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Each human cell has 23 pairs of chromosomes: one set of chromosomes is inherited from the mother and the other set is inherited from the father. There is also a mitochondrial genome, inherited exclusively from the mother, which can be involved in inherited genetic disorders. On each chromosome, there are thousands of genes that are responsible for determining the genotype and phenotype of the individual. A gene is defined as a sequence of DNA that codes for a functional product. The human haploid genome contains 3 billion base pairs and has between 20,000 and 25,000 functional genes.
• 14.0: Prelude to DNA Structure and Function
The three letters “DNA” have now become synonymous with crime solving, paternity testing, human identification, and genetic testing. DNA can be retrieved from hair, blood, or saliva. Each person’s DNA is unique, and it is possible to detect differences between individuals within a species on the basis of these unique features.
• 14.1: Historical Basis of Modern Understanding
Modern understandings of DNA have evolved from the discovery of nucleic acid to the development of the double-helix model. In the 1860s, Friedrich Miescher, a physician by profession, was the first person to isolate phosphate-rich chemicals from white blood cells or leukocytes. He named these chemicals (which would eventually be known as RNA and DNA) nuclein because they were isolated from the nuclei of the cells.
• 14.2: DNA Structure and Sequencing
The building blocks of DNA are nucleotides. The important components of the nucleotide are a nitrogenous base, deoxyribose (5-carbon sugar), and a phosphate group. The nucleotide is named depending on the nitrogenous base. The nitrogenous base can be a purine such as adenine (A) and guanine (G), or a pyrimidine such as cytosine (C) and thymine (T).
• 14.3: Basics of DNA Replication
The elucidation of the structure of the double helix provided a hint as to how DNA divides and makes copies of itself. This model suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. What was not clear was how the replication took place. There were three models suggested: conservative, semi-conservative, and dispersive.
• 14.4: DNA Replication in Prokaryotes
DNA replication has been extremely well studied in prokaryotes primarily because of the small size of the genome and the mutants that are available. E. coli has 4.6 million base pairs in a single circular chromosome and all of it gets replicated in approximately 42 minutes, starting from a single origin of replication and proceeding around the circle in both directions. This means that approximately 1000 nucleotides are added per second. The process is rapid and occurs without many mistakes.
• 14.5: DNA Replication in Eukaryotes
Eukaryotic genomes are much more complex and larger in size than prokaryotic genomes. The human genome has three billion base pairs per haploid set of chromosomes, and 6 billion base pairs are replicated during the S phase of the cell cycle. There are multiple origins of replication on the eukaryotic chromosome; humans can have up to 100,000 origins of replication.
• 14.6: DNA Repair
DNA replication is a highly accurate process, but mistakes can occasionally occur, such as a DNA polymerase inserting a wrong base. Uncorrected mistakes may sometimes lead to serious consequences, such as cancer. Repair mechanisms correct the mistakes. In rare cases, mistakes are not corrected, leading to mutations; in other cases, repair enzymes are themselves mutated or defective.
• 14.E: DNA Structure and Function (Exercises)
Thumbnail: DNA molecule. (CC BY-SA 3.0 / frame from original animation; Dcirovic via Wikimedia Commons).
14: DNA Structure and Function
The three letters “DNA” have now become synonymous with crime solving, paternity testing, human identification, and genetic testing. DNA can be retrieved from hair, blood, or saliva. Each person’s DNA is unique, and it is possible to detect differences between individuals within a species on the basis of these unique features.
DNA analysis has many practical applications beyond forensics. In humans, DNA testing is applied to numerous uses: determining paternity, tracing genealogy, identifying pathogens, archeological research, tracing disease outbreaks, and studying human migration patterns. In the medical field, DNA is used in diagnostics, new vaccine development, and cancer therapy. It is now possible to determine predisposition to diseases by looking at genes.
Each human cell has 23 pairs of chromosomes: one set of chromosomes is inherited from the mother and the other set is inherited from the father. There is also a mitochondrial genome, inherited exclusively from the mother, which can be involved in inherited genetic disorders. On each chromosome, there are thousands of genes that are responsible for determining the genotype and phenotype of the individual. A gene is defined as a sequence of DNA that codes for a functional product. The human haploid genome contains 3 billion base pairs and has between 20,000 and 25,000 functional genes. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/14%3A_DNA_Structure_and_Function/14.0%3A_Prelude_to_DNA_Structure_and_Function.txt |
Skills to Develop
• Explain transformation of DNA
• Describe the key experiments that helped identify that DNA is the genetic material
• State and explain Chargaff’s rules
Modern understandings of DNA have evolved from the discovery of nucleic acid to the development of the double-helix model. In the 1860s, Friedrich Miescher (Figure \(1\)), a physician by profession, was the first person to isolate phosphate-rich chemicals from white blood cells or leukocytes. He named these chemicals (which would eventually be known as RNA and DNA) nuclein because they were isolated from the nuclei of the cells.
Link to Learning
To see Miescher conduct an experiment step-by-step, click through this review of how he discovered the key role of DNA and proteins in the nucleus.
A half century later, British bacteriologist Frederick Griffith was perhaps the first person to show that hereditary information could be transferred from one cell to another “horizontally,” rather than by descent. In 1928, he reported the first demonstration of bacterial transformation, a process in which external DNA is taken up by a cell, thereby changing morphology and physiology. He was working with Streptococcus pneumoniae, the bacterium that causes pneumonia. Griffith worked with two strains, rough (R) and smooth (S). The R strain is non-pathogenic (does not cause disease) and is called rough because its outer surface is a cell wall and lacks a capsule; as a result, the cell surface appears uneven under the microscope. The S strain is pathogenic (disease-causing) and has a capsule outside its cell wall. As a result, it has a smooth appearance under the microscope. Griffith injected the live R strain into mice and they survived. In another experiment, when he injected mice with the heat-killed S strain, they also survived. In a third set of experiments, a mixture of live R strain and heat-killed S strain were injected into mice, and—to his surprise—the mice died. Upon isolating the live bacteria from the dead mouse, only the S strain of bacteria was recovered. When this isolated S strain was injected into fresh mice, the mice died. Griffith concluded that something had passed from the heat-killed S strain into the live R strain and transformed it into the pathogenic S strain, and he called this the transforming principle (Figure \(2\)). These experiments are now famously known as Griffith's transformation experiments.
Scientists Oswald Avery, Colin MacLeod, and Maclyn McCarty (1944) were interested in exploring this transforming principle further. They isolated the S strain from the dead mice and isolated the proteins and nucleic acids, namely RNA and DNA, as these were possible candidates for the molecule of heredity. They conducted a systematic elimination study. They used enzymes that specifically degraded each component and then used each mixture separately to transform the R strain. They found that when DNA was degraded, the resulting mixture was no longer able to transform the bacteria, whereas all of the other combinations were able to transform the bacteria. This led them to conclude that DNA was the transforming principle.
Career Connection: Forensic Scientists and DNA Analysis
DNA evidence was used for the first time to solve an immigration case. The story started with a teenage boy returning to London from Ghana to be with his mother. Immigration authorities at the airport were suspicious of him, thinking that he was traveling on a forged passport. After much persuasion, he was allowed to go live with his mother, but the immigration authorities did not drop the case against him. All types of evidence, including photographs, were provided to the authorities, but deportation proceedings were started nevertheless. Around the same time, Dr. Alec Jeffreys of Leicester University in the United Kingdom had invented a technique known as DNA fingerprinting. The immigration authorities approached Dr. Jeffreys for help. He took DNA samples from the mother and three of her children, plus an unrelated mother, and compared the samples with the boy’s DNA. Because the biological father was not in the picture, DNA from the three children was compared with the boy’s DNA. He found a match in the boy’s DNA for both the mother and his three siblings. He concluded that the boy was indeed the mother’s son.
Forensic scientists analyze many items, including documents, handwriting, firearms, and biological samples. They analyze the DNA content of hair, semen, saliva, and blood, and compare it with a database of DNA profiles of known criminals. Analysis includes DNA isolation, sequencing, and sequence analysis; most forensic DNA analysis involves polymerase chain reaction (PCR) amplification of short tandem repeat (STR) loci and electrophoresis to determine the length of the PCR-amplified fragment. Only mitochondrial DNA is sequenced for forensics. Forensic scientists are expected to appear at court hearings to present their findings. They are usually employed in crime labs of city and state government agencies. Geneticists experimenting with DNA techniques also work for scientific and research organizations, pharmaceutical industries, and college and university labs. Students wishing to pursue a career as a forensic scientist should have at least a bachelor's degree in chemistry, biology, or physics, and preferably some experience working in a laboratory.
Experiments conducted by Martha Chase and Alfred Hershey in 1952 provided confirmatory evidence that DNA was the genetic material and not proteins. Chase and Hershey were studying a bacteriophage, which is a virus that infects bacteria. Viruses typically have a simple structure: a protein coat, called the capsid, and a nucleic acid core that contains the genetic material, either DNA or RNA. The bacteriophage infects the host bacterial cell by attaching to its surface, and then it injects its nucleic acids inside the cell. The phage DNA makes multiple copies of itself using the host machinery, and eventually the host cell bursts, releasing a large number of bacteriophages. Hershey and Chase labeled one batch of phage with radioactive sulfur, 35S, to label the protein coat. Another batch of phage were labeled with radioactive phosphorus, 32P. Because phosphorous is found in DNA, but not protein, the DNA and not the protein would be tagged with radioactive phosphorus.
Each batch of phage was allowed to infect the cells separately. After infection, the phage bacterial suspension was put in a blender, which caused the phage coat to be detached from the host cell. The phage and bacterial suspension was spun down in a centrifuge. The heavier bacterial cells settled down and formed a pellet, whereas the lighter phage particles stayed in the supernatant. In the tube that contained phage labeled with 35S, the supernatant contained the radioactively labeled phage, whereas no radioactivity was detected in the pellet. In the tube that contained the phage labeled with 32P, the radioactivity was detected in the pellet that contained the heavier bacterial cells, and no radioactivity was detected in the supernatant. Hershey and Chase concluded that it was the phage DNA that was injected into the cell and carried information to produce more phage particles, thus providing evidence that DNA was the genetic material and not proteins (Figure \(3\)).
Around this same time, Austrian biochemist Erwin Chargaff examined the content of DNA in different species and found that the amounts of adenine, thymine, guanine, and cytosine were not found in equal quantities, and that it varied from species to species, but not between individuals of the same species. He found that the amount of adenine equals the amount of thymine, and the amount of cytosine equals the amount of guanine, or A = T and G = C. This is also known as Chargaff’s rules. This finding proved immensely useful when Watson and Crick were getting ready to propose their DNA double helix model.
Summary
DNA was first isolated from white blood cells by Friedrich Miescher, who called it nuclein because it was isolated from nuclei. Frederick Griffith's experiments with strains of Streptococcus pneumoniae provided the first hint that DNA may be the transforming principle. Avery, MacLeod, and McCarty proved that DNA is required for the transformation of bacteria. Later experiments by Hershey and Chase using bacteriophage T2 proved that DNA is the genetic material. Chargaff found that the ratio of A = T and C = G, and that the percentage content of A, T, G, and C is different for different species.
Glossary
transformation
process in which external DNA is taken up by a cell | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/14%3A_DNA_Structure_and_Function/14.1%3A_Historical_Basis_of_Modern_Understanding.txt |
Skills to Develop
• Describe the structure of DNA
• Explain the Sanger method of DNA sequencing
• Discuss the similarities and differences between eukaryotic and prokaryotic DNA
The building blocks of DNA are nucleotides. The important components of the nucleotide are a nitrogenous base, deoxyribose (5-carbon sugar), and a phosphate group (Figure \(1\)). The nucleotide is named depending on the nitrogenous base. The nitrogenous base can be a purine such as adenine (A) and guanine (G), or a pyrimidine such as cytosine (C) and thymine (T).
The nucleotides combine with each other by covalent bonds known as phosphodiester bonds or linkages. The purines have a double ring structure with a six-membered ring fused to a five-membered ring. Pyrimidines are smaller in size; they have a single six-membered ring structure. The carbon atoms of the five-carbon sugar are numbered 1', 2', 3', 4', and 5' (1' is read as “one prime”). The phosphate residue is attached to the hydroxyl group of the 5' carbon of one sugar of one nucleotide and the hydroxyl group of the 3' carbon of the sugar of the next nucleotide, thereby forming a 5'-3' phosphodiester bond.
In the 1950s, Francis Crick and James Watson worked together to determine the structure of DNA at the University of Cambridge, England. Other scientists like Linus Pauling and Maurice Wilkins were also actively exploring this field. Pauling had discovered the secondary structure of proteins using X-ray crystallography. In Wilkins’ lab, researcher Rosalind Franklin was using X-ray diffraction methods to understand the structure of DNA. Watson and Crick were able to piece together the puzzle of the DNA molecule on the basis of Franklin's data because Crick had also studied X-ray diffraction (Figure \(2\)). In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Medicine. Unfortunately, by then Franklin had died, and Nobel prizes are not awarded posthumously.
Watson and Crick proposed that DNA is made up of two strands that are twisted around each other to form a right-handed helix. Base pairing takes place between a purine and pyrimidine; namely, A pairs with T and G pairs with C. Adenine and thymine are complementary base pairs, and cytosine and guanine are also complementary base pairs. The base pairs are stabilized by hydrogen bonds; adenine and thymine form two hydrogen bonds and cytosine and guanine form three hydrogen bonds. The two strands are anti-parallel in nature; that is, the 3' end of one strand faces the 5' end of the other strand. The sugar and phosphate of the nucleotides form the backbone of the structure, whereas the nitrogenous bases are stacked inside. Each base pair is separated from the other base pair by a distance of 0.34 nm, and each turn of the helix measures 3.4 nm. Therefore, ten base pairs are present per turn of the helix. The diameter of the DNA double helix is 2 nm, and it is uniform throughout. Only the pairing between a purine and pyrimidine can explain the uniform diameter. The twisting of the two strands around each other results in the formation of uniformly spaced major and minor grooves (Figure \(3\)).
DNA Sequencing Techniques
Until the 1990s, the sequencing of DNA (reading the sequence of DNA) was a relatively expensive and long process. Using radiolabeled nucleotides also compounded the problem through safety concerns. With currently available technology and automated machines, the process is cheap, safer, and can be completed in a matter of hours. Fred Sanger developed the sequencing method used for the human genome sequencing project, which is widely used today (Figure \(4\)).
Link to Learning
Visit this site to watch a video explaining the DNA sequence reading technique that resulted from Sanger’s work.
The method is known as the dideoxy chain termination method. The sequencing method is based on the use of chain terminators, the dideoxynucleotides (ddNTPs). The dideoxynucleotides, or ddNTPSs, differ from the deoxynucleotides by the lack of a free 3' OH group on the five-carbon sugar. If a ddNTP is added to a growing a DNA strand, the chain is not extended any further because the free 3' OH group needed to add another nucleotide is not available. By using a predetermined ratio of deoxyribonucleotides to dideoxynucleotides, it is possible to generate DNA fragments of different sizes.
The DNA sample to be sequenced is denatured or separated into two strands by heating it to high temperatures. The DNA is divided into four tubes in which a primer, DNA polymerase, and all four nucleotides (A, T, G, and C) are added. In addition to each of the four tubes, limited quantities of one of the four dideoxynucleotides are added to each tube respectively. The tubes are labeled as A, T, G, and C according to the ddNTP added. For detection purposes, each of the four dideoxynucleotides carries a different fluorescent label. Chain elongation continues until a fluorescent dideoxy nucleotide is incorporated, after which no further elongation takes place. After the reaction is over, electrophoresis is performed. Even a difference in length of a single base can be detected. The sequence is read from a laser scanner. For his work on DNA sequencing, Sanger received a Nobel Prize in chemistry in 1980.
Link to Learning
Sanger’s genome sequencing has led to a race to sequence human genomes at a rapid speed and low cost, often referred to as the \$1000 in one day sequence. Learn more by selecting the Sequencing at Speed animation here.
Gel electrophoresis is a technique used to separate DNA fragments of different sizes. Usually the gel is made of a chemical called agarose. Agarose powder is added to a buffer and heated. After cooling, the gel solution is poured into a casting tray. Once the gel has solidified, the DNA is loaded on the gel and electric current is applied. The DNA has a net negative charge and moves from the negative electrode toward the positive electrode. The electric current is applied for sufficient time to let the DNA separate according to size; the smallest fragments will be farthest from the well (where the DNA was loaded), and the heavier molecular weight fragments will be closest to the well. Once the DNA is separated, the gel is stained with a DNA-specific dye for viewing it (Figure \(5\)).
Evolution Connection: Neanderthal Genome - How Are We Related?
The first draft sequence of the Neanderthal genome was recently published by Richard E. Green et al. in 2010.1 Neanderthals are the closest ancestors of present-day humans. They were known to have lived in Europe and Western Asia before they disappeared from fossil records approximately 30,000 years ago. Green’s team studied almost 40,000-year-old fossil remains that were selected from sites across the world. Extremely sophisticated means of sample preparation and DNA sequencing were employed because of the fragile nature of the bones and heavy microbial contamination. In their study, the scientists were able to sequence some four billion base pairs. The Neanderthal sequence was compared with that of present-day humans from across the world. After comparing the sequences, the researchers found that the Neanderthal genome had 2 to 3 percent greater similarity to people living outside Africa than to people in Africa. While current theories have suggested that all present-day humans can be traced to a small ancestral population in Africa, the data from the Neanderthal genome may contradict this view. Green and his colleagues also discovered DNA segments among people in Europe and Asia that are more similar to Neanderthal sequences than to other contemporary human sequences. Another interesting observation was that Neanderthals are as closely related to people from Papua New Guinea as to those from China or France. This is surprising because Neanderthal fossil remains have been located only in Europe and West Asia. Most likely, genetic exchange took place between Neanderthals and modern humans as modern humans emerged out of Africa, before the divergence of Europeans, East Asians, and Papua New Guineans.
Several genes seem to have undergone changes from Neanderthals during the evolution of present-day humans. These genes are involved in cranial structure, metabolism, skin morphology, and cognitive development. One of the genes that is of particular interest is RUNX2, which is different in modern day humans and Neanderthals. This gene is responsible for the prominent frontal bone, bell-shaped rib cage, and dental differences seen in Neanderthals. It is speculated that an evolutionary change in RUNX2 was important in the origin of modern-day humans, and this affected the cranium and the upper body.
Link to Learning
Watch Svante Pääbo’s talk explaining the Neanderthal genome research at the 2011 annual TED (Technology, Entertainment, Design) conference.
DNA Packaging in Cells
When comparing prokaryotic cells to eukaryotic cells, prokaryotes are much simpler than eukaryotes in many of their features (Figure \(6\)). Most prokaryotes contain a single, circular chromosome that is found in an area of the cytoplasm called the nucleoid.
Exercise \(1\)
In eukaryotic cells, DNA and RNA synthesis occur in a separate compartment from protein synthesis. In prokaryotic cells, both processes occur together. What advantages might there be to separating the processes? What advantages might there be to having them occur together?
Answer
Compartmentalization enables a eukaryotic cell to divide processes into discrete steps so it can build more complex protein and RNA products. But there is an advantage to having a single compartment as well: RNA and protein synthesis occurs much more quickly in a prokaryotic cell.
The size of the genome in one of the most well-studied prokaryotes, E.coli, is 4.6 million base pairs (approximately 1.1 mm, if cut and stretched out). So how does this fit inside a small bacterial cell? The DNA is twisted by what is known as supercoiling. Supercoiling means that DNA is either under-wound (less than one turn of the helix per 10 base pairs) or over-wound (more than 1 turn per 10 base pairs) from its normal relaxed state. Some proteins are known to be involved in the supercoiling; other proteins and enzymes such as DNA gyrase help in maintaining the supercoiled structure.
Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus (Figure \(7\)). At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The histones are evolutionarily conserved proteins that are rich in basic amino acids and form an octamer. The DNA (which is negatively charged because of the phosphate groups) is wrapped tightly around the histone core. This nucleosome is linked to the next one with the help of a linker DNA. This is also known as the “beads on a string” structure. This is further compacted into a 30 nm fiber, which is the diameter of the structure. At the metaphase stage, the chromosomes are at their most compact, are approximately 700 nm in width, and are found in association with scaffold proteins.
In interphase, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. The tightly packaged region is known as heterochromatin, and the less dense region is known as euchromatin. Heterochromatin usually contains genes that are not expressed, and is found in the regions of the centromere and telomeres. The euchromatin usually contains genes that are transcribed, with DNA packaged around nucleosomes but not further compacted.
Summary
The currently accepted model of the double-helix structure of DNA was proposed by Watson and Crick. Some of the salient features are that the two strands that make up the double helix are complementary and anti-parallel in nature. Deoxyribose sugars and phosphates form the backbone of the structure, and the nitrogenous bases are stacked inside. The diameter of the double helix, 2 nm, is uniform throughout. A purine always pairs with a pyrimidine; A pairs with T, and G pairs with C. One turn of the helix has ten base pairs. During cell division, each daughter cell receives a copy of the DNA by a process known as DNA replication. Prokaryotes are much simpler than eukaryotes in many of their features. Most prokaryotes contain a single, circular chromosome. In general, eukaryotic chromosomes contain a linear DNA molecule packaged into nucleosomes, and have two distinct regions that can be distinguished by staining, reflecting different states of packaging and compaction.
Footnotes
1. 1 Richard E. Green et al., “A Draft Sequence of the Neandertal Genome,” Science 328 (2010): 710-22.
Glossary
electrophoresis
technique used to separate DNA fragments according to size | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/14%3A_DNA_Structure_and_Function/14.2%3A_DNA_Structure_and_Sequencing.txt |
Skills to Develop
• Explain how the structure of DNA reveals the replication process
• Describe the Meselson and Stahl experiments
The elucidation of the structure of the double helix provided a hint as to how DNA divides and makes copies of itself. This model suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. What was not clear was how the replication took place. There were three models suggested (Figure \(1\)): conservative, semi-conservative, and dispersive.
In conservative replication, the parental DNA remains together, and the newly formed daughter strands are together. The semi-conservative method suggests that each of the two parental DNA strands act as a template for new DNA to be synthesized; after replication, each double-stranded DNA includes one parental or “old” strand and one “new” strand. In the dispersive model, both copies of DNA have double-stranded segments of parental DNA and newly synthesized DNA interspersed.
Meselson and Stahl were interested in understanding how DNA replicates. They grew E. coli for several generations in a medium containing a “heavy” isotope of nitrogen (15N) that gets incorporated into nitrogenous bases, and eventually into the DNA (Figure \(2\)).
The E. coli culture was then shifted into medium containing 14N and allowed to grow for one generation. The cells were harvested and the DNA was isolated. The DNA was centrifuged at high speeds in an ultracentrifuge. Some cells were allowed to grow for one more life cycle in 14N and spun again. During the density gradient centrifugation, the DNA is loaded into a gradient (typically a salt such as cesium chloride or sucrose) and spun at high speeds of 50,000 to 60,000 rpm. Under these circumstances, the DNA will form a band according to its density in the gradient. DNA grown in 15N will band at a higher density position than that grown in 14N. Meselson and Stahl noted that after one generation of growth in 14N after they had been shifted from 15N, the single band observed was intermediate in position in between DNA of cells grown exclusively in 15N and 14N. This suggested either a semi-conservative or dispersive mode of replication. The DNA harvested from cells grown for two generations in 14N formed two bands: one DNA band was at the intermediate position between 15N and 14N, and the other corresponded to the band of 14N DNA. These results could only be explained if DNA replicates in a semi-conservative manner. Therefore, the other two modes were ruled out.
During DNA replication, each of the two strands that make up the double helix serves as a template from which new strands are copied. The new strand will be complementary to the parental or “old” strand. When two daughter DNA copies are formed, they have the same sequence and are divided equally into the two daughter cells.
Link to Learning
Click through this tutorial on DNA replication.
Summary
The model for DNA replication suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. In conservative replication, the parental DNA is conserved, and the daughter DNA is newly synthesized. The semi-conservative method suggests that each of the two parental DNA strands acts as template for new DNA to be synthesized; after replication, each double-stranded DNA includes one parental or “old” strand and one “new” strand. The dispersive mode suggested that the two copies of the DNA would have segments of parental DNA and newly synthesized DNA.
Contributors and Attributions
• Connie Rye (East Mississippi Community College), Robert Wise (University of Wisconsin, Oshkosh), Vladimir Jurukovski (Suffolk County Community College), Jean DeSaix (University of North Carolina at Chapel Hill), Jung Choi (Georgia Institute of Technology), Yael Avissar (Rhode Island College) among other contributing authors. Original content by OpenStax (CC BY 4.0; Download for free at http://cnx.org/contents/[email protected]). | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/14%3A_DNA_Structure_and_Function/14.3%3A_Basics_of_DNA_Replication.txt |
Skills to Develop
• Explain the process of DNA replication in prokaryotes
• Discuss the role of different enzymes and proteins in supporting this process
DNA replication has been extremely well studied in prokaryotes primarily because of the small size of the genome and the mutants that are available. E. coli has 4.6 million base pairs in a single circular chromosome and all of it gets replicated in approximately 42 minutes, starting from a single origin of replication and proceeding around the circle in both directions. This means that approximately 1000 nucleotides are added per second. The process is quite rapid and occurs without many mistakes.
DNA replication employs a large number of proteins and enzymes, each of which plays a critical role during the process. One of the key players is the enzyme DNA polymerase, also known as DNA pol, which adds nucleotides one by one to the growing DNA chain that are complementary to the template strand. The addition of nucleotides requires energy; this energy is obtained from the nucleotides that have three phosphates attached to them, similar to ATP which has three phosphate groups attached. When the bond between the phosphates is broken, the energy released is used to form the phosphodiester bond between the incoming nucleotide and the growing chain. In prokaryotes, three main types of polymerases are known: DNA pol I, DNA pol II, and DNA pol III. It is now known that DNA pol III is the enzyme required for DNA synthesis; DNA pol I and DNA pol II are primarily required for repair.
How does the replication machinery know where to begin? It turns out that there are specific nucleotide sequences called origins of replication where replication begins. In E. coli, which has a single origin of replication on its one chromosome (as do most prokaryotes), it is approximately 245 base pairs long and is rich in AT sequences. The origin of replication is recognized by certain proteins that bind to this site. An enzyme called helicase unwinds the DNA by breaking the hydrogen bonds between the nitrogenous base pairs. ATP hydrolysis is required for this process. As the DNA opens up, Y-shaped structures called replication forks are formed. Two replication forks are formed at the origin of replication and these get extended bi- directionally as replication proceeds. Single-strand binding proteins coat the single strands of DNA near the replication fork to prevent the single-stranded DNA from winding back into a double helix. DNA polymerase is able to add nucleotides only in the 5' to 3' direction (a new DNA strand can be only extended in this direction). It also requires a free 3'-OH group to which it can add nucleotides by forming a phosphodiester bond between the 3'-OH end and the 5' phosphate of the next nucleotide. This essentially means that it cannot add nucleotides if a free 3'-OH group is not available. Then how does it add the first nucleotide? The problem is solved with the help of a primer that provides the free 3'-OH end. Another enzyme, RNA primase, synthesizes an RNA primer that is about five to ten nucleotides long and complementary to the DNA. Because this sequence primes the DNA synthesis, it is appropriately called the primer. DNA polymerase can now extend this RNA primer, adding nucleotides one by one that are complementary to the template strand (Figure \(1\)).
Exercise \(1\)
You isolate a cell strain in which the joining together of Okazaki fragments is impaired and suspect that a mutation has occurred in an enzyme found at the replication fork. Which enzyme is most likely to be mutated?
Answer
DNA ligase, as this enzyme joins together Okazaki fragments.
The replication fork moves at the rate of 1000 nucleotides per second. DNA polymerase can only extend in the 5' to 3' direction, which poses a slight problem at the replication fork. As we know, the DNA double helix is anti-parallel; that is, one strand is in the 5' to 3' direction and the other is oriented in the 3' to 5' direction. One strand, which is complementary to the 3' to 5' parental DNA strand, is synthesized continuously towards the replication fork because the polymerase can add nucleotides in this direction. This continuously synthesized strand is known as the leading strand. The other strand, complementary to the 5' to 3' parental DNA, is extended away from the replication fork, in small fragments known as Okazaki fragments, each requiring a primer to start the synthesis. Okazaki fragments are named after the Japanese scientist who first discovered them. The strand with the Okazaki fragments is known as the lagging strand.
The leading strand can be extended by one primer alone, whereas the lagging strand needs a new primer for each of the short Okazaki fragments. The overall direction of the lagging strand will be 3' to 5', and that of the leading strand 5' to 3'. A protein called the sliding clamp holds the DNA polymerase in place as it continues to add nucleotides. The sliding clamp is a ring-shaped protein that binds to the DNA and holds the polymerase in place. Topoisomerase prevents the over-winding of the DNA double helix ahead of the replication fork as the DNA is opening up; it does so by causing temporary nicks in the DNA helix and then resealing it. As synthesis proceeds, the RNA primers are replaced by DNA. The primers are removed by the exonuclease activity of DNA pol I, and the gaps are filled in by deoxyribonucleotides. The nicks that remain between the newly synthesized DNA (that replaced the RNA primer) and the previously synthesized DNA are sealed by the enzyme DNA ligase that catalyzes the formation of phosphodiester linkage between the 3'-OH end of one nucleotide and the 5' phosphate end of the other fragment.
Once the chromosome has been completely replicated, the two DNA copies move into two different cells during cell division. The process of DNA replication can be summarized as follows.
DNA replication steps
1. DNA unwinds at the origin of replication.
2. Helicase opens up the DNA-forming replication forks; these are extended bidirectionally.
3. Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA.
4. Topoisomerase binds at the region ahead of the replication fork to prevent supercoiling.
5. Primase synthesizes RNA primers complementary to the DNA strand.
6. DNA polymerase starts adding nucleotides to the 3'-OH end of the primer.
7. Elongation of both the lagging and the leading strand continues.
8. RNA primers are removed by exonuclease activity.
9. Gaps are filled by DNA pol by adding dNTPs.
10. The gap between the two DNA fragments is sealed by DNA ligase, which helps in the formation of phosphodiester bonds.
Table \(1\) summarizes the enzymes involved in prokaryotic DNA replication and the functions of each.
Table \(1\): Prokaryotic DNA Replication: Enzymes and Their Function
Enzyme/protein Specific Function
DNA pol I Exonuclease activity removes RNA primer and replaces with newly synthesized DNA
DNA pol II Repair function
DNA pol III Main enzyme that adds nucleotides in the 5'-3' direction
Helicase Opens the DNA helix by breaking hydrogen bonds between the nitrogenous bases
Ligase Seals the gaps between the Okazaki fragments to create one continuous DNA strand
Primase Synthesizes RNA primers needed to start replication
Sliding Clamp Helps to hold the DNA polymerase in place when nucleotides are being added
Topoisomerase Helps relieve the stress on DNA when unwinding by causing breaks and then resealing the DNA
Single-strand binding proteins (SSB) Binds to single-stranded DNA to avoid DNA rewinding back.
Link to Learning
Review the full process of DNA replication here.
Summary
Replication in prokaryotes starts from a sequence found on the chromosome called the origin of replication—the point at which the DNA opens up. Helicase opens up the DNA double helix, resulting in the formation of the replication fork. Single-strand binding proteins bind to the single-stranded DNA near the replication fork to keep the fork open. Primase synthesizes an RNA primer to initiate synthesis by DNA polymerase, which can add nucleotides only in the 5' to 3' direction. One strand is synthesized continuously in the direction of the replication fork; this is called the leading strand. The other strand is synthesized in a direction away from the replication fork, in short stretches of DNA known as Okazaki fragments. This strand is known as the lagging strand. Once replication is completed, the RNA primers are replaced by DNA nucleotides and the DNA is sealed with DNA ligase, which creates phosphodiester bonds between the 3'-OH of one end and the 5' phosphate of the other strand.
Glossary
helicase
during replication, this enzyme helps to open up the DNA helix by breaking the hydrogen bonds
lagging strand
during replication, the strand that is replicated in short fragments and away from the replication fork
leading strand
strand that is synthesized continuously in the 5'-3' direction which is synthesized in the direction of the replication fork
ligase
enzyme that catalyzes the formation of a phosphodiester linkage between the 3' OH and 5' phosphate ends of the DNA
Okazaki fragment
DNA fragment that is synthesized in short stretches on the lagging strand
primase
enzyme that synthesizes the RNA primer; the primer is needed for DNA pol to start synthesis of a new DNA strand
primer
short stretch of nucleotides that is required to initiate replication; in the case of replication, the primer has RNA nucleotides
replication fork
Y-shaped structure formed during initiation of replication
single-strand binding protein
during replication, protein that binds to the single-stranded DNA; this helps in keeping the two strands of DNA apart so that they may serve as templates
sliding clamp
ring-shaped protein that holds the DNA pol on the DNA strand
topoisomerase
enzyme that causes underwinding or overwinding of DNA when DNA replication is taking place | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/14%3A_DNA_Structure_and_Function/14.4%3A_DNA_Replication_in_Prokaryotes.txt |
Skills to Develop
• Discuss the similarities and differences between DNA replication in eukaryotes and prokaryotes
• State the role of telomerase in DNA replication
Eukaryotic genomes are much more complex and larger in size than prokaryotic genomes. The human genome has three billion base pairs per haploid set of chromosomes, and 6 billion base pairs are replicated during the S phase of the cell cycle. There are multiple origins of replication on the eukaryotic chromosome; humans can have up to 100,000 origins of replication. The rate of replication is approximately 100 nucleotides per second, much slower than prokaryotic replication. In yeast, which is a eukaryote, special sequences known as Autonomously Replicating Sequences (ARS) are found on the chromosomes. These are equivalent to the origin of replication in E. coli.
The number of DNA polymerases in eukaryotes is much more than prokaryotes: 14 are known, of which five are known to have major roles during replication and have been well studied. They are known as pol α, pol β, pol γ, pol δ, and pol ε.
The essential steps of replication are the same as in prokaryotes. Before replication can start, the DNA has to be made available as template. Eukaryotic DNA is bound to basic proteins known as histones to form structures called nucleosomes. The chromatin (the complex between DNA and proteins) may undergo some chemical modifications, so that the DNA may be able to slide off the proteins or be accessible to the enzymes of the DNA replication machinery. At the origin of replication, a pre-replication complex is made with other initiator proteins. Other proteins are then recruited to start the replication process (Table \(1\)).
A helicase using the energy from ATP hydrolysis opens up the DNA helix. Replication forks are formed at each replication origin as the DNA unwinds. The opening of the double helix causes over-winding, or supercoiling, in the DNA ahead of the replication fork. These are resolved with the action of topoisomerases. Primers are formed by the enzyme primase, and using the primer, DNA pol can start synthesis. While the leading strand is continuously synthesized by the enzyme pol δ, the lagging strand is synthesized by pol ε. A sliding clamp protein known as PCNA (Proliferating Cell Nuclear Antigen) holds the DNA pol in place so that it does not slide off the DNA. RNase H removes the RNA primer, which is then replaced with DNA nucleotides. The Okazaki fragments in the lagging strand are joined together after the replacement of the RNA primers with DNA. The gaps that remain are sealed by DNA ligase, which forms the phosphodiester bond.
Telomere replication
Unlike prokaryotic chromosomes, eukaryotic chromosomes are linear. As you’ve learned, the enzyme DNA pol can add nucleotides only in the 5' to 3' direction. In the leading strand, synthesis continues until the end of the chromosome is reached. On the lagging strand, DNA is synthesized in short stretches, each of which is initiated by a separate primer. When the replication fork reaches the end of the linear chromosome, there is no place for a primer to be made for the DNA fragment to be copied at the end of the chromosome. These ends thus remain unpaired, and over time these ends may get progressively shorter as cells continue to divide.
The ends of the linear chromosomes are known as telomeres, which have repetitive sequences that code for no particular gene. In a way, these telomeres protect the genes from getting deleted as cells continue to divide. In humans, a six base pair sequence, TTAGGG, is repeated 100 to 1000 times. The discovery of the enzyme telomerase (Figure \(1\)) helped in the understanding of how chromosome ends are maintained. The telomerase enzyme contains a catalytic part and a built-in RNA template. It attaches to the end of the chromosome, and complementary bases to the RNA template are added on the 3' end of the DNA strand. Once the 3' end of the lagging strand template is sufficiently elongated, DNA polymerase can add the nucleotides complementary to the ends of the chromosomes. Thus, the ends of the chromosomes are replicated.
Telomerase is typically active in germ cells and adult stem cells. It is not active in adult somatic cells. For her discovery of telomerase and its action, Elizabeth Blackburn (Figure \(2\)) received the Nobel Prize for Medicine and Physiology in 2009.
Telomerase and Aging
Cells that undergo cell division continue to have their telomeres shortened because most somatic cells do not make telomerase. This essentially means that telomere shortening is associated with aging. With the advent of modern medicine, preventative health care, and healthier lifestyles, the human life span has increased, and there is an increasing demand for people to look younger and have a better quality of life as they grow older.
In 2010, scientists found that telomerase can reverse some age-related conditions in mice. This may have potential in regenerative medicine.1 Telomerase-deficient mice were used in these studies; these mice have tissue atrophy, stem cell depletion, organ system failure, and impaired tissue injury responses. Telomerase reactivation in these mice caused extension of telomeres, reduced DNA damage, reversed neurodegeneration, and improved the function of the testes, spleen, and intestines. Thus, telomere reactivation may have potential for treating age-related diseases in humans.
Cancer is characterized by uncontrolled cell division of abnormal cells. The cells accumulate mutations, proliferate uncontrollably, and can migrate to different parts of the body through a process called metastasis. Scientists have observed that cancerous cells have considerably shortened telomeres and that telomerase is active in these cells. Interestingly, only after the telomeres were shortened in the cancer cells did the telomerase become active. If the action of telomerase in these cells can be inhibited by drugs during cancer therapy, then the cancerous cells could potentially be stopped from further division.
Table \(1\): Difference between Prokaryotic and Eukaryotic Replication
Property Prokaryotes Eukaryotes
Origin of replication Single Multiple
Rate of replication 1000 nucleotides/s 50 to 100 nucleotides/s
DNA polymerase types 5 14
Telomerase Not present Present
RNA primer removal DNA pol I RNase H
Strand elongation DNA pol III Pol δ, pol ε
Sliding clamp Sliding clamp PCNA
Summary
Replication in eukaryotes starts at multiple origins of replication. The mechanism is quite similar to prokaryotes. A primer is required to initiate synthesis, which is then extended by DNA polymerase as it adds nucleotides one by one to the growing chain. The leading strand is synthesized continuously, whereas the lagging strand is synthesized in short stretches called Okazaki fragments. The RNA primers are replaced with DNA nucleotides; the DNA remains one continuous strand by linking the DNA fragments with DNA ligase. The ends of the chromosomes pose a problem as polymerase is unable to extend them without a primer. Telomerase, an enzyme with an inbuilt RNA template, extends the ends by copying the RNA template and extending one end of the chromosome. DNA polymerase can then extend the DNA using the primer. In this way, the ends of the chromosomes are protected.
Footnotes
1. 1 Jaskelioff et al., “Telomerase reactivation reverses tissue degeneration in aged telomerase-deficient mice,” Nature 469 (2011): 102-7.
Glossary
telomerase
enzyme that contains a catalytic part and an inbuilt RNA template; it functions to maintain telomeres at chromosome ends
telomere
DNA at the end of linear chromosomes | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/14%3A_DNA_Structure_and_Function/14.5%3A_DNA_Replication_in_Eukaryotes.txt |
Skills to Develop
• Discuss the different types of mutations in DNA
• Explain DNA repair mechanisms
DNA replication is a highly accurate process, but mistakes can occasionally occur, such as a DNA polymerase inserting a wrong base. Uncorrected mistakes may sometimes lead to serious consequences, such as cancer. Repair mechanisms correct the mistakes. In rare cases, mistakes are not corrected, leading to mutations; in other cases, repair enzymes are themselves mutated or defective.
Most of the mistakes during DNA replication are promptly corrected by DNA polymerase by proofreading the base that has been just added (Figure \(1\)). In proofreading, the DNA pol reads the newly added base before adding the next one, so a correction can be made. The polymerase checks whether the newly added base has paired correctly with the base in the template strand. If it is the right base, the next nucleotide is added. If an incorrect base has been added, the enzyme makes a cut at the phosphodiester bond and releases the wrong nucleotide. This is performed by the exonuclease action of DNA pol III. Once the incorrect nucleotide has been removed, a new one will be added again.
Some errors are not corrected during replication, but are instead corrected after replication is completed; this type of repair is known as mismatch repair (Figure \(2\)). The enzymes recognize the incorrectly added nucleotide and excise it; this is then replaced by the correct base. If this remains uncorrected, it may lead to more permanent damage. How do mismatch repair enzymes recognize which of the two bases is the incorrect one? In E. coli, after replication, the nitrogenous base adenine acquires a methyl group; the parental DNA strand will have methyl groups, whereas the newly synthesized strand lacks them. Thus, DNA polymerase is able to remove the wrongly incorporated bases from the newly synthesized, non-methylated strand. In eukaryotes, the mechanism is not very well understood, but it is believed to involve recognition of unsealed nicks in the new strand, as well as a short-term continuing association of some of the replication proteins with the new daughter strand after replication has completed.
In another type of repair mechanism, nucleotide excision repair, enzymes replace incorrect bases by making a cut on both the 3' and 5' ends of the incorrect base (Figure \(3\)). The segment of DNA is removed and replaced with the correctly paired nucleotides by the action of DNA pol. Once the bases are filled in, the remaining gap is sealed with a phosphodiester linkage catalyzed by DNA ligase. This repair mechanism is often employed when UV exposure causes the formation of pyrimidine dimers.
A well-studied example of mistakes not being corrected is seen in people suffering from xeroderma pigmentosa (Figure \(4\)). Affected individuals have skin that is highly sensitive to UV rays from the sun. When individuals are exposed to UV, pyrimidine dimers, especially those of thymine, are formed; people with xeroderma pigmentosa are not able to repair the damage. These are not repaired because of a defect in the nucleotide excision repair enzymes, whereas in normal individuals, the thymine dimers are excised and the defect is corrected. The thymine dimers distort the structure of the DNA double helix, and this may cause problems during DNA replication. People with xeroderma pigmentosa may have a higher risk of contracting skin cancer than those who dont have the condition.
Errors during DNA replication are not the only reason why mutations arise in DNA. Mutations, variations in the nucleotide sequence of a genome, can also occur because of damage to DNA. Such mutations may be of two types: induced or spontaneous. Induced mutations are those that result from an exposure to chemicals, UV rays, x-rays, or some other environmental agent. Spontaneous mutations occur without any exposure to any environmental agent; they are a result of natural reactions taking place within the body.
Mutations may have a wide range of effects. Some mutations are not expressed; these are known as silent mutations. Point mutations are those mutations that affect a single base pair. The most common nucleotide mutations are substitutions, in which one base is replaced by another. These can be of two types, either transitions or transversions. Transition substitution refers to a purine or pyrimidine being replaced by a base of the same kind; for example, a purine such as adenine may be replaced by the purine guanine. Transversion substitution refers to a purine being replaced by a pyrimidine, or vice versa; for example, cytosine, a pyrimidine, is replaced by adenine, a purine. Mutations can also be the result of the addition of a base, known as an insertion, or the removal of a base, also known as deletion. Sometimes a piece of DNA from one chromosome may get translocated to another chromosome or to another region of the same chromosome; this is also known as translocation. These mutation types are shown in Figure \(5\).
Exercise \(1\)
A frameshift mutation that results in the insertion of three nucleotides is often less deleterious than a mutation that results in the insertion of one nucleotide. Why?
Answer
If three nucleotides are added, one additional amino acid will be incorporated into the protein chain, but the reading frame won't shift.
Mutations in repair genes have been known to cause cancer. Many mutated repair genes have been implicated in certain forms of pancreatic cancer, colon cancer, and colorectal cancer. Mutations can affect either somatic cells or germ cells. If many mutations accumulate in a somatic cell, they may lead to problems such as the uncontrolled cell division observed in cancer. If a mutation takes place in germ cells, the mutation will be passed on to the next generation, as in the case of hemophilia and xeroderma pigmentosa.
Summary
DNA polymerase can make mistakes while adding nucleotides. It edits the DNA by proofreading every newly added base. Incorrect bases are removed and replaced by the correct base, and then a new base is added. Most mistakes are corrected during replication, although when this does not happen, the mismatch repair mechanism is employed. Mismatch repair enzymes recognize the wrongly incorporated base and excise it from the DNA, replacing it with the correct base. In yet another type of repair, nucleotide excision repair, the incorrect base is removed along with a few bases on the 5' and 3' end, and these are replaced by copying the template with the help of DNA polymerase. The ends of the newly synthesized fragment are attached to the rest of the DNA using DNA ligase, which creates a phosphodiester bond.
Most mistakes are corrected, and if they are not, they may result in a mutation defined as a permanent change in the DNA sequence. Mutations can be of many types, such as substitution, deletion, insertion, and translocation. Mutations in repair genes may lead to serious consequences such as cancer. Mutations can be induced or may occur spontaneously.
Glossary
induced mutation
mutation that results from exposure to chemicals or environmental agents
mutation
variation in the nucleotide sequence of a genome
mismatch repair
type of repair mechanism in which mismatched bases are removed after replication
nucleotide excision repair
type of DNA repair mechanism in which the wrong base, along with a few nucleotides upstream or downstream, are removed
proofreading
function of DNA pol in which it reads the newly added base before adding the next one
point mutation
mutation that affects a single base
silent mutation
mutation that is not expressed
spontaneous mutation
mutation that takes place in the cells as a result of chemical reactions taking place naturally without exposure to any external agent
transition substitution
when a purine is replaced with a purine or a pyrimidine is replaced with another pyrimidine
transversion substitution
when a purine is replaced by a pyrimidine or a pyrimidine is replaced by a purine | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/14%3A_DNA_Structure_and_Function/14.6%3A_DNA_Repair.txt |
14.1: Historical Basis of Modern Understanding
Modern understandings of DNA have evolved from the discovery of nucleic acid to the development of the double-helix model. In the 1860s, Friedrich Miescher, a physician by profession, was the first person to isolate phosphate-rich chemicals from white blood cells or leukocytes. He named these chemicals (which would eventually be known as RNA and DNA) nuclein because they were isolated from the nuclei of the cells.
Review Questions
If DNA of a particular species was analyzed and it was found that it contains 27 percent A, what would be the percentage of C?
1. 27 percent
2. 30 percent
3. 23 percent
4. 54 percent
Answer
C
The experiments by Hershey and Chase helped confirm that DNA was the hereditary material on the basis of the finding that:
1. radioactive phage were found in the pellet
2. radioactive cells were found in the supernatant
3. radioactive sulfur was found inside the cell
4. radioactive phosphorus was found in the cell
Answer
D
Free Response
Explain Griffith's transformation experiments. What did he conclude from them?
Answer
Live R cells acquired genetic information from the heat-killed S cells that “transformed” the R cells into S cells.
Why were radioactive sulfur and phosphorous used to label bacteriophage in Hershey and Chase's experiments?
Answer
Sulfur is an element found in proteins and phosphorus is a component of nucleic acids.
14.2: DNA Structure and Sequencing
The building blocks of DNA are nucleotides. The important components of the nucleotide are a nitrogenous base, deoxyribose (5-carbon sugar), and a phosphate group. The nucleotide is named depending on the nitrogenous base. The nitrogenous base can be a purine such as adenine (A) and guanine (G), or a pyrimidine such as cytosine (C) and thymine (T).
Review Questions
DNA double helix does not have which of the following?
1. antiparallel configuration
2. complementary base pairing
3. major and minor grooves
4. uracil
Answer
D
In eukaryotes, what is the DNA wrapped around?
1. single-stranded binding proteins
2. sliding clamp
3. polymerase
4. histones
Answer
D
Free Response
Provide a brief summary of the Sanger sequencing method.
Answer
The template DNA strand is mixed with a DNA polymerase, a primer, the 4 deoxynucleotides, and a limiting concentration of 4 dideoxynucleotides. DNA polymerase synthesizes a strand complementary to the template. Incorporation of ddNTPs at different locations results in DNA fragments that have terminated at every possible base in the template. These fragments are separated by gel electrophoresis and visualized by a laser detector to determine the sequence of bases.
Describe the structure and complementary base pairing of DNA.
Answer
DNA has two strands in anti-parallel orientation. The sugar-phosphate linkages form a backbone on the outside, and the bases are paired on the inside: A with T, and G with C, like rungs on a spiral ladder.
14.3: Basics of DNA Replication
The elucidation of the structure of the double helix provided a hint as to how DNA divides and makes copies of itself. This model suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. What was not clear was how the replication took place. There were three models suggested: conservative, semi-conservative, and dispersive.
Review Questions
Meselson and Stahl's experiments proved that DNA replicates by which mode?
1. conservative
2. semi-conservative
3. dispersive
4. none of the above
Answer
B
If the sequence of the 5'-3' strand is AATGCTAC, then the complementary sequence has the following sequence:
1. 3'-AATGCTAC-5'
2. 3'-CATCGTAA-5'
3. 3'-TTACGATG-5'
4. 3'-GTAGCATT-5'
Answer
C
Free Response
How did the scientific community learn that DNA replication takes place in a semi-conservative fashion?
Answer
Meselson’s experiments with E. coli grown in 15N deduced this finding.
14.4: DNA Replication in Prokaryotes
DNA replication has been extremely well studied in prokaryotes primarily because of the small size of the genome and the mutants that are available. E. coli has 4.6 million base pairs in a single circular chromosome and all of it gets replicated in approximately 42 minutes, starting from a single origin of replication and proceeding around the circle in both directions. This means that approximately 1000 nucleotides are added per second. The process is quite rapid and occurs without many mistake
Review Questions
Which of the following components is not involved during the formation of the replication fork?
1. single-strand binding proteins
2. helicase
3. origin of replication
4. ligase
Answer
D
Which of the following does the enzyme primase synthesize?
1. DNA primer
2. RNA primer
3. Okazaki fragments
4. phosphodiester linkage
Answer
B
In which direction does DNA replication take place?
1. 5'-3'
2. 3'-5'
3. 5'
4. 3'
Answer
A
Free Response
DNA replication is bidirectional and discontinuous; explain your understanding of those concepts.
Answer
At an origin of replication, two replication forks are formed that are extended in two directions. On the lagging strand, Okazaki fragments are formed in a discontinuous manner.
What are Okazaki fragments and how they are formed?
Answer
Short DNA fragments are formed on the lagging strand synthesized in a direction away from the replication fork. These are synthesized by DNA pol.
If the rate of replication in a particular prokaryote is 900 nucleotides per second, how long would it take 1.2 million base pair genomes to make two copies?
Answer
1333 seconds or 22.2 minutes.
Explain the events taking place at the replication fork. If the gene for helicase is mutated, what part of replication will be affected?
Answer
At the replication fork, the events taking place are helicase action, binding of single-strand binding proteins, primer synthesis, and synthesis of new strands. If there is a mutated helicase gene, the replication fork will not be extended.
What is the role of a primer in DNA replication? What would happen if you forgot to add a primer in a tube containing the reaction mix for a DNA sequencing reaction?
Answer
Primer provides a 3'-OH group for DNA pol to start adding nucleotides. There would be no reaction in the tube without a primer, and no bands would be visible on the electrophoresis.
14.5: DNA Replication in Eukaryotes
Eukaryotic genomes are much more complex and larger in size than prokaryotic genomes. The human genome has three billion base pairs per haploid set of chromosomes, and 6 billion base pairs are replicated during the S phase of the cell cycle. There are multiple origins of replication on the eukaryotic chromosome; humans can have up to 100,000 origins of replication
Review Questions
The ends of the linear chromosomes are maintained by
1. helicase
2. primase
3. DNA pol
4. telomerase
Answer
D
Free Response
How do the linear chromosomes in eukaryotes ensure that its ends are replicated completely?
Answer
Telomerase has an inbuilt RNA template that extends the 3' end, so primer is synthesized and extended. Thus, the ends are protected.
14.6: DNA Repair
DNA replication is a highly accurate process, but mistakes can occasionally occur, such as a DNA polymerase inserting a wrong base. Uncorrected mistakes may sometimes lead to serious consequences, such as cancer. Repair mechanisms correct the mistakes. In rare cases, mistakes are not corrected, leading to mutations; in other cases, repair enzymes are themselves mutated or defective.
Review Questions
During proofreading, which of the following enzymes reads the DNA?
1. primase
2. topoisomerase
3. DNA pol
4. helicase
Answer
C
The initial mechanism for repairing nucleotide errors in DNA is ________.
1. mismatch repair
2. DNA polymerase proofreading
3. nucleotide excision repair
4. thymine dimers
Answer
B
Free Response
What is the consequence of mutation of a mismatch repair enzyme? How will this affect the function of a gene?
Answer
Mutations are not repaired, as in the case of xeroderma pigmentosa. Gene function may be affected or it may not be expressed. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/14%3A_DNA_Structure_and_Function/14.E%3A_DNA_Structure_and_Function_%28Exercises%29.txt |
Since the rediscovery of Mendel’s work in 1900, the definition of the gene has progressed from an abstract unit of heredity to a tangible molecular entity capable of replication, expression, and mutation. Genes are composed of DNA and are linearly arranged on chromosomes. Genes specify the sequences of amino acids, which are the building blocks of proteins. In turn, proteins are responsible for orchestrating nearly every function of the cell. Both genes and the proteins they encode are absolutely essential to life as we know it.
• 15.0: Prelude to Genes and Proteins
Since the rediscovery of Mendel’s work in 1900, the definition of the gene has progressed from an abstract unit of heredity to a tangible molecular entity capable of replication, expression, and mutation. Genes are composed of DNA and are linearly arranged on chromosomes. Genes specify the sequences of amino acids, which are the building blocks of proteins. In turn, proteins are responsible for orchestrating nearly every function of the cell.
• 15.1: The Genetic Code
The cellular process of transcription generates messenger RNA (mRNA), a mobile molecular copy of one or more genes with an alphabet of A, C, G, and uracil (U). Translation of the mRNA template converts nucleotide-based genetic information into a protein product. Protein sequences consist of 20 commonly occurring amino acids; therefore, it can be said that the protein alphabet consists of 20 letters. Each amino acid is defined by a three-nucleotide sequence called the triplet codon.
• 15.2: Prokaryotic Transcription
The prokaryotes, which include bacteria and archaea, are mostly single-celled organisms that, by definition, lack membrane-bound nuclei and other organelles. A bacterial chromosome is a covalently closed circle that, unlike eukaryotic chromosomes, is not organized around histone proteins. The central region of the cell in which prokaryotic DNA resides is called the nucleoid. Prokaryotes often have abundant plasmids that are shorter circular DNA molecules that may only contain one or a few genes.
• 15.3: Eukaryotic Transcription
Prokaryotes and eukaryotes perform fundamentally the same process of transcription, with a few key differences. The most important difference between prokaryotes and eukaryotes is the latter’s membrane-bound nucleus and organelles. With the genes bound in a nucleus, the eukaryotic cell must be able to transport its mRNA to the cytoplasm and must protect its mRNA from degrading before it is translated.
• 15.4: RNA Processing in Eukaryotes
After transcription, eukaryotic pre-mRNAs must undergo several processing steps before they can be translated. Eukaryotic (and prokaryotic) tRNAs and rRNAs also undergo processing before they can function as components in the protein synthesis machinery.
• 15.5: Ribosomes and Protein Synthesis
The synthesis of proteins consumes more of a cell’s energy than any other metabolic process. In turn, proteins account for more mass than any other component of living organisms (other than water), and proteins perform virtually every function of a cell. The process of translation, or protein synthesis, involves the decoding of an mRNA message into a polypeptide product. Amino acids are covalently bonded by interlinking peptide bonds in lengths ranging from ~50 amino acid residues to >1,000.
• 15.E: Genes and Proteins (Exercises)
Thumbnail: RNA Polymerase producing mRNA from a double-stranded DNA template. (CC BY-SA 3.0; Thomas Splettstoesser via Wikimedia Commons).
15: Genes and Proteins
Since the rediscovery of Mendel’s work in 1900, the definition of the gene has progressed from an abstract unit of heredity to a tangible molecular entity capable of replication, expression, and mutation (Figure \(1\)). Genes are composed of DNA and are linearly arranged on chromosomes. Genes specify the sequences of amino acids, which are the building blocks of proteins. In turn, proteins are responsible for orchestrating nearly every function of the cell. Both genes and the proteins they encode are absolutely essential to life as we know it. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/15%3A_Genes_and_Proteins/15.0%3A_Prelude_to_Genes_and_Proteins.txt |
Skills to Develop
• Explain the “central dogma” of protein synthesis
• Describe the genetic code and how the nucleotide sequence prescribes the amino acid and the protein sequence
The cellular process of transcription generates messenger RNA (mRNA), a mobile molecular copy of one or more genes with an alphabet of A, C, G, and uracil (U). Translation of the mRNA template converts nucleotide-based genetic information into a protein product. Protein sequences consist of 20 commonly occurring amino acids; therefore, it can be said that the protein alphabet consists of 20 letters (Figure $1$). Each amino acid is defined by a three-nucleotide sequence called the triplet codon. Different amino acids have different chemistries (such as acidic versus basic, or polar and nonpolar) and different structural constraints. Variation in amino acid sequence gives rise to enormous variation in protein structure and function.
The Central Dogma: DNA Encodes RNA; RNA Encodes Protein
The flow of genetic information in cells from DNA to mRNA to protein is described by the Central Dogma (Figure $2$), which states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis, while keeping the DNA itself intact and protected. The copying of DNA to RNA is relatively straightforward, with one nucleotide being added to the mRNA strand for every nucleotide read in the DNA strand. The translation to protein is a bit more complex because three mRNA nucleotides correspond to one amino acid in the polypeptide sequence. However, the translation to protein is still systematic and colinear, such that nucleotides 1 to 3 correspond to amino acid 1, nucleotides 4 to 6 correspond to amino acid 2, and so on.
The Genetic Code Is Degenerate and Universal
Given the different numbers of “letters” in the mRNA and protein “alphabets,” scientists theorized that combinations of nucleotides corresponded to single amino acids. Nucleotide doublets would not be sufficient to specify every amino acid because there are only 16 possible two-nucleotide combinations (42). In contrast, there are 64 possible nucleotide triplets (43), which is far more than the number of amino acids. Scientists theorized that amino acids were encoded by nucleotide triplets and that the genetic code was degenerate. In other words, a given amino acid could be encoded by more than one nucleotide triplet. This was later confirmed experimentally; Francis Crick and Sydney Brenner used the chemical mutagen proflavin to insert one, two, or three nucleotides into the gene of a virus. When one or two nucleotides were inserted, protein synthesis was completely abolished. When three nucleotides were inserted, the protein was synthesized and functional. This demonstrated that three nucleotides specify each amino acid. These nucleotide triplets are called codons. The insertion of one or two nucleotides completely changed the triplet reading frame, thereby altering the message for every subsequent amino acid (Figure $4$). Though insertion of three nucleotides caused an extra amino acid to be inserted during translation, the integrity of the rest of the protein was maintained.
Scientists painstakingly solved the genetic code by translating synthetic mRNAs in vitro and sequencing the proteins they specified (Figure $3$).
In addition to instructing the addition of a specific amino acid to a polypeptide chain, three of the 64 codons terminate protein synthesis and release the polypeptide from the translation machinery. These triplets are called nonsense codons, or stop codons. Another codon, AUG, also has a special function. In addition to specifying the amino acid methionine, it also serves as the start codon to initiate translation. The reading frame for translation is set by the AUG start codon near the 5' end of the mRNA.
The genetic code is universal. With a few exceptions, virtually all species use the same genetic code for protein synthesis. Conservation of codons means that a purified mRNA encoding the globin protein in horses could be transferred to a tulip cell, and the tulip would synthesize horse globin. That there is only one genetic code is powerful evidence that all of life on Earth shares a common origin, especially considering that there are about 1084 possible combinations of 20 amino acids and 64 triplet codons.
Link to Learning
Transcribe a gene and translate it to protein using complementary pairing and the genetic code at this site.
Degeneracy is believed to be a cellular mechanism to reduce the negative impact of random mutations. Codons that specify the same amino acid typically only differ by one nucleotide. In addition, amino acids with chemically similar side chains are encoded by similar codons. This nuance of the genetic code ensures that a single-nucleotide substitution mutation might either specify the same amino acid but have no effect or specify a similar amino acid, preventing the protein from being rendered completely nonfunctional.
Scientific Method Connection: Which Has More DNA: A Kiwi or a Strawberry?
Question: Would a kiwifruit and strawberry that are approximately the same size (Figure $5$) also have approximately the same amount of DNA?
Background: Genes are carried on chromosomes and are made of DNA. All mammals are diploid, meaning they have two copies of each chromosome. However, not all plants are diploid. The common strawberry is octoploid (8n) and the cultivated kiwi is hexaploid (6n). Research the total number of chromosomes in the cells of each of these fruits and think about how this might correspond to the amount of DNA in these fruits’ cell nuclei. Read about the technique of DNA isolation to understand how each step in the isolation protocol helps liberate and precipitate DNA.
Hypothesis: Hypothesize whether you would be able to detect a difference in DNA quantity from similarly sized strawberries and kiwis. Which fruit do you think would yield more DNA?
Test your hypothesis: Isolate the DNA from a strawberry and a kiwi that are similarly sized. Perform the experiment in at least triplicate for each fruit.
1. Prepare a bottle of DNA extraction buffer from 900 mL water, 50 mL dish detergent, and two teaspoons of table salt. Mix by inversion (cap it and turn it upside down a few times).
2. Grind a strawberry and a kiwifruit by hand in a plastic bag, or using a mortar and pestle, or with a metal bowl and the end of a blunt instrument. Grind for at least two minutes per fruit.
3. Add 10 mL of the DNA extraction buffer to each fruit, and mix well for at least one minute.
4. Remove cellular debris by filtering each fruit mixture through cheesecloth or porous cloth and into a funnel placed in a test tube or an appropriate container.
5. Pour ice-cold ethanol or isopropanol (rubbing alcohol) into the test tube. You should observe white, precipitated DNA.
6. Gather the DNA from each fruit by winding it around separate glass rods.
Record your observations: Because you are not quantitatively measuring DNA volume, you can record for each trial whether the two fruits produced the same or different amounts of DNA as observed by eye. If one or the other fruit produced noticeably more DNA, record this as well. Determine whether your observations are consistent with several pieces of each fruit.
Analyze your data: Did you notice an obvious difference in the amount of DNA produced by each fruit? Were your results reproducible?
Draw a conclusion: Given what you know about the number of chromosomes in each fruit, can you conclude that chromosome number necessarily correlates to DNA amount? Can you identify any drawbacks to this procedure? If you had access to a laboratory, how could you standardize your comparison and make it more quantitative?
Summary
The genetic code refers to the DNA alphabet (A, T, C, G), the RNA alphabet (A, U, C, G), and the polypeptide alphabet (20 amino acids). The Central Dogma describes the flow of genetic information in the cell from genes to mRNA to proteins. Genes are used to make mRNA by the process of transcription; mRNA is used to synthesize proteins by the process of translation. The genetic code is degenerate because 64 triplet codons in mRNA specify only 20 amino acids and three nonsense codons. Almost every species on the planet uses the same genetic code.
Glossary
Central Dogma
states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins
codon
three consecutive nucleotides in mRNA that specify the insertion of an amino acid or the release of a polypeptide chain during translation
colinear
in terms of RNA and protein, three “units” of RNA (nucleotides) specify one “unit” of protein (amino acid) in a consecutive fashion
degeneracy
(of the genetic code) describes that a given amino acid can be encoded by more than one nucleotide triplet; the code is degenerate, but not ambiguous
nonsense codon
one of the three mRNA codons that specifies termination of translation
reading frame
sequence of triplet codons in mRNA that specify a particular protein; a ribosome shift of one or two nucleotides in either direction completely abolishes synthesis of that protein | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/15%3A_Genes_and_Proteins/15.1%3A_The_Genetic_Code.txt |
Skills to Develop
• List the different steps in prokaryotic transcription
• Discuss the role of promoters in prokaryotic transcription
• Describe how and when transcription is terminated
The prokaryotes, which include bacteria and archaea, are mostly single-celled organisms that, by definition, lack membrane-bound nuclei and other organelles. A bacterial chromosome is a covalently closed circle that, unlike eukaryotic chromosomes, is not organized around histone proteins. The central region of the cell in which prokaryotic DNA resides is called the nucleoid. In addition, prokaryotes often have abundant plasmids, which are shorter circular DNA molecules that may only contain one or a few genes. Plasmids can be transferred independently of the bacterial chromosome during cell division and often carry traits such as antibiotic resistance.
Transcription in prokaryotes (and in eukaryotes) requires the DNA double helix to partially unwind in the region of mRNA synthesis. The region of unwinding is called a transcription bubble. Transcription always proceeds from the same DNA strand for each gene, which is called the template strand. The mRNA product is complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate strand. The only difference is that in mRNA, all of the T nucleotides are replaced with U nucleotides. In an RNA double helix, A can bind U via two hydrogen bonds, just as in A–T pairing in a DNA double helix.
The nucleotide pair in the DNA double helix that corresponds to the site from which the first 5' mRNA nucleotide is transcribed is called the +1 site, or the initiation site. Nucleotides preceding the initiation site are given negative numbers and are designated upstream. Conversely, nucleotides following the initiation site are denoted with “+” numbering and are called downstream nucleotides.
Initiation of Transcription in Prokaryotes
Prokaryotes do not have membrane-enclosed nuclei. Therefore, the processes of transcription, translation, and mRNA degradation can all occur simultaneously. The intracellular level of a bacterial protein can quickly be amplified by multiple transcription and translation events occurring concurrently on the same DNA template. Prokaryotic transcription often covers more than one gene and produces polycistronic mRNAs that specify more than one protein.
Our discussion here will exemplify transcription by describing this process in Escherichia coli, a well-studied bacterial species. Although some differences exist between transcription in E. coli and transcription in archaea, an understanding of E. coli transcription can be applied to virtually all bacterial species.
Prokaryotic RNA Polymerase
Prokaryotes use the same RNA polymerase to transcribe all of their genes. In E. coli, the polymerase is composed of five polypeptide subunits, two of which are identical. Four of these subunits, denoted α, α, β, and β' comprise the polymerase core enzyme. These subunits assemble every time a gene is transcribed, and they disassemble once transcription is complete. Each subunit has a unique role; the two α-subunits are necessary to assemble the polymerase on the DNA; the β-subunit binds to the ribonucleoside triphosphate that will become part of the nascent “recently born” mRNA molecule; and the β' binds the DNA template strand. The fifth subunit, σ, is involved only in transcription initiation. It confers transcriptional specificity such that the polymerase begins to synthesize mRNA from an appropriate initiation site. Without σ, the core enzyme would transcribe from random sites and would produce mRNA molecules that specified protein gibberish. The polymerase comprised of all five subunits is called the holoenzyme.
Prokaryotic Promoters
A promoter is a DNA sequence onto which the transcription machinery binds and initiates transcription. In most cases, promoters exist upstream of the genes they regulate. The specific sequence of a promoter is very important because it determines whether the corresponding gene is transcribed all the time, some of the time, or infrequently. Although promoters vary among prokaryotic genomes, a few elements are conserved. At the -10 and -35 regions upstream of the initiation site, there are two promoter consensus sequences, or regions that are similar across all promoters and across various bacterial species (Figure \(1\)). The -10 consensus sequence, called the -10 region, is TATAAT. The -35 sequence, TTGACA, is recognized and bound by σ. Once this interaction is made, the subunits of the core enzyme bind to the site. The A–T-rich -10 region facilitates unwinding of the DNA template, and several phosphodiester bonds are made. The transcription initiation phase ends with the production of abortive transcripts, which are polymers of approximately 10 nucleotides that are made and released.
Link to Learning
View this MolecularMovies animation to see the first part of transcription and the base sequence repetition of the TATA box.
Elongation and Termination in Prokaryotes
The transcription elongation phase begins with the release of the σ subunit from the polymerase. The dissociation of σ allows the core enzyme to proceed along the DNA template, synthesizing mRNA in the 5' to 3' direction at a rate of approximately 40 nucleotides per second. As elongation proceeds, the DNA is continuously unwound ahead of the core enzyme and rewound behind it (Figure \(2\)). The base pairing between DNA and RNA is not stable enough to maintain the stability of the mRNA synthesis components. Instead, the RNA polymerase acts as a stable linker between the DNA template and the nascent RNA strands to ensure that elongation is not interrupted prematurely.
Prokaryotic Termination Signals
Once a gene is transcribed, the prokaryotic polymerase needs to be instructed to dissociate from the DNA template and liberate the newly made mRNA. Depending on the gene being transcribed, there are two kinds of termination signals. One is protein-based and the other is RNA-based. Rho-dependent termination is controlled by the rho protein, which tracks along behind the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase encounters a run of G nucleotides on the DNA template and it stalls. As a result, the rho protein collides with the polymerase. The interaction with rho releases the mRNA from the transcription bubble.
Rho-independent termination is controlled by specific sequences in the DNA template strand. As the polymerase nears the end of the gene being transcribed, it encounters a region rich in C–G nucleotides. The mRNA folds back on itself, and the complementary C–G nucleotides bind together. The result is a stable hairpin that causes the polymerase to stall as soon as it begins to transcribe a region rich in A–T nucleotides. The complementary U–A region of the mRNA transcript forms only a weak interaction with the template DNA. This, coupled with the stalled polymerase, induces enough instability for the core enzyme to break away and liberate the new mRNA transcript.
Upon termination, the process of transcription is complete. By the time termination occurs, the prokaryotic transcript would already have been used to begin synthesis of numerous copies of the encoded protein because these processes can occur concurrently. The unification of transcription, translation, and even mRNA degradation is possible because all of these processes occur in the same 5' to 3' direction, and because there is no membranous compartmentalization in the prokaryotic cell (Figure \(3\)). In contrast, the presence of a nucleus in eukaryotic cells precludes simultaneous transcription and translation.
Link to Learning
Visit this BioStudio animation to see the process of prokaryotic transcription.
Summary
In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template comprising two consensus sequences that recruit RNA polymerase. The prokaryotic polymerase consists of a core enzyme of four protein subunits and a σ protein that assists only with initiation. Elongation synthesizes mRNA in the 5' to 3' direction at a rate of 40 nucleotides per second. Termination liberates the mRNA and occurs either by rho protein interaction or by the formation of an mRNA hairpin.
Glossary
consensus
DNA sequence that is used by many species to perform the same or similar functions
core enzyme
prokaryotic RNA polymerase consisting of α, α, β, and β' but missing σ; this complex performs elongation
downstream
nucleotides following the initiation site in the direction of mRNA transcription; in general, sequences that are toward the 3' end relative to a site on the mRNA
hairpin
structure of RNA when it folds back on itself and forms intramolecular hydrogen bonds between complementary nucleotides
holoenzyme
prokaryotic RNA polymerase consisting of α, α, β, β', and σ; this complex is responsible for transcription initiation
initiation site
nucleotide from which mRNA synthesis proceeds in the 5' to 3' direction; denoted with a “+1”
nontemplate strand
strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except that T nucleotides in the DNA are replaced by U nucleotides in the mRNA
plasmid
extrachromosomal, covalently closed, circular DNA molecule that may only contain one or a few genes; common in prokaryotes
promoter
DNA sequence to which RNA polymerase and associated factors bind and initiate transcription
Rho-dependent termination
in prokaryotes, termination of transcription by an interaction between RNA polymerase and the rho protein at a run of G nucleotides on the DNA template
Rho-independent
termination sequence-dependent termination of prokaryotic mRNA synthesis; caused by hairpin formation in the mRNA that stalls the polymerase
TATA box
conserved promoter sequence in eukaryotes and prokaryotes that helps to establish the initiation site for transcription
template strand
strand of DNA that specifies the complementary mRNA molecule
transcription bubble
region of locally unwound DNA that allows for transcription of mRNA
upstream
nucleotides preceding the initiation site; in general, sequences toward the 5' end relative to a site on the mRNA | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/15%3A_Genes_and_Proteins/15.2%3A_Prokaryotic_Transcription.txt |
Skills to Develop
• List the steps in eukaryotic transcription
• Discuss the role of RNA polymerases in transcription
• Compare and contrast the three RNA polymerases
• Explain the significance of transcription factors
Prokaryotes and eukaryotes perform fundamentally the same process of transcription, with a few key differences. The most important difference between prokaryotes and eukaryotes is the latter’s membrane-bound nucleus and organelles. With the genes bound in a nucleus, the eukaryotic cell must be able to transport its mRNA to the cytoplasm and must protect its mRNA from degrading before it is translated. Eukaryotes also employ three different polymerases that each transcribe a different subset of genes. Eukaryotic mRNAs are usually monogenic, meaning that they specify a single protein.
Initiation of Transcription in Eukaryotes
Unlike the prokaryotic polymerase that can bind to a DNA template on its own, eukaryotes require several other proteins, called transcription factors, to first bind to the promoter region and then help recruit the appropriate polymerase.
The Three Eukaryotic RNA Polymerases
The features of eukaryotic mRNA synthesis are markedly more complex those of prokaryotes. Instead of a single polymerase comprising five subunits, the eukaryotes have three polymerases that are each made up of 10 subunits or more. Each eukaryotic polymerase also requires a distinct set of transcription factors to bring it to the DNA template.
RNA polymerase I is located in the nucleolus, a specialized nuclear substructure in which ribosomal RNA (rRNA) is transcribed, processed, and assembled into ribosomes (Table \(1\)). The rRNA molecules are considered structural RNAs because they have a cellular role but are not translated into protein. The rRNAs are components of the ribosome and are essential to the process of translation. RNA polymerase I synthesizes all of the rRNAs except for the 5S rRNA molecule. The “S” designation applies to “Svedberg” units, a nonadditive value that characterizes the speed at which a particle sediments during centrifugation.
Table \(1\): Locations, Products, and Sensitivities of the Three Eukaryotic RNA Polymerases
RNA Polymerase Cellular Compartment Product of Transcription α-Amanitin Sensitivity
I Nucleolus All rRNAs except 5S rRNA Insensitive
II Nucleus All protein-coding nuclear pre-mRNAs Extremely sensitive
III Nucleus 5S rRNA, tRNAs, and small nuclear RNAs Moderately sensitive
RNA polymerase II is located in the nucleus and synthesizes all protein-coding nuclear pre-mRNAs. Eukaryotic pre-mRNAs undergo extensive processing after transcription but before translation. For clarity, this module’s discussion of transcription and translation in eukaryotes will use the term “mRNAs” to describe only the mature, processed molecules that are ready to be translated. RNA polymerase II is responsible for transcribing the overwhelming majority of eukaryotic genes.
RNA polymerase III is also located in the nucleus. This polymerase transcribes a variety of structural RNAs that includes the 5S pre-rRNA, transfer pre-RNAs (pre-tRNAs), and small nuclear pre-RNAs. The tRNAs have a critical role in translation; they serve as the adaptor molecules between the mRNA template and the growing polypeptide chain. Small nuclear RNAs have a variety of functions, including “splicing” pre-mRNAs and regulating transcription factors.
A scientist characterizing a new gene can determine which polymerase transcribes it by testing whether the gene is expressed in the presence of a particular mushroom poison, α-amanitin (table above). Interestingly, α-amanitin produced by Amanita phalloides, the Death Cap mushroom, affects the three polymerases very differently. RNA polymerase I is completely insensitive to α-amanitin, meaning that the polymerase can transcribe DNA in vitro in the presence of this poison. In contrast, RNA polymerase II is extremely sensitive to α-amanitin, and RNA polymerase III is moderately sensitive. Knowing the transcribing polymerase can clue a researcher into the general function of the gene being studied. Because RNA polymerase II transcribes the vast majority of genes, we will focus on this polymerase in our subsequent discussions about eukaryotic transcription factors and promoters.
Structure of an RNA Polymerase II Promoter
Eukaryotic promoters are much larger and more complex than prokaryotic promoters, but both have a TATA box. For example, in the mouse thymidine kinase gene, the TATA box is located at approximately -30 relative to the initiation (+1) site (Figure \(1\)). For this gene, the exact TATA box sequence is TATAAAA, as read in the 5' to 3' direction on the nontemplate strand. This sequence is not identical to the E. coli TATA box, but it conserves the A–T rich element. The thermostability of A–T bonds is low and this helps the DNA template to locally unwind in preparation for transcription.
Art Connection
A scientist splices a eukaryotic promoter in front of a bacterial gene and inserts the gene in a bacterial chromosome. Would you expect the bacteria to transcribe the gene?
The mouse genome includes one gene and two pseudogenes for cytoplasmic thymidine kinase. Pseudogenes are genes that have lost their protein-coding ability or are no longer expressed by the cell. These pseudogenes are copied from mRNA and incorporated into the chromosome. For example, the mouse thymidine kinase promoter also has a conserved CAAT box (GGCCAATCT) at approximately -80. This sequence is essential and is involved in binding transcription factors. Further upstream of the TATA box, eukaryotic promoters may also contain one or more GC-rich boxes (GGCG) or octamer boxes (ATTTGCAT). These elements bind cellular factors that increase the efficiency of transcription initiation and are often identified in more “active” genes that are constantly being expressed by the cell.
Transcription Factors for RNA Polymerase II
The complexity of eukaryotic transcription does not end with the polymerases and promoters. An army of basal transcription factors, enhancers, and silencers also help to regulate the frequency with which pre-mRNA is synthesized from a gene. Enhancers and silencers affect the efficiency of transcription but are not necessary for transcription to proceed. Basal transcription factors are crucial in the formation of a preinitiation complex on the DNA template that subsequently recruits RNA polymerase II for transcription initiation.
The names of the basal transcription factors begin with “TFII” (this is the transcription factor for RNA polymerase II) and are specified with the letters A–J. The transcription factors systematically fall into place on the DNA template, with each one further stabilizing the preinitiation complex and contributing to the recruitment of RNA polymerase II.
The processes of bringing RNA polymerases I and III to the DNA template involve slightly less complex collections of transcription factors, but the general theme is the same. Eukaryotic transcription is a tightly regulated process that requires a variety of proteins to interact with each other and with the DNA strand. Although the process of transcription in eukaryotes involves a greater metabolic investment than in prokaryotes, it ensures that the cell transcribes precisely the pre-mRNAs that it needs for protein synthesis.
Evolution Connection: The Evolution of Promoters
The evolution of genes may be a familiar concept. Mutations can occur in genes during DNA replication, and the result may or may not be beneficial to the cell. By altering an enzyme, structural protein, or some other factor, the process of mutation can transform functions or physical features. However, eukaryotic promoters and other gene regulatory sequences may evolve as well. For instance, consider a gene that, over many generations, becomes more valuable to the cell. Maybe the gene encodes a structural protein that the cell needs to synthesize in abundance for a certain function. If this is the case, it would be beneficial to the cell for that gene’s promoter to recruit transcription factors more efficiently and increase gene expression.
Scientists examining the evolution of promoter sequences have reported varying results. In part, this is because it is difficult to infer exactly where a eukaryotic promoter begins and ends. Some promoters occur within genes; others are located very far upstream, or even downstream, of the genes they are regulating. However, when researchers limited their examination to human core promoter sequences that were defined experimentally as sequences that bind the preinitiation complex, they found that promoters evolve even faster than protein-coding genes.
It is still unclear how promoter evolution might correspond to the evolution of humans or other higher organisms. However, the evolution of a promoter to effectively make more or less of a given gene product is an intriguing alternative to the evolution of the genes themselves.1
Promoter Structures for RNA Polymerases I and III
In eukaryotes, the conserved promoter elements differ for genes transcribed by RNA polymerases I, II, and III. RNA polymerase I transcribes genes that have two GC-rich promoter sequences in the -45 to +20 region. These sequences alone are sufficient for transcription initiation to occur, but promoters with additional sequences in the region from -180 to -105 upstream of the initiation site will further enhance initiation. Genes that are transcribed by RNA polymerase III have upstream promoters or promoters that occur within the genes themselves.
Eukaryotic Elongation and Termination
Following the formation of the preinitiation complex, the polymerase is released from the other transcription factors, and elongation is allowed to proceed as it does in prokaryotes with the polymerase synthesizing pre-mRNA in the 5' to 3' direction. As discussed previously, RNA polymerase II transcribes the major share of eukaryotic genes, so this section will focus on how this polymerase accomplishes elongation and termination.
Although the enzymatic process of elongation is essentially the same in eukaryotes and prokaryotes, the DNA template is more complex. When eukaryotic cells are not dividing, their genes exist as a diffuse mass of DNA and proteins called chromatin. The DNA is tightly packaged around charged histone proteins at repeated intervals. These DNA–histone complexes, collectively called nucleosomes, are regularly spaced and include 146 nucleotides of DNA wound around eight histones like thread around a spool.
For polynucleotide synthesis to occur, the transcription machinery needs to move histones out of the way every time it encounters a nucleosome. This is accomplished by a special protein complex called FACT, which stands for “facilitates chromatin transcription.” This complex pulls histones away from the DNA template as the polymerase moves along it. Once the pre-mRNA is synthesized, the FACT complex replaces the histones to recreate the nucleosomes.
The termination of transcription is different for the different polymerases. Unlike in prokaryotes, elongation by RNA polymerase II in eukaryotes takes place 1,000–2,000 nucleotides beyond the end of the gene being transcribed. This pre-mRNA tail is subsequently removed by cleavage during mRNA processing. On the other hand, RNA polymerases I and III require termination signals. Genes transcribed by RNA polymerase I contain a specific 18-nucleotide sequence that is recognized by a termination protein. The process of termination in RNA polymerase III involves an mRNA hairpin similar to rho-independent termination of transcription in prokaryotes.
Summary
Transcription in eukaryotes involves one of three types of polymerases, depending on the gene being transcribed. RNA polymerase II transcribes all of the protein-coding genes, whereas RNA polymerase I transcribes rRNA genes, and RNA polymerase III transcribes rRNA, tRNA, and small nuclear RNA genes. The initiation of transcription in eukaryotes involves the binding of several transcription factors to complex promoter sequences that are usually located upstream of the gene being copied. The mRNA is synthesized in the 5' to 3' direction, and the FACT complex moves and reassembles nucleosomes as the polymerase passes by. Whereas RNA polymerases I and III terminate transcription by protein- or RNA hairpin-dependent methods, RNA polymerase II transcribes for 1,000 or more nucleotides beyond the gene template and cleaves the excess during pre-mRNA processing.
Art Connections
Figure \(2\): A scientist splices a eukaryotic promoter in front of a bacterial gene and inserts the gene in a bacterial chromosome. Would you expect the bacteria to transcribe the gene?
Answer
No. Prokaryotes use different promoters than eukaryotes.
Footnotes
1. 1 H Liang et al., “Fast evolution of core promoters in primate genomes,” Molecular Biology and Evolution 25 (2008): 1239–44.
Glossary
CAAT box
(GGCCAATCT) essential eukaryotic promoter sequence involved in binding transcription factors
FACT
complex that “facilitates chromatin transcription” by disassembling nucleosomes ahead of a transcribing RNA polymerase II and reassembling them after the polymerase passes by
GC-rich box
(GGCG) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter
Octamer box
(ATTTGCAT) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter
preinitiation complex
cluster of transcription factors and other proteins that recruit RNA polymerase II for transcription of a DNA template
small nuclear RNA
molecules synthesized by RNA polymerase III that have a variety of functions, including splicing pre-mRNAs and regulating transcription factors | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/15%3A_Genes_and_Proteins/15.3%3A_Eukaryotic_Transcription.txt |
Skills to Develop
• Describe the different steps in RNA processing
• Understand the significance of exons, introns, and splicing
• Explain how tRNAs and rRNAs are processed
After transcription, eukaryotic pre-mRNAs must undergo several processing steps before they can be translated. Eukaryotic (and prokaryotic) tRNAs and rRNAs also undergo processing before they can function as components in the protein synthesis machinery.
mRNA Processing
The eukaryotic pre-mRNA undergoes extensive processing before it is ready to be translated. The additional steps involved in eukaryotic mRNA maturation create a molecule with a much longer half-life than a prokaryotic mRNA. Eukaryotic mRNAs last for several hours, whereas the typical E. coli mRNA lasts no more than five seconds.
Pre-mRNAs are first coated in RNA-stabilizing proteins; these protect the pre-mRNA from degradation while it is processed and exported out of the nucleus. The three most important steps of pre-mRNA processing are the addition of stabilizing and signaling factors at the 5' and 3' ends of the molecule, and the removal of intervening sequences that do not specify the appropriate amino acids. In rare cases, the mRNA transcript can be “edited” after it is transcribed.
Evolution Connection: RNA Editing in Trypanosomes
The trypanosomes are a group of protozoa that include the pathogen Trypanosoma brucei, which causes sleeping sickness in humans (Figure \(1\)). Trypanosomes, and virtually all other eukaryotes, have organelles called mitochondria that supply the cell with chemical energy. Mitochondria are organelles that express their own DNA and are believed to be the remnants of a symbiotic relationship between a eukaryote and an engulfed prokaryote. The mitochondrial DNA of trypanosomes exhibit an interesting exception to The Central Dogma: their pre-mRNAs do not have the correct information to specify a functional protein. Usually, this is because the mRNA is missing several U nucleotides. The cell performs an additional RNA processing step called RNA editing to remedy this.
Other genes in the mitochondrial genome encode 40- to 80-nucleotide guide RNAs. One or more of these molecules interacts by complementary base pairing with some of the nucleotides in the pre-mRNA transcript. However, the guide RNA has more A nucleotides than the pre-mRNA has U nucleotides to bind with. In these regions, the guide RNA loops out. The 3' ends of guide RNAs have a long poly-U tail, and these U bases are inserted in regions of the pre-mRNA transcript at which the guide RNAs are looped. This process is entirely mediated by RNA molecules. That is, guide RNAs—rather than proteins—serve as the catalysts in RNA editing.
RNA editing is not just a phenomenon of trypanosomes. In the mitochondria of some plants, almost all pre-mRNAs are edited. RNA editing has also been identified in mammals such as rats, rabbits, and even humans. What could be the evolutionary reason for this additional step in pre-mRNA processing? One possibility is that the mitochondria, being remnants of ancient prokaryotes, have an equally ancient RNA-based method for regulating gene expression. In support of this hypothesis, edits made to pre-mRNAs differ depending on cellular conditions. Although speculative, the process of RNA editing may be a holdover from a primordial time when RNA molecules, instead of proteins, were responsible for catalyzing reactions.
5' Capping
While the pre-mRNA is still being synthesized, a 7-methylguanosine cap is added to the 5' end of the growing transcript by a phosphate linkage. This moiety (functional group) protects the nascent mRNA from degradation. In addition, factors involved in protein synthesis recognize the cap to help initiate translation by ribosomes.
3' Poly-A Tail
Once elongation is complete, the pre-mRNA is cleaved by an endonuclease between an AAUAAA consensus sequence and a GU-rich sequence, leaving the AAUAAA sequence on the pre-mRNA. An enzyme called poly-A polymerase then adds a string of approximately 200 A residues, called the poly-A tail. This modification further protects the pre-mRNA from degradation and signals the export of the cellular factors that the transcript needs to the cytoplasm.
Pre-mRNA Splicing
Eukaryotic genes are composed of exons, which correspond to protein-coding sequences (ex-on signifies that they are expressed), and intervening sequences called introns (int-ron denotes their intervening role), which may be involved in gene regulation but are removed from the pre-mRNA during processing. Intron sequences in mRNA do not encode functional proteins.
The discovery of introns came as a surprise to researchers in the 1970s who expected that pre-mRNAs would specify protein sequences without further processing, as they had observed in prokaryotes. The genes of higher eukaryotes very often contain one or more introns. These regions may correspond to regulatory sequences; however, the biological significance of having many introns or having very long introns in a gene is unclear. It is possible that introns slow down gene expression because it takes longer to transcribe pre-mRNAs with lots of introns. Alternatively, introns may be nonfunctional sequence remnants left over from the fusion of ancient genes throughout evolution. This is supported by the fact that separate exons often encode separate protein subunits or domains. For the most part, the sequences of introns can be mutated without ultimately affecting the protein product.
All of a pre-mRNA’s introns must be completely and precisely removed before protein synthesis. If the process errs by even a single nucleotide, the reading frame of the rejoined exons would shift, and the resulting protein would be dysfunctional. The process of removing introns and reconnecting exons is called splicing (Figure \(2\)). Introns are removed and degraded while the pre-mRNA is still in the nucleus. Splicing occurs by a sequence-specific mechanism that ensures introns will be removed and exons rejoined with the accuracy and precision of a single nucleotide. The splicing of pre-mRNAs is conducted by complexes of proteins and RNA molecules called spliceosomes.
Art Connection
Errors in splicing are implicated in cancers and other human diseases. What kinds of mutations might lead to splicing errors? Think of different possible outcomes if splicing errors occur.
Note that more than 70 individual introns can be present, and each has to undergo the process of splicing—in addition to 5' capping and the addition of a poly-A tail—just to generate a single, translatable mRNA molecule.
Link to Learning
See how introns are removed during RNA splicing at this website.
Processing of tRNAs and rRNAs
The tRNAs and rRNAs are structural molecules that have roles in protein synthesis; however, these RNAs are not themselves translated. Pre-rRNAs are transcribed, processed, and assembled into ribosomes in the nucleolus. Pre-tRNAs are transcribed and processed in the nucleus and then released into the cytoplasm where they are linked to free amino acids for protein synthesis.
Most of the tRNAs and rRNAs in eukaryotes and prokaryotes are first transcribed as a long precursor molecule that spans multiple rRNAs or tRNAs. Enzymes then cleave the precursors into subunits corresponding to each structural RNA. Some of the bases of pre-rRNAs are methylated; that is, a –CH3 moiety (methyl functional group) is added for stability. Pre-tRNA molecules also undergo methylation. As with pre-mRNAs, subunit excision occurs in eukaryotic pre-RNAs destined to become tRNAs or rRNAs.
Mature rRNAs make up approximately 50 percent of each ribosome. Some of a ribosome’s RNA molecules are purely structural, whereas others have catalytic or binding activities. Mature tRNAs take on a three-dimensional structure through intramolecular hydrogen bonding to position the amino acid binding site at one end and the anticodon at the other end (Figure \(3\)). The anticodon is a three-nucleotide sequence in a tRNA that interacts with an mRNA codon through complementary base pairing.
Summary
Eukaryotic pre-mRNAs are modified with a 5' methylguanosine cap and a poly-A tail. These structures protect the mature mRNA from degradation and help export it from the nucleus. Pre-mRNAs also undergo splicing, in which introns are removed and exons are reconnected with single-nucleotide accuracy. Only finished mRNAs that have undergone 5' capping, 3' polyadenylation, and intron splicing are exported from the nucleus to the cytoplasm. Pre-rRNAs and pre-tRNAs may be processed by intramolecular cleavage, splicing, methylation, and chemical conversion of nucleotides. Rarely, RNA editing is also performed to insert missing bases after an mRNA has been synthesized.
Art Connections
Figure \(2\): Errors in splicing are implicated in cancers and other human diseases. What kinds of mutations might lead to splicing errors? Think of different possible outcomes if splicing errors occur.
Answer
Mutations in the spliceosome recognition sequence at each end of the intron, or in the proteins and RNAs that make up the spliceosome, may impair splicing. Mutations may also add new spliceosome recognition sites. Splicing errors could lead to introns being retained in spliced RNA, exons being excised, or changes in the location of the splice site.
Glossary
7-methylguanosine cap
modification added to the 5' end of pre-mRNAs to protect mRNA from degradation and assist translation
anticodon
three-nucleotide sequence in a tRNA molecule that corresponds to an mRNA codon
exon
sequence present in protein-coding mRNA after completion of pre-mRNA splicing
intron
non–protein-coding intervening sequences that are spliced from mRNA during processing
poly-A tail
modification added to the 3' end of pre-mRNAs to protect mRNA from degradation and assist mRNA export from the nucleus
RNA editing
direct alteration of one or more nucleotides in an mRNA that has already been synthesized
splicing
process of removing introns and reconnecting exons in a pre-mRNA | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/15%3A_Genes_and_Proteins/15.4%3A_RNA_Processing_in_Eukaryotes.txt |
Skills to Develop
• Describe the different steps in protein synthesis
• Discuss the role of ribosomes in protein synthesis
The synthesis of proteins consumes more of a cell’s energy than any other metabolic process. In turn, proteins account for more mass than any other component of living organisms (with the exception of water), and proteins perform virtually every function of a cell. The process of translation, or protein synthesis, involves the decoding of an mRNA message into a polypeptide product. Amino acids are covalently strung together by interlinking peptide bonds in lengths ranging from approximately 50 amino acid residues to more than 1,000. Each individual amino acid has an amino group (NH2) and a carboxyl (COOH) group. Polypeptides are formed when the amino group of one amino acid forms an amide (i.e., peptide) bond with the carboxyl group of another amino acid (Figure $1$). This reaction is catalyzed by ribosomes and generates one water molecule.
The Protein Synthesis Machinery
In addition to the mRNA template, many molecules and macromolecules contribute to the process of translation. The composition of each component may vary across species; for instance, ribosomes may consist of different numbers of rRNAs and polypeptides depending on the organism. However, the general structures and functions of the protein synthesis machinery are comparable from bacteria to human cells. Translation requires the input of an mRNA template, ribosomes, tRNAs, and various enzymatic factors.
Link to Learning
Click through the steps of this PBS interactive to see protein synthesis in action.
Ribosomes
Even before an mRNA is translated, a cell must invest energy to build each of its ribosomes. In E. coli, there are between 10,000 and 70,000 ribosomes present in each cell at any given time. A ribosome is a complex macromolecule composed of structural and catalytic rRNAs, and many distinct polypeptides. In eukaryotes, the nucleolus is completely specialized for the synthesis and assembly of rRNAs.
Ribosomes exist in the cytoplasm in prokaryotes and in the cytoplasm and rough endoplasmic reticulum in eukaryotes. Mitochondria and chloroplasts also have their own ribosomes in the matrix and stroma, which look more similar to prokaryotic ribosomes (and have similar drug sensitivities) than the ribosomes just outside their outer membranes in the cytoplasm. Ribosomes dissociate into large and small subunits when they are not synthesizing proteins and reassociate during the initiation of translation. In E. coli, the small subunit is described as 30S, and the large subunit is 50S, for a total of 70S (recall that Svedberg units are not additive). Mammalian ribosomes have a small 40S subunit and a large 60S subunit, for a total of 80S. The small subunit is responsible for binding the mRNA template, whereas the large subunit sequentially binds tRNAs. Each mRNA molecule is simultaneously translated by many ribosomes, all synthesizing protein in the same direction: reading the mRNA from 5' to 3' and synthesizing the polypeptide from the N terminus to the C terminus. The complete mRNA/poly-ribosome structure is called a polysome.
tRNAs
The tRNAs are structural RNA molecules that were transcribed from genes by RNA polymerase III. Depending on the species, 40 to 60 types of tRNAs exist in the cytoplasm. Serving as adaptors, specific tRNAs bind to sequences on the mRNA template and add the corresponding amino acid to the polypeptide chain. Therefore, tRNAs are the molecules that actually “translate” the language of RNA into the language of proteins.
Of the 64 possible mRNA codons—or triplet combinations of A, U, G, and C—three specify the termination of protein synthesis and 61 specify the addition of amino acids to the polypeptide chain. Of these 61, one codon (AUG) also encodes the initiation of translation. Each tRNA anticodon can base pair with one of the mRNA codons and add an amino acid or terminate translation, according to the genetic code. For instance, if the sequence CUA occurred on an mRNA template in the proper reading frame, it would bind a tRNA expressing the complementary sequence, GAU, which would be linked to the amino acid leucine.
As the adaptor molecules of translation, it is surprising that tRNAs can fit so much specificity into such a small package. Consider that tRNAs need to interact with three factors: 1) they must be recognized by the correct aminoacyl synthetase (see below); 2) they must be recognized by ribosomes; and 3) they must bind to the correct sequence in mRNA.
Aminoacyl tRNA Synthetases
The process of pre-tRNA synthesis by RNA polymerase III only creates the RNA portion of the adaptor molecule. The corresponding amino acid must be added later, once the tRNA is processed and exported to the cytoplasm. Through the process of tRNA “charging,” each tRNA molecule is linked to its correct amino acid by a group of enzymes called aminoacyl tRNA synthetases. At least one type of aminoacyl tRNA synthetase exists for each of the 20 amino acids; the exact number of aminoacyl tRNA synthetases varies by species. These enzymes first bind and hydrolyze ATP to catalyze a high-energy bond between an amino acid and adenosine monophosphate (AMP); a pyrophosphate molecule is expelled in this reaction. The activated amino acid is then transferred to the tRNA, and AMP is released.
The Mechanism of Protein Synthesis
As with mRNA synthesis, protein synthesis can be divided into three phases: initiation, elongation, and termination. The process of translation is similar in prokaryotes and eukaryotes. Here we’ll explore how translation occurs in E. coli, a representative prokaryote, and specify any differences between prokaryotic and eukaryotic translation.
Initiation of Translation
Protein synthesis begins with the formation of an initiation complex. In E. coli, this complex involves the small 30S ribosome, the mRNA template, three initiation factors (IFs; IF-1, IF-2, and IF-3), and a special initiator tRNA, called $\text{tRNA}_\text{f}^\text{Met}$. The initiator tRNA interacts with the start codon AUG (or rarely, GUG), links to a formylated methionine called fMet, and can also bind IF-2. Formylated methionine is inserted by $\text{fMet} - \text{tRNA}_\text{f}^\text{Met}$ at the beginning of every polypeptide chain synthesized by E. coli, but it is usually clipped off after translation is complete. When an in-frame AUG is encountered during translation elongation, a non-formylated methionine is inserted by a regular Met-tRNAMet.
In E. coli mRNA, a sequence upstream of the first AUG codon, called the Shine-Dalgarno sequence (AGGAGG), interacts with the rRNA molecules that compose the ribosome. This interaction anchors the 30S ribosomal subunit at the correct location on the mRNA template. Guanosine triphosphate (GTP), which is a purine nucleotide triphosphate, acts as an energy source during translation—both at the start of elongation and during the ribosome’s translocation.
In eukaryotes, a similar initiation complex forms, comprising mRNA, the 40S small ribosomal subunit, IFs, and nucleoside triphosphates (GTP and ATP). The charged initiator tRNA, called Met-tRNAi, does not bind fMet in eukaryotes, but is distinct from other Met-tRNAs in that it can bind IFs.
Instead of depositing at the Shine-Dalgarno sequence, the eukaryotic initiation complex recognizes the 7-methylguanosine cap at the 5' end of the mRNA. A cap-binding protein (CBP) and several other IFs assist the movement of the ribosome to the 5' cap. Once at the cap, the initiation complex tracks along the mRNA in the 5' to 3' direction, searching for the AUG start codon. Many eukaryotic mRNAs are translated from the first AUG, but this is not always the case. According to Kozak’s rules, the nucleotides around the AUG indicate whether it is the correct start codon. Kozak’s rules state that the following consensus sequence must appear around the AUG of vertebrate genes: 5'-gccRccAUGG-3'. The R (for purine) indicates a site that can be either A or G, but cannot be C or U. Essentially, the closer the sequence is to this consensus, the higher the efficiency of translation.
Once the appropriate AUG is identified, the other proteins and CBP dissociate, and the 60S subunit binds to the complex of Met-tRNAi, mRNA, and the 40S subunit. This step completes the initiation of translation in eukaryotes.
Translation, Elongation, and Termination
In prokaryotes and eukaryotes, the basics of elongation are the same, so we will review elongation from the perspective of E. coli. The 50S ribosomal subunit of E. coli consists of three compartments: the A (aminoacyl) site binds incoming charged aminoacyl tRNAs. The P (peptidyl) site binds charged tRNAs carrying amino acids that have formed peptide bonds with the growing polypeptide chain but have not yet dissociated from their corresponding tRNA. The E (exit) site releases dissociated tRNAs so that they can be recharged with free amino acids. There is one exception to this assembly line of tRNAs: in E. coli, $\text{fMet} - \text{tRNA}_\text{f}^\text{Met}$ is capable of entering the P site directly without first entering the A site. Similarly, the eukaryotic Met-tRNAi, with help from other proteins of the initiation complex, binds directly to the P site. In both cases, this creates an initiation complex with a free A site ready to accept the tRNA corresponding to the first codon after the AUG.
During translation elongation, the mRNA template provides specificity. As the ribosome moves along the mRNA, each mRNA codon comes into register, and specific binding with the corresponding charged tRNA anticodon is ensured. If mRNA were not present in the elongation complex, the ribosome would bind tRNAs nonspecifically.
Elongation proceeds with charged tRNAs entering the A site and then shifting to the P site followed by the E site with each single-codon “step” of the ribosome. Ribosomal steps are induced by conformational changes that advance the ribosome by three bases in the 3' direction. The energy for each step of the ribosome is donated by an elongation factor that hydrolyzes GTP. Peptide bonds form between the amino group of the amino acid attached to the A-site tRNA and the carboxyl group of the amino acid attached to the P-site tRNA. The formation of each peptide bond is catalyzed by peptidyl transferase, an RNA-based enzyme that is integrated into the 50S ribosomal subunit. The energy for each peptide bond formation is derived from GTP hydrolysis, which is catalyzed by a separate elongation factor. The amino acid bound to the P-site tRNA is also linked to the growing polypeptide chain. As the ribosome steps across the mRNA, the former P-site tRNA enters the E site, detaches from the amino acid, and is expelled (Figure $2$). Amazingly, the E. coli translation apparatus takes only 0.05 seconds to add each amino acid, meaning that a 200-amino acid protein can be translated in just 10 seconds.
Art Connection
Many antibiotics inhibit bacterial protein synthesis. For example, tetracycline blocks the A site on the bacterial ribosome, and chloramphenicol blocks peptidyl transfer. What specific effect would you expect each of these antibiotics to have on protein synthesis?
Tetracycline would directly affect:
1. tRNA binding to the ribosome
2. ribosome assembly
3. growth of the protein chain
Chloramphenicol would directly affect
1. tRNA binding to the ribosome
2. ribosome assembly
3. growth of the protein chain
Termination of translation occurs when a nonsense codon (UAA, UAG, or UGA) is encountered. Upon aligning with the A site, these nonsense codons are recognized by release factors in prokaryotes and eukaryotes that instruct peptidyl transferase to add a water molecule to the carboxyl end of the P-site amino acid. This reaction forces the P-site amino acid to detach from its tRNA, and the newly made protein is released. The small and large ribosomal subunits dissociate from the mRNA and from each other; they are recruited almost immediately into another translation initiation complex. After many ribosomes have completed translation, the mRNA is degraded so the nucleotides can be reused in another transcription reaction.
Protein Folding, Modification, and Targeting
During and after translation, individual amino acids may be chemically modified, signal sequences may be appended, and the new protein “folds” into a distinct three-dimensional structure as a result of intramolecular interactions. A signal sequence is a short tail of amino acids that directs a protein to a specific cellular compartment. These sequences at the amino end or the carboxyl end of the protein can be thought of as the protein’s “train ticket” to its ultimate destination. Other cellular factors recognize each signal sequence and help transport the protein from the cytoplasm to its correct compartment. For instance, a specific sequence at the amino terminus will direct a protein to the mitochondria or chloroplasts (in plants). Once the protein reaches its cellular destination, the signal sequence is usually clipped off.
Many proteins fold spontaneously, but some proteins require helper molecules, called chaperones, to prevent them from aggregating during the complicated process of folding. Even if a protein is properly specified by its corresponding mRNA, it could take on a completely dysfunctional shape if abnormal temperature or pH conditions prevent it from folding correctly.
Summary
The players in translation include the mRNA template, ribosomes, tRNAs, and various enzymatic factors. The small ribosomal subunit forms on the mRNA template either at the Shine-Dalgarno sequence (prokaryotes) or the 5' cap (eukaryotes). Translation begins at the initiating AUG on the mRNA, specifying methionine. The formation of peptide bonds occurs between sequential amino acids specified by the mRNA template according to the genetic code. Charged tRNAs enter the ribosomal A site, and their amino acid bonds with the amino acid at the P site. The entire mRNA is translated in three-nucleotide “steps” of the ribosome. When a nonsense codon is encountered, a release factor binds and dissociates the components and frees the new protein. Folding of the protein occurs during and after translation.
Art Connections
Figure $2$: Many antibiotics inhibit bacterial protein synthesis. For example, tetracycline blocks the A site on the bacterial ribosome, and chloramphenicol blocks peptidyl transfer. What specific effect would you expect each of these antibiotics to have on protein synthesis?
Tetracycline would directly affect:
1. tRNA binding to the ribosome
2. ribosome assembly
3. growth of the protein chain
Chloramphenicol would directly affect
1. tRNA binding to the ribosome
2. ribosome assembly
3. growth of the protein chain
Answer
Tetracycline: a; Chloramphenicol: c.
Glossary
aminoacyl tRNA synthetase
enzyme that “charges” tRNA molecules by catalyzing a bond between the tRNA and a corresponding amino acid
initiator tRNA
in prokaryotes, called $\text{tRNA}_\text{f}^\text{Met}$; in eukaryotes, called tRNAi; a tRNA that interacts with a start codon, binds directly to the ribosome P site, and links to a special methionine to begin a polypeptide chain
Kozak’s rules
determines the correct initiation AUG in a eukaryotic mRNA; the following consensus sequence must appear around the AUG: 5’-GCC(purine)CCAUGG-3’; the bolded bases are most important
peptidyl transferase
RNA-based enzyme that is integrated into the 50S ribosomal subunit and catalyzes the formation of peptide bonds
polysome
mRNA molecule simultaneously being translated by many ribosomes all going in the same direction
Shine-Dalgarno sequence
(AGGAGG); initiates prokaryotic translation by interacting with rRNA molecules comprising the 30S ribosome
signal sequence
short tail of amino acids that directs a protein to a specific cellular compartment
start codon
AUG (or rarely, GUG) on an mRNA from which translation begins; always specifies methionine | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/15%3A_Genes_and_Proteins/15.5%3A_Ribosomes_and_Protein_Synthesis.txt |
15.1: The Genetic Code
Review Questions
The AUC and AUA codons in mRNA both specify isoleucine. What feature of the genetic code explains this?
1. complementarity
2. nonsense codons
3. universality
4. degeneracy
Answer
D
How many nucleotides are in 12 mRNA codons?
1. 12
2. 24
3. 36
4. 48
Answer
C
Free Response
Imagine if there were 200 commonly occurring amino acids instead of 20. Given what you know about the genetic code, what would be the shortest possible codon length? Explain.
Answer
For 200 commonly occurring amino acids, codons consisting of four types of nucleotides would have to be at least four nucleotides long, because 44 = 256. There would be much less degeneracy in this case.
Discuss how degeneracy of the genetic code makes cells more robust to mutations.
Answer
Codons that specify the same amino acid typically only differ by one nucleotide. In addition, amino acids with chemically similar side chains are encoded by similar codons. This nuance of the genetic code ensures that a single-nucleotide substitution mutation might either specify the same amino acid and have no effect, or may specify a similar amino acid, preventing the protein from being rendered completely nonfunctional.
15.2: Prokaryotic Transcription
Review Questions
Which subunit of the E. coli polymerase confers specificity to transcription?
1. α
2. β
3. β'
4. σ
Answer
D
The -10 and -35 regions of prokaryotic promoters are called consensus sequences because ________.
1. they are identical in all bacterial species
2. they are similar in all bacterial species
3. they exist in all organisms
4. they have the same function in all organisms
Answer
B
Free Response
If mRNA is complementary to the DNA template strand and the DNA template strand is complementary to the DNA nontemplate strand, then why are base sequences of mRNA and the DNA nontemplate strand not identical? Could they ever be?
Answer
DNA is different from RNA in that T nucleotides in DNA are replaced with U nucleotides in RNA. Therefore, they could never be identical in base sequence.
In your own words, describe the difference between rho-dependent and rho-independent termination of transcription in prokaryotes.
Answer
Rho-dependent termination is controlled by the rho protein, which tracks along behind the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase stalls at a run of G nucleotides on the DNA template. The rho protein collides with the polymerase and releases mRNA from the transcription bubble. Rho-independent termination is controlled by specific sequences in the DNA template strand. As the polymerase nears the end of the gene being transcribed, it encounters a region rich in C–G nucleotides. This creates an mRNA hairpin that causes the polymerase to stall right as it begins to transcribe a region rich in A–T nucleotides. Because A–U bonds are less thermostable, the core enzyme falls away.
15.3: Eukaryotic Transcription
Review Questions
Which feature of promoters can be found in both prokaryotes and eukaryotes?
1. GC box
2. TATA box
3. octamer box
4. -10 and -35 sequences
Answer
B
What transcripts will be most affected by low levels of α-amanitin?
1. 18S and 28S rRNAs
2. pre-mRNAs
3. 5S rRNAs and tRNAs
4. other small nuclear RNAs
Answer
B
15.4: RNA Processing in Eukaryotes
Review Questions
Which pre-mRNA processing step is important for initiating translation?
1. poly-A tail
2. RNA editing
3. splicing
4. 7-methylguanosine cap
Answer
D
What processing step enhances the stability of pre-tRNAs and pre-rRNAs?
1. methylation
2. nucleotide modification
3. cleavage
4. splicing
Answer
A
15.5: Ribosomes and Protein Synthesis
Review Questions
The RNA components of ribosomes are synthesized in the ________.
1. cytoplasm
2. nucleus
3. nucleolus
4. endoplasmic reticulum
Answer
C
In any given species, there are at least how many types of aminoacyl tRNA synthetases?
1. 20
2. 40
3. 100
4. 200
Answer
A
Free Response
Transcribe and translate the following DNA sequence (nontemplate strand): 5'-ATGGCCGGTTATTAAGCA-3'
Answer
The mRNA would be: 5'-AUGGCCGGUUAUUAAGCA-3'. The protein would be: MAGY. Even though there are six codons, the fifth codon corresponds to a stop, so the sixth codon would not be translated.
Explain how single nucleotide changes can have vastly different effects on protein function.
Answer
Nucleotide changes in the third position of codons may not change the amino acid and would have no effect on the protein. Other nucleotide changes that change important amino acids or create or delete start or stop codons would have severe effects on the amino acid sequence of the protein. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/15%3A_Genes_and_Proteins/15.E%3A_Genes_and_Proteins_%28Exercises%29.txt |
Whereas each cell shares the same genome and DNA sequence, each cell does not turn on, or express, the same set of genes. Each cell type needs a different set of proteins to perform its function. Therefore, only a small subset of proteins is expressed in a cell. For the proteins to be expressed, the DNA must be transcribed into RNA and the RNA must be translated into protein. In a given cell type, not all genes encoded in the DNA are transcribed into RNA or translated into protein because specific cells in our body have specific functions. Specialized proteins that make up the eye (iris, lens, and cornea) are only expressed in the eye, whereas the specialized proteins in the heart (pacemaker cells, heart muscle, and valves) are only expressed in the heart. At any given time, only a subset of all of the genes encoded by our DNA are expressed and translated into proteins. The expression of specific genes is a highly regulated process with many levels and stages of control. This complexity ensures the proper expression in the proper cell at the proper time.
• 16.0: Prelude to Gene Expression
Each somatic cell in the body generally contains the same DNA. A few exceptions include red blood cells, which contain no DNA in their mature state, and some immune system cells that rearrange their DNA while producing antibodies. In general, however, the genes that determine whether you have green eyes, brown hair, and how fast you metabolize food are the same in the cells in your eyes and your liver, even though these organs function quite differently.
• 16.1: Regulation of Gene Expression
The regulation of gene expression conserves energy and space. It would require a significant amount of energy for an organism to express every gene at all times, so it is more energy efficient to turn on the genes only when they are required. In addition, only expressing a subset of genes in each cell saves space because DNA must be unwound from its tightly coiled structure to transcribe and translate the DNA.
• 16.2: Prokaryotic Gene Regulation
The DNA of prokaryotes is organized into a circular chromosome supercoiled in the nucleoid region of the cell cytoplasm. Proteins that are needed for a specific function, or that are involved in the same biochemical pathway, are encoded together in blocks called operons. For example, all of the genes needed to use lactose as an energy source are coded next to each other in the lactose (or lac) operon.
• 16.3: Eukaryotic Epigenetic Gene Regulation
Eukaryotic gene expression is more complex than prokaryotic gene expression because the processes of transcription and translation are physically separated. Unlike prokaryotic cells, eukaryotic cells can regulate gene expression at many different levels. Eukaryotic gene expression begins with control of access to the DNA. This form of regulation, called epigenetic regulation, occurs even before transcription is initiated.
• 16.4: Eukaryotic Transcription Gene Regulation
Like prokaryotic cells, the transcription of genes in eukaryotes requires the actions of an RNA polymerase to bind to a sequence upstream of a gene to initiate transcription. However, unlike prokaryotic cells, the eukaryotic RNA polymerase requires other proteins, or transcription factors, to facilitate transcription initiation. Transcription factors are proteins that bind to the promoter sequence and other regulatory sequences to control the transcription of the target gene.
• 16.5: Eukaryotic Post-transcriptional Gene Regulation
RNA is transcribed, but must be processed into a mature form before translation can begin. This processing after an RNA molecule has been transcribed, but before it is translated into a protein, is called post-transcriptional modification. As with the epigenetic and transcriptional stages of processing, this post-transcriptional step can also be regulated to control gene expression in the cell. If the RNA is not processed, shuttled, or translated, then no protein will be synthesized.
• 16.6: Eukaryotic Translational and Post-translational Gene Regulation
After the RNA has been transported to the cytoplasm, it is translated into protein. Control of this process is largely dependent on the RNA molecule. As previously discussed, the stability of the RNA will have a large impact on its translation into a protein. As the stability changes, the amount of time that it is available for translation also changes.
• 16.7: Cancer and Gene Regulation
Cancer is not a single disease but includes many different diseases. In cancer cells, mutations modify cell-cycle control and cells don’t stop growing as they normally would. Mutations can also alter the growth rate or the progression of the cell through the cell cycle. One example of a gene modification that alters the growth rate is increased phosphorylation of cyclin B, a protein that controls the progression of a cell through the cell cycle and serves as a cell-cycle checkpoint protein.
• 16.E: Gene Expression (Exercises)
Thumbnail: Nucleosomes spaced far apart so that the DNA is exposed. Transcription factors can bind, allowing gene expression to occur. (CC BY 4.0 / modified from original; OpenStax).
16: Gene Expression
Each somatic cell in the body generally contains the same DNA. A few exceptions include red blood cells, which contain no DNA in their mature state, and some immune system cells that rearrange their DNA while producing antibodies. In general, however, the genes that determine whether you have green eyes, brown hair, and how fast you metabolize food are the same in the cells in your eyes and your liver, even though these organs function quite differently. If each cell has the same DNA, how is it that cells or organs are different? Why do cells in the eye differ so dramatically from cells in the liver?
Whereas each cell shares the same genome and DNA sequence, each cell does not turn on, or express, the same set of genes. Each cell type needs a different set of proteins to perform its function. Therefore, only a small subset of proteins is expressed in a cell. For the proteins to be expressed, the DNA must be transcribed into RNA and the RNA must be translated into protein. In a given cell type, not all genes encoded in the DNA are transcribed into RNA or translated into protein because specific cells in our body have specific functions. Specialized proteins that make up the eye (iris, lens, and cornea) are only expressed in the eye, whereas the specialized proteins in the heart (pacemaker cells, heart muscle, and valves) are only expressed in the heart. At any given time, only a subset of all of the genes encoded by our DNA are expressed and translated into proteins. The expression of specific genes is a highly regulated process with many levels and stages of control. This complexity ensures the proper expression in the proper cell at the proper time. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/16%3A_Gene_Expression/16.0%3A_Prelude_to_Gene_Expression.txt |
Skills to Develop
• Discuss why every cell does not express all of its genes
• Describe how prokaryotic gene regulation occurs at the transcriptional level
• Discuss how eukaryotic gene regulation occurs at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels
For a cell to function properly, necessary proteins must be synthesized at the proper time. All cells control or regulate the synthesis of proteins from information encoded in their DNA. The process of turning on a gene to produce RNA and protein is called gene expression. Whether in a simple unicellular organism or a complex multi-cellular organism, each cell controls when and how its genes are expressed. For this to occur, there must be a mechanism to control when a gene is expressed to make RNA and protein, how much of the protein is made, and when it is time to stop making that protein because it is no longer needed.
The regulation of gene expression conserves energy and space. It would require a significant amount of energy for an organism to express every gene at all times, so it is more energy efficient to turn on the genes only when they are required. In addition, only expressing a subset of genes in each cell saves space because DNA must be unwound from its tightly coiled structure to transcribe and translate the DNA. Cells would have to be enormous if every protein were expressed in every cell all the time.
The control of gene expression is extremely complex. Malfunctions in this process are detrimental to the cell and can lead to the development of many diseases, including cancer.
Prokaryotic versus Eukaryotic Gene Expression
To understand how gene expression is regulated, we must first understand how a gene codes for a functional protein in a cell. The process occurs in both prokaryotic and eukaryotic cells, just in slightly different manners.
Prokaryotic organisms are single-celled organisms that lack a cell nucleus, and their DNA therefore floats freely in the cell cytoplasm. To synthesize a protein, the processes of transcription and translation occur almost simultaneously. When the resulting protein is no longer needed, transcription stops. As a result, the primary method to control what type of protein and how much of each protein is expressed in a prokaryotic cell is the regulation of DNA transcription. All of the subsequent steps occur automatically. When more protein is required, more transcription occurs. Therefore, in prokaryotic cells, the control of gene expression is mostly at the transcriptional level.
Eukaryotic cells, in contrast, have intracellular organelles that add to their complexity. In eukaryotic cells, the DNA is contained inside the cell’s nucleus and there it is transcribed into RNA. The newly synthesized RNA is then transported out of the nucleus into the cytoplasm, where ribosomes translate the RNA into protein. The processes of transcription and translation are physically separated by the nuclear membrane; transcription occurs only within the nucleus, and translation occurs only outside the nucleus in the cytoplasm. The regulation of gene expression can occur at all stages of the process (Figure \(1\)). Regulation may occur when the DNA is uncoiled and loosened from nucleosomes to bind transcription factors (epigenetic level), when the RNA is transcribed (transcriptional level), when the RNA is processed and exported to the cytoplasm after it is transcribed (post-transcriptional level), when the RNA is translated into protein (translational level), or after the protein has been made (post-translational level).
The differences in the regulation of gene expression between prokaryotes and eukaryotes are summarized below. The regulation of gene expression is discussed in detail in subsequent modules.
Table \(1\): Differences in the Regulation of Gene Expression of Prokaryotic and Eukaryotic Organisms
Prokaryotic organisms Eukaryotic organisms
Lack nucleus Contain nucleus
DNA is found in the cytoplasm DNA is confined to the nuclear compartment
RNA transcription and protein formation occur almost simultaneously RNA transcription occurs prior to protein formation, and it takes place in the nucleus. Translation of RNA to protein occurs in the cytoplasm.
Gene expression is regulated primarily at the transcriptional level Gene expression is regulated at many levels (epigenetic, transcriptional, nuclear shuttling, post-transcriptional, translational, and post-translational)
Evolution Connection: Evolution of Gene Regulation
Prokaryotic cells can only regulate gene expression by controlling the amount of transcription. As eukaryotic cells evolved, the complexity of the control of gene expression increased. For example, with the evolution of eukaryotic cells came compartmentalization of important cellular components and cellular processes. A nuclear region that contains the DNA was formed. Transcription and translation were physically separated into two different cellular compartments. It therefore became possible to control gene expression by regulating transcription in the nucleus, and also by controlling the RNA levels and protein translation present outside the nucleus.
Some cellular processes arose from the need of the organism to defend itself. Cellular processes such as gene silencing developed to protect the cell from viral or parasitic infections. If the cell could quickly shut off gene expression for a short period of time, it would be able to survive an infection when other organisms could not. Therefore, the organism evolved a new process that helped it survive, and it was able to pass this new development to offspring.
Summary
While all somatic cells within an organism contain the same DNA, not all cells within that organism express the same proteins. Prokaryotic organisms express the entire DNA they encode in every cell, but not necessarily all at the same time. Proteins are expressed only when they are needed. Eukaryotic organisms express a subset of the DNA that is encoded in any given cell. In each cell type, the type and amount of protein is regulated by controlling gene expression. To express a protein, the DNA is first transcribed into RNA, which is then translated into proteins. In prokaryotic cells, these processes occur almost simultaneously. In eukaryotic cells, transcription occurs in the nucleus and is separate from the translation that occurs in the cytoplasm. Gene expression in prokaryotes is regulated only at the transcriptional level, whereas in eukaryotic cells, gene expression is regulated at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels.
Glossary
epigenetic
heritable changes that do not involve changes in the DNA sequence
gene expression
processes that control the turning on or turning off of a gene
post-transcriptional
control of gene expression after the RNA molecule has been created but before it is translated into protein
post-translational
control of gene expression after a protein has been created | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/16%3A_Gene_Expression/16.1%3A_Regulation_of_Gene_Expression.txt |
Skills to Develop
• Describe the steps involved in prokaryotic gene regulation
• Explain the roles of activators, inducers, and repressors in gene regulation
The DNA of prokaryotes is organized into a circular chromosome supercoiled in the nucleoid region of the cell cytoplasm. Proteins that are needed for a specific function, or that are involved in the same biochemical pathway, are encoded together in blocks called operons. For example, all of the genes needed to use lactose as an energy source are coded next to each other in the lactose (or lac) operon.
In prokaryotic cells, there are three types of regulatory molecules that can affect the expression of operons: repressors, activators, and inducers. Repressors are proteins that suppress transcription of a gene in response to an external stimulus, whereas activators are proteins that increase the transcription of a gene in response to an external stimulus. Finally, inducers are small molecules that either activate or repress transcription depending on the needs of the cell and the availability of substrate.
The trp Operon: A Repressor Operon
Bacteria such as E. coli need amino acids to survive. Tryptophan is one such amino acid that E. coli can ingest from the environment. E. coli can also synthesize tryptophan using enzymes that are encoded by five genes. These five genes are next to each other in what is called the tryptophan (trp) operon (Figure \(1\)). If tryptophan is present in the environment, then E. coli does not need to synthesize it and the switch controlling the activation of the genes in the trp operon is switched off. However, when tryptophan availability is low, the switch controlling the operon is turned on, transcription is initiated, the genes are expressed, and tryptophan is synthesized.
A DNA sequence that codes for proteins is referred to as the coding region. The five coding regions for the tryptophan biosynthesis enzymes are arranged sequentially on the chromosome in the operon. Just before the coding region is the transcriptional start site. This is the region of DNA to which RNA polymerase binds to initiate transcription. The promoter sequence is upstream of the transcriptional start site; each operon has a sequence within or near the promoter to which proteins (activators or repressors) can bind and regulate transcription.
A DNA sequence called the operator sequence is encoded between the promoter region and the first trp coding gene. This operator contains the DNA code to which the repressor protein can bind. When tryptophan is present in the cell, two tryptophan molecules bind to the trp repressor, which changes shape to bind to the trp operator. Binding of the tryptophan–repressor complex at the operator physically prevents the RNA polymerase from binding, and transcribing the downstream genes.
When tryptophan is not present in the cell, the repressor by itself does not bind to the operator; therefore, the operon is active and tryptophan is synthesized. Because the repressor protein actively binds to the operator to keep the genes turned off, the trp operon is negatively regulated and the proteins that bind to the operator to silence trp expression are negative regulators.
Link to Learning
Watch this video to learn more about the trp operon.
Catabolite Activator Protein (CAP): An Activator Regulator
Just as the trp operon is negatively regulated by tryptophan molecules, there are proteins that bind to the operator sequences that act as a positive regulator to turn genes on and activate them. For example, when glucose is scarce, E. coli bacteria can turn to other sugar sources for fuel. To do this, new genes to process these alternate genes must be transcribed. When glucose levels drop, cyclic AMP (cAMP) begins to accumulate in the cell. The cAMP molecule is a signaling molecule that is involved in glucose and energy metabolism in E. coli. When glucose levels decline in the cell, accumulating cAMP binds to the positive regulator catabolite activator protein (CAP), a protein that binds to the promoters of operons that control the processing of alternative sugars. When cAMP binds to CAP, the complex binds to the promoter region of the genes that are needed to use the alternate sugar sources (Figure \(2\)). In these operons, a CAP binding site is located upstream of the RNA polymerase binding site in the promoter. This increases the binding ability of RNA polymerase to the promoter region and the transcription of the genes.
The lac Operon: An Inducer Operon
The third type of gene regulation in prokaryotic cells occurs through inducible operons, which have proteins that bind to activate or repress transcription depending on the local environment and the needs of the cell. The lac operon is a typical inducible operon. As mentioned previously, E. coli is able to use other sugars as energy sources when glucose concentrations are low. To do so, the cAMP–CAP protein complex serves as a positive regulator to induce transcription. One such sugar source is lactose. The lac operon encodes the genes necessary to acquire and process the lactose from the local environment. CAP binds to the operator sequence upstream of the promoter that initiates transcription of the lac operon. However, for the lac operon to be activated, two conditions must be met. First, the level of glucose must be very low or non-existent. Second, lactose must be present. Only when glucose is absent and lactose is present will the lac operon be transcribed (Figure \(3\)). This makes sense for the cell, because it would be energetically wasteful to create the proteins to process lactose if glucose was plentiful or lactose was not available.
Art Connection
In E. coli, the trp operon is on by default, while the lac operon is off. Why do you think this is the case?
If glucose is absent, then CAP can bind to the operator sequence to activate transcription. If lactose is absent, then the repressor binds to the operator to prevent transcription. If either of these requirements is met, then transcription remains off. Only when both conditions are satisfied is the lac operon transcribed (Table \(1\)).
Table \(1\): Signals that Induce or Repress Transcription of the lac Operon
Glucose CAP binds Lactose Repressor binds Transcription
+ - - + No
+ - + - Some
- + - + No
- + + - Yes
Link to Learning
Watch an animated tutorial about the workings of lac operon here.
Summary
The regulation of gene expression in prokaryotic cells occurs at the transcriptional level. There are three ways to control the transcription of an operon: repressive control, activator control, and inducible control. Repressive control, typified by the trp operon, uses proteins bound to the operator sequence to physically prevent the binding of RNA polymerase and the activation of transcription. Therefore, if tryptophan is not needed, the repressor is bound to the operator and transcription remains off. Activator control, typified by the action of CAP, increases the binding ability of RNA polymerase to the promoter when CAP is bound. In this case, low levels of glucose result in the binding of cAMP to CAP. CAP then binds the promoter, which allows RNA polymerase to bind to the promoter better. In the last example—the lac operon—two conditions must be met to initiate transcription. Glucose must not be present, and lactose must be available for the lac operon to be transcribed. If glucose is absent, CAP binds to the operator. If lactose is present, the repressor protein does not bind to its operator. Only when both conditions are met will RNA polymerase bind to the promoter to induce transcription.
Art Connections
Figure \(3\): In E. coli, the trp operon is on by default, while the lac operon is off. Why do you think that this is the case?
Answer
Tryptophan is an amino acid essential for making proteins, so the cell always needs to have some on hand. However, if plenty of tryptophan is present, it is wasteful to make more, and the expression of the trp receptor is repressed. Lactose, a sugar found in milk, is not always available. It makes no sense to make the enzymes necessary to digest an energy source that is not available, so the lac operon is only turned on when lactose is present.
Glossary
activator
protein that binds to prokaryotic operators to increase transcription
catabolite activator protein (CAP)
protein that complexes with cAMP to bind to the promoter sequences of operons that control sugar processing when glucose is not available
inducible operon
operon that can be activated or repressed depending on cellular needs and the surrounding environment
lac operon
operon in prokaryotic cells that encodes genes required for processing and intake of lactose
negative regulator
protein that prevents transcription
operator
region of DNA outside of the promoter region that binds activators or repressors that control gene expression in prokaryotic cells
operon
collection of genes involved in a pathway that are transcribed together as a single mRNA in prokaryotic cells
positive regulator
protein that increases transcription
repressor
protein that binds to the operator of prokaryotic genes to prevent transcription
transcriptional start site
site at which transcription begins
trp operon
series of genes necessary to synthesize tryptophan in prokaryotic cells
tryptophan
amino acid that can be synthesized by prokaryotic cells when necessary | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/16%3A_Gene_Expression/16.2%3A_Prokaryotic_Gene_Regulation.txt |
Skills to Develop
• Explain the process of epigenetic regulation
• Describe how access to DNA is controlled by histone modification
Eukaryotic gene expression is more complex than prokaryotic gene expression because the processes of transcription and translation are physically separated. Unlike prokaryotic cells, eukaryotic cells can regulate gene expression at many different levels. Eukaryotic gene expression begins with control of access to the DNA. This form of regulation, called epigenetic regulation, occurs even before transcription is initiated.
Epigenetic Control: Regulating Access to Genes within the Chromosome
The human genome encodes over 20,000 genes; each of the 23 pairs of human chromosomes encodes thousands of genes. The DNA in the nucleus is precisely wound, folded, and compacted into chromosomes so that it will fit into the nucleus. It is also organized so that specific segments can be accessed as needed by a specific cell type.
The first level of organization, or packing, is the winding of DNA strands around histone proteins. Histones package and order DNA into structural units called nucleosome complexes, which can control the access of proteins to the DNA regions (Figure \(1\)a). Under the electron microscope, this winding of DNA around histone proteins to form nucleosomes looks like small beads on a string (Figure \(1\)b). These beads (histone proteins) can move along the string (DNA) and change the structure of the molecule.
If DNA encoding a specific gene is to be transcribed into RNA, the nucleosomes surrounding that region of DNA can slide down the DNA to open that specific chromosomal region and allow for the transcriptional machinery (RNA polymerase) to initiate transcription (Figure \(2\)). Nucleosomes can move to open the chromosome structure to expose a segment of DNA, but do so in a very controlled manner.
Art Connection
In females, one of the two X chromosomes is inactivated during embryonic development because of epigenetic changes to the chromatin. What impact do you think these changes would have on nucleosome packing?
How the histone proteins move is dependent on signals found on both the histone proteins and on the DNA. These signals are tags added to histone proteins and DNA that tell the histones if a chromosomal region should be open or closed (Figure \(3\)) depicts modifications to histone proteins and DNA). These tags are not permanent, but may be added or removed as needed. They are chemical modifications (phosphate, methyl, or acetyl groups) that are attached to specific amino acids in the protein or to the nucleotides of the DNA. The tags do not alter the DNA base sequence, but they do alter how tightly wound the DNA is around the histone proteins. DNA is a negatively charged molecule; therefore, changes in the charge of the histone will change how tightly wound the DNA molecule will be. When unmodified, the histone proteins have a large positive charge; by adding chemical modifications like acetyl groups, the charge becomes less positive.
The DNA molecule itself can also be modified. This occurs within very specific regions called CpG islands. These are stretches with a high frequency of cytosine and guanine dinucleotide DNA pairs (CG) found in the promoter regions of genes. When this configuration exists, the cytosine member of the pair can be methylated (a methyl group is added). This modification changes how the DNA interacts with proteins, including the histone proteins that control access to the region. Highly methylated (hypermethylated) DNA regions with deacetylated histones are tightly coiled and transcriptionally inactive.
This type of gene regulation is called epigenetic regulation. Epigenetic means “around genetics.” The changes that occur to the histone proteins and DNA do not alter the nucleotide sequence and are not permanent. Instead, these changes are temporary (although they often persist through multiple rounds of cell division) and alter the chromosomal structure (open or closed) as needed. A gene can be turned on or off depending upon the location and modifications to the histone proteins and DNA. If a gene is to be transcribed, the histone proteins and DNA are modified surrounding the chromosomal region encoding that gene. This opens the chromosomal region to allow access for RNA polymerase and other proteins, called transcription factors, to bind to the promoter region, located just upstream of the gene, and initiate transcription. If a gene is to remain turned off, or silenced, the histone proteins and DNA have different modifications that signal a closed chromosomal configuration. In this closed configuration, the RNA polymerase and transcription factors do not have access to the DNA and transcription cannot occur (Figure \(3\)).
Link to Learning
View this video that describes how epigenetic regulation controls gene expression.
Summary
In eukaryotic cells, the first stage of gene expression control occurs at the epigenetic level. Epigenetic mechanisms control access to the chromosomal region to allow genes to be turned on or off. These mechanisms control how DNA is packed into the nucleus by regulating how tightly the DNA is wound around histone proteins. The addition or removal of chemical modifications (or flags) to histone proteins or DNA signals to the cell to open or close a chromosomal region. Therefore, eukaryotic cells can control whether a gene is expressed by controlling accessibility to transcription factors and the binding of RNA polymerase to initiate transcription.
Art Connections
Figure \(2\): In females, one of the two X chromosomes is inactivated during embryonic development because of epigenetic changes to the chromatin. What impact do you think these changes would have on nucleosome packing?
Answer
The nucleosomes would pack more tightly together.
Glossary
transcription factor
protein that binds to the DNA at the promoter or enhancer region and that influences transcription of a gene | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/16%3A_Gene_Expression/16.3%3A_Eukaryotic_Epigenetic_Gene_Regulation.txt |
Skills to Develop
• Discuss the role of transcription factors in gene regulation
• Explain how enhancers and repressors regulate gene expression
Like prokaryotic cells, the transcription of genes in eukaryotes requires the actions of an RNA polymerase to bind to a sequence upstream of a gene to initiate transcription. However, unlike prokaryotic cells, the eukaryotic RNA polymerase requires other proteins, or transcription factors, to facilitate transcription initiation. Transcription factors are proteins that bind to the promoter sequence and other regulatory sequences to control the transcription of the target gene. RNA polymerase by itself cannot initiate transcription in eukaryotic cells. Transcription factors must bind to the promoter region first and recruit RNA polymerase to the site for transcription to be established.
Link to Learning
View the process of transcription—the making of RNA from a DNA template—at this site.
The Promoter and the Transcription Machinery
Genes are organized to make the control of gene expression easier. The promoter region is immediately upstream of the coding sequence. This region can be short (only a few nucleotides in length) or quite long (hundreds of nucleotides long). The longer the promoter, the more available space for proteins to bind. This also adds more control to the transcription process. The length of the promoter is gene-specific and can differ dramatically between genes. Consequently, the level of control of gene expression can also differ quite dramatically between genes. The purpose of the promoter is to bind transcription factors that control the initiation of transcription.
Within the promoter region, just upstream of the transcriptional start site, resides the TATA box. This box is simply a repeat of thymine and adenine dinucleotides (literally, TATA repeats). RNA polymerase binds to the transcription initiation complex, allowing transcription to occur. To initiate transcription, a transcription factor (TFIID) is the first to bind to the TATA box. Binding of TFIID recruits other transcription factors, including TFIIB, TFIIE, TFIIF, and TFIIH to the TATA box. Once this complex is assembled, RNA polymerase can bind to its upstream sequence. When bound along with the transcription factors, RNA polymerase is phosphorylated. This releases part of the protein from the DNA to activate the transcription initiation complex and places RNA polymerase in the correct orientation to begin transcription; DNA-bending protein brings the enhancer, which can be quite a distance from the gene, in contact with transcription factors and mediator proteins (Figure \(1\)).
In addition to the general transcription factors, other transcription factors can bind to the promoter to regulate gene transcription. These transcription factors bind to the promoters of a specific set of genes. They are not general transcription factors that bind to every promoter complex, but are recruited to a specific sequence on the promoter of a specific gene. There are hundreds of transcription factors in a cell that each bind specifically to a particular DNA sequence motif. When transcription factors bind to the promoter just upstream of the encoded gene, it is referred to as a cis-acting element, because it is on the same chromosome just next to the gene. The region that a particular transcription factor binds to is called the transcription factor binding site. Transcription factors respond to environmental stimuli that cause the proteins to find their binding sites and initiate transcription of the gene that is needed.
Enhancers and Transcription
In some eukaryotic genes, there are regions that help increase or enhance transcription. These regions, called enhancers, are not necessarily close to the genes they enhance. They can be located upstream of a gene, within the coding region of the gene, downstream of a gene, or may be thousands of nucleotides away.
Enhancer regions are binding sequences, or sites, for transcription factors. When a DNA-bending protein binds, the shape of the DNA changes (Figure \(1\)). This shape change allows for the interaction of the activators bound to the enhancers with the transcription factors bound to the promoter region and the RNA polymerase. Whereas DNA is generally depicted as a straight line in two dimensions, it is actually a three-dimensional object. Therefore, a nucleotide sequence thousands of nucleotides away can fold over and interact with a specific promoter.
Turning Genes Off: Transcriptional Repressors
Like prokaryotic cells, eukaryotic cells also have mechanisms to prevent transcription. Transcriptional repressors can bind to promoter or enhancer regions and block transcription. Like the transcriptional activators, repressors respond to external stimuli to prevent the binding of activating transcription factors.
Summary
To start transcription, general transcription factors, such as TFIID, TFIIH, and others, must first bind to the TATA box and recruit RNA polymerase to that location. The binding of additional regulatory transcription factors to cis-acting elements will either increase or prevent transcription. In addition to promoter sequences, enhancer regions help augment transcription. Enhancers can be upstream, downstream, within a gene itself, or on other chromosomes. Transcription factors bind to enhancer regions to increase or prevent transcription.
Glossary
cis-acting element
transcription factor binding sites within the promoter that regulate the transcription of a gene adjacent to it
enhancer
segment of DNA that is upstream, downstream, perhaps thousands of nucleotides away, or on another chromosome that influence the transcription of a specific gene
trans-acting element
transcription factor binding site found outside the promoter or on another chromosome that influences the transcription of a particular gene
transcription factor binding site
sequence of DNA to which a transcription factor binds | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/16%3A_Gene_Expression/16.4%3A_Eukaryotic_Transcription_Gene_Regulation.txt |
Skills to Develop
• Understand RNA splicing and explain its role in regulating gene expression
• Describe the importance of RNA stability in gene regulation
RNA is transcribed, but must be processed into a mature form before translation can begin. This processing after an RNA molecule has been transcribed, but before it is translated into a protein, is called post-transcriptional modification. As with the epigenetic and transcriptional stages of processing, this post-transcriptional step can also be regulated to control gene expression in the cell. If the RNA is not processed, shuttled, or translated, then no protein will be synthesized.
RNA splicing, the first stage of post-transcriptional control
In eukaryotic cells, the RNA transcript often contains regions, called introns, that are removed prior to translation. The regions of RNA that code for protein are called exons (Figure \(1\)). After an RNA molecule has been transcribed, but prior to its departure from the nucleus to be translated, the RNA is processed and the introns are removed by splicing.
Evolution Connection: Alternative RNA Splicing
In the 1970s, genes were first observed that exhibited alternative RNA splicing. Alternative RNA splicing is a mechanism that allows different protein products to be produced from one gene when different combinations of introns, and sometimes exons, are removed from the transcript (Figure \(2\)). This alternative splicing can be haphazard, but more often it is controlled and acts as a mechanism of gene regulation, with the frequency of different splicing alternatives controlled by the cell as a way to control the production of different protein products in different cells or at different stages of development. Alternative splicing is now understood to be a common mechanism of gene regulation in eukaryotes; according to one estimate, 70 percent of genes in humans are expressed as multiple proteins through alternative splicing.
How could alternative splicing evolve? Introns have a beginning and ending recognition sequence; it is easy to imagine the failure of the splicing mechanism to identify the end of an intron and instead find the end of the next intron, thus removing two introns and the intervening exon. In fact, there are mechanisms in place to prevent such intron skipping, but mutations are likely to lead to their failure. Such “mistakes” would more than likely produce a nonfunctional protein. Indeed, the cause of many genetic diseases is alternative splicing rather than mutations in a sequence. However, alternative splicing would create a protein variant without the loss of the original protein, opening up possibilities for adaptation of the new variant to new functions. Gene duplication has played an important role in the evolution of new functions in a similar way by providing genes that may evolve without eliminating the original, functional protein.
Link to Learning
Visualize how mRNA splicing happens by watching the process in action in this video. NDSU Virtual Cell Animations Project animation 'mRNA Splicing'.
Control of RNA Stability
Before the mRNA leaves the nucleus, it is given two protective "caps" that prevent the end of the strand from degrading during its journey. The 5' cap, which is placed on the 5' end of the mRNA, is usually composed of a methylated guanosine triphosphate molecule (GTP). The poly-A tail, which is attached to the 3' end, is usually composed of a series of adenine nucleotides. Once the RNA is transported to the cytoplasm, the length of time that the RNA resides there can be controlled. Each RNA molecule has a defined lifespan and decays at a specific rate. This rate of decay can influence how much protein is in the cell. If the decay rate is increased, the RNA will not exist in the cytoplasm as long, shortening the time for translation to occur. Conversely, if the rate of decay is decreased, the RNA molecule will reside in the cytoplasm longer and more protein can be translated. This rate of decay is referred to as the RNA stability. If the RNA is stable, it will be detected for longer periods of time in the cytoplasm.
Binding of proteins to the RNA can influence its stability. Proteins, called RNA-binding proteins, or RBPs, can bind to the regions of the RNA just upstream or downstream of the protein-coding region. These regions in the RNA that are not translated into protein are called the untranslated regions, or UTRs. They are not introns (those have been removed in the nucleus). Rather, these are regions that regulate mRNA localization, stability, and protein translation. The region just before the protein-coding region is called the 5' UTR, whereas the region after the coding region is called the 3' UTR (Figure \(3\)). The binding of RBPs to these regions can increase or decrease the stability of an RNA molecule, depending on the specific RBP that binds.
RNA Stability and microRNAs
In addition to RBPs that bind to and control (increase or decrease) RNA stability, other elements called microRNAs can bind to the RNA molecule. These microRNAs, or miRNAs, are short RNA molecules that are only 21–24 nucleotides in length. The miRNAs are made in the nucleus as longer pre-miRNAs. These pre-miRNAs are chopped into mature miRNAs by a protein called dicer. Like transcription factors and RBPs, mature miRNAs recognize a specific sequence and bind to the RNA; however, miRNAs also associate with a ribonucleoprotein complex called the RNA-induced silencing complex (RISC). RISC binds along with the miRNA to degrade the target mRNA. Together, miRNAs and the RISC complex rapidly destroy the RNA molecule.
Summary
Post-transcriptional control can occur at any stage after transcription, including RNA splicing, nuclear shuttling, and RNA stability. Once RNA is transcribed, it must be processed to create a mature RNA that is ready to be translated. This involves the removal of introns that do not code for protein. Spliceosomes bind to the signals that mark the exon/intron border to remove the introns and ligate the exons together. Once this occurs, the RNA is mature and can be translated. RNA is created and spliced in the nucleus, but needs to be transported to the cytoplasm to be translated. RNA is transported to the cytoplasm through the nuclear pore complex. Once the RNA is in the cytoplasm, the length of time it resides there before being degraded, called RNA stability, can also be altered to control the overall amount of protein that is synthesized. The RNA stability can be increased, leading to longer residency time in the cytoplasm, or decreased, leading to shortened time and less protein synthesis. RNA stability is controlled by RNA-binding proteins (RPBs) and microRNAs (miRNAs). These RPBs and miRNAs bind to the 5' UTR or the 3' UTR of the RNA to increase or decrease RNA stability. Depending on the RBP, the stability can be increased or decreased significantly; however, miRNAs always decrease stability and promote decay.
Glossary
3' UTR
3' untranslated region; region just downstream of the protein-coding region in an RNA molecule that is not translated
5' cap
a methylated guanosine triphosphate (GTP) molecule that is attached to the 5' end of a messenger RNA to protect the end from degradation
5' UTR
5' untranslated region; region just upstream of the protein-coding region in an RNA molecule that is not translated
dicer
enzyme that chops the pre-miRNA into the mature form of the miRNA
microRNA (miRNA)
small RNA molecules (approximately 21 nucleotides in length) that bind to RNA molecules to degrade them
poly-A tail
a series of adenine nucleotides that are attached to the 3' end of an mRNA to protect the end from degradation
RNA-binding protein (RBP)
protein that binds to the 3' or 5' UTR to increase or decrease the RNA stability
RNA stability
how long an RNA molecule will remain intact in the cytoplasm
untranslated region
segment of the RNA molecule that are not translated into protein. These regions lie before (upstream or 5') and after (downstream or 3') the protein-coding region
RISC
protein complex that binds along with the miRNA to the RNA to degrade it | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/16%3A_Gene_Expression/16.5%3A_Eukaryotic_Post-transcriptional_Gene_Regulation.txt |
Skills to Develop
• Understand the process of translation and discuss its key factors
• Describe how the initiation complex controls translation
• Explain the different ways in which the post-translational control of gene expression takes place
After the RNA has been transported to the cytoplasm, it is translated into protein. Control of this process is largely dependent on the RNA molecule. As previously discussed, the stability of the RNA will have a large impact on its translation into a protein. As the stability changes, the amount of time that it is available for translation also changes.
The Initiation Complex and Translation Rate
Like transcription, translation is controlled by proteins that bind and initiate the process. In translation, the complex that assembles to start the process is referred to as the initiation complex. The first protein to bind to the RNA to initiate translation is the eukaryotic initiation factor-2 (eIF-2). The eIF-2 protein is active when it binds to the high-energy molecule guanosine triphosphate (GTP). GTP provides the energy to start the reaction by giving up a phosphate and becoming guanosine diphosphate (GDP). The eIF-2 protein bound to GTP binds to the small 40S ribosomal subunit. When bound, the methionine initiator tRNA associates with the eIF-2/40S ribosome complex, bringing along with it the mRNA to be translated. At this point, when the initiator complex is assembled, the GTP is converted into GDP and energy is released. The phosphate and the eIF-2 protein are released from the complex and the large 60S ribosomal subunit binds to translate the RNA. The binding of eIF-2 to the RNA is controlled by phosphorylation. If eIF-2 is phosphorylated, it undergoes a conformational change and cannot bind to GTP. Therefore, the initiation complex cannot form properly and translation is impeded (Figure \(1\)). When eIF-2 remains unphosphorylated, it binds the RNA and actively translates the protein.
Art Connection
An increase in phosphorylation levels of eIF-2 has been observed in patients with neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and Huntington’s. What impact do you think this might have on protein synthesis?
Chemical Modifications, Protein Activity, and Longevity
Proteins can be chemically modified with the addition of groups including methyl, phosphate, acetyl, and ubiquitin groups. The addition or removal of these groups from proteins regulates their activity or the length of time they exist in the cell. Sometimes these modifications can regulate where a protein is found in the cell—for example, in the nucleus, the cytoplasm, or attached to the plasma membrane.
Chemical modifications occur in response to external stimuli such as stress, the lack of nutrients, heat, or ultraviolet light exposure. These changes can alter epigenetic accessibility, transcription, mRNA stability, or translation—all resulting in changes in expression of various genes. This is an efficient way for the cell to rapidly change the levels of specific proteins in response to the environment. Because proteins are involved in every stage of gene regulation, the phosphorylation of a protein (depending on the protein that is modified) can alter accessibility to the chromosome, can alter translation (by altering transcription factor binding or function), can change nuclear shuttling (by influencing modifications to the nuclear pore complex), can alter RNA stability (by binding or not binding to the RNA to regulate its stability), can modify translation (increase or decrease), or can change post-translational modifications (add or remove phosphates or other chemical modifications).
The addition of an ubiquitin group to a protein marks that protein for degradation. Ubiquitin acts like a flag indicating that the protein lifespan is complete. These proteins are moved to the proteasome, an organelle that functions to remove proteins, to be degraded (Figure \(2\)). One way to control gene expression, therefore, is to alter the longevity of the protein.
Summary
Changing the status of the RNA or the protein itself can affect the amount of protein, the function of the protein, or how long it is found in the cell. To translate the protein, a protein initiator complex must assemble on the RNA. Modifications (such as phosphorylation) of proteins in this complex can prevent proper translation from occurring. Once a protein has been synthesized, it can be modified (phosphorylated, acetylated, methylated, or ubiquitinated). These post-translational modifications can greatly impact the stability, degradation, or function of the protein.
Art Connections
Figure \(1\): An increase in phosphorylation levels of eIF-2 has been observed in patients with neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and Huntington’s. What impact do you think this might have on protein synthesis?
Answer
Protein synthesis would be inhibited.
Glossary
eukaryotic initiation factor-2 (eIF-2)
protein that binds first to an mRNA to initiate translation
guanine diphosphate (GDP)
molecule that is left after the energy is used to start translation
guanine triphosphate (GTP)
energy-providing molecule that binds to eIF-2 and is needed for translation
initiation complex
protein complex containing eIF2-2 that starts translation
large 60S ribosomal subunit
second, larger ribosomal subunit that binds to the RNA to translate it into protein
proteasome
organelle that degrades proteins
small 40S ribosomal subunit
ribosomal subunit that binds to the RNA to translate it into protein | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/16%3A_Gene_Expression/16.6%3A_Eukaryotic_Translational_and_Post-translational_Gene_Regulation.txt |
Skills to Develop
• Describe how changes to gene expression can cause cancer
• Explain how changes to gene expression at different levels can disrupt the cell cycle
• Discuss how understanding regulation of gene expression can lead to better drug design
Cancer is not a single disease but includes many different diseases. In cancer cells, mutations modify cell-cycle control and cells don’t stop growing as they normally would. Mutations can also alter the growth rate or the progression of the cell through the cell cycle. One example of a gene modification that alters the growth rate is increased phosphorylation of cyclin B, a protein that controls the progression of a cell through the cell cycle and serves as a cell-cycle checkpoint protein.
For cells to move through each phase of the cell cycle, the cell must pass through checkpoints. This ensures that the cell has properly completed the step and has not encountered any mutation that will alter its function. Many proteins, including cyclin B, control these checkpoints. The phosphorylation of cyclin B, a post-translational event, alters its function. As a result, cells can progress through the cell cycle unimpeded, even if mutations exist in the cell and its growth should be terminated. This post-translational change of cyclin B prevents it from controlling the cell cycle and contributes to the development of cancer.
Cancer: Disease of Altered Gene Expression
Cancer can be described as a disease of altered gene expression. There are many proteins that are turned on or off (gene activation or gene silencing) that dramatically alter the overall activity of the cell. A gene that is not normally expressed in that cell can be switched on and expressed at high levels. This can be the result of gene mutation or changes in gene regulation (epigenetic, transcription, post-transcription, translation, or post-translation).
Changes in epigenetic regulation, transcription, RNA stability, protein translation, and post-translational control can be detected in cancer. While these changes don’t occur simultaneously in one cancer, changes at each of these levels can be detected when observing cancer at different sites in different individuals. Therefore, changes in histone acetylation (epigenetic modification that leads to gene silencing), activation of transcription factors by phosphorylation, increased RNA stability, increased translational control, and protein modification can all be detected at some point in various cancer cells. Scientists are working to understand the common changes that give rise to certain types of cancer or how a modification might be exploited to destroy a tumor cell.
Tumor Suppressor Genes, Oncogenes, and Cancer
In normal cells, some genes function to prevent excess, inappropriate cell growth. These are tumor suppressor genes, which are active in normal cells to prevent uncontrolled cell growth. There are many tumor suppressor genes in cells. The most studied tumor suppressor gene is p53, which is mutated in over 50 percent of all cancer types. The p53 protein itself functions as a transcription factor. It can bind to sites in the promoters of genes to initiate transcription. Therefore, the mutation of p53 in cancer will dramatically alter the transcriptional activity of its target genes.
Link to Learning
Watch this animation to learn more about the use of p53 in fighting cancer.
Proto-oncogenes are positive cell-cycle regulators. When mutated, proto-oncogenes can become oncogenes and cause cancer. Overexpression of the oncogene can lead to uncontrolled cell growth. This is because oncogenes can alter transcriptional activity, stability, or protein translation of another gene that directly or indirectly controls cell growth. An example of an oncogene involved in cancer is a protein called myc. Myc is a transcription factor that is aberrantly activated in Burkett’s Lymphoma, a cancer of the lymph system. Overexpression of myc transforms normal B cells into cancerous cells that continue to grow uncontrollably. High B-cell numbers can result in tumors that can interfere with normal bodily function. Patients with Burkett’s lymphoma can develop tumors on their jaw or in their mouth that interfere with the ability to eat.
Cancer and Epigenetic Alterations
Silencing genes through epigenetic mechanisms is also very common in cancer cells. There are characteristic modifications to histone proteins and DNA that are associated with silenced genes. In cancer cells, the DNA in the promoter region of silenced genes is methylated on cytosine DNA residues in CpG islands. Histone proteins that surround that region lack the acetylation modification that is present when the genes are expressed in normal cells. This combination of DNA methylation and histone deacetylation (epigenetic modifications that lead to gene silencing) is commonly found in cancer. When these modifications occur, the gene present in that chromosomal region is silenced. Increasingly, scientists understand how epigenetic changes are altered in cancer. Because these changes are temporary and can be reversed—for example, by preventing the action of the histone deacetylase protein that removes acetyl groups, or by DNA methyl transferase enzymes that add methyl groups to cytosines in DNA—it is possible to design new drugs and new therapies to take advantage of the reversible nature of these processes. Indeed, many researchers are testing how a silenced gene can be switched back on in a cancer cell to help re-establish normal growth patterns.
Genes involved in the development of many other illnesses, ranging from allergies to inflammation to autism, are thought to be regulated by epigenetic mechanisms. As our knowledge of how genes are controlled deepens, new ways to treat diseases like cancer will emerge.
Cancer and Transcriptional Control
Alterations in cells that give rise to cancer can affect the transcriptional control of gene expression. Mutations that activate transcription factors, such as increased phosphorylation, can increase the binding of a transcription factor to its binding site in a promoter. This could lead to increased transcriptional activation of that gene that results in modified cell growth. Alternatively, a mutation in the DNA of a promoter or enhancer region can increase the binding ability of a transcription factor. This could also lead to the increased transcription and aberrant gene expression that is seen in cancer cells.
Researchers have been investigating how to control the transcriptional activation of gene expression in cancer. Identifying how a transcription factor binds, or a pathway that activates where a gene can be turned off, has led to new drugs and new ways to treat cancer. In breast cancer, for example, many proteins are overexpressed. This can lead to increased phosphorylation of key transcription factors that increase transcription. One such example is the overexpression of the epidermal growth factor receptor (EGFR) in a subset of breast cancers. The EGFR pathway activates many protein kinases that, in turn, activate many transcription factors that control genes involved in cell growth. New drugs that prevent the activation of EGFR have been developed and are used to treat these cancers.
Cancer and Post-transcriptional Control
Changes in the post-transcriptional control of a gene can also result in cancer. Recently, several groups of researchers have shown that specific cancers have altered expression of miRNAs. Because miRNAs bind to the 3' UTR of RNA molecules to degrade them, overexpression of these miRNAs could be detrimental to normal cellular activity. Too many miRNAs could dramatically decrease the RNA population leading to a decrease in protein expression. Several studies have demonstrated a change in the miRNA population in specific cancer types. It appears that the subset of miRNAs expressed in breast cancer cells is quite different from the subset expressed in lung cancer cells or even from normal breast cells. This suggests that alterations in miRNA activity can contribute to the growth of breast cancer cells. These types of studies also suggest that if some miRNAs are specifically expressed only in cancer cells, they could be potential drug targets. It would, therefore, be conceivable that new drugs that turn off miRNA expression in cancer could be an effective method to treat cancer.
Cancer and Translational/Post-translational Control
There are many examples of how translational or post-translational modifications of proteins arise in cancer. Modifications are found in cancer cells from the increased translation of a protein to changes in protein phosphorylation to alternative splice variants of a protein. An example of how the expression of an alternative form of a protein can have dramatically different outcomes is seen in colon cancer cells. The c-Flip protein, a protein involved in mediating the cell death pathway, comes in two forms: long (c-FLIPL) and short (c-FLIPS). Both forms appear to be involved in initiating controlled cell death mechanisms in normal cells. However, in colon cancer cells, expression of the long form results in increased cell growth instead of cell death. Clearly, the expression of the wrong protein dramatically alters cell function and contributes to the development of cancer.
New Drugs to Combat Cancer: Targeted Therapies
Scientists are using what is known about the regulation of gene expression in disease states, including cancer, to develop new ways to treat and prevent disease development. Many scientists are designing drugs on the basis of the gene expression patterns within individual tumors. This idea, that therapy and medicines can be tailored to an individual, has given rise to the field of personalized medicine. With an increased understanding of gene regulation and gene function, medicines can be designed to specifically target diseased cells without harming healthy cells. Some new medicines, called targeted therapies, have exploited the overexpression of a specific protein or the mutation of a gene to develop a new medication to treat disease. One such example is the use of anti-EGF receptor medications to treat the subset of breast cancer tumors that have very high levels of the EGF protein. Undoubtedly, more targeted therapies will be developed as scientists learn more about how gene expression changes can cause cancer.
Career Connection: Clinical Trial Coordinator
A clinical trial coordinator is the person managing the proceedings of the clinical trial. This job includes coordinating patient schedules and appointments, maintaining detailed notes, building the database to track patients (especially for long-term follow-up studies), ensuring proper documentation has been acquired and accepted, and working with the nurses and doctors to facilitate the trial and publication of the results. A clinical trial coordinator may have a science background, like a nursing degree, or other certification. People who have worked in science labs or in clinical offices are also qualified to become a clinical trial coordinator. These jobs are generally in hospitals; however, some clinics and doctor’s offices also conduct clinical trials and may hire a coordinator.
Summary
Cancer can be described as a disease of altered gene expression. Changes at every level of eukaryotic gene expression can be detected in some form of cancer at some point in time. In order to understand how changes to gene expression can cause cancer, it is critical to understand how each stage of gene regulation works in normal cells. By understanding the mechanisms of control in normal, non-diseased cells, it will be easier for scientists to understand what goes wrong in disease states including complex ones like cancer.
Glossary
DNA methylation
epigenetic modification that leads to gene silencing; commonly found in cancer cells
histone acetylation
epigenetic modification that leads to gene silencing; commonly found in cancer cells found in cancer cells
myc
oncogene that causes cancer in many cancer cells | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/16%3A_Gene_Expression/16.7%3A_Cancer_and_Gene_Regulation.txt |
16.1: Regulation of Gene Expression
Review Questions
Control of gene expression in eukaryotic cells occurs at which level(s)?
1. only the transcriptional level
2. epigenetic and transcriptional levels
3. epigenetic, transcriptional, and translational levels
4. epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels
Answer
D
Post-translational control refers to:
1. regulation of gene expression after transcription
2. regulation of gene expression after translation
3. control of epigenetic activation
4. period between transcription and translation
Answer
B
Free Response
Name two differences between prokaryotic and eukaryotic cells and how these differences benefit multicellular organisms.
Answer
Eukaryotic cells have a nucleus, whereas prokaryotic cells do not. In eukaryotic cells, DNA is confined within the nuclear region. Because of this, transcription and translation are physically separated. This creates a more complex mechanism for the control of gene expression that benefits multicellular organisms because it compartmentalizes gene regulation.
Gene expression occurs at many stages in eukaryotic cells, whereas in prokaryotic cells, control of gene expression only occurs at the transcriptional level. This allows for greater control of gene expression in eukaryotes and more complex systems to be developed. Because of this, different cell types can arise in an individual organism.
Describe how controlling gene expression will alter the overall protein levels in the cell.
Answer
The cell controls which proteins are expressed and to what level each protein is expressed in the cell. Prokaryotic cells alter the transcription rate to turn genes on or off. This method will increase or decrease protein levels in response to what is needed by the cell. Eukaryotic cells change the accessibility (epigenetic), transcription, or translation of a gene. This will alter the amount of RNA and the lifespan of the RNA to alter the amount of protein that exists. Eukaryotic cells also control protein translation to increase or decrease the overall levels. Eukaryotic organisms are much more complex and can manipulate protein levels by changing many stages in the process.
16.2: Prokaryotic Gene Regulation
Review Questions
If glucose is absent, but so is lactose, the lac operon will be ________.
1. activated
2. repressed
3. activated, but only partially
4. mutated
Answer
B
Prokaryotic cells lack a nucleus. Therefore, the genes in prokaryotic cells are:
1. all expressed, all of the time
2. transcribed and translated almost simultaneously
3. transcriptionally controlled because translation begins before transcription ends
4. b and c are both true
Answer
D
Free Response
Describe how transcription in prokaryotic cells can be altered by external stimulation such as excess lactose in the environment.
Answer
Environmental stimuli can increase or induce transcription in prokaryotic cells. In this example, lactose in the environment will induce the transcription of the lac operon, but only if glucose is not available in the environment.
What is the difference between a repressible and an inducible operon?
Answer
A repressible operon uses a protein bound to the promoter region of a gene to keep the gene repressed or silent. This repressor must be actively removed in order to transcribe the gene. An inducible operon is either activated or repressed depending on the needs of the cell and what is available in the local environment.
16.3: Eukaryotic Epigenetic Gene Regulation
Review Questions
What are epigenetic modifications?
1. the addition of reversible changes to histone proteins and DNA
2. the removal of nucleosomes from the DNA
3. the addition of more nucleosomes to the DNA
4. mutation of the DNA sequence
Answer
A
Which of the following are true of epigenetic changes?
1. allow DNA to be transcribed
2. move histones to open or close a chromosomal region
3. are temporary
4. all of the above
Answer
D
Free Response
In cancer cells, alteration to epigenetic modifications turns off genes that are normally expressed. Hypothetically, how could you reverse this process to turn these genes back on?
Answer
You can create medications that reverse the epigenetic processes (to add histone acetylation marks or to remove DNA methylation) and create an open chromosomal configuration.
16.4: Eukaryotic Transcription Gene Regulation
Review Questions
The binding of ________ is required for transcription to start.
1. a protein
2. DNA polymerase
3. RNA polymerase
4. a transcription factor
Answer
C
What will result from the binding of a transcription factor to an enhancer region?
1. decreased transcription of an adjacent gene
2. increased transcription of a distant gene
3. alteration of the translation of an adjacent gene
4. initiation of the recruitment of RNA polymerase
Answer
B
Free Response
A mutation within the promoter region can alter transcription of a gene. Describe how this can happen.
Answer
A mutation in the promoter region can change the binding site for a transcription factor that normally binds to increase transcription. The mutation could either decrease the ability of the transcription factor to bind, thereby decreasing transcription, or it can increase the ability of the transcription factor to bind, thus increasing transcription.
What could happen if a cell had too much of an activating transcription factor present?
Answer
If too much of an activating transcription factor were present, then transcription would be increased in the cell. This could lead to dramatic alterations in cell function.
16.5: Eukaryotic Post-transcriptional Gene Regulation
Review Questions
Which of the following are involved in post-transcriptional control?
1. control of RNA splicing
2. control of RNA shuttling
3. control of RNA stability
4. all of the above
Answer
D
Binding of an RNA binding protein will ________ the stability of the RNA molecule.
1. increase
2. decrease
3. neither increase nor decrease
4. either increase or decrease
Answer
D
Free Response
Describe how RBPs can prevent miRNAs from degrading an RNA molecule.
Answer
RNA binding proteins (RBP) bind to the RNA and can either increase or decrease the stability of the RNA. If they increase the stability of the RNA molecule, the RNA will remain intact in the cell for a longer period of time than normal. Since both RBPs and miRNAs bind to the RNA molecule, RBP can potentially bind first to the RNA and prevent the binding of the miRNA that will degrade it.
How can external stimuli alter post-transcriptional control of gene expression?
Answer
External stimuli can modify RNA-binding proteins (i.e., through phosphorylation of proteins) to alter their activity.
16.6: Eukaryotic Translational and Post-translational Gene Regulation
Review Questions
Post-translational modifications of proteins can affect which of the following?
1. protein function
2. transcriptional regulation
3. chromatin modification
4. all of the above
Answer
A
Free Response
Protein modification can alter gene expression in many ways. Describe how phosphorylation of proteins can alter gene expression.
Answer
Because proteins are involved in every stage of gene regulation, phosphorylation of a protein (depending on the protein that is modified) can alter accessibility to the chromosome, can alter translation (by altering the transcription factor binding or function), can change nuclear shuttling (by influencing modifications to the nuclear pore complex), can alter RNA stability (by binding or not binding to the RNA to regulate its stability), can modify translation (increase or decrease), or can change post-translational modifications (add or remove phosphates or other chemical modifications).
Alternative forms of a protein can be beneficial or harmful to a cell. What do you think would happen if too much of an alternative protein bound to the 3' UTR of an RNA and caused it to degrade?
Answer
If the RNA degraded, then less of the protein that the RNA encodes would be translated. This could have dramatic implications for the cell.
Changes in epigenetic modifications alter the accessibility and transcription of DNA. Describe how environmental stimuli, such as ultraviolet light exposure, could modify gene expression.
Answer
Environmental stimuli, like ultraviolet light exposure, can alter the modifications to the histone proteins or DNA. Such stimuli may change an actively transcribed gene into a silenced gene by removing acetyl groups from histone proteins or by adding methyl groups to DNA.
16.7: Cancer and Gene Regulation
Review Questions
Cancer causing genes are called ________.
1. transformation genes
2. tumor suppressor genes
3. oncogenes
4. mutated genes
Answer
C
Targeted therapies are used in patients with a set gene expression pattern. A targeted therapy that prevents the activation of the estrogen receptor in breast cancer would be beneficial to which type of patient?
1. patients who express the EGFR receptor in normal cells
2. patients with a mutation that inactivates the estrogen receptor
3. patients with lots of the estrogen receptor expressed in their tumor
4. patients that have no estrogen receptor expressed in their tumor
Answer
C
Free Response
New drugs are being developed that decrease DNA methylation and prevent the removal of acetyl groups from histone proteins. Explain how these drugs could affect gene expression to help kill tumor cells.
Answer
These drugs will keep the histone proteins and the DNA methylation patterns in the open chromosomal configuration so that transcription is feasible. If a gene is silenced, these drugs could reverse the epigenetic configuration to re-express the gene.
How can understanding the gene expression pattern in a cancer cell tell you something about that specific form of cancer?
Answer
Understanding which genes are expressed in a cancer cell can help diagnose the specific form of cancer. It can also help identify treatment options for that patient. For example, if a breast cancer tumor expresses the EGFR in high numbers, it might respond to specific anti-EGFR therapy. If that receptor is not expressed, it would not respond to that therapy. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/16%3A_Gene_Expression/16.E%3A_Gene_Expression_%28Exercises%29.txt |
• 17.0: Introduction
The study of nucleic acids began with the discovery of DNA, progressed to the study of genes and small fragments, and has now exploded to the field of genomics. Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species. The advances in genomics have been made possible by DNA sequencing technology.
• 17.1: Biotechnology
Biotechnology is the use of biological agents for technological advancement. Biotechnology was used for breeding livestock and crops long before the scientific basis of these techniques was understood. Biotechnology has grown rapidly through both academic research and private companies. The primary applications of this technology are in medicine (production of vaccines and antibiotics) and agriculture (genetic modification of crops, such as to increase yields).
• 17.2: Mapping Genomes
Genome mapping is the process of finding the locations of genes on each chromosome. The maps created by genome mapping are comparable to the maps that we use to navigate streets. A genetic map is an illustration that lists genes and their location on a chromosome. Genetic maps provide the big picture and use genetic markers. A genetic marker is a gene or sequence on a chromosome that co-segregates (shows genetic linkage) with a specific trait.
• 17.3: Whole-Genome Sequencing
Although there have been significant advances in the medical sciences in recent years, doctors are still confounded by some diseases, and they are using whole-genome sequencing to get to the bottom of the problem. Whole-genome sequencing is a process that determines the DNA sequence of an entire genome. Whole-genome sequencing is a brute-force approach to problem solving when there is a genetic basis at the core of a disease.
• 17.4: Applying Genomics
The introduction of DNA sequencing and whole genome sequencing projects, particularly the Human Genome project, has expanded the applicability of DNA sequence information. Genomics is now being used in a wide variety of fields, such as metagenomics, pharmacogenomics, and mitochondrial genomics. The most commonly known application of genomics is to understand and find cures for diseases.
• 17.5: Genomics and Proteomics
Proteins are the final products of genes, which help perform the function encoded by the gene. Proteins are composed of amino acids and play important roles in the cell. All enzymes (except ribozymes) are proteins that act as catalysts to affect the rate of reactions. Proteins are also regulatory molecules, and some are hormones. Transport proteins, such as hemoglobin, help transport oxygen to various organs. Antibodies that defend against foreign particles are also proteins.
• 17.E: Biotechnology and Genomics (Exercises)
Thumbnail: Gel electrophoresis. (CC BY-SA 3.0; Mnolf via Wikimedia Commons).
17: Biotechnology and Genomics
The study of nucleic acids began with the discovery of DNA, progressed to the study of genes and small fragments, and has now exploded to the field of genomics. Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species. The advances in genomics have been made possible by DNA sequencing technology. Just as information technology has led to Google maps that enable people to get detailed information about locations around the globe, genomic information is used to create similar maps of the DNA of different organisms. These findings have helped anthropologists to better understand human migration and have aided the field of medicine through the mapping of human genetic diseases. The ways in which genomic information can contribute to scientific understanding are varied and quickly growing. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/17%3A_Biotechnology_and_Genomics/17.0%3A_Introduction.txt |
Skills to Develop
• Describe gel electrophoresis
• Explain molecular and reproductive cloning
• Describe uses of biotechnology in medicine and agriculture
Biotechnology is the use of biological agents for technological advancement. Biotechnology was used for breeding livestock and crops long before the scientific basis of these techniques was understood. Since the discovery of the structure of DNA in 1953, the field of biotechnology has grown rapidly through both academic research and private companies. The primary applications of this technology are in medicine (production of vaccines and antibiotics) and agriculture (genetic modification of crops, such as to increase yields). Biotechnology also has many industrial applications, such as fermentation, the treatment of oil spills, and the production of biofuels (Figure \(1\)).
Basic Techniques to Manipulate Genetic Material (DNA and RNA)
To understand the basic techniques used to work with nucleic acids, remember that nucleic acids are macromolecules made of nucleotides (a sugar, a phosphate, and a nitrogenous base) linked by phosphodiester bonds. The phosphate groups on these molecules each have a net negative charge. An entire set of DNA molecules in the nucleus is called the genome. DNA has two complementary strands linked by hydrogen bonds between the paired bases. The two strands can be separated by exposure to high temperatures (DNA denaturation) and can be reannealed by cooling. The DNA can be replicated by the DNA polymerase enzyme. Unlike DNA, which is located in the nucleus of eukaryotic cells, RNA molecules leave the nucleus. The most common type of RNA that is analyzed is the messenger RNA (mRNA) because it represents the protein-coding genes that are actively expressed. However, RNA molecules present some other challenges to analysis, as they are often less stable than DNA.
DNA and RNA Extraction
To study or manipulate nucleic acids, the DNA or RNA must first be isolated or extracted from the cells. Various techniques are used to extract different types of DNA (Figure \(2\)). Most nucleic acid extraction techniques involve steps to break open the cell and use enzymatic reactions to destroy all macromolecules that are not desired (such as degradation of unwanted molecules and separation from the DNA sample). Cells are broken using a lysis buffer (a solution which is mostly a detergent); lysis means “to split.” These enzymes break apart lipid molecules in the cell membranes and nuclear membranes. Macromolecules are inactivated using enzymes such as proteases that break down proteins, and ribonucleases (RNAses) that break down RNA. The DNA is then precipitated using alcohol. Human genomic DNA is usually visible as a gelatinous, white mass. The DNA samples can be stored frozen at –80°C for several years.
RNA analysis is performed to study gene expression patterns in cells. RNA is naturally very unstable because RNAses are commonly present in nature and very difficult to inactivate. Similar to DNA, RNA extraction involves the use of various buffers and enzymes to inactivate macromolecules and preserve the RNA.
Gel Electrophoresis
Because nucleic acids are negatively charged ions at neutral or basic pH in an aqueous environment, they can be mobilized by an electric field. Gel electrophoresis is a technique used to separate molecules on the basis of size, using this charge. The nucleic acids can be separated as whole chromosomes or fragments. The nucleic acids are loaded into a slot near the negative electrode of a semisolid, porous gel matrix and pulled toward the positive electrode at the opposite end of the gel. Smaller molecules move through the pores in the gel faster than larger molecules; this difference in the rate of migration separates the fragments on the basis of size. There are molecular weight standard samples that can be run alongside the molecules to provide a size comparison. Nucleic acids in a gel matrix can be observed using various fluorescent or colored dyes. Distinct nucleic acid fragments appear as bands at specific distances from the top of the gel (the negative electrode end) on the basis of their size (Figure \(3\)). A mixture of genomic DNA fragments of varying sizes appear as a long smear, whereas uncut genomic DNA is usually too large to run through the gel and forms a single large band at the top of the gel.
Amplification of Nucleic Acid Fragments by Polymerase Chain Reaction
Although genomic DNA is visible to the naked eye when it is extracted in bulk, DNA analysis often requires focusing on one or more specific regions of the genome. Polymerase chain reaction (PCR) is a technique used to amplify specific regions of DNA for further analysis (Figure \(4\)). PCR is used for many purposes in laboratories, such as the cloning of gene fragments to analyze genetic diseases, identification of contaminant foreign DNA in a sample, and the amplification of DNA for sequencing. More practical applications include the determination of paternity and detection of genetic diseases.
DNA fragments can also be amplified from an RNA template in a process called reverse transcriptase PCR (RT-PCR). The first step is to recreate the original DNA template strand (called cDNA) by applying DNA nucleotides to the mRNA. This process is called reverse transcription. This requires the presence of an enzyme called reverse transcriptase. After the cDNA is made, regular PCR can be used to amplify it.
Link to Learning
Deepen your understanding of the polymerase chain reaction by clicking through this interactive exercise.
Hybridization, Southern Blotting, and Northern Blotting
Nucleic acid samples, such as fragmented genomic DNA and RNA extracts, can be probed for the presence of certain sequences. Short DNA fragments called probes are designed and labeled with radioactive or fluorescent dyes to aid detection. Gel electrophoresis separates the nucleic acid fragments according to their size. The fragments in the gel are then transferred onto a nylon membrane in a procedure called blotting (Figure \(5\)). The nucleic acid fragments that are bound to the surface of the membrane can then be probed with specific radioactively or fluorescently labeled probe sequences. When DNA is transferred to a nylon membrane, the technique is called Southern blotting, and when RNA is transferred to a nylon membrane, it is called northern blotting. Southern blots are used to detect the presence of certain DNA sequences in a given genome, and northern blots are used to detect gene expression.
Molecular Cloning
In general, the word “cloning” means the creation of a perfect replica; however, in biology, the re-creation of a whole organism is referred to as “reproductive cloning.” Long before attempts were made to clone an entire organism, researchers learned how to reproduce desired regions or fragments of the genome, a process that is referred to as molecular cloning.
Cloning small fragments of the genome allows for the manipulation and study of specific genes (and their protein products), or noncoding regions in isolation. A plasmid (also called a vector) is a small circular DNA molecule that replicates independently of the chromosomal DNA. In cloning, the plasmid molecules can be used to provide a "folder" in which to insert a desired DNA fragment. Plasmids are usually introduced into a bacterial host for proliferation. In the bacterial context, the fragment of DNA from the human genome (or the genome of another organism that is being studied) is referred to as foreign DNA, or a transgene, to differentiate it from the DNA of the bacterium, which is called the host DNA.
Plasmids occur naturally in bacterial populations (such as Escherichia coli) and have genes that can contribute favorable traits to the organism, such as antibiotic resistance (the ability to be unaffected by antibiotics). Plasmids have been repurposed and engineered as vectors for molecular cloning and the large-scale production of important reagents, such as insulin and human growth hormone. An important feature of plasmid vectors is the ease with which a foreign DNA fragment can be introduced via the multiple cloning site (MCS). The MCS is a short DNA sequence containing multiple sites that can be cut with different commonly available restriction endonucleases. Restriction endonucleases recognize specific DNA sequences and cut them in a predictable manner; they are naturally produced by bacteria as a defense mechanism against foreign DNA. Many restriction endonucleases make staggered cuts in the two strands of DNA, such that the cut ends have a 2- or 4-base single-stranded overhang. Because these overhangs are capable of annealing with complementary overhangs, these are called “sticky ends.” Addition of an enzyme called DNA ligase permanently joins the DNA fragments via phosphodiester bonds. In this way, any DNA fragment generated by restriction endonuclease cleavage can be spliced between the two ends of a plasmid DNA that has been cut with the same restriction endonuclease (Figure \(6\)).
Recombinant DNA Molecules
Plasmids with foreign DNA inserted into them are called recombinant DNA molecules because they are created artificially and do not occur in nature. They are also called chimeric molecules because the origin of different parts of the molecules can be traced back to different species of biological organisms or even to chemical synthesis. Proteins that are expressed from recombinant DNA molecules are called recombinant proteins. Not all recombinant plasmids are capable of expressing genes. The recombinant DNA may need to be moved into a different vector (or host) that is better designed for gene expression. Plasmids may also be engineered to express proteins only when stimulated by certain environmental factors, so that scientists can control the expression of the recombinant proteins.
Art Connection
You are working in a molecular biology lab and, unbeknownst to you, your lab partner left the foreign genomic DNA that you are planning to clone on the lab bench overnight instead of storing it in the freezer. As a result, it was degraded by nucleases, but still used in the experiment. The plasmid, on the other hand, is fine. What results would you expect from your molecular cloning experiment?
1. There will be no colonies on the bacterial plate.
2. There will be blue colonies only.
3. There will be blue and white colonies.
4. The will be white colonies only.
Link to Learning
View an animation of recombination in cloning from the DNA Learning Center.
Cellular Cloning
Unicellular organisms, such as bacteria and yeast, naturally produce clones of themselves when they replicate asexually by binary fission; this is known as cellular cloning. The nuclear DNA duplicates by the process of mitosis, which creates an exact replica of the genetic material.
Reproductive Cloning
Reproductive cloning is a method used to make a clone or an identical copy of an entire multicellular organism. Most multicellular organisms undergo reproduction by sexual means, which involves genetic hybridization of two individuals (parents), making it impossible for generation of an identical copy or a clone of either parent. Recent advances in biotechnology have made it possible to artificially induce asexual reproduction of mammals in the laboratory.
Parthenogenesis, or “virgin birth,” occurs when an embryo grows and develops without the fertilization of the egg occurring; this is a form of asexual reproduction. An example of parthenogenesis occurs in species in which the female lays an egg and if the egg is fertilized, it is a diploid egg and the individual develops into a female; if the egg is not fertilized, it remains a haploid egg and develops into a male. The unfertilized egg is called a parthenogenic, or virgin, egg. Some insects and reptiles lay parthenogenic eggs that can develop into adults.
Sexual reproduction requires two cells; when the haploid egg and sperm cells fuse, a diploid zygote results. The zygote nucleus contains the genetic information to produce a new individual. However, early embryonic development requires the cytoplasmic material contained in the egg cell. This idea forms the basis for reproductive cloning. Therefore, if the haploid nucleus of an egg cell is replaced with a diploid nucleus from the cell of any individual of the same species (called a donor), it will become a zygote that is genetically identical to the donor. Somatic cell nuclear transfer is the technique of transferring a diploid nucleus into an enucleated egg. It can be used for either therapeutic cloning or reproductive cloning.
The first cloned animal was Dolly, a sheep who was born in 1996. The success rate of reproductive cloning at the time was very low. Dolly lived for seven years and died of respiratory complications (Figure 17.1.7). There is speculation that because the cell DNA belongs to an older individual, the age of the DNA may affect the life expectancy of a cloned individual. Since Dolly, several animals such as horses, bulls, and goats have been successfully cloned, although these individuals often exhibit facial, limb, and cardiac abnormalities. There have been attempts at producing cloned human embryos as sources of embryonic stem cells, sometimes referred to as cloning for therapeutic purposes. Therapeutic cloning produces stem cells to attempt to remedy detrimental diseases or defects (unlike reproductive cloning, which aims to reproduce an organism). Still, therapeutic cloning efforts have met with resistance because of bioethical considerations.
Art Connection
Do you think Dolly was a Finn-Dorset or a Scottish Blackface sheep?
Genetic Engineering
Genetic engineering is the alteration of an organism’s genotype using recombinant DNA technology to modify an organism’s DNA to achieve desirable traits. The addition of foreign DNA in the form of recombinant DNA vectors generated by molecular cloning is the most common method of genetic engineering. The organism that receives the recombinant DNA is called a genetically modified organism (GMO). If the foreign DNA that is introduced comes from a different species, the host organism is called transgenic. Bacteria, plants, and animals have been genetically modified since the early 1970s for academic, medical, agricultural, and industrial purposes. In the US, GMOs such as Roundup-ready soybeans and borer-resistant corn are part of many common processed foods.
Gene Targeting
Although classical methods of studying the function of genes began with a given phenotype and determined the genetic basis of that phenotype, modern techniques allow researchers to start at the DNA sequence level and ask: "What does this gene or DNA element do?" This technique, called reverse genetics, has resulted in reversing the classic genetic methodology. This method would be similar to damaging a body part to determine its function. An insect that loses a wing cannot fly, which means that the function of the wing is flight. The classical genetic method would compare insects that cannot fly with insects that can fly, and observe that the non-flying insects have lost wings. Similarly, mutating or deleting genes provides researchers with clues about gene function. The methods used to disable gene function are collectively called gene targeting. Gene targeting is the use of recombinant DNA vectors to alter the expression of a particular gene, either by introducing mutations in a gene, or by eliminating the expression of a certain gene by deleting a part or all of the gene sequence from the genome of an organism.
Biotechnology in Medicine and Agriculture
It is easy to see how biotechnology can be used for medicinal purposes. Knowledge of the genetic makeup of our species, the genetic basis of heritable diseases, and the invention of technology to manipulate and fix mutant genes provides methods to treat the disease. Biotechnology in agriculture can enhance resistance to disease, pest, and environmental stress, and improve both crop yield and quality.
Genetic Diagnosis and Gene Therapy
The process of testing for suspected genetic defects before administering treatment is called genetic diagnosis by genetic testing. Depending on the inheritance patterns of a disease-causing gene, family members are advised to undergo genetic testing. For example, women diagnosed with breast cancer are usually advised to have a biopsy so that the medical team can determine the genetic basis of cancer development. Treatment plans are based on the findings of genetic tests that determine the type of cancer. If the cancer is caused by inherited gene mutations, other female relatives are also advised to undergo genetic testing and periodic screening for breast cancer. Genetic testing is also offered for fetuses (or embryos with in vitro fertilization) to determine the presence or absence of disease-causing genes in families with specific debilitating diseases.
Gene therapy is a genetic engineering technique used to cure disease. In its simplest form, it involves the introduction of a good gene at a random location in the genome to aid the cure of a disease that is caused by a mutated gene. The good gene is usually introduced into diseased cells as part of a vector transmitted by a virus that can infect the host cell and deliver the foreign DNA (Figure \(8\)). More advanced forms of gene therapy try to correct the mutation at the original site in the genome, such as is the case with treatment of severe combined immunodeficiency (SCID).
Production of Vaccines, Antibiotics, and Hormones
Traditional vaccination strategies use weakened or inactive forms of microorganisms to mount the initial immune response. Modern techniques use the genes of microorganisms cloned into vectors to mass produce the desired antigen. The antigen is then introduced into the body to stimulate the primary immune response and trigger immune memory. Genes cloned from the influenza virus have been used to combat the constantly changing strains of this virus.
Antibiotics are a biotechnological product. They are naturally produced by microorganisms, such as fungi, to attain an advantage over bacterial populations. Antibiotics are produced on a large scale by cultivating and manipulating fungal cells.
Recombinant DNA technology was used to produce large-scale quantities of human insulin in E. coli as early as 1978. Previously, it was only possible to treat diabetes with pig insulin, which caused allergic reactions in humans because of differences in the gene product. In addition, human growth hormone (HGH) is used to treat growth disorders in children. The HGH gene was cloned from a cDNA library and inserted into E. coli cells by cloning it into a bacterial vector.
Transgenic Animals
Although several recombinant proteins used in medicine are successfully produced in bacteria, some proteins require a eukaryotic animal host for proper processing. For this reason, the desired genes are cloned and expressed in animals, such as sheep, goats, chickens, and mice. Animals that have been modified to express recombinant DNA are called transgenic animals. Several human proteins are expressed in the milk of transgenic sheep and goats, and some are expressed in the eggs of chickens. Mice have been used extensively for expressing and studying the effects of recombinant genes and mutations.
Transgenic Plants
Manipulating the DNA of plants (i.e., creating GMOs) has helped to create desirable traits, such as disease resistance, herbicide and pesticide resistance, better nutritional value, and better shelf-life (Figure \(9\)). Plants are the most important source of food for the human population. Farmers developed ways to select for plant varieties with desirable traits long before modern-day biotechnology practices were established.
Plants that have received recombinant DNA from other species are called transgenic plants. Because they are not natural, transgenic plants and other GMOs are closely monitored by government agencies to ensure that they are fit for human consumption and do not endanger other plant and animal life. Because foreign genes can spread to other species in the environment, extensive testing is required to ensure ecological stability. Staples like corn, potatoes, and tomatoes were the first crop plants to be genetically engineered.
Transformation of Plants Using Agrobacterium tumefaciens
Gene transfer occurs naturally between species in microbial populations. Many viruses that cause human diseases, such as cancer, act by incorporating their DNA into the human genome. In plants, tumors caused by the bacterium Agrobacterium tumefaciens occur by transfer of DNA from the bacterium to the plant. Although the tumors do not kill the plants, they make the plants stunted and more susceptible to harsh environmental conditions. Many plants, such as walnuts, grapes, nut trees, and beets, are affected by A. tumefaciens. The artificial introduction of DNA into plant cells is more challenging than in animal cells because of the thick plant cell wall.
Researchers used the natural transfer of DNA from Agrobacterium to a plant host to introduce DNA fragments of their choice into plant hosts. In nature, the disease-causing A. tumefaciens have a set of plasmids, called the Ti plasmids (tumor-inducing plasmids), that contain genes for the production of tumors in plants. DNA from the Ti plasmid integrates into the infected plant cell’s genome. Researchers manipulate the Ti plasmids to remove the tumor-causing genes and insert the desired DNA fragment for transfer into the plant genome. The Ti plasmids carry antibiotic resistance genes to aid selection and can be propagated in E. coli cells as well.
The Organic Insecticide Bacillus thuringiensis
Bacillus thuringiensis (Bt) is a bacterium that produces protein crystals during sporulation that are toxic to many insect species that affect plants. Bt toxin has to be ingested by insects for the toxin to be activated. Insects that have eaten Bt toxin stop feeding on the plants within a few hours. After the toxin is activated in the intestines of the insects, death occurs within a couple of days. Modern biotechnology has allowed plants to encode their own crystal Bt toxin that acts against insects. The crystal toxin genes have been cloned from Bt and introduced into plants. Bt toxin has been found to be safe for the environment, non-toxic to humans and other mammals, and is approved for use by organic farmers as a natural insecticide.
Flavr Savr Tomato
The first GM crop to be introduced into the market was the Flavr Savr Tomato produced in 1994. Antisense RNA technology was used to slow down the process of softening and rotting caused by fungal infections, which led to increased shelf life of the GM tomatoes. Additional genetic modification improved the flavor of this tomato. The Flavr Savr tomato did not successfully stay in the market because of problems maintaining and shipping the crop.
Summary
Nucleic acids can be isolated from cells for the purposes of further analysis by breaking open the cells and enzymatically destroying all other major macromolecules. Fragmented or whole chromosomes can be separated on the basis of size by gel electrophoresis. Short stretches of DNA or RNA can be amplified by PCR. Southern and northern blotting can be used to detect the presence of specific short sequences in a DNA or RNA sample. The term “cloning” may refer to cloning small DNA fragments (molecular cloning), cloning cell populations (cellular cloning), or cloning entire organisms (reproductive cloning). Genetic testing is performed to identify disease-causing genes, and gene therapy is used to cure an inheritable disease.
Transgenic organisms possess DNA from a different species, usually generated by molecular cloning techniques. Vaccines, antibiotics, and hormones are examples of products obtained by recombinant DNA technology. Transgenic plants are usually created to improve characteristics of crop plants.
Art Connections
Figure \(6\): You are working in a molecular biology lab and, unbeknownst to you, your lab partner left the foreign genomic DNA that you are planning to clone on the lab bench overnight instead of storing it in the freezer. As a result, it was degraded by nucleases, but still used in the experiment. The plasmid, on the other hand, is fine. What results would you expect from your molecular cloning experiment?
1. There will be no colonies on the bacterial plate.
2. There will be blue colonies only.
3. There will be blue and white colonies.
4. The will be white colonies only.
Answer
B. The experiment would result in blue colonies only.
Figure \(7\): Do you think Dolly was a Finn-Dorset or a Scottish Blackface sheep?
Answer
Dolly was a Finn-Dorset sheep because even though the original cell came from a Scottish blackface sheep and the surrogate mother was a Scottish blackface, the DNA came from a Finn-Dorset.
Glossary
antibiotic resistance
ability of an organism to be unaffected by the actions of an antibiotic
biotechnology
use of biological agents for technological advancement
cellular cloning
production of identical cell populations by binary fission
clone
exact replica
foreign DNA
DNA that belongs to a different species or DNA that is artificially synthesized
gel electrophoresis
technique used to separate molecules on the basis of size using electric charge
gene targeting
method for altering the sequence of a specific gene by introducing the modified version on a vector
gene therapy
technique used to cure inheritable diseases by replacing mutant genes with good genes
genetic diagnosis
diagnosis of the potential for disease development by analyzing disease-causing genes
genetic engineering
alteration of the genetic makeup of an organism
genetic testing
process of testing for the presence of disease-causing genes
genetically modified organism (GMO)
organism whose genome has been artificially changed
host DNA
DNA that is present in the genome of the organism of interest
lysis buffer
solution used to break the cell membrane and release cell contents
molecular cloning
cloning of DNA fragments
multiple cloning site (MCS)
site that can be recognized by multiple restriction endonucleases
northern blotting
transfer of RNA from a gel to a nylon membrane
polymerase chain reaction (PCR)
technique used to amplify DNA
probe
small DNA fragment used to determine if the complementary sequence is present in a DNA sample
protease
enzyme that breaks down proteins
recombinant DNA
combination of DNA fragments generated by molecular cloning that does not exist in nature; also known as a chimeric molecule
recombinant protein
protein product of a gene derived by molecular cloning
reproductive cloning
cloning of entire organisms
restriction endonuclease
enzyme that can recognize and cleave specific DNA sequences
reverse genetics
method of determining the function of a gene by starting with the gene itself instead of starting with the gene product
reverse transcriptase PCR (RT-PCR)
PCR technique that involves converting RNA to DNA by reverse transcriptase
ribonuclease
enzyme that breaks down RNA
Southern blotting
transfer of DNA from a gel to a nylon membrane
Ti plasmid
plasmid system derived from Agrobacterium tumifaciens that has been used by scientists to introduce foreign DNA into plant cells
transgenic
organism that receives DNA from a different species | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/17%3A_Biotechnology_and_Genomics/17.1%3A_Biotechnology.txt |
Skills to Develop
• Define genomics
• Describe genetic and physical maps
• Describe genomic mapping methods
Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species. Genome mapping is the process of finding the locations of genes on each chromosome. The maps created by genome mapping are comparable to the maps that we use to navigate streets. A genetic map is an illustration that lists genes and their location on a chromosome. Genetic maps provide the big picture (similar to a map of interstate highways) and use genetic markers (similar to landmarks). A genetic marker is a gene or sequence on a chromosome that co-segregates (shows genetic linkage) with a specific trait. Early geneticists called this linkage analysis. Physical maps present the intimate details of smaller regions of the chromosomes (similar to a detailed road map). A physical map is a representation of the physical distance, in nucleotides, between genes or genetic markers. Both genetic linkage maps and physical maps are required to build a complete picture of the genome. Having a complete map of the genome makes it easier for researchers to study individual genes. Human genome maps help researchers in their efforts to identify human disease-causing genes related to illnesses like cancer, heart disease, and cystic fibrosis. Genome mapping can be used in a variety of other applications, such as using live microbes to clean up pollutants or even prevent pollution. Research involving plant genome mapping may lead to producing higher crop yields or developing plants that better adapt to climate change.
Genetic Maps
The study of genetic maps begins with linkage analysis, a procedure that analyzes the recombination frequency between genes to determine if they are linked or show independent assortment. The term linkage was used before the discovery of DNA. Early geneticists relied on the observation of phenotypic changes to understand the genotype of an organism. Shortly after Gregor Mendel (the father of modern genetics) proposed that traits were determined by what are now known as genes, other researchers observed that different traits were often inherited together, and thereby deduced that the genes were physically linked by being located on the same chromosome. The mapping of genes relative to each other based on linkage analysis led to the development of the first genetic maps.
Observations that certain traits were always linked and certain others were not linked came from studying the offspring of crosses between parents with different traits. For example, in experiments performed on the garden pea, it was discovered that the color of the flower and shape of the plant’s pollen were linked traits, and therefore the genes encoding these traits were in close proximity on the same chromosome. The exchange of DNA between homologous pairs of chromosomes is called genetic recombination, which occurs by the crossing over of DNA between homologous strands of DNA, such as nonsister chromatids. Linkage analysis involves studying the recombination frequency between any two genes. The greater the distance between two genes, the higher the chance that a recombination event will occur between them, and the higher the recombination frequency between them. Two possibilities for recombination between two nonsister chromatids during meiosis are shown in Figure \(1\). If the recombination frequency between two genes is less than 50 percent, they are said to be linked.
The generation of genetic maps requires markers, just as a road map requires landmarks (such as rivers and mountains). Early genetic maps were based on the use of known genes as markers. More sophisticated markers, including those based on non-coding DNA, are now used to compare the genomes of individuals in a population. Although individuals of a given species are genetically similar, they are not identical; every individual has a unique set of traits. These minor differences in the genome between individuals in a population are useful for the purposes of genetic mapping. In general, a good genetic marker is a region on the chromosome that shows variability or polymorphism (multiple forms) in the population.
Some genetic markers used in generating genetic maps are restriction fragment length polymorphisms (RFLP), variable number of tandem repeats (VNTRs), microsatellite polymorphisms, and the single nucleotide polymorphisms (SNPs). RFLPs (sometimes pronounced “rif-lips”) are detected when the DNA of an individual is cut with a restriction endonuclease that recognizes specific sequences in the DNA to generate a series of DNA fragments, which are then analyzed by gel electrophoresis. The DNA of every individual will give rise to a unique pattern of bands when cut with a particular set of restriction endonucleases; this is sometimes referred to as an individual’s DNA “fingerprint.” Certain regions of the chromosome that are subject to polymorphism will lead to the generation of the unique banding pattern. VNTRs are repeated sets of nucleotides present in the non-coding regions of DNA. Non-coding, or “junk,” DNA has no known biological function; however, research shows that much of this DNA is actually transcribed. While its function is uncertain, it is certainly active, and it may be involved in the regulation of coding genes. The number of repeats may vary in individual organisms of a population. Microsatellite polymorphisms are similar to VNTRs, but the repeat unit is very small. SNPs are variations in a single nucleotide.
Because genetic maps rely completely on the natural process of recombination, mapping is affected by natural increases or decreases in the level of recombination in any given area of the genome. Some parts of the genome are recombination hotspots, whereas others do not show a propensity for recombination. For this reason, it is important to look at mapping information developed by multiple methods.
Physical Maps
A physical map provides detail of the actual physical distance between genetic markers, as well as the number of nucleotides. There are three methods used to create a physical map: cytogenetic mapping, radiation hybrid mapping, and sequence mapping. Cytogenetic mapping uses information obtained by microscopic analysis of stained sections of the chromosome. It is possible to determine the approximate distance between genetic markers using cytogenetic mapping, but not the exact distance (number of base pairs). Radiation hybrid mapping uses radiation, such as x-rays, to break the DNA into fragments. The amount of radiation can be adjusted to create smaller or larger fragments. This technique overcomes the limitation of genetic mapping and is not affected by increased or decreased recombination frequency. Sequence mapping resulted from DNA sequencing technology that allowed for the creation of detailed physical maps with distances measured in terms of the number of base pairs. The creation of genomic libraries and complementary DNA (cDNA) libraries (collections of cloned sequences or all DNA from a genome) has sped up the process of physical mapping. A genetic site used to generate a physical map with sequencing technology (a sequence-tagged site, or STS) is a unique sequence in the genome with a known exact chromosomal location. An expressed sequence tag (EST) and a single sequence length polymorphism (SSLP) are common STSs. An EST is a short STS that is identified with cDNA libraries, while SSLPs are obtained from known genetic markers and provide a link between genetic maps and physical maps.
Integration of Genetic and Physical Maps
Genetic maps provide the outline and physical maps provide the details. It is easy to understand why both types of genome mapping techniques are important to show the big picture. Information obtained from each technique is used in combination to study the genome. Genomic mapping is being used with different model organisms that are used for research. Genome mapping is still an ongoing process, and as more advanced techniques are developed, more advances are expected. Genome mapping is similar to completing a complicated puzzle using every piece of available data. Mapping information generated in laboratories all over the world is entered into central databases, such as GenBank at the National Center for Biotechnology Information (NCBI). Efforts are being made to make the information more easily accessible to researchers and the general public. Just as we use global positioning systems instead of paper maps to navigate through roadways, NCBI has created a genome viewer tool to simplify the data-mining process.
Scientific Method Connection: How to Use a Genome Map Viewer
Problem statement: Do the human, macaque, and mouse genomes contain common DNA sequences?
Develop a hypothesis.
To test the hypothesis, click here.
In Search box on the left panel, type any gene name or phenotypic characteristic, such as iris pigmentation (eye color). Select the species you want to study, and then press Enter. The genome map viewer will indicate which chromosome encodes the gene in your search. Click each hit in the genome viewer for more detailed information. This type of search is the most basic use of the genome viewer; it can also be used to compare sequences between species, as well as many other complicated tasks.
Is the hypothesis correct? Why or why not?
Link to Learning
Online Mendelian Inheritance in Man (OMIM) is a searchable online catalog of human genes and genetic disorders. This website shows genome mapping information, and also details the history and research of each trait and disorder. Click this link to search for traits (such as handedness) and genetic disorders (such as diabetes).
Summary
Genome mapping is similar to solving a big, complicated puzzle with pieces of information coming from laboratories all over the world. Genetic maps provide an outline for the location of genes within a genome, and they estimate the distance between genes and genetic markers on the basis of recombination frequencies during meiosis. Physical maps provide detailed information about the physical distance between the genes. The most detailed information is available through sequence mapping. Information from all mapping and sequencing sources is combined to study an entire genome.
Glossary
cytogenetic mapping
technique that uses a microscope to create a map from stained chromosomes
expressed sequence tag (EST)
short STS that is identified with cDNA
genetic map
outline of genes and their location on a chromosome
genetic marker
gene or sequence on a chromosome with a known location that is associated with a specific trait
genetic recombination
exchange of DNA between homologous pairs of chromosomes
genome mapping
process of finding the location of genes on each chromosome
cDNA library
collection of cloned cDNA sequences
genomic library
collection of cloned DNA which represents all of the sequences and fragments from a genome
genomics
study of entire genomes including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species
linkage analysis
procedure that analyzes the recombination of genes to determine if they are linked
microsatellite polymorphism
variation between individuals in the sequence and number of repeats of microsatellite DNA
physical map
representation of the physical distance between genes or genetic markers
radiation hybrid mapping
information obtained by fragmenting the chromosome with x-rays
restriction fragment length polymorphism (RFLP)
variation between individuals in the length of DNA fragments generated by restriction endonucleases
sequence mapping
mapping information obtained after DNA sequencing
single nucleotide polymorphism (SNP)
variation between individuals in a single nucleotide
variable number of tandem repeats (VNTRs)
variation in the number of tandem repeats between individuals in the population | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/17%3A_Biotechnology_and_Genomics/17.2%3A_Mapping_Genomes.txt |
Skills to Develop
• Describe three types of sequencing
• Define whole-genome sequencing
Although there have been significant advances in the medical sciences in recent years, doctors are still confounded by some diseases, and they are using whole-genome sequencing to get to the bottom of the problem. Whole-genome sequencing is a process that determines the DNA sequence of an entire genome. Whole-genome sequencing is a brute-force approach to problem solving when there is a genetic basis at the core of a disease. Several laboratories now provide services to sequence, analyze, and interpret entire genomes.
For example, whole-exome sequencing is a lower-cost alternative to whole genome sequencing. In exome sequencing, only the coding, exon-producing regions of the DNA are sequenced. In 2010, whole-exome sequencing was used to save a young boy whose intestines had multiple mysterious abscesses. The child had several colon operations with no relief. Finally, whole-exome sequencing was performed, which revealed a defect in a pathway that controls apoptosis (programmed cell death). A bone-marrow transplant was used to overcome this genetic disorder, leading to a cure for the boy. He was the first person to be successfully treated based on a diagnosis made by whole-exome sequencing. Today, human genome sequencing is more readily available and can be completed in a day or two for about \$1000.
Strategies Used in Sequencing Projects
The basic sequencing technique used in all modern day sequencing projects is the chain termination method (also known as the dideoxy method), which was developed by Fred Sanger in the 1970s. The chain termination method involves DNA replication of a single-stranded template with the use of a primer and a regular deoxynucleotide (dNTP), which is a monomer, or a single unit, of DNA. The primer and dNTP are mixed with a small proportion of fluorescently labeled dideoxynucleotides (ddNTPs). The ddNTPs are monomers that are missing a hydroxyl group (–OH) at the site at which another nucleotide usually attaches to form a chain (Figure \(1\)).
Each ddNTP is labeled with a different color of fluorophore. Every time a ddNTP is incorporated in the growing complementary strand, it terminates the process of DNA replication, which results in multiple short strands of replicated DNA that are each terminated at a different point during replication. When the reaction mixture is processed by gel electrophoresis after being separated into single strands, the multiple newly replicated DNA strands form a ladder because of the differing sizes. Because the ddNTPs are fluorescently labeled, each band on the gel reflects the size of the DNA strand and the ddNTP that terminated the reaction. The different colors of the fluorophore-labeled ddNTPs help identify the ddNTP incorporated at that position. Reading the gel on the basis of the color of each band on the ladder produces the sequence of the template strand (Figure \(2\)).
Early Strategies: Shotgun Sequencing and Pair-Wise End Sequencing
In shotgun sequencing method, several copies of a DNA fragment are cut randomly into many smaller pieces (somewhat like what happens to a round shot cartridge when fired from a shotgun). All of the segments are then sequenced using the chain-sequencing method. Then, with the help of a computer, the fragments are analyzed to see where their sequences overlap. By matching up overlapping sequences at the end of each fragment, the entire DNA sequence can be reformed. A larger sequence that is assembled from overlapping shorter sequences is called a contig. As an analogy, consider that someone has four copies of a landscape photograph that you have never seen before and know nothing about how it should appear. The person then rips up each photograph with their hands, so that different size pieces are present from each copy. The person then mixes all of the pieces together and asks you to reconstruct the photograph. In one of the smaller pieces you see a mountain. In a larger piece, you see that the same mountain is behind a lake. A third fragment shows only the lake, but it reveals that there is a cabin on the shore of the lake. Therefore, from looking at the overlapping information in these three fragments, you know that the picture contains a mountain behind a lake that has a cabin on its shore. This is the principle behind reconstructing entire DNA sequences using shotgun sequencing.
Originally, shotgun sequencing only analyzed one end of each fragment for overlaps. This was sufficient for sequencing small genomes. However, the desire to sequence larger genomes, such as that of a human, led to the development of double-barrel shotgun sequencing, more formally known as pairwise-end sequencing. In pairwise-end sequencing, both ends of each fragment are analyzed for overlap. Pairwise-end sequencing is, therefore, more cumbersome than shotgun sequencing, but it is easier to reconstruct the sequence because there is more available information.
Next-generation Sequencing
Since 2005, automated sequencing techniques used by laboratories are under the umbrella of next-generation sequencing, which is a group of automated techniques used for rapid DNA sequencing. These automated low-cost sequencers can generate sequences of hundreds of thousands or millions of short fragments (25 to 500 base pairs) in the span of one day. These sequencers use sophisticated software to get through the cumbersome process of putting all the fragments in order.
Evolution Connection: Comparing Sequences
A sequence alignment is an arrangement of proteins, DNA, or RNA; it is used to identify regions of similarity between cell types or species, which may indicate conservation of function or structures. Sequence alignments may be used to construct phylogenetic trees. The following website uses a software program called BLAST (basic local alignment search tool).
Under “Basic Blast,” click “Nucleotide Blast.” Input the following sequence into the large "query sequence" box: ATTGCTTCGATTGCA. Below the box, locate the "Species" field and type "human" or "Homo sapiens". Then click “BLAST” to compare the inputted sequence against known sequences of the human genome. The result is that this sequence occurs in over a hundred places in the human genome. Scroll down below the graphic with the horizontal bars and you will see short description of each of the matching hits. Pick one of the hits near the top of the list and click on "Graphics". This will bring you to a page that shows where the sequence is found within the entire human genome. You can move the slider that looks like a green flag back and forth to view the sequences immediately around the selected gene. You can then return to your selected sequence by clicking the "ATG" button.
Use of Whole-Genome Sequences of Model Organisms
The first genome to be completely sequenced was of a bacterial virus, the bacteriophage fx174 (5368 base pairs); this was accomplished by Fred Sanger using shotgun sequencing. Several other organelle and viral genomes were later sequenced. The first organism whose genome was sequenced was the bacterium Haemophilus influenzae; this was accomplished by Craig Venter in the 1980s. Approximately 74 different laboratories collaborated on the sequencing of the genome of the yeast Saccharomyces cerevisiae, which began in 1989 and was completed in 1996, because it was 60 times bigger than any other genome that had been sequenced. By 1997, the genome sequences of two important model organisms were available: the bacterium Escherichia coli K12 and the yeast Saccharomyces cerevisiae. Genomes of other model organisms, such as the mouse Mus musculus, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, and humans Homo sapiens are now known. A lot of basic research is performed in model organisms because the information can be applied to genetically similar organisms. A model organism is a species that is studied as a model to understand the biological processes in other species represented by the model organism. Having entire genomes sequenced helps with the research efforts in these model organisms. The process of attaching biological information to gene sequences is called genome annotation. Annotation of gene sequences helps with basic experiments in molecular biology, such as designing PCR primers and RNA targets.
Link to Learning
Click through each step of HHMI genome sequencing site.
Uses of Genome Sequences
DNA microarrays are methods used to detect gene expression by analyzing an array of DNA fragments that are fixed to a glass slide or a silicon chip to identify active genes and identify sequences. Almost one million genotypic abnormalities can be discovered using microarrays, whereas whole-genome sequencing can provide information about all six billion base pairs in the human genome. Although the study of medical applications of genome sequencing is interesting, this discipline tends to dwell on abnormal gene function. Knowledge of the entire genome will allow future onset diseases and other genetic disorders to be discovered early, which will allow for more informed decisions to be made about lifestyle, medication, and having children. Genomics is still in its infancy, although someday it may become routine to use whole-genome sequencing to screen every newborn to detect genetic abnormalities.
In addition to disease and medicine, genomics can contribute to the development of novel enzymes that convert biomass to biofuel, which results in higher crop and fuel production, and lower cost to the consumer. This knowledge should allow better methods of control over the microbes that are used in the production of biofuels. Genomics could also improve the methods used to monitor the impact of pollutants on ecosystems and help clean up environmental contaminants. Genomics has allowed for the development of agrochemicals and pharmaceuticals that could benefit medical science and agriculture.
It sounds great to have all the knowledge we can get from whole-genome sequencing; however, humans have a responsibility to use this knowledge wisely. Otherwise, it could be easy to misuse the power of such knowledge, leading to discrimination based on a person's genetics, human genetic engineering, and other ethical concerns. This information could also lead to legal issues regarding health and privacy.
Summary
Whole-genome sequencing is the latest available resource to treat genetic diseases. Some doctors are using whole-genome sequencing to save lives. Genomics has many industrial applications including biofuel development, agriculture, pharmaceuticals, and pollution control. The basic principle of all modern-day sequencing strategies involves the chain termination method of sequencing.
Although the human genome sequences provide key insights to medical professionals, researchers use whole-genome sequences of model organisms to better understand the genome of the species. Automation and the decreased cost of whole-genome sequencing may lead to personalized medicine in the future.
Glossary
chain termination method
method of DNA sequencing using labeled dideoxynucleotides to terminate DNA replication; it is also called the dideoxy method or the Sanger method
contig
larger sequence of DNA assembled from overlapping shorter sequences
deoxynucleotide
individual monomer (single unit) of DNA
dideoxynucleotide
individual monomer of DNA that is missing a hydroxyl group (–OH)
DNA microarray
method used to detect gene expression by analyzing an array of DNA fragments that are fixed to a glass slide or a silicon chip to identify active genes and identify sequences
genome annotation
process of attaching biological information to gene sequences
model organism
species that is studied and used as a model to understand the biological processes in other species represented by the model organism
next-generation sequencing
group of automated techniques used for rapid DNA sequencing
shotgun sequencing
method used to sequence multiple DNA fragments to generate the sequence of a large piece of DNA
whole-genome sequencing
process that determines the DNA sequence of an entire genome | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/17%3A_Biotechnology_and_Genomics/17.3%3A_Whole-Genome_Sequencing.txt |
Skills to Develop
• Explain pharmacogenomics
• Define polygenic
The introduction of DNA sequencing and whole genome sequencing projects, particularly the Human Genome project, has expanded the applicability of DNA sequence information. Genomics is now being used in a wide variety of fields, such as metagenomics, pharmacogenomics, and mitochondrial genomics. The most commonly known application of genomics is to understand and find cures for diseases.
Predicting Disease Risk at the Individual Level
Predicting the risk of disease involves screening currently healthy individuals by genome analysis at the individual level. Intervention with lifestyle changes and drugs can be recommended before disease onset. However, this approach is most applicable when the problem resides within a single gene defect. Such defects only account for approximately 5 percent of diseases in developed countries. Most of the common diseases, such as heart disease, are multi-factored or polygenic, which is a phenotypic characteristic that involves two or more genes, and also involve environmental factors such as diet. In April 2010, scientists at Stanford University published the genome analysis of a healthy individual (Stephen Quake, a scientist at Stanford University, who had his genome sequenced); the analysis predicted his propensity to acquire various diseases. A risk assessment was performed to analyze Quake’s percentage of risk for 55 different medical conditions. A rare genetic mutation was found, which showed him to be at risk for sudden heart attack. He was also predicted to have a 23 percent risk of developing prostate cancer and a 1.4 percent risk of developing Alzheimer’s. The scientists used databases and several publications to analyze the genomic data. Even though genomic sequencing is becoming more affordable and analytical tools are becoming more reliable, ethical issues surrounding genomic analysis at a population level remain to be addressed.
Art Connection
In 2011, the United States Preventative Services Task Force recommended against using the PSA test to screen healthy men for prostate cancer. Their recommendation is based on evidence that screening does not reduce the risk of death from prostate cancer. Prostate cancer often develops very slowly and does not cause problems, while the cancer treatment can have severe side effects. The PCA3 test is considered to be more accurate, but screening may still result in men who would not have been harmed by the cancer itself suffering side effects from treatment. What do you think? Should all healthy men be screened for prostate cancer using the PCA3 or PSA test? Should people in general be screened to find out if they have a genetic risk for cancer or other diseases?
Pharmacogenomics and Toxicogenomics
Pharmacogenomics, also called toxicogenomics, involves evaluating the effectiveness and safety of drugs on the basis of information from an individual's genomic sequence. Genomic responses to drugs can be studied using experimental animals (such as laboratory rats or mice) or live cells in the laboratory before embarking on studies with humans. Studying changes in gene expression could provide information about the transcription profile in the presence of the drug, which can be used as an early indicator of the potential for toxic effects. For example, genes involved in cellular growth and controlled cell death, when disturbed, could lead to the growth of cancerous cells. Genome-wide studies can also help to find new genes involved in drug toxicity. Personal genome sequence information can be used to prescribe medications that will be most effective and least toxic on the basis of the individual patient’s genotype. The gene signatures may not be completely accurate, but can be tested further before pathologic symptoms arise.
Microbial Genomics: Metagenomics
Traditionally, microbiology has been taught with the view that microorganisms are best studied under pure culture conditions, which involves isolating a single type of cell and culturing it in the laboratory. Because microorganisms can go through several generations in a matter of hours, their gene expression profiles adapt to the new laboratory environment very quickly. In addition, the vast majority of bacterial species resist being cultured in isolation. Most microorganisms do not live as isolated entities, but in microbial communities known as biofilms. For all of these reasons, pure culture is not always the best way to study microorganisms. Metagenomics is the study of the collective genomes of multiple species that grow and interact in an environmental niche. Metagenomics can be used to identify new species more rapidly and to analyze the effect of pollutants on the environment (Figure \(2\)).
Microbial Genomics: Creation of New Biofuels
Knowledge of the genomics of microorganisms is being used to find better ways to harness biofuels from algae and cyanobacteria. The primary sources of fuel today are coal, oil, wood, and other plant products, such as ethanol. Although plants are renewable resources, there is still a need to find more alternative renewable sources of energy to meet our population’s energy demands. The microbial world is one of the largest resources for genes that encode new enzymes and produce new organic compounds, and it remains largely untapped. Microorganisms are used to create products, such as enzymes that are used in research, antibiotics, and other anti-microbial mechanisms. Microbial genomics is helping to develop diagnostic tools, improved vaccines, new disease treatments, and advanced environmental cleanup techniques.
Mitochondrial Genomics
Mitochondria are intracellular organelles that contain their own DNA. Mitochondrial DNA mutates at a rapid rate and is often used to study evolutionary relationships. Another feature that makes studying the mitochondrial genome interesting is that the mitochondrial DNA in most multicellular organisms is passed on from the mother during the process of fertilization. For this reason, mitochondrial genomics is often used to trace genealogy.
Information and clues obtained from DNA samples found at crime scenes have been used as evidence in court cases, and genetic markers have been used in forensic analysis. Genomic analysis has also become useful in this field. In 2001, the first use of genomics in forensics was published. It was a collaborative attempt between academic research institutions and the FBI to solve the mysterious cases of anthrax communicated via the US Postal Service. Using microbial genomics, researchers determined that a specific strain of anthrax was used in all the mailings.
Genomics in Agriculture
Genomics can reduce the trials and failures involved in scientific research to a certain extent, which could improve the quality and quantity of crop yields in agriculture. Linking traits to genes or gene signatures helps to improve crop breeding to generate hybrids with the most desirable qualities. Scientists use genomic data to identify desirable traits, and then transfer those traits to a different organism. Scientists are discovering how genomics can improve the quality and quantity of agricultural production. For example, scientists could use desirable traits to create a useful product or enhance an existing product, such as making a drought-sensitive crop more tolerant of the dry season.
Summary
Imagination is the only barrier to the applicability of genomics. Genomics is being applied to most fields of biology; it is being used for personalized medicine, prediction of disease risks at an individual level, the study of drug interactions before the conduct of clinical trials, and the study of microorganisms in the environment as opposed to the laboratory. It is also being applied to developments such as the generation of new biofuels, genealogical assessment using mitochondria, advances in forensic science, and improvements in agriculture.
Art Connections
Figure \(1\): In 2011, the United States Preventative Services Task Force recommended against using the PSA test to screen healthy men for prostate cancer. Their recommendation is based on evidence that screening does not reduce the risk of death from prostate cancer. Prostate cancer often develops very slowly and does not cause problems, while the cancer treatment can have severe side effects. The PCA3 test is considered to be more accurate, but screening may still result in men who would not have been harmed by the cancer itself suffering side effects from treatment. What do you think? Should all healthy men be screened for prostate cancer using the PCA3 or PSA test? Should people in general be screened to find out if they have a genetic risk for cancer or other diseases?
Answer
There are no right or wrong answers to these questions. While it is true that prostate cancer treatment itself can be harmful, many men would rather be aware that they have cancer so they can monitor the disease and begin treatment if it progresses. And while genetic screening may be useful, it is expensive and may cause needless worry. People with certain risk factors may never develop the disease, and preventative treatments may do more harm than good.
Glossary
metagenomics
study of the collective genomes of multiple species that grow and interact in an environmental niche
pharmacogenomics
study of drug interactions with the genome or proteome; also called toxicogenomics
polygenic
phenotypic characteristic caused by two or more genes
pure culture
growth of a single type of cell in the laboratory | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/17%3A_Biotechnology_and_Genomics/17.4%3A_Applying_Genomics.txt |
Skills to Develop
• Explain systems biology
• Describe a proteome
• Define protein signature
Proteins are the final products of genes, which help perform the function encoded by the gene. Proteins are composed of amino acids and play important roles in the cell. All enzymes (except ribozymes) are proteins that act as catalysts to affect the rate of reactions. Proteins are also regulatory molecules, and some are hormones. Transport proteins, such as hemoglobin, help transport oxygen to various organs. Antibodies that defend against foreign particles are also proteins. In the diseased state, protein function can be impaired because of changes at the genetic level or because of direct impact on a specific protein.
A proteome is the entire set of proteins produced by a cell type. Proteomes can be studied using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins. The study of the function of proteomes is called proteomics. Proteomics complements genomics and is useful when scientists want to test their hypotheses that were based on genes. Even though all cells of a multicellular organism have the same set of genes, the set of proteins produced in different tissues is different and dependent on gene expression. Thus, the genome is constant, but the proteome varies and is dynamic within an organism. In addition, RNAs can be alternately spliced (cut and pasted to create novel combinations and novel proteins) and many proteins are modified after translation by processes such as proteolytic cleavage, phosphorylation, glycosylation, and ubiquitination. There are also protein-protein interactions, which complicate the study of proteomes. Although the genome provides a blueprint, the final architecture depends on several factors that can change the progression of events that generate the proteome.
Metabolomics is related to genomics and proteomics. Metabolomics involves the study of small molecule metabolites found in an organism. The metabolome is the complete set of metabolites that are related to the genetic makeup of an organism. Metabolomics offers an opportunity to compare genetic makeup and physical characteristics, as well as genetic makeup and environmental factors. The goal of metabolome research is to identify, quantify, and catalogue all of the metabolites that are found in the tissues and fluids of living organisms.
Basic Techniques in Protein Analysis
The ultimate goal of proteomics is to identify or compare the proteins expressed from a given genome under specific conditions, study the interactions between the proteins, and use the information to predict cell behavior or develop drug targets. Just as the genome is analyzed using the basic technique of DNA sequencing, proteomics requires techniques for protein analysis. The basic technique for protein analysis, analogous to DNA sequencing, is mass spectrometry. Mass spectrometry is used to identify and determine the characteristics of a molecule. Advances in spectrometry have allowed researchers to analyze very small samples of protein. X-ray crystallography, for example, enables scientists to determine the three-dimensional structure of a protein crystal at atomic resolution. Another protein imaging technique, nuclear magnetic resonance (NMR), uses the magnetic properties of atoms to determine the three-dimensional structure of proteins in aqueous solution. Protein microarrays have also been used to study interactions between proteins. Large-scale adaptations of the basic two-hybrid screen (Figure \(1\)) have provided the basis for protein microarrays. Computer software is used to analyze the vast amount of data generated for proteomic analysis.
Genomic- and proteomic-scale analyses are part of systems biology. Systems biology is the study of whole biological systems (genomes and proteomes) based on interactions within the system. The European Bioinformatics Institute and the Human Proteome Organization (HUPO) are developing and establishing effective tools to sort through the enormous pile of systems biology data. Because proteins are the direct products of genes and reflect activity at the genomic level, it is natural to use proteomes to compare the protein profiles of different cells to identify proteins and genes involved in disease processes. Most pharmaceutical drug trials target proteins. Information obtained from proteomics is being used to identify novel drugs and understand their mechanisms of action.
The challenge of techniques used for proteomic analyses is the difficulty in detecting small quantities of proteins. Although mass spectrometry is good for detecting small amounts of proteins, variations in protein expression in diseased states can be difficult to discern. Proteins are naturally unstable molecules, which makes proteomic analysis much more difficult than genomic analysis.
Cancer Proteomics
Genomes and proteomes of patients suffering from specific diseases are being studied to understand the genetic basis of the disease. The most prominent disease being studied with proteomic approaches is cancer. Proteomic approaches are being used to improve screening and early detection of cancer; this is achieved by identifying proteins whose expression is affected by the disease process. An individual protein is called a biomarker, whereas a set of proteins with altered expression levels is called a protein signature. For a biomarker or protein signature to be useful as a candidate for early screening and detection of a cancer, it must be secreted in body fluids, such as sweat, blood, or urine, such that large-scale screenings can be performed in a non-invasive fashion. The current problem with using biomarkers for the early detection of cancer is the high rate of false-negative results. A false negative is an incorrect test result that should have been positive. In other words, many cases of cancer go undetected, which makes biomarkers unreliable. Some examples of protein biomarkers used in cancer detection are CA-125 for ovarian cancer and PSA for prostate cancer. Protein signatures may be more reliable than biomarkers to detect cancer cells. Proteomics is also being used to develop individualized treatment plans, which involves the prediction of whether or not an individual will respond to specific drugs and the side effects that the individual may experience. Proteomics is also being used to predict the possibility of disease recurrence.
The National Cancer Institute has developed programs to improve the detection and treatment of cancer. The Clinical Proteomic Technologies for Cancer and the Early Detection Research Network are efforts to identify protein signatures specific to different types of cancers. The Biomedical Proteomics Program is designed to identify protein signatures and design effective therapies for cancer patients.
Summary
Proteomics is the study of the entire set of proteins expressed by a given type of cell under certain environmental conditions. In a multicellular organism, different cell types will have different proteomes, and these will vary with changes in the environment. Unlike a genome, a proteome is dynamic and in constant flux, which makes it both more complicated and more useful than the knowledge of genomes alone.
Proteomics approaches rely on protein analysis; these techniques are constantly being upgraded. Proteomics has been used to study different types of cancer. Different biomarkers and protein signatures are being used to analyze each type of cancer. The future goal is to have a personalized treatment plan for each individual.
Glossary
biomarker
individual protein that is uniquely produced in a diseased state
false negative
incorrect test result that should have been positive
metabolome
complete set of metabolites which are related to the genetic makeup of an organism
metabolomics
study of small molecule metabolites found in an organism
protein signature
set of uniquely expressed proteins in the diseased state
proteome
entire set of proteins produced by a cell type
proteomics
study of the function of proteomes
systems biology
study of whole biological systems (genomes and proteomes) based on interactions within the system | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/17%3A_Biotechnology_and_Genomics/17.5%3A_Genomics_and_Proteomics.txt |
17.1: Biotechnology
Biotechnology is the use of biological agents for technological advancement. Biotechnology was used for breeding livestock and crops long before the scientific basis of these techniques was understood. Biotechnology has grown rapidly through both academic research and private companies. The primary applications of this technology are in medicine (production of vaccines and antibiotics) and agriculture (genetic modification of crops, such as to increase yields).
Review Questions
GMOs are created by ________.
1. generating genomic DNA fragments with restriction endonucleases
2. introducing recombinant DNA into an organism by any means
3. overexpressing proteins in E. coli.
4. all of the above
Answer
B
Gene therapy can be used to introduce foreign DNA into cells ________.
1. for molecular cloning
2. by PCR
3. of tissues to cure inheritable disease
4. all of the above
Answer
C
Insulin produced by molecular cloning:
1. is of pig origin
2. is a recombinant protein
3. is made by the human pancreas
4. is recombinant DNA
Answer
B
Bt toxin is considered to be ________.
1. a gene for modifying insect DNA
2. an organic insecticide produced by bacteria
3. useful for humans to fight against insects
4. a recombinant protein
Answer
B
The Flavr Savr Tomato:
1. is a variety of vine-ripened tomato in the supermarket
2. was created to have better flavor and shelf-life
3. does not undergo soft rot
4. all of the above
Answer
D
Free Response
Describe the process of Southern blotting.
Answer
Southern blotting is the transfer of DNA that has been enzymatically cut into fragments and run on an agarose gel onto a nylon membrane. The DNA fragments that are on the nylon membrane can be denatured to make them single-stranded, and then probed with small DNA fragments that are radioactively or fluorescently labeled, to detect the presence of specific sequences. An example of the use of Southern blotting would be in analyzing the presence, absence, or variation of a disease gene in genomic DNA from a group of patients.
A researcher wants to study cancer cells from a patient with breast cancer. Is cloning the cancer cells an option?
Answer
Cellular cloning of the breast cancer cells will establish a cell line, which can be used for further analysis
How would a scientist introduce a gene for herbicide resistance into a plant?
Answer
By identifying an herbicide resistance gene and cloning it into a plant expression vector system, like the Ti plasmid system from Agrobacterium tumefaciens. The scientist would then introduce it into the plant cells by transformation, and select cells that have taken up and integrated the herbicide-resistance gene into the genome.
If you had a chance to get your genome sequenced, what are some questions you might be able to have answered about yourself?
Answer
What diseases am I prone to and what precautions should I take? Am I a carrier for any disease-causing genes that may be passed on to children?
17.2: Mapping Genomes
Genome mapping is the process of finding the locations of genes on each chromosome. The maps created by genome mapping are comparable to the maps that we use to navigate streets. A genetic map is an illustration that lists genes and their location on a chromosome. Genetic maps provide the big picture and use genetic markers. A genetic marker is a gene or sequence on a chromosome that co-segregates (shows genetic linkage) with a specific trait.
Review Questions
ESTs are ________.
1. generated after a cDNA library is made
2. unique sequences in the genome
3. useful for mapping using sequence information
4. all of the above
Answer
D
Linkage analysis ________.
1. is used to create a physical map
2. is based on the natural recombination process
3. requires radiation hybrid mapping
4. involves breaking and re-joining of DNA artificially
Answer
B
Genetic recombination occurs by which process?
1. independent assortment
2. crossing over
3. chromosome segregation
4. sister chromatids
Answer
B
Individual genetic maps in a given species are:
1. genetically similar
2. genetically identical
3. genetically dissimilar
4. not useful in species analysis
Answer
A
Information obtained by microscopic analysis of stained chromosomes is used in:
1. radiation hybrid mapping
2. sequence mapping
3. RFLP mapping
4. cytogenetic mapping
Answer
D
Free Response
Why is so much effort being poured into genome mapping applications?
Answer
Genome mapping has many different applications and provides comprehensive information that can be used for predictive purposes.
How could a genetic map of the human genome help find a cure for cancer?
Answer
A human genetic map can help identify genetic markers and sequences associated with high cancer risk, which can help to screen and provide early detection of different types of cancer.
17.3: Whole-Genome Sequencing
Although there have been significant advances in the medical sciences in recent years, doctors are still confounded by some diseases, and they are using whole-genome sequencing to get to the bottom of the problem. Whole-genome sequencing is a process that determines the DNA sequence of an entire genome. Whole-genome sequencing is a brute-force approach to problem solving when there is a genetic basis at the core of a disease.
Review Questions
The chain termination method of sequencing:
1. uses labeled ddNTPs
2. uses only dideoxynucleotides
3. uses only deoxynucleotides
4. uses labeled dNTPs
Answer
A
Whole-genome sequencing can be used for advances in:
1. the medical field
2. agriculture
3. biofuels
4. all of the above
Answer
D
Sequencing an individual person’s genome
1. is currently possible
2. could lead to legal issues regarding discrimination and privacy
3. could help make informed choices about medical treatment
4. all of the above
Answer
D
What is the most challenging issue facing genome sequencing?
1. the inability to develop fast and accurate sequencing techniques
2. the ethics of using information from genomes at the individual level
3. the availability and stability of DNA
4. all of the above
Answer
B
17.4: Applying Genomics
The introduction of DNA sequencing and whole genome sequencing projects, particularly the Human Genome project, has expanded the applicability of DNA sequence information. Genomics is now being used in a wide variety of fields, such as metagenomics, pharmacogenomics, and mitochondrial genomics. The most commonly known application of genomics is to understand and find cures for diseases.
Review Questions
Genomics can be used in agriculture to:
1. generate new hybrid strains
2. improve disease resistance
3. improve yield
4. all of the above
Answer
D
Genomics can be used on a personal level to:
1. decrease transplant rejection
2. Predict genetic diseases that a person may have inherited
3. Determine the risks of genetic diseases for an individual’s children
4. All the above
Answer
A
Free Response
Explain why metagenomics is probably the most revolutionary application of genomics.
Answer
Metagenomics is revolutionary because it replaced the practice of using pure cultures. Pure cultures were used to study individual species in the laboratory, but did not accurately represent what happens in the environment. Metagenomics studies the genomes of bacterial populations in their environmental niche.
How can genomics be used to predict disease risk and treatment options?
Answer
Genomics can provide the unique DNA sequence of an individual, which can be used for personalized medicine and treatment options.
17.5: Genomics and Proteomics
Proteins are the final products of genes, which help perform the function encoded by the gene. Proteins are composed of amino acids and play important roles in the cell. All enzymes (except ribozymes) are proteins that act as catalysts to affect the rate of reactions. Proteins are also regulatory molecules, and some are hormones. Transport proteins, such as hemoglobin, help transport oxygen to various organs. Antibodies that defend against foreign particles are also proteins.
Review Questions
What is a biomarker?
1. the color coding of different genes
2. a protein that is uniquely produced in a diseased state
3. a molecule in the genome or proteome
4. a marker that is genetically inherited
Answer
B
A protein signature is:
1. the path followed by a protein after it is synthesized in the nucleus
2. the path followed by a protein in the cytoplasm
3. a protein expressed on the cell surface
4. a unique set of proteins present in a diseased state
Answer
D
Free Response
How has proteomics been used in cancer detection and treatment?
Answer
Proteomics has provided a way to detect biomarkers and protein signatures, which have been used to screen for the early detection of cancer.
What is personalized medicine?
Answer
Personalized medicine is the use of an individual's genomic sequence to predict the risk for specific diseases. When a disease does occur, it can be used to develop a personalized treatment plan. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/17%3A_Biotechnology_and_Genomics/17.E%3A_Biotechnology_and_Genomics_%28Exercises%29.txt |
The theory of evolution is the unifying theory of biology, meaning it is the framework within which biologists ask questions about the living world. Its power is that it provides direction for predictions about living things that are borne out in experiment after experiment. The Ukrainian-born American geneticist Theodosius Dobzhansky famously wrote that “nothing makes sense in biology except in the light of evolution." He meant that the tenet that all life has evolved and diversified from a common ancestor is the foundation from which we approach all questions in biology.
• 18.0: Evolution
All species of living organisms, from bacteria to baboons to blueberries, evolved at some point from a different species. Although it may seem that living things today stay much the same, that is not the case—evolution is an ongoing process.
• 18.1: Understanding Evolution
Evolution by natural selection describes a mechanism for how species change over time. That species change had been suggested and debated well before Darwin began to explore this idea. The view that species were static and unchanging was grounded in the writings of Plato, yet there were also ancient Greeks who expressed evolutionary ideas.
• 18.2: Formation of New Species
Although all life on earth shares various genetic similarities, only certain organisms combine genetic information by sexual reproduction and have offspring that can then successfully reproduce. Scientists call such organisms members of the same biological species.
• 18.3: Reconnection and Rates of Speciation
Speciation occurs over a span of evolutionary time, so when a new species arises, there is a transition period during which the closely related species continue to interact.
• 18.E: Evolution and the Origin of Species (Exercises)
Thumbnail: A silhouette of human evolution. (CC BY-SA 3.0; Tkgd2007 via Wikimedia Commons).
18: Evolution and the Origin of Species
All species of living organisms, from bacteria to baboons to blueberries, evolved at some point from a different species. Although it may seem that living things today stay much the same, that is not the case—evolution is an ongoing process.
The theory of evolution is the unifying theory of biology, meaning it is the framework within which biologists ask questions about the living world. Its power is that it provides direction for predictions about living things that are borne out in experiment after experiment. The Ukrainian-born American geneticist Theodosius Dobzhansky famously wrote that “nothing makes sense in biology except in the light of evolution.”1 He meant that the tenet that all life has evolved and diversified from a common ancestor is the foundation from which we approach all questions in biology.
Footnotes
1. 1 Theodosius Dobzhansky. “Biology, Molecular and Organismic.” American Zoologist 4, no. 4 (1964): 449.
18.1: Understanding Evolution
Skills to Develop
• Describe how the present-day theory of evolution was developed
• Define adaptation
• Explain convergent and divergent evolution
• Describe homologous and vestigial structures
• Discuss misconceptions about the theory of evolution
Evolution by natural selection describes a mechanism for how species change over time. That species change had been suggested and debated well before Darwin began to explore this idea. The view that species were static and unchanging was grounded in the writings of Plato, yet there were also ancient Greeks who expressed evolutionary ideas. In the eighteenth century, ideas about the evolution of animals were reintroduced by the naturalist Georges-Louis Leclerc Comte de Buffon who observed that various geographic regions have different plant and animal populations, even when the environments are similar. It was also accepted that there were extinct species.
During this time, James Hutton, a Scottish naturalist, proposed that geological change occurred gradually by the accumulation of small changes from processes operating like they are today over long periods of time. This contrasted with the predominant view that the geology of the planet was a consequence of catastrophic events occurring during a relatively brief past. Hutton’s view was popularized in the nineteenth century by the geologist Charles Lyell who became a friend to Darwin. Lyell’s ideas were influential on Darwin’s thinking: Lyell’s notion of the greater age of Earth gave more time for gradual change in species, and the process of change provided an analogy for gradual change in species. In the early nineteenth century, Jean-Baptiste Lamarck published a book that detailed a mechanism for evolutionary change. This mechanism is now referred to as an inheritance of acquired characteristics by which modifications in an individual are caused by its environment, or the use or disuse of a structure during its lifetime, could be inherited by its offspring and thus bring about change in a species. While this mechanism for evolutionary change was discredited, Lamarck’s ideas were an important influence on evolutionary thought.
Charles Darwin and Natural Selection
In the mid-nineteenth century, the actual mechanism for evolution was independently conceived of and described by two naturalists: Charles Darwin and Alfred Russel Wallace. Importantly, each naturalist spent time exploring the natural world on expeditions to the tropics. From 1831 to 1836, Darwin traveled around the world on H.M.S. Beagle, including stops in South America, Australia, and the southern tip of Africa. Wallace traveled to Brazil to collect insects in the Amazon rainforest from 1848 to 1852 and to the Malay Archipelago from 1854 to 1862. Darwin’s journey, like Wallace’s later journeys to the Malay Archipelago, included stops at several island chains, the last being the Galápagos Islands west of Ecuador. On these islands, Darwin observed species of organisms on different islands that were clearly similar, yet had distinct differences. For example, the ground finches inhabiting the Galápagos Islands comprised several species with a unique beak shape (Figure \(1\)). The species on the islands had a graded series of beak sizes and shapes with very small differences between the most similar. He observed that these finches closely resembled another finch species on the mainland of South America. Darwin imagined that the island species might be species modified from one of the original mainland species. Upon further study, he realized that the varied beaks of each finch helped the birds acquire a specific type of food. For example, seed-eating finches had stronger, thicker beaks for breaking seeds, and insect-eating finches had spear-like beaks for stabbing their prey.
Wallace and Darwin both observed similar patterns in other organisms and they independently developed the same explanation for how and why such changes could take place. Darwin called this mechanism natural selection. Natural selection, also known as “survival of the fittest,” is the more prolific reproduction of individuals with favorable traits that survive environmental change because of those traits; this leads to evolutionary change.
For example, a population of giant tortoises found in the Galapagos Archipelago was observed by Darwin to have longer necks than those that lived on other islands with dry lowlands. These tortoises were “selected” because they could reach more leaves and access more food than those with short necks. In times of drought when fewer leaves would be available, those that could reach more leaves had a better chance to eat and survive than those that couldn’t reach the food source. Consequently, long-necked tortoises would be more likely to be reproductively successful and pass the long-necked trait to their offspring. Over time, only long-necked tortoises would be present in the population.
Natural selection, Darwin argued, was an inevitable outcome of three principles that operated in nature. First, most characteristics of organisms are inherited, or passed from parent to offspring. Although no one, including Darwin and Wallace, knew how this happened at the time, it was a common understanding. Second, more offspring are produced than are able to survive, so resources for survival and reproduction are limited. The capacity for reproduction in all organisms outstrips the availability of resources to support their numbers. Thus, there is competition for those resources in each generation. Both Darwin and Wallace’s understanding of this principle came from reading an essay by the economist Thomas Malthus who discussed this principle in relation to human populations. Third, offspring vary among each other in regard to their characteristics and those variations are inherited. Darwin and Wallace reasoned that offspring with inherited characteristics which allow them to best compete for limited resources will survive and have more offspring than those individuals with variations that are less able to compete. Because characteristics are inherited, these traits will be better represented in the next generation. This will lead to change in populations over generations in a process that Darwin called descent with modification. Ultimately, natural selection leads to greater adaptation of the population to its local environment; it is the only mechanism known for adaptive evolution.
Papers by Darwin and Wallace (Figure \(2\)) presenting the idea of natural selection were read together in 1858 before the Linnean Society in London. The following year Darwin’s book, On the Origin of Species, was published. His book outlined in considerable detail his arguments for evolution by natural selection.
Demonstrations of evolution by natural selection are time consuming and difficult to obtain. One of the best examples has been demonstrated in the very birds that helped to inspire Darwin’s theory: the Galápagos finches. Peter and Rosemary Grant and their colleagues have studied Galápagos finch populations every year since 1976 and have provided important demonstrations of natural selection. The Grants found changes from one generation to the next in the distribution of beak shapes with the medium ground finch on the Galápagos island of Daphne Major. The birds have inherited variation in the bill shape with some birds having wide deep bills and others having thinner bills. During a period in which rainfall was higher than normal because of an El Niño, the large hard seeds that large-billed birds ate were reduced in number; however, there was an abundance of the small soft seeds which the small-billed birds ate. Therefore, survival and reproduction were much better in the following years for the small-billed birds. In the years following this El Niño, the Grants measured beak sizes in the population and found that the average bill size was smaller. Since bill size is an inherited trait, parents with smaller bills had more offspring and the size of bills had evolved to be smaller. As conditions improved in 1987 and larger seeds became more available, the trend toward smaller average bill size ceased.
Career Connection: Field Biologist
Many people hike, explore caves, scuba dive, or climb mountains for recreation. People often participate in these activities hoping to see wildlife. Experiencing the outdoors can be incredibly enjoyable and invigorating. What if your job was to be outside in the wilderness? Field biologists by definition work outdoors in the “field.” The term field in this case refers to any location outdoors, even under water. A field biologist typically focuses research on a certain species, group of organisms, or a single habitat (Figure \(3\)).
One objective of many field biologists includes discovering new species that have never been recorded. Not only do such findings expand our understanding of the natural world, but they also lead to important innovations in fields such as medicine and agriculture. Plant and microbial species, in particular, can reveal new medicinal and nutritive knowledge. Other organisms can play key roles in ecosystems or be considered rare and in need of protection. When discovered, these important species can be used as evidence for environmental regulations and laws.
Processes and Patterns of Evolution
Natural selection can only take place if there is variation, or differences, among individuals in a population. Importantly, these differences must have some genetic basis; otherwise, the selection will not lead to change in the next generation. This is critical because variation among individuals can be caused by non-genetic reasons such as an individual being taller because of better nutrition rather than different genes.
Genetic diversity in a population comes from two main mechanisms: mutation and sexual reproduction. Mutation, a change in DNA, is the ultimate source of new alleles, or new genetic variation in any population. The genetic changes caused by mutation can have one of three outcomes on the phenotype. A mutation affects the phenotype of the organism in a way that gives it reduced fitness—lower likelihood of survival or fewer offspring. A mutation may produce a phenotype with a beneficial effect on fitness. And, many mutations will also have no effect on the fitness of the phenotype; these are called neutral mutations. Mutations may also have a whole range of effect sizes on the fitness of the organism that expresses them in their phenotype, from a small effect to a great effect. Sexual reproduction also leads to genetic diversity: when two parents reproduce, unique combinations of alleles assemble to produce the unique genotypes and thus phenotypes in each of the offspring.
A heritable trait that helps the survival and reproduction of an organism in its present environment is called an adaptation. Scientists describe groups of organisms becoming adapted to their environment when a change in the range of genetic variation occurs over time that increases or maintains the “fit” of the population to its environment. The webbed feet of platypuses are an adaptation for swimming. The snow leopards’ thick fur is an adaptation for living in the cold. The cheetahs’ fast speed is an adaptation for catching prey.
Whether or not a trait is favorable depends on the environmental conditions at the time. The same traits are not always selected because environmental conditions can change. For example, consider a species of plant that grew in a moist climate and did not need to conserve water. Large leaves were selected because they allowed the plant to obtain more energy from the sun. Large leaves require more water to maintain than small leaves, and the moist environment provided favorable conditions to support large leaves. After thousands of years, the climate changed, and the area no longer had excess water. The direction of natural selection shifted so that plants with small leaves were selected because those populations were able to conserve water to survive the new environmental conditions.
The evolution of species has resulted in enormous variation in form and function. Sometimes, evolution gives rise to groups of organisms that become tremendously different from each other. When two species evolve in diverse directions from a common point, it is called divergent evolution. Such divergent evolution can be seen in the forms of the reproductive organs of flowering plants which share the same basic anatomies; however, they can look very different as a result of selection in different physical environments and adaptation to different kinds of pollinators (Figure \(4\)).
In other cases, similar phenotypes evolve independently in distantly related species. For example, flight has evolved in both bats and insects, and they both have structures we refer to as wings, which are adaptations to flight. However, the wings of bats and insects have evolved from very different original structures. This phenomenon is called convergent evolution, where similar traits evolve independently in species that do not share a recent common ancestry. The two species came to the same function, flying, but did so separately from each other.
These physical changes occur over enormous spans of time and help explain how evolution occurs. Natural selection acts on individual organisms, which in turn can shape an entire species. Although natural selection may work in a single generation on an individual, it can take thousands or even millions of years for the genotype of an entire species to evolve. It is over these large time spans that life on earth has changed and continues to change.
Evidence of Evolution
The evidence for evolution is compelling and extensive. Looking at every level of organization in living systems, biologists see the signature of past and present evolution. Darwin dedicated a large portion of his book, On the Origin of Species, to identifying patterns in nature that were consistent with evolution, and since Darwin, our understanding has become clearer and broader.
Fossils
Fossils provide solid evidence that organisms from the past are not the same as those found today, and fossils show a progression of evolution. Scientists determine the age of fossils and categorize them from all over the world to determine when the organisms lived relative to each other. The resulting fossil record tells the story of the past and shows the evolution of form over millions of years (Figure \(5\)). For example, scientists have recovered highly detailed records showing the evolution of humans and horses (Figure \(5\)). The whale flipper shares a similar morphology to appendages of birds and mammals (Figure \(6\)) indicating that these species share a common ancestor.
Anatomy and Embryology
Another type of evidence for evolution is the presence of structures in organisms that share the same basic form. For example, the bones in the appendages of a human, dog, bird, and whale all share the same overall construction (Figure \(6\)) resulting from their origin in the appendages of a common ancestor. Over time, evolution led to changes in the shapes and sizes of these bones in different species, but they have maintained the same overall layout. Scientists call these synonymous parts homologous structures.
Some structures exist in organisms that have no apparent function at all, and appear to be residual parts from a past common ancestor. These unused structures without function are called vestigial structures. Other examples of vestigial structures are wings on flightless birds, leaves on some cacti, and hind leg bones in whales.
Link to Learning
Visit this interactive site to guess which bones structures are homologous and which are analogous, and see examples of evolutionary adaptations to illustrate these concepts.
Another evidence of evolution is the convergence of form in organisms that share similar environments. For example, species of unrelated animals, such as the arctic fox and ptarmigan, living in the arctic region have been selected for seasonal white phenotypes during winter to blend with the snow and ice (Figure \(7\)). These similarities occur not because of common ancestry, but because of similar selection pressures—the benefits of not being seen by predators.
Embryology, the study of the development of the anatomy of an organism to its adult form, also provides evidence of relatedness between now widely divergent groups of organisms. Mutational tweaking in the embryo can have such magnified consequences in the adult that embryo formation tends to be conserved. As a result, structures that are absent in some groups often appear in their embryonic forms and disappear by the time the adult or juvenile form is reached. For example, all vertebrate embryos, including humans, exhibit gill slits and tails at some point in their early development. These disappear in the adults of terrestrial groups but are maintained in adult forms of aquatic groups such as fish and some amphibians. Great ape embryos, including humans, have a tail structure during their development that is lost by the time of birth.
Biogeography
The geographic distribution of organisms on the planet follows patterns that are best explained by evolution in conjunction with the movement of tectonic plates over geological time. Broad groups that evolved before the breakup of the supercontinent Pangaea (about 200 million years ago) are distributed worldwide. Groups that evolved since the breakup appear uniquely in regions of the planet, such as the unique flora and fauna of northern continents that formed from the supercontinent Laurasia and of the southern continents that formed from the supercontinent Gondwana. The presence of members of the plant family Proteaceae in Australia, southern Africa, and South America is best explained by their presence prior to the southern supercontinent Gondwana breaking up.
The great diversification of marsupials in Australia and the absence of other mammals reflect Australia’s long isolation. Australia has an abundance of endemic species—species found nowhere else—which is typical of islands whose isolation by expanses of water prevents species from migrating. Over time, these species diverge evolutionarily into new species that look very different from their ancestors that may exist on the mainland. The marsupials of Australia, the finches on the Galápagos, and many species on the Hawaiian Islands are all unique to their one point of origin, yet they display distant relationships to ancestral species on mainlands.
Molecular Biology
Like anatomical structures, the structures of the molecules of life reflect descent with modification. Evidence of a common ancestor for all of life is reflected in the universality of DNA as the genetic material and in the near universality of the genetic code and the machinery of DNA replication and expression. Fundamental divisions in life between the three domains are reflected in major structural differences in otherwise conservative structures such as the components of ribosomes and the structures of membranes. In general, the relatedness of groups of organisms is reflected in the similarity of their DNA sequences—exactly the pattern that would be expected from descent and diversification from a common ancestor.
DNA sequences have also shed light on some of the mechanisms of evolution. For example, it is clear that the evolution of new functions for proteins commonly occurs after gene duplication events that allow the free modification of one copy by mutation, selection, or drift (changes in a population’s gene pool resulting from chance), while the second copy continues to produce a functional protein.
Misconceptions of Evolution
Although the theory of evolution generated some controversy when it was first proposed, it was almost universally accepted by biologists, particularly younger biologists, within 20 years after publication of On the Origin of Species. Nevertheless, the theory of evolution is a difficult concept and misconceptions about how it works abound
Link to Learning
This site addresses some of the main misconceptions associated with the theory of evolution.
Evolution Is Just a Theory
Critics of the theory of evolution dismiss its importance by purposefully confounding the everyday usage of the word “theory” with the way scientists use the word. In science, a “theory” is understood to be a body of thoroughly tested and verified explanations for a set of observations of the natural world. Scientists have a theory of the atom, a theory of gravity, and the theory of relativity, each of which describes understood facts about the world. In the same way, the theory of evolution describes facts about the living world. As such, a theory in science has survived significant efforts to discredit it by scientists. In contrast, a “theory” in common vernacular is a word meaning a guess or suggested explanation; this meaning is more akin to the scientific concept of “hypothesis.” When critics of evolution say evolution is “just a theory,” they are implying that there is little evidence supporting it and that it is still in the process of being rigorously tested. This is a mischaracterization.
Individuals Evolve
Evolution is the change in genetic composition of a population over time, specifically over generations, resulting from differential reproduction of individuals with certain alleles. Individuals do change over their lifetime, obviously, but this is called development and involves changes programmed by the set of genes the individual acquired at birth in coordination with the individual’s environment. When thinking about the evolution of a characteristic, it is probably best to think about the change of the average value of the characteristic in the population over time. For example, when natural selection leads to bill-size change in medium-ground finches in the Galápagos, this does not mean that individual bills on the finches are changing. If one measures the average bill size among all individuals in the population at one time and then measures the average bill size in the population several years later, this average value will be different as a result of evolution. Although some individuals may survive from the first time to the second, they will still have the same bill size; however, there will be many new individuals that contribute to the shift in average bill size.
Evolution Explains the Origin of Life
It is a common misunderstanding that evolution includes an explanation of life’s origins. Conversely, some of the theory’s critics believe that it cannot explain the origin of life. The theory does not try to explain the origin of life. The theory of evolution explains how populations change over time and how life diversifies the origin of species. It does not shed light on the beginnings of life including the origins of the first cells, which is how life is defined. The mechanisms of the origin of life on Earth are a particularly difficult problem because it occurred a very long time ago, and presumably it just occurred once. Importantly, biologists believe that the presence of life on Earth precludes the possibility that the events that led to life on Earth can be repeated because the intermediate stages would immediately become food for existing living things.
However, once a mechanism of inheritance was in place in the form of a molecule like DNA either within a cell or pre-cell, these entities would be subject to the principle of natural selection. More effective reproducers would increase in frequency at the expense of inefficient reproducers. So while evolution does not explain the origin of life, it may have something to say about some of the processes operating once pre-living entities acquired certain properties.
Organisms Evolve on Purpose
Statements such as “organisms evolve in response to a change in an environment” are quite common, but such statements can lead to two types of misunderstandings. First, the statement must not be understood to mean that individual organisms evolve. The statement is shorthand for “a population evolves in response to a changing environment.” However, a second misunderstanding may arise by interpreting the statement to mean that the evolution is somehow intentional. A changed environment results in some individuals in the population, those with particular phenotypes, benefiting and therefore producing proportionately more offspring than other phenotypes. This results in change in the population if the characteristics are genetically determined.
It is also important to understand that the variation that natural selection works on is already in a population and does not arise in response to an environmental change. For example, applying antibiotics to a population of bacteria will, over time, select a population of bacteria that are resistant to antibiotics. The resistance, which is caused by a gene, did not arise by mutation because of the application of the antibiotic. The gene for resistance was already present in the gene pool of the bacteria, likely at a low frequency. The antibiotic, which kills the bacterial cells without the resistance gene, strongly selects individuals that are resistant, since these would be the only ones that survived and divided. Experiments have demonstrated that mutations for antibiotic resistance do not arise as a result of antibiotic.
In a larger sense, evolution is not goal directed. Species do not become “better” over time; they simply track their changing environment with adaptations that maximize their reproduction in a particular environment at a particular time. Evolution has no goal of making faster, bigger, more complex, or even smarter species, despite the commonness of this kind of language in popular discourse. What characteristics evolve in a species are a function of the variation present and the environment, both of which are constantly changing in a non-directional way. What trait is fit in one environment at one time may well be fatal at some point in the future. This holds equally well for a species of insect as it does the human species.
Summary
Evolution is the process of adaptation through mutation which allows more desirable characteristics to be passed to the next generation. Over time, organisms evolve more characteristics that are beneficial to their survival. For living organisms to adapt and change to environmental pressures, genetic variation must be present. With genetic variation, individuals have differences in form and function that allow some to survive certain conditions better than others. These organisms pass their favorable traits to their offspring. Eventually, environments change, and what was once a desirable, advantageous trait may become an undesirable trait and organisms may further evolve. Evolution may be convergent with similar traits evolving in multiple species or divergent with diverse traits evolving in multiple species that came from a common ancestor. Evidence of evolution can be observed by means of DNA code and the fossil record, and also by the existence of homologous and vestigial structures.
Glossary
adaptation
heritable trait or behavior in an organism that aids in its survival and reproduction in its present environment
convergent evolution
process by which groups of organisms independently evolve to similar forms
divergent evolution
process by which groups of organisms evolve in diverse directions from a common point
homologous structures
parallel structures in diverse organisms that have a common ancestor
natural selection
reproduction of individuals with favorable genetic traits that survive environmental change because of those traits, leading to evolutionary change
variation
genetic differences among individuals in a population
vestigial structure
physical structure present in an organism but that has no apparent function and appears to be from a functional structure in a distant ancestor | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/4%3A_Evolutionary_Processes/18%3A_Evolution_and_the_Origin_of_Species/18.0%3A_Evolution.txt |
Skills to Develop
• Define species and describe how species are identified as different
• Describe genetic variables that lead to speciation
• Identify prezygotic and postzygotic reproductive barriers
• Explain allopatric and sympatric speciation
• Describe adaptive radiation
Although all life on earth shares various genetic similarities, only certain organisms combine genetic information by sexual reproduction and have offspring that can then successfully reproduce. Scientists call such organisms members of the same biological species.
Species and the Ability to Reproduce
A species is a group of individual organisms that interbreed and produce fertile, viable offspring. According to this definition, one species is distinguished from another when, in nature, it is not possible for matings between individuals from each species to produce fertile offspring.
Members of the same species share both external and internal characteristics, which develop from their DNA. The closer relationship two organisms share, the more DNA they have in common, just like people and their families. People’s DNA is likely to be more like their father or mother’s DNA than their cousin or grandparent’s DNA. Organisms of the same species have the highest level of DNA alignment and therefore share characteristics and behaviors that lead to successful reproduction.
Species’ appearance can be misleading in suggesting an ability or inability to mate. For example, even though domestic dogs (Canis lupus familiaris) display phenotypic differences, such as size, build, and coat, most dogs can interbreed and produce viable puppies that can mature and sexually reproduce (Figure \(1\)).
In other cases, individuals may appear similar although they are not members of the same species. For example, even though bald eagles (Haliaeetus leucocephalus) and African fish eagles (Haliaeetus vocifer) are both birds and eagles, each belongs to a separate species group (Figure \(2\)). If humans were to artificially intervene and fertilize the egg of a bald eagle with the sperm of an African fish eagle and a chick did hatch, that offspring, called a hybrid (a cross between two species), would probably be infertile—unable to successfully reproduce after it reached maturity. Different species may have different genes that are active in development; therefore, it may not be possible to develop a viable offspring with two different sets of directions. Thus, even though hybridization may take place, the two species still remain separate.
Populations of species share a gene pool: a collection of all the variants of genes in the species. Again, the basis to any changes in a group or population of organisms must be genetic for this is the only way to share and pass on traits. When variations occur within a species, they can only be passed to the next generation along two main pathways: asexual reproduction or sexual reproduction. The change will be passed on asexually simply if the reproducing cell possesses the changed trait. For the changed trait to be passed on by sexual reproduction, a gamete, such as a sperm or egg cell, must possess the changed trait. In other words, sexually-reproducing organisms can experience several genetic changes in their body cells, but if these changes do not occur in a sperm or egg cell, the changed trait will never reach the next generation. Only heritable traits can evolve. Therefore, reproduction plays a paramount role for genetic change to take root in a population or species. In short, organisms must be able to reproduce with each other to pass new traits to offspring.
Speciation
The biological definition of species, which works for sexually reproducing organisms, is a group of actually or potentially interbreeding individuals. There are exceptions to this rule. Many species are similar enough that hybrid offspring are possible and may often occur in nature, but for the majority of species this rule generally holds. In fact, the presence in nature of hybrids between similar species suggests that they may have descended from a single interbreeding species, and the speciation process may not yet be completed.
Given the extraordinary diversity of life on the planet there must be mechanisms for speciation: the formation of two species from one original species. Darwin envisioned this process as a branching event and diagrammed the process in the only illustration found in On the Origin of Species (Figure \(3\)a). Compare this illustration to the diagram of elephant evolution (Figure \(3\)b), which shows that as one species changes over time, it branches to form more than one new species, repeatedly, as long as the population survives or until the organism becomes extinct.
For speciation to occur, two new populations must be formed from one original population and they must evolve in such a way that it becomes impossible for individuals from the two new populations to interbreed. Biologists have proposed mechanisms by which this could occur that fall into two broad categories. Allopatric speciation (allo- = "other"; -patric = "homeland") involves geographic separation of populations from a parent species and subsequent evolution. Sympatric speciation (sym- = "same"; -patric = "homeland") involves speciation occurring within a parent species remaining in one location.
Biologists think of speciation events as the splitting of one ancestral species into two descendant species. There is no reason why there might not be more than two species formed at one time except that it is less likely and multiple events can be conceptualized as single splits occurring close in time.
Allopatric Speciation
A geographically continuous population has a gene pool that is relatively homogeneous. Gene flow, the movement of alleles across the range of the species, is relatively free because individuals can move and then mate with individuals in their new location. Thus, the frequency of an allele at one end of a distribution will be similar to the frequency of the allele at the other end. When populations become geographically discontinuous, that free-flow of alleles is prevented. When that separation lasts for a period of time, the two populations are able to evolve along different trajectories. Thus, their allele frequencies at numerous genetic loci gradually become more and more different as new alleles independently arise by mutation in each population. Typically, environmental conditions, such as climate, resources, predators, and competitors for the two populations will differ causing natural selection to favor divergent adaptations in each group.
Isolation of populations leading to allopatric speciation can occur in a variety of ways: a river forming a new branch, erosion forming a new valley, a group of organisms traveling to a new location without the ability to return, or seeds floating over the ocean to an island. The nature of the geographic separation necessary to isolate populations depends entirely on the biology of the organism and its potential for dispersal. If two flying insect populations took up residence in separate nearby valleys, chances are, individuals from each population would fly back and forth continuing gene flow. However, if two rodent populations became divided by the formation of a new lake, continued gene flow would be unlikely; therefore, speciation would be more likely.
Biologists group allopatric processes into two categories: dispersal and vicariance. Dispersal is when a few members of a species move to a new geographical area, and vicariance is when a natural situation arises to physically divide organisms.
Scientists have documented numerous cases of allopatric speciation taking place. For example, along the west coast of the United States, two separate sub-species of spotted owls exist. The northern spotted owl has genetic and phenotypic differences from its close relative: the Mexican spotted owl, which lives in the south (Figure \(4\)).
Additionally, scientists have found that the further the distance between two groups that once were the same species, the more likely it is that speciation will occur. This seems logical because as the distance increases, the various environmental factors would likely have less in common than locations in close proximity. Consider the two owls: in the north, the climate is cooler than in the south; the types of organisms in each ecosystem differ, as do their behaviors and habits; also, the hunting habits and prey choices of the southern owls vary from the northern owls. These variances can lead to evolved differences in the owls, and speciation likely will occur.
Adaptive Radiation
In some cases, a population of one species disperses throughout an area, and each finds a distinct niche or isolated habitat. Over time, the varied demands of their new lifestyles lead to multiple speciation events originating from a single species. This is called adaptive radiation because many adaptations evolve from a single point of origin; thus, causing the species to radiate into several new ones. Island archipelagos like the Hawaiian Islands provide an ideal context for adaptive radiation events because water surrounds each island which leads to geographical isolation for many organisms. The Hawaiian honeycreeper illustrates one example of adaptive radiation. From a single species, called the founder species, numerous species have evolved, including the six shown in Figure \(5\).
Notice the differences in the species’ beaks in Figure \(5\). Evolution in response to natural selection based on specific food sources in each new habitat led to evolution of a different beak suited to the specific food source. The seed-eating bird has a thicker, stronger beak which is suited to break hard nuts. The nectar-eating birds have long beaks to dip into flowers to reach the nectar. The insect-eating birds have beaks like swords, appropriate for stabbing and impaling insects. Darwin’s finches are another example of adaptive radiation in an archipelago.
Link to Learning
Click through this interactive site to see how island birds evolved in evolutionary increments from 5 million years ago to today.
Sympatric Speciation
Can divergence occur if no physical barriers are in place to separate individuals who continue to live and reproduce in the same habitat? The answer is yes. The process of speciation within the same space is called sympatric speciation; the prefix “sym” means same, so “sympatric” means “same homeland” in contrast to “allopatric” meaning “other homeland.” A number of mechanisms for sympatric speciation have been proposed and studied.
One form of sympatric speciation can begin with a serious chromosomal error during cell division. In a normal cell division event chromosomes replicate, pair up, and then separate so that each new cell has the same number of chromosomes. However, sometimes the pairs separate and the end cell product has too many or too few individual chromosomes in a condition called aneuploidy (Figure \(6\)).
Art Connection
Which is most likely to survive, offspring with 2n+1 chromosomes or offspring with 2n-1 chromosomes?
Polyploidy is a condition in which a cell or organism has an extra set, or sets, of chromosomes. Scientists have identified two main types of polyploidy that can lead to reproductive isolation of an individual in the polyploidy state. Reproductive isolation is the inability to interbreed. In some cases, a polyploid individual will have two or more complete sets of chromosomes from its own species in a condition called autopolyploidy (Figure \(7\)). The prefix “auto-” means “self,” so the term means multiple chromosomes from one’s own species. Polyploidy results from an error in meiosis in which all of the chromosomes move into one cell instead of separating.
For example, if a plant species with 2n = 6 produces autopolyploid gametes that are also diploid (2n = 6, when they should be n = 3), the gametes now have twice as many chromosomes as they should have. These new gametes will be incompatible with the normal gametes produced by this plant species. However, they could either self-pollinate or reproduce with other autopolyploid plants with gametes having the same diploid number. In this way, sympatric speciation can occur quickly by forming offspring with 4n called a tetraploid. These individuals would immediately be able to reproduce only with those of this new kind and not those of the ancestral species.
The other form of polyploidy occurs when individuals of two different species reproduce to form a viable offspring called an allopolyploid. The prefix “allo-” means “other” (recall from allopatric): therefore, an allopolyploid occurs when gametes from two different species combine. Figure \(8\) illustrates one possible way an allopolyploid can form. Notice how it takes two generations, or two reproductive acts, before the viable fertile hybrid results.
The cultivated forms of wheat, cotton, and tobacco plants are all allopolyploids. Although polyploidy occurs occasionally in animals, it takes place most commonly in plants. (Animals with any of the types of chromosomal aberrations described here are unlikely to survive and produce normal offspring.) Scientists have discovered more than half of all plant species studied relate back to a species evolved through polyploidy. With such a high rate of polyploidy in plants, some scientists hypothesize that this mechanism takes place more as an adaptation than as an error.
Reproductive Isolation
Given enough time, the genetic and phenotypic divergence between populations will affect characters that influence reproduction: if individuals of the two populations were to be brought together, mating would be less likely, but if mating occurred, offspring would be non-viable or infertile. Many types of diverging characters may affect the reproductive isolation, the ability to interbreed, of the two populations.
Reproductive isolation can take place in a variety of ways. Scientists organize them into two groups: prezygotic barriers and postzygotic barriers. Recall that a zygote is a fertilized egg: the first cell of the development of an organism that reproduces sexually. Therefore, a prezygotic barrier is a mechanism that blocks reproduction from taking place; this includes barriers that prevent fertilization when organisms attempt reproduction. A postzygotic barrier occurs after zygote formation; this includes organisms that don’t survive the embryonic stage and those that are born sterile.
Some types of prezygotic barriers prevent reproduction entirely. Many organisms only reproduce at certain times of the year, often just annually. Differences in breeding schedules, called temporal isolation, can act as a form of reproductive isolation. For example, two species of frogs inhabit the same area, but one reproduces from January to March, whereas the other reproduces from March to May (Figure \(9\)).
In some cases, populations of a species move or are moved to a new habitat and take up residence in a place that no longer overlaps with the other populations of the same species. This situation is called habitat isolation. Reproduction with the parent species ceases, and a new group exists that is now reproductively and genetically independent. For example, a cricket population that was divided after a flood could no longer interact with each other. Over time, the forces of natural selection, mutation, and genetic drift will likely result in the divergence of the two groups (Figure \(10\)).
Behavioral isolation occurs when the presence or absence of a specific behavior prevents reproduction from taking place. For example, male fireflies use specific light patterns to attract females. Various species of fireflies display their lights differently. If a male of one species tried to attract the female of another, she would not recognize the light pattern and would not mate with the male.
Other prezygotic barriers work when differences in their gamete cells (eggs and sperm) prevent fertilization from taking place; this is called a gametic barrier. Similarly, in some cases closely related organisms try to mate, but their reproductive structures simply do not fit together. For example, damselfly males of different species have differently shaped reproductive organs. If one species tries to mate with the female of another, their body parts simply do not fit together (Figure \(11\)).
In plants, certain structures aimed to attract one type of pollinator simultaneously prevent a different pollinator from accessing the pollen. The tunnel through which an animal must access nectar can vary widely in length and diameter, which prevents the plant from being cross-pollinated with a different species (Figure \(12\)).
When fertilization takes place and a zygote forms, postzygotic barriers can prevent reproduction. Hybrid individuals in many cases cannot form normally in the womb and simply do not survive past the embryonic stages. This is called hybrid inviability because the hybrid organisms simply are not viable. In another postzygotic situation, reproduction leads to the birth and growth of a hybrid that is sterile and unable to reproduce offspring of their own; this is called hybrid sterility.
Habitat Influence on Speciation
Sympatric speciation may also take place in ways other than polyploidy. For example, consider a species of fish that lives in a lake. As the population grows, competition for food also grows. Under pressure to find food, suppose that a group of these fish had the genetic flexibility to discover and feed off another resource that was unused by the other fish. What if this new food source was found at a different depth of the lake? Over time, those feeding on the second food source would interact more with each other than the other fish; therefore, they would breed together as well. Offspring of these fish would likely behave as their parents: feeding and living in the same area and keeping separate from the original population. If this group of fish continued to remain separate from the first population, eventually sympatric speciation might occur as more genetic differences accumulated between them.
This scenario does play out in nature, as do others that lead to reproductive isolation. One such place is Lake Victoria in Africa, famous for its sympatric speciation of cichlid fish. Researchers have found hundreds of sympatric speciation events in these fish, which have not only happened in great number, but also over a short period of time. Figure \(13\) shows this type of speciation among a cichlid fish population in Nicaragua. In this locale, two types of cichlids live in the same geographic location but have come to have different morphologies that allow them to eat various food sources.
Summary
Speciation occurs along two main pathways: geographic separation (allopatric speciation) and through mechanisms that occur within a shared habitat (sympatric speciation). Both pathways isolate a population reproductively in some form. Mechanisms of reproductive isolation act as barriers between closely related species, enabling them to diverge and exist as genetically independent species. Prezygotic barriers block reproduction prior to formation of a zygote, whereas postzygotic barriers block reproduction after fertilization occurs. For a new species to develop, something must cause a breach in the reproductive barriers. Sympatric speciation can occur through errors in meiosis that form gametes with extra chromosomes (polyploidy). Autopolyploidy occurs within a single species, whereas allopolyploidy occurs between closely related species.
Art Connections
Figure \(6\): Which is most likely to survive, offspring with 2n+1 chromosomes or offspring with 2n-1 chromosomes?
Answer
Loss of genetic material is almost always lethal, so offspring with 2n+1 chromosomes are more likely to survive.
Glossary
adaptive radiation
speciation when one species radiates out to form several other species
allopatric speciation
speciation that occurs via geographic separation
allopolyploid
polyploidy formed between two related, but separate species
aneuploidy
condition of a cell having an extra chromosome or missing a chromosome for its species
autopolyploid
polyploidy formed within a single species
behavioral isolation
type of reproductive isolation that occurs when a specific behavior or lack of one prevents reproduction from taking place
dispersal
allopatric speciation that occurs when a few members of a species move to a new geographical area
gametic barrier
prezygotic barrier occurring when closely related individuals of different species mate, but differences in their gamete cells (eggs and sperm) prevent fertilization from taking place
habitat isolation
reproductive isolation resulting when populations of a species move or are moved to a new habitat, taking up residence in a place that no longer overlaps with the other populations of the same species
hybrid
offspring of two closely related individuals, not of the same species
postzygotic barrier
reproductive isolation mechanism that occurs after zygote formation
prezygotic barrier
reproductive isolation mechanism that occurs before zygote formation
reproductive isolation
situation that occurs when a species is reproductively independent from other species; this may be brought about by behavior, location, or reproductive barriers
speciation
formation of a new species
species
group of populations that interbreed and produce fertile offspring
sympatric speciation
speciation that occurs in the same geographic space
temporal isolation
differences in breeding schedules that can act as a form of prezygotic barrier leading to reproductive isolation
vicariance
allopatric speciation that occurs when something in the environment separates organisms of the same species into separate groups | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/4%3A_Evolutionary_Processes/18%3A_Evolution_and_the_Origin_of_Species/18.2%3A_Formation_of_New_Species.txt |
Skills to Develop
• Describe pathways of species evolution in hybrid zones
• Explain the two major theories on rates of speciation
Speciation occurs over a span of evolutionary time, so when a new species arises, there is a transition period during which the closely related species continue to interact.
Reconnection
After speciation, two species may recombine or even continue interacting indefinitely. Individual organisms will mate with any nearby individual who they are capable of breeding with. An area where two closely related species continue to interact and reproduce, forming hybrids, is called a hybrid zone. Over time, the hybrid zone may change depending on the fitness of the hybrids and the reproductive barriers (Figure \(1\)). If the hybrids are less fit than the parents, reinforcement of speciation occurs, and the species continue to diverge until they can no longer mate and produce viable offspring. If reproductive barriers weaken, fusion occurs and the two species become one. Barriers remain the same if hybrids are fit and reproductive: stability may occur and hybridization continues.
Art Connection
If two species eat a different diet but one of the food sources is eliminated and both species are forced to eat the same foods, what change in the hybrid zone is most likely to occur?
Hybrids can be either less fit than the parents, more fit, or about the same. Usually hybrids tend to be less fit; therefore, such reproduction diminishes over time, nudging the two species to diverge further in a process called reinforcement. This term is used because the low success of the hybrids reinforces the original speciation. If the hybrids are as fit or more fit than the parents, the two species may fuse back into one species (Figure \(1\)). Scientists have also observed that sometimes two species will remain separate but also continue to interact to produce some hybrid individuals; this is classified as stability because no real net change is taking place.
Varying Rates of Speciation
Scientists around the world study speciation, documenting observations both of living organisms and those found in the fossil record. As their ideas take shape and as research reveals new details about how life evolves, they develop models to help explain rates of speciation. In terms of how quickly speciation occurs, two patterns are currently observed: gradual speciation model and punctuated equilibrium model.
In the gradual speciation model, species diverge gradually over time in small steps. In the punctuated equilibrium model, a new species undergoes changes quickly from the parent species, and then remains largely unchanged for long periods of time afterward (Figure \(2\)). This early change model is called punctuated equilibrium, because it begins with a punctuated or periodic change and then remains in balance afterward. While punctuated equilibrium suggests a faster tempo, it does not necessarily exclude gradualism.
Art Connection
Which of the following statements is false?
1. Punctuated equilibrium is most likely to occur in a small population that experiences a rapid change in its environment.
2. Punctuated equilibrium is most likely to occur in a large population that lives in a stable climate.
3. Gradual speciation is most likely to occur in species that live in a stable climate.
4. Gradual speciation and punctuated equilibrium both result in the divergence of species.
The primary influencing factor on changes in speciation rate is environmental conditions. Under some conditions, selection occurs quickly or radically. Consider a species of snails that had been living with the same basic form for many thousands of years. Layers of their fossils would appear similar for a long time. When a change in the environment takes place—such as a drop in the water level—a small number of organisms are separated from the rest in a brief period of time, essentially forming one large and one tiny population. The tiny population faces new environmental conditions. Because its gene pool quickly became so small, any variation that surfaces and that aids in surviving the new conditions becomes the predominant form.
Link to Learning
Visit this website to continue the speciation story of the snails.
Summary
Speciation is not a precise division: overlap between closely related species can occur in areas called hybrid zones. Organisms reproduce with other similar organisms. The fitness of these hybrid offspring can affect the evolutionary path of the two species. Scientists propose two models for the rate of speciation: one model illustrates how a species can change slowly over time; the other model demonstrates how change can occur quickly from a parent generation to a new species. Both models continue to follow the patterns of natural selection.
Art Connections
Figure \(1\): If two species eat a different diet but one of the food sources is eliminated and both species are forced to eat the same foods, what change in the hybrid zone is most likely to occur?
Answer
Fusion is most likely to occur because the two species will interact more and similar traits in food acquisition will be selected.
Figure \(2\): Which of the following statements is false?
1. Punctuated equilibrium is most likely to occur in a small population that experiences a rapid change in its environment.
2. Punctuated equilibrium is most likely to occur in a large population that lives in a stable climate.
3. Gradual speciation is most likely to occur in species that live in a stable climate.
4. Gradual speciation and punctuated equilibrium both result in the evolution of new species.
Answer
B
Glossary
gradual speciation model
model that shows how species diverge gradually over time in small steps
hybrid zone
area where two closely related species continue to interact and reproduce, forming hybrids
punctuated equilibrium
model for rapid speciation that can occur when an event causes a small portion of a population to be cut off from the rest of the population
reinforcement
continued speciation divergence between two related species due to low fitness of hybrids between them | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/4%3A_Evolutionary_Processes/18%3A_Evolution_and_the_Origin_of_Species/18.3%3A_Reconnection_and_Rates_of_Speciation.txt |
18.1: Understanding Evolution
Review Questions
Which scientific concept did Charles Darwin and Alfred Wallace independently discover?
1. mutation
2. natural selection
3. overbreeding
4. sexual reproduction
Answer
B
Which of the following situations will lead to natural selection?
1. The seeds of two plants land near each other and one grows larger than the other.
2. Two types of fish eat the same kind of food, and one is better able to gather food than the other.
3. Male lions compete for the right to mate with females, with only one possible winner.
4. all of the above
Answer
D
Which description is an example of a phenotype?
1. A certain duck has a blue beak.
2. A mutation occurred to a flower.
3. Most cheetahs live solitary lives.
4. both a and c
Answer
D
Which situation is most likely an example of convergent evolution?
1. Squid and humans have eyes similar in structure.
2. Worms and snakes both move without legs.
3. Some bats and birds have wings that allow them to fly
4. all of the above
Answer
D
Free Response
If a person scatters a handful of garden pea plant seeds in one area, how would natural selection work in this situation?
Answer
The plants that can best use the resources of the area, including competing with other individuals for those resources will produce more seeds themselves and those traits that allowed them to better use the resources will increase in the population of the next generation.
Why do scientists consider vestigial structures evidence for evolution?
Answer
Vestigial structures are considered evidence for evolution because most structures do not exist in an organism without serving some function either presently or in the past. A vestigial structure indicates a past form or function that has since changed, but the structure remains present because it had a function in the ancestor.
How does the scientific meaning of “theory” differ from the common vernacular meaning?
Answer
In science, a theory is a thoroughly tested and verified set of explanations for a body of observations of nature. It is the strongest form of knowledge in science. In contrast, a theory in common vernacular can mean a guess or speculation about something, meaning that the knowledge implied by the theory is very weak.
Explain why the statement that a monkey is more evolved than a mouse is incorrect.
Answer
The statement implies that there is a goal to evolution and that the monkey represents greater progress to that goal than the mouse. Both species are likely to be well adapted to their particular environments, which is the outcome of natural selection.
18.2: Formation of New Species
Review Questions
Which situation would most likely lead to allopatric speciation?
1. flood causes the formation of a new lake.
2. A storm causes several large trees to fall down.
3. A mutation causes a new trait to develop.
4. An injury causes an organism to seek out a new food source.
Answer
A
What is the main difference between dispersal and vicariance?
1. One leads to allopatric speciation, whereas the other leads to sympatric speciation.
2. One involves the movement of the organism, and the other involves a change in the environment.
3. One depends on a genetic mutation occurring, and the other does not.
4. One involves closely related organisms, and the other involves only individuals of the same species.
Answer
B
Which variable increases the likelihood of allopatric speciation taking place more quickly?
1. lower rate of mutation
2. longer distance between divided groups
3. increased instances of hybrid formation
4. equivalent numbers of individuals in each population
Answer
B
What is the main difference between autopolyploid and allopolyploid?
1. the number of chromosomes
2. the functionality of the chromosomes
3. the source of the extra chromosomes
4. the number of mutations in the extra chromosomes
Answer
C
Which reproductive combination produces hybrids?
1. when individuals of the same species in different geographical areas reproduce
2. when any two individuals sharing the same habitat reproduce
3. when members of closely related species reproduce
4. when offspring of the same parents reproduce
Answer
C
Which condition is the basis for a species to be reproductively isolated from other members?
1. It does not share its habitat with related species.
2. It does not exist out of a single habitat.
3. It does not exchange genetic information with other species.
4. It does not undergo evolutionary changes for a significant period of time.
Answer
C
Which situation is not an example of a prezygotic barrier?
1. Two species of turtles breed at different times of the year.
2. Two species of flowers attract different pollinators.
3. Two species of birds display different mating dances.
4. Two species of insects produce infertile offspring.
Answer
D
Free Response
Why do island chains provide ideal conditions for adaptive radiation to occur?
Answer
Organisms of one species can arrive to an island together and then disperse throughout the chain, each settling into different niches and exploiting different food resources to reduce competition.
Two species of fish had recently undergone sympatric speciation. The males of each species had a different coloring through which the females could identify and choose a partner from her own species. After some time, pollution made the lake so cloudy that it was hard for females to distinguish colors. What might take place in this situation?
Answer
It is likely the two species would start to reproduce with each other. Depending on the viability of their offspring, they may fuse back into one species.
Why can polyploidy individuals lead to speciation fairly quickly?
Answer
The formation of gametes with new n numbers can occur in one generation. After a couple of generations, enough of these new hybrids can form to reproduce together as a new species.
18.3: Reconnection and Rates of Speciation
Review Questions
Which term is used to describe the continued divergence of species based on the low fitness of hybrid offspring?
1. reinforcement
2. fusion
3. stability
4. punctuated equilibrium
Answer
A
Which components of speciation would be least likely to be a part of punctuated equilibrium?
1. a division of populations
2. a change in environmental conditions
3. ongoing gene flow among all individuals
4. a large number of mutations taking place at once
Answer
C
Free Response
What do both rate of speciation models have in common?
Answer
Both models continue to conform to the rules of natural selection, and the influences of gene flow, genetic drift, and mutation.
Describe a situation where hybrid reproduction would cause two species to fuse into one.
Answer
If the hybrid offspring are as fit or more fit than the parents, reproduction would likely continue between both species and the hybrids, eventually bringing all organisms under the umbrella of one species. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/4%3A_Evolutionary_Processes/18%3A_Evolution_and_the_Origin_of_Species/18.E%3A_Evolution_and_the_Origin_of_Species_%28Exercises%29.txt |
Natural selection is one of the most dominant evolutionary forces. Natural selection acts to promote traits and behaviors that increase an organism’s chances of survival and reproduction, while eliminating those traits and behaviors that are to the organism’s detriment. But natural selection can only, as its name implies, select—it cannot create. The introduction of novel traits and behaviors falls on the shoulders of another evolutionary force—mutation. Mutation and other sources of variation among individuals, as well as the evolutionary forces that act upon them, alter populations and species. This combination of processes has led to the world of life we see today.
• 19.0: Introduction
All life on Earth is related. Evolutionary theory states that humans, beetles, plants, and bacteria all share a common ancestor, but that millions of years of evolution have shaped each of these organisms into the forms seen today. Scientists consider evolution a key concept to understanding life. Natural selection is one of the most dominant evolutionary forces.
• 19.1: Population Evolution
Initially, the newly discovered particulate nature of genes made it difficult for biologists to understand how gradual evolution could occur. But over the next few decades genetics and evolution were integrated in what became known as the modern synthesis—the coherent understanding of the relationship between natural selection and genetics that took shape by the 1940s and is generally accepted today.
• 19.2: Population Genetics
Individuals of a population often display different phenotypes, or express different alleles of a particular gene, referred to as polymorphisms. Populations with two or more variations of particular characteristics are called polymorphic. The distribution of phenotypes among individuals, known as the population variation, is influenced by a number of factors, including the population’s genetic structure and the environment.
• 19.3: Adaptive Evolution
Fitness is often quantifiable and is measured by scientists in the field. However, it is not the absolute fitness of an individual that counts, but rather how it compares to the other organisms in the population. This concept, called relative fitness, allows researchers to determine which individuals are contributing additional offspring to the next generation, and thus, how the population might evolve.
• 19.E: The Evolution of Populations (Exercises)
19: The Evolution of Populations
All life on Earth is related. Evolutionary theory states that humans, beetles, plants, and bacteria all share a common ancestor, but that millions of years of evolution have shaped each of these organisms into the forms seen today. Scientists consider evolution a key concept to understanding life. Natural selection is one of the most dominant evolutionary forces. Natural selection acts to promote traits and behaviors that increase an organism’s chances of survival and reproduction, while eliminating those traits and behaviors that are to the organism’s detriment. But natural selection can only, as its name implies, select—it cannot create. The introduction of novel traits and behaviors falls on the shoulders of another evolutionary force—mutation. Mutation and other sources of variation among individuals, as well as the evolutionary forces that act upon them, alter populations and species. This combination of processes has led to the world of life we see today. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/4%3A_Evolutionary_Processes/19%3A_The_Evolution_of_Populations/19.0%3A_Introduction.txt |
Skills to Develop
• Define population genetics and describe how population genetics is used in the study of the evolution of populations
• Define the Hardy-Weinberg principle and discuss its importance
The mechanisms of inheritance, or genetics, were not understood at the time Charles Darwin and Alfred Russel Wallace were developing their idea of natural selection. This lack of understanding was a stumbling block to understanding many aspects of evolution. In fact, the predominant (and incorrect) genetic theory of the time, blending inheritance, made it difficult to understand how natural selection might operate. Darwin and Wallace were unaware of the genetics work by Austrian monk Gregor Mendel, which was published in 1866, not long after publication of Darwin's book, On the Origin of Species. Mendel’s work was rediscovered in the early twentieth century at which time geneticists were rapidly coming to an understanding of the basics of inheritance. Initially, the newly discovered particulate nature of genes made it difficult for biologists to understand how gradual evolution could occur. But over the next few decades genetics and evolution were integrated in what became known as the modern synthesis—the coherent understanding of the relationship between natural selection and genetics that took shape by the 1940s and is generally accepted today. In sum, the modern synthesis describes how evolutionary processes, such as natural selection, can affect a population’s genetic makeup, and, in turn, how this can result in the gradual evolution of populations and species. The theory also connects this change of a population over time, called microevolution, with the processes that gave rise to new species and higher taxonomic groups with widely divergent characters, called macroevolution.
Everyday Connection: Evolution and Flu Vaccines
Every fall, the media starts reporting on flu vaccinations and potential outbreaks. Scientists, health experts, and institutions determine recommendations for different parts of the population, predict optimal production and inoculation schedules, create vaccines, and set up clinics to provide inoculations. You may think of the annual flu shot as a lot of media hype, an important health protection, or just a briefly uncomfortable prick in your arm. But do you think of it in terms of evolution?
The media hype of annual flu shots is scientifically grounded in our understanding of evolution. Each year, scientists across the globe strive to predict the flu strains that they anticipate being most widespread and harmful in the coming year. This knowledge is based in how flu strains have evolved over time and over the past few flu seasons. Scientists then work to create the most effective vaccine to combat those selected strains. Hundreds of millions of doses are produced in a short period in order to provide vaccinations to key populations at the optimal time.
Because viruses, like the flu, evolve very quickly (especially in evolutionary time), this poses quite a challenge. Viruses mutate and replicate at a fast rate, so the vaccine developed to protect against last year’s flu strain may not provide the protection needed against the coming year’s strain. Evolution of these viruses means continued adaptions to ensure survival, including adaptations to survive previous vaccines.
Population Genetics
Recall that a gene for a particular character may have several alleles, or variants, that code for different traits associated with that character. For example, in the ABO blood type system in humans, three alleles determine the particular blood-type protein on the surface of red blood cells. Each individual in a population of diploid organisms can only carry two alleles for a particular gene, but more than two may be present in the individuals that make up the population. Mendel followed alleles as they were inherited from parent to offspring. In the early twentieth century, biologists in a field of study known as population genetics began to study how selective forces change a population through changes in allele and genotypic frequencies.
The allele frequency (or gene frequency) is the rate at which a specific allele appears within a population. Until now we have discussed evolution as a change in the characteristics of a population of organisms, but behind that phenotypic change is genetic change. In population genetics, the term evolution is defined as a change in the frequency of an allele in a population. Using the ABO blood type system as an example, the frequency of one of the alleles, IA, is the number of copies of that allele divided by all the copies of the ABO gene in the population. For example, a study in Jordan1 found a frequency of IA to be 26.1 percent. The IB and I0 alleles made up 13.4 percent and 60.5 percent of the alleles respectively, and all of the frequencies added up to 100 percent. A change in this frequency over time would constitute evolution in the population.
The allele frequency within a given population can change depending on environmental factors; therefore, certain alleles become more widespread than others during the process of natural selection. Natural selection can alter the population’s genetic makeup; for example, if a given allele confers a phenotype that allows an individual to better survive or have more offspring. Because many of those offspring will also carry the beneficial allele, and often the corresponding phenotype, they will have more offspring of their own that also carry the allele, thus, perpetuating the cycle. Over time, the allele will spread throughout the population. Some alleles will quickly become fixed in this way, meaning that every individual of the population will carry the allele, while detrimental mutations may be swiftly eliminated if derived from a dominant allele from the gene pool. The gene pool is the sum of all the alleles in a population.
Sometimes, allele frequencies within a population change randomly with no advantage to the population over existing allele frequencies. This phenomenon is called genetic drift. Natural selection and genetic drift usually occur simultaneously in populations and are not isolated events. It is hard to determine which process dominates because it is often nearly impossible to determine the cause of change in allele frequencies at each occurrence. An event that initiates an allele frequency change in an isolated part of the population, which is not typical of the original population, is called the founder effect. Natural selection, random drift, and founder effects can lead to significant changes in the genome of a population.
Hardy-Weinberg Principle of Equilibrium
In the early twentieth century, English mathematician Godfrey Hardy and German physician Wilhelm Weinberg stated the principle of equilibrium to describe the genetic makeup of a population. The theory, which later became known as the Hardy-Weinberg principle of equilibrium, states that a population’s allele and genotype frequencies are inherently stable— unless some kind of evolutionary force is acting upon the population, neither the allele nor the genotypic frequencies would change. The Hardy-Weinberg principle assumes conditions with no mutations, migration, emigration, or selective pressure for or against genotype, plus an infinite population; while no population can satisfy those conditions, the principle offers a useful model against which to compare real population changes.
Working under this theory, population geneticists represent different alleles as different variables in their mathematical models. The variable p, for example, often represents the frequency of a particular allele, say Y for the trait of yellow in Mendel’s peas, while the variable q represents the frequency of y alleles that confer the color green. If these are the only two possible alleles for a given locus in the population, p + q = 1. In other words, all the p alleles and all the q alleles make up all of the alleles for that locus that are found in the population.
But what ultimately interests most biologists is not the frequencies of different alleles, but the frequencies of the resulting genotypes, known as the population’s genetic structure, from which scientists can surmise the distribution of phenotypes. If the phenotype is observed, only the genotype of the homozygous recessive alleles can be known; the calculations provide an estimate of the remaining genotypes. Since each individual carries two alleles per gene, if the allele frequencies (p and q) are known, predicting the frequencies of these genotypes is a simple mathematical calculation to determine the probability of getting these genotypes if two alleles are drawn at random from the gene pool. So in the above scenario, an individual pea plant could be pp (YY), and thus produce yellow peas; pq (Yy), also yellow; or qq (yy), and thus producing green peas (Figure \(1\)). In other words, the frequency of pp individuals is simply p2; the frequency of pq individuals is 2pq; and the frequency of qq individuals is q2. And, again, if p and q are the only two possible alleles for a given trait in the population, these genotypes frequencies will sum to one: p2 + 2pq + q2 = 1.
Exercise \(1\)
In plants, violet flower color (V) is dominant over white (v). If p = 0.8 and q = 0.2 in a population of 500 plants, how many individuals would you expect to be homozygous dominant (VV), heterozygous (Vv), and homozygous recessive (vv)? How many plants would you expect to have violet flowers, and how many would have white flowers?
Answer
The expected distribution is 320 VV, 160Vv, and 20 vv plants. Plants with VV or Vv genotypes would have violet flowers, and plants with the vv genotype would have white flowers, so a total of 480 plants would be expected to have violet flowers, and 20 plants would have white flowers.
In theory, if a population is at equilibrium—that is, there are no evolutionary forces acting upon it—generation after generation would have the same gene pool and genetic structure, and these equations would all hold true all of the time. Of course, even Hardy and Weinberg recognized that no natural population is immune to evolution. Populations in nature are constantly changing in genetic makeup due to drift, mutation, possibly migration, and selection. As a result, the only way to determine the exact distribution of phenotypes in a population is to go out and count them. But the Hardy-Weinberg principle gives scientists a mathematical baseline of a non-evolving population to which they can compare evolving populations and thereby infer what evolutionary forces might be at play. If the frequencies of alleles or genotypes deviate from the value expected from the Hardy-Weinberg equation, then the population is evolving.
Summary
The modern synthesis of evolutionary theory grew out of the cohesion of Darwin’s, Wallace’s, and Mendel’s thoughts on evolution and heredity, along with the more modern study of population genetics. It describes the evolution of populations and species, from small-scale changes among individuals to large-scale changes over paleontological time periods. To understand how organisms evolve, scientists can track populations’ allele frequencies over time. If they differ from generation to generation, scientists can conclude that the population is not in Hardy-Weinberg equilibrium, and is thus evolving.
Footnotes
1. 1 Sahar S. Hanania, Dhia S. Hassawi, and Nidal M. Irshaid, “Allele Frequency and Molecular Genotypes of ABO Blood Group System in a Jordanian Population,” Journal of Medical Sciences 7 (2007): 51-58, doi:10.3923/jms.2007.51.58.
Glossary
allele frequency
(also, gene frequency) rate at which a specific allele appears within a population
founder effect
event that initiates an allele frequency change in part of the population, which is not typical of the original population
gene pool
all of the alleles carried by all of the individuals in the population
genetic structure
distribution of the different possible genotypes in a population
macroevolution
broader scale evolutionary changes seen over paleontological time
microevolution
changes in a population’s genetic structure
modern synthesis
overarching evolutionary paradigm that took shape by the 1940s and is generally accepted today
population genetics
study of how selective forces change the allele frequencies in a population over time | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/4%3A_Evolutionary_Processes/19%3A_The_Evolution_of_Populations/19.1%3A_Population_Evolution.txt |
Skills to Develop
• Describe the different types of variation in a population
• Explain why only heritable variation can be acted upon by natural selection
• Describe genetic drift and the bottleneck effect
• Explain how each evolutionary force can influence the allele frequencies of a population
Individuals of a population often display different phenotypes, or express different alleles of a particular gene, referred to as polymorphisms. Populations with two or more variations of particular characteristics are called polymorphic. The distribution of phenotypes among individuals, known as the population variation, is influenced by a number of factors, including the population’s genetic structure and the environment (Figure \(1\)). Understanding the sources of a phenotypic variation in a population is important for determining how a population will evolve in response to different evolutionary pressures.
Genetic Variance
Natural selection and some of the other evolutionary forces can only act on heritable traits, namely an organism’s genetic code. Because alleles are passed from parent to offspring, those that confer beneficial traits or behaviors may be selected for, while deleterious alleles may be selected against. Acquired traits, for the most part, are not heritable. For example, if an athlete works out in the gym every day, building up muscle strength, the athlete’s offspring will not necessarily grow up to be a body builder. If there is a genetic basis for the ability to run fast, on the other hand, this may be passed to a child.
Heritability is the fraction of phenotype variation that can be attributed to genetic differences, or genetic variance, among individuals in a population. The greater the hereditability of a population’s phenotypic variation, the more susceptible it is to the evolutionary forces that act on heritable variation.
The diversity of alleles and genotypes within a population is called genetic variance. When scientists are involved in the breeding of a species, such as with animals in zoos and nature preserves, they try to increase a population’s genetic variance to preserve as much of the phenotypic diversity as they can. This also helps reduce the risks associated with inbreeding, the mating of closely related individuals, which can have the undesirable effect of bringing together deleterious recessive mutations that can cause abnormalities and susceptibility to disease. For example, a disease that is caused by a rare, recessive allele might exist in a population, but it will only manifest itself when an individual carries two copies of the allele. Because the allele is rare in a normal, healthy population with unrestricted habitat, the chance that two carriers will mate is low, and even then, only 25 percent of their offspring will inherit the disease allele from both parents. While it is likely to happen at some point, it will not happen frequently enough for natural selection to be able to swiftly eliminate the allele from the population, and as a result, the allele will be maintained at low levels in the gene pool. However, if a family of carriers begins to interbreed with each other, this will dramatically increase the likelihood of two carriers mating and eventually producing diseased offspring, a phenomenon known as inbreeding depression.
Changes in allele frequencies that are identified in a population can shed light on how it is evolving. In addition to natural selection, there are other evolutionary forces that could be in play: genetic drift, gene flow, mutation, nonrandom mating, and environmental variances.
Genetic Drift
The theory of natural selection stems from the observation that some individuals in a population are more likely to survive longer and have more offspring than others; thus, they will pass on more of their genes to the next generation. A big, powerful male gorilla, for example, is much more likely than a smaller, weaker one to become the population’s silverback, the pack’s leader who mates far more than the other males of the group. The pack leader will father more offspring, who share half of his genes, and are likely to also grow bigger and stronger like their father. Over time, the genes for bigger size will increase in frequency in the population, and the population will, as a result, grow larger on average. That is, this would occur if this particular selection pressure, or driving selective force, were the only one acting on the population. In other examples, better camouflage or a stronger resistance to drought might pose a selection pressure.
Another way a population’s allele and genotype frequencies can change is genetic drift (Figure \(2\)), which is simply the effect of chance. By chance, some individuals will have more offspring than others—not due to an advantage conferred by some genetically-encoded trait, but just because one male happened to be in the right place at the right time (when the receptive female walked by) or because the other one happened to be in the wrong place at the wrong time (when a fox was hunting).
Exercise \(1\)
Do you think genetic drift would happen more quickly on an island or on the mainland?
Answer
Genetic drift is likely to occur more rapidly on an island where smaller populations are expected to occur.
Small populations are more susceptible to the forces of genetic drift. Large populations, on the other hand, are buffered against the effects of chance. If one individual of a population of 10 individuals happens to die at a young age before it leaves any offspring to the next generation, all of its genes—1/10 of the population’s gene pool—will be suddenly lost. In a population of 100, that’s only 1 percent of the overall gene pool; therefore, it is much less impactful on the population’s genetic structure.
Genetic drift can also be magnified by natural events, such as a natural disaster that kills—at random—a large portion of the population. Known as the bottleneck effect, it results in a large portion of the genome suddenly being wiped out (Figure \(3\)). In one fell swoop, the genetic structure of the survivors becomes the genetic structure of the entire population, which may be very different from the pre-disaster population.
Another scenario in which populations might experience a strong influence of genetic drift is if some portion of the population leaves to start a new population in a new location or if a population gets divided by a physical barrier of some kind. In this situation, those individuals are unlikely to be representative of the entire population, which results in the founder effect. The founder effect occurs when the genetic structure changes to match that of the new population’s founding fathers and mothers. The founder effect is believed to have been a key factor in the genetic history of the Afrikaner population of Dutch settlers in South Africa, as evidenced by mutations that are common in Afrikaners but rare in most other populations. This is likely due to the fact that a higher-than-normal proportion of the founding colonists carried these mutations. As a result, the population expresses unusually high incidences of Huntington’s disease (HD) and Fanconi anemia (FA), a genetic disorder known to cause blood marrow and congenital abnormalities—even cancer.1
Link to Learning
Watch this short video to learn more about the founder and bottleneck effects.
Scientific Method Connection: Testing the Bottleneck Effect
Question: How do natural disasters affect the genetic structure of a population?
Background: When much of a population is suddenly wiped out by an earthquake or hurricane, the individuals that survive the event are usually a random sampling of the original group. As a result, the genetic makeup of the population can change dramatically. This phenomenon is known as the bottleneck effect.
Hypothesis: Repeated natural disasters will yield different population genetic structures; therefore, each time this experiment is run, the results will vary.
Test the hypothesis: Count out the original population using different colored beads. For example, red, blue, and yellow beads might represent red, blue, and yellow individuals. After recording the number of each individual in the original population, place them all in a bottle with a narrow neck that will only allow a few beads out at a time. Then, pour 1/3 of the bottle’s contents into a bowl. This represents the surviving individuals after a natural disaster kills a majority of the population. Count the number of the different colored beads in the bowl, and record it. Then, place all of the beads back in the bottle and repeat the experiment four more times.
Analyze the data: Compare the five populations that resulted from the experiment. Do the populations all contain the same number of different colored beads, or do they vary? Remember, these populations all came from the same exact parent population.
Form a conclusion: Most likely, the five resulting populations will differ quite dramatically. This is because natural disasters are not selective—they kill and spare individuals at random. Now think about how this might affect a real population. What happens when a hurricane hits the Mississippi Gulf Coast? How do the seabirds that live on the beach fare?
Gene Flow
Another important evolutionary force is gene flow: the flow of alleles in and out of a population due to the migration of individuals or gametes (Figure \(4\)). While some populations are fairly stable, others experience more flux. Many plants, for example, send their pollen far and wide, by wind or by bird, to pollinate other populations of the same species some distance away. Even a population that may initially appear to be stable, such as a pride of lions, can experience its fair share of immigration and emigration as developing males leave their mothers to seek out a new pride with genetically unrelated females. This variable flow of individuals in and out of the group not only changes the gene structure of the population, but it can also introduce new genetic variation to populations in different geological locations and habitats.
Mutation
Mutations are changes to an organism’s DNA and are an important driver of diversity in populations. Species evolve because of the accumulation of mutations that occur over time. The appearance of new mutations is the most common way to introduce novel genotypic and phenotypic variance. Some mutations are unfavorable or harmful and are quickly eliminated from the population by natural selection. Others are beneficial and will spread through the population. Whether or not a mutation is beneficial or harmful is determined by whether it helps an organism survive to sexual maturity and reproduce. Some mutations do not do anything and can linger, unaffected by natural selection, in the genome. Some can have a dramatic effect on a gene and the resulting phenotype.
Nonrandom Mating
If individuals nonrandomly mate with their peers, the result can be a changing population. There are many reasons nonrandom mating occurs. One reason is simple mate choice; for example, female peahens may prefer peacocks with bigger, brighter tails. Traits that lead to more matings for an individual become selected for by natural selection. One common form of mate choice, called assortative mating, is an individual’s preference to mate with partners who are phenotypically similar to themselves.
Another cause of nonrandom mating is physical location. This is especially true in large populations spread over large geographic distances where not all individuals will have equal access to one another. Some might be miles apart through woods or over rough terrain, while others might live immediately nearby.
Environmental Variance
Genes are not the only players involved in determining population variation. Phenotypes are also influenced by other factors, such as the environment (Figure \(5\)). A beachgoer is likely to have darker skin than a city dweller, for example, due to regular exposure to the sun, an environmental factor. Some major characteristics, such as gender, are determined by the environment for some species. For example, some turtles and other reptiles have temperature-dependent sex determination (TSD). TSD means that individuals develop into males if their eggs are incubated within a certain temperature range, or females at a different temperature range.
Geographic separation between populations can lead to differences in the phenotypic variation between those populations. Such geographical variation is seen between most populations and can be significant. One type of geographic variation, called a cline, can be seen as populations of a given species vary gradually across an ecological gradient. Species of warm-blooded animals, for example, tend to have larger bodies in the cooler climates closer to the earth’s poles, allowing them to better conserve heat. This is considered a latitudinal cline. Alternatively, flowering plants tend to bloom at different times depending on where they are along the slope of a mountain, known as an altitudinal cline.
If there is gene flow between the populations, the individuals will likely show gradual differences in phenotype along the cline. Restricted gene flow, on the other hand, can lead to abrupt differences, even speciation.
Summary
Both genetic and environmental factors can cause phenotypic variation in a population. Different alleles can confer different phenotypes, and different environments can also cause individuals to look or act differently. Only those differences encoded in an individual’s genes, however, can be passed to its offspring and, thus, be a target of natural selection. Natural selection works by selecting for alleles that confer beneficial traits or behaviors, while selecting against those for deleterious qualities. Genetic drift stems from the chance occurrence that some individuals in the germ line have more offspring than others. When individuals leave or join the population, allele frequencies can change as a result of gene flow. Mutations to an individual’s DNA may introduce new variation into a population. Allele frequencies can also be altered when individuals do not randomly mate with others in the group.
Footnotes
1. 1 A. J. Tipping et al., “Molecular and Genealogical Evidence for a Founder Effect in Fanconi Anemia Families of the Afrikaner Population of South Africa,” PNAS 98, no. 10 (2001): 5734-5739, doi: 10.1073/pnas.091402398.
Glossary
assortative mating
when individuals tend to mate with those who are phenotypically similar to themselves
bottleneck effect
magnification of genetic drift as a result of natural events or catastrophes
cline
gradual geographic variation across an ecological gradient
gene flow
flow of alleles in and out of a population due to the migration of individuals or gametes
genetic drift
effect of chance on a population’s gene pool
genetic variance
diversity of alleles and genotypes in a population
geographical variation
differences in the phenotypic variation between populations that are separated geographically
heritability
fraction of population variation that can be attributed to its genetic variance
inbreeding
mating of closely related individuals
inbreeding depression
increase in abnormalities and disease in inbreeding populations
nonrandom mating
changes in a population’s gene pool due to mate choice or other forces that cause individuals to mate with certain phenotypes more than others
population variation
distribution of phenotypes in a population
selective pressure
environmental factor that causes one phenotype to be better than another | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/4%3A_Evolutionary_Processes/19%3A_The_Evolution_of_Populations/19.2%3A_Population_Genetics.txt |
Skills to Develop
• Explain the different ways natural selection can shape populations
• Describe how these different forces can lead to different outcomes in terms of the population variation
Natural selection only acts on the population’s heritable traits: selecting for beneficial alleles and thus increasing their frequency in the population, while selecting against deleterious alleles and thereby decreasing their frequency—a process known as adaptive evolution. Natural selection does not act on individual alleles, however, but on entire organisms. An individual may carry a very beneficial genotype with a resulting phenotype that, for example, increases the ability to reproduce (fecundity), but if that same individual also carries an allele that results in a fatal childhood disease, that fecundity phenotype will not be passed on to the next generation because the individual will not live to reach reproductive age. Natural selection acts at the level of the individual; it selects for individuals with greater contributions to the gene pool of the next generation, known as an organism’s evolutionary (Darwinian) fitness.
Fitness is often quantifiable and is measured by scientists in the field. However, it is not the absolute fitness of an individual that counts, but rather how it compares to the other organisms in the population. This concept, called relative fitness, allows researchers to determine which individuals are contributing additional offspring to the next generation, and thus, how the population might evolve.
There are several ways selection can affect population variation: stabilizing selection, directional selection, diversifying selection, frequency-dependent selection, and sexual selection. As natural selection influences the allele frequencies in a population, individuals can either become more or less genetically similar and the phenotypes displayed can become more similar or more disparate.
Stabilizing Selection
If natural selection favors an average phenotype, selecting against extreme variation, the population will undergo stabilizing selection (Figure \(1\)). In a population of mice that live in the woods, for example, natural selection is likely to favor individuals that best blend in with the forest floor and are less likely to be spotted by predators. Assuming the ground is a fairly consistent shade of brown, those mice whose fur is most closely matched to that color will be most likely to survive and reproduce, passing on their genes for their brown coat. Mice that carry alleles that make them a bit lighter or a bit darker will stand out against the ground and be more likely to fall victim to predation. As a result of this selection, the population’s genetic variance will decrease.
Directional Selection
When the environment changes, populations will often undergo directional selection (Figure \(1\)), which selects for phenotypes at one end of the spectrum of existing variation. A classic example of this type of selection is the evolution of the peppered moth in eighteenth- and nineteenth-century England. Prior to the Industrial Revolution, the moths were predominately light in color, which allowed them to blend in with the light-colored trees and lichens in their environment. But as soot began spewing from factories, the trees became darkened, and the light-colored moths became easier for predatory birds to spot. Over time, the frequency of the melanic form of the moth increased because they had a higher survival rate in habitats affected by air pollution because their darker coloration blended with the sooty trees. Similarly, the hypothetical mouse population may evolve to take on a different coloration if something were to cause the forest floor where they live to change color. The result of this type of selection is a shift in the population’s genetic variance toward the new, fit phenotype.
Diversifying Selection
Sometimes two or more distinct phenotypes can each have their advantages and be selected for by natural selection, while the intermediate phenotypes are, on average, less fit. Known as diversifying selection (Figure \(1\)), this is seen in many populations of animals that have multiple male forms. Large, dominant alpha males obtain mates by brute force, while small males can sneak in for furtive copulations with the females in an alpha male’s territory. In this case, both the alpha males and the “sneaking” males will be selected for, but medium-sized males, which can’t overtake the alpha males and are too big to sneak copulations, are selected against. Diversifying selection can also occur when environmental changes favor individuals on either end of the phenotypic spectrum. Imagine a population of mice living at the beach where there is light-colored sand interspersed with patches of tall grass. In this scenario, light-colored mice that blend in with the sand would be favored, as well as dark-colored mice that can hide in the grass. Medium-colored mice, on the other hand, would not blend in with either the grass or the sand, and would thus be more likely to be eaten by predators. The result of this type of selection is increased genetic variance as the population becomes more diverse.
Exercise \(1\)
In recent years, factories have become cleaner, and less soot is released into the environment. What impact do you think this has had on the distribution of moth color in the population?
Answer
Moths have shifted to a lighter color.
Frequency-dependent Selection
Another type of selection, called frequency-dependent selection, favors phenotypes that are either common (positive frequency-dependent selection) or rare (negative frequency-dependent selection). An interesting example of this type of selection is seen in a unique group of lizards of the Pacific Northwest. Male common side-blotched lizards come in three throat-color patterns: orange, blue, and yellow. Each of these forms has a different reproductive strategy: orange males are the strongest and can fight other males for access to their females; blue males are medium-sized and form strong pair bonds with their mates; and yellow males (Figure \(2\)) are the smallest, and look a bit like females, which allows them to sneak copulations. Like a game of rock-paper-scissors, orange beats blue, blue beats yellow, and yellow beats orange in the competition for females. That is, the big, strong orange males can fight off the blue males to mate with the blue’s pair-bonded females, the blue males are successful at guarding their mates against yellow sneaker males, and the yellow males can sneak copulations from the potential mates of the large, polygynous orange males.
In this scenario, orange males will be favored by natural selection when the population is dominated by blue males, blue males will thrive when the population is mostly yellow males, and yellow males will be selected for when orange males are the most populous. As a result, populations of side-blotched lizards cycle in the distribution of these phenotypes—in one generation, orange might be predominant, and then yellow males will begin to rise in frequency. Once yellow males make up a majority of the population, blue males will be selected for. Finally, when blue males become common, orange males will once again be favored.
Negative frequency-dependent selection serves to increase the population’s genetic variance by selecting for rare phenotypes, whereas positive frequency-dependent selection usually decreases genetic variance by selecting for common phenotypes.
Sexual Selection
Males and females of certain species are often quite different from one another in ways beyond the reproductive organs. Males are often larger, for example, and display many elaborate colors and adornments, like the peacock’s tail, while females tend to be smaller and duller in decoration. Such differences are known as sexual dimorphisms (Figure \(3\)), which arise from the fact that in many populations, particularly animal populations, there is more variance in the reproductive success of the males than there is of the females. That is, some males—often the bigger, stronger, or more decorated males—get the vast majority of the total matings, while others receive none. This can occur because the males are better at fighting off other males, or because females will choose to mate with the bigger or more decorated males. In either case, this variation in reproductive success generates a strong selection pressure among males to get those matings, resulting in the evolution of bigger body size and elaborate ornaments to get the females’ attention. Females, on the other hand, tend to get a handful of selected matings; therefore, they are more likely to select more desirable males.
Sexual dimorphism varies widely among species, of course, and some species are even sex-role reversed. In such cases, females tend to have a greater variance in their reproductive success than males and are correspondingly selected for the bigger body size and elaborate traits usually characteristic of males.
The selection pressures on males and females to obtain matings is known as sexual selection; it can result in the development of secondary sexual characteristics that do not benefit the individual’s likelihood of survival but help to maximize its reproductive success. Sexual selection can be so strong that it selects for traits that are actually detrimental to the individual’s survival. Think, once again, about the peacock’s tail. While it is beautiful and the male with the largest, most colorful tail is more likely to win the female, it is not the most practical appendage. In addition to being more visible to predators, it makes the males slower in their attempted escapes. There is some evidence that this risk, in fact, is why females like the big tails in the first place. The speculation is that large tails carry risk, and only the best males survive that risk: the bigger the tail, the more fit the male. This idea is known as the handicap principle.
The good genes hypothesis states that males develop these impressive ornaments to show off their efficient metabolism or their ability to fight disease. Females then choose males with the most impressive traits because it signals their genetic superiority, which they will then pass on to their offspring. Though it might be argued that females should not be picky because it will likely reduce their number of offspring, if better males father more fit offspring, it may be beneficial. Fewer, healthier offspring may increase the chances of survival more than many, weaker offspring.
In both the handicap principle and the good genes hypothesis, the trait is said to be an honest signal of the males’ quality, thus giving females a way to find the fittest mates— males that will pass the best genes to their offspring.
No Perfect Organism
Natural selection is a driving force in evolution and can generate populations that are better adapted to survive and successfully reproduce in their environments. But natural selection cannot produce the perfect organism. Natural selection can only select on existing variation in the population; it does not create anything from scratch. Thus, it is limited by a population’s existing genetic variance and whatever new alleles arise through mutation and gene flow.
Natural selection is also limited because it works at the level of individuals, not alleles, and some alleles are linked due to their physical proximity in the genome, making them more likely to be passed on together (linkage disequilibrium). Any given individual may carry some beneficial alleles and some unfavorable alleles. It is the net effect of these alleles, or the organism’s fitness, upon which natural selection can act. As a result, good alleles can be lost if they are carried by individuals that also have several overwhelmingly bad alleles; likewise, bad alleles can be kept if they are carried by individuals that have enough good alleles to result in an overall fitness benefit.
Furthermore, natural selection can be constrained by the relationships between different polymorphisms. One morph may confer a higher fitness than another, but may not increase in frequency due to the fact that going from the less beneficial to the more beneficial trait would require going through a less beneficial phenotype. Think back to the mice that live at the beach. Some are light-colored and blend in with the sand, while others are dark and blend in with the patches of grass. The dark-colored mice may be, overall, more fit than the light-colored mice, and at first glance, one might expect the light-colored mice be selected for a darker coloration. But remember that the intermediate phenotype, a medium-colored coat, is very bad for the mice—they cannot blend in with either the sand or the grass and are more likely to be eaten by predators. As a result, the light-colored mice would not be selected for a dark coloration because those individuals that began moving in that direction (began being selected for a darker coat) would be less fit than those that stayed light.
Finally, it is important to understand that not all evolution is adaptive. While natural selection selects the fittest individuals and often results in a more fit population overall, other forces of evolution, including genetic drift and gene flow, often do the opposite: introducing deleterious alleles to the population’s gene pool. Evolution has no purpose—it is not changing a population into a preconceived ideal. It is simply the sum of the various forces described in this chapter and how they influence the genetic and phenotypic variance of a population.
Summary
Because natural selection acts to increase the frequency of beneficial alleles and traits while decreasing the frequency of deleterious qualities, it is adaptive evolution. Natural selection acts at the level of the individual, selecting for those that have a higher overall fitness compared to the rest of the population. If the fit phenotypes are those that are similar, natural selection will result in stabilizing selection, and an overall decrease in the population’s variation. Directional selection works to shift a population’s variance toward a new, fit phenotype, as environmental conditions change. In contrast, diversifying selection results in increased genetic variance by selecting for two or more distinct phenotypes.
Other types of selection include frequency-dependent selection, in which individuals with either common (positive frequency-dependent selection) or rare (negative frequency-dependent selection) are selected for. Finally, sexual selection results from the fact that one sex has more variance in the reproductive success than the other. As a result, males and females experience different selective pressures, which can often lead to the evolution of phenotypic differences, or sexual dimorphisms, between the two.
Glossary
adaptive evolution
increase in frequency of beneficial alleles and decrease in deleterious alleles due to selection
directional selection
selection that favors phenotypes at one end of the spectrum of existing variation
diversifying selection
selection that favors two or more distinct phenotypes
evolutionary fitness
(also, Darwinian fitness) individual’s ability to survive and reproduce
frequency-dependent selection
selection that favors phenotypes that are either common (positive frequency-dependent selection) or rare (negative frequency-dependent selection)
good genes hypothesis
theory of sexual selection that argues individuals develop impressive ornaments to show off their efficient metabolism or ability to fight disease
handicap principle
theory of sexual selection that argues only the fittest individuals can afford costly traits
honest signal
trait that gives a truthful impression of an individual’s fitness
relative fitness
individual’s ability to survive and reproduce relative to the rest of the population
sexual dimorphism
phenotypic difference between the males and females of a population
stabilizing selection
selection that favors average phenotypes | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/4%3A_Evolutionary_Processes/19%3A_The_Evolution_of_Populations/19.3%3A_Adaptive_Evolution.txt |
19.1: Population Evolution
Initially, the newly discovered particulate nature of genes made it difficult for biologists to understand how gradual evolution could occur. But over the next few decades genetics and evolution were integrated in what became known as the modern synthesis—the coherent understanding of the relationship between natural selection and genetics that took shape by the 1940s and is generally accepted today.
Review Questions
What is the difference between micro- and macroevolution?
1. Microevolution describes the evolution of small organisms, such as insects, while macroevolution describes the evolution of large organisms, like people and elephants.
2. Microevolution describes the evolution of microscopic entities, such as molecules and proteins, while macroevolution describes the evolution of whole organisms.
3. Microevolution describes the evolution of organisms in populations, while macroevolution describes the evolution of species over long periods of time.
4. Microevolution describes the evolution of organisms over their lifetimes, while macroevolution describes the evolution of organisms over multiple generations.
Answer
C
Population genetics is the study of:
1. how selective forces change the allele frequencies in a population over time
2. the genetic basis of population-wide traits
3. whether traits have a genetic basis
4. the degree of inbreeding in a population
Answer
A
Which of the following populations is not in Hardy-Weinberg equilibrium?
1. a population with 12 homozygous recessive individuals (yy), 8 homozygous dominant individuals (YY), and 4 heterozygous individuals (Yy)
2. a population in which the allele frequencies do not change over time
3. p2 + 2pq + q2 = 1
4. a population undergoing natural selection
Answer
D
One of the original Amish colonies rose from a ship of colonists that came from Europe. The ship’s captain, who had polydactyly, a rare dominant trait, was one of the original colonists. Today, we see a much higher frequency of polydactyly in the Amish population. This is an example of:
1. natural selection
2. genetic drift
3. founder effect
4. b and c
Answer
D
Free Response
Solve for the genetic structure of a population with 12 homozygous recessive individuals (yy), 8 homozygous dominant individuals (YY), and 4 heterozygous individuals (Yy).
Answer
p = (8*2 + 4)/48 = .42; q = (12*2 + 4)/48 = .58; p2 = .17; 2pq = .48; q2 = .34
Explain the Hardy-Weinberg principle of equilibrium theory.
Answer
The Hardy-Weinberg principle of equilibrium is used to describe the genetic makeup of a population. The theory states that a population’s allele and genotype frequencies are inherently stable: unless some kind of evolutionary force is acting upon the population, generation after generation of the population would carry the same genes, and individuals would, as a whole, look essentially the same.
Imagine you are trying to test whether a population of flowers is undergoing evolution. You suspect there is selection pressure on the color of the flower: bees seem to cluster around the red flowers more often than the blue flowers. In a separate experiment, you discover blue flower color is dominant to red flower color. In a field, you count 600 blue flowers and 200 red flowers. What would you expect the genetic structure of the flowers to be?
Answer
Red is recessive so q2 = 200/800 = 0.25; q = 0.5; p = 1-q = 0.5; p2 = 0.25; 2pq = 0.5. You would expect 200 homozygous blue flowers, 400 heterozygous blue flowers, and 200 red flowers.
19.2: Population Genetics
Individuals of a population often display different phenotypes, or express different alleles of a particular gene, referred to as polymorphisms. Populations with two or more variations of particular characteristics are called polymorphic. The distribution of phenotypes among individuals, known as the population variation, is influenced by a number of factors, including the population’s genetic structure and the environment.
Review Questions
When male lions reach sexual maturity, they leave their group in search of a new pride. This can alter the allele frequencies of the population through which of the following mechanisms?
1. natural selection
2. genetic drift
3. gene flow
4. random mating
Answer
C
Which of the following evolutionary forces can introduce new genetic variation into a population?
1. natural selection and genetic drift
2. mutation and gene flow
3. natural selection and nonrandom mating
4. mutation and genetic drift
Answer
B
What is assortative mating?
1. when individuals mate with those who are similar to themselves
2. when individuals mate with those who are dissimilar to themselves
3. when individuals mate with those who are the most fit in the population
4. when individuals mate with those who are least fit in the population
Answer
A
When closely related individuals mate with each other, or inbreed, the offspring are often not as fit as the offspring of two unrelated individuals. Why?
1. Close relatives are genetically incompatible.
2. The DNA of close relatives reacts negatively in the offspring.
3. Inbreeding can bring together rare, deleterious mutations that lead to harmful phenotypes.
4. Inbreeding causes normally silent alleles to be expressed.
Answer
C
What is a cline?
1. the slope of a mountain where a population lives
2. the degree to which a mutation helps an individual survive
3. the number of individuals in the population
4. gradual geographic variation across an ecological gradient
Answer
D
Free Response
Describe a situation in which a population would undergo the bottleneck effect and explain what impact that would have on the population’s gene pool.
Answer
A hurricane kills a large percentage of a population of sand-dwelling crustaceans—only a few individuals survive. The alleles carried by those surviving individuals would represent the entire population’s gene pool. If those surviving individuals are not representative of the original population, the post-hurricane gene pool will differ from the original gene pool.
Describe natural selection and give an example of natural selection at work in a population.
Answer
The theory of natural selection stems from the observation that some individuals in a population survive longer and have more offspring than others: thus, more of their genes are passed to the next generation. For example, a big, powerful male gorilla is much more likely than a smaller, weaker one to become the population’s silverback: the pack’s leader who mates far more than the other males of the group. Therefore, the pack leader will father more offspring who share half of his genes and are likely to grow bigger and stronger like their father. Over time, the genes for bigger size will increase in frequency in the population, and the average body size, as a result, grow larger on average.
Explain what a cline is and provide examples.
Answer
A cline is a type of geographic variation that is seen in populations of a given species that vary gradually across an ecological gradient. For example, warm-blooded animals tend to have larger bodies in the cooler climates closer to the earth’s poles, allowing them to better conserve heat. This is considered a latitudinal cline. Flowering plants tend to bloom at different times depending on where they are along the slope of a mountain. This is known as an altitudinal cline.
19.3: Adaptive Evolution
Fitness is often quantifiable and is measured by scientists in the field. However, it is not the absolute fitness of an individual that counts, but rather how it compares to the other organisms in the population. This concept, called relative fitness, allows researchers to determine which individuals are contributing additional offspring to the next generation, and thus, how the population might evolve.
Review Questions
Which type of selection results in greater genetic variance in a population?
1. stabilizing selection
2. directional selection
3. diversifying selection
4. positive frequency-dependent selection
Answer
C
When males and females of a population look or act differently, it is referred to as ________.
1. sexual dimorphism
2. sexual selection
3. diversifying selection
4. a cline
Answer
A
The good genes hypothesis is a theory that explains what?
1. why more fit individuals are more likely to have more offspring
2. why alleles that confer beneficial traits or behaviors are selected for by natural selection
3. why some deleterious mutations are maintained in the population
4. why individuals of one sex develop impressive ornamental traits
Answer
D
Free Response
Give an example of a trait that may have evolved as a result of the handicap principle and explain your reasoning.
Answer
The peacock’s tail is a good example of the handicap principle. The tail, which makes the males more visible to predators and less able to escape, is clearly a disadvantage to the bird’s survival. But because it is a disadvantage, only the most fit males should be able to survive with it. Thus, the tail serves as an honest signal of quality to the females of the population; therefore, the male will earn more matings and greater reproductive success.
List the ways in which evolution can affect population variation and describe how they influence allele frequencies.
Answer
There are several ways evolution can affect population variation: stabilizing selection, directional selection, diversifying selection, frequency-dependent selection, and sexual selection. As these influence the allele frequencies in a population, individuals can either become more or less related, and the phenotypes displayed can become more similar or more disparate. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/4%3A_Evolutionary_Processes/19%3A_The_Evolution_of_Populations/19.E%3A_The_Evolution_of_Populations_%28Exercises%29.txt |
By following pathways of similarities and changes—both visible and genetic—scientists seek to map the evolutionary past of how life developed from single-celled organisms to the tremendous collection of creatures that have germinated, crawled, floated, swam, flown, and walked on this planet.
• 20.0: Introduction
This bee and Echinacea flower could not look more different, yet they are related, as are all living organisms on Earth.
• 20.1: Organizing Life on Earth
In scientific terms, the evolutionary history and relationship of an organism or group of organisms is called phylogeny. Phylogeny describes the relationships of an organism, such as from which organisms it is thought to have evolved, to which species it is most closely related, and so forth. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different.
• 20.2: Determining Evolutionary Relationships
Scientists must collect accurate information that allows them to make evolutionary connections among organisms. Similar to detective work, scientists must use evidence to uncover the facts. In the case of phylogeny, evolutionary investigations focus on two types of evidence: morphologic (form and function) and genetic.
• 20.3: Perspectives on the Phylogenetic Tree
The concepts of phylogenetic modeling are constantly changing. It is one of the most dynamic fields of study in all of biology. Over the last several decades, new research has challenged scientists’ ideas about how organisms are related. New models of these relationships have been proposed for consideration by the scientific community.
• 20.E: Phylogenies and the History of Life (Exercises)
20: Phylogenies and the History of Life
This bee and Echinacea flower could not look more different, yet they are related, as are all living organisms on Earth. By following pathways of similarities and changes—both visible and genetic—scientists seek to map the evolutionary past of how life developed from single-celled organisms to the tremendous collection of creatures that have germinated, crawled, floated, swam, flown, and walked on this planet.
20.1: Organizing Life on Earth
Skills to Develop
• Discuss the need for a comprehensive classification system
• List the different levels of the taxonomic classification system
• Describe how systematics and taxonomy relate to phylogeny
• Discuss the components and purpose of a phylogenetic tree
In scientific terms, the evolutionary history and relationship of an organism or group of organisms is called phylogeny. Phylogeny describes the relationships of an organism, such as from which organisms it is thought to have evolved, to which species it is most closely related, and so forth. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different.
Phylogenetic Trees
Scientists use a tool called a phylogenetic tree to show the evolutionary pathways and connections among organisms. A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past since one cannot go back to confirm the proposed relationships. In other words, a “tree of life” can be constructed to illustrate when different organisms evolved and to show the relationships among different organisms (Figure \(1\)).
Unlike a taxonomic classification diagram, a phylogenetic tree can be read like a map of evolutionary history. Many phylogenetic trees have a single lineage at the base representing a common ancestor. Scientists call such trees rooted, which means there is a single ancestral lineage (typically drawn from the bottom or left) to which all organisms represented in the diagram relate. Notice in the rooted phylogenetic tree that the three domains— Bacteria, Archaea, and Eukarya—diverge from a single point and branch off. The small branch that plants and animals (including humans) occupy in this diagram shows how recent and miniscule these groups are compared with other organisms. Unrooted trees don’t show a common ancestor but do show relationships among species.
In a rooted tree, the branching indicates evolutionary relationships (Figure \(2\)). The point where a split occurs, called a branch point, represents where a single lineage evolved into a distinct new one. A lineage that evolved early from the root and remains unbranched is called basal taxon. When two lineages stem from the same branch point, they are called sister taxa. A branch with more than two lineages is called a polytomy and serves to illustrate where scientists have not definitively determined all of the relationships. It is important to note that although sister taxa and polytomy do share an ancestor, it does not mean that the groups of organisms split or evolved from each other. Organisms in two taxa may have split apart at a specific branch point, but neither taxa gave rise to the other.
The diagrams above can serve as a pathway to understanding evolutionary history. The pathway can be traced from the origin of life to any individual species by navigating through the evolutionary branches between the two points. Also, by starting with a single species and tracing back towards the "trunk" of the tree, one can discover that species' ancestors, as well as where lineages share a common ancestry. In addition, the tree can be used to study entire groups of organisms.
Another point to mention on phylogenetic tree structure is that rotation at branch points does not change the information. For example, if a branch point was rotated and the taxon order changed, this would not alter the information because the evolution of each taxon from the branch point was independent of the other.
Many disciplines within the study of biology contribute to understanding how past and present life evolved over time; these disciplines together contribute to building, updating, and maintaining the “tree of life.” Information is used to organize and classify organisms based on evolutionary relationships in a scientific field called systematics. Data may be collected from fossils, from studying the structure of body parts or molecules used by an organism, and by DNA analysis. By combining data from many sources, scientists can put together the phylogeny of an organism; since phylogenetic trees are hypotheses, they will continue to change as new types of life are discovered and new information is learned.
Limitations of Phylogenetic Trees
It may be easy to assume that more closely related organisms look more alike, and while this is often the case, it is not always true. If two closely related lineages evolved under significantly varied surroundings or after the evolution of a major new adaptation, it is possible for the two groups to appear more different than other groups that are not as closely related. For example, the phylogenetic tree in Figure \(3\) shows that lizards and rabbits both have amniotic eggs, whereas frogs do not; yet lizards and frogs appear more similar than lizards and rabbits.
Another aspect of phylogenetic trees is that, unless otherwise indicated, the branches do not account for length of time, only the evolutionary order. In other words, the length of a branch does not typically mean more time passed, nor does a short branch mean less time passed— unless specified on the diagram. For example, in Figure \(3\), the tree does not indicate how much time passed between the evolution of amniotic eggs and hair. What the tree does show is the order in which things took place. Again using Figure \(3\), the tree shows that the oldest trait is the vertebral column, followed by hinged jaws, and so forth. Remember that any phylogenetic tree is a part of the greater whole, and like a real tree, it does not grow in only one direction after a new branch develops. So, for the organisms in Figure \(3\), just because a vertebral column evolved does not mean that invertebrate evolution ceased, it only means that a new branch formed. Also, groups that are not closely related, but evolve under similar conditions, may appear more phenotypically similar to each other than to a close relative.
Link to Learning
Head to this website to see interactive exercises that allow you to explore the evolutionary relationships among species.
The Levels of Classification
Taxonomy (which literally means “arrangement law”) is the science of classifying organisms to construct internationally shared classification systems with each organism placed into more and more inclusive groupings. Think about how a grocery store is organized. One large space is divided into departments, such as produce, dairy, and meats. Then each department further divides into aisles, then each aisle into categories and brands, and then finally a single product. This organization from larger to smaller, more specific categories is called a hierarchical system.
The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish botanist, zoologist, and physician) uses a hierarchical model. Moving from the point of origin, the groups become more specific, until one branch ends as a single species. For example, after the common beginning of all life, scientists divide organisms into three large categories called a domain: Bacteria, Archaea, and Eukarya. Within each domain is a second category called a kingdom. After kingdoms, the subsequent categories of increasing specificity are: phylum, class, order, family, genus, and species (Figure \(4\)).
The kingdom Animalia stems from the Eukarya domain. For the common dog, the classification levels would be as shown in Figure \(4\). Therefore, the full name of an organism technically has eight terms. For the dog, it is: Eukarya, Animalia, Chordata, Mammalia, Carnivora, Canidae, Canis, and lupus. Notice that each name is capitalized except for species, and the genus and species names are italicized. Scientists generally refer to an organism only by its genus and species, which is its two-word scientific name, in what is called binomial nomenclature. Therefore, the scientific name of the dog is Canis lupus. The name at each level is also called a taxon. In other words, dogs are in order Carnivora. Carnivora is the name of the taxon at the order level; Canidae is the taxon at the family level, and so forth. Organisms also have a common name that people typically use, in this case, dog. Note that the dog is additionally a subspecies: the “familiaris” in Canis lupus familiaris. Subspecies are members of the same species that are capable of mating and reproducing viable offspring, but they are considered separate subspecies due to geographic or behavioral isolation or other factors.
Figure \(5\) shows how the levels move toward specificity with other organisms. Notice how the dog shares a domain with the widest diversity of organisms, including plants and butterflies. At each sublevel, the organisms become more similar because they are more closely related. Historically, scientists classified organisms using characteristics, but as DNA technology developed, more precise phylogenies have been determined.
Art Connection
At what levels are cats and dogs considered to be part of the same group?
Recent genetic analysis and other advancements have found that some earlier phylogenetic classifications do not align with the evolutionary past; therefore, changes and updates must be made as new discoveries occur. Recall that phylogenetic trees are hypotheses and are modified as data becomes available. In addition, classification historically has focused on grouping organisms mainly by shared characteristics and does not necessarily illustrate how the various groups relate to each other from an evolutionary perspective. For example, despite the fact that a hippopotamus resembles a pig more than a whale, the hippopotamus may be the closest living relative of the whale.
Summary
Scientists continually gain new information that helps understand the evolutionary history of life on Earth. Each group of organisms went through its own evolutionary journey, called its phylogeny. Each organism shares relatedness with others, and based on morphologic and genetic evidence, scientists attempt to map the evolutionary pathways of all life on Earth. Historically, organisms were organized into a taxonomic classification system. However, today many scientists build phylogenetic trees to illustrate evolutionary relationships.
Art Connections
Figure \(5\): At what levels are cats and dogs considered to be part of the same group?
Answer
Cats and dogs are part of the same group at five levels: both are in the domain Eukarya, the kingdom Animalia, the phylum Chordata, the class Mammalia, and the order Carnivora.
Glossary
basal taxon
branch on a phylogenetic tree that has not diverged significantly from the root ancestor
binomial nomenclature
system of two-part scientific names for an organism, which includes genus and species names
branch point
node on a phylogenetic tree where a single lineage splits into distinct new ones
class
division of phylum in the taxonomic classification system
family
division of order in the taxonomic classification system
genus
division of family in the taxonomic classification system; the first part of the binomial scientific name
kingdom
division of domain in the taxonomic classification system
order
division of class in the taxonomic classification system
phylogenetic tree
diagram used to reflect the evolutionary relationships among organisms or groups of organisms
phylogeny
evolutionary history and relationship of an organism or group of organisms
phylum
(plural: phyla) division of kingdom in the taxonomic classification system
polytomy
branch on a phylogenetic tree with more than two groups or taxa
rooted
single ancestral lineage on a phylogenetic tree to which all organisms represented in the diagram relate
sister taxa
two lineages that diverged from the same branch point
systematics
field of organizing and classifying organisms based on evolutionary relationships
taxon
(plural: taxa) single level in the taxonomic classification system
taxonomy
science of classifying organisms | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/4%3A_Evolutionary_Processes/20%3A_Phylogenies_and_the_History_of_Life/20.0%3A_Introduction.txt |
Skills to Develop
• Compare homologous and analogous traits
• Discuss the purpose of cladistics
• Describe maximum parsimony
Scientists must collect accurate information that allows them to make evolutionary connections among organisms. Similar to detective work, scientists must use evidence to uncover the facts. In the case of phylogeny, evolutionary investigations focus on two types of evidence: morphologic (form and function) and genetic.
Two Options for Similarities
In general, organisms that share similar physical features and genomes tend to be more closely related than those that do not. Such features that overlap both morphologically (in form) and genetically are referred to as homologous structures; they stem from developmental similarities that are based on evolution. For example, the bones in the wings of bats and birds have homologous structures (Figure \(1\)).
Notice it is not simply a single bone, but rather a grouping of several bones arranged in a similar way. The more complex the feature, the more likely any kind of overlap is due to a common evolutionary past. Imagine two people from different countries both inventing a car with all the same parts and in exactly the same arrangement without any previous or shared knowledge. That outcome would be highly improbable. However, if two people both invented a hammer, it would be reasonable to conclude that both could have the original idea without the help of the other. The same relationship between complexity and shared evolutionary history is true for homologous structures in organisms.
Misleading Appearances
Some organisms may be very closely related, even though a minor genetic change caused a major morphological difference to make them look quite different. Similarly, unrelated organisms may be distantly related, but appear very much alike. This usually happens because both organisms were in common adaptations that evolved within similar environmental conditions. When similar characteristics occur because of environmental constraints and not due to a close evolutionary relationship, it is called an analogy or homoplasy. For example, insects use wings to fly like bats and birds, but the wing structure and embryonic origin is completely different. These are called analogous structures (Figure \(2\)).
Similar traits can be either homologous or analogous. Homologous structures share a similar embryonic origin; analogous organs have a similar function. For example, the bones in the front flipper of a whale are homologous to the bones in the human arm. These structures are not analogous. The wings of a butterfly and the wings of a bird are analogous but not homologous. Some structures are both analogous and homologous: the wings of a bird and the wings of a bat are both homologous and analogous. Scientists must determine which type of similarity a feature exhibits to decipher the phylogeny of the organisms being studied.
Molecular Comparisons
With the advancement of DNA technology, the area of molecular systematics, which describes the use of information on the molecular level including DNA analysis, has blossomed. New computer programs not only confirm many earlier classified organisms, but also uncover previously made errors. As with physical characteristics, even the DNA sequence can be tricky to read in some cases. For some situations, two very closely related organisms can appear unrelated if a mutation occurred that caused a shift in the genetic code. An insertion or deletion mutation would move each nucleotide base over one place, causing two similar codes to appear unrelated.
Sometimes two segments of DNA code in distantly related organisms randomly share a high percentage of bases in the same locations, causing these organisms to appear closely related when they are not. For both of these situations, computer technologies have been developed to help identify the actual relationships, and, ultimately, the coupled use of both morphologic and molecular information is more effective in determining phylogeny.
Evolution Connection: Why Does Phylogeny Matter?
Evolutionary biologists could list many reasons why understanding phylogeny is important to everyday life in human society. For botanists, phylogeny acts as a guide to discovering new plants that can be used to benefit people. Think of all the ways humans use plants—food, medicine, and clothing are a few examples. If a plant contains a compound that is effective in treating cancer, scientists might want to examine all of the relatives of that plant for other useful drugs.
A research team in China identified a segment of DNA thought to be common to some medicinal plants in the family Fabaceae (the legume family) and worked to identify which species had this segment (Figure \(3\)). After testing plant species in this family, the team found a DNA marker (a known location on a chromosome that enabled them to identify the species) present. Then, using the DNA to uncover phylogenetic relationships, the team could identify whether a newly discovered plant was in this family and assess its potential medicinal properties.
Building Phylogenetic Trees
How do scientists construct phylogenetic trees? After the homologous and analogous traits are sorted, scientists often organize the homologous traits using a system called cladistics. This system sorts organisms into clades: groups of organisms that descended from a single ancestor. For example, in Figure \(4\), all of the organisms in the orange region evolved from a single ancestor that had amniotic eggs. Consequently, all of these organisms also have amniotic eggs and make a single clade, also called a monophyletic group. Clades must include all of the descendants from a branch point.
Art Connection
Which animals in this figure belong to a clade that includes animals with hair? Which evolved first, hair or the amniotic egg?
Clades can vary in size depending on which branch point is being referenced. The important factor is that all of the organisms in the clade or monophyletic group stem from a single point on the tree. This can be remembered because monophyletic breaks down into “mono,” meaning one, and “phyletic,” meaning evolutionary relationship. Figure \(5\) shows various examples of clades. Notice how each clade comes from a single point, whereas the non-clade groups show branches that do not share a single point.
Art Connection
What is the largest clade in this diagram?
Shared Characteristics
Organisms evolve from common ancestors and then diversify. Scientists use the phrase “descent with modification” because even though related organisms have many of the same characteristics and genetic codes, changes occur. This pattern repeats over and over as one goes through the phylogenetic tree of life:
1. A change in the genetic makeup of an organism leads to a new trait which becomes prevalent in the group.
2. Many organisms descend from this point and have this trait.
3. New variations continue to arise: some are adaptive and persist, leading to new traits.
4. With new traits, a new branch point is determined (go back to step 1 and repeat).
If a characteristic is found in the ancestor of a group, it is considered a shared ancestral character because all of the organisms in the taxon or clade have that trait. The vertebrate in Figure \(4\) is a shared ancestral character. Now consider the amniotic egg characteristic in the same figure. Only some of the organisms in Figure \(4\) have this trait, and to those that do, it is called a shared derived character because this trait derived at some point but does not include all of the ancestors in the tree.
The tricky aspect to shared ancestral and shared derived characters is the fact that these terms are relative. The same trait can be considered one or the other depending on the particular diagram being used. Returning to Figure \(5\), note that the amniotic egg is a shared ancestral character for the Amniota clade, while having hair is a shared derived character for some organisms in this group. These terms help scientists distinguish between clades in the building of phylogenetic trees.
Choosing the Right Relationships
Imagine being the person responsible for organizing all of the items in a department store properly—an overwhelming task. Organizing the evolutionary relationships of all life on Earth proves much more difficult: scientists must span enormous blocks of time and work with information from long-extinct organisms. Trying to decipher the proper connections, especially given the presence of homologies and analogies, makes the task of building an accurate tree of life extraordinarily difficult. Add to that the advancement of DNA technology, which now provides large quantities of genetic sequences to be used and analyzed. Taxonomy is a subjective discipline: many organisms have more than one connection to each other, so each taxonomist will decide the order of connections.
To aid in the tremendous task of describing phylogenies accurately, scientists often use a concept called maximum parsimony, which means that events occurred in the simplest, most obvious way. For example, if a group of people entered a forest preserve to go hiking, based on the principle of maximum parsimony, one could predict that most of the people would hike on established trails rather than forge new ones.
For scientists deciphering evolutionary pathways, the same idea is used: the pathway of evolution probably includes the fewest major events that coincide with the evidence at hand. Starting with all of the homologous traits in a group of organisms, scientists look for the most obvious and simple order of evolutionary events that led to the occurrence of those traits.
These tools and concepts are only a few of the strategies scientists use to tackle the task of revealing the evolutionary history of life on Earth. Recently, newer technologies have uncovered surprising discoveries with unexpected relationships, such as the fact that people seem to be more closely related to fungi than fungi are to plants. Sound unbelievable? As the information about DNA sequences grows, scientists will become closer to mapping the evolutionary history of all life on Earth.
Summary
To build phylogenetic trees, scientists must collect accurate information that allows them to make evolutionary connections between organisms. Using morphologic and molecular data, scientists work to identify homologous characteristics and genes. Similarities between organisms can stem either from shared evolutionary history (homologies) or from separate evolutionary paths (analogies). Newer technologies can be used to help distinguish homologies from analogies. After homologous information is identified, scientists use cladistics to organize these events as a means to determine an evolutionary timeline. Scientists apply the concept of maximum parsimony, which states that the order of events probably occurred in the most obvious and simple way with the least amount of steps. For evolutionary events, this would be the path with the least number of major divergences that correlate with the evidence.
Art Connections
Figure \(4\): Which animals in this figure belong to a clade that includes animals with hair? Which evolved first, hair or the amniotic egg?
Answer
Rabbits and humans belong in the clade that includes animals with hair. The amniotic egg evolved before hair because the Amniota clade is larger than the clade that encompasses animals with hair.
Figure \(5\): What is the largest clade in this diagram?
Answer
The largest clade encompasses the entire tree.
Glossary
analogy
(also, homoplasy) characteristic that is similar between organisms by convergent evolution, not due to the same evolutionary path
cladistics
system used to organize homologous traits to describe phylogenies
maximum parsimony
applying the simplest, most obvious way with the least number of steps
molecular systematics
technique using molecular evidence to identify phylogenetic relationships
monophyletic group
(also, clade) organisms that share a single ancestor
shared ancestral character
describes a characteristic on a phylogenetic tree that is shared by all organisms on the tree
shared derived character
describes a characteristic on a phylogenetic tree that is shared only by a certain clade of organisms | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/4%3A_Evolutionary_Processes/20%3A_Phylogenies_and_the_History_of_Life/20.2%3A_Determining_Evolutionary_Relationships.txt |
Skills to Develop
• Describe horizontal gene transfer
• Illustrate how prokaryotes and eukaryotes transfer genes horizontally
• Identify the web and ring models of phylogenetic relationships and describe how they differ from the original phylogenetic tree concept
The concepts of phylogenetic modeling are constantly changing. It is one of the most dynamic fields of study in all of biology. Over the last several decades, new research has challenged scientists’ ideas about how organisms are related. New models of these relationships have been proposed for consideration by the scientific community.
Many phylogenetic trees have been shown as models of the evolutionary relationship among species. Phylogenetic trees originated with Charles Darwin, who sketched the first phylogenetic tree in 1837 (Figure \(1\)a), which served as a pattern for subsequent studies for more than a century. The concept of a phylogenetic tree with a single trunk representing a common ancestor, with the branches representing the divergence of species from this ancestor, fits well with the structure of many common trees, such as the oak (Figure \(1\)b). However, evidence from modern DNA sequence analysis and newly developed computer algorithms has caused skepticism about the validity of the standard tree model in the scientific community.
Limitations to the Classic Model
Classical thinking about prokaryotic evolution, included in the classic tree model, is that species evolve clonally. That is, they produce offspring themselves with only random mutations causing the descent into the variety of modern-day and extinct species known to science. This view is somewhat complicated in eukaryotes that reproduce sexually, but the laws of Mendelian genetics explain the variation in offspring, again, to be a result of a mutation within the species. The concept of genes being transferred between unrelated species was not considered as a possibility until relatively recently. Horizontal gene transfer (HGT), also known as lateral gene transfer, is the transfer of genes between unrelated species. HGT has been shown to be an ever-present phenomenon, with many evolutionists postulating a major role for this process in evolution, thus complicating the simple tree model. Genes have been shown to be passed between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to the understanding of phylogenetic relationships.
The various ways that HGT occurs in prokaryotes is important to understanding phylogenies. Although at present HGT is not viewed as important to eukaryotic evolution, HGT does occur in this domain as well. Finally, as an example of the ultimate gene transfer, theories of genome fusion between symbiotic or endosymbiotic organisms have been proposed to explain an event of great importance—the evolution of the first eukaryotic cell, without which humans could not have come into existence.
Horizontal Gene Transfer
Horizontal gene transfer (HGT) is the introduction of genetic material from one species to another species by mechanisms other than the vertical transmission from parent(s) to offspring. These transfers allow even distantly related species to share genes, influencing their phenotypes. It is thought that HGT is more prevalent in prokaryotes, but that only about 2% of the prokaryotic genome may be transferred by this process. Some researchers believe such estimates are premature: the actual importance of HGT to evolutionary processes must be viewed as a work in progress. As the phenomenon is investigated more thoroughly, it may be revealed to be more common. Many scientists believe that HGT and mutation appear to be (especially in prokaryotes) a significant source of genetic variation, which is the raw material for the process of natural selection. These transfers may occur between any two species that share an intimate relationship (Table \(1\)).
Table \(1\): Summary of Mechanisms of Prokaryotic and Eukaryotic HGT
Mechanism Mode of Transmission Example
Prokaryotes transformation DNA uptake many prokaryotes
transduction bacteriophage (virus) bacteria
conjugation pilus many prokaryotes
gene transfer agents phage-like particles purple non-sulfur bacteria
Eukaryotes from food organisms unknown aphid
jumping genes transposons rice and millet plants
epiphytes/parasites unknown yew tree fungi
from viral infections
HGT in Prokaryotes
The mechanism of HGT has been shown to be quite common in the prokaryotic domains of Bacteria and Archaea, significantly changing the way their evolution is viewed. The majority of evolutionary models, such as in the Endosymbiont Theory, propose that eukaryotes descended from multiple prokaryotes, which makes HGT all the more important to understanding the phylogenetic relationships of all extant and extinct species.
The fact that genes are transferred among common bacteria is well known to microbiology students. These gene transfers between species are the major mechanism whereby bacteria acquire resistance to antibiotics. Classically, this type of transfer has been thought to occur by three different mechanisms:
1. Transformation: naked DNA is taken up by a bacteria
2. Transduction: genes are transferred using a virus
3. Conjugation: the use of a hollow tube called a pilus to transfer genes between organisms
More recently, a fourth mechanism of gene transfer between prokaryotes has been discovered. Small, virus-like particles called gene transfer agents (GTAs) transfer random genomic segments from one species of prokaryote to another. GTAs have been shown to be responsible for genetic changes, sometimes at a very high frequency compared to other evolutionary processes. The first GTA was characterized in 1974 using purple, non-sulfur bacteria. These GTAs, which are thought to be bacteriophages that lost the ability to reproduce on their own, carry random pieces of DNA from one organism to another. The ability of GTAs to act with high frequency has been demonstrated in controlled studies using marine bacteria. Gene transfer events in marine prokaryotes, either by GTAs or by viruses, have been estimated to be as high as 1013 per year in the Mediterranean Sea alone. GTAs and viruses are thought to be efficient HGT vehicles with a major impact on prokaryotic evolution.
As a consequence of this modern DNA analysis, the idea that eukaryotes evolved directly from Archaea has fallen out of favor. While eukaryotes share many features that are absent in bacteria, such as the TATA box (found in the promoter region of many genes), the discovery that some eukaryotic genes were more homologous with bacterial DNA than Archaea DNA made this idea less tenable. Furthermore, the fusion of genomes from Archaea and Bacteria by endosymbiosis has been proposed as the ultimate event in eukaryotic evolution.
HGT in Eukaryotes
Although it is easy to see how prokaryotes exchange genetic material by HGT, it was initially thought that this process was absent in eukaryotes. After all, prokaryotes are but single cells exposed directly to their environment, whereas the sex cells of multicellular organisms are usually sequestered in protected parts of the body. It follows from this idea that the gene transfers between multicellular eukaryotes should be more difficult. Indeed, it is thought that this process is rarer in eukaryotes and has a much smaller evolutionary impact than in prokaryotes. In spite of this fact, HGT between distantly related organisms has been demonstrated in several eukaryotic species, and it is possible that more examples will be discovered in the future.
In plants, gene transfer has been observed in species that cannot cross-pollinate by normal means. Transposons or “jumping genes” have been shown to transfer between rice and millet plant species. Furthermore, fungal species feeding on yew trees, from which the anti-cancer drug TAXOL® is derived from the bark, have acquired the ability to make taxol themselves, a clear example of gene transfer.
In animals, a particularly interesting example of HGT occurs within the aphid species (Figure \(2\)). Aphids are insects that vary in color based on carotenoid content. Carotenoids are pigments made by a variety of plants, fungi, and microbes, and they serve a variety of functions in animals, who obtain these chemicals from their food. Humans require carotenoids to synthesize vitamin A, and we obtain them by eating orange fruits and vegetables: carrots, apricots, mangoes, and sweet potatoes. On the other hand, aphids have acquired the ability to make the carotenoids on their own. According to DNA analysis, this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food. A carotenoid enzyme called a desaturase is responsible for the red coloration seen in certain aphids, and it has been further shown that when this gene is inactivated by mutation, the aphids revert back to their more common green color (Figure \(2\)).
Genome Fusion and the Evolution of Eukaryotes
Scientists believe the ultimate in HGT occurs through genome fusion between different species of prokaryotes when two symbiotic organisms become endosymbiotic. This occurs when one species is taken inside the cytoplasm of another species, which ultimately results in a genome consisting of genes from both the endosymbiont and the host. This mechanism is an aspect of the Endosymbiont Theory, which is accepted by a majority of biologists as the mechanism whereby eukaryotic cells obtained their mitochondria and chloroplasts. However, the role of endosymbiosis in the development of the nucleus is more controversial. Nuclear and mitochondrial DNA are thought to be of different (separate) evolutionary origin, with the mitochondrial DNA being derived from the circular genomes of bacteria that were engulfed by ancient prokaryotic cells. Mitochondrial DNA can be regarded as the smallest chromosome. Interestingly enough, mitochondrial DNA is inherited only from the mother. The mitochondrial DNA degrades in sperm when the sperm degrades in the fertilized egg or in other instances when the mitochondria located in the flagellum of the sperm fails to enter the egg.
Within the past decade, the process of genome fusion by endosymbiosis has been proposed by James Lake of the UCLA/NASA Astrobiology Institute to be responsible for the evolution of the first eukaryotic cells (Figure \(3\)a). Using DNA analysis and a new mathematical algorithm called conditioned reconstruction (CR), his laboratory proposed that eukaryotic cells developed from an endosymbiotic gene fusion between two species, one an Archaea and the other a Bacteria. As mentioned, some eukaryotic genes resemble those of Archaea, whereas others resemble those from Bacteria. An endosymbiotic fusion event, such as Lake has proposed, would clearly explain this observation. On the other hand, this work is new and the CR algorithm is relatively unsubstantiated, which causes many scientists to resist this hypothesis.
More recent work by Lake (Figure \(3\)b) proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, indeed resulted from an endosymbiotic fusion of archaeal and bacterial species. The double membrane would be a direct result of the endosymbiosis, with the endosymbiont picking up the second membrane from the host as it was internalized. This mechanism has also been used to explain the double membranes found in mitochondria and chloroplasts. Lake’s work is not without skepticism, and the ideas are still debated within the biological science community. In addition to Lake’s hypothesis, there are several other competing theories as to the origin of eukaryotes. How did the eukaryotic nucleus evolve? One theory is that the prokaryotic cells produced an additional membrane that surrounded the bacterial chromosome. Some bacteria have the DNA enclosed by two membranes; however, there is no evidence of a nucleolus or nuclear pores. Other proteobacteria also have membrane-bound chromosomes. If the eukaryotic nucleus evolved this way, we would expect one of the two types of prokaryotes to be more closely related to eukaryotes.
The nucleus-first hypothesis proposes that the nucleus evolved in prokaryotes first (Figure \(4\)a), followed by a later fusion of the new eukaryote with bacteria that became mitochondria. The mitochondria-first hypothesis proposes that mitochondria were first established in a prokaryotic host (Figure \(4\)b), which subsequently acquired a nucleus, by fusion or other mechanisms, to become the first eukaryotic cell. Most interestingly, the eukaryote-first hypothesis proposes that prokaryotes actually evolved from eukaryotes by losing genes and complexity (Figure \(4\)c). All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis is best supported by data.
Web and Network Models
The recognition of the importance of HGT, especially in the evolution of prokaryotes, has caused some to propose abandoning the classic “tree of life” model. In 1999, W. Ford Doolittle proposed a phylogenetic model that resembles a web or a network more than a tree. The hypothesis is that eukaryotes evolved not from a single prokaryotic ancestor, but from a pool of many species that were sharing genes by HGT mechanisms. As shown in Figure \(5\)a, some individual prokaryotes were responsible for transferring the bacteria that caused mitochondrial development to the new eukaryotes, whereas other species transferred the bacteria that gave rise to chloroplasts. This model is often called the “web of life.” In an effort to save the tree analogy, some have proposed using the Ficus tree (Figure \(5\)b) with its multiple trunks as a phylogenetic to represent a diminished evolutionary role for HGT.
Ring of Life Models
Others have proposed abandoning any tree-like model of phylogeny in favor of a ring structure, the so-called “ring of life” (Figure \(6\)); a phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes. Lake, again using the conditioned reconstruction algorithm, proposes a ring-like model in which species of all three domains—Archaea, Bacteria, and Eukarya—evolved from a single pool of gene-swapping prokaryotes. His laboratory proposes that this structure is the best fit for data from extensive DNA analyses performed in his laboratory, and that the ring model is the only one that adequately takes HGT and genomic fusion into account. However, other phylogeneticists remain highly skeptical of this model.
In summary, the “tree of life” model proposed by Darwin must be modified to include HGT. Does this mean abandoning the tree model completely? Even Lake argues that all attempts should be made to discover some modification of the tree model to allow it to accurately fit his data, and only the inability to do so will sway people toward his ring proposal.
This doesn’t mean a tree, web, or a ring will correlate completely to an accurate description of phylogenetic relationships of life. A consequence of the new thinking about phylogenetic models is the idea that Darwin’s original conception of the phylogenetic tree is too simple, but made sense based on what was known at the time. However, the search for a more useful model moves on: each model serving as hypotheses to be tested with the possibility of developing new models. This is how science advances. These models are used as visualizations to help construct hypothetical evolutionary relationships and understand the massive amount of data being analyzed.
Summary
The phylogenetic tree, first used by Darwin, is the classic “tree of life” model describing phylogenetic relationships among species, and the most common model used today. New ideas about HGT and genome fusion have caused some to suggest revising the model to resemble webs or rings.
Glossary
eukaryote-first hypothesis
proposal that prokaryotes evolved from eukaryotes
gene transfer agent (GTA)
bacteriophage-like particle that transfers random genomic segments from one species of prokaryote to another
genome fusion
fusion of two prokaryotic genomes, presumably by endosymbiosis
horizontal gene transfer (HGT)
(also, lateral gene transfer) transfer of genes between unrelated species
mitochondria-first hypothesis
proposal that prokaryotes acquired a mitochondrion first, followed by nuclear development
nucleus-first hypothesis
proposal that prokaryotes acquired a nucleus first, and then the mitochondrion
ring of life
phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes
web of life
phylogenetic model that attempts to incorporate the effects of horizontal gene transfer on evolution | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/4%3A_Evolutionary_Processes/20%3A_Phylogenies_and_the_History_of_Life/20.3%3A_Perspectives_on_the_Phylogenetic_Tree.txt |
20.1: Organizing Life on Earth
Review Questions
What is used to determine phylogeny?
1. mutations
2. DNA
3. evolutionary history
4. organisms on earth
Answer
C
What do scientists in the field of systematics accomplish?
1. discover new fossil sites
2. organize and classify organisms
3. name new species
4. communicate among field biologists
Answer
B
Which statement about the taxonomic classification system is correct?
1. There are more domains than kingdoms.
2. Kingdoms are the top category of classification.
3. Classes are divisions of orders.
4. Subspecies are the most specific category of classification.
Answer
D
On a phylogenetic tree, which term refers to lineages that diverged from the same place?
1. sister taxa
2. basal taxa
3. rooted taxa
4. dichotomous taxa
Answer
A
Free Response
How does a phylogenetic tree relate to the passing of time?
Answer
The phylogenetic tree shows the order in which evolutionary events took place and in what order certain characteristics and organisms evolved in relation to others. It does not relate to time.
Some organisms that appear very closely related on a phylogenetic tree may not actually be closely related. Why is this?
Answer
In most cases, organisms that appear closely related actually are; however, there are cases where organisms evolved through convergence and appear closely related but are not.
List the different levels of the taxonomic classification system.
Answer
domain, kingdom, phylum, class, order, family, genus, species
20.2: Determining Evolutionary Relationships
Review Questions
Which statement about analogies is correct?
1. They occur only as errors.
2. They are synonymous with homologous traits.
3. They are derived by similar environmental constraints.
4. They are a form of mutation.
Answer
C
What do scientists use to apply cladistics?
1. homologous traits
2. homoplasies
3. analogous traits
4. monophyletic groups
Answer
A
What is true about organisms that are a part of the same clade?
1. They all share the same basic characteristics.
2. They evolved from a shared ancestor.
3. They usually fall into the same classification taxa.
4. They have identical phylogenies.
Answer
B
Why do scientists apply the concept of maximum parsimony?
1. to decipher accurate phylogenies
2. to eliminate analogous traits
3. to identify mutations in DNA codes
4. to locate homoplasies
Answer
A
Free Response
Dolphins and fish have similar body shapes. Is this feature more likely a homologous or analogous trait?
Answer
Dolphins are mammals and fish are not, which means that their evolutionary paths (phylogenies) are quite separate. Dolphins probably adapted to have a similar body plan after returning to an aquatic lifestyle, and, therefore, this trait is probably analogous.
Why is it so important for scientists to distinguish between homologous and analogous characteristics before building phylogenetic trees?
Answer
Phylogenetic trees are based on evolutionary connections. If an analogous similarity were used on a tree, this would be erroneous and, furthermore, would cause the subsequent branches to be inaccurate.
Describe maximum parsimony.
Answer
Maximum parsimony hypothesizes that events occurred in the simplest, most obvious way, and the pathway of evolution probably includes the fewest major events that coincide with the evidence at hand.
20.3: Perspectives on the Phylogenetic Tree
Review Questions
The transfer of genes by a mechanism not involving asexual reproduction is called:
1. meiosis
2. web of life
3. horizontal gene transfer
4. gene fusion
Answer
C
Particles that transfer genetic material from one species to another, especially in marine prokaryotes:
1. horizontal gene transfer
2. lateral gene transfer
3. genome fusion device
4. gene transfer agents
Answer
D
What does the trunk of the classic phylogenetic tree represent?
1. single common ancestor
2. pool of ancestral organisms
3. new species
4. old species
Answer
A
Which phylogenetic model proposes that all three domains of life evolved from a pool of primitive prokaryotes?
1. tree of life
2. web of life
3. ring of life
4. network model
Answer
C
Free Response
Compare three different ways that eukaryotic cells may have evolved.
Answer
Some hypotheses propose that mitochondria were acquired first, followed by the development of the nucleus. Others propose that the nucleus evolved first and that this new eukaryotic cell later acquired the mitochondria. Still others hypothesize that prokaryotes descended from eukaryotes by the loss of genes and complexity.
Describe how aphids acquired the ability to change color.
Answer
Aphids have acquired the ability to make the carotenoids on their own. DNA analysis has demonstrated that this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/4%3A_Evolutionary_Processes/20%3A_Phylogenies_and_the_History_of_Life/20.E%3A_Phylogenies_and_the_History_of_Life_%28Exercises%29.txt |
Viruses are acellular, parasitic entities that are not classified within any kingdom. Viruses are not cells and cannot divide. They infect a host cell and use the host’s replication processes to produce identical progeny virus particles. Viruses infect organisms as diverse as bacteria, plants, and animals and exist in a netherworld between a living organism and a nonliving entity. Living things grow, metabolize, and reproduce. Viruses replicate, but to do so, they are entirely dependent on their host cells.
• 21.0: Prelude to Viruses
Viruses are acellular, parasitic entities that are not classified within any kingdom. Unlike most living organisms, viruses are not cells and cannot divide. Instead, they infect a host cell and use the host’s replication processes to produce identical progeny virus particles. Viruses infect organisms as diverse as bacteria, plants, and animals. They exist in a netherworld between a living organism and a nonliving entity.
• 21.1: Viral Evolution, Morphology, and Classification
Viruses are diverse entities. They vary in their structure, their replication methods, and in their target hosts. Nearly all forms of life—from bacteria and archaea to eukaryotes such as plants, animals, and fungi—have viruses that infect them. While most biological diversity can be understood through evolutionary history, such as how species have adapted to conditions and environments, much about virus origins and evolution remains unknown.
• 21.2: Virus Infections and Hosts
Viruses can be seen as obligate, intracellular parasites. A virus must attach to a living cell, be taken inside, manufacture its proteins and copy its genome, and find a way to escape the cell so that the virus can infect other cells. Viruses can infect only certain species of hosts and only certain cells within that host. Cells that a virus may use to replicate are called permissive.
• 21.3: Prevention and Treatment of Viral Infections
Viruses cause a variety of diseases in animals, including humans, ranging from the common cold to potentially fatal illnesses like meningitis. These diseases can be treated by antiviral drugs or by vaccines, but some viruses, such as HIV, are capable of both avoiding the immune response and mutating to become resistant to antiviral drugs.
• 21.4: Other Acellular Entities - Prions and Viroids
Prions and viroids are pathogens (agents with the ability to cause disease) that have simpler structures than viruses but, in the case of prions, still can produce deadly diseases.
• 21.E: Viruses (Exercises)
Thumbnail: Ebola virus. (Public Domain; CDC).
21: Viruses
No one knows exactly when viruses emerged or from where they came, since viruses do not leave historical footprints such as fossils. Modern viruses are thought to be a mosaic of bits and pieces of nucleic acids picked up from various sources along their respective evolutionary paths. Viruses are acellular, parasitic entities that are not classified within any kingdom. Unlike most living organisms, viruses are not cells and cannot divide. Instead, they infect a host cell and use the host’s replication processes to produce identical progeny virus particles. Viruses infect organisms as diverse as bacteria, plants, and animals. They exist in a netherworld between a living organism and a nonliving entity. Living things grow, metabolize, and reproduce. Viruses replicate, but to do so, they are entirely dependent on their host cells. They do not metabolize or grow, but are assembled in their mature form. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/21%3A_Viruses/21.0%3A_Prelude_to_Viruses.txt |
Skills to Develop
• Describe how viruses were first discovered and how they are detected
• Discuss three hypotheses about how viruses evolved
• Recognize the basic shapes of viruses
• Understand past and emerging classification systems for viruses
Viruses are diverse entities. They vary in their structure, their replication methods, and in their target hosts. Nearly all forms of life—from bacteria and archaea to eukaryotes such as plants, animals, and fungi—have viruses that infect them. While most biological diversity can be understood through evolutionary history, such as how species have adapted to conditions and environments, much about virus origins and evolution remains unknown.
Discovery and Detection
Viruses were first discovered after the development of a porcelain filter, called the Chamberland-Pasteur filter, which could remove all bacteria visible in the microscope from any liquid sample. In 1886, Adolph Meyer demonstrated that a disease of tobacco plants, tobacco mosaic disease, could be transferred from a diseased plant to a healthy one via liquid plant extracts. In 1892, Dmitri Ivanowski showed that this disease could be transmitted in this way even after the Chamberland-Pasteur filter had removed all viable bacteria from the extract. Still, it was many years before it was proven that these “filterable” infectious agents were not simply very small bacteria but were a new type of very small, disease-causing particle.
Virions, single virus particles, are very small, about 20–250 nanometers in diameter. These individual virus particles are the infectious form of a virus outside the host cell. Unlike bacteria (which are about 100-times larger), we cannot see viruses with a light microscope, with the exception of some large virions of the poxvirus family. It was not until the development of the electron microscope in the late 1930s that scientists got their first good view of the structure of the tobacco mosaic virus (TMV) (Figure \(1\)) and other viruses (Figure \(1\)). The surface structure of virions can be observed by both scanning and transmission electron microscopy, whereas the internal structures of the virus can only be observed in images from a transmission electron microscope. The use of these technologies has allowed for the discovery of many viruses of all types of living organisms. They were initially grouped by shared morphology. Later, groups of viruses were classified by the type of nucleic acid they contained, DNA or RNA, and whether their nucleic acid was single- or double-stranded. More recently, molecular analysis of viral replicative cycles has further refined their classification.
Evolution of Viruses
Although biologists have accumulated a significant amount of knowledge about how present-day viruses evolve, much less is known about how viruses originated in the first place. When exploring the evolutionary history of most organisms, scientists can look at fossil records and similar historic evidence. However, viruses do not fossilize, so researchers must conjecture by investigating how today’s viruses evolve and by using biochemical and genetic information to create speculative virus histories.
While most findings agree that viruses don’t have a single common ancestor, scholars have yet to find a single hypothesis about virus origins that is fully accepted in the field. One such hypothesis, called devolution or the regressive hypothesis, proposes to explain the origin of viruses by suggesting that viruses evolved from free-living cells. However, many components of how this process might have occurred are a mystery. A second hypothesis (called escapist or the progressive hypothesis) accounts for viruses having either an RNA or a DNA genome and suggests that viruses originated from RNA and DNA molecules that escaped from a host cell. A third hypothesis posits a system of self-replication similar to that of other self-replicating molecules, likely evolving alongside the cells they rely on as hosts; studies of some plant pathogens support this hypothesis.
As technology advances, scientists may develop and refine further hypotheses to explain the origin of viruses. The emerging field called virus molecular systematics attempts to do just that through comparisons of sequenced genetic material. These researchers hope to one day better understand the origin of viruses, a discovery that could lead to advances in the treatments for the ailments they produce.
Viral Morphology
Viruses are acellular, meaning they are biological entities that do not have a cellular structure. They therefore lack most of the components of cells, such as organelles, ribosomes, and the plasma membrane. A virion consists of a nucleic acid core, an outer protein coating or capsid, and sometimes an outer envelope made of protein and phospholipid membranes derived from the host cell. Viruses may also contain additional proteins, such as enzymes. The most obvious difference between members of viral families is their morphology, which is quite diverse. An interesting feature of viral complexity is that the complexity of the host does not correlate with the complexity of the virion. Some of the most complex virion structures are observed in bacteriophages, viruses that infect the simplest living organisms, bacteria.
Morphology
Viruses come in many shapes and sizes, but these are consistent and distinct for each viral family. All virions have a nucleic acid genome covered by a protective layer of proteins, called a capsid. The capsid is made up of protein subunits called capsomeres. Some viral capsids are simple polyhedral “spheres,” whereas others are quite complex in structure.
In general, the shapes of viruses are classified into four groups: filamentous, isometric (or icosahedral), enveloped, and head and tail. Filamentous viruses are long and cylindrical. Many plant viruses are filamentous, including TMV. Isometric viruses have shapes that are roughly spherical, such as poliovirus or herpesviruses. Enveloped viruses have membranes surrounding capsids. Animal viruses, such as HIV, are frequently enveloped. Head and tail viruses infect bacteria and have a head that is similar to icosahedral viruses and a tail shape like filamentous viruses.
Many viruses use some sort of glycoprotein to attach to their host cells via molecules on the cell called viral receptors (Figure \(2\)). For these viruses, attachment is a requirement for later penetration of the cell membrane, so they can complete their replication inside the cell. The receptors that viruses use are molecules that are normally found on cell surfaces and have their own physiological functions. Viruses have simply evolved to make use of these molecules for their own replication. For example, HIV uses the CD4 molecule on T lymphocytes as one of its receptors. CD4 is a type of molecule called a cell adhesion molecule, which functions to keep different types of immune cells in close proximity to each other during the generation of a T lymphocyte immune response.
Among the most complex virions known, the T4 bacteriophage, which infects the Escherichia coli bacterium, has a tail structure that the virus uses to attach to host cells and a head structure that houses its DNA.
Adenovirus, a non-enveloped animal virus that causes respiratory illnesses in humans, uses glycoprotein spikes protruding from its capsomeres to attach to host cells. Non-enveloped viruses also include those that cause polio (poliovirus), plantar warts (papillomavirus), and hepatitis A (hepatitis A virus).
Enveloped virions like HIV, the causative agent in AIDS, consist of nucleic acid (RNA in the case of HIV) and capsid proteins surrounded by a phospholipid bilayer envelope and its associated proteins. Glycoproteins embedded in the viral envelope are used to attach to host cells. Other envelope proteins are the matrix proteins that stabilize the envelope and often play a role in the assembly of progeny virions. Chicken pox, influenza, and mumps are examples of diseases caused by viruses with envelopes. Because of the fragility of the envelope, non-enveloped viruses are more resistant to changes in temperature, pH, and some disinfectants than enveloped viruses.
Overall, the shape of the virion and the presence or absence of an envelope tell us little about what disease the virus may cause or what species it might infect, but they are still useful means to begin viral classification (Figure \(3\)).
Exercise \(1\)
Which of the following statements about virus structure is true?
1. All viruses are encased in a viral membrane.
2. The capsomere is made up of small protein subunits called capsids.
3. DNA is the genetic material in all viruses.
4. Glycoproteins help the virus attach to the host cell.
Answer
D
Types of Nucleic Acid
Unlike nearly all living organisms that use DNA as their genetic material, viruses may use either DNA or RNA as theirs. The virus core contains the genome or total genetic content of the virus. Viral genomes tend to be small, containing only those genes that encode proteins that the virus cannot get from the host cell. This genetic material may be single- or double-stranded. It may also be linear or circular. While most viruses contain a single nucleic acid, others have genomes that have several, which are called segments.
In DNA viruses, the viral DNA directs the host cell’s replication proteins to synthesize new copies of the viral genome and to transcribe and translate that genome into viral proteins. DNA viruses cause human diseases, such as chickenpox, hepatitis B, and some venereal diseases, like herpes and genital warts.
RNA viruses contain only RNA as their genetic material. To replicate their genomes in the host cell, the RNA viruses encode enzymes that can replicate RNA into DNA, which cannot be done by the host cell. These RNA polymerase enzymes are more likely to make copying errors than DNA polymerases, and therefore often make mistakes during transcription. For this reason, mutations in RNA viruses occur more frequently than in DNA viruses. This causes them to change and adapt more rapidly to their host. Human diseases caused by RNA viruses include hepatitis C, measles, and rabies.
Virus Classification
To understand the features shared among different groups of viruses, a classification scheme is necessary. As most viruses are not thought to have evolved from a common ancestor, however, the methods that scientists use to classify living things are not very useful. Biologists have used several classification systems in the past, based on the morphology and genetics of the different viruses. However, these earlier classification methods grouped viruses differently, based on which features of the virus they were using to classify them. The most commonly used classification method today is called the Baltimore classification scheme and is based on how messenger RNA (mRNA) is generated in each particular type of virus.
Past Systems of Classification
Viruses are classified in several ways: by factors such as their core content (Table \(1\) and Figure \(2\)), the structure of their capsids, and whether they have an outer envelope. The type of genetic material (DNA or RNA) and its structure (single- or double-stranded, linear or circular, and segmented or non-segmented) are used to classify the virus core structures.
Table \(1\): Virus Classification by Genome Structure and Core
Core Classifications Examples
• RNA
• DNA
• Rabies virus, retroviruses
• Herpesviruses, smallpox virus
• Single-stranded
• Double-stranded
• Rabies virus, retroviruses
• Herpesviruses, smallpox virus
• Linear
• Circular
• Rabies virus, retroviruses, herpesviruses, smallpox virus
• Papillomaviruses, many bacteriophages
• Non-segmented: genome consists of a single segment of genetic material
• Segmented: genome is divided into multiple segments
• Parainfluenza viruses
• Influenza viruses
Viruses can also be classified by the design of their capsids (Figure \(3\) and Figure \(4\)). Capsids are classified as naked icosahedral, enveloped icosahedral, enveloped helical, naked helical, and complex (Figure \(5\) and Figure \(6\)). The type of genetic material (DNA or RNA) and its structure (single- or double-stranded, linear or circular, and segmented or non-segmented) are used to classify the virus core structures (Table \(2\)).
Table \(2\): Virus Classification by Capsid Structure
Capsid Classification Examples
Naked icosahedral Hepatitis A virus, polioviruses
Enveloped icosahedral Epstein-Barr virus, herpes simplex virus, rubella virus, yellow fever virus, HIV-1
Enveloped helical Influenza viruses, mumps virus, measles virus, rabies virus
Naked helical Tobacco mosaic virus
Complex with many proteins; some have combinations of icosahedral and helical capsid structures Herpesviruses, smallpox virus, hepatitis B virus, T4 bacteriophage
Baltimore Classification
The most commonly used system of virus classification was developed by Nobel Prize-winning biologist David Baltimore in the early 1970s. In addition to the differences in morphology and genetics mentioned above, the Baltimore classification scheme groups viruses according to how the mRNA is produced during the replicative cycle of the virus.
Group I viruses contain double-stranded DNA (dsDNA) as their genome. Their mRNA is produced by transcription in much the same way as with cellular DNA. Group II viruses have single-stranded DNA (ssDNA) as their genome. They convert their single-stranded genomes into a dsDNA intermediate before transcription to mRNA can occur. Group III viruses use dsRNA as their genome. The strands separate, and one of them is used as a template for the generation of mRNA using the RNA-dependent RNA polymerase encoded by the virus. Group IV viruses have ssRNA as their genome with a positive polarity. Positive polarity means that the genomic RNA can serve directly as mRNA. Intermediates of dsRNA, called replicative intermediates, are made in the process of copying the genomic RNA. Multiple, full-length RNA strands of negative polarity (complimentary to the positive-stranded genomic RNA) are formed from these intermediates, which may then serve as templates for the production of RNA with positive polarity, including both full-length genomic RNA and shorter viral mRNAs. Group V viruses contain ssRNA genomes with a negative polarity, meaning that their sequence is complementary to the mRNA. As with Group IV viruses, dsRNA intermediates are used to make copies of the genome and produce mRNA. In this case, the negative-stranded genome can be converted directly to mRNA. Additionally, full-length positive RNA strands are made to serve as templates for the production of the negative-stranded genome. Group VI viruses have diploid (two copies) ssRNA genomes that must be converted, using the enzyme reverse transcriptase, to dsDNA; the dsDNA is then transported to the nucleus of the host cell and inserted into the host genome. Then, mRNA can be produced by transcription of the viral DNA that was integrated into the host genome. Group VII viruses have partial dsDNA genomes and make ssRNA intermediates that act as mRNA, but are also converted back into dsDNA genomes by reverse transcriptase, necessary for genome replication. The characteristics of each group in the Baltimore classification are summarized in the Table \(3\) with examples of each group.
Table \(3\): Baltimore Classification
Group Characteristics Mode of mRNA Production Example
I Double-stranded DNA mRNA is transcribed directly from the DNA template Herpes simplex (herpesvirus)
II Single-stranded DNA DNA is converted to double-stranded form before RNA is transcribed Canine parvovirus (parvovirus)
III Double-stranded RNA mRNA is transcribed from the RNA genome Childhood gastroenteritis (rotavirus)
IV Single stranded RNA (+) Genome functions as mRNA Common cold (pircornavirus)
V Single stranded RNA (-) mRNA is transcribed from the RNA genome Rabies (rhabdovirus)
VI Single stranded RNA viruses with reverse transcriptase Reverse transcriptase makes DNA from the RNA genome; DNA is then incorporated in the host genome; mRNA is transcribed from the incorporated DNA Human immunodeficiency virus (HIV)
VII Double stranded DNA viruses with reverse transcriptase The viral genome is double-stranded DNA, but viral DNA is replicated through an RNA intermediate; the RNA may serve directly as mRNA or as a template to make mRNA Hepatitis B virus (hepadnavirus)
Summary
Viruses are tiny, acellular entities that can usually only be seen with an electron microscope. Their genomes contain either DNA or RNA—never both—and they replicate using the replication proteins of a host cell. Viruses are diverse, infecting archaea, bacteria, fungi, plants, and animals. Viruses consist of a nucleic acid core surrounded by a protein capsid with or without an outer lipid envelope. The capsid shape, presence of an envelope, and core composition dictate some elements of the classification of viruses. The most commonly used classification method, the Baltimore classification, categorizes viruses based on how they produce their mRNA.
Glossary
acellular
lacking cells
capsid
protein coating of the viral core
capsomere
protein subunit that makes up the capsid
envelope
lipid bilayer that envelopes some viruses
group I virus
virus with a dsDNA genome
group II virus
virus with a ssDNA genome
group III virus
virus with a dsRNA genome
group IV virus
virus with a ssRNA genome with positive polarity
group V virus
virus with a ssRNA genome with negative polarity
group VI virus
virus with a ssRNA genomes converted into dsDNA by reverse transcriptase
group VII virus
virus with a single-stranded mRNA converted into dsDNA for genome replication
matrix protein
envelope protein that stabilizes the envelope and often plays a role in the assembly of progeny virions
negative polarity
ssRNA viruses with genomes complimentary to their mRNA
positive polarity
ssRNA virus with a genome that contains the same base sequences and codons found in their mRNA
replicative intermediate
dsRNA intermediate made in the process of copying genomic RNA
reverse transcriptase
enzyme found in Baltimore groups VI and VII that converts single-stranded RNA into double-stranded DNA
viral receptor
glycoprotein used to attach a virus to host cells via molecules on the cell
virion
individual virus particle outside a host cell
virus core
contains the virus genome | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/21%3A_Viruses/21.1%3A_Viral_Evolution_Morphology_and_Classification.txt |
Skills to Develop
• List the steps of replication and explain what occurs at each step
• Describe the lytic and lysogenic cycles of virus replication
• Explain the transmission and diseases of animal and plant viruses
• Discuss the economic impact of animal and plant viruses
Viruses can be seen as obligate, intracellular parasites. A virus must attach to a living cell, be taken inside, manufacture its proteins and copy its genome, and find a way to escape the cell so that the virus can infect other cells. Viruses can infect only certain species of hosts and only certain cells within that host. Cells that a virus may use to replicate are called permissive. For most viruses, the molecular basis for this specificity is that a particular surface molecule known as the viral receptor must be found on the host cell surface for the virus to attach. Also, metabolic and host cell immune response differences seen in different cell types based on differential gene expression are a likely factor in which cells a virus may target for replication. The permissive cell must make the substances that the virus needs or the virus will not be able to replicate there.
Steps of Virus Infections
A virus must use cell processes to replicate. The viral replication cycle can produce dramatic biochemical and structural changes in the host cell, which may cause cell damage. These changes, called cytopathic (causing cell damage) effects, can change cell functions or even destroy the cell. Some infected cells, such as those infected by the common cold virus known as rhinovirus, die through lysis (bursting) or apoptosis (programmed cell death or “cell suicide”), releasing all progeny virions at once. The symptoms of viral diseases result from the immune response to the virus, which attempts to control and eliminate the virus from the body, and from cell damage caused by the virus. Many animal viruses, such as HIV (human immunodeficiency virus), leave the infected cells of the immune system by a process known as budding, where virions leave the cell individually. During the budding process, the cell does not undergo lysis and is not immediately killed. However, the damage to the cells that the virus infects may make it impossible for the cells to function normally, even though the cells remain alive for a period of time. Most productive viral infections follow similar steps in the virus replication cycle: attachment, penetration, uncoating, replication, assembly, and release (Figure \(1\)).
Attachment
A virus attaches to a specific receptor site on the host cell membrane through attachment proteins in the capsid or via glycoproteins embedded in the viral envelope. The specificity of this interaction determines the host—and the cells within the host—that can be infected by a particular virus. This can be illustrated by thinking of several keys and several locks, where each key will fit only one specific lock.
Entry
The nucleic acid of bacteriophages enters the host cell naked, leaving the capsid outside the cell. Plant and animal viruses can enter through endocytosis, in which the cell membrane surrounds and engulfs the entire virus. Some enveloped viruses enter the cell when the viral envelope fuses directly with the cell membrane. Once inside the cell, the viral capsid is degraded, and the viral nucleic acid is released, which then becomes available for replication and transcription.
Replication and Assembly
The replication mechanism depends on the viral genome. DNA viruses usually use host cell proteins and enzymes to make additional DNA that is transcribed to messenger RNA (mRNA), which is then used to direct protein synthesis. RNA viruses usually use the RNA core as a template for synthesis of viral genomic RNA and mRNA. The viral mRNA directs the host cell to synthesize viral enzymes and capsid proteins, and assemble new virions. Of course, there are exceptions to this pattern. If a host cell does not provide the enzymes necessary for viral replication, viral genes supply the information to direct synthesis of the missing proteins. Retroviruses, such as HIV, have an RNA genome that must be reverse transcribed into DNA, which then is incorporated into the host cell genome. They are within group VI of the Baltimore classification scheme. To convert RNA into DNA, retroviruses must contain genes that encode the virus-specific enzyme reverse transcriptase that transcribes an RNA template to DNA. Reverse transcription never occurs in uninfected host cells—the needed enzyme reverse transcriptase is only derived from the expression of viral genes within the infected host cells. The fact that HIV produces some of its own enzymes not found in the host has allowed researchers to develop drugs that inhibit these enzymes. These drugs, including the reverse transcriptase inhibitor AZT, inhibit HIV replication by reducing the activity of the enzyme without affecting the host’s metabolism. This approach has led to the development of a variety of drugs used to treat HIV and has been effective at reducing the number of infectious virions (copies of viral RNA) in the blood to non-detectable levels in many HIV-infected individuals.
Egress
The last stage of viral replication is the release of the new virions produced in the host organism, where they are able to infect adjacent cells and repeat the replication cycle. As you’ve learned, some viruses are released when the host cell dies, and other viruses can leave infected cells by budding through the membrane without directly killing the cell.
Exercise \(1\)
Influenza virus is packaged in a viral envelope that fuses with the plasma membrane. This way, the virus can exit the host cell without killing it. What advantage does the virus gain by keeping the host cell alive?
Answer
The host cell can continue to make new virus particles.
Link to Learning
Watch a video on viruses, identifying structures, modes of transmission, replication, and more.
Different Hosts and Their Viruses
As you’ve learned, viruses are often very specific as to which hosts and which cells within the host they will infect. This feature of a virus makes it specific to one or a few species of life on Earth. On the other hand, so many different types of viruses exist on Earth that nearly every living organism has its own set of viruses that tries to infect its cells. Even the smallest and simplest of cells, prokaryotic bacteria, may be attacked by specific types of viruses.
Bacteriophages
Bacteriophages are viruses that infect bacteria (Figure \(2\)). When infection of a cell by a bacteriophage results in the production of new virions, the infection is said to be productive. If the virions are released by bursting the cell, the virus replicates by means of a lytic cycle (Figure \(3\)).
An example of a lytic bacteriophage is T4, which infects Escherichia coli found in the human intestinal tract. Sometimes, however, a virus can remain within the cell without being released. For example, when a temperate bacteriophage infects a bacterial cell, it replicates by means of a lysogenic cycle (Figure \(3\)), and the viral genome is incorporated into the genome of the host cell. When the phage DNA is incorporated into the host cell genome, it is called a prophage. An example of a lysogenic bacteriophage is the λ (lambda) virus, which also infects the E. coli bacterium. Viruses that infect plant or animal cells may also undergo infections where they are not producing virions for long periods. An example is the animal herpesviruses, including herpes simplex viruses, the cause of oral and genital herpes in humans. In a process called latency, these viruses can exist in nervous tissue for long periods of time without producing new virions, only to leave latency periodically and cause lesions in the skin where the virus replicates. Even though there are similarities between lysogeny and latency, the term lysogenic cycle is usually reserved to describe bacteriophages. Latency will be described in more detail below.
Exercise \(2\)
Which of the following statements is false?
1. In the lytic cycle, new phage are produced and released into the environment.
2. In the lysogenic cycle, phage DNA is incorporated into the host genome.
3. An environmental stressor can cause the phage to initiate the lysogenic cycle.
4. Cell lysis only occurs in the lytic cycle.
Answer
C
Animal Viruses
Animal viruses, unlike the viruses of plants and bacteria, do not have to penetrate a cell wall to gain access to the host cell. Non-enveloped or “naked” animal viruses may enter cells in two different ways. As a protein in the viral capsid binds to its receptor on the host cell, the virus may be taken inside the cell via a vesicle during the normal cell process of receptor-mediated endocytosis. An alternative method of cell penetration used by non-enveloped viruses is for capsid proteins to undergo shape changes after binding to the receptor, creating channels in the host cell membrane. The viral genome is then “injected” into the host cell through these channels in a manner analogous to that used by many bacteriophages. Enveloped viruses also have two ways of entering cells after binding to their receptors: receptor-mediated endocytosis, or fusion. Many enveloped viruses enter the cell by receptor-mediated endocytosis in a fashion similar to some non-enveloped viruses. On the other hand, fusion only occurs with enveloped virions. These viruses, which include HIV among others, use special fusion proteins in their envelopes to cause the envelope to fuse with the plasma membrane of the cell, thus releasing the genome and capsid of the virus into the cell cytoplasm.
After making their proteins and copying their genomes, animal viruses complete the assembly of new virions and exit the cell. As we have already discussed using the example of HIV, enveloped animal viruses may bud from the cell membrane as they assemble themselves, taking a piece of the cell’s plasma membrane in the process. On the other hand, non-enveloped viral progeny, such as rhinoviruses, accumulate in infected cells until there is a signal for lysis or apoptosis, and all virions are released together.
As you will learn in the next module, animal viruses are associated with a variety of human diseases. Some of them follow the classic pattern of acute disease, where symptoms get increasingly worse for a short period followed by the elimination of the virus from the body by the immune system and eventual recovery from the infection. Examples of acute viral diseases are the common cold and influenza. Other viruses cause long-term chronic infections, such as the virus causing hepatitis C, whereas others, like herpes simplex virus, only cause intermittent symptoms. Still other viruses, such as human herpesviruses 6 and 7, which in some cases can cause the minor childhood disease roseola, often successfully cause productive infections without causing any symptoms at all in the host, and thus we say these patients have an asymptomatic infection.
In hepatitis C infections, the virus grows and reproduces in liver cells, causing low levels of liver damage. The damage is so low that infected individuals are often unaware that they are infected, and many infections are detected only by routine blood work on patients with risk factors such as intravenous drug use. On the other hand, since many of the symptoms of viral diseases are caused by immune responses, a lack of symptoms is an indication of a weak immune response to the virus. This allows for the virus to escape elimination by the immune system and persist in individuals for years, all the while producing low levels of progeny virions in what is known as a chronic viral disease. Chronic infection of the liver by this virus leads to a much greater chance of developing liver cancer, sometimes as much as 30 years after the initial infection.
As already discussed, herpes simplex virus can remain in a state of latency in nervous tissue for months, even years. As the virus “hides” in the tissue and makes few if any viral proteins, there is nothing for the immune response to act against, and immunity to the virus slowly declines. Under certain conditions, including various types of physical and psychological stress, the latent herpes simplex virus may be reactivated and undergo a lytic replication cycle in the skin, causing the lesions associated with the disease. Once virions are produced in the skin and viral proteins are synthesized, the immune response is again stimulated and resolves the skin lesions in a few days by destroying viruses in the skin. As a result of this type of replicative cycle, appearances of cold sores and genital herpes outbreaks only occur intermittently, even though the viruses remain in the nervous tissue for life. Latent infections are common with other herpesviruses as well, including the varicella-zoster virus that causes chickenpox. After having a chickenpox infection in childhood, the varicella-zoster virus can remain latent for many years and reactivate in adults to cause the painful condition known as “shingles” (Figure \(4\)).
Some animal-infecting viruses, including the hepatitis C virus discussed above, are known as oncogenic viruses: They have the ability to cause cancer. These viruses interfere with the normal regulation of the host cell cycle either by either introducing genes that stimulate unregulated cell growth (oncogenes) or by interfering with the expression of genes that inhibit cell growth. Oncogenic viruses can be either DNA or RNA viruses. Cancers known to be associated with viral infections include cervical cancer caused by human papillomavirus (HPV) (Figure \(5\)), liver cancer caused by hepatitis B virus, T-cell leukemia, and several types of lymphoma.
Link to Learning
Visit the interactive animations showing the various stages of the replicative cycles of animal viruses and click on the flash animation links.
Plant Viruses
Plant viruses, like other viruses, contain a core of either DNA or RNA. You have already learned about one of these, the tobacco mosaic virus. As plant viruses have a cell wall to protect their cells, these viruses do not use receptor-mediated endocytosis to enter host cells as is seen with animal viruses. For many plant viruses to be transferred from plant to plant, damage to some of the plants’ cells must occur to allow the virus to enter a new host. This damage is often caused by weather, insects, animals, fire, or human activities like farming or landscaping. Additionally, plant offspring may inherit viral diseases from parent plants. Plant viruses can be transmitted by a variety of vectors, through contact with an infected plant’s sap, by living organisms such as insects and nematodes, and through pollen. When plants viruses are transferred between different plants, this is known as horizontal transmission, and when they are inherited from a parent, this is called vertical transmission.
Symptoms of viral diseases vary according to the virus and its host (Table \(1\)). One common symptom is hyperplasia, the abnormal proliferation of cells that causes the appearance of plant tumors known as galls. Other viruses induce hypoplasia, or decreased cell growth, in the leaves of plants, causing thin, yellow areas to appear. Still other viruses affect the plant by directly killing plant cells, a process known as cell necrosis. Other symptoms of plant viruses include malformed leaves, black streaks on the stems of the plants, altered growth of stems, leaves, or fruits, and ring spots, which are circular or linear areas of discoloration found in a leaf.
Table \(1\): Some Common Symptoms of Plant Viral Diseases
Symptom Appears as
Hyperplasia Galls (tumors)
Hypoplasia Thinned, yellow splotches on leaves
Cell necrosis Dead, blackened stems, leaves, or fruit
Abnormal growth patterns Malformed stems, leaves, or fruit
Discoloration Yellow, red, or black lines, or rings in stems, leaves, or fruit
Plant viruses can seriously disrupt crop growth and development, significantly affecting our food supply. They are responsible for poor crop quality and quantity globally, and can bring about huge economic losses annually. Others viruses may damage plants used in landscaping. Some viruses that infect agricultural food plants include the name of the plant they infect, such as tomato spotted wilt virus, bean common mosaic virus, and cucumber mosaic virus. In plants used for landscaping, two of the most common viruses are peony ring spot and rose mosaic virus. There are far too many plant viruses to discuss each in detail, but symptoms of bean common mosaic virus result in lowered bean production and stunted, unproductive plants. In the ornamental rose, the rose mosaic disease causes wavy yellow lines and colored splotches on the leaves of the plant.
Summary
Viral replication within a living cell always produces changes in the cell, sometimes resulting in cell death and sometimes slowly killing the infected cells. There are six basic stages in the virus replication cycle: attachment, penetration, uncoating, replication, assembly, and release. A viral infection may be productive, resulting in new virions, or nonproductive, which means that the virus remains inside the cell without producing new virions. Bacteriophages are viruses that infect bacteria. They have two different modes of replication: the lytic cycle, where the virus replicates and bursts out of the bacteria, and the lysogenic cycle, which involves the incorporation of the viral genome into the bacterial host genome. Animal viruses cause a variety of infections, with some causing chronic symptoms (hepatitis C), some intermittent symptoms (latent viruses such a herpes simplex virus 1), and others that cause very few symptoms, if any (human herpesviruses 6 and 7). Oncogenic viruses in animals have the ability to cause cancer by interfering with the regulation of the host cell cycle. Viruses of plants are responsible for significant economic damage in both agriculture and plants used for ornamentation.
Glossary
acute disease
disease where the symptoms rise and fall within a short period of time
asymptomatic disease
disease where there are no symptoms and the individual is unaware of being infected unless lab tests are performed
AZT
anti-HIV drug that inhibits the viral enzyme reverse transcriptase
bacteriophage
virus that infects bacteria
budding
method of exit from the cell used in certain animal viruses, where virions leave the cell individually by capturing a piece of the host plasma membrane
cell necrosis
cell death
chronic infection
describes when the virus persists in the body for a long period of time
cytopathic
causing cell damage
fusion
method of entry by some enveloped viruses, where the viral envelope fuses with the plasma membrane of the host cell
gall
appearance of a plant tumor
horizontal transmission
transmission of a disease from parent to offspring
hyperplasia
abnormally high cell growth and division
hypoplasia
abnormally low cell growth and division
intermittent symptom
symptom that occurs periodically
latency
virus that remains in the body for a long period of time but only causes intermittent symptoms
lysis
bursting of a cell
lytic cycle
type of virus replication in which virions are released through lysis, or bursting, of the cell
lysogenic cycle
type of virus replication in which the viral genome is incorporated into the genome of the host cell
oncogenic virus
virus that has the ability to cause cancer
permissive
cell type that is able to support productive replication of a virus
productive
viral infection that leads to the production of new virions
prophage
phage DNA that is incorporated into the host cell genome
vertical transmission
transmission of disease between unrelated individuals | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/21%3A_Viruses/21.2%3A_Virus_Infections_and_Hosts.txt |
Skills to Develop
• Identify major viral illnesses that affect humans
• Compare vaccinations and anti-viral drugs as medical approaches to viruses
Viruses cause a variety of diseases in animals, including humans, ranging from the common cold to potentially fatal illnesses like meningitis (Figure \(1\)). These diseases can be treated by antiviral drugs or by vaccines, but some viruses, such as HIV, are capable of both avoiding the immune response and mutating to become resistant to antiviral drugs.
Vaccines for Prevention
While we do have limited numbers of effective antiviral drugs, such as those used to treat HIV and influenza, the primary method of controlling viral disease is by vaccination, which is intended to prevent outbreaks by building immunity to a virus or virus family (Figure\(1\)). Vaccines may be prepared using live viruses, killed viruses, or molecular subunits of the virus. The killed viral vaccines and subunit viruses are both incapable of causing disease.
Live viral vaccines are designed in the laboratory to cause few symptoms in recipients while giving them protective immunity against future infections. Polio was one disease that represented a milestone in the use of vaccines. Mass immunization campaigns in the 1950s (killed vaccine) and 1960s (live vaccine) significantly reduced the incidence of the disease, which caused muscle paralysis in children and generated a great amount of fear in the general population when regional epidemics occurred. The success of the polio vaccine paved the way for the routine dispensation of childhood vaccines against measles, mumps, rubella, chickenpox, and other diseases.
The danger of using live vaccines, which are usually more effective than killed vaccines, is the low but significant danger that these viruses will revert to their disease-causing form by back mutations. Live vaccines are usually made by attenuating (weakening) the “wild-type” (disease-causing) virus by growing it in the laboratory in tissues or at temperatures different from what the virus is accustomed to in the host. Adaptations to these new cells or temperatures induce mutations in the genomes of the virus, allowing it to grow better in the laboratory while inhibiting its ability to cause disease when reintroduced into conditions found in the host. These attenuated viruses thus still cause infection, but they do not grow very well, allowing the immune response to develop in time to prevent major disease. Back mutations occur when the vaccine undergoes mutations in the host such that it readapts to the host and can again cause disease, which can then be spread to other humans in an epidemic. This type of scenario happened as recently as 2007 in Nigeria where mutations in a polio vaccine led to an epidemic of polio in that country.
Some vaccines are in continuous development because certain viruses, such as influenza and HIV, have a high mutation rate compared to other viruses and normal host cells. With influenza, mutations in the surface molecules of the virus help the organism evade the protective immunity that may have been obtained in a previous influenza season, making it necessary for individuals to get vaccinated every year. Other viruses, such as those that cause the childhood diseases measles, mumps, and rubella, mutate so infrequently that the same vaccine is used year after year.
Link to Learning
Watch this NOVA video to learn how microbiologists are attempting to replicate the deadly 1918 Spanish influenza virus so they can understand more about virology.
Vaccines and Anti-viral Drugs for Treatment
In some cases, vaccines can be used to treat an active viral infection. The concept behind this is that by giving the vaccine, immunity is boosted without adding more disease-causing virus. In the case of rabies, a fatal neurological disease transmitted via the saliva of rabies virus-infected animals, the progression of the disease from the time of the animal bite to the time it enters the central nervous system may be 2 weeks or longer. This is enough time to vaccinate an individual who suspects that they have been bitten by a rabid animal, and their boosted immune response is sufficient to prevent the virus from entering nervous tissue. Thus, the potentially fatal neurological consequences of the disease are averted, and the individual only has to recover from the infected bite. This approach is also being used for the treatment of Ebola, one of the fastest and most deadly viruses on earth. Transmitted by bats and great apes, this disease can cause death in 70–90 percent of infected humans within 2 weeks. Using newly developed vaccines that boost the immune response in this way, there is hope that affected individuals will be better able to control the virus, potentially saving a greater percentage of infected persons from a rapid and very painful death.
Another way of treating viral infections is the use of antiviral drugs. These drugs often have limited success in curing viral disease, but in many cases, they have been used to control and reduce symptoms for a wide variety of viral diseases. For most viruses, these drugs can inhibit the virus by blocking the actions of one or more of its proteins. It is important that the targeted proteins be encoded by viral genes and that these molecules are not present in a healthy host cell. In this way, viral growth is inhibited without damaging the host. There are large numbers of antiviral drugs available to treat infections, some specific for a particular virus and others that can affect multiple viruses.
Antivirals have been developed to treat genital herpes (herpes simplex II) and influenza. For genital herpes, drugs such as acyclovir can reduce the number and duration of episodes of active viral disease, during which patients develop viral lesions in their skin cells. As the virus remains latent in nervous tissue of the body for life, this drug is not curative but can make the symptoms of the disease more manageable. For influenza, drugs like Tamiflu (oseltamivir) (Figure \(3\)) can reduce the duration of “flu” symptoms by 1 or 2 days, but the drug does not prevent symptoms entirely. Tamiflu works by inhibiting an enzyme (viral neuraminidase) that allows new virions to leave their infected cells. Thus, Tamiflu inhibits the spread of virus from infected to uninfected cells. Other antiviral drugs, such as Ribavirin, have been used to treat a variety of viral infections, although its mechanism of action against certain viruses remains unclear.
By far, the most successful use of antivirals has been in the treatment of the retrovirus HIV, which causes a disease that, if untreated, is usually fatal within 10–12 years after infection. Anti-HIV drugs have been able to control viral replication to the point that individuals receiving these drugs survive for a significantly longer time than the untreated.
Anti-HIV drugs inhibit viral replication at many different phases of the HIV replicative cycle (Figure \(4\)). Drugs have been developed that inhibit the fusion of the HIV viral envelope with the plasma membrane of the host cell (fusion inhibitors), the conversion of its RNA genome into double-stranded DNA (reverse transcriptase inhibitors), the integration of the viral DNA into the host genome (integrase inhibitors), and the processing of viral proteins (protease inhibitors).
When any of these drugs are used individually, the high mutation rate of the virus allows it to easily and rapidly develop resistance to the drug, limiting the drug’s effectiveness. The breakthrough in the treatment of HIV was the development of HAART, highly active anti-retroviral therapy, which involves a mixture of different drugs, sometimes called a drug “cocktail.” By attacking the virus at different stages of its replicative cycle, it is much more difficult for the virus to develop resistance to multiple drugs at the same time. Still, even with the use of combination HAART therapy, there is concern that, over time, the virus will develop resistance to this therapy. Thus, new anti-HIV drugs are constantly being developed with the hope of continuing the battle against this highly fatal virus.
Everyday Connection: Applied Virology
The study of viruses has led to the development of a variety of new ways to treat non-viral diseases. Viruses have been used in gene therapy. Gene therapy is used to treat genetic diseases such as severe combined immunodeficiency (SCID), a heritable, recessive disease in which children are born with severely compromised immune systems. One common type of SCID is due to the lack of an enzyme, adenosine deaminase (ADA), which breaks down purine bases. To treat this disease by gene therapy, bone marrow cells are taken from a SCID patient and the ADA gene is inserted. This is where viruses come in, and their use relies on their ability to penetrate living cells and bring genes in with them. Viruses such as adenovirus, an upper respiratory human virus, are modified by the addition of the ADA gene, and the virus then transports this gene into the cell. The modified cells, now capable of making ADA, are then given back to the patients in the hope of curing them. Gene therapy using viruses as carrier of genes (viral vectors), although still experimental, holds promise for the treatment of many genetic diseases. Still, many technological problems need to be solved for this approach to be a viable method for treating genetic disease.
Another medical use for viruses relies on their specificity and ability to kill the cells they infect. Oncolytic viruses are engineered in the laboratory specifically to attack and kill cancer cells. A genetically modified adenovirus known as H101 has been used since 2005 in clinical trials in China to treat head and neck cancers. The results have been promising, with a greater short-term response rate to the combination of chemotherapy and viral therapy than to chemotherapy treatment alone. This ongoing research may herald the beginning of a new age of cancer therapy, where viruses are engineered to find and specifically kill cancer cells, regardless of where in the body they may have spread.
A third use of viruses in medicine relies on their specificity and involves using bacteriophages in the treatment of bacterial infections. Bacterial diseases have been treated with antibiotics since the 1940s. However, over time, many bacteria have developed resistance to antibiotics. A good example is methicillin-resistant Staphylococcus aureus (MRSA, pronounced “mersa”), an infection commonly acquired in hospitals. This bacterium is resistant to a variety of antibiotics, making it difficult to treat. The use of bacteriophages specific for such bacteria would bypass their resistance to antibiotics and specifically kill them. Although phage therapy is in use in the Republic of Georgia to treat antibiotic-resistant bacteria, its use to treat human diseases has not been approved in most countries. However, the safety of the treatment was confirmed in the United States when the U.S. Food and Drug Administration approved spraying meats with bacteriophages to destroy the food pathogen Listeria. As more and more antibiotic-resistant strains of bacteria evolve, the use of bacteriophages might be a potential solution to the problem, and the development of phage therapy is of much interest to researchers worldwide.
Summary
Viruses cause a variety of diseases in humans. Many of these diseases can be prevented by the use of viral vaccines, which stimulate protective immunity against the virus without causing major disease. Viral vaccines may also be used in active viral infections, boosting the ability of the immune system to control or destroy the virus. A series of antiviral drugs that target enzymes and other protein products of viral genes have been developed and used with mixed success. Combinations of anti-HIV drugs have been used to effectively control the virus, extending the lifespans of infected individuals. Viruses have many uses in medicines, such as in the treatment of genetic disorders, cancer, and bacterial infections.
Glossary
attenuation
weakening of a virus during vaccine development
back mutation
when a live virus vaccine reverts back to it disease-causing phenotype
gene therapy
treatment of genetic disease by adding genes, using viruses to carry the new genes inside the cell
oncolytic virus
virus engineered to specifically infect and kill cancer cells
phage therapy
treatment of bacterial diseases using bacteriophages specific to a particular bacterium
vaccine
weakened solution of virus components, viruses, or other agents that produce an immune response | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/21%3A_Viruses/21.3%3A_Prevention_and_Treatment_of_Viral_Infections.txt |
Skills to Develop
• Describe prions and their basic properties
• Define viroids and their targets of infection
Prions and viroids are pathogens (agents with the ability to cause disease) that have simpler structures than viruses but, in the case of prions, still can produce deadly diseases.
Prions
Prions, so-called because they are proteinaceous, are infectious particles—smaller than viruses—that contain no nucleic acids (neither DNA nor RNA). Historically, the idea of an infectious agent that did not use nucleic acids was considered impossible, but pioneering work by Nobel Prize-winning biologist Stanley Prusiner has convinced the majority of biologists that such agents do indeed exist.
Fatal neurodegenerative diseases, such as kuru in humans and bovine spongiform encephalopathy (BSE) in cattle (commonly known as “mad cow disease”) were shown to be transmitted by prions. The disease was spread by the consumption of meat, nervous tissue, or internal organs between members of the same species. Kuru, native to humans in Papua New Guinea, was spread from human to human via ritualistic cannibalism. BSE, originally detected in the United Kingdom, was spread between cattle by the practice of including cattle nervous tissue in feed for other cattle. Individuals with kuru and BSE show symptoms of loss of motor control and unusual behaviors, such as uncontrolled bursts of laughter with kuru, followed by death. Kuru was controlled by inducing the population to abandon its ritualistic cannibalism.
On the other hand, BSE was initially thought to only affect cattle. Cattle dying of the disease were shown to have developed lesions or “holes” in the brain, causing the brain tissue to resemble a sponge. Later on in the outbreak, however, it was shown that a similar encephalopathy in humans known as variant Creutzfeldt-Jakob disease (CJD) could be acquired from eating beef from animals with BSE, sparking bans by various countries on the importation of British beef and causing considerable economic damage to the British beef industry (Figure \(1\)). BSE still exists in various areas, and although a rare disease, individuals that acquire CJD are difficult to treat. The disease can be spread from human to human by blood, so many countries have banned blood donation from regions associated with BSE.
The cause of spongiform encephalopathies, such as kuru and BSE, is an infectious structural variant of a normal cellular protein called PrP (prion protein). It is this variant that constitutes the prion particle. PrP exists in two forms, PrPc, the normal form of the protein, and PrPsc, the infectious form. Once introduced into the body, the PrPsc contained within the prion binds to PrPc and converts it to PrPsc. This leads to an exponential increase of the PrPsc protein, which aggregates. PrPsc is folded abnormally, and the resulting conformation (shape) is directly responsible for the lesions seen in the brains of infected cattle. Thus, although not without some detractors among scientists, the prion seems likely to be an entirely new form of infectious agent, the first one found whose transmission is not reliant upon genes made of DNA or RNA.
Viroids
Viroids are plant pathogens: small, single-stranded, circular RNA particles that are much simpler than a virus. They do not have a capsid or outer envelope, but like viruses can reproduce only within a host cell. Viroids do not, however, manufacture any proteins, and they only produce a single, specific RNA molecule. Human diseases caused by viroids have yet to be identified.
Viroids are known to infect plants (Figure \(2\)) and are responsible for crop failures and the loss of millions of dollars in agricultural revenue each year. Some of the plants they infect include potatoes, cucumbers, tomatoes, chrysanthemums, avocados, and coconut palms.
Career Connection: Virologist
Virology is the study of viruses, and a virologist is an individual trained in this discipline. Training in virology can lead to many different career paths. Virologists are actively involved in academic research and teaching in colleges and medical schools. Some virologists treat patients or are involved in the generation and production of vaccines. They might participate in epidemiologic studies (Figure \(3\)) or become science writers, to name just a few possible careers.
If you think you may be interested in a career in virology, find a mentor in the field. Many large medical centers have departments of virology, and smaller hospitals usually have virology labs within their microbiology departments. Volunteer in a virology lab for a semester or work in one over the summer. Discussing the profession and getting a first-hand look at the work will help you decide whether a career in virology is right for you. The American Society of Virology’s website is a good resource for information regarding training and careers in virology.
Summary
Prions are infectious agents that consist of protein, but no DNA or RNA, and seem to produce their deadly effects by duplicating their shapes and accumulating in tissues. They are thought to contribute to several progressive brain disorders, including mad cow disease and Creutzfeldt-Jakob disease. Viroids are single-stranded RNA pathogens that infect plants. Their presence can have a severe impact on the agriculture industry.
Glossary
pathogen
agent with the ability to cause disease
prion
infectious particle that consists of proteins that replicate without DNA or RNA
PrPc
normal prion protein
PrPsc
infectious form of a prion protein
viroid
plant pathogen that produces only a single, specific RNA | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/21%3A_Viruses/21.4%3A_Other_Acellular_Entities_-_Prions_and_Viroids.txt |
21.1: Viral Evolution, Morphology, and Classification
Viruses are diverse entities. They vary in their structure, their replication methods, and in their target hosts. Nearly all forms of life—from bacteria and archaea to eukaryotes such as plants, animals, and fungi—have viruses that infect them. While most biological diversity can be understood through evolutionary history, such as how species have adapted to conditions and environments, much about virus origins and evolution remains unknown.
Review Questions
Which statement is true?
1. A virion contains DNA and RNA.
2. Viruses are acellular.
3. Viruses replicate outside of the cell.
4. Most viruses are easily visualized with a light microscope.
Answer
B
The viral ________ plays a role in attaching a virion to the host cell.
1. core
2. capsid
3. envelope
4. both b and c
Answer
D
Viruses_______.
1. all have a round shape
2. cannot have a long shape
3. do not maintain any shape
4. vary in shape
Answer
D
Free Response
The first electron micrograph of a virus (tobacco mosaic virus) was produced in 1939. Before that time, how did scientists know that viruses existed if they could not see them? (Hint: Early scientists called viruses “filterable agents.”)
Answer
Viruses pass through filters that eliminated all bacteria that were visible in the light microscopes at the time. As the bacteria-free filtrate could still cause infections when given to a healthy organism, this observation demonstrated the existence of very small infectious agents. These agents were later shown to be unrelated to bacteria and were classified as viruses.
21.2: Virus Infections and Hosts
Viruses can be seen as obligate, intracellular parasites. A virus must attach to a living cell, be taken inside, manufacture its proteins and copy its genome, and find a way to escape the cell so that the virus can infect other cells. Viruses can infect only certain species of hosts and only certain cells within that host. Cells that a virus may use to replicate are called permissive.
Review Questions
Which statement is not true of viral replication?
1. A lysogenic cycle kills the host cell.
2. There are six basic steps in the viral replication cycle.
3. Viral replication does not affect host cell function.
4. Newly released virions can infect adjacent cells.
Answer
D
Which statement is true of viral replication?
1. In the process of apoptosis, the cell survives.
2. During attachment, the virus attaches at specific sites on the cell surface.
3. The viral capsid helps the host cell produce more copies of the viral genome.
4. mRNA works outside of the host cell to produce enzymes and proteins.
Answer
B
Which statement is true of reverse transcriptase?
1. It is a nucleic acid.
2. It infects cells.
3. It transcribes RNA to make DNA.
4. It is a lipid.
Answer
C
Oncogenic virus cores can be_______.
1. RNA
2. DNA
3. neither RNA nor DNA
4. either RNA or DNA
Answer
D
Which is true of DNA viruses?
1. They use the host cell’s machinery to produce new copies of their genome.
2. They all have envelopes.
3. They are the only kind of viruses that can cause cancer.
4. They are not important plant pathogens.
Answer
A
A bacteriophage can infect ________.
1. the lungs
2. viruses
3. prions
4. bacteria
Answer
D
Free Response
Why can’t dogs catch the measles?
Answer
The virus can’t attach to dog cells, because dog cells do not express the receptors for the virus and/or there is no cell within the dog that is permissive for viral replication.
One of the first and most important targets for drugs to fight infection with HIV (a retrovirus) is the reverse transcriptase enzyme. Why?
Answer
Reverse transcriptase is needed to make more HIV-1 viruses, so targeting the reverse transcriptase enzyme may be a way to inhibit the replication of the virus. Importantly, by targeting reverse transcriptase, we do little harm to the host cell, since host cells do not make reverse transcriptase. Thus, we can specifically attack the virus and not the host cell when we use reverse transcriptase inhibitors.
In this section, you were introduced to different types of viruses and viral diseases. Briefly discuss the most interesting or surprising thing you learned about viruses.
Answer
Answer is open and will vary.
Although plant viruses cannot infect humans, what are some of the ways in which they affect humans?
Answer
Plant viruses infect crops, causing crop damage and failure, and considerable economic losses.
21.3: Prevention and Treatment of Viral Infections
Viruses cause a variety of diseases in animals, including humans, ranging from the common cold to potentially fatal illnesses like meningitis . These diseases can be treated by antiviral drugs or by vaccines, but some viruses, such as HIV, are capable of both avoiding the immune response and mutating to become resistant to antiviral drugs.
Review Questions
Which of the following is NOT used to treat active viral disease?
1. vaccines
2. antiviral drugs
3. antibiotics
4. phage therapy
Answer
C
Vaccines_______.
1. are similar to viroids
2. are only needed once
3. kill viruses
4. stimulate an immune response
Answer
D
Free Response
Why is immunization after being bitten by a rabid animal so effective and why aren’t people vaccinated for rabies like dogs and cats are?
Answer
Rabies vaccine works after a bite because it takes week for the virus to travel from the site of the bite to the central nervous system, where the most severe symptoms of the disease occur. Adults are not routinely vaccinated for rabies for two reasons: first, because the routine vaccination of domestic animals makes it unlikely that humans will contract rabies from an animal bite; second, if one is bitten by a wild animal or a domestic animal that one cannot confirm has been immunized, there is still time to give the vaccine and avoid the often fatal consequences of the disease.
21.4: Other Acellular Entities - Prions and Viroids
Prions and viroids are pathogens (agents with the ability to cause disease) that have simpler structures than viruses but, in the case of prions, still can produce deadly diseases.
Review Questions
Which of the following is not associated with prions?
1. replicating shapes
2. mad cow disease
3. DNA
4. toxic proteins
Answer
C
Which statement is true of viroids?
1. They are single-stranded RNA particles.
2. They reproduce only outside of the cell.
3. They produce proteins.
4. They affect both plants and animals.
Answer
A
Free Response
Prions are responsible for variant Creutzfeldt-Jakob Disease, which has resulted in over 100 human deaths in Great Britain during the last 10 years. How do humans obtain this disease?
Answer
This prion-based disease is transmitted through human consumption of infected meat.
How are viroids like viruses?
Answer
They both replicate in a cell, and they both contain nucleic acid. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/21%3A_Viruses/21.E%3A_Viruses_%28Exercises%29.txt |
• 22.0: Prelude to Prokaryotes
Based on differences in the structure of cell membranes and in rRNA, Woese and his colleagues proposed that all life on Earth evolved along three lineages, called domains. The domain Bacteria comprises all organisms in the kingdom Bacteria, the domain Archaea comprises the rest of the prokaryotes, and the domain Eukarya comprises all eukaryotes—including organisms in the kingdoms Animalia, Plantae, Fungi, and Protista.
• 22.1: Prokaryotic Diversity
Prokaryotes are ubiquitous. They cover every imaginable surface where there is sufficient moisture, and they live on and inside of other living things. In the typical human body, prokaryotic cells outnumber human body cells by about ten to one. They comprise the majority of living things in all ecosystems. Some prokaryotes thrive in environments that are inhospitable for most living things.
• 22.2: Structure of Prokaryotes
There are many differences between prokaryotic and eukaryotic cells. However, all cells have four common structures: the plasma membrane, which functions as a barrier for the cell and separates the cell from its environment; the cytoplasm, a jelly-like substance inside the cell; nucleic acids, the genetic material of the cell; and ribosomes, where protein synthesis takes place.
• 22.3: Prokaryotic Metabolism
Prokaryotes are metabolically diverse organisms. There are many different environments on Earth with various energy and carbon sources, and variable conditions. Prokaryotes have been able to live in every environment by using whatever energy and carbon sources are available. Prokaryotes fill many niches on Earth, including being involved in nutrient cycles such as nitrogen and carbon cycles, decomposing dead organisms, and thriving inside living organisms, including humans.
• 22.4: Bacterial Diseases in Humans
Devastating pathogen-borne diseases and plagues, both viral and bacterial in nature, have affected humans since the beginning of human history. The true cause of these diseases was not understood at the time, and some people thought that diseases were a spiritual punishment. Over time, people came to realize that staying apart from afflicted persons, and disposing of the corpses and personal belongings of victims of illness, reduced their own chances of getting sick.
• 22.5: Beneficial Prokaryotes
Not all prokaryotes are pathogenic. On the contrary, pathogens represent only a very small percentage of the diversity of the microbial world. In fact, our life would not be possible without prokaryotes. Just think about the role of prokaryotes in biogeochemical cycles.
• 22.E: Prokaryotes - Bacteria and Archaea (Exercises)
Thumbnail: Scanning electron micrograph of neutrophil ingesting methicillin-resistant Staphylococcus aureus bacteria. (Public Domain; NIAID/NIH).
22: Prokaryotes - Bacteria and Archaea
In the recent past, scientists grouped living things into five kingdoms—animals, plants, fungi, protists, and prokaryotes—based on several criteria, such as the absence or presence of a nucleus and other membrane-bound organelles, the absence or presence of cell walls, multicellularity, and so on. In the late 20th century, the pioneering work of Carl Woese and others compared sequences of small-subunit ribosomal RNA (SSU rRNA), which resulted in a more fundamental way to group organisms on Earth. Based on differences in the structure of cell membranes and in rRNA, Woese and his colleagues proposed that all life on Earth evolved along three lineages, called domains. The domain Bacteria comprises all organisms in the kingdom Bacteria, the domain Archaea comprises the rest of the prokaryotes, and the domain Eukarya comprises all eukaryotes—including organisms in the kingdoms Animalia, Plantae, Fungi, and Protista.
Two of the three domains—Bacteria and Archaea—are prokaryotic. Prokaryotes were the first inhabitants on Earth, appearing 3.5 to 3.8 billion years ago. These organisms are abundant and ubiquitous; that is, they are present everywhere. In addition to inhabiting moderate environments, they are found in extreme conditions: from boiling springs to permanently frozen environments in Antarctica; from salty environments like the Dead Sea to environments under tremendous pressure, such as the depths of the ocean; and from areas without oxygen, such as a waste management plant, to radioactively contaminated regions, such as Chernobyl. Prokaryotes reside in the human digestive system and on the skin, are responsible for certain illnesses, and serve an important role in the preparation of many foods. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/22%3A_Prokaryotes_-_Bacteria_and_Archaea/22.0%3A_Prelude_to_Prokaryotes.txt |
Skills to Develop
• Describe the evolutionary history of prokaryotes
• Discuss the distinguishing features of extremophiles
• Explain why it is difficult to culture prokaryotes
Prokaryotes are ubiquitous. They cover every imaginable surface where there is sufficient moisture, and they live on and inside of other living things. In the typical human body, prokaryotic cells outnumber human body cells by about ten to one. They comprise the majority of living things in all ecosystems. Some prokaryotes thrive in environments that are inhospitable for most living things. Prokaryotes recycle nutrients—essential substances (such as carbon and nitrogen)—and they drive the evolution of new ecosystems, some of which are natural and others man-made. Prokaryotes have been on Earth since long before multicellular life appeared.
Prokaryotes, the First Inhabitants of Earth
When and where did life begin? What were the conditions on Earth when life began? Prokaryotes were the first forms of life on Earth, and they existed for billions of years before plants and animals appeared. The Earth and its moon are thought to be about 4.54 billion years old. This estimate is based on evidence from radiometric dating of meteorite material together with other substrate material from Earth and the moon. Early Earth had a very different atmosphere (contained less molecular oxygen) than it does today and was subjected to strong radiation; thus, the first organisms would have flourished where they were more protected, such as in ocean depths or beneath the surface of the Earth. At this time too, strong volcanic activity was common on Earth, so it is likely that these first organisms—the first prokaryotes—were adapted to very high temperatures. Early Earth was prone to geological upheaval and volcanic eruption, and was subject to bombardment by mutagenic radiation from the sun. The first organisms were prokaryotes that could withstand these harsh conditions.
Microbial Mats
Microbial mats or large biofilms may represent the earliest forms of life on Earth; there is fossil evidence of their presence starting about 3.5 billion years ago. A microbial mat is a multi-layered sheet of prokaryotes (Figure \(1\)) that includes mostly bacteria, but also archaea. Microbial mats are a few centimeters thick, and they typically grow where different types of materials interface, mostly on moist surfaces. The various types of prokaryotes that comprise them carry out different metabolic pathways, and that is the reason for their various colors. Prokaryotes in a microbial mat are held together by a glue-like sticky substance that they secrete called extracellular matrix.
The first microbial mats likely obtained their energy from chemicals found near hydrothermal vents. A hydrothermal vent is a breakage or fissure in the Earth’s surface that releases geothermally heated water. With the evolution of photosynthesis about 3 billion years ago, some prokaryotes in microbial mats came to use a more widely available energy source—sunlight—whereas others were still dependent on chemicals from hydrothermal vents for energy and food.
Stromatolites
Fossilized microbial mats represent the earliest record of life on Earth. A stromatolite is a sedimentary structure formed when minerals are precipitated out of water by prokaryotes in a microbial mat (Figure \(2\)). Stromatolites form layered rocks made of carbonate or silicate. Although most stromatolites are artifacts from the past, there are places on Earth where stromatolites are still forming. For example, growing stromatolites have been found in the Anza-Borrego Desert State Park in San Diego County, California.
The Ancient Atmosphere
Evidence indicates that during the first two billion years of Earth’s existence, the atmosphere was anoxic, meaning that there was no molecular oxygen. Therefore, only those organisms that can grow without oxygen—anaerobic organisms—were able to live. Autotrophic organisms that convert solar energy into chemical energy are called phototrophs, and they appeared within one billion years of the formation of Earth. Then, cyanobacteria, also known as blue-green algae, evolved from these simple phototrophs one billion years later. Cyanobacteria (Figure \(3\)) began the oxygenation of the atmosphere. Increased atmospheric oxygen allowed the development of more efficient O2-utilizing catabolic pathways. It also opened up the land to increased colonization, because some O2 is converted into O3 (ozone) and ozone effectively absorbs the ultraviolet light that would otherwise cause lethal mutations in DNA. Ultimately, the increase in O2 concentrations allowed the evolution of other life forms.
Microbes Are Adaptable: Life in Moderate and Extreme Environments
Some organisms have developed strategies that allow them to survive harsh conditions. Prokaryotes thrive in a vast array of environments: Some grow in conditions that would seem very normal to us, whereas others are able to thrive and grow under conditions that would kill a plant or animal. Almost all prokaryotes have a cell wall, a protective structure that allows them to survive in both hyper- and hypo-osmotic conditions. Some soil bacteria are able to form endospores that resist heat and drought, thereby allowing the organism to survive until favorable conditions recur. These adaptations, along with others, allow bacteria to be the most abundant life form in all terrestrial and aquatic ecosystems.
Other bacteria and archaea are adapted to grow under extreme conditions and are called extremophiles, meaning “lovers of extremes.” Extremophiles have been found in all kinds of environments: the depth of the oceans, hot springs, the Artic and the Antarctic, in very dry places, deep inside Earth, in harsh chemical environments, and in high radiation environments (Figure \(4\)), just to mention a few. These organisms give us a better understanding of prokaryotic diversity and open up the possibility of finding new prokaryotic species that may lead to the discovery of new therapeutic drugs or have industrial applications. Because they have specialized adaptations that allow them to live in extreme conditions, many extremophiles cannot survive in moderate environments. There are many different groups of extremophiles: They are identified based on the conditions in which they grow best, and several habitats are extreme in multiple ways. For example, a soda lake is both salty and alkaline, so organisms that live in a soda lake must be both alkaliphiles and halophiles (Table \(1\)). Other extremophiles, like radioresistant organisms, do not prefer an extreme environment (in this case, one with high levels of radiation), but have adapted to survive in it (Figure \(4\)).
Table \(1\): Extremophiles and Their Preferred Conditions
Extremophile Type Conditions for Optimal Growth
Acidophiles pH 3 or below
Alkaliphiles pH 9 or above
Thermophiles Temperature 60–80 °C (140–176 °F)
Hyperthermophiles Temperature 80–122 °C (176–250 °F)
Psychrophiles Temperature of -15-10 °C (5-50 °F) or lower
Halophiles Salt concentration of at least 0.2 M
Osmophiles High sugar concentration
Prokaryotes in the Dead Sea
One example of a very harsh environment is the Dead Sea, a hypersaline basin that is located between Jordan and Israel. Hypersaline environments are essentially concentrated seawater. In the Dead Sea, the sodium concentration is 10 times higher than that of seawater, and the water contains high levels of magnesium (about 40 times higher than in seawater) that would be toxic to most living things. Iron, calcium, and magnesium, elements that form divalent ions (Fe2+, Ca2+, and Mg2+), produce what is commonly referred to as “hard” water. Taken together, the high concentration of divalent cations, the acidic pH (6.0), and the intense solar radiation flux make the Dead Sea a unique, and uniquely hostile, ecosystem1 (Figure \(5\)).
What sort of prokaryotes do we find in the Dead Sea? The extremely salt-tolerant bacterial mats include Halobacterium, Haloferax volcanii (which is found in other locations, not only the Dead Sea), Halorubrum sodomense, and Halobaculum gomorrense, and the archaea Haloarcula marismortui, among others.
Unculturable Prokaryotes and the Viable-but-Non-Culturable State
Microbiologists typically grow prokaryotes in the laboratory using an appropriate culture medium containing all the nutrients needed by the target organism. The medium can be liquid, broth, or solid. After an incubation time at the right temperature, there should be evidence of microbial growth (Figure \(6\)). The process of culturing bacteria is complex and is one of the greatest discoveries of modern science. German physician Robert Koch is credited with discovering the techniques for pure culture, including staining and using growth media. His assistant Julius Petri invented the Petri dish whose use persists in today’s laboratories. Koch worked primarily with the Mycobacterium tuberculosis bacterium that causes tuberculosis and developed postulates to identify disease-causing organisms that continue to be widely used in the medical community. Koch’s postulates include that an organism can be identified as the cause of disease when it is present in all infected samples and absent in all healthy samples, and it is able to reproduce the infection after being cultured multiple times. Today, cultures remain a primary diagnostic tool in medicine and other areas of molecular biology.
Some prokaryotes, however, cannot grow in a laboratory setting. In fact, over 99 percent of bacteria and archaea are unculturable. For the most part, this is due to a lack of knowledge as to what to feed these organisms and how to grow them; they have special requirements for growth that remain unknown to scientists, such as needing specific micronutrients, pH, temperature, pressure, co-factors, or co-metabolites. Some bacteria cannot be cultured because they are obligate intracellular parasites and cannot be grown outside a host cell.
In other cases, culturable organisms become unculturable under stressful conditions, even though the same organism could be cultured previously. Those organisms that cannot be cultured but are not dead are in a viable-but-non-culturable (VBNC) state. The VBNC state occurs when prokaryotes respond to environmental stressors by entering a dormant state that allows their survival. The criteria for entering into the VBNC state are not completely understood. In a process called resuscitation, the prokaryote can go back to “normal” life when environmental conditions improve.
Is the VBNC state an unusual way of living for prokaryotes? In fact, most of the prokaryotes living in the soil or in oceanic waters are non-culturable. It has been said that only a small fraction, perhaps one percent, of prokaryotes can be cultured under laboratory conditions. If these organisms are non-culturable, then how is it known whether they are present and alive? Microbiologists use molecular techniques, such as the polymerase chain reaction (PCR), to amplify selected portions of DNA of prokaryotes, demonstrating their existence. Recall that PCR can make billions of copies of a DNA segment in a process called amplification.
The Ecology of Biofilms
Until a couple of decades ago, microbiologists used to think of prokaryotes as isolated entities living apart. This model, however, does not reflect the true ecology of prokaryotes, most of which prefer to live in communities where they can interact. A biofilm is a microbial community (Figure \(7\)) held together in a gummy-textured matrix that consists primarily of polysaccharides secreted by the organisms, together with some proteins and nucleic acids. Biofilms grow attached to surfaces. Some of the best-studied biofilms are composed of prokaryotes, although fungal biofilms have also been described as well as some composed of a mixture of fungi and bacteria.
Biofilms are present almost everywhere: they can cause the clogging of pipes and readily colonize surfaces in industrial settings. In recent, large-scale outbreaks of bacterial contamination of food, biofilms have played a major role. They also colonize household surfaces, such as kitchen counters, cutting boards, sinks, and toilets, as well as places on the human body, such as the surfaces of our teeth.
Interactions among the organisms that populate a biofilm, together with their protective exopolysaccharidic (EPS) environment, make these communities more robust than free-living, or planktonic, prokaryotes. The sticky substance that holds bacteria together also excludes most antibiotics and disinfectants, making biofilm bacteria hardier than their planktonic counterparts. Overall, biofilms are very difficult to destroy because they are resistant to many common forms of sterilization.
Art Connection
Compared to free-floating bacteria, bacteria in biofilms often show increased resistance to antibiotics and detergents. Why do you think this might be the case?
Summary
Prokaryotes existed for billions of years before plants and animals appeared. Hot springs and hydrothermal vents may have been the environments in which life began. Microbial mats are thought to represent the earliest forms of life on Earth, and there is fossil evidence of their presence about 3.5 billion years ago. A microbial mat is a multi-layered sheet of prokaryotes that grows at interfaces between different types of material, mostly on moist surfaces. During the first 2 billion years, the atmosphere was anoxic and only anaerobic organisms were able to live. Cyanobacteria evolved from early phototrophs and began the oxygenation of the atmosphere. The increase in oxygen concentration allowed the evolution of other life forms. Fossilized microbial mats are called stromatolites and consist of laminated organo-sedimentary structures formed by precipitation of minerals by prokaryotes. They represent the earliest fossil record of life on Earth.
Bacteria and archaea grow in virtually every environment. Those that survive under extreme conditions are called extremophiles (extreme lovers). Some prokaryotes cannot grow in a laboratory setting, but they are not dead. They are in the viable-but-non-culturable (VBNC) state. The VBNC state occurs when prokaryotes enter a dormant state in response to environmental stressors. Most prokaryotes are social and prefer to live in communities where interactions take place. A biofilm is a microbial community held together in a gummy-textured matrix.
Art Connections
Figure \(7\): Compared to free-floating bacteria, bacteria in biofilms often show increased resistance to antibiotics and detergents. Why do you think this might be the case?
Answer
The extracellular matrix and outer layer of cells protects the inner bacteria. The close proximity of cells also facilitates lateral gene transfer, a process by which genes such as antibiotic resistance genes are transferred from one bacterium to another. And even if lateral gene transfer does not occur, one bacterium that produces an exo-enzyme that destroys antibiotic may save neighboring bacteria.
Footnotes
1. 1 Bodaker, I, Itai, S, Suzuki, MT, Feingersch, R, Rosenberg, M, Maguire, ME, Shimshon, B, and others. Comparative community genomics in the Dead Sea: An increasingly extreme environment. The ISME Journal 4 (2010): 399–407, doi:10.1038/ismej.2009.141. published online 24 December 2009.
Glossary
acidophile
organism with optimal growth pH of three or below
alkaliphile
organism with optimal growth pH of nine or above
anaerobic
refers to organisms that grow without oxygen
anoxic
without oxygen
biofilm
microbial community that is held together by a gummy-textured matrix
cyanobacteria
bacteria that evolved from early phototrophs and oxygenated the atmosphere; also known as blue-green algae
extremophile
organism that grows under extreme or harsh conditions
halophile
organism that require a salt concentration of at least 0.2 M
hydrothermal vent
fissure in Earth’s surface that releases geothermally heated water
hyperthermophile
organism that grows at temperatures between 80–122 °C
microbial mat
multi-layered sheet of prokaryotes that may include bacteria and archaea
nutrient
essential substances for growth, such as carbon and nitrogen
osmophile
organism that grows in a high sugar concentration
phototroph
organism that is able to make its own food by converting solar energy to chemical energy
psychrophile
organism that grows at temperatures of -15 °C or lower
radioresistant
organism that grows in high levels of radiation
resuscitation
process by which prokaryotes that are in the VBNC state return to viability
stromatolite
layered sedimentary structure formed by precipitation of minerals by prokaryotes in microbial mats
thermophile
organism that lives at temperatures between 60–80 °C
viable-but-non-culturable (VBNC) state
survival mechanism of bacteria facing environmental stress conditions | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/22%3A_Prokaryotes_-_Bacteria_and_Archaea/22.1%3A_Prokaryotic_Diversity.txt |
Skills to Develop
• Describe the basic structure of a typical prokaryote
• Describe important differences in structure between Archaea and Bacteria
There are many differences between prokaryotic and eukaryotic cells. However, all cells have four common structures: the plasma membrane, which functions as a barrier for the cell and separates the cell from its environment; the cytoplasm, a jelly-like substance inside the cell; nucleic acids, the genetic material of the cell; and ribosomes, where protein synthesis takes place. Prokaryotes come in various shapes, but many fall into three categories: cocci (spherical), bacilli (rod-shaped), and spirilli (spiral-shaped) (Figure \(1\)).
The Prokaryotic Cell
Recall that prokaryotes (Figure \(2\)) are unicellular organisms that lack organelles or other internal membrane-bound structures. Therefore, they do not have a nucleus but instead generally have a single chromosome—a piece of circular, double-stranded DNA located in an area of the cell called the nucleoid. Most prokaryotes have a cell wall outside the plasma membrane.
Recall that prokaryotes are divided into two different domains, Bacteria and Archaea, which together with Eukarya, comprise the three domains of life (Figure \(3\)).
The composition of the cell wall differs significantly between the domains Bacteria and Archaea. The composition of their cell walls also differs from the eukaryotic cell walls found in plants (cellulose) or fungi and insects (chitin). The cell wall functions as a protective layer, and it is responsible for the organism’s shape. Some bacteria have an outer capsule outside the cell wall. Other structures are present in some prokaryotic species, but not in others (Table \(1\)). For example, the capsule found in some species enables the organism to attach to surfaces, protects it from dehydration and attack by phagocytic cells, and makes pathogens more resistant to our immune responses. Some species also have flagella (singular, flagellum) used for locomotion, and pili (singular, pilus) used for attachment to surfaces. Plasmids, which consist of extra-chromosomal DNA, are also present in many species of bacteria and archaea.
Characteristics of phyla of Bacteria are described in Figure \(4\) and Figure \(5\); Archaea are described in Figure \(6\).
The Plasma Membrane
The plasma membrane is a thin lipid bilayer (6 to 8 nanometers) that completely surrounds the cell and separates the inside from the outside. Its selectively permeable nature keeps ions, proteins, and other molecules within the cell and prevents them from diffusing into the extracellular environment, while other molecules may move through the membrane. Recall that the general structure of a cell membrane is a phospholipid bilayer composed of two layers of lipid molecules. In archaeal cell membranes, isoprene (phytanyl) chains linked to glycerol replace the fatty acids linked to glycerol in bacterial membranes. Some archaeal membranes are lipid monolayers instead of bilayers (Figure \(7\)).
The Cell Wall
The cytoplasm of prokaryotic cells has a high concentration of dissolved solutes. Therefore, the osmotic pressure within the cell is relatively high. The cell wall is a protective layer that surrounds some cells and gives them shape and rigidity. It is located outside the cell membrane and prevents osmotic lysis (bursting due to increasing volume). The chemical composition of the cell walls varies between archaea and bacteria, and also varies between bacterial species.
Bacterial cell walls contain peptidoglycan, composed of polysaccharide chains that are cross-linked by unusual peptides containing both L- and D-amino acids including D-glutamic acid and D-alanine. Proteins normally have only L-amino acids; as a consequence, many of our antibiotics work by mimicking D-amino acids and therefore have specific effects on bacterial cell wall development. There are more than 100 different forms of peptidoglycan. S-layer (surface layer) proteins are also present on the outside of cell walls of both archaea and bacteria.
Bacteria are divided into two major groups: Gram positive and Gram negative, based on their reaction to Gram staining. Note that all Gram-positive bacteria belong to one phylum; bacteria in the other phyla (Proteobacteria, Chlamydias, Spirochetes, Cyanobacteria, and others) are Gram-negative. The Gram staining method is named after its inventor, Danish scientist Hans Christian Gram (1853–1938). The different bacterial responses to the staining procedure are ultimately due to cell wall structure. Gram-positive organisms typically lack the outer membrane found in Gram-negative organisms (Figure \(8\)). Up to 90 percent of the cell wall in Gram-positive bacteria is composed of peptidoglycan, and most of the rest is composed of acidic substances called teichoic acids. Teichoic acids may be covalently linked to lipids in the plasma membrane to form lipoteichoic acids. Lipoteichoic acids anchor the cell wall to the cell membrane. Gram-negative bacteria have a relatively thin cell wall composed of a few layers of peptidoglycan (only 10 percent of the total cell wall), surrounded by an outer envelope containing lipopolysaccharides (LPS) and lipoproteins. This outer envelope is sometimes referred to as a second lipid bilayer. The chemistry of this outer envelope is very different, however, from that of the typical lipid bilayer that forms plasma membranes.
Art Connection
Which of the following statements is true?
1. Gram-positive bacteria have a single cell wall anchored to the cell membrane by lipoteichoic acid.
2. Porins allow entry of substances into both Gram-positive and Gram-negative bacteria.
3. The cell wall of Gram-negative bacteria is thick, and the cell wall of Gram-positive bacteria is thin.
4. Gram-negative bacteria have a cell wall made of peptidoglycan, whereas Gram-positive bacteria have a cell wall made of lipoteichoic acid.
Archaean cell walls do not have peptidoglycan. There are four different types of Archaean cell walls. One type is composed of pseudopeptidoglycan, which is similar to peptidoglycan in morphology but contains different sugars in the polysaccharide chain. The other three types of cell walls are composed of polysaccharides, glycoproteins, or pure protein.
Table \(1\): Structural Differences and Similarities between Bacteria and Archaea
Structural Characteristic Bacteria Archaea
Cell type Prokaryotic Prokaryotic
Cell morphology Variable Variable
Cell wall Contains peptidoglycan Does not contain peptidoglycan
Cell membrane type Lipid bilayer Lipid bilayer or lipid monolayer
Plasma membrane lipids Fatty acids Phytanyl groups
Reproduction
Reproduction in prokaryotes is asexual and usually takes place by binary fission. Recall that the DNA of a prokaryote exists as a single, circular chromosome. Prokaryotes do not undergo mitosis. Rather the chromosome is replicated and the two resulting copies separate from one another, due to the growth of the cell. The prokaryote, now enlarged, is pinched inward at its equator and the two resulting cells, which are clones, separate. Binary fission does not provide an opportunity for genetic recombination or genetic diversity, but prokaryotes can share genes by three other mechanisms.
In transformation, the prokaryote takes in DNA found in its environment that is shed by other prokaryotes. If a nonpathogenic bacterium takes up DNA for a toxin gene from a pathogen and incorporates the new DNA into its own chromosome, it too may become pathogenic. In transduction, bacteriophages, the viruses that infect bacteria, sometimes also move short pieces of chromosomal DNA from one bacterium to another. Transduction results in a recombinant organism. Archaea are not affected by bacteriophages but instead have their own viruses that translocate genetic material from one individual to another. In conjugation, DNA is transferred from one prokaryote to another by means of a pilus, which brings the organisms into contact with one another. The DNA transferred can be in the form of a plasmid or as a hybrid, containing both plasmid and chromosomal DNA. These three processes of DNA exchange are shown in Figure \(9\).
Reproduction can be very rapid: a few minutes for some species. This short generation time coupled with mechanisms of genetic recombination and high rates of mutation result in the rapid evolution of prokaryotes, allowing them to respond to environmental changes (such as the introduction of an antibiotic) very quickly.
Evolution Connection: The Evolution of Prokaryotes
How do scientists answer questions about the evolution of prokaryotes? Unlike with animals, artifacts in the fossil record of prokaryotes offer very little information. Fossils of ancient prokaryotes look like tiny bubbles in rock. Some scientists turn to genetics and to the principle of the molecular clock, which holds that the more recently two species have diverged, the more similar their genes (and thus proteins) will be. Conversely, species that diverged long ago will have more genes that are dissimilar.
Scientists at the NASA Astrobiology Institute and at the European Molecular Biology Laboratory collaborated to analyze the molecular evolution of 32 specific proteins common to 72 species of prokaryotes.1 The model they derived from their data indicates that three important groups of bacteria—Actinobacteria, Deinococcus, and Cyanobacteria (which the authors call Terrabacteria)—were the first to colonize land. (Recall that Deinococcus is a genus of prokaryote—a bacterium—that is highly resistant to ionizing radiation.) Cyanobacteria are photosynthesizers, while Actinobacteria are a group of very common bacteria that include species important in decomposition of organic wastes.
The timelines of divergence suggest that bacteria (members of the domain Bacteria) diverged from common ancestral species between 2.5 and 3.2 billion years ago, whereas archaea diverged earlier: between 3.1 and 4.1 billion years ago. Eukarya later diverged off the Archaean line. The work further suggests that stromatolites that formed prior to the advent of cyanobacteria (about 2.6 billion years ago) photosynthesized in an anoxic environment and that because of the modifications of the Terrabacteria for land (resistance to drying and the possession of compounds that protect the organism from excess light), photosynthesis using oxygen may be closely linked to adaptations to survive on land.
Summary
Prokaryotes (domains Archaea and Bacteria) are single-celled organisms lacking a nucleus. They have a single piece of circular DNA in the nucleoid area of the cell. Most prokaryotes have a cell wall that lies outside the boundary of the plasma membrane. Some prokaryotes may have additional structures such as a capsule, flagella, and pili. Bacteria and Archaea differ in the lipid composition of their cell membranes and the characteristics of the cell wall. In archaeal membranes, phytanyl units, rather than fatty acids, are linked to glycerol. Some archaeal membranes are lipid monolayers instead of bilayers.
The cell wall is located outside the cell membrane and prevents osmotic lysis. The chemical composition of cell walls varies between species. Bacterial cell walls contain peptidoglycan. Archaean cell walls do not have peptidoglycan, but they may have pseudopeptidoglycan, polysaccharides, glycoproteins, or protein-based cell walls. Bacteria can be divided into two major groups: Gram positive and Gram negative, based on the Gram stain reaction. Gram-positive organisms have a thick cell wall, together with teichoic acids. Gram-negative organisms have a thin cell wall and an outer envelope containing lipopolysaccharides and lipoproteins.
Art Connections
Figure \(8\): Which of the following statements is true?
1. Gram-positive bacteria have a single cell wall anchored to the cell membrane by lipoteichoic acid.
2. Porins allow entry of substances into both Gram-positive and Gram-negative bacteria.
3. The cell wall of Gram-negative bacteria is thick, and the cell wall of Gram-positive bacteria is thin.
4. Gram-negative bacteria have a cell wall made of peptidoglycan, whereas Gram-positive bacteria have a cell wall made of lipoteichoic acid.
Answer
A
Footnotes
1. 1 Battistuzzi, FU, Feijao, A, and Hedges, SB. A genomic timescale of prokaryote evolution: Insights into the origin of methanogenesis, phototrophy, and the colonization of land. BioMed Central: Evolutionary Biology 4 (2004): 44, doi:10.1186/1471-2148-4-44.
Glossary
capsule
external structure that enables a prokaryote to attach to surfaces and protects it from dehydration
conjugation
process by which prokaryotes move DNA from one individual to another using a pilus
Gram negative
bacterium whose cell wall contains little peptidoglycan but has an outer membrane
Gram positive
bacterium that contains mainly peptidoglycan in its cell walls
peptidoglycan
material composed of polysaccharide chains cross-linked to unusual peptides
pilus
surface appendage of some prokaryotes used for attachment to surfaces including other prokaryotes
pseudopeptidoglycan
component of archaea cell walls that is similar to peptidoglycan in morphology but contains different sugars
S-layer
surface-layer protein present on the outside of cell walls of archaea and bacteria
teichoic acid
polymer associated with the cell wall of Gram-positive bacteria
transduction
process by which a bacteriophage moves DNA from one prokaryote to another
transformation
process by which a prokaryote takes in DNA found in its environment that is shed by other prokaryotes | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/22%3A_Prokaryotes_-_Bacteria_and_Archaea/22.2%3A_Structure_of_Prokaryotes.txt |
Skills to Develop
• Identify the macronutrients needed by prokaryotes, and explain their importance
• Describe the ways in which prokaryotes get energy and carbon for life processes
• Describe the roles of prokaryotes in the carbon and nitrogen cycles
Prokaryotes are metabolically diverse organisms. There are many different environments on Earth with various energy and carbon sources, and variable conditions. Prokaryotes have been able to live in every environment by using whatever energy and carbon sources are available. Prokaryotes fill many niches on Earth, including being involved in nutrient cycles such as nitrogen and carbon cycles, decomposing dead organisms, and thriving inside living organisms, including humans. The very broad range of environments that prokaryotes occupy is possible because they have diverse metabolic processes.
Needs of Prokaryotes
The diverse environments and ecosystems on Earth have a wide range of conditions in terms of temperature, available nutrients, acidity, salinity, and energy sources. Prokaryotes are very well equipped to make their living out of a vast array of nutrients and conditions. To live, prokaryotes need a source of energy, a source of carbon, and some additional nutrients.
Macronutrients
Cells are essentially a well-organized assemblage of macromolecules and water. Recall that macromolecules are produced by the polymerization of smaller units called monomers. For cells to build all of the molecules required to sustain life, they need certain substances, collectively called nutrients. When prokaryotes grow in nature, they obtain their nutrients from the environment. Nutrients that are required in large amounts are called macronutrients, whereas those required in smaller or trace amounts are called micronutrients. Just a handful of elements are considered macronutrients—carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. (A mnemonic for remembering these elements is the acronym CHONPS.)
Why are these macronutrients needed in large amounts? They are the components of organic compounds in cells, including water. Carbon is the major element in all macromolecules: carbohydrates, proteins, nucleic acids, lipids, and many other compounds. Carbon accounts for about 50 percent of the composition of the cell. Nitrogen represents 12 percent of the total dry weight of a typical cell and is a component of proteins, nucleic acids, and other cell constituents. Most of the nitrogen available in nature is either atmospheric nitrogen (N2) or another inorganic form. Diatomic (N2) nitrogen, however, can be converted into an organic form only by certain organisms, called nitrogen-fixing organisms. Both hydrogen and oxygen are part of many organic compounds and of water. Phosphorus is required by all organisms for the synthesis of nucleotides and phospholipids. Sulfur is part of the structure of some amino acids such as cysteine and methionine, and is also present in several vitamins and coenzymes. Other important macronutrients are potassium (K), magnesium (Mg), calcium (Ca), and sodium (Na). Although these elements are required in smaller amounts, they are very important for the structure and function of the prokaryotic cell.
Micronutrients
In addition to these macronutrients, prokaryotes require various metallic elements in small amounts. These are referred to as micronutrients or trace elements. For example, iron is necessary for the function of the cytochromes involved in electron-transport reactions. Some prokaryotes require other elements—such as boron (B), chromium (Cr), and manganese (Mn)—primarily as enzyme cofactors.
The Ways in Which Prokaryotes Obtain Energy
Prokaryotes can use different sources of energy to assemble macromolecules from smaller molecules. Phototrophs (or phototrophic organisms) obtain their energy from sunlight. Chemotrophs (or chemosynthetic organisms) obtain their energy from chemical compounds. Chemotrophs that can use organic compounds as energy sources are called chemoorganotrophs. Those that can also use inorganic compounds as energy sources are called chemolitotrophs.
The Ways in Which Prokaryotes Obtain Carbon
Prokaryotes not only can use different sources of energy but also different sources of carbon compounds. Recall that organisms that are able to fix inorganic carbon are called autotrophs. Autotrophic prokaryotes synthesize organic molecules from carbon dioxide. In contrast, heterotrophic prokaryotes obtain carbon from organic compounds. To make the picture more complex, the terms that describe how prokaryotes obtain energy and carbon can be combined. Thus, photoautotrophs use energy from sunlight, and carbon from carbon dioxide and water, whereas chemoheterotrophs obtain energy and carbon from an organic chemical source. Chemolitoautotrophs obtain their energy from inorganic compounds, and they build their complex molecules from carbon dioxide. Table \(1\) summarizes carbon and energy sources in prokaryotes.
Table \(1\): Carbon and Energy Sources in Prokaryotes
Energy Sources Carbon Sources
Light Chemicals Carbon dioxide Organic compounds
Phototrophs Chemotrophs Autotrophs Heterotrophs
Organic chemicals Inorganic chemicals
Chemo-organotrophs Chemolithotrophs
Role of Prokaryotes in Ecosystems
Prokaryotes are ubiquitous: There is no niche or ecosystem in which they are not present. Prokaryotes play many roles in the environments they occupy. The roles they play in the carbon and nitrogen cycles are vital to life on Earth.
Prokaryotes and the Carbon Cycle
Carbon is one of the most important macronutrients, and prokaryotes play an important role in the carbon cycle (Figure \(1\)). Carbon is cycled through Earth’s major reservoirs: land, the atmosphere, aquatic environments, sediments and rocks, and biomass. The movement of carbon is via carbon dioxide, which is removed from the atmosphere by land plants and marine prokaryotes, and is returned to the atmosphere via the respiration of chemoorganotrophic organisms, including prokaryotes, fungi, and animals. Although the largest carbon reservoir in terrestrial ecosystems is in rocks and sediments, that carbon is not readily available.
A large amount of available carbon is found in land plants. Plants, which are producers, use carbon dioxide from the air to synthesize carbon compounds. Related to this, one very significant source of carbon compounds is humus, which is a mixture of organic materials from dead plants and prokaryotes that have resisted decomposition. Consumers such as animals use organic compounds generated by producers and release carbon dioxide to the atmosphere. Then, bacteria and fungi, collectively called decomposers, carry out the breakdown (decomposition) of plants and animals and their organic compounds. The most important contributor of carbon dioxide to the atmosphere is microbial decomposition of dead material (dead animals, plants, and humus) that undergo respiration.
In aqueous environments and their anoxic sediments, there is another carbon cycle taking place. In this case, the cycle is based on one-carbon compounds. In anoxic sediments, prokaryotes, mostly archaea, produce methane (CH4). This methane moves into the zone above the sediment, which is richer in oxygen and supports bacteria called methane oxidizers that oxidize methane to carbon dioxide, which then returns to the atmosphere.
Prokaryotes and the Nitrogen Cycle
Nitrogen is a very important element for life because it is part of proteins and nucleic acids. It is a macronutrient, and in nature, it is recycled from organic compounds to ammonia, ammonium ions, nitrate, nitrite, and nitrogen gas by myriad processes, many of which are carried out only by prokaryotes. As illustrated in Figure \(2\), prokaryotes are key to the nitrogen cycle. The largest pool of nitrogen available in the terrestrial ecosystem is gaseous nitrogen from the air, but this nitrogen is not usable by plants, which are primary producers. Gaseous nitrogen is transformed, or “fixed” into more readily available forms such as ammonia through the process of nitrogen fixation. Ammonia can be used by plants or converted to other forms.
Another source of ammonia is ammonification, the process by which ammonia is released during the decomposition of nitrogen-containing organic compounds. Ammonia released to the atmosphere, however, represents only 15 percent of the total nitrogen released; the rest is as N2 and N2O. Ammonia is catabolized anaerobically by some prokaryotes, yielding N2 as the final product. Nitrification is the conversion of ammonium to nitrite and nitrate. Nitrification in soils is carried out by bacteria belonging to the genera Nitrosomas, Nitrobacter, and Nitrospira. The bacteria performs the reverse process, the reduction of nitrate from the soils to gaseous compounds such as N2O, NO, and N2, a process called denitrification.
Art Connection
Which of the following statements about the nitrogen cycle is false?
1. Nitrogen fixing bacteria exist on the root nodules of legumes and in the soil.
2. Denitrifying bacteria convert nitrates (\(\ce{NO_3^-}\)) into nitrogen gas (\(\ce{N_2}\)).
3. Ammonification is the process by which ammonium ion (\(\ce{NH_4^+}\)) is released from decomposing organic compounds.
4. Nitrification is the process by which nitrites (\(\ce{NO_2^-}\)) are converted to ammonium ion (\(\ce{NH_4^+}\)).
Summary
Prokaryotes are the most metabolically diverse organisms; they flourish in many different environments with various carbon energy and carbon sources, variable temperature, pH, pressure, and water availability. Nutrients required in large amounts are called macronutrients, whereas those required in trace amounts are called micronutrients or trace elements. Macronutrients include C, H, O, N, P, S, K, Mg, Ca, and Na. In addition to these macronutrients, prokaryotes require various metallic elements for growth and enzyme function. Prokaryotes use different sources of energy to assemble macromolecules from smaller molecules. Phototrophs obtain their energy from sunlight, whereas chemotrophs obtain energy from chemical compounds.
Prokaryotes play roles in the carbon and nitrogen cycles. Carbon is returned to the atmosphere by the respiration of animals and other chemoorganotrophic organisms. Consumers use organic compounds generated by producers and release carbon dioxide into the atmosphere. The most important contributor of carbon dioxide to the atmosphere is microbial decomposition of dead material. Nitrogen is recycled in nature from organic compounds to ammonia, ammonium ions, nitrite, nitrate, and nitrogen gas. Gaseous nitrogen is transformed into ammonia through nitrogen fixation. Ammonia is anaerobically catabolized by some prokaryotes, yielding N2 as the final product. Nitrification is the conversion of ammonium into nitrite. Nitrification in soils is carried out by bacteria. Denitrification is also performed by bacteria and transforms nitrate from soils into gaseous nitrogen compounds, such as N2O, NO, and N2.
Art Connections
Figure \(2\): Which of the following statements about the nitrogen cycle is false?
1. Nitrogen fixing bacteria exist on the root nodules of legumes and in the soil.
2. Denitrifying bacteria convert nitrates (NO3-) into nitrogen gas (N2).
3. Ammonification is the process by which ammonium ion (NH4+) is released from decomposing organic compounds.
4. Nitrification is the process by which nitrites (NO2-) are converted to ammonium ion (NH4+).
Answer
D
Glossary
ammonification
process by which ammonia is released during the decomposition of nitrogen-containing organic compounds
chemotroph
organism that obtains energy from chemical compounds
decomposer
organism that carries out the decomposition of dead organisms
denitrification
transformation of nitrate from soil to gaseous nitrogen compounds such as N2O, NO and N2
nitrification
conversion of ammonium into nitrite and nitrate in soils
nitrogen fixation
process by which gaseous nitrogen is transformed, or “fixed” into more readily available forms such as ammonia | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/22%3A_Prokaryotes_-_Bacteria_and_Archaea/22.3%3A_Prokaryotic_Metabolism.txt |
Skills to Develop
• Identify bacterial diseases that caused historically important plagues and epidemics
• Describe the link between biofilms and foodborne diseases
• Explain how overuse of antibiotic may be creating “super bugs”
• Explain the importance of MRSA with respect to the problems of antibiotic resistance
Devastating pathogen-borne diseases and plagues, both viral and bacterial in nature, have affected humans since the beginning of human history. The true cause of these diseases was not understood at the time, and some people thought that diseases were a spiritual punishment. Over time, people came to realize that staying apart from afflicted persons, and disposing of the corpses and personal belongings of victims of illness, reduced their own chances of getting sick.
Epidemiologists study how diseases affect a population. An epidemic is a disease that occurs in an unusually high number of individuals in a population at the same time. A pandemic is a widespread, usually worldwide, epidemic. An endemic disease is a disease that is constantly present, usually at low incidence, in a population.
Long History of Bacterial Disease
There are records about infectious diseases as far back as 3000 B.C. A number of significant pandemics caused by bacteria have been documented over several hundred years. Some of the most memorable pandemics led to the decline of cities and nations.
In the 21st century, infectious diseases remain among the leading causes of death worldwide, despite advances made in medical research and treatments in recent decades. A disease spreads when the pathogen that causes it is passed from one person to another. For a pathogen to cause disease, it must be able to reproduce in the host’s body and damage the host in some way.
The Plague of Athens
In 430 B.C., the Plague of Athens killed one-quarter of the Athenian troops that were fighting in the great Peloponnesian War and weakened Athens’ dominance and power. The plague impacted people living in overcrowded Athens as well as troops aboard ships that had to return to Athens. The source of the plague may have been identified recently when researchers from the University of Athens were able to use DNA from teeth recovered from a mass grave. The scientists identified nucleotide sequences from a pathogenic bacterium, Salmonella enterica serovar Typhi (Figure \(1\)), which causes typhoid fever.1 This disease is commonly seen in overcrowded areas and has caused epidemics throughout recorded history.
Bubonic Plagues
From 541 to 750, an outbreak of what was likely a bubonic plague (the Plague of Justinian), eliminated one-quarter to one-half of the human population in the eastern Mediterranean region. The population in Europe dropped by 50 percent during this outbreak. Bubonic plague would strike Europe more than once.
One of the most devastating pandemics was the Black Death (1346 to 1361) that is believed to have been another outbreak of bubonic plague caused by the bacterium Yersinia pestis. It is thought to have originated initially in China and spread along the Silk Road, a network of land and sea trade routes, to the Mediterranean region and Europe, carried by rat fleas living on black rats that were always present on ships. The Black Death reduced the world’s population from an estimated 450 million to about 350 to 375 million. Bubonic plague struck London hard again in the mid-1600s (Figure \(2\)). In modern times, approximately 1,000 to 3,000 cases of plague arise globally each year. Although contracting bubonic plague before antibiotics meant almost certain death, the bacterium responds to several types of modern antibiotics, and mortality rates from plague are now very low.
Link to Learning
Watch a video on the modern understanding of the Black Death—bubonic plague in Europe during the 14th century.
Migration of Diseases to New Populations
Over the centuries, Europeans tended to develop genetic immunity to endemic infectious diseases, but when European conquerors reached the western hemisphere, they brought with them disease-causing bacteria and viruses, which triggered epidemics that completely devastated populations of Native Americans, who had no natural resistance to many European diseases. It has been estimated that up to 90 percent of Native Americans died from infectious diseases after the arrival of Europeans, making conquest of the New World a foregone conclusion.
Emerging and Re-emerging Diseases
The distribution of a particular disease is dynamic. Therefore, changes in the environment, the pathogen, or the host population can dramatically impact the spread of a disease. According to the World Health Organization (WHO) an emerging disease (Figure \(3\)) is one that has appeared in a population for the first time, or that may have existed previously but is rapidly increasing in incidence or geographic range. This definition also includes re-emerging diseases that were previously under control. Approximately 75 percent of recently emerging infectious diseases affecting humans are zoonotic diseases, zoonoses, diseases that primarily infect animals and are transmitted to humans; some are of viral origin and some are of bacterial origin. Brucellosis is an example of a prokaryotic zoonosis that is re-emerging in some regions, and necrotizing fasciitis (commonly known as flesh-eating bacteria) has been increasing in virulence for the last 80 years for unknown reasons.
Some of the present emerging diseases are not actually new, but are diseases that were catastrophic in the past (Figure \(4\)). They devastated populations and became dormant for a while, just to come back, sometimes more virulent than before, as was the case with bubonic plague. Other diseases, like tuberculosis, were never eradicated but were under control in some regions of the world until coming back, mostly in urban centers with high concentrations of immunocompromised people. The WHO has identified certain diseases whose worldwide re-emergence should be monitored. Among these are two viral diseases (dengue fever and yellow fever), and three bacterial diseases (diphtheria, cholera, and bubonic plague). The war against infectious diseases has no foreseeable end.
Biofilms and Disease
Recall that biofilms are microbial communities that are very difficult to destroy. They are responsible for diseases such as infections in patients with cystic fibrosis, Legionnaires’ disease, and otitis media. They produce dental plaque and colonize catheters, prostheses, transcutaneous and orthopedic devices, contact lenses, and internal devices such as pacemakers. They also form in open wounds and burned tissue. In healthcare environments, biofilms grow on hemodialysis machines, mechanical ventilators, shunts, and other medical equipment. In fact, 65 percent of all infections acquired in the hospital (nosocomial infections) are attributed to biofilms. Biofilms are also related to diseases contracted from food because they colonize the surfaces of vegetable leaves and meat, as well as food-processing equipment that isn’t adequately cleaned.
Biofilm infections develop gradually; sometimes, they do not cause symptoms immediately. They are rarely resolved by host defense mechanisms. Once an infection by a biofilm is established, it is very difficult to eradicate, because biofilms tend to be resistant to most of the methods used to control microbial growth, including antibiotics. Biofilms respond poorly or only temporarily to antibiotics; it has been said that they can resist up to 1,000 times the antibiotic concentrations used to kill the same bacteria when they are free-living or planktonic. An antibiotic dose that large would harm the patient; therefore, scientists are working on new ways to get rid of biofilms.
Antibiotics: Are We Facing a Crisis?
The word antibiotic comes from the Greek anti meaning “against” and bios meaning “life.” An antibiotic is a chemical, produced either by microbes or synthetically, that is hostile to the growth of other organisms. Today’s news and media often address concerns about an antibiotic crisis. Are the antibiotics that easily treated bacterial infections in the past becoming obsolete? Are there new “superbugs”—bacteria that have evolved to become more resistant to our arsenal of antibiotics? Is this the beginning of the end of antibiotics? All these questions challenge the healthcare community.
One of the main causes of resistant bacteria is the abuse of antibiotics. The imprudent and excessive use of antibiotics has resulted in the natural selection of resistant forms of bacteria. The antibiotic kills most of the infecting bacteria, and therefore only the resistant forms remain. These resistant forms reproduce, resulting in an increase in the proportion of resistant forms over non-resistant ones. Another major misuse of antibiotics is in patients with colds or the flu, for which antibiotics are useless. Another problem is the excessive use of antibiotics in livestock. The routine use of antibiotics in animal feed promotes bacterial resistance as well. In the United States, 70 percent of the antibiotics produced are fed to animals. These antibiotics are given to livestock in low doses, which maximize the probability of resistance developing, and these resistant bacteria are readily transferred to humans.
Link to Learning
Watch a recent news report on the problem of routine antibiotic administration to livestock and antibiotic-resistant bacteria.
One of the Superbugs: MRSA
The imprudent use of antibiotics has paved the way for bacteria to expand populations of resistant forms. For example, Staphylococcus aureus, often called “staph,” is a common bacterium that can live in the human body and is usually easily treated with antibiotics. A very dangerous strain, however, methicillin-resistant Staphylococcus aureus (MRSA) has made the news over the past few years (Figure \(5\)). This strain is resistant to many commonly used antibiotics, including methicillin, amoxicillin, penicillin, and oxacillin. MRSA can cause infections of the skin, but it can also infect the bloodstream, lungs, urinary tract, or sites of injury. While MRSA infections are common among people in healthcare facilities, they have also appeared in healthy people who haven’t been hospitalized but who live or work in tight populations (like military personnel and prisoners). Researchers have expressed concern about the way this latter source of MRSA targets a much younger population than those residing in care facilities. The Journal of the American Medical Association reported that, among MRSA-afflicted persons in healthcare facilities, the average age is 68, whereas people with “community-associated MRSA” (CA-MRSA) have an average age of 23.2
In summary, the medical community is facing an antibiotic crisis. Some scientists believe that after years of being protected from bacterial infections by antibiotics, we may be returning to a time in which a simple bacterial infection could again devastate the human population. Researchers are developing new antibiotics, but it takes many years to of research and clinical trials, plus financial investments in the millions of dollars, to generate an effective and approved drug.
Foodborne Diseases
Prokaryotes are everywhere: They readily colonize the surface of any type of material, and food is not an exception. Most of the time, prokaryotes colonize food and food-processing equipment in the form of a biofilm. Outbreaks of bacterial infection related to food consumption are common. A foodborne disease (colloquially called “food poisoning”) is an illness resulting from the consumption the pathogenic bacteria, viruses, or other parasites that contaminate food. Although the United States has one of the safest food supplies in the world, the U.S. Centers for Disease Control and Prevention (CDC) has reported that “76 million people get sick, more than 300,000 are hospitalized, and 5,000 Americans die each year from foodborne illness.”
The characteristics of foodborne illnesses have changed over time. In the past, it was relatively common to hear about sporadic cases of botulism, the potentially fatal disease produced by a toxin from the anaerobic bacterium Clostridium botulinum. Some of the most common sources for this bacterium were non-acidic canned foods, homemade pickles, and processed meat and sausages. The can, jar, or package created a suitable anaerobic environment where Clostridium could grow. Proper sterilization and canning procedures have reduced the incidence of this disease.
While people may tend to think of foodborne illnesses as associated with animal-based foods, most cases are now linked to produce. There have been serious, produce-related outbreaks associated with raw spinach in the United States and with vegetable sprouts in Germany, and these types of outbreaks have become more common. The raw spinach outbreak in 2006 was produced by the bacterium E. coli serotype O157:H7. A serotype is a strain of bacteria that carries a set of similar antigens on its cell surface, and there are often many different serotypes of a bacterial species. Most E. coli are not particularly dangerous to humans, but serotype O157:H7 can cause bloody diarrhea and is potentially fatal.
All types of food can potentially be contaminated with bacteria. Recent outbreaks of Salmonella reported by the CDC occurred in foods as diverse as peanut butter, alfalfa sprouts, and eggs. A deadly outbreak in Germany in 2010 was caused by E. coli contamination of vegetable sprouts (Figure \(6\)). The strain that caused the outbreak was found to be a new serotype not previously involved in other outbreaks, which indicates that E. coli is continuously evolving.
Career Connection: Epidemiologist
Epidemiology is the study of the occurrence, distribution, and determinants of health and disease in a population. It is, therefore, part of public health. An epidemiologist studies the frequency and distribution of diseases within human populations and environments.
Epidemiologists collect data about a particular disease and track its spread to identify the original mode of transmission. They sometimes work in close collaboration with historians to try to understand the way a disease evolved geographically and over time, tracking the natural history of pathogens. They gather information from clinical records, patient interviews, surveillance, and any other available means. That information is used to develop strategies, such as vaccinations (Figure \(7\)), and design public health policies to reduce the incidence of a disease or to prevent its spread. Epidemiologists also conduct rapid investigations in case of an outbreak to recommend immediate measures to control it.
An epidemiologist has a bachelor’s degree, plus a master’s degree in public health (MPH). Many epidemiologists are also physicians (and have an M.D.), or they have a Ph.D. in an associated field, such as biology or microbiology.
Summary
Devastating diseases and plagues have been among us since early times. There are records about microbial diseases as far back as 3000 B.C. Infectious diseases remain among the leading causes of death worldwide. Emerging diseases are those rapidly increasing in incidence or geographic range. They can be new or re-emerging diseases (previously under control). Many emerging diseases affecting humans, such as brucellosis, are zoonoses. The WHO has identified a group of diseases whose re-emergence should be monitored: Those caused by bacteria include bubonic plague, diphtheria, and cholera.
Biofilms are considered responsible for diseases such as bacterial infections in patients with cystic fibrosis, Legionnaires’ disease, and otitis media. They produce dental plaque; colonize catheters, prostheses, transcutaneous, and orthopedic devices; and infect contact lenses, open wounds, and burned tissue. Biofilms also produce foodborne diseases because they colonize the surfaces of food and food-processing equipment. Biofilms are resistant to most of the methods used to control microbial growth. The excessive use of antibiotics has resulted in a major global problem, since resistant forms of bacteria have been selected over time. A very dangerous strain, methicillin-resistant Staphylococcus aureus (MRSA), has wreaked havoc recently. Foodborne diseases result from the consumption of contaminated food, pathogenic bacteria, viruses, or parasites that contaminate food.
Footnotes
1. 1 Papagrigorakis MJ, Synodinos PN, and Yapijakis C. Ancient typhoid epidemic reveals possible ancestral strain of Salmonella enterica serovar Typhi. Infect Genet Evol 7 (2007): 126–7, Epub 2006 Jun.
2. 2 Naimi, TS, LeDell, KH, Como-Sabetti, K, et al. Comparison of community- and health care-associated methicillin-resistant Staphylococcus aureus infection. JAMA 290 (2003): 2976–84, doi: 10.1001/jama.290.22.2976.
Glossary
antibiotic
biological substance that, in low concentration, is antagonistic to the growth of prokaryotes
Black Death
devastating pandemic that is believed to have been an outbreak of bubonic plague caused by the bacterium Yersinia pestis
botulism
disease produce by the toxin of the anaerobic bacterium Clostridium botulinum
CA-MRSA
MRSA acquired in the community rather than in a hospital setting
emerging disease
disease making an initial appearance in a population or that is increasing in incidence or geographic range
endemic disease
disease that is constantly present, usually at low incidence, in a population
epidemic
disease that occurs in an unusually high number of individuals in a population at the same time
foodborne disease
any illness resulting from the consumption of contaminated food, or of the pathogenic bacteria, viruses, or other parasites that contaminate food
MRSA
(methicillin-resistant Staphylococcus aureus) very dangerous Staphylococcus aureus strain resistant to multiple antibiotics
pandemic
widespread, usually worldwide, epidemic disease
serotype
strain of bacteria that carries a set of similar antigens on its cell surface, often many in a bacterial species
zoonosis
disease that primarily infects animals that is transmitted to humans | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/22%3A_Prokaryotes_-_Bacteria_and_Archaea/22.4%3A_Bacterial_Diseases_in_Humans.txt |
Skills to Develop
• Explain the need for nitrogen fixation and how it is accomplished
• Identify foods in which prokaryotes are used in the processing
• Describe the use of prokaryotes in bioremediation
• Describe the beneficial effects of bacteria that colonize our skin and digestive tracts
Not all prokaryotes are pathogenic. On the contrary, pathogens represent only a very small percentage of the diversity of the microbial world. In fact, our life would not be possible without prokaryotes. Just think about the role of prokaryotes in biogeochemical cycles.
Cooperation between Bacteria and Eukaryotes: Nitrogen Fixation
Nitrogen is a very important element to living things, because it is part of nucleotides and amino acids that are the building blocks of nucleic acids and proteins, respectively. Nitrogen is usually the most limiting element in terrestrial ecosystems, with atmospheric nitrogen, N2, providing the largest pool of available nitrogen. However, eukaryotes cannot use atmospheric, gaseous nitrogen to synthesize macromolecules. Fortunately, nitrogen can be “fixed,” meaning it is converted into ammonia (NH3) either biologically or abiotically. Abiotic nitrogen fixation occurs as a result of lightning or by industrial processes.
Biological nitrogen fixation (BNF) is exclusively carried out by prokaryotes: soil bacteria, cyanobacteria, and Frankia spp. (filamentous bacteria interacting with actinorhizal plants such as alder, bayberry, and sweet fern). After photosynthesis, BNF is the second most important biological process on Earth. The equation representing the process is as follows
$\text{N}_2 + 16\text{ATP} + 8\text{e}^- + 8\text{H}^+ \rightarrow 2\text{NH}_3 + 16\text{ADP} + 16\text{Pi} + \text{H}_2 \nonumber$
where Pi stands for inorganic phosphate. The total fixed nitrogen through BNF is about 100 to 180 million metric tons per year. Biological processes contribute 65 percent of the nitrogen used in agriculture.
Cyanobacteria are the most important nitrogen fixers in aquatic environments. In soil, members of the genus Clostridium are examples of free-living, nitrogen-fixing bacteria. Other bacteria live symbiotically with legume plants, providing the most important source of BNF. Symbionts may fix more nitrogen in soils than free-living organisms by a factor of 10. Soil bacteria, collectively called rhizobia, are able to symbiotically interact with legumes to form nodules, specialized structures where nitrogen fixation occurs (Figure $1$). Nitrogenase, the enzyme that fixes nitrogen, is inactivated by oxygen, so the nodule provides an oxygen-free area for nitrogen fixation to take place. This process provides a natural and inexpensive plant fertilizer, as it reduces atmospheric nitrogen to ammonia, which is easily usable by plants. The use of legumes is an excellent alternative to chemical fertilization and is of special interest to sustainable agriculture, which seeks to minimize the use of chemicals and conserve natural resources. Through symbiotic nitrogen fixation, the plant benefits from using an endless source of nitrogen: the atmosphere. Bacteria benefit from using photosynthates (carbohydrates produced during photosynthesis) from the plant and having a protected niche. Additionally, the soil benefits from being naturally fertilized. Therefore, the use of rhizobia as biofertilizers is a sustainable practice.
Why are legumes so important? Some, like soybeans, are key sources of agricultural protein. Some of the most important grain legumes are soybean, peanuts, peas, chickpeas, and beans. Other legumes, such as alfalfa, are used to feed cattle.
Early Biotechnology: Cheese, Bread, Wine, Beer, and Yogurt
According to the United Nations Convention on Biological Diversity, biotechnology is “any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use."1 The concept of “specific use” involves some sort of commercial application. Genetic engineering, artificial selection, antibiotic production, and cell culture are current topics of study in biotechnology. However, humans have used prokaryotes before the term biotechnology was even coined. In addition, some of the goods and services are as simple as cheese, bread, wine, beer, and yogurt, which employ both bacteria and other microbes, such as yeast, a fungus (Figure $2$).
Cheese production began around 4,000–7,000 years ago when humans began to breed animals and process their milk. Fermentation in this case preserves nutrients: Milk will spoil relatively quickly, but when processed as cheese, it is more stable. As for beer, the oldest records of brewing are about 6,000 years old and refer to the Sumerians. Evidence indicates that the Sumerians discovered fermentation by chance. Wine has been produced for about 4,500 years, and evidence suggests that cultured milk products, like yogurt, have existed for at least 4,000 years.
Using Prokaryotes to Clean up Our Planet: Bioremediation
Microbial bioremediation is the use of prokaryotes (or microbial metabolism) to remove pollutants. Bioremediation has been used to remove agricultural chemicals (pesticides, fertilizers) that leach from soil into groundwater and the subsurface. Certain toxic metals and oxides, such as selenium and arsenic compounds, can also be removed from water by bioremediation. The reduction of SeO4-2 to SeO3-2 and to Se0 (metallic selenium) is a method used to remove selenium ions from water. Mercury is an example of a toxic metal that can be removed from an environment by bioremediation. As an active ingredient of some pesticides, mercury is used in industry and is also a by-product of certain processes, such as battery production. Methyl mercury is usually present in very low concentrations in natural environments, but it is highly toxic because it accumulates in living tissues. Several species of bacteria can carry out the biotransformation of toxic mercury into nontoxic forms. These bacteria, such as Pseudomonas aeruginosa, can convert Hg+2 into Hg0, which is nontoxic to humans.
One of the most useful and interesting examples of the use of prokaryotes for bioremediation purposes is the cleanup of oil spills. The importance of prokaryotes to petroleum bioremediation has been demonstrated in several oil spills in recent years, such as the Exxon Valdez spill in Alaska (1989) (Figure $3$), the Prestige oil spill in Spain (2002), the spill into the Mediterranean from a Lebanon power plant (2006), and more recently, the BP oil spill in the Gulf of Mexico (2010). To clean up these spills, bioremediation is promoted by the addition of inorganic nutrients that help bacteria to grow. Hydrocarbon-degrading bacteria feed on hydrocarbons in the oil droplet, breaking down the hydrocarbons. Some species, such as Alcanivorax borkumensis, produce surfactants that solubilize the oil, whereas other bacteria degrade the oil into carbon dioxide. In the case of oil spills in the ocean, ongoing, natural bioremediation tends to occur, inasmuch as there are oil-consuming bacteria in the ocean prior to the spill. In addition to naturally occurring oil-degrading bacteria, humans select and engineer bacteria that possess the same capability with increased efficacy and spectrum of hydrocarbon compounds that can be processed. Under ideal conditions, it has been reported that up to 80 percent of the nonvolatile components in oil can be degraded within one year of the spill. Other oil fractions containing aromatic and highly branched hydrocarbon chains are more difficult to remove and remain in the environment for longer periods of time.
Everyday Connection: Microbes on the Human Body
The commensal bacteria that inhabit our skin and gastrointestinal tract do a host of good things for us. They protect us from pathogens, help us digest our food, and produce some of our vitamins and other nutrients. These activities have been known for a long time. More recently, scientists have gathered evidence that these bacteria may also help regulate our moods, influence our activity levels, and even help control weight by affecting our food choices and absorption patterns. The Human Microbiome Project has begun the process of cataloging our normal bacteria (and archaea) so we can better understand these functions.
A particularly fascinating example of our normal flora relates to our digestive systems. People who take high doses of antibiotics tend to lose many of their normal gut bacteria, allowing a naturally antibiotic-resistant species called Clostridium difficile to overgrow and cause severe gastric problems, especially chronic diarrhea (Figure $4$). Obviously, trying to treat this problem with antibiotics only makes it worse. However, it has been successfully treated by giving the patients fecal transplants from healthy donors to reestablish the normal intestinal microbial community. Clinical trials are underway to ensure the safety and effectiveness of this technique.
Scientists are also discovering that the absence of certain key microbes from our intestinal tract may set us up for a variety of problems. This seems to be particularly true regarding the appropriate functioning of the immune system. There are intriguing findings that suggest that the absence of these microbes is an important contributor to the development of allergies and some autoimmune disorders. Research is currently underway to test whether adding certain microbes to our internal ecosystem may help in the treatment of these problems as well as in treating some forms of autism.
Summary
Pathogens are only a small percentage of all prokaryotes. In fact, our life would not be possible without prokaryotes. Nitrogen is usually the most limiting element in terrestrial ecosystems; atmospheric nitrogen, the largest pool of available nitrogen, is unavailable to eukaryotes. Nitrogen can be “fixed,” or converted into ammonia (NH3) either biologically or abiotically. Biological nitrogen fixation (BNF) is exclusively carried out by prokaryotes. After photosynthesis, BNF is the second most important biological process on Earth. The most important source of BNF is the symbiotic interaction between soil bacteria and legume plants.
Microbial bioremediation is the use of microbial metabolism to remove pollutants. Bioremediation has been used to remove agricultural chemicals that leach from soil into groundwater and the subsurface. Toxic metals and oxides, such as selenium and arsenic compounds, can also be removed by bioremediation. Probably one of the most useful and interesting examples of the use of prokaryotes for bioremediation purposes is the cleanup of oil spills.
Human life is only possible due to the action of microbes, both those in the environment and those species that call us home. Internally, they help us digest our food, produce crucial nutrients for us, protect us from pathogenic microbes, and help train our immune systems to function correctly.
Footnotes
1. 1 http://www.cbd.int/convention/articles/?a=cbd-02, United Nations Convention on Biological Diversity: Article 2: Use of Terms.
Glossary
biological nitrogen fixation
conversion of atmospheric nitrogen into ammonia exclusively carried out by prokaryotes
bioremediation
use of microbial metabolism to remove pollutants
biotechnology
any technological application that uses living organisms, biological systems, or their derivatives to produce or modify other products
nodule
novel structure on the roots of certain plants (legumes) that results from the symbiotic interaction between the plant and soil bacteria, is the site of nitrogen fixation | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/22%3A_Prokaryotes_-_Bacteria_and_Archaea/22.5%3A_Beneficial_Prokaryotes.txt |
22.1: Prokaryotic Diversity
Prokaryotes are ubiquitous. They cover every imaginable surface where there is sufficient moisture, and they live on and inside of other living things. In the typical human body, prokaryotic cells outnumber human body cells by about ten to one. They comprise the majority of living things in all ecosystems. Some prokaryotes thrive in environments that are inhospitable for most living things.
Review Questions
The first forms of life on Earth were thought to be_________.
1. single-celled plants
2. prokaryotes
3. insects
4. large animals such as dinosaurs
Answer
A
Microbial mats __________.
1. are the earliest forms of life on Earth
2. obtained their energy and food from hydrothermal vents
3. are multi-layered sheet of prokaryotes including mostly bacteria but also archaea
4. all of the above
Answer
D
The first organisms that oxygenated the atmosphere were
1. cyanobacteria
2. phototrophic organisms
3. anaerobic organisms
4. all of the above
Answer
A
Halophiles are organisms that require________.
1. a salt concentration of at least 0.2 M
2. high sugar concentration
3. the addition of halogens
4. all of the above
Answer
A
Free Response
Describe briefly how you would detect the presence of a non-culturable prokaryote in an environmental sample.
Answer
As the organisms are non-culturable, the presence could be detected through molecular techniques, such as PCR.
Why do scientists believe that the first organisms on Earth were extremophiles?
Answer
Because the environmental conditions on Earth were extreme: high temperatures, lack of oxygen, high radiation, and the like.
22.2: Structure of Prokaryotes
There are many differences between prokaryotic and eukaryotic cells. However, all cells have four common structures: the plasma membrane, which functions as a barrier for the cell and separates the cell from its environment; the cytoplasm, a jelly-like substance inside the cell; nucleic acids, the genetic material of the cell; and ribosomes, where protein synthesis takes place.
Review Questions
The presence of a membrane-enclosed nucleus is a characteristic of ________.
1. prokaryotic cells
2. eukaryotic cells
3. all cells
4. viruses
Answer
B
Which of the following consist of prokaryotic cells?
1. bacteria and fungi
2. archaea and fungi
3. protists and animals
4. bacteria and archaea
Answer
D
The cell wall is ________.
1. interior to the cell membrane
2. exterior to the cell membrane
3. a part of the cell membrane
4. interior or exterior, depending on the particular cell
Answer
B
Organisms most likely to be found in extreme environments are ________.
1. fungi
2. bacteria
3. viruses
4. archaea
Answer
B
Prokaryotes stain as Gram-positive or Gram-negative because of differences in the cell _______.
1. wall
2. cytoplasm
3. nucleus
4. chromosome
Answer
A
Pseudopeptidoglycan is a characteristic of the walls of ________.
1. eukaryotic cells
2. bacterial prokaryotic cells
3. archaean prokaryotic cells
4. bacterial and archaean prokaryotic cells
Answer
C
The lipopolysaccharide layer (LPS) is a characteristic of the wall of ________.
1. archaean cells
2. Gram-negative bacteria
3. bacterial prokaryotic cells
4. eukaryotic cells
Answer
B
Free Response
Mention three differences between bacteria and archaea.
Answer
Responses will vary. A possible answer is: Bacteria contain peptidoglycan in the cell wall; archaea do not. The cell membrane in bacteria is a lipid bilayer; in archaea, it can be a lipid bilayer or a monolayer. Bacteria contain fatty acids on the cell membrane, whereas archaea contain phytanyl.
Explain the statement that both types, bacteria and archaea, have the same basic structures, but built from different chemical components.
Answer
Both bacteria and archaea have cell membranes and they both contain a hydrophobic portion. In the case of bacteria, it is a fatty acid; in the case of archaea, it is a hydrocarbon (phytanyl). Both bacteria and archaea have a cell wall that protects them. In the case of bacteria, it is composed of peptidoglycan, whereas in the case of archaea, it is pseudopeptidoglycan, polysaccharides, glycoproteins, or pure protein. Bacterial and archaeal flagella also differ in their chemical structure.
22.3: Prokaryotic Metabolism
Prokaryotes are metabolically diverse organisms. There are many different environments on Earth with various energy and carbon sources, and variable conditions. Prokaryotes have been able to live in every environment by using whatever energy and carbon sources are available. Prokaryotes fill many niches on Earth, including being involved in nutrient cycles such as nitrogen and carbon cycles, decomposing dead organisms, and thriving inside living organisms, including humans.
Review Questions
Which of the following elements is not a micronutrient?
1. boron
2. calcium
3. chromium
4. manganese
Answer
B
Prokaryotes that obtain their energy from chemical compounds are called _____.
1. phototrophs
2. auxotrophs
3. chemotrophs
4. lithotrophs
Answer
C
Ammonification is the process by which _____.
1. ammonia is released during the decomposition of nitrogen-containing organic compounds
2. ammonium is converted to nitrite and nitrate in soils
3. nitrate from soil is transformed to gaseous nitrogen compounds such as NO, N2O, and N2
4. gaseous nitrogen is fixed to yield ammonia
Answer
A
Plants use carbon dioxide from the air and are therefore called _____.
1. consumers
2. producers
3. decomposer
4. carbon fixers
Answer
B
Free Response
Think about the conditions (temperature, light, pressure, and organic and inorganic materials) that you may find in a deep-sea hydrothermal vent. What type of prokaryotes, in terms of their metabolic needs (autotrophs, phototrophs, chemotrophs, etc.), would you expect to find there?
Answer
Responses will vary. In a deep-sea hydrothermal vent, there is no light, so prokaryotes would be chemotrophs instead of phototrophs. The source of carbon would be carbon dioxide dissolved in the ocean, so they would be autotrophs. There is not a lot of organic material in the ocean, so prokaryotes would probably use inorganic sources, thus they would be chemolitotrophs. The temperatures are very high in the hydrothermal vent, so the prokaryotes would be thermophilic.
22.4: Bacterial Diseases in Humans
Devastating pathogen-borne diseases and plagues, both viral and bacterial in nature, have affected humans since the beginning of human history. The true cause of these diseases was not understood at the time, and some people thought that diseases were a spiritual punishment. Over time, people came to realize that staying apart from afflicted persons, and disposing of the corpses and personal belongings of victims of illness, reduced their own chances of getting sick.
Review Questions
A disease that is constantly present in a population is called _____.
1. pandemic
2. epidemic
3. endemic
4. re-emerging
Answer
C
Which of the statements about biofilms is incorrect?
1. Biofilms are considered responsible for diseases such as cystic fibrosis.
2. Biofilms produce dental plaque, and colonize catheters and prostheses.
3. Biofilms colonize open wounds and burned tissue.
4. All statements are incorrect.
Answer
D
Which of these statements is true?
1. An antibiotic is any substance produced by a organism that is antagonistic to the growth of prokaryotes.
2. An antibiotic is any substance produced by a prokaryote that is antagonistic to the growth of other viruses.
3. An antibiotic is any substance produced by a prokaryote that is antagonistic to the growth of eukaryotic cells.
4. An antibiotic is any substance produced by a prokaryote that prevents growth of the same prokaryote.
Answer
A
Free Response
Explain the reason why the imprudent and excessive use of antibiotics has resulted in a major global problem.
Answer
Antibiotics kill bacteria that are sensitive to them; thus, only the resistant ones will survive. These resistant bacteria will reproduce, and therefore, after a while, there will be only resistant bacteria.
Researchers have discovered that washing spinach with water several times does not prevent foodborne diseases due to E. coli. How can you explain this fact?
Answer
E. coli colonizes the surface of the leaf, forming a biofilm that is more difficult to remove than free (planktonic) cells. Additionally, bacteria can be taken up in the water that plants are grown in, thereby entering the plant tissues rather than simply residing on the leaf surface.
22.5: Beneficial Prokaryotes
Not all prokaryotes are pathogenic. On the contrary, pathogens represent only a very small percentage of the diversity of the microbial world. In fact, our life would not be possible without prokaryotes. Just think about the role of prokaryotes in biogeochemical cycles.
Review Questions
Which of these occurs through symbiotic nitrogen fixation?
1. The plant benefits from using an endless source of nitrogen.
2. The soil benefits from being naturally fertilized.
3. Bacteria benefit from using photosynthates from the plant.
4. All of the above occur.
Answer
D
Synthetic compounds found in an organism but not normally produced or expected to be present in that organism are called _____.
1. pesticides
2. bioremediators
3. recalcitrant compounds
4. xenobiotics
Answer
D
Bioremediation includes _____.
1. the use of prokaryotes that can fix nitrogen
2. the use of prokaryotes to clean up pollutants
3. the use of prokaryotes as natural fertilizers
4. All of the above
Answer
B
Free Response
Your friend believes that prokaryotes are always detrimental and pathogenic. How would you explain to them that they are wrong?
Answer
Remind them of the important roles prokaryotes play in decomposition and freeing up nutrients in biogeochemical cycles; remind them of the many prokaryotes that are not human pathogens and that fill very specialized niches. Furthermore, our normal bacterial symbionts are crucial for our digestion and in protecting us from pathogens. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/22%3A_Prokaryotes_-_Bacteria_and_Archaea/22.E%3A_Prokaryotes_-_Bacteria_and_Archaea_%28Exercises%29.txt |
Most protists are microscopic, unicellular organisms that are abundant in soil, freshwater, brackish, and marine environments. They are also common in the digestive tracts of animals and in the vascular tissues of plants.
• 23.0: Prelude to Protists
Most protists are microscopic, unicellular organisms that are abundant in soil, freshwater, brackish, and marine environments. They are also common in the digestive tracts of animals and in the vascular tissues of plants. Others invade the cells of other protists, animals, and plants. Not all protists are microscopic. Some have huge, macroscopic cells, such as the plasmodia (giant amoebae) of myxomycete slime molds or the marine green alga Caulerpa.
• 23.1: Eukaryotic Origins
Living things fall into three large groups: Archaea, Bacteria, and Eukarya. The first two have prokaryotic cells, and the third contains all eukaryotes. A relatively sparse fossil record is available to help discern what the first members of each of these lineages looked like, so it is possible that all the events that led to the last common ancestor of extant eukaryotes will remain unknown. However, comparative biology of extant organisms and the limited fossil record provide some insight.
• 23.2: Characteristics of Protists
There are over 100,000 described living species of protists, and it is unclear how many undescribed species may exist. Since many protists live as commensals or parasites in other organisms and these relationships are often species-specific, there is a huge potential for protist diversity that matches the diversity of hosts. As the catchall term for eukaryotic organisms that are not animal, plant, or fungi, it is not surprising that very few characteristics are common to all protists.
• 23.3: Groups of Protists
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging.
• 23.4: Ecology of Protists
Protists function in various ecological niches. Whereas some protist species are essential components of the food chain and generators of biomass, others function in the decomposition of organic materials. Still other protists are dangerous human pathogens or causative agents of devastating plant diseases.
• 23.E: Protists (Exercises)
Thumbnail: This scanning electron micrograph (SEM) revealed some of the external ultrastructural details displayed by a flagellated Giardia lamblia protozoan parasite. G. lamblia is the organism responsible for causing the diarrheal disease "giardiasis". (Public Domain; CDC / Janice Haney Carr).
23: Protists
Humans have been familiar with macroscopic organisms (organisms big enough to see with the unaided eye) since before there was a written history, and it is likely that most cultures distinguished between animals and land plants, and most probably included the macroscopic fungi as plants. Therefore, it became an interesting challenge to deal with the world of microorganisms once microscopes were developed a few centuries ago. Many different naming schemes were used over the last couple of centuries, but it has become the most common practice to refer to eukaryotes that are not land plants, animals, or fungi as protists.
This name was first suggested by Ernst Haeckel in the late nineteenth century. It has been applied in many contexts and has been formally used to represent a kingdom-level taxon called Protista. However, many modern systematists (biologists who study the relationships among organisms) are beginning to shy away from the idea of formal ranks such as kingdom and phylum. Instead, they are naming taxa as groups of organisms thought to include all the descendants of a last common ancestor (monophyletic group). During the past two decades, the field of molecular genetics has demonstrated that some protists are more related to animals, plants, or fungi than they are to other protists. Therefore, not including animals, plants and fungi make the kingdom Protista a paraphyletic group, or one that does not include all descendents of its common ancestor. For this reason, protist lineages originally classified into the kingdom Protista continue to be examined and debated. In the meantime, the term “protist” still is used informally to describe this tremendously diverse group of eukaryotes.
Most protists are microscopic, unicellular organisms that are abundant in soil, freshwater, brackish, and marine environments. They are also common in the digestive tracts of animals and in the vascular tissues of plants. Others invade the cells of other protists, animals, and plants. Not all protists are microscopic. Some have huge, macroscopic cells, such as the plasmodia (giant amoebae) of myxomycete slime molds or the marine green alga Caulerpa. Some protists are multicellular, such as the red, green, and brown seaweeds. It is among the protists that one finds the wealth of ways that organisms can grow. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/23%3A_Protists/23.0%3A_Prelude_to_Protists.txt |
Skills to Develop
• List the unifying characteristics of eukaryotes
• Describe what scientists know about the origins of eukaryotes based on the last common ancestor
• Explain endosymbiotic theory
Living things fall into three large groups: Archaea, Bacteria, and Eukarya. The first two have prokaryotic cells, and the third contains all eukaryotes. A relatively sparse fossil record is available to help discern what the first members of each of these lineages looked like, so it is possible that all the events that led to the last common ancestor of extant eukaryotes will remain unknown. However, comparative biology of extant organisms and the limited fossil record provide some insight into the history of Eukarya.
The earliest fossils found appear to be Bacteria, most likely cyanobacteria. They are about 3.5 billion years old and are recognizable because of their relatively complex structure and, for prokaryotes, relatively large cells. Most other prokaryotes have small cells, 1 or 2 µm in size, and would be difficult to pick out as fossils. Most living eukaryotes have cells measuring 10 µm or greater. Structures this size, which might be fossils, appear in the geological record about 2.1 billion years ago.
Characteristics of Eukaryotes
Data from these fossils have led comparative biologists to the conclusion that living eukaryotes are all descendants of a single common ancestor. Mapping the characteristics found in all major groups of eukaryotes reveals that the following characteristics must have been present in the last common ancestor, because these characteristics are present in at least some of the members of each major lineage.
1. Cells with nuclei surrounded by a nuclear envelope with nuclear pores. This is the single characteristic that is both necessary and sufficient to define an organism as a eukaryote. All extant eukaryotes have cells with nuclei.
2. Mitochondria. Some extant eukaryotes have very reduced remnants of mitochondria in their cells, whereas other members of their lineages have “typical” mitochondria.
3. A cytoskeleton containing the structural and motility components called actin microfilaments and microtubules. All extant eukaryotes have these cytoskeletal elements.
4. Flagella and cilia, organelles associated with cell motility. Some extant eukaryotes lack flagella and/or cilia, but they are descended from ancestors that possessed them.
5. Chromosomes, each consisting of a linear DNA molecule coiled around basic (alkaline) proteins called histones. The few eukaryotes with chromosomes lacking histones clearly evolved from ancestors that had them.
6. Mitosis, a process of nuclear division wherein replicated chromosomes are divided and separated using elements of the cytoskeleton. Mitosis is universally present in eukaryotes.
7. Sex, a process of genetic recombination unique to eukaryotes in which diploid nuclei at one stage of the life cycle undergo meiosis to yield haploid nuclei and subsequent karyogamy, a stage where two haploid nuclei fuse together to create a diploid zygote nucleus.
8. Members of all major lineages have cell walls, and it might be reasonable to conclude that the last common ancestor could make cell walls during some stage of its life cycle. However, not enough is known about eukaryotes’ cell walls and their development to know how much homology exists among them. If the last common ancestor could make cell walls, it is clear that this ability must have been lost in many groups.
Endosymbiosis and the Evolution of Eukaryotes
In order to understand eukaryotic organisms fully, it is necessary to understand that all extant eukaryotes are descendants of a chimeric organism that was a composite of a host cell and the cell(s) of an alpha-proteobacterium that “took up residence” inside it. This major theme in the origin of eukaryotes is known as endosymbiosis, one cell engulfing another such that the engulfed cell survives and both cells benefit. Over many generations, a symbiotic relationship can result in two organisms that depend on each other so completely that neither could survive on its own. Endosymbiotic events likely contributed to the origin of the last common ancestor of today’s eukaryotes and to later diversification in certain lineages of eukaryotes (Figure \(4\)). Before explaining this further, it is necessary to consider metabolism in prokaryotes.
Prokaryotic Metabolism
Many important metabolic processes arose in prokaryotes, and some of these, such as nitrogen fixation, are never found in eukaryotes. The process of aerobic respiration is found in all major lineages of eukaryotes, and it is localized in the mitochondria. Aerobic respiration is also found in many lineages of prokaryotes, but it is not present in all of them, and many forms of evidence suggest that such anaerobic prokaryotes never carried out aerobic respiration nor did their ancestors.
While today’s atmosphere is about one-fifth molecular oxygen (O2), geological evidence shows that it originally lacked O2. Without oxygen, aerobic respiration would not be expected, and living things would have relied on fermentation instead. At some point before, about 3.5 billion years ago, some prokaryotes began using energy from sunlight to power anabolic processes that reduce carbon dioxide to form organic compounds. That is, they evolved the ability to photosynthesize. Hydrogen, derived from various sources, was captured using light-powered reactions to reduce fixed carbon dioxide in the Calvin cycle. The group of Gram-negative bacteria that gave rise to cyanobacteria used water as the hydrogen source and released O2 as a waste product.
Eventually, the amount of photosynthetic oxygen built up in some environments to levels that posed a risk to living organisms, since it can damage many organic compounds. Various metabolic processes evolved that protected organisms from oxygen, one of which, aerobic respiration, also generated high levels of ATP. It became widely present among prokaryotes, including in a group we now call alpha-proteobacteria. Organisms that did not acquire aerobic respiration had to remain in oxygen-free environments. Originally, oxygen-rich environments were likely localized around places where cyanobacteria were active, but by about 2 billion years ago, geological evidence shows that oxygen was building up to higher concentrations in the atmosphere. Oxygen levels similar to today’s levels only arose within the last 700 million years.
Recall that the first fossils that we believe to be eukaryotes date to about 2 billion years old, so they appeared as oxygen levels were increasing. Also, recall that all extant eukaryotes descended from an ancestor with mitochondria. These organelles were first observed by light microscopists in the late 1800s, where they appeared to be somewhat worm-shaped structures that seemed to be moving around in the cell. Some early observers suggested that they might be bacteria living inside host cells, but these hypotheses remained unknown or rejected in most scientific communities.
Endosymbiotic Theory
As cell biology developed in the twentieth century, it became clear that mitochondria were the organelles responsible for producing ATP using aerobic respiration. In the 1960s, American biologist Lynn Margulis developed endosymbiotic theory, which states that eukaryotes may have been a product of one cell engulfing another, one living within another, and evolving over time until the separate cells were no longer recognizable as such. In 1967, Margulis introduced new work on the theory and substantiated her findings through microbiological evidence. Although Margulis’ work initially was met with resistance, this once-revolutionary hypothesis is now widely (but not completely) accepted, with work progressing on uncovering the steps involved in this evolutionary process and the key players involved. Much still remains to be discovered about the origins of the cells that now make up the cells in all living eukaryotes.
Broadly, it has become clear that many of our nuclear genes and the molecular machinery responsible for replication and expression appear closely related to those in Archaea. On the other hand, the metabolic organelles and genes responsible for many energy-harvesting processes had their origins in bacteria. Much remains to be clarified about how this relationship occurred; this continues to be an exciting field of discovery in biology. For instance, it is not known whether the endosymbiotic event that led to mitochondria occurred before or after the host cell had a nucleus. Such organisms would be among the extinct precursors of the last common ancestor of eukaryotes.
Mitochondria
One of the major features distinguishing prokaryotes from eukaryotes is the presence of mitochondria. Eukaryotic cells may contain anywhere from one to several thousand mitochondria, depending on the cell’s level of energy consumption. Each mitochondrion measures 1 to 10 or greater micrometers in length and exists in the cell as an organelle that can be ovoid to worm-shaped to intricately branched (Figure \(1\)). Mitochondria arise from the division of existing mitochondria; they may fuse together; and they may be moved around inside the cell by interactions with the cytoskeleton. However, mitochondria cannot survive outside the cell. As the atmosphere was oxygenated by photosynthesis, and as successful aerobic prokaryotes evolved, evidence suggests that an ancestral cell with some membrane compartmentalization engulfed a free-living aerobic prokaryote, specifically an alpha-proteobacterium, thereby giving the host cell the ability to use oxygen to release energy stored in nutrients. Alpha-proteobacteria are a large group of bacteria that includes species symbiotic with plants, disease organisms that can infect humans via ticks, and many free-living species that use light for energy. Several lines of evidence support that mitochondria are derived from this endosymbiotic event. Most mitochondria are shaped like alpha-proteobacteria and are surrounded by two membranes, which would result when one membrane-bound organism was engulfed into a vacuole by another membrane-bound organism. The mitochondrial inner membrane is extensive and involves substantial infoldings called cristae that resemble the textured, outer surface of alpha-proteobacteria. The matrix and inner membrane are rich with the enzymes necessary for aerobic respiration.
Mitochondria divide independently by a process that resembles binary fission in prokaryotes. Specifically, mitochondria are not formed from scratch (de novo) by the eukaryotic cell; they reproduce within it and are distributed with the cytoplasm when a cell divides or two cells fuse. Therefore, although these organelles are highly integrated into the eukaryotic cell, they still reproduce as if they are independent organisms within the cell. However, their reproduction is synchronized with the activity and division of the cell. Mitochondria have their own (usually) circular DNA chromosome that is stabilized by attachments to the inner membrane and carries genes similar to genes expressed by alpha-proteobacteria. Mitochondria also have special ribosomes and transfer RNAs that resemble these components in prokaryotes. These features all support that mitochondria were once free-living prokaryotes.
Mitochondria that carry out aerobic respiration have their own genomes, with genes similar to those in alpha-proteobacteria. However, many of the genes for respiratory proteins are located in the nucleus. When these genes are compared to those of other organisms, they appear to be of alpha-proteobacterial origin. Additionally, in some eukaryotic groups, such genes are found in the mitochondria, whereas in other groups, they are found in the nucleus. This has been interpreted as evidence that genes have been transferred from the endosymbiont chromosome to the host genome. This loss of genes by the endosymbiont is probably one explanation why mitochondria cannot live without a host.
Some living eukaryotes are anaerobic and cannot survive in the presence of too much oxygen. Some appear to lack organelles that could be recognized as mitochondria. In the 1970s to the early 1990s, many biologists suggested that some of these eukaryotes were descended from ancestors whose lineages had diverged from the lineage of mitochondrion-containing eukaryotes before endosymbiosis occurred. However, later findings suggest that reduced organelles are found in most, if not all, anaerobic eukaryotes, and that all eukaryotes appear to carry some genes in their nuclei that are of mitochondrial origin. In addition to the aerobic generation of ATP, mitochondria have several other metabolic functions. One of these functions is to generate clusters of iron and sulfur that are important cofactors of many enzymes. Such functions are often associated with the reduced mitochondrion-derived organelles of anaerobic eukaryotes. Therefore, most biologists accept that the last common ancestor of eukaryotes had mitochondria.
Plastids
Some groups of eukaryotes are photosynthetic. Their cells contain, in addition to the standard eukaryotic organelles, another kind of organelle called a plastid. When such cells are carrying out photosynthesis, their plastids are rich in the pigment chlorophyll a and a range of other pigments, called accessory pigments, which are involved in harvesting energy from light. Photosynthetic plastids are called chloroplasts (Figure \(2\)).
Like mitochondria, plastids appear to have an endosymbiotic origin. This hypothesis was also championed by Lynn Margulis. Plastids are derived from cyanobacteria that lived inside the cells of an ancestral, aerobic, heterotrophic eukaryote. This is called primary endosymbiosis, and plastids of primary origin are surrounded by two membranes. The best evidence is that this has happened twice in the history of eukaryotes. In one case, the common ancestor of the major lineage/supergroup Archaeplastida took on a cyanobacterial endosymbiont; in the other, the ancestor of the small amoeboid rhizarian taxon, Paulinella, took on a different cyanobacterial endosymbiont. Almost all photosynthetic eukaryotes are descended from the first event, and only a couple of species are derived from the other.
Cyanobacteria are a group of Gram-negative bacteria with all the conventional structures of the group. However, unlike most prokaryotes, they have extensive, internal membrane-bound sacs called thylakoids. Chlorophyll is a component of these membranes, as are many of the proteins of the light reactions of photosynthesis. Cyanobacteria also have the peptidoglycan wall and lipopolysaccharide layer associated with Gram-negative bacteria.
Chloroplasts of primary origin have thylakoids, a circular DNA chromosome, and ribosomes similar to those of cyanobacteria. Each chloroplast is surrounded by two membranes. In the group of Archaeplastida called the glaucophytes and in Paulinella, a thin peptidoglycan layer is present between the outer and inner plastid membranes. All other plastids lack this relictual cyanobacterial wall. The outer membrane surrounding the plastid is thought to be derived from the vacuole in the host, and the inner membrane is thought to be derived from the plasma membrane of the symbiont.
There is also, as with the case of mitochondria, strong evidence that many of the genes of the endosymbiont were transferred to the nucleus. Plastids, like mitochondria, cannot live independently outside the host. In addition, like mitochondria, plastids are derived from the division of other plastids and never built from scratch. Researchers have suggested that the endosymbiotic event that led to Archaeplastida occurred 1 to 1.5 billion years ago, at least 5 hundred million years after the fossil record suggests that eukaryotes were present.
Not all plastids in eukaryotes are derived directly from primary endosymbiosis. Some of the major groups of algae became photosynthetic by secondary endosymbiosis, that is, by taking in either green algae or red algae (both from Archaeplastida) as endosymbionts (Figure \(3\)). Numerous microscopic and genetic studies have supported this conclusion. Secondary plastids are surrounded by three or more membranes, and some secondary plastids even have clear remnants of the nucleus of endosymbiotic alga. Others have not “kept” any remnants. There are cases where tertiary or higher-order endosymbiotic events are the best explanations for plastids in some eukaryotes.
Art Connection
What evidence is there that mitochondria were incorporated into the ancestral eukaryotic cell before chloroplasts?
Evolution Connection: Secondary Endosymbiosis in Chlorarachniophytes
Endosymbiosis involves one cell engulfing another to produce, over time, a coevolved relationship in which neither cell could survive alone. The chloroplasts of red and green algae, for instance, are derived from the engulfment of a photosynthetic cyanobacterium by an early prokaryote.
This leads to the question of the possibility of a cell containing an endosymbiont to itself become engulfed, resulting in a secondary endosymbiosis. Molecular and morphological evidence suggest that the chlorarachniophyte protists are derived from a secondary endosymbiotic event. Chlorarachniophytes are rare algae indigenous to tropical seas and sand that can be classified into the rhizarian supergroup. Chlorarachniophytes extend thin cytoplasmic strands, interconnecting themselves with other chlorarachniophytes, in a cytoplasmic network. These protists are thought to have originated when a eukaryote engulfed a green alga, the latter of which had already established an endosymbiotic relationship with a photosynthetic cyanobacterium (Figure \(5\)).
Several lines of evidence support that chlorarachniophytes evolved from secondary endosymbiosis. The chloroplasts contained within the green algal endosymbionts still are capable of photosynthesis, making chlorarachniophytes photosynthetic. The green algal endosymbiont also exhibits a stunted vestigial nucleus. In fact, it appears that chlorarachniophytes are the products of an evolutionarily recent secondary endosymbiotic event. The plastids of chlorarachniophytes are surrounded by four membranes: The first two correspond to the inner and outer membranes of the photosynthetic cyanobacterium, the third corresponds to the green alga, and the fourth corresponds to the vacuole that surrounded the green alga when it was engulfed by the chlorarachniophyte ancestor. In other lineages that involved secondary endosymbiosis, only three membranes can be identified around plastids. This is currently rectified as a sequential loss of a membrane during the course of evolution.
The process of secondary endosymbiosis is not unique to chlorarachniophytes. In fact, secondary endosymbiosis of green algae also led to euglenid protists, whereas secondary endosymbiosis of red algae led to the evolution of dinoflagellates, apicomplexans, and stramenopiles.
Summary
The oldest fossil evidence of eukaryotes is about 2 billion years old. Fossils older than this all appear to be prokaryotes. It is probable that today’s eukaryotes are descended from an ancestor that had a prokaryotic organization. The last common ancestor of today’s Eukarya had several characteristics, including cells with nuclei that divided mitotically and contained linear chromosomes where the DNA was associated with histones, a cytoskeleton and endomembrane system, and the ability to make cilia/flagella during at least part of its life cycle. It was aerobic because it had mitochondria that were the result of an aerobic alpha-proteobacterium that lived inside a host cell. Whether this host had a nucleus at the time of the initial symbiosis remains unknown. The last common ancestor may have had a cell wall for at least part of its life cycle, but more data are needed to confirm this hypothesis. Today’s eukaryotes are very diverse in their shapes, organization, life cycles, and number of cells per individual.
Art Connections
Figure \(4\): What evidence is there that mitochondria were incorporated into the ancestral eukaryotic cell before chloroplasts?
Answer
All eukaryotic cells have mitochondria, but not all eukaryotic cells have chloroplasts.
Glossary
endosymbiosis
engulfment of one cell within another such that the engulfed cell survives, and both cells benefit; the process responsible for the evolution of mitochondria and chloroplasts in eukaryotes
endosymbiotic theory
theory that states that eukaryotes may have been a product of one cell engulfing another, one living within another, and evolving over time until the separate cells were no longer recognizable as such
plastid
one of a group of related organelles in plant cells that are involved in the storage of starches, fats, proteins, and pigments | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/23%3A_Protists/23.1%3A_Eukaryotic_Origins.txt |
Skills to Develop
• Describe the cell structure characteristics of protists
• Describe the metabolic diversity of protists
• Describe the life cycle diversity of protists
There are over 100,000 described living species of protists, and it is unclear how many undescribed species may exist. Since many protists live as commensals or parasites in other organisms and these relationships are often species-specific, there is a huge potential for protist diversity that matches the diversity of hosts. As the catchall term for eukaryotic organisms that are not animal, plant, or fungi, it is not surprising that very few characteristics are common to all protists.
Cell Structure
The cells of protists are among the most elaborate of all cells. Most protists are microscopic and unicellular, but some true multicellular forms exist. A few protists live as colonies that behave in some ways as a group of free-living cells and in other ways as a multicellular organism. Still other protists are composed of enormous, multinucleate, single cells that look like amorphous blobs of slime, or in other cases, like ferns. In fact, many protist cells are multinucleated; in some species, the nuclei are different sizes and have distinct roles in protist cell function.
Single protist cells range in size from less than a micrometer to three meters in length to hectares. Protist cells may be enveloped by animal-like cell membranes or plant-like cell walls. Others are encased in glassy silica-based shells or wound with pellicles of interlocking protein strips. The pellicle functions like a flexible coat of armor, preventing the protist from being torn or pierced without compromising its range of motion.
Metabolism
Protists exhibit many forms of nutrition and may be aerobic or anaerobic. Protists that store energy by photosynthesis belong to a group of photoautotrophs and are characterized by the presence of chloroplasts. Other protists are heterotrophic and consume organic materials (such as other organisms) to obtain nutrition. Amoebas and some other heterotrophic protist species ingest particles by a process called phagocytosis, in which the cell membrane engulfs a food particle and brings it inward, pinching off an intracellular membranous sac, or vesicle, called a food vacuole (Figure \(1\)). The vesicle containing the ingested particle, the phagosome, then fuses with a lysosome containing hydrolytic enzymes to produce a phagolysosome, and the food particle is broken down into small molecules that can diffuse into the cytoplasm and be used in cellular metabolism. Undigested remains ultimately are expelled from the cell via exocytosis.
Subtypes of heterotrophs, called saprobes, absorb nutrients from dead organisms or their organic wastes. Some protists can function as mixotrophs, obtaining nutrition by photoautotrophic or heterotrophic routes, depending on whether sunlight or organic nutrients are available.
Motility
The majority of protists are motile, but different types of protists have evolved varied modes of movement (Figure \(2\)). Some protists have one or more flagella, which they rotate or whip. Others are covered in rows or tufts of tiny cilia that they coordinately beat to swim. Still others form cytoplasmic extensions called pseudopodia anywhere on the cell, anchor the pseudopodia to a substrate, and pull themselves forward. Some protists can move toward or away from a stimulus, a movement referred to as taxis. Movement toward light, termed phototaxis, is accomplished by coupling their locomotion strategy with a light-sensing organ.
Life Cycles
Protists reproduce by a variety of mechanisms. Most undergo some form of asexual reproduction, such as binary fission, to produce two daughter cells. In protists, binary fission can be divided into transverse or longitudinal, depending on the axis of orientation; sometimes Paramecium exhibits this method. Some protists such as the true slime molds exhibit multiple fission and simultaneously divide into many daughter cells. Others produce tiny buds that go on to divide and grow to the size of the parental protist. Sexual reproduction, involving meiosis and fertilization, is common among protists, and many protist species can switch from asexual to sexual reproduction when necessary. Sexual reproduction is often associated with periods when nutrients are depleted or environmental changes occur. Sexual reproduction may allow the protist to recombine genes and produce new variations of progeny that may be better suited to surviving in the new environment. However, sexual reproduction is often associated with resistant cysts that are a protective, resting stage. Depending on their habitat, the cysts may be particularly resistant to temperature extremes, desiccation, or low pH. This strategy also allows certain protists to “wait out” stressors until their environment becomes more favorable for survival or until they are carried (such as by wind, water, or transport on a larger organism) to a different environment, because cysts exhibit virtually no cellular metabolism.
Protist life cycles range from simple to extremely elaborate. Certain parasitic protists have complicated life cycles and must infect different host species at different developmental stages to complete their life cycle. Some protists are unicellular in the haploid form and multicellular in the diploid form, a strategy employed by animals. Other protists have multicellular stages in both haploid and diploid forms, a strategy called alternation of generations that is also used by plants.
Habitats
Nearly all protists exist in some type of aquatic environment, including freshwater and marine environments, damp soil, and even snow. Several protist species are parasites that infect animals or plants. A few protist species live on dead organisms or their wastes, and contribute to their decay.
Summary
Protists are extremely diverse in terms of their biological and ecological characteristics, partly because they are an artificial assemblage of phylogenetically unrelated groups. Protists display highly varied cell structures, several types of reproductive strategies, virtually every possible type of nutrition, and varied habitats. Most single-celled protists are motile, but these organisms use diverse structures for transportation.
Glossary
mixotroph
organism that can obtain nutrition by autotrophic or heterotrophic means, usually facultatively
pellicle
outer cell covering composed of interlocking protein strips that function like a flexible coat of armor, preventing cells from being torn or pierced without compromising their range of motion
phagolysosome
cellular body formed by the union of a phagosome containing the ingested particle with a lysosome that contains hydrolytic enzymes | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/23%3A_Protists/23.2%3A_Characteristics_of_Protists.txt |
Skills to Develop
• Describe representative protist organisms from each of the six presently recognized supergroups of eukaryotes
• Identify the evolutionary relationships of plants, animals, and fungi within the six presently recognized supergroups of eukaryotes
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging. The emerging classification scheme groups the entire domain Eukaryota into six “supergroups” that contain all of the protists as well as animals, plants, and fungi that evolved from a common ancestor (Figure \(1\)). The supergroups are believed to be monophyletic, meaning that all organisms within each supergroup are believed to have evolved from a single common ancestor, and thus all members are most closely related to each other than to organisms outside that group. There is still evidence lacking for the monophyly of some groups.
The classification of eukaryotes is still in flux, and the six supergroups may be modified or replaced by a more appropriate hierarchy as genetic, morphological, and ecological data accumulate. Keep in mind that the classification scheme presented here is just one of several hypotheses, and the true evolutionary relationships are still to be determined. When learning about protists, it is helpful to focus less on the nomenclature and more on the commonalities and differences that define the groups themselves.
Excavata
Many of the protist species classified into the supergroup Excavata are asymmetrical, single-celled organisms with a feeding groove “excavated” from one side. This supergroup includes heterotrophic predators, photosynthetic species, and parasites. Its subgroups are the diplomonads, parabasalids, and euglenozoans.
Diplomonads
Among the Excavata are the diplomonads, which include the intestinal parasite, Giardia lamblia (Figure \(2\)). Until recently, these protists were believed to lack mitochondria. Mitochondrial remnant organelles, called mitosomes, have since been identified in diplomonads, but these mitosomes are essentially nonfunctional. Diplomonads exist in anaerobic environments and use alternative pathways, such as glycolysis, to generate energy. Each diplomonad cell has two identical nuclei and uses several flagella for locomotion.
Parabasalids
A second Excavata subgroup, the parabasalids, also exhibits semi-functional mitochondria. In parabasalids, these structures function anaerobically and are called hydrogenosomes because they produce hydrogen gas as a byproduct. Parabasalids move with flagella and membrane rippling. Trichomonas vaginalis, a parabasalid that causes a sexually transmitted disease in humans, employs these mechanisms to transit through the male and female urogenital tracts. T. vaginalis causes trichamoniasis, which appears in an estimated 180 million cases worldwide each year. Whereas men rarely exhibit symptoms during an infection with this protist, infected women may become more susceptible to secondary infection with human immunodeficiency virus (HIV) and may be more likely to develop cervical cancer. Pregnant women infected with T. vaginalis are at an increased risk of serious complications, such as pre-term delivery.
Euglenozoans
Euglenozoans includes parasites, heterotrophs, autotrophs, and mixotrophs, ranging in size from 10 to 500 µm. Euglenoids move through their aquatic habitats using two long flagella that guide them toward light sources sensed by a primitive ocular organ called an eyespot. The familiar genus, Euglena, encompasses some mixotrophic species that display a photosynthetic capability only when light is present. In the dark, the chloroplasts of Euglena shrink up and temporarily cease functioning, and the cells instead take up organic nutrients from their environment.
The human parasite, Trypanosoma brucei, belongs to a different subgroup of Euglenozoa, the kinetoplastids. The kinetoplastid subgroup is named after the kinetoplast, a DNA mass carried within the single, oversized mitochondrion possessed by each of these cells. This subgroup includes several parasites, collectively called trypanosomes, which cause devastating human diseases and infect an insect species during a portion of their life cycle. T. brucei develops in the gut of the tsetse fly after the fly bites an infected human or other mammalian host. The parasite then travels to the insect salivary glands to be transmitted to another human or other mammal when the infected tsetse fly consumes another blood meal. T. brucei is common in central Africa and is the causative agent of African sleeping sickness, a disease associated with severe chronic fatigue, coma, and can be fatal if left untreated.
Trypanosoma brucei
Watch this video to see T. brucei swimming. https://youtu.be/EnsydwITLYk
Chromalveolata
Current evidence suggests that species classified as chromalveolates are derived from a common ancestor that engulfed a photosynthetic red algal cell, which itself had already evolved chloroplasts from an endosymbiotic relationship with a photosynthetic prokaryote. Therefore, the ancestor of chromalveolates is believed to have resulted from a secondary endosymbiotic event. However, some chromalveolates appear to have lost red alga-derived plastid organelles or lack plastid genes altogether. Therefore, this supergroup should be considered a hypothesis-based working group that is subject to change. Chromalveolates include very important photosynthetic organisms, such as diatoms, brown algae, and significant disease agents in animals and plants. The chromalveolates can be subdivided into alveolates and stramenopiles.
Alveolates: Dinoflagellates, Apicomplexians, and Ciliates
A large body of data supports that the alveolates are derived from a shared common ancestor. The alveolates are named for the presence of an alveolus, or membrane-enclosed sac, beneath the cell membrane. The exact function of the alveolus is unknown, but it may be involved in osmoregulation. The alveolates are further categorized into some of the better-known protists: the dinoflagellates, the apicomplexans, and the ciliates.
Dinoflagellates exhibit extensive morphological diversity and can be photosynthetic, heterotrophic, or mixotrophic. Many dinoflagellates are encased in interlocking plates of cellulose. Two perpendicular flagella fit into the grooves between the cellulose plates, with one flagellum extending longitudinally and a second encircling the dinoflagellate (Figure \(4\)). Together, the flagella contribute to the characteristic spinning motion of dinoflagellates. These protists exist in freshwater and marine habitats, and are a component of plankton, the typically microscopic organisms that drift through the water and serve as a crucial food source for larger aquatic organisms.
Some dinoflagellates generate light, called bioluminescence, when they are jarred or stressed. Large numbers of marine dinoflagellates (billions or trillions of cells per wave) can emit light and cause an entire breaking wave to twinkle or take on a brilliant blue color (Figure \(5\)). For approximately 20 species of marine dinoflagellates, population explosions (also called blooms) during the summer months can tint the ocean with a muddy red color. This phenomenon is called a red tide, and it results from the abundant red pigments present in dinoflagellate plastids. In large quantities, these dinoflagellate species secrete an asphyxiating toxin that can kill fish, birds, and marine mammals. Red tides can be massively detrimental to commercial fisheries, and humans who consume these protists may become poisoned.
The apicomplexan protists are so named because their microtubules, fibrin, and vacuoles are asymmetrically distributed at one end of the cell in a structure called an apical complex (Figure \(6\)). The apical complex is specialized for entry and infection of host cells. Indeed, all apicomplexans are parasitic. This group includes the genus Plasmodium, which causes malaria in humans. Apicomplexan life cycles are complex, involving multiple hosts and stages of sexual and asexual reproduction.
The ciliates, which include Paramecium and Tetrahymena, are a group of protists 10 to 3,000 micrometers in length that are covered in rows, tufts, or spirals of tiny cilia. By beating their cilia synchronously or in waves, ciliates can coordinate directed movements and ingest food particles. Certain ciliates have fused cilia-based structures that function like paddles, funnels, or fins. Ciliates also are surrounded by a pellicle, providing protection without compromising agility. The genus Paramecium includes protists that have organized their cilia into a plate-like primitive mouth, called an oral groove, which is used to capture and digest bacteria (Figure \(7\)). Food captured in the oral groove enters a food vacuole, where it combines with digestive enzymes. Waste particles are expelled by an exocytic vesicle that fuses at a specific region on the cell membrane, called the anal pore. In addition to a vacuole-based digestive system, Paramecium also uses contractile vacuoles, which are osmoregulatory vesicles that fill with water as it enters the cell by osmosis and then contract to squeeze water from the cell.
Link to Learning
Watch the video of the contractile vacuole of Paramecium expelling water to keep the cell osmotically balanced.
Paramecium has two nuclei, a macronucleus and a micronucleus, in each cell. The micronucleus is essential for sexual reproduction, whereas the macronucleus directs asexual binary fission and all other biological functions. The process of sexual reproduction in Paramecium underscores the importance of the micronucleus to these protists. Paramecium and most other ciliates reproduce sexually by conjugation. This process begins when two different mating types of Paramecium make physical contact and join with a cytoplasmic bridge (Figure \(8\)). The diploid micronucleus in each cell then undergoes meiosis to produce four haploid micronuclei. Three of these degenerate in each cell, leaving one micronucleus that then undergoes mitosis, generating two haploid micronuclei. The cells each exchange one of these haploid nuclei and move away from each other. A similar process occurs in bacteria that have plasmids. Fusion of the haploid micronuclei generates a completely novel diploid pre-micronucleus in each conjugative cell. This pre-micronucleus undergoes three rounds of mitosis to produce eight copies, and the original macronucleus disintegrates. Four of the eight pre-micronuclei become full-fledged micronuclei, whereas the other four perform multiple rounds of DNA replication and go on to become new macronuclei. Two cell divisions then yield four new Paramecia from each original conjugative cell.
Exercise
Which of the following statements about Paramecium sexual reproduction is false?
1. The macronuclei are derived from micronuclei.
2. Both mitosis and meiosis occur during sexual reproduction.
3. The conjugate pair swaps macronucleii.
4. Each parent produces four daughter cells.
Stramenopiles: Diatoms, Brown Algae, Golden Algae and Oomycetes
The other subgroup of chromalveolates, the stramenopiles, includes photosynthetic marine algae and heterotrophic protists. The unifying feature of this group is the presence of a textured, or “hairy,” flagellum. Many stramenopiles also have an additional flagellum that lacks hair-like projections (Figure \(9\)). Members of this subgroup range in size from single-celled diatoms to the massive and multicellular kelp.
The diatoms are unicellular photosynthetic protists that encase themselves in intricately patterned, glassy cell walls composed of silicon dioxide in a matrix of organic particles (Figure \(10\)). These protists are a component of freshwater and marine plankton. Most species of diatoms reproduce asexually, although some instances of sexual reproduction and sporulation also exist. Some diatoms exhibit a slit in their silica shell, called a raphe. By expelling a stream of mucopolysaccharides from the raphe, the diatom can attach to surfaces or propel itself in one direction.
During periods of nutrient availability, diatom populations bloom to numbers greater than can be consumed by aquatic organisms. The excess diatoms die and sink to the sea floor where they are not easily reached by saprobes that feed on dead organisms. As a result, the carbon dioxide that the diatoms had consumed and incorporated into their cells during photosynthesis is not returned to the atmosphere. In general, this process by which carbon is transported deep into the ocean is described as the biological carbon pump, because carbon is “pumped” to the ocean depths where it is inaccessible to the atmosphere as carbon dioxide. The biological carbon pump is a crucial component of the carbon cycle that maintains lower atmospheric carbon dioxide levels.
Like diatoms, golden algae are largely unicellular, although some species can form large colonies. Their characteristic gold color results from their extensive use of carotenoids, a group of photosynthetic pigments that are generally yellow or orange in color. Golden algae are found in both freshwater and marine environments, where they form a major part of the plankton community.
The brown algae are primarily marine, multicellular organisms that are known colloquially as seaweeds. Giant kelps are a type of brown algae. Some brown algae have evolved specialized tissues that resemble terrestrial plants, with root-like holdfasts, stem-like stipes, and leaf-like blades that are capable of photosynthesis. The stipes of giant kelps are enormous, extending in some cases for 60 meters. A variety of algal life cycles exists, but the most complex is alternation of generations, in which both haploid and diploid stages involve multicellularity. Compare this life cycle to that of humans, for instance. Haploid gametes produced by meiosis (sperm and egg) combine in fertilization to generate a diploid zygote that undergoes many rounds of mitosis to produce a multicellular embryo and then a fetus. However, the individual sperm and egg themselves never become multicellular beings. Terrestrial plants also have evolved alternation of generations. In the brown algae genus Laminaria, haploid spores develop into multicellular gametophytes, which produce haploid gametes that combine to produce diploid organisms that then become multicellular organisms with a different structure from the haploid form (Figure \(11\)). Certain other organisms perform alternation of generations in which both the haploid and diploid forms look the same.
Exercise
Which of the following statements about the Laminaria life cycle is false?
1. 1n zoospores form in the sporangia.
2. The sporophyte is the 2n plant.
3. The gametophyte is diploid.
4. Both the gametophyte and sporophyte stages are multicellular.
The water molds, oomycetes (“egg fungus”), were so-named based on their fungus-like morphology, but molecular data have shown that the water molds are not closely related to fungi. The oomycetes are characterized by a cellulose-based cell wall and an extensive network of filaments that allow for nutrient uptake. As diploid spores, many oomycetes have two oppositely directed flagella (one hairy and one smooth) for locomotion. The oomycetes are nonphotosynthetic and include many saprobes and parasites. The saprobes appear as white fluffy growths on dead organisms (Figure \(12\)). Most oomycetes are aquatic, but some parasitize terrestrial plants. One plant pathogen is Phytophthora infestans, the causative agent of late blight of potatoes, such as occurred in the nineteenth century Irish potato famine.
Rhizaria
The Rhizaria supergroup includes many of the amoebas, most of which have threadlike or needle-like pseudopodia (Figure \(13\)). Pseudopodia function to trap and engulf food particles and to direct movement in rhizarian protists. These pseudopods project outward from anywhere on the cell surface and can anchor to a substrate. The protist then transports its cytoplasm into the pseudopod, thereby moving the entire cell. This type of motion, called cytoplasmic streaming, is used by several diverse groups of protists as a means of locomotion or as a method to distribute nutrients and oxygen.
Link to Learning
Take a look at this video to see cytoplasmic streaming in a green alga.
Forams
Foraminiferans, or forams, are unicellular heterotrophic protists, ranging from approximately 20 micrometers to several centimeters in length, and occasionally resembling tiny snails (Figure \(14\)). As a group, the forams exhibit porous shells, called tests that are built from various organic materials and typically hardened with calcium carbonate. The tests may house photosynthetic algae, which the forams can harvest for nutrition. Foram pseudopodia extend through the pores and allow the forams to move, feed, and gather additional building materials. Typically, forams are associated with sand or other particles in marine or freshwater habitats. Foraminiferans are also useful as indicators of pollution and changes in global weather patterns.
Radiolarians
A second subtype of Rhizaria, the radiolarians, exhibit intricate exteriors of glassy silica with radial or bilateral symmetry (Figure \(15\)). Needle-like pseudopods supported by microtubules radiate outward from the cell bodies of these protists and function to catch food particles. The shells of dead radiolarians sink to the ocean floor, where they may accumulate in 100 meter-thick depths. Preserved, sedimented radiolarians are very common in the fossil record.
Archaeplastida
Red algae and green algae are included in the supergroup Archaeplastida. It was from a common ancestor of these protists that the land plants evolved, since their closest relatives are found in this group. Molecular evidence supports that all Archaeplastida are descendents of an endosymbiotic relationship between a heterotrophic protist and a cyanobacterium. The red and green algae include unicellular, multicellular, and colonial forms.
Red Algae
Red algae, or rhodophytes, are primarily multicellular, lack flagella, and range in size from microscopic, unicellular protists to large, multicellular forms grouped into the informal seaweed category. The red algae life cycle is an alternation of generations. Some species of red algae contain phycoerythrins, photosynthetic accessory pigments that are red in color and outcompete the green tint of chlorophyll, making these species appear as varying shades of red. Other protists classified as red algae lack phycoerythrins and are parasites. Red algae are common in tropical waters where they have been detected at depths of 260 meters. Other red algae exist in terrestrial or freshwater environments.
Green Algae: Chlorophytes and Charophytes
The most abundant group of algae is the green algae. The green algae exhibit similar features to the land plants, particularly in terms of chloroplast structure. That this group of protists shared a relatively recent common ancestor with land plants is well supported. The green algae are subdivided into the chlorophytes and the charophytes. The charophytes are the closest living relatives to land plants and resemble them in morphology and reproductive strategies. Charophytes are common in wet habitats, and their presence often signals a healthy ecosystem.
The chlorophytes exhibit great diversity of form and function. Chlorophytes primarily inhabit freshwater and damp soil, and are a common component of plankton. Chlamydomonas is a simple, unicellular chlorophyte with a pear-shaped morphology and two opposing, anterior flagella that guide this protist toward light sensed by its eyespot. More complex chlorophyte species exhibit haploid gametes and spores that resemble Chlamydomonas.
The chlorophyte Volvox is one of only a few examples of a colonial organism, which behaves in some ways like a collection of individual cells, but in other ways like the specialized cells of a multicellular organism (Figure \(16\)). Volvox colonies contain 500 to 60,000 cells, each with two flagella, contained within a hollow, spherical matrix composed of a gelatinous glycoprotein secretion. Individual Volvox cells move in a coordinated fashion and are interconnected by cytoplasmic bridges. Only a few of the cells reproduce to create daughter colonies, an example of basic cell specialization in this organism.
True multicellular organisms, such as the sea lettuce, Ulva, are represented among the chlorophytes. In addition, some chlorophytes exist as large, multinucleate, single cells. Species in the genus Caulerpa exhibit flattened fern-like foliage and can reach lengths of 3 meters (Figure \(17\)). Caulerpa species undergo nuclear division, but their cells do not complete cytokinesis, remaining instead as massive and elaborate single cells.
Amoebozoa
The amoebozoans characteristically exhibit pseudopodia that extend like tubes or flat lobes, rather than the hair-like pseudopodia of rhizarian amoeba (Figure \(18\)). The Amoebozoa include several groups of unicellular amoeba-like organisms that are free-living or parasites.
Slime Molds
A subset of the amoebozoans, the slime molds, has several morphological similarities to fungi that are thought to be the result of convergent evolution. For instance, during times of stress, some slime molds develop into spore-generating fruiting bodies, much like fungi.
The slime molds are categorized on the basis of their life cycles into plasmodial or cellular types. Plasmodial slime molds are composed of large, multinucleate cells and move along surfaces like an amorphous blob of slime during their feeding stage (Figure \(19\)). Food particles are lifted and engulfed into the slime mold as it glides along. Upon maturation, the plasmodium takes on a net-like appearance with the ability to form fruiting bodies, or sporangia, during times of stress. Haploid spores are produced by meiosis within the sporangia, and spores can be disseminated through the air or water to potentially land in more favorable environments. If this occurs, the spores germinate to form ameboid or flagellate haploid cells that can combine with each other and produce a diploid zygotic slime mold to complete the life cycle.
The cellular slime molds function as independent amoeboid cells when nutrients are abundant (Figure \(20\)). When food is depleted, cellular slime molds pile onto each other into a mass of cells that behaves as a single unit, called a slug. Some cells in the slug contribute to a 2–3-millimeter stalk, drying up and dying in the process. Cells atop the stalk form an asexual fruiting body that contains haploid spores. As with plasmodial slime molds, the spores are disseminated and can germinate if they land in a moist environment. One representative genus of the cellular slime molds is Dictyostelium, which commonly exists in the damp soil of forests.
Link to Learning
View this site to see the formation of a fruiting body by a cellular slime mold.
Opisthokonta
The opisthokonts include the animal-like choanoflagellates, which are believed to resemble the common ancestor of sponges and, in fact, all animals. Choanoflagellates include unicellular and colonial forms, and number about 244 described species. These organisms exhibit a single, apical flagellum that is surrounded by a contractile collar composed of microvilli. The collar uses a similar mechanism to sponges to filter out bacteria for ingestion by the protist. The morphology of choanoflagellates was recognized early on as resembling the collar cells of sponges, and suggesting a possible relationship to animals.
The Mesomycetozoa form a small group of parasites, primarily of fish, and at least one form that can parasitize humans. Their life cycles are poorly understood. These organisms are of special interest, because they appear to be so closely related to animals. In the past, they were grouped with fungi and other protists based on their morphology.
Summary
The process of classifying protists into meaningful groups is ongoing, but genetic data in the past 20 years have clarified many relationships that were previously unclear or mistaken. The majority view at present is to order all eukaryotes into six supergroups: Excavata, Chromalveolata, Rhizaria, Archaeplastida, Amoebozoa, and Opisthokonta. The goal of this classification scheme is to create clusters of species that all are derived from a common ancestor. At present, the monophyly of some of the supergroups are better supported by genetic data than others. Although tremendous variation exists within the supergroups, commonalities at the morphological, physiological, and ecological levels can be identified.
Art Connections
Figure \(8\): Which of the following statements about Paramecium sexual reproduction is false?
1. The macronuclei are derived from micronuclei.
2. Both mitosis and meiosis occur during sexual reproduction.
3. The conjugate pair swaps macronuclei.
4. Each parent produces four daughter cells.
Answer
C
Figure \(11\): Which of the following statements about the Laminaria life cycle is false?
1. 1n zoospores form in the sporangia.
2. The sporophyte is the 2n plant.
3. The gametophyte is diploid.
4. Both the gametophyte and sporophyte stages are multicellular.
Answer
C
Glossary
biological carbon pump
process by which inorganic carbon is fixed by photosynthetic species that then die and fall to the sea floor where they cannot be reached by saprobes and their carbon dioxide consumption cannot be returned to the atmosphere
bioluminescence
generation and emission of light by an organism, as in dinoflagellates
contractile vacuole
vesicle that fills with water (as it enters the cell by osmosis) and then contracts to squeeze water from the cell; an osmoregulatory vesicle
cytoplasmic streaming
movement of cytoplasm into an extended pseudopod such that the entire cell is transported to the site of the pseudopod
hydrogenosome
organelle carried by parabasalids (Excavata) that functions anaerobically and outputs hydrogen gas as a byproduct; likely evolved from mitochondria
kinetoplast
mass of DNA carried within the single, oversized mitochondrion, characteristic of kinetoplastids (phylum: Euglenozoa)
mitosome
nonfunctional organelle carried in the cells of diplomonads (Excavata) that likely evolved from a mitochondrion
plankton
diverse group of mostly microscopic organisms that drift in marine and freshwater systems and serve as a food source for larger aquatic organisms
raphe
slit in the silica shell of diatoms through which the protist secretes a stream of mucopolysaccharides for locomotion and attachment to substrates
test
porous shell of a foram that is built from various organic materials and typically hardened with calcium carbonate | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/23%3A_Protists/23.3%3A_Groups_of_Protists.txt |
Skills to Develop
• Describe the role that protists play in the ecosystem
• Describe important pathogenic species of protists
Protists function in various ecological niches. Whereas some protist species are essential components of the food chain and generators of biomass, others function in the decomposition of organic materials. Still other protists are dangerous human pathogens or causative agents of devastating plant diseases.
Primary Producers/Food Sources
Protists are essential sources of nutrition for many other organisms. In some cases, as in plankton, protists are consumed directly. Alternatively, photosynthetic protists serve as producers of nutrition for other organisms. For instance, photosynthetic dinoflagellates called zooxanthellae use sunlight to fix inorganic carbon. In this symbiotic relationship, these protists provide nutrients for coral polyps (Figure \(1\)) that house them, giving corals a boost of energy to secrete a calcium carbonate skeleton. In turn, the corals provide the protist with a protected environment and the compounds needed for photosynthesis. This type of symbiotic relationship is important in nutrient-poor environments. Without dinoflagellate symbionts, corals lose algal pigments in a process called coral bleaching, and they eventually die. This explains why reef-building corals do not reside in waters deeper than 20 meters: insufficient light reaches those depths for dinoflagellates to photosynthesize.
The protists themselves and their products of photosynthesis are essential—directly or indirectly—to the survival of organisms ranging from bacteria to mammals (Figure \(2\)). As primary producers, protists feed a large proportion of the world’s aquatic species. (On land, terrestrial plants serve as primary producers.) In fact, approximately one-quarter of the world’s photosynthesis is conducted by protists, particularly dinoflagellates, diatoms, and multicellular algae.
Protists do not create food sources only for sea-dwelling organisms. For instance, certain anaerobic parabasalid species exist in the digestive tracts of termites and wood-eating cockroaches, where they contribute an essential step in the digestion of cellulose ingested by these insects as they bore through wood.
Human Pathogens
A pathogen is anything that causes disease. Parasites live in or on an organism and harm the organism. A significant number of protists are pathogenic parasites that must infect other organisms to survive and propagate. Protist parasites include the causative agents of malaria, African sleeping sickness, and waterborne gastroenteritis in humans. Other protist pathogens prey on plants, effecting massive destruction of food crops.
Plasmodium Species
Members of the genus Plasmodium must colonize both a mosquito and a vertebrate to complete their life cycle. In vertebrates, the parasite develops in liver cells and goes on to infect red blood cells, bursting from and destroying the blood cells with each asexual replication cycle (Figure \(3\)). Of the four Plasmodium species known to infect humans, P. falciparum accounts for 50 percent of all malaria cases and is the primary cause of disease-related fatalities in tropical regions of the world. In 2010, it was estimated that malaria caused between one-half and one million deaths, mostly in African children. During the course of malaria, P. falciparum can infect and destroy more than one-half of a human’s circulating blood cells, leading to severe anemia. In response to waste products released as the parasites burst from infected blood cells, the host immune system mounts a massive inflammatory response with episodes of delirium-inducing fever as parasites lyse red blood cells, spilling parasite waste into the bloodstream. P. falciparum is transmitted to humans by the African malaria mosquito, Anopheles gambiae. Techniques to kill, sterilize, or avoid exposure to this highly aggressive mosquito species are crucial to malaria control.
Trypanosomes
Trypanosoma brucei, the parasite that is responsible for African sleeping sickness, confounds the human immune system by changing its thick layer of surface glycoproteins with each infectious cycle (Figure \(4\)). The glycoproteins are identified by the immune system as foreign antigens, and a specific antibody defense is mounted against the parasite. However, T. brucei has thousands of possible antigens, and with each subsequent generation, the protist switches to a glycoprotein coating with a different molecular structure. In this way, T. brucei is capable of replicating continuously without the immune system ever succeeding in clearing the parasite. Without treatment, T. brucei attacks red blood cells, causing the patient to lapse into a coma and eventually die. During epidemic periods, mortality from the disease can be high. Greater surveillance and control measures lead to a reduction in reported cases; some of the lowest numbers reported in 50 years (fewer than 10,000 cases in all of sub-Saharan Africa) have happened since 2009.
In Latin America, another species, T. cruzi, is responsible for Chagas disease. T. cruzi infections are mainly caused by a blood-sucking bug. The parasite inhabits heart and digestive system tissues in the chronic phase of infection, leading to malnutrition and heart failure due to abnormal heart rhythms. An estimated 10 million people are infected with Chagas disease, and it caused 10,000 deaths in 2008.
Plant Parasites
Protist parasites of terrestrial plants include agents that destroy food crops. The oomycete Plasmopara viticola parasitizes grape plants, causing a disease called downy mildew (Figure \(5\)). Grape plants infected with P. viticola appear stunted and have discolored, withered leaves. The spread of downy mildew nearly collapsed the French wine industry in the nineteenth century.
Phytophthora infestans is an oomycete responsible for potato late blight, which causes potato stalks and stems to decay into black slime (Figure \(6\)). Widespread potato blight caused by P. infestans precipitated the well-known Irish potato famine in the nineteenth century that claimed the lives of approximately 1 million people and led to the emigration of at least 1 million more from Ireland. Late blight continues to plague potato crops in certain parts of the United States and Russia, wiping out as much as 70 percent of crops when no pesticides are applied.
Agents of Decomposition
The fungus-like protist saprobes are specialized to absorb nutrients from nonliving organic matter, such as dead organisms or their wastes. For instance, many types of oomycetes grow on dead animals or algae. Saprobic protists have the essential function of returning inorganic nutrients to the soil and water. This process allows for new plant growth, which in turn generates sustenance for other organisms along the food chain. Indeed, without saprobe species, such as protists, fungi, and bacteria, life would cease to exist as all organic carbon became “tied up” in dead organisms.
Summary
Protists function at several levels of the ecological food web: as primary producers, as direct food sources, and as decomposers. In addition, many protists are parasites of plants and animals that can cause deadly human diseases or destroy valuable crops. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/23%3A_Protists/23.4%3A_Ecology_of_Protists.txt |
23.1: Eukaryotic Origins
Living things fall into three large groups: Archaea, Bacteria, and Eukarya. The first two have prokaryotic cells, and the third contains all eukaryotes. A relatively sparse fossil record is available to help discern what the first members of each of these lineages looked like, so it is possible that all the events that led to the last common ancestor of extant eukaryotes will remain unknown. However, comparative biology of extant organisms and the limited fossil record provide some insight into
Review Questions
What event is thought to have contributed to the evolution of eukaryotes?
1. global warming
2. glaciation
3. volcanic activity
4. oxygenation of the atmosphere
Answer
D
Which characteristic is shared by prokaryotes and eukaryotes?
1. cytoskeleton
2. nuclear envelope
3. DNA-based genome
4. mitochondria
Answer
C
Mitochondria most likely evolved by _____________.
1. a photosynthetic cyanobacterium
2. cytoskeletal elements
3. endosymbiosis
4. membrane proliferation
Answer
C
Which of these protists is believed to have evolved following a secondary endosymbiosis?
1. green algae
2. cyanobacteria
3. red algae
4. chlorarachniophytes
Answer
D
Free Response
Describe the hypothesized steps in the origin of eukaryotic cells.
Answer
Eukaryotic cells arose through endosymbiotic events that gave rise to the energy-producing organelles within the eukaryotic cells such as mitochondria and chloroplasts. The nuclear genome of eukaryotes is related most closely to the Archaea, so it may have been an early archaean that engulfed a bacterial cell that evolved into a mitochondrion. Mitochondria appear to have originated from an alpha-proteobacterium, whereas chloroplasts originated as a cyanobacterium. There is also evidence of secondary endosymbiotic events. Other cell components may also have resulted from endosymbiotic events.
23.2: Characteristics of Protists
There are over 100,000 described living species of protists, and it is unclear how many undescribed species may exist. Since many protists live as commensals or parasites in other organisms and these relationships are often species-specific, there is a huge potential for protist diversity that matches the diversity of hosts. As the catchall term for eukaryotic organisms that are not animal, plant, or fungi, it is not surprising that very few characteristics are common to all protists.
Review Questions
Protists that have a pellicle are surrounded by ______________.
1. silica dioxide
2. calcium carbonate
3. carbohydrates
4. proteins
Answer
D
Protists with the capabilities to perform photosynthesis and to absorb nutrients from dead organisms are called ______________.
1. photoautotrophs
2. mixotrophs
3. saprobes
4. heterotrophs
Answer
B
Which of these locomotor organs would likely be the shortest?
1. a flagellum
2. a cilium
3. an extended pseudopod
4. a pellicle
Answer
B
Alternation of generations describes which of the following?
1. The haploid form can be multicellular; the diploid form is unicellular.
2. The haploid form is unicellular; the diploid form can be multicellular.
3. Both the haploid and diploid forms can be multicellular.
4. Neither the haploid nor the diploid forms can be multicellular.
Answer
C
Free Response
Explain in your own words why sexual reproduction can be useful if a protist’s environment changes.
Answer
The ability to perform sexual reproduction allows protists to recombine their genes and produce new variations of progeny that may be better suited to the new environment. In contrast, asexual reproduction generates progeny that are clones of the parent.
Giardia lamblia is a cyst-forming protist parasite that causes diarrhea if ingested. Given this information, against what type(s) of environments might G. lamblia cysts be particularly resistant?
Answer
As an intestinal parasite, Giardia cysts would be exposed to low pH in the stomach acids of its host. To survive this environment and reach the intestine, the cysts would have to be resistant to acidic conditions.
23.3: Groups of Protists
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging.
Review Questions
Which protist group exhibits mitochondrial remnants with reduced functionality?
1. slime molds
2. diatoms
3. parabasalids
4. dinoflagellates
Answer
C
Conjugation between two Paramecia produces ________ total daughter cells.
1. 2
2. 4
3. 8
4. 16
Answer
C
What is the function of the raphe in diatoms?
1. locomotion
2. defense
3. capturing food
4. photosynthesis
Answer
A
What genus of protists appears to contradict the statement that unicellularity restricts cell size?
1. Dictyostelium
2. Ulva
3. Plasmodium
4. Caulerpa
Answer
D
Free Response
The chlorophyte (green algae) genera Ulva and Caulerpa both have macroscopic leaf-like and stem-like structures, but only Ulva species are considered truly multicellular. Explain why.
Answer
Unlike Ulva, protists in the genus Caulerpa actually are large, multinucleate, single cells. Because these organisms undergo mitosis without cytokinesis and lack cytoplasmic divisions, they cannot be considered truly multicellular.
Why might a light-sensing eyespot be ineffective for an obligate saprobe? Suggest an alternative organ for a saprobic protist.
Answer
By definition, an obligate saprobe lacks the ability to perform photosynthesis, so it cannot directly obtain nutrition by searching for light. Instead, a chemotactic mechanism that senses the odors released during decay might be a more effective sensing organ for a saprobe.
23.4: Ecology of Protists
Protists function in various ecological niches. Whereas some protist species are essential components of the food chain and generators of biomass, others function in the decomposition of organic materials. Still other protists are dangerous human pathogens or causative agents of devastating plant diseases.
Review Questions
An example of carbon fixation is _____________.
1. photosynthesis
2. decomposition
3. phagocytosis
4. parasitism
Answer
A
Which parasitic protist evades the host immune system by altering its surface proteins with each generation?
1. Paramecium caudatum
2. Trypanosoma brucei
3. Plasmodium falciparum
4. Phytophthora infestans
Answer
B
Free Response
How does killing Anopheles mosquitoes affect the Plasmodium protists?
Answer
Plasmodium parasites infect humans and cause malaria. However, they must complete part of their life cycle within Anopheles mosquitoes, and they can only infect humans via the bite wound of a mosquito. If the mosquito population is decreased, then fewer Plasmodium would be able to develop and infect humans, thereby reducing the incidence of human infections with this parasite.
Without treatment, why does African sleeping sickness invariably lead to death?
Answer
The trypanosomes that cause this disease are capable of expressing a glycoprotein coat with a different molecular structure with each generation. Because the immune system must respond to specific antigens to raise a meaningful defense, the changing nature of trypanosome antigens prevents the immune system from ever clearing this infection. Massive trypanosome infection eventually leads to host organ failure and death. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/23%3A_Protists/23.E%3A_Protists_%28Exercises%29.txt |
The kingdom Fungi includes an enormous variety of living organisms collectively referred to as Eucomycota, or true Fungi. While scientists have identified about 100,000 species of fungi, this is only a fraction of the 1.5 million species of fungus likely present on Earth. Edible mushrooms, yeasts, black mold, and the producer of the antibiotic penicillin, Penicillium notatum, are all members of the kingdom Fungi, which belongs to the domain Eukarya.
• 24.0: Prelude to Fungi
The word fungus comes from the Latin word for mushrooms. Indeed, the familiar mushroom is a reproductive structure used by many types of fungi. However, there are also many fungi species that don't produce mushrooms at all. Being eukaryotes, a typical fungal cell contains a true nucleus and many membrane-bound organelles. The kingdom Fungi includes an enormous variety of living organisms collectively referred to as Eucomycota, or true Fungi.
• 24.1: Characteristics of Fungi
Although humans have used yeasts and mushrooms since prehistoric times, until recently, the biology of fungi was poorly understood. Up until the mid-20th century, many scientists classified fungi as plants. Fungi, like plants, arose mostly sessile and seemingly rooted in place. They possess a stem-like structure similar to plants, as well as having a root-like fungal mycelium in the soil. In addition, their mode of nutrition was poorly understood.
• 24.2: Classifications of Fungi
The kingdom Fungi contains five major phyla that were established according to their mode of sexual reproduction or using molecular data. Polyphyletic, unrelated fungi that reproduce without a sexual cycle, are placed for convenience in a sixth group called a “form phylum”. Not all mycologists agree with this scheme. Rapid advances in molecular biology and the sequencing of 18S rRNA (a part of RNA) continue to show new and different relationships between the various categories of fungi.
• 24.3: Ecology of Fungi
Fungi play a crucial role in the balance of ecosystems. They colonize most habitats on Earth, preferring dark, moist conditions. They can thrive in seemingly hostile environments, such as the tundra, thanks to a most successful symbiosis with photosynthetic organisms like algae to produce lichens. Fungi are not obvious in the way large animals or tall trees appear. Yet, like bacteria, they are the major decomposers of nature.
• 24.4: Fungal Parasites and Pathogens
Parasitism describes a symbiotic relationship in which one member of the association benefits at the expense of the other. Both parasites and pathogens harm the host; however, the pathogen causes a disease, whereas the parasite usually does not. Commensalism occurs when one member benefits without affecting the other.
• 24.5: Importance of Fungi in Human Life
Although we often think of fungi as organisms that cause disease and rot food, fungi are important to human life on many levels. As we have seen, they influence the well-being of human populations on a large scale because they are part of the nutrient cycle in ecosystems. They have other ecosystem roles as well. As animal pathogens, fungi help to control the population of damaging pests. These fungi are very specific to the insects they attack, and do not infect animals or plants.
• 24.E: Fungi (Exercises)
Thumbnail: A cluster of mushrooms. (Modification of work by Chris Wee).
24: Fungi
The word fungus comes from the Latin word for mushrooms. Indeed, the familiar mushroom is a reproductive structure used by many types of fungi. However, there are also many fungi species that don't produce mushrooms at all. Being eukaryotes, a typical fungal cell contains a true nucleus and many membrane-bound organelles. The kingdom Fungi includes an enormous variety of living organisms collectively referred to as Eucomycota, or true Fungi. While scientists have identified about 100,000 species of fungi, this is only a fraction of the 1.5 million species of fungus likely present on Earth. Edible mushrooms, yeasts, black mold, and the producer of the antibiotic penicillin, Penicillium notatum, are all members of the kingdom Fungi, which belongs to the domain Eukarya.
Fungi, once considered plant-like organisms, are more closely related to animals than plants. Fungi are not capable of photosynthesis: they are heterotrophic because they use complex organic compounds as sources of energy and carbon. Some fungal organisms multiply only asexually, whereas others undergo both asexual reproduction and sexual reproduction with alternation of generations. Most fungi produce a large number of spores, which are haploid cells that can undergo mitosis to form multicellular, haploid individuals. Like bacteria, fungi play an essential role in ecosystems because they are decomposers and participate in the cycling of nutrients by breaking down organic materials to simple molecules.
Fungi often interact with other organisms, forming beneficial or mutualistic associations. For example most terrestrial plants form symbiotic relationships with fungi. The roots of the plant connect with the underground parts of the fungus forming mycorrhizae. Through mycorrhizae, the fungus and plant exchange nutrients and water, greatly aiding the survival of both species Alternatively, lichens are an association between a fungus and its photosynthetic partner (usually an alga). Fungi also cause serious infections in plants and animals. For example, Dutch elm disease, which is caused by the fungus Ophiostoma ulmi, is a particularly devastating type of fungal infestation that destroys many native species of elm (Ulmus sp.) by infecting the tree’s vascular system. The elm bark beetle acts as a vector, transmitting the disease from tree to tree. Accidentally introduced in the 1900s, the fungus decimated elm trees across the continent. Many European and Asiatic elms are less susceptible to Dutch elm disease than American elms.
In humans, fungal infections are generally considered challenging to treat. Unlike bacteria, fungi do not respond to traditional antibiotic therapy, since they are eukaryotes. Fungal infections may prove deadly for individuals with compromised immune systems.
Fungi have many commercial applications. The food industry uses yeasts in baking, brewing, and cheese and wine making. Many industrial compounds are byproducts of fungal fermentation. Fungi are the source of many commercial enzymes and antibiotics.
Glossary
spore
a haploid cell that can undergo mitosis to form a multicellular, haploid individua
mycorrhizae
a mutualistic relationship between a plant and a fungus. Mycorrhizae are connections between fungal hyphae, which provide soil minerals to the plant, and plant roots, which provide carbohydrates to the fungus | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/24%3A_Fungi/24.0%3A_Prelude_to_Fungi.txt |
Skills to Develop
• List the characteristics of fungi
• Describe the composition of the mycelium
• Describe the mode of nutrition of fungi
• Explain sexual and asexual reproduction in fungi
Although humans have used yeasts and mushrooms since prehistoric times, until recently, the biology of fungi was poorly understood. Up until the mid-20th century, many scientists classified fungi as plants. Fungi, like plants, arose mostly sessile and seemingly rooted in place. They possess a stem-like structure similar to plants, as well as having a root-like fungal mycelium in the soil. In addition, their mode of nutrition was poorly understood. Progress in the field of fungal biology was the result of mycology: the scientific study of fungi. Based on fossil evidence, fungi appeared in the pre-Cambrian era, about 450 million years ago. Molecular biology analysis of the fungal genome demonstrates that fungi are more closely related to animals than plants. They are a polyphyletic group of organisms that share characteristics, rather than sharing a single common ancestor.
Career Connection: Mycologist
Mycologists are biologists who study fungi. Mycology is a branch of microbiology, and many mycologists start their careers with a degree in microbiology. To become a mycologist, a bachelor's degree in a biological science (preferably majoring in microbiology) and a master's degree in mycology are minimally necessary. Mycologists can specialize in taxonomy and fungal genomics, molecular and cellular biology, plant pathology, biotechnology, or biochemistry. Some medical microbiologists concentrate on the study of infectious diseases caused by fungi (mycoses). Mycologists collaborate with zoologists and plant pathologists to identify and control difficult fungal infections, such as the devastating chestnut blight, the mysterious decline in frog populations in many areas of the world, or the deadly epidemic called white nose syndrome, which is decimating bats in the Eastern United States.
Government agencies hire mycologists as research scientists and technicians to monitor the health of crops, national parks, and national forests. Mycologists are also employed in the private sector by companies that develop chemical and biological control products or new agricultural products, and by companies that provide disease control services. Because of the key role played by fungi in the fermentation of alcohol and the preparation of many important foods, scientists with a good understanding of fungal physiology routinely work in the food technology industry. Oenology, the science of wine making, relies not only on the knowledge of grape varietals and soil composition, but also on a solid understanding of the characteristics of the wild yeasts that thrive in different wine-making regions. It is possible to purchase yeast strains isolated from specific grape-growing regions. The great French chemist and microbiologist, Louis Pasteur, made many of his essential discoveries working on the humble brewer’s yeast, thus discovering the process of fermentation.
Cell Structure and Function
Fungi are eukaryotes, and as such, have a complex cellular organization. As eukaryotes, fungal cells contain a membrane-bound nucleus. The DNA in the nucleus is wrapped around histone proteins, as is observed in other eukaryotic cells. A few types of fungi have structures comparable to bacterial plasmids (loops of DNA); however, the horizontal transfer of genetic information from one mature bacterium to another rarely occurs in fungi. Fungal cells also contain mitochondria and a complex system of internal membranes, including the endoplasmic reticulum and Golgi apparatus.
Unlike plant cells, fungal cells do not have chloroplasts or chlorophyll. Many fungi display bright colors arising from other cellular pigments, ranging from red to green to black. The poisonous Amanita muscaria (fly agaric) is recognizable by its bright red cap with white patches (Figure \(1\)). Pigments in fungi are associated with the cell wall and play a protective role against ultraviolet radiation. Some fungal pigments are toxic.
Like plant cells, fungal cells have a thick cell wall. The rigid layers of fungal cell walls contain complex polysaccharides called chitin and glucans. Chitin, also found in the exoskeleton of insects, gives structural strength to the cell walls of fungi. The wall protects the cell from desiccation and predators. Fungi have plasma membranes similar to other eukaryotes, except that the structure is stabilized by ergosterol: a steroid molecule that replaces the cholesterol found in animal cell membranes. Most members of the kingdom Fungi are nonmotile. Flagella are produced only by the gametes in the primitive Phylum Chytridiomycota.
Growth
The vegetative body of a fungus is a unicellular or multicellular thallus. Dimorphic fungi can change from the unicellular to multicellular state depending on environmental conditions. Unicellular fungi are generally referred to as yeasts. Saccharomyces cerevisiae (baker’s yeast) and Candida species (the agents of thrush, a common fungal infection) are examples of unicellular fungi (Figure \(2\)).
Most fungi are multicellular organisms. They display two distinct morphological stages: the vegetative and reproductive. The vegetative stage consists of a tangle of slender thread-like structures called hyphae (singular, hypha), whereas the reproductive stage can be more conspicuous. The mass of hyphae is a mycelium (Figure \(3\)). It can grow on a surface, in soil or decaying material, in a liquid, or even on living tissue. Although individual hyphae must be observed under a microscope, the mycelium of a fungus can be very large, with some species truly being “the fungus humongous.” The giant Armillaria solidipes (honey mushroom) is considered the largest organism on Earth, spreading across more than 2,000 acres of underground soil in eastern Oregon; it is estimated to be at least 2,400 years old.
Most fungal hyphae are divided into separate cells by endwalls called septa (singular, septum) (Figure \(4\)). In most phyla of fungi, tiny holes in the septa allow for the rapid flow of nutrients and small molecules from cell to cell along the hypha. They are described as perforated septa. The hyphae in bread molds (which belong to the Phylum Zygomycota) are not separated by septa. Instead, they are formed by large cells containing many nuclei, an arrangement described as coenocytic hyphae (Figure 24.1.4).
Fungi thrive in environments that are moist and slightly acidic, and can grow with or without light. They vary in their oxygen requirement. Most fungi are obligate aerobes, requiring oxygen to survive. Other species, such as the Chytridiomycota that reside in the rumen of cattle, are are obligate anaerobes, in that they only use anaerobic respiration because oxygen will disrupt their metabolism or kill them. Yeasts are intermediate, being faculative anaerobes. This means that they grow best in the presence of oxygen using aerobic respiration, but can survive using anaerobic respiration when oxygen is not available. The alcohol produced from yeast fermentation is used in wine and beer production.
Nutrition
Like animals, fungi are heterotrophs; they use complex organic compounds as a source of carbon, rather than fix carbon dioxide from the atmosphere as do some bacteria and most plants. In addition, fungi do not fix nitrogen from the atmosphere. Like animals, they must obtain it from their diet. However, unlike most animals, which ingest food and then digest it internally in specialized organs, fungi perform these steps in the reverse order; digestion precedes ingestion. First, exoenzymes are transported out of the hyphae, where they process nutrients in the environment. Then, the smaller molecules produced by this external digestion are absorbed through the large surface area of the mycelium. As with animal cells, the polysaccharide of storage is glycogen, rather than starch, as found in plants.
Fungi are mostly saprobes (saprophyte is an equivalent term): organisms that derive nutrients from decaying organic matter. They obtain their nutrients from dead or decomposing organic matter: mainly plant material. Fungal exoenzymes are able to break down insoluble polysaccharides, such as the cellulose and lignin of dead wood, into readily absorbable glucose molecules. The carbon, nitrogen, and other elements are thus released into the environment. Because of their varied metabolic pathways, fungi fulfill an important ecological role and are being investigated as potential tools in bioremediation. For example, some species of fungi can be used to break down diesel oil and polycyclic aromatic hydrocarbons (PAHs). Other species take up heavy metals, such as cadmium and lead.
Some fungi are parasitic, infecting either plants or animals. Smut and Dutch elm disease affect plants, whereas athlete’s foot and candidiasis (thrush) are medically important fungal infections in humans. In environments poor in nitrogen, some fungi resort to predation of nematodes (small non-segmented roundworms). Species of Arthrobotrys fungi have a number of mechanisms to trap nematodes. One mechanism involves constricting rings within the network of hyphae. The rings swell when they touch the nematode, gripping it in a tight hold. The fungus penetrates the tissue of the worm by extending specialized hyphae called haustoria. Many parasitic fungi possess haustoria, as these structures penetrate the tissues of the host, release digestive enzymes within the host's body, and absorb the digested nutrients.
Reproduction
Fungi reproduce sexually and/or asexually. Perfect fungi reproduce both sexually and asexually, while the so-called imperfect fungi reproduce only asexually (by mitosis).
In both sexual and asexual reproduction, fungi produce spores that disperse from the parent organism by either floating on the wind or hitching a ride on an animal. Fungal spores are smaller and lighter than plant seeds. The giant puffball mushroom bursts open and releases trillions of spores. The huge number of spores released increases the likelihood of landing in an environment that will support growth (Figure \(5\)).
Asexual Reproduction
Fungi reproduce asexually by fragmentation, budding, or producing spores. Fragments of hyphae can grow new colonies. Somatic cells in yeast form buds. During budding (a type of cytokinesis), a bulge forms on the side of the cell, the nucleus divides mitotically, and the bud ultimately detaches itself from the mother cell (Figure \(6\)).
The most common mode of asexual reproduction is through the formation of asexual spores, which are produced by one parent only (through mitosis) and are genetically identical to that parent (Figure \(7\)). Spores allow fungi to expand their distribution and colonize new environments. They may be released from the parent thallus either outside or within a special reproductive sac called a sporangium.
There are many types of asexual spores. Conidiospores are unicellular or multicellular spores that are released directly from the tip or side of the hypha. Other asexual spores originate in the fragmentation of a hypha to form single cells that are released as spores; some of these have a thick wall surrounding the fragment. Yet others bud off the vegetative parent cell. Sporangiospores are produced in a sporangium (Figure \(8\)).
Sexual Reproduction
Sexual reproduction introduces genetic variation into a population of fungi. In fungi, sexual reproduction often occurs in response to adverse environmental conditions. During sexual reproduction, two mating types are produced. When both mating types are present in the same mycelium, it is called homothallic, or self-fertile. Heterothallic mycelia require two different, but compatible, mycelia to reproduce sexually.
Although there are many variations in fungal sexual reproduction, all include the following three stages (Figure \(7\)). First, during plasmogamy (literally, “marriage or union of cytoplasm”), two haploid cells fuse, leading to a dikaryotic stage where two haploid nuclei coexist in a single cell. During karyogamy (“nuclear marriage”), the haploid nuclei fuse to form a diploid zygote nucleus. Finally, meiosis takes place in the gametangia (singular, gametangium) organs, in which gametes of different mating types are generated. At this stage, spores are disseminated into the environment.
Link to Learning
Review the characteristics of fungi by visiting this interactive site from Wisconsin-online.
Summary
Fungi are eukaryotic organisms that appeared on land more than 450 million years ago. They are heterotrophs and contain neither photosynthetic pigments such as chlorophyll, nor organelles such as chloroplasts. Because fungi feed on decaying and dead matter, they are saprobes. Fungi are important decomposers that release essential elements into the environment. External enzymes digest nutrients that are absorbed by the body of the fungus, which is called a thallus. A thick cell wall made of chitin surrounds the cell. Fungi can be unicellular as yeasts, or develop a network of filaments called a mycelium, which is often described as mold. Most species multiply by asexual and sexual reproductive cycles and display an alternation of generations. Another group of fungi do not have a sexual cycle. Sexual reproduction involves plasmogamy (the fusion of the cytoplasm), followed by karyogamy (the fusion of nuclei). Meiosis regenerates haploid individuals, resulting in haploid spores.
Glossary
coenocytic hypha
single hypha that lacks septa and contains many nuclei
faculative anaerobes
organisms that can perform both aerobic and anaerobic respiration and can survive in oxygen-rich and oxygen-poor environment
haustoria
modified hyphae on many parasitic fungi that penetrate the tissues of their hosts, release digestive enzymes, and/or absorb nutrients from the host
heterothallic
describes when only one mating type is present in an individual mycelium
homothallic
describes when both mating types are present in mycelium
hypha
fungal filament composed of one or more cells
karyogamy
fusion of nuclei
mycelium
mass of fungal hyphae
mycology
scientific study of fungi
obligate aerobes
organisms, such as humans, that must perform aerobic respiration to survive
obligate anaerobes
organisms that only perform anaerobic respiration and often cannot survive in the presence of oxygen
plasmogamy
fusion of cytoplasm
saprobe
organism that derives nutrients from decaying organic matter; also saprophyte
septa
cell wall division between hyphae
sporangium
reproductive sac that contains spores
thallus
vegetative body of a fungus
yeast
general term used to describe unicellular fungi | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/24%3A_Fungi/24.1%3A_Characteristics_of_Fungi.txt |
Skills to Develop
• Classify fungi into the five major phyla
• Describe each phylum in terms of major representative species and patterns of reproduction
The kingdom Fungi contains five major phyla that were established according to their mode of sexual reproduction or using molecular data. Polyphyletic, unrelated fungi that reproduce without a sexual cycle, are placed for convenience in a sixth group called a “form phylum”. Not all mycologists agree with this scheme. Rapid advances in molecular biology and the sequencing of 18S rRNA (a part of RNA) continue to show new and different relationships between the various categories of fungi.
The five true phyla of fungi are the Chytridiomycota (Chytrids), the Zygomycota (conjugated fungi), the Ascomycota (sac fungi), the Basidiomycota (club fungi) and the recently described Phylum Glomeromycota. An older classification scheme grouped fungi that strictly use asexual reproduction into Deuteromycota, a group that is no longer in use.
Note
Note: “-mycota” is used to designate a phylum while “-mycetes” formally denotes a class or is used informally to refer to all members of the phylum.
Chytridiomycota: The Chytrids
The only class in the Phylum Chytridiomycota is the Chytridiomycetes. The chytrids are the simplest and most primitive Eumycota, or true fungi. The evolutionary record shows that the first recognizable chytrids appeared during the late pre-Cambrian period, more than 500 million years ago. Like all fungi, chytrids have chitin in their cell walls, but one group of chytrids has both cellulose and chitin in the cell wall. Most chytrids are unicellular; a few form multicellular organisms and hyphae, which have no septa between cells (coenocytic). They produce gametes and diploid zoospores that swim with the help of a single flagellum.
The ecological habitat and cell structure of chytrids have much in common with protists. Chytrids usually live in aquatic environments, although some species live on land. Some species thrive as parasites on plants, insects, or amphibians (Figure \(1\)), while others are saprobes. The chytrid species Allomyces is well characterized as an experimental organism. Its reproductive cycle includes both asexual and sexual phases. Allomyces produces diploid or haploid flagellated zoospores in a sporangium.
Zygomycota: The Conjugated Fungi
The zygomycetes are a relatively small group of fungi belonging to the Phylum Zygomycota. They include the familiar bread mold, Rhizopus stolonifer, which rapidly propagates on the surfaces of breads, fruits, and vegetables. Most species are saprobes, living off decaying organic material; a few are parasites, particularly of insects. Zygomycetes play a considerable commercial role. The metabolic products of other species of Rhizopus are intermediates in the synthesis of semi-synthetic steroid hormones.
Zygomycetes have a thallus of coenocytic hyphae in which the nuclei are haploid when the organism is in the vegetative stage. The fungi usually reproduce asexually by producing sporangiospores (Figure \(2\)). The black tips of bread mold are the swollen sporangia packed with black spores (Figure \(3\)). When spores land on a suitable substrate, they germinate and produce a new mycelium. Sexual reproduction starts when conditions become unfavorable. Two opposing mating strains (type + and type –) must be in close proximity for gametangia from the hyphae to be produced and fuse, leading to karyogamy. The developing diploid zygospores have thick coats that protect them from desiccation and other hazards. They may remain dormant until environmental conditions are favorable. When the zygospore germinates, it undergoes meiosis and produces haploid spores, which will, in turn, grow into a new organism. This form of sexual reproduction in fungi is called conjugation (although it differs markedly from conjugation in bacteria and protists), giving rise to the name “conjugated fungi”.
Ascomycota: The Sac Fungi
The majority of known fungi belong to the Phylum Ascomycota, which is characterized by the formation of an ascus (plural, asci), a sac-like structure that contains haploid ascospores. Many ascomycetes are of commercial importance. Some play a beneficial role, such as the yeasts used in baking, brewing, and wine fermentation, plus truffles and morels, which are held as gourmet delicacies. Aspergillus oryzae is used in the fermentation of rice to produce sake. Other ascomycetes parasitize plants and animals, including humans. For example, fungal pneumonia poses a significant threat to AIDS patients who have a compromised immune system. Ascomycetes not only infest and destroy crops directly; they also produce poisonous secondary metabolites that make crops unfit for consumption. Filamentous ascomycetes produce hyphae divided by perforated septa, allowing streaming of cytoplasm from one cell to the other. Conidia and asci, which are used respectively for asexual and sexual reproductions, are usually separated from the vegetative hyphae by blocked (non-perforated) septa.
Asexual reproduction is frequent and involves the production of conidiophores that release haploid conidiospores (Figure \(4\)). Sexual reproduction starts with the development of special hyphae from either one of two types of mating strains (Figure \(4\)). The “male” strain produces an antheridium and the “female” strain develops an ascogonium. At fertilization, the antheridium and the ascogonium combine in plasmogamy without nuclear fusion. Special ascogenous hyphae arise, in which pairs of nuclei migrate: one from the “male” strain and one from the “female” strain. In each ascus, two or more haploid ascospores fuse their nuclei in karyogamy. During sexual reproduction, thousands of asci fill a fruiting body called the ascocarp. The diploid nucleus gives rise to haploid nuclei by meiosis. The ascospores are then released, germinate, and form hyphae that are disseminated in the environment and start new mycelia (Figure \(5\)).
Art Connection
Which of the following statements is true?
1. A dikaryotic ascus that forms in the ascocarp undergoes karyogamy, meiosis, and mitosis to form eight ascospores.
2. A diploid ascus that forms in the ascocarp undergoes karyogamy, meiosis, and mitosis to form eight ascospores.
3. A haploid zygote that forms in the ascocarp undergoes karyogamy, meiosis, and mitosis to form eight ascospores.
4. A dikaryotic ascus that forms in the ascocarp undergoes plasmogamy, meiosis, and mitosis to form eight ascospores.
Basidiomycota: The Club Fungi
The fungi in the Phylum Basidiomycota are easily recognizable under a light microscope by their club-shaped fruiting bodies called basidia (singular, basidium), which are the swollen terminal cell of a hypha. The basidia, which are the reproductive organs of these fungi, are often contained within the familiar mushroom, commonly seen in fields after rain, on the supermarket shelves, and growing on your lawn (Figure \(6\)). These mushroom-producing basidiomyces are sometimes referred to as “gill fungi” because of the presence of gill-like structures on the underside of the cap. The “gills” are actually compacted hyphae on which the basidia are borne. This group also includes shelf fungus, which cling to the bark of trees like small shelves. In addition, the basidiomycota includes smuts and rusts, which are important plant pathogens; toadstools, and shelf fungi stacked on tree trunks. Most edible fungi belong to the Phylum Basidiomycota; however, some basidiomycetes produce deadly toxins. For example, Cryptococcus neoformans causes severe respiratory illness.
The lifecycle of basidiomycetes includes alternation of generations (Figure \(7\)). Spores are generally produced through sexual reproduction, rather than asexual reproduction. The club-shaped basidium carries spores called basidiospores. In the basidium, nuclei of two different mating strains fuse (karyogamy), giving rise to a diploid zygote that then undergoes meiosis. The haploid nuclei migrate into basidiospores, which germinate and generate monokaryotic hyphae. The mycelium that results is called a primary mycelium. Mycelia of different mating strains can combine and produce a secondary mycelium that contains haploid nuclei of two different mating strains. This is the dikaryotic stage of the basidiomyces lifecyle and and it is the dominant stage. Eventually, the secondary mycelium generates a basidiocarp, which is a fruiting body that protrudes from the ground—this is what we think of as a mushroom. The basidiocarp bears the developing basidia on the gills under its cap.
Art Connection
Which of the following statements is true?
1. A basidium is the fruiting body of a mushroom-producing fungus, and it forms four basidiocarps.
2. The result of the plasmogamy step is four basidiospores.
3. Karyogamy results directly in the formation of mycelia.
4. A basidiocarp is the fruiting body of a mushroom-producing fungus.
Asexual Ascomycota and Basidiomycota
Imperfect fungi—those that do not display a sexual phase—use to be classified in the form phylum Deuteromycota, , a classification group no longer used in the present, ever-developing classification of organisms. While Deuteromycota use to be a classification group, recent moleclular analysis has shown that the members classified in this group belong to the Ascomycota or the Basidiomycota classifications. Since they do not possess the sexual structures that are used to classify other fungi, they are less well described in comparison to other members. Most members live on land, with a few aquatic exceptions. They form visible mycelia with a fuzzy appearance and are commonly known as mold.
Reproduction of the fungi in this group is strictly asexual and occurs mostly by production of asexual conidiospores (Figure \(8\)). Some hyphae may recombine and form heterokaryotic hyphae. Genetic recombination is known to take place between the different nuclei.
The fungi in this group have a large impact on everyday human life. The food industry relies on them for ripening some cheeses. The blue veins in Roquefort cheese and the white crust on Camembert are the result of fungal growth. The antibiotic penicillin was originally discovered on an overgrown Petri plate, on which a colony of Penicillium fungi killed the bacterial growth surrounding it. Other fungi in this group cause serious diseases, either directly as parasites (which infect both plants and humans), or as producers of potent toxic compounds, as seen in the aflatoxins released by fungi of the genus Aspergillus.
Glomeromycota
The Glomeromycota is a newly established phylum which comprises about 230 species that all live in close association with the roots of trees. Fossil records indicate that trees and their root symbionts share a long evolutionary history. It appears that all members of this family form arbuscular mycorrhizae: the hyphae interact with the root cells forming a mutually beneficial association where the plants supply the carbon source and energy in the form of carbohydrates to the fungus, and the fungus supplies essential minerals from the soil to the plant.
The glomeromycetes do not reproduce sexually and do not survive without the presence of plant roots. Although they have coenocytic hyphae like the zygomycetes, they do not form zygospores. DNA analysis shows that all glomeromycetes probably descended from a common ancestor, making them a monophyletic lineage.
Summary
Chytridiomycota (chytrids) are considered the most primitive group of fungi. They are mostly aquatic, and their gametes are the only fungal cells known to have flagella. They reproduce both sexually and asexually; the asexual spores are called zoospores. Zygomycota (conjugated fungi) produce non-septated hyphae with many nuclei. Their hyphae fuse during sexual reproduction to produce a zygospore in a zygosporangium. Ascomycota (sac fungi) form spores in sacs called asci during sexual reproduction. Asexual reproduction is their most common form of reproduction. Basidiomycota (club fungi) produce showy fruiting bodies that contain basidia in the form of clubs. Spores are stored in the basidia. Most familiar mushrooms belong to this division. Fungi that have no known sexual cycle were classified in the form phylum Deuteromycota, which the present classification puts in the phyla Ascomycota and Basidiomycota. Glomeromycota form tight associations (called mycorrhizae) with the roots of plants.
Art Connections
Figure \(4\): Which of the following statements is true?
1. A dikaryotic ascus that forms in the ascocarp undergoes karyogamy, meiosis, and mitosis to form eight ascospores.
2. A diploid ascus that forms in the ascocarp undergoes karyogamy, meiosis, and mitosis to form eight ascospores.
3. A haploid zygote that forms in the ascocarp undergoes karyogamy, meiosis, and mitosis to form eight ascospores.
4. A dikaryotic ascus that forms in the ascocarp undergoes plasmogamy, meiosis, and mitosis to form eight ascospores.
Answer
A
Figure \(7\): Which of the following statements is true?
1. A basidium is the fruiting body of a mushroom-producing fungus, and it forms four basidiocarps.
2. The result of the plasmogamy step is four basidiospores.
3. Karyogamy results directly in the formation of mycelia.
4. A basidiocarp is the fruiting body of a mushroom-producing fungus.
Answer
D
Glossary
Arbuscular mycorrhizae
mycorrhizae commonly involving Glomeromycetes in which the fungal hyphae penetrate the cell walls of the plant root cells (but not the cell membranes)
ascocarp
fruiting body of ascomycetes
Ascomycota
(also, sac fungi) phylum of fungi that store spores in a sac called ascus
basidiocarp
fruiting body that protrudes from the ground and bears the basidia
Basidiomycota
(also, club fungi) phylum of fungi that produce club-shaped structures (basidia) that contain spores
basidium
club-shaped fruiting body of basidiomycetes
Chytridiomycota
(also, chytrids) primitive phylum of fungi that live in water and produce gametes with flagella
Deuteromycota
former form phylum of fungi that do not have a known sexual reproductive cycle (presently members of two phyla: Ascomycota and Basidiomycota)
Ectomycorrhizae
mycorrhizae in which the fungal hyphae do not penetrate the root cells of the plant
Glomeromycota
phylum of fungi that form symbiotic relationships with the roots of trees
mold
tangle of visible mycelia with a fuzzy appearance
Zygomycota
(also, conjugated fungi) phylum of fungi that form a zygote contained in a zygospore
zygospore
structure with thick cell wall that contains the zygote in zygomycetes | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/24%3A_Fungi/24.2%3A_Classifications_of_Fungi.txt |
Skills to Develop
• Describe the role of fungi in the ecosystem
• Describe mutualistic relationships of fungi with plant roots and photosynthetic organisms
• Describe the beneficial relationship between some fungi and insects
Fungi play a crucial role in the balance of ecosystems. They colonize most habitats on Earth, preferring dark, moist conditions. They can thrive in seemingly hostile environments, such as the tundra, thanks to a most successful symbiosis with photosynthetic organisms like algae to produce lichens. Fungi are not obvious in the way large animals or tall trees appear. Yet, like bacteria, they are the major decomposers of nature. With their versatile metabolism, fungi break down organic matter, which would not otherwise be recycled.
Habitats
Although fungi are primarily associated with humid and cool environments that provide a supply of organic matter, they colonize a surprising diversity of habitats, from seawater to human skin and mucous membranes. Chytrids are found primarily in aquatic environments. Other fungi, such as Coccidioides immitis, which causes pneumonia when its spores are inhaled, thrive in the dry and sandy soil of the southwestern United States. Fungi that parasitize coral reefs live in the ocean. However, most members of the Kingdom Fungi grow on the forest floor, where the dark and damp environment is rich in decaying debris from plants and animals. In these environments, fungi play a major role as decomposers and recyclers, making it possible for members of the other kingdoms to be supplied with nutrients and live.
Decomposers and Recyclers
The food web would be incomplete without organisms that decompose organic matter (Figure \(1\)). Some elements—such as nitrogen and phosphorus—are required in large quantities by biological systems, and yet are not abundant in the environment. The action of fungi releases these elements from decaying matter, making them available to other living organisms. Trace elements present in low amounts in many habitats are essential for growth, and would remain tied up in rotting organic matter if fungi and bacteria did not return them to the environment via their metabolic activity.
The ability of fungi to degrade many large and insoluble molecules is due to their mode of nutrition. As seen earlier, digestion precedes ingestion. Fungi produce a variety of exoenzymes to digest nutrients. The enzymes are either released into the substrate or remain bound to the outside of the fungal cell wall. Large molecules are broken down into small molecules, which are transported into the cell by a system of protein carriers embedded in the cell membrane. Because the movement of small molecules and enzymes is dependent on the presence of water, active growth depends on a relatively high percentage of moisture in the environment.
As saprobes, fungi help maintain a sustainable ecosystem for the animals and plants that share the same habitat. In addition to replenishing the environment with nutrients, fungi interact directly with other organisms in beneficial, and sometimes damaging, ways (Figure \(2\)).
Mutualistic Relationships
Symbiosis is the ecological interaction between two organisms that live together. The definition does not describe the quality of the interaction. When both members of the association benefit, the symbiotic relationship is called mutualistic. Fungi form mutualistic associations with many types of organisms, including cyanobacteria, algae, plants, and animals.
Fungus/Plant Mutualism
One of the most remarkable associations between fungi and plants is the establishment of mycorrhizae. Mycorrhiza, which comes from the Greek words myco meaning fungus and rhizo meaning root, refers to the association between vascular plant roots and their symbiotic fungi. Somewhere between 80 and 90 percent of all plant species have mycorrhizal partners. In a mycorrhizal association, the fungal mycelia use their extensive network of hyphae and large surface area in contact with the soil to channel water and minerals from the soil into the plant. In exchange, the plant supplies the products of photosynthesis to fuel the metabolism of the fungus.
There are a number of types of mycorrhizae. Ectomycorrhizae (“outside” mycorrhiza) depend on fungi enveloping the roots in a sheath (called a mantle) and a Hartig net of hyphae that extends into the roots between cells (Figure 24.3.3). The fungal partner can belong to the Ascomycota, Basidiomycota or Zygomycota. In a second type, the Glomeromycete fungi form vesicular–arbuscular interactions with arbuscular mycorrhiza (sometimes called endomycorrhizae). In these mycorrhiza, the fungi form arbuscules that penetrate root cells and are the site of the metabolic exchanges between the fungus and the host plant (Figure \(3\) and Figure \(4\)). The arbuscules (from the Latin for little trees) have a shrub-like appearance. Orchids rely on a third type of mycorrhiza. Orchids are epiphytes that form small seeds without much storage to sustain germination and growth. Their seeds will not germinate without a mycorrhizal partner (usually a Basidiomycete). After nutrients in the seed are depleted, fungal symbionts support the growth of the orchid by providing necessary carbohydrates and minerals. Some orchids continue to be mycorrhizal throughout their lifecycle.
Art Connection
If symbiotic fungi are absent from the soil, what impact do you think this would have on plant growth?
Other examples of fungus–plant mutualism include the endophytes: fungi that live inside tissue without damaging the host plant. Endophytes release toxins that repel herbivores, or confer resistance to environmental stress factors, such as infection by microorganisms, drought, or heavy metals in soil.
Evolution Connection: Coevolution of Land Plants and Mycorrhizae
Mycorrhizae are the mutually beneficial symbiotic association between roots of vascular plants and fungi. A well-accepted theory proposes that fungi were instrumental in the evolution of the root system in plants and contributed to the success of Angiosperms. The bryophytes (mosses and liverworts), which are considered the most primitive plants and the first to survive on dry land, do not have a true root system; some have vesicular–arbuscular mycorrhizae and some do not. They depend on a simple rhizoid (an underground organ) and cannot survive in dry areas. True roots appeared in vascular plants. Vascular plants that developed a system of thin extensions from the rhizoids (found in mosses) are thought to have had a selective advantage because they had a greater surface area of contact with the fungal partners than the mosses and liverworts, thus availing themselves of more nutrients in the ground.
Fossil records indicate that fungi preceded plants on dry land. The first association between fungi and photosynthetic organisms on land involved moss-like plants and endophytes. These early associations developed before roots appeared in plants. Slowly, the benefits of the endophyte and rhizoid interactions for both partners led to present-day mycorrhizae; up to about 90 percent of today’s vascular plants have associations with fungi in their rhizosphere. The fungi involved in mycorrhizae display many characteristics of primitive fungi; they produce simple spores, show little diversification, do not have a sexual reproductive cycle, and cannot live outside of a mycorrhizal association. The plants benefited from the association because mycorrhizae allowed them to move into new habitats because of increased uptake of nutrients, and this gave them a selective advantage over plants that did not establish symbiotic relationships.
Lichens
Lichens display a range of colors and textures (Figure \(5\)) and can survive in the most unusual and hostile habitats. They cover rocks, gravestones, tree bark, and the ground in the tundra where plant roots cannot penetrate. Lichens can survive extended periods of drought, when they become completely desiccated, and then rapidly become active once water is available again.
Link to Learning
Explore the world of lichens using this site from Oregon State University.
Lichens are not a single organism, but rather an example of a mutualism, in which a fungus (usually a member of the Ascomycota or Basidiomycota phyla) lives in close contact with a photosynthetic organism (a eukaryotic alga or a prokaryotic cyanobacterium) (Figure \(6\)). Generally, neither the fungus nor the photosynthetic organism can survive alone outside of the symbiotic relationship. The body of a lichen, referred to as a thallus, is formed of hyphae wrapped around the photosynthetic partner. The photosynthetic organism provides carbon and energy in the form of carbohydrates. Some cyanobacteria fix nitrogen from the atmosphere, contributing nitrogenous compounds to the association. In return, the fungus supplies minerals and protection from dryness and excessive light by encasing the algae in its mycelium. The fungus also attaches the symbiotic organism to the substrate.
The thallus of lichens grows very slowly, expanding its diameter a few millimeters per year. Both the fungus and the alga participate in the formation of dispersal units for reproduction. Lichens produce soredia, clusters of algal cells surrounded by mycelia. Soredia are dispersed by wind and water and form new lichens.
Lichens are extremely sensitive to air pollution, especially to abnormal levels of nitrogen and sulfur. The U.S. Forest Service and National Park Service can monitor air quality by measuring the relative abundance and health of the lichen population in an area. Lichens fulfill many ecological roles. Caribou and reindeer eat lichens, and they provide cover for small invertebrates that hide in the mycelium. In the production of textiles, weavers used lichens to dye wool for many centuries until the advent of synthetic dyes.
Link to Learning
Lichens are used to monitor the quality of air. Read more on this site from the United States Forest Service.
Fungus/Animal Mutualism
Fungi have evolved mutualisms with numerous insects in Phylum Arthropoda: jointed, legged invertebrates. Arthropods depend on the fungus for protection from predators and pathogens, while the fungus obtains nutrients and a way to disseminate spores into new environments. The association between species of Basidiomycota and scale insects is one example. The fungal mycelium covers and protects the insect colonies. The scale insects foster a flow of nutrients from the parasitized plant to the fungus. In a second example, leaf-cutting ants of Central and South America literally farm fungi. They cut disks of leaves from plants and pile them up in gardens (Figure \(7\)). Fungi are cultivated in these disk gardens, digesting the cellulose in the leaves that the ants cannot break down. Once smaller sugar molecules are produced and consumed by the fungi, the fungi in turn become a meal for the ants. The insects also patrol their garden, preying on competing fungi. Both ants and fungi benefit from the association. The fungus receives a steady supply of leaves and freedom from competition, while the ants feed on the fungi they cultivate.
Fungivores
Animal dispersal is important for some fungi because an animal may carry spores considerable distances from the source. Fungal spores are rarely completely degraded in the gastrointestinal tract of an animal, and many are able to germinate when they are passed in the feces. Some dung fungi actually require passage through the digestive system of herbivores to complete their lifecycle. The black truffle—a prized gourmet delicacy—is the fruiting body of an underground mushroom. Almost all truffles are ectomycorrhizal, and are usually found in close association with trees. Animals eat truffles and disperse the spores. In Italy and France, truffle hunters use female pigs to sniff out truffles. Female pigs are attracted to truffles because the fungus releases a volatile compound closely related to a pheromone produced by male pigs.
Summary
Fungi have colonized nearly all environments on Earth, but are frequently found in cool, dark, moist places with a supply of decaying material. Fungi are saprobes that decompose organic matter. Many successful mutualistic relationships involve a fungus and another organism. Many fungi establish complex mycorrhizal associations with the roots of plants. Some ants farm fungi as a supply of food. Lichens are a symbiotic relationship between a fungus and a photosynthetic organism, usually an alga or cyanobacterium. The photosynthetic organism provides energy derived from light and carbohydrates, while the fungus supplies minerals and protection. Some animals that consume fungi help disseminate spores over long distances.
Art Connections
Figure \(3\): If symbiotic fungi are absent from the soil, what impact do you think this would have on plant growth?
Answer
Without mycorrhiza, plants cannot absorb adequate nutrients, which stunts their growth. Addition of fungal spores to sterile soil can alleviate this problem.
Glossary
arbuscular mycorrhiza
mycorrhizal association in which the fungal hyphae enter the root cells and form extensive networks
ectomycorrhiza
mycorrhizal fungi that surround the roots with a mantle and have a Hartig net that extends into the roots between cells
lichen
close association of a fungus with a photosynthetic alga or bacterium that benefits both partners
mycorrhiza
mutualistic association between fungi and vascular plant roots
soredia
clusters of algal cells and mycelia that allow lichens to propagate | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/24%3A_Fungi/24.3%3A_Ecology_of_Fungi.txt |
Skills to Develop
• Describe fungal parasites and pathogens of plants
• Describe the different types of fungal infections in humans
• Explain why antifungal therapy is hampered by the similarity between fungal and animal cells
Parasitism describes a symbiotic relationship in which one member of the association benefits at the expense of the other. Both parasites and pathogens harm the host; however, the pathogen causes a disease, whereas the parasite usually does not. Commensalism occurs when one member benefits without affecting the other.
Plant Parasites and Pathogens
The production of sufficient good-quality crops is essential to human existence. Plant diseases have ruined crops, bringing widespread famine. Many plant pathogens are fungi that cause tissue decay and eventual death of the host (Figure \(1\)). In addition to destroying plant tissue directly, some plant pathogens spoil crops by producing potent toxins. Fungi are also responsible for food spoilage and the rotting of stored crops. For example, the fungus Claviceps purpurea causes ergot, a disease of cereal crops (especially of rye). Although the fungus reduces the yield of cereals, the effects of the ergot's alkaloid toxins on humans and animals are of much greater significance. In animals, the disease is referred to as ergotism. The most common signs and symptoms are convulsions, hallucination, gangrene, and loss of milk in cattle. The active ingredient of ergot is lysergic acid, which is a precursor of the drug LSD. Smuts, rusts, and powdery or downy mildew are other examples of common fungal pathogens that affect crops.
Aflatoxins are toxic, carcinogenic compounds released by fungi of the genus Aspergillus. Periodically, harvests of nuts and grains are tainted by aflatoxins, leading to massive recall of produce. This sometimes ruins producers and causes food shortages in developing countries.
Animal and Human Parasites and Pathogens
Fungi can affect animals, including humans, in several ways. A mycosis is a fungal disease that results from infection and direct damage. Fungi attack animals directly by colonizing and destroying tissues. Mycotoxicosis is the poisoning of humans (and other animals) by foods contaminated by fungal toxins (mycotoxins). Mycetismus describes the ingestion of preformed toxins in poisonous mushrooms. In addition, individuals who display hypersensitivity to molds and spores develop strong and dangerous allergic reactions. Fungal infections are generally very difficult to treat because, unlike bacteria, fungi are eukaryotes. Antibiotics only target prokaryotic cells, whereas compounds that kill fungi also harm the eukaryotic animal host.
Many fungal infections are superficial; that is, they occur on the animal’s skin. Termed cutaneous (“skin”) mycoses, they can have devastating effects. For example, the decline of the world’s frog population in recent years may be caused by the chytrid fungus Batrachochytrium dendrobatidis, which infects the skin of frogs and presumably interferes with gaseous exchange. Similarly, more than a million bats in the United States have been killed by white-nose syndrome, which appears as a white ring around the mouth of the bat. It is caused by the cold-loving fungus Geomyces destructans, which disseminates its deadly spores in caves where bats hibernate. Mycologists are researching the transmission, mechanism, and control of G. destructans to stop its spread.
Fungi that cause the superficial mycoses of the epidermis, hair, and nails rarely spread to the underlying tissue (Figure \(2\)). These fungi are often misnamed “dermatophytes”, from the Greek words dermis meaning skin and phyte meaning plant, although they are not plants. Dermatophytes are also called “ringworms” because of the red ring they cause on skin. They secrete extracellular enzymes that break down keratin (a protein found in hair, skin, and nails), causing conditions such as athlete’s foot and jock itch. These conditions are usually treated with over-the-counter topical creams and powders, and are easily cleared. More persistent superficial mycoses may require prescription oral medications.
Systemic mycoses spread to internal organs, most commonly entering the body through the respiratory system. For example, coccidioidomycosis (valley fever) is commonly found in the southwestern United States, where the fungus resides in the dust. Once inhaled, the spores develop in the lungs and cause symptoms similar to those of tuberculosis. Histoplasmosis is caused by the dimorphic fungus Histoplasma capsulatum. It also causes pulmonary infections, and in rarer cases, swelling of the membranes of the brain and spinal cord. Treatment of these and many other fungal diseases requires the use of antifungal medications that have serious side effects.
Opportunistic mycoses are fungal infections that are either common in all environments, or part of the normal biota. They mainly affect individuals who have a compromised immune system. Patients in the late stages of AIDS suffer from opportunistic mycoses that can be life threatening. The yeast Candida sp., a common member of the natural biota, can grow unchecked and infect the vagina or mouth (oral thrush) if the pH of the surrounding environment, the person’s immune defenses, or the normal population of bacteria are altered.
Mycetismus can occur when poisonous mushrooms are eaten. It causes a number of human fatalities during mushroom-picking season. Many edible fruiting bodies of fungi resemble highly poisonous relatives, and amateur mushroom hunters are cautioned to carefully inspect their harvest and avoid eating mushrooms of doubtful origin. The adage “there are bold mushroom pickers and old mushroom pickers, but are there no old, bold mushroom pickers” is unfortunately true.
Scientific Method Connection: Dutch Elm Disease
Question: Do trees resistant to Dutch elm disease secrete antifungal compounds?
Hypothesis: Construct a hypothesis that addresses this question.
Background: Dutch elm disease is a fungal infestation that affects many species of elm (Ulmus) in North America. The fungus infects the vascular system of the tree, which blocks water flow within the plant and mimics drought stress. Accidently introduced to the United States in the early 1930s, it decimated shade trees across the continent. It is caused by the fungus Ophiostoma ulmi. The elm bark beetle acts as a vector and transmits the disease from tree to tree. Many European and Asiatic elms are less susceptible to the disease than are American elms.
Test the hypothesis: A researcher testing this hypothesis might do the following. Inoculate several Petri plates containing a medium that supports the growth of fungi with fragments of Ophiostoma mycelium. Cut (with a metal punch) several disks from the vascular tissue of susceptible varieties of American elms and resistant European and Asiatic elms. Include control Petri plates inoculated with mycelia without plant tissue to verify that the medium and incubation conditions do not interfere with fungal growth. As a positive control, add paper disks impregnated with a known fungicide to Petri plates inoculated with the mycelium.
Incubate the plates for a set number of days to allow fungal growth and spreading of the mycelium over the surface of the plate. Record the diameter of the zone of clearing, if any, around the tissue samples and the fungicide control disk.
Record your observations in the following table.
Table \(1\): Results of Antifungal Testing of Vascular Tissue from Different Species of Elm
Disk Zone of Inhibition (mm)
Distilled Water
Fungicide
Tissue from Susceptible Elm #1
Tissue from Susceptible Elm #2
Tissue from Resistant Elm #1
Tissue from Resistant Elm #2
Analyze the data and report the results. Compare the effect of distilled water to the fungicide. These are negative and positive controls that validate the experimental set up. The fungicide should be surrounded by a clear zone where the fungus growth was inhibited. Is there a difference among different species of elm?
Draw a conclusion: Was there antifungal activity as expected from the fungicide? Did the results support the hypothesis? If not, how can this be explained? There are several possible explanations for resistance to a pathogen. Active deterrence of infection is only one of them.
Summary
Fungi establish parasitic relationships with plants and animals. Fungal diseases can decimate crops and spoil food during storage. Compounds produced by fungi can be toxic to humans and other animals. Mycoses are infections caused by fungi. Superficial mycoses affect the skin, whereas systemic mycoses spread through the body. Fungal infections are difficult to cure.
Glossary
commensalism
symbiotic relationship in which one member benefits while the other member is not affected
mycetismus
ingestion of toxins in poisonous mushrooms
mycosis
fungal infection
mycotoxicosis
poisoning by a fungal toxin released in food
parasitism
symbiotic relationship in which one member of the association benefits at the expense of the other | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/24%3A_Fungi/24.4%3A_Fungal_Parasites_and_Pathogens.txt |
Skills to Develop
• Describe the importance of fungi to the balance of the environment
• Summarize the role of fungi in food and beverage preparation
• Describe the importance of fungi in the chemical and pharmaceutical industries
• Discuss the role of fungi as model organisms
Although we often think of fungi as organisms that cause disease and rot food, fungi are important to human life on many levels. As we have seen, they influence the well-being of human populations on a large scale because they are part of the nutrient cycle in ecosystems. They have other ecosystem roles as well. As animal pathogens, fungi help to control the population of damaging pests. These fungi are very specific to the insects they attack, and do not infect animals or plants. Fungi are currently under investigation as potential microbial insecticides, with several already on the market. For example, the fungus Beauveria bassiana is a pesticide being tested as a possible biological control agent for the recent spread of emerald ash borer. It has been released in Michigan, Illinois, Indiana, Ohio, West Virginia and Maryland (Figure \(1\)).
The mycorrhizal relationship between fungi and plant roots is essential for the productivity of farm land. Without the fungal partner in root systems, 80–90 percent of trees and grasses would not survive. Mycorrhizal fungal inoculants are available as soil amendments from gardening supply stores and are promoted by supporters of organic agriculture.
We also eat some types of fungi. Mushrooms figure prominently in the human diet. Morels, shiitake mushrooms, chanterelles, and truffles are considered delicacies (Figure \(2\)). The humble meadow mushroom, Agaricus campestris, appears in many dishes. Molds of the genus Penicillium ripen many cheeses. They originate in the natural environment such as the caves of Roquefort, France, where wheels of sheep milk cheese are stacked in order to capture the molds responsible for the blue veins and pungent taste of the cheese.
Fermentation—of grains to produce beer, and of fruits to produce wine—is an ancient art that humans in most cultures have practiced for millennia. Wild yeasts are acquired from the environment and used to ferment sugars into CO2 and ethyl alcohol under anaerobic conditions. It is now possible to purchase isolated strains of wild yeasts from different wine-making regions. Louis Pasteur was instrumental in developing a reliable strain of brewer’s yeast, Saccharomyces cerevisiae, for the French brewing industry in the late 1850s. This was one of the first examples of biotechnology patenting.
Many secondary metabolites of fungi are of great commercial importance. Antibiotics are naturally produced by fungi to kill or inhibit the growth of bacteria, limiting their competition in the natural environment. Important antibiotics, such as penicillin and the cephalosporins, are isolated from fungi. Valuable drugs isolated from fungi include the immunosuppressant drug cyclosporine (which reduces the risk of rejection after organ transplant), the precursors of steroid hormones, and ergot alkaloids used to stop bleeding. Psilocybin is a compound found in fungi such as Psilocybe semilanceata and Gymnopilus junonius, which have been used for their hallucinogenic properties by various cultures for thousands of years.
As simple eukaryotic organisms, fungi are important model research organisms. Many advances in modern genetics were achieved by the use of the red bread mold Neurospora crassa. Additionally, many important genes originally discovered in S. cerevisiae served as a starting point in discovering analogous human genes. As a eukaryotic organism, the yeast cell produces and modifies proteins in a manner similar to human cells, as opposed to the bacterium Escherichia coli, which lacks the internal membrane structures and enzymes to tag proteins for export. This makes yeast a much better organism for use in recombinant DNA technology experiments. Like bacteria, yeasts grow easily in culture, have a short generation time, and are amenable to genetic modification.
Summary
Fungi are important to everyday human life. Fungi are important decomposers in most ecosystems. Mycorrhizal fungi are essential for the growth of most plants. Fungi, as food, play a role in human nutrition in the form of mushrooms, and also as agents of fermentation in the production of bread, cheeses, alcoholic beverages, and numerous other food preparations. Secondary metabolites of fungi are used as medicines, such as antibiotics and anticoagulants. Fungi are model organisms for the study of eukaryotic genetics and metabolism. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/24%3A_Fungi/24.5%3A_Importance_of_Fungi_in_Human_Life.txt |
24.1: Characteristics of Fungi
Review Questions
Which polysaccharide is usually found in the cell wall of fungi?
1. starch
2. glycogen
3. chitin
4. cellulose
Answer
C
Which of these organelles is not found in a fungal cell?
1. chloroplast
2. nucleus
3. mitochondrion
4. Golgi apparatus
Answer
A
The wall dividing individual cells in a fungal filament is called a
1. thallus
2. hypha
3. mycelium
4. septum
Answer
D
During sexual reproduction, a homothallic mycelium contains
1. all septated hyphae
2. all haploid nuclei
3. both mating types
4. none of the above
Answer
C
Free Response
What are the evolutionary advantages for an organism to reproduce both asexually and sexually?
Answer
Asexual reproduction is fast and best under favorable conditions. Sexual reproduction allows the recombination of genetic traits and increases the odds of developing new adaptations better suited to a changed environment.
Compare plants, animals, and fungi, considering these components: cell wall, chloroplasts, plasma membrane, food source, and polysaccharide storage. Be sure to indicate fungi’s similarities and differences to plants and animals.
Answer
Animals have no cell walls; fungi have cell walls containing chitin; plants have cell walls containing cellulose. Chloroplasts are absent in both animals and fungi but are present in plants. Animal plasma membranes are stabilized with cholesterol, while fungi plasma membranes are stabilized with ergosterol, and plant plasma membranes are stabilized with phytosterols. Animals obtain N and C from food sources via internal digestion. Fungi obtain N and C from food sources via external digestion. Plants obtain organic N from the environment or through symbiotic N-fixing bacteria; they obtain C from photosynthesis. Animals and fungi store polysaccharides as glycogen, while plants store them as starch.
24.2: Classifications of Fungi
Review Questions
The most primitive phylum of fungi is the ________.
1. Chytridiomycota
2. Zygomycota
3. Glomeromycota
4. Ascomycota
Answer
A
Members of which phylum produce a club-shaped structure that contains spores?
1. Chytridiomycota
2. Basidiomycota
3. Glomeromycota
4. Ascomycota
Answer
B
Members of which phylum establish a successful symbiotic relationship with the roots of trees?
1. Ascomycota
2. Deuteromycota
3. Basidiomycota
4. Glomeromycota
Answer
D
The fungi that do not reproduce sexually use to be classified as ________.
1. Ascomycota
2. Deuteromycota
3. Basidiomycota
4. Glomeromycota
Answer
B
Free Response
What is the advantage for a basidiomycete to produce a showy and fleshy fruiting body?
Answer
By ingesting spores and disseminating them in the environment as waste, animals act as agents of dispersal. The benefit to the fungus outweighs the cost of producing fleshy fruiting bodies.
For each of the four groups of perfect fungi (Chytridiomycota, Zygomycota, Ascomycota, and Basidiomycota), compare the body structure and features, and provide an example.
Answer
Chytridiomycota (Chytrids) may have a unicellular or multicellular body structure; some are aquatic with motile spores with flagella; an example is the Allomyces. Zygomycota (conjugated fungi) have a multicellular body structure; features include zygospores and presence in soil; examples are bread and fruit molds. Ascomycota (sac fungi) may have unicellular or multicellular body structure; a feature is sexual spores in sacs (asci); examples include the yeasts used in bread, wine, and beer production. Basidiomycota (club fungi) have multicellular bodies; features includes sexual spores in the basidiocarp (mushroom) and that they are mostly decomposers; mushroom-producing fungi are an example.
24.3: Ecology of Fungi
Review Questions
What term describes the close association of a fungus with the root of a tree?
1. a rhizoid
2. a lichen
3. a mycorrhiza
4. an endophyte
Answer
C
Why are fungi important decomposers?
1. They produce many spores.
2. They can grow in many different environments.
3. They produce mycelia.
4. They recycle carbon and inorganic minerals by the process of decomposition.
Answer
D
Free Response
Why does protection from light actually benefit the photosynthetic partner in lichens?
Answer
Protection from excess light that may bleach photosynthetic pigments allows the photosynthetic partner to survive in environments unfavorable to plants.
24.4: Fungal Parasites and Pathogens
Review Questions
A fungus that climbs up a tree reaching higher elevation to release its spores in the wind and does not receive any nutrients from the tree or contribute to the tree’s welfare is described as a ________.
1. commensal
2. mutualist
3. parasite
4. pathogen
Answer
A
A fungal infection that affects nails and skin is classified as ________.
1. systemic mycosis
2. mycetismus
3. superficial mycosis
4. mycotoxicosis
Answer
C
Free Response
Why can superficial mycoses in humans lead to bacterial infections?
Answer
Dermatophytes that colonize skin break down the keratinized layer of dead cells that protects tissues from bacterial invasion. Once the integrity of the skin is breached, bacteria can enter the deeper layers of tissues and cause infections.
24.5: Importance of Fungi in Human Life
Review Questions
Yeast is a facultative anaerobe. This means that alcohol fermentation takes place only if:
1. the temperature is close to 37°C
2. the atmosphere does not contain oxygen
3. sugar is provided to the cells
4. light is provided to the cells
Answer
B
The advantage of yeast cells over bacterial cells to express human proteins is that:
1. yeast cells grow faster
2. yeast cells are easier to manipulate genetically
3. yeast cells are eukaryotic and modify proteins similarly to human cells
4. yeast cells are easily lysed to purify the proteins
Answer
C
Free Response
Historically, artisanal breads were produced by capturing wild yeasts from the air. Prior to the development of modern yeast strains, the production of artisanal breads was long and laborious because many batches of dough ended up being discarded. Can you explain this fact?
Answer
The dough is often contaminated by toxic spores that float in the air. It was one of Louis Pasteur’s achievements to purify reliable strains of baker’s yeast to produce bread consistently. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/24%3A_Fungi/24.E%3A_Fungi_%28Exercises%29.txt |
Seedless plants reproduce and spread through spores, but do not flower or seed to replicate.
• 25.0: Prelude to Seedless Plants
The evolutionary transition from water to land imposed severe constraints on plants. They had to develop strategies to avoid drying out, to disperse reproductive cells in air, for structural support, and for capturing and filtering sunlight. While seed plants developed adaptations that allowed them to populate even the most arid habitats on Earth, full independence from water did not happen in all plants. Most seedless plants still require a moist environment.
• 25.1: Early Plant Life
The kingdom Plantae constitutes large and varied groups of organisms. There are more than 300,000 species of catalogued plants. Of these, more than 260,000 are seed plants. Mosses, ferns, conifers, and flowering plants are all members of the plant kingdom. Most biologists also consider green algae to be plants, although others exclude all algae from the plant kingdom.
• 25.2: Green Algae - Precursors of Land Plants
Green algae contain the same carotenoids and chlorophyll a and b as land plants, whereas other algae have different accessory pigments and types of chlorophyll molecules in addition to chlorophyll a. Both green algae and land plants also store carbohydrates as starch. Cells in green algae divide along cell plates called phragmoplasts, and their cell walls are layered in the same manner as the cell walls of embryophytes.
• 25.3: Bryophytes
Bryophytes are the group of plants that are the closest extant relative of early terrestrial plants. The first bryophytes (liverworts) most likely appeared in the Ordovician period, about 450 million years ago. Because of the lack of lignin and other resistant structures, the likelihood of bryophytes forming fossils is rather small. Some spores protected by sporopollenin have survived and are attributed to early bryophytes.
• 25.4: Seedless Vascular Plants
The vascular plants, or tracheophytes, are the dominant and most conspicuous group of land plants. More than 260,000 species of tracheophytes represent more than 90 percent of Earth’s vegetation. Several evolutionary innovations explain their success and their ability to spread to all habitats.
• 25.E: Seedless Plants (Exercises)
Thumbnail: Fern plants. (CC BY-SA 3.0; Sanjay ach via Wikimedia Commons).
25: Seedless Plants
An incredible variety of seedless plants populates the terrestrial landscape. Mosses may grow on a tree trunk, and horsetails may display their jointed stems and spindly leaves across the forest floor. Today, seedless plants represent only a small fraction of the plants in our environment; yet, three hundred million years ago, seedless plants dominated the landscape and grew in the enormous swampy forests of the Carboniferous period. Their decomposition created large deposits of coal that we mine today.
Current evolutionary thought holds that all plants—green algae as well as land dwellers—are monophyletic; that is, they are descendants of a single common ancestor. The evolutionary transition from water to land imposed severe constraints on plants. They had to develop strategies to avoid drying out, to disperse reproductive cells in air, for structural support, and for capturing and filtering sunlight. While seed plants developed adaptations that allowed them to populate even the most arid habitats on Earth, full independence from water did not happen in all plants. Most seedless plants still require a moist environment. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/25%3A_Seedless_Plants/25.0%3A_Prelude_to_Seedless_Plants.txt |
Skills to Develop
• Discuss the challenges to plant life on land
• Describe the adaptations that allowed plants to colonize the land
• Describe the timeline of plant evolution and the impact of land plants on other living things
The kingdom Plantae constitutes large and varied groups of organisms. There are more than 300,000 species of catalogued plants. Of these, more than 260,000 are seed plants. Mosses, ferns, conifers, and flowering plants are all members of the plant kingdom. Most biologists also consider green algae to be plants, although others exclude all algae from the plant kingdom. The reason for this disagreement stems from the fact that only green algae, the Charophytes, share common characteristics with land plants (such as using chlorophyll a and b plus carotene in the same proportion as plants). These characteristics are absent in other types of algae.
Evolution Connection: Algae and Evolutionary Paths to Photosynthesis
Some scientists consider all algae to be plants, while others assert that only the Charophytes belong in the kingdom Plantae. These divergent opinions are related to the different evolutionary paths to photosynthesis selected for in different types of algae. While all algae are photosynthetic—that is, they contain some form of a chloroplast—they didn’t all become photosynthetic via the same path.
The ancestors to the green algae became photosynthetic by endosymbiosing a green, photosynthetic bacterium about 1.65 billion years ago. That algal line evolved into the Charophytes, and eventually into the modern mosses, ferns, gymnosperms, and angiosperms. Their evolutionary trajectory was relatively straight and monophyletic. In contrast, the other algae—red, brown, golden, stramenopiles, and so on—all became photosynthetic by secondary, or even tertiary, endosymbiotic events; that is, they endosymbiosed cells that had already endosymbiosed a cyanobacterium. These latecomers to photosynthesis are parallels to the Charophytes in terms of autotrophy, but they did not expand to the same extent as the Charophytes, nor did they colonize the land.
The different views on whether all algae are Plantae arise from how these evolutionary paths are viewed. Scientists who solely track evolutionary straight lines (that is, monophyly), consider only the Charophytes as plants. To biologists who cast a broad net over living things that share a common characteristic (in this case, photosynthetic eukaryotes), all algae are plants.
Link to Learning
Go to this interactive website to get a more in-depth view of the Charophytes.
Plant Adaptations to Life on Land
As organisms adapted to life on land, they had to contend with several challenges in the terrestrial environment. Water has been described as “the stuff of life.” The cell’s interior is a watery soup: in this medium, most small molecules dissolve and diffuse, and the majority of the chemical reactions of metabolism take place. Desiccation, or drying out, is a constant danger for an organism exposed to air. Even when parts of a plant are close to a source of water, the aerial structures are likely to dry out. Water also provides buoyancy to organisms. On land, plants need to develop structural support in a medium that does not give the same lift as water. The organism is also subject to bombardment by mutagenic radiation, because air does not filter out ultraviolet rays of sunlight. Additionally, the male gametes must reach the female gametes using new strategies, because swimming is no longer possible. Therefore, both gametes and zygotes must be protected from desiccation. The successful land plants developed strategies to deal with all of these challenges. Not all adaptations appeared at once. Some species never moved very far from the aquatic environment, whereas others went on to conquer the driest environments on Earth.
To balance these survival challenges, life on land offers several advantages. First, sunlight is abundant. Water acts as a filter, altering the spectral quality of light absorbed by the photosynthetic pigment chlorophyll. Second, carbon dioxide is more readily available in air than in water, since it diffuses faster in air. Third, land plants evolved before land animals; therefore, until dry land was colonized by animals, no predators threatened plant life. This situation changed as animals emerged from the water and fed on the abundant sources of nutrients in the established flora. In turn, plants developed strategies to deter predation: from spines and thorns to toxic chemicals.
Early land plants, like the early land animals, did not live very far from an abundant source of water and developed survival strategies to combat dryness. One of these strategies is called tolerance. Many mosses, for example, can dry out to a brown and brittle mat, but as soon as rain or a flood makes water available, mosses will absorb it and are restored to their healthy green appearance. Another strategy is to colonize environments with high humidity, where droughts are uncommon. Ferns, which are considered an early lineage of plants, thrive in damp and cool places such as the understory of temperate forests. Later, plants moved away from moist or aquatic environments using resistance to desiccation, rather than tolerance. These plants, like cacti, minimize the loss of water to such an extent they can survive in extremely dry environments.
The most successful adaptation solution was the development of new structures that gave plants the advantage when colonizing new and dry environments. Four major adaptations are found in all terrestrial plants: the alternation of generations, a sporangium in which the spores are formed, a gametangium that produces haploid cells, and apical meristem tissue in roots and shoots. The evolution of a waxy cuticle and a cell wall with lignin also contributed to the success of land plants. These adaptations are noticeably lacking in the closely related green algae—another reason for the debate over their placement in the plant kingdom.
Alternation of Generations
Alternation of generations describes a life cycle in which an organism has both haploid and diploid multicellular stages (Figure \(1\)).
Haplontic refers to a lifecycle in which there is a dominant haploid stage, and diplontic refers to a lifecycle in which the diploid is the dominant life stage. Humans are diplontic. Most plants exhibit alternation of generations, which is described as haplodiplodontic: the haploid multicellular form, known as a gametophyte, is followed in the development sequence by a multicellular diploid organism: the sporophyte. The gametophyte gives rise to the gametes (reproductive cells) by mitosis. This can be the most obvious phase of the life cycle of the plant, as in the mosses, or it can occur in a microscopic structure, such as a pollen grain, in the higher plants (a common collective term for the vascular plants). The sporophyte stage is barely noticeable in lower plants (the collective term for the plant groups of mosses, liverworts, and lichens). Towering trees are the diplontic phase in the lifecycles of plants such as sequoias and pines.
Protection of the embryo is a major requirement for land plants. The vulnerable embryo must be sheltered from desiccation and other environmental hazards. In both seedless and seed plants, the female gametophyte provides protection and nutrients to the embryo as it develops into the new generation of sporophyte. This distinguishing feature of land plants gave the group its alternate name of embryophytes.
Sporangia in Seedless Plants
The sporophyte of seedless plants is diploid and results from syngamy (fusion) of two gametes. The sporophyte bears the sporangia (singular, sporangium): organs that first appeared in the land plants. The term “sporangia” literally means “spore in a vessel,” as it is a reproductive sac that contains spores Figure \(2\). Inside the multicellular sporangia, the diploid sporocytes, or mother cells, produce haploid spores by meiosis, where the 2n chromosome number is reduced to 1n (note that many plant sporophytes are polyploid: for example, durum wheat is tetraploid, bread wheat is hexaploid, and some ferns are 1000-ploid). The spores are later released by the sporangia and disperse in the environment. Two different types of spores are produced in land plants, resulting in the separation of sexes at different points in the lifecycle. Seedless non-vascular plants produce only one kind of spore and are called homosporous. The gametophyte phase is dominant in these plants. After germinating from a spore, the resulting gametophyte produces both male and female gametangia, usually on the same individual. In contrast, heterosporous plants produce two morphologically different types of spores. The male spores are called microspores, because of their smaller size, and develop into the male gametophyte; the comparatively larger megaspores develop into the female gametophyte. Heterospory is observed in a few seedless vascular plants and in all seed plants.
When the haploid spore germinates in a hospitable environment, it generates a multicellular gametophyte by mitosis. The gametophyte supports the zygote formed from the fusion of gametes and the resulting young sporophyte (vegetative form). The cycle then begins anew.
The spores of seedless plants are surrounded by thick cell walls containing a tough polymer known as sporopollenin. This complex substance is characterized by long chains of organic molecules related to fatty acids and carotenoids: hence the yellow color of most pollen. Sporopollenin is unusually resistant to chemical and biological degradation. In seed plants, which use pollen to transfer the male sperm to the female egg, the toughness of sporopollenin explains the existence of well-preserved pollen fossils. Sporopollenin was once thought to be an innovation of land plants; however, the green algae Coleochaetes forms spores that contain sporopollenin.
Gametangia in Seedless Plants
Gametangia (singular, gametangium) are structures observed on multicellular haploid gametophytes. In the gametangia, precursor cells give rise to gametes by mitosis. The male gametangium (antheridium) releases sperm. Many seedless plants produce sperm equipped with flagella that enable them to swim in a moist environment to the archegonia: the female gametangium. The embryo develops inside the archegonium as the sporophyte. Gametangia are prominent in seedless plants, but are very rarely found in seed plants.
Apical Meristems
Shoots and roots of plants increase in length through rapid cell division in a tissue called the apical meristem, which is a small zone of cells found at the shoot tip or root tip (Figure \(3\)). The apical meristem is made of undifferentiated cells that continue to proliferate throughout the life of the plant. Meristematic cells give rise to all the specialized tissues of the organism. Elongation of the shoots and roots allows a plant to access additional space and resources: light in the case of the shoot, and water and minerals in the case of roots. A separate meristem, called the lateral meristem, produces cells that increase the diameter of tree trunks.
Additional Land Plant Adaptations
As plants adapted to dry land and became independent from the constant presence of water in damp habitats, new organs and structures made their appearance. Early land plants did not grow more than a few inches off the ground, competing for light on these low mats. By developing a shoot and growing taller, individual plants captured more light. Because air offers substantially less support than water, land plants incorporated more rigid molecules in their stems (and later, tree trunks). In small plants such as single-celled algae, simple diffusion suffices to distribute water and nutrients throughout the organism. However, for plants to evolve larger forms, the evolution of vascular tissue for the distribution of water and solutes was a prerequisite. The vascular system contains xylem and phloem tissues. Xylem conducts water and minerals absorbed from the soil up to the shoot, while phloem transports food derived from photosynthesis throughout the entire plant. A root system evolved to take up water and minerals from the soil, and to anchor the increasingly taller shoot in the soil.
In land plants, a waxy, waterproof cover called a cuticle protects the leaves and stems from desiccation. However, the cuticle also prevents intake of carbon dioxide needed for the synthesis of carbohydrates through photosynthesis. To overcome this, stomata or pores that open and close to regulate traffic of gases and water vapor appeared in plants as they moved away from moist environments into drier habitats.
Water filters ultraviolet-B (UVB) light, which is harmful to all organisms, especially those that must absorb light to survive. This filtering does not occur for land plants. This presented an additional challenge to land colonization, which was met by the evolution of biosynthetic pathways for the synthesis of protective flavonoids and other compounds: pigments that absorb UV wavelengths of light and protect the aerial parts of plants from photodynamic damage.
Plants cannot avoid being eaten by animals. Instead, they synthesize a large range of poisonous secondary metabolites: complex organic molecules such as alkaloids, whose noxious smells and unpleasant taste deter animals. These toxic compounds can also cause severe diseases and even death, thus discouraging predation. Humans have used many of these compounds for centuries as drugs, medications, or spices. In contrast, as plants co-evolved with animals, the development of sweet and nutritious metabolites lured animals into providing valuable assistance in dispersing pollen grains, fruit, or seeds. Plants have been enlisting animals to be their helpers in this way for hundreds of millions of years.
Evolution of Land Plants
No discussion of the evolution of plants on land can be undertaken without a brief review of the timeline of the geological eras. The early era, known as the Paleozoic, is divided into six periods. It starts with the Cambrian period, followed by the Ordovician, Silurian, Devonian, Carboniferous, and Permian. The major event to mark the Ordovician, more than 500 million years ago, was the colonization of land by the ancestors of modern land plants. Fossilized cells, cuticles, and spores of early land plants have been dated as far back as the Ordovician period in the early Paleozoic era. The oldest-known vascular plants have been identified in deposits from the Devonian. One of the richest sources of information is the Rhynie chert, a sedimentary rock deposit found in Rhynie, Scotland (Figure \(4\)), where embedded fossils of some of the earliest vascular plants have been identified.
Paleobotanists distinguish between extinct species, as fossils, and extant species, which are still living. The extinct vascular plants, classified as zosterophylls and trimerophytes, most probably lacked true leaves and roots and formed low vegetation mats similar in size to modern-day mosses, although some trimetophytes could reach one meter in height. The later genus Cooksonia, which flourished during the Silurian, has been extensively studied from well-preserved examples. Imprints of Cooksonia show slender branching stems ending in what appear to be sporangia. From the recovered specimens, it is not possible to establish for certain whether Cooksonia possessed vascular tissues. Fossils indicate that by the end of the Devonian period, ferns, horsetails, and seed plants populated the landscape, giving rising to trees and forests. This luxuriant vegetation helped enrich the atmosphere in oxygen, making it easier for air-breathing animals to colonize dry land. Plants also established early symbiotic relationships with fungi, creating mycorrhizae: a relationship in which the fungal network of filaments increases the efficiency of the plant root system, and the plants provide the fungi with byproducts of photosynthesis.
Career Connection: Paleobotanist
How organisms acquired traits that allow them to colonize new environments—and how the contemporary ecosystem is shaped—are fundamental questions of evolution. Paleobotany (the study of extinct plants) addresses these questions through the analysis of fossilized specimens retrieved from field studies, reconstituting the morphology of organisms that disappeared long ago. Paleobotanists trace the evolution of plants by following the modifications in plant morphology: shedding light on the connection between existing plants by identifying common ancestors that display the same traits. This field seeks to find transitional species that bridge gaps in the path to the development of modern organisms. Fossils are formed when organisms are trapped in sediments or environments where their shapes are preserved. Paleobotanists collect fossil specimens in the field and place them in the context of the geological sediments and other fossilized organisms surrounding them. The activity requires great care to preserve the integrity of the delicate fossils and the layers of rock in which they are found.
One of the most exciting recent developments in paleobotany is the use of analytical chemistry and molecular biology to study fossils. Preservation of molecular structures requires an environment free of oxygen, since oxidation and degradation of material through the activity of microorganisms depend on its presence. One example of the use of analytical chemistry and molecular biology is the identification of oleanane, a compound that deters pests. Up to this point, oleanane appeared to be unique to flowering plants; however, it has now been recovered from sediments dating from the Permian, much earlier than the current dates given for the appearance of the first flowering plants. Paleobotanists can also study fossil DNA, which can yield a large amount of information, by analyzing and comparing the DNA sequences of extinct plants with those of living and related organisms. Through this analysis, evolutionary relationships can be built for plant lineages.
Some paleobotanists are skeptical of the conclusions drawn from the analysis of molecular fossils. For example, the chemical materials of interest degrade rapidly when exposed to air during their initial isolation, as well as in further manipulations. There is always a high risk of contaminating the specimens with extraneous material, mostly from microorganisms. Nevertheless, as technology is refined, the analysis of DNA from fossilized plants will provide invaluable information on the evolution of plants and their adaptation to an ever-changing environment.
The Major Divisions of Land Plants
The green algae and land plants are grouped together into a subphylum called the Streptophytina, and thus are called Streptophytes. In a further division, land plants are classified into two major groups according to the absence or presence of vascular tissue, as detailed in Figure \(5\). Plants that lack vascular tissue, which is formed of specialized cells for the transport of water and nutrients, are referred to as non-vascular plants. Liverworts, mosses, and hornworts are seedless, non-vascular plants that likely appeared early in land plant evolution. Vascular plants developed a network of cells that conduct water and solutes. The first vascular plants appeared in the late Ordovician and were probably similar to lycophytes, which include club mosses (not to be confused with the mosses) and the pterophytes (ferns, horsetails, and whisk ferns). Lycophytes and pterophytes are referred to as seedless vascular plants, because they do not produce seeds. The seed plants, or spermatophytes, form the largest group of all existing plants, and hence dominate the landscape. Seed plants include gymnosperms, most notably conifers (Gymnosperms), which produce “naked seeds,” and the most successful of all plants, the flowering plants (Angiosperms). Angiosperms protect their seeds inside chambers at the center of a flower; the walls of the chamber later develop into a fruit.
Art Connection
Which of the following statements about plant divisions is false?
1. Lycophytes and pterophytes are seedless vascular plants.
2. All vascular plants produce seeds.
3. All nonvascular embryophytes are bryophytes.
4. Seed plants include angiosperms and gymnosperms.
Summary
Land plants acquired traits that made it possible to colonize land and survive out of the water. All land plants share the following characteristics: alternation of generations, with the haploid plant called a gametophyte, and the diploid plant called a sporophyte; protection of the embryo, formation of haploid spores in a sporangium, formation of gametes in a gametangium, and an apical meristem. Vascular tissues, roots, leaves, cuticle cover, and a tough outer layer that protects the spores contributed to the adaptation of plants to dry land. Land plants appeared about 500 million years ago in the Ordovician period.
Art Connections
Figure \(5\): Which of the following statements about plant divisions is false?
1. Lycophytes and pterophytes are seedless vascular plants.
2. All vascular plants produce seeds.
3. All nonvascular embryophytes are bryophytes.
4. Seed plants include angiosperms and gymnosperms.
Answer
B.
Glossary
antheridium
male gametangium
archegonium
female gametangium
charophyte
other term for green algae; considered the closest relative of land plants
diplontic
diploid stage is the dominant stage
embryophyte
other name for land plant; embryo is protected and nourished by the sporophyte
extant
still-living species
extinct
no longer existing species
gametangium
structure on the gametophyte in which gametes are produced
haplodiplodontic
haploid and diploid stages alternate
haplontic
haploid stage is the dominant stage
heterosporous
produces two types of spores
homosporous
produces one type of spore
megaspore
female spore
microspore
male spore
non-vascular plant
plant that lacks vascular tissue, which is formed of specialized cells for the transport of water and nutrients
seedless vascular plant
plant that does not produce seeds
sporocyte
diploid cell that produces spores by meiosis
sporopollenin
tough polymer surrounding the spore
vascular plant
plant containing a network of cells that conducts water and solutes through the organism | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/25%3A_Seedless_Plants/25.1%3A_Early_Plant_Life.txt |
Skills to Develop
• Describe the traits shared by green algae and land plants
• Explain the reasons why Charales are considered the closest relative to land plants
• Understand that current phylogenetic relationships are reshaped by comparative analysis of DNA sequences
Streptophytes
Until recently, all photosynthetic eukaryotes were considered members of the kingdom Plantae. The brown, red, and gold algae, however, have been reassigned to the Protista kingdom. This is because apart from their ability to capture light energy and fix CO2, they lack many structural and biochemical traits that distinguish plants from protists. The position of green algae is more ambiguous. Green algae contain the same carotenoids and chlorophyll a and b as land plants, whereas other algae have different accessory pigments and types of chlorophyll molecules in addition to chlorophyll a. Both green algae and land plants also store carbohydrates as starch. Cells in green algae divide along cell plates called phragmoplasts, and their cell walls are layered in the same manner as the cell walls of embryophytes. Consequently, land plants and closely related green algae are now part of a new monophyletic group called Streptophyta.
The remaining green algae, which belong to a group called Chlorophyta, include more than 7000 different species that live in fresh or brackish water, in seawater, or in snow patches. A few green algae even survive on soil, provided it is covered by a thin film of moisture in which they can live. Periodic dry spells provide a selective advantage to algae that can survive water stress. Some green algae may already be familiar, in particular Spirogyra and desmids. Their cells contain chloroplasts that display a dizzying variety of shapes, and their cell walls contain cellulose, as do land plants. Some green algae are single cells, such as Chlorella and Chlamydomonas, which adds to the ambiguity of green algae classification, because plants are multicellular. Other algae, like Ulva (commonly called sea lettuce), form colonies (Figure \(1\)).
Reproduction of Green Algae
Green algae reproduce both asexually, by fragmentation or dispersal of spores, or sexually, by producing gametes that fuse during fertilization. In a single-celled organism such as Chlamydomonas, there is no mitosis after fertilization. In the multicellular Ulva, a sporophyte grows by mitosis after fertilization. Both Chlamydomonas and Ulva produce flagellated gametes.
Charales
Green algae in the order Charales, and the coleochaetes (microscopic green algae that enclose their spores in sporopollenin), are considered the closest living relatives of embryophytes. The Charales can be traced back 420 million years. They live in a range of fresh water habitats and vary in size from a few millimeters to a meter in length. The representative species is Chara (Figure \(2\)), often called muskgrass or skunkweed because of its unpleasant smell. Large cells form the thallus: the main stem of the alga. Branches arising from the nodes are made of smaller cells. Male and female reproductive structures are found on the nodes, and the sperm have flagella. Unlike land plants, Charales do not undergo alternation of generations in their lifecycle. Charales exhibit a number of traits that are significant in their adaptation to land life. They produce the compounds lignin and sporopollenin, and form plasmodesmata that connect the cytoplasm of adjacent cells. The egg, and later, the zygote, form in a protected chamber on the parent plant.
New information from recent, extensive DNA sequence analysis of green algae indicates that the Zygnematales are more closely related to the embryophytes than the Charales. The Zygnematales include the familiar genus Spirogyra. As techniques in DNA analysis improve and new information on comparative genomics arises, the phylogenetic connections between species will change. Clearly, plant biologists have not yet solved the mystery of the origin of land plants.
Summary
Green algae share more traits with land plants than other algae, according to structure and DNA analysis. Charales form sporopollenin and precursors of lignin, phragmoplasts, and have flagellated sperm. They do not exhibit alternation of generations.
Glossary
streptophytes
group that includes green algae and land plants | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/25%3A_Seedless_Plants/25.2%3A_Green_Algae_-_Precursors_of_Land_Plants.txt |
Skills to Develop
• Identify the main characteristics of bryophytes
• Describe the distinguishing traits of liverworts, hornworts, and mosses
• Chart the development of land adaptations in the bryophytes
• Describe the events in the bryophyte lifecycle
Bryophytes are the group of plants that are the closest extant relative of early terrestrial plants. The first bryophytes (liverworts) most likely appeared in the Ordovician period, about 450 million years ago. Because of the lack of lignin and other resistant structures, the likelihood of bryophytes forming fossils is rather small. Some spores protected by sporopollenin have survived and are attributed to early bryophytes. By the Silurian period, however, vascular plants had spread through the continents. This compelling fact is used as evidence that non-vascular plants must have preceded the Silurian period.
More than 25,000 species of bryophytes thrive in mostly damp habitats, although some live in deserts. They constitute the major flora of inhospitable environments like the tundra, where their small size and tolerance to desiccation offer distinct advantages. They generally lack lignin and do not have actual tracheids (xylem cells specialized for water conduction). Rather, water and nutrients circulate inside specialized conducting cells. Although the term non-tracheophyte is more accurate, bryophytes are commonly called nonvascular plants.
In a bryophyte, all the conspicuous vegetative organs—including the photosynthetic leaf-like structures, the thallus, stem, and the rhizoid that anchors the plant to its substrate—belong to the haploid organism or gametophyte. The sporophyte is barely noticeable. The gametes formed by bryophytes swim with a flagellum, as do gametes in a few of the tracheophytes. The sporangium—the multicellular sexual reproductive structure—is present in bryophytes and absent in the majority of algae. The bryophyte embryo also remains attached to the parent plant, which protects and nourishes it. This is a characteristic of land plants.
The bryophytes are divided into three phyla: the liverworts or Hepaticophyta, the hornworts or Anthocerotophyta, and the mosses or true Bryophyta.
Liverworts
Liverworts (Hepaticophyta) are viewed as the plants most closely related to the ancestor that moved to land. Liverworts have colonized every terrestrial habitat on Earth and diversified to more than 7000 existing species (Figure \(1\)). Some gametophytes form lobate green structures, as seen in Figure \(2\). The shape is similar to the lobes of the liver, and hence provides the origin of the name given to the phylum.
Openings that allow the movement of gases may be observed in liverworts. However, these are not stomata, because they do not actively open and close. The plant takes up water over its entire surface and has no cuticle to prevent desiccation. Figure \(3\) represents the lifecycle of a liverwort. The cycle starts with the release of haploid spores from the sporangium that developed on the sporophyte. Spores disseminated by wind or water germinate into flattened thalli attached to the substrate by thin, single-celled filaments. Male and female gametangia develop on separate, individual plants. Once released, male gametes swim with the aid of their flagella to the female gametangium (the archegonium), and fertilization ensues. The zygote grows into a small sporophyte still attached to the parent gametophyte. It will give rise, by meiosis, to the next generation of spores. Liverwort plants can also reproduce asexually, by the breaking of branches or the spreading of leaf fragments called gemmae. In this latter type of reproduction, the gemmae—small, intact, complete pieces of plant that are produced in a cup on the surface of the thallus (shown in Figure \(3\))—are splashed out of the cup by raindrops. The gemmae then land nearby and develop into gametophytes.
Hornworts
The hornworts (Anthocerotophyta) belong to the broad bryophyte group. They have colonized a variety of habitats on land, although they are never far from a source of moisture. The short, blue-green gametophyte is the dominant phase of the lifecycle of a hornwort. The narrow, pipe-like sporophyte is the defining characteristic of the group. The sporophytes emerge from the parent gametophyte and continue to grow throughout the life of the plant (Figure \(4\)).
Stomata appear in the hornworts and are abundant on the sporophyte. Photosynthetic cells in the thallus contain a single chloroplast. Meristem cells at the base of the plant keep dividing and adding to its height. Many hornworts establish symbiotic relationships with cyanobacteria that fix nitrogen from the environment.
The lifecycle of hornworts (Figure \(5\)) follows the general pattern of alternation of generations. The gametophytes grow as flat thalli on the soil with embedded gametangia. Flagellated sperm swim to the archegonia and fertilize eggs. The zygote develops into a long and slender sporophyte that eventually splits open, releasing spores. Thin cells called pseudoelaters surround the spores and help propel them further in the environment. Unlike the elaters observed in horsetails, the hornwort pseudoelaters are single-celled structures. The haploid spores germinate and give rise to the next generation of gametophyte.
Mosses
More than 10,000 species of mosses have been catalogued. Their habitats vary from the tundra, where they are the main vegetation, to the understory of tropical forests. In the tundra, the mosses’ shallow rhizoids allow them to fasten to a substrate without penetrating the frozen soil. Mosses slow down erosion, store moisture and soil nutrients, and provide shelter for small animals as well as food for larger herbivores, such as the musk ox. Mosses are very sensitive to air pollution and are used to monitor air quality. They are also sensitive to copper salts, so these salts are a common ingredient of compounds marketed to eliminate mosses from lawns.
Mosses form diminutive gametophytes, which are the dominant phase of the lifecycle. Green, flat structures—resembling true leaves, but lacking vascular tissue—are attached in a spiral to a central stalk. The plants absorb water and nutrients directly through these leaf-like structures. Some mosses have small branches. Some primitive traits of green algae, such as flagellated sperm, are still present in mosses that are dependent on water for reproduction. Other features of mosses are clearly adaptations to dry land. For example, stomata are present on the stems of the sporophyte, and a primitive vascular system runs up the sporophyte’s stalk. Additionally, mosses are anchored to the substrate—whether it is soil, rock, or roof tiles—by multicellular rhizoids. These structures are precursors of roots. They originate from the base of the gametophyte, but are not the major route for the absorption of water and minerals. The lack of a true root system explains why it is so easy to rip moss mats from a tree trunk. The moss lifecycle follows the pattern of alternation of generations as shown in Figure \(6\). The most familiar structure is the haploid gametophyte, which germinates from a haploid spore and forms first a protonema—usually, a tangle of single-celled filaments that hug the ground. Cells akin to an apical meristem actively divide and give rise to a gametophore, consisting of a photosynthetic stem and foliage-like structures. Rhizoids form at the base of the gametophore. Gametangia of both sexes develop on separate gametophores. The male organ (the antheridium) produces many sperm, whereas the archegonium (the female organ) forms a single egg. At fertilization, the sperm swims down the neck to the venter and unites with the egg inside the archegonium. The zygote, protected by the archegonium, divides and grows into a sporophyte, still attached by its foot to the gametophyte.
Art Connection
Which of the following statements about the moss life cycle is false?
1. The mature gametophyte is haploid.
2. The sporophyte produces haploid spores.
3. The calyptra buds to form a mature gametophyte.
4. The zygote is housed in the venter.
The slender seta (plural, setae), as seen in Figure \(7\), contains tubular cells that transfer nutrients from the base of the sporophyte (the foot) to the sporangium or capsule.
A structure called a peristome increases the spread of spores after the tip of the capsule falls off at dispersal. The concentric tissue around the mouth of the capsule is made of triangular, close-fitting units, a little like “teeth”; these open and close depending on moisture levels, and periodically release spores.
Summary
Seedless nonvascular plants are small, having the gametophyte as the dominant stage of the lifecycle. Without a vascular system and roots, they absorb water and nutrients on all their exposed surfaces. Collectively known as bryophytes, the three main groups include the liverworts, the hornworts, and the mosses. Liverworts are the most primitive plants and are closely related to the first land plants. Hornworts developed stomata and possess a single chloroplast per cell. Mosses have simple conductive cells and are attached to the substrate by rhizoids. They colonize harsh habitats and can regain moisture after drying out. The moss sporangium is a complex structure that allows release of spores away from the parent plant.
Art Connections
Figure \(6\): Which of the following statements about the moss life cycle is false?
1. The mature gametophyte is haploid.
2. The sporophyte produces haploid spores.
3. The rhizoid buds to form a mature gametophyte.
4. The zygote is housed in the venter.
Answer
C.
Glossary
capsule
case of the sporangium in mosses
gemma
(plural, gemmae) leaf fragment that spreads for asexual reproduction
hornworts
group of non-vascular plants in which stomata appear
liverworts
most primitive group of the non-vascular plants
mosses
group of bryophytes in which a primitive conductive system appears
peristome
tissue that surrounds the opening of the capsule and allows periodic release of spores
protonema
tangle of single celled filaments that forms from the haploid spore
rhizoids
thin filaments that anchor the plant to the substrate
seta
stalk that supports the capsule in mosses | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/25%3A_Seedless_Plants/25.3%3A_Bryophytes.txt |
Skills to Develop
• Identify the new traits that first appear in tracheophytes
• Discuss the importance of adaptations to life on land
• Describe the classes of seedless tracheophytes
• Describe the lifecycle of a fern
• Explain the role of seedless vascular plants in the ecosystem
The vascular plants, or tracheophytes, are the dominant and most conspicuous group of land plants. More than 260,000 species of tracheophytes represent more than 90 percent of Earth’s vegetation. Several evolutionary innovations explain their success and their ability to spread to all habitats.
Bryophytes may have been successful at the transition from an aquatic habitat to land, but they are still dependent on water for reproduction, and absorb moisture and nutrients through the gametophyte surface. The lack of roots for absorbing water and minerals from the soil, as well as a lack of reinforced conducting cells, limits bryophytes to small sizes. Although they may survive in reasonably dry conditions, they cannot reproduce and expand their habitat range in the absence of water. Vascular plants, on the other hand, can achieve enormous heights, thus competing successfully for light. Photosynthetic organs become leaves, and pipe-like cells or vascular tissues transport water, minerals, and fixed carbon throughout the organism.
In seedless vascular plants, the diploid sporophyte is the dominant phase of the lifecycle. The gametophyte is now an inconspicuous, but still independent, organism. Throughout plant evolution, there is an evident reversal of roles in the dominant phase of the lifecycle. Seedless vascular plants still depend on water during fertilization, as the sperm must swim on a layer of moisture to reach the egg. This step in reproduction explains why ferns and their relatives are more abundant in damp environments.
Vascular Tissue: Xylem and Phloem
The first fossils that show the presence of vascular tissue date to the Silurian period, about 430 million years ago. The simplest arrangement of conductive cells shows a pattern of xylem at the center surrounded by phloem. Xylem is the tissue responsible for the storage and long-distance transport of water and nutrients, as well as the transfer of water-soluble growth factors from the organs of synthesis to the target organs. The tissue consists of conducting cells, known as tracheids, and supportive filler tissue, called parenchyma. Xylem conductive cells incorporate the compound lignin into their walls, and are thus described as lignified. Lignin itself is a complex polymer that is impermeable to water and confers mechanical strength to vascular tissue. With their rigid cell walls, the xylem cells provide support to the plant and allow it to achieve impressive heights. Tall plants have a selective advantage by being able to reach unfiltered sunlight and disperse their spores or seeds further away, thus expanding their range. By growing higher than other plants, tall trees cast their shadow on shorter plants and limit competition for water and precious nutrients in the soil.
Phloem is the second type of vascular tissue; it transports sugars, proteins, and other solutes throughout the plant. Phloem cells are divided into sieve elements (conducting cells) and cells that support the sieve elements. Together, xylem and phloem tissues form the vascular system of plants.
Roots: Support for the Plant
Roots are not well preserved in the fossil record. Nevertheless, it seems that roots appeared later in evolution than vascular tissue. The development of an extensive network of roots represented a significant new feature of vascular plants. Thin rhizoids attached bryophytes to the substrate, but these rather flimsy filaments did not provide a strong anchor for the plant; neither did they absorb substantial amounts of water and nutrients. In contrast, roots, with their prominent vascular tissue system, transfer water and minerals from the soil to the rest of the plant. The extensive network of roots that penetrates deep into the soil to reach sources of water also stabilizes trees by acting as a ballast or anchor. The majority of roots establish a symbiotic relationship with fungi, forming mycorrhizae, which benefit the plant by greatly increasing the surface area for absorption of water and soil minerals and nutrients.
Leaves, Sporophylls, and Strobili
A third innovation marks the seedless vascular plants. Accompanying the prominence of the sporophyte and the development of vascular tissue, the appearance of true leaves improved their photosynthetic efficiency. Leaves capture more sunlight with their increased surface area by employing more chloroplasts to trap light energy and convert it to chemical energy, which is then used to fix atmospheric carbon dioxide into carbohydrates. The carbohydrates are exported to the rest of the plant by the conductive cells of phloem tissue.
The existence of two types of morphology suggests that leaves evolved independently in several groups of plants. The first type of leaf is the microphyll, or “little leaf,” which can be dated to 350 million years ago in the late Silurian. A microphyll is small and has a simple vascular system. A single unbranched vein—a bundle of vascular tissue made of xylem and phloem—runs through the center of the leaf. Microphylls may have originated from the flattening of lateral branches, or from sporangia that lost their reproductive capabilities. Microphylls are present in the club mosses and probably preceded the development of megaphylls, or “big leaves”, which are larger leaves with a pattern of branching veins. Megaphylls most likely appeared independently several times during the course of evolution. Their complex networks of veins suggest that several branches may have combined into a flattened organ, with the gaps between the branches being filled with photosynthetic tissue.
In addition to photosynthesis, leaves play another role in the life of the plants. Pine cones, mature fronds of ferns, and flowers are all sporophylls—leaves that were modified structurally to bear sporangia. Strobili are cone-like structures that contain sporangia. They are prominent in conifers and are commonly known as pine cones.
Ferns and Other Seedless Vascular Plants
By the late Devonian period, plants had evolved vascular tissue, well-defined leaves, and root systems. With these advantages, plants increased in height and size. During the Carboniferous period, swamp forests of club mosses and horsetails—some specimens reaching heights of more than 30 m (100 ft)—covered most of the land. These forests gave rise to the extensive coal deposits that gave the Carboniferous its name. In seedless vascular plants, the sporophyte became the dominant phase of the lifecycle.
Water is still required for fertilization of seedless vascular plants, and most favor a moist environment. Modern-day seedless tracheophytes include club mosses, horsetails, ferns, and whisk ferns.
Phylum Lycopodiophyta: Club Mosses
The club mosses, or phylum Lycopodiophyta, are the earliest group of seedless vascular plants. They dominated the landscape of the Carboniferous, growing into tall trees and forming large swamp forests. Today’s club mosses are diminutive, evergreen plants consisting of a stem (which may be branched) and microphylls (Figure \(1\)). The phylum Lycopodiophyta consists of close to 1,200 species, including the quillworts (Isoetales), the club mosses (Lycopodiales), and spike mosses (Selaginellales), none of which are true mosses or bryophytes.
Lycophytes follow the pattern of alternation of generations seen in the bryophytes, except that the sporophyte is the major stage of the lifecycle. The gametophytes do not depend on the sporophyte for nutrients. Some gametophytes develop underground and form mycorrhizal associations with fungi. In club mosses, the sporophyte gives rise to sporophylls arranged in strobili, cone-like structures that give the class its name. Lycophytes can be homosporous or heterosporous.
Phylum Monilophyta: Class Equisetopsida (Horsetails)
Horsetails, whisk ferns and ferns belong to the phylum Monilophyta, with horsetails placed in the Class Equisetopsida. The single genus Equisetum is the survivor of a large group of plants, known as Arthrophyta, which produced large trees and entire swamp forests in the Carboniferous. The plants are usually found in damp environments and marshes (Figure \(2\)).
The stem of a horsetail is characterized by the presence of joints or nodes, hence the name Arthrophyta (arthro- = "joint"; -phyta = "plant"). Leaves and branches come out as whorls from the evenly spaced joints. The needle-shaped leaves do not contribute greatly to photosynthesis, the majority of which takes place in the green stem (Figure \(3\)).
Silica collects in the epidermal cells, contributing to the stiffness of horsetail plants. Underground stems known as rhizomes anchor the plants to the ground. Modern-day horsetails are homosporous and produce bisexual gametophytes.
Phylum Monilophyta: Class Psilotopsida (Whisk Ferns)
While most ferns form large leaves and branching roots, the whisk ferns, Class Psilotopsida, lack both roots and leaves, probably lost by reduction. Photosynthesis takes place in their green stems, and small yellow knobs form at the tip of the branch stem and contain the sporangia. Whisk ferns were considered an early pterophytes. However, recent comparative DNA analysis suggests that this group may have lost both vascular tissue and roots through evolution, and is more closely related to ferns.
Phylum Monilophyta: Class Psilotopsida (Ferns)
With their large fronds, ferns are the most readily recognizable seedless vascular plants. They are considered the most advanced seedless vascular plants and display characteristics commonly observed in seed plants. More than 20,000 species of ferns live in environments ranging from tropics to temperate forests. Although some species survive in dry environments, most ferns are restricted to moist, shaded places. Ferns made their appearance in the fossil record during the Devonian period and expanded during the Carboniferous.
The dominant stage of the lifecycle of a fern is the sporophyte, which consists of large compound leaves called fronds. Fronds fulfill a double role; they are photosynthetic organs that also carry reproductive organs. The stem may be buried underground as a rhizome, from which adventitious roots grow to absorb water and nutrients from the soil; or, they may grow above ground as a trunk in tree ferns (Figure \(5\)). Adventitious organs are those that grow in unusual places, such as roots growing from the side of a stem.
The tip of a developing fern frond is rolled into a crozier, or fiddlehead (Figure \(6\)). Fiddleheads unroll as the frond develops.
The lifecycle of a fern is depicted in Figure \(7\).
Art Connection
Which of the following statements about the fern life cycle is false?
1. Sporangia produce haploid spores.
2. The sporophyte grows from a gametophyte.
3. The sporophyte is diploid and the gametophyte is haploid.
4. Sporangia form on the underside of the gametophyte.
Link to Learning
To see an animation of the lifecycle of a fern and to test your knowledge, go to the website.
Most ferns produce the same type of spores and are therefore homosporous. The diploid sporophyte is the most conspicuous stage of the lifecycle. On the underside of its mature fronds, sori (singular, sorus) form as small clusters where sporangia develop (Figure \(8\)).
Inside the sori, spores are produced by meiosis and released into the air. Those that land on a suitable substrate germinate and form a heart-shaped gametophyte, which is attached to the ground by thin filamentous rhizoids (Figure \(9\)).
The inconspicuous gametophyte harbors both sex gametangia. Flagellated sperm released from the antheridium swim on a wet surface to the archegonium, where the egg is fertilized. The newly formed zygote grows into a sporophyte that emerges from the gametophyte and grows by mitosis into the next generation sporophyte.
Career Connection: Landscape Designer
Looking at the well-laid parterres of flowers and fountains in the grounds of royal castles and historic houses of Europe, it’s clear that the gardens’ creators knew about more than art and design. They were also familiar with the biology of the plants they chose. Landscape design also has strong roots in the United States’ tradition. A prime example of early American classical design is Monticello: Thomas Jefferson’s private estate. Among his many interests, Jefferson maintained a strong passion for botany. Landscape layout can encompass a small private space, like a backyard garden; public gathering places, like Central Park in New York City; or an entire city plan, like Pierre L’Enfant’s design for Washington, DC.
A landscape designer will plan traditional public spaces—such as botanical gardens, parks, college campuses, gardens, and larger developments—as well as natural areas and private gardens. The restoration of natural places encroached on by human intervention, such as wetlands, also requires the expertise of a landscape designer.
With such an array of necessary skills, a landscape designer’s education includes a solid background in botany, soil science, plant pathology, entomology, and horticulture. Coursework in architecture and design software is also required for the completion of the degree. The successful design of a landscape rests on an extensive knowledge of plant growth requirements, such as light and shade, moisture levels, compatibility of different species, and susceptibility to pathogens and pests. Mosses and ferns will thrive in a shaded area, where fountains provide moisture; cacti, on the other hand, would not fare well in that environment. The future growth of individual plants must be taken into account, to avoid crowding and competition for light and nutrients. The appearance of the space over time is also of concern. Shapes, colors, and biology must be balanced for a well-maintained and sustainable green space. Art, architecture, and biology blend in a beautifully designed and implemented landscape.
The Importance of Seedless Vascular Plants
Mosses and liverworts are often the first macroscopic organisms to colonize an area, both in a primary succession—where bare land is settled for the first time by living organisms—or in a secondary succession, where soil remains intact after a catastrophic event wipes out many existing species. Their spores are carried by the wind, birds, or insects. Once mosses and liverworts are established, they provide food and shelter for other species. In a hostile environment, like the tundra where the soil is frozen, bryophytes grow well because they do not have roots and can dry and rehydrate rapidly once water is again available. Mosses are at the base of the food chain in the tundra biome. Many species—from small insects to musk oxen and reindeer—depend on mosses for food. In turn, predators feed on the herbivores, which are the primary consumers. Some reports indicate that bryophytes make the soil more amenable to colonization by other plants. Because they establish symbiotic relationships with nitrogen-fixing cyanobacteria, mosses replenish the soil with nitrogen.
At the end of the nineteenth century, scientists observed that lichens and mosses were becoming increasingly rare in urban and suburban areas. Since bryophytes have neither a root system for absorption of water and nutrients, nor a cuticle layer that protects them from desiccation, pollutants in rainwater readily penetrate their tissues; they absorb moisture and nutrients through their entire exposed surfaces. Therefore, pollutants dissolved in rainwater penetrate plant tissues readily and have a larger impact on mosses than on other plants. The disappearance of mosses can be considered a bioindicator for the level of pollution in the environment.
Ferns contribute to the environment by promoting the weathering of rock, accelerating the formation of topsoil, and slowing down erosion by spreading rhizomes in the soil. The water ferns of the genus Azolla harbor nitrogen-fixing cyanobacteria and restore this important nutrient to aquatic habitats.
Seedless plants have historically played a role in human life through uses as tools, fuel, and medicine. Dried peat moss, Sphagnum, is commonly used as fuel in some parts of Europe and is considered a renewable resource. Sphagnum bogs (Figure \(11\)) are cultivated with cranberry and blueberry bushes. The ability of Sphagnum to hold moisture makes the moss a common soil conditioner. Florists use blocks of Sphagnum to maintain moisture for floral arrangements.
The attractive fronds of ferns make them a favorite ornamental plant. Because they thrive in low light, they are well suited as house plants. More importantly, fiddleheads are a traditional spring food of Native Americans in the Pacific Northwest, and are popular as a side dish in French cuisine. The licorice fern, Polypodium glycyrrhiza, is part of the diet of the Pacific Northwest coastal tribes, owing in part to the sweetness of its rhizomes. It has a faint licorice taste and serves as a sweetener. The rhizome also figures in the pharmacopeia of Native Americans for its medicinal properties and is used as a remedy for sore throat.
Link to Learning
Go to this website to learn how to identify fern species based upon their fiddleheads.
By far the greatest impact of seedless vascular plants on human life, however, comes from their extinct progenitors. The tall club mosses, horsetails, and tree-like ferns that flourished in the swampy forests of the Carboniferous period gave rise to large deposits of coal throughout the world. Coal provided an abundant source of energy during the Industrial Revolution, which had tremendous consequences on human societies, including rapid technological progress and growth of large cities, as well as the degradation of the environment. Coal is still a prime source of energy and also a major contributor to global warming.
Summary
Vascular systems consist of xylem tissue, which transports water and minerals, and phloem tissue, which transports sugars and proteins. With the development of the vascular system, there appeared leaves to act as large photosynthetic organs, and roots to access water from the ground. Small uncomplicated leaves are microphylls. Large leaves with vein patterns are megaphylls. Modified leaves that bear sporangia are sporophylls. Some sporophylls are arranged in cone structures called strobili.
The seedless vascular plants include club mosses, which are the most primitive; whisk ferns, which lost leaves and roots by reductive evolution; and horsetails and ferns. Ferns are the most advanced group of seedless vascular plants. They are distinguished by large leaves called fronds and small sporangia-containing structures called sori, which are found on the underside of the fronds.
Mosses play an essential role in the balance of the ecosystems; they are pioneering species that colonize bare or devastated environments and make it possible for a succession to occur. They contribute to the enrichment of the soil and provide shelter and nutrients for animals in hostile environments. Mosses and ferns can be used as fuels and serve culinary, medical, and decorative purposes.
Art Connections
Figure \(7\): Which of the following statements about the fern life cycle is false?
1. Sporangia produce haploid spores.
2. The sporophyte grows from a gametophyte.
3. The sporophyte is diploid and the gametophyte is haploid.
4. Sporangia form on the underside of the gametophyte.
Answer
D.
Glossary
adventitious
describes an organ that grows in an unusual place, such as a roots growing from the side of a stem
club mosses
earliest group of seedless vascular plants
fern
seedless vascular plant that produces large fronds; the most advanced group of seedless vascular plants
horsetail
seedless vascular plant characterized by joints
lignin
complex polymer impermeable to water
lycophyte
club moss
megaphyll
larger leaves with a pattern of branching veins
microphyll
small size and simple vascular system with a single unbranched vein
peat moss
Sphagnum
phloem
tissue responsible for transport of sugars, proteins, and other solutes
sporophyll
leaf modified structurally to bear sporangia
strobili
cone-like structures that contain the sporangia
tracheophyte
vascular plant
vein
bundle of vascular tissue made of xylem and phloem
whisk fern
seedless vascular plant that lost roots and leaves by reduction
xylem
tissue responsible for long-distance transport of water and nutrients | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/25%3A_Seedless_Plants/25.4%3A_Seedless_Vascular_Plants.txt |
25.1: Early Plant Life
Review Questions
The land plants are probably descendants of which of these groups?
1. green algae
2. red algae
3. brown algae
4. angiosperms
Answer
A
Alternation of generations means that plants produce:
1. only haploid multicellular organisms
2. only diploid multicellular organisms
3. only diploid multicellular organisms with single-celled haploid gametes
4. both haploid and diploid multicellular organisms
Answer
D
Which of the following traits of land plants allows them to grow in height?
1. alternation of generations
2. waxy cuticle
3. tracheids
4. sporopollenin
Answer
C
Free Response
Why did land plants lose some of the accessory pigments present in brown and red algae?
Answer
Sunlight is not filtered by water or other algae on land; therefore, there is no need to collect light at additional wavelengths made available by other pigment coloration.
What is the difference between extant and extinct?
Answer
Paleobotanists distinguish between extinct species, which no longer live, and extant species, which are still living.
25.2: Green Algae - Precursors of Land Plants
Review Questions
What characteristic of Charales would enable them to survive a dry spell?
1. sperm with flagella
2. phragmoplasts
3. sporopollenin
4. chlorophyll a
Answer
C
Which one of these characteristics is present in land plants and not in Charales?
1. alternation of generations
2. flagellated sperm
3. phragmoplasts
4. plasmodesmata
Answer
A
Free Response
To an alga, what is the main advantage of producing drought-resistant structures?
Answer
It allows for survival through periodic droughts and colonization of environments where the supply of water fluctuates.
25.3: Bryophytes
Review Questions
Which of the following structures is not found in bryophytes?
1. a cellulose cell wall
2. chloroplast
3. sporangium
4. root
Answer
D
Stomata appear in which group of plants?
1. Charales
2. liverworts
3. hornworts
4. mosses
Answer
C
The chromosome complement in a moss protonema is:
1. 1n
2. 2n
3. 3n
4. varies with the size of the protonema
Answer
A
Why do mosses grow well in the Arctic tundra?
1. They grow better at cold temperatures.
2. They do not require moisture.
3. They do not have true roots and can grow on hard surfaces.
4. There are no herbivores in the tundra.
Answer
C
Free Response
In areas where it rains often, mosses grow on roofs. How do mosses survive on roofs without soil?
Answer
Mosses absorb water and nutrients carried by the rain and do not need soil because they do not derive much nutrition from the soil.
What are the three classes of bryophytes?
Answer
The bryophytes are divided into three phyla: the liverworts or Hepaticophyta, the hornworts or Anthocerotophyta, and the mosses or true Bryophyta.
25.4: Seedless Vascular Plants
Review Questions
Microphylls are characteristic of which types of plants?
1. mosses
2. liverworts
3. club mosses
4. ferns
Answer
C
A plant in the understory of a forest displays a segmented stem and slender leaves arranged in a whorl. It is probably a ________.
1. club moss
2. whisk fern
3. fern
4. horsetail
Answer
D
The following structures are found on the underside of fern leaves and contain sporangia:
1. sori
2. rhizomes
3. megaphylls
4. microphylls
Answer
A
The dominant organism in fern is the ________.
1. sperm
2. spore
3. gamete
4. sporophyte
Answer
D
What seedless plant is a renewable source of energy?
1. club moss
2. horsetail
3. sphagnum moss
4. fern
Answer
C
How do mosses contribute to returning nitrogen to the soil?
1. Mosses fix nitrogen from the air.
2. Mosses harbor cyanobacteria that fix nitrogen.
3. Mosses die and return nitrogen to the soil.
4. Mosses decompose rocks and release nitrogen.
Answer
D
Free Response
How did the development of a vascular system contribute to the increase in size of plants?
Answer
Plants became able to transport water and nutrients and not be limited by rates of diffusion. Vascularization allowed the development of leaves, which increased efficiency of photosynthesis and provided more energy for plant growth.
Which plant is considered the most advanced seedless vascular plant and why?
Answer
Ferns are considered the most advanced seedless vascular plants, because they display characteristics commonly observed in seed plants—they form large leaves and branching roots. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/25%3A_Seedless_Plants/25.E%3A_Seedless_Plants_%28Exercises%29.txt |
Seed plants, such as palms, have broken free from the need to rely on water for their reproductive needs. They play an integral role in all aspects of life on the planet, shaping the physical terrain, influencing the climate, and maintaining life as we know it.
• 26.0: Prelude to Seed Plants
For millennia, human societies have depended on seed plants for nutrition and medicinal compounds: and more recently, for industrial by-products, such as timber and paper, dyes, and textiles. Palms provide materials including rattans, oils, and dates. Wheat is grown to feed both human and animal populations. The fruit of the cotton boll flower is harvested as a boll, with its fibers transformed into clothing or pulp for paper.
• 26.1: Evolution of Seed Plants
The first plants to colonize land were most likely closely related to modern day mosses (bryophytes) and are thought to have appeared about 500 million years ago. They were followed by liverworts (also bryophytes) and primitive vascular plants—the pterophytes—from which modern ferns are derived.
• 26.2: Gymnosperms
Gymnosperms, meaning “naked seeds,” are a diverse group of seed plants and are paraphyletic. Paraphyletic groups are those in which not all members are descendants of a single common ancestor. Their characteristics include naked seeds, separate female and male gametes, pollination by wind, and tracheids (which transport water and solutes in the vascular system).
• 26.3: Angiosperms
From their humble and still obscure beginning during the early Jurassic period, the angiosperms—or flowering plants—have evolved to dominate most terrestrial ecosystems. With more than 250,000 species, the angiosperm phylum (Anthophyta) is second only to insects in terms of diversification.
• 26.4: The Role of Seed Plants
Without seed plants, life as we know it would not be possible. Plants play a key role in the maintenance of terrestrial ecosystems through stabilization of soils, cycling of carbon, and climate moderation. Large tropical forests release oxygen and act as carbon dioxide sinks. Seed plants provide shelter to many life forms, as well as food for herbivores, thereby indirectly feeding carnivores. Plant secondary metabolites are used for medicinal purposes and industrial production.
• 26.E: Seed Plants (Exercises)
Thumbnail: Sunflower (Sunfola variety) against a blue sky. (CC BY-NC 3.0 / cropped from original; Fir0002/Flagstaffotos via Wikipedia).
26: Seed Plants
The lush palms on tropical shorelines do not depend on water for the dispersal of their pollen, fertilization, or the survival of the zygote—unlike mosses, liverworts, and ferns of the terrain. Seed plants, such as palms, have broken free from the need to rely on water for their reproductive needs. They play an integral role in all aspects of life on the planet, shaping the physical terrain, influencing the climate, and maintaining life as we know it. For millennia, human societies have depended on seed plants for nutrition and medicinal compounds: and more recently, for industrial by-products, such as timber and paper, dyes, and textiles. Palms provide materials including rattans, oils, and dates. Wheat is grown to feed both human and animal populations. The fruit of the cotton boll flower is harvested as a boll, with its fibers transformed into clothing or pulp for paper. The showy opium poppy is valued both as an ornamental flower and as a source of potent opiate compounds. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/26%3A_Seed_Plants/26.0%3A_Prelude_to_Seed_Plants.txt |
Skills to Develop
• Explain when seed plants first appeared and when gymnosperms became the dominant plant group
• Describe the two major innovations that allowed seed plants to reproduce in the absence of water
• Discuss the purpose of pollen grains and seeds
• Describe the significance of angiosperms bearing both flowers and fruit
The first plants to colonize land were most likely closely related to modern day mosses (bryophytes) and are thought to have appeared about 500 million years ago. They were followed by liverworts (also bryophytes) and primitive vascular plants—the pterophytes—from which modern ferns are derived. The lifecycle of bryophytes and pterophytes is characterized by the alternation of generations, like gymnosperms and angiosperms; what sets bryophytes and pterophytes apart from gymnosperms and angiosperms is their reproductive requirement for water. The completion of the bryophyte and pterophyte life cycle requires water because the male gametophyte releases sperm, which must swim—propelled by their flagella—to reach and fertilize the female gamete or egg. After fertilization, the zygote matures and grows into a sporophyte, which in turn will form sporangia or "spore vessels." In the sporangia, mother cells undergo meiosis and produce the haploid spores. Release of spores in a suitable environment will lead to germination and a new generation of gametophytes.
In seed plants, the evolutionary trend led to a dominant sporophyte generation, and at the same time, a systematic reduction in the size of the gametophyte: from a conspicuous structure to a microscopic cluster of cells enclosed in the tissues of the sporophyte. Whereas lower vascular plants, such as club mosses and ferns, are mostly homosporous (produce only one type of spore), all seed plants, or spermatophytes, are heterosporous. They form two types of spores: megaspores (female) and microspores (male). Megaspores develop into female gametophytes that produce eggs, and microspores mature into male gametophytes that generate sperm. Because the gametophytes mature within the spores, they are not free-living, as are the gametophytes of other seedless vascular plants. Heterosporous seedless plants are seen as the evolutionary forerunners of seed plants.
Seeds and pollen—two critical adaptations to drought, and to reproduction that doesn’t require water—distinguish seed plants from other (seedless) vascular plants. Both adaptations were required for the colonization of land begun by the bryophytes and their ancestors. Fossils place the earliest distinct seed plants at about 350 million years ago. The first reliable record of gymnosperms dates their appearance to the Pennsylvanian period, about 319 million years ago (Figure \(1\)). Gymnosperms were preceded by progymnosperms, the first naked seed plants, which arose about 380 million years ago. Progymnosperms were a transitional group of plants that superficially resembled conifers (cone bearers) because they produced wood from the secondary growth of the vascular tissues; however, they still reproduced like ferns, releasing spores into the environment. Gymnosperms dominated the landscape in the early (Triassic) and middle (Jurassic) Mesozoic era. Angiosperms surpassed gymnosperms by the middle of the Cretaceous (about 100 million years ago) in the late Mesozoic era, and today are the most abundant plant group in most terrestrial biomes.
Pollen and seed were innovative structures that allowed seed plants to break their dependence on water for reproduction and development of the embryo, and to conquer dry land. The pollen grains are the male gametophytes, which contain the sperm (gametes) of the plant. The small haploid (1n) cells are encased in a protective coat that prevents desiccation (drying out) and mechanical damage. Pollen grains can travel far from their original sporophyte, spreading the plant’s genes. The seed offers the embryo protection, nourishment, and a mechanism to maintain dormancy for tens or even thousands of years, ensuring germination can occur when growth conditions are optimal. Seeds therefore allow plants to disperse the next generation through both space and time. With such evolutionary advantages, seed plants have become the most successful and familiar group of plants, in part because of their size and striking appearance.
Evolution of Gymnosperms
The fossil plant Elkinsia polymorpha, a "seed fern" from the Devonian period—about 400 million years ago—is considered the earliest seed plant known to date. Seed ferns (Figure \(2\)) produced their seeds along their branches without specialized structures. What makes them the first true seed plants is that they developed structures called cupules to enclose and protect the ovule—the female gametophyte and associated tissues—which develops into a seed upon fertilization. Seed plants resembling modern tree ferns became more numerous and diverse in the coal swamps of the Carboniferous period.
Fossil records indicate the first gymnosperms (progymnosperms) most likely originated in the Paleozoic era, during the middle Devonian period: about 390 million years ago. Following the wet Mississippian and Pennsylvanian periods, which were dominated by giant fern trees, the Permian period was dry. This gave a reproductive edge to seed plants, which are better adapted to survive dry spells. The Ginkgoales, a group of gymnosperms with only one surviving species—the Gingko biloba—were the first gymnosperms to appear during the lower Jurassic. Gymnosperms expanded in the Mesozoic era (about 240 million years ago), supplanting ferns in the landscape, and reaching their greatest diversity during this time. The Jurassic period was as much the age of the cycads (palm-tree-like gymnosperms) as the age of the dinosaurs. Gingkoales and the more familiar conifers also dotted the landscape. Although angiosperms (flowering plants) are the major form of plant life in most biomes, gymnosperms still dominate some ecosystems, such as the taiga (boreal forests) and the alpine forests at higher mountain elevations (Figure \(3\)) because of their adaptation to cold and dry growth conditions.
Seeds and Pollen as an Evolutionary Adaptation to Dry Land
Unlike bryophyte and fern spores (which are haploid cells dependent on moisture for rapid development of gametophytes), seeds contain a diploid embryo that will germinate into a sporophyte. Storage tissue to sustain growth and a protective coat give seeds their superior evolutionary advantage. Several layers of hardened tissue prevent desiccation, and free reproduction from the need for a constant supply of water. Furthermore, seeds remain in a state of dormancy—induced by desiccation and the hormone abscisic acid—until conditions for growth become favorable. Whether blown by the wind, floating on water, or carried away by animals, seeds are scattered in an expanding geographic range, thus avoiding competition with the parent plant.
Pollen grains (Figure \(4\)) are male gametophytes and are carried by wind, water, or a pollinator. The whole structure is protected from desiccation and can reach the female organs without dependence on water. Male gametes reach female gametophyte and the egg cell gamete though a pollen tube: an extension of a cell within the pollen grain. The sperm of modern gymnosperms lack flagella, but in cycads and the Gingko, the sperm still possess flagella that allow them to swim down the pollen tube to the female gamete; however, they are enclosed in a pollen grain.
Evolution of Angiosperms
Undisputed fossil records place the massive appearance and diversification of angiosperms in the middle to late Mesozoic era. Angiosperms (“seed in a vessel”) produce a flower containing male and/or female reproductive structures. Fossil evidence (Figure \(5\)) indicates that flowering plants first appeared in the Lower Cretaceous, about 125 million years ago, and were rapidly diversifying by the Middle Cretaceous, about 100 million years ago. Earlier traces of angiosperms are scarce. Fossilized pollen recovered from Jurassic geological material has been attributed to angiosperms. A few early Cretaceous rocks show clear imprints of leaves resembling angiosperm leaves. By the mid-Cretaceous, a staggering number of diverse flowering plants crowd the fossil record. The same geological period is also marked by the appearance of many modern groups of insects, including pollinating insects that played a key role in ecology and the evolution of flowering plants.
Although several hypotheses have been offered to explain this sudden profusion and variety of flowering plants, none have garnered the consensus of paleobotanists (scientists who study ancient plants). New data in comparative genomics and paleobotany have, however, shed some light on the evolution of angiosperms. Rather than being derived from gymnosperms, angiosperms form a sister clade (a species and its descendents) that developed in parallel with the gymnosperms. The two innovative structures of flowers and fruit represent an improved reproductive strategy that served to protect the embryo, while increasing genetic variability and range. Paleobotanists debate whether angiosperms evolved from small woody bushes, or were basal angiosperms related to tropical grasses. Both views draw support from cladistics studies, and the so-called woody magnoliid hypothesis—which proposes that the early ancestors of angiosperms were shrubs—also offers molecular biological evidence.
The most primitive living angiosperm is considered to be Amborella trichopoda, a small plant native to the rainforest of New Caledonia, an island in the South Pacific. Analysis of the genome of A. trichopoda has shown that it is related to all existing flowering plants and belongs to the oldest confirmed branch of the angiosperm family tree. A few other angiosperm groups called basal angiosperms, are viewed as primitive because they branched off early from the phylogenetic tree. Most modern angiosperms are classified as either monocots or eudicots, based on the structure of their leaves and embryos. Basal angiosperms, such as water lilies, are considered more primitive because they share morphological traits with both monocots and eudicots.
Flowers and Fruits as an Evolutionary Adaptation
Angiosperms produce their gametes in separate organs, which are usually housed in a flower. Both fertilization and embryo development take place inside an anatomical structure that provides a stable system of sexual reproduction largely sheltered from environmental fluctuations. Flowering plants are the most diverse phylum on Earth after insects; flowers come in a bewildering array of sizes, shapes, colors, smells, and arrangements. Most flowers have a mutualistic pollinator, with the distinctive features of flowers reflecting the nature of the pollination agent. The relationship between pollinator and flower characteristics is one of the great examples of coevolution.
Following fertilization of the egg, the ovule grows into a seed. The surrounding tissues of the ovary thicken, developing into a fruit that will protect the seed and often ensure its dispersal over a wide geographic range. Not all fruits develop from an ovary; such structures are “false fruits.” Like flowers, fruit can vary tremendously in appearance, size, smell, and taste. Tomatoes, walnut shells and avocados are all examples of fruit. As with pollen and seeds, fruits also act as agents of dispersal. Some may be carried away by the wind. Many attract animals that will eat the fruit and pass the seeds through their digestive systems, then deposit the seeds in another location. Cockleburs are covered with stiff, hooked spines that can hook into fur (or clothing) and hitch a ride on an animal for long distances. The cockleburs that clung to the velvet trousers of an enterprising Swiss hiker, George de Mestral, inspired his invention of the loop and hook fastener he named Velcro.
Evolution Connection: Building Phylogenetic Trees with Analysis of DNA Sequence Alignments
All living organisms display patterns of relationships derived from their evolutionary history. Phylogeny is the science that describes the relative connections between organisms, in terms of ancestral and descendant species. Phylogenetic trees, such as the plant evolutionary history shown in Figure \(6\), are tree-like branching diagrams that depict these relationships. Species are found at the tips of the branches. Each branching point, called a node, is the point at which a single taxonomic group (taxon), such as a species, separates into two or more species.
Phylogenetic trees have been built to describe the relationships between species since Darwin’s time. Traditional methods involve comparison of homologous anatomical structures and embryonic development, assuming that closely related organisms share anatomical features during embryo development. Some traits that disappear in the adult are present in the embryo; for example, a human fetus, at one point, has a tail. The study of fossil records shows the intermediate stages that link an ancestral form to its descendants. Most of these approaches are imprecise and lend themselves to multiple interpretations. As the tools of molecular biology and computational analysis have been developed and perfected in recent years, a new generation of tree-building methods has taken shape. The key assumption is that genes for essential proteins or RNA structures, such as the ribosomal RNA, are inherently conserved because mutations (changes in the DNA sequence) could compromise the survival of the organism. DNA from minute amounts of living organisms or fossils can be amplified by polymerase chain reaction (PCR) and sequenced, targeting the regions of the genome that are most likely to be conserved between species. The genes encoding the ribosomal RNA from the small 18S subunit and plastid genes are frequently chosen for DNA alignment analysis.
Once the sequences of interest are obtained, they are compared with existing sequences in databases such as GenBank, which is maintained by The National Center for Biotechnology Information. A number of computational tools are available to align and analyze sequences. Sophisticated computer analysis programs determine the percentage of sequence identity or homology. Sequence homology can be used to estimate the evolutionary distance between two DNA sequences and reflect the time elapsed since the genes separated from a common ancestor. Molecular analysis has revolutionized phylogenetic trees. In some cases, prior results from morphological studies have been confirmed: for example, confirming Amborella trichopoda as the most primitive angiosperm known. However, some groups and relationships have been rearranged as a result of DNA analysis.
Summary
Seed plants appeared about one million years ago, during the Carboniferous period. Two major innovations—seed and pollen—allowed seed plants to reproduce in the absence of water. The gametophytes of seed plants shrank, while the sporophytes became prominent structures and the diploid stage became the longest phase of the lifecycle. Gymnosperms became the dominant group during the Triassic. In these, pollen grains and seeds protect against desiccation. The seed, unlike a spore, is a diploid embryo surrounded by storage tissue and protective layers. It is equipped to delay germination until growth conditions are optimal. Angiosperms bear both flowers and fruit. The structures protect the gametes and the embryo during its development. Angiosperms appeared during the Mesozoic era and have become the dominant plant life in terrestrial habitats.
Glossary
flower
branches specialized for reproduction found in some seed-bearing plants, containing either specialized male or female organs or both male and female organs
fruit
thickened tissue derived from ovary wall that protects the embryo after fertilization and facilitates seed dispersal
ovule
female gametophyte
pollen grain
structure containing the male gametophyte of the plant
pollen tube
extension from the pollen grain that delivers sperm to the egg cell
progymnosperm
transitional group of plants that resembled conifers because they produced wood, yet still reproduced like ferns
seed
structure containing the embryo, storage tissue and protective coat
spermatophyte
seed plant; from the Greek sperm (seed) and phyte (plant) | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/26%3A_Seed_Plants/26.1%3A_Evolution_of_Seed_Plants.txt |
Skills to Develop
• Discuss the type of seeds produced by gymnosperms, as well as other characteristics of gymnosperms
• State which period saw the first appearance of gymnosperms and explain when they were the dominant plant life
• List the four groups of modern-day gymnosperms and provide examples of each
Gymnosperms, meaning “naked seeds,” are a diverse group of seed plants and are paraphyletic. Paraphyletic groups are those in which not all members are descendants of a single common ancestor. Their characteristics include naked seeds, separate female and male gametes, pollination by wind, and tracheids (which transport water and solutes in the vascular system).
Gymnosperm seeds are not enclosed in an ovary; rather, they are exposed on cones or modified leaves. Sporophylls are specialized leaves that produce sporangia. The term strobilus (plural = strobili) describes a tight arrangement of sporophylls around a central stalk, as seen in cones. Some seeds are enveloped by sporophyte tissues upon maturation. The layer of sporophyte tissue that surrounds the megasporangium, and later, the embryo, is called the integument.
Gymnosperms were the dominant phylum in Mesozoic era. They are adapted to live where fresh water is scarce during part of the year, or in the nitrogen-poor soil of a bog. Therefore, they are still the prominent phylum in the coniferous biome or taiga, where the evergreen conifers have a selective advantage in cold and dry weather. Evergreen conifers continue low levels of photosynthesis during the cold months, and are ready to take advantage of the first sunny days of spring. One disadvantage is that conifers are more susceptible than deciduous trees to infestations because conifers do not lose their leaves all at once. They cannot, therefore, shed parasites and restart with a fresh supply of leaves in spring.
The life cycle of a gymnosperm involves alternation of generations, with a dominant sporophyte in which the female gametophyte resides, and reduced gametophytes. All gymnosperms are heterosporous. The male and female reproductive organs can form in cones or strobili. Male and female sporangia are produced either on the same plant, described as monoecious (“one home” or bisexual), or on separate plants, referred to as dioecious (“two homes” or unisexual) plants. The life cycle of a conifer will serve as our example of reproduction in gymnosperms.
Life Cycle of a Conifer
Pine trees are conifers (cone bearing) and carry both male and female sporophylls on the same mature sporophyte. Therefore, they are monoecious plants. Like all gymnosperms, pines are heterosporous and generate two different types of spores: male microspores and female megaspores. In the male cones, or staminate cones, the microsporocytes give rise to pollen grains by meiosis. In the spring, large amounts of yellow pollen are released and carried by the wind. Some gametophytes will land on a female cone. Pollination is defined as the initiation of pollen tube growth. The pollen tube develops slowly, and the generative cell in the pollen grain divides into two haploid sperm cells by mitosis. At fertilization, one of the sperm cells will finally unite its haploid nucleus with the haploid nucleus of a haploid egg cell.
Female cones, or ovulate cones, contain two ovules per scale. One megaspore mother cell, or megasporocyte, undergoes meiosis in each ovule. Three of the four cells break down; only a single surviving cell will develop into a female multicellular gametophyte, which encloses archegonia (an archegonium is a reproductive organ that contains a single large egg). Upon fertilization, the diploid egg will give rise to the embryo, which is enclosed in a seed coat of tissue from the parent plant. Fertilization and seed development is a long process in pine trees: it may take up to two years after pollination. The seed that is formed contains three generations of tissues: the seed coat that originates from the sporophyte tissue, the gametophyte that will provide nutrients, and the embryo itself.
Figure \(1\) illustrates the life cycle of a conifer. The sporophyte (2n) phase is the longest phase in the life of a gymnosperm. The gametophytes (1n)—microspores and megaspores—are reduced in size. It may take more than year between pollination and fertilization while the pollen tube grows towards the megasporocyte (2n), which undergoes meiosis into megaspores. The megaspores will mature into eggs (1n).
Exercise \(1\)
At what stage does the diploid zygote form?
1. when the female cone begins to bud from the tree
2. at fertilization
3. when the seeds drop from the tree
4. when the pollen tube begins to grow
Video \(1\): Watch this video to see the process of seed production in gymnosperms.
Diversity of Gymnosperms
Modern gymnosperms are classified into four phyla. Coniferophyta, Cycadophyta, and Ginkgophyta are similar in their production of secondary cambium (cells that generate the vascular system of the trunk or stem and are partially specialized for water transportation) and their pattern of seed development. However, the three phyla are not closely related phylogenetically to each other. Gnetophyta are considered the closest group to angiosperms because they produce true xylem tissue.
Conifers (Coniferophyta)
Conifers are the dominant phylum of gymnosperms, with the most variety of species (Figure \(2\)). Most are typically tall trees that usually bear scale-like or needle-like leaves. Water evaporation from leaves is reduced by their thin shape and the thick cuticle. Snow slides easily off needle-shaped leaves, keeping the load light and decreasing breaking of branches. Adaptations to cold and dry weather explain the predominance of conifers at high altitudes and in cold climates. Conifers include familiar evergreen trees such as pines, spruces, firs, cedars, sequoias, and yews. A few species are deciduous and lose their leaves in fall. The European larch and the tamarack are examples of deciduous conifers (Figure \(2\)c). Many coniferous trees are harvested for paper pulp and timber. The wood of conifers is more primitive than the wood of angiosperms; it contains tracheids, but no vessel elements, and is therefore referred to as “soft wood.”
Cycads
Cycads thrive in mild climates, and are often mistaken for palms because of the shape of their large, compound leaves. Cycads bear large cones (Figure \(3\)), and may be pollinated by beetles rather than wind: unusual for a gymnosperm. They dominated the landscape during the age of dinosaurs in the Mesozoic, but only a hundred or so species persisted to modern times. They face possible extinction, and several species are protected through international conventions. Because of their attractive shape, they are often used as ornamental plants in gardens in the tropics and subtropics.
Gingkophytes
The single surviving species of the gingkophytes group is the Gingko biloba (Figure \(4\)). Its fan-shaped leaves—unique among seed plants because they feature a dichotomous venation pattern—turn yellow in autumn and fall from the tree. For centuries, G. biloba was cultivated by Chinese Buddhist monks in monasteries, which ensured its preservation. It is planted in public spaces because it is unusually resistant to pollution. Male and female organs are produced on separate plants. Typically, gardeners plant only male trees because the seeds produced by the female plant have an off-putting smell of rancid butter.
Gnetophytes
Gnetophytes are the closest relative to modern angiosperms, and include three dissimilar genera of plants: Ephedra, Gnetum, and Welwitschia (Figure \(5\)). Like angiosperms, they have broad leaves. In tropical and subtropical zones, gnetophytes are vines or small shrubs. Ephedra occurs in dry areas of the West Coast of the United States and Mexico. Ephedra’s small, scale-like leaves are the source of the compound ephedrine, which is used in medicine as a potent decongestant. Because ephedrine is similar to amphetamines, both in chemical structure and neurological effects, its use is restricted to prescription drugs. Like angiosperms, but unlike other gymnosperms, all gnetophytes possess vessel elements in their xylem.
Summary
Gymnosperms are heterosporous seed plants that produce naked seeds. They appeared in the Paleozoic period and were the dominant plant life during the Mesozoic. Modern-day gymnosperms belong to four phyla. The largest phylum, Coniferophyta, is represented by conifers, the predominant plants at high altitude and latitude. Cycads (phylum Cycadophyta) resemble palm trees and grow in tropical climates. Gingko biloba is the only representative of the phylum Gingkophyta. The last phylum, Gnetophyta, is a diverse group of shrubs that produce vessel elements in their wood.
Art Connections
Figure \(1\): At what stage does the diploid zygote form?
1. When the female cone begins to bud from the tree
2. At fertilization
3. When the seeds drop from the tree
4. When the pollen tube begins to grow
Answer
B. The diploid zygote forms after the pollen tube has finished forming, so that the male generative nuclei can fuse with the female gametophyte.
Glossary
conifer
dominant phylum of gymnosperms with the most variety of trees
cycad
gymnosperm that grows in tropical climates and resembles a palm tree; member of the phylum Cycadophyta
dioecious
describes a species in which the male and female reproductive organs are carried on separate specimens
gingkophyte
gymnosperm with one extant species, the Gingko biloba: a tree with fan-shaped leaves
gnetophyte
gymnosperm shrub with varied morphological features that produces vessel elements in its woody tissues; the phylum includes the genera Ephedra, Gnetum and Welwitschia
gymnosperm
seed plant with naked seeds (seeds exposed on modified leaves or in cones)
integument
layer of sporophyte tissue that surrounds the megasporangium, and later, the embryo
megasporocyte
megaspore mother cell; larger spore that germinates into a female gametophyte in a heterosporous plant
microsporocyte
smaller spore that produces a male gametophyte in a heterosporous plant
monoecious
describes a species in which the male and female reproductive organs are on the same plant
ovulate cone
cone containing two ovules per scale
strobilus
plant structure with a tight arrangement of sporophylls around a central stalk, as seen in cones or flowers; the male strobilus produces pollen, and the female strobilus produces eggs | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/26%3A_Seed_Plants/26.2%3A_Gymnosperms.txt |
Skills to Develop
• Explain why angiosperms are the dominant form of plant life in most terrestrial ecosystems
• Describe the main parts of a flower and their purpose
• Detail the life cycle of an angiosperm
• Discuss the two main groups of flowering plants
From their humble and still obscure beginning during the early Jurassic period, the angiosperms—or flowering plants—have evolved to dominate most terrestrial ecosystems (Figure \(1\)). With more than 250,000 species, the angiosperm phylum (Anthophyta) is second only to insects in terms of diversification.
The success of angiosperms is due to two novel reproductive structures: flowers and fruit. The function of the flower is to ensure pollination. Flowers also provide protection for the ovule and developing embryo inside a receptacle. The function of the fruit is seed dispersal. They also protect the developing seed. Different fruit structures or tissues on fruit—such as sweet flesh, wings, parachutes, or spines that grab—reflect the dispersal strategies that help spread seeds.
Flowers
Flowers are modified leaves, or sporophylls, organized around a central stalk. Although they vary greatly in appearance, all flowers contain the same structures: sepals, petals, carpels, and stamens. The peduncle attaches the flower to the plant. A whorl of sepals (collectively called the calyx) is located at the base of the peduncle and encloses the unopened floral bud. Sepals are usually photosynthetic organs, although there are some exceptions. For example, the corolla in lilies and tulips consists of three sepals and three petals that look virtually identical. Petals, collectively the corolla, are located inside the whorl of sepals and often display vivid colors to attract pollinators. Flowers pollinated by wind are usually small, feathery, and visually inconspicuous. Sepals and petals together form the perianth. The sexual organs (carpels and stamens) are located at the center of the flower.
As illustrated in Figure \(2\), styles, stigmas, and ovules constitute the female organ: the gynoecium or carpel. Flower structure is very diverse, and carpels may be singular, multiple, or fused. Multiple fused carpels comprise a pistil. The megaspores and the female gametophytes are produced and protected by the thick tissues of the carpel. A long, thin structure called a style leads from the sticky stigma, where pollen is deposited, to the ovary, enclosed in the carpel. The ovary houses one or more ovules, each of which will develop into a seed upon fertilization. The male reproductive organs, the stamens (collectively called the androecium), surround the central carpel. Stamens are composed of a thin stalk called a filament and a sac-like structure called the anther. The filament supports the anther, where the microspores are produced by meiosis and develop into pollen grains.
Fruit
As the seed develops, the walls of the ovary thicken and form the fruit. The seed forms in an ovary, which also enlarges as the seeds grow. In botany, a fertilized and fully grown, ripened ovary is a fruit. Many foods commonly called vegetables are actually fruit. Eggplants, zucchini, string beans, and bell peppers are all technically fruit because they contain seeds and are derived from the thick ovary tissue. Acorns are nuts, and winged maple whirligigs (whose botanical name is samara) are also fruit. Botanists classify fruit into more than two dozen different categories, only a few of which are actually fleshy and sweet.
Mature fruit can be fleshy or dry. Fleshy fruit include the familiar berries, peaches, apples, grapes, and tomatoes. Rice, wheat, and nuts are examples of dry fruit. Another distinction is that not all fruits are derived from the ovary. For instance, strawberries are derived from the receptacle and apples from the pericarp, or hypanthium. Some fruits are derived from separate ovaries in a single flower, such as the raspberry. Other fruits, such as the pineapple, form from clusters of flowers. Additionally, some fruits, like watermelon and orange, have rinds. Regardless of how they are formed, fruits are an agent of seed dispersal. The variety of shapes and characteristics reflect the mode of dispersal. Wind carries the light dry fruit of trees and dandelions. Water transports floating coconuts. Some fruits attract herbivores with color or perfume, or as food. Once eaten, tough, undigested seeds are dispersed through the herbivore’s feces. Other fruits have burs and hooks to cling to fur and hitch rides on animals.
The Life Cycle of an Angiosperm
The adult, or sporophyte, phase is the main phase of an angiosperm’s life cycle (Figure \(3\)). Like gymnosperms, angiosperms are heterosporous. Therefore, they generate microspores, which will generate pollen grains as the male gametophytes, and megaspores, which will form an ovule that contains female gametophytes. Inside the anthers’ microsporangia, male gametophytes divide by meiosis to generate haploid microspores, which, in turn, undergo mitosis and give rise to pollen grains. Each pollen grain contains two cells: one generative cell that will divide into two sperm and a second cell that will become the pollen tube cell.
Art Connection
If a flower lacked a megasporangium, what type of gamete would not form? If the flower lacked a microsporangium, what type of gamete would not form?
The ovule, sheltered within the ovary of the carpel, contains the megasporangium protected by two layers of integuments and the ovary wall. Within each megasporangium, a megasporocyte undergoes meiosis, generating four megaspores—three small and one large. Only the large megaspore survives; it produces the female gametophyte, referred to as the embryo sac. The megaspore divides three times to form an eight-cell stage. Four of these cells migrate to each pole of the embryo sac; two come to the equator, and will eventually fuse to form a 2n polar nucleus; the three cells away from the egg form antipodals, and the two cells closest to the egg become the synergids.
The mature embryo sac contains one egg cell, two synergids or “helper” cells, three antipodal cells, and two polar nuclei in a central cell. When a pollen grain reaches the stigma, a pollen tube extends from the grain, grows down the style, and enters through the micropyle: an opening in the integuments of the ovule. The two sperm cells are deposited in the embryo sac.
A double fertilization event then occurs. One sperm and the egg combine, forming a diploid zygote—the future embryo. The other sperm fuses with the 2n polar nuclei, forming a triploid cell that will develop into the endosperm, which is tissue that serves as a food reserve. The zygote develops into an embryo with a radicle, or small root, and one (monocot) or two (dicot) leaf-like organs called cotyledons. This difference in the number of embryonic leaves is the basis for the two major groups of angiosperms: the monocots and the eudicots. Seed food reserves are stored outside the embryo, in the form of complex carbohydrates, lipids or proteins. The cotyledons serve as conduits to transmit the broken-down food reserves from their storage site inside the seed to the developing embryo. The seed consists of a toughened layer of integuments forming the coat, the endosperm with food reserves, and at the center, the well-protected embryo.
Most flowers are monoecious or bisexual, which means that they carry both stamens and carpels; only a few species self-pollinate. Monoecious flowers are also known as “perfect” flowers because they contain both types of sex organs (Figure \(2\)). Both anatomical and environmental barriers promote cross-pollination mediated by a physical agent (wind or water), or an animal, such as an insect or bird. Cross-pollination increases genetic diversity in a species.
Diversity of Angiosperms
Angiosperms are classified in a single phylum: the Anthophyta. Modern angiosperms appear to be a monophyletic group, which means that they originate from a single ancestor. Flowering plants are divided into two major groups, according to the structure of the cotyledons, pollen grains, and other structures. Monocots include grasses and lilies, and eudicots or dicots form a polyphyletic group. Basal angiosperms are a group of plants that are believed to have branched off before the separation into monocots and eudicots because they exhibit traits from both groups. They are categorized separately in many classification schemes. The Magnoliidae (magnolia trees, laurels, and water lilies) and the Piperaceae (peppers) belong to the basal angiosperm group.
Basal Angiosperms
The Magnoliidae are represented by the magnolias: tall trees bearing large, fragrant flowers that have many parts and are considered archaic (Figure \(4\)d). Laurel trees produce fragrant leaves and small, inconspicuous flowers. The Laurales grow mostly in warmer climates and are small trees and shrubs. Familiar plants in this group include the bay laurel, cinnamon, spice bush (Figure \(4\)a), and avocado tree. The Nymphaeales are comprised of the water lilies, lotus (Figure \(4\)c), and similar plants; all species thrive in freshwater biomes, and have leaves that float on the water surface or grow underwater. Water lilies are particularly prized by gardeners, and have graced ponds and pools for thousands of years. The Piperales are a group of herbs, shrubs, and small trees that grow in the tropical climates. They have small flowers without petals that are tightly arranged in long spikes. Many species are the source of prized fragrance or spices, for example the berries of Piper nigrum (Figure \(4\)b) are the familiar black peppercorns that are used to flavor many dishes.
Monocots
Plants in the monocot group are primarily identified as such by the presence of a single cotyledon in the seedling. Other anatomical features shared by monocots include veins that run parallel to the length of the leaves, and flower parts that are arranged in a three- or six-fold symmetry. True woody tissue is rarely found in monocots. In palm trees, vascular and parenchyma tissues produced by the primary and secondary thickening meristems form the trunk. The pollen from the first angiosperms was monosulcate, containing a single furrow or pore through the outer layer. This feature is still seen in the modern monocots. Vascular tissue of the stem is not arranged in any particular pattern. The root system is mostly adventitious and unusually positioned, with no major tap root. The monocots include familiar plants such as the true lilies (which are at the origin of their alternate name of Liliopsida), orchids, grasses, and palms. Many important crops are monocots, such as rice and other cereals, corn, sugar cane, and tropical fruits like bananas and pineapples (Figure \(5\)).
Eudicots
Eudicots, or true dicots, are characterized by the presence of two cotyledons in the developing shoot. Veins form a network in leaves, and flower parts come in four, five, or many whorls. Vascular tissue forms a ring in the stem; in monocots, vascular tissue is scattered in the stem. Eudicots can be herbaceous (like grasses), or produce woody tissues. Most eudicots produce pollen that is trisulcate or triporate, with three furrows or pores. The root system is usually anchored by one main root developed from the embryonic radicle. Eudicots comprise two-thirds of all flowering plants. The major differences between monocots and eudicots are summarized in the table below. Many species exhibit characteristics that belong to either group; as such, the classification of a plant as a monocot or a eudicot is not always clearly evident.
Table \(1\): Comparison of Structural Characteristics of Monocots and Eudicots
Characteristic Monocot Eudicot
Cotyledon One Two
Veins in Leaves Parallel Network (branched)
Stem Vascular Tissue Scattered Arranged in ring pattern
Roots Network of adventitious roots Tap root with many lateral roots
Pollen Monosulcate Trisulcate
Flower Parts Three or multiple of three Four, five, multiple of four or five and whorls
Summary
Angiosperms are the dominant form of plant life in most terrestrial ecosystems, comprising about 90 percent of all plant species. Most crops and ornamental plants are angiosperms. Their success comes from two innovative structures that protect reproduction from variability in the environment: the flower and the fruit. Flowers were derived from modified leaves. The main parts of a flower are the sepals and petals, which protect the reproductive parts: the stamens and the carpels. The stamens produce the male gametes in pollen grains. The carpels contain the female gametes (the eggs inside the ovules), which are within the ovary of a carpel. The walls of the ovary thicken after fertilization, ripening into fruit that ensures dispersal by wind, water, or animals.
The angiosperm life cycle is dominated by the sporophyte stage. Double fertilization is an event unique to angiosperms. One sperm in the pollen fertilizes the egg, forming a diploid zygote, while the other combines with the two polar nuclei, forming a triploid cell that develops into a food storage tissue called the endosperm. Flowering plants are divided into two main groups, the monocots and eudicots, according to the number of cotyledons in the seedlings. Basal angiosperms belong to an older lineage than monocots and eudicots.
Art Connections
Figure \(3\): If a flower lacked a megasporangium, what type of gamete would not form? If the flower lacked a microsporangium, what type of gamete would not form?
Answer
Without a megasporangium, an egg would not form; without a microsporangium, pollen would not form.
Glossary
anther
sac-like structure at the tip of the stamen in which pollen grains are produced
Anthophyta
phylum to which angiosperms belong
basal angiosperms
a group of plants that probably branched off before the separation of monocots and eudicots
calyx
whorl of sepals
carpel
single unit of the pistil
corolla
collection of petals
cotyledon
primitive leaf that develop in the zygote; monocots have one cotyledon, and dicots have two cotyledons
dicot
(also, eudicot) related group of angiosperms whose embryos possess two cotyledons
filament
thin stalk that links the anther to the base of the flower
gynoecium
(also, carpel) structure that constitute the female reproductive organ
herbaceous
grass-like plant noticeable by the absence of woody tissue
monocot
related group of angiosperms that produce embryos with one cotyledon and pollen with a single ridge
ovary
chamber that contains and protects the ovule or female megasporangium
perianth
part of the plant consisting of the calyx (sepals) and corolla (petals)
petal
modified leaf interior to the sepals; colorful petals attract animal pollinators
pistil
fused group of carpels
sepal
modified leaf that encloses the bud; outermost structure of a flower
stamen
structure that contains the male reproductive organs
stigma
uppermost structure of the carpel where pollen is deposited
style
long, thin structure that links the stigma to the ovary | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/26%3A_Seed_Plants/26.3%3A_Angiosperms.txt |
Skills to Develop
• Explain how angiosperm diversity is due, in part, to multiple interactions with animals
• Describe ways in which pollination occurs
• Discuss the roles that plants play in ecosystems and how deforestation threatens plant biodiversity
Without seed plants, life as we know it would not be possible. Plants play a key role in the maintenance of terrestrial ecosystems through stabilization of soils, cycling of carbon, and climate moderation. Large tropical forests release oxygen and act as carbon dioxide sinks. Seed plants provide shelter to many life forms, as well as food for herbivores, thereby indirectly feeding carnivores. Plant secondary metabolites are used for medicinal purposes and industrial production.
Animals and Plants: Herbivory
Coevolution of flowering plants and insects is a hypothesis that has received much attention and support, especially because both angiosperms and insects diversified at about the same time in the middle Mesozoic. Many authors have attributed the diversity of plants and insects to pollination and herbivory, or consumption of plants by insects and other animals. This is believed to have been as much a driving force as pollination. Coevolution of herbivores and plant defenses is observed in nature. Unlike animals, most plants cannot outrun predators or use mimicry to hide from hungry animals. A sort of arms race exists between plants and herbivores. To “combat” herbivores, some plant seeds—such as acorn and unripened persimmon—are high in alkaloids and therefore unsavory to some animals. Other plants are protected by bark, although some animals developed specialized mouth pieces to tear and chew vegetal material. Spines and thorns (Figure \(1\)) deter most animals, except for mammals with thick fur, and some birds have specialized beaks to get past such defenses.
Herbivory has been used by seed plants for their own benefit in a display of mutualistic relationships. The dispersal of fruit by animals is the most striking example. The plant offers to the herbivore a nutritious source of food in return for spreading the plant’s genetic material to a wider area.
An extreme example of collaboration between an animal and a plant is the case of acacia trees and ants. The trees support the insects with shelter and food. In return, ants discourage herbivores, both invertebrates and vertebrates, by stinging and attacking leaf-eating insects.
Animals and Plants: Pollination
Grasses are a successful group of flowering plants that are wind pollinated. They produce large amounts of powdery pollen carried over large distances by the wind. The flowers are small and wisp-like. Large trees such as oaks, maples, and birches are also wind pollinated.
More than 80 percent of angiosperms depend on animals for pollination: the transfer of pollen from the anther to the stigma. Consequently, plants have developed many adaptations to attract pollinators. The specificity of specialized plant structures that target animals can be very surprising. It is possible, for example, to determine the type of pollinator favored by a plant just from the flower’s characteristics. Many bird or insect-pollinated flowers secrete nectar, which is a sugary liquid. They also produce both fertile pollen, for reproduction, and sterile pollen rich in nutrients for birds and insects.
Butterflies and bees can detect ultraviolet light. Flowers that attract these pollinators usually display a pattern of low ultraviolet reflectance that helps them quickly locate the flower's center and collect nectar while being dusted with pollen (Figure \(2\)). Large, red flowers with little smell and a long funnel shape are preferred by hummingbirds, who have good color perception, a poor sense of smell, and need a strong perch. White flowers opened at night attract moths. Other animals—such as bats, lemurs, and lizards—can also act as pollinating agents. Any disruption to these interactions, such as the disappearance of bees as a consequence of colony collapse disorders, can lead to disaster for agricultural industries that depend heavily on pollinated crops.
Scientific Method Connection: Testing Attraction of Flies by Rotting Flesh Smell
Question: Will flowers that offer cues to bees attract carrion flies if sprayed with compounds that smell like rotten flesh?
Background: Visitation of flowers by pollinating flies is a function mostly of smell. Flies are attracted by rotting flesh and carrions. The putrid odor seems to be the major attractant. The polyamines putrescine and cadaverine, which are the products of protein breakdown after animal death, are the source of the pungent smell of decaying meat. Some plants strategically attract flies by synthesizing polyamines similar to those generated by decaying flesh and thereby attract carrion flies.
Flies seek out dead animals because they normally lay their eggs on them and their maggots feed on the decaying flesh. Interestingly, time of death can be determined by a forensic entomologist based on the stages and type of maggots recovered from cadavers.
Hypothesis: Because flies are drawn to other organisms based on smell and not sight, a flower that is normally attractive to bees because of its colors will attract flies if it is sprayed with polyamines similar to those generated by decaying flesh.
Test the hypothesis:
1. Select flowers usually pollinated by bees. White petunia may be good choice.
2. Divide the flowers into two groups, and while wearing eye protection and gloves, spray one group with a solution of either putrescine or cadaverine. (Putrescine dihydrochloride is typically available in 98 percent concentration; this can be diluted to approximately 50 percent for this experiment.)
3. Place the flowers in a location where flies are present, keeping the sprayed and unsprayed flowers separated.
4. Observe the movement of the flies for one hour. Record the number of visits to the flowers using a table similar to Table \(1\). Given the rapid movement of flies, it may be beneficial to use a video camera to record the fly–flower interaction. Replay the video in slow motion to obtain an accurate record of the number of fly visits to the flowers.
5. Repeat the experiment four more times with the same species of flower, but using different specimens.
6. Repeat the entire experiment with a different type of flower that is normally pollinated by bees.
Table \(1\): Results of number of visits by flies to sprayed and control/ unsprayed flowers
Trial # Sprayed Flowers Unsprayed Flowers
1
2
3
4
5
Analyze your data: Review the data you have recorded. Average the number of visits that flies made to sprayed flowers over the course of the five trials (on the first flower type) and compare and contrast them to the average number of visits that flies made to the unsprayed/control flowers. Can you draw any conclusions regarding the attraction of the flies to the sprayed flowers?
For the second flower type used, average the number of visits that flies made to sprayed flowers over the course of the five trials and compare and contrast them to the average number of visits that flies made to the unsprayed/control flowers. Can you draw any conclusions regarding the attraction of the flies to the sprayed flowers?
Compare and contrast the average number of visits that flies made to the two flower types. Can you draw any conclusions about whether the appearance of the flower had any impact on the attraction of flies? Did smell override any appearance differences, or were the flies attracted to one flower type more than another?
Form a conclusion: Do the results support the hypothesis? If not, how can this be explained?
The Importance of Seed Plants in Human Life
Seed plants are the foundation of human diets across the world (Figure \(3\)). Many societies eat almost exclusively vegetarian fare and depend solely on seed plants for their nutritional needs. A few crops (rice, wheat, and potatoes) dominate the agricultural landscape. Many crops were developed during the agricultural revolution, when human societies made the transition from nomadic hunter–gatherers to horticulture and agriculture. Cereals, rich in carbohydrates, provide the staple of many human diets. Beans and nuts supply proteins. Fats are derived from crushed seeds, as is the case for peanut and rapeseed (canola) oils, or fruits such as olives. Animal husbandry also consumes large amounts of crops.
Staple crops are not the only food derived from seed plants. Fruits and vegetables provide nutrients, vitamins, and fiber. Sugar, to sweeten dishes, is produced from the monocot sugarcane and the eudicot sugar beet. Drinks are made from infusions of tea leaves, chamomile flowers, crushed coffee beans, or powdered cocoa beans. Spices come from many different plant parts: saffron and cloves are stamens and buds, black pepper and vanilla are seeds, the bark of a bush in the Laurales family supplies cinnamon, and the herbs that flavor many dishes come from dried leaves and fruit, such as the pungent red chili pepper. The volatile oils of flowers and bark provide the scent of perfumes. Additionally, no discussion of seed plant contribution to human diet would be complete without the mention of alcohol. Fermentation of plant-derived sugars and starches is used to produce alcoholic beverages in all societies. In some cases, the beverages are derived from the fermentation of sugars from fruit, as with wines and, in other cases, from the fermentation of carbohydrates derived from seeds, as with beers.
Seed plants have many other uses, including providing wood as a source of timber for construction, fuel, and material to build furniture. Most paper is derived from the pulp of coniferous trees. Fibers of seed plants such as cotton, flax, and hemp are woven into cloth. Textile dyes, such as indigo, were mostly of plant origin until the advent of synthetic chemical dyes.
Lastly, it is more difficult to quantify the benefits of ornamental seed plants. These grace private and public spaces, adding beauty and serenity to human lives and inspiring painters and poets alike.
The medicinal properties of plants have been known to human societies since ancient times. There are references to the use of plants’ curative properties in Egyptian, Babylonian, and Chinese writings from 5,000 years ago. Many modern synthetic therapeutic drugs are derived or synthesized de novo from plant secondary metabolites. It is important to note that the same plant extract can be a therapeutic remedy at low concentrations, become an addictive drug at higher doses, and can potentially kill at high concentrations. The table below presents a few drugs, their plants of origin, and their medicinal applications.
Table \(2\): Plant origin of medicinal compounds and applications
Plant Compound Application
Deadly nightshade (Atropa belladonna ) Atropine Dilate eye pupils for eye exams
Foxglove (Digitalis purpurea) Digitalis Heart disease, stimulates heart beat
Yam (Dioscorea spp.) Steroids Steroid hormones: contraceptive pill and cortisone
Ephedra (Ephedra spp.) Ephedrine Decongestant and bronchiole dilator
Pacific yew (Taxus brevifolia) Taxol Cancer chemotherapy; inhibits mitosis
Opium poppy (Papaver somniferum) Opioids Analgesic (reduces pain without loss of consciousness) and narcotic (reduces pain with drowsiness and loss of consciousness) in higher doses
Quinine tree (Cinchona spp.) Quinine Antipyretic (lowers body temperature) and antimalarial
Willow (Salix spp.) Salicylic acid (aspirin) Analgesic and antipyretic
Career Connection: Ethnobotanist
The relatively new field of ethnobotany studies the interaction between a particular culture and the plants native to the region. Seed plants have a large influence on day-to-day human life. Not only are plants the major source of food and medicine, they also influence many other aspects of society, from clothing to industry. The medicinal properties of plants were recognized early on in human cultures. From the mid-1900s, synthetic chemicals began to supplant plant-based remedies.
Pharmacognosy is the branch of pharmacology that focuses on medicines derived from natural sources. With massive globalization and industrialization, there is a concern that much human knowledge of plants and their medicinal purposes will disappear with the cultures that fostered them. This is where ethnobotanists come in. To learn about and understand the use of plants in a particular culture, an ethnobotanist must bring in knowledge of plant life and an understanding and appreciation of diverse cultures and traditions. The Amazon forest is home to an incredible diversity of vegetation and is considered an untapped resource of medicinal plants; yet, both the ecosystem and its indigenous cultures are threatened with extinction.
To become an ethnobotanist, a person must acquire a broad knowledge of plant biology, ecology and sociology. Not only are the plant specimens studied and collected, but also the stories, recipes, and traditions that are linked to them. For ethnobotanists, plants are not viewed solely as biological organisms to be studied in a laboratory, but as an integral part of human culture. The convergence of molecular biology, anthropology, and ecology make the field of ethnobotany a truly multidisciplinary science.
Biodiversity of Plants
Biodiversity ensures a resource for new food crops and medicines. Plant life balances ecosystems, protects watersheds, mitigates erosion, moderates climate and provides shelter for many animal species. Threats to plant diversity, however, come from many angles. The explosion of the human population, especially in tropical countries where birth rates are highest and economic development is in full swing, is leading to human encroachment into forested areas. To feed the larger population, humans need to obtain arable land, so there is massive clearing of trees. The need for more energy to power larger cities and economic growth therein leads to the construction of dams, the consequent flooding of ecosystems, and increased emissions of pollutants. Other threats to tropical forests come from poachers, who log trees for their precious wood. Ebony and Brazilian rosewood, both on the endangered list, are examples of tree species driven almost to extinction by indiscriminate logging.
The number of plant species becoming extinct is increasing at an alarming rate. Because ecosystems are in a delicate balance, and seed plants maintain close symbiotic relationships with animals—whether predators or pollinators—the disappearance of a single plant can lead to the extinction of connected animal species. A real and pressing issue is that many plant species have not yet been catalogued, and so their place in the ecosystem is unknown. These unknown species are threatened by logging, habitat destruction, and loss of pollinators. They may become extinct before we have the chance to begin to understand the possible impacts from their disappearance. Efforts to preserve biodiversity take several lines of action, from preserving heirloom seeds to barcoding species. Heirloom seeds come from plants that were traditionally grown in human populations, as opposed to the seeds used for large-scale agricultural production. Barcoding is a technique in which one or more short gene sequences, taken from a well-characterized portion of the genome, are used to identify a species through DNA analysis.
Summary
Angiosperm diversity is due in part to multiple interactions with animals. Herbivory has favored the development of defense mechanisms in plants, and avoidance of those defense mechanism in animals. Pollination (the transfer of pollen to a carpel) is mainly carried out by wind and animals, and angiosperms have evolved numerous adaptations to capture the wind or attract specific classes of animals.
Plants play a key role in ecosystems. They are a source of food and medicinal compounds, and provide raw materials for many industries. Rapid deforestation and industrialization, however, threaten plant biodiversity. In turn, this threatens the ecosystem.
Glossary
barcoding
molecular biology technique in which one or more short gene sequences taken from a well-characterized portion of the genome is used to identify a species
crop
cultivated plant
heirloom seed
seed from a plant that was grown historically, but has not been used in modern agriculture on a large scale
herbivory
consumption of plants by insects and other animals
nectar
liquid rich in sugars produced by flowers to attract animal pollinators
pollination
transfer of pollen from the anther to the stigma | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/26%3A_Seed_Plants/26.4%3A_The_Role_of_Seed_Plants.txt |
26.1: Evolution of Seed Plants
The first plants to colonize land were most likely closely related to modern day mosses (bryophytes) and are thought to have appeared about 500 million years ago. They were followed by liverworts (also bryophytes) and primitive vascular plants—the pterophytes—from which modern ferns are derived.
Review Questions
Seed plants are ________.
1. all homosporous.
2. mostly homosporous with some heterosporous.
3. mostly heterosporous with some homosporous.
4. all heterosporous.
Answer
D
Besides the seed, what other major structure diminishes a plant’s reliance on water for reproduction?
1. flower
2. fruit
3. pollen
4. spore
Answer
A
In which of the following geological periods would gymnosperms dominate the landscape?
1. Carboniferous
2. Permian
3. Triassic
4. Eocene (present)
Answer
C
Which of the following structures widens the geographic range of a species and is an agent of dispersal?
1. seed
2. flower
3. leaf
4. root
Answer
A
Free Response
The Triassic Period was marked by the increase in number and variety of angiosperms. Insects also diversified enormously during the same period. Can you propose the reason or reasons that could foster coevolution?
Answer
Both pollination and herbivory contributed to diversity, with plants needing to attract some insects and repel others.
What role did the adaptations of seed and pollen play in the development and expansion of seed plants?
Answer
Seeds and pollen allowed plants to reproduce in absence of water. This allowed them to expand their range onto dry land and to survive drought conditions.
26.2: Gymnosperms
Gymnosperms, meaning “naked seeds,” are a diverse group of seed plants and are paraphyletic. Paraphyletic groups are those in which not all members are descendants of a single common ancestor. Their characteristics include naked seeds, separate female and male gametes, pollination by wind, and tracheids (which transport water and solutes in the vascular system).
Review Questions
Which of the following traits characterizes gymnosperms?
1. The plants carry exposed seeds on modified leaves.
2. Reproductive structures are located in a flower.
3. After fertilization, the ovary thickens and forms a fruit.
4. The gametophyte is longest phase of the life cycle.
Answer
A
Megasporocytes will eventually produce which of the following?
1. pollen grain
2. sporophytes
3. male gametophytes
4. female gametophytes
Answer
D
What is the ploidy of the following structures: gametophyte, seed, spore, sporophyte?
1. 1n, 1n, 2n, 2n
2. 1n, 2n, 1n, 2n
3. 2n, 1n, 2n, 1n
4. 2n, 2n, 1n, 1n
Answer
B
In the northern forests of Siberia, a tall tree is most likely a:
1. conifer
2. cycad
3. Gingko biloba
4. gnetophyte
Answer
A
Free Response
The Mediterranean landscape along the sea shore is dotted with pines and cypresses. The weather is not cold, and the trees grow at sea level. What evolutionary adaptation of conifers makes them suitable to the Mediterranean climate?
Answer
The trees are adapted to arid weather, and do not lose as much water due to transpiration as non-conifers.
What are the four modern-day phyla of gymnosperms?
Answer
The four modern-day phyla of gymnosperms are Coniferophyta, Cycadophyta, Gingkophyta, and Gnetophyta.
26.3: Angiosperms
From their humble and still obscure beginning during the early Jurassic period, the angiosperms—or flowering plants—have evolved to dominate most terrestrial ecosystems. With more than 250,000 species, the angiosperm phylum (Anthophyta) is second only to insects in terms of diversification.
Review Questions
Which of the following structures in a flower is not directly involved in reproduction?
1. the style
2. the stamen
3. the sepal
4. the anther
Answer
C
Pollen grains develop in which structure?
1. the anther
2. the stigma
3. the filament
4. the carpel
Answer
A
In the course of double fertilization, one sperm cell fuses with the egg and the second one fuses with ________.
1. the synergids
2. the polar nuclei of the center cell
3. the egg as well
4. the antipodal cells
Answer
B
Corn develops from a seedling with a single cotyledon, displays parallel veins on its leaves, and produces monosulcate pollen. It is most likely:
1. a gymnosperm
2. a monocot
3. a eudicot
4. a basal angiosperm
Answer
B
Free Response
Some cycads are considered endangered species and their trade is severely restricted. Customs officials stop suspected smugglers who claim that the plants in their possession are palm trees, not cycads. How would a botanist distinguish between the two types of plants?
Answer
The resemblance between cycads and palm trees is only superficial. Cycads are gymnosperms and do not bear flowers or fruit. Cycads produce cones: large, female cones that produce naked seeds, and smaller male cones on separate plants. Palms do not.
What are the two structures that allow angiosperms to be the dominant form of plant life in most terrestrial ecosystems?
Answer
Angiosperms are successful because of flowers and fruit. These structures protect reproduction from variability in the environment.
26.4: The Role of Seed Plants
Without seed plants, life as we know it would not be possible. Plants play a key role in the maintenance of terrestrial ecosystems through stabilization of soils, cycling of carbon, and climate moderation. Large tropical forests release oxygen and act as carbon dioxide sinks. Seed plants provide shelter to many life forms, as well as food for herbivores, thereby indirectly feeding carnivores. Plant secondary metabolites are used for medicinal purposes and industrial production.
Review Questions
Which of the following plant structures is not a defense against herbivory?
1. thorns
2. spines
3. nectar
4. alkaloids
Answer
C
White and sweet-smelling flowers with abundant nectar are probably pollinated by
1. bees and butterflies
2. flies
3. birds
4. wind
Answer
A
Abundant and powdery pollen produced by small, indistinct flowers is probably transported by:
1. bees and butterflies
2. flies
3. birds
4. wind
Answer
D
Plants are a source of ________.
1. food
2. fuel
3. medicine
4. all of the above
Answer
D
Free Response
Biosynthesis of nectar and nutrient-rich pollen is energetically very expensive for a plant. Yet, plants funnel large amounts of energy into animal pollination. What are the evolutionary advantages that offset the cost of attracting animal pollinators?
Answer
Using animal pollinators promotes cross-pollination and increases genetic diversity. The odds that the pollen will reach another flower are greatly increased compared with the randomness of wind pollination.
What is biodiversity and why is it important to an ecosystem?
Answer
Biodiversity is the variation in all forms of life. It can refer to variation within a species, within an ecosystem, or on an entire planet. It is important because it ensures a resource for new food crops and medicines. Plant life balances the ecosystems, protects watersheds, mitigates erosion, moderates climate, and provides shelter for many animal species. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/26%3A_Seed_Plants/26.E%3A_Seed_Plants_%28Exercises%29.txt |
Thumbnail: Animal diversity. (CC BY-SA 2.5 / cropped from original; via Wikimedia Commons).
27: Introduction to Animal Diversity
Animal evolution began in the ocean over 600 million years ago with tiny creatures that probably do not resemble any living organism today. Since then, animals have evolved into a highly diverse kingdom. Although over one million extant (currently living) species of animals have been identified, scientists are continually discovering more species as they explore ecosystems around the world. The number of extant species is estimated to be between 3 and 30 million.
But what is an animal? While we can easily identify dogs, birds, fish, spiders, and worms as animals, other organisms, such as corals and sponges, are not as easy to classify. Animals vary in complexity—from sea sponges to crickets to chimpanzees—and scientists are faced with the difficult task of classifying them within a unified system. They must identify traits that are common to all animals as well as traits that can be used to distinguish among related groups of animals. The animal classification system characterizes animals based on their anatomy, morphology, evolutionary history, features of embryological development, and genetic makeup. This classification scheme is constantly developing as new information about species arises. Understanding and classifying the great variety of living species help us better understand how to conserve the diversity of life on earth.
27.1: Features of the Animal Kingdom
Skills to Develop
• List the features that distinguish the kingdom Animalia from other kingdoms
• Explain the processes of animal reproduction and embryonic development
• Describe the roles that Hox genes play in development
Even though members of the animal kingdom are incredibly diverse, most animals share certain features that distinguish them from organisms in other kingdoms. All animals are eukaryotic, multicellular organisms, and almost all animals have a complex tissue structure with differentiated and specialized tissues. Most animals are motile, at least during certain life stages. All animals require a source of food and are therefore heterotrophic, ingesting other living or dead organisms; this feature distinguishes them from autotrophic organisms, such as most plants, which synthesize their own nutrients through photosynthesis. As heterotrophs, animals may be carnivores, herbivores, omnivores, or parasites (Figure \(1\)). Most animals reproduce sexually, and the offspring pass through a series of developmental stages that establish a determined and fixed body plan. The body plan refers to the morphology of an animal, determined by developmental cues.
Complex Tissue Structure
As multicellular organisms, animals differ from plants and fungi because their cells don’t have cell walls, their cells may be embedded in an extracellular matrix (such as bone, skin, or connective tissue), and their cells have unique structures for intercellular communication (such as gap junctions). In addition, animals possess unique tissues, absent in fungi and plants, which allow coordination (nerve tissue) of motility (muscle tissue). Animals are also characterized by specialized connective tissues that provide structural support for cells and organs. This connective tissue constitutes the extracellular surroundings of cells and is made up of organic and inorganic materials. In vertebrates, bone tissue is a type of connective tissue that supports the entire body structure. The complex bodies and activities of vertebrates demand such supportive tissues. Epithelial tissues cover, line, protect, and secrete. Epithelial tissues include the epidermis of the integument, the lining of the digestive tract and trachea, and make up the ducts of the liver and glands of advanced animals.
The animal kingdom is divided into Parazoa (sponges) and Eumetazoa (all other animals). As very simple animals, the organisms in group Parazoa (“beside animal”) do not contain true specialized tissues; although they do possess specialized cells that perform different functions, those cells are not organized into tissues. These organisms are considered animals since they lack the ability to make their own food. Animals with true tissues are in the group Eumetazoa (“true animals”). When we think of animals, we usually think of Eumetazoans, since most animals fall into this category.
The different types of tissues in true animals are responsible for carrying out specific functions for the organism. This differentiation and specialization of tissues is part of what allows for such incredible animal diversity. For example, the evolution of nerve tissues and muscle tissues has resulted in animals’ unique ability to rapidly sense and respond to changes in their environment. This allows animals to survive in environments where they must compete with other species to meet their nutritional demands.
Link to Learning
Watch a presentation by biologist E.O. Wilson on the importance of diversity.
Animal Reproduction and Development
Most animals are diploid organisms, meaning that their body (somatic) cells are diploid and haploid reproductive (gamete) cells are produced through meiosis. Some exceptions exist: For example, in bees, wasps, and ants, the male is haploid because it develops from unfertilized eggs. Most animals undergo sexual reproduction: This fact distinguishes animals from fungi, protists, and bacteria, where asexual reproduction is common or exclusive. However, a few groups, such as cnidarians, flatworm, and roundworms, undergo asexual reproduction, although nearly all of those animals also have a sexual phase to their life cycle.
Processes of Animal Reproduction and Embryonic Development
During sexual reproduction, the haploid gametes of the male and female individuals of a species combine in a process called fertilization. Typically, the small, motile male sperm fertilizes the much larger, sessile female egg. This process produces a diploid fertilized egg called a zygote.
Some animal species—including sea stars and sea anemones, as well as some insects, reptiles, and fish—are capable of asexual reproduction. The most common forms of asexual reproduction for stationary aquatic animals include budding and fragmentation, where part of a parent individual can separate and grow into a new individual. In contrast, a form of asexual reproduction found in certain insects and vertebrates is called parthenogenesis (or “virgin beginning”), where unfertilized eggs can develop into new male offspring. This type of parthenogenesis is called haplodiploidy. These types of asexual reproduction produce genetically identical offspring, which is disadvantageous from the perspective of evolutionary adaptability because of the potential buildup of deleterious mutations. However, for animals that are limited in their capacity to attract mates, asexual reproduction can ensure genetic propagation.
After fertilization, a series of developmental stages occur during which primary germ layers are established and reorganize to form an embryo. During this process, animal tissues begin to specialize and organize into organs and organ systems, determining their future morphology and physiology. Some animals, such as grasshoppers, undergo incomplete metamorphosis, in which the young resemble the adult. Other animals, such as some insects, undergo complete metamorphosis where individuals enter one or more larval stages that may in differ in structure and function from the adult (Figure \(2\)). For the latter, the young and the adult may have different diets, limiting competition for food between them. Regardless of whether a species undergoes complete or incomplete metamorphosis, the series of developmental stages of the embryo remains largely the same for most members of the animal kingdom.
The process of animal development begins with the cleavage, or series of mitotic cell divisions, of the zygote (Figure \(3\)). Three cell divisions transform the single-celled zygote into an eight-celled structure. After further cell division and rearrangement of existing cells, a 6–32-celled hollow structure called a blastula is formed. Next, the blastula undergoes further cell division and cellular rearrangement during a process called gastrulation. This leads to the formation of the next developmental stage, the gastrula, in which the future digestive cavity is formed. Different cell layers (called germ layers) are formed during gastrulation. These germ layers are programmed to develop into certain tissue types, organs, and organ systems during a process called organogenesis.
Link to Learning
Watch the following video to see how human embryonic development (after the blastula and gastrula stages of development) reflects evolution.
The Role of Homeobox (Hox) Genes in Animal Development
Since the early 19th century, scientists have observed that many animals, from the very simple to the complex, shared similar embryonic morphology and development. Surprisingly, a human embryo and a frog embryo, at a certain stage of embryonic development, look remarkably alike. For a long time, scientists did not understand why so many animal species looked similar during embryonic development but were very different as adults. They wondered what dictated the developmental direction that a fly, mouse, frog, or human embryo would take. Near the end of the 20th century, a particular class of genes was discovered that had this very job. These genes that determine animal structure are called “homeotic genes,” and they contain DNA sequences called homeoboxes. The animal genes containing homeobox sequences are specifically referred to as Hox genes. This family of genes is responsible for determining the general body plan, such as the number of body segments of an animal, the number and placement of appendages, and animal head-tail directionality. The first Hox genes to be sequenced were those from the fruit fly (Drosophila melanogaster). A single Hox mutation in the fruit fly can result in an extra pair of wings or even appendages growing from the “wrong” body part.
While there are a great many genes that play roles in the morphological development of an animal, what makes Hox genes so powerful is that they serve as master control genes that can turn on or off large numbers of other genes. Hox genes do this by coding transcription factors that control the expression of numerous other genes. Hox genes are homologous in the animal kingdom, that is, the genetic sequences of Hox genes and their positions on chromosomes are remarkably similar across most animals because of their presence in a common ancestor, from worms to flies, mice, and humans (Figure \(4\)). One of the contributions to increased animal body complexity is that Hox genes have undergone at least two duplication events during animal evolution, with the additional genes allowing for more complex body types to evolve.
Art Connection
If a Hox 13 gene in a mouse was replaced with a Hox 1 gene, how might this alter animal development?
Summary
Animals constitute an incredibly diverse kingdom of organisms. Although animals range in complexity from simple sea sponges to human beings, most members of the animal kingdom share certain features. Animals are eukaryotic, multicellular, heterotrophic organisms that ingest their food and usually develop into motile creatures with a fixed body plan. A major characteristic unique to the animal kingdom is the presence of differentiated tissues, such as nerve, muscle, and connective tissues, which are specialized to perform specific functions. Most animals undergo sexual reproduction, leading to a series of developmental embryonic stages that are relatively similar across the animal kingdom. A class of transcriptional control genes called Hox genes directs the organization of the major animal body plans, and these genes are strongly homologous across the animal kingdom.
Art Connections
Figure \(4\): If a Hox 13 gene in a mouse was replaced with a Hox 1 gene, how might this alter animal development?
Answer
The animal might develop two heads and no tail.
Glossary
blastula
16–32 cell stage of development of an animal embryo
body plan
morphology or constant shape of an organism
cleavage
cell division of a fertilized egg (zygote) to form a multicellular embryo
gastrula
stage of animal development characterized by the formation of the digestive cavity
germ layer
collection of cells formed during embryogenesis that will give rise to future body tissues, more pronounced in vertebrate embryogenesis
Hox gene
(also, homeobox gene) master control gene that can turn on or off large numbers of other genes during embryogenesis
organogenesis
formation of organs in animal embryogenesis | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/27%3A_Introduction_to_Animal_Diversity/27.0%3A_Introduction.txt |
Skills to Develop
• Explain the differences in animal body plans that support basic animal classification
• Compare and contrast the embryonic development of protostomes and deuterostomes
Scientists have developed a classification scheme that categorizes all members of the animal kingdom, although there are exceptions to most “rules” governing animal classification (Figure \(1\)). Animals are primarily classified according to morphological and developmental characteristics, such as a body plan. One of the most prominent features of the body plan of true animals is that they are morphologically symmetrical. This means that their distribution of body parts is balanced along an axis. Additional characteristics include the number of tissue layers formed during development, the presence or absence of an internal body cavity, and other features of embryological development, such as the origin of the mouth and anus.
Art Connection
Which of the following statements is false?
1. Eumetazoans have specialized tissues and parazoans don’t.
2. Lophotrochozoa and Ecdysozoa are both Bilataria.
3. Acoela and Cnidaria both possess radial symmetry.
4. Arthropods are more closely related to nematodes than they are to annelids.
Animal Characterization Based on Body Symmetry
At a very basic level of classification, true animals can be largely divided into three groups based on the type of symmetry of their body plan: radially symmetrical, bilaterally symmetrical, and asymmetrical. Asymmetry is a unique feature of Parazoa (Figure \(2\)). Only a few animal groups display radial symmetry. All types of symmetry are well suited to meet the unique demands of a particular animal’s lifestyle.
Radial symmetry is the arrangement of body parts around a central axis, as is seen in a drinking glass or pie. It results in animals having top and bottom surfaces but no left and right sides, or front or back. The two halves of a radially symmetrical animal may be described as the side with a mouth or “oral side,” and the side without a mouth (the “aboral side”). This form of symmetry marks the body plans of animals in the phyla Ctenophora and Cnidaria, including jellyfish and adult sea anemones (Figure 27.2.2). Radial symmetry equips these sea creatures (which may be sedentary or only capable of slow movement or floating) to experience the environment equally from all directions.
Bilateral symmetry involves the division of the animal through a sagittal plane, resulting in two mirror image, right and left halves, such as those of a butterfly (Figure \(2\)), crab, or human body. Animals with bilateral symmetry have a “head” and “tail” (anterior vs. posterior), front and back (dorsal vs. ventral), and right and left sides (Figure \(3\)). All true animals except those with radial symmetry are bilaterally symmetrical. The evolution of bilateral symmetry that allowed for the formation of anterior and posterior (head and tail) ends promoted a phenomenon called cephalization, which refers to the collection of an organized nervous system at the animal’s anterior end. In contrast to radial symmetry, which is best suited for stationary or limited-motion lifestyles, bilateral symmetry allows for streamlined and directional motion. In evolutionary terms, this simple form of symmetry promoted active mobility and increased sophistication of resource-seeking and predator-prey relationships.
Animals in the phylum Echinodermata (such as sea stars, sand dollars, and sea urchins) display radial symmetry as adults, but their larval stages exhibit bilateral symmetry. This is termed secondary radial symmetry. They are believed to have evolved from bilaterally symmetrical animals; thus, they are classified as bilaterally symmetrical.
Link to Learning
Watch this video to see a quick sketch of the different types of body symmetry.
Animal Characterization Based on Features of Embryological Development
Most animal species undergo a separation of tissues into germ layers during embryonic development. Recall that these germ layers are formed during gastrulation, and that they are predetermined to develop into the animal’s specialized tissues and organs. Animals develop either two or three embryonic germs layers (Figure \(4\)). The animals that display radial symmetry develop two germ layers, an inner layer (endoderm) and an outer layer (ectoderm). These animals are called diploblasts. Diploblasts have a non-living layer between the endoderm and ectoderm. More complex animals (those with bilateral symmetry) develop three tissue layers: an inner layer (endoderm), an outer layer (ectoderm), and a middle layer (mesoderm). Animals with three tissue layers are called triploblasts.
Art Connection
Which of the following statements about diploblasts and triploblasts is false?
1. Animals that display radial symmetry are diploblasts.
2. Animals that display bilateral symmetry are triploblasts.
3. The endoderm gives rise to the lining of the digestive tract and the respiratory tract.
4. The mesoderm gives rise to the central nervous system.
Each of the three germ layers is programmed to give rise to particular body tissues and organs. The endoderm gives rise to the lining of the digestive tract (including the stomach, intestines, liver, and pancreas), as well as to the lining of the trachea, bronchi, and lungs of the respiratory tract, along with a few other structures. The ectoderm develops into the outer epithelial covering of the body surface, the central nervous system, and a few other structures. The mesoderm is the third germ layer; it forms between the endoderm and ectoderm in triploblasts. This germ layer gives rise to all muscle tissues (including the cardiac tissues and muscles of the intestines), connective tissues such as the skeleton and blood cells, and most other visceral organs such as the kidneys and the spleen.
Presence or Absence of a Coelom
Further subdivision of animals with three germ layers (triploblasts) results in the separation of animals that may develop an internal body cavity derived from mesoderm, called a coelom, and those that do not. This epithelial cell-lined coelomic cavity represents a space, usually filled with fluid, which lies between the visceral organs and the body wall. It houses many organs such as the digestive system, kidneys, reproductive organs, and heart, and contains the circulatory system. In some animals, such as mammals, the part of the coelom called the pleural cavity provides space for the lungs to expand during breathing. The evolution of the coelom is associated with many functional advantages. Primarily, the coelom provides cushioning and shock absorption for the major organ systems. Organs housed within the coelom can grow and move freely, which promotes optimal organ development and placement. The coelom also provides space for the diffusion of gases and nutrients, as well as body flexibility, promoting improved animal motility.
Triploblasts that do not develop a coelom are called acoelomates, and their mesoderm region is completely filled with tissue, although they do still have a gut cavity. Examples of acoelomates include animals in the phylum Platyhelminthes, also known as flatworms. Animals with a true coelom are called eucoelomates (or coelomates) (Figure \(5\)). A true coelom arises entirely within the mesoderm germ layer and is lined by an epithelial membrane. This membrane also lines the organs within the coelom, connecting and holding them in position while allowing them some free motion. Annelids, mollusks, arthropods, echinoderms, and chordates are all eucoelomates. A third group of triploblasts has a slightly different coelom derived partly from mesoderm and partly from endoderm, which is found between the two layers. Although still functional, these are considered false coeloms, and those animals are called pseudocoelomates. The phylum Nematoda (roundworms) is an example of a pseudocoelomate. True coelomates can be further characterized based on certain features of their early embryological development.
Embryonic Development of the Mouth
Bilaterally symmetrical, tribloblastic eucoelomates can be further divided into two groups based on differences in their early embryonic development. Protostomes include arthropods, mollusks, and annelids. Deuterostomes include more complex animals such as chordates but also some simple animals such as echinoderms. These two groups are separated based on which opening of the digestive cavity develops first: mouth or anus. The word protostome comes from the Greek word meaning “mouth first,” and deuterostome originates from the word meaning “mouth second” (in this case, the anus develops first). The mouth or anus develops from a structure called the blastopore (Figure \(6\)). The blastopore is the indentation formed during the initial stages of gastrulation. In later stages, a second opening forms, and these two openings will eventually give rise to the mouth and anus (Figure \(6\)). It has long been believed that the blastopore develops into the mouth of protostomes, with the second opening developing into the anus; the opposite is true for deuterostomes. Recent evidence has challenged this view of the development of the blastopore of protostomes, however, and the theory remains under debate.
Another distinction between protostomes and deuterostomes is the method of coelom formation, beginning from the gastrula stage. The coelom of most protostomes is formed through a process called schizocoely, meaning that during development, a solid mass of the mesoderm splits apart and forms the hollow opening of the coelom. Deuterostomes differ in that their coelom forms through a process called enterocoely. Here, the mesoderm develops as pouches that are pinched off from the endoderm tissue. These pouches eventually fuse to form the mesoderm, which then gives rise to the coelom.
The earliest distinction between protostomes and deuterostomes is the type of cleavage undergone by the zygote. Protostomes undergo spiral cleavage, meaning that the cells of one pole of the embryo are rotated, and thus misaligned, with respect to the cells of the opposite pole. This is due to the oblique angle of the cleavage. Deuterostomes undergo radial cleavage, where the cleavage axes are either parallel or perpendicular to the polar axis, resulting in the alignment of the cells between the two poles.
There is a second distinction between the types of cleavage in protostomes and deuterostomes. In addition to spiral cleavage, protostomes also undergo determinate cleavage. This means that even at this early stage, the developmental fate of each embryonic cell is already determined. A cell does not have the ability to develop into any cell type. In contrast, deuterostomes undergo indeterminate cleavage, in which cells are not yet pre-determined at this early stage to develop into specific cell types. These cells are referred to as undifferentiated cells. This characteristic of deuterostomes is reflected in the existence of familiar embryonic stem cells, which have the ability to develop into any cell type until their fate is programmed at a later developmental stage.
Evolution Connection: The Evolution of the Coelom
One of the first steps in the classification of animals is to examine the animal’s body. Studying the body parts tells us not only the roles of the organs in question but also how the species may have evolved. One such structure that is used in classification of animals is the coelom. A coelom is a body cavity that forms during early embryonic development. The coelom allows for compartmentalization of the body parts, so that different organ systems can evolve and nutrient transport is possible. Additionally, because the coelom is a fluid-filled cavity, it protects the organs from shock and compression. Simple animals, such as worms and jellyfish, do not have a coelom. All vertebrates have a coelom that helped them evolve complex organ systems.
Animals that do not have a coelom are called acoelomates. Flatworms and tapeworms are examples of acoelomates. They rely on passive diffusion for nutrient transport across their body. Additionally, the internal organs of acoelomates are not protected from crushing.
Animals that have a true coelom are called eucoelomates; all vertebrates are eucoelomates. The coelom evolves from the mesoderm during embryogenesis. The abdominal cavity contains the stomach, liver, gall bladder, and other digestive organs. Another category of invertebrates animals based on body cavity is pseudocoelomates. These animals have a pseudo-cavity that is not completely lined by mesoderm. Examples include nematode parasites and small worms. These animals are thought to have evolved from coelomates and may have lost their ability to form a coelom through genetic mutations. Thus, this step in early embryogenesis—the formation of the coelom—has had a large evolutionary impact on the various species of the animal kingdom.
Summary
Organisms in the animal kingdom are classified based on their body morphology and development. True animals are divided into those with radial versus bilateral symmetry. Generally, the simpler and often non-motile animals display radial symmetry. Animals with radial symmetry are also generally characterized by the development of two embryological germ layers, the endoderm and ectoderm, whereas animals with bilateral symmetry are generally characterized by the development of a third embryological germ layer, the mesoderm. Animals with three germ layers, called triploblasts, are further characterized by the presence or absence of an internal body cavity called a coelom. The presence of a coelom affords many advantages, and animals with a coelom may be termed true coelomates or pseudocoelomates, depending on which tissue gives rise to the coelom. Coelomates are further divided into one of two groups called protostomes and deuterostomes, based on a number of developmental characteristics, including differences in zygote cleavage and method of coelom formation.
Art Connections
Figure \(1\): Which of the following statements is false?
1. Eumetazoans have specialized tissues and parazoans don’t.
2. Lophotrochozoa and Ecdysozoa are both Bilataria.
3. Acoela and Cnidaria both possess radial symmetry.
4. Arthropods are more closely related to nematodes than they are to annelids.
Answer
C
Figure \(4\): Which of the following statements about diploblasts and triploblasts is false?
1. Animals that display radial symmetry are diploblasts.
2. Animals that display bilateral symmetry are triploblasts.
3. The endoderm gives rise to the lining of the digestive tract and the respiratory tract.
4. The mesoderm gives rise to the central nervous system.
Answer
D
Glossary
acoelomate
animal without a body cavity
bilateral symmetry
type of symmetry in which there is only one plane of symmetry, so the left and right halves of an animal are mirror images
blastopore
indentation formed during gastrulation, evident in the gastrula stage
coelom
lined body cavity
determinate cleavage
developmental tissue fate of each embryonic cell is already determined
deuterostome
blastopore develops into the anus, with the second opening developing into the mouth
diploblast
animal that develops from two germ layers
enterocoely
mesoderm of deuterostomes develops as pouches that are pinched off from endodermal tissue, cavity contained within the pouches becomes coelom
eucoelomate
animal with a body cavity completely lined with mesodermal tissue
indeterminate cleavage
early stage of development when germ cells or “stem cells” are not yet pre-determined to develop into specific cell types
protostome
blastopore develops into the mouth of protostomes, with the second opening developing into the anus
pseudocoelomate
animal with a body cavity located between the mesoderm and endoderm
radial cleavage
cleavage axes are parallel or perpendicular to the polar axis, resulting in the alignment of cells between the two poles
radial symmetry
type of symmetry with multiple planes of symmetry, with body parts (rays) arranged around a central disk
schizocoely
during development of protostomes, a solid mass of mesoderm splits apart and forms the hollow opening of the coelom
spiral cleavage
cells of one pole of the embryo are rotated or misaligned with respect to the cells of the opposite pole
triploblast
animal that develops from three germ layers | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/27%3A_Introduction_to_Animal_Diversity/27.2%3A_Features_Used_to_Classify_Animals.txt |
Skills to Develop
• Interpret the metazoan phylogenetic tree
• Describe the types of data that scientists use to construct and revise animal phylogeny
• List some of the relationships within the modern phylogenetic tree that have been discovered as a result of modern molecular data
Biologists strive to understand the evolutionary history and relationships of members of the animal kingdom, and all of life, for that matter. The study of phylogeny aims to determine the evolutionary relationships between phyla. Currently, most biologists divide the animal kingdom into 35 to 40 phyla. Scientists develop phylogenetic trees, which serve as hypotheses about which species have evolved from which ancestors
Recall that until recently, only morphological characteristics and the fossil record were used to determine phylogenetic relationships among animals. Scientific understanding of the distinctions and hierarchies between anatomical characteristics provided much of this knowledge. Used alone, however, this information can be misleading. Morphological characteristics may evolve multiple times, and independently, through evolutionary history. Analogous characteristics may appear similar between animals, but their underlying evolution may be very different. With the advancement of molecular technologies, modern phylogenetics is now informed by genetic and molecular analyses, in addition to traditional morphological and fossil data. With a growing understanding of genetics, the animal evolutionary tree has changed substantially and continues to change as new DNA and RNA analyses are performed on additional animal species.
Constructing an Animal Phylogenetic Tree
The current understanding of evolutionary relationships between animal, or Metazoa, phyla begins with the distinction between “true” animals with true differentiated tissues, called Eumetazoa, and animal phyla that do not have true differentiated tissues (such as the sponges), called Parazoa. Both Parazoa and Eumetazoa evolved from a common ancestral organism that resembles the modern-day protists called choanoflagellates. These protist cells strongly resemble the sponge choanocyte cells today (Figure \(1\)).
Eumetazoa are subdivided into radially symmetrical animals and bilaterally symmetrical animals, and are thus classified into clade Bilateria or Radiata, respectively. As mentioned earlier, the cnidarians and ctenophores are animal phyla with true radial symmetry. All other Eumetazoa are members of the Bilateria clade. The bilaterally symmetrical animals are further divided into deuterostomes (including chordates and echinoderms) and two distinct clades of protostomes (including ecdysozoans and lophotrochozoans) (Figure \(2\)). Ecdysozoa includes nematodes and arthropods; they are so named for a commonly found characteristic among the group: exoskeletal molting (termed ecdysis). Lophotrochozoa is named for two structural features, each common to certain phyla within the clade. Some lophotrochozoan phyla are characterized by a larval stage called trochophore larvae, and other phyla are characterized by the presence of a feeding structure called a lophophore.
Link to Learning
Explore an interactive tree of life here. Zoom and click to learn more about the organisms and their evolutionary relationships.
Modern Advances in Phylogenetic Understanding Come from Molecular Analyses
The phylogenetic groupings are continually being debated and refined by evolutionary biologists. Each year, new evidence emerges that further alters the relationships described by a phylogenetic tree diagram.
Link to Learning
Watch the following video to learn how biologists use genetic data to determine relationships among organisms.
Nucleic acid and protein analyses have greatly informed the modern phylogenetic animal tree. These data come from a variety of molecular sources, such as mitochondrial DNA, nuclear DNA, ribosomal RNA (rRNA), and certain cellular proteins. Many evolutionary relationships in the modern tree have only recently been determined due to molecular evidence. For example, a previously classified group of animals called lophophorates, which included brachiopods and bryozoans, were long-thought to be primitive deuterostomes. Extensive molecular analysis using rRNA data found these animals to be protostomes, more closely related to annelids and mollusks. This discovery allowed for the distinction of the protostome clade, the lophotrochozoans. Molecular data have also shed light on some differences within the lophotrochozoan group, and some scientists believe that the phyla Platyhelminthes and Rotifera within this group should actually belong to their own group of protostomes termed Platyzoa.
Molecular research similar to the discoveries that brought about the distinction of the lophotrochozoan clade has also revealed a dramatic rearrangement of the relationships between mollusks, annelids, arthropods, and nematodes, and a new ecdysozoan clade was formed. Due to morphological similarities in their segmented body types, annelids and arthropods were once thought to be closely related. However, molecular evidence has revealed that arthropods are actually more closely related to nematodes, now comprising the ecdysozoan clade, and annelids are more closely related to mollusks, brachiopods, and other phyla in the lophotrochozoan clade. These two clades now make up the protostomes.
Another change to former phylogenetic groupings because of molecular analyses includes the emergence of an entirely new phylum of worm called Acoelomorpha. These acoel flatworms were long thought to belong to the phylum Platyhelminthes because of their similar “flatworm” morphology. However, molecular analyses revealed this to be a false relationship and originally suggested that acoels represented living species of some of the earliest divergent bilaterians. More recent research into the acoelomorphs has called this hypothesis into question and suggested a closer relationship with deuterostomes. The placement of this new phylum remains disputed, but scientists agree that with sufficient molecular data, their true phylogeny will be determined.
Summary
Scientists are interested in the evolutionary history of animals and the evolutionary relationships among them. There are three main sources of data that scientists use to create phylogenetic evolutionary tree diagrams that illustrate such relationships: morphological information (which includes developmental morphologies), fossil record data, and, most recently, molecular data. The details of the modern phylogenetic tree change frequently as new data are gathered, and molecular data has recently contributed to many substantial modifications of the understanding of relationships between animal phyla.
Glossary
Ecdysozoa
clade of protostomes that exhibit exoskeletal molting (ecdysis)
Eumetazoa
group of animals with true differentiated tissues
Lophotrochozoa
clade of protostomes that exhibit a trochophore larvae stage or a lophophore feeding structure
Metazoa
group containing all animals
Parazoa
group of animals without true differentiated tissues | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/27%3A_Introduction_to_Animal_Diversity/27.3%3A_Animal_Phylogeny.txt |
Skills to Develop
• Describe the features that characterized the earliest animals and when they appeared on earth
• Explain the significance of the Cambrian period for animal evolution and the changes in animal diversity that took place during that time
• Describe some of the unresolved questions surrounding the Cambrian explosion
• Discuss the implications of mass animal extinctions that have occurred in evolutionary history
Many questions regarding the origins and evolutionary history of the animal kingdom continue to be researched and debated, as new fossil and molecular evidence change prevailing theories. Some of these questions include the following: How long have animals existed on Earth? What were the earliest members of the animal kingdom, and what organism was their common ancestor? While animal diversity increased during the Cambrian period of the Paleozoic era, 530 million years ago, modern fossil evidence suggests that primitive animal species existed much earlier.
Pre-Cambrian Animal Life
The time before the Cambrian period is known as the Ediacaran period (from about 635 million years ago to 543 million years ago), the final period of the late Proterozoic Neoproterozoic Era (Figure \(1\)). It is believed that early animal life, termed Ediacaran biota, evolved from protists at this time. Some protest species called choanoflagellates closely resemble the choanocyte cells in the simplest animals, sponges. In addition to their morphological similarity, molecular analyses have revealed similar sequence homologies in their DNA.
The earliest life comprising Ediacaran biota was long believed to include only tiny, sessile, soft-bodied sea creatures. However, recently there has been increasing scientific evidence suggesting that more varied and complex animal species lived during this time, and possibly even before the Ediacaran period.
Fossils believed to represent the oldest animals with hard body parts were recently discovered in South Australia. These sponge-like fossils, named Coronacollina acula, date back as far as 560 million years, and are believed to show the existence of hard body parts and spicules that extended 20–40 cm from the main body (estimated about 5 cm long). Other fossils from the Ediacaran period are shown in Figure \(2\).
Another recent fossil discovery may represent the earliest animal species ever found. While the validity of this claim is still under investigation, these primitive fossils appear to be small, one-centimeter long, sponge-like creatures. These fossils from South Australia date back 650 million years, actually placing the putative animal before the great ice age extinction event that marked the transition between the Cryogenian period and the Ediacaran period. Until this discovery, most scientists believed that there was no animal life prior to the Ediacaran period. Many scientists now believe that animals may in fact have evolved during the Cryogenian period.
The Cambrian Explosion of Animal Life
The Cambrian period, occurring between approximately 542–488 million years ago, marks the most rapid evolution of new animal phyla and animal diversity in Earth’s history. It is believed that most of the animal phyla in existence today had their origins during this time, often referred to as the Cambrian explosion (Figure 27.4.3). Echinoderms, mollusks, worms, arthropods, and chordates arose during this period. One of the most dominant species during the Cambrian period was the trilobite, an arthropod that was among the first animals to exhibit a sense of vision (Figure \(4\)).
The cause of the Cambrian explosion is still debated. There are many theories that attempt to answer this question. Environmental changes may have created a more suitable environment for animal life. Examples of these changes include rising atmospheric oxygen levels and large increases in oceanic calcium concentrations that preceded the Cambrian period (Figure \(5\)). Some scientists believe that an expansive, continental shelf with numerous shallow lagoons or pools provided the necessary living space for larger numbers of different types of animals to co-exist. There is also support for theories that argue that ecological relationships between species, such as changes in the food web, competition for food and space, and predator-prey relationships, were primed to promote a sudden massive coevolution of species. Yet other theories claim genetic and developmental reasons for the Cambrian explosion. The morphological flexibility and complexity of animal development afforded by the evolution of Hox control genes may have provided the necessary opportunities for increases in possible animal morphologies at the time of the Cambrian period. Theories that attempt to explain why the Cambrian explosion happened must be able to provide valid reasons for the massive animal diversification, as well as explain why it happened when it did. There is evidence that both supports and refutes each of the theories described above, and the answer may very well be a combination of these and other theories.
However, unresolved questions about the animal diversification that took place during the Cambrian period remain. For example, we do not understand how the evolution of so many species occurred in such a short period of time. Was there really an “explosion” of life at this particular time? Some scientists question the validity of the this idea, because there is increasing evidence to suggest that more animal life existed prior to the Cambrian period and that other similar species’ so-called explosions (or radiations) occurred later in history as well. Furthermore, the vast diversification of animal species that appears to have begun during the Cambrian period continued well into the following Ordovician period. Despite some of these arguments, most scientists agree that the Cambrian period marked a time of impressively rapid animal evolution and diversification that is unmatched elsewhere during history.
Link to Learning
View an animation of what ocean life may have been like during the Cambrian explosion.
Post-Cambrian Evolution and Mass Extinctions
The periods that followed the Cambrian during the Paleozoic Era are marked by further animal evolution and the emergence of many new orders, families, and species. As animal phyla continued to diversify, new species adapted to new ecological niches. During the Ordovician period, which followed the Cambrian period, plant life first appeared on land. This change allowed formerly aquatic animal species to invade land, feeding directly on plants or decaying vegetation. Continual changes in temperature and moisture throughout the remainder of the Paleozoic Era due to continental plate movements encouraged the development of new adaptations to terrestrial existence in animals, such as limbed appendages in amphibians and epidermal scales in reptiles.
Changes in the environment often create new niches (living spaces) that contribute to rapid speciation and increased diversity. On the other hand, cataclysmic events, such as volcanic eruptions and meteor strikes that obliterate life, can result in devastating losses of diversity. Such periods of mass extinction (Figure \(6\)) have occurred repeatedly in the evolutionary record of life, erasing some genetic lines while creating room for others to evolve into the empty niches left behind. The end of the Permian period (and the Paleozoic Era) was marked by the largest mass extinction event in Earth’s history, a loss of roughly 95 percent of the extant species at that time. Some of the dominant phyla in the world’s oceans, such as the trilobites, disappeared completely. On land, the disappearance of some dominant species of Permian reptiles made it possible for a new line of reptiles to emerge, the dinosaurs. The warm and stable climatic conditions of the ensuing Mesozoic Era promoted an explosive diversification of dinosaurs into every conceivable niche in land, air, and water. Plants, too, radiated into new landscapes and empty niches, creating complex communities of producers and consumers, some of which became very large on the abundant food available.
Another mass extinction event occurred at the end of the Cretaceous period, bringing the Mesozoic Era to an end. Skies darkened and temperatures fell as a large meteor impact and tons of volcanic ash blocked incoming sunlight. Plants died, herbivores and carnivores starved, and the mostly cold-blooded dinosaurs ceded their dominance of the landscape to more warm-blooded mammals. In the following Cenozoic Era, mammals radiated into terrestrial and aquatic niches once occupied by dinosaurs, and birds, the warm-blooded offshoots of one line of the ruling reptiles, became aerial specialists. The appearance and dominance of flowering plants in the Cenozoic Era created new niches for insects, as well as for birds and mammals. Changes in animal species diversity during the late Cretaceous and early Cenozoic were also promoted by a dramatic shift in Earth’s geography, as continental plates slid over the crust into their current positions, leaving some animal groups isolated on islands and continents, or separated by mountain ranges or inland seas from other competitors. Early in the Cenozoic, new ecosystems appeared, with the evolution of grasses and coral reefs. Late in the Cenozoic, further extinctions followed by speciation occurred during ice ages that covered high latitudes with ice and then retreated, leaving new open spaces for colonization.
Link to Learning
Watch the following video to learn more about the mass extinctions.
Career Connection: Paleontologist
Natural history museums contain the fossil casts of extinct animals and information about how these animals evolved, lived, and died. Paleontogists are scientists who study prehistoric life. They use fossils to observe and explain how life evolved on Earth and how species interacted with each other and with the environment. A paleontologist needs to be knowledgeable in biology, ecology, chemistry, geology, and many other scientific disciplines. A paleontologist’s work may involve field studies: searching for and studying fossils. In addition to digging for and finding fossils, paleontologists also prepare fossils for further study and analysis. Although dinosaurs are probably the first animals that come to mind when thinking about paleontology, paleontologists study everything from plant life, fungi, and fish to sea animals and birds.
An undergraduate degree in earth science or biology is a good place to start toward the career path of becoming a paleontologist. Most often, a graduate degree is necessary. Additionally, work experience in a museum or in a paleontology lab is useful.
Summary
The most rapid diversification and evolution of animal species in all of history occurred during the Cambrian period of the Paleozoic Era, a phenomenon known as the Cambrian explosion. Until recently, scientists believed that there were only very few tiny and simplistic animal species in existence before this period. However, recent fossil discoveries have revealed that additional, larger, and more complex animals existed during the Ediacaran period, and even possibly earlier, during the Cryogenian period. Still, the Cambrian period undoubtedly witnessed the emergence of the majority of animal phyla that we know today, although many questions remain unresolved about this historical phenomenon.
The remainder of the Paleozoic Era is marked by the growing appearance of new classes, families, and species, and the early colonization of land by certain marine animals. The evolutionary history of animals is also marked by numerous major extinction events, each of which wiped out a majority of extant species. Some species of most animal phyla survived these extinctions, allowing the phyla to persist and continue to evolve into species that we see today.
Glossary
Cambrian explosion
time during the Cambrian period (542–488 million years ago) when most of the animal phyla in existence today evolved
Cryogenian period
geologic period (850–630 million years ago) characterized by a very cold global climate
Ediacaran period
geological period (630–542 million years ago) when the oldest definite multicellular organisms with tissues evolved
mass extinction
event that wipes out the majority of species within a relatively short geological time period | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/27%3A_Introduction_to_Animal_Diversity/27.4%3A_The_Evolutionary_History_of_the_Animal_Kingdom.txt |
27.1: Features of the Animal Kingdom
Review Questions
Which of the following is not a feature common to most animals?
1. development into a fixed body plan
2. asexual reproduction
3. specialized tissues
4. heterotrophic nutrient sourcing
Answer
B
During embryonic development, unique cell layers develop and distinguish during a stage called ________.
1. the blastula stage
2. the germ layer stage
3. the gastrula stage
4. the organogenesis stage
Answer
C
Which of the following phenotypes would most likely be the result of a Hox gene mutation?
1. abnormal body length or height
2. two different eye colors
3. the contraction of a genetic illness
4. two fewer appendages than normal
Answer
D
Free Response
Why might the evolution of specialized tissues be important for animal function and complexity?
Answer
The development of specialized tissues affords more complex animal anatomy and physiology because differentiated tissue types can perform unique functions and work together in tandem to allow the animal to perform more functions. For example, specialized muscle tissue allows directed and efficient movement, and specialized nervous tissue allows for multiple sensory modalities as well as the ability to respond to various sensory information; these functions are not necessarily available to other non-animal organisms.
Describe and give examples of how humans display all of the features common to the animal kingdom.
Answer
Humans are multicellular organisms. They also contain differentiated tissues, such as epithelial, muscle, and nervous tissue, as well as specialized organs and organ systems. As heterotrophs, humans cannot produce their own nutrients and must obtain them by ingesting other organisms, such as plants, fungi, and animals. Humans undergo sexual reproduction, as well as the same embryonic developmental stages as other animals, which eventually lead to a fixed and motile body plan controlled in large part by Hox genes.
How have Hox genes contributed to the diversity of animal body plans?
Answer
Altered expression of homeotic genes can lead to major changes in the morphology of the individual. Hox genes can affect the spatial arrangements of organs and body parts. If a Hox gene was mutated or duplicated, it could affect where a leg might be on a fruit fly or how far apart a person’s fingers are.
27.2: Features Used to Classify Animals
Review Questions
Which of the following organism is most likely to be a diploblast?
1. sea star
2. shrimp
3. jellyfish
4. insect
Answer
C
Which of the following is not possible?
1. radially symmetrical diploblast
2. diploblastic eucoelomate
3. protostomic coelomate
4. bilaterally symmetrical deuterostome
Answer
B
An animal whose development is marked by radial cleavage and enterocoely is ________.
1. a deuterostome
2. an annelid or mollusk
3. either an acoelomate or eucoelomate
4. none of the above
Answer
A
Free Response
Using the following terms, explain what classifications and groups humans fall into, from the most general to the most specific: symmetry, germ layers, coelom, cleavage, embryological development.
Answer
Humans have body plans that are bilaterally symmetrical and are characterized by the development of three germ layers, making them triploblasts. Humans have true coeloms and are thus eucoelomates. As deuterostomes, humans are characterized by radial and indeterminate cleavage.
Explain some of the advantages brought about through the evolution of bilateral symmetry and coelom formation.
Answer
The evolution of bilateral symmetry led to designated head and tail body regions, and promoted more efficient mobility for animals. This improved mobility allowed for more skillful seeking of resources and prey escaping from predators. The appearance of the coelom in coelomates provides many internal organs with shock absorption, making them less prone to physical damage from bodily assault. A coelom also gives the body greater flexibility, which promotes more efficient movement. The relatively loose placement of organs within the coelom allows them to develop and grow with some spatial freedom, which promoted the evolution of optimal organ arrangement. The coelom also provides space for a circulatory system, which is an advantageous way to distribute body fluids and gases.
27.3: Animal Phylogeny
Review Questions
Consulting the modern phylogenetic tree of animals, which of the following would not constitute a clade?
1. deuterostomes
2. lophotrochozoans
3. Parazoa
4. Bilateria
Answer
C
Which of the following is thought to be the most closely related to the common animal ancestor?
1. fungal cells
2. protist cells
3. plant cells
4. bacterial cells
Answer
B
As with the emergence of the Acoelomorpha phylum, it is common for ____ data to misplace animals in close relation to other species, whereas ____ data often reveals a different and more accurate evolutionary relationship.
1. molecular : morphological
2. molecular : fossil record
3. fossil record : morphological
4. morphological : molecular
Answer
D
Free Response
Describe at least two major changes to the animal phylogenetic tree that have come about due to molecular or genetic findings.
Answer
Two new clades that comprise the two major groups of protostomes are called the lophotrochozoans and the ecdysozoans. The formation of these two clades came about through molecular research from DNA and protein data. Also, the novel phylum of worm called Acoelomorpha was determined due to molecular data that distinguished them from other flatworms.
How is it that morphological data alone might lead scientists to group animals into erroneous evolutionary relationships?
Answer
In many cases, morphological similarities between animals may be only superficial similarities and may not indicate a true evolutionary relationship. One of the reasons for this is that certain morphological traits can evolve along very different evolutionary branches of animals for similar ecological reasons.
27.4: The Evolutionary History of the Animal Kingdom
Review Questions
Which of the following periods is the earliest during which animals may have appeared?
1. Ordovician period
2. Cambrian period
3. Ediacaran period
4. Cryogenian period
Answer
D
What type of data is primarily used to determine the existence and appearance of early animal species?
1. molecular data
2. fossil data
3. morphological data
4. embryological development data
Answer
B
The time between 542–488 million years ago marks which period?
1. Cambrian period
2. Silurian period
3. Ediacaran period
4. Devonian period
Answer
A
Until recent discoveries suggested otherwise, animals existing before the Cambrian period were believed to be:
1. small and ocean-dwelling
2. small and non-motile
3. small and soft-bodied
4. small and radially symmetrical or asymmetrical
Answer
C
Plant life first appeared on land during which of the following periods?
1. Cambrian period
2. Ordovician period
3. Silurian period
4. Devonian period
Answer
B
Approximately how many mass extinction events occurred throughout the evolutionary history of animals?
1. 3
2. 4
3. 5
4. more than 5
Answer
D
Free Response
Briefly describe at least two theories that attempt to explain the cause of the Cambrian explosion.
Answer
One theory states that environmental factors led to the Cambrian explosion. For example, the rise in atmospheric oxygen and oceanic calcium levels helped to provide the right environmental conditions to allow such a rapid evolution of new animal phyla. Another theory states that ecological factors such as competitive pressures and predator-prey relationships reached a threshold that supported the rapid animal evolution that took place during the Cambrian period.
How is it that most, if not all, of the extant animal phyla today evolved during the Cambrian period if so many massive extinction events have taken place since then?
Answer
It is true that multiple mass extinction events have taken place since the Cambrian period, when most currently existing animal phyla appeared, and the majority of animal species were commonly wiped out during these events. However, a small number of animal species representing each phylum were usually able to survive each extinction event, allowing the phylum to continue to evolve rather than become altogether extinct. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/27%3A_Introduction_to_Animal_Diversity/27.E%3A_Introduction_to_Animal_Diversity_%28Exercises%29.txt |
Invertebrate animals are those without a cranium and defined vertebral column or spine. In addition to lacking a spine, most invertebrates also lack an endoskeleton. A large number of invertebrates are aquatic animals, and scientific research suggests that many of the world’s species are aquatic invertebrates that have not yet been documented.
• 28.0: Prelude to Invertebrates
A brief look at any magazine pertaining to our natural world, such as National Geographic, would show a rich variety of vertebrates, especially mammals and birds. To most people, these are the animals that attract our attention. Concentrating on vertebrates, however, gives us a rather biased and limited view of biodiversity, because it ignores nearly 97 percent of the animal kingdom, namely the invertebrates.
• 28.1: Phylum Porifera
The simplest of all the invertebrates are the Parazoans, which include only the phylum Porifera: the sponges. Parazoans (“beside animals”) do not display tissue-level organization, although they do have specialized cells that perform specific functions. Sponge larvae are able to swim; however, adults are non-motile and spend their life attached to a substratum.
• 28.2: Phylum Cnidaria
Phylum Cnidaria includes animals that show radial or biradial symmetry and are diploblastic, that is, they develop from two embryonic layers. Nearly all (about 99 percent) cnidarians are marine species. Cnidarians contain specialized cells known as cnidocytes (“stinging cells”) containing organelles called nematocysts (stingers). These cells are present around the mouth and tentacles, and serve to immobilize prey with toxins contained within the cells.
• 28.3: Superphylum Lophotrochozoa
Animals belonging to superphylum Lophotrochozoa are protostomes, in which the blastopore, or the point of involution of the ectoderm or outer germ layer, becomes the mouth opening to the alimentary canal. This is called protostomy or “first mouth.” In protostomy, solid groups of cells split from the endoderm or inner germ layer to form a central mesodermal layer of cells. This layer multiplies into a band and then splits internally to form the coelom.
• 28.4: Superphylum Ecdysozoa
The superphylum Ecdysozoa contains an incredibly large number of species. This is because it contains two of the most diverse animal groups: phylum Nematoda (the roundworms) and Phylum Arthropoda (the arthropods). The most prominant distinguising feature of Ecdysozoans is their tough external covering called the cuticle. The cuticle provides a tough, but flexible exoskeleton tht protects these animals from water loss, predators and other aspects of the external environment.
• 28.5: Superphylum Deuterostomia
The phyla Echinodermata and Chordata (the phylum in which humans are placed) both belong to the superphylum Deuterostomia. Recall that protostome and deuterostomes differ in certain aspects of their embryonic development, and they are named based on which opening of the digestive cavity develops first. The word deuterostome comes from the Greek word meaning “mouth second,” indicating that the anus is the first to develop.
• 28.E: Invertebrates (Exercises)
Thumbnail: Drosophila melanogaster. (CC BY-SA 2.5; André Karwath aka Aka via Wikimedia Commons).
28: Invertebrates
A brief look at any magazine pertaining to our natural world, such as National Geographic, would show a rich variety of vertebrates, especially mammals and birds. To most people, these are the animals that attract our attention. Concentrating on vertebrates, however, gives us a rather biased and limited view of biodiversity, because it ignores nearly 97 percent of the animal kingdom, namely the invertebrates. Invertebrate animals are those without a cranium and defined vertebral column or spine. In addition to lacking a spine, most invertebrates also lack an endoskeleton. A large number of invertebrates are aquatic animals, and scientific research suggests that many of the world’s species are aquatic invertebrates that have not yet been documented. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/28%3A_Invertebrates/28.0%3A_Prelude_to_Invertebrates.txt |
Skills to Develop
• Describe the organizational features of the simplest multicellular organisms
• Explain the various body forms and bodily functions of sponges
The invertebrates, or invertebrata, are animals that do not contain bony structures, such as the cranium and vertebrae. The simplest of all the invertebrates are the Parazoans, which include only the phylum Porifera: the sponges (Figure \(1\)). Parazoans (“beside animals”) do not display tissue-level organization, although they do have specialized cells that perform specific functions. Sponge larvae are able to swim; however, adults are non-motile and spend their life attached to a substratum. Since water is vital to sponges for excretion, feeding, and gas exchange, their body structure facilitates the movement of water through the sponge. Structures such as canals, chambers, and cavities enable water to move through the sponge to nearly all body cells.
Morphology of Sponges
The morphology of the simplest sponges takes the shape of a cylinder with a large central cavity, the spongocoel, occupying the inside of the cylinder. Water can enter into the spongocoel from numerous pores in the body wall. Water entering the spongocoel is extruded via a large common opening called the osculum. However, sponges exhibit a range of diversity in body forms, including variations in the size of the spongocoel, the number of osculi, and where the cells that filter food from the water are located.
While sponges (excluding the hexactinellids) do not exhibit tissue-layer organization, they do have different cell types that perform distinct functions. Pinacocytes, which are epithelial-like cells, form the outermost layer of sponges and enclose a jelly-like substance called mesohyl. Mesohyl is an extracellular matrix consisting of a collagen-like gel with suspended cells that perform various functions. The gel-like consistency of mesohyl acts like an endoskeleton and maintains the tubular morphology of sponges. In addition to the osculum, sponges have multiple pores called ostia on their bodies that allow water to enter the sponge. In some sponges, ostia are formed by porocytes, single tube-shaped cells that act as valves to regulate the flow of water into the spongocoel. In other sponges, ostia are formed by folds in the body wall of the sponge.
Choanocytes (“collar cells”) are present at various locations, depending on the type of sponge, but they always line the inner portions of some space through which water flows (the spongocoel in simple sponges, canals within the body wall in more complex sponges, and chambers scattered throughout the body in the most complex sponges). Whereas pinacocytes line the outside of the sponge, choanocytes tend to line certain inner portions of the sponge body that surround the mesohyl. The structure of a choanocyte is critical to its function, which is to generate a water current through the sponge and to trap and ingest food particles by phagocytosis. Note the similarity in appearance between the sponge choanocyte and choanoflagellates (Protista). This similarity suggests that sponges and choanoflagellates are closely related and likely share a recent common ancestry. The cell body is embedded in mesohyl and contains all organelles required for normal cell function, but protruding into the “open space” inside of the sponge is a mesh-like collar composed of microvilli with a single flagellum in the center of the column. The cumulative effect of the flagella from all choanocytes aids the movement of water through the sponge: drawing water into the sponge through the numerous ostia, into the spaces lined by choanocytes, and eventually out through the osculum (or osculi). In the meantime, food particles, including waterborne bacteria and algae, are trapped by the sieve-like collar of the choanocytes, slide down into the body of the cell, are ingested by phagocytosis, and become encased in a food vacuole. Lastly, choanocytes will differentiate into sperm for sexual reproduction, where they will become dislodged from the mesohyl and leave the sponge with expelled water through the osculum.
The second crucial cells in sponges are called amoebocytes (or archaeocytes), named for the fact that they move throughout the mesohyl in an amoeba-like fashion. Amoebocytes have a variety of functions: delivering nutrients from choanocytes to other cells within the sponge, giving rise to eggs for sexual reproduction (which remain in the mesohyl), delivering phagocytized sperm from choanocytes to eggs, and differentiating into more-specific cell types. Some of these more-specific cell types include collencytes and lophocytes, which produce the collagen-like protein to maintain the mesohyl, sclerocytes, which produce spicules in some sponges, and spongocytes, which produce the protein spongin in the majority of sponges. These cells produce collagen to maintain the consistency of the mesohyl. The different cell types in sponges are shown in Figure \(2\).
Exercise \(1\)
Which of the following statements is false?
1. Choanocytes have flagella that propel water through the body.
2. Pinacocytes can transform into any cell type.
3. Lophocytes secrete collagen.
4. Porocytes control the flow of water through pores in the sponge body.
Answer
B
In some sponges, sclerocytes secrete small spicules into the mesohyl, which are composed of either calcium carbonate or silica, depending on the type of sponge. These spicules serve to provide additional stiffness to the body of the sponge. Additionally, spicules, when present externally, may ward off predators. Another type of protein, spongin, may also be present in the mesohyl of some sponges.
The presence and composition of spicules/spongin are the differentiating characteristics of the three classes of sponges (Figure \(3\)): Class Calcarea contains calcium carbonate spicules and no spongin, class Hexactinellida contains six-rayed siliceous spicules and no spongin, and class Demospongia contains spongin and may or may not have spicules; if present, those spicules are siliceous. Spicules are most conspicuously present in class Hexactinellida, the order consisting of glass sponges. Some of the spicules may attain giant proportions (in relation to the typical size range of glass sponges of 3 to 10 mm) as seen in Monorhaphis chuni, which grows up to 3 m long.
Physiological Processes in Sponges
Sponges, despite being simple organisms, regulate their different physiological processes through a variety of mechanisms. These processes regulate their metabolism, reproduction, and locomotion.
Digestion
Sponges lack complex digestive, respiratory, circulatory, reproductive, and nervous systems. Their food is trapped when water passes through the ostia and out through the osculum. Bacteria smaller than 0.5 microns in size are trapped by choanocytes, which are the principal cells engaged in nutrition, and are ingested by phagocytosis. Particles that are larger than the ostia may be phagocytized by pinacocytes. In some sponges, amoebocytes transport food from cells that have ingested food particles to those that do not. For this type of digestion, in which food particles are digested within individual cells, the sponge draws water through diffusion. The limit of this type of digestion is that food particles must be smaller than individual cells.
All other major body functions in the sponge (gas exchange, circulation, excretion) are performed by diffusion between the cells that line the openings within the sponge and the water that is passing through those openings. All cell types within the sponge obtain oxygen from water through diffusion. Likewise, carbon dioxide is released into seawater by diffusion. In addition, nitrogenous waste produced as a byproduct of protein metabolism is excreted via diffusion by individual cells into the water as it passes through the sponge.
Reproduction
Sponges reproduce by sexual as well as asexual methods. The typical means of asexual reproduction is either fragmentation (where a piece of the sponge breaks off, settles on a new substrate, and develops into a new individual) or budding (a genetically identical outgrowth grows from the parent and eventually detaches or remains attached to form a colony). An atypical type of asexual reproduction is found only in freshwater sponges and occurs through the formation of gemmules. Gemmules are environmentally resistant structures produced by adult sponges wherein the typical sponge morphology is inverted. In gemmules, an inner layer of amoebocytes is surrounded by a layer of collagen (spongin) that may be reinforced by spicules. The collagen that is normally found in the mesohyl becomes the outer protective layer. In freshwater sponges, gemmules may survive hostile environmental conditions like changes in temperature and serve to recolonize the habitat once environmental conditions stabilize. Gemmules are capable of attaching to a substratum and generating a new sponge. Since gemmules can withstand harsh environments, are resistant to desiccation, and remain dormant for long periods, they are an excellent means of colonization for a sessile organism.
Sexual reproduction in sponges occurs when gametes are generated. Sponges are monoecious (hermaphroditic), which means that one individual can produce both gametes (eggs and sperm) simultaneously. In some sponges, production of gametes may occur throughout the year, whereas other sponges may show sexual cycles depending upon water temperature. Sponges may also become sequentially hermaphroditic, producing oocytes first and spermatozoa later. Oocytes arise by the differentiation of amoebocytes and are retained within the spongocoel, whereas spermatozoa result from the differentiation of choanocytes and are ejected via the osculum. Ejection of spermatozoa may be a timed and coordinated event, as seen in certain species. Spermatozoa carried along by water currents can fertilize the oocytes borne in the mesohyl of other sponges. Early larval development occurs within the sponge, and free-swimming larvae are then released via the osculum.
Locomotion
Sponges are generally sessile as adults and spend their lives attached to a fixed substratum. They do not show movement over large distances like other free-swimming marine invertebrates. However, sponge cells are capable of creeping along substrata via organizational plasticity. Under experimental conditions, researchers have shown that sponge cells spread on a physical support demonstrate a leading edge for directed movement. It has been speculated that this localized creeping movement may help sponges adjust to microenvironments near the point of attachment. It must be noted, however, that this pattern of movement has been documented in laboratories, but it remains to be observed in natural sponge habitats.
Summary
Animals included in phylum Porifera are Parazoans because they do not show the formation of true tissues (except in class Hexactinellida). These organisms show very simple organization, with a rudimentary endoskeleton. Sponges have multiple cell types that are geared toward executing various metabolic functions. Although these animals are very simple, they perform several complex physiological functions.
Glossary
amoebocyte
sponge cell with multiple functions, including nutrient delivery, egg formation, sperm delivery, and cell differentiation
choanocyte
(also, collar cell) sponge cell that functions to generate a water current and to trap and ingest food particles via phagocytosis
gemmule
structure produced by asexual reproduction in freshwater sponges where the morphology is inverted
invertebrata
(also, invertebrates) category of animals that do not possess a cranium or vertebral column
mesohyl
collagen-like gel containing suspended cells that perform various functions in the sponge
osculum
large opening in the sponge’s body through which water leaves
ostium
pore present on the sponge’s body through which water enters
pinacocyte
epithelial-like cell that forms the outermost layer of sponges and encloses a jelly-like substance called mesohyl
Porifera
phylum of animals with no true tissues, but a porous body with rudimentary endoskeleton
sclerocyte
cell that secretes silica spicules into the mesohyl
spicule
structure made of silica or calcium carbonate that provides structural support for sponges
spongocoel
central cavity within the body of some sponges | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/28%3A_Invertebrates/28.1%3A_Phylum_Porifera.txt |
Skills to Develop
• Compare structural and organization characteristics of Porifera and Cnidaria
• Describe the progressive development of tissues and their relevance to animal complexity
Phylum Cnidaria includes animals that show radial or biradial symmetry and are diploblastic, that is, they develop from two embryonic layers. Nearly all (about 99 percent) cnidarians are marine species.
Cnidarians contain specialized cells known as cnidocytes (“stinging cells”) containing organelles called nematocysts (stingers). These cells are present around the mouth and tentacles, and serve to immobilize prey with toxins contained within the cells. Nematocysts contain coiled threads that may bear barbs. The outer wall of the cell has hairlike projections called cnidocils, which are sensitive to touch. When touched, the cells are known to fire coiled threads that can either penetrate the flesh of the prey or predators of cnidarians (see Figure \(1\)) or ensnare it. These coiled threads release toxins into the target and can often immobilize prey or scare away predators.
Animals in this phylum display two distinct morphological body plans: polyp or “stalk” and medusa or “bell” (Figure \(2\)). An example of the polyp form is Hydra spp.; perhaps the most well-known medusoid animals are the jellies (jellyfish). Polyp forms are sessile as adults, with a single opening to the digestive system (the mouth) facing up with tentacles surrounding it. Medusa forms are motile, with the mouth and tentacles hanging down from an umbrella-shaped bell.
Some cnidarians are polymorphic, that is, they have two body plans during their life cycle. An example is the colonial hydroid called an Obelia. The sessile polyp form has, in fact, two types of polyps, shown in Figure \(3\). The first is the gastrozooid, which is adapted for capturing prey and feeding; the other type of polyp is the gonozooid, adapted for the asexual budding of medusa. When the reproductive buds mature, they break off and become free-swimming medusa, which are either male or female (dioecious). The male medusa makes sperm, whereas the female medusa makes eggs. After fertilization, the zygote develops into a blastula, which develops into a planula larva. The larva is free swimming for a while, but eventually attaches and a new colonial reproductive polyp is formed.
All cnidarians show the presence of two membrane layers in the body that are derived from the endoderm and ectoderm of the embryo. The outer layer (from ectoderm) is called the epidermis and lines the outside of the animal, whereas the inner layer (from endoderm) is called the gastrodermis and lines the digestive cavity. Between these two membrane layers is a non-living, jelly-like mesoglea connective layer. In terms of cellular complexity, cnidarians show the presence of differentiated cell types in each tissue layer, such as nerve cells, contractile epithelial cells, enzyme-secreting cells, and nutrient-absorbing cells, as well as the presence of intercellular connections. However, the development of organs or organ systems is not advanced in this phylum.
The nervous system is primitive, with nerve cells scattered across the body. This nerve net may show the presence of groups of cells in the form of nerve plexi (singular plexus) or nerve cords. The nerve cells show mixed characteristics of motor as well as sensory neurons. The predominant signaling molecules in these primitive nervous systems are chemical peptides, which perform both excitatory and inhibitory functions. Despite the simplicity of the nervous system, it coordinates the movement of tentacles, the drawing of captured prey to the mouth, the digestion of food, and the expulsion of waste.
The cnidarians perform extracellular digestion in which the food is taken into the gastrovascular cavity, enzymes are secreted into the cavity, and the cells lining the cavity absorb nutrients. The gastrovascular cavity has only one opening that serves as both a mouth and an anus, which is termed an incomplete digestive system. Cnidarian cells exchange oxygen and carbon dioxide by diffusion between cells in the epidermis with water in the environment, and between cells in the gastrodermis with water in the gastrovascular cavity. The lack of a circulatory system to move dissolved gases limits the thickness of the body wall and necessitates a non-living mesoglea between the layers. There is no excretory system or organs, and nitrogenous wastes simply diffuse from the cells into the water outside the animal or in the gastrovascular cavity. There is also no circulatory system, so nutrients must move from the cells that absorb them in the lining of the gastrovascular cavity through the mesoglea to other cells.
The phylum Cnidaria contains about 10,000 described species divided into four classes: Anthozoa, Scyphozoa, Cubozoa, and Hydrozoa. The anthozoans, the sea anemones and corals, are all sessile species, whereas the scyphozoans (jellyfish) and cubozoans (box jellies) are swimming forms. The hydrozoans contain sessile forms and swimming colonial forms like the Portuguese Man O’ War.
Class Anthozoa
The class Anthozoa includes all cnidarians that exhibit a polyp body plan only; in other words, there is no medusa stage within their life cycle. Examples include sea anemones (Figure \(4\)), sea pens, and corals, with an estimated number of 6,100 described species. Sea anemones are usually brightly colored and can attain a size of 1.8 to 10 cm in diameter. These animals are usually cylindrical in shape and are attached to a substrate. A mouth opening is surrounded by tentacles bearing cnidocytes.
The mouth of a sea anemone is surrounded by tentacles that bear cnidocytes. The slit-like mouth opening and pharynx are lined by a groove called a siphonophore. The pharynx is the muscular part of the digestive system that serves to ingest as well as egest food, and may extend for up to two-thirds the length of the body before opening into the gastrovascular cavity. This cavity is divided into several chambers by longitudinal septa called mesenteries. Each mesentery consists of one ectodermal and one endodermal cell layer with the mesoglea sandwiched in between. Mesenteries do not divide the gastrovascular cavity completely, and the smaller cavities coalesce at the pharyngeal opening. The adaptive benefit of the mesenteries appears to be an increase in surface area for absorption of nutrients and gas exchange.
Sea anemones feed on small fish and shrimp, usually by immobilizing their prey using the cnidocytes. Some sea anemones establish a mutualistic relationship with hermit crabs by attaching to the crab’s shell. In this relationship, the anemone gets food particles from prey caught by the crab, and the crab is protected from the predators by the stinging cells of the anemone. Anemone fish, or clownfish, are able to live in the anemone since they are immune to the toxins contained within the nematocysts.
Anthozoans remain polypoid throughout their lives and can reproduce asexually by budding or fragmentation, or sexually by producing gametes. Both gametes are produced by the polyp, which can fuse to give rise to a free-swimming planula larva. The larva settles on a suitable substratum and develops into a sessile polyp.
Class Scyphozoa
Class Scyphozoa includes all the jellies and is exclusively a marine class of animals with about 200 known species. The defining characteristic of this class is that the medusa is the prominent stage in the life cycle, although there is a polyp stage present. Members of this species range from 2 to 40 cm in length but the largest scyphozoan species, Cyanea capillata, can reach a size of 2 m across. Scyphozoans display a characteristic bell-like morphology (Figure \(5\)).
In the jellyfish, a mouth opening is present on the underside of the animal, surrounded by tentacles bearing nematocysts. Scyphozoans live most of their life cycle as free-swimming, solitary carnivores. The mouth leads to the gastrovascular cavity, which may be sectioned into four interconnected sacs, called diverticuli. In some species, the digestive system may be further branched into radial canals. Like the septa in anthozoans, the branched gastrovascular cells serve two functions: to increase the surface area for nutrient absorption and diffusion; thus, more cells are in direct contact with the nutrients in the gastrovascular cavity.
In scyphozoans, nerve cells are scattered all over the body. Neurons may even be present in clusters called rhopalia. These animals possess a ring of muscles lining the dome of the body, which provides the contractile force required to swim through water. Scyphozoans are dioecious animals, that is, the sexes are separate. The gonads are formed from the gastrodermis and gametes are expelled through the mouth. Planula larvae are formed by external fertilization; they settle on a substratum in a polypoid form known as scyphistoma. These forms may produce additional polyps by budding or may transform into the medusoid form. The life cycle (Figure \(6\)) of these animals can be described as polymorphic, because they exhibit both a medusal and polypoid body plan at some point in their life cycle.
Class Cubozoa
This class includes jellies that have a box-shaped medusa, or a bell that is square in cross-section; hence, are colloquially known as “box jellyfish.” These species may achieve sizes of 15–25 cm. Cubozoans display overall morphological and anatomical characteristics that are similar to those of the scyphozoans. A prominent difference between the two classes is the arrangement of tentacles. This is the most venomous group of all the cnidarians (Figure \(7\)).
The cubozoans contain muscular pads called pedalia at the corners of the square bell canopy, with one or more tentacles attached to each pedalium. These animals are further classified into orders based on the presence of single or multiple tentacles per pedalium. In some cases, the digestive system may extend into the pedalia. Nematocysts may be arranged in a spiral configuration along the tentacles; this arrangement helps to effectively subdue and capture prey. Cubozoans exist in a polypoid form that develops from a planula larva. These polyps show limited mobility along the substratum and, like scyphozoans, may bud to form more polyps to colonize a habitat. Polyp forms then transform into the medusoid forms.
Class Hydrozoa
Hydrozoa includes nearly 3,200 species; most are marine, although some freshwater species are known (Figure \(8\)). Animals in this class are polymorphs, and most exhibit both polypoid and medusoid forms in their lifecycle, although this is variable.
The polyp form in these animals often shows a cylindrical morphology with a central gastrovascular cavity lined by the gastrodermis. The gastrodermis and epidermis have a simple layer of mesoglea sandwiched between them. A mouth opening, surrounded by tentacles, is present at the oral end of the animal. Many hydrozoans form colonies that are composed of a branched colony of specialized polyps that share a gastrovascular cavity, such as in the colonial hydroid Obelia. Colonies may also be free-floating and contain medusoid and polypoid individuals in the colony as in Physalia (the Portuguese Man O’ War) or Velella (By-the-wind sailor). Even other species are solitary polyps (Hydra) or solitary medusae (Gonionemus). The true characteristic shared by all of these diverse species is that their gonads for sexual reproduction are derived from epidermal tissue, whereas in all other cnidarians they are derived from gastrodermal tissue.
Summary
Cnidarians represent a more complex level of organization than Porifera. They possess outer and inner tissue layers that sandwich a noncellular mesoglea. Cnidarians possess a well-formed digestive system and carry out extracellular digestion. The cnidocyte is a specialized cell for delivering toxins to prey as well as warning off predators. Cnidarians have separate sexes and have a lifecycle that involves morphologically distinct forms. These animals also show two distinct morphological forms—medusoid and polypoid—at various stages in their lifecycle.
Glossary
Cnidaria
phylum of animals that are diploblastic and have radial symmetry
cnidocyte
specialized stinging cell found in Cnidaria
epidermis
outer layer (from ectoderm) that lines the outside of the animal
extracellular digestion
food is taken into the gastrovascular cavity, enzymes are secreted into the cavity, and the cells lining the cavity absorb nutrients
gastrodermis
inner layer (from endoderm) that lines the digestive cavity
gastrovascular cavity
opening that serves as both a mouth and an anus, which is termed an incomplete digestive system
medusa
free-floating cnidarian body plan with mouth on underside and tentacles hanging down from a bell
mesoglea
non-living, gel-like matrix present between ectoderm and endoderm in cnidarians
nematocyst
harpoon-like organelle within cnidocyte with pointed projectile and poison to stun and entangle prey
polyp
stalk-like sessile life form of a cnidarians with mouth and tentacles facing upward, usually sessile but may be able to glide along surface
polymorphic
possessing multiple body plans within the lifecycle of a group of organisms
siphonophore
tubular structure that serves as an inlet for water into the mantle cavity | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/28%3A_Invertebrates/28.2%3A_Phylum_Cnidaria.txt |
Skills to Develop
• Describe the unique anatomical and morphological features of flatworms, rotifers, Nemertea, mollusks, and annelids
• Describe the development of an extracoelomic cavity
• Discuss the advantages of true body segmentation
• Explain the key features of Platyhelminthes and their importance as parasites
• Describe the features of animals classified in phylum Annelida
Animals belonging to superphylum Lophotrochozoa are protostomes, in which the blastopore, or the point of involution of the ectoderm or outer germ layer, becomes the mouth opening to the alimentary canal. This is called protostomy or “first mouth.” In protostomy, solid groups of cells split from the endoderm or inner germ layer to form a central mesodermal layer of cells. This layer multiplies into a band and then splits internally to form the coelom; this protostomic coelom is hence termed schizocoelom.
As lophotrochozoans, the organisms in this superphylum possess either a lophophore or trochophore larvae. The lophophores include groups that are united by the presence of the lophophore, a set of ciliated tentacles surrounding the mouth. Lophophorata include the flatworms and several other phyla. These clades are upheld when RNA sequences are compared. Trochophore larvae are characterized by two bands of cilia around the body.
The lophotrochozoans are triploblastic and possess an embryonic mesoderm sandwiched between the ectoderm and endoderm found in the diploblastic cnidarians. These phyla are also bilaterally symmetrical, meaning that a longitudinal section will divide them into right and left sides that are symmetrical. It also means the beginning of cephalization, the evolution of a concentration of nervous tissues and sensory organs in the head of the organism, which is where it first encounters its environment.
Phylum Platyhelminthes
The flatworms are acoelomate organisms that include many free-living and parasitic forms. Most of the flatworms are classified in the superphylum Lophotrochozoa, which also includes the mollusks and annelids. The Platyhelminthes consist of two lineages: the Catenulida and the Rhabditophora. The Catenulida, or "chain worms" is a small clade of just over 100 species. These worms typically reproduce asexually by budding. However, the offspring do not fully attach from the parents and, resemble a chain in appearance. All of the remaining flatworms discussed here are part of the Rhabditophora. Many flatworms are parasitic, including important parasites of humans. Flatworms have three embryonic tissue layers that give rise to surfaces that cover tissues (from ectoderm), internal tissues (from mesoderm), and line the digestive system (from endoderm). The epidermal tissue is a single layer cells or a layer of fused cells (syncytium) that covers a layer of circular muscle above a layer of longitudinal muscle. The mesodermal tissues include mesenchymal cells that contain collagen and support secretory cells that secrete mucus and other materials at the surface. The flatworms are acoelomates, so their bodies are solid between the outer surface and the cavity of the digestive system.
Physiological Processes of Flatworms
The free-living species of flatworms are predators or scavengers. Parasitic forms feed on the tissues of their hosts. Most flatworms, such as the planarian shown in Figure \(1\), have a gastrovascular cavity rather than a complete digestive system. In such animals, the “mouth” is also used to expel waste materials from the digestive system. Some species also have an anal opening. The gut may be a simple sac or highly branched. Digestion is extracellular, with digested materials taken in to the cells of the gut lining by phagocytosis. One group, the cestodes, lacks a digestive system. Flatworms have an excretory system with a network of tubules throughout the body with openings to the environment and nearby flame cells, whose cilia beat to direct waste fluids concentrated in the tubules out of the body. The system is responsible for the regulation of dissolved salts and the excretion of nitrogenous wastes. The nervous system consists of a pair of nerve cords running the length of the body with connections between them and a large ganglion or concentration of nerves at the anterior end of the worm, where there may also be a concentration of photosensory and chemosensory cells.
There is neither a circulatory nor respiratory system, with gas and nutrient exchange dependent on diffusion and cell-cell junctions. This necessarily limits the thickness of the body in these organisms, constraining them to be “flat” worms.
Most flatworm species are monoecious, and fertilization is typically internal. Asexual reproduction is common in some groups.
Diversity of Flatworms
Platyhelminthes are traditionally divided into four classes: Turbellaria, Monogenea, Trematoda, and Cestoda (Figure \(2\)). As discussed above, the relationships among members of these classes is being reassessed, with the turbellarians in particular now viewed as a paraphyletic group, a group that does not have a single common ancestor.
The class Turbellaria includes mainly free-living, marine species, although some species live in freshwater or moist terrestrial environments. The ventral epidermis of turbellarians is ciliated and facilitates their locomotion. Some turbellarians are capable of remarkable feats of regeneration in which they may regrow the body, even from a small fragment.
The monogeneans are ectoparasites, mostly of fish, with simple lifecycles that consist of a free-swimming larva that attaches to a fish to begin transformation to the parasitic adult form. The parasite has only one host and that host is usually only one species. The worms may produce enzymes that digest the host tissues or simply graze on surface mucus and skin particles. Most monogeneans are hermaphroditic, but the male gametes develop first and so cross-fertilization is quite common.
The trematodes, or flukes, are internal parasites of mollusks and many other groups, including humans. Trematodes have complex lifecycles that involve a primary host in which sexual reproduction occurs, and one or more secondary hosts in which asexual reproduction occurs. The primary host is almost always a mollusk. Trematodes are responsible for serious human diseases including schistosomiasis, a blood fluke. The disease infects an estimated 200 million people in the tropics, leading to organ damage and chronic symptoms like fatigue. Infection occurs when the human enters the water and a larva, released from the primary snail host, locates and penetrates the skin. The parasite infects various organs in the body and feeds on red blood cells before reproducing. Many of the eggs are released in feces and find their way into a waterway, where they are able to reinfect the primary snail host.
The cestodes, or tapeworms, are also internal parasites, mainly of vertebrates (Figure \(3\)). Tapeworms live in the intestinal tract of the primary host and remain fixed using a sucker on the anterior end, or scolex, of the tapeworm body. The remaining body of the tapeworm is made up of a long series of units called proglottids, each of which may contain an excretory system with flame cells, but contain reproductive structures, both male and female. Tapeworms do not possess a digestive system; instead, they absorb nutrients from the food matter passing them in the host’s intestine.
Proglottids are produced at the scolex and gradually migrate to the end of the tapeworm; at this point, they are “mature” and all structures except fertilized eggs have degenerated. Most reproduction occurs by cross-fertilization. The proglottid detaches from the body of the worm and is released into the feces of the organism. The eggs are eaten by an intermediate host. The juvenile worm infects the intermediate host and takes up residence, usually in muscle tissue. When the muscle tissue is eaten by the primary host, the cycle is completed. There are several tapeworm parasites of humans that are transmitted by eating uncooked or poorly cooked pork, beef, and fish.
Phylum Rotifera
The rotifers are a microscopic (about 100 µm to 30 mm) group of mostly aquatic organisms that get their name from the corona, a rotating, wheel-like structure that is covered with cilia at their anterior end (Figure \(4\)). Although their taxonomy is currently in flux, one treatment places the rotifers in three classes: Bdelloidea, Monogononta, and Seisonidea. The classification of the group is currently under revision, however, as more phylogenetic evidence becomes available. It is possible that the “spiny headed worms” currently in phylum Acanthocephala will be incorporated into this group in the future.
The body form of rotifers consists of a head (which contains the corona), a trunk (which contains the organs), and the foot. Rotifers are typically free-swimming and truly planktonic organisms, but the toes or extensions of the foot can secrete a sticky material forming a holdfast to help them adhere to surfaces. The head contains sensory organs in the form of a bi-lobed brain and small eyespots near the corona.
The rotifers are filter feeders that will eat dead material, algae, and other microscopic living organisms, and are therefore very important components of aquatic food webs. Rotifers obtain food that is directed toward the mouth by the current created from the movement of the corona. The food particles enter the mouth and travel to the mastax (pharynx with jaw-like structures). Food then passes by digestive and salivary glands, and into the stomach, then onto the intestines. Digestive and excretory wastes are collected in a cloacal bladder before being released out the anus.
Rotifers are pseudocoelomates commonly found in fresh water and some salt water environments throughout the world. Figure \(5\) shows the anatomy of a rotifer belonging to class Bdelloidea. About 2,200 species of rotifers have been identified. Rotifers are dioecious organisms (having either male or female genitalia) and exhibit sexual dimorphism (males and females have different forms). Many species are parthenogenic and exhibit haplodiploidy, a method of gender determination in which a fertilized egg develops into a female and an unfertilized egg develops into a male. In many dioecious species, males are short-lived and smaller with no digestive system and a single testis. Females can produce eggs that are capable of dormancy for protection during harsh environmental conditions.
Phylum Nemertea
The Nemertea are colloquially known as ribbon worms. Most species of phylum Nemertea are marine, predominantly benthic or bottom dwellers, with an estimated 900 species known. However, nemertini have been recorded in freshwater and terrestrial habitats as well. Most nemerteans are carnivores, feeding on worms, clams, and crustaceans. Some species are scavengers, and some nemertini species, like Malacobdella grossa, have also evolved commensalistic relationships with some mollusks. Some species have devastated commercial fishing of clams and crabs. Nemerteans have almost no predators and two species are sold as fish bait.
Morphology
Ribbon worms vary in size from 1 cm to several meters. They show bilateral symmetry and remarkable contractile properties. Because of their contractility, they can change their morphological presentation in response to environmental cues. Animals in phylum Nemertea show a flattened morphology, that is, they are flat from front to back, like a flattened tube. Nemertea are soft and unsegmented animals (Figure \(6\)).
A unique characteristic of this phylum is the presence of a proboscis enclosed in a rhynchocoel. The proboscis serves to capture food and may be ornamented with barbs in some species. The rhynchocoel is a fluid-filled cavity that extends from the head to nearly two-thirds of the length of the gut in these animals (Figure \(7\)). The proboscis may be extended or retracted by the retractor muscle attached to the wall of the rhynchocoel.
Digestive System
The nemertini show a very well-developed digestive system. A mouth opening that is ventral to the rhynchocoel leads into the foregut, followed by the intestine. The intestine is present in the form of diverticular pouches and ends in a rectum that opens via an anus. Gonads are interspersed with the intestinal diverticular pouches and open outwards via genital pores. A circulatory system consists of a closed loop of a pair of lateral blood vessels. The circulatory system is derived from the coelomic cavity of the embryo. Some animals may also have cross-connecting vessels in addition to lateral ones. Although these are called blood vessels, since they are of coelomic origin, the circulatory fluid is colorless. Some species bear hemoglobin as well as other yellow or green pigments. The blood vessels are connected to the rhynchocoel. The flow of fluid in these vessels is facilitated by the contraction of muscles in the body wall. A pair of protonephridia, or primitive kidneys, is present in these animals to facilitate osmoregulation. Gaseous exchange occurs through the skin in the nemertini.
Nervous System
Nemertini have a ganglion or “brain” situated at the anterior end between the mouth and the foregut, surrounding the digestive system as well as the rhynchocoel. A ring of four nerve masses called “ganglia” composes the brain in these animals. Paired longitudinal nerve cords emerge from the brain ganglia and extend to the posterior end. Ocelli or eyespots are present in pairs, in multiples of two in the anterior portion of the body. It is speculated that the eyespots originate from neural tissue and not from the epidermis.
Reproduction
Animals in phylum Nemertea show sexual dimorphism, although freshwater species may be hermaphroditic. Eggs and sperm are released into the water, and fertilization occurs externally. The zygote then develops into a planuliform larva. In some nemertine species, a pilidium larva may develop inside the young worm, from a series of imaginal discs. This larval form, characteristically shaped like a deerstalker cap, devours tissues from the young worm for survival before metamorphosing into the adult-like morphology.
Phylum Mollusca
Phylum Mollusca is the predominant phylum in marine environments. It is estimated that 23 percent of all known marine species are mollusks; there are over 75,000 described species, making them the second most diverse phylum of animals. The name “mollusca” signifies a soft body, since the earliest descriptions of mollusks came from observations of unshelled cuttlefish. Mollusks are predominantly a marine group of animals; however, they are known to inhabit freshwater as well as terrestrial habitats. Mollusks display a wide range of morphologies in each class and subclass, but share a few key characteristics, including a muscular foot, a visceral mass containing internal organs, and a mantle that may or may not secrete a shell of calcium carbonate (Figure \(8\)).
Exercise \(1\)
Which of the following statements about the anatomy of a mollusk is false?
1. Mollusks have a radula for grinding food.
2. A digestive gland is connected to the stomach.
3. The tissue beneath the shell is called the mantle.
4. The digestive system includes a gizzard, a stomach, a digestive gland, and the intestine.
Answer
d
Mollusks have a muscular foot, which is used for locomotion and anchorage, and varies in shape and function, depending on the type of mollusk under study. In shelled mollusks, this foot is usually the same size as the opening of the shell. The foot is a retractable as well as an extendable organ. The foot is the ventral-most organ, whereas the mantle is the limiting dorsal organ. Mollusks are eucoelomate, but the coelomic cavity is restricted to a cavity around the heart in adult animals. The mantle cavity develops independently of the coelomic cavity.
The visceral mass is present above the foot, in the visceral hump. This includes digestive, nervous, excretory, reproductive, and respiratory systems. Mollusk species that are exclusively aquatic have gills for respiration, whereas some terrestrial species have lungs for respiration. Additionally, a tongue-like organ called a radula, which bears chitinous tooth-like ornamentation, is present in many species, and serves to shred or scrape food. The mantle (also known as the pallium) is the dorsal epidermis in mollusks; shelled mollusks are specialized to secrete a chitinous and hard calcareous shell.
Most mollusks are dioecious animals and fertilization occurs externally, although this is not the case in terrestrial mollusks, such as snails and slugs, or in cephalopods. In some mollusks, the zygote hatches and undergoes two larval stages—trochophore and veliger—before becoming a young adult; bivalves may exhibit a third larval stage, glochidia.
Classification of Phylum Mollusca
Phylum Mollusca is a very diverse (85,000 species) group of mostly marine species. Mollusks have a dramatic variety of form, ranging from large predatory squids and octopus, some of which show a high degree of intelligence, to grazing forms with elaborately sculpted and colored shells. This phylum can be segregated into seven classes: Aplacophora, Monoplacophora, Polyplacophora, Bivalvia, Gastropoda, Cephalopoda, and Scaphopoda.
Class Aplacophora (“bearing no plates”) includes worm-like animals primarily found in benthic marine habitats. These animals lack a calcareous shell but possess aragonite spicules on their epidermis. They have a rudimentary mantle cavity and lack eyes, tentacles, and nephridia (excretory organs). Members of class Monoplacophora (“bearing one plate”) posses a single, cap-like shell that encloses the body. The morphology of the shell and the underlying animal can vary from circular to ovate. A looped digestive system, multiple pairs of excretory organs, many gills, and a pair of gonads are present in these animals. The monoplacophorans were believed extinct and only known via fossil records until the discovery of Neopilina galathaea in 1952. Today, scientists have identified nearly two dozen extant species.
Animals in the class Polyplacophora (“bearing many plates”) are commonly known as “chitons” and bear an armor-like eight-plated shell (Figure \(9\)). These animals have a broad, ventral foot that is adapted for suction to rocks and other substrates, and a mantle that extends beyond the shell in the form of a girdle. Calcareous spines may be present on the girdle to offer protection from predators. Respiration is facilitated by ctenidia (gills) that are present ventrally. These animals possess a radula that is modified for scraping. The nervous system is rudimentary with only buccal or “cheek” ganglia present at the anterior end. Eyespots are absent in these animals. A single pair of nephridia for excretion is present.
Class Bivalvia (“two shells”) includes clams, oysters, mussels, scallops, and geoducks. Members of this class are found in marine as well as freshwater habitats. As the name suggests, bivalves are enclosed in a pair of shells (valves are commonly called “shells”) that are hinged at the dorsal end by shell ligaments as well as shell teeth (Figure \(10\)). The overall morphology is laterally flattened, and the head region is poorly developed. Eyespots and statocysts may be absent in some species. Since these animals are suspension feeders, a radula is absent in this class of mollusks. Respiration is facilitated by a pair of ctenidia, whereas excretion and osmoregulation are brought about by a pair of nephridia. Bivalves often possess a large mantle cavity. In some species, the posterior edges of the mantle may fuse to form two siphons that serve to take in and exude water.
One of the functions of the mantle is to secrete the shell. Some bivalves like oysters and mussels possess the unique ability to secrete and deposit a calcareous nacre or “mother of pearl” around foreign particles that may enter the mantle cavity. This property has been commercially exploited to produce pearls.
Animals in class Gastropoda (“stomach foot”) include well-known mollusks like snails, slugs, conchs, sea hares, and sea butterflies. Gastropoda includes shell-bearing species as well as species with a reduced shell. These animals are asymmetrical and usually present a coiled shell (Figure \(11\)). Shells may be planospiral (like a garden hose wound up), commonly seen in garden snails, or conispiral, (like a spiral staircase), commonly seen in marine conches.
The visceral mass in the shelled species displays torsion around the perpendicular axis on the center of the foot, which is the key characteristic of this group, along with a foot that is modified for crawling (Figure \(12\)). Most gastropods bear a head with tentacles, eyes, and a style. A complex radula is used by the digestive system and aids in the ingestion of food. Eyes may be absent in some gastropods species. The mantle cavity encloses the ctenidia as well as a pair of nephridia.
Everyday Connection: Can Snail Venom Be Used as a Pharmacological Painkiller?
Marine snails of the genus Conus (Figure \(13\)) attack prey with a venomous sting. The toxin released, known as conotoxin, is a peptide with internal disulfide linkages. Conotoxins can bring about paralysis in humans, indicating that this toxin attacks neurological targets. Some conotoxins have been shown to block neuronal ion channels. These findings have led researchers to study conotoxins for possible medical applications.
Conotoxins are an exciting area of potential pharmacological development, since these peptides may be possibly modified and used in specific medical conditions to inhibit the activity of specific neurons. For example, these toxins may be used to induce paralysis in muscles in specific health applications, similar to the use of botulinum toxin. Since the entire spectrum of conotoxins, as well as their mechanisms of action, are not completely known, the study of their potential applications is still in its infancy. Most research to date has focused on their use to treat neurological diseases. They have also shown some efficacy in relieving chronic pain, and the pain associated with conditions like sciatica and shingles. The study and use of biotoxins—toxins derived from living organisms—are an excellent example of the application of biological science to modern medicine.
Class Cephalopoda (“head foot” animals), include octopuses, squids, cuttlefish, and nautilus. Cephalopods are a class of shell-bearing animals as well as mollusks with a reduced shell. They display vivid coloration, typically seen in squids and octopuses, which is used for camouflage. All animals in this class are carnivorous predators and have beak-like jaws at the anterior end. All cephalopods show the presence of a very well-developed nervous system along with eyes, as well as a closed circulatory system. The foot is lobed and developed into tentacles, and a funnel, which is used as their mode of locomotion. Suckers are present on the tentacles in octopuses and squid. Ctenidia are enclosed in a large mantle cavity and are serviced by large blood vessels, each with its own heart associated with it; the mantle has siphonophores that facilitate exchange of water.
Locomotion in cephalopods is facilitated by ejecting a stream of water for propulsion. This is called “jet” propulsion. A pair of nephridia is present within the mantle cavity. Sexual dimorphism is seen in this class of animals. Members of a species mate, and the female then lays the eggs in a secluded and protected niche. Females of some species care for the eggs for an extended period of time and may end up dying during that time period. Cephalopods such as squids and octopuses also produce sepia or a dark ink, which is squirted upon a predator to assist in a quick getaway.
Reproduction in cephalopods is different from other mollusks in that the egg hatches to produce a juvenile adult without undergoing the trochophore and veliger larval stages.
In the shell-bearing Nautilus spp., the spiral shell is multi-chambered. These chambers are filled with gas or water to regulate buoyancy. The shell structure in squids and cuttlefish is reduced and is present internally in the form of a squid pen and cuttlefish bone, respectively. Examples are shown in Figure \(14\).
Members of class Scaphopoda (“boat feet”) are known colloquially as “tusk shells” or “tooth shells,” as evident when examining Dentalium, one of the few remaining scaphopod genera (Figure \(15\)). Scaphopods are usually buried in sand with the anterior opening exposed to water. These animals bear a single conical shell, which has both ends open. The head is rudimentary and protrudes out of the posterior end of the shell. These animals do not possess eyes, but they have a radula, as well as a foot modified into tentacles with a bulbous end, known as captaculae. Captaculae serve to catch and manipulate prey. Ctenidia are absent in these animals.
Phylum Annelida
Phylum Annelida includes segmented worms. These animals are found in marine, terrestrial, and freshwater habitats, but a presence of water or humidity is a critical factor for their survival, especially in terrestrial habitats. The name of the phylum is derived from the Latin word annellus, which means a small ring. Animals in this phylum show parasitic and commensal symbioses with other species in their habitat. Approximately 16,500 species have been described in phylum Annelida. The phylum includes earthworms, polychaete worms, and leeches. Annelids show protostomic development in embryonic stages and are often called “segmented worms” due to their key characteristic of metamerism, or true segmentation.
Morphology
Annelids display bilateral symmetry and are worm-like in overall morphology. Annelids have a segmented body plan wherein the internal and external morphological features are repeated in each body segment. Metamerism allows animals to become bigger by adding “compartments” while making their movement more efficient. This metamerism is thought to arise from identical teloblast cells in the embryonic stage, which give rise to identical mesodermal structures. The overall body can be divided into head, body, and pygidium (or tail). The clitellum is a reproductive structure that generates mucus that aids in sperm transfer and gives rise to a cocoon within which fertilization occurs; it appears as a fused band in the anterior third of the animal (Figure \(16\)).
Anatomy
The epidermis is protected by an acellular, external cuticle, but this is much thinner than the cuticle found in the ecdysozoans and does not require periodic shedding for growth. Circular as well as longitudinal muscles are located interior to the epidermis. Chitinous hairlike extensions, anchored in the epidermis and projecting from the cuticle, called setae/chaetae are present in every segment. Annelids show the presence of a true coelom, derived from embryonic mesoderm and protostomy. Hence, they are the most advanced worms. A well-developed and complete digestive system is present in earthworms (oligochaetes) with a mouth, muscular pharynx, esophagus, crop, and gizzard being present. The gizzard leads to the intestine and ends in an anal opening. A cross-sectional view of a body segment of an earthworm (a terrestrial type of annelid) is shown in Figure \(17\); each segment is limited by a membranous septum that divides the coelomic cavity into a series of compartments.
Annelids possess a closed circulatory system of dorsal and ventral blood vessels that run parallel to the alimentary canal as well as capillaries that service individual tissues. In addition, these vessels are connected by transverse loops in every segment. These animals lack a well-developed respiratory system, and gas exchange occurs across the moist body surface. Excretion is facilitated by a pair of metanephridia (a type of primitive “kidney” that consists of a convoluted tubule and an open, ciliated funnel) that is present in every segment towards the ventral side. Annelids show well-developed nervous systems with a nerve ring of fused ganglia present around the pharynx. The nerve cord is ventral in position and bears enlarged nodes or ganglia in each segment.
Annelids may be either monoecious with permanent gonads (as in earthworms and leeches) or dioecious with temporary or seasonal gonads that develop (as in polychaetes). However, cross-fertilization is preferred in hermaphroditic animals. These animals may also show simultaneous hermaphroditism and participate in simultaneous sperm exchange when they are aligned for copulation.
Classification of Phylum Annelida
Phylum Annelida contains the class Polychaeta (the polychaetes) and the class Oligochaeta (the earthworms, leeches and their relatives).
Earthworms are the most abundant members of the class Oligochaeta, distinguished by the presence of the clitellum as well as few, reduced chaetae (“oligo- = “few”; -chaetae = “hairs”). The number and size of chaetae are greatly diminished in Oligochaeta compared to the polychaetes (poly=many, chaetae = hairs). The many chetae of polychaetes are also arranged within fleshy, flat, paired appendages that protrude from each segment called parapodia, which may be specialized for different functions in the polychates. The subclass Hirudinea includes leeches such as Hirudo medicinalis and Hemiclepsis marginata. The class Oligochaeta includes the subclass Hirudinia and the subclass Brachiobdella. A significant difference between leeches and other annelids is the development of suckers at the anterior and posterior ends and a lack of chaetae. Additionally, the segmentation of the body wall may not correspond to the internal segmentation of the coelomic cavity. This adaptation possibly helps the leeches to elongate when they ingest copious quantities of blood from host vertebrates. The subclass Brachiobdella includes species like Branchiobdella balcanica sketi and Branchiobdella astaci, worms that show similarity with leeches as well as oligochaetes.
Summary
Phylum Annelida includes vermiform, segmented animals. Segmentation is seen in internal anatomy as well, which is called metamerism. Annelids are protostomes. These animals have well-developed neuronal and digestive systems. Some species bear a specialized band of segments known as a clitellum. Annelids show the presence numerous chitinous projections termed chaetae, and polychaetes possess parapodia. Suckers are seen in order Hirudinea. Reproductive strategies include sexual dimorphism, hermaphroditism, and serial hermaphroditism. Internal segmentation is absent in class Hirudinea.
Flatworms are acoelomate, triploblastic animals. They lack circulatory and respiratory systems, and have a rudimentary excretory system. This digestive system is incomplete in most species. There are four traditional classes of flatworms, the largely free-living turbellarians, the ectoparasitic monogeneans, and the endoparasitic trematodes and cestodes. Trematodes have complex lifecycles involving a molluscan secondary host and a primary host in which sexual reproduction takes place. Cestodes, or tapeworms, infect the digestive systems of primary vertebrate hosts.
The rotifers are microscopic, multicellular, mostly aquatic organisms that are currently under taxonomic revision. The group is characterized by the rotating, ciliated, wheel-like structure, the corona, on their head. The mastax or jawed pharynx is another structure unique to this group of organisms.
The nemertini are the simplest eucoelomates. These ribbon-shaped animals bear a specialized proboscis enclosed within a rhynchocoel. The development of a closed circulatory system derived from the coelom is a significant difference seen in this species compared to other pseudocoelomate phyla. Alimentary, nervous, and excretory systems are more developed in the nemertini than in less advanced phyla. Embryonic development of nemertine worms proceeds via a planuliform larval stage.
Phylum Mollusca is a large, marine group of invertebrates. Mollusks show a variety of morphological variations within the phylum. This phylum is also distinct in that some members exhibit a calcareous shell as an external means of protection. Some mollusks have evolved a reduced shell. Mollusks are protostomes. The dorsal epidermis in mollusks is modified to form the mantle, which encloses the mantle cavity and visceral organs. This cavity is quite distinct from the coelomic cavity, which in the adult animal surrounds the heart. Respiration is facilitated by gills known as ctenidia. A chitinous-toothed tongue called the radula is present in most mollusks. Early development in some species occurs via two larval stages: trochophore and veliger. Sexual dimorphism is the predominant sexual strategy in this phylum. Mollusks can be divided into seven classes, each with distinct morphological characteristics.
Glossary
Annelida
phylum of vermiform animals with metamerism
captacula
tentacle-like projection that is present in tusks shells to catch prey
clitellum
specialized band of fused segments, which aids in reproduction
conispiral
shell shape coiled around a horizontal axis
corona
wheel-like structure on the anterior portion of the rotifer that contains cilia and moves food and water toward the mouth
ctenidium
specialized gill structure in mollusks
mantle
(also, pallium) specialized epidermis that encloses all visceral organs and secretes shells
mastax
jawed pharynx unique to the rotifers
metamerism
series of body structures that are similar internally and externally, such as segments
Mollusca
phylum of protostomes with soft bodies and no segmentation
nacre
calcareous secretion produced by bivalves to line the inner side of shells as well as to coat intruding particulate matter
Nemertea
phylum of dorsoventrally flattened protostomes known as ribbon worms
parapodium
fleshy, flat, appendage that protrudes in pairs from each segment of polychaetes
pilidium
larval form found in some nemertine species
planospiral
shell shape coiled around a vertical axis
planuliform
larval form found in phylum Nemertea
radula
tongue-like organ with chitinous ornamentation
rhynchocoel
cavity present above the mouth that houses the proboscis
schizocoelom
coelom formed by groups of cells that split from the endodermal layer
seta/chaeta
chitinous projection from the cuticle
trochophore
first of the two larval stages in mollusks
veliger
second of the two larval stages in mollusks
| textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/28%3A_Invertebrates/28.3%3A_Superphylum_Lophotrochozoa.txt |
Skills to Develop
• Describe the structural organization of nematodes
• Understand the importance of Caenorhabditis elegans in research
• Compare the internal systems and appendage specializations of phylum Arthropoda
• Discuss the environmental importance of arthropods
• Discuss the reasons for arthropod success and abundance
The superphylum Ecdysozoa contains an incredibly large number of species. This is because it contains two of the most diverse animal groups: phylum Nematoda (the roundworms) and Phylum Arthropoda (the arthropods). The most prominant distinguising feature of Ecdysozoans is their tough external covering called the cuticle. The cuticle provides a tough, but flexible exoskeleton tht protects these animals from water loss, predators and other aspects of the external environment. All members of this superphylum periodically molt, or shed their cuticle as they grow. After molting, they secrete a new cuticle that will last until their next growth phase. The process of molting and replacing the cuticle is called ecdysis, which is how the superphylum derived its name.
Phylum Nematoda
The Nematoda, like most other animal phyla, are triploblastic and possess an embryonic mesoderm that is sandwiched between the ectoderm and endoderm. They are also bilaterally symmetrical, meaning that a longitudinal section will divide them into right and left sides that are symmetrical. Furthermore, the nematodes, or roundworms, possess a pseudocoelom and consist of both free-living and parasitic forms.
It has been said that were all the non-nematode matter of the biosphere removed, there would remain a shadow of the former world in the form of nematodes.1 The arthropods, one of the most successful taxonomic groups on the planet, are coelomate organisms characterized by a hard exoskeleton and jointed appendages. Both the nematodes and arthropods belong to the superphylum Ecdysozoa that is believed to be a clade consisting of all evolutionary descendants from one common ancestor. The name derives from the word ecdysis, which refers to the shedding, or molting, of the exoskeleton. The phyla in this group have a hard cuticle that covers their bodies, which must be periodically shed and replaced for them to increase in size.
Phylum Nematoda includes more than 28,000 species with an estimated 16,000 being parasitic in nature. The name Nematoda is derived from the Greek word “Nemos,” which means “thread” and includes roundworms. Nematodes are present in all habitats with a large number of individuals of each species present in each. The free-living nematode, Caenorhabditis elegans has been extensively used as a model system in laboratories all over the world.
Morphology
In contrast with cnidarians, nematodes show a tubular morphology and circular cross-section. These animals are pseudocoelomates and show the presence of a complete digestive system with a distinct mouth and anus. This is in contrast with the cnidarians, where only one opening is present (an incomplete digestive system).
The cuticle of Nematodes is rich in collagen and a carbohydrate-protein polymer called chitin, and forms an external “skeleton” outside the epidermis. The cuticle also lines many of the organs internally, including the pharynx and rectum. The epidermis can be either a single layer of cells or a syncytium, which is a multinucleated cell formed from the fusion of uninucleated cells.
The overall morphology of these worms is cylindrical, as seen in Figure \(1\). The head is radially symmetrical. A mouth opening is present at the anterior end with three or six lips as well as teeth in some species in the form of cuticle extensions. Some nematodes may present other external modifications like rings, head shields, or warts. Rings, however, do not reflect true internal body segmentation. The mouth leads to a muscular pharynx and intestine, which leads to a rectum and anal opening at the posterior end. The muscles of nematodes differ from those of most animals: They have a longitudinal layer only, which accounts for the whip-like motion of their movement.
Excretory System
In nematodes, specialized excretory systems are not well developed. Nitrogenous wastes may be lost by diffusion through the entire body or into the pseudocoelom (body cavity), where they are removed by specialized cells. Regulation of water and salt content of the body is achieved by renette glands, present under the pharynx in marine nematodes.
Nervous system
Most nematodes possess four longitudinal nerve cords that run along the length of the body in dorsal, ventral, and lateral positions. The ventral nerve cord is better developed than the dorsal or lateral cords. All nerve cords fuse at the anterior end, around the pharynx, to form head ganglia or the “brain” of the worm (which take the form of a ring around the pharynx) as well as at the posterior end to form the tail ganglia. In C. elegans, the nervous system accounts for nearly one-third of the total number of cells in the animal.
Reproduction
Nematodes employ a variety of reproductive strategies that range from monoecious to dioecious to parthenogenic, depending upon the species under consideration. C. elegans is a monoecious species and shows development of ova contained in a uterus as well as sperm contained in the spermatheca. The uterus has an external opening known as the vulva. The female genital pore is near the middle of the body, whereas the male’s is at the tip. Specialized structures at the tail of the male keep him in place while he deposits sperm with copulatory spicules. Fertilization is internal, and embryonic development starts very soon after fertilization. The embryo is released from the vulva during the gastrulation stage. The embryonic development stage lasts for 14 hours; development then continues through four successive larval stages with ecdysis between each stage—L1, L2, L3, and L4—ultimately leading to the development of a young male or female adult worm. Adverse environmental conditions like overcrowding and lack of food can result in the formation of an intermediate larval stage known as the dauer larva.
Everyday Connection: C. elegans: The Model System for Linking Developmental Studies with Genetics
If biologists wanted to research how nicotine dependence develops in the body, how lipids are regulated, or observe the attractant or repellant properties of certain odors, they would clearly need to design three very different experiments. However, they might only need one object of study: C. elegans. The nematode Caenorhabditis elegans was brought into the focus of mainstream biological research by Dr. Sydney Brenner. Since 1963, Dr. Brenner and scientists worldwide have used this animal as a model system to study various physiological and developmental mechanisms.
C. elegans is a free-living organism found in soil. It is easy to culture this organism on agar plates (10,000 worms/plate), it feeds on Escherichia coli (another long-term resident of biological laboratories worldwide), and therefore, it can be readily grown and maintained in a laboratory. The biggest asset of this nematode is its transparency, which helps researchers to observe and monitor changes within the animal with ease. It is also a simple organism with fewer than 1,000 cells and a genome of 20,000 genes. It shows chromosomal organization of DNA into five pairs of autosomes plus a pair of sex chromosomes, making it an ideal candidate to study genetics. Since every cell can be visualized and identified, this organism is useful for studying cellular phenomena like cell-cell interactions, cell-fate determinations, cell division, apoptosis, and intracellular transport.
Another tremendous asset is the short life cycle of this worm (Figure \(2\)). It takes only 3 days to achieve the “egg to adult to daughter egg;” therefore, tracking genetic changes is easier in this animal. The total life span of C. elegans is 2 to 3 weeks; hence, age-related phenomena are easy to observe. Another feature that makes C. elegans an excellent experimental model system is that the position and number of the 959 cells present in adult hermaphrodites of this organism is constant. This feature is extremely significant when studying cell differentiation, cell-cell communication, and apoptosis. Lastly, C. elegans is also amenable to genetic manipulations using molecular methods, rounding off its usefulness as a model system.
Biologists worldwide have created information banks and groups dedicated to research using C. elegans. Their findings have led, for example, to better understandings of cell communication during development, neuronal signaling and insight into lipid regulation (which is important in addressing health issues like the development of obesity and diabetes). In recent years, studies have enlightened the medical community with a better understanding of polycystic kidney disease. This simple organism has led biologists to complex and significant findings, growing the field of science in ways that touch the everyday world.
A number of common parasitic nematodes serve as prime examples of parasitism. These animals exhibit complex lifecycles that involve multiple hosts, and they can have significant medical and veterinary impacts. Humans may become infected by Dracunculus medinensis, known as guinea worms, when they drink unfiltered water containing copepods (Figure \(3\)). Hookworms, such as Ancyclostoma and Necator, infest the intestines and feed on the blood of mammals, especially in dogs, cats, and humans. Trichina worms (Trichinella) are the causal organism of trichinosis in humans, often resulting from the consumption of undercooked pork; Trichinella can infect other mammalian hosts as well. Ascaris, a large intestinal roundworm, steals nutrition from its human host and may create physical blockage of the intestines. The filarial worms, such as Dirofilaria and Wuchereria, are commonly vectored by mosquitoes, which pass the infective agents among mammals through their blood-sucking activity. Dirofilaria immitis, a blood-infective parasite, is the notorious dog heartworm species. Wuchereria bancrofti infects the lymph nodes of humans, resulting in the non-lethal but deforming condition called elephantiasis, in which parts of the body become swelled to gigantic proportions due to obstruction of lymphatic drainage and inflammation of lymphatic tissues.
Phylum Arthropoda
The name “arthropoda” means “jointed legs” (in the Greek, “arthros” means “joint” and “podos” means “leg”); it aptly describes the enormous number of invertebrates included in this phylum. Arthropoda dominate the animal kingdom with an estimated 85 percent of known species included in this phylum and many arthropods yet undocumented. The principal characteristics of all the animals in this phylum are functional segmentation of the body and presence of jointed appendages. Arthropods also show the presence of an exoskeleton made principally of chitin, which is a waterproof, tough polysaccharide. Phylum Arthropoda is the largest phylum in the animal world, and insects form the single largest class within this phylum. Arthropods are eucoelomate, protostomic organisms.
Phylum Arthropoda includes animals that have been successful in colonizing terrestrial, aquatic, and aerial habitats. This phylum is further classified into five subphyla: Trilobitomorpha (trilobites, all extinct), Hexapoda (insects and relatives), Myriapoda (millipedes, centipedes, and relatives), Crustaceans (crabs, lobsters, crayfish, isopods, barnacles, and some zooplankton), and Chelicerata (horseshoe crabs, arachnids, scorpions, and daddy longlegs). Trilobites are an extinct group of arthropods found chiefly in the pre-Cambrian Era that are probably most closely related to the Chelicerata. These are identified based on fossil records (Figure \(4\)).
Morphology
A unique feature of animals in the arthropod phylum is the presence of a segmented body and fusion of sets of segments that give rise to functional body regions called tagma. Tagma may be in the form of a head, thorax, and abdomen, or a cephalothorax and abdomen, or a head and trunk. A central cavity, called the hemocoel (or blood cavity), is present, and the open circulatory system is regulated by a tubular or single-chambered heart. Respiratory systems vary depending on the group of arthropod: insects and myriapods use a series of tubes (tracheae) that branch through the body, open to the outside through openings called spiracles, and perform gas exchange directly between the cells and air in the tracheae, whereas aquatic crustaceans utilize gills, terrestrial chelicerates employ book lungs, and aquatic chelicerates use book gills (Figure \(5\)). The book lungs of arachnids (scorpions, spiders, ticks and mites) contain a vertical stack of hemocoel wall tissue that somewhat resembles the pages of a book. Between each of the "pages" of tissue is an air space. This allows both sides of the tissue to be in contact with the air at all times, greatly increasing the efficiency of gas exchange. The gills of crustaceans are filamentous structures that exchange gases with the surrounding water. Groups of arthropods also differ in the organs used for excretion, with crustaceans possessing green glands and insects using Malpighian tubules, which work in conjunction with the hindgut to reabsorb water while ridding the body of nitrogenous waste. The cuticle is the covering of an arthropod. It is made up of two layers: the epicuticle, which is a thin, waxy water-resistant outer layer containing no chitin, and the layer beneath it, the chitinous procuticle. Chitin is a tough, flexible polysaccharide. In order to grow, the arthropod must shed the exoskeleton during a process called ecdysis (“to strip off”); this is a cumbersome method of growth, and during this time, the animal is vulnerable to predation. The characteristic morphology of representative animals from each subphylum is described below.
Subphylum Hexapoda
The name Hexapoda denotes the presence of six legs (three pairs) in these animals as differentiated from the number of pairs present in other arthropods. Hexapods are characterized by the presence of a head, thorax, and abdomen, constituting three tagma. The thorax bears the wings as well as six legs in three pairs. Many of the common insects we encounter on a daily basis—including ants, cockroaches, butterflies, and flies—are examples of Hexapoda.
Amongst the hexapods, the insects (Figure \(6\)) are the largest class in terms of species diversity as well as biomass in terrestrial habitats. Typically, the head bears one pair of sensory antennae, mandibles as mouthparts, a pair of compound eyes, and some ocelli (simple eyes) along with numerous sensory hairs. The thorax bears three pairs of legs (one pair per segment) and two pairs of wings, with one pair each on the second and third thoracic segments. The abdomen usually has eleven segments and bears reproductive apertures. Hexapoda includes insects that are winged (like fruit flies) and wingless (like fleas).
Exercise \(1\)
Which of the following statements about insects is false?
1. Insects have both dorsal and ventral blood vessels.
2. Insects have spiracles, openings that allow air to enter.
3. The trachea is part of the digestive system.
4. Insects have a developed digestive system with a mouth, crop, and intestine.
Answer
c
Subphylum Myriapoda
Subphylum Myriapoda includes arthropods with numerous legs. Although the name is hyperbolic in suggesting that myriad legs are present in these invertebrates, the number of legs may vary from 10 to 750. This subphylum includes 13,000 species; the most commonly found examples are millipedes and centipedes. All myriapods are terrestrial animals and prefer a humid environment.
Myriapods are typically found in moist soils, decaying biological material, and leaf litter. Subphylum Myriapoda is divided into four classes: Chilopoda, Symphyla, Diplopoda, and Pauropoda. Centipedes like Scutigera coleoptrata (Figure 28.4.7) are classified as chilopods. These animals bear one pair of legs per segment, mandibles as mouthparts, and are somewhat dorsoventrally flattened. The legs in the first segment are modified to form forcipules (poison claws) that deliver poison to prey like spiders and cockroaches, as these animals are all predatory. Millipedes bear two pairs of legs per diplosegment, a feature that results from embryonic fusion of adjacent pairs of body segments, are usually rounder in cross-section, and are herbivores or detritivores. Millipedes have visibly more numbers of legs as compared to centipedes, although they do not bear a thousand legs (Figure \(7\)).
Subphylum Crustacea
Crustaceans are the most dominant aquatic arthropods, since the total number of marine crustacean species stands at 67,000, but there are also freshwater and terrestrial crustacean species. Krill, shrimp, lobsters, crabs, and crayfish are examples of crustaceans (Figure \(8\)). Terrestrial species like the wood lice (Armadillidium spp.) (also called pill bugs, rolly pollies, potato bugs, or isopods) are also crustaceans, although the number of non-aquatic species in this subphylum is relatively low.
Crustaceans possess two pairs of antennae, mandibles as mouthparts, and biramous (“two branched”) appendages, which means that their legs are formed in two parts, as distinct from the uniramous (“one branched”) myriapods and hexapods (Figure \(9\)).
Unlike that of the Hexapoda, the head and thorax of most crustaceans is fused to form a cephalothorax (Figure \(10\)), which is covered by a plate called the carapace, thus producing a body structure of two tagma. Crustaceans have a chitinous exoskeleton that is shed by molting whenever the animal increases in size. The exoskeletons of many species are also infused with calcium carbonate, which makes them even stronger than in other arthropods. Crustaceans have an open circulatory system where blood is pumped into the hemocoel by the dorsally located heart. Hemocyanin and hemoglobin are the respiratory pigments present in these animals.
Most crustaceans are dioecious, which means that the sexes are separate. Some species like barnacles may be hermaphrodites. Serial hermaphroditism, where the gonad can switch from producing sperm to ova, may also be seen in some species. Fertilized eggs may be held within the female of the species or may be released in the water. Terrestrial crustaceans seek out damp spaces in their habitats to lay eggs.
Larval stages—nauplius and zoea—are seen in the early development of crustaceans. A cypris larva is also seen in the early development of barnacles (Figure \(11\)).
Crustaceans possess a tripartite brain and two compound eyes. Most crustaceans are carnivorous, but herbivorous and detritivorous species are also known. Crustaceans may also be cannibalistic when extremely high populations of these organisms are present.
Subphylum Chelicerata
This subphylum includes animals such as spiders, scorpions, horseshoe crabs, and sea spiders. This subphylum is predominantly terrestrial, although some marine species also exist. An estimated 77,000 species are included in subphylum Chelicerata. Chelicerates are found in almost all habitats.
The body of chelicerates may be divided into two parts: prosoma and opisthosoma, which are basically the equivalents of cephalothorax (usually smaller) and abdomen (usually larger). A “head” tagmum is not usually discernible. The phylum derives its name from the first pair of appendages: the chelicerae (Figure \(12\)), which are specialized, claw-like or fang-like mouthparts. These animals do not possess antennae. The second pair of appendages is known as pedipalps. In some species, like sea spiders, an additional pair of appendages, called ovigers, is present between the chelicerae and pedipalps.
Chelicerae are mostly used for feeding, but in spiders, these are often modified into fangs that inject venom into their prey before feeding (Figure \(13\)). Members of this subphylum have an open circulatory system with a heart that pumps blood into the hemocoel. Aquatic species have gills, whereas terrestrial species have either trachea or book lungs for gaseous exchange.
Most chelicerates ingest food using a preoral cavity formed by the chelicerae and pedipalps. Some chelicerates may secrete digestive enzymes to pre-digest food before ingesting it. Parasitic chelicerates like ticks and mites have evolved blood-sucking apparatuses.
The nervous system in chelicerates consists of a brain and two ventral nerve cords. These animals use external fertilization as well as internal fertilization strategies for reproduction, depending upon the species and its habitat. Parental care for the young ranges from absolutely none to relatively prolonged care.
Summary
Nematodes are pseudocoelomate animals akin to flatworms, yet display more advanced neuronal development, a complete digestive system, and a body cavity. This phylum includes free-living as well as parasitic organisms like Caenorhabditis elegans and Ascaris spp., respectively. They include dioeceous as well as hermaphroditic species. Nematodes also possess an excretory system that is not quite well developed. Embryonic development is external and proceeds via three larval stages. A peculiar feature of nematodes is the secretion of a collagenous/chitinous cuticle outside the body.
Arthropods represent the most successful phylum of animal on Earth, in terms of the number of species as well as the number of individuals. These animals are characterized by a segmented body as well as the presence of jointed appendages. In the basic body plan, a pair of appendages is present per body segment. Within the phylum, traditional classification is based on mouthparts, number of appendages, and modifications of appendages present. Arthropods bear a chitinous exoskeleton. Gills, trachea, and book lungs facilitate respiration. Sexual dimorphism is seen in this phylum, and embryonic development includes multiple larval stages.
Footnotes
1. 1 Stoll, N. R., “This wormy world. 1947,” Journal of Parasitology 85(3) (1999): 392-396.
Glossary
Arthropoda
phylum of animals with jointed appendages
biramous
referring to two branches per appendage
cephalothorax
fused head and thorax in some species
chelicera
modified first pair of appendages in subphylum Chelicerata
cuticle (animal)
the tough, external layer possessed by members of the invertebrate class Ecdysozoa that is periodically molted and replaced
cypris
larval stage in the early development of crustaceans
hemocoel
internal body cavity seen in arthropods
hermaphrodite
referring to an animal where both male and female gonads are present in the same individual
nauplius
larval stage in the early development of crustaceans
Nematoda
phylum of worm-like animals that are triploblastic, pseudocoelomates that can be free-living or parasitic
oviger
additional pair of appendages present on some arthropods between the chelicerae and pedipalps
pedipalp
second pair of appendages in Chelicerata
uniramous
referring to one branch per appendage
zoea
larval stage in the early development of crustaceans
| textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/28%3A_Invertebrates/28.4%3A_Superphylum_Ecdysozoa.txt |
Skills to Develop
• Describe the distinguishing characteristics of echinoderms
• Describe the distinguishing characteristics of chordates
The phyla Echinodermata and Chordata (the phylum in which humans are placed) both belong to the superphylum Deuterostomia. Recall that protostome and deuterostomes differ in certain aspects of their embryonic development, and they are named based on which opening of the digestive cavity develops first. The word deuterostome comes from the Greek word meaning “mouth second,” indicating that the anus is the first to develop. There are a series of other developmental characteristics that differ between protostomes and deuterostomes, including the mode of formation of the coelom and the early cell division of the embryo. In deuterostomes, internal pockets of the endodermal lining called the archenteron fuse to form the coelom. The endodermal lining of the archenteron (or the primitive gut) forms membrane protrusions that bud off and become the mesodermal layer. These buds, known as coelomic pouches, fuse to form the coelomic cavity, as they eventually separate from the endodermal layer. The resultant coelom is termed an enterocoelom. The archenteron develops into the alimentary canal, and a mouth opening is formed by invagination of ectoderm at the pole opposite the blastopore of the gastrula. The blastopore forms the anus of the alimentary system in the juvenile and adult forms. The fates of embryonic cells in deuterostomes can be altered if they are experimentally moved to a different location in the embryo due to indeterminant cleavage in early embryogenesis.
Phylum Echinodermata
Echinodermata are so named owing to their spiny skin (from the Greek “echinos” meaning “spiny” and “dermos” meaning “skin”), and this phylum is a collection of about 7,000 described living species. Echinodermata are exclusively marine organisms. Sea stars (Figure \(1\)), sea cucumbers, sea urchins, sand dollars, and brittle stars are all examples of echinoderms. To date, no freshwater or terrestrial echinoderms are known.
Morphology and Anatomy
Adult echinoderms exhibit pentaradial symmetry and have a calcareous endoskeleton made of ossicles, although the early larval stages of all echinoderms have bilateral symmetry. The endoskeleton is developed by epidermal cells and may possess pigment cells, giving vivid colors to these animals, as well as cells laden with toxins. Gonads are present in each arm. In echinoderms like sea stars, every arm bears two rows of tube feet on the oral side. These tube feet help in attachment to the substratum. These animals possess a true coelom that is modified into a unique circulatory system called a water vascular system. An interesting feature of these animals is their power to regenerate, even when over 75 percent of their body mass is lost.
Water Vascular System
Echinoderms possess a unique ambulacral or water vascular system, consisting of a central ring canal and radial canals that extend along each arm. Water circulates through these structures and facilitates gaseous exchange as well as nutrition, predation, and locomotion. The water vascular system also projects from holes in the skeleton in the form of tube feet. These tube feet can expand or contract based on the volume of water present in the system of that arm. By using hydrostatic pressure, the animal can either protrude or retract the tube feet. Water enters the madreporite on the aboral side of the echinoderm. From there, it passes into the stone canal, which moves water into the ring canal. The ring canal connects the radial canals (there are five in a pentaradial animal), and the radial canals move water into the ampullae, which have tube feet through which the water moves. By moving water through the unique water vascular system, the echinoderm can move and force open mollusk shells during feeding.
Nervous System
The nervous system in these animals is a relatively simple structure with a nerve ring at the center and five radial nerves extending outward along the arms. Structures analogous to a brain or derived from fusion of ganglia are not present in these animals.
Excretory System
Podocytes, cells specialized for ultrafiltration of bodily fluids, are present near the center of echinoderms. These podocytes are connected by an internal system of canals to an opening called the madreporite.
Reproduction
Echinoderms are sexually dimorphic and release their eggs and sperm cells into water; fertilization is external. In some species, the larvae divide asexually and multiply before they reach sexual maturity. Echinoderms may also reproduce asexually, as well as regenerate body parts lost in trauma.
Classes of Echinoderms
This phylum is divided into five extant classes: Asteroidea (sea stars), Ophiuroidea (brittle stars), Echinoidea (sea urchins and sand dollars), Crinoidea (sea lilies or feather stars), and Holothuroidea (sea cucumbers) (Figure \(2\)).
The most well-known echinoderms are members of class Asteroidea, or sea stars. They come in a large variety of shapes, colors, and sizes, with more than 1,800 species known so far. The key characteristic of sea stars that distinguishes them from other echinoderm classes includes thick arms (ambulacra) that extend from a central disk where organs penetrate into the arms. Sea stars use their tube feet not only for gripping surfaces but also for grasping prey. Sea stars have two stomachs, one of which can protrude through their mouths and secrete digestive juices into or onto prey, even before ingestion. This process can essentially liquefy the prey and make digestion easier.
Brittle stars belong to the class Ophiuroidea. Unlike sea stars, which have plump arms, brittle stars have long, thin arms that are sharply demarcated from the central disk. Brittle stars move by lashing out their arms or wrapping them around objects and pulling themselves forward. Sea urchins and sand dollars are examples of Echinoidea. These echinoderms do not have arms, but are hemispherical or flattened with five rows of tube feet that help them in slow movement; tube feet are extruded through pores of a continuous internal shell called a test. Sea lilies and feather stars are examples of Crinoidea. Both of these species are suspension feeders. Sea cucumbers of class Holothuroidea are extended in the oral-aboral axis and have five rows of tube feet. These are the only echinoderms that demonstrate “functional” bilateral symmetry as adults, because the uniquely extended oral-aboral axis compels the animal to lie horizontally rather than stand vertically.
Phylum Chordata
Animals in the phylum Chordata share four key features that appear at some stage of their development: a notochord, a dorsal hollow nerve cord, pharyngeal slits, and a post-anal tail. In some groups, some of these traits are present only during embryonic development. In addition to containing vertebrate classes, the phylum Chordata contains two clades of invertebrates: Urochordata (tunicates) and Cephalochordata (lancelets). Most tunicates live on the ocean floor and are suspension feeders. Lancelets are suspension feeders that feed on phytoplankton and other microorganisms.
Summary
Echinoderms are deuterostomic marine organisms. This phylum of animals bears a calcareous endoskeleton composed of ossicles. These animals also have spiny skin. Echinoderms possess water-based circulatory systems. A pore termed the madreporite is the point of entry and exit for water into the water vascular system. Osmoregulation is carried out by specialized cells known as podocytes.
The characteristic features of Chordata are a notochord, a dorsal hollow nerve cord, pharyngeal slits, and a post-anal tail. Chordata contains two clades of invertebrates: Urochordata (tunicates) and Cephalochordata (lancelets), together with the vertebrates in Vertebrata. Most tunicates live on the ocean floor and are suspension feeders. Lancelets are suspension feeders that feed on phytoplankton and other microorganisms.
Glossary
archenteron
primitive gut cavity within the gastrula that opens outwards via the blastopore
Chordata
phylum of animals distinguished by their possession of a notochord, a dorsal, hollow nerve cord, pharyngeal slits, and a post-anal tail at some point in their development
Echinodermata
phylum of deuterostomes with spiny skin; exclusively marine organisms
enterocoelom
coelom formed by fusion of coelomic pouches budded from the endodermal lining of the archenteron
madreporite
pore for regulating entry and exit of water into the water vascular system
water vascular system
system in echinoderms where water is the circulatory fluid | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/28%3A_Invertebrates/28.5%3A_Superphylum_Deuterostomia.txt |
28.1: Phylum Porifera
The simplest of all the invertebrates are the Parazoans, which include only the phylum Porifera: the sponges. Parazoans (“beside animals”) do not display tissue-level organization, although they do have specialized cells that perform specific functions. Sponge larvae are able to swim; however, adults are non-motile and spend their life attached to a substratum.
Review Questions
Mesohyl contains:
1. a polysaccharide gel and dead cells
2. a collagen-like gel and suspended cells for various functions
3. spicules composed of silica or calcium carbonate
4. multiple pores
Answer
B
The large central opening in the Parazoan body is called the:
1. gemmule
2. spicule
3. ostia
4. osculum
Answer
D
Cnidocytes are found in _____.
1. phylum Porifera
2. phylum Nemertea
3. phylum Nematoda
4. phylum Cnidaria
Answer
D
Cubozoans are ________.
1. polyps
2. medusoids
3. polymorphs
4. sponges
Answer
C
Free Response
Describe the different cell types and their functions in sponges.
Answer
Pinacocytes are epithelial-like cells, form the outermost layer of sponges, and enclose a jelly-like substance called mesohyl. In some sponges, porocytes form ostia, single tube-shaped cells that act as valves to regulate the flow of water into the spongocoel. Choanocytes (“collar cells”) are present at various locations, depending on the type of sponge, but they always line some space through which water flows and are used in feeding.
Describe the feeding mechanism of sponges and identify how it is different from other animals.
Answer
The sponges draw water carrying food particles into the spongocoel using the beating of flagella on the choanocytes. The food particles are caught by the collar of the choanocyte and are brought into the cell by phagocytosis. Digestion of the food particle takes place inside the cell. The difference between this and the mechanisms of other animals is that digestion takes place within cells rather than outside of cells. It means that the organism can feed only on particles smaller than the cells themselves.
Explain the function of nematocysts in cnidarians.
Answer
Nematocysts are “stinging cells” designed to paralyze prey. The nematocysts contain a neurotoxin that renders prey immobile.
Compare the structural differences between Porifera and Cnidaria.
Answer
Poriferans do not possess true tissues, while cnidarians do have tissues. Because of this difference, poriferans do not have a nervous system or muscles for locomotion, which cnidarians have.
28.2: Phylum Cnidaria
Phylum Cnidaria includes animals that show radial or biradial symmetry and are diploblastic, that is, they develop from two embryonic layers. Nearly all (about 99 percent) cnidarians are marine species. Cnidarians contain specialized cells known as cnidocytes (“stinging cells”) containing organelles called nematocysts (stingers). These cells are present around the mouth and tentacles, and serve to immobilize prey with toxins contained within the cells.
Review Questions
Annelids have a:
1. pseudocoelom
2. a true coelom
3. no coelom
4. none of the above
Answer
B
Which group of flatworms are primarily ectoparasites of fish?
1. monogeneans
2. trematodes
3. cestodes
4. turbellarians
Answer
A
A mantle and mantle cavity are present in:
1. phylum Echinodermata
2. phylum Adversoidea
3. phylum Mollusca
4. phylum Nemertea
Answer
C
The rhynchocoel is a ________.
1. circulatory system
2. fluid-filled cavity
3. primitive excretory system
4. proboscis
Answer
B
Free Response
Describe the morphology and anatomy of mollusks.
Answer
Mollusks have a large muscular foot that may be modified in various ways, such as into tentacles, but it functions in locomotion. They have a mantle, a structure of tissue that covers and encloses the dorsal portion of the animal, and secretes the shell when it is present. The mantle encloses the mantle cavity, which houses the gills (when present), excretory pores, anus, and gonadopores. The coelom of mollusks is restricted to the region around the systemic heart. The main body cavity is a hemocoel. Many mollusks have a radula near the mouth that is used for scraping food.
What are the anatomical differences between nemertines and mollusks?
Answer
Mollusks have a shell, even if it is a reduced shell. Nemertines do not have a shell. Nemertines have a proboscis; mollusks do not. Nemertines have a closed circulatory system, whereas Mollusks have an open circulatory system.
28.3: Superphylum Lophotrochozoa
Animals belonging to superphylum Lophotrochozoa are protostomes, in which the blastopore, or the point of involution of the ectoderm or outer germ layer, becomes the mouth opening to the alimentary canal. This is called protostomy or “first mouth.” In protostomy, solid groups of cells split from the endoderm or inner germ layer to form a central mesodermal layer of cells. This layer multiplies into a band and then splits internally to form the coelom.
28.4: Superphylum Ecdysozoa
The superphylum Ecdysozoa contains an incredibly large number of species. This is because it contains two of the most diverse animal groups: phylum Nematoda (the roundworms) and Phylum Arthropoda (the arthropods). The most prominant distinguising feature of Ecdysozoans is their tough external covering called the cuticle. The cuticle provides a tough, but flexible exoskeleton tht protects these animals from water loss, predators and other aspects of the external environment.
Review Questions
The embryonic development in nematodes can have up to __________ larval stages.
1. one
2. two
3. three
4. five
Answer
D
The nematode cuticle contains _____.
1. glucose
2. skin cells
3. chitin
4. nerve cells
Answer
C
Crustaceans are _____.
1. ecdysozoans
2. nematodes
3. arachnids
4. parazoans
Answer
A
Flies are_______.
1. chelicerates
2. hexapods
3. arachnids
4. crustaceans
Answer
B
Free Response
Enumerate features of Caenorhabditis elegans that make it a valuable model system for biologists.
Answer
It is a true animal with at least rudiments of the physiological systems—feeding, nervous, muscle, and reproductive—found in “higher animals” like mice and humans. It is so small that large numbers can be raised in Petri dishes. It reproduces rapidly. It is transparent so that every cell in the living animal can be seen under the microscope. Before it dies (after 2–3 weeks), it shows signs of aging and thus may provide general clues as to the aging process.
What are the different ways in which nematodes can reproduce?
Answer
There are nematodes with separate sexes and hermaphrodites in addition to species that reproduce parthenogentically. The nematode Caenorhabditis elegans has a self-fertilizing hermaphrodite sex and a pure male sex.
Describe the various superclasses that phylum Arthropoda can be divided into.
Answer
The Arthropoda include the Hexapoda, which are mandibulates with six legs, the Myriapoda, which are mandibulates with many legs and include the centipedes and millipedes, the Crustacea, which are mostly marine mandibulates, and the Chelicerata, which include the spiders and scorpions and their kin.
Compare and contrast the segmentation seen in phylum Annelida with that seen in phylum Arthropoda.
Answer
Arthropods have an exoskeleton, which is missing in annelids. Arthropod segmentation is more specialized with major organs concentrated in body tagma. Annelid segmentation is usually more uniform with the intestine extending through most segments.
28.5: Superphylum Deuterostomia
The phyla Echinodermata and Chordata (the phylum in which humans are placed) both belong to the superphylum Deuterostomia. Recall that protostome and deuterostomes differ in certain aspects of their embryonic development, and they are named based on which opening of the digestive cavity develops first. The word deuterostome comes from the Greek word meaning “mouth second,” indicating that the anus is the first to develop.
Review Questions
Echinoderms have _____.
1. triangular symmetry
2. radial symmetry
3. hexagonal symmetry
4. pentaradial symmetry
Answer
D
The circulatory fluid in echinoderms is _____.
1. blood
2. mesohyl
3. water
4. saline
Answer
C
Free Response
Describe the different classes of echinoderms using examples.
Answer
The Asteroidea are the sea stars, the Echinoidea are the sea urchins and sand dollars, the Ophiuroidea are the brittle stars, the Crinoidea are the sea lilies and feather stars, the Holothuroidea are the sea cucumbers. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/28%3A_Invertebrates/28.E%3A_Invertebrates_%28Exercises%29.txt |
Vertebrates are among the most recognizable organisms of the animal kingdom. More than 62,000 vertebrate species have been identified. The vertebrate species now living represent only a small portion of the vertebrates that have existed. The best-known extinct vertebrates are the dinosaurs, a unique group of reptiles, which reached sizes not seen before or after in terrestrial animals. They were the dominant terrestrial animals for 150 million years, until they died out in a mass extinction near the end of the Cretaceous period. Although it is not known with certainty what caused their extinction, a great deal is known about the anatomy of the dinosaurs, given the preservation of skeletal elements in the fossil record.
• 29.0: Prelude to Vertebrates
Currently, a number of vertebrate species face extinction primarily due to habitat loss and pollution. According to the International Union for the Conservation of Nature, more than 6,000 vertebrate species are classified as threatened. Amphibians and mammals are the classes with the greatest percentage of threatened species, with 29 percent of all amphibians and 21 percent of all mammals classified as threatened.
• 29.1: Chordates
Animals in the phylum Chordata share four key features that appear at some stage during their development: a notochord, a dorsal hollow nerve cord, pharyngeal slits, and a post-anal tail. In some groups, some of these are present only during embryonic development. The chordates are named for the notochord, which is a flexible, rod-shaped structure that is found in the embryonic stage of all chordates and in the adult stage of some chordate species.
• 29.2: Fishes
Modern fishes include an estimated 31,000 species. Fishes were the earliest vertebrates, with jawless species being the earliest and jawed species evolving later. They are active feeders, rather than sessile, suspension feeders. Jawless fishes—the hagfishes and lampreys—have a distinct cranium and complex sense organs including eyes, distinguishing them from the invertebrate chordates.
• 29.3: Amphibians
Amphibians are vertebrate tetrapods. Amphibia includes frogs, salamanders, and caecilians. The term amphibian loosely translates from the Greek as “dual life,” which is a reference to the metamorphosis that many frogs and salamanders undergo and their mixture of aquatic and terrestrial environments in their life cycle. Amphibians evolved during the Devonian period and were the earliest terrestrial tetrapods.
• 29.4: Reptiles
The amniotes —reptiles, birds, and mammals—are distinguished from amphibians by their terrestrially adapted egg, which is protected by amniotic membranes. The evolution of amniotic membranes meant that the embryos of amniotes were provided with their own aquatic environment, which led to less dependence on water for development and thus allowed the amniotes to branch out into drier environments.
• 29.5: Birds
The most obvious characteristic that sets birds apart from other modern vertebrates is the presence of feathers, which are modified scales. While vertebrates like bats fly without feathers, birds rely on feathers and wings, along with other modifications of body structure and physiology, for flight.
• 29.6: Mammals
Mammals are vertebrates that possess hair and mammary glands. Several other characteristics are distinctive to mammals, including certain features of the jaw, skeleton, integument, and internal anatomy. Modern mammals belong to three clades: monotremes, marsupials, and eutherians (or placental mammals).
• 29.7: The Evolution of Primates
Order Primates of class Mammalia includes lemurs, tarsiers, monkeys, apes, and humans. Non-human primates live primarily in the tropical or subtropical regions of South America, Africa, and Asia. They range in size from the mouse lemur at 30 grams (1 ounce) to the mountain gorilla at 200 kilograms (441 pounds). The characteristics and evolution of primates is of particular interest to us as it allows us to understand the evolution of our own species.
• 29.E: Vertebrates (Exercises)
Thumbnail: Red-eyed tree frog (Agalychnis callidryas). (CC BY-SA 3.0; Charlesjsharp).
29: Vertebrates
Vertebrates are among the most recognizable organisms of the animal kingdom. More than 62,000 vertebrate species have been identified. The vertebrate species now living represent only a small portion of the vertebrates that have existed. The best-known extinct vertebrates are the dinosaurs, a unique group of reptiles, which reached sizes not seen before or after in terrestrial animals. They were the dominant terrestrial animals for 150 million years, until they died out in a mass extinction near the end of the Cretaceous period. Although it is not known with certainty what caused their extinction, a great deal is known about the anatomy of the dinosaurs, given the preservation of skeletal elements in the fossil record.
Currently, a number of vertebrate species face extinction primarily due to habitat loss and pollution. According to the International Union for the Conservation of Nature, more than 6,000 vertebrate species are classified as threatened. Amphibians and mammals are the classes with the greatest percentage of threatened species, with 29 percent of all amphibians and 21 percent of all mammals classified as threatened. Attempts are being made around the world to prevent the extinction of threatened species. For example, the Biodiversity Action Plan is an international program, ratified by 188 countries, which is designed to protect species and habitats. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/29%3A_Vertebrates/29.0%3A_Prelude_to_Vertebrates.txt |
Skills to Develop
• Describe the distinguishing characteristics of chordates
• Identify the derived character of craniates that sets them apart from other chordates
• Describe the developmental fate of the notochord in vertebrates
Vertebrates are members of the kingdom Animalia and the phylum Chordata (Figure \(1\)). Recall that animals that possess bilateral symmetry can be divided into two groups—protostomes and deuterostomes—based on their patterns of embryonic development. The deuterostomes, whose name translates as “second mouth,” consist of two phyla: Chordata and Echinodermata. Echinoderms are invertebrate marine animals that have pentaradial symmetry and a spiny body covering, a group that includes sea stars, sea urchins, and sea cucumbers. The most conspicuous and familiar members of Chordata are vertebrates, but this phylum also includes two groups of invertebrate chordates.
Characteristics of Chordata
Animals in the phylum Chordata share four key features that appear at some stage during their development: a notochord, a dorsal hollow nerve cord, pharyngeal slits, and a post-anal tail (Figure \(2\)). In some groups, some of these are present only during embryonic development.
The chordates are named for the notochord, which is a flexible, rod-shaped structure that is found in the embryonic stage of all chordates and in the adult stage of some chordate species. It is located between the digestive tube and the nerve cord, and provides skeletal support through the length of the body. In some chordates, the notochord acts as the primary axial support of the body throughout the animal’s lifetime. In vertebrates, the notochord is present during embryonic development, at which time it induces the development of the neural tube and serves as a support for the developing embryonic body. The notochord, however, is not found in the postnatal stage of vertebrates; at this point, it has been replaced by the vertebral column (that is, the spine).
Art Connection
Which of the following statements about common features of chordates is true?
1. The dorsal hollow nerve cord is part of the chordate central nervous system.
2. In vertebrate fishes, the pharyngeal slits become the gills.
3. Humans are not chordates because humans do not have a tail.
4. Vertebrates do not have a notochord at any point in their development; instead, they have a vertebral column.
The dorsal hollow nerve cord derives from ectoderm that rolls into a hollow tube during development. In chordates, it is located dorsal to the notochord. In contrast, other animal phyla are characterized by solid nerve cords that are located either ventrally or laterally. The nerve cord found in most chordate embryos develops into the brain and spinal cord, which compose the central nervous system.
Pharyngeal slits are openings in the pharynx (the region just posterior to the mouth) that extend to the outside environment. In organisms that live in aquatic environments, pharyngeal slits allow for the exit of water that enters the mouth during feeding. Some invertebrate chordates use the pharyngeal slits to filter food out of the water that enters the mouth. In vertebrate fishes, the pharyngeal slits are modified into gill supports, and in jawed fishes, into jaw supports. In tetrapods, the slits are modified into components of the ear and tonsils. Tetrapod literally means “four-footed,” which refers to the phylogenetic history of various groups that evolved accordingly, even though some now possess fewer than two pairs of walking appendages. Tetrapods include amphibians, reptiles, birds, and mammals.
The post-anal tail is a posterior elongation of the body, extending beyond the anus. The tail contains skeletal elements and muscles, which provide a source of locomotion in aquatic species, such as fishes. In some terrestrial vertebrates, the tail also helps with balance, courting, and signaling when danger is near. In humans, the post-anal tail is vestigial, that is, reduced in size and nonfunctional.
Link to Learning
Click for a video discussing the evolution of chordates and five characteristics that they share.
Chordates and the Evolution of Vertebrates
Chordata also contains two clades of invertebrates: Urochordata and Cephalochordata. Members of these groups also possess the four distinctive features of chordates at some point during their development.
Urochordata
Members of Urochordata are also known as tunicates (Figure \(3\)). The name tunicate derives from the cellulose-like carbohydrate material, called the tunic, which covers the outer body of tunicates. Although adult tunicates are classified as chordates, they do not have a notochord, a dorsal hollow nerve cord, or a post-anal tail, although they do have pharyngeal slits. The larval form, however, possesses all four structures. Most tunicates are hermaphrodites. Tunicate larvae hatch from eggs inside the adult tunicate’s body. After hatching, a tunicate larva swims for a few days until it finds a suitable surface on which it can attach, usually in a dark or shaded location. It then attaches via the head to the surface and undergoes metamorphosis into the adult form, at which point the notochord, nerve cord, and tail disappear.
Most tunicates live a sessile existence on the ocean floor and are suspension feeders. The primary foods of tunicates are plankton and detritus. Seawater enters the tunicate’s body through its incurrent siphon. Suspended material is filtered out of this water by a mucous net (pharyngeal slits) and is passed into the intestine via the action of cilia. The anus empties into the excurrent siphon, which expels wastes and water. Tunicates are found in shallow ocean waters around the world.
Cephalochordata
Members of Cephalochordata possess a notochord, dorsal hollow nerve cord, pharyngeal slits, and a post-anal tail in the adult stage (Figure \(4\)). The notochord extends into the head, which gives the subphylum its name. Extinct members of this subphylum include Pikaia, which is the oldest known cephalochordate. Pikaia fossils were recovered from the Burgess shales of Canada and dated to the middle of the Cambrian age, making them more than 500 million years old.
Extant members of Cephalochordata are the lancelets, named for their blade-like shape. Lancelets are only a few centimeters long and are usually found buried in sand at the bottom of warm temperate and tropical seas. Like tunicates, they are suspension feeders.
Craniata and Vertebrata
A cranium is a bony, cartilaginous, or fibrous structure surrounding the brain, jaw, and facial bones (Figure \(5\)). Most bilaterally symmetrical animals have a head; of these, those that have a cranium compose the clade Craniata. Craniata includes the hagfishes (Myxini), which have a cranium but lack a backbone, and all of the organisms called “vertebrates.”
Vertebrates are members of the clade Vertebrata. Vertebrates display the four characteristic features of the chordates; however, members of this group also share derived characteristics that distinguish them from invertebrate chordates. Vertebrata is named for the vertebral column, composed of vertebrae, a series of separate bones joined together as a backbone (Figure \(6\)). In adult vertebrates, the vertebral column replaces the notochord, which is only seen in the embryonic stage.
Based on molecular analysis, vertebrates appear to be more closely related to lancelets (cephalochordates) than to tunicates (urochordates) among the invertebrate chordates. This evidence suggests that the cephalochordates diverged from Urochordata and the vertebrates subsequently diverged from the cephalochordates. This hypothesis is further supported by the discovery of a fossil in China from the genus Haikouella. This organism seems to be an intermediate form between cephalochordates and vertebrates. The Haikouella fossils are about 530 million years old and appear similar to modern lancelets. These organisms had a brain and eyes, as do vertebrates, but lack the skull found in craniates.1 This evidence suggests that vertebrates arose during the Cambrian explosion. Recall that the “Cambrian explosion” is the name given to a relatively brief span of time during the Cambrian period during which many animal groups appeared and rapidly diversified. Most modern animal phyla originated during the Cambrian explosion.
Vertebrates are the largest group of chordates, with more than 62,000 living species. Vertebrates are grouped based on anatomical and physiological traits. More than one classification and naming scheme is used for these animals. Here we will consider the traditional groups Agnatha, Chondrichthyes, Osteichthyes, Amphibia, Reptilia, Aves, and Mammalia, which constitute classes in the subphylum Vertebrata. Many modern authors classify birds within Reptilia, which correctly reflects their evolutionary heritage. We consider them separately only for convenience. Further, we will consider hagfishes and lampreys together as jawless fishes, the agnathans, although emerging classification schemes separate them into chordate jawless fishes (the hagfishes) and vertebrate jawless fishes (the lampreys).
Animals that possess jaws are known as gnathostomes, which means “jawed mouth.” Gnathostomes include fishes and tetrapods—amphibians, reptiles, birds, and mammals. Tetrapods can be further divided into two groups: amphibians and amniotes. Amniotes are animals whose eggs are adapted for terrestrial living, and this group includes mammals, reptiles, and birds. Amniotic embryos, developing in either an externally shed egg or an egg carried by the female, are provided with a water-retaining environment and are protected by amniotic membranes.
Summary
The characteristic features of Chordata are a notochord, a dorsal hollow nerve cord, pharyngeal slits, and a post-anal tail. Chordata contains two clades of invertebrates: Urochordata (tunicates) and Cephalochordata (lancelets), together with the vertebrates in Vertebrata. Most tunicates live on the ocean floor and are suspension feeders. Lancelets are suspension feeders that feed on phytoplankton and other microorganisms. Vertebrata is named for the vertebral column, which is a feature of almost all members of this clade.
Art Connections
Figure \(2\): Which of the following statements about common features of chordates is true?
1. The dorsal hollow nerve cord is part of the chordate central nervous system.
2. In vertebrate fishes, the pharyngeal slits become the gills.
3. Humans are not chordates because humans do not have a tail.
4. Vertebrates do not have a notochord at any point in their development; instead, they have a vertebral column.
Answer
A
Footnotes
1. 1 Chen, J. Y., Huang, D. Y., and Li, C. W., “An early Cambrian craniate-like chordate,” Nature 402 (1999): 518–522, doi:10.1038/990080.
Glossary
Cephalochordata
chordate clade whose members possess a notochord, dorsal hollow nerve cord, pharyngeal slits, and a post-anal tail in the adult stage
Chordata
phylum of animals distinguished by their possession of a notochord, a dorsal hollow nerve cord, pharyngeal slits, and a post-anal tail at some point during their development
Craniata
clade composed of chordates that possess a cranium; includes Vertebrata together with hagfishes
cranium
bony, cartilaginous, or fibrous structure surrounding the brain, jaw, and facial bones
dorsal hollow nerve cord
hollow, tubular structure derived from ectoderm, which is located dorsal to the notochord in chordates
lancelet
member of Cephalochordata; named for its blade-like shape
notochord
flexible, rod-shaped support structure that is found in the embryonic stage of all chordates and in the adult stage of some chordates
pharyngeal slit
opening in the pharynx
post-anal tail
muscular, posterior elongation of the body extending beyond the anus in chordates
tetrapod
phylogenetic reference to an organism with a four-footed evolutionary history; includes amphibians, reptiles, birds, and mammals
tunicate
sessile chordate that is a member of Urochordata
Urochordata
clade composed of tunicates
vertebral column
series of separate bones joined together as a backbone
Vertebrata
members of the phylum Chordata that possess a backbone | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/29%3A_Vertebrates/29.1%3A_Chordates.txt |
Skills to Develop
• Describe the difference between jawless and jawed fishes
• Discuss the distinguishing features of sharks and rays compared to other modern fishes
Modern fishes include an estimated 31,000 species. Fishes were the earliest vertebrates, with jawless species being the earliest and jawed species evolving later. They are active feeders, rather than sessile, suspension feeders. Jawless fishes—the hagfishes and lampreys—have a distinct cranium and complex sense organs including eyes, distinguishing them from the invertebrate chordates.
Jawless Fishes
Jawless fishes are craniates that represent an ancient vertebrate lineage that arose over one half-billion years ago. In the past, the hagfishes and lampreys were classified together as agnathans. Today, hagfishes and lampreys are recognized as separate clades, primarily because lampreys are true vertebrates, whereas hagfishes are not. A defining feature is the lack of paired lateral appendages (fins). Some of the earliest jawless fishes were the ostracoderms (which translates to “shell-skin”). Ostracoderms were vertebrate fishes encased in bony armor, unlike present-day jawless fishes, which lack bone in their scales.
Myxini: Hagfishes
The clade Myxini includes at least 20 species of hagfishes. Hagfishes are eel-like scavengers that live on the ocean floor and feed on dead invertebrates, other fishes, and marine mammals (Figure \(1\)). Hagfishes are entirely marine and are found in oceans around the world, except for the polar regions. A unique feature of these animals is the slime glands beneath the skin that release mucus through surface pores. This mucus allows the hagfish to escape from the grip of predators. Hagfish can also twist their bodies in a knot to feed and sometimes eat carcasses from the inside out.
The skeleton of a hagfish is composed of cartilage, which includes a cartilaginous notochord that runs the length of the body. This notochord provides support to the hagfish’s body. Hagfishes do not replace the notochord with a vertebral column during development, as do true vertebrates.
Petromyzontidae: Lampreys
The clade Petromyzontidae includes approximately 35–40 or more species of lampreys. Lampreys are similar to hagfishes in size and shape; however, lampreys possess some vertebral elements. Lampreys lack paired appendages and bone, as do the hagfishes. As adults, lampreys are characterized by a toothed, funnel-like sucking mouth. Many species have a parasitic stage of their life cycle during which they are ectoparasites of fishes (Figure \(2\)).
Lampreys live primarily in coastal and fresh waters, and have a worldwide distribution, except for in the tropics and polar regions. Some species are marine, but all species spawn in fresh water. Eggs are fertilized externally, and the larvae distinctly differ from the adult form, spending 3 to 15 years as suspension feeders. Once they attain sexual maturity, the adults reproduce and die within days.
Lampreys possess a notochord as adults; however, this notochord is surrounded by a cartilaginous structure called an arcualia, which may resemble an evolutionarily early form of the vertebral column.
Gnathostomes: Jawed Fishes
Gnathostomes or “jaw-mouths” are vertebrates that possess jaws. One of the most significant developments in early vertebrate evolution was the development of the jaw, which is a hinged structure attached to the cranium that allows an animal to grasp and tear its food. The evolution of jaws allowed early gnathostomes to exploit food resources that were unavailable to jawless fishes.
Early gnathostomes also possessed two sets of paired fins, allowing the fishes to maneuver accurately. Pectoral fins are typically located on the anterior body, and pelvic fins on the posterior. Evolution of the jaw and paired fins permitted gnathostomes to expand from the sedentary suspension feeding of jawless fishes to become mobile predators. The ability of gnathostomes to exploit new nutrient sources likely is one reason that they replaced most jawless fishes during the Devonian period. Two early groups of gnathostomes were the acanthodians and placoderms (Figure \(3\)), which arose in the late Silurian period and are now extinct. Most modern fishes are gnathostomes that belong to the clades Chondrichthyes and Osteichthyes.
Chondrichthyes: Cartilaginous Fishes
The clade Chondrichthyes is diverse, consisting of sharks (Figure \(4\)), rays, and skates, together with sawfishes and a few dozen species of fishes called chimaeras, or “ghost” sharks.” Chondrichthyes are jawed fishes that possess paired fins and a skeleton made of cartilage. This clade arose approximately 370 million years ago in the early or middle Devonian. They are thought to be descended from the placoderms, which had skeletons made of bone; thus, the cartilaginous skeleton of Chondrichthyes is a later development. Parts of shark skeleton are strengthened by granules of calcium carbonate, but this is not the same as bone.
Most cartilaginous fishes live in marine habitats, with a few species living in fresh water for a part or all of their lives. Most sharks are carnivores that feed on live prey, either swallowing it whole or using their jaws and teeth to tear it into smaller pieces. Shark teeth likely evolved from the jagged scales that cover their skin, called placoid scales. Some species of sharks and rays are suspension feeders that feed on plankton.
Sharks have well-developed sense organs that aid them in locating prey, including a keen sense of smell and electroreception, with the latter perhaps the most sensitive of any animal. Organs called ampullae of Lorenzini allow sharks to detect the electromagnetic fields that are produced by all living things, including their prey. Electroreception has only been observed in aquatic or amphibious animals. Sharks, together with most fishes and aquatic and larval amphibians, also have a sense organ called the lateral line, which is used to detect movement and vibration in the surrounding water, and is often considered homologous to “hearing” in terrestrial vertebrates. The lateral line is visible as a darker stripe that runs along the length of a fish’s body.
Sharks reproduce sexually, and eggs are fertilized internally. Most species are ovoviviparous: The fertilized egg is retained in the oviduct of the mother’s body and the embryo is nourished by the egg yolk. The eggs hatch in the uterus, and young are born alive and fully functional. Some species of sharks are oviparous: They lay eggs that hatch outside of the mother’s body. Embryos are protected by a shark egg case or “mermaid’s purse” (Figure \(5\)) that has the consistency of leather. The shark egg case has tentacles that snag in seaweed and give the newborn shark cover. A few species of sharks are viviparous: The young develop within the mother’s body and she gives live birth.
Rays and skates comprise more than 500 species and are closely related to sharks. They can be distinguished from sharks by their flattened bodies, pectoral fins that are enlarged and fused to the head, and gill slits on their ventral surface (Figure \(6\)). Like sharks, rays and skates have a cartilaginous skeleton. Most species are marine and live on the sea floor, with nearly a worldwide distribution.
Osteichthyes: Bony Fishes
Members of the clade Osteichthyes, also called bony fishes, are characterized by a bony skeleton. The vast majority of present-day fishes belong to this group, which consists of approximately 30,000 species, making it the largest class of vertebrates in existence today.
Nearly all bony fishes have an ossified skeleton with specialized bone cells (osteocytes) that produce and maintain a calcium phosphate matrix. This characteristic has only reversed in a few groups of Osteichthyes, such as sturgeons and paddlefish, which have primarily cartilaginous skeletons. The skin of bony fishes is often covered by overlapping scales, and glands in the skin secrete mucus that reduces drag when swimming and aids the fish in osmoregulation. Like sharks, bony fishes have a lateral line system that detects vibrations in water.
All bony fishes use gills to breathe. Water is drawn over gills that are located in chambers covered and ventilated by a protective, muscular flap called the operculum. Many bony fishes also have a swim bladder, a gas-filled organ that helps to control the buoyancy of the fish. Bony fishes are further divided into two extant clades: Actinopterygii (ray-finned fishes) and Sarcopterygii (lobe-finned fishes).
Actinopterygii, the ray-finned fishes, include many familiar fishes—tuna, bass, trout, and salmon (Figure \(7\)), among others. Ray-finned fishes are named for their fins that are webs of skin supported by bony spines called rays. In contrast, the fins of Sarcopterygii are fleshy and lobed, supported by bone (Figure \(7\)). Living members of this clade include the less-familiar lungfishes and coelacanths.
Summary
The earliest vertebrates that diverged from the invertebrate chordates were the jawless fishes. Fishes with jaws (gnathostomes) evolved later. Jaws allowed early gnathostomes to exploit new food sources. Agnathans include the hagfishes and lampreys. Hagfishes are eel-like scavengers that feed on dead invertebrates and other fishes. Lampreys are characterized by a toothed, funnel-like sucking mouth, and most species are parasitic on other fishes. Gnathostomes include the cartilaginous fishes and the bony fishes, as well as all other tetrapods. Cartilaginous fishes include sharks, rays, skates, and ghost sharks. Most cartilaginous fishes live in marine habitats, with a few species living in fresh water for part or all of their lives. The vast majority of present-day fishes belong to the clade Osteichthyes, which consists of approximately 30,000 species. Bony fishes can be divided into two clades: Actinopterygii (ray-finned fishes, virtually all extant species) and Sarcopterygii (lobe-finned fishes, comprising fewer than 10 extant species but which are the ancestors of tetrapods).
Glossary
Actinopterygii
ray-finned fishes
ampulla of Lorenzini
sensory organ that allows sharks to detect electromagnetic fields produced by living things
Chondrichthyes
jawed fish with paired fins and a skeleton made of cartilage
gnathostome
jawed fish
hagfish
eel-like jawless fish that live on the ocean floor and are scavengers
lamprey
jawless fish characterized by a toothed, funnel-like, sucking mouth
lateral line
sense organ that runs the length of a fish’s body; used to detect vibration in the water
Myxini
hagfishes
Osteichthyes
bony fish
ostracoderm
one of the earliest jawless fish covered in bone
Petromyzontidae
clade of lampreys
Sarcopterygii
lobe-finned fish
swim bladder
in fishes, a gas filled organ that helps to control the buoyancy of the fish | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/29%3A_Vertebrates/29.2%3A_Fishes.txt |
Skills to Develop
• Describe the important difference between the life cycle of amphibians and the life cycles of other vertebrates
• Distinguish between the characteristics of Urodela, Anura, and Apoda
• Describe the evolutionary history of amphibians
Amphibians are vertebrate tetrapods. Amphibia includes frogs, salamanders, and caecilians. The term amphibian loosely translates from the Greek as “dual life,” which is a reference to the metamorphosis that many frogs and salamanders undergo and their mixture of aquatic and terrestrial environments in their life cycle. Amphibians evolved during the Devonian period and were the earliest terrestrial tetrapods.
Link to Learning
Watch this series of Animal Planet videos on tetrapod evolution:
1: The evolution from fish to earliest tetrapod
2: Fish to Earliest Tetrapod
3: The discovery of coelacanth and Acanthostega fossils
4: The number of fingers on “legs”
Characteristics of Amphibians
As tetrapods, most amphibians are characterized by four well-developed limbs. Some species of salamanders and all caecilians are functionally limbless; their limbs are vestigial. An important characteristic of extant amphibians is a moist, permeable skin that is achieved via mucus glands that keep the skin moist; thus, exchange of oxygen and carbon dioxide with the environment can take place through it (cutaneous respiration). Additional characteristics of amphibians include pedicellate teeth—teeth in which the root and crown are calcified, separated by a zone of noncalcified tissue—and a papilla amphibiorum and papilla basilaris, structures of the inner ear that are sensitive to frequencies below and above 10,00 hertz, respectively. Amphibians also have an auricular operculum, which is an extra bone in the ear that transmits sounds to the inner ear. All extant adult amphibians are carnivorous, and some terrestrial amphibians have a sticky tongue that is used to capture prey.
Evolution of Amphibians
The fossil record provides evidence of the first tetrapods: now-extinct amphibian species dating to nearly 400 million years ago. Evolution of tetrapods from fishes represented a significant change in body plan from one suited to organisms that respired and swam in water, to organisms that breathed air and moved onto land; these changes occurred over a span of 50 million years during the Devonian period. One of the earliest known tetrapods is from the genus Acanthostega. Acanthostega was aquatic; fossils show that it had gills similar to fishes. However, it also had four limbs, with the skeletal structure of limbs found in present-day tetrapods, including amphibians. Therefore, it is thought that Acanthostega lived in shallow waters and was an intermediate form between lobe-finned fishes and early, fully terrestrial tetrapods. What preceded Acanthostega?
In 2006, researchers published news of their discovery of a fossil of a “tetrapod-like fish,” Tiktaalik roseae, which seems to be an intermediate form between fishes having fins and tetrapods having limbs (Figure \(1\)). Tiktaalik likely lived in a shallow water environment about 375 million years ago.1
The early tetrapods that moved onto land had access to new nutrient sources and relatively few predators. This led to the widespread distribution of tetrapods during the early Carboniferous period, a period sometimes called the “age of the amphibians.”
Modern Amphibians
Amphibia comprises an estimated 6,770 extant species that inhabit tropical and temperate regions around the world. Amphibians can be divided into three clades: Urodela (“tailed-ones”), the salamanders; Anura (“tail-less ones”), the frogs; and Apoda (“legless ones”), the caecilians.
Urodela: Salamanders
Salamanders are amphibians that belong to the order Urodela. Living salamanders (Figure \(1\)) include approximately 620 species, some of which are aquatic, other terrestrial, and some that live on land only as adults. Adult salamanders usually have a generalized tetrapod body plan with four limbs and a tail. They move by bending their bodies from side to side, called lateral undulation, in a fish-like manner while “walking” their arms and legs fore and aft. It is thought that their gait is similar to that used by early tetrapods. Respiration differs among different species. The majority of salamanders are lungless, and respiration occurs through the skin or through external gills. Some terrestrial salamanders have primitive lungs; a few species have both gills and lungs.
Unlike frogs, virtually all salamanders rely on internal fertilization of the eggs. The only male amphibians that possess copulatory structures are the caecilians, so fertilization among salamanders typically involves an elaborate and often prolonged courtship. Such a courtship allows the successful transfer of sperm from male to female via a spermatophore. Development in many of the most highly evolved salamanders, which are fully terrestrial, occurs during a prolonged egg stage, with the eggs guarded by the mother. During this time, the gilled larval stage is found only within the egg capsule, with the gills being resorbed, and metamorphosis being completed, before hatching. Hatchlings thus resemble tiny adults.
Link to Learning
View River Monsters: Fish With Arms and Hands? to see a video about an unusually large salamander species.
Anura: Frogs
Frogs are amphibians that belong to the order Anura (Figure \(3\)). Anurans are among the most diverse groups of vertebrates, with approximately 5,965 species that occur on all of the continents except Antarctica. Anurans have a body plan that is more specialized for movement. Adult frogs use their hind limbs to jump on land. Frogs have a number of modifications that allow them to avoid predators, including skin that acts as camouflage. Many species of frogs and salamanders also release defensive chemicals from glands in the skin that are poisonous to predators.
Frog eggs are fertilized externally, and like other amphibians, frogs generally lay their eggs in moist environments. A moist environment is required as eggs lack a shell and thus dehydrate quickly in dry environments. Frogs demonstrate a great diversity of parental behaviors, with some species laying many eggs and exhibiting little parental care, to species that carry eggs and tadpoles on their hind legs or backs. The life cycle of frogs, as other amphibians, consists of two distinct stages: the larval stage followed by metamorphosis to an adult stage. The larval stage of a frog, the tadpole, is often a filter-feeding herbivore. Tadpoles usually have gills, a lateral line system, long-finned tails, and lack limbs. At the end of the tadpole stage, frogs undergo metamorphosis into the adult form (Figure \(4\)). During this stage, the gills, tail, and lateral line system disappear, and four limbs develop. The jaws become larger and are suited for carnivorous feeding, and the digestive system transforms into the typical short gut of a predator. An eardrum and air-breathing lungs also develop. These changes during metamorphosis allow the larvae to move onto land in the adult stage.
Apoda: Caecilians
An estimated 185 species comprise caecilians, a group of amphibians that belong to the order Apoda. Although they are vertebrates, a complete lack of limbs leads to their resemblance to earthworms in appearance. They are adapted for a soil-burrowing or aquatic lifestyle, and they are nearly blind. These animals are found in the tropics of South America, Africa, and Southern Asia. They have vestigial limbs, evidence that they evolved from a legged ancestor.
Evolution Connection: The Paleozoic Era and the Evolution of Vertebrates
The climate and geography of Earth was vastly different during the Paleozoic Era, when vertebrates arose, as compared to today. The Paleozoic spanned from approximately 542 to 251 million years ago. The landmasses on Earth were very different from those of today. Laurentia and Gondwana were continents located near the equator that subsumed much of the current day landmasses in a different configuration (Figure \(5\)). At this time, sea levels were very high, probably at a level that hasn’t been reached since. As the Paleozoic progressed, glaciations created a cool global climate, but conditions warmed near the end of the first half of the Paleozoic. During the latter half of the Paleozoic, the landmasses began moving together, with the initial formation of a large northern block called Laurasia. This contained parts of what is now North America, along with Greenland, parts of Europe, and Siberia. Eventually, a single supercontinent, called Pangaea, was formed, starting in the latter third of the Paleozoic. Glaciations then began to affect Pangaea’s climate, affecting the distribution of vertebrate life.
During the early Paleozoic, the amount of carbon dioxide in the atmosphere was much greater than it is today. This may have begun to change later, as land plants became more common. As the roots of land plants began to infiltrate rock and soil began to form, carbon dioxide was drawn out of the atmosphere and became trapped in the rock. This reduced the levels of carbon dioxide and increased the levels of oxygen in the atmosphere, so that by the end of the Paleozoic, atmospheric conditions were similar to those of today.
As plants became more common through the latter half of the Paleozoic, microclimates began to emerge and ecosystems began to change. As plants and ecosystems continued to grow and become more complex, vertebrates moved from the water to land. The presence of shoreline vegetation may have contributed to the movement of vertebrates onto land. One hypothesis suggests that the fins of aquatic vertebrates were used to maneuver through this vegetation, providing a precursor to the movement of fins on land and the development of limbs. The late Paleozoic was a time of diversification of vertebrates, as amniotes emerged and became two different lines that gave rise, on one hand, to mammals, and, on the other hand, to reptiles and birds. Many marine vertebrates became extinct near the end of the Devonian period, which ended about 360 million years ago, and both marine and terrestrial vertebrates were decimated by a mass extinction in the early Permian period about 250 million years ago.
Link to Learning
View Earth’s Paleogeography: Continental Movements Through Time to see changes in Earth as life evolved.
Summary
As tetrapods, most amphibians are characterized by four well-developed limbs, although some species of salamanders and all caecilians are limbless. The most important characteristic of extant amphibians is a moist, permeable skin used for cutaneous respiration. The fossil record provides evidence of amphibian species, now extinct, that arose over 400 million years ago as the first tetrapods. Amphibia can be divided into three clades: salamanders (Urodela), frogs (Anura), and caecilians (Apoda). The life cycle of frogs, like the majority of amphibians, consists of two distinct stages: the larval stage and metamorphosis to an adult stage. Some species in all orders bypass a free-living larval stage.
Footnotes
1. 1 Daeschler, E. B., Shubin, N. H., and Jenkins, F. J. “A Devonian tetrapod-like fish and the evolution of the tetrapod body plan,” Nature 440 (2006): 757–763, doi:10.1038/nature04639, http://www.nature.com/nature/journal/v440/n7085/abs/nature04639.html.
Glossary
Acanthostega
one of the earliest known tetrapods
Amphibia
frogs, salamanders, and caecilians
Anura
frogs
Apoda
caecilians
caecilian
legless amphibian that belongs to the clade Apoda
cutaneous respiration
gas exchange through the skin
frog
tail-less amphibian that belongs to the clade Anura
salamander
tailed amphibian that belongs to the clade Urodela
tadpole
larval stage of a frog
Urodela
salamanders | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/29%3A_Vertebrates/29.3%3A_Amphibians.txt |
Skills to Develop
• Describe the main characteristics of amniotes
• Explain the difference between anapsids, synapsids, and diapsids, and give an example of each
• Identify the characteristics of reptiles
• Discuss the evolution of reptiles
The amniotes —reptiles, birds, and mammals—are distinguished from amphibians by their terrestrially adapted egg, which is protected by amniotic membranes. The evolution of amniotic membranes meant that the embryos of amniotes were provided with their own aquatic environment, which led to less dependence on water for development and thus allowed the amniotes to branch out into drier environments. This was a significant development that distinguished them from amphibians, which were restricted to moist environments due their shell-less eggs. Although the shells of various amniotic species vary significantly, they all allow retention of water. The shells of bird eggs are composed of calcium carbonate and are hard, but fragile. The shells of reptile eggs are leathery and require a moist environment. Most mammals do not lay eggs (except for monotremes). Instead, the embryo grows within the mother’s body; however, even with this internal gestation, amniotic membranes are still present.
Characteristics of Amniotes
The amniotic egg is the key characteristic of amniotes. In amniotes that lay eggs, the shell of the egg provides protection for the developing embryo while being permeable enough to allow for the exchange of carbon dioxide and oxygen. The albumin, or egg white, provides the embryo with water and protein, whereas the fattier egg yolk is the energy supply for the embryo, as is the case with the eggs of many other animals, such as amphibians. However, the eggs of amniotes contain three additional extra-embryonic membranes: the chorion, amnion, and allantois (Figure \(1\)). Extra-embryonic membranes are membranes present in amniotic eggs that are not a part of the body of the developing embryo. While the inner amniotic membrane surrounds the embryo itself, the chorion surrounds the embryo and yolk sac. The chorion facilitates exchange of oxygen and carbon dioxide between the embryo and the egg’s external environment. The amnion protects the embryo from mechanical shock and supports hydration. The allantois stores nitrogenous wastes produced by the embryo and also facilitates respiration. In mammals, membranes that are homologous to the extra-embryonic membranes in eggs are present in the placenta.
Art Connection
Which of the following statements about the parts of an egg are false?
1. The allantois stores nitrogenous waste and facilitates respiration.
2. The chorion facilitates gas exchange.
3. The yolk provides food for the growing embryo.
4. The amniotic cavity is filled with albumen.
Additional derived characteristics of amniotes include waterproof skin, due to the presence of lipids, and costal (rib) ventilation of the lungs.
Evolution of Amniotes
The first amniotes evolved from amphibian ancestors approximately 340 million years ago during the Carboniferous period. The early amniotes diverged into two main lines soon after the first amniotes arose. The initial split was into synapsids and sauropsids. Synapsids include all mammals, including extinct mammalian species. Synapsids also include therapsids, which were mammal-like reptiles from which mammals evolved. Sauropsids include reptiles and birds, and can be further divided into anapsids and diapsids. The key differences between the synapsids, anapsids, and diapsids are the structures of the skull and the number of temporal fenestrae behind each eye (Figure \(2\)). Temporal fenestrae are post-orbital openings in the skull that allow muscles to expand and lengthen. Anapsids have no temporal fenestrae, synapsids have one, and diapsids have two. Anapsids include extinct organisms and may, based on anatomy, include turtles. However, this is still controversial, and turtles are sometimes classified as diapsids based on molecular evidence. The diapsids include birds and all other living and extinct reptiles.
The diapsids diverged into two groups, the Archosauromorpha (“ancient lizard form”) and the Lepidosauromorpha (“scaly lizard form”) during the Mesozoic period (Figure \(3\)). The lepidosaurs include modern lizards, snakes, and tuataras. The archosaurs include modern crocodiles and alligators, and the extinct pterosaurs (“winged lizard”) and dinosaurs (“terrible lizard”). Clade Dinosauria includes birds, which evolved from a branch of dinosaurs.
Art Connection
Members of the order Testudines have an anapsid-like skull with one opening. However, molecular studies indicate that turtles descended from a diapsid ancestor. Why might this be the case?
In the past, the most common division of amniotes has been into the classes Mammalia, Reptilia, and Aves. Birds are descended, however, from dinosaurs, so this classical scheme results in groups that are not true clades. We will consider birds as a group distinct from reptiles for the purpose of this discussion with the understanding that this does not completely reflect phylogenetic history and relationships.
Characteristics of Reptiles
Reptiles are tetrapods. Limbless reptiles—snakes and other squamates—have vestigial limbs and, like caecilians, are classified as tetrapods because they are descended from four-limbed ancestors. Reptiles lay eggs enclosed in shells on land. Even aquatic reptiles return to the land to lay eggs. They usually reproduce sexually with internal fertilization. Some species display ovoviviparity, with the eggs remaining in the mother’s body until they are ready to hatch. Other species are viviparous, with the offspring born alive.
One of the key adaptations that permitted reptiles to live on land was the development of their scaly skin, containing the protein keratin and waxy lipids, which reduced water loss from the skin. This occlusive skin means that reptiles cannot use their skin for respiration, like amphibians, and thus all breathe with lungs.
Reptiles are ectotherms, animals whose main source of body heat comes from the environment. This is in contrast to endotherms, which use heat produced by metabolism to regulate body temperature. In addition to being ectothermic, reptiles are categorized as poikilotherms, or animals whose body temperatures vary rather than remain stable. Reptiles have behavioral adaptations to help regulate body temperature, such as basking in sunny places to warm up and finding shady spots or going underground to cool down. The advantage of ectothermy is that metabolic energy from food is not required to heat the body; therefore, reptiles can survive on about 10 percent of the calories required by a similarly sized endotherm. In cold weather, some reptiles such as the garter snake brumate. Brumation is similar to hibernation in that the animal becomes less active and can go for long periods without eating, but differs from hibernation in that brumating reptiles are not asleep or living off fat reserves. Rather, their metabolism is slowed in response to cold temperatures, and the animal is very sluggish.
Evolution of Reptiles
Reptiles originated approximately 300 million years ago during the Carboniferous period. One of the oldest known amniotes is Casineria, which had both amphibian and reptilian characteristics. One of the earliest undisputed reptiles was Hylonomus. Soon after the first amniotes appeared, they diverged into three groups—synapsids, anapsids, and diapsids—during the Permian period. The Permian period also saw a second major divergence of diapsid reptiles into archosaurs (predecessors of crocodilians and dinosaurs) and lepidosaurs (predecessors of snakes and lizards). These groups remained inconspicuous until the Triassic period, when the archosaurs became the dominant terrestrial group due to the extinction of large-bodied anapsids and synapsids during the Permian-Triassic extinction. About 250 million years ago, archosaurs radiated into the dinosaurs and the pterosaurs.
Although they are sometimes mistakenly called dinosaurs, the pterosaurs were distinct from true dinosaurs (Figure \(4\)). Pterosaurs had a number of adaptations that allowed for flight, including hollow bones (birds also exhibit hollow bones, a case of convergent evolution). Their wings were formed by membranes of skin that attached to the long, fourth finger of each arm and extended along the body to the legs.
The dinosaurs were a diverse group of terrestrial reptiles with more than 1,000 species identified to date. Paleontologists continue to discover new species of dinosaurs. Some dinosaurs were quadrupeds (Figure \(5\)); others were bipeds. Some were carnivorous, whereas others were herbivorous. Dinosaurs laid eggs, and a number of nests containing fossilized eggs have been found. It is not known whether dinosaurs were endotherms or ectotherms. However, given that modern birds are endothermic, the dinosaurs that served as ancestors to birds likely were endothermic as well. Some fossil evidence exists for dinosaurian parental care, and comparative biology supports this hypothesis since the archosaur birds and crocodilians display parental care.
Dinosaurs dominated the Mesozoic Era, which was known as the “age of reptiles.” The dominance of dinosaurs lasted until the end of the Cretaceous, the last period of the Mesozoic Era. The Cretaceous-Tertiary extinction resulted in the loss of most of the large-bodied animals of the Mesozoic Era. Birds are the only living descendants of one of the major clades of dinosaurs.
Link to Learning
Visit this site to see a video discussing the hypothesis that an asteroid caused the Cretaceous-Triassic (KT) extinction.
Modern Reptiles
Class Reptilia includes many diverse species that are classified into four living clades. These are the 25 species of Crocodilia, 2 species of Sphenodontia, approximately 9,200 Squamata species, and the Testudines, with about 325 species.
Crocodilia
Crocodilia (“small lizard”) arose with a distinct lineage by the middle Triassic; extant species include alligators, crocodiles, and caimans. Crocodilians (Figure \(6\)) live throughout the tropics and subtropics of Africa, South America, Southern Florida, Asia, and Australia. They are found in freshwater, saltwater, and brackish habitats, such as rivers and lakes, and spend most of their time in water. Some species are able to move on land due to their semi-erect posture.
Sphenodontia
Sphenodontia (“wedge tooth”) arose in the Mesozoic era and includes only one living genus, Tuatara, comprising two species that are found in New Zealand (Figure \(7\)). Tuataras measure up to 80 centimeters and weigh about 1 kilogram. Although quite lizard-like in gross appearance, several unique features of the skull and jaws clearly define them and distinguish the group from the squamates.
Squamata
Squamata (“scaly”) arose in the late Permian, and extant species include lizards and snakes. Both are found on all continents except Antarctica. Lizards and snakes are most closely related to tuataras, both groups having evolved from a lepidosaurian ancestor. Squamata is the largest extant clade of reptiles (Figure \(8\)). Most lizards differ from snakes by having four limbs, although these have been variously lost or significantly reduced in at least 60 lineages. Snakes lack eyelids and external ears, which are present in lizards. Lizard species range in size from chameleons and geckos, which are a few centimeters in length, to the Komodo dragon, which is about 3 meters in length. Most lizards are carnivorous, but some large species, such as iguanas, are herbivores.
Snakes are thought to have descended from either burrowing lizards or aquatic lizards over 100 million years ago (Figure \(9\)). Snakes comprise about 3,000 species and are found on every continent except Antarctica. They range in size from 10 centimeter-long thread snakes to 10 meter-long pythons and anacondas. All snakes are carnivorous and eat small animals, birds, eggs, fish, and insects. The snake body form is so specialized that, in its general morphology, a “snake is a snake.” Their specializations all point to snakes having evolved to feed on relatively large prey (even though some current species have reversed this trend). Although variations exist, most snakes have a skull that is very flexible, involving eight rotational joints. They also differ from other squamates by having mandibles (lower jaws) without either bony or ligamentous attachment anteriorly. Having this connection via skin and muscle allows for great expansion of the gape and independent motion of the two sides—both advantages in swallowing big items.
Testudines
Turtles are members of the clade Testudines (“having a shell”) (Figure \(10\)). Turtles are characterized by a bony or cartilaginous shell. The shell consists of the ventral surface called the plastron and the dorsal surface called the carapace, which develops from the ribs. The plastron is made of scutes or plates; the scutes can be used to differentiate species of turtles. The two clades of turtles are most easily recognized by how they retract their necks. The dominant group, which includes all North American species, retracts its neck in a vertical S-curve. Turtles in the less speciose clade retract the neck with a horizontal curve.
Turtles arose approximately 200 million years ago, predating crocodiles, lizards, and snakes. Similar to other reptiles, turtles are ectotherms. They lay eggs on land, although many species live in or near water. None exhibit parental care. Turtles range in size from the speckled padloper tortoise at 8 centimeters (3.1 inches) to the leatherback sea turtle at 200 centimeters (over 6 feet). The term “turtle” is sometimes used to describe only those species of Testudines that live in the sea, with the terms “tortoise” and “terrapin” used to refer to species that live on land and in fresh water, respectively.
Summary
The amniotes are distinguished from amphibians by the presence of a terrestrially adapted egg protected by amniotic membranes. The amniotes include reptiles, birds, and mammals. The early amniotes diverged into two main lines soon after the first amniotes arose. The initial split was into synapsids (mammals) and sauropsids. Sauropsids can be further divided into anapsids (turtles) and diapsids (birds and reptiles). Reptiles are tetrapods either having four limbs or descending from such. Limbless reptiles (snakes) are classified as tetrapods, as they are descended from four-limbed organisms. One of the key adaptations that permitted reptiles to live on land was the development of scaly skin containing the protein keratin, which prevented water loss from the skin. Reptilia includes four living clades: Crocodilia (crocodiles and alligators), Sphenodontia (tuataras), Squamata (lizards and snakes), and Testudines (turtles).
Art Connections
Figure \(1\): Which of the following statements about the parts of an egg are false?
1. The allantois stores nitrogenous waste and facilitates respiration.
2. The chorion facilitates gas exchange.
3. The yolk provides food for the growing embryo.
4. The amniotic cavity is filled with albumen.
Answer
D
Figure \(3\): Members of the order Testudines have an anapsid-like skull with one opening. However, molecular studies indicate that turtles descended from a diapsid ancestor. Why might this be the case?
Answer
The ancestor of modern Testudines may at one time have had a second opening in the skull, but over time this might have been lost.
Glossary
amniote
animal that produces a terrestrially adapted egg protected by amniotic membranes
allantois
membrane of the egg that stores nitrogenous wastes produced by the embryo; also facilitates respiration
amnion
membrane of the egg that protects the embryo from mechanical shock and prevents dehydration
anapsid
animal having no temporal fenestrae in the cranium
archosaur
modern crocodilian or bird, or an extinct pterosaur or dinosaur
brumation
period of much reduced metabolism and torpor that occurs in any ectotherm in cold weather
Casineria
one of the oldest known amniotes; had both amphibian and reptilian characteristics
chorion
membrane of the egg that surrounds the embryo and yolk sac
Crocodilia
crocodiles and alligators
diapsid
animal having two temporal fenestrae in the cranium
Hylonomus
one of the earliest reptiles
lepidosaur
modern lizards, snakes, and tuataras
sauropsid
reptile or bird
Sphenodontia
clade of tuataras
Squamata
clade of lizards and snakes
synapsid
mammal having one temporal fenestra
temporal fenestra
non-orbital opening in the skull that may allow muscles to expand and lengthen
Testudines
order of turtles | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/29%3A_Vertebrates/29.4%3A_Reptiles.txt |
Skills to Develop
• Describe the evolutionary history of birds
• Describe the derived characteristics in birds that facilitate flight
The most obvious characteristic that sets birds apart from other modern vertebrates is the presence of feathers, which are modified scales. While vertebrates like bats fly without feathers, birds rely on feathers and wings, along with other modifications of body structure and physiology, for flight.
Characteristics of Birds
Birds are endothermic, and because they fly, they require large amounts of energy, necessitating a high metabolic rate. Like mammals, which are also endothermic, birds have an insulating covering that keeps heat in the body: feathers. Specialized feathers called down feathers are especially insulating, trapping air in spaces between each feather to decrease the rate of heat loss. Certain parts of a bird’s body are covered in down feathers, and the base of other feathers have a downy portion, whereas newly hatched birds are covered in down.
Feathers not only act as insulation but also allow for flight, enabling the lift and thrust necessary to become airborne. The feathers on a wing are flexible, so the collective feathers move and separate as air moves through them, reducing the drag on the wing. Flight feathers are asymmetrical, which affects airflow over them and provides some of the lifting and thrusting force required for flight (Figure \(1\)). Two types of flight feathers are found on the wings, primary feathers and secondary feathers. Primary feathers are located at the tip of the wing and provide thrust. Secondary feathers are located closer to the body, attach to the forearm portion of the wing and provide lift. Contour feathers are the feathers found on the body, and they help reduce drag produced by wind resistance during flight. They create a smooth, aerodynamic surface so that air moves smoothly over the bird’s body, allowing for efficient flight.
Flapping of the entire wing occurs primarily through the actions of the chest muscles, the pectoralis and the supracoracoideus. These muscles are highly developed in birds and account for a higher percentage of body mass than in most mammals. These attach to a blade-shaped keel, like that of a boat, located on the sternum. The sternum of birds is larger than that of other vertebrates, which accommodates the large muscles required to generate enough upward force to generate lift with the flapping of the wings. Another skeletal modification found in most birds is the fusion of the two clavicles (collarbones), forming the furcula or wishbone. The furcula is flexible enough to bend and provide support to the shoulder girdle during flapping.
An important requirement of flight is a low body weight. As body weight increases, the muscle output required for flying increases. The largest living bird is the ostrich, and while it is much smaller than the largest mammals, it is flightless. For birds that do fly, reduction in body weight makes flight easier. Several modifications are found in birds to reduce body weight, including pneumatization of bones. Pneumatic bones are bones that are hollow, rather than filled with tissue (Figure \(2\)). They contain air spaces that are sometimes connected to air sacs, and they have struts of bone to provide structural reinforcement. Pneumatic bones are not found in all birds, and they are more extensive in large birds than in small birds. Not all bones of the skeleton are pneumatic, although the skulls of almost all birds are.
Other modifications that reduce weight include the lack of a urinary bladder. Birds possess a cloaca, a structure that allows water to be reabsorbed from waste back into the bloodstream. Uric acid is not expelled as a liquid but is concentrated into urate salts, which are expelled along with fecal matter. In this way, water is not held in the urinary bladder, which would increase body weight. Most bird species only possess one ovary rather than two, further reducing body mass.
The air sacs that extend into bones to form pneumatic bones also join with the lungs and function in respiration. Unlike mammalian lungs in which air flows in two directions, as it is breathed in and out, airflow through bird lungs travels in one direction (Figure \(3\)). Air sacs allow for this unidirectional airflow, which also creates a cross-current exchange system with the blood. In a cross-current or counter-current system, the air flows in one direction and the blood flows in the opposite direction, creating a very efficient means of gas exchange.
Evolution of Birds
The evolutionary history of birds is still somewhat unclear. Due to the fragility of bird bones, they do not fossilize as well as other vertebrates. Birds are diapsids, meaning they have two fenestrations or openings in their skulls. Birds belong to a group of diapsids called the archosaurs, which also includes crocodiles and dinosaurs. It is commonly accepted that birds evolved from dinosaurs.
Dinosaurs (including birds) are further subdivided into two groups, the Saurischia (“lizard like”) and the Ornithischia (“bird like”). Despite the names of these groups, it was not the bird-like dinosaurs that gave rise to modern birds. Rather, Saurischia diverged into two groups: One included the long-necked herbivorous dinosaurs, such as Apatosaurus. The second group, bipedal predators called theropods, includes birds. This course of evolution is suggested by similarities between theropod fossils and birds, specifically in the structure of the hip and wrist bones, as well as the presence of the wishbone, formed by the fusing of the clavicles.
One important fossil of an animal intermediate to dinosaurs and birds is Archaeopteryx, which is from the Jurassic period (Figure \(4\)). Archaeopteryx is important in establishing the relationship between birds and dinosaurs, because it is an intermediate fossil, meaning it has characteristics of both dinosaurs and birds. Some scientists propose classifying it as a bird, but others prefer to classify it as a dinosaur. The fossilized skeleton of Archaeopteryx looks like that of a dinosaur, and it had teeth whereas birds do not, but it also had feathers modified for flight, a trait associated only with birds among modern animals. Fossils of older feathered dinosaurs exist, but the feathers do not have the characteristics of flight feathers.
It is still unclear exactly how flight evolved in birds. Two main theories exist, the arboreal (“tree”) hypothesis and the terrestrial (“land”) hypothesis. The arboreal hypothesis posits that tree-dwelling precursors to modern birds jumped from branch to branch using their feathers for gliding before becoming fully capable of flapping flight. In contrast to this, the terrestrial hypothesis holds that running was the stimulus for flight, as wings could be used to improve running and then became used for flapping flight. Like the question of how flight evolved, the question of how endothermy evolved in birds still is unanswered. Feathers provide insulation, but this is only beneficial if body heat is being produced internally. Similarly, internal heat production is only viable if insulation is present to retain that heat. It has been suggested that one or the other—feathers or endothermy—evolved in response to some other selective pressure.
During the Cretaceous period, a group known as the Enantiornithes was the dominant bird type (Figure \(5\)). Enantiornithes means “opposite birds,” which refers to the fact that certain bones of the feet are joined differently than the way the bones are joined in modern birds. These birds formed an evolutionary line separate from modern birds, and they did not survive past the Cretaceous. Along with the Enantiornithes, Ornithurae birds (the evolutionary line that includes modern birds) were also present in the Cretaceous. After the extinction of Enantiornithes, modern birds became the dominant bird, with a large radiation occurring during the Cenozoic Era. Referred to as Neornithes (“new birds”), modern birds are now classified into two groups, the Paleognathae (“old jaw”) or ratites, a group of flightless birds including ostriches, emus, rheas, and kiwis, and the Neognathae (“new jaw”), which includes all other birds.
Career Connection: Veterinarian
Veterinarians treat diseases, disorders, and injuries in animals, primarily vertebrates. They treat pets, livestock, and animals in zoos and laboratories. Veterinarians usually treat dogs and cats, but also treat birds, reptiles, rabbits, and other animals that are kept as pets. Veterinarians that work with farms and ranches treat pigs, goats, cows, sheep, and horses.
Veterinarians are required to complete a degree in veterinary medicine, which includes taking courses in animal physiology, anatomy, microbiology, and pathology, among many other courses. The physiology and biochemistry of different vertebrate species differ greatly.
Veterinarians are also trained to perform surgery on many different vertebrate species, which requires an understanding of the vastly different anatomies of various species. For example, the stomach of ruminants like cows has four compartments versus one compartment for non-ruminants. Birds also have unique anatomical adaptations that allow for flight.
Some veterinarians conduct research in academic settings, broadening our knowledge of animals and medical science. One area of research involves understanding the transmission of animal diseases to humans, called zoonotic diseases. For example, one area of great concern is the transmission of the avian flu virus to humans. One type of avian flu virus, H5N1, is a highly pathogenic strain that has been spreading in birds in Asia, Europe, Africa, and the Middle East. Although the virus does not cross over easily to humans, there have been cases of bird-to-human transmission. More research is needed to understand how this virus can cross the species barrier and how its spread can be prevented.
Summary
Birds are endothermic, meaning they produce their own body heat and regulate their internal temperature independently of the external temperature. Feathers not only act as insulation but also allow for flight, providing lift with secondary feathers and thrust with primary feathers. Pneumatic bones are bones that are hollow rather than filled with tissue, containing air spaces that are sometimes connected to air sacs. Airflow through bird lungs travels in one direction, creating a cross-current exchange with the blood. Birds are diapsids and belong to a group called the archosaurs. Birds are thought to have evolved from theropod dinosaurs. The oldest known fossil of a bird is that of Archaeopteryx, which is from the Jurassic period. Modern birds are now classified into two groups, Paleognathae and Neognathae.
Glossary
Archaeopteryx
transition species from dinosaur to bird from the Jurassic period
contour feather
feather that creates an aerodynamic surface for efficient flight
down feather
feather specialized for insulation
Enantiornithes
dominant bird group during the Cretaceous period
flight feather
feather specialized for flight
furcula
wishbone formed by the fusing of the clavicles
Neognathae
birds other than the Paleognathae
Neornithes
modern birds
Paleognathae
ratites; flightless birds, including ostriches and emus
pneumatic bone
air-filled bone
primary feather
feather located at the tip of the wing that provides thrust
secondary feather
feather located at the base of the wing that provides lift
theropod
dinosaur group ancestral to birds | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/5%3A_Biological_Diversity/29%3A_Vertebrates/29.5%3A_Birds.txt |
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