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In order to function, proteins must fold into the correct three-dimensional shape, and be targeted to the correct part of the cell.
Learning Objectives
• Discuss how post-translational events affect the proper function of a protein
Key Points
• Protein folding is a process in which a linear chain of amino acids attains a defined three-dimensional structure, but there is a possibility of forming misfolded or denatured proteins, which are often inactive.
• Proteins must also be located in the correct part of the cell in order to function correctly; therefore, a signal sequence is often attached to direct the protein to its proper location, which is removed after it attains its location.
• Protein misfolding is the cause of numerous diseases, such as mad cow disease, Creutzfeldt-Jakob disease, and cystic fibrosis.
Key Terms
• prion: a self-propagating misfolded conformer of a protein that is responsible for a number of diseases that affect the brain and other neural tissue
• chaperone: a protein that assists the non-covalent folding/unfolding of other proteins
Protein Folding
After being translated from mRNA, all proteins start out on a ribosome as a linear sequence of amino acids. This linear sequence must “fold” during and after the synthesis so that the protein can acquire what is known as its native conformation. The native conformation of a protein is a stable three-dimensional structure that strongly determines a protein’s biological function. When a protein loses its biological function as a result of a loss of three-dimensional structure, we say that the protein has undergone denaturation. Proteins can be denatured not only by heat, but also by extremes of pH; these two conditions affect the weak interactions and the hydrogen bonds that are responsible for a protein’s three-dimensional structure. 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. The denatured state of the protein does not equate with the unfolding of the protein and randomization of conformation. Actually, denatured proteins exist in a set of partially-folded states that are currently poorly understood. Many proteins fold spontaneously, but some proteins require helper molecules, called chaperones, to prevent them from aggregating during the complicated process of folding.
Protein Modification and Targeting
During and after translation, individual amino acids may be chemically modified and signal sequences may be appended to the protein. 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.
Misfolding
It is very important for proteins to achieve their native conformation since failure to do so may lead to serious problems in the accomplishment of its biological function. Defects in protein folding may be the molecular cause of a range of human genetic disorders. For example, cystic fibrosis is caused by defects in a membrane-bound protein called cystic fibrosis transmembrane conductance regulator (CFTR). This protein serves as a channel for chloride ions. The most common cystic fibrosis-causing mutation is the deletion of a Phe residue at position 508 in CFTR, which causes improper folding of the protein. Many of the disease-related mutations in collagen also cause defective folding.
A misfolded protein, known as prion, appears to be the agent of a number of rare degenerative brain diseases in mammals, like the mad cow disease. Related diseases include kuru and Creutzfeldt-Jakob. The diseases are sometimes referred to as spongiform encephalopathies, so named because the brain becomes riddled with holes. Prion, the misfolded protein, is a normal constituent of brain tissue in all mammals, but its function is not yet known. Prions cannot reproduce independently and not considered living microoganisms. A complete understanding of prion diseases awaits new information about how prion protein affects brain function, as well as more detailed structural information about the protein. Therefore, improved understanding of protein folding may lead to new therapies for cystic fibrosis, Creutzfeldt-Jakob, and many other diseases.
Contributions and Attributions
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44529/latest...ol11448/latest. License: CC BY: Attribution
• ribosome. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/ribosome. License: CC BY-SA: Attribution-ShareAlike
• Ribosome. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Ribosome. License: CC BY-SA: Attribution-ShareAlike
• Transfer RNA. Provided by: Wikipedia. Located at: commons.wikimedia.org/wiki/Fi...e_yeast_en.svg. License: CC BY-SA: Attribution-ShareAlike
• Transfer RNA. Provided by: Wikepedia. Located at: commons.wikimedia.org/wiki/Fi...e_yeast_en.svg. License: CC BY-SA: Attribution-ShareAlike
• Translation (biology). Provided by: Wikepedia. Located at: en.Wikipedia.org/wiki/Transla...slation_en.svg. License: Public Domain: No Known Copyright
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44529/latest...ol11448/latest. License: CC BY: Attribution
• translation. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/translation. License: CC BY-SA: Attribution-ShareAlike
• Ribosome. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Ribosome. License: CC BY-SA: Attribution-ShareAlike
• Transfer RNA. Provided by: Wikipedia. Located at: commons.wikimedia.org/wiki/Fi...e_yeast_en.svg. License: CC BY-SA: Attribution-ShareAlike
• Transfer RNA. Provided by: Wikepedia. Located at: commons.wikimedia.org/wiki/Fi...e_yeast_en.svg. License: CC BY-SA: Attribution-ShareAlike
• Translation (biology). Provided by: Wikepedia. Located at: en.Wikipedia.org/wiki/Transla...slation_en.svg. License: Public Domain: No Known Copyright
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44529/latest...ol11448/latest. License: CC BY: Attribution
• Lydia Kavraki, Protein Folding. November 4, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m11467/latest/. License: CC BY: Attribution
• prion. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/prion. License: CC BY-SA: Attribution-ShareAlike
• chaperone. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/chaperone. License: CC BY-SA: Attribution-ShareAlike
• Ribosome. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Ribosome. License: CC BY-SA: Attribution-ShareAlike
• Transfer RNA. Provided by: Wikipedia. Located at: commons.wikimedia.org/wiki/Fi...e_yeast_en.svg. License: CC BY-SA: Attribution-ShareAlike
• Transfer RNA. Provided by: Wikepedia. Located at: commons.wikimedia.org/wiki/Fi...e_yeast_en.svg. License: CC BY-SA: Attribution-ShareAlike
• Translation (biology). Provided by: Wikepedia. Located at: en.Wikipedia.org/wiki/Transla...slation_en.svg. License: Public Domain: No Known Copyright
• Protein folding. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Protein_folding.png. License: Public Domain: No Known Copyright | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/15%3A_Genes_and_Proteins/15.12%3A_Ribosomes_and_Protein_Synthesis_-_Protein_Folding_Modification_and_Targeting.txt |
Learning Objectives
• Discuss how the genome and proteome contribute to the specialization of a cell
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 that constitutes its proteome. 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.
In this section, you will learn about the various methods of gene regulation and the mechanisms used to control gene expression, such as: epigenetic, transcriptional, post-transcriptional, translational, and post-translational controls in eukaryotic gene expression, and transcriptional control in prokaryotic gene expression.
Key Points
• Every cell within an organism shares the same genome (with exceptions, i.e. mature red blood cells), but has variation between its proteomes.
• Gene expression involves the process of transcribing DNA into RNA and then translating RNA into proteins.
• Gene expression is a highly complex and tightly-regulated process.
Key Terms
• somatic: part of, or relating to the body of an organism
• genome: the cell’s complete genetic information packaged as a double-stranded DNA molecule
• proteome: the complete set of proteins encoded by a particular genome
16.02: Regulation of Gene Expression - Prokaryotic versus Eukaryotic Gene Expression
Learning Objectives
• Compare and contrast prokaryotic and eukaryotic gene expression
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 defined nucleus; therefore, their DNA floats freely within the cell cytoplasm. To synthesize a protein, the processes of transcription (DNA to RNA) and translation (RNA to protein) occur almost simultaneously. When the resulting protein is no longer needed, transcription stops. Thus, the regulation of transcription is the primary method to control what type of protein and how much of each protein is expressed in a prokaryotic cell. 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 where 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 within the cytoplasm. The regulation of gene expression can occur at all stages of the process. Regulation may occur when the DNA is uncoiled and loosened from nucleosomes to bind transcription factors (epigenetics), 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).
Key Points
• Prokaryotic gene expression is primarily controlled at the level of transcription.
• Eukaryotic gene expression is controlled at the levels of epigenetics, transcription, post-transcription, translation, and post-translation.
• Prokaryotic gene expression (both transcription and translation) occurs within the cytoplasm of a cell due to the lack of a defined nucleus; thus, the DNA is freely located within the cytoplasm.
• Eukaryotic gene expression occurs in both the nucleus (transcription) and cytoplasm (translation).
Key Terms
• epigenetics: the study of heritable changes caused by the activation and deactivation of genes without any change in DNA sequence
• nucleosome: any of the subunits that repeat in chromatin; a coil of DNA surrounding a histone core
Contributions and Attributions
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44533/latest...ol11448/latest. License: CC BY: Attribution
• somatic. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/somatic. License: CC BY-SA: Attribution-ShareAlike
• proteome. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/proteome. License: CC BY-SA: Attribution-ShareAlike
• genome. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/genome. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Introduction. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44533/latest...e_16_00_01.jpg. License: CC BY: Attribution
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44534/latest...ol11448/latest. License: CC BY: Attribution
• epigenetics. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/epigenetics. License: CC BY-SA: Attribution-ShareAlike
• nucleosome. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/nucleosome. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Introduction. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44533/latest...e_16_00_01.jpg. License: CC BY: Attribution
• OpenStax College, Regulation of Gene Expression. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44534/latest...e_16_01_01.jpg. License: CC BY: Attribution | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.01%3A_Regulation_of_Gene_Expression_-_The_Process_and_Purpose_of_Gene_Expression_Regulation.txt |
Learning Objectives
• Explain the relationship between structure and function of an operon and the ways in which repressors regulate gene expression
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. If tryptophan is present in the environment, then E. coli does not need to synthesize it; the switch controlling the activation of the genes in the trp operon is turned 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.
Key Points
• The operator sequence is encoded between the promoter region and the first trp-coding gene.
• The trp operon is repressed when tryptophan levels are high by binding the repressor protein to the operator sequence via a corepressor which blocks RNA polymerase from transcribing the trp-related genes.
• The trp operon is activated when tryptophan levels are low by dissociation of the repressor protein to the operator sequence which allows RNA polymerase to transcribe the trp genes in the operon.
Key Terms
• repressor: any protein that binds to DNA and thus regulates the expression of genes by decreasing the rate of transcription
• operon: a unit of genetic material that functions in a coordinated manner by means of an operator, a promoter, and structural genes that are transcribed together
16.04: Prokaryotic Gene Regulation - Catabolite Activator Protein (CAP)- An Activator Regulator
Learning Objectives
• Explain how an activator works to increase transcription of a gene
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. This type of process can be seen in the lac operon which is turned on in the presence of lactose and absence of glucose.
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, such as the lac operon. The CAP assists in production in the absence of glucose. CAP is a transcriptional activator that exists as a homodimer in solution, with each subunit comprising a ligand-binding domain at the N-terminus, which is also responsible for the dimerization of the protein and a DNA-binding domain at the C-terminus. Two cAMP molecules bind dimeric CAP with negative cooperativity and function as allosteric effectors by increasing the protein’s affinity for DNA. CAP has a characteristic helix-turn-helix structure that allows it to bind to successive major grooves on DNA. This opens up the DNA molecule, allowing RNA polymerase to bind and transcribe the genes involved in lactose catabolism. When cAMP binds to CAP, the complex binds to the promoter region of the genes that are needed to use the alternate sugar sources. 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. As cAMP-CAP is required for transcription of the lac operon, this requirement reflects the greater simplicity with which glucose may be metabolized in comparison to lactose.
Key Points
• Catabolite activator protein (CAP) must bind to cAMP to activate transcription of the lac operon by RNA polymerase.
• CAP is a transcriptional activator with a ligand-binding domain at the N-terminus and a DNA -binding domain at the C-terminus.
• cAMP molecules bind to CAP and function as allosteric effectors by increasing CAP’s affinity to DNA.
Key Terms
• RNA polymerase: a DNA-dependent RNA polymerase, an enzyme, that produces RNA
• operon: a unit of genetic material that functions in a coordinated manner by means of an operator, a promoter, and structural genes that are transcribed together
• promoter: the section of DNA that controls the initiation of RNA transcription
16.05: Prokaryotic Gene Regulation - The lac Operon- An Inducer Operon
Learning Objectives
• Describe the components of the lac operon and their role in its function
A major type of gene regulation that occurs in prokaryotic cells utilizes and occurs through inducible operons. Inducible operons have proteins that can bind to either 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, which includes the structural genes lacZ, lacY, and lacA. lacZ encodes β-galactosidase (LacZ), an intracellular enzyme that cleaves the disaccharide lactose into glucose and galactose. lacY encodes β-galactoside permease (LacY), a membrane-bound transport protein that pumps lactose into the cell. lacA encodes β-galactoside transacetylase (LacA), an enzyme that transfers an acetyl group from acetyl-CoA to β-galactosides. Only lacZ and lacY appear to be necessary for lactose catabolism.
CAP binds to the operator sequence upstream of the promoter that initiates transcription of the lac operon. The lac operon uses a two-part control mechanism to ensure that the cell expends energy producing β-galactosidase, β-galactoside permease, and thiogalactoside transacetylase (also known as galactoside O-acetyltransferase) only when necessary. 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. 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. The cell can use lactose as an energy source by producing the enzyme b-galactosidase to digest that lactose into glucose and galactose. Only when both conditions are satisfied is the lac operon transcribed, such as when glucose is absent and lactose is present. This process is beneficial and makes most sense for the cell as it would be energetically wasteful to create the proteins to process lactose if glucose were plentiful or if lactose were not available.
Key Points
• The lac operon contains an operator, promoter, and structural genes that are transcribed together and are under the control of the catabolite activator protein (CAP) or repressor.
• The lac operon is not activated and transcription remains off when the level of glucose is low or non-existent, but lactose is absent.
• The lac operon encodes for the genes needed to utilize lactose as an energy source.
Key Terms
• operator: a segment of DNA to which a transcription factor protein binds
• repressor: any protein that binds to DNA and thus regulates the expression of genes by decreasing the rate of transcription | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.03%3A_Prokaryotic_Gene_Regulation_-_The_trp_Operon-_A_Repressor_Operon.txt |
Learning Objectives
• Describe the role of promoters in RNA transcription
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 transcription initiation 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.
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, they are referred to as cis-acting elements because they are 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.
Key Points
• The purpose of the promoter is to bind transcription factors that control the initiation of transcription.
• The promoter region can be short or quite long; the longer the promoter is, the more available space for proteins to bind.
• To initiate transcription, a transcription factor (TFIID) binds to the TATA box, which causes other transcription factors to subsequently bind to the TATA box.
• Once the transcription initiation complex is assembled, RNA polymerase can bind to its upstream sequence and is then phosphorylated.
• Phosphorylation of RNA polymerase 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.
• Transcription factors respond to environmental stimuli that cause the proteins to find their binding sites and initiate transcription of the gene that is needed.
Key Terms
• TATA box: a DNA sequence (cis-regulatory element) found in the promoter region of genes in archaea and eukaryotes
• transcription factor: a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to mRNA
• promoter: the section of DNA that controls the initiation of RNA transcription
16.07: Eukaryotic Gene Regulation - Transcriptional Enhancers and Repressors
Learning Objectives
• Explain how enhancers and repressors regulate gene expression
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 to an enhancer, the shape of the DNA changes. This shape change allows the interaction between the activators bound to the enhancers and the transcription factors bound to the promoter region and the RNA polymerase to occur. 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.
A corepressor is a protein that decreases gene expression by binding to a transcription factor that contains a DNA-binding domain. The corepressor is unable to bind DNA by itself. The corepressor can repress transcriptional initiation by recruiting histone deacetylase, which catalyzes the removal of acetyl groups from lysine residues. This increases the positive charge on histones, which strengthens the interaction between the histones and DNA, making the DNA less accessible to the process of transcription.
Key Points
• Enhancers can be located upstream of a gene, within the coding region of the gene, downstream of a gene, or thousands of nucleotides away.
• When a DNA -bending protein binds to the enhancer, the shape of the DNA changes, which allows interactions between the activators and transcription factors to occur.
• Repressors respond to external stimuli to prevent the binding of activating transcription factors.
• Corepressors can repress transcriptional initiation by recruiting histone deacetylase.
• Histone deactylation increases the positive charge on histones, which strengthens the interaction between the histones and DNA, making the DNA less accessible to transcription.
Key Terms
• enhancer: a short region of DNA that can increase transcription of genes
• repressor: any protein that binds to DNA and thus regulates the expression of genes by decreasing the rate of transcription
• activator: any chemical or agent which regulates one or more genes by increasing the rate of transcription | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.06%3A_Eukaryotic_Gene_Regulation_-_The_Promoter_and_the_Transcription_Machinery.txt |
Learning Objectives
• Discuss how eukaryotic gene regulation occurs at the epigenetic level and the various epigenetic changes that can be made to DNA
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. Under the electron microscope, this winding of DNA around histone proteins to form nucleosomes looks like small beads on a string. 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. Nucleosomes can move to open the chromosome structure to expose a segment of DNA, but do so in a very controlled manner.
How the histone proteins move is dependent on signals found on both the histone proteins and on the DNA. These signals are tags, or modifications, added to histone proteins and DNA that tell the histones if a chromosomal region should be open or closed. 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, such as 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. These changes to DNA are inherited from parent to offspring, such that while the DNA sequence is not altered, the pattern of gene expression is passed to the next generation.
This type of gene regulation is called epigenetic regulation. Epigenetics means “above 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.
Key Points
• DNA is packaged by wrapping around histone proteins into structures called nucleosomes, which resemble beads on a string.
• When DNA is to be transcribed, the nucleosomes can slide away from that region of DNA, opening it up to the transcription machinery of the cell.
• Chemical modifications to either the histone proteins or the DNA itself signals whether or not a particular region of the genome should be “open” or “closed” to the transcription machinery.
• Modifications such as acetylation or methylation of the histones can alter how tightly DNA is wrapped around them, while methylation of DNA changes how the DNA interacts with proteins, including the histone proteins that control access to the region.
• This type of genetic regulation is called epigenetic regulation (“above genetics”) as it does not change the nucleotide sequence of the DNA.
Key Terms
• nucleosome: any of the subunits that repeat in chromatin; a coil of DNA surrounding a histone core
• epigenetics: the study of heritable changes caused by the activation and deactivation of genes without any change in DNA sequence
• histone: any of various simple water-soluble proteins that are rich in the basic amino acids lysine and arginine and are complexed with DNA in the nucleosomes of eukaryotic chromatin | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.08%3A_Eukaryotic_Gene_Regulation_-_Epigenetic_Control-_Regulating_Access_to_Genes_within_the_Chromosome.txt |
Learning Objectives
• Explain the role of RNA splicing in regulating gene expression
RNA splicing, the first stage of post-transcriptional control
Gene expression is the process that transfers genetic information from a gene made of DNA to a functional gene product made of RNA or protein. Genetic Information flows from DNA to RNA by the process of transcription and then from RNA to protein by the process of translation. In order to ensure that the proper products are produced, gene expression is regulated at many different stages during and in between transcription and translation. In eukaryotes, the gene contains extra sequences that do not code for protein. In these organisms, transcription of DNA produces pre-mRNA. These pre-mRNA transcripts often contain regions, called introns, that are intervening sequences which must be removed prior to translation by the process of splicing. The regions of RNA that code for protein are called exons. Splicing can be regulated so that different mRNAs can contain or lack exons, in a process called alternative splicing. Alternative splicing allows more than one protein to be produced from a gene and is an important regulatory step in determining which functional proteins are produced from gene expression. Thus, splicing is the first stage of post-transcriptional control.
Alternative Splicing
Alternative splicing is a process that occurs during gene expression and allows for the production of multiple proteins (protein isoforms) from a single gene coding. Alternative splicing can occur due to the different ways in which an exon can be excluded from or included in the messenger RNA. It can also occur if portions on an exon are excluded/included or if there is an inclusion of introns. For example, if a pre-mRNA has four exons (A, B, C, and D), these can be spliced and translated in a number of different combinations. Exons A, B, and C can be translated together or Exons A, C, and D can be translated. This results in what is called alternative splicing. The pattern of splicing and production of alternatively-spliced messenger RNA is controlled by the binding of regulatory proteins (trans-acting proteins that contain the genes) to cis-acting sites that are found on the pre-RNA. Some of these regulatory proteins include splicing activators (proteins that promote certain splicing sites) and splicing repressors (proteins that reduce the use of certain sites). Some common splicing repressors include: heterogeneous nuclear ribonucleoprotein (hnRNP) and polypyrimidine tract binding protein (PTB). Proteins that are translated from alternatively-spliced messenger RNAs differ in the sequence of their amino acids which results in altered function of the protein. This is one reason why the human genome can encode a wide diversity of proteins. Alternative splicing is a common process that occurs in eukaryotes; most of the multi-exonic genes in humans are spliced alternatively. Unfortunately, abnormal variations in splicing are also the reason why there are many genetic diseases and disorders.
Spliceosome
The splicing of messenger RNA is accomplished and catalyzed by a macro-molecule complex known as the spliceosome. The areas for ligation and cleavage are determined by the many sub-units of the spliceosome which include the branch site (A) and the 5′ and 3′ splice sites. Interactions between these sub-units and the small nuclear ribonucleoproteins (snRNP) found in the spliceosome create a spliceosome A complex which helps determine which introns to leave out and which exons to keep and bind together. Once the introns are cleaved and removed, the exons are joined together by a phosphodiester bond.
Regulatory Proteins
As noted above, splicing is regulated by repressor proteins and activator proteins, which are are also known as trans-acting proteins. Equally as important are the silencers and enhancers that are found on the messenger RNAs, also known as cis-acting sites. These regulatory functions work together in order to create splicing code that determines alternative splicing.
Key Points
• Introns are intervening sequences within a pre-mRNA molecule that do not code for proteins and are removed during RNA processing by a spliceosome.
• Exons are expressing sequences within a pre-mRNA molecule that are spliced together once introns are removed to form mature mRNA molecules that are translated into proteins.
• Alternative splicing allows for the production of various protein isoforms from one single gene coding.
• A spliceosome is a complex comprised of both RNA molecules and proteins which determine which introns to leave out and which exons to keep and bind together.
Key Terms
• intron: a portion of a split gene that is included in pre-RNA transcripts but is removed during RNA processing and rapidly degraded
• exon: a region of a transcribed gene present in the final functional RNA molecule
• spliceosome: a dynamic complex of RNA and protein subunits that removes introns from precursor mRNA | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.09%3A_Eukaryotic_Gene_Regulation_-_RNA_Splicing.txt |
Learning Objectives
• Discuss how eukaryotes assemble ribosomes on the mRNA to begin translation
Ribosome Assembly and Translation Rate
Like transcription, translation is controlled by proteins that bind and initiate the process. In translation, before protein synthesis can begin, ribosome assembly has to be completed. This is a multi-step process.
In ribosome assembly, the large and small ribosomal subunits and an initiator tRNA (tRNAi) containing the first amino acid of the final polypeptide chain all come together at the translation start codon on an mRNA to allow translation to begin. First, the small ribosomal subunit binds to the tRNAi which carries methionine in eukaryotes and archaea and carries N-formyl-methionine in bacteria. (Because the tRNAi is carrying an amino acid, it is said to be charged.) Next, the small ribosomal subunit with the charged tRNAi still bound scans along the mRNA strand until it reaches the start codon AUG, which indicates where translation will begin. The start codon also establishes the reading frame for the mRNA strand, which is crucial to synthesizing the correct sequence of amino acids. A shift in the reading frame results in mistranslation of the mRNA. The anticodon on the tRNAi then binds to the start codon via basepairing. The complex consisting of mRNA, charged tRNAi, and the small ribosomal subunit attaches to the large ribosomal subunit, which completes ribosome assembly. These components are brought together by the help of proteins called initiation factors which bind to the small ribosomal subunit during initiation and are found in all three domains of life. In addition, the cell spends GTP energy to help form the initiation complex. Once ribosome assembly is complete, the charged tRNAi is positioned in the P site of the ribosome and the empty A site is ready for the next aminoacyl-tRNA. The polypeptide synthesis begins and always proceeds from the N-terminus to the C-terminus, called the N-to-C direction.
In eukaryotes, several eukaryotic initiation factor proteins (eIFs) assist in ribosome assembly. The eukaryotic initiation factor-2 (eIF-2) is active when it binds to guanosine triphosphate (GTP). With GTP bound to it, eIF-2 protein binds to the small 40S ribosomal subunit. Next, the initiatior tRNA charged with methionine (Met-tRNAi) associates with the GTP-eIF-2/40S ribosome complex, and once all these components are bound to each other, they are collectively called the 43S complex.
Eukaryotic initiation factors eIF1, eIF3, eIF4, and eIF5 help bring the 43S complex to the 5′-m7G cap of an mRNA be translated. Once bound to the mRNA’s 5′ m7G cap, the 43S complex starts travelling down the mRNA until it reaches the initiation AUG codon at the start of the mRNA’s reading frame. Sequences around the AUG may help ensure the correct AUG is used as the initiation codon in the mRNA.
Once the 43S complex is at the initiation AUG, the tRNAi-Met is positioned over the AUG. The anticodon on tRNAi-Met basepairs with the AUG codon. At this point, the GTP bound to eIF2 in the 43S complexx is hydrolyzed to GDP + phosphate, and energy is released. This energy is used to release the eIF2 (with GDP bound to it) from the 43S complex, leaving the 40S ribosomal subunit and the tRNAi-Met at the translation start site of the mRNA.
Next, eIF5 with GTP bound binds to the 40S ribosomal subunit complexed to the mRNA and the tRNAi-Met. The eIF5-GTP allows the 60S large ribosomal subunit to bind. Once the 60S ribosomal subunit arrives, eIF5 hydrolyzes its bound GTP to GDP + phosphate, and energy is released. This energy powers assembly of the two ribosomal subunits into the intact 80S ribosome, with tRNAi-Met in its P site while also basepaired to the initiation AUG codon on the mRNA. Translation is ready to begin.
The binding of eIF-2 to the 40S ribosomal subunit is controlled by phosphorylation. If eIF-2 is phosphorylated, it undergoes a conformational change and cannot bind to GTP. Therefore, the 43S complex cannot form properly and translation is impeded. When eIF-2 remains unphosphorylated, it binds the 40S ribosomal subunit and actively translates the protein.
The ability to fully assemble the ribosome directly affects the rate at which translation occurs. But protein synthesis is regulated at various other levels as well, including mRNA synthesis, tRNA synthesis, rRNA synthesis, and eukaryotic initiation factor synthesis. Alteration in any of these components affects the rate at which translation can occur.
Key Points
• The components involved in ribosome assembly are brought together by the help of proteins called initiation factors which bind to the small ribosomal subunit.
• Initiator tRNA is used to locate the start codon AUG (the amino acid methionine) which establishes the reading frame for the mRNA strand.
• GTP carried by eIF2 is the energy source used for loading the initiator tRNA carried by the small ribosomal subunit on the correct start codon in the mRNA.
• GTP carried by eIF5 is the energy source for assembling the large and small ribosomal subunits together.
Key Terms
• reading frame: either of three possible triplets of codons in which a DNA sequence could be transcribed
• phosphorylation: the addition of a phosphate group to a compound; often catalyzed by enzymes | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.10%3A_Eukaryotic_Gene_Regulation_-_The_Initiation_Complex_and_Translation_Rate.txt |
Learning Objectives
• Explain how chemical modifications affect protein activity and longevity
Chemical Modifications, Protein Activity, and Longevity
Proteins can be chemically modified with the addition of 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 protein function, 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 abundance 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). All of these protein activities are affected by the phosphorylation process. The enzymes which are responsible for phosphorylation are known as protein kinases. The addition of a phosphate group to a protein can result in either activation or deactivation; it is protein dependent.
Another example of chemical modifications affecting protein activity include the addition or removal of methyl groups. Methyl groups are added to proteins via the process of methylation; this is the most common form of post-translational modification. The addition of methyl groups to a protein can result in protein-protein interactions that allows for transcriptional regulation, response to stress, protein repair, nuclear transport, and even differentiation processes. Methylation on side chain nitrogens is considered largely irreversible while methylation of the carboxyl groups is potentially reversible. Methylation in the proteins negates the negative charge on it and increases the hydrophobicity of the protein. Methylation on carboxylate side chains covers up a negative charge and adds hydrophobicity. The addition of this chemical group changes the property of the protein and, thus, affects it activity.
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. One way to control gene expression is to alter the longevity of the protein: ubiquitination shortens a protein’s lifespan.
Key Points
• Proteins can be chemically modified by adding methyl, phosphate, acetyl, and ubiquitin groups.
• Protein longevity can be affected by altering stages of gene regulation, including but not limited to altering: accessibility to chromosomal DNA for transcription, rate of translation, nuclear shuttling, RNA stability, and post-translational modifications.
• Ubiquitin is added to a protein to mark it for degradation by the proteasome.
Key Terms
• ubiquitin: a small polypeptide present in the cells of all eukaryotes; it plays a part in modifying and degrading proteins
• proteasome: a complex protein, found in bacterial, archaeal and eukaryotic cells, that breaks down other proteins via proteolysis | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.11%3A_Eukaryotic_Gene_Regulation_-_Regulating_Protein_Activity_and_Longevity.txt |
Learning Objectives
• Discuss the types of cell division that can occur to add cells during development
Adding cells through cellular division
Stem cells are undifferentiated biological cells found in multicellular organisms, that can differentiate into specialized cells (asymmetric division) or can divide to produce more stem cells (symmetric division). In mammals, there are two broad types of stem cells: embryonic stem cells, which are isolated from the inner cell mass of blastocysts, and adult stem cells, which are found in various tissues. In adult organisms, stem cells and progenitor cells act as a repair system for the body by replenishing adult tissues. In a developing embryo, stem cells can differentiate into all of the specialized cells (including ectoderm, endoderm and mesoderm cells) but also maintain the normal turnover of regenerative organs, such as blood, skin, or intestinal tissues. The pathway that is taken to produced specialized cells included: the embryonic cells develop from totipotent cells, to pluripotent cells which undergo differentiation and become more specialized. The key component however, in the ability to maintain tissues is the ability to maintain a key of stem cells.
There are three accessible sources of autologous adult stem cells in humans: (1) bone marrow, which requires extraction by harvesting (i.e., drilling into bone); (2) adipose tissue (lipid cells), which requires extraction by liposuction; and (3) blood, which requires extraction through apheresis (wherein blood is drawn from the donor, passed through a machine that extracts the stem cells, and returned to the donor). Stem cells can also be taken from umbilical cord blood just after birth. Of all the stem cell types, autologous harvesting involves the least risk. By definition, autologous cells are obtained from one’s own body, just as one may bank his or her own blood for elective surgical procedures. Highly plastic adult stem cells are routinely used in medical therapies, for example in bone marrow transplantation. Stem cells can now be artificially grown and differentiated into specialized cell types with characteristics consistent with muscle or nerve cells through cell culture. Embryonic cell lines and autologous embryonic stem cells generated through therapeutic cloning have also been proposed as promising candidates for future therapies.
Symmetric and asymmetric cell division
To ensure self-renewal, stem cells undergo two types of cell division: symmetric and asymmetric. Symmetric division gives rise to two identical daughter cells both endowed with stem cell properties. Asymmetric division, on the other hand, produces only one stem cell and a progenitor cell with limited self-renewal potential. Progenitors can go through several rounds of cell division themselves before terminally differentiating into a mature cell.. It is possible that the molecular distinction between symmetric and asymmetric division lies in differential segregation of cell membrane proteins between the daughter cells. An alternative theory is that stem cells remain undifferentiated due to environmental cues in their particular niche. Stem cells differentiate when they leave that niche or no longer receive those signals.
An asymmetric cell division produces two daughter cells with different cellular fates. This is in contrast to normal symmetric cell divisions, which give rise to daughter cells of equivalent fates. Notably, stem cells divide asymmetrically to give rise to two distinct daughter cells: one copy of the original stem cell as well as a second daughter programmed to differentiate into a non-stem cell fate.
In principle, there are two mechanisms by which distinct properties may be conferred on the daughters of a dividing cell. In one, the daughter cells are initially equivalent but a difference is induced by signaling between the cells, from surrounding cells, or from the precursor cell. This mechanism is known as extrinsic asymmetric cell division. Extrinsic factors involve interactions with neighboring cells and the micro and macro environment of the precursor cell.
In the second mechanism, the prospective daughter cells are inherently different at the time of division of the mother cell. Because this latter mechanism does not depend on interactions of cells with each other or with their environment, it must rely on intrinsic asymmetry. The term asymmetric cell division usually refers to such intrinsic asymmetric divisions. Intrinsic factors generally involve differing amounts of cell-fate determinants being distributed into each daughter cell.
Animals are made up of a vast number of distinct cell types. During development, the zygote undergoes many cell divisions that give rise to various cell types, including embryonic stem cells. Asymmetric divisions of these embryonic cells gives rise to one cell of the same potency (self-renewal), and another that may be of the same potency or stimulated to further differentiate into specialized cell types such as neurons. Asymmetric division of stem cells plays a key role in development by allowing for the differentiation of a subset of daughter cells while maintaining stem cell pluripotency. Since it can be controlled by both intrinsic and extrinsic factors, upon delineating these particular factors it may be possible to use this knowledge in applications of tissue and whole organ generation.
Key Points
• Symmetric cell division of stem cells ensures that a constant pool of stem cells is available by giving rise to two identical daughter cells both endowed with stem cell properties.
• Asymmetric division of stem cells results in the production of only one stem cell and a progenitor cell with limited self-renewal potential.
• Progenitor cells that are produced via asymmetric cell division will go through additional rounds of cell division until they are terminally differentiated into a mature, specialized cell.
• Asymmetric division can be controlled by both intrinsic and extrinsic factors.
• Intrinsic factors involve differing amounts of cell-fate determinants being distributed into each daughter cell, while extrinsic factors involve interactions with neighboring cells and the micro and macro environment of the precursor cell.
Key Terms
• totipotency: the ability of a cell to produce differentiated cells upon division
• progenitor cell: a biological cell that, like a stem cell, has a tendency to differentiate into a specific type of cell, but is already more specific than a stem cell and is pushed to differentiate into its “target” cell.
• autologous: derived from part of the same individual (i.e. from the recipient rather than the donor)
• morula: a spherical mass of blastomeres that forms following the splitting of a zygote; it becomes the blastula
• pluripotent: able to develop into more than one mature cell or tissue type, but not all | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.12%3A_Regulating_Gene_Expression_in_Cell_Development_-_Gene_Expression_in_Stem_Cells.txt |
Learning Objectives
• Discuss how differentiated cells can serve different functions
To develop a multicellular organisms, cells must differentiate to specialize for different functions. Three basic categories of cells make up the mammalian body: germ cells, somatic cells, and stem cells. Each of the approximately 100 trillion cells in an adult human has its own copy or copies of the genome except certain cell types, such as red blood cells, that lack nuclei in their fully differentiated state. Most cells are diploid; they have two copies of each chromosome. The process of cellular differentiation is regulated by transcription factors and growth factors, and results in expression or inhibition of various genes between the cell types, thereby resulting in varying proteomes between cell types. The variation in proteomes between cell types is what drives differentiation and thus, specialization of cells. The ability of transcription factors to control whether a gene will be transcribed or not that contributes to specialization and growth factors to aid in the division process are key components of cell differentiation.
Somatic cells are diploid cells that make up most of the human body, such as the skin and muscle. Germ cells are any line of cells that give rise to gametes—eggs and sperm—and thus are continuous through the generations. Stem cells, on the other hand, have the ability to divide for indefinite periods and to give rise to specialized cells. They are best described in the context of normal human development.
Embryonic Development
Development begins when a sperm fertilizes an egg and creates a single cell that has the potential to form an entire organism. In the first hours after fertilization, this cell divides into identical cells. In humans, approximately four days after fertilization and after several cycles of cell division, these cells begin to specialize, forming a hollow sphere of cells, called a blastocyst. The blastocyst has an outer layer of cells, and inside this hollow sphere, there is a cluster of cells called the inner cell mass. The cells of the inner cell mass go on to form virtually all of the tissues of the human body. Although the cells of the inner cell mass can form virtually every type of cell found in the human body, they cannot form an organism. These cells are referred to as pluripotent.
Pluripotent stem cells undergo further specialization into multipotent progenitor cells that then give rise to functional cells. Examples of stem and progenitor cells include:
1. Hematopoietic stem cells (adult stem cells) from the bone marrow that give rise to red blood cells, white blood cells, and platelets
2. Mesenchymal stem cells (adult stem cells) from the bone marrow that give rise to stromal cells, fat cells, and types of bone cells;
3. Epithelial stem cells (progenitor cells) that give rise to the various types of skin cells
4. Muscle satellite cells (progenitor cells) that contribute to differentiated muscle tissue
A pathway that is guided by the cell adhesion molecules is created as the cellular blastomere differentiates from the single-layered blastula to the three primary layers of germ cells in mammals, namely the ectoderm, mesoderm and endoderm (listed from most distal, or exterior, to the most proximal, or interior). The ectoderm ends up forming the skin and the nervous system, the mesoderm forms the bones and muscular tissue, and the endoderm forms the internal organ tissues.
Key Points
• The three major cell types in the mammalian body include germ cells (which develop into gametes), somatic cells ( diploid cells that develop into a majority of the human body) and stem cells (cells that can divide indefinitely).
• In human development, the inner cell mass exhibits the ability to differentiate and form all tissues of the body; however, they cannot form an organism.
• The various types of stem and progenitor cells included in the body that will differentiate to develop more specialized cells includes: hematopoietic stem cells, mesenchymal stem cells, epithelial stem cells and muscle satellite cells.
• To develop a multicellular oragnisms, cells must differentiate to specialize for different functions.
Key Terms
• blastocyst: the mammalian blastula formed during development where the inner cell mass can be found which forms the embryo
• inner cell mass: a mass of cells within a primordial embryo that will eventually develop into the distinct form of a fetus in most eutherian mammals
• proteome: the complete set of proteins encoded by a particular genome
• pluripotent: able to develop into more than one mature cell or tissue type, but not all | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.13%3A_Regulating_Gene_Expression_in_Cell_Development_-_Cellular_Differentiation.txt |
Learning Objectives
• Summarize how a cell can differentiate into a specialized cell
Cellular differentiation
How does a complex organism such as a human develop from a single cell—a fertilized egg—into the vast array of cell types such as nerve cells, muscle cells, and epithelial cells that characterize the adult? Throughout development and adulthood, the process of cellular differentiation leads cells to assume their final morphology and physiology. Differentiation is the process by which unspecialized cells become specialized to carry out distinct functions.
Stem Cells
A stem cell is an unspecialized cell that can divide without limit as needed and can, under specific conditions, differentiate into specialized cells. Stem cells are divided into several categories according to their potential to differentiate. The first embryonic cells that arise from the division of the zygote are the ultimate stem cells; these stems cells are described as totipotent because they have the potential to differentiate into any of the cells needed to enable an organism to grow and develop. The embryonic cells that develop from totipotent stem cells and are precursors to the fundamental tissue layers of the embryo are classified as pluripotent. A pluripotent stem cell is one that has the potential to differentiate into any type of human tissue but cannot support the full development of an organism. These cells then become slightly more specialized, and are referred to as multipotent cells. A multipotent stem cell has the potential to differentiate into different types of cells within a given cell lineage or small number of lineages, such as a red blood cell or white blood cell.
Finally, multipotent cells can become further specialized oligopotent cells. An oligopotent stem cell is limited to becoming one of a few different cell types. In contrast, a unipotent cell is fully specialized and can only reproduce to generate more of its own specific cell type. Stem cells are unique in that they can also continually divide and regenerate new stem cells instead of further specializing.
There are different stem cells present at different stages of a human’s life, including the embryonic stem cells of the embryo, fetal stem cells of the fetus, and adult stem cells in the adult. One type of adult stem cell is the epithelial stem cell, which gives rise to the keratinocytes (cells that produce keratin, the primary protein in nails and hair) in the multiple layers of epithelial cells in the epidermis of skin. Adult bone marrow has three distinct types of stem cells: hematopoietic stem cells, which give rise to red blood cells, white blood cells, and platelets; endothelial stem cells, which give rise to the endothelial cell types that line blood and lymph vessels; and mesenchymal stem cells, which give rise to the different types of muscle cells.
Differentiation
When a cell differentiates (i.e., becomes more specialized), it may undertake major changes in its size, shape, metabolic activity, and overall function. Because all cells in the body, beginning with the fertilized egg, contain the same DNA, how do the different cell types come to be so different? The answer is analogous to a movie script. Different actors in a movie all read from the same script, but each one only reads their own part of the script. Similarly, all cells contain the same full complement of DNA, but each type of cell only “reads” the portions of DNA that are relevant to its own functioning. In other terms, each cell has the genome but will only express specific genes, thereby having unique proteomes. In biology, this is referred to as the unique genetic expression of each cell. In order for a cell to differentiate into its specialized form and function, it need only manipulate those genes (and thus those proteins) that will be expressed, and not those that will remain silent.
Mechanism
The primary mechanism by which genes are turned “on” or “off” is through transcription factors. A transcription factor is one of a class of proteins that bind to specific genes on the DNA molecule and either promote or inhibit their transcription. The primary mechanism that determines which genes will be expressed and which ones will not is through the use of different transcription factor proteins, which bind to DNA and promote or hinder the transcription of different genes. Through the action of these transcription factors, cells specialize into one of hundreds of different cell types in the human body.
Key Points
• Different types of stem cells exhibit varying abilities to differentiate into specialized cells (from the most unlimited stem cell to the most restricted): totipotent, pluripotent, multipotent to oligopotent.
• Totipotent cells have the potential to differentiate into any of the cells needed to enable an organism to grow and develop; pluripotent cells have the potential to differentiate into any type of human tissue but cannot support the full development of an organism.
• A multipotent stem cell has the potential to differentiate into different types of cells within a given cell lineage or small number of lineages, while an oligopotent stem cell is limited to becoming one of a few different cell types.
• The process of cellular differentiation is under strict regulation by transcription factors which can either activate or repress expression of genes that will affect the proteome of the cell and thus, provide the necessary components it needs to become a specialized cell.
• All cells contain the same complement of DNA, or genome, but once differentiation occurs, it is the changes in the proteome that will distinguish one cell type from another.
Key Terms
• differentiate: to produce distinct cells, organs or to achieve specific functions by a process of development
• proteome: the complete set of proteins encoded by a particular genome
• transcription: the synthesis of RNA under the direction of DNA | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.14%3A_Regulating_Gene_Expression_in_Cell_Development_-_Mechanics_of_Cellular_Differentation.txt |
Learning Objectives
• Summarize the mechanisms and cell types that establish the body axes
Vertebrate axis formation
During development, as the germ layers form, the ball of cells still retains its spherical shape. However, animal bodies have lateral-medial (left-right), dorsal-ventral (back-belly), and anterior-posterior (head-feet) axes. How are these established? In one of the most seminal experiments ever to be carried out in developmental biology, Spemann and Mangold took dorsal cells from one embryo and transplanted them into the belly region of another embryo. They found that the transplanted embryo now had two notochords: one at the dorsal site from the original cells and another at the transplanted site. This suggested that the dorsal cells were genetically programmed to form the notochord and define the axis. Since then, researchers have identified many genes that are responsible for axis formation. Mutations in these genes leads to the loss of symmetry required for organism development. Animal bodies have externally visible symmetry. However, the internal organs are not symmetric. For example, the heart is on the left side and the liver on the right. The formation of the central left-right axis is an important process during development. This internal asymmetry is established very early during development and involves many genes. Research is still ongoing to fully understand the developmental implications of these genes.
Neural tube
In the developing chordate (including vertebrates), the neural tube is the embryo’s precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal, the ectodermal wall of which forms the rudiment of the nervous system.
Primary and secondary neurulation
The neural tube develops in two ways: primary neurulation and secondary neurulation. Primary neurulation divides the ectoderm into three cell types: the internally located neural tube, the externally located epidermis, and the neural crest cells, which develop in the region between the neural tube and epidermis but then migrate to new locations. Primary neurulation begins after the neural plate forms. The edges of the neural plate start to thicken and lift upward, forming the neural folds. The center of the neural plate remains grounded, allowing a U-shaped neural groove to form. This neural groove sets the boundary between the right and left sides of the embryo. The neural folds pinch in towards the midline of the embryo and fuse together to form the neural tube. In secondary neurulation, the cells of the neural plate form a cord-like structure that migrates inside the embryo and hollows to form the tube.
Each organism uses primary and secondary neurulation to varying degrees. Neurulation in fish proceeds only via the secondary form. In avian species the posterior regions of the tube develop using secondary neurulation and the anterior regions develop by primary neurulation. In mammals, secondary neurulation begins around the 35th somite. Mammalian neural tubes close in the head in the opposite order that they close in the trunk. In the head, neural crest cells migrate, the neural tube closes, and the overlying ectoderm closes. In the trunk, overlying ectoderm closes, the neural tube closes and neural crest cells migrate.
Neural tube subdivisions
Four neural tube subdivisions eventually develop into distinct regions of the central nervous system by the division of neuroepithelial cells: the prosencephalon, the mesencephalon, the rhombencephalon and the spinal cord. The prosencephalon further goes on to develop into the telencephalon (the forebrain or cerebrum) and the diencephalon (the optic vesicles and hypothalamus). The mesencephalon develops into the midbrain. The rhombencephalon develops into the metencephalon (the pons and cerebellum) and the myelencephalon (the medulla oblongata).
For a short time, the neural tube is open both cranially and caudally. These openings, called neuropores, close during the fourth week in the human. Improper closure of the neuropores can result in neural tube defects such as anencephaly or spina bifida. The dorsal part of the neural tube contains the alar plate, which is primarily associated with sensation. The ventral part of the neural tube contains the basal plate, which is primarily associated with motor (i.e., muscle) control.
Signaling molecules and other factors
The neural tube patterns along the dorsal-ventral axis establish defined compartments of neural progenitor cells that lead to distinct classes of neurons. This patterning occurs early in development and results from the activity of several secreted signaling molecules. Sonic hedgehog (Shh) is a key player in patterning the ventral axis, while Bone morphogenic proteins (Bmp) and Wnt family members play an important role in patterning the dorsal axis. Other factors shown to provide positional information to the neural progenitor cells include Fibroblast growth factors (FGF) and Retinoic Acid. Retinoic acid is required ventrally along with Shh to induce Pax6 and Olig2 during differentiation of motor neurons. Three main ventral cell types are established during early neural tube development: the floor plate cells, which form at the ventral midline during the neural fold stage; as well as the more dorsally located motor neurons and interneurons. These cell types are specified by the secretion of Shh from the notochord (located ventrally to the neural tube), and later from the floor plate cells. Shh acts as a morphogen, meaning that it acts in a concentration-dependent manner to specify cell types as it moves further from its source. The different combinations of expression of transcription factors along the dorsal-ventral axis of the neural tube are responsible for creating the identity of the neuronal progenitor cells.
Key Points
• The three axes of the animal body are established in development via the expression of specific sets of genes that regulate which cells will develop into specific structures.
• During development, the dorsal cells are genetically programmed to develop into the notochord and define the axis.
• The neural tube can develop in two ways: primary or secondary neurulation, which are used by organisms in varying degrees to establish the neural tube that will develop into the central nervous system (brain and spinal cord).
• Specific patterns along the neural tube that are established via secretion and production of specific signaling molecules (such as Wnt, Shh, BMP and retinoic acid) play a key role in patterning the dorsal and ventral axes.
Key Terms
• neural tube: hollow longitudinal dorsal tube formed in the folding and subsequent fusion of the opposite ectodermal folds in the embryo that gives rise to the brain and spinal cord
• neurulation: the process by which the beginnings of the vertebrate nervous system is formed in embryos
• anencephaly: a lethal birth defect in which most of the brain and parts of the skull are missing; absence of the encephalon
• notochord: a flexible rodlike structure that forms the main support of the body in the lowest chordates; a primitive spine | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.15%3A_Regulating_Gene_Expression_in_Cell_Development_-_Establishing_Body_Axes_during_Development.txt |
Learning Objectives
• Describe the role genes play in development and ensuring proper spatial positioning
Genes provide positional information
Gastrulation leads to the formation of the three germ layers that give rise, during further development, to the different organs in the animal body. This process, known as organogenesis, is characterized by rapid and precise movements of the cells within the embryo.
Organogenesis
Organs form from the germ layers through the process of differentiation. During differentiation, the embryonic stem cells express specific sets of genes which will determine their ultimate cell type. For example, some cells in the ectoderm (the outer tissue layer of the embryo) will express the genes specific to skin cells. As a result, these cells will differentiate into epidermal cells. The process of differentiation is regulated by cellular signaling cascades. Scientists study organogenesis extensively in the lab in fruit flies (Drosophila) and the nematode Caenorhabditis elegans. Drosophila have segments along their bodies, and the patterning associated with the segment formation has allowed scientists to study which genes play important roles in organogenesis along the length of the embryo at different time points. The nematode C.elegans has roughly 1000 somatic cells and scientists have studied the fate of each of these cells during their development in the nematode life cycle. There is little variation in patterns of cell lineage between individuals, unlike in mammals where cell development from the embryo is dependent on cellular cues.
In vertebrates, one of the primary steps during organogenesis is the formation of the neural system. The ectoderm forms epithelial cells and tissues, as well as neuronal tissues. During the formation of the neural system, special signaling molecules called growth factors signal some cells at the edge of the ectoderm to become epidermis cells. The remaining cells in the center form the neural plate. If the signaling by growth factors were disrupted, then the entire ectoderm would differentiate into neural tissue. The neural plate undergoes a series of cell movements where it rolls up and forms a tube called the neural tube. In further development, the neural tube will give rise to the brain and the spinal cord. The mesoderm that lies on either side of the vertebrate neural tube will develop into the various connective tissues of the animal body. A spatial pattern of gene expression reorganizes the mesoderm into groups of cells called somites with spaces between them. The somites will further develop into the ribs, lungs, and segmental (spine) muscle. The mesoderm also forms a structure called the notochord, which is rod-shaped and forms the central axis of the animal body.
Key Points
• Organogenesis results in the formation of the various organs in the body; however it will only occur if specific sets of genes are expressed to determine ultimate cell type.
• The ability of specific cells to migrate to the the edge of the ectoderm is highly regulated by specific gene expression and allows for differentiation into epidermal cells; in contrast, the cells which remain in the center will develop into the neural plate.
• The expression of specific sets of genes will also regulate the reorganization of the mesoderm into distinct groups of cells, called somites, which develop into the ribs, lungs, spine muscle and notochord.
Key Terms
• gastrulation: the stage of embryo development at which a gastrula is formed from the blastula by the inward migration of cells
• organogenesis: the formation and development of the organs of an organism from embryonic cells
• somite: one of the paired masses of mesoderm distributed along the sides of the neural tube that will eventually become dermis, skeletal muscle, or vertebrae | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.16%3A_Regulating_Gene_Expression_in_Cell_Development_-_Gene_Expression_for_Spatial_Positioning.txt |
Learning Objectives
• Describe how cells can migrate within an organism
Cell migration
Cell migration is a central process in the development and maintenance of multicellular organisms. Processes such as tissue formation during embryonic development, wound healing, and immune responses, all require the orchestrated movement of cells in particular directions to specific locations. Errors during this process have serious consequences, including intellectual disability, vascular disease, tumor formation and metastasis. An understanding of the mechanism by which cells migrate may lead to the development of novel therapeutic strategies for controlling, for example, invasive tumor cells.
Cells often migrate in response to specific external signals, including chemical signals and mechanical signals. Due to a highly viscous environment, cells need to permanently produce forces in order to move. Cells achieve active movement by very different mechanisms. Many less complex prokaryotic organisms (and sperm cells) use flagella or cilia to propel themselves. Eukaryotic cell migration typically is far more complex and can consist of combinations of different migration mechanisms. It generally involves drastic changes in cell shape which are driven by the cytoskeleton, for instance a series of contractions and expansions due to cytoplasmic displacement. Two very distinct migration scenarios are crawling motion (most commonly studied) and blebbing motility.
The migration of cultured cells attached to a surface is commonly studied using microscopy. As cell movement is very slow (only a few µm/minute), time-lapse microscopy videos are recorded of the migrating cells to speed up the movement. Such videos reveal that the leading cell front is very active with a characteristic behavior of successive contractions and expansions. It is generally accepted that the leading front is the main motor that pulls the cell forward.
Cell Migration: Phase images of BSC 1 cells migrating in a scratch assay in the absence of serum over a period of 15 hours.
Common features of cell migration
The processes underlying mammalian cell migration are believed to be consistent with those of (non-spermatozoic) locomotion. Observations in common include cytoplasmic displacement at the leading front and laminar removal of dorsally-accumulated debris toward trailing end. The latter feature is most easily observed when aggregates of a surface molecule are cross-linked with a fluorescent antibody or when small beads become artificially bound to the front of the cell. Other eukaryotic cells are observed to migrate similarly. The amoeba Dictyostelium discoideum is useful to researchers because they consistently exhibit chemotaxis in response to cyclic AMP; they move more quickly than cultured mammalian cells; and they have a haploid genome that simplifies the process of connecting a particular gene product with its effect on cellular behavior.
Key Points
• The disruption or dysfunction of cell migration processes can lead to formation of various diseases such as metastasis, tumor formation and vascular disease.
• In prokaryotic organisms, and some eukaryotic cells such as sperm cells, cell migration occurs via the use of a cilia or flagella to propel forward.
• In eukaryotic organisms, cell migration is a much more complex process and can include, but is not excluded to, changes in the cytoskeleton, motor proteins, blebbing, and cytoplasmic displacement; it involves both external and internal signals that mediate these processes.
Key Terms
• bleb: an irregular bulge in the plasma membrane of a cell
• chemotaxis: the movement of a cell or an organism in response to a chemical stimulant
• laminar: of fluid motion, smooth and regular, flowing as though in different layers
• metastasis: the transference of a bodily function or disease to another part of the body; specifically the development of a secondary area of disease remote from the original site, as with some cancers | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.17%3A_Regulating_Gene_Expression_in_Cell_Development_-_Cell_Migration_in_Multicellular_Organisms.txt |
Learning Objectives
• Explain the importance of programmed cell death, including apoptosis and autophagy
Programmed cell death
Programmed cell-death (or PCD) is death of a cell in any form, mediated by an intracellular program. PCD is carried out in a regulated process, which usually confers advantage during an organism’s life-cycle. For example, the differentiation of fingers and toes in a developing human embryo occurs because cells between the fingers apoptose, or die; the result is that the digits are separate. PCD serves fundamental functions during both plant and metazoa (multicellular animal) tissue development. Apoptosis and autophagy are both forms of PCD, but necrosis is a non-physiological process that occurs as a result of infection or injury.
Apoptosis
Apoptosis is the process of PCD that may occur in multicellular organisms. Biochemical events lead to characteristic cell changes ( morphology ) and death. These changes include blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation, and chromosomal DNA fragmentation. There appears to be some variation in the morphology and indeed the biochemistry of these “suicide” pathways. Some tread the path of apoptosis, while others follow a more generalized pathway to deletion; however both are usually genetically and synthetically motivated. There is some evidence that certain symptoms of apoptosis, such as endonuclease activation, can be spuriously induced without engaging a genetic cascade; however, it is presumed that true apoptosis and PCD must be genetically mediated. It is also becoming clear that mitosis (the division of the cell nucleus) and apoptosis are linked in some way, and that the balance achieved depends on signals received from appropriate growth or survival factors.
When a cell is damaged, superfluous, or potentially dangerous to an organism, a cell can initiate a mechanism to trigger apoptosis. Apoptosis allows a cell to die in a controlled manner that prevents the release of potentially damaging molecules from inside the cell. There are many internal checkpoints that monitor a cell’s health; if abnormalities are observed, a cell can spontaneously initiate the process of apoptosis. However, in some cases, such as a viral infection or uncontrolled cell division due to cancer, the cell’s normal checks and balances fail.
Apoptosis can also be initiated via external signaling. For example, most normal animal cells have receptors that interact with the extracellular matrix, a network of glycoproteins that provides structural support for cells in an organism. The binding of cellular receptors to the extracellular matrix initiates a signaling cascade within the cell. However, if the cell moves away from the extracellular matrix, the signaling ceases, and the cell undergoes apoptosis. This system keeps cells from traveling through the body and proliferating out of control, as happens with tumor cells that metastasize.
Another example of external signaling that leads to apoptosis occurs in T-cell development. T-cells are immune cells that bind to foreign macromolecules and particles, and target them for destruction by the immune system. Normally, T-cells do not target “self” proteins (those of their own organism), a process that can lead to autoimmune diseases. In order to develop the ability to discriminate between self and non-self, immature T-cells undergo screening to determine whether they bind to so-called self proteins. If the T-cell receptor binds to self proteins, the cell initiates apoptosis to remove the potentially dangerous cell.
Apoptosis is also essential for normal embryological development. In vertebrates, for example, early stages of development include the formation of web-like tissue between individual fingers and toes. During the course of normal development, these unneeded cells must be eliminated, enabling fully separated fingers and toes to form. A cell signaling mechanism triggers apoptosis, which destroys the cells between the developing digits.
Autophagy
Macroautophagy, often referred to as autophagy, is a type of programmed cell death accomplished through self-digestion. It is a catabolic process that results in the autophagosomic-lysosomal degradation of bulk cytoplasmic contents, abnormal protein aggregates, and excess or damaged organelles. Autophagy is generally activated by conditions of nutrient deprivation but has also been associated with physiological as well as pathological processes such as development, differentiation, neurodegenerative diseases, stress (physiology), infection and cancer.
Necrosis
Necrosis is the death of a cell caused by external factors such as trauma or infection and occurs in several different forms. Recently a form of programmed necrosis, called necroptosis, has been recognized as an alternate form of PCD. It is hypothesized that necroptosis can serve as a cell-death backup to apoptosis when the apoptosis signaling is blocked by endogenous or exogenous factors, such as viruses or mutations.
Key Points
• Programmed cell death can provide an advantage to an organism during development, for instance by maintaining homeostasis and protection against potentially disruptive issues which may arise during the life of a cell.
• Apoptosis is a process of programmed cell death that is regulated by numerous biochemical events and appears to be genetically mediated.
• Autophagy is a process of programmed cell death that is characterized as a catabolic process via formation of an autophagolysosome which degrades damaged cellular contents.
• Necrosis occurs when cellular death is caused by external factors and is characterized as an alternate form of programmed cell death, called necroptosis.
Key Terms
• apoptosis: a process of programmed cell death
• extracellular matrix: All the connective tissues and fibres that are not part of a cell, but rather provide support.
• autophagy: a type of programmed cell death accomplished through self-digestion | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.18%3A_Regulating_Gene_Expression_in_Cell_Development_-_Programmed_Cell_Death.txt |
Learning Objectives
• Describe how cancer is caused by uncontrolled cell growth
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 do not 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, but the one most studied 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.
Another type of gene often deregulated in cancers are proto-oncogenes which 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 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.
Key Points
• Cancer results from a gene that is not normally expressed in a cell, but is switched on and expressed at high levels due to mutations or alterations in gene regulation.
• Alterations in histone acetylation, activation of transcription factors, increased RNA stability, increased translational control, and protein modification are all observed in cancer cells.
• Tumor suppressor genes, active in normal cells, work to prevent uncontrolled cell growth.
• Proto- oncogenes, which are positive cell-cycle regulators, can become oncogenes and cause cancer when mutated.
Key Terms
• oncogene: any gene that contributes to the conversion of a normal cell into a cancerous cell when mutated or expressed at high levels
• proto-oncogene: a gene that promotes the specialization and division of normal cells that becomes an oncogene following mutation
• cancer: a disease in which the cells of a tissue undergo uncontrolled (and often rapid) proliferation | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.19%3A_Cancer_and_Gene_Regulation_-_Altered_Gene_Expression_in_Cancer.txt |
Learning Objectives
• Describe the role played by epigenetic alterations to gene expression in the development of cancer
Cancer and Epigenetic Alterations
Cancer epigenetics is the study of epigenetic modifications to the genome of cancer cells that do not involve a change in the nucleotide sequence. Epigenetic alterations are as important as genetic mutations in a cell’s transformation to cancer. Mechanisms of epigenetic silencing of tumor suppressor genes and activation of oncogenes include: alteration in CpG island methylation patterns, histone modifications, and dysregulation of DNA binding proteins.
Silencing genes through epigenetic mechanisms is very common in cancer cells and include 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, genomic regions that contain a high frequency of CpG sites, where a cytosine nucleotide occurs next to a guanine nucleotide. Histone proteins that surround that region lack the acetylation modification (the addition of an acetyl group) 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 are understanding how these 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 also thought to be regulated by epigenetic mechanisms. As our knowledge deepens of how genes are controlled, new ways to treat these diseases and cancer will emerge.
Key Points
• The DNA in the promoter region of silenced genes in cancer cells is methylated on cytosine DNA residues in CpG islands.
• Histone proteins that surround the promoter region of silenced genes lack the acetylation modification that is present when the genes are expressed in normal cells.
• When the combination of DNA methylation and histone deacetylation occur within cancer cells, the gene present in that chromosomal region is silenced.
• Epigenetic changes that are altered in cancer can be reversed and may, therefore, be helpful in new drug and therapy design.
Key Terms
• epigenetic: the study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence
• methylation: the addition of a methyl group to cytosine and adenine residues in DNA that leads to the epigenetic modification of DNA and the reduction of gene expression and protein production
• acetylation: the reaction of a substance with acetic acid or one of its derivatives; the introduction of one or more acetyl groups into a substance | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.20%3A_Cancer_and_Gene_Regulation_-_Epigenetic_Alterations_in_Cancer.txt |
Learning Objectives
• Explain the role of transcription factors in cancer
Cancer and Transcriptional Control
Many transcription factors, especially some that are proto-oncogenes or tumor suppressors, help regulate the cell cycle and, as such, determine how large a cell will get and when it can divide into two daughter cells. 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.
Key Points
• The mutations that activate transcription factors can increase the binding of a transcription factor to its binding site in a promoter leading to increased transcriptional activation of that gene and resulting in altered cell growth.
• A mutation in the DNA of a promoter or enhancer region may increase the binding ability of a transcription factor, which may then lead to the increased transcription and anomalous gene expression that is seen in cancer cells.
• Studying how to control the transcriptional activation of gene expression in cancer cells along with identifying how a transcription factor binds or a pathway activates where a gene can be turned off has led researchers to new drugs and novel ways of treating cancer.
Key Terms
• transcription factor: a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to mRNA
16.22: Cancer and Gene Regulation - Cancer and Post-Transcriptional Control
Learning Objectives
• Explain how post-transcriptional control can result in cancer
Cancer and Post-transcriptional Control
Post-transcriptional regulation is the control of gene expression at the RNA level; therefore, between the transcription and the translation of the gene. After being produced, the stability and distribution of the different transcripts is regulated (post-transcriptional regulation) by means of RNA-binding proteins (RBP) that control the various steps and rates of the transcripts: events such as alternative splicing, nuclear degradation (exosome), processing, nuclear export (three alternative pathways), sequestration in DCP2-bodies for storage or degradation, and, ultimately, translation.
Changes in the post-transcriptional control of a gene can result in cancer. Recently, several groups of researchers have shown that specific cancers have altered expression of microRNAs (miRNAs). miRNAs bind to the 3′ UTR or 5′ UTR of RNA molecules to degrade them. Overexpression of these miRNAs could be detrimental to normal cellular activity. An increase in 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.
Key Points
• Specific cancers have altered expression of miRNAs; changes in the miRNA population of particular cancers varies depending on the type of cancer.
• Having too many miRNAs can dramatically decrease the RNA population leading to a decrease in protein expression.
• Studies have found that some miRNAs are specifically expressed only in cancer cells.
Key Terms
• microRNA: a single-stranded, non-coding form of RNA, having only about 20-30 nucleotides, that has a number of functions including the regulation of gene expression
• exosome: a vesicle responsible for the selective removal of plasma membrane proteins
16.23: Cancer and Gene Regulation - Cancer and Translational Control
Learning Objectives
• Determine how translational or post-translational modifications can lead to cancer
There are many examples of translational or post-translational modifications of proteins that 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 Therapy
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.
Key Points
• Protein modifications from the increased translation of a protein to changes in protein phosphorylation to alternative splice variants of a protein are found in cancer cells.
• The expression of the wrong protein dramatically alters cell function and contributes to the progression of cancer.
• Gene regulation and gene function provide scientists with the opportunity to design medicines and therapies that specifically target diseased cells or exploit the overexpression of specific proteins as cancer treatment.
Key Terms
• targeted therapy: a type of medication that blocks the growth of cancer cells by interfering with specific targeted molecules rather than by interfering with rapidly dividing cells
• cancer: a disease in which the cells of a tissue undergo uncontrolled (and often rapid) proliferation
• post-translational modification: the chemical modification of a protein after its translation; one of the later steps in protein biosynthesis, and thus gene expression, for many proteins | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/16%3A_Gene_Expression/16.21%3A_Cancer_and_Gene_Regulation_-_Cancer_and_Transcriptional_Control.txt |
Relying on the study of DNA, genomics analyzes entire genomes, while biotechnology uses biological agents for technological advancements.
Learning Objectives
• Justify an overview of the field of biotechnology
Key Points
• Genomics includes the study of a complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species.
• Through DNA sequencing, genomic information is used to create maps of the DNA of different organisms.
• Biotechnology, or the use of biological agents for technological progression, has applications in medicine, agriculture, and in industry, which include processes such as fermentation and the production of biofuels.
Key Terms
• genomics: the study of the complete genome of an organism
• sequencing: the procedure of determining the order of amino acids in the polypeptide chain of a protein (protein sequencing) or of nucleotides in a DNA section comprising a gene (gene sequencing)
• biotechnology: the use of living organisms (especially microorganisms) in industrial, agricultural, medical, and other technological applications
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.
Another rapidly-advancing field that utilizes DNA is biotechnology. This field involves 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.
17.1B: Basic Techniques to Manipulate Genetic Material (DNA and RNA)
Basic techniques used in genetic material manipulation include extraction, gel electrophoresis, PCR, and blotting methods.
Learning Objectives
• Distinguish among the basic techniques used to manipulate DNA and RNA
Key Points
• The first step to study or work with nucleic acids includes the isolation or extraction of DNA or RNA from cells.
• Gel electrophoresis depends on the negatively-charged ions present on nucleic acids at neutral or basic pH to separate molecules on the basis of size.
• Specific regions of DNA can be amplified through the use of polymerase chain reaction for further analysis.
• Southern blotting involves the transfer of DNA to a nylon membrane, while northern blotting is the transfer of RNA to a nylon membrane; these techniques allow samples to be probed for the presence of certain sequences.
Key Terms
• denaturation: the change of folding structure of a protein (and thus of physical properties) caused by heating, changes in pH, or exposure to certain chemicals
• electrophoresis: a method for the separation and analysis of large molecules, such as proteins or nucleic acids, by migrating a colloidal solution of them through a gel under the influence of an electric field
• polymerase chain reaction: a technique in molecular biology for creating multiple copies of DNA from a sample
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.
DNA and RNA Extraction
To study or manipulate nucleic acids, the DNA or RNA must first be isolated or extracted from the cells. This can be done through various techniques. 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 that is mostly a detergent); lysis means “to split.” These enzymes break apart lipid molecules in the membranes of the cell and the nucleus. 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. Samples can be stored at –80°C for 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 and may be separated as whole chromosomes or fragments. The nucleic acids are loaded into a slot near the negative electrode of a 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.
Amplification of Nucleic Acid Fragments by Polymerase Chain Reaction
Polymerase chain reaction (PCR) is a technique used to amplify specific regions of DNA for further analysis. 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.
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. 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; 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/17%3A_Biotechnology_and_Genomics/17.01%3A_Biotechnology/17.1A%3A_Biotechnology.txt |
Molecular cloning reproduces the desired regions or fragments of a genome, enabling the manipulation and study of genes.
Learning Objectives
• Describe the process of molecular cloning
Key Points
• Cloning small fragments of a genome allows specific genes, their protein products, and non-coding regions to be studied in isolation.
• A plasmid, also known as a vector, is a small circular DNA molecule that replicates independently of the chromosomal DNA; it can be used to provide a “folder” in which to insert a desired DNA fragment.
• Recombinant DNA molecules are plasmids with foreign DNA inserted into them; they are created artificially as they do not occur in nature.
• Bacteria and yeast naturally produce clones of themselves when they replicate asexually through cellular cloning.
Key Terms
• recombinant DNA: DNA that has been engineered by splicing together fragments of DNA from multiple species and introduced into the cells of a host
• molecular cloning: a biological method that creates many identical DNA molecules and directs their replication within a host organism
• plasmid: a circle of double-stranded DNA that is separate from the chromosomes, which is found in bacteria and protozoa
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.
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.
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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/17%3A_Biotechnology_and_Genomics/17.01%3A_Biotechnology/17.1C%3A_Molecular_and_Cellular_Cloning.txt |
Reproductive cloning, possible through artificially-induced asexual reproduction, is a method used to make a clone of an entire organism.
Learning Objectives
• Differentiate reproductive cloning from cellular and molecular cloning
Key Points
• A form of asexual reproduction, parthenogenesis, occurs when an embryo grows and develops without the fertilization of the egg.
• In reproductive cloning, if the haploid nucleus of an egg cell is replaced with a diploid nucleus from the cell of an individual of the same species, it will become a zygote that is genetically identical to the donor.
• Reproductive cloning has become successful, but still has limitations as cloned individuals often exhibit facial, limb, and cardiac abnormalities.
• Therapeutic cloning, the cloning of human embryos as a source of embryonic stem cells, has been attempted in order to produce cells that can be used to treat detrimental diseases or defects.
Key Terms
• clone: a living organism produced asexually from a single ancestor, to which it is genetically identical
• stem cell: a primal undifferentiated cell from which a variety of other cells can develop through the process of cellular differentiation
• parthenogenesis: a form of asexual reproduction where growth and development of embryos occur without fertilization
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 to generate an identical copy or 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. 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. 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. 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 (e.g. 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, the technique produces stem cells that 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/17%3A_Biotechnology_and_Genomics/17.01%3A_Biotechnology/17.1D%3A_Reproductive_Cloning.txt |
In genetic engineering, an organism’s genotype is altered using recombinant DNA, created by molecular cloning, to modify an organism’s DNA.
Learning Objectives
• Discuss how genetic engineering leads to DNA modification.
Key Points
• A genetically modified organism receives recombinant DNA generated through molecular cloning.
• Transgenic host organisms receive their foreign DNA from a different species.
• The use of recombinant DNA vectors to alter the expression of a particular gene is known as gene targeting, which is done through the addition of mutations in a gene or the exclusion of the expression of a certain gene.
• Recombinant DNA technology involves transferring a DNA fragment of interest from one organism to another by inserting it into a vector.
Key Terms
• recombinant DNA: DNA that has been engineered by splicing together fragments of DNA from multiple species and introduced into the cells of a host
• genetic engineering: the deliberate modification of the genetic structure of an organism
• genetically modified organism: an organism whose genetic material has been altered using genetic engineering techniques
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. Recombinant DNA technology, or DNA cloning, is the process of transferring a DNA fragment of interest from one organism to a self-replicating genetic element, such as a bacteria plasmid, which is called a vector. The DNA of interest can then be propagated in another organism. 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/17%3A_Biotechnology_and_Genomics/17.01%3A_Biotechnology/17.1E%3A__Genetic_Engineering.txt |
Transgenic modification, adding recombinant DNA to a species, has led to the expression of desirable genes in plants and animals.
Learning Objectives
• Describe how research on transgenic plants and animals aids humans.
Key Points
• Transgenic animals are those that have been modified to express recombinant DNA from another species.
• Manipulation of transgenic plants, those that have received recombinant DNA from other species, has led to the creation of species that display disease resistance, herbicide and pesticide resistance, better nutritional value, and better shelf-life.
• The thickness of a plant’s cell wall makes the artificial introduction of DNA into plant cells much more challenging than in animal cells.
Key Terms
• transgenic: of or pertaining to an organism whose genome has been changed by the addition of a gene from another species; genetically modified
• genetically modified organism: an organism whose genetic material has been altered using genetic engineering techniques
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, while others 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 (or creating genetically modified organisms called GMOs) has helped to create desirable traits, such as disease resistance, herbicide and pesticide resistance, better nutritional value, and better shelf-life. 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 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 stunt the plants, which become 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/17%3A_Biotechnology_and_Genomics/17.01%3A_Biotechnology/17.1F%3A__Genetically_Modified_Organisms_%28GMOs%29.txt |
From manipulation of mutant genes to enhanced resistance to disease, biotechnology has allowed advances in medicine.
Learning Objectives
• Give examples of how biotechnology is used in medicine.
Key Points
• The study of pharmacogenomics can result in the development of tailor-made vaccines for people, more accurate means of determining drug dosages, improvements in drug discovery and approval, and the development of safer vaccines.
• Modern biotechnology can be used to manufacture drugs more easily and cheaply, as they can be produced in larger quantities from existing genetic sources.
• Genetic diagnosis involves the process of testing for suspected genetic defects before administering treatment through genetic testing.
• In gene therapy, a good gene is introduced at a random location in the genome to aid the cure of a disease that is caused by a mutated gene.
Key Terms
• gene therapy: any of several therapies involving the insertion of genes into a patient’s cells in order to replace defective ones
• pharmacogenomics: the study of genes that code for enzymes that metabolize drugs, and the design of tailor-made drugs adapted to an individual’s genetic make-up
• immunodeficiency: a depletion in the body’s natural immune system, or in some component of it
Biotechnology in Medicine
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.
Pharmacogenomics is the study of how the genetic inheritance of an individual affects his/her body’s response to drugs. It is a coined word derived from the words “pharmacology” and ” genomics “. It is, therefore, the study of the relationship between pharmaceuticals and genetics. The vision of pharmacogenomics is to be able to design and produce drugs that are adapted to each person’s genetic makeup. Pharmacogenomics results in the following benefits:
1. Development of tailor-made medicines. Using pharmacogenomics, pharmaceutical companies can create drugs based on the proteins, enzymes, and RNA molecules that are associated with specific genes and diseases. These tailor-made drugs promise not only to maximize therapeutic effects, but also to decrease damage to nearby healthy cells.
2. More accurate methods of determining appropriate drug dosages. Knowing a patient’s genetics will enable doctors to determine how well the patient’s body can process and metabolize a medicine. This will maximize the value of the medicine and decrease the likelihood of overdose.
3. Improvements in the drug discovery and approval process. The discovery of potential therapies will be made easier using genome targets. Genes have been associated with numerous diseases and disorders. With modern biotechnology, these genes can be used as targets for the development of effective new therapies, which could significantly shorten the drug discovery process.
4. Better vaccines. Safer vaccines can be designed and produced by organisms transformed by means of genetic engineering. These vaccines will elicit the immune response without the attendant risks of infection. They will be inexpensive, stable, easy to store, and capable of being engineered to carry several strains of pathogen at once.
Modern biotechnology can be used to manufacture existing drugs more easily and cheaply. The first genetically-engineered products were medicines designed to combat human diseases. In 1978, Genentech joined a gene for insulin with a plasmid vector and put the resulting gene into a bacterium called Escherichia coli. Insulin, widely used for the treatment of diabetes, was previously extracted from sheep and pigs. It was very expensive and often elicited unwanted allergic responses. The resulting genetically-engineered bacterium enabled the production of vast quantities of human insulin at low cost. Since then, modern biotechnology has made it possible to produce more easily and cheaply the human growth hormone, clotting factors for hemophiliacs, fertility drugs, erythropoietin, and other drugs. Genomic knowledge of the genes involved in diseases, disease pathways, and drug-response sites are expected to lead to the discovery of thousands more new targets.
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. 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 to determine the presence or absence of disease-causing genes in families with specific, debilitating diseases.
Genetic testing involves the direct examination of the DNA molecule itself. A scientist scans a patient’s DNA sample for mutated sequences. There are two major types of gene tests. In the first type, a researcher may design short pieces of DNA whose sequences are complementary to the mutated sequences. These probes will seek their complement among the base pairs of an individual’s genome. If the mutated sequence is present in the patient’s genome, the probe will bind to it and flag the mutation. In the second type, a researcher may conduct the gene test by comparing the sequence of DNA bases in a patient’s gene to a normal version of the gene.
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. 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).
17.1H: Production of Vaccines Antibiotics and Hormones
Biotechnological advances in gene manipulation techniques have further resulted in the production of vaccines, antibiotics, and hormones.
Learning Objectives
• Discuss the methods by which biotechnology is used to produce vaccines, antibiotics, and hormones.
Key Points
• Vaccines use weakened or inactive forms of microorganisms to mount the initial immune response through the use of antigens, which are produced through use the genes of microbes that are cloned into vectors.
• Antibiotics, agents that inhibit bacterial growth or kill bacteria, are produced by cultivating and manipulating fungal cells.
• Hormones, such as the human growth hormone (HGH), can be formulated through recombinant DNA technology; for example, HGH can be cloned from a cDNA library and inserted into E. coli cells by cloning it into a bacterial vector.
Key Terms
• bactericidal: that which kills bacteria
• bacteriostatic: that which slows down or stalls bacterial growth
• antigen: a substance that binds to a specific antibody; may cause an immune response
Vaccines
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
Antibiotics are biotechnological products that inhibit bacterial growth or kill bacteria. 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. Many antibacterial compounds are classified on the basis of their chemical or biosynthetic origin into natural, semisynthetic, and synthetic. Another classification system is based on biological activity. In this classification, antibiotics are divided into two broad groups according to their biological effect on microorganisms: bactericidal agents kill bacteria, and bacteriostatic agents slow down or stall bacterial growth.
Hormones
Recombinant DNA technology was used to produce large-scale quantities of human insulin (a hormone) 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 recent times, human growth hormone (HGH) has been 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. The bacteria was then grown and the hormone isolated, enabling large scale commercial production. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/17%3A_Biotechnology_and_Genomics/17.01%3A_Biotechnology/17.1G%3A_Biotechnology_in_Medicine.txt |
Genetic maps provide information about which chromosomes contain specific genes and precisely where the genes lie on that chromosome.
Learning Objectives
• Describe the different types of genetic markers that are used in generating genetic maps of DNA
Key Points
• Genetic mapping, often called linkage mapping, provides information about the location of a specific gene along a chromosome.
• Gene linkage describes the phenomenon that certain genes are physically linked by being located on the same chromosome and have a tendency to be inherited together.
• Genetic recombination involves the production of a novel set of genetic information by breaking and rejoining DNA fragments that have a great distance between them along the chromosome.
• The construction of genetic maps is reliant on the natural process of recombination which results in the ability to identify genetic markers with variability within a population.
• Genetic markers that can be used in generating genetic maps include restriction length polymorphisms ( RFLP ); variable number of tandem repeats (VNTRs); microsatellite polymorphisms; and single nucleotide polymorphisms ( SNPs ).
Key Terms
• polymorphism: the regular existence of two or more different genotypes within a given species or population
• SNP: single nucleotide polymorphism is single base pair of DNA which is polymorphic with respect to a population
• microsatellite: any of a group of polymorphic loci in DNA that consist of repeat units of just a few base pairs
• RFLP: restriction fragment length polymorphism is a section of DNA whose length varies among individuals and which is delimited by a base which does not occur within it
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; 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. 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 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; 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; thus, it is often referred to as short tandem repeats(STRs). 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/17%3A_Biotechnology_and_Genomics/17.02%3A_Mapping_Genomes/17.2A%3A_Genetic_Maps.txt |
Physical maps display the physical distance between genes and can be constructed using cytogenetic, radiation hybrid, or sequence mapping.
Learning Objectives
• Describe the methods used to physically map genes: cytogenetic mapping, radiation hybrid mapping, and sequence mapping
Key Points
• Physical maps provide specified detail about the number of bases and physical distance that exists between genetic markers.
• Cytogenetic mapping is a method used to construct physical maps that uses stained sections of chromosomes to approximate the distance between genetic markers.
• Radiation hybrid mapping is a method used to construct physical maps that uses radiation or x-rays to break DNA into fragments to determine the distance between genetic markers and their order on the chromosome.
• Sequence mapping is a method used to construct physical maps that uses already-known locations of genetic markers to determine distances in number of base pairs.
Key Terms
• cytogenetic: of or pertaining to the origin and development of cells
• physical map: a map showing how much DNA separates two genes and is measured in base pairs
• expressed sequence tag: a short sub-sequence of a cDNA sequence that may be used to identify gene transcripts
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 research organisms. Genome mapping is an-ongoing process; as better 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 worldwide 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/17%3A_Biotechnology_and_Genomics/17.02%3A_Mapping_Genomes/17.2B%3A_Physical_Maps_and_Integration_with_Genetic_Maps.txt |
The strategies used for sequencing genomes include the Sanger method, shotgun sequencing, pairwise end, and next-generation sequencing.
Learning Objectives
• Compare the different strategies used for whole-genome sequencing: Sanger method, shotgun sequencing, pairwise-end sequencing, and next-generation sequencing
Key Points
• The Sanger method is a basic sequencing technique that uses fluorescently-labeled dideoxynucleotides (ddNTPs) during DNA replication which results in multiple short strands of replicated DNA that terminate at different points, based on where the ddNTP was incorporated.
• Shotgun sequencing is a method that randomly cuts DNA fragments into smaller pieces and then, with the help of a computer, takes the DNA fragments, analyzes them for overlapping sequences, and reassembles the entire DNA sequence.
• Pairwise-end sequencing is a type of shotgun sequencing which is used for larger genomes and analyzes both ends of the DNA fragments for overlap.
• Next-generation sequencing is a type of sequencing which is automated and relies on sophisticated software for rapid DNA sequencing.
Key Terms
• fluorophore: a molecule or functional group which is capable of fluorescence
• contig: a set of overlapping DNA segments, derived from a single source of genetic material, from which the complete sequence may be deduced
• dideoxynucleotide: any nucleotide formed from a deoxynucleotide by loss of an a second hydroxyl group from the deoxyribose group
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. 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 due to their 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.
Early Strategies: Shotgun Sequencing and Pair-Wise End Sequencing
In the 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 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. Sophisticated software is used to manage the cumbersome process of putting all the fragments in order. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/17%3A_Biotechnology_and_Genomics/17.03%3A_Whole-Genome_Sequencing/17.3A%3A_Strategies_Used_in_Sequencing_Projects.txt |
Sequencing genomes of model organisms allows scientists to study homologous proteins in more complex eukaryotes, such as humans.
Learning Objectives
• Describe the model organisms used in whole-genome sequencing
Key Points
• The first genome to be completely sequenced was the bacterial virus, bacteriophage fx174, which is 5368 base pairs.
• Scientists utilize genome sequencing from model organisms to study homologous proteins and establish evolutionary relationships.
• Genome annotation is the process of attaching biological information to gene sequences identified using whole-genome sequencing.
• Model organisms include the fruit fly (Drosophila melanogaster), brewers yeast (Saccharomyces cerevisiae), the nematode, Caenorhabditis elegans, and the mouse (Mus musculus).
Key Terms
• genome annotation: the process of attaching biological information to gene sequences.
• model organism: any organism (e.g. the fruit fly) that has been extensively studied as an example of many others and from which general principles may be established
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, which 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. It took this long because it was 60 times bigger than any other genome that had been sequenced at that point. 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 the human Homo sapiens are now known. Much basic research is performed using model organisms because the information can be applied to the biological processes of genetically-similar organisms. Having entire genomes sequenced aids these research efforts.
The process of attaching biological information to gene sequences is called genome annotation. Annotation aids researchers doing basic experiments in molecular biology, such as designing PCR primers and RNA targets.
Sequencing genomes allows scientists to identify homologous proteins and establish evolutionary relationships. Furthermore, if a newly-discovered protein is homologous to a known protein, through homology, scientists can make an educated guess as to how the new protein functions.
Eukaryotes are organisms containing cells that enclose complex organelles within a well-defined cell membrane. The defining characteristic that sets eukaryotes and prokaryotes apart is the eukaryotes’ nucleus, or nuclear envelope, in which an organism’s genetic information is contained. The first eukaryotic genome to be sequenced was that of S. cerevisiae, which is the yeast used in baking and brewing. It is the most-studied eukaryotic model organism in molecular and cell biology, similar to E. coli‘s role in the study of prokaryotic organisms. Research on many proteins that are important to humans is done by examining their homologs in yeasts. For example, signaling proteins and protein-processing enzymes were discovered through the help of yeast genome.
17.3C: Uses of Genome Sequences
Genome sequences and expression can be analyzed using DNA microarrays, which can contribute to detection of disease and genetic disorders.
Learning Objectives
• Describe the various uses of genome sequences
Key Points
• DNA microarrays can be used to detect gene expression within specific samples by analyzing active genes and sequences using an array of DNA fragments fixed to a slide.
• Genome sequences can be used to discover the possibility of disease and genetic disorders prior to onset.
• Genome sequences can also be used to develop agrochemicals and pharmaceuticals.
Key Terms
• microarray: any of several devices containing a two-dimensional array of small quantities of biological material used for various types of assays
• genomics: the study of the complete genome of an organism
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. In addition, 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/17%3A_Biotechnology_and_Genomics/17.03%3A_Whole-Genome_Sequencing/17.3B%3A__Use_of_Whole-Genome_Sequences_of_Model_Organisms.txt |
Genome analysis is used to predict the level of disease risk in healthy individuals.
Learning Objectives
• Explain how analysis of an individual’s genome can aid in predicting disease risk
Key Points
• Genome sequencing can predict the risk of developing diseases brought on by a single gene defect, but these defects only account for five percent of common diseases.
• Most diseases are polygenic or are brought on by environmental factors; genome sequencing cannot predict the risk of acquiring these diseases.
• Genome sequencing is becoming more reliable, but many scientists still question if it reduces the risk of death from certain diseases such as prostate cancer.
Key Terms
• Human Genome Project: an organized international scientific endeavor to determine the complete structure of human genetic material (DNA) to identify all the genes and understand their function
• genome sequencing: a laboratory process that determines the complete DNA sequence of an organism’s genome at a single time
• polygenic: a phenotypic characteristic controlled by the interaction of two or more genes with the environment
Predicting Disease Risk at the Individual Level
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 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 five 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 interacting with 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.
In 2011, the United States Preventative Services Task Force recommended against using the PSA test to screen healthy men for prostate cancer. Their recommendation was 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 suffering side effects from treatment who would not have been harmed by the cancer itself. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/17%3A_Biotechnology_and_Genomics/17.04%3A_Applying_Genomics/17.4A%3A_Predicting_Disease_Risk_at_the_Individual_Level.txt |
Learning Objectives
• Explain how microbial metagenomics can give researchers a more complete picture of a particular environment
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.
Key Points
• Pharmacogenomics 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 or live cells in the laboratory, which help indicate the potentially toxic effects of a drug.
• Personal genome sequence information can be used to prescribe medications that will be most effective and least toxic on an individual level.
• Metagenomics, the study of the collective genomes of multiple species that grow and interact in an environmental niche, is often a better way to study microrganisms rather than pure culture.
Key Terms
• pharmacogenomics: the study of genes that code for enzymes that metabolize drugs, and the design of tailor-made drugs adapted to an individual’s genetic make-up
• metagenomics: the study of the collective genomes of multiple species that grow and interact in an environmental niche
17.4C: Genomics and Biofuels
Microbial genomics can be used to create new biofuels.
Learning Objectives
• Explain the process of creating new biofuels by using microbial genomics
Key Points
• Microorganisms can encode new enzymes and produce new organic compounds that can be used as biofuels.
• Genomic analysis of the fungus Pichia will allow optimization of its use in fermenting ethanol fuels.
• Analysis of the microbes in the hindgut of termites have found 500 genes that may be useful in enzymatic destruction of cellulose.
• Genetic markers have been used in forensic analysis, like in 2001 when the FBI used microbial genomics to determine a specific strain of anthrax that was found in several pieces of mail.
• Genomics is used in agriculture to develop plants with more desirable traits, such as drought and disease resistance.
Key Terms
• renewable resource: a natural resource such that it is replenished by natural processes at a rate comparable to its rate of consumption by humans or other users
• biofuel: any fuel that is obtained from a renewable biological resource
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.
For microbial biomass breakdown, many candidates have already been identified. These include Clostridia species for their ability to degrade cellulose, and fungi that express genes associated with the decomposition of the most recalcitrant features of the plant cell wall, lignin, the phenolic “glue” that imbues the plant with structural integrity and pest resistance. The white rot fungus Phanerochaete chrysosporium produces unique extracellular oxidative enzymes that effectively degrade lignin by gaining access through the protective matrix surrounding the cellulose microfibrils of plant cell walls.
Another fungus, the yeast Pichia stipitis, ferments the five-carbon “wood sugar” xylose abundant in hardwoods and agricultural harvest residue. Pichia‘s recently-sequenced genome has revealed insights into the metabolic pathways responsible for this process, guiding efforts to optimize this capability in commercial production strains. Pathway engineering promises to produce a wider variety of organisms able to ferment the full repertoire of sugars derived from cellulose and hemicellulose and tolerate higher ethanol concentrations to optimize fuel yields. For instance, the hindgut contents of nature’s own bioreactor, the termite, has yielded more than 500 genes related to the enzymatic deconstruction of cellulose and hemicellulose. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/17%3A_Biotechnology_and_Genomics/17.04%3A_Applying_Genomics/17.4B%3A_Pharmacogenomics_Toxicogenomics_and_Metagenomics.txt |
Learning Objectives
• Explain how the field of genomics led to the development of proteomics
Proteomics is a relatively-recent field; the term was coined in 1994 while the science itself had its origins in electrophoresis techniques of the 1970’s and 1980’s. The study of proteins, however, has been a scientific focus for a much longer time. Studying proteins generates insight into how they affect cell processes. Conversely, this study also investigates how proteins themselves are affected by cell processes or the external environment. Proteins provide intricate control of cellular machinery; they are, in many cases, components of that same machinery. They serve a variety of functions within the cell; there are thousands of distinct proteins and peptides in almost every organism. The goal of proteomics is to analyze the varying proteomes of an organism at different times in order to highlight differences between them. Put more simply, proteomics analyzes the structure and function of biological systems. For example, the protein content of a cancerous cell is often different from that of a healthy cell. Certain proteins in the cancerous cell may not be present in the healthy cell, making these unique proteins good targets for anti-cancer drugs. The realization of this goal is difficult; both purification and identification of proteins in any organism can be hindered by a multitude of biological and environmental factors.
The study of the function of proteomes is called proteomics. A proteome is the entire set of proteins produced by a cell type. Genomics led to proteomics (via transcriptomics) as a logical step. 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. 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.
Key Points
• Proteomics investigates how proteins affect and are affected by cell processes or the external environment.
• Within an individual organism, the genome is constant, but the proteome varies and is dynamic.
• Every cell in an individual organism has the same set of genes, but the set of proteins produced in different tissues differ from one another and are dependent on gene expression.
Key Terms
• proteomics: the branch of molecular biology that studies the set of proteins expressed by the genome of an organism
• proteome: the complete set of proteins encoded by a particular genome
• genomics: the study of the complete genome of an organism | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/17%3A_Biotechnology_and_Genomics/17.05%3A_Genomics_and_Proteomics/17.5A%3A_Genomics_and_Proteomics.txt |
Learning Objectives
• Describe the techniques used in proteomics to analyze proteins
Basic Techniques in Protein Analysis
The ultimate goal of proteomics is to identify or compare the proteins expressed in 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
Mass spectrometry is used to identify and determine the characteristics of a molecule. It is a technique in which gas phase molecules are ionized and their mass-to-charge ratio is measured by observing acceleration differences of ions when an electric field is applied. Lighter ions will accelerate faster and be detected first. If the mass is measured with precision, then the composition of the molecule can be identified. In the case of proteins, the sequence can be identified. The challenge of techniques used for proteomic analyses is the difficulty in detecting small quantities of proteins, but advances in spectrometry have allowed researchers to analyze very small samples of protein. Variations in protein expression in diseased states, however, can be difficult to discern. Proteins are naturally-unstable molecules, which makes proteomic analysis much more difficult than genomic analysis.
X-ray crystallography and Nuclear Magnetic Resonance
X-ray crystallography enables scientists to determine the three-dimensional structure of a protein crystal at atomic resolution. Crystallographers aim high-powered X-rays at a tiny crystal containing trillions of identical molecules. The crystal scatters the X-rays onto an electronic detector that is the same type used to capture images in a digital camera. After each blast of X-rays, lasting from a few seconds to several hours, the researchers precisely rotate the crystal by entering its desired orientation into the computer that controls the X-ray apparatus. This enables the scientists to capture in three dimensions how the crystal scatters, or diffracts, X-rays. The intensity of each diffracted ray is fed into a computer, which uses a mathematical equation to calculate the position of every atom in the crystallized molecule. The result is a three-dimensional digital image of the molecule.
Another protein imaging technique, nuclear magnetic resonance (NMR), uses the magnetic properties of atoms to determine the three-dimensional structure of proteins. NMR spectroscopy is unique in being able to reveal the atomic structure of macromolecules in solution, provided that highly-concentrated solution can be obtained. This technique depends on the fact that certain atomic nuclei are intrinsically magnetic. The chemical shift of nuclei depends on their local environment. The spins of neighboring nuclei interact with each other in ways that provide definitive structural information that can be used to determine complete three-dimensional structures of proteins.
Protein Microarrays and Two- Hybrid Screening
Protein microarrays have also been used to study interactions between proteins. These are large-scale adaptations of the basic two-hybrid screen. The premise behind the two-hybrid screen is that most eukaryotic transcription factors have modular activating and binding domains that can still activate transcription even when split into two separate fragments, as long as the fragments are brought within close proximity to each other. Generally, the transcription factor is split into a DNA-binding domain (BD) and an activation domain (AD). One protein of interest is genetically fused to the BD and another protein is fused to the AD. If the two proteins of interest bind each other, then the BD and AD will also come together and activate a reporter gene that signals interaction of the two hybrid proteins.
Western Blot
The western blot, or protein immunoblot, is a technique that combines protein electrophoresis and antibodies to detect proteins in a sample. A western blot is fairly quick and simple compared to the above techniques and, thus, can serve as an assay to validate results from other experiments. The protein sample is first separated by gel electrophoresis, then transferred to a nitrocellulose or other type of membrane, and finally stained with a primary antibody that specifically binds the protein of interest. A fluorescent or radioactive-labeled secondary antibody binds to the primary antibody and provides a means of detection via either photography or x-ray film, respectively.
Key Points
• Mass Spectrometry is a technique that is useful for determining the size of a protein or protein complex.
• X-ray crystallography and NMR are techniques useful for determining the 3-D structure of a protein or protein complex.
• Protein microarrays are useful for determining protein-protein interactions.
Key Terms
• microarray: any of several devices containing a two-dimensional array of small quantities of biological material used for various types of assays
• reporter gene: a gene that researchers attach to a regulatory sequence of another gene of interest and whose product is easily identifiable in assays | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/17%3A_Biotechnology_and_Genomics/17.05%3A_Genomics_and_Proteomics/17.5B%3A_Basic_Techniques_in_Protein_Analysis.txt |
Learning Objectives
• Explain the ways in which cancer proteomics may lead to better treatments
Genomes and proteomes of patients suffering from specific diseases are being studied to understand the genetic basis of diseases. The most prominent set of diseases being studied with proteomic approaches is cancer. Proteomic approaches are being used to improve screening and early detection of cancer, which is achieved by identifying proteins whose expression is affected by the disease process.
An individual protein that indicates disease 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 (e.g. 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. In addition, proteomics can be 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.
Key Points
• Identifying those proteins whose expression is affected by disease processes can be used to improve screening and early detection of cancer.
• Different biomarkers and protein signatures are being used to analyze each type of cancer.
• A future goal of cancer proteomics is to have a personalized treatment plan for each individual.
Key Terms
• biomarker: a substance used as an indicator of a biological state, most commonly disease
Contributions and Attributions
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44558/latest...ol11448/latest. License: CC BY: Attribution
• Proteomics/Introduction to Proteomics. Provided by: Wikibooks. Located at: en.wikibooks.org/wiki/Proteom..._to_Proteomics. License: CC BY-SA: Attribution-ShareAlike
• proteomics. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/proteomics. License: CC BY-SA: Attribution-ShareAlike
• proteome. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/proteome. License: CC BY-SA: Attribution-ShareAlike
• genomics. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/genomics. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Genomics and Proteomics. November 12, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m45485/latest/. License: CC BY: Attribution
• Structural Biochemistry/Proteins/Western Blotting. Provided by: Wikibooks. Located at: en.wikibooks.org/wiki/Structu...stern_Blotting. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44558/latest...ol11448/latest. License: CC BY: Attribution
• Structural Biochemistry/Proteins/NMR Spectroscopy. Provided by: Wikibooks. Located at: en.wikibooks.org/wiki/Structu...R_Spectroscopy. License: CC BY-SA: Attribution-ShareAlike
• Proteomics/Protein Identification - Mass Spectrometry. Provided by: Wikibooks. Located at: en.wikibooks.org/wiki/Proteom...s_Spectrometry. License: CC BY-SA: Attribution-ShareAlike
• Structural Biochemistry/Proteins/X-ray Crystallography. Provided by: Wikibooks. Located at: en.wikibooks.org/wiki/Structu...rystallography. License: CC BY-SA: Attribution-ShareAlike
• Two-hybrid screening. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Two-hybrid_screening. License: CC BY-SA: Attribution-ShareAlike
• reporter gene. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/reporter%20gene. License: CC BY-SA: Attribution-ShareAlike
• microarray. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/microarray. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Genomics and Proteomics. November 12, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m45485/latest/. License: CC BY: Attribution
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• Cancer biomarkers. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Cancer_biomarkers. License: Public Domain: No Known Copyright | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/17%3A_Biotechnology_and_Genomics/17.05%3A_Genomics_and_Proteomics/17.5C%3A_Cancer_Proteomics.txt |
Evolution, the unifying theory of biology, describes a mechanism for the change and diversification of species over time.
Learning Objectives
• Describe the historical influences on Darwin’s theory of evolution
Key Points
• Ancient Greeks expressed ideas about evolution, which were reintroduced in the eighteenth century by Georges-Louis Leclerc Comte de Buffon who observed different environments had different plant and animal populations.
• James Hutton proposed that geological changes occur gradually over time via the accumulation of small changes rather than through large catastrophic events.
• Charles Lyell popularized James Hutton’s theory; this theory of incremental change influenced Darwin’s theory of evolution.
• Jean-Baptiste Lamarck proposed the theory of the inheritance of acquired characterstics; this theory has now been discredited, but it served as an important influence on the theory of evolution.
Key Terms
• evolution: the change in the genetic composition of a population over successive generations
• inheritance of acquired characteristics: hypothesis that physiological changes acquired over the life of an organism may be transmitted to its offspring
Introduction: Evolution
All species of living organisms, including bacteria and chimpanzees, evolved at some point from a different species. Although it may seem that living things today stay the same, this is not the case: evolution is a gradual and 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. The Ukrainian-born American geneticist Theodosius Dobzhansky famously wrote that “nothing makes sense in biology except in the light of evolution.” The tenet that all species have evolved and diversified from a common ancestor is the foundation from which we approach all questions in biology. It provides a direction for predictions about living things, which has been validated through extensive scientific experimentation.
Evolution by natural selection describes a mechanism for the change of species over time. Well before Darwin began to explore the concept of evolution, the idea that species change over time had already been suggested and debated. The view that species are static and unchanging was grounded in the writings of Plato, yet there were also ancient Greeks who expressed ideas about evolution. During 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 are extinct species.
During this time, a Scottish naturalist named James Hutton proposed that geological change occurs gradually by the accumulation of small changes over long periods of time. This theory contrasted with the predominant view of the time: that the geology of the planet is a consequence of catastrophic events that occurred during a relatively brief past. During the nineteenth century, Hutton’s views were popularized by the geologist Charles Lyell, who was a friend of Charles Darwin. Lyell’s ideas, in turn, influenced Darwin’s concept of evolution. The greater age of the earth proposed by Lyell supported the gradual evolution that Darwin proposed, and the slow process of geological change provided an analogy for the gradual change in species.
In the early nineteenth century, Jean-Baptiste Lamarck published a book that detailed a different mechanism for evolutionary change. This mechanism is now referred to as an inheritance of acquired characteristics. This idea states that modifications in an individual are caused by its environment, or the use or disuse of a structure during its lifetime, and that these changes can be inherited by its offspring, bringing about change in a species. While this mechanism for evolutionary change was discredited, Lamarck’s ideas were an important influence on the concept of evolution. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.01%3A_Understanding_Evolution/18.1A%3A_What_is_Evolution.txt |
Charles Darwin and Alfred Wallace independently developed the theories of evolution and its main operating principle: natural selection.
Learning Objectives
• Explain how natural selection can lead to evolution
Key Points
• Wallace traveled to Brazil to collect and observe insects from the Amazon rainforest.
• Darwin observed that finches in the Galápagos Islands had different beaks than finches in South America; these adaptations equiped the birds to acquire specific food sources.
• Wallace and Darwin observed similar patterns in the variation of organisms and independently developed the same explanation for how such variations could occur over time, a mechanism Darwin called natural selection.
• According to natural selection, also known as “survival of the fittest,” individuals with traits that enable them to survive are more reproductively successful; this leads to those traits becoming predominant within a population.
• Natural selection is an inevitable outcome of three principles: most characteristics are inherited, more offspring are produced than are able to survive, and offspring with more favorable characteristics will survive and have more offspring than those individuals with less favorable traits.
Key Terms
• natural selection: a process in which individual organisms or phenotypes that possess favorable traits are more likely to survive and reproduce
• descent with modification: change in populations over generations
Charles Darwin and Natural Selection
In the mid-nineteenth century, the 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 to places like 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, as with 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 that species of organisms on different islands were clearly similar, yet had distinct differences. For example, the ground finches inhabiting the Galápagos Islands comprised several species with a unique beak shape. 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 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, while insect-eating finches had spear-like beaks for stabbing their prey.
Natural Selection
Wallace and Darwin observed similar patterns in other organisms and 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, the trait becoming predominant within a population. For example, Darwin observed that a population of giant tortoises found in the Galapagos Archipelago 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 could not reach the food source. Consequently, long-necked tortoises would more probably 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 how traits were inherited was unknown. Second, more offspring are produced than are able to survive. 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 were influenced by an essay written by economist Thomas Malthus who discussed this principle in relation to human populations. Third, Darwin and Wallace reasoned that offspring with the inherited characteristics that 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 successive 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 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 his arguments for evolution by natural selection. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.01%3A_Understanding_Evolution/18.1B%3A_Charles_Darwin_and_Natural_Selection.txt |
The differences in shape and size of beaks in Darwin’s finches illustrate ongoing evolutionary change.
Learning Objectives
• Describe how finches provide visible evidence of evolution
Key Points
• Darwin observed the Galapagos finches had a graded series of beak sizes and shapes and predicted these species were modified from one original mainland species.
• Darwin called differences among species natural selection, which is caused by the inheritance of traits, competition between individuals, and the variation of traits.
• Offspring with inherited characteristics that allow them to best compete will survive and have more offspring than those individuals with variations that are less able to compete.
• Large-billed finches feed more efficiently on large, hard seeds, whereas smaller billed finches feed more efficiently on small, soft seeds.
• When small, soft seeds become rare, large-billed finches will survive better, and there will be more larger-billed birds in the following generation; when large, hard seeds become rare, the opposite will occur.
Key Terms
• natural selection: a process in which individual organisms or phenotypes that possess favorable traits are more likely to survive and reproduce
• evolution: the change in the genetic composition of a population over successive generations
Visible Evidence of Ongoing Evolution: Darwin’s Finches
From 1831 to 1836, Darwin traveled around the world, observing animals on different continents and islands. On the Galapagos Islands, Darwin observed several species of finches with unique beak shapes. He observed these finches closely resembled another finch species on the mainland of South America and that the group of species in the Galápagos formed a graded series of beak sizes and shapes, with very small differences between the most similar. Darwin imagined that the island species might be all species modified from one original mainland species. In 1860, he wrote, “seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends.”
Natural Selection
Darwin called this mechanism of change natural selection. Natural selection, Darwin argued, was an inevitable outcome of three principles that operated in nature. First, the characteristics of organisms are inherited, or passed from parent to offspring. Second, more offspring are produced than are able to survive; in other words, resources for survival and reproduction are limited. The capacity for reproduction in all organisms exceeds the availability of resources to support their numbers. Thus, there is a competition for those resources in each generation. Third, offspring vary among each other in regard to their characteristics and those variations are inherited. Out of these three principles, Darwin reasoned that offspring with inherited characteristics that 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,” or evolution.
Studies of Natural Selection After Darwin
Demonstrations of evolution by natural selection can be time consuming. Peter and Rosemary Grant and their colleagues have studied Galápagos finch populations every year since 1976 and have provided important demonstrations of the operation of natural selection. The Grants found changes from one generation to the next in the beak shapes of the medium ground finches on the Galápagos island of Daphne Major.
The medium ground finch feeds on seeds. The birds have inherited variation in the bill shape with some individuals having wide, deep bills and others having thinner bills. Large-billed birds feed more efficiently on large, hard seeds, whereas smaller billed birds feed more efficiently on small, soft seeds. During 1977, a drought period altered vegetation on the island. After this period, the number of seeds declined dramatically; the decline in small, soft seeds was greater than the decline in large, hard seeds. The large-billed birds were able to survive better than the small-billed birds the following year.
The year following the drought when the Grants measured beak sizes in the much-reduced population, they found that the average bill size was larger. This was clear evidence for natural selection of bill size caused by the availability of seeds. The Grants had studied the inheritance of bill sizes and knew that the surviving large-billed birds would tend to produce offspring with larger bills, so the selection would lead to evolution of bill size. Subsequent studies by the Grants have demonstrated selection on and evolution of bill size in this species in response to other changing conditions on the island. The evolution has occurred both to larger bills, as in this case, and to smaller bills when large seeds became rare. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.01%3A_Understanding_Evolution/18.1C%3A_The_Galapagos_Finches_and_Natural_Selection.txt |
Natural selection can only occur in the presence of genetic variation; environmental conditions determine which traits are selected.
Learning Objectives
• Explain why only heritable variation can be acted upon by natural selection
Key Points
• Genetic variation within a population is a result of mutations and sexual reproduction.
• A mutation may be neutral, reduce an organism’s fitness, or increase an organism’s fitness.
• An adaptation is a heritable trait that increases the survival and rate of reproduction of an organism in its present environment.
• Divergent evolution describes the process in which two species evolve in diverse directions from a common point.
• Convergent evolution is the process in which similar traits evolve independently in species that do not share a recent common ancestry.
Key Terms
• adaptation: modification of something or its parts that makes it more fit for existence under the conditions of its current environment
• divergent evolution: the process by which a species with similar traits become groups that are tremendously different from each other over many generations
• convergent evolution: a trait of evolution in which species not of similar recent origin acquire similar properties due to natural selection
Variation
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 due to better nutrition rather than different genes.
Genetic diversity within a population comes from two main mechanisms: mutation and sexual reproduction. Mutation, a change in the DNA sequence, 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:
• Many mutations will have no effect on the fitness of the phenotype; these are called neutral mutations.
• A mutation may affect the phenotype of the organism in a way that gives it reduced fitness (a lower likelihood of survival or fewer offspring).
• A mutation may produce a phenotype with a beneficial effect on fitness. Different mutations will have a range of effects on the fitness of an 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. However, sexual reproduction can not lead to new genes, but rather provides a new combination of genes in a given individual.
Adaptations
A heritable trait that aids 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 “fitness” 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.
In other cases, similar phenotypes evolve independently in distantly-related species. For example, flight has evolved in both bats and insects; 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.01%3A_Understanding_Evolution/18.1D%3A_Processes_and_Patterns_of_Evolution.txt |
Evidence for evolution has been obtained through fossil records, embryology, geography, and molecular biology.
Learning Objectives
• Explain the development of the theory of evolution
Key Points
• Fossils serve to highlight the differences and similarities between current and extinct species, showing the evolution of form over time.
• Similar anatomy across different species highlights their common origin and can be seen in homologous and vestigial structures.
• Embryology provides evidence for evolution since the embryonic forms of divergent groups are extremely similar.
• The natural distribution of species across different continents supports evolution; species that evolved before the breakup of the supercontinent are distributed worldwide, whereas species that evolved more recently are more localized.
• Molecular biology indicates that the molecular basis for life evolved very early and has been maintained with little variation across all life on the planet.
Key Terms
• homologous structure: the traits of organisms that result from sharing a common ancestor; such traits often have similar embryological origins and development
• biogeography: the study of the geographical distribution of living things
• vestigial structure: genetically determined structures or attributes that have apparently lost most or all of their ancestral function in a given species
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. Since Darwin, our understanding has become clearer and broader.
Fossils, Anatomy, and Embryology
Fossils provide solid evidence that organisms from the past are not the same as those found today; they show a progression of evolution. Scientists calculate the age of fossils and categorize them 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. For example, scientists have recovered highly-detailed records showing the evolution of humans and horses. The whale flipper shares a similar morphology to appendages of birds and mammals, indicating that these species share 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, appearing to be residual parts from a common ancestor. These unused structures (such as wings on flightless birds, leaves on some cacti, and hind leg bones in whales) are vestigial.
Embryology, the study of the development of the anatomy of an organism to its adult form, provides evidence for evolution as embryo formation in widely-divergent groups of organisms tends to be conserved. Structures that are absent in the adults of some groups often appear in their embryonic forms, disappearing 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 adults 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 birth.
Another form of 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. These similarities occur not because of common ancestry, but because of similar selection pressures: the benefits of not being seen by predators.
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 compared to that of the southern continents that formed from the supercontinent Gondwana.
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 (those 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, in the near universality of the genetic code, and in the machinery of DNA replication and expression. In general, the relatedness of groups of organisms is reflected in the similarity of their DNA sequences. This is 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 duplications 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.01%3A_Understanding_Evolution/18.1E%3A_Evidence_of_Evolution.txt |
There are many misconceptions about evolution, including the meaning of the word theory, the way populations change, and the origin of life.
Learning Objectives
• Discuss misconceptions about the theory of evolution
Key Points
• Attacks on the theory of evolution sometimes take issue with the word “theory”, which in the vernacular means a guess or suggested explanation. In scientific language, “theory” indicates a body of thoroughly-tested and verified explanations for a set of observations of the natural world.
• Evolution does not take place on an individual level; evolution is the average change of a characteristic within an entire population.
• Evolution does not explain the origin of life; the theory of evolution instead explains how populations change over time and how traits are selected in order to increase the fitness of a population.
• Favorable traits do not arise as a result of the environment as these traits are already present; individuals with favorable traits are more likely to survive and, thus, will have greater fitness than individuals with less desirable traits.
• Evolution and natural selection are not synonymous. Natural selection is just one mechanism by which evolution occurs.
Key Terms
• theory: a well-substantiated explanation of some aspect of the natural world based on knowledge that has been repeatedly confirmed through observation and experimentation
Misconceptions of Evolution
Although the theory of evolution generated controversy when it was first proposed, it was almost universally accepted by biologists within 20 years of the publication of On the Origin of Species. Nevertheless, the theory of evolution is a difficult concept and misconceptions about it abound.
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. A theory in science has also 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 mis-characterization.
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 that population several years later, this average value of the population will be different as a result of evolution.
Evolution Explains the Origin of Life
It is a common misunderstanding that evolution includes an explanation of life’s origins. The theory of evolution explains how populations change over time. 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 occurred just once. However, 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. 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.
Organisms Evolve on Purpose
Statements such as “organisms evolve in response to a change in an environment” may lead to the misunderstanding that 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 important to understand that the variation that natural selection works on is already present 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, probably 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 antibiotics.
In a larger sense, evolution is not goal directed. Species do not become “better” over time; they track their changing environment with adaptations that maximize their reproduction. The characteristics that evolve in a species are a function of preexisting variation and the environment, both of which are constantly changing non-directionally. A trait that is fit in one environment at one time may also be fatal at some point in the future.
Evolution = Natural Selection
The terms “evolution” and “natural selection” are often conflated, as the two concepts are closely related. They are not, however, synonymous. Natural selection refers to the process by which organisms better suited for their environment are more likely to survive and produce offspring, thereby proliferating those favorable genetics in a population. Evolution is defined more broadly as any change in the genetic makeup of a population over time. As expounded by Darwin, natural selection is a major driving force of evolution, but it is not the only one.
Genetic drift, for example, is another mechanism by which evolution may occurs. Genetic drift occurs when allelic frequency is altered due to random sampling. It is evolution by chance, and the smaller the population, the more significant the effects on genetic distribution due to sampling error. For example, a population bottleneck, which occurs when an event such as a natural disaster dramatically reduces the size of a population, can result in the elimination or significant reduction of a trait within a population, regardless of how beneficial that trait may be to survival or reproduction. Thus evolution can occur without natural selection. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.01%3A_Understanding_Evolution/18.1F%3A_Misconceptions_of_Evolution.txt |
A species is defined as a group of individuals that, in nature, are able to mate and produce viable, fertile offspring.
Learning Objectives
• Explain the biological species concept
Key Points
• Members of the same species are similar both in their external appearance and their internal physiology; the closer the relationship between two organisms, the more similar they will be in these features.
• Some species can look very dissimilar, such as two very different breeds of dogs, but can still mate and produce viable offspring, which signifies that they belong to the same species.
• Some species may look very similar externally, but can be dissimilar enough in their genetic makeup that they cannot produce viable offspring and are, therefore, different species.
• Mutations can occur in any cell of the body, but if a change does not occur in a sperm or egg cell, it cannot be passed on to the organism’s offspring.
Key Terms
• species: a group of organsms that, in nature, are capable of mating and producing viable, fertile offspring
• hybrid: offspring resulting from cross-breeding different entities, e.g. two different species or two purebred parent strains
• gene pool: the complete set of unique alleles that would be found by inspecting the genetic material of every living member of a species or population
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’s 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.
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. 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.02%3A_Formation_of_New_Species/18.2A%3A_The_Biological_Species_Concept.txt |
Reproductive isolation, through mechanical, behavioral, and physiological barriers, is an important component of speciation.
Learning Objectives
• Explain how reproductive isolation can result in speciation
Key Points
• Reproductive isolation can be either prezygotic (barriers that prevent fertilization ) or postzygotic (barriers that occur after zygote formation such as organisms that die as embryos or those that are born sterile).
• Some species may be prevented from mating with each other by the incompatibility of their anatomical mating structures, or a resulting offspring may be prevented by the incompatibility of their gametes.
• Postzygotic barriers include the creation of hybrid individuals that do not survive past the embryonic stages ( hybrid inviability ) or the creation of a hybrid that is sterile and unable to produce offspring ( hybrid sterility ).
• Temporal isolation can result in species that are physically similar and may even live in the same habitat, but if their breeding schedules do not overlap then interbreeding will never occur.
• Behavioral isolation, in which the behaviors involved in mating are so unique as to prevent mating, is a prezygotic barrier that can cause two otherwise-compatible species to be uninterested in mating with each other.
• Behavioral isolation, in which the behaviors involved in mating are so unique as to prevent mating, is a prezygotic barrier that can cause two otherwise compatible species to be uninterested in mating with each other.
Key Terms
• reproductive isolation: a collection of mechanisms, behaviors, and physiological processes that prevent two different species that mate from producing offspring, or which ensure that any offspring produced is not fertile
• temporal isolation: factors that prevent potentially fertile individuals from meeting that reproductively isolate the members of distinct species
• behavioral isolation: the presence or absence of a specific behavior that prevents reproduction between two species from taking place
• prezygotic barrier: a mechanism that blocks reproduction from taking place by preventing fertilization
• postzygotic barrier: a mechanism that blocks reproduction after fertilization and zygote formation
• hybrid inviability: a situation in which a mating between two individuals creates a hybrid that does not survive past the embryonic stages
• hybrid sterility: a situation in which a mating between two individuals creates a hybrid that is sterile
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 improbable, but if mating did occur, offspring would be non-viable or infertile. Many types of diverging characters may affect reproductive isolation, the ability to interbreed, of the two populations. Reproductive isolation is a collection of mechanisms, behaviors, and physiological processes that prevent the members of two different species that cross or mate from producing offspring, or which ensure that any offspring that may be produced is not fertile.
Scientists classify reproductive isolation in 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.
In some cases, populations of a species move to a new habitat and take up residence in a place that no longer overlaps with other populations of the same species; this 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.
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 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 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..
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 in length and diameter, which prevents the plant from being cross-pollinated with a different species.
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. 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.02%3A_Formation_of_New_Species/18.2B%3A_Reproductive_Isolation.txt |
Speciation is an event in which a single species may branch to form two or more new species.
Learning Objectives
• Define speciation and discuss the ways in which it may occur
Key Points
• For the majority of species, the definition of a species is a group of animals that can potentially interbreed, although some different species are capable of producing hybrid offspring.
• Darwin was the first to envision speciation as the branching of two or more new species from one ancestral species; indicated by a diagram he made that bears a striking resemblance to modern-day phylogenetic diagrams.
• For a new species to be formed from an old species, certain events or changes must occur such that the new population is no longer capable of interbreeding with the old one.
• Speciation can occur either through allopatric speciation, when a population is geographically separated from one another, or through sympatric speciation, in which the two new species are not geographically separated.
• Speciation, the formation of two species from one original species, occurs as one species changes over time and branches to form more than one new species.
Key Terms
• sympatric: living in the same territory without interbreeding
• allopatric: not living in the same territory; geographically isolated and thus unable to crossbreed
• speciation: the process by which new distinct species evolve
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: 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, which bears some resemblance to the more modern phylogenetic diagram of elephant evolution. The diagram shows that as one species changes over time, it branches repeatedly to form more than one new species 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; 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 and sympatric speciation. 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; multiple events can be conceptualized as single splits occurring close in time. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.02%3A_Formation_of_New_Species/18.2C%3A_Speciation.txt |
Allopatric speciation occurs when a single species becomes geographically separated; each group evolves new and distinctive traits.
Learning Objectives
• Give examples of allopatric speciation
Key Points
• When a population is geographically continuous, the allele frequencies among its members are similar; however, when a population becomes separated, the allele frequencies between the two groups can begin to vary.
• If the separation between groups continues for a long period of time, the differences between their alleles can become more and more pronounced due to differences in climate, predation, food sources, and other factors, eventually leading to the formation of a new species.
• Geographic separation between populations can occur in many ways; the severity of the separation depends on the travel capabilities of the species.
• Allopatric speciation events can occur either by dispersal, when a few members of a species move to a new geographical area, or by vicariance, when a natural situation, such as the formation of a river or valley, physically divide organisms.
• When a population disperses throughout an area, into new, different and often isolated habitats, multiple speciation events can occur in which the single original species gives rise to many new species; this phenomenon is called adaptive radiation.
Key Terms
• vicariance: the separation of a group of organisms by a geographic barrier, resulting in differentiation of the original group into new varieties or species
• adaptive radiation: the diversification of species into separate forms that each adapt to occupy a specific environmental niche
• dispersal: the movement of a few members of a species to a new geographical area, resulting in differentiation of the original group into new varieties or species
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 continues for a period of time, the two populations are able to evolve along different trajectories. This is known as allopatric speciation. 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 improbable; therefore, speciation would be probably occur.
Biologists group allopatric processes into two categories: dispersal and vicariance. Dispersal occurs when a few members of a species move to a new geographical area, while vicariance occurs when a natural situation arises to physically divide organisms.
Scientists have documented numerous cases of allopatric speciation. 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.
Additionally, scientists have found that the further the distance between two groups that once were the same species, the more probable it is that speciation will occur. This seems logical because as the distance increases, the various environmental factors would generally have less in common than locations in close proximity. Consider the two owls: in the north, the climate is cooler than in the south causing 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, resulting in speciation.
Adaptive Radiation
In some cases, a population of one species disperses throughout an area with each finding 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, 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.
In Hawaiian honeycreepers, the response to natural selection based on specific food sources in each new habitat led to the evolution of a different beak suited to the specific food source. The seed-eating birds have 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.02%3A_Formation_of_New_Species/18.2D%3A_Allopatric_Speciation.txt |
Sympatric speciation occurs when two individual populations diverge from an ancestral species without being separated geographically.
Learning Objectives
• Give examples of sympatric speciation
Key Points
• Sympatric speciation can occur when one individual develops an abnormal number of chromosomes, either extra chromosomes ( polyploidy ) or fewer, such that viable interbreeding can no longer occur.
• When the extra sets of chromosomes in a polyploid originate with the individual because their own gametes do not undergo cytokinesis after meiosis, the result is autopolyploidy.
• When individuals of two different species reproduce to form a viable offspring, such that the extra chromosomes come from two different species, the result is an allopolyploid.
• Once a species develops an abnormal number of chromosomes, it can then only interbreed with members of the population that have the same abnormal number, which can lead to the development of a new species.
Key Terms
• sympatric speciation: the process through which new species evolve from a single ancestral species while inhabiting the same geographic region
• autopolyploid: having more than two sets of chromosomes, derived from the same species, as a result of redoubling
• allopolyploid: having multiple complete sets of chromosomes derived from different species
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.
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, or the inability to interbreed with normal individuals, of an individual in the polyploidy state. In some cases, a polyploid individual will have two or more complete sets of chromosomes from its own species in a condition called autopolyploidy. 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: 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. 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.02%3A_Formation_of_New_Species/18.2E%3A_Sympatric_Speciation.txt |
Over time, two species may further diverge or reconnect, depending on the fitness strength and the reproductive barriers of the hybrids.
Learning Objectives
• Discuss how the fitness of a hybrid will lead to changes in the hybrid zone over time
Key Points
• After speciation, or sufficient evolutionary change for one species to become two distinct species, the two species may continue to co-habitate and interact.
• The area in which two closely-related species interact and reproduce is known as the hybrid zone; their offspring are known as hybrids.
• Depending on the fitness of the hybrid offspring relative to the parents, the two species may either stay as two distinct species (reinforcement), or become one species again ( reconnection ).
Key Terms
• hybrid zone: an area where the ranges of two interbreeding species meet and interbreed
• hybrid speciation: the formation of a new species as the direct result of mating between members of two existing species
• reconnection: a convergence of two species over time
Reconnection After Speciation
Speciation occurs over a span of evolutionary time. When a new species arises, there is a transition period during which the closely-related species continue to interact.
After speciation, two species may recombine or even continue interacting indefinitely. Individual organisms will mate with any nearby individual with which they are capable of breeding. 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 strength and the reproductive barriers of the hybrids.
Hybrids can have less fitness, more fitness, or about the same fitness level as the purebred parents. Usually, hybrids tend to be less fit; therefore, reproduction to produce hybrids will diminish over time, which nudges 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 less fit than the parents, reinforcement of speciation occurs, and the species will continue to diverge until they can no longer mate and produce viable offspring.
If the hybrids are as fit or more fit than the parents, or the reproductive barriers weaken, the two species may fuse back into one species (reconnection). For a hybrid form to persist, it will generally have to be able to exploit the available resources better than either parent species, with which, in most cases, it will have to compete.
Over time, via a process called hybrid speciation, the hybrids themselves can become a separate species. Reproductive isolation between hybrids and their parents was once thought to be particularly difficult to achieve; thus, hybrid species were thought to be extremely rare. With DNA analysis becoming more accessible in the 1990s, hybrid speciation has been shown to be a fairly common phenomenon, particularly in plants.
Scientists have also observed that sometimes two species will remain separate, but continue to interact to produce some hybrid individuals; this is classified as stability because no real net change is taking place. For a hybrid zone to be stable, the offspring produced by the hybrids have to be less fit than members of the parent species.
18.3B: Varying Rates of Speciation
Two patterns are currently observed in the rates of speciation: gradual speciation and punctuated equilibrium.
Learning Objectives
• Explain how the interaction of an organism’s population size in association with environmental changes can lead to different rates of speciation
Key Points
• In the gradual speciation model, species diverge slowly over time in small steps while in the punctuated equilibrium model, a new species diverges rapidly from the parent species.
• The two key influencing factors on the change in speciation rate are the environmental conditions and the population size.
• Gradual speciation is most likely to occur in large populations that live in a stable environment, while the punctuation equilibrium model is more likely to occur in a small population with rapid environmental change.
Key Terms
• punctuated equilibrium: a theory of evolution holding that evolutionary change tends to be characterized by long periods of stability, with infrequent episodes of very fast development
• gradualism: in evolutionary biology, belief that evolution proceeds at a steady pace, without the sudden development of new species or biological features from one generation to the next
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: the gradual speciation model and the punctuated equilibrium model.
In the gradual speciation model, species diverge gradually over time in small steps. In the punctuated equilibrium model, a new species changes quickly from the parent species and then remains largely unchanged for long periods of time afterward. 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.
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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.03%3A_Hybrid_Zones_and_Rates_of_Speciation/18.3A%3A_Hybrid_Zones.txt |
Genomic similarities between distant species can be established via analysis of genomes using advanced technology.
Learning Objectives
• Discuss the evolutionary implications of observed genome similarities between distant species
Key Points
• Genomic similarities between distant species can be explained by the theory that all organisms share a common ancestor.
• Genomic similarities between distant species can be analysed using genomic analysis tools to create phylogenetic trees that explain these relationships.
• Genetic distance is used to explain the genetic divergence between species or between populations within a species and can indicate how closely related they are and whether they have a recent common ancestor or recent interbreeding has taken place.
• Horizontal gene transfer (HGT) occurs when two unrelated species exchange genes, usually two prokaryotes, although HGT occurs in some eurokaryotes as well.
Key Terms
• conjugation: the temporary fusion of organisms, especially as part of sexual reproduction
• phylogeny: the evolutionary history of an organism
• horizontal gene transfer: the transfer of genetic material from one organism to another one that is not its offspring; especially common among bacteria
• transformation: the alteration of a bacterial cell caused by the transfer of DNA from another, especially if pathogenic
• transduction: horizontal gene transfer mechanism in prokaryotes where genes are transferred using a virus
Genomic Similarities Between Distant Species
Genetic distance refers to the genetic divergence between species or between populations within a species. Smaller genetic distances indicate that the populations have more similar genes, which indicates they are closely related; they have a recent common ancestor, or recent interbreeding has taken place. Genetic distance is useful in reconstructing the history of populations. For example, evidence from genetic distance suggests that humans arrived in America about 30,000 years ago. By examining the difference between allele frequencies between the populations, genetic distance can estimate how long ago the two populations were together.
Phylogenetic Relationships
Phylogeny describes the relationships of an organism, such as the relationship with its ancestors and the species it is most closely related. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different. The use of advanced genomic analysis has allowed us to establish phylogenetic trees, which map the relationship between species at a genetic and molecular level. The ability to use these technologies has established previously unknown relationships and has contributed to a more complex evolutionary history. These technologies have established genomic similarities between distant species by establishing genetic distances. In addition, the mechanisms by which genomic similarities between distant species occur can include horizontal gene transfer.
Horizontal Gene Transfer
Horizontal gene transfer (HGT), also known as lateral gene transfer, is the transfer of genes between unrelated species. 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.
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. 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: transformation, transduction and conjugation.
Although it is easy to see how prokaryotes exchange genetic material by HGT, it was initially thought that this process was absent in eukaryotes, followed by the idea that the gene transfers between multicellular eukaryotes should be more difficult. In spite of this fact, HGT between distantly related organisms has been demonstrated in several eukaryotic species.
In animals, a particularly interesting example of HGT occurs within the aphid species. 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.04%3A_Evolution_of_Genomes/18.4A%3A_Genomic_Similiarities_between_Distant_Species.txt |
Processes such as mutations, duplications, exon shuffling, transposable elements and pseudogenes have contributed to genomic evolution.
Learning Objectives
• Explain the importance of genomic changes in an evolutionary context
Key Points
• Gene and whole genome duplications have contributed accumulations that have contributed to genome evolution.
• Mutations are constantly occurring in an organism’s genome and can cause either a negative effect, positive effect or no effect at all; however, it will still result in changes to the genome.
• Transposable elements are regions of DNA that can be inserted into the genetic code and will causes changes within the genome.
• Pseudogenes are dysfunctional genes derived from previously functional gene relatives and will become a pseudogene by deletion or insertion of one or multiple nucleotides.
• Exon shuffling occurs when two or more exons from different genes are combined together or when exons are duplicated, and will result in new genes.
• Species can also exhibit genome reduction when subsets of their genes are not needed anymore.
Key Terms
• intron: a portion of a split gene that is included in pre-RNA transcripts but is removed during RNA processing and rapidly degraded
• exon: a region of a transcribed gene present in the final functional RNA molecule
• pseudogene: a segment of DNA that is part of the genome of an organism, and which is similar to a gene but does not code for a gene product
Accumulating Changes Over Time
The evolution of the genome is characterized by the accumulation of changes. The analaysis of genomes and their changes in sequence or size over time involves various fields. There are various mechanisms that have contributed to genome evolution and these include gene and genome duplications, polyploidy, mutation rates, transposable elements, pseudogenes, exon shuffling and genomic reduction and gene loss. The concepts of gene and whole-genome duplication are discussed as their own independent concepts, thus, the focus will be on other mechanisms.
Mutation Rates
Mutation rates differ between species and even between different regions of the genome of a single species. Spontaneous mutations often occur which can cause various changes in the genome. Mutations can result in the addition or deletion of one or more nucleotide bases. A change in the code can result in a frameshift mutation which causes the entire code to be read in the wrong order and thus often results in a protein becoming non-functional. A mutation in a promoter region, enhancer region or a region coding for transcription factors can also result in either a loss of function or and upregulation or downregulation in transcription of that gene. Mutations are constantly occurring in an organism’s genome and can cause either a negative effect, positive effect or no effect at all.
Transposable Elements
Transposable elements are regions of DNA that can be inserted into the genetic code through one of two mechanisms. These mechanisms work similarly to “cut-and-paste” and “copy-and-paste” functionalities in word processing programs. The “cut-and-paste” mechanism works by excising DNA from one place in the genome and inserting itself into another location in the code. The “copy-and-paste” mechanism works by making a genetic copy or copies of a specific region of DNA and inserting these copies elsewhere in the code. The most common transposable element in the human genome is the Alu sequence, which is present in the genome over one million times.
Pseudogenes
Often a result of spontaneous mutation, pseudogenes are dysfunctional genes derived from previously functional gene relatives. There are many mechanisms by which a functional gene can become a pseudogene including the deletion or insertion of one or multiple nucleotides. This can result in a shift of reading frame, causing the gene to longer code for the expected protein, a premature stop codon or a mutation in the promoter region. Often cited examples of pseudogenes within the human genome include the once functional olfactory gene families. Over time, many olfactory genes in the human genome became pseudogenes and were no longer able to produce functional proteins, explaining the poor sense of smell humans possess in comparison to their mammalian relatives.
Exon Shuffling
Exon shuffling is a mechanism by which new genes are created. This can occur when two or more exons from different genes are combined together or when exons are duplicated. Exon shuffling results in new genes by altering the current intron-exon structure. This can occur by any of the following processes: transposon mediated shuffling, sexual recombination or illegitimate recombination. Exon shuffling may introduce new genes into the genome that can be either selected against and deleted or selectively favored and conserved.
Genome Reduction and Gene Loss
Many species exhibit genome reduction when subsets of their genes are not needed anymore. This typically happens when organisms adapt to a parasitic life style, e.g. when their nutrients are supplied by a host. As a consequence, they lose the genes need to produce these nutrients. In many cases, there are both free living and parasitic species that can be compared and their lost genes identified. Good examples are the genomes of Mycobacterium tuberculosis and Mycobacterium leprae, the latter of which has a dramatically reduced genome. Another beautiful example are endosymbiont species. For instance, Polynucleobacter necessarius was first described as a cytoplasmic endosymbiont of the ciliate Euplotes aediculatus. The latter species dies soon after being cured of the endosymbiont. In the few cases in which P. necessarius is not present, a different and rarer bacterium apparently supplies the same function. No attempt to grow symbiotic P. necessarius outside their hosts has yet been successful, strongly suggesting that the relationship is obligate for both partners. Yet, closely related free-living relatives of P. necessarius have been identified. The endosymbionts have a significantly reduced genome when compared to their free-living relatives (1.56 Mbp vs. 2.16 Mbp). | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.04%3A_Evolution_of_Genomes/18.4B%3A_Genome_Evolution.txt |
Whole-genome duplication is characterized by an organisms entire genetic information being copied once or multiple times.
Learning Objectives
• State the evolutionary implications of whole-genome duplication
Key Points
• Whole- genome duplication can provide an evolutionary advantage by providing the organism with multiple copies of a gene that is considered favorable.
• Whole-genome duplication can result in divergence and formation of new species over time.
• Whole-genome duplication can result in mutation and cause disease if the genes are rendered non-functional.
Key Terms
• polyploidy: having more than the usual two homologous sets of chromosomes
• palaeopolyploidization: the development of polyploid organisms in the geologic past
• sympatric speciation: the process through which new species evolve from a single ancestral species while inhabiting the same geographic region
Whole-Genome Duplication
Gene duplication is the process by which a region of DNA coding for a gene creates additional copies of the gene. Similar to gene duplication, whole-genome duplication is the process by which an organism’s entire genetic information is copied, once or multiple times, which is known as polyploidy. This may provide an evolutionary benefit to the organism by supplying it with multiple copies of a gene, thus, creating a greater possibility of functional and selectively favored genes.
Evolutionary importance
Paleopolyploidization events lead to massive cellular changes, including doubling of the genetic material, changes in gene expression and increased cell size. Gene loss during diploidization is not completely random, but heavily selected. Genes from large gene families are duplicated. On the other hand, individual genes are not duplicated. Overall, paleopolyploidy can have both short-term and long-term evolutionary effects on an organism’s fitness in the natural environment.
Genome diversity
Genome doubling provides organisms with redundant alleles that can evolve freely with little selection pressure. The duplicated genes can undergo neofunctionalization or subfunctionalization which could help the organism adapt to the new environment or survive different stress conditions.
Speciation
Sympatric speciation can begin with a chromosomal error during meiosis or the formation of a hybrid individual with too many chromosomes, such as polyploidy which can occur during whole-genome duplication. Scientists have identified types of polyploidy that can lead to reproductive isolation of an individual in the polyploid state. In some cases a polyploid individual will have two or more complete sets of chromosomes from its own species in a condition called autopolyploidy. 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.
It has been suggested that many polyploidization events created new species, via a gain of adaptive traits, or by sexual incompatibility with their diploid counterparts. An example would be the recent speciation of allopolyploid Spartina — S. anglica; the polyploid plant is so successful that it is listed as an invasive species in many regions.
Evidence of Whole-Genome Duplication
In 1997, Wolfe & Shields gave evidence for an ancient duplication of the Saccharomyces cerevisiae (Yeast) genome. It was initially noted that this yeast genome contained many individual gene duplications. Wolfe & Shields hypothesized that this was actually the result of an entire genome duplication in the yeast’s distant evolutionary history. They found 32 pairs of homologous chromosomal regions, accounting for over half of the yeast’s genome. They also noted that although homologs were present, they were often located on different chromosomes. Based on these observations, they determined that Saccharomyces cerevisiae underwent a whole-genome duplication soon after its evolutionary split from Kluyveromyces, a genus of ascomycetous yeasts. Over time, many of the duplicate genes were deleted and rendered non-functional. A number of chromosomal rearrangements broke the original duplicate chromosomes into the current manifestation of homologous chromosomal regions. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.04%3A_Evolution_of_Genomes/18.4C%3A_Whole-Genome_Duplication.txt |
Learning Objectives
• Explain the mechanisms of gene duplication and divergence
Gene Duplication
Gene duplication is the process by which a region of DNA coding for a gene is copied. Gene duplication can occur as the result of an error in recombination or through a retrotransposition event. Duplicate genes are often immune to the selective pressure under which genes normally exist. This can result in a large number of mutations accumulating in the duplicate gene code. This may render the gene non-functional or in some cases confer some benefit to the organism. There are multiple mechanisms by which gene duplication can occur.
Ectopic Recombination
Duplications can arise from unequal crossing-over that occurs during meiosis between misaligned homologous chromosomes. The product of this recombination is a duplication at the site of the exchange and a reciprocal deletion. Ectopic recombination is typically mediated by sequence similarity at the duplicate breakpoints, which form direct repeats. Repetitive genetic elements, such as transposable elements, offer one source of repetitive DNA that can facilitate recombination, and they are often found at duplication breakpoints in plants and mammals.
Replication Slippage
Replication slippage is an error in DNA replication, which can produce duplications of short genetic sequences. During replication, DNA polymerase begins to copy the DNA, and at some point during the replication process, the polymerase dissociates from the DNA and replication stalls. When the polymerase reattaches to the DNA strand, it aligns the replicating strand to an incorrect position and incidentally copies the same section more than once. Replication slippage is also often facilitated by repetitive sequence but requires only a few bases of similarity.
Retrotransposition
During cellular invasion by a replicating retroelement or retrovirus, viral proteins copy their genome by reverse transcribing RNA to DNA. If viral proteins attach irregularly to cellular mRNA, they can reverse-transcribe copies of genes to create retrogenes. Retrogenes usually lack intronic sequence and often contain poly A sequences that are also integrated into the genome. Many retrogenes display changes in gene regulation in comparison to their parental gene sequences, which sometimes results in novel functions.
Aneuploidy
Aneuploidy occurs when nondisjunction at a single chromosome results in an abnormal number of chromosomes. Aneuploidy is often harmful and in mammals regularly leads to spontaneous abortions. Some aneuploid individuals are viable. For example, trisomy 21 in humans leads to Down syndrome, but it is not fatal. Aneuploidy often alters gene dosage in ways that are detrimental to the organism and therefore, will not likely spread through populations.
Gene duplication as an evolutionary event
Gene duplications are an essential source of genetic novelty that can lead to evolutionary innovation. Duplication creates genetic redundancy and if one copy of a gene experiences a mutation that affects its original function, the second copy can serve as a ‘spare part’ and continue to function correctly. Thus, duplicate genes accumulate mutations faster than a functional single-copy gene, over generations of organisms, and it is possible for one of the two copies to develop a new and different function. This is an examples of neofunctionalization.
Gene duplication is believed to play a major role in evolution; this stance has been held by members of the scientific community for over 100 years. It has been argued that gene duplication is the most important evolutionary force since the emergence of the universal common ancestor.
Another possible fate for duplicate genes is that both copies are equally free to accumulate degenerative mutations, so long as any defects are complemented by the other copy. This leads to a neutral “subfunctionalization” model, in which the functionality of the original gene is distributed among the two copies. Neither gene can be lost, as both now perform important non-redundant functions, but ultimately neither is able to achieve novel functionality. Subfunctionalization can occur through neutral processes in which mutations accumulate with no detrimental or beneficial effects. However, in some cases subfunctionalization can occur with clear adaptive benefits. If an ancestral gene is pleiotropic and performs two functions, often times neither one of these two functions can be changed without affecting the other function. In this way, partitioning the ancestral functions into two separate genes can allow for adaptive specialization of subfunctions, thereby providing an adaptive benefit.
Divergence
Genetic divergence is the process in which two or more populations of an ancestral species accumulate independent genetic changes through time, often after the populations have become reproductively isolated for some period of time. In some cases, subpopulations living in ecologically distinct peripheral environments can exhibit genetic divergence from the remainder of a population, especially where the range of a population is very large. The genetic differences among divergent populations can involve silent mutations (that have no effect on the phenotype) or give rise to significant morphological and/or physiological changes. Genetic divergence will always accompany reproductive isolation, either due to novel adaptations via selection and/or due to genetic drift, and is the principal mechanism underlying speciation.
Genetic drift or allelic drift is the change in the frequency of a gene variant ( allele ) in a population due to random sampling. The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces. A population’s allele frequency is the fraction of the copies of one gene that share a particular form. Genetic drift may cause gene variants to disappear completely and thereby reduce genetic variation. When there are few copies of an allele, the effect of genetic drift is larger, and when there are many copies the effect is smaller. These changes in gene frequency can contribute to divergence.
Divergent evolution is usually a result of diffusion of the same species to different and isolated environments, which blocks the gene flow among the distinct populations allowing differentiated fixation of characteristics through genetic drift and natural selection.Divergent evolution can also be applied to molecular biology characteristics. This could apply to a pathway in two or more organisms or cell types. This can apply to genes and proteins, such as nucleotide sequences or protein sequences that are derived from two or more homologous genes. Both orthologous genes (resulting from a speciation event) and paralogous genes (resulting from gene duplication within a population) can be said to display divergent evolution.
Key Points
• Ectopic recombination occurs when there is an unequal crossing-over and the product of this recombination are a duplication at the site of the exchange and a reciprocal deletion.
• Gene duplications do not always result in detrimental mutations; they can contribute to divergent evolution, which causes genetic differences between groups to develop and eventually form new species.
• Replication slippage can occur when there is an error during DNA replication and duplications of short genetic sequences are produced.
• Retrotranspositions occur when a retrovirus copies their genome by reverse transcribing RNA to DNA and aberrantly attach to cellular mRNA and reverse transcribe copies of genes to create retrogenes.
• Aneuploidy can occur when there is a nondisjunction even at a single chromosome thus, the result is an abnormal number of chromosomes.
• Genetic divergence can occur by mechanisms such as genetic drift which contibute to the accumulation of independent genetic changes of two or more populations derived from a common ancestor.
Key Terms
• paralogous: having a similar structure indicating divergence from a common ancestral gene
• nondisjunction: the failure of chromosome pairs to separate properly during meiosis
• retrogene: a DNA gene copied back from RNA by reverse transcription
• genetic drift: an overall shift of allele distribution in an isolated population, due to random fluctuations in the frequencies of individual alleles of the genes | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.04%3A_Evolution_of_Genomes/18.4D%3A_Gene_Duplications_and_Divergence.txt |
Noncoding DNA are sequences of DNA that do not encode protein sequences but can be transcribed to produce important regulatory molecules.
Learning Objectives
• Summarize the importance of noncoding DNA
Key Points
• In the human genome, over 98% of DNA is classified as noncoding DNA and can be transcribed to regulatory noncoding RNAs (i.e. tRNAs, rRNAs), origins of DNA replication, centromeres, telomeres and scaffold attachment regions (SARs).
• Noncoding regions are most commonly referred to as ‘junk DNA’, however, this term is misleading as noncoding DNA does have functional importance.
• The proportion of coding and noncoding DNA within organisms varies and the amount of noncoding DNA typically correlates with organism complexity, though there are many notable exceptions.
Key Terms
• intergenic: describing the noncoding sections of nucleic acid between genes
• noncoding: DNA which does not code for protein
• intron: a portion of a split gene that is included in pre-RNA transcripts but is removed during RNA processing and rapidly degraded
Noncoding DNA
In genomics and related disciplines, noncoding DNA sequences are components of an organism’s DNA that do not encode protein sequences. Some noncoding DNA is transcribed into functional noncoding RNA molecules (e.g. transfer RNA, ribosomal RNA, and regulatory RNAs), while others are not transcribed or give rise to RNA transcripts of unknown function. The amount of noncoding DNA varies greatly among species. For example, over 98% of the human genome is noncoding DNA, while only about 2% of a typical bacterial genome is noncoding DNA.
Initially, a large proportion of noncoding DNA had no known biological function and was therefore sometimes referred to as “junk DNA”, particularly in the lay press. However, many types of noncoding DNA sequences do have important biological functions, including the transcriptional and translational regulation of protein-coding sequences, origins of DNA replication, centromeres, telomeres, scaffold attachment regions (SARs), genes for functional RNAs, and many others. Other noncoding sequences have likely, but as-yet undetermined, functions. Some sequences may have no biological function for the organism, such as endogenous retroviruses.
Genomic Variation between Organisms
The amount of total genomic DNA varies widely between organisms, and the proportion of coding and noncoding DNA within these genomes varies greatly as well. More than 98% of the human genome does not encode protein sequences, including most sequences within introns and most intergenic DNA. While overall genome size, and by extension the amount of noncoding DNA, are correlated to organism complexity, there are many exceptions. For example, the genome of the unicellular Polychaos dubium (formerly known as Amoeba dubia) has been reported to contain more than 200 times the amount of DNA in humans. The pufferfish Takifugu rubripes genome is only about one eighth the size of the human genome, yet seems to have a comparable number of genes; approximately 90% of the Takifugu genome is noncoding DNA.
In 2013, a new “record” for most efficient genome was discovered. Utricularia gibba, a bladderwort plant, has only 3% noncoding DNA. The extensive variation in nuclear genome size among eukaryotic species is known as the C-value enigma or C-value paradox. Most of the genome size difference appears to lie in the noncoding DNA. About 80 percent of the nucleotide bases in the human genome may be transcribed, but transcription does not necessarily imply function. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.04%3A_Evolution_of_Genomes/18.4E%3A_Noncoding_DNA.txt |
The genome size does not always correlate with the complexity of the organism and, in fact, shows great variation in size and gene number.
Learning Objectives
• Describe how variations in the size and number of genes can arise through evolutionary mechanisms
Key Points
• Harmless mutations and sexual recombination of chromosomes may allow the evolution of new characteristics.
• Genome size can be affected by various events, including duplication, insertion, recombination, deletion and polyploidization events.
• Genome size can be affected by evolution of an organism and result is an increased or decreased need for specific genes for survival based on behavior.
• The human genome exemplifies the concept that complexity does not always correlate with an increase in genome size; there are fewer protein coding genes present than expected relative to the genome size.
Key Terms
• polyploidization: hybridization that leads to polyploidy
• pseudogene: a segment of DNA that is part of the genome of an organism, and which is similar to a gene but does not code for a gene product
• genome: the cell’s complete genetic information packaged as a double-stranded DNA molecule
Variations in Size and Number of Genes
Genetic diversity refers to any variation in the nucleotides, genes, chromosomes, or whole genomes of organisms. Genetic diversity at its most elementary level is represented by differences in the sequences of nucleotides (adenine, cytosine, guanine, and thymine) that form the DNA (deoxyribonucleic acid) within the cells of the organism. The DNA is contained in the chromosomes present within the cell; some chromosomes are contained within specific organelles in the cell (for example, the chromosomes of mitochondria and chloroplast). Nucleotide variation is measured for discrete sections of the chromosomes, called genes. Thus, each gene compromises a hereditary section of DNA that occupies a specific place of the chromosome, and controls a particular characteristic of an organism.
Chromosomes
Most organisms are diploid, having two sets of chromosomes, and therefore two copies (called alleles ) of each gene. However, some organisms can be haploid, triploid, or tetraploid (having one, three, or four sets of chromosomes respectively). Within any single organism, there may be variation between the two (or more) alleles for each gene. This variation is introduced either through mutation of one of the alleles, or as a result of sexual reproduction.
During sexual reproduction, offspring inherit alleles from both parents and these alleles might be slightly different, especially if there has been migration or hybridization of organisms, so that the parents may come from different populations and gene pools. Also, when the offspring’s chromosomes are copied after fertilization, genes can be exchanged in a process called sexual recombination. Harmless mutations and sexual recombination may allow the evolution of new characteristics.
Genome Size and Number
Genome size is usually measured in base pairs (or bases in single-stranded DNA or RNA). The C-value is another measure of genome size. The C-value refers to the amount, in picograms, of DNA contained within a haploid nucleus (e.g. a gamete) or one half the amount in a diploid somatic cell of a eukaryotic organism. In some cases (notably among diploid organisms), the terms C-value and genome size are used interchangeably, however in polyploids the C-value may represent two or more genomes contained within the same nucleus.
Different species can have different numbers of genes within the entire DNA or genome of the organism. However, a greater total number of genes might not correspond with a greater observable complexity in the anatomy and physiology of the organism (i.e. greater phenotypic complexity). For example, the predicted size of the human genome is not much larger than the genomes of some invertebrates and plants, and may even be smaller than the Indian rice genome. In humans, more proteins are encoded per gene than in other species. In prokaryotic genomes, research has shown that there is a significant positive correlation between the C-value of prokaryotes and the amount of genes that compose the genome. This indicates that gene number is the main factor influencing the size of the prokaryotic genome.
Genes vs Genome Size
In eukaryotic organisms, there is a paradox observed, namely that the number of genes that make up the genome does not correlate with genome size. In other words, the genome size is much larger than would be expected given the total number of protein coding genes. Genome size can increase by duplication, insertion, or polyploidization and the process of recombination can lead to both DNA loss or gain. It is also possible that genomes can shrink due to deletions.
A famous example for such gene decay is the genome of Mycobacterium leprae, the causative agent of leprosy. M.leprae has lost many once-functional genes over time due to the formation of pseudogenes. This is evident in looking at its closest ancestor Mycobacterium tuberculosis. M. leprae lives inside and replicates inside of a host and due to this arrangement it does not have a need for many of the genes it once carried which allowed it to live and prosper outside of the host. Thus over time these genes have lost their function through mechanisms such as mutation causing them to become pseudogenes. It is beneficial to an organism to rid itself of non-essential genes because it makes replicating its DNA much faster and more energy-efficient.
An example of increasing genome size over time is seen in filamentous plant pathogens. These plant pathogen genomes have been growing larger over the years due to repeat-driven expansion. The repeat-rich regions contain genes coding for host interaction proteins. With the addition of more and more repeats to these regions the plants increase the possibility of developing new virulence factors through mutation and other forms of genetic recombination. In this way it is beneficial for these plant pathogens to have larger genomes.
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• Genome evolution. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Genome_evolution. License: CC BY-SA: Attribution-ShareAlike
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• Ian Harrison, Melina Laverty, and Eleanor Sterling, Genetic Diversity. December 6, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m12158/latest/. License: CC BY: Attribution
• genome. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/genome. License: CC BY-SA: Attribution-ShareAlike
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• pseudogene. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/pseudogene. License: CC BY-SA: Attribution-ShareAlike
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• Gene-duplication. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Gene-duplication.png. License: Public Domain: No Known Copyright
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• Gene. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Gene%23Number_of_genes. License: Public Domain: No Known Copyright | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.04%3A_Evolution_of_Genomes/18.4F%3A_Variations_in_Size_and_Number_of_Genes.txt |
Fossils tell us when organisms lived, as well as provide evidence for the progression and evolution of life on earth over millions of years.
Learning Objectives
• Synthesize the contributions of the fossil record to our understanding of evolution
Key Points
• Fossils are the preserved remains or traces of animals, plants, and other organisms from the past.
• Fossils are important evidence for evolution because they show that life on earth was once different from life found on earth today.
• Usually only a portion of an organism is preserved as a fossil, such as body fossils (bones and exoskeletons ), trace fossils (feces and footprints), and chemofossils (biochemical signals).
• Paleontologists can determine the age of fossils using methods like radiometric dating and categorize them to determine the evolutionary relationships between organisms.
Key Terms
• biomarker: A substance used as an indicator of a biological state, most commonly disease.
• trace fossil: A type of fossil reflecting the reworking of sediments and hard substrates by organisms including structures like burrows, trails, and impressions.
• fossil record: All discovered and undiscovered fossils and their placement in rock formations and sedimentary layers.
• strata: Layers of sedimentary rock.
• fossiliferous: Containing fossils.
What Fossils Tell Us
Fossils are the preserved remains or traces of animals, plants, and other organisms from the past. Fossils range in age from 10,000 to 3.48 billion years old. The observation that certain fossils were associated with certain rock strata led 19th century geologists to recognize a geological timescale. Like extant organisms, fossils vary in size from microscopic, like single-celled bacteria, to gigantic, like dinosaurs and trees.
Permineralization
Permineralization is a process of fossilization that occurs when an organism is buried. The empty spaces within an organism (spaces filled with liquid or gas during life) become filled with mineral-rich groundwater. Minerals precipitate from the groundwater, occupying the empty spaces. This process can occur in very small spaces, such as within the cell wall of a plant cell. Small-scale permineralization can produce very detailed fossils. For permineralization to occur, the organism must be covered by sediment soon after death, or soon after the initial decay process.
The degree to which the remains are decayed when covered determines the later details of the fossil. Fossils usually consist of the portion of the organisms that was partially mineralized during life, such as the bones and teeth of vertebrates or the chitinous or calcareous exoskeletons of invertebrates. However, other fossils contain traces of skin, feathers or even soft tissues.
Trace Fossils
Fossils may also consist of the marks left behind by the organism while it was alive, such as footprints or feces. These types of fossils are called trace fossils, or ichnofossils, as opposed to body fossils. Past life may also leave some markers that cannot be seen but can be detected in the form of biochemical signals; these are known as chemofossils or biomarkers.
The Fossil Record
The totality of fossils, both discovered and undiscovered, and their placement in fossiliferous (fossil-containing) rock formations and sedimentary layers (strata) is known as the fossil record. The fossil record was one of the early sources of data underlying the study of evolution and continues to be relevant to the history of life on Earth. The development of radiometric dating techniques in the early 20th century allowed geologists to determine the numerical or “absolute” age of various strata and their included fossils.
Evidence for Evolution
Fossils provide solid evidence that organisms from the past are not the same as those found today; fossils show a progression of evolution. Fossils, along with the comparative anatomy of present-day organisms, constitute the morphological, or anatomical, record. By comparing the anatomies of both modern and extinct species, paleontologists can infer the lineages of those species. This approach is most successful for organisms that had hard body parts, such as shells, bones or teeth. The resulting fossil record tells the story of the past and shows the evolution of form over millions of years. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.05%3A_Evidence_of_Evolution/18.5A%3A_The_Fossil_Record_as_Evidence_for_Evolution.txt |
Fossils can form under ideal conditions by preservation, permineralization, molding (casting), replacement, or compression.
Learning Objectives
• Predict the conditions suitable to fossil formation
Key Points
• Preservation of remains in amber or other substances is the rarest from of fossilization; this mechanism allows scientists to study the skin, hair, and organs of ancient creatures.
• Permineralization, where minerals like silica fill the empty spaces of shells, is the most common form of fossilization.
• Molds form when shells or bones dissolve, leaving behind an empty depression; a cast is then formed when the depression is filled by sediment.
• Replacement occurs when the original shell or bone dissolves away and is replaced by a different mineral; when this occurs with permineralization, it is called petrification.
• In compression, the most common form of fossilization of leaves and ferns, a dark imprint of the fossil remains.
• Decay, chemical weathering, erosion, and predators are factors that deter fossilization.
• Fossilization of soft body parts is rare, and hard parts are better preserved when buried.
Key Terms
• amber: a hard, generally yellow to brown translucent fossil resin
• permineralization: form of fossilization in which minerals are deposited in the pores of bone and similar hard animal parts
• petrification: process by which organic material is converted into stone through the replacement of the original material and the filling of the original pore spaces with minerals
Fossil Formation
The process of a once living organism becoming a fossil is called fossilization. Fossilization is a very rare process, and of all the organisms that have lived on Earth, only a tiny percentage of them ever become fossils. To see why, imagine an antelope that dies on the African plain. Most of its body is quickly eaten by scavengers, and the remaining flesh is soon eaten by insects and bacteria, leaving behind only scattered bones. As the years go by, the bones are scattered and fragmented into small pieces, eventually turning into dust and returning their nutrients to the soil. As a result, it would be rare for any of the antelope’s remains to actually be preserved as a fossil.
Fossilization can occur in many ways. Most fossils are preserved in one of five processes:
• preserved remains
• permineralization
• molds and casts
• replacement
• compression
Preserved Remains
The rarest form of fossilization is the preservation of original skeletal material and even soft tissue. For example, some insects have been preserved perfectly in amber, which is ancient tree sap. In addition, several mammoths and even a Neanderthal hunter have been discovered frozen in glaciers. These preserved remains allow scientists the rare opportunity to examine the skin, hair, and organs of ancient creatures. Scientists have collected DNA from these remains and compared the DNA sequences to those of modern creatures.
Permineralization
The most common method of fossilization is permineralization. After a bone, wood fragment, or shell is buried in sediment, it may be exposed to mineral-rich water that moves through the sediment. This water will deposit minerals, typically silica, into empty spaces, producing a fossil. Fossilized dinosaur bones, petrified wood, and many marine fossils were formed by permineralization.
Molds and Casts
In some cases, the original bone or shell dissolves away, leaving behind an empty space in the shape of the shell or bone. This depression is called a mold. Later, the space may be filled with other sediments to form a matching cast in the shape of the original organism. Many mollusks (bivalves, snails, and squid) are commonly found as molds and casts because their shells dissolve easily.
Replacement
In some cases, the original shell or bone dissolves away and is replaced by a different mineral. For example, shells that were originally calcite may be replaced by dolomite, quartz, or pyrite. If quartz fossils are surrounded by a calcite matrix, the calcite can be dissolved away by acid, leaving behind an exquisitely preserved quartz fossil. When permineralization and replacement occur together, the organism is said to have undergone petrification, the process of turning organic material into stone. However, replacement can occur without permineralization and vice versa.
Compression
Some fossils form when their remains are compressed by high pressure. This can leave behind a dark imprint of the fossil. Compression is most common for fossils of leaves and ferns but also can occur with other organisms.
Conditions for Fossilization
Following the death of an organism, several forces contribute to the dissolution of its remains. Decay, predators, or scavengers will typically rapidly remove the flesh. The hard parts, if they are separable at all, can be dispersed by predators, scavengers, or currents. The individual hard parts are subject to chemical weathering and erosion, as well as to splintering by predators or scavengers, which will crunch up bones for marrow and shells to extract the flesh inside. Also, an animal swallowed whole by a predator, such as a mouse swallowed by a snake, will have not just its flesh but some, and perhaps all, its bones destroyed by the gastric juices of the predator.
It would not be an exaggeration to say that the typical vertebrate fossil consists of a single bone, or tooth, or fish scale. The preservation of an intact skeleton with the bones in the relative positions they had in life requires a remarkable circumstances, such as burial in volcanic ash, burial in aeolian sand due to the sudden slumping of a sand dune, burial in a mudslide, burial by a turbidity current, and so forth. The mineralization of soft parts is even less common and is seen only in exceptionally rare chemical and biological conditions. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.05%3A_Evidence_of_Evolution/18.5B%3A_Fossil_Formation.txt |
Because not all animals have bodies which fossilize easily, the fossil record is considered incomplete.
Learning Objectives
• Explain the gap in the fossil record
Key Points
• The number of species known about through fossils is less than 1% of all species that have ever lived.
• Because hard body parts are more easily preserved than soft body parts, there are more fossils of animals with hard body parts, such as vertebrates, echinoderms, brachiopods, and some groups of arthropods.
• Very few fossils have been found in the period from 360 to 345 million years ago, known as Romer’s gap. Theories to explain this include the period’s geochemistry, errors in excavation, and limited vertebrate diversity.
Key Terms
• transitional fossil: Fossilized remains of a life form that exhibits traits common to both an ancestral group and its derived descendant group.
• Romer’s gap: A period in the tetrapod fossil record (360 to 345 million years ago) from which excavators have not yet found relevant fossils.
Incompleteness of the Fossil Record
Each fossil discovery represents a snapshot of the process of evolution. Because of the specialized and rare conditions required for a biological structure to fossilize, many important species or groups may never leave fossils at all. Even if they do leave fossils, humans may never find them—for example, if they are buried under hundreds of feet of ice in Antarctica. The number of species known about through the fossil record is less than 5% of the number of species alive today. Fossilized species may represent less than 1% of all the species that have ever lived.
Types of Fossils in the Fossil Record
The fossil record is very uneven and is mostly comprised of fossils of organisms with hard body parts, leaving most groups of soft-bodied organisms with little to no fossil record. Groups considered to have a good fossil record, including transitional fossils between these groups, are the vertebrates, the echinoderms, the brachiopods, and some groups of arthropods. Their hard bones and shells fossilize easily, unlike the bodies of organisms like cephalopods or jellyfish.
Romer’s Gap
Romer’s gap is an example of an apparent gap in the tetrapod fossil record used in the study of evolutionary biology. These gaps represent periods from which no relevant fossils have been found. Romer’s gap is named after paleontologist Alfred Romer, who first recognized it. Romer’s gap spanned from approximately 360 to 345 million years ago, corresponding to the first 15 million years of the Carboniferous Period.
There has been much debate over why there are so few fossils from this time period. Some scientists have suggested that the geochemistry of the time period caused bad conditions for fossil formation, so few organisms were fossilized. Another theory suggests that scientists have simply not yet discovered an excavation site for these fossils, due to inaccessibility or random chance.
18.5D: Carbon Dating and Estimating Fossil Age
The age of fossils can be determined using stratigraphy, biostratigraphy, and radiocarbon dating.
Learning Objectives
• Summarize the available methods for dating fossils
Key Points
• Determining the ages of fossils is an important step in mapping out how life evolved across geologic time.
• The study of stratigraphy enables scientists to determine the age of a fossil if they know the age of layers of rock that surround it.
• Biostratigraphy enables scientists to match rocks with particular fossils to other rocks with those fossils to determine age.
• Paleontology seeks to map out how life evolved across geologic time. A substantial hurdle is the difficulty of working out fossil ages.
• Scientists use carbon dating when determining the age of fossils that are less than 60,000 years old, and that are composed of organic materials such as wood or leather.
Key Terms
• half-life: The time required for half of the nuclei in a sample of a specific isotope to undergo radioactive decay.
• stratigraphy: The study of rock layers and the layering process.
• radiocarbon dating: A method of estimating the age of an artifact or biological vestige based on the relative amounts of various isotopes of carbon present in a sample.
Determining Fossil Ages
Paleontology seeks to map out how life evolved across geologic time. A substantial hurdle is the difficulty of working out fossil ages. There are several different methods for estimating the ages of fossils, including:
1. stratigraphy
2. biostratigraphy
3. carbon dating
Stratigraphy
Paleontologists rely on stratigraphy to date fossils. Stratigraphy is the science of understanding the strata, or layers, that form the sedimentary record. Strata are differentiated from each other by their different colors or compositions and are exposed in cliffs, quarries, and river banks. These rocks normally form relatively horizontal, parallel layers, with younger layers forming on top.
If a fossil is found between two layers of rock whose ages are known, the fossil’s age is thought to be between those two known ages. Because rock sequences are not continuous, but may be broken up by faults or periods of erosion, it is difficult to match up rock beds that are not directly adjacent.
Biostratigraphy
Fossils of species that survived for a relatively short time can be used to match isolated rocks: this technique is called biostratigraphy. For instance, the extinct chordate Eoplacognathus pseudoplanus is thought to have existed during a short range in the Middle Ordovician period. If rocks of unknown age have traces of E. pseudoplanus, they have a mid-Ordovician age. Such index fossils must be distinctive, globally distributed, and occupy a short time range to be useful. Misleading results can occur if the index fossils are incorrectly dated.
Relative Dating
Stratigraphy and biostratigraphy can in general provide only relative dating (A was before B), which is often sufficient for studying evolution. This is difficult for some time periods, however, because of the barriers involved in matching rocks of the same age across continents. Family-tree relationships can help to narrow down the date when lineages first appeared. For example, if fossils of B date to X million years ago and the calculated “family tree” says A was an ancestor of B, then A must have evolved earlier.
It is also possible to estimate how long ago two living branches of a family tree diverged by assuming that DNA mutations accumulate at a constant rate. However, these “molecular clocks” are sometimes inaccurate and provide only approximate timing. For example, they are not sufficiently precise and reliable for estimating when the groups that feature in the Cambrian explosion first evolved, and estimates produced by different approaches to this method may vary as well.
Carbon Dating
Together with stratigraphic principles, radiometric dating methods are used in geochronology to establish the geological time scale. Beds that preserve fossils typically lack the radioactive elements needed for radiometric dating (” radiocarbon dating ” or simply “carbon dating”). The principle of radiocarbon dating is simple: the rates at which various radioactive elements decay are known, and the ratio of the radioactive element to its decay products shows how long the radioactive element has existed in the rock. This rate is represented by the half-life, which is the time it takes for half of a sample to decay.
The half-life of carbon-14 is 5,730 years, so carbon dating is only relevant for dating fossils less than 60,000 years old. Radioactive elements are common only in rocks with a volcanic origin, so the only fossil-bearing rocks that can be dated radiometrically are volcanic ash layers. Carbon dating uses the decay of carbon-14 to estimate the age of organic materials, such as wood and leather. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.05%3A_Evidence_of_Evolution/18.5C%3A_Gaps_in_the_Fossil_Record.txt |
Learning Objectives
• Analyze the fossil record to understand the evolution of horses
Fossils provide evidence that organisms from the past are not the same as those found today, and demonstrate a progression of evolution. Scientists date and categorize fossils 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 forms over millions of years.
Case Study: Evolution of the Modern Horse
Highly detailed fossil records have been recovered for sequences in the evolution of modern horses. The fossil record of horses in North America is especially rich and contains transition fossils: fossils that show intermediate stages between earlier and later forms. The fossil record extends back to a dog-like ancestor some 55 million years ago, which gave rise to the first horse-like species 55 to 42 million years ago in the genus Eohippus.
The first equid fossil was found in the gypsum quarries in Montmartre, Paris in the 1820s. The tooth was sent to the Paris Conservatory, where Georges Cuvier identified it as a browsing equine related to the tapir. His sketch of the entire animal matched later skeletons found at the site. During the H.M.S. Beagle survey expedition, Charles Darwin had remarkable success with fossil hunting in Patagonia. In 1833 in Santa Fe, Argentina, he was “filled with astonishment” when he found a horse’s tooth in the same stratum as fossils of giant armadillos and wondered if it might have been washed down from a later layer, but concluded this was “not very probable.” In 1836, the anatomist Richard Owen confirmed the tooth was from an extinct species, which he subsequently named Equus curvidens.
The original sequence of species believed to have evolved into the horse was based on fossils discovered in North America in the 1870s by paleontologist Othniel Charles Marsh. The sequence, from Eohippus to the modern horse (Equus), was popularized by Thomas Huxley and became one of the most widely known examples of a clear evolutionary progression. The sequence of transitional fossils was assembled by the American Museum of Natural History into an exhibit that emphasized the gradual, “straight-line” evolution of the horse.
Since then, as the number of equid fossils has increased, the actual evolutionary progression from Eohippus to Equus has been discovered to be much more complex and multibranched than was initially supposed. Detailed fossil information on the rate and distribution of new equid species has also revealed that the progression between species was not as smooth and consistent as was once believed.
Although some transitions were indeed gradual progressions, a number of others were relatively abrupt in geologic time, taking place over only a few million years. Both anagenesis, a gradual change in an entire population ‘s gene frequency, and cladogenesis, a population “splitting” into two distinct evolutionary branches, occurred, and many species coexisted with “ancestor” species at various times.
Adaptation for Grazing
The series of fossils tracks the change in anatomy resulting from a gradual drying trend that changed the landscape from a forested habitat to a prairie habitat. Early horse ancestors were originally specialized for tropical forests, while modern horses are now adapted to life on drier land. Successive fossils show the evolution of teeth shapes and foot and leg anatomy to a grazing habit with adaptations for escaping predators.
The horse belongs to the order Perissodactyla (odd-toed ungulates), the members of which all share hoofed feet and an odd number of toes on each foot, as well as mobile upper lips and a similar tooth structure. This means that horses share a common ancestry with tapirs and rhinoceroses. Later species showed gains in size, such as those of Hipparion, which existed from about 23 to 2 million years ago. The fossil record shows several adaptive radiations in the horse lineage, which is now much reduced to only one genus, Equus, with several species. Paleozoologists have been able to piece together a more complete outline of the modern horse’s evolutionary lineage than that of any other animal.
Key Points
• A dog-like organism gave rise to the first horse ancestors 55-42 million years ago.
• The fossil record shows modern horses moved from tropical forests to prairie habitats, developed teeth, and grew in size.
• The first equid fossil was a tooth from the extinct species Equus curvidens found in Paris in the 1820s.
• Thomas Huxley popularized the evolutionary sequence of horses, which became one of the most common examples of clear evolutionary progression.
• Horse evolution was previously believed to be a linear progress, but after more fossils were discovered, it was determined the evolution of horses was more complex and multi-branched.
• Horses have evolved from gradual change ( anagenesis ) as well as abrupt progression and division ( cladogenesis ).
Key Terms
• cladogenesis: An evolutionary splitting event in which each branch and its smaller branches forms a clade.
• equid: A member of the horse family.
• anagenesis: Evolution of a new species through a large scale change in gene frequency so that the new species replaces the old, rather than branching to produce an additional species. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.05%3A_Evidence_of_Evolution/18.5E%3A_The_Fossil_Record_and_the_Evolution_of_the_Modern_Horse.txt |
Homologous structures are similar structures that evolved from a common ancestor.
Learning Objectives
• Describe the connection between evolution and the appearance of homologous structures
Key Points
• Homology is a relationship defined between structures or DNA derived from a common ancestor and illustrates descent from a common ancestor.
• Analogous structures are physically (but not genetically) similar structures that were not present the last common ancestor.
• Homology can also be partial; new structures can evolve through the combination or parts of developmental pathways.
• Analogy may also be referred to as homoplasy, which is further divided into parallelism, reversal, and convergence.
Key Terms
• homology: A correspondence of structures in two life forms with a common evolutionary origin, such as flippers and hands.
• analogy: The relationship between characteristics that are apparently similar but did not develop from the same structure
• homoplasy: A correspondence between the parts or organs of different species acquired as the result of parallel evolution or convergence.
Homologous Structures
Homology is the relationship between structures or DNA derived from the most recent common ancestor. A common example of homologous structures in evolutionary biology are the wings of bats and the arms of primates. Although these two structures do not look similar or have the same function, genetically, they come from the same structure of the last common ancestor. Homologous traits of organisms are therefore explained by descent from a common ancestor.
It’s important to note that defining two structures as homologous depends on what ancestor is being described as the common ancestor. If we go all the way back to the beginning of life, all structures are homologous!
In genetics, homology is measured by comparing protein or DNA sequences. Homologous gene sequences share a high similarity, supporting the hypothesis that they share a common ancestor.
Homology can also be partial: new structures can evolve through the combination of developmental pathways or parts of them. As a result, hybrid or mosaic structures can evolve that exhibit partial homologies. For example, certain compound leaves of flowering plants are partially homologous both to leaves and shoots because they combine some traits of leaves and some of shoots.
Paralogous Structures
Homologous sequences are considered paralogous if they were separated by a gene duplication event; if a gene in an organism is duplicated to occupy two different positions in the same genome, then the two copies are paralogous.
A set of sequences that are paralogous are called paralogs of each other. Paralogs typically have the same or similar function, but sometimes do not. It is considered that due to lack of the original selective pressure upon one copy of the duplicated gene, this copy is free to mutate and acquire new functions.
Paralogous genes often belong to the same species, but not always. For example, the hemoglobin gene of humans and the myoglobin gene of chimpanzees are considered paralogs. This is a common problem in bioinformatics; when genomes of different species have been sequenced and homologous genes have been found, one can not immediately conclude that these genes have the same or similar function, as they could be paralogs whose function has diverged.
Analogous Structures
The opposite of homologous structures are analogous structures, which are physically similar structures between two taxa that evolved separately (rather than being present in the last common ancestor). Bat wings and bird wings evolved independently and are considered analogous structures. Genetically, a bat wing and a bird wing have very little in common; the last common ancestor of bats and birds did not have wings like either bats or birds. Wings evolved independently in each lineage after diverging from ancestors with forelimbs that were not used as wings (terrestrial mammals and theropod dinosaurs, respectively).
It is important to distinguish between different hierarchical levels of homology in order to make informative biological comparisons. In the above example, the bird and bat wings are analogous as wings, but homologous as forelimbs because the organ served as a forearm (not a wing) in the last common ancestor of tetrapods.
Analogy is different than homology. Although analogous characteristics are superficially similar, they are not homologous because they are phylogenetically independent. The wings of a maple seed and the wings of an albatross are analogous but not homologous (they both allow the organism to travel on the wind, but they didn’t both develop from the same structure). Analogy is commonly also referred to as homoplasy. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.05%3A_Evidence_of_Evolution/18.5F%3A_Homologous_Structures.txt |
Convergent evolution occurs in different species that have evolved similar traits independently of each other.
Learning Objectives
• Predict the circumstances supporting convergent evolution of two species
Key Points
• Examples of convergent evolution include the relationship between bat and insect wings, shark and dolphin bodies, and vertebrate and cephalopod eyes.
• Analogous structures arise from convergent evolution, but homologous structures do not.
• Convergent evolution is the opposite of divergent evolution, in which related species evolve different traits.
• Convergent evolution is similar to parallel evolution, in which two similar but independent species evolve in the same direction and independently acquire similar characteristics.
Key Terms
• parallel evolution: the development of a similar trait in related, but distinct, species descending from the same ancestor, but from different clades
• convergent evolution: a trait of evolution in which species not of similar recent origin acquire similar properties due to natural selection
• divergent evolution: the process by which a species with similar traits become groups that are tremendously different from each other over many generations
• morphology: the form and structure of an organism
Convergent Evolution
Sometimes, similar phenotypes evolve independently in distantly related species. For example, flight has evolved in both bats and insects, and they both have 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.
Examples of Convergent Evolution
Convergent evolution describes the independent evolution of similar features in species of different lineages. The two species came to the same function, flying, but did so separately from each other. They have “converged” on this useful trait. Both sharks and dolphins have similar body forms, yet are only distantly related: sharks are fish and dolphins are mammals. Such similarities are a result of both populations being exposed to the same selective pressures. Within both groups, changes that aid swimming have been favored. Thus, over time, they developed similar appearances (morphology), even though they are not closely related.
One of the most well-known examples of convergent evolution is the camera eye of cephalopods (e.g., octopus), vertebrates (e.g., mammals), and cnidaria (e.g., box jellies). Their last common ancestor had at most a very simple photoreceptive spot, but a range of processes led to the progressive refinement of this structure to the advanced camera eye. There is, however, one subtle difference: the cephalopod eye is “wired” in the opposite direction, with blood and nerve vessels entering from the back of the retina, rather than the front as in vertebrates.
Convergent evolution is similar to, but distinguishable from, the phenomenon of parallel evolution. Parallel evolution occurs when two independent but similar species evolve in the same direction and thus independently acquire similar characteristics; for example, gliding frogs have evolved in parallel from multiple types of tree frog.
Analogous Structures
Traits arising through convergent evolution are analogous structures, in contrast to homologous structures, which have a common origin, but not necessarily similar function. The British anatomist Richard Owen was the first scientist to recognize the fundamental difference between analogies and homologies. Bat and pterosaur wings are an example of analogous structures, while the bat wing is homologous to human and other mammal forearms, sharing an ancestral state despite serving different functions.
Divergent Evolution
The opposite of convergent evolution is divergent evolution, whereby related species evolve different traits. On a molecular level, this can happen due to random mutation unrelated to adaptive changes. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.05%3A_Evidence_of_Evolution/18.5G%3A_Convergent_Evolution.txt |
Vestigial structures have no function but may still be inherited to maintain fitness.
Learning Objectives
• Discuss the connection between evolution and the existence of vestigial structures
Key Points
• Structures that have no apparent function and appear to be residual parts from a past ancestor are called vestigial structures.
• Examples of vestigial structures include the human appendix, the pelvic bone of a snake, and the wings of flightless birds.
• Vestigial structures can become detrimental, but in most cases these structures are harmless; however, these structures, like any other structure, require extra energy and are at risk for disease.
• Vestigial structures, especially non-harmful ones, take a long time to be phased out since eliminating them would require major alterations that could result in negative side effects.
Key Terms
• vestigial structure: Genetically determined structures or attributes that have lost most or all of their ancestral function in a given species.
• adaptation: A modification of something or its parts that makes it more fit for existence under the conditions of its current environment.
What Are Vestigial Structures?
Some organisms possess structures with no apparent function which appear to be residual parts from a past ancestor. For example, some snakes have pelvic bones despite having no legs because they descended from reptiles that did have legs. Another example of a structure with no function is the human vermiform appendix. These unused structures without function are called vestigial structures. Other examples of vestigial structures are wings (which may have other functions) on flightless birds like the ostrich, leaves on some cacti, traces of pelvic bones in whales, and the sightless eyes of cave animals.
There are also several reflexes and behaviors that are considered to be vestigial. The formation of goose bumps in humans under stress is a vestigial reflex its function in human ancestors was to raise the body’s hair, making the ancestor appear larger and scaring off predators. The arrector pili muscle, which is a band of smooth muscle that connects the hair follicle to connective tissue, contracts and creates the goose bumps on skin.
Vestigial Structures in Evolution
Vestigial structures are often homologous to structures that function normally in other species. Therefore, vestigial structures can be considered evidence for evolution, the process by which beneficial heritable traits arise in populations over an extended period of time. The existence of vestigial traits can be attributed to changes in the environment and behavior patterns of the organism in question. As the function of the trait is no longer beneficial for survival, the likelihood that future offspring will inherit the “normal” form of it decreases. In some cases the structure becomes detrimental to the organism.
If there are no selection pressures actively lowering the fitness of the individual, the trait will persist in future generations unless the trait is eliminated through genetic drift or other random events.
Although in many cases the vestigial structure is of no direct harm, all structures require extra energy in terms of development, maintenance, and weight and are also a risk in terms of disease (e.g., infection, cancer). This provides some selective pressure for the removal of parts that do not contribute to an organism’s fitness, but a structure that is not directly harmful will take longer to be ‘phased out’ than one that is. Some vestigial structures persist due to limitations in development, such that complete loss of the structure could not occur without major alterations of the organism’s developmental pattern, and such alterations would likely produce numerous negative side-effects.
The vestigial versions of a structure can be compared to the original version of the structure in other species in order to determine the homology of the structure. Homologous structures indicate common ancestry with those organisms that have a functional version of the structure. Vestigial traits can still be considered adaptations because an adaptation is often defined as a trait that has been favored by natural selection. Adaptations, therefore, need not be adaptive, as long as they were at some point. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.05%3A_Evidence_of_Evolution/18.5H%3A_Vestigial_Structures.txt |
The biological distribution of species is based on the movement of tectonic plates over a period of time.
Learning Objectives
• Relate biogeography and the distribution of species
Key Points
• Biogeography is the study of geological species distribution, which is influenced by both biotic and abiotic factors.
• Some species are endemic and are only found in a particular region, while others are generalists and are distributed worldwide.
• Species that evolved before the breakup of continents are distributed worldwide.
• Species that evolved after the breakup of continents are found in only certain regions of the planet.
Key Terms
• endemic: unique to a particular area or region; not found in other places
• generalist: species which can thrive in a wide variety of environmental conditions
• Pangaea: supercontinent that included all the landmasses of the earth before the Triassic period and that broke up into Laurasia and Gondwana
Distribution of Species
Biogeography is the study of the geographic distribution of living things and the abiotic factors that affect their distribution. Abiotic factors, such as temperature and rainfall, vary based on latitude and elevation, primarily. As these abiotic factors change, the composition of plant and animal communities also changes.
Patterns of Species Distribution
Ecologists who study biogeography examine patterns of species distribution. No species exists everywhere; for example, the Venus flytrap is endemic to a small area in North and South Carolina. An endemic species is one which is naturally found only in a specific geographic area that is usually restricted in size. Other species are generalists: species which live in a wide variety of geographic areas; the raccoon, for example, is native to most of North and Central America.
Since species distribution patterns are based on biotic and abiotic factors and their influences during the very long periods of time required for species evolution, early studies of biogeography were closely linked to the emergence of evolutionary thinking in the eighteenth century. Some of the most distinctive assemblages of plants and animals occur in regions that have been physically separated for millions of years by geographic barriers. Biologists estimate that Australia, for example, has between 600,000 and 700,000 species of plants and animals. Approximately 3/4 of living plant and mammal species are endemic species found solely in Australia.
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 Proteaceae in Australia, southern Africa, and South America is best explained by the plant family’s presence there prior to the southern supercontinent Gondwana breaking up.
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• OpenStax College, Biogeography. December 7, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44857/latest/. License: CC BY: Attribution | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/18%3A_Evolution_and_the_Origin_of_Species/18.05%3A_Evidence_of_Evolution/18.5I%3A_Biogeography_and_the_Distribution_of_Species.txt |
Genetic variation in a population is determined by mutations, natural selection, genetic drift, genetic hitchhiking, and gene flow.
Learning Objectives
• Describe how the forces of genetic drift, genetic hitchhiking, gene flow, and mutation can lead to differences in population variation
Key Points
• The theory of evolution gives us a unifying theory to explain the similarities and differences within life’s organisms and processes.
• Populations (or gene pools ) evolve as gene frequencies change; individual organisms cannot evolve.
• Variation in populations is determined by the genes present in the population’s gene pool, which may be directly altered by mutation.
• Natural selection is the gradual process that increases the frequency of advantageous inherited traits (allowing it to survive and reproduce) and decreases the frequency of detrimental inherited traits within a population.
• A population’s genetic makeup can also be affected by random chance events like genetic drift, or when genes are inherited together in genetic hitchhiking.
Key Terms
• gene flow: the transfer of alleles or genes from one population to another
• genetic hitchhiking: a phenomenon in which a gene increases in a population because it lies near genes on the same chromosome that are advantageous to an organism
• genetic drift: an overall shift of allele distribution in an isolated population, due to random fluctuations in the frequencies of individual alleles of the genes
• fitness: an individual’s ability to propagate its genes
• natural selection: a process in which individual organisms or phenotypes that possess favorable traits are more likely to survive and reproduce
• mutation: any heritable change of the base-pair sequence of genetic material
The Evolution of Populations
According to evolutionary theory, every organism from humans to beetles to plants to bacteria share a common ancestor. Millions of years of evolutionary pressure caused some organisms to died while others survived, leaving earth with the diverse life forms we have today. Within this diversity is unity; for example, all organisms are composed of cells and use DNA. The theory of evolution gives us a unifying theory to explain the similarities and differences within life’s organisms and processes.
Genetic Variation in Populations
A population is a group of individuals that can all interbreed, often distinguished as a species. Because these individuals can share genes and pass on combinations of genes to the next generation, the collection of these genes is called a gene pool. The process of evolution occurs only in populations and not in individuals. A single individual cannot evolve alone; evolution is the process of changing the gene frequencies within a gene pool. Five forces can cause genetic variation and evolution in a population: mutations, natural selection, genetic drift, genetic hitchhiking, and gene flow.
Mutations
Why do some organisms survive while others die? These surviving organisms generally possess traits or characteristics that bestow benefits that help them survive (e.g., better camouflage, faster swimming, or more efficient digestion). Each of these characteristics is the result of a mutation, or a change in the genetic code. Mutations occur spontaneously, but not all mutations are heritable; they are passed down to offspring only if the mutations occur in the gametes. These heritable mutations are responsible for the rise of new traits in a population.
Natural Selection
Just as mutations cause new traits in a population, natural selection acts on the frequency of those traits. Because there are more organisms than resources, all organisms are in a constant struggle for existence. In natural selection, those individuals with superior traits will be able to produce more offspring. The more offspring an organism can produce, the higher its fitness. As novel traits and behaviors arise from mutation, natural selection perpetuates the traits that confer a benefit.
Genetic Drift
When selective forces are absent or relatively weak, gene frequencies tend to “drift” due to random events. This drift halts when the variation of the gene becomes “fixed” by either disappearing from the population or replacing the other variations completely. Even in the absence of selective forces, genetic drift can cause two separate populations that began with the same genetic structure to drift apart into two divergent populations.
Genetic Hitchhiking
When recombination occurs during sexual reproduction, genes are usually shuffled so that each parent gives its offspring a random assortment of its genetic variation. However, genes that are close together on the same chromosome are often assorted together. Therefore, the frequency of a gene may increase in a population through genetic hitchhiking if its proximal genes confer a benefit.
Gene Flow
Gene flow is the exchange of genes between populations or between species.If the gene pools between two populations are different, the exchange of genes can introduce variation that is advantageous or disadvantageous to one of the populations. If advantageous, this gene variation may replace all the other variations until the entire population exhibits that trait. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/19%3A_The_Evolution_of_Populations/19.01%3A_Population_Evolution/19.1A%3A_Defining_Population_Evolution.txt |
Population genetics is the study of the distributions and changes of allele frequency in a population.
Learning Objectives
• Define a population gene pool and explain how the size of the gene pool can affect the evolutionary success of a population
Key Points
• A gene pool is the sum of all the alleles (variants of a gene) in a population.
• Allele frequencies range from 0 (present in no individuals) to 1 (present in all individuals); all allele frequencies for a given gene add up to 100 percent in a population.
• The smaller a population, the more susceptible it is to mechanisms like natural selection and genetic drift, as the effects of such mechanisms are magnified when the gene pool is small.
• The founder effect occurs when part of an original population establishes a new population with a separate gene pool, leading to less genetic variation in the new population.
Key Terms
• allele: one of a number of alternative forms of the same gene occupying a given position on a chromosome
• gene pool: the complete set of unique alleles that would be found by inspecting the genetic material of every living member of a species or population
• founder effect: a decrease in genetic variation that occurs when an entire population descends from a small number of founders
Population Genetics
A gene for a particular characteristic may have several variations called alleles. These variations code for different traits associated with that characteristic. For example, in the ABO blood type system in humans, three alleles (IA, IB, or i) determine the particular blood-type protein on the surface of red blood cells. A human with a type IA allele will display A-type proteins (antigens) on the surface of their red blood cells. Individuals with the phenotype of type A blood have the genotype IAIA or IAi, type B have IBIB or IBi, type AB have IAIB, and type O have ii.
A diploid organism can only carry two alleles for a particular gene. In human blood type, the combinations are composed of two alleles such as IAIA or IAIB. Although each organism can only carry two alleles, more than those two alleles may be present in the larger population. For example, in a population of fifty people where all the blood types are represented, there may be more IA alleles than i alleles. Population genetics is the study of how selective forces change a population through changes in allele and genotypic frequencies.
Allele Frequency
The allele frequency (or gene frequency) is the rate at which a specific allele appears within a population. In population genetics, the term evolution is defined as a change in the frequency of an allele in a population. Frequencies range from 0, present in no individuals, to 1, present in all individuals. The gene pool is the sum of all the alleles at all genes in a population.
Using the ABO blood type system as an example, the frequency of one of the alleles, for example IA, is the number of copies of that allele divided by all the copies of the ABO gene in the population, i.e. all the alleles. Allele frequencies can be expressed as a decimal or as a percent and always add up to 1, or 100 percent, of the total population. For example, in a sample population of humans, the frequency of the IA allele might be 0.26, which would mean that 26% of the chromosomes in that population carry the IA allele. If we also know that the frequency of the IB allele in this population is 0.14, then the frequency of the i allele is 0.6, which we obtain by subtracting all the known allele frequencies from 1 (thus: 1 – 0.26 – 0.14 = 0.6). A change in any of these allele frequencies over time would constitute evolution in the population.
Population Size and Evolution
When allele frequencies within a population change randomly with no advantage to the population over existing allele frequencies, the phenomenon is called genetic drift. The smaller a population, the more susceptible it is to mechanisms such as genetic drift as alleles are more likely to become fixed at 0 (absent) or 1 (universally present). Random events that alter allele frequencies will have a much larger effect when the gene pool is small. Genetic drift and natural selection usually occur simultaneously in populations, but the cause of the frequency change is often impossible to determine.
Natural selection also affects allele frequency. If an allele confers a phenotype that enables an individual to better survive or have more offspring, the frequency of that allele will increase. Because many of those offspring will also carry the beneficial allele and, therefore, the phenotype, they will have more offspring of their own that also carry the allele. Over time, the allele will spread throughout the population and may become fixed: every individual in the population carries the allele. If an allele is dominant but detrimental, it may be swiftly eliminated from the gene pool when the individual with the allele does not reproduce. However, a detrimental recessive allele can linger for generations in a population, hidden by the dominant allele in heterozygotes. In such cases, the only individuals to be eliminated from the population are those unlucky enough to inherit two copies of such an allele.
The Founder Effect
The founder effect occurs when part of a population becomes isolated and establishes a separate gene pool with its own allele frequencies. When a small number of individuals become the basis of a new population, this new population can be very different genetically from the original population if the founders are not representative of the original. Therefore, many different populations, with very different and uniform gene pools, can all originate from the same, larger population. Together, the forces of natural selection, genetic drift, and founder effect can lead to significant changes in the gene pool of a population. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/19%3A_The_Evolution_of_Populations/19.01%3A_Population_Evolution/19.1B%3A_Population_Genetics.txt |
Learning Objectives
• Use the Hardy Weinberg equation to calculate allelic and genotypic frequencies in a population
The Hardy-Weinberg principle states that a population’s allele and genotype frequencies will remain constant in the absence of evolutionary mechanisms. Ultimately, the Hardy-Weinberg principle models a population without evolution under the following conditions:
1. no mutations
2. no immigration/emigration
3. no natural selection
4. no sexual selection
5. a large population
Although no real-world population can satisfy all of these conditions, the principle still offers a useful model for population analysis.
Hardy-Weinberg Equations and Analysis
According to the Hardy-Weinberg principle, the variable p often represents the frequency of a particular allele, usually a dominant one. For example, assume that p represents the frequency of the dominant allele, Y, for yellow pea pods. The variable q represents the frequency of the recessive allele, y, for green pea pods. If p and q are the only two possible alleles for this characteristic, then the sum of the frequencies must add up to 1, or 100 percent. We can also write this as p + q = 1.If the frequency of the Y allele in the population is 0.6, then we know that the frequency of the y allele is 0.4.
From the Hardy-Weinberg principle and the known allele frequencies, we can also infer the frequencies of the genotypes. Since each individual carries two alleles per gene (Y or y), we can predict the frequencies of these genotypes with a chi square. If two alleles are drawn at random from the gene pool, we can determine the probability of each genotype.
In the example, our three genotype possibilities are: pp (YY), producing yellow peas; pq (Yy), also yellow; or qq (yy), producing green peas. The frequency of homozygous pp individuals is p2; the frequency of hereozygous pq individuals is 2pq; and the frequency of homozygous qq individuals is q2. 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.
In our example, the possible genotypes are homozygous dominant (YY), heterozygous (Yy), and homozygous recessive (yy). If we can only observe the phenotypes in the population, then we know only the recessive phenotype (yy). For example, in a garden of 100 pea plants, 86 might have yellow peas and 16 have green peas. We do not know how many are homozygous dominant (Yy) or heterozygous (Yy), but we do know that 16 of them are homozygous recessive (yy).
Therefore, by knowing the recessive phenotype and, thereby, the frequency of that genotype (16 out of 100 individuals or 0.16), we can calculate the number of other genotypes. If q2 represents the frequency of homozygous recessive plants, then q2 = 0.16. Therefore, q = 0.4.Because p + q = 1, then 1 – 0.4 = p, and we know that p = 0.6. The frequency of homozygous dominant plants (p2) is (0.6)2 = 0.36. Out of 100 individuals, there are 36 homozygous dominant (YY) plants. The frequency of heterozygous plants (2pq) is 2(0.6)(0.4) = 0.48. Therefore, 48 out of 100 plants are heterozygous yellow (Yy).
Applications of Hardy-Weinberg
The genetic variation of natural populations is constantly changing from genetic drift, mutation, migration, and natural and sexual selection. The Hardy-Weinberg principle gives scientists a mathematical baseline of a non-evolving population to which they can compare evolving populations. If scientists record allele frequencies over time and then calculate the expected frequencies based on Hardy-Weinberg values, the scientists can hypothesize the mechanisms driving the population’s evolution.
Key Points
• The Hardy-Weinberg principle assumes that in a given population, the population is large and is not experiencing mutation, migration, natural selection, or sexual selection.
• The frequency of alleles in a population can be represented by p + q = 1, with p equal to the frequency of the dominant allele and q equal to the frequency of the recessive allele.
• The frequency of genotypes in a population can be represented by p2+2pq+q2= 1, with p2 equal to the frequency of the homozygous dominant genotype, 2pq equal to the frequency of the heterozygous genotype, and q2 equal to the frequency of the recessive genotype.
• The frequency of alleles can be estimated by calculating the frequency of the recessive genotype, then calculating the square root of that frequency in order to determine the frequency of the recessive allele.
Key Terms
• genotype: the combination of alleles, situated on corresponding chromosomes, that determines a specific trait of an individual, such as “Aa” or “aa”
• phenotype: the appearance of an organism based on a multifactorial combination of genetic traits and environmental factors, especially used in pedigrees
Contributions and Attributions
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44575/latest...ol11448/latest. License: CC BY: Attribution
• Evolution. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Evolution%23Mechanisms. License: CC BY-SA: Attribution-ShareAlike
• gene flow. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/gene%20flow. License: CC BY-SA: Attribution-ShareAlike
• Boundless. Provided by: Boundless Learning. Located at: www.boundless.com//biology/de...ic-hitchhiking. License: CC BY-SA: Attribution-ShareAlike
• fitness. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/fitness. License: CC BY-SA: Attribution-ShareAlike
• mutation. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/mutation. License: CC BY-SA: Attribution-ShareAlike
• Natural Selection. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Natural_selection. License: CC BY-SA: Attribution-ShareAlike
• genetic drift. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/genetic_drift. License: CC BY-SA: Attribution-ShareAlike
• natural selection. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/natural_selection. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Introduction. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44575/latest...e_19_00_01.jpg. License: CC BY: Attribution
• Mutation and selection diagram. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Mu...on_diagram.svg. License: CC BY-SA: Attribution-ShareAlike
• Random sampling genetic drift. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Ra...etic_drift.svg. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44582/latest...ol11448/latest. License: CC BY: Attribution
• allele. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/allele. License: CC BY-SA: Attribution-ShareAlike
• Population Genetics. Provided by: Wikpedia. Located at: en.Wikipedia.org/wiki/Population_genetics. License: CC BY-SA: Attribution-ShareAlike
• founder effect. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/founder_effect. License: CC BY-SA: Attribution-ShareAlike
• gene pool. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/gene_pool. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Introduction. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44575/latest...e_19_00_01.jpg. License: CC BY: Attribution
• Mutation and selection diagram. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Mu...on_diagram.svg. License: CC BY-SA: Attribution-ShareAlike
• Random sampling genetic drift. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Ra...etic_drift.svg. License: CC BY-SA: Attribution-ShareAlike
• ABO Blood type. Provided by: Wikimedia. Located at: en.Wikipedia.org/wiki/ABO_blo...blood_type.svg. License: Public Domain: No Known Copyright
• Founder effect. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Founder_effect.png. License: Public Domain: No Known Copyright
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44582/latest...ol11448/latest. License: CC BY: Attribution
• genotype. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/genotype. License: CC BY-SA: Attribution-ShareAlike
• phenotype. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/phenotype. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Introduction. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44575/latest...e_19_00_01.jpg. License: CC BY: Attribution
• Mutation and selection diagram. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Mu...on_diagram.svg. License: CC BY-SA: Attribution-ShareAlike
• Random sampling genetic drift. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Ra...etic_drift.svg. License: CC BY-SA: Attribution-ShareAlike
• ABO Blood type. Provided by: Wikimedia. Located at: en.Wikipedia.org/wiki/ABO_blo...blood_type.svg. License: Public Domain: No Known Copyright
• Founder effect. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Founder_effect.png. License: Public Domain: No Known Copyright
• OpenStax College, Population Evolution. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44582/latest...e_19_01_01.png. License: CC BY: Attribution
• Hardy-Weinberg. Provided by: Wikimedia. Located at: en.Wikipedia.org/wiki/Hardy-W...y-Weinberg.svg. License: CC BY-SA: Attribution-ShareAlike | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/19%3A_The_Evolution_of_Populations/19.01%3A_Population_Evolution/19.1C%3A_Hardy-Weinberg_Principle_of_Equilibrium.txt |
Genetic variation is a measure of the variation that exists in the genetic makeup of individuals within population.
Learning Objectives
• Assess the ways in which genetic variance affects the evolution of populations
Key Points
• Genetic variation is an important force in evolution as it allows natural selection to increase or decrease frequency of alleles already in the population.
• Genetic variation can be caused by mutation (which can create entirely new alleles in a population), random mating, random fertilization, and recombination between homologous chromosomes during meiosis (which reshuffles alleles within an organism’s offspring).
• Genetic variation is advantageous to a population because it enables some individuals to adapt to the environment while maintaining the survival of the population.
Key Terms
• genetic diversity: the level of biodiversity, refers to the total number of genetic characteristics in the genetic makeup of a species
• crossing over: the exchange of genetic material between homologous chromosomes that results in recombinant chromosomes
• phenotypic variation: variation (due to underlying heritable genetic variation); a fundamental prerequisite for evolution by natural selection
• genetic variation: variation in alleles of genes that occurs both within and among populations
Genetic Variation
Genetic variation is a measure of the genetic differences that exist within a population. The genetic variation of an entire species is often called genetic diversity. Genetic variations are the differences in DNA segments or genes between individuals and each variation of a gene is called an allele.For example, a population with many different alleles at a single chromosome locus has a high amount of genetic variation. Genetic variation is essential for natural selection because natural selection can only increase or decrease frequency of alleles that already exist in the population.
Genetic variation is caused by:
• mutation
• random mating between organisms
• random fertilization
• crossing over (or recombination) between chromatids of homologous chromosomes during meiosis
The last three of these factors reshuffle alleles within a population, giving offspring combinations which differ from their parents and from others.
Evolution and Adaptation to the Environment
Variation allows some individuals within a population to adapt to the changing environment. Because natural selection acts directly only on phenotypes, more genetic variation within a population usually enables more phenotypic variation. Some new alleles increase an organism’s ability to survive and reproduce, which then ensures the survival of the allele in the population. Other new alleles may be immediately detrimental (such as a malformed oxygen-carrying protein) and organisms carrying these new mutations will die out. Neutral alleles are neither selected for nor against and usually remain in the population. Genetic variation is advantageous because it enables some individuals and, therefore, a population, to survive despite a changing environment.
Geographic Variation
Some species display geographic variation as well as variation within a population. Geographic variation, or the distinctions in the genetic makeup of different populations, often occurs when populations are geographically separated by environmental barriers or when they are under selection pressures from a different environment. One example of geographic variation are clines: graded changes in a character down a geographic axis.
Sources of Genetic Variation
Gene duplication, mutation, or other processes can produce new genes and alleles and increase genetic variation. New genetic variation can be created within generations in a population, so a population with rapid reproduction rates will probably have high genetic variation. However, existing genes can be arranged in new ways from chromosomal crossing over and recombination in sexual reproduction. Overall, the main sources of genetic variation are the formation of new alleles, the altering of gene number or position, rapid reproduction, and sexual reproduction. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/19%3A_The_Evolution_of_Populations/19.02%3A_Population_Genetics/19.2A%3A_Genetic_Variation.txt |
Genetic drift is the change in allele frequencies of a population due to random chance events, such as natural disasters.
Learning Objectives
• Distinguish between selection and genetic drift
Key Points
• Genetic drift is the change in the frequency of an allele in a population due to random sampling and the random events that influence the survival and reproduction of those individuals.
• The bottleneck effect occurs when a natural disaster or similar event randomly kills a large portion (i.e. random sample) of the population, leaving survivors that have allele frequencies that were very different from the previous population.
• The founder effect occurs when a portion of the population (i.e. “founders”) separates from the old population to start a new population with different allele frequencies.
• Small populations are more susceptible genetic drift than large populations, whose larger numbers can buffer the population against chance events.
Key Terms
• genetic drift: an overall shift of allele distribution in an isolated population, due to random sampling
• founder effect: a decrease in genetic variation that occurs when an entire population descends from a small number of founders
• random sampling: a subset of individuals (a sample) chosen from a larger set (a population) by chance
Genetic Drift vs. Natural Selection
Genetic drift is the converse of natural selection. The theory of natural selection maintains that some individuals in a population have traits that enable to survive and produce more offspring, while other individuals have traits that are detrimental and may cause them to die before reproducing. Over successive generation, these selection pressures can change the gene pool and the traits within the population. For example, a big, powerful male gorilla will mate with more females than a small, weak male and therefore more of his genes will be passed on to the next generation. His offspring may continue to dominate the troop and pass on their genes as well. Over time, the selection pressure will cause the allele frequencies in the gorilla population to shift toward large, strong males.
Unlike natural selection, genetic drift describes the effect of chance on populations in the absence of positive or negative selection pressure. Through random sampling, or the survival or and reproduction of a random sample of individuals within a population, allele frequencies within a population may change. Rather than a male gorilla producing more offspring because he is stronger, he may be the only male available when a female is ready to mate. His genes are passed on to future generation because of chance, not because he was the biggest or the strongest. Genetic drift is the shift of alleles within a population due to chance events that cause random samples of the population to reproduce or not.
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 leaving 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 individual represents only 1 percent of the overall gene pool; therefore, genetic drift has much less impact on the larger population’s genetic structure.
The Bottleneck Effect
Genetic drift can also be magnified by natural events, such as a natural disaster that kills a large portion of the population at random. The bottleneck effect occurs when only a few individuals survive and reduces variation in the gene pool of a population. The genetic structure of the survivors becomes the genetic structure of the entire population, which may be very different from the pre-disaster population.
The Founder Effect
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, it is improbable that those individuals are 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 was probably 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.
Drift and fixation
The Hardy–Weinberg principle states that within sufficiently large populations, the allele frequencies remain constant from one generation to the next unless the equilibrium is disturbed by migration, genetic mutation, or selection.
Because the random sampling can remove, but not replace, an allele, and because random declines or increases in allele frequency influence expected allele distributions for the next generation, genetic drift drives a population towards genetic uniformity over time. When an allele reaches a frequency of 1 (100%) it is said to be “fixed” in the population and when an allele reaches a frequency of 0 (0%) it is lost. Once an allele becomes fixed, genetic drift for that allele comes to a halt, and the allele frequency cannot change unless a new allele is introduced in the population via mutation or gene flow. Thus even while genetic drift is a random, directionless process, it acts to eliminate genetic variation over time. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/19%3A_The_Evolution_of_Populations/19.02%3A_Population_Genetics/19.2B%3A_Genetic_Drift.txt |
A population’s genetic variation changes as individuals migrate into or out of a population and when mutations introduce new alleles.
Learning Objectives
• Explain how gene flow and mutations can influence the allele frequencies of a population
Key Points
• Plant populations experience gene flow by spreading their pollen long distances.
• Animals experience gene flow when individuals leave a family group or herd to join other populations.
• The flow of individuals in and out of a population introduces new alleles and increases genetic variation within that population.
• Mutations are changes to an organism’s DNA that create diversity within a population by introducing new alleles.
• Some mutations are harmful and are quickly eliminated from the population by natural selection; harmful mutations prevent organisms from reaching sexual maturity and reproducing.
• Other mutations are beneficial and can increase in a population if they help organisms reach sexual maturity and reproduce.
Key Terms
• gene flow: the transfer of alleles or genes from one population to another
• mutation: any heritable change of the base-pair sequence of genetic material
Gene Flow
An important evolutionary force is gene flow: the flow of alleles in and out of a population due to the migration of individuals or gametes. While some populations are fairly stable, others experience more movement and fluctuation. Many plants, for example, send their pollen by wind, insects, or birds 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 receive new genetic variation as developing males leave their mothers to form new prides 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 can also introduce new genetic variation to populations in different geological locations and habitats.
Maintained gene flow between two populations can also lead to a combination of the two gene pools, reducing the genetic variation between the two groups. Gene flow strongly acts against speciation, by recombining the gene pools of the groups, and thus, repairing the developing differences in genetic variation that would have led to full speciation and creation of daughter species.
For example, if a species of grass grows on both sides of a highway, pollen is likely to be transported from one side to the other and vice versa. If this pollen is able to fertilize the plant where it ends up and produce viable offspring, then the alleles in the pollen have effectively linked the population on one side of the highway with the other.
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 have no effect on an organism and can linger, unaffected by natural selection, in the genome while others can have a dramatic effect on a gene and the resulting phenotype. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/19%3A_The_Evolution_of_Populations/19.02%3A_Population_Genetics/19.2C%3A_Gene_Flow_and_Mutation.txt |
Population structure can be altered by nonrandom mating (the preference of certain individuals for mates) as well as the environment.
Learning Objectives
• Explain how environmental variance and nonrandom mating can change gene frequencies in a population
Key Points
• Nonrandom mating can occur when individuals prefer mates with particular superior physical characteristics or by the preference of individuals to mate with individuals similar to themselves.
• Nonrandom mating can also occur when mates are chosen based on physical accessibility; that is, the availability of some mates over others.
• Phenotypes of individuals can also be influenced by the environment in which they live, such as temperature, terrain, or other factors.
• A cline occurs when populations of a given species vary gradually across an ecological gradient.
Key Terms
• cline: a gradation in a character or phenotype within a species or other group
• sexual selection: a mode of natural selection in which some individuals out-reproduce others of a population because they are better at securing mates
• assortative mating: between males and females of a species, the mutual attraction or selection, for reproductive purposes, of individuals with similar characteristics
Nonrandom Mating
If individuals nonrandomly mate with other individuals in the population, i.e. they choose their mate, choices can drive evolution within a population. There are many reasons nonrandom mating occurs. One reason is simple mate choice or sexual selection; for example, female peahens may prefer peacocks with bigger, brighter tails. Traits that lead to more matings for an individual lead to more offspring and through natural selection, eventually lead to a higher frequency of that trait in the population. One common form of mate choice, called positive assortative mating, is an individual’s preference to mate with partners that 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. 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.
Geographic variation in moose: This graph shows geographical variation in moose; body mass increase positively with latitude. Bergmann’s Rule is an ecologic principle which states that as latitude increases the body mass of a particular species increases. The data are taken from a Swedish study investigating the size of moose as latitude increases as shows the positive relationship between the two, supporting Bergmann’s Rule.
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.
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• mutation. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/mutation. License: CC BY-SA: Attribution-ShareAlike
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• American Robin Close-Up. Provided by: Wikimedia. Located at: en.Wikipedia.org/wiki/America...n_Close-Up.JPG. License: CC BY-SA: Attribution-ShareAlike | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/19%3A_The_Evolution_of_Populations/19.02%3A_Population_Genetics/19.2D%3A_Nonrandom_Mating_and_Environmental_Variance.txt |
Natural selection drives adaptive evolution by selecting for and increasing the occurrence of beneficial traits in a population.
Learning Objectives
• Explain how natural selection leads to adaptive evolution
Key Points
• Natural selection increases or decreases biological traits within a population, thereby selecting for individuals with greater evolutionary fitness.
• An individual with a high evolutionary fitness will provide more beneficial contributions to the gene pool of the next generation.
• Relative fitness, which compares an organism’s fitness to the others in the population, allows researchers to establish how a population may evolve by determining which individuals are contributing additional offspring to the next generation.
• Stabilizing selection, directional selection, diversifying selection, frequency -dependent selection, and sexual selection all contribute to the way natural selection can affect variation within a population.
Key Terms
• natural selection: a process in which individual organisms or phenotypes that possess favorable traits are more likely to survive and reproduce
• fecundity: number, rate, or capacity of offspring production
• Darwinian fitness: the average contribution to the gene pool of the next generation that is made by an average individual of the specified genotype or phenotype
An Introduction to Adaptive Evolution
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. This process is 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 fitness (or 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
• 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. In the end, natural selection cannot produce perfect organisms from scratch, it can only generate populations that are better adapted to survive and successfully reproduce in their environments through the aforementioned selections.
Galápagos with David Attenborough: Two hundred years after Charles Darwin set foot on the shores of the Galápagos Islands, David Attenborough travels to this wild and mysterious archipelago. Amongst the flora and fauna of these enchanted volcanic islands, Darwin formulated his groundbreaking theories on evolution. Journey with Attenborough to explore how life on the islands has continued to evolve in biological isolation, and how the ever-changing volcanic landscape has given birth to species and sub-species that exist nowhere else in the world. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/19%3A_The_Evolution_of_Populations/19.03%3A_Adaptive_Evolution/19.3A%3A_Natural_Selection_and_Adaptive_Evolution.txt |
Stabilizing, directional, and diversifying selection either decrease, shift, or increase the genetic variance of a population.
Learning Objectives
• Contrast stabilizing selection, directional selection, and diversifying selection.
Key Points
• Stabilizing selection results in a decrease of a population ‘s genetic variance when natural selection favors an average phenotype and selects against extreme variations.
• In directional selection, a population’s genetic variance shifts toward a new phenotype when exposed to environmental changes.
• Diversifying or disruptive selection increases genetic variance when natural selection selects for two or more extreme phenotypes that each have specific advantages.
• In diversifying or disruptive selection, average or intermediate phenotypes are often less fit than either extreme phenotype and are unlikely to feature prominently in a population.
Key Terms
• directional selection: a mode of natural selection in which a single phenotype is favored, causing the allele frequency to continuously shift in one direction
• disruptive selection: (or diversifying selection) a mode of natural selection in which extreme values for a trait are favored over intermediate values
• stabilizing selection: a type of natural selection in which genetic diversity decreases as the population stabilizes on a particular trait value
Stabilizing Selection
If natural selection favors an average phenotype by selecting against extreme variation, the population will undergo stabilizing selection. For example, in a population of mice that live in the woods, natural selection will tend 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 most probably survive and reproduce, passing on their genes for their brown coat. Mice that carry alleles that make them slightly lighter or slightly darker will stand out against the ground and will more probably die from predation. As a result of this stabilizing selection, the population’s genetic variance will decrease.
Stabilizing selection: Stabilizing selection occurs when the population stabilizes on a particular trait value and genetic diversity decreases.
Directional Selection
When the environment changes, populations will often undergo directional selection, 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. As soot began spewing from factories, the trees darkened and the light-colored moths became easier for predatory birds to spot.
Directional selection: Directional selection occurs when a single phenotype is favored, causing the allele frequency to continuously shift in one direction.
Over time, the frequency of the melanic form of the moth increased because their darker coloration provided camouflage against the sooty tree; they had a higher survival rate in habitats affected by air pollution. Similarly, the hypothetical mouse population may evolve to take on a different coloration if their forest floor habitat changed. The result of this type of selection is a shift in the population’s genetic variance toward the new, fit phenotype.
Diversifying (or Disruptive) Selection
Sometimes natural selection can select for two or more distinct phenotypes that each have their advantages. In these cases, the intermediate phenotypes are often less fit than their extreme counterparts. Known as diversifying or disruptive selection, this is seen in many populations of animals that have multiple male mating strategies, such as lobsters. 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 cannot overtake the alpha males and are too big to sneak copulations, are selected against.
Diversifying (or disruptive) selection: Diversifying selection occurs when extreme values for a trait are favored over the intermediate values.This type of selection often drives speciation.
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, thus, would more probably be eaten by predators. The result of this type of selection is increased genetic variance as the population becomes more diverse. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/19%3A_The_Evolution_of_Populations/19.03%3A_Adaptive_Evolution/19.3B%3A_Stabilizing_Directional_and_Diversifying_Selection.txt |
In frequency-dependent selection, phenotypes that are either common or rare are favored through natural selection.
Learning Objectives
• Describe frequency-dependent selection
Key Points
• Negative frequency -dependent selection selects for rare phenotypes in a population and increases a population’s genetic variance.
• Positive frequency-dependent selection selects for common phenotypes in a population and decreases genetic variance.
• In the example of male side-blotched lizards, populations of each color pattern increase or decrease at various stages depending on their frequency; this ensures that both common and rare phenotypes continue to be cyclically present.
• Infectious agents such as microbes can exhibit negative frequency-dependent selection; as a host population becomes immune to a common strain of the microbe, less common strains of the microbe are automatically favored.
• Variation in color pattern mimicry by the scarlet kingsnake is dependent on the prevalence of the eastern coral snake, the model for this mimicry, in a particular geographical region. The more prevalent the coral snake is in a region, the more common and variable the scarlet kingsnake’s color pattern will be, making this an example of positive frequency-dependent selection.
Key Terms
• frequency-dependent selection: the term given to an evolutionary process where the fitness of a phenotype is dependent on its frequency relative to other phenotypes in a given population
• polygynous: having more than one female as mate
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).
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 are the smallest and look a bit like female, allowing 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. 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.
An example of negative frequency-dependent selection can also be seen in the interaction between the human immune system and various infectious microbes such as pathogenic bacteria or viruses. As a particular human population is infected by a common strain of microbe, the majority of individuals in the population become immune to it. This then selects for rarer strains of the microbe which can still infect the population because of genome mutations; these strains have greater evolutionary fitness because they are less common.
Positive Frequency-dependent Selection
An example of positive frequency-dependent selection is the mimicry of the warning coloration of dangerous species of animals by other species that are harmless. The scarlet kingsnake, a harmless species, mimics the coloration of the eastern coral snake, a venomous species typically found in the same geographical region. Predators learn to avoid both species of snake due to the similar coloration, and as a result the scarlet kingsnake becomes more common, and its coloration phenotype becomes more variable due to relaxed selection. This phenotype is therefore more “fit” as the population of species that possess it (both dangerous and harmless) becomes more numerous. In geographic areas where the coral snake is less common, the pattern becomes less advantageous to the kingsnake, and much less variable in its expression, presumably because predators in these regions are not “educated” to avoid the pattern.
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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/19%3A_The_Evolution_of_Populations/19.03%3A_Adaptive_Evolution/19.3C%3A_Frequency-Dependent_Selection.txt |
Sexual selection, the selection pressure on males and females to obtain matings, can result in traits designed to maximize sexual success.
Learning Objectives
• Discuss the effects of sexual dimorphism on the reproductive potential of an organism
Key Points
• Sexual selection often results in the development of secondary sexual characteristics, which help to maximize a species ‘ reproductive success, but do not provide any survival benefits.
• The handicap principle states that only the best males survive the risks from traits that may actually be detrimental to a species; therefore, they are more fit as mating partners.
• In the good genes hypothesis, females will choose males that show off impressive traits to ensure they pass on genetic superiority to their offspring.
• Sexual dimorphisms, obvious morphological differences between the sexes of a species, arise when there is more variance in the reproductive success of either males or females.
Key Terms
• sexual dimorphism: a physical difference between male and female individuals of the same species
• sexual selection: a type of natural selection, where members of the sexes acquire distinct forms because members choose mates with particular features or because competition for mates with certain traits succeed
• handicap principle: a theory that suggests that animals of greater biological fitness signal this status through a behavior or morphology that effectively lowers their chances of survival
Sexual Selection
The selection pressures on males and females to obtain matings is known as sexual selection. Sexual selection takes two major forms: intersexual selection (also known as ‘mate choice’ or ‘female choice’) in which males compete with each other to be chosen by females; and intrasexual selection (also known as ‘male–male competition’) in which members of the less limited sex (typically males) compete aggressively among themselves for access to the limiting sex. The limiting sex is the sex which has the higher parental investment, which therefore faces the most pressure to make a good mate decision.
Sexual Dimorphism
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, such as the peacock’s tail, while females tend to be smaller and duller in decoration. These differences are called sexual dimorphisms and arise from the variation in male reproductive success.
Females almost always mate, while mating is not guaranteed for males. The bigger, stronger, or more decorated males usually obtain the vast majority of the total matings, while other males 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 obtain those matings, resulting in the evolution of bigger body size and elaborate ornaments in order to increase their chances of mating. 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; some species are even sex-role reversed. In such cases, females tend to have a greater variation in their reproductive success than males and are, correspondingly, selected for the bigger body size and elaborate traits usually characteristic of males.
The Handicap Principle
Sexual selection can be so strong that it selects for traits that are actually detrimental to the individual’s survival, even though they maximize its reproductive success. For example, while the male peacock’s tail is beautiful and the male with the largest, most colorful tail will more probably win the female, it is not a 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. Because large tails carry risk, only the best males survive that risk and therefore the bigger the tail, the more fit the male. This idea is known as the handicap principle.
The Good Genes Hypothesis
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 so selective 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.
BBC Planet Earth – Birds of Paradise mating dance: Extraordinary Courtship displays from these weird and wonderful creatures. From episode 1 “Pole to Pole”. This is an example of the extreme behaviors that arise from intense sexual selection pressure. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/19%3A_The_Evolution_of_Populations/19.03%3A_Adaptive_Evolution/19.3D%3A_Sexual_Selection.txt |
Natural selection cannot create novel, perfect species because it only selects on existing variations in a population.
Learning Objectives
• Explain the limitations encountered in natural selection
Key Points
• Natural selection is limited by a population ‘s existing genetic variation.
• Natural selection is limited through linkage disequilibrium, where alleles that are physically proximate on the chromosome are passed on together at greater frequencies.
• In a polymorphic population, two phenotypes may be maintained in the population despite the higher fitness of one morph if the intermediate phenotype is detrimental.
• Evolution is not purposefully adaptive; it is the result of various selection forces working together to influence genetic and phenotypical variances within a population.
Key Terms
• linkage disequilibrium: a non-random association of two or more alleles at two or more loci; normally caused by an interaction between genes
• genetic hitchhiking: changes in the frequency of an allele because of linkage with a positively or negatively selected allele at another locus
• polymorphism: the regular existence of two or more different genotypes within a given species or population
No Perfect Organism
Natural selection is a driving force in evolution and can generate populations that are adapted to survive and successfully reproduce in their environments. However, natural selection cannot produce the perfect organism. Natural selection can only select on existing variation in the population; it cannot create anything from scratch. Therefore, the process of evolution is limited by a population’s existing genetic variance, the physical proximity of alleles, non-beneficial intermediate morphs in a polymorphic population, and non-adaptive evolutionary forces.
Natural Selection Acts on Individuals, not Alleles
Natural selection is also limited because it acts on the phenotypes of individuals, not alleles. Some alleles may be more likely to be passed on with alleles that confer a beneficial phenotype because of their physical proximity on the chromosomes. Alleles that are carried together are in linkage disequilibrium. When a neutral allele is linked to beneficial allele, consequently meaning that it has a selective advantage, the allele frequency can increase in the population through genetic hitchhiking (also called genetic draft).
Any given individual may carry some beneficial alleles and some unfavorable alleles. Natural selection acts on the net effect of these alleles and corresponding fitness of the phenotype. As a result, good alleles can be lost if they are carried by individuals that also have several overwhelmingly bad alleles; similarly, bad alleles can be kept if they are carried by individuals that have enough good alleles to result in an overall fitness benefit.
Polymorphism
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 because the intermediate morph is detrimental.
Polymorphism in the grove snail: Color and pattern morphs of the grove snail, Cepaea nemoralis.The polymorphism, when two or more different genotypes exist within a given species, in grove snails seems to have several causes, including predation by thrushes.
For example, consider a hypothetical population of mice that live in the desert. Some are light-colored and blend in with the sand, while others are dark and blend in with the patches of black rock. The dark-colored mice may be more fit than the light-colored mice, and according to the principles of natural selection the frequency of light-colored mice is expected to decrease over time. However, the intermediate phenotype of a medium-colored coat is very bad for the mice: these cannot blend in with either the sand or the rock and will more vulnerable to predators. As a result, the frequency of a dark-colored mice would not increase because the intermediate morphs are less fit than either light-colored or dark-colored mice. This a common example of disruptive selection.
Not all Evolution is Adaptive
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 by 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 various forces and their influence on the genetic and phenotypic variance of a population.
Contributions and Attributions
• natural selection. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/natural_selection. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44586/latest...ol11448/latest. License: CC BY: Attribution
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• Frequency-dependent selection. Provided by: WIKIPEDIA. Located at: en.Wikipedia.org/wiki/Frequen...dent_selection. License: CC BY-SA: Attribution-ShareAlike
• frequency-dependent selection. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/frequen...nt%20selection. License: CC BY-SA: Attribution-ShareAlike
• Evolution sm. Provided by: Wikimedia. Located at: en.Wikipedia.org/wiki/Adaptiv...olution_sm.png. License: Public Domain: No Known Copyright
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• Peppered moth evolution. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Peppered_moth_evolution. License: Public Domain: No Known Copyright
• OpenStax College, Biology. November 9, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44586/latest...ol11448/latest. License: CC BY: Attribution
• Coral snake. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Coral_009.jpg. License: CC BY-SA: Attribution-ShareAlike
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• sexual selection. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/sexual_selection. License: CC BY-SA: Attribution-ShareAlike
• Evolution sm. Provided by: Wikimedia. Located at: en.Wikipedia.org/wiki/Adaptiv...olution_sm.png. License: Public Domain: No Known Copyright
• Galu00e1pagos with David Attenborough. Located at: http://www.youtube.com/watch?v=czpPbDGHOZA. License: Public Domain: No Known Copyright. License Terms: Standard YouTube license
• Peppered moth evolution. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Peppered_moth_evolution. License: Public Domain: No Known Copyright
• OpenStax College, Biology. November 9, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44586/latest...ol11448/latest. License: CC BY: Attribution
• Coral snake. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Coral_009.jpg. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Adaptive Evolution. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44586/latest...e_19_03_02.jpg. License: CC BY: Attribution
• Lampropeltis elapsoides. Provided by: WikiPedia. Located at: en.Wikipedia.org/wiki/File:G-Bartolotti_SK.jpg. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Adaptive Evolution. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44586/latest...9_03_03abc.jpg. License: CC BY: Attribution
• Bull elk bugling during the fall mating season. Provided by: Wikimedia. Located at: en.Wikipedia.org/wiki/File:Bu...ing_season.jpg. License: Public Domain: No Known Copyright
• Ribbon-tailed Astrapia. Provided by: Wikimedia. Located at: en.Wikipedia.org/wiki/Bird-of...d_Astrapia.jpg. License: CC BY-SA: Attribution-ShareAlike
• BBC Planet Earth - Birds of Paradise mating dance. Located at: http://www.youtube.com/watch?v=W7QZnwKqopo. License: Public Domain: No Known Copyright. License Terms: Standard YouTube license
• linkage disequilibrium. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/linkage_disequilibrium. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44586/latest...ol11448/latest. License: CC BY: Attribution
• polymorphism. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/polymorphism. License: CC BY-SA: Attribution-ShareAlike
• Genetic Hitchhiking. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Genetic_draft. License: CC BY-SA: Attribution-ShareAlike
• Evolution sm. Provided by: Wikimedia. Located at: en.Wikipedia.org/wiki/Adaptiv...olution_sm.png. License: Public Domain: No Known Copyright
• Galu00e1pagos with David Attenborough. Located at: http://www.youtube.com/watch?v=czpPbDGHOZA. License: Public Domain: No Known Copyright. License Terms: Standard YouTube license
• Peppered moth evolution. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Peppered_moth_evolution. License: Public Domain: No Known Copyright
• OpenStax College, Biology. November 9, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44586/latest...ol11448/latest. License: CC BY: Attribution
• Coral snake. Provided by: Wikipedia. Located at: http://en.Wikipedia.org/wiki/File:Coral_009.jpg. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Adaptive Evolution. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44586/latest...e_19_03_02.jpg. License: CC BY: Attribution
• Lampropeltis elapsoides. Provided by: WikiPedia. Located at: en.Wikipedia.org/wiki/File:G-Bartolotti_SK.jpg. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Adaptive Evolution. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44586/latest...9_03_03abc.jpg. License: CC BY: Attribution
• Bull elk bugling during the fall mating season. Provided by: Wikimedia. Located at: en.Wikipedia.org/wiki/File:Bu...ing_season.jpg. License: Public Domain: No Known Copyright
• Ribbon-tailed Astrapia. Provided by: Wikimedia. Located at: en.Wikipedia.org/wiki/Bird-of...d_Astrapia.jpg. License: CC BY-SA: Attribution-ShareAlike
• BBC Planet Earth - Birds of Paradise mating dance. Located at: http://www.youtube.com/watch?v=W7QZnwKqopo. License: Public Domain: No Known Copyright. License Terms: Standard YouTube license
• Polymorphism in Cepaea nemoralis. Provided by: Wikimedia. Located at: commons.wikimedia.org/wiki/Fi..._nemoralis.jpg. License: CC BY-SA: Attribution-ShareAlike | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/19%3A_The_Evolution_of_Populations/19.03%3A_Adaptive_Evolution/19.3E%3A_No_Perfect_Organism.txt |
Learning Objectives
• Describe the various types of phylogenetic trees and how they organize life
Scientists use a tool called a phylogenetic tree, a type of diagram, to show the evolutionary pathways and connections among 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”, as it is sometimes called, can be constructed to illustrate when different organisms evolved and to show the relationships among different organisms.
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. 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.
Rooted phylogenetic trees 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; together, these disciplines 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.
Key Points
• Rooted trees have a single lineage at the base representing a common ancestor that connects all organisms presented in a phylogenetic diagram.
• Branch points in a phylogenetic tree represent a split where a single lineage evolved into a distinct new one, while basal taxon depict unbranched lineages that evolved early from the root.
• Unrooted trees portray relationships among species, but do not depict their common ancestor.
• Phylogenetic trees are hypotheses and are, therefore, modified as data becomes available.
• Systematics uses data from fossils, the study of bodily structures, molecules used by a species, and DNA analysis to contribute to the building, updating, and maintaining of phylogenetic trees.
Key Terms
• polytomy: a section of a phylogeny in which the evolutionary relationships cannot be fully resolved to dichotomies
• basal taxon: a lineage, displayed using a phylogenetic tree, that evolved early from the root and from which no other branches have diverged
• systematics: research into the relationships of organisms; the science of systematic classification
• phylogeny: the visual representation of the evolutionary history of organisms; based on rigorous analyses | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/20%3A_Phylogenies_and_the_History_of_Life/20.01%3A_Organizing_Life_on_Earth/20.1A%3A_Phylogenetic_Trees.txt |
Learning Objectives
• Identify the limitations of phylogenetic trees as representations of the organization of life
It may be easy to assume that more closely-related organisms look more alike; 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 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. A tree may 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. For example, the tree in the diagram shows that the oldest trait is the vertebral column, followed by hinged jaws, and so forth. Remember, any phylogenetic tree is a part of the greater whole and, as with a real tree, it does not grow in only one direction after a new branch develops. So, simply 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.
Key Points
• Closely-related species may not always look more alike, while groups that are not closely related yet evolved under similar conditions, may appear more similar to each other.
• In phylogenetic trees, branches do not usually account for length of time and only depict evolutionary order.
• Phylogenetic trees are like real trees in that they do not simply grow in only one direction after a new branch forms; the evolution of one organism does not necessarily signify the evolutionary end of another.
Key Terms
• phenotypical: of or pertaining to a phenotype: the appearance of an organism based on a multifactorial combination of genetic traits and environmental factors
20.1C: The Levels of Classification
Learning Objectives
• Describe how taxonomic classification of organisms is accomplished and detail the levels of taxonomic classification from domain to species
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 domains: 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.
The kingdom Animalia stems from the Eukarya domain. The full name of an organism technically has eight terms. For dogs, it is: Eukarya, Animalia, Chordata, Mammalia, Carnivora, Canidae, Canis, and lupus. Notice that each name is capitalized except for species and that 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.
Dogs actually share a domain (Eukarya) 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 physical characteristics, but as DNA technology developed, more precise phylogenies have been determined.
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 to the whale.
Key Points
• Categories within taxonomic classification are arranged in increasing specificity.
• The most general category in taxonomic classification is domain, which is the point of origin for all species; all species belong to one of these domains: Bacteria, Archaea, and Eukarya.
• Within each of the three domains, we find kingdoms, the second category within taxonomic classification, followed by subsequent categories that include phylum, class, order, family, genus, and species.
• At each classification category, organisms become more similar because they are more closely related.
• As scientific technology advances, changes to the taxonomic classification of many species must be altered as inaccuracies in classifications are discovered and corrected.
Key Terms
• binomial nomenclature: the scientific system of naming each species of organism with a Latinized name in two parts
• taxon: any of the taxonomic categories such as phylum or subspecies
• Linnaeus: Swedish botanist, physician and zoologist who laid the foundations for the modern scheme of nomenclature; known as the “father of modern taxonomy” | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/20%3A_Phylogenies_and_the_History_of_Life/20.01%3A_Organizing_Life_on_Earth/20.1B%3A_Limitations_of_Phylogenetic_Trees.txt |
Learning Objectives
• Explain the difference between homologous and analogous structures
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.
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 probable that any 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 similar. This usually happens because both organisms developed 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.
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. Ultimately, the coupled use of both morphologic and molecular information is more effective in determining phylogeny.
Key Points
• Organisms may be very closely related, even though they look quite different, due to a minor genetic change that caused a major morphological difference.
• Unrelated organisms may appear very similar because both organisms developed common adaptations that evolved within similar environmental conditions.
• To determine the phylogeny of an organism, scientists must determine whether a similarity is homologous or analogous.
• The advancement of DNA technology, the area of molecular systematics, describes the use of information on the molecular level, including DNA analysis.
Key Terms
• analogous: when similar similar physical features occur in organisms because of environmental constraints and not due to a close evolutionary relationship
• homologous: when similar physical features and genomes stem from developmental similarities that are based on evolution
• phylogeny: the evolutionary history of an organism
• molecular systematics: molecular phylogenetics is the analysis of hereditary molecular differences, mainly in DNA sequences, to gain information on an organism’s evolutionary relationships | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/20%3A_Phylogenies_and_the_History_of_Life/20.02%3A_Determining_Evolutionary_Relationships/20.2A%3A__Distinguishing_between_Similar_Traits.txt |
Learning Objectives
• Describe the cladistics as a method used to create 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, 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.
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. Notice in the various examples of clades how each clade comes from a single point, whereas the non-clade groups show branches that do not share a single point.
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 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. Now, consider the amniotic egg characteristic in the same figure. Only some of the organisms have this trait; 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. 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.
Key Points
• Phylogenetic trees sort organisms into clades: groups of organisms that descended from a single ancestor.
• Organisms of a single clade are called a monophyletic group.
• Scientists use the phrase “descent with modification” because genetic changes occur even though related organisms have many of the same characteristics and genetic codes.
• A characteristic is considered a shared-ancestral character if it is found in the ancestor of a group and all of the organisms in the taxon or clade have that trait.
• If only some of the organisms have a certain trait, it is called a shared- derived character because this trait derived at some point, but does not include all of the ancestors in the clade.
• Scientists often use a concept called maximum parsimony, which means that events occurred in the simplest, most obvious way, to aid in the tremendous task of describing phylogenies accurately.
Key Terms
• monophyletic: of, pertaining to, or affecting a single phylum (or other taxon) of organisms
• derived: of, or pertaining to, conditions unique to the descendant species of a clade, and not found in earlier ancestral species
• clades: groups of organisms that descended from a single ancestor
• ancestral: of, pertaining to, derived from, or possessed by, an ancestor or ancestors; as, an ancestral estate
• maximum parsimony: the preferred phylogenetic tree is the tree that requires the least evolutionary change to explain some observed data | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/20%3A_Phylogenies_and_the_History_of_Life/20.02%3A_Determining_Evolutionary_Relationships/20.2B%3A_Building_Phylogenetic_Trees.txt |
Learning Objectives
• Identify the limitations to the classic model of phylogenetic trees
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, 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. 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.
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 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. 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.
Key Points
• Charles Darwin sketched the first phylogenetic tree in 1837.
• A single trunk on a phylogenetic tree represents a common ancestor and the branches represent the divergence of species from this ancestor.
• Prokaryotes are assumed to evolve clonally in the classic tree model.
• Horizontal gene transfer is the transfer of genes between unrelated species and, as such, complicates the simple tree model.
• Ultimate gene transfer has provided theories of genome fusion between symbiotic or endosymbiotic organisms.
Key Terms
• phylogenetic: of, or relating to the evolutionary development of organisms
• clonal: pertaining to asexual reproduction
• horizontal gene transfer: the transfer of genetic material from one organism to another one that is not its offspring; especially common among bacteria
20.3B: Horizontal Gene Transfer
Learning Objectives
• Explain how horizontal gene transfer can make resolution of phylogenies difficult
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 (using standard phylogeny) 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 these 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 evolutionists postulate a major role for this process in evolution, thus complicating the simple tree model. A number of 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, thus adding a layer of complexity to the understanding or resolution of phylogenetic relationships.
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. These gene transfers between species are the major mechanism whereby bacteria acquire resistance to antibiotics. Classically, this type of transfer was thought to occur by three different mechanisms:
• Transformation: naked DNA is taken up by a bacteria.
• Transduction: genes are transferred using a virus.
• Conjugation: the use 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.
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 only 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. 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. Aphids are insects that vary in color based on carotenoid content. Carotenoids are pigments made by a variety of plants, fungi, and microbes, which 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. Furthermore, it has been shown that when this gene is inactivated by mutation, the aphids revert back to their more common green color.
Key Points
• It is thought that HGT is more prevalent in prokaryotes than eukaryotes, but that only about 2% of the prokaryotic genome may be transferred by this process.
• 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.
• HGT in prokaryotes occurs by four different mechanisms: transformation, transduction, conjugation, and via gene transfer agents.
• HGT occurs in plants through transposons (jumping genes), which transfer between different species of plants.
• An example of HGT in animals is the transfer (through consumption) of fungal genes into insects called aphids, which allows the aphids the ability to make carotenoids on their own.
Key Terms
• transformation: the alteration of a bacterial cell caused by the transfer of DNA from another, especially if pathogenic
• transduction: horizontal gene transfer mechanism in prokaryotes where genes are transferred using a virus
• conjugation: the temporary fusion of organisms, especially as part of sexual reproduction | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/20%3A_Phylogenies_and_the_History_of_Life/20.03%3A_Perspectives_on_the_Phylogenetic_Tree/20.3A%3A_Limitations_to_the_Classic_Model_of_Phylogenetic_Trees.txt |
Learning Objectives
• Describe the genome fusion hypothesis and its relationship to the evolution of eukaryotes
Genome Fusion and the Evolution of Eukaryotes
Scientists believe the ultimate event in HGT (horizontal gene transfer) occurs through genome fusion between different species 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 to be responsible for the evolution of the first eukaryotic cells. Using DNA analysis and a new mathematical algorithm called conditioned reconstruction (CR), it has been 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 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 proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, did result from an endosymbiotic fusion of archaeal and bacterial species. The double membrane would be a direct result of 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. A lot of skepticism still surrounds this hypothesis; the ideas are still debated within the biological science community.
There are several other competing hypotheses as to the origin of eukaryotes and the nucleus. One idea about how the eukaryotic nucleus evolved is that prokaryotic cells produced an additional membrane which 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. Another hypothesis, the nucleus-first hypothesis, proposes the nucleus evolved in prokaryotes first, followed by a later fusion of the new eukaryote with bacteria that became mitochondria. The mitochondria-first hypothesis, however, proposes mitochondria were first established in a prokaryotic host, which subsequently acquired a nucleus (by fusion or other mechanisms) to become the first eukaryotic cell. Most interestingly, the eukaryote-first hypothesis proposes prokaryotes actually evolved from eukaryotes by losing genes and complexity. All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis is best supported by data.
Key Points
• Two symbiotic organisms become endosymbiotic when one species is taken inside the cytoplasm of another species, resulting in genome fusion.
• Genome fusion, by endosymbiosis, between two species, one an Archaea and the other a Bacteria, has been proposed as responsible for the evolution of the first eukaryotic cells.
• Gram-negative bacteria are proposed to result from an endosymbiotic fusion of archaeal and bacterial species through a mechanism that has also been used to explain the double membranes found in mitochondria and chloroplasts.
• The nucleus-first hypothesis proposes the nucleus evolved in prokaryotes first, followed by a later fusion of the new eukaryote with bacteria that became mitochondria.
• The mitochondria-first hypothesis proposes mitochondria were first established in a prokaryotic host, which subsequently acquired a nucleus to become the first eukaryotic cell.
• The eukaryote-first hypothesis proposes prokaryotes actually evolved from eukaryotes by losing genes and complexity.
Key Terms
• genome fusion: a result of endosymbiosis when a genome consists of genes from both the endosymbiont and the host.
• symbiotic: of a relationship with mutual benefit between two individuals or organisms
• endosymbiosis: when one symbiotic species is taken inside the cytoplasm of another symbiotic species and both become endosymbiotic
20.3D: Web Network and Ring of Life Models
Learning Objectives
• Describe the web, network, and ring of life models of phylogenetic trees
The recognition of the importance of Horizontal gene transfer (HGT), especially in the evolution of prokaryotes, has caused some to propose abandoning the classic “tree of life” model. In 1999, a phylogenetic model that resembles a web or a network more than a tree was proposed. 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. Some individual prokaryotes were responsible for transferring the bacteria that caused mitochondrial development in 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 with its multiple trunks as a phylogenetic tree to represent the evolutionary role for HGT.
Others have proposed abandoning any tree-like model of phylogeny in favor of a ring structure. The ” ring of life ” is a phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes. Using the conditioned reconstruction algorithm, it 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. This structure is proposed as the best fit for data from extensive DNA analyses; the ring model is the only one that adequately takes HGT and genomic fusion into account. However, phylogeneticists remain highly skeptical of this model.
In summary, the “tree of life” model proposed by Darwin must be modified to include HGT. This does not 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 that time.
Key Points
• A phylogenetic model that resembles a web or a network was proposed since eukaryotes evolved not from a single prokaryotic ancestor, but from a pool of many species that were sharing genes by HGT mechanisms.
• A phylogenetic model that resembles a ring was proposed in which species of all three domains, Archaea, Bacteria, and Eukarya, evolved from a single pool of gene-swapping prokaryotes.
• Phylogenetic models will continue to evolve as phylogeneticists remain highly skeptical of the current tree, web, and ring models.
Key Terms
• web of life: a phylogenetic model that resembles a web or a network more than a tree
• ring of life: a phylogenetic model where all three domains of life (Archaea, Bacteria, and Eukarya) evolved from a pool of primitive prokaryotes | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/20%3A_Phylogenies_and_the_History_of_Life/20.03%3A_Perspectives_on_the_Phylogenetic_Tree/20.3C%3A_Endosymbiotic_Theory_and_the_Evolution_of_Eukaryotes.txt |
Thumbnail: Ebola virus. (Public Domain; CDC).
21: Viruses
Learning Objectives
• Describe how viruses were first discovered and how they are detected
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 tiny, 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) and other viruses. 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 enabled 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.
Key Points
• Virions, single virus particles, are 20–250 nanometers in diameter.
• In the past, viruses were classified by the type of nucleic acid they contained, DNA or RNA, and whether they had single- or double-stranded nucleic acid.
• Molecular analysis of viral replicative cycles is now more routinely used to classify viruses.
Key Terms
• virus: a submicroscopic infectious organism, now understood to be a non-cellular structure consisting of a core of DNA or RNA surrounded by a protein coat
• virion: a single individual particle of a virus (the viral equivalent of a cell)
21.1B: Evolution of Viruses
Learning Objectives
• Describe the difficulties in determining the origin 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 one hypothesis about virus origins that is fully accepted in the field. One possible 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, probably 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.
Key Points
• Scientists agree that viruses don’t have a single common ancestor, but have yet to agree on a single hypothesis about virus origins.
• The devolution or the regressive hypothesis suggests that viruses evolved from free-living cells.
• The escapist or the progressive hypothesis suggests that viruses originated from RNA and DNA molecules that escaped from a host cell.
• The self-replicating hypothesis posits a system of self-replication that most probably involves evolution alongside the host cells.
Key Terms
• self-replicating: able to generate a copy of itself
• devolution: degeneration (as opposed to evolution) | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/21%3A_Viruses/21.01%3A_Viral_Evolution_Morphology_and_Classification/21.1A%3A_Discovery_and_Detection_of_Viruses.txt |
Learning Objectives
• Describe the relationship between the viral genome, capsid, and envelope
Viruses are acellular, meaning they are biological entities that do not have a cellular structure. Therefore, they 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. The capsid is made up of protein subunits called capsomeres. 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 host and virion complexity are uncorrelated. Some of the most intricate 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. 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 (tobacco mosaic virus). 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. They 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. For these viruses, attachment is a requirement for later penetration of the cell membrane, allowing them to 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.
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. 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 consist of nucleic acid 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 include 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 are enveloped viruses.
Types of Nucleic Acid
Unlike nearly all living organisms that use DNA as their genetic material, viruses may use either DNA or RNA. 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 obtain 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, 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.
Key Points
• Viruses are classified into four groups based on shape: filamentous, isometric (or icosahedral), enveloped, and head and tail.
• Many viruses attach to their host cells to facilitate penetration of the cell membrane, allowing their replication inside the cell.
• Non-enveloped viruses can be more resistant to changes in temperature, pH, and some disinfectants than are enveloped viruses.
• The virus core contains the small single- or double-stranded genome that encodes the proteins that the virus cannot get from the host cell.
Key Terms
• capsid: the outer protein shell of a virus
• envelope: an enclosing structure or cover, such as a membrane
• filamentous: Having the form of threads or filaments
• isometric: of, or being a geometric system of three equal axes lying at right angles to each other (especially in crystallography) | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/21%3A_Viruses/21.01%3A_Viral_Evolution_Morphology_and_Classification/21.1C%3A_Viral_Morphology.txt |
Learning Objectives
• Describe how viruses are classified
To understand the features shared among different groups of viruses, a classification scheme is necessary. However, most viruses are not thought to have evolved from a common ancestor, so 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 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 which is based on how messenger RNA (mRNA) is generated in each particular type of virus. 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.
Past Systems of Classification
Viruses are classified in several ways: by factors such as their core content, the structure of their capsids, and whether they have an outer envelope. Viruses may use either DNA or RNA as their genetic material. 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 obtain 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. 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.
Viruses can also be classified by the design of their capsids. 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. Capsids are classified as naked icosahedral, enveloped icosahedral, enveloped helical, naked helical, and complex. For example, the tobacco mosaic virus has a naked helical capsid. The adenovirus has an icosahedral capsid.
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. Viruses can contain double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), double-stranded RNA (dsRNA), single-stranded RNA with a positive polarity (ssRNA), ssRNA with a negative polarity, diploid (two copies) ssRNA, and partial dsDNA genomes. Positive polarity means that the genomic RNA can serve directly as mRNA and a negative polarity means that their sequence is complementary to the mRNA.
Key Points
• The type of genetic material, either DNA or RNA, and whether its structure is single- or double-stranded, linear or circular, and segmented or non-segmented are factors for classification.
• Virus capsids can be classified as naked icosahedral, enveloped icosahedral, enveloped helical, naked helical, and complex.
• Virus can either have an envelope or not.
• A more recent system, the Baltimore classification scheme, groups viruses into seven classes according to how the mRNA is produced during the replicative cycle of the virus.
Key Terms
• Baltimore classification: a classification scheme that groups viruses into seven classes according to how the mRNA is produced during the replicative cycle of the virus
• messenger RNA: Messenger RNA (mRNA) is a molecule of RNA that encodes a chemical “blueprint” for a protein product. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/21%3A_Viruses/21.01%3A_Viral_Evolution_Morphology_and_Classification/21.1D%3A_Virus_Classification.txt |
Viral infection involves the incorporation of viral DNA into a host cell, replication of that material, and the release of the new viruses.
Learning Objectives
• List the steps of viral replication and explain what occurs at each step
Key Points
• Viral replication involves six steps: attachment, penetration, uncoating, replication, assembly, and release.
• During attachment and penetration, the virus attaches itself to a host cell and injects its genetic material into it.
• During uncoating, replication, and assembly, the viral DNA or RNA incorporates itself into the host cell’s genetic material and induces it to replicate the viral genome.
• During release, the newly-created viruses are released from the host cell, either by causing the cell to break apart, waiting for the cell to die, or by budding off through the cell membrane.
Key Terms
• virion: a single individual particle of a virus (the viral equivalent of a cell)
• glycoprotein: a protein with covalently-bonded carbohydrates
• retrovirus: a virus that has a genome consisting of RNA
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.
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 to 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.
To convert RNA into DNA, retroviruses must contain genes that encode the virus-specific enzyme reverse transcriptase, which 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. They are then able to infect adjacent cells and repeat the replication cycle. As you have learned, some viruses are released when the host cell dies, while other viruses can leave infected cells by budding through the membrane without directly killing the cell. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/21%3A_Viruses/21.02%3A_Virus_Infections_and_Hosts/21.2A%3A_Steps_of_Virus_Infections.txt |
Bacteriophages, viruses that infect bacteria, may undergo a lytic or lysogenic cycle.
Learning Objectives
• Describe the lytic and lysogenic cycles of bacteriophages
Key Points
• Viruses are species specific, but almost every species on Earth can be affected by some form of virus.
• The lytic cycle involves the reproduction of viruses using a host cell to manufacture more viruses; the viruses then burst out of the cell.
• The lysogenic cycle involves the incorporation of the viral genome into the host cell genome, infecting it from within.
Key Terms
• latency: The ability of a pathogenic virus to lie dormant within a cell.
• bacteriophage: A virus that specifically infects bacteria.
• lytic cycle: The normal process of viral reproduction involving penetration of the cell membrane, nucleic acid synthesis, and lysis of the host cell.
• lysogenic cycle: A form of viral reproduction involving the fusion of the nucleic acid of a bacteriophage with that of a host, followed by proliferation of the resulting prophage.
Different Hosts and Their Viruses
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. So many different types of viruses exist that nearly every living organism has its own set of viruses that try 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. Bacteriophages may have a lytic cycle or a lysogenic cycle, and a few viruses are capable of carrying out both. When infection of a cell by a bacteriophage results in the production of new virions, the infection is said to be productive.
Lytic Cycle
With lytic phages, bacterial cells are broken open (lysed) and destroyed after immediate replication of the virion. As soon as the cell is destroyed, the phage progeny can find new hosts to infect. An example of a lytic bacteriophage is T4, which infects E. coli found in the human intestinal tract. Lytic phages are more suitable for phage therapy.
Some lytic phages undergo a phenomenon known as lysis inhibition, where completed phage progeny will not immediately lyse out of the cell if extracellular phage concentrations are high.
Lysogenic Cycle
In contrast, the lysogenic cycle does not result in immediate lysing of the host cell. Those phages able to undergo lysogeny are known as temperate phages. Their viral genome will integrate with host DNA and replicate along with it fairly harmlessly, or may even become established as a plasmid. The virus remains dormant until host conditions deteriorate, perhaps due to depletion of nutrients; then, the endogenous phages (known as prophages) become active. At this point they initiate the reproductive cycle, resulting in lysis of the host cell. As the lysogenic cycle allows the host cell to continue to survive and reproduce, the virus is reproduced in all of the cell’s offspring. An example of a bacteriophage known to follow the lysogenic cycle and the lytic cycle is the phage lambda of E. coli.
Latency Period
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 herpes viruses, including herpes simplex viruses, which cause 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/21%3A_Viruses/21.02%3A_Virus_Infections_and_Hosts/21.2B%3A_The_Lytic_and_Lysogenic_Cycles_of_Bacteriophages.txt |
Animal viruses have their genetic material copied by a host cell after which they are released into the environment to cause disease.
Learning Objectives
• Describe various animal viruses and the diseases they cause
Key Points
• Animal viruses may enter a host cell by either receptor -mediated endocytosis or by changing shape and entering the cell through the cell membrane.
• Viruses cause diseases in humans and other animals; they often have to run their course before symptoms disappear.
• Examples of viral animal diseases include hepatitis C, chicken pox, and shingles.
Key Terms
• receptor-mediated endocytosis: a process by which cells internalize molecules (endocytosis) by the inward budding of plasma membrane vesicles containing proteins with receptor sites specific to the molecules being internalized
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. When 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 and 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. 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.
Animal viruses are associated with a variety of human diseases. Some of them follow the classic pattern of acute disease, where symptoms worsen for a short period followed by the elimination of the virus from the body by the immune system with 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, cause only intermittent symptoms. Still other viruses, such as human herpes viruses 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; 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, with many infections only detected by routine blood work on patients with risk factors such as intravenous drug use. 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 the virus to escape elimination by the immune system and persist in individuals for years, while continuing to produce 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 mentioned, 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; 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 herpes viruses 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”. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/21%3A_Viruses/21.02%3A_Virus_Infections_and_Hosts/21.2C%3A_Animal_Viruses.txt |
Plant viruses can cause damage to stems, leaves, and fruits and can have a major impact on the economy because of food supply disruptions.
Learning Objectives
• Give examples of plant viruses and explain why they can be costly to the economy
Key Points
• Plants have cell walls which protect them from viruses entering their cells, so some type of damage must occur in order for them to become infected.
• When viruses are passed between plants, it is called horizontal transmission; when they are passed from the parent plant to the offspring, it is called vertical transmission.
• Symptoms of plant virus infection include malformed leaves, black streaks on the stems, discoloration of the leaves and fruits, and ring spots.
• Plant viruses can cause major disruptions to crop growth, which in turn can have a major impact on the economy.
Key Terms
• horizontal transmission: the transmission of an infectious agent, such as bacterial, fungal, or viral infection, between members of the same species that are not in a parent-child relationship
• vertical transmission: the transmission of an infection or other disease from the female of the species to the offspring
Plant Viruses
Plant viruses, like other viruses, contain a core of either DNA or RNA. As plant viruses have a cell wall to protect their cells, their 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 such as 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 plant viruses are transferred between different plants, this is known as horizontal transmission; when they are inherited from a parent, this is called vertical transmission.
Symptoms of viral diseases vary according to the virus and its host. 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.
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. Other 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/21%3A_Viruses/21.02%3A_Virus_Infections_and_Hosts/21.2D%3A_Plant_Viruses.txt |
Vaccinations prevent viruses from spreading by building immunity to the virus.
Learning Objectives
• Explain how vaccination protects vaccinated individuals and the community
Key Points
• Vaccinations are prepared with live viruses, killed viruses, or molecular subunits of the virus.
• A live vaccine consists of a small dose of the active virus.
• A killed vaccine contains the inactivated virus.
• It is possible, though rare, for live vaccines to cause the disease they’re used to prevent.
• Live vaccines are made by growing the virus in a lab, which causes mutations that allow them to grow better in the lab than in the host, thereby inhibiting their ability to cause disease.
• Even though live vaccines are designed to cause few symptoms, back mutations can occur and cause the virus to readapt to the host and the disease to spread.
Key Terms
• vaccination: inoculation in order to protect against a particular disease or strain of disease; causes a primary immune response without illness, allowing the secondary response to destroy subsequent infection
• live vaccine: consists of an active microbe (virus or bacteria)
• killed vaccine: (inactivated vaccine) consists of virus particles which are grown in culture and then killed using a method such as with heat or formaldehyde
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. 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 and 1960s significantly reduced the incidence of the disease, which caused muscle paralysis in children and generated great 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 low, but significant since the possibility that these viruses will revert to their disease-causing form by back mutations is still present. 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 still cause infection, but since they do not grow very well, they allow 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/21%3A_Viruses/21.03%3A_Prevention_and_Treatment_of_Viral_Infections/21.3A%3A_Vaccines_and_Immunity.txt |
Vaccines and anti-viral drugs can be used to inhibit the virus and reduce symptoms in individuals suffering from viral infections.
Learning Objectives
• Give examples of treatments with anti-viral drugs
Key Points
• Vaccines can boost an individual’s immune response and control viruses, such as Ebola and rabies, before they become deadly.
• Anti-viral drugs inhibit the virus by blocking the actions of its proteins; they are used to control and reduce symptoms for viral diseases.
• Tamiflu can reduce flu symptoms by inhibiting the enzyme neuraminidase, which blocks the virus from spreading to uninfected cells.
• Anti-HIV drugs inhibit and control viral replication at many different phases of the HIV replication cycle, so patients taking these drugs have a higher survival rate.
• Viruses can develop resistance to individual anti-viral drugs.
• The treatment of HIV involves a mixture of different drugs (fusion inhibitors, reverse transcriptase inhibitors, integrase inhibitors, and protease inhibitors) in a cocktail; viruses have greater difficulty gaining resistance to multiple drugs.
Key Terms
• virion: a single individual particle of a virus (the viral equivalent of a cell)
• anti-viral drug: a class of medication, such as antibiotics, that inhibits the virus by blocking the actions of one or more of its proteins
• Ebola virus: an extremely contagious virus of African origin that causes Ebola fever, spread through contact with bodily fluids or secretions of infected persons and by airborne particles
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 two weeks or longer. This is enough time to vaccinate an individual who suspects that they have been bitten by a rabid animaL; 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; the individual only has to recover from the infected bite. This approach is also being used for the treatment of Ebola virus, 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 two 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) can reduce the duration of “flu” symptoms by one or two 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.
Anti-HIV Drugs
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. 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/21%3A_Viruses/21.03%3A_Prevention_and_Treatment_of_Viral_Infections/21.3B%3A_Vaccines_and_Anti-Viral_Drugs_for_Treatment.txt |
Prions are infectious particles that contain no nucleic acids, and viroids are small plant pathogens that do not encode proteins.
Learning Objectives
• Describe prions and viroids and their basic properties
Key Points
• The prion appears to be the first infectious agent found whose transmission is not reliant upon genes made of DNA or RNA.
• An infectious structural variant of a normal cellular protein called PrP (prion protein) is known to cause spongiform encephalopathies.
• Prions have been implicated in fatal neurodegenerative diseases, such as kuru in humans and bovine spongiform encephalopathy (BSE) in cattle.
• Loss of motor control and unusual behaviors are common symptoms of individuals with kuru and BSE; symptoms are usually followed by death.
• Viroids do not have a capsid or outer envelope and can reproduce only within a host cell.
• Viroids are not known to cause any human diseases, but they are responsible for crop failures and the loss of millions of dollars in agricultural revenue each year.
Key Terms
• prion: a self-propagating misfolded conformer of a protein that is responsible for a number of diseases that affect the brain and other neural tissue
• proteinaceous: of, pertaining to, or consisting of protein
• viroid: plant pathogens that consist of just a short section of RNA, but without the protein coat typical of viruses
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, 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 affect only cattle. Cattle that died of BSE had 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. BSE still exists in various areas. Although a rare disease, individuals that acquire CJD are difficult to treat. The disease spreads 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; 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 appears 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, as with viruses, can reproduce only within a host cell. Viroids do not, however, manufacture any proteins. They produce only a single, specific RNA molecule. Human diseases caused by viroids have yet to be identified.
Viroid-infected plants 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/21%3A_Viruses/21.04%3A_Prions_and_Viroids/21.4.01%3A_21-4A-_Prions_and_Viroids.txt |
Thumbnail: Scanning electron micrograph of neutrophil ingesting methicillin-resistant Staphylococcus aureus bacteria. (Public Domain; NIAID/NIH).
22: Prokaryotes- Bacteria and Archaea
Prokaryotic organisms were the first living things on earth and still inhabit every environment, no matter how extreme.
Learning Objectives
• Discuss the origins of prokaryotic organisms in terms of the geologic timeline
Key Points
• All living things can be classified into three main groups called domains; these include the Archaea, the Bacteria, and the Eukarya.
• Prokaryotes arose during the Precambrian Period 3.5 to 3.8 billion years ago.
• Prokaryotic organisms can live in every type of environment on Earth, from very hot, to very cold, to super haline, to very acidic.
• The domains Bacteria and Archaea are the ones containing prokaryotic organisms.
• The Archaea are prokaryotes that inhabit extreme environments, such as inside of volcanoes, while Bacteria are more common organisms, such as E. coli.
Key Terms
• prokaryote: an organism whose cell (or cells) are characterized by the absence of a nucleus or any other membrane-bound organelles
• domain: in the three-domain system, the highest rank in the classification of organisms, above kingdom: Bacteria, Archaea, and Eukarya
• archaea: a taxonomic domain of single-celled organisms lacking nuclei, formerly called archaebacteria, but now known to differ fundamentally from bacteria
Evolution of Prokaryotes
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, etc. 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.
The current model of the evolution of the first, living organisms is that these were some form of prokaryotes, which may have evolved out of protobionts. In general, the eukaryotes are thought to have evolved later in the history of life. However, some authors have questioned this conclusion, arguing that the current set of prokaryotic species may have evolved from more complex eukaryotic ancestors through a process of simplification. Others have argued that the three domains of life arose simultaneously, from a set of varied cells that formed a single gene pool.
Two of the three domains, Bacteria and Archaea, are prokaryotic. Based on fossil evidence, prokaryotes were the first inhabitants on Earth, appearing 3.5 to 3.8 billion years ago during the Precambrian Period. 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/Book%3A_General_Biology_(Boundless)/22%3A_Prokaryotes-_Bacteria_and_Archaea/22.01%3A_Prokaryotic_Diversity/22.1A%3A_Classification_of_Prokaryotes.txt |
Archaea are believed to have evolved from gram-positive bacteria and can occupy more extreme environments.
Learning Objectives
• Distinguish bacteria from archaea in terms of their origins
Key Points
• The first prokaryotes were adapted to the extreme conditions of early earth.
• It has been proposed that archaea evolved from gram-positive bacteria as a response to antibiotic selection pressures.
• Microbial mats and stromatolites represent some of the earliest prokaryotic formations that have been found.
Key Terms
• stromatolite: a laminated, columnar, rock-like structure built over geologic time by microorganisms such as cyanobacteria
• gram-positive: that is stained violet by Gram’s method due to the presence of a peptidoglycan cell wall
• sacculus: a small sac
• indel: either an insertion or deletion mutation in the genetic code
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, existing 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. Also at this time, strong volcanic activity was common on Earth. It is probable 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.
Although probable prokaryotic cell fossils date to almost 3.5 billion years ago, most prokaryotes do not have distinctive morphologies; fossil shapes cannot be used to identify them as Archaea. Instead, chemical fossils of unique lipids are more informative because such compounds do not occur in other organisms. Some publications suggest that archaean or eukaryotic lipid remains are present in shales dating from 2.7 billion years ago. Such lipids have also been detected in Precambrian formations. The oldest such traces come from the Isua district of west Greenland, which include earth’s oldest sediments, formed 3.8 billion years ago. The archaeal lineage may be the most ancient that exists on earth.
Within prokaryotes, archaeal cell structure is most similar to that of gram-positive bacteria, largely because both have a single lipid bilayer and usually contain a thick sacculus of varying chemical composition. In phylogenetic trees based upon different gene / protein sequences of prokaryotic homologs, the archaeal homologs are more closely related to those of Gram-positive bacteria. Archaea and gram-positive bacteria also share conserved indels in a number of important proteins, such as Hsp70 and glutamine synthetase.
It has been proposed that the archaea evolved from gram-positive bacteria in response to antibiotic selection pressure. This is suggested by the observation that archaea are resistant to a wide variety of antibiotics that are primarily produced by gram-positive bacteria and that these antibiotics primarily act on the genes that distinguish archaea from bacteria. The evolution of Archaea in response to antibiotic selection, or any other competitive selective pressure, could also explain their adaptation to extreme environments (such as high temperature or acidity) as the result of a search for unoccupied niches to escape from antibiotic-producing organisms.
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 that includes mostly bacteria, but also archaea. Microbial mats are a few centimeters thick, typically growing where different types of materials interface, mostly on moist surfaces. The various types of prokaryotes that comprise the mats use different metabolic pathways, which 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. 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/22%3A_Prokaryotes-_Bacteria_and_Archaea/22.01%3A_Prokaryotic_Diversity/22.1B%3A_The_Origins_of_Archaea_and_Bacteria.txt |
Prokaryotes are well adapted to living in all types of conditions, including extreme ones, and prefer to live in colonies called biofilms.
Learning Objectives
• Discuss the distinguishing features of extremophiles and the environments that produce biofilms
Key Points
• Prokaryotes live in all environments, no matter how extreme they may be.
• Bacteria that prefer very salty environments are called halophiles, while those that live in very acidic environments are called acidophiles.
• An example of a habitat that halophiles can colonize is the Dead Sea, a body of water that is 10 times saltier than regular ocean water.
• A biofilm is a microbial community held together in a gummy-textured matrix that consists primarily of polysaccharides secreted by the organisms.
• Biofilms can be found clogging pipes, on kitchen counters, or even on the surface of one’s teeth.
Key Terms
• extremophile: an organism that lives under extreme conditions of temperature, salinity, etc; commercially important as a source of enzymes that operate under similar conditions
• halophile: an organism that lives and thrives in an environment of high salinity, often requiring such an environment; a form of extremophile
• alkaliphile: any organism that lives and thrives in an alkaline environment, such as a soda lake; a form of extremophile
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 Arctic and the Antarctic, in very dry places, deep inside earth, in harsh chemical environments, and in high radiation environments, just to mention a few. These organisms give us a better understanding of prokaryotic diversity and raise 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. 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. 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.
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. The water also 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, ecosystem.
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 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/22%3A_Prokaryotes-_Bacteria_and_Archaea/22.01%3A_Prokaryotic_Diversity/22.1C%3A_Extremophiles_and_Biofilms.txt |
Prokaryotes, found in both Domain Archaea and Bacteria, are unicellular organisms that lack membrane-bound organelles and a defined nucleus.
Learning Objectives
• Describe the basic structure of a typical prokaryote
Key Points
• Prokaryotic cells lack a defined nucleus, but have a region in the cell, termed the nucleoid, in which a single chromosomal, circular, double-stranded DNA molecule is located.
• Archaeal membranes have replaced the fatty acids of bacterial membranes with isoprene; some archaeal membranes are monolayer rather than bilayer.
• Prokaryotes can be further classified based on the composition of the cell wall in terms of the amount of peptidoglycan present.
• Gram-positive organisms typically lack the outer membrane found in gram-negative organisms and contain a large amount of peptidoglycan in the cell wall, roughly 90%.
• Gram-negative bacteria have a relatively thin cell wall composed of a few layers of peptidoglycan.
• Gram-negative bacteria have a relatively thin cell wall composed of a few layers of peptidoglycan.
Key Terms
• nucleoid: the irregularly-shaped region within a prokaryote cell where the genetic material is localized
• plasmid: a circle of double-stranded DNA that is separate from the chromosomes, which is found in bacteria and protozoa
• osmotic pressure: the hydrostatic pressure exerted by a solution across a semipermeable membrane from a pure solvent
The Prokaryotic Cell
Prokaryotes 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.
The composition of the cell wall differs significantly between the domains Bacteria and Archaea, the two domains of life into which prokaryotes are divided. 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 is responsible for the organism’s shape. Some bacteria have a capsule outside the cell wall. Other structures are present in some prokaryotic species, but not in others. 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 increases its resistance to our immune responses. Some species also have flagella used for locomotion and pili used for attachment to surfaces. Plasmids, which consist of extra-chromosomal DNA, are also present in many species of bacteria and archaea.
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, preventing them from diffusing into the extracellular environment, while other molecules may move through the membrane. 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.
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. It 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. Up to 90 percent of the cell wall in gram-positive bacteria is composed of peptidoglycan, with most of the rest 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.
22.2B: Prokaryotic Reproduction
Prokaryotes reproduce asexually by binary fission; they can also exchange genetic material by transformation, transduction, and conjugation.
Learning Objectives
• Distinguish among the types of reproduction in prokaryotes
Key Points
• Binary fission is a type of reproduction in which the chromosome is replicated and the resultant prokaryote is an exact copy of the parental prokaryate, thus leaving no opportunity for genetic diversity.
• Transformation is a type of prokaryotic reproduction in which a prokaryote can take up DNA found within the environment that has originated from other prokaryotes.
• Transduction is a type of prokaryotic reproduction in which a prokaryote is infected by a virus which injects short pieces of chromosomal DNA from one bacterium to another.
• Conjugation is a type of prokaryotic reproduction in which DNA is transferred between prokaryotes by means of a pilus.
Key Terms
• transformation: the alteration of a bacterial cell caused by the transfer of DNA from another, especially if pathogenic
• transduction: horizontal gene transfer mechanism in prokaryotes where genes are transferred using a virus
• binary fission: the process whereby a cell divides asexually to produce two daughter cells
• conjugation: the temporary fusion of organisms, especially as part of sexual reproduction
• pilus: a hairlike appendage found on the cell surface of many bacteria
Reproduction
Reproduction in prokaryotes is asexual and usually takes place by binary fission. The DNA of a prokaryote exists as 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.
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 rapidly. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/22%3A_Prokaryotes-_Bacteria_and_Archaea/22.02%3A_Structure_of_Prokaryotes/22.2A%3A_Basic_Structures_of_Prokaryotic_Cells.txt |
Prokaryotes need a source of energy, a source of carbon, macronutrients, and micronutrients to survive.
Learning Objectives
• Summarize what prokaryotes need to remain alive and functioning
Key Points
• The main components of the organic compounds in a prokaryotic cell are macronutrients (such as carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur) that make up important biomolecules, including proteins and nucleic acids.
• Nutrients that are needed by prokaryotes in small quantities to perform cellular functions, including certain electron transport chain reactions, are known as micronutrients (e.g., iron, boron, chromium, and manganese).
• Autotrophic prokaryotes are able to fix inorganic compounds, such as carbon dioxide, to obtain carbon, while heterotrophic prokaryotes use organic compounds as their source of carbon.
Key Terms
• macronutrient: any of the elements required in large amounts by all living things
• chemotroph: an organism that obtains energy by the oxidation of electron-donating molecules in the environment
• micronutrient: a mineral, vitamin, or other substance that is essential, even in very small quantities, for growth or metabolism
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. 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. It 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 chemolithotrophs.
The Ways in Which Prokaryotes Obtain Carbon
Just as prokaryotes can use different sources of energy, they can also utilize 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. Chemolithoautotrophs obtain their energy from inorganic compounds, while building their complex molecules from carbon dioxide. Table 1 summarizes carbon and energy sources in prokaryotes. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/22%3A_Prokaryotes-_Bacteria_and_Archaea/22.03%3A_Prokaryotic_Metabolism/22.3A%3A_Energy_and_Nutrient_Requirements_for_Prokaryotes.txt |
Prokaryotes play vital roles in the movement of carbon dioxide and nitrogen in the carbon and nitrogen cycles.
Learning Objectives
• Give examples of the beneficial roles played by prokaryotes in different ecosystems
Key Points
• Carbon and nitrogen are both macronutrients that are necessary for life on earth; prokaryotes play vital roles in their cycles.
• The carbon cycle is maintained by prokaryotes that remove carbon dioxide and return it to the atmosphere.
• Prokaryotes play a major role in the nitrogen cycle by fixing atomspheric nitrogen into ammonia that plants can use and by converting ammonia into other forms of nitrogen sources.
Key Terms
• carbon cycle: the physical cycle of carbon through the earth’s biosphere, geosphere, hydrosphere, and atmosphere that includes such processes as photosynthesis, decomposition, respiration and carbonification
• nitrogen cycle: the natural circulation of nitrogen, in which atmospheric nitrogen is converted to nitrogen oxides and deposited in the soil, where it is used by organisms or decomposed back to elemental nitrogen
• nitrogen fixation: the conversion of atmospheric nitrogen into ammonia and organic derivatives, by natural means, especially by microorganisms in the soil, into a form that can be assimilated by plants
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, but 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. Prokaryotes play an important role in the carbon cycle. 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, which are producers that 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, releasing 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).
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. As a macronutrient 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 solely by prokaryotes; they 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 by natural means, especially by microorganisms (prokayotes) in the soil. Ammonia can then 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 perform the reverse process, the reduction of nitrate from the soils to gaseous compounds such as N2O, NO, and N2, a process called denitrification. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/22%3A_Prokaryotes-_Bacteria_and_Archaea/22.03%3A_Prokaryotic_Metabolism/22.3B%3A_The_Role_of_Prokaryotes_in_Ecosystems.txt |
Learning Objectives
• Give examples of historical, new, and re-emerging bacterial diseases in humans
There are records about infectious diseases as far back as 3000 B.C.E. 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.E., 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, which causes typhoid fever. This disease is commonly seen in overcrowded areas and has caused epidemics throughout recorded history.
Bubonic Plagues
From 541 to 750 C.E.., 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. The 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. 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; mortality rates from plague are now very low.
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 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, are of both viral and bacterial origins. Brucellosis is an example of a prokaryotic zoonosis that is re-emerging in some regions. Necrotizing fasciitis (commonly known as flesh-eating bacteria) has been increasing in virulence for the last 80 years, for unknown reasons.
Some of the currently-emerging diseases are not actually new, but are diseases that were catastrophic in the past. They devastated populations, became dormant for a while, but have re-emerged, sometimes more virulent than before. Such was the case with bubonic plague. Other diseases, like tuberculosis, were never eradicated, but were under control in some regions of the world until re-emerging, 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.
Key Points
• A pathogen must be able to reproduce in the host’s body and damage the host in some way to cause disease.
• Before antibiotics, contracting plagues usually meant death; however, most bacterium associated with these plagues respond to modern antibiotics; mortality rates from these diseases are now very low.
• Emerging diseases include those that have appeared in a population for the first time or that may have existed previously, but are rapidly spreading; this also includes re-emerging diseases that were previously under control.
• The spread of disease can be impacted dramatically by changes in the environment, the pathogen, or the host population.
Key Terms
• zoonosis: an animal disease that can be transmitted to humans
• plague: an epidemic or pandemic caused by any pestilence
• pathogen: any organism or substance, especially a microorganism, capable of causing disease, such as bacteria, viruses, protozoa, or fungi
22.4B: Biofilms and Disease
Biofilms, complex colonies of bacteria acting as a unit in their release of toxins, are highly resistant to antibiotics and host defense.
Learning Objectives
• Give examples of the roles played by biofilms in human diseases
Key Points
• Once a biofilm infection is established, it is very difficult to eradicate because biofilms exhibit great resistance to most methods used to control microbial growth, including antibiotics.
• Biofilms are able to grow anywhere there is an optimal combination of moisture, nutrients, and a surface.
• Biofilms are responsible for diseases such as infections in patients and readily settle within wounds and burns; they can also easily colonize medical devices and other surfaces where sterility is vital for health.
Key Terms
• biofilm: a thin film of mucus created by and containing a colony of bacteria and other microorganisms
• nosocomial: contracted in a hospital, or arising from hospital treatment
Biofilms and Disease
Biofilms are complex colonies of bacteria (often containing several species) that exchange chemical signals to coordinate the release of toxins that will attack the host. Once established, they are very difficult to destroy as they are highly resistant to antimicrobial treatments and host defense. Biofilms form when microorganisms adhere to the surface of some object in a moist environment and begin to reproduce. They grow virtually everywhere in almost any environment where there is a combination of moisture, nutrients, and a surface. Biofilms 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 is not adequately cleaned.
Biofilm infections develop gradually and often do not cause immediate symptoms. 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 eradicate biofilms. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/22%3A_Prokaryotes-_Bacteria_and_Archaea/22.04%3A_Bacterial_Diseases_in_Humans/22.4A%3A_History_of_Bacterial_Diseases.txt |
Learning Objectives
• Discuss antibiotic resistance.
The word antibiotic comes from the Greek word “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 other 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; 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. There is also the excessive use of antibiotics in livestock along with the routine use of antibiotics in animal feed, both of which promote bacterial resistance. In the United States, 70 percent of the antibiotics produced are fed to animals. Because they are given to livestock in low doses, the probability of resistance developing is maximized. These resistant bacteria are readily transferred to humans.
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. 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 have not 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 (JAMA) 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.
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 of research and clinical trials, plus financial investments in the millions of dollars, to generate an effective and approved drug.
Key Points
• In antibiotic resistance, antibiotics will kill most of the infecting bacteria leaving behind only the resistant forms, which reproduce, resulting in an increase in the proportion of resistant forms over non-resistant ones.
• Cold and flu treatments and the medication of livestock are examples of antibiotic misuse responsible for bacterial resistance.
• Methicillin-resistant Staphylococcus aureus (MRSA) is an example of a dangerous antibiotic-resistant strain of bacteria that can infect sick, as well as healthy people.
• Due to the growing resistance to antibiotics, scientists believe that we may be returning to a time in which a simple bacterial infection could again detrimentally impact human populations.
Key Terms
• antibiotic: any substance that can destroy or inhibit the growth of bacteria and similar microorganisms
Reference
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.
22.4D: Bacterial Foodborne Diseases
Learning Objectives
• Give examples of bacterial foodborne diseases in humans
Prokaryotes are everywhere. They readily colonize the surface of any type of material. 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 of 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, sporadic cases of botulism, the potentially fatal disease produced by a toxin from the anaerobic bacterium Clostridium botulinum, were relatively common. Some of the 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. However, 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. 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. 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. 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.
Key Points
• Food and food-processing equipment are usually colonized by biofilms.
• A foodborne disease is an illness resulting from the consumption of pathogenic bacteria, viruses, or other parasites that contaminate animal or plant-based food.
• Proper sterilization techniques and canning procedures have reduced the incidence of botulism.
• E. coli outbreaks have become more common as new strains continue to evolve.
Key Terms
• serotype: a group of microorganisms characterized by a specific set of antigens
• botulism: poisoning caused by the toxin from Clostridium botulinum, a type of anaerobic bacteria that grows in improperly-prepared food | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/22%3A_Prokaryotes-_Bacteria_and_Archaea/22.04%3A_Bacterial_Diseases_in_Humans/22.4C%3A_Antibiotics-_Are_We_Facing_a_Crisis.txt |
Prokaryotes fix nitrogen into a form that can be used by eukaryotes.
Learning Objectives
• Explain the need for nitrogen fixation and how it is accomplished
Key Points
• Prokaryotes perform biological nitrogen fixation (BNF) to convert nitrogen gas from the atmosphere into ammonia, which can be used by eukaryotes to form important biomolecules such as amino acids and nucleic acids.
• Although most nitrogen fixation is performed by prokaryotes, abiotic processes, such as industrial processes and lightning, can also fix nitrogen.
• Some bacteria form symbiotic relationships with legumes, which provide oxygen-free nodules on their roots for nitrogen fixation to occur; this process allows ammonia to form naturally from atomspheric nitrogen to act as fertilizer for soils.
Key Terms
• abiotic: nonliving, inanimate, characterized by the absence of life; of inorganic matter
• nitrogen fixation: the conversion of atmospheric nitrogen into ammonia and organic derivatives, by natural means, especially by microorganisms in the soil, into a form that can be assimilated by plants
• legume: a large family of herbs, shrubs, and trees that bear nodules on the roots that contain nitrogen-fixing bacteria
Cooperation between Bacteria and Eukaryotes: Nitrogen Fixation
Nitrogen is a very important element for living things because it is part of the 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. Atmospheric nitrogen, N2, provides 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.
Bacterial Nitrogen Fixation
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 and cellular respiration, BNF is the second most important biological process on Earth. The equation representing the process is as follows, where Pi stands for inorganic phosphate: N2 + 16ATP + 8 + 8H+ 2NH3 + 16ADP + 16Pi + H2
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.
Types of Bacteria
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. 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 converts (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.
Some legumes, like soybeans, are also key sources of agricultural protein. Some of the most important legumes are soybean, peanuts, peas, chickpeas, and beans. Other legumes, such as alfalfa, are used to feed cattle. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/22%3A_Prokaryotes-_Bacteria_and_Archaea/22.05%3A_Beneficial_Prokaryotes/22.5A%3A_Symbiosis_between_Bacteria_and_Eukaryotes.txt |
Some of the earliest biotechnology used prokaryotes for the production of food products such as cheese, bread, wine, beer, and yogurt.
Learning Objectives
• Discuss the origins of food biotechnology as indicated by the production of cheese, bread, wine, beer, and yogurt
Key Points
• Prokaryotes and other microbes are beneficial to some food production by transforming textures, providing flavors, producing ethanol, and providing protection from unwanted microbes.
• Bacteria breakdown proteins and fats into a complex mix of amino acids, amines, and fatty acids; this processing alters the food product.
• Many food production processes rely on the fermentation of prokaryotes and other microbes to produce the desired flavors; in the case of beer and wine, they also affect the desired amount of ethanol.
Key Terms
• fermentation: an anaerobic biochemical reaction, in yeast, for example, in which enzymes catalyze the conversion of sugars to alcohol or acetic acid with the evolution of carbon dioxide
• biotechnology: the use of living organisms (especially microorganisms) in industrial, agricultural, medical, and other technological applications
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. ” 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. Some of the products are as simple as cheese, bread, wine, beer, and yogurt,which employ both bacteria and other microbes, such as yeast.
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 because milk will spoil relatively quickly, but when processed as cheese, it is more stable. A required step in cheese-making is separating the milk into solid curds and liquid whey. This usually is done by acidifying the milk and adding rennet. The acidification can be accomplished directly by the addition of an acid like vinegar, but usually starter bacteria are employed instead. These starter bacteria convert milk sugars into lactic acid. The same bacteria (and the enzymes they produce) also play a large role in the eventual flavor of aged cheeses. Most cheeses are made with starter bacteria from the Lactococci, Lactobacilli, or Streptococci families. As a cheese ages, microbes and enzymes transform texture and intensify flavor. This transformation is largely a result of the breakdown of casein proteins and milkfat into a complex mix of amino acids, amines, and fatty acids. Some cheeses have additional bacteria or molds intentionally introduced before or during aging. In traditional cheesemaking, these microbes might already be present in the aging room; they are simply allowed to settle and grow on the stored cheeses. More often today, prepared cultures are used, giving more consistent results and putting fewer constraints on the environment where the cheese ages.
Records of brewing beer date back about 6,000 years to the Sumerians. Evidence indicates that the Sumerians discovered fermentation by chance. Wine has been produced for about 4,500 years. The production of beer and wine use microbes, including both yeast and bacteria, to produce ethanol during fermentation as well as provide flavor to the beverage. Similarly, bread is one of the oldest prepared foods. Bread-making also uses the fermentation of yeast and some bacteria for leavening and flavor. Additionally, evidence suggests that cultured milk products, such as yogurt, have existed for at least 4,000 years. These products use prokaryotes (as with cheese) to provide flavor and to protect the food product from other unwanted microbes. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/22%3A_Prokaryotes-_Bacteria_and_Archaea/22.05%3A_Beneficial_Prokaryotes/22.5B%3A_Early_Biotechnology-_Cheese_Bread_Wine_Beer_and_Yogurt.txt |
Bioremediation occurs when prokaryotes clean up a polluted environment through the natural breakdown of pollutants.
Learning Objectives
• Give examples of the use of prokaryotes in enviromental bioremediation
Key Points
• To clean up oil spills, bacteria are introduced to the area of the spill where they break down the hydrocarbons of the oil into carbon dioxide; this is an example of bioremediation.
• Toxic metals, such as mercury (II), can be converted into nontoxic forms, such as mercury (0), by bacteria.
• Using natural organisms as examples, scientists can engineer bacteria for improved bioremediation of desired pollutants.
• Bioremediation can remove oil, some pesticides, fertilizers, and toxic chemicals, such as arsenic, from the environment.
Key Terms
• bioremediation: the use of biological organisms, usually microorganisms, to remove contaminants, especially from soil or polluted water
• biotransformation: the changes (both chemical and physical) that occur to a substance (especially a drug) by the actions of enzymes within an organism
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 elemental 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), 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 if 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 the spectrum of hydrocarbon compounds that can be processed. Under ideal conditions, it has been reported that up to 80 percent of the non-volatile 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. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/22%3A_Prokaryotes-_Bacteria_and_Archaea/22.05%3A_Beneficial_Prokaryotes/22.5C%3A_Prokaryotes_and_Environmental_Bioremediation.txt |
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
Learning Objectives
• Discuss the origins of eukaryotes in terms of the geologic time line
Origins of Eukaryotes
Humans have been familiar with macroscopic organisms (organisms big enough to see with the unaided eye) since before there was a written history. It is likely that most cultures distinguished between animals and land plants, but 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.
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, which can have single cells that can be several meters in size. 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. They are among the first organisms to evolve with the rise of eukaryotes.
Eukaryotes in a Geological Time Frame
The oldest fossil evidence of eukaryotes, cells measuring 10 µm or greater, is about 2 billion years old. All fossils older than this appear to be prokaryotes. It is probable that today’s eukaryotes are descended from an ancestor that had a prokaryotic cellular organization. The last common ancestor (LCA) of today’s Eukarya had several characteristics that included: 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. The LCA 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 LCA 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.
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; living things would have relied on fermentation instead. At some point before about 3.5 billion years ago, some prokaryotes evolved the ability to photosynthesize. Cyanobacteria used water as a hydrogen source and released O2 as a waste product. Originally, oxygen-rich environments were probably 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.
Key Points
• On a geological time line, protists are among the first organisms that evolved after prokaryotes.
• Today’s eukaryotes evolved from a common ancestor with the following features: a nucleus that divided via mitosis, DNA associated with histones, a cytoskeleton and endomembrane system, the ability to make cilia/flagella.
• Protists vary widely in size, from single cells approximately 10 µm in size to multicellular seaweeds that are visible with the naked eye.
Key Terms
• cyanobacteria: photosynthetic prokaryotic microorganisms, of phylum Cyanobacteria, once known as blue-green algae
• aerobic: living or occurring only in the presence of oxygen
• endomembrane: all the membraneous components inside a eukaryotic cell, including the nuclear envelope, endoplastic reticulum, and Golgi apparatus | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/23%3A_Protists/23.01%3A_Eukaryotic_Origins/23.1A%3A_Early_Eukaryotes.txt |
Eukaryotes, having probably evolved from prokaryotes, have more complex traits in both cell and DNA organization.
Learning Objectives
• Compare and contrast prokaryotic DNA to eukaryotic DNA
Key Points
• Prokaryotic genomic DNA is attached to the plasma membrane in the form of a nucleoid, in contrast to eukaryotic DNA, which is located in a nucleus.
• Eukaryotic DNA is linear, compacted into chromosomes by histones, and has telomeres at each end to protect from deterioration.
• Prokaryotes contain circular DNA in addition to smaller, transferable DNA plasmids.
• Eukaryotic cells contain mitochondrial DNA in addition to nuclear DNA.
• Eukaryotes separate replicated chromosomes by mitosis, using cytoskeletal proteins, whereas prokaryotes divide more simply via binary fission.
Key Terms
• telomere: either of the repetitive nucleotide sequences at each end of a eukaryotic chromosome, which protect the chromosome from degradation
• plasmid: a circle of double-stranded DNA that is separate from the chromosomes, which is found in bacteria and protozoa
Characteristics of Eukaryotic DNA compared to Prokaryotic DNA
Prokaryotic cells are known to be much less complex than eukaryotic cells since eukaryotic cells are considered to be present at a later point of evolution. It is probable that eukaryotic cells evolved from prokaryotic cells. Differences in complexity can be seen at the cellular level.
The single characteristic that is both necessary and sufficient to define an organism as a eukaryote is a nucleus surrounded by a nuclear envelope with nuclear pores. All extant eukaryotes have cells with nuclei; most of a eukaryotic cell’s genetic material is contained within the nucleus. In contrast, prokaryotic DNA is not contained within a nucleus, but rather is attached to the plasma membrane and contained in the form of a nucleoid, an irregularly-shaped region that is not surrounded by a nuclear membrane.
Eukaryotic DNA is packed into bundles of chromosomes, each consisting of a linear DNA molecule coiled around basic (alkaline) proteins called histones, which wind the DNA into a more compact form. Prokaryotic DNA is found in circular, non-chromosomal form. In addition, prokaryotes have plasmids, which are smaller pieces of circular DNA that can replicate separately from prokaryotic genomic DNA. Because of the linear nature of eukaryotic DNA, repeating non-coding DNA sequences called telomeres are present on either end of the chromosomes as protection from deterioration.
Mitosis, a process of nuclear division wherein replicated chromosomes are divided and separated using elements of the cytoskeleton, is universally present in eukaryotes. The cytoskeleton contains structural and motility components called actin microfilaments and microtubules. All extant eukaryotes have these cytoskeletal elements. Prokaryotes on the other hand undergo binary fission in a process where the DNA is replicated, then separates to two poles of the cell, and, finally, the cell fully divides.
A major DNA difference between eukaryotes and prokaryotes is the presence of mitochondrial DNA (mtDNA) in eukaryotes. Because eukaryotes have mitochondria and prokaryotes do not, eukaryotic cells contain mitochondrial DNA in addition to DNA contained in the nucleus and ribosomes. The mtDNA is composed of significantly fewer base pairs than nuclear DNA and encodes only a few dozen genes, depending on the organism. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/23%3A_Protists/23.01%3A_Eukaryotic_Origins/23.1B%3A_Characteristics_of_Eukaryotic_DNA.txt |
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