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Cell_Biology_Alberts_110	Cell_Biology_Alberts	molecular Biology Began with a spotlight on E. coli Because living organisms are so complex, the more we learn about any particular species, the more attractive it becomes as an object for further study. Each discovery raises new questions and provides new tools with which to tackle general questions in the context of the chosen organism. For this reason, large communities of biologists have become dedicated to studying different aspects of the same model organism.	Cell_Biology_Alberts. molecular Biology Began with a spotlight on E. coli Because living organisms are so complex, the more we learn about any particular species, the more attractive it becomes as an object for further study. Each discovery raises new questions and provides new tools with which to tackle general questions in the context of the chosen organism. For this reason, large communities of biologists have become dedicated to studying different aspects of the same model organism.
Cell_Biology_Alberts_111	Cell_Biology_Alberts	In the early days of molecular biology, the spotlight focused intensely on just one species: the Escherichia coli, or E. coli, bacterium (see Figures 1–13 and 1–14). This small, rod-shaped bacterial cell normally lives in the gut of humans and other vertebrates, but it can be grown easily in a simple nutrient broth in a culture bottle. It adapts to variable chemical conditions and reproduces rapidly, and it can evolve by mutation and selection at a remarkable speed. As with other bacteria, different strains of E. coli, though classified as members of a single species, differ genetically to a much greater degree than do different varieties of a sexually reproducing organism such as a plant or animal. One E. coli strain may possess many hundreds of genes that are absent from another, and the two strains could have as little as 50% of their genes in common. The standard laboratory strain	Cell_Biology_Alberts. In the early days of molecular biology, the spotlight focused intensely on just one species: the Escherichia coli, or E. coli, bacterium (see Figures 1–13 and 1–14). This small, rod-shaped bacterial cell normally lives in the gut of humans and other vertebrates, but it can be grown easily in a simple nutrient broth in a culture bottle. It adapts to variable chemical conditions and reproduces rapidly, and it can evolve by mutation and selection at a remarkable speed. As with other bacteria, different strains of E. coli, though classified as members of a single species, differ genetically to a much greater degree than do different varieties of a sexually reproducing organism such as a plant or animal. One E. coli strain may possess many hundreds of genes that are absent from another, and the two strains could have as little as 50% of their genes in common. The standard laboratory strain
Cell_Biology_Alberts_112	Cell_Biology_Alberts	E. coli K-12 has a genome of approximately 4.6 million nucleotide pairs, contained in a single circular molecule of DNA that codes for about 4300 different kinds of proteins (Figure 1–24). In molecular terms, we know more about E. coli than about any other living organism. Most of our understanding of the fundamental mechanisms of life— for example, how cells replicate their DNA, or how they decode the instructions represented in the DNA to direct the synthesis of specific proteins—initially came from studies of E. coli. The basic genetic mechanisms have turned out to be highly conserved throughout evolution: these mechanisms are essentially the same in our own cells as in E. coli.	Cell_Biology_Alberts. E. coli K-12 has a genome of approximately 4.6 million nucleotide pairs, contained in a single circular molecule of DNA that codes for about 4300 different kinds of proteins (Figure 1–24). In molecular terms, we know more about E. coli than about any other living organism. Most of our understanding of the fundamental mechanisms of life— for example, how cells replicate their DNA, or how they decode the instructions represented in the DNA to direct the synthesis of specific proteins—initially came from studies of E. coli. The basic genetic mechanisms have turned out to be highly conserved throughout evolution: these mechanisms are essentially the same in our own cells as in E. coli.
Cell_Biology_Alberts_113	Cell_Biology_Alberts	Prokaryotes (cells without a distinct nucleus) are biochemically the most diverse organisms and include species that can obtain all their energy and nutrients from inorganic chemical sources, such as the reactive mixtures of minerals released at hydrothermal vents on the ocean floor—the sort of diet that may have nourished the first living cells 3.5 billion years ago. DNA sequence comparisons reveal the family relationships of living organisms and show that the prokaryotes fall into two groups that diverged early in the course of evolution: the bacteria (or eubacteria) and the archaea. Together with the eukaryotes (cells with a membrane-enclosed nucleus), these constitute the three primary branches of the tree of life.	Cell_Biology_Alberts. Prokaryotes (cells without a distinct nucleus) are biochemically the most diverse organisms and include species that can obtain all their energy and nutrients from inorganic chemical sources, such as the reactive mixtures of minerals released at hydrothermal vents on the ocean floor—the sort of diet that may have nourished the first living cells 3.5 billion years ago. DNA sequence comparisons reveal the family relationships of living organisms and show that the prokaryotes fall into two groups that diverged early in the course of evolution: the bacteria (or eubacteria) and the archaea. Together with the eukaryotes (cells with a membrane-enclosed nucleus), these constitute the three primary branches of the tree of life.
Cell_Biology_Alberts_114	Cell_Biology_Alberts	Most bacteria and archaea are small unicellular organisms with compact genomes comprising 1000–6000 genes. Many of the genes within a single organism show strong family resemblances in their DNA sequences, implying that they originated from the same ancestral gene through gene duplication and divergence. Family resemblances (homologies) are also clear when gene sequences are compared between different species, and more than 200 gene families have been so highly (A) 4,639,221 nucleotide pairs Escherichia coli K-12 origin of replication terminus of replication (B) Figure 1–24 The genome of E. coli. (A) A cluster of E. coli cells. (B) A diagram of the genome of	Cell_Biology_Alberts. Most bacteria and archaea are small unicellular organisms with compact genomes comprising 1000–6000 genes. Many of the genes within a single organism show strong family resemblances in their DNA sequences, implying that they originated from the same ancestral gene through gene duplication and divergence. Family resemblances (homologies) are also clear when gene sequences are compared between different species, and more than 200 gene families have been so highly (A) 4,639,221 nucleotide pairs Escherichia coli K-12 origin of replication terminus of replication (B) Figure 1–24 The genome of E. coli. (A) A cluster of E. coli cells. (B) A diagram of the genome of
Cell_Biology_Alberts_115	Cell_Biology_Alberts	E. coli strain k-12. The diagram is circular because the dnA of E. coli, like that of other prokaryotes, forms a single, closed loop. Protein-coding genes are shown as yellow or orange bars, depending on the dnA strand from which they are transcribed; genes encoding only RnA molecules are indicated by green arrows. some genes are transcribed from one strand of the dnA double helix (in a clockwise direction in this diagram), others from the other strand (counterclockwise). (A, courtesy of dr. Tony Brain and david Parker/Photo Researchers; B, adapted from F.R. Blattner et al., Science 277:1453–1462, 1997.) conserved that they can be recognized as common to most species from all three domains of the living world. Thus, given the DNA sequence of a newly discovered gene, it is often possible to deduce the gene’s function from the known function of a homologous gene in an intensively studied model organism, such as the bacterium E. coli.	Cell_Biology_Alberts. E. coli strain k-12. The diagram is circular because the dnA of E. coli, like that of other prokaryotes, forms a single, closed loop. Protein-coding genes are shown as yellow or orange bars, depending on the dnA strand from which they are transcribed; genes encoding only RnA molecules are indicated by green arrows. some genes are transcribed from one strand of the dnA double helix (in a clockwise direction in this diagram), others from the other strand (counterclockwise). (A, courtesy of dr. Tony Brain and david Parker/Photo Researchers; B, adapted from F.R. Blattner et al., Science 277:1453–1462, 1997.) conserved that they can be recognized as common to most species from all three domains of the living world. Thus, given the DNA sequence of a newly discovered gene, it is often possible to deduce the gene’s function from the known function of a homologous gene in an intensively studied model organism, such as the bacterium E. coli.
Cell_Biology_Alberts_116	Cell_Biology_Alberts	E. coli. Eukaryotic cells, in general, are bigger and more elaborate than prokaryotic cells, and their genomes are bigger and more elaborate, too. The greater size is accompanied by radical differences in cell structure and function. Moreover, many classes of eukaryotic cells form multicellular organisms that attain levels of complexity unmatched by any prokaryote.	Cell_Biology_Alberts. E. coli. Eukaryotic cells, in general, are bigger and more elaborate than prokaryotic cells, and their genomes are bigger and more elaborate, too. The greater size is accompanied by radical differences in cell structure and function. Moreover, many classes of eukaryotic cells form multicellular organisms that attain levels of complexity unmatched by any prokaryote.
Cell_Biology_Alberts_117	Cell_Biology_Alberts	Because they are so complex, eukaryotes confront molecular biologists with a special set of challenges that will concern us in the rest of this book. Increasingly, biologists attempt to meet these challenges through the analysis and manipulation of the genetic information within cells and organisms. It is therefore important at the outset to know something of the special features of the eukaryotic genome. We begin by briefly discussing how eukaryotic cells are organized, how this reflects their way of life, and how their genomes differ from those of prokaryotes. This leads us to an outline of the strategy by which cell biologists, by exploiting genetic and biochemical information, are attempting to discover how eukaryotic organisms work. eukaryotic cells may have originated as Predators	Cell_Biology_Alberts. Because they are so complex, eukaryotes confront molecular biologists with a special set of challenges that will concern us in the rest of this book. Increasingly, biologists attempt to meet these challenges through the analysis and manipulation of the genetic information within cells and organisms. It is therefore important at the outset to know something of the special features of the eukaryotic genome. We begin by briefly discussing how eukaryotic cells are organized, how this reflects their way of life, and how their genomes differ from those of prokaryotes. This leads us to an outline of the strategy by which cell biologists, by exploiting genetic and biochemical information, are attempting to discover how eukaryotic organisms work. eukaryotic cells may have originated as Predators
Cell_Biology_Alberts_118	Cell_Biology_Alberts	By definition, eukaryotic cells keep their DNA in an internal compartment called the nucleus. The nuclear envelope, a double layer of membrane, surrounds the nucleus and separates the DNA from the cytoplasm. Eukaryotes also have other features that set them apart from prokaryotes (Figure 1–25). Their cells are, typically, 10 times bigger in linear dimension and 1000 times larger in volume. They have an elaborate cytoskeleton—a system of protein filaments crisscrossing the cytoplasm and forming, together with the many proteins that attach to them, a system of girders, ropes, and motors that gives the cell mechanical strength, controls its shape, and drives and guides its movements (Movie 1.1). And the nuclear envelope is only one part of a set of internal membranes, each structurally similar to the plasma membrane and enclosing different types of spaces inside the cell, many of them involved in digestion and secretion. Lacking the tough cell wall of most bacteria, animal cells and the	Cell_Biology_Alberts. By definition, eukaryotic cells keep their DNA in an internal compartment called the nucleus. The nuclear envelope, a double layer of membrane, surrounds the nucleus and separates the DNA from the cytoplasm. Eukaryotes also have other features that set them apart from prokaryotes (Figure 1–25). Their cells are, typically, 10 times bigger in linear dimension and 1000 times larger in volume. They have an elaborate cytoskeleton—a system of protein filaments crisscrossing the cytoplasm and forming, together with the many proteins that attach to them, a system of girders, ropes, and motors that gives the cell mechanical strength, controls its shape, and drives and guides its movements (Movie 1.1). And the nuclear envelope is only one part of a set of internal membranes, each structurally similar to the plasma membrane and enclosing different types of spaces inside the cell, many of them involved in digestion and secretion. Lacking the tough cell wall of most bacteria, animal cells and the
Cell_Biology_Alberts_119	Cell_Biology_Alberts	to the plasma membrane and enclosing different types of spaces inside the cell, many of them involved in digestion and secretion. Lacking the tough cell wall of most bacteria, animal cells and the free-living eukaryotic cells called protozoa can change their shape rapidly and engulf other cells and small objects by phagocytosis (Figure 1–26).	Cell_Biology_Alberts. to the plasma membrane and enclosing different types of spaces inside the cell, many of them involved in digestion and secretion. Lacking the tough cell wall of most bacteria, animal cells and the free-living eukaryotic cells called protozoa can change their shape rapidly and engulf other cells and small objects by phagocytosis (Figure 1–26).
Cell_Biology_Alberts_120	Cell_Biology_Alberts	How all of the unique properties of eukaryotic cells evolved, and in what sequence, is still a mystery. One plausible view, however, is that they are all reflections of the way of life of a primordial cell that was a predator, living by capturing other cells and eating them (Figure 1–27). Such a way of life requires a large cell with a flexible plasma membrane, as well as an elaborate cytoskeleton to support Figure 1–25 The major features of eukaryotic cells. The drawing depicts a typical animal cell, but almost all the same components are found in plants and fungi as well as in single-celled eukaryotes such as yeasts and protozoa. Plant cells contain chloroplasts in addition to the components shown here, and their plasma membrane is surrounded by a tough external wall formed of cellulose.	Cell_Biology_Alberts. How all of the unique properties of eukaryotic cells evolved, and in what sequence, is still a mystery. One plausible view, however, is that they are all reflections of the way of life of a primordial cell that was a predator, living by capturing other cells and eating them (Figure 1–27). Such a way of life requires a large cell with a flexible plasma membrane, as well as an elaborate cytoskeleton to support Figure 1–25 The major features of eukaryotic cells. The drawing depicts a typical animal cell, but almost all the same components are found in plants and fungi as well as in single-celled eukaryotes such as yeasts and protozoa. Plant cells contain chloroplasts in addition to the components shown here, and their plasma membrane is surrounded by a tough external wall formed of cellulose.
Cell_Biology_Alberts_121	Cell_Biology_Alberts	and move this membrane. It may also require that the cell’s long, fragile DNA molecules be sequestered in a separate nuclear compartment, to protect the genome from damage by the movements of the cytoskeleton.	Cell_Biology_Alberts. and move this membrane. It may also require that the cell’s long, fragile DNA molecules be sequestered in a separate nuclear compartment, to protect the genome from damage by the movements of the cytoskeleton.
Cell_Biology_Alberts_122	Cell_Biology_Alberts	A predatory way of life helps to explain another feature of eukaryotic cells. All such cells contain (or at one time did contain) mitochondria (Figure 1–28). These small bodies in the cytoplasm, enclosed by a double layer of membrane, take up oxygen and harness energy from the oxidation of food molecules—such as sugars—to produce most of the ATP that powers the cell’s activities. Mitochondria are similar in size to small bacteria, and, like bacteria, they have their own genome in the form of a circular DNA molecule, their own ribosomes that differ from those elsewhere in the eukaryotic cell, and their own transfer RNAs. It is now generally accepted that mitochondria originated from free-living oxygen-metabolizing (aerobic) bacteria that were engulfed by an ancestral cell that could otherwise make no such use of oxygen (that is, was anaerobic). Escaping digestion, these bacteria evolved in symbiosis with the engulfing cell and its progeny, receiving	Cell_Biology_Alberts. A predatory way of life helps to explain another feature of eukaryotic cells. All such cells contain (or at one time did contain) mitochondria (Figure 1–28). These small bodies in the cytoplasm, enclosed by a double layer of membrane, take up oxygen and harness energy from the oxidation of food molecules—such as sugars—to produce most of the ATP that powers the cell’s activities. Mitochondria are similar in size to small bacteria, and, like bacteria, they have their own genome in the form of a circular DNA molecule, their own ribosomes that differ from those elsewhere in the eukaryotic cell, and their own transfer RNAs. It is now generally accepted that mitochondria originated from free-living oxygen-metabolizing (aerobic) bacteria that were engulfed by an ancestral cell that could otherwise make no such use of oxygen (that is, was anaerobic). Escaping digestion, these bacteria evolved in symbiosis with the engulfing cell and its progeny, receiving
Cell_Biology_Alberts_123	Cell_Biology_Alberts	Figure 1–27 A single-celled eukaryote that eats other cells. (A) Didinium is a carnivorous protozoan, belonging to the group known as ciliates. It has a globular body, about 150 μm in diameter, encircled by two fringes of cilia—sinuous, whiplike appendages that beat continually; its front end is flattened except for a single protrusion, rather like a snout. (B) A Didinium engulfing its prey. Didinium normally swims around in the water at high speed by means of the synchronous beating of its cilia. When it encounters a suitable prey (yellow), usually another type of protozoan, it releases numerous small paralyzing darts from its snout region. Then, the Didinium attaches to and devours the other cell by phagocytosis, inverting like a hollow ball to engulf its victim, which can be almost as large as itself. (courtesy of d. Barlow.)	Cell_Biology_Alberts. Figure 1–27 A single-celled eukaryote that eats other cells. (A) Didinium is a carnivorous protozoan, belonging to the group known as ciliates. It has a globular body, about 150 μm in diameter, encircled by two fringes of cilia—sinuous, whiplike appendages that beat continually; its front end is flattened except for a single protrusion, rather like a snout. (B) A Didinium engulfing its prey. Didinium normally swims around in the water at high speed by means of the synchronous beating of its cilia. When it encounters a suitable prey (yellow), usually another type of protozoan, it releases numerous small paralyzing darts from its snout region. Then, the Didinium attaches to and devours the other cell by phagocytosis, inverting like a hollow ball to engulf its victim, which can be almost as large as itself. (courtesy of d. Barlow.)
Cell_Biology_Alberts_124	Cell_Biology_Alberts	Figure 1–26 Phagocytosis. This series of stills from a movie shows a human white blood cell (a neutrophil) engulfing a red blood cell (artificially colored red) that has been treated with an antibody that marks it for destruction (see movie 13.5). (courtesy of stephen e. malawista and Anne de Boisfleury chevance.) shelter and nourishment in return for the power generation they performed for their hosts. This partnership between a primitive anaerobic predator cell and an aerobic bacterial cell is thought to have been established about 1.5 billion years ago, when the Earth’s atmosphere first became rich in oxygen. As indicated in Figure 1–29, recent genomic analyses suggest that the first eukaryotic cells formed after an archaeal cell engulfed an aerobic bacterium. This would explain why all eukaryotic cells today, including those that live as strict anaerobes show clear evidence that they once contained mitochondria.	Cell_Biology_Alberts. Figure 1–26 Phagocytosis. This series of stills from a movie shows a human white blood cell (a neutrophil) engulfing a red blood cell (artificially colored red) that has been treated with an antibody that marks it for destruction (see movie 13.5). (courtesy of stephen e. malawista and Anne de Boisfleury chevance.) shelter and nourishment in return for the power generation they performed for their hosts. This partnership between a primitive anaerobic predator cell and an aerobic bacterial cell is thought to have been established about 1.5 billion years ago, when the Earth’s atmosphere first became rich in oxygen. As indicated in Figure 1–29, recent genomic analyses suggest that the first eukaryotic cells formed after an archaeal cell engulfed an aerobic bacterium. This would explain why all eukaryotic cells today, including those that live as strict anaerobes show clear evidence that they once contained mitochondria.
Cell_Biology_Alberts_125	Cell_Biology_Alberts	Many eukaryotic cells—specifically, those of plants and algae—also contain another class of small membrane-enclosed organelles somewhat similar to mitochondria—the chloroplasts (Figure 1–30). Chloroplasts perform photosynthesis, using the energy of sunlight to synthesize carbohydrates from atmospheric carbon dioxide and water, and deliver the products to the host cell as food. Like mitochondria, chloroplasts have their own genome. They almost certainly originated as symbiotic photosynthetic bacteria, acquired by eukaryotic cells that already possessed mitochondria (Figure 1–31).	Cell_Biology_Alberts. Many eukaryotic cells—specifically, those of plants and algae—also contain another class of small membrane-enclosed organelles somewhat similar to mitochondria—the chloroplasts (Figure 1–30). Chloroplasts perform photosynthesis, using the energy of sunlight to synthesize carbohydrates from atmospheric carbon dioxide and water, and deliver the products to the host cell as food. Like mitochondria, chloroplasts have their own genome. They almost certainly originated as symbiotic photosynthetic bacteria, acquired by eukaryotic cells that already possessed mitochondria (Figure 1–31).
Cell_Biology_Alberts_126	Cell_Biology_Alberts	A eukaryotic cell equipped with chloroplasts has no need to chase after other cells as prey; it is nourished by the captive chloroplasts it has inherited from its ancestors. Correspondingly, plant cells, although they possess the cytoskeletal equipment for movement, have lost the ability to change shape rapidly and to engulf other cells by phagocytosis. Instead, they create around themselves a tough, protective cell wall. If the first eukaryotic cells were predators on other organisms, we can view plant cells as cells that have made the transition from hunting to farming. Fungi represent yet another eukaryotic way of life. Fungal cells, like animal cells, possess mitochondria but not chloroplasts; but in contrast with animal cells and protozoa, they have a tough outer wall that limits their ability to move rapidly Figure 1–28 A mitochondrion. (A) A cross section, as seen in the electron microscope.	Cell_Biology_Alberts. A eukaryotic cell equipped with chloroplasts has no need to chase after other cells as prey; it is nourished by the captive chloroplasts it has inherited from its ancestors. Correspondingly, plant cells, although they possess the cytoskeletal equipment for movement, have lost the ability to change shape rapidly and to engulf other cells by phagocytosis. Instead, they create around themselves a tough, protective cell wall. If the first eukaryotic cells were predators on other organisms, we can view plant cells as cells that have made the transition from hunting to farming. Fungi represent yet another eukaryotic way of life. Fungal cells, like animal cells, possess mitochondria but not chloroplasts; but in contrast with animal cells and protozoa, they have a tough outer wall that limits their ability to move rapidly Figure 1–28 A mitochondrion. (A) A cross section, as seen in the electron microscope.
Cell_Biology_Alberts_127	Cell_Biology_Alberts	Figure 1–28 A mitochondrion. (A) A cross section, as seen in the electron microscope. (B) A drawing of a mitochondrion with part of it cut away to show the three-dimensional structure (Movie 1.2). (c) A schematic eukaryotic cell, with the interior space of a mitochondrion, containing the mitochondrial dnA and ribosomes, colored. note the smooth outer membrane and the convoluted inner membrane, which houses the proteins that generate ATP from the oxidation of food molecules. (A, courtesy of daniel s. Friend.) Figure 1–29 The origin of mitochondria. archaeon) is thought to have engulfed the bacterial ancestor of mitochondria, initiating a symbiotic relationship. clear evidence of a dual bacterial and archaeal inheritance can be discerned today in the genomes of all eukaryotes.	Cell_Biology_Alberts. Figure 1–28 A mitochondrion. (A) A cross section, as seen in the electron microscope. (B) A drawing of a mitochondrion with part of it cut away to show the three-dimensional structure (Movie 1.2). (c) A schematic eukaryotic cell, with the interior space of a mitochondrion, containing the mitochondrial dnA and ribosomes, colored. note the smooth outer membrane and the convoluted inner membrane, which houses the proteins that generate ATP from the oxidation of food molecules. (A, courtesy of daniel s. Friend.) Figure 1–29 The origin of mitochondria. archaeon) is thought to have engulfed the bacterial ancestor of mitochondria, initiating a symbiotic relationship. clear evidence of a dual bacterial and archaeal inheritance can be discerned today in the genomes of all eukaryotes.
Cell_Biology_Alberts_128	Cell_Biology_Alberts	or to swallow up other cells. Fungi, it seems, have turned from hunters into scavengers: other cells secrete nutrient molecules or release them upon death, and fungi feed on these leavings—performing whatever digestion is necessary extracellularly, by secreting digestive enzymes to the exterior.	Cell_Biology_Alberts. or to swallow up other cells. Fungi, it seems, have turned from hunters into scavengers: other cells secrete nutrient molecules or release them upon death, and fungi feed on these leavings—performing whatever digestion is necessary extracellularly, by secreting digestive enzymes to the exterior.
Cell_Biology_Alberts_129	Cell_Biology_Alberts	The genetic information of eukaryotic cells has a hybrid origin—from the ancestral anaerobic archaeal cell, and from the bacteria that it adopted as symbionts. Most of this information is stored in the nucleus, but a small amount remains inside the mitochondria and, for plant and algal cells, in the chloroplasts. When mitochondrial DNA and the chloroplast DNA are separated from the nuclear DNA and individually analyzed and sequenced, the mitochondrial and chloroplast genomes are found to be degenerate, cut-down versions of the corresponding bacterial genomes. In a human cell, for example, the mitochondrial genome consists of only 16,569 nucleotide pairs, and codes for only 13 proteins, 2 ribosomal RNA components, and 22 transfer RNAs.	Cell_Biology_Alberts. The genetic information of eukaryotic cells has a hybrid origin—from the ancestral anaerobic archaeal cell, and from the bacteria that it adopted as symbionts. Most of this information is stored in the nucleus, but a small amount remains inside the mitochondria and, for plant and algal cells, in the chloroplasts. When mitochondrial DNA and the chloroplast DNA are separated from the nuclear DNA and individually analyzed and sequenced, the mitochondrial and chloroplast genomes are found to be degenerate, cut-down versions of the corresponding bacterial genomes. In a human cell, for example, the mitochondrial genome consists of only 16,569 nucleotide pairs, and codes for only 13 proteins, 2 ribosomal RNA components, and 22 transfer RNAs.
Cell_Biology_Alberts_130	Cell_Biology_Alberts	Figure 1–30 Chloroplasts. These organelles capture the energy of sunlight in plant cells and some single-celled eukaryotes. (A) A single cell isolated from a leaf of a flowering plant, seen in the light microscope, showing the green chloroplasts (Movie 1.3 and see movie 14.9). (B) A drawing of one of the chloroplasts, showing the highly folded system of internal membranes containing the chlorophyll molecules by which light is absorbed. (A, courtesy of Preeti dahiya.) early eukaryotic cell eukaryotic cell capable of photosynthesis	Cell_Biology_Alberts. Figure 1–30 Chloroplasts. These organelles capture the energy of sunlight in plant cells and some single-celled eukaryotes. (A) A single cell isolated from a leaf of a flowering plant, seen in the light microscope, showing the green chloroplasts (Movie 1.3 and see movie 14.9). (B) A drawing of one of the chloroplasts, showing the highly folded system of internal membranes containing the chlorophyll molecules by which light is absorbed. (A, courtesy of Preeti dahiya.) early eukaryotic cell eukaryotic cell capable of photosynthesis
Cell_Biology_Alberts_131	Cell_Biology_Alberts	Many of the genes that are missing from the mitochondria and chloroplasts have not been lost; instead, they have moved from the symbiont genome into the DNA of the host cell nucleus. The nuclear DNA of humans contains many genes coding for proteins that serve essential functions inside the mitochondria; in plants, the nuclear DNA also contains many genes specifying proteins required in chloroplasts. In both cases, the DNA sequences of these nuclear genes show clear evidence of their origin from the bacterial ancestor of the respective organelle.	Cell_Biology_Alberts. Many of the genes that are missing from the mitochondria and chloroplasts have not been lost; instead, they have moved from the symbiont genome into the DNA of the host cell nucleus. The nuclear DNA of humans contains many genes coding for proteins that serve essential functions inside the mitochondria; in plants, the nuclear DNA also contains many genes specifying proteins required in chloroplasts. In both cases, the DNA sequences of these nuclear genes show clear evidence of their origin from the bacterial ancestor of the respective organelle.
Cell_Biology_Alberts_132	Cell_Biology_Alberts	Natural selection has evidently favored mitochondria with small genomes. By contrast, the nuclear genomes of most eukaryotes seem to have been free to enlarge. Perhaps the eukaryotic way of life has made large size an advantage: predators typically need to be bigger than their prey, and cell size generally increases in proportion to genome size. Whatever the reason, aided by a massive accumulation of DNA segments derived from parasitic transposable elements (discussed in Chapter 5), the genomes of most eukaryotes have become orders of magnitude larger than those of bacteria and archaea (Figure 1–32). The freedom to be extravagant with DNA has had profound implications. Eukaryotes not only have more genes than prokaryotes; they also have vastly more DNA that does not code for protein. The human genome contains 1000 times as many nucleotide pairs as the genome of a typical bacterium, perhaps 10 times as Figure 1–31 The origin of chloroplasts.	Cell_Biology_Alberts. Natural selection has evidently favored mitochondria with small genomes. By contrast, the nuclear genomes of most eukaryotes seem to have been free to enlarge. Perhaps the eukaryotic way of life has made large size an advantage: predators typically need to be bigger than their prey, and cell size generally increases in proportion to genome size. Whatever the reason, aided by a massive accumulation of DNA segments derived from parasitic transposable elements (discussed in Chapter 5), the genomes of most eukaryotes have become orders of magnitude larger than those of bacteria and archaea (Figure 1–32). The freedom to be extravagant with DNA has had profound implications. Eukaryotes not only have more genes than prokaryotes; they also have vastly more DNA that does not code for protein. The human genome contains 1000 times as many nucleotide pairs as the genome of a typical bacterium, perhaps 10 times as Figure 1–31 The origin of chloroplasts.
Cell_Biology_Alberts_133	Cell_Biology_Alberts	Figure 1–31 The origin of chloroplasts. An early eukaryotic cell, already possessing mitochondria, engulfed a photosynthetic bacterium (a cyanobacterium) and retained it in symbiosis. Present-day chloroplasts are thought to trace their ancestry back to a single species of cyanobacterium that was adopted as an internal symbiont (an endosymbiont) over a billion years ago. Figure 1–32 Genome sizes compared. Genome size is measured in nucleotide pairs of dnA per haploid genome, that is, per single copy of the genome. (The cells of sexually reproducing organisms such as ourselves are generally diploid: they contain two copies of the genome, one inherited from the mother, the other from the father.) closely related organisms can vary widely in the quantity of dnA in their genomes, even though they contain similar numbers of functionally distinct genes. (data from	Cell_Biology_Alberts. Figure 1–31 The origin of chloroplasts. An early eukaryotic cell, already possessing mitochondria, engulfed a photosynthetic bacterium (a cyanobacterium) and retained it in symbiosis. Present-day chloroplasts are thought to trace their ancestry back to a single species of cyanobacterium that was adopted as an internal symbiont (an endosymbiont) over a billion years ago. Figure 1–32 Genome sizes compared. Genome size is measured in nucleotide pairs of dnA per haploid genome, that is, per single copy of the genome. (The cells of sexually reproducing organisms such as ourselves are generally diploid: they contain two copies of the genome, one inherited from the mother, the other from the father.) closely related organisms can vary widely in the quantity of dnA in their genomes, even though they contain similar numbers of functionally distinct genes. (data from
Cell_Biology_Alberts_134	Cell_Biology_Alberts	W.h. li, molecular evolution, pp. 380–383. sunderland, mA: sinauer, 1997.) many genes, and a great deal more noncoding DNA (~98.5% of the genome for a human does not code for proteins, as opposed to 11% of the genome for the bacterium E. coli). The estimated genome sizes and gene numbers for some eukaryotes are compiled for easy comparison with E. coli in Table 1–2; we shall discuss how each of these eukaryotes serves as a model organism shortly.	Cell_Biology_Alberts. W.h. li, molecular evolution, pp. 380–383. sunderland, mA: sinauer, 1997.) many genes, and a great deal more noncoding DNA (~98.5% of the genome for a human does not code for proteins, as opposed to 11% of the genome for the bacterium E. coli). The estimated genome sizes and gene numbers for some eukaryotes are compiled for easy comparison with E. coli in Table 1–2; we shall discuss how each of these eukaryotes serves as a model organism shortly.
Cell_Biology_Alberts_135	Cell_Biology_Alberts	Much of our noncoding DNA is almost certainly dispensable junk, retained like a mass of old papers because, when there is little pressure to keep an archive small, it is easier to retain everything than to sort out the valuable information and discard the rest. Certain exceptional eukaryotic species, such as the puffer fish, bear witness to the profligacy of their relatives; they have somehow managed to rid themselves of large quantities of noncoding DNA. Yet they appear similar in structure, behavior, and fitness to related species that have vastly more such DNA (see Figure 4–71).	Cell_Biology_Alberts. Much of our noncoding DNA is almost certainly dispensable junk, retained like a mass of old papers because, when there is little pressure to keep an archive small, it is easier to retain everything than to sort out the valuable information and discard the rest. Certain exceptional eukaryotic species, such as the puffer fish, bear witness to the profligacy of their relatives; they have somehow managed to rid themselves of large quantities of noncoding DNA. Yet they appear similar in structure, behavior, and fitness to related species that have vastly more such DNA (see Figure 4–71).
Cell_Biology_Alberts_136	Cell_Biology_Alberts	Even in compact eukaryotic genomes such as that of puffer fish, there is more noncoding DNA than coding DNA, and at least some of the noncoding DNA certainly has important functions. In particular, it regulates the expression of adjacent genes. With this regulatory DNA, eukaryotes have evolved distinctive ways of controlling when and where a gene is brought into play. This sophisticated gene regulation is crucial for the formation of complex multicellular organisms. The Genome defines the Program of multicellular development The cells in an individual animal or plant are extraordinarily varied. Fat cells, skin cells, bone cells, nerve cells—they seem as dissimilar as any cells could be (Figure 1–33). Yet all these cell types are the descendants of a single fertilized egg cell, and all (with minor exceptions) contain identical copies of the genome of the species.	Cell_Biology_Alberts. Even in compact eukaryotic genomes such as that of puffer fish, there is more noncoding DNA than coding DNA, and at least some of the noncoding DNA certainly has important functions. In particular, it regulates the expression of adjacent genes. With this regulatory DNA, eukaryotes have evolved distinctive ways of controlling when and where a gene is brought into play. This sophisticated gene regulation is crucial for the formation of complex multicellular organisms. The Genome defines the Program of multicellular development The cells in an individual animal or plant are extraordinarily varied. Fat cells, skin cells, bone cells, nerve cells—they seem as dissimilar as any cells could be (Figure 1–33). Yet all these cell types are the descendants of a single fertilized egg cell, and all (with minor exceptions) contain identical copies of the genome of the species.
Cell_Biology_Alberts_137	Cell_Biology_Alberts	The differences result from the way in which the cells make selective use of their genetic instructions according to the cues they get from their surroundings in the developing embryo. The DNA is not just a shopping list specifying the molecules that every cell must have, and the cell is not an assembly of all the items on the list. Rather, the cell behaves as a multipurpose machine, with sensors to receive environmental signals and with highly developed abilities to call different sets of genes into action according to the sequences of signals to which the cell has been exposed. The genome in each cell is big enough to accommodate the Figure 1–33 Cell types can vary enormously in size and shape. An animal nerve cell is compared here with a neutrophil, a type of white blood cell. Both are drawn to scale. information that specifies an entire multicellular organism, but in any individual cell only part of that information is used.	Cell_Biology_Alberts. The differences result from the way in which the cells make selective use of their genetic instructions according to the cues they get from their surroundings in the developing embryo. The DNA is not just a shopping list specifying the molecules that every cell must have, and the cell is not an assembly of all the items on the list. Rather, the cell behaves as a multipurpose machine, with sensors to receive environmental signals and with highly developed abilities to call different sets of genes into action according to the sequences of signals to which the cell has been exposed. The genome in each cell is big enough to accommodate the Figure 1–33 Cell types can vary enormously in size and shape. An animal nerve cell is compared here with a neutrophil, a type of white blood cell. Both are drawn to scale. information that specifies an entire multicellular organism, but in any individual cell only part of that information is used.
Cell_Biology_Alberts_138	Cell_Biology_Alberts	information that specifies an entire multicellular organism, but in any individual cell only part of that information is used. A large number of genes in the eukaryotic genome code for proteins that regulate the activities of other genes. Most of these transcription regulators act by binding, directly or indirectly, to the regulatory DNA adjacent to the genes that are to be controlled, or by interfering with the abilities of other proteins to do so. The expanded genome of eukaryotes therefore not only specifies the hardware of the cell, but also stores the software that controls how that hardware is used (Figure 1–34).	Cell_Biology_Alberts. information that specifies an entire multicellular organism, but in any individual cell only part of that information is used. A large number of genes in the eukaryotic genome code for proteins that regulate the activities of other genes. Most of these transcription regulators act by binding, directly or indirectly, to the regulatory DNA adjacent to the genes that are to be controlled, or by interfering with the abilities of other proteins to do so. The expanded genome of eukaryotes therefore not only specifies the hardware of the cell, but also stores the software that controls how that hardware is used (Figure 1–34).
Cell_Biology_Alberts_139	Cell_Biology_Alberts	Cells do not just passively receive signals; rather, they actively exchange signals with their neighbors. Thus, in a developing multicellular organism, the same control system governs each cell, but with different consequences depending on the messages exchanged. The outcome, astonishingly, is a precisely patterned array of cells in different states, each displaying a character appropriate to its position in the multicellular structure. many eukaryotes live as solitary cells	Cell_Biology_Alberts. Cells do not just passively receive signals; rather, they actively exchange signals with their neighbors. Thus, in a developing multicellular organism, the same control system governs each cell, but with different consequences depending on the messages exchanged. The outcome, astonishingly, is a precisely patterned array of cells in different states, each displaying a character appropriate to its position in the multicellular structure. many eukaryotes live as solitary cells
Cell_Biology_Alberts_140	Cell_Biology_Alberts	many eukaryotes live as solitary cells Many species of eukaryotic cells lead a solitary life—some as hunters (the protozoa), some as photosynthesizers (the unicellular algae), some as scavengers (the unicellular fungi, or yeasts). Figure 1–35 conveys something of the astonishing variety of the single-celled eukaryotes. The anatomy of protozoa, especially, is often elaborate and includes such structures as sensory bristles, photoreceptors, sinuously beating cilia, leglike appendages, mouth parts, stinging darts, and musclelike contractile bundles. Although they are single cells, protozoa can be as intricate, as versatile, and as complex in their behavior as many multicellular organisms (see Figure 1–27, Movie 1.4, and Movie 1.5).	Cell_Biology_Alberts. many eukaryotes live as solitary cells Many species of eukaryotic cells lead a solitary life—some as hunters (the protozoa), some as photosynthesizers (the unicellular algae), some as scavengers (the unicellular fungi, or yeasts). Figure 1–35 conveys something of the astonishing variety of the single-celled eukaryotes. The anatomy of protozoa, especially, is often elaborate and includes such structures as sensory bristles, photoreceptors, sinuously beating cilia, leglike appendages, mouth parts, stinging darts, and musclelike contractile bundles. Although they are single cells, protozoa can be as intricate, as versatile, and as complex in their behavior as many multicellular organisms (see Figure 1–27, Movie 1.4, and Movie 1.5).
Cell_Biology_Alberts_141	Cell_Biology_Alberts	In terms of their ancestry and DNA sequences, the unicellular eukaryotes are far more diverse than the multicellular animals, plants, and fungi, which arose as three comparatively late branches of the eukaryotic pedigree (see Figure 1–17). As with prokaryotes, humans have tended to neglect them because they are microscopic. Only now, with the help of genome analysis, are we beginning to understand their positions in the tree of life, and to put into context the glimpses these strange creatures can offer us of our distant evolutionary past. A yeast serves as a minimal model eukaryote The molecular and genetic complexity of eukaryotes is daunting. Even more than for prokaryotes, biologists need to concentrate their limited resources on a few selected model organisms to unravel this complexity. Figure 1–34 Genetic control of the program of multicellular development.	Cell_Biology_Alberts. In terms of their ancestry and DNA sequences, the unicellular eukaryotes are far more diverse than the multicellular animals, plants, and fungi, which arose as three comparatively late branches of the eukaryotic pedigree (see Figure 1–17). As with prokaryotes, humans have tended to neglect them because they are microscopic. Only now, with the help of genome analysis, are we beginning to understand their positions in the tree of life, and to put into context the glimpses these strange creatures can offer us of our distant evolutionary past. A yeast serves as a minimal model eukaryote The molecular and genetic complexity of eukaryotes is daunting. Even more than for prokaryotes, biologists need to concentrate their limited resources on a few selected model organisms to unravel this complexity. Figure 1–34 Genetic control of the program of multicellular development.
Cell_Biology_Alberts_142	Cell_Biology_Alberts	Figure 1–34 Genetic control of the program of multicellular development. The role of a regulatory gene is demonstrated in the snapdragon Antirrhinum. In this example, a mutation in a single gene coding for a regulatory protein causes leafy shoots to develop in place of flowers: because a regulatory protein has been changed, the cells adopt characters that would be appropriate to a different location in the normal plant. The mutant is on the left, the normal plant on the right. (courtesy of enrico coen and Rosemary carpenter.) To analyze the internal workings of the eukaryotic cell without the additional problems of multicellular development, it makes sense to use a species that is unicellular and as simple as possible. The popular choice for this role of minimal model eukaryote has been the yeast Saccharomyces cerevisiae (Figure 1–36)—the same species that is used by brewers of beer and bakers of bread.	Cell_Biology_Alberts. Figure 1–34 Genetic control of the program of multicellular development. The role of a regulatory gene is demonstrated in the snapdragon Antirrhinum. In this example, a mutation in a single gene coding for a regulatory protein causes leafy shoots to develop in place of flowers: because a regulatory protein has been changed, the cells adopt characters that would be appropriate to a different location in the normal plant. The mutant is on the left, the normal plant on the right. (courtesy of enrico coen and Rosemary carpenter.) To analyze the internal workings of the eukaryotic cell without the additional problems of multicellular development, it makes sense to use a species that is unicellular and as simple as possible. The popular choice for this role of minimal model eukaryote has been the yeast Saccharomyces cerevisiae (Figure 1–36)—the same species that is used by brewers of beer and bakers of bread.
Cell_Biology_Alberts_143	Cell_Biology_Alberts	S. cerevisiae is a small, single-celled member of the kingdom of fungi and thus, according to modern views, is at least as closely related to animals as it is to plants. It is robust and easy to grow in a simple nutrient medium. Like other fungi, it has a tough cell wall, is relatively immobile, and possesses mitochondria but not chloroplasts. When nutrients are plentiful, it grows and divides almost as rapidly as a bacterium. It can reproduce either vegetatively (that is, by simple cell division), or sexually: two yeast cells that are haploid (possessing a single copy of the genome) can fuse to create a cell that is diploid (containing a double genome); and the diploid cell can undergo meiosis (a reduction division) to produce cells that are once again haploid (Figure 1–37). In contrast with higher plants and animals, the yeast can divide indefinitely in either the haploid or the diploid state, and the process leading from one state to the other can be induced at will by changing the	Cell_Biology_Alberts. S. cerevisiae is a small, single-celled member of the kingdom of fungi and thus, according to modern views, is at least as closely related to animals as it is to plants. It is robust and easy to grow in a simple nutrient medium. Like other fungi, it has a tough cell wall, is relatively immobile, and possesses mitochondria but not chloroplasts. When nutrients are plentiful, it grows and divides almost as rapidly as a bacterium. It can reproduce either vegetatively (that is, by simple cell division), or sexually: two yeast cells that are haploid (possessing a single copy of the genome) can fuse to create a cell that is diploid (containing a double genome); and the diploid cell can undergo meiosis (a reduction division) to produce cells that are once again haploid (Figure 1–37). In contrast with higher plants and animals, the yeast can divide indefinitely in either the haploid or the diploid state, and the process leading from one state to the other can be induced at will by changing the
Cell_Biology_Alberts_144	Cell_Biology_Alberts	higher plants and animals, the yeast can divide indefinitely in either the haploid or the diploid state, and the process leading from one state to the other can be induced at will by changing the growth conditions.	Cell_Biology_Alberts. higher plants and animals, the yeast can divide indefinitely in either the haploid or the diploid state, and the process leading from one state to the other can be induced at will by changing the growth conditions.
Cell_Biology_Alberts_145	Cell_Biology_Alberts	In addition to these features, the yeast has a further property that makes it a convenient organism for genetic studies: its genome, by eukaryotic standards, is exceptionally small. Nevertheless, it suffices for all the basic tasks that every eukaryotic cell must perform. Mutants are available for essentially every gene, Figure 1–35 An assortment of protozoa: a small sample of an extremely diverse class of organisms. The drawings are done to different scales, but in each case the scale bar represents 10 μm. The organisms in (A), (c), and (G) are ciliates; is a heliozoan; (d) is an amoeba; is a dinoflagellate; and (F) is a euglenoid. (From m.A. sleigh, Biology of Protozoa. cambridge, uk: cambridge university Press, 1973.)	Cell_Biology_Alberts. In addition to these features, the yeast has a further property that makes it a convenient organism for genetic studies: its genome, by eukaryotic standards, is exceptionally small. Nevertheless, it suffices for all the basic tasks that every eukaryotic cell must perform. Mutants are available for essentially every gene, Figure 1–35 An assortment of protozoa: a small sample of an extremely diverse class of organisms. The drawings are done to different scales, but in each case the scale bar represents 10 μm. The organisms in (A), (c), and (G) are ciliates; is a heliozoan; (d) is an amoeba; is a dinoflagellate; and (F) is a euglenoid. (From m.A. sleigh, Biology of Protozoa. cambridge, uk: cambridge university Press, 1973.)
Cell_Biology_Alberts_146	Cell_Biology_Alberts	Figure 1–36 The yeast Saccharomyces cerevisiae. (A) A scanning electron micrograph of a cluster of the cells. This species is also known as budding yeast; it proliferates by forming a protrusion or bud that enlarges and then separates from the rest of the original cell. many cells with buds are visible in this micrograph. (B) A transmission electron micrograph of a cross section of a yeast cell, showing its nucleus, mitochondrion, and thick cell wall. (A, courtesy of Ira herskowitz and eric schabatach.) Figure 1–37 The reproductive cycles of the yeast S. cerevisiae.	Cell_Biology_Alberts. Figure 1–36 The yeast Saccharomyces cerevisiae. (A) A scanning electron micrograph of a cluster of the cells. This species is also known as budding yeast; it proliferates by forming a protrusion or bud that enlarges and then separates from the rest of the original cell. many cells with buds are visible in this micrograph. (B) A transmission electron micrograph of a cross section of a yeast cell, showing its nucleus, mitochondrion, and thick cell wall. (A, courtesy of Ira herskowitz and eric schabatach.) Figure 1–37 The reproductive cycles of the yeast S. cerevisiae.
Cell_Biology_Alberts_147	Cell_Biology_Alberts	Figure 1–37 The reproductive cycles of the yeast S. cerevisiae. depending on environmental conditions and on details of the genotype, cells of this species can exist in either a diploid (2n) state, with a double chromosome set, or a haploid (n) state, with a single chromosome set. The diploid form can either proliferate by ordinary cell-division cycles or undergo meiosis to produce haploid cells. The haploid form can either proliferate by ordinary cell-division cycles or undergo sexual fusion with another haploid cell to become diploid. meiosis is triggered by starvation and gives rise to spores—haploid cells in a dormant state, resistant to harsh environmental conditions.	Cell_Biology_Alberts. Figure 1–37 The reproductive cycles of the yeast S. cerevisiae. depending on environmental conditions and on details of the genotype, cells of this species can exist in either a diploid (2n) state, with a double chromosome set, or a haploid (n) state, with a single chromosome set. The diploid form can either proliferate by ordinary cell-division cycles or undergo meiosis to produce haploid cells. The haploid form can either proliferate by ordinary cell-division cycles or undergo sexual fusion with another haploid cell to become diploid. meiosis is triggered by starvation and gives rise to spores—haploid cells in a dormant state, resistant to harsh environmental conditions.
Cell_Biology_Alberts_148	Cell_Biology_Alberts	and studies on yeasts (using both S. cerevisiae and other species) have provided a key to many crucial processes, including the eukaryotic cell-division cycle—the critical chain of events by which the nucleus and all the other components of a cell are duplicated and parceled out to create two daughter cells from one. The control system that governs this process has been so well conserved over the course of evolution that many of its components can function interchangeably in yeast and human cells: if a mutant yeast lacking an essential yeast cell-division-cycle gene is supplied with a copy of the homologous cell-division-cycle gene from a human, the yeast is cured of its defect and becomes able to divide normally. The expression levels of All the Genes of An organism can Be monitored simultaneously	Cell_Biology_Alberts. and studies on yeasts (using both S. cerevisiae and other species) have provided a key to many crucial processes, including the eukaryotic cell-division cycle—the critical chain of events by which the nucleus and all the other components of a cell are duplicated and parceled out to create two daughter cells from one. The control system that governs this process has been so well conserved over the course of evolution that many of its components can function interchangeably in yeast and human cells: if a mutant yeast lacking an essential yeast cell-division-cycle gene is supplied with a copy of the homologous cell-division-cycle gene from a human, the yeast is cured of its defect and becomes able to divide normally. The expression levels of All the Genes of An organism can Be monitored simultaneously
Cell_Biology_Alberts_149	Cell_Biology_Alberts	The expression levels of All the Genes of An organism can Be monitored simultaneously The complete genome sequence of S. cerevisiae, determined in 1997, consists of approximately 13,117,000 nucleotide pairs, including the small contribution (78,520 nucleotide pairs) of the mitochondrial DNA. This total is only about 2.5 times as much DNA as there is in E. coli, and it codes for only 1.5 times as many distinct proteins (about 6600 in all). The way of life of S. cerevisiae is similar in many ways to that of a bacterium, and it seems that this yeast has likewise been subject to selection pressures that have kept its genome compact.	Cell_Biology_Alberts. The expression levels of All the Genes of An organism can Be monitored simultaneously The complete genome sequence of S. cerevisiae, determined in 1997, consists of approximately 13,117,000 nucleotide pairs, including the small contribution (78,520 nucleotide pairs) of the mitochondrial DNA. This total is only about 2.5 times as much DNA as there is in E. coli, and it codes for only 1.5 times as many distinct proteins (about 6600 in all). The way of life of S. cerevisiae is similar in many ways to that of a bacterium, and it seems that this yeast has likewise been subject to selection pressures that have kept its genome compact.