Molecular Biology of the Cell

Last updated Feb 18, 2023

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• CiteKey:: albertsMolecularBiologyCell2022
• Type:: book
• Author:: Bruce Alberts Rebecca Heald Alexander Johnson David Morgan Martin Raff Keith Roberts Peter Walter John Wilson Tim Hunt
• Editor::
• Publisher:: W. W. Norton & Company
• Series::
• Series Number::
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• Volume::
• Issue::
• Pages:: 1552
• Year:: 2022
• DOI::
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• ISBN:: 978-0-393-88482-1
• Format:: PDF

Abstract

The definitive text in cell biology now with the Digital Problems Book in Smartwork   For more than four decades, Molecular Biology of the Cell has distilled the vast amount of scientific knowledge to illuminate basic principles, enduring concepts, and cutting-edge research. The Seventh Edition has been extensively revised and updated with the latest research, and has been thoroughly vetted by experts and instructors. The classic companion text, The Problems Book, has been reimagined as the Digital Problems Book in Smartwork, an interactive digital assessment course with a wide selection of questions and automatic-grading functionality. The digital format with embedded animations and dynamic question types makes the Digital Problems Book in Smartwork easier to assign than ever before―for both in-person and online classes.

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Alberts, B., Heald, R., Johnson, A., Morgan, D., Raff, M., Roberts, K., Walter, P., Wilson, J., & Hunt, T. (2022). Molecular Biology of the Cell (Seventh edition). W. W. Norton & Company. ^bib

• A textbook provides what open-ended Internet searches cannot—a curation of knowledge and an expert, accurate guide to the beauty and complexities of cells. Page 6
• The surface of our planet is populated by living things—organisms—curious, intricately organized chemical factories that take in matter from their surroundings and use these raw materials to generate copies of themselves. Page 40 ^ff4ee0
• All living things are made of cells: small, membrane-enclosed units filled with a concentrated aqueous solution of chemicals and endowed with the extraordinary ability to create copies of themselves by growing and then dividing in two. Page 40
• Because cells are the fundamental units of life, it is to cell biology—the study of the structure, function, and behavior of cells—that we must look for answers to the questions of what life is and how it works. Page 40
• The pioneering cell biologist E. B. Wilson, “the key to every biological problem must finally be sought in the cell; for every living organism is, or at some time has been, a cell.” Page 40
• The whole of biology is thus a counterpoint between two themes: astonishing variety in individual particulars and astonishing constancy in fundamental mechanisms. Page 40
• Viruses are now recognized to be the most abundant biological entities on the planet. Page 41
• The parent organism hands down information specifying, in extraordinary detail, the characteristics that the offspring will have. This phenomenon of heredity is central to the definition of life: it distinguishes life from other processes Page 41
• A living organism must consume free energy to exist, as does a candle flame. But life employs this free energy to drive a very complex system of chemical reactions that create and maintain the intricate organization of its cells, all as specified by the hereditary information in those cells. Page 41
• Most living organisms are single cells. Others, such as us, are like vast multicellular cities in which groups of cells perform specialized functions that are linked by intricate systems of intercellular communication. Page 41
• But even for the aggregate of more than 1013 cells that makes up a human body, the whole organism has been generated by cell divisions from a single cell. The single cell therefore contains all of the hereditary information that defines a species Page 41
• The cell must also contain all of the machinery needed to gather raw materials from the environment and to construct from them a new cell in its own image, complete with a new copy of the hereditary information of its parent Page 41
• All Cells Store Their Hereditary Information in the Form of Double-Strand DNA Molecules Page 41
• Living cells, like computers, store information, and it is estimated that they have been evolving and diversifying for more than 3.5 billion years. One might not expect that they would all store their information in the same form or that the hereditary information carried by one type of cell should be readable by the information-handling machinery of another. And yet it is so. This fact provides compelling evidence that all living things on Earth have inherited the form of their genetic instructions, as well as how to use them, from a universal common ancestral cell. Page 41
• All cells on Earth today store their hereditary information in the form of double-strand molecules of DNA—long, unbranched, paired polymer chains, which are always composed of the same four types of monomers. These monomers, chemical compounds known as nucleotides, have nicknames drawn from a four-letter alphabet—A, T, C, G—and they are strung together in a long linear sequence that encodes the hereditary information Page 42
• We can take a piece of DNA from a human cell and insert it into a bacterium or a piece of bacterial DNA and insert it into a human cell, and, with only a few minor modifications, the information will be successfully read, interpreted, and copied. Page 42
• scientists can now rapidly read out the sequence of nucleotides in any DNA molecule and thereby determine the complete DNA sequence of any cell’s genome—the totality of its hereditary information embodied in the linear sequence of nucleotides in its DNA. Page 42
• All Cells Replicate Their Hereditary Information by Templated Polymerization Page 42
• Each monomer in a single DNA strand—that is, each nucleotide—consists of two parts: a sugar (deoxyribose) with a phosphate group attached to it, and a base Page 42
• Figure 1–1 The hereditary information in the fertilized egg cell determines the nature of the whole multicellular organism that will develop from it. As indicated, although their starting cells look superficially similar, the egg of a sea urchin gives rise to a sea urchin (A and B), the egg of a mouse gives rise to a mouse (C and D), and the egg of the seaweed Fucus gives rise to a Fucus seaweed (E and F). Page 42
• Figure 1–2 DNA and its building blocks. (A) DNA is made from simple subunits, called nucleotides. Each nucleotide consists of a specific arrangement of about 35 covalently linked atoms, forming a sugar–phosphate molecule with a nitrogencontaining side group, or base, attached to it. The bases are of four types (adenine, guanine, cytosine, and thymine), corresponding to four distinct nucleotides, labeled A, G, C, and T. (B) A single strand of DNA consists of nucleotides joined together by sugar–phosphate linkages. Note that the individual sugar–phosphate units are asymmetric, giving the backbone of the strand a definite directionality, or polarity. This directionality guides the molecular processes by which the information in DNA is both interpreted and copied (replicated) in cells: the information is always “read” in a consistent order, just as written English text is read from left to right. (C) Through templated polymerization, the sequence of nucleotides in an existing DNA strand controls the sequence in which nucleotides are joined together in a new DNA strand; T in one strand pairs with A in the other, and G in one strand with C in the other. The new strand therefore has a nucleotide sequence complementary to that of the old strand and a backbone with opposite directionality: thus, GTAA… in the original strand, is …TTAC in the new strand. (D) A normal DNA molecule consists of two such complementary strands. The nucleotides within each strand are linked by strong (covalent) chemical bonds; the complementary nucleotides on opposite strands are held together more weakly, by hydrogen bonds. (E) The two strands twist around each other to form a double helix—a robust structure that can accommodate any sequence of nucleotides without altering its basic double-helical structure Page 43
• DNA is the information store for heredity, and templated polymerization is the way in which this information is copied throughout the living world. Page 44
• All Cells Transcribe Portions of Their DNA into RNA Molecules Page 44
• To carry out its information-bearing function, DNA must do more than copy itself. It must also express its information, by letting the information guide the synthesis of other molecules in the cell. This expression occurs by a mechanism that is the same in all living organisms, leading first and foremost to the production of two other crucial classes of biological polymers: RNA molecules and protein molecules. The process begins with a templated polymerization called transcription, in which segments of the DNA sequence are used as templates for the synthesis of shorter molecules of the closely related polymer ribonucleic acid, or RNA. Subsequently, in a process called translation, many of these RNA molecules direct the synthesis of polymers of a radically different chemical class—the proteins Page 44
• The backbone of an RNA molecule is formed by a slightly different sugar from that in DNA—ribose instead of deoxyribose; in addition, one of the four bases is slightly different—uracil (U) replaces thymine (T). Most important, however, the other three bases—A, C, and G—are identical to those in DNA, and all four bases will pair with their complementary counterparts in DNA—the A, U, C, and G of RNA with the T, A, G, and C of DNA, respectively. Page 44
• The same segment of DNA can be used repeatedly to guide the synthesis of many identical RNA molecules Page 44
• RNA transcripts are mass-produced and disposable. Most of these transcripts function as intermediates in the transfer of genetic information by serving as messenger RNA (mRNA) molecules that guide the synthesis of proteins according to the genetic instructions stored in the DNA. Page 44
• Figure 1–3 The copying of genetic information by DNA replication. In this process, the two strands of a DNA double helix are pulled apart, and each serves as a template for the synthesis of a new complementary strand. The end result is two daughter DNA double helices that are identical in sequence to the parent double helix. Page 44
• Figure 1–4 From DNA to protein. In addition to DNA replication (shown at the top of the figure), genetic information is read out and put to use through a two-step process: First, in transcription, segments of the DNA sequence are used to guide the synthesis of molecules of RNA. Then, in translation, RNA molecules are used to guide the synthesis of proteins, which are polymers made of amino acid subunits (discussed shortly). Page 44
• All Cells Use Proteins as Catalysts Page 45
• Like DNA and RNA molecules, protein molecules are long unbranched polymer chains Page 45
• Like DNA and RNA, proteins carry information in the form of a linear sequence of subunits Page 45
• The subunits of proteins are the amino acids, which are quite different from the nucleotides of DNA and RNA, and there are 20 types instead of 4. Page 45
• Each protein molecule is a polypeptide chain that is created by joining its amino acids in a particular sequence; this sequence determines how the polypeptide folds up, giving the protein its unique three-dimensional structure. Through several billion years of evolution, these sequences have been selected to give each protein a useful function. Page 45
• Proteins, above all, are the main molecules that put the cell’s genetic information into action. Thus, polynucleotides (DNA and mRNAs) specify the amino acid sequences of proteins. Proteins, in turn, serve as catalysts to cause many different chemical reactions to occur, including those that synthesize new DNA and RNA molecules. Page 45
• In everyday speech, a catalyst refers to “any agent that provokes or speeds significant change or action.” But in chemistry, the term catalyst is defined more narrowly, being applied to any molecule that speeds up a specific chemical reaction without itself being changed. Page 45
• From the most fundamental point of view, a living cell is a self-replicating collection of catalysts that takes in food, processes this food to provide both the building blocks and energy needed to make more catalysts, and discards the materials left over as waste Page 45
• All Cells Translate RNA into Protein in the Same Way Page 45
• Figure 1–5 Life as an autocatalytic process. (A) The living cell is a selfreplicating collection of catalysts. (B) Life can be viewed as an autocatalytic process. DNA and RNA molecules provide the nucleotide sequence information (green arrows) that is used both to produce proteins and to copy themselves. Proteins, in turn, provide the catalytic activity (red arrows) needed to synthesize DNA, RNA, and proteins themselves. Together, these feedback loops create the self-replicating system that endows cells with the ability to reproduce. Although the great majority of the catalysts in the cell are proteins (known as enzymes), a few RNA molecules (known as ribozymes) also have this property, Page 45
• The translation of genetic information from the 4-letter alphabet of polynucleotides into the 20-letter alphabet of proteins is a complex process. The rules of this translation seem in some respects neat and rational but in other respects strangely arbitrary, given that they are (with minor exceptions) identical in all living things. These arbitrary features, it is thought, reflect frozen accidents in the early history of life. They stem from the chance properties of the earliest organisms that were passed on by heredity and have become so deeply embedded in the constitution of all living cells that they cannot be changed without disastrous consequences Page 46
• the information in the sequence of a messenger RNA (mRNA) molecule is read out in groups of three nucleotides at a time: each triplet of nucleotides, or codon, specifies (codes for, or encodes) a single amino acid in a corresponding protein. Because the number of distinct triplets that can be formed from four nucleotides is 43, there are 64 possible codons, all of which occur in nature. However, there are only 20 naturally occurring amino acids, which means there are necessarily many cases in which several codons correspond to the same amino acid. This genetic code is read out by a special class of small RNA molecules, called transfer RNAs (tRNAs). Each type of tRNA becomes attached at one end to a specific amino acid and displays at its other end a specific sequence of three nucleotides—an anticodon—that enables it to recognize, through base-pairing, a particular codon or subset of codons in mRNA. The intricate chemistry that enables these tRNAs to translate a specific sequence of A, C, G, and U nucleotides in an mRNA molecule into a specific sequence of amino acids in a protein molecule occurs on a ribosome, a large multimolecular machine composed of both protein and ribosomal RNA. Page 46
• Each Protein Is Encoded by a Specific Gene Page 46
• Special sequences in the DNA serve as punctuation, defining where the information for each RNA and protein begins and ends. And individual segments of the long DNA sequence are transcribed into separate mRNA molecules, coding for different proteins. Each such DNA segment represents one gene. Page 46
• A gene therefore is defined as the segment of DNA sequence corresponding either to a single protein (but sometimes to a set of closely related, alternative protein variants) or to a single catalytic, regulatory, or structural RNA molecule Page 46
• In all cells, the expression of individual genes is regulated Page 46
• the genome of the cell dictates not only the nature of the cell’s proteins but also when and where they are to be made. Page 46
• Life Requires a Continual Input of Free Energy Page 46
• A living cell is a dynamic chemical system, operating far from chemical equilibrium. For a cell to grow or to make a new cell in its own image, it must take in free energy from the environment, as well as raw materials, to drive the necessary synthetic reactions. This consumption of free energy is fundamental to life. When this energy is not available, a cell decays toward chemical equilibrium and soon dies Page 46
• free energy must be spent for the creation of order.
  To replicate its genetic information faithfully, and indeed to make all its complex molecules according to the correct specifications, the cell therefore requires free energy Page 47
• All Cells Function as Biochemical Factories Page 47
• Although all cells function as biochemical factories of a broadly similar type, many of the details of their small-molecule transactions differ. Page 47
• All Cells Are Enclosed in a Plasma Membrane Across Which Nutrients and Waste Materials Must Pass Page 47
• Without a plasma membrane, the cell could not maintain its integrity as a coordinated chemical system. Page 47
• The molecules that form cell membranes have the simple physicochemical property of being amphiphilic; that is, they consist of one part that is hydrophilic (water-soluble) and another part that is hydrophobic (water-insoluble). Page 47
• Figure 1–6 Behavior of phospholipid molecules in water. (A) A phospholipid molecule is amphiphilic, having a hydrophilic (water-loving) phosphate head group and a hydrophobic (wateravoiding) hydrocarbon tail. (B) At an interface between oil and water, phospholipids arrange themselves as a single sheet (a monolayer), with their head groups facing the water and their tail groups facing the oil. When immersed in water, however, phospholipids aggregate to form lipid bilayers that fold in on themselves to form sealed aqueous compartments known as vesicles. Page 47
• the hydrophobic tails of the predominant lipid molecules in all cells are hydrocarbon polymers (–CH2–CH2–CH2–) Page 48
• cells produce molecules whose chemical properties cause them to self-assemble into the structures that a cell needs. Page 48
• The cell boundary cannot be totally impermeable. If a cell is to grow and reproduce, it must be able to import raw materials and export waste across its plasma membrane. All cells therefore have specialized proteins embedded in their plasma membrane that transport specific molecules from one side to the other. Page 48
• The transport proteins in the plasma membrane largely determine which molecules enter the cell, while the catalytic proteins (enzymes) inside the cell determine the reactions that the entering molecules undergo. Page 48
• Cells Operate at a Microscopic Scale Dominated by Random Thermal Motion Page 48
• even the simplest cell is highly ordered internally Page 48
• random thermal motions of molecules (including water) are prominent at the scale of cells—whose dimensions can be as small as a micrometer (10–6 meters) in diameter. This type of spontaneous movement, called thermal or Brownian motion, was first observed by Robert Brown in 1827 Page 48
• Brownian motion drives a process called diffusion, and it determines the rates of biochemical reactions as molecules collide with one another within the interior of a cell Page 48
• A Living Cell Can Exist with 500 Genes Page 49
• A species that has one of the smallest known genomes is the bacterium Mycoplasma genitalium, which causes a common, sexually transmitted, human disease (Figure 1–8). This organism lives as a parasite in mammals, where the environment provides it with many of the small molecules it needs ready-made. Nevertheless, it still has to make all the large molecules—DNA, RNAs, and proteins. It has 525 genes, most of which are essential. Page 49
• The individual cell is the minimal self-reproducing unit of life. A cell consists of a self-replicating collection of catalysts, enclosed in a plasma membrane. All cells operate as biochemical factories, driven by the free energy released in a complicated network of chemical reactions. Central to a cell’s ability to reproduce is the transmission of its genetic information to its progeny cells when it divides. All cells store their genetic information in double-strand DNA, and the complete sequence of DNA nucleotides for each organism is known as its genome. The cell replicates this information by separating the paired DNA strands and using each as a template for polymerization to make a new DNA strand with a complementary sequence of nucleotide subunits. The same strategy of templated polymerization is used in the transcription of portions of the DNA into molecules of the closely related polynucleotide polymer, RNA. Most of these RNA molecules are mRNAs that in turn guide the synthesis of protein molecules by the process of translation. Proteins are polymers of amino acid subunits and are the catalysts for almost all the cell’s chemical reactions. They are also responsible for the selective import and export of molecules across the plasma membrane that surrounds each cell. The specific shape and function of each protein depend on its amino acid sequence, which is specified by the nucleotide sequence of a corresponding segment of the DNA—the gene that codes for that protein. In this way, the DNA of the cell determines the cell’s chemistry, which is fundamentally similar in all cells, reflecting their ultimate origin from a common ancestor cell that existed on Earth more than 3.5 billion years ago. Page 49
• Figure 1–7 How membrane protrusion is driven by a simple Brownian ratchet. A single actin filament is shown abutting the plasma membrane, which is fluctuating back and forth because of random thermal motions. When the membrane happens to move away from the end of the filament, it creates sufficient space for an additional subunit, which quickly adds on. The slightly longer filament acts as a ratchet and prevents the membrane from moving back to its original position. In a migrating animal cell, this Brownian ratchet process drives protrusion of the membrane and contributes to forward movement of the cell Page 49
• Figure 1–8 The small bacterium Mycoplasma genitalium. It is viewed here in cross section in an electron microscope, which uses a beam of electrons instead of light to create an image with a resolution that is many times higher than that of an image viewed in a conventional light microscope. Of the 525 genes this bacterium contains, 43 code for transfer RNAs, ribosomal RNAs, and other nonprotein-coding RNAs. Of the 482 protein-coding genes, 154 are involved in replication, transcription, translation, and related processes involving DNA, RNA, and protein; 98 are involved in the membrane and surface structures of the cell; 46 are involved in the transport of nutrients and other molecules across the plasma membrane; and 71 are involved in energy conversion and the synthesis and degradation of small molecules. (Courtesy of Roger Cole, in Medical Page 49
• The Tree of Life Has Three Major Domains: Eukaryotes, Bacteria, and Archaea Page 50
• For constructing a comprehensive tree of life, it is necessary to begin with a segment of DNA that is easily recognized in the genomes of all organisms. Page 51
• Ribosomes are fundamentally similar in all organisms, and an especially well-conserved component of them is the RNA molecules that make up their core. Page 51
• Although the exact sequence of these ribosomal RNAs (rRNAs) differs across organisms, they are similar enough to use them as a ruler to judge how closely two species are related: the more similar the ribosomal RNA sequences, the more recently the two species diverged from a common ancestor and the more related they must be. Page 51
• Figure 1–9 A global tree of life, based on genome comparisons, shows the three major divisions (domains) of the living world. The lengths of the branches are proportional to differences among genomes using common genes that can be recognized and compared across many different species. Some of the organisms discussed in this and later chapters are indicated. Of the three domains of life (bacteria, archaea, and eukaryotes), bacteria encompass by far the greatest diversity, commensurate with their ability to colonize nearly every ecological niche on the planet. So many new bacterial species are currently being identified through DNA sequencing of environmental samples that simply naming them has become a challenge. Although eukaryotes (and especially animals) are the main focus of this book, they comprise only a small slice of the global diversity Page 51
• Eukaryotes Make Up the Domain of Life That Is Most Familiar to Us Page 52
• The great variety of living creatures that we see around us are eukaryotes. The name is from the Greek, meaning “truly nucleated” (from the words eu, “well” or “truly,” and karyon, “kernel” or “nucleus”), reflecting the fact that the cells of these organisms have their DNA enclosed in a membrane-bound organelle called the nucleus. Page 52
• The genomes of eukaryotes also tend to run much larger—containing more than 20,000 genes for humans and corals, for example, compared with 4000–6000 genes for the typical bacteria or archaea. Page 52
• In addition to plants and animals, the eukaryotes include fungi (such as mushrooms or the yeasts used in beerand bread-making), as well as an astonishing variety of single-celled, microscopic forms of life. Page 52
• On the Basis of Genome Analysis, Bacteria Are the Most Diverse Group of Organisms on the Planet Page 52
• Figure 1–10 Shapes and sizes of some bacteria. Although most are small, as shown, measuring a few micrometers in linear dimension, there are also some giant species. An extreme example is the cigar-shaped bacterium Epulopiscium fishelsoni, which lives in the gut of a surgeonfish and can be up to 600 μm long Page 52
• Figure 1–11 Bacterial structure. (A) A drawing of the bacterium Vibrio cholerae, showing its simple internal organization. This species can infect the human small intestine to cause cholera; the severe diarrhea that accompanies this disease kills more than 100,000 people a year worldwide. Like many other bacteria, Vibrio has a helical appendage at one end—a flagellum—that rotates as a propeller to drive the cell forward. (B) An electron micrograph of a longitudinal section through the widely studied bacterium Escherichia coli (E. coli). E. coli is part of our normal intestinal microbiota, the complete collection of microbes in our gut. It has many flagella distributed over its surface, but they are not visible in this section. Both of the bacteria shown here are Gram negative, having both an outer and an inner (plasma) membrane. However, many bacterial species lack the outer membrane; these are classified as Gram positive. Page 53
• Figure 1–12 Photosynthetic bacteria. (A) A light micrograph of the bacterium Anabaena cylindrica. Its cells form long chains, in which most of the cells (labeled V) perform photosynthesis (and thereby capture CO2 and incorporate C into organic compounds); others (labeled H) become specialized for fixing N from N2; and still others (labeled S) develop into spores, which can resist unfavorable conditions. (B) An electron micrograph of a related photosynthetic bacterium, Phormidium laminosum, which shows the intracellular membranes where photosynthesis occurs. As shown in these micrographs, some prokaryotes have intracellular membranes and form colonies that resemble simple multicellular organisms. Page 53
• Archaea: The Most Mysterious Domain of Life Page 54
• Of the three domains of life, archaea remains the most poorly understood. Most of its members have been identified only by DNA sequencing of samples from the environment, and relatively few have been cultured and studied up close in the laboratory Page 54
• Like bacteria, the archaea we know most about are small and lack the internal, membrane-bound organelles that distinguish the eukaryotes. But they differ from bacteria in many ways, including the chemistry of their cell walls, the kinds of lipids that make up their membrane, and the range of biochemical reactions that they can carry out. Another surprising conclusion came from genome comparisons: although archaea resemble bacteria in their outward appearances, their genomes are much more closely related to eukaryotes than to bacteria Page 54
• At first it was thought that archaea occupied only extreme environments such as volcanoes, salt lakes, acid hot springs, and the stomachs of cattle, but they are now recognized to be present also in more congenial surroundings such as soils, seawater, and our skin. Commensurate with the wide variety of ecological niches in which they have been found, different species of archaea have highly diverse chemistries. They are believed to be the predominant life-form in soil and seawater, and they play major roles in recycling nitrogen and carbon, two of the most important elements for all cells. Page 54
• Organisms inhabit nearly all of the planet, and we continue to discover new habitats. Page 54
• The human biomass is 10 times greater than that of all measurable wild animals together, and—while human biomass continues to increase—that of wild animals is falling, largely as a result of human activities. Page 54
• Cells Can Be Powered by a Wide Variety of Free-Energy Sources Page 54
• Organisms obtain the free energy needed for life in different ways. Some—such as animals, fungi, and the many different bacteria that live in the human gut— get it by feeding on other living things or the organic chemicals they produce; such organisms are called organotrophic Page 54
• Figure 1–13 The bacterium Beggiatoa. It lives in sulfurous environments (for example, see Figure 1–15) and gets its energy by oxidizing H2S; it can fix carbon even in the dark. Note the yellow deposits of sulfur inside the cells Page 54
• Figure 1–14 The distribution of living biomass on Earth. The total biomass on Earth expressed as gigatons of carbon (Gt C) is estimated to be ∼550 Gt C. In the graph shown, the area of each taxon represented is proportional to the taxon’s global biomass, so plants account for about 80% (450/550) of the total biomass, whereas animals account for 0.4% (2/550). These recent estimates are based on various advanced techniques, including DNA sequencing and remote sensing. Page 54
• Others derive their free energy directly from the nonliving world. These primary energy converters fall into two classes: those that harvest the energy of sunlight, and those that capture their energy from energy-rich systems of inorganic chemicals in the environment (chemical systems that are far from chemical equilibrium). Organisms of the former class are called phototrophic (feeding on sunlight); those of the latter are called lithotrophic (feeding on rock). Page 55
• Figure 1–15 The geology of a hot hydrothermal vent in the ocean floor. As indicated, seawater percolates down toward the hot, molten, volcanic rock upwelling (basalt) from Earth’s interior and is heated and driven back upward, carrying a mixture of minerals leached from the hot rock. A temperature gradient is set up, from more than 350°C near the core of the vent, down to 2–3°C in the surrounding ocean. Minerals precipitate from the water as it cools, forming a chimney. Different classes of organisms, thriving at different temperatures, live in different neighborhoods of the chimney. A typical chimney might be a few meters tall, spewing out hot, mineral-rich water. The locations of lithotrophic bacteria and the invertebrate marine animals that depend on them are also shown Page 55
• Some Cells Fix Nitrogen and Carbon Dioxide for Other Cells Page 56
• DNA, RNA, and protein are composed of just six elements: hydrogen, carbon, nitrogen, oxygen, sulfur, and phosphorus Page 56
• Figure 1–16 Organisms living at a depth of 2500 meters near a vent in the ocean floor. Close to the vent, at temperatures up to about 120°C, various lithotrophic species of bacteria and archaea live, directly fueled by geochemical energy. A little further away, where the temperature is lower, various invertebrate animals live by feeding on these microorganisms. Most remarkable are the giant (2-meter-long) tube worms, Riftia pachyptila, which are shown in the photograph. Rather than feed on the lithotrophic microbes, these worms live in symbiosis with them: specialized organs in the worms harbor huge numbers of symbiotic sulfur-oxidizing bacteria, which harness geochemical energy and supply nourishment to their hosts, which have no mouth, gut, or anus. The tube worms are thought to have evolved from more conventional animals and to have become secondarily adapted to life at hydrothermal vents. Page 56
• Genomes Diversify Over Evolutionary Time, Producing New Types of Organisms Page 57
• In storing and copying genetic information, random accidents and errors occur, altering the nucleotide sequence; that is, creating mutations. Therefore, when a cell divides, the genomes of its two daughters are often not quite identical to each other or to that of the parent cell. On rare occasions, the error may represent a change for the better; more probably, it will cause no significant difference in the cell’s prospects. But in some cases, the error will cause serious damage; for example, by disrupting the coding sequence for a key protein or RNA molecule. Changes due to mistakes of the first type will tend to be perpetuated, because the altered cell has an increased likelihood of surviving and reproducing itself. Changes due to mistakes of the second type—neutral changes—may be perpetuated or not: in the competition for limited resources, it is a matter of chance whether the altered cell or its cousins will succeed. But changes that cause serious damage lead nowhere: the cell that suffers them dies, leaving no progeny. Page 57
• Some parts of the genome will change more readily than others in the course of evolution. A segment of DNA that does not code for protein or RNA and has no significant regulatory role is free to change at a rate limited only by the frequency of random errors. In contrast, a gene that codes for a highly optimized, essential protein or RNA molecule cannot alter so easily: when mistakes occur, the faulty cells are almost always disabled and eliminated. Genes of this latter sort are therefore highly conserved. Through 3.5 billion years or more of evolutionary history, many DNA sequences have changed beyond all recognition, but the most highly conserved genes remain perfectly recognizable in all living species. Page 57
• The ribosomal RNA genes are exceptional in being so well conserved, whereas most parts of genomes have diversified much more dramatically over evolutionary time Page 57
• Figure 1–17 Genetic information conserved since the days of the last universal common ancestor of all living things. A part of the gene that codes for the smaller of the two main ribosomal RNA (rRNA) molecules in the ribosome is shown. (The complete molecule is about 1500–1900 nucleotides long, depending on the species.) Corresponding segments of nucleotide sequences from an archaeon (Methanococcus jannaschii), a bacterium (Escherichia coli), and a eukaryote (Homo sapiens) are aligned. The red vertical lines indicate sites where the nucleotides are identical between the species; the human sequence is repeated at the bottom of the alignment so that all three two-way comparisons can be seen. The black dot halfway along the E. coli sequence denotes a site where a nucleotide has been either deleted from the bacterial lineage in the course of evolution or inserted in the other two lineages. Note that the sequences from these three organisms, representative of the three domains of the living world, still retain unmistakable similarities. Page 57
• New Genes Are Generated from Preexisting Genes Page 58
• Figure 1–18 Four modes of genetic innovation and their effects on the DNA sequence of an organism. A special form of horizontal transfer occurs when cells of two different species enter into a permanent symbiotic association; genes from one of the cells may subsequently be transferred to the genome of the other, as we will see later when we discuss the likely evolutionary origins of mitochondria and chloroplasts. Page 58
• Gene Duplications Give Rise to Families of Related Genes Within a Single Genome Page 59
• A cell duplicates its entire genome each time it divides into two daughter cells. However, accidents occasionally result in the inappropriate duplication of just part of the genome, with retention of both the original and duplicate segments in a single cell. Once a gene has been duplicated in this way (see mode 2 in Figure 1–18), the two gene copies can acquire mutations and become specialized to perform different functions within the same cell and its descendants. Repeated rounds of this process of gene duplication and divergence, over many millions of years, have enabled one gene to give rise to a family of related genes within a single genome. Page 59
• Genes that are related by descent in this way—that is, genes in two separate species that derive from the same ancestral gene in the last common ancestor of those two species—are called orthologs. Related genes that have resulted from a gene duplication event within a single genome—and are likely to have diverged in their function—are called paralogs. Genes that are related by descent in either way are called homologs, a general term used to cover both types of relationship Page 59
• The Function of a Gene Can Often Be Deduced from Its Nucleotide Sequence Page 59
• Family relationships among genes are important not just for their evolutionary interest, but also because they simplify the task of deciphering gene functions. Page 59
• Figure 1–19 Families of evolutionarily related genes in the genome of Bacillus subtilis. The largest gene family in this bacterium consists of 77 genes coding for varieties of a class of membrane transport proteins called ABC transporters, which are found in all three domains of the living world Page 59
• More Than 200 Gene Families Are Common to All Three Domains of Life MBoC7 m1.21/1.20 Page 60
• Figure 1–20 Two types of gene homology based on different evolutionary pathways. (A) Orthologs. (B) Paralogs. Genes related by either mechanism are called homologs Page 60
• Many of the genes within a single organism or species 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 conserved that they can be recognized as common to most species from all three domains of the living world, suggesting they were present in the ancestral cell from which all life evolved. Given the DNA sequence of a newly discovered gene in any organism, it is therefore often possible to deduce the gene’s function from the known function of a homologous gene in a better-studied organism Page 61
• Eukaryotic Cells Contain a Variety of Organelles Page 62
• By definition, eukaryotic cells keep almost all their DNA in a membrane-enclosed internal compartment—the nucleus, which is usually the most conspicuous organelle (Figure 1–21). The long DNA polymers in the nucleus are packaged with proteins to form chromosomes, which only become visible in a light microscope when they condense in preparation for cell division. The nuclear envelope, a double layer of membrane, surrounds the nucleus and separates the nuclear DNA from the cytoplasm, which, in a eukaryotic cell, includes everything between the plasma membrane and the nucleus. As shown in the figure, the nuclear envelope is perforated by nuclear pores, which are channels formed by protein complexes that mediate the two-way traffic of large molecules between the nucleus and the cytoplasm. Page 62
• Figure 1–21 The major features of eukaryotic cells. The drawing depicts the major contents of a typical animal cell seen in cross section, but almost all the same components are found in plant cells and fungi, as well as in single-cell eukaryotes. The cytoskeleton (discussed in Chapter 16) consists of three types of protein filaments: actin filaments (red), microtubules (green), and intermediate filaments (blue). Plant cells (not shown) contain chloroplasts in addition to the components shown here; they also have a rigid external cell wall that contains cellulose surrounding their plasma membrane, which means they are largely immobile. The interior of cells is, in reality, much more crowded than depicted in this simplified diagram. Page 62
• Lacking the kind of tough cell wall characteristic of bacteria and archaea, these eukaryotic cells can change their shape rapidly, in some cases enabling them to move and engulf other cells and small objects by a process called phagocytosis Page 63
• There are many other membrane-enclosed organelles in eukaryotic cells. Unlike the nucleus, most of them are enclosed by single membranes. The most extensive organelle is the endoplasmic reticulum (ER), which is where most cell membrane components are made, along with materials destined for secretion to the outside of the cell. The Golgi apparatus receives these molecules from the ER and modifies and packages them for secretion or transport to another cell compartment. Lysosomes are small irregularly shaped organelles in which intracellular digestion occurs. Peroxisomes are small vesicles where hydrogen peroxide is used to inactivate toxic molecules MBoC7 e15.32/1.22 Page 63
• A continual exchange of materials occurs between these single-membraneenclosed organelles, mediated mainly by small transport vesicles that pinch off from the membrane of one organelle and fuse with that of another. To connect the eukaryotic cell with its surroundings, a similar vesicle-mediated exchange goes on continually at the cell surface. Here, portions of the plasma membrane pinch in to form intracellular vesicles that carry material captured from the external medium into the cell—a process called endocytosis; and in the reverse process, called exocytosis, vesicles from inside the cell fuse with the plasma membrane and release their contents to the exterior Page 63
• Besides the nucleus, there are two other eukaryotic cell organelles that are enclosed in double membranes—mitochondria and, in plant cells and algae, chloroplasts. Mitochondria take up oxygen and harness energy from the oxidation of food molecules, such as sugars and fats, to produce most of the ATP (adenosine triphosphate) that powers the cell’s activities. Chloroplasts perform photosynthesis in plant cells and algae, using the energy of sunlight to synthesize carbohydrates from atmospheric CO2 and water, delivering these energy-rich products to the host cell as food. Page 63
• In many eukaryotic cells, roughly half of the cytoplasm is occupied by membrane-enclosed organelles. The surrounding fluid is called the cytosol. It contains ribosomes, which translate RNAs into proteins, and it is also where most of the cell’s other metabolic reactions take place Page 63
• Figure 1–22 Phagocytosis. An electron micrograph of a mammalian phagocytic white blood cell (a neutrophil) ingesting a bacterium that is in the process of dividing. Only the part of the cell that is extending surface protrusions to engulf the bacterium is shown. Page 63
• Figure 1–23 Endocytosis and exocytosis across the plasma membrane. Eukaryotic cells import extracellular materials by endocytosis and secrete intracellular materials by exocytosis. The endocytosed material is first delivered to singlemembrane-enclosed organelles called endosomes Page 63
• Mitochondria Evolved from a Symbiotic Bacterium Captured by an Ancient Archaeon Page 64
• A fundamental question in both evolution and cell biology is how did the first eukaryotic cell arise? The evidence suggests that it happened when an archaeal and a bacterial cell merged about 2 billion years ago, in a world that had contained only prokaryotes for more than 1.5 billion years. Page 64
• All eukaryotic cells contain (or at one time did contain) mitochondria Page 64
• The mitochondria contain their own DNA, with genes that resemble bacterial genes; they also contain their own ribosomes and translation factors that resemble those in bacteria. These and other similarities between mitochondria and present-day bacteria provide strong evidence that mitochondria evolved from an aerobic bacterium (one that harvested energy by combining electrons derived from foodstuffs with oxygen gas) Page 64
• Figure 1–24 Membrane-enclosed organelles are distributed throughout the eukaryotic cell cytoplasm. The membrane-enclosed organelles, shown in different colors, are each specialized to perform a different function. The cytoplasm that fills the space outside of these organelles is called the cytosol. Page 64
• Figure 1–25 A mitochondrion. (A) An electron micrograph of the organelle seen in cross section. (B) A drawing of a mitochondrion with part of it cut away to show the three-dimensional structure Page 64
• These two cells (and their descendants) were then able to evolve an endosymbiotic relationship, providing mutual metabolic support within a common cytoplasm. Page 64
• There are also good reasons to believe that the ancestral capturing cell was an archaeon. As we have seen, the genomes of present-day archaea encode many proteins that are characteristic of present-day eukaryotic cells. Those archaea with the most eukaryotic-like genes belong to the Asgard lineage, first identified by sequencing DNA fragments obtained from the seabed. But no living example had been seen or cultivated—until very recently, when, after a heroic 12-yearlong isolation procedure, the first Asgard archaeon was propagated in culture. This remarkable, living, anaerobic archaeon looked like no other prokaryote— having long branching protrusions—and it seemed to live in an ectosymbiotic relationship with another bacterium and another archaeon, both of which were isolated with it Page 65
• Chloroplasts Evolved from a Symbiotic Photosynthetic Bacterium Engulfed by an Ancient Eukaryotic Cell Page 65
• Chloroplasts (Figure 1–28) perform photosynthesis in plant cells and algae, using the energy of sunlight to synthesize their own “food” (in the form of carbohydrates) from atmospheric CO2 and water. Like mitochondria, they are enclosed in double membranes, have their own “circular” genomes, and reproduce by dividing. They almost certainly evolved from a symbiotic photosynthetic bacterium that was captured by an ancient eukaryotic cell that already possessed mitochondria. This bacterium may have been captured by phagocytosis, a frequent process in eukaryotes Page 65
• Figure 1–26 A scanning electron micrograph of an Asgard archaeon in culture. This anaerobic cell proliferates very slowly, doubling only about every 20 days (compared to every half hour or so for the bacterium E. coli). It can be seen to extend elaborate membranous protrusions from its surface—including “blebs” and unique branched and unbranched structures. These protrusions are intimately associated with two other species—one bacterial, one archaeal—that were isolated with the Asgard strain as ectosymbionts, as indicated. The scientists had maintained the deep marine sediment under anaerobic conditions in a bioreactor for more than 2000 days, mimicking conditions of the seabed, and they attempted to culture samples from this bioreactor under a range of different conditions. Only after many years and repeated subculturing were they able to isolate this archaeon with its ectosymbionts. Page 65
• Figure 1–27 A possible model for some early steps in eukaryotic cell evolution. In this model, the surface protrusions of an ancient Asgard archaeon expanded and surrounded an ectosymbiotic aerobic bacterium to create a symbiotic relationship between the two types of cells. Eventually, the protrusions fused with one another, trapping the bacterium as an endosymbiont in the archaeon cytoplasm, where it was initially enclosed by an internal membrane derived from the archaeon’s plasma membrane (the bacterium itself retaining its own membranes). At some point, the endosymbiont escaped from the enclosing archaeon-derived membrane and entered the cytosol, where it eventually evolved into a mitochondrion—with both its DNA and membranes derived from the engulfed bacterium. As shown, it is postulated that the internal archaeon membranes generated by this mechanism of protrusion expansion and fusion progressively formed both the nucleus and single-membraneenclosed organelles, such as the endoplasmic reticulum Page 65
• If some eukaryotic cells can be viewed as hunters, then one might view plant cells as having given up hunting for farming. Page 66
• Fungi represent yet another eukaryotic way of life. Fungal cells, like animal cells, possess mitochondria but not chloroplasts; they have a tough outer wall that limits their ability to move rapidly or to take up other cells. Fungi, it seems, have turned from hunters into scavengers. Other cells secrete nutrient molecules or release them after death, and fungi feed on these leavings—often performing whatever digestion is necessary extracellularly, by secreting digestive enzymes to the exterior. Page 66
• Eukaryotes Have Hybrid Genomes Page 66
• the genetic information of eukaryotic cells has a hybrid origin— from an ancestral anaerobic archaeon and from the bacteria it adopted as endosymbionts Page 66
• Figure 1–28 Chloroplasts. In plant cells and single-celled photosynthetic eukaryotes, these organelles capture the energy of sunlight. (A) A light micrograph of a single cell isolated from a leaf of a flowering plant, showing the green chloroplasts (Movie 1.3 and see Movie 14.10). (B) A drawing of one chloroplast, showing the highly folded system of internal membranes containing the chlorophyll molecules that absorb light. Page 66
• Figure 1–29 A model for the evolution of eukaryotic cells in the tree of life. All living cells are thought to have evolved from an ancestral prokaryotic cell (the last universal common ancestor) between 3.5 and 3.8 billion years ago). Many millions of years later, it seems an anaerobic archaeon acquired an aerobic bacterial symbiont, which evolved into mitochondria (see Figure 1–27). Later still, a mitochondria-containing eukaryotic cell acquired a photosynthetic bacterium, which evolved into chloroplasts. Mitochondria are essentially the same in plants, animals, and fungi, indicating that they were acquired before these three lineages diverged about 1.5 billion years ago. Page 66
• When the mitochondrial DNA and the chloroplast DNA are separated from the nuclear DNA and individually sequenced, both the mitochondrial and chloroplast genomes are found to be cut-down versions of the corresponding bacterial genomes Page 67
• Many of the genes that are missing from the mitochondria and chloroplasts have not been lost; instead, they have moved from the endosymbiont genomes into the DNA of the host-cell nucleus. Thus the nuclear DNA of animals contains many genes coding for proteins that serve essential functions inside the mitochondria; in plants and algae, the nuclear DNA contains many genes specifying proteins required in chloroplasts. In both cases, the DNA sequences of these nuclear genes still show clear evidence of their bacterial origins. Page 67
• Eukaryotic Genomes Are Big Page 67
• 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: predatory cells, for example, typically need to be bigger than their prey, and cell size generally increases in proportion to genome size. Whatever the reason, the genomes of most eukaryotes have become hundreds of times larger than those of bacteria and archaea Page 67
• 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 or RNA. The human genome contains about 700 times as many nucleotide pairs as the genome of a typical bacterium such as E. coli, but it contains only about 4.5 times as many protein-coding genes because a much greater proportion of the human genome does not code for protein (∼98.5% compared to 11% in E. coli). Page 67
• Eukaryotic Genomes Are Rich in Regulatory DNA Page 67
• much of our nonprotein-coding DNA is almost certainly dispensable “junk,” retained during evolution like a mass of old papers because, when there is little pressure to keep an archive small, it is easier to retain Page 67
• Figure 1–30 Genome sizes compared. Genome size is measured in nucleotide (base) pairs of DNA per haploid genome, that is, per single copy of the genome. (The body cells of sexually reproducing, multicellular organisms such as ourselves are generally diploid: they contain two copies of the genome, one inherited from the mother, the other from the father.) Note that closely related organisms can vary widely in the quantity of DNA in their genomes (as indicated by the length of the green bars), even though they contain similar numbers of protein-coding genes. Page 67
• 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 nonprotein-coding DNA, and, yet, they appear similar in structure, behavior, and fitness to related species that have vastly more such DNA. Page 68
• Even in compact eukaryotic genomes such as that of the puffer fish, there is more nonprotein-coding DNA than protein-coding DNA. Page 68
• As in all eukaryotic organisms, at least some of the noncoding DNA certainly has important functions. In particular, it regulates the expression of genes. With this regulatory DNA, eukaryotes have evolved distinctive, highly sophisticated ways of controlling when and where a gene is brought into play. Elaborate mechanisms for gene regulation are especially crucial for the formation and function of complex multicellular organisms, which have many different cell types, each with different functions Page 68
• Eukaryotic Genomes Define the Program of Multicellular Development Page 68
• The cells in an individual animal or plant are extraordinarily varied. Blood cells, skin cells, bone cells, nerve cells—they seem as dissimilar as any cells could be (Figure 1–31). Yet all these cell types are the descendants of a single fertilized egg cell, and all (with very minor exceptions) contain identical copies of the genome of the species. Page 68

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• Figure 1–31 Cell types can vary enormously in size and shape. A human nerve cell is compared here with a human neutrophil, a type of white blood cell. Both are drawn to scale. Page 68
• Figure 1–32 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 the regulator 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. Page 69