Chapter 1: Cells, Genomes, and the Diversity of Life PDF

PA R T I II III IV V INTRODUCTION TO THE CELL CHAPTER Cells,...

PA R T I II III IV V INTRODUCTION TO THE CELL CHAPTER Cells, Genomes, and the Diversity of Life 1 The surface of our planet is populated by living things—organisms—curious, intricately organized chemical factories that take in matter from their sur- IN THIS CHAPTER roundings and use these raw materials to generate copies of themselves. These organisms appear extraordinarily diverse. What could be more different than a The Universal Features of Life tiger and a piece of seaweed or a butterfly and a tree? Yet our ancestors, knowing nothing of cells or DNA, saw that all these things had something in common. on Earth They called that something “life,” marveled at it, struggled to define it, and Genome Diversification and the despaired of explaining what it was or how it worked in terms that relate to non- living matter. Tree of Life The remarkable discoveries of the past 100 years or so have not diminished the marvel—quite the contrary. But they have removed the central mystery regarding Eukaryotes and the Origin of the the nature of life. We can now see that all living things are made of cells: small, Eukaryotic Cell membrane-enclosed units filled with a concentrated aqueous solution of chemi- cals and endowed with the extraordinary ability to create copies of themselves by Model Organisms growing and then dividing in two. 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. With a deeper understand- ing of cells and their evolution, we can begin to tackle the grand historical problems of life on Earth: its mysterious origins, its stunning diversity, and its invasion of every conceivable habitat. Indeed, as emphasized long ago by 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.” Despite their apparent diversity, living things are fundamentally similar inside. The whole of biology is thus a counterpoint between two themes: aston- ishing variety in individual particulars and astonishing constancy in fundamental mechanisms. In this chapter, we begin by outlining the universal features com- mon to all life on our planet, along with some of the fundamental properties of their cells. We then discuss how an analysis of DNA genomes allows scientists to position the wide variety of organisms in an evolutionary “tree of life.” This 1 MBOC7_ptr_ch01_001-048.indd 1 02/12/21 12:53 PM  2 Chapter 1: Cells, Genomes, and the Diversity of Life approach, which quantifies how closely organisms are related to one another, allows us to identify the three major branches of life on Earth, eukaryotes, bacte- ria, and archaea—each with unique qualities. We shall see that the familiar world of plants and animals—the focus of scientists for many centuries—makes up only a small slice of the complete diversity of life, the vast majority of which is invisible to the unaided human eye. After exploring some of the ways that genomes change over evolutionary times, we highlight the handful of model organisms that biologists have chosen to focus on to dissect the molecular mechanisms underlying life. A few specific viruses, including SARS-CoV-2, pose grave threats to humans, so they too have become objects of intensive study. For this reason, this section also includes an introduction to viruses, the ubiquitous parasites that have evolved to feed on cells. Viruses are now recognized to be the most abundant biological entities on the planet. THE UNIVERSAL FEATURES OF LIFE ON EARTH There are more than 2 million described species living on Earth today, but many, many more are yet to be discovered. Each species is different, and each repro- duces itself faithfully, yielding progeny that are unique to that species. Thus, 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, such as the growth of a crystal, or the burning of a candle, or the formation of waves on water, in which structures are generated without the same type of link between the peculiarities of parents and offspring. 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 intri- cate organization of its cells, all as specified by the hereditary information in those cells. Most living organisms are single cells. Others, such as us, are like vast multicel- lular cities in which groups of cells perform specialized functions that are linked by intricate systems of intercellular communication. 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 con- tains all of the hereditary information that defines a species (Figure 1–1). 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. Every cell on Earth is truly amazing. All Cells Store Their Hereditary Information in the Form of Double-Strand DNA Molecules Computers have made us familiar with the concept of information as a measur- able quantity—106 bytes to record a few hundred pages of text or an image from a digital camera, 109 bytes for a 60-minute video streamed from the Internet, and so on. Computers have also made us well aware that the same information can be recorded in many different physical forms: the discs and tapes that we used 25 years ago for our electronic archives have become unreadable on present-day machines. 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 pro- vides 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 com- mon ancestral cell. This ancestor is thought to have existed roughly 3.5–3.8 billion years ago. MBOC7_ptr_ch01_001-048.indd 2 02/12/21 12:53 PM  THE UNIVERSAL FEATURES OF LIFE ON EARTH 3 (A) (C) (E) 100 µm 50 µm 50 µm (B) (D) (F) 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). (A, courtesy of David McClay; B, courtesy of Tim Hunt; C, courtesy of Patricia Calarco, from G. Martin, Science 209:768–776, 1980. With permission from AAAS; D, Rudmer Zwerver/Alamy Stock Photo; E and F, courtesy of Colin Brownlee.) 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 fourMBoC7 of monomers. These mono- types m1.01/1.01 mers, 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, just as the sequence of 1’s and 0’s encodes the information in a computer file. 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. As we describe in Chapter 8, scien- tists 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 nucleo­ tides in its DNA. As a result, we now know the complete genome sequences for tens of thousands of species, ranging from the smallest bacterium to the largest plants and animals on Earth. All Cells Replicate Their Hereditary Information by Templated Polymerization The mechanisms that make life possible depend on the structure of the double-strand DNA molecule. We discuss this remarkable molecule in detail in Chapters 4 and 5; here we provide only an overview of its structure and means of reproduction. 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, which may be either adenine (A), guanine (G), MBOC7_ptr_ch01_001-048.indd 3 02/12/21 12:53 PM  4 Chapter 1: Cells, Genomes, and the Diversity of Life (A) building block of DNA (D) double-strand DNA phosphate sugar + G C T T C C T A G A G sugar– base G phosphate G A A G G A nucleotide T C T C (B) DNA strand sugar–phosphate G T A A C G G T C A backbone hydrogen-bonded base pairs (E) DNA double helix (C) templated polymerization of new strand nucleotide monomers C C A T A C A G A T G G G G T G C C A T T G C A C A G T A A C G G T C A C 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 nitrogen- containing 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 (see Movie 4.1). cytosine (C), or thymine (T) (Figure 1–2). Each sugarm1.02/1.02 MBoC7 is linked to the next via the phosphate group, creating a polymer chain composed of a repetitive sugar– phosphate backbone with a series of bases protruding from it. The DNA polymer is extended by adding monomers at one end. For a single isolated strand, these monomers can, in principle, be added in any order, because each one links to the next in the same way, through the part of the molecule that is the same for all of them. In the living cell, however, DNA is not synthesized as a free strand in isolation, but on a template formed by a preexisting DNA strand. The bases that protrude from this template can bind to bases of the strand being synthe- sized, according to a strict rule defined by the complementary structures of the bases: A binds to T, and C binds to G. This base-pairing holds fresh monomers in place and thereby controls the selection of which one of the four monomers will next be added to a growing strand. In this way, a double-strand structure is created, consisting of two exactly complementary sequences of A’s, C’s, T’s, and G’s. These two strands twist around each other, forming a DNA double helix (see Figure 1–2E). Compared with the covalent sugar–phosphate bonds, the hydrogen bonds between the base pairs are weak, which allows the two DNA strands to be MBOC7_ptr_ch01_001-048.indd 4 02/12/21 12:53 PM  THE UNIVERSAL FEATURES OF LIFE ON EARTH 5 template strand 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 new strand complementary strand. The end result is two daughter DNA double helices that are identical in sequence to the parent new strand double helix. parent DNA double helix template strand pulled apart without breakage of their backbones. Each strand then can serve as a template, in the way just described, for the synthesis of a fresh DNA strand complementary to itself—a fresh copy, that is, of the hereditary information (Figure 1–3). In different types of cells, this process of DNA replication occurs at different rates, with different controls to start it or stop it, and with different MBoC7 m1.03/1.03 auxiliary molecules to help the process along (discussed in Chapters 5 and 17). But the basics are universal: DNA is the information store for heredity, and tem- plated polymerization is the way in which this information is copied throughout the living world. All Cells Transcribe Portions of Their DNA into RNA Molecules 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 mole- DNA cules. The process begins with a templated polymerization called transcription, in which segments of the DNA sequence are used as templates for the synthe- sis of shorter molecules of the closely related polymer ribonucleic acid, or RNA. Subsequently, in a process called translation, many of these RNA molecules DNA synthesis direct the synthesis of polymers of a radically different chemical class—the pro- REPLICATION DNA teins (Figure 1–4). The detailed chemical reactions involved are presented in Chapter 6; here they will only be briefly outlined. 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 RNA synthesis nucleotides TRANSCRIPTION 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 RNA 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. During transcription, this pair- ing allows the RNA monomers to be lined up and selected for polymerization on protein synthesis TRANSLATION a template strand of DNA, just as DNA monomers are selected during replication. The outcome is a single-strand polymer molecule whose sequence of nucleotides PROTEIN faithfully represents a portion of the cell’s genetic information, even though it is written in a slightly different alphabet—consisting of the four RNA monomers amino acids instead of the four DNA monomers. The same segment of DNA can be used repeatedly to guide the synthesis Figure 1–4 From DNA to protein. In addition to DNA replication (shown at the of many identical RNA molecules. Thus, whereas the cell’s archive of genetic top of the figure), genetic information is information in the form of DNA is fixed and sacrosanct, RNA transcripts are read out and put to use through a two-step mass-produced and disposable. Most of these transcripts function as intermedi- process: First, in transcription, segments ates in the transfer of genetic information by serving as messenger RNA (mRNA) of the DNA sequence are used to guide the synthesis of molecules of RNA. Then, molecules that guide the synthesis of proteins according to the genetic instruc- MBoC7RNA in translation, m1.04/1.04 molecules are used to tions stored in the DNA. But as we discuss in Chapter 6, some RNA transcripts guide the synthesis of proteins, which are do not serve as information carriers; instead, they function directly in the cell to polymers made of amino acid subunits carry out a variety of other functions. (discussed shortly). MBOC7_ptr_ch01_001-048.indd 5 02/12/21 12:53 PM  6 Chapter 1: Cells, Genomes, and the Diversity of Life All Cells Use Proteins as Catalysts Like DNA and RNA molecules, protein molecules are long unbranched poly- mer chains, formed by stringing together monomeric building blocks (subunits) drawn from a standard repertoire that is the same for all living cells. Like DNA and RNA, proteins carry information in the form of a linear sequence of subunits in the same way as a human message written in an alphabetic script. There are many different protein molecules in each cell, and—if we ignore water molecules—they form the major portion of the cell’s mass. 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. Each amino acid is built around a core structure that allows it to be covalently linked in a standard way to any other amino acid in the set; attached to this core is a side group of atoms that gives each amino acid a distinctive chemical character. 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. By folding into a precise structure that binds with high specificity to other molecules, each protein performs a specific function according to its genetically specified sequence of amino acids. Proteins form and maintain diverse cell and extracellular structures, generate movements, sense signals, and so on. Many have reactive sites on their surface, allowing them to act as enzymes that cata- lyze reactions that make or break specific covalent bonds. 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. In everyday speech, a catalyst refers to “any agent that provokes or speeds sig- Figure 1–5 Life as an autocatalytic process. (A) The living cell is a self- nificant change or action.” But in chemistry, the term catalyst is defined more replicating collection of catalysts. (B) Life narrowly, being applied to any molecule that speeds up a specific chemical reac- can be viewed as an autocatalytic process. tion without itself being changed. From the most fundamental point of view, a DNA and RNA molecules provide the living cell is a self-replicating collection of catalysts that takes in food, processes nucleotide sequence information (green this food to provide both the building blocks and energy needed to make more arrows) that is used both to produce proteins and to copy themselves. Proteins, catalysts, and discards the materials left over as waste (Figure 1–5A). Together, in turn, provide the catalytic activity (red these feedback loops that connect proteins and polynucleotides form the basis for arrows) needed to synthesize DNA, RNA, this autocatalytic, self-reproducing behavior of all living organisms (Figure 1–5B). and proteins themselves. Together, these feedback loops create the self-replicating system that endows cells with the ability to All Cells Translate RNA into Protein in the Same Way reproduce. Although the great majority of the catalysts in the cell are proteins (known How the information in DNA specifies the production of proteins was a complete as enzymes), a few RNA molecules (known mystery in the 1950s when the double-strand structure of DNA was first revealed as ribozymes) also have this property, as as the basis of heredity. But in subsequent years, scientists discovered the elegant we will see in Chapter 6. (A) FOOD IN WASTE OUT (B) building SEQUENCE blocks INFORMATION DNA and RNA energy nucleotides cell's collection CATALYTIC of catalysts ACTIVITY proteins amino acids CELL'S COLLECTION OF CATALYSTS COLLABORATE TO REPRODUCE THE ENTIRE COLLECTION BEFORE A CELL DIVIDES MBOC7_ptr_ch01_001-048.indd 6 MBoC7 m1.08/1.05 02/12/21 12:53 PM  THE UNIVERSAL FEATURES OF LIFE ON EARTH 7 mechanisms involved. 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. It turns out that 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 nucleo- tides 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. All of these processes will be described in detail in Chapter 6. Each Protein Is Encoded by a Specific Gene DNA molecules as a rule are very large, containing the specifications for thou- sands of proteins and RNA molecules. 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. As previously mentioned, some DNA segments—a smaller number—are transcribed into RNA molecules that are not translated into protein but have other functions in the cell; such DNA segments also count as genes. A gene therefore is defined as the segment of DNA sequence correspond- ing 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. In all cells, the expression of individual genes is regulated: instead of manu- facturing its full repertoire of possible proteins and RNAs at full tilt all the time, the cell adjusts the rate of transcription and translation of different genes inde- pendently, according to need. As we shall see in Chapter 7, stretches of regulatory DNA are interspersed among the segments that code for protein, and these noncoding regions bind to special protein molecules that control the rate of transcription of individual genes. The organization of this regulatory DNA varies widely from one class of organisms to another, but the basic strategy is univer- sal. In this way, 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. Life Requires a Continual Input of Free Energy A living cell is a dynamic chemical system, operating far from chemical equilib- rium. 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 neces- sary 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. MBOC7_ptr_ch01_001-048.indd 7 02/12/21 12:53 PM  8 Chapter 1: Cells, Genomes, and the Diversity of Life As one example, free energy is required for the propagation of genetic infor- mation. Picture the molecules in a cell as a swarm of objects endowed with thermal energy, moving around violently at random, buffeted by collisions with one another. To copy genetic information—in the form of a DNA sequence, for example—nucleotide molecules from this wild crowd must be captured, arranged in a specific order defined by a preexisting template, and linked together in a fixed relationship. The bonds that hold the nucleotides in their proper places on the template and join them together must be strong enough to resist the disor- dering effect of thermal motion, which we describe shortly. The joining process is driven forward by a consumption of free energy, which is needed to ensure that the correct bonds are made, and made robustly. As an analogy, the molecules might be compared with spring-loaded traps, ready to snap into a more stable, lower-energy attached state when they meet their proper partners. As they snap together into the bonded arrangement, their available stored energy—their free energy—like the energy of the spring in the trap, is released and dissipated as heat. In a cell, the chemical processes underlying information transfer are more complex, but the same basic principle applies: free energy must be spent for the creation of order. To replicate its genetic information faithfully, and indeed to make all its com- plex molecules according to the correct specifications, the cell therefore requires free energy, which has to be imported somehow from the surroundings. As we will discuss in detail in Chapter 2, the free energy required by animal cells is derived hydrophilic from chemical bonds in food molecules that the animals eat, whereas plants get head their free energy from sunlight. hydrophobic tails (A) All Cells Function as Biochemical Factories phospholipid Because all cells make DNA, RNA, and protein, they all have to contain and monolayer manipulate a similar collection of small organic (carbon-containing) molecules, including simple sugars, nucleotides, and amino acids, as well as other substances that are universally required. All cells, for example, require the phosphorylated OIL nucleotide ATP (adenosine triphosphate), not only as a building block for the syn- thesis of DNA and RNA but also as a carrier of the free energy that is needed to drive a huge number of chemical reactions in the cell. Although all cells function as biochemical factories of a broadly similar type, many of the details of their small-molecule transactions differ. Plants, for exam- ple, require only the simplest of nutrients because they harness the energy of sunlight to make all their own small organic molecules. Other organisms, such phospholipid as animals and some bacteria, feed on living (or once living) organisms and bilayer forming must obtain many of their organic molecules ready-made. We return to this a vesicle point later in the chapter. All Cells Are Enclosed in a Plasma Membrane Across Which WATER Nutrients and Waste Materials Must Pass Each living cell is enclosed by a membrane—the plasma membrane. This mem- (B) brane acts as a selective barrier that enables the cell to concentrate nutrients Figure 1–6 Behavior of phospholipid gathered from its environment and retain the products it synthesizes for its own molecules in water. (A) A phospholipid use, while excreting its waste products. Without a plasma membrane, the cell molecule is amphiphilic, having a could not maintain its integrity as a coordinated chemical system. hydrophilic (water-loving) phosphate The molecules that form cell membranes have the simple physicochemical head group and a hydrophobic (water- avoiding) hydrocarbon tail. (B) At property of being amphiphilic; that is, they consist of one part that is hydrophilic an interface between oil and water, (water-soluble) and another part that is hydrophobic (water-insoluble). Such MBoC7 m1.09/1.06 phospholipids arrange themselves as a molecules placed in water aggregate spontaneously, arranging their hydropho- single sheet (a monolayer), with their bic portions to be as much in contact with one another as possible to hide them head groups facing the water and their from the water, while keeping their hydrophilic portions exposed. Amphiphilic tail groups facing the oil. When immersed in water, however, phospholipids molecules of appropriate shape, such as the phospholipid molecules that com- aggregate to form lipid bilayers that fold pose most of the molecules of the plasma membrane, spontaneously aggregate in in on themselves to form sealed aqueous water to create a bilayer that forms small closed vesicles (Figure 1–6). compartments known as vesicles. MBOC7_ptr_ch01_001-048.indd 8 02/12/21 12:53 PM  THE UNIVERSAL FEATURES OF LIFE ON EARTH 9 Although the chemical details vary, the hydrophobic tails of the predominant lipid molecules in all cells are hydrocarbon polymers (–CH2–CH2–CH2–), and their spontaneous assembly into a lipid bilayer is but one of many examples of an important general principle: cells produce molecules whose chemical properties cause them to self-assemble into the structures that a cell needs. 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. Some of these membrane transport proteins, like some of the proteins that catalyze the fundamental small-molecule reactions inside the cell, have been so well conserved over the course of evolution that we can recognize the fam- ily resemblances between them when even the most distantly related organisms are compared. 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. Thus, by specifying the RNAs and proteins that the cell produces, the genetic information recorded in the DNA sequence dictates the entire chemistry of the cell—in fact, not only its chemistry but also its form and its behavior, for these too are chiefly determined and controlled by the cell’s proteins. Cells Operate at a Microscopic Scale Dominated by Random Thermal Motion Thus far we have described the cell as a self-replicating, membrane-bound bag of chemicals and macromolecules; but, as the unit of life, the cell is much more than the sum of its parts. Although not obvious from microscopy images, even the simplest cell is highly ordered internally: its individual components must self-assemble and become highly organized for the cell to function. And the cell contents are in perpetual motion. The most obvious movements are catalyzed by motor proteins, enzymes that use the energy of ATP hydrolysis for a wide variety of purposes; these include pumping ions across the plasma membrane, translo- cating large assemblies from one intracellular site to another, and propelling the cell through its environment. In addition, and as previously mentioned, 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 diam- eter. This type of spontaneous movement, called thermal or Brownian motion, was first observed by Robert Brown in 1827, while looking through a microscope at pollen grains immersed in water. Caused by random molecular collisions, the constant fluctuating movement has important repercussions. Brownian motion drives a process called diffusion, and it determines the rates of biochemical reac- tions as molecules collide with one another within the interior of a cell (described in Chapter 2; see Movie 2.4). Even though random, the cell can harness Brownian motion for its own advantage. For example, during one step in the crawling migration of animal cells, the plasma membrane at the leading edge extends forward (see Chapter 16). This movement does not involve motor proteins. Instead, a cytoskeletal filament (an actin polymer) polymerizes adjacent to the inner membrane surface. When the membrane fluctuates in the forward direction, actin quickly fills in the gap so that the membrane cannot slip back to its original position. This phenome- non, in which random thermal motions are harnessed in a directed way, creates a Brownian ratchet (Figure 1–7). Because an object at the micrometer scale is constantly buffeted by water mol- ecules, its movement requires overcoming high viscous drag forces. As a result, the directed movement of a complex of molecules inside the cell (by a motor pro- tein, for example) will stop immediately when the motor disengages, leaving the complex to be randomly buffeted by thermal motion. There is no “gliding” inside the cell. MBOC7_ptr_ch01_001-048.indd 9 02/12/21 12:53 PM  10 Chapter 1: Cells, Genomes, and the Diversity of Life Figure 1–7 How membrane protrusion plasma membrane 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 actin filament contributes to forward movement of the cell, as described in Chapter 16 (see pp. 956–957). A Living Cell Can Exist with 500 Genes We have seen how genomes carry the information for all the proteins and RNA molecules of a cell, and how, through catalysis, all the other building blocks of the cell are made. But how complex are real living cells? In particular, what are the minimum requirements of a living cell? One measure of complexity is based on the total number of genesMBoC7inn1.110/1.07 an organism’s genome. 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 organ- ism 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. Its genome of 580,070 nucleotide pairs represents 145,018 bytes of information—about as much as it takes to record the text of one chapter of this book. Cell biology may be complicated, but it is not unimaginably so. Summary 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 trans- 0.2 µm mission 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 Figure 1–8 The small bacterium DNA nucleotides for each organism is known as its genome. The cell replicates this Mycoplasma genitalium. It is viewed information by separating the paired DNA strands and using each as a template here in cross section in an electron for polymerization to make a new DNA strand with a complementary sequence of microscope, which uses a beam of nucleotide subunits. The same strategy of templated polymerization is used in the electrons instead of light to create an image with a resolution that is many times transcription of portions of the DNA into molecules of the closely related polynu- higher than that of an image viewed in a cleotide polymer, RNA. Most of these RNA molecules are mRNAs that in turn guide conventional light microscope. Of the the synthesis of protein molecules by the process of translation. Proteins are poly- 525 genes this bacterium contains, mers of amino acid subunits and are the catalysts for almost all the cell’s chemical 43 code for transfer RNAs, ribosomal RNAs, and other nonprotein-coding reactions. They are also responsible for the selective import and export of molecules RNAs. Of the 482 protein-coding across the plasma membrane that surrounds each cell. The specific shape and func- genes, 154 are involved MBoC7 in replication, m1.10/1.08 tion of each protein depend on its amino acid sequence, which is specified by the transcription, translation, and related nucleotide sequence of a corresponding segment of the DNA—the gene that codes processes involving DNA, RNA, and for that protein. In this way, the DNA of the cell determines the cell’s chemistry, protein; 98 are involved in the membrane and surface structures of the cell; 46 which is fundamentally similar in all cells, reflecting their ultimate origin from a are involved in the transport of nutrients common ancestor cell that existed on Earth more than 3.5 billion years ago. and other molecules across the plasma membrane; and 71 are involved in energy conversion and the synthesis GENOME DIVERSIFICATION AND THE TREE OF LIFE and degradation of small molecules. (Courtesy of Roger Cole, in Medical The success of living organisms based on DNA, RNA, and protein has been spec- Microbiology, 4th ed. [S. Baron, ed.]. tacular. Through its billions of years of proliferation, life has populated the oceans, Galveston: University of Texas Medical covered the land, penetrated deep into Earth’s crust, and molded the surface of Branch, 1996.) MBOC7_ptr_ch01_001-048.indd 10 02/12/21 12:53 PM  GENOME DIVERSIFICATION AND THE TREE OF LIFE 11 our planet. Our oxygen-rich atmosphere, the deposits of coal and oil, the layers of iron ores, the cliffs of chalk and limestone and marble—all these are products, directly or indirectly, of past biological activity on Earth. Living things are not confined to the familiar temperate realm of land, water, and sunlight inhabited by plants and animals. They are found in the darkest depths of the ocean, in hot volcanic mud, in pools beneath the frozen surface of the Antarctic, and buried kilometers deep in Earth’s crust. The creatures that live in these extreme environments are generally unfamiliar, not only because they are inaccessible, but also because they are mostly microscopic and cannot be maintained in a laboratory. Even in more familiar habitats, most organisms are too small for us to see without special equipment: they tend to go unnoticed, unless they cause a disease or rot the timbers of our houses. Yet such microor- ganisms (microbes) are by far the most numerous living organisms on our planet. Only recently, through new methods of molecular analysis including rapid DNA sequencing, have we begun to get a picture of life on Earth that is not grossly dis- torted by our biased perspective as large animals living on dry land. In this section, we consider—in very broad terms—the diversity of organisms on our planet and the relationships among them. Because the genetic informa- tion for every organism is written in the universal language of DNA sequences, and because the DNA sequence of any organism’s genome can be readily determined, it is now possible to characterize, catalog, and compare any set of living organisms with reference to these sequences. From such comparisons we can specify the place of each organism in the family tree of living species—the “tree of life.” The Tree of Life Has Three Major Domains: Eukaryotes, Bacteria, and Archaea The classification of living things has traditionally depended on comparisons of their outward appearances: we can see that a fish has eyes, jaws, backbone, brain, and so on, just as humans do, and that a worm does not—just as we can see that a rosebush is more similar to an apple tree than to grass. As Darwin showed, we can readily interpret such close family resemblances in terms of an evolution from common ancestors, and we can find the remains of many of these ancestors pre- served in the fossil record. In this way, it became possible to draw a family tree of living organisms, showing the various lines of descent, as well as branch points in evolutionary history, where the ancestors of one group of species became differ- ent from those of another. When the disparities between organisms become very great, however, these methods begin to fail. How do we decide whether a fungus is more closely related to a plant or to an animal? When it comes to microscopic organisms such as bacteria, the task becomes harder still: one tiny rod or sphere can look much like another. Moreover, much of our knowledge of the microbial world was tra- ditionally restricted to those species that can be isolated and cultured in the laboratory. But direct DNA sequencing of populations of microbes in their natural habitats—such as soil, ocean water, or even the human mouth—has taught us that the vast majority of microbes cannot be easily cultured in the laboratory. Often, they thrive in the wild as components of complex ecosystems and—when separated from their natural surroundings—cannot survive. Until modern DNA sequencing was developed, these organisms were largely unknown to us, espe- cially those that inhabit extreme environments such as the deep Earth’s crust or seawater miles below the ocean surface. Genome analysis has now provided us with a simple, direct, and powerful way to determine evolutionary relationships. The complete DNA sequence of an organism defines its nature with almost perfect precision and in exhaustive detail. Moreover, this specification is in a digital form—a string of letters—that can be entered into a computer and compared with the corresponding information for any other organism. Because DNA is subject to random changes that accumu- late over long periods of time (as we will see shortly), the number of differences MBOC7_ptr_ch01_001-048.indd 11 02/12/21 12:53 PM  12 Chapter 1: Cells, Genomes, and the Diversity of Life between the DNA sequences of two organisms can provide a direct, objective, and quantitative indication of the evolutionary distance between them. 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. We discussed earlier how all cells use the same fundamental mechanism to translate a nucleotide sequence into a protein sequence, and we saw that the ribosome is the “decoding machine” that carries this out. Ribosomes are fundamentally simi­ lar in all organisms, and an especially well-conserved component of them is the RNA molecules that make up their core. 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. Once a rough approxi­ mation of the tree of life has been obtained in this way, many additional DNA sequences in genomes—those that might not be identifiable in all organisms— can accurately determine relationships among more closely related species. This approach has revealed that the living world consists of three major divi- sions, or domains: eukaryotes, bacteria, and archaea, as illustrated in Figure 1–9; in the following paragraphs, we briefly introduce each in turn. Spirochetes Rickettsia E. coli Salmonella Neisseria Yersinia Vibrio Beggiatoa PVC superphylum (includes Chlamydia) Proteobacteria Actinobacteria (includes Streptomyces) Chloroflexi based largely on genome sequencing of environmental samples Firmicutes (includes Clostridium, Streptococcus, ARCHAEA Staphylococcus, and Listeria) Cyanobacteria Asgard (includes Anabaena and Phormidium) animals and fungi EUKARYOTES plants BACTERIA 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. An expanded eukaryotic tree is shown in Figure 1–35, and an expanded tree of mammals is given in Figure 4–67. (Adapted from C.J. Castelle and J.F. Banfield, Cell 172:1181–1197, 2018.) MBoC7 n1.283/1.09 MBOC7_ptr_ch01_001-048.indd 12 02/12/21 12:53 PM  GENOME DIVERSIFICATION AND THE TREE OF LIFE 13 Eukaryotes Make Up the Domain of Life That Is Most Familiar to Us 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. Visible by simple light microscopy, this feature was used in the early twentieth century to classify living organisms as either eukaryotes (those with a nucleus) or prokaryotes (those without a nucleus). We now know that prokary- otes comprise two of the three major domains of life, the bacteria and archaea. Eukaryotic cells are typically much larger than those of bacteria and archaea; in addition to a nucleus, they typically contain a variety of membrane-bound organelles that are also lacking in the prokaryotes. 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. In addition to plants and animals, the eukaryotes include fungi (such as mush- rooms or the yeasts used in beer- and bread-making), as well as an astonishing variety of single-celled, microscopic forms of life. Most of this book is focused on the cell biology of eukaryotic organisms (especially animals); in the final sec- tions of this chapter, we shall return to eukaryotes and focus on the variety within this group. On the Basis of Genome Analysis, Bacteria Are the Most Diverse Group of Organisms on the Planet When modern trees of life were constructed using genome information, one of the big surprises was how much more evolutionarily diverse the bacterial world is compared with the eukaryotes; we now know that this great diversity reflects the much earlier appearance of bacteria in the evolutionary history of the planet. Bacteria are usually very small (and invisible to the unaided eye), and they gener- ally live as independent individuals or in loosely organized communities, rather than as multicellular organisms. They are typically spherical or rod-shaped and measure a few micrometers (μm) in linear dimension (Figure 1–10). They often have a tough protective coat, called a cell wall, beneath which a plasma mem- brane encloses a single cytoplasmic compartment—the cytoplasm—containing DNA, RNA, proteins, and the many small molecules needed for life (Figure 1–11). Although difficult to discern in the light microscope, the interior of a bacterium is nevertheless highly organized, a topic we discuss in Chapter 16. Commensurate with the diversity of their genomes, bacteria live in an enor- mous variety of ecological niches, and they are astonishingly varied in their 2 µm spherical rod-shaped cells, the smallest spiral cells, cells, e.g., e.g., Escherichia coli, cells, e.g., e.g., Treponema pallidum Streptococcus Salmonella Mycoplasma, Spiroplasma 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 (not shown). MBOC7_ptr_ch01_001-048.indd 13 MBoC7 m1.13/1.10 02/12/21 12:53 PM  14 Chapter 1: Cells, Genomes, and the Diversity of Life (A) Figure 1–11 Bacterial structure. (A) A flagellum drawing of the bacterium Vibrio cholerae, showing its simple internal organization. 1 µm This species can infect the human small intestine to cause cholera; the severe diarrhea that accompanies this disease ribosomes in cytosol kills more than 100,000 people a year worldwide. Like many other bacteria, Vibrio cell plasma DNA outer cytoplasm has a helical appendage at one end—a wall membrane membrane flagellum—that rotates as a propeller to (B) 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 1 µm bacterial species lack the outer membrane; these are classified as Gram positive. (B, courtesy of E. Kellenberger.) biochemical capabilities. There exist species that can utilize virtually any type of organic molecule as food, ranging from sugars and amino acids to hydrocar- bons, including the simplest hydrocarbon, methane gas (CH4). Other species (Figure 1–12) harvest light energy in a variety of ways; some, like plants, carry out photosynthesis and generate oxygen as a by-product. Still others can feed on a MBoC7 m1.14a,e1.11/1.11 plain diet of inorganic nutrients, getting their carbon from CO2, and relying on a host of other chemicals that occur in the environment to fuel their energy needs— including H2, Fe2+, H2S, and elemental sulfur (Figure 1–13). A wide range of bacteria directly affect human health. The bubonic plague of the Middle Ages (estimated to have killed half the population of Europe) and the current tuberculosis pandemic (more than a million deaths a year) are each due to a specific species of bacteria. And thousands of different bacterial species reside in our gut and on our skin, where they are often beneficial to us. We shall dis- cuss bacteria throughout the book, as it is the study of these relatively simple cells that led to much of our understanding of basic biological processes—including DNA replication, transcription, and translation. We focus again on bacteria in Chapter 24 when we examine the cell biology of infectious disease. Finally, genetic H S V 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 (A) capture CO2 and incorporate C into organic 10 µm 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. (A, courtesy of (B) David Adams; B, courtesy of D.P. Hill and 1 µm C.J. Howe.) MBoC7 e1.12/1.12 MBOC7_ptr_ch01_001-048.indd 14 02/12/21 12:53 PM  GENOME DIVERSIFICATION AND THE TREE OF LIFE 15 engineering techniques allow bacteria to be put to use as small “factories” to pro- duce human pharmaceuticals, biofuels, and other high-value chemical products, as we discuss in Chapter 8. Archaea: The Most Mysterious Domain of Life 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. 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 bio- chemical 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 (see Figure 1–9). It has even been proposed that the tree of life should be considered to have only two principal domains, with the archaea and eukaryotes 6 µm making up one domain and bacteria constituting the other. The close relationship of archaea and eukaryotes has also changed our views on how the earliest eukary- Figure 1–13 The bacterium Beggiatoa. It lives in sulfurous environments (for otic cell evolved, a topic addressed later in this chapter. example, see Figure 1–15) and gets its At first it was thought that archaea occupied only extreme environments such energy by oxidizing H2S; it can fix carbon as volcanoes, salt lakes, acid hot springs, and the stomachs of cattle, but they are even in the dark. Note the yellow deposits now recognized to be present also in more congenial surroundings such as soils, of sulfur inside the cells. (Courtesy of Ralph seawater, and our skin. Commensurate with the wide variety of ecological niches S. Wolfe.) 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 seawa- ter, and they play major roles in recycling nitrogen and carbon, two of the most important elements for all cells. MBoC7 m1.16/1.13 Organisms Occupy Most of Our Planet To understand life on Earth, we need to understand more than its diversity; we also need to know where life is found on our planet and how various living species are distributed. Organisms inhabit nearly all of the planet, and we con- tinue to discover new habitats. Amazingly, some bacteria and archaea even live archaea 7 Gt C miles down in Earth’s deep crust and in the deepest and most hostile parts of the oceans. viruses How are the main groups of organisms distributed among different envi- 0.2 Gt C ronments? DNA sequencing and other advanced technologies have been used plants recently to address this question. The total biomass on Earth is estimated to con- 450 Gt C tain ∼550 gigatons (1015 grams) of carbon, of which 450 gigatons of carbon (Gt C) bacteria is plants, 70 Gt C is bacteria, 7 Gt C is archaea, and 2 Gt C is animals (Figure 1–14). 70 Gt C The plants are mainly terrestrial; the bacteria and archaea are mainly in the soil and Earth’s crust. Total terrestrial biomass is 100 times greater than that in the oceans, although most of the animal mass is found in the oceans. The human protists fungi animals 4 Gt C 12 Gt C 2 Gt C 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 fall­ Figure 1–14 The distribution of living ing, largely as a result of human activities. biomass on Earth. The total biomass on Although humans and other animals make up a small fraction of Earth’s Earth expressed as gigatons of carbon (Gt C) is estimated to be ∼550 Gt C. In biomass, their existence depends completely on other forms of life. In the next the graph shown, the area of each taxon section, we shall see some of the ways that these different life-forms work together represented is proportional to the taxon’s to capture and recycle energy from Earth’s inanimate features. global biomass, MBoC7 n1.103/1.14 so plants account for about 80% (450/550) of the total biomass, whereas animals account for 0.4% (2/550). Cells Can Be Powered by a Wide Variety of Free-Energy Sources These recent estimates are based on Organisms obtain the free energy needed for life in different ways. Some—such various advanced techniques, including DNA sequencing and remote sensing. as animals, fungi, and the many different bacteria that live in the human gut— (Adapted from Y.M. Bar-On et al., Proc. get it by feeding on other living things or the organic chemicals they produce; Natl. Acad. Sci. USA 115:6506–6511, such organisms are called organotrophic (from the Greek word trophe, meaning 2018. With permission from the authors.) MBOC7_ptr_ch01_001-048.indd 15 02/12/21 12:53 PM  16 Chapter 1: Cells, Genomes, and the Diversity of Life “food”). 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 inor- ganic 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). The organo- trophic organisms like ourselves could not exist without these primary energy converters, which are the most plentiful form of life. The phototrophic organisms include many types of bacteria, as well as algae and plants, on which we—and virtually all the living things that we ordinarily see around us—depend. Phototrophic organisms have changed the whole chemistry of our environment: as a prime example, the oxygen in Earth’s atmosphere is a by-product of their biosynthetic activities. Lithotrophic organisms are not such an obvious feature of our world, because they are microscopic and mostly live in habitats that humans do not frequent—deep in the ocean, buried in Earth’s crust, or in various other seem- ingly inhospitable environments. But they are a major part of the living world, and they are especially important in any consideration of the history of life on Earth. Some lithotrophs get energy from aerobic reactions, which use molecular oxy- gen from the environment; because atmospheric O2 is ultimately the product of living phototrophic organisms, these aerobic lithotrophs are, in a sense, feeding on the products of past life. There are, however, many other lithotrophs that live anaerobically, in places where little or no molecular oxygen is present; these are circumstances similar to those that existed in the early days of life on Earth, before oxygen had accumulated. The most dramatic of the anaerobic sites are the hot hydrothermal vents on the floor of the Pacific and Atlantic Oceans. They are located where the ocean floor is spreading as new portions of Earth’s crust form by a gradual upwelling of material from Earth’s interior (Figure 1–15). Downward-percolating seawater is heated and driven back upward as a submarine geyser, carrying with it a cur- rent of chemicals from the hot rocks below. A typical cocktail might include H2S, H2, CO, Mn2+, Fe2+, Ni2+, CH4, NH4+, and phosphorus-containing compounds. SEA dark cloud of hot, mineral-rich water hydrothermal anaerobic lithotrophic vent bacteria invertebrate chimney made from animal community Figure 1–15 The geology of a hot precipitated metal sulfides hydrothermal vent in the ocean floor. As indicated, seawater percolates down 2–3°C 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 seafloor 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 350°C surrounding ocean. Minerals precipitate percolation core from the water as it cools, forming a of seawater chimney. Different classes of organisms, thriving at different temperatures, live in different neighborhoods of the chimney. A hot mineral solution typical chimney might be a few meters tall, spewing out hot, mineral-rich water. The locations of lithotrophic bacteria and the hot basalt invertebrate marine animals that depend on them are also shown (see Figure 1–16). MBOC7_ptr_ch01_001-048.indd 16 02/12/21 12:53 PM  GENOME DIVERSIFICATION AND THE TREE OF LIFE 17 geochemical energy and Figure 1–16 Organisms living at a depth inorganic raw materials 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, bacteria and archaea directly fueled by geochemical energy. A little further away, where the temperature is lower, various invertebrate animals live by feeding on these microorganisms. Most multicellular animals, e.g., tube worms 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. (Science History Images/Alamy Stock Photo.) 1m A dense population of microorganisms lives in the neighborhood of the vent, thriving on this austere diet and harvesting free energy from reactions between the available chemicals. Various invertebrate marine animals—clams, mussels, and giant marine worms—in turn, live off the microbes at the vent, forming an entire ecosystem analogous to MBoC7 m1.12/1.16 the world of plants and animals that we belong to, but one powered by geochemical energy instead of light (Figure 1–16). Some Cells Fix Nitrogen and Carbon Dioxide for Other Cells To make a living cell requires matter, as well as free energy. DNA, RNA, and pro- tein are composed of just six elements: hydrogen, carbon, nitrogen, oxygen, sulfur, and phosphorus. These are all plentiful in the nonliving environment, in Earth’s rocks, water, and atmospher