Cells, Genomes, and the Diversity of Life (Chapter 1)

PA R T I II III IV V INTRODUCTION TO THE CELL Cells, Genomes, and the Diversity of Life 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. These organisms appear extraordinarily diverse. What could be more different than a 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. They called that something “life,” marveled at it, struggled to define it, and despaired of explaining what it was or how it worked in terms that relate to nonliving matter. 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 the nature of life. We can now see that 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. 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 understanding 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: astonishing variety in individual particulars and astonishing constancy in fundamental mechanisms. In this chapter, we begin by outlining the universal features common 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 MBOC7_ptr_ch01_001-048.indd 1 CHAPTER 1 IN THIS CHAPTER The Universal Features of Life on Earth Genome Diversification and the Tree of Life Eukaryotes and the Origin of the Eukaryotic Cell Model Organisms 02/12/21 12:53 PM approach, which quantifies how closely organisms are related to one another, allows us to identify the three major branches of life on Earth, eukaryotes, bacteria, 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 reproduces 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 intricate 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 multicellular 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 contains 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 measurable 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 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. 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 (A) (B) (C) 100 µm (E) 50 µm (D) 50 µm (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 types m1.01/1.01 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, 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, 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 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 (A) building block of DNA (D) double-strand DNA phosphate sugar + sugar– phosphate (B) G G base nucleotide A T T G C C A G T G T A A C G G T C A DNA strand G T A A C G G T sugar–phosphate backbone A C (E) (C) C hydrogen-bonded base pairs DNA double helix templated polymerization of new strand nucleotide monomers C C A T T G T A A G G T C C G G G C A A C A T G G C A G T A T C G A C C A 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 (see Movie 4.1). cytosine (C), or thymine (T) (Figure 1–2). Each sugarm1.02/1.02 is linked to the next via MBoC7 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 synthesized, 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). MBOC7_ptr_ch01_001-048.indd 4 02/12/21 12:53 PM