CHAPTER Biochemistry:An Evolving Science 1 such as the on theight.The p PeterAgre,M.D. s.Since the OUTLINE 1.1 Biochemical Unity Underlies of life with great intensity.Through these investigations,many of the most Biological Diversity fundamental mysteries of how living things function at a biochemical level have now been solved.However,much remains to be investigated.As is often the case,each discovery raises at least as many new questions as it "urt our trem ofbiocSgpotun Biological Molecules rav.and many other fields.We begin our journey into biochemistry with one of the most startling discoveries 1.4 The Genomic Revolution s Transforming Biochemis of the past century:namely,the great unity of all living things at the Medicine,and Other Fields biochemical level. 1.1 Biochemical Unity Underlies Biological Diversity The biological world is magnificently diverse.The animal kingdom is elephants
1 Biochemistry: An Evolving Science 1 CHAPTER O U T L I N E 1.1 Biochemical Unity Underlies Biological Diversity 1.2 DNA Illustrates the Interplay BetweenForm and Function 1.3 Concepts from Chemistry Explain the Properties of Biological Molecules 1.4 The Genomic Revolution Is Transforming Biochemistry, Medicine, and Other Fields Biochemistry is the study of the chemistry of life processes. Since the discovery that biological molecules such as urea could be synthesized from nonliving components in 1828, scientists have explored the chemistry of life with great intensity. Through these investigations, many of the most fundamental mysteries of how living things function at a biochemical level have now been solved. However, much remains to be investigated. As is often the case, each discovery raises at least as many new questions as it answers. Furthermore, we are now in an age of unprecedented opportunity for the application of our tremendous knowledge of biochemistry to problems in medicine, dentistry, agriculture, forensics, anthropology, environmental sciences, alternative energy, and many other fields. We begin our journey into biochemistry with one of the most startling discoveries of the past century: namely, the great unity of all living things at the biochemical level. 1.1 Biochemical Unity Underlies Biological Diversity The biological world is magnificently diverse. The animal kingdom is rich with species ranging from nearly microscopic insects to elephants and whales. The plant kingdom includes species as small and relatively Chemistry in action.Human activities require energy. The interconversionof different forms of energy requires large biochemical machines comprising many thousands of atoms such as the complex shown above. Yet, the functions of these elaborate assemblies depend on simple chemical processes such as the protonationand deprotonationof the carboxylic acid groups shown on the right. The photograph is of Nobel Prize winners Peter Agre , M.D., and Carol Greider , Ph.D., who used, respectively, biochemical techniques to reveal key mechanisms of how water is transported into and out of cells, and how chromosomes are replicated faithfully. [Keith Weller for Johns Hopkins Medicine.] C C H O O C H2 H2 C H+ + H OC HN C C H O O C H2 H2 C OC HN —
CHAPTER 1 Biochemistry: extends futher h mcroscopic world.Organisms nd into the mic An Evolving Scienc water,in soil,and on or within larger organisms.Some organisms can survive and even thrive in seemingly hostile environments such as hot celled organisms are lRofoel and micr rent from their outward been tremendously supported and expanded.At the biochemical level,all ns me nterplay -H OH such as glu CH2OH cose and glycerol,referred to as metabolites,that are chemically transformed in biological processes OH Glycerol Members of both these classes of molecules are common,with minor vaiatono th that playm dimensional structures(Figure 1.1). opsis thal
2 CHAPTER 1 Biochemistry: An Evolving Science simple as algae and as large and complex as giant sequoias. This diversity extends further when we descend into the microscopic world. Organisms such as protozoa, yeast, and bacteria are present with great diversity in water, in soil, and on or within larger organisms. Some organisms can survive and even thrive in seemingly hostile environments such as hot springs and glaciers. The development of the microscope revealed a key unifying feature that underlies this diversity. Large organisms are built up of cells, resembling, to some extent, single-celled microscopic organisms. The construction of animals, plants, and microorganisms from cells suggested that these diverse organisms might have more in common than is apparent from their outward appearance. With the development of biochemistry, this suggestion has been tremendously supported and expanded. At the biochemical level, all organisms have many common features (Figure 1.1). As mentioned earlier, biochemistry is the study of the chemistry of life processes. These processes entail the interplay of two different classes of molecules: large molecules such as proteins and nucleic acids, referred to as biological macromolecules, and low-molecular-weight molecules such as glucose and glycerol, referred to as metabolites, that are chemically transformed in biological processes. Members of both these classes of molecules are common, with minor variations, to all living things. For example, deoxyribonucleic acid (DNA) stores genetic information in all cellular organisms. Proteins, the macromolecules that are key participants in most biological processes, are built from the same set of 20 building blocks in all organisms. Furthermore, proteins that play similar roles in different organisms often have very similar threedimensional structures (Figure 1.1). O OH OH CH2OH OH HO Glucose Glycerol HO C H CH2OH CH2OH Sulfolobus archaea Arabidopsis thaliana Homo sapiens FIGURE 1.1 Biological diversity and similarity. The shape of a key molecule in gene regulation (the TATA-box-binding protein) is similar in three very different organisms that are separated from one another by billions of years of evolution. [(Left) Eye of Science/Science Source; (middle) Holt Studios/Photo Researchers; (right) Time Life Pictures/Getty Images.]
1.1 Unity and Diversity 35 30 2.5 20 1.0 0.5 0.0 Billions of years le time line for ical ev t life on E eings emerged quite recent Key metabolic For )and human beir entical ngs fver es tha appear to be quite distinct often have common features at the biochemical level.Remarkably,the biochemical processes by which plants capture light energy and convert it into more-useful forms are strikingly similar to steps used in animals to capture energy released from the brea wn of glucose ese observations overwhelmingly Earth have a c om this that Geolo have line fo pres of their biochemical characteristics the diverse nisms of the modern world can be divided into three fundamental groups called domains:Eukarya (eukaryotes),Bacteria,and Archaea.Domain Eukarya comprises all multicel ular organisms,including human beings as well as many microscopic unice lular organisms such as yeast. eukaryotes is the which ed each cell. oeoedc assified ery in 1977 that certain bacteria-like These organisms,now recognized as having diverged from bacteria early in evolution,are the archaea.Evolutionary on the 13 Figure and the associated biol pore the chemical molecules olites that are found in biological pr sses common to all organisms.The unity of life at the biochemical level makes this approach possible.At the same time,different epending on tr in wh In most cases,these challenges are addressed by the adap tation of existing macromolecules to new roles rather than by the evolution of entirely new ones. Biochemistry has been greatly enriched by our ability IGURE 1.3 The tree of life.A onal struc nmon ancestor anp of the tree to organisms found in the modem world at the top
3 1.1 Unity and Diversity Key metabolic processes also are common to many organisms. For example, the set of chemical transformations that converts glucose and oxygen into carbon dioxide and water is essentially identical in simple bacteria such as Escherichia coli (E. coli) and human beings. Even processes that appear to be quite distinct often have common features at the biochemical level. Remarkably, the biochemical processes by which plants capture light energy and convert it into more-useful forms are strikingly similar to steps used in animals to capture energy released from the breakdown of glucose. These observations overwhelmingly suggest that all living things on Earth have a common ancestor and that modern organisms have evolved from this ancestor into their present forms. Geological and biochemical findings support a time line for this evolutionary path (Figure 1.2). On the basis of their biochemical characteristics, the diverse organisms of the modern world can be divided into three fundamental groups called domains: Eukarya (eukaryotes), Bacteria, and Archaea . Domain Eukarya comprises all multicellular organisms, including human beings as well as many microscopic unicellular organisms such as yeast. The defining characteristic of eukaryotes is the presence of a well-defined nucleus within each cell. Unicellular organisms such as bacteria, which lack a nucleus, are referred to as prokaryotes . The prokaryotes were reclassified as two separate domains in response to Carl Woese’s discovery in 1977 that certain bacteria-like organisms are biochemically quite distinct from other previously characterized bacterial species. These organisms, now recognized as having diverged from bacteria early in evolution, are the archaea . Evolutionary paths from a common ancestor to modern organisms can be deduced on the basis of biochemical information. One such path is shown in Figure 1.3. Much of this book will explore the chemical reactions and the associated biological macromolecules and metabolites that are found in biological processes common to all organisms. The unity of life at the biochemical level makes this approach possible. At the same time, different organisms have specific needs, depending on the particular biological niche in which they evolved and live. By comparing and contrasting details of particular biochemical pathways in different organisms, we can learn how biological challenges are solved at the biochemical level. In most cases, these challenges are addressed by the adaptation of existing macromolecules to new roles rather than by the evolution of entirely new ones. Biochemistry has been greatly enriched by our ability to examine the three-dimensional structures of biological macromolecules in great detail. Some of these structures 4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0.0 Earth formed Microorganisms Cells with nuclei Macroscopic organisms Dinosaurs Human beings Oxygen atmosphere forming Billions of years FIGURE 1.2 A possible time line for biochemical evolution. Selected key events are indicated. Note that life on Earth began approximately 3.5 billion years ago, whereas human beings emerged quite recently. Escherichia Bacillus BACTERIA EUKARYA ARCHAEA Salmonella Homo Saccharomyces Zea Methanococcus Archaeoglobus Halobacterium FIGURE 1.3 The tree of life. A possible evolutionary path from a common ancestor approximately 3.5 billion years ago at the bottom of the tree to organisms found in the modern world at the top
AEoeRsoaecamsr s provide an es tial fran wok2oplicated.han incredibly c function.We begin our exploration of the interplay between structure and function with the genetic material,DNA. 1.2 DNA Illustrates the Interplay Between Form and Function A fundamental biochemical feature common to all cellular organisms is the use of DNA for the storage of genetic information.The discovery that DNA plays this central role was first made in studies of bacteria in the 1940s.This discovery was for the three-dimension structure o an even field the stage I r many of the presen l to all biolo es the int and function.The remarkable properties of this chemical substance allow i to function as a very efficient and robust vehicle for storing information.We start with an examination of the covalent structure of DNA and its exten- sion into three dimensions. DNA is constructed from four building blocks DNA is a linear polymer made up of four different types of monomers.It has a fixed backbone from which protrude variable substituents,referred to as sugars re mole rom w es It kag sugar is co two pho nate groups throus ONA strand ha oined toeac deoxrbose is one of four possible bases:adenine(A).cyto sine(C),guanine(G),and thymine(T). mymine (T) These bases are connected to the sugar components in the DNA backn the wn significantl ther respects base 1.4 Coval om thesr-phosphate 0
4 CHAPTER 1 Biochemistry: An Evolving Science are simple and elegant, whereas others are incredibly complicated. In any case, these structures provide an essential framework for understanding function. We begin our exploration of the interplay between structure and function with the genetic material, DNA. 1.2 DNA Illustrates the Interplay Between Form and Function A fundamental biochemical feature common to all cellular organisms is the use of DNA for the storage of genetic information. The discovery that DNA plays this central role was first made in studies of bacteria in the 1940s. This discovery was followed by a compelling proposal for the three-dimensional structure of DNA in 1953, an event that set the stage for many of the advances in biochemistry and many other fields, extending to the present. The structure of DNA powerfully illustrates a basic principle common to all biological macromolecules: the intimate relation between structure and function. The remarkable properties of this chemical substance allow it to function as a very efficient and robust vehicle for storing information. We start with an examination of the covalent structure of DNA and its extension into three dimensions. DNA is constructed from four building blocks DNA is a linear polymer made up of four different types of monomers. It has a fixed backbone from which protrude variable substituents , referred to as bases (Figure 1.4). The backbone is built of repeating sugar–phosphate units. The sugars are molecules of deoxyribose from which DNA receives its name. Each sugar is connected to two phosphate groups through different linkages. Moreover, each sugar is oriented in the same way, and so each DNA strand has directionality, with one end distinguishable from the other. Joined to each deoxyribose is one of four possible bases: adenine (A), cytosine (C), guanine (G), and thymine (T). These bases are connected to the sugar components in the DNA backbone through the bonds shown in black in Figure 1.4. All four bases are planar but differ significantly in other respects. Thus, each monomer of DNA consists of a sugar–phosphate unit and one of four bases attached to the sugar. These bases can be arranged in any order along a strand of DNA. N N N N H H NH2 N N N H O NH2 N N H H NH2 O N N H O O H CH3 Adenine (A) Cytosine (C) Guanine (G) Thymine (T) N H FIGURE 1.4 Covalent structure of DNA. Each unit of the polymeric structure is composed of a sugar (deoxyribose), a phosphate, and a variable base that protrudes from the sugar–phosphate backbone. O O O base1 base2 base3 O P O O O O O P O O O O O P O O –– – Sugar Phosphate
Two single strands of DNA combine to form a double helix Most DNA molecules consist of not one but two strands(Figure 1.5).In 1.2 DNA:Fom and Functior 1953,James Watson and Francis Crick deduced the arrangement of these ter and arrange on on th is th and the ba on the the sug p rs(bp)held together by hyd 13 nine pairs with cytosine(G-C).as shown in Figure 1.6.Hydrogen bonds are much weaker than covalent bonds such as the carbon- define the struc tures o Such wea onds al e crucia systems they are weak bones of the two chains are shown in red and blue,and the ye rticularly with resoect double helix. Adenine (A) Thymine(T) (G ytosine (C) FIGURE 1.6 Watson mine(A-T),and gua DNA structure explains heredity and the storage of information The structure importar thus fit equally well into the center of the double-helical str sequence.Without any constraints.the sequence of bases along a N strand can act as an efficient means of storing information.Indeed,the ncof bases along DNA strands is how genetic information is stored. A sequence determines the sequence of the ribonucleic acid(RNA) and prote mole at carry out most of the ac thin cells ecause of b se-pairing of b enc As uone stran GT AA C that the we have postulated immediately ing mechanism for the genetic materialThus if the DNAdouble hei eparated n -U..0_ single strands,each strand can act as a template for the generation of its formation(Figure 1.7).The three FIGURE 1.7 DNA replication.If a DNA strcture of DN beautifuyustrates the close connection form and function
Two single strands of DNA combine to form a double helix Most DNA molecules consist of not one but two strands (Figure 1.5). In 1953, James Watson and Francis Crick deduced the arrangement of these strands and proposed a three-dimensional structure for DNA molecules. This structure is a double helix composed of two intertwined strands arranged such that the sugar–phosphate backbone lies on the outside and the bases on the inside. The key to this structure is that the bases form specific base pairs ( bp ) held together by hydrogen bonds (Section 1.3): adenine pairs with thymine (A–T) and guanine pairs with cytosine (G–C), as shown in Figure 1.6. Hydrogen bonds are much weaker than covalent bonds such as the carbon– carbon or carbon–nitrogen bonds that define the structures of the bases themselves. Such weak bonds are crucial to biochemical systems; they are weak enough to be reversibly broken in biochemical processes, yet they are strong enough, particularly when many form simultaneously, to help stabilize specific structures such as the double helix. FIGURE 1.5 The double helix. The double-helical structure of DNA proposed by Watson and Crick. The sugar–phosphate backbones of the two chains are shown in red and blue, and the bases are shown in green, purple, orange, and yellow. The two strands are antiparallel, running in opposite directions with respect to the axis of the double helix, as indicated by the arrows. N N N N N H H N N O O H CH3 Adenine (A) Thymine (T) N N N N O N H H H N N O N H H Guanine (G) Cytosine (C) FIGURE 1.6 Watson–Crick base pairs. Adenine pairs with thymine (A – T), and guanine with cytosine (G – C). The dashed green lines represent hydrogen bonds. C G T A T A A T C C G C A T G C G G C G T A C G Newly synthesized strands FIGURE 1.7 DNA replication. If a DNA molecule is separated into two strands, each strand can act as the template for the generation of its partner strand. 5 1.2 DNA: Form and Function DNA structure explains heredity and the storage of information The structure proposed by Watson and Crick has two properties of central importance to the role of DNA as the hereditary material. First, the structure is compatible with any sequence of bases. While the bases are distinct in structure, the base pairs have essentially the same shape (Figure 1.6) and thus fit equally well into the center of the double-helical structure of any sequence. Without any constraints, the sequence of bases along a DNA strand can act as an efficient means of storing information. Indeed, the sequence of bases along DNA strands is how genetic information is stored. The DNA sequence determines the sequences of the ribonucleic acid (RNA) and protein molecules that carry out most of the activities within cells. Second, because of base-pairing, the sequence of bases along one strand completely determines the sequence along the other strand. As Watson and Crick so coyly wrote: “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” Thus, if the DNA double helix is separated into two single strands, each strand can act as a template for the generation of its partner strand through specific base-pair formation (Figure 1.7). The threedimensional structure of DNA beautifully illustrates the close connection between molecular form and function