xxxii Contents ATP binding and hydrolysis induce changes in the 36.2 Drug Candidates Can Be Discovered conformation and binding affinity of motor proteins 1010 by Serendipity,Screening,or Design 1037 35.2 Myosins Move Along Actin Filaments 1012 Serendipitous observations can drive drug Actin is a polar,self-assembling,dynamic polymer 1012 development 1037 Myosin head domains bind to actin filaments 1014 Screening libraries of compounds can yield drugs Motions of single motor proteins can be directly or drug leads 1039 observed 1014 Drugs can be designed on the basis of Phosphate release triggers the myosin power stroke 1015 three-dimensional structural information 1042 Muscle is a complex of myosin and actin 1015 about their targets The length of the lever arm determines motor 36.3 Analyses of Genomes Hold Great velocity 1018 Promise for Drug Discovery 1045 35.3 Kinesin and Dynein Move Along Potential targets can be identified in the human 1045 Microtubules 1018 proteome Animal models can be developed to test the Microtubules are hollow cylindrical polymers 1018 validity of potential drug targets 1046 Kinesin motion is highly processive 1020 Potential targets can be identified in the genomes 35.4 A Rotary Motor Drives Bacterial Motion 1022 of pathogens 1046 Bacteria swim by rotating their flagella 1022 Genetic differences influence individual responses Proton flow drives bacterial flagellar rotation 1022 to drugs 1047 Bacterial chemotaxis depends on reversal of the 36.4 The Development of Drugs Proceeds direction of flagellar rotation 1024 Through Several Stages 1048 Clinical trials are time consuming and expensive 1048 Chapter 36 Drug Development 1029 The evolution of drug resistance can limit 36.1 The Development of Drugs Presents the utility of drugs for infectious agents and cancer 1050 Huge Challenges 1030 Drug candidates must be potent modulators of their targets 1030 Answers to Problems A1 Drugs must have suitable properties to reach their Selected Readings B1 targets 1031 Toxicity can limit drug effectiveness 1036 Index C1
xxxii Contents ATP binding and hydrolysis induce changes in the conformation and binding affinity of motor proteins 1010 35.2 Myosins Move Along Actin Filaments 1012 Actin is a polar, self-assembling, dynamic polymer 1012 Myosin head domains bind to actin filaments 1014 Motions of single motor proteins can be directly observed 1014 Phosphate release triggers the myosin power stroke 1015 Muscle is a complex of myosin and actin 1015 The length of the lever arm determines motor velocity 1018 35.3 Kinesin and Dynein Move Along Microtubules 1018 Microtubules are hollow cylindrical polymers 1018 Kinesin motion is highly processive 1020 35.4 A Rotary Motor Drives Bacterial Motion 1022 Bacteria swim by rotating their flagella 1022 Proton flow drives bacterial flagellar rotation 1022 Bacterial chemotaxis depends on reversal of the direction of flagellar rotation 1024 Chapter 36 Drug Development 1029 36.1 The Development of Drugs Presents Huge Challenges 1030 Drug candidates must be potent modulators of their targets 1030 Drugs must have suitable properties to reach their targets 1031 Toxicity can limit drug effectiveness 1036 36.2 Drug Candidates Can Be Discovered by Serendipity, Screening, or Design 1037 Serendipitous observations can drive drug development 1037 Screening libraries of compounds can yield drugs or drug leads 1039 Drugs can be designed on the basis of three-dimensional structural information about their targets 1042 36.3 Analyses of Genomes Hold Great Promise for Drug Discovery 1045 Potential targets can be identified in the human proteome 1045 Animal models can be developed to test the validity of potential drug targets 1046 Potential targets can be identified in the genomes of pathogens 1046 Genetic differences influence individual responses to drugs 1047 36.4 The Development of Drugs Proceeds Through Several Stages 1048 Clinical trials are time consuming and expensive 1048 The evolution of drug resistance can limit the utility of drugs for infectious agents and cancer 1050 Answers to Problems A1 Selected Readings B1 Index C1
CHAPTER Biochemistry:An Evolving Science Chemistry in action.Human activities require energy.The interconversion of 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 protonation and deprotonation of 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 biochemical techniques to study the structure and function of proteins. [Courtesy of Johns Hopkins Medicine.] Diochemistry is the study of the chemistry of life processes.Since the dis- OUTLINE Dcovery that biological molecules such as urea could be synthesized from nonliving components in 1828,scientists have explored the chemistry of life 1.1 Biochemical Unity Underlies with great intensity.Through these investigations,many of the most funda- Biological Diversity mental mysteries of how living things function at a biochemical level have 1.2 DNA Illustrates the Interplay now been solved.However,much remains to be investigated.As is often the Between Form and Function 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 1.3 Concepts from Chemistry Explain application of our tremendous knowledge of biochemistry to problems in the Properties of Biological medicine,dentistry,agriculture,forensics,anthropology,environmental Molecules sciences,and many other fields.We begin our journey into biochemistry 1.4 The Genomic Revolution Is with one of the most startling discoveries of the past century:namely,the Transforming Biochemistry and great unity of all living things at the biochemical level. Medicine 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 simple 1
CHAPTER 1 Biochemistry: An Evolving Science 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, 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 simple Chemistry in action. Human activities require energy. The interconversion of 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 protonation and deprotonation of 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 biochemical techniques to study the structure and function of proteins. [Courtesy of Johns Hopkins Medicine.] 1 OUTLINE 1.1 Biochemical Unity Underlies Biological Diversity 1.2 DNA Illustrates the Interplay Between Form and Function 1.3 Concepts from Chemistry Explain the Properties of Biological Molecules 1.4 The Genomic Revolution Is Transforming Biochemistry and 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 n ~
as algae and as large and complex as giant sequoias.This diversity extends CHAPTER 1 Biochemistry: further when we descend into the microscopic world.Single-celled organ- An Evolving Science isms 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 ani- mals,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). CH2OH As mentioned earlier,biochemistry is the study of the chemistry of life processes.These processes entail the interplay of two different classes of mol- 0 CH>OH ecules:large molecules such as proteins and nucleic acids,referred to as bio- OH HO- C-H logical macromolecules,and low-molecular-weight molecules such as glucose HO OH CH2OH and glycerol,referred to as metabolites,that are chemically transformed in biological processes.Members of both these classes of molecules are com- OH Glycerol mon,with minor variations,to all living things.For example,deoxyribonucleic Glucose 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 three-dimensional structures(see Figure 1.1). Sulfolobus acidicaldarius 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)Dr.T.J.Beveridge/Visuals Unlimited;(middle) Holt Studios/Photo Researchers;(right)Time Life Pictures/Getty Images.]
2 CHAPTER 1 Biochemistry: An Evolving Science as algae and as large and complex as giant sequoias. This diversity extends further when we descend into the microscopic world. Single-celled 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 three-dimensional structures (see Figure 1.1). Sulfolobus acidicaldarius 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) Dr. T. J. Beveridge/Visuals Unlimited; (middle) Holt Studios/Photo Researchers; (right) Time Life Pictures/Getty Images.] O OH OH CH2OH OH HO Glucose Glycerol HO C H CH2OH CH2OH
3 1.1 Biochemical Unity Oxygen atmosphere sunesou!d forming 4.0 3.5 3.0 2.5 2.0 15 1.0 0.5 0.0 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. Key metabolic processes also are common to many organisms.For example,the set of chemical transformations that converts glucose and oxy- gen 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 char- acteristic 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 sepa- rate domains in response to Carl Woese's discovery in 1977 that certain bacteria-like organisms are biochemically quite distinct from other previ- ously characterized bacterial species.These organisms, now recognized as having diverged from bacteria early in evolution,are the archaea.Evolutionary paths from a BACTERIA EUKARYA ARCHAEA common ancestor to modern organisms can be deduced on the basis of biochemical information.One such path is shown in Figure 1.3. 1 Much of this book will explore the chemical reactions and the associated biological macromolecules and metab- olites 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 particu- lar biological niche in which they evolved and live.By comparing and contrasting details of particular biochemi- cal 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 adap- tation of existing macromolecules to new roles rather than by the evolution of entirely new ones. Figure 1.3 The tree of life.A possible evolutionary path from a Biochemistry has been greatly enriched by our ability to common ancestor approximately 3.5 billion years ago at the bottom of examine the three-dimensional structures of biological the tree to organisms found in the moder world at the top
3 1.1 Biochemical Unity 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 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
macromolecules in great detail.Some of these structures are simple and ele- CHAPTER 1 Biochemistry: gant,whereas others are incredibly complicated but,in any case,these struc- An Evolving Science tures 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 the elucidation of the three-dimensional struc- ture 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 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(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 ori- ented 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 possi- ble bases:adenine(A),cytosine(C),guanine(G),and thymine(T). NH2 NH2 NH Adenine(A) Cytosine(C) Guanine(G) hymine(①) These bases are connected to the sugar components in the DNA back- bone through the bonds shown in black in Figure 1.4.All four bases are pla- nar 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. base base2 bases 0 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 0 0 from the sugar-phosphate backbone. Sugar Phosphate
4 CHAPTER 1 Biochemistry: An Evolving Science macromolecules in great detail. Some of these structures are simple and elegant, whereas others are incredibly complicated but, 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 the elucidation of 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 (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. O O O base1 base2 base3 O P O O O O O P O O O O O P O O –– – Sugar Phosphate 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. 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) Guanine (G) Cytosine (C) Thymine (T) N H