Lehninger Principles of Biochemistry, Fourth Edition PDF

 Lehninger PRINCIPLES OF BIOCHEMISTRY Fourth Edition David L. Nelson (University of Wisconsin–Madison) Michael M. Cox (University of Wisconsin–Madison) New to This Edition Every chapter fully updated: Including coverage of the human genome and genomics integrated througho...

 Lehninger PRINCIPLES OF BIOCHEMISTRY Fourth Edition David L. Nelson (University of Wisconsin–Madison) Michael M. Cox (University of Wisconsin–Madison) New to This Edition Every chapter fully updated: Including coverage of the human genome and genomics integrated throughout, and key developments since the publication of the third edition, such as the structure of the ribosome. New treatment of metabolic regulation: NEW Chapter 15 gives students the most up-to- date picture of how cells maintain biochemical homeostasis by including modern concepts in metabolic regulation. New, earlier coverage of DNA-based information technologies (Chapter 9): Shows how advances in DNA technology are revolutionizing medicine and biotechnology; examines cloning and genetic engineering, as well as the implications of human gene therapy. Glycolysis and gluconeogenesis now presented in a single chapter (Chapter 14). Redesigned and Expanded Treatment of Enzyme Mechanisms: NEW Mechanism Figures designed to lead students through these reactions step by step. The first reaction mechanism treated in the book, chymotrypsin, presents a refresher on how to follow and understand reaction mechanism diagrams. Twelve new mechanisms have been added, including lysozyme. New Medical and Life Sciences Examples: This edition adds boxed features of biochemical methods, medical applications, and the history of biochemistry, adding to those already present of medicine, biotechnology, and other aspects of daily life. Web site at: www.whfreeman.com/lehninger4e For students: Biochemistry in 3D molecular structure tutorials: Self-paced, interactive tutorials based on the Chemscape Chime molecular visualization browser plug-in. Chime tutorial archive provides links to some of the best Chime tutorials available on the Web. Online support for the Biochemistry on the Internet problems in the textbook. Flashcards on key terms from the text. Online quizzing for each chapter, a new way for students to review material and prepare for exams. Animated mechanisms viewed in Flash or PowerPoint formats give students and instructors a way to visualize mechanisms in a two-dimensional format. Living Graphs illustrate graphed material featured in the text. Bonus Material from Lehninger, Principles of Biochemistry, Third Edition: fundamental Chapters 1, 2, and 3 from the third edition that instructors find useful for their students as a basis for their biochemistry studies. For instructors: All the figures from the book optimized for projection, available in PowerPoint and JPEG format; also available on the IRCD (see below). CHIME Student CD, 0-7167-7049-0 This CD allows students to view Chime tutorials without having to install either the older version of Netscape or the Chime plug-in. Available packaged with Lehninger for free,this optional Student CD-ROM also includes the animated mechanisms and living graphs from the Web site. Instructor's Resource CD-ROM with Test Bank, 0-7167-5953-5 All the images and tables from the text in JPEG and PowerPoint formats, optimized for projection with enhanced colors, higher resolution and enlarged fonts for easy reading in the lecture hall. Animated enzyme mechanisms. Living Graphs Test Bank organized by chapter in the form of.pdf files and editable Word files. Supplements For Instructors Printed Test Bank, Terry Platt and Eugene Barber, University of Rochester Medical Cente), David L. Nelson and Brook Chase Soltvedt, University of Wisconsin-Madison, 0-7167-5952-7 The new Test Bank contains 25% new multiple-choice and short-answer problems and solutions with approximately 50 problems and solutions per chapter. Each problem is keyed to the corresponding chapter of the text and rated by level of difficulty. Overhead Transparency Set, 0-7167-5956-X The full-color transparency set contains 150 key illustrations from the text, with enlarged labels that project more clearly for lecture hall presentation. For Students The Absolute, Ultimate Guide to Lehninger, Principles of Biochemistry, Fourth Edition: Study Guide and Solutions Manual, Marcy Osgood, University of New Mexico, and Karen Ocorr, University of California, San Diego, 0-7167-5955-1 The Absolute, Ultimate Guide combines an innovative study guide with a reliable solutions manual in one convenient volume. A poster-size Cellular Metabolic Map is packaged with the Guide, on which students can draw the reactions and pathways of metabolism in their proper compartments within the cell. Exploring Genomes, Paul G. Young (Queens University), 0-7167-5738-2 Used in conjunction with the online tutorials found at www.whfreeman.com/young, Exploring Genomes guides students through live searches and analyses on the most commonly used National Center for Biotechnology Information (NCBI) database. Lecture Notebook, 0-7167-5954-3 Bound volume of black and white reproductions of all the text's line art and tables, allowing students to concentrate on the lecture instead of copying illustrations. Also includes: Essential reaction equations and mathematical equations with identifying labels Complete pathway diagrams and individual reaction diagrams for all metabolic pathways in the book References that key the material in the text to the CD-ROM and Web Site Lehninger Principles of Biochemistry Fourth Edition David L. Nelson (U. of Wisconsin–Madison) Michael M. Cox (U. of Wisconsin–Madison) 1. The Foundations of Biochemistry 1.1 Cellular Foundations 1.2 Chemical Foundations 1.3 Physical Foundations 1.4 Genetic Foundations 1.5 Evolutionary Foundations Distilled and reorganized from Chapters 1–3 of the previous edition, this overview provides a refresher on the cellular, chemical, physical, genetic, and evolutionary background to biochemistry, while orienting students toward what is unique about biochemistry. PART I. STRUCTURE AND CATALYSIS 2. Water 2.1 Weak Interactions in Aqueous Systems 2.2 Ionization of Water, Weak Acids, and Weak Bases 2.3 Buffering against pH Changes in Biological Systems 2.4 Water as a Reactant 2.5 The Fitness of the Aqueous Environment for Living Organisms Includes new coverage of the concept of protein-bound water, illustrated with molecular graphics. 3. Amino Acids, Peptides, and Proteins 3.1 Amino Acids 3.2 Peptides and Proteins 3.3 Working with Proteins 3.4 The Covalent Structure of Proteins 3.5 Protein Sequences and Evolution Adds important new material on genomics and proteomics and their implications for the study of protein structure, function, and evolution. 4. The Three-Dimensional Structure of Proteins 4.1 Overview of Protein Structure 4.2 Protein Secondary Structure 4.3 Protein Tertiary and Quaternary Structures 4.4 Protein Denaturation and Folding Adds a new box on scurvy. 5. Protein Function 5.1 Reversible Binding of a Protein to a Ligand: Oxygen-Binding Proteins 5.2 Complementary Interactions between Proteins and Ligands: The Immune System and Immunoglobulins 5.3 Protein Interactions Modulated by Chemical Energy: Actin, Myosin, and Molecular Motors Adds a new box on carbon monoxide poisoning 6. Enzymes 6.1 An Introduction to Enzymes 6.2 How Enzymes Work 6.3 Enzyme Kinetics as An Approach to Understanding Mechanism 6.4 Examples of Enzymatic Reactions 6.5 Regulatory Enzymes Offers a revised presentation of the mechanism of chymotrypsin (the first reaction mechanism in the book), featuring a two-page figure that takes students through this particular mechanism, while serving as a step-by-step guide to interpreting any reaction mechanism Features new coverage of the mechanism for lysozyme including the controversial aspects of the mechanism and currently favored resolution based on work published in 2001. 7. Carbohydrates and Glycobiology 7.1 Monosaccharides and Disaccharides 7.2 Polysaccharides 7.3 Glycoconjugates: Proteoglycans, Glycoproteins, and Glycolipids 7.4 Carbohydrates as Informational Molecules: The Sugar Code 7.5 Working with Carbohydrates Includes new section on polysaccharide conformations. A striking new discussion of the "sugar code" looks at polysaccharides as informational molecules, with detailed discussions of lectins, selectins, and oligosaccharide-bearing hormones. Features new material on structural heteropolysaccharides and proteoglycans Covers recent techniques for carbohydrate analysis. 8. Nucleotides and Nucleic Acids 8.1 Some Basics 8.2 Nucleic Acid Structure 8.3 Nucleic Acid Chemistry 8.4 Other Functions of Nucleotides 9. DNA-Based Information Technologies 9.1 DNA Cloning: The Basics 9.2 From Genes to Genomes 9.3 From Genomes to Proteomes 9.4 Genome Alterations and New Products of Biotechnology Introduces the human genome. Biochemical insights derived from the human genome are integrated throughout the text. Tracking the emergence of genomics and proteomics, this chapter establishes DNA technology as a core topic and a path to understanding metabolism, signaling, and other topics covered in the middle chapters of this edition. Includes up-to-date coverage of microarrays, protein chips, comparative genomics, and techniques in cloning and analysis. 10. Lipids 10.1 Storage Lipids 10.2 Structural Lipids in Membranes 10.3 Lipids as Signals, Cofactors, and Pigments 10.4 Working with Lipids Integrates new topics specific to chloroplasts and archaebacteria Adds material on lipids as signal molecules. 11. Biological Membranes and Transport 11.1 The Composition and Architecture of Membranes 11.2 Membrane Dynamics 11.3 Solute Transport across Membranes Includes a description of membrane rafts and microdomains within membranes, and a new box on the use of atomic force microscopy to visualize them. Looks at the role of caveolins in the formation of membrane caveolae Covers the investigation of hop diffusion of membrane lipids using FRAP (fluorescence recovery after photobleaching) Adds new details to the discussion of the mechanism of Ca2- ATPase (SERCA pump), revealed by the recently available high-resolution view of its structure Explores new facets of the mechanisms of the K+ selectivity filter, brought to light by recent high-resolution structures of the K+ channel Illuminates the structure, role, and mechanism of aquaporins with important new details Describes ABC transporters, with particular attention to the multidrug transporter (MDR1) Includes the newly solved structure of the lactose transporter of E. coli. 12. Biosignaling 12.1 Molecular Mechanisms of Signal Transduction 12.2 Gated Ion Channels 12.3 Receptor Enzymes 12.4 G Protein-Coupled Receptors and Second Messengers 12.5 Multivalent Scaffold Proteins and Membrane Rafts 12.6 Signaling in Microorganisms and Plants 12.7 Sensory Transduction in Vision, Olfaction, and Gustation 12.8 Regulation of Transcription by Steroid Hormones 12.9 Regulation of the Cell Cycle by Protein Kinases 12.10 Oncogenes, Tumor Suppressor Genes, and Programmed Cell Death Updates the previous edition's groundbreaking chapter to chart the continuing rapid development of signaling research Includes discussion on general mechanisms for activation of protein kinases in cascades Now covers the roles of membrane rafts and caveolae in signaling pathways, including the activities of AKAPs (A Kinase Anchoring Proteins) and other scaffold proteins Examines the nature and conservation of families of multivalent protein binding modules, which combine to create many discrete signaling pathways Adds a new discussion of signaling in plants and bacteria, with comparison to mammalian signaling pathways Features a new box on visualizing biochemistry with fluorescence resonance energy transfer (FRET) with green fluorescent protein (GFP) PART II: BIOENERGETICS AND METABOLISM 13. Principles of Bioenergetics 13.1 Bioenergetics and Thermodynamics 13.2 Phosphoryl Group Transfers and ATP 13.3 Biological Oxidation-Reduction Reactions Examines the increasing awareness of the multiple roles of polyphosphate Adds a new discussion of niacin deficiency and pellagra. 14. Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway 14.1 Glycolysis 14.2 Feeder Pathways for Glycolysis 14.3 Fates of Pyruvate under Anaerobic Conditions: Fermentation 14.4 Gluconeogenesis 14.5 Pentose Phosphate Pathway of Glucose Oxidation Now covers gluconeogenesis immediately after glycolysis, discussing their relatedness, differences, and coordination and setting up the completely new chapter on metabolic regulation that follows Adds coverage of the mechanisms of phosphohexose isomerase and aldolase Revises the presentation of the mechanism of glyceraldehyde 3-phosphate dehydrogenase. New Chapter 15. Principles of Metabolic Regulation, Illustrated with Glucose and Glycogen Metabolism  15.1 The Metabolism of Glycogen in Animals 15.2 Regulation of Metabolic Pathways 15.3 Coordinated Regulation of Glycolysis and Gluconeogenesis 15.4 Coordinated Regulation of Glycogen Synthesis and Breakdown 15.5 Analysis of Metabolic Control Brings together the concepts and principles of metabolic regulation in one chapter Concludes with the latest conceptual approaches to the regulation of metabolism, including metabolic control analysis and contemporary methods for studying and predicting the flux through metabolic pathways 16. The Citric Acid Cycle 16.1 Production of Acetyl-CoA (Activated Acetate) 16.2 Reactions of the Citric Acid Cycle 16.3 Regulation of the Citric Acid Cycle 16.4 The Glyoxylate Cycle Expands and updates the presentation of the mechanism for pyruvate carboxylase. Adds coverage of the mechanisms of isocitrate dehydrogenase and citrate synthase. 17. Fatty Acid Catabolism 17.1 Digestion, Mobilization, and Transport of Fats 17.2 Oxidation of Fatty Acids 17.3 Ketone Bodies Updates coverage of trifunctional protein New section on the role of perilipin phosphorylation in the control of fat mobilization New discussion of the role of acetyl-CoA in the integration of fatty acid oxidation and synthesis Updates coverage of the medical consequences of genetic defects in fatty acyl–CoA dehydrogenases Takes a fresh look at medical issues related to peroxisomes 18. Amino Acid Oxidation and the Production of Urea 18.1 Metabolic Fates of Amino Groups 18.2 Nitrogen Excretion and the Urea Cycle 18.3 Pathways of Amino Acid Degradation Integrates the latest on regulation of reactions throughout the chapter, with new material on genetic defects in urea cycle enzymes, and updated information on the regulatory function of N-acetylglutamate synthase. Reorganizes coverage of amino acid degradation to focus on the big picture Adds new material on the relative importance of several degradative pathways Includes a new description of the interplay of the pyridoxal phosphate and tetrahydrofolate cofactors in serine and glycine metabolism 19. Oxidative Phosphorylation and Photophosphorylation Oxidative Phosporylation 19.1 Electron-Transfer Reactions in Mitochondria 19.2 ATP Synthesis 19.3 Regulation of Oxidative Phosphorylation 19.4 Mitochondrial Genes: Their Origin and the Effects of Mutations 19.5 The Role of Mitochondria in Apoptosis and Oxidative Stress Photosynthesis: Harvesting Light Energy 19.6 General Features of Photophosphorylation 19.7 Light Absorption 19.8 The Central Photochemical Event: Light-Driven Electron Flow 19.9 ATP Synthesis by Photophosphorylation Adds a prominent new section on the roles of mitochondria in apoptosis and oxidative stress Now covers the role of IF1 in the inhibition of ATP synthase during ischemia  Includes revelatory details on the light-dependent pathways of electron transfer in photosynthesis, based on newly available molecular structures 20. Carbohydrate Biosynthesis in Plants and Bacteria 20.1 Photosynthetic Carbohydrate Synthesis 20.2 Photorespiration and the C4 and CAM Pathways 20.3 Biosynthesis of Starch and Sucrose 20.4 Synthesis of Cell Wall Polysaccharides: Plant Cellulose and Bacterial Peptidoglycan 20.5 Integration of Carbohydrate Metabolism in the Plant Cell Reorganizes the coverage of photosynthesis and the C4 and CAM pathways Adds a major new section on the synthesis of cellulose and bacterial peptidoglycan 21. Lipid Biosynthesis 21.1 Biosynthesis of Fatty Acids and Eicosanoids 21.2 Biosynthesis of Triacylglycerols 21.3 Biosynthesis of Membrane Phospholipids 21.4 Biosynthesis of Cholesterol, Steroids, and Isoprenoids Features an important new section on glyceroneogenesis and the triacylglycerol cycle between adipose tissue and liver, including their roles in fatty acid metabolism (especially during starvation) and the emergence of thiazolidinediones as regulators of glyceroneogenesis in the treatment of type II diabetes Includes a timely new discussion on the regulation of cholesterol metabolism at the genetic level, with consideration of sterol regulatory element-binding proteins (SREBPs). 22. Biosynthesis of Amino Acids, Nucleotides, and Related Molecules 22.1 Overview of Nitrogen Metabolism 22.2 Biosynthesis of Amino Acids 22.3 Molecules Derived from Amino Acids 22.4 Biosynthesis and Degradation of Nucleotides Adds material on the regulation of nitrogen metabolism at the level of transcription Significantly expands coverage of synthesis and degradation of heme 23. Integration and Hormonal Regulation of Mammalian Metabolism 23.1 Tissue-Specific Metabolism: The Division of Labor 23.2 Hormonal Regulation of Fuel Metabolism 23.3 Long Term Regulation of Body Mass 23.4 Hormones: Diverse Structures for Diverse Functions Reorganized presentation leads students through the complex interactions of integrated metabolism step by step Features extensively revised coverage of insulin and glucagon metabolism that includes the integration of carbohydrate and fat metabolism New discussion of the role of AMP-dependent protein kinase in metabolic integration Updates coverage of the fast-moving field of obesity, regulation of body mass, and the leptin and adiponectin regulatory systems Adds a discussion of Ghrelin and PYY3-36 as regulators of short-term eating behavior Covers the effects of diet on the regulation of gene expression, considering the role of peroxisome proliferator-activated receptors (PPARs) PART III. INFORMATION PATHWAYS 24. Genes and Chromosomes 24.1 Chromosomal Elements 24.2 DNA Supercoiling 24.3 The Structure of Chromosomes  Integrates important new material on the structure of chromosomes, including the roles of SMC proteins and cohesins, the features of chromosomal DNA, and the organization of genes in DNA 25. DNA Metabolism 25.1 DNA Replication 25.2 DNA Repair 25.3 DNA Recombination Adds a section on the "replication factories" of bacterial DNA Includes latest perspectives on DNA recombination and repair 26. RNA Metabolism 26.1 DNA-Dependent Synthesis of RNA 26.2 RNA Processing 26.3 RNA-Dependent Synthesis of RNA and DNA Updates coverage on mechanisms of mRNA processing Adds a subsection on the 5' cap of eukaryotic mRNAs Adds important new information about the structure of bacterial RNA polymerase and its mechanism of action. 27. Protein Metabolism 27.1 The Genetic Code 27.2 Protein Synthesis 27.3 Protein Targeting and Degradation Includes a presentation and analysis of the long-awaited structure of the ribosome- -one of the most important updates in this new edition Adds a new box on the evolutionary significance of ribozyme-catalyzed peptide synthesis. 28. Regulation of Gene Expression 28.1 Principles of Gene Regulation 28.2 Regulation of Gene Expression in Prokaryotes 28.3 Regulation of Gene Expression in Eukaryotes Adds a new section on RNA interference (RNAi), including the medical potential of gene silencing. 8885d_c01_01-46 10/27/03 7:48 AM Page 1 mac76 mac76:385_reb: chapter 1 THE FOUNDATIONS OF BIOCHEMISTRY 1.1 Cellular Foundations 3 life arose—simple microorganisms with the ability to ex- 1.2 Chemical Foundations 12 tract energy from organic compounds or from sunlight, which they used to make a vast array of more complex 1.3 Physical Foundations 21 biomolecules from the simple elements and compounds 1.4 Genetic Foundations 28 on the Earth’s surface. 1.5 Evolutionary Foundations 31 Biochemistry asks how the remarkable properties of living organisms arise from the thousands of differ- ent lifeless biomolecules. When these molecules are iso- With the cell, biology discovered its atom... To lated and examined individually, they conform to all the characterize life, it was henceforth essential to study the physical and chemical laws that describe the behavior cell and analyze its structure: to single out the common of inanimate matter—as do all the processes occurring denominators, necessary for the life of every cell; in living organisms. The study of biochemistry shows how the collections of inanimate molecules that consti- alternatively, to identify differences associated with the tute living organisms interact to maintain and perpetu- performance of special functions. ate life animated solely by the physical and chemical —François Jacob, La logique du vivant: une histoire de l’hérédité laws that govern the nonliving universe. (The Logic of Life: A History of Heredity), 1970 Yet organisms possess extraordinary attributes, properties that distinguish them from other collections We must, however, acknowledge, as it seems to me, that of matter. What are these distinguishing features of liv- man with all his noble qualities... still bears in his ing organisms? bodily frame the indelible stamp of his lowly origin. A high degree of chemical complexity and —Charles Darwin, The Descent of Man, 1871 microscopic organization. Thousands of differ- ent molecules make up a cell’s intricate internal structures (Fig. 1–1a). Each has its characteristic ifteen to twenty billion years ago, the universe arose F as a cataclysmic eruption of hot, energy-rich sub- atomic particles. Within seconds, the simplest elements sequence of subunits, its unique three-dimensional structure, and its highly specific selection of binding partners in the cell. (hydrogen and helium) were formed. As the universe Systems for extracting, transforming, and expanded and cooled, material condensed under the in- using energy from the environment (Fig. fluence of gravity to form stars. Some stars became 1–1b), enabling organisms to build and maintain enormous and then exploded as supernovae, releasing their intricate structures and to do mechanical, the energy needed to fuse simpler atomic nuclei into the chemical, osmotic, and electrical work. Inanimate more complex elements. Thus were produced, over bil- matter tends, rather, to decay toward a more lions of years, the Earth itself and the chemical elements disordered state, to come to equilibrium with its found on the Earth today. About four billion years ago, surroundings. 1 8885d_c01_002 11/3/03 1:38 PM Page 2 mac76 mac76:385_reb: 2 Chapter 1 The Foundations of Biochemistry This is true not only of macroscopic structures, such as leaves and stems or hearts and lungs, but also of microscopic intracellular structures and indi- vidual chemical compounds. The interplay among the chemical components of a living organism is dy- namic; changes in one component cause coordinat- ing or compensating changes in another, with the whole ensemble displaying a character beyond that of its individual parts. The collection of molecules carries out a program, the end result of which is (a) reproduction of the program and self-perpetuation of that collection of molecules—in short, life. A history of evolutionary change. Organisms change their inherited life strategies to survive in new circumstances. The result of eons of evolution is an enormous diversity of life forms, superficially very different (Fig. 1–2) but fundamentally related through their shared ancestry. Despite these common properties, and the funda- mental unity of life they reveal, very few generalizations (b) about living organisms are absolutely correct for every organism under every condition; there is enormous di- versity. The range of habitats in which organisms live, from hot springs to Arctic tundra, from animal intestines to college dormitories, is matched by a correspondingly wide range of specific biochemical adaptations, achieved (c) FIGURE 1–1 Some characteristics of living matter. (a) Microscopic complexity and organization are apparent in this colorized thin sec- tion of vertebrate muscle tissue, viewed with the electron microscope. (b) A prairie falcon acquires nutrients by consuming a smaller bird. (c) Biological reproduction occurs with near-perfect fidelity. A capacity for precise self-replication and self-assembly (Fig. 1–1c). A single bacterial cell placed in a sterile nutrient medium can give rise to a billion identical “daughter” cells in 24 hours. Each cell contains thousands of different molecules, some extremely complex; yet each bacterium is a faithful copy of the original, its construction FIGURE 1–2 Diverse living organisms share common chemical fea- directed entirely from information contained tures. Birds, beasts, plants, and soil microorganisms share with hu- within the genetic material of the original cell. mans the same basic structural units (cells) and the same kinds of Mechanisms for sensing and responding to macromolecules (DNA, RNA, proteins) made up of the same kinds of alterations in their surroundings, constantly monomeric subunits (nucleotides, amino acids). They utilize the same adjusting to these changes by adapting their pathways for synthesis of cellular components, share the same genetic internal chemistry. code, and derive from the same evolutionary ancestors. Shown here Defined functions for each of their compo- is a detail from “The Garden of Eden,” by Jan van Kessel the Younger nents and regulated interactions among them. (1626–1679). 8885d_c01_003 12/20/03 7:03 AM Page 3 mac76 mac76:385_reb: 1.1 Cellular Foundations 3 within a common chemical framework. For the sake of Nucleus (eukaryotes) clarity, in this book we sometimes risk certain general- or nucleoid (bacteria) Contains genetic material–DNA and izations, which, though not perfect, remain useful; we associated proteins. Nucleus is also frequently point out the exceptions that illuminate membrane-bounded. scientific generalizations. Plasma membrane Biochemistry describes in molecular terms the struc- Tough, flexible lipid bilayer. tures, mechanisms, and chemical processes shared by Selectively permeable to all organisms and provides organizing principles that polar substances. Includes membrane proteins that underlie life in all its diverse forms, principles we refer function in transport, to collectively as the molecular logic of life. Although in signal reception, biochemistry provides important insights and practical and as enzymes. applications in medicine, agriculture, nutrition, and industry, its ultimate concern is with the wonder of life itself. In this introductory chapter, then, we describe (briefly!) the cellular, chemical, physical (thermody- namic), and genetic backgrounds to biochemistry and the overarching principle of evolution—the develop- ment over generations of the properties of living cells. Cytoplasm As you read through the book, you may find it helpful Aqueous cell contents and to refer back to this chapter at intervals to refresh your suspended particles memory of this background material. and organelles. centrifuge at 150,000 g 1.1 Cellular Foundations The unity and diversity of organisms become apparent Supernatant: cytosol even at the cellular level. The smallest organisms consist Concentrated solution of enzymes, RNA, of single cells and are microscopic. Larger, multicellular monomeric subunits, organisms contain many different types of cells, which metabolites, vary in size, shape, and specialized function. Despite inorganic ions. these obvious differences, all cells of the simplest and Pellet: particles and organelles most complex organisms share certain fundamental Ribosomes, storage granules, properties, which can be seen at the biochemical level. mitochondria, chloroplasts, lysosomes, endoplasmic reticulum. Cells Are the Structural and Functional Units of All FIGURE 1–3 The universal features of living cells. All cells have a Living Organisms nucleus or nucleoid, a plasma membrane, and cytoplasm. The cytosol Cells of all kinds share certain structural features (Fig. is defined as that portion of the cytoplasm that remains in the super- natant after centrifugation of a cell extract at 150,000 g for 1 hour. 1–3). The plasma membrane defines the periphery of the cell, separating its contents from the surroundings. It is composed of lipid and protein molecules that form The internal volume bounded by the plasma mem- a thin, tough, pliable, hydrophobic barrier around the brane, the cytoplasm (Fig. 1–3), is composed of an cell. The membrane is a barrier to the free passage of aqueous solution, the cytosol, and a variety of sus- inorganic ions and most other charged or polar com- pended particles with specific functions. The cytosol is pounds. Transport proteins in the plasma membrane al- a highly concentrated solution containing enzymes and low the passage of certain ions and molecules; receptor the RNA molecules that encode them; the components proteins transmit signals into the cell; and membrane (amino acids and nucleotides) from which these macro- enzymes participate in some reaction pathways. Be- molecules are assembled; hundreds of small organic cause the individual lipids and proteins of the plasma molecules called metabolites, intermediates in biosyn- membrane are not covalently linked, the entire struc- thetic and degradative pathways; coenzymes, com- ture is remarkably flexible, allowing changes in the pounds essential to many enzyme-catalyzed reactions; shape and size of the cell. As a cell grows, newly made inorganic ions; and ribosomes, small particles (com- lipid and protein molecules are inserted into its plasma posed of protein and RNA molecules) that are the sites membrane; cell division produces two cells, each with its of protein synthesis. own membrane. This growth and cell division (fission) All cells have, for at least some part of their life, ei- occurs without loss of membrane integrity. ther a nucleus or a nucleoid, in which the genome— 8885d_c01_01-46 10/27/03 7:48 AM Page 4 mac76 mac76:385_reb: 4 Chapter 1 The Foundations of Biochemistry the complete set of genes, composed of DNA—is stored molecular oxygen by diffusion from the surrounding and replicated. The nucleoid, in bacteria, is not sepa- medium through its plasma membrane. The cell is so rated from the cytoplasm by a membrane; the nucleus, small, and the ratio of its surface area to its volume is in higher organisms, consists of nuclear material en- so large, that every part of its cytoplasm is easily reached closed within a double membrane, the nuclear envelope. by O2 diffusing into the cell. As cell size increases, how- Cells with nuclear envelopes are called eukaryotes ever, surface-to-volume ratio decreases, until metabo- (Greek eu, “true,” and karyon, “nucleus”); those with- lism consumes O2 faster than diffusion can supply it. out nuclear envelopes—bacterial cells—are prokary- Metabolism that requires O2 thus becomes impossible otes (Greek pro, “before”). as cell size increases beyond a certain point, placing a theoretical upper limit on the size of the cell. Cellular Dimensions Are Limited by Oxygen Diffusion There Are Three Distinct Domains of Life Most cells are microscopic, invisible to the unaided eye. Animal and plant cells are typically 5 to 100
m in di- All living organisms fall into one of three large groups ameter, and many bacteria are only 1 to 2
m long (see (kingdoms, or domains) that define three branches of the inside back cover for information on units and their evolution from a common progenitor (Fig. 1–4). Two abbreviations). What limits the dimensions of a cell? The large groups of prokaryotes can be distinguished on bio- lower limit is probably set by the minimum number of chemical grounds: archaebacteria (Greek arche-, “ori- each type of biomolecule required by the cell. The gin”) and eubacteria (again, from Greek eu, “true”). smallest cells, certain bacteria known as mycoplasmas, Eubacteria inhabit soils, surface waters, and the tissues are 300 nm in diameter and have a volume of about of other living or decaying organisms. Most of the well- 10
14 mL. A single bacterial ribosome is about 20 nm in studied bacteria, including Escherichia coli, are eu- its longest dimension, so a few ribosomes take up a sub- bacteria. The archaebacteria, more recently discovered, stantial fraction of the volume in a mycoplasmal cell. are less well characterized biochemically; most inhabit The upper limit of cell size is probably set by the extreme environments—salt lakes, hot springs, highly rate of diffusion of solute molecules in aqueous systems. acidic bogs, and the ocean depths. The available evi- For example, a bacterial cell that depends upon oxygen- dence suggests that the archaebacteria and eubacteria consuming reactions for energy production must obtain diverged early in evolution and constitute two separate Eubacteria Eukaryotes Animals Ciliates Green Fungi Gram- positive nonsulfur Plants Purple bacteria bacteria bacteria Flagellates Cyanobacteria Flavobacteria Microsporidia Thermotoga Extreme halophiles Methanogens Extreme thermophiles Archaebacteria FIGURE 1–4 Phylogeny of the three domains of life. Phylogenetic relationships are often illustrated by a “family tree” of this type. The fewer the branch points between any two organisms, the closer is their evolutionary relationship. 8885d_c01_005 12/20/03 7:04 AM Page 5 mac76 mac76:385_reb: 1.1 Cellular Foundations 5 All organisms Phototrophs Chemotrophs (energy from (energy from chemical light) compounds) Autotrophs Heterotrophs Heterotrophs (carbon from (carbon from (carbon from organic CO2) organic compounds) compounds) Examples: Cyanobacteria Examples: Plants Purple bacteria Green bacteria Lithotrophs Organotrophs (energy from (energy from inorganic organic compounds) compounds) Examples: Examples: Sulfur bacteria Most prokaryotes FIGURE 1–5 Organisms can be classified according to their source Hydrogen bacteria All nonphototrophic of energy (sunlight or oxidizable chemical compounds) and their eukaryotes source of carbon for the synthesis of cellular material. domains, sometimes called Archaea and Bacteria. All eu- atoms exclusively from CO2 (that is, no chemotrophs karyotic organisms, which make up the third domain, are autotrophs), but the chemotrophs may be further Eukarya, evolved from the same branch that gave rise classified according to a different criterion: whether the to the Archaea; archaebacteria are therefore more fuels they oxidize are inorganic (lithotrophs) or or- closely related to eukaryotes than to eubacteria. ganic (organotrophs). Within the domains of Archaea and Bacteria are sub- Most known organisms fall within one of these four groups distinguished by the habitats in which they live. broad categories—autotrophs or heterotrophs among the In aerobic habitats with a plentiful supply of oxygen, photosynthesizers, lithotrophs or organotrophs among some resident organisms derive energy from the trans- the chemical oxidizers. The prokaryotes have several gen- fer of electrons from fuel molecules to oxygen. Other eral modes of obtaining carbon and energy. Escherichia environments are anaerobic, virtually devoid of oxy- coli, for example, is a chemoorganoheterotroph; it re- gen, and microorganisms adapted to these environments quires organic compounds from its environment as fuel obtain energy by transferring electrons to nitrate (form- and as a source of carbon. Cyanobacteria are photo- ing N2), sulfate (forming H2S), or CO2 (forming CH4). lithoautotrophs; they use sunlight as an energy source Many organisms that have evolved in anaerobic envi- and convert CO2 into biomolecules. We humans, like E. ronments are obligate anaerobes: they die when ex- coli, are chemoorganoheterotrophs. posed to oxygen. We can classify organisms according to how they Escherichia coli Is the Most-Studied Prokaryotic Cell obtain the energy and carbon they need for synthesiz- ing cellular material (as summarized in Fig. 1–5). There Bacterial cells share certain common structural fea- are two broad categories based on energy sources: pho- tures, but also show group-specific specializations (Fig. totrophs (Greek trophe-, “nourishment”) trap and use 1–6). E. coli is a usually harmless inhabitant of the hu- sunlight, and chemotrophs derive their energy from man intestinal tract. The E. coli cell is about 2
m long oxidation of a fuel. All chemotrophs require a source of and a little less than 1
m in diameter. It has a protec- organic nutrients; they cannot fix CO2 into organic com- tive outer membrane and an inner plasma membrane pounds. The phototrophs can be further divided into that encloses the cytoplasm and the nucleoid. Between those that can obtain all needed carbon from CO2 (au- the inner and outer membranes is a thin but strong layer totrophs) and those that require organic nutrients of polymers called peptidoglycans, which gives the cell (heterotrophs). No chemotroph can get its carbon its shape and rigidity. The plasma membrane and the 8885d_c01_006 11/3/03 1:39 PM Page 6 mac76 mac76:385_reb: 6 Chapter 1 The Foundations of Biochemistry Ribosomes Bacterial ribosomes are smaller than FIGURE 1–6 Common structural features of bacterial cells. Because eukaryotic ribosomes, but serve the same function— of differences in the cell envelope structure, some eubacteria (gram- protein synthesis from an RNA message. positive bacteria) retain Gram’s stain, and others (gram-negative bacteria) do not. E. coli is gram-negative. Cyanobacteria are also Nucleoid Contains a single, simple, long circular DNA eubacteria but are distinguished by their extensive internal membrane molecule. system, in which photosynthetic pigments are localized. Although the cell envelopes of archaebacteria and gram-positive eubacteria look Pili Provide similar under the electron microscope, the structures of the membrane points of lipids and the polysaccharides of the cell envelope are distinctly dif- adhesion to ferent in these organisms. surface of other cells. Flagella layers outside it constitute the cell envelope. In the Propel cell Archaea, rigidity is conferred by a different type of poly- through its surroundings. mer (pseudopeptidoglycan). The plasma membranes of eubacteria consist of a thin bilayer of lipid molecules penetrated by proteins. Archaebacterial membranes have a similar architecture, although their lipids differ strikingly from those of the eubacteria. The cytoplasm of E. coli contains about 15,000 ribosomes, thousands of copies each of about 1,000 Cell envelope different enzymes, numerous metabolites and cofac- Structure varies tors, and a variety of inorganic ions. The nucleoid with type of contains a single, circular molecule of DNA, and the bacteria. cytoplasm (like that of most bacteria) contains one or more smaller, circular segments of DNA called plas- mids. In nature, some plasmids confer resistance to toxins and antibiotics in the environment. In the labo- ratory, these DNA segments are especially amenable to experimental manipulation and are extremely use- ful to molecular geneticists. Most bacteria (including E. coli) lead existences as individual cells, but in some bacterial species cells tend Outer membrane Peptidoglycan layer to associate in clusters or filaments, and a few (the Peptidoglycan layer Inner membrane myxobacteria, for example) demonstrate simple social Inner membrane behavior. Eukaryotic Cells Have a Variety of Membranous Organelles, Which Can Be Isolated for Study Gram-negative bacteria Gram-positive bacteria Typical eukaryotic cells (Fig. 1–7) are much larger than Outer membrane; No outer membrane; prokaryotic cells—commonly 5 to 100
m in diameter, peptidoglycan layer thicker peptidoglycan layer with cell volumes a thousand to a million times larger than those of bacteria. The distinguishing characteristics of eukaryotes are the nucleus and a variety of membrane- bounded organelles with specific functions: mitochondria, endoplasmic reticulum, Golgi complexes, and lysosomes. Plant cells also contain vacuoles and chloroplasts (Fig. 1–7). Also present in the cytoplasm of many cells are granules or droplets containing stored nutrients such as starch and fat. Cyanobacteria Archaebacteria In a major advance in biochemistry, Albert Claude, Gram-negative; tougher No outer membrane; peptidoglycan layer; peptidoglycan layer outside Christian de Duve, and George Palade developed meth- extensive internal plasma membrane ods for separating organelles from the cytosol and from membrane system with each other—an essential step in isolating biomolecules photosynthetic pigments and larger cell components and investigating their 8885d_c01_007 1/15/04 3:28 PM Page 7 mac76 mac76:385_reb: 1.1 Cellular Foundations 7 (a) Animal cell Ribosomes are protein- synthesizing machines Peroxisome destroys peroxides Cytoskeleton supports cell, aids in movement of organells Lysosome degrades intracellular debris Transport vesicle shuttles lipids and proteins between ER, Golgi, and plasma membrane Golgi complex processes, packages, and targets proteins to other organelles or for export Smooth endoplasmic reticulum (SER) is site of lipid synthesis and drug metabolism Nuclear envelope segregates Nucleolus is site of ribosomal chromatin (DNA
protein) RNA synthesis from cytoplasm Nucleus contains the Rough endoplasmic reticulum (RER) is site of much protein genes (chromatin) Plasma membrane separates cell synthesis from environment, regulates movement of materials into and Ribosomes Cytoskeleton out of cell Mitochondrion oxidizes fuels to produce ATP Golgi complex Chloroplast harvests sunlight, produces ATP and carbohydrates Starch granule temporarily stores carbohydrate products of photosynthesis Thylakoids are site of light- driven ATP synthesis Cell wall provides shape and rigidity; protects cell from osmotic swelling Vacuole degrades and recycles macromolecules, stores metabolites Plasmodesma provides path Cell wall of adjacent cell between two plant cells Glyoxysome contains enzymes of the glyoxylate cycle FIGURE 1–7 Eukaryotic cell structure. Schematic illustrations of the (b) Plant cell two major types of eukaryotic cell: (a) a representative animal cell and (b) a representative plant cell. Plant cells are usually 10 to 100
m in diameter—larger than animal cells, which typically range from 5 to 30
m. Structures labeled in red are unique to either animal or plant cells.  8885d_c01_01-46 10/27/03 7:48 AM Page 8 mac76 mac76:385_reb: 8 Chapter 1 The Foundations of Biochemistry structures and functions. In a typical cell fractionation Differential centrifugation results in a rough fraction- (Fig. 1–8), cells or tissues in solution are disrupted by ation of the cytoplasmic contents, which may be further gentle homogenization. This treatment ruptures the purified by isopycnic (“same density”) centrifugation. In plasma membrane but leaves most of the organelles in- this procedure, organelles of different buoyant densities tact. The homogenate is then centrifuged; organelles (the result of different ratios of lipid and protein in each such as nuclei, mitochondria, and lysosomes differ in type of organelle) are separated on a density gradient. By size and therefore sediment at different rates. They also carefully removing material from each region of the gra- differ in specific gravity, and they “float” at different dient and observing it with a microscope, the biochemist levels in a density gradient. can establish the sedimentation position of each organelle FIGURE 1–8 Subcellular fractionation of tissue. A tissue such as liver is first mechanically homogenized to break cells and disperse their contents in an aqueous buffer. The sucrose medium has an osmotic pressure similar to that in organelles, thus preventing diffusion of wa- ter into the organelles, which would swell and burst. (a) The large and small particles in the suspension can be separated by centrifugation at different speeds, or (b) particles of different density can be sepa- rated by isopycnic centrifugation. In isopycnic centrifugation, a cen- trifuge tube is filled with a solution, the density of which increases (a) Differential from top to bottom; a solute such as sucrose is dissolved at different centrifugation concentrations to produce the density gradient. When a mixture of ❚ organelles is layered on top of the density gradient and the tube is ❚ Tissue centrifuged at high speed, individual organelles sediment until their ❚ ❚ homogenization ❚ buoyant density exactly matches that in the gradient. Each layer can ❚ be collected separately. ❚ ❚ ❚ ❚ ❚ Low-speed centrifugation ❚ ❚ ❚ ❚ ❚ ❚ (1,000 g, 10 min) ❚ ❚ ❚ ❚ ▲▲ ❚ ❚ ❚ ❚ ▲ ▲ ▲❚ ▲ ❚ ❚ ▲ Supernatant subjected to ❚ ❚ ❚ ❚ ❚ ❚ ▲ (b) Isopycnic medium-speed centrifugation ❚ ▲ ❚▲ ▲ ❚ ▲ ❚ ▲❚ (20,000 g, 20 min) (sucrose-density) ❚ ▲ ❚ ❚ ❚ ❚ ❚ centrifugation ❚ ▲ ❚ ▲ ❚ ❚ ❚ ▲ ▲ ❚ ❚▲ ❚ ▲ Supernatant subjected ▲ ❚ ▲ ▲ ❚ ❚ ❚ ❚ ▲ to high-speed ❚ ❚ ▲ ❚ ❚ ❚ centrifugation ▲ Tissue ❚ Centrifugation ❚ ❚ ▲ ❚▲ (80,000 g, 1 h) homogenate ❚ ▲ ▲ ❚ ❚ ❚ ❚ ❚ ▲ ❚ ▲ Supernatant ▲❚ ▲ ❚ ▲ ▲ ❚ ❚ subjected to ▲ ▲ ❚ ▲ ❚ ❚❚ ❚ ❚ ❚ very high-speed ❚ ❚ Pellet ❚ centrifugation ❚ ❚ ❚ contains ❚ (150,000 g, 3 h) ❚ ❚ ❚ ❚ ❚ ❚ whole cells, ❚ ❚❚ ❚❚ ❚ ❚ ❚ ❚ ❚ ❚ nuclei, ❚ ❚ ❚ ▲ ▲ ❚ ▲ cytoskeletons, ❚ ▲▲ ❚ ▲ ▲ ❚ ❚ ▲ ❚ ❚ ❚ ▲ ❚ ❚ ❚ plasma ❚ ❚❚ ❚ ❚ ❚ ❚ membranes ❚ ❚ Pellet ❚ ❚ contains Sample ❚❚ ❚ ❚ ❚ mitochondria, ❚❚ ❚ ❚ ❚ ❚ ❚ lysosomes, Supernatant Sucrose ❚ ❚ ❚ contains peroxisomes ❚ ❚ ❚ ❚ ❚ ❚❚❚❚ ❚ gradient ❚ ❚❚ soluble ❚ ❚ ❚ ❚ ❚ Pellet proteins ❚ ❚ ❚ ❚ ❚ contains Less dense ❚❚ ❚ ❚ ❚ microsomes (fragments of ER), component ❚ ❚ small vesicles Fractionation More dense Pellet contains component ribosomes, large macromolecules 8 7 6 5 4 3 2 1 8885d_c01_009 12/20/03 7:04 AM Page 9 mac76 mac76:385_reb: 1.1 Cellular Foundations 9 and obtain purified organelles for further study. For into their protein subunits and reassembly into fila- example, these methods were used to establish that ments. Their locations in cells are not rigidly fixed but lysosomes contain degradative enzymes, mitochondria may change dramatically with mitosis, cytokinesis, contain oxidative enzymes, and chloroplasts contain amoeboid motion, or changes in cell shape. The assem- photosynthetic pigments. The isolation of an organelle en- bly, disassembly, and location of all types of filaments riched in a certain enzyme is often the first step in the are regulated by other proteins, which serve to link or purification of that enzyme. bundle the filaments or to move cytoplasmic organelles along the filaments. The Cytoplasm Is Organized by the Cytoskeleton The picture that emerges from this brief survey of cell structure is that of a eukaryotic cell with a and Is Highly Dynamic meshwork of structural fibers and a complex system of Electron microscopy reveals several types of protein fila- membrane-bounded compartments (Fig. 1–7). The fila- ments crisscrossing the eukaryotic cell, forming an inter- ments disassemble and then reassemble elsewhere. Mem- locking three-dimensional meshwork, the cytoskeleton. branous vesicles bud from one organelle and fuse with There are three general types of cytoplasmic filaments— another. Organelles move through the cytoplasm along actin filaments, microtubules, and intermediate filaments protein filaments, their motion powered by energy de- (Fig. 1–9)—differing in width (from about 6 to 22 nm), pendent motor proteins. The endomembrane system composition, and specific function. All types provide segregates specific metabolic processes and provides structure and organization to the cytoplasm and shape surfaces on which certain enzyme-catalyzed reactions to the cell. Actin filaments and microtubules also help to occur. Exocytosis and endocytosis, mechanisms of produce the motion of organelles or of the whole cell. transport (out of and into cells, respectively) that involve Each type of cytoskeletal component is composed membrane fusion and fission, provide paths between the of simple protein subunits that polymerize to form fila- cytoplasm and surrounding medium, allowing for secre- ments of uniform thickness. These filaments are not per- tion of substances produced within the cell and uptake manent structures; they undergo constant disassembly of extracellular materials. Actin stress fibers Microtubules Intermediate filaments (a) (b) (c) FIGURE 1–9 The three types of cytoskeletal filaments. The upper pan- lin, or intermediate filament proteins are covalently attached to a els show epithelial cells photographed after treatment with antibodies fluorescent compound. When the cell is viewed with a fluorescence that bind to and specifically stain (a) actin filaments bundled together microscope, only the stained structures are visible. The lower panels to form “stress fibers,” (b) microtubules radiating from the cell center, show each type of filament as visualized by (a, b) transmission or and (c) intermediate filaments extending throughout the cytoplasm. For (c) scanning electron microscopy. these experiments, antibodies that specifically recognize actin, tubu- 8885d_c01_010 1/15/04 3:28 PM Page 10 mac76 mac76:385_reb: 10 Chapter 1 The Foundations of Biochemistry Although complex, this organization of the cyto- reversible, and subject to regulation in response to var- plasm is far from random. The motion and the position- ious intracellular and extracellular signals. ing of organelles and cytoskeletal elements are under tight regulation, and at certain stages in a eukaryotic Cells Build Supramolecular Structures cell’s life, dramatic, finely orchestrated reorganizations, Macromolecules and their monomeric subunits differ such as the events of mitosis, occur. The interactions be- greatly in size (Fig. 1–10). A molecule of alanine is less tween the cytoskeleton and organelles are noncovalent, than 0.5 nm long. Hemoglobin, the oxygen-carrying pro- tein of erythrocytes (red blood cells), consists of nearly (a) Some of the amino acids of proteins 600 amino acid subunits in four long chains, folded into globular shapes and associated in a structure 5.5 nm in


diameter. In turn, proteins are much smaller than ribo- COO COO COO A  A  A somes (about 20 nm in diameter), which are in turn H3NOCOH H3NOCOH H3NOCOH much smaller than organelles such as mitochondria, typ- A A A CH3 CH2OH CH2 ically 1,000 nm in diameter. It is a long jump from sim- A ple biomolecules to cellular structures that can be seen
Alanine Serine COO Aspartate

COO COO A  A
FIGURE 1–10 The organic compounds from which most cellular COO H3NOCOH H3NOCOH  A A A materials are constructed: the ABCs of biochemistry. Shown here are H3NOCOH CH2 CH2 A (a) six of the 20 amino acids from which all proteins are built (the A NH CH2 side chains are shaded pink); (b) the five nitrogenous bases, two five- C A CH SH carbon sugars, and phosphoric acid from which all nucleic acids are HC  NH built; (c) five components of membrane lipids; and (d) D-glucose, the Cysteine parent sugar from which most carbohydrates are derived. Note that OH Histidine phosphoric acid is a component of both nucleic acids and membrane Tyrosine lipids. (b) The components of nucleic acids (c) Some components of lipids O O NH2 COO
COO
CH2OH C C CH3 CH2 CH2 CHOH HN CH HN C N CH CH2 CH2 CH2OH C CH C CH C CH Glycerol O N O N O N CH2 CH2 H H H CH2 CH2 Uracil Thymine Cytosine CH3 CH2 CH2  CH3 N CH2CH2OH NH2 O CH2 CH2 CH3 C C O
CH2 CH2 Choline N N N C HN C CH CH2 CH CH HO P OH HC C C C CH CH2 N N H2N N N O H H Phosphoric acid CH2 CH2 Adenine Guanine (d) The parent sugar CH2 CH2 Nitrogenous bases CH2 CH2 HOCH2 O H HOCH2 O CH2 CH2 CH 2OH H H H CH2 CH2 O H H H H H OH H H OH CH2 CH3 OH H OH OH OH H Palmitate HO OH CH2  -D-Ribose H OH 2-Deoxy--D-ribose CH3 Five-carbon sugars Oleate  -D-Glucose 8885d_c01_011 12/20/03 7:04 AM Page 11 mac76 mac76:385_reb: 1.1 Cellular Foundati