Tài liệu Lehninger principle of biochemistry 4th

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-todate 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: 1 chapter THE FOUNDATIONS OF BIOCHEMISTRY 1.1 1.2 1.3 1.4 1.5 Cellular Foundations 3 Chemical Foundations 12 Physical Foundations 21 Genetic Foundations 28 Evolutionary Foundations 31 With the cell, biology discovered its atom . . . To characterize life, it was henceforth essential to study the cell and analyze its structure: to single out the common denominators, necessary for the life of every cell; alternatively, to identify differences associated with the performance of special functions. —François Jacob, La logique du vivant: une histoire de l’hérédité (The Logic of Life: A History of Heredity), 1970 We must, however, acknowledge, as it seems to me, that man with all his noble qualities . . . still bears in his bodily frame the indelible stamp of his lowly origin. —Charles Darwin, The Descent of Man, 1871 ifteen to twenty billion years ago, the universe arose as a cataclysmic eruption of hot, energy-rich subatomic particles. Within seconds, the simplest elements (hydrogen and helium) were formed. As the universe expanded and cooled, material condensed under the influence of gravity to form stars. Some stars became enormous and then exploded as supernovae, releasing the energy needed to fuse simpler atomic nuclei into the more complex elements. Thus were produced, over billions of years, the Earth itself and the chemical elements found on the Earth today. About four billion years ago, F life arose—simple microorganisms with the ability to extract energy from organic compounds or from sunlight, which they used to make a vast array of more complex biomolecules from the simple elements and compounds on the Earth’s surface. Biochemistry asks how the remarkable properties of living organisms arise from the thousands of different lifeless biomolecules. When these molecules are isolated and examined individually, they conform to all the physical and chemical laws that describe the behavior of inanimate matter—as do all the processes occurring in living organisms. The study of biochemistry shows how the collections of inanimate molecules that constitute living organisms interact to maintain and perpetuate life animated solely by the physical and chemical laws that govern the nonliving universe. Yet organisms possess extraordinary attributes, properties that distinguish them from other collections of matter. What are these distinguishing features of living organisms? A high degree of chemical complexity and microscopic organization. Thousands of different molecules make up a cell’s intricate internal structures (Fig. 1–1a). Each has its characteristic sequence of subunits, its unique three-dimensional structure, and its highly specific selection of binding partners in the cell. Systems for extracting, transforming, and using energy from the environment (Fig. 1–1b), enabling organisms to build and maintain their intricate structures and to do mechanical, chemical, osmotic, and electrical work. Inanimate matter tends, rather, to decay toward a more disordered state, to come to equilibrium with its surroundings. 1 8885d_c01_002 2 11/3/03 Chapter 1 1:38 PM Page 2 mac76 mac76:385_reb: The Foundations of Biochemistry (a) (b) This is true not only of macroscopic structures, such as leaves and stems or hearts and lungs, but also of microscopic intracellular structures and individual chemical compounds. The interplay among the chemical components of a living organism is dynamic; changes in one component cause coordinating 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 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 fundamental unity of life they reveal, very few generalizations about living organisms are absolutely correct for every organism under every condition; there is enormous diversity. 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 section 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 directed entirely from information contained within the genetic material of the original cell. Mechanisms for sensing and responding to alterations in their surroundings, constantly adjusting to these changes by adapting their internal chemistry. Defined functions for each of their components and regulated interactions among them. FIGURE 1–2 Diverse living organisms share common chemical features. Birds, beasts, plants, and soil microorganisms share with humans the same basic structural units (cells) and the same kinds of macromolecules (DNA, RNA, proteins) made up of the same kinds of monomeric subunits (nucleotides, amino acids). They utilize the same pathways for synthesis of cellular components, share the same genetic code, and derive from the same evolutionary ancestors. Shown here is a detail from “The Garden of Eden,” by Jan van Kessel the Younger (1626–1679). 8885d_c01_003 12/20/03 7:03 AM Page 3 mac76 mac76:385_reb: 1.1 within a common chemical framework. For the sake of clarity, in this book we sometimes risk certain generalizations, which, though not perfect, remain useful; we also frequently point out the exceptions that illuminate scientific generalizations. Biochemistry describes in molecular terms the structures, mechanisms, and chemical processes shared by all organisms and provides organizing principles that underlie life in all its diverse forms, principles we refer to collectively as the molecular logic of life. Although biochemistry provides important insights and practical 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 (thermodynamic), and genetic backgrounds to biochemistry and the overarching principle of evolution—the development over generations of the properties of living cells. As you read through the book, you may find it helpful to refer back to this chapter at intervals to refresh your memory of this background material. 1.1 Cellular Foundations The unity and diversity of organisms become apparent even at the cellular level. The smallest organisms consist of single cells and are microscopic. Larger, multicellular organisms contain many different types of cells, which vary in size, shape, and specialized function. Despite these obvious differences, all cells of the simplest and most complex organisms share certain fundamental properties, which can be seen at the biochemical level. Cells Are the Structural and Functional Units of All Living Organisms Cells of all kinds share certain structural features (Fig. 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 a thin, tough, pliable, hydrophobic barrier around the cell. The membrane is a barrier to the free passage of inorganic ions and most other charged or polar compounds. Transport proteins in the plasma membrane allow the passage of certain ions and molecules; receptor proteins transmit signals into the cell; and membrane enzymes participate in some reaction pathways. Because the individual lipids and proteins of the plasma membrane are not covalently linked, the entire structure is remarkably flexible, allowing changes in the shape and size of the cell. As a cell grows, newly made lipid and protein molecules are inserted into its plasma membrane; cell division produces two cells, each with its own membrane. This growth and cell division (fission) occurs without loss of membrane integrity. Cellular Foundations 3 Nucleus (eukaryotes) or nucleoid (bacteria) Contains genetic material–DNA and associated proteins. Nucleus is membrane-bounded. Plasma membrane Tough, flexible lipid bilayer. Selectively permeable to polar substances. Includes membrane proteins that function in transport, in signal reception, and as enzymes. Cytoplasm Aqueous cell contents and suspended particles and organelles. centrifuge at 150,000 g Supernatant: cytosol Concentrated solution of enzymes, RNA, monomeric subunits, metabolites, inorganic ions. Pellet: particles and organelles Ribosomes, storage granules, mitochondria, chloroplasts, lysosomes, endoplasmic reticulum. FIGURE 1–3 The universal features of living cells. All cells have a nucleus or nucleoid, a plasma membrane, and cytoplasm. The cytosol is defined as that portion of the cytoplasm that remains in the supernatant after centrifugation of a cell extract at 150,000 g for 1 hour. The internal volume bounded by the plasma membrane, the cytoplasm (Fig. 1–3), is composed of an aqueous solution, the cytosol, and a variety of suspended particles with specific functions. The cytosol is a highly concentrated solution containing enzymes and the RNA molecules that encode them; the components (amino acids and nucleotides) from which these macromolecules are assembled; hundreds of small organic molecules called metabolites, intermediates in biosynthetic and degradative pathways; coenzymes, compounds essential to many enzyme-catalyzed reactions; inorganic ions; and ribosomes, small particles (composed of protein and RNA molecules) that are the sites of protein synthesis. All cells have, for at least some part of their life, either a nucleus or a nucleoid, in which the genome— 8885d_c01_01-46 4 10/27/03 7:48 AM Page 4 mac76 mac76:385_reb: The Foundations of Biochemistry Chapter 1 the complete set of genes, composed of DNA—is stored and replicated. The nucleoid, in bacteria, is not separated from the cytoplasm by a membrane; the nucleus, in higher organisms, consists of nuclear material enclosed within a double membrane, the nuclear envelope. Cells with nuclear envelopes are called eukaryotes (Greek eu, “true,” and karyon, “nucleus”); those without nuclear envelopes—bacterial cells—are prokaryotes (Greek pro, “before”). molecular oxygen by diffusion from the surrounding medium through its plasma membrane. The cell is so small, and the ratio of its surface area to its volume is so large, that every part of its cytoplasm is easily reached by O2 diffusing into the cell. As cell size increases, however, surface-to-volume ratio decreases, until metabolism consumes O2 faster than diffusion can supply it. Metabolism that requires O2 thus becomes impossible 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 Most cells are microscopic, invisible to the unaided eye. Animal and plant cells are typically 5 to 100
m in diameter, and many bacteria are only 1 to 2
m long (see the inside back cover for information on units and their abbreviations). What limits the dimensions of a cell? The lower limit is probably set by the minimum number of each type of biomolecule required by the cell. The smallest cells, certain bacteria known as mycoplasmas, are 300 nm in diameter and have a volume of about 10
14 mL. A single bacterial ribosome is about 20 nm in its longest dimension, so a few ribosomes take up a substantial fraction of the volume in a mycoplasmal cell. The upper limit of cell size is probably set by the rate of diffusion of solute molecules in aqueous systems. For example, a bacterial cell that depends upon oxygenconsuming reactions for energy production must obtain There Are Three Distinct Domains of Life All living organisms fall into one of three large groups (kingdoms, or domains) that define three branches of evolution from a common progenitor (Fig. 1–4). Two large groups of prokaryotes can be distinguished on biochemical grounds: archaebacteria (Greek arche-, “origin”) and eubacteria (again, from Greek eu, “true”). Eubacteria inhabit soils, surface waters, and the tissues of other living or decaying organisms. Most of the wellstudied bacteria, including Escherichia coli, are eubacteria. The archaebacteria, more recently discovered, are less well characterized biochemically; most inhabit extreme environments—salt lakes, hot springs, highly acidic bogs, and the ocean depths. The available evidence suggests that the archaebacteria and eubacteria diverged early in evolution and constitute two separate Eubacteria Eukaryotes Animals Purple bacteria Grampositive bacteria Green nonsulfur bacteria Ciliates Fungi Plants 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 (energy from light) Autotrophs (carbon from CO2) Examples: •Cyanobacteria •Plants Chemotrophs (energy from chemical compounds) Heterotrophs (carbon from organic compounds) Heterotrophs (carbon from organic compounds) Examples: •Purple bacteria •Green bacteria FIGURE 1–5 Organisms can be classified according to their source of energy (sunlight or oxidizable chemical compounds) and their source of carbon for the synthesis of cellular material. domains, sometimes called Archaea and Bacteria. All eukaryotic organisms, which make up the third domain, Eukarya, evolved from the same branch that gave rise to the Archaea; archaebacteria are therefore more closely related to eukaryotes than to eubacteria. Within the domains of Archaea and Bacteria are subgroups distinguished by the habitats in which they live. In aerobic habitats with a plentiful supply of oxygen, some resident organisms derive energy from the transfer of electrons from fuel molecules to oxygen. Other environments are anaerobic, virtually devoid of oxygen, and microorganisms adapted to these environments obtain energy by transferring electrons to nitrate (forming N2), sulfate (forming H2S), or CO2 (forming CH4). Many organisms that have evolved in anaerobic environments are obligate anaerobes: they die when exposed to oxygen. We can classify organisms according to how they obtain the energy and carbon they need for synthesizing cellular material (as summarized in Fig. 1–5). There are two broad categories based on energy sources: phototrophs (Greek trophe-, “nourishment”) trap and use sunlight, and chemotrophs derive their energy from oxidation of a fuel. All chemotrophs require a source of organic nutrients; they cannot fix CO2 into organic compounds. The phototrophs can be further divided into those that can obtain all needed carbon from CO2 (autotrophs) and those that require organic nutrients (heterotrophs). No chemotroph can get its carbon Lithotrophs (energy from inorganic compounds) Organotrophs (energy from organic compounds) Examples: •Sulfur bacteria •Hydrogen bacteria Examples: •Most prokaryotes •All nonphototrophic eukaryotes atoms exclusively from CO2 (that is, no chemotrophs are autotrophs), but the chemotrophs may be further classified according to a different criterion: whether the fuels they oxidize are inorganic (lithotrophs) or organic (organotrophs). Most known organisms fall within one of these four broad categories—autotrophs or heterotrophs among the photosynthesizers, lithotrophs or organotrophs among the chemical oxidizers. The prokaryotes have several general modes of obtaining carbon and energy. Escherichia coli, for example, is a chemoorganoheterotroph; it requires organic compounds from its environment as fuel and as a source of carbon. Cyanobacteria are photolithoautotrophs; they use sunlight as an energy source and convert CO2 into biomolecules. We humans, like E. coli, are chemoorganoheterotrophs. Escherichia coli Is the Most-Studied Prokaryotic Cell Bacterial cells share certain common structural features, but also show group-specific specializations (Fig. 1–6). E. coli is a usually harmless inhabitant of the human intestinal tract. The E. coli cell is about 2
m long and a little less than 1
m in diameter. It has a protective outer membrane and an inner plasma membrane that encloses the cytoplasm and the nucleoid. Between the inner and outer membranes is a thin but strong layer of polymers called peptidoglycans, which gives the cell its shape and rigidity. The plasma membrane and the 8885d_c01_006 6 11/3/03 Chapter 1 1:39 PM Page 6 mac76 mac76:385_reb: The Foundations of Biochemistry Ribosomes Bacterial ribosomes are smaller than eukaryotic ribosomes, but serve the same function— protein synthesis from an RNA message. Nucleoid Contains a single, simple, long circular DNA molecule. Pili Provide points of adhesion to surface of other cells. Flagella Propel cell through its surroundings. Cell envelope Structure varies with type of bacteria. Outer membrane Peptidoglycan layer Peptidoglycan layer Inner membrane Inner membrane FIGURE 1–6 Common structural features of bacterial cells. Because of differences in the cell envelope structure, some eubacteria (grampositive bacteria) retain Gram’s stain, and others (gram-negative bacteria) do not. E. coli is gram-negative. Cyanobacteria are also eubacteria but are distinguished by their extensive internal membrane system, in which photosynthetic pigments are localized. Although the cell envelopes of archaebacteria and gram-positive eubacteria look similar under the electron microscope, the structures of the membrane lipids and the polysaccharides of the cell envelope are distinctly different in these organisms. layers outside it constitute the cell envelope. In the Archaea, rigidity is conferred by a different type of polymer (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 different enzymes, numerous metabolites and cofactors, and a variety of inorganic ions. The nucleoid contains a single, circular molecule of DNA, and the cytoplasm (like that of most bacteria) contains one or more smaller, circular segments of DNA called plasmids. In nature, some plasmids confer resistance to toxins and antibiotics in the environment. In the laboratory, these DNA segments are especially amenable to experimental manipulation and are extremely useful to molecular geneticists. Most bacteria (including E. coli) lead existences as individual cells, but in some bacterial species cells tend to associate in clusters or filaments, and a few (the myxobacteria, for example) demonstrate simple social behavior. Eukaryotic Cells Have a Variety of Membranous Organelles, Which Can Be Isolated for Study Gram-negative bacteria Outer membrane; peptidoglycan layer Gram-positive bacteria No outer membrane; thicker peptidoglycan layer Cyanobacteria Gram-negative; tougher peptidoglycan layer; extensive internal membrane system with photosynthetic pigments Archaebacteria No outer membrane; peptidoglycan layer outside plasma membrane Typical eukaryotic cells (Fig. 1–7) are much larger than prokaryotic cells—commonly 5 to 100
m in diameter, 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 membranebounded 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. In a major advance in biochemistry, Albert Claude, Christian de Duve, and George Palade developed methods for separating organelles from the cytosol and from each other—an essential step in isolating biomolecules 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 proteinsynthesizing 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 chromatin (DNA
protein) from cytoplasm Nucleolus is site of ribosomal RNA synthesis Nucleus contains the Rough endoplasmic reticulum genes (chromatin) (RER) is site of much protein synthesis Plasma membrane separates cell from environment, regulates movement of materials into and out of cell Ribosomes Cytoskeleton 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 lightdriven ATP synthesis Cell wall provides shape and rigidity; protects cell from osmotic swelling Vacuole degrades and recycles macromolecules, stores metabolites Plasmodesma provides path between two plant cells Cell wall of adjacent cell Glyoxysome contains enzymes of the glyoxylate cycle FIGURE 1–7 Eukaryotic cell structure. Schematic illustrations of the 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. (b) Plant cell 8885d_c01_01-46 10/27/03 Page 8 mac76 mac76:385_reb: The Foundations of Biochemistry Chapter 1 8 7:48 AM structures and functions. In a typical cell fractionation (Fig. 1–8), cells or tissues in solution are disrupted by gentle homogenization. This treatment ruptures the plasma membrane but leaves most of the organelles intact. The homogenate is then centrifuged; organelles such as nuclei, mitochondria, and lysosomes differ in size and therefore sediment at different rates. They also differ in specific gravity, and they “float” at different levels in a density gradient. 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 water 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 separated by isopycnic centrifugation. In isopycnic centrifugation, a centrifuge tube is filled with a solution, the density of which increases from top to bottom; a solute such as sucrose is dissolved at different concentrations to produce the density gradient. When a mixture of organelles is layered on top of the density gradient and the tube is centrifuged at high speed, individual organelles sediment until their buoyant density exactly matches that in the gradient. Each layer can be collected separately. ❚ (a) Differential centrifugation ❚ ❚ Tissue homogenization ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚❚ ❚ ❚ ❚ ❚ ❚ ▲▲ Pellet contains mitochondria, lysosomes, peroxisomes Sample ❚ ❚ ❚ ❚ ❚ ❚ ▲ ❚❚ ▲❚ ▲ ▲ ❚ ❚ Supernatant subjected to very high-speed centrifugation (150,000 g, 3 h) ❚❚❚❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚❚ ❚ ❚ ❚ ❚ ❚❚ ❚❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚❚ ❚ ❚ ❚ Centrifugation ▲ ▲ ▲ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚❚ ❚ ❚ ❚ ▲ ▲ Pellet contains whole cells, nuclei, cytoskeletons, plasma membranes ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ▲ ❚ ❚ ❚ ▲ ▲ ▲ ▲ ❚ ❚ ❚ ❚ ❚ ❚ Supernatant subjected to high-speed centrifugation (80,000 g, 1 h) ❚ ▲ ❚▲ ❚ ❚ ❚ ❚ ❚ ❚ ▲ (b) Isopycnic (sucrose-density) centrifugation ▲ ▲ ▲ ❚ ▲ ▲❚ ❚▲ ▲ ❚ ❚ ❚▲ ❚ ❚ ▲ ❚ ❚ ▲ ▲ Tissue homogenate ▲ ❚ ❚ ❚ ▲ ▲ ▲ ❚ ▲ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ▲ ▲ ❚ ▲ ▲ Supernatant subjected to medium-speed centrifugation (20,000 g, 20 min) ❚ ▲ ▲ ❚ ❚ ▲ ▲▲ ▲❚ ▲ ▲ ❚ ❚ ❚ ❚ ▲ ❚ Low-speed centrifugation (1,000 g, 10 min) ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ Differential centrifugation results in a rough fractionation of the cytoplasmic contents, which may be further purified by isopycnic (“same density”) centrifugation. In this procedure, organelles of different buoyant densities (the result of different ratios of lipid and protein in each type of organelle) are separated on a density gradient. By carefully removing material from each region of the gradient and observing it with a microscope, the biochemist can establish the sedimentation position of each organelle Pellet contains microsomes (fragments of ER), small vesicles Supernatant contains soluble proteins Pellet contains ribosomes, large macromolecules Sucrose gradient Less dense component Fractionation More dense component 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 into their protein subunits and reassembly into filaments. Their locations in cells are not rigidly fixed but may change dramatically with mitosis, cytokinesis, amoeboid motion, or changes in cell shape. The assembly, disassembly, and location of all types of filaments are regulated by other proteins, which serve to link or bundle the filaments or to move cytoplasmic organelles along the filaments. The picture that emerges from this brief survey of cell structure is that of a eukaryotic cell with a meshwork of structural fibers and a complex system of membrane-bounded compartments (Fig. 1–7). The filaments disassemble and then reassemble elsewhere. Membranous vesicles bud from one organelle and fuse with another. Organelles move through the cytoplasm along protein filaments, their motion powered by energy dependent motor proteins. The endomembrane system segregates specific metabolic processes and provides surfaces on which certain enzyme-catalyzed reactions occur. Exocytosis and endocytosis, mechanisms of transport (out of and into cells, respectively) that involve membrane fusion and fission, provide paths between the cytoplasm and surrounding medium, allowing for secretion of substances produced within the cell and uptake of extracellular materials. and obtain purified organelles for further study. For example, these methods were used to establish that lysosomes contain degradative enzymes, mitochondria contain oxidative enzymes, and chloroplasts contain photosynthetic pigments. The isolation of an organelle enriched in a certain enzyme is often the first step in the purification of that enzyme. The Cytoplasm Is Organized by the Cytoskeleton and Is Highly Dynamic Electron microscopy reveals several types of protein filaments crisscrossing the eukaryotic cell, forming an interlocking three-dimensional meshwork, the cytoskeleton. There are three general types of cytoplasmic filaments— actin filaments, microtubules, and intermediate filaments (Fig. 1–9)—differing in width (from about 6 to 22 nm), composition, and specific function. All types provide structure and organization to the cytoplasm and shape to the cell. Actin filaments and microtubules also help to produce the motion of organelles or of the whole cell. Each type of cytoskeletal component is composed of simple protein subunits that polymerize to form filaments of uniform thickness. These filaments are not permanent structures; they undergo constant disassembly Actin stress fibers Microtubules Intermediate filaments (a) (b) (c) FIGURE 1–9 The three types of cytoskeletal filaments. The upper panels show epithelial cells photographed after treatment with antibodies that bind to and specifically stain (a) actin filaments bundled together to form “stress fibers,” (b) microtubules radiating from the cell center, and (c) intermediate filaments extending throughout the cytoplasm. For these experiments, antibodies that specifically recognize actin, tubu- 9 lin, or intermediate filament proteins are covalently attached to a fluorescent compound. When the cell is viewed with a fluorescence microscope, only the stained structures are visible. The lower panels show each type of filament as visualized by (a, b) transmission or (c) scanning electron microscopy.