《生物化学》课程教学资源（书籍文献）Biochemistry, sixth edition 2017, Reginald H. Garrett, Charles M. Grisham, University of Virginia

biochemistry SIXTH EDITION Reginald H.Garrett Charles M.Grisham University of Virginia With molecular graphic images by Michal Sabat,University of Virginia CemIngGE AustraliarMexicoSingaporeUnited Kingdom.United Stater

Reginald H. Garrett | Charles M. Grisham University of Virginia With molecular graphic images by Michal Sabat, University of Virginia biochemistry sixth edition Australia ● Brazil ● Mexico ● Singapore ● United Kingdom ● United States Copyright 2017 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it

ABOUT THE AUTHORS Reginald H.Garret Charles M Grisham and raised in Minneap 1日 d hi his Ph.D.in biology in 1968.Since that time,he has been at the B.S.in chemistry from the Illinois Institute of Technology in1969 University of Virginia,where he is currently Professor Emeritus and his Ph.D.in chemistry from the University of Minn esota in of Bi logy. 973.F lowing a pos University of Virginia.where he is Professor of Chemistry.He is genetic,and molecular biological aspects of inorganic nitrogen the author of previous editions of Biochemistry and Principlesof metabolism.His research interests focused on the pathway of Biochemistry (Cengage,Brooks/Cole),and numerous papers and filamentous fungi.His investigations con ctive transport ol sodium,po um. an etics ic udy systems approaches to the metabolic basis of nutrition-related CD-ROM and Workhe ook,a tutorial CD for students.His work diseases supported by the National Insti has ed by he National Institutes of He alth,the ar He is er ght Schol Unand pr t Bodenkultur in Vienna.Austria and served as Visiting Scholar at ociation.and the American Chemical Society.He isa Research the University of Cambridge on two separate occasions.During Caree Dev lopment Awardee of the National Institutes of in D and 19 siting S Sabatier/Toulouse inl and the of Chem of Sa Scientifique.Institute for Pharmacology and Structural Biology Diego He has taught biochemistry.introductory chemistry.and in France.He ta aught biochemistry at the University of Virginia American p: Society for Charles M.Grisham and Reginald H.Garrett iv

iv Charles M. Grisham was born and raised in Minneapolis, Minnesota, and educated at Benilde High School. He received his B.S. in chemistry from the Illinois Institute of Technology in 1969 and his Ph.D. in chemistry from the University of Minnesota in 1973. Following a postdoctoral appointment at the Institute for Cancer Research in Philadelphia, he joined the faculty of the University of Virginia, where he is Professor of Chemistry. He is the author of previous editions of Biochemistry and Principles of Biochemistry (Cengage, Brooks/Cole), and numerous papers and review articles on active transport of sodium, potassium, and calcium in mammalian systems, on protein kinase C, and on the applications of NMR and EPR spectroscopy to the study of biological systems. He has also authored Interactive Biochemistry CD-ROM and Workbook, a tutorial CD for students. His work has been supported by the National Institutes of Health, the National Science Foundation, the Muscular Dystrophy Associa￾tion of America, the Research Corporation, the American Heart Association, and the American Chemical Society. He is a Research Career Development Awardee of the National Institutes of Health, and in 1983 and 1984 he was a Visiting Scientist at the Aarhus University Institute of Physiology Denmark. In 1999, he was Knapp Professor of Chemistry at the University of San Diego. He has taught biochemistry, introductory chemistry, and physical chemistry at the University of Virginia for more than 40 years. He is a member of the American Society for Biochemis￾try and Molecular Biology. Reginald H. Garrett was educated in the Baltimore city public schools and at the Johns Hopkins University, where he received his Ph.D. in biology in 1968. Since that time, he has been at the University of Virginia, where he is currently Professor Emeritus of Biology. He is the author of previous editions of Biochemis￾try, as well as Principles of Biochemistry (Cengage, Brooks/Cole), and numerous papers and review articles on the biochemical, genetic, and molecular biological aspects of inorganic nitrogen metabolism. His research interests focused on the pathway of nitrate assimilation in filamentous fungi. His investigations con￾tributed substantially to our understanding of the enzymology, genetics, and regulation of this major pathway of biological nitrogen acquisition. More recently, he has collaborated in systems approaches to the metabolic basis of nutrition-related diseases. His research has been supported by the National Insti￾tutes of Health, the National Science Foundation, and private industry. He is a former Fulbright Scholar at the Universität für Bodenkultur in Vienna, Austria and served as Visiting Scholar at the University of Cambridge on two separate occasions. During the second, he was Thomas Jefferson Visiting Fellow in Downing College. In 2003, he was Professeur Invité at the Université Paul Sabatier/Toulouse III and the Centre National de la Recherche Scientifique, Institute for Pharmacology and Structural Biology in France. He taught biochemistry at the University of Virginia for 46 years. He is a member of the American Society for Biochemistry and Molecular Biology. Charles M. Grisham and Reginald H. Garrett Georgia Cobb Garrett About the Authors Copyright 2017 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it

CONTENTS IN BRIEF PART I Molecular Components of Cells 1 The Facts of Life: Is the Logic of Biological Phenomena 1 Water:The Medium of Life 31 of Biological Systems 53 4 Amino Acids and the Peptide Bo d 79 5 Proteins:Their Primary Structure and Biological Functions 105 6 Proteins Secondary Tertiary and Quaternary Structure 147 7 Carbohydrates and the Glycoconjugates of Cell Surfaces 203 8 Lipids 245 9 Membranes and Membrane Transport 273 10 Nucleotides and Nucleic Acids 325 11 Structure of Nucleic Acids 353 12 Recombinant DNA,Cloning.Chimeric Genes.and Synthetic Biology 399 PART II Protein Dynamics 437 13 Enzymes-Kinetics and Specificity 437 14 Mechanisms of Enzyme Action 477 15 Enzyme Regulation 513 16 Molecular Motors 547 PART III Metabolism and Its Regulation 583 17 Metabolism:An Overview 583 18 Glycolysis 611 19 The Tricarboxylic Acid Cycle 643 20 Electron Transport and Oxidative Phosphorylation 679 21 Photosynthesis 719 22 Gluconeogenesis,Glycogen Metabolism,and the Pentose Phosphate Pathway 755 23 Fatty Acid Catabolism 795 24 Lipid Biosynthesis 825 25 Nitrogen Acquisition and Amino Acid Metabolism 877 26 Synthesis and Degradation of Nucleotides 927 27 Metabolic Integration and Organ Specialization 957 PART IV Information Transfer 985 28 DNA Metabolism:Replication,Recombination,and Repair 985 29 Transcription and the Regulation of Gene Expression 1035 30 Protein Synthesis 1091 31 Completing the Protein Life Cycle:Folding.Processing.and Degradation 1131 32 The Reception and Transmission of Extracellular Information 1161 Abbreviated A-1 ndex 1-1 cee

v Part I Molecular Components of Cells 1 1 The Facts of Life: Chemistry Is the Logic of Biological Phenomena 1 2 Water: The Medium of Life 31 3 Thermodynamics of Biological Systems 53 4 Amino Acids and the Peptide Bond 79 5 Proteins: Their Primary Structure and Biological Functions 105 6 Proteins: Secondary, Tertiary, and Quaternary Structure 147 7 Carbohydrates and the Glycoconjugates of Cell Surfaces 203 8 Lipids 245 9 Membranes and Membrane Transport 273 10 Nucleotides and Nucleic Acids 325 11 Structure of Nucleic Acids 353 12 Recombinant DNA, Cloning, Chimeric Genes, and Synthetic Biology 399 Part II Protein Dynamics 437 13 Enzymes—Kinetics and Specificity 437 14 Mechanisms of Enzyme Action 477 15 Enzyme Regulation 513 16 Molecular Motors 547 Part III Metabolism and Its Regulation 583 17 Metabolism: An Overview 583 18 Glycolysis 611 19 The Tricarboxylic Acid Cycle 643 20 Electron Transport and Oxidative Phosphorylation 679 21 Photosynthesis 719 22 Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway 755 23 Fatty Acid Catabolism 795 24 Lipid Biosynthesis 825 25 Nitrogen Acquisition and Amino Acid Metabolism 877 26 Synthesis and Degradation of Nucleotides 927 27 Metabolic Integration and Organ Specialization 957 Part IV Information Transfer 985 28 DNA Metabolism: Replication, Recombination, and Repair 985 29 Transcription and the Regulation of Gene Expression 1035 30 Protein Synthesis 1091 31 Completing the Protein Life Cycle: Folding, Processing, and Degradation 1131 32 The Reception and Transmission of Extracellular Information 1161 Abbreviated Answers to Problems A-1 Index I-1 Contents in Brief Copyright 2017 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it

DETAILED CONTENTS PARTI MOLECULAR COMPONENTS OF CELLS EgoaaowenswBooenTrSrte 1 The Facts of Life:Chemistry Is the Logic How Many Genes Doesa Cell Need?1 of Biological Phenomena 1 1.1 What Are the Distinctive Properties of Living The structural oreanization of Eukaryotic cells is more Systems?1 Complex Than That of Prokaryotic Cells 20 1.2 What Kinds of Molecules Are Biomolecules?4 1.6 What Are Viruses?22 Biomolecules Are Carbon Compounds 5 SUMMARY 26 13 FOUNDATIONAL BIOCHEMISTRY 27 PROBLEMS 27 Metabolites Are Used to Form the Building Blocks FURTHER READING 29 of Macromolecules 2 Water:The Medium of Life 31 21 What Are the Properties of Water?32 Water Has Unusual Properties 32 The Unit of Life is the Cell 10 Hydrogen Bonding in Water Is Key to Its Properties 32 14 The Structure of lce Is Based on H-Bond Formation 32 How Do the Properties of Biomolecules Reflect Their Fitness to the Living Condition?10 olbgcdlhecromeetsandTterBuldinglocs nt Properties of Water Derive from Its Pola omol Water Can lonize to Form H+and OH-37 2.2 What Is pH>38 ctrolytes dissociate co Weak Forces Maintain Biological Structure and Determine Biomolecular Interactions 12 ate Only Slightly in Water 40 The Henderson-Ha n Bonds Are Important in Biomolecular Presenc Titration Curves lustrate the Progressive Dissociation Through Structura of a Weak Acid 42 Phosphoric Acid Has Three Dissociable H+43 Chemedated byWek Biomolecular Rec 2.3 What Are Buffers,and What Do They Do?44 Range Metabolic Reactions 16 Serves HUMAN BIOCHEMISTRY:The Bicarbonate Buffer System 1.5 What Are of Cells of Blood Plasma 46 H

vi Critical Developments in Biochemistry: Synthetic Life 18 How Many Genes Does a Cell Need? 19 Archaea and Bacteria Have a Relatively Simple Structural Organization 20 The Structural Organization of Eukaryotic Cells Is More Complex Than That of Prokaryotic Cells 20 1.6 What Are Viruses? 22 SUMMARY 26 Foundational Biochemistry 27 PROBLEMS 27 Further Reading 29 2 Water: The Medium of Life 31 2.1 What Are the Properties of Water? 32 Water Has Unusual Properties 32 Hydrogen Bonding in Water Is Key to Its Properties 32 The Structure of Ice Is Based on H-Bond Formation 32 Molecular Interactions in Liquid Water Are Based on H Bonds 33 The Solvent Properties of Water Derive from Its Polar Nature 34 Water Can Ionize to Form H1 and OH2 37 2.2 What Is pH? 38 Strong Electrolytes Dissociate Completely in Water 39 Weak Electrolytes Are Substances That Dissociate Only Slightly in Water 40 The Henderson–Hasselbalch Equation Describes the Dissociation of a Weak Acid in the Presence of Its Conjugate Base 41 Titration Curves Illustrate the Progressive Dissociation of a Weak Acid 42 Phosphoric Acid Has Three Dissociable H1 43 2.3 What Are Buffers, and What Do They Do? 44 The Phosphate Buffer System Is a Major Intracellular Buffering System 45 The Imidazole Group of Histidine Also Serves as an Intracellular Buffering System 45 Human Biochemistry: The Bicarbonate Buffer System of Blood Plasma 46 “Good” Buffers Are Buffers Useful Within Physiological pH Ranges 47 Part I Molecular Components of Cells 1 The Facts of Life: Chemistry Is the Logic of Biological Phenomena 1 1.1 What Are the Distinctive Properties of Living Systems? 1 1.2 What Kinds of Molecules Are Biomolecules? 4 Biomolecules Are Carbon Compounds 5 1.3 What Is the Structural Organization of Complex Biomolecules? 7 Metabolites Are Used to Form the Building Blocks of Macromolecules 7 Organelles Represent a Higher Order in Biomolecular Organization 9 Membranes Are Supramolecular Assemblies That Define the Boundaries of Cells 9 The Unit of Life Is the Cell 10 1.4 How Do the Properties of Biomolecules Reflect Their Fitness to the Living Condition? 10 Biological Macromolecules and Their Building Blocks Have a “Sense” or Directionality 10 Biological Macromolecules Are Informational 10 Biomolecules Have Characteristic Three-Dimensional Architecture 12 Weak Forces Maintain Biological Structure and Determine Biomolecular Interactions 12 Van der Waals Attractive Forces Play an Important Role in Biomolecular Interactions 12 Hydrogen Bonds Are Important in Biomolecular Interactions 13 The Defining Concept of Biochemistry Is “Molecular Recognition Through Structural Complementarity” 14 Biomolecular Recognition Is Mediated by Weak Chemical Forces 15 Weak Forces Restrict Organisms to a Narrow Range of Environmental Conditions 15 Enzymes Catalyze Metabolic Reactions 16 The Time Scale of Life 17 1.5 What Are the Organization and Structure of Cells? 18 The Eukaryotic Cell Likely Emerged from an Archaeal Lineage 18 Detailed Contents Copyright 2017 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it

Detailed Contents HUMAN BIOCHEMISTRY:Blood ph and respiration 47 Standard Reduction Potentials Are Measured in Reaction 2.4 Half.Cells71 Vaes Can Be Used o Predict the Direction SUMMARY 48 FOUNDATIONAL BIOCHEMISTRY 49 in Redox Reactions 7 to Analyze Energy Changes PROBLEMS 50 The Reduction Potential Depends on Concentration 74 FURTHER READING 51 SUMMARY 74 FOUNDATIONAL BIOCHEMISTRY 75 3 Thermodynamics of Biological Systems 53 3.1 FURTHER READING 77 Reactions 54 4 Amino Acids and the Peptide Bond 79 the Structures and Properties of Amino ation,and the mino Acids Contain a Central Tetrahedral Carbor FoEeepodeas9peCteionforEaulbrium56 Atom 79 Amino Acids Can Join via Peptide Bonds 80 3.2 There Are 20 Common Amino Acids 81 Are There Other Ways to Classify Amino Acids?84 33 cfHond-Fr Amino Acids 21 and 22-and More?84 A DEEPER LOOK:Selenocysteine and Selenoproteins 84 Several Amino Acids Occur Only Rarely in Proteins 85 4.2 What Are the Acid-Base Properties of Amino 3.4 What Can Thermodynamic Parameters tell us about Acids?85 Biochemical Events?59 5 What Are the Characteristics of High-Energy Amino Acids Are Weak Polyprotic Acids 85 Biomolecules?60 ATP Is an Intermediate Energy-Shuttle Molecule 62 Acids 86 esno人u ric Acid Anhydrides Is Highly 4.3 What Reactions Do Amino Acids Undergo?89 4.4 What Are the Optical and Stereochemical Properties The Hydrolysis AG'of ATP and ADP Is Greater Than That of AMP66 of Amino Acids?89 Amino Acids Are Chiral Molecules 89 Acetyl Phosphate and 1.3.Bisphosp Chiral Molecules Are Described by the Dand (R.S) orylating Agents66 onventions 9 3.6 scentProtein TheLight Fantasi of H Jellyfish to Gene Expression9 olysis for ATP Is pH-De endent 67 4.5 What Are the Spectroscopic Properties of Amino of ATP 68 Acids?91 CTPegoaAcstheFetnegyofhdos overy of Absolute Configuration 92 Why Are Coupled Processes Important to Living Things?6 a 3.8 What Is the Daily Human Requirement for ATP?69 amino Aci Can Be Characterized by Nuclear Magnetic ADEEPER LOOK The Murchison Meteorite-Discovery of 39 Extraterrestrial Handedness 93 What Are Reduction Potentials,and How Are or Free Energy Change

Detailed Contents vii Standard Reduction Potentials Are Measured in Reaction Half-Cells 71 %o9 Values Can Be Used to Predict the Direction of Redox Reactions 72 %o9 Values Can Be Used to Analyze Energy Changes in Redox Reactions 72 The Reduction Potential Depends on Concentration 74 SUMMARY 74 Foundational Biochemistry 75 PROBLEMS 76 Further Reading 77 4 Amino Acids and the Peptide Bond 79 4.1 What Are the Structures and Properties of Amino Acids? 79 Typical Amino Acids Contain a Central Tetrahedral Carbon Atom 79 Amino Acids Can Join via Peptide Bonds 80 There Are 20 Common Amino Acids 81 Are There Other Ways to Classify Amino Acids? 84 Amino Acids 21 and 22—and More? 84 A Deeper Look: Selenocysteine and Selenoproteins 84 Several Amino Acids Occur Only Rarely in Proteins 85 4.2 What Are the Acid–Base Properties of Amino Acids? 85 Amino Acids Are Weak Polyprotic Acids 85 Critical Developments in Biochemistry: Adding New Chemistry to Proteins with Unnatural Amino Acids 86 Side Chains of Amino Acids Undergo Characteristic Ionizations 88 4.3 What Reactions Do Amino Acids Undergo? 89 4.4 What Are the Optical and Stereochemical Properties of Amino Acids? 89 Amino Acids Are Chiral Molecules 89 Chiral Molecules Are Described by the d,l and (R,S) Naming Conventions 90 Critical Developments in Biochemistry: Green Fluorescent Protein—The “Light Fantastic” from Jellyfish to Gene Expression 91 4.5 What Are the Spectroscopic Properties of Amino Acids? 91 Critical Developments in Biochemistry: Discovery of Optically Active Molecules and Determination of Absolute Configuration 92 Phenylalanine, Tyrosine, and Tryptophan Absorb Ultraviolet Light 92 Amino Acids Can Be Characterized by Nuclear Magnetic Resonance 92 A Deeper Look: The Murchison Meteorite—Discovery of Extraterrestrial Handedness 93 Critical Developments in Biochemistry: Rules for Description of Chiral Centers in the (R,S) System 94 Human Biochemistry: Blood pH and Respiration 47 2.4 What Properties of Water Give It a Unique Role in the Environment? 48 SUMMARY 48 Foundational Biochemistry 49 PROBLEMS 50 Further Reading 51 3 Thermodynamics of Biological Systems 53 3.1 What Are the Basic Concepts of Thermodynamics? 54 Three Quantities Describe the Energetics of Biochemical Reactions 54 All Reactions and Processes Follow the Laws of Thermodynamics 55 A Deeper Look: Entropy, Information, and the Importance of “Negentropy” 56 Free Energy Provides a Simple Criterion for Equilibrium 56 3.2 What Is the Effect of Concentration on Net Free Energy Changes? 57 3.3 What Is the Effect of pH on Standard-State Free Energies? 58 A Deeper Look: Comparing Standard State, Equilibrium, and Cellular Conditions 58 3.4 What Can Thermodynamic Parameters Tell Us About Biochemical Events? 59 3.5 What Are the Characteristics of High-Energy Biomolecules? 60 ATP Is an Intermediate Energy-Shuttle Molecule 62 Group Transfer Potentials Quantify the Reactivity of Functional Groups 62 The Hydrolysis of Phosphoric Acid Anhydrides Is Highly Favorable 63 The Hydrolysis DG89 of ATP and ADP Is Greater Than That of AMP 66 Acetyl Phosphate and 1,3-Bisphosphoglycerate Are Phosphoric-Carboxylic Anhydrides 66 Enol Phosphates Are Potent Phosphorylating Agents 66 3.6 What Are the Complex Equilibria Involved in ATP Hydrolysis? 67 The DG89 of Hydrolysis for ATP Is pH-Dependent 67 Metal Ions Affect the Free Energy of Hydrolysis of ATP 68 Concentration Affects the Free Energy of Hydrolysis of ATP 68 3.7 Why Are Coupled Processes Important to Living Things? 69 3.8 What Is the Daily Human Requirement for ATP? 69 A Deeper Look: ATP Changes the Keq by a Factor of 108  70 3.9 What Are Reduction Potentials, and How Are They Used to Account for Free Energy Changes in Redox Reactions? 71 Copyright 2017 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it

Detailed Contents 4.6 Step 1.Separation of Polypeptide Chains117 eSeparated by 47 hat Ist此 Fundamental Structural Pattern in Step 2 Cleavage of Disulfide Bridges 118 Step 3.N-and CTerminal Analysis 118 Peptide Bond Has Partial Double-ond Character97 Steps 4 and 5.Fragmentation of the Polypeptide Chain 120 toHow Many Amin 8eggeconrposadcfonecrMoePohpepide Acids They Contain 99 The amino acid sea FOUNDATIONAL BIOCHEMISTRY 10 5.5 PROBLEMS 102 What Is the Nature of Amino Acid Sequences?127 FURTHER READING 103 Homologous Prote 5 Proteins:Their Primary Structure and Biological Homoloy betwen Proteins 12 equences and Discove Functions 105 Related Proteins Sharea Common Evolutionary Origin 130 5.1 What Architectural Arrangements Characterize Protein Structure?105 AMoRoegne5agenwnhaSiehyDierenl 5.6 Can poly in the Labep tides Be Synthesized tor?134 Noncovalent Forces Drive Formation of the Higher Orders Solid.Phase Methods Are Very Useful in Peptide of Protein Structure 107 Synthesis 135 proten's Can Described as Its Overall 57 Do Proteins Have Chemical Groups Other Than Amino Acids?135 5.2 5.8 What Are the Many Biological Functions of Proteins?137 ation Methods Exploit Differences in Size and Charge 110 5.9 What is the Proteome and what Does it Tell Us>140 CRITICAL DEVELOPMENTS IN BIOCHEMISTRY:TWO New Suin Molecular Biology and Biochemistry:m ADEEPER LOOK:Techniques Used in Protein the Proteome ofa Cell 141 Purification 111 SUMMARY 5.3 How Is the Amino Acid Analysis of Proteins FOUNDATIONAL BIOCHEMISTRY 143 Performed?115 PROBLEMS 143 Acid Hydrolysis Liberates the Amino Acids FURTHER READING 145 6 Proteins:Secondary,Tertiary,and Quaternary The Amino Acid Compositions of Different Proteins Structure 147 What No Are Different 116 6.1 actions stabilize the Higher 5.4 How Is the Primary Structure of a Protein Levels of Protein Structure?148 Determined?116 Hydrogen Bonds Are Formed Whenever Possible 148 Hydrophobic Interactions Drive Protein Folding 148 The of Amino Acids in a Protein Is lonic Interactions Usually Occur on the Protein Was the First to Determine the Sequence Surface 149 ofa Protein 117 Van der Waals Interactions Are Ubiquitous 149 Both Methodologies Are Used in 6.2 Protein Sequencing 1

viii Detailed Contents Step 1. Separation of Polypeptide Chains 117 A Deeper Look: The Virtually Limitless Number of Different Amino Acid Sequences 118 Step 2. Cleavage of Disulfide Bridges 118 Step 3. N- and C-Terminal Analysis 118 Steps 4 and 5. Fragmentation of the Polypeptide Chain 120 Step 6. Reconstruction of the Overall Amino Acid Sequence 122 The Amino Acid Sequence of a Protein Can Be Determined by Mass Spectrometry 122 Sequence Databases Contain the Amino Acid Sequences of Millions of Different Proteins 126 5.5 What Is the Nature of Amino Acid Sequences? 127 Homologous Proteins from Different Organisms Have Homologous Amino Acid Sequences 128 Computer Programs Can Align Sequences and Discover Homology between Proteins 128 Related Proteins Share a Common Evolutionary Origin 130 Apparently Different Proteins May Share a Common Ancestry 130 A Mutant Protein Is a Protein with a Slightly Different Amino Acid Sequence 133 5.6 Can Polypeptides Be Synthesized in the Laboratory? 134 Solid-Phase Methods Are Very Useful in Peptide Synthesis 135 5.7 Do Proteins Have Chemical Groups Other Than Amino Acids? 135 5.8 What Are the Many Biological Functions of Proteins? 137 5.9 What Is the Proteome and What Does It Tell Us? 140 The Proteome Is Dynamic 140 Critical Developments in Biochemistry: Two New Suffixes in Molecular Biology and Biochemistry: “-ome” and “-omics” 140 Determining the Proteome of a Cell 141 SUMMARY 141 Foundational Biochemistry 143 PROBLEMS 143 Further Reading 145 6 Proteins: Secondary, Tertiary, and Quaternary Structure 147 6.1 What Noncovalent Interactions Stabilize the Higher Levels of Protein Structure? 148 Hydrogen Bonds Are Formed Whenever Possible 148 Hydrophobic Interactions Drive Protein Folding 148 Ionic Interactions Usually Occur on the Protein Surface 149 Van der Waals Interactions Are Ubiquitous 149 6.2 What Role Does the Amino Acid Sequence Play in Protein Structure? 149 4.6 How Are Amino Acid Mixtures Separated and Analyzed? 95 Amino Acids Can Be Separated by Chromatography 95 4.7 What Is the Fundamental Structural Pattern in Proteins? 96 The Peptide Bond Has Partial Double-Bond Character 97 The Polypeptide Backbone Is Relatively Polar 99 Peptides Can Be Classified According to How Many Amino Acids They Contain 99 Proteins Are Composed of One or More Polypeptide Chains 99 SUMMARY 101 Foundational Biochemistry 101 PROBLEMS 102 Further Reading 103 5 Proteins: Their Primary Structure and Biological Functions 105 5.1 What Architectural Arrangements Characterize Protein Structure? 105 Proteins Fall into Three Basic Classes According to Shape and Solubility 105 Protein Structure Is Described in Terms of Four Levels of Organization 106 Noncovalent Forces Drive Formation of the Higher Orders of Protein Structure 107 A Protein’s Conformation Can Be Described as Its Overall Three-Dimensional Structure 109 5.2 How Are Proteins Isolated and Purified from Cells? 109 A Number of Protein Separation Methods Exploit Differences in Size and Charge 110 A Deeper Look: Estimation of Protein Concentrations in Solutions of Biological Origin 110 A Typical Protein Purification Scheme Uses a Series of Separation Methods 111 A Deeper Look: Techniques Used in Protein Purification 111 5.3 How Is the Amino Acid Analysis of Proteins Performed? 115 Acid Hydrolysis Liberates the Amino Acids of a Protein 115 Chromatographic Methods Are Used to Separate the Amino Acids 116 The Amino Acid Compositions of Different Proteins Are Different 116 5.4 How Is the Primary Structure of a Protein Determined? 116 The Sequence of Amino Acids in a Protein Is Distinctive 116 Sanger Was the First to Determine the Sequence of a Protein 117 Both Chemical and Enzymatic Methodologies Are Used in Protein Sequencing 117 Copyright 2017 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it

Detailed Contents ix 63 What Are the Elements of Secondary Stru HUMAN BIOCHEMISTRY -A Tale All Protein Structure Is Based on the Amide Plane 150 HUMAN BIOCHEMISTRY:Diseases of Protein Folding 191 The Alpha-Helix is a Key Secondary Structure 151 HUMAN BIOCHEMISTRY:Structural Genomics 191 A DEEPER LOOK:Knowing What the Right Hand and Left There Is Symmetry in Quaternary Structures 192 Quaternary Association Is Driven by Weak Forces 192 heet Is a Co 冬人9 Structure in Pr Open Quatemary Structures Can Polymerize 194 ther 19 e Features and a Nobel Prize 156 ionalAd antages Helix-Sheet Composites in Spider Silk 156 HUMAN BIOCHEMISTRY:Faster-Acting Insulin:Geneti Engine ring So ves a Quaternary Structure Problem 19 6.4 How D n Thee-Dmen SUMMARY 197 tein FOUNDATIONAL BIOCHEMISTRY 19 p. PROBLEMS 198 tif in protein 161 FURTHER READING 199 164 Helices and Sheets Make up the Core of Most Globular 7 Carbohydrates and the Glycoconjugates Proteins 165 Waters on the Protein Surface Stabilize the Structure 166 of Cell Surfaces 203 7.1 How Are Carbohydrates Named?204 Packing Considerations 166 72 HUMAN BIOCHEMISTRY:Collagen-Related Diseases 168 What Are the Structure and Chemistry of Monosaccharides?204 ot Nature Modua Strategy HUMAN BIOCHEMIS TDV.D and Ke Monosaccharides Exist in Cyclic and Anomeric Forms 206 Haworth Projections Are a Convenient Device A DEEPER LOOK:Protein Sectors:Evolutionary Units for Drawing Sugars 207 of Three-Dimensional Structure 171 Monosacc Be Converted to Severa Denaturatis toLoss of Protein Structure DEE RLOOK Honey-An Ancestral Carbohydrat Anfinsen's Classic Experiment Proved That Sequence Treat 212 Determines Structure 176 73 What Are the Structure and Chemistry Is There a Single Mechanism for Protein Folding?177 of Oligosaccharides?214 Disaccharides Are the Simplest Oligosaccharides 214 A DEEPER LOOK Trehalose-A Natural Protectant Marginal Stability of the Tertiary Structure Makes Proteins MNph-Cal and Red Mea Flexible180 A Variety of Higher Oligosaccharides Occur Motion in Globular Proteins 180 in Nature 217 7.4 What Are the Structure and Chemistry of Polysaccharides?217 A DEEPER LOOK:Meta -A Consequence Polysacch grbamengooeoirousoue Most Glo and Protection Functions 218 Storage,Structure, glso85gsAePoiainsTitHepohe Polysaccharides Provide Stores of Energy 218 Some Proteins Are Intrinsically Unstructured 186 Polysaccharides Provide Physical Structure and Strength How do protein Subunits Inte eract at the Quatemary Level of Protein Structure?189 e年

Detailed Contents ix Human Biochemistry: a1-Antitrypsin—A Tale of Molecular Mousetraps and a Folding Disease 190 Human Biochemistry: Diseases of Protein Folding 191 Human Biochemistry: Structural Genomics 191 There Is Symmetry in Quaternary Structures 192 Quaternary Association Is Driven by Weak Forces 192 Open Quaternary Structures Can Polymerize 194 A Deeper Look: Immunoglobulins—All the Features of Protein Structure Brought Together 195 There Are Structural and Functional Advantages to Quaternary Association 195 Human Biochemistry: Faster-Acting Insulin: Genetic Engineering Solves a Quaternary Structure Problem 195 SUMMARY 197 Foundational Biochemistry 197 PROBLEMS 198 Further Reading 199 7 Carbohydrates and the Glycoconjugates of Cell Surfaces 203 7.1 How Are Carbohydrates Named? 204 7.2 What Are the Structure and Chemistry of Monosaccharides? 204 Monosaccharides Are Classified as Aldoses and Ketoses 204 Stereochemistry Is a Prominent Feature of Monosaccharides 204 Monosaccharides Exist in Cyclic and Anomeric Forms 206 Haworth Projections Are a Convenient Device for Drawing Sugars 207 Monosaccharides Can Be Converted to Several Derivative Forms 210 A Deeper Look: Honey—An Ancestral Carbohydrate Treat 212 7.3 What Are the Structure and Chemistry of Oligosaccharides? 214 Disaccharides Are the Simplest Oligosaccharides 214 A Deeper Look: Trehalose—A Natural Protectant for Bugs 215 Human Biochemistry: Alpha-Gal and Red Meat Allergy 216 A Variety of Higher Oligosaccharides Occur in Nature 217 7.4 What Are the Structure and Chemistry of Polysaccharides? 217 Nomenclature for Polysaccharides Is Based on Their Composition and Structure 217 Polysaccharides Serve Energy Storage, Structure, and Protection Functions 218 Polysaccharides Provide Stores of Energy 218 Polysaccharides Provide Physical Structure and Strength to Organisms 219 A Deeper Look: Billiard Balls, Exploding Teeth, and Dynamite—The Colorful History of Cellulose 220 6.3 What Are the Elements of Secondary Structure in Proteins, and How Are They Formed? 150 All Protein Structure Is Based on the Amide Plane 150 The Alpha-Helix Is a Key Secondary Structure 151 A Deeper Look: Knowing What the Right Hand and Left Hand Are Doing 152 The b-Pleated Sheet Is a Core Structure in Proteins 155 Critical Developments in Biochemistry: In Bed with a Cold, Pauling Stumbles onto the a-Helix and a Nobel Prize 156 Helix–Sheet Composites in Spider Silk 156 b-Turns Allow the Protein Strand to Change Direction 158 6.4 How Do Polypeptides Fold into Three-Dimensional Protein Structures? 159 Fibrous Proteins Usually Play a Structural Role 160 A Deeper Look: The Coiled-Coil Motif in Proteins 161 Globular Proteins Mediate Cellular Function 164 Helices and Sheets Make up the Core of Most Globular Proteins 165 Waters on the Protein Surface Stabilize the Structure 166 Packing Considerations 166 Human Biochemistry: Collagen-Related Diseases 168 Protein Domains Are Nature’s Modular Strategy for Protein Design 168 Human Biochemistry: Domain-Based Engineering of Proteins Forms the Basis of a Novel Cancer Treatment 169 Classification Schemes for the Protein Universe Are Based on Domains 170 A Deeper Look: Protein Sectors: Evolutionary Units of Three-Dimensional Structure 171 Denaturation Leads to Loss of Protein Structure and Function 174 Anfinsen’s Classic Experiment Proved That Sequence Determines Structure 176 Is There a Single Mechanism for Protein Folding? 177 A Deeper Look: Measuring Friction in the Protein Folding Process 178 What Is the Thermodynamic Driving Force for Folding of Globular Proteins? 180 Marginal Stability of the Tertiary Structure Makes Proteins Flexible 180 Motion in Globular Proteins 180 The Folding Tendencies and Patterns of Globular Proteins 181 A Deeper Look: Metamorphic Proteins—A Consequence of Dynamism and Marginal Stability 182 Most Globular Proteins Belong to One of Four Structural Classes 184 Molecular Chaperones Are Proteins That Help Other Proteins to Fold 186 Some Proteins Are Intrinsically Unstructured 186 6.5 How Do Protein Subunits Interact at the Quaternary Level of Protein Structure? 189 Copyright 2017 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it

Detailed Contents 83 A DEEPER LOOK:A Complex Polysaccharide in Red is Are the Most Common Wine-The Strange Story of Rhamnogalacturonan ll 224 ADEEPER LOOK:Will the Real Glycophospholipid Come Forward?25 Fruits of ts of Phloem and the Large ycerophos Peptidoglycan s the Polysaccharide of BacteriaCell HUMAN RICO HEMISTRY:Platelet-Activating Factor Walls 226 A Potent Glyceroether Mediator 254 Animals Display a Variety of Cell Surface Polysaccharides 228 8.4 7.5 c8ropoindHowoognion egg2ndHeoAempotn 8.5 and How Are They Used?254 A DEEPER LOOK:Novel Lipids with Valuable Properties 256 O-GleNAc Signaling Is Altered in Diabetes and Cancer 230 86 es, ance e3257 O-Linked Saccharides Form Rigid Extended Extracellular Structures 230 A DEEPER LOOK:Why Do Plants Emit Is ne3259 Polar Fish Depend on Antifreeze Glycoproteins 230 HUMAN BIOCHEMISTRY:Coumadin or Warfarin- -Agent of Life or Death 259 87 What are steroids and what are their Cellulat A DEEPER LOOKD nds a Sweet Spot 232 Functions?260 Sialic Acid te des Cholesterol 260 Steroid Hormones Are Derived from Cholesterol 26 ADEEPER LOOK:N-Linked Oligosaccharides Help and Stanol E2 old by Both Intrinsic and Extrinsi 17B.H Sialic Acid Cleavage Can Ser ve asa Timing Device Dehydrogenase 3 Deficiency 262 for Protein Degradation 233 8.8 How Do Lipids and Their Metabolites Act 7.6 How Do Proteoglycans Modulate Processes as Biological Signals?263 in Cells and Organisms?234 A DEEPER LOOK:Glycerophospholipid Degradation: aes2Poioashoendngooa One of the Effects of Sna e Venom 26 MnOaDnsope2neP HUMAN BIO 7.7 Do Carbohydrates Provide a Structural Code?3 8.9 What Can Lipidomics Tell Us about Cell,Tissue,and Sugar Code Organ Physiology?267 SUMMARY 269 Mediators of Inflammation,Immunity. FOUNDATIONAL RIOCHEMISTRY 270 and Cancer 240 PRORIEMS 270 CReactive Protein-A Lectin That Limits Inflammation FURTHER READING 27 SUMMARY 241 Membranes and Membrane Transport 273 FOUNDATIONAL BIOCHEMISTRY 242 9.1 What are the chemical and physical properties PROBLEMS 242 of Membranes>274 FURTHER READING 243 The Composition of Membranes Suits Their Functions 274 Lipids Form Ordered Structures Spontaneously in Water 275 8 Lipids 245 8.1 The Fluid Mosaic Model Describes Membrane What Are the Structures and Chemistry of Fatty Dynamics 27 Acids?245 9.2 82 What Are the St 5224 s and Chemistry of Mem of Tri ADEEPER LOOK:Polar Bears Prefer Nonpolar Food 249 RphelMmrrngotensAsocateLoseh p

x Detailed Contents 8.3 What Are the Structures and Chemistry of Glycerophospholipids? 250 Glycerophospholipids Are the Most Common Phospholipids 250 A Deeper Look: Will the Real Glycophospholipid Come Forward? 251 Ether Glycerophospholipids Include PAF and Plasmalogens 253 Human Biochemistry: Platelet-Activating Factor: A Potent Glyceroether Mediator 254 8.4 What Are Sphingolipids, and How Are They Important for Higher Animals? 254 8.5 What Are Waxes, and How Are They Used? 254 A Deeper Look: Novel Lipids with Valuable Properties 256 8.6 What Are Terpenes, and What Is Their Relevance to Biological Systems? 257 A Deeper Look: Why Do Plants Emit Isoprene? 259 Human Biochemistry: Coumadin or Warfarin—Agent of Life or Death 259 8.7 What Are Steroids, and What Are Their Cellular Functions? 260 Cholesterol 260 Steroid Hormones Are Derived from Cholesterol 261 Human Biochemistry: Plant Sterols and Stanols— Natural Cholesterol Fighters 261 Human Biochemistry: 17b-Hydroxysteroid Dehydrogenase 3 Deficiency 262 8.8 How Do Lipids and Their Metabolites Act as Biological Signals? 263 A Deeper Look: Glycerophospholipid Degradation: One of the Effects of Snake Venom 264 Human Biochemistry: The Endocannabinoid Signaling System: A Target for Next-Generation Therapeutics 264 Human Biochemistry: Fingolimod—a Sphingosine-1-P Mimic Is an Oral Drug for Multiple Sclerosis 266 8.9 What Can Lipidomics Tell Us about Cell, Tissue, and Organ Physiology? 267 SUMMARY 269 Foundational Biochemistry 270 PROBLEMS 270 Further Reading 271 9 Membranes and Membrane Transport 273 9.1 What Are the Chemical and Physical Properties of Membranes? 274 The Composition of Membranes Suits Their Functions 274 Lipids Form Ordered Structures Spontaneously in Water 275 The Fluid Mosaic Model Describes Membrane Dynamics 277 9.2 What Are the Structure and Chemistry of Membrane Proteins? 279 Peripheral Membrane Proteins Associate Loosely with the Membrane 279 A Deeper Look: Ruth Benerito and Wrinkle-Free Cotton Fabrics 222 A Deeper Look: A Complex Polysaccharide in Red Wine—The Strange Story of Rhamnogalacturonan II 224 Polysaccharides Provide Strength and Rigidity to Bacterial Cell Walls 225 A Deeper Look: The Secrets of Phloem and the Large Fruits of Cucurbitaceae 225 Peptidoglycan Is the Polysaccharide of Bacterial Cell Walls 226 Animals Display a Variety of Cell Surface Polysaccharides 228 7.5 What Are Glycoproteins, and How Do They Function in Cells? 228 Carbohydrates on Proteins Can Be O-Linked or N-Linked 228 O-GlcNAc Signaling Is Altered in Diabetes and Cancer 230 O-Linked Saccharides Form Rigid Extended Extracellular Structures 230 Polar Fish Depend on Antifreeze Glycoproteins 230 N-Linked Oligosaccharides Can Affect the Physical Properties and Functions of a Protein 231 A Deeper Look: Drug Research Finds a Sweet Spot 232 Sialic Acid Terminates the Oligosaccharides of Glycoproteins and Glycolipids 232 A Deeper Look: N-Linked Oligosaccharides Help Proteins Fold by Both Intrinsic and Extrinsic Effects 233 Sialic Acid Cleavage Can Serve as a Timing Device for Protein Degradation 233 7.6 How Do Proteoglycans Modulate Processes in Cells and Organisms? 234 Functions of Proteoglycans Involve Binding to Other Proteins 234 Proteoglycans May Modulate Cell Growth Processes 236 Proteoglycans Make Cartilage Flexible and Resilient 237 7.7 Do Carbohydrates Provide a Structural Code? 237 Lectins Translate the Sugar Code 238 Selectins, Rolling Leukocytes, and the Inflammatory Response 239 Galectins—Mediators of Inflammation, Immunity, and Cancer 240 C-Reactive Protein—A Lectin That Limits Inflammation Damage 240 SUMMARY 241 Foundational Biochemistry 242 PROBLEMS 242 Further Reading 243 8 Lipids 245 8.1 What Are the Structures and Chemistry of Fatty Acids? 245 8.2 What Are the Structures and Chemistry of Triacylglycerols? 248 A Deeper Look: Polar Bears Prefer Nonpolar Food 249 Copyright 2017 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it

Detailed Contents Integral Membrane Proteins Are Firmly Anchored The properties of pyrimidines and purines can be traced in the Membrane 280 to Their Electron-Rich Nature 327 Lipid-Anchored Membrane Poten Are Switching 10.2 What Are Nucleosides?328 HUMAN BIOCHEMISTRY:Adenosine:A Nucleoside with Physiological Activity 328 10.3 93 What Are the Structure and Chemistry of Nucleotides?329 Structures 290 Cyclic Nucleotides Are Cyclic Phosphodiesters 330 94 What are the dynamic Processes that modulate phosphates Are 330 Membrane Function?291 HUMAN BIOCHEMISTRY Lipids and Proteins Undergo a Variety of Movements mbranes NDPs and NTPs Are Polyprotic Acids 332 embrane Lipids Can BeOrdered to Different Extents 292 Nucleosie 5'Triphosphates Are Carriers of Chemical 9.5 nergy 33. 10.4 What Are Nucleic Acids?333 9.6 What Is Passive Diffusion?301 10.5 What Are the Different Classes of Nucleic Acids?334 How Does Facilitated Diffusion Occur?301 ne Fundamenta s a D Membrane Channel Proteins Facilitate Diffusion 30. arious Forms RNA Serve Differen es in Cells 337 The esa Variation Practical Applications?339 Coa Pentameric 305 A DEEPER LOOK-The rNA world and farly fvolution 342 Chloride Water.Glyce erol.and Ammonia Flow Through The Chemical Differences Between DNA and RNA Have Single-Subunit Pores 306 Biological Significance 342 98 How Does Energy Input Drive Active Transport 10.6 Are Nucleic Acids Susceptible to Hydrolysis?343 Processes?307 RNA Is Susceptible to Hydrolysis by Base.but DNA nspor sem Are Eergy-oupin s Not 343 y Nucleases Differ in Their Specificity for Different Forms of Nucleic Acid 345 ABC Transporters Use ATP to Drive Import and Export Functions and Provide Multidrug Resistance 313 9.9 How Are Certain Transport Processes Driven e Useful by Light Energy?315 the Structureo 9.10 lary Active Transport Driven by lon SUMMARY 349 321 FOUNDATIONAL BIOCHEMISTRY 350 Naand HDrive Secondary Active Tra ort 316 PROBLEMS 351 AcrB Is a Secondary Active Tr. FURTHER READING 352 SUMMARY 318 11 Structure of Nucleic Acids 353 BIOCHEMISTRY 319 1 PROBLEMS 319 FURTHER READING 321 ence of DNa Can be d nad 10 Nucleotides and nucleic Acids 325 from the Electrophoretic Mig of Polynu 10.1 What Are the stru re and Chemistry of Nitroge nous Bases?326 ocanomeDte2ahodUse Three P rimidines and Two Purines Are Commonly Found of Polynucleotide Fragments 354 in Cells 326 Next-Generation Sequencing 356 ee ce

Detailed Contents xi The Properties of Pyrimidines and Purines Can Be Traced to Their Electron-Rich Nature 327 10.2 What Are Nucleosides? 328 Human Biochemistry: Adenosine: A Nucleoside with Physiological Activity 328 10.3 What Are the Structure and Chemistry of Nucleotides? 329 Cyclic Nucleotides Are Cyclic Phosphodiesters 330 Nucleoside Diphosphates and Triphosphates Are Nucleotides with Two or Three Phosphate Groups 330 Human Biochemistry: cGAMP, A Cyclic Dinucleotide That Triggers a Response to Infection 331 NDPs and NTPs Are Polyprotic Acids 332 Nucleoside 59-Triphosphates Are Carriers of Chemical Energy 332 10.4 What Are Nucleic Acids? 333 The Base Sequence of a Nucleic Acid Is Its Defining Characteristic 333 10.5 What Are the Different Classes of Nucleic Acids? 334 The Fundamental Structure of DNA Is a Double Helix 334 Various Forms of RNA Serve Different Roles in Cells 337 A Deeper Look: Do the Properties of DNA Invite Practical Applications? 339 A Deeper Look: The RNA World and Early Evolution 342 The Chemical Differences Between DNA and RNA Have Biological Significance 342 10.6 Are Nucleic Acids Susceptible to Hydrolysis? 343 RNA Is Susceptible to Hydrolysis by Base, but DNA Is Not 343 The Enzymes That Hydrolyze Nucleic Acids Are Phosphodiesterases 343 Nucleases Differ in Their Specificity for Different Forms of Nucleic Acid 345 Restriction Enzymes Are Nucleases That Cleave Double-Stranded DNA Molecules 345 Type II Restriction Endonucleases Are Useful for Manipulating DNA in the Lab 346 Restriction Endonucleases Can Be Used to Map the Structure of a DNA Fragment 349 SUMMARY 349 Foundational Biochemistry 350 PROBLEMS 351 Further Reading 352 11 Structure of Nucleic Acids 353 11.1 How Do Scientists Determine the Primary Structure of Nucleic Acids? 353 The Nucleotide Sequence of DNA Can Be Determined from the Electrophoretic Migration of a Defined Set of Polynucleotide Fragments 354 Sanger’s Chain Termination or Dideoxy Method Uses DNA Replication to Generate a Defined Set of Polynucleotide Fragments 354 Next-Generation Sequencing 356 Integral Membrane Proteins Are Firmly Anchored in the Membrane 280 Lipid-Anchored Membrane Proteins Are Switching Devices 287 Human Biochemistry: “Fat-Free Proteins” May Point the Way to Drugs for Sleeping Sickness 289 9.3 How Are Biological Membranes Organized? 290 Membranes Are Asymmetric and Heterogeneous Structures 290 9.4 What Are the Dynamic Processes That Modulate Membrane Function? 291 Lipids and Proteins Undergo a Variety of Movements in Membranes 291 Membrane Lipids Can Be Ordered to Different Extents 292 9.5 How Does Transport Occur Across Biological Membranes? 300 9.6 What Is Passive Diffusion? 301 Charged Species May Cross Membranes by Passive Diffusion 301 9.7 How Does Facilitated Diffusion Occur? 301 Membrane Channel Proteins Facilitate Diffusion 302 The B. cereus NaK Channel Uses a Variation on the K1 Selectivity Filter 304 CorA Is a Pentameric Mg21 Channel 305 Chloride, Water, Glycerol, and Ammonia Flow Through Single-Subunit Pores 306 9.8 How Does Energy Input Drive Active Transport Processes? 307 All Active Transport Systems Are Energy-Coupling Devices 307 Many Active Transport Processes Are Driven by ATP 308 A Deeper Look: Cardiac Glycosides: Potent Drugs from Ancient Times 312 ABC Transporters Use ATP to Drive Import and Export Functions and Provide Multidrug Resistance 313 9.9 How Are Certain Transport Processes Driven by Light Energy? 315 Bacteriorhodopsin Uses Light Energy to Drive Proton Transport 315 9.10 How Is Secondary Active Transport Driven by Ion Gradients? 316 Na1 and H1 Drive Secondary Active Transport 316 AcrB Is a Secondary Active Transport System 316 SUMMARY 318 Foundational Biochemistry 319 PROBLEMS 319 Further Reading 321 10 Nucleotides and Nucleic Acids 325 10.1 What Are the Structure and Chemistry of Nitrogenous Bases? 326 Three Pyrimidines and Two Purines Are Commonly Found in Cells 326 Copyright 2017 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it

xii Detailed Contents High-T Wha e Secondary and Tertiary Structures Ilumina Next-Gen Sequencing 358 :The Human Cenome RNA AIS Order Structure 1.2 What Sorts of Secondary Structures Car e-5 anded D p 2360 re Are oli cifically selected for Their Ligand-Binding Ability 393 SUMMARY 393 Molecules 362 founDATIONAL BIOCHEMISTRY 395 Watson-Crick Base Pairs Have Virtually Identical PROBLEMS 395 Di FURTHER READING 397 e DNA Doub Helixsa Stable Str A DEEPE Why Just Two s36 Adopt a Number of Stable 12 Recombinant DNA,Cloning,Chimeric ctures can Genes,and Synthetic Biology 399 A-Form DNA Is an Alternative Form of Right-Handed 12.1 What Does It Mean "To Clone"?399 DNA 366 Plasmids Are Very Useful in Cloning Genes 400 ninthe Form Shuttle Ve nic Structure 369 Be Create 12.2 What Is a DNA Library?406 Alternative Hydrogen-Bonding Interactions Give Rise red from the Total DNA in an Oreanism 406 13 CRITICAL DEVELOPMENTS IN BIOCHEMISTRY: Combinatorial Libraries 40 tion of DNA Can Be Observed an for the Presenc of by Changes in UV Absorbance 374 Probes for scree ne libraries can be prepared in a H-onding Solutes Denature Variety of Ways 40 PCR Is Used to Clone and Amplify Specific Genes 408 nded DNA Can Renature to Form DNA DNA Libraries Prepared PMENTS IN BIOCHEMIS Specific DNA Se nces b A D PER LOO he Buoyant Density of DNA 376 606ouhemBog A Stra DNA M 1.4 123 Kind of s of High plexity?377 the Clo enes in Libraries d41 in DNA 377 ad so That the n.5 What Is the Str e of Fuka es Are the Fundamental Structural Unit es?379 in Chromatin 380 meric DNA M Next to an Easily Expressible Gene Product 416 Gives Rise to 05383 nization east Iw 1.6 Can Nucleic Acids Be Synthesized Chemically?383 419 orm 12.4 How Is RN Jsed to Revea nes?41 Genes Can Be Synthesized Chemically 385 Jsing Synthetic shRN A5420

xii Detailed Contents 11.7 What Are the Secondary and Tertiary Structures of RNA? 386 Transfer RNA Adopts Higher-Order Structure Through Intrastrand Base Pairing 387 Messenger RNA Adopts Higher-Order Structure Through Intrastrand Base Pairing 390 Ribosomal RNA Also Adopts Higher-Order Structure Through Intrastrand Base Pairing 391 Aptamers Are Oligonucleotides Specifically Selected for Their Ligand-Binding Ability 393 SUMMARY 393 Foundational Biochemistry 395 PROBLEMS 395 Further Reading 397 12 Recombinant DNA, Cloning, Chimeric Genes, and Synthetic Biology 399 12.1 What Does It Mean “To Clone”? 399 Plasmids Are Very Useful in Cloning Genes 400 Shuttle Vectors Are Plasmids That Can Propagate in Two Different Organisms 405 Artificial Chromosomes Can Be Created from Recombinant DNA 405 12.2 What Is a DNA Library? 406 Genomic Libraries Are Prepared from the Total DNA in an Organism 406 Critical Developments in Biochemistry: Combinatorial Libraries 406 Libraries Can Be Screened for the Presence of Specific Genes 407 Probes for Screening Libraries Can Be Prepared in a Variety of Ways 408 PCR Is Used to Clone and Amplify Specific Genes 408 cDNA Libraries Are DNA Libraries Prepared from mRNA 409 Critical Developments in Biochemistry: Identifying Specific DNA Sequences by Southern Blotting (Southern Hybridization) 410 DNA Microarrays (Gene Chips) Are Arrays of Different Oligonucleotides Immobilized on a Chip 412 12.3 Can the Cloned Genes in Libraries Be Expressed? 413 Expression Vectors Are Engineered So That the RNA or Protein Products of Cloned Genes Can Be Expressed 413 Reporter Gene Constructs Are Chimeric DNA Molecules Composed of Gene Regulatory Sequences Positioned Next to an Easily Expressible Gene Product 416 Specific Protein–Protein Interactions Can Be Identified Using the Yeast Two-Hybrid System 417 In Vitro Mutagenesis 419 12.4 How Is RNA Interference Used to Reveal the Function of Genes? 419 RNAi Using Synthetic shRNAs 420 High-Throughput DNA Sequencing by the Light of Fireflies 356 Illumina Next-Gen Sequencing 358 Emerging Technologies to Sequence DNA Are Based on Single-Molecule Sequencing Strategies 358 Human Biochemistry: The Human Genome Project 360 11.2 What Sorts of Secondary Structures Can Double-Stranded DNA Molecules Adopt? 360 Conformational Variation in Polynucleotide Strands 360 DNA Usually Occurs in the Form of Double-Stranded Molecules 362 Watson–Crick Base Pairs Have Virtually Identical Dimensions 362 The DNA Double Helix Is a Stable Structure 362 A Deeper Look: Why Just Two Base Pairs? 363 Double Helical Structures Can Adopt a Number of Stable Conformations 365 A-Form DNA Is an Alternative Form of Right-Handed DNA 366 Z-DNA Is a Conformational Variation in the Form of a Left-Handed Double Helix 367 The Double Helix Is a Very Dynamic Structure 369 Human Biochemistry: DNA Methylation, CpG Islands, and Epigenetics 369 Alternative Hydrogen-Bonding Interactions Give Rise to Novel DNA Structures: Cruciforms, Triplexes, and Quadruplexes 371 11.3 Can the Secondary Structure of DNA Be Denatured and Renatured? 374 Thermal Denaturation of DNA Can Be Observed by Changes in UV Absorbance 374 pH Extremes or Strong H-Bonding Solutes also Denature DNA Duplexes 375 Single-Stranded DNA Can Renature to Form DNA Duplexes 375 The Rate of DNA Renaturation Is an Index of DNA Sequence Complexity 375 A Deeper Look: The Buoyant Density of DNA 376 Nucleic Acid Hybridization: Different DNA Strands of Similar Sequence Can Form Hybrid Duplexes 376 11.4 Can DNA Adopt Structures of Higher Complexity? 377 Supercoils Are One Kind of Structural Complexity in DNA 377 11.5 What Is the Structure of Eukaryotic Chromosomes? 379 Nucleosomes Are the Fundamental Structural Unit in Chromatin 380 Higher-Order Structural Organization of Chromatin Gives Rise to Chromosomes 381 SMC Proteins Establish Chromosome Organization and Mediate Chromosome Dynamics 383 11.6 Can Nucleic Acids Be Synthesized Chemically? 383 Phosphoramidite Chemistry Is Used to Form Oligonucleotides from Nucleotides 384 Genes Can Be Synthesized Chemically 385 Copyright 2017 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it