Biochemistry

Cover 1 Table of Contents 2 Dedication 10 About the authors 10 Preface 10 Tools and Techniques 15 Clinical Applications 18 Molecular Evolution 22 Supplements Supporting Biochemistry, Fifth Edition 25 Acknowledgments 28 I. The Molecular Design of Life 34 1. Prelude: Biochemistry and the Genomic Revolution 35 1.1. DNA Illustrates the Relation between Form and Function 37 1.2. Biochemical Unity Underlies Biological Diversity 41 1.3. Chemical Bonds in Biochemistry 43 1.4. Biochemistry and Human Biology 52 Appendix: Depicting Molecular Structures 53 2. Biochemical Evolution 57 2.1. Key Organic Molecules Are Used by Living Systems 58 2.2. Evolution Requires Reproduction, Variation, and Selective Pressure 60 2.3. Energy Transformations Are Necessary to Sustain Living Systems 67 2.4. Cells Can Respond to Changes in Their Environments 73 Summary 79 Problems 81 3. Protein Structure and Function 84 3.1. Proteins Are Built from a Repertoire of 20 Amino Acids 86 3.2. Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains 97 3.3. Secondary Structure: Polypeptide Chains Can Fold Into Regular Structures Such as the Alpha Helix, the Beta Sheet, and Turns and Loops 104 3.4. Tertiary Structure: Water-Soluble Proteins Fold Into Compact Structures with Nonpolar Cores 112 3.5. Quaternary Structure: Polypeptide Chains Can Assemble Into Multisubunit Structures 115 3.6. The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure 117 Summary 127 Appendix: Acid-Base Concepts 129 Problems 133 4. Exploring Proteins 137 4.1. The Purification of Proteins Is an Essential First Step in Understanding Their Function 138 4.2. Amino Acid Sequences Can Be Determined by Automated Edman Degradation 156 4.3. Immunology Provides Important Techniques with Which to Investigate Proteins 165 4.4. Peptides Can Be Synthesized by Automated Solid-Phase Methods 173 4.5. Three-Dimensional Protein Structure Can Be Determined by NMR Spectroscopy and X-Ray Crystallography 177 Summary 186 Problems 188 5. DNA, RNA, and the Flow of Genetic Information 194 5.1. A Nucleic Acid Consists of Four Kinds of Bases Linked to a Sugar-Phosphate Backbone 196 5.2. A Pair of Nucleic Acid Chains with Complementary Sequences Can Form a Double-Helical Structure 201 5.3. DNA Is Replicated by Polymerases that Take Instructions from Templates 212 5.4. Gene Expression Is the Transformation of DNA Information Into Functional Molecules 214 5.5. Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point 221 5.6. Most Eukaryotic Genes Are Mosaics of Introns and Exons 224 Summary 228 Problems 230 6. Exploring Genes 236 6.1. The Basic Tools of Gene Exploration 237 6.2. Recombinant DNA Technology Has Revolutionized All Aspects of Biology 249 6.3. Manipulating the Genes of Eukaryotes 257 6.4. Novel Proteins Can Be Engineered by Site-Specific Mutagenesis 267 Summary 271 Problems 273 7. Exploring Evolution 278 7.1. Homologs Are Descended from a Common Ancestor 280 7.2. Statistical Analysis of Sequence Alignments Can Detect Homology 281 7.3. Examination of Three-Dimensional Structure Enhances Our Understanding of Evolutionary Relationships 287 7.4. Evolutionary Trees Can Be Constructed on the Basis of Sequence Information 293 7.5. Modern Techniques Make the Experimental Exploration of Evolution Possible 294 Summary 297 Problems 299 8. Enzymes: Basic Concepts and Kinetics 302 8.1. Enzymes Are Powerful and Highly Specific Catalysts 304 8.2. Free Energy Is a Useful Thermodynamic Function for Understanding Enzymes 309 8.3. Enzymes Accelerate Reactions by Facilitating the Formation of the Transition State 313 8.4. The Michaelis-Menten Model Accounts for the Kinetic Properties of Many Enzymes 319 8.5. Enzymes Can Be Inhibited by Specific Molecules 330 8.6. Vitamins Are Often Precursors to Coenzymes 341 Summary 346 Appendix: V 348 and K 348 Can Be Determined by Double-Reciprocal Plots 348 Problems 351 9. Catalytic Strategies 357 9.1. Proteases: Facilitating a Difficult Reaction 359 9.2. Making a Fast Reaction Faster: Carbonic Anhydrases 373 9.3. Restriction Enzymes: Performing Highly Specific DNA-Cleavage Reactions 379 9.4. Nucleoside Monophosphate Kinases: Catalyzing Phosphoryl Group Exchange between Nucleotides Without Promoting Hydrolysis 389 Summary 395 Problems 397 10. Regulatory Strategies: Enzymes and Hemoglobin 403 10.1. Aspartate Transcarbamoylase Is Allosterically Inhibited by the End Product of Its Pathway 404 10.2. Hemoglobin Transports Oxygen Efficiently by Binding Oxygen Cooperatively 414 10.3. Isozymes Provide a Means of Regulation Specific to Distinct Tissues and Developmental Stages 422 10.4. Covalent Modification Is a Means of Regulating Enzyme Activity 423 10.5. Many Enzymes Are Activated by Specific Proteolytic Cleavage 429 Summary 443 Problems 446 11. Carbohydrates 454 11.1. Monosaccharides Are Aldehydes or Ketones with Multiple Hydroxyl Groups 455 11.2. Complex Carbohydrates Are Formed by Linkage of Monosaccharides 463 11.3. Carbohydrates Can Be Attached to Proteins to Form Glycoproteins 469 11.4. Lectins Are Specific Carbohydrate-Binding Proteins 478 Summary 480 Problems 483 12. Lipids and Cell Membranes 488 12.1. Many Common Features Underlie the Diversity of Biological Membranes 490 12.2. Fatty Acids Are Key Constituents of Lipids 490 12.3. There Are Three Common Types of Membrane Lipids 493 12.4. Phospholipids and Glycolipids Readily Form Bimolecular Sheets in Aqueous Media 498 12.5. Proteins Carry Out Most Membrane Processes 502 12.6. Lipids and Many Membrane Proteins Diffuse Rapidly in the Plane of the Membrane 512 12.7. Eukaryotic Cells Contain Compartments Bounded by Internal Membranes 516 Summary 521 Problems 523 13. Membrane Channels and Pumps 528 13.1. The Transport of Molecules Across a Membrane May Be Active or Passive 529 13.2. A Family of Membrane Proteins Uses ATP Hydrolysis to Pump Ions Across Membranes 531 13.3. Multidrug Resistance and Cystic Fibrosis Highlight a Family of Membrane Proteins with ATP-Binding Cassette Domains 536 13.4. Secondary Transporters Use One Concentration Gradient to Power the Formation of Another 538 13.5. Specific Channels Can Rapidly Transport Ions Across Membranes 540 13.6. Gap Junctions Allow Ions and Small Molecules to Flow between Communicating Cells 555 Summary 557 Problems 559 II. Transducing and Storing Energy 568 14. Metabolism: Basic Concepts and Design 568 14.1. Metabolism Is Composed of Many Coupled, Interconnecting Reactions 570 14.2. The Oxidation of Carbon Fuels Is an Important Source of Cellular Energy 578 14.3. Metabolic Pathways Contain Many Recurring Motifs 582 Summary 592 Problems 594 15. Signal-Transduction Pathways: An Introduction to Information Metabolism 599 15.1. Seven-Transmembrane-Helix Receptors Change Conformation in Response to Ligand Binding and Activate G Proteins 603 15.2. The Hydrolysis of Phosphatidyl Inositol Bisphosphate by Phospholipase C Generates Two Messengers 611 15.3. Calcium Ion Is a Ubiquitous Cytosolic Messenger 617 15.4. Some Receptors Dimerize in Response to Ligand Binding and Signal by Cross-phosphorylation 623 15.5. Defects in Signaling Pathways Can Lead to Cancer and Other Diseases 630 15.6. Recurring Features of Signal-Transduction Pathways Reveal Evolutionary Relationships 634 Summary 635 Problems 637 16. Glycolysis and Gluconeogenesis 644 16.1. Glycolysis Is an Energy-Conversion Pathway in Many Organisms 648 16.2. The Glycolytic Pathway Is Tightly Controlled 668 16.3. Glucose Can Be Synthesized from Noncarbohydrate Precursors 676 16.4. Gluconeogenesis and Glycolysis Are Reciprocally Regulated 684 Summary 689 Problems 691 17. The Citric Acid Cycle 698 17.1. The Citric Acid Cycle Oxidizes Two-Carbon Units 702 17.2. Entry to the Citric Acid Cycle and Metabolism Through It Are Controlled 718 17.3. The Citric Acid Cycle Is a Source of Biosynthetic Precursors 721 17.4. The Glyoxylate Cycle Enables Plants and Bacteria to Grow on Acetate 724 Summary 726 Problems 727 18. Oxidative Phosphorylation 734 18.1. Oxidative Phosphorylation in Eukaryotes Takes Place in Mitochondria 736 18.2. Oxidative Phosphorylation Depends on Electron Transfer 739 18.3. The Respiratory Chain Consists of Four Complexes: Three Proton Pumps and a Physical Link to the Citric Acid Cycle 744 18.4. A Proton Gradient Powers the Synthesis of ATP 759 18.5. Many Shuttles Allow Movement Across the Mitochondrial Membranes 769 18.6. The Regulation of Cellular Respiration Is Governed Primarily by the Need for ATP 773 Summary 778 Problems 780 19. The Light Reactions of Photosynthesis 788 19.1. Photosynthesis Takes Place in Chloroplasts 791 19.2. Light Absorption by Chlorophyll Induces Electron Transfer 793 19.3. Two Photosystems Generate a Proton Gradient and NADPH in Oxygenic Photosynthesis 798 19.4. A Proton Gradient Across the Thylakoid Membrane Drives ATP Synthesis 807 19.5. Accessory Pigments Funnel Energy Into Reaction Centers 812 19.6. The Ability to Convert Light Into Chemical Energy Is Ancient 819 Summary 820 Problems 822 20. The Calvin Cycle and the Pentose Phosphate Pathway 826 20.1. The Calvin Cycle Synthesizes Hexoses from Carbon Dioxide and Water 828 20.2. The Activity of the Calvin Cycle Depends on Environmental Conditions 839 20.3 the Pentose Phosphate Pathway Generates NADPH and Synthesizes Five-Carbon Sugars 844 20.4. The Metabolism of Glucose 6-Phosphate by the Pentose Phosphate Pathway Is Coordinated with Glycolysis 851 20.5. Glucose 6-Phosphate Dehydrogenase Plays a Key Role in Protection Against Reactive Oxygen Species 854 Summary 857 Problems 859 21. Glycogen Metabolism 865 21.1. Glycogen Breakdown Requires the Interplay of Several Enzymes 867 21.2. Phosphorylase Is Regulated by Allosteric Interactions and Reversible Phosphorylation 873 21.3. Epinephrine and Glucagon Signal the Need for Glycogen Breakdown 877 21.4. Glycogen Is Synthesized and Degraded by Different Pathways 879 21.5. Glycogen Breakdown and Synthesis Are Reciprocally Regulated 884 Summary 890 Problems 892 22. Fatty Acid Metabolism 898 22.1. Triacylglycerols Are Highly Concentrated Energy Stores 901 22.2. The Utilization of Fatty Acids as Fuel Requires Three Stages of Processing 903 22.3. Certain Fatty Acids Require Additional Steps for Degradation 911 22.4. Fatty Acids Are Synthesized and Degraded by Different Pathways 920 22.5. Acetyl Coenzyme A Carboxylase Plays a Key Role in Controlling Fatty Acid Metabolism 929 22.6. Elongation and Unsaturation of Fatty Acids Are Accomplished by Accessory Enzyme Systems 932 Summary 935 Problems 937 23. Protein Turnover and Amino Acid Catabolism 943 23.1. Proteins Are Degraded to Amino Acids 945 23.2. Protein Turnover Is Tightly Regulated 946 23.3. The First Step in Amino Acid Degradation Is the Removal of Nitrogen 953 23.4. Ammonium Ion Is Converted Into Urea in Most Terrestrial Vertebrates 960 23.5. Carbon Atoms of Degraded Amino Acids Emerge as Major Metabolic Intermediates 967 23.6. Inborn Errors of Metabolism Can Disrupt Amino Acid Degradation 975 Summary 977 Problems 979 III. Synthesizing the Molecules of Life 986 24. The Biosynthesis of Amino Acids 987 24.1. Nitrogen Fixation: Microorganisms Use ATP and a Powerful Reductant to Reduce Atmospheric Nitrogen to Ammonia 989 24.2. Amino Acids Are Made from Intermediates of the Citric Acid Cycle and Other Major Pathways 995 24.3. Amino Acid Biosynthesis Is Regulated by Feedback Inhibition 1011 24.4. Amino Acids Are Precursors of Many Biomolecules 1017 Summary 1023 Problems 1025 25. Nucleotide Biosynthesis 1030 25.1. In de Novo Synthesis, the Pyrimidine Ring Is Assembled from Bicarbonate, Aspartate, and Glutamine 1032 25.2. Purine Bases Can Be Synthesized de Novo or Recycled by Salvage Pathways 1038 25.3. Deoxyribonucleotides Synthesized by the Reduction of Ribonucleotides Through a Radical Mechanism 1044 25.4. Key Steps in Nucleotide Biosynthesis Are Regulated by Feedback Inhibition 1050 25.5. NAD+, FAD, and Coenzyme A Are Formed from ATP 1051 25.6. Disruptions in Nucleotide Metabolism Can Cause Pathological Conditions 1052 Summary 1054 Problems 1056 26. The Biosynthesis of Membrane Lipids and Steroids 1062 26.1. Phosphatidate Is a Common Intermediate in the Synthesis of Phospholipids and Triacylglycerols 1064 26.2. Cholesterol Is Synthesized from Acetyl Coenzyme A in Three Stages 1072 26.3. The Complex Regulation of Cholesterol Biosynthesis Takes Place at Several Levels 1078 26.4. Important Derivatives of Cholesterol Include Bile Salts and Steroid Hormones 1086 Summary 1096 Problems 1098 27. DNA Replication, Recombination, and Repair 1104 27.1. DNA Can Assume a Variety of Structural Forms 1107 27.2. DNA Polymerases Require a Template and a Primer 1113 27.3. Double-Stranded DNA Can Wrap Around Itself to Form Supercoiled Structures 1119 27.4. DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites 1125 27.5. Double-Stranded DNA Molecules with Similar Sequences Sometimes Recombine 1135 27.6. Mutations Involve Changes in the Base Sequence of DNA 1138 Summary 1148 Problems 1151 28. RNA Synthesis and Splicing 1158 28.1. Transcription Is Catalyzed by RNA Polymerase 1161 28.2. Eukaryotic Transcription and Translation Are Separated in Space and Time 1172 28.3. The Transcription Products of All Three Eukaryotic Polymerases Are Processed 1179 28.4. The Discovery of Catalytic RNA Was Revealing in Regard to Both Mechanism and Evolution 1188 Summary 1192 Problems 1194 29. Protein Synthesis 1202 29.1. Protein Synthesis Requires the Translation of Nucleotide Sequences Into Amino Acid Sequences 1204 29.2. Aminoacyl-Transfer RNA Synthetases Read the Genetic Code 1209 29.3. A Ribosome Is a Ribonucleoprotein Particle (70S) Made of a Small (30S) and a Large (50S) Subunit 1217 29.4. Protein Factors Play Key Roles in Protein Synthesis 1230 29.5. Eukaryotic Protein Synthesis Differs from Prokaryotic Protein Synthesis Primarily in Translation Initiation 1235 Summary 1240 Problems 1242 30. The Integration of Metabolism 1250 30.1. Metabolism Consist of Highly Interconnected Pathways 1251 30.2. Each Organ Has a Unique Metabolic Profile 1260 30.3. Food Intake and Starvation Induce Metabolic Changes 1264 30.4. Fuel Choice During Exercise Is Determined by Intensity and Duration of Activity 1270 30.5. Ethanol Alters Energy Metabolism in the Liver 1272 Summary 1273 Problems 1275 31. The Control of Gene Expression 1280 31.1. Prokaryotic DNA-Binding Proteins Bind Specifically to Regulatory Sites in Operons 1282 31.2. The Greater Complexity of Eukaryotic Genomes Requires Elaborate Mechanisms for Gene Regulation 1290 31.3. Transcriptional Activation and Repression Are Mediated by Protein-Protein Interactions 1297 31.4. Gene Expression Can Be Controlled at Posttranscriptional Levels 1307 Summary 1311 Problems 1314 IV. Responding to Environmental Changes 1320 32. Sensory Systems 1320 32.1. A Wide Variety of Organic Compounds Are Detected by Olfaction 1322 32.2. Taste Is a Combination of Senses that Function by Different Mechanisms 1329 32.3. Photoreceptor Molecules in the Eye Detect Visible Light 1336 32.4. Hearing Depends on the Speedy Detection of Mechanical Stimuli 1343 32.5. Touch Includes the Sensing of Pressure, Temperature, and Other Factors 1347 Summary 1350 Problems 1352 33. The Immune System 1356 33.1. Antibodies Possess Distinct Antigen-Binding and Effector Units 1358 33.2. The Immunoglobulin Fold Consists of a Beta-Sandwich Framework with Hypervariable Loops 1363 33.3. Antibodies Bind Specific Molecules Through Their Hypervariable Loops 1364 33.4. Diversity Is Generated by Gene Rearrangements 1367 33.5. Major-Histocompatibility-Complex Proteins Present Peptide Antigens on Cell Surfaces for Recognition by T-Cell Receptors 1372 33.6. Immune Responses Against Self-Antigens Are Suppressed 1386 Summary 1388 Problems 1391 34. Molecular Motors 1398 34.1. Most Molecular-Motor Proteins Are Members of the P-Loop NTPase Superfamily 1400 34.2. Myosins Move Along Actin Filaments 1407 34.3. Kinesin and Dynein Move Along Microtubules 1414 34.4. A Rotary Motor Drives Bacterial Motion 1420 Summary 1425 Problems 1427 Appendix A: Physical Constants and Conversion of Units 1432 Appendix B: Acidity Constants 1434 Appendix C: Standard Bond Lengths 1436 Glossary of Compounds 1436 Answers to Problems 1452 Chapter 2 1453 Chapter 3 1454 Chapter 4 1456 Chapter 5 1458 Chapter 12 1461 Chapter 14 1463 Chapter 15 1465 Chapter 16 1467 Chapter 17 1470 Chapter 18 1474 Chapter 19 1477 Chapter 20 1479 Chapter 21 1482 Chapter 22 1486 Chapter 23 1489 Chapter 24 1492 Chapter 25 1494 Chapter 26 1496 Chapter 27 1499 Chapter 29 1501 Chapter 30 1503 Chapter 31 1507 Chapter 33 1508 Chapter 34 1510