BRIEF CONTENTS CONTENTS Part I THE MOLECULAR DESIGN OF LIFE Preface 1 Biochemistry:An Evolvina Science 1 Part I THE MOLECULAR DESIGN OF LIFE 2 Protein Composition and Structure 27 3 Exploring Proteins and Proteomes 65 CHAPTER1 Biochemistry:An Evolving Science 1 4 DNA,RNA,and the Flow of Genetic Information 105 1.1 Biochemical Unity Underlies Biological Diversity 5 Exploring Genes and Genomes 135 6Exploring Evolution and Bioinformatics169 .2DNA ustrates the Interplay Between Fomm and 7 Hemoglobin:Portrait of a Protein in Action 191 DNA is const 8 Enzymes:Basic Concepts and Kinetics 215 mbine to form a double helix DNA structure explains heredity and the storage of 9 Catalytic Strategies 251 information 5 10 Regulatory Stra 285 11 Carbohydrates 315 .Chemistry Explain the Properties 12 Lipids and Cell Membranes 341 NA double helix pl 13 Membrane Channels and Pumps 367 Covalent and nt for 14 Signal-Tra ways 307 the structure and stability of biological molecules Part II TRANSDUCING AND STORING ENERGY The double helix is an expression of the rules of chemistry 15 Metabolism:Basic Concepts and Design 423 16 Glycolysis and Gluconeogenesis 449 Heat is released in the formation of the double helix 12 Acid-base reactions are central in many biochemical 17 The Citric Acid Cycle 495 18 Oxidative Phosphorylation 523 11. can dig upt 19The Light Reactions of Photosynthesis 565 nd in the lab atory 20nd h Pentose Phosphate athway 公 21 Glycogen Metabolism 617 ncing has transformed biochemistry 22 Fatty Acid Metabolism 643 23 Protein Turnover and Amino Acid Catabolism 681 nistry Part IlI SYNTHESIZING THE MOLECULES OF LIFE APPENDIX:Visualizing Molecular Structures I: 24 The Biosynthesis of Amino Acids 713 mall Molecules 25 Nucleotide Biosynthesis 743 26of Membrane pids and CHAPTER 2 Protein Composition and Structure 27 The Integration of Metabolism 801 2.1 Proteins Are Built from a Repertoire of 20 Amino 28 DNA Replication.Repair.and Recombination 827 Acids 29 29 RNA Synthesis and Processing 859 2.2 Primary Structure:Amino Acids Are Linked by 30 Protein Synthesis 893 Peptide Bonds to Form Polypeptide Chains 35 The Control of Gene Expression in Prokaryotes 925 Proteins have unique amino acid sequences specified 37 32 The Control of Gene Expression in Eukaryotes 941 tide chains are flexible yet conformationally 38 Part IV RESPONDING TO ENVIRONMENTAL CHANGES 2.3 Secondary Structure:Polypeptide Chains Can e Alpha 33 Sensory Systems 96 34 The Immune System 981 35 Molecular Motors 1011 % 36 Drug Development 1033 bonding pep BRIEF CONTENTS Part I THE MOLECULAR DESIGN OF LIFE 1 Biochemistry: An Evolving Science 1 2 Protein Composition and Structure 27 3 Exploring Proteins and Proteomes 65 4 DNA, RNA, and the Flow of Genetic Information 105 5 Exploring Genes and Genomes 135 6 Exploring Evolution and Bioinformatics 169 7 Hemoglobin: Portrait of a Protein in Action 191 8 Enzymes: Basic Concepts and Kinetics 215 9 Catalytic Strategies 251 10 Regulatory Strategies 285 11 Carbohydrates 315 12 Lipids and Cell Membranes 341 13 Membrane Channels and Pumps 367 14 Signal-Transduction Pathways 397 Part II TRANSDUCING AND STORING ENERGY 15 Metabolism: Basic Concepts and Design 423 16 Glycolysis and Gluconeogenesis 449 17 The Citric Acid Cycle 495 18 Oxidative Phosphorylation 523 19 The Light Reactions of Photosynthesis 565 20 The Calvin Cycle and the Pentose Phosphate Pathway 589 21 Glycogen Metabolism 617 22 Fatty Acid Metabolism 643 23 Protein Turnover and Amino Acid Catabolism 681 Part III SYNTHESIZING THE MOLECULES OF LIFE 24 The Biosynthesis of Amino Acids 713 25 Nucleotide Biosynthesis 743 26 The Biosynthesis of Membrane Lipids and Steroids 767 27 The Integration of Metabolism 801 28 DNA Replication, Repair, and Recombination 827 29 RNA Synthesis and Processing 859 30 Protein Synthesis 893 31 The Control of Gene Expression in Prokaryotes 925 32 The Control of Gene Expression in Eukaryotes 941 Part IV RESPONDING TO ENVIRONMENTAL CHANGES 33 Sensory Systems 961 34 The Immune System 981 35 Molecular Motors 1011 36 Drug Development 1033 Preface v Part I THE MOLECULAR DESIGN OF LIFE 1 CHAPTER 1 Biochemistry: An Evolving Science 1 1.1 Biochemical Unity Underlies Biological Diversity 1 1.2 DNA Illustrates the Interplay Between Form and Function 4 DNA is constructed from four building blocks 4 Two single strands of DNA combine to form a double helix 5 DNA structure explains heredity and the storage of information 5 1.3 Concepts from Chemistry Explain the Properties of Biological Molecules 6 The formation of the DNA double helix as a key example 6 The double helix can form from its component strands 6 Covalent and noncovalent bonds are important for the structure and stability of biological molecules 6 The double helix is an expression of the rules of chemistry 9 The laws of thermodynamics govern the behavior of biochemical systems 10 Heat is released in the formation of the double helix 12 Acid–base reactions are central in many biochemical processes 13 Acid–base reactions can disrupt the double helix 14 Buffers regulate pH in organisms and in the laboratory 15 1.4 The Genomic Revolution Is Transforming Biochemistry, Medicine, and Other Fields 17 Genome sequencing has transformed biochemistry and other fields 17 Environmental factors influence human biochemistry 20 Genome sequences encode proteins and patterns of expression 21 APPENDIX: Visualizing Molecular Structures I: Small Molecules 22 CHAPTER 2 Protein Composition and Structure 27 2.1 Proteins Are Built from a Repertoire of 20 Amino Acids 29 2.2 Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains 35 Proteins have unique amino acid sequences specified by genes 37 Polypeptide chains are flexible yet conformationally restricted 38 2.3 Secondary Structure: Polypeptide Chains Can Fold into Regular Structures Such As the Alpha Helix, the Beta Sheet, and Turns and Loops 40 The alpha helix is a coiled structure stabilized by intrachain hydrogen bonds 40 Beta sheets are stabilized by hydrogen bonding between polypeptide strands 42 CHAPTER 1 Biochemistry: An Evolving Science 1 CHAPTER 2 Protein Composition and Structure 27 CONTENTS