Contents

• Dedication
• About the authors
• Preface
• Acknowledgments
• Part I. The Molecular Design of Life
  • Chapter 1. Prelude: Biochemistry and the Genomic Revolution
    • 1.1 DNA Illustrates the Relation between Form and Function
    • 1.2 Biochemical Unity Underlies Biological Diversity
    • 1.3 Chemical Bonds in Biochemistry
    • 1.4 Biochemistry and Human Biology
    • Appendix: Depicting Molecular Structures
  • Chapter 2. Biochemical Evolution
    • 2.1 Key Organic Molecules Are Used by Living Systems
    • 2.2 Evolution Requires Reproduction, Variation, and Selective Pressure
    • 2.3 Energy Transformations Are Necessary to Sustain Living Systems
    • 2.4 Cells Can Respond to Changes in Their Environments
    • Summary
    • Problems
    • Selected Readings
  • Chapter 3. Protein Structure and Function
    • 3.1 Proteins Are Built from a Repertoire of 20 Amino Acids
    • 3.2 Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains
    • 3.3 Secondary Structure: Polypeptide Chains Can Fold Into Regular Structures Such as the Alpha Helix, the Beta Sheet, and Turns and Loops
    • 3.4 Tertiary Structure: Water-Soluble Proteins Fold Into Compact Structures with Nonpolar Cores
    • 3.5 Quaternary Structure: Polypeptide Chains Can Assemble Into Multisubunit Structures
    • 3.6 The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure
    • Summary
    • Appendix: Acid-Base Concepts
    • Problems
    • Selected Readings
  • Chapter 4. Exploring Proteins
    • 4.1 The Purification of Proteins Is an Essential First Step in Understanding Their Function
    • 4.2 Amino Acid Sequences Can Be Determined by Automated Edman Degradation
    • 4.3 Immunology Provides Important Techniques with Which to Investigate Proteins
    • 4.4 Peptides Can Be Synthesized by Automated Solid-Phase Methods
    • 4.5 Three-Dimensional Protein Structure Can Be Determined by NMR Spectroscopy and X-Ray Crystallography
    • Summary
    • Problems
    • Selected Readings
  • Chapter 5. DNA, RNA, and the Flow of Genetic Information
    • 5.1 A Nucleic Acid Consists of Four Kinds of Bases Linked to a Sugar-Phosphate Backbone
    • 5.2 A Pair of Nucleic Acid Chains with Complementary Sequences Can Form a Double-Helical Structure
    • 5.3 DNA Is Replicated by Polymerases that Take Instructions from Templates
    • 5.4 Gene Expression Is the Transformation of DNA Information Into Functional Molecules
    • 5.5 Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point
    • 5.6 Most Eukaryotic Genes Are Mosaics of Introns and Exons
    • Summary
    • Problems
    • Selected Readings
  • Chapter 6. Exploring Genes
    • 6.1 The Basic Tools of Gene Exploration
    • 6.2 Recombinant DNA Technology Has Revolutionized All Aspects of Biology
    • 6.3 Manipulating the Genes of Eukaryotes
    • 6.4 Novel Proteins Can Be Engineered by Site-Specific Mutagenesis
    • Summary
    • Problems
    • Selected Reading
  • Chapter 7. Exploring Evolution
    • 7.1 Homologs Are Descended from a Common Ancestor
    • 7.2 Statistical Analysis of Sequence Alignments Can Detect Homology
    • 7.3 Examination of Three-Dimensional Structure Enhances Our Understanding of Evolutionary Relationships
    • 7.4 Evolutionary Trees Can Be Constructed on the Basis of Sequence Information
    • 7.5 Modern Techniques Make the Experimental Exploration of Evolution Possible
    • Summary
    • Problems
    • Selected Readings
  • Chapter 8. Enzymes: Basic Concepts and Kinetics
    • 8.1 Enzymes Are Powerful and Highly Specific Catalysts
    • 8.2 Free Energy Is a Useful Thermodynamic Function for Understanding Enzymes
    • 8.3 Enzymes Accelerate Reactions by Facilitating the Formation of the Transition State
    • 8.4 The Michaelis-Menten Model Accounts for the Kinetic Properties of Many Enzymes
    • 8.5 Enzymes Can Be Inhibited by Specific Molecules
    • 8.6 Vitamins Are Often Precursors to Coenzymes
    • Summary
    • Appendix: V_max and K_M Can Be Determined by Double-Reciprocal Plots
    • Problems
    • Selected Readings
  • Chapter 9. Catalytic Strategies
    • 9.1 Proteases: Facilitating a Difficult Reaction
    • 9.2 Making a Fast Reaction Faster: Carbonic Anhydrases
    • 9.3 Restriction Enzymes: Performing Highly Specific DNA-Cleavage Reactions
    • 9.4 Nucleoside Monophosphate Kinases: Catalyzing Phosphoryl Group Exchange between Nucleotides Without Promoting Hydrolysis
    • Summary
    • Problems
    • Selected Readings
  • Chapter 10. Regulatory Strategies: Enzymes and Hemoglobin
    • 10.1 Aspartate Transcarbamoylase Is Allosterically Inhibited by the End Product of Its Pathway
    • 10.2 Hemoglobin Transports Oxygen Efficiently by Binding Oxygen Cooperatively
    • 10.3 Isozymes Provide a Means of Regulation Specific to Distinct Tissues and Developmental Stages
    • 10.4 Covalent Modification Is a Means of Regulating Enzyme Activity
    • 10.5 Many Enzymes Are Activated by Specific Proteolytic Cleavage
    • Summary
    • Problems
    • Selected Readings
  • Chapter 11. Carbohydrates
    • 11.1 Monosaccharides Are Aldehydes or Ketones with Multiple Hydroxyl Groups
    • 11.2 Complex Carbohydrates Are Formed by Linkage of Monosaccharides
    • 11.3 Carbohydrates Can Be Attached to Proteins to Form Glycoproteins
    • 11.4 Lectins Are Specific Carbohydrate-Binding Proteins
    • Summary
    • Problems
    • Selected Readings
  • Chapter 12. Lipids and Cell Membranes
    • 12.1 Many Common Features Underlie the Diversity of Biological Membranes
    • 12.2 Fatty Acids Are Key Constituents of Lipids
    • 12.3 There Are Three Common Types of Membrane Lipids
    • 12.4 Phospholipids and Glycolipids Readily Form Bimolecular Sheets in Aqueous Media
    • 12.5 Proteins Carry Out Most Membrane Processes
    • 12.6 Lipids and Many Membrane Proteins Diffuse Rapidly in the Plane of the Membrane
    • 12.7 Eukaryotic Cells Contain Compartments Bounded by Internal Membranes
    • Summary
    • Problems
    • Selected Readings
  • Chapter 13. Membrane Channels and Pumps
    • 13.1 The Transport of Molecules Across a Membrane May Be Active or Passive
    • 13.2 A Family of Membrane Proteins Uses ATP Hydrolysis to Pump Ions Across Membranes
    • 13.3 Multidrug Resistance and Cystic Fibrosis Highlight a Family of Membrane Proteins with ATP-Binding Cassette Domains
    • 13.4 Secondary Transporters Use One Concentration Gradient to Power the Formation of Another
    • 13.5 Specific Channels Can Rapidly Transport Ions Across Membranes
    • 13.6 Gap Junctions Allow Ions and Small Molecules to Flow between Communicating Cells
    • Summary
    • Problems
    • Selected Readings
• Part II. Transducing and Storing Energy
  • Chapter 14. Metabolism: Basic Concepts and Design
    • 14.1 Metabolism Is Composed of Many Coupled, Interconnecting Reactions
    • 14.2 The Oxidation of Carbon Fuels Is an Important Source of Cellular Energy
    • 14.3 Metabolic Pathways Contain Many Recurring Motifs
    • Summary
    • Problems
    • Selected Readings
  • Chapter 15. Signal-Transduction Pathways: An Introduction to Information Metabolism
    • 15.1 Seven-Transmembrane-Helix Receptors Change Conformation in Response to Ligand Binding and Activate G Proteins
    • 15.2 The Hydrolysis of Phosphatidyl Inositol Bisphosphate by Phospholipase C Generates Two Messengers
    • 15.3 Calcium Ion Is a Ubiquitous Cytosolic Messenger
    • 15.4 Some Receptors Dimerize in Response to Ligand Binding and Signal by Cross-phosphorylation
    • 15.5 Defects in Signaling Pathways Can Lead to Cancer and Other Diseases
    • 15.6 Recurring Features of Signal-Transduction Pathways Reveal Evolutionary Relationships
    • Summary
    • Problems
    • Selected Readings
  • Chapter 16. Glycolysis and Gluconeogenesis
    • 16.1 Glycolysis Is an Energy-Conversion Pathway in Many Organisms
    • 16.2 The Glycolytic Pathway Is Tightly Controlled
    • 16.3 Glucose Can Be Synthesized from Noncarbohydrate Precursors
    • 16.4 Gluconeogenesis and Glycolysis Are Reciprocally Regulated
    • Summary
    • Problems
    • Selected Readings
  • Chapter 17. The Citric Acid Cycle
    • 17.1 The Citric Acid Cycle Oxidizes Two-Carbon Units
    • 17.2 Entry to the Citric Acid Cycle and Metabolism Through It Are Controlled
    • 17.3 The Citric Acid Cycle Is a Source of Biosynthetic Precursors
    • 17.4 The Glyoxylate Cycle Enables Plants and Bacteria to Grow on Acetate
    • Summary
    • Problems
    • Selected Readings
  • Chapter 18. Oxidative Phosphorylation
    • 18.1 Oxidative Phosphorylation in Eukaryotes Takes Place in Mitochondria
    • 18.2 Oxidative Phosphorylation Depends on Electron Transfer
    • 18.3 The Respiratory Chain Consists of Four Complexes: Three Proton Pumps and a Physical Link to the Citric Acid Cycle
    • 18.4 A Proton Gradient Powers the Synthesis of ATP
    • 18.5 Many Shuttles Allow Movement Across the Mitochondrial Membranes
    • 18.6 The Regulation of Cellular Respiration Is Governed Primarily by the Need for ATP
    • Summary
    • Problems
    • Selected Readings
  • Chapter 19. The Light Reactions of Photosynthesis
    • 19.1 Photosynthesis Takes Place in Chloroplasts
    • 19.2 Light Absorption by Chlorophyll Induces Electron Transfer
    • 19.3 Two Photosystems Generate a Proton Gradient and NADPH in Oxygenic Photosynthesis
    • 19.4 A Proton Gradient Across the Thylakoid Membrane Drives ATP Synthesis
    • 19.5 Accessory Pigments Funnel Energy Into Reaction Centers
    • 19.6 The Ability to Convert Light Into Chemical Energy Is Ancient
    • Summary
    • Problems
    • Selected Readings
  • Chapter 20. The Calvin Cycle and the Pentose Phosphate Pathway
    • 20.1 The Calvin Cycle Synthesizes Hexoses from Carbon Dioxide and Water
    • 20.2 The Activity of the Calvin Cycle Depends on Environmental Conditions
    • 20.3 the Pentose Phosphate Pathway Generates NADPH and Synthesizes Five-Carbon Sugars
    • 20.4 The Metabolism of Glucose 6-Phosphate by the Pentose Phosphate Pathway Is Coordinated with Glycolysis
    • 20.5 Glucose 6-Phosphate Dehydrogenase Plays a Key Role in Protection Against Reactive Oxygen Species
    • Summary
    • Problems
    • Selected Readings
  • Chapter 21. Glycogen Metabolism
    • 21.1 Glycogen Breakdown Requires the Interplay of Several Enzymes
    • 21.2 Phosphorylase Is Regulated by Allosteric Interactions and Reversible Phosphorylation
    • 21.3 Epinephrine and Glucagon Signal the Need for Glycogen Breakdown
    • 21.4 Glycogen Is Synthesized and Degraded by Different Pathways
    • 21.5 Glycogen Breakdown and Synthesis Are Reciprocally Regulated
    • Summary
    • Problems
    • Selected Readings
  • Chapter 22. Fatty Acid Metabolism
    • 22.1 Triacylglycerols Are Highly Concentrated Energy Stores
    • 22.2 The Utilization of Fatty Acids as Fuel Requires Three Stages of Processing
    • 22.3 Certain Fatty Acids Require Additional Steps for Degradation
    • 22.4 Fatty Acids Are Synthesized and Degraded by Different Pathways
    • 22.5 Acetyl Coenzyme A Carboxylase Plays a Key Role in Controlling Fatty Acid Metabolism
    • 22.6 Elongation and Unsaturation of Fatty Acids Are Accomplished by Accessory Enzyme Systems
    • Summary
    • Problems
    • Selected Readings
  • Chapter 23. Protein Turnover and Amino Acid Catabolism
    • 23.1 Proteins Are Degraded to Amino Acids
    • 23.2 Protein Turnover Is Tightly Regulated
    • 23.3 The First Step in Amino Acid Degradation Is the Removal of Nitrogen
    • 23.4 Ammonium Ion Is Converted Into Urea in Most Terrestrial Vertebrates
    • 23.5 Carbon Atoms of Degraded Amino Acids Emerge as Major Metabolic Intermediates
    • 23.6 Inborn Errors of Metabolism Can Disrupt Amino Acid Degradation
    • Summary
    • Problems
    • Selected Readings
• Part III. Synthesizing the Molecules of Life
  • Chapter 24. The Biosynthesis of Amino Acids
    • 24.1 Nitrogen Fixation: Microorganisms Use ATP and a Powerful Reductant to Reduce Atmospheric Nitrogen to Ammonia
    • 24.2 Amino Acids Are Made from Intermediates of the Citric Acid Cycle and Other Major Pathways
    • 24.3 Amino Acid Biosynthesis Is Regulated by Feedback Inhibition
    • 24.4 Amino Acids Are Precursors of Many Biomolecules
    • Summary
    • Problems
    • Selected Readings
  • Chapter 25. Nucleotide Biosynthesis
    • 25.1 In de Novo Synthesis, the Pyrimidine Ring Is Assembled from Bicarbonate, Aspartate, and Glutamine
    • 25.2 Purine Bases Can Be Synthesized de Novo or Recycled by Salvage Pathways
    • 25.3 Deoxyribonucleotides Synthesized by the Reduction of Ribonucleotides Through a Radical Mechanism
    • 25.4 Key Steps in Nucleotide Biosynthesis Are Regulated by Feedback Inhibition
    • 25.5 NAD⁺, FAD, and Coenzyme A Are Formed from ATP
    • 25.6 Disruptions in Nucleotide Metabolism Can Cause Pathological Conditions
    • Summary
    • Problems
    • Selected Readings
  • Chapter 26. The Biosynthesis of Membrane Lipids and Steroids
    • 26.1 Phosphatidate Is a Common Intermediate in the Synthesis of Phospholipids and Triacylglycerols
    • 26.2 Cholesterol Is Synthesized from Acetyl Coenzyme A in Three Stages
    • 26.3 The Complex Regulation of Cholesterol Biosynthesis Takes Place at Several Levels
    • 26.4 Important Derivatives of Cholesterol Include Bile Salts and Steroid Hormones
    • Summary
    • Problems
    • Selected Readings
  • Chapter 27. DNA Replication, Recombination, and Repair
    • 27.1 DNA Can Assume a Variety of Structural Forms
    • 27.2 DNA Polymerases Require a Template and a Primer
    • 27.3 Double-Stranded DNA Can Wrap Around Itself to Form Supercoiled Structures
    • 27.4 DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites
    • 27.5 Double-Stranded DNA Molecules with Similar Sequences Sometimes Recombine
    • 27.6 Mutations Involve Changes in the Base Sequence of DNA
    • Summary
    • Problems
    • Selected Readings
  • Chapter 28. RNA Synthesis and Splicing
    • 28.1 Transcription Is Catalyzed by RNA Polymerase
    • 28.2 Eukaryotic Transcription and Translation Are Separated in Space and Time
    • 28.3 The Transcription Products of All Three Eukaryotic Polymerases Are Processed
    • 28.4 The Discovery of Catalytic RNA Was Revealing in Regard to Both Mechanism and Evolution
    • Summary
    • Problems
    • Selected Readings
  • Chapter 29. Protein Synthesis
    • 29.1 Protein Synthesis Requires the Translation of Nucleotide Sequences Into Amino Acid Sequences
    • 29.2 Aminoacyl-Transfer RNA Synthetases Read the Genetic Code
    • 29.3 A Ribosome Is a Ribonucleoprotein Particle (70S) Made of a Small (30S) and a Large (50S) Subunit
    • 29.4 Protein Factors Play Key Roles in Protein Synthesis
    • 29.5 Eukaryotic Protein Synthesis Differs from Prokaryotic Protein Synthesis Primarily in Translation Initiation
    • Summary
    • Problems
    • Selected Readings
  • Chapter 30. The Integration of Metabolism
    • 30.1 Metabolism Consist of Highly Interconnected Pathways
    • 30.2 Each Organ Has a Unique Metabolic Profile
    • 30.3 Food Intake and Starvation Induce Metabolic Changes
    • 30.4 Fuel Choice During Exercise Is Determined by Intensity and Duration of Activity
    • 30.5 Ethanol Alters Energy Metabolism in the Liver
    • Summary
    • Problems
    • Selected Readings
  • Chapter 31. The Control of Gene Expression
    • 31.1 Prokaryotic DNA-Binding Proteins Bind Specifically to Regulatory Sites in Operons
    • 31.2 The Greater Complexity of Eukaryotic Genomes Requires Elaborate Mechanisms for Gene Regulation
    • 31.3 Transcriptional Activation and Repression Are Mediated by Protein-Protein Interactions
    • 31.4 Gene Expression Can Be Controlled at Posttranscriptional Levels
    • Summary
    • Problems
    • Selected Readings
• Part IV. Responding to Environmental Changes
  • Chapter 32. Sensory Systems
    • 32.1 A Wide Variety of Organic Compounds Are Detected by Olfaction
    • 32.2 Taste Is a Combination of Senses that Function by Different Mechanisms
    • 32.3 Photoreceptor Molecules in the Eye Detect Visible Light
    • 32.4 Hearing Depends on the Speedy Detection of Mechanical Stimuli
    • 32.5 Touch Includes the Sensing of Pressure, Temperature, and Other Factors
    • Summary
    • Problems
    • Selected Readings
  • Chapter 33. The Immune System
    • 33.1 Antibodies Possess Distinct Antigen-Binding and Effector Units
    • 33.2 The Immunoglobulin Fold Consists of a Beta-Sandwich Framework with Hypervariable Loops
    • 33.3 Antibodies Bind Specific Molecules Through Their Hypervariable Loops
    • 33.4 Diversity Is Generated by Gene Rearrangements
    • 33.5 Major-Histocompatibility-Complex Proteins Present Peptide Antigens on Cell Surfaces for Recognition by T-Cell Receptors
    • 33.6 Immune Responses Against Self-Antigens Are Suppressed
    • Summary
    • Problems
    • Selected Readings
  • Chapter 34. Molecular Motors
    • 34.1 Most Molecular-Motor Proteins Are Members of the P-Loop NTPase Superfamily
    • 34.2 Myosins Move Along Actin Filaments
    • 34.3 Kinesin and Dynein Move Along Microtubules
    • 34.4 A Rotary Motor Drives Bacterial Motion
    • Summary
    • Problems
    • Selected Readings
• Appendices
  • Appendix A: Physical Constants and Conversion of Units
  • Appendix B: Acidity Constants
  • Appendix C: Standard Bond Lengths
• Glossary of Compounds
• Common Abbreviations in Biochemistry