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
      • 1.1.1. DNA Is Constructed from Four Building Blocks
      • 1.1.2. Two Single Strands of DNA Combine to Form a Double Helix
      • 1.1.3. RNA Is an Intermediate in the Flow of Genetic Information
      • 1.1.4. Proteins, Encoded by Nucleic Acids, Perform Most Cell Functions
    • 1.2. Biochemical Unity Underlies Biological Diversity
    • 1.3. Chemical Bonds in Biochemistry
      • 1.3.1. Reversible Interactions of Biomolecules Are Mediated by Three Kinds of Noncovalent Bonds
      • 1.3.2. The Properties of Water Affect the Bonding Abilities of Biomolecules
      • 1.3.3. Entropy and the Laws of Thermodynamics
      • 1.3.4. Protein Folding Can Be Understood in Terms of Free-Energy Changes
    • 1.4. Biochemistry and Human Biology
    • Appendix: Depicting Molecular Structures
      • Stereochemical Renderings
      • Fischer Projections
      • Key Terms
  • Chapter 2. Biochemical Evolution
    • 2.1. Key Organic Molecules Are Used by Living Systems
      • 2.1.1. Many Components of Biochemical Macromolecules Can Be Produced in Simple, Prebiotic Reactions
      • 2.1.2. Uncertainties Obscure the Origins of Some Key Biomolecules
    • 2.2. Evolution Requires Reproduction, Variation, and Selective Pressure
      • 2.2.1. The Principles of Evolution Can Be Demonstrated in Vitro
      • 2.2.2. RNA Molecules Can Act As Catalysts
      • 2.2.3. Amino Acids and Their Polymers Can Play Biosynthetic and Catalytic Roles
      • 2.2.4. RNA Template-Directed Polypeptide Synthesis Links the RNA and Protein Worlds
      • 2.2.5. The Genetic Code Elucidates the Mechanisms of Evolution
      • 2.2.6. Transfer RNAs Illustrate Evolution by Gene Duplication
      • 2.2.7. DNA Is a Stable Storage Form for Genetic Information
    • 2.3. Energy Transformations Are Necessary to Sustain Living Systems
      • 2.3.1. ATP, a Common Currency for Biochemical Energy, Can Be Generated Through the Breakdown of Organic Molecules
      • 2.3.2. Cells Were Formed by the Inclusion of Nucleic Acids Within Membranes
      • 2.3.3. Compartmentalization Required the Development of Ion Pumps
      • 2.3.4. Proton Gradients Can Be Used to Drive the Synthesis of ATP
      • 2.3.5. Molecular Oxygen, a Toxic By-Product of Some Photosynthetic Processes, Can Be Utilized for Metabolic Purposes
    • 2.4. Cells Can Respond to Changes in Their Environments
      • 2.4.1. Filamentous Structures and Molecular Motors Enable Intracellular and Cellular Movement
      • 2.4.2. Some Cells Can Interact to Form Colonies with Specialized Functions
      • 2.4.3. The Development of Multicellular Organisms Requires the Orchestrated Differentiation of Cells
      • 2.4.4. The Unity of Biochemistry Allows Human Biology to Be Effectively Probed Through Studies of Other Organisms
    • Summary
      • Key Organic Molecules Are Used by Living Systems
      • Evolution Requires Reproduction, Variation, and Selective Pressure
      • Energy Transformations Are Necessary to Sustain Living Systems
      • Cells Can Respond to Changes in Their Environments
      • Key Terms
    • Problems
    • Selected Readings
      • Where to start
      • Books
      • Prebiotic chemistry
      • In vitro evolution
      • Replication and catalytic RNA
      • Transition from RNA to DNA
      • Membranes
      • Multicellular organisms and development
  • 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
      • 3.2.1. Proteins Have Unique Amino Acid Sequences That Are Specified by Genes
      • 3.2.2. Polypeptide Chains Are Flexible Yet Conformationally Restricted
    • 3.3. Secondary Structure: Polypeptide Chains Can Fold Into Regular Structures Such as the Alpha Helix, the Beta Sheet, and Turns and Loops
      • 3.3.1. The Alpha Helix Is a Coiled Structure Stabilized by Intrachain Hydrogen Bonds
      • 3.3.2. Beta Sheets Are Stabilized by Hydrogen Bonding Between Polypeptide Strands
      • 3.3.3. Polypeptide Chains Can Change Direction by Making Reverse 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
      • 3.6.1. Amino Acids Have Different Propensities for Forming Alpha Helices, Beta Sheets, and Beta Turns
      • 3.6.2. Protein Folding Is a Highly Cooperative Process
      • 3.6.3. Proteins Fold by Progressive Stabilization of Intermediates Rather Than by Random Search
      • 3.6.4. Prediction of Three-Dimensional Structure from Sequence Remains a Great Challenge
      • 3.6.5. Protein Modification and Cleavage Confer New Capabilities
    • Summary
      • Proteins Are Built from a Repertoire of 20 Amino Acids
      • Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains
      • Secondary Structure: Polypeptide Chains Can Fold into Regular Structures Such as the Alpha Helix, the Beta Sheet, and Turns and Loops
      • Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures with Nonpolar Cores
      • Quaternary Structure: Polypeptide Chains Can Assemble into Multisubunit Structures
      • The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure
      • Key Terms
    • Appendix: Acid-Base Concepts
      • Ionization of Water
      • Definition of Acid and Base
      • Definition of pH and pK
      • Henderson-Hasselbalch Equation
      • Buffers
      • pK_a Values of Amino Acids
    • Problems
      • Media Problem
    • Selected Readings
      • Where to start
      • Books
      • Conformation of proteins
      • Alpha helices, beta sheets, and loops
      • Domains
      • Protein folding
      • Covalent modification of proteins
      • Molecular graphics
  • Chapter 4. Exploring Proteins
    • 4.1. The Purification of Proteins Is an Essential First Step in Understanding Their Function
      • 4.1.1. The Assay: How Do We Recognize the Protein That We Are Looking For?
      • 4.1.2. Proteins Must Be Released from the Cell to Be Purified
      • 4.1.3. Proteins Can Be Purified According to Solubility, Size, Charge, and Binding Affinity
      • 4.1.4. Proteins Can Be Separated by Gel Electrophoresis and Displayed
      • 4.1.5. A Protein Purification Scheme Can Be Quantitatively Evaluated
      • 4.1.6. Ultracentrifugation Is Valuable for Separating Biomolecules and Determining Their Masses
      • 4.1.7. The Mass of a Protein Can Be Precisely Determined by Mass Spectrometry
    • 4.2. Amino Acid Sequences Can Be Determined by Automated Edman Degradation
      • 4.2.1. Proteins Can Be Specifically Cleaved into Small Peptides to Facilitate Analysis
      • 4.2.2. Amino Acid Sequences Are Sources of Many Kinds of Insight
      • 4.2.3. Recombinant DNA Technology Has Revolutionized Protein Sequencing
    • 4.3. Immunology Provides Important Techniques with Which to Investigate Proteins
      • 4.3.1. Antibodies to Specific Proteins Can Be Generated
      • 4.3.2. Monoclonal Antibodies with Virtually Any Desired Specificity Can Be Readily Prepared
      • 4.3.3. Proteins Can Be Detected and Quantitated by Using an Enzyme-Linked Immunosorbent Assay
      • 4.3.4. Western Blotting Permits the Detection of Proteins Separated by Gel Electrophoresis
      • 4.3.5. Fluorescent Markers Make Possible the Visualization of Proteins in the Cell
    • 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
      • 4.5.1. Nuclear Magnetic Resonance Spectroscopy Can Reveal the Structures of Proteins in Solution
      • 4.5.2. X-Ray Crystallography Reveals Three-Dimensional Structure in Atomic Detail
    • Summary
      • The Purification of Proteins Is an Essential Step in Understanding Their Function
      • Amino Acid Sequences Can Be Determined by Automated Edman Degradation
      • Immunology Provides Important Techniques with Which to Investigate Proteins
      • Peptides Can Be Synthesized by Automated Solid-Phase Methods
      • Three-Dimensional Protein Structure Can Be Determined by NMR Spectroscopy and X-Ray Crystallography
      • Key Terms
    • Problems
      • Chapter Integration Problems
      • Data Interpretation Problems
    • Selected Readings
      • Where to start
      • Books
      • Protein purification and analysis
      • Ultracentrifugation and mass spectrometry
      • X-ray crystallography and spectroscopy
      • Monoclonal antibodies and fluorescent molecules
      • Chemical synthesis of proteins
  • 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
      • 5.1.1. RNA and DNA Differ in the Sugar Component and One of the Bases
      • 5.1.2. Nucleotides Are the Monomeric Units of Nucleic Acids
    • 5.2. A Pair of Nucleic Acid Chains with Complementary Sequences Can Form a Double-Helical Structure
      • 5.2.1. The Double Helix Is Stabilized by Hydrogen Bonds and Hydrophobic Interactions
      • 5.2.2. The Double Helix Facilitates the Accurate Transmission of Hereditary Information
      • 5.2.3. The Double Helix Can Be Reversibly Melted
      • 5.2.4. Some DNA Molecules Are Circular and Supercoiled
      • 5.2.5. Single-Stranded Nucleic Acids Can Adopt Elaborate Structures
    • 5.3. DNA Is Replicated by Polymerases that Take Instructions from Templates
      • 5.3.1. DNA Polymerase Catalyzes Phosphodiester-Bond Formation
      • 5.3.2. The Genes of Some Viruses Are Made of RNA
    • 5.4. Gene Expression Is the Transformation of DNA Information Into Functional Molecules
      • 5.4.1. Several Kinds of RNA Play Key Roles in Gene Expression
      • 5.4.2. All Cellular RNA Is Synthesized by RNA Polymerases
      • 5.4.3. RNA Polymerases Take Instructions from DNA Templates
      • 5.4.4. Transcription Begins near Promoter Sites and Ends at Terminator Sites
      • 5.4.5. Transfer RNA Is the Adaptor Molecule in Protein Synthesis
    • 5.5. Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point
      • 5.5.1. Major Features of the Genetic Code
      • 5.5.2. Messenger RNA Contains Start and Stop Signals for Protein Synthesis
      • 5.5.3. The Genetic Code Is Nearly Universal
    • 5.6. Most Eukaryotic Genes Are Mosaics of Introns and Exons
      • 5.6.1. RNA Processing Generates Mature RNA
      • 5.6.2. Many Exons Encode Protein Domains
    • Summary
      • A Nucleic Acid Consists of Four Kinds of Bases Linked to a Sugar-Phosphate Backbone
      • A Pair of Nucleic Acid Chains with Complementary Sequences Can Form a Double-Helical Structure
      • DNA Is Replicated by Polymerases That Take Instructions from Templates
      • Gene Expression Is the Transformation of DNA Information into Functional Molecules
      • Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point
      • Most Eukaryotic Genes Are Mosaics of Introns and Exons
      • Key Terms
    • Problems
      • Chapter Integration Problems
      • Media Problem
    • Selected Readings
      • Where to start
      • Books
      • DNA structure
      • DNA replication
      • Discovery of messenger RNA
      • Genetic code
      • Introns, exons, and split genes
      • Reminiscences and historical accounts
  • Chapter 6. Exploring Genes
    • 6.1. The Basic Tools of Gene Exploration
      • 6.1.1. Restriction Enzymes Split DNA into Specific Fragments
      • 6.1.2. Restriction Fragments Can Be Separated by Gel Electrophoresis and Visualized
      • 6.1.3. DNA Is Usually Sequenced by Controlled Termination of Replication (Sanger Dideoxy Method)
      • 6.1.4. DNA Probes and Genes Can Be Synthesized by Automated Solid-Phase Methods
      • 6.1.5. Selected DNA Sequences Can Be Greatly Amplified by the Polymerase Chain Reaction
      • 6.1.6. PCR Is a Powerful Technique in Medical Diagnostics, Forensics, and Molecular Evolution
    • 6.2. Recombinant DNA Technology Has Revolutionized All Aspects of Biology
      • 6.2.1. Restriction Enzymes and DNA Ligase Are Key Tools in Forming Recombinant DNA Molecules
      • 6.2.2. Plasmids and Lambda Phage Are Choice Vectors for DNA Cloning in Bacteria
      • 6.2.3. Specific Genes Can Be Cloned from Digests of Genomic DNA
      • 6.2.4. Long Stretches of DNA Can Be Efficiently Analyzed by Chromosome Walking
    • 6.3. Manipulating the Genes of Eukaryotes
      • 6.3.1. Complementary DNA Prepared from mRNA Can Be Expressed in Host Cells
      • 6.3.2. Gene-Expression Levels Can Be Comprehensively Examined
      • 6.3.3. New Genes Inserted into Eukaryotic Cells Can Be Efficiently Expressed
      • 6.3.4. Transgenic Animals Harbor and Express Genes That Were Introduced into Their Germ Lines
      • 6.3.5. Gene Disruption Provides Clues to Gene Function
      • 6.3.6. Tumor-Inducing Plasmids Can Be Used to Introduce New Genes into Plant Cells
    • 6.4. Novel Proteins Can Be Engineered by Site-Specific Mutagenesis
      • 6.4.1. Proteins with New Functions Can Be Created Through Directed Changes in DNA
      • 6.4.2. Recombinant DNA Technology Has Opened New Vistas
    • Summary
      • The Basic Tools of Gene Exploration
      • Recombinant DNA Technology Has Revolutionized All Aspects of Biology
      • Manipulating the Genes of Eukaryotes
      • Novel Proteins Can Be Engineered by Site-Specific Mutagenesis
      • Key Terms
    • Problems
      • Chapter Integration Problem
      • Chapter Integration and Data Analysis Problem
      • Data Interpretation Problem
    • Selected Reading
      • Where to start
      • Books on recombinant DNA technology
      • DNA sequencing and synthesis
      • Polymerase chain reaction (PCR)
      • DNA arrays
      • Introduction of genes into animal cells
      • Genetic engineering of plants
  • Chapter 7. Exploring Evolution
    • 7.1. Homologs Are Descended from a Common Ancestor
    • 7.2. Statistical Analysis of Sequence Alignments Can Detect Homology
      • 7.2.1. The Statistical Significance of Alignments Can Be Estimated by Shuffling
      • 7.2.2. Distant Evolutionary Relationships Can Be Detected Through the Use of Substitution Matrices
      • 7.2.3. Databases Can Be Searched to Identify Homologous Sequences
    • 7.3. Examination of Three-Dimensional Structure Enhances Our Understanding of Evolutionary Relationships
      • 7.3.1. Tertiary Structure Is More Conserved Than Primary Structure
      • 7.3.2. Knowledge of Three-Dimensional Structures Can Aid in the Evaluation of Sequence Alignments
      • 7.3.3. Repeated Motifs Can Be Detected by Aligning Sequences with Themselves
      • 7.3.4. Convergent Evolution: Common Solutions to Biochemical Challenges
      • 7.3.5. Comparison of RNA Sequences Can Be a Source of Insight into Secondary Structures
    • 7.4. Evolutionary Trees Can Be Constructed on the Basis of Sequence Information
    • 7.5. Modern Techniques Make the Experimental Exploration of Evolution Possible
      • 7.5.1. Ancient DNA Can Sometimes Be Amplified and Sequenced
      • 7.5.2. Molecular Evolution Can Be Examined Experimentally
    • Summary
      • Homologs Are Descended from a Common Ancestor
      • Statistical Analysis of Sequence Alignments Can Detect Homology
      • Examination of Three-Dimensional Structure Enhances Our Understanding of Evolutionary Relationships
      • Evolutionary Trees Can Be Constructed on the Basis of Sequence Information
      • Modern Techniques Make the Experimental Exploration of Evolution Possible
      • Key Terms
    • Problems
      • Media Problem
    • Selected Readings
      • Book
      • Sequence alignment
      • Structure comparison
      • Domain detection
      • Evolutionary trees
      • Ancient DNA
      • Evolution in the laboratory
      • Web sites
  • Chapter 8. Enzymes: Basic Concepts and Kinetics
    • 8.1. Enzymes Are Powerful and Highly Specific Catalysts
      • 8.1.1. Many Enzymes Require Cofactors for Activity
      • 8.1.2. Enzymes May Transform Energy from One Form into Another
      • 8.1.3. Enzymes Are Classified on the Basis of the Types of Reactions That They Catalyze
    • 8.2. Free Energy Is a Useful Thermodynamic Function for Understanding Enzymes
      • 8.2.1. The Free-Energy Change Provides Information About the Spontaneity but Not the Rate of a Reaction
      • 8.2.2. The Standard Free-Energy Change of a Reaction Is Related to the Equilibrium Constant
      • 8.2.3. Enzymes Alter Only the Reaction Rate and Not the Reaction Equilibrium
    • 8.3. Enzymes Accelerate Reactions by Facilitating the Formation of the Transition State
      • 8.3.1. The Formation of an Enzyme-Substrate Complex Is the First Step in Enzymatic Catalysis
      • 8.3.2. The Active Sites of Enzymes Have Some Common Features
    • 8.4. The Michaelis-Menten Model Accounts for the Kinetic Properties of Many Enzymes
      • 8.4.1. The Significance of K_M and V_max Values
      • 8.4.2. Kinetic Perfection in Enzymatic Catalysis: The k_cat/K_M Criterion
      • 8.4.3. Most Biochemical Reactions Include Multiple Substrates
      • 8.4.4. Allosteric Enzymes Do Not Obey Michaelis-Menten Kinetics
    • 8.5. Enzymes Can Be Inhibited by Specific Molecules
      • 8.5.1. Competitive and Noncompetitive Inhibition Are Kinetically Distinguishable
      • 8.5.2. Irreversible Inhibitors Can Be Used to Map the Active Site
      • 8.5.3. Transition-State Analogs Are Potent Inhibitors of Enzymes
      • 8.5.4. Catalytic Antibodies Demonstrate the Importance of Selective Binding of the Transition State to Enzymatic Activity
      • 8.5.5. Penicillin Irreversibly Inactivates a Key Enzyme in Bacterial Cell-Wall Synthesis
    • 8.6. Vitamins Are Often Precursors to Coenzymes
      • 8.6.1. Water-Soluble Vitamins Function As Coenzymes
      • 8.6.2. Fat-Soluble Vitamins Participate in Diverse Processes Such as Blood Clotting and Vision
    • Summary
      • Enzymes are Powerful and Highly Specific Catalysts
      • Free Energy Is a Useful Thermodynamic Function for Understanding Enzymes
      • Enzymes Accelerate Reactions by Facilitating the Formation of the Transition State
      • The Michaelis-Menten Model Accounts for the Kinetic Properties of Many Enzymes
      • Enzymes Can Be Inhibited by Specific Molecules
      • Vitamins Are Often Precursors to Coenzymes
      • Key Terms
    • Appendix: V_max and K_M Can Be Determined by Double-Reciprocal Plots
    • Problems
      • Data Interpretation Problems
      • Chapter Integration Problems
      • Media Problem
    • Selected Readings
      • Where to start
      • Books
      • Transition-state stabilization, analogs, and other enzyme inhibitors
      • Catalytic antibodies
      • Enzyme kinetics and mechanisms
  • Chapter 9. Catalytic Strategies
    • 9.1. Proteases: Facilitating a Difficult Reaction
      • 9.1.1. Chymotrypsin Possesses a Highly Reactive Serine Residue
      • 9.1.2. Chymotrypsin Action Proceeds in Two Steps Linked by a Covalently Bound Intermediate
      • 9.1.3. Serine is Part of a Catalytic Triad That Also Includes Histidine and Aspartic Acid
      • 9.1.4. Catalytic Triads Are Found in Other Hydrolytic Enzymes
      • 9.1.5. The Catalytic Triad Has Been Dissected by Site-Directed Mutagenesis
      • 9.1.6. Cysteine, Aspartyl, and Metalloproteases Are Other Major Classes of Peptide-Cleaving Enzymes
      • 9.1.7. Protease Inhibitors Are Important Drugs
    • 9.2. Making a Fast Reaction Faster: Carbonic Anhydrases
      • 9.2.1. Carbonic Anhydrase Contains a Bound Zinc Ion Essential for Catalytic Activity
      • 9.2.2. Catalysis Entails Zinc Activation of Water
      • 9.2.3. A Proton Shuttle Facilitates Rapid Regeneration of the Active Form of the Enzyme
      • 9.2.4. Convergent Evolution Has Generated Zinc-Based Active Sites in Different Carbonic Anhydrases
    • 9.3. Restriction Enzymes: Performing Highly Specific DNA-Cleavage Reactions
      • 9.3.1. Cleavage Is by In-Line Displacement of 3′ Oxygen from Phosphorus by Magnesium-Activated Water
      • 9.3.2. Restriction Enzymes Require Magnesium for Catalytic Activity
      • 9.3.3. The Complete Catalytic Apparatus Is Assembled Only Within Complexes of Cognate DNA Molecules, Ensuring Specificity
      • 9.3.4. Type II Restriction Enzymes Have a Catalytic Core in Common and Are Probably Related by Horizontal Gene Transfer
    • 9.4. Nucleoside Monophosphate Kinases: Catalyzing Phosphoryl Group Exchange between Nucleotides Without Promoting Hydrolysis
      • 9.4.1. NMP Kinases Are a Family of Enzymes Containing P-Loop Structures
      • 9.4.2. Magnesium (or Manganese) Complexes of Nucleoside Triphosphates Are the True Substrates for Essentially All NTP-Dependent Enzymes
      • 9.4.3. ATP Binding Induces Large Conformational Changes
      • 9.4.4. P-Loop NTPase Domains Are Present in a Range of Important Proteins
    • Summary
      • Proteases: Facilitating a Difficult Reaction
      • Carbonic Anhydrases: Making a Fast Reaction Faster
      • Restriction Enzymes: Performing Highly Specific DNA Cleavage Reactions
      • Nucleoside Monophosphate Kinases: Catalyzing Phosphoryl Group Exchange Without Promoting Hydrolysis
      • Key Terms
    • Problems
      • Mechanism Problem
      • Media Problems
    • Selected Readings
      • Where to start
      • Books
      • Chymotrypsin and other serine proteases
      • Other proteases
      • Carbonic anhydrase
      • Restriction enzymes
      • NMP kinases
  • Chapter 10. Regulatory Strategies: Enzymes and Hemoglobin
    • 10.1. Aspartate Transcarbamoylase Is Allosterically Inhibited by the End Product of Its Pathway
      • 10.1.1. ACTase Consists of Separable Catalytic and Regulatory Subunits
      • 10.1.2. Allosteric Interactions in ATCase Are Mediated by Large Changes in Quaternary Structure
      • 10.1.3. Allosterically Regulated Enzymes Do Not Follow Michaelis-Menten Kinetics
      • 10.1.4. Allosteric Regulators Modulate the T-to-R Equilibrium
      • 10.1.5. The Concerted Model Can Be Formulated in Quantitative Terms
      • 10.1.6. Sequential Models Also Can Account for Allosteric Effects
    • 10.2. Hemoglobin Transports Oxygen Efficiently by Binding Oxygen Cooperatively
      • 10.2.1. Oxygen Binding Induces Substantial Structural Changes at the Iron Sites in Hemoglobin
      • 10.2.2. Oxygen Binding Markedly Changes the Quaternary Structure of Hemoglobin
      • 10.2.3. Tuning the Oxygen Affinity of Hemoglobin: The Effect of 2,3-Bisphosphoglycerate
      • 10.2.4. The Bohr Effect: Hydrogen Ions and Carbon Dioxide Promote the Release of Oxygen
    • 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
      • 10.4.1. Phosphorylation Is a Highly Effective Means of Regulating the Activities of Target Proteins
      • 10.4.2. Cyclic AMP Activates Protein Kinase A by Altering the Quaternary Structure
      • 10.4.3. ATP and the Target Protein Bind to a Deep Cleft in the Catalytic Subunit of Protein Kinase A
    • 10.5. Many Enzymes Are Activated by Specific Proteolytic Cleavage
      • 10.5.1. Chymotrypsinogen Is Activated by Specific Cleavage of a Single Peptide Bond
      • 10.5.2. Proteolytic Activation of Chymotrypsinogen Leads to the Formation of a Substrate-Binding Site
      • 10.5.3. The Generation of Trypsin from Trypsinogen Leads to the Activation of Other Zymogens
      • 10.5.4. Some Proteolytic Enzymes Have Specific Inhibitors
      • 10.5.5. Blood Clotting Is Accomplished by a Cascade of Zymogen Activations
      • 10.5.6. Fibrinogen Is Converted by Thrombin into a Fibrin Clot
      • 10.5.7. Prothrombin Is Readied for Activation by a Vitamin K-Dependent Modification
      • 10.5.8. Hemophilia Revealed an Early Step in Clotting
      • 10.5.9. The Clotting Process Must Be Precisely Regulated
    • Summary
      • Aspartate Transcarbamoylase Is Allosterically Inhibited by the End Product of Its Pathway
      • Hemoglobin Transports Oxygen Efficiently by Binding Oxygen Cooperatively
      • Isozymes Provide a Means of Regulation Specific to Distinct Tissues and Developmental Stages
      • Covalent Modification Is a Means of Regulating Enzyme Activity
      • Many Enzymes Are Activated by Specific Proteolytic Cleavage
      • Key Terms
    • Problems
      • Data Interpretation Problems
      • Chapter Integration Problem
      • Mechanism Problems
      • Media Problem
    • Selected Readings
      • Where to start
      • Aspartate transcarbamoylase and allosteric interactions
      • Hemoglobin
      • Covalent modification
      • Protein kinase A
      • Zymogen activation
      • Protease inhibitors
      • Clotting cascade
  • Chapter 11. Carbohydrates
    • 11.1. Monosaccharides Are Aldehydes or Ketones with Multiple Hydroxyl Groups
      • 11.1.1. Pentoses and Hexoses Cyclize to Form Furanose and Pyranose Rings
      • 11.1.2. Conformation of Pyranose and Furanose Rings
      • 11.1.3. Monosaccharides Are Joined to Alcohols and Amines Through Glycosidic Bonds
    • 11.2. Complex Carbohydrates Are Formed by Linkage of Monosaccharides
      • 11.2.1. Sucrose, Lactose, and Maltose Are the Common Disaccharides
      • 11.2.2. Glycogen and Starch Are Mobilizable Stores of Glucose
      • 11.2.3. Cellulose, the Major Structural Polymer of Plants, Consists of Linear Chains of Glucose Units
      • 11.2.4. Glycosaminoglycans Are Anionic Polysaccharide Chains Made of Repeating Disaccharide Units
      • 11.2.5. Specific Enzymes Are Responsible for Oligosaccharide Assembly
    • 11.3. Carbohydrates Can Be Attached to Proteins to Form Glycoproteins
      • 11.3.1. Carbohydrates May Be Linked to Proteins Through Asparagine (N-Linked) or Through Serine or Threonine (O-Linked) Residues
      • 11.3.2. Protein Glycosylation Takes Place in the Lumen of the Endoplasmic Reticulum and in the Golgi Complex
      • 11.3.3. N-Linked Glycoproteins Acquire Their Initial Sugars from Dolichol Donors in the Endoplasmic Reticulum
      • 11.3.4. Transport Vesicles Carry Proteins from the Endoplasmic Reticulum to the Golgi Complex for Further Glycosylation and Sorting
      • 11.3.5. Mannose 6-phosphate Targets Lysosomal Enzymes to Their Destinations
      • 11.3.6. Glucose Residues Are Added and Trimmed to Aid in Protein Folding
      • 11.3.7. Oligosaccharides Can Be “Sequenced”
    • 11.4. Lectins Are Specific Carbohydrate-Binding Proteins
      • 11.4.1. Lectins Promote Interactions Between Cells
      • 11.4.2. Influenza Virus Binds to Sialic Acid Residues
    • Summary
      • Monosaccharides Are Aldehydes or Ketones with Multiple Hydroxyl Groups
      • Complex Carbohydrates Are Formed by Linkage of Monosaccharides
      • Carbohydrates Can Attach to Proteins to Form Glycoproteins
      • Lectins Are Specific Carbohydrate-Binding Proteins
      • Key Terms
    • Problems
      • Chapter Integration Problem
    • Selected Readings
      • Where to start
      • Books
      • Structure of carbohydrate-binding proteins
      • Glycoproteins
      • Carbohydrates in recognition processes
      • Carbohydrate sequencing
  • 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
      • 12.2.1. The Naming of Fatty Acids
      • 12.2.2. Fatty Acids Vary in Chain Length and Degree of Unsaturation
    • 12.3. There Are Three Common Types of Membrane Lipids
      • 12.3.1. Phospholipids Are the Major Class of Membrane Lipids
      • 12.3.2. Archaeal Membranes Are Built from Ether Lipids with Branched Chains
      • 12.3.3. Membrane Lipids Can Also Include Carbohydrate Moieties
      • 12.3.4. Cholesterol Is a Lipid Based on a Steroid Nucleus
      • 12.3.5. A Membrane Lipid Is an Amphipathic Molecule Containing a Hydrophilic and a Hydrophobic Moiety
    • 12.4. Phospholipids and Glycolipids Readily Form Bimolecular Sheets in Aqueous Media
      • 12.4.1. Lipid Vesicles Can Be Formed from Phospholipids
      • 12.4.2. Lipid Bilayers Are Highly Impermeable to Ions and Most Polar Molecules
    • 12.5. Proteins Carry Out Most Membrane Processes
      • 12.5.1. Proteins Associate with the Lipid Bilayer in a Variety of Ways
      • 12.5.2. Proteins Interact with Membranes in a Variety of Ways
      • 12.5.3. Some Proteins Associate with Membranes Through Covalently Attached Hydrophobic Groups
      • 12.5.4. Transmembrane Helices Can Be Accurately Predicted from Amino Acid Sequences
    • 12.6. Lipids and Many Membrane Proteins Diffuse Rapidly in the Plane of the Membrane
      • 12.6.1. The Fluid Mosaic Model Allows Lateral Movement but Not Rotation Through the Membrane
      • 12.6.2. Membrane Fluidity Is Controlled by Fatty Acid Composition and Cholesterol Content
      • 12.6.3. All Biological Membranes Are Asymmetric
    • 12.7. Eukaryotic Cells Contain Compartments Bounded by Internal Membranes
      • 12.7.1. Proteins Are Targeted to Specific Compartments by Signal Sequences
      • 12.7.2. Membrane Budding and Fusion Underlie Several Important Biological Processes
    • Summary
      • Many Common Features Underlie the Diversity of Biological Membranes
      • Fatty Acids Are Key Constituents of Lipids
      • There Are Three Common Types of Membrane Lipids
      • Phospholipids and Glycolipids Readily Form Bimolecular Sheets in Aqueous Media
      • Proteins Carry Out Most Membrane Processes
      • Lipids and Many Membrane Proteins Diffuse Rapidly in the Plane of the Membrane
      • Eukaryotic Cells Contain Compartments Bounded by Internal Membranes
      • Key Terms
    • Problems
      • Data Interpretation Problems
      • Chapter Integration Problem
    • Selected Readings
      • Where to start
      • Books
      • Membrane lipids and dynamics
      • Structure of membrane proteins
      • Intracellular membranes
  • Chapter 13. Membrane Channels and Pumps
    • 13.1. The Transport of Molecules Across a Membrane May Be Active or Passive
      • 13.1.1. Many Molecules Require Protein Transporters to Cross Membranes
      • 13.1.2. Free Energy Stored in Concentration Gradients Can Be Quantified
    • 13.2. A Family of Membrane Proteins Uses ATP Hydrolysis to Pump Ions Across Membranes
      • 13.2.1. The Sarcoplasmic Reticulum Ca²⁺ ATPase Is an Integral Membrane Protein
      • 13.2.2. P-Type ATPases Are Evolutionarily Conserved and Play a Wide Range of Roles
      • 13.2.3. Digitalis Specifically Inhibits the Na⁺-K⁺ Pump by Blocking Its Dephosphorylation
    • 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
      • 13.5.1. Patch-Clamp Conductance Measurements Reveal the Activities of Single Channels
      • 13.5.2. Ion-Channel Proteins Are Built of Similar Units
      • 13.5.3. Action Potentials Are Mediated by Transient Changes in Na⁺ and K⁺ Permeability
      • 13.5.4. The Sodium Channel Is an Example of a Voltage-Gated Channel
      • 13.5.5. Potassium Channels Are Homologous to the Sodium Channel
      • 13.5.6. The Structure of a Potassium Channel Reveals the Basis of Rapid Ion Flow with Specificity
      • 13.5.7. The Structure of the Potassium Channel Explains Its Rapid Rates of Transport
      • 13.5.8. A Channel Can Be Inactivated by Occlusion of the Pore: The Ball-and-Chain Model
    • 13.6. Gap Junctions Allow Ions and Small Molecules to Flow between Communicating Cells
    • Summary
      • The Transport of Molecules Across a Membrane May Be Active or Passive
      • A Family of Membrane Proteins Uses ATP Hydrolysis to Pump Ions Across Membranes
      • Multidrug Resistance and Cystic Fibrosis Highlight a Family of Membrane Proteins with ATP-Binding Cassette Domains
      • Secondary Transporters Use One Concentration Gradient to Power the Formation of Another
      • Specific Channels Can Rapidly Transport Ions Across Membranes
      • Gap Junctions Allow Ions and Small Molecules to Flow Between Communicating Cells
      • Key Terms
    • Problems
      • Chapter Integration Problem
      • Mechanism Problem
      • Data Interpretation Problem
      • Media Problem
    • Selected Readings
      • Where to start
      • Books
      • Voltage-gated ion channels
      • Ligand-gated ion channels
      • ATP-driven ion pumps
      • ATP-binding cassette (ABC) proteins
      • Symporters and antiporters
      • Gap junctions
• Part II. Transducing and Storing Energy
  • Chapter 14. Metabolism: Basic Concepts and Design
    • 14.1. Metabolism Is Composed of Many Coupled, Interconnecting Reactions
      • 14.1.1. A Thermodynamically Unfavorable Reaction Can Be Driven by a Favorable Reaction
      • 14.1.2. ATP Is the Universal Currency of Free Energy in Biological Systems
      • 14.1.3. ATP Hydrolysis Drives Metabolism by Shifting the Equilibrium of Coupled Reactions
      • 14.1.4. Structural Basis of the High Phosphoryl Transfer Potential of ATP
      • 14.1.5. Phosphoryl Transfer Potential Is an Important Form of Cellular Energy Transformation
    • 14.2. The Oxidation of Carbon Fuels Is an Important Source of Cellular Energy
      • 14.2.1. High Phosphoryl Transfer Potential Compounds Can Couple Carbon Oxidation to ATP Synthesis
      • 14.2.2. Ion Gradients Across Membranes Provide an Important Form of Cellular Energy That Can Be Coupled to ATP Synthesis
      • 14.2.3. Stages in the Extraction of Energy from Foodstuffs
    • 14.3. Metabolic Pathways Contain Many Recurring Motifs
      • 14.3.1. Activated Carriers Exemplify the Modular Design and Economy of Metabolism
      • 14.3.2. Key Reactions Are Reiterated Throughout Metabolism
      • 14.3.3. Metabolic Processes Are Regulated in Three Principal Ways
      • 14.3.4. Evolution of Metabolic Pathways
    • Summary
      • Metabolism Is Composed of Many Coupled, Interconnecting Reactions
      • The Oxidation of Carbon Fuels Is an Important Source of Cellular Energy
      • Metabolic Pathways Contain Many Recurring Motifs
      • Key Terms
    • Problems
      • Chapter Integration Problem
      • Data Interpretation
      • Media Problem
    • Selected Readings
      • Where to start
      • Books
      • Thermodynamics
      • Bioenergetics and metabolism
      • Regulation of metabolism
      • Historical aspects
  • 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
      • 15.1.1. Ligand Binding to 7TM Receptors Leads to the Activation of G Proteins
      • 15.1.2. G Proteins Cycle Between GDP- and GTP-Bound Forms
      • 15.1.3. Activated G Proteins Transmit Signals by Binding to Other Proteins
      • 15.1.4. G Proteins Spontaneously Reset Themselves Through GTP Hydrolysis
      • 15.1.5. Cyclic AMP Stimulates the Phosphorylation of Many Target Proteins by Activating Protein Kinase A
    • 15.2. The Hydrolysis of Phosphatidyl Inositol Bisphosphate by Phospholipase C Generates Two Messengers
      • 15.2.1. Inositol 1,4,5-trisphosphate Opens Channels to Release Calcium Ions from Intracellular Stores
      • 15.2.2. Diacylglycerol Activates Protein Kinase C, Which Phosphorylates Many Target Proteins
    • 15.3. Calcium Ion Is a Ubiquitous Cytosolic Messenger
      • 15.3.1. Ionophores Allow the Visualization of Changes in Calcium Concentration
      • 15.3.2. Calcium Activates the Regulatory Protein Calmodulin, Which Stimulates Many Enzymes and Transporters
    • 15.4. Some Receptors Dimerize in Response to Ligand Binding and Signal by Cross-phosphorylation
      • 15.4.1. Some Receptors Contain Tyrosine Kinase Domains Within Their Covalent Structures
      • 15.4.2. Ras, Another Class of Signaling G Protein
    • 15.5. Defects in Signaling Pathways Can Lead to Cancer and Other Diseases
      • 15.5.1. Protein Kinase Inhibitors May Be Effective Anticancer Drugs
      • 15.5.2. Cholera and Whooping Cough Are Due to Altered G-Protein Activity
    • 15.6. Recurring Features of Signal-Transduction Pathways Reveal Evolutionary Relationships
    • Summary
      • Seven-Transmembrane-Helix Receptors Change Conformation in Response to Ligand Binding and Activate G Proteins
      • The Hydrolysis of Phosphatidyl Inositol Bisphosphate by Phospholipase C Generates Two Messengers
      • Calcium Ion Is a Ubiquitous Cytosolic Messenger
      • Some Receptors Dimerize in Response to Ligand Binding and Signal by Cross-Phosphorylation
      • Defects in Signaling Pathways Can Lead to Cancer and Other Diseases
      • Recurring Features of Signal-Transduction Pathways Reveal Evolutionary Relationships
      • Key Terms
    • Problems
      • Chapter Integration Problem
      • Mechanism Problem
      • Data Interpretation Problems
      • Media Problem
    • Selected Readings
      • Where to start
      • G proteins and 7TM receptors
      • cAMP cascade
      • Phosphoinositide cascade
      • Calcium
      • Protein kinases, including receptor tyrosine kinases
      • Ras
      • Cancer
  • Chapter 16. Glycolysis and Gluconeogenesis
    • 16.1. Glycolysis Is an Energy-Conversion Pathway in Many Organisms
      • 16.1.1. Hexokinase Traps Glucose in the Cell and Begins Glycolysis
      • 16.1.2. The Formation of Fructose 1,6-bisphosphate from Glucose 6-phosphate
      • 16.1.3. The Six-Carbon Sugar Is Cleaved into Two Three-Carbon Fragments by Aldolase
      • 16.1.4. Triose phosphate isomerase Salvages a Three-Carbon Fragment
      • 16.1.5. Energy Transformation: Phosphorylation Is Coupled to the Oxidation of Glyceraldehyde 3-phosphate by a Thioester Intermediate
      • 16.1.6. The Formation of ATP from 1,3-Bisphosphoglycerate
      • 16.1.7. The Generation of Additional ATP and the Formation of Pyruvate
      • 16.1.8. Energy Yield in the Conversion of Glucose into Pyruvate
      • 16.1.9. Maintaining Redox Balance: The Diverse Fates of Pyruvate
      • 16.1.10. The Binding Site for NAD⁺ Is Similar in Many Dehydrogenases
      • 16.1.11. The Entry of Fructose and Galactose into Glycolysis
      • 16.1.12. Many Adults Are Intolerant of Milk Because They Are Deficient in Lactase
      • 16.1.13. Galactose Is Highly Toxic If the Transferase Is Missing
    • 16.2. The Glycolytic Pathway Is Tightly Controlled
      • 16.2.1. Phosphofructokinase Is the Key Enzyme in the Control of Glycolysis
      • 16.2.2. A Regulated Bifunctional Enzyme Synthesizes and Degrades Fructose 2,6 -bisphosphate
      • 16.2.3. Hexokinase and Pyruvate kinase Also Set the Pace of Glycolysis
      • 16.2.4. A Family of Transporters Enables Glucose to Enter and Leave Animal Cells
      • 16.2.5. Cancer and Glycolysis
    • 16.3. Glucose Can Be Synthesized from Noncarbohydrate Precursors
      • 16.3.1. Gluconeogenesis Is Not a Reversal of Glycolysis
      • 16.3.2. The Conversion of Pyruvate into Phosphoenolpyruvate Begins with the Formation of Oxaloacetate
      • 16.3.3. Oxaloacetate Is Shuttled into the Cytosol and Converted into Phosphoenolpyruvate
      • 16.3.4. The Conversion of Fructose 1,6-bisphosphate into Fructose 6-phosphate and Orthophosphate Is an Irreversible Step
      • 16.3.5. The Generation of Free Glucose Is an Important Control Point
      • 16.3.6. Six High Transfer Potential Phosphoryl Groups Are Spent in Synthesizing Glucose from Pyruvate
    • 16.4. Gluconeogenesis and Glycolysis Are Reciprocally Regulated
      • 16.4.1. Substrate Cycles Amplify Metabolic Signals and Produce Heat
      • 16.4.2. Lactate and Alanine Formed by Contracting Muscle Are Used by Other Organs
      • 16.4.3. Glycolysis and Gluconeogenesis Are Evolutionarily Intertwined
    • Summary
      • Glycolysis Is an Energy-Conversion Pathway in Many Organisms
      • The Glycolytic Pathway Is Tightly Controlled
      • Glucose Can Be Synthesized from Noncarbohydrate Precursors
      • Gluconeogenesis and Glycolysis Are Reciprocally Regulated
      • Key Terms
    • Problems
      • Mechanism Problem
      • Chapter Integration Problem
      • Data Interpretation Problem
      • Media Problems
    • Selected Readings
      • Where to start
      • Books
      • Structure of glycolytic and gluconeogenic enzymes
      • Catalytic mechanisms
      • Regulation
      • Sugar transporters
      • Genetic diseases
      • Evolution
      • Historical aspects
  • Chapter 17. The Citric Acid Cycle
    • 17.1. The Citric Acid Cycle Oxidizes Two-Carbon Units
      • 17.1.1. The Formation of Acetyl Coenzyme A from Pyruvate
      • 17.1.2. Flexible Linkages Allow Lipoamide to Move Between Different Active Sites
      • 17.1.3. Citrate Synthase Forms Citrate from Oxaloacetate and Acetyl Coenzyme A
      • 17.1.4. Citrate Is Isomerized into Isocitrate
      • 17.1.5. Isocitrate Is Oxidized and Decarboxylated to α-Ketoglutarate
      • 17.1.6. Succinyl Coenzyme A Is Formed by the Oxidative Decarboxylation of α-Ketoglutarate
      • 17.1.7. A High Phosphoryl-Transfer Potential Compound Is Generated from Succinyl Coenzyme A
      • 17.1.8. Oxaloacetate Is Regenerated by the Oxidation of Succinate
      • 17.1.9. Stoichiometry of the Citric Acid Cycle
    • 17.2. Entry to the Citric Acid Cycle and Metabolism Through It Are Controlled
      • 17.2.1. The Pyruvate Dehydrogenase Complex Is Regulated Allosterically and by Reversible Phosphorylation
      • 17.2.2. The Citric Acid Cycle Is Controlled at Several Points
    • 17.3. The Citric Acid Cycle Is a Source of Biosynthetic Precursors
      • 17.3.1. The Citric Acid Cycle Must Be Capable of Being Rapidly Replenished
      • 17.3.2. The Disruption of Pyruvate Metabolism Is the Cause of Beriberi and Poisoning by Mercury and Arsenic
      • 17.3.3. Speculations on the Evolutionary History of the Citric Acid Cycle
    • 17.4. The Glyoxylate Cycle Enables Plants and Bacteria to Grow on Acetate
    • Summary
      • The Citric Acid Cycle Oxidizes Two-Carbon Units
      • Entry to the Citric Acid Cycle and Metabolism Through It Are Controlled
      • The Citric Acid Cycle Is a Source of Biosynthetic Precursors
      • The Glyoxylate Cycle Enables Plants and Bacteria to Grow on Acetate
      • Key Terms
    • Problems
      • Chapter Integration Problem
      • Mechanism Problems
      • Data Interpretation
    • Selected Readings
      • Where to start
      • Pyruvate dehydrogenase complex
      • Structure of citric acid cycle enzymes
      • Organization of the citric acid cycle
      • Regulation
      • Evolutionary aspects
      • Discovery of the citric acid cycle
  • Chapter 18. Oxidative Phosphorylation
    • 18.1. Oxidative Phosphorylation in Eukaryotes Takes Place in Mitochondria
      • 18.1.1. Mitochondria Are Bounded by a Double Membrane
      • 18.1.2. Mitochondria Are the Result of an Endosymbiotic Event
    • 18.2. Oxidative Phosphorylation Depends on Electron Transfer
      • 18.2.1. High-Energy Electrons: Redox Potentials and Free-Energy Changes
      • 18.2.2. A 1.14-Volt Potential Difference Between NADH and O₂ Drives Electron Transport Through the Chain and Favors the Formation of a Proton Gradient
      • 18.2.3. Electrons Can Be Transferred Between Groups That Are Not in Contact
    • 18.3. The Respiratory Chain Consists of Four Complexes: Three Proton Pumps and a Physical Link to the Citric Acid Cycle
      • 18.3.1. The High-Potential Electrons of NADH Enter the Respiratory Chain at NADH-Q Oxidoreductase
      • 18.3.2. Ubiquinol Is the Entry Point for Electrons from FADH₂ of Flavoproteins
      • 18.3.3. Electrons Flow from Ubiquinol to Cytochrome c Through Q-Cytochrome c Oxidoreductase
      • 18.3.4. Transmembrane Proton Transport: The Q Cycle
      • 18.3.5. Cytochrome c Oxidase Catalyzes the Reduction of Molecular Oxygen to Water
      • 18.3.6. Toxic Derivatives of Molecular Oxygen Such as Superoxide Radical Are Scavenged by Protective Enzymes
      • 18.3.7. The Conformation of Cytochrome c Has Remained Essentially Constant for More Than a Billion Years
    • 18.4. A Proton Gradient Powers the Synthesis of ATP
      • 18.4.1. ATP Synthase Is Composed of a Proton-Conducting Unit and a Catalytic Unit
      • 18.4.2. Proton Flow Through ATP Synthase Leads to the Release of Tightly Bound ATP: The Binding-Change Mechanism
      • 18.4.3. The World's Smallest Molecular Motor: Rotational Catalysis
      • 18.4.4. Proton Flow Around the c Ring Powers ATP Synthesis
      • 18.4.5. ATP Synthase and G Proteins Have Several Common Features
    • 18.5. Many Shuttles Allow Movement Across the Mitochondrial Membranes
      • 18.5.1. Electrons from Cytosolic NADH Enter Mitochondria by Shuttles
      • 18.5.2. The Entry of ADP into Mitochondria Is Coupled to the Exit of ATP by ATP-ADP Translocase
      • 18.5.3. Mitochondrial Transporters for Metabolites Have a Common Tripartite Motif
    • 18.6. The Regulation of Cellular Respiration Is Governed Primarily by the Need for ATP
      • 18.6.1. The Complete Oxidation of Glucose Yields About 30 Molecules of ATP
      • 18.6.2. The Rate of Oxidative Phosphorylation Is Determined by the Need for ATP
      • 18.6.3. Oxidative Phosphorylation Can Be Inhibited at Many Stages
      • 18.6.4. Regulated Uncoupling Leads to the Generation of Heat
      • 18.6.5. Mitochondrial Diseases Are Being Discovered
      • 18.6.6. Mitochondria Play a Key Role in Apoptosis
      • 18.6.7. Power Transmission by Proton Gradients: A Central Motif of Bioenergetics
    • Summary
      • Oxidative Phosphorylation in Eukaryotes Takes Place in Mitochondria
      • Oxidative Phosphorylation Depends on Electron Transfer
      • The Respiratory Chain Consists of Four Complexes: Three Proton Pumps and a Physical Link to the Citric Acid Cycle
      • A Proton Gradient Powers the Synthesis of ATP
      • Many Shuttles Allow Movement Across the Mitochondrial Membranes
      • The Regulation of Oxidative Phosphorylation Is Governed Primarily by the Need for ATP
      • Key Terms
    • Problems
      • Chapter Integration Problem
      • Data Interpretation Problem
      • Mechanism Problem
      • Media Problem
    • Selected Readings
      • Where to start
      • Books
      • Electron-transport chain
      • ATP synthase
      • Translocators
      • Superoxide dismutase and catalase
      • Mitochondrial diseases
      • Apoptosis
      • Historical aspects
  • Chapter 19. The Light Reactions of Photosynthesis
    • 19.1. Photosynthesis Takes Place in Chloroplasts
      • 19.1.1. The Primary Events of Photosynthesis Take Place in Thylakoid Membranes
      • 19.1.2. The Evolution of Chloroplasts
    • 19.2. Light Absorption by Chlorophyll Induces Electron Transfer
      • 19.2.1. Photosynthetic Bacteria and the Photosynthetic Reaction Centers of Green Plants Have a Common Core
      • 19.2.2. A Special Pair of Chlorophylls Initiates Charge Separation
    • 19.3. Two Photosystems Generate a Proton Gradient and NADPH in Oxygenic Photosynthesis
      • 19.3.1. Photosystem II Transfers Electrons from Water to Plastoquinone and Generates a Proton Gradient
      • 19.3.2. Cytochrome bf Links Photosystem II to Photosystem I
      • 19.3.3. Photosystem I Uses Light Energy to Generate Reduced Ferredoxin, a Powerful Reductant
      • 19.3.4. Ferredoxin-NADP⁺ Reductase Converts NADP⁺ into NADPH
    • 19.4. A Proton Gradient Across the Thylakoid Membrane Drives ATP Synthesis
      • 19.4.1. The ATP Synthase of Chloroplasts Closely Resembles Those of Mitochondria and Prokaryotes
      • 19.4.2. Cyclic Electron Flow Through Photosystem I Leads to the Production of ATP Instead of NADPH
      • 19.4.3. The Absorption of Eight Photons Yields One O₂, Two NADPH, and Three ATP Molecules
    • 19.5. Accessory Pigments Funnel Energy Into Reaction Centers
      • 19.5.1. Resonance Energy Transfer Allows Energy to Move from the Site of Initial Absorbance to the Reaction Center
      • 19.5.2. Light-Harvesting Complexes Contain Additional Chlorophylls and Carotinoids
      • 19.5.3. Phycobilisomes Serve as Molecular Light Pipes in Cyanobacteria and Red Algae
      • 19.5.4. Components of Photosynthesis Are Highly Organized
      • 19.5.5. Many Herbicides Inhibit the Light Reactions of Photosynthesis
    • 19.6. The Ability to Convert Light Into Chemical Energy Is Ancient
    • Summary
      • Photosynthesis Takes Place in Chloroplasts
      • Light Absorption by Chlorophyll Induces Electron Transfer
      • Two Photosystems Generate a Proton Gradient and NADPH in Oxygenic Photosynthesis
      • A Proton Gradient Across the Thylakoid Membrane Drives ATP Synthesis
      • Accessory Pigments Funnel Energy into Reaction Centers
      • The Ability to Convert Light into Chemical Energy Is Ancient
      • Key Terms
    • Problems
      • Mechanism Problem
      • Data Interpretation and Chapter Integration Problem
    • Selected Readings
      • Where to start
      • Books and general reviews
      • Electron-transfer mechanisms
      • Photosystem II
      • Oxygen evolution
      • Photosystem I and cytochrome bf
      • ATP synthase
      • Light-harvesting assemblies
      • Evolution
  • Chapter 20. The Calvin Cycle and the Pentose Phosphate Pathway
    • 20.1. The Calvin Cycle Synthesizes Hexoses from Carbon Dioxide and Water
      • 20.1.1. Carbon Dioxide Reacts with Ribulose 1,5-bisphosphate to Form Two Molecules of 3-Phosphoglycerate
      • 20.1.2. Catalytic Imperfection: Rubisco Also Catalyzes a Wasteful Oxygenase Reaction
      • 20.1.3. Hexose Phosphates Are Made from Phosphoglycerate, and Ribulose 1,5-bisphosphate Is Regenerated
      • 20.1.4. Three Molecules of ATP and Two Molecules of NADPH Are Used to Bring Carbon Dioxide to the Level of a Hexose
      • 20.1.5. Starch and Sucrose Are the Major Carbohydrate Stores in Plants
    • 20.2. The Activity of the Calvin Cycle Depends on Environmental Conditions
      • 20.2.1. Rubisco Is Activated by Light-Driven Changes in Proton and Magnesium Ion Concentrations
      • 20.2.2. Thioredoxin Plays a Key Role in Regulating the Calvin Cycle
      • 20.2.3. The C₄ Pathway of Tropical Plants Accelerates Photosynthesis by Concentrating Carbon Dioxide
      • 20.2.4. Crassulacean Acid Metabolism Permits Growth in Arid Ecosystems
    • 20.3 the Pentose Phosphate Pathway Generates NADPH and Synthesizes Five-Carbon Sugars
      • 20.3.1. Two Molecules of NADPH Are Generated in the Conversion of Glucose 6-phosphate into Ribulose 5-phosphate
      • 20.3.2. The Pentose Phosphate Pathway and Glycolysis Are Linked by Transketolase and Transaldolase
      • 20.3.3. Transketolase and Transaldolase Stabilize Carbanionic Intermediates by Different Mechanisms
    • 20.4. The Metabolism of Glucose 6-Phosphate by the Pentose Phosphate Pathway Is Coordinated with Glycolysis
      • 20.4.1. The Rate of the Pentose Phosphate Pathway Is Controlled by the Level of NADP⁺
      • 20.4.2. The Flow of Glucose 6-phosphate Depends on the Need for NADPH, Ribose 5-phosphate, and ATP
      • 20.4.3. Through the Looking Glass: The Calvin Cycle and the Pentose Phosphate Pathway
    • 20.5. Glucose 6-Phosphate Dehydrogenase Plays a Key Role in Protection Against Reactive Oxygen Species
      • 20.5.1. Glucose 6-phosphate Dehydrogenase Deficiency Causes a Drug-Induced Hemolytic Anemia
      • 20.5.2. A Deficiency of Glucose 6-phosphate Dehydrogenase Confers an Evolutionary Advantage in Some Circumstances
    • Summary
      • The Calvin Cycle Synthesizes Hexoses from Carbon Dioxide and Water
      • The Activity of the Calvin Cycle Depends on Environmental Conditions
      • The Pentose Phosphate Pathway Generates NADPH and Synthesizes Five-Carbon Sugars
      • The Metabolism of Glucose 6-phosphate by the Pentose Phosphate Pathway Is Coordinated with Glycolysis
      • Glucose 6-phosphate Dehydrogenase Plays a Key Role in Protection Against Reactive Oxygen Species
      • Key Terms
    • Problems
      • Mechanism Problems
      • Chapter Integration Problems
      • Date Interpretation Problem
    • Selected Readings
      • Where to start
      • Books and general reviews
      • Enzymes and reaction mechanisms
      • Carbon dioxide fixation and rubisco
      • Regulation
      • Glucose 6-phosphate dehydrogenase
      • Evolution
  • Chapter 21. Glycogen Metabolism
    • 21.1. Glycogen Breakdown Requires the Interplay of Several Enzymes
      • 21.1.1. Phosphorylase Catalyzes the Phosphorolytic Cleavage of Glycogen to Release Glucose 1-phosphate
      • 21.1.2. A Debranching Enzyme Also Is Needed for the Breakdown of Glycogen
      • 21.1.3. Phosphoglucomutase Converts Glucose 1-phosphate into Glucose 6-phosphate
      • 21.1.4. Liver Contains Glucose 6-phosphatase, a Hydrolytic Enzyme Absent from Muscle
      • 21.1.5. Pyridoxal Phosphate Participates in the Phosphorolytic Cleavage of Glycogen
    • 21.2. Phosphorylase Is Regulated by Allosteric Interactions and Reversible Phosphorylation
      • 21.2.1. Muscle Phosphorylase Is Regulated by the Intracellular Energy Charge
      • 21.2.2. Liver Phosphorylase Produces Glucose for Use by Other Tissues
      • 21.2.3. Phosphorylase Kinase Is Activated by Phosphorylation and Calcium Ions
    • 21.3. Epinephrine and Glucagon Signal the Need for Glycogen Breakdown
      • 21.3.1. G Proteins Transmit the Signal for the Initiation of Glycogen Breakdown
      • 21.3.2. Glycogen Breakdown Must Be Capable of Being Rapidly Turned Off
      • 21.3.3. The Regulation of Glycogen Phosphorylase Became More Sophisticated as the Enzyme Evolved
    • 21.4. Glycogen Is Synthesized and Degraded by Different Pathways
      • 21.4.1. UDP-Glucose Is an Activated Form of Glucose
      • 21.4.2. Glycogen Synthase Catalyzes the Transfer of Glucose from UDP-Glucose to a Growing Chain
      • 21.4.3. A Branching Enzyme Forms α-1,6 Linkages
      • 21.4.4. Glycogen Synthase Is the Key Regulatory Enzyme in Glycogen Synthesis
      • 21.4.5. Glycogen Is an Efficient Storage Form of Glucose
    • 21.5. Glycogen Breakdown and Synthesis Are Reciprocally Regulated
      • 21.5.1. Protein Phosphatase 1 Reverses the Regulatory Effects of Kinases on Glycogen Metabolism
      • 21.5.2. Insulin Stimulates Glycogen Synthesis by Activating Protein Phosphatase 1
      • 21.5.3. Glycogen Metabolism in the Liver Regulates the Blood-Glucose Level
      • 21.5.4. A Biochemical Understanding of Glycogen-Storage Diseases Is Possible
    • Summary
      • Glycogen Breakdown Requires the Interplay of Several Enzymes
      • Phosphorylase Is Regulated by Allosteric Interactions and Reversible Phosphorylation
      • Epinephrine and Glucagon Signal the Need for Glycogen Breakdown
      • Glycogen Is Synthesized and Degraded by Different Pathways
      • Glycogen Breakdown and Synthesis Are Reciprocally Regulated
      • Key Terms
    • Problems
      • Mechanism Problem
      • Chapter Integration and Data Interpretation Problems
      • Media Problem
    • Selected Readings
      • Where to start
      • Books and general reviews
      • X-ray crystallographic studies
      • Priming of glycogen synthesis
      • Catalytic mechanisms
      • Regulation of glycogen metabolism
      • Genetic diseases
      • Evolution
  • Chapter 22. Fatty Acid Metabolism
    • 22.1. Triacylglycerols Are Highly Concentrated Energy Stores
      • 22.1.1. Dietary Lipids Are Digested by Pancreatic Lipases
      • 22.1.2. Dietary Lipids Are Transported in Chylomicrons
    • 22.2. The Utilization of Fatty Acids as Fuel Requires Three Stages of Processing
      • 22.2.1. Triacylglycerols Are Hydrolyzed by Cyclic AMP-Regulated Lipases
      • 22.2.2. Fatty Acids Are Linked to Coenzyme A Before They Are Oxidized
      • 22.2.3. Carnitine Carries Long-Chain Activated Fatty Acids into the Mitochondrial Matrix
      • 22.2.4. Acetyl CoA, NADH, and FADH₂ Are Generated in Each Round of Fatty Acid Oxidation
      • 22.2.5. The Complete Oxidation of Palmitate Yields 106 Molecules of ATP
    • 22.3. Certain Fatty Acids Require Additional Steps for Degradation
      • 22.3.1. An Isomerase and a Reductase Are Required for the Oxidation of Unsaturated Fatty Acids
      • 22.3.2. Odd-Chain Fatty Acids Yield Propionyl Coenzyme A in the Final Thiolysis Step
      • 22.3.3. Propionyl CoA Is Converted into Succinyl CoA in a Reaction That Requires Vitamin B₁₂
      • 22.3.4. Fatty Acids Are Also Oxidized in Peroxisomes
      • 22.3.5. Ketone Bodies Are Formed from Acetyl Coenzyme A When Fat Breakdown Predominates
      • 22.3.6. Ketone Bodies Are a Major Fuel in Some Tissues
      • 22.3.7. Animals Cannot Convert Fatty Acids into Glucose
    • 22.4. Fatty Acids Are Synthesized and Degraded by Different Pathways
      • 22.4.1. The Formation of Malonyl Coenzyme A Is the Committed Step in Fatty Acid Synthesis
      • 22.4.2. Intermediates in Fatty Acid Synthesis Are Attached to an Acyl Carrier Protein
      • 22.4.3. The Elongation Cycle in Fatty Acid Synthesis
      • 22.4.4. Fatty Acids Are Synthesized by a Multifunctional Enzyme Complex in Eukaryotes
      • 22.4.5. The Flexible Phosphopantetheinyl Unit of ACP Carries Substrate from One Active Site to Another
      • 22.4.6. The Stoichiometry of Fatty Acid Synthesis
      • 22.4.7. Citrate Carries Acetyl Groups from Mitochondria to the Cytosol for Fatty Acid Synthesis
      • 22.4.8. Sources of NADPH for Fatty Acid Synthesis
      • 22.4.9. Fatty Acid Synthase Inhibitors May Be Useful Drugs
      • 22.4.10. Variations on a Theme: Polyketide and Nonribosomal Peptide Synthetases Resemble Fatty Acid Synthase
    • 22.5. Acetyl Coenzyme A Carboxylase Plays a Key Role in Controlling Fatty Acid Metabolism
      • Global Regulation
      • Local Regulation
      • Response to Diet
    • 22.6. Elongation and Unsaturation of Fatty Acids Are Accomplished by Accessory Enzyme Systems
      • 22.6.1. Membrane-Bound Enzymes Generate Unsaturated Fatty Acids
      • 22.6.2. Eicosanoid Hormones Are Derived from Polyunsaturated Fatty Acids
    • Summary
      • Triacylglycerols Are Highly Concentrated Energy Stores
      • The Utilization of Fatty Acids as Fuel Requires Three Stages of Processing
      • Certain Fatty Acids Require Additional Steps for Degradation
      • Fatty Acids Are Synthesized and Degraded by Different Pathways
      • Acetyl Coenzyme A Carboxylase Plays a Key Role in Controlling Fatty Acid Metabolism
      • Elongation and Unsaturation of Fatty Acids Are Accomplished by Accessory Enzyme Systems
      • Key Terms
    • Problems
      • Mechanism Problems
      • Chapter Integration Problems
      • Data Interpretation Problem
      • Media Problem
    • Selected Readings
      • Where to start
      • Books
      • Fatty acid oxidation
      • Fatty acid synthesis
      • Acetyl CoA carboxylase
      • Eicosanoids
      • Genetic diseases
  • Chapter 23. Protein Turnover and Amino Acid Catabolism
    • 23.1. Proteins Are Degraded to Amino Acids
      • 23.1.1. The Digestion and Absorption of Dietary Proteins
      • 23.1.2. Cellular Proteins Are Degraded at Different Rates
    • 23.2. Protein Turnover Is Tightly Regulated
      • 23.2.1. Ubiquitin Tags Proteins for Destruction
      • 23.2.2. The Proteasome Digests the Ubiquitin-Tagged Proteins
      • 23.2.3. Protein Degradation Can Be Used to Regulate Biological Function
      • 23.2.4. The Ubiquitin Pathway and the Proteasome Have Prokaryotic Counterparts
    • 23.3. The First Step in Amino Acid Degradation Is the Removal of Nitrogen
      • 23.3.1. Alpha-Amino Groups Are Converted into Ammonium Ions by the Oxidative Deamination of Glutamate
      • 23.3.2. Pyridoxal Phosphate Forms Schiff-Base Intermediates in Aminotransferases
      • 23.3.3. Aspartate Aminotransferase Is a Member of a Large and Versatile Family of Pyridoxal-Dependent Enzymes
      • 23.3.4. Serine and Threonine Can Be Directly Deaminated
      • 23.3.5. Peripheral Tissues Transport Nitrogen to the Liver
    • 23.4. Ammonium Ion Is Converted Into Urea in Most Terrestrial Vertebrates
      • 23.4.1. The Urea Cycle Begins with the Formation of Carbamoyl Phosphate
      • 23.4.2. The Urea Cycle Is Linked to the Citric Acid Cycle
      • 23.4.3. The Evolution of the Urea Cycle
      • 23.4.4. Inherited Defects of the Urea Cycle Cause Hyperammonemia and Can Lead to Brain Damage
      • 23.4.5. Urea Is Not the Only Means of Disposing of Excess Nitrogen
    • 23.5. Carbon Atoms of Degraded Amino Acids Emerge as Major Metabolic Intermediates
      • 23.5.1. Pyruvate as an Entry Point into Metabolism
      • 23.5.2. Oxaloacetate as an Entry Point into Metabolism
      • 23.5.3. Alpha-Ketoglutarate as an Entry Point into Metabolism
      • 23.5.4. Succinyl Coenzyme A Is a Point of Entry for Several Nonpolar Amino Acids
      • 23.5.5. Methionine Degradation Requires the Formation of a Key Methyl Donor, S-Adenosylmethionine
      • 23.5.6. The Branched-Chain Amino Acids Yield Acetyl CoA, Acetoacetate, or Propionyl CoA
      • 23.5.7. Oxygenases Are Required for the Degradation of Aromatic Amino Acids
    • 23.6. Inborn Errors of Metabolism Can Disrupt Amino Acid Degradation
    • Summary
      • Proteins Are Degraded to Amino Acids
      • Protein Turnover Is Tightly Regulated
      • The First Step in Amino Acid Degradation Is the Removal of Nitrogen
      • Ammonium Ion Is Converted into Urea in Most Terrestrial Vertebrates
      • Carbon Atoms of Degraded Amino Acids Emerge as Major Metabolic Intermediates
      • Inborn Errors of Metabolism Can Disrupt Amino Acid Degradation
      • Key Terms
    • Problems
      • Mechanism Problems
      • Chapter Integration Problems
      • Data Interpretation Problem
    • Selected Readings
      • Where to start
      • Books
      • Ubiquitin and the proteasome
      • Pyridoxal phosphate-dependent enzymes
      • Urea-cycle enzymes
      • Amino acid degradation
      • Genetic diseases
      • Historical aspects and the process of discovery
• 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
      • 24.1.1. The Iron-Molybdenum Cofactor of Nitrogenase Binds and Reduces Atmospheric Nitrogen
      • 24.1.2. Ammonium Ion Is Assimilated into an Amino Acid Through Glutamate and Glutamine
    • 24.2. Amino Acids Are Made from Intermediates of the Citric Acid Cycle and Other Major Pathways
      • 24.2.1. Human Beings Can Synthesize Some Amino Acids but Must Obtain Others from the Diet
      • 24.2.2. A Common Step Determines the Chirality of All Amino Acids
      • 24.2.3. An Adenylated Intermediate Is Required to Form Asparagine from Aspartate
      • 24.2.4. Glutamate Is the Precursor of Glutamine, Proline, and Arginine
      • 24.2.5. Serine, Cysteine, and Glycine Are Formed from 3-Phosphoglycerate
      • 24.2.6. Tetrahydrofolate Carries Activated One-Carbon Units at Several Oxidation Levels
      • 24.2.7. S-Adenosylmethionine Is the Major Donor of Methyl Groups
      • 24.2.8. Cysteine Is Synthesized from Serine and Homocysteine
      • 24.2.9. High Homocysteine Levels Are Associated with Vascular Disease
      • 24.2.10. Shikimate and Chorismate Are Intermediates in the Biosynthesis of Aromatic Amino Acids
      • 24.2.11. Tryptophan Synthetase Illustrates Substrate Channeling in Enzymatic Catalysis
    • 24.3. Amino Acid Biosynthesis Is Regulated by Feedback Inhibition
      • 24.3.1. Branched Pathways Require Sophisticated Regulation
      • 24.3.2. The Activity of Glutamine Synthetase Is Modulated by an Enzymatic Cascade
    • 24.4. Amino Acids Are Precursors of Many Biomolecules
      • 24.4.1. Glutathione, a Gamma-Glutamyl Peptide, Serves as a Sulfhydryl Buffer and an Antioxidant
      • 24.4.2. Nitric Oxide, a Short-Lived Signal Molecule, Is Formed from Arginine
      • 24.4.3. Mammalian Porphyrins Are Synthesized from Glycine and Succinyl Coenzyme A
      • 24.4.4. Porphyrins Accumulate in Some Inherited Disorders of Porphyrin Metabolism
    • Summary
      • Nitrogen Fixation: Microorganisms Use ATP and a Powerful Reductant to Reduce Atmospheric Nitrogen to Ammonia
      • Amino Acids Are Made from Intermediates of the Citric Acid Cycle and Other Major Pathways
      • Amino Acid Biosynthesis Is Regulated by Feedback Inhibition
      • Amino Acids Are Precursors of Many Biomolecules
      • Key Terms
    • Problems
      • Mechanism Problems
      • Chapter Integration Problems
      • Chapter Integration and Data Interpretation Problem
    • Selected Readings
      • Where to start
      • Books
      • Nitrogen fixation
      • Regulation of amino acid biosynthesis
      • Aromatic amino acid biosynthesis
      • Glutathione
      • Ethylene and nitric oxide
      • Biosynthesis of porphyrins
  • Chapter 25. Nucleotide Biosynthesis
    • 25.1. In de Novo Synthesis, the Pyrimidine Ring Is Assembled from Bicarbonate, Aspartate, and Glutamine
      • 25.1.1. Bicarbonate and Other Oxygenated Carbon Compounds Are Activated by Phosphorylation
      • 25.1.2. The Side Chain of Glutamine Can Be Hydrolyzed to Generate Ammonia
      • 25.1.3. Intermediates Can Move Between Active Sites by Channeling
      • 25.1.4. Orotate Acquires a Ribose Ring from PRPP to Form a Pyrimidine Nucleotide and Is Converted into Uridylate
      • 25.1.5. Nucleotide Mono-, Di-, and Triphosphates Are Interconvertible
      • 25.1.6. CTP Is Formed by Amination of UTP
    • 25.2. Purine Bases Can Be Synthesized de Novo or Recycled by Salvage Pathways
      • 25.2.1. Salvage Pathways Economize Intracellular Energy Expenditure
      • 25.2.2. The Purine Ring System Is Assembled on Ribose Phosphate
      • 25.2.3. The Purine Ring Is Assembled by Successive Steps of Activation by Phosphorylation Followed by Displacement
      • 25.2.4. AMP and GMP Are Formed from IMP
    • 25.3. Deoxyribonucleotides Synthesized by the Reduction of Ribonucleotides Through a Radical Mechanism
      • 25.3.1. Thymidylate Is Formed by the Methylation of Deoxyuridylate
      • 25.3.2. Dihydrofolate Reductase Catalyzes the Regeneration of Tetrahydrofolate, a One-Carbon Carrier
      • 25.3.3. Several Valuable Anticancer Drugs Block the Synthesis of Thymidylate
    • 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
      • 25.6.1. Purines Are Degraded to Urate in Human Beings
      • 25.6.2. Lesch-Nyhan Syndrome Is a Dramatic Consequence of Mutations in a Salvage-Pathway Enzyme
    • Summary
      • In de Novo Synthesis, the Pyrimidine Ring Is Assembled from Bicarbonate, Aspartate, and Glutamine
      • Purines Bases Can Be Synthesized de Novo or Recycled by Salvage Pathways
      • Deoxyribonucleotides Are Synthesized by the Reduction of Ribonucleotides Through a Radical Mechanism
      • Key Steps in Nucleotide Biosynthesis Are Regulated by Feedback Inhibition
      • NAD⁺, FAD, and Coenzyme A Are Formed from ATP
      • Disruptions in Nucleotide Metabolism Can Cause Pathological Conditions
      • Key Terms
    • Problems
      • Mechanism Problems
      • Chapter Integration Problems
    • Selected Readings
      • Where to start
      • Pyrimidine biosynthesis
      • Purine biosynthesis
      • Ribonucleotide reductases
      • Thymidylate synthase and dihydrofolate reductase
      • Genetic diseases
  • Chapter 26. The Biosynthesis of Membrane Lipids and Steroids
    • 26.1. Phosphatidate Is a Common Intermediate in the Synthesis of Phospholipids and Triacylglycerols
      • 26.1.1. The Synthesis of Phospholipids Requires an Activated Intermediate
      • 26.1.2. Plasmalogens and Other Ether Phospholipids Are Synthesized from Dihydroxyacetone Phosphate
      • 26.1.3. Sphingolipids Are Synthesized from Ceramide
      • 26.1.4. Gangliosides Are Carbohydrate-Rich Sphingolipids That Contain Acidic Sugars
      • 26.1.5. Sphingolipids Confer Diversity on Lipid Structure and Function
      • 26.1.6. Respiratory Distress Syndrome and Tay-Sachs Disease Result from the Disruption of Lipid Metabolism
    • 26.2. Cholesterol Is Synthesized from Acetyl Coenzyme A in Three Stages
      • 26.2.1. The Synthesis of Mevalonate, Which Is Activated as Isopentenyl Pyrophosphate, Initiates the Synthesis of Cholesterol
      • 26.2.2. Squalene (C₃₀) Is Synthesized from Six Molecules of Isopentenyl Pyrophosphate (C₅)
      • 26.2.3. Squalene Cyclizes to Form Cholesterol
    • 26.3. The Complex Regulation of Cholesterol Biosynthesis Takes Place at Several Levels
      • 26.3.1. Lipoproteins Transport Cholesterol and Triacylglycerols Throughout the Organism
      • 26.3.2. The Blood Levels of Certain Lipoproteins Can Serve Diagnostic Purposes
      • 26.3.3. Low-Density Lipoproteins Play a Central Role in Cholesterol Metabolism
      • 26.3.4. The LDL Receptor Is a Transmembrane Protein Having Five Different Functional Regions
      • 26.3.5. The Absence of the LDL Receptor Leads to Hypercholesteremia and Atherosclerosis
      • 26.3.6. The Clinical Management of Cholesterol Levels Can Be Understood at a Biochemical Level
    • 26.4. Important Derivatives of Cholesterol Include Bile Salts and Steroid Hormones
      • Bile Salts
      • Steroid Hormones
      • 26.4.1. The Nomenclature of Steroid Hormones
      • 26.4.2. Steroids Are Hydroxylated by Cytochrome P450 Monooxygenases That Utilize NADPH and O₂
      • 26.4.3. The Cytochrome P450 System Is Widespread and Performs a Protective Function
      • 26.4.4. Pregnenolone, a Precursor for Many Other Steroids, Is Formed from Cholesterol by Cleavage of Its Side Chain
      • 26.4.5. The Synthesis of Progesterone and Corticosteroids from Pregnenolone
      • 26.4.6. The Synthesis of Androgens and Estrogens from Pregnenolone
      • 26.4.7. Vitamin D Is Derived from Cholesterol by the Ring-Splitting Activity of Light
      • 26.4.8. Isopentenyl Pyrophosphate Is a Precursor for a Wide Variety of Biomolecules
    • Summary
      • Phosphatidate Is a Common Intermediate in the Synthesis of Phospholipids and Triacylglycerols
      • Cholesterol Is Synthesized from Acetyl Coenzyme A in Three Stages
      • The Complex Regulation of Cholesterol Biosynthesis Takes Place at Several Levels
      • Important Derivatives of Cholesterol Include Bile Salts and Steroid Hormones
      • Key Terms
    • Problems
      • Mechanism Problem
      • Data Interpretation and Chapter Integration Problems
    • Selected Readings
      • Where to start
      • Books
      • Phospholipids and sphingolipids
      • Biosynthesis of cholesterol and steroids
      • Lipoproteins and their receptors
      • Oxygen activation and P450 catalysis
  • Chapter 27. DNA Replication, Recombination, and Repair
    • 27.1. DNA Can Assume a Variety of Structural Forms
      • 27.1.1. A-DNA Is a Double Helix with Different Characteristics from Those of the More Common B-DNA
      • 27.1.2. The Major and Minor Grooves Are Lined by Sequence-Specific Hydrogen-Bonding Groups
      • 27.1.3. The Results of Studies of Single Crystals of DNA Revealed Local Variations in DNA Structure
      • 27.1.4. Z-DNA Is a Left-Handed Double Helix in Which Backbone Phosphates Zigzag
    • 27.2. DNA Polymerases Require a Template and a Primer
      • 27.2.1. All DNA Polymerases Have Structural Features in Common
      • 27.2.2. Two Bound Metal Ions Participate in the Polymerase Reaction
      • 27.2.3. The Specificity of Replication Is Dictated by Hydrogen Bonding and the Complementarity of Shape Between Bases
      • 27.2.4. Many Polymerases Proofread the Newly Added Bases and Excise Errors
      • 27.2.5. The Separation of DNA Strands Requires Specific Helicases and ATP Hydrolysis
    • 27.3. Double-Stranded DNA Can Wrap Around Itself to Form Supercoiled Structures
      • 27.3.1. The Linking Number of DNA, a Topological Property, Determines the Degree of Supercoiling
      • 27.3.2. Helical Twist and Superhelical Writhe Are Correlated with Each Other Through the Linking Number
      • 27.3.3. Type I Topoisomerases Relax Supercoiled Structures
      • 27.3.4. Type II Topoisomerases Can Introduce Negative Supercoils Through Coupling to ATP Hydrolysis
    • 27.4. DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites
      • 27.4.1. An RNA Primer Synthesized by Primase Enables DNA Synthesis to Begin
      • 27.4.2. One Strand of DNA Is Made Continuously, Whereas the Other Strand Is Synthesized in Fragments
      • 27.4.3. DNA Ligase Joins Ends of DNA in Duplex Regions
      • 27.4.4. DNA Replication Requires Highly Processive Polymerases
      • 27.4.5. The Leading and Lagging Strands Are Synthesized in a Coordinated Fashion
      • 27.4.6. DNA Synthesis Is More Complex in Eukaryotes Than in Prokaryotes
      • 27.4.7. Telomeres Are Unique Structures at the Ends of Linear Chromosomes
      • 27.4.8. Telomeres Are Replicated by Telomerase, a Specialized Polymerase That Carries Its Own RNA Template
    • 27.5. Double-Stranded DNA Molecules with Similar Sequences Sometimes Recombine
      • 27.5.1. Recombination Reactions Proceed Through Holliday Junction Intermediates
      • 27.5.2. Recombinases Are Evolutionarily Related to Topoisomerases
    • 27.6. Mutations Involve Changes in the Base Sequence of DNA
      • 27.6.1. Some Chemical Mutagens Are Quite Specific
      • 27.6.2. Ultraviolet Light Produces Pyrimidine Dimers
      • 27.6.3. A Variety of DNA-Repair Pathways Are Utilized
      • 27.6.4. The Presence of Thymine Instead of Uracil in DNA Permits the Repair of Deaminated Cytosine
      • 27.6.5. Many Cancers Are Caused by Defective Repair of DNA
      • 27.6.6. Some Genetic Diseases Are Caused by the Expansion of Repeats of Three Nucleotides
      • 27.6.7. Many Potential Carcinogens Can Be Detected by Their Mutagenic Action on Bacteria
    • Summary
      • DNA Can Assume a Variety of Structural Forms
      • DNA Polymerases Require a Template and a Primer
      • Double-Stranded DNA Can Wrap Around Itself to Form Supercoiled Structures
      • DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites
      • Double-Stranded DNA Molecules with Similar Sequences Sometimes Recombine
      • Mutations Are Produced by Several Types of Changes in the Base Sequence of DNA
      • Key Terms
    • Problems
      • Mechanism Problems
      • Data Interpretation and Chapter Integration Problems
      • Media Problem
    • Selected Readings
      • Where to begin
      • Books
      • DNA structure
      • DNA topology and topoisomerases
      • Mechanism of replication
      • DNA polymerases and other enzymes of replication
      • Recombinases
      • Mutations and DNA repair
      • Defective DNA repair and cancer
  • Chapter 28. RNA Synthesis and Splicing
    • 28.1. Transcription Is Catalyzed by RNA Polymerase
      • 28.1.1. Transcription Is Initiated at Promoter Sites on the DNA Template
      • 28.1.2. Sigma Subunits of RNA Polymerase Recognize Promoter Sites
      • 28.1.3. RNA Polymerase Must Unwind the Template Double Helix for Transcription to Take Place
      • 28.1.4. RNA Chains Are Formed de Novo and Grow in the 5′-to-3′ Direction
      • 28.1.5. Elongation Takes Place at Transcription Bubbles That Move Along the DNA Template
      • 28.1.6. An RNA Hairpin Followed by Several Uracil Residues Terminates the Transcription of Some Genes
      • 28.1.7. The Rho Protein Helps Terminate the Transcription of Some Genes
      • 28.1.8. Precursors of Transfer and Ribosomal RNA Are Cleaved and Chemically Modified After Transcription
      • 28.1.9. Antibiotic Inhibitors of Transcription
    • 28.2. Eukaryotic Transcription and Translation Are Separated in Space and Time
      • 28.2.1. RNA in Eukaryotic Cells Is Synthesized by Three Types of RNA Polymerase
      • 28.2.2. Cis- And Trans-Acting Elements: Locks and Keys of Transcription
      • 28.2.3. Most Promoters for RNA Polymerase II Contain a TATA Box Near the Transcription Start Site
      • 28.2.4. The TATA-Box-Binding Protein Initiates the Assembly of the Active Transcription Complex
      • 28.2.5. Multiple Transcription Factors Interact with Eukaryotic Promoters
      • 28.2.6. Enhancer Sequences Can Stimulate Transcription at Start Sites Thousands of Bases Away
    • 28.3. The Transcription Products of All Three Eukaryotic Polymerases Are Processed
      • 28.3.1. The Ends of the Pre-mRNA Transcript Acquire a 5′ Cap and a 3′ Poly(A) Tail
      • 28.3.2. RNA Editing Changes the Proteins Encoded by mRNA
      • 28.3.3. Splice Sites in mRNA Precursors Are Specified by Sequences at the Ends of Introns
      • 28.3.4. Splicing Consists of Two Transesterification Reactions
      • 28.3.5. Small Nuclear RNAs in Spliceosomes Catalyze the Splicing of mRNA Precursors
      • 28.3.6. Some Pre-mRNA Molecules Can Be Spliced in Alternative Ways to Yield Different mRNAs
    • 28.4. The Discovery of Catalytic RNA Was Revealing in Regard to Both Mechanism and Evolution
    • Summary
      • Transcription Is Catalyzed by RNA Polymerase
      • Eukaryotic Transcription and Translation Are Separated in Space and Time
      • The Transcription Products of All Three Eukaryotic Polymerases Are Processed
      • The Discovery of Catalytic RNA Was Revealing with Regard to Both Mechanism And Evolution
      • Key Terms
    • Problems
      • Mechanism Problem
      • Chapter Integration Problems
      • Data Interpretation Problems
    • Selected Readings
      • Where to begin
      • Books
      • RNA polymerases
      • Initiation and elongation
      • Promoters, enhancers, and transcription factors
      • Termination
      • 5′-Cap formation and polyadenylation
      • RNA editing
      • Splicing of mRNA precursors
      • Self-splicing and RNA catalysis
  • Chapter 29. Protein Synthesis
    • 29.1. Protein Synthesis Requires the Translation of Nucleotide Sequences Into Amino Acid Sequences
      • 29.1.1. The Synthesis of Long Proteins Requires a Low Error Frequency
      • 29.1.2. Transfer RNA Molecules Have a Common Design
      • 29.1.3. The Activated Amino Acid and the Anticodon of tRNA Are at Opposite Ends of the L-Shaped Molecule
    • 29.2. Aminoacyl-Transfer RNA Synthetases Read the Genetic Code
      • 29.2.1. Amino Acids Are First Activated by Adenylation
      • 29.2.2. Aminoacyl-tRNA Synthetases Have Highly Discriminating Amino Acid Activation Sites
      • 29.2.3. Proofreading by Aminoacyl-tRNA Synthetases Increases the Fidelity of Protein Synthesis
      • 29.2.4. Synthetases Recognize the Anticodon Loops and Acceptor Stems of Transfer RNA Molecules
      • 29.2.5. Aminoacyl-tRNA Synthetases Can Be Divided into Two Classes
    • 29.3. A Ribosome Is a Ribonucleoprotein Particle (70S) Made of a Small (30S) and a Large (50S) Subunit
      • 29.3.1. Ribosomal RNAs (5S, 16S, and 23S rRNA) Play a Central Role in Protein Synthesis
      • 29.3.2. Proteins Are Synthesized in the Amino-to-Carboxyl Direction
      • 29.3.3. Messenger RNA Is Translated in the 5′-to-3′ Direction
      • 29.3.4. The Start Signal Is AUG (or GUG) Preceded by Several Bases That Pair with 16S rRNA
      • 29.3.5. Bacterial Protein Synthesis Is Initiated by Formylmethionyl Transfer RNA
      • 29.3.6. Ribosomes Have Three tRNA-Binding Sites That Bridge the 30S and 50S Subunits
      • 29.3.7. The Growing Polypeptide Chain Is Transferred Between tRNAs on Peptide-Bond Formation
      • 29.3.8. Only the Codon-Anticodon Interactions Determine the Amino Acid That Is Incorporated
      • 29.3.9. Some Transfer RNA Molecules Recognize More Than One Codon Because of Wobble in Base-Pairing
    • 29.4. Protein Factors Play Key Roles in Protein Synthesis
      • 29.4.1. Formylmethionyl-tRNA_f Is Placed in the P Site of the Ribosome During Formation of the 70S Initiation Complex
      • 29.4.2. Elongation Factors Deliver Aminoacyl-tRNA to the Ribosome
      • 29.4.3. The Formation of a Peptide Bond Is Followed by the GTP-Driven Translocation of tRNAs and mRNA
      • 29.4.4. Protein Synthesis Is Terminated by Release Factors That Read Stop Codons
    • 29.5. Eukaryotic Protein Synthesis Differs from Prokaryotic Protein Synthesis Primarily in Translation Initiation
      • 29.5.1. Many Antibiotics Work by Inhibiting Protein Synthesis
      • 29.5.2. Diphtheria Toxin Blocks Protein Synthesis in Eukaryotes by Inhibiting Translocation
    • Summary
      • Protein Synthesis Requires the Translation of Nucleotide Sequences into Amino Acid Sequences
      • Aminoacyl-Transfer-RNA Synthetases Read the Genetic Code
      • A Ribosome Is a Ribonucleoprotein Particle (70S) Made of a Small (30S) and a Large (50S) Subunit
      • Protein Factors Play Key Roles in Protein Synthesis
      • Eukaryotic Protein Synthesis Differs from Prokaryotic Protein Synthesis Primarily in Translation Initiation
      • Key Terms
    • Problems
      • Mechanism Problems
      • Chapter Integration Problems
      • Data Interpretation Problem
      • Media Problem
    • Selected Readings
      • Where to start
      • Books
      • Aminoacyl-tRNA synthetases
      • Transfer RNA
      • Ribosomes and ribosomal RNAs
      • Initiation factors
      • Elongation factors
      • Peptide-bond formation and translocation
      • Termination
      • Fidelity and proofreading
      • Eukaryotic protein synthesis
      • Antibiotics and toxins
  • Chapter 30. The Integration of Metabolism
    • 30.1. Metabolism Consist of Highly Interconnected Pathways
      • 30.1.1. Recurring Motifs in Metabolic Regulation
      • 30.1.2. Major Metabolic Pathways and Control Sites
      • 30.1.3. Key Junctions: Glucose 6-phosphate, Pyruvate, and Acetyl CoA
    • 30.2. Each Organ Has a Unique Metabolic Profile
    • 30.3. Food Intake and Starvation Induce Metabolic Changes
      • 30.3.1. Metabolic Adaptations in Prolonged Starvation Minimize Protein Degradation
      • 30.3.2. Metabolic Derangements in Diabetes Result from Relative Insulin Insufficiency and Glucagon Excess
      • 30.3.3. Caloric Homeostasis: A Means of Regulating Body Weight
    • 30.4. Fuel Choice During Exercise Is Determined by Intensity and Duration of Activity
    • 30.5. Ethanol Alters Energy Metabolism in the Liver
    • Summary
      • Metabolism Consists of Highly Interconnected Pathways
      • Each Organ Has a Unique Metabolic Profile
      • Food Intake and Starvation Induce Metabolic Changes
      • Fuel Choice During Exercise Is Determined by Intensity and Duration of Activity
      • Ethanol Alters Energy Metabolism in the Liver
      • Key Terms
    • Problems
    • Selected Readings
      • Where to start
      • Books
      • Fuel metabolism
      • Metabolic adaptations in starvation
      • Diabetes mellitus
      • Exercise metabolism
      • Ethanol metabolism
  • Chapter 31. The Control of Gene Expression
    • 31.1. Prokaryotic DNA-Binding Proteins Bind Specifically to Regulatory Sites in Operons
      • 31.1.1. An Operon Consists of Regulatory Elements and Protein-Encoding Genes
      • 31.1.2. The lac Operator Has a Symmetric Base Sequence
      • 31.1.3. The lac Repressor Protein in the Absence of Lactose Binds to the Operator and Blocks Transcription
      • 31.1.4. Ligand Binding Can Induce Structural Changes in Regulatory Proteins
      • 31.1.5. The Operon Is a Common Regulatory Unit in Prokaryotes
      • 31.1.6. Transcription Can Be Stimulated by Proteins That Contact RNA Polymerase
      • 31.1.7. The Helix-Turn-Helix Motif Is Common to Many Prokaryotic DNA-Binding Proteins
    • 31.2. The Greater Complexity of Eukaryotic Genomes Requires Elaborate Mechanisms for Gene Regulation
      • 31.2.1. Nucleosomes Are Complexes of DNA and Histones
      • 31.2.2. Eukaryotic DNA Is Wrapped Around Histones to Form Nucleosomes
      • 31.2.3. The Control of Gene Expression Requires Chromatin Remodeling
      • 31.2.4. Enhancers Can Stimulate Transcription by Perturbing Chromatin Structure
      • 31.2.5. The Modification of DNA Can Alter Patterns of Gene Expression
    • 31.3. Transcriptional Activation and Repression Are Mediated by Protein-Protein Interactions
      • 31.3.1. Steroids and Related Hydrophobic Molecules Pass Through Membranes and Bind to DNA-Binding Receptors
      • 31.3.2. Nuclear Hormone Receptors Regulate Transcription by Recruiting Coactivators and Corepressors to the Transcription Complex
      • 31.3.3. Steroid-Hormone Receptors Are Targets for Drugs
      • 31.3.4. Chromatin Structure Is Modulated Through Covalent Modifications of Histone Tails
      • 31.3.5. Histone Deacetylases Contribute to Transcriptional Repression
      • 31.3.6. Ligand Binding to Membrane Receptors Can Regulate Transcription Through Phosphorylation Cascades
      • 31.3.7. Chromatin Structure Effectively Decreases the Size of the Genome
    • 31.4. Gene Expression Can Be Controlled at Posttranscriptional Levels
      • 31.4.1. Attenuation Is a Prokaryotic Mechanism for Regulating Transcription Through Modulation of Nascent RNA Secondary Structure
      • 31.4.2. Genes Associated with Iron Metabolism Are Translationally Regulated in Animals
    • Summary
      • Prokaryotic DNA-Binding Proteins Bind Specifically to Regulatory Sites in Operons
      • The Greater Complexity of Eukaryotic Genomes Requires Elaborate Mechanisms for Gene Regulation
      • Transcriptional Activation and Repression Are Mediated by Protein-Protein Interactions
      • Gene Expression Can Be Controlled at Posttranscriptional Levels
      • Key Terms
    • Problems
      • Mechanism Problem
      • Chapter Integration Problem
      • Data Interpretation Problem
    • Selected Readings
      • Where to start
      • Books
      • Prokaryotic gene regulation
      • Nucleosomes and histones
      • Nuclear hormone receptors
      • Chromatin and chromatin remodeling
      • Posttranscriptional regulation
      • Historical aspects
• Part IV. Responding to Environmental Changes
  • Chapter 32. Sensory Systems
    • 32.1. A Wide Variety of Organic Compounds Are Detected by Olfaction
      • 32.1.1. Olfaction Is Mediated by an Enormous Family of Seven-Transmembrane-Helix Receptors
      • 32.1.2. Odorants Are Decoded by a Combinatorial Mechanism
      • 32.1.3. Functional Magnetic Resonance Imaging Reveals Regions of the Brain Processing Sensory Information
    • 32.2. Taste Is a Combination of Senses that Function by Different Mechanisms
      • 32.2.1. Sequencing the Human Genome Led to the Discovery of a Large Family of 7TM Bitter Receptors
      • 32.2.2. A Family of 7TM Receptors Almost Certainly Respond to Sweet Compounds
      • 32.2.3. Salty Tastes Are Detected Primarily by the Passage of Sodium Ions Through Channels
      • 32.2.4. Sour Tastes Arise from the Effects of Hydrogen Ions (Acids) on Channels
      • 32.2.5. Umami, the Taste of Glutamate, Is Detected by a Specialized Form of Glutamate Receptor
    • 32.3. Photoreceptor Molecules in the Eye Detect Visible Light
      • 32.3.1. Rhodopsin, a Specialized 7TM Receptor, Absorbs Visible Light
      • 32.3.2. Light Absorption Induces a Specific Isomerization of Bound 11-cis-Retinal
      • 32.3.3. Light-Induced Lowering of the Calcium Level Coordinates Recovery
      • 32.3.4. Color Vision Is Mediated by Three Cone Receptors That Are Homologs of Rhodopsin
      • 32.3.5. Rearrangements in the Genes for the Green and Red Pigments Lead to “Color Blindness”
    • 32.4. Hearing Depends on the Speedy Detection of Mechanical Stimuli
      • 32.4.1. Hair Cells Use a Connected Bundle of Stereocilia to Detect Tiny Motions
      • 32.4.2. Mechanosensory Channels Have Been Identified in Drosophila and Bacteria
    • 32.5. Touch Includes the Sensing of Pressure, Temperature, and Other Factors
      • 32.5.1. Studies of Capsaicin, the Active Ingredient in “Hot” Peppers, Reveal a Receptor for Sensing High Temperatures and Other Painful Stimuli
      • 32.5.2. Subtle Sensory Systems Detect Other Environmental Factors Such as Earth's Magnetic Field
    • Summary
      • Smell, Taste, Vision, Hearing, and Touch Are Based on Signal-Transduction Pathways Activated by Signals from the Environment
      • A Wide Variety of Organic Compounds Are Detected by Olfaction
      • Taste Is a Combination of Senses That Function by Different Mechanisms
      • Photoreceptor Molecules in the Eye Detect Visible Light
      • Hearing Depends on the Speedy Detection of Mechanical Stimuli
      • Touch Includes the Sensing of Pressure, Temperature, and Other Factors
      • Key Terms
    • Problems
      • Chapter Integration Problem
      • Mechanism Problem
      • Media Problems
    • Selected Readings
      • Where to start
      • Olfaction
      • Taste
      • Vision
      • Hearing
      • Touch and pain reception
      • Other sensory systems
  • 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
      • 33.3.1. X-Ray Analyses Have Revealed How Antibodies Bind Antigens
      • 33.3.2. Large Antigens Bind Antibodies with Numerous Interactions
    • 33.4. Diversity Is Generated by Gene Rearrangements
      • 33.4.1. J (Joining) Genes and D (Diversity) Genes Increase Antibody Diversity
      • 33.4.2. More Than 10⁸ Antibodies Can Be Formed by Combinatorial Association and Somatic Mutation
      • 33.4.3. The Oligomerization of Antibodies Expressed on the Surface of Immature B Cells Triggers Antibody Secretion
      • 33.4.4. Different Classes of Antibodies Are Formed by the Hopping of V_H Genes
    • 33.5. Major-Histocompatibility-Complex Proteins Present Peptide Antigens on Cell Surfaces for Recognition by T-Cell Receptors
      • 33.5.1. Peptides Presented by MHC Proteins Occupy a Deep Groove Flanked by Alpha Helices
      • 33.5.2. T-Cell Receptors Are Antibody-like Proteins Containing Variable and Constant Regions
      • 33.5.3. CD8 on Cytotoxic T Cells Acts in Concert with T-Cell Receptors
      • 33.5.4. Helper T Cells Stimulate Cells That Display Foreign Peptides Bound to Class II MHC Proteins
      • 33.5.5. Helper T Cells Rely on the T-Cell Receptor and CD4 to Recognize Foreign Peptides on Antigen-Presenting Cells
      • 33.5.6. MHC Proteins Are Highly Diverse
      • 33.5.7. Human Immunodeficiency Viruses Subvert the Immune System by Destroying Helper T Cells
    • 33.6. Immune Responses Against Self-Antigens Are Suppressed
      • 33.6.1. T Cells Are Subject to Positive and Negative Selection in the Thymus
      • 33.6.2. Autoimmune Diseases Result from the Generation of Immune Responses Against Self-Antigens
      • 33.6.3. The Immune System Plays a Role in Cancer Prevention
    • Summary
      • Antibodies Possess Distinct Antigen-Binding and Effector Units
      • The Immunoglobulin Fold Consists of a Beta-Sandwich Framework with Hypervariable Loops
      • Antibodies Bind Specific Molecules Through Their Hypervariable Loops
      • Diversity Is Generated by Gene Rearrangements
      • Major-Histocompatibility-Complex Proteins Present Peptide Antigens on Cell Surfaces for Recognition by T-Cell Receptors
      • Immune Responses Against Self-Antigens Are Suppressed
      • Key Terms
    • Problems
      • Mechanism Problem
      • Chapter Integration Problem
      • Data Interpretation Problem
    • Selected Readings
      • Where to start
      • Books
      • Structure of antibodies and antibody-antigen complexes
      • Generation of diversity
      • MHC proteins and antigen processing
      • T-cell receptors and signaling complexes
      • HIV and AIDS
      • Discovery of major concepts
  • Chapter 34. Molecular Motors
    • 34.1. Most Molecular-Motor Proteins Are Members of the P-Loop NTPase Superfamily
      • 34.1.1. A Motor Protein Consists of an ATPase Core and an Extended Structure
      • 34.1.2. ATP Binding and Hydrolysis Induce Changes in the Conformation and Binding Affinity of Motor Proteins
    • 34.2. Myosins Move Along Actin Filaments
      • 34.2.1. Muscle Is a Complex of Myosin and Actin
      • 34.2.2. Actin Is a Polar, Self-Assembling, Dynamic Polymer
      • 34.2.3. Motions of Single Motor Proteins Can Be Directly Observed
      • 34.2.4. Phosphate Release Triggers the Myosin Power Stroke
      • 34.2.5. The Length of the Lever Arm Determines Motor Velocity
    • 34.3. Kinesin and Dynein Move Along Microtubules
      • 34.3.1. Microtubules Are Hollow Cylindrical Polymers
      • 34.3.2. Kinesin Motion Is Highly Processive
      • 34.3.3. Small Structural Changes Can Reverse Motor Polarity
    • 34.4. A Rotary Motor Drives Bacterial Motion
      • 34.4.1. Bacteria Swim by Rotating Their Flagella
      • 34.4.2. Proton Flow Drives Bacterial Flagellar Rotation
      • 34.4.3. Bacterial Chemotaxis Depends on Reversal of the Direction of Flagellar Rotation
    • Summary
      • Most Molecular-Motor Proteins Are Members of the P-Loop NTPase Superfamily
      • Myosins Move Along Actin Filaments
      • Kinesin and Dynein Move Along Microtubules
      • A Rotary Motor Drives Bacterial Motion
      • Key Terms
    • Problems
      • Mechanism Problem
      • Chapter Integration Problem
      • Data Interpretation Problem
    • Selected Readings
      • Where to start
      • Books
      • Myosin and actin
      • Kinesin, dynein, and microtubules
      • Bacterial motion and chemotaxis
      • Historical aspects
• 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