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Cover of Biochemistry

Biochemistry, 5th edition

, , and .

Author Information
New York: W H Freeman; .
ISBN-10: 0-7167-3051-0

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
        • pKa 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 KM and Vmax Values
        • 8.4.2. Kinetic Perfection in Enzymatic Catalysis: The kcat/KM 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: Vmax and KM 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-tRNAf 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 VH 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

By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed.

Copyright © 2002, W. H. Freeman and Company.
Bookshelf ID: NBK21154

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