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• About this Book
• Cover Page
• Halftitle Page
• Title Page
• Copyright
• Dedication
• About the Authors
• A Note on the Nature of Science
• Overview of key features
• Tools and Resources to Support Teaching
• Acknowledgments
• Contents in Brief
• Contents
• Chapter 1 The Foundations of Biochemistry
• 1.1 Cellular Foundations
• Cells Are the Structural and Functional Units of All Living Organisms
• Cellular Dimensions Are Limited by Diffusion
• Organisms Belong to Three Distinct Domains of Life
• Organisms Differ Widely in Their Sources of Energy and Biosynthetic Precursors
• Bacterial and Archaeal Cells Share Common Features but Differ in Important Ways
• Eukaryotic Cells Have a Variety of Membranous Organelles, Which Can Be Isolated for Study
• The Cytoplasm Is Organized by the Cytoskeleton and Is Highly Dynamic
• Cells Build Supramolecular Structures
• In Vitro Studies May Overlook Important Interactions among Molecules
• 1.2 Chemical Foundations
• Biomolecules Are Compounds of Carbon with a Variety of Functional Groups
• Cells Contain a Universal Set of Small Molecules
• Macromolecules Are the Major Constituents of Cells
• Three-Dimensional Structure Is Described by Configuration and Conformation
• Interactions between Biomolecules Are Stereospecific
• 1.3 Physical Foundations
• Living Organisms Exist in a Dynamic Steady State, Never at Equilibrium with Their Surroundings
• Organisms Transform Energy and Matter from Their Surroundings
• Creating and Maintaining Order Requires Work and Energy
• Energy Coupling Links Reactions in Biology
• K[eq] and ΔG° Are Measures of a Reaction’s Tendency to Proceed Spontaneously
• Enzymes Promote Sequences of Chemical Reactions
• Metabolism Is Regulated to Achieve Balance and Economy
• 1.4 Genetic Foundations
• Genetic Continuity Is Vested in Single DNA Molecules
• The Structure of DNA Allows Its Replication and Repair with Near-Perfect Fidelity
• The Linear Sequence in DNA Encodes Proteins with Three-Dimensional Structures
• 1.5 Evolutionary Foundations
• Changes in the Hereditary Instructions Allow Evolution
• Biomolecules First Arose by Chemical Evolution
• RNA or Related Precursors May Have Been the First Genes and Catalysts
• Biological Evolution Began More Than Three and a Half Billion Years Ago
• The First Cell Probably Used Inorganic Fuels
• Eukaryotic Cells Evolved from Simpler Precursors in Several Stages
• Molecular Anatomy Reveals Evolutionary Relationships
• Functional Genomics Shows the Allocations of Genes to Specific Cellular Processes
• Genomic Comparisons Have Increasing Importance in Medicine
• Chapter Review
• Key Terms
• Problems
• Part I Structure and Catalysis
• Chapter 2 Water, The Solvent of Life
• 2.1 Weak Interactions in Aqueous Systems
• Hydrogen Bonding Gives Water Its Unusual Properties
• Water Forms Hydrogen Bonds with Polar Solutes
• Water Interacts Electrostatically with Charged Solutes
• Nonpolar Gases Are Poorly Soluble in Water
• Nonpolar Compounds Force Energetically Unfavorable Changes in the Structure of Water
• van der Waals Interactions Are Weak Interatomic Attractions
• Weak Interactions Are Crucial to Macromolecular Structure and Function
• Concentrated Solutes Produce Osmotic Pressure
• 2.2 Ionization of Water, Weak Acids, and Weak Bases
• Pure Water Is Slightly Ionized
• The Ionization of Water Is Expressed by an Equilibrium Constant
• The pH Scale Designates the H[+] and H[−] Concentrations
• Weak Acids and Bases Have Characteristic Acid Dissociation Constants
• Titration Curves Reveal the p[Ka] of Weak Acids
• 2.3 Buffering against pH Changes in Biological Systems
• Buffers Are Mixtures of Weak Acids and Their Conjugate Bases
• The Henderson-Hasselbalch Equation Relates pH, p[Ka], and Buffer Concentration
• Weak Acids or Bases Buffer Cells and Tissues against pH Changes
• Untreated Diabetes Produces Life-Threatening Acidosis
• Chapter Review
• Key Terms
• Problems
• Chapter 3 Amino Acids, Peptides, and Proteins
• 3.1 Amino Acids
• Amino Acids Share Common Structural Features
• The Amino Acid Residues in Proteins Are L Stereoisomers
• Amino Acids Can Be Classified by R Group
• Uncommon Amino Acids Also Have Important Functions
• Amino Acids Can Act as Acids and Bases
• Amino Acids Differ in Their Acid-Base Properties
• 3.2 Peptides and Proteins
• Peptides Are Chains of Amino Acids
• Peptides Can Be Distinguished by Their Ionization Behavior
• Biologically Active Peptides and Polypeptides Occur in a Vast Range of Sizes and Compositions
• Some Proteins Contain Chemical Groups Other Than Amino Acids
• 3.3 Working with Proteins
• Proteins Can Be Separated and Purified
• Proteins Can Be Separated and Characterized by Electrophoresis
• Unseparated Proteins Are Detected and Quantified Based on Their Functions
• 3.4 The Structure of Proteins: Primary Structure
• The Function of a Protein Depends on Its Amino Acid Sequence
• Protein Structure Is Studied Using Methods That Exploit Protein Chemistry
• Mass Spectrometry Provides Information on Molecular Mass, Amino Acid Sequence, and Entire Proteomes
• Small Peptides and Proteins Can Be Chemically Synthesized
• Amino Acid Sequences Provide Important Biochemical Information
• Protein Sequences Help Elucidate the History of Life on Earth
• Chapter Review
• Key Terms
• Problems
• Chapter 4 The Three-Dimensional Structure of Proteins
• 4.1 Overview of Protein Structure
• A Protein’s Conformation Is Stabilized Largely by Weak Interactions
• Packing of Hydrophobic Amino Acids Away from Water Favors Protein Folding
• Polar Groups Contribute Hydrogen Bonds and Ion Pairs to Protein Folding
• Individual van der Waals Interactions Are Weak but Combine to Promote Folding
• The Peptide Bond Is Rigid and Planar
• 4.2 Protein Secondary Structure
• The α Helix Is a Common Protein Secondary Structure
• Amino Acid Sequence Affects Stability of the α Helix
• The β Conformation Organizes Polypeptide Chains into Sheets
• β Turns Are Common in Proteins
• Common Secondary Structures Have Characteristic Dihedral Angles
• Common Secondary Structures Can Be Assessed by Circular Dichroism
• 4.3 Protein Tertiary and Quaternary Structures
• Fibrous Proteins Are Adapted for a Structural Function
• Structural Diversity Reflects Functional Diversity in Globular Proteins
• Myoglobin Provided Early Clues about the Complexity of Globular Protein Structure
• Globular Proteins Have a Variety of Tertiary Structures
• Some Proteins or Protein Segments Are Intrinsically Disordered
• Protein Motifs Are the Basis for Protein Structural Classification
• Protein Quaternary Structures Range from Simple Dimers to Large Complexes
• 4.4 Protein Denaturation and Folding
• Loss of Protein Structure Results in Loss of Function
• Amino Acid Sequence Determines Tertiary Structure
• Polypeptides Fold Rapidly by a Stepwise Process
• Some Proteins Undergo Assisted Folding
• Defects in Protein Folding Are the Molecular Basis for Many Human Genetic Disorders
• 4.5 Determination of Protein and Biomolecular Structures
• X-ray Diffraction Produces Electron Density Maps from Protein Crystals
• Distances between Protein Atoms Can Be Measured by Nuclear Magnetic Resonance
• Thousands of Individual Molecules Are Used to Determine Structures by Cryo-Electron Microscopy
• Chapter Review
• Key Terms
• Problems
• Chapter 5 Protein Function
• 5.1 Reversible Binding of a Protein to a Ligand: Oxygen-Binding Proteins
• Oxygen Can Bind to a Heme Prosthetic Group
• Globins Are a Family of Oxygen-Binding Proteins
• Myoglobin Has a Single Binding Site for Oxygen
• Protein-Ligand Interactions Can Be Described Quantitatively
• Protein Structure Affects How Ligands Bind
• Hemoglobin Transports Oxygen in Blood
• Hemoglobin Subunits Are Structurally Similar to Myoglobin
• Hemoglobin Undergoes a Structural Change on Binding Oxygen
• Hemoglobin Binds Oxygen Cooperatively
• Cooperative Ligand Binding Can Be Described Quantitatively
• Two Models Suggest Mechanisms for Cooperative Binding
• Hemoglobin Also Transports H[+] and CO[2]
• Oxygen Binding to Hemoglobin Is Regulated by 2,3-Bisphosphoglycerate
• Sickle Cell Anemia Is a Molecular Disease of Hemoglobin
• 5.2 Complementary Interactions between Proteins and Ligands: The Immune System and Immunoglobulins
• The Immune Response Includes a Specialized Array of Cells and Proteins
• Antibodies Have Two Identical Antigen-Binding Sites
• Antibodies Bind Tightly and Specifically to Antigen
• The Antibody-Antigen Interaction Is the Basis for a Variety of Important Analytical Procedures
• 5.3 Protein Interactions Modulated by Chemical Energy: Actin, Myosin, and Molecular Motors
• The Major Proteins of Muscle Are Myosin and Actin
• Additional Proteins Organize the Thin and Thick Filaments into Ordered Structures
• Myosin Thick Filaments Slide along Actin Thin Filaments
• Chapter Review
• Key Terms
• Problems
• Chapter 6 Enzymes
• 6.1 An Introduction to Enzymes
• Most Enzymes Are Proteins
• Enzymes Are Classified by the Reactions They Catalyze
• 6.2 How Enzymes Work
• Enzymes Affect Reaction Rates, Not Equilibria
• Reaction Rates and Equilibria Have Precise Thermodynamic Definitions
• A Few Principles Explain the Catalytic Power and Specificity of Enzymes
• Noncovalent Interactions between Enzyme and Substrate Are Optimized in the Transition State
• Covalent Interactions and Metal Ions Contribute to Catalysis
• 6.3 Enzyme Kinetics as an Approach to Understanding Mechanism
• Substrate Concentration Affects the Rate of Enzyme-Catalyzed Reactions
• The Relationship between Substrate Concentration and Reaction Rate Can Be Expressed with the Michaelis-Menten Equation
• Michaelis-Menten Kinetics Can Be Analyzed Quantitatively
• Kinetic Parameters Are Used to Compare Enzyme Activities
• Many Enzymes Catalyze Reactions with Two or More Substrates
• Enzyme Activity Depends on pH
• Pre–Steady State Kinetics Can Provide Evidence for Specific Reaction Steps
• Enzymes Are Subject to Reversible or Irreversible Inhibition
• 6.4 Examples of Enzymatic Reactions
• The Chymotrypsin Mechanism Involves Acylation and Deacylation of a Ser Residue
• An Understanding of Protease Mechanisms Leads to New Treatments for HIV Infection
• Hexokinase Undergoes Induced Fit on Substrate Binding
• The Enolase Reaction Mechanism Requires Metal Ions
• An Understanding of Enzyme Mechanism Produces Useful Antibiotics
• 6.5 Regulatory Enzymes
• Allosteric Enzymes Undergo Conformational Changes in Response to Modulator Binding
• The Kinetic Properties of Allosteric Enzymes Diverge from Michaelis-Menten Behavior
• Some Enzymes Are Regulated by Reversible Covalent Modification
• Phosphoryl Groups Affect the Structure and Catalytic Activity of Enzymes
• Multiple Phosphorylations Allow Exquisite Regulatory Control
• Some Enzymes and Other Proteins Are Regulated by Proteolytic Cleavage of an Enzyme Precursor
• A Cascade of Proteolytically Activated Zymogens Leads to Blood Coagulation
• Some Regulatory Enzymes Use Several Regulatory Mechanisms
• Chapter Review
• Key Terms
• Problems
• Chapter 7 Carbohydrates and Glycobiology
• 7.1 Monosaccharides and Disaccharides
• The Two Families of Monosaccharides Are Aldoses and Ketoses
• Monosaccharides Have Asymmetric Centers
• The Common Monosaccharides Have Cyclic Structures
• Organisms Contain a Variety of Hexose Derivatives
• Sugars That Are, or Can Form, Aldehydes Are Reducing Sugars
• 7.2 Polysaccharides
• Some Homopolysaccharides Are Storage Forms of Fuel
• Some Homopolysaccharides Serve Structural Roles
• Steric Factors and Hydrogen Bonding Influence Homopolysaccharide Folding
• Peptidoglycan Reinforces the Bacterial Cell Wall
• Glycosaminoglycans Are Heteropolysaccharides of the Extracellular Matrix
• 7.3 Glycoconjugates: Proteoglycans, Glycoproteins, and Glycolipids
• Proteoglycans Are Glycosaminoglycan-Containing Macromolecules of the Cell Surface and Extracellular Matrix
• Glycoproteins Have Covalently Attached Oligosaccharides
• Glycolipids and Lipopolysaccharides Are Membrane Components
• 7.4 Carbohydrates as Informational Molecules: The Sugar Code
• Oligosaccharide Structures Are Information-Dense
• Lectins Are Proteins That Read the Sugar Code and Mediate Many Biological Processes
• Lectin-Carbohydrate Interactions Are Highly Specific and Often Multivalent
• 7.5 Working with Carbohydrates
• Chapter Review
• Key Terms
• Problems
• Chapter 8 Nucleotides and Nucleic Acids
• 8.1 Some Basic Definitions and Conventions
• Nucleotides and Nucleic Acids Have Characteristic Bases and Pentoses
• Phosphodiester Bonds Link Successive Nucleotides in Nucleic Acids
• The Properties of Nucleotide Bases Affect the Three-Dimensional Structure of Nucleic Acids
• 8.2 Nucleic Acid Structure
• DNA Is a Double Helix That Stores Genetic Information
• DNA Can Occur in Different Three-Dimensional Forms
• Certain DNA Sequences Adopt Unusual Structures
• Messenger RNAs Code for Polypeptide Chains
• Many RNAs Have More Complex Three-Dimensional Structures
• 8.3 Nucleic Acid Chemistry
• Double-Helical DNA and RNA Can Be Denatured
• Nucleotides and Nucleic Acids Undergo Nonenzymatic Transformations
• Some Bases of DNA Are Methylated
• The Chemical Synthesis of DNA Has Been Automated
• Gene Sequences Can Be Amplified with the Polymerase Chain Reaction
• The Sequences of Long DNA Strands Can Be Determined
• DNA Sequencing Technologies Are Advancing Rapidly
• 8.4 Other Functions of Nucleotides
• Nucleotides Carry Chemical Energy in Cells
• Adenine Nucleotides Are Components of Many Enzyme Cofactors
• Some Nucleotides Are Regulatory Molecules
• Adenine Nucleotides Also Serve as Signals
• Chapter Review
• Key Terms
• Problems
• Chapter 9 DNA-Based Information Technologies
• 9.1 Studying Genes and Their Products
• Genes Can Be Isolated by DNA Cloning
• Restriction Endonucleases and DNA Ligases Yield Recombinant DNA
• Cloning Vectors Allow Amplification of Inserted DNA Segments
• Cloned Genes Can Be Expressed to Amplify Protein Production
• Many Different Systems Are Used to Express Recombinant Proteins
• Alteration of Cloned Genes Produces Altered Proteins
• Terminal Tags Provide Handles for Affinity Purification
• The Polymerase Chain Reaction Offers Many Options for Cloning Experiments
• DNA Libraries Are Specialized Catalogs of Genetic Information
• 9.2 Exploring Protein Function on the Scale of Cells or Whole Organisms
• Sequence or Structural Relationships Can Suggest Protein Function
• When and Where a Protein Is Present in a Cell Can Suggest Protein Function
• Knowing What a Protein Interacts with Can Suggest Its Function
• The Effect of Deleting or Altering a Protein Can Suggest Its Function
• Many Proteins Are Still Undiscovered
• 9.3 Genomics and the Human Story
• The Human Genome Contains Many Types of Sequences
• Genome Sequencing Informs Us about Our Humanity
• Genome Comparisons Help Locate Genes Involved in Disease
• Genome Sequences Inform Us about Our Past and Provide Opportunities for the Future
• Chapter Review
• Key Terms
• Problems
• Chapter 10 Lipids
• 10.1 Storage Lipids
• Fatty Acids Are Hydrocarbon Derivatives
• Triacylglycerols Are Fatty Acid Esters of Glycerol
• Triacylglycerols Provide Stored Energy and Insulation
• Partial Hydrogenation of Cooking Oils Improves Their Stability but Creates Fatty Acids with Harmful Health Effects
• Waxes Serve as Energy Stores and Water Repellents
• 10.2 Structural Lipids in Membranes
• Glycerophospholipids Are Derivatives of Phosphatidic Acid
• Some Glycerophospholipids Have Ether-Linked Fatty Acids
• Galactolipids of Plants and Ether-Linked Lipids of Archaea Are Environmental Adaptations
• Sphingolipids Are Derivatives of Sphingosine
• Sphingolipids at Cell Surfaces Are Sites of Biological Recognition
• Phospholipids and Sphingolipids Are Degraded in Lysosomes
• Sterols Have Four Fused Carbon Rings
• 10.3 Lipids as Signals, Cofactors, and Pigments
• Phosphatidylinositols and Sphingosine Derivatives Act as Intracellular Signals
• Eicosanoids Carry Messages to Nearby Cells
• Steroid Hormones Carry Messages between Tissues
• Vascular Plants Produce Thousands of Volatile Signals
• Vitamins A and D Are Hormone Precursors
• Vitamins E and K and the Lipid Quinones Are Oxidation-Reduction Cofactors
• Dolichols Activate Sugar Precursors for Biosynthesis
• Many Natural Pigments Are Lipidic Conjugated Dienes
• Polyketides Are Natural Products with Potent Biological Activities
• 10.4 Working with Lipids
• Lipid Extraction Requires Organic Solvents
• Adsorption Chromatography Separates Lipids of Different Polarity
• Gas Chromatography Resolves Mixtures of Volatile Lipid Derivatives
• Specific Hydrolysis Aids in Determination of Lipid Structure
• Mass Spectrometry Reveals Complete Lipid Structure
• Lipidomics Seeks to Catalog All Lipids and Their Functions
• Chapter Review
• Key Terms
• Problems
• Chapter 11 Biological Membranes and Transport
• 11.1 The Composition and Architecture of Membranes
• The Lipid Bilayer Is Stable in Water
• Bilayer Architecture Underlies the Structure and Function of Biological Membranes
• The Endomembrane System Is Dynamic and Functionally Differentiated
• Membrane Proteins Are Receptors, Transporters, and Enzymes
• Membrane Proteins Differ in the Nature of Their Association with the Membrane Bilayer
• The Topology of an Integral Membrane Protein Can Often Be Predicted from Its Sequence
• Covalently Attached Lipids Anchor or Direct Some Membrane Proteins
• 11.2 Membrane Dynamics
• Acyl Groups in the Bilayer Interior Are Ordered to Varying Degrees
• Transbilayer Movement of Lipids Requires Catalysis
• Lipids and Proteins Diffuse Laterally in the Bilayer
• Sphingolipids and Cholesterol Cluster Together in Membrane Rafts
• Membrane Curvature and Fusion Are Central to Many Biological Processes
• Integral Proteins of the Plasma Membrane Are Involved in Surface Adhesion, Signaling, and Other Cellular Processes
• 11.3 Solute Transport across Membranes
• Transport May Be Passive or Active
• Transporters and Ion Channels Share Some Structural Properties but Have Different Mechanisms
• The Glucose Transporter of Erythrocytes Mediates Passive Transport
• The Chloride-Bicarbonate Exchanger Catalyzes Electroneutral Cotransport of Anions across the Plasma Membrane
• Active Transport Results in Solute Movement against a Concentration or Electrochemical Gradient
• P-Type ATPases Undergo Phosphorylation during Their Catalytic Cycles
• V-Type and F-Type ATPases Are ATP-Driven Proton Pumps
• ABC Transporters Use ATP to Drive the Active Transport of a Wide Variety of Substrates
• Ion Gradients Provide the Energy for Secondary Active Transport
• Aquaporins Form Hydrophilic Transmembrane Channels for the Passage of Water
• Ion-Selective Channels Allow Rapid Movement of Ions across Membranes
• The Structure of a K[+] Channel Reveals the Basis for Its Specificity
• Chapter Review
• Key Terms
• Problems
• Chapter 12 Biochemical Signaling
• 12.1 General Features of Signal Transduction
• Signal-Transducing Systems Share Common Features
• The General Process of Signal Transduction in Animals Is Universal
• 12.2 G Protein–Coupled Receptors and Second Messengers
• The β-Adrenergic Receptor System Acts through the Second Messenger cAMP
• Cyclic AMP Activates Protein Kinase A
• Several Mechanisms Cause Termination of the β-Adrenergic Response
• The β-Adrenergic Receptor Is Desensitized by Phosphorylation and by Association with Arrestin
• Cyclic AMP Acts as a Second Messenger for Many Regulatory Molecules
• G Proteins Act as Self-Limiting Switches in Many Processes
• Diacylglycerol, Inositol Trisphosphate, and Ca2+ Have Related Roles as Second Messengers
• Calcium Is a Second Messenger That Is Limited in Space and Time
• 12.3 GPCRs in Vision, Olfaction, and Gustation
• The Vertebrate Eye Uses Classic GPCR Mechanisms
• Vertebrate Olfaction and Gustation Use Mechanisms Similar to the Visual System
• All GPCR Systems Share Universal Features
• 12.4 Receptor Tyrosine Kinases
• Stimulation of the Insulin Receptor Initiates a Cascade of Protein Phosphorylation Reactions
• The Membrane Phospholipid PIP3 Functions at a Branch in Insulin Signaling
• Cross Talk among Signaling Systems Is Common and Complex
• 12.5 Multivalent Adaptor Proteins and Membrane Rafts
• Protein Modules Bind Phosphorylated Tyr, Ser, or Thr Residues in Partner Proteins
• Membrane Rafts and Caveolae Segregate Signaling Proteins
• 12.6 Gated Ion Channels
• Ion Channels Underlie Rapid Electrical Signaling in Excitable Cells
• Voltage-Gated Ion Channels Produce Neuronal Action Potentials
• Neurons Have Receptor Channels That Respond to Different Neurotransmitters
• Toxins Target Ion Channels
• 12.7 Regulation of Transcription by Nuclear Hormone Receptors
• 12.8 Regulation of the Cell Cycle by Protein Kinases
• The Cell Cycle Has Four Stages
• Levels of Cyclin-Dependent Protein Kinases Oscillate
• CDKs Are Regulated by Phosphorylation, Cyclin Degradation, Growth Factors, and Specific Inhibitors
• CDKs Regulate Cell Division by Phosphorylating Critical Proteins
• 12.9 Oncogenes, Tumor Suppressor Genes, and Programmed Cell Death
• Oncogenes Are Mutant Forms of the Genes for Proteins That Regulate the Cell Cycle
• Defects in Certain Genes Remove Normal Restraints on Cell Division
• Apoptosis Is Programmed Cell Suicide
• Chapter Review
• Key Terms
• Problems
• Part II Bioenergetics and Metabolism
• Chapter 13 Introduction to Metabolism
• 13.1 Bioenergetics and Thermodynamics
• Biological Energy Transformations Obey the Laws of Thermodynamics
• Standard Free-Energy Change Is Directly Related to the Equilibrium Constant
• Actual Free-Energy Changes Depend on Reactant and Product Concentrations
• Standard Free-Energy Changes Are Additive
• 13.2 Chemical Logic and Common Biochemical Reactions
• Biochemical Reactions Occur in Repeating Patterns
• Biochemical and Chemical Equations Are Not Identical
• 13.3 Phosphoryl Group Transfers and ATP
• The Free-Energy Change for ATP Hydrolysis Is Large and Negative
• Other Phosphorylated Compounds and Thioesters Also Have Large, Negative Free Energies of Hydrolysis
• ATP Provides Energy by Group Transfers, Not by Simple Hydrolysis
• ATP Donates Phosphoryl, Pyrophosphoryl, and Adenylyl Groups
• Assembly of Informational Macromolecules Requires Energy
• Transphosphorylations between Nucleotides Occur in All Cell Types
• 13.4 Biological Oxidation-Reduction Reactions
• The Flow of Electrons Can Do Biological Work
• Oxidation-Reductions Can Be Described as Half-Reactions
• Biological Oxidations Often Involve Dehydrogenation
• Reduction Potentials Measure Affinity for Electrons
• Standard Reduction Potentials Can Be Used to Calculate Free-Energy Change
• A Few Types of Coenzymes and Proteins Serve as Universal Electron Carriers
• NAD Has Important Functions in Addition to Electron Transfer
• Flavin Nucleotides Are Tightly Bound in Flavoproteins
• 13.5 Regulation of Metabolic Pathways
• Cells and Organisms Maintain a Dynamic Steady State
• Both the Amount and the Catalytic Activity of an Enzyme Can Be Regulated
• Reactions Far from Equilibrium in Cells Are Common Points of Regulation
• Adenine Nucleotides Play Special Roles in Metabolic Regulation
• Chapter Review
• Key Terms
• Problems
• Chapter 14 Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway
• 14.1 Glycolysis
• An Overview: Glycolysis Has Two Phases
• The Preparatory Phase of Glycolysis Requires ATP
• The Payoff Phase of Glycolysis Yields ATP and NADH
• The Overall Balance Sheet Shows a Net Gain of Two ATP and Two NADH Per Glucose
• 14.2 Feeder Pathways for Glycolysis
• Endogenous Glycogen and Starch Are Degraded by Phosphorolysis
• Dietary Polysaccharides and Disaccharides Undergo Hydrolysis to Monosaccharides
• 14.3 Fates of Pyruvate
• The Pasteur and Warburg Effects Are Due to Dependence on Glycolysis Alone for ATP Production
• Pyruvate Is the Terminal Electron Acceptor in Lactic Acid Fermentation
• Ethanol Is the Reduced Product in Ethanol Fermentation
• Fermentations Produce Some Common Foods and Industrial Chemicals
• 14.4 Gluconeogenesis
• The First Bypass: Conversion of Pyruvate to Phosphoenolpyruvate Requires Two Exergonic Reactions
• The Second and Third Bypasses Are Simple Dephosphorylations by Phosphatases
• Gluconeogenesis Is Energetically Expensive, But Essential
• Mammals Cannot Convert Fatty Acids to Glucose; Plants and Microorganisms Can
• 14.5 Coordinated Regulation of Glycolysis and Gluconeogenesis
• Hexokinase Isozymes Are Affected Differently by Their Product, Glucose 6-Phosphate
• Phosphofructokinase-1 and Fructose 1,6-Bisphosphatase Are Reciprocally Regulated
• Fructose 2,6-Bisphosphate Is a Potent Allosteric Regulator of PFK-1 and FBPase-1
• Xylulose 5-Phosphate Is a Key Regulator of Carbohydrate and Fat Metabolism
• The Glycolytic Enzyme Pyruvate Kinase Is Allosterically Inhibited by ATP
• Conversion of Pyruvate to Phosphoenolpyruvate Is Stimulated When Fatty Acids Are Available
• Transcriptional Regulation Changes the Number of Enzyme Molecules
• 14.6 Pentose Phosphate Pathway of Glucose Oxidation
• The Oxidative Phase Produces NADPH and Pentose Phosphates
• The Nonoxidative Phase Recycles Pentose Phosphates to Glucose 6-Phosphate
• Glucose 6-Phosphate Is Partitioned between Glycolysis and the Pentose Phosphate Pathway
• Thiamine Deficiency Causes Beriberi and Wernicke-Korsakoff Syndrome
• Chapter Review
• Key Terms
• Problems
• Chapter 15 The Metabolism of Glycogen in Animals
• 15.1 The Structure and Function of Glycogen
• Vertebrate Animals Require a Ready Fuel Source for Brain and Muscle
• Glycogen Granules Have Many Tiers of Branched Chains of d-Glucose
• 15.2 Breakdown and Synthesis of Glycogen
• Glycogen Breakdown Is Catalyzed by Glycogen Phosphorylase
• Glucose 1-Phosphate Can Enter Glycolysis or, in Liver, Replenish Blood Glucose
• The Sugar Nucleotide UDP-Glucose Donates Glucose for Glycogen Synthesis
• Glycogenin Primes the Initial Sugar Residues in Glycogen
• 15.3 Coordinated Regulation of Glycogen Breakdown and Synthesis
• Glycogen Phosphorylase Is Regulated by Hormone-Stimulated Phosphorylation and by Allosteric Effectors
• Glycogen Synthase Also Is Subject to Multiple Levels of Regulation
• Allosteric and Hormonal Signals Coordinate Carbohydrate Metabolism Globally
• Carbohydrate and Lipid Metabolism Are Integrated by Hormonal and Allosteric Mechanisms
• Chapter Review
• Key Terms
• Problems
• Chapter 16 The Citric Acid Cycle
• 16.1 Production of Acetyl-CoA (Activated Acetate)
• Pyruvate Is Oxidized to Acetyl-CoA and CO2
• The PDH Complex Employs Three Enzymes and Five Coenzymes to Oxidize Pyruvate
• The PDH Complex Channels Its Intermediates through Five Reactions
• 16.2 Reactions of the Citric Acid Cycle
• The Sequence of Reactions in the Citric Acid Cycle Makes Chemical Sense
• The Citric Acid Cycle Has Eight Steps
• The Energy of Oxidations in the Cycle Is Efficiently Conserved
• 16.3 The Hub of Intermediary Metabolism
• The Citric Acid Cycle Serves in Both Catabolic and Anabolic Processes
• Anaplerotic Reactions Replenish Citric Acid Cycle Intermediates
• Biotin in Pyruvate Carboxylase Carries One-Carbon (CO2) Groups
• 16.4 Regulation of the Citric Acid Cycle
• Production of Acetyl-CoA by the PDH Complex Is Regulated by Allosteric and Covalent Mechanisms
• The Citric Acid Cycle Is Also Regulated at Three Exergonic Steps
• Citric Acid Cycle Activity Changes in Tumors
• Certain Intermediates Are Channeled through Metabolons
• Chapter Review
• Key Terms
• Problems
• Chapter 17 Fatty Acid Catabolism
• 17.1 Digestion, Mobilization, and Transport of Fats
• Dietary Fats Are Absorbed in the Small Intestine
• Hormones Trigger Mobilization of Stored Triacylglycerols
• Fatty Acids Are Activated and Transported into Mitochondria
• 17.2 Oxidation of Fatty Acids
• The β Oxidation of Saturated Fatty Acids Has Four Basic Steps
• The Four β-Oxidation Steps Are Repeated to Yield Acetyl-CoA and ATP
• Acetyl-CoA Can Be Further Oxidized in the Citric Acid Cycle
• Oxidation of Unsaturated Fatty Acids Requires Two Additional Reactions
• Complete Oxidation of Odd-Number Fatty Acids Requires Three Extra Reactions
• Fatty Acid Oxidation Is Tightly Regulated
• Transcription Factors Turn on the Synthesis of Proteins for Lipid Catabolism
• Genetic Defects in Fatty Acyl–CoA Dehydrogenases Cause Serious Disease
• Peroxisomes Also Carry Out β Oxidation
• Phytanic Acid Undergoes α Oxidation in Peroxisomes
• 17.3 Ketone Bodies
• Ketone Bodies, Formed in the Liver, Are Exported to Other Organs as Fuel
• Ketone Bodies Are Overproduced in Diabetes and during Starvation
• Chapter Review
• Key Terms
• Problems
• Chapter 18 Amino Acid Oxidation and the Production of Urea
• 18.1 Metabolic Fates of Amino Groups
• Dietary Protein Is Enzymatically Degraded to Amino Acids
• Pyridoxal Phosphate Participates in the Transfer of α-Amino Groups to α-Ketoglutarate
• Glutamate Releases Its Amino Group as Ammonia in the Liver
• Glutamine Transports Ammonia in the Bloodstream
• Alanine Transports Ammonia from Skeletal Muscles to the Liver
• Ammonia Is Toxic to Animals
• 18.2 Nitrogen Excretion and the Urea Cycle
• Urea Is Produced from Ammonia in Five Enzymatic Steps
• The Citric Acid and Urea Cycles Can Be Linked
• The Activity of the Urea Cycle Is Regulated at Two Levels
• Pathway Interconnections Reduce the Energetic Cost of Urea Synthesis
• Genetic Defects in the Urea Cycle Can Be Life-Threatening
• 18.3 Pathways of Amino Acid Degradation
• Some Amino Acids Can Contribute to Gluconeogenesis, Others to Ketone Body Formation
• Several Enzyme Cofactors Play Important Roles in Amino Acid Catabolism
• Six Amino Acids Are Degraded to Pyruvate
• Seven Amino Acids Are Degraded to Acetyl-CoA
• Phenylalanine Catabolism Is Genetically Defective in Some People
• Five Amino Acids Are Converted to -Ketoglutarate
• Four Amino Acids Are Converted to Succinyl-CoA
• Branched-Chain Amino Acids Are Not Degraded in the Liver
• Asparagine and Aspartate Are Degraded to Oxaloacetate
• Chapter Review
• Key Terms
• Problems
• Chapter 19 Oxidative Phosphorylation
• 19.1 The Mitochondrial Respiratory Chain
• Electrons Are Funneled to Universal Electron Acceptors
• Electrons Pass through a Series of Membrane-Bound Carriers
• Electron Carriers Function in Multienzyme Complexes
• Mitochondrial Complexes Associate in Respirasomes
• Other Pathways Donate Electrons to the Respiratory Chain via Ubiquinone
• The Energy of Electron Transfer Is Efficiently Conserved in a Proton Gradient
• Reactive Oxygen Species Are Generated during Oxidative Phosphorylation
• 19.2 ATP Synthesis
• In the Chemiosmotic Model, Oxidation and Phosphorylation Are Obligately Coupled
• ATP Synthase Has Two Functional Domains, F[0] and F[1]
• ATP Is Stabilized Relative to ADP on the Surface of F[1]
• The Proton Gradient Drives the Release of ATP from the Enzyme Surface
• Each β Subunit of ATP Synthase Can Assume Three Different Conformations
• Rotational Catalysis Is Key to the Binding-Change Mechanism for ATP Synthesis
• Chemiosmotic Coupling Allows Nonintegral Stoichiometries of O[2] Consumption and ATP Synthesis
• The Proton-Motive Force Energizes Active Transport
• Shuttle Systems Indirectly Convey Cytosolic NADH into Mitochondria for Oxidation
• 19.3 Regulation of Oxidative Phosphorylation
• Oxidative Phosphorylation Is Regulated by Cellular Energy Needs
• An Inhibitory Protein Prevents ATP Hydrolysis during Hypoxia
• Hypoxia Leads to ROS Production and Several Adaptive Responses
• ATP-Producing Pathways Are Coordinately Regulated
• 19.4 Mitochondria in Thermogenesis, Steroid Synthesis, and Apoptosis
• Uncoupled Mitochondria in Brown Adipose Tissue Produce Heat
• Mitochondrial P-450 Monooxygenases Catalyze Steroid Hydroxylations
• Mitochondria Are Central to the Initiation of Apoptosis
• 19.5 Mitochondrial Genes: Their Origin and the Effects of Mutations
• Mitochondria Evolved from Endosymbiotic Bacteria
• Mutations in Mitochondrial DNA Accumulate throughout the Life of the Organism
• Some Mutations in Mitochondrial Genomes Cause Disease
• A Rare Form of Diabetes Results from Defects in the Mitochondria of Pancreatic β Cells
• Chapter Review
• Key Terms
• Problems
• Chapter 20 Photosynthesis and Carbohydrate Synthesis in Plants
• 20.1 Light Absorption
• Chloroplasts Are the Site of Light-Driven Electron Flow and Photosynthesis in Plants
• Chlorophylls Absorb Light Energy for Photosynthesis
• Chlorophylls Funnel Absorbed Energy to Reaction Centers by Exciton Transfer
• 20.2 Photochemical Reaction Centers
• Photosynthetic Bacteria Have Two Types of Reaction Center
• In Vascular Plants, Two Reaction Centers Act in Tandem
• The Cytochrome b[6]f Complex Links Photosystems II and I, Conserving the Energy of Electron Transfer
• Cyclic Electron Transfer Allows Variation in the Ratio of ATP/NADPH Synthesized
• State Transitions Change the Distribution of LHCII between the Two Photosystems
• Water Is Split at the Oxygen-Evolving Center
• 20.3 Evolution of a Universal Mechanism for ATP Synthesis
• A Proton Gradient Couples Electron Flow and Phosphorylation
• The Approximate Stoichiometry of Photophosphorylation Has Been Established
• The ATP Synthase Structure and Mechanism Are Nearly Universal
• 20.4 CO[2]-Assimilation Reactions
• Carbon Dioxide Assimilation Occurs in Three Stages
• Synthesis of Each Triose Phosphate from CO[2] Requires Six NADPH and Nine ATP
• A Transport System Exports Triose Phosphates from the Chloroplast and Imports Phosphate
• Four Enzymes of the Calvin Cycle Are Indirectly Activated by Light
• 20.5 Photorespiration and the C[4] and CAM Pathways
• Photorespiration Results from Rubisco’s Oxygenase Activity
• Phosphoglycolate Is Salvaged in a Costly Set of Reactions in C[3] Plants
• In C[4] Plants, CO[2] Fixation and Rubisco Activity Are Spatially Separated
• In CAM Plants, CO[2] Capture and Rubisco Action Are Temporally Separated
• 20.6 Biosynthesis of Starch, Sucrose, and Cellulose
• ADP-Glucose Is the Substrate for Starch Synthesis in Plant Plastids and for Glycogen Synthesis in Bacteria
• UDP-Glucose Is the Substrate for Sucrose Synthesis in the Cytosol of Leaf Cells
• Conversion of Triose Phosphates to Sucrose and Starch Is Tightly Regulated
• The Glyoxylate Cycle and Gluconeogenesis Produce Glucose in Germinating Seeds
• Cellulose Is Synthesized by Supramolecular Structures in the Plasma Membrane
• Pools of Common Intermediates Link Pathways in Different Organelles
• Chapter Review
• Key Terms
• Problems
• Chapter 21 Lipid Biosynthesis
• 21.1 Biosynthesis of Fatty Acids and Eicosanoids
• Malonyl-CoA Is Formed from Acetyl-CoA and Bicarbonate
• Fatty Acid Synthesis Proceeds in a Repeating Reaction Sequence
• The Mammalian Fatty Acid Synthase Has Multiple Active Sites
• Fatty Acid Synthase Receives the Acetyl and Malonyl Groups
• The Fatty Acid Synthase Reactions Are Repeated to Form Palmitate
• Fatty Acid Synthesis Is a Cytosolic Process in Most Eukaryotes but Takes Place in the Chloroplasts in Plants
• Acetate Is Shuttled out of Mitochondria as Citrate
• Fatty Acid Biosynthesis Is Tightly Regulated
• Long-Chain Saturated Fatty Acids Are Synthesized from Palmitate
• Desaturation of Fatty Acids Requires a Mixed-Function Oxidase
• Eicosanoids Are Formed from 20- and 22-Carbon Polyunsaturated Fatty Acids
• 21.2 Biosynthesis of Triacylglycerols
• Triacylglycerols and Glycerophospholipids Are Synthesized from the Same Precursors
• Triacylglycerol Biosynthesis in Animals Is Regulated by Hormones
• Adipose Tissue Generates Glycerol 3-Phosphate by Glyceroneogenesis
• Thiazolidinediones Treat Type 2 Diabetes by Increasing Glyceroneogenesis
• 21.3 Biosynthesis of Membrane Phospholipids
• Cells Have Two Strategies for Attaching Phospholipid Head Groups
• Pathways for Phospholipid Biosynthesis Are Interrelated
• Eukaryotic Membrane Phospholipids Are Subject to Remodeling
• Plasmalogen Synthesis Requires Formation of an Ether-Linked Fatty Alcohol
• Sphingolipid and Glycerophospholipid Synthesis Share Precursors and Some Mechanisms
• Polar Lipids Are Targeted to Specific Cellular Membranes
• 21.4 Cholesterol, Steroids, and Isoprenoids: Biosynthesis, Regulation, and Transport
• Cholesterol Is Made from Acetyl-CoA in Four Stages
• Cholesterol Has Several Fates
• Cholesterol and Other Lipids Are Carried on Plasma Lipoproteins
• HDL Carries Out Reverse Cholesterol Transport
• Cholesteryl Esters Enter Cells by Receptor-Mediated Endocytosis
• Cholesterol Synthesis and Transport Are Regulated at Several Levels
• Dysregulation of Cholesterol Metabolism Can Lead to Cardiovascular Disease
• Reverse Cholesterol Transport by HDL Counters Plaque Formation and Atherosclerosis
• Steroid Hormones Are Formed by Side-Chain Cleavage and Oxidation of Cholesterol
• Intermediates in Cholesterol Biosynthesis Have Many Alternative Fates
• Chapter Review
• Key Terms
• Problems
• Chapter 22 Biosynthesis of Amino Acids, Nucleotides, and Related Molecules
• 22.1 Overview of Nitrogen Metabolism
• A Global Nitrogen Cycling Network Maintains a Pool of Biologically Available Nitrogen
• Nitrogen Is Fixed by Enzymes of the Nitrogenase Complex
• Ammonia Is Incorporated into Biomolecules through Glutamate and Glutamine
• Glutamine Synthetase Is a Primary Regulatory Point in Nitrogen Metabolism
• Several Classes of Reactions Play Special Roles in the Biosynthesis of Amino Acids and Nucleotides
• 22.2 Biosynthesis of Amino Acids
• Organisms Vary Greatly in Their Ability to Synthesize the 20 Common Amino Acids
• α-Ketoglutarate Gives Rise to Glutamate, Glutamine, Proline, and Arginine
• Serine, Glycine, and Cysteine Are Derived from 3-Phosphoglycerate
• Three Nonessential and Six Essential Amino Acids Are Synthesized from Oxaloacetate and Pyruvate
• Chorismate Is a Key Intermediate in the Synthesis of Tryptophan, Phenylalanine, and Tyrosine
• Histidine Biosynthesis Uses Precursors of Purine Biosynthesis
• Amino Acid Biosynthesis Is under Allosteric Regulation
• 22.3 Molecules Derived from Amino Acids
• Glycine Is a Precursor of Porphyrins
• Heme Degradation Has Multiple Functions
• Amino Acids Are Precursors of Creatine and Glutathione
• d-Amino Acids Are Found Primarily in Bacteria
• Aromatic Amino Acids Are Precursors of Many Plant Substances
• Biological Amines Are Products of Amino Acid Decarboxylation
• Arginine Is the Precursor for Biological Synthesis of Nitric Oxide
• 22.4 Biosynthesis and Degradation of Nucleotides
• De Novo Purine Nucleotide Synthesis Begins with PRPP
• Purine Nucleotide Biosynthesis Is Regulated by Feedback Inhibition
• Pyrimidine Nucleotides Are Made from Aspartate, PRPP, and Carbamoyl Phosphate
• Pyrimidine Nucleotide Biosynthesis Is Regulated by Feedback Inhibition
• Nucleoside Monophosphates Are Converted to Nucleoside Triphosphates
• Ribonucleotides Are the Precursors of Deoxyribonucleotides
• Thymidylate Is Derived from dCDP and dUMP
• Degradation of Purines and Pyrimidines Produces Uric Acid and Urea, Respectively
• Purine and Pyrimidine Bases Are Recycled by Salvage Pathways
• Excess Uric Acid Causes Gout
• Many Chemotherapeutic Agents Target Enzymes in Nucleotide Biosynthetic Pathways
• Chapter Review
• Key Terms
• Problems
• Chapter 23 Hormonal Regulation and Integration of Mammalian Metabolism
• 23.1 Hormone Structure and Action
• Hormones Act through Specific High-Affinity Cellular Receptors
• Hormones Are Chemically Diverse
• Some Hormones Are Released by a “Top-Down” Hierarchy of Neuronal and Hormonal Signals
• “Bottom-Up” Hormonal Systems Send Signals Back to the Brain and to Other Tissues
• 23.2 Tissue-Specific Metabolism
• The Liver Processes and Distributes Nutrients
• Adipose Tissues Store and Supply Fatty Acids
• Brown and Beige Adipose Tissues Are Thermogenic
• Muscles Use ATP for Mechanical Work
• The Brain Uses Energy for Transmission of Electrical Impulses
• Blood Carries Oxygen, Metabolites, and Hormones
• 23.3 Hormonal Regulation of Fuel Metabolism
• Insulin Counters High Blood Glucose in the Well-Fed State
• Pancreatic β Cells Secrete Insulin in Response to Changes in Blood Glucose
• Glucagon Counters Low Blood Glucose
• During Fasting and Starvation, Metabolism Shifts to Provide Fuel for the Brain
• Epinephrine Signals Impending Activity
• Cortisol Signals Stress, Including Low Blood Glucose
• 23.4 Obesity and the Regulation of Body Mass
• Adipose Tissue Has Important Endocrine Functions
• Leptin Stimulates Production of Anorexigenic Peptide Hormones
• Leptin Triggers a Signaling Cascade That Regulates Gene Expression
• Adiponectin Acts through AMPK to Increase Insulin Sensitivity
• AMPK Coordinates Catabolism and Anabolism in Response to Metabolic Stress
• The mTORC1 Pathway Coordinates Cell Growth with the Supply of Nutrients and Energy
• Diet Regulates the Expression of Genes Central to Maintaining Body Mass
• Short-Term Eating Behavior Is Influenced by Ghrelin, PPY3–36, and Cannabinoids
• Microbial Symbionts in the Gut Influence Energy Metabolism and Adipogenesis
• 23.5 Diabetes Mellitus
• Diabetes Mellitus Arises from Defects in Insulin Production or Action
• Carboxylic Acids (Ketone Bodies) Accumulate in the Blood of Those with Untreated Diabetes
• In Type 2 Diabetes the Tissues Become Insensitive to Insulin
• Type 2 Diabetes Is Managed with Diet, Exercise, Medication, and Surgery
• Chapter Review
• Key Terms
• Problems
• Part III Information Pathways
• Chapter 24 Genes and Chromosomes
• 24.1 Chromosomal Elements
• Genes Are Segments of DNA That Code for Polypeptide Chains and RNAs
• DNA Molecules Are Much Longer than the Cellular or Viral Packages That Contain Them
• Eukaryotic Genes and Chromosomes Are Very Complex
• 24.2 DNA Supercoiling
• Most Cellular DNA Is Underwound
• DNA Underwinding Is Defined by Topological Linking Number
• Topoisomerases Catalyze Changes in the Linking Number of DNA
• DNA Compaction Requires a Special Form of Supercoiling
• 24.3 The Structure of Chromosomes
• Chromatin Consists of DNA, Proteins, and RNA
• Histones Are Small, Basic Proteins
• Nucleosomes Are the Fundamental Organizational Units of Chromatin
• Nucleosomes Are Packed into Highly Condensed Chromosome Structures
• Condensed Chromosome Structures Are Maintained by SMC Proteins
• Bacterial DNA Is Also Highly Organized
• Chapter Review
• Key Terms
• Problems
• Chapter 25 DNA Metabolism
• 25.1 DNA Replication
• DNA Replication Follows a Set of Fundamental Rules
• DNA Is Degraded by Nucleases
• DNA Is Synthesized by DNA Polymerases
• Replication Is Very Accurate
• E. coli Has at Least Five DNA Polymerases
• DNA Replication Requires Many Enzymes and Protein Factors
• Replication of the E. coli Chromosome Proceeds in Stages
• Replication in Eukaryotic Cells Is Similar but More Complex
• Viral DNA Polymerases Provide Targets for Antiviral Therapy
• 25.2 DNA Repair
• Mutations Are Linked to Cancer
• All Cells Have Multiple DNA Repair Systems
• The Interaction of Replication Forks with DNA Damage Can Lead to Error-Prone Translesion DNA Synthesis
• 25.3 DNA Recombination
• Bacterial Homologous Recombination Is a DNA Repair Function
• Eukaryotic Homologous Recombination Is Required for Proper Chromosome Segregation during Meiosis
• Some Double-Strand Breaks Are Repaired by Nonhomologous End Joining
• Site-Specific Recombination Results in Precise DNA Rearrangements
• Transposable Genetic Elements Move from One Location to Another
• Immunoglobulin Genes Assemble by Recombination
• Chapter Review
• Key Terms
• Problems
• Chapter 26 RNA Metabolism
• 26.1 DNA-Dependent Synthesis of RNA
• RNA Is Synthesized by RNA Polymerases
• RNA Synthesis Begins at Promoters
• Transcription Is Regulated at Several Levels
• Specific Sequences Signal Termination of RNA Synthesis
• Eukaryotic Cells Have Three Kinds of Nuclear RNA Polymerases
• RNA Polymerase II Requires Many Other Protein Factors for Its Activity
• RNA Polymerases Are Drug Targets
• 26.2 RNA Processing
• Eukaryotic mRNAs Are Capped at the 5′ End
• Both Introns and Exons Are Transcribed from DNA into RNA
• RNA Catalyzes the Splicing of Introns
• In Eukaryotes the Spliceosome Carries out Nuclear pre-mRNA Splicing
• Proteins Catalyze Splicing of tRNAs
• Eukaryotic mRNAs Have a Distinctive 3′ End Structure
• A Gene Can Give Rise to Multiple Products by Differential RNA Processing
• Ribosomal RNAs and tRNAs Also Undergo Processing
• Special-Function RNAs Undergo Several Types of Processing
• Cellular mRNAs Are Degraded at Different Rates
• 26.3 RNA-Dependent Synthesis of RNA and DNA
• Reverse Transcriptase Produces DNA from Viral RNA
• Some Retroviruses Cause Cancer and AIDS
• Many Transposons, Retroviruses, and Introns May Have a Common Evolutionary Origin
• Telomerase Is a Specialized Reverse Transcriptase
• Some RNAs Are Replicated by RNA-Dependent RNA Polymerase
• RNA-Dependent RNA Polymerases Share a Common Structural Fold
• 26.4 Catalytic RNAs and the RNA World Hypothesis
• Ribozymes Share Features with Protein Enzymes
• Ribozymes Participate in a Variety of Biological Processes
• Ribozymes Provide Clues to the Origin of Life in an RNA World
• Chapter Review
• Key Terms
• Problems
• Chapter 27 Protein Metabolism
• 27.1 The Genetic Code
• The Genetic Code Was Cracked Using Artificial mRNA Templates
• Wobble Allows Some tRNAs to Recognize More than One Codon
• The Genetic Code Is Mutation-Resistant
• Translational Frameshifting Affects How the Code Is Read
• Some mRNAs Are Edited before Translation
• 27.2 Protein Synthesis
• The Ribosome Is a Complex Supramolecular Machine
• Transfer RNAs Have Characteristic Structural Features
• Stage 1: Aminoacyl-tRNA Synthetases Attach the Correct Amino Acids to Their tRNAs
• Stage 2: A Specific Amino Acid Initiates Protein Synthesis
• Stage 3: Peptide Bonds Are Formed in the Elongation Stage
• Stage 4: Termination of Polypeptide Synthesis Requires a Special Signal
• Stage 5: Newly Synthesized Polypeptide Chains Undergo Folding and Processing
• Protein Synthesis Is Inhibited by Many Antibiotics and Toxins
• 27.3 Protein Targeting and Degradation
• Posttranslational Modification of Many Eukaryotic Proteins Begins in the Endoplasmic Reticulum
• Glycosylation Plays a Key Role in Protein Targeting
• Signal Sequences for Nuclear Transport Are Not Cleaved
• Bacteria Also Use Signal Sequences for Protein Targeting
• Cells Import Proteins by Receptor-Mediated Endocytosis
• Protein Degradation Is Mediated by Specialized Systems in All Cells
• Chapter Review
• Key Terms
• Problems
• Chapter 28 Regulation of Gene Expression
• 28.1 The Proteins and RNAs of Gene Regulation
• RNA Polymerase Binds to DNA at Promoters
• Transcription Initiation Is Regulated by Proteins and RNAs
• Many Bacterial Genes Are Clustered and Regulated in Operons
• The lac Operon Is Subject to Negative Regulation
• Regulatory Proteins Have Discrete DNA-Binding Domains
• Regulatory Proteins Also Have Protein-Protein Interaction Domains
• 28.2 Regulation of Gene Expression in Bacteria
• The lac Operon Undergoes Positive Regulation
• Many Genes for Amino Acid Biosynthetic Enzymes Are Regulated by Transcription Attenuation
• Induction of the SOS Response Requires Destruction of Repressor Proteins
• Synthesis of Ribosomal Proteins Is Coordinated with rRNA Synthesis
• The Function of Some mRNAs Is Regulated by Small RNAs in Cis or in Trans
• Some Genes Are Regulated by Genetic Recombination
• 28.3 Regulation of Gene Expression in Eukaryotes
• Transcriptionally Active Chromatin Is Structurally Distinct from Inactive Chromatin
• Most Eukaryotic Promoters Are Positively Regulated
• DNA-Binding Activators and Coactivators Facilitate Assembly of the Basal Transcription Factors
• The Genes of Galactose Metabolism in Yeast Are Subject to Both Positive and Negative Regulation
• Transcription Activators Have a Modular Structure
• Eukaryotic Gene Expression Can Be Regulated by Intercellular and Intracellular Signals
• Regulation Can Result from Phosphorylation of Nuclear Transcription Factors
• Many Eukaryotic mRNAs Are Subject to Translational Repression
• Posttranscriptional Gene Silencing Is Mediated by RNA Interference
• RNA-Mediated Regulation of Gene Expression Takes Many Forms in Eukaryotes
• Development Is Controlled by Cascades of Regulatory Proteins
• Stem Cells Have Developmental Potential That Can Be Controlled
• Chapter Review
• Key Terms
• Problems
• Note
• Abbreviated Solutions to Problems
• Glossary
• Index
• Resources
• Back Cover