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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

UM RAFBÆKUR Á HEIMKAUP.IS

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