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• Title:Lehninger principles of biochemistry / David L. Nelson, Michael M. Cox.
  
•    
• Variant Title:Principles of biochemistry.
  
• Author/Creator:Nelson, David L. (David Lee), 1942- author.
  
• Other Contributors/Collections:Cox, Michael M., author.
  Lehninger, Albert L. Principles of biochemistry.
  
• Published/Created:New York : W.H. Freeman, [2017].
  c2017.
  

• Holdings

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  • Location:OKANAGAN LIBRARY stacksWhere is this?
    
  • Call Number: QU4 .N425l 2017
    
  • Number of Items:1
    
  • Status:Available
    

  • Location: c.1  Temporarily shelved at WOODWARD LIBRARY reserve collectionWhere is this?
    
  • Call Number: QU4 .N425l 2017
    
  • Number of Items:1
    
  • Status:Available
    

   
• Library of Congress Subjects:Biochemistry.
  Biochemistry--Problems, exercises, etc.
  
• Medical Subjects: Biochemistry.
  
• Genre/Form:Problems and exercises.
  Textbooks.
  
• Edition:7th edition
  
• Description:xxxiv, 1, 172, AS-34, G-20, I-45 pages : illustrations (chiefly color), color maps ; 29 cm
  
• Summary:"Lehninger Principles of Biochemistry ... brings clarity and coherence to an often unwieldy discipline, offering a thoroughly updated survey of biochemistry's enduring principles, definitive discoveries, and groundbreaking new advances with each edition.This new Seventh Edition maintains the qualities that have distinguished the text since Albert Lehninger's original edition--clear writing, careful explanations of difficult concepts, helpful problem-solving support, and insightful communication of contemporary biochemistry's core ideas, new techniques, and pivotal discoveries. Again, David Nelson and Michael Cox introduce students to an extraordinary amount of exciting new findings without an overwhelming amount of extra discussion or detail." -- Publisher description.
  
• Notes:Supplementary material available via the World Wide Web.
  Includes bibliographic references and index.
  
• ISBN:9781464126116
  1464126119
  1464187975
  9781464187971
  
• Contents:Machine generated contents note: 1. 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
  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
  BOX 1-1 Molecular Weight, Molecular Mass, and Their Correct Units
  Cells Contain a Universal Set of Small Molecules
  Macromolecules Are the Major Constituents of Cells
  Three-Dimensional Structure Is Described by Configuration and Conformation
  Box 1-2 Louis Pasteur and Optical Activity: In Vino, Veritas
  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
  Box 1-3 Entropy: Things Fall Apart
  Flow of Electrons Provides Energy for Organisms
  Creating and Maintaining Order Requires Work and Energy
  Energy Coupling Links Reactions in Biology
  Keq 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
  Structure of DNA Allows Its Replication and Repair with Near-Perfect Fidelity
  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
  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 Human Biology and Medicine
  I. STRUCTURE AND CATALYSIS
  2. Water
  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
  Entropy Increases as Crystalline Substances Dissolve
  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
  Solutes Affect the Colligative Properties of Aqueous Solutions
  2.2. Ionization of Water, Weak Acids, and Weak Bases
  Pure Water Is Slightly Ionized
  Ionization of Water Is Expressed by an Equilibrium Constant
  pH Scale Designates the H+ and OH~ Concentrations
  Weak Acids and Bases Have Characteristic Acid Dissociation Constants
  Titration Curves Reveal the pKa of Weak Acids
  2.3. Buffering against pH Changes in Biological Systems
  Buffers Are Mixtures of Weak Acids and Their Conjugate Bases
  Henderson-Hasselbalch Equation Relates pH, pka, and Buffer Concentration
  Weak Acids or Bases Buffer Cells and Tissues against pH Changes
  Untreated Diabetes Produces Life-Threatening Acidosis
  BOX 2-1 MEDICINE On Being One's Own Rabbit (Don't Try This at Home!)
  2.4. Water as a Reactant
  2.5. Fitness of the Aqueous Environment for Living Organisms
  3. Amino Acids, Peptides, and Proteins
  3.1. Amino Acids
  Amino Acids Share Common Structural Features
  Amino Acid Residues in Proteins Are L Stereoisomers
  Amino Acids Can Be Classified by R Group
  BOX 3-1 METHODS Absorption of Light by Molecules: The Lambert-Beer Law
  Uncommon Amino Acids Also Have Important Functions
  Amino Acids Can Act as Acids and Bases
  Amino Acids Have Characteristic Titration Curves
  Titration Curves Predict the Electric Charge of Amino Acids
  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 Can Be Quantified
  3.4. Structure of Proteins: Primary Structure
  Function of a Protein Depends on Its Amino Acid Sequence
  Amino Acid Sequences of Millions of Proteins Have Been Determined
  Protein Chemistry Is Enriched by Methods Derived from Classical Polypeptide Sequencing
  Mass Spectrometry Offers an Alternative Method to Determine Amino Acid Sequences
  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
  BOX 3-2 Consensus Sequences and Sequence Logos
  4. Three-Dimensional Structure of Proteins
  4.1. Overview of Protein Structure
  Protein's Conformation Is Stabilized Largely by Weak Interactions
  Peptide Bond Is Rigid and Planar
  4.2. Protein Secondary Structure
  α Helix Is a Common Protein Secondary Structure
  BOX 4-1 METHODS Knowing the Right Hand from the Left
  Amino Acid Sequence Affects Stability of the a Helix
  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
  BOX 4-2 Permanent Waving Is Biochemical Engineering
  BOX 4-3 MEDICINE Why Sailors, Explorers, and College Students Should Eat Their Fresh Fruits and Vegetables
  Structural Diversity Reflects Functional Diversity in Globular Proteins
  Myoglobin Provided Early Clues about the Complexity of Globular Protein Structure
  BOX 4-4 Protein Data Bank
  Globular Proteins Have a Variety of Tertiary Structures
  BOX 4-5 METHODS Methods for Determining the Three-Dimensional Structure of a Protein
  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 Provide the Molecular Basis for a Wide Range of Human Genetic Disorders
  BOX 4-6 MEDICINE Death by Misfolding: The Prion Diseases
  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
  BOX 5-1 MEDICINE Carbon Monoxide: A Stealthy Killer
  Hemoglobin Also Transports H+ and CO2
  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
  Immune Response Includes a Specialized Array of Cells and Proteins
  Antibodies Have Two Identical Antigen-Binding Sites
  Antibodies Bind Tightly and Specifically to Antigen
  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
  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
  6. Enzymes
  6.1. 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
  Few Principles Explain the Catalytic Power and Specificity of Enzymes
  Weak Interactions between Enzyme and Substrate Are Optimized in the Transition State
  Contents note continued: Binding Energy Contributes to Reaction Specificity and Catalysis
  Specific Catalytic Groups Contribute to Catalysis
  6.3. Enzyme Kinetics as an Approach to Understanding Mechanism
  Substrate Concentration Affects the Rate of Enzyme-Catalyzed Reactions
  Relationship between Substrate Concentration and Reaction Rate Can Be Expressed Quantitatively
  Kinetic Parameters Are Used to Compare Enzyme Activities
  BOX 6-1 Transformations of the Michael is-Men ten Equation: The Double-Reciprocal Plot
  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
  BOX 6-2 Kinetic Tests for Determining Inhibition Mechanisms
  BOX 6-3 MEDICINE Curing African Sleeping Sickness with a Biochemical Trojan Horse
  6.4. Examples of Enzymatic Reactions
  Chymotrypsin Mechanism Involves Acylation and Deacylation of a Ser Residue
  Understanding of Protease Mechanisms Leads to New Treatments for HIV Infections
  Hexokinase Undergoes Induced Fit on Substrate Binding
  Enolase Reaction Mechanism Requires Metal Ions
  Lysozyme Uses Two Successive Nucleophilic Displacement Reactions
  Understanding of Enzyme Mechanism Produces Useful Antibiotics
  6.5. Regulatory Enzymes
  Allosteric Enzymes Undergo Conformational Changes in Response to Modulator Binding
  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
  Cascade of Proteolytically Activated Zymogens Leads to Blood Coagulation
  Some Regulatory Enzymes Use Several Regulatory Mechanisms
  7. Carbohydrates and Glycobiology
  7.1. Monosaccharides and Disaccharides
  Two Families of Monosaccharides Are Aldoses and Ketoses
  Monosaccharides Have Asymmetric Centers
  Common Monosaccharides Have Cyclic Structures
  Organisms Contain a Variety of Hexose Derivatives
  BOX 7-1 MEDICINE Blood Glucose Measurements in the Diagnosis and Treatment of Diabetes
  Monosaccharides Are Reducing Agents
  Disaccharides Contain a Glycosidic Bond
  BOX 7-2 Sugar Is Sweet, and So Are... a Few Other Things
  7.2. Polysaccharides
  Some Homopolysaccharides Are Storage Forms of Fuel
  Some Homopolysaccharides Serve Structural Roles
  Steric Factors and Hydrogen Bonding Influence Homopolysaccharide Folding
  Bacterial and Algal Cell Walls Contain Structural Heteropolysaccharides
  Glycosaminoglycans Are Heteropolysaccharides of the Extracellular Matrix
  7.3. Glycoconjugates: Proteoglycans, Glycoproteins, and Glycosphingolipids
  Proteoglycans Are Glycosaminoglycan-Containing Macromolecules of the Cell Surface and Extracellular Matrix
  MEDICINE Defects in the Synthesis or Degradation of Sulfated Glycosaminoglycans Can Lead to Serious Human Disease
  Glycoproteins Have Covalently Attached Oligosaccharides
  Glycolipids and Lipopolysaccharides Are Membrane Components
  7.4. Carbohydrates as Informational Molecules: The Sugar Code
  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
  8. Nucleotides and Nucleic Acids
  8.1. Some Basics
  Nucleotides and Nucleic Acids Have Characteristic Bases and Pentoses
  Phosphodiester Bonds Link Successive Nucleotides in Nucleic Acids
  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
  Chemical Synthesis of DNA Has Been Automated
  Gene Sequences Can Be Amplified with the Polymerase Chain Reaction
  Sequences of Long DNA Strands Can Be Determined
  BOX 8-1 Potent Weapon in Forensic Medicine
  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
  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
  Polymerase Chain Reaction Can Be Adapted for Convenient Cloning
  9.2. Using DNA-Based Methods to Understand Protein Function
  DNA Libraries Are Specialized Catalogs of Genetic Information
  Sequence or Structural Relationships Provide Information on Protein Function
  Fusion Proteins and Immunofluorescence Can Reveal the Location of Proteins in Cells
  Protein-Protein Interactions Can Help Elucidate Protein Function
  DNA Microarrays Reveal RNA Expression Patterns and Other Information
  Inactivating or Altering a Gene with CRISPR Can Reveal Gene Function
  9.3. Genomics and the Human Story
  BOX 9-1 MEDICINE Personalized Genomic Medicine
  Annotation Provides a Description of the Genome
  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
  BOX 9-2 Getting to Know Humanity's Next of Kin
  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
  Chloroplasts Contain Galactolipids and Sulfolipids
  Archaea Contain Unique Membrane Lipids
  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
  BOX 10-1 MEDICINE Abnormal Accumulations of Membrane Lipids: Some Inherited Human Diseases
  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
  11. Biological Membranes and Transport
  11.1. Composition and Architecture of Membranes
  Each Type of Membrane Has Characteristic Lipids and Proteins
  All Biological Membranes Share Some Fundamental Properties
  Lipid Bilayer Is the Basic Structural Element of Membranes
  Three Types of Membrane Proteins Differ in the Nature of Their Association with the Membrane
  Many Integral Membrane Proteins Span the Lipid Bilayer
  Hydrophobic Regions of Integral Proteins Associate with Membrane Lipids
  Topology of an Integral Membrane Protein Can Often Be Predicted from Its Sequence
  Covalently Attached Lipids Anchor Some Membrane Proteins
  Amphitropic Proteins Associate Reversibly with the Membrane
  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
  Contents note continued: Glucose Transporter of Erythrocytes Mediates Passive Transport
  Chloride-Bicarbonate Exchanger Catalyzes Electroneutral Cotransport of Anions across the Plasma Membrane
  BOX 11-1 MEDICINE Defective Glucose and Water Transport in Two Forms of Diabetes
  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
  BOX 11-2 MEDICINE A Defective Ion Channel in Cystic Fibrosis
  Aquaporins Form Hydrophilic Transmembrane Channels for the Passage of Water
  Ion-Selective Channels Allow Rapid Movement of Ions across Membranes
  Ion-Channel Function Is Measured Electrically
  Structure of a K+ Channel Reveals the Basis for Its Specificity
  Gated Ion Channels Are Central in Neuronal Function
  Defective Ion Channels Can Have Severe Physiological Consequences
  12. Biosignaling
  12.1. General Features of Signal Transduction
  12.2. G Protein
  Coupled Receptors and Second Messengers
  β-Adrenergic Receptor System Acts through the Second Messenger cAMP
  BOX 12-1 G Proteins: Binary Switches in Health and Disease
  Several Mechanisms Cause Termination of the β-Adrenergic Response
  0-Adrenergic Receptor Is Desensitized by Phosphorylation and by Association with Arrestin
  Cyclic AMP Acts as a Second Messenger for Many Regulatory Molecules
  Diacylglycerol, Inositol Trisphosphate, and Ca2+ Have Related Roles as Second Messengers
  BOX 12-2 METHODS FRET: Biochemistry Visualized in a Living Cell
  Calcium Is a Second Messenger That Is Localized in Space and Time
  12.3. GPCRs in Vision, Olfaction, and Gustation
  Vertebrate Eye Uses Classic GPCR Mechanisms
  BOX 12-3 MEDICINE Color Blindness: John Dalton's Experiment from the Grave
  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
  Membrane Phospholipid PIP3 Functions at a Branch in Insulin Signaling
  Cross Talk among Signaling Systems Is Common and Complex
  12.5. Receptor Guanylyl Cyclases, cGMP, and Protein Kinase G
  12.6. 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
  12.7. Gated Ion Channels
  Ion Channels Underlie 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
  12.8. Regulation of Transcription by Nuclear Hormone Receptors
  12.9. Signaling in Microorganisms and Plants
  Bacterial Signaling Entails Phosphorylation in a Two-Component System
  Signaling Systems of Plants Have Some of the Same Components Used by Microbes and Mammals
  12.10. Regulation of the Cell Cycle by Protein Kinases
  Cell Cycle Has Four Stages
  Levels of Cyclin-Dependent Protein Kinases Oscillate
  CDKs Regulate Cell Division by Phosphorylating Critical Proteins
  12.11. Oncogenes, Tumor Suppressor Genes, and Programmed Cell Death
  Oncogenes Are Mutant Forms of the Genes for Proteins That Regulate the Cell Cycle
  BOX 12-3 MEDICINE Development of Protein Kinase Inhibitors for Cancer Treatment
  Defects in Certain Genes Remove Normal Restraints on Cell Division
  Apoptosis Is Programmed Cell Suicide
  II. BIOENERGETICS AND METABOLISM
  13. Bioenergetics and Biochemical Reaction Types
  13.1. Bioenergetics and Thermodynamics
  Biological Energy Transformations Obey the Laws of Thermodynamics
  Cells Require Sources of Free Energy
  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 and Chemical Equations Are Not Identical
  13.3. Phosphoryl Group Transfers and ATP
  Free-Energy Change for ATP Hydrolysis Is Large and Negative
  Other Phosphorylated Compounds and Thioesters Also Have Large 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
  ATP Energizes Active Transport and Muscle Contraction
  BOX 13-1 Firefly Flashes: Glowing Reports of ATP
  Transphosphorylations between Nucleotides Occur in All Cell Types
  Inorganic Polyphosphate Is a Potential Phosphoryl Group Donor
  13.4. Biological Oxidation-Reduction Reactions
  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
  Cellular Oxidation of Glucose to Carbon Dioxide Requires Specialized Electron Carriers
  Few Types of Coenzymes and Proteins Serve as Universal Electron Carriers
  NADH and NADPH Act with Dehydrogenases as Soluble Electron Carriers
  NAD Has Important Functions in Addition to Electron Transfer
  Dietary Deficiency of Niacin, the Vitamin Form of NAD and NADP, Causes Pellagra
  Flavin Nucleotides Are Tightly Bound in Flavoproteins
  14. Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway
  14.1. Glycolysis
  Overview: Glycolysis Has Two Phases
  Preparatory Phase of Glycolysis Requires ATP
  Payoff Phase of Glycolysis Yields ATP and NADH
  Overall Balance Sheet Shows a Net Gain of ATP
  Glycolysis Is under Tight Regulation
  BOX 14-1 MEDICINE High Rate of Glycolysis in Tumors Suggests Targets for Chemotherapy and Facilitates Diagnosis
  Glucose Uptake Is Deficient in Type
  Diabetes Mellitus
  14.2. Feeder Pathways for Glycolysis
  Dietary Polysaccharides and Disaccharides Undergo Hydrolysis to Monosaccharides
  Endogenous Glycogen and Starch Are Degraded by Phosphorolysis
  Other Monosaccharides Enter the Glycolytic Pathway at Several Points
  14.3. Fates of Pyruvate under Anaerobic Conditions: Fermentation
  Pyruvate Is the Terminal Electron Acceptor in Lactic Acid Fermentation
  BOX 14-2 Athletes, Alligators, and Coelacanths: Glycolysis at Limiting Concentrations of Oxygen
  Ethanol Is the Reduced Product in Ethanol Fermentation
  Thiamine Pyrophosphate Carries "Active Acetaldehyde" Groups
  BOX 14-3 Ethanol Fermentations: Brewing Beer and Producing Biofuels
  Fermentations Are Used to Produce Some Common Foods and Industrial Chemicals
  14.4. Gluconeogenesis
  Conversion of Pyruvate to Phosphoenolpyruvate Requires Two Exergonic Reactions
  Conversion of Fructose 1,6-Bisphosphate to Fructose 6-Phosphate Is the Second Bypass
  Conversion of Glucose 6-Phosphate to Glucose Is the Third Bypass
  Gluconeogenesis Is Energetically Expensive, but Essential
  Citric Acid Cycle Intermediates and Some Amino Acids Are Glucogenic
  Mammals Cannot Convert Fatty Acids to Glucose
  Glycolysis and Gluconeogenesis Are Reciprocally Regulated
  14.5. Pentose Phosphate Pathway of Glucose Oxidation
  Oxidative Phase Produces Pentose Phosphates and NADPH
  BOX 14-3 MEDICINE Why Pythagoras Wouldn't Eat Falafel: Glucose 6-Phosphate Dehydrogenase Deficiency
  Nonoxidative Phase Recycles Pentose Phosphates to Glucose 6-Phosphate
  Wernicke-Korsakoff Syndrome Is Exacerbated by a Defect in Transketolase
  Glucose 6-Phosphate Is Partitioned between Glycolysis and the Pentose Phosphate Pathway
  15. Principles of Metabolic Regulation
  15.1. 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
  15.2. Analysis of Metabolic Control
  Contribution of Each Enzyme to Flux through a Pathway Is Experimentally Measurable
  Flux Control Coefficient Quantifies the Effect of a Change in Enzyme Activity on Metabolite Flux through a Pathway
  Elasticity Coefficient Is Related to an Enzyme's Responsiveness to Changes in Metabolite or Regulator Concentrations
  BOX 15-1 METHODS Metabolic Control Analysis: Quantitative Aspects
  Response Coefficient Expresses the Effect of an Outside Controller on Flux through a Pathway
  Metabolic Control Analysis Has Been Applied to Carbohydrate Metabolism, with Surprising Results
  Metabolic Control Analysis Suggests a General Method for Increasing Flux through a Pathway
  15.3. Coordinated Regulation of Glycolysis and Gluconeogenesis
  Hexokinase Isozymes of Muscle and Liver Are Affected Differently by Their Product, Glucose 6-Phosphate
  BOX 15.2 Isozymes: Different Proteins That Catalyze the Same Reaction
  Hexokinase IV (Glucokinase) and Glucose 6-Phosphatase Are Transcriptionally Regulated
  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
  Contents note continued: Glycolytic Enzyme Pyruvate Kinase Is Allosterically Inhibited by ATP
  Gluconeogenic Conversion of Pyruvate to Phosphoenolpyruvate Is under Multiple Types of Regulation
  Transcriptional Regulation of Glycolysis and Gluconeogenesis Changes the Number of Enzyme Molecules
  BOX 15-2 MEDICINE Genetic Mutations That Lead to Rare Forms of Diabetes
  15.4. Metabolism of Glycogen in Animals
  Glycogen Breakdown Is Catalyzed by Glycogen Phosphorylase
  Glucose 1-Phosphate Can Enter Glycolysis or, in Liver, Replenish Blood Glucose
  Sugar Nucleotide UDP-Glucose Donates Glucose for Glycogen Synthesis
  BOX 15-3 Carl and Gerty Cori: Pioneers in Glycogen Metabolism and Disease
  Glycogenin Primes the Initial Sugar Residues in Glycogen
  15.5. Coordinated Regulation of Glycogen Breakdown and Synthesis
  Glycogen Phosphorylase Is Regulated Allosterically and Hormonally
  Glycogen Synthase Is Also Regulated by Phosphorylation and Dephosphorylation
  Glycogen Synthase Kinase 3 Mediates Some of the Actions of Insulin
  Phosphoprotein Phosphatase 1 Is Central to Glycogen Metabolism
  Allosteric and Hormonal Signals Coordinate Carbohydrate Metabolism Globally
  Carbohydrate and Lipid Metabolism Are Integrated by Hormonal and Allosteric Mechanisms
  16. Citric Acid Cycle
  16.1. Production of Acetyl-CoA (Activated Acetate)
  Pyruvate Is Oxidized to Acetyl-CoA and CO2
  Pyruvate Dehydrogenase Complex Employs Five Coenzymes
  Pyruvate Dehydrogenase Complex Consists of Three Distinct Enzymes
  In Substrate Channeling, Intermediates Never Leave the Enzyme Surface
  16.2. Reactions of the Citric Acid Cycle
  Sequence of Reactions in the Citric Acid Cycle Makes Chemical Sense
  Citric Acid Cycle Has Eight Steps
  BOX 16-1 Moonlighting Enzymes: Proteins with More Than One Job
  BOX 16-2 Synthases and Synthetases; Ligases and Lyases; Kinases, Phosphatases, and Phosphorylases: Yes, the Names Are Confusing!
  Energy of Oxidations in the Cycle Is Efficiently Conserved
  BOX 15-3 Citrate: A Symmetric Molecule That Reacts Asymmetrically
  Why Is the Oxidation of Acetate So Complicated?
  Citric Acid Cycle Components Are Important Biosynthetic Intermediates
  Anaplerotic Reactions Replenish Citric Acid Cycle Intermediates
  Biotin in Pyruvate Carboxylase Carries CO2 Groups
  16.3. Regulation of the Citric Acid Cycle
  Production of Acetyl-CoA by the Pyruvate Dehydrogenase Complex Is Regulated by Allosteric and Covalent Mechanisms
  Citric Acid Cycle Is Regulated at Its Three Exergonic Steps
  Substrate Channeling through Multienzyme Complexes May Occur in the Citric Acid Cycle
  Some Mutations in Enzymes of the Citric Acid Cycle Lead to Cancer
  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
  β Oxidation of Saturated Fatty Acids Has Four Basic Steps
  Four β-Oxidation Steps Are Repeated to Yield Acetyl-CoA and ATP
  Acetyl-CoA Can Be Further Oxidized in the Citric Acid Cycle
  BOX 17-1 Long Winter's Nap: Oxidizing Fats during Hibernation
  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
  BOX 17-2 Coenzyme B12: A Radical Solution to a Perplexing Problem
  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
  β-Oxidation Enzymes of Different Organelles Have Diverged during Evolution
  w Oxidation of Fatty Acids Occurs in the Endoplasmic Reticulum
  Phytanic Acid Undergoes a 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
  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 Q-Amino Groups to a-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
  Citric Acid and Urea Cycles Can Be Linked
  Activity of the Urea Cycle Is Regulated at Two Levels
  BOX 18-1 MEDICINE Assays for Tissue Damage
  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 Are Converted to Glucose, Others to Ketone Bodies
  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 a-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
  BOX 18-2 MEDICINE Scientific Sleuths Solve a Murder Mystery
  19. Oxidative Phosphorylation
  19.1. 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
  BOX 19-1 METHODS Determining Three-Dimensional Structures of Large Macromolecular Complexes by Single-Particle Cryo-Electron Microscopy
  Energy of Electron Transfer Is Efficiently Conserved in a Proton Gradient
  Reactive Oxygen Species Are Generated during Oxidative Phosphorylation
  Plant Mitochondria Have Alternative Mechanisms for Oxidizing NADH
  BOX 19-2 Hot, Stinking Plants and Alternative Respiratory Pathways
  19.2. ATP Synthesis
  In the Chemiosmotic Model, Oxidation and Phosphorylation Are Obligately Coupled
  ATP Synthase Has Two Functional Domains, F0 and F1
  ATP Is Stabilized Relative to ADP on the Surface of F1
  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
  How Does Proton Flow through the F1 Complex Produce Rotary Motion?
  BOX 19-2 Atomic Force Microscopy to Visualize Membrane Proteins
  Chemiosmotic Coupling Allows Nonintegral Stoichiometries of O2 Consumption and ATP Synthesis
  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
  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
  Rare Form of Diabetes Results from Defects in the Mitochondria of Pancreatic β Cells
  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
  Accessory Pigments Extend the Range of Light Absorption
  Chlorophylls Funnel Absorbed Energy to Reaction Centers by Exciton Transfer
  20.2. Photochemical Reaction Centers
  Photosynthetic Bacteria Have Two Types of Reaction Center
  Kinetic and Thermodynamic Factors Prevent the Dissipation of Energy by Internal Conversion
  In Plants, Two Reaction Centers Act in Tandem
  Cytochrome b6f Complex Links Photosystems II and I
  Cyclic Electron Flow between PSI and the Cytochrome b6f Complex Increases the Production of ATP Relative to NADPH
  State Transitions Change the Distribution of LHCII between the Two Photosystems
  Water Is Split by the Oxygen-Evolving Complex
  20.3. ATP Synthesis by Photophosphorylation
  Proton Gradient Couples Electron Flow and Phosphorylation
  Approximate Stoichiometry of Photophosphorylation Has Been Established
  ATP Synthase of Chloroplasts Resembles That of Mitochondria
  20.4. Evolution of Oxygenic Photosynthesis
  Chloroplasts Evolved from Ancient Photosynthetic Bacteria
  In Halobacterium, a Single Protein Absorbs Light and Pumps Protons to Drive ATP Synthesis
  20.5. Carbon-Assimilation Reactions
  Carbon Dioxide Assimilation Occurs in Three Stages
  Contents note continued: Synthesis of Each Triose Phosphate from CO2 Requires Six NADPH and Nine ATP
  Transport System Exports Triose Phosphates from the Chloroplast and Imports Phosphate
  Four Enzymes of the Calvin Cycle Are Indirectly Activated by Light
  20.6. Photorespiration and the C4 and CAM Pathways
  Photorespiration Results from Rubisco's Oxygenase Activity
  Salvage of Phosphoglycolate Is Costly
  In C4 Plants, CO2 Fixation and Rubisco Activity Are Spatially Separated
  BOX 20-1 Will Genetic Engineering of Photosynthetic Organisms Increase Their Efficiency?
  In CAM Plants, CO2 Capture and Rubisco Action Are Temporally Separated
  20.7. 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
  Glyoxylate Cycle and Gluconeogenesis Produce Glucose in Germinating Seeds
  Cellulose Is Synthesized by Supramolecular Structures in the Plasma Membrane
  20.8. Integration of Carbohydrate Metabolism in Plants
  Pools of Common Intermediates Link Pathways in Different Organelles
  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
  Mammalian Fatty Acid Synthase Has Multiple Active Sites
  Fatty Acid Synthase Receives the Acetyl and Malonyl Groups
  Fatty Acid Synthase Reactions Are Repeated to Form Palmitate
  Fatty Acid Synthesis Is a Cytosolic Process in Many Organisms 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
  BOX 21-1 MEDICINE Oxidases, Oxygenases, Cytochrome P-450 Enzymes, and Drug Overdoses
  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
  Phospholipid Synthesis in E. coli Employs CDP-Diacylglycerol
  Eukaryotes Synthesize Anionic Phospholipids from CDP-Diacylglycerol
  Eukaryotic Pathways to Phosphatidylserine, Phosphatidylethanolamine, and Phosphatidylcholine Are Interrelated
  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
  BOX 21-2 MEDICINE ApoE Alleles Predict Incidence of Alzheimer Disease
  Cholesteryl Esters Enter Cells by Receptor-Mediated Endocytosis
  HDL Carries Out Reverse Cholesterol Transport
  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
  BOX 21-3 MEDICINE The Lipid Hypothesis and the Development of Statins
  Steroid Hormones Are Formed by Side-Chain Cleavage and Oxidation of Cholesterol
  Intermediates in Cholesterol Biosynthesis Have Many Alternative Fates
  22. Biosynthesis of Amino Acids, Nucleotides, and Related Molecules
  22.1. Overview of Nitrogen Metabolism
  Nitrogen Cycle Maintains a Pool of Biologically Available Nitrogen
  Nitrogen Is Fixed by Enzymes of the Nitrogenase Complex
  BOX 22-1 Unusual Lifestyles of the Obscure but Abundant
  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
  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
  BOX 22-1 MEDICINE On Kings and Vampires
  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
  23. Hormonal Regulation and Integration of Mammalian Metabolism
  23.1. Hormones: Diverse Structures for Diverse Functions
  Detection and Purification of Hormones Requires a Bioassay
  BOX 23-1 MEDICINE How Is a Hormone Discovered? The Arduous Path to Purified Insulin
  Hormones Act through Specific High-Affinity Cellular Receptors
  Hormones Are Chemically Diverse
  Hormone Release Is Regulated 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 Division of Labor
  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
  BOX 23-2 Creatine and Creatine Kinase: Invaluable Diagnostic Aids and the Muscle Builder's Friends
  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
  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
  Diabetes Mellitus Arises from Defects in Insulin Production or Action
  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
  Leptin System May Have Evolved to Regulate the Starvation Response
  Insulin Also Acts in the Arcuate Nucleus to Regulate Eating and Energy Conservation
  Adiponectin Acts through AMPK to Increase Insulin Sensitivity
  AMPK Coordinates Catabolism and Anabolism in Response to Metabolic Stress
  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, PYY3-36, and Cannabinoids
  Microbial Symbionts in the Gut Influence Energy Metabolism and Adipogenesis
  23.5. Obesity, Metabolic Syndrome, and Type 2 Diabetes
  In Type 2 Diabetes the Tissues Become Insensitive to Insulin
  Type 2 Diabetes Is Managed with Diet, Exercise, Medication, and Surgery
  III. INFORMATION PATHWAYS
  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
  BOX 24-1 MEDICINE Curing Disease by Inhibiting Topoisomerases
  DNA Compaction Requires a Special Form of Supercoiling
  24.3. Structure of Chromosomes
  Chromatin Consists of DNA and Proteins
  Histones Are Small, Basic Proteins
  Nucleosomes Are the Fundamental Organizational Units of Chromatin
  Contents note continued: Nucleosomes Are Packed into Highly Condensed Chromosome Structures
  BOX 24-2 METHODS Epigenetics, Nucleosome Structure, and Histone Variants
  Condensed Chromosome Structures Are Maintained by SMC Proteins
  Bacterial DNA Is Also Highly Organized
  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
  Interaction of Replication Forks with DNA Damage Can Lead to Error-Prone Translesion DNA Synthesis
  BOX 25-1 MEDICINE DNA Repair and Cancer
  25.3. DNA Recombination
  Bacterial Homologous Recombination Is a DNA Repair Function
  Eukaryotic Homologous Recombination Is Required for Proper Chromosome Segregation during Meiosis
  Recombination during Meiosis Is Initiated with Double-Strand Breaks
  BOX 25-2 MEDICINE Why Proper Segregation of Chromosomes Matters
  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
  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
  BOX 26-1 METHODS RNA Polymerase Leaves Its Footprint on a Promoter
  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
  DNA-Dependent RNA Polymerase Undergoes Selective Inhibition
  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
  Eukaryotic mRNAs Have a Distinctive 3' End Structure
  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
  RNA Enzymes Are the Catalysts of Some Events in RNA Metabolism
  Cellular mRNAs Are Degraded at Different Rates
  Polynucleotide Phosphorylase Makes Random RNA-like Polymers
  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
  BOX 26.2 MEDICINE Fighting AIDS with Inhibitors of HIV Reverse Transcriptase
  Telomerase Is a Specialized Reverse Transcriptase
  Some RNAs Are Replicated by RNA-Dependent RNA Polymerase
  RNA Synthesis Provides Clues to the Origin of Life in an RNA World
  BOX 26-2 METHODS The SELEX Method for Generating RNA Polymers with New Functions
  27. Protein Metabolism
  27.1. Genetic Code
  Genetic Code Was Cracked Using Artificial mRNA Templates
  BOX 27-1 Exceptions That Prove the Rule: Natural Variations in the Genetic Code
  Wobble Allows Some tRNAs to Recognize More than One Codon
  Genetic Code Is Mutation-Resistant
  Translational Frameshifting and RNA Editing Affect How the Code Is Read
  27.2. Protein Synthesis
  Protein Biosynthesis Takes Place in Five Stages
  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 Specific Amino Acid Initiates Protein Synthesis
  BOX 27-2 Natural and Unnatural Expansion of the Genetic Code
  Stage 3 Peptide Bonds Are Formed in the Elongation Stage
  Stage 4 Termination of Polypeptide Synthesis Requires a Special Signal
  Induced Variation in the Genetic Code: Nonsense Suppression
  Stage 5 Newly Synthesized Polypeptide Chains Undergo Folding and Processing
  Ribosome Profiling Provides a Snapshot of Cellular Translation
  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
  28. Regulation of Gene Expression
  28.1. Principles 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
  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
  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
  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
  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
  BOX 28-1 Of Fins, Wings, Beaks, and Things.