Table of contents for Fundamentals of biochemistry : life at the molecular level / Donald Voet, Judith G. Voet, Charlotte W. Pratt.


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PART I: INTRODUCTION.
Chapter 1. Introduction to the Chemistry of Life.
1._The Origin of Life
_____ A._Biological Molecules Arose from Inorganic Materials
_____ B._Complex Self-replicating Systems Evolved from Simple Molecules
2._Cellular Architecture
_____ A._Cells Evolved to Carry Out Metabolic Reactions
_____ B._There Are Two Types of Cells: Prokaryotes and Eukaryotes
_____ C._Molecular Data Reveal Three Evolutionary Domains of Organisms
_____ D._Organisms Continue to Evolve
3._Thermodynamics
_____ A._The First Law of Thermodynamics States that Energy Is Conserved
_____ B._The Second Law of Thermodynamics States that Entropy Tends to Increase
_____ C._The Free Energy Change Determines the Spontaneity of a Process
_____ D._Free Energy Changes Can Be Calculated from Equilibrium Concentrations
_____ E._Life Obeys the Laws of Thermodynamics
Box 1-1 Pathways of Discovery
Lynn Margulis and the Theory of Endosymbiosis
Box 1-2 Perspectives in Biochemistry
Biochemical Conventions
Chapter 2. Water.
1._Physical Properties of Water
__ A._Water Is a Polar Molecule
__ B._Hydrophilic Substances Dissolve in Water
__ C._The Hydrophobic Effect Causes Nonpolar Substances to Aggregate in Water
__ D._Water Moves by Osmosis and Solutes Move by Diffusion
2._Chemical Properties of Water
__ A._Water Ionizes to Form H+ and OH–
__ B._Acids and Bases Alter the pH
__ C._Buffers Resist Changes in pH
Box 2-1 Biochemistry in Health and Disease
The Blood Buffering System
PART II: BIOMOLECULES.
Chapter 3. Nucleotides, Nucleic Acids, and Genetic Information.
1._Nucleotides
2._Introduction to Nucleic Acid Structure
__ A._Nucleic Acids Are Polymers of Nucleotides
__ B._The DNA Forms a Double Helix
__ C._RNA Is a Single-Stranded Nucleic Acid
3._Overview of Nucleic Acid Function
__ A._DNA Carries Genetic Information
__ B._Genes Direct Protein Synthesis
4._Nucleic Acid Sequencing
__ A._Restriction Endonucleases Cleave DNA at Specific Sequences
__ B._Electrophoresis Separates Nucleic Acids According to Size
__ C._DNA Is Sequenced by the Chain-Terminator Method
__ D._Entire Genomes Have Been Sequenced
__ E._Evolution Results from Sequence Mutations
5._Manipulating DNA
__ A._Cloned DNA Is an Amplified Copy
__ B._DNA Libraries Are Collections of Cloned DNA
__ C._DNA Is Amplified by the Polymerase Chain Reaction
__ D._Recombinant DNA Technology Has Numerous Practical Applications
Box 3-1 Pathways of Discovery
Francis Collins and the Gene for Cystic Fibrosis
Box 3-2 Perspectives in Biochemistry
DNA Fingerprinting
Box 3-3 Perspectives in Biochemistry
Ethical Aspects of Recombinant DNA Technology
Chapter 4. Amino Acids.
1._Amino Acid Structure
__ A._Amino Acids Are Dipolar Ions
__ B._Peptide Bonds Link Amino Acids
__ C._Amino Acid Side Chains Are Nonpolar, Polar, or Charged
__ D._The pK Values of Ionizable Groups Depend on Nearby Groups
__ E._Amino Acid Names Are Abbreviated
2._Stereochemistry
3._Amino Acid Derivatives
__ A._Protein Side Chains May be Modified
__ B._Some Amino Acids Are Biologically Active
Box 4-1 Pathways of Discovery
William C. Rose and the Discovery of Threonine
Box 4-2 Perspectives in Biochemistry
The RS System
Box 4-3 Perspectives in Biochemistry
Green Fluorescent Protein
Chapter 5. Proteins: Primary Structure.
1._Polypeptide Diversity
2._Protein Purification and Analysis
__ A._Purifying a Protein Requires a Strategy
__ B._Salting Out Separates Proteins by Their Solubility
__ C._Chromatography Involves Interaction with Mobile and Stationary Phases
__ D._Electrophoresis Separates Molecules According to Charge and Size
3._Protein Sequencing
__ A._The First Step Is to Separate Subunits
__ B. _The Polypeptide Chains Are Cleaved
__ C._Edman Degradation Removes a Peptide’s First Amino Acid Residue
__ D._Mass Spectrometry Determines the Molecular Masses of Peptides
__ E._Reconstructed Protein Sequences Are Stored in Databases
4._Protein Evolution
__ A._Protein Sequences Reveal Evolutionary Relationships
__ B._Proteins Evolve by the Duplication of Genes or Gene Segments
Box 5-1 Pathways of Discovery
Frederick Sanger and Protein Sequencing
Chapter 6. Proteins: Three-Dimensional Structure.
1._Secondary Structure
__ A._The Planar Peptide Group Limits Polypeptide Conformations
__ B._The Most Common Regular Secondary Structures Are the_a_Helix and the ß Sheet
__ C._Fibrous Proteins Have Repeating Secondary Structures
__ D._Most Proteins Include Nonrepetitive Structure
2._Tertiary Structure
__ A._Most Protein Structures Have Been Determined by X-Ray Crystallography or Nuclear Magnetic Resonance
__ B._Side Chain Location Varies with Polarity
__ C._Tertiary Structures Contain Combinations of Secondary Structure
__ D._Structure Is Conserved More than Sequence
__ E._Structural Bioinformatics Provides Tools for Storing, Visualizing, and Comparing Protein Structural Information
3._Quaternary Structure and Symmetry
4._Protein Stability
__ A._Proteins Are Stabilized by Several Forces
__ B._Proteins Can Undergo Denaturation and Renaturation
5._Protein Folding
__ A._Proteins Follow Folding Pathways
__ B._Molecular Chaperones Assist Protein Folding
__ C._Some Diseases Are Caused by Protein Misfolding
Box 6-1 Pathways of Discovery
Linus Pauling and Structural Biochemistry
Box 6-2 Biochemistry in Health and Disease
Collagen Diseases
Box 6-3 Perspectives in Biochemistry
Thermostable Proteins
Box 6-4 Perspectives in Biochemistry
Protein Structure Prediction and Protein Design
Chapter 7. Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies
1._Oxygen Binding to Myoglobin and Hemoglobin
__ A._Myoglobin Is a Monomeric Oxygen-Binding Protein
__ B. _Hemoglobin Is a Tetramer with Two Conformations
__ C._Oxygen Binds Cooperatively to Hemoglobin
__ D. _Hemoglobin’s Two Conformations Exhibit Different Affinities for Oxygen
__ E._Mutations May Alter Hemoglobin’s Structure and Function
2._Muscle Contraction
__ A. _Muscle Consists of Interdigitated Thick and Thin Filaments
__ B. _Muscle Contraction Occurs When Myosin Heads Walk Up Thin Filaments
__ C. _Actin Forms Microfilaments in Nonmuscle Cells
3._Antibodies
__ A. _Antibodies Have Constant and Variable Regions
__ B. _Antibodies Recognize a Huge Variety of Antigens
Box 7-1 Perspectives in Biochemistry
Other Oxygen-Transport Proteins
Box 7-2 Pathways of Discovery
Max Perutz and the Structure and Function of Hemoglobin
Box 7-3 Biochemistry in Health and Disease
High-Altitude Adaptation
Box 7-4 Pathways of Discovery
Hugh Huxley and the Sliding Filament Model
Box 7-5 Perspectives in Biochemistry
Monoclonal Antibodies
Chapter 8. Carbohydrates.
1._Monosaccharides
__ A._Monosaccharides Are Aldoses or Ketoses
__ B._Monosaccharides Vary in Configuration and Conformation
__ C._Sugars Can Be Modified and Covalently Linked
2._Polysaccharides
__ A._Lactose and Sucrose Are Disaccharides
__ B._Cellulose and Chitin Are Structural Polysaccharides
__ C._Starch and Glycogen Are Storage Polysaccharides
__ D._Glycosaminoglycans Form Highly Hydrated Gels
3._Glycoproteins
__ A._Proteoglycans Contain Glycosaminoglycans
__ B._Bacterial Cell Walls Are Made of Peptidoglycan
__ C._Many Eukaryotic Proteins Are Glycosylated
__ D._Oligosaccharides May Determine Glycoprotein Structure, Function, and Recognition
Box 8-1 Biochemistry in Health and Disease
Lactose Intolerance
Box 8-2 Perspectives in Biochemistry
Artificial Sweeteners
Box 8-3 Biochemistry in Health and Disease
Peptidoglycan-Specific Antibiotics
Chapter 9. Lipids and Biological Membranes.
1._Lipid Classification
__ A._The Properties of Fatty Acids Depend on Their Hydrocarbon Chains
__ B._Triacylglycerols Contain Three Esterified Fatty Acids
__ C._Glycerophospholipids Are Amphiphilic
__ D._Sphingolipids Are Amino Alcohol Derivatives
__ E._Steroids Contain Four Fused Rings
__ F._Other Lipids Perform a Variety of Metabolic Roles
2._Lipid Bilayers
__ A._Bilayer Formation Is Driven by the Hydrophobic Effect
__ B._Lipid Bilayers Have Fluidlike Properties
3._Membrane Proteins
__ A._Integral Membrane Proteins Interact with Hydrophobic Lipids
__ B._Lipid-Linked Proteins Are Anchored to the Bilayer
__ C._Peripheral Proteins Associate Loosely with Membranes
4._Membrane Structure and Assembly
__ A._The Fluid Mosaic Model Accounts for Lateral Diffusion
__ B._The Membrane Skeleton Helps Define Cell Shape
__ C._Membrane Lipids Are Distributed Asymmetrically
__ D._The Secretory Pathway Generates Secreted and Transmembrane Proteins
__ E._Intracellular Vesicles Transport Proteins
__ F. Proteins Mediate Vesicle Fusion
Box 9-1 Biochemistry in Health and Disease
Lung Surfactant
Box 9-2 Pathways of Discovery
Richard Henderson and the Structure of Bacteriorhodopsin
Box 9-3 Biochemistry in Health and Disease
Tetanus and Botulinum Toxins Specifically Cleave SNAREs
Chapter 10. Membrane Transport.
1._Thermodynamics of Transport
2._Passive-Mediated Transport
__ A._Ionophores Carry Ions across Membranes
__ B._Porins Contain ? Barrels
__ C._Ion Channels Are Highly Selective
__ D._Aquaporins Mediate the Transmembrane Movement of Water
__ E._Transport Proteins Alternate between Two Conformations
3._Active Transport
__ A._The (Na+–K+)–ATPase Transports Ions in Opposite Directions
__ B._The Ca2+–ATPase Pumps Ca2+ out of the Cytosol
__ C._ABC Transporters Are Responsible for Drug Resistance
__ D._Active Transport May Be Driven by Ion Gradients
Box 10-1 Perspectives in Biochemistry
Gap Junctions
Box 10-2 Perspectives in Biochemistry
Differentiating Mediated and Nonmediated Transport
Box 10-3 Biochemistry in Health and Disease
The Action of Cardiac Glycosides
PART III: ENZYMES.
Chapter 11. Enzymatic Catalysis.
1._General Properties of Enzymes
__ A._Enzymes Are Classified by the Type of Reaction They Catalyze
__ B._Enzymes Act on Specific Substrates
__ C._Some Enzymes Require Cofactors
2._Activation Energy and the Reaction Coordinate
3._Catalytic Mechanisms
__ A._Acid–Base Catalysis Occurs by Proton Transfer
__ B._Covalent Catalysis Usually Requires a Nucleophile
__ C._Metal Ion Cofactors Act as Catalysts
__ D._Catalysis Can Occur through Proximity and Orientation Effects
__ E._Enzymes Catalyze Reactions by Preferentially Binding the Transition State
4._Lysozyme
__ A._Lysozyme’s Catalytic Site Was Identified through Model Building
__ B._The Lysozyme Reaction Proceeds via a Covalent Intermediate
5._Serine Proteases
__ A._The Active Site Residues Were Identified by Chemical Labeling
__ B._X-Ray Structures Provided Information about Catalysis, Substrate Specificity, and Evolution
__ C._Serine Proteases Use Several Catalytic Mechanisms
__ D._Zymogens Are Inactive Enzyme Precursors
Box 11-1 Perspectives in Biochemistry
Effects of pH on Enzyme Activity
Box 11-2 Perspectives in Biochemistry
Observing Enzyme Action by X-Ray Crystallography
Box 11-3 Biochemistry in Health and Disease
Nerve Poisons
Box 11-4 Biochemistry in Health and Disease
The Blood Coagulation Cascade
Chapter 12. Enzyme Kinetics, Inhibition, and Control.
1._Reaction Kinetics
__ A._Chemical Kinetics Is Described by Rate Equations
__ B._Enzyme Kinetics Often Follows the Michaelis–Menten Equation
__ C._Kinetic Data Can Provide Values of Vmax and KM
__ D._Bisubstrate Reactions Follow One of Several Rate Equations
2._Enzyme Inhibition
__ A._Competitive Inhibition Involves Inhibitor Binding at an Enzyme’s Substrate Binding Site
__ B._Uncompetitive Inhibition Involves Inhibitor Binding to the Enzyme–Substrate Complex
__ C._Mixed Inhibition Involves Inhibitor Binding to Both the Free Enzyme and the Enzyme–Substrate Complex
3._Control of Enzyme Activity
__ A. _Allosteric Control Involves Binding at a Site Other Than the Active Site
__ B. _Control by Covalent Modification Often Involves Protein Phosphorylation
4._Drug Design
__ A._Drug Discovery Employs a Variety of Techniques
__ B._A Drug’s Bioavailability Depends on How It Is Absorbed and Transported in the Body
__ C._Clinical Trials Test for Efficacy and Safety
__ D._Cytochromes P450 Are Often Implicated in Adverse Drug Reactions
Box 12-1 Perspectives in Biochemistry
Isotopic Labeling
Box 12-2 Pathways of Discovery
J.B.S. Haldane and Enzyme Action
Box 12-3 Perspectives in Biochemistry
Kinetics and Transition State Theory
Box 12-4 Biochemistry in Health and Disease
HIV Enzyme Inhibitors
Chapter 13. Biochemical Signaling
1._Hormones
__ A. _Pancreatic Islet Hormones Control Fuel Metabolism
__ B. _Epinephrine and Norepinephrine Prepare the Body for Action
__ C. _Steroid Hormones Regulate a Wide Variety of Metabolic and Sexual Processes
__ D. _Growth Hormone Binds to Receptors in Muscle, Bone, and Cartilage
2._Receptor Tyrosine Kinases
__ A.__Receptor Tyrosine Kinases Transmit Signals across the Cell Membrane
__ B.__Kinase Cascades Relay Signals to the Nucleus
__ C. _Some Receptors Are Associated with Nonreceptor Tyrosine Kinases
__ D.__Protein Phosphatases Are Signaling Proteins in Their Own Right
3._Heterotrimeric G Proteins
__ A. _G Protein–Coupled Receptors Contain Seven Transmembrane Helices
__ B.__Heterotrimeric G Proteins Dissociate on Activation
__ C.__Adenylate Cyclase Synthesizes cAMP to Activate Protein Kinase A
__ D. _Phosphodiesterases Limit Second Messenger Activity
4._The Phosphoinositide Pathway
__ A. _Ligand Binding Results in the Cytoplasmic Release of the Second Messengers IP3 and Ca2+
__ B. _Calmodulin Is a Ca2+-Activated Switch
__ C. _DAG Is a Lipid-Soluble Second Messenger that Activates Protein Kinase C
__ D. _Epilog: Complex Systems Have Emergent Properties
Box 13-1 Pathways of Discovery
Rosalyn Yalow and the Radioimmunoassay (RIA)
Box 13-2 Perspectives in Biochemistry
Receptor-Ligand Binding Can Be Quantitated
Box 13-3 Biochemistry in Health and Disease
Oncogenes and Cancer
Box 13-4 Biochemistry in Health and Disease
Drugs and Toxins That Affect Cell Signaling
Box 13-5 Biochemistry in Health and Disease
Anthrax
PART IV: METABOLISM.
Chapter 14. Introduction to Metabolism.
1._Overview of Metabolism
__ A. _Nutrition Involves Food Intake and Use
__ B. _Vitamins and Minerals Assist Metabolic Reactions
__ C._Metabolic Pathways Consist of Series of Enzymatic Reactions
__ D._Thermodynamics Dictates the Direction and Regulatory Capacity of Metabolic Pathways
__ E._Metabolic Flux Must Be Controlled
2._“High-Energy” Compounds
__ A._ATP Has a High Phosphoryl Group-Transfer Potential
__ B._Coupled Reactions Drive Endergonic Processes
__ C._Some Other Phosphorylated Compounds Have High Phosphoryl Group-Transfer Potentials
__ D._Thioesters Are Energy-Rich Compounds
3._Oxidation–Reduction Reactions
__ A._NAD+ and FAD Are Electron Carriers
__ B._The Nernst Equation Describes Oxidation–Reduction Reactions
__ C._Spontaneity Can Be Determined by Measuring Reduction Potential Differences
4._Experimental Approaches to the Study of Metabolism
__ A._Labeled Metabolites Can Be Traced
__ B._Studying Metabolic Pathways Often Involves Perturbing the System
__ C. _Systems Biology Has Entered the Study of Metabolism
Box 14-1 Perspectives in Biochemistry
Oxidation States of Carbon
Box 14-2 Perspectives in Biochemistry
Mapping Metabolic Pathways
Box 14-3 Pathways of Discovery
Fritz Lipmann and “High-energy” Compounds
Box 14-4 Perspectives in Biochemistry
ATP and_DG
Chapter 15. Glucose Catabolism.
1._Overview of Glycolysis
2._The Reactions of Glycolysis
__ A._Hexokinase Uses the First ATP
__ B._Phosphoglucose Isomerase Converts Glucose-6-Phosphate to Fructose-6-Phosphate
__ C._Phosphofructokinase Uses the Second ATP
__ D._Aldolase Converts a 6-Carbon Compound to Two 3-Carbon Compounds
__ E._Triose Phosphate Isomerase Interconverts Dihydroxyacetone Phosphate and Glyceraldehyde-3-Phosphate
__ F._Glyceraldehyde-3-Phosphate Dehydrogenase Forms the First “High-Energy” Intermediate
__ G._Phosphoglycerate Kinase Generates the First ATP
__ H._Phosphoglycerate Mutase Interconverts 3-Phosphoglycerate and 2-Phosphoglycerate
__ I._Enolase Forms the Second “High-Energy” Intermediate
__ J._Pyruvate Kinase Generates the Second ATP
3._Fermentation: The Anaerobic Fate of Pyruvate
__ A._Homolactic Fermentation Converts Pyruvate to Lactate
__ B._Alcoholic Fermentation Converts Pyruvate to Ethanol and CO2
__ C._Fermentation is Energetically Favorable
4._Regulation of Glycolysis
__ A.____ Phosphofructokinase is The Major Flux-Controlling Enzyme of Glycolysis in Muscle
__ B._Substrate Cycling Fine-Tunes Flux Control
5._Metabolism of Hexoses Other than Glucose
__ A._Fructose Is Converted to Fructose-6-Phosphate or Glyceraldehyde-3-Phosphate
__ B._Galactose Is Converted to Glucose-6-Phosphate
__ C._Mannose Is Converted to Fructose-6-Phosphate
6._The Pentose Phosphate Pathway
__ A._Oxidative Reactions Produce NADPH in Stage 1
__ B._Isomerization and Epimerization of Ribulose-5-Phosphate Occur in Stage 2
__ C._Stage 3 Involves Carbon–Carbon Bond Cleavage and Formation
__ D._The Pentose Phosphate Pathway Must Be Regulated
Box 15-1 Pathways of Discovery
Otto Warburg and Studies of Metabolism
Box 15-2 Perspectives in Biochemistry
Synthesis of 2,3-Bisphosphoglycerate in Erythrocytes and Its Effect on the Oxygen Carrying Capacity of the Blood
Box 15-3 Perspectives in Biochemistry
Glycolytic ATP Production in Muscle
Box 15-4 Biochemistry in Health and Disease
Glucose-6-Phosphate Dehydrogenase Deficiency
Chapter 16. Glycogen Metabolism and Gluconeogenesis.
1._Glycogen Breakdown
__ A._Glycogen Phosphorylase Degrades Glycogen to Glucose-1-Phosphate
__ B._Glycogen Debranching Enzyme Acts as a Glucosyltransferase
__ C._Phosphoglucomutase Interconverts Glucose-1-Phosphate and Glucose-6-Phosphate
2._Glycogen Synthesis
__ A._UDP–Glucose Pyrophosphorylase Activates Glucosyl Units
__ B._Glycogen Synthase Extends Glycogen Chains
__ C._Glycogen Branching Enzyme Transfers Seven-Residue Glycogen Segments
3._Control of Glycogen Metabolism
__ A._Glycogen Phosphorylase and Glycogen Synthase Are Under Allosteric Control
__ B._Glycogen Phosphorylase and Glycogen Synthase Undergo Control by Covalent Modification
__ C._Glycogen Metabolism Is Subject to Hormonal Control
4._Gluconeogenesis
__ A._Pyruvate Is Converted to Phosphoenolpyruvate in Two Steps
__ B._Hydrolysis Reactions Bypass Irreversible Glycolytic Reactions
__ C._Gluconeogenesis and Glycolysis Are Independently Regulated
5._Other Carbohydrate Biosynthetic Pathways
Box 16-1 Pathways of Discovery
Carl and Gerty Cori and Glucose Metabolism
Box 16-2 Biochemistry in Health and Disease
Glycogen Storage Diseases
Box 16-3 Perspectives in Biochemistry
Optimizing Glycogen Structure
Box 16-4 Perspectives in Biochemistry
Lactose Synthesis
Chapter 17. Citric Acid Cycle.
1._Overview of the Citric Acid Cycle
2._Synthesis of Acetyl-Coenzyme A
__ A._Pyruvate Dehydrogenase Is a Multienzyme Complex
__ B._The Pyruvate Dehydrogenase Complex Catalyzes Five Reactions
3._Enzymes of the Citric Acid Cycle
__ A._Citrate Synthase Joins an Acetyl Group to Oxaloacetate
__ B._Aconitase Interconverts Citrate and Isocitrate
__ C._NAD+-Dependent Isocitrate Dehydrogenase Releases CO2
__ D._a-Ketoglutarate Dehydrogenase Resembles Pyruvate Dehydrogenase
__ E._Succinyl-CoA Synthetase Produces GTP
__ F._Succinate Dehydrogenase Generates FADH2
__ G._Fumarase Produces Malate
__ H._Malate Dehydrogenase Regenerates Oxaloacetate
4._Regulation of the Citric Acid Cycle
__ A._Pyruvate Dehydrogenase Is Regulated by Product Inhibition and Covalent Modification
__ B._Three Enzymes Control the Rate of the Citric Acid Cycle
5._Reactions Related to the Citric Acid Cycle
__ A._Other Pathways Use Citric Acid Cycle Intermediates
__ B._Some Reactions Replenish Citric Acid Cycle Intermediates
__ C._The Glyoxylate Cycle Shares Some Steps with the Citric Acid Cycle
Box 17-1 Pathways of Discovery
Hans Krebs and the Citric Acid Cycle
Box 17-2 Biochemistry in Health and Disease
Arsenic Poisoning
Box 17-3 Perspectives in Biochemistry
Evolution of the Citric Acid Cycle
Chapter 18. Electron Transport and Oxidative Phosphorylation.
1._The Mitochondrion
__ A._Mitochondria Contain a Highly Folded Inner Membrane
__ B._Ions and Metabolites Enter Mitochondria via Transporters
2._Electron Transport
__ A._Electron Transport Is an Exergonic Process
__ B._Electron Carriers Operate in Sequence
__ C._Complex I Accepts Electrons from NADH
__ D._Complex II Contributes Electrons to Coenzyme Q
__ E._Complex III Translocates Protons via the Q Cycle
__ F._Complex IV Reduces Oxygen to Water
3._Oxidative Phosphorylation
__ A._The Chemiosmotic Theory Links Electron Transport to ATP Synthesis
__ B._ATP Synthase Is Driven by the Flow of Protons
__ C._The P/O Ratio Relates the Amount of ATP Synthesized to the Amount of Oxygen Reduced
__ D._Oxidative Phosphorylation Can be Uncoupled from Electron Transport
4._Control of Oxidative Metabolism
__ A._The Rate of Oxidative Phosphorylation Depends on the ATP and NADH Concentrations
__ B._Aerobic Metabolism Has Some Disadvantages
Box 18-1 Perspectives in Biochemistry
Cytochromes Are Electron-Transport Heme Proteins
Box 18-2 Pathways of Discovery
Peter Mitchell and the Chemiosmotic Theory
Box 18-3 Perspectives in Biochemistry
Bacterial Electron Transport and Oxidative Phosphorylation
Box 18-4 Perspectives in Biochemistry
Uncoupling in Brown Adipose Tissue Generates Heat
Box 18-5 Biochemistry in Health and Disease
Oxygen Deprivation in Heart Attack and Stroke
Chapter 19. Photosynthesis.
1._Chloroplasts
__ A._The Light Reactions Take Place in the Thylakoid Membrane
__ B._Pigment Molecules Absorb Light
2._The Light Reactions
__ A._Light Energy Is Transformed to Chemical Energy
__ B._Electron Transport in Photosynthetic Bacteria Follows a Circular Path
__ C._Two-Center Electron Transport Is a Linear Pathway That Produces O2 and NADPH
__ D. The Proton Gradient Drives ATP Synthesis by Photophosphorylation
3._The Dark Reactions
__ A._The Calvin Cycle Fixes CO2
__ B._Calvin Cycle Products Are Converted to Starch, Sucrose, and Cellulose
__ C._The Calvin Cycle Is Controlled Indirectly by Light
__ D._Photorespiration Competes with Photosynthesis
Box 19-1 Perspectives in Biochemistry
Segregation of PSI and PSII
Chapter 20. Lipid Metabolism.
1._Lipid Digestion, Absorption, and Transport
__ A._Triacylglycerols Are Digested before They Are Absorbed
__ B._Lipids Are Transported as Lipoproteins
2._Fatty Acid Oxidation
__ A._Fatty Acids Are Activated by Their Attachment to Coenzyme A
__ B._Carnitine Carries Acyl Groups across the Mitochondrial Membrane
__ C._? Oxidation Degrades Fatty Acids to Acetyl-CoA
__ D._Oxidation of Unsaturated Fatty Acids Requires Additional Enzymes
__ E._Oxidation of Odd-Chain Fatty Acids Yields Propionyl-CoA
F._Peroxisomal ? Oxidation Differs from Mitochondrial ? Oxidation
3._Ketone Bodies
4._Fatty Acid Biosynthesis
__ A._Mitochondrial Acetyl-CoA Must Be Transported into the Cytosol
__ B._Acetyl-CoA Carboxylase Produces Malonyl-CoA
__ C._Fatty Acid Synthase Catalyzes Seven Reactions
__ D._Fatty Acids May Be Elongated and Desaturated
__ E._Fatty Acids Are Esterified to Form Triacylglycerols
5._Regulation of Fatty Acid Metabolism
6._Synthesis of Other Lipids
__ A._Glycerophospholipids Are Built from Intermediates of Triacylglycerol Synthesis
__ B._Sphingolipids Are Built from Palmitoyl-CoA and Serine
__ C._C20 Fatty Acids Are the Precursors of Prostaglandins
7._Cholesterol Metabolism
__ A._Cholesterol Is Synthesized from Acetyl-CoA
__ B._HMG-CoA Reductase Controls the Rate of Cholesterol Synthesis
__ C._Abnormal Cholesterol Transport Leads to Atherosclerosis
Box 20-1 Biochemistry in Health and Disease
Vitamin B12 Deficiency
Box 20-2 Pathways of Discovery
Dorothy Crowfoot Hodgkin and the Structure of Vitamin B12
Box 20-3 Perspectives in Biochemistry
Triclosan: An Inhibitor of Fatty Acid Synthesis
Box 20-4 Biochemistry in Health and Disease
Sphingolipid Degradation and Lipid Storage Diseases
Chapter 21. Amino Acid Metabolism.
Chapter 22. Mammalian Fuel Metabolism: Integration and Regulation.
PART V: GENE EXPRESSION AND REPLICATION.
Chapter 23. Nucleotide Metabolism.
Chapter 24. Nucleic Acid Structure.
Chapter 25. DNA Replication, Repair, and Recombination.
Chapter 26. Transcription and RNA Processing.
Chapter 27. Protein Synthesis.
Chapter 28. Regulation of Gene Expression.
1._Genome Organization
__ A._Gene Number Varies among Organisms
__ B._Some Genes Occur in Clusters
__ C._Eukaryotic Genomes Contain Repetitive DNA Sequences
2._Regulation of Prokaryotic Gene Expression
__ A._The lac Operon Is Controlled by a Repressor
__ B._Catabolite-Repressed Operons Can Be Activated
__ C._Attenuation Regulates Transcription Termination
__ D._Riboswitches Are Metabolite-Sensing RNAs
3._Regulation of Eukaryotic Gene Expression
__ A._Chromatin Structure Influences Gene Expression
__ B._Eukaryotes Contain Multiple Transcriptional Activators
__ C._Posttranscriptional Control Mechanisms Include RNA Degradation
__ D._Antibody Diversity Results from Somatic Recombination and Hypermutation
4. _The Cell Cycle, Cancer, and Apoptosis
__ A._Progress Through the Cell Cycle Is Tightly Regulated
__ B. _Tumor Suppressors Prevent Cancer
__ C. _Apoptosis Is an Orderly Process
__ D. _Development Has a Molecular Basis
Box 28-1 Biochemistry in Health and Disease
Trinucleotide Repeat Diseases
Box 28-2 Perspectives in Biochemistry
X Chromosome Inactivation
Box 28-3 Perspectives in Biochemistry
Nonsense-Mediated Decay
Appendices:
Solutions to Problems.
Glossary.
Index. _



Library of Congress subject headings for this publication:
Biochemistry -- Textbooks.