Chapter Introduction
ABOUT THE AUTHORS
PREFACE
MEDIA AND ASSESSMENT
MOLECULAR EVOLUTION
CLINICAL APPLICATIONS
ACKNOWLEDGMENTS
BRIEF CONTENTS
CONTENTS
Chapter Introduction
1.1: Biochemical Unity Underlies Biological Diversity
1.2: DNA Illustrates the Interplay Between Form and Function
1.3: Concepts from Chemistry Explain the Properties of Biological Molecules
1.4: The Genomic Revolution Is Transforming Biochemistry, Medicine, and Other Fields
APPENDIX: Visualizing Molecular Structures I: Small Molecules
KEY TERMS
PROBLEMS
Chapter Introduction
2.1: Proteins Are Built from a Repertoire of 20 Amino Acids
2.2: Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains
2.3: Secondary Structure: Polypeptide Chains Can Fold into Regular Structures Such As the Alpha Helix, the Beta Sheet, and Turns and Loops
2.4: Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures with Nonpolar Cores
2.5: Quaternary Structure: Polypeptide Chains Can Assemble into Multisubunit Structures
2.6: The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure
SUMMARY
APPENDIX: Visualizing Molecular Structures II: Proteins
KEY TERMS
PROBLEMS
Chapter Introduction
3.1: The Purification of Proteins Is an Essential First Step in Understanding Their Function
3.2: Immunology Provides Important Techniques with Which to Investigate Proteins
3.3: Mass Spectrometry is a Powerful Technique for the Identification of Peptides and Proteins
3.4: Peptides Can Be Synthesized by Automated Solid-Phase Methods
3.5: Three-Dimensional Protein Structure Can Be Determined by X-ray Crystallography and NMR Spectroscopy
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
4.1: A Nucleic Acid Consists of Four Kinds of Bases Linked to a Sugar-Phosphate Backbone
4.2: A Pair of Nucleic Acid Strands with Complementary Sequences Can Form a Double-Helical Structure
4.3: The Double Helix Facilitates the Accurate Transmission of Hereditary Information
4.4: DNA Is Replicated by Polymerases That Take Instructions from Templates
4.5: Gene Expression Is the Transformation of DNA Information into Functional Molecules
4.6: Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point
4.7: Most Eukaryotic Genes Are Mosaics of Introns and Exons
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
5.1: The Exploration of Genes Relies on Key Tools
5.2: Recombinant DNA Technology Has Revolutionized All Aspects of Biology
5.3: Complete Genomes Have Been Sequenced and Analyzed
5.4: Eukaryotic Genes Can Be Quantitated and Manipulated with Considerable Precision
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
6.1: Homologs Are Descended from a Common Ancestor
6.2: Statistical Analysis of Sequence Alignments Can Detect Homology
6.3: Examination of Three-Dimensional Structure Enhances Our Understanding of Evolutionary Relationships
6.4: Evolutionary Trees Can Be Constructed on the Basis of Sequence Information
6.5: Modern Techniques Make the Experimental Exploration of Evolution Possible
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
7.1: Myoglobin and Hemoglobin Bind Oxygen at Iron Atoms in Heme
7.2: Hemoglobin Binds Oxygen Cooperatively
7.3: Hydrogen Ions and Carbon Dioxide Promote the Release of Oxygen: The Bohr Effect
7.4: Mutations in Genes Encoding Hemoglobin Subunits Can Result in Disease
SUMMARY
APPENDIX: Binding Models Can Be Formulated in Quantitative Terms: The Hill Plot and the Concerted Model
KEY TERMS
PROBLEMS
Chapter Introduction
8.1: Enzymes Are Powerful and Highly Specific Catalysts
8.2: Gibbs Free Energy Is a Useful Thermodynamic Function for Understanding Enzymes
8.3: Enzymes Accelerate Reactions by Facilitating the Formation of the Transition State
8.4: The Michaelis-Menten Model Accounts for the Kinetic Properties of Many Enzymes
8.5: Enzymes Can Be Inhibited by Specific Molecules
8.6: Enzymes Can Be Studied One Molecule at a Time
SUMMARY
APPENDIX: Enzymes are Classified on the Basis of the Types of Reactions That They Catalyze
KEY TERMS
PROBLEMS
Chapter Introduction
9.1 Proteases Facilitate a Fundamentally Difficult Reaction
9.2 Carbonic Anhydrases Make a Fast Reaction Faster
9.3 Restriction Enzymes Catalyze Highly Specific DNA-Cleavage Reactions
9.4 Myosins Harness Changes in Enzyme Conformation to Couple ATP Hydrolysis to Mechanical Work
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
10.1 Aspartate Transcarbamoylase Is Allosterically Inhibited by the End Product of Its Pathway
10.2 Isozymes Provide a Means of Regulation Specific to Distinct Tissues and Developmental Stages
10.3 Covalent Modification Is a Means of Regulating Enzyme Activity
10.4 Many Enzymes are Activated by Specific Proteolytic Cleavage
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
11.1 Monosaccharides Are the Simplest Carbohydrates
11.2 Monosaccharides Are Linked to Form Complex Carbohydrates
11.3 Carbohydrates Can Be Linked to Proteins to Form Glycoproteins
11.4 Lectins Are Specific Carbohydrate-Binding Proteins
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
12.1 Fatty Acids Are Key Constituents of Lipids
12.2 There Are Three Common Types of Membrane Lipids
12.3 Phospholipids and Glycolipids Readily Form Bimolecular Sheets in Aqueous Media
12.4 Proteins Carry Out Most Membrane Processes
12.5 Lipids and Many Membrane Proteins Diffuse Rapidly in the Plane of the Membrane
12.6 Eukaryotic Cells Contain Compartments Bounded by Internal Membranes
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
13.1 The Transport of Molecules Across a Membrane May Be Active or Passive
13.2 Two Families of Membrane Proteins Use ATP Hydrolysis to Pump Ions and Molecules Across Membranes
13.3 Lactose Permease Is an Archetype of Secondary Transporters That Use One Concentration Gradient to Power the Formation of Another
13.4 Specific Channels Can Rapidly Transport Ions Across Membranes
13.5 Gap Junctions Allow Ions and Small Molecules to Flow Between Communicating Cells
13.6 Specific Channels Increase the Permeability of Some Membranes to Water
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
14.1 Heterotrimeric G Proteins Transmit Signals and Reset Themselves
14.2 Insulin Signaling: Phosphorylation Cascades Are Central to Many Signal-Transduction Processes
14.3 EGF Signaling: Signal-Transduction Pathways Are Poised to Respond
14.4 Many Elements Recur with Variation in Different Signal-Transduction Pathways
14.5 Defects in Signal-Transduction Pathways Can Lead to Cancer and Other Diseases
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
15.1 Metabolism Is Composed of Many Coupled, Interconnecting Reactions
15.2 ATP Is the Universal Currency of Free Energy in Biological Systems
15.3 The Oxidation of Carbon Fuels Is an Important Source of Cellular Energy
15.4 Metabolic Pathways Contain Many Recurring Motifs
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
16.1 Glycolysis Is an Energy-Conversion Pathway in Many Organisms
16.2 The Glycolytic Pathway Is Tightly Controlled
16.3 Glucose Can Be Synthesized from Noncarbohydrate Precursors
16.4 Gluconeogenesis and Glycolysis Are Reciprocally Regulated
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
17.1 The Pyruvate Dehydrogenase Complex Links Glycolysis to the Citric Acid Cycle
17.2 The Citric Acid Cycle Oxidizes Two-Carbon Units
17.3 Entry to the Citric Acid Cycle and Metabolism Through It Are Controlled
17.4 The Citric Acid Cycle Is a Source of Biosynthetic Precursors
17.5 The Glyoxylate Cycle Enables Plants and Bacteria to Grow on Acetate
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
18.1 Eukaryotic Oxidative Phosphorylation Takes Place in Mitochondria
18.2 Oxidative Phosphorylation Depends on Electron Transfer
18.3 The Respiratory Chain Consists of Four Complexes: Three Proton Pumps and a Physical Link to the Citric Acid Cycle
18.4 A Proton Gradient Powers the Synthesis of ATP
18.5 Many Shuttles Allow Movement Across Mitochondrial Membranes
18.6 The Regulation of Cellular Respiration Is Governed Primarily by the Need for ATP
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
19.1 Photosynthesis Takes Place in Chloroplasts
19.2 Light Absorption by Chlorophyll Induces Electron Transfer
19.3 Two Photosystems Generate a Proton Gradient and NADPH in Oxygenic Photosynthesis
19.4 A Proton Gradient across the Thylakoid Membrane Drives ATP Synthesis
19.5 Accessory Pigments Funnel Energy into Reaction Centers
19.6 The Ability to Convert Light into Chemical Energy Is Ancient
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
20.1 The Calvin Cycle Synthesizes Hexoses from Carbon Dioxide and Water
20.2 The Activity of the Calvin Cycle Depends on Environmental Conditions
20.3 The Pentose Phosphate Pathway Generates NADPH and Synthesizes Five-Carbon Sugars
20.4 The Metabolism of Glucose 6-Phosphate by the Pentose Phosphate Pathway Is Coordinated with Glycolysis
20.5 Glucose 6-Phosphate Dehydrogenase Plays a Key Role in Protection Against Reactive Oxygen Species
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
21.1 Glycogen Breakdown Requires the Interplay of Several Enzymes
21.2 Phosphorylase Is Regulated by Allosteric Interactions and Reversible Phosphorylation
21.3 Epinephrine and Glucagon Signal the Need for Glycogen Breakdown
21.4 Glycogen Is Synthesized and Degraded by Different Pathways
21.5 Glycogen Breakdown and Synthesis Are Reciprocally Regulated
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
22.1 Triacylglycerols Are Highly Concentrated Energy Stores
22.2 The Use of Fatty Acids as Fuel Requires Three Stages of Processing
22.3 Unsaturated and Odd-Chain Fatty Acids Require Additional Steps for Degradation
22.4 Fatty Acids Are Synthesized by Fatty Acid Synthase
22.5 The Elongation and Unsaturation of Fatty Acids Are Accomplished by Accessory Enzyme Systems
22.6 Acetyl CoA Carboxylase Plays a Key Role in Controlling Fatty Acid Metabolism
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
23.1 Proteins Are Degraded to Amino Acids
23.2 Protein Turnover Is Tightly Regulated
23.3 The First Step in Amino Acid Degradation Is the Removal of Nitrogen
23.4 Ammonium Ion Is Converted into Urea in Most Terrestrial Vertebrates
23.5 Carbon Atoms of Degraded Amino Acids Emerge as Major Metabolic Intermediates
23.6 Inborn Errors of Metabolism Can Disrupt Amino Acid Degradation
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
24.1 Nitrogen Fixation: Microorganisms Use ATP and a Powerful Reductant to Reduce Atmospheric Nitrogen to Ammonia
24.2 Amino Acids Are Made from Intermediates of the Citric Acid Cycle and Other Major Pathways
24.3 Feedback Inhibition Regulates Amino Acid Biosynthesis
24.4 Amino Acids Are Precursors of Many Biomolecules
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
25.1 The Pyrimidine Ring Is Assembled de Novo or Recovered by Salvage Pathways
25.2 Purine Bases Can Be Synthesized de Novo or Recycled by Salvage Pathways
25.3 Deoxyribonucleotides Are Synthesized by the Reduction of Ribonucleotides Through a Radical Mechanism
25.4 Key Steps in Nucleotide Biosynthesis Are Regulated by Feedback Inhibition
25.5 Disruptions in Nucleotide Metabolism Can Cause Pathological Conditions
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
26.1 Phosphatidate Is a Common Intermediate in the Synthesis of Phospholipids and Triacylglycerols
26.2 Cholesterol Is Synthesized from Acetyl Coenzyme A in Three Stages
26.3 The Complex Regulation of Cholesterol Biosynthesis Takes Place at Several Levels
26.4 Important Derivatives of Cholesterol Include Bile Salts and Steroid Hormones
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
27.1 Caloric Homeostasis Is a Means of Regulating Body Weight
27.2 The Brain Plays a Key Role in Caloric Homeostasis
27.3 Diabetes Is a Common Metabolic Disease Often Resulting from Obesity
27.4 Exercise Beneficially Alters the Biochemistry of Cells
27.5 Food Intake and Starvation Induce Metabolic Changes
27.6 Ethanol Alters Energy Metabolism in the Liver
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
28.1 DNA Replication Proceeds by the Polymerization of Deoxyribonucleoside Triphosphates Along a Template
28.2 DNA Unwinding and Supercoiling Are Controlled by Topoisomerases
28.3 DNA Replication Is Highly Coordinated
28.4 Many Types of DNA Damage Can Be Repaired
28.5 DNA Recombination Plays Important Roles in Replication, Repair, and Other Processes
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
29.1 RNA Polymerases Catalyze Transcription
29.2 Transcription in Eukaryotes Is Highly Regulated
29.3 The Transcription Products of Eukaryotic Polymerases Are Processed
29.4 The Discovery of Catalytic RNA Was Revealing in Regard to Both Mechanism and Evolution
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
30.1 Protein Synthesis Requires the Translation of Nucleotide Sequences into Amino Acid Sequences
30.2 Aminoacyl Transfer RNA Synthetases Read the Genetic Code
30.3 The Ribosome Is the Site of Protein Synthesis
30.4 Eukaryotic Protein Synthesis Differs from Bacterial Protein Synthesis Primarily in Translation Initiation
30.5 A Variety of Antibiotics and Toxins Can Inhibit Protein Synthesis
30.6 Ribosomes Bound to the Endoplasmic Reticulum Manufacture Secretory and Membrane Proteins
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
31.1 Many DNA-Binding Proteins Recognize Specific DNA Sequences
31.2 Prokaryotic DNA-Binding Proteins Bind Specifically to Regulatory Sites in Operons
31.3 Regulatory Circuits Can Result in Switching Between Patterns of Gene Expression
31.4 Gene Expression Can Be Controlled at Posttranscriptional Levels
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
32.1 Eukaryotic DNA Is Organized into Chromatin
32.2 Transcription Factors Bind DNA and Regulate Transcription Initiation
32.3 The Control of Gene Expression Can Require Chromatin Remodeling
32.4 Eukaryotic Gene Expression Can Be Controlled at Posttranscriptional Levels
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
33.1 A Wide Variety of Organic Compounds Are Detected by Olfaction
33.2 Taste Is a Combination of Senses That Function by Different Mechanisms
33.3 Photoreceptor Molecules in the Eye Detect Visible Light
33.4 Hearing Depends on the Speedy Detection of Mechanical Stimuli
33.5 Touch Includes the Sensing of Pressure, Temperature, and Other Factors
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
34.1 Antibodies Possess Distinct Antigen-Binding and Effector Units
34.2 Antibodies Bind Specific Molecules Through Hypervariable Loops
34.3 Diversity Is Generated by Gene Rearrangements
34.4 Major-Histocompatibility-Complex Proteins Present Peptide Antigens on Cell Surfaces for Recognition by T-Cell Receptors
34.5 The Immune System Contributes to the Prevention and the Development of Human Diseases
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
35.1 Most Molecular-Motor Proteins Are Members of the P-Loop NTPase Superfamily
35.2 Myosins Move Along Actin Filaments
35.3 Kinesin and Dynein Move Along Microtubules
35.4 A Rotary Motor Drives Bacterial Motion
SUMMARY
KEY TERMS
PROBLEMS
Chapter Introduction
36.1 The Development of Drugs Presents Huge Challenges
36.2 Drug Candidates Can Be Discovered by Serendipity, Screening, or Design
36.3 Analyses of Genomes Hold Great Promise for Drug Discovery
36.4 The Clinical Development of Drugs Proceeds Through Several Phases
SUMMARY
KEY TERMS
PROBLEMS
Chapter 1
Chapter 2
Chapter 3
Chapter 4
Chapter 5
Chapter 6
Chapter 7
Chapter 8
Chapter 9
Chapter 10
Chapter 11
Chapter 12
Chapter 13
Chapter 14
Chapter 15
Chapter 16
Chapter 17
Chapter 18
Chapter 19
Chapter 20
Chapter 21
Chapter 22
Chapter 23
Chapter 24
Chapter 25
Chapter 26
Chapter 27
Chapter 28
Chapter 29
Chapter 30
Chapter 31
Chapter 32
Chapter 33
Chapter 34
Chapter 35
Chapter 36
Chapter 2
Chapter 3
Chapter 4
Chapter 5
Chapter 6
Chapter 7
Chapter 8
Chapter 9
Chapter 10
Chapter 11
Chapter 12
Chapter 13
Chapter 14
Chapter 15
Chapter 16
Chapter 17
Chapter 18
Chapter 19
Chapter 20
Chapter 21
Chapter 22
Chapter 23
Chapter 24
Chapter 25
Chapter 26
Chapter 27
Chapter 28
Chapter 29
Chapter 30
Chapter 31
Chapter 32
Chapter 33
Chapter 34
Chapter 35
Chapter 36
Index
ACIDITY CONSTANTS
STANDARD BOND LENGTHS