4. The Three-Dimensional Structure of Proteins 
4.1 Overview of Protein Structure 
4.2 Protein Secondary Structure 
Box 4–1 Methods: Knowing the Right Hand from the Left  
4.3 Protein Tertiary and Quaternary Structures 
Box 4–2 Permanent Waving Is Biochemical Engineering 
Box 4–3 Why Sailors, Explorers, and College Students Should Eat Their Fresh Fruits and Vegetables 
Box 4–4 The Protein Data Bank 
Box 4–5 Methods: Methods for Determining the Three-Dimensional Structure of a Protein 
4.4 Protein Denaturation and Folding 
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 
Box 5–1 Medicine: Carbon Monoxide: A Stealthy Killer
5.2 Complementary Interactions between Proteins and Ligands: The Immune System and Immunoglobulins 
5.3 Protein Interactions Modulated by Chemical Energy: Actin, Myosin, and Molecular Motors  

6. Enzymes 
6.1 An Introduction to Enzymes 
6.2 How Enzymes Work 
6.3 Enzyme Kinetics as an Approach to Understanding Mechanism 
Box 6–1 Transformations of the Michaelis-Menten Equation: The Double-Reciprocal Plot
Box 6–2 Kinetic Tests for Determining Inhibition Mechanisms 
Box 6–3 Curing African Sleeping Sickness with a Biochemical Trojan Horse 
6.4 Examples of Enzymatic Reactions 
6.5 Regulatory Enzymes 

7. Carbohydrates and Glycobiology 
7.1 Monosaccharides and Disaccharides 
Box 7–1 Medicine: Blood Glucose Measurements in the Diagnosis and Treatment of Diabetes
Box 7–2 Sugar Is Sweet, and So Are . . . a Few Other Things 
7.2 Polysaccharides 
7.3 Glycoconjugates: Proteoglycans, Glycoproteins, and Glycolipids 
7.4 Carbohydrates as Informational Molecules: The Sugar Code  
7.5 Working with Carbohydrates  

8. Nucleotides and Nucleic Acids  
8.1 Some Basics 
8.2 Nucleic Acid Structure 
8.3 Nucleic Acid Chemistry 
8.4 Other Functions of Nucleotides  

9.  DNA-Based Information Technologies 
9.1 Studying Genes and Their Products 
Box 9–1 A Powerful Tool in Forensic Medicine 
9.2 Using DNA-Based Methods to Understand Protein Function 
9.3 Genomics and the Human Story 
Box 9–2 Medicine: Personalized Genomic Medicine 
Box 9–3 Getting to Know the Neanderthals  

10. Lipids 
10.1 Storage Lipids 
10.2 Structural Lipids in Membranes 
Box 10–1 Medicine: Abnormal Accumulations of Membrane Lipids: Some Inherited Human Diseases 
10.3 Lipids as Signals, Cofactors, and Pigments  
10.4 Working with Lipids 

11. Biological Membranes and Transport  
11.1 The Composition and Architecture of Membranes 
11.2 Membrane Dynamics 
11.3 Solute Transport across Membranes 
Box 11–1 Medicine: Defective Glucose and Water Transport in Two Forms of Diabetes
Box 11–2 Medicine: A Defective Ion Channel in Cystic Fibrosis

12. Biosignaling 
12.1 General Features of Signal Transduction 
Box 12–1 Methods Scatchard Analysis Quantifies the Receptor-Ligand Interaction 
12.2 Protein–Coupled Receptors and Second Messengers 
Box 12–2 Medicine: G Proteins: Binary Switches in Health and Disease 
Box 12–3 Methods: FRET: Biochemistry Visualized in a Living Cell 
12.3 Receptor Tyrosine Kinases 
12.4 Receptor Guanylyl Cyclases, cGMP, and Protein Kinase G 
12.5 Multivalent Adaptor Proteins and Membrane Rafts 
12.6 Gated Ion Channels 
12.7 Integrins: Bidirectional Cell Adhesion Receptors 
12.8 Regulation of Transcription by Nuclear Hormone Receptors 
12.9 Signaling in Microorganisms and Plants 
12.10 Sensory Transduction in Vision, Olfaction, and Gustation 
Box 12–4 Medicine: Color Blindness: John Dalton’s Experiment from the Grave 
12.11 Regulation of the Cell Cycle by Protein Kinases 
12.12 Oncogenes, Tumor Suppressor Genes, and Programmed Cell Death 
Box 12–5 Medicine: Development of Protein Kinase Inhibitors for Cancer Treatment 

13. Bioenergetics and Biochemical Reaction Types 
13.1 Bioenergetics and Thermodynamics 
13.2 Chemical Logic and Common Biochemical Reactions 
13.3 Phosphoryl Group Transfers and ATP 
Box 13–1 Firefly Flashes: Glowing Reports of ATP 
13.4 Biological Oxidation-Reduction Reactions 

14. Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway 
14.1 Glycolysis 
Box 14–1 Medicine: High Rate of Glycolysis in Tumors Suggests Targets for Chemotherapy and Facilitates Diagnosis  
14.2 Feeder Pathways for Glycolysis 
14.3 Fates of Pyruvate under Anaerobic Conditions: Fermentation 
Box 14–2 Athletes, Alligators, and Coelacanths: Glycolysis at Limiting Concentrations of Oxygen 
Box 14–3 Ethanol Fermentations: Brewing Beer and Producing Biofuels
14.4 Gluconeogenesis 
14.5 Pentose Phosphate Pathway of Glucose Oxidation 
Box 14–4 Medicine: Why Pythagoras Wouldn’t Eat Falafel: Glucose 6-Phosphate Dehydrogenase Deficiency 

15. Principles of Metabolic Regulation 
15.1 Regulation of Metabolic Pathways 
15.2 Analysis of Metabolic Control  
Box 15–1 Methods: Metabolic Control Analysis: Quantitative Aspects 
15.3 Coordinated Regulation of Glycolysis and Gluconeogenesis 
Box 15–2 Isozymes: Different Proteins That Catalyze the Same Reaction 
Box 15–3 Medicine: Genetic Mutations That Lead to Rare Forms of Diabetes 
15.4 The Metabolism of Glycogen in Animals 
Box 15–4 Carl and Gerty Cori: Pioneers in Glycogen Metabolism and Disease 
15.5 Coordinated Regulation of Glycogen Synthesis and Breakdown 

16. The Citric Acid Cycle 
16.1 Production of Acetyl-CoA (Activated Acetate) 
16.2 Reactions of the Citric Acid Cycle 
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! 
Box 16–3 Citrate: A Symmetric Molecule That Reacts Asymmetrically 
16.3 Regulation of the Citric Acid Cycle 
16.4 The Glyoxylate Cycle 

17. Fatty Acid Catabolism 
17.1 Digestion, Mobilization, and Transport of Fats 
17.2 Oxidation of Fatty Acids 
Box 17–1 Fat Bears Carry Out β Oxidation in Their Sleep 
Box 17–2 Coenzyme B12: A Radical Solution to a Perplexing Problem  
17.3 Ketone Bodies  

18. Amino Acid Oxidation and the Production of Urea 
18.1 Metabolic Fates of Amino Groups 
18.2 Nitrogen Excretion and the Urea Cycle 
Box 18–1 Medicine: Assays for Tissue Damage 
18.3 Pathways of Amino Acid Degradation 
Box 18–2 Medicine:Scientific Sleuths Solve a Murder Mystery  

19.  Oxidative Phosphorylation and Photophosphorylation Oxidative Phosphorylation 
19.1 Electron-Transfer Reactions in Mitochondria 
Box 19–1 Hot, Stinking Plants and Alternative Respiratory Pathways  
19.2 ATP Synthesis 
Box 19–2 Methods: Atomic Force Microscopy to Visualize Membrane Proteins  
19.3 Regulation of Oxidative Phosphorylation 
19.4 Mitochondria in Thermogenesis, Steroid Synthesis, and Apoptosis 
19.5 Mitochondrial Genes: Their Origin and the Effects of Mutations  
Photosynthesis: Harvesting Light Energy
19.6 General Features of Photophosphorylation 
19.7 Light Absorption 
19.8 The Central Photochemical Event: Light-Driven Electron Flow  
19.9 ATP Synthesis by Photophosphorylation 
19.10 The Evolution of Oxygenic Photosynthesis 

20. Carbohydrate Biosynthesis in Plants and Bacteria  
20.1 Photosynthetic Carbohydrate Synthesis 
20.2 Photorespiration and the C4 and CAM Pathways 
Box 20–1 Will Genetic Engineering of Photosynthetic Organisms Increase Their Efficiency?
20.3 Biosynthesis of Starch and Sucrose 
20.4 Synthesis of Cell Wall Polysaccharides: Plant Cellulose and Bacterial Peptidoglycan 
20.5 Integration of Carbohydrate Metabolism in the Plant Cell  

21. Lipid Biosynthesis 
21.1 Biosynthesis of Fatty Acids and Eicosanoids 
Box 21–1 Medicine: Mixed-Function Oxidases, Cytochrome P-450s and Drug Overdoses 
21.2 Biosynthesis of Triacylglycerols 
21.3 Biosynthesis of Membrane Phospholipids 
21.4 Cholesterol, Steroids, and Isoprenoids: Biosynthesis, Regulation, and Transport  
Box 21–2 Medicine: ApoE Alleles Predict Incidence of Alzheimer’s Disease 
Box 21–3 Medicine: The Lipid Hypothesis and the Development of Statins 

22. Biosynthesis of Amino Acids, Nucleotides, and Related Molecules 
22.1 Overview of Nitrogen Metabolism 
Box 22–1 Unusual Lifestyles of the Obscure but Abundant 
22.2 Biosynthesis of Amino Acids 
22.3 Molecules Derived from Amino Acids 
Box 22–2 On Kings and Vampires 
22.4 Biosynthesis and Degradation of Nucleotides 

23. Hormonal Regulation and Integration of Mammalian Metabolism  
23.1 Hormones: Diverse Structures for Diverse Functions 
Box 23–1 Medicine: How Is a Hormone Discovered? The Arduous Path to Purified Insulin 
23.2 Tissue-Specific Metabolism: The Division of Labor 
Box 23–2 Creatine and Creatine Kinase: Invaluable Diagnostic Aids and the Muscle Builder’s Friends 
23.3 Hormonal Regulation of Fuel Metabolism 
23.4 Obesity and the Regulation of Body Mass 
23.5 Obesity, the Metabolic Syndrome, and Type 2 Diabetes 

24. Genes and Chromosomes 
24.1 Chromosomal Elements 
24.2 DNA Supercoiling 
Box 24–1 Medicine: Curing Disease by Inhibiting Topoisomerases 
24.3 The Structure of Chromosomes 
Box 24–2 Medicine: Epigenetics, Nucleosome Structure, and Histone Variants 

25. DNA Metabolism 
25.1 DNA Replication 
25.2 DNA Repair 
Box 25–1 Medicine: DNA Repair and Cancer 
25.3 DNA Recombination 
Box 25–2 Medicine:Why Proper Chromosomal Segregation Matters 

26. RNA Metabolism 
26.1 DNA-Dependent Synthesis of RNA 
Box 26–1 Methods: RNA Polymerase Leaves Its Footprint on a Promoter  
26.2 RNA Processing  
26.3 RNA-Dependent Synthesis of RNA and DNA  
Box 26–2 Medicine: Fighting AIDS with Inhibitors of HIV Reverse Transcriptase 
Box 26–3 Methods: The SELEX Method for Generating RNA Polymers with New Functions 
Box 26–4 An Expanding RNA Universe Filled with TUF RNAs 

27. Protein Metabolism 
27.1 The Genetic Code 
Box 27–1 Exceptions That Prove the Rule: Natural Variations in the Genetic Code 
27.2 Protein Synthesis 
Box 27–2 From an RNA World to a Protein World 
Box 27–3 Natural and Unnatural Expansion of the Genetic Code 
Box 27–4 Induced Variation in the Genetic Code: Nonsense Suppression  
27.3 Protein Targeting and Degradation 

28. Regulation of Gene Expression  
28.1 Principles of Gene Regulation  
28.2 Regulation of Gene Expression in Bacteria 
28.3 Regulation of Gene Expression in Eukaryotes 
Box 28–1 Of Fins, Wings, Beaks, and Things 

Appendix A Common Abbreviations in the Biochemical Research Literature
Appendix B Abbreviated Solutions to Problems
Glossary
Credits
Index

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