Essential Biochemistry. 3rd Edition

Table of Contents

PART ONE FOUNDATIONS

1 THE CHEMICAL BASIS OF LIFE 1

1–1 What is Biochemistry? 2

1–2 Biological Molecules 3

1–3 Energy and Metabolism 10

1–4 The Origin and Evolution of Life 14

2 AQUEOUS CHEMISTRY 24

2–1 Water Molecules form Hydrogen Bonds 25

2–2 The Hydrophobic Effect 30

2–3 Acid Base Chemistry 33

2–4 Tools and Techniques: Buffers 41

PART TWO MOLECULAR STRUCTURE AND FUNCTION

3 FROM GENES TO PROTEINS 51

3–1 DNA Is the Genetic Material 52

3–2 Genes Encode Proteins 61

3–3 Genomics 65

3–4 Tools and Techniques: Manipulating DNA 70

4 PROTEIN STRUCTURE 87

4–1 Proteins Are Chains of Amino Acids 89

4–2 Secondary Structure: The Conformation of the Peptide Group 96

4–3 Tertiary Structure and Protein Stability 99

4–4 Quaternary Structure 107

4–5 Tools and Techniques: Analyzing Protein Structure 108

5 PROTEIN FUNCTION 121

5–1 Myoglobin and Hemoglobin: Oxygen–Binding Proteins 122

5–2 Structural Proteins 133

5–3 Motor Proteins 144

6 HOW ENZYMES WORK 158

6–1 What Is an Enzyme? 159

6–2 The Chemistry of Catalysis 162

6–3 The Unique Properties of Enzyme Catalysts 171

6–4 Some Additional Features of Enzymes 174

7 ENZYME KINETICS AND INHIBITION 188

7–1 Introduction to Enzyme Kinetics 189

7–2 Derivation and Meaning of the Michaelis Menten Equation 191

7–3 Enzyme Inhibition 200

8 LIPIDS AND MEMBRANES 220

8–1 Lipids 221

8–2 The Lipid Bilayer 227

8–3 Membrane Proteins 230

8–4 The Fluid Mosaic Model 233

9 MEMBRANE TRANSPORT 241

9–1 The Thermodynamics of Membrane Transport 242

9–2 Passive Transport 246

9–3 Active Transport 252

9–4 Membrane Fusion 255

10 SIGNALING 266

10–1 General Features of Signaling Pathways 267

10–2 G Protein Signaling Pathways 271

10–3 Receptor Tyrosine Kinases 277

10–4 Lipid Hormone Signaling 281

11 CARBOHYDRATES 290

11–1 Monosaccharides 291

11–2 Polysaccharides 294

11–3 Glycoproteins 299

PART THREE METABOLISM

12 METABOLISM AND BIOENERGETICS 308

12–1 Food and Fuel 309

12–2 Metabolic Pathways 314

12–3 Free Energy Changes in Metabolic Reactions 323

13 GLUCOSE METABOLISM 338

13–1 Glycolysis 339

13–2 Gluconeogenesis 354

13–3 Glycogen Synthesis and Degradation 357

13–4 The Pentose Phosphate Pathway 361

14 THE CITRIC ACID CYCLE 370

14–1 The Pyruvate Dehydrogenase Reaction 371

14–2 The Eight Reactions of the Citric Acid Cycle 374

14–3 Anabolic and Catabolic Functions of the Citric Acid Cycle 384

15 OXIDATIVE PHOSPHORYLATION 394

15–1 The Thermodynamics of Oxidation Reduction Reactions 395

15–2 Mitochondrial Electron Transport 399

15–3 Chemiosmosis 408

15–4 ATP Synthase 410

16 PHOTOSYNTHESIS 420

16–1 Chloroplasts and Solar Energy 422

16–2 The Light Reactions 425

16–3 Carbon Fixation 432

17 LIPID METABOLISM 442

17–1 Fatty Acid Oxidation 445

17–2 Fatty Acid Synthesis 453

17–3 Synthesis of Other Lipids 463

18 NITROGEN METABOLISM 475

18–1 Nitrogen Fixation and Assimilation 476

18–2 Amino Acid Biosynthesis 480

18–3 Nucleotide Biosynthesis 488

18–4 Amino Acid Catabolism 494

18–5 Nitrogen Disposal: The Urea Cycle 498

19 REGULATION OF MAMMALIAN FUEL METABOLISM 509

19–1 Integration of Fuel Metabolism 510

19–2 Hormonal Control of Fuel Metabolism 515

19–3 Disorders of Fuel Metabolism 520

PART FOUR GENETIC INFORMATION

20 DNA REPLICATION AND REPAIR 529

20–1 DNA Supercoiling 530

20–2 The DNA Replication Machinery 533

20–3 Telomeres 540

20–4 DNA Damage and Repair 543

20–5 DNA Packaging 552

21 TRANSCRIPTION AND RNA 561

21–1 Transcription Initiation 563

21–2 RNA Polymerase 571

21–3 RNA Processing 576

22 PROTEIN SYNTHESIS 590

22–1 tRNA Aminoacylation 592

22–2 Ribosome Structure 596

22–3 Translation 599

22–4 Post–translational Events 608

GLOSSARY 617

SOLUTIONS 629

ANSWERS TO PRACTICE PROBLEMS PP–1

ANSWERS TO CLINICAL CONNECTION

QUESTIONS CC–1

INDEX I–1

Authors

Charlott Pratt received her Ph.D. in biochemistry from Duke University. She did post–doctoral research at the University of North Carolina at Chapel Hill and has contributed to numerous primary research articles and reviews. She is presently in the Department of Chemistry at Seattle Pacific University. She is co–author with Donald Voet and Judith Voet of Fundamentals of Biochemistry, also published by Wiley.

Kathleen Cornely received her Ph.D. in biochemistry from Cornell University. She has published numerous research articles and is presently Professor in the Department of Chemistry and Biochemistry at Providence College. She is a member of the Educational and Professional Development Committee of the American Society for Biochemistry and Molecular Biology and is on the editorial borad for the journal, Biochemistry and Molecular Biology Education.