Preface xii
Acknowledgments xv
PART I INTRODUCTION
1 Life, Cell and Thermodynamics 1
1 The Origin of Life 2
2 Cellular Architecture 5
3 Thermodynamics 11
2 Physical and Chemical Properties of Water 23
1 Physical Properties of Water 24
2 Chemical Properties of Water 31
PART I I BIOMOLECULES
3 Overview of DNA Structure, Function, and Engineering 42
1 Nucleotides 43
2 Introduction to Nucleic Acid Structure 46
3 Overview of Nucleic Acid Function 50
4 Nucleic Acid Sequencing 53
5 Manipulating DNA 66
4 Amino Acids 80
1 Amino Acid Structure 81
2 Stereochemistry 88
3 Amino Acid Derivatives 91
5 Polypeptide Analysis, Sequencing and Evolution 97
1 Polypeptide Diversity 98
2 Protein Purifi cation and Analysis 99
3 Protein Sequencing 110
4 Protein Evolution 119
6 Proteins: Structure and Folding 131
1 Secondary Structure 132
2 Tertiary Structure 145
3 Quaternary Structure and Symmetry 158
4 Protein Stability 160
5 Protein Folding 165
7 Physiological Activities of Proteins 180
1 Oxygen Binding to Myoglobin and Hemoglobin 181
2 Muscle Contraction 200
3 Antibodies 212
8 Saccharide Chemistry 221
1 Monosaccharides 222
2 Polysaccharides 228
3 Glycoproteins 234
9 Lipids, Bilayer and Membranes 245
1 Lipid Classifi cation 246
2 Lipid Bilayers 259
3 Membrane Proteins 262
4 Membrane Structure and Assembly 269
10 Passive and Active Transport 293
1 Thermodynamics of Transport 294
2 Passive-Mediated Transport 295
3 Active Transport 309
PART I I I ENZYMES
11 Mechanisms of Enzyme Action 322
1 General Properties of Enzymes 323
2 Activation Energy and the Reaction Coordinate 327
3 Catalytic Mechanisms 330
4 Lysozyme 339
5 Serine Proteases 345
12 Properties of Enzymes 361
1 Reaction Kinetics 362
2 Enzyme Inhibition 374
3 Control of Enzyme Activity 382
4 Drug Design 391
13 Hormones and Signal Transduction 402
1 Hormones 403
2 Receptor Tyrosine Kinases 408
3 Heterotrimeric G Proteins 423
4 The Phosphoinositide Pathway 432
PART IV METABOLISM
14 Bioenergetics 442
1 Overview of Metabolism 443
2 “High-Energy” Compounds 452
3 Oxidation–Reduction Reactions 462
4 Experimental Approaches to the Study of Metabolism 468
15 Glycolysis and the Pentose Phosphate Pathway 478
1 Overview of Glycolysis 479
2 The Reactions of Glycolysis 481
3 Fermentation: The Anaerobic Fate of Pyruvate 497
4 Regulation of Glycolysis 502
5 Metabolism of Hexoses Other than Glucose 508
6 The Pentose Phosphate Pathway 512
16 Additional Pathways in Carbohydrate Metabolism 523
1 Glycogen Breakdown 524
2 Glycogen Synthesis 532
3 Control of Glycogen Metabolism 536
4 Gluconeogenesis 544
5 Other Carbohydrate Biosynthetic Pathways 551
17 The Citric Acid Cycle 558
1 Overview of the Citric Acid Cycle 559
2 Synthesis of Acetyl-Coenzyme A 562
3 Enzymes of the Citric Acid Cycle 568
4 Regulation of the Citric Acid Cycle 575
5 Reactions Related to the Citric Acid Cycle 579
18 Mitochondrial ATP Synthesis 588
1 The Mitochondrion 589
2 Electron Transport 593
3 Oxidative Phosphorylation 609
4 Control of Oxidative Metabolism 620
19 Photosynthesis 630
1 Chloroplasts 631
2 The Light Reactions 635
3 The Dark Reactions 651
20 Synthesis and Degradation of lipids 664
1 Lipid Digestion, Absorption, and Transport 664
2 Fatty Acid Oxidation 671
3 Ketone Bodies 685
4 Fatty Acid Biosynthesis 686
5 Regulation of Fatty Acid Metabolism 697
6 Synthesis of Other Lipids 700
7 Cholesterol Metabolism 706
21 Synthesis and Degradation of Amino Acids 718
1 Protein Degradation 719
2 Amino Acid Deamination 724
3 The Urea Cycle 728
4 Breakdown of Amino Acids 733
5 Amino Acid Biosynthesis 746
6 Other Products of Amino Acid Metabolism 758
7 Nitrogen Fixation 764
22 Regulation of Fuel Metabolism 773
1 Organ Specialization 774
2 Hormonal Control of Fuel Metabolism 781
3 Metabolic Homeostasis: The Regulation of Energy Metabolism, Appetite, and Body Weight 786
4 Disturbances in Fuel Metabolism 790
PART V GENE EXPRESSION AND REPLICATION
23 Nucleotide Synthesis and Degradation 802
1 Synthesis of Purine Ribonucleotides 802
2 Synthesis of Pyrimidine Ribonucleotides 809
3 Formation of Deoxyribonucleotides 812
4 Nucleotide Degradation 820
24 DNA structure and Interactions with Proteins 831
1 The DNA Helix 832
2 Forces Stabilizing Nucleic Acid Structures 848
3 Fractionation of Nucleic Acids 856
4 DNA–Protein Interactions 859
5 Eukaryotic Chromosome Structure 868
25 DNA Synthesis and Repair 879
1 Overview of DNA Replication 880
2 Prokaryotic DNA Replication 882
3 Eukaryotic DNA Replication 898
4 DNA Damage 904
5 DNA Repair 909
6 Recombination 916
26 RNA Metabolism 938
1 Prokaryotic RNA Transcription 939
2 Transcription in Eukaryotes 948
3 Posttranscriptional Processing 961
27 The Genetic Code and Translation 982
1 The Genetic Code 983
2 Transfer RNA and Its Aminoacylation 988
3 Ribosomes 996
4 Translation 1004
5 Posttranslational Processing 1024
28 Gene Expression in Prokaryotes and Eukaryotes 1033
1 Genome Organization 1034
2 Regulation of Prokaryotic Gene Expression 1043
3 Regulation of Eukaryotic Gene Expression 1052
4 The Cell Cycle, Cancer, Apoptosis, and Development 1080
Glossary G-1 Index I-1
SOLUTIONS to Odd-Numbered Problems SP-1
