Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology, 2nd Edition
Now in its second edition, Biochemical Pathways continues to garner praise from students, instructors, and researchers for its clear, full-color illustrations of the pathways and networks that determine biological function.
Biochemical Pathways examines the biochemistry of bacteria, plants, and animals. It offers a quick overview of the metabolic sequences in biochemical pathways, the chemistry and enzymology of conversions, the regulation of turnover, the expression of genes, the immunological interactions, and the metabolic background of health disorders. A standard set of conventions is used in all illustrations, enabling readers to easily gather information and compare the key elements of different biochemical pathways. For both quick and in-depth understanding, the book uses a combination of:
Illustrations integrating many different features of the reactions and their interrelationships
Tables listing the important system components and their function
Text supplementing and expanding on the illustrated facts
In the second edition, the volume has been expanded by 50 percent. Text and figures have undergone a thorough revision and update, reflecting the tremendous progress in biochemical knowledge in recent years. A guide to the relevant biochemical databases facilitates access to the extensive documentation of scientific knowledge.
Biochemical Pathways, Second Edition is recommended for all students and researchers in such fields as biochemistry, molecular biology, medicine, organic chemistry, and pharmacology. The book’s illustrated pathways aids the reader in understanding the complex set of biochemical reactions that occur in biological systems.
Table of Contents
Preface to the Second Edition IX
From the Preface to the First Edition X
Contributors XI
1 Introduction and General Aspects 1 Gerhard Michal and Dietmar Schomburg
1.1 Organization of This Book 1
1.1.1 Conventions Used in This Book 3
1.1.2 Common Abbreviations 3
1.2 Carbohydrate Chemistry and Structure 4
1.2.1 Structure and Classification 4
1.2.2 Glycosidic Bonds 5
1.3 Amino Acid Chemistry and Structure 5
1.3.1 Structure and Classification 6
1.3.2 Peptide Bonds 6
1.4 Lipid Chemistry and Structure 6
1.4.1 Fatty acids 6
1.4.2 Acylglycerols and Derivatives 7
1.4.3 Waxes 7
1.4.4 Glycerophospholipids 7
1.4.5 Plasmalogens 7
1.4.6 Sphingolipids 7
1.4.7 Steroids 8
1.4.8 Lipoproteins 8
1.5 Physico-Chemical Aspects of Biochemical Processess 8
1.5.1 Energetics of Chemical Reactions 8
1.5.2 Redox Reactions 9
1.5.3 Transport Through Membranes 9
1.5.4 Enzyme Kinetics 10
2 The Cell and Its Contents 14 Gerhard Michal and Dietmar Schomburg
2.1 Classification of Living Organisms 14
2.2 Structure of Cells 14
2.2.1 Prokaryotic Cells 14
2.2.2 General Characteristics of Eukaryotic Cells 15
2.2.3 Special Structures of Plant Cells 17
2.2.4 Special Structures of Animal Cells 18
2.3 Protein Structure and Function 18
2.3.1 Levels of Organization 19
2.3.2 Protein Function 21
2.4 Enzymes 21
2.4.1 Catalytic Mechanism 21
2.4.2 Isoenzymes 23
2.4.3 Multienzyme Complexes 23
2.4.4 Reaction Rate 23
2.4.5 Classification of Enzymes 23
2.5 Regulation of the Enzyme Activity 24
2.5.1 Regulation of the Quantity of Enzymes 24
2.5.2 Regulation of the Activity of Enzymes 24
2.5.3 Site of Regulation 26
2.6 Nucleic Acid Structure 26
2.6.1 Components of Nucleic Acids 26
2.6.2 Properties of RNA Chains 27
2.6.3 Properties of DNA Chains 27
2.6.4 Compaction Levels of DNA Chains 28
2.7 Genetic Code and the Flow of Information 30
2.7.1 From DNA to RNA 30
2.7.2 From Nucleic Acids to Proteins – The Genetic Code 30
2.7.3 Influence of Errors 31
2.8 Polymeric Carbohydrates 31
2.8.1 Polymeric Carbohydrates in Energy Storage 31
2.8.2 Polymeric Carbohydrates as Structural Elements 32
2.9 Glycosylated Proteins and Peptides 32
2.9.1 Glycoproteins 33
2.9.2 Proteoglycans 33
2.9.3 Peptidoglycans 35
2.10 Lipid Aggregates and Membranes 35
3 Metabolism 37
3.1 Carbohydrate Metabolism and Citrate Cycle 37 Röbbe Wünschiers
3.1.1 Glycolysis and Gluconeogenesis 37
3.1.2 Polysaccharide Metabolism 42
3.1.3 Pyruvate Turnover and Acetyl-Coenzyme A 46
3.1.4 Di- and Oligosaccharides 48
3.1.5 Metabolism of Hexose Derivatives 48
3.1.6 Pentose Metabolism 51
3.1.7 Amino Sugars 54
3.1.8 Citrate Cycle 55
3.1.9 Glyoxylate Metabolism 57
3.2 Amino Acids and Derivatives 58 Röbbe Wünschiers
3.2.1 Nitrogen Fixation and Metabolism 58
3.2.2 Glutamate, Glutamine, Alanine, Aspartate, Asparagine and Ammonia Turnover 59
3.2.3 Proline and Hydroxyproline 62
3.2.4 Serine and Glycine 62
3.2.5 Lysine, Threonine, Methionine, Cysteine and Sulfur Metabolism 65
3.2.6 Leucine, Isoleucine and Valine 72
3.2.7 Phenylalanine, Tyrosine, Tryptophan and Derivatives 74
3.2.8 Histidine 79
3.2.9 Urea Cycle, Arginine and Associated Reactions 80
3.3 Tetrapyrroles 82 Martina Jahn and Dieter Jahn
3.3.1 Pathways for the Biosynthesis of Tetrapyrroles 82
3.3.2 Heme and Cytochrome Biosynthesis 86
3.3.3 Linear Tetrapyrroles 87
3.3.4 Biosynthesis of Chlorophylls 90
3.3.5 Biosynthesis of Cobalamins 91
3.3.6 Siroheme Biosynthesis 91
3.4 Lipids and Glycolipids 93 Röbbe Wünschiers
3.4.1 Fatty Acids and Acyl-CoA 93
3.4.2 Triacylglycerols (Triglycerides) 98
3.4.3 Phospholipids 100
3.4.4 Glycolipids 104
3.5 Steroids and Isoprenoids 107 Röbbe Wünschiers
3.5.1 Cholesterol 107
3.5.2 Hopanoids, Steroids of Plants and Insects 110
3.5.3 Isoprenoids 111
3.5.4 Steroid Hormones 114
3.5.5 Gestagen 115
3.5.6 Androgens 116
3.5.7 Estrogens 117
3.5.8 Corticosteroids 119
3.5.9 Bile Acids 121
3.6 Nucleotides and Nucleosides 124 Röbbe Wünschiers
3.6.1 Purine Nucleotides and Nucleosides 124
3.6.2 Pyrimidine Nucleotides and Nucleosides 130
3.7 Cofactors and Vitamins 133 Ida Schomburg
3.7.1 Retinol (Vitamin A) 133
3.7.2 Thiamin (Vitamin B1) 134
3.7.3 Riboflavin (Vitamin B2), FMN and FAD 135
3.7.4 Pyridoxine (Vitamin B6) 136
3.7.5 Cobalamin (Coenzyme B12, Vitamin B12) 137
3.7.6 Folate and Pterines 138
3.7.7 Pantothenate, Coenzyme A and Acyl Carrier Protein (ACP) 141
3.7.8 Biotin 141
3.7.9 Nicotinate, NAD+ and NADP+ 143
3.7.10 Ascorbate (Vitamin C) 145
3.7.11 Calciferol (Vitamin D) 146
3.7.12 Tocopherol (Vitamin E) 148
3.7.13 Phylloquinone and Menaquinone (Vitamin K) 148
3.7.14 Other Compounds 149
3.8 Nucleic Acid Metabolism in Bacteria 149 Susanne Peifer and Elmar Heinzle
3.8.1 Bacterial DNA Replication 149
3.8.2 Bacterial DNA Repair 151
3.8.3 Degradation of Nucleic Acids 156
3.9 Nucleic Acid Metabolism in Eukarya 157 Helmut Burtscher
3.9.1 Eukaryotic DNA Replication 157
3.9.2 Eukaryotic DNA Repair 162
3.10 Special Bacterial Metabolism and Biosynthesis of Antimicrobials 164 Julia Garbe, Annika Steen and Max Schobert
3.10.1 Bacterial Envelope 164
3.10.2 Bacterial Protein Export across the Cytoplasmic Membrane 166
3.10.3 Protein Transport across the Outer Membrane of Gram-Negative Bacteria 167
3.10.4 Bacterial Transport Systems 168
3.10.5 Bacterial Fermentations 169
3.10.6 Anaerobic Respiration 173
3.10.7 Chemolithotrophy 175
3.10.8 Quinoenzymes, Alkane and Methane Oxidation 178
3.10.9 Antibiotics 179
3.11 Electron Transfer Reactions and Oxidative Phosphorylation 183 Martina Jahn and Dieter Jahn
3.11.1 General Principles 183
3.11.2 Different types of electron transport chains 183
3.11.3 The Energetic Basis of the Oxidative Phosphorylation 183
3.11.4 Electron Transport System in Mitochondria and Bacteria 184
3.12 Photosynthesis 188 Dieter Oesterhelt and Josef Wachtveitl