Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology

Cover......Page 1
Title Page......Page 5
Copyright......Page 6
Preface......Page 11
Contributors......Page 13
Contents......Page 7
1.1 Organization of This Book......Page 14
1.1.2 Common Abbreviations......Page 16
1.2.1 Structure and Classification......Page 17
1.3 Amino Acid Chemistry and Structure......Page 18
1.4.1 Fatty acids......Page 19
1.4.6 Sphingolipids......Page 20
1.5.1 Energetics of Chemical Reactions......Page 21
1.5.3 Transport Through Membranes......Page 22
1.5.4 Enzyme Kinetics......Page 23
2.2.1 Prokaryotic Cells......Page 27
2.2.2 General Characteristics of Eukaryotic Cells......Page 28
2.2.3 Special Structures of Plant Cells......Page 30
2.3 Protein Structure and Function......Page 31
2.3.1 Levels of Organization......Page 32
2.4.1 Catalytic Mechanism......Page 34
2.4.5 Classification of Enzymes......Page 36
2.5.2 Regulation of the Activity of Enzymes......Page 37
2.6.1 Components of Nucleic Acids......Page 39
2.6.3 Properties of DNA Chains......Page 40
2.6.4 Compaction Levels of DNA Chains......Page 41
2.7.2 From Nucleic Acids to Proteins – The Genetic Code......Page 43
2.8.1 Polymeric Carbohydrates in Energy Storage......Page 44
2.9 Glycosylated Proteins and Peptides......Page 45
2.9.2 Proteoglycans......Page 46
2.10 Lipid Aggregates and Membranes......Page 48
3.1.1 Glycolysis and Gluconeogenesis......Page 50
3.1.2 Polysaccharide Metabolism......Page 55
3.1.3 Pyruvate Turnover and Acetyl-Coenzyme A......Page 59
3.1.5 Metabolism of Hexose Derivatives......Page 61
3.1.6 Pentose Metabolism......Page 64
3.1.7 Amino Sugars......Page 67
3.1.8 Citrate Cycle......Page 68
3.1.9 Glyoxylate Metabolism......Page 70
3.2.1 Nitrogen Fixation and Metabolism......Page 71
3.2.2 Glutamate, Glutamine, Alanine, Aspartate, Asparagine and Ammonia Turnover......Page 72
3.2.4 Serine and Glycine......Page 75
3.2.5 Lysine, Threonine, Methionine, Cysteine and Sulfur Metabolism......Page 78
3.2.6 Leucine, Isoleucine and Valine......Page 85
3.2.7 Phenylalanine, Tyrosine, Tryptophan and Derivatives......Page 87
3.2.8 Histidine......Page 92
3.2.9 Urea Cycle, Arginine and Associated Reactions......Page 93
3.3.1 Pathways for the Biosynthesis of Tetrapyrroles......Page 95
3.3.2 Heme and Cytochrome Biosynthesis......Page 99
3.3.3 Linear Tetrapyrroles......Page 100
3.3.4 Biosynthesis of Chlorophylls......Page 103
3.3.6 Siroheme Biosynthesis......Page 104
3.4.1 Fatty Acids and Acyl-CoA......Page 106
3.4.2 Triacylglycerols (Triglycerides)......Page 111
3.4.3 Phospholipids......Page 113
3.4.4 Glycolipids......Page 117
3.5.1 Cholesterol......Page 120
3.5.2 Hopanoids, Steroids of Plants and......Page 123
3.5.3 Isoprenoids......Page 124
3.5.4 Steroid Hormones......Page 127
3.5.5 Gestagen......Page 128
3.5.6 Androgens......Page 129
3.5.7 Estrogens......Page 130
3.5.8 Corticosteroids......Page 132
3.5.9 Bile Acids......Page 134
3.6.1 Purine Nucleotides and Nucleosides......Page 137
3.6.2 Pyrimidine Nucleotides and Nucleosides......Page 143
3.7.1 Retinol (Vitamin A)......Page 146
3.7.2 Thiamin (Vitamin B1)......Page 147
3.7.3 Riboflavin (Vitamin B2), FMN and FAD......Page 148
3.7.4 Pyridoxine (Vitamin B6)......Page 149
3.7.5 Cobalamin (Coenzyme B12, Vitamin B12)......Page 150
3.7.6 Folate and Pterines......Page 151
3.7.8 Biotin......Page 154
3.7.9 Nicotinate, NAD+ and NADP+......Page 156
3.7.10 Ascorbate (Vitamin C)......Page 158
3.7.11 Calciferol (Vitamin D)......Page 159
3.7.13 Phylloquinone and Menaquinone (Vitamin K)......Page 161
3.8.1 Bacterial DNA Replication......Page 162
3.8.2 Bacterial DNA Repair......Page 164
3.8.3 Degradation of Nucleic Acids......Page 169
3.9.1 Eukaryotic DNA Replication......Page 170
3.9.2 Eukaryotic DNA Repair......Page 175
3.10.1 Bacterial Envelope......Page 177
3.10.2 Bacterial Protein Export across the Cytoplasmic Membrane......Page 179
3.10.3 Protein Transport across the Outer Membrane of Gram-Negative Bacteria......Page 180
3.10.4 Bacterial Transport Systems......Page 181
3.10.5 Bacterial Fermentations......Page 182
3.10.6 Anaerobic Respiration......Page 186
3.10.7 Chemolithotrophy......Page 188
3.10.8 Quinoenzymes, Alkane and Methane Oxidation......Page 191
3.10.9 Antibiotics......Page 192
3.11.3 The Energetic Basis of the Oxidative Phosphorylation......Page 196
3.11.4 Electron Transport System in Mitochondria and Bacteria......Page 197
3.12.1 Light Reaction......Page 201
3.12.2 Dark Reactions......Page 205
3.13 Plant Secondary Metabolism......Page 206
3.13.1 Phenolics......Page 207
3.13.2 Terpenoids......Page 211
3.13.3 Nitrogen-containing Secondary Metabolites......Page 214
4.1.1 Bacterial Transcription......Page 223
4.1.2 Regulation of Bacterial Gene Expression......Page 225
4.1.3 Bacterial Protein Synthesis......Page 227
4.1.4 Degradation of Nucleic Acids......Page 230
4.2.1 Eukaryotic Transcription......Page 232
4.2.2 Regulation of Eukaryotic Transcription......Page 239
4.2.3 Eukaryotic Translation......Page 241
4.2.5 mRNA Degradation......Page 244
4.3.1 Core Components of the Cell Cycle Machinery......Page 245
4.3.3 G1 to S Transition in Mammalian Cells......Page 247
4.3.5 Mitosis in Mammalian Cells......Page 248
4.3.6 Cell Cycle Checkpoints......Page 249
4.4.1 Protein Processing in the Endoplasmic Reticulum......Page 251
4.4.2 Glycosylation Reactions in the Golgi Apparatus......Page 254
4.4.3 Terminal Carbohydrate Structures of Glycoconjugates......Page 256
4.5.1 Folding of Proteins......Page 257
4.5.2 Vesicular Transport and Secretion of Proteins......Page 261
4.5.3 Protein Transport into the Nucleus......Page 262
4.5.4 Protein Transport into Mitochondria......Page 265
4.5.5 Protein Transport into Chloroplasts......Page 267
4.5.6 Protein Degradation......Page 269
4.5.7 Protein Degradation by the Ubiquitin-Proteasome System......Page 271
5.1.1 Genomic Characteristics of Viruses......Page 274
5.1.2 Structure......Page 276
5.2.1 Papillomavirus......Page 277
5.3.1 Hepatitis C Virus......Page 280
5.4.1 Human Immunodeficiency Virus (HIV)......Page 281
6.1.2 Channels / Pores......Page 285
6.1.3 Solute Carriers......Page 289
6.1.4 Primary Active Transport Systems......Page 290
6.1.6 The Cytoskeleton as Means for Intracellular Transport and Cellular Movements in Eukarya......Page 291
6.2.2 Plasma Lipoprotein Metabolism......Page 292
6.2.4 Lipoprotein Receptors......Page 294
6.3.1 Biosynthesis and Properties of Hemoglobin and Myoglobin......Page 295
6.3.2 Oxygen Binding to Hemo- and Myoglobin......Page 296
6.3.3 Hemoglobin Diseases in Humans......Page 298
7.1.2 General Characteristics of Receptors......Page 299
7.1.5 Hypothalamus-Anterior Pituitary Hormone System......Page 300
7.1.6 Placental Hormones......Page 304
7.1.8 Hormones Regulating the Na+ Concentration and the Water Balance......Page 305
7.1.9 Hormones of the Gastrointestinal Tract......Page 306
7.2.3 Transmitter Gated Signalling at the Synapse......Page 307
7.3 Principles of Intracellular Communication......Page 309
7.4 Receptors Coupled to Heterotrimeric G-Proteins......Page 312
7.4.1 Mechanism of Heterotrimeric G-Protein Action......Page 313
7.4.3 Activation of Phospholipase C and Protein Kinase C......Page 315
7.4.4 Metabolic Role of Inositol Phosphates and Ca++......Page 316
7.4.5 Muscle Contraction......Page 318
7.4.6 Visual Process......Page 320
7.4.7 Olfactory and Gustatory Processes......Page 321
7.4.8 Arachidonate Metabolism and Eicosanoids......Page 322
7.5.2 Components of the Signal Cascades......Page 324
7.5.3 Receptor Tyrosine Kinases......Page 325
7.5.4. Tyrosine Kinase-Associated Receptors (TKaR)......Page 328
7.6 Programmed Cell Death (Apoptosis)......Page 332
7.7 Receptors for Steroid and Thyroid Hormones, for Retinoids and Vitamin D......Page 334
7.8 Cyclic GMP Dependent Pathways and Effects of Nitric Oxide (NO)......Page 335
7.8.3 Protein Kinase G......Page 336
8.1.1 Innate, Non Adaptive Immune System......Page 338
8.1.3 Development and Maturation of the Cellular Components......Page 341
8.1.4 Antigen Receptor of B Lymphocytes, Antibodies......Page 343
8.1.5 Complement System......Page 347
8.1.6 Antigen Receptor of T Lymphocytes......Page 349
8.1.7 Antigen Presentation by MHC Molecules......Page 350
8.1.8 Cytokines, Chemokines and Receptors......Page 351
8.2.1 Activation of T Cells......Page 356
8.2.2 CD4+ T Effector Cells, Regulation of the Immune Response......Page 357
8.2.4 Lymphocyte Circulation and Generation of Cellular and Humoral Immune Responses in Lymphoid Tissue......Page 358
8.2.5 Cellular Cytotoxicity and Apoptosis......Page 360
8.2.7 Immunological Tolerance......Page 363
8.2.8 Induction of Specific Immune Responses against Pathogens......Page 364
8.3.1 IgE-Mediated Hypersensitivity of the Immediate Type......Page 365
8.3.2 Autoimmunity......Page 366
8.4 Adhesion of Leukocytes......Page 367
9.1 Hemostasis......Page 370
9.2.3 Generation of Binding Surfaces......Page 371
9.3.3 Key Events......Page 372
9.3.4 Controlled Propagation......Page 373
9.3.5 Generation of Fibrin......Page 374
9.4 Platelets (Thrombocytes)......Page 375
9.5.1 Pathways of Plasminogen Activation......Page 377
9.5.2 Control of Fibrinolysis......Page 378
10.3.1 Overview......Page 379
10.3.2 Detailed Description of Some Databases......Page 380
Index......Page 387