Microbial Biochemistry (eBook)

G.N. Cohen (Autor)

eBook Download: PDF

2011 | 2nd ed. 2011
XXVIII, 558 Seiten
Springer Netherland (Verlag)
978-90-481-9437-7 (ISBN)

Infos

Microbial physiology, biochemistry, and genetics allowed the formulation of concepts that turned out to be important in the study of higher organisms. In the first section, the principles of bacterial growth are given, as well as the description of the different layers that enclose the bacterial cytoplasm, and their role in obtaining nutrients from the outside media through different permeability mechanism described in detail. A chapter is devoted to allostery and is indispensable for the comprehension of many regulatory mechanisms described throughout the book. Another section analyses the mechanisms by which cells obtain the energy necessary for their growth, glycolysis, the pentose phosphate pathway, the tricarboxylic and the anaplerotic cycles. Two chapters are devoted to classes of microorganisms rarely dealt with in textbooks, namely the Archaea, mainly the methanogenic bacteria, and the methylotrophs. Eight chapters describe the principles of the regulations at the transcriptional level, with the necessary knowledge of the machineries of transcription and translation. The next fifteen chapters deal with the biosynthesis of the cell building blocks, amino acids, purine and pyrimidine nucleotides and deoxynucleotides, water-soluble vitamins and coenzymes, isoprene and tetrapyrrole derivatives and vitamin B12. The two last chapters are devoted to the study of protein-DNA interactions and to the evolution of biosynthetic pathways. The considerable advances made in the last thirty years in the field by the introduction of gene cloning and sequencing and by the exponential development of physical methods such as X-ray crystallography or nuclear magnetic resonance have helped presenting metabolism under a multidisciplinary attractive angle. The level of readership presupposes some knowledge of chemistry and genetics at the undergraduate level. The target group is graduate students, researchers in academia and industry.

Inhalt

Foreword 6
Contents 8
Abbreviations 22
Introduction 28
Chapter 1: Bacterial Growth 30
The Lag Phase 30
The Exponential Phase 30
Linear Growth 31
The Yield of Growth 32
Variation of the Growth Rate at Limiting Carbon Source Concentrations 33
Continuous Growth: The Chemostat 34
Advantages of the Continuous Exponential Culture 36
Diauxic Growth 36
Selected References 39
Bacterial Growth: Diauxie 39
Linear Growth 39
Continuous Growth: The Chemostat 39
Influence of Growth Rate on Cellular Constituents 39
Adaptive (Inducible) Enzymes: Prehistory 39
Chapter 2: The Outer Membrane of Gram-negative Bacteria and the Cytoplasmic Membrane 40
The Outer Membrane of Gram-Negative Bacteria 40
The Cytoplasmic Membrane 41
Energy Generation 42
ATP Synthase 42
Subunit Composition of the ATP Synthase 43
ATP Synthesis in Archaea 45
Selected References 45
ATP Synthase 45
Chapter 3: Peptidoglycan Synthesis and Cell Division 46
General Structure 46
Assembly of the Peptidoglycan Unit 47
The Membrane Steps 48
Assembly of the Murein Sacculus 49
Penicillin Sensitivity 49
Cell Division 50
Selected References 51
Cell Division 51
Chapter 4: Cellular Permeability 52
Accumulation, Crypticity, and Selective Permeability 53
beta-Galactoside Permease 54
Accumulation in Induced Cells: Kinetics and Specificity 55
The Induced Synthesis of Galactoside Permease 58
Functional Significance of Galactoside Permease: Specific Crypticity 59
Functional Relationships of Permease: Induction 61
Genetic Relationships of Galactosidase and Galactoside Permease 61
Galactoside Permease as Protein 62
Periplasmic Binding Proteins and ATP Binding Cassettes 65
Phosphotransferases: The PTS System 68
TRAP Transporters 70
A Few Well-identified Cases of Specific Cellular Permeability 71
Amino Acid Permeases 71
Peptide Permeases 72
Porins 74
Iron Uptake 76
Conclusion 77
Selected References 77
beta-Galactoside Permease 77
Amino Acid Permeases 77
Periplasmic Proteins and ATP-Binding Cassettes 77
Phosphotransferase System 78
Peptide Permeaes 78
TRAP Transporters 78
Porins 78
Chapter 5: Allosteric Enzymes 79
Allosteric Inhibition and Activation 82
An Alternative Model 89
Conclusion 90
Selected References 90
Chapter 6: Glycolysis, Gluconeogenesis and Glycogen Synthesis 91
Glycogen Degradation 91
Glycolysis 91
Hexokinase 93
Glucose 6-Phosphate Isomerase 93
Phosphofructokinase 94
A Second Phosphorylation Follows the Isomerization Step 94
Regulation of Phosphofructokinase in Bacteria 95
Fructose 1,6-Bisphosphate Aldolase 96
Triose Phosphate Isomerase 96
As for the Preceding Enzyme, This One Is not Subject to Metabolic Regulation 96
Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) 96
Phosphoglycerate Kinase 97
Phosphoglyceromutase 97
Enolase 97
Pyruvate Kinase 98
Gluconeogenesis 98
Fructose Bisphosphatase in Microorganisms 98
Glycogen Synthesis 99
Glycogen Synthase 99
Control of Glycogen Biosynthesis 100
Branching Enzyme 100
Chapter 7: The Pentose Phosphate and Entner-Doudoroff Pathways 101
The Pentose Phosphate Pathway 101
The Enzymes of the Oxidative Phase 101
Glucose 6-Phosphate Dehydrogenase 101
6-Phosphogluconolactonase 102
6-Phosphogluconate Dehydrogenase (Decarboxylating) 102
Ribose Phosphate Isomerase 102
The Enzymes of the Non-oxidative Phase 102
Transketolase 103
Transaldolase 104
Ribulose-5-Phosphate-3-Epimerase 104
Regulation of the Pentose Phosphate Pathway 105
The Entner-Doudoroff Pathway 105
Chapter 8: The Tricarboxylic Acid Cycle and the Glyoxylate Bypass 106
The origin of acetyl CoA: The Pyruvate Dehydrogenase Complex 106
Overview of the Tricarboxylic Acid (TCA) Cycle 108
Origin of the Oxaloacetate 108
Organization of the Enzymes of the Tricarboxylic Acid Cycle 123
The Tricarboxylic Acid Cycle Is a Source of Biosynthetic Precursors 124
The Anaplerotic Glyoxylic Pathway Bypass 124
Chapter 9: ATP-Generating Processes: Respiration and Fermentation 127
Respiration 127
Fermentation 130
Acetone-Butanol Fermentation 130
The Stickland Reaction 131
Ornithine Fermentation 131
Glycine and Proline Degradation 132
Threonine Degradation 132
Glutamate Degradation 133
Lysine Degradation 134
Arginine Fermentation 135
Methionine Degradation 136
D-Selenocystine and D-Cysteine Degradation 136
Selected References 137
NADH-Ubiquinone Oxidoreductases 137
Erom Quinones to Oxygen 137
The Stickland Reaction 137
Arginîne and Ornithine Degradation 137
Threonine Degradation 138
Glycine Degradation 138
Proline Degradation 138
Glutamate Degradation 138
Lysine Degradation 138
Methionine gamma-Lyase 138
D-Selenocystine and D-Cysteine Degradation 139
Chapter 10: Biosynthesis of Lipids 140
Biosynthesis of Short Chain Fatty Acids 140
Biosynthesis of Long-Chain Fatty Acids 141
Synthesis of Acetyl CoA 141
Synthesis of Malonyl CoA 141
From Malonyl CoA to Palmitate 142
Regulation of Yeast Fatty Acid Synthesis at the Genetic Level 145
Regulation of Fatty Acid Synthesis in Bacteria 147
Biosynthesis of Triglycerides 147
Biosynthesis of Phosphoglycerides 147
Cyclopropane Fatty Acid Synthase (CFA Synthase) 148
Selected References 150
Short Chain Fatty Acid Synthesis 150
Fatty Acid Synthesis and Its Regulation 150
Cyclopropane Fatty Acid Synthetase 150
Chapter 11: Iron-Sulfur Proteins 151
Iron-Sulfur Clusters 151
2Fe-2S Clusters 152
4Fe-4S Clusters 152
3Fe-4S Clusters 153
Other Fe-S Clusters 153
Biosynthesis of Fe-S Clusters 153
Iron-Sulfur Proteins 154
Selected References 156
Chapter 12: The Archaea 157
Chemical Characteristics of Archaea 159
Archaea: Fossil Record 160
Economic Importance of the Archaea 161
Selected References 161
Chapter 13: Methanogens and Methylotrophs 162
Methanogens and Methanogenesis 163
Reduction of CO2 163
Formylmethanofuran Dehydrogenase 165
Formylmethanofuran: Tetrahydromethanopterin Formyltransferase 166
Methenyltetrahydromethanopterin Cyclohydrolase 167
5, 10-Methylenetetrahydromethanopterin Dehydrogenase 167
5, 10-Methylenetetrahydromethanopterin F420 Oxidoreductase 168
The Methylreductase: Methyl Coenzyme M Reductase 168
Simplification of the Methylreductase System 170
Structure of the Methylreductase 171
Source of the Energy Needed for the Growth of Methanogens 172
Biosynthesis of Some Cofactors Involved in Methanogenesis 172
Methanofuran 172
Methanopterin 172
Coenzyme M 173
7-Mercaptoheptanoylthreoninephosphate (Coenzyme B) 174
Biosynthesis of Coenzyme F420 175
Biosynthesis of Factor F430 175
Biosynthesis of Factor III 176
Methylotrophs 176
Methanotrophs 176
Metabolism of Methyl Compounds 177
Methanol Dehydrogenase (MDH) 178
Anaerobic Oxidation of Methane 178
Methylamine Dehydrogenase 179
Carbon Assimilation by Methylotrophs 179
Carboxydotrophs 181
Selected References 183
Methanogenesis 183
Biosynthesis of the Methanogenic Cofactors 183
Biosynthesis of Methanofuran 183
Biosynthesis of Methanopterin 183
Biosynthesis of Coenzyme M 183
Biosynthesis of 7-Mercaptoheptanoylthreoninephosphate (Coenzyme B) 183
Biosynthesis of Coenzyme F420 184
Biosynthesis of Factor F430 184
Anaerobic Oxidation of Methane 184
Carboxydotrophs 184
Chapter 14: Enzyme Induction in Catabolic Systems 185
The Specificity of Induction 185
De Novo Synthesis of beta-Galactosidase 186
Constitutive Mutants 188
Pleiotropy of the Constitutive Mutants 189
The Genetic Control and the Cytoplasmic Expression of Inducibility in the Synthesis of beta-Galactosidase in E. coli. The Lac R 190
Operators and Operons 196
Selected References 199
Specificity of Induction. De Novo Synthesis 199
Pleiotropy of the i Gene 199
Thiogalactoside Transacetylase 199
Genetics 199
Repressors and Operators 199
Chapter 15: Transcription: RNA Polymerase 200
The Synthesis of Messenger RNA: The Bacterial RNA Polymerase 201
Termination of Transcription in Prokaryotes 204
Yeast RNA Polymerases 205
Archaeal RNA Polymerases 206
Transcription Termination and PolyA Tails 207
Selected References 207
Trans-acting Transcription Factors 207
Eukaryotic RNA Polymerases 207
Termination of Transcription 208
Chapter 16: Negative Regulation 209
Induction Is Correlated with the Synthesis of a Specific Messenger 209
Isolation of the Lac Repressor 211
The lac Operator Is a DNA sequence 213
Direct Observation of Transcription Factor Dynamics in a Living Cell 219
Selected References 219
Messenger RNA 219
Isolation of Lac Repressor and lac Operator 220
Operators 02 and 03 220
Formation of Loop Structures in DNA 220
Quantifying lac Repressor Kinetics 220
Chapter 17: Enzyme Repression in Anabolic Pathways 221
Description of the Phenomenon 221
Isolation of Derepressed (Constitutive) Mutants in Biosynthetic Pathways. The Use of Structural Analogues 225
Replacement of Methionine by Selenomethionine in Proteins 226
Selected References 227
Repression of the Biosynthesis of Anabolic Enzymes 227
Incorporation of Amino Acid Analogs into Proteins 227
Chapter 18: Positive Regulation 228
The Promoter Region 229
Role of Cyclic AMP and of the CAP Protein in the Binding of RNA Polymerase to the Promoter Region 230
The Synthesis and Degradation of Cyclic AMP 232
How Does Glucose Exert Its Inhibitory Effect on E. coli beta-Galactosidase Synthesis? 233
Selected References 233
Catabolic Repression 233
Effects of Cyclic AMP on the Glucose Effect 234
The Promoter 234
The CAP Protein 234
Mode of Action of Cyclic AMP 234
Chapter 19: The Ribosomes 235
The Components of E. coli Ribosomes 236
The Ribosomes of Eukaryotes and of Archaea 237
Mechanistic Aspects of Translation of Messenger RNA to Protein by Ribosomes 238
Selected References 239
General 239
Eukaryotic Ribosomes 240
Crystallography 240
Chapter 20: The Genetic Code, the Transfer RNAs and the Aminoacyl-tRNA-Synthetases 241
The Genetic Code 241
The Transfer RNAs 244
Selected References 249
Colinearity of Genes and Proteins 249
The Genetic Code 249
Selenocysteine and Pyrrolysine 249
Transfer RNAs 249
Aminoacyl-tRNA Synthetases 249
RNA-Dependent Cysteine Biosynthesis in Archaea 249
Chapter 21: Attenuation 250
Regulation of the trp Operon in Bacillus subtilis 254
General Remarks on Regulatory Mechanisms 254
Selected References 255
Attenuation 255
TRAP Protein 256
Chapter 22: Riboswitches 257
Mechanisms of Riboswitches 259
Selected References 260
Chapter 23: The Biological Fixation of Nitrogen 261
Control of Nitrogenase Synthesis and Activity 264
Selected References 266
General Reviews 266
Fe-Protein 266
Mo-Fe Protein 266
Fe-MoCo 266
Oxygen Relations of Nitrogen Fixation in Cyanobacteria 266
Chapter 24: How Biosynthetic Pathways have been Established 267
Use of Isotopes 267
Use of Auxotrophic Mutants 270
Enzymatic Analysis 272
Selected References 272
Isotopic Competition 272
Isolation of Auxotrophic Mutants 272
Chapter 25: The Aspartic Acid Family of Amino Acids: Biosynthesis 273
The Biosynthesis of Aspartic Acid and Asparagine 273
Biosynthesis of Lysine from Aspartate Semialdehyde in Bacteria 276
The Synthesis of Dipicolinic Acid, a Substance Present in the Spores of Gram-Positive Bacilli 278
The Reduction of Aspartate Semialdehyde to Homoserine, the Common Precursor of Methionine and Threonine 279
Biosynthesis of Methionine from Homoserine 279
S-Adenosylmethionine (SAM) Biosynthesis 284
Biosynthesis of Threonine from Homoserine 285
Biosynthetic Threonine Dehydratase 286
Isoleucine Biosynthesis 287
Summary of the Biosynthetic Pathway of the Aspartate Family of Amino Acids 288
Ectoine Biosynthesis 289
Selected References 289
Asparagine 290
Threonine Synthase 290
Diaminopimelate Decarboxylase 290
Methionine Biosynthesis Direct Sulfhydrylation Pathway
Chapter 26: Regulation of the Biosynthesis of the Amino Acids of the Aspartic Acid Family in Enterobacteriacea 291
A Paradigm of Isofunctional and Multifunctional Enzymes and of the Allosteric Equilibrium 291
Two Aspartokinases in E. coli 292
The Threonine-Sensitive Homoserine Dehydrogenase of E. coli 294
Isolation of a Mutant Lacking the Lysine-Sensitive Aspartokinase and of Revertants Thereof 294
Evidence That the Threonine-Sensitive Aspartokinase and Homoserine Dehydrogenase of E. coli Are Carried by the Same Bifunctiona 297
The Binding of Threonine to Aspartokinase I-Homoserine Dehydrogenase I 297
The Binding of Pyridine Nucleotides to Aspartokinase I-Homoserine Dehydrogenase I 299
The Effects of Threonine on Aspartokinase I-Homoserine Dehydrogenase I Are Not Only Due to Direct Interactions 300
The Allosteric Transition of Aspartokinase I-Dehydrogenase I 302
Aspartokinase II-Homoserine Dehydrogenase II 305
Aspartokinase III 307
From Homoserine to Methionine 307
From Threonine to Isoleucine 308
Multifunctional Proteins 309
Regulations at the Genetic Level 310
The Threonine Operon 310
Regulation of the Lysine Regulon at the Genetic Level 312
Regulation of Methionine Biosynthesis at the Genetic Level 312
The Methionine Repressor 314
The metR Gene and Its Product 318
The Regulation of Isoleucine Synthesis at the Genetic Level 320
Appendix: More on Regulons 320
Selected References 321
Isofunctional Aspartokinases 321
Aspartokinases-Homoserine Dehydrogenases I and II. Structure and Regulation of Activity 321
The Threonine Operon and Its Regulation 322
Aspartokinase III. Crystallography 322
Regulation of Methionine Biosynthesis. The Methionine Repressor 322
Regulation of the Synthesis of the Branched-Chain Amino Acids 322
The Leucine-Lrp Regulon 322
Chapter 27: Other Patterns of Regulation of the Synthesis of Amino Acids of the Aspartate Family 323
Concerted Feedback Inhibition of Aspartokinase Activity in Rhodobacter capsulatus (Formerly Rhodopseudomonas capsulata) 323
Pseudomonads 324
Specific Reversal of a Particular Feedback Inhibition by Other Essential Metabolites. The Case of Rhodospirillum rubrum 326
The Particular Case of Spore-Forming bacilli 327
Some Other Cases 330
Conclusion 330
Selected References 330
Concerted Feedback Inhibition 330
Pseudomonads 331
Rhodospirillum rubrum 331
Spore-Forming bacilli 331
Chapter 28: Biosynthesis of the Amino Acids of the Glutamic Acid Family and Its Regulation 332
The Biosynthesis of Glutamine 332
Biosynthesis of Glutamine: Cumulative Feedback Inhibition 332
Biosynthesis of Glutamine: The Covalent Modification of Glutamine Synthetase 334
Glutamine Synthetase Structure 335
Reversible Adenylylation of the Glutamine Synthetase 338
Regulation of Glutamine Synthetase Activity by Covalent Adenylylation 339
The Regulation of the Synthesis of Glutamine Synthetase also Involves the Two Forms of PII and UTase/UR 340
Glutamine Synthetase in Other Microorganisms 342
The Biosynthesis of Glutamate 344
Glutamate Dehydrogenase 344
Glutamate Synthase 344
Biosynthesis of Proline 345
Utilization of Proline 347
The Biosynthesis of Arginine and Polyamines 348
Biosynthesis of Arginine 348
Regulation of Arginine Biosynthesis at the Transcriptional Level 351
The Arginine Repressor 351
Polyamine Biosynthesis 352
Utilization of Arginine as Sole Nitrogen Source by B. subtilis 355
Nitric Oxide Synthase in Bacteria 356
The Biosynthesis of Lysine in Yeasts and Molds 356
The Aminoadipic Acid Pathway 357
Selected References 360
Glutamine Synthetase Activity and Its Regulation by Covalent Modification: Structure 360
Glutamine Synthetase: Regulation of Gene Expression 360
The Levels of Glutamine Synthetase Are also Regulated by Oxidation Followed by Proteolytic Degradation 360
Glutamate Synthase 360
Proline Biosynthesis 360
Arginine Biosynthesis and Regulation 361
The Arginine Repressor 361
The Methionine Salvage Pathway 361
Nitric Oxide Synthase 361
Aminoadipic Acid Pathway 361
Chapter 29: Biosynthesis of Amino Acids Derived from Phosphoglyceric Acid and Pyruvic Acid 362
Biosynthesis of Glycine and Serine 362
Regulation of Serine Hydroxymethyltransferase at the Transcriptional Level 364
Biosynthesis of Cysteine 365
O-Acetylation of Serine 367
Cysteine Synthesis in Methanogens 367
Allosteric Regulation of Cysteine Synthesis 368
Regulation of Cysteine Synthesis at the Genetic Level 368
Biosynthesis of Alanine 369
Biosynthesis of Valine 370
Biosynthesis of Leucine 372
Isoleucine Synthesis from Pyruvate 374
Regulation of Valine, Isoleucine and Leucine Biosynthesis 374
Selected References 375
Serine Biosynthesis 375
Serine Hydroxymethylase 376
Sulfite Reductase 376
Cysteine Synthesis in Methanogens 376
Valine and Leucine 376
Isoleucine Synthesis from Pyruvate 376
Aspartate-beta-Decarboxylase 376
Chapter 30: Selenocysteine and Selenoproteins 377
Outlook 377
Enzymes Containing Selenocysteine 378
Formate Dehydrogenases 378
The Glycine Reductase Complex 378
The Nicotinic Acid Hydroxylase of Clostridium barkeri 379
Hydrogenases 380
Xanthine Dehydrogenase 380
Acetoacetyl CoA Thiolase 381
Gene Products Involved in Selenocysteine Biosynthesis and Incorporation 381
Selenocysteine Synthase 382
Selenophosphate Synthetase 382
Selenocysteine Lyase 382
Selenocysteyl tRNA 382
Insertion Sequences (SECIS Elements) 384
Selenocysteine and Archaea 384
Biochemical Function of the Selenocysteine Residue in Catalysis 385
Selected References 385
Chapter 31: Biosynthesis of Aromatic Amino Acids and Its Regulation 386
The Common Pathway (Shikimic Pathway) 386
Formation of Shikimic Acid 386
Formation of Chorismic Acid 390
Physiological Aspects of the Regulation of the Common Pathway 391
Characteristics of the Common Pathway in Several Organisms 392
Biosynthesis of Phenylalanine and Tyrosine from Chorismic Acid 393
The tyrR Regulon 394
Regulation of the pheA Gene by Attenuation 395
Other Organisms: The Arogenate Pathway of Phenylalanine and Tyrosine Biosynthesis 395
Aspartate as a Presursor of Aromatic Amino Acids 396
The Biosynthesis of Tryptophan from Chorismic Acid 397
Anthranilate Synthase-Anthranilate Phosphoribosyltransferase 398
Phosphoribosylanthranilate Isomerase-Indoleglycerophosphate Synthase 399
Tryptophan Synthase 400
Regulation of Tryptophan Biosynthesis at the Genetic Level: The Tryptophan Repressor 404
A Unitary Model for Induction and Repression 406
Isolation of the Trp Repressor 406
Enterochelin (Enterobactin) Biosynthesis 408
The Synthesis of 2,3-Dihydroxybenzoic Acid 408
Selected References 410
The Common Pathway 410
Biosynthesis of Phenylalanine and Tyrosine 410
DKFP Pathway: Aspartate as a Precursor of Aromatic Amino Acids 410
TyrR 411
Tryptophan Synthesis 411
Tryptophan Repressor: Functional Aspects 411
Enterochelin 411
Chapter 32: The Biosynthesis of Histidine and Its Regulation 412
Regulation of Histidine Biosynthesis at the Genetic Level 415
Synthesis of Diphthamide, a Modified Histidine, by Archaea 420
Selected References 421
Histidine Biosynthesis and Its Regulation 421
PR-ATP Pyrophosphorylase 421
Attenuation 421
Diphthamide in Archaea 421
Chapter 33: The Biosynthesis of Nucleotides 422
The Biosynthesis of Pyrimidine Nucleotides 422
Synthesis of 5-Phosphoribosyl-1-Pyrophosphate (PRPP) 422
Synthesis of Carbamylphosphate 423
The Synthesis of Cytidine and Uridine Triphosphates 425
Direct Utilization of Pyrimidines and of Their Derivatives 427
Aspartate Transcarbamylase of E. coli 427
The Aspartate Transcarbamylase of Other Organisms 433
Regulation of Pyrimidine Nucleotide Synthesis at the Genetic Level 434
The Biosynthesis of Purine Nucleotides 435
Biosynthesis of 5-Amino-4-Imidazole Carboxamide Ribonucleotide 435
Synthesis of Inosinic Acid 438
The Synthesis of Guanylic and Adenylic Acids 439
Remarks on the Control of Purine Nucleotide Biosynthesis 440
From Nucleoside Monophosphates to Nucleoside Diphosphates and Triphosphates 442
Selected References 442
Carbamylphosphate Synthetase 442
PRPP Synthetase 442
Aspartate Transcarbamylase 442
CAD Protein 443
Nucleoside Diphosphokinase 443
PRPP Amidotransferase 443
Chapter 34: The Biosynthesis of Deoxyribonucleotides 444
The Formation of Deoxyribonucleoside Diphosphates from Ribose Nucleoside Diphosphates 444
The Ribosenucleoside Diphosphate (NDP) Reductase System of E. coli 444
Thioredoxin and Thioredoxin Reductase 444
Ribonucleoside Reductase 447
Regulation of the Activity of Ribonucleoside Diphosphate Reductase 449
dCMP Deaminase and Thymidylate Synthase 450
dUTPase 452
The Ribonucleoside Phosphate Reductase of Other Organisms 452
A Ribonucleotide Triphosphate Reductase Reaction in E. coli Grown Under Anaerobic Conditions 453
The Synthesis of Deoxyribonucleoside Triphosphates from the Diphosphates 454
Organization of DNA Precursor Synthesis in Eukaryotic Cells 454
Selected References 455
Thioredoxin and Glutaredoxin 455
Ribonucleoside Diphosphate and Triphosphate Reductases 455
Thymidylate Kinases 455
Nucleoside Diphosphate Kinase 455
Chapter 35: Biosynthesis of Some Water-Soluble Vitamins and of Their Coenzyme Forms 456
Biosynthesis of Thiamin and Cocarboxylase 456
Control of Thiamin Biosynthesis 458
Biosynthesis of Riboflavin 460
Biosynthesis of Nicotinamide, NAD+ and NADP+ 462
Regulation of the Biosynthesis of Nicotinamide and Its Derivatives 465
NAD+ and the ADP-Ribosylation of Proteins 466
Biosynthesis of Para-Aminobenzoic Acid, of Folic Acid and Its Derivatives 467
Biosynthesis of Vitamin B6 Pyridoxine, and of Its Derivatives, Pyridoxal, Pyridoxamine and Pyridoxal Phosphate 470
Biosynthesis of Biotin, Biotin CO2, and Biocytin 472
The Biotin Operon and Its Repressor 475
Biosynthesis of Lipoic Acid 476
Biosynthesis of Pantothenate and Coenzyme A 477
The Synthesis of Pantothenic Acid 477
The Synthesis of Coenzyme A from Pantothenic Acid 479
The Acyl Carrier Protein 480
The Biosynthesis of Inositol 480
Biosynthesis of Pyrroloquinoline Quinone 480
Selected References 483
Thiamin 483
Riboflavin 483
Pyridoxal Phosphate 483
Chapter 36: Biosynthesis of Carotene, Vitamin A, Sterols, Ubiquinones and Menaquinones 484
Synthesis of the Common Precursor 484
The Non-mevalonate Pathway of Isoprenoid Precursor (Dimethylallyl Pyrophosphate) Biosynthesis 486
Synthesis of beta-Carotene, Carotenoids and Vitamin A 488
Synthesis of the Carotenoids 488
Regulation of Carotenoid Synthesis 491
Synthesis of Vitamin A 492
Synthesis of Sterols 492
The Biosynthesis of Ubiquinones and Menaquinones 494
Selected References 497
Mevalonate and Non-mevalonate Pathways 497
Biosynthesis of Water-Soluble Vitamins 498
Pyridoxine 498
Carotenoids 498
Menaquinones 498
Chapter 37: Biosynthesis of the Tetrapyrrole Ring System 499
Synthesis of Protoporphyrin 499
Synthesis of Heme from Protoporphyrin 504
Heme Biosynthesis in Archaea 505
Synthesis of Chlorophyll from Protoporphyrin 505
Biosynthesis of the Phycobilin Chromophores. Chromatic Adaptation 508
A Type of Chromatic Adaptation Under Conditions of Sulfur Starvation 511
Selected References 512
The Tetrapyrroles 512
ALA Synthesis 512
Heme Biosynthesis in Archaea 512
Phycobilins 512
Complementary Chromatic Adaptation 513
The Effect of Sulfur Starvation on Chromatic Adaptation 513
Chapter 38: Biosynthesis of Cobalamins Including Vitamin B12 514
Cobinamide Biosynthesis 518
From GDP-Cobinamide to Cobalamin 520
Selected References 521
Threonine Kinase and the Origin of the Aminopropanol Residue 521
Origin of the Dimethylbenzimidazole 521
Many References to Previous Work Will be Found in the Last Two Papers 522
Chapter 39: Interactions Between Proteins and DNA 523
DNA-Binding Proteins 523
Study of the Protein-DNA Complexes 525
Some Other Types of DNA-Binding Proteins 531
Selected References 534
Trp Repressor. Structural Aspects 534
Met Repressor 534
Chapter 40: Evolution of Biosynthetic Pathways 535
Principles of Protein Evolution 535
Two Theories for the Evolution of Biosynthetic Pathways 535
The Methionine and Cysteine Biosynthetic Pathways 536
The Threonine, Isoleucine, Cysteine and Tryptophan Biosynthetic Pathways 539
The Evolutionary Pathway Leading to the Three Isofunctional Aspartokinases in Escherichia coli 545
Transmembrane Facilitators 552
DNA-Binding Regulator Proteins 553
Selected References 553
Two Books 553
Two Different Theories on the Evolution of Biosynthetic Pathways 553
Common Origin of Cystathionine-gamma-Synthase and Cystathionase 553
Common Origin of Threonine Synthase, Threonine Dehydratase, D-Serine Dehydratase, and the B Chain of Tryptophan Synthase 554
Comparison of arg Genes with Homologous and Analogous Enzymes 554
Evolution of the E. coli Aspartokinases and Homoserine Dehydrogenases 554
Structural and Evolutionary Relationships Between E. coli Aspartokinase-Homoserine Dehydrogenases and Monofunctional Homoserine 554
Superfamily of Transmembrane Facilitators 554
DNA-Binding Regulator Proteins 554
Index 555

Produkt-Details

• Erscheint lt. Verlag: 2.2.2011
• Zusatzinfo: XXVIII, 558 p. 141 illus., 6 illus. in color.
• Verlagsort: Dordrecht
• Sprache: englisch
• Themenwelt: Medizin / Pharmazie ► Medizinische Fachgebiete ► Mikrobiologie / Infektologie / Reisemedizin
• Themenwelt: Studium ► 1. Studienabschnitt (Vorklinik) ► Biochemie / Molekularbiologie
• Themenwelt: Studium ► 1. Studienabschnitt (Vorklinik) ► Physiologie
• Themenwelt: Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie
• Themenwelt: Naturwissenschaften ► Biologie ► Zellbiologie
• Themenwelt: Technik
• Schlagworte: biosynthetic pathways • Permeability • regulation,archaea
• ISBN-10: 90-481-9437-7 / 9048194377
• ISBN-13: 978-90-481-9437-7 / 9789048194377