Amino Acid Metabolism
3. Edition August 2012
478 Pages, Hardcover
Wiley & Sons Ltd
ISBN:
978-0-470-66151-2
John Wiley & Sons
Amino Acid Metabolism, 3rd Edition covers all aspects of the biochemistry and nutritional biochemistry of the amino acids. Starting with an overview of nitrogen fixation and the incorporation of inorganic nitrogen into amino acids, the book then details other major nitrogenous compounds in micro-organisms, plants and animals. Contents include a discussion of the catabolism of amino acids and other nitrogenous compounds in animals, and the microbiological reactions involved in release of nitrogen gas back into the atmosphere. Mammalian (mainly human) protein and amino acid requirements are considered in detail, and the methods that are used to determine them.
Chapters consider individual amino acids, grouped according to their metabolic origin, and discussing their biosynthesis (in plants and micro-organisms for those that are dietary essentials for human beings), major metabolic roles (mainly in human metabolism) and catabolism (again mainly in human metabolism). There is also discussion of regulatory mechanisms for all these metabolic pathways, and of metabolic and genetic diseases affecting the (human) metabolism of amino acids.
Throughout the book the emphasis is on the nutritional importance of amino acids, integration and control of metabolism and metabolic and other disturbances of relevance to human biochemistry and health.
* Completely revised edition of this comprehensive text covering all the latest findings in amino acid metabolism research
* Written by an authority in the field
* Covers new advances in structural biology
* Clear illustrations of all structures and metabolic pathways
* Full list of recommended further reading for each chapter and bibliography of papers cited in the text
Figures xiii
Tables xvii
Preface xix
1 Nitrogen Metabolism 1
1.1 Nitrogen fixation 3
1.1.1 Nitrogenase 5
1.2 Nitrification and denitrification 11
1.2.1 The anammox (ANaerobic AMMonium OXidation) reaction 12
1.3 The incorporation of fi xed nitrogen into organic compounds 12
1.3.1 Utilization of nitrite and nitrate in plants 12
1.3.2 Incorporation of ammonium into organic compounds 13
1.4 The synthesis and catabolism of purine and pyrimidine nucleotides 23
1.4.1 Purine synthesis 26
1.4.2 Purine catabolism and salvage 31
1.4.3 Pyrimidine synthesis 38
1.4.4 Pyrimidine catabolism and salvage 43
1.5 Deamination of amino acids 45
1.5.1 Amino acid oxidases 45
1.5.2 Amine oxidases 47
1.5.3 Glutamate and alanine dehydrogenases 48
1.5.4 Non-oxidative deamination of amino acids 49
1.5.5 Glutaminase and asparaginase 50
1.6 Excretion of nitrogenous waste 51
1.6.1 Uricotelic and purinotelic species 51
1.6.2 Ureotelic species 52
1.7 Other nitrogenous compounds in human urine 61
1.7.1 Aminoacidurias 62
Further reading 65
2 Nitrogen Balance and Protein Turnover - Protein and Amino Acids in Human Nutrition 67
2.1 Nitrogen balance and protein requirements 67
2.1.1 Protein digestion and absorption 69
2.1.2 Protein digestibility and unavailable amino acids in dietary proteins 74
2.1.3 Obligatory nitrogen losses 75
2.1.4 Dynamic equilibrium and tissue protein turnover 76
2.1.5 Tissue protein catabolism 77
2.1.6 Whole body protein turnover 81
2.2 Requirements for individual amino acids 86
2.2.1 Nitrogen balance studies 89
2.2.2 Isotope tracer studies 90
2.2.3 Control of protein synthesis by the availability of amino acids 91
2.2.4 Protein quality (protein nutritional value) 92
2.3 The fate of amino acid carbon skeletons and the thermic effect of protein 94
2.4 Inter-organ metabolism of amino acids 99
2.5 Transport of amino acids across membranes 100
2.5.1 Families of amino acid transporters 101
Further reading 104
3 The Role of Vitamin B6 in Amino Acid Metabolism 105
3.1 Pyridoxal phosphate-dependent reactions 106
3.1.1 Families of pyridoxal phosphate-dependent enzymes 111
3.2 Amino acid racemases 112
3.2.1 Bacterial alanine racemase 112
3.2.2 Eukaryotic serine racemase 113
3.2.3 D-Aspartate in eukaryotes 114
3.2.4 D-Amino acids in aquatic invertebrates 115
3.2.5 D-Amino acids in gene-encoded peptides and proteins 115
3.3 Transamination 117
3.3.1 Dual substrate recognition in transaminases 120
3.3.2 Aspartate transaminase and the malate-aspartate shuttle 120
3.4 Decarboxylation and side-chain elimination and replacement reactions 122
3.4.1 Transamination of decarboxylases and enzymes catalyzing side-chain limination reactions 122
3.5 Pyruvate-containing enzymes 124
3.6 Vitamin B6 defi ciency and dependency 125
Further reading 128
4 Glycine, Serine and the One-Carbon Pool 129
4.1 Sources of glycine 130
4.1.1 Choline as a source of glycine 130
4.1.2 Glycine transaminase 132
4.2 The interconversion of glycine and serine 132
4.2.1 Serine hydroxymethyltransferase 133
4.2.2 The glycine cleavage system 135
4.2.3 Serine hydroxymethyltransferase and the glycine cleavage system in photosynthetic tissue 136
4.2.4 Non-ketotic and ketotic hyperglycinaemia 137
4.3 Glycine oxidase and glyoxylate metabolism 138
4.3.1 Primary hyperoxaluria 140
4.4 One-carbon metabolism 141
4.5 Serine biosynthesis 141
4.6 Serine catabolism 144
4.6.1 Serine transamination 144
4.6.2 Serine deaminase 145
4.7 Peptidyl glycine hydroxylase (peptide alpha-amidase) 146
4.8 5-Aminolevulinic acid and porphyrin synthesis 147
4.8.1 Porphyrias - diseases of porphyrin synthesis 151
4.9 Selenocysteine 152
Further reading 154
5 Amino Acids Synthesized from Glutamate: Glutamine, Proline, Ornithine, Citrulline and Arginine 157
5.1 Synthesis of 5-aminolevulinic acid from glutamate in plants 159
5.2 The catabolism of glutamate 160
5.3 Glutamine 161
5.3.1 Indirect formation of glutamine-tRNA 163
5.3.2 Glutaminases 164
5.3.3 Transglutaminases 165
5.4 Glutathione and the gamma-glutamyl cycle 168
5.4.1 Glutathione peroxidases 170
5.4.2 Glutathione reductase 171
5.4.3 Glutathione S-transferases 171
5.4.4 Glutathione synthesis 174
5.4.5 The gamma-glutamyl cycle 176
5.5 Glutamate decarboxylase and the GABA shunt 178
5.5.1 Glutamate decarboxylase 180
5.5.2 Alternative pathways of GABA synthesis 181
5.5.3 GABA catabolism 183
5.6 Glutamate carboxylase and vitamin K-dependent post-synthetic modification of proteins 184
5.6.1 Vitamin K-dependent proteins in blood clotting 187
5.6.2 Osteocalcin and matrix Gla protein 189
5.6.3 Vitamin K-dependent proteins in cell signalling - Gas-6 and protein S 190
5.7 Proline 190
5.7.1 Proline synthesis and catabolism 192
5.7.2 Peptide prolyl hydroxylase 196
5.8 The polyamines 198
5.8.1 Ornithine decarboxylase 199
5.8.2 S-Adenosylmethionine decarboxylase and polyamine synthesis 201
5.8.3 Polyamine catabolism and the interconversion pathway 203
5.8.4 Hypusine 204
5.9 Arginine, citrulline and ornithine 205
5.9.1 Arginine biosynthesis 206
5.9.2 Arginine catabolism in microorganisms 209
5.9.3 Nitric oxide 210
5.9.4 Agmatine 216
5.9.5 Post-synthetic methylation of arginine in proteins 217
5.9.6 Post-synthetic formation of citrulline in proteins 218
5.9.7 Creatine 219
Further reading 222
6 Amino Acids Synthesized from Aspartate: Lysine, Methionine (and Cysteine), Threonine and Isoleucine 225
6.1 Regulation of the pathway of amino acid synthesis from aspartate 227
6.1.1 Aspartate kinase 228
6.1.2 Homoserine dehydrogenase 230
6.1.3 Homoserine kinase 231
6.1.4 Threonine synthase 232
6.1.5 Threonine catabolism 232
6.2 Lysine 235
6.2.1 Lysine biosynthesis in bacteria and plants - the diaminopimelate pathway 236
6.2.2 Lysine biosynthesis in yeasts and fungi - the alpha-amino adipic acid pathway 239
6.2.3 Lysine catabolism 242
6.2.4 Post-synthetic modifi cation of lysine in proteins 245
6.2.5 Carnitine 252
6.3 Methionine and cysteine 255
6.3.1 Methionine biosynthesis 256
6.3.2 S-Adenosylmethionine and the methylation cycle 260
6.3.3 Transsulphuration and cysteine synthesis in animals 265
6.3.4 Ethylene synthesis in plants 268
6.3.5 Radical SAM enzymes 271
6.3.6 Hydrogen sulphide 272
6.3.7 Taurine and the catabolism of cysteine 273
Further reading 276
7 The Branched-Chain Amino Acids: Leucine, Isoleucine and Valine 279
7.1 Synthesis of the branched-chain amino acids 280
7.1.1 Acetohydroxyacid synthase 282
7.1.2 Acetohydroxyacid reducto-isomerase, dihydroxyacid dehydratase and transamination of the oxo-acids 283
7.1.3 Leucine synthesis 284
7.2 Mammalian catabolism of the branched-chain amino acids 287
7.2.1 Branched-chain amino acid transaminases 289
7.2.2 Branched-chain 2-oxo-acid dehydrogenase 290
7.2.3 Branched-chain acyl CoA dehydrogenases 293
7.2.4 Leucine catabolism 295
7.2.5 Isoleucine catabolism 296
7.2.6 Valine catabolism 297
7.2.7 Biotin-dependent carboxylation reactions 299
Further reading 302
8 Histidine 305
8.1 Biosynthesis of histidine 306
8.2 Histidine catabolism 310
8.2.1 The urocanic acid pathway of histidine catabolism 311
8.2.2 The hydantoin propionate pathway 315
8.2.3 The transaminase pathway of histidine catabolism 316
8.3 Histamine 316
8.3.1 Bacterial histamine poisoning (scombroid poisoning) 317
8.3.2 Histidine decarboxylase 318
8.3.3 Histamine catabolism 319
8.4 Methylhistidine 321
8.5 Carnosine and related histidine-containing peptides 321
Further reading 322
9 The Aromatic Amino Acids: Phenylalanine, Tyrosine and Tryptophan 323
9.1 Biosynthesis of phenylalanine, tyrosine and tryptophan 324
9.1.1 The shikimate pathway 325
9.1.2 Synthesis of phenylalanine and tyrosine 328
9.1.3 Synthesis of tryptophan 331
9.2 Metabolism of phenylalanine and tyrosine 335
9.2.1 Phenylalanine ammonia lyase and lignin biosynthesis in plants 335
9.2.2 Polyphenol biosynthesis in plants 338
9.2.3 Phenylalanine hydroxylase and phenylketonuria 339
9.2.4 The catecholamines: dopamine, noradrenaline and adrenaline 342
9.2.5 Tyrosinase and melanin synthesis 349
9.2.6 The thyroid hormones, thyroxine and tri-iodothyronine 352
9.3 Catabolism of phenylalanine and tyrosine 355
9.4 Metabolism of tryptophan 357
9.4.1 Auxin (indoleacetic acid) 357
9.4.2 Indole formation 358
9.4.3 Serotonin and melatonin 359
9.4.4 The kynurenine pathway of tryptophan metabolism 363
9.4.5 Pellagra 370
9.5 Quinone cofactors in amine oxidases 374
Further reading 375
Bibliography 377
Index 431
Tables xvii
Preface xix
1 Nitrogen Metabolism 1
1.1 Nitrogen fixation 3
1.1.1 Nitrogenase 5
1.2 Nitrification and denitrification 11
1.2.1 The anammox (ANaerobic AMMonium OXidation) reaction 12
1.3 The incorporation of fi xed nitrogen into organic compounds 12
1.3.1 Utilization of nitrite and nitrate in plants 12
1.3.2 Incorporation of ammonium into organic compounds 13
1.4 The synthesis and catabolism of purine and pyrimidine nucleotides 23
1.4.1 Purine synthesis 26
1.4.2 Purine catabolism and salvage 31
1.4.3 Pyrimidine synthesis 38
1.4.4 Pyrimidine catabolism and salvage 43
1.5 Deamination of amino acids 45
1.5.1 Amino acid oxidases 45
1.5.2 Amine oxidases 47
1.5.3 Glutamate and alanine dehydrogenases 48
1.5.4 Non-oxidative deamination of amino acids 49
1.5.5 Glutaminase and asparaginase 50
1.6 Excretion of nitrogenous waste 51
1.6.1 Uricotelic and purinotelic species 51
1.6.2 Ureotelic species 52
1.7 Other nitrogenous compounds in human urine 61
1.7.1 Aminoacidurias 62
Further reading 65
2 Nitrogen Balance and Protein Turnover - Protein and Amino Acids in Human Nutrition 67
2.1 Nitrogen balance and protein requirements 67
2.1.1 Protein digestion and absorption 69
2.1.2 Protein digestibility and unavailable amino acids in dietary proteins 74
2.1.3 Obligatory nitrogen losses 75
2.1.4 Dynamic equilibrium and tissue protein turnover 76
2.1.5 Tissue protein catabolism 77
2.1.6 Whole body protein turnover 81
2.2 Requirements for individual amino acids 86
2.2.1 Nitrogen balance studies 89
2.2.2 Isotope tracer studies 90
2.2.3 Control of protein synthesis by the availability of amino acids 91
2.2.4 Protein quality (protein nutritional value) 92
2.3 The fate of amino acid carbon skeletons and the thermic effect of protein 94
2.4 Inter-organ metabolism of amino acids 99
2.5 Transport of amino acids across membranes 100
2.5.1 Families of amino acid transporters 101
Further reading 104
3 The Role of Vitamin B6 in Amino Acid Metabolism 105
3.1 Pyridoxal phosphate-dependent reactions 106
3.1.1 Families of pyridoxal phosphate-dependent enzymes 111
3.2 Amino acid racemases 112
3.2.1 Bacterial alanine racemase 112
3.2.2 Eukaryotic serine racemase 113
3.2.3 D-Aspartate in eukaryotes 114
3.2.4 D-Amino acids in aquatic invertebrates 115
3.2.5 D-Amino acids in gene-encoded peptides and proteins 115
3.3 Transamination 117
3.3.1 Dual substrate recognition in transaminases 120
3.3.2 Aspartate transaminase and the malate-aspartate shuttle 120
3.4 Decarboxylation and side-chain elimination and replacement reactions 122
3.4.1 Transamination of decarboxylases and enzymes catalyzing side-chain limination reactions 122
3.5 Pyruvate-containing enzymes 124
3.6 Vitamin B6 defi ciency and dependency 125
Further reading 128
4 Glycine, Serine and the One-Carbon Pool 129
4.1 Sources of glycine 130
4.1.1 Choline as a source of glycine 130
4.1.2 Glycine transaminase 132
4.2 The interconversion of glycine and serine 132
4.2.1 Serine hydroxymethyltransferase 133
4.2.2 The glycine cleavage system 135
4.2.3 Serine hydroxymethyltransferase and the glycine cleavage system in photosynthetic tissue 136
4.2.4 Non-ketotic and ketotic hyperglycinaemia 137
4.3 Glycine oxidase and glyoxylate metabolism 138
4.3.1 Primary hyperoxaluria 140
4.4 One-carbon metabolism 141
4.5 Serine biosynthesis 141
4.6 Serine catabolism 144
4.6.1 Serine transamination 144
4.6.2 Serine deaminase 145
4.7 Peptidyl glycine hydroxylase (peptide alpha-amidase) 146
4.8 5-Aminolevulinic acid and porphyrin synthesis 147
4.8.1 Porphyrias - diseases of porphyrin synthesis 151
4.9 Selenocysteine 152
Further reading 154
5 Amino Acids Synthesized from Glutamate: Glutamine, Proline, Ornithine, Citrulline and Arginine 157
5.1 Synthesis of 5-aminolevulinic acid from glutamate in plants 159
5.2 The catabolism of glutamate 160
5.3 Glutamine 161
5.3.1 Indirect formation of glutamine-tRNA 163
5.3.2 Glutaminases 164
5.3.3 Transglutaminases 165
5.4 Glutathione and the gamma-glutamyl cycle 168
5.4.1 Glutathione peroxidases 170
5.4.2 Glutathione reductase 171
5.4.3 Glutathione S-transferases 171
5.4.4 Glutathione synthesis 174
5.4.5 The gamma-glutamyl cycle 176
5.5 Glutamate decarboxylase and the GABA shunt 178
5.5.1 Glutamate decarboxylase 180
5.5.2 Alternative pathways of GABA synthesis 181
5.5.3 GABA catabolism 183
5.6 Glutamate carboxylase and vitamin K-dependent post-synthetic modification of proteins 184
5.6.1 Vitamin K-dependent proteins in blood clotting 187
5.6.2 Osteocalcin and matrix Gla protein 189
5.6.3 Vitamin K-dependent proteins in cell signalling - Gas-6 and protein S 190
5.7 Proline 190
5.7.1 Proline synthesis and catabolism 192
5.7.2 Peptide prolyl hydroxylase 196
5.8 The polyamines 198
5.8.1 Ornithine decarboxylase 199
5.8.2 S-Adenosylmethionine decarboxylase and polyamine synthesis 201
5.8.3 Polyamine catabolism and the interconversion pathway 203
5.8.4 Hypusine 204
5.9 Arginine, citrulline and ornithine 205
5.9.1 Arginine biosynthesis 206
5.9.2 Arginine catabolism in microorganisms 209
5.9.3 Nitric oxide 210
5.9.4 Agmatine 216
5.9.5 Post-synthetic methylation of arginine in proteins 217
5.9.6 Post-synthetic formation of citrulline in proteins 218
5.9.7 Creatine 219
Further reading 222
6 Amino Acids Synthesized from Aspartate: Lysine, Methionine (and Cysteine), Threonine and Isoleucine 225
6.1 Regulation of the pathway of amino acid synthesis from aspartate 227
6.1.1 Aspartate kinase 228
6.1.2 Homoserine dehydrogenase 230
6.1.3 Homoserine kinase 231
6.1.4 Threonine synthase 232
6.1.5 Threonine catabolism 232
6.2 Lysine 235
6.2.1 Lysine biosynthesis in bacteria and plants - the diaminopimelate pathway 236
6.2.2 Lysine biosynthesis in yeasts and fungi - the alpha-amino adipic acid pathway 239
6.2.3 Lysine catabolism 242
6.2.4 Post-synthetic modifi cation of lysine in proteins 245
6.2.5 Carnitine 252
6.3 Methionine and cysteine 255
6.3.1 Methionine biosynthesis 256
6.3.2 S-Adenosylmethionine and the methylation cycle 260
6.3.3 Transsulphuration and cysteine synthesis in animals 265
6.3.4 Ethylene synthesis in plants 268
6.3.5 Radical SAM enzymes 271
6.3.6 Hydrogen sulphide 272
6.3.7 Taurine and the catabolism of cysteine 273
Further reading 276
7 The Branched-Chain Amino Acids: Leucine, Isoleucine and Valine 279
7.1 Synthesis of the branched-chain amino acids 280
7.1.1 Acetohydroxyacid synthase 282
7.1.2 Acetohydroxyacid reducto-isomerase, dihydroxyacid dehydratase and transamination of the oxo-acids 283
7.1.3 Leucine synthesis 284
7.2 Mammalian catabolism of the branched-chain amino acids 287
7.2.1 Branched-chain amino acid transaminases 289
7.2.2 Branched-chain 2-oxo-acid dehydrogenase 290
7.2.3 Branched-chain acyl CoA dehydrogenases 293
7.2.4 Leucine catabolism 295
7.2.5 Isoleucine catabolism 296
7.2.6 Valine catabolism 297
7.2.7 Biotin-dependent carboxylation reactions 299
Further reading 302
8 Histidine 305
8.1 Biosynthesis of histidine 306
8.2 Histidine catabolism 310
8.2.1 The urocanic acid pathway of histidine catabolism 311
8.2.2 The hydantoin propionate pathway 315
8.2.3 The transaminase pathway of histidine catabolism 316
8.3 Histamine 316
8.3.1 Bacterial histamine poisoning (scombroid poisoning) 317
8.3.2 Histidine decarboxylase 318
8.3.3 Histamine catabolism 319
8.4 Methylhistidine 321
8.5 Carnosine and related histidine-containing peptides 321
Further reading 322
9 The Aromatic Amino Acids: Phenylalanine, Tyrosine and Tryptophan 323
9.1 Biosynthesis of phenylalanine, tyrosine and tryptophan 324
9.1.1 The shikimate pathway 325
9.1.2 Synthesis of phenylalanine and tyrosine 328
9.1.3 Synthesis of tryptophan 331
9.2 Metabolism of phenylalanine and tyrosine 335
9.2.1 Phenylalanine ammonia lyase and lignin biosynthesis in plants 335
9.2.2 Polyphenol biosynthesis in plants 338
9.2.3 Phenylalanine hydroxylase and phenylketonuria 339
9.2.4 The catecholamines: dopamine, noradrenaline and adrenaline 342
9.2.5 Tyrosinase and melanin synthesis 349
9.2.6 The thyroid hormones, thyroxine and tri-iodothyronine 352
9.3 Catabolism of phenylalanine and tyrosine 355
9.4 Metabolism of tryptophan 357
9.4.1 Auxin (indoleacetic acid) 357
9.4.2 Indole formation 358
9.4.3 Serotonin and melatonin 359
9.4.4 The kynurenine pathway of tryptophan metabolism 363
9.4.5 Pellagra 370
9.5 Quinone cofactors in amine oxidases 374
Further reading 375
Bibliography 377
Index 431
"Summing Up: Recommended. Upper-division undergraduates through professionals." (Choice, 1 March 2013)
"Bender writes succinctly and clearly, in a manner which serves well for quick referencing or for reading whole chapters at a time. The chapters are well organised and arranged logically." (Phenotype, 1 February 2013)
"Bender writes succinctly and clearly, in a manner which serves well for quick referencing or for reading whole chapters at a time. The chapters are well organised and arranged logically." (Phenotype, 1 February 2013)
