David A. Bender, Senior Lecturer, Department of Biochemistry and Molecular Biology, University College London, London, UK; Assistant Faculty Tutor (Life Sciences, Medical) and Sub-Dean (Teaching), Royal Free and University College Medical School.

Tables xvii

Preface xix

1 Nitrogen Metabolism 1

1.1 Nitrogen fixation 3

1.1.1 Nitrogenase 5

1.1.1.1 The nitrogen fixation gene cluster 7

1.1.1.2 Regulation of nitrogenase by the availability of fixed nitrogen and ATP 7

1.1.1.3 Protection of nitrogenase against oxygen 9

1.1.1.4 Respiratory protection in aerobic microorganisms 9

1.1.1.5 Conformational changes in nitrogenase 10

1.1.1.6 Heterocyst formation in filamentous cyanobacteria 10

1.1.1.7 Symbiotic Rhizobium spp. in root nodules 10

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

1.3.2.1 Reductive amination – the glutamate pathway of ammonium incorporation 14

1.3.2.2 Glutamate dehydrogenase 16

1.3.2.3 Mammalian glutamate dehydrogenase 17

1.3.2.4 Glutamate synthase – the glutamine pathway of ammonium incorporation 18

1.3.2.5 Synthesis of aspartate and asparagine 21

1.4 The synthesis and catabolism of purine and pyrimidine nucleotides 23

1.4.1 Purine synthesis 26

1.4.1.1 Phosphoribosyl pyrophosphate (PRPP) synthetase 28

1.4.1.2 PRPP amidotransferase 30

1.4.2 Purine catabolism and salvage 31

1.4.2.1 Adenosine deaminase deficiency – severe combined immune deficiency 34

1.4.2.2 Gout and hyperuricaemia 35

1.4.2.3 HGPRT deficiency – the Lesch-Nyhan syndrome 37

1.4.3 Pyrimidine synthesis 38

1.4.3.1 Orotic aciduria 42

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

1.6.2.1 Urea synthesis 52

1.6.2.2 Inborn errors of metabolism affecting the urea synthesis cycle 57

1.6.2.3 Entero-hepatic circulation of urea 59

1.6.2.4 Canavanine 60

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

2.1.5.1 Lysosomal autophagy 78

2.1.5.2 Ubiquitin and the proteasome 79

2.1.5.3 Active site proteolysis of apo-enzymes 81

2.1.6 Whole body protein turnover 81

2.1.6.1 The constant infusion, labelled precursor method 82

2.1.6.2 The constant infusion, labelled end product method 82

2.1.6.3 Rates of whole-body protein turnover 83

2.1.6.4 The catabolic drive and amino acid oxidation 83

2.1.6.5 The energy cost of protein turnover 84

2.1.6.6 Diurnal variation in protein turnover 85

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

2.2.4.1 Biological assays of protein quality 93

2.2.4.2 Chemical analysis and protein quality 94

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

2.5.1.1 Dipeptide transport 104

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 α-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

5.3.2.1 Glutamine-dependent amidotransferases 164

5.3.3 Transglutaminases 165

5.4 Glutathione and the γ-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

5.4.4.1 Glutamate cysteine ligase 174

5.4.4.2 Glutathione synthetase 175

5.4.5 The γ-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

5.7.1.1 Δ1-pyrroline-5-carboxylate reductase and proline oxidase 192

5.7.1.2 Hydroxyproline catabolism 194

5.7.2 Peptide prolyl hydroxylase 196

5.7.2.1 The hypoxia-inducible factor 198

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

5.9.1.1 The role of citrulline in arginine biosynthesis in mammals 208

5.9.2 Arginine catabolism in microorganisms 209

5.9.3 Nitric oxide 210

5.9.3.1 Nitric oxide synthase 211

5.9.3.2 Arginase and the control of arginine availability for nitric oxide synthesis or polyamine synthesis 214

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

6.1.1.1 Aspartate kinase in post-synthetic modification of proteins 230

6.1.1.2 Aspartic semialdehyde dehydrogenase 230

6.1.2 Homoserine dehydrogenase 230

6.1.3 Homoserine kinase 231

6.1.4 Threonine synthase 232

6.1.5 Threonine catabolism 232

6.1.5.1 Threonine deaminase 234

6.2 Lysine 235

6.2.1 Lysine biosynthesis in bacteria and plants – the diaminopimelate pathway 236

6.2.1.1 Diaminopimelate and dipicolinate in sporulating bacteria 238

6.2.2 Lysine biosynthesis in yeasts and fungi – the α-amino adipic acid pathway 239

6.2.3 Lysine catabolism 242

6.2.3.1 The saccharopine pathway of lysine catabolism 243

6.2.3.2 The pipecolic acid pathway of lysine catabolism 245

6.2.4 Post-synthetic modifi cation of lysine in proteins 245

6.2.4.1 Hydroxylysine, lysine aldehyde (allysine) and cross-links in collagen and elastin 247

6.2.4.2 Methyl lysine 249

6.2.4.3 Pyrrolysine 251

6.2.5 Carnitine 252

6.3 Methionine and cysteine 255

6.3.1 Methionine biosynthesis 256

6.3.1.1 Cystathionine γ-synthase and cystathionine β-lyase 258

6.3.1.2 Methionine synthase 259

6.3.1.3 S-Methylmethionine in plants 260

6.3.2 S-Adenosylmethionine and the methylation cycle 260

6.3.2.1 Glycine N-methyltransferase 263

6.3.2.2 Megaloblastic anaemia and the methyl folate trap 264

6.3.2.3 Methionine γ-lyase 264

6.3.3 Transsulphuration and cysteine synthesis in animals 265

6.3.3.1 Homocystinuria, hyperhomocysteinaemia and cardiovascular disease 266

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

7.1.3.1 The pyruvate pathway of isoleucine synthesis 286

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

7.2.2.1 Maple syrup urine disease 293

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

7.2.7.1 Multiple carboxylase deficiency 300

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

8.2.1.1 The histidine load test (FIGLU test) for folate nutritional status 314

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

9.1.3.1 The trp operon 333

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

9.2.4.1 Parkinson’s disease and inhibitors of dopa decarboxylase 346

9.2.4.2 Catabolism of the catecholamines 346

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

9.4.3.1 Melatonin synthesis and catabolism 362

9.4.4 The kynurenine pathway of tryptophan metabolism 363

9.4.4.1 Regulation of tryptophan dioxygenase 365

9.4.4.2 Kynurenine metabolism 367

9.4.4.3 Kynureninase and the tryptophan load test for vitamin B6 nutritional status 368

9.4.4.4 De novo synthesis of NAD 369

9.4.5 Pellagra 370

9.4.5.1 The pellagragenic effect of excess dietary leucine 372

9.4.5.2 Inborn errors of tryptophan metabolism 372

9.4.5.3 Carcinoid syndrome 373

9.4.5.4 Drug-induced pellagra 373

9.5 Quinone cofactors in amine oxidases 374

Further reading 375

Bibliography 377

Index 431

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