Biochemical Pathway

Index 388

Lysergic acid amides (e.g. LSD) 205 277 Mannosyl-oligosaccharide 1,3-1,6-a-mannosidase Methenyl-THF-cyclohydrolase (EC 3.5.4.9) 139
Lysergic acid peptide derivatives 205–206 (EC 3.2.1.114) 241 Methenyltetrahydrofolate cyclohydrolase
L-Lysine 5
– amino acids 59 Maroteaux-Lamy’s syndrome 34 (EC 3.5.4.9) 175
– biosynthesis 65 Mass, characterized 8 L-Methionine 5
– cysteine metabolism 69 Mast cells – C1 metabolism 138
– eukaryotic genome 28 – cytokines 341 – human amino acids 59
– genetic code 30 – innate immune system 326 – metabolism 65–67
– metabolism 67 Matricaria 198 Methionine adenosyltransferase (EC 2.5.1.6) 67
– peptidoglycans 35 Matrix-associated regions (MARs) 28 Methionyl-tRNA formyltransferase (EC 2.1.2.9) 139,
Lysinetyrosylquinone (LTQ) 178 Matrix targeting signal, mitochondrial protein
Lysoglycerophospholipids 7 216
Lysophospholipase (EC 3.1.1.5) 102 transport 252 Methoctramine 298
Lysophosphatidate 99 Matter, quantity of 8 Methylaminobutanal 203
Lysosomes Maximum reaction rate 10 Methylaspartate ammonia-lyase (EC 4.3.1.2) 172
– lipoprotein receptors 281 M cyclins Methylaspartate mutase (EC 5.4.99.1) 60, 172
– pollymeric carbohydrates 32 – eukaryotic cell cycle 232, 235 Methylation
– structure and function 16 Measures and constants 8 – DNA 28
– vesicular transport 248 Mediators, in transcription 219
Lysosomal ATPase, H+-transporting (TC 3.A.2.2.3) Medical studies. See Disease(s); Human studies – long patch repair 154
Lysozyme (EC 3.2.1.17), immune system 325 Melanocyte-stimulating hormones (MSH) 288 – rRNA processing 223
Melatonin 76 Methylcobalamin 137–138
M Membrane associated receptors, signal cascades 312 – biosynthesis 91
Membrane-attack complex (MAC) 336 Methylcoclaurine 3¢-monooxygenase
MACiE database 372 Membrane-bound endoplasmic reticulum, protein
Macrolides (EC 1.14.13.71) 207
– antibiotics 179 location 239 Methylcrotonyl CoA carboxylase (EC 6.4.1.4) 72, 107
– classification 181 Membrane molecules, T cell activation 343 2C-Methyl-D-erythritol 2,4-cyclodiphosphate synthase
Macrophage colony stimulating factor Membrane potential 294
Membrane(s) (EC 4.6.1.12) 112
(M CSF) receptors 312 – cholesterol in 109 2C-Methyl-D-erythritol 4-phosphate citidyltransferase
Macrophages – fluidity 96
– complement system 336 – fusion 101 (EC 2.7.7.60) 112
– cytokines 341 – lipid membranes 36 2C-Methyl-D-erythriol 4-phosphate (MEP) pathway 112
– immune response regulation 344 – proteins 336 Methyl-directed mismatch repair (MMR) 154
– immune system development 330 – translocation 240 5,10-Methylene-THF 138
– innate immune system 326 Membrane transport 5,10-Methylenetetrahydromethanopterin reductase
MadCAM-1, 356 – primary active transport systems 277–278
Magnesium (Mg++), hormone regulation 292 – proteins 367 (EC 1.5.99.11) 174
Maize, carbon dioxide pumping 193 – solute carriers 275–277 Methylene-THF dehydrogenase (EC 1.5.1.15) 139
Major facilitator superfamily, bacterial transport 168 Memory, specific, in immunology 325 Methylene-THF reductase (NAD(P)+)
Major histocompatibility complex (MHC) Menaquinone (Vitamin K)
– antigen presentation 337–338 – bacteria biosynthesis 75 (EC 1.5.1.20) 139
– immune system 336–338 – biosynthesis and metabolism 148–149 3-Methyl glutaconyl-CoA Hydratase (EC 4.2.1.18) 107
– ubiquitylation 260 – branched-chain amino acids 73 Methyl groups 23
Malate-CoA ligase (EC 6.2.1.9) 179 Menstrual cycle, hypothalamo-pituitary-uterus N-Methylhydantoinase (EC 3.5.2.14) 81
Malate dehydrogenase (EC 1.1.1.37) 179, 170, 56, 93, 56 L-6-N-Methyllysine 6
Malate shuttle 47 axis 290–291 Methylmalonyl-CoA carboxytransferase
– glyoxalate metabolism 57–58 3-Mercaptopyruvate sulfurtransferase (EC 2.8.1.2) 68
Malate synthase (EC 4.1.3.2), fatty acid oxidation 98 MEROPS database 371 (EC 2.1.3.1) 47, 170
MalE, maltose binding (TC 3.A.1.1.1) 169 – peptidase inhibitors 258 Methylmalonyl-CoA epimerase (EC 5.1.99.1) 68, 170
Maleylacetoacetate isomerase (EC 5.2.1.2) 76 Messenger RNA (mRNA). See also pre-MRNA Methylmalonyl-CoA mutase (EC 5.4.99.2) 68, 170
Malic enzyme (EC 1.1.1.38) 46, 93 – bacterial ribosome 215 Methylobacterium 178
Malonamoyl-CoA, tetracycline biosynthesis 182 – bacterial translation 216 5-Methyl-THF 138
Maltose 5, 44 – capping 221 3-Methyl-2-oxobutanoate dehydrogenase
Malvidin 197 – characterized 2
Mammal(s). See also Animal cells – deadenylation-mediated degradation 231 (2-methylpropanoyl-transferring) (EC 1.2.4.4) 71
– bile acid metabolism 123 – decoding 6 3-Methyl-2-oxobutanoate hydroxymethyltransferase
– cell cycle 232–236 – eukaryotic mRNA structure 228
– eukaryotic translation 228 (EC 2.1.2.11) 71, 142
– fatty acid desaturation 95 – functions of 27 5-Methyltetrahydropteroyltriglutamate-homocysteine
– fatty acid oxidation in 97–98 – genetic code 30
– gangliosides 105 – half-life, enzyme regulation 24 S-methyltransferase (EC 2.1.1.14) 67
– glycogen metabolism in 44–45 – metabolic reactions 115 C-1 Methyltransferase (EC 2.1.1.152) 92
– mitochondria 31 – nucleic acid degradation 217 C-2 Methyltransferase (EC 2.1.1.107) 85
– multienzyme complexes 23 – processing 222–223 C-11 Methyltransferase (EC 2.1.1.133) 92
– NAD+/NADP+ biosynthesis and reaction 144 – protein coding 211–212 C-17 Methyltransferase (EC 2.1.1.131) 92
– polyadenylation 222 – transcription 219–221 C-2,C-7 Methyltransferase (EC 2.5.1.17) 91
– protein processing in 240 Metabolic fluxes, modeling of 366 C-20 Methyltransferase (EC 2.1.1.130) 91
– respiratory chain 184 Metabolome analysis 366 C-5,C-6 Methyltransferase (EC 2.1.1.132) 92
– chylomicrons in 280 Metabolome 80 Methyltrophs, carbon assimilation 178–179
– G-protein coupled receptor activity 300–301 MetaCyc database 372 Metmyoglobin 283
– Ras signalling cascades 314 Metal ions 22–23 Mevalonate kinase (EC 2.7.1.36) 107, 109
Manganese (II) ions (Mn++) 175 Metallopeptidases Mevalonate (MVA) pathway
Manihot sp. 201 – reaction mechanisms 257–258 – isoprenoid metabolism 112
Mannan-binding lectin (MBL) Metaphase, animal cell mitosis 235 – terpene, carotenoid, retinoid metabolism 113
– complement system 334–336 Methylotrophs, obligate 178–179 – terpenoid biosynthesis 198
– innate immune system 325 Methane MgtE-like Mg++ transporter (TC 9.A.19.4) 276
Mannose 37 – methanogenesis 174 Mg-Protoporphyrin IX chelatase 90
– glycoprotein synthesis 241 – oxidation 178–179 Mg-Protoporphyrin IX O-methyl transferase
– metabolism 51 Methane monooxygenase (soluble) (EC 1.14.13.25) 179
Mannose Isomerase (EC 5.3.1.7) 37 Methanogenesis 174 (EC 2.1.1.11) 90
Mannose 6-phosphate isomerase (EC 5.3.1.8) 51 Methanogenic archaea 174 Micelles, spherical 35
a-1,6-Mannosyl-glycoprotein 2-b-N- Methanopterin Michaelis constant 10
acetylglucosaminyltransferase (EC 2.4.1.143) 241 – biosynthesis 141 Michaelis-Menten equation
b-1,4-Mannosyl-glycoprotein 4-b-N- – in folate biosynthesis 138 – enzyme kinetics 10
acetylglucosaminyltransferase (EC 2.4.1.144) 241 Methanothermobacter sp. 174 – enzyme regulation 24
Mannosyl-oligosaccharide 1,2-a-mannosidase Methemoglobin 283 – hormone receptor kinetics 287
(EC 3.2.1.113) 239–241 Methemoglobinemias Michaelis-Menten theory 13
– hemo- and myoglobin oxygen binding 283 Microparticle formation, platelet function 362
– hemoglobin oxygenation 285 Microtubules
– anaphase of mitosis 236
– functions of 17
– intracellular transport 278–279
Mineralocorticoids
– intercellular signal transmission 286
– metabolism 119–121
– steroid hormone biosynthesis 114
Miniband, mitosis and 29
miRNA 27

389 Index Multidrug resistance transporter – innate immune system 326
(TC 3.A.1.201.1 … 3) 277 – receptors and ligands 350
Mismatch repair Natural rubber 201
– defined 154–155 Multifunctional anion exchanger (TC 2.A.53.1 … 2) 275 Natural Treg, regulatory T cells 345
– in eukaryotes 163–164 Multienzyme complexes 23 Negative control, RNA binding 212
– post-replicative 162 Multimeric signalosome complex, T cell receptors 317 Negative strand virus 261
Mitochondria Multiple enzyme control, tryptophan biosynthesis 75 Neopterin biosynthesis 139–140
– codon differences in 31 Mumps virus 263 Nernst equation 9
– cytochromes 87 Murein Nerve conduction, synaptic transmission 294–296
– electron transport system and 183–184 – bacterial cell walls 35 Nerve growth factor (NGF) receptors 318
– functions of 17–18 – bacterial envelope and synthesis of 164–165 Nerve muscle synapse 297
– heat generation 188 – biosynthesis 54 Neuraminidase (EC 4.4.2.1) 55
– membrane transfer 47 Muscarine receptors 297–298 Neurodegenerative diseases, protein degradation 258
– protein transport in 252–254 Muscle(s). See also specific muscles and muscle types Neuroendocrine system, immune system
– respiratory chain in 185–186 – contraction 305–307
– urea cycle 80 – cytokines 341 interaction 350–351
Mitochondrial apoptotic pathway 347–348 Muscular endplate, signal transmission 296 Neuropeptide(s)
MItochondrial ATP synthase, H+ transporting C-11,C-12 Mutase (EC 5.4.1.2) 92 – hypothalamus-anterior pituitary
Mycobacteria 166
(TC 3.A.2.1.3) 277 Mycoplasms 15, 149 homone system 288
Mitochondrial carrier family (TC 2.A.29) 275, 276 Mycosterols 110–111 – neurotransmission 297
Mitogen-activated protein kinase (MAPK, EC 2.7.11.24) Myelomonocitic cells, immune system development 330 – receptors 297–298
– EGF receptor activation 313 Myeloperoxidase (EC 1.11.2.2) 70 Neuropeptide Y 99
– T cell receptors 317 Myofibrils, muscle structure 305 Neurotransmitters
Mitosis Myoglobin – characteristics 296–297
– eukaryotic chromosomes 29 – biosynthesis and properties 282–283 – cysteine-loop neurotransmitters 273
– intracellular transport 278–279 – dissociation curves 284–285 – intercellular signal transmission 286
– mammalian cells 235–236 – oxygen binding to 283–285 Neurotransmitter:sodium symporter (NSS) family
Mitotic centromere-associated kinesin (MCAK), Myo-inositol
– calcium release 304–305 (TC 2.A.22) 276
mammalian cell mitosis 236 – synthesis and degradation 49 Neurotropin growth factor (NGF) receptors
Mixed inhibition 24 Myo-Inositol oxygenase (EC 1.13.99.1) 50 – enzyme degradation inhibition 81
– enzyme activities 11–12 L-Myo-inositol phosphatase (EC 3.1.3.25) 50 – protein-tyrosine kinase activity 312
Mixed lineage kinases (MLKs), signal cascades 312 Myosin Neutrophilic cells
Mixotroph 176 – muscle contraction 305–306 – complement receptors 336
Molecular chaperones, protein folding 245 – protein function 21 – immune response regulation 344
Molecular mimicry 354 Myosin light chain kinase (MLCK, EC 2.7.11.18), – immune system development 330
Molecular scavengers 71 – innate immune system 326
Mollusks 32 muscle contraction 307 Neutrophilic chemotactic factor (NCF), IgE-mediated
Molten globules, protein folding 244–245 Myrosinase (EC 3.2.1.147) 202
Molybdenum 127 Myristic acid 6 hypersensitivity 353
Molybdenum cofactor cytidylyltransferase Myristoylation 19 N-glycans, glycosylation reactions 241
Nicotiana sp. 198, 209
(EC 2.7.7.76) 140 N Nicotiana tobacco alkaloids 201–203
Molybdenum cofactor guanylyltransferase Nicotinamidase (EC 3.5.1.19) 144
N-acetylglutamate synthase (EC 2.3.1.1) deficiency 80 Nicotinamide adenine dinucleotide (NAD+/NADH)
(EC 2.7.7.77) 140 N-acetylneuraminic acid, biosynthesis 54–55 – aromatic amino acids 74, 76
Molybdenum/tungsten cofactors (MoCo) NAD(P)+-Arginine ADP-ribosyltransferase – biosynthesis and degradation 143–145
– biosynthesis 140–141 – citrate cycle and 55, 57
– folate metabolism 138 (EC 2.4.2.31) 145 – coenzymes 144–145
Molybdopterin adenylyltransferase (EC 2.7.7.75) 140 NADH: Ubiquinone oxidoreductase (EC 1.6.5.3) 184 – dehydrogenase, electron transport 183–184
Molybdopterin molybdotransferase (EC 2.10.1.1) 140 NAD+ Kinase (EC 2.7.1.23) 144 – electron transport 183
Molybdopterin sulfurtransferase (EC 2.8.1.7) 140 NAD+ [or NAD(P)+] Nucleosidase (EC 3.2.2.5) 144 – enzyme catalysis 22–23
Molybdopterin synthase (EC 2.8.1.12) 140 NAD+ Pyrophosphatase (EC 3.6.1.22) 144 – glutamate metabolism 61
Monensin 181 NAD+ Synthase (glutamine-hydrolyzing) – ligase/ADP-ribosylation reactions 145
Monoamine oxidase (EC 1.4.3.4) 76, 77 – lysine degradation 65
Monocarboxylate transporter (TC 2.A.1.13) 275 (EC 6.3.5.1) 144 – nucleotides and nucleosides 124
Monocyclic monoterpenes 198 NAD(P) Transhydrogenase (EC 1.6.1.1) 144 – photosynthesis 190–191
Monocyclic sesquiterpenes 198 NADH Dehydrogenase (EC 1.6.99.3) 97, 176 – pyruvate dehydrogenase regulation 47–48
Monocytes NADH Dehydrogenase (quinone) (EC 1.6.99.5) 97, 176 – respiratory chain, extramitochondrial carrier
– complement receptors 336 NADH Peroxidase (EC 1.11.1.1) 144
– cytokines 341 NADPH Ferrohemoprotein reductase systems 187
– immune system development 330 – tryptophan degradation 76
– innate immune system 326 (EC 1.18.1.2) 89 Nicotinamide adenine dinucleotide phosphate
Monod-Changeux-Wyman symmetry model 25 Na+: bile salt cotransporter (TC 2.A.28.1) 275
Monodehydroascorbate reductase (NAD) 147 Na+: Ca++ + K+ exchanger (TC 2.A.19.4) 275 (NADP+/NADPH)
12a-Monoxygenase (EC 1.14.13.95) 121 Na+-Cl−-dependent Na+-neurotransmitter – aromatic amino acids 74, 76
24-Monooxygenase (EC 2.3.1.154) 122 – ascorbate metabolism 145
Monooxygenases, ascorbate symporters (TC 2.A.22.1 - 6) 275 – biosynthesis and degradation 143–145
– metabolism 145 Na+-coupled neutral amino acid transporter (TC – dark reactions 192
Monoterpenes – fatty acid reaction sequence 93–94
– classification 198–199 2.A.18.6) 275 – glutamate metabolism 61
– indole alkaloids 203, 205 Na+-coupled nucleoside symporter (TC 2.A.41.2) 275 – glutathione metabolism 69
– nicotine biosynthesis 203 Na+-dependent ascorbic acid symporter – morphine biosynthesis 207
Monounsaturated fatty acids 6 – pentose phosphate cycle 51–52
Moorella sp. 175 (TC 2.A.40.6) 275 – photosynthesis 190–191
Morphine biosynthesis 207, 209 Na+:glucose cotransporter (GLUT 1...5) – reactive oxyten species 70
Morphine 6-dehydrogenase (EC 1.1.1.218) 207 – tryptophan degradation 76
Morphine-type compounds 206 (TC 2.A.21.3 … 8) 41, 275 Nicotinamide coenzymes 144–145
Morquio syndrome 34 Na+ / H+ exchanger (TC 2.A.36.1., -.8) 275 Nicotinamide mononucleotide (NMN), in NAD+/NADP+
Motifs, protein structure 19–20 Na+/ K+-ATPases (TC 3.A.3.1.1 … 2) 277, 278
Motor model Na+/K+ exchanging ATPases biosynthesis 143
– chloroplast protein transport 255 Nicotinamide riboside kinase (EC 2.7.1.22) 144
– mitochondrial protein transport 253 (TC 3.A.3.1, 3.A.3.2) 277–278 Nicotinate N-methyltransferase (EC 2.1.1.7) 67
Mouse studies 123 Naked DNA 159 Nicotinate/nicotinamide nucleotide adenylyltransferase
M phase, eukaryotic cell cycle 232 Na+:PO43− cotransporter Type III (TC 2.A.20.2) 275
mRNA. See Messenger RNA (mRNA) Na+: sulfate/carboxylate cotransporter (EC 2.7.7.18) 144
mRNPs 222 Nicotinate, in NAD+/NADP+ biosynthesis 143–144
Mucins 33 (TC 2.A.47.1) 275 Nicotinate phosphoribosyltransferase (EC 2.4.2.11) 144
Mucopolysaccharides 34 Naltrindole 298 Nicotine, biosynthesis of 203
Mucopolysaccharidosis 34 Naringenin 3-dioxygenase (EC 1.14.11.9) 196 Nicotine N-demethylase (EC 1.14.13.B3) 203
Muir-Torre syndrome 164 NarXL regulon 213 Nicotine synthase 203
Müllerian inhibitory substance (MIS) 289 Natural antibodies 333 Nicotinic acetylcholine receptor/ion channels
Natural immune system 325
Natural killer (NK) cells (TC 1.A.9.1.1) 273–274
– antibody-dependent cell-mediated cytotoxicity 350 Nicotinic acid 203
– apoptosis 347
– cytokines 341

Index 390

Nicotinic receptors, neurotransmission 297 Nucleosome filament 28–29 Oxidation
Nikkomycin 181 5¢-Nucleotidase (EC 3.1.3.5) 127, 129, 131, 132 – chemolithotrophy 176–177
Nitrate ammonification 174 Nucleotide(s) – DNA damage 151–153
Nitric oxide (NO) – alkylation 151 – fatty acids 97–98
– cGMP dependent pathways 322–323 – -binding structures 19 – tocopherol 148
– guanylate cyclase activation and metabolism 323 – characterized 124–133 Oxidative phosphorylation
– vasodilatory/antiaggregatory effects 324 – eukaryotic DNA repair 162–163 – chemolithotrophy 175
Nitric oxide synthase (EC 1.6.99.1) 323 – excision repair, DNA repair systems 153–154, – electron transport 183–184
Nitrification 176 – mitochondria and bacteria 185–186
Nitrite, chemolithotrophy 177 162–163 Oxidoreductases 23
Nitrobacter 177 – long patch repair 154–155 2,3-Oxidosqualene-b-amyrin cyclase 200
Nitrogen – pentose phosphate cycle 52 2,3-Oxidosqualene-a-amyrin cyclase
– circulation of 59 – purine bases 124–125
– fixation and metabolism 58–59 – pyrimidine bases 130–131 (EC 5.4.99.40) 200
– secondary plant metabolites 201–209 – sequence databases 367 2,3-Oxido-squalene-cycloartenol-cyclase
Nitrogenase (EC 1.18.6.1), composition 58–59 – sugars 48
Nitrogen monoxide, hemoglobin/myoglobin oxygen Nucleotide sugar transporters (NSTs, (EC 5.4.99.8) 200
3-Oxoacid CoA-transferase (EC 2.8.3.5) 97
binding 283 TC 2.A.7.10 - 15) 277 3-Oxoacyl-[acyl-carrier-protein] reductase
Nitrogenous compounds 171–172 Nucleus, protein transport in 249–251
Nitrosomonas 176–177 (EC 1.1.1.100) 94
N-linked glycans, protein folding 247 O 3-Oxoacyl-[acyl-carrier-protein]synthase
N-linked glycosylation, protein processing 238–239
NMDA (N-methyl-D-aspartate) O-antigen 165 (EC 2.3.1.41) 94
– ligand-gated ion channels 274 Obligate anaerobic bacteria 187 2-Oxoglutarate dehydrogenase (EC 1.2.4.2) 56, 149
NMDA receptors (TC 1.A.10.1.3) 298 Obligate methylotrophs 178 Oxo groups 133
Nod-like receptors (NLRs) 326–327 O-Glycans, glycoprotein synthesis 241 5-Oxoprolinase (ATP-hydrolysing) (EC 3.5.2.9) 69
Nodosomes 327 Okazaki fragments 3-Oxo-5b-steroid d4-dehydrogenase
Non-adaptive immune system. See Innate, non-adaptive – eukaryotic DNA replication 159–160
– synthesis 151 (EC 1.3.99.6) 120, 122
immune system Oleoyl-[acyl-carrier-protein] hydrolase Oxygen saturation, hemoglobin/myoglobin 284–285
Noncompetitive inhibition 11–12, 24 Oxygen transport, hemoglobin/myoglobin 282–285
Noncyclic electron flow 188–189 (EC 3.1.2.14) 94 OxyR regulon 213
Non-distributive action, nucleic acid degradation 217 Oligomeric enzymes 25 Oxytocin, uterus contraction 293
Non-genomic effects, corticosterid metabolism 119–121 Oligosaccharides
Non-glycolytic fermentation 171–172 – dolichol-bound synthesis 239 P
Non-glycosylated pentacyclic triterpenes 201 – glycosylation 32
Non-hydrolyzable tannins 197 – metabolism 48 P2X family, ligand-gated ion channels 297
Non-mevalonate pathway 112 Oligoterpenes 201 (TC 1.A.7.1.1- TC 1.A.7.1.3) 273–274
Nonmuscle cells, structure and function 307 O-linked glycosylation, protein processing 238
Non-procressive action O-mannosylation, protein processing 238 p53 protein, cell cycle checkpoints 236–237
– DNA polymerases 158 OMIM-Online Mendelian Inheritance in Man p67 polypeptide, hemoglobin oxygen transport and
– nucleic acid degradation 217
Non-proteinogenic amino acids 201 database 367, 373 biosynthesis 282–283
Nonsense-mediated mRNA decay (NMD) 231 Oncogenes, cell growth and function 311 Paclitaxel 198
Non-translated region (NTR), hepatitis C viral Ondansetron 298 Paeonidin 197
One-substrate reactions 10 Palmitic acid 6
genome 267 Open initiation complex 219 Palmitoylation 19
Noradrenaline. See norepinephrine Open reading frame (ORF), hepatitis C viral Pancreatic hormones, synthesis and regulation 293
Norcoclaurine 6-O methyltransferase (EC 2.1.1.128) 207 Pancreozymin (PZ) 293
Norepinephrine genome 267 Pantetheine-phosphate adenylyltransferase
– biosynthesis and degradation 78 Opsonizing receptors
– neurotransmission 297–298 – complement system 336 (EC 2.7.7.3) 142
– regulation and metabolic effects 287–288 – innate immune system 326 PANTHER database 368
(S)-norcoclaurine synthase (EC 4.2.1.78) 207 Ordered multistep model, mRNA transcription 220 Pantoate-b-alanine ligase (EC 6.3.2.1) 142
Nornicotine 203 Ordered sequential, generally Pantothenate 141–142
Ntr regulon 213 – mechanism 21 Pantothenate kinase (EC 2.7.1.33) 142
Nuclear DNA 17 – reaction 12 Papaver sp. 206
Nuclear envelope breakdown, mammalian cell cycle 235 Organic anion transporter (TC 2.A.60.1) 275 Papillomavirus 264–266
Nuclear hormone receptors 321 Organic cation/anion/zwitterions antiporter Paracoccus sp. 186–187
Nuclear import and integration, Paracrine cytokines 338
(TC 2.A.1.19) 275 Paramecia 30
HIV replication 269–270 oriC protein, replication initiation 149–150 Parasympathetic nervous system, neurotransmission
Nuclear localization sequence (NLS) 250–251 Origin recognition complex (ORC) 157 Parathyroid hormone
Nuclear pore complex (NPC) 250–251 Oripavine 6-O-demethylase (EC 1.14.11.31) 207 – intercellular transmission 286
Nuclear receptors L-Ornithine 6 – ion channel regulation 292
– activation model 322 – glutamate conversion 61 Passive transport, bacteria 168–169
– superfamily 322 – nicotine biosynthesis 203 Pathogen-associated molecular patterns (PAMPS)
Nuclear scaffold proteins 28 – polyamine metabolism 81–82 – immune response regulation 344
Nucleic acids – tropane alkaloids 208 – innate immune system 326
– components 26–27 Ornithine aminotransferase (EC 2.6.1.13) 60 Pathologic immune reponses
– degradation 217–218 Ornithine carbamoyltransferase (EC 2.1.3.3) 81 – autoimmunity 353–354
Ornithine decarboxylase (EC 4.1.1.17) 81, 203, 208 – G-protein coupled receptor activity 301
– Type I/Type II/Type IIS/Type III enzymes 156–157 Orotate phosphoribosyl transferase (EC 2.4.2.10) 132 – IgE-mediated hypersensitivity of the immediate
– fractal enyzme kinetics 13 Orotate reductase (EC 1.3.1.14) 132
– structure of 26–29 Orotidine-5¢-phosphate decarboxylase type 352–353
Nucleolar organizer region (NOR) 223 – lysis of pathogens 336
Nucleophilic substitution reaction, cholesterol (EC 4.1.1.23) 132 – soluble factors and receptors 326
Orphan channels, membrane transport 274 Pattern recognition receptors (PRRs) 326
biosynthesis 107 Oryza sativa 101 Pectate 17
Nucleoplasmic transport 251–252 Osmoprotection 104 Pelargonidin 197
Nucleoporins 250–251 Osteomalacia 148 Penicillin
Nucleosidase (EC 3.2.2.9) 131 Outer membrane envelope – biosynthesis of 179–180
Nucleoside diphosphates 124 – bacteria 164–165 – precursor peptides 19
Nucleoside diphosphatase (EC 3.6.1.6) 127, 131 – chloroplast protein transport 255–256 – semisynthetic 179
Nucleoside diphosphate kinase – mitochondrial protein transport 252–253 Penicillin amidase (EC 3.5.1.11) 180
– protein transport 166 Penicillinium sp. 181
(EC 2.7.4.6) 128–130, 132 – viruses 263 Pentanoic acid 298
Nucleoside(s) Ovalalbumin 21 Pentose 124
– characterized 124–133 Oxalate CoA transferase (EC 2.8.3.2) 58 – chemistry and structure 4
– diphosphates 23 Oxalate decarboxylase (EC 4.1.1.2) 58 – metabolism
– purine bases 124–130 Oxaloacetate decarboxylase (EC 4.1.1.3) 171
– pyrimidine 130–133 Oxalyl-CoA decarboxylase (EC 4.1.1.8) 58 – decarboxylation reactions 52–53
Nucleoside triphosphates 124 Oxidases, fatty acid degradation 97 – in humans 54
– overview 1, 51–54
– pentose phosphate cycle 50–52
– plant cell walls 53–54

391 Index

Pentose phosphate cycle Phosphatidyl-N-methylethanolamine N-methyltransferase – glycogen metabolism 44
– hexose metabolism 50–51 (EC 2.1.1.71) 100 – HMG-CoA reductase 109
– mechanisms of 51–52 – in signal cascades 311–317
– plant cell decarboxylation and cell wall Phosphatidylserine (PS) – potential 183
– characteristics 36 – primary active transport systems 277
synthesis 53–54 – metabolism 100–101 – protein kinase G 324
Pentraxins, immune system 325–326 Phosphatidylserine decarboxylase (EC 4.1.1.65) 100 – protein structure 19
PEP-carboxykinase (EC 4.1.1.32) 47 Phosphoacetylglucosamine mutase (EC 5.4.2.3) 54 – RNA polymerase transcription factors 219
Pepsin (EC 3.4.23.1), reaction mechanisms 257–258 Phospho-N-acetylmuramoyl-pentapeptide-transferase – small G-proteins 315
Peptidases, classification 256–258 Phosphoserine phosphatase (EC 3.1.3.3) 64
Peptide(s) (EC 2.7.8.13) 165 Phosphoserine transaminase (EC 2.6.1.52) 38, 64
– bonds 6 3¢-Phosphoadenylylsulfate (PAPS) 69 Phosphotransferase systems (PTS)
– bound peptides 337 Phosphoadenylyl-sulfate reductase (thioredoxin) – bacterial transport 169
– chain 32 – gene regulation 213
– enzyme regulation 24 (EC 1.8.4.8) 66 Phosporibosyl-formyl-glycinamidine cycloligase
– glycosylated 32–35 Phosphoarginine 80–81
– in protein structure 18–19 Phosphocreatine 80–81 (EC 6.3.3.1) 126
– redox stabilization 69 Phosphodiesterase (PDE, EC 3.1.11.1), visual Phosporibosyl-formyl-glycinamidine synthase
Peptidoglycans
– bacterial envelope 15, 164–165 process 307 (EC 6.3.5.3) 125
– glycosylation 32, 35 Phosphoenolpyruvate carboxykinase Photoreactivation
Peptidyltransferase (EC 2.3.2.12) 229 – DNA damage repair 153, 162
Peptostreptococcus sp. 172 (EC 4.1.1.31) 46, 47 Photorespiration
Peripheral (dominant) tolerance 351 Phosphoenolpyruvate carboxylase – C4 cycle 193
Periplasmic proteins – glycine metabolism 65
– bacterial translation 216 (EC 4.1.1.31) 47, 170 – glyoxylate reactions 58
– transport mechanisms 166 Phosphoenolpyruvate (PEP) 46–47 Photosynthesis
Peroxidase (EC 1.11.1.7) 70 – branched-chain amino acids 72–73 – chloroplasts 17
Peroxide radicals 70 1-Phosphofructokinase (EC 2.7.1.56) 37, 38 – cytochromes 87
Peroxisomes 16–17 6-Phosphofructo-1-kinase (PFK, EC 2.7.1.11) 37–38 – dark reactions 192–193
Peroxynitrite 70 – glycolysis and dephosphorylation 39–40 – hexose derivatives 49–51
Pertussis toxin, G-protein coupled receptor Phosphoglucokinase (EC 2.7.1.10) 37, 43 – light reaction 188–191
Phosphoglucomutase (EC 5.4.2.2) 37, 38, 181 – starch synthesis and degradation 43–44
activity 301 Phosphogluconate dehydratase (EC 4.2.1.12) 171 Photosystem(s)
PEST sequence, protein degradation 238 Phosphogluconate dehydrogenase (decarboxylating) – I and II 188–190
Petunidin 197 – in purple bacteria 190
Pfam database 366, 368 (EC 1.1.1.44) 52, 171 Phycobiliproteins 88
Phagocytic cells, pathogen defense 326 6-Phosphogluconolactonase (EC 3.1.1.31) 52 Phycobilisomes 189
Phagocytosis Phosphoglycerate dehydrogenase (EC 1.1.1.95) 64 3Z-Phycoerythrobilin-ferredoxin oxidoreductase
– cellular uptake 278 Phosphoglycerate mutase (EC 5.4.2.1) 37, 38
– complement system 336 Phosphoglycerides 7, 100–101 (EC 1.3.7.3) 89
Phenolic compounds, in plant metabolism 194 Phosphoglyceromutase (EC 2.7.5.3) 179 3Z-Phycocyanobilin-ferredoxin oxidoreductase
L-Phenylanine 5 Phosphoglycolate phosphatase (EC 3.1.3.18) 179
– biosynthesis 74 D-3-Phosphoglyerate dehydrogenase (EC 1.3.7.5) 89
– derivatives and degradation 76 Phylloquinone 148–149
– genetic code 30 (EC 1.1.1.95) 38 – bacterial biosynthesis 75
– essential amino acid 59 3-Phosphoglyerate kinase (EC 2.7.2.3) 37, 38 – branched-chain amino acids 73
– phenylpropanoid compounds 195 Phosphoinositol 314 – enzyme catalysis 23
Phenylalanine ammonia-lyase (EC 4.3.1.24) 195 Phosphoketolase (EC 4.1.2.9) 171 Phylogenetic tree, papillomaviruses 264–266
Phenylalanine 4-monooxygenase (EC 1.14.16.1) 74, 76 Phospholipase A1 (EC 3.1.1.4) 102 PhysicalEntities, Reactome database 373
Phenylethanolamine N-methyltransferase Phospholipase A1 (EC 3.1.1.32) 102 Phytoalexins 197
Phospholipase A2 (EC 3.1.1.4) 102 Phytochrome 88
(EC 2.1.1.28) 78 Phospholipase C (PLC, EC 3.1.4.3) 102 Phytochromibilin synthase (EC 1.3.7.4) 89
Phenylpropane 195–196 – activation 302–303 Phytoecdysteroids 201
Phenylpropanoids, in plants 195 – arachidonic acid release 309 Phytoene 201
pH levels – olfactory processes 308 Phytols 198
– chemolithotrophy 177 Phospholipase D (EC 3.1.4.4) 102 Phytosterols 198
– enzyme catalysis 22 Phospholipase D (PLD, EC 3.1.4.4), arachidonic acid – biosynthesis 110–111
– hemoglobin/myoglobin oxygenation 284 Phytyl-PP 114
Phosphagens 80–81 release 309 PI 3K pathway, insulin receptor activation 313–314
Phosphatase 144 Phospholipases (PL), survey 101–102 Pierotoxin 298
Phosphatase activation Phospholipids Pili 15
– glycogen synthesis and degradation 45 – contact activation 358–359 Pimeloyl-CoA, biotin biosynthesis 141, 143
– signal cascades 312 – metabolism 100–103 Ping-pong reaction 12–13, 22
Phosphatase I (PP1, EC 3.1.3.16) 44 – species distribution 101 Pinocytosis, vesicular transport 278
5¢-Phosphatase (EC 3.1.3.73) 92 Phosphomevalonate kinase (EC 2.7.4.2) 107 Piperidine 203
Phosphate(s) Phospho-pantothenate-cysteine ligase (EC 6.3.2.5) 142 Pirenzapine 298
– hormone regulation of 292 Phospho-pantothenoylcysteine decarboxylase PIRSF database 368
– intercellular transmission 286 Placental hormones 291–292
– respiratory chain carrier 187 (EC 4.1.1.36) 142 Planck’s constant 8
Phosphate acetyltransferase (EC 2.3.1.8) 170–172 Phosphonopropionic acid 298 Plant cell
Phosphatidate cytidylyltransferase (EC 2.7.7.41) 100 Phosphoribosyl-amine-glycine ligase (EC 6.3.4.13) 125 – cell walls 53–54
Phosphatidate phosphatase-1 (PAP-1, EC 3.1.3.4) 99 Phosphoribosyl-aminoimidazole-carboxamide – decarboxylation in 52–54
Phosphatidic acid 7 – fatty acid oxidation 97–98
Phosphatidylcholine 36 formyltransferase (EC 2.1.2.3) 126 – general structure 16
Phosphatidylcholine-retinol D-acyltransferase Phosphoribosyl-aminoimidazole-succino-carboxamide – primary and secondary 53
– purine nucleotide oxidation 127
(EC 2.3.1.35) 113 synthase (EC 6.3.2.6) 126 – starch synthesis 43–44
Phosphatidylethanolamine (PE) 101 Phosphoribosyl-AMP cyclohydrolase (EC 3.5.4.19) 79 – sterols 110–111
– characteristics 36 Phosphoribosylanthranilate isomerase (EC 5.3.1.24) 74 – synthesis 53
Phosphatidylethanolamine N-methyltransferase Phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) 79 – wood degradation 53–54
5-Phosphoribosyl-1-pyrophosphate (PRPP) 124–12 Plants
(EC 2.1.1.17) 100 – in pyrimidine biosynthesis 130 – biosynthetic reactions 2
Phosphatidylglycerol (PG) 101 Phosphoribosylglycinamide formyltransferase – cell structures 17
Phosphatidylinositol (PI) – chloroplasts 253–256
Phosphatidylinositol N-acetylglucosaminyltransferase (GART, EC 2.1.2.2) 124–125 – energy storage 31
Phosphoribosyl-PP, histidine synthesis 80 – glycerophospholipid synthesis 101, 104
(EC 3.5.1.89) 239–240 Phosphorylases – linear tetrapyrroles 88
3-Phosphatidyl-1-D-myo-inositol (PI) – allosteric mechanisms 45 – nitrogen-containing secondary metabolites 201–209
– cellular communication and 318 – dephosphorylation 44 – phosphate bonds 56
– membrane anchors 238 Phosphorylase a (EC 2.4.1.1) 45 – photosystems in 188–189
– metabolism 100–101 Phosphorylase b (EC 2.4.1.1) 45
– phosphates, reconstitution 305 Phosphorylase kinase (EC 2.7.11.19) 45
Phosphorylation
– ADP 126
– aspartate/asparagine metabolism 61
– chemolithotrophy 175
– DNA chain compaction 28
– enzyme regulation 26
– glucose 39

Index 392

– phytochelatins 69 Polyterpenes 201 Promoter regions
– plastids 95 Polytranslational glycosylation 238 – bacterial transcription 210
– protein processing in 240 Polyunsaturated fatty acids (PUFA), metabolism 309 – dispersed promoters, eukaryotic transcription 226
– secondary metabolism 193–209 Pompe’s disease 46 – gene regulation 213
– signals 197 P/O quotient 183 Proofreading
– sterols in 110–111 Porphilinogen deaminase (EC 2.5.1.61) 85 – replication fidelity 162
Plasma Porphobilinogen, conversion 87 – translesion synthesis 164
– hormone concentrations 291 Porphobilinogen deaminase (PBGD, EC 2.5.1.61) 84, 87 Proopiomelanocortin (POMC), hypothalamus-anterior
– lipid transport in 279–282 Porphobilinogen synthase (EC 4.2.1.24) 84, 85
– lipoproteins Porphyrias 85–86 pituitary homone system 288
Porphyrins 85 Prophase, mammalian cell mitosis 235
– classification and properties 279–281 Positive control, RNA binding 212 Propionyl-CoA carboxylase (EC 6.4.1.3) 68
– structures 279 Positive cooperativity, hemoglobin oxygenation 284 Propionyl-CoA, tetracycline biosynthesis 182
– long-lived plasma cells 347 Positive regulatory domains, eukaryotic Proprionbacterium 172
– proteins 336 PROSITE database 368
Plasmalogens 100, 102 transcription 228 Prostacyclins, structure and function 309
– chemistry and structure 7 Positive-stranded viruses 261 Prostaglandins
Plasmamylcholine 102 Postreplication repair 155 – classification 309
Plasmanylethanolamine 102 Postsynaptic receptors – metabolism and 101
Plasmanylethanolamine desaturase – agonists and antagonists 296, 298 Prostanoids
(EC 1.14.99.19) 103 – organization 296 – classification 309
Plasmatic factor 358 – reactions 294 – cyclooxygenase pathway and
Plasmids 15 Posttranslational carboxylation 61
Plasmin (EC 3.4.4.14) 364–365 Posttranslational modification biosynthesis 310
– blood coagulation and hemostasis 357 – implications of 6, 28 Prosteoglycans, synthesis 241
Plasminogen activation 364 – in proteins 238–244 Prosthetic groups
Plasmodesmata 17 – Sec-dependent transport 167 – enzyme catalysis 22
Plastocyanin, chloroplast protein transport 254 – of tubulin 278 – nucleotide/nucleoside metabolism 133
Plastoquinone, branched-chain amino acids 73 Potassium (K+) channels Protease inhibitors
Platelet activating factors (PAFs) 353 – hormone regulation 292 – coagulation factors and 361
– ether lipid biosynthesis 102–103 – nerve conduction and synaptic transmission 294 – protein function and 21
Platelet derived growth factor (PDGF) receptors – neurotransmission 297 Protease(s)
– enzyme degradation inhibition 81 – voltage-gated 272–273 – blood coagulation mechanisms 359, 361
– protein-tyrosine kinase activity 312 (p)ppGppp synthase I (RelA) 214 – protein degradation 256–259
Platelet endothelial cell adhesion molecule Precorrin 3B synthase (EC 1.14.13.83) 91 Proteasomes
(PECAM) 356 Precorrin reductase (EC 1.3.1.54) 92 – large, multifunctional 338
Platelets Pregnenolone 115 – ubiquitylation 259–260
– cell flattening and diapedesis 356 Preinitiation complex in transcription 219–220, 223 Protein(s). See also specific proteins
– immune system development 330 Pre-integration complex (PIC), retroviruses 268–271 – biosynthesis in bacteria 210–217,
– membrane receptors 363 Prekallikrein (PK), contact activation 358 – biosynthesis in eukarya 219–231
– structure and function 362–363 Pre-messenger RNA (pre-mRNA), immunoglobin – cell cycle analogies/homologies 234
Pleotropism, cytokines 338 – coagulation cascade 359
Plumbago indica 194 diversity 332 – degradation 256–260
Pluripotent stem cells 328 Prenylation 114
Point mutations, immunoglobulin genes 331 Prephenate dehydratase (EC 4.2.1.51) 74 – cell cycle 238
Pollinators, attraction of 193–194, 197 Prephenate dehydrogenase (NADP+) (EC 1.3.1.13) 74 – disulfide bond formation and isomerization 246
Poly(A) Pre-replication complex assembly 158, 234 – endoplasmic reticulum-Golgi
– characterized 221 Presequence, mitochondrial protein transport 252
– polymerase (PAP) 222 Pressure, defined 8 transport system 249
Poly(A) binding protein 1 (Pab1) 231 Presynaptic reactions, transmitter gated signalling 294 – family databases 367
Polyadenylation Pre-tRNAs – folding 244–247
– eukaryotic transcription 219 – modification and processing 224–225 – function databases 366–367
– mRNA processing 222 – nucleotide sequences 212 – glycosylated 32–35
Polyamine(s) P-Ribosyl-PP, in nucleotide biosynthesis 124–125 – kinases (See Protein kinases)
– degradation 82 Primary activator, eukaryotic cell cycle 232 – lipid-anchored 239–240
– synthesis 81–82 Primary active transport systems – lipid transport 281
Polyamine oxidase (EC 1.5.3.11) 82 – membrane transport 277–278 – location 238–239
Polycistronic operons 211 – TC classification 272 – membrane proteins 336
Polygalacturonase (EC 3.2.1.15) 53 Primary bile acids 123 – posttranslational modification 238–244
Polyglutamylation of reduced folate 138 Primary metabolism, plants 193–194 – secretion pathways 167
Polyketide pathway 194–195 Primary structure, in proteins 19 – secretion systems Type I - Type VI 167
Polymerase switch, eukaryotic DNA replication 159 Primase enzyme 150 – selenocysteine-containing,
Polymeric carbohydrates Primosome 150 – special functions database 367
– energy storage 31 PRINTS database 368 – species 371
– structural elements 32 Prions, structure and function 261 – structure and function of 18–21
Polypeptide(s) Proapoptotic proteins 348 – structure databases 367
– chain 19 Processing bodies (PB), mRNA degradation 231 – transport
– genetic code 30 Processive action, nucleic acid degradation 217
– globin synthesis 282–283 Procollagen-proline dioxygenase (EC 1.14.11.2) 63 – chloroplast proteins 254–256
– immune system development 330 Proenzyme activation 24 – cytoplasmic membranes 166–167
– immunoglobulin disulfide bridges 331–332 Progesterone – mitochondrial proteins 252–254
– nuclear protein transport 249–251 – biosynthesis 114, 115–116 – nuclear transport 249–251
– synthesis 215–217 – hypothalamo-pituitary-uterus axis 290 – viral, expression 269
Polypeptide N-acetylgalactosaminyltransferase Prokarya Protein Data Bank (PDB) 372
(EC 2.4.1.41) 241 – classification of 14 Protein Database 371–372
Polypodium sp. 201 – electron transport 183 Protein Information Resource (PIR) 368
Polyprotein processing 267 – structure of 14–15 Protein kinase A (EC 2.7.10.2) 94
Polyribonucleotide nucleotidyl transferase Prolactin Protein kinase A (PKA, EC 2.7.11.1) 302
(EC 2.7.7.8) 128, 131 – cytokine receptors 318 – activation 302–303
Polysaccharides – hypothalamo-pituitary-testis axis 289 – substrates 302
– bacterial cell envelope 165–166 – receptors 316 Protein kinase B (PKB = AKT, EC 2.7.11.1) 314
– catabolism of 44 L-Proline 5 Protein kinase C (PKC, EC 2.7.11.13) 302
– disease aspects 45 – essential amino acis 59 – activation 302–303
– functions of 31–32 – genetic code 30 – substrates 303
– metabolism 42–46 – metabolism 62–63 – T cell receptors 317
– prokaryotic cells 15 – structure 32 Protein kinase G (PKG, EC 2.7.11.12) 323–324
Polysaturated fatty acids 6 Proline dehydrogenase (EC 1.5.99.8) 59, 63 Protein kinases (generally)
Polysome(s), translational factors 215 D-Proline reductase (dithiol) (EC 1.21.4.1) 63 – cascades 311–319
Prometaphase, mammalian cell mitosis 235 – DNA repair 164
– downstream 315
Protein phosphatase 2A (EC 3.1.3.16) 94
Protein phosphatase 2C (EC 3.1.3.16) 94

393 Index

Protein synthesis Pyrophosphatase (EC 3.6.1.1) 96, 127 Reaction, generally
– enzyme regulation 24 Pyroptosis 326 – specificity 21
– priciples of information transfer 30–31 1-Pyrroline-4-hydroxy-2-carboxylate deaminase – substrate reactions 21–22
Protein tyrosine kinases (PTK, EC 2.7.10.2) 312–319 – velocity 10
– receptor associations 319 (EC 3.5.4.22) 63 Reaction rate, enzymes 23–24
– signal cascades 312 1-Pyrroline-5-carboxylate dehydrogenase (EC Reaction center regneration, photosynthesis 190
Proteoglycans 32–33 Reactive oxygen species (ROS)
Proteolysis 1.5.1.12) 60, 63 – damage and protection mechanisms 70–71
– limited and unlimited 256 Pyrroline-2-carboxylate reductase (EC 1.5.1.1) 63 – innate immune system 326
– ubiquitin regulation 259 Pyrroline-5-carboxylate reductase Reactome database 372–373
Proteolytic activation cascade 357 REBASE database 371
Proteome analysis 366 (EC 1.5.1.2) 59, 63 Receptor interacting protein-2 (RIP2) 327
Proto-alkaloids 202 Pyrrolinium 203 Receptor-mediated effect
Protochlorophyllide oxidoreductase Pyrrolizidine alkaloids – apoptotic response 321
– amino acid precursor 202 – corticoid metabolism 119
(POR, EC 1.3.1.33) 90 – bioactivation 205 Receptor(s). See also specific receptor types
Protochlorophyllide reductase (EC 1.3.1.33) 90 – nicotine biosynthesis 203 – binding, hepatitis C virus 267
Protoheme – structure 202–203 – heterotrimeric G-protein coupling 299–311
– bilin formation and degradation 89 – synthesis and structures 204 – intercellular transmission 286–287
– heme oxidation 84–85 Pyrrolo-quinolone quinone (PQQ) – intracellular communication 298–299
Proton motive force (PMF), bacterial transport 168 – enzyme catalysis 23 – postsynaptic 296
Proto-oncogenes 311 – quinoenzymes 178 – protein function 21
Protopectin 53 Pyrrolysine 6, 18 – proteins 296
Protoporphyrins Pyruvate – signal cascade 313
– biosynthetic reactions 2 – branched-chain amino acids 71 – tyrosine kinases (RTKs) 311–319
– chlorophyll biosynthesis 90 – citrate cycle regulation 57 – phospholipase activation 302–303
Protoporphyrinogen oxidase (EC 1.3.3.4) 86 – cysteine metabolism 68 – signaling system cross talk 314
Protozoans, mitochondria 31 – lipoate biochemistry 149 – structure 312–313
Provirus DNA, in HIV replication 269–270 – oxidation 46 Recombinases, immunoglobin diversity 332
Proximal sequence element (PSE) 223 – pantothenate biosynthesis 142 Recombination
Proximity effects, enzyme catalysis 22 – pyridoxine metabolism 136 – class switch recombination 332–333
Prunus sp. 201 – quinone cofactor biosynthesis 75 – DNA repair 154–155
P-Selectin 354 – reactions of 38 – double-strand DNA repair 164
Pseudoalkaloids – sugar fermentation 169–170 – immunoglobulin genes 331–332
– in plant metabolism 201–202 – thiamine biosynthesis 134 Redox reactions
– secondary metabolites 194 – turnover 46–47 – chemolithotrophy 175–177
Pseudomonas sp. Pyruvate carboxylase (EC 6.4.1.1) 46–48, 93 – effects 22
– biotin metabolism 141–142 Pyruvate decarboxylase (EC 4.1.1.1) 48, 170, 171 – electron transport 173, 184
– chemolithotrophy 177 Pyruvate dehydrogenase (EC 1.2.1.51) 46–48 – lipoate 149
– cobalamin synthesis 137 Pyruvate dehydrogenase (acetyl-transferring) – NAD+/NADP+ biosynthesis 144
– fermentation 172 – oxidative phosphorylation 184
– linear tetrapyrroles 88 (EC 1.2.4.1) 134, 171 – photosynthesis 191
– peptidase specificity 257 Pyruvate kinase (EC 2.7.1.40) 37, 38, 170 – potentials 9, 173, 191
– Sec-independent secretion 167 – citrate cycle 56 Reductive citrate cycle 55
– transcription inhibition 225 – regulation mechanisms 40 Redundancy, in cytokines 338
PSI-BLAST database 368 6-Pyruvoyltetrahydropterin synthase Regulating DNA sequence elements, eukaryotic
Psicose 4
Pteridines, biosynthesis 140 (EC 4.6.1.10) 139 transcription 226
Pterin-4a-carbinolamine dehydratase (EC 4.2.1.96) 139 Regulatory particles (RPs), ubiquitylation 259–260
Pterines 138–141 Q Regulatory proteins, transcription initiation 212
PUBCHEM database 367 Regulatory systems, two-component 212
Purine Q-cycle Regulatory T cells
– alkaloids 202, 204 – in photosynthesis 189–190 – adaptive immune system 328
– bases 124–125 – in respiratory chain 185–186 – immune response regulation 345
– deoxyribonucleotide interconversion and Quantitative metabolic flow analysis 366 Regulon 80
Quantity of matter, characterized 8 Releasing hormones 114
degradtion 129 Quaternary structure, in proteins 21 Renin-angiotensin system 293
– nucleotides and nucleosides 124–130 Quinine 205 b-Replacement 137
– ribonucleotide interconversion and degradation 125 Quinoenzymes 178 Replicase assembly 267
– in thiamine biosynthesis 134 Quinolinate 77 Replication
Purine nucleosidase (EC 3.2.2.1) 127 Quinolinate phosphoribosyltransferase – cell cycle checkpoints 237
Purine nucleoside phosphorylase (EC 2.4.2.1) 127, 129 – bacterial DNA 149–153
Puromycin 181 (decarboxylating) (EC 2.4.2.19) 144
Purple bacteria Quinolinate synthase (EC 2.5.1.72) 144 – cell cycle 149
– cytochromes 87 Quinolizidine alkaloids 202–203 – fidelity 151
– photosynthesis 188–189 Quinone(s) – initiation 149–150
– photosystems in 190 – chloroplast protein transport 256 – reaction mechanisms 150
– redox reactions 191 – cofactors 75 – eukaryotic DNA 157–162
Putrescine 203–204 – functions of 23 – cell cycle 157
– polyamine synthesis 81–82 Quinone reductase (EC 1.6.5.1) 148 – fidelity 162
Putrescine N-methyltransferase (EC 2.1.1.53) 208, 203 Quinoprotein methanol dehydrogenase – initiation 157–158
Pyranose 4 – forks 159–160
Pyridine alkaloids 202 (EC 1.1.2.7) 179 – genomes 157
Pyridoxal kinase (EC 2.7.1.35) 136 – in papillomavirus 265–266
Pyridoxal phosphate 23 R – in retroviruses 268–271
Pyridoxamine-P 136 – in yeast 157–158
Pyridoxamine-P oxidase (EC 1.4.3.5) 136 Rab families 315 Repression mechanisms, gene regulation 213
Pyridoxine (Vitamin B6) 136–137 Rabies virus 263 Repressor proteins
Pyridoxine 4-dehydrogenase (EC 1.1.1.65) 136 Racemizations 137 – eukaryotic elements 227
Pyrimidine Rac/Rho family 315 – protein function 21
– bases 124 Radical compounds – transcription modulation 227
– DNA damage 151 – translational regulation 231
– deoxyribonucleotide interconversion and – tocopherol 148 Resistance-nodulation-cell-division superfamily
degradation 132 Ramachandran diagrams 6 (TC 2.A.6 - 7) 169
Ran-dependent transport 250–251 Respiration, redox reaction free energies 184
– dimerization 151 Random sequential reaction 12 Respiratory chain
– nucleotides and nucleosides 130–133 – enzymes 21–22 – citrate cycle regulation 57
Ran family 315 – extramitochondrial hydrogen carrier
– ribonucleotide interconversion and degradation 131 Ran-independent transport 251
– transketolase reaction mechanism 135 Rapamycin 314 systems 187
Pyrimidine deaminase (EC 1.3.1.1) 135 Ras family
Pyrimidine nucleoside phosphorylase (EC 2.4.2.4) 131 – signaling cascades 314–315
Ras/Raf/MAPK pathway 316
Rat studies 123

Index 394

– mammalian mitochondria 184 Ribose Rod cells 307
– mitochondria and bacteria 185–186 – chemistry and structure 4 Rohmer pathway 112, 198
Resting state, eukaryotic cell cycle 232 – histidine biosynthesis and degradation 79 – terpenoid biosynthesis 198
Restriction endonucleases 218 – metabolism 51 Rolling circle mechanism
– Type I/Type II/Type IIS/Type III enzymes 218 Ribose 5-P – DNA replication 149
– degradation 156 – metabolism 51–52 – DNA viruses 264
Restriction-modification (R-M) systems 218 – purine biosynthesis 124 – leukocyte adhesion 354
Resveratrol 196 Ribose-phosphate diphosphokinase (EC 2.7.6.1) 79 Root structure, glycosphingolipids 104–105
Resveratrol synthase (EC 2.3.1.95) 196 Ribose-5-phosphate isomerase (EC 5.3.1.6) 52 RORgT 344
Reticulocytes 231 Ribose-phosphate pyrophosphokinase Rosmarinus 198
– globin biosynthesis 282–283 Rotavirus 263
Retinal dehydrogenase (EC 1.2.1.36) 113 (EC 2.7.6.1) 52, 125, 132 Rough endoplasmic reticulum 16
Retinal rods 307 Ribosomal proteins Rous sarcoma virus 268
Retinoic acid – biosynthesis 215 R state, hemoglobin oxygenation 284
– biochemical function 134 – rRNA transcription 223 Rubber cis-polyprenyl cis-transferase
– intracellular communication 298 Ribosomal recycling factor (RRF)
Retinoids – E. coli translator 215 (EC 2.5.1.20) 113
– metabolism 112–113 – eukaryotic translation 231 Rubredoxin-NAD+ reductase (EC 1.18.1.1) 178
– receptors 321–322 – nucleic acid degradation 217 Ryanodine-inositol-P family
Retinol dehydrogenase (EC 1.1.1.1) 113 Ribosomal RNAs (rRNAs) – calcium metabolism 304
Retinol fatty-acyltransferase (EC 2.3.1.76) 113 – protein coding 211 – ligand-gated ion channels 274
Retinol (Vitamin A) 133–134 – transcription and processing 223–224 Ryanodine receptor family (TC 1.A.3.11) 274
Retinol-protein complexes 112 Ribosomal subunits
Retinylpalmitate esterase (EC 3.1.1.21) 113 – eukaryotic translation 230 S
Retrograde movement, membrane – rRNA transcription and processing 223–224
Ribosomal synthesis 19 Saccharides 32. See also polysaccharides
transport 278 Ribosomes – chemistry and structure 4
Retroviruses – bacterial translation 215 Saccharomyces cerivisae
– classification and structure 268–271 – eukaryotic translation 228–229 – cell cycle regulation 234
– genomic characteristics 261 – protein folding, endoplasmic reticulum 247 – DNA replication 157–158
– prokaryotic cells 15 – rRNA transcription 223 – double-strand DNA repair 164
Reversed electron pumping 175–176 Ribozymes – fermentation 172
Reverse transcription, human immunodeficiency – bacterial transcription 210 – mitochondrial codon differences 31
– histidine synthesis 80 – mitochondrial protein transport 252
virus 268–269, 271 – ribonuclease differentiation 157 Saccharopine dehydrogenase (NAD+,
RGS family 300 – RNA protein coding 211
Rh ammonium transporter (TC 1.A.11.4) 275 – translational factors 215 L-glutamate-forming) (EC 1.5.1.9) 68
Rhamnose – untranslated RNA 212 Saccharopine dehydrogenase (NAD+, L-lysine-forming)
– pentose phosphate cycle 51 Ribulokinase (EC 2.7.1.16) 53
– in plant cell wall 53 D-Ribulokinase (EC 2.7.1.47) 52 (EC 1.5.1.7) 68
Rhamnosidase (a: EC 3.2.1.40, b: Ribulose 4 Saccharopine dehydrogenase (NADP+,
– reduction 52
EC 3.2.1.43) 54 Ribulose 5-P L-glutamate-forming) (EC 1.5.1.10) 68
Rhesus-system, blood groups 243 – pentose phosphate cycle 51–52 Saccharopine dehydrogenase (NADP+,
Rhizobium 58 – transketolase reaction mechanism 135
Rhodobacter sp. 188 Ribulose bisphosphate carboxylase/oxygenase L-lysine-forming) (EC 1.5.1.8) 68
– chlorophyll biosynthesis 90 Saccharopolyspora 181
Rhodopseudomonas sp. (Rubisco, EC 4.1.1.39) 192 S-adenosylhomomocysteine (SAH) 66
– lysine metabolism 65 – Calvin cycle regulation 192–193 S-adenosyl methionine (SAM)
– photosynthesis 190 Ribulose monophosphate pathway 179 – chlorophyll biosynthesis 90
Rhodopsin L-Ribulose-phosphate 3-epimerase (EC 5.1.3.1) 52, 53, 171 – coproporphyrinogen III dehydrogenase
– protein function 21 L-Ribulose-phosphate 4-epimerase (EC 5.3.1.4) 52, 53
– visual process 307–308 Rickets 148 (EC 1.3.99.22) 88–89
r-independent DNA, bacterial transcription 211 Rieske-iron-sulfur protein 185 – enzyme catalysis 23
Ribitol 52 RIG-like receptors (RLRs) 326–327 – methionine metabolism 66
Ribitol dehydrogenase (EC 1.1.1.56) 52 Ritonavar® 258 – ribonucleotide reduction 126
Riboflavin 135–136 RNA. See also specific types of RNA Salmonellae
Riboflavin kinase (EC 2.7.1.26) 135 – chain properties 27 – fermentation 172
Riboflavin synthase (EC 2.5.1.9) 135 – serotyping 165
Ribokinase (EC 2.7.1.15) 52 – degradation 156 – thiamin biosynthesis 134
Ribonuclease (EC 2.7.7.16) 128 – double-stranded viruses 263 Salt wasting syndrome 119
Ribonuclease D (EC 3.1.13.5) 211 – exonucleases 218 Salutaridine reductase (NADPH) (EC 1.1.1.248) 207
Ribonuclease E (EC 3.1.26.12) 211 – overview 1–2 Salutaridine synthase (EC 1.1.3.35) 207
Ribonuclease F (EC 3.1.27.7) 211 – processing, in bacterial transcription 211–212 Salutaridinol 7-O-acetyltransferase
Ribonuclease H (EC 3.1.26.4) 161 – replication 267
Ribonuclease M5 (EC 3.1.26.8) 211 – retroviruses 261–263 (EC 2.3.1.150) 207
Ribonuclease P (EC 3.1.26.5) 211 – single-strand viruses 263 Salvage reactions
Ribonucleases (RNases) – untranslated 210–212 – NAD+/NADP+ biosynthesis and reaction 143
– degradation 157 – viroids 261 – purine regulation 125
– nucleic acid degradation 217–218 – viruses 267 Sandhoff disease 105
– RNA processing 212 RNA-directed RNA polymerase Sanfilippo’s syndrome B 34
Ribonucleic acid. See RNA Saponins, triterpenes 200–201
Ribonucleoprotein complexes (RNP) 222 (EC 2.7.7.48) 128, 131, 132 Saquinavar® 258
Ribonucleoside-diphosphate-reductase RNA exosome 231 Sarcina sp. 172
RNA polymerases PolI/PolII/PolIII (EC 2.7.7.6) Sarcosine 104
(EC 1.17.4.1) 129, 132 – bacterial 210 Sarcosine dehydrogenase (EC 1.5.99.1) 104
Ribonucleoside-diphosphate reductases – core promoters 226 Sarcosine oxidase (EC 1.5.3.1) 104
– classes I/II/III (EC 1.17.4.1) 126 – elongation and termination 151 Saturated fatty acids 6
– E. coli reaction mechanism 128–129 – eukaryotic 219–220 Saturation curves 25
– imbalance 130 – gene regulation 213 Scaffold-attached regions (SARs) 28
Ribonucleoside-triphosphate reductase – HIV replication 269 Scatchard plot, hormone-receptor interaction 287
– RNA polymerase I 219 Scavenger pathway, lipid transport 281
(EC 1.17.4.2) 132 Schiff base, pyridoxine catalysis 136
Ribonucleotides – core promoters 226 SCOP database 372
– cobalamin 138 – transcription factors 223 Scurvy, ascorate metabolism 145
– E. coli reaction mechanism 128 – RNA polymerase II 219 SEC 61 complex, protein processing 238
– interconversion of 125 – core promoters 226 Sec-independent secretion 167
– purines 124–126 – mRNA transcription 219 Secondary aldosteronism 119
– pyrimidines 130, 133 – RNA polymerase III 219 Secondary bile acids 123
– pyrimidine synthesis 131 – 5S rRNA transcription, transcription factors 225 Secondary hyperuricemia 130
– reduction of 69 – RNA polymerase s subunits (EC 2.7.7.6) 210 Secondary metabolism, plants 192–209
– reduction to deoxyribonucleotides 126–127 – 30S RNA primary transcript, cleavage of 211 Secondary structure, in proteins 19
Secondary transport systems, bacterial

transport 168–169

395 Index s-factor Sorbitol 51
– bacterial transcription 210, 212 – and glycolysis 38
Second messengers – DNA replication 149 D-Sorbitol dehydrogenase (EC 1.1.1.14) 146
– G-protein system 302 – DNA viruses 264 L-Sorbose dehydrogenase (EC 1.1.99.32) 146
– intracellular communication 296 Signal amplification, heterotrimeric G-protein Sorghum sp. 201
Second order reactions 12 SOS repair system
Sec-pathway coupling 300 – bacterial DNA repair 154
– bacterial protein transport 166 Signal cascades – damage tolerance mechanism 155
– chloroplast protein transport 256 – components 311–312 – regulon 213
Sec/Tat dependent secretion – receptor activation 313–314 SoxRX regulon 213
Signal integration, synaptic transmission 295 Spectrin 19
(TC 3.A.1, 3.A.5, 3.A.6, 3.A.7) 166, 167 Signalling mechanisms Spermidine 204
Secretin 286 – B cells 320–321 – polyamine metabolism 82
Secretory IgA, biological function 334 – T cell receptor activation 318 Spermidine synthase (EC 2.5.1.16) 81
Secretory phospholipase A (sPLA, EC 3.1.1.4) 309 Signal peptides, lipid-anchored proteins 239–240 Spermine 82
– arachidonic acid release 309 Signal recognition particle (SRP, EC 3.6.5.4) Spermine synthase (EC 2.5.1.22) 81
Secretory proteins, protein processing 238 – protein folding 246–247 S phase
Sedoheptulose 52 – protein processing 238, 240 – checkpoints 236–237
L-Selenocysteine (Sec, 6) – related small G-proteins 315 – eukaryotic cell cycle 232, 234
– biosynthesis 217 Signal sequence, protein processing 238 – mammalian cells, G1 transition 234–235
– protein structure and function 18–19 Signal transduction Spherical micelles 35
Self proteins, modification of 353 – components of 21 Sphingolipids 35
Self-splicing, mRNA processing 222 – cyclic GMP dependent pathways 322–323 – chemistry and structure 7
Semi-conservative mechanism 149 – heterotrimeric G-protein coupled receptors 299–311 Sphingomyelin phosphodiesterase (EC 3.1.4.12) 103
Semliki forest virus 263 – intracellular communication principles 296, Sphingomyelins 103
Senecionine 204–205 – characteristics 36
Senecionine N-oxygenase (EC 1.14.13.101) 205 298–299 – chemistry and structure 7
Sepiapterin reductase (EC 1.1.1.153) 139 – mechanism 101 Sphingophospholipids 101, 103
Sepsis 119 – nerve conduction and synaptic transmission 294–296 Sphingosine 7
Sequence databases 366 – pathways 314 – glycosphingolipid degradation 106
Sequential control, quinone cofactor – programmed cell death 319–321 Sphingosine-1-phosphate (S1P),
– receptor tyrosine kinases 311–319
biosynthesis 75 – steroid and thyroid hormones 321–322 cellular/humoral immune response 346
Sequential model, enzyme activity 26 Signal transmission Spindle assembly, in cell cycle 236–237
Sequential reaction, defined 12 – interneural synapses 296 Spiperone 298
Serglycin 348 – intracellular hormones 287–293 Spiroxatine 298
L-Serine 5 – muscular endplate 296 Spliceosome, mRNA processing 222
– degradation 63 Silencers, eukaryotic transcription 219, 226 Splicing
– genetic code 30 Silencers, in transcription, eukaryotic transcription 219 – eukaryotic transcription 219
– glycine synthesis 64 Sinapate 196 – immunoglobulin diversity 332–333
– human essential amino acids 59 Single replication origin 149–150 – mRNA 221
– metabolism 62 Single-stranded nucleic acids, viruses 261–263 Spontaneous reactions, DNA damage 151
– methionine metabolism 67 Single-substrate reactions 21 Squalene
– pathway 179 Singlet oxygen 70–71 – cholesterol biosynthesis 107–108
– reconversion 63 siRNA 27 – hopanoid biosynthesis 111
Serine dehydratase (EC 4.3.1.17) 63 Siroheme – terpene, carotenoid, retinoid metabolism 113
L-Serine dehydratase (EC 4.2.1.13) 64 – biosynthesis 91–92 – triterpene derivation 200
Serine glyoxylate transaminase (EC 2.6.1.45) 38 – derivation 138 Squalene hopene cyclase (EC 5.4.99.17) 111
Serine C-palmitoyltransferase (EC 2.3.1.50) 103 – structure of 83 Squalene monooxygenase
Serine peptidases Skeletal muscle 46
– inhibitors 258 Small molecule information database 367 (EC 1.14.13.132) 108, 111, 200
– reaction mechanisms 257–258 Small nuclear ribonucleoparticles (snRNPs) 223 Squalene synthase (EC 2.5.1.21) 200
Serine-pyruvate transaminase (EC 2.6.1.51) 64 Small nuclear RNA (snRNA) Src family 319
Serine/threonine kinases – nucleic acid structure 27 Staphylococcus sp.
– cell cycle machinery 232–233 – transcription 223 – peptidase specificity 257
– glycosylation reactions 241–242 Small nuclear RNA activating protein complex – peptidoglycans 35
– posttranslational protein modification 238–239 Starch 32, 42
– signal cascades 312 (SNAPc) 226 – Calvin cycle regulation 192–193
Serotonin (5-hydroxytryptamine 5HT) SMART database 368 – dark reactions 192
– ligand-gated ion channels 273–274 S/M checkpoints, mammalian cell cycle 237 – degradation 44
– neurotransmission 297–298 Smooth muscle contraction 307 – energy storage 31
– tetrahydrobiopterin synthesis 140 Snake studies 123 – glycolysis 37–38
Serotonin (5-HT3) receptor (TC 1.A.9.2.1) 274 – protein function 21 – polysaccharide biosynthesis 41–42
Serotyping, bacterial envelope structure 165 SNARE proteins 248–249 – synthesis 43–44
Serpentine receptors, G-protein coupling 299 snoRNA 27 Starch phosphorylase (EC 2.4.1.1) 43
Serpins (serine protease inhibitors) 258 Sodium (Na+) Starch synthase (EC 2.4.1.21) 43
Serprocidins 325 – hormone regulation 292–293 START signal, yeast cell cycle regulation 234
Serum – nerve conduction and synaptic transmission 294 Starvation, glucose transport and 42
– albumin 21 – water turnover 293 Statins
– starvation 235 Sodium (Na+) ion channels, ligand- and voltage- – hypothalamus-anterior pituitary homone system 288
Sesquiterpenes 198–199 – steroid hormone synthesis 114
Seven transmembrane receptors (7TMRs) 298 gated 273 STAT proteins 316–317
Severe combined immunodeficiency syndrome Solamen sp. 198 STB-ENZYME Nomenclature Database 366
Solanum sp. 201 Stearoyl-CoA 9-desaturase (EC 1.14.19.1) 95
(SCID) 130 Solenoids 28–29 Stearoyl-CoA desaturase (EC 1.14.99.5) 95
Sex hormone binding globulin (SBG) 116–117 Soluble endoplasmic reticulum proteins 239 Stercobilin 88
Sex hormones. See also specific hormones Soluble guanylate cyclases 323 Stereospecificity
– intercellular transmission 286 Soluble N-ethylmaleimide-sensitive factor attachment – NAD+/NADP+ biosynthesis 144
Shemin pathway 84 Steroid(s). See also specific types of steroids
Shewanella sp. 175 protein receptor (SNARE) proteins 248–249 – binding receptors 298
Shikimate dehydrogenase (EC 1.1.1.25) 73 Solute carriers, in transport systems 275–277 – cholesterol 107–110
Shikimate kinase (EC 2.7.1.71) 73 Solute:sodium symporter (SSS) family (TC 2.A.21) 276 – functions of 8
Shikimate pathway Somatic hypermutations – hormones (see Steroid hormones)
– aromatic amino acids 74–75 – cellular/humoral immune response 347 – of plants and insects 110–111
– plant secondary metabolism 194 – immunoglobin diversity 332 – triterpenes 200
Short patch system, in DNA repair 163–164 Somatic point mutations, immunoglobulin Steroidal alkaloids 200–201
Short-term regulation, cholesterol Steroid 16a-monooxygenase (EC 1.14.99.9) 117
genes 331–332 Steroid 17a-monooxygenase (EC 1.14.99.9) 117, 120
homeostasis 109 Somatic recombination, immunoglobulin Steroid 11b-monooxygenase (EC 1.14.15.4) 120
Sialate, amino sugar biosynthesis 55
Sialic acid 105 genes 331–332
– biosynthesis 54–55 Somatostatin 288
Sickle cell anemia 285 Somatotropin 288
Sorangion cellulosum 149

Index 396

Steroid D-isomerase (EC 5.3.3.1) 115, 116, 120 Sulfur metabolism 66, 69, 176–177 297 Tetrahydromethanopterin (THMPT), pterine
D7-Sterol 5-desaturase (EC 1.14.21.6) 108 Sulpiride 298 biosynthesis 138–139
Steroid hormones Superantigen(s)
– biological activation and regulation of 114–115 – binding 344 Tetrahymena 222
– biosynthesis 114 – stimulation 354 – genetic code 30
– degradation of 115 Supercoiling DNA helix 28–29 Tetrapyrroles
– receptors 321–322 SUPERFAMILY database 368 – biosynthetic pathways 82, 84–87
– synthesis and secretion of 115 Superoxide dismutase (SOD, EC 1.15.1.1) 70 – linear 82, 87–89
– transport 115 Superoxide radical 70 – natural sources 82–83
Steroid 11-hydroxylase (EC 1.14.15.4) 117 Supersecondary protein structures 19–20 Tetraterpenes 201
Steroid 21-monooxygenase (EC 1.14.99.10) 120 Surfactant proteins 325 Thalassemias, a and b 285
D6-Steroid reductase (EC 1.3.1.21) 122 Survivin 348 Thebaine 6-O-demethylase (EC 1.14.11.31) 207
Sterol regulatory element 1 (SRE-1), cholesterol Swiss-Prot database 366, 368 T helper cells 1 (Th1 cells)
Syk family 319 – adaptive immune system 328
homeostasis 110 Symmetry model, enzyme activity 25 – immune response regulation 344–345
Sterols 110–111 Sympathetic nervous system, neurotransmission – immune system development 330
– chemistry and structure 7 Symport, bacterial transport 168 – pathogenic immune response 351–352
Steryl sulfatase (EC 3.1.6.2) 117 Synaptic transmission Theobroma sp. 202
Sticky end, restriction endonuclease cleavage 218 – nerve conduction 294–296 Theobromine 204
Stilbenes, in plant metabolism 196–197 – transmitter gated signalling 294–295 Theophylline 204
Stimulons 213 – types 295 Thermal denaturation 13
Stop transfer effector (STE) sequences, transmembrane Synaptotagmin, in nerve terminals 249 Thermus sp. 184
Systems biology and networks 366 q-mechanism
proteins 238 Syzygium sp. 198 – DNA replication 149
Storage, proteins 21 – DNA viruses 264
Store-operated Ca++ channel (TC 1.A.4.3.1, T Thiamin kinase (EC 2.7.1.89) 134
Thiamin monophosphate kinase (EC 2.7.4.16) 134
TC 1.A.5.2.1.1) 274 Tannins, in plant metabolism 197–198 Thiamin-P pyrophosphorylase (EC 2.5.1.3) 134
Streptococci, bacterial envelope 165 T-antigen, glycoprotein synthesis 241 Thiamine pyrophosphate (ThPP) 52
Streptomyces sp. 180–181 TAP1/TAP2 molecules, MHC complex 338 – enzyme catalysis 23
Streptomycin, biosynthesis of 180–182 Targeting model, chloroplast protein transport 255–256 Thiobacillus sp.
Striated (voluntary) muscles 305–306 Tarui’s disease 46 – chemolithotrophy 177
Strictosidine, biosynthesis of 206 TATA box, eukaryotic transcription 226 – electron transport 183
Strictosidine synthase (EC 4.3.3.2) 206 Tat-pathway, chloroplast protein transport 256 Thioesters, ubiquitylation 259
Stringent response, in protein synthesis 214 Taurine 123, 298 Thioredoxin (EC 1.8.1.8)
Strophantus 110 – cysteine metabolism 68 – protein folding, disulfide bond formation 246
Structural domains 20 Tay-Sachs disease 105 Thioredoxin-disulfide reductase (EC 1.8.1.9) 246
Strychnine 298 T cells Thioredoxin reductase (NADPH) (EC 1.6.4.5) 129, 131
– indole alkaloids 205 – activation of 343–344, 353–354 Thiosulfate oxidation 176
Suberin 196 – adaptive immune system 328 Thiosulfate sulfurtransferase (EC 2.8.1.1) 68
Substrate channeling – antigen-induced clonal proliferation 344 L-Threonate dehydrogenase (EC 1.1.1.129) 146
– fatty acid oxidation 97 – antigen receptors 336–337 L-Threonine 5
– urea cycle 80 – complement system 336 – branched-chain amino acids 71
Substrate specificity 21 – cytokines 341 – cell cycle machinery 232–233
Succinate – immune system development 330 – genetic code 30
– electron transport 184 – membrane molecules 343 – glycosylation reactions 241–242
– glycolytic and lactate converting fermentation 170 – metabolic reactions 130 – human essential amino acids 59
– polyamine metabolism 81–82 – receptors (TCRs) 336–337 – metabolism 65–67
Succinate CoA ligase (EC 6.2.1.4/5) 56, 56 – peptidase specificity 257
Succinate dehydrogenase (EC 1.3.5.1) 56 – structure and properties 317–318 – posttranslational protein modification 238–239
Succinate dehydrogenase (EC 1.3.99.1) 184 – regulatory 345 Threonine dehydratase (EC 4.2.1.16) 67, 71
Succinate-semialdehyde dehydrogenase [NAD(P)+] Threonine synthase (EC 4.2.3.1) 67
– specific adaptive immune system 328 Threose 4
(EC 1.2.1.16) 60, 82 – regulatory, suppression by 351 Thrombin (EC 3.4.4.13) 359–361
O-Succinylbenzoate synthase (EC 4.2.1.113) 73 – tyrosine kinase-associated receptors 315 Thrombocytes
O-Succinylbenzoate-CoA ligase (EC 6.2.1.26) 73 dTDP-Glucose 4,6-dehydratase (EC 4.2.1.46) 181 – platelet structure and function 362
Succinyl-CoA Teichoic acids 106 – vesicular compounds 363
– chlorophyll biosynthesis 91 Telomeres 160–162 Thrombomodulin (TM) 360–361
– heme biosynthesis 85 – mitosis 29 Thromboplastin factor 358
Succinyl CoA Hydrolase (EC 3.1.2.3) 56 Telophase, mammalian cell mitosis 235 Thromboxanes
Succinyl-diaminopimelate desuccinylase Temperature dependence – IgE-mediated autoimmune response 352
– characterized 8 – structure and function 309
(EC 3.5.1.18) 68 – dependence of reaction on 13 Thylakoid lumen proteins, transport mechanisms 256
O-Succinylhomoserine (thiol)-lyase (EC 4.2.99.9) 67 – enzyme catalysis 21–23 Thymidilate kinase 132
2-Succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate – transition 35 Thymidilate synthase (EC 2.4.2.6) 132
Terminal differentiation, adaptive immune response Thymidine 27
synthase (EC 4.2.99.20) 73 Thymidine kinase (EC 2.7.1.75) 132
Sucrose 48–49 cessation 347 Thymidine phosphorylase (EC 2.4.2.4) 132
– Calvin cycle regulation 192–193 Terminal electron acceptor 175–176 Thymidine triphosphatase (EC 3.6.1.39) 132
Sucrose phosphatase (EC 3.1.3.24) 49 Termination Thymidylate synthase (EC 2.1.1.45) 133
Sucrose-P synthase (EC 2.4.1.14) 48 – bacterial DNA replication 151 Thymine, bacterial transcription 210
Sucrose synthase (EC 2.4.1.13) 48 – bacterial transcription 211 Thymineless death 133
Sugar – bacterial translation 217 Thyamin pyrophosphate (ThPP) 134
– fermentation 169–170 – rRNA transcription 223 Thymus sp. 198
– metabolism 193 (See also specific types of sugars) Ternary intermediate complex (EAB) 21 Thyreocalcitonin 286
Sugar-PO43−/PO43− exchanger (TC 2.A.1.4) 275 Terpenes, metabolism 112–113 Thyroid hormones
Sugar residues, nucleic acid components 26–27 Terpenoids, in plant metabolism 194, 198 – bile acid metabolism 123
“Suicidal” mechanism, bacterial DNA repair 154 Tertiary structure, in proteins 19–20 – biosynthesis and degradation 78–79
Sulfate 66, 69 Testosterone – hypothalamo-pituitary-thyroid axis 288
Sulfate adenylyltransferase (EC 2.7.7.4) 66 – hypothalamo-pituitary-testis axis 289–290 – intercellular signal transmission 286
Sulfate adenylyltransferase (ADP) (EC 2.7.7.5) 178 – metabolism 116 – intracellular communication 298
Sulfides Tetracycline, biosynthesis of 181–182 – receptors 321–322
– chemolithotrophy 177 Tetrahydrobiopterin (THB) – tyrosine derivatives 75
– metabolism 69 – biosynthesis 140 Thyroxine 78–79
Sulfinoalanine decarboxylase (EC 4.1.1.29) 68 – folate synthesis 138 TIGRFAMS database 368
Sulfite dehydrogenase (EC 1.8.2.1) 176 – pterine biosynthesis 139 TIM complex, mitochondrial protein transport 252–253
Sulfite oxidase (EC 1.8.3.1), molybdoenzyme Tetrahydrofolate (THF), pterine biosynthesis 138–139 Time, characterized 8
Tetrahydrofolylpolyglutamate 138 Time-resolved simulation of biochemical networks 366
synthesis 141 Tetrahydrofolyl-polyglutamate synthase
Sulfite reductase (ferredoxin) (EC 1.8.7.1) 66
Sulfite reductase (NADPH) (EC 1.8.1.2) 67 (EC 6.3.2.17) 139
Sulfolobus 177
Sulfuric acid conjugates 123
Sulfur dioxygenase (EC 1.13.11.18) 176

397 Index Transketolase (TK, EC 2.2.1.1) 52 Trypsin (EC 3.4.4.4)
– pentose phosphate cycle 51–52 – protein function 21
T-independent antigens 345 – reaction mechanism 135 – zymogen activation 24
Tissue factor (TF), coagulation initiation 358 Translation Tryptamine 76
Tissue factor pathway inhibitor (TFPI) 360 – bacterial 215–217 Tryptase (EC 3.4.21.59), IgE-mediated
Tissue plasminogen activator – eukaryotic 228–231
– hepatitis C virus 267 autoimmune response 352
(t-PA, EC 3.4.21.68) 364–365 – viral proteins 267 L-Tryptophan 5
T lymphocytes. See T cells Translational start codon 210 – biosynthesis 74–75, 213
dTMP Kinase (EC 2.7.4.9) 132 Translesion synthesis 164 – derivatives and degradation 76–77
Tn-antigen, glycoprotein synthesis 241 Translocation – human essential amino acids 59
Tobacco, alkaloids 202 – motor model 255 – NAD+/NADP+ biosynthesis and reaction 144
Tobacco mosaic virus (TMV) 261, 263 – protein structure 19
Tocopherol (Vitamin E) – mitochondrial protein transport 253 – strictosidine biosynthesis 206
– biosynthesis and metabolism 148–149 – protein processing 240 Tryptophan decarboxylase (EC 4.1.1.27) 206
– phenylalanine and tyrosine derivation 75 – targeting model 255 Tryptophan 2,3-dioxygenase (EC 1.13.11.11) 77
TOC/TIC complex, chloroplast protein Translocon, protein processing 238 Tryptophan 5-monooxygenase (EC 1.14.16.4) 77
Transmembrane proteins Tryptophan transaminase (EC 2.6.1.27) 77
transport 254–256 – globular proteins 20 Tryptophanase (EC 4.1.99.1) 74
Toll-like receptors (TLRs) – hormones 286 Tryptophantryptophylquinone (TTQ) 178
– apoptotic pathways 348 – lipids 36 T state, hemoglobin oxygenation 284
– cytokines 316, 318 – prokaryotic cells 15 Tubocurarin 205
– innate immune systems 326–327 – protein processing 238 Tubulin 21
TOM complex (EC 3.6.3.51), mitochondrial protein Transmitter gated signaling Tumor necrosis factor (TNF)
– ion channels 298 – cytokine receptors 318, 339
transport 252–253 – synaptic transmission 294–295 – MHC antigen presentation 337
Topoisomerase (EC 5.99.1.2) 28 Transport – receptor family, cytokines 316
– eukaryotic DNA replication 158–160 – bacterial 168–169 – receptor superfamily (TNFRs) 320
Topological analysis, of biochemical – chloroplast proteins 254–256 Tumor necrosis factor-a (TNF-a)
– electron carriers 272 – immune response regulation 344
networks 366 – fatty acids 96 – pathogenic immune response 352
Topology, CATH database 372 – glucose 41 Tumor(s). See also Cancer
Toxiferin 205 – hemoglobin oxygen transport 282–285 – cell, migration 356
Transaldolase (TA, EC 2.2.1.2) 51–52 – intracellular 278–279 – estrogen therapy 119
Transamination – lipid proteins, plasma transport 279–282 – viruses, DNA 264
– ammonia metabolism 61–62 – membrane transport 272–279 Tumor suppressor genes 311
– cobalamin metabolism 137 – proteins 21 Tungsten (W)
Transcarboxylation – solute carriers 275–277 – cofactors 140–141
– biotin biosynthesis 143 – vesicular 248–249 – folate metabolism 138
Trans-cinnamate 195–196 Transporter Commission (TC) Turnover number 11
Trans-cinnamate 2-monooxygenase Two-component regulatory systems 212
system 24, 272, 371 Two-substrate reactions 12–13, 21–22
(EC 1.14.13.14) 195 Transport vesicles, structure and Two-substrate two-product (Bi-Bi) reactions 12
Trans-cinnamate 4-monooxygenase Type III polyketide synthase (EC 2.3.1.94) 194
interrelationships 16 L-Tyrosine 5
(EC 1.14.13.11) 195 Trans-unsaturated acids (TFA) 96 – aromatic amino acids 74–76
Transcription TrEMBL database 366 – catecholamine biosynthesis and degradation 78
– accuracy of 212 Triacylglycerol lipase (EC 3.1.1.3) 99 – derivatives and degradation 76
– bacterial 210–212 – metabolism 279 – genetic code 30
– bubble 210 Triacylglycerol(s) – glycosylation 32
– eukaryotic regulation 226–228 – chemistry and structure 7–8 – human essential amino acids 59
– eukaryotic 226–228 – lipid aggregates and membranes 35 – thyroid hormone biosynthesis and
– genetic code 30 – metabolism 98–99
– HIV replication 269 Triacylglycerols, lipoprotein metabolism 279–281 degradation 78–79
– human immunodeficiency virus (HIV) 268–271 Tricarboxylic acid cycle. See citrate cycle Tyrosine kinase-associated receptors
– inhibitors 212, 225 Trigger factor (TF, EC 5.2.1.8) 246
– initiation 212 Triglycerides (TKaR) 315–319
– modulation 227–228 – chemistry and structure 7 Tyrosine kinases
– mRNA 219–221 – energy storage 31 – intracellular communication 298
– papillomavirus 264–266 – glycolysis and gluconeogenesis 38 – phospholipase activation 302
– termination of 223 – metabolism 98–99 – receptors (TKRs) 311–319
Transcriptional start site 210 3a,7a,12a-Trihydroxy-5b-cholestanate CoA ligase – signal transduction receptors 311–319
Transcription-coupled DNA repair 162 Tyrosine 3-monooxygenase (EC 1.14.16.2) 76
Transcription factors (EC 6.2.1.29) 122 Tyrosine transaminase (EC 2.6.1.5) 74, 76
– domains 227 3a,7a,12a-Trihydroxycholestane 26-al 26-oxidoreductase
– human interferon enhanceosome 227–228 U
– receptor protein tyrosine kinases) 319 (EC 1.1.1.161) 122
– RNA polymerase II (EC 2.7.7.6) 219 Trihydroxyphenylalanine quinone (TPQ) 178 Ubiquinol 185–186
– signal cascades 312 Trihydroxy-stilbene synthase Ubiquinone
Transcription-repair coupling factor, – branched-chain amino acids 73
(EC 2.3.1.95) 195 – cofactor biosynthesis 75
nucleotide excision repair 154 3,5,3¢-Triiodothyronine 78–79 – enzyme catalysis 23
Transcriptome analysis 366 Trimethyllysine dioxygenase (EC 1.14.11.8) 68 Ubiquinone oxidoreductases 184–185
TRANSFAC database 371 Triose-phosphate isomerase (EC 5.3.1.1) 179 Ubiquitin-activating enzyme (EC 6.3.2.B1) 258
Transferases 23–24 Triplet codons 30 Ubiquitin-proteasome system (UPS), protein
Transferrin, immune system 326 Triterpenes
Transfer RNAs (tRNAs) – derivatives 198, 200 degradation 238, 258–260
– aminoacylation 215 – non-glycosylated pentacycle structure 201 Ubiquitin-protein ligase (EC 6.3.2.19) 258
– bacterial protein synthesis 214–215 Triterpenins, permacyclic 198 Ubiquitylation, protein degradation 259–260
– characterized 6 tRNA nucleotidyltransferase UDP-galactose /UMP antiporter family
– charged 228
– DNA information storage 27 (EC 2.7.7.56) 211, 225 (TC 2.A.7.11) 277
– genetic code 30 Tropane alkaloids UDP Galacturonate decarboxylase (EC 4.1.1.67) 53
– modification and processing 224–225 – amino acid precursor 202 UDP Glucuronate decarboxylase (EC 4.1.1.35) 53
– modification examples 212 – biosynthesis 208–209 UDP-N-Acetylglucosamine 1-carboxyvinyl transferase
– secondary structure 214 Trophic hormones 114
– transcription 223 Tropinone acyltransferase 208 (EC 2.5.1.7) 54
– translation systems 228–229 Tropinone reductase I (EC 1.1.1.206) 208 UDP-N-Acetylglucosamine 2-epimerase
– untranslated 211 Tropinone reductase II (EC 1.1.1.236) 208
Transforming growth factor-a (TGF-a), Tropins 114 (EC 5.1.3.14) 54
trp operons 213–214 UDP-N-Acetylglucosamine 4-epimerase
placental hormones 291 True alkaloids 202
Transforming growth factor b (TNF b), Trypanosoma (EC 5.1.3.7) 54
– genetic code 30 UDP-N-Acetylglucosamine pyrophosphorylase
mammalian cell cycle 235
Transglycosylation, sucrose metabolism 48 (EC 2.7.7.23) 54
Transition complexes 21
– temperature and activation energy 13

Index 398

UDP-N-Acetylglucosamine-dolichyl-phosphate Urotelic animals 80 – fat soluble 133
N-acetylglucosaminephosphotransferase UTP-glucose 1-phosphate uridyl transferase – FNM 135–136
(EC 2.7.8.15) 239–240 – menaquinone (Vitamin K) 148–149
(EC 2.7.7.10) 43, 49 – phylloquinone 148–149
UDP-N-Acetylglucosamine-lysosomal-enzyme – pterines 138–141
N-acetylglucosaminephosphotransferase V – pyridoxine (Vitamin B6) 136–137
(EC 2.7.8.17) 241 – retinol (Vitamin A) 133–134
Vaccinia virus 263 – riboflavin (Vitamin B2) 135–136
UDP-N-Acetylmuramate-L-alanine ligase – siroheme and coenzyme F430 138
(EC 6.3.2.8) 165 Vacuoles 18 – thiamine (Vitamin B1) 134
– tocopherol (Vitamin E) 75, 148
UDP-N-Acetylmuramoyl-L-alanine-D-glutamate ligase L-Valine 5 – water-soluble 133
(EC 6.3.2.9) 165 Voltage gated ion channels
– branched-chain amino acids 72 – membrane transport 272–273
UDP-N-Acetylmuramoyl-L-alanyl-D-glutamate-2,6- – nerve conduction and synaptic transmission
diaminopimelate ligase (EC 6.3.2.13) 165 – genetic code 30 – synaptic signalling 296
Volume, characterized 8
UDPG 4-Epimerase (EC 5.1.3.2) 49 – human essential amino acids 59 V-oncogenes 311
UDPG-Hexose 1-phosphate uridyltransferase von Gierke’s disease 46
– pantothenate biosynthesis 142 von Willebrand factor, platelet function 362
(EC 2.7.7.10) 49
Uncharged molecules, membrane transport 9 – penicillin/cephalosporin biosynthesis 180
– energy requirements 272
Uncompetitive inhibition, enzyme regulation 25 Variable (V) immunoglobulin domains 330–331 294
Uncoupling protein 99
Undecaprenyl diphosphatase (EC 3.6.1.27) 113, 165 Vascular cell adhesion molecule-1 (VCAM-1) 356
Uniport, bacterial transport 168
UniProt protein sequences database 366–368 Vascular effects, platelet function 362
Universal DNA repair system 162
Unlimited proteolysis, protein degradation 256–259 Vascular endothelial growth factor
Unsaturated fatty acids
– biosynthesis 96 (VEGF, EC 3.4.21.46) 312
– characterization 6
Untranslated RNA, processing 210–212 Vasoconstrictive compounds 357
Upstream binding factor (UBF)
– eukaryotic transcription 226 Vasopressin
– rRNA transcription 223
Upstream control element (UCE) – intercellular signal transmission 286 W
– core promoter 227
– rRNA transcription 223 – regulation 293 Waterson Friederichsen syndrome 119
Upstream non-coding region 210 Water volume and turnover,
Upstream open reading frames (uORFs), translational Veiled cells 346
hormone regulation 292–293
regulation 231 Very-low-density lipoproteins (VLDLs), Watson-Crick base pairing
Upstream regulator sequence, bacterial gene – bacterial DNA replication 149
metabolism 279–281 – nucleic acid structure 27
regulation 212–213 Waxes, chemistry and structure 7
Uracil Very short patch DNA repair 154 Wobble hypothesis
– bacterial transcription 210 – eukaryotic translation 229–230
– pyrimidine interconversion 130 Vesicular transport – genetic code 30
Uracil-DNA glycosylase (EC 3.2.2.27) 153 Wolinella succinogenes
Uracil reductase (EC 1.3.1.1) 135 – pathways 248 – chemolithotrophy 177
Uracil dehydrogenase (EC 1.17.99.4) 131, 132 – fumarate electron acceptors 187
Urate 127, 130 – vesicles 248–249 – redox reaction and electron transport 173
Urate oxidase (EC 1.7.3.3) 128 Wood, degradation of 53–54
Urate ribonucleoside phosphorylase (EC 2.4.2.16) 128 – clathrin coated vesicles 278 Worldwide Protein Data Bank 371
Urea cycle 80–81
Urea transporter (TC 1.A.28.1) 275 Vesicular amine transporter (TC 2.A.1.2) 275
Urease (EC 3.5.1.5) 128
Ureidoglycolate lyase (EC 4.3.2.3) 128 Vesicular glutamate transporter (TC 2.A.1.14) 275
3-Ureidopropionase (EC 3.5.1.6) 131, 132
Ureidosuccinase (EC 3.5.1.7) 131 Vesicular inhibitory amino acid transporter
Uricotelic animals
– urate metabolism 127 (TC 2.A.18.5) 275
– urea cycle 80
Uridine 5¢-diphosphate (UDP) 130–132 Veterbrate viruses 262–263
– glycosylation 240
– pentose phosphate cycle 52–53 Vimetin 17
– sucrose synthesis 48–49
Uridine kinase (EC 2.7.1.48) 131 Vinblastine 205
Uridine 5¢-monophosphate (UMP) 130
– pyrimidine interconversion and degradation 131–132 Vinyl reductase (EC 1.3.1.33) 90
Uridine nucleosidase (EC 3.2.2.3) 131
Uridine phosphorylase (EC 2.4.2.3) 131 Violaxanthin de-epoxidase (EC 1.10.99.3) 113
Uridine 5¢-triphosphate (UTP) 130–132
– pyrimidine interconversion and degradation 131–132 Viral replicase (EC 2.7.7.48), RNA viral assembly 267 X
Uridylate kinase (EC 2.7.4.22) 131
Uriporphyrinogen III synthase Virion assembly Xanthine, urate oxidation 127
Xanthine oxidase (EC 1.2.3.2) 127
(UROS, EC 4.2.1.75) 84 – HIV replication 269–271 Xanthine oxidase (EC 1.2.3.2)
Urobilin 88 – molybdoenzyme synthesis 141
Urocanate hydratase (EC 4.2.1.49) 79 – papillomaviruses 264–266 – purine biosynthesis and degradation 127, 129
Urokinase type plasminogen activator (u-PA, EC Xanthophylls
– RNA viruses 267 – characterized 112
3.4.21.73) 364 – cycle 188–189
Uronic acids Viroids, in plants 261 Xanthosine-5¢-monophosphate 125
– metabolism 48–49 Xanthosine nucleotide, biosynthetic reactions 1
Uroporphyrinogen III 84 Viruses. See also specific types of viruses XDP-sugars 106
– conversion 87 Xylose, in plant cell wall 53
– siroheme 92 – assembly mechanisms 269 Xylose isomerase (EC 5.3.1.5) 37
Uroporphyrinogen decarboxylase (EC 4.1.1.37) 86, 87 Xylose kinase 47, 53
Uroporphyrinogen III synthase (EC 4.2.1.75) 85 – budding Xylose-1-phosphate uridyltransferase (EC 2.7.7.11)
Xylulose 5-P 52
– HIV virus 271 – pentose metabolism 54
Xylulokinase (EC 2.7.1.17) 52, 53
– RNA viruses 267

– DNA 264–266

– genomic characteristics 261–263

– general characteristics 261–263

– maturation 271

– protein synthesis 267 53

– reproductive information flow 261

– retroviruses 268–271

– genomic characteristics 261

– RNA 267

– genomic characteristics 261–263 Y

– information storage 27

– structure of 263 Yeast. See also specific types of yeast
– anaplerotic reactions 46
– vertebrates 262 – cell cycle in 234
– deadenylation-mediated mRNA degradation
Visual processes 307–308 – genome replication 157–158
– glycerophospholipid synthesis 101
Vitamin D binding protein 147 – lactate dehydrogenase 87 231
– pre-replication complex assembly 234
Vitamin K epoxide reductase (EC 1.1.4.1) 148 Yohimbine 205

Vitamin(s)

– ascorbate (Vitamin C) 145–146

– hexose metabolism 50

– calciferol (Vitamin D2) 146–148
– hopanoid biosynthesis 110

– intercellular signal transmission 286 Z

– receptors 321–322 Z-DNA 28
Zeaxanthin epoxidase (EC 1.14.13.90) 113
– characterized 133–149 Zn++ transporter (TC 2.A.4.2 … 3) 276
Zellweger’s syndrome 123
– cholecalciferol (Vitamin D3) 110 Zinc activated channels 273–274
– cobalamin (coenzyme B12, Zollinger-Ellison’s syndrome 123
Zymogen activation 24
Vitamin B12) 137–138 Zymomonas sp. 172
– biosynthesis 91–92

– essential amino acids 149

– essential fatty acids (Vitamin F) 149

– FAD 135–136

Common Abbreviations
(Other abbreviations are defined in the text)

aa Amino acid
Acc, AccH2 Acceptor, reduced acceptor (unspecified)
ACP Acyl carrier protein
ATP, ADP, AMP, A Adenosine tri-, di-, monophosphate, adenosine
bp, kbp base pair (in DNA), kilobase pairs
cAMP Cyclic AMP = adenosine 3¢,5¢-monophosphate
cGMP Cyclic GMP = guanosine 3¢,5¢-monophosphate
CoA-SH, CoA-S- Coenzyme A
CTP, CDP, CMP, C Cytidine tri-, di-, monophosphate, cytidine
Cyt Cytochrome
Da, kDa Dalton, kilodalton (unit of molecular mass)
dATP, dADP, dAMP, dA Deoxyadenosine tri-, di-, monophosphate, deoxyadenosine
dCTP, dCDP, dCMP, dC Deoxycytidine tri-, di-, monophosphate, deoxycytidine
dGTP, dGDP, dGMP, dG Deoxyguanosine tri-, di-, monophosphate, deoxyguanosine
dTTP, dTDP, dTMP, dT Deoxythymidine tri-, di-, monophosphate, deoxythymidine
DNA Deoxyribonucleic acid
E Enzyme
EC number Enzyme classification according to the IUBMB EC classification
ER Endoplasmatic reticulum
ETF Electron transferring flavoprotein
F430 A corrinoid coenzyme (Ni)
FAD, FADH2 Flavin-adenine dinucleotide, reduced flavin-adenine dinucleotide
Fd Ferredoxin
FMN, FMNH2 Flavin mononucleotide, reduced flavin mononucleotide
Fp Flavoprotein
DG Change of free energy (see 1.5.1)
G6P Glucose 6-phosphate
GSH, GSSG Glutathione, oxidized glutathione
GTP, GDP, GMP, G Guanosine tri-, di-, monophosphate, guanosine
Ig Immunoglobulin
ITP, IDP, IMP, I Inosine tri-, di-, monophosphate, inosine
k Velocity constant of a reaction (1.5.4)
K Equilibrium constant of a reaction (see 1.5.1)
KS, KI, KD Dissociation constants (see 1.5.4, 7.1.2)
KM Michaelis constant (see 1.5.4)
kb Kilobases (103 bases)
l Wavelength of light

a-Lipoic acid, oxidized a-lipoic acid

NAD+, NADH + H+ Nicotinamide-adenine dinucleotide, reduced nicotinamide-adenine dinucleotide

NADP+, NADPH + H+ Nicotinamide-adenine dinucleotide phosphate, reduced nicotinamide-adenine dinucleotide phosphate

nt Nucleotide

NTP, NDP, NMP, N Any nucleotide tri-, di-, monophosphate or nucleoside

PAP Adenosine 3,5-diphosphate

PAPS 3-Phosphoadenylylsulfate

PEP Phosphoenolpyruvate

Pi, PPi Inorganic phosphate, inorganic pyrophosphate
pH Negative decadic logarithm of the H+ concentration

pK Negative decadic logarithm of a dissociation constant

PQQ Pyrroloquinoline quinone

PRPP a-D-5-Phosphoribosylpyrophosphate

PyrP Pyridoxal phosphate

RNA Ribonucleic acid

mRNA, rRNA, tRNA Messenger-, ribosomal-, transfer ribonucleic acid

R-S-S-R Disulfide group of amino acids or peptides

S Svedberg units (sedimentation coefficient)

SAH S-Adenosylhomocysteine

SAM S-Adenosylmethionine

THF 5,6,7,8-Tetrahydrofolate

THMPT 5,6,7,8-Tetrahydromethanopterin

ThPP Thiamin pyrophosphate

UDPG Uridine diphosphate glucose

UQ, UQH2 Ubiquinone, reduced ubiquinone
UTP, UDP, UMP, U Uridine tri-, di-, monophosphate, uridine

Abbreviations for amino acids are listed in Figure 1.3.2, abbreviations for sugars in Figure 4.4.1-1.

Organization of the Chapters

This book was organized in a decimal classification system, which is Biosynthetic Reactions in General Metabolism
also used for the index and for the numerous cross-references.

The Figures on this and on the facing page present the majority of the
pathways in this book in a schematized way. The chapter and section
numbers, which are shown in the drawings, can be used for quick
location of the reactions.

The general setup is as follows:
Chapter 1: Introduction and general aspects, chemistry and physical
chemistry
Chapter 2: The cell and its contents: Enzymes, nucleic acids, polymeric
carbohydrates and lipids
Chapter 3: General metabolism in animals, plants and bacteria
Chapter 4:.Protein biosynthesis, modifications and degradation
Chapter 5: Viruses
Chapter 6: Transport systems
Chapter 7: Signal transduction and cellular communication
Chapter 8: Immune system
Chapter 9: Blood coagulation and fibrinolysis
Chapter 10: Biochemical networks, bioinformatics and systems biology

Key to the Background Colors:

green = carbohydrates 3.6.1
3.2.8
blue = amino acids

red = lipids including steroids

orange = nucleotides

brown = tetrapyrroles

none = compounds involved in general

interconversions

The colors of the frames are for easy
differentiation only.

Conventions for the reaction arrows

black line arrows = general pathway

blue line arrows = observed in animals

green line arrows = observed in plants and

yeasts

red line arrows = observed in bacteria and 3.5
3.6.2
archaea 3.7 3.2.7

dashed line arrows = of primarily catabolic 3.1.6

importance, 3.1.1

full line arrows = either of primarily 3.12

anabolic importance or

frequently passed through

in both directions

3.2.9

3.1.2 3.1.3
3.1.4

3.4.1

3.2.4 3.2.6

3.11 3.4.3 3.4.2

Cellular Communication Protein Biosynthesis

3.8.1 3.8.2
3.9.1 3.9.2

4.1.1 4.2.1
4.1.2 4.2.2

4.1.3 4.2.3 4.4
3.10.2 4.5.2...4.5.5

3.6.2

3.2.2 3.2.5
3.3.1, 3.3.2
3.2.9

3.7.5 3.3.3

3.3.3

3.1.8 3.3.2 3.5.9

3.5.9 16.1
3.5.4
3.5.3 3.5.2