Index: Index Terms Links A

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INDEX
Index Terms A acetal acetoacetate acetoacetyl-CoA and ketone bodies acetyl group structure acetyl-CoA no connection to glucose TCA-cycle and tracking carbon atoms in transport from mitochondria acid definition dissociation constant dissociation constants-table weak acid-base behavior 284 223 223 284 156 200 154 238 158 242 244 243 244 Links
catalysis equation imbalance imbalance table stoichiometry titration acidic groups on proteins acidosis aconitase geometry of recognition of citrate actinomycin D activation energy active site active site residues active transport pumps acyl group structure adenylate cyclase adipose tissue metabolic role of response to metabolic signals agarose alanine cycle aldoase
Co py rig hte dM ate ria l

224 239 240 241 246 251 256 94 249 258 260 245 245 254 258 239 240 240 38 82 81 81 29 284 196 242 247 252 257 243 248 253 258 244 249 254 259 245 250 255 260 259 260 246 276 97 212 212 65 222 236 213 213 223 237
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320
Index Terms aligned recombination alkalosis alkane, structure of alkene, structure of alkyne, structure of allosteric effectors allosterism concerted model alternative splicing amide, structure of amine pKa structure of amino acids acidic acidic and basic apolar degradation essential glucogenic hydrophilic hydrophobic ketogenic metabolism nitrogen disposal from nonessential polar sidechains synthesis amino group, structure of aminoacyl tRNA aminoacyl tRNA synthetases amounts amphipathic amplifiers anaerobic glycolysis anaplerotic reactions annealing antibody diagram recombination in Western blots and antimycin antiparallel antisense strand apolar APRTase arginine in urea cycle Links 47 257 284 284 284 121 117 119 54 284 243 284
258
259
260

254 7 8 187 187 187 8 7 187 186 211 186 8 7 186 284 57 59 96 14 125 192 192 38 50 47 67 181 19 41 8 228 226 210 211 211 187 188 189 136 137 193 51 48 49 53 55

321
Index Terms arginosuccinate arsenate ascorbic acid function structure aspartate transcarbamoylase assay curvature in ATP fatty acid synthesis cost gluconeogenesis cost glycogen cost glycogen yield glycolysis yield metabolism -oxidation yield synthesis ATPase as membrane pumps atractyloside autophosphorylation autoradiography B Links 226 144 285 285 231 98 100
B6, see pyridoxal B12 function and one-carbon metabolism structure base pairing bases, pKa basic amino acids basic groups on protein benzyl group, structure bicarbonate reclamation by the kidney bicarbonate buffer equation binding, ligand biotin function and pyruvate carboxylase structure blood pH blotting diagram Northern

157 145 150 150 144 192 166 176 176 31 181 129 66 146 192 32 172 285 234 285 35 245 254 254 284 258 254 256 20 172 285 193 285 257 67 68 67
101

322
Index Terms blood pH (Continued) Southern Western bongkrekate brain metabolic role of response to metabolic signals buffers capacity example C Links
67 67 181 213 213 248 251 249
calcium cAMP glucagon and glycogen and protein kinase activation by synthesis by adenylate cyclase capping mRNA carbamoyl phosphate and pyrimidine metabolism carbamoyl phosphate synthetase carbon dioxide breathing and dissolved pKa carbon oxidation states carboxyl group structure carboxylic acid pKa carnitine shuttle diagram CAT (RNA polyermase promoter) catalysis acid-base chemical electrostatic cDNA cDNA library chemical catalysis chemical structures chimera cholesterol effect on membrane fluidity citrate source of cytosolic acetyl-CoA symmetry of

134 133 196 149 197 197 53 226 231 226 254 256 256 243 233 284 243 164 166 55 83 94 93 93 71 71 93 284 72 24 27 158 240 135 134 136 55 28 159

323
Index Terms citrulline cloning screening selecting steps in vector Cobalamin. see B12 structure codon codon table coenzyme A function structure concentration concentration gradient concepts concerted allosteric model conformation change conjugate acid and base connection of storage pools consensus sequence cooperation of tissues cooperativity in enzymes negative positive Cori cycle diagram coupling free energies cyanide and electron transport cyclase cystathionine cysteine synthesis cytoplasm D Links 226 70 71 71 70 71 285 59 59
72
decarboxylation deletion mutagenesis G. see free energy denaturation DNA protein de novo purine synthesis deoxynucleotide synthesis diabetes dideoxynucleotide sequencing dielectric constant dihydroxy acetone phosphate dinitrophenol

286 286 96 29 2 119 84 244 213 56 211 117 117 117 221 268 181 134 234 234 26 245 118 118 118 188 75 37 15 228 228 194 73 8 236 180 229 195 74 196

324
Index Terms directionality in DNA/RNA synthesis disulfide structure DNA antisense strand base pairs B-form chimeric codon consensus sequence directions gels major groove metabolism methylation mutagenesis pitch polymerase probe promoter replication sense strand sequencing stability structure supercoiling Z-form DNA polymerase from prokaryotes and eukaryotes types DNP (dinitrophenol) driving force E Links 41 284 41 35 36 72 59 56 19 65 37 40 55 72 38 43 67 55 42 41 73 35 35 44 36 53 55
Eadie-Hofstee plot effector-allosteric effectors effectors of metabolism electrochemical gradient electron transport see also oxidative phosphorylation ATP yield from connections diagram flavin-linked substrates inhibitors P/O rations

28 75 56 43 53 74 36 55 37 46 45 180 273 274 111 121 125 198 180 112 173 178 173 176 175 176 180 178 174 179 174 175 180 176 181 177 182 181 182

325
Index Terms electron transport (Continued) regulation sites of ATP synthesis substrate shuttles uncouplers electroporation electrostatic catalysis elongation factor endergonic reactions enhancer enthalpy and free energy entropy ad free energy and organization enzyme active site active-site residues allosterism and cooperativity assay catalysis conformation change hyperbolic kinetics inhibition initial velocity interaction with substrate kinetic constants kinetic plots kinetics mechanism Michaelis-Menten equation nomenclature proteolytic rate acceleration restriction saturation specific activity steady-state transition state binding transition state stabilization units velocity vs. substrate epinephrine and protein phosphorylation equilibrium constant relation to G and thermodynamics ester structure Links

50 87 88 81 81 117 98 83 84 104 113 100 81 105 111 96 80 103 96 92 108 62 104 97 109 91 88 97 105 197 197 262 263 262 284 97 98 106 112 101 107 102 105 98 99 100 198 198
178 176 177 179 73 93 58 263 49 273 273 10 273 273
177

326
Index Terms ethidium bromide exams excitement metabolic movements in metabolic pathways during metabolic signals in exergonic reactions exon exothermic reaction expression vector F Links 38 2 194 217 220 217 263 55 273 72 66 195 218 196 219
facilitated diffusion channels farnesyl fasting diagram metabolic movements in metabolic responses to fat cant be converted to carbohydrate as energy storage metabolic movements metabolic pathway metabolic scheme organ utilization as a storage molecule fatty acids delta nomenclature desaturation elongation naming nomenclature numbering omega nomenclature oxidation See -oxidation fatty acid synthase reactions fatty acid synthesis citrate and connections diagram energy costs equation function location

29 26 194 216 216 214 195 196 207 207 207 207 208 207 193 208 209 160 160 160 161 160 160 160 164 168 156 160 162 161 162 164 169 165 170 166 171 167 172 158 157 156 157 159 156 156

327
Index Terms fatty acid synthesis (Continued) regulation 2,6-FBP. See fructose-2,6-bisphosphate feeding metabolic diagram metabolic movements during metabolic response to metabolic signals in F1F0 ATPase first-order reaction equation half-time time coursediagram velocity ofdiagram fluid-mosaic model folding of proteins folic acid and amino acid metabolism function oxidation states structure formyl tetrahydrofolate free energy (G) of activation adding calculating calculating-example coupling definition G0 G0 diagram equation example and protein synthesis relation to enthalpy and entropy relation to equilibrium constant standard state units useful work and fructose-1,6-bisphosphatase fructose-2,6-bisphosphatase effects of phosphorylation fructose-1,6-bisphosphate fructose-2,6-bisphosphate during excitement effects on glycolysis and gluconeogenesis liver Links
157 194 215 214 214 214 176 8 278 279 279 279 26 18

278 279 188 285 235 285 235 263 276 268 266 266 268 264 265 266 264 263 266 268 273 263 265 266 264 142 204 204 142 198 219 203 204 265 266 269 267 201 204

328
Index Terms fructose-2,6 bisphosphate (Continued) muscle synthesis and degradation functional groups structure futile cycle G gels agarose DNA gene deletion duplication expression-regulation regulation genomic library geranylgeranyl glossary glucagon and cAMP and increased protein phosphorylation gluconeogenesis absence in muscle alanine as source ATP costs connections diagram effect of fructose-2,6-bisphosphate equations fructose-2,6-bisphosphate regulation function glucagon effect glycerol and insulin effect location regulation glucose conversion to pyruvate effect of glucagon effect of insulin epithelial cells and lack of synthesis by muscle maintaining supplies metabolism of labeled molecule molecular signals for numbering glucose-6-phosphate dehydrogenase Links
204 203 284 200
201

65 65 47 47 49 50 49 50 71 26 287318 196 197 197 196 197 145 146 145 145 146 146 145 142 198 198 146 146 145 145 146 145 146 145 146 145 145 146 236 196 195 32 205 192 236 198 236 184 53 53 197 196

329
Index Terms glutathione glycerol glycerol phosphate shuttle glycogen ATP cost for synthesis ATP yield branch points branching connections debranching degradation diagram depletion enzymes and function glucose-6-phosphate effect insulin and glucagon and location metabolic diagram metabolic movements metabolic regulation regulation regulation by phosphorylation as storage form of glucose as a storage molecule structure synthase synthesis diagram glycogen debrancher glycogen phosphorylase glycolipid glycolysis anaerobic arsenate effect ATP from connections diagram effect of fructose-2,6-bisphosphate enzymes epinephrine equations fructose-2,6-bisphosphate function glucagon insulin lactate from phosphorylation pyruvate from red cells and Links 184 146 177 150 150 151 152 148 151 149 213 149 147 150 205 147 206 205 204 148 148 204 193 151 148 149 151 148 24 141 143 144 144 143 142 198 142 143 144 143 143 143 143 144 143 145 192
152

152 152 152 25 145 145 145

330
Index Terms glycolysis (Continued) regulation tracing labeled carbons G protein gradient membranes and guanine nucleotide exchange factors guanine nucleotide release proteins H Links
143 236 131 28 132 132
132
136
196
hairpin half-time Hanes-Wolf plot helix hemiacetal structure hemiketal structure Henderson-Hasselbalch equation deriving heterotropic effectors hexose monophosphate pathway HGPRTase high energy signals HMP pathway equations regulation hnRNA homocysteine homologous recombination homotropic effectors hydrochloric acid pKa hydrogen bonding cooperativity DNA enthalpy changes in entropy changes in thermodynamics of hydrophobic interaction 3-hydroxyacyl-CoA hydroxybutyrate hydroxyl group structure hydroxymethylglutaryl-CoA hyperbolic kinetics hyperchromicity hyperventilation hypoventilation hypoxanthine

38 279 111 12 284 284 249 251 117 183 228 198 183 183 183 55 234 47 117 243 11 275 35 274 274 274 9 169 223 284 224 103 38 257 257 229 112 184 185 184 185 224 104

331
Index Terms hypoxanthine-guanine phosphoriboxyltransferase (HGPRTase) I imidazole structure imine indole induced fit diagram inducible information metabolism regulation inhibition competitive noncompetitive product slope and intercept effects uncompetitive inhibitor electron transport ad transition state analog inhibitors initial velocity initiation factor inosine insertion mutagenesis instructions insulin integration of metabolism makes sense understanding integrators diagram interactions in protein folding bad good intercalating agents interorgan cycles intron ionophore isoelectric point estimating K KdaD kdcatD kdcatD/KdmD 244 106 107 284 284 284 83 86 49 52 Links
228

113 113 100 113 114 114 114 101 114 180 181 91 92 125 138 100 58 229 75 1 2 195 196 190224 191 191 125 137 138 17 17 38 220 53 180 254 254 139 138 55

332
Index Terms KdmD ketal structure ketone bodies metabolism synthesis utilization kidneys role in pH balance kinetics Links 107 284 223 223 223 223 257 275 280 117 105 95 117 153
224 224 224 224 276 281 277 282 278 283 279
allosteric diagram enzyme sigmoid Krebs cycle. see TCA cycle L
labeled carbons and metabolism lactate anaerobic glycolysis and Cori cycle and recycline to glucose by liver lagging strand leading strand library ligand ligand binding and thermodynamic cycles ligase Lineweaver-Burk plot lipids acidic neutral lipoic acid function structure liver metabolic function metabolic responses to signals lock and key diagram logarithms London forces low energy signals lungs role in pH balance

236 237 238 239 240 145 221 221 42 42 71 20 270 72 111 23 23 23 286 286 112 212 212 83 84 245 11 198 257 246 247 248

333
Index Terms M major groove in DNA malate-aspartate shuttle malic enzyme malonyl-CoA mechanisms of enzyme catalysis 37 177 193 156 80 85 90 37 19 29 Links
melting DNA protein membrane potential membrane proteins integral peripheral membranes channels composition diffusion fluidity general function membrane proteins and
movement of ions and molecules structure transport metabolic acidosis/alkalosis metabolic regulation secondary signals metabolic signals for glucose metabolic states metabolism during feeding generalities integration storage pools methenyl tetrahydrofolate methionine and one-carbon metabolism methylene tetrahydrofolate 7-methyl guanosine methyl-malonyl-CoA methyl-malonyl-CoA mutase Michaelis-Menton equation assumptions derivation diagram

33 25 25 26 29 23 28 27 22 22 27 32 28 25 29 258 198 194 198 194 30 28 23 23 28 33 29 30 29 24 29 34 25 30 26 31 31 213 214 199 190224 213 235 234 235 229 235 53 55 171 171 103 109 110 110 111 105
81 86 91
82 87 92
83 88 93
84 89 94

334
Index Terms Michaelis-Menton equation (Continued) transformation and graphs minor groove in DNA Monod-Wyman-Changeaux muscle metabolic responses to signals metabolic role of mutagenesis deletion random site-directed diagram mutations, temperature sensitive N Links
111 37 119 212 212 72 75 75 72 19
NADH and glycolysis NADPH in GSSG reduction reduction negative cooperativity Nernst equation example nicotinamide function structure nonaligned recombination nonhomologous recombination nonreproductive binding diagram Northern blot nucleoside phosphorylase O
oligomycin one-carbon metabolism diagram operon organization and entropy origin of replication origin ornithine orotate oxidation oxidation ATP yield

75 77 145 184 184 117 31 32 33 34 285 285 47 47 85 87 67 231 181 233 234 53 1 273 42 43 226 231 173 164 169 166 234 235 2 3 4 5 43 165 170 166 171 167 172 168

335
Index Terms oxidation (Continued) connections diagram equation location malonyl-CoA and odd-chain-length fatty acids reactions regulation unsaturated fatty acids oxidation states of carbon oxidation states of folic acid oxidative phosphorylation see also electron transport diagram inhibitors regulation P Links
palindrome pantothenate function structure partial pressure pCO2 PCR pentose phosphate pathway PFK-2 pH imbalance relation to buffer pKa phenol pKa phenyl group structure phosphate phosphatidic acid phosphodiesterase phosphodiesterases phosphodiester structure phosphofructokinase-1 activation by fructose-1,6-bisphosphate futile cycle and glycolysis and phosphofructokinase-2 phosphofructo-2-kinase effects of phosphorylation phosphogluconate pathway

174 179 175 180 176 181 177 182 175 180 178 181 64 285 285 256 256 76 183 203 246 257 249 243 284 284 163 197 134 284 198 201 142 203 78 184 185 248 204 183 184 185
164 165 167 164 164 172 167 164 168 233 235 173 178
168

336
Index Terms phospholipid bilayer phospholipids structure types phospholipid synthesis phosphomonoester structure phosphopantetheine phosphoric acid pKa phosphorylase phosphorylase kinase phosphorylation diagram effect on enzyme activities metabolic regulation by remembering phosphotriester structure pI pitch pKa polar poly A tailing polylinker polymerase chain reaction diagram polymorphism P/O ratios positive cooperativity posttranslational modification primary transcript primase primer probe product inhibition product/reactant ratio promoter proofreading propionyl-CoA propionyl-CoA carboxylase protein binding denaturation folding glucose ad energy storage in interactions with ligands metabolic movements metabolic pathway stability synthesis Links 24 163 23 23 163 284 159 243 148 148
24

139 202 196 203 284 254 38 244 8 55 72 76 78 69 178 117 26 53 44 44 67 100 262 55 59 171 172 202 204 248 55 101 56 20 19 16 209 20 209 209 15 57 210 210 18 59

337
Index Terms protein kinase cascade metabolic role protein phosphatases protein synthesis ATP requirement free energy and GTP requirement proton proton concentration and pH proton gradient pseudoknot purine degradation purine metabolism purine salvage pathway purine synthesis pathway pyridoxal function structure pyridoxal phosphate pyrimidine degradation pyrimidine salvage pyrimidine synthesis pyruvate carbon atoms from glucose in conversion to malate and oxaloacetate numbering pyruvate carboxylase R Links 136 197 196 197 57 60 269 60 242 248 180 38 229 227 228 229 229 137 197 58 59 196 197 202
Ras pathway diagram rate definition rate constants mechanism related to rate law reaction coordinate diagram receptors acetyl choline enzyme coupled G protein coupled ion-channel coupled soluble intracellular transmembrane

228 229 285 285 188 232 231 230 231 237 193 236 193 131 98 275 102 283 278 80 125 133 128 131 132 127 128 103 277 81 126 82 127 277 129 132 133 130

338
Index Terms reciprocal control of synthesis and degradation recombination reducing sugar reduction regulation information metabolism integration of metabolism replication replication fork repressible repressor respiratory acidosis/alkalosis restriction enzymes cleavage ends mapping orientation sequence restriction fragment-linked polymorphism (RFLP) restriction fragments, joining restriction mapping RFLP riboflavin function structure ribonucleotide reductase ribose synthesis ribsome RNA capping metabolism poly (A) tailing polymerase primary transcript secondary structure splicing RNA polymerase RNAse H rotenone R state RT-PCR S saturation saturation kinetics 105 103 106 105 Links
200 47 151 173 52 190224 42 44 49 49 258 62 64 64 63 65 63 69 66 48 69

49 286 286 228 184 58 53 40 56 53 53 38 53 53 44 181 119 77 55 57 55 55 55 55 106

339
Index Terms screening secondary metabolic signals secondary structure and hydrophobic interaction RNA stability second messengers second-order reactions diagram rate law selection sense strand sequencing DNA serine serine phosphorylation serine transhydroxymethylase serum pH SH2 domain SH3 domain -sheet sigmoid kinetics signals common metabolic transduction pathways and signal transduction pathways Links 71 198 12 14 38 13 125 102 282 280 71 41 73 137 202 234 257 130 130 12 117 125 126 198 125 123 128 133 138 140 123 124 43 72 13 67 97 20 24 53 54 35 18 15 265 194 218
common signals and pathways model organization single-strand binding protein site-directed mutagenesis solvation Southern blot specific activity specificity sphingomyelin splicing alternative stability DNA energetics protein standard state, definition starvation diagram of metabolism

53 55 124 129 134 139 124 125 130 135 140 126 131 136 127 132 137 73 75 77 98 99 100 55 37 195
14 133 280
134
135
136

340
Index Terms starvation (Continued) metabolic movements metabolic signals in stoichiometry of acid-base reactions storage molecules strain and distortion stringency structure amino acids DNA protein Links
217 217 245 191 88 67 6 35 6 10 14 18 12 2 239 240
218
193 89
213
protein, secondary studying succinate symmetry of succinate dehydrogenase and labeled carbons sulfide structure supercoiling surface area synthase definition synthetase definition T
TATA box TCA cycle acetyl-CoA entry ATP from connections diagram equations function location pyruvate and regulation tracking carbon atoms telomere termination factor tetrahydrofolate thermodynamic box thermodynamic cycles

7 7 11 15 19 8 12 16 20 9 13 17 21 240 212 284 44 11 159 159 213 56 153 153 153 154 153 153 153 153 153 238 44 58 235 271 269 272 270

341
Index Terms thermodynamics Links 261 266 271 276 281 286 184 286 262 267 272 277 282 263 268 273 278 283 264 269 274 279 265 270 275 280
thiamin function HMP pathway and structure thiol pKa structure thiol ester thioredoxin threonine threonine phosphorylation thymidylate synthase time, not wasting tissue cooperation titration amino acids curve of acetic acid example stoichiometry topoisomerase tracking carbon atoms through metabolism transaldolase transamination in alanine cycle transcript, primary transcription activation of transcription factor transducers transition state stabilization theory transition state analog transketolase translation tricarboxylic acid cycle triglycerides and adipose triglyceride synthesis triose phosphate isomerase trivia tRNA T state

243 284 284 228 137 202 229 4 211 229 5 253 251 251 245 44 252 246 247 236 184 188 222 53 53 127 55 125 81 88 276 91 184 57 154 163 163 236 2 57 119 237 238 239 240 223 55 56 82 89 92 279 58 59 237 3 59 4 5
185

342
Index Terms Links 12
-turn
U UDP glucose uncouplers ATP synthesis and units of enzyme activity urea urea cycle diagram function uric acid V
valinomycin van der Waals interactions vector velocity change in definition of diagram vitamin A function structure vitamin B6 in one-carbon metabolism vitamin B12 vitamin C structure vitamin E structure vitamin K structure vitamin structures Vmax diagram W
water pKa weak acid Western blot wobble hypothesis X xanthine

226 180 11 71 98 101 275 99 72 286 286 188 234 172 285 286 286 285 106 105 286 9 243 243 67 59 244 229
149 179 179 97 226 225 226 226 229
152 180 180

343
Index Terms Z zero-order reactions 103 281 282 Links

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allosteric diagram enzyme sigmoid Krebs cycle. see TCA cycle L

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