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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
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
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
101
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Index Terms blood pH (Continued) Southern Western bongkrekate brain metabolic role of response to metabolic signals buffers capacity example C Links
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
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
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
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
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
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
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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
201
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
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Index Terms glycolysis (Continued) regulation tracing labeled carbons G protein gradient membranes and guanine nucleotide exchange factors guanine nucleotide release proteins H Links
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
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
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
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
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
81 86 91
82 87 92
83 88 93
84 89 94
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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
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
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
164 165 167 164 164 172 167 164 168 233 235 173 178
168
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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
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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
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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
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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
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
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
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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
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
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Index Terms Z zero-order reactions 103 281 282 Links