Index I-25 Polar bear, 223B Polar solute, 31 Polarity of protein polypeptide, 89 structural, 10 of water, 30 Poly(A) polymerase, 941 Poly(A) tail, 303, 940 3Ј-Polyadenylation of eukaryotic mRNA, 940–941 Polyadenylylation, 940 Polyalanine, 142 Polyamino acid, 142 Polycistronic mRNA, single, 912–913 Poly(Gly-Pro-Pro), 151F Polyleucine, 142 Polylinker, 357 Polymerase core, 907 DNA, 317, 863–864, 865–870, 865T, 866F, 867T, 868F, 868G, 869T, 870B, 870F, 874 poly(A), 941 RNA in eukaryote, 924–925, 925G, 926T in prokaryote, 908, 909F, 910–911 Polymerase chain reaction, 373–375, 374F, 375F, 377F, 378F Polymerization initiation of, 911 microtubule, 494B by open quaternary structures, 177 Polyneuropathy, familial amyloidotic, 172B Polynucleotide, 297 Polynucleotide chain, cleavage in, 309F Polynucleotide fragment, 316–317 Polyol pathway, 687B Polypeptide, 89D backbone, 167D folding of, 96F, 96G, 146 Hsp70 chaperones and, 989 laboratory synthesis of, 117, 119 polarity of, 89 in pyrimidine synthesis, 828 structure of, 10S synthesis of, 118F, 119 Polypeptide chain, 89 conformation of, 96–97 in E. coli polymerase, 866 fragmentation of, 103–105, 104F, 105T separation of, 101 twist in, 166F Polypeptide hormone, 1010 Polyprenol, 231 Polyprotic acid, weak, 76–78 Polyribosome, 976 Polysaccharide, 181D, 194D in bacterial cell walls, 201–204, 202S, 203F branched, glycogen and, 674 cell surface, 204 description of, 213 function of, 194–195 naming of, 194 storage, 194 structural, 196–201 structure of, 10S Polysome electron micrograph of, 976F in protein synthesis, 976, 976F Polyunsaturated fatty acid, 219D degradation of, 714, 715F docosahexaenoic acid as, 736B in mammals, 735 Porcine ribonuclease inhibitor, 169 F Porin, 255, 258F, 593 Portal vein system, 680, 680F Positive control system, 917–918 Positive supercoiling, 335F Positron emission tomography , 555B Postsynaptic cell, 1046 Post-transcriptional processing of mRNA, 940–941 Post-transcriptional regulation of gene expression, 979 Post-translation modification of protein, 119, 993 Potassium action potential and, 1044–1046, 1045F transport of, 272–274 Potassium channels, 272, 274, 274F–275F Potassium ion, hydrolysis of ATP and, 64 Potential action, 1044–1046, 1045F electrical, in neuron, 1044 electrochemical, 271 group transfer, 58–59 phosphorylation, 844 reduction, 593–596, 594F, 595T thermodynamic, 66 transfer, types of, 59T Potentiality, thermodynamic, 382 Power, catalytic, 383 Power stroke, 489 PPT, 801B pp60 v-src , 1023 Precursor inosinic acid as, to GMP and AMP, 814, 815F, 816–818, 820F to plasmalogens, 743–744 zymogens as, 454–455, 454F–455F, 454T Pregnenolone, 238S, 763 Prehybridization, 364B Preinitiation complex, 931–932, 977F, 978 Prenyl, thioether-linked, 257 Prenylation reaction, 259B Prephenate, 799 Preproalbumin, 995 Preprohormone, 1010 Prepro-opiomelanocortin, 1010 Prereplication complex, 872 Pressure, osmotic, 34, 34F Presynaptic cell, 1046 Pribnow box, 908 Primary structure fundamental, 86–89, 87F, 88F, 89, 90T of nucleic acids, 316–320, 317F, 318F, 321F of protein, 94F, 100–110. See also Amino acid sequencing Primase, 869 Primed synthesis method, 317 Primer, 317, 865 Priming reaction in glycolysis, 538, 541F, 542–543, 542F Prion, 893, 895 Prion protein, 893, 895 Pro ␣-2 collagen gene, 940 Probe heterologous, 363 in Southern blotting, 364B Processive movement, 500 Prochirality, 224S Product formation, 391 Proenzyme, 434, 454, 454F Progesterone, 233, 234S, 763 Proinsulin, 454, 454F Projection Fischer, 183–185 Haworth, 185–187 Prokaryote gene transcription in, 906–912, 909F, 910F, 911F, 913F reg ulation of, 912–923, 914F, 915F, 916T, 917B, 917T, 918F, 918G, 919F, 921F, 922F metabolic diversity of, 511 metabolic pathways in, 527 mRNA in, 304F peptide chain initiation in, 966–968, 967F ribosomes of, 305F, 962–963 RNA polymerases, 906–907 translocation of proteins in, 994 Prokar yotic cell, 17, 20, 20T Prokaryotic promoter, 908, 910–911 Prolactin, 1009F Proliferating cell nuclear antigen, 874 Proline hydroxylated residues of, 150S pK a value for, 77T structure of, 72S, 150S synthesis of, 783 Proline racemase, 423 Proline racemase reaction, 423F Prolyl hydroxylases, 559 Promoter, 357, 907 cloning, 357 in eukaryote, 927, 928F prokaryotic, 908, 910–911 Promoter complex, 908 Propeller twist, 323, 323F Propionyl-CoA, conversion of, 711F Prostaglandin, 737, 747, 747B Prostaglandin endoperoxide H synthase, 747, 749F Prosthetic group, 81B, 120, 385, 598 Protease aspartic, 437, 440–441, 441F, 441S HIV-1, 440F, 441–442 HtrA, 1003 naming of, 384 serine, 434–437, 436F, 438F, 439B Proteasome, 947, 998, 1000 Proteasome activator-700 kD, 1000 Proteasome inhibitors, 425B, 1003B Protein. See also Protein synthesis acetylcholine transport, 1050 actin-anchoring, 486B amino acid sequences of analysis of, 99–100 databases of, 109–110 nature of, 110–117, 110F, 113F, 114F, 115F, 116G, 117T in structure, 136 annexin, 1031 biological functions of, 120–123 biotin carboxyl carrier, 724 I-26 Index Protein (continued) calcium-binding, 1031 cAMP receptor, 917 catabolite activator, 916 catalytic, 121 chemistry of, 93 cholesterol ester transfer, 758 classification schemes for, 157–159 of cloned genes, 369–372, 369F, 371F coiled-coil motif in, 148B conjugated, 120T definition of, 89D degradation of, 208–209, 998–1005, 999F, 1000F, 1001F, 1004B, 1004F denaturation of, 51T, 159–161, 160F DNA-binding, 923 domains of, 155–156 EF hand, 1031, 1033 energy in, 698T in eukaryotes, 995 extrinsic, 246 in fatty acid synthesis, 727, 727F folding of, 987–992 diseases of, 172B of globular protein, 166–167 Hsp70 chaperones for, 988–989, 989F hydrophobic interactions in, 135 mechanism of, 162–163, 163F molecular chaperones for, 168 N-linked oligosaccharides in, 209B polypeptide, 96F, 96G, 146 thermodynamics, 163–164 functions of, 120–123 fusion, 371T G GPCR signals transduced by, 1024–1025 muscarinic receptors and, 1050–1052 phospholipase C activation by, 1030 as signal transducer, 1027–1028 gene regulatory, 935–939, 939F globular, 152–170. See also Globular protein green fluorescent, 81B, 81G, 372 GTP-binding, 466 heat shock, 168, 988 with helix-turn-helix motif, 936 hybrid, 371F hydrophobic, 203 indirect readout and, 937 inte gral, 246 integral membrane, 270 intrinsic, 246 intrinsically unstructured, 168, 170F iron–sulfur, 598 isolation and purification of, 97–98, 98B, 99T link, 213 lipid-anchored, 256–258, 257B, 258F, 260 location in cell, 994F, 994–998, 996F, 997F membrane, 248–260, 995 aggregation of, 272–273 bacteriorhodopsin as, 250–251, 251F porins as, 255, 258F with single transmembrane segment, 249–250, 249F as switching device, 256–258, 257B, 258F, 260 mitochondrial, 997 motor, 481 multifunctional, 725 multimeric, 175F mutant, 117, 171 B noncovalent interactions in, 134–136 nonhistone chromosomal, 302–303, 336 nutritional requirement for , 531 oligomeric state of, 458–459 oxygen-storage, myoglobin as, 468 peripheral, 246 post-translation modification of, 993 primary structure of architectural arrangement of, 93–97, 94F, 95F, 96G, 97F fundamental, 86–89, 87F, 88F, 90T, 93 prion, 893, 895 quaternary structure of, 173–178 polymerization of, 178 symmetry of, 174, 176F variety of, 177 weak forces in, 174, 176 ras, 259B, 1027, 1027G RecA, 881–883 receptor, 1043 regulatory, 913 ribosomal, 962 Rieske, 604 Ruv, 880, 883–885 scaffolding, 266–267 secondary structure of, 136–146 alpha-helix in, 137, 139–142, 140F, 141F amide plane in, 136–137, 137F, 138F beta-pleated sheets in, 141F, 142–144, 143B, 144F beta-turns in, 144–145, 145F parallel sheets in, 143 simple, 119 single-stranded DNA-binding, 863 size of molecules of, 90T SMC, 338–339, 339F structure of, 169F targeting of molecules by, 121–122 tertiary structure of, 146–172 fibrous proteins and, 146–151, 147F, 149F, 150S, 151F, 151S globular proteins and, 152–170. See also Globular protein marginal stability of, 164 triage of, 1004B Tus, 870 ubiquitin-carrier, 998 unfolding of, 55, 55F viral transforming, 1023 whimsical names for, 1040B Protein binding, 122 Protein deposit, diseases with, 988B Protein interaction domains, 1011 Protein isoform, 944 Protein kinase covalent modification and, 453 description of, 453F, 460–461 mitogen-activated, 1034B Protein kinase A, 460, 460F, 1035 Protein kinase C, 1029–1031, 1035–1036 Protein phosphatase 2A, 693 Protein sequence, conventions used in expressing, 907B Protein splicing, 896B Protein synthesis, 952–986 aminoacyl-tRNA synthetases in, 953, 955–958, 955T, 956F, 957G codon–anticodon pairing in, 958–961, 959 F, 959 T, 961T Escherichia coli glutaminyl-tRNA syn- thetase in, 958, 958G in eukar yotic cells, 976–984, 977F, 978T, 980B, 980F, 982T genetic code and, 952–953, 953F, 954B, 954T G:U base pair in, 958 inhibitors of, 981–984, 982T messenger RNA and, 303 mRNA translation in, 965–976. See also mRNA translation in protein syn- thesis ribosomes in, 961–965, 962T, 963F, 965T steps in, 965F Protein transfer potential, 59T Protein translocation, 994 Protein tyrosine kinase pp60 c-src , 1036, 1036F Protein tyrosine phosphatase SHP-2, 1036–1037, 1036G Protein-coding gene, 925–926 Protein-protein interaction, 123, 372–373, 922–923 Proteoglycan, 209–213 cell growth and, 211–212 function of, 209–211 Proteoglycan-hyaluronate aggregate, 213 Proteolytic cleavage in post-translational processing, 993 Proteolytic enzyme digestive, 454–455, 454F in polypeptide cleavage procedures, 105T Proteome, 120 Proteomics, 367B, 513 Prothrombin, 232B Proton gradient flagella and, 503–504 synthesis of ATP and, 611–620, 614F, 616F–617F, 618F, 619B, 619F Proton pump, 283F Proton symport, 286 Proton transport, 604–605 Proto-oncogene, 1029B Provirus, 877 Prozac, 1054B–1055B PrP, 893, 895 PRPP in Lesch-Nyhan syndrome, 822B PS decarboxylase, 741 PsaD, 645 Pseudoknot formation, 344 Pseudosubstrate sequence, 460, 845 Pseudouridine, 305S, 345 PSI complex, 637–638, 638F, 640, 645, 646F, 647 PSII complex, 637–638, 638F, 640–641 D-Psicose, 183S Pump, proton, 283F Pure noncompetitive inhibition, 400 Purification affinity, 97 protein, 98, 99T Index I-27 Purine, 291–294, 292F, 293S catabolism of, 821, 823–826, 824F, 826F salvage of, 821, 821F synthesis of, 802, 804, 813–821 ATP-dependent kinases in, 820–821 inosinic acid in, 814, 815F, 816–818, 819F regulation of, 819–820 Purine nucleoside cycle, 823, 824F Purine nucleoside phosphorylase, 823 Purine ring, 292F Puromycin, 983S Purple patches, 285 Pyranose, 184 Pyranose form of D-glucose, 186S of D-ribose, 186S Pyridoxine, 524T Pyrimidine, 291–294, 292F, 293S degradation of, 830, 830F fluoro-substituted, 835B synthesis of, 826–830, 827F, 828F Pyrimidine dimer repair, 890 Pyrimidine ring, 292F Pyroglutamic acid, 75S, 76 Pyrophosphate, 57T Pyrophosphomevalonate decarboxylase, 755 Pyrrolysine, 75S Pyruvate gluconeogenesis and, 662 in glycolysis, 552–553, 553F glycolysis production of, 537F metabolism of, 552–553, 553F synthesis of, 805F transamination of, 851F in tricarboxylic acid cycle, 564F, 566 Pyruvate carboxylase, 582, 664–665 compartmentalized, 666 in gluconeogenesis, 665–666, 665F Pyruvate decarboxylase, 553 Pyruvate dehydrogenase complex, 566, 567F, 568B–569B, 571F Pyruvate dehydrogenase E3-binding pro- tein, 566 Pyruvate dehydrogenase kinase, 584–586 Pyruvate dehydrogenase reaction, 566 Pyruvate family of amino acids, 781T, 793, 794F, 795F Pyruvate kinase, 550–551, 550F, 552F Pyruvate-Pi dikinase, 658 Pyruvic acid, 191S PYY 3–36 , 855 Q cycle, 603, 604–606, 605F Q a -SNARE, 268 Q bc -SNARE, 268 Quadruplexes, 329, 330F Quality control, protein, 1003–1005, 1004B Quantum yield of photosynthesis, 637, 647–648 Quaternary structure allosteric properties and, 467–468 of hemoglobin, 469, 471 of protein, 95, 173–178 Racker, Efraim, 616 Radiation, ultraviolet, 82 Radical, free cationic, 636, 638 in ribonucleotide reduction, 832F RAG recombinase, 901 Ramachandran plot, 137, 138F Random coil, 153 Random reaction, 403 RANTES, 1042 Ras protein, 259B, 1027, 1027G Rat cartilage proteoglycan, 210F Rat growth hormone gene, 889B Rate constant, 386 Rate of enzyme catalysis, 386, 419 Rate-limiting step, 437 Ratio, 393 equilibrium, ATP changing, 67B H ϩ /2e Ϫ , 611 k cat /K m , 393–394 molar, of nucleic acids, 300T P/O, 620 Rational drug design, 404B Reactant, 386 Reaction aminotransferase, 782B anaplerotic, 582, 584 beta-oxidation, 704–709, 704F, 706F bimolecular, 387 in Calvin–Benson cycle, 653, 653T, 655 DNA strand exchange, 881–883 filling up, 582, 584 fructose-1,6-bisphosphatase, 667 in gluconeogenesis, 665–669, 667F, 668F, 669F glucose-6-phosphate dehydrogenase, 684, 685F glutamine synthase, 776F glycogen phosphorylase, 462–467, 462S, 463F, 463S, 464F, 674, 675F glycogen synthase, 676, 678F of glycolysis, 538T malate dehydrogenase, 578 nitrogenase, 772–773, 772F nucleoside diphosphate kinase, 576 PEP carboxykinase, 666F 6-phosphogluconate dehydrogenase, 684, 686, 686F phosphopentose isomerase in, 686–687, 687F photosynthetic, 632–633, 632F priming, 538 redox, 595–596 ribulose-1,5-bisphosphate carboxylase, 651, 651F second-order, 387 serine dehydratase, 807B splicing , 942–943 succinate dehydrogenase, 576 thymidylate synthase, 836F transaldolase, 689–690, 690F transamination, 782B transketolase, 688–689, 688F in tricarboxylic acid cycle, 572T UDP-glucose pyrophosphorylase, 676, 676F Reaction center, photosynthetic, 638, 641–647, 642F, 643F, 643G Reaction half-cell, 594 Reactive-center loop, 171B Readout, indirect, 937 Reagent, Edman’s, 102 Reannealing, 331 RecA, 499 RecA protein, 881–883, 882G RecBCD enzyme, 880 RecBCD-dependent initiation of recombi- nation, 881F Receptor acetylcholine, 1047, 1048F asialoglycoprotein, 209 G-protein-coupled, 1013, 1015 lambda, 255 LDL, 760 lymphocyte homing, 212 muscarinic, 1050–1052 nicotinic acetylcholine, 1050 nitric oxide, 1024 signal-transducing, 1012F, 1013–1024, 1013F, 1013G, 1024B TMS, 1015 Receptor protein, 1043 cAMP , 917 Receptor signal transduction, 1024–1034 Receptor tyrosine kinase, 1016–1017, 1030, 1030F Recognition matrix, 937 Recognition particle, signal, 995 Recombinant DNA, 354–381 artificial chromosomes from, 360 cloning and, 354–360. See also Cloning directed changes in heredity and, 375–377, 377F, 378B, 378F DNA libraries and, 360–368, 361B, 362 F–363F, 364B, 365F, 366F, 367B, 368F–370F, 371T polymerase chain reaction and, 373–375, 374F, 375F Recombinant DNA molecule, 354 Recombinant plasmid, 355 Recombinase, 881 Recombination, genetic, 877–886. See also Genetic recombination Recombination-activating gene, 901 Recombination-dependent replication, 884B, 885 Recycling factor, ribosome, 974 Red blood cell, sickle cell anemia and, 476–478 Red wine, polysaccharide in, 199B Redox couple, 594 Redox reaction, 595–596 Reducing end, 192 Reducing sugars, 188 Reductase aldose, 687B nitrogenase, 771, 773G Reduction of ␤-carbonyl group, in fatty acid synthe- sis, 729–730 oxidation, transduction of light energy and, 636 Reduction potential, 593–596, 594F, 595T concentration and, 596 Reductive citric acid cycle, 583B Reductive cleavage, of disulfide bridges, 102F Reentrant loops, 253 Reference half-cell, 594 Refsum’s disease, 717B I-28 Index Regular structure, of protein, 94F Regulation allosteric. See Allosteric regulation autogenous, 920 of carbon dioxide fixation, 655–656, 655F by enzyme, 383–385 of gene transcription, 912–923, 914F, 915F, 916T, 917B, 917T, 918F, 918G, 919F, 921F, 922F of gluconeogenesis, 669–673, 671F, 672F of glutamine synthetase, 776–779, 777F, 777G, 778F of glycogen metabolism, 678–683 of glycogen synthase, 676–679 of isocitrate dehydrogenase, 586 metabolic, 16 negative, 915 of nitrogen fixation, 773F of phosphofructokinase, 542G post-transcriptional, 979 of purine synthesis, 819–820, 820F of pyrimidine synthesis, 830 of tricarboxylic acid cycle, 584–586, 585F Regulators of G-protein signaling, 1038 Regulatory enzyme definition of, 383D nonlinear Lineweaver–Burk or Hanes–Woolf plots, 395 Reg ulatory gene, 914–915 Regulatory protein, 913 gene, 935–939, 939F Relaxed DNA, 334 Relaxed form of hemoglobin subunits, 473 Release factor, 974 Remodeling, bone, 282–283 Renaturation of DNA, 331–332 Rep helicase, 500 Repair of DNA, 887–891, 890F, 892F of genetic deficiency, 376, 377, 378B Repeat, inverted, 327, 328F Replacement therapy, gene, 376, 377 Replication, DNA, 862–876. See also DNA, replication of Replication activator protein, 872 Replication factory, 870 Replication fork, 863, 868–869 Replication licensing factors, 872 Replication switch, 872 Replicator, 355 Reporter gene, 371 Repressible operon, 918 Repression, 452, 914D Repressor lac, 915–916, 915F, 917B, 917T Trp, 920 Repulsion, electrostatic, 60, 61F Reserpine, 1054B–1055B Residue amino acid, 89, 433B in alpha-helix, 139 hydroxylated of collagen, 150F of proline, 150S invariant, 113 sialic acid, 208S Resistance, drug, 283, 285 Resonance competing, 60 peptide bond, 87, 89, 136 stabilization of hydrolysis products by , 60 Resonance-stabilized carbanion intermedi- ate, 711F Respiratory acidosis, 44B Respiratory alkalosis, 44B Response element, 927, 928–929 cAMP, 936B Restriction endonuclease, 310–313, 311T, 312F, 313 Restriction endonuclease EcoRI, 356F Restriction enzyme, 310–313 Restriction fragment size, 312–313 Reticulum endoplasmic, 20 of animal cell, 23T of plant cell, 24T signal peptidase and, 996–997 sarcoplasmic, 280 Retina, docosahexaenoic acid in, 736B Retinal, 285S Retrograde translocation, 997 Retrovirus, 876B Reunion of DNA strands, 877–878 Reverse transcriptase, 363, 876–877 Reverse transcriptase polymerase chain reaction, 373 Reverse transcriptase-driven synthesis of cDNA, 366F RF, 974 RGS proteins, 1039, 1039F Rhamnogalacturonan II, 199B ␣- L-Rhamnose, 189S Rho termination factor, 912 Rhodopseudomonas viridis photosynthetic reaction center, 642–645, 642F, 643F, 643G Rhodopsin, 252F Ribbon, extended, 197 Ribbon structure of protein, 156F Ribitol, 189 Ribitol phosphate, 204 Riboflavin, 524T ␤- D-Ribofuranose, 295 Ribonuclease bovine, 152 unfolding of, 161F Ribonuclease A, 94F, 152F, 152G size of molecule of, 90T Ribonucleic acid. See mRNA; RNA Ribonucleoprotein particle, 941 small nuclear, 305 Ribonucleotide, 294F, 295D Ribonucleotide reductase, 831–832, 832F D-Ribose, 186S Ribose zipper, 344 Ribose-5-P, 691–692 ␣- D-Ribose-5-phosphate, 189F Ribose-5-phosphate pyrophosphokinase, 814 Ribosomal protein, 962 Ribosomal RNA, 299, 303–304, 304F, 305F, 306, 962–963, 963F intrastrand base pairing and, 346, 348 Ribosomal subunit, 974, 976F Ribosome assembly of, 961–965 catalytic power of, 970–971 definition of, 961D eukaryotic, 305F, 964–965, 965F life cycle of, 976F in plant cell, 24T prokaryotic, 305F, 962–963 prokaryotic cell, 20T spontaneous self-assembly of, 963 structural organization of, 961–965, 962T, 963F, 965T translocon and, 995 tRNA-binding sites on, 966F Ribosome binding site, 967 Ribosome nascent chain:SP complex, 995–996 Ribosome recycling factor, 974 Ribosome RNA secondary structure of, 349F tertiary structure of, 349F, 349G Riboswitches, 350 Ribothymidine, 305S Ribothymidylic acid, 304 Ribozyme, 410–412, 411F Ribulose, 90T D-Ribulose, 183S Ribulose bisphosphate, 651 Ribulose bisphosphate carboxylase, 656 Ribulose-1,5-bisphosphate, 651, 651G Ribulose-1,5-bisphosphate carboxylase reac- tion, 651 Ribulose-5-phosphate kinase, 653 Rieske protein, 169F, 604 Right-handed DNA, 323, 324F Ring furanose, 187 purine, 292F pyrimidine, 292F Ritonavir, 443S RLFs, 872 RNA biological significance of, 307 of cloned genes, 369–372, 369F, 370F definition of, 297D double-stranded, 375 eukaryotic transcript, 305 hydrolysis of, 307 messenger. See mRNA entries micro, 306 noncoding, 306 ribosomal, 303–304, 304F, 305F, 306 intrastrand base pairing and, 346, 348 operons of, 963F ribozymes, 410–412, 411F secondary structure of, 341–350, 345F, 345S, 346S, 347S, 348F, 349F small, 305, 306 small interfering, 375 splicing of, 944 transfer, 304–305 unusual bases of, 305S vincinal -OH groups of, 308F RNA editing, 945–946 RNA enzyme, 411–412, 412F RNA expression, 369 RNA genome, replication of, 876–877, 876B RNA interference, 375 RNA polymerase in eukaryotes, 924–925, 925G, 926T, 930 I, 924 Index I-29 II, 924, 925G, 926T III, 924 in prokaryotes, 908, 909F, 910–911 RNA polymerase holoenzyme, 906–907 RNA-directed DNA polymerase activity, 876 RNA-induced silencing complex, 375 RNase, 309 RNase H, 876 RNase PH, 947 RNC-SRP, 995–996 Robinson, Sir Robert, 753B Rosanoff, M.A., 82B Rosanoff convention, 82B Rossman fold, 501 Rotating molecular motor, 481 Rotation of flagella, 503–504 optical, 80 Rotation axis, twofold, 174 Rotenone, 617S Rough endoplasmic reticulum, 21F Rous sarcoma virus, 1023 RRF, 974 rRNA, 962–963, 963F (R,S) system, 81–82, 84B R-SNARE, 269 RT-PCR, 373 Rubisco, 651 Rubisco activase, 652 Rule, Chargaff’s, 300T RuvA, 880, 883–885 RuvB, 880, 883–885 RuvC, 880, 883–885 RuvC resolvase, 885 70S complex, 974 48S initiation complex, 979F 80S initiation complex, 979 43S preinitiation complex, 977F, 978 20S proteasome, 1000 26S proteasome, 1000, 1000G 19S regulator, 1000 70S ribosome:RF1:RF3-GTP:termination signal complex, 974 Saccharide, 204, 205S, 206F Saccharopine, 787 Saccharopine pathway, 809 SAGA complex, 933 SAICAR synthase, 815F Salivary ␣-amylase, 196 Salmonella, 204 Salt, bile, 700 Salt bridge between subunits of hemoglo- bin, 473F Salting-in of protein, 98 Salvage of purines, 821, 821F SAM, 790, 997–998 Sample half-cell, 594 Sanger, F., 316 Sanger’s chain termination, 317–320 Saponification, 222 Saquinavir, 425B, 443S Sarcolemma, 483 Sarcoma virus, Rous, 1023 Sarcomeres, 483 Sarcoplasmic reticulum, 280, 483 Sarin, 1051S, 1052 Saturated fatty acid, 219D Saturation behavior, 271 Saturation curve, 122, 122F oxygen, 474F substrate, 389 Saturation effect, 389 Saxitoxin, 1049B Scaffolding proteins, 266–267 Schiff base linkage, 285S Schizosaccharomyces pombe, 845 Schönbein, Christian, 201B Schultze, Major E., 201B SCID, 378B, 822B SCOP, 158 Scramblases, 262 Screening of DNA library, 362, 362F, 370 Scurvy, 155B SDS-PAGE, 131 SDS-polyacrylamide gel electrophoresis, 130–131 Seawater, 5T Sec61 complex, 996 SECIS element, 954B Second genetic code, 953, 955 Second messenger calcium as, 1031 cyclic AMP as, 466, 1025–1026, 1026F, 1026G, 1026T intracellular, 1026T phosphatidylcholine generating, 1031 released by phospholipase, 1028 Secondar y active transport, 286–287 Secondary structure of DNA, 320–333. See also DNA, sec- ondary structure of of proteins, 136–146. See also Protein, secondary structure of of RNA, 341–350, 345F, 345S, 346S, 347S, 348F, 349F Second-order reaction, 387 Secreted polypeptide hormone, 1010 Secretion insulin, 680 of pancreatic juice, 699F retrograde translocation preventing, 997 Secretory protein, 995 Sedimentation coefficient, 132–133, 303 Sedoheptulose-1,7-bisphosphatase, 653 Selectable marker, 355 Selectins, 213T, 214, 214F Selectivity filter, 272, 274 Selenocysteine, 75S, 954B Self-replication, 3–4 Self-splicing, 411 Sensor, 923 Separation, protein, 97–98, 98B Sequence consensus, 908D, 928T DNA cloning of, 355–356, 356F gene regulatory proteins and, 935–939, 939F insertion, 886 intervening, 303 nucleic acid, 907B signal, 994 stop-transfer, 997 upstream activation, 927 Sequence tag, expressed, 366 Sequence-specific transcription factor, 937 Sequencing amino acid, 100–110. See also Amino acid sequencing DNA, 318F automated, 318–320 genome, 17–18 Sequencing gel, dideoxy, 318–320 Sequential reaction, 403 Serglycin, 210F Serine catabolism of, 804 ethanolamine and, 741 in green fluorescent protein, 81B in lipid synthesis, 741 pK a value for, 77T sphingolipid synthesis and, 744–745 structure of, 72S synthesis of, 793, 796F Serine acetyltransferase, 795 Serine dehydratase reaction, 807B Serine hydroxymethyltransferase, 816B Serine phosphatase, 793 Serine protease, 434, 436F, 437, 438F, 439B Serotonin, 75S, 76 Serpin, 171B Serum albumin, 90T Serum cholesterol, 761 Seryl tRNA synthetase, 148B Sesquiterpene, 229, 230S, 231 Severe combined immunodeficiency syn- drome, 378B, 822B Sex hormone, 763 SH modification in cleavage of disulfide bridges, 102F Sheet ␤. See Beta sheet in globular proteins, 152–153, 152G, 154G parallel, in proteins, 143 Shift chemical, 83–84, 85F hyperchromic, 330 keto-enol tautomeric, 293 Shikimate pathway, 793, 799F Shine-Dalgarno sequence, 967, 967F Short-chain acyl-CoA dehydrogenase, 705 Shuttle, malate–aspartate, 621 Shuttle vector, 360, 360F Sialic acid, 191S, 208S, 228 Sickle cell anemia, 476–478 Side chain, amino acid, 78–79 Sigma factors, 907 Sigmoid curve, 456 Signal GPCR, 1024–1025 polyadenylation, 940 Signal peptidase, 994, 996–997 Signal peptide, 996 Signal receptor, 994 Signal recog nition particle, 994, 995 Signal sequence, 994 Signal transduction pathway, 257, 992–993, 1010–1013, 1012F Signal transduction unit, 1025 Signalsome, 1011 Signal-transducing receptor, 1012F–1013F, 1013–1024, 1013G, 1024B Silencer, 927 Silencing, gene, 306–307 I-30 Index Silk, spider, 144 Silk fibroin, 149F Simple protein, 119 Simple sugar, 181D Singer, S. J., 245 Single polycistronic mRNA, 912–913 Single transmembrane segment, 249–250, 249F Single-displacement bisubstrate mecha- nism, 403F Single-displacement reaction, 403, 403F, 405–406 Single-strand assimilation, 882–883 Single-stranded DNA damage, 887 description of, 331 Single-stranded DNA-binding protein, 863 siRNA, 306 Siroheme, 770 Site active, 389, 398 catalytic, 178 cloning, 355 substrate-binding, 398 Sitosterol, 236S Size exclusion chromatography, 130–131 Skeletal muscle, 481–490. See also Muscle contraction energy metabolism of, 848T metabolic role of, 849–851, 850B structure of, 482F Skeletal muscle troponin T isoform, 945 Sliding filament, 486, 487F, 488–490 Slow-twitch muscles, 708B Small interfering RNA, 306, 375 Small intestine, 699F Small nuclear ribonucleoprotein particle, 306 Small RNA, 306 SMC proteins, 338–339, 339F SMC1/SMC3 heterodimers, 339 SMC2/SMC4 heterodimers, 339 Smooth endoplasmic reticulum, 21F Smooth muscle effectors, 482B Snake venom, 235B, 308F SNARE, 268–269, 269F snRNP, 305, 943 Soap, 222 Sodium, action potential and, 1044–1046, 1045F, 1046 F Sodium channel toxin, 1049B Sodium ion hydrolysis of ATP and, 64 secondary active transport and, 286 Solar energy. See Light energy Solid phase oligonucleotide synthesis, 341F Solid-ordered state, 262 Solid-phase synthesis, of peptide, 118F Solubility, of globular protein, 98F Soluble protein, unfolding of, 55, 55F Solute colligative properties and, 33–34 polar, 31 water properties and, 33 Solution, double helix in, 327 Solvent, water as, 30–34, 44 Soma, 1044 Somatic recombination, 877 Somatostatin, 1009F Sorbitol, 189 D-Sorbose, 183S Sorting and assembly complex, 997–998 Southern, E. M., 364B Southern blotting, 364B Southern hybridization, 362–363 Space intermembrane, 592 thylakoid, 631 Specialization, organ, 847, 848F, 848T, 849–853, 851B, 851F Specific acid–base catalysis, 430 Specific activity, 393 Specific linking difference, 335 Specificity definition of, 383 enzyme, 383 Specificity site of ribonucleotide reductase, 832–833 Spectrin, 265 Spectrometry amino acid properties, 82–85 mass, 105–109, 106T, 107F–108F, 109F Spectroscopy, nuclear magnetic resonance, 526–527, 527F Spectrum, absorption, of nucleic acid bases, 293–294, 293F Spermaceti, 229B Sphingolipid, 227–229, 228F, 737, 744–745, 745F Sphingomyelin, 227, 746F, 1031 Sphingomyelinase, 1031 Sphingosine, 227 Sphingosine-1-phosphate, 235 Spider web, 144 Spirogyra, 632F Spliceosome, 943, 943F Splicing, 411F, 939–940 nuclear pre-mRNA, 940–941 protein, 896B Splicing reaction, 942–943 Split gene, 939–940 Squalene, 230S, 231, 752, 753, 754F Squalene monooxygenase, 757 SRP, 995 SRs, 994 SSB protein, 863 S-shaped curve, 456 Stability of quaternary structure, 177 Stabilization of hydrolysis products, 60 transition-state, in serine protease, 439B Stacking , coaxial, 344 Standard reduction potential, 59T Standard state, 50 Standard-state free energy, 54–55 Standard-state free energy change, 53 Stanozolol, 764, 764F Staphvax, 207B Staphylococcal protease, 103 Starch, 195–196, 196S catabolism of, 673–674, 673F Starch phosphorylase, 195 State function, 49 Statins, 424B, 755B Statistical thermodynamics, 51 Stator, 612 Steady state, 2 Steady-state assumption, 390 Stearic acid, 6F, 219, 220T, 221G, 221S, 222G, 222S Stearoyl-CoA desaturase, 734 1-Stearoyl-2-oleoyl-phosphatidylcholine, 226, 226F, 226G Steitz, Thomas, 870B Stem-loop structure, 342, 912 Stereochemistry of amino acid, 79–82 of monosaccharides, 183–184 Stereoisomer, 83B Stereospecificity in NAD ϩ -dependent dehy- drogenase, 579B Steroid anabolic, 764, 764F cardiotonic, 280, 280G, 280S, 282B structure and function of, 233, 234F, 234S, 236B, 238S Steroid hormone action of, 1008–1009 definition of, 1008D synthesis of, 762–764 Stigmastanol, 236S Stoeckenius, Walther, 616 Stoichiometry, 841–843, 841D Stomata of desert plant, 659 Stop-transfer sequence, 997 Stop-transfer signal, 994 Storage, long-term memory, 936B Storage granule, 20T Storage polysaccharide, 194 Stored metabolic fuel, 698T Strain, structural, 422 ␤-Strand, 95F Strand exchange, 879 Streptococcus lividans, 274, 274F Streptomycin, 194F, 983S Stroma, 631 magnesium ions moving into, 656 Strong electrolyte, 46 Structural complementarity, 14, 14G Structural gene, 914–915 Structural genomics, 172B Structural polarity, 10 Structural polysaccharide, 196–201 Structural strain, 422 Strychnine, 1053 Substrate binding of, 389 definition of, 383 of gluconeogenesis, 662, 672–673 in glycolysis, 554–558, 556F, 558B leadin g, 405 obligatory, 405 suicide, 401–403 Substrate saturation curve, 389 Substrate specificity site, 831, 832–833 Substrate-binding site, 398 Substrate-level control mechanism in gluco- neogenesis, 669–671, 671F Substrate-level phosphorylation, 575–576 Subunit cytochrome, 642F of E. coli polymerase III homoenzyme, 867T identical, dimer of, 441 of prokaryotic ribosomes, 961–962 protein, 95, 173 Succinate oxidation of, 601–603, 602F structure of, 150S in TCA cycle, 576 Index I-31 Succinate dehydrogenase competitive inhibition and, 399–400, 400F as FAD-dependent, 576 Succinate dehydrogenase reaction, 576 Succinate thiokinase, 575 Succinate-coenzyme Q reductase, 598 N-Succinyl-5-aminoimidazole-4-carboxamide ribonucleotide, 815F Succinyl-CoA amino acid catabolism and, 807 oxidation of, 711F, 712 Succinyl-CoA synthetase, in TCA cycle, 575–576 Sucrose, 192F, 192G, 192S, 193, 408 Sugar amino, 190 deoxy, 189 simple, 181D structure of, 10S Sugar acid, 187–188, 188S Sugar alcohol, 189, 189S Sugar code description of, 213 lectin translation of, 213 Sugar ester, 189, 189S Sugar nucleotide, 675, 675G, 675S Suicide substrate, 401–403 Sulfate assimilation of, 797F sulfide synthesis from, 796–797 Sulfatide, 228 Sulfide synthesis, 796–797, 797F Sulfite oxidase, wild-type, 396B Sulfmeturon methyl, 801B Sumoylation, 933 Supercoil, 333–336, 335F, 336F, 911F Superfamily, 158, 499, 499T, 500F Superhelix density, 335 Suppressor tRNA, 960–961 Supramolecular complex, 6, 8F membrane as, 9 membrane-spanning, 638 virus as, 21–22 Surface tension, of water, 45 Switch membrane protein as, 256–258, 257B, 258F, 260 replication, 872 Symmetry, 174 Symmetry model, 457–459 Symport, 286 Synapse, 1044, 1046–1047 Synapsis, chromosome, 879, 879F Synaptic bulb, 1044 Synaptic cleft, 1044, 1048, 1050 Synaptic junction, 1052 Synaptic knob, 1044 Synaptic terminal, 1044 Synaptotagmin, 269 Synchrony, 204 Syndecan, 209–210, 210F Synechococcus elongatus, 644–645, 644F Synonymous codon, 953 Synthesis amino acid, 779–810. See also Amino acid synthesis of ATP, 611–620, 614F, 616F–617F, 618F, 619B, 619F of cDNA, 366F cholesterol, 750–757 dehydration, 191 DNA, deoxyribonucleotide formation in, 830–833, 831F, 833F of eicosanoids, 747–750 fatty acid, 722–737. See also Fatty acid synthesis of fructose-2,6-bisphosphatase, 672F of gene, 340 glycogen, 675–677, 675G, 675S, 676F, 680–683 of hexose, 647–648, 653, 655 of hybrid protein, 371F lethal, 834B macromolecular , 839–840 of nucleic acid, 339–340 polypeptide, 118F, 119 protein, 952–986. See also Protein synthesis of pyrimidines, 826–830, 827F, 828F of secretory proteins, 995 solid phase oligonucletotide, 341F of thymine nucleotide, 833–836, 834B, 835B, 836F Synthesis method, primed, 317 Synthetase Acyl-CoA, 702 arginosuccinate, 784 glutamine, 774, 775F regulation of, 776–779, 777F, 777G, 778F Synthetic combinatorial library, 361B Synvinolin, 755B Szent-Györgyi, Albert, 488 T lymphocyte, 897 Tabun, 1051S, 1052 TAF, 930 Tag, expressed sequence, 366 D-Tagatose, 183S Tail, myosin, 484 D-Talose, 182S Tamiflu, 425B Tandem enzyme, 671 Tandem mass spectrometry, 107–108, 109F Tangle, neurofibrillary, 988B TATA box, 927, 927F Taurocholic acid, 761F Taut form of hemoglobin subunits, 473 Tautomeric shift, keto-enol, 293 Taxol, 494B TBP, 930 Teichoic acid, 204 Telomerase, 875 Telomere, 299D, 340B, 874, 875B, 875F Temperature enzymatic activity and, 397, 397F melting, 331 of water, 44–45 Template, 317 DNA, 862, 862D Template DNA, 908, 910–911 Template strand, 907B Tense form of hemoglobin subunits, 473 Ter region, 869–870 Terminal, synaptic, 1044 Terminal chain segment, glycogen, 677–678, 678F Termination, 966 peptide chain, 974, 975F in eukaryotes, 981 in protein synthesis, 974, 975F Sanger’s chain, 317–320 Termination codon, 953 Termination site, 912 Terminator, 922 Terpene, 229–232, 230S, 231B, 231S, 232B Tertiary structure of DNA. See also DNA, tertiary structure of of protein, 95, 146–172. See also Protein, tertiary structure of of rRNA, 348, 349G of transfer RNA, 345, 346F, 348 Testosterone, 233, 234S, 238S, 1009F Tetracycline, 983S Tetrahedral oxyanion transition state, 439B Tetrahydrofolate, 816B Tetraloop, 343 Tetrodotoxin, 1049B Tetrulose, 183 TF, 988 TFII, 930, 933 TFIII, 925 Therapy, gene, 376, 377, 378B Thermal cycler, 373 Thermal denaturation, of DNA, 330–331, 333F Thermal properties of water, 44–45 Thermoacidophile, 19 Thermodynamic parameters for protein denaturation, 51T Thermodynamic potential, 66, 382 Thermodynamics, 48–69 ATP hydrolysis and, 64 coupled processes and, 66 electron transport and, 611 enthalpy and, 49–51 first law of, 48–49 of glycolysis, 538T high-energy biomolecules and, 56, 57T parameters of, 55–56 pH and, 54–55 requirement for ATP and, 66 second law of, 51–52 third law of, 52 Thermogenin, 619B, 852 Thiamine, 524T Thiamine pyrophosphate, 350F, 568B Thick filament, 484–485 Thin filament, 483F, 484 Thioester -linked fatty acyl, 257 Thioether-linked prenyl, 257 Thiokinase, fatty acid, 702 Thiolase, 707, 752–753 Thiolase reaction, 707F Thioredoxin, 831–832 Thioredoxin reductase, 831, 832 4-Thiouridine, 305S Third-base degeneracy, 953 Threonine, 790, 791F pK a value for, 77T stereoisomers of, 83B structure of, 73S synthesis of, 790, 791F Threonine deaminase, 793 Threonine synthase, 790 D-Threose, 182S I-32 Index Thrombin, 113 Thromboxane, 747 Thylakoid lumen, 631 Thylakoid membrane, 631 Thylakoid space, 631 Thylakoid vesicle, 631, 656 Thymidine, 294 Thymidylate synthase, 169F, 835, 836F Thymidylate synthase reaction, 836F Thymine, 292, 292F, 301S Thymine nucleotide synthesis, 833–836, 834B, 835B, 836F Tight turn in protein, 145 TIM, 998 TIM barrel, 159 Titration, 78F, 79F Titration curve, 39 7-TMS protein, 1015 TMS receptor, 1015 Toluene, 56 TOM, 997 Tomography, positron emission, 555B Top-of-power stroke, 489 Topoisomerase, 334 Topology, supercoil, 333–334 Total adenine nucleotide pool, 843–844 Toxic shock syndrome, 227B Toxin diphtheria, peptide chain termination in, 980B tetrodotoxin, 1049B TPP-dependent transketolase reaction, 689F Tracer, isotopic, 525–526, 525T, 526F TRAM, 996 Transaldolase, 689–690, 690F Transamination of pyruvate to alanine, 851F Transamination reaction, 782B Transcarboxylase, 724 trans-complex, 269 Transcriptase, reverse, 363 Transcription, 906–951 DNA, 291, 292F eukaryotic, 305, 924–925, 925G, 926T initiation of, 931F, 931G Mediator effects on, 932 in prokaryotes, 906–912, 909F, 910B, 911F, 913F regulation of, 912–923, 914F, 915F, 916T, 917B, 918F, 918G, 919F, 921F, 922F steroid hormones and, 763 supercoiling vs., 911F Transcription activator, 934 Transcription attenuation, 920 Transcription factor, 924 CREB-type, 936B general, 929 heat shock, 929 sequence-specific, 937 Transcription start site, 908 Transcriptional activator, 923 Transcriptome, 367D Transcriptomics, 513 Transduction energy, 522, 636 of GPCR signals, 1024–1025 Transduction pathway, 1031F signal, 257, 1010–1013, 1012F Transfer, peptidyl, 969 T ransfer potential group, 58–59 types of, 59T Transfer protein, cholesterol ester, 758 Transfer RNA. See tRNA Transferase adenylyl, 777 peptidyl, 964, 969 phosphoethanolamine, 741 Transformation experiment, bacterial, 359F Transforming growth factor ␤, 212 Transgenic animal, 889B Trans-hydration of fumarase, 577 Transient receptor potential, 275 Transition state, 387, 419 tetrahedral oxyanion, 439B Transition-state analogs, 423, 424B–425B Transition-state stabilization, in serine pro- tease, 439B Transketolase, 688–689, 688F Translation, 291, 292F Translocase acylcarnitine and, 702 ATP–ADP, 618, 619F Translocases, 498 Translocation, 964, 969 protein, 994 retrograde, 997 Translocon, 996 Transmembrane segment, single, 249–250, 249F 7-Transmembrane segment protein, 1015 Transpeptidation, 969 Transport electron, 592–629. See also Electron transport membrane, 260, 269–287. See also Membrane, transport across Transposable element, 886 Transposition, 877, 886 Transposon, 886, 886F Transverse asymmetry, 260–261 Transverse tubules, 483 Tranylcypromine, 1055B Treadmilling, 490 Trehalose, 193B Triacylglycerol, 737, 757–758 energy stored as, 697 fatty acids liberated from, 698F structure and function of, 222, 222G, 222S, 223 Triacylglycerol lipase, 700 Triage, protein, 1004B Triantennary oligosaccharide, 209 Tricarboxylic acid cycle, 532B, 563–591 aconitase reaction in, 573, 573F, 573G chemical logic of, 564 citrate synthase in, 571–574, 571F, 572G diagram of, 565F energetic consequences of, 578–581 enzymes and reactions of, 572T fluoroacetate blocking, 573–574 intermediates in, 581–582 isocitrate dehydrogenase in, 574, 574F, 574G isocitrate formation in, 572–574 ␣-ketoglutarate dehydrogenase in, 575 overview of, 563–564, 564F oxaloactetate and, 575–578 oxidation of succinyl CoA and, 712 pyruvate and, 566 pyruvate dehydrogenase complex in, 571F regulation of, 584–586, 585F Trigger factor, 988 Trioleoylglycerol, 222 Triose, 183 Triose kinase, 555 Triose phosphate isomerase, 159F, 394T backbone structures of, 167F in glycolysis, 544, 545F, 545G T riple helix of collagen, 150–151, 151F, 151S Triplet code, 952–953 Tristearin, 222G, 222S Tristearoylglycerol, 222 Triterpene, 230S, 231 Triton X-100, 245S tRNA, 299, 304–305 aminoacyl-tRNA synthetase recognizing, 956–958 cognate, 955 intrastrand base pairing and, 344–345 structure of, 953S general, 953F secondary, 345 tertiary, 345, 346F, 348 suppressor, nonsense codons and, 960–961 tRNA Ala , 958 tRNA-binding site, 966F tRNA i Met , 977 Trojan horse substrate, 402 Tropocollagen, 150 Tropomyosin, 483D Troponin, 483D Troponin C, 849, 1031 Troponin T isoform, muscle, 945 trp operon, 914, 920 trp repressor, 920 Trypsin naming of, 384 in polypeptide fragmentation, 103, 104F as serine protease, 113 trypsinogen, 434, 435F Tryptophan pK a value for, 77T structure of, 73S synthesis of, 799–802, 800F, 802G ultraviolet light absorbed by, 82 Tryptophan synthase, 802, 802F, 802G d-Tubocurarine, 1050 Tubulin, 490 Tumor. See also Cancer positron emission tomography of, 555B telomeres and, 340B Tumor-suppressor gene, 1029B Tunneling, 433B, 802 Turnover number, 393, 393T Tus protein, 870 Twist, 334 helical, 323F propeller, 323, 323F Two-dimensional gel electrophoresis, 131–132, 131F Twofold rotation axis, 174 Two-state transition, 160 Tyk2, 1037 Index I-33 Type 1 diabetes, 717B Type 2 diabetes, 717B Tyrosine catabolism of, 809–810, 809F catecholamine transmitters derived from, 1056 in green fluorescent protein, 81B pK a value for, 77T structure of, 73S synthesis of, 798–799, 800F, 801F ultraviolet light absorbed by, 82 Tyrosine hydroxylase, 1056 Tyrosine kinase, 1015 nonreceptor, 1023–1024 phospholipase C activation by, 1030 Tyrosine kinase pp60 c-src , 1036, 1036F Tyrosine kinase pp60 v-src , 1023 Tyrosine kinases, 461 Ubiquinone, 598 Ubiquitin, 998 Ubiquitin-activating enzyme, 998 Ubiquitination, 998 Ubiquitin-carrier protein, 998 Ubiquitin-protein ligase, 998 UCP1, 619B UDP–glucose pyrophosphorylase, 556, 557F, 676, 676F UDP–glucose-4-epimerase, 556 Ultracentrifugation, 132–133 Ultrafiltration, 129 Ultraviolet light amino acid absorbing, 82 denaturation of DNA and, 330 pyrimidine dimer repair and, 890 pyrimidines and purines and, 293, 293F UMP synthase, 828 Uncharged amino acid, 74 Uncompetitive inhibition, 401 Uncoupler, 618, 619B Uncoupling protein-1, 619B, 852 Undecaprenyl alcohol, 231S Unfolded protein, natively, 168 Unfolding of protein, 55 Unilamellar vesicle, 244F, 245 Unsaturated fatty acid, 219D, 733–734 oxidation of, 713–714 Unstructured protein, 168 Unwinding of helix, 863 Upstream, 908 Upstream activation sequence, 927 Uptake, single-strand, 883 Uracil, 292, 292F, 307S Urate oxidase, 825 Urea, 810 Urea cycle, 783, 785, 786F, 787, 787B Urease, 420T, 826 Urease reaction, 419 Ureido group, 784 Ureotelic, 810 Uric acid, 293S, 810, 813 gout caused by, 824–825 purine catabolism and, 823 structure of, 814S Uricotelic organism, 810 Uridine, 294, 295S Uridine 5Ј-diphosphate, 296 Uridine diphosphate glucose, 675G, 675S, 676 Uridine diphosphoglucose, 57 T Uridine 5Ј-monophosphate, 296S Uridylic acid, 295 Uridylylation, 461T Uroguanylin, 1021 Uronic acid, 188 UTP, UMP synthesis and, 829 U-turn, 343 Vacuolar ATPase, 282 Vacuole, 20, 24T Vacuum blotting, 364B Valine catabolism of, 807, 808F pK a value for, 77T structure of, 72S synthesis of, 793, 794F van der Waals contact distance, 12 van der Waals forces, 12, 12F van der Waals interaction description of, 11T DNA and, 321–322 ubiquitousness of, 136 van der Waals interaction energy, 12F Vancocin, 207B Van’t Hoff plot, 50 Vaporization, 44 Variable loop, 345 Vasoactive intestinal peptide, 1056 V(D)J recombinase, 900–902 Vector cloning, 355, 355F expression, 369, 369F, 370F expression-cloning, 370F plasmid, 356F shuttle, 360, 360F Vein, portal, 680, 680F Velocity of enzyme-catalyzed reaction, 386 in Michaelis–Menten equation, 390–391 Venom, snake, 308F Versican, 209, 210F Very long-chain acyl-CoA dehydrogenase, 704–705, 705F Very-low-density lipoprotein, 757, 758 Vesicle coated, 758 multilamellar, 244F, 245 thylakoid, 631, 656 unilamellar, 244F, 245 Vesicle-mediated transport, 268F Vevesca, 207B VH gene, 900 Viagra, 404B, 404S Viceroy butterfly, 282B Vicinal XOH groups of RNA, 308F Vinblastine, 284F, 494B Vinca alkaloids, 494B Vincristine, 284F, 494B Viracept, 443S Viral neuraminidase inhibitor, 425B Viral transforming protein, 1023 Virus, 876B in g ene delivery system, 377, 378F Rous sarcoma, 1023 structure and function of, 21–22, 24F–25F Vitamin B 12 activation of, 712B catalysis of, 711–712 Vitamin C deficiency, 155B Vitamin K epoxide reductase, 232B Vitamin K reductase, 232B Vitamins, 523, 524T Vitellogenin gene, 940 VLDL, 757, 758 Voltage-dependent anion channel, 624 Voltage-gated ion channel, 1044 von Gierke disease, 681B V-type ATPase, 1050 Walker, John, 613 Wall, cell, 19, 20T bacterial, 201–204, 202S, 203F of plant cell, 24T Warburg, Otto, 535 Warfarin, 232B Water, 28–47 buffers and, 41–44 environmental role of, 44–45 lipid structures formed in, 244–245, 244F, 245S metabolic, 710 pH and, 35–40, 36T properties of, 28–35 colligative, 33–34 forming ions, 34–35 hydrogen bonding as, 29–30 solvent, 30–34 unusual, 28 structure of, 29S Water:plastoquinone oxidoreductase, 638 Watson, J. D., 862 Watson–Crick base pair, 321 Watson–Crick postulate of double helix, 301, 301F Wavelength, 634 Wax, 229, 229B, 230S WD40 repeat domain, 625 Weak acid, polyprotic, 76–78 Weak electrolyte, 37 Weak force chemical, 11, 11T biomolecular recognition and, 14–15 environmental conditions and, 15 quaternary protein structure and, 174, 176 Web, spider, 144 Western blotting, 364B Wheel, helical, 153, 1033, 1033F Whole genome sequencing, 17–18 Wild-type human sulfite oxidase, 396 B Wobble hypothesis of codon–anticodon pairing, 959 Woodward, R. B., 753B Work, mechanical, 49 Writhe, 334 Wyman, Jeffries, 457 Wza, 256 Xanthine, 293S Xanthine oxidase, 823–824, 825F Xylitol, 189 ␣-Xylosyl-threonine, 205S D-Xylulose, 183S Xyluose-5-phosphate, 692–693, 692F I-34 Index YAC, 360 Yeast enolase, 550F hexokinase, 540F phenylalanine tRNA, 346F, 347F, 347G RNA polymerase II subunits of, 926T rRNA of, 348F Yeast artificial chromosome, 360 Yeast mating factor, 260 Yeast two-hybrid system, 372–373, 372F Z line, 483 Z scheme, 638, 639F, 640 Z-DNA, 323–324, 324F, 325T, 326 cytosine methylation and, 326 Zero-order kinetics, 389 Zinc finger, 936, 937F Zipper, ribose, 344 Zipper motif, 938 Zn finger motif, 937–938, 937F Zn-finger, 936, 937F Z-variant of protein, 171B Zwitterion, 70D, 76F Zymogen, 434 as enzyme precursor, 454–455, 454F–455F, 454T gastric and pancreatic, 454–455, 454T . 976F in protein synthesis, 976, 976F Polyunsaturated fatty acid, 219D degradation of, 714, 715F docosahexaenoic acid as, 736B in mammals, 735 Porcine ribonuclease inhibitor, 169 F Porin, 255,. 20 of animal cell, 23T of plant cell, 24T signal peptidase and, 996–997 sarcoplasmic, 280 Retina, docosahexaenoic acid in, 736B Retinal, 285S Retrograde translocation, 997 Retrovirus, 876B Reunion