Molecular biology

physical evidence for, 10 site-specific, 747–781 in phage λ integration, 748–751, 748f, 749f, 750f, 751f in Salmonella, 751–753, 752f, 753f Recombination repair, 676–677, 677f Recombination-activating genes, in immunoglobulin gene rearrangement, 764–767, 765f, 766f Recruitment eukaryotic, 354–360 transcription factor IIB in, 355–358, 356f, 357f transcription factor IID in, 354–355, 355f transcription factor IIE in, 358–359, 358f, 359f transcription factor IIF in, 358–359, 358f prokaryotic, 354 Release factors, 53 eukaryotic, 600–602, 601t, 602f prokaryotic, 597–600, 599f, 600t, 601f Reovirus, caps of, 463–464, 463f, 464f, 466, 466f, 467, 468f Replica plating, 64, 64f Replication. See DNA replication Replicon, 652 Reporter gene transcription, 121–122, 123f Restriction endonucleases, 60–63, 61t names for, 60 Restriction fragment length polymorphisms, 110–111, 110f, 113f, 788–789, 789f Restriction–modification (R-M) system, 61, 62f Retrohoming, 777, 777f Retrotransposition, of group II introns, 776–780, 777f, 778f, 779f Retrotransposons, 767, 771–780 LTR-containing, 771–773, 772f nonautonomous, 776 non-LTR-containing, 773–776, 773f, 774f, 775f Retroviruses, 767–771 replication of, 767, 767f, 768f, 769–771, 769f, 771f Reverse transcriptase, 767–768, 767f, 769–771, 770f, 771f in cDNA library construction, 75, 77f primer for, 768, 770f Reverse transcriptase polymerase chain reaction (RT-PCR), 78–79, 78f RF-A, 657 Rho loading site, 170, 171f Rho-dependent terminator, 168–171, 170f, 171f chain elongation and, 168–169 hairpin of, 170, 171f RNA binding of, 170, 171f transcript length and, 169, 170f transcript release and, 170, 171f Rho-independent terminator, 165–168, 167f hairpin of, 166, 168, 168f inverted repeat of, 166, 168 structure of, 167–168, 168f, 169f Ribonuclear proteins (RNP), small nuclear (snRNP), 264, 264t, 266, 430 U1, 430, 430f, 431f, 432f, 468–470, 469f U2, 434–435, 435f U4, 437–438, 438f U5, 435–437, 436f, 437f, 438f U6, 431–434, 432f, 433f, 438, 438f Ribonuclease H, in cDNA library construction, 75, 77f Ribonucleic acid. See RNA Ribonucleoside triphosphates, in transcription, 46 Riboprobes, 116 Ribose, 19, 21f Ribosomes, 4, 4f, 49–50, 50f, 607–625 A (aminoacyl) site of, 52–53, 576, 577f, 578–580, 579f, 580t aminoacyl-tRNA binding to, 580–586, 581f, 582t, 583f, 584f antibiotic binding to, 576, 578f assembly of, 613–614, 613f, 614f composition of, 612–613, 612f cycling of, 532–534, 534f dissociation of, 529–534, 530f, 531f initiation factors in, 531–532, 532f, 533f E (exit) site of, 53, 576, 579–580, 580t fine structure of, 608–610, 610f, 611f, 612f gross structure of, 607–608, 607f, 608f, 609f P (peptidyl) site of, 52, 576, 577f, 578–580, 579f, 580f, 580t peptidyl transferase of, 587–589, 587f, 588f, 589f, 621–624, 622f, 623f, 624f 30S subunit of antibiotic interaction with, 617–620, 618f, 619f, 620f, 621f assembly of, 613–614, 613f composition of, 612–613, 612f dissociation of, 529–534, 530f, 531f, 532f, 533f fMet-tRNAf Met binding to, 540–542, 541f, 541t, 542 mRNA binding to, 536–539, 537f, 538f, 539f, 540t paromomycin interaction with, 619–620, 620f 16S rRNA of, 613–614, 613f, 615–616, 616f, 617f streptomycin interaction with, 617–618, 619f structure of, 607f, 608f, 611f, 614–617, 615f, 616f, 617f 50S subunit of assembly of, 614 composition of, 612–613, 612f dissociation of, 529–534, 530f, 531f, 532f, 533f 23S rRNA of, 621–624, 624f structure of, 608f, 611f, 621–624, 622f, 623f, 624f 70S subunit of, structure of, 607–610, 609f, 610f, 611f, 612f three-site model of, 578–580, 579f, 580f, 580t in translation, 49–50, 50f Ribozymes, 454 Ricin, 73 Rifampicin, prokaryotic RNA polymerase sensitivity to, 143f, 144, 155, 155f R-looping, 419–420, 420f R-M (restriction–modification) system, 61, 62f RNA, 17 chemical composition of, 19, 21–23, 21f, 22f discovery of, 10 DNA hybridization to, 33, 33f. See also Hybridization EBER2, 266, 290 5'-end of primer extension mapping of, 118, 118f S1 mapping of, 115–116, 116f 3'-end of, S1 mapping of, 116, 117f 7LS, 289–290 phosphorimaging of, 98–99, 99f primer extension mapping of, 117–118, 118f restriction endonuclease cutting of, 60–63, 61t, 62f S1 mapping of, 115–117, 116f, 117f 7SK, 266, 290, 290f 7SL, 266 synthesis of, 46–49, 48f, 49f. See also Transcription U6, 290 VA (virus-associated), 266 dsRNA, 520–524, 522f, 523f, 524f gRNA, 510–511, 511f, 512f hnRNA, 264, 264t, 420–421. See also mRNA splicing mRNA, 12, 39, 39f cap protection of, 467, 468f capping of, 463–470. See also Capping; Cap(s) casein, 513, 513t discovery of, 45–46, 47f editing of, 509–513, 510f, 511f, 512f in 30S initiation complex, 536–539, 537f, 538t, 539f maternal, 487–488, 489f poly(A) protection of, 471, 472f, 473f polyadenylation of, 470–489. See also Poly(A); Polyadenylation polycistronic, 176 splicing of. See mRNA splicing transferrin receptor, 514–520. See also Transferrin receptor transport of, from nucleus, 468–470, 469f trans-splicing of, 505–509, 505f, 506f, 507f, 508f 3'-UTR of, 53f, 54 5'-UTR of, 53f, 54 rRNA, 12, 50, 50f eukaryotic, 498–501, 498f, 499f, 500f introns in, 419 processing of, 498–501, 498f, 499f, 500f, 501f prokaryotic, 501, 501f 23S, 588–589, 623–624, 624f self-splicing of, 450–456, 452f, 453f, 454f, 455f Index 853RNase PH, 503–504, 505f RNase PII, 503 RNase T, 503–504, 505f RNase T1, 424–425, 424f RNase T2, 425, 427f snRNP (snurps), 430–439 U1, 430, 430f, 431f, 432f U2, 434–435, 435f U4, 437–438, 438f U5, 435–437, 436f, 437f, 438f U6, 431–434, 432f, 433f, 438, 438f rrn genes, 140 rrnB P1 promoter, 140, 141f, 152–154, 153f, 154f rrnD operon, of Escherichia coli, 501, 501f RSF1010 plasmid, 61–62, 62f Run-off transcription, 118–120, 119f Run-on transcription, 120–121, 121f RuvA, 721, 721f, 729–734, 730f, 731f, 732f, 733f, 734f RuvA-RuvB-Holliday junction complex, 729–734, 730f, 731f, 732f, 733f, 734f RuvB, 729–734, 730f, 731f, 732f, 733f, 734f in recombination, 721, 721f RuvC, 734–737, 736f, 738f, 739f in recombination, 721, 721f S1 mapping, 115–117, 116f, 117f S1 nuclease, 115–116, 116f S10, in antitermination, 218, 219f Saccharomyces cerevisiae DNA replication in, 690–693, 692f meiotic recombination in, 739–742, 741f, 742f, 743f 2-micron plasmid of, 84–85 RNA polymerase II of, 266t, 267–272, 267t, 268f, 269f, 270f, 271f transposons of, 772–773, 772f SAGA complex, 311 SalI, in S1 mapping, 115, 116f Salmonella typhimurium DNA decatenation in, 706–708, 707f site-specific recombination in, 751–753, 752f, 753f Sanger chain-termination DNA sequencing, 105–109, 106f, 107f SC35, in mRNA splicing, 443–444, 444f, 445f Sedimentation coefficient, of Escherichia coli ribosomes, 49–50, 50f Sequence-tagged connector, 792–793, 792f Sequence-tagged sites, 790, 790f Serial analysis of gene expression, 800–802, 801f Serine, 40f Sex chromosome, 3 SF1, 446f, 447 SF2/ASF, in mRNA splicing, 443–444, 445f SH2 domains, in MAP kinase pathway, 375f, 376 SH3 domains, in MAP kinase pathway, 375f, 376 Shine-Dalgarno sequence, 52, 536–539 Shotgun sequencing, 792–793, 792f Shuttle expression vectors, 84–85, 86f Sickle cell disease, 55–56, 55f, 56f, 57f Sigma (σ) subunit(s), 134–136, 134f, 134t, 136f in Anabaena, 213, 213f in Bacillus subtilis, 146–151, 148f in Bacillus subtilis sporulation, 208–212, 209f, 210f, 211f, 212f competition between, 215 in DNA–polymerase dissociation, 151, 151f in Escherichia coli, 146–151, 148f, 149f, 150f, 151f, 208, 208f, 213–215, 213f, 214f functions of, 141–146, 143f, 144f, 151, 151f in glnA transcription, 213, 213f, 214f in htpR transcription, 214–215, 214f in λ phage repressor-RNA polymerase interaction, 226, 226f in phage SPO1-infected Bacillus subtilis, 206–208, 206f, 207f in phage T7-infected Escherichia coli, 208, 208f in promoter–polymerase binding, 137–140, 138f, 139f, 146–151, 148f, 150f region 1 of, 148–149, 148f, 149f region 2 of, 148f, 149, 149f region 3 of, 149, 149f region 4 of, 149–150, 149f, 150f reuse of, 143–144, 143f in spoIID transcription, 210, 210f in spoIIIC transcription, 210, 211f in spoIVCB transcription, 210, 211f in spoVG transcription, 211–212, 212f structure of, 147–151, 148f, 149f, 150f switching model of, 206–208, 206f, 207f in transcription initiation, 141–146, 143f, 144f Signal transduction pathways, 371, 374–376, 375f Silencers, 291–293 Silencing, histone deacetylation and, 405 Sin3, 405 Sin3A, 405–406, 406f Sin3B, 405 Single-nucleotide polymorphisms, 811–812 Single-strand DNA-binding proteins, in DNA replication, 655–658, 656f, 656t, 657f SIR2 protein, 409 SIR3 protein, 409 SIR4 protein, 409 SL1, 325–327, 326f, 327f structure of, 329–331, 330f, 331f Slu7, in mRNA splicing, 442–443, 443f SmaI, 60, 61 Snurp(s), 264, 264t, 266, 430–439 U1, 430, 430f, 431f, 432f, 468–470, 469f U2, 434–435, 435f U4, 437–438, 438f U5, 435–437, 436f, 437f, 438f U6, 431–434, 432f, 433f, 438, 438f Sodium dodecyl sulfate (SDS), for polyacrylamide gel electrophoresis, 94, 94f Sos protein, in MAP kinase pathway, 375f, 376 Southern blotting, 100–102, 101f Sp1, TATA-box-binding protein–associated factor interaction with, 308–309, 311f, 312f Specialized genes, 280 Spliced leader, in trans-splicing, 505–507, 506f, 507f, 508f Spliceosomes, 428–430, 429f activation of, 441 assembly of, 439–441, 440f, 441f cycle of, 439–441, 440f, 441f, 442f Split genes, 419–420, 420f Spo11, in meiotic recombination, 741–742, 742f spoIID gene, 210, 210f spoIIIC gene, 210, 211f spoIVCB gene, 210, 211f Sporulation, transcription during, 208–211, 209f, 210f, 211f spoVG gene, 211–212, 212f Squelching, activator, 371 SR proteins, in mRNA splicing, 443–444, 444f, 445f, 450, 450f SRB proteins, 324 Stahl, Franklin, 12f Steroid receptor coactivators, 373 Stopped-flow apparatus, 592 Streptococcus pneumoniae avirulent, 17, 17f, 18f transformation experiments in, 17–19, 18f, 19f, 20f virulent, 17, 17f, 18f Streptolydigin, resistance to, 155–156 Streptomycin, 578f, 586 ribosome subunit interaction with, 617–618, 619f Sturtevant, A. H., 5 Supercoiling, 34, 35f, 165 SV40 virus DNase hypersensitivity regions in, 399, 399f early promoter of, 280–282, 281f, 282f Escherichia coli RNA polymerase interaction with, 145–146, 147f nucleosome-free zones in, 397–399, 397f, 398f nucleosomes of, 385, 385f replication of, 657, 689–690, 690ffactor IIE recruitment and, 358–359, 358f, 359f transcription factor IIF recruitment and, 358–359, 358f transcription-activating domain of, 343, 346, 347f independence of, 352–353, 353f zinc fingers of, 343, 344–346, 344f, 345f zinc modules of, 343, 346–350, 347f, 348f, 349f Transcription bubble, 144–146, 145f, 146f, 147f, 164–165, 165f Transcription elongation, 46–47 nucleosomes and, 410–414, 411f, 412f, 413f, 414f prokaryotic, 154–165 α subunits in, 159–160 core RNA polymerase functions in, 154–159 α subunit and, 159–160 β subunit and, 155–159, 155f, 156f, 157f, 160f β' subunit and, 156–159, 158f, 159f, 160f elongation complexes in, 160–165, 161f, 162f, 163f, 164f rho effects on, 168–169 RNA–DNA hybrid in, 160–161, 161f topology of, 164–165, 164f, 165f transcription factor IIS in, 322–324, 322f, 323f Transcription factor(s), 291, 298–336 architectural, 367–369, 367f, 368f, 369f class I, 325–331. See also SL1; UBF class II, 298–325. See also specific factors class III, 331–336. See also specific factors Transcription factor GCN4, 351, 351f Transcription factor IIA, 298–300, 298f, 299f, 300f, 312, 314–315, 315f mutations in, 314 structure of, 314 Transcription factor IIB, 298–300, 299f, 300f, 301f, 314–315, 315f, 321f recruitment of, 355–358, 356f, 357f structure of, 314–315 Transcription factor IID, 298–300, 298f, 299f, 300f, 301–312 of Drosophila, 307f recruitment of, 354–355, 355f Sp1 interaction with, 308–309, 311f, 312f structure of, 305, 307f TATA-box-binding protein of, 301–306, 302f, 303f, 304f, 305f, 306f, 307f TATA-box-binding protein–associated factors of, 305–309, 307f, 308f, 309f, 310f, 311f mutations in, 309–311, 314t Transcription factor IIE, 316–321, 317f, 321f activator recruitment of, 358–359, 358f, 359f Transcription factor IIF, 298–300, 299f, 300f, 301f, 315–316, 316f activator recruitment of, 358–359, 358f structure of, 315 Transcription factor IIH, 316–321, 317f, 318f, 319f, 320f, 321f Transcription factor IIS, 322–324, 322f, 323f Transcription factor IIIA, 331–332, 332f Transcription factor IIIB, 332–334, 333f, 334f, 335f, 336f Transcription factor IIIC, 332–334, 333f, 334f, 335f Transcription factor SL1, 325–327, 326f, 327f structure of, 329–331, 330f, 331f Transcription factor UBF, 328–329, 328f, 329f Transcription factor VP16, 354–355, 355f Transcription initiation, 46 prokaryotic, 141–154, 142f σ functions in, 141–146, 143f, 144f. See also Sigma (σ) subunit(s) σ reuse in, 143–144, 143f stages of, 141, 142f Transcription mediators, 371–374, 371f, 372f, 373f, 374f Transcription termination, 47 prokaryotic, 165–171 attenuator in, 166, 167f hairpin in, 166, 167–168, 168f, 170, 171f inverted repeats in, 166 model for, 167–168, 168f rho-dependent, 168–171, 170f, 171f rho-independent, 165–168, 167f, 168f, 169f Transcription unit, 475 Transcription-activating domain, of activator, 343 Transcriptomics, 812 Trans-dominant mutation, 179, 181f Transfection, definition of, 85 Transferrin receptor mRNA degradation pathway in, 519–520, 520f, 521f mRNA stability in, 514–520 iron response elements and, 514–515, 514f, 515f, 518–519, 519f rapid turnover determinant and, 515–518, 516f, 517f, 518f Transformation in bacteria, 17–19, 18f, 19f, 20f definition of, 85 Transgenic plants, 88, 88f Translation, 39, 39f, 49–54 AUG codon in, 52, 545–550, 545f, 550f capping and, 467–468, 469t direction of, 568–569, 568f, 569f elongation phase of, 52–53, 52f, 576–594. See also Translation elongation error rate of, 586 initiation of, 52, 528–563. See also Translation initiation poly(A) and, 471–474, 472f, 473f, 474f proofreading in, 585–586, 585f reading frame in, 53–54, 53f ribosomes in, 49–50, 50f, 607–625. See also Ribosomes speed of, 585–586, 585f termination phase of S