Bisc 320 lectures 2008

Bisc 320 lectures 2008 - Bisc 320, Molecular Biology, Fall,...

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Bisc 320, Molecular Biology, Fall, 2008. The following notes are meant to be of help in understanding the lectures. These notes are outlines of a portion of the material presented and do not contain many of the details given in the actual lectures. 1. Bisc 320, Molecular Biology, Fall, 2008. Beginning October 29 th , lectures by R. Baker Some notes on: Transcription See also, Watson, et al., chapter 12 in either the 5 th or 6 th edition. Procaryotes Fig 12-1, Table 12-1, Fig 12-2, 12-3, 12-4 either the 5 th or 6 th edition. Transcription initiation in prokaryotes by core RNA polymerase [alpha, alpha, beta, beta prime, omega]: Sigma 70 associates with the core and gives start site specificity. Rapidly dividing E. coli cells each contain about 5000 copies of core RNA polymerase. About one half are engaged in active transcription; about one fourth are attached to transcription initiation sites, but are not engaged in transcription; approximately one fourth are attached to other DNA positions and about 1% are free. The double stranded, circular E. coli genome has 4,639,221 base pairs, which includes 4,377 genes; 4,290 of these genes encode proteins; the rest code for ribosomal and transfer RNAs. (Rifampicin can bind to the beta subunit of core RNA polymerase, halting transcription.) See Fig 12-5 and Box 12-1 in the 5 th or 6 th edition of Watson et al. Other sigmas: 54 = used in transcription of nitrogen metabolism genes, 38 = stationery phase genes, 35 = heat shock genes, 28 = motility and chemotaxis genes Figs 12-6, 16-14, 16-15, 16-16 in the 5 th or 6 th edition. Within bacterial genomic DNA: ---UP sequence (where two CTDs, one on each of the alpha RNA polymerase subunits, attach)------ TTGACA[ (-) 35] TATAAAT[ (-) 10]----A/G [+1, start of transcription]------AGGAGG (Shine Dalgarno where 30S ribosome subunit attaches to mRNA)----AUG (translation start codon, where 50S ribosome subunit attaches to mRNA)-------- Fig 12-7, 12-8 in either the 5 th or 6 th edition. Proofreading: Gre factor = hydrolytic editor factor (still ~ 1 in 10 to the 4 th error frequency (e.g., DNA rep has ~ 1 in 10 to the 7 th errors). Prokaryotic mRNA has an ~ 3 minute ½ life. Traveling, open DNA transcription bubble is ~ 14 BP. Termination of transcription: Is rho-independent when the RNA snapback handle of a tennis racket is G+C rich and the 3’ end of the mRNA has 6 or >U’s, hydrogen bonded to the template DNA. Rho-dependent termination utilizes a rho factor (6 copies of a 55K Dalton monomer per rho factor) +ATP ( ADP) and the handle is less G+C rich; the 3’ end of the mRNA has <U’s. Fig 12-9, 12-10, 12-11 in the 5 th edition; Figs 11, 12, 13 in the 6 th edition. Eukaryotes RNA Pol I (has 32 subunits) synthesizes ribosomal RNA, Pol II (has 12 subunits) synthesizes pre-mRNA, Pol III (has 34 subunits) synthesizes tRNA, 5S, and a few other small RNAs.
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Pre-mRNA synthesis by RNA pol II Fig 12-12, 12-13, 12-14, Table 12-2, Fig 12-15 in the 5 th edition; Fig 12-14, 12-15, 12-16, Table 12-2,
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Bisc 320 lectures 2008 - Bisc 320, Molecular Biology, Fall,...

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