Bisc 320, Molecular Biology, Fall, 2009, lectures by R. Baker
The following notes are meant to be of help in understanding the lectures.
are outlines of a portion of the material presented and do not contain many of the details
given in the actual lectures.
Some notes on:
See also, Watson, et al., chapter 12 in either the 5
Chapters 12 and 13 + blackboard
Fig 12-1, Table 12-1, Fig 12-2, 12-3, 12-4 either the 5
Transcription initiation in prokaryotes by core RNA polymerase [alpha, alpha, beta, beta
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.
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.
If we look at one gene
the idea is that in order to transcribe it, we have to place an RNA polymerase and it
copies along one strand of DNA and comes off.
(Rifampicin can bind to the beta subunit
of core RNA polymerase, halting transcription.)
See Fig 12-5 and Box 12-1 in the 5
edition of Watson et al.
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
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
Gre factor = hydrolytic editor factor (still ~ 1 in 10 to the 4
error frequency (e.g., DNA rep has ~ 1 in 10 to the 7
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
edition; Figs 11,
12, 13 in the 6