bacterial transcription (ch. 8)

four stages of transcription

promoter recognition, transcription initiation, chain elongation, chain termination

bacterial RNA polymerase composition

holoenzyme = pentameric core enzyme + sigma subunit

pentameric core enzyme contains (counterclockwise): beta’, omega, alpha 2, alpha 1, beta

cannot bind to promoter/initiate synthesis without the sigma subunit

alternative sigma subunits bind to different promoters - regulation (alter the core enzyme conformation) (TATA = sigma 70)

bacterial promoters

RNA pol. binding site (binds to -10/-35 and occupies space between and around)

short distance upstream of coding sequence, within a few nucleotides of +1

includes -10 (Pribnow box) and -35 consensus sequences

-10/Pribnow box: 5’-TATAAT-3’

-35 sequence: 5’-TTGACA-3’

what are the areas between the promoter and the start codon; and between the stop codon and the termination region

5’ UTR and 3’ UTR

where are the promoter consensus sequences located

upstream 5’-3’ WRITTEN ON THE CODING STRAND

transcription initiation

step 1: holoenzyme makes loose attachment to promoter to form the closed promoter complex

step 2: holoenzyme (HELICASE FUNCTION) unwinds 18bp of DNA around the -10 area to form open promoter complex

holoenzyme progresses down and initiates RNA synth. at +1 site

when does sigma subunit dissociate

after the first 8-10 RNA nucleotides are added

how big is the transcription bubble//elongation

about 18bp

RNA pol. unwinds DNA as it goes and the DNA reforms behind RNA pol.

termination of transcription in bacteria

transcription ends at the termination sequence (two different types)w

core enzyme dissociates from DNA

what are the two types of bacterial termination of transcription

intrinsic termination - MORE COMMON

rho-dependent termination

intrinsic termination

have an inverted repeat followed by a string of adenine

inverted repeat causes mRNA to create a stem loop (hairpin)

the polyadenine sequence adds a bunch of U’s which makes RNA pol. slow down and destabilize, A-U strand breaks, releasing the mRNA and detach from DNA

rho-dependent termination

Rho utilization site on DNA codes for a C-rich area of ~50 nucleotides

rho protein binds to rut sequence on mRNA and moves toward 3’ end (towards the RNA pol) - activated by ATP binding to allow binding to rut sequence

RNA pol. stops at termination sequence after stem loop formation

rho protein reaches RNA pol. and releases it as well as the mRNA

bacterial tRNA processing

multiple tRNA’s cleaved from large precursor transcript

nucleotides trimmed from each end

tRNA’s fold into 3d structures (double stranded stems, single stranded loops)

post-transcriptional addition of bases: add CCA to 3’ end