01:694:301 Lecture Notes - Lecture 29: Pribnow Box, Transcription Bubble, Phosphodiester Bond

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Chapter 29‘RNA Synthesis and Processing’
Understand the ‘overview’ and KNOW the 5 items (852-853) (focus: prokaryotic transcript)
o DNA stores genetic info in a stable form that can be replicated
o Expressing this genetic info requires flow from DNA ! RNA
o RNA synthesis or
is the process of making RNA transcript with sequence
info from DNA template
" 3 stages of transcription: promoter binding and initiation, elongation, and termination
o RNA polymerases catalyze the synthesis of RNA and have multiple functions:
" 1) They search for DNA initiation sites (promoter sites)
" 2) They unwind short stretch of double helical DNA ! ss DNA templates from which
sequences can be read
" 3) They select correct rNTP and catalyze formation of phosphodiester bond; it’s
completely processive
" 4) They detect termination signals where transcript ends
" 5) They interact w/ activator and repressor proteins that modulate rate of
transcription initiation
RNA chains grow in 5’ ! 3’ direction; no primer is required to begin synthesis
o The coding strand DNA ‘sense’ (+) has same sequence as RNA (except T ! U)
o The template strand ‘antisense’ (--) is complement of RNA transcript
o The first base transcribed is always
, so new unprocessed RNA always starts with
pppA or ppp
The promoter site has a ‘-35 region’ and sequence centered around -10 (‘Pribnow box’)
The efficiency or strength of a promoter sequence serves to regulate transcription
o The promoter is found only in the DNA and is NOT transcribed
The RNA Pol holoenzyme, including the σ (sigma) subunit as well αββ2 must be present for
transcription to start
o RNA Pol take place in complex of DNA known as
transcription bubble
(has unwound ds
DNA with exposed base pairs
o The σ subunit is only present during initiation and then drops off; is responsible for the
specific binding of the RNA polymerase to a promoter site on the template DNA
o The β subunit contains the polymerase active site and binds to promoter
o RNA Pol use backtracking as means of proofreading;
" In backtracked position, hydrolysis takes place cleaving phosphodiester bond and
releases a dinucleotide containing incorrect nucleotide
o Note that RNA synthesis has lower fidelity than DNA replication
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