transcription 1 Flashcards
what is the coding strand
strand of DNA that has the same sequence as the mRNA
how many RNA polymerases in prokaryotes and eukaryotes
1 RNA polymerase in prokaryotes and 3 RNA polymerases in eukaryotes
what does a sigma factor do
confers specifity to bind to a promoter on DNA in Prokaryotes
what confers specifity in eukaryotes?
transcription factors
can an RNA polymerase assemble from an αNTD domain
yes
what domain is involved in activation?
the αCTD domain
what is the name of the specific DNA sequence that sigma factor confers on RNA polymerase to bind to
the promoter
what is the primary sigma factor in E.coli
sig70
what is the primary sigma factor in bacillus subtilis
sigA
how many domains does σ70/σ4 have
4 main domains
what does region 1 domain of σ70/σ4 do?
it is self inhibitory
what does region 2 of σ70/σ4 do?
2 has 4 sub domains some unassigned others melt DNA and recognise and interacts with the -10 region (TATAAT) of the promoter
what does region 3 of the σ70/σ4 do?
interacts with DNA upstream of the -10 region of promoter
what does region 4 of σ70/σ4 do ?
has 2 sub domains 4.1 has no specific function. 4.2 interacts with the -35 region of the promoter
what is suppressor analysis
Suppressor analysis is a technique used in genetics and molecular biology to identify genes or mutations that can restore the function of a mutant protein or RNA molecule.
what do you need to identify in terms of suppressor analysis methodology?
you need to identify the DNA operational sites (the promoters)
what are the steps following on for the suppressor analysis methodology?
- promoter probes plasmids 2. suppressor analysis 3. primer extension analysis 4. footprinting 5. bioinformatic information
where and how is the transcriptor fired?
it is fired bythe promoter onto a piece of DNA and all of its copies.
what is transcriptional fusion?
Transcriptional fusion is a molecular biology technique used to study gene expression by joining the regulatory regions of one gene with the coding sequence of another gene, resulting in a single mRNA transcript that can be used to measure gene expression levels.
where does fusion occur
just at the level of transcription
where do you find the promoter?
Promoter is the sequence usually at 5’ end of operons that RNA pol binds to specifically to initiate transcription
what spacing portion is critical for the promoter?
the spacing between -10 and -35
what does the addition of bases do ?
it doesnt elongate the helix, it just moves the helix around itself.
what happens when 5 bases are added to the -10 and -35 spacing?
it can completely alter the positioning of further base pairs.
what is the consensus promoter sequence?
it presents the bases most commonly found at each position of the promoter for a particular promoter family
what happens to promoters that deviate from the consensus sequence?
usually weaker
what is the series of stages that initiation of prokaryotic transcription occurs at?
R + P ->RPc <–>RP1 <–> RP0, where RPc is closed complex, RP1 is intermediate complex, RP0 is open complex.
what is the formation of RP0 required for?
to initiate transcription.
give two statements regarding consensus promoters
1 they are very strong since cell needs to balance promoter strength (limited amount of RNA pol) 2 their activity is fully on, so can only be controlled by turning them off.
do most promoters deviate from the consensus
yes
what happens when these promoters are activated and repressed
activated: transcription can be increased
repressed: transcription can be turned off
what happens when there is an increase in RPc formation ?
affinity increased of DNA promoter for RNA polymerase
what happens when RPo is increased?
increases conversion of RPc into RPo.
what do activator proteins do
bind to RNA polymerase and to promoter DNA, also provide contact between RNA polymerase and DNA therefore increase affinity between them. they also increase rate of RP0 formation
how many interactions has RNA polymerase when bound to the promoter?
two interactions: -35 DNA sequence and region 4.2 of sig70, and -10 DNA sequence and region 2.4 of sig70
what is an UP element
a DNA sequence which alpha CTD domain of RNA polymerase can bind to, making it three interactions
what indirectly happens due to the UP element
affinity increased between RNA pol and DNA and increased RPc formation / increased transcription
how is transcription increased ?
by increased clearance of promoter and by increased affinity between RNA polymerase and the promoter.
