General mechanism of Transcription Flashcards
what is a coding strand
aka sense strand
5’ to 3’
has same sequence as RNA that’s produced
what is template strand
aka antisense strand
3’ - 5’
has complementory sequence to the RNA that’s producced
what does a promoter do
tells RNA Polymerase:
where to start transc
what direction to transc in
what are the sequences that an RNA pol recognises on a promoter
-10 = TATAAATG
-35 = TTGACA
only recognises this sequences then it knows what to attach to and which direction to go in
see onenote for diagram
what are the 3 phases of transcription
initiation
elongation
termination
main enzyme involved in transc
RNA polymerase
initiation
RNA pol binds to promoter
seperates strands for DNA
template strand used to make mRNA strand
elongation
using the template strand, complementary mRNA strand is produced
complementary nucleotides added to form strand
(remember not T but U in RNA strand)
termination
stop signal from terminator gene
mRNA released from trancription complex
this strand is called pre mRNA (not yet ready to leave nucleus
prokaryotic RNA polymerase enzyme subunits
sigma
2 alpha
2 beta (beta and beta’)
omega
prok RNA pol subunits function: sigma
promoter recognition
recognises the -35 and -10 boxes
prok RNA pol subunits function: alpha
assembly and transcription activation
prok RNA pol subunits function: beta
catalysis (adding nucleotides to growing RNA chain)
termination
prok RNA pol subunits function: omega
involved in assembly
folding
in some genes and not others
difference between RNA holoenzyme and core enzyme
holoenzyme - whole thing with all subunits
core enzyme - when polymerase starts transcribing, sigma subunit breaks off leaving the core enzyme (alpha, beta and omega units only)
why does sigma subunit need to break off`
only needed during inititation to detect the start codon
after this, the enzyme must turn non-specific for any particular sequence
so polymerase only has general affinity for DNA
euk RNA polymerase, the 3 types and their functions
pol I = makes ribosomal RNA genes
pol II = makes protein coding genes (mRNA)
and small nuclear RNA (snRNA)
pol III = transfer RNA (tRNA)
also, rRNA and snRNA
euk RNA Pol II features
large enzyme
~10 core subunitsk
how does euk rna pol II interact with the promoter sequence?
must be recruited by transcription factors
e.g. TF2D (aka TFIID so basically transcription factor for rna pol II)
what is function of TFIID and what is it made up of
allows the RNA pol II to recognise and bind to promoter site
TFIID is a multisubunit protein
made of these subunits:
TATA binding protein (TBP) = the bit that acc binds to the promoter site
and
TBP Associated factors (TAFs)
what is the TFIID similar to
similar sequence to the sigma subunit
promoters are very TA rich (similar to the -10 sequence in prok promoters)
other transcription factors needed in eukaryotes during initiation
TFIIA - helps TFIID bind
TFIIB - measures distance between core promoter sequence (the AT rich one) and the transcritption start site
other transcription factors needed and their general functions
TFII E, F, H, J and K
- blocks non specific binding of pol II to DNA (liek sigma)
- promoter clearance > starts to elongate and make chain
- helicase > unwinding the DNA
- procesivity > so once it starts, it continues to full transribe the chain
- DNA repair > scanning chain for errors and repairs it
RNA Pol I main elements
core element - contains transcription start site
Upstream control element (UCE)
these 2 bind with protein called Upstream Binding Factor (UBF)
which allows the DNA to kinda loop through
see onenote for diagram
what is the main transcription factor for RNA pol I and its components
SL1
made up of TBP and pol I specific TAFs
difference bwtween the TBP in RNA pol II and RNA pol I
in RNA pol II = itneracts with the DNA
in RNA pol I = acts binding site to keep all the TAFs together
whats the difference in the transcription start site in a tRNA gene transcribing promoter
the promoter is actually ‘downstream’ from the transc start site
so the promoter is within the coding region
promoter is made up of an A box and a B box
see onenote diagram
what are the A box and B box bound by in a tRNA gene
TFIIIC
what are the 2 transcription factors used in the tRNA gene (RNA Pol III)
TFIIIC
TFIIIB - made up of TBP and pol III specific TAFs
what happens after TFIII B is recruited ?
TF IIIC is dispensible
Rna pol III c
what happens after TFIII B is recruited ?
TF IIIC is dispensible
Rna pol III can then bind without any obstruction
See diagram one note hehe
What is the difference between the tRNA genes and the 5s rRNA genes in terms of what factors they use
rRNA use an extra factor TFIIIA to recruit TFIIIC
Instead of TFIIIB which is used in tRNA
everything else is pretty much the same
