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CMB2001 EXAM QUESTIONS AND VERIFIED ANSWERS
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CMB2001 EXAM QUESTIONS ANDVERIFIED ANSWERS
In prokaryotes, RNA polymerase requires what co-factor? - ANSWER 70 sigma
factor
Forms the holoenzyme
The promoter is formed of two hexameric sequences at what positions? -
ANSWER -35 and -10
The amount of product transcribed is dependant on how close the promoter
sequences are to what? - ANSWER Consensus sequence
Eukaryotic promoters have a basal region which can contain a TATA box, initiator
(Lnr), BRE (TFIIV recognition element) and what other element? - ANSWER
Downstream core promoter (DPE)
CPG islands are located near promoters, if the cysteine residues are methylated are
genes turned on or off? - ANSWER Off
Hypomethylation = turned on
UAS is interchangeable with what term which increases transcription? - ANSWER
Enhancer
URS = silencer
What is an example of a reporter gene which can help analyse gene expression and
how strong a promoter is? - ANSWER Lac-Z
What does RNA polymerase I transcribe? - ANSWER rRNA (nucleolus)
What does RNA polymerase II transcribe? - ANSWER mRNA, snRNA, miRNA
12 subunit complex
,What does RNA polymerase III transcribe? - ANSWER tRNA 5s RNA, U6 RNA,
7S RBA
Where do the general transcription factors bind in eukaryotes to recruit RNA
polymerase II? - ANSWER Over the TATA box
TFIID binds the TATA box and recruits what? - ANSWER TFIIA
TFIID, then TFIIA, the next factor binds and recruits RNA polymerase II and
TFIIF what is it? - ANSWER TFIIB
After the recruitment of TFIIF with RNA polymerase what are the last two factors
to bind? - ANSWER TFIIE then TFIIH
This whole complex = the pre-initiation complex
Which subunit has helicase activity to unwind the start site to start unwinding the
DNA? After promoter melting - ANSWER TFIIH
Uses ATP hydrolysis
After RNA polymerase transcribes and clears the promoter what is
hyperphosphorylated? - ANSWER The C-terminal domain
TFIIH has two parts ATPase called XPB which causes promoter melting, CORE
region and what other region? - ANSWER CAK - the kinase that phosphorylates
the C- terminal domain
TFIID has a trilobular structure and binds the TATA box, what other factors bind to
it? - ANSWER TATA-binding protein (TBP is the main subunit), TBP associated
factors (TAFs) = interact with elements which bind to the promoter region
TAF6 = DPE
Promoters with only the basal or core regions will only have low levels of
transcription, enhancer elements can increase the level of transcription. There are
three typical activators which hind constitutively active activators, GC box = factor
sp1, CAAT box = NFY factor, and what is the third? - ANSWER Octamer binds
the Oct-1 factor
Enhancers can be upstream or downstream of the start site due to the flexible nature
, of DNA
response elements give additional control as they require factors to bind to them to
activate genes. SRE binds serum response factor which induces growth and HSE
binds what? - ANSWER Heat shock factor
Eukaryotic activators are split into what two domains? In prokaryotes they are
combined. - ANSWER Activation domain - binds activator domain can be more
than one, interact with TAFs
DNA binding domain - leucine zippers, zinc fingers, homeodomains
Electrophoretic Mobility Shift Assay (EMSA) uses denaturing acrylamide gel to
separate out DNA which is free which runs down from what? - ANSWER DNA
bound to a protein activator which stays at the top
In vitro
Another in vitro technique is using a transcription assay, if the activator works with
the DNA sample what appears on the gel? - ANSWER RNA transcript
Reporter genes are an example of in vivo analysis of an activator works, what other
technique which involves immunoprecipation of proteins bound to DNA can be
used? - ANSWER Chromatin immunoprecipitation (CHIPseq)
PCR after reverse cross link and then sequence
What creates a bridge between activators and RNA polymerase II, it has a head
middle and tail domain which can each bind a different activator protein to enhance
pre initiation complex formation? - ANSWER Mediators (22polypeptide subunit)
Activators can work in a few different ways, they can promote the binding of an
additional activator, stimulate complex assembly (TAFs, mediators to promote pre
initiation complex) or to aid RNA polymerase in what way? - ANSWER Release
the stalled RNA polymerase, which can stall near the promoter
in the absence if Heat shock factor the RNA will pause after 50nts, HSF can release
it.
Can also aid in chromatin remodelling
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