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CMB2001 FINAL EXAM (326) QUESTIONS WITH VERIFIED ANSWERS
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CMB2001 FINAL EXAM (326) QUESTIONS WITHVERIFIED ANSWERS 2024-2025
What is gene expression? - ANSWER dsDNA is decoded to ssRNA/proteins by an
mRNA intermediate using A/U/C/GTPs and RNA polymerase
Where is the consensus sequence in prokaryotic promoters? - ANSWER at -10 and
-35 upstream of the transcription start site
What recognises the consensus sequences in prokaryotes? - ANSWER the
holoenzyme
What is a holoenzyme? - ANSWER a closed complex with a core enzyme and
sigma factor 70
What does the holoenzyme do? - ANSWER causes the dsDNA to open and allows
for elongation to happen, after 10 bases are added the sigma factor is released
What does eukaryotic DNA have near the transcription start site? - ANSWER
core/basal regions
What is a possible core/basal region? - ANSWER TATA box
Where is a TATA box located? - ANSWER -26/-31
What is a possible core/basal region? - ANSWER initiator (INR)
Where is the initiator located? - ANSWER -2/+4
What is a possible core/basal region? - ANSWER downstream core promoter
(DPE)
Where is the downstream core promoter located? - ANSWER +30
What is a possible core/basal region? - ANSWER TFIIB recognition element
(BRE)
Where is the TFIIB recognition element located? - ANSWER -37/-32
What is a possible core/basal region? - ANSWER CpG islands
,What are CpG islands? - ANSWER DNA regions with many cytosine bases
adjacent to guanine bases
What makes CpG islands different? - ANSWER normally the C residues next to G
are methylated to 5-methyl C but in the islands they are not
What effect does methylation have on gene transcription? - ANSWER can either
increase or decrease transcription of genes depending on which amino acids are
methylated, and how many methyl groups are attached
What does eukaryotic DNA have upstream of the transcription start site? -
ANSWER upstream regulatory regions
Whats an examples of upstream regulatory regions? - ANSWER CAAT box which
is an UAS (upstream activating sequences)
Whats an examples of upstream regulatory regions? - ANSWER GC box (UAS)
What are UAS/URS? - ANSWER upstream activating/repressor sequences without
activator sequences the formation of PIC is ineffective and leads to poor
transcription
A way to identify promoter elements? - ANSWER sequence comparison
How does sequence comparison work? - ANSWER comparing 30 bp sequences of
start sites and can look at the frequency of the different bases in different positions
to find the consensus sequence
Whats a drawback with sequence comparison? - ANSWER gives no functional
information
What does reporter analysis do? - ANSWER measures transcriptional levels
What do reporter genes do? - ANSWER encode enzymes whose level of
transcription are easy to measure
How does reporter analysis work? - ANSWER the reporter gene is clones into a
plasmid and controlled by the same promoter whose activity is being investigated
What does the measurable product from the enzyme reporter show? - ANSWER it's
proportional to the activity of the investigated promoter so can be used to
,investigate parts of the promoter elements through promotor bashing
What is promoter bashing? - ANSWER make a series of promoters each with a
little less to see how this alters the protein expression to show the importance
activator/repressor sequences
Whats an example of when reporter analysis has been used? - ANSWER in mice
embryos to see location of expression of genes using the LacZ reporter gene with a
Ure2 promoter
Whats does eukaryotic RNA polymerase I transcribe? - ANSWER 28s, 18s and
5.8s rRNA in the nucleolus
Whats does eukaryotic RNA polymerase II transcribe? - ANSWER mRNA, snRNA
and miRNA in the nucleus
Whats does eukaryotic RNA polymerase III transcribe? - ANSWER tRNA, 5s
rRNA, U6RNA and 7sRNA in the nucleus
Whats the basic structure of eukaryotic polymerases? - ANSWER basic crab claw
with 12 subunits
Whats a homologue of RPB2 in eukaryotes? - ANSWER beta in prokaryotes
How was the eukaryotic Pre-initiation complex (PIC) assembly order worked out? -
ANSWER in vitro trial and error by adding different factors to give an order
What does TFIID do? - ANSWER binds to TATA box (core promoter) and recruits
TFIIB
What stabilises TFIIB? - ANSWER TFIIA
What does TFIIB do? - ANSWER recruits polymerase II and TFIIF which are
needed for start site selection
What does TFIIF do? - ANSWER stimulates elongation and destabilises non
specific DNA polymerase interactions
What does TFIIE do? - ANSWER recruits and modulates TFIIH's activities
What does TFIIH do? - ANSWER has helicase activity to separate the 2 strands by
ATP hydrolysis
, What is TFIIH made of? - ANSWER made of 9-10 subunits and can be split into
CORE and CAK parts
What does the CAK part of TFIIH do? - ANSWER contains kinase to
phosphorylate the CTD and DNA helicases which are involved in promoter
clearance, DNA repair and coupling
What is the CTD? - ANSWER C-terminal domain which is a series of repeats at the
C-terminal of the largest beta subunit of polymerase II
What DNA helicases does the TFIIH have? - ANSWER XPD and XPB
What does XPB play a part in? - ANSWER promoter melting
What happens to TFIID and TFIIA do as transcription happens? - ANSWER they
stay behind
What happens to TFIIF do as transcription happens? - ANSWER moves along with
the polymerase II
What happens to TFIIB, TFIIE and TFIIH do as transcription happens? - ANSWER
released
What is the central RNA pol II transcription factor? - ANSWER TFIID
What is TFIID made of? - ANSWER TATA binding protein (TBP) and TBP
associated factors (TAFs), in a tri-lobular structure
What is the TATA binding protein? - ANSWER a molecular saddle that fits on top
of the DNA and directs assembly of the PIC on the TATA box, this can be done
without TAFS when TATA box is present (if not needs help from TAFS)
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