CMB2001 Exam Questions With Verified
Answers.
What is gene expression? - answerdsDNA 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? - answerat -10 and -35 upstream
of the the transcription start...
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 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
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