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CMB2001 Questions and Answer | Latest Update 2024/2025
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Core Promoter Elements ~~> TATA box = repetitive sequence of thymine and adenine Initiator (INR) = sequence of pyramidines like thymine and cytosine DPE = downstream promoter elements found along the DNA Common to have >1 promoter but not all of them CpG islands ~~> Sequences hig...

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  • September 15, 2024
  • 51
  • 2024/2025
  • Exam (elaborations)
  • Questions & answers

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  • cmb2001 questions and answer latest update 2024
  • core promoter elements tata box repetitive

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1 | P a g e | © copyright 2024/2025 | Grade A+




CMB2001 Questions and Answer |
Latest Update 2024/2025
Core Promoter Elements


✓ ~~> TATA box = repetitive sequence of thymine and adenine

✓ Initiator (INR) = sequence of pyramidines like thymine and cytosine

✓ DPE = downstream promoter elements found along the DNA




Common to have >1 promoter but not all of them




CpG islands


✓ ~~> Sequences high in CG frequency. They are able to escape

methylation which would lead to gene silencing. Demethylation would

lead to over expression of genes.




Regulatory Promoter Elements


✓ ~~> UAS and URS found proximal upstream; silence and repressor

found distalling upstream

UAS + activator = Activator binding site


URS + silencer = Repressor binding site




Master01 | September, 2024/2025 | Latest update

, 2 | P a g e | © copyright 2024/2025 | Grade A+


Identifying promoter elements


✓ ~~> 1. Sequence comparison - high frequency base at particular

point = consensus sequence

2. Reporter Gene Assay using GFP, luciferase, lac-Z; amount of reporter is the

amount of gene expressed




5' deletion series


✓ ~~> Otherwise known as protein bashing:

1. Recombinant DNA techniques applied


2. Ligate vector carrying reporter gene


3. Transform E.coli and isolate plasmid DNA


4. Transfect each type of plasmid and culture cells


5. Prepare cell extract and carry out reporter assay which will show the effect

of the deletion




Reporters are used to identify


✓ ~~> - When a gene is expressed

- Where a gene is expressed


- What signal causes it's expression




Master01 | September, 2024/2025 | Latest update

, 3 | P a g e | © copyright 2024/2025 | Grade A+


- What factors and sequences are involved




RNA polymerase I


✓ ~~> Found in the nucleolus produces rRNA such as 28S, 18S and 5.8S




RNA polymerase II


✓ ~~> Found in the nucleus and produces mRNAs including siRNA and

miRNAs




RNA polymerase III


✓ ~~> Found in the nucleus and produces tRNA




How is the prokaryotic RNA polymerase II different to eukaryotic RNA

polymerase II?


✓ ~~> Prokaryotic = 2 x alpha, beta, beta', omega subunits

Requires sigma cofactor to recognise DNA


Eukaryotic = much more complex. Has 12 subunits (some which are similar to

the prokaryotic subunits) and sigma cofactor is replaced by Transcription

factors which will recruit RNA polymerase II to the promoter site




Master01 | September, 2024/2025 | Latest update

, 4 | P a g e | © copyright 2024/2025 | Grade A+


The sequence of TFII binding


✓ ~~> D -> A -> B -> F + RNA polymerase II -> E + H




CTD on RNA polymerase II


✓ ~~> C-terminus domain on beta' subunit is highly phosphorylated

during transcription




TFII fate during transcription


✓ ~~> - TFII D and A remain at the promoter site

- TFIIF remains with the RNA polymerase II


- TFII H, E and B




TFIIA


✓ ~~> Promotes binding of TFIID and has antirepressing function




TFIIB


✓ ~~> Recruits RNA polymerase II and TFIIF so is important for start site

selection




TFIID


Master01 | September, 2024/2025 | Latest update

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