Term
| Where does transcription start? |
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Definition
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Term
| What is the most common core promoter? |
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Definition
| CpG Islands, 70% of promoters are these |
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Term
| What makes up 20% of core promoters, and is the most studied and understood? |
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Definition
| BreU and BreD, a TATA box, Inr, and DPE |
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Term
| What makes up 10% of core promoters? |
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Definition
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Term
| Why is CpG rare in the genome apart from these promoters? |
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Definition
| The cytosine is methylated to 5-methyl cytosine, which overtime is spontaneously deaminated into T, turning it into CpT |
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Term
| What is TBP, and what is it's structure? |
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Definition
| TATA box binding protein, part of TFIID, contains two 66 amino acid long repeats that flank a basic region, which forms a molecular saddle that binds the DNA in the minor groove. The underside of the saddle is a beta pleated sheet, the topside is an alpha helix. the beta pleated sheet is five stranded and anti-parralel. Four strands form the conclave underside that binds to DNA. |
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Term
| What is the structure of RNAPII's CTD tail, and how is it regulated when transcription begins? |
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Definition
52 repeats of YSPTSPS, 31 being imperfect repeats - the CTD forms a 'landing pad for enzymes
1st the 5ths S is phosphorylated by Cdk7, as RNAPII begins transcription, then the 2nd S is phosphorylated to transcribe further into the gene (attracts cleavage and polyadenylation, the S2 phosphorylation is lost at this point) |
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Term
| What are the two forms of RNAP2? |
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Definition
A (Unphosphorylated CTD)
O (Phosphorylated CTD - active) |
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Term
| What is the stepwise assembly model, and what is the evidence for it? |
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Definition
| GTFs added one by one to build up the transcription complex. Buratowski used band shift assays to show that complex was build up sequentially - may not be true in vivo. In 2013, fluorescence resonance energy transfer was used to monitor protein interactions. PCNA sliding clamps (Protein complexes that allow the holoenzyme to slide along DNA) are quickly removed from DNA unless RNAPII is present - suggests holoenzyme not fully assembled, or that this is the wrong order |
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Term
| What is the holoenzyme model, and what evidence is it based on? |
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Definition
| The holoenzyme is preassembled before interacting with promoter DNA - based on biochemical purification of RNAPII |
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Term
| What does the holoenzyme contain? |
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Definition
| The GTFs, the mediator complex, Swi/Snf and RNAPII |
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Term
| What is the mediator complexes structure? |
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Definition
| Formed of 25 proteins, has 4 regions - head, tail, middle and kinase modules. The head binds to TF2 and TF2H |
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Term
| What is proximal pausing and where does it occur? |
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Definition
| It is pausing at the proximal promoter that allows for rapidly induced synthesis at a later point. |
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