BIOS 390 Exam 2 - required to initiate transcription at PolII cor...

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BIOS 390 Exam 2

1. GTF

–Answer general transcription factors required to initiate transcription at PolII core promoters mostly multimeric proteins, highly conserved

2. TFIID

–Answer 1/14 subunits is TBP (TATA box binding protein) interacts with minor groove of TATA box, bends DNA

3. TFIIB

–Answer CTD interacts with TBP and RNAPII

4. TFIIA

–Answer Stabilizes interaction of TBP and TFIIB in vivo

5. TFIIF

–Answer Associated with RNAPII Prevents nonspecific interaction by capturing nontemplate strand

6. TFIIE

–Answer docking site for TFIIH

7. TFIIH

–Answer helicase activity –Answer unwinds DNA duplex 1 / 3

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kinase activity –Answer phosphorylates PolII in beginning of elongation (Ser5, pauses)

• other factors required for eukaryotic in vivo transcription

–Answer chromatin remod- eler upstream factors to promote DNA looping mediator complexes

• CTD of RNAPII

–Answer contains repeats of 7mer (diff number of repeats depending on species) landing pad for proteins involved in elongation and post-transcriptional modification

• Pausing

–Answer Ser5 phosphorylated by TFIIH –Answer pauses In pause, 5' cap added capping triggers phosphorylation of Ser2 by p-TEFb, resumes

• pTEFb

–Answer phosphorylates ser2 to resume elongation after 5' capping

• release of initiation complex

–Answer conformational change in promoter clearance causes RNAPII grip to switch from initiation factors to strand

• RNAPII proofreading mechanisms

–Answer kinetic and nucleolytic 2 / 3

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• kinetic proofreading

–Answer aka pyrophosphorolytic edition incorrect base stalls polII, pyrophosphate acts as nucleophile to break phosphodi- ester bond product –Answer rNTP

• nucleolytic proofreading

–Answer aka hydrolytic editing intrinsic activity to RNAPII RNAPII backtracks, water lyses phosphodiester bond to release several bases product –Answer NMPs

• 2 enzymatic activities of RNAPII active site

–Answer 1) nucleotidyl addition 2) hydrolysis compare to DNAP which is associated to exonuclease

• RNAPII double check of incoming NTPS

–Answer

• binds at preinsertion site, discrim- inates NTP/dNTP

–Answer spatial arrangement of 2 Mg2+ has to be correct for catalysis

• trigger loop

–Answer folds to form 3-helix bundle with bridge helix. active center checks for complementarity

18. TFIIS

–Answer

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