RNA polymerase function in transcription.txt

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RNA polymerase function in transcription.txt
2012-03-25 21:44:02
RNA polymerase function updated

updated RNA polymerase function
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  1. Function of RNA polymerase sigma factor
    • *prokaryotic subunit
    • 1. binds to core enzyme to yield holoenzyme
    • 2. sigma 4 binds to BOTH DNA strands. Indirectly binds to template strand thru H2O binding (hydrophobic regions of RNA polymerase and DNA bind and polymerase unwind)
  2. Holoenzyme importance and role
    • Essential in:
    • LOCATING and BINDING promoter
    • OPENING of helix (unwinding of DNA)
    • acts as TARGET for transcription factors
  3. Eukaryotic Polymerases
    • RNA pol I: rRNA
    • RNA pol 2: mRNA
    • RNA pol 3: tRNA
  4. RNAP I
    • has conserved C-terminal domain (CTD)
    • Synthesizes NON-coding RNA, ie rRNA.
  5. RNAP 2
    • Contains 12 subunits.
    • Transcribes genes that code for PROTEIN (mRNA)
    • Scans for DNA damage & modifies surrounding chromatin
    • acts as platform for mRNA processing factors for mRNA modification
  6. RNAP 3
    synthesizes NON-coding RNA, ie tRNA
  7. Role of CTD (carboxyl tail domain)
    • 26-52 repeats of specific amino acids
    • Caps and SPLICES RNA transcript
    • undergoes PHOSPHORYLATION events on Ser2 and Ser5 repeats
    • Hydrophilic
  8. Ser2 role
    • allows for ELONGATION of Transcription (2nd phosphorylation step)
    • Phosphorylates solely to TERMINATE process
    • undergo phosphorylation by CTD kinase-1, which promotes elongation
  9. Ser5 role
    • Occurs after binding to TFIIH and mediator (start initiation)
    • Phosphorylated by TFIIH, initiates transcription (1st phosphorylation step)
  10. Role of Rpb 1 & 2 in elongation
    • form active site of core domain of RNA polymerase II
    • nucleotides added in this active site
    • has a conserved domain
    • Highly POSITIVE charge, helps in stabilizing template DNA entering active site
  11. Mechanism for elongation at active site
    • 3 aspartates in a loop on template DNA
    • 1 Mg ion in the middle
    • Loops shrinks when RNA pol is absorbing an NTP
    • Loop expands when RNAP is completing add'n of nucleotide
    • Shrinking loop PUSHES Mg up out of ring & it is now able to access 3'-OH group of nucleotide base
    • series of reactions result in phosphodiester bond formation between nucleotides
  12. Role of Mg ions
    • role in catalytic add'n of incoming NTPs during elongation of transcription
    • Stabilizes nucleophilic add'n of NTP's
    • 1st Mg ion located in Asp triad: frees up Oxygen of the 3'-OH group through H-Bond FORMATION (results in formation of phosphodiester bond)
    • 2nd Mg ion associated w/incoming base: stabilizes pyrophosphate that is a biproduct of elongation