Transcription
Terms
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- RNA exit channel
- RNA exits RNA pol here
- Promoter escape
- When abortive transcription does not occur and the polymerase has moved ~10 nt
- RNA Pol III
- tRNA genes, 5S rRNA
- Template strand (T) channel
- melted template strand moves through here
- Upstrream DNA channel
- DNA leaves RNA pol here
- sigma70
- E. coli RNA pol holoenzyme member that converts the core such that txn only initiates at promoter sequences
- NTP uptake channel
- allows ribonucleotides to enter the active center of RNA polymerase
- Downstream DNA channel
- DNA enters RNA pol here
- RNA Pol II
- Eukaryotic mRNA txn
- de novo txn
- first ribonucleotide is an A because there must be a rigid hold for the next NTP to be added
- RNA Pol I
- Eukaryotic specialized RNA txn
- Phosphorolytic editing
- the active site of RNA pol uses the back-reaction to catalyze the removal of an incorrectly intersted ribonucleotide by reincorporation of PPi; time dependent
- Sigma 3/4 linker
- mimics RNA and blocks the RNA exit channel, dissociates with sigma factor during elongation
- Single-subunit polymerase
- encoded in some phage genomes, chloroplasts, mitochondria
- Rho-dependent transcription termination
- uses rut sites on ssRNA and then ATPase activity to cause complex dissociation
- Sigma region 1.1 in holoenzme
- a molecular mimic of DNA (negatively charged)
- -35 and -10 elements
- E. coli/prok. 6nt relatively well conserved promoter sequences bound by sigma70, melting occurs in the -10 element
- UP-element
- upstream promoter element that increases binding by interaction with the alphaCTD of RNA pol (Ex. rRNA genes)
- Transcription initiation
- requires 1 Mg2+ in active site and the first two rNTPs with divalent ions of their own
- Non-template strand (NT) channel
- melted non-template strand moves through here
- Promoter
- Sequence that initially binds RNA poly
- isomerization
- transition to open complex; does not require ATP and is essentially irreversible
- TRCF-mediated nucleotide excision repair [Uvr(A)BC]
- repair at stalled polymerases due to DNA damage, uses ATPase to push polymerase forward.
- Hydrolytic editing
- cleavage of incorrect 3' rNT stimulated by Gre factors
- discriminator
- found in prok. promoters just downstream of -10 element, increases stability of txn init. complex
- 1/10,000
- Txn Error Rate
- extended -10 element
- another bacterial promoter (Ex. E. coli gal genes)