RNA polymerases and transcription Flashcards
Where is snRNA used for?
mRNA splicing and gene regulation in eukaryotes
What is miRNA used for?
inhibition of mRNA transcription
Is primer needed for RNA transcription?
NO
What is the difference between antisense and sense strand?
Antisense is template for RNA transcription, sense is unused nontranscribed DNA strand (same seqUence as RNA except U)
What is RNA polymerase made up of in bacteria?
Sigma factor, and polymerase core
What is the role of core polymerase? (2)
1) helicase
2) nucleotidyl transferase
What is the role of sigma factor?
recognize promoter
Where are promoters sequences found for prokaryotes?
-35 and -10 consensus sequence
What is another name for -10 consensus sequence?
Pribnow Box
What does variation in promoter sequences mean?
variation results in variation in the binding ability of RNA polymerase and affect the rate of transcription.
What does holoenzyme mean?
core RNA polymerase + sigma factor
What are the steps of initiation and elongation of prokaryotic RNA transcription? (5)
- Holoenzyme binds to -35 and -10 regions.
- DNA molecule is unwound by 17 bp at -10 regions (helicase activity)
- After 8-9 nt have been polymerized, sigma factor dissociates from the core enzyme.
- Polymerization proceeds
- Transcription terminates once termination sequence is reached.
Role of TBP (TATA-box binding protein)
a subunit of TFIID, binds to the TATA box of a gene promoter region
Role of TFIIA (2)
Stabilize TBP binding to TATA box, and blocks binding of repressor proteins.
Role of TFIID
Causes a distortion in the DNA helix allowing the recruitment of other TFs
Role of TFIIB
Recognize BRE element , involved in RNA polymerase interacitons
Role of TFIIH (2)
Contain DNA helicase to unwind DNA
Activate RNA pol by phosphorylation
Role of TFIIE
Involved in positioning of RNA POL
Describe assembly of TFs at the core promotor region
- TFIID which contain TBP recognize TATA box of promotor.
- TFIIA facilitates TBP binding to TATA box.
- TFIIB then comes and recognize BRE element.
- TFIIE then associate with growing assembly and attracts TFIIH.
- TFIIF then stabilizes RNA polymerase by interacting with TBP&TFIIB and helps attracting TFIIH.
- TFIIH unwind DNA and phosphorylate CTD of RNA pol to activate for initiation of transcription.
- Phosphorylation of CTD will change conformation of RNA pol, releasing most of TFs.
What disease is rifampin used for?
TB
What is the mechanism of rifampin and effect?
Binds to prokaryotic RNA polymerase, thus blocking formation of the first phosphodiester bond, which inhibits initiation of transcription.
What can lead to rifampin-resistance?
Mutation in genes encoding RNA polymerase or topoisomerase
Is rifampin specific on prokaryotic cell?
YES
What genes does RNA pol I transcribe?
5.8s, 18S, 28S rRNA genes
What genes does RNA pol II transcribe?
all protein-coding genes (mRNA), some snRNA and miRNA
What genes does RNA pol III transcribe?
tRNA genes and some snRNA
What is alpha-amanitin
potent inhibitor of RNA pol II
Effect of alpha-amanitin clinically?
GI symptoms such as diarrhea and vomiting (1-2 days)
hepatic phase (renal and liver failure)
If untreated, death can occur in 7-10 days
What is the treatment of alpha amanitin?
high dose penicillin which inhibit amnitin activity in liver
GI decontamination
Liver transplant
bacterial gyrase inhibitor (name of drug) (2)
courmarins and quinolones (ciprofloxacin)
What is Rho-independent termination process? in prokaryotes
GC-rich palindrome precedes a sequence of 6-7 U residues in RNA, which leads to hairpin loop structure just before oligo U residues. Oligo U which is bound to oligo A at DNA template is very weak allowing separation of RNA from template.
What is Rho-dependent termination process? in prokaryotes
- Rho protein attaches to recognition site on RNA
- Rho moves along the RNA following RNA pol.
- RNA pol pauses at terminator and rho catches up
- Rho unwinds DNA-RNA hybrid and separates RNA polymerase, leading to termination (release)
