RNA Transcription Flashcards
Rnase P
Ribozyme. Generate mature tRNA from pre-RNA. Endonuclease. Has a protein part and a RNA part. Protein part to prevent RNA-RNA repulsion. RNA part is catalyst
Ribozyme
RNA molecules that catalyze specific reactions, such as splicing & formation of peptide bonds during protein synthesis
Pseudoknots
Energetically unfavorable for translation, can be used for regulation. Used for modulating gene expression in gag-pol operon (virus)
How does region 2 of sigma factor interact with the promotor?
Binds to the -10 element and stabilize melted DNA
How does region 4 of sigma factor interact with the promotor?
Recognizes and binds to -35 using helix-turn-helix
Rho-independent termination
Hairpin structure followed by multiple A(:U)
Stepwise assembly of eukaryotic pol II preinitiation complex
TFIID/TBP -> TFIIA -> TFIIB -> TFIIF/RNA pol II -> TFIIE -> TFIIH
How is eukaryotic DNA transcribed despite histone proteins?
FACT removes H2A.H2B dimers from nucleosome
Formation of 5’ RNA cap
Dephosphorylation of 5’ end?. Happens before polyA-tail
Differences between transcription in prokaryotes and eukaryotes
Coupled transcription/translation in bacteria
Splicing, 5’ cap and polyA tail in eukaryotes.
TATA, TFII-X in eukaryotes, sigma factor and -10 and -35 consensus seq. in bacteria
Autocatalytic property of RNA
If in alkaline solutions, the 2’ OH group can attack the phosphodiester bond and cleave itself. In acidic conditions, this doesnt happen
Topoisomerase role in transcription
DNA is only unwound inside the RNA pol which could cause positive supercoiling in front of it
RNA polymerase holoenzyme
Core enzyme (2 beta (beta and beta prime) subunits, 2 alpha subunits), Sigma subunit. Resembles crab claw with catalytic center in cleft.
RNA pol beta subunits
Main body of the polymerase, contains catalytic center
RNA pol alpha subunits
Responsible for enzyme assembly and transcription start
Sigma factor
Recognize promotor region in bacteria. 4 factors. Involved in initiation, release lead to elongation step as it blocks RNA exit site.
Sigma factor 2
Recognizes -10 (TATAAT), flips bases into body of sigma factor, melts open the DNA
Sigma factor 1.1
Neg aas, stop polymerase from moving until sigma 2 unwinds DNA
Sigma factor 4
Interacts with major groove at -35 with helix turn helix DNA binding. Blocks RNA exit tunnel
Consensus sequence in bacteria
A form of gene regulation, the closer to the consensus sequence the higher expression
Consensus sequence in eukaryotes
TATA box (-30), then the start point and some downstream promotor elements
Main RNA polymerase in eukaryotes
RNA pol II, makes pre mRNA and snoRNA.
Other RNA pol in eukaryotes
RNA pol I makes rRNA, RNA pol III makes tRNA
TFIID+TBP
Binds to TATA box (at minor groove), causes distortion of DNA and sets landmark for RNA pol. Recruits -A and -B
TFII-E
Helicase loader, recruits TFIIH and melts DNA
TFII-H
H for Helicase. Also kinase, will start phosphorylating RNA pol “tail”, causing promotor release.
TFIIF
Sits on RNA pol
Histone acetylase
Adds acetyl groups to histone tails, decreasing interaction of histone-DNA, making it possible to unpack DNA
Promotor escape in eukaryotes
Phosphorylation of serine-5 on RNA pol tail leads to promotor escape and capping
Proofreading in RNA pol
Hydrolytic editing - stimulate RNase activity?
Phosphorylatic editing - PPi are allowed to do “backwards” reaction , GnB controls that the strand is not distorted, if it is then neutralizes metal ion which slows down addition of next NTP -> higher chance of backwards PPi reaction.
Rho dependent termination
Rho binds to specific seq. when that RNA is exposed. Helicase that unwinds RNA-DNA hybrid. ATPase.
Functional domains on Rho hexamer
P, Q and R-loop. P is ATP binding and activity, Q and R is RNA binding.
TFIIS
Elongation factor that stimulates RNA proofreading by hydrolytic editing
Hammerhead ribozyme
Forms 2’ 3’ cyclic phosphate by attack of 2’ OH at 3’ diphosphate linkage, sequence specific ribonuclease. Self cleaving RNA in viruses.
