RR8 Flashcards
Why is a carboxyl domain on a large subunit highly critical?
In the phosphorylated form, it is associates with highly transcribed genes.
What is the CTD composed of?
It is composed of the heptapeptide sequence.
In terms of CTD, what phosphorylation is actually taking place?
There are two important transcription reactions.
1) Serine in position 5
2) Serine in position 2
What is the process of phosphorylation of CTD of RNA Pol II?
During transcription, conditions are optimal. TF2H melts DNA, CDK7 phosphorylates on Serine 5. The Carboxyl Terminal Tail is phosphorylated when RNA Pol II paused at first nucleosome. It squeaks along the heptatpeptide sequence and moves slowly and innefficiently. There is now a phosphorylated P on Serine 5 which caps the 5’ end. The capping enzyme recognizes the serine 5 and sits near the 5’ end.
During the phosphorylation of CTD of RNA Pol II, what is the function of the CAP?
- Protects pre mRNA
- Facilitates nuclear export
- Recognition by translation factors
Why does RNA polymerase II pause after initiation?
This allows for change in factors. From those blocking elongation (NELF) to factors that enhance it (DSIF, SPT6 and PAF). It is mediated and dependent on CDK9/P-TEFb phosphorylation. It allows RNA to elongate more proccessively.
What is splicing? When does it take place?
It takes place from pre-mRNA to mRNA. Eukaryotic genes have introns and exons are in mature mRNA. Introns can encode regulatory information and they were discovered due to discrepancy between mRNA size and gene size. Introns need to be spliced out because they don’t have the proper coding information.
How can we identify intron borders?
You can identify them by looking at where sequences don’t match. For example, GUAG, it is invarient at 5’ end of intron, associated with boundaries.
What do you need 5 snRNPs for?
At least five different kinds of snRNPs make up the spliceosome; U1 snRNA, U2 snRNA, U4 snRNA, U5 snRNA, and U6 snRNA.
U1 contacts 5’ borders of introns and branch point region (U2). The branch point is nor paired and it bulges out.
Why is RNA:RNA pairing critical?
It is critical for U1 function in splicing. And their function is to contact the 5’ borders which is important.
What is the process of trans-esterification reactions in intron splicing?
There are two reactions, and the result of the reactions is the joining of 2 exons and the release of a intron lariat. There will be immediate interactio at 5’ end of exon sequence - directed by SnRNPs.
first reaction: hydroxyl group of residue at branch point attacks 5’ phosphate group of 1st intron residue, leading to the formation of ‘lariat.’
second reaction: free 3’ end of preceding exon attacks 5’ phosphate group of first residue in the following exon.
What is the use of radio-labelled RNA?
Intermediate splicing product can be separated and quantified during a splicing reaction.
Describe the spliceosome cycle:
SnRNPs assemble sequentially on the Intron. There are rearranging events in RNA:RNA interactions between the pre-mRNA and snRNAs, the U1 and U4 exit complex leaving the active spliceosome. Following, there is spliceosome formation, transesterification occurs, with no net energy expenditure.
Do self-splicing introns need a protein?
Not always, RNA can be catalytic.
What are most introns spliced by?
The spliceosome.
