Lecture 11 - Transcription elongation and termination, introduction to RNA processing Flashcards
In most animal ________, Pol II _____ after transcribing ___________
promoters, pauses, <100 bp
Why Pol II pauses during elongation
facilitates recruitment of the 5’ capping enzyme complex that stabilizes the 5’ end of the nascent message (nascent RNA)
in beginning of elongation (from ___ to ___ bp) elongation is still ____ and is in a ______ phase (but elongation is said to be ____)
20 - 100, unstable, double-check. but said to be stable
5’ end that comes out of ______ is vulnerable to ______ (means ______- that are always ____) solution : _______
RNAP II, exonucleases, enzymes that cleave nucleotides one at a time from end of polynucleotide chain, always around, sol: capping
______ and _____ (___) and _____ act together to _____ transcription elongation beyong ____ - ____ nucleotides
Spt4 Spt4 (DSIF), NELF, inhibit, 20-60
For further ____ to occur, _____ must _______ specific residues in ____, ____ and _____
elongation, P-TEFb (not to know), phosphorylate, NELF, Spt5 and CTD (long C-terminal domain of Pol II)
phosphorylation of residues by P-TEFb induces 3 things
dissociation of NELF, switch in Spt5 from being a repressor to an activator of transcription, and production of full-length transcript by RNAP II
elongating Pol II can move trough some regions ___________ than others and this was proved with the _____ experiment
faster. ChIP
Pol II does not ______ transcription until after transcription of a ______ that directs ______ and _______ of the RNA at its ______ end
terminate, sequence, cleavage, polyadenylation, 3’
Pol II can _____ transcription at multiple ________ located ________ downstream of this __________ site
terminate, sites, 500-2000 bp PolyA addition
Everything that has to do with _______ (so transcription) comes from _________ or _________ influence
mRNA, environmental, developmental
what part of initiation complex not required for Pol 1 and Pol III
Kinase (no CTD …) and helicase activity of TFIIH (where it undwinds the DNA helix)
Transcription initiation with Pol I ( __)and Pol III (___) is similar to ______ but requires _________
rRNA, tRNA and other stuff, Pol II, different GTFs
Pol I transcribes ____ precursor of ____, ____ and ____ rRNA from _____ of the _________
45S, 18S, 5.8S, 28S, multiple copies, pre-rRNA gene
Pol III transcribes ____, _____ and ______ of unknown function
tRNAs, 5s RNA, additional small stable RNAs
Pol II is regulated by ________ and ________
development and cell cycle
Pol I and Pol III respond to signals that __________________ so they are regulated by ________ signals. They also respond to ________________
say if they have enough ‘food’, if the cell has enough resources for synthesis, environmental signals, cues from cell cycle regulated factors
Pol I major difference with pol II
many promotor elements involved within the coding region
In Pol III, ________ is controlled by an _____________. It is bound by a ______ subunit of a specialized form of _________ binding to a _______
U6 snRNA, upstream promoter, TBP-like, TFIIB, tata box
In Pol III, there are _____ ______ elements for ______ and _______ genes so Pol III has some specific _______
internal promoter, TRNA, 5sRNA, GTFs
Pol I and Pol III deal with 2 different signals ( __, __) (that are the ____ they bind to?)
Do you wanna go ahead (commit to transcription), does the cell have enough resources. (some GTFs ?)
You can recruit _______ with ________ to bacterial RNAP recruitment to a promoter but in __________
RNAP (III), homology, different ways
you need ________ for translating housekeepings genes necessary for _______ and _________ of Rna. the _______ is required for recruiting these proteins
ribosomes, housekeeping, capping and polyadenylation, ctd tail required
first step of pre mRNA processing
5’ capping
second step of pre mRNA processing
cleavage at poly(A) site by endonuclease
3rd step in pre mRNA processing
Polyadenylation by Poly (A) polymerase (PAP) and ATP (add 100-250 at 3’ end)
4th step in pre mRNA processing
RNA Splicing
5’ cap structure briefly : ________ is added to the 5’ end of the nascent mRNA when it is _______nt long
7-methylguanosine, 25-30 nt long
first step addition of 5’ cap structure : ______ capping enzyme associates with ___________ (exact 4 steps not really to know)
dimeric, CTD tail of RNA pol II
2nd step addition of 5’ cap structure (exact 4 steps not really to know)
subunit of enzyme removes gamma-phosphate from 5´ end of RNA
third step addition of 5’ cap structure (exact 4 steps not really to know)
other subunit transfers guanosine monophosphate (nucleotide that caps) from GTP to the 5’ diphosphate of the nascent transcript
4th step addition of 5’ cap structure (exact 4 steps not really to know)
seperate enzymes transfer methyl groups to the N7 position of the guanine
To always remember : Nascent RNa transcripts and mRNA processing intermediates do not ________________
exist as free molecules in a cell (always associated with proteins)
what proteins associate with pre-mRNAs/what is called the associatio of pre-mRNAs/intermediates of processing with proteins called
diverse set of proteins with conserved binding domains . association called : hnRNPs - heterogeneous ribonucleoprotein particles
3 things contained by hnRNPs
1) hnRNAs (Pre-mRNAs and RNA processing intermediates containing one or more introns)
2) Proteins involved in different steps of RNA processing and transport of mRNAs to cytoplasm
3) Proteins with RNA binding domains and domains that interact with other proteins
Transcription and RNA processing are ______ to________________ within nuclei. They happen _________
restricted to discrete physical sites. Happen seperately
RNA binding domains : where discovered
in hnRNPs, proteins that associate with pre-mRNAs
Most common RNA binding domain and what it is made of
RNA recognition motif : 80 a.a, folds into 4-stranded beta sheet flanked by 2 alpha helices. Contains RNP1 and RNP2 that contact the phosphates of RNA
Interaction of prot with ____ is similar with ____
RNA/DNA
First other RNA binding motif
RGG box : contains 5 Arg-Gly-Gly repeats interspersed with aromatic amino acids (Phe, Tyr, Trp). Structure unknown
Second RNA binding motif
KH motif : 45 residues, similar structure to RRM domain but RNA binds by interacting with hydrophobic surface formed by the alpha helices and one beta strand
CTD of RNAP II is _______ and very _____ in comparison with the _______ part
unfolded, very long, globular part
CTD of Pol II associates with _______ and ________ factors, thus linking these processes with __________
splicing and polyadenylation, transcription
RNAPs can be recruited to different ________ in the __________
elements, genomes
The different RNAPs mainly differ because the _________ are placed differently. For some, they are ______ and for others they are _______. Different parts of ________ interact with these
promoters, within the gene, upstream, RNAP
RNAP II responds to information from ________
outside the cell
RNAP I and II respond to information from __________ and if you’re starving to death/cell needs resources, you’re gonna produce ________
outside the cell, ribosomes
RNA is less well known because proteins that bind to it are very __________ and RNA is less ________ and more difficult to _________
heterogeneous, stable, isolate
Termination sequences are not _____________ . The sites will vary according to _________ mechanisms in cell.
specific, signaling
