Lecture 11 - Transcription elongation and termination, introduction to RNA processing

Question 1

In most animal ________, Pol II _____ after transcribing ___________

Answer 1

promoters, pauses, <100 bp

Question 2

Why Pol II pauses during elongation

Answer 2

facilitates recruitment of the 5’ capping enzyme complex that stabilizes the 5’ end of the nascent message (nascent RNA)

Question 3

in beginning of elongation (from ___ to ___ bp) elongation is still ____ and is in a ______ phase (but elongation is said to be ____)

Answer 3

20 - 100, unstable, double-check. but said to be stable

Question 4

5’ end that comes out of ______ is vulnerable to ______ (means ______- that are always ____) solution : _______

Answer 4

RNAP II, exonucleases, enzymes that cleave nucleotides one at a time from end of polynucleotide chain, always around, sol: capping

Question 5

______ and _____ (___) and _____ act together to _____ transcription elongation beyong ____ - ____ nucleotides

Answer 5

Spt4 Spt4 (DSIF), NELF, inhibit, 20-60

Question 6

For further ____ to occur, _____ must _______ specific residues in ____, ____ and _____

Answer 6

elongation, P-TEFb (not to know), phosphorylate, NELF, Spt5 and CTD (long C-terminal domain of Pol II)

Question 7

phosphorylation of residues by P-TEFb induces 3 things

Answer 7

dissociation of NELF, switch in Spt5 from being a repressor to an activator of transcription, and production of full-length transcript by RNAP II

Question 8

elongating Pol II can move trough some regions ___________ than others and this was proved with the _____ experiment

Answer 8

faster. ChIP

Question 9

Pol II does not ______ transcription until after transcription of a ______ that directs ______ and _______ of the RNA at its ______ end

Answer 9

terminate, sequence, cleavage, polyadenylation, 3’

Question 10

Pol II can _____ transcription at multiple ________ located ________ downstream of this __________ site

Answer 10

terminate, sites, 500-2000 bp PolyA addition

Question 11

Everything that has to do with _______ (so transcription) comes from _________ or _________ influence

Answer 11

mRNA, environmental, developmental

Question 12

what part of initiation complex not required for Pol 1 and Pol III

Answer 12

Kinase (no CTD …) and helicase activity of TFIIH (where it undwinds the DNA helix)

Question 13

Transcription initiation with Pol I ( __)and Pol III (___) is similar to ______ but requires _________

Answer 13

rRNA, tRNA and other stuff, Pol II, different GTFs

Question 14

Pol I transcribes ____ precursor of ____, ____ and ____ rRNA from _____ of the _________

Answer 14

45S, 18S, 5.8S, 28S, multiple copies, pre-rRNA gene

Question 15

Pol III transcribes ____, _____ and ______ of unknown function

Answer 15

tRNAs, 5s RNA, additional small stable RNAs

Question 16

Pol II is regulated by ________ and ________

Answer 16

development and cell cycle

Question 17

Pol I and Pol III respond to signals that __________________ so they are regulated by ________ signals. They also respond to ________________

Answer 17

say if they have enough ‘food’, if the cell has enough resources for synthesis, environmental signals, cues from cell cycle regulated factors

Question 18

Pol I major difference with pol II

Answer 18

many promotor elements involved within the coding region

Question 19

In Pol III, ________ is controlled by an _____________. It is bound by a ______ subunit of a specialized form of _________ binding to a _______

Answer 19

U6 snRNA, upstream promoter, TBP-like, TFIIB, tata box

Question 20

In Pol III, there are _____ ______ elements for ______ and _______ genes so Pol III has some specific _______

Answer 20

internal promoter, TRNA, 5sRNA, GTFs

Question 21

Pol I and Pol III deal with 2 different signals ( __, __) (that are the ____ they bind to?)

Answer 21

Do you wanna go ahead (commit to transcription), does the cell have enough resources. (some GTFs ?)

Question 22

You can recruit _______ with ________ to bacterial RNAP recruitment to a promoter but in __________

Answer 22

RNAP (III), homology, different ways

Question 23

you need ________ for translating housekeepings genes necessary for _______ and _________ of Rna. the _______ is required for recruiting these proteins

Answer 23

ribosomes, housekeeping, capping and polyadenylation, ctd tail required

Question 24

first step of pre mRNA processing

Answer 24

5’ capping

Question 25

second step of pre mRNA processing

Answer 25

cleavage at poly(A) site by endonuclease

Question 26

3rd step in pre mRNA processing

Answer 26

Polyadenylation by Poly (A) polymerase (PAP) and ATP (add 100-250 at 3’ end)

Question 27

4th step in pre mRNA processing

Answer 27

RNA Splicing

Question 28

5’ cap structure briefly : ________ is added to the 5’ end of the nascent mRNA when it is _______nt long

Answer 28

7-methylguanosine, 25-30 nt long

Question 29

first step addition of 5’ cap structure : ______ capping enzyme associates with ___________ (exact 4 steps not really to know)

Answer 29

dimeric, CTD tail of RNA pol II

Question 30

2nd step addition of 5’ cap structure (exact 4 steps not really to know)

Answer 30

subunit of enzyme removes gamma-phosphate from 5´ end of RNA

Question 31

third step addition of 5’ cap structure (exact 4 steps not really to know)

Answer 31

other subunit transfers guanosine monophosphate (nucleotide that caps) from GTP to the 5’ diphosphate of the nascent transcript

Question 32

4th step addition of 5’ cap structure (exact 4 steps not really to know)

Answer 32

seperate enzymes transfer methyl groups to the N7 position of the guanine

Question 33

To always remember : Nascent RNa transcripts and mRNA processing intermediates do not ________________

Answer 33

exist as free molecules in a cell (always associated with proteins)

Question 34

what proteins associate with pre-mRNAs/what is called the associatio of pre-mRNAs/intermediates of processing with proteins called

Answer 34

diverse set of proteins with conserved binding domains . association called : hnRNPs - heterogeneous ribonucleoprotein particles

Question 35

3 things contained by hnRNPs

Answer 35

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

Question 36

Transcription and RNA processing are ______ to________________ within nuclei. They happen _________

Answer 36

restricted to discrete physical sites. Happen seperately

Question 37

RNA binding domains : where discovered

Answer 37

in hnRNPs, proteins that associate with pre-mRNAs

Question 38

Most common RNA binding domain and what it is made of

Answer 38

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

Question 39

Interaction of prot with ____ is similar with ____

Answer 39

RNA/DNA

Question 40

First other RNA binding motif

Answer 40

RGG box : contains 5 Arg-Gly-Gly repeats interspersed with aromatic amino acids (Phe, Tyr, Trp). Structure unknown

Question 41

Second RNA binding motif

Answer 41

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

Question 42

CTD of RNAP II is _______ and very _____ in comparison with the _______ part

Answer 42

unfolded, very long, globular part

Question 43

CTD of Pol II associates with _______ and ________ factors, thus linking these processes with __________

Answer 43

splicing and polyadenylation, transcription

Question 44

RNAPs can be recruited to different ________ in the __________

Answer 44

elements, genomes

Question 45

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

Answer 45

promoters, within the gene, upstream, RNAP

Question 46

RNAP II responds to information from ________

Answer 46

outside the cell

Question 47

RNAP I and II respond to information from __________ and if you’re starving to death/cell needs resources, you’re gonna produce ________

Answer 47

outside the cell, ribosomes

Question 48

RNA is less well known because proteins that bind to it are very __________ and RNA is less ________ and more difficult to _________

Answer 48

heterogeneous, stable, isolate

Question 49

Termination sequences are not _____________ . The sites will vary according to _________ mechanisms in cell.

Answer 49

specific, signaling