RNA transcription

Question 1

Where does the capping protein start and then where does it go?

Answer 1

Starts on RNA pol tail, then caps 5’ end of RNA and stays there until translation.

Question 2

Processing factors

Answer 2

e.g. spliceosome, etc. Recruited by pattern of phosphorylation on c-term RNA pol tail

Question 3

What do splicing proteins do?

Answer 3

remove introns, join exons

Question 4

What do 3’ end processing proteins do? What are some of their other effects?

Answer 4

Recognize cleavage/polyadenylation signals in mRNA, cleave at 3’ end. Destabilizes RNA pol

Question 5

How does RNA pol dissociate?

Answer 5

3’ end processing proteins destabilize, then it’s dephosphrylated by phosphotases

Question 6

Benefits of RNA splicing

Answer 6

Exon shuffling from recombination can generate novel domains, more coding potential with alternative splicing

Question 7

Alternative splicing

Answer 7

Some exons are spliced out in between introns sometimes

Question 8

Consensus sequences in pre-mRNA

Answer 8

GU on 5’ end of intron, ‘A’ at branch site, AG at 3’ end

Question 9

Lariat formation

Answer 9

Two transesterifications
No energy req for transesterification
New bond on 2’ deoxyribose of ‘A’ branch site from G in GU

snRNP’s stay on it when it leaves

Question 10

Mechanism of splicing

Answer 10

1. U1 snRNP to 5’ splice site, U2AF/BBP to branch site
2. U2 snRNP replaces U2AF/BBP
3. U4/U6 snRNP come in with U5, form the loop
4. U1 replaced by U6, branch site with U2 comes in at 5’ splice site
5. U6 at 5’ splice site goes to 3’ splice site and breaks the loop off

Question 11

What are spliceosomes?

Answer 11

ribonucleoprotein complexes. Contain snRNA’s that base pair.

Question 12

Where does the Exon Junction Complex bind?

Answer 12

Binds to mRNA at the place where the intron used to be and stays there

Question 13

RNA-RNA rearrangements in spliceosome - what rearranges and what’s needed to do it?

Answer 13

When U1 is replaced by U6, ATP is needed.

Question 14

What are snRNA’s/snRNP’s?

Answer 14

Small nuclear RNA, U1-U6. Complexed with protein subunits to form snRNP’s.

Question 15

Exon-marking proteins

Answer 15

Sit on exons while mRNA is being transcribed

Question 16

Poly-A Binding Proteins

Answer 16

Sit at 3’ end, help with poly-A tail

Question 17

What do 3’ end processing proteins do and when? Where are they before that?

Answer 17

Sit at RNA pol tail, then cleave at 3’ end once polyadenylation/cleavage signals happen

Question 18

What happens when RNA pol dissociates?

Answer 18

Dephosphorylated by phosphotases, then can go do more transcription

Question 19

polycistronic

Answer 19

Encodes more than one gene

Question 20

What is different about prokaryotic mRNA compared to eukaryotic?

Answer 20

polycistronic, no exons, small noncoding sequences in the middle, no cap or AAA tail

Question 21

Eukaryotic mRNA (compared to prok)

Answer 21

5’ cap > 5’ untranslated region > coding sequence > 3’ UTR > poly-A tail

Question 22

UTR

Answer 22

Untranslated region in eukaryotic mRNA. This is how ribosomes recognize it

Question 23

5’ cap structure

Answer 23

5’-5’ triphosphate bridge, then 7-methylguanosine attached to its 2’ carbon. Bound by cap-binding complex.

Question 24

Cleavage factor

Answer 24

protein factors that cleave mRNA at the 3’ end when it’s done transcribing

Question 25

Polyadenylation factor

Answer 25

Help add poly-A tail

Question 26

Cleavage/polyadenylation factor similarities

Answer 26

Proteins that bind to signals coded in DNA, bind to RNA sequences as soon as RNA pol makes them.

Question 27

Poly-A polymerase

Answer 27

Jumps on and makes poly-A tail when polyadenylation factors bind to RNA

Question 28

Poly-A binding protein

Answer 28

Binds to poly-A tail to show that it's ready to export. Lots of them bind, it's not just one across the whole thing

Question 29

Where do cleavage/polyadenylation factors start?

Answer 29

RNA pol c-terminus tail

Question 30

mRNA as it goes through the nucleus

Answer 30

Still has exon-marking proteins, exon junction complex, a nuclear export receptor, poly-A binding proteins, cap binding complex and 5’ cap. Some proteins leave as it goes through

Question 31

mRNA right after it exits nuclear pore

Answer 31

Initiation factors for protein synth bind to it (elF4G, elF4E), then nonsense-mediated decay, then translation. Nuclear-specific proteins leave.

Question 32

When does pol tail phosphorylation happen and why is it important?

Answer 32

Happens gradually during transcription initiation. Allows new proteins to bind to the tail.

Question 33

What distinguishes mRNA from other RNA molecules?

Answer 33

5' cap

Question 34

What letter sequence is at the 3' splice site?

Answer 34

AG (GU at 5')

Question 35

How do snRNP's connect to intron splice sites?

Answer 35

base-pairing

Question 36

What's the first phosphoryl-transferase reaction in splicing?

Answer 36

U6 displaces U1, letting active site catalyze it. Doesn't need ATP

Question 37

What fidelity mechanisms increase splicing accuracy?

Answer 37

1. Splicing happens during transcription (snRNP's only have one site to bind to at a time) 2. Exon definition: SR ('serine/arginine') proteins bind to

Question 38

Why are SR proteins called that?

Answer 38

They have lots of serine / arginine

Question 39

What do hnRNP proteins do?

Answer 39

Bind to introns to signal mRNA hasn't been fully processed

Question 40

What do SR proteins do?

Answer 40

Attach to newly made mRNA to stop it from binding to DNA strand