Transcription in Eukaryotes part 3

Question 1

When does the addition of the 5’ cap happen?

Answer 1

As soon as the first 20-30 nt have exited the RNA pol.

Question 2

What is the role of guanyl transferase

Answer 2

It converts and GTP into GMP, and then adds it to the rNDP at the 5’ end to make an unusual 5’-5’ linkage

Question 3

What enzyme adds a methyl group to position seven of the final guanine on a strand at the 5’ end?

Answer 3

ribonucleotide methyl transferase

Question 4

What are three functions of the 5’ cap?

Answer 4

1. distinguish transcripts made by RNA pol. II
2. protect mRNA from degradation by exoribonucleases
3. facilitate interaction with the Cap Binding complex

Question 5

Define the first transesterfication reaction in the context of splicing

Answer 5

A special “A” in a sequence motif in an intron attacks the phospodiester bond present between G/G sequence present at the beginning of the intron sequence, cutting it.

Question 6

Define the second transesterfication reaction in the context of splicing

Answer 6

The free -OH group on the first exon attacks the phosphodiester bond present between the G/G at the end of the intron sequence, fully separating the intron from the second exon.

Question 7

In the context of the spliceosome, what is responsible for cleaving introns?

Answer 7

small nuclear RNA (snRNA) with catalytic activity, linked to a complex of proteins called small nuclear ribonucleoprotein (snRNP). Often have names such as U2, U4, U5, etc.

Question 8

What two proteins attract U2 snRNP to the 3’ splice site?

Answer 8

BBP and U2AF

Question 9

What three snRNPs form the “triple snRNP?

Answer 9

U4, U5, U6

Question 10

What proteins put the two exons together at the end of splicing?

Answer 10

the exon junction complex

Question 11

What is the role of RNA helicase in splicing

Answer 11

It modifies the RNA-RNA hybrids in such a way that the catalytic centers are optimally oriented

Question 12

What snRNP replaces for U1?

Answer 12

U6

Question 13

What snRNP helps facilitate joining of the exons together?

Answer 13

U5

Question 14

What is the exon definition hypothesis?

Answer 14

predicts that the relative constancy of the exon size in eukaryotes (100-200nt) is used to facilitate formation of splice-site machinery

Question 15

Define hnRNPs

Answer 15

1. heterogenous nuclear ribonucleoprotein
2. preferentially bind to cryptic bind sites in introns to mask them
3. condense large introns to help facilitate their excision

Question 16

Define SR proteins

Answer 16

Proteins high in serine and arginine that bind to exon splice sites to help facilitate attraction of snRNPs.

Question 17

Define minor form of spliceosome

Answer 17

just recognizes different consensus sequecne

Question 18

Define trans splicing

Answer 18

a single 5’ exon is spliced onto the 5’ end of many different mRNAs

Question 19

Phosphorylation of the CTD allows the recruitment of what two factors?

Answer 19

CPSF (cleavage and polyadenylation specificity factor) andCstF (cleavage stimulation factor F)

Question 20

What is PAP and what does it do?

Answer 20

Poly A polymerase. It adds close to 200 A’s to the 3’ end of the mRNA.

Question 21

What is the role of the poly-A binding protein?

Answer 21

Bind to the poly A region at the end of the mRNA. They are responsible for preventing degradation from the 3’ direction

Question 22

What six factors must be present in order for mRNA to be “acceptable” to leave the nucleus?

Answer 22

1. the cap binding complex
2. SR proteins
3. PABP
4. hnRNPs
5. Export factors
6. Exon Junction complex

Question 23

The CTD is made of a heptamter that is repeated 52 times in humans. What is the sequence of the heptameter?

Answer 23

Tyr-Ser-Pro-Thr-Ser-Pro-Ser

Question 24

What occurs in the individual heptameters of the CTD during the transition from initiation to elongation?

Answer 24

Serine residues 2 and 5 are phosphorylated