Lecture 4 - Exam 2

Question 1

In eukaryotes, pre-mRNAs are modified before export from the nucleus. What are some of these modifications? What coordinates these processes?

Answer 1

5’ Capping and Polyadenylation. These reactions are coupled to transcription.
The C-terminal domain (CTD) of RNA polymerase II coordinates these processes by serving as a binding site for the enzyme complexes involved in these processes.

Question 2

Describe 5’ Capping.

Answer 2

The 5’ end of the transcript is modified by enzymes interacting with the phosphorylated CTD following transcription of ~20-30 nukes.

Question 3

In 5’ capping, the enzymes add..?

Answer 3

The enzymes add a 7-methylguanosine cap.

Question 4

The 5’ cap does what to the RNA and ribosome?

Answer 4

The 5’ cap stabilizes the RNA and aligned it on the ribosome during translation.

Question 5

The 5’ cap is formed by…?

Answer 5

The 5’ cap is formed by the addition of a guanosine triphosphate (GTP) in reverse orientation to the 5’ end of the mRNA, forming a 5’ to 5’ linkages.

Question 6

At the 3’ end of the pre-mRNA, what happens?

Answer 6

At the 3’ end, a poly-A tail is added by polyadenylation.

Question 7

What are the signals for polyadenylation?

Answer 7

Signals for polyadenylation are the hexanucleotide AAUAAA, and a GU-rich downstream element.

Question 8

What does the recognition of the polyadenylation signal lead to?

Answer 8

Recognition of the polyadenylation signal leads to termination of transcription, cleavage, and polyadenylation of the mRNA.

Question 9

Poly-A polymerase then adds…?

Answer 9

About 200 adenines to form the poly-A tail.

Question 10

What is removed from pre-mRNA by splicing?

Answer 10

Introns (noncoding sequences).

Question 11

In mammals, most genes contain ________ introns.

Answer 11

Multiple.

Question 12

Splicing proceeds in two steps:

Answer 12

1. Cleavage at the 5’ splice site (SS) and joining of the 5’ end of the intron to adenine within the intron (branch point). The intron forms a loop.
2. Cleavage at the 3’ SS and simultaneous ligations of the exons excises the intron loop.

Question 13

What is ligation?

Answer 13

The joining of two DNA strands or other molecules by a phosphate ester linkage.

Question 14

Splicing takes place in large complexes, called _________, which have…?

Answer 14

Spliceosomes.
Have five types of small nuclear RNAs (snRNAs) coupled with proteins – U1, U2, U4, U5, and U6.

Question 15

The U proteins are complexed with small nuclear RNAs that recognize…?

Answer 15

Consensus sequences at the branch and splice sites, and also catalyze the splicing reaction.

Question 16

Describe the assembly of the spliceosome.

Answer 16

1) U1 SnRNP binds to the 5’ splice site of pre-mRNA.
2) U2 snRNP binds to the branch point by similar complimentary pairing between branchpoint DNA and U2.
3) Preformed U4/U6 and U5 snRNPs join the complex.
The complex rearranges and the rxn is catalyzed by U2, U5, and U6.

Question 17

Mutations in splicing sites can alter….?

Answer 17

The ultimate expression of a particular gene.

Question 18

What is one way that different proteins can be made?

Answer 18

Different proteins can be made by splicing together different exon combinations!

Question 19

What is SXL?

Answer 19

A repressor that prevents U2AF from binding a specific splice site, but there can be activators that recruit the spliceosome to sites they normally would not see!!!

Question 20

How can you figure out the total number of different mRNAs from a gene?

Answer 20

Alternative splicing :
(# of alternative exons in Exon) x (# of alternative exons in Exon)…..

Question 21

Describe mRNA degradation.

Answer 21

Degradation of mRNAs is usually initiated by shortening the poly-A tail (deadenylation).
This is followed either by removal of the 5’ cap and degradation from the 5’ end (5’ to 3’ degradation) or by degradation from the 3’ end (3’ to 5’ degradation).

Question 22

Every somatic cell contains the __________.

Answer 22

Complete genome

Question 23

Unused genes retain the potential for ____?

Answer 23

Expression

Question 24

How much of the genome is expressed in each cell?

Answer 24

Small percentage.