Eukaryotic gene expression

Question 1

How many RNA pols in eukaryotic?

Answer 1

3.
I
II
III

Question 2

What does RNA pol I transcribe for?

Answer 2

rRNA

Question 3

What does RNA pol II transcribe for?

Answer 3

mRNA (via hnRNA)

Question 4

What does RNA pol III transcribe for?

Answer 4

tRNA (and other small RNAs)

Question 5

What are the general factors that interact with RNA pol II?

Answer 5

Form basal transcriptional apparatus along with RNA pol II.

Question 6

What are the upstream factors that interact with RNA pol II?

Answer 6

DNA-binding factors recognising short consensus sequences, not regulated and required for adequate transcription.

Question 7

What are the inducible factors that interact with RNA pol II?

Answer 7

as upstram factors, but regulated to provide control of gene expression in eg stimulus specific manner.

Question 8

What are the general factors known?

Answer 8

(TFII)D, A, B, F, E, H
combine with RNAPII to start basal transcription apparatus.

Question 9

What is used to recognise promoters?

Answer 9

TFIID = TBP + TAFs
= TATA-binding protein + TBP-associated factors
Positions RNAPII in right place.
Only general initiation factor which binds promoters in sequence specific manner.
Binds to DNA in minor groove.
Bends DNA by 80 degrees.

Question 10

What happens to CTD of RNA pol II?

Answer 10

Reversibly phosphorylated, allowing promoter release and coordinating post-transcriptional events.

Question 11

What are cis-acting control elements (DNA)?

Answer 11

Promoters
Enhancers/repressors.

Question 12

What are trans-acting transcription factors (proteins)?

Answer 12

Consitutively expressed or induced.
2 domains - DNA binding and activation domains.

Question 13

Where do down mutations happen?

Answer 13

3 locations corresponding to 3 elements which make up promoter.
GC box -90
CAAT box -75
TATA box -30

Question 14

What is needed for transcription to be activated?

Answer 14

Particular combo of control elements can activate transcription only when the appropriate activator proteins are present (and potentially expressed).

Question 15

What do DNA binding domains do?

Answer 15

Recognise target sequences in enhancers or promoters.

Question 16

What do activation domains do?

Answer 16

Function to influence transcription by contacting basal apparatus.

Question 17

Where does the transcriptional co-activator bind?

Answer 17

Does not bind DNA itself, but bridges btwn activator and basal transcription apparatus.

Question 18

What controls gene expression?

Answer 18

Cis-acting (consesus) sequences and trans-acting (transcription) factors in combinational fshion.

Question 19

How do transcription factors uses 2 domains?

Answer 19

bind upstream of tsp, contacting basal transcriptional apparatus (via mediator) to increase transcriptional initiation.

Question 20

What is chromatin?

Answer 20

the material of which the chromosomes of organisms other than bacteria (i.e. eukaryotes) are composed, consisting of protein, RNA, and DNA.

Question 21

What is a nucleosome?

Answer 21

a structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled around a core of histones.

Question 22

What are the two types of nucleosome remodellers?

Answer 22

2 main classes:
ATP-dependent nucleosome remodellers.
Modifiers of histone acetylation

Question 23

What does acetylation/deacetylation?

Answer 23

HAT/HDAC; acetylation both alters nuclesomal structure and recruits bromodomain containing proteins

Question 24

What happens in pre-mRNA processing?

Answer 24

1. Transcription, 5’ capping (at 25-30 nt of elongation)
2. Cleavage at Poly(A) site
3. Polyadenylation
4. RNA splicing

Question 25

What bits are 100% conserved in exon-intron junctions?

Answer 25

GU
Branch point (A)

Question 26

What is lariat formation?

Answer 26

Lariat formation involves cleavage of the precursor at the 5’ splice site (5’ SS) and the formation of a 2’-5’ phosphodiester bond between the guanosine residue at the 5’ end of the intron and an adenosine within the intron. Intron AKA lariat separates and allows exons to join together.

Question 27

How many U-rich small nuclear RNAs (snRNAs) are involved in splicing.

Answer 27

5 U1,2,4,5,6

Question 28

WHat does the U2 RNA do?

Answer 28

Pairs in such away that the A of the branch sticks out, allowing it to take part in the first transesterification reaction.

Question 29

How does splicing of pre-MRNA occur?

Answer 29

snRNPs assemble on pre-mRNA to form a spliceosome.
1st U1, U2 bind.
then 4, 5 and 6 enter as a complex.
Spliceosome rearranges - release 1, 4 - transesterification occurs.
2nd rearrangement leads to 2nd transesterification to occur.
Excised intron and snRNPs dissociate.

Question 30

What do -ve factors do to U1 and U2?

Answer 30

Prevent binding or block spliceosome assembly after U1 or U2 binding

Question 31

What do +ve factors do?

Answer 31

Enhance spliceosome assembly at sites that are poorly recognised

Question 32

What needs to happen to CTD for initiation to occur?

Answer 32

Phosphorylation

Question 33

Do mRNA have diff half lives?

Answer 33

Yes diff stabilities.
short = regulatory proteins - AU rich in 3’-UTR (AUUUA)
long = structural proteins/ key metabolic enzymes

Question 34

What does 5’ cap do?

Answer 34

Aids mRNA nuclear export
Protects from 5’-3’ exonuclease degradation in cytoplasm.
Enhances translatability of transcript

Question 35

What does poly-A tail do?

Answer 35

Participates in termination of transcription.
Aids mRNA nuclear export
Protects from 5’-3’ exonuclease degradation in cytoplasm.
Enhances translatability of transcript

Question 36

Is mRNA exported?

Answer 36

Yes it is exported by mRNA exporter.
Leaves via pore of nucleus

Question 37

What can regulate mRNAs in cytoplasm?

Answer 37

Proteins that bind to it - regulates translation and degredation.