eukaryotic genes and gene expression 2

Question 1

3 RNA process mechanisms

all occur while RNA pol 2 is actively elongating the RNA chain

Answer 1

capping
polyadenylation
splicing

Question 2

Capping what is used and what does it do

Answer 2

7 methylguanosine

protects mRNA from degradation and increases translation efficiency

Question 3

capping what happens

Answer 3

5’ end capped
terminal Phosphate of 5’ (usually on A or G) is cleaved and 5’ terminal G added in the reverse orientation
the G is connected to 5’ end using 5’ to 5’ triphosphate bridge
G is then methylated at the 7th position to get m7G cap

Question 4

polyadenylation what is the signal and what happens

Answer 4

polyadenylation signal (aauaaa)
this is recognised and mRNA cleaved 11-30 nb downstream
multiple A are added to the end 
importance is for mRNA stability and efficiency of translation

Question 5

splicing

Answer 5

introns recognised by splicing machinery (sliceosome)
joining of exon
forms mRNA which contains all the exon

Question 6

splicing processes 1

what do introns have

Answer 6

they have conserved 5’donor site, 3’ acceptor site and interval branch site
U1 binds to donor site (AG/GU)
U2 binds to branch sequence (CUR(A)YY)

Question 7

slicing processes
what is a spliceosome
what happens to branch point

Answer 7

U4, U5, U6 come in (spliceosome)

branch point brought closer to donor site

Question 8

splicing processes 3

what happens to introns and exons

Answer 8

introns are excised as a lariet

exon are ligated together

Question 9

alternative splicing what is it and what does it do

and problems

Answer 9

greatly increases protein diversity
choice of exons used regulated again by tissue specific or developmental stage specific manner
problems are commonly atypical cystic fibrosis and retinitis pigmeatosa

Question 10

negative control of alternative RNA splicing

and what introns cause

Answer 10

repressor protein may bind to the pre mRNA
this blocks access of the splicing machinery
intron will be retained
introns may contain stop codon and cause frame shift causing degradation

Question 11

positive control of alternative RNA splicing

Answer 11

activator proteins may bind to pre mRNA
recruit splicing machinery
introns will be spliced out
binding sites for activator proteins can be remote from the splice site (splicing enhancer)

Question 12

what does mRNA contain

Answer 12

a cap made from mod of G nucleotide and a poly A tail

untranslatedregion UTRs at 5’ and 3’ end

Question 13

open reading frame ORF,

Answer 13

containing triplet code used for assembly of polypeptide

Question 14

how does the ORF begin and end

Answer 14

usually starts with AUG
ends with either UAG
UAA
UGA

Question 15

elF

Answer 15

eukaryotic initiation factor

Question 16

PABP

Answer 16

poly a binding protein

Question 17

what is requires for transcriptional initiation

Answer 17

PABP
elF4G
elF4E

Question 18

formation of the transcriptional initiation complex

Answer 18

requires poly a tail and a cap

Question 19

3 steps of translation

Answer 19

initiation elFs
elongation eEFs
termination eEFs

Question 20

initiation elFs what happens

Answer 20

scanning of the small ribosomal subunit from cap to initiation codon
joining of large ribosomal subunit to make whole 80s ribosome

Question 21

elongation eEFs

Answer 21

ensures correct AA is added in correct protein chain

Question 22

termination eEFs

Answer 22

releases a complete polypeptide and recycle of ribosomal subunits

Question 23

what is the limiting step of translation

Answer 23

initiation

Question 24

transcriptional control mechanisms

Answer 24

global control

specific control

Question 25

global control

Answer 25

changes in TF and Ribosomal activity
kinase signalling via p38 MAPK
cleavage of initiation factor during viral infection and apoptosis

Question 26

specific control

Answer 26

signals in mRNA define the Efficiency of their translation
cap independent translation
multiple product from same mRNA

Question 27

what do viruses do to elF4G

Answer 27

they cleave it disabaling translation of host cell mRNA

Question 28

how does a virus initiate translation

Answer 28

IRES

internal ribosomal entry site

Question 29

alternative initiation codon usage (leaky scanning)

Answer 29

isoforms with different n-termini can be produced by leaky scanning
from alternative AUG and near cognate initiation codons

Question 30

mRNA degradation in 2 phases

Answer 30

deadenylation and 3’-5’ decay

decapping and 5’-3’ decay

Question 31

AREs what are they

Answer 31

AU rich elements

more vulnerable to degradation

Question 32

AREs ate typified by

and they can control

Answer 32

single or tandem repeatsof AUUUA pentamer

they can control transcriptional efficiancy as well as deadenylation and decapping

Question 33

NMD

Answer 33

nonsense mediated mRNA decay

Question 34

NMD is what

Answer 34

a survalence mechanism to detect and destroy aberrupt mRNA containing premature terminal codons PTCs before multiple rounds of translation

Question 35

what does NMD prevent

Answer 35

accumalation of proteins with C-terminal trucations which create incatve or even dominant negative versions

Question 36

splicing and the exon junction complex what is it

Answer 36

protein complex which is deposeted during splicing

20-24 nucleotide upstream

Question 37

NMD has a recruitment of what

Answer 37

surf complex between pioneer ribosome and EJC

Question 38

NMD has rapid degradation via

Answer 38

deadenylation
decapping
endonuclease attack near the ptc

Question 39

MircoRNA what is it

Answer 39

small regulatory RNA
targeted to 3’ UTRs
if imperfect match downregulate translation
If perfect, mRNA cleaved