1.7: Regulation of the Proteome

Question 1

what do prokaryotes and eukaryotes use translational control mechanisms to regulate protein expression in response to

Answer 1

stressful situations

Question 2

explain the method of translational regulation in prokaryotes

Answer 2

mRNAs have 6 nucleotide shine dalgarno (sd) sequences upstream of the AUG start codon (it’s inside the 5’ UTR) - it correctly positions AUG in the ribosome and provides translational control mechanisms

Question 3

state and define the 4 mechanisms of translational regulation in prokaryotes

Answer 3

1: a specific rna binding protein blocks access to the sd sequence = no translation = no protein
2: temperature regulated rna structures – usually stem-loop structure to block access to sd and increased temperature opens it up
3: riboswitch (eg s-adenosyl methionine): small molecule causes structural rearrangement of rna blocking sd
4: antisense rna (eg iron storage proteins): antisense rna produced elsewhere in the genome base pairs w mRNA and blocks sd

Question 4

what process are sd sequences needed for

Answer 4

translation in prokaryotes

Question 5

do prokaryotes and eukaryotes have SIMILAR translational regulation mechs

Answer 5

yes

Question 6

what does aconitase do

Answer 6

translational repressors can bind near initiator aug and inhibit translation in eukaryotes

ferritin binds iron and releases it in a controlled manner - ferritin isn’t needed when iron is low so aconitase binds to the ferritin rna near the start site and blocks translation - when iron is in excess, aconitase binds iron, there is a conformatonal change in aconitase, and ferritin rna is released

Question 7

what other receptor does aconitase regulate, apart from ferritin

Answer 7

transferrin

Question 8

in eukaryotes, what interferes w 5’ cap and 3’ poly a tail interactions that are required for efficient translation

Answer 8

repressor proteins

Question 9

t/f can miRNAs regulate EUKARYOTIC translation

Answer 9

true

Question 10

describe the regulation of eukaryotic initiation factors (long answer)

Answer 10

• eIF2 (very important) forms a complex w GTP and recruits the initiator tRNA (methionyl) to the small ribosomal subunit <– binds the 5’ end of mRNA and scans for the first AUG
• when found first AUG, eIF2 hydrolyzes gtp to gdp
• gtp hydrolysis causes a conformational change in eIF2
• eIF2 bound to gdp is released and is inactive
• reactivation of eIF2 requires eIF2B which is a guanine nucleotide exchange factor (GEF) - means it causes the exchange of gdp for gtp

Question 11

which initiation factor is crucial in translation initiation

Answer 11

eIF2

Question 12

does gef cause phosphorylation in eukaryotic translation initiation

Answer 12

no! it is an exchange of gdp to gtp

Question 13

what are reactivation of eIF2 require in eukaryotic translation initiation

Answer 13

eIF2b

Question 14

what modification regulated eIF2 REACTIVATION

Answer 14

phosphorylation - phosphorylated eIF2 sequesters eIF2B as an inactive complex

Question 15

which is more abundant in cells eIF2 or eIF2B

Answer 15

eIF2

Question 16

are all mRNAs equally affected by eIF2 phosphorylation and why

Answer 16

no, there is a different mechanism for a couple of important proteins

Question 17

what happens when eIF2B is all sequestered by eIF2

Answer 17

translation is dramatically reduced

Question 18

can you reverse the inactivation of eIF2B

Answer 18

yes, just dephosphorylate it

Question 19

list the steps that protein must undergo to become functional

Answer 19

1. proteins must fold properly to adopt their 3d structure
2. proteins are covalently modified w chemical groups (eg sugars, phosphate)
3. proteins interact w other proteins and small molecules (cofactors)
   *typical order but doesn’t have to be like this

Question 20

hydrophobic aa are buried in the ________________

Answer 20

interior core

Question 21

t/f for some proteins, folding begins as they emerge from ribosomes but some are completely folded after synthesis

Answer 21

t

Question 22

most proteins require a special class of proteins called? for proper folding

Answer 22

chaperones

Question 23

why are many chaperones called heat-shock proteins (hsp)

Answer 23

they are synthesized to high amounts by cells at elevated temperatures

Question 24

will you only see heat shock proteins at high temp

Answer 24

no

Question 25

what hsps make up chaperonin

Answer 25

hsp70 and hsp60

Question 26

list 3 commonalities between hsp70 and hsp60

Answer 26

both assist protein folding, interact w exposed hydrophobic residues of misfolded proteins and both use energy from atp hydrolysis to promote proper folding

Question 27

can both hsp complexes function at the same time

Answer 27

no -

Question 28

why do chaperone proteins function like an isolation chamber

Answer 28

they need atp to get the GroES cap, keep the protein in there to give it time to fold, use atp to take the cap out

Question 29

improperly folded proteins can ________ and become toxic to cells

Answer 29

aggregate

Question 30

what enzyme monitors improperly folded proteins and how does it work

Answer 30

proteasome, it degrades proteins by using exposed hydrophobic residues to mark proteins for degradation

Question 31

what do chaperons and proteasomes compete for

Answer 31

misfolded proteins

Question 32

the _______ time to fold, the higher the chance of being degraded

Answer 32

longer

Question 33

How many of the following statements are correct?
i. Treatment of cells with HSP inhibitors should result in a decrease in protein
degradation.
ii. Treatment of cells with an iron chelator (which removes excess cellular iron)
should result in a decrease in ferritin transcription.
iii. Treatment of cells with a miRNA complementary to eIF2B should result in
an increase in transcription.
a. 0
b. 1
c. 2
d. 3

Answer 33

a. 0
i is wrong is it should increase protein degradation
ii is wrong bc it decreases ferritin translation, not transcription
iii is wrong bc it should lead to a decrease in translation