Protein Folding and Misfolding

Question 1

In what compartments of the cell does protein folding occur?

Answer 1

*Cytoplasm *ER Mitochondria Chloroplasts Peroxisomes Others

Question 2

Where does protein synthesis occur?

Answer 2

Ribosomes

Question 3

What are types of covalent modifications of proteins?

Answer 3

Glycosylation

Phosphorylation

Acetylation

Question 4

What end of the polypeptide chain is synthesized first?

Answer 4

N terminus

Question 5

The native conformation of a protein is its ______ energy state

Answer 5

lowest

Question 6

What do chaperones do?

Answer 6

Prevent inappropriate contacts during protein folding. e.g. protecting hydrophobic regions

Question 7

How do chaperones speed up folding?

Answer 7

By restricting the folding pathway so the number of possible intermediate states is limited

Question 8

Do chaperones change the thermodynamics of protein folding?

Answer 8

No!

Question 9

What are three common protein families of chaperones?

Answer 9

*Hsp 70 *Hsp 60 (chaperonins) Hsp 90 * = most common

Question 10

How were chaperones first discovered?

Answer 10

heat shock experiments

Question 11

Do chaperones use ATP to fold the protein?

Answer 11

Yes

Question 12

What causes the clamp of the hsp to close? What does this facilitate? What follows?

Answer 12

ATP hydrolysis brings the relevant pieces of the protein together

Then ADP is exchanged for ATP (?)

Question 13

What is Hsp60 responsible for?

Answer 13

Folding OTC (responsible for breaking down urea) within the mitochondrial membrane

Question 14

What are the two subunits of Hsp60? Which one is the cap?

Answer 14

GroES and GroEL GroES is the cap

Question 15

Can folded proteins enter organelles?

Answer 15

No! Must enter in the unfolded state through protein-conducting pores

Question 16

What is BiP?

Answer 16

An important Hsp70 chaperone in the ER

Question 17

What does BiP do?

Answer 17

binds to hydrophobic regions of translocating proteins in the ER

Question 18

Are unfolded proteins dangerous?

Answer 18

Yes when they accumulate they can stick together and cause problems

Question 19

What is the UPR? Where does it occur?

Answer 19

Unfolded protein response that occurs in the lumen of the ER

Question 20

What role does BiP play in the UPR?

Answer 20

BiP is upregulated/increased expression to take care of the accumulation of unfolded proteins in the ER

BiP attaches to the unfolded proteins which is sensed by the cell causing a protein kinase, PERK to increase gene expression of chaperone-coding genes

PERK also reduces the number of proteins entering the ER until the ER can catch up

Question 22

Where are misfolded proteins degraded?

Answer 22

The proteasome

Question 23

What cell marker/signal attaches to proteins to tell the proteasome to degrade it?

Answer 23

Ubiquitin (forms a polyubiquitin chain)

Question 24

What are the 2 subunits of the proteasome? Which one is the “core” which is the cap?

Answer 24

Alpha and Beta

beta = core

alpha = cap

Question 25

Which subunit of the proteasome has proteolytic activity?

Answer 25

Beta subunit

Question 26

What is the function of the alpha cap of the proteasome?

Answer 26

19s cap is the “unfoldase” so that the chain can reach the beta subunit for proteolysis

Question 27

How is ubiquitin attached?

Answer 27

E1 ubiquiting activating enzyme (+ATP)

->

E2/E3 complex: ubiquitin ligase

Question 28

Once one ubiquitin is attached, what adds additional ub to create the poly-ubiquitin chain?

Answer 28

E2/E3 but E1 must be present

Question 29

What bond is between each ubiquitin in a poly-ubiquitin chain? What is it composed of?

Answer 29

Isopeptide bond

Protein substrate C terminus - Glycine - Lysine 48 - Glycine - Lysine 48, etc.

Question 30

Can misfolded proteins in the ER be retrotranslocated to the cytoplasm to be digested by the proteasome?

Answer 30

Yes