Lecture 7 - Protein Folding II

Question 1

How can we predict whether a sequence will be an α-helix, β-sheet, or reverse turn?

L7 S4

Answer 1

Propensity: the natural inclination of an AA residue to be found in a certain structure. Propensities were found by Chou and Fasman using X-ray crystallography

Question 2

What is the tertiary structure of a protein?

L7 S5

Answer 2

Arrangement of secondary structures with regards to one another and disulfide bonds.

Question 3

What amino acid is responsible for disulfide bridges?

L7 S7

Answer 3

Cysteine

Question 4

Differentiate between interchain disulfide bonds and intrachain disulfide bonds.

L7 S7

Answer 4

Interchain:
-between different polypeptides

Intrachain:
-within the same polypeptide

Question 5

What is the quaternary structure of a protein?

L7 S9

Answer 5

Arrangement of different subunits (polypeptides) to form a final, functional protein.

Not all proteins have a quaternary structure.

Question 6

What are the main different types of accessory proteins used in protein folding and what are their functions?

L7 S11

Answer 6

Protein disulfide isomerases (PDI):
-rearranges disulfide bonds

Peptidyl prolly cis-trans isomerases:
-switches AAs between cis- and trans- isomers

Chaperones:

• help to fold new proteins
• help to unfold and refold misfolded proteins
• unfolds and folds trafficked proteins

Question 7

What factors can cause a protein to become denatured?

L7 S12

Answer 7

• heat
• pH
• agitation
• detergents (SDS)
• chaotropic agents (urea)
• organic solvents (TCA/trichloroacetic acid)

Question 8

What methods can be used to assess if proteins are denatured?

L7 S13

Answer 8

• turbidity
• circular dichroism
• UV absorption
• fluorescence
• biological activity

Question 9

What are the two classes of chaperons?

L7 S17

Answer 9

Heat shock proteins (Hsp)

• Hsp70 family: directs substrates for unfolding, disaggregation, refolding, or degradation
• Hsp90 family: signaling function/late stage folding

Chaperoning (protein folding containers):

• Hsp60 proteins
• Hsp10 proteins

Question 10

What is a proteasome and what signal directs a protein to a proteasome?

L7 S21

Answer 10

Protein complex that breaks down other proteins into small fragments.
Ubiquinated proteins are directed to proteasomes.