Lecture 7: Protein folding 2

Question 1

Describe the tertiary structure of a protein

Answer 1

Disulfide bonds are formed between amino acid residues that are far apart allowing for a more compact structure

Question 2

Describe the protein disulfide isomerase

Answer 2

rearranges the sulfide bonds if they are incorrectly paired; allows for correct protein folding

Question 3

Describe bovine insulin (he has had this on two lectures no so that is why this is here)

Answer 3

2 chainz

has 2 interchain disulfide bonds with an intrachain disulfide bond

Question 4

Describe the major difference between extracellular and intracellular proteins

Answer 4

extracellular have several S-S bonds and intracellular lack S-S bonds

Question 5

Describe the quaternary structure

Answer 5

spatial arrangement of subunits and their interactions

Question 6

Who are the two accessory proteins that are involved in protein folding?

Answer 6

PDI and PPI

Question 7

Describe HSP70

Answer 7

ATP driven

helps to reverse misfolds and can unfold or refold trafficked proteins

Question 8

List the molecular chaperones

Answer 8

HSP 70 
chaperonins 
HSP 90 
nucleoplasmins 
small HSP

Question 9

What are the conditions that are able to denature proteins

Answer 9

heat
pH
agitation

Question 10

What are the chemicals that are able to denature proteins?

Answer 10

Detergents
Chaotropic agens
Organic solvents (TCA)

Question 11

List the methods of analysis in protein denaturation

Answer 11

1. turbidity
2. circular dichroism
3. UV absorption
4. Fluorescence
5. Biological activity

Question 12

What does a molecular chaperone do?

Answer 12

bind to unfolded and partially folded polypeptide chains

prevent unwanted bonding between hydrophobic segments

allow refolding to native conformations

Question 13

What are the two classes of chaperones?

Answer 13

1. heat shock proteins (70 and 90)

2. chaperonins (protein folding container- HSP60 and HSP 10)

Question 14

What does the HSP 90 family do?

Answer 14

integrates signaling functions and acts at a late stage of folding substrates

Question 15

Describe the mechanism of the chaperonins

Answer 15

1. Unfolded polypeptide enters the cylinder
2. cap attaches and the cylinder changes shape to create a hydrophilic environment for the folding of the polypeptide
3. cap comes off and the properly folded protein is released

Question 16

Describe the proteasome

Answer 16

protein degradation that digests ubiquinated proteins

Question 17

Describe in detail the 26S proteasome

Answer 17

There are two 19S regulatory subunits that sandwich a 20S catalytic core.

19S: recognized ubiquinated proteins and cleaves off the ubiquitin with isopeptidase then send the protein to the core

20S: 28 subunits, sealed barrel

Question 18

Which of the following interactions determines protein folding ability?

a. covalent bonds between atoms
b. double bonds
c. hydrogen bonds
d. disulfide bridge
e. high energy phosphate bond

Answer 18

C- hydrogen bonds

Question 19

Protease enzyme hydrolyzes the peptide bond of a protein. How might a protease bind a target protein so that vulnerable peptide bond will be exposed?

a. protease bond to target protein via forming H bonds
b. Protease and target protein form extended parallel beta strand without requiring H bonds
c. protease and target protein form an alpha helix structure to expose a peptide bond
d. protease enzyme work only in hydrophobic conditions

Answer 19

B-protease and target protein form extended parallel beta strand without requiring H bonds

Question 20

Many of the loops in proteins are exposed to the environment. Why might this be the case?

Answer 20

Exposed loops should be hydrophilic due to aqueous environment