Protein Folding I and II

Question 1

What type of interaction is a major factor in the folding stability of proteins?

Answer 1

Hydrophobic

Question 2

H bonds are stronger or weaker than covalent bonds?

Answer 2

Weaker, but longer than covalent

Question 3

Why are hydrogen bonds important for folding stabiltiy rather than covalent or disulfide bridges?

Answer 3

Hydrogen bonds provides stability and flexibility. Covalent bonds are too strong to bend as well as di sulfide bridges, they would break.

Question 4

What is the hydrophobic effect?

Answer 4

Hydrophobic amino acids will be in the sequence will be found in the center of the structure to escape the hydrophillic environment.

Question 5

Which secondary structure is more flexible?

Answer 5

Alpha helices are more flexible than beta sheets. They are enriched with hydrogen bonds which give it flexiblity and save space. Beta sheets are less flexible and mostly a parallel structure. Both provide stability.

Question 6

What bonds stabilize alpha helices?

Answer 6

Hydrogen bonds between the NH and C=O groups

Question 7

What form are alpha helices in proteins mostly found in?

Answer 7

Right handed more energetically favorable

Question 8

Describe the superhelix alpha helical coiled coil.

Answer 8

Provides proteins with long fibers and serves a structural role such as alpha keratin, collagen cytoskeleton, or muscle proteins. Also involved in biological functions such as gene regulation. **Region of 300 aa with heptad repeats

Question 9

Describe the Folding Funnel.

Answer 9

Rapid formation of secondary structures occurs with high energy. Then formation of domains through cooperative aggregation occurs. Next formation of assembled domains (molten globule). Then adjustment of conformation occurs and finally left with a rigid structure

Question 10

What is the repeating motif in calmodulin?

Answer 10

Calcium binding sites

Question 11

What is calmodulin?

Answer 11

Calcium sensor with four similar subunits in one polypeptide chain.

Question 12

Context dependent folding??

Answer 12

??

Question 13

What is the molten globule state?

Answer 13

an intermediate conformational state between a native and unfolded protein.

Question 14

What are five characteristics of molten globule state?

Answer 14

1. Presence of native like content in secondary structure
2. Absence of specific tertiary structures due to compact AA
3. Compactness in shape of the protein radius is 10-30% large
4. Presence of loosely packed hydrophobic core exposure to the hydrophillic solvent
5. Not specific and occurs in early stages of folding

Question 15

What stabilizes the molten globule state?

Answer 15

Nonspecific hydrophobic interactions

Question 16

What is the Chou-Fasman method?

Answer 16

A way to predict the secondary structures in proteins.

F= aa in alpha helix/ all aa

P= f/ all aa

P= propensity/ natural inclination

Question 17

What is a PDI?

Answer 17

Protein disulfide isomerase, which re arranges the polypeptide’s non native disulfide bonds

Question 18

What chaperones are responsible for reversing misfolds, newly synthesized proteins, unfolding and refolding trafficked proteins?

Answer 18

HSP 70 and 40

Question 19

Can a protien be unfolded or folded half way?

Answer 19

No, it is all or none

Question 20

What conditions can denature proteins?

Answer 20

• Heat
• pH
• agitation
• Detergents (SDS)
• Chaotropic agents such as urea and guanidine hydrochloride
• Organic solvents such as TCA

Question 21

What is circular dichroism used for?

Answer 21

To study the conformation of proteins in a solution. It uses absorption of right and left hand circularly polarized light from the molecular asymmetry with a chromophore group.

Question 22

What are the two major classes of chaperones?

Answer 22

1. Heat shock proteins:
   
   1. HSP70 which directs substrates for unfolding refolding disaggregation or degradation
   2. Hsp90 which integrates signaling functions at late stage folding
2. Chaperonins: folding container
   
   1. Hsp60
   2. Hsp10

Question 23

Describe the mechanism for chaperonins.

Answer 23

An unfolded pp enters cylinder and a cap attaches causing cylinder to change shape and create a hydrophillic environment. This helps the protiein fold correctly and then the cap comes off and releases the protein.

Question 24

What is the proteasome?

Answer 24

Protein degradation machinery it digests ubiquinated proteins.

Isopeptidase, part of the 19s, cleaves of ubiquitin and directs the protein into the 20s catalytic core.