Lecture 6: Protein folding 1

Question 1

What are the non-covalent interactions that govern the protein folding stability?

Answer 1

Van der waals
hydrogen bonds
electrostatic forces

Question 2

Which interaction is the major factor in the folding and stability of proteins?

Answer 2

hydrophobic interactions

Question 3

What are the 4 determinants of protein folding?

Answer 3

1. secondary structures
2. hierarchical folding
3. hydrophobic effect
4. context dependent

Question 4

What kids of interactions is the alpha helix stabilized by?

Answer 4

hydrogen bonds between the NH and CO groups

Question 5

What is the most energetically favorable screw? (right handed or left handed?)

Answer 5

right handed

Question 6

Describe the amino acid residues in an alpha helix

Answer 6

rise of 1.5 A along the helix axis

100 degrees of rotation

3.6 aa residue per turn of helix

Question 7

Describe B sheets

Answer 7

distance between aa is 3.5 A

can be anti-parallel or parallel

Question 8

Describe how a polypeptide chain is able to turn or make loops

Answer 8

1. reverse turns
2. Beta turns
3. Hairpin turn

loops are often rigid and participate in protein protein interactions and other molecules

Question 9

Describe a superhelix

Answer 9

two helices that are held together by weak interactions including ionic and van der waals forces

serve a structural role and is involved in biological function

Question 10

Describe the events that take place in the folding funnel

Answer 10

1. secondary structure formed rapidly
2. cooperative aggregation forms domains
3. assembled domains form
4. adjustment of conformation
5. a more rigid structure is obtained

Question 11

Which protein exists in two conformations that are in equilibrium? both an alpha and a beta sheet

Answer 11

Lymphotactin

Question 12

Describe a molten globule state

Answer 12

intermediate state between the native and the fully unfolded states of a protein; so something that is partially unfolded

tertiary is absent because of the tight packing of the side chains

radius is slightly larger than the native state with a loosely packed hydrophobic core

stabilized by a nonspecific hydrophobic interactions

Question 13

Describe the “context dependent” portion of the 4 types of the protein formation

Answer 13

sequences are able to adopt other conformations, depending on what the cell needs or what it is “instructed” or thermodynamically expected to do; it just depends on the context (sequence VDLLKN can be seen in alpha and beta conformations)

Question 14

Describe bovine insulin

Answer 14

2 chains that are linked by disulfide bonds

extracellular have several SS bonds and intracellular usually lack