Lecture 6- Protein Folding I

Question 1

Describe the different types of non-covalent interactions:

Answer 1

VdW- charges (e-) fluctuate around an atom, forming temporary dipole moments
electrostatic- charges on one atom interact with charges on another, as described by Coulomb’s law
hydrogen bonding- partial charges from hydrogen interact with Nitrogen and Oxygen
short range repulsion-

Question 2

Protein folding is a highly (random/cooperative) process

Answer 2

cooperative

Question 3

Secondary structure plays an important part in the ____ of proteins.

Answer 3

compact folding

Question 4

The conformation of a protein is the result of specific _____.

Answer 4

AA sequences

Question 5

How does hydrophobicity act as a determinant of folding?

Answer 5

Hydrophobic AAs tend to “cluster together” in pockets of hydrophobicity (usually found within the plasma membrane)

Question 6

Draw/describe the steps of protein folding.

Answer 6

1) Secondary structure is rapidly achieved (high E* state)
2) Format’n of hydrophobic domains (cooperative) leading to “core protein”
3) Formation of a molten globule
4) Adjustment of structure to native, low E* structure

Question 7

The dynamic conformational state between native protein and full-unfolded protein

Answer 7

Molten globule

Question 8

Why is the concept of the “molten globule” important?

Answer 8

The molten globule exists as the protein tries to find a low E*, highly ordered, thermodynamically stable structure

Question 9

What two major types of interactions determine protein folding?

Answer 9

Non-covalent and hydrophobic interactions

Question 10

Describe the characteristics of the “molten globule”

Answer 10

1) Presence of some 2* “native structure” elements - the beginnings of final form are taking shape
2) No specific 3* structure - no packing of side chains
3) Compact into the overall shape of the protein, but radius is still 10-30% larger than final native protein’s radius
4) Loosely packed hydrophobic core

Question 11

Repeating secondary structure present in many proteins that exhibit similar f(x)s

Answer 11

Domain

Question 12

Structural charachteristics of a protein (ex: repeated alpha-helices)

Answer 12

motif

Question 13

A specific functional region of a protein

Answer 13

domain (ex: antigen binding domain on an anti-body)

Question 14

List the “non-covalent” interactions responsible for protein folding:

Answer 14

• van der Walls
• electrostatic interaction
• Hydrogen bonds
• short range repulsion