Lecture 6 - Protein Folding I

Question 1

What sort of interactions govern protein folding?

L6 S4

Answer 1

Non-covalent:

• Van der Waals
• hydrogen bonding
• electrostatic forces (ion pairing)

Hydrophobic:
-favor interacting with other hydrophobic groups and avoid interacting with water

Question 2

What is the hydrophobic effect?

L6 S9

Answer 2

Hydrophobic molecules will tend to associate/aggregate when in a polar environment.

Question 3

What is the structure of an α-helix?

L6 S12

Answer 3

Coiled structure stabilized by hydrogen bonds between amine and carboxyl group of every 4th AA residue

Each amino acid is 1.5 Å up from the other and is rotated 100 degrees.

Each full turn is 3.6 AA residues

Coil can be right handed (clockwise, more favored) or left handed (counter-clockwise, less favored)

Question 4

What is the structure of a β-sheet?

L6 S14

Answer 4

Interaction of two or more adjacent polypeptide chains called β-strands that can be parallel or anitparallel.

Distance between AA residues is 3.5 Å.

Stabilized by hydrogen bonding of amine and carboxyl groups of opposing strands

Question 5

What is the primary determining factor of a proteins folded/native conformation?

L6 S18;25

Answer 5

The protein will attempt to fold into the lowest energy state for the environment it is in.

Question 6

What is meant by “context dependent folding”?

L6 S20

Answer 6

Depending on the environment, the same amino acid sequence could fold in a different manner.

ie. It could be part of an α-helix in certain condition and part of a β-sheet in others

Question 8

Which of the following interactions determines protein folding stability?

A. Covalent bonds between atoms
B. Double bonds
C. Hydrogen bonds
D. Disulfide bonds
E. High energy phosphate bond

Answer 8

C. Hydrogen bonds

Question 9

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

A. Protease bind to target proteins via formation H bonds
B. Protease and target protein form extended parallel β-strand without requiring H bonds
C. Protease and target protein form α-helix structure to expose peptide bond
D. Protease enzyme works in only hydrophobic conditions

Answer 9

B. Protease and target protein form extended parallel β-strand without requiring H bonds

Question 10

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

A. Loop-regions are almost always made from hydrophobic amino acids
B. Exposed loops should be hydrophilic due to aqueous environment
C. Loops do not fit into the protein core; therefore they are exposed

Answer 10

B. Exposed loops should be hydrophilic due to aqueous environment

Question 12

What is a molten globule?

L6 S22-24

Answer 12

It is the state(s) between a protein being unfolded and one that is fully folded.