Lecture 5.5: Protein Structure- Folding Problem

Question 1

Factors that Determine How a Protein will Fold?

Answer 1

Hydrophobic effect

Minimize steric effects

Question 2

Levels of Protein Structure

Answer 2

Primary, secondary, tertiary, quaternary

Question 3

Primary Structure

Answer 3

Linear sequence

Question 4

Secondary structure

Answer 4

Involves H-bonds between NH and CO along polypeptide backbone
Ex. a-helix, b-sheet, b-turns
Both a-helix and b-sheet are repetitive structures
Stabilized by H bonding along polypeptide backbone
No R groups participation

Question 5

A-Helix

Answer 5

Stabilized by H bonds
Each petite bond is connected by H-bonds to a peptide bond 4 amino acids away
H bonding: each carbonyl O h-bonded with amide (NH)
R groups project outward
Phi and psi angles are similar

Question 6

Constraints on a-Helix

Answer 6

Steric: less common = Valine, isoleucine, threonine
Reactivity: less common = serine, aspartic acid, asparagine
Side chains are h-bond donors or acceptors that compete with main CO and NH groups
Phi angle not consistent with helix
Proline: unique, rigid ring structure; cannot be in middle of helix, can be at ends; helix breaker
Glycine destabilizes
Has H side chain; rotation around a-carbon unconstrained

Question 7

B-Strand

Answer 7

Extended structure
Lots of H bonds
R groups extend above and below plane; can accommodate bulky R groups

Question 8

B-strand

Answer 8

B-sheet: 2 or more B-strands linked by H bonds
Antiparallel: ends (NH & CO) face each other
Parallel: ends (NH & NH or CO & CO) run in same direction
Enables change of direction in proteins or connects strands
Not a repetitive structure
Lie on protein’s surface; participates in interactions

Question 9

Tertiary Structure

Answer 9

Noncovalent interactions between aa R groups & the pattern of disulfide bonds
Independent regions that are connected in a single polypep chain
Importance: aa far apart in primary structure are brought closer and interact via noncovalent interactions

Question 10

Myoglobin

Answer 10

Role of hydrophobic effect: nonpolar amino acids in interior of structure, away from water

Question 11

Oligoneric Proteins: Proteins with Quaternary Structure

Answer 11

2 or more polypep chains (subunits) stabilized by noncovalent interactions and sometimes disulfide (covalent) bonds
Interact to form the functional protein