Proteins, Muscles, Antibodies COPY

Question 1

What value describes the conformation of a polypeptide backbone?

Answer 1

Torsion angles

Question 2

What are the two torsion angles of a polypeptide backbone?

Answer 2

⍦ - C-C bond

∅ - C-N bond

-amide bond has little rotation because it is planar and has some double bond character

Question 3

What is a Romachandran diagram?

Answer 3

• indicates allowed conformations for a polypeptide (due to side chains only certain are allowed)
• ⍦ vs ∅ plotted

Question 4

What are the two exceptions to the romachandran diagram?

Answer 4

Proline and glycine

Question 5

Describe proline’s torsion angles.

Answer 5

• ∅ values are restricted to -60
• restricted to one side of the plot, can only rotate on the side that has the H, not on the side with the R-group
• more restrained motion

Question 6

Describe glycine’s torsion angles.

Answer 6

• less steric hinderance, allowed angles are greater
• no R group, just 2 Hs

Question 7

Describe the structure of a typical alpha helix.

(handed, residues, pitch, bonds, side chains)

Answer 7

• right handed helix
• 3.6 amino acids/residues per turn
• pitch (distance covered per turn) = 5.4Ă
• carbonyl (C=O) of Nth residue is hydrogen bonded to the N-H of the N+4th residues
• side chains point outward and downward

Question 8

How are beta sheets stabilized?

Answer 8

• held together by H-bonds
• H-bonds are between neighboring polypeptide chains

Question 9

What are the two types of beta sheets?

Answer 9

parallel and antiparallel

Question 10

Describe parallel beta sheets.

Answer 10

• polypeptides run in the same direction (N-C) and (N-C)
• H-bonds between the strands are angled
• the crossover connection between strands is longer and goes out of the plane

Question 11

Describe antiparallel beta sheets.

Answer 11

• polypeptides run in opposite directions (N-C) and (C-N)
• H-bonds between the strands are parallel
• the crossover connection between strands is shorter and on the same plane

Question 12

What are the two classes of proteins?

Answer 12

• fibrous and globular

Question 13

Describe fibrous proteins.

Answer 13

• have repeating second degree structures
• are structural proteins: hair, nails, muscle tendons
• keratin and collagen are examples

Question 14

How are disulfide bonds formed?

Answer 14

cysteine residues have thiol groups that form disulfide bonds under oxidizing conditions

Question 15

Describe globular proteins.

Answer 15

have non-repetitive second degree structures

Question 16

What is the tertiary structure of a protein?

Answer 16

• the folding of second degree structural elements
• positions of each atom in a protein, including side chains
• Where is every atom located in 3D space?

Question 17

Describe the quaternary structure of proteins.

Answer 17

• more than one polypeptide chain
• eg. dimer, trimer
• geometry of association of multiple polypeptides
• non-covalent associations

Question 18

What is the hydropathy scale?

Answer 18

• (-4.5) - (4.5)
• number rating how hydrophobic each amino acid is
• larger = more hydrophobic

Question 19

What are two examples of chaotropic agents?

Answer 19

urea, guanidinium

Question 20

What are intrinsically disordered proteins?

Answer 20

• unfolded
• fold when in contact with their binding partner

Question 21

When proteins fold, they go from _______ to _______

Answer 21

• high energy, high entropy
• low energy, low entropy

Question 22

Describe the process of protein folding.

Answer 22

1. Secondary structural elements and local segments of second degree structure form (Rapid process)
2. Tertiary structure forms, second degree elements collapse to form tertiary structure (Slow process)

Question 23

What chart illustrates protein folding?

Answer 23

• folding funnel
• energy x entropy
• local energy minima are the dips
• the lowest point is the most stable native structure

Question 24

What do chaperone proteins do?

Answer 24

• assist with protein folding when stuck in minima
• eg. heat shock proteins (Hsp70/90)
• many of these are ATPases that catalyze the hydrolysis of a phosphate to allow a reaction that would not otherwise occur happen