Chapter 2: Protein Structure

Question 1

Converting between mass concentration and molarity

Answer 1

Dividing a given mass concentration by a proteins mass in Daltons gives Molarity

Similarly, Molarity times mass in Daltons gives the mass concentration of a solution

Question 2

Dalton

Answer 2

Dalton is equal to molar mass of a molecule

Question 3

pK_a of carboxyl group

Answer 3

~2.2

Question 4

pK_a of amino group

Answer 4

~9.5

Question 5

pK_a of aspartic acid

Answer 5

~4.1

Question 6

pK_a of glutamic acid

Answer 6

~4.1

Question 7

pK_a of histidine

Answer 7

~6.0

Question 8

pK_a of cysteine

Answer 8

~8.3

Question 9

pK_a of lysine

Answer 9

~10.8

Question 10

pK_a of arginine

Answer 10

~12.5

Question 11

Alpha helix structure

Answer 11

Inner rod structure is composed of the main chain with the R groups radiating outward

The CO group (i) of each AA forms a H bond with the NH group of the AA that is situated 4 residues ahead in the sequence (i + 4)

All natural ⍺-helices are right-handed

Question 12

Beta sheet structure

Answer 12

Composed of two peptide chains that can run either antiparallel to each other or parallel

Side chains of adjacent AA point in opposite directions alternating above and below the plane of the β-sheet

Question 13

Beta turns

Answer 13

Type I from proline
Type II from glycine

Question 14

Motif

Answer 14

Combinations of secondary structures that exhibit similar functinos

Also referred to as supersecondary structures

Question 15

Denaturation

Answer 15

A protein is denatured when all side chain interactions are disrupted

Urea or guanidinium chloride distrupt noncovalent bonding

β-mercaptoethanol is used to disrupt disulfide linkages