Chapter 3: Amino Acids, Peptides, and Proteins

Question 1

What are the names for the one-letter codes for the 20 standard amino acids?

Answer 1

Nonpolar: Gly (G), Ala (A), Val (V), Leu (L), Ile (I), Met (M), Phe (F), Pro (P), Trp (W)
Polar uncharged: Ser (S), Thr (T), Cys (C), Asn (N), Gln (Q), Tyr (Y)
Polar charged: Asp (D), Glu (E), Lys (K), Arg (R), His (H)

Question 2

How are amino acids classified based on their R groups?

Answer 2

Nonpolar, hydrophobic: Akyl and aromatic side chains
Polar, uncharged: Contain -OH, -NH2, or -SH
Polar, charged: Acidic (-COOH) or basic (-NH2)

Question 3

What makes amino acids act as weak acids and bases?

Answer 3

Amino acids that have ionizable groups:
Carboxyl group (-COOH) acts as a weak acids, donating H+
Amino group (-NH2) acts as a weak base, accepting H+

Question 4

What is the buffering capacity of amino acids?

Answer 4

Amino acids buffer best near the pKA values of their ionizable groups, where they can resist changes in pH by accepting or donating protons

Question 5

What is an amino acid’s titration curve, and what information can be obtained from it?

Answer 5

A titration curve shoes pH changes as a function of added base.

pKa values are the midpoints of the buffering regions.
Isoelectric point (pI) is the pH at which the amino acid’s strength has no net charge (zwitterion form).

Question 6

How is the isoelectric point (pI) calculated for amino acids?

Answer 6

pI = 1/2(pKa1 + pKa2)

Question 7

What is a peptide, and how are amino acids linked to form peptides?

Answer 7

A peptide is a chain of amino acids linked by peptide bonds, formed through condensation reactions between the carboxyl group of one amino acid and the amino group of another.

Question 8

What is the primary structure of a protein?

Answer 8

The primary structure is the linear sequence of amino acids in a polypeptide chain, determined by genetic information

Question 9

How do you determine the overall charge of a peptide at a specific pH?

Answer 9

Consider the pKa values of all ionizable groups (N-terminus, C-terminus, and R groups). Compare the pH to each pKa to determine if each group is protonated or deprotonated, then sum the charges

Question 10

What are the amino (N-) and carboxyl (C-) termini of a peptide?

Answer 10

Amino (N-) terminus: The free amino group at the start of a peptide.
Carboxyl (C-) terminus: The free carboxyl group at the end of a peptide.