Amino Acids, Peptides, Proteins

Question 1

Stereochemistry

Answer 1

The stereochemistry of the a-carbon is L for all chiral
amino acids in eukaryotes. (carbohydrates are D-config).
All chiral amino acids except cysteine have (S)
configuration and all amino acids are chiral except for
Glycine.

Question 2

Amphoteric

Answer 2

Amino acids can act as a base or an acid.

Question 3

pKa

Answer 3

The pH at which half of the species is deprotonated;
[HA] = [A-
].

Question 4

Dipeptide:

Answer 4

2 residues

Question 5

Tripeptide:

Answer 5

3 residues

Question 6

Oligopeptides:

Answer 6

Less than 20 residues

Question 7

Polypeptides:

Answer 7

Greater than 20 residues

Question 8

Formation of a Peptide bond

Answer 8

Forming a peptide bond is a dehydration reaction. The
nucleophilic amino group of one amino acid attacks the
electrophilic carbonyl group of another amino acid.

Question 9

Amide Bonds

Answer 9

The C-N bond of a peptide bond. Rigid due to resonance.

Question 10

Breaking peptide bonds

Answer 10

Breaking a peptide bond is a hydrolysis reaction.

Question 11

1° Structure:

Answer 11

Linear sequence of amino acids in a peptide. Stabilized by
peptide bonds. The AA sequence is written N-terminus to Cterminus. N-terminus is POSITIVELY charged due to –NH3
+.

Question 12

2° Structure:

Answer 12

The local structure of neighboring amino acid. Is stabilized
by hydrogen bonding between amino groups and
nonadjacent carboxyl groups.

Question 13

a-helices:

Answer 13

: A common 2° structure. Clockwise coils around a central axis.

Question 14

b-pleated

sheets:

Answer 14

A common 2° structure. Rippled strands that can be parallel

or antiparallel.

Question 15

The effects of proline on secondary structure

Answer 15

Can interrupt secondary structure because of its rigid cyclic structure

Question 16

3° Structure:

Answer 16

3-D shape of a single polypeptide chain, and is
stabilized by hydrophobic interactions, acid-base
interactions, H-bonds, and disulfide bonds.

Question 17

Hydrophobic

Interactions

Answer 17

Push hydrophobic R groups to the interior or a
protein, which increases entropy of the surrounding
water molecules and creates a negative Gibbs free
energy.

Question 18

Disulfide Bonds:

Answer 18

Occur when two cysteine molecules are oxidized and
create a covalent bond between their thiol groups.
This forms cystine.

Question 19

4° Structure

Answer 19

The interaction between peptides in proteins that

contain multiple subunits

Question 20

Conjugated Proteins

Answer 20

Proteins with covalently attached molecules.

Question 21

Prosthetic Group

Answer 21

The attached molecule in a conjugated protein. Can
be a metal ion, vitamin, lipid, carbohydrate, or
nucleic acid

Question 22

Denaturation:

Answer 22

The loss of 3-D structure. Caused by heat or solute

concentration.