Sec. 2: Protein Composition and Structure

Question 1

Describe the structure of an alpha-amino acid

Answer 1

A central carbon atom (alpha carbon) linked to a primary amino group, a carboxylic acid group, a hydrogen atom and a side chain (R group).

Question 2

What part of the structure differs between alpha-amino acids?

Answer 2

The side chain (R group)

Question 3

Why are amino acids asymmetrical?

Answer 3

Alpha carbon is chiral because it has four different groups attached.

Question 4

What is the consequence of amino acids being asymmetrical?

Answer 4

Amino acids exist in two mirror-image forms: L isomer and D isomer.

Question 5

Which stereoisomer of amino acids are in proteins?

Answer 5

Only L isomer

Question 6

What is a possible explanation for the preference of L amino acids in proteins?

Answer 6

1. Pure L or D amino acids are slightly more soluble than a stable DL crystal
2. By chance, L amino acid was slightly in excess of D amino acid.
3. Solubility difference amplified L amino acid and became dominant.

Question 7

What is a zwitterion?

Answer 7

A dipolar ion; a molecule that is neutral because it has full positive and negative charges in its structure.

Question 8

Describe the three ionization states of an amino acid

Answer 8

1. at pH less than pKa of COOH, amino group is protonated (NH3+) and carboxylic acid is protonated (COOH)
2. at pH greater than pKa of COOH and less than pKa of NH3, amino group is protonated (NH3+) and carboxylic acid is deprotonated (COO-) [zwitterion]
3. at pH greater than pKa of NH3, amino group is deprotonated (NH2) and carboxylic acid is deprotonated (COO-)

Question 9

At physiological pH, what ionization state is an amino acid in?

Answer 9

Zwitterion (amino group is protonated and carboxylic acid is deprotonated)

Question 10

The twenty side chains of amino acids vary in what six (6) characteristics?

Answer 10

(SS CC HH)

1. size
2. shape
3. charge
4. chemical reactivity
5. hydrogen-bonding capacity
6. hydrophobic character

Question 11

Identify the four (4) main classes of amino acids

Answer 11

1. Hydrophobic amino acids with [nonpolar R groups]
2. Polar amino acids with [neutral R groups but the charge is not evenly distributed]
3. Positively charged amino acids with [R groups that have a positive charge at physiological pH]
4. Negative charged amino acids with [R groups that have a negative charge at physiological pH]

Question 12

Hydrophobic amino acids mostly have side chains containing what atoms?

Answer 12

carbon and hydrogen (hydrocarbon side chains)

Question 13

How many amino acids have nonpolar R groups?

Answer 13

Nine

Question 14

How many amino acids have neutral, polar R groups

Answer 14

Six

Question 15

How many amino acids have positively charged R groups at physiological pH?

Answer 15

Three

Question 16

How many amino acids have negatively charged R groups at physiological pH?

Answer 16

Two

Question 17

Which five (5) hydrophobic amino acids have linear, aliphatic R groups?

Answer 17

1. Glycine
2. Alanine
3. Valine
4. Leucine
5. Isoleucine

Question 18

Which hydrophobic amino acid has a cyclic, aliphatic R group?

Answer 18

Proline

Question 19

Which hydrophobic amino acid has a thioether (-S-) group?

Answer 19

Methionine

Question 20

Which hydrophobic amino acid contains a phenyl group?

Answer 20

Phenylalanine

Question 21

Which hydrophobic amino acid contains an indole group?

Answer 21

Tryptophan

Question 22

Which three (3) polar amino acids have hydroxyl groups?

Answer 22

1. Serine
2. Threonine
3. Tyrosine

Question 23

Which polar amino acid has a sulfhydryl group?

Answer 23

Cysteine

Question 24

Which two (2) polar amino acids has a terminal carboxamide group?

Answer 24

1. Asparagine

2. Glutamine

Question 25

Which positive amino acid has a side chain with a terminal amino group?

Answer 25

Lysine

Question 26

Which positive amino acid has a side chain with a terminal guanidinium group?

Answer 26

Arginine