Amino Acids

Basic Amino Acid Structure

Must know:

1) Names

2) 3 and 1 letter abbreviations

3) Side Chain Structure and Characteristics

4) Charge/ Behavior at Different pH Levels

Glycine

3-letter: Gly

1-letter: G

Side chain: R group = H

Characteristics: Smallest and simplest amino acid; achiral because the R group is H, the same as the other H attached to Cα. The slideshow also groups glycine with the polar amino acids, even though it cannot hydrogen bond because of its backbone.

Charge/pH behavior: Side chain stays uncharged. The amino and carboxyl groups still change with pH.

Alanine

3-letter: Ala

1-letter: A

Side chain/structure: –CH₃

Characteristics: Small, nonpolar, hydrophobic.

Charge/pH behavior: Side chain remains uncharged across normal biological pH ranges.

Valine

3-letter: Val

1-letter: V

Side chain/structure: –CH(CH₃)₂

Characteristics: Nonpolar, hydrophobic, branched.

Charge/pH behavior: Side chain remains uncharged.

Leucine

3-letter: Leu

1-letter: L

Side chain/structure: –CH₂–CH(CH₃)₂

Characteristics: Nonpolar, hydrophobic, branched.

Charge/pH behavior: Side chain remains uncharged.

Isoleucine

3-letter: Ile

1-letter: I

Side chain/structure: –CH(CH₃)–CH₂–CH₃

Characteristics: Nonpolar, hydrophobic, branched.

Charge/pH behavior: Side chain remains uncharged.

Methionine

3-letter: Met

1-letter: M

Side chain/structure: –CH₂–CH₂–S–CH₃

Characteristics: Nonpolar, hydrophobic; contains sulfur.

Charge/pH behavior: Side chain remains uncharged.

Proline

3-letter: Pro

1-letter: P

Side chain/structure: –(CH₂)₃– forms a ring back to the amino nitrogen.

Characteristics: Nonpolar; rigid ring structure; restricts flexibility of the protein backbone.

Charge/pH behavior: Side chain itself remains uncharged.

Phenylalanine

3-letter: Phe

1-letter: F

Side chain/structure: –CH₂–phenyl ring

Characteristics: Nonpolar, hydrophobic, aromatic.

Charge/pH behavior: Side chain remains uncharged.

Tryptophan

3-letter: Trp

1-letter: W

Side chain/structure: –CH₂–indole ring

Characteristics: Nonpolar, hydrophobic, aromatic; contains nitrogen in its ring.

Charge/pH behavior: Side chain is generally uncharged at physiological pH.

Serine

3-letter: Ser

1-letter: S

Side chain/structure: –CH₂–OH

Characteristics: Polar; contains a hydroxyl (–OH) group; interacts strongly with water.

Charge/pH behavior: Usually uncharged at physiological pH; the OH can lose H⁺ at very high pH.

Threonine

3-letter: Thr

1-letter: T

Side chain/structure: –CH(OH)–CH₃

Characteristics: Polar; contains a hydroxyl group.

Charge/pH behavior: Usually uncharged at physiological pH; can lose H⁺ at high pH.

Tyrosine

3-letter: Tyr

1-letter: Y

Side chain/structure: –CH₂–phenyl–OH

Characteristics: Polar; aromatic ring + hydroxyl group.

Charge/pH behavior: Usually uncharged at physiological pH; OH can lose H⁺ at sufficiently high pH.

Asparagine

3-letter: Asn

1-letter: N

Side chain/structure: –CH₂–CONH₂

Characteristics: Polar; contains an amide group; can hydrogen bond with water.

Charge/pH behavior: Side chain is generally uncharged.

Glutamine

3-letter: Gln

1-letter: Q

Side chain/structure: –CH₂–CH₂–CONH₂

Characteristics: Polar; contains an amide group.

Charge/pH behavior: Side chain is generally uncharged.

Cysteine

3-letter: Cys

1-letter: C

Side chain/structure: –CH₂–SH

Characteristics: Polar; can participate in chemical reactions. Can ionize at high pH. Two cysteine groups can undergo oxidation to form a disulfide bond, which is a covalent bond.

Charge/pH: At high pH, the –SH can lose H⁺ and become –S⁻. Protonation state depends on pH.

Important: Two cysteines can oxidize to form a disulfide bond (S–S), which helps stabilize protein structure.

Histidine

3-letter: His

1-letter: H

Side chain/structure: –CH₂–imidazole ring

Characteristics: Polar; ionizable; can participate in chemical reactions.

Charge/pH behavior: Can gain or lose H⁺ near physiological pH.

• Protonated → +1

• Deprotonated → 0

Important: Histidine can act as a buffer because it can switch between these states.

Lysine

3-letter: Lys

1-letter: K

Side chain/structure: –(CH₂)₄–NH₃⁺

Characteristics: Polar, basic, positively charged.

Charge/pH behavior:

• Lower pH → +1

• Physiological pH → +1

• High pH → eventually loses H⁺ → 0

Important: One of the amino acids with a positively charged side chain at physiological pH.

Arginine

3-letter: Arg

1-letter: R

Side chain/structure: –(CH₂)₃–NH–C(=NH₂⁺)–NH₂ (guanidinium group)

Characteristics: Polar, basic, positively charged.

• Charge/pH behavior:

• Lower/physiological pH → +1

• Very high pH → eventually loses H⁺ → 0

Important: Positively charged at physiological pH.

Aspartate

3-letter: Asp

1-letter: D

Side chain/structure: –CH₂–COO⁻

Characteristics: Polar, acidic, negatively charged.

Charge/pH behavior:

• Low pH → –COOH = 0

• Physiological pH → –COO⁻ = −1

• High pH → remains −1

Easy distinction: Aspartate has ONE CH₂ before its carboxyl group.

Glutamate

3-letter: Glu

1-letter: E

Side chain/structure: –CH₂–CH₂–COO⁻

Characteristics: Polar, acidic, negatively charged.

Charge/pH behavior:

• Low pH → –COOH = 0

• Physiological pH → –COO⁻ = −1

• High pH → remains −1

Easy distinction: Glutamate has TWO CH₂s before its carboxyl group.

What determines which amino acid it is?

The R group (side chain) determines the amino acid's identity and properties.

What happens when pH < pKa?

The group is protonated (has gained H⁺).

What happens when pH > pKa?

The group is deprotonated (has lost H⁺).

How do nonpolar vs. polar side chains interact with water?

Nonpolar: weak interaction with water.

Polar: strong interaction with water.

What are the 4 amino acids with charged side chains at physiological pH?

Lysine (+), Arginine (+), Aspartate (−), Glutamate (−)