Amino Acids: Structure, Classification, and Properties Ch 3

Amino Acids: Structure and Stereochemistry

Definition and General Structure

Amino acids are organic compounds that serve as the building blocks of proteins. Each amino acid contains both an amino group (-NH2) and a carboxyl group (-COOH) attached to a central (α) carbon atom. The α-carbon is also bonded to a hydrogen atom and a distinctive side chain (R group) that determines the identity and properties of the amino acid.

• α-Amino acid: Has the amino group attached to the carbon adjacent to the carboxyl group.

• Chirality: With the exception of glycine, all protein-derived amino acids have at least one stereocenter (the α-carbon) and are chiral (exist as stereoisomers).

• Configuration: The vast majority of α-amino acids in proteins have the L-configuration at the α-carbon.

• Proline: The only proteinogenic amino acid with a secondary amino group (imino acid).

Amino acids can be referred to by their full names, three-letter, or one-letter codes.

Table: Names and Abbreviations of the Common Amino Acids

Amino Acid	Three-Letter Abbreviation	One-Letter Abbreviation
Alanine	Ala	A
Arginine	Arg	R
Asparagine	Asn	N
Aspartic acid	Asp	D
Cysteine	Cys	C
Glutamic acid	Glu	E
Glutamine	Gln	Q
Glycine	Gly	G
Histidine	His	H
Isoleucine	Ile	I
Leucine	Leu	L
Lysine	Lys	K
Methionine	Met	M
Phenylalanine	Phe	F
Proline	Pro	P
Serine	Ser	S
Threonine	Thr	T
Tryptophan	Trp	W
Tyrosine	Tyr	Y
Valine	Val	V

Classification of Amino Acids

Group A: Amino Acids with Nonpolar Side Chains

These amino acids have side chains that are hydrophobic and do not interact favorably with water. They are often found in the interior of proteins.

• Examples: Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Proline (Pro), Phenylalanine (Phe), Tryptophan (Trp), Methionine (Met)

• Structural features:

  • Aliphatic hydrocarbon groups: Ala, Val, Leu, Ile, Pro

  • Cyclic structure: Proline

  • Aromatic rings: Phe (phenyl), Trp (indole)

  • Sulfur atom: Met

Group B: Amino Acids with Neutral Polar Side Chains

These amino acids have side chains that can form hydrogen bonds and are more hydrophilic.

• Examples: Serine (Ser), Threonine (Thr), Tyrosine (Tyr), Cysteine (Cys), Glutamine (Gln), Asparagine (Asn)

• Structural features:

  • Hydroxyl groups: Ser, Thr, Tyr

  • Thiol group: Cys

  • Amide groups: Gln, Asn

Group C: Acidic Amino Acids

These amino acids have side chains containing a carboxyl group, which is negatively charged at physiological pH.

• Examples: Aspartic acid (Asp), Glutamic acid (Glu)

• Structural features: Side chain carboxyl group (–COOH), which ionizes to –COO− at neutral pH.

Group D: Basic Amino Acids

These amino acids have side chains that are positively charged at physiological pH.

• Examples: Lysine (Lys), Arginine (Arg), Histidine (His)

• Structural features:

  • Amino group: Lys

  • Guanidino group: Arg

  • Imidazole group: His

Spectroscopic Detection of Aromatic Amino Acids

UV Absorbance Properties

Aromatic amino acids absorb light in the ultraviolet (UV) region, typically with maxima around 275–280 nm. Tryptophan and tyrosine are the strongest chromophores among the amino acids.

• Quantification: Protein concentration can be determined by UV-visible spectrophotometry using the Beer-Lambert law:

$A = \varepsilon \cdot c \cdot l$

• A: Absorbance (unitless)

• ε: Molar absorptivity or extinction coefficient (M−1 cm−1)

• c: Concentration (mol/L)

• l: Path length (cm)

Cysteine and Disulfide Bonds

Special Properties of Cysteine

Cysteine contains a thiol (-SH) group, which can be oxidized to form a disulfide bond (S–S) with another cysteine, resulting in the formation of cystine. Disulfide bonds play important structural and biochemical roles in stabilizing protein structure.

$2 \text{Cysteine} \xrightarrow{\text{oxidation}} \text{Cystine} + 2H^+ + 2e^-$

• Disulfide bonds: Covalent links that stabilize the tertiary and quaternary structure of proteins.

Summary Table: Key Properties of Amino Acid Groups

Group	Examples	Key Side Chain Feature	Charge at pH 7
Nonpolar	Ala, Val, Leu, Ile, Pro, Phe, Trp, Met	Hydrocarbon, aromatic, or sulfur	0
Polar, uncharged	Ser, Thr, Tyr, Cys, Gln, Asn	Hydroxyl, thiol, or amide	0
Acidic	Asp, Glu	Carboxylate	−1
Basic	Lys, Arg, His	Amino, guanidino, imidazole	+1 (His can be neutral)

Additional info:

• Stereochemistry: Isoleucine and threonine each have a second stereocenter in their side chains.

• Proteinogenic amino acids: The 20 standard amino acids incorporated into proteins during translation.

• Importance of knowing codes: Three-letter and one-letter codes are essential for interpreting protein sequences and bioinformatics data.