Amino Acids: Structure and Stereochemistry

Definition and General Structure

Amino acids are organic compounds containing both an amino group (-NH2) and a carboxyl group (-COOH) attached to the same carbon atom, known as the α-carbon. The α-carbon is also bound to a variable side chain (R group) that determines the identity and properties of each amino acid.

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

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

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

• Amino acids are commonly referred to by their three-letter or one-letter codes.

Table: Names and Abbreviations of the Common Amino Acids

Classification of Amino Acids

Group A: Nonpolar Side Chains

Nonpolar amino acids have hydrophobic side chains, often consisting of aliphatic or aromatic hydrocarbon groups. These amino acids are typically found in the interior of proteins, stabilizing structure through hydrophobic interactions.

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

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

• Proline has a cyclic structure, restricting backbone flexibility.

• Aromatic hydrocarbon: Phe, Trp

• Indole ring side chain: Trp

• Sulfur atom in side chain: Met

Group B: Neutral Polar Side Chains

Polar amino acids have side chains capable of forming hydrogen bonds, making them hydrophilic and often found on protein surfaces.

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

• Ser, Thr, Tyr: Side chain contains a hydroxyl group (-OH)

• Cys: Side chain contains a thiol group (-SH)

• Asn, Gln: Side chain contains an amide group

Group C: Acidic Side Chains

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

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

• Side chain is a carboxylate ion (-COO-) at neutral pH

Group D: Basic Side Chains

Basic amino acids have side chains that are positively charged at physiological pH due to the presence of amino groups.

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

• Lys: ε-amino group

• Arg: Guanidino group

• His: Imidazole group (can be protonated or neutral at pH 7)

Spectroscopic Properties of Aromatic Amino Acids

UV Absorbance

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

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

• A: Absorbance (unitless)

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

• c: Concentration (mol/L)

• l: Path length (cm)

Special Properties: Cysteine and Disulfide Bonds

Cysteine Oxidation

Under certain conditions, two free sulfhydryl groups (-SH) of cysteine residues can be oxidized to form a disulfide bond (S-S), resulting in the formation of cystine. Disulfide bonds play important structural and biochemical roles, stabilizing protein tertiary and quaternary structures.

Reaction:

• Disulfide bonds are covalent and contribute to protein stability.

Summary of Amino Acid Features

• All 20 standard amino acids are α-amino acids.

• For 19 of the 20, the α-amino group is primary; for proline, it is secondary.

• With the exception of glycine, the α-carbon of each amino acid is a stereocenter (chiral).

• Isoleucine and threonine contain a second stereocenter.

• Each amino acid has unique three-letter and one-letter codes.

Additional info:

• The classification of amino acids by side chain properties is essential for understanding protein structure and function.

• Knowledge of amino acid abbreviations is fundamental for interpreting protein sequences and biochemical literature.