Amino Acids: Structure, Stereochemistry, Classification, and Properties

Amino Acids

Introduction to Amino Acids

Amino acids are the fundamental building blocks of proteins and play crucial roles in biochemistry. Each amino acid contains a central carbon atom (the α-carbon) bonded to an amino group, a carboxylic acid group, a hydrogen atom, and a unique side chain (R group).

• General Structure: The α-carbon is central, with four different groups attached: amino group (–NH2), carboxyl group (–COOH), hydrogen atom, and side chain (R group).

• Zwitterion: At neutral pH, amino acids exist as zwitterions, where the amino group is protonated (–NH3+) and the carboxyl group is deprotonated (–COO−).

• Asymmetric Center: When the R group is not hydrogen, the α-carbon is a chiral center, leading to stereoisomerism.

Structure of an α-Amino Acid

Chemical Structure

The chemical structure of an α-amino acid can be represented as follows:

• Central α-carbon: Tetrahedral geometry.

• Functional groups: Amino group, carboxyl group, hydrogen atom, and side chain (R group).

• Zwitterionic form: At physiological pH, the amino group is –NH3+ and the carboxyl group is –COO−.

Example: Glycine is the simplest amino acid, with R = H.

Amino Acid Stereochemistry

Chirality and Stereoisomers

Most amino acids (except glycine) have a chiral α-carbon, resulting in two possible stereoisomers: L- and D-forms.

• Chiral Center: The α-carbon is attached to four different groups, making it a stereocenter.

• Enantiomers: L-alanine and D-alanine are non-superimposable mirror images (enantiomers).

• Fischer Projection: A two-dimensional representation used to depict stereochemistry.

Example: All proteinogenic amino acids in proteins are L-amino acids.

Classification of Naturally Occurring Amino Acids

Categories Based on Side Chain Properties

The 20 common amino acids found in proteins are classified according to the chemical nature of their side chains (R groups):

Class	Examples	Properties
Nonpolar, Aliphatic	Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Methionine	Hydrophobic, found in protein interiors
Aromatic	Phenylalanine, Tyrosine, Tryptophan	Contain aromatic rings, absorb UV light
Polar, Uncharged	Serine, Threonine, Cysteine, Asparagine, Glutamine	Hydrophilic, can form hydrogen bonds
Positively Charged (Basic)	Lysine, Arginine, Histidine	Basic side chains, positively charged at physiological pH
Negatively Charged (Acidic)	Aspartic acid, Glutamic acid	Acidic side chains, negatively charged at physiological pH

Example: Tyrosine and tryptophan are aromatic amino acids that absorb UV light at 280 nm, useful for protein quantification.

General Properties of Amino Acids

Physical and Chemical Properties

• UV Absorption: Aromatic amino acids (phenylalanine, tyrosine, tryptophan) absorb UV light, especially at 280 nm.

• Ionization: Amino acids have ionizable groups with characteristic pKa values. The amino group, carboxyl group, and some side chains can gain or lose protons depending on pH.

• Zwitterion Formation: At neutral pH, amino acids exist as zwitterions with both positive and negative charges.

Equation:

$\text{Amino acid (zwitterion):} \quad ^{+}H_3N-CHR-COO^{-}$

Example: The titration curve of histidine shows multiple ionization steps due to its ionizable side chain.

Summary Table: Amino Acid Classification

Group	Amino Acids	Key Features
Nonpolar, Aliphatic	Gly, Ala, Val, Leu, Ile, Pro, Met	Hydrophobic, nonpolar side chains
Aromatic	Phe, Tyr, Trp	Aromatic rings, UV absorption
Polar, Uncharged	Ser, Thr, Cys, Asn, Gln	Hydrophilic, can form H-bonds
Positively Charged	Lys, Arg, His	Basic, positively charged at pH 7
Negatively Charged	Asp, Glu	Acidic, negatively charged at pH 7

Additional info:

• The L-form of amino acids is the predominant form found in proteins.

• Glycine is achiral because its R group is hydrogen.

• Amino acids are linked by peptide bonds to form proteins.