Amino Acids: Structure, Classification, and Biochemical Properties

Topic 3 - Amino Acids

General Structure and Properties of Amino Acids

Amino acids are the fundamental building blocks of proteins and play a central role in biochemistry. Each amino acid contains at least two functional groups: a carboxyl group (–COOH) and an amino group (–NH2), attached to a central (alpha) carbon atom, which also bears a unique side chain (R group) specific to each amino acid.

• Definition: An amino acid is a simple organic compound containing both a carboxyl and an amino functional group.

• General formula: $\mathrm{NH_2{-}CHR{-}COOH}$

• Side chain (R group): Determines the identity and properties of each amino acid.

• Zwitterion: At physiological pH, amino acids exist as dipolar ions (zwitterions), carrying both a positive and a negative charge.

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

Peptides, Polypeptides, and Proteins

Amino acids link together via peptide (amide) bonds to form peptides, polypeptides, and ultimately proteins. The length and arrangement of these chains determine their classification and biological function.

• Peptide: Short chain of amino acid monomers linked by peptide bonds. Examples include dipeptides, tripeptides, and tetrapeptides.

• Polypeptide: Long, continuous, and unbranched peptide chain, typically containing up to ~50 amino acids.

• Protein: Consists of one or more polypeptides arranged in a biologically functional way.

The 20 Common Amino Acids

Humans genetically code for 20 standard amino acids, which are incorporated into proteins. These amino acids are classified as either essential (cannot be synthesized by the body) or non-essential (can be synthesized).

• Essential amino acids: Must be obtained from the diet.

• Non-essential amino acids: Can be synthesized by the body.

• Storage: Amino acids cannot be stored in the body like fats; a low protein diet slows protein synthesis.

• Biological importance: Amino acids are the second-largest component of human muscles, cells, and tissues (after water).

Classification of Amino Acids

Amino acids are classified based on the location of their functional groups and the nature of their side chains (R groups).

• By core structure:

  • Alpha (α) amino acids: Most common, with the amino group attached to the α-carbon.

  • Beta (β), gamma (γ), delta (δ), epsilon (ε) amino acids: Less common, with the amino group attached to further carbons from the carboxyl group.

• By side chain (R group):

  • Aliphatic (non-polar): e.g., Glycine, Alanine, Valine

  • Aromatic (generally non-polar): e.g., Phenylalanine, Tyrosine, Tryptophan

  • Polar (uncharged): e.g., Serine, Threonine, Cysteine

  • Negatively charged (acidic): e.g., Aspartate, Glutamate

  • Positively charged (basic): e.g., Lysine, Arginine, Histidine

Aromatic vs. Aliphatic Compounds

Organic compounds composed of carbon and hydrogen are divided into two classes: aromatic and aliphatic.

• Aromatic compounds: Contain an aromatic-ring configuration of atoms, such as benzene.

• Aliphatic compounds: Do not contain aromatic rings.

Chemical Properties and Reactions

Amino acids possess characteristic chemical reactivity due to their functional groups.

• Primary amines: All amino acids except proline are primary amines, where one hydrogen in ammonia is replaced by an alkyl or aromatic group.

• Characteristic reactions:

  • Carboxyl group: Esterification

  • Amino group: Acetylation or formylation

• Post-translational modifications: Amino acids in proteins can be modified after translation, introducing new functional groups (e.g., phosphate, acetate, amide, methyl).

Ninhydrin Reaction

The ninhydrin reaction is a chemical test used to detect and quantify amino acids and amines.

• Principle: Ninhydrin reacts with ammonia or primary and secondary amines to produce a deep blue or purple color known as Ruhemann's purple.

• Applications: Used to detect fingerprints and terminal amines of lysine residues in peptides and proteins.

• Reaction equation: $\text{Amino acid} + \text{Ninhydrin} \rightarrow \text{CO}_2 + \text{R-CHO} + \text{Ruhemann's purple (color)}$

Enantiomers and Stereoisomerism

The α-carbon of amino acids (except glycine) is asymmetric, allowing for stereoisomerism. Enantiomers are chiral molecules that are non-superimposable mirror images of each other.

• Stereoisomers: Same molecular formula and sequence of bonded atoms, but differ in 3D orientation.

• Enantiomers: Chiral molecules that are mirror images; they rotate plane-polarized light in opposite directions.

• Biological activity: Only L-amino acids are synthesized and used in biological systems; chemical synthesis yields racemic mixtures (equal quantities of L- and D- forms).

• Example: L-Alanine vs. D-Alanine

Table: Classification of Amino Acids by Side Chain Properties

Class	Examples	Properties
Aliphatic (non-polar)	Glycine, Alanine, Valine, Leucine, Isoleucine	Hydrophobic, found in protein interiors
Aromatic	Phenylalanine, Tyrosine, Tryptophan	Ring structure, generally non-polar, absorb UV light
Polar (uncharged)	Serine, Threonine, Cysteine, Asparagine, Glutamine	Hydrophilic, participate in hydrogen bonding
Negatively charged (acidic)	Aspartate, Glutamate	Carry negative charge at physiological pH
Positively charged (basic)	Lysine, Arginine, Histidine	Carry positive charge at physiological pH

Table: Essential vs. Non-Essential Amino Acids

Essential Amino Acids	Non-Essential Amino Acids
Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine	Alanine, Arginine, Asparagine, Aspartate, Cysteine, Glutamate, Glutamine, Glycine, Proline, Serine, Tyrosine

Additional info: The notes infer the importance of stereochemistry in enzyme specificity and the role of post-translational modifications in protein function.