Structure and Chemical properties of Amino Acids

Amino Acid

Organic compound containing an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen, and a variable side chain (R group) all bonded to a central α-carbon.

➡ Basic building blocks of proteins.

α-Carbon

The central carbon atom in an amino acid that bonds to the amino group, carboxyl group, hydrogen atom, and side chain (R group).

➡ Determines the amino acid’s structure and chirality.

Zwitterion

A molecule with both a positive charge (on the –NH₃⁺ group) and a negative charge (on the –COO⁻ group) but overall neutral charge.

➡ Amino acids exist as zwitterions in solid form and physiological pH.

Ionization

Process where a molecule gains or loses protons (H⁺) depending on the pH.

➡ Determines whether the amino acid is positively, negatively, or neutrally charged.

Acid

A proton donor (releases H⁺).

➡ In amino acids, the carboxyl group (–COOH) acts as an acid.

Base

A proton acceptor (binds H⁺).

➡ In amino acids, the amino group (–NH₂) acts as a base.

Weak Acid / Weak Base

A compound that partially ionizes in solution.

➡ Amino acids are weak acids and bases, allowing them to act as buffers.

Buffer

A solution that resists changes in pH when small amounts of acid or base are added.

➡ Amino acids and proteins act as buffers near their pKa values.

pKa

The acid dissociation constant, expressed as a pH value, showing how easily a group donates a proton.

➡ Lower pKa = stronger acid (gives up proton easily).

➡ Higher pKa = weaker acid.

pI (Isoelectric Point)

The pH at which an amino acid has no net charge — equal number of positive and negative charges.

➡ The amino acid will not move in an electric field at its pI.

Titration

A laboratory technique used to determine the concentration or pKa values of an amino acid by adding acid or base and measuring pH changes.

Titration Curve

A graph of pH vs. amount of base added, showing the ionization steps of an amino acid.

➡ Each inflection point = a pKa value.

Glycine

The simplest amino acid, with hydrogen as its R group.

➡ Example used to illustrate titration behavior; pKa₁ = 2.34 (–COOH), pI ≈ 6.0.

Transamination

Reaction where an amino group is transferred from one amino acid to a keto acid, forming a new amino acid.

➡ Important in amino acid synthesis and metabolism.

Oxidative Deamination

Reaction that removes an amino group from an amino acid, producing ammonia (NH₃) and a keto acid.

➡ Step in nitrogen metabolism.

Decarboxylation

Reaction that removes CO₂ from an amino acid.

➡ Produces biologically active amines (e.g., neurotransmitters).

Ammonia Detoxification

The process of converting toxic NH₃ → urea in the urea cycle.

➡ Prevents ammonia buildup in the body.

Peptide Bond

A covalent amide bond between the α-carboxyl group of one amino acid and the α-amino group of another.

➡ Formed via condensation reaction (water is released).

➡ Backbone of all protein structures.

Condensation Reaction

Chemical reaction where two molecules join and release water (H₂O) as a byproduct.

➡ Used to form peptide bonds.

Hydrolysis

Reverse of condensation — breaking a bond by adding water.

➡ Used to break peptide bonds under strong acid/base or enzyme action.

Partial Double-Bond Character

Property of peptide bonds caused by resonance between carbon and nitrogen atoms.

➡ Makes bond rigid, planar, and strong — prevents rotation.

Planar Structure

A flat molecular geometry where atoms are in the same plane.

➡ Peptide bonds are planar, stabilizing protein structure.

Cis vs. Trans Peptide Bond

• Trans: bulky R groups on opposite sides (more stable).

• Cis: R groups on same side (less stable, but sometimes necessary for folding).

➡ Interconversion affects protein folding and function.

L-Configuration

The natural stereochemical form of amino acids found in proteins.

➡ Determines spatial arrangement and 3D structure of proteins.

UV Absorption (190–230 nm)

Peptide bonds absorb ultraviolet light in this range.

➡ Used in spectrophotometry to measure protein concentration.

Spectrophotometry

Analytical method measuring light absorption by molecules at specific wavelengths.

➡ Used to analyze proteins and peptide bonds.

Internal Salt

A compound that forms when a molecule has both positive and negative ions within itself.

➡ Zwitterionic amino acids are internal salts.

α-Ketoacid

A carbon skeleton left after the amino group of an amino acid is removed.

➡ Can enter metabolic pathways for energy production.

Catecholamines

Biogenic amines (dopamine, norepinephrine, epinephrine) derived from amino acids.

➡ Produced through decarboxylation and hydroxylation reactions.

Urea Cycle

Metabolic pathway that converts ammonia (NH₃) into urea for safe excretion.

➡ Main detoxification route for nitrogen waste.