Amino Acids

Definition and General Structure

Basic Composition

Amino acids: organic molecules with amino (-NH₂) and carboxyl (-COOH) groups attached to a central α-carbon. Also feature a variable side chain (R group) defining identity.

General Formula

Formula: NH₂-CHR-COOH. Chirality: L-configuration predominant in proteins. Exceptions: glycine (achiral).

Structural Components

Components: α-carbon, amino group, carboxyl group, hydrogen, and side chain (R group). Side chain determines chemical properties and reactivity.

 H |H2N-C-COOH | R

Classification of Amino Acids

By Side Chain Polarity

Categories: nonpolar (hydrophobic), polar uncharged, acidic (negatively charged), basic (positively charged).

By Essentiality

Essential: must be obtained from diet. Non-essential: synthesized endogenously.

Special Functional Groups

Sulfur-containing (cysteine, methionine), aromatic (phenylalanine, tyrosine, tryptophan), imino acid (proline).

Chemical Properties

Acid-Base Behavior

Amino acids: amphoteric. Amino group basic, carboxyl group acidic. Ionization depends on pH.

Reactivity of Side Chains

Side chains: nucleophilic, electrophilic, or hydrophobic. Reactivity determines enzyme catalysis, binding.

Optical Activity

Except glycine, amino acids are chiral, exhibit optical activity. L-isomers predominate in nature.

Zwitterions and Isoelectric Point

Zwitterionic Form

At physiological pH (~7.4), amino acids exist mainly as zwitterions: NH₃⁺ and COO⁻ groups coexist.

Isoelectric Point (pI)

pI: pH where net charge is zero. Calculated by averaging pKa values of ionizable groups.

Effect on Solubility and Migration

At pI, amino acids have minimal solubility, do not migrate in electric fields; exploited in electrophoresis.

pI = (pKa1 + pKa2) / 2 (for simple amino acids)

Essential and Non-Essential Amino Acids

Essential Amino Acids

Humans require 9 essential amino acids: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine.

Non-Essential Amino Acids

Can be synthesized de novo: alanine, asparagine, aspartic acid, glutamic acid, serine, etc.

Conditionally Essential Amino Acids

Required under special conditions: arginine, cysteine, glutamine, tyrosine, glycine, proline, serine.

Biosynthesis and Metabolism

Pathways of Synthesis

Synthesis from metabolic intermediates: glycolysis, TCA cycle, pentose phosphate pathway.

Transamination Reactions

Key mechanism: transfer of amino group via aminotransferases. Requires vitamin B6 cofactor.

Catabolism and Urea Cycle

Degradation produces ammonia, converted to urea for excretion. Involves liver enzymes.

Glutamate + α-ketoglutarate ⇌ α-ketoglutarate + glutamate (transamination)

Peptide Bonds and Protein Formation

Formation Mechanism

Peptide bond: amide linkage between carboxyl group of one amino acid and amino group of another. Condensation reaction releasing water.

Directionality

Peptides synthesized from N-terminus to C-terminus.

Structural Importance

Peptide bonds confer rigidity, planarity; backbone of protein secondary structure.

Side Chain Functional Groups

Hydrophobic Side Chains

Aliphatic and aromatic groups: stabilize protein core via hydrophobic interactions.

Polar and Charged Side Chains

Involved in hydrogen bonding, ionic interactions, catalysis.

Reactive Side Chains

Examples: cysteine thiol forms disulfide bonds; serine hydroxyl participates in catalysis.

Analytical Techniques

Chromatography

Separation based on polarity, charge. Techniques: ion exchange, HPLC.

Spectroscopy

UV absorbance for aromatic amino acids; circular dichroism for secondary structure.

Electrophoresis

Separation by charge at different pH; isoelectric focusing to determine pI.

Industrial and Medical Applications

Pharmaceuticals

Amino acids used in drug synthesis, nutrition supplements, intravenous nutrition.

Food Industry

Flavor enhancers (glutamate), fortification, fermentation substrates.

Biotechnology

Protein engineering, enzyme immobilization, biosensors.

Structural Variants and Modifications

D-Amino Acids

Rare in nature; found in bacterial cell walls, some peptides; resist proteolysis.

Post-Translational Modifications

Phosphorylation, methylation, acetylation alter function and activity.

Non-Standard Amino Acids

Selenocysteine and pyrrolysine incorporated via specialized mechanisms.

References

• Nelson, D.L., Cox, M.M. "Lehninger Principles of Biochemistry," 7th ed., W.H. Freeman, 2017, pp. 123-178.
• Berg, J.M., Tymoczko, J.L., Gatto, G.J. "Biochemistry," 8th ed., W.H. Freeman, 2015, pp. 45-98.
• Stryer, L. "Biochemistry," 5th ed., W.H. Freeman, 2002, pp. 65-112.
• Voet, D., Voet, J.G. "Biochemistry," 4th ed., Wiley, 2011, pp. 150-200.
• Alberts, B. et al. "Molecular Biology of the Cell," 6th ed., Garland Science, 2014, pp. 320-365.