Amino Acids: Structure and Properties

Amino Acid Structure - Alpha's Anatomy

• Fundamental Unit: Each amino acid has a central α-carbon (Cα) bonded to four distinct groups:
  • An amino group ($-NH_2$)
  • A carboxyl group ($-COOH$)
  • A hydrogen atom ($-H$)
  • A variable R-group (side chain), unique to each, defining its properties.
• General formula: $H_2N-CHR-COOH$.
• L-Amino Acids Predominate: Proteins consist almost exclusively of L-amino acids.
  • 📌 CORN rule (L-isomers): With H atom away, COOH, R, NH2 groups are clockwise around Cα.
• Chirality: All amino acids (except glycine) possess a chiral α-carbon (asymmetric center), making them optically active.

  ⭐ Glycine is the only achiral amino acid; its R-group is a hydrogen atom, so its α-carbon is not asymmetric. oka

Amino Acid Classification - Side Chain Symphony

Amino acids are classified based on the polarity and charge of their side chains (R-groups) at physiological pH (~7.4). This dictates their interactions and protein structure.

AA Properties & Special Types - pH & Special Stars

• Acid-Base Properties:

  • Amino acids are amphoteric, existing as zwitterions ($R-CH(NH_3^+)-COO^-$) at physiological pH.

    ⭐ At physiological pH (~7.4), amino acids exist as zwitterions.

  • Isoelectric point (pI): pH where net charge is zero. For neutral AAs: $pI = (pK_1 + pK_2)/2$.
  • Typical pKa values: α-carboxyl ~2.0; α-amino ~9.0-10.0.
  • Buffering action: Resist pH changes near their pKa values due to ionizable groups.

  

• Special Amino Acids:

  • Proline (P): Imino acid; its rigid ring structure disrupts α-helices (helix breaker).
  • Cysteine (C): Contains a sulfhydryl (-SH) group; forms disulfide bonds (-S-S-), crucial for protein tertiary structure.
  • Selenocysteine (U): The 21st amino acid; contains selenium; vital for specific antioxidant enzymes like glutathione peroxidase.

• Essential & Non-Essential AAs:

  • Essential AAs (must be obtained from diet): 📌 PVT TIM HALL (Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine *, Leucine, Lysine).
    
    *Arginine is semi-essential.
  • Non-essential AAs are synthesized by the body (e.g., Alanine, Aspartate, Glutamate).

Peptide Bond Formation - Bond & Build

• Formation: Amino acids link via peptide bonds ($-CO-NH-$) by dehydration synthesis (condensation), releasing H₂O.
• Characteristics:
  • Rigid & Planar: Due to partial double bond character.
  • Trans configuration favored (less steric hindrance).
  • Restricted rotation around peptide bond; free around α-carbons.
• Polypeptide Chain:
  • N-terminus: Free -NH₃⁺ group.
  • C-terminus: Free -COO⁻ group.
  • Read N → C terminus.

⭐ The peptide bond has partial double bond character, making it rigid and planar, which is crucial for protein folding.

High‑Yield Points - ⚡ Biggest Takeaways

• Glycine: only achiral amino acid; others are L-isomers.
• Proline: imino acid, forms kinks in polypeptide chains.
• Essential AAs (PVT TIM HALL) are dietary requirements.
• Aromatic AAs (Trp, Tyr, Phe) absorb UV at 280 nm.
• Cysteine forms disulfide bonds, stabilizing protein structure.
• Basic AAs (Arg, Lys, His) are +ve charged; Acidic AAs (Asp, Glu) -ve charged at physiological pH.
• Amino acids are zwitterions (dipolar ions) at physiological pH_._