amino acid

Overview of Proteins and Amino Acids

  • Proteins are the most abundant and functionally diverse molecules in living organisms.

  • They are composed of amino acids that are linear polymers.

  • Functions:

    • Enzymes and hormones: Regulate metabolism.

    • Contractile proteins: Facilitate movement in muscles.

    • Collagen: Provides structure in bones.

    • Hemoglobin and albumin: Transport molecules; immunoglobulins combat infections.

  • The chapter explores amino acid properties and protein structures formed by these building blocks.

Structure of Amino Acids

  • Common Amino Acids: Over 300 amino acids exist, but 20 are commonly found in mammalian proteins.

  • Each amino acid has:

    • A carboxyl group (COOH)

    • A primary amino group (NH2)

    • A distinctive side chain (R-group) bonded to the alpha carbon.

  • Physiologic pH (around 7.4): The carboxyl group becomes negatively charged.

Classes of Amino Acids

1. Nonpolar Side Chains

  • Characteristics:

    • Do not gain/lose protons or form hydrogen/ionic bonds.

    • Exhibit hydrophobic interactions.

  • Location in Proteins:

    • Cluster internally in aqueous solutions.

    • Found on the exterior in membrane proteins.

  • Examples:

    • Glycine: Smallest, with hydrogen as R-group.

    • Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Methionine, Proline.

2. Uncharged Polar Side Chains

  • Characteristics:

    • Zero net charge at neutral pH.

    • Can participate in hydrogen bonds.

  • Examples:

    • Serine, Threonine, Tyrosine: Each has a hydroxyl group.

    • Asparagine, Glutamine: Contain carbonyl and amide groups.

    • Cysteine: Contains a sulfhydryl group, capable of forming disulfide bonds.

3. Acidic Side Chains

  • Characteristics:

    • Proton donors; fully ionized and negatively charged at physiologic pH.

  • Examples:

    • Aspartic Acid (Aspartate)

    • Glutamic Acid (Glutamate).

4. Basic Side Chains

  • Characteristics:

    • Proton acceptors; positively charged at physiologic pH.

    • Lysine and Arginine: Fully ionized.

    • Histidine: Weakly basic, can be positive or neutral in protein.

Abbreviations and Symbols of Amino Acids

  • Each amino acid has a unique three-letter abbreviation and a one-letter symbol:

    • Alanine (Ala = A)

    • Glycine (Gly = G)

    • Others include: Valine (Val = V), Proline (Pro = P), Lysine (Lys = K).

  • Special cases:

    • B for both Aspartate/Asparagine (Asx), Z for Glutamate/Glutamine (Glx).

Optical Properties of Amino Acids

  • The alpha carbon is a chiral or optically active carbon, except in glycine (not chiral).

  • Exists in two stereoisomeric forms: D and L configurations.

  • All proteins consist predominantly of L-amino acids, while D-amino acids are found in some antibiotics and specific cell structures.