Understanding Protein Structure, Function, and Classification

Posted on Mar 17, 2025 in Human Nutrition and Dietetics

Protein Functions

  • Structural: All cellular and extracellular structures contain proteins.
  • Catalytic: Enzymes are proteins that accelerate a diverse range of (bio)chemical reactions.
  • Transport: Gases (hemoglobin, myoglobin); mineral cations (transferrin (Fe++)/ceruloplasmin (Cu++)); organic anions and lipids (retinol binding protein, transcortin, albumin).
  • Regulatory: Hormones (TSH, LH, FSH, GH, etc.); growth factors; cytokines.
  • Defense: Antibodies, lectins, complement, blood clotting factors.
  • Motor functions: Fibrils and units of our muscles.
  • Energy formation: Proteins of the electron transport chain.

Hetero-, Iso-, and Alloproteins or Enzymes

  • Heteroproteins: Protein variants with the same function but found in different species.
  • Isoproteins: Variants of proteins, found in each species, with the same function but in different locations, with different structures, thermostability, etc.
  • Alloproteins: Variants of proteins found in different individuals of the same species, often as a result of variant alleles of a gene.

Peptides, Polypeptides, and Proteins

  • Peptides and proteins are polymers of amino acids bound with peptide bonds.
  • Oligopeptides: 2-20 amino acids (e.g., glutathione, ADH, oxytocin, gastrin).
  • Polypeptides: 20-100 amino acids (e.g., insulin, glucagon, CCK).
  • Proteins: >100 amino acids.
  • Peptides with biological functions: hormonal activity (insulin, glucagon); releasing factors from the hypothalamus; natural opiates (enkephalin, endorphins); tissue hormones (gastrin, VIP); toxic compounds (phalloidin, amanitin); glutathione.
  • Proteins range from small to large, depending on the number of amino acids, but most are in a medium range. Some proteins are simple, consisting of only one polypeptide chain, whereas others appear as a combination of two or more polypeptide chains (oligomeric proteins).

Amino Acids as Structural Units of Proteins

  • Proteogenic amino acids are those responsible for the formation of peptides and, ultimately, proteins.
  • There are 20 proteogenic amino acids, essential or non-essential, depending on the organism’s ability to synthesize them.
  • Essential amino acids must be supplied by nutrition (Val, Leu, Ile, Lys, Met, Phe, Thr, Trp, His).
  • Peptide bonds are strong, covalent, and planar.

Classification According to Chemical Nature and Polarity at pH 7.0

  • Nonpolar vs. polar amino acids:
    • Nonpolar + aliphatic R-group: Ala, Val, Leu, Ile, Met, Pro, Gly
    • Nonpolar + aromatic R-group: Phe, Trp, Tyr
    • Polar + uncharged R-group: Cys, Asn, Ser, Thr, Gln
    • Polar + charged R-group: Asp, Glu (-); Lys, His, Arg (+)
  • The behavior at a pH of 7.0 likely refers to zwitterions.

Levels of Organization of Protein Molecules: Primary Structure

  • Four levels usually occur in protein molecules: primary, secondary, tertiary, and quaternary structure.
  • Conformation: The spatial arrangement of atoms in a protein.
  • The 3D structure of a protein defines its function.
  • Primary structure:
    • Strong covalent peptide bonds arranged in a planar manner with restricted rotation around the C-N bond.
    • Linear formations.
    • Weak hydrogen bonding due to the presence of proton donors in the peptide structures themselves. H atoms also originate from aqueous environments.
    • Weak hydrophobic forces arise from hydrophobic R-groups of the amino acids, driving these specific groups away from the watery environment.
    • Weak electrostatic forces (charge-charge, charge-dipole, dipole-dipole).
    • Van der Waals forces.
    • A protein’s conformation is largely stabilized by weak interactions.