JG

Recording-2025-08-29T17:14:05.479Z

Protein Building Blocks and Why They Matter

  • Everything happening inside the cell is chemistry; proteins are key players in most cellular processes (enzymes, transporters, receptors, structural components, motors).
  • Enzymes catalyze reactions by lowering activation energy to drive metabolism and energy production.
  • Transport proteins facilitate movement of substances across membranes.
  • Receptors gather signals (e.g., in neurons) and relay information to the cell to elicit responses.
  • Structural proteins (e.g., collagen) provide mechanical support and shape to tissues.
  • Motor proteins drive movement within cells.

Amino Acids: Structure, Drawing, and Classification

  • Building blocks of proteins are amino acids; a 2D drawing is expected for exam familiarity:

    • Central carbon (Cα) bonded to a hydrogen (H), an amino group (–NH₂), a carboxyl group (–COOH), and an R group (side chain).
    • The side chain (R) distinguishes amino acids and drives chemical behavior.
    • A peptide bond links amino acids covalently between the carboxyl carbon of one amino acid and the amide nitrogen of the next, forming –(N–H)–C(=O)– linkage with the next residue. This bond has resonance, giving partial double-bond character and restricting rotation.
    • Rotation about the peptide bond is limited; leading to backbone dihedral angles φ (phi) and ψ (psi).
    • Primary structure is the linear amino acid sequence; it determines how the protein will fold.

  • Important directions: proteins are read from N-terminus (amino end) to C-terminus (carboxyl end). The sequence direction matters for structure and function.

  • Polymerization via peptide bonds creates a backbone with side chains (R groups) protruding from it.

  • You should be able to draw any amino acid and identify its side chain; you do not need to memorize 3-letter or 1-letter abbreviations, though some familiarity is helpful.

  • pH-dependent protonation: amino and carboxyl groups can be protonated/deprotonated depending on physiological pH, altering charge states of side chains.

  • Common amino acid categories (by R-group properties):

    • Nonpolar (hydrophobic): equal electron sharing with little to no charge
    • Polar (uncharged): electronegativity differences create partial charges
    • Positively charged (basic): Lysine (Lys, K), Arginine (Arg, R)
    • Negatively charged (acidic): Aspartate (Asp, D), Glutamate (Glu, E)
    • Aromatic: rings with conjugated pi systems (e.g., Tryptophan, Phenylalanine, Tyrosine)

  • Key illustrative amino acids discussed:

    • Glycine (Gly, G): smallest side chain (H); highly flexible.
    • Cysteine (Cys, C): contains sulfur; can form disulfide bonds (–S–S–) that stabilize proteins; disulfide bonds are sensitive to redox state and pH.
    • Proline (Pro, P): R-group forms a ring with the backbone N; introduces kinks and rigidity, influencing backbone conformation.
    • Lysine (Lys, K) and Arginine (Arg, R): positively charged side chains; can be modified (e.g., in histones) for signaling and regulation.
    • Aspartate (Asp, D) and Glutamate (Glu, E): negatively charged carboxylate side chains.

  • Aromatic rings and stacking: aromatic amino acids participate in pi-pi interactions; tryptophan (Trp) is a common aromatic example.

  • Amino acid side chains and charge states depend on pH; exam-friendly approach accepts drawn/charged forms appropriate to the pH context rather than enumerating every protonation state.

  • Practical note: focus on recognizing structures and general chemistry principles (bonding, charge, hydrophobic/h