Chapter 33 — Key Takeaways

What you should leave Chapter 33 with

  1. Amino acids are α-amino carboxylic acids with the general structure $H_2N-CHR-COOH$. The 20 proteinogenic amino acids differ in side chain $R$.

  2. All natural proteinogenic amino acids except glycine are L-configured. L corresponds to (S) at the α-carbon for most amino acids (except cysteine, which is (R) due to priority differences with sulfur).

  3. The 20 amino acids classified by side chain: - Nonpolar aliphatic: Gly, Ala, Val, Leu, Ile, Met, Pro. - Aromatic: Phe, Tyr, Trp. - Polar uncharged: Ser, Thr, Cys, Asn, Gln. - Positively charged: Lys (pKaH 10.5), Arg (pKaH 12), His (pKaH 6). - Negatively charged: Asp (pKa 4), Glu (pKa 4).

  4. Zwitterion: at physiological pH, the α-COOH is deprotonated (-COO⁻) and the α-NH₂ is protonated (-NH₃⁺). Net charge zero. This is the dominant form of amino acids in water.

  5. Isoelectric point (pI): the pH at which the molecule has zero net charge. For amino acids with no ionizable side chains, pI ≈ (pKa COOH + pKaH NH₂)/2 ≈ 6. For acidic amino acids (Asp, Glu): pI ≈ 3. For basic amino acids (Lys, Arg, His): pI ≈ 10.

  6. Peptide bond: an amide between α-COOH of one amino acid and α-NH₂ of the next. Section 26.6 chemistry.

  7. The peptide bond's properties (from Ch 24 case study 2): - Planar (the 6 atoms Cα-C-O-N-H-Cα coplanar) due to N→C=O resonance. - Restricted rotation (~99% trans). - N-H is a good hydrogen-bond donor. - Slow hydrolysis (half-life ~600 years uncatalyzed).

  8. Protein structure has four levels: - Primary: amino acid sequence. - Secondary: local backbone H-bond patterns (α-helix, β-sheet). - Tertiary: 3D fold of a single polypeptide. - Quaternary: assembly of multiple chains (e.g., hemoglobin's 4 subunits).

  9. α-helix: right-handed helix, ~3.6 residues per turn, ~5.4 Å pitch. Backbone H-bond from CO of residue i to NH of residue i+4.

  10. β-sheet: extended chains in parallel or antiparallel arrangement; backbone H-bonds between adjacent strands.

  11. Protein folding is mostly thermodynamic (Anfinsen 1961). Driven by:

    • Hydrophobic effect (dominant): nonpolar side chains cluster in interior, releasing water (entropy gain).
    • Hydrogen bonding (backbone + polar side chains).
    • Electrostatics (salt bridges).
    • Van der Waals (tight packing in interior).
    • Disulfide bonds (Cys-Cys, oxidatively-formed S-S linkages).

  12. Solid-Phase Peptide Synthesis (SPPS) invented by Bruce Merrifield (Nobel 1984). Modern Fmoc strategy:

    • Protect each amino acid's α-amine with Fmoc.
    • Activate α-COOH with HBTU or HATU.
    • Couple to the resin-bound peptide's free amine.
    • Remove Fmoc with piperidine.
    • Repeat for next amino acid.
    • Cleave from resin with TFA + scavengers.

  13. Peptide drugs (insulin analogs, GLP-1 agonists, octreotide, bivalirudin) are made by:

    • SPPS for shorter peptides (≤50 amino acids).
    • Recombinant DNA for larger proteins.

  14. Modern peptide drugs include:

    • Insulin analogs: lispro (rapid-acting), glargine (long-acting), detemir (albumin-binding).
    • GLP-1 agonists: semaglutide (Ozempic, Wegovy), liraglutide, tirzepatide.
    • Octreotide: somatostatin analog.
    • Bivalirudin: anticoagulant.

  15. Enzyme catalysis uses amino acid side chains. The serine protease catalytic triad (Ser-His-Asp) is the canonical example:

    • Ser: nucleophile (attacks substrate carbonyl).
    • His: general acid/base (transfers protons).
    • Asp: orienting/stabilizing residue.
    • Mechanism: nucleophilic acyl substitution + acid/base catalysis + covalent intermediate. Rate enhancement: 10⁹-10¹².

  16. Other enzyme classes:

    • Cysteine proteases: use Cys-SH instead of Ser-OH.
    • Aspartic proteases (HIV protease, pepsin): use two Asp side chains; no covalent intermediate.
    • Metalloproteases (thermolysin, MMPs): use Zn²⁺ to activate water.
    • Glycosidases: similar acid/base + nucleophilic catalysis on glycosidic bonds.
    • Kinases: transfer phosphate from ATP to substrate.

  17. AlphaFold (2020) revolutionized structure prediction. Predicts 3D structure from amino acid sequence with near-experimental accuracy. ~200 million predicted structures freely available in AlphaFold Database (2022).

  18. AlphaFold's implicit chemistry: hydrophobic packing, hydrogen bonding, electrostatics, disulfides, geometric constraints, coevolutionary signal.

  19. Nobel Prize 2024: Hassabis, Jumper (DeepMind, AlphaFold) + Baker (UW, Rosetta) for computational protein design and structure prediction.

  20. Misfolding diseases:

    • Alzheimer's (amyloid-β plaques).
    • Parkinson's (α-synuclein aggregates).
    • Prion diseases (mad cow, CJD).
    • Cystic fibrosis (CFTR misfolding).
    • Many others. Drugs targeting misfolded proteins are an active area (e.g., tafamidis for transthyretin amyloidosis).

Cross-references

  • Chapter 24 — Carbonyl group; the amide is at the bottom of the reactivity ladder.
  • Chapter 25 — Imine formation (PLP enzymes use this).
  • Chapter 26 — Acyl substitution; peptide bond formation and hydrolysis.
  • Chapter 27 — α-Carbon chemistry; PLP-mediated amino acid reactions.
  • Chapter 30 — Amine chemistry; amino acid backbone amine.
  • Chapter 32 — Carbohydrates (glycoproteins).
  • Chapter 34 — Lipids and cell membranes.
  • Chapter 35 — Drug design (peptide drugs, enzyme inhibitors).
  • Appendix B — pKa table (amino acid side chains).
  • Appendix F — Named reactions (SPPS chemistry).

Study tip

Memorize the 20 amino acids and their pKa values. For each, identify: 1. Side chain class (nonpolar, aromatic, polar uncharged, charged). 2. pKa of any ionizable side chain. 3. Whether it's likely to be in the protein interior or surface.

If you can recall this for all 20 amino acids in 2 minutes, you've internalized Chapter 33's foundational chemistry. Then peptide synthesis, protein folding, and enzyme catalysis become applications of that knowledge.