Chapter 33 — Quiz

Twenty-five questions on amino acids, peptides, proteins, and enzyme catalysis. ∗ marks questions answered in the answer key.

Multiple choice

1.∗ Natural proteinogenic amino acids are predominantly: (a) D-configured (b) L-configured (c) racemic (d) achiral

2.∗ A free amino acid in water at physiological pH 7.4 is mostly: (a) neutral, fully protonated (b) zwitterion (COO⁻ and NH₃⁺) (c) fully deprotonated (d) cationic

3.∗ Lysine's side chain pKaH is approximately: (a) ~4 (b) ~8 (c) ~10 (d) ~12

4.∗ Aspartate's side chain pKa is approximately: (a) ~4 (b) ~7 (c) ~10 (d) ~12

5.∗ A peptide bond is: (a) an ester (b) an amide (c) an aldehyde (d) an ether

6.∗ An α-helix is: (a) primary structure (b) secondary structure (c) tertiary structure (d) quaternary structure

7.∗ AlphaFold predicts: (a) protein folding kinetics (b) protein 3D structure from amino acid sequence (c) DNA sequences (d) enzyme mechanisms

8.∗ Solid-phase peptide synthesis (SPPS) was invented by: (a) Bruce Merrifield (Nobel 1984) (b) Linus Pauling (c) Albert Hofmann (d) Carl Djerassi

9.∗ Why is proline special among amino acids? (a) it has a cyclic structure that constrains its backbone, making it favor cis configurations (b) it has no chirality (c) it has a sulfur atom (d) it is achiral

10.∗ Histidine's imidazolium pKa is approximately: (a) ~2 (b) ~6 (c) ~10 (d) ~12

11.∗ The peptide bond's partial double-bond character comes from: (a) the nitrogen lone pair donating into the C=O π system (resonance) (b) the nitrogen being sp³ (c) the nitrogen being sp² (d) carbon-carbon bonding

12.∗ Modern SPPS uses Fmoc protection rather than Boc because: (a) Fmoc is removed by base (piperidine), allowing use of acid-labile side-chain protections (b) Fmoc is more water-soluble (c) Fmoc is faster (d) Fmoc is cheaper

13.∗ The serine protease catalytic triad consists of: (a) Ser, His, Asp (b) Cys, Lys, Glu (c) Ser, Lys, Tyr (d) Tyr, Cys, Met

14.∗ Why does the hydrophobic effect drive protein folding? (a) nonpolar side chains cluster in the protein interior, releasing water from their surfaces (entropy gain) (b) it's electrostatic (c) it's a hydrogen-bond effect (d) it has no role in folding

15.∗ A protein is denatured by 8 M urea. The result: (a) the polypeptide is unfolded; secondary and tertiary structure are lost (b) the peptide bonds break (c) only the side chains are affected (d) the protein refolds tighter

16.∗ Anfinsen's experiment proved that: (a) the primary structure (amino acid sequence) determines the 3D fold (b) external chaperones are required for folding (c) folding is irreversible (d) folding requires energy input

17.∗ Insulin is a: (a) single polypeptide of 51 amino acids (b) two polypeptide chains (A and B), linked by disulfide bonds (c) a sugar (d) a lipid

18.∗ Modern peptide drugs (semaglutide, octreotide, bivalirudin) are made by: (a) chemical SPPS or recombinant DNA (b) extraction from plants (c) random mutagenesis (d) only by organic synthesis

19.∗ AlphaFold's predicted structures for ~200 million proteins: (a) are freely available in the AlphaFold Database (b) are kept proprietary (c) only cover human proteins (d) are mostly inaccurate

20.∗ Trypsin cleaves peptide bonds: (a) after every amino acid (b) after Lys or Arg (c) before Pro (d) only at glycine

Short answer

21. Sketch the zwitterion of glycine and predict its pI from the pKa values (α-COOH 2.34, α-NH₃⁺ 9.60).

22. Sketch the structure of the dipeptide Ala-Gly. Identify the peptide bond, the α-carbons, and the side chains.

23. Outline the SPPS synthesis of Gly-Ala-Val using Fmoc strategy. Show the deprotection and coupling steps.

24. Sketch the serine protease catalytic mechanism. Identify the acyl-enzyme intermediate and explain how the Ser/His/Asp triad accelerates catalysis.

25. Explain why AlphaFold is a major scientific advance. What problem did it solve? What chemistry does it implicitly use?

Answer key

  1. b — L-configured amino acids dominate.
  2. b — Zwitterion at physiological pH.
  3. c — Lysine pKaH ~10.
  4. a — Aspartate side chain pKa ~4.
  5. b — Peptide bond is an amide.
  6. b — α-helix is secondary structure.
  7. b — AlphaFold predicts 3D structure.
  8. a — Merrifield invented SPPS.
  9. a — Proline's cyclic structure constrains backbone.
  10. b — Histidine pKa ~6.
  11. a — N lone pair donation via resonance.
  12. a — Fmoc + base; allows acid-labile side-chain protections.
  13. a — Ser, His, Asp triad.
  14. a — Hydrophobic effect drives folding.
  15. a — Urea unfolds proteins.
  16. a — Sequence determines fold.
  17. b — Insulin is two chains linked by disulfides.
  18. a — Modern peptide drugs are made by SPPS or recombinant DNA.
  19. a — AlphaFold structures freely available.
  20. b — Trypsin cleaves after Lys or Arg.

21. Zwitterion of glycine: ⁺H₃N-CH₂-COO⁻. Net charge zero. Both proton (on N) and deprotonated COO⁻ are present simultaneously. pI = (2.34 + 9.60) / 2 = 5.97. At pH 5.97, the molecule has zero net charge.

22. Ala-Gly dipeptide: H₂N-CH(CH₃)-CO-NH-CH₂-COOH (in N-to-C order). The peptide bond is the central -CO-NH-. The α-carbons are: (1) the C of Ala bearing CH₃, NH₂, and COOH (now in amide), and (2) the C of Gly bearing two H's. Side chains: Ala = CH₃; Gly = H.

23. SPPS Gly-Ala-Val (N-to-C order; resin attached at C-terminus): - Step 1: Attach Fmoc-Val to resin via -COOH (this is the C-terminal residue). - Step 2: Remove Fmoc with 20% piperidine in DMF. Wash. - Step 3: Couple Fmoc-Ala (with α-COOH activated by HBTU + HOBt + DIEA): forms Ala-Val on resin. - Step 4: Remove Fmoc with piperidine. Wash. - Step 5: Couple Fmoc-Gly (HBTU + DIEA). - Step 6: Remove Fmoc. - Step 7: Cleave from resin with TFA + scavengers; free peptide Gly-Ala-Val.

24. Serine protease mechanism (chymotrypsin): - Step 1: Substrate binds; substrate's C=O is positioned next to Ser195-OH. - Step 2: His57 (with Asp102 orientation) deprotonates Ser-OH; Ser-O⁻ attacks substrate C=O. - Step 3: Tetrahedral intermediate; the substrate's amide N is now connected to Ser via a tetrahedral C. - Step 4: Amide N-C bond breaks; the leaving amine takes a proton from His; "acyl-enzyme intermediate" forms (substrate's C-terminus is covalently attached to Ser). - Step 5: Water enters; His deprotonates water; HO⁻ attacks the acyl-enzyme C=O. - Step 6: Second tetrahedral intermediate; Ser-O leaves; acid product (the C-terminal half of the substrate's first half) is released. The triad accelerates by: (a) acid/base catalysis (His + Asp activate Ser, protonate leaving group, activate water), (b) covalent catalysis (acyl-enzyme intermediate), (c) substrate orientation (Bürgi-Dunitz pre-organization). Combined: ~10⁹–10¹² rate enhancement.

25. AlphaFold solved the protein folding problem: predicting 3D structure from amino acid sequence. For 60 years this was the central open problem in computational biology. AlphaFold uses deep learning trained on the Protein Data Bank (~200,000 known structures) to predict structures with accuracy near experimental methods. The model implicitly learns: (a) hydrogen bonding between amides; (b) hydrophobic clustering; (c) electrostatics; (d) disulfide bonds; (e) coevolutionary signals from multiple sequence alignment. Impact: ~200 million predicted structures freely available; structural biology research that took years now done in seconds; Nobel Prize 2024 to Hassabis & Jumper.