Amino Acid Structure and Classification (1A) - Bio & Biochem

1. Which amino acid side chain commonly forms disulfide bonds in oxidizing environments?

   Cysteine. Its thiol group can oxidize to form covalent disulfide bridges, stabilizing protein tertiary and quaternary structures.

2. Which amino acids have hydroxyl-containing side chains (alcohol functional group)?

   Serine and threonine. Their side chains contain alcohol groups, which are polar and can form hydrogen bonds or be phosphorylated.

3. Which amino acids are polar uncharged at physiological pH on the MCAT?

   Ser, Thr, Asn, Gln, Cys, Tyr. These side chains have polar functional groups like hydroxyls, amides, or thiols but remain neutral at pH 7.4.

4. Which amino acids are classified as branched-chain amino acids (BCAAs)?

   Valine, leucine, isoleucine. These amino acids have branched aliphatic side chains, which are metabolized via specific pathways in muscle tissue.

5. Which amino acids have carboxylate side chains (acidic side chains)?

   Aspartate (Asp) and glutamate (Glu). Their additional carboxylic acid groups deprotonate at physiological pH, conferring acidity and negative charge.

6. Which amino acid has a guanidinium side chain and is strongly basic at physiological pH?

   Arginine. The guanidinium group has a very high pKa, ensuring it stays protonated and basic in physiological conditions.

7. What is the definition of an amino acid side-chain $pK_a$ in acidbase terms?

   $pK_a$ is the pH where the group is $50\%$ protonated. It represents the equilibrium point where half of the side-chain groups are protonated and half are deprotonated.

8. Which amino acids are classified as nonpolar (hydrophobic) aliphatic side chains on the MCAT?

   Gly, Ala, Val, Leu, Ile, Met, Pro. These amino acids have hydrocarbon side chains that lack polarity, promoting hydrophobic interactions in proteins.

9. Which amino acids have side chains that are positively charged at physiological pH?

   Lysine (Lys), Arginine (Arg), Histidine (His). Their basic side chains have high pKa values, remaining protonated and positively charged at physiological pH.

10. At pH $7.4$, which side chain is most likely to act as a general acid/base in enzyme active sites?

    Histidine. Its imidazole side chain has a pKa near 6.5, enabling proton donation or acceptance at physiological pH in catalysis.

11. Which amino acids have side chains that are negatively charged at physiological pH?

    Aspartate (Asp), Glutamate (Glu). Their carboxylic acid side chains have low pKa values, leading to deprotonation and negative charge at pH 7.4.

12. Which amino acid is sulfur-containing but is not capable of forming disulfide bonds?

    Methionine. Its thioether side chain contains sulfur but lacks the reactive thiol needed for disulfide formation.

13. Identify the amino acid that is both polar and aromatic in standard MCAT classifications.

    Tyrosine. Its phenolic side chain combines an aromatic ring with a polar hydroxyl group, fitting both categories.

14. Which amino acid is not chiral among the 20 standard amino acids?

    Glycine. Its side chain is a hydrogen atom, making the α-carbon non-asymmetric and thus achiral.

15. Which amino acids have amide side chains (carboxamide functional group)?

    Asparagine (Asn) and glutamine (Gln). Amide groups in their side chains are derived from aspartate and glutamate but are neutral and polar.

16. Which three amino acids are the most common targets for phosphorylation in proteins?

    Serine, threonine, tyrosine. Their side-chain hydroxyl groups serve as nucleophiles for phosphate attachment in post-translational modifications.

17. Which amino acids are aromatic on the MCAT classification scheme?

    Phe, Tyr, Trp. Their side chains contain aromatic rings, which can participate in π-π stacking and hydrophobic interactions.

18. Which amino acid has a side chain that is a primary amine and is typically positively charged?

    Lysine. The ε-amino group has a high pKa, remaining protonated and positively charged at physiological pH.

19. Which amino acid has a phenolic side chain and is often a phosphorylation site?

    Tyrosine. The phenolic hydroxyl group can be phosphorylated by kinases, regulating protein function in signaling pathways.

20. Which amino acid has an imidazole side chain and can be neutral or positive near physiological pH?

    Histidine. The imidazole ring has a pKa around 6, allowing it to toggle between protonated and deprotonated states near pH 7.

21. What is the zwitterion form of a typical amino acid at physiological pH?

    $\mathrm{NH_3^+}$ and $\mathrm{COO^-}$ on the same molecule. At physiological pH, the amino group is protonated and the carboxyl group is deprotonated, forming a dipolar ion.

Study these flashcards