Describe the general structure of an amino acid and provide examples of amino acids with hydroxyl, sulfur-containing, aromatic, and basic side chains, including their structures.

Here are the answers to questions 4 and 5:

4. Amino acid classification and structures:

The general structure of an amino acid is:

$$\begin{array}{c} \text{H} \\ | \\ \text{H}_{2}\text{N} - \underset{|}{\text{C}} - \text{COOH} \\ \text{R} \end{array}$$

where R represents the side chain.

• i. Amino acids with hydroxyl side chain:

  • Serine (Ser, S): $$\begin{array}{c} \text{H} \\ | \\ \text{H}_{2}\text{N} - \underset{|}{\text{C}} - \text{COOH} \\ \text{CH}_{2}\text{OH} \end{array}$$
  • Tyrosine (Tyr, Y): $$\begin{array}{c} \text{H} \\ | \\ \text{H}_{2}\text{N} - \underset{|}{\text{C}} - \text{COOH} \\ \text{CH}_{2}-\text{C}_{6}\text{H}_{4}\text{OH} \end{array}$$

• ii. Amino acids with sulfur-containing side chains:

  • Methionine (Met, M): $$\begin{array}{c} \text{H} \\ | \\ \text{H}_{2}\text{N} - \underset{|}{\text{C}} - \text{COOH} \\ \text{CH}_{2}\text{CH}_{2}\text{SCH}_{3} \end{array}$$

• iii. Aromatic amino acids:

  • Tyrosine (Tyr, Y): (Structure shown above)

• iv. Basic amino acids:

  • Lysine (Lys, K): $$\begin{array}{c} \text{H} \\ | \\ \text{H}_{2}\text{N} - \underset{|}{\text{C}} - \text{COOH} \\ (\text{CH}_{2})_{4}\text{NH}_{2} \end{array}$$

• v. Acidic amino acids:

  • Aspartate (Asp, D): $$\begin{array}{c} \text{H} \\ | \\ \text{H}_{2}\text{N} - \underset{|}{\text{C}} - \text{COOH} \\ \text{CH}_{2}\text{COOH} \end{array}$$

• vi. Essential amino acids from the list:

  • Valine
  • Leucine
  • Methionine
  • Lysine

5. (a) i. Outline the characteristics of a peptide bond

• A peptide bond is an amide linkage formed by a dehydration reaction between the carboxyl group of one amino acid and the amino group of another amino acid.
• It exhibits partial double-bond character due to resonance between the carbonyl oxygen and the amide nitrogen, making it rigid and planar.
• This partial double-bond character restricts rotation around the $\text{C}-\text{N}$ bond, but allows rotation around the $\text{N}-\text{C}_{\alpha}$ and $\text{C}_{\alpha}-\text{C}$ bonds.
• The atoms involved in the peptide bond ($\text{C}_{\alpha}-\text{C}(=\text{O})-\text{N}(\text{H})-\text{C}_{\alpha}$) lie in a single plane.
• The peptide bond is uncharged, but the carbonyl oxygen can act as a hydrogen bond acceptor and the amide hydrogen as a hydrogen bond donor, which are crucial for protein secondary structures.

5. (a) ii. Define Isoelectric point (pI)

The isoelectric point ($\text{pI}$) is the specific pH at which an amino acid, peptide, or protein has no net electrical charge. At this pH, the molecule exists predominantly as a zwitterion, meaning it has an equal number of positive and negative charges, and therefore, its overall charge is zero. At its pI, the molecule will not migrate in an electric field.