Look at the amino acids below. You do not need to memorize the amino acids for this class but be able to identify the chemical properties of the side chains.

In Enzyme B, serine, threonine, and aspartic acid are crucial for the binding of the substrate at the active site. Which of the following characteristics do you predict that the substrate of Enzyme B will possess?

Question

Look at the amino acids below.  You do not need to memorize the amino acids for this class but be able to identify the chemical properties of the side chains.

In Enzyme B,   serine, threonine, and aspartic acid are crucial for the binding of the substrate at the active site. Which of the following characteristics  do you predict that the substrate  of Enzyme B will possess?

BlackTom AI · Accepted Answer

Serine and threonine contain polar, uncharged hydroxyl side chains able to form hydrogen bonds; aspartic acid has a carboxyl side chain that is negatively charged at physiological pH. These chemical properties determine what kind of substrate will be favored at the active site.

1) Relevant knowledge points and concepts
- Serine (–CH2–OH) and threonine (–CH(OH)–CH3) are polar and form hydrogen bonds (hydrophilic, uncharged side chains).
- Aspartic acid (–CH2–COOH) has a side chain with pKa ≈ 3.9; at physiological pH (~7.4) it is deprotonated and negatively charged (–COO–).
- Electrostatic attraction: oppositely charged groups attract; like charges repel.
- Hydrophilic active sites favor polar/charged substrates; hydrophobic sites favor nonpolar substrates.

2) Step-by-step reasoning
- The active site presents two hydrogen-bonding polar groups (Ser, Thr) and one negatively charged group (Asp).
- Polar groups suggest the enzyme binds a polar (hydrophilic) substrate able to form H-bonds.
- The negatively charged Asp will preferentially interact with a positively charged part of the substrate (electrostatic attraction), stabilizing binding.

3) Calculations / intermediate steps
- Use Henderson–Hasselbalch to confirm Asp is deprotonated: pH = pKa + log([A–]/[HA]).
- 7.4 = 3.9 + log([A–]/[HA]) → log([A–]/[HA]) = 3.5 → [A–]/[HA] ≈ 10^3.5 ≈ 3162.
- This shows Asp is overwhelmingly in the deprotonated (negative) form at physiological pH.

4) Why the correct answer is correct
- A substrate that is hydrophilic and positively charged can form hydrogen bonds with Ser/Thr and electrostatic attraction with Asp–, making “hydrophilic, with a positive charge” the best fit for complementary interactions.

5) Why the other options are incorrect
- Hydrophilic with a negative charge: would be repelled by Asp– (like charges repel) and less favorably bound.
- Relatively hydrophobic: would not interact well with polar Ser/Thr and would be destabilized in a polar active site.
- Hydrophilic but without a charge: could H-bond with Ser/Thr but would miss the favorable electrostatic interaction with Asp–, so less likely as the optimal substrate.

6) Conclusion
- Therefore the predicted substrate characteristics are hydrophilic and positively charged, matching the provided correct answer: hydrophilic, with a positive charge.

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