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 C, lysine, arginine, and histidine 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 C 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 C,   lysine, arginine, and histidine  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 C will possess?

BlackTom AI · Accepted Answer

Lysine, arginine, and histidine have side chains that are basic and tend to carry positive charges at or near physiological pH, so the substrate will be negatively charged and water‑soluble.

1) Relevant knowledge points and concepts
- Lysine and arginine contain side chains with amine/guanidinium groups that are positively charged at physiological pH; histidine has an imidazole ring with a pKa near physiological pH and can be protonated (positively charged) in many enzyme active sites.
- Opposite charges attract (electrostatic/ionic interactions, salt bridges), and charged groups make molecules hydrophilic (water‑soluble).
- Enzyme active sites commonly place charged residues to form complementary interactions with the substrate (charge complementarity).

2) Step‑by‑step reasoning
Step 1: Identify the chemical character of the three residues: lysine (positively charged), arginine (positively charged), histidine (often positively charged in active sites).
Step 2: Consider what substrate would form favorable interactions: a substrate presenting one or more negative charges (for example carboxylate or phosphate groups) will experience strong electrostatic attraction to those positive side chains.
Step 3: Negative charges (carboxylates, phosphates, sulfates) make the substrate polar and water‑soluble, i.e., hydrophilic.
Step 4: Therefore the best predicted substrate property is hydrophilic with negative charges enabling ionic bonding to the active site residues.

3) Calculations
- No numeric calculations are required; reasoning is qualitative based on charge interactions and side‑chain chemistry.

4) Why the correct answer is correct
Because three basic/positively charged residues are used for binding, the substrate most likely carries negative charges to maximize favorable ionic interactions and will be hydrophilic due to those charged groups.

5) Why the other options are incorrect
- Hydrophilic with a positive charge: would be electrostatically repelled by the positively charged side chains.
- Relatively hydrophobic: lacks polar/charged groups, so cannot form strong ionic interactions with those residues.
- Hydrophilic but without a charge: could form hydrogen bonds but would not take full advantage of multiple positive charges the active site provides; ionic interactions are stronger and more likely.

Conclusion: The substrate is best predicted to be hydrophilic with negative charges, which matches the provided answer.

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