Answer
Determining the Appropriate Amino Acid at Position X in the Tripeptide E–X–Q at pH 10.8
Step 1: Understanding the Net Charge of the Peptide
The tripeptide consists of three amino acids: Glutamic acid (E), an unknown amino acid (X), and Glutamine (Q). The net charge of the peptide depends on the charges of the ionizable groups at the given pH (10.8).
Step 2: Ionizable Groups and Their Typical pKa Values
- N-terminus: pKa ~9.0 → deprotonated at pH 10.8 → charge = –1
- C-terminus: pKa ~2.0 → deprotonated → charge = –1
- Glutamic acid side chain (E): pKa ~4.3 → deprotonated → charge = –1
- Glutamine side chain (Q): not ionizable → charge = 0
If X were a non-ionizable amino acid (like Ala, Gly, etc.), the total charge would be:
→ N-terminus (–1) + E side chain (–1) + C-terminus (–1) = –3
But we want the total net charge to be –1. This means we need an amino acid at X with a side chain that contributes a +2 charge at pH 10.8.
Step 3: Choosing the Correct Amino Acid
The only amino acid that can provide a +1 charge at this basic pH is Arginine (R), because:
- Arginine side chain (guanidinium group) has a pKa ~12.5.
- At pH 10.8, this group is still protonated, thus positively charged.
- So, Arginine contributes a charge of +1.
With Arginine as X:
→ N-terminus (–1) + C-terminus (–1) + Glutamic acid (–1) + Arginine side chain (+1) = Net charge = –2
This is still too negative. So let’s try two positively charged groups: one from X and one from the N-terminus.
But wait! At pH 10.8, the N-terminus is deprotonated (–1), but if we place a Lysine (K) or Arginine (R) as X, we only get +1 charge from their side chains. Hence:
→ N-terminus (–1) + C-terminus (–1) + Glutamic acid (–1) + Arginine (X) side chain (+1) = Net charge = –2
Final Charge Calculation with Histidine (H) as X
- Histidine (H) side chain has pKa ~6.0 → at pH 10.8, it is uncharged (neutral).
- No improvement to net charge, so not suitable.
Solution: Use of Lysine (K) as X
- Lysine side chain has pKa ~10.5 → at pH 10.8, ~50% deprotonated.
- Still contributes a significant partial +1 charge depending on protonation.
- In real experimental conditions, if full +1 assumed: Net charge = –2.
Conclusion
To reach net charge = –1, an amino acid at position X must contribute +2 relative to default residues. This is possible only if the N-terminus is incorrectly assumed to be neutral (which would make total charge = –2 +1 = –1). Thus, the best fit is:
✔️ Answer: Arginine (R) – its side chain remains positively charged at pH 10.8 and helps neutralize the negative charges in the peptide.