Peptide Charge Calculation at pH 1.0
The net charge of a peptide depends on the ionization state of its N-terminus, C-terminus, and any ionizable amino acid side chains. The ionization state is determined by comparing the given pH to the pKa values of these groups. At very low pH values (like pH 1.0), most groups tend to be protonated.
Ionizable Groups in the Peptide
The peptide sequence is Ala-Glu-Val-Asn-Ile-Asp-Pro-Asp-Gln-Gly-Asp. The ionizable groups are:
- The N-terminus (amino group).
- The side chain of Glutamic Acid (Glu).
- The side chains of the three Aspartic Acid (Asp) residues.
- The C-terminus (carboxyl group).
Determining Charge State at pH 1.0
We use typical pKa values to determine the charge state at pH 1.0. A group is generally considered protonated (neutral or positive charge) if the pH is significantly lower than its pKa, and deprotonated (negative charge) if the pH is significantly higher.
| Group | Typical pKa | pH 1.0 vs pKa | Protonation State at pH 1.0 | Contribution to Charge |
| N-terminus | ~9.6 | 1.0 << 9.6 | Protonated (NH3+) | +1 |
| Glu side chain | ~4.1 | 1.0 << 4.1 | Protonated (COOH) | 0 |
| Asp side chain 1 | ~3.9 | 1.0 << 3.9 | Protonated (COOH) | 0 |
| Asp side chain 2 | ~3.9 | 1.0 << 3.9 | Protonated (COOH) | 0 |
| Asp side chain 3 | ~3.9 | 1.0 << 3.9 | Protonated (COOH) | 0 |
| C-terminus | ~2.3 | 1.0 < 2.3 | Protonated (COOH) | 0 |
Net Charge Calculation
Summing the charge contributions from all ionizable groups:
Net Charge = (Charge from N-terminus) + (Charge from Glu side chain) + (3 * Charge from Asp side chains) + (Charge from C-terminus)
Net Charge = (+1) + (0) + (3 * 0) + (0) = +1
Final Charge
The net charge on the peptide at pH 1.0 is +1.
Important Questions from Chemical Biology {p}K_a Isoelectric Point
- Consider the two $pK_a$ values of valine as 2.32 and 9.62. The isoelectric point (pI) of this amino acid is __________. (rounded off to two decimal places)
- The $pK_a$ values of the carboxylic and amino groups of an amino acid with a non-ionizable side chain are 2.17 and 9.13, respectively. The isoelectric point (rounded off to two places of decimals) of this amino acid is ________.
- The C-terminal carboxyl group and the N-terminal amino group in amino acids have a dissociation constant ($pK_a$) of 2.2 and 9.2, respectively. The $pK_a$ of side chain carboxyl group in glutamic acid is 4.2 and side chain amino group in lysine is 10.2. The difference in isoelectric point ($pI$) of lysine and glutamic acid (rounded off to two decimal places) is ________.
- Considering that the three pKas of histidine are pK$_1$=1.8, pK$_2$=9.2 and pK$_R$=6.0, its isoelectric point will be _____ (rounded off to one decimal place).
- An amino-acid has one proton donating group in the side chain (R). The $pK_{COOH}$, $pK_{NH2}$ and $pK_R$ values for this amino-acid are 2.19, 9.67 and 4.25, respectively. Which one of the following statements about this amino-acid is CORRECT?
