Free MCAT tool
pKa and Charge at pH Trainer
Practice Henderson-Hasselbalch the way the MCAT uses it: is a group protonated, and what is the net charge of a short peptide at a given pH? The working is shown every time.
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The idea behind the trainer
Every ionizable group is an acid-base pair, and the Henderson-Hasselbalch equation, pH = pKa + log([A-]/[HA]), tells you how the two forms split at any pH. If the pH is below the pKa, the protonated form wins. If it is above, the deprotonated form wins. At the pKa the two are equal. A difference of one pH unit corresponds to a ratio of ten to one, which is about 91 percent in the favored form.
Whether that matters for charge depends on the kind of group. An acidic group (a carboxyl, a thiol, a phenol) is neutral when protonated and negative when deprotonated. A basic group (an amino, imidazole or guanidinium group) is positive when protonated and neutral when deprotonated. Mixing those two up is the most common mistake on charge questions, which is why the first mode makes you commit to protonated or deprotonated before it shows the arithmetic.
The peptide mode scales the same logic up. A short peptide has one free N-terminus, one free C-terminus and a side chain for each ionizable residue. Add one charge contribution per group and you have the net charge. The tool lists every group, its pKa, the distance from the pH and the fraction in the charged form, so you can see exactly where your own estimate went wrong. The explorer lets you slide the pH and watch charge and pI change for any residue.
For background, read The Henderson-Hasselbalch Equation for the MCAT and Amino Acid pKa Values and Charge at pH 7.4. Values are typical textbook numbers and sources differ by a few tenths.
Questions
What is the Henderson-Hasselbalch equation?
pH = pKa + log([A-]/[HA]). When the pH equals the pKa the group is half protonated. Each unit above or below the pKa changes the ratio of the two forms by a factor of 10.
Which pKa values are used for peptide termini?
A teaching convention of 2.0 for the C-terminal carboxyl and 9.0 for the N-terminal amino group. Real peptide termini shift by up to about a unit depending on neighbors, so follow the values given in your exam passage.
Why does the trainer avoid pH values very close to a pKa?
Right at the pKa a group is about half charged, which makes a whole-number answer ambiguous. The questions keep a clear margin so there is one defensible answer.
Is this a substitute for my course materials?
No. It is a practice aid built from standard facts. Always check numbers against the reference your exam or instructor provides.
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