Amino acids: ionic forms with pH, isoelectric point and peptide bonds
ChemistryBiomolecules & PolymersAges 17–18
Use it with your class: students open it from a link or a QR code, with no account needed.
Next in Biomolecules & Polymers
In ion mode, drag the pH slider from 0 to 14 and watch the amino acid's structure change instantly — a cation in acid, a zwitterion near the isoelectric point, an anion in base; the fraction bar and the average charge are computed from real pKa values, and the molecule migrates toward the cathode or anode in an electric field, staying still exactly at its pI. In peptide mode, choose the number of residues and press Run to watch the amino acids link up through –CO–NH– bonds, each one releasing a water molecule.
Lesson: Amino acids: amphoteric behavior, zwitterion form, isoelectric point; peptides and the peptide bond
What it shows
Amino acids carry an acidic –COOH group and a basic –NH₂ group, so they are amphoteric and exist mainly as zwitterions. Their charge depends on pH: below the isoelectric point (pI) the cation dominates, above it the anion, and at the pI the average charge is zero. The simulation computes the share of each form from real pKa values and links it to electrophoresis, where charged molecules move toward the opposite electrode. Extra acidic or basic side chains, as in glutamic acid and lysine, shift the pI away from neutral. Each peptide bond that forms releases one water molecule.
How to use
With Content set to Ionic form vs pH and electrophoresis, choose an Amino acid and drag the Solution pH slowly from 0 to 14, watching the structure, the fraction bar and the direction of migration. Press Go to pI to find where the molecule stops moving, then compare lysine with glutamic acid. Switch Content to Form peptide bonds, set the number of residues and press Run to count the water molecules released.
Parameters you can change
- Amino acid Glycine (pI 5.97), Alanine (pI 6.00), Lysine (pI 9.74), Glutamic acid (pI 3.22)
- Solution pH 0–14
- Content Ionic form vs pH and electrophoresis, Form peptide bonds
- Number of amino acid residues in the chain 2–5 residues
Questions to explore
- At pH 7, which form of lysine dominates, and toward which electrode does it migrate?
- Why is the pI of glutamic acid so much lower than the pI of glycine?
- How many peptide bonds and water molecules are involved when a pentapeptide forms, and how does this affect its molar mass?
