34.4 Amino acids
- Syllabus
- 9701–2028–2029
- Topic
- 34.4
- Level
- A2
Learning objectives
34.4.1Acid / base properties of amino acids• Describe the acid / base properties of amino acids and the formation of zwitterions, to include the isoelectric point34.4.2Peptide bond formation• Describe the formation of amide (peptide) bonds between amino acids to give di- and tripeptides34.4.3And predict the results of electrophoresis• Interpret and predict the results of electrophoresis on mixtures of amino acids and dipeptides at varying pHs (the assembling of the apparatus will not be tested)
Use pH and the isoelectric point to choose an amino acid's ionic form
An amino acid is amphoteric because its -NH2 group can accept H+ and its -COOH group can donate H+. Proton transfer gives a zwitterion containing both -NH3+ and -COO- on the same molecule.
| pH condition | Predominant general form | Net charge | Acid-base change from zwitterion |
|---|---|---|---|
| pH below pI | +H3N-CH(R)-COOH | positive | -COO- accepts H+ |
| pH at pI | +H3N-CH(R)-COO- | zero overall | zwitterionic form predominates |
| pH above pI | H2N-CH(R)-COO- | negative | -NH3+ loses H+ |
The isoelectric point, pI, is the pH at which the amino acid has zero average net charge and therefore shows no net movement in an electric field. Internal positive and negative charges can still be present.
If the side chain contains another acidic or basic group, include its protonation state when finding the total charge; do not infer net charge only from the alpha-amino and alpha-carboxyl groups.
A zwitterion is not uncharged at every atom: its separated charges sum to zero. The pI is a particular pH, not a claim that the amino acid is always neutral in solution.
Condensation joins amino acids through amide peptide bonds
The -COOH group of one amino acid reacts with the -NH2 group of another in condensation. OH from -COOH and H from -NH2 leave as H2O, and the new covalent amide link is the peptide bond -CO-NH-.
| Product | Amino-acid residues | Peptide bonds | H2O molecules eliminated on formation |
|---|---|---|---|
| dipeptide | 2 | 1 | 1 |
| tripeptide | 3 | 2 | 2 |
A peptide retains a free amino end (N-terminus) and a free carboxyl end (C-terminus), so a dipeptide can condense with a third amino acid to form a tripeptide.
Sequence matters: glycine followed by alanine (Gly-Ala) and alanine followed by glycine (Ala-Gly) contain the same residues but have different orders and are different dipeptides. Draw each -CO-NH- link between consecutive residues.
Do not join two -NH2 groups or two -COOH groups, and do not count residues as peptide bonds: a chain of n residues contains n-1 peptide bonds.
Predict each electrophoresis band from net charge at the buffer pH
Electrophoresis separates charged amino acids and dipeptides in an electric field. A positive species moves toward the negative electrode, a negative species moves toward the positive electrode, and a zero-net-charge species has no net migration from the origin.
| Compare buffer pH with the species' pI | Likely net charge | Direction |
|---|---|---|
| pH < pI | positive | toward negative electrode (cathode) |
| pH = pI | zero overall | remains at/near origin |
| pH > pI | negative | toward positive electrode (anode) |
For every amino acid or dipeptide in the mixture: 1) identify every ionisable -NH3+/-COO- group, including side chains and free peptide termini; 2) determine its net charge at the stated pH; 3) assign the opposite electrode; 4) only then compare distance travelled. Greater charge tends to increase migration, while larger species tend to move more slowly.
A dipeptide's internal peptide-bond nitrogen and carbonyl are not counted as a free amino and carboxyl pair. Start with its free N-terminus, free C-terminus and any ionisable side chains when predicting charge.
Do not send every amino acid to the same side or assume every dipeptide is neutral. At a fixed buffer pH, different pI values and ionisable side chains can give different net charges; distance also cannot be interpreted from charge alone when sizes differ.