Part 1: Amino acids, zwitterions and peptides

Draw the correct amino-acid form at a stated pH and build or hydrolyse peptide structures without losing side chains.

An α-amino acid has both groups on the adjacent carbon

A typical α-amino acid is H₂N–CH(R)–COOH: its amino group is attached to the carbon next to the carboxyl carbon. The R group identifies the amino acid. Glycine has R = H, alanine R = CH₃ and serine R = CH₂OH. Use the supplied data-booklet structures rather than assuming every side chain is non-polar.

The α-carbon of the standard protein amino acids is chiral except in glycine, where it has two H atoms. The syllabus does not require memorising a list described as “20 essential amino acids”: the standard protein amino acids and the subset nutritionally essential to humans are different categories.

Internal charges can add to zero

A proton can transfer from COOH to NH₂ to give H₃N⁺–CH(R)–COO⁻, a zwitterion with both positive and negative charges but no net charge. Zwitterionic forms predominate in ordinary amino-acid crystals and in appropriate aqueous pH ranges. Strong ionic interactions help explain their high melting/decomposition temperatures compared with simple neutral molecules.

For an amino acid with an uncharged side chain, low pH protonates COO⁻ to COOH, giving a net +1 ion; high pH removes H⁺ from NH₃⁺, giving a net −1 ion. The dominant species depends on pH and the molecule’s dissociation equilibria, not on a rule that the neutral drawn form can never exist.

Every ionisable side-chain group also matters

Aspartic acid has an extra COOH in its CH₂COOH side chain. At sufficiently high pH, both acid groups are COO⁻ and the amino group is NH₂, giving total charge −2. Lysine has an extra NH₂ in its (CH₂)₄NH₂ side chain; at sufficiently low pH both amino groups are NH₃⁺ and COOH is neutral, giving +2.

State the pH condition before adding charges and check each group independently. An amino acid’s isoelectric point is where its average net charge is zero; it is not necessarily pH 7. Side chains can also undergo their own reactions, so supplied structures must be read in full.

A peptide link is an amide link

Condensation between one amino acid’s COOH and another’s NH₂ forms –C(=O)–NH– and eliminates water. The two α-carbons are not directly joined. For two different amino acids, order matters: glycylalanine and alanylglycine have different sequences even though their molecular formulae match.

Using neutral shorthand, a glycine–alanine dipeptide is H₂NCH₂CONHCH(CH₃)COOH. A glycine–alanine–serine tripeptide is H₂NCH₂CONHCH(CH₃)CONHCH(CH₂OH)COOH and contains two peptide links. Retain the N-terminal and C-terminal groups for a finite peptide; a section of a longer protein instead needs continuing bonds.

Constructed mass example: glycine Mᵣ = 75.0 and alanine Mᵣ = 89.0 form a dipeptide of Mᵣ = 75.0 + 89.0 − 18.0 = 146.0. A tripeptide also containing serine, Mᵣ = 105.0, has Mᵣ = 75.0 + 89.0 + 105.0 − 2 × 18.0 = 233.0.

Cut each peptide bond and restore the groups

Heating with strong aqueous acid or alkali can hydrolyse peptide links. Under acidic conditions the amino-acid amino groups are protonated; under alkaline conditions their carboxyl groups are carboxylates. Hydrolysis of a mixed peptide gives its constituent amino acids but does not by itself reveal their original sequence.

For a neutral shorthand equation, add one water per peptide bond broken. Then adjust all ionisable groups for the actual medium. June 2022 Paper 2 Q04.2 distinguished a protein-chain section from a complete dipeptide: draw the type of structure actually requested.

Identify hydrolysis products by TLC

Spot the amino-acid hydrolysate and known standards on a pencil baseline above the solvent level of a suitable TLC plate. Develop in a covered chamber, mark the solvent front immediately, then locate the colourless spots with a suitable developing agent such as ninhydrin using the laboratory method. UV visualisation needs an appropriate plate and compounds that can be detected that way; it is not guaranteed for every amino acid.

Calculate Rf = distance from baseline to spot centre / distance from baseline to solvent front. A constructed spot travelling 3.6 cm while the front travels 6.0 cm has Rf = 0.60. Compare with standards run under the same solvent, stationary-phase and temperature conditions. A matching spot supports identity but co-elution can hide more than one amino acid; hydrolysis/TLC identifies composition, not the original peptide sequence.

Quick checks

Original Finesse questions. Reveal the indicative worked solutions after attempting each question; these are not official AQA mark allocations.

Sources