ProteinsAQA A-Level Chemistry: Revision notes
Section 1
Peptide links and polypeptides
Amino acids join by condensation: the –COOH of one reacts with the –NH₂ of the next, losing H₂O and forming an amide link, –CONH–, called the peptide link.
Two amino acids make a dipeptide, three a tripeptide, and many a polypeptide. A protein is a polypeptide with a specific shape.
Example: glycine + alanine → H₂NCH₂–CO–NH–CH(CH₃)–COOH + H₂O. The order matters: Gly–Ala differs from Ala–Gly.
Count the water lost: a tripeptide forms with 2 H₂O, so n amino acids give n – 1 peptide links.
Section 2
Hydrolysis of peptides
Heating a peptide with aqueous acid (for example 6 mol dm⁻³ HCl) or alkali breaks every peptide link and gives the constituent amino acids.
tripeptide + 2H₂O → three amino acids
To find the amino acids from a section of peptide, break each C–N link, add –OH to the C=O and –H to the N. In acid the amino acids are present as their –NH₃⁺ forms.
Do not break the C–C bond. The cleaved bond is the C–N bond of the –CONH– group.
Section 3
Primary and secondary structure
Primary structure: the sequence of amino acids in the polypeptide chain, held by peptide (covalent) links.
Secondary structure: regular folding of the chain into an α-helix (a spiral) or β-pleated sheet (side-by-side chains). It is held by hydrogen bonds between the N–H of one peptide link and the C=O of another.
Section 4
Tertiary structure
Tertiary structure is the further folding of the whole chain into a specific three-dimensional shape. It is maintained by:
- hydrogen bonds between side chains (R groups)
- sulfur–sulfur bonds (disulfide bridges) between the side chains of cysteine residues. These are covalent and strong.
The shape of a protein decides its function, for example the active site of an enzyme.
Secondary-structure hydrogen bonds involve the peptide backbone. Tertiary-structure hydrogen bonds involve the side chains.
Section 5
Separating amino acids by TLC
A mixture of amino acids is separated by thin-layer chromatography. Spot the sample on a baseline, stand the plate in solvent, and let the solvent rise. Amino acids are colourless, so locate them with ninhydrin spray (coloured spots) or ultraviolet light (fluorescent plate).
Rf = distance moved by the spot ÷ distance moved by the solvent front
Example: spot at 3.6 cm, solvent front at 8.0 cm: Rf = 3.6 ÷ 8.0 = 0.45. Compare with known Rf values measured under the same conditions to identify each amino acid.
Rf is always between 0 and 1, so divide spot distance by solvent distance and not the other way round.
That's the notes covered.
Carry on to the next subtopic.
Exam questions on Proteins
- Glycine, H₂NCH₂COOH, and alanine, CH₃CH(NH₂)COOH, can join together to form dipeptides.Give the structural formula of the dipeptide in which the –COOH group of glycine has reacted with the –NH₂ group of alanine, and identify the peptide link.2 marks
- A mixture of amino acids from the hydrolysis of a protein is separated by thin-layer chromatography (TLC). The plate is then sprayed with ninhydrin. The solvent front moved 8.0 cm from the baseline. The centre of spot 1 is 3.6 cm above the baseline and the centre of spot 2 is 5.2 cm above the baseline.Calculate the Rf value of spot 2 and explain how it can be used to identify the amino acid.2 marks
- Keratin, the protein in hair, contains regions that are coiled into an α-helix. Its shape is also held by sulfur–sulfur bonds between cysteine residues.Describe what is meant by the primary structure and the secondary structure of a protein such as keratin.3 marks
Written by the Exaim team, led by Shaun Daswani (Head of Upper Secondary, Improve ME Institute; MSc Financial Mathematics, Imperial College London; BSc, UCL) and Jason Daswani (operational lead, Improve ME Institute; LSE).