Unit 1 Question Bank
Numerically it is the pH midway between the pKa values of the ionisations on either side of the isoelectric species. For alanine (pKa 2.35 and 9.69) the pI is about 6.0.
Application: the basis of electrophoresis and isoelectric focusing — above its pI a protein is net negative and moves to the anode; below it, net positive and moves to the cathode.Harper's ch.3, p.20
Amino acids exist as zwitterions in blood and most tissues (–COO⁻ and –NH₃⁺). The fully uncharged structure cannot exist in aqueous solution, because there is no pH at which both the carboxyl group is protonated and the amino group is not.Harper's ch.3, p.20
It possesses partial double-bond character, so the peptide unit is rigid and planar and normally in the trans configuration; rotation in the backbone is restricted to the N–Cα (φ) and Cα–C (ψ) bonds.Harper's ch.3, p.15
Harper's counts ten such nutritionally essential L-α-amino acids.Harper's ch.3, p.15
It occurs in proteins from every domain of life; humans contain about two dozen selenoproteins, including certain peroxidases and reductases and the iodothyronine deiodinases that convert thyroxine (T₄) to T₃. It is incorporated co-translationally at a recoded UGA codon rather than having a codon of its own.Harper's ch.3, p.16
The sole exception is glycine, whose R group is a hydrogen atom, so the α-carbon carries two identical substituents and is not chiral. Only L-isomers occur in proteins.TMU Lecture 1 Slide 14 · Harper's ch.3
General structure
All amino acids in proteins are L-α-amino acids. Each has an α-carbon bearing four groups: an amino group (–NH₃⁺), a carboxyl group (–COO⁻), a hydrogen, and a variable R group (side chain).
Because the four groups differ, the α-carbon is chiral — with the single exception of glycine, whose R group is a hydrogen. Only the L configuration occurs in proteins, although free D-serine and D-aspartate exist in brain tissue.
Classification by side chain
| Class | Members |
|---|---|
| Non-polar aliphatic | Gly · Ala · Val · Leu · Ile · Pro · Met |
| Aromatic | Phe · Tyr · Trp — absorb UV at 280 nm |
| Polar uncharged | Ser · Thr · Cys · Asn · Gln |
| Acidic | Asp · Glu — low pI |
| Basic | Lys · Arg · His — high pI |
Points worth adding
- The genetic code specifies 20 amino acids; selenocysteine is regarded as the 21st
- Ten are nutritionally essential
- Some residues are modified after translation — 4-hydroxyproline and 5-hydroxylysine in collagen, plus methylation, acetylation, prenylation and phosphorylation
Two ionisable groups
Every amino acid carries at least two groups that ionise in opposite directions — an α-carboxyl group that loses a proton and an α-amino group that gains one. Some side chains add a third ionisable group.
The zwitterion
At the pH of blood and most tissues, the carboxyl group exists as –COO⁻ and the amino group as –NH₃⁺. The molecule therefore carries equal positive and negative charges and no net charge: this is a zwitterion.
The fully uncharged form cannot exist in aqueous solution, because at any pH low enough to protonate the carboxyl group the amino group would also be protonated, and at any pH high enough for a neutral amino group the carboxyl would already be ionised.
The isoelectric point
The isoelectric pH (pI) is the pH at which the molecule bears no net charge and does not migrate in a direct-current electrical field. It is the pH midway between the pKa values on either side of the isoelectric species.
For alanine, with pKa values of 2.35 and 9.69, the pI is approximately 6.0. Acidic amino acids have a low pI, basic amino acids a high pI.
Application
Above its pI a molecule is net negative and migrates to the anode; below its pI it is net positive and migrates to the cathode. This is the basis of electrophoresis and isoelectric focusing, used clinically for serum protein electrophoresis and haemoglobin variant detection.
Formation
A peptide bond is the amide linkage formed between the α-carboxyl group of one amino acid and the α-amino group of the next, with the elimination of a molecule of water (a condensation reaction). Repeated, it produces the polypeptide backbone.
Partial double-bond character
The lone pair of electrons on the peptide nitrogen is delocalised onto the carbonyl oxygen, so the C–N bond behaves as though partly a double bond. Two consequences follow:
- The six atoms of the peptide unit — Cα, C, O, N, H and the next Cα — lie in a single rigid plane, almost always in the trans configuration, which keeps bulky side chains apart.
- Rotation about the C–N bond is not possible. Only the two other backbone bonds can rotate: the N–Cα bond (angle φ, phi) and the Cα–C bond (angle ψ, psi).
Why this determines conformation
A backbone free to rotate about every bond would have an effectively infinite number of conformations and could never fold reproducibly. Because rotation is restricted to φ and ψ, and because steric clashes further restrict which combinations of those angles are allowed, the chain has a limited and predictable set of stable conformations.
Those permitted conformations are precisely the regular secondary structures: the α-helix, stabilised by hydrogen bonds between backbone carbonyl and amide groups four residues apart, and the β-sheet, stabilised by hydrogen bonds between adjacent extended strands.
Directionality and nomenclature
Peptides are numbered and written from the N-terminus to the C-terminus, and are synthesised in that direction. Residues within a chain take the suffix -yl (glycyl, alanyl); only the C-terminal residue keeps its full name.
Where the rule breaks — and why that matters
Proline is the exception. Its side chain bonds back to the α-nitrogen, fixing φ and removing the amide hydrogen needed for backbone hydrogen bonding. Proline therefore disrupts α-helices and is common at bends — a direct illustration that the conformation of a protein is dictated by what the peptide bond will and will not allow.