Classification of Proteins: MDCAT Chemistry notes
Classification of Proteins for MDCAT: amino acids, zwitterions, peptide bonds, simple, conjugated and derived proteins, collagen and gelatine.
Amino acids: the building blocks
Proteins are polymers of $\alpha$-amino acids, $\mathrm{H_2N{-}CH(R){-}COOH}$, which carry an amino group and a carboxyl group on the same carbon. They are bifunctional compounds. About 20 different amino acids occur in proteins.
- Glycine is the simplest (R = H); alanine has R = $\mathrm{CH_3}$. Lysine, leucine and glutamic acid are other common amino acids.
- Lactic acid ($\mathrm{CH_3CH(OH)COOH}$) is a hydroxy acid, and folic acid is a vitamin; neither is an amino acid.
Zwitterion and amphoteric nature
Inside the molecule the $-\mathrm{COOH}$ group donates its proton to the $-\mathrm{NH_2}$ group, giving a dipolar ion (zwitterion), $\mathrm{H_3N^+{-}CHR{-}COO^-}$. It is amphoteric:
- When acid is added, the $\mathrm{-COO^-}$ group accepts $\mathrm{H^+}$ (acts as the base).
- When base is added, the $\mathrm{-NH_3^+}$ group gives up $\mathrm{H^+}$ (acts as the acid).
Peptide bond
The $-\mathrm{COOH}$ of one amino acid condenses with the $-\mathrm{NH_2}$ of another, losing water and forming the peptide (amide) linkage, $-\mathrm{CO{-}NH-}$. Two amino acids give a dipeptide, three a tripeptide, many a polypeptide.
Worked example: how many different tetrapeptides can be made from four different amino acids if each is used once? The order matters, so the number is $4! = 24$. For three different amino acids used once each, $3! = 6$.
Levels of protein structure
| Level | What it is | Held by |
|---|---|---|
| Primary | Sequence of amino acids | Peptide bonds |
| Secondary | $\alpha$-helix, $\beta$-pleated sheet | Hydrogen bonds between the N–H of one peptide group and the C=O of another |
| Tertiary | Folding of the whole chain | H-bonds, ionic bonds, disulphide bridges, hydrophobic forces |
| Quaternary | Association of several chains (e.g. haemoglobin) | Same forces between chains |
Classification by physico-chemical properties
Proteins are classified into three types: simple, compound (conjugated) and derived.
| Class | Definition | Examples |
|---|---|---|
| Simple proteins | Give only amino acids on hydrolysis | Albumins, globulins, collagen, keratin |
| Compound (conjugated) proteins | Protein + non-protein prosthetic group | Phosphoproteins (casein), glycoproteins, lipoproteins, chromoproteins (haemoglobin), nucleoproteins |
| Derived proteins | Formed from natural proteins by partial hydrolysis or denaturation | Gelatine, proteoses, peptones |
- Collagen, a fibrous simple protein, is the most abundant protein of the animal kingdom, forming about 25–35% of body protein.
- Heating (boiling) bones, skin and tendons partially hydrolyses collagen to gelatine, a derived protein.
- Simple proteins are further divided by shape into fibrous (collagen, keratin) and globular (albumin, haemoglobin chains, enzymes).
Common MDCAT traps
- Phosphoprotein is conjugated, not simple or derived.
- In zwitterion formation COOH donates, $\mathrm{NH_2}$ accepts.
- The $\alpha$-helix is held by hydrogen bonds, not van der Waals forces or disulphide bridges.
- The link joining amino acids is the peptide bond, not an ester linkage.
- For $n$ different amino acids used once each, the number of peptides is $n!$, not $n^2$.
Quick revision
- Glycine = simplest amino acid.
- Peptide linkage: $-\mathrm{CO{-}NH-}$.
- Classes: simple, conjugated, derived.
- Gelatine comes from collagen of bones.
- Collagen: 25–35% of body protein.