Proteins

General structure. Every amino acid has the same four groups attached to a central α-carbon:

• An amine group (—NH₂)
• A carboxyl group (—COOH)
• A hydrogen atom (—H)
• A variable R group (side chain) — this is what makes each amino acid different.

There are 20 R groups found in human proteins. They fall into broad chemical categories: non-polar (e.g. alanine, valine), polar uncharged (e.g. serine, asparagine), positively charged (e.g. lysine, arginine), negatively charged (e.g. glutamate, aspartate), and special cases (e.g. glycine with R = H, cysteine with R = —CH₂—SH).

Peptide bond formation. When the —COOH of one amino acid meets the —NH₂ of the next, a condensation reaction removes one molecule of water (—OH from the carboxyl, —H from the amine). The remaining —CO— and —NH— form a covalent peptide bond (—CO—NH—). The product of two amino acids is a dipeptide; many amino acids in a chain form a polypeptide.

The reverse reaction, hydrolysis, adds a water molecule and breaks the peptide bond — this is what occurs during digestion of proteins in the gut and intracellular turnover by proteases.

Primary structure is the sequence of amino acids in a polypeptide. Conventionally written from the N-terminus (free —NH₂) to the C-terminus (free —COOH). The sequence is dictated by the DNA codon sequence of the gene. A single amino acid substitution (e.g. valine for glutamate at position 6 of β-globin) can radically alter protein function — this is the cause of sickle-cell anaemia.

Secondary structure is local coiling or folding driven by hydrogen bonds between peptide backbone groups — specifically between the —C=O of one peptide group and the —N—H of another. Two patterns dominate:

• α-helix — a right-handed corkscrew with 3.6 residues per turn. R groups project outward.
• β-pleated sheet — strands of polypeptide lying side by side, connected by H-bonds at right angles to the strand direction.

It is crucial to note that secondary structure depends on the peptide backbone, not on R groups.

Tertiary structure is the overall 3D fold of a single polypeptide. It is stabilised by interactions between R groups:

• Hydrogen bonds between polar R groups.
• Ionic (salt) bonds between full-charge R groups.
• Disulfide bridges (—S—S—) — covalent bonds between two cysteine R groups; the strongest stabilising interaction.
• Hydrophobic interactions — non-polar R groups cluster in the interior, away from water, driven by the entropy of surrounding water molecules.

Tertiary structure determines the precise geometry of an enzyme's active site, an antibody's binding region or a receptor's ligand-binding pocket.

Quaternary structure is the arrangement of two or more polypeptide subunits held together by the same R-group interactions as in tertiary structure. Many quaternary proteins also incorporate a non-protein prosthetic group (e.g. the iron-containing haem of haemoglobin). The functional protein is the assembled complex; individual subunits typically have little or no biological activity on their own.

Type. Haemoglobin (Hb) is a globular protein — roughly spherical, soluble in the cytoplasm of red blood cells.

Quaternary structure. Four polypeptide subunits:

• Two α-globin chains (141 amino acids each)
• Two β-globin chains (146 amino acids each)

The four subunits are held together by hydrogen bonds, ionic bonds and hydrophobic interactions between R groups at the subunit interfaces.

Prosthetic group. Each of the four subunits contains a non-protein haem group: a flat porphyrin ring with a central Fe²⁺ ion. Each Fe²⁺ reversibly binds one O₂ molecule. A single haemoglobin can therefore carry up to four oxygen molecules.

Why globular?

• Hydrophobic R groups are packed in the interior, away from water.
• Hydrophilic R groups face outward, making Hb soluble.
• The compact shape gives a large internal volume for the four haem groups to sit in pockets where they bind O₂ but resist oxidation of Fe²⁺ to Fe³⁺.

Cooperative binding. Binding of the first O₂ molecule causes a small conformational change that increases the affinity of the remaining three subunits for O₂. This positive cooperativity produces the characteristic sigmoid (S-shaped) oxygen dissociation curve: O₂ is taken up efficiently at the high partial pressures of the lungs and released efficiently at the low partial pressures of respiring tissues.

Bohr effect. High CO₂ and low pH (in respiring tissue) shift the dissociation curve to the right, unloading O₂ where it is needed.

Type. Collagen is a fibrous protein. It is the most abundant protein in the human body, providing tensile strength to tendons, ligaments, the bone matrix, skin and the walls of blood vessels.

Polypeptide structure. Each polypeptide is a left-handed helix — different from the α-helix because of the high proline content. Three such polypeptides wind around each other to form a right-handed triple helix — the tropocollagen molecule. Hydrogen bonds form between the three chains and stabilise the triple helix.

Every third amino acid is glycine. Because glycine's R group is a single hydrogen atom, it is small enough to fit at the centre of the triple helix where the three chains converge. Any other R group would be too bulky and would distort the helix.

Covalent cross-links. Many tropocollagen molecules line up end-to-end and side-to-side. Covalent cross-links form between the lysine (and hydroxylysine) R groups of adjacent tropocollagen molecules, locking the structure together.

Staggered ends. Adjacent tropocollagens are offset by about a quarter of their length — staggered like bricks in a wall. This avoids planes of weakness and produces the characteristic ~67 nm banded appearance of collagen fibres under electron microscopy.

Insolubility. Hydrophobic R groups point outward in collagen — the opposite of globular proteins. The molecule is therefore insoluble in water, ideal for a permanent structural role.

Tensile strength. Tendons made of collagen have a tensile strength comparable to that of steel cable — they can withstand the forces transmitted from muscle to bone during locomotion.

Denaturation is the loss of a protein's secondary, tertiary and quaternary structure caused by disruption of the weaker stabilising bonds. The primary sequence (peptide bonds) remains intact — denaturation is not the same as hydrolysis.

Common causes.

• High temperature — adds kinetic energy, breaks hydrogen bonds.
• Extremes of pH — alters the ionisation of R groups, breaking ionic bonds and disrupting H-bonds.
• Heavy metals (e.g. Hg²⁺, Pb²⁺) — interact with —SH and —COO⁻ groups.
• Organic solvents and detergents — disrupt hydrophobic clusters.
• Strong reducing agents — break disulfide bridges (—S—S— → 2 —SH).

Visible effect. A denatured protein exposes its previously buried hydrophobic interior, which then aggregates non-specifically with other denatured molecules. Cooked egg white turns from clear to opaque because of this aggregation.

Functional effect. Because a protein's function depends on a precise 3D arrangement of R groups — an enzyme's active site, haemoglobin's haem pocket, an antibody's antigen-binding region — loss of that arrangement abolishes the function. Denaturation is the molecular basis of fever-induced metabolic failure, of cell death by heat shock, and (deliberately) of food preservation by cooking.

Denaturation is usually irreversible in practice, because the chance of refolding from a tangled aggregate is vanishingly small.