Proteins are complex macromolecules whose function is intimately linked to their three-dimensional structure. Protein structure is described at four levels of organisation, each representing a different level of complexity. Understanding these levels is essential for understanding how proteins fold, function, and interact. The four levels are: (1) Primary structure — the linear sequence of amino acids, (2) Secondary structure — local regular folding patterns stabilised by hydrogen bonds, (3) Tertiary structure — the overall 3D shape of a single polypeptide chain, (4) Quaternary structure — the arrangement of multiple polypeptide chains in multi-subunit proteins. Each level builds on the one below it, and each is stabilised by different types of chemical interactions.

The primary structure of a protein is the linear sequence of amino acids connected by peptide bonds (−CO−NH−). It is determined directly by the gene sequence (via the genetic code). The primary structure is read from the amino terminus (N-terminus, free −NH₂ group) to the carboxy terminus (C-terminus, free −COOH group). The primary structure determines all higher levels of structure — a protein with a specific amino acid sequence will fold into a specific 3D structure (Anfinsen's dogma). Primary structure is stabilised by covalent peptide bonds, which are very strong and require enzymatic action (proteases) to break. Even a single amino acid change (point mutation) can alter protein function dramatically — as seen in sickle cell anaemia where Glu→Val at position 6 of β-globin changes the protein's entire behaviour.

Secondary structure refers to the regular, locally folded arrangements within a polypeptide chain, stabilised by hydrogen bonds between backbone atoms (−NH and −C=O groups). The two most common secondary structures are the α-helix and the β-pleated sheet. α-Helix: the polypeptide backbone coils into a right-handed spiral. Each turn of the helix contains 3.6 amino acid residues. The helix is stabilised by hydrogen bonds between the −C=O of each amino acid and the −NH of the amino acid that is 4 residues ahead (i → i+4 H-bonds). R-groups (side chains) project outward from the helix axis. Linus Pauling and Robert Corey first described the α-helix in 1951. β-Pleated sheet: adjacent polypeptide strands are extended and arranged side by side, forming a sheet-like structure. H-bonds form between −NH and −C=O groups on neighbouring strands. Can be parallel (same N→C direction) or antiparallel (opposite N→C directions). Antiparallel β-sheets are more stable.

Tertiary structure is the overall three-dimensional conformation of a complete single polypeptide chain, including all its secondary structure elements and the loops/turns connecting them. It is stabilised by multiple types of non-covalent interactions and one type of covalent bond: Hydrophobic interactions: non-polar R-groups cluster together away from water (inside the protein core). This is the major driving force for protein folding. Hydrogen bonds: between polar R-groups and backbone groups. Ionic bonds (salt bridges): between oppositely charged R-groups (e.g., Asp/Glu with Arg/Lys). Van der Waals interactions: weak, short-range attraction between atoms in close contact. Disulfide bonds (−S−S−): covalent bonds between cysteine residues. The ONLY covalent interactions in tertiary structure. Stabilise proteins against denaturation. The 3D structure determines the protein's function — the active site of an enzyme, the antigen-binding site of an antibody, the ion channel of a receptor, are all features of tertiary structure.

Quaternary structure is present only in proteins composed of more than one polypeptide chain (subunit). It describes the arrangement and interactions of these subunits. Each polypeptide chain is a subunit. Subunits may be identical (homooligomers) or different (heterooligomers). Stabilised by same interactions as tertiary structure (hydrophobic, H-bonds, ionic bonds, disulfide bonds between subunits). Classic example: Haemoglobin — composed of 4 subunits (2 α-chains + 2 β-chains). Each subunit has its own tertiary structure (globin fold). The 4 subunits assemble to form the functional tetramer. Cooperative binding: oxygen binding to one subunit increases affinity of others (sigmoid O₂-dissociation curve). Other examples: collagen (triple helix of 3 polypeptide chains), DNA polymerase, RNA polymerase, ion channels, viral capsids.

Based on shape and function, proteins are classified as fibrous or globular. Fibrous proteins: elongated, thread-like shape. Often structural/mechanical roles. Rich in regular secondary structure. Generally insoluble in water. Examples: Collagen (connective tissue — most abundant protein in body, triple helix of 3 α-chains, tensile strength, Gly-X-Y repeat). Keratin (hair, nails, wool — α-helix wound into coiled coil). Fibrin (blood clot — β-sheet structure). Silk fibroin (β-sheets, strong and flexible). Globular proteins: compact, spherical/ellipsoidal shape. Soluble in water (hydrophilic surfaces). Functional roles (catalysis, transport, regulation, immune response). Mix of α-helices, β-sheets, random coil. Examples: enzymes (all globular), antibodies (IgG — Y-shaped), haemoglobin, myoglobin, insulin, albumin.

Denaturation is the loss of a protein's native three-dimensional structure (secondary, tertiary, quaternary) without breaking peptide bonds (primary structure intact). Causes: heat (disrupts weak interactions, vibrational energy > stabilising forces), extreme pH (alters ionic states of R-groups, disrupts ionic bonds and H-bonds), detergents/urea/guanidinium chloride (disrupt hydrophobic interactions), heavy metal ions (Hg²⁺, Pb²⁺ form bonds with −SH groups, disrupt structure), organic solvents (compete with hydrophobic core). Result: polypeptide unfolds → random coil → loss of function. Renaturation: if denaturing agent is gently removed, some proteins can spontaneously refold to their native structure. Christian Anfinsen demonstrated renaturation of ribonuclease A (Nobel 1972) → proved that sequence determines structure (Anfinsen's dogma). In cell: protein folding is assisted by chaperones (heat shock proteins: Hsp70, Hsp90, GroEL/ES) that prevent aggregation.

Twenty standard amino acids with different R-group properties determine protein characteristics. Non-polar (hydrophobic): glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, methionine. These form the hydrophobic core of proteins. Polar (uncharged): serine, threonine, cysteine, asparagine, glutamine, tyrosine. Participate in H-bonds. Cysteine forms disulfide bonds. Acidic (negatively charged at pH 7): aspartate (Asp, D) and glutamate (Glu, E). Form ionic bonds with positive R-groups. Basic (positively charged at pH 7): lysine (Lys, K), arginine (Arg, R), histidine (His, H at certain pH). Histidine (pKa ~6) acts as both acid and base near physiological pH → often found in enzyme active sites. Essential amino acids (humans): valine, leucine, isoleucine, lysine, methionine, phenylalanine, threonine, tryptophan (+ histidine, arginine semi-essential). Cannot be synthesised — must come from diet.