AS Biology 9700: Protein Structure from Primary to Quaternary

Proteins are polymers of amino acids, and their function depends on the way the polypeptide chain folds and, in some cases, associates with other chains.

(a) State what is meant by the primary structure of a protein, and name the type of bond that links adjacent amino acids together. [2]

(b) Describe the two common types of secondary structure found in proteins, stating the type of bond responsible for maintaining each. [2]

(c) Explain, with reference to at least three different types of interaction between R-groups, how the tertiary structure of a protein is formed and maintained. [3]

(d) Haemoglobin is a globular protein with a quaternary structure, while collagen is an insoluble fibrous protein. Explain how the structure of haemoglobin, and separately the structure of collagen, is related to its function. [3]

Part (a): Primary structure

Primary structure is the specific linear sequence of amino acids that make up a polypeptide chain. Adjacent amino acids are joined together by peptide bonds, formed by condensation reactions between the amino group (-NH2) of one amino acid and the carboxyl group (-COOH) of the next, with a molecule of water released at each bond formed.

Part (b): Secondary structure

The polypeptide chain folds locally into regular, repeating shapes. In an α-helix, the chain coils into a spiral. In a β-pleated sheet, sections of the chain lie alongside one another in a folded, zig-zag arrangement. Both structures are held in shape by hydrogen bonds that form between the C=O group of one amino acid and the N-H group of another amino acid further along the backbone, not by interactions between R-groups.

Part (c): Tertiary structure

Tertiary structure is the overall three-dimensional folding of a single polypeptide chain, produced and held in place by interactions between the R-groups of amino acids that may lie far apart in the primary sequence. These interactions include:

Hydrogen bonds between polar R-groups.
Ionic bonds between R-groups carrying opposite charges.
Disulfide bonds, covalent bonds that form between the sulfur atoms of two cysteine R-groups.
Hydrophobic interactions, where non-polar R-groups cluster together away from water.

Together, these interactions fold the chain into its precise, functional three-dimensional shape.

Haemoglobin is a globular protein: its polypeptide chains fold so that hydrophilic R-groups face outwards and hydrophobic R-groups are tucked inwards, making the molecule roughly spherical and soluble in the aqueous environment of the red blood cell and blood plasma. It has a quaternary structure made of four polypeptide subunits, each associated with a haem group that binds one oxygen molecule, so the whole molecule can carry up to four oxygen molecules at once, a structure well suited to its transport function.

Collagen is a fibrous protein: three polypeptide chains, each rich in the small amino acid glycine, wind around one another to form a rope-like triple helix, stabilised by hydrogen bonds between the chains. Many triple-helix molecules are then cross-linked together to form long, insoluble fibres. This structure gives collagen high tensile strength but no solubility, suiting its structural role in tissues that must resist stretching, such as tendons, skin, cartilage and the walls of blood vessels.

Final answers

(a) Primary structure = the amino acid sequence, linked by peptide bonds.
(b) α-helix and β-pleated sheet, both held in shape by hydrogen bonds along the polypeptide backbone.
(c) Tertiary structure is held together by hydrogen bonds, ionic bonds, disulfide bonds and hydrophobic interactions between R-groups.
(d) Haemoglobin (globular, quaternary, four haem-bearing subunits) is suited to soluble oxygen transport; collagen (fibrous, triple helix, cross-linked fibres) is suited to structural strength.