B1.2 ProteinsIB Biology HL: Revision notes

Every amino acid has an alpha carbon bonded to an amine group (–NH₂), a carboxyl group (–COOH), a hydrogen atom and an R-group. Condensation between the carboxyl group of one amino acid and the amine group of another forms a peptide bond and releases water:

amino acid + amino acid → dipeptide + water

A chain of n amino acids has n − 1 peptide bonds. Hydrolysis reverses this, using one water per bond.

Essential amino acids cannot be synthesized and must come from food; non-essential ones can be made from other amino acids. Vegan diets must combine plant proteins to supply all essential amino acids.

With 20 amino acids, in any order and chains of any length, there are 20ⁿ possible sequences, giving almost infinite variety (examples: insulin, collagen, titin).

Heat and extremes of pH break the bonds holding the three-dimensional shape: denaturation.

R-groups are the basis of the immense diversity in protein form and function. R-groups are hydrophobic (non-polar) or hydrophilic; hydrophilic R-groups are polar or charged, and charged ones are acidic (–COO⁻) or basic (–NH₃⁺).

The primary structure is the sequence of amino acids. The sequence and precise position of each amino acid determines the protein's three-dimensional conformation, so proteins have precise, predictable and repeatable structures despite their complexity.

Secondary structure: hydrogen bonds form in regular positions between the C=O and N–H groups of the backbone, coiling the chain into alpha helices or folding it into beta-pleated sheets.

Tertiary structure: further folding, held by bonds between R-groups:

• hydrogen bonds between polar R-groups;
• ionic bonds between R-groups that have become charged by gaining or losing H⁺ (–NH₃⁺ and –COO⁻), which is why pH affects shape;
• disulfide bonds: covalent bonds between pairs of cysteines;
• hydrophobic interactions between non-polar R-groups.

In water-soluble globular proteins, hydrophobic amino acids cluster in the core, away from water, and hydrophilic ones are on the surface. Integral membrane proteins have regions of hydrophobic amino acids that embed them in the hydrophobic core of the membrane.

Quaternary structure is two or more polypeptides linked together. Non-conjugated proteins contain only polypeptides: insulin (two chains) and collagen (three chains). Conjugated proteins also have a non-polypeptide part: haemoglobin (four chains, each with a haem group).

Globular proteins (e.g. insulin) are compact and usually soluble, with precise shapes for binding. Fibrous proteins (e.g. collagen) are long, insoluble and strong. Collagen's triple helix gives high tensile strength for skin, tendons and bone; insulin's shape lets it bind to specific receptors.

NOS: cryogenic electron microscopy has allowed single protein molecules and their interactions to be imaged, which would be impossible with the unaided senses.