Proteins — IB Diploma Biology HL

Revision notes

8 short notes, in the order of the specification. Each one in short:

1. Amino acids and peptide bonds

   Practical

   An amino acid has a central alpha carbon atom bonded to an amine group, a carboxyl group, a hydrogen atom and a variable R-group. In a condensation reaction the carboxyl group of one amino acid reacts with the amine group of another, forming a peptide bond and releasing water. Repeating this produces a polypeptide.

2. Dietary amino acids and the variety of peptide chains

   Essential amino acids cannot be synthesised by the body and must be obtained from food, while non-essential amino acids can be made from other amino acids. The genetic code codes for 20 amino acids, and a chain can have any number of them, from a few to thousands, in any order, so the variety is effectively infinite.

3. Effect of pH and temperature on protein structure

   Practical

   Denaturation is a change in the three-dimensional structure of a protein that is usually permanent, so the protein can no longer carry out its function. High temperatures make the molecule vibrate until weak bonds holding its shape break. Extremes of pH change the charges on R-groups, breaking ionic and hydrogen bonds. Peptide bonds are not broken.

4. R-groups and primary structure

   HL only

   The R-groups of the 20 amino acids are chemically diverse: some are hydrophobic and others hydrophilic, and hydrophilic R-groups are polar or charged, acidic or basic. R-groups determine the properties of a polypeptide. The primary structure, the sequence of amino acids, determines how the chain folds, so proteins have precise, predictable and repeatable three-dimensional shapes.

5. Secondary structure: alpha helices and beta-pleated sheets

   HL only

   Secondary structure is the regular coiling or pleating of parts of a polypeptide, stabilised by hydrogen bonds in regular positions between the C=O of one peptide bond and the N–H of another. In an alpha helix the chain coils, with each C=O bonded to the N–H four amino acids along; in a beta-pleated sheet, neighbouring stretches lie side by side.

6. Tertiary structure and the effect of polar and non-polar amino acids

   HL only

   Tertiary structure is the overall three-dimensional folding of a polypeptide. It depends on interactions between R-groups: hydrogen bonds, ionic bonds, disulfide covalent bonds between pairs of cysteines, and hydrophobic interactions. In water-soluble globular proteins, hydrophobic amino acids cluster in the core, while integral membrane proteins have hydrophobic regions that embed in the membrane.

7. Quaternary structure: non-conjugated and conjugated proteins

   HL only

   Quaternary structure is the linking of two or more polypeptides to form a single protein. Non-conjugated proteins consist only of polypeptides, for example insulin (two chains) and collagen (three chains). Conjugated proteins also contain a non-polypeptide component, for example haemoglobin, which has four polypeptides each with a haem group containing iron that binds oxygen.

8. Form and function in globular and fibrous proteins

   HL only

   Globular proteins are rounded, compact and usually soluble, with a specific shape that suits roles such as hormones and enzymes; insulin is an example. Fibrous proteins are long, narrow and insoluble, with repetitive structure that gives strength; collagen is an example. In both, form is related to function: insulin binds a receptor, while collagen resists pulling forces.