2.5 Proteins

1. 2.5 Proteins Specification reference: 3.1.2

2. Learning Objectives • How are amino acids linked to form polypeptides – the primary structure of proteins? • How are polypeptides arranged to form the secondary structure and then the tertiary structure of a protein? • How is the quaternary structure of a protein formed? • How are proteins identified?

3. Starter Activity: Word-Search ALPHA HELIX AMINO ACID BIURET CONDENSATION DIPEPTIDE DISULPHIDE BOND GLOBULAR HAEMOGLOBIN HYDROGEN BOND HYDROLYSIS IONIC BOND MONOMER PEPTIDE BOND POLYMER POLYMERISATION POLYPEPTIDE PROSTHETIC TERTIARY QUATERNARY

4. Why are Proteins polymers? Proteins consist of long chains of amino acids.

7. There are over 20 naturally occurring amino acids, which differ in the composition of the R group.

8. Two amino acids may be linked together by a condensation reaction to form a ‘dipeptide’.

9. Since the amino acids may be joined in any sequence there is an almost infinite variety of possible proteins.

10. The chain of amino acids is referred to as the protein’s primary structure.

11. The chain is folded (often into a helix) to give the secondary structure.

12. The secondary structure is folded on itself to form the tertiary structure.

13. The combination of a number of polypeptide chains along with associated non-protein groups results in the quaternary.

14. Quaternary Structure Of A Protein

15. These shapes are due to the fact that proteins are amphoteric, i.e. they have both positive and negative charges on them. • The attraction of these opposite charges forms weak electrostatic (hydrogen) bonds causing the chain to form a complex 3D structure – globular proteins.

16. Ionic bonds, disulphide bridges, hydrogen bonds and hydrophobic interactions all contribute to the final shape of a given protein molecule.

17. All enzymes and some hormones are globular proteins and their functions depend on the precise shape of the protein molecule.

18. Sometimes the protein consists of long parallel chains with cross-links – fibrous proteins. • These are insoluble and have structural functions, e.g. collagen in cartilage; keratin in hooves, feathers and hair, actin and myosin in muscle.

19. If a globular protein is heated or treated with a strong acid or alkali the hydrogen bonds are broken and it reverts to a more fibrous nature – a process called DENATURATION.

20. Proteins sometimes occur in combination with a non-protein substance (prosthetic group); these are called conjugated proteins, e.g. haemoglobin.

21. Test for Proteins The Biuret test detects peptide bonds. • Place a sample of the solution to be tested in a test tube and add an equal volume of sodium hydroxide solution at room temperature. • Add a few drops of very dilute (0.5%) copper (II) sulphate solution and mix gently. • A purple coloration indicates the presence of peptide bonds and hence a protein. If no protein is present, the solution remains blue. • Alternatively use Biuret reagent to test for protein. A purple colour shows protein is present; a blue colour indicates that protein is absent.

22. Protein shape and function Proteins perform many different roles in living organisms. Their roles depend on their molecular shape, which can be of 2 basic types. • Fibrous proteins, such as collagen, have structural functions. • Globular proteins, such as enzymes and haemoglobin, carry out metabolic functions. It is the very different structure and shape of each of these types of proteins that enables them to carry out their functions.

23. Fibrous Proteins e.g. Collagen These form long chains which run parallel to one another. These chains are linked by cross-bridges and so form very stable molecules. One example is collagen. Its molecular structure is as follows: • The primary structure is an unbranched polypeptide chain. • In the secondary structure the polypeptide chain is very tightly wound. • In the tertiary structure the chain is twisted into a second helix. • Its quaternary structure is made up of 3 such polypeptide chains wound together in the same way as individual fibres are wound together in a rope.

24. Collagen is found in tendons. Tendons join muscles to bones. When a muscle contracts the bone is pulled in the direction of the contraction. The individual collagen polypeptide chains in the fibres are held together by cross-linkages between amino acids of adjacent chains. • The points where one collagen molecule ends and the next begins are spread throughout the fibre rather than all being in the same position along it.

25. Questions • Explain why the quaternary structure of collagen makes it a suitable molecule for a tendon. • Suggest how the cross-linkages between the amino acids of polypeptide chains increase the strength and stability of a collagen fibre. • Explain why the arrangement of collagen molecules is necessary for the efficient functioning of a tendon.

26. Answers • It has 3 polypeptide chains wound together to form a strong, rope-like structure that has strength in the direction of pull of a tendon. • It prevents the individual polypeptide chains from sliding past one another and so they gain strength because they act as a single unit. • The junctions between adjacent collagen are points of weakness. If they all occurred at the same point in a fibre, this would be a major weak point at which the fibre might break.

27. Plenary: Use the following key words to write an essay on proteins. You must include all key words! Monomer Peptide Bond Polymer Polymerisation Polypeptide Primary Prosthetic Secondary Tertiary Quaternary Alpha Helix Amino Acid Biuret Condensation Dipeptide Disulphide Bond Globular Haemoglobin Hydrogen Bond Hydrolysis Ionic Bond

28. Learning Objectives • How are amino acids linked to form polypeptides – the primary structure of proteins? • How are polypeptides arranged to form the secondary structure and then the tertiary structure of a protein? • How is the quaternary structure of a protein formed? • How are proteins identified?