However, it is not enough that the two molecules (enzyme and substrate/cofactor) have complementary shapes; they must also have complementary amino acid sequence at a specific site known as the binding site, so that they can attach to each other and carry out reaction faster. The amino acids at the catalytic site must also be of specific sequence and arranged in a suitable shape such that a reaction can take place with the other molecule bound to the protein in a specific orientation.
The type and location of interactions between polypeptide chains also affects the function of the protein, in determining whether it is an enzyme or a structural fibrous protein. For e.g., in collagen, bonds form between side chains of lysine in polypeptide chains lying next to each other---these cross-links hold many collagen molecules together forming fibres with added tensile strength; thus function of collagen protein is that of providing structural support (as in tendons).
Amino acid sequence of the protein affects the type of bonding that occurs, because the different polar or non-polar R groups on the amino acids react with each other or with other parts of the amino acid chain differently---the relative positions of each group affect what kind of bonds form and where. The bonding that occurs is such that the protein molecule is as stable as possible, so it cannot be broken down easily and can carry out its specific functions properly. For e.g., in collagen there is a small glycine amino acid for every third amino acid in the chain, so three polypeptide chains can interact closely at these points in the chains forming a tight triple helix structure needed to confer strength in tendons. The bonding also creates the protein’s unique shape essential in determining its specific function, especially in enzymes which can only bind to and react with specific molecules.
Configuration of the protein also affects its solubility, which affects the medium in which it is carried and thus the role it plays in the body. For example, globular proteins tend to curl up so their non-polar, hydrophobic side chains point to the center and the hydrophilic side chains remain on the outside---this makes them soluble and allows them to be transported in the blood, e.g. haemoglobin carries oxygen to respiring cells all over the body via blood vessels.
Proteins may sometimes contain prosthetic groups which aid in their function, e.g. haemoglobin contains haem groups which bind to oxygen which the protein is supposed to transport.
In conclusion, the structure of proteins provide the conditions and/or limitations which gives the proteins their unique function(s) in organisms.
Vera Goh
2S03C
29/1/03
