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Enzymes are proteins that can increase the rate of a chemical reaction, like a catalyst, by lowering the activation energy. Most processes in a cell rely on enzymatic reactions to turn substrates into products, which occurs at a significant rate. Although enzymes can speed up reactions, millions of times faster than un-catalyzed, only a few reactions are possible due to enzymes being selective to specific substrates. The metabolic pathways which occur in a cell are determined by the set of enzymes made in that cell. Like all catalysts, enzymes are not destroyed by the reaction they catalyse, they also, do not alter the equilibrium of the reaction.
Most enzymes are globular proteins, which are also known as stereoprotiens, due to their spherical shape. The spherical shape of a globular protein is determined by four key structures during the enzymes development.
The primary structure of a protein can contain hundreds of amino acids. The different types of amino acids and their chained sequence determine the function of the protein. A simple change in one amino acid can completely change the properties of a protein.
A polypeptide forms an Î±- helix due to interactions between amino acids. The attraction between the CO group of one amino acid and the NH group of an amino acid four places ahead, bond through non-covalent forces, this is called a hydrogen bond. This is due to electron sharing on the NH group, leaving a slightly positive charge. In turn, the oxygen in the CO group carries a slightly negative charge, this causes the hydrogen and oxygen to attract each other. Hydrogen bonds hold the Î±- helix shape.
The tertiary structure is formed by an Î±-helix coiling or folding, which forms a precise 3D structure. This precise structure is held in place by bonds between different amino acids, in different parts of the chain. There are four types of bonds which help fold and hold proteins in into a precise shape.
Disulphide bonds form between cystine molecules, Hydrogen bonds which form between R groups, ionic bonds form between ionised amine and carboxyl acid groups and van der waals forces which attract non polar side chains together.
Many proteins contain different polypeptide chains in them. They are often held in place by non- covalent, the same forces which stabilize the tertiary structure of proteins. A protein with multiple polypeptide chains is called a oligomeric protein. A structure which is formed by monomer - monomer attractions in a oligomeric protein form the quaternary structure. Oligomeric proteins can contain many identical protein subunits are called homo-oligomers, proteins which contain different protein subunits are called hetero-oligomers.
The oxygen carrying protein of the blood, haemoglobin, is a good example of an hetero-oligomer. The Haemoglobin structure contains 2 Î± and 2 Î² subunits, this arrangement forms an Î±2Î²2 quaternary structure.
Enzymes are generally globular proteins which which are composed of 'globe' shaped proteins which are soluble in water and other aqueous solutions. Enzymes are larger than the substrate they act upon, yet only a small area of the enzyme is involved, directly, with catalysis
The abilities of an enzyme are influenced by their Three dimensional shape, the area of the three dimensional structure which binds the substrate and forms the product is called the active site. There are also binding sites on an enzyme for binding cofactors, needed for catalysis. Thesbinding sites can also bind other small molecules, which can inhibit or activate an enzyme, which can provide a means for feedback regulation.
As enzymes are proteins, they have long, linear chains of amino acids, which produce there 3d shape. Due to the specific shape produced by the amino acid sequence, the enzyme is given unique properties. Most enzymes can be denatured by chemical denaturants or by temperature changes which cause the 3D structure to unfold, thus denature. If the environment changes are not too severe, an enzyme denaturation may be reversed.
The unique shape enzymes fold into give the enzyme specificity to only a few substrates. The specific requirements in which a substrate must engage are the complimentary shape of the enzyme, the hydrophobic/ hydrophilic nature and charge of both enzymes and substrates.
The geometric shape of both substrates and enzyme are complimentary to each other. This is refereed to as the "lock and key" method, which explains enzyme specificity, it does not however, explain stabilization of the transition state an enzyme must achieve.
It was suggested by Daniel Koshland in 1958, that a modification to the lock and key method could explain the stabilization of the transition state. The theory stated that enzymes are flexible, with a continuously reshaping active site. The reshaping is caused by the substrate as it interacts with the enzyme. This results in amino acid side chains, which make up the active site, remoulding into the precise shape of the substrate, allowing catalysis to occur. The active site continuously changes shape until the substrate is fully bound, the charge and final shape are decided.
Effects of change in pH
pH has an effect on an enzyme by effecting the state of ionisation of acidic and basic amino acids. Each acidic amino acid has a carboxyl functioning group in its side chain. In turn, a basic amino acid has an amine functioning group in its side chain. The state of ionization determines the proteins shape, if any alteration in the ionic bonds retaining the structure occur, the protein itself is altered. This can result in protein denaturation or may cause the substrate to not recognise the enzymes active site. The change in pH can not only affect the structure of the enzyme, but can also change the charge properties of the substrate. This may cause difficulty in substrate binding or it may prevent catalysis.