The many biochemical pathways found within living cells often involve chemical reactions which do not easily take place at normal temperatures and pressures. For this reason there is a need for catalysts to be present in the cell to ensure that the rates of reaction are fast enough to maintain the living system. The main catalysts occurring in living organisms are formed from protein molecules. They have a complex 3-D shape which in certain regions have the ability to link temporarily to other molecules. These active sites can impose forces upon the linked molecule at the atomic level which will allow specific reactions to occur very easily. Most reactions require an input of energy to start them off, a fire is a good example! The job of the enzyme is two-fold:

1. It lowers the activation energy requirement of the reaction allowing it to occur at much lower temperatures and pressures than it otherwise would;
2. It creates the necessary stresses, or associations between chemical groupings so that only one particular reaction can occur.

The alteration of a protein's active site can seriously interfere with its efficiency as a catalyst. The shape is held by hydrogen, ionic and disulphide bonds and also by the hydrophobic-hydrophilic reactions of its component amino acids. Any factor which can interfere with these shaping forces will alter the rate of an enzyme controlled reaction. Organisms which live in extreme environments, such as hot springs at 70^oC, have enzymes with many strong disulphide bonds rather than the weaker hydrogen bonds.

Enzyme reactions can be classified into two main categories, anabolic (building reactions) and catabolic (breakdown reactions). The sum of all of these reactions is referred to as the metabolism. As the reaction pathways of an organism are all inter-linked it is very important that the various reactions run at speeds which create an overall balance to the reaction pathways. Alteration of one reaction pathway can have serious repercussions upon other reaction pathways. For example, a dose of cyanide prevents one enzyme in the respiratory pathways from working. This leads to a failure to produce adequate ATP. The lack of ATP prevents most other reactions from working and the organism ceases to function. You must be aware that the biochemical pathways are a dynamic set of reactions which must be controlled if they are to produce the overall result of a living organism.

Temperature is a major influence upon reaction rates. Initial the rate increases by doubling with each 10^oC rise in temperature (Q₁₀rule). Then a peak is reached and the enzyme rapidly loses its catalytic ability as its active site is disrupted by the high temperatures inducing hydrogen bond instability. If the disruption of the protein's shape is extreme enough then the protein will be permanently denatured. You can imagine this as a spring being stretched, if you let it go it bounces back to its former shape, but if you stretch it to far it remains distorted out of shape.

In this graph we see two enzymes which have similar reaction profiles but with their optima at different pH's. The number of H⁺ or OH^- in a solution has a powerful affect upon the stability of hydrogen and ionic bonds, which are weak +ve and -ve attractions between different parts of the protein.

The amount of substrate available for a reaction will clearly be linearly related to the rate of reaction. However, a point is reached at which the concentration of the substrate is so great that when the product is released by the enzyme another substrate attaches. There is no idle time between reactions and a maximum rate is achieved.

An enzyme only carries out one reaction because its active site is designed to fit only to its substrate molecule or molecules. Sometimes a molecule with a shape or arrangement of chemical groups similar to the substrates gets onto the enzyme's active site. While this 'foreign' molecule is blocking the active site no reactions can take place. The reaction is inhibited. The inhibitor can have a number of styles of action. It may hop onto the active site and then be thrown off. While it is off, the correct substrate can get on. This type of action is called competitive inhibition. If the inhibitor attaches to the enzyme and either permanently blocks the active site or deforms the enzyme, rendering the active site useless, we call it a non-competitive inhibitor. Often in biochemical pathways, the final product of the pathway can inhibit the action of an enzyme in the pathway to reduce the activity of the system, if too much product is being made. For example ATP inhibits an enzyme in the glycolysis pathway if a very high concentration of ATP exists. Many heavy metals act as inhibitors. Lead for example will alter the solubility of enzyme proteins and affect their ability to catalyse reactions.

Many enzymes require the presence of cofactors to enable them to function. These may be as simple as particular ions Cl^- or Mg⁺⁺. Sometimes the cofactor is a bigger molecule referred to as a coenzyme.

Cofactors you should know about:

Coenzyme A: forms a complex with an enzyme to create a 2C acetyl group from a 3C acid.

NAD, FAD and NADP are hydrogen acceptors without which dehydrogenase reactions will not work.

Many of the B group of vitamins are cofactors in the respiratory pathways.

Phosphorylase adds a phosphate group.

Dephosphorylase takes off a phosphate group.

Hydrogenase adds hydrogen.

Dehydrogenase removes hydrogen.

Carboxylase adds carbon dioxide.

Decarboxylase removes carbon dioxide.

Isomerase changes one isomer into another.

Kinase moves a group from one position to another on a molecule.

Endopeptidase breaks the bond between two adjacent amino acids within the polypeptide chain.

Exopeptidase breaks the bond between amino acids on the ends of polypeptide chain.

Polymerase produces a polymer from its component monomers.

Restriction endonuclease cuts nucleic acids (DNA) into sections at specific code sequences.

Ligase bonds sections of DNA together.

 The name for most enzymes includes the name of its substrate, for example, Ribulose bisphosphate carboxylase is the enzyme responsible for adding Carbon dioxide onto Ribulose bisphosphate in the light independent stage of photosynthesis.