Structural Biochemistry/Enzyme/Reaction intermediates

The transition state is the highest energy intermediate of a reaction and thus tends to be the shortest-lived intermediate along a reaction coordinate. Upon formation of the transition state, the intermediate can spontaneously proceed to product formation.

This transition state of intermediates are indicated by double dagger. Transition state has a higher free energy or delta G than reactants and products. Therefore, the intermediates are less stable than reactants and products.

The energy difference between reactant and transition state is called activation energy. The activation energy determine the rate of reactions. Since the activation energy is the difference in energy between the reactant and the intermediate, it acts as a barrier for the reactant to overcome. As a result, enough energy must be added to the reactants in order to overcome the activation energy and transform into product. Therefore, the higher the activation energy, the harder it will be for the reactant to be converted into product. The rate limiting step, which is sometimes related to formation of the highest energy intermediate determines the rate of the reaction. The activation energy depends on a number of factors including temperature, the specific reaction involved and the presence of catalysts.

An enzyme generally accelerates the rate of reaction by stabilizing the transition state intermediate. Enzymes simply lower the activation energy of the intermediates by changing the conformation of the intermediates into a more favorable and stabilized conformation. A stabilized intermediate means lower activation energy and as mentioned above, lower activation energy means lower activation barrier so the reactants can form products at a faster rate. The result is generally a very large increase in reaction rates on the order of millions of times.

Enzymes do not alter reaction equilibrium because they do not change the potential energy of either starting material or products. Furthermore, the rates of the forward and reverse reactions are changed equally, meaning that the ratio of k_forward and k_reverse is the same at all times.