There are two primary reasons for not letting chemical reactions occur naturally.
First, sometimes the reactions would not naturally occur. For example, the Calcium and Phosphorus do not naturally react to form a material similar to bones. Since the reaction is so vital, it needs to be "helped along" by the enzyme to make sure it occurs.
Second, sometimes the reactions that do occur naturally are dangerous. A massive exothermic reaction in your brain, or a severe endothermic reaction in a bone, would be unpleasant if not fatal. Enzymes within cells alter how these reactions occur keeping them from having undesirable side-effects.