The region that associates with the ligand is known as the binding or active site (this is also where the reaction takes place) and it is usually a cavity that is arranged to allow the correct ligand to fit in but excludes other molecules.
There are a few models to describe how the enzyme binds to the substrate. The induced fit model involves the enzyme firstly binding weakly to the substrate and this binding inducing a conformational change in the enzyme that allows the substrate to fit into the binding site. The lock and key theory suggests that the enzyme binding site is already the exact shape of the substrate. Most of the rest of the protein is present simply to maintain the protein in the correct shape so that the ligand can be bound although some parts with be involved in regulation of the enzyme by other molecules.
Non-protein molecules known as co-factors are sometimes associated with proteins to help with their function. For example, hemoglobin's that carry oxygen around the body are proteins plus an associated haem group.
So how does an enzyme work? Well firstly its important to point out that enzymes can't make a reaction occur that would normally be impossible. They can only speed up chemical reactions that would normally not proceed fast enough to be of any use to the cell. It works by firstly bringing together the substrates of the chemical reaction so that they are close enough to react. Secondly, they stabilize the transition states of the reaction to allow the reaction to take place. To explain what I mean by this, I have drawn you a pretty little picture.
OK, this graph shows the process of a simple reaction that converts the substrate, S, to the product, P. To reach the product, the substrate must go through several intermediate states, which tend to be very unstable. Everything likes to be in the lowest possible energy state so something with a high energy tends to be very unstable. The intermediate state with the highest energy is known as the transition state and this determines what is known as the activation energy.
Activation energy is the energy that has to be put into a reaction so that the substrate can reach the high energy transition state and therefore be converted into the product. On the graph the activation energy is shown as the difference between the energy of the substrate and the energy of the transition state. The enzyme works by reducing the energy of this transition state and stabilizing it- they do this by binding to the transition state much more strongly that the more stable substrate. This means that the reaction can proceed more easily and faster than it would normally.
Enzymes can also speed up reactions by covalently binding themselves
to the substrate and then allowing another reaction to break the
bond. This is an advantage if the two separate reactions have
lower activation energies that the single step reaction.
