Enzyme Characteristics

..Catalytic Power

..Specificity

..Structure

..Classification

Mechanism of Action

..Fit of Substrate and Active Site

..Balancing Bond Breaking and Bond Making

Enzymes are the catalysts which make possible biochemical reactions. Consider that bichemistry takes place at about 37 degrees C in water and contrast that to typical reaction conditions in organic chemistry. For example, to hydrolyze (saponify) fats we boil them with concentrated sodium hydroxide solution for a few hours. Enzymes called lipases do the same thing at body temperature in minutes. Without enzymes, our body chemistry would not occur, and life would not exist. This illustrates the impressive power of enzymes as catalysts.

Remember that catalysts increase the rate of a reaction, but are not themselves consumed or produced by the reaction. Also, they do not change the equilibrium constant of a reaction. This means that any catalyst which catalyzes a reaction in one direction (e.g., esterification) also catalyzes the reverse (e.g., ester hydrolysis) reaction. To say these things another way, catalysts do not change the energy balance between reactants and products; catalysts do lower the energy barrier between reactants and products. These statements are true of enzymes as well as other types of catalysts.

Enzymes differ from simple catalysts another very important way. Enzymes are much more specific. Sulfuric acid as a source of H⁺ will catalyze the formation of any ester from the appropriate alcohol and carboxylic acid, but many enzymes are so specialized that they will catalyze a reaction of one molecule, but will leave untouched a very similar molecule. Amylase, a digestive enzyme, will hydrolyze starch, but not cellulose. Both molecules are polymers of glucose. They differ in the orientation of one bond at the junction of glucose units. Other enzymes can work effectively on a broader range of substrates (the molecule whose reaction is being catalyzed.

This broader specificity is useful in the case of an enzyme like papain which is important in protein digestion. It can catalyze the hydrolysis of peptide (amide) bonds in a variety of proteins, which means that the body does not need to maintain a stock of more specific enzymes to tackle specific proteins.

As always, we will expect to find explanations for these enzyme characteristics in the structure of enzymes. The first thing to notice is that enzymes are almost all proteins. They are often globular proteins. Thus we can describe them in terms of their primary, secondary, tertiary, and in many cases, quaternary structure. They are long chains of amino acid units held together by peptide bonds, looped and folded into secondary and tertiary (and often quaternary) structures by disulfide bonds, hydrophobic interactions, and salt bridges.

In addition, active enzymes usually involve "cofactors." These are small molecules (sometimes inorganic ions) which are needed complete the catalytically active structure of the enzyme. In such instances, the enzyme without the cofactor is called an apoenzyme, and the apoenzyme-cofactor complex is called a holoenzyme. We will see that the protein chain of an apoenzyme can have functional groups on its side chains (R groups) which are important to its catalytic function, but other important functional groups are introduced by way of cofactors.

Enzymes are classified according to the reactions they catalyze. In some cases, the terms used are fairly clear; in others, less so. Examples:

 

Oxidoreductases:

These are enzymes which catalyze the reduction or oxidation of a molecule. Remember that oxidation is the reverse of reduction and that an enzyme has to catalyze the forward and reverse reactions to the same degree. Any enzyme which catalyzes a reduction has to also catalyze the reverse (oxidation) reaction, thus the double-barreled name "oxidoreductase."

Transferases:

These enzymes catalyze the transfer of a group of atoms from one molecule to another. A common example involves transfer of a phosphate between ATP and a sugar molecule.

Hydrolases:

As the name suggests, these enzymes catalyze hydrolysis reactions (and their reverse reactions). The hydrolysis of an ester would be an example of such a reaction.

Isomerases:

These enzymes catalyze the conversion of a molecule into an isomer. The cis-trans interconversion of maleate and fumarate is an example.

Lyases:

Reactions which add a small molecule such as water or ammonia to a double bond (and the reverse, elimination, reactions) are catalyzed by lyases.

Ligases:

These enzymes catalyze reactions which make bonds to join together (ligate) smaller molecules to make larger ones.

Each of these classes has more specific subclasses as well. The key to using this classification scheme is to look at the reaction the enzyme catalyzes, decide which type of reaction it is, and apply the appropriate name.

Specific enzyme names are systematically derived by specifiying the substrate (the molecule being acted upon -- the reactant), the type of reaction, and appending the suffix ase. Alcohol dehydrogenase thus is an enzyme which acts on an alcohol and takes hydrogen (oxidizes) from it: it is therefore classified as an oxidoreductase. We can tell a lot about what an enzyme does from its name.

Catalytic power and specificity are the two characteristics of enzymes which require explanation. The structure of the enzyme's active site [the part of the enzyme's structure where the substrate, the enzyme's functional groups and the cofactor (if any) come together] will provide us with the beginnings of an explanation.

Since a catalyst must come in contact with the substrate to initiate any reaction, there must be a fit between the substrate and the active site. Right away, some substrate molecules will fit and others will not, so some substrates will react and others will not. This is specificity. The fit can come about either because the molecule fits easily into the enzyme's active site (lock-and-key model) or because the enzyme's structure adjusts to the substrate's entry (induced fit model).

How does catalysis occur, or, what reduces the energy barrier for reaction. Let's keep in mind that making bonds lowers the energy of a molecule, and breaking bonds raises it. Since reactions involve both bond breaking and bond making, a reaction's energy barrier is reduced if, in each step, the energy required to break one bond is supplied by making another. Let's illustrate this idea by tracing through the mechanism of a well studied reaction, the hydrolysis of a peptide bond by the enzyme chymotrypsin.

Information provided by: http://www.chem.wsu.edu