BIOCHEMISTRY

Chemical Reactions

Some reactions require energy. Energy must be added in order to make these reactions happen and the product(s) will be at a higher energy level than the reactants. In metabolism, many anabolic reactions fall into this category.

Some reactions release energy. In such reactions the product(s) will be at a lower energy level than the reactants. For example metallic sodium will react with water to form sodium hydroxide, hydrogen gas and heat. In addition to being energetically favored and exothermic this reaction is also spontaneous.

Not all energetically favored, exothermic reactions are spontaneous. Many times some energy of activation needs to be added. For example, paper (cellulose = C6H12O6) exists stably in the presence of oxygen. Even though the rapid oxidation of the cellulose to form CO2, H2O and C is energetically favored, the paper won't burn (burning = the rapid oxidation of cellulose) unless activation energy (heat) is applied.

ENZYMES

In the cell, the energy needed to drive anabolic reactions as well as the activation energy needed to get many catabolic reactions going cannot be directly applied as heat. Instead, cells use enzymes to lower the amount of energy needed to cause the reactions to occur. Thus enzymes are called catalysts because the facilitate reactions and speed them up but they don't enter into the reactions.

Enzymes lower the activation energy of reactions because enzymes are able to (1) bind to the reactants (substrate), (2) force the reactants (substrate molecules) very close to each other and (3) bend the substrate molecules and destabilize their electron configurations. This makes the molecules unstable and reactive. We can call these unstable reactant molecules unstable intermediates or reactive intermediates. The place on the enzyme where substrate binds is called the substrate binding site or the active site of the enzyme. (See Tortora pg. 107, fig. 5.3 to see a computer simulation of how enzymes bind to substrate.)

There is an unique enzyme for every reaction within the cell. Enzymes are usually named after the reaction they catalyze and their name often ends with the suffix -ase. (See Tortora page 105, Table 5.1 for a list of enzyme types.)

Variations on the Enzyme Theme:

(1). Holoenzyme = Apoenzyme + Cofactor

In these enzymes the binding site is not active until a cofactor binds to it. Cofactors are non-protein atoms or molecules which bind to the apoenzyme. These are often metal ions or a variety of organic molecules. (See pg. 105, fig.5.2 for a description of holoenzymes. Pg. 106, table 5.2 for a short list of organic cofactors (coenzymes)).

(2). Allosteric Enzymes

These enzymes have an extra binding site, the allosteric site, into which a cofactor can bind. This allows the cofactor to act like a switch turning the enzyme either on or off. If the cofactor turns the enzyme on it can be called an activator. If the cofactor turns the enzyme off it can be called an non-competitive inhibitor. (Non-competitive because the cofactor doesn't compete with the substrate for binding to the active site.) These cofactors are often metal ions. Another important cofactor for some allosteric enzymes is the nucleotide cAMP. (See pg. 109, fig. 5.6c and pg.110 fig. 5.7 for some examples of allosteric enzymes.)

Competitive Inhibition

Sometimes the wrong molecule will bind to the active site of an enzyme. This can be thought of as a case of mistaken identity or molecular mimicry. The classic example of this is with the enzyme which we can call folic acid synthetase. This enzyme binds PABA and converts it to folic acid. The drug sulfanilamide has a chemical structure very similar to PABA and the drug will bind to the active site of the enzyme. Folic acid synthetase however is incapable of converting sulfanilamide into anything. Therefore once the drug is in the active site of the enzyme, that enzyme becomes inactive. This is called competitive inhibition because the inhibitor competes with the substrate for binding to the active site of the enzyme. (See pg. 108 for diagrams of the chemical structure of PABA and sulfanilamide. See pg.109, fig. 5.6b for a model of competitive inhibition.)

The enzymes active in metabolism are arranged in pathways. There are biosynthetic pathways (anabolic pathways) and there are energy producing pathways (catabolic pathways).

These pathways are controlled (turned on or off) by a variety of means:

(1.) Genetic control - genes can be turned on or off and since an enzyme can only be made if its gene is on this is an effective way to control how much enzyme is present inside the cell.

(2.) Protein (enzyme) stability - each enzyme has a life-span. Some enzymes are more stable than others. Enzyme stability is affected by various physical parameters such as: pH, temperature and salt concentration. Each enzyme has an optimum pH, temperature and salt concentration at which it works best (optimally). If these physical conditions are changed drastically from the optimum the enzyme denatures and becomes inactive. (See pg. 108, fig. 5.4 for a description of temperature and pH effects on enzymes. See pg. 109, fig. 5.5 for a description of denaturation.)

(3.) Cofactors - control apoenzymes and allosteric enzymes as described in the above discussion.

(4.) In addition to the above influences on enzyme activity, note that there are a number of substances such as cyanide, heavy metals and nerve gas which can inactivate specific enzymes.