Chemical Reactions in Metabolic Processes

In order for a chemical reaction to take place, the reacting molecules (or atoms) must first collide and then have sufficient energy (activation energy) to trigger the formation of new bonds.

Although many reactions can occur spontaneously, the presence of a catalyst accelerates the rate of the reaction because it lowers the activation energy required for the reaction to take place. A catalyst is any substance that accelerates a reaction but does not undergo a chemical change itself.

Since the catalyst is not changed by the reaction, it can be used over and over again. Chemical reactions that occur in biological systems are referred to as metabolism. Metabolism includes the breakdown of substances (catabolism), the formation of new products (synthesis or anabolism), or the transferring of energy from one substance to another. Metabolic processes have the following characteristics in common:

1. The net direction of metabolic reactions, that is, whether the overall reaction proceeds in the forward direction or in the reverse direction, is determined by the concentration of the reactants and the end products. Chemical equilibrium describes the condition where the rate of reaction in the forward direction equals the rate in the reverse direction and, as a result, there is no net production of reactants or products.

2. Enzymes are globular proteins that act as catalysts (activators or accelerators) for metabolic reactions. Note the following characteristics of enzymes:

• The substrate is the substance or substances upon which the enzyme acts. For example, amylase catalyzes the breakdown of the substrate amylose (starch).

• Enzymes are substrate specific. The enzyme amylase, for example, catalyzes the reaction that breaks the á-glycosidic linkage in starch but cannot break the â-glycosidic linkage in cellulose.

• The induced-fit model describes how enzymes work. Within the protein (the enzyme), there is an active site with which the reactants readily interact because of the shape, polarity, or other characteristics of the active site. The interaction of the reactants (substrate) and the enzyme causes the enzyme to change shape. The new position places the substrate molecules into a position favorable to their reaction. Once the reaction takes place, the product is released.

• An enzyme is unchanged as a result of a reaction. It can perform its enzymatic function repeatedly.

• The efficiency of an enzyme is affected by temperature and pH. The human body, for example, is maintained at a temperature of 98.6°, near the optimal temperature for most human enzymes. Above 104°, these enzymes begin to lose their ability to catalyze reactions as they become denatured, that is, they lose their three-dimensional shape as hydrogen bonds and peptide bonds begin to break down. The enzyme pepsinogen, which digests proteins in the stomach, becomes active only at a low pH (very acidic). • The standard suffix for enzymes is “ase,” so it is easy to identify enzymes that use this ending (some do not).

3. Cofactors are nonprotein molecules that assist enzymes. A holoenzyme is the union of the cofactor and the enzyme (called an apoenzyme when part of a holoenzyme).

• Coenzymes are organic cofactors that usually function to donate or accept some component of a reaction, often electrons. Some vitamins are coenzymes or components of coenzymes.

• Inorganic cofactors are often metal ions, like Fe2+.

4. ATP (adenosine triphosphate) is a common source of activation energy for metabolic reactions. ATP is essentially an RNA adenine nucleotide with two additional phosphate groups. The wavy lines between these two phosphate groups indicate highenergy bonds. When ATP supplies energy to a reaction, it is usually the energy in the last bond that is delivered to the reaction. In the process of giving up this energy, the last phosphate bond is broken and the ATP molecule is converted to ADP (adenosine diphosphate) and a phosphate group (indicated by Pi). In contrast, new ATP molecules are assembled by phosphorylation when ADP combines with a phosphate group using energy obtained from some energy-rich molecule (like glucose).

How do living systems regulate chemical reactions? How do they know when to start a reaction and when to shut it off? One way of regulating a reaction is by regulating its enzyme. Here are four common ways in which this is done:

1. Allosteric enzymes have two kinds of binding sites—one an active site for the substrate and one an allosteric site for an allosteric effector. There are two kinds of allosteric effectors:

• An allosteric activator binds to the enzyme and induces the enzyme’s active form.

• An allosteric inhibitor binds to the enzyme and induces the enzyme’s inactive form. In feedback inhibition, an end product of a series of reactions acts as an allosteric inhibitor, shutting down one of the enzymes catalyzing the reaction series.

2. In competitive inhibition, a substance that mimics the substrate inhibits an enzyme by occupying the active site. The mimic displaces the substrate and prevents the enzyme from catalyzing the substrate.

3. A noncompetitor inhibitor binds to an enzyme at locations other than an active or allosteric site. The inhibitor changes the shape of the enzyme which disables its enzymatic activity.

4. In cooperativity, an enzyme becomes more receptive to additional substrate molecules after one substrate molecule attaches to an active site. This occurs, for example, in enzymes that consist of two or more subunits (quaternary structure), each with its own active site. A common example of this process (though not an enzyme) is hemoglobin, whose binding capacity to additional oxygen molecules increases after the first oxygen binds to an active site.