Enzymes

INTRODUCTION

Almost all cellular reactions are controlled by enzymes. Enzymes are globular proteins, each with a specific structure (native conformation), function, distribution of electrical charges, and surface geometry whose specificity depends on their tertiary structure. The tertiary structure determines the three-dimensional shape. They are each responsible for control of a single reaction and are thus responsible for control of metabolism.

There are about 700 enzymes in a typical prokaryotic cell and there are thousands in a eukaryotic cell.

Enzymes function as catalysts, which are substances that facilitate (speed up) reactions without actually entering into the reaction. They are used over and over and a single enzyme molecule may mediate thousands of reactions in a single second.

Enzymes operate on reactants, which are known as substrates, and convert them into products. The reaction may require energy or it may release energy. The enzyme is unaffected by the reaction.

A + B + ENZYME -------> AB + ENZYME

substrates ---------> product

Chemical reactions depend on the energy of the substrates being sufficient to cause the molecules to move and thus collide. This is usually accomplished with heat. Heat increases the motion of molecules and makes it more likely they will collide. The heat necessary to accomplish this is often inappropriate inside a cell. Enzymes can be used instead of heat to increase the likelihood that reactants will collide, and collide in the correct position. Enzymes bring reactants together and hold them in the correct position with respect to each other.

Reactions occur between atoms and involve changes in the distribution of electrons.

Energy of Activation

Reactions involve making and breaking bonds. Some bonds must be broken at the start of a reaction and this requires energy. No matter how exergonic the overall reaction may be, some energy must be added initially to break the necessary bonds and get the reaction started. (E.g. match to paper, spark to cylinder). This is the energy of activation (Ea). This energy often supplied as heat but this may not be practical in a cell.

All organic molecules contain energy that could be released by the breakdown of the molecule. Such a reaction would be strongly exergonic and, in fact, is favored by the laws of thermodynamics. It does not happen spontaneously because the activation energy must be provided to get the reaction started and this energy is usually not available. There are times, however, when it is advantageous to the cell for such a reaction to occur. To accomplish this it is necessary to provide the activation energy, or else reduce the amount of activation energy needed.

Enzymes make reactions more likely by reducing the energy of activation required. Presumably by holding the reactants (substrates) in exactly the right orientation to each other so that contact will result in a reaction each time.

GEOMETRIC MODEL

Enzymes are thought to operate on a geometric principle. The tertiary and quaternary structures of an enzyme render it exactly appropriate to bind closely with molecules of the substrate it is designed to utilize. Enzymes change shape slightly when the substrate enters, a process known as induced fit. The changed shape lowers the energy of activation by either stressing an existing bond or correctly orienting two molecules to favor a reaction. The enzyme holds the substrate molecules in exactly the right position relative to each other to facilitate the reaction due to geometric and electrical configuration. The reaction occurs and the new product molecule leaves the enzyme due to diffusion gradients, or to new repulsive electrical forces or the shape changes in either the enzyme or the product. New substrate molecules move into position.

If there is only one substrate the enzyme stresses the bond making it more likely it will break.

Anabolic reactions, endergonic

A + B C

Endergonic reactions do not occur spontaneously. In them the system moves from low to high potential energy

Catabolic reactions are exergonic

C A + B

Exergonic reactions usually do not happen spontaneously because the activation energy is not available in the cell. If an enzyme is present to lower the activation energy there may then be enough energy present for the reaction to occur.

PATHWAYS

Enzymes typically work in chains called METABOLIC PATHWAYS in which the product of one reaction is the substrate of the next. We will soon consider the glycolytic pathway for example in which glucose is broken down in a stepwise fashion to pyruvic acid.

substrate--->A---->B---->C---->D---->E--->F---->G---> product

For example, (simplified) glucose fructose phosphoglygeraldehyde pyruvate

OPTIMA

Activity of enzymes is closely controlled by environmental (cellular environment) factors such as temperature and pH. Enzymes always exhibit typical temperature and pH optima that are characteristics of that enzyme and appropriate for its function.

Mammalian enzymes for example always show temperature optima around 37 while those of the ice fish are around 0 . Most enzymes are denatured at 45 or so, but not those of thermophilic organisms.

INHIBITION

Enzymes may be regulated in several ways. By temp and pH as mentioned, by control of synthesis somewhere between DNA and the ribosome, or locally. We are interested in the latter here. There are many types of inhibitors. Some are deleterious (poisons) some are important regulatory mechanisms. Some inhibitions are deliberate control mechanisms, some are detrimental to the organism.

Enzymes are often inactivated by some molecule (an inhibitor) that changes their shape or blocks the active site.

A. COMPETITIVE INHIBITORS are molecules that bind reversibly or irreversibly to the active site. They compete with the substrate for space in the active site. Most naturally occuring competitive inhibitors are irreversible.

1. REVERSIBLE. These competitors are not the substrate molecule and they thus compete with the substrate. If they are in high concentration they may essentially inactivate the enzyme. These are of limited importance in natural systems. The competition is reversible and the competitor can be overwhelmed by high concentration of substrate.

SUCCINIC ACID -------------------->FUMARIC ACID

succinic dehydrogenase is the enzyme

2. IRREVERSIBLE COMPETITIVE. The competitor and substrate both compete for the active site but the competitor occupies the active site permanently thus deactivating the enzyme.

Carbon monoxide is an irreversible competitive inhibitor of hemoglobin. Oxygen is the substrate. Penicillin is an irreversible competitive inhibitor.

B. NON-COMPETITIVE INHIBITION:

In non-competitive inhibition the inhibitor and substrate do not compete for space in the active site. The substrate enters the active site but the inhibitor reacts with some other part of the enzyme molecule. It may be reversible or non-reversible. Reversible non-competitive inhibition is a major metabolic control mechanism.

1. REVERSIBLE NON-COMPETITIVE This type of inhibition involves two binding sites on the enzyme molecule. The usual active site and a second regulatory site where the inhibitor binds. The inhibitor and the substrate do not compete for the same site. If the regulatory site is occupied by the inhibitor then the shape of the active site is changed so that the substrate molecules cannot fit and react. This type of inhibition,often called allosteric control, is very important in regulating metabolic pathways in the cell.

In allosteric control the final product molecule often acts as an inhibitor of one of the enzymes in the pathway, typically the first.

When high concentrations of final product accumulate, some of them react with the first enzymes at its regulatory site and render it inactive. This eventually results in a decrease in the concentration of the product. When this happens the inhibitor will drop out of the regulatory site and the enzyme will become active again. This is an example of negative feedback. This is a type of reaction that we will see over and over again in biology...at all levels from cell to ecosystem. Negative feedback prevents runaway reactions. The thermostat on your furnace at home is a negative feed back mechanism. When too much heat is produced the furnace is turned off.

The conversion of fructose 6, PO4 to fructose 1, 6 diphosphate is controlled by an enzyme that exerts allosteric control over glycolysis. When [ATP] as high, ATP Binds to a regulatory site on the enzyme and renders the enzyme inoperative. This blocks the production of fructose 1, 6, phosphate and hence the remainder of glycolysis and aerobic respiration. The resulting accumulation of fructose 6 phosphate drives the preceding reaction backward to glucose 6 phosphate then to glucose. There is thus no accumulation of intermediates. High concentrations of ADP or AMP result in their tying up the regulatory site to the exclusion of ATP but do not deform the enzyme. ADP and AMP enhance the activity of the enzyme.

2. IRREVERSIBLE NON-COMPETITIVE. These inhibitors do not compete with the substrate for space in the active site in the sense that they bind irreversible and there is thus no opportunity for competition. They bind irreversible with some other part of the enzyme (or to the active site) and permanently denature or inactivate it. They permanently alter the native conformation of the protein. They include heavy metals, cyanide, nerve gas, and arsenic.

COFACTORS

Proteins are often associated with other chemical groups known as cofactors or prosthetic groups. Enzymes are no exception.

Often molecules, atoms or ions other than proteins are necessary for the functioning of enzyme molecules.

These may be a permanent part of the molecule, as are most ions (Zn, Mg, Fe) or may be only temporarily associated with the protein.

Small organic prosthetic groups are often called coenzymes. If the coenzyme cannot be synthesized by the organism they are called vitamins.

Proteins other than enzymes have prosthetic groups

nucleoproteins: nucleic acid prosthetic group

glycoproteins: carbohydrate prosthetic group

lipoproteins: lipid prosthetic group