The Role of Enzymes in Biological Systems

I. We will concern ourselves with three types of biochemical reactions: anabolic or synthetic , catabolic or decomposition reactions and redox (reduction-oxidation) reactions. Taken together, these reactions make up what is loosely defined as metabolism. Products of these reactions are referred to as metabolites.

A. In reference to  anabolic and catabolic reactions respectively, covalent bonds are formed or broken. The redox reactions involve the transfer of electrons from one molecule or atom to another. These reactions would occur very slowly if no catalyst were present. Enzymes are the catalysts which are responsible for allowing all of the catabolic and anabolic reactions within the body to proceed. For the most part enzymes consist of proteins, though enzymes which consist in part or totally of RNA have been discovered. These RNA based enzymes are sometimes referred to as ribozymes. Though ribozymes participate in important metabolic reactions we will concentrate on the protein based enzymes.

1. In any reaction, the molecule (or molecules) acted upon by an enzyme is called a substrate and the molecule (or molecules) formed during the reaction is referred to as the product. For a reaction to occur a certain amount of energy must be added to the substrate to allow the covalent bond to be formed or broken; this is referred to as the energy of activation. Without a catalyst, this activation energy is fairly great and acts as a barrier to the occurrence of the reaction. Enzymes act by lowering the energy of activation of a reaction and thus allowing that reaction to go forward at a relatively rapid rate. (How this is accomplished requires a greater understanding of molecular structure and the physics involved in bond formation.)
2. The tertiary structure of an enzymatic protein results in the formation of a cleft or pocket that is capable of binding the substrate or substrates and bringing them into proper alignment for the reaction to occur. This pocket or cleft is referred to as the active site.
3. Enzymes which consist of nothing but protein are referred to as simple enzymes. Often a nonprotein component is needed for the protein to gain enzymatic activity. Organic non-proteinacous components are referred to as coenzymes. Inorganic components of enzymes are referred to as cofactors. Many vitamins and minerals act as coenzymes or cofactors. Enzymes that are combinations of protein, cofactors and/or coenzymes are referred to as a conjugated enzyme or holoenzyme..

B. Enzymes are all made within the cell by the process of protein synthesis. Some enzymes are secreted from the cell and act upon substrates in the extracellular fluids. This type of enzyme is referred to as a exoenzyme. Other enzymes act upon substrates within the cytoplasm or organelles of the cell this type of enzyme is referred to as an endoenzyme. Constitutive enzymes are made by the cell at a constant rate regardless of the level of the substrates for that enzyme. Inducible enzymes are produced in response to the exposure of the cell to the substrates for that enzyme. The Lac operon is an example of a mechanism that allows for enzyme induction.

C. Usually biochemical reactions occur in pathways. A biochemical pathway is a chain of reactions in which the products of one reaction become the substrates for the next reaction. Each reaction in a pathway requires the presence of a specific enzyme (or sometimes many enzymes). If any reaction in a pathway does not occur, the product of that pathway will cease to be produced.

D. Enzymatic activity is greatly effected by environmental conditions. This is due to the fact that enzymes are proteins that must have a very particular three-dimension shape for them to function. The shape of an enzyme is is important for two major reasons: 1) substrates have a particular shape and fit into an active site on the enzyme which must also have a particular shape; 2) most enzymes consist of several proteins that fit together in a very precise way.  Any change in the shape of these proteins will destroy their ability to interact properly with each other and thus the enzyme can not be formed.

1. Environmental factors to be considered include: temperature, osmolarity, and pH.  Many enzymes are only active in a very narrow range of these conditions.

2. In the human body these conditions are tightly controlled in a healthy individual. If any of these conditions change greatly the body will not function correctly.

3. Bacteria do not have the luxury of controlling their environmental conditions. Consequently bacterial enzymes generally will have greater tolerance to changes in environmental conditions. But even bacteria have limits and when these limits are exceeded the bacteria cease to be able to grow. Many of our methods for limiting spoilage of food involve alteration of the environment so that the bacterial enzymes cannot function and thus bacteria cannot grow. Refrigeration is an example of this.   

      

E. Enzymatic activity can be regulated in several ways.

1. One way involves increasing or decreasing the levels of an enzyme. This level of control involves controlling the rate at which the enzyme is made. This can involve control of transcript (synthesis of RNA) or control of the release of enzymes from the cell. When a cell is stimulated to make more of an enzyme it is referred to as enzyme induction whereas when it is stimulated to decrease production of the enzyme it is referred to as enzyme repression.

2.The concentration of the substrate and the product will also influence the rate at which an enzyme functions. Obviously, when little or no substrate is present the rate at which product is created will be diminished. Not so obvious is the fact that as product concentration rises the rate at which the reaction occurs will slow. This is referred to as feedback inhibition.

3. Allosteric enzymes are effected by binding of a non-substrate molecule (an allosteric effector) to another site on the enzyme (the allosteric or regulatory regulatory site). Binding of the allosteric effector results in a change in the shape of the protein molecule such that it binds the substrates with a different efficiency. 

Example: The pathway that results in the synthesis of the amino acid isoleucine from the amino acid threonine involves several biochemical reactions and each reaction must have a specific enzyme. The first reaction involves the allosteric enzyme threonine deaminase. This enzyme acts upon the amino acid threonine. When the level of isoleucine is high in the cytoplasm, no more synthesis of isoleucine is needed. Isoleucine itself binds to the allosteric site of the enzyme threonine deaminase, this binding of isoleucine to the enzyme results in a change in the shape of the threonine deaminase. This shape change causes the enzyme to be unable to bind to threonine so it can not begin the pathway. This type of control over the activity of an enzyme (allosteric regulation) is another form of feedback inhibition.

4. Enzymes can also have chemical alterations so that they increase or decrease their activity. There are many enzymes that become active only if a phosphate group is covalently attached to the enzyme. Other enzymes become less active if the same modification occurs. This is referred to as phosphorylation. Enzymes which add phosphate groups to proteins are referred to as kinases. The enzymes which remove phosphate groups are referred to as dephosphorylases.