Possibly the most important means for controlling the flux of metabolites through catabolic and anabolic pathways, and for integrating the numerous different pathways in the cell, is through the regulation of either the activity or the synthesis of key (pacemaker) enzymes. It was recognized in the 1950s, largely from work with microorganisms, that pacemaker enzymes can interact with small molecules at more than one site on the surface of the enzyme molecule.
The reaction between an enzyme and its substrate—defined as the compound with which the enzyme acts to form a product—occurs at a specific site on the enzyme known as the catalytic, or active, site; the proper fit between the substrate and the active site is an essential prerequisite for the occurrence of a reaction catalyzed by an enzyme. Interactions at other, so-called regulatory sites on the enzyme, however, do not result in a chemical reaction but cause changes in the shape of the protein; the changes profoundly affect the catalytic properties of the enzyme, either inhibiting or stimulating the rate of the reaction.
Modulation of the activity of pacemaker enzymes may be effected by metabolites of the pathway in which the enzyme acts or by those of another pathway; the process may be described as a “fine control” of metabolism. Very small changes in the chemical environment thus produce important and immediate effects on the rates at which individual metabolic processes occur.
Most catabolic pathways are regulated by the relative proportions of ATP, ADP, and AMP in the cell. It is reasonable to suppose that a pathway that serves to make ATP available for energy-requiring reactions would be less active if sufficient ATP were already present, than if ADP or AMP were to accumulate. The relative amounts of the adenine nucleotides (i.e., ATP, ADP, and AMP) thus modulate the overall rate of catabolic pathways.
They do so by reacting with specific regulatory sites on pacemaker enzymes necessary for the catabolic pathways, which do not participate in the anabolic routes that effect the opposite reactions. Similarly, it is reasonable to suppose that many anabolic processes, which require energy, are inhibited by ADP or AMP; elevated levels of these nucleotides may be regarded therefore as cellular distress signals indicating a lack of energy.
Since one way in which anabolic pathways differ from catabolic routes is that the former result in identifiable end products, it is not unexpected that the pacemaker enzymes of many anabolic pathways—particularly those effecting the biosynthesis of amino acids and nucleotides —are regulated by the end products of these pathways or, in cases in which branching of pathways occurs, by end products of each branch.
Such pacemaker enzymes usually act at the first step unique to a particular anabolic route. If branching occurs, the first step of each branch is controlled. By this so-called negative feedback system, the cellular concentrations of products determine the rates of their formation, thus ensuring that the cell synthesizes only as much of the products as it needs.
A second and less immediately responsive, or “coarse,” control is exerted over the synthesis of pacemaker enzymes. The rate of protein synthesis reflects the activity of appropriate genes, which contain the information that directs all cellular processes. Coarse control is therefore exerted on genetic material rather than on enzymes. Preferential synthesis of a pacemaker enzyme is particularly required to accommodate a cell to major changes in its chemical milieu.
Such changes occur in multicellular organisms only to a minor extent, so that this type of control mechanism is less important in animals than in microorganisms. In the latter, however, it may determine the ease with which a cell previously growing in one nutrient medium can grow after transfer to another. In cases in which several types of organism compete in the same medium for available carbon sources, the operation of coarse controls may well be decisive in ensuring survival.
Alterations in the differential rates of synthesis of pacemaker enzymes in microorganisms responding to changes in the composition of their growth medium also manifest the properties of negative feedback systems. Depending on the nature of the metabolic pathway of which a pacemaker enzyme is a constituent, the manner in which the alterations are elicited may be distinguished. Thus, an increase in the rates at which enzymes of catabolic routes are synthesized results from the addition of inducers—usually compounds that exhibit some structural similarity to the substrates on which the enzymes act.
A classic example of an inducible enzyme of this type is β-galactosidase. Escherichia coli growing in nutrient medium containing glucose do not utilize the milk sugar, lactose (glucose-4-β-D-galactoside); however, if the bacteria are placed in a growth medium containing lactose as the sole source of carbon, they synthesize β-galactosidase and can therefore utilize lactose. The reaction catalyzed by the enzyme is the hydrolysis (i.e., breakdown involving water) of lactose to its two constituent sugars, glucose and galactose; the preferential synthesis of the enzyme thus allows the bacteria to use the lactose for growth and energy.
Another characteristic of the process of enzyme induction is that it continues only as long as the inducer (in this case, lactose) is present; if cells synthesizing β-galactosidase are transferred to a medium containing no lactose, synthesis of β-galactosidase ceases, and the amount of the enzyme in the cells is diluted as they divide, until the original low level of the enzyme is reestablished.
In contrast, the differential rates of synthesis of pacemaker enzymes of anabolic routes are usually not increased by the presence of inducers. Instead, the absence of small molecules that act to repress enzyme synthesis accelerates enzyme formation. Similar to the fine control processes described above is the regulation by coarse control of many pacemaker enzymes of amino-acid biosynthesis. Like the end product inhibitors, the repressors in these cases also appear to be the amino-acid end products themselves. It is useful to regard the acceleration of the enzyme-forming machinery as the consequence, metaphorically, of either placing a foot on the accelerator or removing it from the brake.