Metabolism and the Regulation of Enzymes

A major characteristic of life is homeostasis, the maintenance of stable internal conditions. Regulation of the rates at which our thousands of different enzymes operate contributes to metabolic homeostasis. In the remainder of this chapter, we will investigate the role of enzymes in organizing and regulating metabolism. In living cells, the activity of enzymes can be activated or inhibited in various ways, so the presence of an enzyme does not necessarily ensure that it is functioning. There are mechanisms that alter the rate at which some enzymes catalyze reactions making enzymes the target points at which entire sequences of chemical reactions can be regulated. Finally, we examine how the environment—namely, temperature and pH—affects enzyme activity.

Metabolism is organized into pathways

An organism’s metabolismis the totality of the biochemical reactions that take place within it. Metabolism transforms raw materials and stored potential energy into forms that can be used by living cells. Metabolism consists of sequences of enzyme-catalyzed chemical reactions called pathways. In these sequences, the product of one reaction is the substrate for the next: Some metabolic pathways are anabolic synthesizing the important chemical building blocks from which macromolecules are built. Others are catabolic, breaking down molecules for usable free energy, recycling monomers or inactivating toxic substances. The balance among these anabolic and catabolic pathways may change depending on the cell’s (and the organism’s) needs. So a cell must regulate all its metabolic pathways constantly.

Enzyme activity is subject to regulation by inhibitors

Various inhibitors can bind to enzymes, slowing down the rates of enzyme-catalyzed reactions. Some inhibitors occur naturally in cells; others are artificial. Naturally occurring inhibitors regulate metabolism; artificial ones can be used to treat disease, to kill pests or in the laboratory to study how enzymes work. Some inhibitors irreversibly inhibit the enzyme by permanently binding to it. Others have reversible effects; that is, they can become unbound from the enzyme.

Allosteric enzymes control their activity by changing their shape

The change in enzyme shape due to noncompetitive inhibitor binding is an example of allostery(allo-, “different”; -stery, “shape”). In that case, the binding of the inhibitor induces the protein to change its shape. More common are enzymes that already exist in the cell in more than one possible shape. The inactive form of the enzyme has a shape that cannot bind the substrate, while the active form has the proper shape at the active site to bind the substrate. These two forms can interconvert, and this process is regulated by the binding of an allosteric regulatorto a site on the enzyme away from the active site. Regulator binding is just like substrate binding: it is highly specific. So an enzyme may have several sites for binding: one for the substrate(s) and others for regulators.

Allosteric regulators work in two ways:

Positive regulators stabilize the active form of the enzyme.

Negative regulators stabilize the inactive form of the enzyme.

Most (but not all) enzymes that are allosterically regulated are proteins with quaternary structure; that is, they are made up of multiple polypeptide subunits. The active site is present on one subunit, called the catalytic subunit, while the regulatory site(s) are present on different subunit(s), the regulatory subunit(s). Allosteric enzymes and nonallosteric enzymes differ greatly in their reaction rates when the substrate concentration is low. Graphs of reaction rate plotted against substrate concentration show this relationship. The reaction rate first increases very sharply with increasing substrate concentration, then tapers off to a constant maximum rate as the supply of enzyme becomes saturated with substrate. The plot for many allosteric enzymes is radically different, having a sigmoid (S-shaped) appearance. The increase in reaction rate with increasing substrate concentration is slight at low substrate concentrations but within a certain range, the reaction rate is extremely sensitive to relatively small changes in substrate concentration. Because of this sensitivity, allosteric enzymes are important in regulating entire metabolic pathways.

Allosteric effects regulate metabolism

Metabolic pathways typically involve a starting material, various intermediate products, and an end product that is used for some purpose by the cell. In each pathway, there are a number of reactions, each forming an intermediate product and each catalyzed by a different enzyme. The first step in a pathway is called the commitment step, meaning that once this enzyme-catalyzed reaction occurs, the “ball is rolling,” and the other reactions happen in sequence, leading to the end product. But what if the cell has no need for that product—for example, if that product is available from its environment in adequate amounts? It would be energetically wasteful for the cell to continue making something it does not need. One way that cells solve this problem is to shut down the metabolic pathway by having the final product allosterically. inhibit the enzyme that catalyzes the commitment step. This mechanism is known as end-product inhibition or feedback inhibition. When the end product is present in a high concentration, some of it binds to an allosteric site on the commitment step enzyme, thereby causing it to become inactive.

Enzymes are affected by their environment

Enzymes enable cells to perform chemical reactions and carry out complex processes rapidly without using the extremes of temperature and pH employed by chemists in the laboratory. However, because of their three-dimensional structures and the chemistry of the side chains in their active sites, enzymes are highly sensitive to temperature and pH. Here, we will examine their effects on enzyme function, which, of course, depends on enzyme structure and chemistry.

pH affects enzymes activity

The rates of most enzyme-catalyzed reactions depend on the pH of the medium in which they occur. Each enzyme is most active at a particular pH; its activity decreases as the solution is made more acidic or more basic than its “ideal” (optimal) pH. Several factors contribute to this effect. One is the ionization of carboxyl, amino, and other groups on either the substrate or the enzyme. In neutral or basic solutions, carboxyl groups (—COOH) release H⁺ to become negatively charged carboxylate groups (—COO–). Similarly, amino groups (—NH₂) accept H⁺ ions in neutral or acidic solutions, becoming positively charged —NH₃⁺ groups. Thus, in a neutral solution, a molecule with an amino group is attracted electrically to another molecule that has a carboxyl group, because both groups are ionized and the two groups have opposite charges. If the pH changes, however, the ionization of these groups may change. For example, at a low pH (high H⁺ concentration), the excess H⁺ may react with the —COO– to form COOH. If this happens, the group is no longer charged and cannot interact with other charged groups in the protein, so the folding of the protein may be altered. If such a change occurs at the active site of an enzyme, the enzyme may no longer have the correct shape to bind to its substrate.

Temperature affects enzymes activity

In general, warming increases the rate of an enzyme-catalyzed reaction because at higher temperatures, a greater fraction of the reactant molecules have enough energy to provide the activation energy for the reaction. Temperatures that are too high, however, inactivate enzymes, because at high temperatures enzyme molecules vibrate and twist so rapidly that some of their noncovalent bonds break. When heat changes their tertiary structure, enzymes become inactivated or thermally denatured. Some enzymes denature at temperatures only slightly above that of the human body, but a few are stable even at the boiling or freezing points of water. All enzymes, however, show an optimal temperature for activity. Individual organisms adapt to changes in the environment in many ways, one of which is based on groups of enzymes, called isozymes, that catalyze the same reaction but have different chemical compositions and physical properties. Different isozymes within a given group may have different optimal temperatures. The rainbow trout, for example, has several isozymes of the enzyme acetylcholinesterase, whose operation is essential to the normal transmission of nerve impulses. If a rainbow trout is transferred from warm water to near-freezing water (2°C), the fish produces an isozyme of acetylcholinesterase that is different from the one it produces at the higher temperature. The new isozyme has a lower optimal temperature, allowing the fish to perform normally in the colder water. In general, enzymes adapted to warm temperatures fail to denature at those temperatures because their tertiary structures are held together largely by covalent bonds, such as disulfide bridges, instead of the more heat-sensitive weak chemical interactions. Most enzymes in humans are more stable at high temperatures than those of the bacteria that infect them, so that a moderate fever tends to denature bacterial enzymes but not our own.

2.1.3. Photosynthesis: Energy from the Sun

Powered by sunlight, green plants convert CO₂ and water into carbohydrates by a process called photosynthesis. The emergence of this metabolic pathway was a key event in the evolution of life. Photosynthesizing organisms, called autotrophs (“self-feeders”), use solar energy to make their own food from simple chemicals in the environment. In this way, they provide an entry point to the biosphere for chemical energy. Heterotrophs (“other-feeders”) cannot photosynthesize, and they depend on autotrophs (or other heterotrophs) for the raw materials of metabolism, such as glucose. The “food chain” from autotrophs to heterotrophs requires a lot of photosynthesis. On the African plain, it takes 6 acres of grassland to convert enough CO₂ into plant matter to support the growth of one gazelle that consumes the grass. Globally, more than 10 billion tons of carbon is fixed—converted from being part of a simple gas (CO₂) into a more complex molecule (carbohydrate)—by plants every year. This huge amount of photosynthetically-fixed carbon is available for use by all species that need it. Humans consume a huge amount of Earth’s photosynthetic output. Recent calculations of total plant growth in agriculture, pastures, and forests and the products consumed by people indicate that one-third of all the carbon fixed annually is appropriated by humans, leaving two-thirds for the entire remainder of the biosphere. This is by far the greatest proportion of consumption for any single species in known history. Is this situation sustainable? Conferences such as the 2002 United Nations Conference on Sustainability have demonstrated concern for our photosynthetic future. An important first step in examining ecological sustainability is a thorough understanding of photosynthesis. The process of photosynthesis can be neatly broken down into two steps. The first step is the conversion of energy from light to chemical bonds in reduced electron carriers and ATP. In the second step, these two sources of chemical energy are used to drive the synthesis of carbohydrates from carbon dioxide. In this chapter, we will examine these two processes and show how they are related to each other and to plant growth.