Category: 4. Metabolism, Catabolism and Anabolism

Fine control

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.

Coarse control

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.

Catabolic pathways effect the transformation of food materials into interconvertible intermediates. Anabolic pathways, on the other hand, are sequences of enzyme-catalyzed reactions in which the component building blocks of large molecules, or macromolecules (e.g., proteins, carbohydrates, and fats), are constructed from the same intermediates. Thus, catabolic routes have clearly defined beginnings but no unambiguously identifiable end products; anabolic routes, on the other hand, lead to clearly distinguishable end products from diffuse beginnings.

The two types of pathway are linked through reactions of phosphate transfer, involving ADP, AMP, and ATP, and also through electron transfers, which enable reducing equivalents (i.e., hydrogen atoms or electrons), which have been released during catabolic reactions, to be utilized for biosynthesis. But, although catabolic and anabolic pathways are closely linked, and although the overall effect of one type of route is obviously the opposite of the other, they have few steps in common. The anabolic pathway for the synthesis of a particular molecule generally starts from intermediate compounds quite different from those produced as a result of catabolism of that molecule; for example, microorganisms catabolize aromatic (i.e., containing a ring, or cyclic, structure) amino acids to acetyl coenzyme A and an intermediate compound of the TCA cycle.

The biosynthesis of these amino acids, however, starts with a compound derived from pyruvate and an intermediate compound of the metabolism of pentose (a general name for sugars with five carbon atoms). Similarly, histidine is synthesized from a pentose sugar but is catabolized to α-oxoglutarate.

Even in cases in which a product of catabolism is used in an anabolic pathway, differences emerge; thus, fatty acids, which are catabolized to acetyl coenzyme A, are synthesized not from acetyl coenzyme A directly but from a derivative of it, malonyl coenzyme A (see below Lipid components). Furthermore, even enzymes that catalyze apparently identical steps in catabolic and anabolic routes may exhibit different properties. In general, therefore, the way down (catabolism) is different from the way up (anabolism). These differences are important because they allow for the regulation of catabolic and anabolic processes in the cell.

In eukaryotic cells (i.e., those with a well-defined nucleus, characteristic of organisms higher than bacteria) the enzymes of catabolic and anabolic pathways are often located in different cellular compartments. This also contributes to the manner of their cellular control; for example, the formation of acetyl coenzyme A from fatty acids, referred to above, occurs in animal cells in small sausage-shaped components, or organelles, called mitochondria, which also contain the enzymes for terminal respiration and for oxidative phosphorylation. The biosynthesis of fatty acids from acetyl coenzyme A, on the other hand, occurs in the cytoplasm.

Total oxidation of the relatively few products of phase II occurs in a cyclic sequence of chemical reactions known as the tricarboxylic acid (TCA) cycle, or the Krebs cycle, after its discoverer, Sir Hans Krebs; it represents phase III of energy release from foods. Each turn of this cycle (see below The tricarboxylic acid [TCA] cycle) is initiated by the formation of citrate, with six carbon atoms, from oxaloacetate (with four carbons) and acetyl coenzyme A; subsequent reactions result in the reformation of oxaloacetate and the formation of two molecules of carbon dioxide. The carbon atoms that go into the formation of carbon dioxide are no longer available to the cell.

The concomitant stepwise oxidations—in which hydrogen atoms or electrons are removed from intermediate compounds formed during the cycle and, via a system of carriers, are transferred ultimately to oxygen to form water—are quantitatively the most important means of generating ATP from ADP and inorganic phosphate. These events are known as terminal respiration and oxidative phosphorylation (see below Biological energy transduction).

Some microorganisms, incapable of completely converting their carbon compounds to carbon dioxide, release energy by fermentation reactions, in which the intermediate compounds of catabolic routes either directly or indirectly accept or donate hydrogen atoms.

Such secondary changes in intermediate compounds result in considerably less energy being made available to the cell than occurs with the pathways that are linked to oxidative phosphorylation; however, fermentation reactions yield a large variety of commercially important products. Thus, for example, if the oxidation (removal of electrons or hydrogen atoms) of some catabolic intermediate is coupled to the reduction of pyruvate or of acetaldehyde derived from pyruvate, the products formed are lactic acid and ethyl alcohol, respectively.

In the second phase of the release of energy from food (phase II), the small molecules produced in the first phase—sugars, glycerol, a number of fatty acids, and about 20 varieties of amino acids—are incompletely oxidized (in this sense, oxidation means the removal of electrons or hydrogen atoms), the end product being (apart from carbon dioxide and water) one of only three possible substances: the two-carbon compound acetate, in the form of a compound called acetyl coenzyme A; the four-carbon compound oxaloacetate; and the five-carbon compound α-oxoglutarate. The first, acetate in the form of acetyl coenzyme A, constitutes by far the most common product—it is the product of two-thirds of the carbon incorporated into carbohydrates and glycerol; all of the carbon in most fatty acids; and approximately half of the carbon in amino acids. The end product of several amino acids is α-oxoglutarate; that of a few others is oxaloacetate, which is formed either directly or indirectly (from fumarate). These processes occur in animals, plants, bacteria, fungi, and other organisms capable of oxidizing their food materials wholly to carbon dioxide and water.

The release of chemical energy from food materials essentially occurs in three phases. In the first phase (phase I), the large molecules that make up the bulk of food materials are broken down into small constituent units: proteins are converted to the 20 or so different amino acids of which they are composed; carbohydrates (polysaccharides such as starch in plants and glycogen in animals) are degraded to sugars such as glucose; and fats (lipids) are broken down into fatty acids and glycerol. The amounts of energy liberated in phase I are relatively small: only about 0.6 percent of the free, or useful, energy of proteins and carbohydrates, and about 0.1 percent of that of fats, is released during this phase. Because this energy is liberated largely as heat, it cannot be used by the cell. The purpose of the reactions of phase I, which can be grouped under the term digestion and which, in animals, occur mainly in the intestinal tract and in tissues in which reserve materials are prepared, or mobilized, for energy production, is to prepare the foodstuffs for the energy-releasing processes.

At any given time, a neutral molecule of water dissociates into a hydrogen ion (H⁺) and a hydroxide ion (OH⁻), and the ions are continually re-forming into the neutral molecule. Under normal conditions (neutrality), the concentration of hydrogen ions (acidic ions) is equal to that of the hydroxide ions (basic ions); each are at a concentration of 10⁻⁷ mole per litre, which is described as a pH of 7.

All cells either are bounded by membranes or contain organelles that have membranes. These membranes do not permit water or the ions derived from water to pass into or out of the cells or organelles. In green plants, sunlight is absorbed by chlorophyll and other pigments in the chloroplasts of the cells, called photosystem II. As shown previously, when a water molecule is split by light energy, one-half of an oxygen molecule and two hydrogen atoms (which dissociate to two electrons and two hydrogen ions, H⁺) are formed.

When excited by sunlight, chlorophyll loses one electron to an electron carrier molecule but quickly recovers it from a hydrogen atom of the split water molecule, which sends H⁺ into solution in the process. Two oxygen atoms come together to form a molecule of oxygen gas (O₂). The free electrons are passed to photosystem I, but, in doing so, an excess concentration of positively charged hydrogen ions (H⁺) appears on one side of the membrane in the chloroplast, whereas an excess of negatively charged hydroxide ions (OH⁻) builds up on the other side. The free energy released as H⁺ ions move through a specific “pore” in the membrane, to equalize the concentrations of ions, is sufficient to make some biological processes work, such as the uptake of certain nutrients by bacteria and the rotation of the whiplike protein-based propellers that enable such bacteria to move.

Equally important, however, is that this gradient across the membrane powers the formation of adenosine triphosphate (ATP) from inorganic phosphate (HPO₄²⁻, abbreviated P_i) and adenosine diphosphate (ADP). ATP is the major carrier of biologically utilizable energy in all forms of living matter. The interrelationships of energy-yielding and energy-requiring metabolic reactions may be considered largely as processes that couple the formation of ATP with its breakdown.

Synthesis of ATP by green plants is similar to the synthesis of ATP that takes place in the mitochondria of animal, plant, and fungus cells, and in the plasma membranes of bacteria that use oxygen (or other inorganic electron acceptors, such as nitrate) to accept electrons from the removal of hydrogen atoms from a molecule of food (see below Biological energy transduction).

Through these processes most of the energy stored in food materials is released and converted into the molecules that fuel life processes. It must also be remembered, however, that many living organisms (usually bacteria and protozoa) cannot tolerate oxygen; they form ATP from inorganic phosphate and ADP by substrate-level phosphorylations (the addition of a phosphate group) that do not involve the establishment and collapse of proton gradients across membranes. (Such processes are discussed in detail below in The catabolism of glucose.) It must also be borne in mind that the fuels of life and the cellular “furnace” in which they are “burned” are made of the same types of material: if the fires burn too brightly, not only the fuel but also the furnace is consumed. It is therefore essential to release energy at small, discrete, readily utilizable intervals. The relative complexity of the catabolic pathways (by which food materials are broken down) and the complexity of the anabolic pathways (by which cell components are synthesized) reflect this need and offer the possibility for simple feedback systems to control the rate at which materials travel along these sequences of enzymic reactions.

The energy changes associated with physicochemical processes are the province of thermodynamics, a subdiscipline of physics. The first two laws of thermodynamics state, in essence, that energy can be neither created nor destroyed and that the effect of physical and chemical changes is to increase the disorder, or randomness (i.e., entropy), of the universe. Although it might be supposed that biological processes—through which organisms grow in a highly ordered and complex manner, maintain order and complexity throughout their life, and pass on the instructions for order to succeeding generations—are in contravention of these laws, this is not so. Living organisms neither consume nor create energy: they can only transform it from one form to another. From the environment they absorb energy in a form useful to them; to the environment they return an equivalent amount of energy in a biologically less useful form. The useful energy, or free energy, may be defined as energy capable of doing work under isothermal conditions (conditions in which no temperature differential exists); free energy is associated with any chemical change. Energy less useful than free energy is returned to the environment, usually as heat. Heat cannot perform work in biological systems because all parts of cells have essentially the same temperature and pressure.

The unity of life

At the cellular level of organization, the main chemical processes of all living matter are similar, if not identical. This is true for animals, plants, fungi, or bacteria; where variations occur (such as, for example, in the secretion of antibodies by some molds), the variant processes are but variations on common themes. Thus, all living matter is made up of large molecules called proteins, which provide support and coordinated movement, as well as storage and transport of small molecules, and, as catalysts, enable chemical reactions to take place rapidly and specifically under mild temperature, relatively low concentration, and neutral conditions (i.e., neither acidic nor basic). Proteins are assembled from some 20 amino acids, and, just as the 26 letters of the alphabet can be assembled in specific ways to form words of various lengths and meanings, so may tens or even hundreds of the 20 amino-acid “letters” be joined to form specific proteins. Moreover, those portions of protein molecules involved in performing similar functions in different organisms often comprise the same sequences of amino acids.

There is the same unity among cells of all types in the manner in which living organisms preserve their individuality and transmit it to their offspring. For example, hereditary information is encoded in a specific sequence of bases that make up the DNA (deoxyribonucleic acid) molecule in the nucleus of each cell. Only four bases are used in synthesizing DNA: adenine, guanine, cytosine, and thymine. Just as the Morse Code consists of three simple signals—a dash, a dot, and a space—the precise arrangement of which suffices to convey coded messages, so the precise arrangement of the bases in DNA contains and conveys the information for the synthesis and assembly of cell components. Some primitive life-forms, however, use RNA (ribonucleic acid; a nucleic acid differing from DNA in containing the sugar ribose instead of the sugar deoxyribose and the base uracil instead of the base thymine) in place of DNA as a primary carrier of genetic information. The replication of the genetic material in these organisms must, however, pass through a DNA phase. With minor exceptions, the genetic code used by all living organisms is the same.

The chemical reactions that take place in living cells are similar as well. Green plants use the energy of sunlight to convert water (H₂O) and carbon dioxide (CO₂) to carbohydrates (sugars and starches), other organic (carbon-containing) compounds, and molecular oxygen (O₂). The process of photosynthesis requires energy, in the form of sunlight, to split one water molecule into one-half of an oxygen molecule (O₂; the oxidizing agent) and two hydrogen atoms (H; the reducing agent), each of which dissociates to one hydrogen ion (H⁺) and one electron. Through a series of oxidation-reduction reactions, electrons (denoted e⁻) are transferred from a donating molecule (oxidation), in this case water, to an accepting molecule (reduction) by a series of chemical reactions; this “reducing power” may be coupled ultimately to the reduction of carbon dioxide to the level of carbohydrate. In effect, carbon dioxide accepts and bonds with hydrogen, forming carbohydrates (C_n[H₂O]_n).

Living organisms that require oxygen reverse this process: they consume carbohydrates and other organic materials, using oxygen synthesized by plants to form water, carbon dioxide, and energy. The process that removes hydrogen atoms (containing electrons) from the carbohydrates and passes them to the oxygen is an energy-yielding series of reactions.

In plants, all but two of the steps in the process that converts carbon dioxide to carbohydrates are the same as those steps that synthesize sugars from simpler starting materials in animals, fungi, and bacteria. Similarly, the series of reactions that take a given starting material and synthesize certain molecules that will be used in other synthetic pathways are similar, or identical, among all cell types. From a metabolic point of view, the cellular processes that take place in a lion are only marginally different from those that take place in a dandelion.

metabolism, the sum of the chemical reactions that take place within each cell of a living organism and that provide energy for vital processes and for synthesizing new organic material.

Living organisms are unique in that they can extract energy from their environments and use it to carry out activities such as movement, growth and development, and reproduction. But how do living organisms—or, their cells—extract energy from their environments, and how do cells use this energy to synthesize and assemble the components from which the cells are made?

The answers to these questions lie in the enzyme-mediated chemical reactions that take place in living matter (metabolism). Hundreds of coordinated, multistep reactions, fueled by energy obtained from nutrients and/or solar energy, ultimately convert readily available materials into the molecules required for growth and maintenance.