Metabolism

Metabolism refers to the highly integrated network of chemical reactions by which living cells grow and sustain themselves. This network is composed of two major types of pathways: anabolism and catabolism. Anabolism uses energy stored in the form of adenosine triphosphate (ATP) to build larger molecules from smaller molecules. Catabolic reactions degrade larger molecules in order to produce ATP and raw materials for anabolic reactions.

Together, these two general metabolic networks have three major functions: (1) to extract energy from nutrients or solar energy; (2) to synthesize the building blocks that make up the large molecules of life: proteins, fats, carbohydrates, nucleic acids, and combinations of these substances; and (3) to synthesize and degrade molecules required for special functions in the cell.

These reactions are controlled by enzymes, protein catalysts that increase the speed of chemical reactions in the cell without themselves being changed. Each enzyme catalyzes a specific chemical reaction by acting on a specific substrate, or raw material. Each reaction is just one of a in a sequence of catalytic steps known as metabolic pathways. These sequences may be composed of up to 20 enzymes, each one creating a product that becomes the substrate—or raw material—for the subsequent enzyme. Often, an additional molecule called a coenzyme, is required for the enzyme to function. For example, some coenzymes accept an electron that is released from the substrate during the enzymatic reaction. Most of the water-soluble vitamins of the B complex serve as coenzymes; riboflavin (vitamin B₂) for example, is a precursor of the coenzyme flavine adenine dinucleotide, while pantothenate is a component of coenzyme A, an important intermediate metabolite.

The series of products created by the sequential enzymatic steps of anabolism or catabolism are called metabolic intermediates, or metabolites. Each step represents a small change in the molecule, usually the removal, transfer, or addition of a specific atom, molecule or group of atoms that serves as a functional group, such as the amino groups (-NH₂) of proteins.

Most such metabolic pathways are linear, that is, they begin with a specific substrate and end with a specific product. However, some pathways, such as the Krebs cycle, are cyclic. Often, metabolic pathways also have branches that feed into or out of them. The specific sequences of intermediates in the pathways of cell metabolism are called intermediary metabolism.

Among the many hundreds of chemical reactions there are only a few that are central to the activity of the cell, and these pathways are identical in most forms of life.

All reactions of metabolism, however, are part of the overall goal of the organism to maintain its internal orderliness, whether that organism is a single celled protozoan or a human. Organisms maintain this orderliness by removing energy from nutrients or sunlight and returning to their environment an equal amount of energy in a less useful form, mostly heat. This heat becomes dissipated throughout the rest of the organism's environment.

According to the first law of thermodynamics, in any physical or chemical change, the total amount of energy in the universe remains constant, that is, energy cannot be created or destroyed. Thus, when the energy stored in nutrient molecules is released and captured in the form of ATP, some energy is lost as heat. But the total amount of energy is unchanged.

The second law of thermodynamics states that physical and chemical changes proceed in such a direction that useful energy undergoes irreversible degradation into a randomized form—entropy. The dissipation of energy during metabolism represents an increase in the randomness, or disorder, of the organism's environment. Because this disorder is irreversible, it provides the driving force and direction to all metabolic enzymatic reactions.

Even in the simplest cells, such as bacteria, there are at least a thousand such reactions. Regardless of the number, all cellular reactions can be classified as one of two types of metabolism: anabolism and catabolism. These reactions, while opposite in nature, are linked through the common bond of energy. Anabolism, or biosynthesis, is the synthetic phase of metabolism during which small building block molecules, or precursors, are built into large molecular components of cells, such as carbohydrates and proteins.

Catabolic reactions are used to capture and save energy from nutrients, as well as to degrade larger molecules into smaller, molecular raw materials for reuse by the cell. The energy is stored in the form of energy-rich ATP, which powers the reactions of anabolism. The useful energy of ATP is stored in the form of a high-energy bond between the second and third phosphate groups of ATP. The cell makes ATP by adding a phosphate group to the molecule adenosine diphosphate (ADP). Therefore, ATP is the major chemical link between the energy-yielding reactions of catabolism, and the energy-requiring reactions of anabolism.

In some cases, energy is also conserved as energy-rich hydrogen atoms in the coenzyme nicotinamide adenine dinucleotide phosphate in the reduced form of NADPH. The NADPH can then be used as a source of high-energy hydrogen atoms during certain biosynthetic reactions of anabolism.

In addition to the obvious difference in the direction of their metabolic goals, anabolism and catabolism differ in other significant ways. For example, the various degradative pathways of catabolism are convergent. That is, many hundreds of different proteins, polysaccharides and lipids are broken down into relatively few catabolic end products. The hundreds of anabolic pathways, however, are divergent. That is, the cell uses relatively few biosynthetic precursor molecules to synthesize a vast number of different proteins, polysaccharides and lipids.

The opposing pathways of anabolism and catabolism may also use different reaction intermediates or different enzymatic reactions in some of the steps. For example, there are 11 enzymatic steps in the breakdown of glucose into pyruvic acid in the liver. But the liver uses only nine of those same steps in the synthesis of glucose, replacing the other two steps with a different set of enzyme-catalyzed reactions. This occurs because the pathway to degradation of glucose releases energy, while the anabolic process of glucose synthesis requires energy. The two different reactions of anabolism are required to overcome the energy barrier that would otherwise prevent the synthesis of glucose.

Another reason for having slightly different pathways is that the corresponding anabolic and catabolic routes must be independently regulated. Otherwise, if the two phases of metabolism shared the exact pathway (only in reverse) a slowdown in the anabolic pathway would slow catabolism, and vice versa.

In addition to regulating the direction of metabolic pathways, cells, especially those in multicellular organisms, also exert control at three different levels: allosteric enzymes, hormones, and enzyme concentration.

Allosteric enzymes in metabolic pathways change their activity in response to molecules that either stimulate or inhibit their catalytic activity. While the end product of an enzyme cascade is used up, the cascade continues to synthesize that product. The result is a steady-state condition in which the product is used up as it is produced and there is no significant accumulation of product. However, when the product accumulates above the steady-state level for any reason, that is, in excess of the cell's needs, the end product acts as an inhibitor of the first enzyme of the sequence. This is called allosteric inhibition, and is a type of feedback inhibition.

A classic example of allosteric inhibition is the case of the enzymatic conversion of L-threonine into L-isoleucine by bacteria. The first of five enzymes, threonine dehydratase is inhibited by the end product, isoleucine. This inhibition is very specific, and is accomplished only by isoleucine, which binds to a site on the enzyme molecule called the regulatory, or allosteric, site. This site is different from the active site of the enzyme, which is the site of the catalytic action of the enzyme on the substrate, or molecule being acted on by the enzyme.

Moreover, some allosteric enzymes may be stimulated by modulator molecules. These molecules are not the end product of a series of reactions, but rather may be the substrate molecule itself. These enzymes have two or more substrate binding sites, which serve a dual function as both catalytic sites and regulatory sites. Such allosteric enzymes respond to excessive concentrations of substrates that must be removed. Furthermore, some enzymes have two or more modulators that may be opposite in effect and have their own specific allosteric site. When occupied, one site may speed up the catalytic reaction, while the other may slow it down. ADP and AMP ( adenosine monophosphate) stimulate certain metabolic pathway enzymes, for example, while ATP inhibits the same allosteric enzymes.

The activity of allosteric enzymes in one pathway may also be modulated by intermediate or final products from other pathways. Such cross-reaction is an important way in which the rates of different enzyme systems can be coordinate with each other.

Hormone control of metabolism is regulated by chemical messengers secreted into the blood by different endocrine glands. These messengers, called hormones, travel to other tissues or organs, where they may stimulate or inhibit specific metabolic pathways.

A classic example of hormonal control of metabolism is the hormone adrenaline, which is secreted by the medulla of the adrenal gland and carried by the blood to the liver. In the liver adrenaline stimulates the breakdown of glycogen to glucose, increasing the blood sugar level. In the skeletal muscles, adrenaline stimulates the breakdown of glycogen to lactate ATP.

Adrenaline exerts its effect by binding to a receptor site on the cell surfaces of liver and muscle cells, where it initiates a series of signals that ultimately causes an inactive form of the enzyme glycogen phosphorylase to become active. This enzyme is the first in a sequence that leads to the breakdown of glycogen to glucose and other products.

Finally, the concentration of the enzymes themselves exert a profound influence on the rate of metabolic activity. For example, the ability of the liver to turn enzymes on and off—a process called enzyme induction—assures that adequate amounts of needed enzymes are available, while inhibiting the cell from wasting its energy and other resources on making enzymes that are not needed.

For example, in the presence of a high-carbohydrate, low-protein diet, the liver enzymes that degrade amino acids are present in low concentrations. In the presence of a high-protein diet, however, the liver produces increased amounts of enzymes needed for degrading these molecules.

The basis of both anabolic and catabolic pathways is the reactions of reduction and oxidation. Oxidation refers to the combination of an atom or molecule with oxygen, or the loss from it of hydrogen or of one or more electrons. Reduction, the opposite of oxidation, is the gain of one or more electrons by an atom or molecule. The nature of these reactions requires them to occur together; i.e., oxidation always occurs in conjunction with reduction. The term "redox" refers to this coupling of reduction and oxidation.

Redox reactions form the basis of metabolism and are the basis of oxidative phosphorylation, the process by which electrons from organic substances such as glucose are transferred from organic compounds such as glucose to electron carriers (usually coenzymes), and then are passed through a series of different electron carriers to molecules of oxygen molecules. The transfer of electrons in oxidative phosphorylation occurs along the electron transport chain. During this process, called aerobic respiration, energy is released, some of which is used to make ATP from ADP. The major electron carriers are the coenzymes nicotinamide adenine dinucleotide (NADH) or flavin adenine dinucleotide (FADH₂). Oxidative phosphorylation is the major source of ATP in aerobic organisms, from bacteria to humans.

Some anaerobic bacteria, however, also carry out respiration, but use other inorganic molecules, such as nitrate (NO₃ ^-) or sulfate (SO₄^2- ) ions as the final electron acceptors. In this form of respiration, called anaerobic respiration, nitrate is reduced to nitrite ion (NO₂^- ), nitrous oxide (N₂O) or nitrogen gas (N₂), and sulfate is reduced to form hydrogen sulfide (H₂S).

Much of the metabolic activity of cells consists largely of central metabolic pathways that transform large amounts of proteins, fats and carbohydrates. Foremost among these pathways are glycolysis, which can occur in either aerobic or anaerobic conditions, and the Krebs cycle, which is coupled to the electron transport chain, which accepts electrons removed from reduced coenzymes of glycolysis and the Krebs cycle. The final electron acceptor of the chain is usually oxygen, but some bacteria use specific, oxidized ions as the final acceptor in anaerobic conditions.

As vital as these reactions are, there are other metabolic pathways in which the flow of substrates and products is much smaller, yet the products quite important. These pathways constitute secondary metabolism, which produces specialized molecules needed by the cell or by tissues or organs in small quantities. Such molecules may be coenzymes, hormones, nucleotides, toxins, or antibiotics.

The process of extracting energy by the central metabolic pathways that break down fats, polysaccharides and proteins, and conserving it as ATP, occurs in three stages in aerobic organisms. In anaerobic organisms, only one stage is present. In each case, the first step is glycolysis.

Glycolysis is a ubiquitous central pathway of glucose metabolism among living things, from bacteria to plants and humans. The glycolytic series of reactions converts glucose into the molecule pyruvate, with the production of ATP. This pathway is controlled by both the concentration of substrates entering glycolysis as well as by feedback inhibition of the pathway's allosteric enzymes.

Glucose, a hexose (6-carbon) sugar, enters the pathway through phosphorylation of the number six carbon by the enzyme hexokinase. In this reaction, ATP relinquishes one of its phosphates, becoming ADP, while glucose is converted to glucose-6-phosphate. When the need for further oxidation of glucose-6-phosphate by the cell decreases, the concentration of this metabolite increases, as serves as a feedback inhibitor of the allosteric enzyme hexokinase. In the liver, however, glucose-6-phosphate is converted to glycogen, a storage form of glucose. Thus a buildup of glucose-6-phosphate is normal for liver, and feedback inhibition would interfere with this vital pathway. However, to produce glucose-6-phosphate, the liver uses the enzyme glucokinase, which is not inhibited by an increase in the concentration of glucose-6-phosphate.

In the liver and muscle cells, another enzyme, glycogen phosphorylase, breaks down glycogen into glucose molecules, which then enter glycolysis.

Two other allosteric enzyme regulatory reactions also help to regulate glycolysis: the conversion of fructose 6-phosphate to fructose 1,6-diphosphate by phosphofructokinase and the conversion of phosphoenolpyruvate to pyruvate by pyruvate kinase.

The first stage of glycolysis prepares the glucose molecule for the second stage, during which energy is conserved in the form of ATP. As part of the preparatory state, however, two ATP molecules are consumed.

At the fourth step of glycolysis, the doubly phosphorylated molecule (fructose 1,6-diphosphate) is cleaved into two 3-carbon molecules, dihyroxyacetone phosphate and glyceraldehyde 3-phosphate. These 3-carbon molecules are readily converted from one to another, however it is only glyceraldehyde 3-phosphate that undergoes five further changes during the energy conserving stage. In the first step of this second stage, a molecule of the coenzyme NAD⁺ is reduced to NADH. During oxidative phosphorylation, the NADH will be oxidized, giving up its electrons to the electron transport system.

At steps seven and ten of glycolysis, ADP is phosphorylated to ATP, using phosphate groups added to the original 6-carbon molecule in the preparatory stage. Since this phosphorylation of ADP occurs by enzymatic removal of a phosphate group from each of two substrates of glycolysis, this process is called substrate level phosphorylation of ADP. It differs markedly from the phosphorylation of ADP that occurs in the more complex oxidative phosphorylation processes in the electron transport chain. Since two 3-carbon molecules derived from the original 6-carbon hexose undergo this process, two molecules of ATP are formed from glucose during this stage, for a net overall gain of two ATP (two ATP having been used in the preparatory stage).

Aerobic organisms use glycolysis as the first stage in the complete degradation of glucose to carbon dioxide and water. During this process, the pyruvate formed by glycolysis is oxidized to acetyl-Coenzyme A (acetyl-CoA), with the loss of its carboxyl group as carbon dioxide.

The fate of pyruvate formed by glycolysis differs among species, and within the same species depending on the level of oxygen available for further oxidation of the products of glycolysis.

Under aerobic conditions, or in the case of bacteria using a non-oxygen final electron acceptor, acetyl-CoA, enters the Krebs cycle by combining with citric acid. The Krebs cycle continues the oxidation process, extracting electrons as it does so. These electrons are carried by coenzymes (NADH and FADH) to the electron transport chain, where the final reactions of oxidation produce ATP.

During these reactions, the acetyl group is oxidized completely to carbon dioxide and water by the citric acid cycle. This final oxidative degradation requires oxygen as the final electron acceptor in the electron transport chain.

Organisms that lack the enzyme systems necessary for oxidative phosphorylation also use glycolysis to produce pyruvate and a small amount of ATP. But pyruvate is then converted into lactate, ethanol or other organic alcohols or acids. This process is called fermentation, and does not produce more ATP. The NADH produced during the energy-conserving stage of fermentation is used during the synthesis of other molecules. Thus, glycolysis is the major central pathway of glucose catabolism in virtually all organisms.

While the main function of glycolysis is to produce ATP, there are minor catabolic pathways that produce specialized products for cells. One, the pentose phosphate pathway, produces NADPH and the sugar ribose 5-phosphate. NADPH is used to reduce substrates in the synthesis of fatty acids, and ribose 5-phosphate is used in the synthesis of nucleic acids.

Another secondary pathway for glucose in animal tissues produces D-glucuronate, which is important in detoxifying and excreting foreign organic compounds and in synthesizing vitamin C.

Most of the energy conservation achieved by the oxidative phosphorylation of glucose occurs during the Krebs cycle. Pyruvate is first converted to acetyl-CoA, in an enzymatic step that converts one of its carbons into carbon dioxide, and NAD⁺ is reduced to NADH. Acetyl-CoA enters the 8-step Krebs cycle by combining with the 4-carbon oxaloacetic acid to form the 6-carbon citric acid. During the next 7 steps, three molecules of NAD⁺ and one molecule of FAD⁺ are reduced, one ATP is formed by substrate level phosphorylation, and two carbons are oxidized to CO₂.

The reduced coenzymes produced during conversion of pyruvic acid to acetyl-CoA and the Krebs cycle are oxidized along the electron transport chain. As the electrons released by the coenzymes pass through the stepwise chain of redox reactions, there is a stepwise release of energy that is ultimately used to phosphorylate molecules of ADP to ATP. The energy is converted into a gradient of protons established across the membrane of the bacterial cell or of the organelle of the eucaryotic cells. The energy of the proton flow back into the cell or organelle is used by the enzyme ATP synthetase to phosphorylate ADP molecules.

FADH₂ releases its electrons at a lower level along the chain than does NADH. The electrons of the former coenzyme thus pass along fewer electron acceptors than NADH, and this difference is reflected in the number of ATP molecules produced by the sequential transfer of each coenzymes electrons along the chain. The oxidation of each NADH produces three ATP, while the oxidation of FADH₂ produces two.

The total number of ATP produced by glycolysis and metabolism is 38 molecules, which includes a net of two from glycolysis (substrate level phosphorylation), 30 from the oxidation of 10 NADH molecules, four from oxidation of two FADH₂ molecules, and two from substrate level phosphorylation in the Krebs cycle.

In addition to their role in the catabolism of glucose, glycolysis and the Krebs cycle also participate in the breakdown of proteins and fats. Proteins are initially degraded into constituent amino acids, which may be converted to pyruvic acid or acetyl-CoA before being passed into the Krebs cycle; or they may enter the Krebs cycle directly after being converted into one of the metabolites of this metabolic pathway.

Lipids are first hydrolyzed into glycerol and fatty acids, glycerol being converted to the glyceraldehyde 3-phosphate metabolite of glycolysis, while fatty acids are degraded to acetyl-CoA, which then enters the Krebs cycle.

Although metabolic pathways in both single-celled and multicellular organisms have much in common, especially in the case of certain central metabolic pathways, they may occur in different locations.

In the simplest organisms, the prokaryotes, metabolic pathways are not contained in compartments separated by internal membranes. Rather, glycolysis takes place in the cytosol, while the electron transport chain and lipid synthesis occurs in the cell membrane. Proteins are made on ribosomes in the cytosol.

In eucaryotic cells, glycolysis, gluconeogenesis and fatty acid synthesis takes place in the cytosol, while the Krebs cycle is isolated within mitochondria; glycogen is made in glycogen granules, lipid is synthesized in the endoplasmic reticulum and lysosomes carry on a variety of hydrolytic activities. As in procaryotic cells, ribosomes in the cytosol are the site of protein synthesis.

The metabolic pathways discussed to this point oxidize organic matter to produce ATP. These organic compounds are made by plants and some microorganisms by photosynthesis, which takes place in organelles called chloroplasts. Using this process, these organisms synthesize organic compounds by converting the energy of sunlight into chemical energy, which is then used to convert CO₂ from the atmosphere to more reduced carbon compounds, particularly sugars.