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Enzymes

ENZYMES

CONCEPT

Enzymes are biological catalysts, or chemicals that speed up the rate of reaction between substances without themselves being consumed in the reaction. As such, they are vital to such bodily functions as digestion, and they make possible processes that normally could not occur except at temperatures so high they would threaten the well-being of the body. A type of protein, enzymes sometimes work in tandem with non-proteins called coenzymes. Among the processes in which enzymes play a vital role is fermentation, which takes place in the production of alcohol or the baking of bread and also plays a part in numerous other natural phenomena, such as the purification of wastewater.

HOW IT WORKS

Amino Acids, Proteins, and Biochemistry

Amino acids are organic compounds made of carbon, hydrogen, oxygen, nitrogen, and (in some cases) sulfur bonded in characteristic formations. Strings of 50 or more amino acids are known as proteins, large molecules that serve the functions of promoting normal growth, repairing damaged tissue, contributing to the body's immune system, and making enzymes. The latter are a type of protein that functions as a catalyst, a substance that speeds up a chemical reaction without participating in it. Catalysts, of which enzymes in the bodies of plants and animals are a good example, thus are not consumed in the reaction.

Catalysts

In a chemical reaction, substances known as reactants interact with one another to create new substances, called products. Energy is an important component in the chemical reaction, because a certain threshold, termed the activation energy, must be crossed before a reaction can occur. To increase the rate at which a reaction takes place and to hasten the crossing of the activation energy threshold, it is necessary to do one of three things.

The first two options are to increase either the concentration of reactants or the temperature at which the reaction takes place. It is not always feasible or desirable, however, to do either of these things. Many of the processes that take place in the human body, for instance, normally would require high temperaturestemperatures, in fact, that are too high to sustain human life. Imagine what would happen if the only way we had of digesting starch was to heat it to the boiling point inside our stomachs! Fortunately, there is a third option: the introduction of a catalyst, a substance that speeds up a reaction without participating in it either as a reactant or as a product. Catalysts thus are not consumed in the reaction. Enzymes, which facilitate the necessary reactions in our bodies without raising temperatures or increasing the concentrations of substances, are a prime example of a chemical catalyst.

THE DISCOVERY OF CATALYSIS.

Long before chemists recognized the existence of catalysts, ordinary people had been using the chemical process known as catalysis for numerous purposes: making soap, fermenting wine to create vinegar, or leavening bread, for instance. Early in the nineteenth century, chemists began to take note of this phenomenon. In 1812 the Russian chemist Gottlieb Kirchhoff (1764-1833) was studying the conversion of starches to sugar in the presence of strong acids when he noticed something interesting.

When a suspension of starch (that is, particles of starch suspended in water) was boiled, Kirchhoff observed, no change occurred in the starch. When he added a few drops of concentrated acid before boiling the suspension, however, he obtained a very different result. This time, the starch broke down to form glucose, a simple sugar (see Carbohydrates), whereas the acidwhich clearly had facilitated the reactionunderwent no change. In 1835 the Swedish chemist Jöns Berzelius (1779-1848) provided a name to the process Kirchhoff had observed: catalysis, derived from the Greek words kata ("down") and lyein ("loosen"). Just two years earlier, in 1833, the French physiologist Anselme Payen (1795-1871) had isolated a material from malt that accelerated the conversion of starch to sugar, for instance, in the brewing of beer.

The renowned French chemist Louis Pasteur (1822-1895), who was right about so many things, called these catalysts ferments and pronounced them separate organisms. In 1897, however, the German biochemist Eduard Buchner (1860-1917) isolated the catalysts that bring about the fermentation of alcohol and determined that they were chemical substances, not organisms. By that time, the German physiologist Willy Kahne had suggested the name enzyme for these catalysts in living systems.

Substrates and Active Sites

Each type of enzyme is geared to interact chemically with only one particular substance or type of substance, termed a substrate. The two parts fit together, according to a widely accepted theory introduced in the 1890s by the German chemist Emil Fischer (1852-1919), as a key fits into a lock. Each type of enzyme has a specific three-dimensional shape that enables it to fit with the substrate, which has a complementary shape.

The link between enzymes and substrates is so strong that enzymes often are named after the substrate involved, simply by adding ase to the name of the substrate. For example, lactase is the enzyme that catalyzes the digestion of lactose, or milk sugar, and urease catalyzes the chemical breakdown of urea, a substance in urine. Enzymes bind their reactants or substrates at special folds and clefts, named active sites, in the structure of the substrate. Because numerous interactions are required in their work of catalysis, enzymes must have many active sites, and therefore they are very large, having atomic mass figures as high as one million amu. (An atomic mass unit, or amu, is approximately equal to the mass of a proton, a positively charged particle in the nucleus of an atom.)

Suppose a substrate molecule, such as a starch, needs to be broken apart for the purposes of digestion in a living body. The energy needed to break apart the substrate is quite large, larger than is available in the body. An enzyme with the correct molecular shape arrives on the scene and attaches itself to the substrate molecule, forming a chemical bond within it. The formation of these bonds causes the breaking apart of other bonds within the substrate molecule, after which the enzyme, its work finished, moves on to another uncatalyzed substrate molecule.

Coenzymes

All enzymes belong to the protein family, but many of them are unable to participate in a catalytic reaction until they link with a non protein component called a coenzyme. This can be a medium-size molecule called a prosthetic group, or it can be a metal ion (an atom with a net electric charge), in which case it is known as a cofactor. Quite often, though, coenzymes are composed wholly or partly of vitamins. Although some enzymes are attached very tightly to their coenzymes, others can be parted easily; in either case, the parting almost always deactivates both partners.

The first coenzyme was discovered by the English biochemist Sir Arthur Harden (1865-1940) around the turn of the nineteenth century. Inspired by Buchner, who in 1897 had detected an active enzyme in yeast juice that he had named zymase, Harden used an extract of yeast in most of his studies. He soon discovered that even after boiling, which presumably destroyed the enzymes in yeast, such deactivated yeast could be reactivated. This finding led Harden to the realization that a yeast enzyme apparently consists of two parts: a large, molecular portion that could not survive boiling and was almost certainly a protein and a smaller portion that had survived and was probably not a protein. Harden, who later shared the 1929 Nobel Prize in chemistry for this research, termed the non protein a coferment, but others began calling it a coenzyme.

REAL-LIFE APPLICATIONS

The Body, Food, and Digestion

Enzymes enable the many chemical reactions that are taking place at any second inside the body of a plant or animal. One example of an enzyme is cytochrome, which aids the respiratory system by catalyzing the combination of oxygen with hydrogen within the cells. Other enzymes facilitate the conversion of food to energy and make possible a variety of other necessary biological functions. Enzymes in the human body fulfill one of three basic functions. The largest of all enzyme types, sometimes called metabolic enzymes, assist in a wide range of basic bodily processes, from breathing to thinking. Some such enzymes are devoted to maintaining the immune system, which protects us against disease, and others are involved in controlling the effects of toxins, such as tobacco smoke, converting them to forms that the body can expel more easily.

A second category of enzyme is in the diet and consists of enzymes in raw foods that aid in the process of digesting those foods. They include proteases, which implement the digestion of protein; lipases, which help in digesting lipids or fats; and amylases, which make it possible to digest carbohydrates. Such enzymes set in motion the digestive process even when food is still in the mouth. As these enzymes move with the food into the upper portion of the stomach, they continue to assist with digestion.

The third group of enzymes also is involved in digestion, but these enzymes are already in the body. The digestive glands secrete juices containing enzymes that break down nutrients chemically into smaller molecules that are more easily absorbed by the body. Amylase in the saliva begins the process of breaking down complex carbohydrates into simple sugars. While food is still in the mouth, the stomach begins producing pepsin, which, like protease, helps digest protein.

Later, when food enters the small intestine, the pancreas secretes pancreatic juicewhich contains three enzymes that break down carbohydrates, fats, and proteinsinto the duodenum, which is part of the small intestine. Enzymes from food wind up among the nutrients circulated to the body through plasma, a watery liquid in which red blood cells are suspended. These enzymes in the blood assist the body in everything from growth to protection against infection.

One digestive enzyme that should be in the body, but is not always present, is lactase. As we noted earlier, lactase works on lactose, the principal carbohydrate in milk, to implement its digestion. If a person lacks this enzyme, consuming dairy products may cause diarrhea, bloating, and cramping. Such a person is said to be "lactose intolerant," and if he or she is to consume dairy products at all, they must be in forms that contain lactase. For this reason, Lactaid milk is sold in the specialty dairy section of major supermarkets, while many health-food stores sell lactaid tablets.

Fermentation

Fermentation, in its broadest sense, is a process involving enzymes in which a compound rich in energy is broken down into simpler substances. It also is sometimes identified as a process in which large organic molecules (those containing hydrogen and carbon) are broken down into simpler molecules as the result of the action of microorganisms working anaerobically, or in the absence of oxygen. The most familiar type of fermentation is the conversion of sugars and starches to alcohol by enzymes in yeast. To distinguish this reaction from other kinds of fermentation, the process is sometimes termed alcoholic or ethanolic fermentation.

At some point in human prehistory, humans discovered that foods spoil, or go bad. Yet at the dawn of historythat is, in ancient Sumer and Egyptpeople found that sometimes the "spoilage" (that is, fermentation) of products could have beneficial results. Hence the fermentation of fruit juices, for example, resulted in the formation of primitive forms of wine. Over the centuries that followed, people learned how to make both alcoholic beverages and bread through the controlled use of fermentation.

ALCOHOLIC BEVERAGES.

In fermentation, starch is converted to simple sugars, such as sucrose and glucose, and through a complex sequence of some 12 reactions, these sugars then are converted to ethyl alcohol (the kind of alcohol that can be consumed, as opposed to methyl alcohol and other toxic forms) and carbon dioxide. Numerous enzymes are needed to carry out this sequence of reactions, the most important being zymase, which is found in yeast cells. These enzymes are sensitive to environmental conditions, such that when the concentration of alcohol reaches about 14%, they are deactivated. For this reason, no fermentation product (such as wine) can have an alcoholic concentration of more than about 14%. Stronger alcoholic beverages, such as whisky, are the result of another process, distillation.

The alcoholic beverages that can be produced by fermentation vary widely, depending primarily on two factors: the plant that is fermented and the enzymes used for fermentation. Depending on the materials available to them, various peoples have used grapes, berries, corn, rice, wheat, honey, potatoes, barley, hops, cactus juice, cassava roots, and other plant materials for fermentation to produce wines, beers, and other fermented drinks. The natural product used in making the beverage usually determines the name of the synthetic product. Thus, for instance, wine made with ricea time-honored tradition in Japanis known as sake, while a fermented beverage made from barley, hops, or malt sugar has a name very familiar to Americans: beer. Grapes make wine, but "wine" made from honey is known as mead.

OTHER FOODS.

Of course, ethyl alcohol is not the only useful product of fermentation or even of fermentation using yeast; so, too, are baked goods, such as bread. The carbon dioxide generated during fermentation is an important component of such items. When the batter for bread is mixed, a small amount of sugar and yeast is added. The bread then rises, which is more than just a figure of speech: it actually puffs up as a result of the fermentation of the sugar by enzymes in the yeast, which brings about the formation of carbon dioxide gas. The carbon dioxide gives the batter bulkiness and texture that would be lacking without the fermentation process. Another food-related application of fermentation is the production of one processed type of food from a raw, natural variety. The conversion of raw olives to the olives sold in stores, of cucumbers to pickles, and of cabbage to sauerkraut utilizes a particular bacterium that assists in a type of fermentation.

INDUSTRIAL APPLICATIONS.

There is even ongoing research into the creation of edible products from the fermentation of petroleum. While this may seem a bit far-fetched, it is less difficult to comprehend powering cars with an environmentally friendly product of fermentation known as gasohol. Gasohol first started to make headlines in the 1970s, when an oil embargo and resulting increases in gas prices, combined with growing environmental concerns, raised the need for a type of fuel that would use less petroleum. A mixture of about 90% gasoline and 10% alcohol, gasohol burns more cleanly that gasoline alone and provides a promising method for using renewable resources (plant material) to extend the availability of a nonrenewable resource (petroleum). Furthermore, the alcohol needed for this product can be obtained from the fermentation of agricultural and municipal wastes.

The applications of fermentation span a wide spectrum, from medicines that go into people's bodies to the cleaning of waters containing human waste. Some antibiotics and other drugs are prepared by fermentation: for example, cortisone, used in treating arthritis, can be made by fermenting a plant steroid known as diosgenin. In the treatment of wastewater, anaerobic, or non-oxygen-dependent, bacteria are used to ferment organic material. Thus, solid wastes are converted to carbon dioxide, water, and mineral salts.

WHERE TO LEARN MORE

Asimov, Isaac. The Chemicals of Life: Enzymes, Vitamins, Hormones. New York: Abelard-Schulman, 1954.

"Enzymes: Classification, Structure, Mechanism." Washington State University Department of Chemistry (Web site). <http://www.chem.wsu.edu/Chem102/102-EnzStrClassMech.html>.

"Enzymes." HordeNet: Hardy Research Group, Department of Chemistry, The University of Akron (Web site). <http://ull.chemistry.uakron.edu/genobc/Chapter_20/>.

Fruton, Joseph S. A Skeptical Biochemist. Cambridge, MA: Harvard University Press, 1992.

"Introduction to Enzymes." Worthington Biochemical Corporation (Web site). <http://www.worthingtonbiochem.com/introBiochem/introEnzymes.html>.

Kornberg, Arthur. For the Love of Enzymes: The Odyssey of a Biochemist. Cambridge, MA: Harvard University Press, 1989.

"Milk Makes Me Sick: Exploration of the Basis of Lactose Intolerance." Exploratorium: The Museum of Science, Art, and Human Perception (Web site). <http://www.exploratorium.edu/snacks/milk_makes-me_sick/>.

KEY TERMS

ACTIVATION ENERGY:

A threshold that must be crossed to facilitate a chemical reaction. There are three ways to reach the activation energy: by increasing the concentration of reactants, by raising their temperature, or by introducing a catalyst, such as an enzyme.

ACTIVE SITES:

Folds and clefts on the surface of an enzyme that enable attach ment to its particular substrate.

AMINO ACIDS:

Organic compounds made of carbon, hydrogen, oxygen, nitro gen, and (in some cases) sulfur bonded in characteristic formations. Strings of amino acids make up proteins.

BIOCHEMISTRY:

The area of the bio logical sciences concerned with the chemical substances and processes in organisms.

CARBOHYDRATES:

Naturally occurring compounds, consisting of carbon, hydrogen, and oxygen, whose primary function in the body is to supply energy. Included in the carbohydrate group are sugars, starches, cellulose, and various other substances. Most carbohydrates are produced by green plants in the process of undergoing photosynthesis.

CATALYSIS:

The act or process of cat alyzing, or speeding up the rate of reaction between substances.

CATALYST:

A substance that speeds up a chemical reaction without participating in it. Catalysts, of which enzymes are a good example, thus are not consumed in the reaction.

COENZYME:

A non protein component sometimes required to allow an enzyme to set in motion a catalytic reaction.

ENZYME:

A protein that acts as a catalyst, a material that speeds up chemical reactions in the bodies of plants and animals without itself taking part in, or being consumed by, these reactions.

FERMENTATION:

A process involving enzymes in which a compound rich in energy is broken down into simpler substances.

METABOLISM:

The chemical process by which nutrients are broken down and converted into energy or are used in the construction of new tissue or other materi al in the body.

MOLECULE:

A group of atoms, usual ly but not always representing more than one element, joined in a structure. Compounds typically are made up of molecules.

ORGANIC:

At one time, chemists used the term organic only in reference to living things. Now the word is applied to compounds containing carbon and hydrogen.

PROTEINS:

Large molecules built from long chains of 50 or more amino acids. Proteins serve the functions of promoting normal growth, repairing damaged tissue, contributing to the body's immune system, and making enzymes.

REACTANT:

A substance that interacts with another substance in a chemical reaction, resulting in the formation of a chemical or chemicals known as the product.

STARCHES:

Complex carbohydrates without taste or odor, which are granular or powdery in physical form.

SUBSTRATE:

A reactant that typically is paired with a particular enzyme. Enzymes often are named after their respective substrates by adding the suffix ase (e.g., the enzyme lactase is paired with the substrate lactose).

SUGARS:

One of the three principal types of carbohydrate, along with starches and cellulose. Sugars can be defined as any of various water-soluble carbohydrates of varying sweetness. What we think of as "sugar" (i.e., table sugar) is actually sucrose.

VITAMINS:

Organic substances that, in extremely small quantities, are essential to the nutrition of most animals and some plants. In particular, vitamins work with enzymes in regulating metabolic processes; however, they do not in themselves provide energy, and thus vitamins alone do not qualify as a form of nutrition.

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Enzymes

Enzymes

Enzymes are incredibly efficient and highly specific biological catalysts . In fact, the human body would not exist without enzymes because the chemical reactions required to maintain the body simply would not occur fast enough.

Think about the soda you drank moments ago before hitting the books. The sugar in the soda was converted to CO2, H2O, and chemical energy within seconds of being absorbed by your cells, and this chemical energy enabled you to see, think, and move. However, the 2.2-kilogram (5-pound) bag of sugar in your kitchen cabinet can sit for years and still not be converted to CO2 and H2O. The net reaction (glucose 6 O2 6 CO2 + 6 H2O) is the same in both cases, and both pathways are thermodynamically favorable. However, the human body speeds the overall reaction through a series of enzyme-mediated steps. The key is in the catalytic power of enzymes to drive reactions on a time scale required to digest food, relay signals via the nervous system, and contract muscles.

How do enzymes do what they do? They create an environment to make the reaction energetically more favorable. This environment, the active site , is typically a pocket or groove that is lined with amino acids whose side chains bind the substrate (such as sugar) and aid in its chemical transformation to products (see Figure 1). Therefore, the amino acids that form the active site provide the specificity of substrate binding and the proper chemical environment so that the reaction occurs more rapidly than it otherwise would.

Enzymes are central to every biochemical process that occurs in the body. Most enzymes are proteins . There are exceptions, however. For example, there are catalytic ribonucleic acid (RNA) molecules called ribozymes that are involved in RNA processing, and, in 1994, the first DNA enzyme was engineered. Although no naturally occurring deoxyribozymes have been identified, these laboratory-generated DNA enzymes are being developed as therapeutic agents to fight infectious disease and cancer.

All enzymes are characterized by having a high degree of specificity for their substrates, and they accelerate the rate of chemical reactions tremendously, often by a factor of a million times or more. Most enzymes function in the cellular environment at mild conditions of temperature, pH , and salt. There are few nonbiological catalysts that can be so efficient in this type of environment.

Enzymes play a critical role in everyday life. Many heritable genetic disorders (diabetes, Tay-Sachs disease) occur because there is a deficiency or total absence of one or more enzymes. Other disease conditions (cancer) result because there is an excessive activity of one or more enzymes. Routine medical tests monitor the activity of enzymes in the blood, and many of the prescription drugs (penicillin, methotrexate) exert their effects through interactions with enzymes. Enzymes and their inhibitors can be important tools in medicine, agriculture, and food science.

Four Common Features of Enzymes

Enzymes exhibit four fundamental characteristics. First, enzymes do not make a reaction occur that would not occur on its own, they just make it happen much faster. Second, the enzyme molecule is not permanently altered by the reaction. It may be changed transiently, but the enzyme at the end of the reaction is the same molecule it was at the beginning. Therefore, a single enzyme molecule can be used over and over to catalyze the same reaction. Third, an enzyme can catalyze both the forward and the reverse reaction. One direction may be more favorable than the other, but the unfavorable direction of the reaction can occur. Fourth, enzymes are highly specific for the substrates they bind, meaning they catalyze only one reaction.

How Enzymes Work

Take a look at Figure 2. Note that glucose (C6H12O6) in the presence of oxygen (6 O2) will generate carbon dioxide (6 CO2) and water (6 H2O). The forward reaction from glucose to the top of the energy hill to carbon dioxide and water at the base is energetically favorable, as indicated by the "downhill" position of the products. Because energy is released, the forward reaction sequence is called exergonic. Conversely, to synthesize glucose from CO2 and H2O requires energy input to surmount the energy hill and drive the reaction in reverse; therefore, glucose synthesis is called endergonic.

Every biochemical reaction involves both bond breaking and bond forming. The reactant molecules or substrates must absorb enough energy from their surroundings to start the reaction by breaking bonds in the reactant molecules. This initial energy investment is called the activation energy. The activation energy is represented by the uphill portion of the graph with the energy content of the reactants increasing. It is the height of this hilltop that is lowered by enzymes. At the top of the energetic hill, the reactants are in an unstable condition known as the transition state. At this fleeting moment, the molecules are energized and poised for the reaction to occur. As the molecules settle into their new bonding arrangements, energy is released to the surroundings (the downhill portion of the curve). At the summit of the energy hill, the reaction can occur in either the forward or the reverse direction.

Look again at Figure 2. The products CO2 and H2O can form spontaneously or through a series of enzyme-catalyzed reactions in the cell. What enzymes do to accelerate reactions is to lower the energy activation barrier (green) to allow the transition state to be reached more rapidly. What is so special about the active site that allows it to accomplish this goal? Several mechanisms are involved.

Proximity Effect. Substrate molecules collide infrequently when their concentrations are low. The active site brings the reactants together for collision. The effective concentration of the reactants is increased significantly at the active site and favors transition state formation.

Orientation Effect. Substrate collisions in solution are random and are less likely to be the specific orientation that promotes the approach to the transition state. The amino acids that form the active site play a significant role in orienting the substrate. Substrate interaction with these specific amino acid side chains promotes strain such that some of the bonds are easier to break and thus the new bonds can form.

Promotion of Acid-Base Reactions. For many enzymes, the amino acids that form the active site have functional side chains that are poised to donate or accept hydrogen ions from the substrate. The loss or the addition of a proton (H+) can destabilize the covalent bonds in the substrate to make it easier for the bonds to break. Hydrolysis and electron transfers also work by this mechanism.

Exclusion of Water. Most active sites are sequestered and somewhat hydrophobic to exclude water. This nonpolar environment can lower the activation energy for certain reactions. In addition, substrate binding to the enzyme is mediated by many weak noncovalent interactions. The presence of water with the substrate can actually disrupt these interactions in many cases.

Enzymes can use one or more of these mechanisms to produce the strain that is required to convert substrates to their transition state. Enzymes speed the rate of a reaction by lowering the amount of activation energy required to reach the transition state, which is always the most difficult step in a reaction.

Lock and Key or Induced Fit Model

The first ideas about substrate binding to the active site of an enzyme were based on a lock and key model, with the active site being the keyhole and the substrate being the key. When the right substrate entered the active site, catalysis occurred because the substrate was perfectly complementary to the active site. This model described some enzymes, but not all. For others, binding leads to conformational, or shape changes, in the enzyme active site to enhance the bond breakage and formation required to reach the transition state. In both models, the active site provides the tightest fit for the transition state, and the substrate is drawn into the transition state configuration as a result.

The Cellular Environment Affects Enzyme Activity

Temperature and pH. Enzymes are sensitive to their environmental conditions. Up to a point, the rate of the reaction will increase as a function of temperature because the substrates will collide more frequently with the enzyme active site. At extremes of pH or temperature, either high or low, the native structure of the enzyme will be compromised, and the molecule will become inactive (see Figure 3). Note that there is a sharp decrease in the temperature optimum for typical human enzymes at approximately 40 degrees Celsius (104 degrees Fahrenheit). At temperatures greater than 40 degrees Celsius, the enzyme degrades because the noncovalent interactions that stabilize the native conformation of the enzyme are disrupted. The enzyme in essence falls apart, and the active site is no longer able to function. In contrast, the optimal temperature for enzymes of the thermophilic bacteria (extremophiles) that live in hot springs is quite high at 70 degrees Celsius (158 degrees Fahrenheit), a temperature that would instantly scald skin.

Enzymes also show a pH range at which they are most active (see Figure 3). The pH effect results because of critical amino acids at the active site of the enzyme that participate in substrate binding and catalysis. The ionic or electric charge on the active site amino acids can enhance and stabilize interactions with the substrate. In addition, the ability of the substrate and enzyme to donate or receive an H+ is affected by pH. The pH optimum differs for different enzymes. For example, pepsin is a digestive enzyme in the stomach, and its pH optimum is pH 2. In contrast, trypsin is a digestive enzyme that works in the small intestine where the environment is much less acidic . Its pH optimum is pH 8.

Cofactors and Coenzymes. Many enzymes require additional factors for catalytic activity. The cofactors are inorganic such as the metal atoms, zinc, iron, and copper. Organic molecules that function to assist an enzyme are referred to as coenzymes. Vitamins are the precursors of many essential coenzymes. Cofactors and coenzymes may remain at the active site of the enzyme in the absence of the substrate, or they may be present transiently during catalysis.

Allosteric Inhibitors and Activators. In addition to the active site where the substrate binds, an enzyme may have separate sites, called allosteric sites, where specific molecules can bind to increase or decrease the activity of the enzyme. The allosteric inhibitors and activators bind the enzyme through weak, noncovalent interactions and exert their effects by changing the conformation of the enzyme, a change that is transmitted to the active site. Typically, the allosteric modulators regulate enzyme activity by affecting substrate binding at the active site.

Control of Metabolism

Although biochemical reactions are controlled in part by the specificity of substrate biding and by allosteric regulation, the human body could not function if all enzymes were present together and all operating maximally with no regulation. There would be biochemical chaos with substances being synthesized and degraded at the same time. Instead, the body tightly regulates enzymes through metabolic pathways and by controlling specific enzymes within a pathway. This approach allows an entire pathway to be turned on or off by simply regulating one or a few enzymes. Metabolic pathways can also be regulated by switching specific genes on or off.

Compartmentation. One of the major characteristics of eukaryotic cells is the presence of membrane-bound intracellular organelles . These structures help to segregate specific enzymes and metabolic pathways, especially when the pathways are competing with each other. For example, the enzymes that catalyze synthesis of fatty acids (a type of lipid ) are located in the cytoplasm , while the enzymes that breakdown fatty acids are located in the mitochondria .

Covalent Modification. Enzymes can be activated or inactivated by covalent modification. A common example is phosphorylation of an enzyme (addition of a phosphate group to the amino acids serine, threonine, or tyrosine) mediated by another enzyme called a kinase . The phosphorylation is reversible, and other enzymes called phosphatases typically catalyze the removal of the phosphate group from the enzyme. The phosphorylated form of the enzyme is often, but not always, the active form. For some enzymes, the dephosphorylated form is active, and the phosphorylated state is inactive. Enzymes can also be activated by removing a fragment of the protein. Many of the digestive enzymes (trypsin, chymotrypsin) are synthesized and stored in the pancreas. They are secreted to the small intestine where they are activated by removing or cleaving off a small portion of the protein. This "proteolytic" cleavage to activate an enzyme is irreversible but serves an important function to prevent the digestive enzymes from digesting the pancreas.

Allosteric Regulation. Allosteric modulators can increase or decrease the activity of an entire metabolic pathway by altering the conformation of a single enzyme. Sometimes, the end product of the metabolic pathway acts as an allosteric inhibitor by binding to the enzyme at its allosteric site, causing a conformational change in the enzyme to decrease the activity of the enzyme. This type of regulation is called feedback inhibition (see Figure 4).

Cooperativity. Frequently, enzymes are multisubunit complexes with more than one active site. Binding of the first substrate molecule may lead to conformational changes that are communicated to the other subunit(s) such that the binding of each additional substrate molecule is enhanced. Positive cooperativity can amplify the response of enzymes to substrates and provides an additional mechanism to regulate enzyme activity.

Molecular Motors

Finally, enzymes can be thought of as nanomachines, powering the reactions of the cell to enable the human body to be the entity it is. There is a special class of enzymes called molecular motors that drive all the movements that occur in the body, including muscle contraction (myosin/actin), flagella and cilia beating (dynein/microtubule), and vesicle movements in neurons (kinesin/microtubule). These molecular motors harness the energy from adenosine triphosphate (ATP) to drive actin-based or microtubulebased movements.

see also Cell Motility; Control Mechanisms; Cytoskeleton; Genetic Diseases; Lipids; Mitochondrion; Vitamins and Coenzymes

Susan P. Gilbert

Bibliography

Breaker, Ronald R. "Making Catalytic DNAs." Science 290 (2000): 20952096.

Campbell, Neil A., Jane B. Reece, and Lawrence G. Mitchell. Biology, 5th ed. Menlo Park, CA: Benjamin/Cummings, 1999.

Deeth, Robert J. "Chemical Choreography." New Scientist 155 (1997): 2427.

Koshland, Daniel E., Jr. "Protein Shape and Biological Control." Scientific American 229 (1973): 5264.

Madigan, Michael R., and Barry L. Marrs. "Extremophiles." Scientific American 276 (1997): 8287.

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enzymes

enzymes are most familiarly associated with digestion, as substances in the alimentary tract that are necessary for the breakdown of food into simpler stuffs that can be absorbed into the body proper. These are indeed important, but they are in a small minority among the vast population of the body's enzymes. They also differ from the majority in acting outside rather than inside the cells that make them.

All living cells are teeming with enzymes. The name comes from the Greek meaning ‘in leaven’ or yeast. They are proteins, synthesized in cells, which act as catalysts, causing all the body's chemical processes to advance with the necessary rapidity and completeness. Enzymes are ubiquitous in body cells and fluids, and they are specific — each enzyme is responsible for catalyzing one particular chemical process. Their existence and their function came to be recognized during the nineteenth century; understanding advanced with burgeoning twentieth-century biochemistry; and molecular biologists continue to elucidate their ultimate structure and mode of action, and the genes that make them.

The names and nature of enzymes

The naming of enzymes in most cases reveals their function; ‘-ase’ is added to the name either of the substance (the substrate) on which they act (like peptidase for those acting on peptides), or of the type of reaction induced (such as hydrolase, for those causing hydrolysis, the splitting of a substance with addition of water, or transferase, for those moving some chemical group from one molecule to another). Some of the first enzymes to be discovered have unique names, such as pepsin in the stomach, and trypsin from the pancreas, which are both proteinases.

So what sort of proteins are they, and how do they function? With molecular masses of 10 000 to 1 000 000, enzymes are themselves large molecules, but some also exist in larger complexes that facilitate a sequence of changes. An enzyme molecule is a ‘globular’ protein that has an area on its surface to which can be bound only the specific substrate that the enzyme is designed to accept. This binding leads to changes in both molecules that result in the formation of the required product, and restoration of the enzyme molecule to its original state, ready to take on another substrate molecule. With progressively higher concentrations of substrate the rate of product yield increases, but the increment in rate diminishes as it approaches a maximum at a certain substrate concentration; beyond this point only an increase in the concentration of the enzyme itself can accelerate the process. This behaviour is consistent with progressive occupation of binding sites on all available enzymes, until they are all functioning at a maximal turnover rate.

Range and sites of enzyme function

Enzymes operate at every stage of life. Even the head of the sperm releases an enzyme that dissolves its path through the outer covering of the ovum to reach and penetrate it. Cell division in the embryo and throughout life involves replication of the DNA that carries the genetic information. A series of specific enzymes is needed for this, to unwind the double helix, to replicate it by the synthesis of new strands, and to put it and the new pairs back together again — whilst other enzymes meanwhile supply energy by the breakdown of adenosine triphosphate (ATP). Yet others are involved in the formation of messenger RNA and in all subsequent synthesis of proteins in a cell that results from the genetic coding.

Enzymes implement every event in the internal life of every cell in the body, and in its interaction with its environment. Each enzyme, or chain of enzymes acting in rapid sequence, has a specific function. There are those that are necessary for respiration and energy production; for transport mechanisms across the cell membrane and between internal components; for modifications of cellular metabolism in response to hormones; and for any specialized activity, including secretion by glandular cells, contraction by muscle cells, synthesis, release, and reuptake of neurotransmitters by nerve cells. The continual potential damage to tissues by the generation of free radicals is crucially limited by the body's antioxidant enzymes.

All cells have enzymes in their membrane, in the cytoplasm, and in the organelles within them. Those at the heart of cellular metabolism are the complex sequence of respiratory enzymes in the mitochondria that make possible the utilization of oxygen for the conversion of nutrient substrates to carbon dioxide and water, synthesis of ATP, and its breakdown for release of energy.

Cell membranes are furnished with ‘sodium pumps’ — protein molecules spanning the cell membrane that pump sodium ions out and potassium ions in. Facing inwards is an enzyme site that binds and breaks down ATP to supply the energy for pumping. Other enzyme molecules in the cell membrane may have, in addition to a site for substrate-binding, another that acts as receptor for a ‘messenger’ that activates the catalytic process: for example, the insulin receptor spans the cell membrane of muscle or fat cells; its outer site binds insulin, and its inner site handles the first of a series of enzyme-catalyzed reactions inside the cell that result in the several effects of insulin.

At synapses between nerves, and at neuromuscular junctions, enzymes are present that break down redundant neurotransmitters, preventing persistence of their effects. An example is acetylcholinesterase, found in the synaptic clefts on motor end plates in skeletal muscle, which hydrolyses excess acetylcholine, the neurotransmitter released by the motor nerve terminals.

Within skeletal muscle fibres, the enzymes vary according to their type of metabolism: whether it is predominantly aerobic (utilizing oxygen: ‘slow’ or ‘red’ muscle) or anaerobic (‘fast’ or ‘pale’ muscle). The sequence of events leading from activation of a muscle fibre by neurotransmitter, to contraction by means of interaction between myosin and actin filaments, depends on enzymes at every stage.

Enzymes in the blood

In the circulating blood there are enzymes both inside the blood cells, and outside in the plasma. Blood cells, in common with all cells, have the necessary enzymes for membrane transport and energy production. White blood cells have respiratory enzymes for aerobic metabolism, and others suited to their particular functions. Red blood cells are without mitochondria and respire anaerobically, so have enzymes appropriate to anaerobic glycolysis. Important for their function in whole-body respiratory gas exchange, they contain carbonic anhydrase, which promotes the uptake from the tissues of carbon dioxide and its carriage in the blood as bicarbonate, by catalyzing its combination with water to form carbonic acid, and its release in the lungs by this reaction in reverse.

Some enzymes exist as pro-enzymes or zymogens; they require some molecular change to be triggered into their active forms. These include proteins in the plasma that are involved in blood clotting: prothrombin is synthesized in the liver, and becomes thrombin when clotting is activated, and plasminogen can come into action as plasmin, a clot-dissolving enzyme. In the stomach, pepsinogen is secreted, and activated into pepsin by the acid that is secreted at the same site.

Enzymes that are normally secreted only into the gut or inside cells may, in pathological conditions, appear in significant quantities in the plasma, so that their measurement may be clinically useful. Examples are digestive enzymes that leak into the blood in acute pancreatitis, and creatine kinase, an enzyme from muscle tissue, that can appear in skeletal muscle disorders or, along with other intracellular enzymes, after a coronary thrombosis resulting in breakdown of some of the cardiac muscle.

Conditions for enzyme activity

All enzymes need the right environment for effective function, notably an optimal acidity, which differs in accordance with the site at which a particular enzyme acts (for example, more acidic inside cells than outside, and, for digestive enzymes, acidic in the stomach and alkaline in the duodenum). Like any chemical reactions, the rate of those that are catalyzed by enzymes varies with temperature. Local heat generation, for example in exercising muscle, enhances all such reactions within it. Likewise, whole-body metabolic rate increases in fever and decreases in hypothermia, because of the effect on all enzyme-catalyzed reactions. Extremes of pH or temperature irreversibly abolish enzyme activity, and so also do some substances that bind to the active sites of particular enzymes. These include an organophosphate ‘nerve gas’ that blocks acetylcholinesterase (causing persistent accumulation of acetylcholine at neuromuscular junctions, and thus uncontrollable muscle contraction). Poisoning by cyanide is due to blocking an essential enzyme in mitochondria and so fatally preventing all tissue respiration.

Medical applications

It is possible to inhibit the action of an enzyme without destroying it, and this has important therapeutic implications. There are substances that compete with the natural substrate for binding to an enzyme by having a similar structure, and others that act on other components of the enzyme molecule, preventing its ability to catalyze. Acetylcholinesterase inhibition is again an example — though in this context useful and reversible — in the treatment of the condition of myasthenia gravis, when the receptors on muscles cells for acetylcholine are deficient; the similar molecular structure of neostigmine allows it to bind to the enzyme, preventing binding and breakdown of acetylcholine; this can then accumulate sufficiently to enhance neuromuscular transmission. Drugs are used similarly to reverse the neuromuscular blockade deliberately induced during general anaesthesia. A different and important medical application of enzyme inhibition is in the use of antibiotics that block enzymes in microorganisms that are essential for their life or growth.

There are also many necessary co-enzymes, or co-factors for enzymes — organic non-protein molecules, smaller than the enzymes themselves, which either enhance or are necessary for the enzyme's activity. These again are widespread throughout the body, and are of many different molecular structures. Some require for their synthesis small amounts of essential substances from the diet. This is the basis of the need for the vitamins of the B group — they provide components for co-enzymes which could not otherwise be made in the body. Ions of several metals are also essential as co-factors, as well as for incorporation in some enzyme molecules themselves.

Sheila Jennett


See also alimentary system; cell; cell membrane; metabolism; respiration; transport.

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Enzymes

Enzymes


Enzymes are (mostly) proteins that catalyze biochemical reactions; that is, they increase the rate of a reaction but are not used up in the process. Their importance to life is underscored by the fact that many severe or fatal genetic diseases involve a missing or defective enzyme. Enzymes can also provide targets, with hitting the target the strategy for attacking disease-causing bacteria or viruses. One could design a drug that attaches to or occupies the active site of a target organism's enzyme. For example, penicillin destroys an enzyme crucial to the synthesis of bacterial cell walls. In the treatment of AIDS, HIV protease inhibitors target the viral enzyme protease.

Properties and Mechanism

In some cases, the increase in the rate of an enzyme-catalyzed reaction versus the uncatalyzed rate is a millionfold. As soon as one reaction has been catalyzed, the enzyme is available for another round of catalysis a phenomenon known as turnover. Enzymes operate near physiological temperature and pH, and they are also highly specific in their actionsfor example, an enzyme called hexokinase will place a phosphate group only onto the sixth carbon of a D-glucose molecule. The enzyme has no activity toward L-glucose, and reduced activity toward other D-sugars. Enzymes can also be regulated so that they are switched on only when they are needed by the cell. They may consist of a single polypeptide chain of amino acids (RNAse contains 124 amino acids), or they may require an additional chemical called a coenzyme. Many of the vitamins as well as several metals act as coenzymes.

A study of enzyme catalysis is a study of kinetics, which asks the question "how fast?" However, enzymes cannot alter the outcome or direction of a reaction. For instance, if one were to add a small amount of sodium chloride to a large volume of water, we know that the end result will be that the salt will dissolve in the water. However, the time dissolution takes depends on a number of factors: What is the temperature?; Is it being stirred? This is kinetics. We also know that a swinging pendulum will eventually come to rest at its equilibrium point, which in this case is its pointing straight down toward the center of Earth. Kinetics describes only the time it takes to reach that point. Enzymes cannot alter the equilibrium point of a reaction, only the time it takes to get there.

To proceed to products, reactants must come together with sufficient energy to overcome an energy barrier known as the energy of activation. The apex of this barrier represents the transition state between reactants and products. Enzymes act to lower the energy of activation by stabilizing (lowering the energy of) the transition state.

Mechanistically, an enzyme will bind the reactant, called the substrate, at a very specific site on the enzyme known as the active site. This resulting enzymesubstrate complex (ES), described as a lock-and-key mechanism, involves weak binding and often some structural changesknown as induced fitthat assist in stabilizing the transition state. In the unique microenvironment of the active site, substrate can rapidly be converted to product resulting in an enzyme product (EP) complex that then dissociates to release product.

Nomenclature

Enzyme nomenclature has historically been at the whim of the discoverer of the enzyme. Many enzyme names give clues to their actions or to where they are found. The meat tenderizer papain can be obtained from the papyrus plant. Pepsin is a digestive enzyme found in the stomach. Lysozyme acts to lyse bacterial cell walls. Most enzymes are now named by their function along with the suffix "ase." For instance, ethanol is metabolized in the liver by alcohol dehyrogenase. Phosphates are removed from molecules by phosphatases. An international body known as the Enzyme Commission (EC) has assigned numerical designations, called EC numbers, to enzymes. The EC has listed six categories based on type of activity (oxidation-reduction, hydrolysis, etc.), along with several subcategories, into which enzymes are placed. For example, alcohol dehydrogenase is EC 1.1.1.1.

Enzyme Kinetics

The rate of an enzyme-catalyzed reaction varies with the substrate concentration. At very low substrate concentrations, the rate will be directly proportional to the concentration of the substrate and will exhibit first-order kinetics. However, at very high substrate levels, all of the active sites are occupied and substrate molecules must wait their turn, just as the traffic at a line of tollbooths depends on how fast the cars can pass through the gates. This represents saturation, and the reaction rate is at its maximum and is designated Vmax.

Other factors that influence enzyme activity include pH and temperature. Most mammalian enzymes operate maximally at around physiological pH and body temperature. There are several exceptions. The stomach digestive enzyme pepsin works best at around pH 2.0, the approximate pH of the stomach. Bacteria found in hot springs have enzymes that operate at or near the boiling point of water. In most cases, however, extremes of pH or temperature will destroy enzymes in an enzyme-unfolding process known as denaturation. Only one, very precise, three-dimensional configuration or fold of the chain of amino acids is functional. Denatured or unfolded proteins are inactive. Denaturation can be observed when an egg white is cooked: The proteins in the egg white unfold and form a gel-like aggregate with other unfolded proteins. The same occurs when bacteria spoil milk by lowering its pH sufficiently to unfold and curdle milk proteins.

RNA as an Enzyme

Although enzymes are considered to be proteins, enzyme activity has recently been found in ribonucleic acid (RNA) in certain organisms. These "ribozymes" may yield clues to the origins of life on Earth. DNA needs enzymes to replicate, whereas enzymes need the instructions of DNA. This represents a "chicken-and-egg" question that has stumped researchers. Early life may have used RNA that was able to catalyze its own replication.

see also Catalysis and Catalysts; Coenzyme; Denaturation; Hydrogen; Inhibitors; Kinetics; Proteins; Ribonucleic Acid.

C. Larry Bering

Bibliography

Campbell, Mary K. (1999). Biochemistry, 3rd edition. New York: Saunders.

Voet, Donald, and Voet, Judith G. (1995). Biochemistry, 2nd edition. New York: Wiley.

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Enzymes

Enzymes

Enzymes are molecules that act as critical catalysts in biological systems. Catalysts are substances that increase the rate of chemical reactions without being consumed in the reaction. Without enzymes, many reactions would require higher levels of energy and higher temperatures than exist in biological systems. Enzymes are proteins that possess specific binding sites for other molecules (substrates). A series of weak binding interactions allow enzymes to accelerate reaction rates. Enzyme kinetics is the study of enzymatic reactions and mechanisms. Enzyme inhibitor studies have allowed researchers to develop therapies for the treatment of diseases, including AIDS .

French chemist Louis Pasteur (18221895) was an early investigator of enzyme action. Pasteur hypothesized that the conversion of sugar into alcohol by yeast was catalyzed by "ferments," which he thought could not be separated from living cells. In 1897, German biochemist Eduard Buchner (18601917) isolated the enzymes that catalyze the fermentation of alcohol from living yeast cells. In 1909, English physician Sir Archibald Garrod (18571936) first characterized enzymes genetically through the one gene-one enzyme hypothesis. Garrod studied the human disease alkaptonuria, a hereditary disease characterized by the darkening of excreted urine after exposure to air. He hypothesized that alkaptonurics lack an enzyme that breaks down alkaptans to normal excretion products, that alkaptonurics inherit this inability to produce a specific enzyme, and that they inherit a mutant form of a gene from each of their parents and have two mutant forms of the same gene. Thus, he hypothesized, some genes contain information to specify particular enzymes.

The early twentieth century saw dramatic advancement in enzyme studies. German chemist Emil Fischer (18521919) recognized the importance of substrate shape for binding by enzymes. German-American biochemist Leonor Michaelis (18751949) and Canadian biologist Maud Menten (18791960) introduced a mathematical approach for quantifying enzyme-catalyzed reactions. American chemists James Sumner (18871955) and John Northrop (18911987) were among the first to produce highly ordered enzyme crystals and firmly establish the proteinaceous nature of these biological catalysts. In 1937, German-born British biochemist Hans Krebs (19001981) postulated how a series of enzymatic reactions were coordinated in the citric acid cycle for the production of ATP from glucose metabolites. Today, enzymology is a central part of biochemical study, and the fields of industrial microbiology and genetics employ enzymes in numerous ways, from food production to gene cloning , to advanced therapeutic techniques.

Enzymes are proteins that encompass a large range of molecular size and mass. They may be composed of more than one polypeptide chain. Each polypeptide chain is called a subunit and may have a separate catalytic function. Some enzymes require non-protein groups for enzymatic activity. These components include metal ions and organic molecules called coenzymes. Coenzymes that are tightly or covalently attached to enzymes are termed prosthetic groups. Prosthetic groups contain critical chemical groups which allow the overall catalytic event to occur.

Enzymes bind their substrates at special folds and clefts in their structures called active sites. Because active sites have chemical groups precisely located and orientated for binding the substrate, they generally display a high degree of substrate specificity. The active site of an enzyme consists of two key regions, the catalytic site, which interacts with the substrate during the reaction, and the binding site, the chemical groups of the enzyme that bind the substrate, allowing the interactions at the catalytic site to occur. The crevice of the active site creates a microenvironment whose properties are critical for catalysis. Environmental factors influencing enzyme activity include pH , polarity and hydrophobicity of amino acids in the active site, and a precise arrangement of the chemical groups of the enzyme and its substrate.

Enzymes have high catalytic power, high substrate specificity, and are generally most active in aqueous solvents at mild temperature and physiological pH. Most enzymes catalyze the transfer of electrons, atoms, or groups of atoms. There are thousands of known enzymes, but most can be categorized according to their biological activities into six major classes: oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases.

Enzymes generally have an optimum pH range in which they are most active. The pH of the environment will affect the ionization state of catalytic groups at the active site and the ionization of the substrate. Electrostatic interactions are therefore controlled by pH. The pH of a reaction may also control the conformation of the enzyme by influencing amino acids critical for the three-dimensional shape of the macromolecule.

Inhibitors can diminish the activity of an enzyme by altering the binding of substrates. Inhibitors may resemble the structure of the substrate, thereby binding the enzyme and competing for the correct substrate. Inhibitors may be large organic molecules, small molecules, or ions. They can be used for chemotherapeutic treatment of diseases.

Regulatory enzymes are characterized by increased or decreased activity in response to chemical signals. Metabolic pathways are regulated by controlling the activity of one or more enzymatic steps along that path. Regulatory control allows cells to meet changing demands for energy and metabolites.

See also Biochemical analysis techniques; Biotechnology; Bioremediation; Cloning, application of cloning to biological problems; Enzyme induction and repression; Enzyme-linked immunosorbant assay (ELISA); Food preservation; Food safety; Immunologic therapies; Immunological analysis techniques

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