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Enzyme

Enzyme
ribozymes catalyze reactions, with an important example being some parts of the ribosome.[4][5] Synthetic molecules called artificial enzymes also display enzyme-like catalysis.[6] Enzyme activity can be affected by other molecules. Inhibitors are molecules that decrease enzyme activity; activators are molecules that increase activity. Many drugs and poisons are enzyme inhibitors. Activity is also affected by temperature, chemical environment (e.g., pH), and the concentration of substrate. Some enzymes are used commercially, for example, in the synthesis of antibiotics. In addition, some household products use enzymes to speed up biochemical reactions (e.g., enzymes in biological washing powders break down protein or fat stains on clothes; enzymes in meat tenderizers break down proteins, making the meat easier to chew).

Human glyoxalase I. Two zinc ions that are needed for the enzyme to catalyze its reaction are shown as purple spheres, and an enzyme inhibitor called S-hexylglutathione is shown as a space-filling model, filling the two active sites. Enzymes are biomolecules that catalyze (i.e., increase the rates of) chemical reactions.[1][2] Almost all enzymes are proteins. In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, called the products. Almost all processes in a biological cell need enzymes to occur at significant rates. Since enzymes are selective for their substrates and speed up only a few reactions from among many possibilities, the set of enzymes made in a cell determines which metabolic pathways occur in that cell. Like all catalysts, enzymes work by lowering the activation energy (Ea or ΔG‡) for a reaction, thus dramatically increasing the rate of the reaction. Most enzyme reaction rates are millions of times faster than those of comparable un-catalyzed reactions. As with all catalysts, enzymes are not consumed by the reactions they catalyze, nor do they alter the equilibrium of these reactions. However, enzymes do differ from most other catalysts by being much more specific. Enzymes are known to catalyze about 4,000 biochemical reactions.[3] A few RNA molecules called

Etymology and history
As early as the late 1700s and early 1800s, the digestion of meat by stomach secretions[7] and the conversion of starch to sugars by plant extracts and saliva were known. However, the mechanism by which this occurred had not been identified.[8] In the 19th century, when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur came to the conclusion that this fermentation was catalyzed by a vital force contained within the yeast cells called "ferments", which were thought to function only within living organisms. He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells."[9] In 1878, German physiologist Wilhelm Kühne (1837–1900) first used the term enzyme, which comes from Greek ενζυμον, "in leaven", to describe this process. The word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms.

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Enzyme
However, in 1926, James B. Sumner showed that the enzyme urease was a pure protein and crystallized it; Sumner did likewise for the enzyme catalase in 1937. The conclusion that pure proteins can be enzymes was definitively proved by Northrop and Stanley, who worked on the digestive enzymes pepsin (1930), trypsin and chymotrypsin. These three scientists were awarded the 1946 Nobel Prize in Chemistry.[12] This discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This was first done for lysozyme, an enzyme found in tears, saliva and egg whites that digests the coating of some bacteria; the structure was solved by a group led by David Chilton Phillips and published in 1965.[13] This high-resolution structure of lysozyme marked the beginning of the field of structural biology and the effort to understand how enzymes work at an atomic level of detail.

Eduard Buchner In 1897, Eduard Buchner began to study the ability of yeast extracts that lacked any living yeast cells to ferment sugar. In a series of experiments at the University of Berlin, he found that the sugar was fermented even when there were no living yeast cells in the mixture.[10] He named the enzyme that brought about the fermentation of sucrose "zymase".[11] In 1907, he received the Nobel Prize in Chemistry "for his biochemical research and his discovery of cell-free fermentation". Following Buchner’s example, enzymes are usually named according to the reaction they carry out. Typically, to generate the name of an enzyme, the suffix -ase is added to the name of its substrate (e.g., lactase is the enzyme that cleaves lactose) or the type of reaction (e.g., DNA polymerase forms DNA polymers). Having shown that enzymes could function outside a living cell, the next step was to determine their biochemical nature. Many early workers noted that enzymatic activity was associated with proteins, but several scientists (such as Nobel laureate Richard Willstätter) argued that proteins were merely carriers for the true enzymes and that proteins per se were incapable of catalysis.

Structures and mechanisms
See also: Enzyme catalysis

Ribbon diagram showing carbonic anhydrase II. The grey sphere is the zinc cofactor in the active site. Diagram drawn from PDB 1MOO. Enzymes are generally globular proteins and range from just 62 amino acid residues in size, for the monomer of 4-oxalocrotonate tautomerase,[14] to over 2,500 residues in the animal fatty acid synthase.[15] A small number of RNA-based biological catalysts exist, with the most common being the ribosome;

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these are referred to as either RNA-enzymes or ribozymes. The activities of enzymes are determined by their three-dimensional structure.[16] However, although structure does determine function, predicting a novel enzyme’s activity just from its structure is a very difficult problem that has not yet been solved.[17] Most enzymes are much larger than the substrates they act on, and only a small portion of the enzyme (around 3–4 amino acids) is directly involved in catalysis.[18] The region that contains these catalytic residues, binds the substrate, and then carries out the reaction is known as the active site. Enzymes can also contain sites that bind cofactors, which are needed for catalysis. Some enzymes also have binding sites for small molecules, which are often direct or indirect products or substrates of the reaction catalyzed. This binding can serve to increase or decrease the enzyme’s activity, providing a means for feedback regulation. Like all proteins, enzymes are made as long, linear chains of amino acids that fold to produce a three-dimensional product. Each unique amino acid sequence produces a specific structure, which has unique properties. Individual protein chains may sometimes group together to form a protein complex. Most enzymes can be denatured—that is, unfolded and inactivated—by heating or chemical denaturants, which disrupt the three-dimensional structure of the protein. Depending on the enzyme, denaturation may be reversible or irreversible.

Enzyme
average error rates of less than 1 error in 100 million reactions in high-fidelity mammalian polymerases.[21] Similar proofreading mechanisms are also found in RNA polymerase,[22] aminoacyl tRNA synthetases[23] and ribosomes.[24] Some enzymes that produce secondary metabolites are described as promiscuous, as they can act on a relatively broad range of different substrates. It has been suggested that this broad substrate specificity is important for the evolution of new biosynthetic pathways.[25]

"Lock and key" model
Enzymes are very specific, and it was suggested by Emil Fischer in 1894 that this was because both the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another.[26] This is often referred to as "the lock and key" model. However, while this model explains enzyme specificity, it fails to explain the stabilization of the transition state that enzymes achieve. The "lock and key" model has proven inaccurate, and the induced fit model is the most currently accepted enzyme-substratecoenzyme figure.

Induced fit model

Specificity
Enzymes are usually very specific as to which reactions they catalyze and the substrates that are involved in these reactions. Complementary shape, charge and hydrophilic/hydrophobic characteristics of enzymes and substrates are responsible for this specificity. Enzymes can also show impressive levels of stereospecificity, regioselectivity and chemoselectivity.[19] Some of the enzymes showing the highest specificity and accuracy are involved in the copying and expression of the genome. These enzymes have "proof-reading" mechanisms. Here, an enzyme such as DNA polymerase catalyzes a reaction in a first step and then checks that the product is correct in a second step.[20] This two-step process results in

Diagrams to show the induced fit hypothesis of enzyme action. In 1958, Daniel Koshland suggested a modification to the lock and key model: since enzymes are rather flexible structures, the active site is continually reshaped by interactions with the substrate as the substrate interacts with the enzyme.[27] As a result, the substrate does not simply bind to a rigid active site; the amino acid side chains which make up the active site are moulded into the precise positions that enable the enzyme to perform its catalytic function. In some cases, such as glycosidases, the substrate molecule also changes shape slightly as it enters the active site.[28] The active site continues to change until the substrate is completely

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bound, at which point the final shape and charge is determined.[29]

Enzyme
or even an entire protein domain. These movements occur at various time-scales ranging from femtoseconds to seconds. Networks of protein residues throughout an enzyme’s structure can contribute to catalysis through dynamic motions.[37][38][39][40] Protein motions are vital to many enzymes, but whether small and fast vibrations, or larger and slower conformational movements are more important depends on the type of reaction involved. However, although these movements are important in binding and releasing substrates and products, it is not clear if protein movements help to accelerate the chemical steps in enzymatic reactions.[41] These new insights also have implications in understanding allosteric effects and developing new drugs.

Mechanisms
Enzymes can act in several ways, all of which lower ΔG‡:[30] • Lowering the activation energy by creating an environment in which the transition state is stabilized (e.g. straining the shape of a substrate—by binding the transition-state conformation of the substrate/product molecules, the enzyme distorts the bound substrate(s) into their transition state form, thereby reducing the amount of energy required to complete the transition). • Lowering the energy of the transition state, but without distorting the substrate, by creating an environment with the opposite charge distribution to that of the transition state. • Providing an alternative pathway. For example, temporarily reacting with the substrate to form an intermediate ES complex, which would be impossible in the absence of the enzyme. • Reducing the reaction entropy change by bringing substrates together in the correct orientation to react. Considering ΔH‡ alone overlooks this effect. Interestingly, this entropic effect involves destabilization of the ground state,[31] and its contribution to catalysis is relatively small.[32]

Allosteric modulation
Allosteric enzymes change their structure in response to binding of effectors. Modulation can be direct, where the effector binds directly to binding sites in the enzyme, or indirect, where the effector binds to other proteins or protein subunits that interact with the allosteric enzyme and thus influence catalytic activity.

Cofactors and coenzymes
Cofactors
Some enzymes do not need any additional components to show full activity. However, others require non-protein molecules called cofactors to be bound for activity.[42] Cofactors can be either inorganic (e.g., metal ions and iron-sulfur clusters) or organic compounds (e.g., flavin and heme). Organic cofactors can be either prosthetic groups, which are tightly bound to an enzyme, or coenzymes, which are released from the enzyme’s active site during the reaction. Coenzymes include NADH, NADPH and adenosine triphosphate. These molecules act to transfer chemical groups between enzymes.[43] An example of an enzyme that contains a cofactor is carbonic anhydrase, and is shown in the ribbon diagram above with a zinc cofactor bound as part of its active site.[44] These tightly bound molecules are usually found in the active site and are involved in catalysis. For example, flavin and heme

Transition State Stabilization
The understanding of the origin of the reduction of ΔG‡ requires one to find out how the enzymes can stabilize its transition state more than the transition state of the uncatalyzed reaction. Apparently, the most effective way for reaching large stabilization is the use of electrostatic effects, in particular, by having a relatively fixed polar environment that is oriented toward the charge distribution of the transition state.[33] Such an environment does not exist in the uncatalyzed reaction in water.

Dynamics and function
The internal dynamics of enzymes is connected to their mechanism of catalysis.[34][35][36] Internal dynamics are the movement of parts of the enzyme’s structure, such as individual amino acid residues, a group of amino acids,

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cofactors are often involved in redox reactions. Enzymes that require a cofactor but do not have one bound are called apoenzymes or apoproteins. An apoenzyme together with its cofactor(s) is called a holoenzyme (this is the active form). Most cofactors are not covalently attached to an enzyme, but are very tightly bound. However, organic prosthetic groups can be covalently bound (e.g., thiamine pyrophosphate in the enzyme pyruvate dehydrogenase). The term "holoenzyme" can also be applied to enzymes that contain multiple protein subunits, such as the DNA polymerases, here the holoenzyme is the complete complex containing all the subunits needed for activity.

Enzyme
useful to consider coenzymes to be a special class of substrates, or second substrates, which are common to many different enzymes. For example, about 700 enzymes are known to use the coenzyme NADH.[46] Coenzymes are usually regenerated and their concentrations maintained at a steady level inside the cell: for example, NADPH is regenerated through the pentose phosphate pathway and S-adenosylmethionine by methionine adenosyltransferase.

Thermodynamics

Coenzymes

The energies of the stages of a chemical reaction. Substrates need a lot of energy to reach a transition state, which then decays into products. The enzyme stabilizes the transition state, reducing the energy needed to form products. As all catalysts, enzymes do not alter the position of the chemical equilibrium of the reaction. Usually, in the presence of an enzyme, the reaction runs in the same direction as it would without the enzyme, just more quickly. However, in the absence of the enzyme, other possible uncatalyzed, "spontaneous" reactions might lead to different products, because in those conditions this different product is formed faster. Furthermore, enzymes can couple two or more reactions, so that a thermodynamically favorable reaction can be used to "drive" a thermodynamically unfavorable one. For example, the hydrolysis of ATP is often used to drive other chemical reactions. Enzymes catalyze the forward and backward reactions equally. They do not alter the equilibrium itself, but only the speed at which it is reached. For example, carbonic anhydrase catalyzes its reaction in either

Space-filling model of the coenzyme NADH Coenzymes are small organic molecules that transport chemical groups from one enzyme to another.[45] Some of these chemicals such as riboflavin, thiamine and folic acid are vitamins (compounds which cannot be synthesized by the body and must be acquired from the diet). The chemical groups carried include the hydride ion (H-) carried by NAD or NADP+, the acetyl group carried by coenzyme A, formyl, methenyl or methyl groups carried by folic acid and the methyl group carried by S-adenosylmethionine. Since coenzymes are chemically changed as a consequence of enzyme action, it is

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direction depending on the concentration of its reactants. (in tissues; high CO2 concentration)

Enzyme
chemical step in the reaction and releases the product.

(in lungs; low CO2 concentration) Nevertheless, if the equilibrium is greatly displaced in one direction, that is, in a very exergonic reaction, the reaction is effectively irreversible. Under these conditions the enzyme will, in fact, only catalyze the reaction in the thermodynamically allowed direction.

Kinetics

Saturation curve for an enzyme reaction showing the relation between the substrate concentration (S) and rate (v). Enzymes can catalyze up to several million reactions per second. For example, the reaction catalyzed by orotidine 5’-phosphate decarboxylase will consume half of its substrate in 78 million years if no enzyme is present. However, when the decarboxylase is added, the same process takes just 25 milliseconds.[51] Enzyme rates depend on solution conditions and substrate concentration. Conditions that denature the protein abolish enzyme activity, such as high temperatures, extremes of pH or high salt concentrations, while raising substrate concentration tends to increase activity. To find the maximum speed of an enzymatic reaction, the substrate concentration is increased until a constant rate of product formation is seen. This is shown in the saturation curve on the right. Saturation happens because, as substrate concentration increases, more and more of the free enzyme is converted into the substrate-bound ES form. At the maximum velocity (Vmax) of the enzyme, all the enzyme active sites are bound to substrate, and the amount of ES complex is the same as the total amount of enzyme. However, Vmax is only one kinetic constant of enzymes. The amount of substrate needed to achieve a given rate of reaction is also important. This is given by the Michaelis-Menten constant (Km), which is the substrate concentration required for an enzyme to reach one-half its maximum velocity. Each enzyme has a characteristic Km for a given substrate, and this can show how tight the binding of the substrate is to the enzyme. Another useful constant is kcat,

Mechanism for a single substrate enzyme catalyzed reaction. The enzyme (E) binds a substrate (S) and produces a product (P). Enzyme kinetics is the investigation of how enzymes bind substrates and turn them into products. The rate data used in kinetic analyses are obtained from enzyme assays. In 1902 Victor Henri[47] proposed a quantitative theory of enzyme kinetics, but his experimental data were not useful because the significance of the hydrogen ion concentration was not yet appreciated. After Peter Lauritz Sørensen had defined the logarithmic pH-scale and introduced the concept of buffering in 1909[48] the German chemist Leonor Michaelis and his Canadian postdoc Maud Leonora Menten repeated Henri’s experiments and confirmed his equation which is referred to as Henri-Michaelis-Menten kinetics (sometimes also Michaelis-Menten kinetics).[49] Their work was further developed by G. E. Briggs and J. B. S. Haldane, who derived kinetic equations that are still widely used today.[50] The major contribution of Henri was to think of enzyme reactions in two stages. In the first, the substrate binds reversibly to the enzyme, forming the enzyme-substrate complex. This is sometimes called the Michaelis complex. The enzyme then catalyzes the

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which is the number of substrate molecules handled by one active site per second. The efficiency of an enzyme can be expressed in terms of kcat/Km. This is also called the specificity constant and incorporates the rate constants for all steps in the reaction. Because the specificity constant reflects both affinity and catalytic ability, it is useful for comparing different enzymes against each other, or the same enzyme with different substrates. The theoretical maximum for the specificity constant is called the diffusion limit and is about 108 to 109 (M-1 s-1). At this point every collision of the enzyme with its substrate will result in catalysis, and the rate of product formation is not limited by the reaction rate but by the diffusion rate. Enzymes with this property are called catalytically perfect or kinetically perfect. Example of such enzymes are triosephosphate isomerase, carbonic anhydrase, acetylcholinesterase, catalase, fumarase, βlactamase, and superoxide dismutase. Michaelis-Menten kinetics relies on the law of mass action, which is derived from the assumptions of free diffusion and thermodynamically driven random collision. However, many biochemical or cellular processes deviate significantly from these conditions, because of macromolecular crowding, phaseseparation of the enzyme/substrate/product, or one or two-dimensional molecular movement.[52] In these situations, a fractal Michaelis-Menten kinetics may be applied.[53][54][55][56] Some enzymes operate with kinetics which are faster than diffusion rates, which would seem to be impossible. Several mechanisms have been invoked to explain this phenomenon. Some proteins are believed to accelerate catalysis by drawing their substrate in and pre-orienting them by using dipolar electric fields. Other models invoke a quantum-mechanical tunneling explanation, whereby a proton or an electron can tunnel through activation barriers, although for proton tunneling this model remains somewhat controversial.[57][58] Quantum tunneling for protons has been observed in tryptamine.[59] This suggests that enzyme catalysis may be more accurately characterized as "through the barrier" rather than the traditional model, which requires substrates to go "over" a lowered energy barrier.

Enzyme

Inhibition

Competitive inhibitors bind reversibly to the enzyme, preventing the binding of substrate. On the other hand, binding of substrate prevents binding of the inhibitor. Substrate and inhibitor compete for the enzyme.

Types of inhibition. This classification was introduced by W.W. Cleland.[60] Enzyme reaction rates can be decreased by various types of enzyme inhibitors. Competitive inhibition In competitive inhibition, the inhibitor and substrate compete for the enzyme (i.e., they can not bind at the same time). Often competitive inhibitors strongly resemble the real substrate of the enzyme. For example,

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methotrexate is a competitive inhibitor of the enzyme dihydrofolate reductase, which catalyzes the reduction of dihydrofolate to tetrahydrofolate. The similarity between the structures of folic acid and this drug are shown in the figure to the right bottom. Note that binding of the inhibitor need not be to the substrate binding site (as frequently stated), if binding of the inhibitor changes the conformation of the enzyme to prevent substrate binding and vice versa. In competitive inhibition the maximal velocity of the reaction is not changed, but higher substrate concentrations are required to reach a given velocity, increasing the apparent Km. Uncompetitive inhibition In uncompetitive inhibition the inhibitor can not bind to the free enzyme, but only to the ES-complex. The EIS-complex thus formed is enzymatically inactive. This type of inhibition is rare, but may occur in multimeric enzymes. Non-competitive inhibition Non-competitive inhibitors can bind to the enzyme at the same time as the substrate, i.e. they never bind to the active site. Both the EI and EIS complexes are enzymatically inactive. Because the inhibitor can not be driven from the enzyme by higher substrate concentration (in contrast to competitive inhibition), the apparent Vmax changes. But because the substrate can still bind to the enzyme, the Km stays the same. Mixed inhibition This type of inhibition resembles the noncompetitive, except that the EIS-complex has residual enzymatic activity. In many organisms inhibitors may act as part of a feedback mechanism. If an enzyme produces too much of one substance in the organism, that substance may act as an inhibitor for the enzyme at the beginning of the pathway that produces it, causing production of the substance to slow down or stop when there is sufficient amount. This is a form of negative feedback. Enzymes which are subject to this form of regulation are often multimeric and have allosteric binding sites for regulatory substances. Their substrate/velocity plots are not hyperbolar, but sigmoidal (S-shaped). Irreversible inhibitors react with the enzyme and form a covalent adduct with the protein. The inactivation is irreversible. These compounds include eflornithine a drug used to treat the parasitic disease sleeping

Enzyme

The coenzyme folic acid (left) and the anticancer drug methotrexate (right) are very similar in structure. As a result, methotrexate is a competitive inhibitor of many enzymes that use folates. sickness.[61] Penicillin and Aspirin also act in this manner. With these drugs, the compound is bound in the active site and the enzyme then converts the inhibitor into an activated form that reacts irreversibly with one or more amino acid residues. Uses of inhibitors Since inhibitors modulate the function of enzymes they are often used as drugs. An common example of an inhibitor that is used as a drug is aspirin, which inhibits the COX-1 and COX-2 enzymes that produce the inflammation messenger prostaglandin, thus suppressing pain and inflammation. However, other enzyme inhibitors are poisons. For example, the poison cyanide is an irreversible enzyme inhibitor that combines with the copper and iron in the active site of the enzyme cytochrome c oxidase and blocks cellular respiration.[62]

Biological function
Enzymes serve a wide variety of functions inside living organisms. They are indispensable for signal transduction and cell regulation, often via kinases and phosphatases.[63] They also generate movement, with myosin hydrolysing ATP to generate muscle contraction and also moving cargo around the cell as part of the cytoskeleton.[64] Other ATPases in the cell membrane are ion pumps involved in active transport. Enzymes are also involved in more exotic functions, such as luciferase generating light in fireflies.[65] Viruses can also contain enzymes for infecting cells, such as the HIV integrase and reverse transcriptase, or for viral release from cells, like the influenza virus neuraminidase. An important function of enzymes is in the digestive systems of animals. Enzymes such as amylases and proteases break down large molecules (starch or proteins, respectively) into smaller ones, so they can be absorbed by

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the intestines. Starch molecules, for example, are too large to be absorbed from the intestine, but enzymes hydrolyse the starch chains into smaller molecules such as maltose and eventually glucose, which can then be absorbed. Different enzymes digest different food substances. In ruminants which have herbivorous diets, microorganisms in the gut produce another enzyme, cellulase to break down the cellulose cell walls of plant fiber.[66] Several enzymes can work together in a specific order, creating metabolic pathways. In a metabolic pathway, one enzyme takes the product of another enzyme as a substrate. After the catalytic reaction, the product is then passed on to another enzyme. Sometimes more than one enzyme can catalyze the same reaction in parallel, this can allow more complex regulation: with for example a low constant activity being provided by one enzyme but an inducible high activity from a second enzyme. Enzymes determine what steps occur in these pathways. Without enzymes, metabolism would neither progress through the same steps, nor be fast enough to serve the needs of the cell. Indeed, a metabolic pathway such as glycolysis could not exist independently of enzymes. Glucose, for example, can react directly with ATP to become phosphorylated at one or more of its carbons. In the absence of enzymes, this occurs so slowly as to be insignificant. However, if hexokinase is added, these slow reactions continue to take place except that phosphorylation at carbon 6 occurs so rapidly that if the mixture is tested a short time later, glucose-6-phosphate is found to be the only significant product. Consequently, the network of metabolic pathways within each cell depends on the set of functional enzymes that are present.

Enzyme
induced that hydrolyse the crucial betalactam ring within the penicillin molecule. Another example are enzymes in the liver called cytochrome P450 oxidases, which are important in drug metabolism. Induction or inhibition of these enzymes can cause drug interactions. 2. Enzymes can be , with different metabolic pathways occurring in different cellular compartments. For example, fatty acids are synthesized by one set of enzymes in the cytosol, endoplasmic reticulum and the Golgi apparatus and used by a different set of enzymes as a source of energy in the mitochondrion, through βoxidation.[67] 3. Enzymes can be regulated by . For example, the end product(s) of a metabolic pathway are often inhibitors for one of the first enzymes of the pathway (usually the first irreversible step, called committed step), thus regulating the amount of end product made by the pathways. Such a regulatory mechanism is called a negative feedback mechanism, because the amount of the end product produced is regulated by its own concentration. Negative feedback mechanism can effectively adjust the rate of synthesis of intermediate metabolites according to the demands of the cells. This helps allocate materials and energy economically, and prevents the manufacture of excess end products. The control of enzymatic action helps to maintain a stable internal environment in living organisms. 4. Enzymes can be regulated through . This can include phosphorylation, myristoylation and glycosylation. For example, in the response to insulin, the phosphorylation of multiple enzymes, including glycogen synthase, helps control the synthesis or degradation of glycogen and allows the cell to respond to changes in blood sugar.[68] Another example of post-translational modification is the cleavage of the polypeptide chain. Chymotrypsin, a digestive protease, is produced in inactive form as chymotrypsinogen in the pancreas and transported in this form to the stomach where it is activated. This stops the enzyme from digesting the pancreas or other tissues before it enters the gut. This type of inactive precursor to an enzyme is known as a zymogen.

Control of activity
There are five main ways that enzyme activity is controlled in the cell. 1. (transcription and translation of enzyme genes) can be enhanced or diminished by a cell in response to changes in the cell’s environment. This form of gene regulation is called enzyme induction and inhibition (see enzyme induction). For example, bacteria may become resistant to antibiotics such as penicillin because enzymes called beta-lactamases are

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5. Some enzymes may become (eg. from a reducing (cytoplasm) to an oxidising (periplasm) environment, high pH to low pH etc). For example, hemagglutinin in the influenza virus is activated by a conformational change caused by the acidic conditions, these occur when it is taken up inside its host cell and enters the lysosome.[69]

Enzyme
less able to repair mutations in the genome. This causes a slow accumulation of mutations and results in the development of many types of cancer in the sufferer.

Naming conventions
An enzyme’s name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase. Examples are lactase, alcohol dehydrogenase and DNA polymerase. This may result in different enzymes, called isozymes, with the same function having the same basic name. Isoenzymes have a different amino acid sequence and might be distinguished by their optimal pH, kinetic properties or immunologically. Furthermore, the normal physiological reaction an enzyme catalyzes may not be the same as under artificial conditions. This can result in the same enzyme being identified with two different names. E.g. Glucose isomerase, used industrially to convert glucose into the sweetener fructose, is a xylose isomerase in vivo. The International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers; each enzyme is described by a sequence of four numbers preceded by "EC". The first number broadly classifies the enzyme based on its mechanism: The top-level classification is • EC 1 Oxidoreductases: catalyze oxidation/reduction reactions • EC 2 Transferases: transfer a functional group (e.g. a methyl or phosphate group) • EC 3 Hydrolases: catalyze the hydrolysis of various bonds • EC 4 Lyases: cleave various bonds by means other than hydrolysis and oxidation • EC 5 Isomerases: catalyze isomerization changes within a single molecule • EC 6 Ligases: join two molecules with covalent bonds The complete nomenclature can be browsed at http://www.chem.qmul.ac.uk/iubmb/ enzyme/.

Involvement in disease

Phenylalanine hydroxylase. Created from PDB 1KW0 Since the tight control of enzyme activity is essential for homeostasis, any malfunction (mutation, overproduction, underproduction or deletion) of a single critical enzyme can lead to a genetic disease. The importance of enzymes is shown by the fact that a lethal illness can be caused by the malfunction of just one type of enzyme out of the thousands of types present in our bodies. One example is the most common type of phenylketonuria. A mutation of a single amino acid in the enzyme phenylalanine hydroxylase, which catalyzes the first step in the degradation of phenylalanine, results in build-up of phenylalanine and related products. This can lead to mental retardation if the disease is untreated.[70] Another example is when germline mutations in genes coding for DNA repair enzymes cause hereditary cancer syndromes such as xeroderma pigmentosum. Defects in these enzymes cause cancer since the body is

Industrial applications
Enzymes are used in the chemical industry and other industrial applications when extremely specific catalysts are required. However, enzymes in general are limited in the number of reactions they have evolved to

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catalyze and also by their lack of stability in organic solvents and at high temperatures. Consequently, protein engineering is an active area of research and involves attempts to create new enzymes with novel properties, either through rational design or in vitro evolution.[71][72] These efforts have begun to be successful, and a few enzymes have now been desiged "from scratch" to catalyse reactions that do not occur in nature.[73]

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[8] Williams, H. S. (1904) A History of Science: in Five Volumes. Volume IV: Modern Development of the Chemical and Biological Sciences Harper and Brothers (New York) Accessed 4 April 2007 [9] Dubos J. (1951). "Louis Pasteur: Free Lance of Science, Gollancz. Quoted in Manchester K. L. (1995) Louis Pasteur (1822–1895)—chance and the prepared mind". Trends Biotechnol 13 (12): 511–5. doi:10.1016/S0167-7799(00)89014-9. PMID 8595136. [10] Nobel Laureate Biography of Eduard Buchner at http://nobelprize.org Accessed 4 April 2007 [11] Text of Eduard Buchner’s 1907 Nobel lecture at http://nobelprize.org Accessed 4 April 2007 [12] 1946 Nobel prize for Chemistry laureates at http://nobelprize.org Accessed 4 April 2007 [13] Blake CC, Koenig DF, Mair GA, North AC, Phillips DC, Sarma VR. (1965). "Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Angstrom resolution". Nature 22 (206): 757–61. doi:10.1038/206757a0. PMID 5891407. [14] Chen LH, Kenyon GL, Curtin F, Harayama S, Bembenek ME, Hajipour G, Whitman CP (1992). "4-Oxalocrotonate tautomerase, an enzyme composed of 62 amino acid residues per monomer". J. Biol. Chem. 267 (25): 17716–21. PMID 1339435. [15] Smith S (01 Dec 1994). "The animal fatty acid synthase: one gene, one polypeptide, seven enzymes". Faseb J. 8 (15): 1248–59. PMID 8001737. http://www.fasebj.org/cgi/reprint/8/15/ 1248. [16] Anfinsen C.B. (1973). "Principles that Govern the Folding of Protein Chains". Science 181: 223–30. doi:10.1126/ science.181.4096.223. PMID 4124164. [17] Dunaway-Mariano D (November 2008). "Enzyme function discovery". Structure 16 (11): 1599–600. doi:10.1016/ j.str.2008.10.001. PMID 19000810. [18] The Catalytic Site Atlas at The European Bioinformatics Institute Accessed 4 April 2007 [19] Jaeger KE, Eggert T. (2004). "Enantioselective biocatalysis optimized by directed evolution". Curr Opin

See also
• • • • • • • • • • List of enzymes Enzyme assay Enzyme catalysis The Proteolysis Map RNA Biocatalysis SUMO enzymes Ki Database Proteonomics and protein engineering Immobilized enzyme Kinetic Perfection

References
[1] Smith AL (Ed) et al. (1997). Oxford dictionary of biochemistry and molecular biology. Oxford [Oxfordshire]: Oxford University Press. ISBN 0-19-854768-4. [2] Grisham, Charles M.; Reginald H. Garrett (1999). Biochemistry. Philadelphia: Saunders College Pub. pp. 426–7. ISBN 0-03-022318-0. [3] Bairoch A. (2000). "The ENZYME database in 2000" (PDF). Nucleic Acids Res 28: 304–5. doi:10.1093/nar/28.1.304. PMID 10592255. http://www.expasy.org/ NAR/enz00.pdf. [4] Lilley D (2005). "Structure, folding and mechanisms of ribozymes". Curr Opin Struct Biol 15 (3): 313–23. doi:10.1016/ j.sbi.2005.05.002. PMID 15919196. [5] Cech T (2000). "Structural biology. The ribosome is a ribozyme". Science 289 (5481): 878–9. doi:10.1126/ science.289.5481.878. PMID 10960319. [6] Groves JT (1997). "Artificial enzymes. The importance of being selective". Nature 389 (6649): 329–30. doi:10.1038/ 38602. PMID 9311771. [7] de Réaumur, RAF (1752). "Observations sur la digestion des oiseaux". Histoire de l’academie royale des sciences 1752: 266, 461.

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From Wikipedia, the free encyclopedia
Application Food processing Enzymes used Amylases from fungi and plants. Uses

Enzyme

Amylases catalyze the release of simple sugars from starch Proteases Baby foods Brewing industry Trypsin

Production of sugars from starch, such as in making high-fructose corn syrup.[74] In baking, catalyze breakdown of starch in the flour to sugar. Yeast fermentation of sugar produces the carbon dioxide that raises the dough. Biscuit manufacturers use them to lower the protein level of flour. To predigest baby foods.

Enzymes from barley are released They degrade starch and proteins during the mashing stage of beer to produce simple sugar, amino production. acids and peptides that are used by yeast for fermentation. Industrially produced barley enzymes Widely used in the brewing process to substitute for the natural enzymes found in barley. Split polysaccharides and proteins in the malt. Improve the wort and beer filtration characteristics. Low-calorie beer and adjustment of fermentability. Remove cloudiness produced during storage of beers.

Germinating barley used for malt.

Amylase, glucanases, proteases Betaglucanases and arabinoxylanases Amyloglucosidase and pullulanases Proteases

Acetolactatedecarboxylase (ALDC) Increases fermentation efficiency by reducing diacetyl formation.[75] Fruit juices Dairy industry Cellulases, pectinases Clarify fruit juices Rennin, derived from the stomachs Manufacture of cheese, used to of young ruminant animals (like hydrolyze protein. calves and lambs). Microbially produced enzyme Lipases Roquefort cheese Now finding increasing use in the dairy industry. Is implemented during the production of Roquefort cheese to enhance the ripening of the bluemould cheese. Break down lactose to glucose and galactose. To soften meat for cooking.

Lactases Meat tenderizers Starch industry Papain

Amylases, amyloglucosideases and Converts starch into glucose and glucoamylases various syrups. Glucose isomerase Converts glucose into fructose in production of high fructose syrups from starchy materials. These syrups have enhanced sweetening properties and lower calorific

Glucose

Fructose

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From Wikipedia, the free encyclopedia

Enzyme
values than sucrose for the same level of sweetness.

Paper industry

Amylases, Xylanases, Cellulases and ligninases

A paper mill in South Carolina. Biofuel industry Cellulases

Degrade starch to lower viscosity, aiding sizing and coating paper. Xylanases reduce bleach required for decolorising; cellulases smooth fibers, enhance water drainage, and promote ink removal; lipases reduce pitch and lignin-degrading enzymes remove lignin to soften paper. Used to break down cellulose into sugars that can be fermented (see cellulosic ethanol). Use of lignin waste

Ligninases Cellulose in 3D Biological detergent Primarily proteases, produced in an extracellular form from bacteria Amylases

Used for presoak conditions and direct liquid applications helping with removal of protein stains from clothes. Detergents for machine dish washing to remove resistant starch residues. Used to assist in the removal of fatty and oily stains. Used in biological fabric conditioners. To remove proteins on contact lens to prevent infections. To generate oxygen from peroxide to convert latex into foam rubber. Dissolve gelatin off scrap film, allowing recovery of its silver content. Used to manipulate DNA in genetic engineering, important in pharmacology, agriculture and medicine. Essential for restriction digestion and the polymerase chain reaction. Molecular biology is also important in forensic science.

Lipases Cellulases Contact lens cleaners Rubber industry Photographic industry Molecular biology Proteases Catalase Protease (ficin)

Restriction enzymes, DNA ligase and polymerases

Part of the DNA double helix.

Biotechnol. 15 (4): 305–13. doi:10.1016/ j.copbio.2004.06.007. PMID 15358000. [20] Shevelev IV, Hubscher U. (2002). "The 3’ 5’ exonucleases". Nat Rev Mol Cell Biol. 3 (5): 364–76. doi:10.1038/nrm804. PMID 11988770.

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Further reading
Etymology and history • New Beer in an Old Bottle: Eduard Buchner and the Growth of Biochemical Knowledge, edited by Athel Cornish-Bowden and published by Universitat de València (1997): ISBN 84-370-3328-4, A history of early enzymology. • Williams, Henry Smith, 1863–1943. A History of Science: in Five Volumes. Volume IV: Modern Development of the Chemical Kinetics and inhibition • Cornish-Bowden, Athel. Fundamentals of Enzyme Kinetics. (3rd edition), Portland Press, 2004. ISBN 1-85578-158-1. • Segel Irwin H. Enzyme Kinetics: Behavior and Analysis of Rapid

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From Wikipedia, the free encyclopedia
and Biological Sciences, A textbook from the 19th century. • Kleyn J, Hough J (1971). "The microbiology of brewing". Annu. Rev. Microbiol. 25: 583–608. doi:10.1146/ annurev.mi.25.100171.003055. PMID 4949040. Enzyme structure and mechanism • Fersht, Alan (1999). Structure and mechanism in protein science: a guide to enzyme catalysis and protein folding. San Francisco: W.H. Freeman. ISBN 0-7167-3268-8. • Walsh C (1979). Enzymatic reaction mechanisms. San Francisco: W. H. Freeman. ISBN 0-7167-0070-0. • Page, M. I., and Williams, A. (Eds.). Enzyme Mechanisms. Royal Society of Chemistry, 1987. ISBN 0-85186-947-5. • Bugg, T. Introduction to Enzyme and Coenzyme Chemistry. (2nd edition), Blackwell Publishing Limited, 2004. ISBN 1-40511-452-5. • Warshel, A. Computer Modeling of Chemical Reactions in enzymes and Solutions. John Wiley & Sons Inc., 1991. ISBN 0-471-18440-3. Thermodynamics • "Reactions and Enzymes" Chapter 10 of on-line biology book at Estrella Mountain Community College.

Enzyme

Equilibrium and 7. Acad. Press, Steady-State New York, 1959. Enzyme Systems. Industrial (New Ed edition), applications Wiley• "History of Interscience, industrial 1993. ISBN enzymes", Article 0-471-30309-7. about the history • Baynes, John W. of industrial Medical enzymes from the Biochemistry. late 1900s to the (2nd edition), present times. Elsevier-Mosby, 2005. ISBN 0-7234-3341-0, p. • Structure/Function of Enzymes, Web 57. tutorial on enzyme structure and function. Function and con• UC trol of enzymes inBerkeley video lecture on enzyme structure and function the cell • • Price, N. andEnzymes in diagnosis Role of enzymes in Stevens, L. diagnosis of diseases. • Enzyme spotlight Monthly feature at the Fundamentals of Enzymology: European Bioinformatics Institute on a Cell selected enzyme. and Molecular Biology of • AMFEP, Association of Manufacturers and Formulators of Enzyme Products Catalytic • BRENDA database, a comprehensive Proteins. Oxford compilation of information and literature University Press, 1999. ISBN references about all known enzymes; requires payment by commercial users. 0-19-850229-X. • Enzyme Structures Database links to the • "Nutritional and Metabolic known 3-D structure data of enzymes in Diseases". the Protein Data Bank. • ExPASy enzyme database, links to SwissChapter of the online textbookProt sequence data, entries in other Introduction databases and to related literature to Genes and searches. • the Disease fromKEGG: Kyoto Encyclopedia of Genes and Genomes Graphical and hypertext-based NCBI. information on biochemical pathways and Enzyme-naming conventions enzymes. • Enzyme • MACiE database of enzyme reaction mechanisms. Nomenclature, • MetaCyc database of enzymes and Recommendations metabolic pathways for enzyme names from the • Face-to-Face Interview with Sir John Cornforth who was awarded a Nobel Prize Nomenclature for work on stereochemistry of enzymeCommittee of the Internationalcatalyzed reactions Freeview video by the Vega Science Trust Union of • and BiochemistrySigma Aldrich Enzyme Assays by Enzyme Molecular Name - 100’s of assays sorted by enzyme name. Biology. • Koshland, • Bugg TD (October 2001). "The D. The development of mechanistic enzymology Enzymes, v. I, ch.

External links

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From Wikipedia, the free encyclopedia
in the 20th century". Nat Prod Rep 18 (5): 465–93. doi:10.1039/b009205n. PMID

Enzyme
11699881. http://www.rsc.org/ej/NP/2001/ B009205N/.

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