An enzyme is a biological molecule that catalyzes a chemical reaction. Most enzymes are proteins and the word "enzyme" is often used to mean a protein enzyme, but some RNA molecules also have catalytic activity, and to differentiate them from protein enzymes, they are referred to as RNA enzymes or ribozymes.

Enzymes are essential for life because most chemical reactions in living cells would occur too slowly, or would lead to different products without enzymes.

Like all catalysts, enzymes work by providing an alternate pathway of lower energy for a reaction. This speeds up the reaction, sometimes making it many millions of times faster. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions nor do they alter the equilibrium of a reaction. However, enzymes do differ from most other catalysts in showing much higher levels of specificity.

Enzyme activity can be affected by other molecules. Inhibitors are molecules that decrease or abolish enzyme activity; while activators are molecules that increase activity. Drugs and poisons are often enzyme inhibitors.

While all enzymes have a biological role, some enzymes have commercial uses. Many household products use enzymes to speed up chemical reactions (e.g., enzymes in biological washing powders break down protein or fat stains on clothes).

About 4,000 reactions are known to be catalyzed by enzymes.Bairoch A. The ENZYME database in 2000 Nucleic Acids Res 28:304-305(2000). Enzymes are named according to the reaction they catalyze. Typically the suffix -ase is added to the name of the substrate (e.g., lactase is the enzyme that catalyzes the cleavage of lactose) or the type of reaction (e.g., DNA polymerase catalyzes the formation of DNA polymers).

Etymology and history

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The word enzyme comes from Greek: "in leaven". As early as the late 1700s and early 1800s, the digestion of meat by stomach secretions and the conversion of starch to sugars by plant extracts and saliva were known. However, the mechanism by which this occurred was unknown.Williams, Henry Smith, 1863-1943. A History of Science: in Five Volumes. Volume IV: Modern Development of the Chemical and Biological Sciences

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 a living organisms. He wrote that "Alcoholic fermentation is an act correlated with the life and organisation of the yeast cells, not with the death or putrefaction of the cells."Dubos, 1<. J. (1951) Louis Pasteur: Free Lance of Science, Gollancz. Quoted in Manchester KL. Louis Pasteur (1822-1895)--chance and the prepared mind. Trends Biotechnol. 1995 Dec;13(12):511-5.

In 1878 German physiologist Wilhelm Kühne (1837-1900) coined the term "enzyme," meaning "in leaven," to describe this process. The word enzyme was used later to refer to non-living substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms.

In 1897, Eduard Buchner began to study the ability of yeast extracts to ferment sugar, despite the absence of living yeast cells. 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 Biography of Eduard Buchner. He named the enzyme that brought about the fermentation of sucrose "zymase". Text of Eduard Buchner's 1907 Nobel lecture.

It was not until 1926, however, that pepsin became the first enzyme to be obtained in pure form by Northrop, Sumner and Stanley. Their successful purification and crystallization of pepsin proved that enzymes were proteins and they were awarded the 1946 Nobel prize for Chemistry 1946 Nobel prize for Chemistry laureates.

Enzyme structure and mechanism

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The activities of enzymes are determined by their three-dimensional structureAnfinsen C.B. Principles that Govern the Folding of Protein Chains Science 20 July 1973: 223-230.

As with any protein, each protein is actually produced as a long, linear chain of amino acids, which folds in a particular fashion to produce a three-dimensional product with a tertiary structure. Each amino acid sequence produces a unique structure, which can have unique properties. Individual protein chains may sometimes group together to form a protein complex. Most enzymes can be unfolded or inactivated by heating, which destroys the three-dimensional structure of the protein.

Most enzymes are larger than the substrates they act on and only a very small portion of the enzyme, around 10 amino acids, comes into contact with the substrate(s). This region, where binding of the substrate(s) and then the reaction occurs, is known as the active site. Some enzymes also contain sites that bind cofactors, which are needed for catalysis.

Some enzymes 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 (depending on the molecule and enzyme), providing a means for feedback regulation.

Specificity

Enzymes are usually specific as to the reactions they catalyze and the substrates that are involved in these reactions. Shape, charge complementarity, and hydrophilic/hydrophobic characters of enzymes and substrates are responsible for this specificity. Enzymes show impressive levels of stereospecificity, regioselectivity and chemoselectivity.

"Lock and key" model

Enzymes are very specific and it was suggested by Emil Fischer in the 1890s that this was because the enzyme had a particular shape into which the substrate(s) fit exactly.Fischer E, "Einfluss der configuration auf die wirkung derenzyme" ''Ber. Dt. Chem. Ges.'' 1894 v27, 2985-2993. This is often referred to as "the lock and key" model. An enzyme combines with its substrate(s) to form a short-lived enzyme-substrate complex. However, while this model explains enzyme specificity, it fails to explain the stabilisation of the transition state which occurs.

Induced fit model

In 1958 Daniel Koshland suggested a modification to the "lock and key" model.Koshland DE, Application of a Theory of Enzyme Specificity to Protein Synthesis. Proc. Natl. Acad. Sci. U.S.A. 1958 Feb;44(2):98-104. Enzymes are rather flexible structures. The active site of an enzyme can be modified as the substrate interacts with the enzyme. The amino acids side chains which make up the active site are moulded into a precise shape which enables the enzyme to perform its catalytic function. In some cases the substrate molecule changes shape slightly as it enters the active site. Unlike the "Lock and key" model, this model explains enzyme specificity and the stabilisation of the transition state which occurs.

Modifications

Many enzymes contain not only protein but require other additional modifications. These modifications are made post-translationally; that is, after the polypeptide chain has been synthesized. This usually involves chemical groups being added onto the polypeptide chain, e.g., phosphorylation or glycosylation of the enzyme.

Another kind 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.

Enzyme cofactors

Some enzymes do not need any additional components to exhibit full activity. However, others require non-protein molecules to be bound for activity. Cofactors can be either inorganic (e.g., metal ions and Iron-sulfur clusters) or organic compounds, which are also known as coenzymes (e.g., flavin and heme). An example of an enzyme that contains a cofactor is carbonic anhydrase, and is shown in the diagram above with four zinc cofactors bound in its active sites.

Enzymes that require a cofactor, but do not have one bound are called apoenzymes. An apoenzyme together with its cofactor(s) is called a holoenzyme (i.e., the active form). Most cofactors are not covalently attached to an enzyme, but are tightly bound. However, some cofactors known as prosthetic groups are covalently bound (e.g., thiamine pyrophosphate in the enzyme Pyruvate dehydrogenase).

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.

Thermodynamics

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As with all catalysts, all reactions catalyzed by enzymes must be "spontaneous" (containing a net negative Gibbs free energy). In the presence of an enzyme, a reaction runs in the same direction as it would without the enzyme, just more quickly. However, the uncatalyzed, "spontaneous" reaction might lead to different products than the catalyzed reaction. 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 cleavage of the high-energy compound ATP is often used to drive other, energetically unfavorable 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 direction, depending on the concentration of its reactants.

$\backslash mathrm\{CO\_2\; +\; H\_2O$

{}^\mathrm{\quad Carbonic\ anhydrase} \!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\! \overrightarrow{\qquad\qquad\qquad\qquad} H_2CO_3} (in tissues - high CO₂ concentration)

$\backslash mathrm\{H\_2CO\_3$

{}^\mathrm{\quad Carbonic\ anhydrase} \!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\! \overrightarrow{\qquad\qquad\qquad\qquad} CO_2 + H_2O} (in lungs - low CO₂ concentration)

Nevertheless, if the physiological concentrations of the substrates and products has a large negative Gibbs free energy (exergonic) then the reaction is effectively irreversible. Under these conditions it is possible that the enzyme will only catalyse the reaction in one direction.

Kinetics

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Enzyme kinetics is the investigation of how enzymes bind substrates and turn them into products. In 1913, Leonor Michaelis and Maud Menten proposed a quantitative theory of enzyme kinetics, which is referred to as Michaelis-Menten kinetics.Leonor Michaelis and Maud Menten, Die Kinetik der Invertinwirkung, Biochem. Z. (1913) 49, 333-369. Their work was further developed by G. E. Briggs and J. B. S. Haldane, who derived numerous kinetic equations that are still widely used todayG. E. Briggs and J. B. S. Haldane, A note on the kinetics of enzyme action, Biochem. J., (1925) 19, 339-339..

The major contribution of Michaelis and Menten was to divide enzyme reactions into two stages. In the first, the substrate binds reversibly to the enzyme, forming the enzyme-substrate complex. This is sometimes called the Michaelis-Menten complex in their honour. The enzyme then catalyzes the chemical step in the reaction and releases the product.

Enzymes can catalyze up to several million reactions per second. To find the maximum speed of an enzymatic reaction, the substrate concentration is increased until a constant rate of product formation is seen. This saturation happens because, ss substrate concentration increases, more and more of the free enzyme is converted into the substrate-bound ES form. At the maximum velocity (V_max) of the enzyme, all enzyme active sites are saturated with substrate, and the amount of ES complex is the same as the amount of enzyme.

However, V_max is only one kinetic constant of enzymes. The amount of substrate needed to achieve a given rate of reaction is also of interest. This can be expressed by the Michaelis-Menten constant (K_m), which is the substrate concentration required for an enzyme to reach one-half its maximum velocity. Each enzyme has a characteristic K_m for a given substrate and this can show how tight the binding of the substrate is to the enzyme.

The efficiency of an enzyme can be expressed in terms of k_cat/K_m. 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 triose-phosphate isomerase, carbonic anhydrase, acetylcholinesterase, catalase, fumarase, ß-lactamase, and superoxide dismutase.

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 protons tunneling remains somewhat controversial. Mireia Garcia-Viloca,1 Jiali Gao,1 Martin Karplus,2* Donald G. Truhlar Science 9 January 2004: Vol. 303. no. 5655, pp. 186 - 195 Olsson MH, Siegbahn PE, Warshel A. J Am Chem Soc. 2004 Mar 10;126(9):2820-8.

Coenzymes

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Coenzymes are small molecules that transport chemical groups from one enzyme to another. The chemical groups carried can be as simple as the hydride ion (H+ + 2e-) carried by NAD or the larger acetyl group carried by coenzyme A. Since coenzymes are chemically changed as a consequence of enzyme action, it is often useful to consider coenzymes to be a special class of substrates, or second substrates, which are common to many different enzymes.

Inhibition

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Enzymes reaction rates can be decreased by variuos types of enzyme inhibitors.

Mechanisms of enzyme inhibitors

Competitive inhibition

In competitive inhibition, the inhibitor binds to the substrate binding site as shown (right top), thus preventing substrate from binding. Often competitive inhibitors strongly resemble the real substrate of the enzyme. For example, malonate is a competitive inhibitor of the enzyme succinate dehydrogenase, which catalyzes the oxidation of succinate to fumarate.

Non-competitive inhibition

Non-competitive inhibitors never bind to the active site, but to other parts of the enzyme that can be far away from the substrate binding site, (right, bottom). Consequently, since there is no competition between the substrate and inhibitor for the enzyme, the extent of inhibition depends only on the inhibitor concentration and will not be affected by the substrate concentration.

By changing the conformation (the three-dimensional structure) of the enzyme, the inhibitors disable the ability of the enzyme to bind or turn over its substrate. When the inhibitor is bound, the enzyme has no activity.

Mixed inhibition

Mixed inhibitors can bind to both the enzyme and the enzyme-substrate complex. It has the properties of both competitive and uncompetitive inhibition.

The types of enzyme inhibitor are discussed in more detail in the enzyme inhibition page.

Uses of enzyme inhibitors

Inhibitors are often used as drugs, but they can also act as poisons. However, the difference between a drug and a poison is usually only a matter of amount, since most drugs are toxic at some level, as Paracelsus wrote "The dose makes the poison." Equally, antibiotics and other anti-infective drugs are just specific poisons that can kill a pathogen but not its host.

An example of an inhibitor being 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. The poison cyanide is an irreversible enzyme inhibitor that combines with the copper prosthetic groups of the enzyme cytochrome c oxidase and blocks cellular respiration.

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 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.

Function and control of enzymes in the cell

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Metabolic pathways

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.

Control of enzyme activity

There are three main ways that enzyme activity is controlled in the cell

1. Enzymes can be compartmentalised, with different metabolic pathways occurring in different cellular compartments. For example, fatty acids are synthesised by one set of enzymes in the cytosol, endoplasmic reticulum and golgi and used by a different set of enzymes as a source of energy in the mitochondrion, through β-oxidationFaergeman NJ, Knudsen J. Role of long-chain fatty acyl-CoA esters in the regulation of metabolism and in cell signalling. Biochem J. 1997 Apr 1;323 ( Pt 1):1-12.
2. Enzymes can be regulated by inhibitors and activators. 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 with effective allocations of materials and energy economy, and it prevents the excess manufacture of end products. Like other homeostatic devices, the control of enzymatic action helps to maintain a stable internal environment in living organisms.
3. Enzymes can be regulated through post-translational modification. 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 sugarDoble BW, Woodgett JR GSK-3: tricks of the trade for a multi-tasking kinase. J Cell Sci. 2003 Apr 1;116(Pt 7):1175-86..

Errors in metabolism

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 disease. For example, the most common type of phenylketonuria is caused by a single amino acid mutation in the enzyme phenylalanine hydroxylase, which catalyzes the first step in the degradation of phenylalanine. The resulting build-up of phenylalanine and related products can lead to mental retardation if the disease is untreated Phenylketonuria: NCBI Genes and Disease.

Enzyme-naming conventions

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By common convention, an enzyme's name consists of a description of what it does, with the word ending in -ase. Examples are alcohol dehydrogenase and DNA polymerase. Kinases are enzymes that transfer phosphate groups. This results in different enzymes with the same function having the same basic name; they are therefore distinguished by other characteristics, such as their optimal pH (alkaline phosphatase) or their location (membrane ATPase). Furthermore, the reversibility of chemical reactions means that the normal physiological direction of an enzyme's function may not be observed under laboratory conditions. This can result in the same enzyme being identified with two different names: one coming from the laboratory identification as described above and the other from its behavior in the cell. For instance the enzyme formally known as xylitol:NAD+ 2-oxidoreductase (D-xylulose-forming) is more commonly referred to in the cellular physiological sense as D-xylulose reductase, since the function of the enzyme in the cell is actually the reverse of what is often seen under laboratory conditions.

The International Union of Biochemistry and Molecular Biology has developed a nomenclature for enzymes, the EC numbers; each enzyme is described by a sequence of four numbers, preceded by "EC". However, this is not a perfect solution, as enzymes from different species or even very similar enzymes in the same species may have identical EC numbers.

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/

Industrial Applications

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|rowspan="2"| Starch industry

Application	Enzymes used	Uses	Notes and examples
Biological detergent	Primarily proteases, produced in an extracellular form from bacteria	Used for presoak conditions and direct liquid applications helping with removal of protein stains from clothes.
	Amylase enzymes	Detergents for machine dish washing to remove resistant starch residues.
	Lipase enzymes	Used to assist in the removal of fatty and oily stains
	Cellulase enzymes	Used in biological fabric conditioners
Baking industry	Fungal alpha-amylase enzymes: normally inactivated at about 50 degrees Celsius, destroyed during baking process	Catalyze breakdown of starch in the flour to sugar. Yeast action on sugar produces carbon dioxide. Used in production of white bread, buns, and rolls
	Protease enzymes	Biscuit manufacturers use them to lower the protein level of flour.
Baby foods	Trypsin	To predigest baby foods
Brewing industry	Enzymes from barley are released during the mashing stage of beer production.	They degrade starch and proteins to produce simple sugar, amino 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.
	Amylase, glucanases, proteases	Split polysaccharides and proteins in the malt
	Betaglucosidase	Improve the filtration characteristics.
	Amyloglucosidase	Low-calorie beer
	Proteases	Remove cloudiness produced during storage of beers.
Fruit juices	Cellulases, pectinases	Clarify fruit juices
Dairy industry	Rennin, derived from the stomachs of young ruminant animals (calves, lambs)	Manufacture of cheese, used to hydrolyse protein	Note: As animals age rennin production decreases and is replaced by another protease, pepsin, which is not suitable for cheese production. In recent years the increase in cheese consumption, as well as increased beef production, has resulted in a shortage of rennin and escalating prices.
	Microbially produced enzyme	Now finding increasing use in the dairy industry
	Lipases	Is implemented during the production of Roquefort cheese to enhance the ripening of the blue-mould cheese.
	Lactases	Break down lactose to glucose and galactose
Amylases, amyloglucosideases and glucoamylases	Converts starch into glucose and various syrups

Glucose	Fructose