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۱ کرښه:
[[Imageدوتنه:TPI1 structure.png|thumb|310px|[[Protein structure|Ribbon diagram]] of the enzyme [[triosephosphate isomerase|TIM]], surrounded by the [[space-filling model]] of the protein. TIM is an extremely efficient enzyme involved in the process that converts [[sugar]]s to energy in the body.]]
'''Enzymes''' are [[protein]]s that [[catalysis|catalyze]] (''i.e.'' [[reaction rate|accelerate]]) [[chemical reaction]]s.<ref>Smith AD (Ed) ''et al.'' (1997) ''Oxford Dictionary of Biochemistry and Molecular Biology'' Oxford University Press ISBN 0-19-854768-4</ref> In enzymatic reactions, the [[molecule]]s at the beginning of the process are called [[Substrate (biochemistry)|substratesubstrates]]s, and the enzyme converts them into different molecules, the products. Almost all processes in a [[cell (biology)|biological cell]] need enzymes in order to occur at significant rates. Since enzymes are extremely 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 pathway]]s occur in that cell.
 
Like all catalysts, enzymes work by lowering the [[activation energy]] (''E''<sub>a</sub> or Δ''G''<sup>‡</sup>) for a reaction, thus dramatically accelerating the rate of the reaction. Most enzyme reaction rates are millions of times faster than those of comparable uncatalyzed reactions. As with all catalysts, enzymes are not consumed by the reactions they catalyze, nor do they alter the [[chemical equilibrium|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.<ref>{{cite journal|url=http://www.expasy.org/NAR/enz00.pdf|author= Bairoch A.|year= 2000|title= The ENZYME database in 2000 |journal=Nucleic Acids Res|volume=28|pages=304–305|id= PMID 10592255 }}</ref> Although almost all enzymes are proteins, not all biochemical catalysts are enzymes, since some [[RNA]] molecules called [[ribozyme]]s also catalyze reactions.<ref>{{cite journal |author=Lilley D |title=Structure, folding and mechanisms of ribozymes |journal=Curr Opin Struct Biol |volume=15 |issue=3 |pages=313-23 |year=2005 |pmid=15919196}}</ref> Synthetic molecules called [[artificial enzyme]]s also display enzyme-like catalysis.<ref>{{cite journal |author=Groves JT |title=Artificial enzymes. The importance of being selective |journal=Nature |volume=389 |issue=6649 |pages=329-30 |year=1997 |pmid=9311771}}</ref>
 
Enzyme activity can be affected by other molecules. [[enzyme inhibitor|Inhibitors]] are molecules that decrease enzyme activity; [[enzyme activator|activatoractivators]]s are molecules that increase activity. Many [[drug]]s and [[poison]]s 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 [[antibiotic]]s. In addition, some household products use enzymes to speed up biochemical reactions (''e.g.'', enzymes in biological [[washing powder]]s break down protein or [[fat]] stains on clothes; enzymes in [[meat tenderizer]]s break down proteins, making the meat easier to chew).
 
== Structures and mechanisms ==
 
{{see also|Enzyme catalysis}}
 
[[Imageدوتنه:Carbonic anhydrase.png|thumb|right|300px|Ribbon-diagram showing [[carbonic anhydrase|carbonic anhydrase II]]. The grey sphere is the [[zinc]] cofactor in the active site. Diagram drawn from [http://www.rcsb.org/pdb/explore.do?structureId=1MOO PDB 1MOO].]]
 
Enzymes are generally globular proteins and range from just 62 amino acid residues in size, for the [[monomer]] of [[4-Oxalocrotonate tautomerase|4-oxalocrotonate tautomerase]],<ref>{{cite journal |author=Chen LH, Kenyon GL, Curtin F, Harayama S, Bembenek ME, Hajipour G, Whitman CP |title=4-Oxalocrotonate tautomerase, an enzyme composed of 62 amino acid residues per monomer |journal=J. Biol. Chem. |volume=267 |issue=25 |pages=17716-21 |year=1992 |pmid=1339435}}</ref> to over 2,500 residues in the animal [[fatty acid synthase]].<ref>{{cite journal |author=Smith S |title=The animal fatty acid synthase: one gene, one polypeptide, seven enzymes |url=http://www.fasebj.org/cgi/reprint/8/15/1248 |journal=FASEB J. |volume=8 |issue=15 |pages=1248–59 |year=1994 |pmid=8001737}}</ref> A small number of RNA-based biological catalysts exist, with the most common being the [[ribosome]], these are either referred to as ''RNA-enzymes'', or [[ribozyme]]s. The activities of enzymes are determined by their [[quaternary structure|three-dimensional structure]].<ref>{{cite journal|author=Anfinsen C.B.|year= 1973|title= Principles that Govern the Folding of Protein Chains|journal= Science|pages= 223–230|id= PMID 4124164}}</ref> Most enzymes are much larger than the substrates they act on, and only a small portion of the enzyme (around 3–4 [[amino acid]]s) is directly involved in catalysis.<ref>[http://www.ebi.ac.uk/thornton-srv/databases/CSA/ The Catalytic Site Atlas at The European Bioinformatics Institute] Accessed 04 April 2007</ref> 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 [[Cofactor (biochemistry)|cofactors]], which are needed for catalysis. Some enzymes also have binding sites for small molecules, which are often direct or [[#Metabolic pathways|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.
۱۶ کرښه:
Like all proteins, enzymes are made as long, linear chains of amino acids that [[protein folding|fold]] to produce a [[tertiary structure|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 [[denaturation (biochemistry)|denatured]]—that is, unfolded and inactivated—by heating, which destroys the [[Tertiary structure|three-dimensional structure]] of the protein. Depending on the enzyme, denaturation may be reversible or irreversible.
 
=== Specificity ===
Enzymes are usually very specific as to which reactions they catalyze and the [[substrate (biochemistry)|substratesubstrates]]s 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]].<ref>{{cite journal |author= Jaeger KE, Eggert T.|year= 2004|title= Enantioselective biocatalysis optimized by directed evolution.| journal=Curr Opin Biotechnol.|volume= 15(4)|pages= 305–313|id= PMID 15358000}}</ref>
 
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]] catalyses a reaction in a first step and then checks that the product is correct in a second step.<ref>{{cite journal |author= Shevelev IV, Hubscher U.|year= 2002|title= The 3' 5' exonucleases.| journal= Nat Rev Mol Cell Biol.|volume= 3|issue= 5|pages= 364–376|id= PMID 11988770}}</ref> This two-step process results in average error rates of less than 1 error in 100 million reactions in high-fidelity [[mammal]]ian polymerases.<ref>Berg J., Tymoczko J. and Stryer L. (2002) ''Biochemistry.'' W. H. Freeman and Company ISBN 0-7167-4955-6</ref> Similar proofreading mechanisms are also found in [[RNA polymerase]],<ref>{{cite journal |author= Zenkin N, Yuzenkova Y, Severinov K.|year= 2006|title= Transcript-assisted transcriptional proofreading.| journal= Science.|volume= 313|pages= 518–520|id= PMID 16873663}}</ref> [[aminoacyl tRNA synthetase]]s<ref>{{cite journal |author= Ibba M, Soll D.|year= 2000|title= Aminoacyl-tRNA synthesis.| journal= Annu Rev Biochem.|volume= 69|pages= 617–650|id= PMID 10966471}}</ref> and [[ribosome]]s.<ref>{{cite journal |author= Rodnina MV, Wintermeyer W.|year= 2001|title= Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms.| journal= Annu Rev Biochem.|volume= 70|pages= 415–435|id= PMID 11395413}}</ref>
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Some enzymes that produce [[secondary metabolite]]s 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.<ref>{{cite web |url=http://www-users.york.ac.uk/~drf1/rdf_sp1.htm |title=The Screening Hypothesis - a new explanation of secondary product diversity and function |accessdate=2006-10-11 |last=Firn |first=Richard }}</ref>
 
==== "Lock and key" model ====
Enzymes are very specific, and it was suggested by [[Hermann Emil Fischer|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.<ref>{{cite journal |author= Fischer E.|year= 1894|title= Einfluss der Configuration auf die Wirkung der Enzyme| journal=Ber. Dt.
Chem. Ges.|volume=27|pages=2985–2993|url = http://gallica.bnf.fr/ark:/12148/bpt6k90736r/f364.chemindefer }}</ref> 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-substrate-coenzyme figure.
 
==== Induced fit model ====
[[Imageدوتنه:Induced fit diagram.svg|thumb|450px|Diagrams to show the induced fit hypothesis of enzyme action.]]
In 1958 [[Daniel E. Koshland, Jr.|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.<ref>{{cite journal|url=http://www.pnas.org/cgi/reprint/44/2/98|author=Koshland D. E.|year= 1958|title= Application of a Theory of Enzyme Specificity to Protein Synthesis|journal=Proc. Natl. Acad. Sci.|volume=44|issue=2|pages=98–104|id= PMID 16590179}}</ref> As a result, the substrate does not simply bind to a rigid active site, the amino acid [[side chain]]s 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.<ref>{{cite journal|author=Vasella A, Davies GJ, Bohm M.|year= 2002|title= Glycosidase mechanisms.|journal=Curr Opin Chem Biol.|volume=6|issue=5|pages=619–629|id= PMID 12413546}}</ref> The active site continues to change until the substrate is completely bound, at which point the final shape and charge is determined.<ref>{{cite book |last=Boyer |first=Rodney |title=Concepts in Biochemistry |origyear=2002 |accessdate=2007-04-21 |edition=2nd ed.|publisher=John Wiley & Sons, Inc. |location=New York, Chichester, Weinheim, Brisbane, Singapore, Toronto. |language=English |isbn=0-470-00379-0 |pages=137–138 |chapter=6}}</ref>
 
=== Mechanisms ===
 
Enzymes can act in several ways, all of which lower ΔG<sup>‡</sup>:<ref>Fersht, A (1985) ''Enzyme Structure and Mechanism'' (2nd ed) p50–52 W H Freeman & co, New York ISBN 0-7167-1615-1</ref>
 
* 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<sup>‡</sup> alone overlooks this effect.
 
Interestingly, this entropic effect involves destabilization of the ground state,<ref> Jencks W.P. "Catalysis in Chemistry and Enzymology." 1987, Dover, New York </ref> and its contribution to catalysis is relatively small.<ref>{{cite journal |author=Villa J, Strajbl M, Glennon TM, Sham YY, Chu ZT, Warshel A |title=How important are entropic contributions to enzyme catalysis? |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=97 |issue=22 |pages=11899-904 |year=2000 |pmid=11050223 |url=http://www.pnas.org/cgi/content/full/97/22/11899}}</ref>
 
==== Transition State Stabilization ====
 
The understanding of the origin of the reduction of ΔG<sup>‡</sup> 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.<ref>{{cite journal |author=Warshel A, Sharma PK, Kato M, Xiang Y, Liu H, Olsson MH |title=Electrostatic basis for enzyme catalysis |journal=Chem. Rev. |volume=106 |issue=8 |pages=3210-35 |year=2006 |pmid=16895325}}</ref> Such an environment does not exist in the uncatalyzed reaction in water.
 
==== Dynamics and function ====
 
Recent investigations have provided new insights into the connection between internal dynamics of enzymes and their mechanism of catalysis.<ref> Eisenmesser EZ, Bosco DA, Akke M, Kern D. ''Enzyme dynamics during catalysis.'' Science. 2002 February 22;295(5559):1520–3. PMID: 11859194 </ref><ref> Agarwal PK. ''Role of protein dynamics in reaction rate enhancement by enzymes.'' J Am Chem Soc. 2005 November 2;127(43):15248-56. PMID: 16248667</ref><ref>Eisenmesser EZ, Millet O, Labeikovsky W, Korzhnev DM, Wolf-Watz M, Bosco DA, Skalicky JJ, Kay LE, Kern D. ''Intrinsic dynamics of an enzyme underlies catalysis.'' Nature. 2005 November 3;438(7064):117-21. PMID: 16267559</ref>
۵۷ کرښه:
It should be clarified, however, that the dynamical time-dependent processes are not likely to help to accelerate enzymatic reactions, since such motions randomize and the rate constant is determined by the probability (P) of reaching the transition state, (P = exp {ΔG<sup>‡</sup>/RT}).<ref> Olsson M.H.M., Parson W.W. and Warshel A. "Dynamical Contributions to Enzyme Catalysis: Critical Tests of A Popular Hypothesis" Chem. Rev., 2006 105: 1737-1756 </ref> Furthermore, the reduction of ΔG<sup>‡</sup> requires having relatively smaller motions (in relation to the corresponding motions in solution reactions) for the transition between the reactant and the product states. Thus, it is not clear that motional or dynamical effects contribute to the catalysis of the chemical step.
 
=== Allosteric modulation ===
[[Allosteric]] enzymes change their structure in response to binding of [[effector (biology)|effectoreffectors]]s. Modulation can be direct, where the effector binds directly to [[binding site]]s in the enzyme, or indirect, where the effector binds to other proteins or [[protein subunit]]s that interact with the allosteric enzyme and thus influence catalytic activity.
 
== Cofactors and coenzymes ==
{{main|Cofactor (biochemistry)|Coenzyme}}
=== Cofactors ===
Some enzymes do not need any additional components to show 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 cluster]]s) or [[organic molecules|organic compounds]], (e.g., [[flavin]] and [[heme]]). Organic cofactors (coenzymes) are usually [[prosthetic groups]], which are tightly bound to the enzymes that they assist. These tightly-bound cofactors are distinguished from other coenzymes, such as [[Nicotinamide adenine dinucleotide|NADH]], since they are not released from the active site during the reaction.
 
۶۹ کرښه:
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 very tightly bound. However, organic prosthetic groups can be covalently bound (''e.g.'', [[thiamine pyrophosphate]] in the enzyme [[pyruvate dehydrogenase]]).
 
=== Coenzymes ===
[[Imageدوتنه:NADH-3D-vdW.png|thumb|left|150px|[[Molecular graphics#Space-filling models|Space-filling model]] of the coenzyme NADH]]
Coenzymes are small organic molecules that transport chemical groups from one enzyme to another.<ref>AF Wagner, KA Folkers (1975) ''Vitamins and coenzymes.'' Interscience Publishers New York| ISBN 0-88275-258-8</ref> Some of these chemicals such as [[riboflavin]], [[thiamine]] and [[folic acid]] are [[vitamins]], this is when these compounds cannot be made in the body and must be acquired from the diet. The chemical groups carried include the [[hydride]] ion (H<sup>-</sup>) carried by [[nicotinamide adenine dinucleotide|NAD or NADP<sup>+</sup>]], the acetyl group carried by [[coenzyme A]], formyl, methenyl or methyl groups carried by [[folic acid]] and the methyl group carried by [[S-adenosylmethionine]].
 
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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 ==
{{main |Activation energy|Thermodynamic equilibrium|Chemical equilibrium}}
[[Imageدوتنه:Activation2 updated.svg|thumb|300px|Diagram of a catalytic reaction, showing the energy ''niveau'' at each stage of the reaction. The substrates usually need a large amount of energy to reach the transition state, which then decays into the end product. The enzyme stabilizes the transition state, reducing the energy needed to form this species and thus reducing the energy required 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.
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\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!
\overrightarrow{\qquad\qquad\qquad\qquad}
H_2CO_3}</math> (in [[Biological tissue|tissuetissues]]s; high CO<sub>2</sub> concentration)
: <math>\mathrm{H_2CO_3
{}^\mathrm{\quad Carbonic\ anhydrase}
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== Kinetics ==
{{main|Enzyme kinetics}}
[[Imageدوتنه:Simple mechanism.svg|thumb|left|300px|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 assay]]s.
 
۱۰۹ کرښه:
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 chemical step in the reaction and releases the product.
 
[[Imageدوتنه:Michaelis-Menten saturation curve of an enzyme reaction.svg|thumb|300px|right|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.<ref>{{cite journal |author=Radzicka A, Wolfenden R.|year= 1995|title= A proficient enzyme. |journal= Science |volume=6|issue=267|pages=90–931|id= PMID 7809611}}</ref> 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 (''V''<sub>max</sub>) of the enzyme, all enzyme active sites are saturated with substrate, and the amount of ES complex is the same as the total amount of enzyme.
However, ''V''<sub>max</sub> 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]] (''K''<sub>m</sub>), which is the substrate concentration required for an enzyme to reach one-half its maximum velocity. Each enzyme has a characteristic ''K''<sub>m</sub> for a given substrate, and this can show how tight the binding of the substrate is to the enzyme. Another useful constant is ''k''<sub>cat</sub>, which is the number of substrate molecules handled by one active site per second.
۱۲۰ کرښه:
{{cite journal|author=Olsson M. H., Siegbahn P. E., Warshel A.|year= 2004|title= Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase|journal = J. Am. Chem. Soc.|volume=126|issue=9|pages=2820-1828|id= PMID 14995199}}</ref> Quantum tunneling for protons has been observed in [[tryptamine]].<ref>{{cite journal|author=Masgrau L., Roujeinikova A., Johannissen L. O., Hothi P., Basran J., Ranaghan K. E., Mulholland A. J., Sutcliffe M. J., Scrutton N. S., Leys D.|year= 2006|title= Atomic Description of an Enzyme Reaction Dominated by Proton Tunneling|journal= Science| volume=312|issue=5771|pages=237–241|id= PMID 16614214}}</ref> 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.
 
== Inhibition ==
[[Imageدوتنه:Competitive inhibition.svg|thumb|400px|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.]]
 
[[Imageدوتنه:Inhibition.png|thumb|400px|Types of inhibition. This classification was introduced by [[W.W. Cleland]].<ref>{{cite journal|author=Cleland, W.W.|year=1963|title= The Kinetics of Enzyme-catalyzed Reactions with two or more Substrates or Products 2. {I}nhibition: Nomenclature and Theory|journal=Biochim. Biophys. Acta|volume= 67|pages= 173-187}}</ref>]]
 
{{main|Enzyme inhibitor}}
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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).
 
[[Imageدوتنه:Methotrexate and folic acid compared.png||thumb|400px|right|The coenzyme folic acid (left) and the anti-cancer drug methotrexate (right) are very similar in structure. As a result, methotrexate is a competitive inhibitor of many enzymes that use folates.]]
 
[[Enzyme inhibitor#Irreversible inhibitors|Irreversible inhibitors]] react with the enzyme and form a [[covalent bond|covalent]] adduct with the protein. The inactivation is irreversible. These compounds include [[eflornithine]] a drug used to treat the parasitic disease [[sleeping sickness]].<ref name=Poulin>Poulin R, Lu L, Ackermann B, Bey P, Pegg AE. [http://www.jbc.org/cgi/reprint/267/1/150 ''Mechanism of the irreversible inactivation of mouse ornithine decarboxylase by alpha-difluoromethylornithine. Characterization of sequences at the inhibitor and coenzyme binding sites.''] J Biol Chem. 1992 Jan 5;267(1):150–8. PMID 1730582</ref> [[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 inactivators ===
 
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, "''In all things there is a poison, and there is nothing without a poison.''"<ref>Ball, Philip (2006) ''The Devil's Doctor: Paracelsus and the World of Renaissance Magic and Science.'' Farrar, Straus and Giroux ISBN 0-374-22979-1</ref> Equally, [[antibiotics]] and other anti-infective drugs are just specific poisons that kill a pathogen but not its [[host (biology)|host]].
۱۶۶ کرښه:
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 [[phosphorylation|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.
 
== Control of activity ==
 
There are five main ways that enzyme activity is controlled in the cell.
 
# '''Enzyme production''' ([[Transcription (genetics)|transcription]] and [[Translation (genetics)|translation]] of enzyme genes) can be enhanced or diminished by a cell in response to changes in the cell's environment. This form of [[Regulation of gene expression|gene regulation]] is called [[enzyme induction and inhibition]]. For example, bacteria may become [[Antibiotic resistance|resistant to antibiotics]] such as [[penicillin]] because enzymes called [[beta-lactamase]]s are induced that hydrolyse the crucial [[Beta-lactam|beta-lactam ring]] within the penicillin molecule. Another example are enzymes in the [[liver]] called [[cytochrome P450 oxidase]]s, which are important in [[drug metabolism]]. Induction or inhibition of these enzymes can cause [[drug interaction]]s.
# Enzymes can be '''compartmentalized''', with different metabolic pathways occurring in different [[cellular compartment]]s. 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 [[β-oxidation]].<ref>{{cite journal |url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1218279&blobtype=pdf|author=Faergeman N. J, Knudsen J.|year= 1997|month=April|title= Role of long-chain fatty acyl-CoA esters in the regulation of metabolism and in cell signalling|journal= Biochem J|volume=323|pages=1–12|id= PMID 9173866}}</ref>
# Enzymes can be regulated by '''[[Enzyme inhibitor|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|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. Like other [[homeostasis|homeostatic devices]], the control of enzymatic action helps to maintain a stable internal environment in living organisms.
# Enzymes can be regulated through '''[[post-translational modification]]'''. This can include [[phosphorylation]], [[Myristic acid|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]].<ref>{{cite journal |url=http://jcs.biologists.org/cgi/content/full/116/7/1175|author= Doble B. W., Woodgett J. R. |year=2003|month=April|title= GSK-3: tricks of the trade for a multi-tasking kinase|journal=J. Cell. Sci.|volume=116|pages=1175–1186|id= PMID 12615961}}</ref> 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]].
# Some enzymes may become '''activated when localized to a different environment''' (eg. from a reducing ([[cytoplasm]]) to an oxidising ([[periplasm]]) environment, high pH to low pH etc). For example, [[hemagglutinin]] of the [[influenza]] virus undergoes a conformational change once it encounters the acidic environment of the host cell [[Vesicle (biology)|vesicle]] causing its activation.<ref>{{cite journal|url=http://dx.doi.org/10.1016/0092-8674(93)90260-W|author=Carr C. M., Kim P. S. |year=2003|month=April|title= A spring-loaded mechanism for the conformational change of influenza hemagglutinin|journal=Cell|volume=73|pages=823–832|id= PMID 8500173}}</ref>
 
== Involvement in disease ==
[[Imageدوتنه:Phenylalanine hydroxylase brighter.jpg|thumb|200px|[[Phenylalanine hydroxylase]]. Created from [http://www.rcsb.org/pdb/explore.do?structureId=1KW0 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.
 
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The complete nomenclature can be browsed at http://www.chem.qmul.ac.uk/iubmb/enzyme/.
 
== 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 catalyse and also by their lack of stability in [[organic solvent]]s 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.<ref>{{cite journal|author=Renugopalakrishnan V, Garduno-Juarez R, Narasimhan G, Verma CS, Wei X, Li P.|year= 2005|title= Rational design of thermally stable proteins: relevance to bionanotechnology.|journal= J Nanosci Nanotechnol.|volume=5|issue=11|pages= 1759–1767|id= PMID 16433409}}</ref><ref>{{cite journal|author=Hult K, Berglund P.|year= 2003|title= Engineered enzymes for improved organic synthesis.|journal= Curr Opin Biotechnol.|volume=14|issue=4|pages= 395–400|id= PMID 12943848}}</ref>
 
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|width=38% align=center|'''Uses'''
|-
|style="border-top: solid 3px #aaaaaa;" rowspan="2" | '''[[Baking|Baking industry]]''' [[Imageدوتنه:Amylose.svg|thumb|center|180px|alpha-amylase catalyzes the release of sugar monomers from starch]]
|style="border-top: solid 3px #aaaaaa;" |[[Fungus|Fungal]] alpha-amylase enzymes are normally inactivated at about 50 degrees Celsius, but are destroyed during the baking process.
|style="border-top: solid 3px #aaaaaa;" |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.
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|style="border-top: solid 3px #aaaaaa;" |To predigest baby foods.
|-
|style="border-top: solid 3px #aaaaaa;" rowspan="6" | '''[[Brewing|Brewing industry]]''' [[Imageدوتنه:Sjb whiskey malt.jpg|thumb|center|180px|Germinating [[barley]] used for malt.]]
|style="border-top: solid 3px #aaaaaa;" | Enzymes from barley are released during the mashing stage of beer production.
|style="border-top: solid 3px #aaaaaa;" | They degrade starch and proteins to produce simple sugar, amino acids and peptides that are used by yeast for fermentation.
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|style="border-top: solid 3px #aaaaaa;" | Clarify fruit juices
|-
|style="border-top: solid 3px #aaaaaa;" rowspan="4" | '''[[Dairy|Dairy industry]]''' [[Imageدوتنه:Roquefort cheese.jpg|thumb|center|180px|Roquefort cheese]]
|style="border-top: solid 3px #aaaaaa;" |[[Rennin]], derived from the stomachs of young [[ruminant|ruminant animals]] (like calves and lambs).
|style="border-top: solid 3px #aaaaaa;" |Manufacture of cheese, used to [[hydrolyze]] protein.
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| Converts [[glucose]] into [[fructose]] in production of [[High-fructose corn syrup|high fructose syrups]] from starchy materials. These syrups have enhanced sweetening properties and lower [[calorie|calorific values]] than sucrose for the same level of sweetness.
|-
|style="border-top: solid 3px #aaaaaa;" |'''[[Paper|Paper industry]]'''[[Imageدوتنه:InternationalPaper6413.jpg|160px|thumb|center|A paper mill in [[South Carolina]].]]
|style="border-top: solid 3px #aaaaaa;" |[[Amylase]]s, [[Xylanase]]s, [[Cellulase]]s and [[lignin]]ases
|style="border-top: solid 3px #aaaaaa;" |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.
|-
|style="border-top: solid 3px #aaaaaa;" rowspan="2" |'''[[Biofuel]] industry'''[[Imageدوتنه:Cellulose-3D-balls.png|180px|thumb|center|Cellulose in 3D]]
|style="border-top: solid 3px #aaaaaa;" |[[Cellulase]]s
|style="border-top: solid 3px #aaaaaa;" |Used to break down cellulose into sugars that can be fermented (see [[cellulosic ethanol]]).
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|style="border-top: solid 3px #aaaaaa;" |Dissolve [[gelatin]] off scrap [[Photographic film|film]], allowing recovery of its [[silver]] content.
|-
|style="border-top: solid 3px #aaaaaa;" |'''[[Molecular biology]]''' [[Imageدوتنه:DNA123 rotated.png|180px|thumb|center|Part of the DNA [[double helix]].]]
|style="border-top: solid 3px #aaaaaa;" |[[Restriction enzyme]]s, [[DNA ligase]] and [[polymerases]]
|style="border-top: solid 3px #aaaaaa;" |Used to manipulate DNA in [[genetic engineering]], important in [[pharmacology]], [[agriculture]] and [[medicine]]. Essential for [[Restriction enzyme|restriction digestion]] and the [[polymerase chain reaction]]. Molecular biology is also important in [[forensic science]].
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'''Etymology and history'''
* [http://bip.cnrs-mrs.fr/bip10/buchner.htm 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.
* [http://etext.lib.virginia.edu/toc/modeng/public/Wil4Sci.html Williams, Henry Smith, 1863–1943. A History of Science: in Five Volumes. Volume IV: Modern Development of the Chemical and Biological Sciences], A textbook from the 19th century.
* Kleyn, J. and Hough J. The Microbiology of Brewing. ''Annual Review of Microbiology'' (1971) Vol. 25: 583–608
 
'''Enzyme structure and mechanism'''
* Fersht, A. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. W. H. Freeman, 1998 ISBN 0-7167-3268-8
* Walsh, C., Enzymatic Reaction Mechanisms. W. H. Freeman and Company. 1979. ISBN 0-7167-0070-0
* Page, M. I., and Williams, A. (Eds.), 1987. Enzyme Mechanisms. Royal Society of Chemistry. ISBN 0-85186-947-5
* Bugg, T. Introduction to Enzyme and Coenzyme Chemistry, 2004, Blackwell Publishing Limited; 2nd edition. ISBN 1-405114051-4521452-5
* Warshel, A., Computer Modeling of Chemical Reactions in enzymes and Solutions John Wiley & Sons Inc. 1991. ISBN 0-471-18440-3
 
'''Thermodynamics'''
* [http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookEnzym.html Reactions and Enzymes] Chapter 10 of On-Line Biology Book at Estrella Mountain Community College.
 
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'''Kinetics and inhibition'''
 
* Athel Cornish-Bowden, ''Fundamentals of Enzyme Kinetics''. (3rd edition), Portland Press (2004), ISBN 1-85578-158-1.
* Irwin H. Segel, ''Enzyme Kinetics: Behavior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems''. Wiley-Interscience; New Ed edition (1993), ISBN 0-471-30309-7.
* John W. Baynes, ''Medical Biochemistry'', Elsevier-Mosby; 2th Edition (2005), ISBN 0-7234-3341-0, p. 57.
 
'''Function and control of enzymes in the cell'''
 
* Price, N. and Stevens, L., Fundamentals of Enzymology: Cell and Molecular Biology of Catalytic Proteins Oxford University Press, (1999), ISBN 0-19-850229-X
* [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=gnd.chapter.86 Nutritional and Metabolic Diseases] Chapter of the on-line textbook "Introduction to Genes and Disease" from the NCBI.
 
'''Enzyme-naming conventions'''
* [http://www.chem.qmul.ac.uk/iubmb/enzyme/ Enzyme Nomenclature], Recommendations for enzyme names from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology.
* Koshland D. The Enzymes, v. I, ch. 7, Acad. Press, New York, (1959)
 
'''Industrial applications'''
* [http://www.mapsenzymes.com/History_of_Enzymes.asp History of industrial enzymes], Article about the history of industrial enzymes, from the late 1900s to the present times.
 
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{{commonscat|Enzymes}}
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* [http://tutor.lscf.ucsb.edu/instdev/sears/biochemistry/tw-enz/tabs-enzymes-frames.htm Structure/Function of Enzymes], Web tutorial on enzyme structure and function.
* [http://www.ebi.ac.uk/intenz/spotlight.jsp Enzyme spotlight] Monthly feature at the European Bioinformatics Institute on a selected enzyme.
* [http://www.amfep.org AMFEP], Association of Manufacturers and Formulators of Enzyme Products
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{{Enzymes}}
 
[[Categoryوېشنيزه:Biomolecules]]
[[Categoryوېشنيزه:Enzymes|*]]
[[Categoryوېشنيزه:Metabolism]]
 
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