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80-452: Vitamin K epoxide reductase ( VKOR ) is an enzyme ( EC 1.17.4.4 ) that reduces vitamin K after it has been oxidised in the carboxylation of glutamic acid residues in blood coagulation enzymes. VKOR is a member of a large family of predicted enzymes that are present in vertebrates, Drosophila , plants, bacteria and archaea . In some plant and bacterial homologues , the VKOR domain

160-487: A catalytic triad , stabilize charge build-up on the transition states using an oxyanion hole , complete hydrolysis using an oriented water substrate. Enzymes are not rigid, static structures; instead they have complex internal dynamic motions – that is, movements of parts of the enzyme's structure such as individual amino acid residues, groups of residues forming a protein loop or unit of secondary structure , or even an entire protein domain . These motions give rise to

240-489: A conformational ensemble of slightly different structures that interconvert with one another at equilibrium . Different states within this ensemble may be associated with different aspects of an enzyme's function. For example, different conformations of the enzyme dihydrofolate reductase are associated with the substrate binding, catalysis, cofactor release, and product release steps of the catalytic cycle, consistent with catalytic resonance theory . Substrate presentation

320-511: A type of enzyme rather than being like an enzyme, but even in the decades since ribozymes' discovery in 1980–1982, the word enzyme alone often means the protein type specifically (as is used in this article). An enzyme's specificity comes from its unique three-dimensional structure . Like all catalysts, enzymes increase the reaction rate by lowering its activation energy . Some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example

400-581: A constant, now known as an equilibrium constant . By convention, the products form the numerator . However, the law of mass action is valid only for concerted one-step reactions that proceed through a single transition state and is not valid in general because rate equations do not, in general, follow the stoichiometry of the reaction as Guldberg and Waage had proposed (see, for example, nucleophilic aliphatic substitution by S N 1 or reaction of hydrogen and bromine to form hydrogen bromide ). Equality of forward and backward reaction rates, however,

480-474: A first step and then checks that the product is correct in a second step. This two-step process results in average error rates of less than 1 error in 100 million reactions in high-fidelity mammalian polymerases. Similar proofreading mechanisms are also found in RNA polymerase , aminoacyl tRNA synthetases and ribosomes . Conversely, some enzymes display enzyme promiscuity , having broad specificity and acting on

560-399: A proton may hop from one molecule of acetic acid onto a water molecule and then onto an acetate anion to form another molecule of acetic acid and leaving the number of acetic acid molecules unchanged. This is an example of dynamic equilibrium . Equilibria, like the rest of thermodynamics, are statistical phenomena, averages of microscopic behavior. Le Châtelier's principle (1884) predicts

640-464: A quantitative theory of enzyme kinetics, which is referred to as Michaelis–Menten kinetics . The major contribution of Michaelis and Menten 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–Menten complex in their honor. The enzyme then catalyzes the chemical step in

720-439: A range of different physiologically relevant substrates. Many enzymes possess small side activities which arose fortuitously (i.e. neutrally ), which may be the starting point for the evolutionary selection of a new function. To explain the observed specificity of enzymes, in 1894 Emil Fischer proposed that both the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another. This

800-475: A solution is given by where c i and z i stand for the concentration and ionic charge of ion type i , and the sum is taken over all the N types of charged species in solution. When the concentration of dissolved salt is much higher than the analytical concentrations of the reagents, the ions originating from the dissolved salt determine the ionic strength, and the ionic strength is effectively constant. Since activity coefficients depend on ionic strength,

880-451: A species' normal level; as a result, enzymes from bacteria living in volcanic environments such as hot springs are prized by industrial users for their ability to function at high temperatures, allowing enzyme-catalysed reactions to be operated at a very high rate. Enzymes are usually much larger than their substrates. Sizes range from just 62 amino acid residues, for the monomer of 4-oxalocrotonate tautomerase , to over 2,500 residues in

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960-446: A steady level inside the cell. For example, NADPH is regenerated through the pentose phosphate pathway and S -adenosylmethionine by methionine adenosyltransferase . This continuous regeneration means that small amounts of coenzymes can be used very intensively. For example, the human body turns over its own weight in ATP each day. As with all catalysts, enzymes do not alter the position of

1040-442: A thermodynamically unfavourable one so that the combined energy of the products is lower than the substrates. For example, the hydrolysis of ATP is often used to drive other chemical reactions. Enzyme kinetics is the investigation of how enzymes bind substrates and turn them into products. The rate data used in kinetic analyses are commonly obtained from enzyme assays . In 1913 Leonor Michaelis and Maud Leonora Menten proposed

1120-457: Is k cat , also called the turnover number , 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 k cat / K m . This is also called the specificity constant and incorporates the rate constants for all steps in the reaction up to and including the first irreversible step. Because the specificity constant reflects both affinity and catalytic ability, it

1200-838: Is orotidine 5'-phosphate decarboxylase , which allows a reaction that would otherwise take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, nor do they alter the equilibrium of a reaction. Enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules: inhibitors are molecules that decrease enzyme activity, and activators are molecules that increase activity. Many therapeutic drugs and poisons are enzyme inhibitors. An enzyme's activity decreases markedly outside its optimal temperature and pH , and many enzymes are (permanently) denatured when exposed to excessive heat, losing their structure and catalytic properties. Some enzymes are used commercially, for example, in

1280-405: Is a necessary condition for chemical equilibrium, though it is not sufficient to explain why equilibrium occurs. Despite the limitations of this derivation, the equilibrium constant for a reaction is indeed a constant, independent of the activities of the various species involved, though it does depend on temperature as observed by the van 't Hoff equation . Adding a catalyst will affect both

1360-421: Is a process where the enzyme is sequestered away from its substrate. Enzymes can be sequestered to the plasma membrane away from a substrate in the nucleus or cytosol. Or within the membrane, an enzyme can be sequestered into lipid rafts away from its substrate in the disordered region. When the enzyme is released it mixes with its substrate. Alternatively, the enzyme can be sequestered near its substrate to activate

1440-450: Is a redox protein with an unknown identity, probably a thioredoxin-like protein located in the ER lumen such as TMX1 . There is also a similar gene called VKORC1L1 . The VKORL1 complex it forms is much less efficient at reducing the epoxide, but it has the ability to reduce the quinone form of vitamin K to a diol form (KH 2 ). Although EC 1.17.4.4 notes both paralogs as having both activities,

1520-586: Is bound by a redox-active CXXC motif in the C-terminal helices, similar to the DsbB active site. Two other cysteines to the N-terminal are located in a loop outside of the transmembrane region; they relay electrons with a redox protein (or in the case of the bacterial homolog, its own fused domain). The human gene for VKOR is called VKORC1 (VKOR complex subunit 1). It is the target of anticoagulant warfarin . Its partner

1600-454: Is called enzymology and the field of pseudoenzyme analysis recognizes that during evolution, some enzymes have lost the ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Other biocatalysts are catalytic RNA molecules , also called ribozymes . They are sometimes described as

1680-509: Is considered. The relation between the Gibbs free energy and the equilibrium constant can be found by considering chemical potentials . At constant temperature and pressure in the absence of an applied voltage, the Gibbs free energy , G , for the reaction depends only on the extent of reaction : ξ (Greek letter xi ), and can only decrease according to the second law of thermodynamics . It means that

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1760-437: Is described by "EC" followed by a sequence of four numbers which represent the hierarchy of enzymatic activity (from very general to very specific). That is, the first number broadly classifies the enzyme based on its mechanism while the other digits add more and more specificity. The top-level classification is: These sections are subdivided by other features such as the substrate, products, and chemical mechanism . An enzyme

1840-749: Is fully specified by four numerical designations. For example, hexokinase (EC 2.7.1.1) is a transferase (EC 2) that adds a phosphate group (EC 2.7) to a hexose sugar, a molecule containing an alcohol group (EC 2.7.1). Sequence similarity . EC categories do not reflect sequence similarity. For instance, two ligases of the same EC number that catalyze exactly the same reaction can have completely different sequences. Independent of their function, enzymes, like any other proteins, have been classified by their sequence similarity into numerous families. These families have been documented in dozens of different protein and protein family databases such as Pfam . Non-homologous isofunctional enzymes . Unrelated enzymes that have

1920-411: Is fused with domains of the thioredoxin family of oxidoreductases . Four cysteine residues and one residue, which is either serine or threonine, are identified as likely active-site residues . Solved bacterial VKOR structures has enabled more insights into the catalytic mechanism. All VKORs are transmembrane proteins with at least three TM helices at the catalytic core. The quinone to be reduced

2000-405: Is known, paradoxically, as a thermodynamic equilibrium constant. Before using a published value of an equilibrium constant in conditions of ionic strength different from the conditions used in its determination, the value should be adjusted. A mixture may appear to have no tendency to change, though it is not at equilibrium. For example, a mixture of SO 2 and O 2 is metastable as there

2080-404: Is left out, as it is the solvent and its concentration remains high and nearly constant. A quantitative version is given by the reaction quotient . J. W. Gibbs suggested in 1873 that equilibrium is attained when the Gibbs free energy of the chemical potential of the system is at its minimum value (assuming the reaction is carried out at a constant temperature and pressure). What this means

2160-473: 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 . Different enzymes that catalyze the same chemical reaction are called isozymes . The International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers (for "Enzyme Commission") . Each enzyme

2240-418: Is often referred to as "the lock and key" model. This early model explains enzyme specificity, but fails to explain the stabilization of the transition state that enzymes achieve. In 1958, Daniel Koshland suggested a modification to the lock and key model: since enzymes are rather flexible structures, the active site is continuously reshaped by interactions with the substrate as the substrate interacts with

2320-462: Is only one of several important kinetic parameters. The amount of substrate needed to achieve a given rate of reaction is also important. This is given by the Michaelis–Menten constant ( K m ), which is the substrate concentration required for an enzyme to reach one-half its maximum reaction rate; generally, each enzyme has a characteristic K M for a given substrate. Another useful constant

2400-404: 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 complex. At the maximum reaction rate ( V max ) 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. V max

2480-434: Is that the derivative of the Gibbs energy with respect to reaction coordinate (a measure of the extent of reaction that has occurred, ranging from zero for all reactants to a maximum for all products) vanishes (because dG = 0), signaling a stationary point . This derivative is called the reaction Gibbs energy (or energy change) and corresponds to the difference between the chemical potentials of reactants and products at

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2560-403: Is the ribosome which is a complex of protein and catalytic RNA components. Enzymes must bind their substrates before they can catalyse any chemical reaction. Enzymes are usually very specific as to what substrates they bind and then the chemical reaction catalysed. Specificity is achieved by binding pockets with complementary shape, charge and hydrophilic / hydrophobic characteristics to

2640-474: Is the standard chemical potential ). The definition of the Gibbs energy equation interacts with the fundamental thermodynamic relation to produce Inserting dN i  = ν i  dξ into the above equation gives a stoichiometric coefficient ( ν i   {\displaystyle \nu _{i}~} ) and a differential that denotes the reaction occurring to an infinitesimal extent ( dξ ). At constant pressure and temperature

2720-486: Is the concentration of reagent A, etc. It is possible in principle to obtain values of the activity coefficients, γ. For solutions, equations such as the Debye–Hückel equation or extensions such as Davies equation Specific ion interaction theory or Pitzer equations may be used. However this is not always possible. It is common practice to assume that Γ is a constant, and to use the concentration quotient in place of

2800-447: Is the product of partial pressure and fugacity coefficient. The chemical potential of a species in the real gas phase is given by so the general expression defining an equilibrium constant is valid for both solution and gas phases. In aqueous solution, equilibrium constants are usually determined in the presence of an "inert" electrolyte such as sodium nitrate , NaNO 3 , or potassium perchlorate , KClO 4 . The ionic strength of

2880-790: 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 10 to 10 (M s ). 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 , β-lactamase , and superoxide dismutase . The turnover of such enzymes can reach several million reactions per second. But most enzymes are far from perfect:

2960-611: The DNA polymerases ; here the holoenzyme is the complete complex containing all the subunits needed for activity. Coenzymes are small organic molecules that can be loosely or tightly bound to an enzyme. Coenzymes transport chemical groups from one enzyme to another. Examples include NADH , NADPH and adenosine triphosphate (ATP). Some coenzymes, such as flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), thiamine pyrophosphate (TPP), and tetrahydrofolate (THF), are derived from vitamins . These coenzymes cannot be synthesized by

3040-636: The Gibbs free energy , G , while at constant temperature and volume, one must consider the Helmholtz free energy , A , for the reaction; and at constant internal energy and volume, one must consider the entropy, S , for the reaction. The constant volume case is important in geochemistry and atmospheric chemistry where pressure variations are significant. Note that, if reactants and products were in standard state (completely pure), then there would be no reversibility and no equilibrium. Indeed, they would necessarily occupy disjoint volumes of space. The mixing of

3120-511: The law of mass action , which is derived from the assumptions of free diffusion and thermodynamically driven random collision. Many biochemical or cellular processes deviate significantly from these conditions, because of macromolecular crowding and constrained molecular movement. More recent, complex extensions of the model attempt to correct for these effects. Enzyme reaction rates can be decreased by various types of enzyme inhibitors. A competitive inhibitor and substrate cannot bind to

3200-401: The above equations can be written as which is the Gibbs free energy change for the reaction. This results in: By substituting the chemical potentials: the relationship becomes: which is the standard Gibbs energy change for the reaction that can be calculated using thermodynamical tables. The reaction quotient is defined as: Therefore, At equilibrium: leading to: and Obtaining

3280-437: The active site and are involved in catalysis. For example, flavin and heme cofactors are often involved in redox reactions. Enzymes that require a cofactor but do not have one bound are called apoenzymes or apoproteins . An enzyme together with the cofactor(s) required for activity is called a holoenzyme (or haloenzyme). The term holoenzyme can also be applied to enzymes that contain multiple protein subunits, such as

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3360-502: The active site. Organic cofactors can be either coenzymes , which are released from the enzyme's active site during the reaction, or prosthetic groups , which are tightly bound to an enzyme. Organic prosthetic groups can be covalently bound (e.g., biotin in enzymes such as pyruvate carboxylase ). An example of an enzyme that contains a cofactor is carbonic anhydrase , which uses a zinc cofactor bound as part of its active site. These tightly bound ions or molecules are usually found in

3440-439: The activity coefficients of the species are effectively independent of concentration. Thus, the assumption that Γ is constant is justified. The concentration quotient is a simple multiple of the equilibrium constant. However, K c will vary with ionic strength. If it is measured at a series of different ionic strengths, the value can be extrapolated to zero ionic strength. The concentration quotient obtained in this manner

3520-407: The animal fatty acid synthase . Only a small portion of their structure (around 2–4 amino acids) is directly involved in catalysis: the catalytic site. This catalytic site is located next to one or more binding sites where residues orient the substrates. The catalytic site and binding site together compose the enzyme's active site . The remaining majority of the enzyme structure serves to maintain

3600-578: The average values of k c a t / K m {\displaystyle k_{\rm {cat}}/K_{\rm {m}}} and k c a t {\displaystyle k_{\rm {cat}}} are about 10 5 s − 1 M − 1 {\displaystyle 10^{5}{\rm {s}}^{-1}{\rm {M}}^{-1}} and 10 s − 1 {\displaystyle 10{\rm {s}}^{-1}} , respectively. Michaelis–Menten kinetics relies on

3680-420: The behavior of an equilibrium system when changes to its reaction conditions occur. If a dynamic equilibrium is disturbed by changing the conditions, the position of equilibrium moves to partially reverse the change . For example, adding more S (to the chemical reaction above) from the outside will cause an excess of products, and the system will try to counteract this by increasing the reverse reaction and pushing

3760-502: The body de novo and closely related compounds (vitamins) must be acquired from the diet. The chemical groups carried include: Since coenzymes are chemically changed as a consequence of enzyme action, it is useful to consider coenzymes to be a special class of substrates, or second substrates, which are common to many different enzymes. For example, about 1000 enzymes are known to use the coenzyme NADH. Coenzymes are usually continuously regenerated and their concentrations maintained at

3840-471: The chemical equilibrium of the reaction. In the presence of an enzyme, the reaction runs in the same direction as it would without the enzyme, just more quickly. For example, carbonic anhydrase catalyzes its reaction in either direction depending on the concentration of its reactants: The rate of a reaction is dependent on the activation energy needed to form the transition state which then decays into products. Enzymes increase reaction rates by lowering

3920-406: The composition of the reaction mixture. This criterion is both necessary and sufficient. If a mixture is not at equilibrium, the liberation of the excess Gibbs energy (or Helmholtz energy at constant volume reactions) is the "driving force" for the composition of the mixture to change until equilibrium is reached. The equilibrium constant can be related to the standard Gibbs free energy change for

4000-425: The conversion of starch to sugars by plant extracts and saliva were known but the mechanisms by which these occurred had not been identified. French chemist Anselme Payen was the first to discover an enzyme, diastase , in 1833. A few decades later, when studying the fermentation of sugar to alcohol by yeast , Louis Pasteur concluded that this fermentation was caused by a vital force contained within

4080-405: The derivative of G with respect to ξ must be negative if the reaction happens; at the equilibrium this derivative is equal to zero. In order to meet the thermodynamic condition for equilibrium, the Gibbs energy must be stationary, meaning that the derivative of G with respect to the extent of reaction, ξ , must be zero. It can be shown that in this case, the sum of chemical potentials times

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4160-433: The energy of the transition state. First, binding forms a low energy enzyme-substrate complex (ES). Second, the enzyme stabilises the transition state such that it requires less energy to achieve compared to the uncatalyzed reaction (ES ). Finally the enzyme-product complex (EP) dissociates to release the products. Enzymes can couple two or more reactions, so that a thermodynamically favorable reaction can be used to "drive"

4240-587: The enzyme urease was a pure protein and crystallized it; he did likewise for the enzyme catalase in 1937. The conclusion that pure proteins can be enzymes was definitively demonstrated by John Howard Northrop and Wendell Meredith Stanley , who worked on the digestive enzymes pepsin (1930), trypsin and chymotrypsin . These three scientists were awarded the 1946 Nobel Prize in Chemistry. The discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography . This

4320-483: The enzyme at the same time. Often competitive inhibitors strongly resemble the real substrate of the enzyme. For example, the drug methotrexate is a competitive inhibitor of the enzyme dihydrofolate reductase , which catalyzes the reduction of dihydrofolate to tetrahydrofolate. The similarity between the structures of dihydrofolate and this drug are shown in the accompanying figure. This type of inhibition can be overcome with high substrate concentration. In some cases,

4400-403: The enzyme. As a result, the substrate does not simply bind to a rigid active site; the amino acid side-chains that make up the active site are molded 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. The active site continues to change until

4480-427: The enzyme. For example, the enzyme can be soluble and upon activation bind to a lipid in the plasma membrane and then act upon molecules in the plasma membrane. Allosteric sites are pockets on the enzyme, distinct from the active site, that bind to molecules in the cellular environment. These molecules then cause a change in the conformation or dynamics of the enzyme that is transduced to the active site and thus affects

4560-500: The equilibrium point backward (though the equilibrium constant will stay the same). If mineral acid is added to the acetic acid mixture, increasing the concentration of hydronium ion, the amount of dissociation must decrease as the reaction is driven to the left in accordance with this principle. This can also be deduced from the equilibrium constant expression for the reaction: If {H 3 O } increases {CH 3 CO 2 H} must increase and CH 3 CO − 2 must decrease. The H 2 O

4640-403: The equilibrium position is said to be "far to the left" if hardly any product is formed from the reactants. Guldberg and Waage (1865), building on Berthollet's ideas, proposed the law of mass action : where A, B, S and T are active masses and k + and k − are rate constants . Since at equilibrium forward and backward rates are equal: and the ratio of the rate constants is also

4720-427: The following chemical equation , arrows point both ways to indicate equilibrium. A and B are reactant chemical species, S and T are product species, and α , β , σ , and τ are the stoichiometric coefficients of the respective reactants and products: The equilibrium concentration position of a reaction is said to lie "far to the right" if, at equilibrium, nearly all the reactants are consumed. Conversely

4800-450: The forward reaction and the reverse reaction in the same way and will not have an effect on the equilibrium constant. The catalyst will speed up both reactions thereby increasing the speed at which equilibrium is reached. Although the macroscopic equilibrium concentrations are constant in time, reactions do occur at the molecular level. For example, in the case of acetic acid dissolved in water and forming acetate and hydronium ions,

4880-460: The inhibitor can bind to a site other than the binding-site of the usual substrate and exert an allosteric effect to change the shape of the usual binding-site. Chemical equilibrium The concept of chemical equilibrium was developed in 1803, after Berthollet found that some chemical reactions are reversible . For any reaction mixture to exist at equilibrium, the rates of the forward and backward (reverse) reactions must be equal. In

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4960-468: The mixture. He named the enzyme that brought about the fermentation of sucrose " zymase ". In 1907, he received the Nobel Prize in Chemistry for "his discovery of cell-free fermentation". Following Buchner's example, enzymes are usually named according to the reaction they carry out: the suffix -ase is combined with the name of the substrate (e.g., lactase is the enzyme that cleaves lactose ) or to

5040-576: The precise division of labor in vitro is debated. Enzyme Enzymes ( / ˈ ɛ n z aɪ m z / ) are proteins that act as biological catalysts by accelerating chemical reactions . The molecules upon which enzymes may act are called substrates , and the enzyme converts the substrates into different molecules known as products . Almost all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes

5120-528: The precise orientation and dynamics of the active site. In some enzymes, no amino acids are directly involved in catalysis; instead, the enzyme contains sites to bind and orient catalytic cofactors . Enzyme structures may also contain allosteric sites where the binding of a small molecule causes a conformational change that increases or decreases activity. A small number of RNA -based biological catalysts called ribozymes exist, which again can act alone or in complex with proteins. The most common of these

5200-420: The products and reactants contributes a large entropy increase (known as entropy of mixing ) to states containing equal mixture of products and reactants and gives rise to a distinctive minimum in the Gibbs energy as a function of the extent of reaction. The standard Gibbs energy change, together with the Gibbs energy of mixing, determine the equilibrium state. In this article only the constant pressure case

5280-406: The reaction and releases the product. This work was further developed by G. E. Briggs and J. B. S. Haldane , who derived kinetic equations that are still widely used today. Enzyme rates depend on solution conditions and substrate concentration . To find the maximum speed of an enzymatic reaction, the substrate concentration is increased until a constant rate of product formation

5360-804: The reaction by the equation where R is the universal gas constant and T the temperature . When the reactants are dissolved in a medium of high ionic strength the quotient of activity coefficients may be taken to be constant. In that case the concentration quotient , K c , where [A] is the concentration of A, etc., is independent of the analytical concentration of the reactants. For this reason, equilibrium constants for solutions are usually determined in media of high ionic strength. K c varies with ionic strength , temperature and pressure (or volume). Likewise K p for gases depends on partial pressure . These constants are easier to measure and encountered in high-school chemistry courses. At constant temperature and pressure, one must consider

5440-733: The reaction rate of the enzyme. In this way, allosteric interactions can either inhibit or activate enzymes. Allosteric interactions with metabolites upstream or downstream in an enzyme's metabolic pathway cause feedback regulation, altering the activity of the enzyme according to the flux through the rest of the pathway. Some enzymes do not need additional components to show full activity. Others require non-protein molecules called cofactors to be bound for activity. Cofactors can be either inorganic (e.g., metal ions and iron–sulfur clusters ) or organic compounds (e.g., flavin and heme ). These cofactors serve many purposes; for instance, metal ions can help in stabilizing nucleophilic species within

5520-410: The same enzymatic activity have been called non-homologous isofunctional enzymes . Horizontal gene transfer may spread these genes to unrelated species, especially bacteria where they can replace endogenous genes of the same function, leading to hon-homologous gene displacement. Enzymes are generally globular proteins , acting alone or in larger complexes . The sequence of the amino acids specifies

5600-430: The stoichiometric coefficients of the products is equal to the sum of those corresponding to the reactants. Therefore, the sum of the Gibbs energies of the reactants must be the equal to the sum of the Gibbs energies of the products. where μ is in this case a partial molar Gibbs energy, a chemical potential . The chemical potential of a reagent A is a function of the activity , {A} of that reagent. (where μ A

5680-412: The structure which in turn determines the catalytic activity of the enzyme. Although structure determines function, a novel enzymatic activity cannot yet be predicted from structure alone. Enzyme structures unfold ( denature ) when heated or exposed to chemical denaturants and this disruption to the structure typically causes a loss of activity. Enzyme denaturation is normally linked to temperatures above

5760-519: The substrate is completely bound, at which point the final shape and charge distribution is determined. Induced fit may enhance the fidelity of molecular recognition in the presence of competition and noise via the conformational proofreading mechanism. Enzymes can accelerate reactions in several ways, all of which lower the activation energy (ΔG , Gibbs free energy ) Enzymes may use several of these mechanisms simultaneously. For example, proteases such as trypsin perform covalent catalysis using

5840-405: The substrates. Enzymes can therefore distinguish between very similar substrate molecules to be chemoselective , regioselective and stereospecific . Some of the enzymes showing the highest specificity and accuracy are involved in the copying and expression of the genome . Some of these enzymes have " proof-reading " mechanisms. Here, an enzyme such as DNA polymerase catalyzes a reaction in

5920-399: The synthesis of antibiotics . Some household products use enzymes to speed up chemical reactions: enzymes in biological washing powders break down protein, starch or fat stains on clothes, and enzymes in meat tenderizer break down proteins into smaller molecules, making the meat easier to chew. By the late 17th and early 18th centuries, the digestion of meat by stomach secretions and

6000-477: The thermodynamic equilibrium constant. It is also general practice to use the term equilibrium constant instead of the more accurate concentration quotient . This practice will be followed here. For reactions in the gas phase partial pressure is used in place of concentration and fugacity coefficient in place of activity coefficient. In the real world, for example, when making ammonia in industry, fugacity coefficients must be taken into account. Fugacity, f ,

6080-438: The type of reaction (e.g., DNA polymerase forms DNA polymers). The biochemical identity of enzymes was still unknown in the early 1900s. Many scientists observed that enzymatic activity was associated with proteins, but others (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. In 1926, James B. Sumner showed that

6160-442: The value of the standard Gibbs energy change, allows the calculation of the equilibrium constant. For a reactional system at equilibrium: Q r  =  K eq ; ξ  =  ξ eq . Note that activities and equilibrium constants are dimensionless numbers. The expression for the equilibrium constant can be rewritten as the product of a concentration quotient, K c and an activity coefficient quotient, Γ . [A]

6240-486: 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." In 1877, German physiologist Wilhelm Kühne (1837–1900) first used the term enzyme , which comes from Ancient Greek ἔνζυμον (énzymon)  ' leavened , in yeast', to describe this process. The word enzyme

6320-581: 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. 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. Enzymes can be classified by two main criteria: either amino acid sequence similarity (and thus evolutionary relationship) or enzymatic activity. Enzyme activity . An enzyme's name

6400-451: 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. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897. In a series of experiments at the University of Berlin , he found that sugar was fermented by yeast extracts even when there were no living yeast cells in

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