bio catalyst

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"Biocatalyst" redirects here. For the use of natural catalysts in organic chemistry,

seeBiocatalysis.

Humanglyoxalase I.Twozincions that are needed for the enzyme to catalyze its reaction are shown as purple

spheres, and anenzyme inhibitorcalled S-hexylglutathione is shown as aspace-filling model,filling the two active

sites.

Enzymes/nzamz/are large biologicalmoleculesresponsible for the thousands ofmetabolic

processesthat sustain life.[1][2]They are highly selectivecatalysts,greatly accelerating both the

rate and specificity of metabolic reactions, from the digestion of food to the synthesis ofDNA.

Most enzymes areproteins,although somecatalytic RNA moleculeshave been identified.

Enzymes adopt a specificthree-dimensional structure,and may employ organic (e.g.biotin)andinorganic (e.g.magnesiumion)cofactorsto assist in catalysis.

In enzymatic reactions, the molecules at the beginning of the process, calledsubstrates,are

converted into different molecules, calledproducts.Almost all chemical reactions in abiological

cellneed enzymes in order to occur at rates sufficient for life. Since enzymes are selective for

their substrates and speed up only a few reactions from among many possibilities, the set of

enzymes made in a cell determines whichmetabolic pathwaysoccur in that cell.

Like all catalysts, enzymes work by lowering theactivation energy(Ea) for a reaction, thus

dramatically increasing therate of the reaction.As a result, products are formed faster and

reactions reach their equilibrium state more rapidly. Most enzyme reaction rates are millions of

times faster than those of comparable un-catalyzed reactions. As with all catalysts, enzymes are

not consumed by the reactions they catalyze, nor do they alter theequilibriumof these

reactions. However, enzymes do differ from most other catalysts in that they are highly specific

for their substrates. Enzymes are known to catalyze about 4,000 biochemical reactions.[3]A

fewRNAmolecules calledribozymesalso catalyze reactions, with an important example being
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some parts of theribosome.[4][5]Synthetic molecules calledartificial enzymesalso display

enzyme-like catalysis.[6]

Enzyme activity can be affected by other molecules.Inhibitorsare molecules that decrease

enzyme activity;activatorsare molecules that increase activity. Manydrugsandpoisonsare

enzyme inhibitors. Activity is also affected bytemperature,pressure,chemical environment(e.g.,pH), and theconcentrationof substrate. Some enzymes are used commercially, for

example, in the synthesis ofantibiotics.In addition, some household products use enzymes to

speed up biochemical reactions (e.g., enzymes in biologicalwashing powdersbreak down

protein orfatstains on clothes; enzymes inmeat tenderizersbreak down proteins into smaller

molecules, making the meat easier to chew).

Contents

[hide]

1 Etymology and history

2 Structures and mechanisms

o 2.1 Specificity

2.1.1 "Lock and key" model

o 2.2 Mechanisms

2.2.1 Transition state stabilization

2.2.2 Dynamics and function

o 2.3 Allosteric modulation

3 Cofactors and coenzymes

o 3.1 Cofactors

o 3.2 Coenzymes

4 Thermodynamics

5 Kinetics

6 Inhibition

7 Biological function

8 Control of activity

9 Involvement in disease

10 Naming conventions

11 Industrial applications

12 See also

13 References

14 Further reading
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zymeshttp://en.wikipedia.org/wiki/Enzyme#Allosteric_modulationhttp://en.wikipedia.org/wiki/Enzyme#Dynamics_and_functionhttp://en.wikipedia.org/wiki/Enzyme#Transition_state_stabilizationhttp://en.wikipedia.org/wiki/Enzyme#Mechanismshttp://en.wikipedia.org/wiki/Enzyme#.22Lock_and_key.22_modelhttp://en.wikipedia.org/wiki/Enzyme#Specificityhttp://en.wikipedia.org/wiki/Enzyme#Structures_and_mechanismshttp://en.wikipedia.org/wiki/Enzyme#Etymology_and_historyhttp://en.wikipedia.org/wiki/Enzymehttp://en.wikipedia.org/wiki/Papainhttp://en.wikipedia.org/wiki/Fathttp://en.wikipedia.org/wiki/Washing_powderhttp://en.wikipedia.org/wiki/Antibiotichttp://en.wikipedia.org/wiki/Concentrationhttp://en.wikipedia.org/wiki/PHhttp://en.wikipedia.org/wiki/Pressurehttp://en.wikipedia.org/wiki/Temperaturehttp://en.wikipedia.org/wiki/Poisonhttp://en.wikipedia.org/wiki/Drughttp://en.wikipedia.org/wiki/Enzyme_activatorhttp://en.wikipedia.org/wiki/Enzyme_inhibitorhttp://en.wikipedia.org/wiki/Enzyme#cite_note-6http://en.wikipedia.org/wiki/Artificial_enzymehttp://en.wikipedia.org/wiki/Enzyme#cite_note-4http://en.wikipedia.org/wiki/Enzyme#cite_note-4http://en.wikipedia.org/wiki/Ribosome


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15 External links

Etymology and history

Eduard Buchner

As early as the late 17th and early 18th centuries, the digestion ofmeatby stomach

secretions[7]and the conversion ofstarchtosugarsby plant extracts andsalivawere known.

However, the mechanism by which this occurred had not been identified.[8]

In 1833, French chemistAnselme Payendiscovered the first enzyme,diastase.A few decades

later, when studying thefermentationof sugar toalcoholbyyeast,Louis Pasteurcame to the

conclusion that this fermentation was catalyzed by a vital force contained within the yeast cells

called "ferments", which were thought to function only within living organisms. He wrote that

"alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not

with the death or putrefaction of the cells."[9]

In 1877,GermanphysiologistWilhelm Khne(18371900) first used the termenzyme,which

comes fromGreek, "in leaven", to describe this process.[10]The word enzymewas used

later to refer to nonliving substances such aspepsin,and the word fermentwas used to refer to

chemical activity produced by living organisms.

In 1897,Eduard Buchnersubmitted his first paper on the ability of yeast extracts that lacked any

living yeast cells to ferment sugar. In a series of experiments at theUniversity of Berlin,he

found that the sugar was fermented even when there were no living yeast cells in the

mixture.[11]He named the enzyme that brought about the fermentation of sucrose

"zymase".[12]In 1907, he received theNobel Prize in Chemistry"for his biochemical research

and his discovery of cell-free fermentation". Following Buchner's example, enzymes are usually

named according to the reaction they carry out. Typically, to generate the name of an enzyme,
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the suffix-aseis added to the name of itssubstrate(e.g.,lactaseis the enzyme that

cleaveslactose)or the type of reaction (e.g.,DNA polymeraseforms DNA polymers).[13]

Having shown that enzymes could function outside a living cell, the next step was to determine

their biochemical nature. Many early workers noted that enzymatic activity was associated with

proteins, but several scientists (such as Nobel laureateRichard Willsttter)argued that proteinswere merely carriers for the true enzymes and that proteinsper sewere incapable of

catalysis.[14]However, in 1926,James B. Sumnershowed that the enzymeureasewas a pure

protein and crystallized it; Sumner did likewise for the enzymecatalasein 1937. The conclusion

that pure proteins can be enzymes was definitively proved byNorthropandStanley,who

worked on the digestive enzymes pepsin (1930), trypsin and chymotrypsin. These three

scientists were awarded the 1946 Nobel Prize in Chemistry.[15]

This discovery that enzymes could be crystallized eventually allowed their structures to be

solved byx-ray crystallography.This was first done forlysozyme,an enzyme found in tears,

saliva andegg whitesthat digests the coating of some bacteria; the structure was solved by agroup led byDavid Chilton Phillipsand published in 1965.[16]This high-resolution structure of

lysozyme marked the beginning of the field ofstructural biologyand the effort to understand

how enzymes work at an atomic level of detail.

Structures and mechanisms

See also:Enzyme catalysis

Ribbon diagramshowinghuman carbonic anhydrase II.The grey sphere is thezinccofactor in the active site.

Diagram drawn fromPDB 1MOO.

Enzymes are in generalglobular proteinsand range from just 62 amino acid residues in size, for

themonomerof4-oxalocrotonate tautomerase,[17]to over 2,500 residues in the animalfatty acid
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://en.wikipedia.org/wiki/Enzyme#cite_note-14http://en.wikipedia.org/wiki/Richard_Willst%C3%A4tterhttp://en.wikipedia.org/wiki/Enzyme#cite_note-13http://en.wikipedia.org/wiki/DNA_polymerasehttp://en.wikipedia.org/wiki/Lactosehttp://en.wikipedia.org/wiki/Lactasehttp://en.wikipedia.org/wiki/Substrate_(biochemistry)http://en.wikipedia.org/wiki/-ase


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synthase.[18]A small number of RNA-based biological catalysts exist, with the most common

being theribosome;these are referred to as either RNA-enzymes orribozymes.The activities of

enzymes are determined by theirthree-dimensional structure.[19]However, although structure

does determine function, predicting a novel enzyme's activity just from its structure is a very

difficult problem that has not yet been solved.[20]

Most enzymes are much larger than the substrates they act on, and only a small portion of the

enzyme (around 24amino acids)is directly involved in catalysis.[21]The region that contains

these catalytic residues, binds the substrate, and then carries out the reaction is known as

theactive site.Enzymes can also contain sites that bindcofactors,which are needed for

catalysis. Some enzymes also have binding sites for small molecules, which are often direct

orindirectproducts or substrates of the reaction catalyzed. This binding can serve to increase

or decrease the enzyme's activity, providing a means forfeedbackregulation.

Like all proteins, enzymes are long, linear chains of amino acids that foldto produce athree-

dimensional product.Each unique amino acid sequence produces a specific structure, whichhas unique properties. Individual protein chains may sometimes group together to form a protein

complex.Most enzymes can bedenaturedthat is, unfolded and inactivatedby heating or

chemical denaturants, which disrupt thethree-dimensional structureof the protein. Depending

on the enzyme, denaturation may be reversible or irreversible.

Structures of enzymes with substrates or substrate analogs during a reaction may be obtained

usingTime resolved crystallographymethods.

Specificity

Enzymes are usually very specific as to which reactions they catalyze and thesubstratesthat

are involved in these reactions. Complementary shape, charge

andhydrophilic/hydrophobiccharacteristics of enzymes and substrates are responsible for this

specificity. Enzymes can also show impressive levels

ofstereospecificity,regioselectivityandchemoselectivity.[22]

Some of the enzymes showing the highest specificity and accuracy are involved in the copying

andexpressionof thegenome.These enzymes have "proof-reading" mechanisms. Here, an

enzyme such asDNA polymerasecatalyzes a reaction in a first step and then checks that the

product is correct in a second step.[23]This two-step process results in average error rates of

less than 1 error in 100 million reactions in high-fidelitymammalianpolymerases.[24]Similar

proofreading mechanisms are also found inRNA polymerase,[25]aminoacyl tRNA

synthetases[26]andribosomes.[27]

Whereas some enzymes have broad-specificity, as they can act on a relatively broad 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; this phenomenon is known asenzyme promiscuity.[28]
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ttp://en.wikipedia.org/wiki/Enzyme#cite_note-Tawfik10-28http://en.wikipedia.org/wiki/Enzyme#cite_note-Tawfik10-28http://en.wikipedia.org/wiki/Enzyme#cite_note-Tawfik10-28http://en.wikipedia.org/wiki/Enzyme_promiscuityhttp://en.wikipedia.org/wiki/Neutral_evolutionhttp://en.wikipedia.org/wiki/Enzyme#cite_note-27http://en.wikipedia.org/wiki/Ribosomehttp://en.wikipedia.org/wiki/Aminoacyl_tRNA_synthetasehttp://en.wikipedia.org/wiki/Aminoacyl_tRNA_synthetasehttp://en.wikipedia.org/wiki/Enzyme#cite_note-25http://en.wikipedia.org/wiki/Enzyme#cite_note-25http://en.wikipedia.org/wiki/RNA_polymerasehttp://en.wikipedia.org/wiki/Enzyme#cite_note-24http://en.wikipedia.org/wiki/Mammalhttp://en.wikipedia.org/wiki/Enzyme#cite_note-23http://en.wikipedia.org/wiki/DNA_polymerasehttp://en.wikipedia.org/wiki/Genomehttp://en.wikipedia.org/wiki/Gene_expressionhttp://en.wikipedia.org/wiki/Enzyme#cite_note-22http://en.wikipedia.org/wiki/Chemoselectivityhttp://en.wikipedia.org/wiki/Regioselectivityhttp://en.wikipedia.org/wiki/Stereospecificityhttp://en.wikipedia.org/wiki/Hydrophobichttp://en.wikipedia.org/wiki/Hydrophilichttp://en.wikipedia.org/wiki/Substrate_(biochemistry)http://en.wikipedia.org/wiki/Time_resolved_crystallographyhttp://en.wikipedia.org/wiki/Tertiary_structurehttp://en.wikipedia.org/wiki/Denaturation_(biochemistry)http://en.wikipedia.org/wiki/Protein_complexhttp://en.wikipedia.org/wiki/Protein_complexhttp://en.wikipedia.org/wiki/Tertiary_structurehttp://en.wikipedia.org/wiki/Tertiary_structurehttp://en.wikipedia.org/wiki/Protein_foldinghttp://en.wikipedia.org/wiki/Feedbackhttp://en.wikipedia.org/wiki/Enzyme#Metabolic_pathwayshttp://en.wikipedia.org/wiki/Cofactor_(biochemistry)http://en.wikipedia.org/wiki/Active_sitehttp://en.wikipedia.org/wiki/Enzyme#cite_note-21http://en.wikipedia.org/wiki/Amino_acidhttp://en.wikipedia.org/wiki/Enzyme#cite_note-20http://en.wikipedia.org/wiki/Enzyme#cite_note-19http://en.wikipedia.org/wiki/Quaternary_structurehttp://en.wikipedia.org/wiki/Ribozymehttp://en.wikipedia.org/wiki/Ribosomehttp://en.wikipedia.org/wiki/Enzyme#cite_note-18http://en.wikipedia.org/wiki/Fatty_acid_synthase


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"Lock and key" model

Enzymes are very specific, and it was suggested by theNobel laureateorganic chemistEmil

Fischerin 1894 that this was because both the enzyme and the substrate possess specific

complementary geometric shapes that fit exactly into one another.[29]This is often referred to as

"the lock and key" model. However, while this model explains enzyme specificity, it fails toexplain the stabilization of the transition state that enzymes achieve.

Diagrams to show the induced fit hypothesis of enzyme action

In 1958,Daniel Koshlandsuggested 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 the enzyme.[30]As a result, the substrate does not

simply bind to a rigid active site; the amino acidside-chainsthat 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 substratemoleculealso changes shape slightly as it

enters the active site.[31]The active site continues to change until the substrate is completely

bound, at which point the final shape and charge is determined.[32]Induced fit may enhance the

fidelity of molecular recognition in the presence of competition and noise via the conformational

proofreadingmechanism.[33]

Based on Fischer's lock-and-key model and Koshlands induced fit theory, theChous distorted

key theory for peptide drugswas proposed[34]to develop peptide drugs

againstHIV/AIDSandSARS.[35][36][37]

Mechanisms

Enzymes can act in several ways, all of which lower G

(Gibbs energy):

[38]

Lowering theactivation energyby creating an environment in which the transition state is

stabilized (e.g. straining the shape of a substrateby 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).
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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 correctorientation to react. Considering Halone overlooks this effect.

Increases in temperatures speed up reactions. Thus, temperature increases help the

enzyme function and develop the end product even faster. However, if heated too much, the

enzyme's shape deteriorates and the enzyme becomes denatured. Some enzymes like

thermolabile enzymes work best at low temperatures.

The function of a protein is dependent on its structure so that if the structure is disrupted, so

is its function.

It is interesting that thisentropiceffect involves destabilization of the ground state,[39]and its

contribution to catalysis is relatively small.

[40]

Transition state stabilization

The understanding of the origin of the reduction of Grequires one to find out how the

enzymes can stabilize its transition state more than the transition state of the uncatalyzed

reaction. It seems that the most effective way for reaching large stabilization is the use of

electrostatic effects, in particular, when having a relatively fixed polar environment that is

oriented toward the charge distribution of the transition state.[41]Such an environment does not

exist in the uncatalyzed reaction in water.

Dynamics and function

See also:Protein dynamics

The internal dynamics of enzymes has been suggested to be linked with their mechanism of

catalysis.[42][43][44]Internal dynamics are the movement of parts of the enzyme's structure, such

as individual amino acid residues, a group of amino acids, or even an entireprotein domain.

These movements occur at various time-scales ranging fromfemtosecondsto seconds.

Networks of protein residues throughout an enzyme's structure can contribute to catalysis

through dynamic motions.[45][46][47][48]This is simply seen in thekinetic schemeof the combined

process, enzymatic activity and dynamics; this scheme can have several

independentMichaelis-Menten-like reaction pathways that are connected through fluctuation

rates.[49][50][51]

Protein motions are vital to many enzymes, but whether small and fast vibrations, or larger and

slower conformational movements are more important depends on the type of reaction involved.

However, although these movements are important in binding and releasing substrates and

products, it is not clear if protein movements help to accelerate the chemical steps in enzymatic
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reactions.[52]These new insights also have implications in understanding allosteric effects and

developing new medicines.

Allosteric modulation

Allosteric transition of an enzyme between R and T states, stabilized by an agonist, an inhibitor and a substrate

(theMWC model)

Main article:Allosteric regulation

Allosteric sites are sites on the enzyme that bind to molecules in the cellular environment. The

sites form weak, noncovalent bonds with these molecules, causing a change in the

conformation of the enzyme. This change in conformation translates to the active site, which

then affects the reaction rate of the enzyme.[53]Allosteric interactions can both inhibit and

activate enzymes and are a common way that enzymes are controlled in the body.[54]

Cofactors and coenzymes

Main articles:Cofactor (biochemistry)andCoenzyme

Cofactors

Some enzymes do not need any additional components to show full activity. However, others

require non-protein molecules called cofactors to be bound for activity.[55]Cofactors can be

eitherinorganic(e.g.,metal ionsandiron-sulfur clusters)ororganic

compounds(e.g.,flavinandheme). Organic cofactors can be eitherprosthetic groups,which are

tightly bound to an enzyme, orcoenzymes,which are released from the enzyme's active site

during the reaction. Coenzymes includeNADH,NADPHandadenosine triphosphate.These

molecules transfer chemical groups between enzymes.[56]

An example of an enzyme that contains a cofactor iscarbonic anhydrase,and is shown in

theribbon diagramabove with a zinc cofactor bound as part of its active site.[57]These tightly

bound molecules are usually found in the active site and are involved in catalysis. For example,

flavin and heme cofactors are often involved inredoxreactions.

Enzymes that require a cofactor but do not have one bound are

called apoenzymesor apoproteins. An apoenzyme together with its cofactor(s) is called

a holoenzyme(this is the active form). Most cofactors are not covalently attached to an enzyme,
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but are very tightly bound. However, organic prosthetic groups can be covalently bound

(e.g.,biotinin the enzymepyruvate carboxylase). The term "holoenzyme" can also be applied to

enzymes that contain multiple protein subunits, such as theDNA polymerases;here the

holoenzyme is the complete complex containing all the subunits needed for activity.

Coenzymes

Space-filling modelof the coenzyme NADH

Coenzymes are small organic molecules that can be loosely or tightly bound to an enzyme.

Tightly bound coenzymes can be called prosthetic groups. Coenzymes transport chemical

groups from one enzyme to another.[58]Some of these chemicals such

asriboflavin,thiamineandfolic acidarevitamins(compounds that cannot be synthesized by the

body and must be acquired from the diet). The chemical groups carried include thehydrideion

(H-) carried byNAD or NADP+,the phosphate group carried byadenosine triphosphate,the

acetyl group carried bycoenzyme A,formyl, methenyl or methyl groups carried byfolic acidand

the methyl group carried byS-adenosylmethionine.

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 700 enzymes are known to use the

coenzyme NADH.[59]

Coenzymes are usually continuously regenerated and their concentrations maintained at a

steady level inside the cell: for example, NADPH is regenerated through thepentose phosphate

pathwayand S-adenosylmethionine bymethionine adenosyltransferase.This continuous

regeneration means that even small amounts of coenzymes are used very intensively. For

example, the human body turns over its own weight in ATP each day.[60]

Thermodynamics
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The energies of the stages of achemical reaction.Substrates need a lot of potential energy to reach atransition

state,which then decays into products. The enzyme stabilizes the transition state, reducing the energy needed to

form products.

Main articles:Activation energy,Thermodynamic equilibrium,andChemical equilibrium

As all catalysts, enzymes do not alter the position of the chemical equilibrium of the reaction.

Usually, in the presence of an enzyme, the reaction runs in the same direction as it would

without the enzyme, just more quickly. However, in the absence of the enzyme, other possible

uncatalyzed, "spontaneous" reactions might lead to different products, because in those

conditions this different product is formed faster.

Furthermore, enzymes can couple two or more reactions, so that a thermodynamically favorable

reaction can be used to "drive" a thermodynamically unfavorable one. For example, the

hydrolysis ofATPis often used to drive other chemical reactions.[61]

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 anhydrasecatalyzes its

reaction in either direction depending on the concentration of its reactants.

(intissues;high CO2concentration)

(inlungs;low CO2concentration)

Nevertheless, if the equilibrium is greatly displaced in one direction, that is, in a

veryexergonicreaction, the reaction is in effect irreversible. Under these conditions, the

enzyme will, in fact, catalyze the reaction only in the thermodynamically allowed

direction.

Kinetics

Main article:Enzyme kinetics
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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 commonly obtained fromenzyme

assays,where since the 90s, the dynamics of many enzymes are studied on the level

ofindividual molecules.

In 1902Victor Henriproposed a quantitative theory of enzyme kinetics,

[62]

but hisexperimental data were not useful because the significance of the hydrogen ion

concentration was not yet appreciated. AfterPeter Lauritz Srensenhad defined the

logarithmic pH-scale and introduced the concept of buffering in 1909[63]the German

chemistLeonor Michaelisand his Canadian postdocMaud Leonora Mentenrepeated

Henri's experiments and confirmed his equation, which is referred to asHenri-Michaelis-

Menten kinetics(termed alsoMichaelis-Menten kinetics).[64]Their work was further

developed byG. E. BriggsandJ. B. S. Haldane,who derived kinetic equations that are

still widely considered today a starting point in solving enzymatic activity.[65]

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. Note that the

simpleMichaelis Menten mechanismfor the enzymatic activity is considered today a

basic idea, where many examples show that the enzymatic activity involves structural

dynamics. This is incorporated in the enzymatic mechanism while introducing several

Michaelis Menten pathways that are connected with fluctuating

rates.[49][50][51]Nevertheless, there is a mathematical relation connecting the behavior

obtained from the basic Michaelis Menten mechanism (that was indeed proved correct

in many experiments) with the generalized Michaelis Menten mechanisms involvingdynamics and activity;[66]this means that the measured activity of enzymes on the level

of many enzymes may be explained with the simple Michaelis-Menten equation, yet, the

actual activity of enzymes is richer and involves structural dynamics.
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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, theuncatalyzed decarboxylation oforotidine 5'-monophosphatehas a half life of 78 million

years. However, when the enzymeorotidine 5'-phosphate decarboxylaseis added, the

same process takes just 25 milliseconds.[67]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 when [S] is low. 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 reaction rate (Vmax) of the enzyme, all the enzyme active sites are bound to

substrate, and the amount of ES complex is the same as the total amount of enzyme.

However, Vmaxis 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 theMichaelis-

Menten constant(Km), which is the substrate concentration required for an enzyme to

reach one-half its maximum reaction rate; generally, each enzyme has a

characteristic Kmfor a given substrate. Another useful constant is kcat, which is the rate

of product formation handled by one active site and is generally given in units of inverse

seconds.

The efficiency of an enzyme can be expressed in terms of kcat/Km. This is also called the

specificity constant and incorporates therate constantsfor 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 108to 109(M1s1). At this point every collision of the enzyme with its
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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

perfector kinetically perfect. Example of such enzymes aretriose-phosphate

isomerase,carbonic anhydrase,acetylcholinesterase,catalase,fumarase, -lactamase,

andsuperoxide dismutase.

Michaelis-Menten kinetics relies on thelaw of mass action,which is derived from the

assumptions of freediffusionand thermodynamically driven random collision. However,

many biochemical or cellular processes deviate significantly from these conditions,

because ofmacromolecular crowding,phase-separation of the

enzyme/substrate/product, or one or two-dimensional molecular movement.[68]In these

situations, afractalMichaelis-Menten kineticsmay be applied.[69][70][71][72]

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 theirsubstrate in and pre-orienting them by using dipolar electric fields. Other models invoke

a quantum-mechanicaltunnelingexplanation, whereby a proton or an electron can

tunnel through activation barriers, although for proton tunneling this model remains

somewhat controversial.[73][74]Quantum tunneling for protons has been observed

intryptamine.[75]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
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Competitive inhibitors bind reversibly to the enzyme, preventing the binding of substrate. On the other

hand, binding of substrate prevents binding of the inhibitor. Substrate and inhibitor compete for the

enzyme.

Types of inhibition. This classification was introduced byW.W. Cleland.[76]

Main article:Enzyme inhibitor

Enzyme reaction rates can be decreased by various types ofenzyme inhibitors.

Competitive inhibition

In competitive inhibition, the inhibitor and substrate compete for the enzyme (i.e., they

can not bind at the same time).[77]Often competitive inhibitors strongly resemble the real

substrate of the enzyme. For example,methotrexateis a competitive inhibitor of the

enzymedihydrofolate reductase,which catalyzes the reduction

ofdihydrofolatetotetrahydrofolate.The similarity between the structures of folic acid and
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this drug are shown in the figure to the rightbottom. In some cases, the inhibitor can

bind to a site other than the binding-site of the usual substrate and exert anallosteric

effectto change the shape of the usual binding-site. For example,strychnineacts as an

allosteric inhibitor of the glycine receptor in the mammalian spinal cord and brain stem.

Glycine is a major post-synaptic inhibitory neurotransmitter with a specific receptor site.

Strychnine binds to an alternate site that reduces the affinity of the glycine receptor for

glycine, resulting in convulsions due to lessened inhibition by the glycine.[78]In

competitive inhibition the maximal rate of the reaction is not changed, but higher

substrate concentrations are required to reach a given maximum rate, increasing the

apparent Km.

Uncompetitive inhibition

In uncompetitive inhibition, the inhibitor cannot bind to the free enzyme, only to the ES-

complex. The EIS-complex thus formed is enzymatically inactive. This type of inhibition

is rare, but may occur in multimeric enzymes.

Non-competitive inhibition

Non-competitive inhibitors can bind to the enzyme at the binding site at the sam

bio catalyst

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