Enzymes are proteins that catalyze (i.e., increase the rates of) chemical reactions.

In enzymatic
reactions, the molecules at the beginning of the process are called substrates, and the enzyme
converts them into different molecules, called the products. Almost all processes in a biological
cell need enzymes to occur at significant rates. Since enzymes are selective for their substrates
and speed up only a few reactions from among many possibilities, the set of enzymes made in a
cell determines which metabolic pathways occur in that cell.

Like all catalysts, enzymes work by lowering the activation energy (Ea‡) for a reaction, thus
dramatically increasing the rate of the reaction. Most enzyme reaction rates are millions of times
faster than those of comparable un-catalyzed reactions. As with all catalysts, enzymes are not
consumed by the reactions they catalyze, nor do they alter the equilibrium of these reactions.
However, enzymes do differ from most other catalysts by being much more specific. Enzymes
are known to catalyze about 4,000 biochemical reactions.[3] A few RNA molecules called
ribozymes also catalyze reactions, with an important example being some parts of the ribosome.
[4][5]
Synthetic molecules called artificial enzymes also display enzyme-like catalysis.[6]

Enzyme activity can be affected by other molecules. Inhibitors are molecules that decrease
enzyme activity; activators are molecules that increase activity. Many drugs and poisons are
enzyme inhibitors. Activity is also affected by temperature, chemical environment (e.g., pH), and
the concentration of substrate. Some enzymes are used commercially, for example, in the
synthesis of antibiotics. In addition, some household products use enzymes to speed up
biochemical reactions (e.g., enzymes in biological washing powders break down protein or fat
stains on clothes; enzymes in meat tenderizers break down proteins, making the meat easier to
chew).

Etymology and history

As early as the late 18th and early 19th centuries, the digestion of meat by stomach secretions
and the conversion of starch to sugars by plant extracts and saliva were known. However, the
mechanism by which this occurred had not been identified.

In the 19th century, when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur
came to the conclusion that this fermentation was catalyzed by a vital force contained within the
yeast cells called "ferments", which were thought to function only within living organisms. He
wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast
cells, not with the death or putrefaction of the cells."

In 1877, German physiologist Wilhelm Kühne (1837–1900) first used the term enzyme, which
comes from Greek ενζυμον, "in leaven", to describe this process. The word enzyme was used
later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to
chemical activity produced by living organisms.

In 1897, Eduard Buchner submitted his first paper on the ability of yeast extracts that lacked any
living yeast cells to ferment sugar. In a series of experiments at the University of Berlin, he
found that the sugar was fermented even when there were no living yeast cells in the mixture. He
named the enzyme that brought about the fermentation of sucrose "zymase".In 1907, he received
the Nobel Prize in Chemistry "for his biochemical research and his discovery of cell-free
fermentation". Following Buchner's example, enzymes are usually named according to the
reaction they carry out. Typically, to generate the name of an enzyme, the suffix -ase is added to
the name of its substrate (e.g., lactase is the enzyme that cleaves lactose) or the type of reaction
(e.g., DNA polymerase forms DNA polymers).

Having shown that enzymes could function outside a living cell, the next step was to determine
their biochemical nature. Many early workers noted that enzymatic activity was associated with
proteins, but several scientists (such as Nobel laureate Richard Willstätter) argued that proteins
were merely carriers for the true enzymes and that proteins per se were incapable of catalysis.
However, in 1926, James B. Sumner showed that the enzyme urease was a pure protein and
crystallized it; Sumner did likewise for the enzyme catalase in 1937. The conclusion that pure
proteins can be enzymes was definitively proved by Northrop and Stanley, who worked on the
digestive enzymes pepsin (1930), trypsin and chymotrypsin. These three scientists were awarded
the 1946 Nobel Prize in Chemistry.

This discovery that enzymes could be crystallized eventually allowed their structures to be
solved by x-ray crystallography. This was first done for lysozyme, an enzyme found in tears,
saliva and egg whites that digests the coating of some bacteria; the structure was solved by a
group led by David Chilton Phillips and published in 1965. 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.

Structures and mechanisms

Ribbon diagram showing carbonic anhydrase II. The grey sphere is the zinc cofactor in the active
site. Diagram drawn from PDB 1MOO.

Enzymes are generally globular proteins and range from just 62 amino acid residues in size, for
the monomer of 4-oxalocrotonate tautomerase[ to over 2,500 residues in the animal fatty acid
synthase. A small number of RNA-based biological catalysts exist, with the most common being
the ribosome; these are referred to as either RNA-enzymes or ribozymes. The activities of
enzymes are determined by their three-dimensional structure. 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.

Most enzymes are much larger than the substrates they act on, and only a small portion of the
enzyme (around 3–4 amino acids) is directly involved in catalysis.] The region that contains these
catalytic residues, binds the substrate, and then carries out the reaction is known as the active
site. Enzymes can also contain sites that bind cofactors, which are needed for catalysis. Some
enzymes also have binding sites for small molecules, which are often direct or indirect products
or substrates of the reaction catalyzed. This binding can serve to increase or decrease the
enzyme's activity, providing a means for feedback regulation.

Like all proteins, enzymes are long, linear chains of amino acids that fold to produce a three-
dimensional product. Each unique amino acid sequence produces a specific structure, which has
unique properties. Individual protein chains may sometimes group together to form a protein
complex. Most enzymes can be denatured—that is, unfolded and inactivated—by heating or
chemical denaturants, which disrupt the three-dimensional structure of the protein. Depending on
the enzyme, denaturation may be reversible or irreversible.

Structures of enzymes in complex with substrates or substrate analogs during a reaction may be
obtained using Time resolved crystallography methods.

Specificity

Enzymes are usually very specific as to which reactions they catalyze and the substrates that are
involved in these reactions. Complementary shape, charge and hydrophilic/hydrophobic
characteristics of enzymes and substrates are responsible for this specificity. Enzymes can also
show impressive levels of stereospecificity, regioselectivity and chemoselectivity.[21]

Some of the enzymes showing the highest specificity and accuracy are involved in the copying
and expression of the genome. These enzymes have "proof-reading" mechanisms. Here, an
enzyme such as DNA polymerase catalyzes a reaction in a first step and then checks that the
product is correct in a second step. 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 synthetasesand
ribosomes.

Some enzymes that produce secondary metabolites are described as promiscuous, as they can act
on a relatively broad range of different substrates. It has been suggested that this broad substrate
specificity is important for the evolution of new biosynthetic pathways.
"Lock and key" model

Enzymes are very specific, and it was suggested by the Nobel laureate organic chemist 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. 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.

Diagrams to show the induced fit hypothesis of enzyme action.

In 1958, Daniel Koshland suggested a modification to the lock and key model: since enzymes are
rather flexible structures, the active site is continually reshaped by interactions with the substrate
as the substrate interacts with the enzyme. As a result, the substrate does not simply bind to a
rigid active site; the amino acid side chains which make up the active site are 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 the substrate is completely bound, at which point the final
shape and charge is determined.

Mechanisms

Enzymes can act in several ways, all of which lower ΔG‡:

 Lowering the activation energy by creating an environment in which the transition state is
stabilized (e.g. straining the shape of a substrate—by binding the transition-state
conformation of the substrate/product molecules, the enzyme distorts the bound
substrate(s) into their transition state form, thereby reducing the amount of energy
required to complete the transition).
 Lowering the energy of the transition state, but without distorting the substrate, by
creating an environment with the opposite charge distribution to that of the transition
state.
 Providing an alternative pathway. For example, temporarily reacting with the substrate to
form an intermediate ES complex, which would be impossible in the absence of the
enzyme.
  Reducing the reaction entropy change by bringing substrates together in the correct
orientation to react. Considering ΔH‡ alone overlooks this effect.
 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 only when the temperature comes back to normal
does the enzyme regain its shape. Some enzymes like thermolabile enzymes work best at
low temperatures.

Interestingly, this entropic effect involves destabilization of the ground state, and its contribution
to catalysis is relatively small.

Transition State Stabilization

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

Dynamics and function

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

Allosteric modulation

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

and a substrate (the MWC 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.[44] Allosteric interactions can both inhibit and activate enzymes and
are a common way that enzymes are controlled in the body.[45]

Cofactors and coenzymes

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. Cofactors can be either
inorganic (e.g., metal ions and iron-sulfur clusters) or organic compounds (e.g., flavin and
heme). Organic cofactors can be either prosthetic groups, which are tightly bound to an enzyme,
or coenzymes, which are released from the enzyme's active site during the reaction. Coenzymes
include NADH, NADPH and adenosine triphosphate. These molecules transfer chemical groups
between enzymes.

An example of an enzyme that contains a cofactor is carbonic anhydrase, and is shown in the
ribbon diagram above with a zinc cofactor bound as part of its active site. 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 in redox reactions.

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

Coenzymes

Space-filling model of the coenzyme NADH

Coenzymes are small organic molecules that transport chemical groups from one enzyme to
another. Some of these chemicals such as riboflavin, thiamine and folic acid are vitamins
(compounds which cannot be synthesized by the body and must be acquired from the diet). The
chemical groups carried include the hydride ion (H-) carried by NAD or NADP+, the phosphate group
carried by adenosine triphosphate, the acetyl group carried by coenzyme A, formyl, methenyl or
methyl groups carried by folic acid and the methyl group carried by S-adenosylmethionine.

Since coenzymes are chemically changed as a consequence of enzyme action, it is 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.

Coenzymes are usually continuously 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. 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.

Thermodynamics

The energies of the stages of a chemical reaction. Substrates need a lot of energy to reach a
transition state, which then decays into products. The enzyme stabilizes the transition state,
reducing the energy needed to form products.
Main articles: Activation energy, Thermodynamic equilibrium, and Chemical 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 of ATP is often used to drive other chemical reactions.
Enzymes catalyze the forward and backward reactions equally. They do not alter the equilibrium
itself, but only the speed at which it is reached. For example, carbonic anhydrase catalyzes its
reaction in either direction depending on the concentration of its reactants.

(in tissues; high CO2 concentration)

(in lungs; low CO2 concentration)

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

Kinetics

Mechanism for a single substrate enzyme catalyzed reaction. The enzyme (E) binds a substrate
(S) and produces a product (P).

Enzyme kinetics is the investigation of how enzymes bind substrates and turn them into
products. The rate data used in kinetic analyses are obtained from enzyme assays.

In 1902 Victor Henri proposed a quantitative theory of enzyme kinetics, but his experimental
data were not useful because the significance of the hydrogen ion concentration was not yet
appreciated. After Peter Lauritz Sørensen had defined the logarithmic pH-scale and introduced
the concept of buffering in 1909 the German chemist Leonor Michaelis and his Canadian
postdoc Maud Leonora Menten repeated Henri's experiments and confirmed his equation which).
Their work was further developed by G. E. Briggs and J. B. S. Haldane, who derived kinetic
equations that are still widely used today.

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.
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 uncatalyzed
decarboxylation of orotidine 5'-monophosphate has a half life of 78 million years. However,
when the enzyme orotidine 5'-phosphate decarboxylase is added, the same process takes just 25
milliseconds. Enzyme rates depend on solution conditions and substrate concentration.
Conditions that denature the protein abolish enzyme activity, such as high temperatures,
extremes of pH or high salt concentrations, while raising substrate concentration tends to
increase activity. To find the maximum speed of an enzymatic reaction, the substrate
concentration is increased until a constant rate of product formation is seen. This is shown in the
saturation curve on the right. Saturation happens because, as substrate concentration increases,
more and more of the free enzyme is converted into the substrate-bound ES form. At the
maximum velocity (Vmax) of the enzyme, all the enzyme active sites are bound to substrate, and
the amount of ES complex is the same as the total amount of enzyme. However, Vmax is only one
kinetic constant of enzymes. The amount of substrate needed to achieve a given rate of reaction
is also important. This is given by the Michaelis-Menten constant (Km), which is the substrate
concentration required for an enzyme to reach one-half its maximum velocity. Each enzyme has
a characteristic Km for a given substrate, and this can show how tight the binding of the substrate
is to the enzyme. Another useful constant is kcat, which is the number of substrate molecules
handled by one active site per second.

The efficiency of an enzyme can be expressed in terms of kcat/Km. This is also called the
specificity constant and incorporates the rate constants for all steps in the reaction. Because the
specificity constant reflects both affinity and catalytic ability, it is useful for comparing different
enzymes against each other, or the same enzyme with different substrates. The theoretical
maximum for the specificity constant is called the diffusion limit and is about 108 to 109 (M−1
s−1). At this point every collision of the enzyme with its substrate will result in catalysis, and the
rate of product formation is not limited by the reaction rate but by the diffusion rate. Enzymes
with this property are called catalytically perfect or kinetically perfect. Example of such enzymes
are triose-phosphate isomerase, carbonic anhydrase, acetylcholinesterase, catalase, fumarase, β-
lactamase, and superoxide dismutase.
Michaelis-Menten kinetics relies on the law of mass action, which is derived from the
assumptions of free diffusion and thermodynamically driven random collision. However, many
biochemical or cellular processes deviate significantly from these conditions, because of
macromolecular crowding, phase-separation of the enzyme/substrate/product, or one or two-
dimensional molecular movement. In these situations, a fractal Michaelis-Menten kinetics may
be applied.

Some enzymes operate with kinetics which are faster than diffusion rates, which would seem to
be impossible. Several mechanisms have been invoked to explain this phenomenon. Some
proteins are believed to accelerate catalysis by drawing their substrate in and pre-orienting them
by using dipolar electric fields. Other models invoke a quantum-mechanical tunneling
explanation, whereby a proton or an electron can tunnel through activation barriers, although for
proton tunneling this model remains somewhat controversial. Quantum tunneling for protons has
been observed in tryptamine. 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

Competitive inhibitors bind reversibly to the enzyme, preventing the binding of substrate. On the
other hand, binding of substrate prevents binding of the inhibitor. Substrate and inhibitor
compete for the enzyme.
Types of inhibition. This classification was introduced by W.W. Cleland.[66]
Main article: Enzyme inhibitor

Enzyme reaction rates can be decreased by various types of enzyme inhibitors.

Competitive inhibition

In competitive inhibition, the inhibitor and substrate compete for the enzyme (i.e., they can not
bind at the same time).[67] Often competitive inhibitors strongly resemble the real substrate of the
enzyme. For example, methotrexate is a competitive inhibitor of the enzyme dihydrofolate
reductase, which catalyzes the reduction of dihydrofolate to tetrahydrofolate. The similarity
between the structures of folic acid and this drug are shown in the figure to the right bottom.
Note that binding of the inhibitor need not be to the substrate binding site (as frequently stated),
if binding of the inhibitor changes the conformation of the enzyme to prevent substrate binding
and vice versa. In competitive inhibition the maximal velocity of the reaction is not changed, but
higher substrate concentrations are required to reach a given velocity, increasing the apparent
Km.
Uncompetitive inhibition

In uncompetitive inhibition the inhibitor can not bind to the free enzyme, but only to the ES-
complex. The EIS-complex thus formed is enzymatically inactive. This type of inhibition is rare,
but may occur in multimeric enzymes.

Non-competitive inhibition

Non-competitive inhibitors can bind to the enzyme at the same time as the substrate, i.e. they
never bind to the active site. Both the EI and EIS complexes are enzymatically inactive. Because
the inhibitor can not be driven from the enzyme by higher substrate concentration (in contrast to
competitive inhibition), the apparent Vmax changes. But because the substrate can still bind to the
enzyme, the Km stays the same.

Mixed inhibition

This type of inhibition resembles the non-competitive, except that the EIS-complex has residual
enzymatic activity.

In many organisms inhibitors may act as part of a feedback mechanism. If an enzyme produces
too much of one substance in the organism, that substance may act as an inhibitor for the enzyme
at the beginning of the pathway that produces it, causing production of the substance to slow
down or stop when there is sufficient amount. This is a form of negative feedback. Enzymes
which are subject to this form of regulation are often multimeric and have allosteric binding sites
for regulatory substances. Their substrate/velocity plots are not hyperbolar, but sigmoidal (S-
shaped).

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.

Irreversible inhibitors react with the enzyme and form a covalent adduct with the protein. The
inactivation is irreversible. These compounds include eflornithine a drug used to treat the
parasitic disease sleeping sickness.[68] Penicillin and Aspirin also act in this manner. With these
drugs, the compound is bound in the active site and the enzyme then converts the inhibitor into
an activated form that reacts irreversibly with one or more amino acid residues.

Uses of inhibitors
Since inhibitors modulate the function of enzymes they are often used as drugs. An common
example of an inhibitor that is used as a drug is aspirin, which inhibits the COX-1 and COX-2
enzymes that produce the inflammation messenger prostaglandin, thus suppressing pain and
inflammation. However, other enzyme inhibitors are poisons. For example, the poison cyanide is
an irreversible enzyme inhibitor that combines with the copper and iron in the active site of the
enzyme cytochrome c oxidase and blocks cellular respiration.[69]

[edit] Biological function

Enzymes serve a wide variety of functions inside living organisms. They are indispensable for
signal transduction and cell regulation, often via kinases and phosphatases.[70] They also generate
movement, with myosin hydrolysing ATP to generate muscle contraction and also moving cargo
around the cell as part of the cytoskeleton.[71] Other ATPases in the cell membrane are ion pumps
involved in active transport. Enzymes are also involved in more exotic functions, such as
luciferase generating light in fireflies.[72] Viruses can also contain enzymes for infecting cells,
such as the HIV integrase and reverse transcriptase, or for viral release from cells, like the
influenza virus neuraminidase.

An important function of enzymes is in the digestive systems of animals. Enzymes such as

amylases and proteases break down large molecules (starch or proteins, respectively) into
smaller ones, so they can be absorbed by the intestines. Starch molecules, for example, are too
large to be absorbed from the intestine, but enzymes hydrolyse the starch chains into smaller
molecules such as maltose and eventually glucose, which can then be absorbed. Different
enzymes digest different food substances. In ruminants which have herbivorous diets,
microorganisms in the gut produce another enzyme, cellulase to break down the cellulose cell
walls of plant fiber.[73]

Glycolytic enzymes and their functions in the metabolic pathway of glycolysis

Several enzymes can work together in a specific order, creating metabolic pathways. In a
metabolic pathway, one enzyme takes the product of another enzyme as a substrate. After the
catalytic reaction, the product is then passed on to another enzyme. Sometimes more than one
enzyme can catalyze the same reaction in parallel, this can allow more complex regulation: with
for example a low constant activity being provided by one enzyme but an inducible high activity
from a second enzyme.

Enzymes determine what steps occur in these pathways. Without enzymes, metabolism would
neither progress through the same steps, nor be fast enough to serve the needs of the cell. Indeed,
a metabolic pathway such as glycolysis could not exist independently of enzymes. Glucose, for
example, can react directly with ATP to become phosphorylated at one or more of its carbons. In
the absence of enzymes, this occurs so slowly as to be insignificant. However, if hexokinase is
added, these slow reactions continue to take place except that phosphorylation at carbon 6 occurs
so rapidly that if the mixture is tested a short time later, glucose-6-phosphate is found to be the
only significant product. Consequently, the network of metabolic pathways within each cell
depends on the set of functional enzymes that are present.

[edit] Control of activity

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

1. Enzyme production (transcription and translation of enzyme genes) can be enhanced or

diminished by a cell in response to changes in the cell's environment. This form of gene
regulation is called enzyme induction and inhibition (see enzyme induction). For
example, bacteria may become resistant to antibiotics such as penicillin because enzymes
called beta-lactamases are induced that hydrolyse the crucial beta-lactam ring within the
penicillin molecule. Another example are enzymes in the liver called cytochrome P450
oxidases, which are important in drug metabolism. Induction or inhibition of these
enzymes can cause drug interactions.
2. Enzymes can be compartmentalized, with different metabolic pathways occurring in
different cellular compartments. For example, fatty acids are synthesized by one set of
enzymes in the cytosol, endoplasmic reticulum and the Golgi apparatus and used by a
different set of enzymes as a source of energy in the mitochondrion, through β-oxidation.
[74]

3. Enzymes can be regulated by inhibitors and activators. For example, the end product(s)
of a metabolic pathway are often inhibitors for one of the first enzymes of the pathway
(usually the first irreversible step, called committed step), thus regulating the amount of
end product made by the pathways. Such a regulatory mechanism is called a negative
feedback mechanism, because the amount of the end product produced is regulated by its
own concentration. Negative feedback mechanism can effectively adjust the rate of
synthesis of intermediate metabolites according to the demands of the cells. This helps
allocate materials and energy economically, and prevents the manufacture of excess end
products. The control of enzymatic action helps to maintain a stable internal environment
in living organisms.
4. Enzymes can be regulated through post-translational modification. This can include
phosphorylation, myristoylation and glycosylation. For example, in the response to
insulin, the phosphorylation of multiple enzymes, including glycogen synthase, helps
control the synthesis or degradation of glycogen and allows the cell to respond to changes
 in blood sugar.[75] 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.
5. Some enzymes may become activated when localized to a different environment (e.g.
from a reducing (cytoplasm) to an oxidizing (periplasm) environment, high pH to low pH
etc.). For example, hemagglutinin in the influenza virus is activated by a conformational
change caused by the acidic conditions, these occur when it is taken up inside its host cell
and enters the lysosome.[76]

[edit] Involvement in disease

Phenylalanine hydroxylase. Created from PDB 1KW0

Since the tight control of enzyme activity is essential for homeostasis, any malfunction
(mutation, overproduction, underproduction or deletion) of a single critical enzyme can lead to a
genetic disease. The importance of enzymes is shown by the fact that a lethal illness can be
caused by the malfunction of just one type of enzyme out of the thousands of types present in our
bodies.

One example is the most common type of phenylketonuria. A mutation of a single amino acid in
the enzyme phenylalanine hydroxylase, which catalyzes the first step in the degradation of
phenylalanine, results in build-up of phenylalanine and related products. This can lead to mental
retardation if the disease is untreated.[77]

Another example is when germline mutations in genes coding for DNA repair enzymes cause
hereditary cancer syndromes such as xeroderma pigmentosum. Defects in these enzymes cause
cancer since the body is less able to repair mutations in the genome. This causes a slow
accumulation of mutations and results in the development of many types of cancer in the
sufferer.

[edit] Naming conventions

An enzyme's name is often derived from its substrate or the chemical reaction it catalyzes, with
the word ending in -ase. Examples are lactase, alcohol dehydrogenase and DNA polymerase.
This may result in different enzymes, called isozymes, with the same function having the same
basic name. Isoenzymes have a different amino acid sequence and might be distinguished by
their optimal pH, kinetic properties or immunologically. Furthermore, the normal physiological
reaction an enzyme catalyzes may not be the same as under artificial conditions. This can result
in the same enzyme being identified with two different names. E.g. Glucose isomerase, used
industrially to convert glucose into the sweetener fructose, is a xylose isomerase in vivo.

The International Union of Biochemistry and Molecular Biology have developed a nomenclature
for enzymes, the EC numbers; each enzyme is described by a sequence of four numbers preceded
by "EC". The first number broadly classifies the enzyme based on its mechanism.

The top-level classification is

 EC 1 Oxidoreductases: catalyze oxidation/reduction reactions

 EC 2 Transferases: transfer a functional group (e.g. a methyl or phosphate group)
 EC 3 Hydrolases: catalyze the hydrolysis of various bonds
 EC 4 Lyases: cleave various bonds by means other than hydrolysis and oxidation
 EC 5 Isomerases: catalyze isomerization changes within a single molecule
 EC 6 Ligases: join two molecules with covalent bonds.

The complete nomenclature can be browsed at http://www.chem.qmul.ac.uk/iubmb/enzyme/.

According to the naming conventions, enzymes are generally classified into six main family
classes and many sub-family classes. Some web-servers, e.g., EzyPred [78] and bioinformatics
tools have been developed to predict which main family class [79] and sub-family class [80] [81] an
enzyme molecule belongs to according to its sequence information alone via the pseudo amino
acid composition.

[edit] 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 catalyze and also by their lack of stability in organic solvents and
at high temperatures. Consequently, protein engineering is an active area of research and
involves attempts to create new enzymes with novel properties, either through rational design or
in vitro evolution.[82][83] These efforts have begun to be successful, and a few enzymes have now
been desiged "from scratch" to catalyze reactions that do not occur in nature.[84]

Application Enzymes used Uses

Food processing Amylases from fungi and Production of sugars from
plants. starch, such as in making
high-fructose corn syrup.[85]
In baking, catalyze
 breakdown of starch in the
flour to sugar. Yeast
fermentation of sugar
produces the carbon dioxide
that raises the dough.
Amylases catalyze the release of simple Biscuit manufacturers use
sugars from starch Proteases them to lower the protein
level of flour.
Baby foods Trypsin To predigest baby foods.
They degrade starch and
Enzymes from barley are proteins to produce simple
released during the mashing sugar, amino acids and
stage of beer production. peptides that are used by
yeast for fermentation.
Brewing industry Widely used in the brewing
Industrially produced barley process to substitute for the
enzymes natural enzymes found in
barley.
Amylase, glucanases, Split polysaccharides and
proteases proteins in the malt.
Betaglucanases and Improve the wort and beer
arabinoxylanases filtration characteristics.
Germinating barley used for malt. Low-calorie beer and
Amyloglucosidase and
adjustment of
pullulanases
fermentability.
Remove cloudiness
Proteases produced during storage of
beers.
Increases fermentation
Acetolactatedecarboxylase
efficiency by reducing
(ALDC)
diacetyl formation.[86]
Fruit juices Cellulases, pectinases Clarify fruit juices
Dairy industry Rennin, derived from the
stomachs of young ruminant Manufacture of cheese, used
animals (like calves and to hydrolyze protein.
lambs).
Microbially produced Now finding increasing use
enzyme in the dairy industry.
Lipases Is implemented during the
production of Roquefort
cheese to enhance the
ripening of the blue-mould
 cheese.
Break down lactose to
Roquefort cheese Lactases
glucose and galactose.
Meat tenderizers Papain To soften meat for cooking.
Amylases,
Converts starch into glucose
amyloglucosideases and
and various syrups.
glucoamylases
Starch industry
Converts glucose into
fructose in production of
high fructose syrups from
starchy materials. These
Glucose isomerase syrups have enhanced
sweetening properties and
Glucose Fructose
lower calorific values than
sucrose for the same level of
sweetness.
Degrade starch to lower
Paper industry viscosity, aiding sizing and
coating paper. Xylanases
reduce bleach required for
decolorising; cellulases
Amylases, Xylanases,
smooth fibers, enhance
Cellulases and ligninases
water drainage, and promote
ink removal; lipases reduce
pitch and lignin-degrading
A paper mill in South Carolina. enzymes remove lignin to
soften paper.
Biofuel industry Used to break down
cellulose into sugars that
Cellulases
can be fermented (see
cellulosic ethanol).

Ligninases Use of lignin waste

Cellulose in 3D
Biological detergent Used for presoak conditions
Primarily proteases, and direct liquid
produced in an extracellular applications helping with
form from bacteria removal of protein stains
from clothes.
Detergents for machine dish
Amylases washing to remove resistant
starch residues.
Lipases Used to assist in the
 removal of fatty and oily
stains.
Used in biological fabric
Cellulases
conditioners.
To remove proteins on
Contact lens cleaners Proteases contact lens to prevent
infections.
To generate oxygen from
Rubber industry Catalase peroxide to convert latex
into foam rubber.
Dissolve gelatin off scrap
Photographic industry Protease (ficin) film, allowing recovery of
its silver content.
Used to manipulate DNA in
Molecular biology genetic engineering,
important in pharmacology,
agriculture and medicine.
Restriction enzymes, DNA Essential for restriction
ligase and polymerases digestion and the
polymerase chain reaction.
Molecular biology is also
Part of the DNA double helix. important in forensic
science.

[edit] See also

Enzymes

Function and structure

Enzymes are very efficient catalysts for biochemical reactions. They speed up reactions by
providing an alternative reaction pathway of lower activation energy.

 Reaction profiles: uncatalysed and enzyme-catalysed

Like all catalysts, enzymes take part in the reaction - that is how they provide an alternative
reaction pathway. But they do not undergo permanent changes and so remain unchanged at the
end of the reaction. They can only alter the rate of reaction, not the position of the equilibrium.
Most chemical catalysts catalyse a wide range of reactions. They are not usually very selective.
In contrast enzymes are usually highly selective, catalysing specific reactions only. This
specificity is due to the shapes of the enzyme molecules.

Many enzymes consist of a protein and a non-protein (called the cofactor). The proteins in
enzymes are usually globular. The intra- and intermolecular bonds that hold proteins in their
secondary and tertiary structures are disrupted by changes in temperature and pH. This affects
shapes and so the catalytic activity of an enzyme is pH and temperature sensitive.

Cofactors may be:

 organic groups that are permanently bound to the enzyme (prosthetic groups)
 cations - positively charged metal ions (activators), which temporarily bind to the active site of
the enzyme, giving an intense positive charge to the enzyme's protein
 organic molecules, usually vitamins or made from vitamins (coenzymes), which are not
permanently bound to the enzyme molecule, but combine with the enzyme-substrate complex
temporarily.

Find out more by looking at:

 Proteins

How enzymes work

For two molecules to react they must collide with one another. They must collide in the right
direction (orientation) and with sufficient energy. Sufficient energy means that between them
they have enough energy to overcome the energy barrier to reaction. This is called the activation
energy.

 Reaction profile

Enzymes have an active site. This is part of the molecule that has just the right shape and
functional groups to bind to one of the reacting molecules. The reacting molecule that binds to
the enzyme is called the substrate.

An enzyme-catalysed reaction takes a different 'route'. The enzyme and substrate form a reaction
intermediate. Its formation has a lower activation energy than the reaction between reactants
without a catalyst.

A simplified picture

Route A reactant 1 + reactant 2   product

   
Route B reactant 1 + enzyme     intermediate

  intermediate + reactant 2     product + enzyme

So the enzyme is used to form a reaction intermediate, but when this reacts with another reactant
the enzyme reforms.

 Reaction profiles: uncatalysed and enzyme-catalysed

Lock and key hypothesis

This is the simplest model to represent how an enzyme works. The substrate simply fits into the
active site to form a reaction intermediate.

Induced fit hypothesis

In this model the enzyme molecule changes shape as the substrate molecules gets close. The
change in shape is 'induced' by the approaching substrate molecule. This more sophisticated
model relies on the fact that molecules are flexible because single covalent bonds are free to
rotate.

Factors affecting catalytic activity of enzymes

Temperature
As the temperature rises, reacting molecules have more and more kinetic energy. This increases
the chances of a successful collision and so the rate increases. There is a certain temperature at
which an enzyme's catalytic activity is at its greatest (see graph). This optimal temperature is
usually around human body temperature (37.5 oC) for the enzymes in human cells.

Above this temperature the enzyme structure begins to break down (denature) since at higher
temperatures intra- and intermolecular bonds are broken as the enzyme molecules gain even
more kinetic energy.

pH

Each enzyme works within quite a small pH range. There is a pH at which its activity is greatest
(the optimal pH). This is because changes in pH can make and break intra- and intermolecular
bonds, changing the shape of the enzyme and, therefore, its effectiveness.

Concentration of enzyme and substrate

           

The rate of an enzyme-catalysed reaction depends on the concentrations of enzyme and substrate.
As the concentration of either is increased the rate of reaction increases (see graphs).

For a given enzyme concentration, the rate of reaction increases with increasing substrate
concentration up to a point, above which any further increase in substrate concentration produces
no significant change in reaction rate. This is because the active sites of the enzyme molecules at
any given moment are virtually saturated with substrate. The enzyme/substrate complex has to
dissociate before the active sites are free to accommodate more substrate. (See graph)
Provided that the substrate concentration is high and that temperature and pH are kept constant,
the rate of reaction is proportional to the enzyme concentration. (See graph)

Inhibition of enzyme activity

Some substances reduce or even stop the catalytic activity of enzymes in biochemical reactions.
They block or distort the active site. These chemicals are called inhibitors, because they inhibit
reaction.

Inhibitors that occupy the active site and prevent a substrate molecule from binding to the
enzyme are said to be active site-directed (or competitive, as they 'compete' with the substrate for
the active site).

Inhibitors that attach to other parts of the enzyme molecule, perhaps distorting its shape, are said
to be non-active site-directed (or non competitive).

Immobilized enzymes
Enzymes are widely used commercially, for example in the detergent, food and brewing
industries. Protease enzymes are used in 'biological' washing powders to speed up the breakdown
of proteins in stains like blood and egg. Pectinase is used to produce and clarify fruit juices.
Problems using enzymes commercially include:

 they are water soluble which makes them hard to recover

 some products can inhibit the enzyme activity (feedback inhibition)

Enzymes can be immobilized by fixing them to a solid surface. This has a number of commercial
advantages:

 the enzyme is easily removed

 the enzyme can be packed into columns and used over a long period
 speedy separation of products reduces feedback inhibition
 thermal stability is increased allowing higher temperatures to be used
 higher operating temperatures increase rate of reaction

There are four principal methods of immobilization currently in use:

 covalent bonding to a solid support

 adsorption onto an insoluble substance
 entrapment within a gel
 encapsulation behind a selectively permeable membrane

http://www.rsc.org/education/teachers/learnnet/cfb/enzymes.htm