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Enzyme

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									Enzyme




              Ribbon diagram of the catalytically perfect enzyme TIM.




Factor D enzyme crystal prevents the immune system from inappropriately running
out of control.

An enzyme (from Greek énsimo (ένζυμο), formed by én = at or in and simo = leaven
or yeast) is a protein that catalyzes, or speeds up, a chemical reaction.

Enzymes are essential to sustain life, because most chemical reactions in biological
cells would occur too slowly or would lead to different products without enzymes. A
malfunction (mutation, overproduction, underproduction or deletion) of a single
critical enzyme can lead to severe diseases. For example, phenylketonuria is caused
by an enzyme malfunction in the enzyme phenylalanine hydroxylase, which catalyses
the first step in the degradation of phenylalanine. If this enzyme does not function, the
resulting build-up of phenylalanine leads to mental retardation.
Like all catalysts, enzymes work by lowering the activation energy of a reaction, thus
allowing the reaction to proceed much faster. Enzymes may speed up reactions by a
factor of many thousands. An enzyme, like any catalyst, remains unaltered by the
completed reaction and can therefore continue to function. Because enzymes, like all
catalysts, do not affect the relative energy between the products and reagents, they do
not affect equilibrium of a reaction. However, the advantage of enzymes compared to
most other catalysts is their sterio-, regio- and chemoselectivity and specificity.

Enzyme activity can be affected by other molecules. Inhibitors are molecules that
decrease or abolish enzyme activity; activators are molecules that increase the
activity. Suicide inhibitors are inhibitors that incorporate themselves into the enzyme,
permanently deactivating it. Inhibitors can be either natural or man-made. Many drugs
are enzyme inhibitors. Aspirin, for example, inhibits an enzyme that produces the
inflammation messenger prostaglandin, thus suppressing pain and inflammation.

Enzymes are also used in everyday products such as washing detergents, where they
speed up chemical reactions involved in cleaning the clothes (for example, breaking
down starch stains). For industrial purposes the properties of Enzymes are emulated to
form new kinds of catalytic molecules named Synzymes and Abzyme.

More than 5,000 enzymes are known. To name different enzymes, one typically uses
the ending -ase with the name of the chemical being transformed (substrate), e.g.,
lactase is the enzyme that catalyzes the cleavage of lactose.



Etymology and history




                                   Eduard Buchner

The word enzyme comes from Greek: "in leaven". As early as the late-1700s and
early-1800s, the digestion of meat by stomach secretions and the conversion of starch
to sugars by plant extracts and saliva were observed.
Studying the fermentation of sugar to alcohol by yeast, Louis Pasteur came to the
conclusion that this fermentation was catalyzed by "ferments" in the yeast, which
were thought to function only in the presence of living organisms.

In 1897, Hans and Eduard Buchner inadvertently used yeast extracts to ferment sugar,
despite the absence of living yeast cells. They were interested in making extracts of
yeast cells for medical purposes, and, as one possible way of preserving them, they
added large amounts of sucrose to the extract. To their surprise, they found that the
sugar was fermented, even though there were no living yeast cells in the mixture. The
term "enzyme" was used to describe the substance(s) in yeast extract that brought
about the fermentation of sucrose. An example of an enzyme would be amylase



3D-Structure
In enzymes, as with other proteins, function is determined by structure. An enzyme
can be:

      A monomeric protein, i.e., containing only one polypeptide chain, made up of
       about hundred amino acids or more; or
      an oligomeric protein consisting of several polypeptide chains, different or
       identical, that act together as a unit.

As with any protein, each monomer is actually produced as a long, linear chain of
amino acids, which folds in a particular fashion to produce a three-dimensional
product. Individual monomers may then combine via non-covalent interactions to
form a multimeric protein.




                   Cartoon showing the active site of an enzyme.

Most enzymes are far larger molecules than the substrates they act on and that only a
very small portion of the enzyme, around 10 amino acids, come into direct contact
with the substrate(s). This region, where binding of the substrate(s) and than the
reaction occurs, is known as the active site of the enzyme. Sometimes enzymes
contain additionally other binding sites. Some enzymes have a binding site for a
cofactor, which is needed for catalysis. Some enzymes have a binding site that serve
regulatory functions, which increase or decrease the enzyme's activity. These
typically bind small molecules, often direct or indirect products or substrates of the
reaction catalyzed. This provides a means for feedback regulation.

The amino acid sidechains of an enzyme are either involved in forming the active site
or a binding site, or are needed to form the 3D-structure of the protein. Some amino
acid sidechains are not needed for function or structure of the enzyme.



Specificity
Enzymes are usually specific as to the reactions they catalyze and the substrates that
are involved in these reactions. Shape and charge complementarity of enzyme and
substrate are responsible for this specificity.



"Lock and key" hypothesis




                 Fischer's lock and key hypothesis of enzyme action.

Enzymes are very specific and it was suggested by Emil Fischer in 1890 that this was
because the enzyme had a particular shape into which the substrate(s) fit exactly. This
is often referred to as "the lock and key" hypothesis. An enzyme combines with its
substrate(s) to form a short lived enzyme-substrate complex.

Induced fit hypothesis




       Diagrams to show Koshland's induced fit hypothesis of enzyme action.
In 1958 Daniel Koshland suggested a modification to the "lock and key" hypothesis.
Enzymes are rather flexible structures. The active site of an enzyme could be
modified as the substrate interacts with the enzyme. The amino acids sidechains
which make up the active site are molded into a precise shape which enables the
enzyme to perform its catalytic function. In some cases the substrate molecule
changes shape slightly as it enters the active site.

A suitable analogy would be that of a hand changing the shape of a glove as the glove
is put on.



Modifications
Many enzymes contain not only a protein part but need additionally various
modifications. These modifications are made posttranslational, i.e. after the
polypeptide chain was synthesized. Additional groups can be synthesized onto the
polypeptide chain. E.g. phosphorylation or glycolisation of the enzyme.

Another kind of posttranslational modification is the cleavage and splicing of the
polypeptide chain. E.g. 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 prevents the enzyme from harmful digestion of the pancreas
or other tissue. This type of inactive precursor to an enzyme is known as a zymogen.



Enzyme cofactors
Some enzymes do not need any additional components to exhibit full activities.
However, many enzymes are chemically inactive, and they require additional
components to become active. An enzyme cofactor is the non-protein component of
an enzyme essential for its catalytic activity. There are three types of cofactors,
namely activators, coenzymes, prosthetic groups.



Activators
Certain enzymes require inorganic ions as cofactors. These inorganic ions are called
activators. They are mainly metallic monovalent or divalent cations which are either
loosely or firmly bound to the enzymes. For example in blood clotting, calcium ions,
known as factor IV, are required to activate thrombokinase to convert prothrombin
into thrombin.
Prosthetic groups




                                  Structure of heme.

Non-protein organic cofactors which are firmly bound to the enzyme molecules are
called prosthetic groups. They combine to form an integral part in performing
catalytic functions. FAD, a prosthetic group containing heavy metals, is a prosthetic
group having similar function as NAD and NADP in carrying hydrogen. Heme is a
prosthetic group responsible for carring electrons in the cytochrome system.



Coenzymes
The cofactors of some other enzymes are non-protein organic molecules known as
coenzymes, which are not bonded to enzyme molecules like prosthetic groups. Being
vitamin-derivatives, they usually serve as carriers to transfer atoms or functional
groups from one enzyme to a substrate. Common examples are NAD (derived from
nicotinic acid, a member of vitamin B complex) and NADP, which act as hydrogen
carriers and Coenzyme A that transfers the acetyl groups.

Those inactive protein parts of enzymes are called apoenzymes. An apoenzyme works
effectively only in the presence of non-protein cofactors. An apoenzyme together with
its cofactor constitutes a holoenzyme, i.e., an active enzyme. Most of the cofactors are
either regenerated or chemically unchanged at the end of the reactions.



Allosteric modulation
Allosteric enzymes have either effector binding sites, or multiple protein subunits that
interact with each other and thus influence catalytic activity.
Kinetics
In 1913, Leonor Michaelis and Maud Menten proposed a quantitative theory of
enzyme kinetics which is still widely used today (usually referred to as Michaelis-
Menten kinetics). Enzymes can perform up to several million catalytic reactions per
second; to determine the maximum speed of an enzymatic reaction, the substrate
concentration is increased until a constant rate of product formation is achieved. This
is the maximum velocity (Vmax) of the enzyme. In this state, all enzyme active sites
are saturated with substrate. However, Vmax is only one kinetic parameter that
biochemists are interested in. The amount of substrate needed to achieve a given rate
of reaction is also of interest. This can be expressed by the Michaelis-Menten constant
(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. Since
Vmax cannot be measured directly, both KM and Vmax are usually determined by
extrapolating from a limited data set, using what is known as a double reciprocal, or
Lineweaver-Burk plot.

The efficiency of an enzyme can be expressed in terms of kcat/Km. The quantity kcat,
also called the turnover number, incorporates the rate constants for all steps in the
reaction, and is the product of Vmax and the total enzyme concentration. kcat/Km is a
useful quantity for comparing different enzymes against each other, or the same
enzyme with different substrates, because it takes both affinity and catalytic ability
into consideration. The theoretical maximum for kcat/Km, called diffusion limit, is
about 108 to 109 (l mol-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 that reach this kcat/Km value are called
catalytically perfect or kinetically perfect. Example of such enzymes are triose-
phosphate isomerase, carbonic anhydrase, acetylcholinesterase, catalase, fumarase, ß-
lactamase, and superoxide dismutase.



Thermodynamics




Diagram of a catalytic reaction, showing the energy niveau at each stage of the
reaction. The substrates (A and B) usually need a large amount of energy to reach the
transition state (TS), which then reacts to form the end product (C and D). The
enzyme stabilizes the transition state, reducing the energy niveau of the transition
state and thus the energy required to get over this barrier. Because the lower energy
niveau is easier to reach and therefore occurs more frequently, the reaction is more
likely to take place, thus increasing the reaction speed.

As with all catalysts, all reactions catalyzed by enzymes must be "spontaneous"
(containing a net negative Gibbs free energy). With the enzyme, they run in the same
direction as they would without the enzyme, just more quickly. However, the
uncatalyzed, "spontaneous" reaction might lead to different products than the
catalyzed reaction. Furthermore, enzymes can couple two or more reactions, so that a
thermodynamically favorable reaction can be used to "drive" a thermodynamically
unfavorable one. For example, the cleavage of the high-energy compound ATP is
often used to drive other, energetically unfavorable chemical reactions.

Many reactions catalyzed by an enzyme are reversible.



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 which catalyzes a reaction in either direction depending on the conditions
at the time.

                                                        (in tissues - high CO2
       concentration)
                                                        (in   lungs   -   low   CO2
       concentration)
Inhibition
Enzymes reaction rates can be changed by competitive inhibition, non-competitive
inhibition, uncompetitive inhibition and mixed inhibition.

Competitive inhibition




Competitive inhibition. A competitive inhibitor binds reversibly to the enzyme,
preventing the binding of substrate. On the other hand, binding of substrate prevents
binding of the inhibitor, thus substrate and inhibitor compete for the enzyme.

The inhibitor may bind to the substrate binding site as shown in the figure above, thus
preventing substrate binding. An example for competitive inhibition is the enzyme
succinate dehydrogenase by malonate. Succinate dehydrogenase catalyses the
oxidation of succinate to fumarate.




Action of the enzyme succinate dehydrogenase on succinate (right) and competitive
inhibition of the enzyme by malonate (bottom).
Uncompetitive inhibition
Uncompetitive inhibition occurs when the inhibitor binds only to the enzyme-
substrate complex, not to the free enzyme, the enzyme-inhibitor-substrate (EIS)
complex is catalytically inactive. This mode of inhibition is rare.



Non-competitive inhibition




           Diagram showing the mechanism of non-competitive inhibition.

Non-competitive inhibitors never bind to the active center, but to other parts of the
enzyme that can be far away from the substrate binding site, consequently, there is no
competition between the substrate and inhibitor for the enzyme. The extent of
inhibition depends entirely on the inhibitor concentration and will not be affected by
the substrate concentration. However, these inhibitors bind only loosely with the
enzyme and can be removed to resume the enzymatic activities. For example, cyanide
combines with the copper prosthetic groups of the enzyme cytochrome c oxidase, thus
inhibiting respiration.

By changing the conformation (the three-dimensional structure) of the enzyme, the
inhibitors either disable the ability of the enzyme to bind or turn over its substrate.
The EI and EIS-complex have no catalytic activity.
Partially competitive inhibition
The mechanism of partially competitive is similar to that of non-competitive
inhibition, except that the EIS-complex has catalytic activity, which may be lower or
even higher (partially competitive activation) than that of the ES-complex.



Irreversible inhibitors
Some inhibitor bind irreversibly with the enzyme molecules, inhibiting the catalytic
activities permanently. The enzymatic reactions will stop sooner or later and are not
affected by an increase in substrate concentration. These are irreversible inhibitors.
Examples are heavy metal ions including silver, mercury and lead ions.

Another example of irreversible inhibition is provided by the nerve gas
diisopropylfluorophosphate (DFP) designed for use in warfare. It combines with the
amino acid serine (contains the —SH group) at the active site of the enzyme
acetylcholinesterase. The enzyme deactivates the neurotransmitter acetylcholine.
Neurotransmitters are needed to continue the passage of nerve impulses from one
neurone to another across the synapse. Once the impulse has been transmitted,
acetylcholinesterase functions to deactivate the acetycholine almost immediately by
breaking it down. If the enzyme is inhibited, acetylcholine accumulates and nerve
impulses cannot be stopped, causing prolonged muscle contration. Paralysis occurs
and death may result since the respiratory muscles are affected. Some insecticides
currently in use, including those known as organophosphates (e.g. parathion), have a
similar effect on insects, and can also cause harm to nervous and muscular system of
humans who are overexposed to them.



Metabolic pathways and allosteric enzymes
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. The end product(s) of such a pathway are often inhibitors for one of the first
enzymes of the pathway (usually the first irreversible step, called committed step),
thus regulating the amount of end product made by the pathways. Such a regulatory
mechanism is called a negative feedback mechanism, because the amount of the end
product produced is regulated by its own concentration. Negative feedback
mechanism can effectively adjust the rate of synthesis of intermediate metabolites
according to the demands of the cells. This helps with effective allocations of
materials and energy economy, and it prevents the excess manufacture of end
products. Like other homeostatic devices, the control of enzymatic action helps to
maintain a stable internal environment in living organisms.
Common feedback inhibition mechanisms, (1) The basic feedback inhibition
mechanism, where the product (P) inhibits the committed step (A→B). (2) Sequential
feedback inhibition. The end products P1 and P2 inhibit the first committed step of
their individual pathway (C→D or C→F). If both products are present in abundance,
all pathways from C are blocked. This leads to a buildup of C, which in turn inhibits
the first common committed step A→B. (3) Enzyme multiplicity. Each end product
inhibits both the first individual committed step and one of the enzymes performing
the first common committed step. (4) Concerted feedback inhibition. Each end
product inhibits the first individual committed step. Together, they inhibit the first
common committed step. (5) Cumulative feedback inhibition. Each end product
inhibits the first individual committed step. Also, each end product partially inhibits
the first common committed step.

Enzymes that are regulated by end-production inhibition are usually allosteric
enzymes. An allosteric enzyme molecule has an active site and also an allosteric site.
The allosteric site can bind with allosteric effectors that affect the activity of the
enzyme molecule. Allosteric effectors include allosteric activators and allosteric
inhibitors. The binding with an allosteric activator activates an enzyme molecule
because the active site is in the right conformation to bind with substrate molecules.
The binding with an allosteric inhibitor inactivates the enzyme molecule because the
conformation of the active site is altered. The activation and inhibition of an allosteric
enzyme are reversible.




Allosteric inhibition. In the example ATCase, the enzyme of the first reaction in the
pathway, is an allosteric enzyme, and CTP, the end product, is an allosteric inhibitor
of ATCase.
Enzyme naming conventions
By common convention, an enzyme's name consists of a description of what it does,
with the word ending in -ase. Examples are alcohol dehydrogenase and DNA
polymerase. Kinases are enzymes that transfer phosphate groups. This results in
different enzymes with the same function having the same basic name; they are
therefore distinguished by other characteristics, such their optimal pH (alkaline
phosphatase) or their location (membrane ATPase). Furthermore, the reversibility of
chemical reactions means that the normal physiological direction of an enzyme's
function may not be that observed under laboratory conditions. This can result in the
same enzyme being identified with two different names: one stemming from the
formal laboratory identification as described above, the other representing its behavior
in the cell. For instance the enzyme formally known as xylitol:NAD+ 2-
oxidoreductase (D-xylulose-forming) is more commonly referred to in the cellular
physiological sense as D-xylulose reductase, reflecting the fact that the function of the
enzyme in the cell is actually the reverse of what is often seen under in vitro
conditions.
The International Union of Biochemistry and Molecular Biology has developed a
nomenclature for enzymes, the EC numbers; each enzyme is described by a sequence
of four numbers, preceded by "EC". The first number broadly classifies the enzyme
based on its mechanism:
                                                                     Enzyme
                                                    Typical
Group            Reaction catalyzed                                  example(s) with
                                                    reaction
                                                                     trivial name
EC            1 To catalyze oxidation/reduction     AH + B → A Dehydrogenase,
Oxidoreductases reactions; transfer of H and O      +          BH oxidase
                atoms or electrons from one         (reduced)
                substance to another                A + O → AO
                                                    (oxidized)
EC             2 Transfer of a functional group AB + C → A Transaminase,
Transferases     from one substance to another. + BC       kinase
                 The group may be methyl-,
                 acyl-, amino- or phospate group
EC             3 Formation of two products from AB + H2O → Lipase, amylase,
Hydrolases       a substrate by hydrolysis      AOH + BH   peptidase
EC             4 Non-hydrolytic addition or RCOCOOH
Lyases           removal of groups from → RCOH +
                 substrates. C-C, C-N, C-O or C- CO2
                 S bonds may be cleaved
EC             5 Intramolecule    rearrangement, AB → BA             Isomerase, mutase
Isomerases       i.e.   isomerization     changes
                 within a single molecule
EC             6 Join together two molecules by X + Y+ ATP Synthetase
Ligases          synthesis of new C-O, C-S, C-N → XY + ADP
                 or C-C bonds with simultaneous + Pi
                 breakdown of ATP
     Applications
Application   Enzymes used            Uses               Notes and examples
Biological                         Used         for
detergent                          presoak
                                   conditions and
              Primarily proteases,
                                   direct    liquid
              produced in an
                                   applications
              extracellular form
                                   helping     with
              from bacteria
                                   removal       of
                                   protein stains
                                   from clothes.
                                      Detergents for     Biological washing powders contain protease.
                                      machine
                                      dishwashing to     Note: The amylases and proteases used in
              Amylase enzymes                            detergents are allergenic for the process workers,
                                      remove
                                      resistant starch   although, encapsulation techniques have reduced
                                      residues           this problem.
                                      Catalyze
                                      breakdown of
              Fungal        alpha-    starch in the
              amylase enzymes:        flour to sugar.
              normally                Yeast action on
              inactivates about 50    sugar produces
              degrees      Celsius,   carbon dioxide.
              destroyed     during    Used          in
Baking        baking process          production of alpha-amylase catalyzes          the   release      sugar
industry                              white     bread, monomers (n) from starch
                                      buns, and rolls
                                      Biscuit
                                      manufacturers
                                      use them to
              Protease enzymes
                                      lower        the
                                      protein level of
                                      flour.
                                      To    predigest
Baby foods    Trypsin
                                      baby foods
                                      They degrade
                                      starch      and
                                      proteins      to
              Enzymes        from     produce simple
              barley are released     sugar, amino
              during the mashing      acids       and
Brewing       stage    of     beer    peptides    that
industry      production.             are used by
                                      yeast         to
                                      enhance
                                      fermentation.
              Industrially produced enzymes Germinating barley used for malt.
              now widely used in the brewing
              process to substitute for the
               natural enzymes found in barley:
                                   Split
               Amylase,
                                   polysaccharides
               glucanases,
                                   and proteins in
               proteases
                                   the malt
                                   Improve       the
               Betaglucosidase     filtration
                                   characteristics.
                                   Low-calorie
               Amyloglucosidase
                                   beer
                                   Remove
                                   cloudiness
               Proteases
                                   during storage
                                   of beers.
               Cellulases,         Clarify     fruit
Fruit juices
               pectinases          juices
                                                   Note: As animals age rennin production decreases
               Rennin,      derived
                                                   and is replaced by another protease, pepsin, which
               from the stomachs Manufacture of
                                                   is not suitable for cheese production. In recent
               of young ruminant cheese, used to
                                                   years the increase in cheese consumption, as well
               animals      (calves, split protein
                                                   as increased beef production, has resulted in a
               lambs, kids)
                                                   shortage of rennin and escalating prices.
                                   Now      finding
               Microbially         increasing use
               produced enzyme     in the dairy
                                   industry
Dairy                              Is implemented
industry                           during      the
                                   production of
                                   Roquefort
               Lipases             cheese       to
                                   enhance     the
                                   ripening of the
                                   blue-mould
                                   cheese.
                                                       Roquefort cheese
                                   Break     down
                                   lactose      to
               Lactases
                                   glucose     and
                                   galactose
                                  Converts starch
               Amylases,
                                  into   glucose
               amyloglucosideases
                                  and     various
               and glucoamylases
                                  syrups
Starch                           Converts
industry                         glucose      in
                                 fructose (high
               Glucose isomerase fructose syrups
                                 derived from Glucose                       Fructose
                                 starchy
                                 materials have
                                enhanced
                                sweetening
                                properties and
                                lower calorific
                                values)
                                Production of Note: Although this process is widely used in the
              Immobilised
                                high fructose USA and Japan, legislation in the EEC restricts it’s
              enzymes
                                syrups        use to protect sugar beet farmers.
                                To     generate
                                oxygen from
Rubber
              Catalase          peroxide      to
industry
                                convert latex to
                                foam rubber


                                Degrade starch
                                to        lower
Paper                           viscosity
              Amylases
industry                        product needed
                                for sizing and
                                coating paper

                                                    Paper factories use amylase
                                Dissolve
                                gelatin off the
Photographic                    scrap       film
             Protease (ficin)
industry                        allowing
                                recovery       of
                                silver present

								
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