Enzymes are macromolecules that help accelerate (catalyze) chemical reactions in
biological systems. This is usually done by accelerating reactions by lowering the
transition state or decreasing the activation energy.
Enzyme decreases activation energy
Some biological reactions in the absence of enzymes may be as much as a million times
slower. Virtually all enzymes are proteins, though the converse is not true and other
molecules such as RNA can also catalyze reactions. The most remarkable
characteristics of enzymes are their ability to accelerate chemical reactions and their
specificity for a particular substrate. Enzymes take advantage of the full range of
intermolecular forces (van der waals interactions, polar interactions, hydrophobic
interactions and hydrogen bonding) to bring substrates together in most optimal
orientation so that reaction will occur. Also, enzymes can be inhibited by specific
molecules by called competitive, uncompetitive, and noncompetitive inhibitors.
Catalysis happens at the active site of the enzyme. It contains the residues that directly
participate in the making and breaking of bonds. These residues are called the catalytic
groups. Although enzymes differ widely in structure, specificity, and mode of catalysis a
number of generalizations concerning their active sites can be made:
1. The active site is a three dimensional cleft or crevice formed by groups that come from
different parts of the amino acid sequence - residues far apart in the amino
acid sequence may interact more strongly than adjacent residues in the sequence.
2. The active site takes up a relatively small part of the total volume of an enzyme. Most
of the amino acid residues in an enzyme are not in contact with the substrate, which
raises the question of why enzymes are so big. Nearly all enzymes are made up of more
than 100 amino acid residues. The "extra" amino acids serve as a scaffold to create the
three dimensional active site from the amino acids that are far apart in the primary
structure. In many proteins the remaining amino acids also constitute regulatory sites,
sites of interaction with other proteins, or channels to bring the substrate to the active
sites.
3. Active sites are unique microenvironments. In all enzymes of known structure,
substrate molecules are bound to a cleft or crevice. Water is usually excluded unless it is
a reactant. The nonpolar microenvironment of the cleft enhances the binding of
substrates as well as catalysis. Nevertheless, the cleft may also contain polar residues.
Certain of these polar residues acquire special properties essential for substrate binding
or catalyis.
4. Substrates are bound to enzymes by multiple weak interactions. Stated above
5. The specificity of binding depends on the precise defined arrangement of atoms in
the active site. Because the enzyme and the substrate interact by means of short-range
forces that require close contact, a substrate must have a matching shape to fit into the
site. However, the active site of some enzymes assume a shape that is complementary
to that of the substrate only after the substrate is bound. This process of dynamic
recognition is called induced fit.
Enzymes are highly specific and may require cofactors for catalysis. A cofactor is a nonprotein chemical compound bound to a protein; there are 2 types of cofactors: Metals and
organic/metalloorganic (which are derived from vitamins). An example of a metal cofactor
is zinc and the enzyme, carbonic anhydrase, tightly binds the zinc at the active site. The
process involves binding water to carbon dioxide and deprotonating it into carbonic acid.
Then the carbonic acid becomes a bicarbonate ion due to the displacement of water.
Catalysts can fasten the reaction speed by lowering the activation energy (not
the transition state) of the process. Theactive site is a location on the enzyme which has
complementary shape to the substrate. It is also where the amino acids with a
complementary charge, polarity and shape to the ligand are.
The enzyme function and catalysis result from the ability to stabilize the transition
state in a chemical reaction. Thetransition state is the highest energy species in a
reaction. It is a transitory molecular structure that is no longer the substrate but is not yet
the product. It is the most seldom occupied species along the reaction pathway. The
difference in free energy between the transition state and the substrate is called the
Gibbs free energy of activation or simply the activation energy.
Thus we can see the key to how enzymes operate: Enzymes accelerate reactions by
decreasing the activation energy. The combination of substrate and enzyme creates a
reaction pathway whose transition state is lower than that of the reaction in the absence
of the enzyme. Because the activation energy is lower more substrate molecules have
the energy required to reach the transition state.
It is important to note that enzymes have evolved specifically to recognize the transition
states of chemical reactions. Therefore, enzymes do not bind to any reactive species
before the species have actually begun to react; enzymes only recognize and bind
the transition states of such species. In fact, if enzymes were to bind to the reactants of a
reaction "on sight", or immediately, this would result in an even higher activation energy
than before! For this reason, enzymes recognize only the transition state and bind to
reactive species only when this high-energy state has been achieved. The fact that
enzymes can recognize structures as specific and short-lived as transition states is a
testament to their incredible specificity and efficiency.
Each enzyme is optimized for a particular reaction transition state. This ensures that
enzymes will not compete with each other and hinder cellular reactions instead of help
them. Enzyme inhibition occurs when the activity of a given enzyme is disrupted or
interrupted in some fashion. Inhibitors can be molecules that have a similar shape,
structure, or charge to the substrate in question so that the active site of an enzyme will
"mistake" the inhibitor for the substrate. This affects the affinity of the enzyme for the
substrate, as well as the rate of the overall reaction. Several types of inhibition can occur
in the cell; more detailed explanations on these can be found in the corresponding
sections.
Because of the active sites, enzymes are highly specific catalysts. These catalysts are
governed by the ability to lower the free energy of thermodynamics to
overcome transition states. The Michaelis-Menten Model describes the kinetic properties
of many enzymes.
The interaction between the substrate and the enzyme helps accelerate the reaction, and
the specificity of enzymes result in minimal side reactions.
It is of great importance to note that an enzyme cannot alter the laws of thermodynamics
and consequently cannot alter the equilibrium of the reaction. The amount of product
formed for a reaction utilizing an enzyme is always equal to the amount of product form
of the same reaction occurring in the same reaction mixture without the enzyme. The
enzyme just allows the reaction to reach its equilibrium faster. The equilibrium position is
a function only of the free-energy difference between reactants and products.
6. Enzymes only alter reaction rate, not the reaction equilibrium. Enzyme cannot alter the
laws of thermodynamics; therefore, it cannot alter the equilibrium of a chemical reaction.
Enzyme is present, the amount of products form faster compared with enzyme is absent.
Enzyme is only accelerating the reaction rate, not shipping the position of equilibrium
(free energy, delta G)
Contents
[hide]

1 Lock and Key Model

2 Induced Fit

3 Transition State Theory


4 Methods
5 Enzymatic Strategies and Examples


6 Catalytic Mechanisms
7 Enzyme's Cofactors for Activity

8 Enzyme Classification

9 Kinetics


10 The Michaelis-Menten Model

11 Replicative DNA polymerase
12 Temperature affect on catalytic activity of enzymes

13 References
Lock and Key Model[edit]
The "lock and key" model was first proposed by an organic chemist named Emil Fischer
in 1894. In this model, the "lock" refers to an enzyme and the "key" refers to its
complementary substrate. Each enzyme has a highly specific geometric shape that is
complementary to its substrate. In order to activate an enzyme, its substrate must first
bind to the active site on the enzyme. Only then will a catalytic reaction take place.
However, like a lock and a key, the enzyme and substrate shape must be complementary
and fit perfectly. Designed by evolution the active site for enzymes is generally highly
specific in its substrate recognition and has the ability to distinguish between
stereoisomers.
Induced Fit[edit]
According to the Lock and Key Model, the geometric shape of both enzymes and
substrates can not be changed as they are both predetermined. Thus, the binding of the
substrate to the enzymes active site does not alter the shape of the enzyme. While this
theory helped explain the specificity of the enzyme, it does not explain the stability of the
transition state for it would require more energy to reach the transition state complex.
Thus the induced fit model was proposed in which enzymes like proteins are flexible. The
concept of induced fit is that when a substrate binds to the active site of an enzyme,
there is a conformational change and structural adaptation that makes this binding site
more complementary and tighter. In essence the substrate does not simply bind to a rigid
active site but instead the macromolecules, weak interaction forces, and hydrophobic
characteristics on the enzyme surface mold into a precise formation so that there is an
induced fit where the enzyme can perform maximum catalytic
function.
Transition State Theory[edit]
Stabilization of the transition state by an enzyme.
Transition state theory states that in an enzyme catalysis, the enzyme binds more
strongly to its "transition state complex rather than its ground state reactants." In
essence, the transition state is more stable. The stabilization of the transition state lowers
the activation barrier between reactants and products thus increasing the rate of reaction
or enzymatic activity as this will favor the increase of formation of the transition state
complex.
In the transition state theory, the mechanism of interaction of reactants is irrelevant.
However, the colliding molecules that take place in the reaction must have sufficient
amount of kinetic energy to overcome the activation energy barrier in order to react. In
many cases, temperature, pH, or enzymes can be changed to facilitate the stabilization
of the transition state as well as statistically increasing the probability for molecules
colliding and forming the transition state complex. For a bimolecular reaction such as
Sn2, a transition state is formed when the two molecules’ old bonds are weakened and
new bonds begin to form or the old bonds break first to form the transition state and then
the new bonds form after. The theory suggests that as reactant molecules approach each
other closely they are momentarily in a less stable state than either the reactants or the
products.
Methods[edit]
1. Some catalysts provide a charge to a molecule to make it more attractive to other
reactants. Acids are an example for this kind of catalyst. They give the reacting
species a positive charge to attract the negative or partially negative reactant,
increasing the chance for the two species to collide and react.
2. Some catalysts increase the local concentration of reactants so that they are
more likely to collide.
3. Some catalysts may modify the shape of one reactant to be more susceptible to
other molecule.
Enzymatic Strategies and Examples[edit]
1. Covalent Catalysis - Through the course of catalysis, a powerful nucleophile is
temporarily attached to a part of the substrate. The nucleophile is contained in the active
site. A proteolytic enzyme chymotrypsin is an excellent example of this strategy. It is a
substrate forming a transient covalent bond with residues in the active site or with a
cofacter, which adds additional intermediate and reduce the energy of later transition.
2. General Acid/Base Catalysis - Water often acts as a donor or acceptor, but in
Acid/base catalysis, the molecule which donates or accepts a proton is NOT water. This
strategy incorporates base and acid catalysis to shorten reaction times. In the case of
Chymotrypsin, the enzyme uses a histidine residue as a base catalyst to enhance the
nucloephilicity of serine analogous to how histidine residue in carbonic anhydrase
facilitates the removal of a proton from a zinc bound water molecule to yield hydroxide.
3. Catalysis by approximation - In this method, reactions favored by bring together the
two substrates to a single binding surface on enzymes. The two substrates are brought
together to one area and this increases the rate of the reaction. NMP kinase for example,
brings tow nucleotides together to improve the transferring of phosphoryl groups.
4. Metal Ion Catalysis - Metal ions can be involved as a catalyst in many different ways.
Zinc can help the formation of a nucleophile. It makes the pka of water change from
approximately 14 to 7, which allows it to be protonated at neutral pH. It can also stabilize
negative charges by acting as an electrophile in a complex. Metal ions are also used to
increase the binding energy of substrates, holding them together. A metal ion may also
serve as a bridge between the enzyme and substrate acting as a cofactor in cases of
NMP kinases.
Catalytic Mechanisms[edit]
1. Proteases (chymotrypsin and trypsin): are any enzyme that conducts proteolysis
(protein catabolism) by hydrolysis of the peptide bonds lining amino acids together in the
polypeptide chain.
Sample Experiment: Site-Directed Mutagenesis Applying Polymerase Chain Reaction
(PCR) & Oligonucleotide Primers that contains the desired mutation in a newly
synthesize strand, engineering a mis-match during first cycle DNA can develop a
mutation.
2. Carbonic Anhydrase (metalloenzymes) These enzymes catalyzes the rapid
interconversion of carbon dioxide and water to bicarbonate and protons, a reversible
reaction that occurs rather slowly in the absence of catalyst.
3. Restriction Endonucleases (BamHI) It is a restriction enzyme that cleaves double
stranded DNA at specific recognition nucleotide sequences (restriction site).
4. Nucleaside Monophosphate Kinases (NMP Kinase) These enzymes transfer
phosphate groups from high energy donor molecule (ATP) to specific substrates
(phosphorylation).
Enzyme's Cofactors for Activity[edit]
The succinate dehydrogenase complex showing several cofactors, including flavin, iron-sulfur
centersand heme.
The catalytic activity of enzymes depends on the presence of small molecules called
cofactors. The role of the catalytic activity varies with the enzyme and its cofactors. In
general, those cofactors can execute chemical reactions which cannot be performed by
the standard 20 amino acids. An enzyme without cofactor is called apoenzyme, however
the one with completely catalytically active is called holoenzyme.
Cofactors can be divided into two individual groups: Metal and Coenzymes. Metals are
important for enzymes because they are molecular assistants that play a vital role in
some of the enzymatic reactions that fuel the body metabolism. They also act to stabilize
the shapes of enzymes. For example, iron helps the protein hemoglobin transport oxygen
to organs in the body and copper helps superoxide dismutase in sopping up dangerous
free radicals that accumulate inside the cells. Coenzymes are small organic molecules
that often derived from vitamins. Coenzymes can be either tightly or loosely bound to the
enzyme. Tightly bound ones are called prosthetic groups, while loosely bound
coenzymes are like substrates and products, bind to the enzyme and get released from
it. Enzymes that use the same coenzymes often perform catalysis by the similar
mechanisms.
Enzyme
Classification[edit]
Class
Hydrolases
Type of
Reduction
Examples
Catalyze
Estrases
hydrolysis
Digestive
reactions
enzymes
The classification of an enzyme is
Catalyze
shown within the table as it's class
isomerization
and the type of reduction the
(changing of
enzyme goes through. An example
Isomerases
a molecule
of a name is glucose
into its
phosphotransferase. In this reaction
isomer)
ATP transfers one of its phosphates
Ligases
phosphate group to glucose, it is
formation
Citric acid
coupled with
synthetase
ATP
within the classification of
hydrolysis.
transferases, hence the name
"glucose phosphotransferase."
Catalyze a
Since many enzymes have common
group
names that do not refer to their
elimination in
Lyases
order to form
they catalyze, a enzyme
double bonds
classification system was
(or a ring
established. There are six classes
structure).
of enzymes that were created with
Catalyze
subclasses based on what they
catalyze so that enzymes could
Oxidoreductases
easily be named. Depending on the
classification used for enzymes. For
oxidation-
Dehydrogenases
reduction
Oxidases
transfer of
These classes are
and Ligases. This is the internation
Aldolases
Catalyze the
enzyme can have various names.
Hydrolases, Lyases, Isomerases,
Decarboxylases
reactions
type of reaction catalyzed, an
Oxidoreductases, Transferases,
Fumarase
bond
ADP + D-glucose 6-phosphate.
function or what kind of reaction
isomerase,
Catalyze
to glucose: ATP + D-glucose ->
Since this process "transfers" a
Phospho hexo
Transferases
functional
Transaminase
groups
Kinases
among
molecules.
example, a common oxidoreductase
is dehydrogenase. Dehydrogenase is known as an enzyme that oxidizes a substrate and
transferring protons. Enzymes are normally used for catalyzing the transfer of functional
groups, electrons, or atoms. Since this is the case, they are assigned names by the type
of reaction they catalyze. This allowed for the addition of a four-digit number that would
precede EC(Enzyme Commission) and each enzyme could be identified. The reaction
that an enzyme catalyzes must be know before it can be classified.
Oxidoreductases catalyze oxidation-reduction reactions where electrons are transferred.
These electrons are usually in the form of hydride ions or hydrogen atoms. When a
substrate is being oxidized it is the hydrogen donor. The most common name used is a
dehydrogenase and sometimes reductase will be used. An oxidase is referred to when
the oxygen atom is the acceptor.
Transferases catalyze group transfer reactions. The transfer occurs from one molecule
that will be the donor to another molecule that will be the acceptor. Most of the time, the
donor is a cofactor that is charged with the group about to be transferred.
Hydrolases catalyze reactions that involve hydrolysis. This cases usually involves the
transfer of functional groups to water. When the hydrolase acts on amide, glycosyl,
peptide, ester, or other bonds, they not only catalyze the hydrolytic removal of a group
from the substrate but also a transfer of the group to an acceptor compound. These
enzymes could also be classified under transferaes since hydrolysis can be viewed as a
transfer of a functional group to water as an acceptor. However, as the acceptor's
reaction with water was discovered very early, it's considered the main function of the
enzyme which allows it to fall under this classification.
Lyases catalyze reactions where functional groups are added to break double bonds in
molecules or the reverse where double bonds are formed by the removal of functional
groups.
Isomerases catalyze reactions that transfer functional groups within a molecule so that
isomeric forms are produced. These enzymes allow for structural or geometric changes
within a compound. Sometime the interconverstion is carried out by an intramolecular
oxidoreduction. In this case, one molecule is both the hydrogen acceptor and donor, so
there's no oxidized product. The lack of a oxidized product is the reason this enzyme falls
under this classification. The subclasses are created under this category by the type of
isomerism.
Ligases are used in catalysis where two substrates are litigated and the formation of
carbon-carbon, carbon-sulfide, carbon-nitrogen, and carbon-oxygen bonds due to
condensation reactions. These reactions are couple to the cleavage of ATP.