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ENZYMES
Introduction
 Enzymes are biological catalysts that speed up the rate of the
biochemical reaction.
 Most enzymes are three dimensional globular proteins (tertiary and
quaternary structure).
 Enzymes – are organic catalysts produced by an organisms. The
reactant in an enzyme-catalyzed reaction is called “substrate”.
CHARACTERISTICS
 Enzymes speed up the reaction by lowering the activation energy of
the reaction.
 Their presence does not effect the nature and properties of end product.
 They are highly specific in their action that is each enzyme
can catalyze one kind of substrate.
 Small amount of enzymes can accelerate chemical reactions.
 Enzymes are sensitive to change in pH, temperature and substrate
concentration.
 Turnover number is defined as the number of substrate molecules
transformed per minute by one enzyme molecule
HISTORICAL BACKGROUND
 Berzelius in 1836 coined the term catalysis.
 In 1878, Kuhne used the word enzyme to indicate the catalysis
taking place in the biological systems.
 Isolation of enzyme system from cell-free extract of yeast was
achieved in 1883 by Buchner.
 In 1926, James Sumner first achieved the isolation and
crystallization of the enzyme urease from jack bean and identified
it as a protein.
CHEMICAL NATURE OF AN ENZYME
 Most of the enzymes are protein in nature with large molecular
weight.
 Each enzyme has its own tertiary structure and specific conformation
which is very essential for its catalytic activity.
 The study of enzymes is called enzymology.
 Enzymes are known to catalyze more than 5,000 biochemical
reaction types
STRUCTURE OF ENZYMES
 The active site of an enzyme is the region that binds substrates.
 Active sites generally occupy less than 5% of the total surface area of
enzyme.
 Active site has a specific shape due to tertiary structure of protein.
 A change in the shape of protein affects the shape of active site and
function of the enzyme.
NOMENCLATURE OF ENZYMES
 In the early, days the enzymes were given names by their discovers in
an arbitary manner.
 Enzymes are commonly named by putting the suffix ‘-ase’ to the
name of the substrate or with the catalytic action of the enzyme.
 E.g. a lipase is an enzyme which catalyses the hydrolysis of a lipid, a
fatty acid synthase is an enzyme that catalyzes the synthesis of a fatty
acid.
 These names of the enzymes are called as trivial names.
 While assigning a trivial name to an enzyme however, no systematic
rules are followed.
Systematic Name
 First part is the name of the substrates for the enzyme.
 Second part is the type of reaction catalyzed by the enzyme.This
part ends with the suffix “ase”.
Example: Lactate dehydrogenase
According to the International union Of Biochemistry an enzyme name
has two parts
CLASSIFICATION OF ENZYMES
 For the rational naming of each enzyme, International Union of
Biochemistry and Molecular Biology (IUBMB) adopted a scheme
and suggested functional classification of enzymes and appointed an
Enzyme Commission in 1961.
 Each enzyme is assigned a name and a systematic four digit enzyme
code, commonly known as Enzyme Commission number (E.C.
number). The first number broadly classifies the enzyme based on its
mechanism
 This classification is based on the type of reactions catalyzed by
enzymes.
 There are six major classes.
 Each class is further divided into sub classes, sub sub-classes and so
on, to describe the huge number of different enzyme- catalyzed
reactions.
 The classification does not take into account amino acid sequence
(ie, homology), protein structure, or chemical mechanism
CLASSIFICATION
1. EC 1, Oxidoreductases: catalyze oxidation/reduction
reactions.
2. EC 2, Transferases: transfer a functional group (e.g. a methyl or
phosphate group).
3. EC 3, Hydrolases: catalyze the hydrolysis of various bonds.
4. EC 4, Lyases: cleave various bonds by means other than hydrolysis.
5. EC 5, Isomerases: catalyze isomerization changes within a single
molecule.
6. EC 6, Ligases: join two molecules with covalent bonds.
Example - ATP: Glucose phosphotransferase
Its Enzyme Commission Number (E.C.Number) is 2.7.1.1
2 – denotes the class name (transferase);
7 – denotes subclass (phosphotransferase);
1 – denotes a phosphotransferase with a hydroxyl group as acceptor;
1 – denotes glucose as a phosphoryl group acceptor
EC 1. Oxidoreductases
Catalyze the transfer of hydrogen or oxygen atoms or electrons from
one substrate to another, also called oxidases, dehydrogenases, or
reductases. Note that since these are ‘redox’ reactions, an electron
donor/acceptor is also required to complete the reaction.
EC 2. Transferases
Catalyze group transfer reactions, excluding oxidoreductases (which
transfer hydrogen or oxygen and are EC 1). These are of the general
form:
A-X + B ↔ BX + A
EC 3. Hydrolases
Catalyze hydrolytic reactions. Includes lipases, esterases, nitrilases,
peptidases/proteases. These are of the general form:
A-X + H2O ↔ X-OH + HA
EC 4. Lyases
Catalyze non-hydrolytic (covered in EC 3) removal of functional
groups from substrates, often creating a double bond in the product; or
EC 5. Isomerases
Catalyzes isomerization reactions, including racemizations and cis-
tran isomerizations.
EC 6. Ligases
Catalyzes the synthesis of various (mostly C-X) bonds, coupled with
the breakdown of energy-containing substrates, usually ATP
Factors affecting enzyme activity
 Each enzyme has a pH range within which it can function. This is called “optimum
pH range” for that particular enzyme. For example, the optimum pH range of
pepsin, an enzyme found in gastric juice, is approximately 2.0, whereas the
optimum pH range of trypsin, an enzyme found in pancreatic juice, is near 8.2. The
relationship between enzyme activity and pH is also represented by a bell shaped
curve which has its peak at the optimum pH.
Effect of pH
Effect of pH on enzyme velocity
 Optimum pH for most of the intracellular enzymes is in the neutral
range, i.e. around 7.0.
Temperature
 Velocity of an enzyme reaction increases with increase in
temperature up to a maximum and then declines. A bell-shaped
curve is usually observed.
 The best temperature for enzyme function at which the rate of a
reaction involving an enzyme is the greatest is called the “optimum
temperature”.
 Enzymes are most active at an optimum temperature (usually 37 °C
in humans). show little activity at low temperatures. lose activity at
high temperatures as denaturation occurs
Effect of Product concentration
The accumulation of reaction products generally decreases the enzyme
velocity.
Clinical Significance
 Foods can be preserved in refrigerators (at low temperatures) due to
reduced bacterial enzyme activities.
 Certain surgeries are carried out by lowering the patient’s body
temperature (induced hypothermia), and thus the metabolic rate.
Effect of activators
 Some of the enzymes require certain inorganic metallic cations like Mg2+
Mn2+, Zn2+ etc. for their optimum activity. Metals function as activators of
enzyme velocity through various mechanisms- combining with the
substrate, formation of ES-metal complex.
Exposure of enzymes to ultraviolet, beta, gamma and X-rays inactivates certain
enzymes due to the formation of peroxides. E.g. UV rays inhibit salivary
amylase activity.
Effect of light and radiation
Effect of Substrate Concentration
 As with the all chemical reactions, the speed is increased with an
increase in concentration of substrate. With an increased
concentration of substrate, the rate of the reaction will increase until
available enzyme becomes saturated with substrate.
 Some enzymes also require a non-protein part for their activity.
Based on these, enzymes are categorised into two types
 Simple enzymes – They are only made up of proteins, e.g. trypsin,
pepsin, etc.
 Conjugate enzymes or holoenzymes – They consist of a protein as
well as non-protein part essential for the activity.
Holoenzyme Apoenzyme + Coenzyme
(protein part) (non-protein part)
USEFUL TERMS
 The non-protein, organic, Iow molecular weight and dialysable
substance associated with enzyme function is known as coenzyme.
 The term prosthetic group is used when the non-protein moiety
(covalently) binds with the apoenzyme.
 The coenzyme can be separated by dialysis from the enzyme while
the prosthetic group cannot be.
 Some of the enzymes require the presence of certain molecules, such
as a metal ions for their activity. The inorganic ions, such as Mg2+,
Zn2+ or Cl- required for the catalytic activity of an enzyme are
called as cofactors
ACTIVE SITE
The active site (or active centre) of an enzyme represents as the small
region at which the substrate(s) binds and participates in the catalysis.
Salient features of active site
 The existence of active site is due to the tertiary structure of protein
resulting in three-dimensional native conformation.
 The active site is made up of amino acids (known as catalytic
residues) which are far from each other in the linear sequence of
amino acids (primary structure of protein).
 Active sites are regarded as clefts or crevices or pockets occupying a
small region in a big molecule.
 The active site is not rigid in structure and shape. It is rather flexible
to promote the specific substrate binding.
 Generally, the active site possesses a substrate binding site and a
catalytic site.
 The coenzymes or cofactors on which some enzymes depend are
present as a part of the catalytic site.
 The substrate(s) binds at the active site by weak noncovalent bonds.
 Enzymes are specific in their function due to the existence of active
sites.
 The commonly found amino acids at the active sites are serine,
histidine etc. Among these amino acids, serine is the most frequently
found.
 The substrate [S] binds with the enzyme (E) at the active site to form
enzyme- substrate complex(ES). The product (P) is released after the
catalysis and the enzyme is available for reuse.
THERMODYNAMIC CHANGES
 All chemical reactions have energy barriers between reactants and
products.
 The difference in transitional state and substrate is called
activational barrier.
 Only a few substances cross the activation barrier and change into
products , that is why rate of uncatalyzed reactions is much slow.
 Enzymes provide an alternate pathway for conversion of substrate
into products.
 Enzymes accelerate reaction rates byforming transitional state
having low activational energy.
 Hence, the reaction rate is increased many folds in the presence of
enzymes.
The Free Energy of Activation
 Before a chemical reaction can take place, the reactants must
become activated.
 This needs a certain amount of energy which is termed the energy of
activation.
 It is defined as the minimum amount of energy which is required of
a molecule to take part in a reaction.
 For example,decomposition of hydrogen peroxide without a catalyst
has an energy activation about 18 000. When the enzyme catalase is
added, it is less than 2000.
 The rate of the reaction is proportional to the energy of activation:
 Greater the energy of activation, Slower will be the reaction. While if
the energy of activation is less, The reaction will be faster
Enzyme-substrate complex formation
Formation of enzyme-substrate (ES) complex is the first step in
enzymatic catalysis which ultimately results in the product
formation(p).
E + S ES E + P
MECHANISM OF ENZYME ACTION
Two models for substrate binding to the active site of the enzyme have
been proposed to explain the specificity that an enzyme has for its
substrate.
 Lock and Key model or Rigid Template Model of Emil Fisher
 Induced Fit Model or Hand-in-glove Model of Daniel E
Koshland
 Proposed by a Emil Fischer
 First model purposed to explain an enzyme catalyzed reaction.
 According to this model, the structure of conformation of the enzyme
is rigid.
 The substrate fits to the binding site (now active site) just as a key fits
into the proper lock.
 Thus the active site of an enzyme is a rigid and pre- shaped template
where only a Specific substrate can bind.
Lock and key Model
Lock and key model/ Fischer’s template Model
Drawbacks Lock and key Model
 Does not give any scope for the flexible nature of enzymes
 Totally fails to explain many facts of enzymatic reactions
 Does not explain the effect of allosteric modulator
Induced Fit Model or Hand-in-glove Model of Daniel E Koshland
 Daniel E Koshland in 1958 postulated that the enzymes are flexible
and shapes of the active site can be modified by the binding of the
substrate.
 In the induced fit model, the substrate induces a conformational
change in the enzyme, in the same manner in which placing a hand
(substrate) into a glove (enzyme) induces changes in the glove’s
shape. Therefore, this model is also known as hand-in-glove model.
 The functional groups of the active sites are arranged in a definite
spatial configuration and the enzyme-substrate complex is formed
by multiple bindings (such as by covalent bonds, hydrogen bonds
and electrostatic bonds) of the substrate with the enzyme.
Koshland’s induced fit theory
Koshland’s induced fit theory model was accepted because
 Has sufficient experimental evidence from the X-ray diffraction
studies.
 This model also explains the action of allosteric
modulators and competitive inhibition on enzymes
ENZYME INHIBITION
 Chemical substances which inhibit enzyme activity and reduce the
velocity of an enzyme catalyzed reaction are called inhibitors.
 The phenomenon of a decrease in enzymatic reaction brought about
by the addition of an inhibitor is called enzyme inhibition.
 There are 3 broad categories of Enzyme inhibition.
1. Reversible inhibition
2. Irreversible inhibition
3. Allosteric inhibition
REVERSIBLE INHIBITION
 The inhibitor binds non-covalently with enzyme.
 The enzyme inhibition can be reversed if the inhibitor is removed.
 The reversible inhibition is further sub-divided into
1. Competitive inhibition
2. Non-competitive inhibition
3. Uncompetitive inhibition
Competitive inhibition
 A substance that competes directly with a normal substrate for an
enzyme’s substrate-binding site is known as a competitive inhibitor.
 Chemical structure of the competitive inhibitor closely resembles
with that of the substrate. They are called structural analogs.
 The inhibitor competes with the substrate for binding at the active
site of the enzyme.
 The inhibitor forms a complex with the enzyme called as enzyme-
inhibitor complex (EI), instead of the enzyme substrate complex
(ES).
 A competitive inhibitor thus reduces concentration of free enzyme
available for the substrate binding.
 The relative concentration of the substrate and inhibitor and their respective
affinity with the enzyme determines the degree of competitive inhibition.
 The degree of inhibition can be reduced by increasing the concentration of
the substrate.
 For example, sulphanilamide (a sulfa drug) is an antibacterial agent and
resembles p-aminobenzoic acid (PABA), structurally. The drug is a
competitive inhibitor of the enzyme dihydropteroate synthase, in bacteria.
 Similarly, methotrexate, a structural analog of folate, competitively inhibits
dihydrofolate reductase and is used in the treatment of childhood leukemias.
P-aminobenzoic acid
Sulphanilamide
Clinical applications of competitive enzyme inhibition
Drug Enzyme True substrate Clinical application
Allopurinol Xanthine oxidase Hypoxanthine Gout
Sulfonamides Dihydropteroat
e synthase
Para-amino
benzoic acid
(PABA)
Bacterial infection
Methotrexate Dihydrofolat
e reductase
Dihydrofolate Cancer
Dicumarol Epoxide reductase Vitamin K epoxide Thrombosis
Succinyl choline Acetyl cholinesterase Acetyl choline Muscle relaxant
Non-competitive inhibition (mixed inhibition)
 The inhibitor (I) usually bears no structural similarity to the
substrate(S) and thus there occurs no competition between I and S.
 A non-competitive inhibitor binds at a site other than the substrate
binding site hence the enzyme as well as the enzyme-substrate
complex can bind to inhibitor. Therefore, both binary(EI) and
ternary (ES) complexes can be formed.
 Since ES may breakdown to form a product but at a slower rate,
therefore, this type of inhibition is also known as mixed inhibition.
 Certain analogs of purines and pyrimidines (called antimetabolites)
are non- competitive inhibitors of some of the enzymes and are used
as chemotherapeutic agents, e.g. 5-flurouracil. It is an analog of
thymine and inhibits thymidylate synthetase, noncompetitively.
 Deoxycycline, an antibiotic, functions at low concentrations as a
non- competitive inhibitor of a proteolytic enzyme, collagenase. It is
used to treat periodontal disease.
 Metal ions at lower concentrations act as reversible non-competitive
inhibitors
Uncompetitive inhibition
 Uncompetitive inhibition occurs when the inhibitor binds after the
substrate has bound to the enzyme, and then stops the reaction.
 Uncompetitive inhibitor can bind only to the enzyme-substrate(ES)
complex and such an inhibitor may not resemble the substrate.
 An example is the inhibition of alkaline phosphatase by
phenylalanine.
Irreversible Inhibition
 An irreversible inhibitor bind covalently with the enzymes and
inactivate them which is irreversible.
 Several oxidizing agents, enzyme poisons, and heavy metals cause
irreversible inhibition of enzyme activity.
 These inhibitors bear no structural similarity to the substrate, the
inhibition cannot be reversed by increasing substrate concentration.
 Some of the enzymes possesses additional sites, known as allosteric sites
(Greek: allo- other), besides the active site. Such enzymes are known as
allosteric enzymes or regulatory enzymes.
 Allosteric Enzyme are those enzymes possess additional sites, known
as allosteric sites besides the active site. The allosteric sites are unique
places on the enzyme molecules; allosteric enzymes have one or more
allosteric site.
 The term allosteric has been introduced by the two Noble laureates,
MONOD AND JACOB, to denote an enzyme site, different from the
active site ,which non competitively binds molecule other than the
substrate and may influence the enzyme activity.
ALLOSTERIC INHIBITION
PROPERTIES OF ALLOSTERIC ENZYME
 Allosteric enzyme have one or more allosteric sites
 Allosteric sites are binding sites distinct from an enzyme active site or
substrate binding site
 Molecule that bind to allosteric sites are called effector or modulator
 Effector may be positive or negative, this effector regulate the enzyme
activity.
 The enzyme activity is increased when a positive allosteric effector binds
at the allosteric site known as activator site. On the other hand, negative
allosteric effector bind at the allosteric site called inhibitor site and
inhibit the enzyme activity.
 Binding to allosteric sites alter the activity of the enzyme, this is called
cooperative binding.
 The catalytic site where the substrate binds, and the allosteric site
which is occupied by the effector molecule, are physically distinct
and often located far away from each other.
 The effector may activate an enzymatic reaction (allosteric
activation) and is called as a positive effector or allosteric
activator.
 The binding of the effector molecule may also result in inhibition
of the enzymatic reaction. This is called as allosteric inhibition
and such a effector molecule is called as a negative effector or
allosteric inhibitor
 Reversal of such an inhibition can be brought about by increasing the
amount of the substrate, relative to the amount of the inhibitor.
 If the effector substance is the substrate itself, it is called as the
homotropic effect.
 On the other hand, if the effector molecule is a substance other than
the substrate, then it is called as the heterotropic effect.
Regulation of enzyme activity
 Regulation of enzyme activity is important to coordinate the
different metabolicprocesses.
 It is also important for homeostasis i.e. to maintain the internal
environment of theorganism constant.
Regulation of enzyme activity can be achieved by two
general mechanisms:
1- Control of enzyme quantity : Enzyme quantity is affected by:
A- Altering the rate of enzyme synthesis and degradation,
B- Induction
C- Repression
2- Altering the catalytic efficiency of the enzyme by: Catalytic efficiency
of enzymes is affected by:
A- Allosteric regulation
B- Feedback inhibition
C- Proenzyme (zymogen)
D- Covalent modification
E- Protein – Protein interaction
A- Control of the rates of enzyme synthesis and degradation.
As enzymes are protein in nature, they are synthesized from amino acids under
gene control and degraded again to amino acids after doing its work.
Enzyme quantity depends on the rate of enzyme synthesis and the rate of its
degradation.
 Increased enzyme quantity may be due to an increase in the rate of
synthesis, a decrease in the rate of degradation or both.
 Decreased enzyme quantity may be due to a decrease in the rate of
synthesis, an increase in the rate of degradation or both.
 For example, the quantity of liver arginase enzyme increases after protein
rich meal due to an increase in the rate of its synthesis; also it increases in
starved animals due to a decrease in the rate of its degradation.
1. Control of enzyme quantity
 Induction means an increase in the rate of enzyme synthesis by
substances called inducers
 According to the response to inducers, enzymes are classified into:
i- Constitutive enzymes, the concentration of these enzymes does
not depend on inducers.
ii- Inducible enzymes, the concentration of these enzymes depends
on the presence of inducers
 For example, induction of lactase enzyme in bacteria grown on glucose
media.
B- Induction
 Repression means a decrease in the rate of enzyme synthesis by
substances called repressors.
 Repressors are low molecular weight substances that decrease the
rate of enzyme synthesis at the level of gene expression.
 Repressors are usually end products of biosynthetic reaction, so
repression is sometimes called feedback regulation.
 For example, dietary cholesterol decreases the rate of synthesis of
HMG CoA reductase (β-hydroxy β-methyl glutaryl CoA reductase),
which is a key enzyme in cholesterol biosynthesis.
C- Repression
Allosteric enzyme is formed of more than one protein subunit. It has two
sites; a catalytic site for substrate binding and another site (allosteric
site), that is the regulatory site, to which an effector binds.
Allosteric means another site: If binding of the effector to the enzyme
increases it activity, it is called positive effector or allosteric activator
e.g. ADP is allosteric activator for phosphofructokinase enzyme.
2. Control of catalytic efficiency of enzymes
A- Allosteric Regulation
If binding of the effector to the enzyme causes a decrease in its activity,
it is called negative effector or allosteric inhibitor e.g.
 ATP and citrate are allosteric inhibitors for phosphofructokinase
enzyme.
 Glucose-6-phosphate is allosteric inhibitor for hexokinase enzyme.
Binding of the allosteric effector to the regulatory site causes conformational
changes in the catalytic site, which becomes more fit for substrate binding in
positive effector (allosteric activator), and becomes unfit for substrate binding
in negative effector (allosteric inhibitor) as shown in the following diagram.
Mechanism of allosteric regulation
A representative diagram for the mechanisms of allosteric regulation
In biosynthetic pathways, an end product may directly inhibit an enzyme
early in the pathway. Such enzyme catalyzes the early functionally
irreversible step specific to a particular biosynthetic pathway.
Feedback inhibition may occur by simple feedback loop.as in the
following diagram
Feedback Inhibition
Simple feedback inhibition loop
Where A is the substrate, E is the end product, B, C, D are intermediate
metabolites, E1, E2, E3 and E4 are enzymes in biosynthetic pathway.
Feedback inhibition can occur by multiple feedback inhibition loops as occurs in
branched biosynthetic pathways.
Multiple feedback inhibition loop
 It means that an end product in the reaction decreases the rate of enzyme synthesis at the
level of gene expression.
 It does not affect the enzyme activity.
 It decreases the enzyme quantity through the action on the gene that encodes the
enzyme.
 It is a complicated process that takes hours to days.
 For example, inhibition of HMG CoA reductase enzyme by dietary cholesterol.
Feedback inhibition
 It means that an end product directly inhibits an enzyme early in biosynthetic pathways.
 It does not affect enzyme quantity
 It decreases enzyme activity.
 It is a direct and rapid process that occurs in seconds to minutes.
 For example, CTP inhibits aspartate- transcarbamylase enzyme in pyrimidine synthesis
Feedback regulation is different from feedback inhibition.
Feedback regulation
C. Proenzymes (Zymogens)
 Some enzymes are secreted in inactive forms called proenzymes or
zymogens. Examples for zymogens include pepsinogen, trypsinogen,
chymotrypsinogen, prothrombin and clotting factors.
 Zymogen is inactive because it contains an additional polypeptide
chain that masks (blocks) the active site of the enzyme
 Activation of zymogen occurs by removal of the polypeptide chain
that masks the active site as shown in the following figure.
 Some enzymes are secreted in zymogen form to protect the tissues of origin
from auto digestion.
 Another biological importance of zymogens is to insure rapid mobilization of
enzyme activity at the time of needs in response to physiological demands.
Biological importance of zymogens
It means modification of enzyme activity of many enzymes through
formation of covalent bonds e.g.
1. Methylation (addition of methyl group).
2. Hydroxylation (addition of hydroxyl group).
3. Adenylation (addition of adenylic acid).
4. Phosphorylation (addition of phosphate group)
Covalent modification
Phosphorylation is the most covalent modification used to regulate
enzyme activity. Phosphorylation of the enzyme occurs by addition of
phosphate group to the enzyme at the hydroxyl group of serine, threonine
or tyrosine. This occurs by protein kinase enzyme.
Dephosphorylation of the enzyme occurs by removal of phosphate group
from the hydroxyl group of serine, threonine or tyrosine. This occurs by
phosphatase enzyme. The phosphorylated form is the active form in some
enzymes, while the dephosphorylated form is the active form in other
enzymes.
Examples of enzymes activated by phosphorylation. These are usually
enzymes of degradative (breakdown) reactions e.g.
 Glycogen phosphorylase that breaks down glycogen into glucose.
 Citrate lyase, which breaks down citrate.
 Lipase that hydrolyzes triglyceride into glycerol and 3 fatty acids
Examples of enzymes inactivated by phosphorylation. These are usually
enzymes of biosynthetic reactions e.g.
 Glycogen Synthetase, which catalyzes biosynthesis of glycogen.
 Acetyl CoA carboxylase, an enzyme in fatty acid biosynthesis.
 HMG CoA reductase, an enzyme in cholesterol biosynthesis.
Everything You Need to Know About Enzymes
Everything You Need to Know About Enzymes
Everything You Need to Know About Enzymes
Everything You Need to Know About Enzymes
Everything You Need to Know About Enzymes

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Everything You Need to Know About Enzymes

  • 2. Introduction  Enzymes are biological catalysts that speed up the rate of the biochemical reaction.  Most enzymes are three dimensional globular proteins (tertiary and quaternary structure).  Enzymes – are organic catalysts produced by an organisms. The reactant in an enzyme-catalyzed reaction is called “substrate”.
  • 3. CHARACTERISTICS  Enzymes speed up the reaction by lowering the activation energy of the reaction.  Their presence does not effect the nature and properties of end product.  They are highly specific in their action that is each enzyme can catalyze one kind of substrate.  Small amount of enzymes can accelerate chemical reactions.  Enzymes are sensitive to change in pH, temperature and substrate concentration.  Turnover number is defined as the number of substrate molecules transformed per minute by one enzyme molecule
  • 4. HISTORICAL BACKGROUND  Berzelius in 1836 coined the term catalysis.  In 1878, Kuhne used the word enzyme to indicate the catalysis taking place in the biological systems.  Isolation of enzyme system from cell-free extract of yeast was achieved in 1883 by Buchner.  In 1926, James Sumner first achieved the isolation and crystallization of the enzyme urease from jack bean and identified it as a protein.
  • 5. CHEMICAL NATURE OF AN ENZYME  Most of the enzymes are protein in nature with large molecular weight.  Each enzyme has its own tertiary structure and specific conformation which is very essential for its catalytic activity.  The study of enzymes is called enzymology.  Enzymes are known to catalyze more than 5,000 biochemical reaction types
  • 6. STRUCTURE OF ENZYMES  The active site of an enzyme is the region that binds substrates.  Active sites generally occupy less than 5% of the total surface area of enzyme.  Active site has a specific shape due to tertiary structure of protein.  A change in the shape of protein affects the shape of active site and function of the enzyme.
  • 7.
  • 8. NOMENCLATURE OF ENZYMES  In the early, days the enzymes were given names by their discovers in an arbitary manner.  Enzymes are commonly named by putting the suffix ‘-ase’ to the name of the substrate or with the catalytic action of the enzyme.  E.g. a lipase is an enzyme which catalyses the hydrolysis of a lipid, a fatty acid synthase is an enzyme that catalyzes the synthesis of a fatty acid.  These names of the enzymes are called as trivial names.  While assigning a trivial name to an enzyme however, no systematic rules are followed.
  • 9. Systematic Name  First part is the name of the substrates for the enzyme.  Second part is the type of reaction catalyzed by the enzyme.This part ends with the suffix “ase”. Example: Lactate dehydrogenase According to the International union Of Biochemistry an enzyme name has two parts
  • 10. CLASSIFICATION OF ENZYMES  For the rational naming of each enzyme, International Union of Biochemistry and Molecular Biology (IUBMB) adopted a scheme and suggested functional classification of enzymes and appointed an Enzyme Commission in 1961.  Each enzyme is assigned a name and a systematic four digit enzyme code, commonly known as Enzyme Commission number (E.C. number). The first number broadly classifies the enzyme based on its mechanism
  • 11.  This classification is based on the type of reactions catalyzed by enzymes.  There are six major classes.  Each class is further divided into sub classes, sub sub-classes and so on, to describe the huge number of different enzyme- catalyzed reactions.  The classification does not take into account amino acid sequence (ie, homology), protein structure, or chemical mechanism
  • 12. CLASSIFICATION 1. EC 1, Oxidoreductases: catalyze oxidation/reduction reactions. 2. EC 2, Transferases: transfer a functional group (e.g. a methyl or phosphate group). 3. EC 3, Hydrolases: catalyze the hydrolysis of various bonds. 4. EC 4, Lyases: cleave various bonds by means other than hydrolysis. 5. EC 5, Isomerases: catalyze isomerization changes within a single molecule. 6. EC 6, Ligases: join two molecules with covalent bonds.
  • 13. Example - ATP: Glucose phosphotransferase Its Enzyme Commission Number (E.C.Number) is 2.7.1.1 2 – denotes the class name (transferase); 7 – denotes subclass (phosphotransferase); 1 – denotes a phosphotransferase with a hydroxyl group as acceptor; 1 – denotes glucose as a phosphoryl group acceptor
  • 14. EC 1. Oxidoreductases Catalyze the transfer of hydrogen or oxygen atoms or electrons from one substrate to another, also called oxidases, dehydrogenases, or reductases. Note that since these are ‘redox’ reactions, an electron donor/acceptor is also required to complete the reaction.
  • 15. EC 2. Transferases Catalyze group transfer reactions, excluding oxidoreductases (which transfer hydrogen or oxygen and are EC 1). These are of the general form: A-X + B ↔ BX + A
  • 16. EC 3. Hydrolases Catalyze hydrolytic reactions. Includes lipases, esterases, nitrilases, peptidases/proteases. These are of the general form: A-X + H2O ↔ X-OH + HA
  • 17. EC 4. Lyases Catalyze non-hydrolytic (covered in EC 3) removal of functional groups from substrates, often creating a double bond in the product; or
  • 18. EC 5. Isomerases Catalyzes isomerization reactions, including racemizations and cis- tran isomerizations. EC 6. Ligases Catalyzes the synthesis of various (mostly C-X) bonds, coupled with the breakdown of energy-containing substrates, usually ATP
  • 19. Factors affecting enzyme activity  Each enzyme has a pH range within which it can function. This is called “optimum pH range” for that particular enzyme. For example, the optimum pH range of pepsin, an enzyme found in gastric juice, is approximately 2.0, whereas the optimum pH range of trypsin, an enzyme found in pancreatic juice, is near 8.2. The relationship between enzyme activity and pH is also represented by a bell shaped curve which has its peak at the optimum pH. Effect of pH Effect of pH on enzyme velocity
  • 20.  Optimum pH for most of the intracellular enzymes is in the neutral range, i.e. around 7.0.
  • 21. Temperature  Velocity of an enzyme reaction increases with increase in temperature up to a maximum and then declines. A bell-shaped curve is usually observed.  The best temperature for enzyme function at which the rate of a reaction involving an enzyme is the greatest is called the “optimum temperature”.
  • 22.  Enzymes are most active at an optimum temperature (usually 37 °C in humans). show little activity at low temperatures. lose activity at high temperatures as denaturation occurs
  • 23. Effect of Product concentration The accumulation of reaction products generally decreases the enzyme velocity. Clinical Significance  Foods can be preserved in refrigerators (at low temperatures) due to reduced bacterial enzyme activities.  Certain surgeries are carried out by lowering the patient’s body temperature (induced hypothermia), and thus the metabolic rate.
  • 24. Effect of activators  Some of the enzymes require certain inorganic metallic cations like Mg2+ Mn2+, Zn2+ etc. for their optimum activity. Metals function as activators of enzyme velocity through various mechanisms- combining with the substrate, formation of ES-metal complex. Exposure of enzymes to ultraviolet, beta, gamma and X-rays inactivates certain enzymes due to the formation of peroxides. E.g. UV rays inhibit salivary amylase activity. Effect of light and radiation
  • 25. Effect of Substrate Concentration  As with the all chemical reactions, the speed is increased with an increase in concentration of substrate. With an increased concentration of substrate, the rate of the reaction will increase until available enzyme becomes saturated with substrate.
  • 26.  Some enzymes also require a non-protein part for their activity. Based on these, enzymes are categorised into two types  Simple enzymes – They are only made up of proteins, e.g. trypsin, pepsin, etc.  Conjugate enzymes or holoenzymes – They consist of a protein as well as non-protein part essential for the activity. Holoenzyme Apoenzyme + Coenzyme (protein part) (non-protein part) USEFUL TERMS
  • 27.  The non-protein, organic, Iow molecular weight and dialysable substance associated with enzyme function is known as coenzyme.  The term prosthetic group is used when the non-protein moiety (covalently) binds with the apoenzyme.  The coenzyme can be separated by dialysis from the enzyme while the prosthetic group cannot be.  Some of the enzymes require the presence of certain molecules, such as a metal ions for their activity. The inorganic ions, such as Mg2+, Zn2+ or Cl- required for the catalytic activity of an enzyme are called as cofactors
  • 28. ACTIVE SITE The active site (or active centre) of an enzyme represents as the small region at which the substrate(s) binds and participates in the catalysis.
  • 29. Salient features of active site  The existence of active site is due to the tertiary structure of protein resulting in three-dimensional native conformation.  The active site is made up of amino acids (known as catalytic residues) which are far from each other in the linear sequence of amino acids (primary structure of protein).  Active sites are regarded as clefts or crevices or pockets occupying a small region in a big molecule.  The active site is not rigid in structure and shape. It is rather flexible to promote the specific substrate binding.  Generally, the active site possesses a substrate binding site and a catalytic site.
  • 30.  The coenzymes or cofactors on which some enzymes depend are present as a part of the catalytic site.  The substrate(s) binds at the active site by weak noncovalent bonds.  Enzymes are specific in their function due to the existence of active sites.  The commonly found amino acids at the active sites are serine, histidine etc. Among these amino acids, serine is the most frequently found.  The substrate [S] binds with the enzyme (E) at the active site to form enzyme- substrate complex(ES). The product (P) is released after the catalysis and the enzyme is available for reuse.
  • 31. THERMODYNAMIC CHANGES  All chemical reactions have energy barriers between reactants and products.  The difference in transitional state and substrate is called activational barrier.
  • 32.  Only a few substances cross the activation barrier and change into products , that is why rate of uncatalyzed reactions is much slow.  Enzymes provide an alternate pathway for conversion of substrate into products.  Enzymes accelerate reaction rates byforming transitional state having low activational energy.  Hence, the reaction rate is increased many folds in the presence of enzymes.
  • 33. The Free Energy of Activation  Before a chemical reaction can take place, the reactants must become activated.  This needs a certain amount of energy which is termed the energy of activation.  It is defined as the minimum amount of energy which is required of a molecule to take part in a reaction.  For example,decomposition of hydrogen peroxide without a catalyst has an energy activation about 18 000. When the enzyme catalase is added, it is less than 2000.
  • 34.  The rate of the reaction is proportional to the energy of activation:  Greater the energy of activation, Slower will be the reaction. While if the energy of activation is less, The reaction will be faster
  • 35. Enzyme-substrate complex formation Formation of enzyme-substrate (ES) complex is the first step in enzymatic catalysis which ultimately results in the product formation(p). E + S ES E + P MECHANISM OF ENZYME ACTION
  • 36. Two models for substrate binding to the active site of the enzyme have been proposed to explain the specificity that an enzyme has for its substrate.  Lock and Key model or Rigid Template Model of Emil Fisher  Induced Fit Model or Hand-in-glove Model of Daniel E Koshland
  • 37.  Proposed by a Emil Fischer  First model purposed to explain an enzyme catalyzed reaction.  According to this model, the structure of conformation of the enzyme is rigid.  The substrate fits to the binding site (now active site) just as a key fits into the proper lock.  Thus the active site of an enzyme is a rigid and pre- shaped template where only a Specific substrate can bind. Lock and key Model
  • 38. Lock and key model/ Fischer’s template Model
  • 39. Drawbacks Lock and key Model  Does not give any scope for the flexible nature of enzymes  Totally fails to explain many facts of enzymatic reactions  Does not explain the effect of allosteric modulator
  • 40. Induced Fit Model or Hand-in-glove Model of Daniel E Koshland  Daniel E Koshland in 1958 postulated that the enzymes are flexible and shapes of the active site can be modified by the binding of the substrate.  In the induced fit model, the substrate induces a conformational change in the enzyme, in the same manner in which placing a hand (substrate) into a glove (enzyme) induces changes in the glove’s shape. Therefore, this model is also known as hand-in-glove model.  The functional groups of the active sites are arranged in a definite spatial configuration and the enzyme-substrate complex is formed by multiple bindings (such as by covalent bonds, hydrogen bonds and electrostatic bonds) of the substrate with the enzyme.
  • 42. Koshland’s induced fit theory model was accepted because  Has sufficient experimental evidence from the X-ray diffraction studies.  This model also explains the action of allosteric modulators and competitive inhibition on enzymes
  • 43. ENZYME INHIBITION  Chemical substances which inhibit enzyme activity and reduce the velocity of an enzyme catalyzed reaction are called inhibitors.  The phenomenon of a decrease in enzymatic reaction brought about by the addition of an inhibitor is called enzyme inhibition.  There are 3 broad categories of Enzyme inhibition. 1. Reversible inhibition 2. Irreversible inhibition 3. Allosteric inhibition
  • 44. REVERSIBLE INHIBITION  The inhibitor binds non-covalently with enzyme.  The enzyme inhibition can be reversed if the inhibitor is removed.  The reversible inhibition is further sub-divided into 1. Competitive inhibition 2. Non-competitive inhibition 3. Uncompetitive inhibition
  • 45. Competitive inhibition  A substance that competes directly with a normal substrate for an enzyme’s substrate-binding site is known as a competitive inhibitor.  Chemical structure of the competitive inhibitor closely resembles with that of the substrate. They are called structural analogs.  The inhibitor competes with the substrate for binding at the active site of the enzyme.  The inhibitor forms a complex with the enzyme called as enzyme- inhibitor complex (EI), instead of the enzyme substrate complex (ES).  A competitive inhibitor thus reduces concentration of free enzyme available for the substrate binding.
  • 46.  The relative concentration of the substrate and inhibitor and their respective affinity with the enzyme determines the degree of competitive inhibition.  The degree of inhibition can be reduced by increasing the concentration of the substrate.  For example, sulphanilamide (a sulfa drug) is an antibacterial agent and resembles p-aminobenzoic acid (PABA), structurally. The drug is a competitive inhibitor of the enzyme dihydropteroate synthase, in bacteria.  Similarly, methotrexate, a structural analog of folate, competitively inhibits dihydrofolate reductase and is used in the treatment of childhood leukemias. P-aminobenzoic acid Sulphanilamide
  • 47.
  • 48. Clinical applications of competitive enzyme inhibition Drug Enzyme True substrate Clinical application Allopurinol Xanthine oxidase Hypoxanthine Gout Sulfonamides Dihydropteroat e synthase Para-amino benzoic acid (PABA) Bacterial infection Methotrexate Dihydrofolat e reductase Dihydrofolate Cancer Dicumarol Epoxide reductase Vitamin K epoxide Thrombosis Succinyl choline Acetyl cholinesterase Acetyl choline Muscle relaxant
  • 49. Non-competitive inhibition (mixed inhibition)  The inhibitor (I) usually bears no structural similarity to the substrate(S) and thus there occurs no competition between I and S.  A non-competitive inhibitor binds at a site other than the substrate binding site hence the enzyme as well as the enzyme-substrate complex can bind to inhibitor. Therefore, both binary(EI) and ternary (ES) complexes can be formed.  Since ES may breakdown to form a product but at a slower rate, therefore, this type of inhibition is also known as mixed inhibition.
  • 50.  Certain analogs of purines and pyrimidines (called antimetabolites) are non- competitive inhibitors of some of the enzymes and are used as chemotherapeutic agents, e.g. 5-flurouracil. It is an analog of thymine and inhibits thymidylate synthetase, noncompetitively.  Deoxycycline, an antibiotic, functions at low concentrations as a non- competitive inhibitor of a proteolytic enzyme, collagenase. It is used to treat periodontal disease.  Metal ions at lower concentrations act as reversible non-competitive inhibitors
  • 51.
  • 52. Uncompetitive inhibition  Uncompetitive inhibition occurs when the inhibitor binds after the substrate has bound to the enzyme, and then stops the reaction.  Uncompetitive inhibitor can bind only to the enzyme-substrate(ES) complex and such an inhibitor may not resemble the substrate.  An example is the inhibition of alkaline phosphatase by phenylalanine.
  • 53.
  • 54. Irreversible Inhibition  An irreversible inhibitor bind covalently with the enzymes and inactivate them which is irreversible.  Several oxidizing agents, enzyme poisons, and heavy metals cause irreversible inhibition of enzyme activity.  These inhibitors bear no structural similarity to the substrate, the inhibition cannot be reversed by increasing substrate concentration.
  • 55.  Some of the enzymes possesses additional sites, known as allosteric sites (Greek: allo- other), besides the active site. Such enzymes are known as allosteric enzymes or regulatory enzymes.  Allosteric Enzyme are those enzymes possess additional sites, known as allosteric sites besides the active site. The allosteric sites are unique places on the enzyme molecules; allosteric enzymes have one or more allosteric site.  The term allosteric has been introduced by the two Noble laureates, MONOD AND JACOB, to denote an enzyme site, different from the active site ,which non competitively binds molecule other than the substrate and may influence the enzyme activity. ALLOSTERIC INHIBITION
  • 56. PROPERTIES OF ALLOSTERIC ENZYME  Allosteric enzyme have one or more allosteric sites  Allosteric sites are binding sites distinct from an enzyme active site or substrate binding site  Molecule that bind to allosteric sites are called effector or modulator  Effector may be positive or negative, this effector regulate the enzyme activity.  The enzyme activity is increased when a positive allosteric effector binds at the allosteric site known as activator site. On the other hand, negative allosteric effector bind at the allosteric site called inhibitor site and inhibit the enzyme activity.  Binding to allosteric sites alter the activity of the enzyme, this is called cooperative binding.
  • 57.  The catalytic site where the substrate binds, and the allosteric site which is occupied by the effector molecule, are physically distinct and often located far away from each other.  The effector may activate an enzymatic reaction (allosteric activation) and is called as a positive effector or allosteric activator.  The binding of the effector molecule may also result in inhibition of the enzymatic reaction. This is called as allosteric inhibition and such a effector molecule is called as a negative effector or allosteric inhibitor
  • 58.  Reversal of such an inhibition can be brought about by increasing the amount of the substrate, relative to the amount of the inhibitor.  If the effector substance is the substrate itself, it is called as the homotropic effect.  On the other hand, if the effector molecule is a substance other than the substrate, then it is called as the heterotropic effect.
  • 59.
  • 60. Regulation of enzyme activity  Regulation of enzyme activity is important to coordinate the different metabolicprocesses.  It is also important for homeostasis i.e. to maintain the internal environment of theorganism constant.
  • 61. Regulation of enzyme activity can be achieved by two general mechanisms: 1- Control of enzyme quantity : Enzyme quantity is affected by: A- Altering the rate of enzyme synthesis and degradation, B- Induction C- Repression 2- Altering the catalytic efficiency of the enzyme by: Catalytic efficiency of enzymes is affected by: A- Allosteric regulation B- Feedback inhibition C- Proenzyme (zymogen) D- Covalent modification E- Protein – Protein interaction
  • 62. A- Control of the rates of enzyme synthesis and degradation. As enzymes are protein in nature, they are synthesized from amino acids under gene control and degraded again to amino acids after doing its work. Enzyme quantity depends on the rate of enzyme synthesis and the rate of its degradation.  Increased enzyme quantity may be due to an increase in the rate of synthesis, a decrease in the rate of degradation or both.  Decreased enzyme quantity may be due to a decrease in the rate of synthesis, an increase in the rate of degradation or both.  For example, the quantity of liver arginase enzyme increases after protein rich meal due to an increase in the rate of its synthesis; also it increases in starved animals due to a decrease in the rate of its degradation. 1. Control of enzyme quantity
  • 63.  Induction means an increase in the rate of enzyme synthesis by substances called inducers  According to the response to inducers, enzymes are classified into: i- Constitutive enzymes, the concentration of these enzymes does not depend on inducers. ii- Inducible enzymes, the concentration of these enzymes depends on the presence of inducers  For example, induction of lactase enzyme in bacteria grown on glucose media. B- Induction
  • 64.  Repression means a decrease in the rate of enzyme synthesis by substances called repressors.  Repressors are low molecular weight substances that decrease the rate of enzyme synthesis at the level of gene expression.  Repressors are usually end products of biosynthetic reaction, so repression is sometimes called feedback regulation.  For example, dietary cholesterol decreases the rate of synthesis of HMG CoA reductase (β-hydroxy β-methyl glutaryl CoA reductase), which is a key enzyme in cholesterol biosynthesis. C- Repression
  • 65. Allosteric enzyme is formed of more than one protein subunit. It has two sites; a catalytic site for substrate binding and another site (allosteric site), that is the regulatory site, to which an effector binds. Allosteric means another site: If binding of the effector to the enzyme increases it activity, it is called positive effector or allosteric activator e.g. ADP is allosteric activator for phosphofructokinase enzyme. 2. Control of catalytic efficiency of enzymes A- Allosteric Regulation
  • 66. If binding of the effector to the enzyme causes a decrease in its activity, it is called negative effector or allosteric inhibitor e.g.  ATP and citrate are allosteric inhibitors for phosphofructokinase enzyme.  Glucose-6-phosphate is allosteric inhibitor for hexokinase enzyme.
  • 67. Binding of the allosteric effector to the regulatory site causes conformational changes in the catalytic site, which becomes more fit for substrate binding in positive effector (allosteric activator), and becomes unfit for substrate binding in negative effector (allosteric inhibitor) as shown in the following diagram. Mechanism of allosteric regulation A representative diagram for the mechanisms of allosteric regulation
  • 68. In biosynthetic pathways, an end product may directly inhibit an enzyme early in the pathway. Such enzyme catalyzes the early functionally irreversible step specific to a particular biosynthetic pathway. Feedback inhibition may occur by simple feedback loop.as in the following diagram Feedback Inhibition Simple feedback inhibition loop Where A is the substrate, E is the end product, B, C, D are intermediate metabolites, E1, E2, E3 and E4 are enzymes in biosynthetic pathway.
  • 69. Feedback inhibition can occur by multiple feedback inhibition loops as occurs in branched biosynthetic pathways. Multiple feedback inhibition loop
  • 70.  It means that an end product in the reaction decreases the rate of enzyme synthesis at the level of gene expression.  It does not affect the enzyme activity.  It decreases the enzyme quantity through the action on the gene that encodes the enzyme.  It is a complicated process that takes hours to days.  For example, inhibition of HMG CoA reductase enzyme by dietary cholesterol. Feedback inhibition  It means that an end product directly inhibits an enzyme early in biosynthetic pathways.  It does not affect enzyme quantity  It decreases enzyme activity.  It is a direct and rapid process that occurs in seconds to minutes.  For example, CTP inhibits aspartate- transcarbamylase enzyme in pyrimidine synthesis Feedback regulation is different from feedback inhibition. Feedback regulation
  • 71. C. Proenzymes (Zymogens)  Some enzymes are secreted in inactive forms called proenzymes or zymogens. Examples for zymogens include pepsinogen, trypsinogen, chymotrypsinogen, prothrombin and clotting factors.  Zymogen is inactive because it contains an additional polypeptide chain that masks (blocks) the active site of the enzyme  Activation of zymogen occurs by removal of the polypeptide chain that masks the active site as shown in the following figure.
  • 72.
  • 73.  Some enzymes are secreted in zymogen form to protect the tissues of origin from auto digestion.  Another biological importance of zymogens is to insure rapid mobilization of enzyme activity at the time of needs in response to physiological demands. Biological importance of zymogens
  • 74. It means modification of enzyme activity of many enzymes through formation of covalent bonds e.g. 1. Methylation (addition of methyl group). 2. Hydroxylation (addition of hydroxyl group). 3. Adenylation (addition of adenylic acid). 4. Phosphorylation (addition of phosphate group) Covalent modification
  • 75. Phosphorylation is the most covalent modification used to regulate enzyme activity. Phosphorylation of the enzyme occurs by addition of phosphate group to the enzyme at the hydroxyl group of serine, threonine or tyrosine. This occurs by protein kinase enzyme. Dephosphorylation of the enzyme occurs by removal of phosphate group from the hydroxyl group of serine, threonine or tyrosine. This occurs by phosphatase enzyme. The phosphorylated form is the active form in some enzymes, while the dephosphorylated form is the active form in other enzymes.
  • 76. Examples of enzymes activated by phosphorylation. These are usually enzymes of degradative (breakdown) reactions e.g.  Glycogen phosphorylase that breaks down glycogen into glucose.  Citrate lyase, which breaks down citrate.  Lipase that hydrolyzes triglyceride into glycerol and 3 fatty acids
  • 77. Examples of enzymes inactivated by phosphorylation. These are usually enzymes of biosynthetic reactions e.g.  Glycogen Synthetase, which catalyzes biosynthesis of glycogen.  Acetyl CoA carboxylase, an enzyme in fatty acid biosynthesis.  HMG CoA reductase, an enzyme in cholesterol biosynthesis.