Enzyme

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2.  Definition, classification, specificity and active
site.
 Cofactors.
 Effect of pH temperature and substrate
concentration.
 Introduction to enzyme inhibitors,
proenzymes and isoenzymes.
 Introduction to allosteric regulation, covalent
modification and regulation by induction /
repression
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3.  Enzymes are biological catalysts synthesized by
living cells that accelerate biochemical reactions.
 The orderly course of metabolic processes is only
possible because each cell is equipped with its
own genetically determined set of enzymes
 It is only this that allows coordinated sequences
of reactions - metabolic pathways
 Involved in many regulatory mechanisms.
 Almost all enzymes are proteins except
catalytically active ribonucleic acids, the
ribozymes
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4.  Enzymes are characterized by three distinctive
features:
 Catalytic Power
◦ Ability to catalyses biochemical reaction
◦ Accelerating reaction rates as much as 1016 over
uncatalyzed levels - far greater than any synthetic
catalysts
 Specificity
◦ A given enzyme is very selective
◦ Both in the substances with which it interacts and in the
reaction that it catalyzes
 Regulation
◦ Metabolic inhibitors and activators
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5.  Traditionally, enzymes often were named by
adding the suffix –ase to the substrate upon
which they acted
 Ex: phosphatase, urease, catalase, proteases
 Confusion arose from these trivial naming.
 So a new system of nomenclature of enzyme
was developed based on nature of reaction it
helps
 Six classes of reactions are recognized
◦ Within each class are subclasses, and under each
subclass are subsubclasses within which individual
enzymes are listed
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6.  Enzyme are classified on the basis of action it
performs
◦ Oxidoreductases - oxidation–reduction reactions
 Phosphate dehydrogenase
◦ Transferases - transfer of functional groups
 Methyltransferases, Carboxyltransferases
◦ Hydrolases - hydrolysis reactions
 Carboxylic ester hydrolases
◦ Isomerases - isomerization reactions
 Epimerases
◦ Lyases - addition to double bonds
 Carboxy lyases, Aldehyde lyases
◦ Ligases - formation of bonds with ATP cleavage
 Amino acid–RNA ligases
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7. o Intracellular
o enzymes are synthesized and retained in the cell for
the use of cell itself.
oThey are found in the cytoplasm, nucleus,
mitochondria and chloroplast.
Example: Oxydoreductase catalyses biological
oxidation, Enzymes involved in reduction in the
mitochondria.
o Extracellular
oenzymes are synthesized in the cell but secreted
from the cell to work externally.
Example : Digestive enzyme produced by the
pancreas, are not used by the cells in the pancreas but
are transported to the duodenum.
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8.  Most of enzymes carry out their functions relying
solely on their protein structure
 Many others require non-protein components –
cofactors
◦ Usually metal ion or non-protein organic part (Coenzyme)
 Less complex than proteins, tend to be stable to heat
 Many coenzymes are vitamins or contain vitamins as
part of their structure
 Functional unit of enzyme is known as holoenzyme
◦ Holenzyme = Apoenzyme + Coenzyme
• Apoenzyme : protein without any catalytic
activity
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9.  If the enzyme is made of single polypeptide –
monomeric enzyme. Ex: ribonuclease, trypsin
 If the enzyme is made up of more than one
polypeptide – oligomeric enzyme. Ex: lactate
dehydrogenase, aspartate transcarbamoylase
 Multienzyme complex: have multiple enzyme
unit to carry out different reaction in
sequence
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11.  The quantitative measurement of the rates of
enzyme-catalyzed reactions and the systematic
study of factors that affect these rates
 Helps in analysis, diagnosis, and treatment of the
enzymic imbalances that underlie numerous
human diseases.
 Levels of particular enzymes serve as clinical
indicators for pathologies
◦ myocardial infarctions,
◦ prostate cancer
◦ damage to the liver
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12.  Any biochemical reaction constitute,
A + B C + D
Where A and B are substrate and C + D are product
 Study of enzyme kinetic has 2 component,
i.e.
• Gibs Free Energy : Direction and equilibrium state of
substrate and product
 Activation Energy: Mechanism of reaction
and rate of reaction
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13.  Also called either free energy or Gibbs energy
 It describes in quantitative form both the direction in
which a chemical reaction will tend to proceed and
the concentrations of substrate and products that will
be present at equilibrium
 Mathematically, ΔG = ΔGp – ΔGs
◦ ΔGp : sum of the free energies of formation of the
reaction products
◦ ΔGs : sum of the free energies of formation of the
substrates
• The sign and the magnitude of the free energy change
determine how far the reaction will proceed
• If ΔG is negative then the reaction proceeds in
forward direction spontaneously
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14.  Any reaction doesn’t proceeds directly to product
formation.
 There is always a transition state between ground
state and products
 Activation energy: The difference between the
energy levels of the ground state and the
transition state.
 The function of a catalyst is to increase the rate
of a reaction, it does not affect reaction
equilibria.
 So enzyme just lowers the activation energy.
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16.  The contact between enzyme and substrate is the
most essential pre-requisite for enzyme activity.
 The important factors that influence the enzyme
reaction are
◦ Concentration of Substrate
◦ Concentration of Enzyme
◦ Temperature
◦ pH
◦ Product concentration
◦ Activators
◦ Time
◦ Light and radiation
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17.  The frequency with which
molecules collide is directly
proportionate to their
concentrations
Rate ∝ [A]n[B]m , Rate = k[A]n[B]m
◦ where, nA + mB → P; k = rate
constant
• The sum of the molar ratios of the reactants defines the
kinetic order of the reaction
• In the example above, reaction is said to be of (n+m)
order overall but n order with respect to A and m order
with respect to B
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18.  Also known as Haldane’s Constant
 Substrate concentration to produce half
maximum velocity in an enzyme catalyst
reaction
 Km is constant and a chracterstic feature of a
given enzyme – strength of Enzyme Substrate
(ES) complex
 Low Km value indicates a strong affinity between
enzyme and substrate
 Majority of Enzyme Km value – 10-5 to 10-2
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19. Michaelis-Menten
Reaction
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20.  Reaction velocity is directly proportional to
concentration of enzyme
 Serum enzyme for diagnosis of disease
◦ Known volume of serum and substrate taken at
optimum pH and temperature
◦ Enzyme is assayed in laboratory
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21.  Velocity of an enzyme reaction increase with the
increase in temperature up to a maximum and then
declines
 Increase in temperature causes increases the kinetic
energy of molecules
 A bell-shaped curve is usually observed
 Temperature coefficient Q10 : increase in enzyme
velocity when the temperature is increased by 100C
 Optimum temperature for most of enzyme – 40 – 45
0C
 Beyond 500C there is denaturation of enzyme
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22.  Most intracellular enzymes exhibit optimal activity at
pH values between 6 - 8.
 Balance between enzyme denaturation at high or low
pH and effects on the charged state of the enzyme,
the substrates, or both
 Exception – pepsin (1-2), acid phosphatase (4-5),
alkaline phophatase (10-11)
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23.  Certain metallica cations – Mn, Mg, Zn, Ca, Co, Cu,
Na, K.
 It acts in a various ways
◦ Combining with substrate
◦ Formation of E-S metal complex, direct participation in the
reaction and bringing a conformational changes in enzyme
• There are 2 categories of enzyme
requiring metals for their activity
 Metal activated enzyme:Not tightly held by the enzyme and can
be exchanged easily. Ex: ATPAase (Mg and Ca) and Enolase
 Metalloenzyme: Hold the metal tightly. Ex: alcohol
dehydrogenase, carbonic anhydrase, alkaline phosphatase,
carboxypeptidase
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24.  Product concentration: Accumulation of
reaction products generally decreases the
enzyme velocity
 Light and radiation: exposure to UV, beta-
gamma and X-rays inactivates certain enzyme
◦ Formation of peroxides, ex: UV rays inhibit salivary
amylase activity
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25.  The active site of an enzyme is the region that
binds substrates, co-factors and prosthetic
groups and contains residue that helps to hold
the substrate.
 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.
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26. This model (above) is an enzyme called
Ribonuclease S, that breaks up RNA
molecules. It has three active sites (arrowed).
Active site:
The active site contains both binding
and catalytic regions. The substrate
is drawn to the enzyme’s surface and
the substrate molecule(s) are
positioned in a way to promote a
reaction: either joining two molecules
together or splitting up a larger one.Enzyme molecule:
The complexity of the
active site is what makes
each enzyme so specific
(i.e. precise in terms of the
substrate it acts on).
Substrate molecule:
Substrate molecules are the
chemicals that an enzyme
acts on. They are drawn into
the cleft of the enzyme.
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27. o Active site can be further divided into:
it chooses the substrate It performs the
catalytic
and binds it to active site. action of
enzyme.
Active Site
Binding Site Catalytic Site
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28.  The catalytic efficiency of enzymes is explained by two
perspectives:
Thermodynamic
changes
Processes at the
active site
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29.  All chemical reactions have energy barriers between reactants
and products.
 The difference in transitional state and substrate is called
activational barrier.
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30. Covalent
catalysis
Acid
base
catalysisCatalysis
by strain
Catalysis
by
proximit
y
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31. o Enzymes form covalent linkages with substrate forming
transient enzyme-substrate complex with very low activation
energy.
o Enzyme is released unaltered after completion of reaction.
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32.  Mostly undertaken by oxido- reductases enzyme.
 Mostly at the active site, histdine is present which act as both
proton donor and proton acceptor.
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33.  In this catalysis molecules must come in bond forming
distance.
 When enzyme binds:
 A region of high substrate concentration is produced at active
site.
 This will orient substrate molecules especially in a position
ideal for them.
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34.  Mostly undertaken by lyases.
 The enzyme-substrate binding causes reorientation of
the structure of site due to in a strain condition.
 Thus transitional state is required and here bond is
unstable and eventually broken.
 In this way bond between substrate is broken and
converted into products.
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35.  Proposed by EMIL FISCHER in 1894.
 Lock and key hypothesis assumes the active site of an
enzymes are rigid in its shape.
 There is no change in the active site before and after a
chemical reaction.
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36. The lock and key model of enzyme action, proposed earlier
this century, proposed that the substrate was simply drawn
into a closely matching cleft on the enzyme molecule.
Substrate
Enzyme
Products
Symbolic representation of the lock and key model of enzyme action.
1. A substrate is drawn into the active sites of the enzyme.
2. The substrate shape must be compatible with the enzymes active site in
order to fit and be reacted upon.
3. The enzyme modifies the substrate. In this instance the substrate is
broken down, releasing two products.
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37.  More recent studies have revealed that the process is much
more likely to involve an induced fit model(proposed by
DANIAL KOSH LAND in 1958).
 According to this exposure of an enzyme to substrate cause a
change in enzyme, which causes the active site to change it’s
shape to allow enzyme and substrate to bind.
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38. More recent studies
have revealed that the
process is much more
likely to involve an
induced fit.
The enzyme or the reactants
(substrate) change their shape
slightly.
The reactants become bound
to enzymes by weak chemical
bonds.
This binding can weaken
bonds within the reactants
themselves, allowing the
reaction to proceed more
The enzyme
changes shape,
forcing the substrate
molecules to
combine.
Two substrate
molecules are
drawn into the cleft
of the enzyme.
The resulting end
product is released
by the enzyme
which returns to its
normal shape, ready
to undergo more
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39. 39
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40.  Changes to the shape of the active site will result
in a loss of function. Enzymes are sensitive to
various factors such as temperature & pH.
 When an enzyme has lost its characteristic 3D
shape, it is said to be denatured. Some enzymes
can regain their shape while in others, the
changes are irreversible.
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41. o The prevention of an enzyme process as a result of
interaction of inhibitors with the enzyme.
 INHIBITORS:
Any substance that can diminish the velocity of
an enzyme catalyzed reaction is called an inhibitor.
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42. Inhibition
Reversible
Competitive Uncompetitive Mixed
Non-
competitive
Irreversible
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43. o It is an inhibition of enzyme activity in which the inhibiting
molecular entity can associate and dissociate from the
protein‘s binding site.
TYPES OF REVERSIBLE INHIBITION
o There are four types:
 Competitive inhibition.
 Uncompetitive inhibition.
 Mixed inhibition.
 Non-competitive inhibition.
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44.  In this type of inhibition, the inhibitors compete with the
substrate for the active site. Formation of E.S complex is
reduced while a new E.I complex is formed.
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45.  Statin Drug As Example Of Competitive
Inhibition:
 Statin drugs such as lipitor compete with HMG-
CoA(substrate) and inhibit the active site of HMG CoA-
REDUCTASE (that bring about the catalysis of cholesterol synthesis).
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46.  In this type of inhibition, inhibitor does not compete with the
substrate for the active site of enzyme instead it binds to
another site known as allosteric site.
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47.  Drugs to treat cases of poisoning by methanol or
ethylene glycol act as uncompetitive inhibitors.
 Tetramethylene sulfoxide and 3- butylthiolene 1-oxide
are uncompetitive inhibitors of liver
alcohaldehydrogenase.
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48. o It is a special case of inhibition.
o In this inhibitor has the same affinity for either enzyme
E or the E.S complex.
MIXED INHIBITION
o In this type of inhibition both E.I and E.S.I complexes are
formed.
o Both complexes are catalytically inactive.
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49.  This type of inhibition involves the covalent attachment of the
inhibitor to the enzyme.
 The catalytic activity of enzyme is completely lost.
 It can only be restored only by synthesizing molecules.
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50.  Aspirin which targets and covalently modifies a key enzyme
involved in inflammation is an irreversible inhibitor.
 SUICIDE INHIBITION :
 It is an unusual type of irreversible inhibition where the
enzyme converts the inhibitor into a reactive form in its active
site.
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51.  Enzymes are highly specific in nature, interacting with one or
few substrates and catalyzing only one type of chemical
reaction.
 Substrate specificity is due to complete fitting of active site
and substrate .
Example:
 Oxydoreductase do not catalyze hydrolase reactions and
hydrolase do not catalyze reaction involving oxidation and
reduction.
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52.  Enzymes show different degrees of specificity:
 Bond specificity.
 Group specificity.
 Absolute specificity.
 Optical or stereo-specificity.
 Dual specificity.
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53.  In this type, enzyme acts on substrates that are similar in
structure and contain the same type of bond.
Example :
 Amylase which acts on α-1-4 glycosidic ,bond in starch
dextrin and glycogen, shows bond specificity.
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54.  In this type of specificity, the enzyme is specific not only to
the type of bond but also to the structure surrounding it.
Example:
 Pepsin is an endopeptidase enzyme, that hydrolyzes central
peptide bonds in which the amino group belongs to aromatic
amino acids e. g phenyl alanine, tyrosine and tryptophan.
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55.  In this type of specificity ,the enzymes acts only on one
substrate
Example :
 Uricase ,which acts only on uric acid, shows substrate
specificity.
 Maltase , which acts only on maltose, shows substrate
specificity.
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56.  In this type of specificity , the enzyme is not specific to
substrate but also to its optical configuration
Example:
 D amino acid oxidase acts only on D amino acids.
 L amino acid oxidase acts only on L amino acids.
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57.  There are two types of dual specificity.
 The enzyme may act on one substrate by two different
reaction types.
Example:
 Isocitrate dehydrogenase enzyme acts on isocitrate (one
substrate) by oxidation followed by decarboxylation(two
different reaction types) .
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58.  The enzyme may act on two substrates by one reaction type
Example:
• Xanthine oxidase enzyme acts on xanthine and
hypoxanthine(two substrates) by oxidation (one reaction type)
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59.  Regulation of enzyme occurs in following
ways
◦ Allosteric regulation
◦ Activation of Latent Enzyme
◦ Compartmentation
◦ Control of enzyme synthesis
◦ Enzyme Degradation
◦ Isoenzyme
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60.  Additional sites other than active sites –
Allosteric enzymes
 Types of allosteric enzyme:
◦ K-class: effectors changes the Km
◦ V-class: effectors changes the Vmax
• Most of allosteric enzymes are
oligomeric in nature
• Non-reversible binding of effector
molecule at the allosteric sites –
conformational change in the active site
of enzyme
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61.  Some enzymes remain inactive,
 It gets activated at the site of action by the
breakdown of one or more peptide bonds
 Ex: chymotrypsin, pepsinogen and
plasminogen
 Certain enzymes keeps interconverting from
active to inactive and vice-versa depending
on the need of body
 Ex: Glycogen phosphorylase, Phosphorylase b
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62.  The enzyme remains confined to particular area
of cell/body which makes it exclusive
 For instance: fatty acid synthesis takes place in
cytosol whereas fatty acid oxidation takes in
mitochondria
Organelle Enzyme/metabolic pathway
Cytoplasm Aminotransferase, peptidases, glycolysis, HMP shunt
Mitochondria Fatty acid oxidation, Kreb’s Cycle, Urea Cycle, ETC
Nucleus Biosynthesis of DNA and RNA
Endoplasmic
Reticulum
Protein Biosynthesis, Triacylglycrol and phospholipid
synthesis
Lysosomes Lysozyme, phosphatases, phospholipases, hydrolases,
proteases
Golgi Appartus Glucos-6 phosphatease, glucosyl and galactosyl
transferase
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63.  Most of the enzyme particularly the rate limiting
ones are present in very low concentration
 Based on the amount of enzyme present in the
body, enzymes are
◦ Constitutive enzymes: its levels are not controlled and it
remain almost constant
◦ Adaptive enzymes: their level increases or decreases as
per body needs
• Synthesis of enzyme are regulated by
gene.
• Regulation by induction / repression
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64.  Enzymes have their self-destructing
capabilities.
 But it is highly variable and in general
◦ The key and regulatory enzyme are most rapidly
degraded
◦ Not so important enzyme have longer half life
• Ex: LDH4 – 5-6 days, LDH1 – 8-12
hrs, amylase – 3-5 hrs
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65.  When same reaction is catalyzed by two or more
different molecular forms of an enzyme, it is
called isoenzyme
 It may occur in the same species, in the same
tissue, or even in the same cell.
 The different forms of the enzyme generally
differ in kinetic or regulatory properties
 Ex: hexokinase - 4, lactate dehydrogenase (LDH)
– 5, creatinine phosphate (CPK) - 3 , creatinine
kinase (CK) - 3, Alkaline phosphate (ALP) – 6,
Alcohol dehydrogenase (ADH) - 2
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66.  Estimation of enzyme activities in biological
fluid is of great clinical importance.
 The enzyme can be divided in 2 groups
◦ Plasma Specific or plasma functional enzyme
◦ Non-plasma specific or plasma non-functional
enzyme
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67.  Present in the plasma normally and have specific
fucntion
 Their value is higher in plasma than tissue
 They are mainly synthesized in liver and enter the
circulation
 Ex: Lipoprotein lipase, plasmin, thrombin,
choline esterase, ceruloplasmin
 Impairment of liver function or genetic disorder –
leads to enzyme deficiency
 Wilson disease – deficiency of ceruloplasmin
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68.  These enzymes are present in the low level in
plasma compared to the tissue
• Estimation of activities of these enzymes serves for the
diagnosis and prognosis of several disease - markers of
disease
 The raised enzyme level may indicate
◦ Cellular damage
◦ Increased rate of cell turnover
◦ Proliferation of cells
◦ Increased synthesis of enzymes
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69.  Amylase – Acute pancreatitis
 Serum glutamate pyruvate transferase (SGPT) – liver
disease (hepatitis)
 Serum glutamate oxaloacetate transaminase (SGOT) –
Heart attacks (myocardial infarction)
 Alkaline phosphatase – Rickets, obstructive jaundice
 Acid phophatase – cancer of prostate gland
 Lactate dehydrogenase (LDH) – heart attacks, liver disease
 Creatinine phosphokinase (CPK) – myocardial infarction
 Aldolase – Muscular dystrophy
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70.  Activity increased in acute pancreatitis
 Normal level – 0.2-1.5 IU/l
 Peak value in 8-12 hrs – onset of disease and
returns to normal in 3-4 days
 Urine analysis
 Serum analysis – chronic pancreatitis, acute
parotitis (mumps) and obstruction of
pancreatic duct
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71.  Also known as Alanine transaminase (ALT)
 Normal level – 3-4.0 IU/l
 Acute hepatitis of viral or toxic origin
 Jaundice and cirrohosis of liver
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72.  Also known as Aspartate transaminase
 Normal 4-4.5 IU/l
 Increase in myocardial infarction and also in
liver diseases
 SGPT is more specific for liver disease and
SGOT for MI – SGPT more cytosomal enzyme
while SGOT is cytosol and mitochondria
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73.  Elevated in bone and liver disease
 Normal : 25-90 IU/l
 Diagnosis for
◦ Rickets,
◦ Hyperparathyroidism,
◦ Carcinoma of bone
◦ Obstructive jaundice
◦ Paget’s Disease
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74.  Normal : 0.5 -4 KA units/dl
 Increased in cancer of prostate gland and
Paget’s Disease
 Good tumor marker
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75.  At least five different isozymes
 Assess the timing and extent of heart damage
due to myocardial infarction MI (heart attack)
◦ 12 hrs of MI: blood level of total LDH increases, and
there is more LDH2 than LDH1
◦ 24 hrs of MI: more LDH1 than LDH2
Type Compositio
n
Location
LDH1 HHHH Heart and erythrocyte
LDH2 HHHM Heart and erythrocyte
LDH3 HHMM Brain and kidney
LDH4 HMMM Skeletal muscle and liver
LDH5 MMMM Skeletal muscle and liverFor more Visit us:
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76.  Normal : 10-50 IU/l
 Diagnosis of
◦ MI - Very early detection
◦ Muscular dystrophy
◦ Hypothyroidism
◦ Alcoholism
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77.  Normal ; 2+6 IU/l
 Diagnosis of
◦ Muscular dystrophy
◦ Liver disease
◦ Myocardial infarction
◦ Myasthenia gravis
◦ Leukemia
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78.  Biochemistry – U. Satyanarayan, U.
Chakerpeni
 Color_Atlas_of_Biochemistry_2005
 Harpers_Biochemistry_26th_ed
 Lehninger Principles of Biochemistry, Fourth
Edition - David L. Nelson, Michael M. Cox.
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