enzymes

1. ENZYMES
Dr. Neelam Zaidi

2. INTRODUCTION
▰ Enzymes, biological catalysts
▰ Highly specialized proteins (RNA)
▰ Increase the rate of reactions without
being changed in the overall process
▰ Substrates (called reactants), products
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3. CONT’D
▰ Function in aqueous solutions under very
mild conditions of temp and pH
▰ Most enzymes are three dimensional
globular proteins (tertiary and quaternary
structure)
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4. NOMENCLATURE
▰ Formerly enzyme were given names ending
in “-in”. e.g. pepsin, trypsin
▰ Thecurrent system for naming enzymes
uses the name of the substrate or the type
of reaction involved, with the ending“-ase”.
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5. ENZYME SUBTRATE or REACTION
TYPE
Maltase Maltose
Urease Urea
Protease Proteins
Carbohydrase Carbohydrates
Lipase Lipids
Hydrolase Hydrolysis Reaction
Deaminase Removing amines
Dehydrogenase Removing hydrogens
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6. Enzymes Characteristics
Synthetase Requires ATP
Synthase No ATP required
Phosphatase Use water to remove Pi
Phosphorylase Use Pi to break a bond and generate P-
product
Dehydrogenase NAD+/FAD is an electron acceptor
Oxidase O2 is the acceptor, O atoms are not
incorporated into substrate
Oxygenase One or both O atoms are incorporated
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7. BASIC TERMS
▰ Holoenzyme: refers to the active enzyme with its
nonprotein component
▰ Apoenzyme: the inactive enzyme without its
nonprotein moiety
▰ Cofactor: the nonprotein moiety is a metal ion,
such as Zn2+ or Fe2+
▰ Coenzyme: it is a small organic molecule
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8. BASIC TERMS
▰ Coenzymes commonly are derived from
vitamins
▰ For example, NAD+ contains niacin, and FAD
contains riboflavin
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10. PROPERTIES
▰ ACTIVE SITES
▰ CATALYTIC EFFICIENCY
▰ SPECIFICITY
▰ LOCALIZATION
▰ REGULATION
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11. ACTIVE SITES
▰ A special pocket or
cleft or region in
enzyme molecules
▰ Formed by folding of
the protein
▰ Participate in
substrate binding
and catalysis
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12. CATALYTIC EFFICIENCY
▰ Enzyme-catalyzed reactions are highly
efficient
▰ Two properties: “accelerate”
▰ Enzyme itself doesn’t change
▰ Chemical equilibrium doesn’t change
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13. SPECIFICITY
▰ Highly specific
▰ Interact with one or a few substrates
▰ Catalyze only one type of chemical
reactions
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14. REGULATION
▰ Enzyme activity can be regulated
▰ Increased or decreased
▰ The rate of product formation
responds to cellular need
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15. LOCALIZATION
▰ Many enzymes are localized in specific
organelles within the cell
▰ Or specific localization of the body.
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16. INTRACELLULAR ENZYMES
▰ Lysosome: enzyme required for the degradation of
complex macromolecules
▰ Nucleous: enzymes of DNA and RNAsynthesis
▰ Cytosol: enzyme of glycolysis, fatty acid synthesis, urea
cycle, gluconeogenesis, heme synthesis
▰ Mitochondria: enzymes of TCA cycle, fattyacid
oxidation, oxidative phosphorylation
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17. EXTRACELLULAR ENZYMES
▰ Are secreted and function out of the cell
▰ Mainly digestive enzymes
▰ α-amylase secreted by salivary glands
▰ Pepsin secreted by gastric glands
▰ Lipase, trypsin, chymotrypsin, amylase secreted by
pancreas
▰ Aminopeptidase, dipeptidase, lactase, sucrase, maltase,
isomaltase secreted from intestinal glands
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18. PRECURSOR ENZYME
▰ Some proteolytic enzymes found in the blood or
digestive tract are present in an inactive form
(precursor) known as zymogen or proenzymes
▰ Some examples: prothrombin, proelastase,
chymotrypsinogen, trypsinogen, pepsinogen
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19. HOW ENZYMES WORK
▰ Free energy of activation
▰ Chemistry of the active site
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20. FREE ENERGY OF ACTIVATION
▰ All chemical reactions have an energy barrier
separating substrate (S) and product (P)
▰ This barrier is called free energy of activation
▰ The energy difference between the energy of
the substrate and high energy intermediates in
the transition state
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21. 21

22. CONT’D
▰ Enzymes can lower the activation energies
so that reactions can occur quickly
▰ Doesn’t change equilibrium of the reaction.
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23. CHEMISTRY OF THE ACTIVE SITE
▰ Substrates bind to enzymes then form
an enzyme-substrate complex (ES)
▰ Binding is facilitated by active sites
(flexible molecular template)
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24. TWO MODELS
▰ Two models of substrate binding to the
active site of the enzyme
▰ Lock and key model
▰ Induced fit model
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25. ▰ The substrate and enzyme active site have
complementary shapes in which the
substrate fits exactly into the active site
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26. ▰ The configurations of both the enzyme and
substrate are modified (conformational
changes) by substrate binding
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Induced fit model

27. ENZYME KINETICS
▰ The study of reaction rates and how they
change in response to changes in
experimental parameters
▰ The rate of reaction affected by:
▰ cont of substrate [S]
▰ temp
▰ pH
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28. CONT’D
▰ Initial velocity (Vₒ )
▰ Maximum velocity (Vmax) : when all active sites
on the enzyme are filled with substrates
▰ At saturation levels of substrate,the enzyme
functions at its maximum velocity
▰ The occurrence of higher cont of substrate
cannot increase the velocity further
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30. MICHAELIS CONSTANT ( Km )
▰ Represents the cont of a substrate when the
reaction is at half of its maximum velocity (½Vmax)
▰ Km is an inverse measure of the strength of
binding between the enzyme and substrate.
▰ The lower the Km, the greater the affinity
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31. FACTORS AFFECTING VELOCITY
OF ENZYME REACTION
▰ Substrate cont
▰ Enzyme cont
▰ Product cont
▰ pH/temp
▰ Inhibitors
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34. INHIBITION OF ENZYME
ACTIVITY
▰ Any substance that decrease the velocity of an
enzyme catalyzed reaction is called an inhibitor
▰ Classified into :
▰ Irreversible
▰ Reversible
▰ Competitive
▰ Noncompetitive
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35. IRREVERSIBLE INHIBITION
▰ The inhibitor binds to the
enzyme irreversibly through
formation of a covalent bond
with the enzyme, permanently
inactivating the enzyme
▰ E.g: Ferrochelatase is
irreversibly inhibited by lead
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36. “SUICIDE ” INHIBITOR
▰ A special group of irreversible inhibitor
▰ The inhibitor binds to the enzymes as a substrate
and catalyzed, then generates a chemically
reactive intermediate that inactivates the
enzyme through covalent modification.
▰ Suicide because enzyme participates in its own
irreversible inhibition.
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37. REVERSIBLE INHIBITION
▰ Inhibitor binds with enzyme through
non-covalent bonds – temporary
▰ The activity of enzyme is fully restored
on removing the inhibitor- reversible
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38. CONT’D
▰ Reversible inhibitors are used to control enzyme
activity
▰ The is often an interaction between the substrate
or end product and the enzymes controlling the
reaction
▰ Buildup of the end product or a lack of substrate
may deactivate the enzyme
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39. COMPETITIVE INHIBITION
▰ Inhibitors often have structural features similar to
those of the substrates
▰ Therefore, they directly compete with the substrate
for the same active site on the enzyme.
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reversible

40. CONT’D
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41. CLINICAL APPLICATION
▰ Statin drugs: antihyperlipidemic
agents
▰ Structural analogs
▰ Competitively inhibit HMG-CoA
reductase in cholesterol
biosynthesis.
▰ Lower plasma cholesterol
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42. NONCOMPETITIVE INHIBITION
▰ The inhibitor and substrate bind at different sites on the
enzyme (allosteric site)
▰ Can bind free enzyme or ES complex
▰ Changes the shape of active site on enzyme
▰ Not influenced by the cont of substrate
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43. CLINICAL APPLICATION
▰ Anticancer drugs: inhibit enzymes involved in
DNA synthesis; stop DNA production/ division
of more cancer cells
▰ Cyanide poisoning: Irreversible inhibitor of
cytochrome C, an enzyme in cellular
respiration: stops production of ATP
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44. DO YOU KNOW?
▰ EnzymeinhibitorsasDrugs
▰ While some enzyme inhibitors are poisonous, others
are beneficial to life. Pencillin acts as an enzyme inhibitor
for transpeptide, a substance that bacteria need to build
their cell walls. If the cell wall is lacking, osmotic pressure
causes the bacterial cell to burst and die.
▰ However, new strains of bacteria have developed an
enzyme, penicillinase, that inactivates penicillin. To destroy
these new strains, synthetically modified penicillins have
been prepared so that this antibiotic remains effective.
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45. REGULATION OF ENZYME
ACTIVITY
▰ Regulation of allosteric enzymes
▰ Regulation of enzymes by covalent
modification
▰ Induction and repression of enzyme
synthesis
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46. ALLOSTERIC ENZYMES
▰ Are regulated by noncovalent binding of
modulators / effectors at a site other than the
active site
▰ Composed of multiple subunits
▰ allosteric activators: enhance (cooperativity)
▰ allosteric inhibitors: decrease (feedback)
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Allosteric = other site

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49. HOMOTROPIC EFFECTORS
▰ Substrate itself serves as an effector
(positive)
▰ The presence of S at one site enhances the
activity of other sites, cooperative binding.
▰ E.g. the binding of O2 to Hb
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50. HETEROTROPIC
EFFECTORS
▰ Effector is different from substrate.
▰ Feedback inhibition
▰ E.g: phosphofructokinase-1 is
allosterically inhibited by citrate
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51. COVALENT MODIFICATION
▰ Addition or removal of phosphate groups
▰ Protein phosphorylation is mediated by hormones
▰ Phosphorylation: protein kinases. ATP as donor
▰ Depending on the specific enzymes, Pi-form may
increase or decrease activity.
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52. ENZYME SYNTHESIS
▰ Cells can alter the rate of enzyme degradation
or synthesis.
▰ Induction/ repression
▰ At only one stage of development or under
selected physiologic conditions.
▰ E.g. insulin
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53. REGULATORY ENZYMES
▰ In each enzyme system, there is at least one
enzyme that sets the rate of the overall
sequence because it catalyzes the slowest or
rate-limiting reaction
▰ These regulatory enzymes exhibit increased
or decreased catalytic activity in response to
certain signals
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56. REFERENCES
• NomenclatureCommitteeoftheInternationalUnionofBiochemistryand
MolecularBiology(NC-IUBMB)EnzymeNomenclature
• NationalCenterforBiotechnologyInformation,U.S.NationalLibraryofMedicine
8600RockvillePike,BethesdaMD,20894USA
• Lehninger.Principlesofbochemistry.byNelsonandCox,5thEdition;W.H.Freeman
and Company
• NaikPankaja(2010).Biochemistry.3ededition,JAYPEE
• Emsley,John(2011).Nature'sBuildingBlocks:AnA-ZGuidetotheElements(Newed.).
NewYork,NY:OxfordUniversityPress.ISBN:978-0-19-960563-7
• Guyton,C.Arthur.1985.TextbookofMedicalPhysiology.6thedition,W.B.Company
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