4th SEMESTER – BOTANYKARNATAKA UNIVERSITY, DHARWADKARNATAKA UNIVERSITY, DHARWAD

Modified from various internet resources byDr. Jayakara Bhandary

Associate Professor of BotanyGovernment Arts & Science College

Karwar, Uttara Kannada1

Introduction & History� Enzyme, in Greek means in living (en= in, zyme =

living).� Biocatalysts or Organic catalysts, usually high

molecular weight proteins (exception- Ribozymesmolecular weight proteins (exception- Ribozymesor RNA enzymes).

� Coined by Kuhne in 1878.� First enzyme extract from Yeast cells by Buchner

(1897).� First purified enzyme is urease, by James B.

Summer (1926).

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Enzymes are Biological CatalystsEnzymes are proteins that: � Increase the rate of

reaction by lowering the energy of activation.Catalyze nearly all the energy of activation.

� Catalyze nearly all the chemical reactions taking place in the cells of the body.

� Have unique three-dimensional shapes that fit the shapes of reactants.

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Activation EnergyThink of activation energy as the BARRIERrequired to make a product.Most stable product is the one with

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Most stable product is the one with the lowestenergy.Most reactions require a “push” to get themstarted! “Push” is called “energy of activation” forreaction - Also represented by EA

Trivial Names of EnzymesThe name of an enzyme:� Usually ends in –ase. � Identifies the reacting substance. For

example, example, sucrase catalyzes the reaction of sucrose.

� Describes the function of the enzyme. For example, oxidases catalyze oxidation.

� Could be a common name, particularly for the digestion enzymes such as pepsin and trypsin.

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IUB Classification of Enzymes� Enzymes are classified according to the reaction

they catalyze.Class Reactions catalyzed

� Oxidoreductases Oxidation-reduction� Oxidoreductases Oxidation-reduction� Transferases Transfer groups of atoms� Hydrolases Hydrolysis� Lyases Add atoms/remove atoms

to/from a double bond� Isomerases Rearrange atoms� Ligases Use ATP to combine

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Systematic Name� According to the International union Of Biochemistry

an enzyme name has two parts:-First part is the name of the substrates for the

enzyme.enzyme.-Second part is the type of reaction catalyzed by

the enzyme.This part ends with the suffix “ase”.Example: Lactate dehydrogenase

EC numberEnzymes are classified into six different groups

according to the reaction being catalyzed. The nomenclature was determined by the Enzyme Commission in 1961 (with the latest update having Commission in 1961 (with the latest update having occurred in 1992), hence all enzymes are assigned an “EC” number. The classification does not take into account amino acid sequence (ie, homology), protein structure, or chemical mechanism.

EC numbers§ EC numbers are four digits, for example a.b.c.d, where

“a” is the class, “b” is the subclass, “c” is the sub-subclass, and “d” is the sub-sub-subclass. The “b” and “c” digits describe the reaction, while the “d” digit is “c” digits describe the reaction, while the “d” digit is used to distinguish between different enzymes of the same function based on the actual substrate in the reaction.

§ Example: for Alcohol:NAD+oxidoreductase EC number is 1.1.1.1

The Six Classes

�EC 1. Oxidoreductases �EC 2. Transferases �EC 3. Hydrolases �EC 4. Lyases �EC 5. Isomerases �EC 6. Ligases

EC 1. Oxidoreductases � Catalyze the transfer of hydrogen or oxygen atoms

or electrons from one substrate to another. � Since these are ‘redox’ reactions, an electron

donor/acceptor is also required to complete the reaction.reaction.

A H2 +B → A+ BH2

Ex. Oxidases, Dehydrogenases, Reductases.

EC 2. Transferases§ Catalyze group transfer reactions, excluding

oxidoreductases (which transfer hydrogen or oxygen and are EC 1). These are of the general form: form:

§A-X + B ↔ BX + A§ Ex: Transaminases (transfer amino group),

Kinases (transfer Phosphate group)

EC 3. Hydrolases�Catalyze hydrolytic reactions.

Includes.

A-X + H O ↔ X-OH + A-H �A-X + H2O ↔ X-OH + A-H �Ex: lipases, esterases, Amylases,

peptidases/proteases, etc.

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 the reverse reaction, ie, addition of function groups across a double bond.across a double bond.

A- X +B-Y → A=B + X-YEx: Decarboxylases, Aldolases, Dehydrases,

Deaminases, Synthases, etc.

EC 5. Isomerases� Catalyzes isomerization reactions, including

epimerizations and cis-trans� isomerizations.

A→A’ Ex: Isomerases (Cis-Trans), Epimerases (D—L)

EC 6. Ligases� Catalyzes the synthesis of various (mostly C-X)

bonds, coupled with the breakdown of energy-containing substrates, usually ATP .

A + B → A-BATP → ADP+iP

Ex: Synthetases, Carboxylases

Classification of Enzymes: Oxidoreductases and Transferases

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Classification: Hydrolases and Lyases

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Classification: Isomerases and Ligases

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Active SiteThe active site: � Is a region within an

enzyme that fits the shape of molecules called substrates.

� Contains amino acid R called substrates.

� Contains amino acid R groups that align and bind the substrate.

� Releases products when the reaction is complete.

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Enzyme SpecificityEnzymes may recognize and catalyze:� A single substrate.� A group of similar substrates.� A particular type of bond. � A particular type of bond.

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Mechanism of Enzyme Catalyzed Reactions � The proper fit of a substrate (S) in an active site

forms an enzyme-substrate (ES) complex.E + S ES

� Within the ES complex, the reaction occurs to � Within the ES complex, the reaction occurs to convert substrate to product (P).

ES E + P� The products, which are no longer attracted to

the active site, are released. � Overall, substrate is convert to product.

E + S ES E + P

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Mechanism of Enzyme Action

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Example of An Enzyme Catalyzed Reaction

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1.Lock-and-Key ModelIn the lock-and-key model of enzyme action: � The active site has a rigid shape.� Only substrates with the matching shape can

fit.

Mechanism of Enzyme Action:

fit.� The substrate is a key that fits the lock of the

active site.

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2. Induced-fit ModelIn the induced-fit model of enzyme action:� The active site is flexible, not rigid.� The shapes of the enzyme, active site, and

substrate adjust to maximum the fit, which substrate adjust to maximum the fit, which improves catalysis.

� There is a greater range of substrate specificity.

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Isoenzymes � Isoenzymes

catalyze the same reaction in different tissues in the body.the body.

� Lactate dehydrogenase, which converts lactate to pyruvate, (LDH) consists of five isoenzymes.

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Temperature and Enzyme ActionEnzymes:� Are most active at an

optimum temperature (usually temperature (usually 37°C in humans).

� Show little activity at low temperatures.

� Lose activity at high temperatures as denaturation occurs.

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pH and Enzyme ActionEnzymes:� Are most active at

optimum pH.� Contain R groups of � Contain R groups of

amino acids with proper charges at optimum pH.

� Lose activity in low or high pH as tertiary structure is disrupted.

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Optimum pH Values� Most enzymes of the body have an optimum pH

of about 7.4.� In certain organs, enzymes operate at lower and

higher optimum pH values.higher optimum pH values.

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Enzyme Concentration� The rate of

reaction increases as enzyme concentration increases (at increases (at constant substrate concentration).

� At higher enzyme concentrations, more substrate binds with enzyme.

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Substrate Concentration� The rate of reaction

increases as substrate concentration concentration increases (at constant enzyme concentration).

� Maximum activity occurs when the enzyme is saturated.

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