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Enzymes for Karnataka University Botany IV Semester
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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
molecules6
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
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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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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