The document discusses enzymes, including their properties, nomenclature, and classification. It covers key topics such as the location of enzymes in the body, their uses in catalyzing biochemical reactions, and their practical importance in medicine, pharmaceuticals, food processing, and agriculture. It also examines the components of enzymes including cofactors, metal ions, and active sites. Finally, it explores how enzymes work by lowering the activation energy of reactions, without changing reaction equilibria or being consumed in the process.

1. Enzymes
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2. Assignment

3. - Introduction
- Properties of enzymes
- Nomenclature and Classification
- Mechanism of enzyme-catalyzed reactions
- Kinetics of enzyme-catalyzed reactions
- Inhibition of enzymes
- Regulation of enzymes
- Clinical applications of enzymes
Contents
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4. Enzymes
- Two fundamental conditions for life;
- 1st the living entity must be able to self-replicate
- 2nd the organism should be capable of catalyzing
chemical reactions efficiently & selectively.
- Enzymes are molecules that catalyze (enhance)
biochemical reactions in the biological systems(From Greek
en = in, + zumē= yeast).
– Almost all enzymes are composed of protein except for
Ribozymes.
– Ribozymes are molecules of RNA that catalyze
reactions on the phosphodiester bond of other RNAs.
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5. Location of enzymes
- Found in all tissues and fluids of the body.
– Intracellular enzymes catalyze the rxns of metabolic
pathways,
– Plasma membrane enzymes regulate catalysis within
cells in response to extracellular signals, &
– Enzymes of the circulatory system are responsible for
regulating the clotting of blood.
– Etc.
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6. Use of enzymes
- They catalyze the hundreds of stepwise reactions
- Degrade macromolecules,
- Conserve and transform chemical energy,
- make biological macromolecules from simple precursors.
- Important for cell replication
- Facilitating flow of genetic information
- Waste removal(urea,Co2,urate, lactate, e.t.c).
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7. Practical importance of enzyme study
- Absence or excessive appearance of enzymes can be
used as a tool for diagnosis, Rx & prognosis of diseases
in medicine.
- For drug designing in pharmaceuticals.
- chemical industry, food processing, and in agriculture.
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8. Properties of
Enzymes
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9. Enzymes Chemical catalysts
-Thermolabile - Thermostable
- Organic, biological substances - Mostly inorganic substances
- Protein in nature, denaturable - Non-protein, non-denaturable
- Specific for substrate and nature of the
chemical reaction
- Non-specific.
- Body temperature, pH and pressure are
their optimum.
- Require high temperature, pressure or
extreme pH.
- High catalytic efficiency by forming - Low catalytic efficiency because of absen
enzyme-substrate complex (reaction rate is ce of ES complex.
105-1017 greater than uncatalyzed).
- They are regulated. - Unregulated.
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10. Cont…
- Since, most enzymes are proteins
- Their catalytic activity depends on the integrity of their native
protein conformation.
- like other proteins, they have mwts ranging from about 12,000-
1million.
– Some enzymes require no chemical groups for activity other
than their amino acid residues(apoenzymes).
– Others require an additional chemical component called a
cofactor either one or more inorganic ions, such as Fe2+, Mg2+,
Mn2+, or Zn2+ or a complex organic or metalloorganic molecule
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11. • Simple enzymes: consists of only one peptide chain
• Conjugated enzymes: holoenzyme = apoenzyme + cofactor
- Cofactors: metal ions; small organic molecules
1- A coenzyme-a non-protein organic substance which is
dialyzable, thermo stable and loosely attached to the protein part.
2- A prosthetic group:an organic substance w/c is dialyzable &
thermo stable w/c is firmly attached to the protein or apoenzyme
portion.
3- A metal-ion activator:- Like K+, Fe2+,Fe3+,Cu2+,Zn2+,Mn2+
Molecular Components of enzymes
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12. Cont…
– Some enzymes require both a coenzyme & >1metal ions for
their activity.
– If a coenzyme or metal ion attached tightly or even covalently
bound to the enzyme protein is called a prosthetic group.
– A complete, catalytically active enzyme together with its bound
coenzyme and/or metal ions is called a holoenzyme.
– The protein part of such an enzyme is called the
apoenzyme/apoprotein.
– Coenzymes act as transient carriers of specific functional
groups.
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13. Some coenzymes that serve as transient carriers of specific atoms or
functional groups
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14. Metal ions
-Metal-activated enzyme: ions are necessary but loosely bound.
- Often found in metal-activated enzyme.
-Metalloenzymes:Ions tightly bound.
Particularly in the active center,
- Transfer electrons, bridge the enzyme and substrates, stabilize
enzyme conformation ,neutralize the anions.
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15. Some Inorganic Elements That Serve as Cofactors for Enzymes
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16. How Enzymes Work
- The enzymatic catalysis of rxns is essential to living systems.
- Under biologically relevant conditions, uncatalyzed rxns tend to be slow.
- Most biological molecules are quite stable in the neutral-pH, mild temperature,
aqueous environment inside cells.
- Reactions required to digest food, send nerve signals, contract a muscle etc.
- An enzyme circumvents these problems by providing a specific environment
(active site)where a given rxn(chemical transformation)can occur more rapidly.
- Substrate:The molecule that is bound in the active site and acted upon by the
enzyme.
- Then ES is formed by enclosing ,separating and sequestering the substrate
from the external env’t by enclosing .
- ES Complex was 1st proposed by Charles Adolphe-Wurth in 1880, key for
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17. Components of Enzyme
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18. - Almost all the enzymes are proteins having well defined structures.
- Some functional groups are close enough in space to form a portion
called the active center.
- Active centers look like a cleft or a crevice which are hydrophobic.
Active Center
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19. 2.The substrate-binding site :where the substrate specifically
binds and activates the chemical action along with the
catalytic site.
1.The catalytic site :the region of the enzyme that catalyzes the
chemical reaction(manipulates the substrate to help reaching
the reaction transition state and equilibrium faster.
- It may be slightly separated from the substrate-binding site or
they may be integrated into one site.
The active center has 2 essential components
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20. +
- Catalytic group
Binding group
Substrate
molecule
Protein chain
Active center
Essential groups
outside the
active center
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21. Active centers
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22. + +
+ + No binding due to lowered
substrate affinity
Allosteric enzyme
Allosteric
activator site
Allosteric
inhibitor site
Allosteric
effector Substrate
Active site
Binding
due to
increased
substrate
affinity
The allosteric site is an additional binding site that does not have a catalytic
function but has a regulatory function on the enzyme substrate binding and/or
catalytic functions.
The term allosteric site means “the other steering site”, i.e., other than and
separated from the catalytic/substrate-binding site(s); and, allostery means “a
change in shape”.
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23. 1.Lock-and-key model
-This analogy first postulated by Emil Fisher in 1894.
- In this analogy, the lock is the enzyme and the key is the substrate.
-Only the correctly sized key (substrate) fits into the key hole (active site) of
the lock (enzyme).
-Both E&S are rigid and fixed, so they must be complementary to each other
perfectly in order to have a right match.
Two theories of enzyme and substrate interaction
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24. 2.Induced-fit model(proposed by Koshland)
-The binding induces conformational changes of both E and S,
forcing them to get a perfect match.
- by the analogy of this model , both E and S are flexible.
- Widely accepted and persuasive model.
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25. Enzymes Affect Reaction Rates, Not Equilibria
- A simple enzymatic reaction might be written as;
Equation -1
- Where E, S, and P represent the enzyme, substrate, and product;
ES and EP are transient complexes of the enzyme with the
substrate&product.
- Catalysis do not affect the equilibria but the rate of a rxn.
• Any reaction, such as SP, can be described by a rxn coordinate
diagram, a picture of the energy changes during the reaction.
• Energy in biological systems is described in terms of free
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26. Cont…
• The starting point for either the forward or the reverse rxn is called ground
state.
- The equilibrium b/n S & P reflects the difference in the free energies
of their ground states.
- The free energy of the ground state of P is lower than that of S, so
G’o for the rxn is -ve & the equilibrium favors P.
- The position and direction of equilibrium are not affected by any
catalyst.
- A favorable equilibrium does not mean that the SP conversion
will occur at a detectable rate. There is an Energy barrier between
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27. Cont…
- The energy required for alignment of reacting groups, formation of
transient unstable charges, bond rearrangements, and other
transformations for the reaction to proceed in either direction.
- This is illustrated by the energy “hill” below.
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28. Cont…
 For the rxn to proceed, the molecules must overcome this barrier
and therefore must be raised to a higher energy level.
• Top of the energy hill is a point at which decay to the S or P state
is equally probable (it is downhill either way).
– This is called the transition state.
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29. Cont…
- The transition state is not a chemical species with any significant
stability and should not be confused with a reaction intermediate
(such as ES or EP).
– It is simply a fleeting molecular moment in which events
such as bond breakage, bond formation, & charge
development have proceeded to the precise point at which
decay to either substrate or product is equally likely.
– The difference between the energy levels of the ground state
and the transition state is the activation energy, G‡.
• The rate of a reaction reflects this activation energy:
• Higher activation energy corresponds to a slower reaction.
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30. Cont…
• Reaction rates can be increased by raising the temperature,
thereby increasing the number of molecules with sufficient
energy to overcome the energy barrier.
• Alternatively, the activation energy can be lowered by
adding a catalyst.
• Catalysts enhance rxn rates by lowering activation
energies.
• The activation energies, G‡, for the SP and PS reactions are
indicated. G’o is the overall standard free-energy change in the
direction SP.
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31. A + B → C + D
General Concepts
GG0RTln
[C][D]
[A][B]
- Spontaneous reaction only if G is negative.
- At equilibrium if G is zero.
- Spontaneously impossible if G is positive.
Reaction progress
Free
energy
G for
the reaction
reactants
products
transition state, S
G+ (uncatalyzed)
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32. Catalyzed reactions
- Reactants need to pass over the energy barrier, G+.
- Catalysts reduce the activation energy and assist the
reactants to pass over the activation energy.
Reaction progress
Free
energy
G for
the reaction
reactants
products
transition state, S
G+ (catalyzed)
G+ (uncatalyzed)
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33. Cont…
– The bidirectional arrows in Equation-1 make this point: any
enzyme that catalyzes the reaction SP also catalyzes the
reaction PS.
– The role of enzymes is to accelerate the interconversion of S& P.
– The enzyme neither consumed nor change the equilibrium point
but speed up the rxn rate.
– Activation energies are energy barriers to chemical reactions.
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34. Cont…
- These barriers are crucial to life itself.
– Without such energy barriers, complex macromolecules would
revert spontaneously to much simpler molecular forms, and the
complex and highly ordered structures&metabolic processes of
cells could not exist.
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35. 1. Do not consume themselves
- No changes in quantity and quality before and after the rxns.
2. Do not change the equilibrium points:only enhance the reaction
rates.
3.Apply to the thermodynamically allowable reactions
4. Reduce the activation energy
Unique features
- Enzyme-catalyzed reactions have very high catalytic efficiency.
- Enzymes have a high degree of specificity for their substrates.
- their activities are highly regulated in response to the external
changes.
Common Features Catalysts
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36. Accelerated reaction rates
Enzyme
Non-enzymatic
rate constant
(kn in s-1)
enzymatic
rate constant
(kn in s-1)
accelerated
reaction rate
Carbonic anhydrase 10-1 106 8 x 106
Chymotrypsin 4 x 10-9 4 x 10-2 10-2107
Lysozyme 3 x 10-9 5 x 10-1 2 x 108
Triose phosphate
isomerase
4 x 10-6 4 x 103 109
Urease 3 x 10-10 3 x 104 1014
Mandelate racemase 3 x 10-10 5 x 102 1.7 x 1015
Alkaline
phosphatase
10-15 102 1017
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37. 1- Absolute specificity(can recognize only one type of
substrate and implement their catalytic functions).
e.g., glucokinase,urease etc.
2- Relative specificity(catalyze one class of substrates or one
kind of chemical bond in the same type).
- Protein kinase-A,C&G catalayze the phosphorylation of the –
OH group of Serine and threonine in the substrate proteins,
leading to the activations of proteins. 3- Stereo specificity
High specificity
- Unlike conventional catalysts, enzymes demonstrate the ability to
distinguish different substrates.
- There are three types of substrate specificities.
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38. Absolute specificity
O C
NH2
NH2
+ H2O 2NH3 + CO2
urea
urease
O C
NH
NH2
+ H2O
methyl urea
CH3
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39. - Enzymes catalyze one class of substrates(Aromatic amino
acid decarboxylase0 or one kind of chemical bond in the
same type.
Relative specificity
O
H
OH
H
H
OH
H
OH
CH2OH
H
CH2OH
H
CH2OH
OH H
H OH
O
O
1
1
O
H
OH
H
H
OH
H
OH
CH2
H
CH2OH
H
CH2OH
OH H
H OH
O
O
1
1
O
O
OH
H
H
H
OH
H
OH
CH2OH
H 1
sucrose
raffinose
sucrase
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40. Stereospecificity
The enzyme can act on only one form of isomers of the substrates.
-Lactate dehydrogenase can recognize only the L-form not the D-
form.
High regulation
- Enzyme-catalyzed reactions can be regulated in response to the
external
Stimuli, satisfying the needs of biological processes.
- Regulations can be accomplished through varying the enzyme
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41. Nomenclature
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42. Cont…
Types of names: Trivial, Recommended, & Systematic names.
1)Trivial name: Name is given without scientific base.
– Enzymes were named by their discoverers for a broad function,
before the specific reaction catalyzed was known.
– For example, pepsin, from the Greek pepsis, “digestion,”
- lysozyme was named for its ability to lyse bacterial cell walls.
- Named by source: trypsin, named in part from the Greek
tryein, “to wear down,” was obtained by rubbing pancreatic tissue
with glycerin.
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43. 2.Recommended name:
- Many enzymes have been named by adding the suffix “-ase” to the
name of their substrate or to a word or phrase describing their
activity.
-Thus for example; urease catalyzes hydrolysis of urea,
- DNA polymerase catalyzes the polymerization of
nucleotidesDNA.
- Oxidases catalyze the oxidation rxn.
 It is short & convenient for everyday use.
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44. 3.Systematic name:
 Since sometimes the same enzyme may have two or more names,
or two different enzymes have the same name.
– B/c of such ambiguities, and the ever increasing number of newly
discovered enzymes, biochemists(IUBMB, in 1948), by
international agreement, have adopted a system for naming and
classifying enzymes.
– The enzyme commission divide enzymes to 6 classes then to
subclasses based on the type of reaction they catalyze.
– Assign a unique number, a systematic name, a shorter common
name to each enzyme.
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45. Systematic naming
- Every enzyme is given two names
1. A written systematic name.
2. A code digital identification name.
The written name of an enzyme is formed of
- The substrate/product name , the coenzyme name ,the class of the
chemical rxn suffixed with "-ase".
The digital name of an enzyme is composed of four parts (EC
W.X.Y.Z).
- EC refers to Enzyme Commission numbering system;
- W refers to the enzyme class, i.e., the type of reaction catalyzed;
- X refers to the subclass, i.e.,the general substrate or chemical
group involved;
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46. Cont…
Example, the formal systematic name of the enzyme catalyzing the
reaction
is ATP:Glucose phosphotransferase, which indicates that it
catalyzes the transfer of a phosphoryl group from ATP to glucose.
 Its Enzyme Commission number (E.C. number) is 2.7.1.1.
– the 1st number (2) denotes the class name (transferase);
– the 2nd number (7), the subclass(phosphotransferase);
– the 3rd number (1), a phosphotransferase with a hydroxyl
group as acceptor; and
– the 4th number (1), D-glucose as the phosphoryl group
acceptor.
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47. -Y refers to the sub-sub class,i.e., the specific substrate or
coenzyme; and,
- Z refers to the serial number of the individual enzyme among the
list of the sub-subclass.
- EC classification of enzymes.
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48. Classification of Enzymes with rxn & example
Class Reaction Enzymes
1. Oxidoreductases Ared + Box → Aox + Bred Dehydrogenase, Peroxidase
2. Transferases A-B + C → A + B-C Hexokinase, Transaminase
3. Hydrolases A-B + H2O → A-H + B-OH Alkaline Phosphatase, Trypsin
4. Lyases (synthases) A(XH)-B → A-X + B-H Carbonic Anhydrase, Dehydratases
5. Isomerases A  Iso-A
Triose phosphate isomerase,
Phosphoglucomutase
6. Ligases (synthetases) A + B + ATP → A-B + ADP + Pi Pyruvate Carboxylase, DNA Ligase
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49. Oxidoreductases sub-sub class
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51. Cont…
1.Alcohol:NAD:Oxidoreductase(EC1:1:1:1) ;
-1st 1= an oxidoreductase (class 1) catalyzes ethanol-OH
group oxidation into acetaldehyde (subclass 1 acting on -
OH) on the expense of NAD as electron acceptor (sub-
subclass 1) activated by the enzyme alcohol
dehydrogenase per se listed number 1 in the subsub sub
class (1).
• However, the shorter and more familiar and convenient
trivial names of the 1, 2 and 3 naming systems are still
widely in use.
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52. - They catalyze simultaneously a pair of oxidation and
reduction reactions of substrates, where one compound is
oxidized and the other is reduced by transfer of protons
and/or electrons.
AH2 + B → A + BH2
- Dehydrogenases/reductase -LDH
- Transhydrogenase –NAD/NADPH
- Oxidase –Xanthine oxidase
- Oxygenase -5-lipooxygenase
- Peroxidase-glutathione peroxidase
- Cytochrome oxidase, L-and D-amino acid oxidases.
1.EC1 Oxidoreductases
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53. - They catalyze the transfer of a functional group (e.g.,
phosphate, amino and methyl) or a chemical moiety (e.g.,
ketole and aldole) from one compound (donor) to the other
(acceptor).
A-X + B → A + B-X
-Aminotransferases,glycosyltransferases,methyltransferases,
Phosphotransferases(kinases),Transaldolases,Transketolases
, Sulfotransferases and mutases,
-Hexokinase (ATP:D-hexose 6-phosphotransferase, E.C.2.7.1.1.)
2.EC2 Transferases
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54. - They catalyze hydrolytic cleavage of substrates, i.e., breakdown of
the compound by addition of water;A-B + H2O → AH + BOH
-Thiolases,amidases,ribonucleases,deoxyribonucleases,hydrolytic
deaminases,phospholipases,phosphatases,glycosidases,esterase
&peptidases.
- Lipase (triacylglycerol acyl hydrolase, EC. 3.1.1.3.)
- Adenosine aminohydrolase (EC 3.5.4.4)
- Alkaline phosphatase (EC. 3.1.3.1)
4.EC4–Lyases;They catalyze breakage and reformation of bonds in
substrates by mechanisms other than hydrolysis or oxidation.
- Phosphorylases split substrate by adding phosphate.
3.EC3 -Hydrolases
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55. -A-B + X-Y → AX + BY
Aldolase (ketose 1-phosphate aldehyde lysase, E.C. 4.1.2.7.)
pyruvic decarboxylase,Phosphorylases,Histidase.
5.EC-5-Isomerases;
- They reversibly catalyze interconversion of different types of
isomers that include;A → A’
 Isomerases,epimerases,mutases,racemases
-Triosephosphate isomerase (D-glyceraaldehyde 3-phosphate
ketoisomerase, E.C. 5.3.1.1).
- Retinol isomerase and Phosphohexose isomerase
Cont….
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56. -They catalyze covalent C-C, C-O, C-S or C-N new bond
formation to ligate 2 molecules together in the presence of
ATP (synthetase)
A + B → A-B
- Glutamine synthetase (L-glutamate ammonia ligase, E.C.
6.3.1.2.)
- Acetyl CoA carboxylase, succinate
thiokinase,GDH,Aspargine synthetase.
6.EC6 Ligases or synthetases
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57. Mechanism of Enzyme-Catalyzed
Reactions
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66. Thanks!
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