3. Terms should be learn
• allosteric enzyme; a regulatory enzyme whose affinity
for its substrate is affected by the presence or absence of
other molecules
• Apoenzyme; protein portion of an enzyme (i.e., lacking a
coenzyme)
• Enzyme; protein which catalyzes a biochemical reaction,
an enzyme name ends in -ase (e.g., amylase and carbonic
anhydrase)
• Holoenzyme; complete active enzyme (i.e.,
protein + coenzyme)
Dr. Siham Gritly 3
4. • enzyme classificationl; assignment of an enzyme to one of six groups,
depending on the type of chemical reaction which the enzyme catalyzes
• first order kinetics; rate of reaction is directly proportional to the
concentration of starting materials (i.e., substrate)
• Inhibition; alteration in an enzyme’s activity, usually caused by
modification of the enzyme active site, so that substrate cannot bind to the
enzyme, or substrate can bind but cannot be converted to product, or
product cannot be released
• Michaelis-Menten kinetics; simple mathematical description of a first-
order enzyme reaction [Leonor Michaelis was British and Maud Menten
was Canadian]
• Catalyst; chemical substance that facilitates (or slows) a chemical process, but is
unchanged by the process
• Coenzyme; small, nonprotein group attached to an enzyme; the site on the
enzyme where catalysis occurs
• Cofactor; organic molecule that acts as a coenzyme
• Michaelis constant ( Km ) represent the concentration of a substrate that is found in
an occurring reaction when the reaction is at one half its maximum velocity
Dr. Siham Gritly 4
5. Enzymes
• macromolecular components composed of
protein. They are known as biological catalysts
responsible for supporting almost all of the
chemical reactions that maintain life processes
• Enzymes are found in all tissues and fluids of the
body.
• Enzymes have a high degree of specifity for
types of reaction catalized and for their substrate
• Enzymes are also stereospecific catalysts for
specific stereoisomers (L & D)
Dr. Siham Gritly 5
6. • All enzymes are proteins except ribozymes;
• ribozymes are certain RNA molecules act as
catalysts
• ribozymes catalyzing the cleavage and
synthesis of phosphodiester bond in RNA at
specific sites in RNA
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7. Localization of enzymes
• 1-Enzymes of the intracellular
• Lysosome; enzyme required for the degradation
of complex macromolecules
• Nucleous; enzymes of DNA and RNA synthesis
• Cytosol; enzyme of glycolysis, fatty acid
synthesis, urea cycle, gluconeogenesis, heam
synthesis
• Mitochondria; enzymes of TCA cycle, fatty acid
oxidation, oxidative phosphorylation
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8. • 2-extracellular enzymes
• Are secreted and function out from the cell
• Mainly digestive enzymes
• Alfa amylase secreted by salivary glands
• Pepsin and renin secreted by gastric glands
• Lipase, trypsin, chymotrypsin, amylase secreted
by pancrease
• Aminopeptidase, dipeptidase, lactase, sucrase,
maltase, isomaltase secreted from intestinal
glands
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9. Proenzyme or zymogen (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
which produced and stored as inactive
proenzyme or zymogen
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10. Composition classification of enzymes
• Simple enzymes composed completely of
protein
• complex enzymes, are composed of protein
plus a relatively small organic molecule.
• Complex enzymes are also known as
holoenzymes.
• protein component is known as the
apoenzyme,
• Apoenzymes becomes active enzymes on
Dr. Siham Gritly 10
addition of a cofacter.
11. • Cofactors can be either inorganic (e.g., metal
ions or organic compounds, (e.g.,favin and
heme) or organic
• Organic cofactors can be either prothetic
groups, which are tightly bound to an enzyme,
or coenzymes, which are released from the
enzyme's active site during the reaction
• Coenzymes binds apoenzyme protein
molecule to produce active holoenzyme
Dr. Siham Gritly 11
12. Cofactors can be either inorganic (e.g., metal ions or organic
compounds, (e.g.,favin and heme)
Organic cofactors can be either prothetic groups, which are
tightly bound to an enzyme, or coenzymes, which are released
from the enzyme's active site during the reaction. when the
binding between the apoenzyme and non-protein components is
non-covalent, the small organic molecule is called a coenzyme
Dr. Siham Gritly 12
14. classification and nomenclature of
Enzyme
Reference; Nomenclature Committee of the International Union of
Biochemistry and Molecular Biology (NC-IUBMB) Enzyme Nomenclature
• Functional classification
• enzymes are grouped into six functional
'
classes by the International Union of
Biochemists (I.U.B.).
Dr. Siham Gritly 14
15. • Class 1.Oxidoreductases- this class belong all
enzymes of catalysing oxidoreduction reactions.
• The substrate that is oxidized is regarded as
hydrogen donor.
• Act on many chemical groupings to add or
remove hydrogen atoms
• The common name will be dehydrogenase,
reductase can be used.
• Oxidase is only used in cases where O2 is the
acceptor.
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16. • Class 2. Transferases- transfer chemical groups
from one molecule to another or to another
part of the same molecule.
• Kinases are specialized transferases that
regulate metabolism by transferring phosphate
from ATP to other molecules
Dr. Siham Gritly 16
17. • Class 3. Hydrolases-
• Add water across a bond, hydrolyzing it
• These enzymes catalyse the hydrolytic
cleavage of C-O, C-N, C-C and some other
bonds,
• Although the systematic name always includes
hydrolase, such as digestive enzymes
Dr. Siham Gritly 17
18. • Class 4. Lyases- remove a group from or add a
group to double bonds.
• Add water, ammonia or carbon dioxide across
double bonds, or remove these elements to
produce double bonds
• In the common names, expressions like
decarboxylase, aldolase, dehydratase (in case
of elimination of CO2, aldehyde, or water) are
used
Dr. Siham Gritly 18
19. • Class 5. Isomerases-.
• These enzymes catalyse geometric or
structural changes within one molecule.
According to the type of isomerism
(interconvert isomeric structures by molecular
rearrangements),
• they may be called, cis-trans-isomerases,
isomerases, tautomerases, mutases and L to D
isomerase,
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20. • Class 6. Ligases –
• Ligases are enzymes catalysing the joining together
of two molecules coupled with the hydrolysis of a
diphosphate bond in ATP or a similar triphosphate
• Catalyze reactions in which two chemical groups are
joined (or ligated) with the use of energy from ATP
• pyruvate oxaloacetate
• enzyme = pyruvate carboxylase
Dr. Siham Gritly 20
21. The Catalytic Activity of Enzymes
• enzymes are characterized by two fundamental
properties.
• 1- First, they increase the rate of chemical
reactions without themselves being consumed or
permanently altered by the reaction.
• 2-Second, they increase reaction rates without
altering the chemical equilibrium between
reactants and products,
• a molecule acted upon by an enzyme is called
substrate [S]
• substrate [S] is converted to a product (P)
Dr. Siham Gritly 21
22. • The functional activities depend on
• 1-protein portion of enzyme
• 2-non-protein prothetic group or co-enzyme
• Usually prothetic group is inorganic (metal ions,
Mg, Zn, Cu, Mn, Fe
• Enzyme activity system may affected by;-
• Negative modifiers
• Change on pH
• Change in enzyme concentration
Dr. Siham Gritly 22
23. How enzyme work
energy changes during the enzymatic reaction
• All chemical reactions have an energy barrier
separation reactant (S) and product (P)
• It is known as free energy of activation EA
• Free energy of activation is the energy
difference between the energy of the
reactant and high energy intermediates that
occur during the formation of the products
• The amount of change in the free energy of a
reaction is labeled ΔG
Dr. Siham Gritly 23
24. There are two theories as to how reactions occur:
• 1- the collision theory,
• it is thought that reactions occur because
molecules collide; the faster they collide, the
faster the reaction occurs.
• The energy level that must be reached for the
molecules to collide is called the activation
energy EA Enzymes lower the activation
energies so that reactions can occur quickly
Dr. Siham Gritly 24
25. • 2- the transition state theory,
• substrate are thought to form bonds and then
break bonds until they form products.
• As this forming and breaking happens, free
energy increases until it reaches a transition
state (also called activated complex), which is
viewed as the midpoint between reactants and
products.
• Reactions proceed faster if there is a higher
concentration of activated complex.
Dr. Siham Gritly 25
26. The energies of the stages of a chemical reaction.
Substrates need a lot of potential energy to reach a
transition state, which then convert into products.
Enzymes act by reducing the activation energy, thus
increasing the rate of reaction
Dr. Siham Gritly 26
27. If the free energy of activation EA is high, the transition state is
low, and the reaction is slow.
If the activation energy is lower, the reaction occurs faster
because more activated complexes (transition state) can form.
this figure shows the changes in energy during conversion of
a molecule of reactant or substrate S to product P through
the transition state
Dr. Siham Gritly 27
28. Transition state; in which high energy intermediates are formed
during the conversion of substrate to product
Dr. Siham Gritly 28
29. Active site of an enzyme
• The catalytic activity of enzyme involves the
binding of their substrates to form an enzyme-
substrate complex (ES). In an enzymatic
reaction the substrate binds to a specific region
of the enzyme, called the active site.
• While bound to the active site, the substrate is
converted into the product of the reaction,
which is then released from the enzyme.
Dr. Siham Gritly 29
30. The active site of an enzyme lower EA and speed
the chemical reaction barrier by;-
• 1-orienting substrates correctly
• 2-strain substrate bonds
• 3-providing a favorable micro-
environment
• 4-covalently bonding to the substrate
Dr. Siham Gritly 30
31. Enzyme substrate complex (ES complex)
Enzymatic catalysis of a reaction between two
substrates.
The enzyme provides a template upon which the two
substrates are brought together in the proper position
and orientation to react with each other
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32. Mechanism of enzyme action
• Formation of an enzyme-substrate complexes
is the first step in enzymatic catalysis
• Substrate is bound through multiple non-
covalent interactions at the active site of the
enzyme forming substrate complex which is
then converted to product and free away
enzyme
Dr. Siham Gritly 32
33. • Two model of substrate binding to the active
site of the enzyme;
• -lock and key model
• - induced fit model
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34. lock and key model
the substrate and enzyme active site have complementary shapes
in which the substrate fits exactly into the active site
Dr. Siham Gritly 34
35. induced fit model; the configurations of both the enzyme and
substrate are modified by substrate binding
This model proposes that the initial interaction between enzyme
and substrate is relatively weak, but that these weak interactions
rapidly induce conformational changes in the enzyme that
strengthen binding
Dr. Siham Gritly 35
36. Enzyme Kinetic
• Enzyme kinetics are the study of reaction rates
and how they change in response to changes in
experimental parameters.
• The rate of reaction affected by;
• -the amount of substrate present (S)
• -the effect on initial velocity (Vₒ)of varying
substrate concentration when enzyme
concentration is held constant
• initial velocity is the rate of reaction as soon as
enzyme and substrates are mixed
Dr. Siham Gritly 36
37. Effects of substrate concentration on the initial velocity of an enzyme
catalyzed reaction keeping enzyme concentration constant
Dr. Siham Gritly 37
38. • Low concentrations of substrate, initial
velocity (Vₒ) increases linearly with an
increase in S this condition known as first
order kinetics
• At higher substrate concentration, (Vₒ)
increases by smaller amount in response to
increase in S
• That is, The velocity of an enzyme-catalyzed
reaction increases as the concentration of the
substrate increases
Dr. Siham Gritly 38
39. • When there are small increase in (Vₒ) with increasing
S a condition known as zero order kinetics and a
plateau is called maximum velocity vmax (when all
active sites on the enzyme are filled with
substrate)
• That is to say; At saturation levels of substrate, the
enzyme functions at its maximum velocity (vmax)
• the occurrence of higher concentration of substrate
cannot increase the velocity further
Dr. Siham Gritly 39
40. Factors affecting the Velocity of Enzyme
reaction
• Any substrate that affects the configuration of an
enezyme affects its activity
• Various factors that affect enzyme activity are;-
• 1-substrate concentration
• 2-Enzyme concentration
• 3- Ph (H ions concentration)
• 4-temperature
• 5-product concentration
• 6-inhibitors
Dr. Siham Gritly 40
41. Michaelis-Menten constant Km
• Michaelis constant ( Km ) represent the
concentration of a substrate that is found in an
occurring reaction when the reaction is at one
half its maximum velocity (½ Vmax)
• Km is an inverse measure of the strength of
binding between the enzyme and its substrate.
The lower the Km, the greater the affinity
• E+S ↔ ES-------1
• ES→ E+ P ---------2
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42. If an enzyme has a high Km value then the abundance of
substrate must be present to raise the rate of reaction to half its
maximum the enzyme has a low affinity for its substrate.
e.g, glucokinase the low affinity of glucokinase for glucose
prevents too much glucose being removed from the blood during
period of fasting
substrate concentration versus reaction velocity
Dr. Siham Gritly 42
43. The Michaelis-Menten Equation
represent the concentration of a substrate that is found in an
occurring reaction when the reaction is at one half its
maximum velocity (½ Vmax)
Vₒ initial reaction velocity is the rate of reaction as
=
soon as enzyme and substrates are mixed
Vmax = maximum velocity is observed when all active
sites on the enzyme are filled with substrate
Km = Michaelis-Menten constant is the substrate
concentration at which the reaction rate is half of its
maximum velocity Vmax
[S ] = substrate concentration
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44. Michaelis constant has two significance
• 1-Km is the concentration of substrate at which
half the active site of enzymes are filled, thus Km
provide measure of the substrate concentration
required for the reaction to occur
• 2-Km is the measure for the strength of the ES
complex or the affinity of enzyme to substrate
• -a high Km indicates weak binding with its
substrate
• -a low Km indicates strong affinity or binding to
substrate
Dr. Siham Gritly 44
46. • Noncompetitive Inhibitor;- Binds E or ES
complex other than at the catalytic site.
Substrate binding unaltered, but ES complex
cannot form products. Inhibition cannot be
reversed by substrate.
• Kinetic effect; Km appears unaltered; Vmax is
decreased proportionately to inhibitor
concentration
Dr. Siham Gritly 46
51. Regulatory enzymes
• In each enzyme system, however, there is at
least one enzyme that sets the rate of the
overall sequence because it catalyzes the
slowest or rate-limiting reaction.
• These regnlatory enzymes exhibit increased
or decreased catalytic activity in response to
certain signals.
Dr. Siham Gritly 51
53. Allosteric Enzymes Are Regulated by Noncovalent
Binding of Modulators
• allosteric regulation is the regulation of an
enzyme or other protein by binding an effector
molecule at the protein's allosteric site (that is,
a site other than the protein's active site)
• Effectors that enhance the protein's activity are
referred to as allosteric activators,
• whereas those that decrease the protein's
activity are called allosteric inhibitors
Dr. Siham Gritly 53
55. • Murry K. Robert, Granner K. daryl, Mayes A. peter, Rodwell W. Victor (1999). Harpers
Biochemistry. Appleton and Lange , twent fifth edition
• Cooper GM 2000. The Central Role of Enzymes as Biological CatalystsThe Cell: A Molecular
Approach. 2nd edition. Sunderland (MA): Sinauer Associates; 2000
• Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life.
Boston, Massachusetts: Pearson Prentice Hall
• A. Burtis, Edward R. Ashwood, Norbert W. Tietz (2000), Tietz fundamentals of clinical
chemistry
• Maton, Anthea; Jean Hopkins, Charles William McLaughlin, Susan Johnson, Maryanna Quon
Warner, David LaHart, Jill D. Wright (1993). Human Biology and Health. Englewood Cliffs,
New Jersey, USA: Prentice Hall. pp. 52–59
• Maitland, Jr Jones (1998). Organic Chemistry. W W Norton & Co Inc (Np). p. 139. ISBN 0-
393-97378-6.
• Nelson DL, Cox MM (2005). Lehninger's Principles of Biochemistry (4th ed.). New York,
New York: W. H. Freeman and Company.
• Matthews, C. E.; K. E. Van Holde; K. G. Ahern (1999) Biochemistry. 3rd edition. Benjamin
Cummings.
• http://wiki.answers.com/Q/What_is_dehydration_synthesis#ixzz2BuiK645
Dr. Siham Gritly 55
