enzyme_kinetics(engineering_biophysics).pdf

This lecture include content about enzyme kinetics in biophysics.

1. ENZYME
KINETICS
PHYS BioPhysics : lec2-Enzyme kinetics

2. Outline
ENZYMES & ACTIVEENZYMES & ACTIVE
SITESITE
MECHANISM OF ENZYMEMECHANISM OF ENZYME
ACTIONACTION
SPECIFICITY OF ENZYMESPECIFICITY OF ENZYME
ENZYME KINETICS &ENZYME KINETICS &
REACTION RATEREACTION RATE
KINETICS OF ENZYMEKINETICS OF ENZYME
REACTIONSREACTIONS
PHYS BioPhysics : lec2-Enzyme kinetics
ENZYME INHIBITIONENZYME INHIBITION
ENZYME REGULATIONENZYME REGULATION

3. Enzymes are protein catalysts that increase the rate of reactions without being changed
in the overall process. All Enzymes are protein in nature.
Each specific enzyme binds to a specific substrate.
Enzymes
Enzyme molecules contain a special pocket or cleft called the active site.
The active site, formed by folding of the protein, contains amino acid side chains that
participate in substrate binding and catalysis.
the substrate binds enzyme noncovalently.
Active site
PHYS BioPhysics : lec2-Enzyme kinetics
Enzymes & Active site

4. Activation energy is the energy which
is needed to start a reaction.
Enzymes act as biological catalysts by
lowering this activation energy. They
provide an alternative pathway for the
reaction to occur, requiring less
energy to initiate.
Mechanism of enzyme action
PHYS BioPhysics : lec2-Enzyme kinetics

5. Substrate specificity : Most enzymes bind to a
specific substrate or a very limited group of related
substrates. This precision is crucial for efficient and
controlled biochemical reactions.
Reaction specificity : Each enzyme catalyzes a
particular type of chemical reaction. For example, some
enzymes break bonds, while others form new bonds.
Active site : The specificity of an enzyme is primarily
determined by the shape and chemical properties of its
active site, where the substrate binds.
Lock-and-key model : This model, although simplified,
helps visualize how the enzyme's active site fits
precisely with the substrate, like a lock and key.
Specificity of enzyme
PHYS BioPhysics : lec2-Enzyme kinetics

6. Enzyme kinetics is the study of the rate of reaction catalysed by an
enzyme.
It helps us to understand enzymatic efficiency and to determine the
concentration of an enzyme in a solution or biological sample.
Enzyme kinetics
The reaction rate of an enzyme is determined by the change in the
amount of substrate or product per unit time.
Reaction rate
PHYS BioPhysics : lec2-Enzyme kinetics
Enzyme kinetics & Reaction rate

7. Kinetics of simple enzyme reactions was described in 1902 by Victor
Henri a again in 1913 by Leonor Michaelis a Maud Menten
Michaelis-Menten Model
PHYS BioPhysics : lec2-Enzyme kinetics
KINETICS OF ENZYME REACTIONS
Basic equations

8. PHYS BioPhysics : lec2-Enzyme kinetics
KINETICS OF ENZYME REACTIONS
Michaelis-Menten
Model variables
enzyme
product
substrate
constants of direct
reactions
rate constant of
product P formation
the total concentration of enzyme : in the system remains constant, at any time
moment the sum of concentrations of the free (E) and bound (ES) enzymes is
constants of
inverse reactions

9. PHYS BioPhysics : lec2-Enzyme kinetics
KINETICS OF ENZYME REACTIONS
The Michaelis-Menten equation governs enzymatic reactions.
Most enzymes exhibit Michaelis-Menten type kinetics, in which the graph of initial
velocity (V0) versus substrate concentration ([S]), is of the hyperbolic type.
The representation of V0 with
respect to [S] is a hyperbola

10. PHYS BioPhysics : lec2-Enzyme kinetics
KINETICS OF ENZYME REACTIONS
Origin of the Michaelis-Menten equation
Michaelis-Menten equation (hyperbolic curve):

11. km = substrate concentration at one half
km does not vary with enzyme concentration.
michaels constant is characteristics of an enzyme
and its particular substrate and reflects the affinity of
the enzyme for that substrate.
small km : a numerically small (low) km reflects a high
affinity of the enzyme for substrate, because a low
concentration of substrate is needed to half-saturate
the enzyme (reach one half ).
large Km : a numerically large (high) km reflects a low
affinity of enzyme for substrate because a high
concentration of substrate is needed to half saturate
the enzyme
PHYS BioPhysics : lec2-Enzyme kinetics
KINETICS OF ENZYME REACTIONS
Michaelis constant (Km) (Specificity/affinity)

12. This is an inverse representation of V0 versus [S]:
1/V0 is plotted against 1/[S] and a straight line is
obtained. This is also called a double-reciprocal plot.
This is useful for calculating Km and Vmax more
accurately and the mechanism of action of enzyme
inhibitors.
The intercept on the x-axis is equal to -1/Km,
The y-axis intercept is equal to 1/Vmax.
The slope m = Km/Vmax.
PHYS BioPhysics : lec2-Enzyme kinetics
KINETICS OF ENZYME REACTIONS
Linearization of the Michaelis-Menten equation (Lineweaver-Burk plot)
What is the purpose of inverse representation?
When V0 is plotted against [S], it is not always possible to determine when Vmax has been
achieved due to the gradual upward slope of the curve at high substrate concentrations.

13. ENZYME INHIBITION
ReversibleReversible
PHYS BioPhysics : lec2-Enzyme kinetics
non-competitivenon-competitive
INHIBITIONINHIBITION
competitivecompetitive
irreversibleirreversible

14. Any substance that can decreases the velocity of an enzyme-catalyzed reaction is
called an inhibitor it can be reversible or irreversible.
irreversible inhibitors bind to enzymes through covalent bonds.
Reversible inhibitors bind to enzymes through non-covalent bonds and thus, dilution
of the enzyme-inhibitor complex results in dissociation of the reversibly bound inhibitor
and recovery of enzyme activity.
PHYS BioPhysics : lec2-Enzyme kinetics
ENZYME INHIBITION

15. Competitive inhibitors impair reaction progress by binding to an enzyme, often at the
active site, and preventing the real substrate from binding .
At any given time, only the competitive inhibitor or the substrate can be bound to the
enzyme (not both) .
That is, the inhibitor and substrate compete for the enzyme. Competitive inhibition acts
by decreasing the number of enzyme molecules available to bind the substrate.
By increasing the substrate concentration, the probability of the substrate binding to
the enzyme increases, overcoming the inhibitor. is unchanged
PHYS BioPhysics : lec2-Enzyme kinetics
Reversible competitive inhibitors

16. Non-competitive inhibition occurs when the inhibitor and substrate bind at different
sites on the enzyme (Allosteric site). The noncompetitive inhibitor can bind either free
enzyme or the enzyme- substrate complex, thereby preventing the reaction from
occurring.
Non-competitive inhibition cannot be overcome by increasing the concentration of
substrate.
Non-competitive inhibitors decrease Vmax of the reaction.
PHYS BioPhysics : lec2-Enzyme kinetics
Reversible Non-competitive inhibition

17. Effect of competitive and non-competitive
inhibition on maximum speed
PHYS BioPhysics : lec2-Enzyme kinetics

18. The regulation of the reaction velocity of
enzymes is essential if an organism is to
coordinate its numerous metabolic
processes.
Effectors that inhibit enzyme activity are
negative effectors, whereas those that
increase enzyme activity are positive
effectors.
PHYS BioPhysics : lec2-Enzyme kinetics
Enzyme regulation

19. Test Bank
Explain the mechanism of action of the enzyme , show your answer using figures ?Explain the mechanism of action of the enzyme , show your answer using figures ?
Show Michaelis-Menten model and Origin of the Michaelis-Menten equation?Show Michaelis-Menten model and Origin of the Michaelis-Menten equation?
Explain the difference between competitive inhibitors and non-competitive inhibitors ?Explain the difference between competitive inhibitors and non-competitive inhibitors ?
PHYS BioPhysics : lec2-Enzyme kinetics
Show Effect of competitive and non-competitive inhibition on maximum speed ?Show Effect of competitive and non-competitive inhibition on maximum speed ?

20. References
https://www.slideshare.net/slideshow/enzymhttps://www.slideshare.net/slideshow/enzym
e-kinetics-57408548/57408548e-kinetics-57408548/57408548
https://www.slideshare.net/slideshow/https://www.slideshare.net/slideshow/
enzyme-final/16499463enzyme-final/16499463
Fundamentals of Fundamentals of BiophysicsBiophysics
Andrey B. RubinAndrey B. Rubin
PHYS BioPhysics : lec2-Enzyme kinetics
https://www.youtube.com/watch?https://www.youtube.com/watch?
v=8yLjhR7imyYv=8yLjhR7imyY

21. Thank you
PHYS BioPhysics : lec2-Enzyme kinetics