A diffusion-limited enzyme catalyses a reaction so efficiently that the rate limiting step is that of substrate diffusion into the active site, or product diffusion out. This is also known as kinetic perfection or catalytic perfection. Since the rate of catalysis of such enzymes is set by the diffusion-controlled reaction, it therefore represents an intrinsic, physical constraint on evolution (a maximum peak height in the fitness landscape). Diffusion limited perfect enzymes are very rare. Most enzymes catalyse their reactions to a rate that is 1,000-10,000 times slower than this limit. This is due to both the chemical limitations of difficult reactions, and the evolutionary limitations that such high reaction rates do not confer any extra fitness.

1. Kinetically perfect enzymes
Presented by,
SHRYLI K S
Vth Semester
YMB17118
Molecular Biology,
Yuvaraja's College (Autonomous),
Mysuru
Guided by,
Dr. Ragavendra Hegade Katte
Guest Faculty
Dept. Molecular Biology,
Yuvaraja's College (Autonomous),
Mysuru
24t May, 2020
MINOR SEMINAR
Enzymology

2. Contents
• Introduction
• Michaelis- Menten equation.
• Kinetically perfect enzymes.
• Advantages of kinetically perfect enzymes with respect to biological
systems.
 Triose phosphate isomerase.
 Acetylcholinesterase.
 Superoxide Dismutase.
• Conclusion
• References
• Acknowledgement
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3. Introduction
• Chemical Kinetics- Branch of physical chemistry that is concerned with
understanding the rate of chemical reactions.
• Enzymes are the biological catalyst that play a critical role in accelerating
reactions anywhere from 103 to 1017 times faster than the normal rate of the
reaction.
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4. Michaelis- Menten Enzyme
Kinetics
Fig 01: An enzyme catalyzes the reaction of two substrates and to form one product.
This can be described with the following multistep mechanism.
1
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5. Where k1 , k–1 , k2 , and k–2 are rate constants. The reaction’s rate law for generating the
product [P] is
However, if we make measurement early in the reaction, the concentration of products is
negligible, i.e.,
[P]≈0
And we can ignore the back reaction (second term in right side of Equation 2). Then under
these conditions, the reaction’s rate is,
To be analytically useful we need to write Equation 4 in terms of the reactants (e.g., the
concentrations of enzyme and substrate). To do this we use the steady-state approximation,
in which we assume that the concentration of ES remains essentially constant. Following an
initial period, during which the enzyme–substrate complex first forms, the rate at
which ES forms,
Is equal to the rate at which it disappears,
2
3
4
5
6
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6. where [E]0 is the enzyme’s original concentration. Combining Equations 5 and
6 gives,
which we solve for the concentration of the enzyme–substrate complex,
where Km is the Michaelis constant. Substituting Equation 8 into
Equation 4 leaves us with our final rate equation.
Graph 01: Plot of Equation 9 showing limits for the
analysis of substrates and enzymes in an enzyme-
catalyzed chemical kinetic method of analysis. The
curve in the region highlighted in red obeys
equation 11 and the curve in the area highlighted
in green follows Equation 10.
7
8
9
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7. For high substrate concentrations, where [S]≫Km, Equation 9 simplifies to,
where Vmax is the maximum rate for the catalyzed reaction. Under these
conditions the reaction is zero-order in substrate and we can use Vmax to
calculate the enzyme’s concentration, typically using a variable-time method.
At lower substrate concentrations, where [S]≪Km, Equation 9 becomes,
The reaction is now first-order in substrate, and we can use the rate of the
reaction to determine the substrate’s concentration by a fixed-time method.
The Michaelis constant Km is the substrate concentration at which the reaction
rate is at half-maximum, and is an inverse measure of the substrate's affinity
for the enzyme—as a small Km indicates high affinity, meaning that the rate
will approach Vmax more quickly. The value of Km is dependent on both the
enzyme and the substrate, as well as conditions such as temperature and pH.
10
11
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8. From the last two terms in Equation 11, we can express Vmax in terms of
a turnover number (kcat):
where [E]0 is the enzyme concentration and kcat is the turnover number,
defined as the maximum number of substrate molecules converted to product
per enzyme molecule per second. Hence, the turnover number is defined as the
maximum number of chemical conversions of substrate molecules per second
that a single catalytic site will execute for a given enzyme concentration [E]o.
12
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9. Kinetically Perfect Enzymes
• Efficient.
• Specificity constant Kcat / Km- 108 to 109 M-1 S-1.
Table 01: Some Kinetically Prefect Enzymes.
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10. Advantages of Kinetically Perfect
Enzymes w.r.t. Biological Systems.
• Triose Phosphate Isomerase
• Acetylcholinesterase
• Superoxide Dismutase
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11. Triose Phosphate Isomerase
Fig 03: Structure of TPI enzyme.
Fig 04: Reaction catalysed by TPI
enzyme.
• A crucial enzyme involved in
the glycolytic pathway.
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12. Acetylcholinesterase
Fig 05: Structure of acetylcholinesterase enzyme.
Fig 06: Reaction catalysed by
acetylcholinesterase enzyme.
• A crucial enzyme involved in
nerve impulse transmission.
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13. Superoxide Dismutase
Fig 07: Structure of SOD enzyme.
Fig 08: Reaction catalysed by
SOD enzyme.
• A crucial enzyme involved in
destruction of superoxide
radicals.
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14. Conclusion
• Very important.
• Inability to function as kinetically perfect enzymes leads to severe toxicities
in the body.
• Deficiencies or malfunctioning of these enzymes lead to many
abnormalities such as, affected individuals experience low levels of
circulating red blood cells due to premature destruction of red blood cells
(hemolytic anemia) and severe, progressive neurological symptoms ( for
TPI), neurodegenerative disorders (for AChE), familial amyotrophic lateral
sclerosis a motor neuron disease (for SOD) etc.
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15. References
• N S Punekar, Enzymes: Catalysis, Kinetics & Mechanisms. Springer Nature
Singapore. Ltd, 2018, 560 pp.
• Berg J M, Tymoczko J L, Stryer L, Biochemistry, 5th Edition, W H Freeman &
Company & Sumona. Inc, 2002, 1514pp.
• https://chem.libretexts.org/Courses/University_of_California_Davis/UC
D_Chem_107B%3A_Physical_Chemistry_for_Life_Scientists/Chapters/3%3
A_Enzyme_Kinetics/3.2%3A_The_Equations_of_Enzyme_Kinetics
• https://en.wikipedia.org
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16. Acknowledgements
I would like to thank the department of Molecular Biology
for providing me this opportunity to present my seminar. I
also
thank Dr. Ragavendra Hegade Katte for his valuable
guidance throughout the preparation of my seminar.
Thank you.
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