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Determination of
the kinetic parameters of
enzyme-induced reactions
- learn about the meaning of kinetic parameters
- learn to determine the kinetic parameters
- learn the effects of pH, temperature and substrate
concentration on enzyme activity (or reaction rates)
- learn about inhibited enzyme kinetics
- learn about allosteric enzymes and their kinetics
Prof. R. Shanthini
Updated: 23 Nov 2012
Simple Enzyme Kinetics (in summary)
k1 k3
E+S ES E+P
k2
which is equivalent to
[E]
S P
[E]
S P
rmaxCS
rP = - r S =
KM + CS
KM is a constant
Prof. R. Shanthini
Updated: 23 Nov 2012
Simple Enzyme Kinetics (in summary)
-rs
Catalyzed reaction
rmax
rmaxCS
- rS =
rmax KM + CS uncatalyzed reaction
2
KM Cs
Prof. R. Shanthini
Updated: 23 Nov 2012
An exercise
Consider an industrially important enzyme, which catalyzes the
conversion of a protein substrate to form a much more valuable
product. The enzyme follows the Briggs-Haldane mechanism:
Catalytic step
k1 k3
E+S ES E+P
k2
k3 = kcat
Prof. R. Shanthini
Updated: 23 Nov 2012
- learn about the meaning of kinetic parameters
- learn to determine the kinetic parameters
- learn the effects of pH, temperature and substrate
concentration on enzyme activity (or reaction rates)
- learn about inhibited enzyme kinetics
- learn about allosteric enzymes and their kinetics
Prof. R. Shanthini
Updated: 23 Nov 2012
How to determine the kinetic parameters rmax and KM ?
t Cs - rs
0 given given rmaxCS
- rS =
10 given given KM + CS
15 given given
Prof. R. Shanthini
Updated: 23 Nov 2012
How to determine the M-M kinetics rmax and KM ?
t Cs - rs
0 given given rmaxCS
- rS =
10 given given KM + CS
15 given given
Prof. R. Shanthini
Updated: 23 Nov 2012
We could rearrange rmaxCS
- rS =
KM + CS
to get the following 3 linear forms:
CS KM 1
= + CS (14)
- rS rmax rmax
1 1 KM 1
= + (15)
- rS rmax rmax CS
- rS
- rS = rmax - KM (16)
CS
Prof. R. Shanthini
Updated: 23 Nov 2012
The Langmuir Plot
CS KM 1 CS
= + (14)
- rS rmax rmax
CS
- rS
1
rmax
- KM
Prof. R. Shanthini CS
Updated: 23 Nov 2012
The Langmuir Plot
CS KM 1 CS
= + (14)
- rS rmax rmax
CS
- rS
1 Determine rmax
rmax more accurately
than the other
- KM plots.
Prof. R. Shanthini CS
Updated: 23 Nov 2012
The Lineweaver-Burk Plot
1 1 KM 1
= + (15)
- rS rmax rmax CS
1
- rS
KM
rmax
1
- KM
1
Prof. R. Shanthini
Updated: 23 Nov 2012 CS
The Lineweaver-Burk Plot
1 1 KM 1
= + (15)
- rS rmax rmax CS
1
- Gives good estimates of rmax, but
- rS not necessarily KM
KM
- Data points at low substrate
rmax
concentrations influence the slope
1 and intercept more than data points
- KM at high Cs
1
Prof. R. Shanthini
Updated: 23 Nov 2012 CS
The Eadie-Hofstee Plot
- rS
- rS = rmax - KM (16)
CS
- rS
KM
rmax
KM
-rS
Prof. R. Shanthini
Updated: 23 Nov 2012 CS
The Eadie-Hofstee Plot
- rS
- rS = rmax - KM (16)
CS
- rS
-rS
Prof. R. Shanthini
Updated: 23 Nov 2012 CS
Data:
CS -rS
(mmol/l) -(mmol/l.min)
1 0.20
2 0.22
3 0.30
5 0.45
7 0.41
10 0.50
Determine the M-M kinetic
parameters for all the
three methods discussed
in the previous slides.
Prof. R. Shanthini
Updated: 23 Nov 2012
The Langmuir Plot
25
20
CS/(-rS) min
15
10
y = 1.5866x + 4.6417
5
R2 = 0.9497
0
0 2 4 6 8 10
CS (mmol/l)
rmax = 1 / slope = 1 / 1.5866 = 0.63 mmol/l.min
5
4
3
2
y = 3.4575x + 1.945
1
R2 = 0.8463
0
0 0.2 0.4 0.6 0.8 1
1/CS l/mmol
rmax = 1 / intercept = 1 / 1.945 = 0.51 mmol/l.min
2
0.4 R = 0.6618
0.3
0.2
0.1
0
0 0.05 0.1 0.15 0.2 0.25
(-rS)/CS per min
KM
R2
Prof. R. Shanthini
Updated: 23 Nov 2012
Comparison of the results
Prof. R. Shanthini
Updated: 23 Nov 2012
Comparison of the results
http://www.youtube.com/watch?v=D2j2KGwJXJc
Prof. R. Shanthini
Updated: 23 Nov 2012
Effects of temperature on enzyme activity:
Prof. R. Shanthini
Updated: 23 Nov 2012 http://academic.brooklyn.cuny.edu/biology/bio4fv/page/enz_act.htm
Effects of temperature on enzyme activity:
More energetic collisions:
When molecules collide, the kinetic energy of the molecules can
be converted into chemical potential energy of the molecules.
If the chemical potential energy of the molecules become great
enough, the activation energy of a exergonic reaction can be
achieved and a change in chemical state will result.
Thus the greater the kinetic energy of the molecules in a system,
the greater is the resulting chemical potential energy when two
molecules collide.
As the temperature of a system is increased it is possible that
more molecules per unit time will reach the activation energy.
Thus the rate of the reaction may increase.
Prof. R. Shanthini
Updated: 23 Nov 2012 http://academic.brooklyn.cuny.edu/biology/bio4fv/page/enz_act.htm
Effects of temperature on enzyme activity:
Increase in the number of collisions per unit time:
In order to convert substrate into product, enzymes must collide
with and bind to the substrate at the active site.
Increasing the temperature of a system will increase the
number of collisions of enzyme and substrate per unit time.
Thus, within limits, the rate of the reaction will increase.
Prof. R. Shanthini
Updated: 23 Nov 2012 http://academic.brooklyn.cuny.edu/biology/bio4fv/page/enz_act.htm
Effects of temperature on enzyme activity:
Denaturation of the enzyme:
Enzymes are very large proteins whose three dimensional shape is
vital for their activity.
When proteins are heated up too much they vibrate.
If the heat gets too intense then the enzymes literally shake
themselves out of shape, and the structure breaks down.
The enzyme is said to be denatured.
A denatured enzyme does not have the correct 'lock' structure.
Therefore it cannot function efficiently by accepting the 'key'
substrate molecule.
Prof. R. Shanthini
Updated: 23 Nov 2012 http://www.woisd.net/moodle/mod/resource/view.php?id=44
Effects of temperature on enzyme activity:
Denaturation of the enzyme:
Prof. R. Shanthini
Updated: 23 Nov 2012
Effects of temperature on enzyme activity:
Denaturation of the enzyme:
Enzymes start to
denature at about
45C.
Prof. R. Shanthini
Updated: 23 Nov 2012 http://www.woisd.net/moodle/mod/resource/view.php?id=44
Effects of temperature on enzyme activity:
enzymes
Prof. R. Shanthini
Temperature (deg C)
Updated: 23 Nov 2012 https://wikispaces.psu.edu/display/230/Enzyme+Kinetics+and+Catalysis
Effects of pH on enzyme activity:
Prof. R. Shanthini
Updated: 23 Nov 2012
Effects of pH on enzyme activity:
pH
Prof. R. Shanthini
Updated: 23 Nov 2012 https://wikispaces.psu.edu/display/230/Enzyme+Kinetics+and+Catalysis
Effects of pH on enzyme activity:
Catalase enzyme
Prof. R. Shanthini
Updated: 23 Nov 2012 www.docbrown.info/page01/ExIndChem/ExIndChema.htm
Effects of pH on enzyme activity:
Invertase enzyme
Prof. R. Shanthini
Updated: 23 Nov 2012 www.docbrown.info/page01/ExIndChem/ExIndChema.htm
Effects of pH on enzyme activity:
Maltase enzyme
Prof. R. Shanthini
Updated: 23 Nov 2012 www.docbrown.info/page01/ExIndChem/ExIndChema.htm
Effects of pH on enzyme activity:
Pepsin enzyme
Prof. R. Shanthini
Updated: 23 Nov 2012 www.docbrown.info/page01/ExIndChem/ExIndChema.htm
Effects of pH on enzyme activity:
Trypsin enzyme
Prof. R. Shanthini
Updated: 23 Nov 2012 www.docbrown.info/page01/ExIndChem/ExIndChema.htm
Effects of pH on enzyme activity:
Urease enzyme
Prof. R. Shanthini
Updated: 23 Nov 2012 www.docbrown.info/page01/ExIndChem/ExIndChema.htm
Effects of substrate concentration on enzyme activity:
Prof. R. Shanthini
Updated: 23 Nov 2012 www.docbrown.info/page01/ExIndChem/ExIndChema.htm
Effect of shear
Prof. R. Shanthini
Updated: 23 Nov 2012
Complex enzyme kinetics
Prof. R. Shanthini
Updated: 23 Nov 2012
Inhibited enzyme reactions
Inhibitors are substances that slow down the rate of enzyme
catalyzed reactions.
There are two distinct types of inhibitors:
- Irreversible inhibitors form a stable complex with enzymes
and reduce enzyme activity (e.g. lead, cadmium,
organophosphorous pesticide)
- Reversible inhibitors interact more loosely with enzymes
and can be displaced.
Prof. R. Shanthini
Updated: 23 Nov 2012
Inhibited enzyme reactions - applications
Many drugs and poisons are inhibitors of enzymes in the
nervous system.
Poisons: snake bite, plant alkaloids and nerve gases
Medicines: antibiotics, sulphonamides, sedatives and stimulants
Prof. R. Shanthini
Updated: 23 Nov 2012
Primary constituents of Snake Venom
Enzymes - Spur physiologically disruptive or destructive processes.
Proteolysins - Dissolve cells and tissue at the bite site, causing local
pain and swelling.
Cardiotoxins - Variable effects, some depolarise cardiac muscles and
alter heart contraction, causing heart failure.
Harmorrhagins - Destroy capillary walls, causing haemorrhages near
and distant from the bite.
Coagulation - Retarding compounds prevent blood clotting.
Thromboses - Coagulate blood and foster clot formation throughout
the circulatory system.
Haemolysis - Destroy red blood cells.
Cytolysins - Destroy white blood cells.
Neurotoxins - Block the transmission of nerve impulses to muscles,
especially those associated with the diaphragm and breathing.
Prof. R. Shanthini
Updated: 23 Nov 2012 http://www.writework.com/essay/biochemistry-snake-venom
Inhibited enzyme reactions
Inhibitors are also classified as competitive and non-competitive
inhibitors.
Prof. R. Shanthini
Updated: 23 Nov 2012
Competitive inhibition
Prof. R. Shanthini
Updated: 23 Nov 2012 http://www.elmhurst.edu/~chm/vchembook/573inhibit.html
Competitive inhibition
- The inhibitor is "stuck" on the enzyme and prevents any
substrate molecules from reacting with the enzyme.
- However, a competitive inhibition is usually reversible if
sufficient substrate molecules are available to ultimately
displace the inhibitor.
- Therefore, the amount of enzyme inhibition depends upon
the inhibitor concentration, substrate concentration, and the
relative affinities of the inhibitor and substrate for the active
site.
Prof. R. Shanthini
Updated: 23 Nov 2012 http://www.elmhurst.edu/~chm/vchembook/573inhibit.html
Competitive inhibition
Competitive inhibitors (denoted by I) compete with substrate to
occupy the active site of the enzyme.
k1 k3
E+S ES E+P
k2
k4
E+I EI
k5
where
rP = k3 CES (17)
Prof. R. Shanthini
Updated: 23 Nov 2012
Competitive inhibition
k1 CE CS = k2 CES
k2 CE CS
KM = = (19)
k1 CES
k4 CE CI = k5 CEI
k5 CE CI
KI = = (20)
k4 CEI
Prof. R. Shanthini
Updated: 23 Nov 2012
Competitive inhibition
k3CE0CS rmaxCS
rP = = (21)
KM (1 + CI / KI) + CS KM,app + CS
where
rmax = k3CE0 (5)
KM = k2 / k1 (6)
1
CI > 0
- rS
1 CI = 0 (no inhibitor)
1 - KM, app
- KM 1
rmax
1
CS
Prof. R. Shanthini
Updated: 23 Nov 2012
Competitive inhibition
In the presence of a competitive inhibitor,
the maximal rate of the reaction (rmax) is unchanged,
but the Michaelis constant (KM) is increased.
Prof. R. Shanthini
Updated: 23 Nov 2012
Competitive inhibition an example
Ethanol is metabolized in the body by oxidation to acetaldehyde,
which is a toxic compound and a known carcinogen.
Prof. R. Shanthini
Updated: 23 Nov 2012
Non-competitive inhibition
- The structure of inhibitor molecule is entirely different from
that of the substrate molecule.
- The inhibitor forms complex at a point other than the active
site (remote from or very close to the active site).
- It does not complete with the substrate.
- It alters the structure of the enzyme in such a way that the
substrate can no longer interact with the enzyme to give a
reaction.
Prof. R. Shanthini
Updated: 23 Nov 2012 https://ibhumanbiochemistry.wikispaces.com/C.7.5
Non-competitive inhibition
Prof. R. Shanthini
Updated: 23 Nov 2012 https://ibhumanbiochemistry.wikispaces.com/C.7.5
Non-competitive inhibition
k1 k3
E+S ES E+P
k2
k4
E+I EI
k5
k6
EI + S ESI
k7
k8
ES + I ESI
k9
Prof. R. Shanthini
Updated: 23 Nov 2012
Non-competitive inhibition
We could drive the rate equation (given on the next page)
assuming the following:
k2 k7
= KM = = KIM
k1 k6
k5 k9
= KI = = KMI
k4 k8
Prof. R. Shanthini
Updated: 23 Nov 2012
Non-competitive inhibition
rmax,appCS
rP = (23)
KM + CS
where
rmax
rmax,app = (24)
(1 + CI / KI)
KM = k2 / k1 (6)
Prof. R. Shanthini
Updated: 23 Nov 2012
rmax,app < rmax
Non-competitive inhibition
The Lineweaver-Burk Plot
1
CI > 0
- rS
1
rmax,app
CI = 0 (no inhibitor)
1
- KM 1
rmax
1
CS
Prof. R. Shanthini
Updated: 23 Nov 2012
Non-competitive inhibition
In the presence of a non-competitive inhibitor,
the maximal rate of the reaction (rmax) is lower
but the Michaelis constant (KM) is unchanged.
Prof. R. Shanthini
Updated: 23 Nov 2012
Uncompetitive inhibition
k1 k3
E+S ES E+P
k2
k4
ES + I ESI
k5
Prof. R. Shanthini
Updated: 23 Nov 2012
Uncompetitive inhibition
An uncompetitive inhibitor binds only to the enzyme-substrate
complex preventing the formation or release of the enzymatic
products.
Unlike with competitive inhibition an uncompetitive inhibitor
need not resemble the structure of the enzymes natural
substrate.
An uncompetitive inhibitor is most effective at high substrate
concentration as there will be more enzyme-substrate
complex for it to bind.
Unlike with competitive inhibitors the effects of an
uncompetitive inhibitor cannot be overcome by increasing the
concentration of substrate.
Prof. R. Shanthini
Updated: 23 Nov 2012
Non-competitive inhibition
rmax,appCS
rP = (23)
KM + CS
where
rmax
rmax,app = (24)
(1 + CI / KI)
KM = k2 / k1 (6)
Prof. R. Shanthini
Updated: 23 Nov 2012
rmax,app < rmax
Uncompetitive inhibition
rmax,appCS
rP = (25)
KM,app + CS
where
rmax
rmax,app = (24) rmax,app < rmax
(1 + CI / KI)
KM = k2 / k1 (6)
Prof. R. Shanthini
Updated: 23 Nov 2012
Uncompetitive inhibition
KM is reduced
Prof. R. Shanthini
Updated: 23 Nov 2012
Uncompetitive inhibition
The Lineweaver-Burk Plot
1
- rS CI > 0
1
rmax,app
CI = 0 (no inhibitor)
1
- KM, app
1 1
1 rmax CS
Prof. R. Shanthini - K
Updated: 23 Nov 2012 M
Competitive versus Uncompetitive inhibition
Prof. R. Shanthini
Updated: 23 Nov 2012
Mixed inhibition
Prof. R. Shanthini
Updated: 23 Nov 2012
An exercise
The kinetic properties of the ATPase enzyme, isolated from yeast,
which catalyzes the hydrolysis of ATP to form ADP and Pi, are
assessed by measuring initial rates in solution, with various ATP
concentrations S0 and a total ATPase concentration E0 = 0.60 M.
From these experiments, it is determined that
Vmax = 1.20 M/s; KM = 40 M.
a. Calculate the values of kcat and the catalytic efficiency for ATPase
under these conditions.
b. An inhibitor molecule is added at a concentration of 0.1 mM, and
the experiments are repeated. The apparent Vmax and KM are now
found to be 0.6 M/s, and 20 M, respectively. Speculate on how
this inhibitor works (i.e., specify which species are engaged by the
inhibitor).
Prof. R. Shanthini
Updated: 23 Nov 2012
Substrate / Product inhibition
Prof. R. Shanthini
Updated: 23 Nov 2012
Assignment
Prof. R. Shanthini
Updated: 23 Nov 2012
Food for Thought
Problem 3.13 from Shuler & Kargi: CS -rS
The following substrate reaction rate (-rS) (mg/l) (mg/l.h)
data were obtained from enzymatic 10 5
oxidation of phenol by phenol oxidase at 20 7.5
different phenol concentrations (CS). 30 10
By plotting (-rS) versus (CS) curve, or
otherwise, determine the type of inhibition 50 12.5
described by the data provided? 60 13.7
80 15
90 15
110 21.5
130 9.5
140 7.5
Prof. R. Shanthini 150 5.7
Updated: 23 Nov 2012
Sigmoid/Hill kinetics
A particular class of enzymes exhibit kinetic properties that
cannot be studied using the Michaelis-Menten equation.
rmaxCSn
rP = (27) The Hill
K + CS n equation
Hill constant Hill coefficient
n=6
n=4
n=2
Prof. R. Shanthini
Updated: 23 Nov 2012
Sigmoid kinetics
For an alternative formulation of Hill equation, we could
rewrite (25) in a linear form as follows:
rP CSn
= =
rmax K + CS n
ln = n ln(CS) ln (K) (28)
1-
Prof. R. Shanthini
Updated: 23 Nov 2012 http://chemwiki.ucdavis.edu/Biological_Chemistry/Catalysts/Enzymatic_Kinetics/Sigmoid_Kinetics
Allosteric enzyme
Prof. R. Shanthini
Updated: 23 Nov 2012 http://chemwiki.ucdavis.edu/Biological_Chemistry/Catalysts/Enzymatic_Kinetics/Sigmoid_Kinetics