biocatalysts introduction to molecular cell biology biocatalysts dr. fridoon jawad ahmad hec foreign...
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Introduction to Molecular Cell Biology
Biocatalysts Biocatalysts Dr. Fridoon Jawad AhmadDr. Fridoon Jawad Ahmad
HEC Foreign ProfessorHEC Foreign ProfessorKing Edward Medical UniversityKing Edward Medical University
Visiting Professor LUMS-SSEVisiting Professor LUMS-SSE
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The Miracle Workers
One of biggest miracles of life is that it can perform slow reactions and the ones requiring extreme
conditions, quickly and at physiological conditions.
N2(g) + 3H2(g) 2NH3(g)
N2 + 8H+ + 8e− + 16 ATP 2NH3 + H2 + 16ADP + 16 Pi
The reaction is carried out under conditions of 150-250 atmospheres (atm), 450-500 °C;
resulting in a yield of 10-20%
Nitrogenase
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Energy and Energy Conversions
Energy is the capacity to do work. Potential energy is the energy of state or position; it includes the
energy stored in chemical bonds. Kinetic energy is the energy of motion (and related forms such as
electric energy, light, and heat).
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The Laws of Thermodynamics
Living things, obey the laws of thermodynamics.
1) Energy cannot be created or destroyed.
2) The quantity of energy available to
do work (free energy) decreases
and unusable energy (associated
with entropy) increases.
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Free Energy (ΔG)
total energy = usable energy + unusable energyH = G + TS
(H = Enthalpy, G = free energy, T= absolute temperature, S = entropy)
G = H – TS
Absolute G, H or S can not be measuredΔG (reaction) = G (products) – G (reactants)
Changes in free energy, total energy, temperature, and entropy are related by the equation.
ΔG = ΔH – TΔS
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ΔG of Combustion
CH4 + 2O2 CO2 + 2H2OH = G + TS H = G + TS
500 = 400 + 100 300 = 100 + 200
G = H – TS G = H – TS400 = 500 - 100 100 = 300 - 200
ΔG (reaction) = G (products) – G (reactants)- 300 = 100 - 400
ΔG = - 300ΔH = - 200
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ΔG of Reverse Reaction
CO2 + 2H2O CH4 + 2O2H = G + TS H = G + TS
300 = 100 + 200 500 = 400 + 100
G = H – TS G = H – TS100 = 300 - 200 400 = 500 - 100
ΔG (reaction) = G (products) – G (reactants) 300 = 400 - 100
ΔG = 300ΔH = 200
ΔS = - 100
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Free Energy (ΔG)
If ΔG is negative free energy is releasedIf ΔG is positive free energy is required
ΔH is the total amount of energy added
In living systems magnitude and sign of ΔG can depend significantly on changes in entropy ΔS
ΔS will be positive in hydrolysis
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Water Molecules adjacent to hydrophobic molecule suffer restrictions in orientation as they form hydrogen bonds with other water molecules.
Bonding (hydrogen) also reduces energy state.
Hydrophobicity Counterintuitive ???
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Water Structure
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Exergonic & Endergonic Reactions
Exergonic reactions release free energy and have a negative ΔG.
Endergonic reactions take up
free energy and have a positive ΔG.
Endergonic reactions proceed
only if free energy is provided
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Equilibrium in Reversible Reactions
The change in free energy (ΔG) of a reaction determines its point of chemical equilibrium, at
which the forward and reverse reactions proceed at the same rate.
For exergonic reactions, the equilibrium point lies toward completion (the conversion of all reactants
into products).
@ 0.02M, 25C & pH 7ΔG = -1.7 kcal/mol
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ATP Hydrolysis
ATP (adenosine triphosphate) serves as an energy currency
in cells.
Hydrolysis of ATP releases a relatively large amount of free
energy (-12 kcal/mol).
Oxidation of Luciferin in fire flies is powered by ATP
hydrolysis.
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ATP Hydrolysis Is Coupled
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Biological Catalysts are Enzymes
Change in free energy (ΔG) is indicative of equilibrium point.
The more negative ΔG is, the further the reaction proceeds towards completion.
However ΔG does not tell us any thing about the rate of a reaction (the speed at which it moves towards
equilibrium).
Most Enzymes are proteins (ribozymes are RNA)
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Activation Energy
Exergonic although release energy however they are not generally
spontaneous and proceed only after the reactants
are pushed over the energy barrier by small
amount of added energy (Activation Energy Ea
e.g. CH4 + O2
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Activation Energy
Activation energy changes reactants into unstable molecules forms called transition-state species.
At normal temperatures only few molecules have enough kinetic
energy for this transformation.
Enzymes lower the energy barrier.
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Enzymes are Specific
Reactants (substrates) bind the a particular (active) site of the respective enzyme.
The specificity of this binding is a function of three-dimensional shape, structure and environment of its
active site.
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Enzymes Lower the Energy Barrier
Enzymes Lower the Energy Barrier for both forward and reverse reaction.
Equilibrium and ΔG are not changed by enzymes.
50% 600 poly arginine
degradation by carboxypeptidase 7 years vs. half a
second
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How do Enzymes Work
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How do Enzymes Work
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Induced Fit
Upon binding to substrate, some enzymes change shape, facilitating catalysis.
The shape changes (Induced fitting) modify the active site and exposes/ aligns those regions that
perform catalysis
Water is exclusion at the active site results in transfer
of Pi from ATP to glucose preventing APT hydrolysis
to ADP The active site = the catalytic + binding sites
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Helpers
Cofactors: Inorganic ions (Cu, Zn & Fe) bound to some enzymes and are essential to their function.
Coenzymes: Carbon containing molecules bind enzymes temporarily (by collision) and are
chemically changed during reaction (like substrate).
Prosthetic groups: non-protein component permanently bound
to enzymes (heme group), without its prosthetic group apoprotein vs. holoprotein.
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Cofactors and Coenzymes
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Substrate Concentration
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Enzyme Regulation
Some factors can activate enzymes and other can deactivate them (inhibit their function).
Irreversible inhibitors permanently inhibit enzymes function generally by modifying the active site
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Reversible Inhibitors
Competitive inhibiters are similar to the natural substrate (bind the active site) however they are different enough that no reaction is catalyzed.
When their concentration is lower they come of the enzyme and enzyme can bind the substrate (ADH).
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The Citric Acid Cycle
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Reversible Inhibitors
Noncompetitive inhibiters bind the enzyme at a a site other than active site and cause a
conformational change that prevents enzyme from binding its substrate or slow the catalysis.
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Feed Back/End Product Inhibition
End product can serves as allosteric inhibitor of commitment step enzyme If sufficient amount of end product of a pathway is available in the environment
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Allosteric Regulators
Allostery (different shape) change in enzyme shape due to binding of a noncompetitive inhibiter.
These enzymes exist in more than one shape and have
multiple poly peptide chains.
Allosteric regulator (AR) can be positive or negative.
Enzymes catalyzing commitment step have AR
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Physical Factors Influence Enzymes
Fever?