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Summary Enzymology, BIC20806, WUR
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A summary of the reader of the course Enzymology, BIC20806, at WUR
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Enzymology summaryIntroduction
Catalyst: a compound which enhances the rate of a chemical reaction without being destroyed or
incorporated in the product. Nature uses enzymes as catalysts to enhance reaction rates. Specificity
of the catalyst is caused by recognition of the substrate by the enzyme.
The reaction from substrate (reactant) into a product needs energy input, the activation energy. This
energy is obtained from the kinetic energy of the reactant, mostly because of vibrational energy.
Catalysts can decrease the activation energy by lowering the energy content of the transition state or
by ground state destabilisation.
Enzymes can catalyse chemical reactions in four different ways:
Complexation Temporary formation General acid/base Distortion of the
covalent intermediates catalysis conformation of the
substrate
Bringing the reactants in Between enzyme and Amino acid residues This distortion leads to
the optimum orientation substrate. One reaction is facilitate reaction by ground state
and keeping them there split iton several smaller selective (de)protonation destabilisation. This is
for a short period of time steps (nucleophilic of the substrate rather specific for bio
(does not change catalysis) catalysis.
activation energy, but
does lowers entropy).
In order to exert catalytic activity, a large number of enzymes need extra compounds, the cofactors.
Chapter 1: kinetic data and their interpretation
Stoichiometry: relation between the quantities of substances that take part in a chemical (overall)
reaction, as reactants and products. Stoichiometry says nothing about the rate of a reaction. It is not
allowed to draw a conclusion about the reaction mechanism from the stoichiometry of a reaction.
Monomolecular: one particle disintegrates or reacts within itself
Bimolecular: two particles collide and react
The velocity of a process depends on the rate of individual steps. The slowest step determines the
overall reaction rate and is thus the rate-determining step. The velocity of a reaction can be
measured by monitoring the disappearance of reactants or the formation of products (determine
their concentrations in time). Examples of determining their concentration:
Chromatography, such as HPLC or GC
UV-spectroscopy (UV absorption is excellently suited for quantitative measurements, use
Lambert-Beer’s law)
NMR, which can be used to follow the progress of reactions (use deuterated solvents)
Titration of the formed carboxylic acid by a pH-stat, to monitor the hydrolysis of organic
esters in water (acid produced leads to a pH-decrease, a computer can plot the amount of
base added against time, the slope equals the reaction rate)
Other methods, such as oxygen-sensitive electrodes or conductivity measurements
Usually, the reaction rate changes in time if the concentrations change in time (of reactant/product).
, First-order Second-order Reversible reactions Pre-equilibria reactions
reactions reactions
Found in enzyme A + B -> P A -> B and A <- B. A + B -> A*B -> C, the first step
inactivation, The general rate The change in here is reversible.
radioactive decay equation for second concentration B equals the A nice example of kinetics with
processes and Sn1 order reactions is formation from A minus its pre-equilibria is in the Michaelis-
reactions inconvenient, we reaction to form A. Menten model.
A -> B (+ C) therefore consider ln k 1 ¿ ¿ V max S
Rate equation: pseudo first-order V 0= , where Km is the
= -(k1 + k-1)t KmS
ln ¿ ¿ . Plotting will reactions (the You can use the measure for dissociation of the
give a straight line. concentration of one equilibrium constant K to complex ES (enzyme-substrate). A
Half-life: t1/2 = reactant can be rewrite the formula small Km gives a tight, stable
ln2/k1. neglected)
1,
¿¿
t1/2 = 1/(2k2[A]0)
complex.
The rate of a reaction depends on the energy barrier that has to be taken by a compound on its
way to products. It is easier to take this barrier at higher temperatures (Arrhenius equation,
see image).
Transition state theory: takes only one reaction step into account (can only be
applied if individual steps are known). If two molecules collide, there is an
extremely short period in which there is a situation with maximum Gibbs free
energy (transition state). Reactants are in constant equilibrium with the
transition state (not a normal equilibrium, we therefore use some new
equations, see image). These equations are called the Eyring equations.
Gibbs free energy of activation: determines with which rate a process
runs
Enthalpy of activation: measure for the amount of binding energy that is lost during the
formation of the activated complex (solvation effects have to be taken into account)
Entropy of activation: the amount of order of the activated complex relative to the starting
situation (difference is the disorder between ground state and rate determining step, rate
determining step monomolecular: ΔS = 0, bimolecular: ΔS << 0).
Thermodynamic variables exert their effects on the rate constants in exponential form.
Solvation: hydrogen bonds, dipole-dipole interactions and van der Waals interactions. Solvation has a
tremendous influence on reaction rates. Ions, for example, are more solvated in water (hydrogen
bonding) and they thereby stabilize the ground state. Solvation gives a higher ΔG because of
stabilisation. Small and strongly concentrated negative charged ions (chloride/fluoride) are more
strongly solvated in water than larger ions. The reactions in water of molecules can be sped up by
adding polymers, which bears a hydrophobic side to the mixture. Solvation also affects the pK a.
Enzymes use ground state destabilization in 3 ways:
1. By creating a hydrophobic patch
2. Distortion of the conformation of the substrate
3. Catalysis by complexation (see before).
Energy diagram (see image): visualises the energy course of a
reaction. Combination of two-dimensional graphs for bonds
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