Download Consortium for Educational Communication Answer

Consortium for Educational Communication
Frequently Asked Questions:
1. What is the importance of ES complex in enzyme catalyzed
reactions?
Answer: The formation of an enzyme-substrate complex is
indispensable for enzymatic catalysis. It is only when substrate
binds to the active site of enzyme to form ES complex that the
reaction will proceed. The substrate in ES complex is enclosed
and sequestered completely from solution, getting a specific
environment and surface for the reaction to occur more readily.
The weak non-covalent (binding energy) and transient covalent
interactions between the enzyme and substrate are possible only
in enzyme-substrate (ES) complexes that promote the formation
and stabilization of the transition states in enzyme-substrate (ES)
complexes and result in lowering of the energy of activation through
multiple mechanisms.
2. What do you mean by activation energy? How does activation
energy of catalyzed reactions differ from that of uncatalyzed
reactions?
Answer: Activation energies are energy barriers to chemical
reactions. The difference between the energy levels of the ground
states (substrates or products) and the transition state is called
the Gibbs free energy of activation or simply the activation energy,
∆G‡. For uncatalyzed forward reaction, activation energy is the
difference in free energy between the substrate and the transition
state: ∆G‡uncat = Gs‡ - Gs. However, the activation energy in the
enzyme-catalyzed reaction is the energy difference between ES
complex and ES‡ transition state complex: ∆G‡cat = GES‡ - GES. The
energy barrier between ES and ES‡ is less than the energy barrier
between S and S‡, thereby meaning that the activation energy for
the catalyzed reaction is lower than the activation energy for the
uncatalyzed reaction (∆G‡cat < ∆G‡Uncat).
Consortium for Educational Communication
3. What is the relationship between activation energy and the
reaction rate?
Answer: The relationship between the activation energy and
the reaction rate is given by the equation:
where V is reaction rate; k, rate constant; ∆G‡, activation energy;
[S], substrate concentration; T, absolute temperature; k, the
Boltzmann constant; h, Planck’s constant and R, gas constant.
The relationship between the activation energy and the reaction
rate is inverse and exponential, thereby meaning that the rate
at which a molecule undergoes a particular reaction decreases
as the activation energy for that reaction increases. In simplified
terms, the lower activation energy means a faster reaction rate.
4. What is the source of the energy for the dramatic lowering
of the activation energies for enzyme catalyzed reactions?
Answer: The sources of the energy for the dramatic lowering of
the activation energies for enzyme catalyzed reactions are:
A)Noncovalent interactions between enzyme and substrate:
Formation of a large number of weak, noncovalent bonds
and interactions (hydrogen bonds and hydrophobic and ionic
interactions) between substrate and enzyme in an ES complex is accompanied by a release of free energy called binding energy. Binding energy is a major source of free energy
used by enzymes to lower the activation energies.
B)Transient covalent interactions of enzyme with a substrate
or group transfers to or from a substrate: Besides binding
energy, other sources of energy for the lowering of the activation energies are transient covalent interaction of enzyme
with a substrate or group transfer to or from a substrate.
5. Do enzymes affect reaction equilibria? Do they make nonspontaneous reactions to occur spontaneously?
Consortium for Educational Communication
Answer: Enzymes, like other catalysts, do not affect reaction
equilibria. They do not change the position of reaction equilibria.
The enzyme catalyzes and accelerates the reaction in both the
directions to same extent. However, the reaction reaches equilibrium
much faster when the appropriate enzyme is present. In other
words, enzymes provide a reaction pathway whose transition-state
energy is lower than that of the uncatalyzed reaction. Reaction
equilibria (spontaneity) depend on free-energy change for the
reaction, ∆G; while reaction rates depend on activation energies,
∆G‡. ∆G of the reaction, which tells about the spontaneity of the
reaction, is independent of the activation energy. Since enzymes
lower only the activation energy, therefore, they enhance reaction
rates without altering the free-energy change for the reaction.
Thus, enzymes do not make non-spontaneous reactions to occur
spontaneously.
6. What is the role of binding energy in enzyme catalyzed reactions?
Answer: The binding energy contributes to specificity as well
as to catalysis of reactions. Binding energy is a major source of
free energy used by enzymes to lower the activation energies of
reactions. Under conditions commonly found in cells, a 10-fold
rate enhancement requires a ∆∆G‡cat of only 5.71 kj/mol, while
a million-fold rate enhancement requires a ∆∆G‡cat of ≈ 34 kj/
mol. The binding energy available from formation of a single
weak interaction is generally estimated to be 4 to 30 kJ/mol.
Considering a number of such interactions in ES and ES‡ complex,
the overall binding energy available is therefore sufficient to lower
the activation energies by 60 to 100 kJ/mol, thereby showing such
a large rate enhancements. Besides, specificity is also derived
from the formation of many weak interactions (binding energy)
between the enzyme and its specific substrate molecule. The
binding energy is used to lower the activation energy through
following mechanisms: Stabilization of transition state, Entropy
Loss and destabilization of the ES complex, and Proximity and
orientation effects.
Consortium for Educational Communication
7. Mention the various mechanisms employed by enzymes to
catalyze the reactions?
Answer: The mechanisms employed by enzymes to catalyze the
reactions are:
1 Stabilization of transition state
2 Entropy Loss and destabilization of the ES complex
3 Proximity and orientation effects
4 General Acid–base catalysis
5 Covalent catalysis
6 Metal ion catalysis
8. Name the various mechanisms through which binding energy lowers the activation energy?
Answer: The binding energy is used to lower the activation energy
through following mechanisms: Stabilization of transition state,
Entropy Loss and destabilization of the ES complex and Proximity
and orientation effects.
9. What do you mean by Stabilization of transition state?
Answer: Stabilization of transition state means lowering of its
free energy. Enzymes are “designed” by nature to bind the
transition-state structure more tightly than the substrate (or the
product). In other words, weak interactions are optimized in the
reaction transition state; enzyme active sites are complementary
not to the substrates per se but to the transition states through
which substrates pass as they are converted to products during
Consortium for Educational Communication
an enzymatic reaction. Since these weak interactions occur
preferentially in the reaction transition state, the transition state
has more binding energy and gets therefore stabilized, thereby
lowering the activation energy.
10.
How does entropy loss occur? How does it raise the free
energy of ES complex that lowers the activation energy?
Answer: The loss of entropy occurs due to the binding of substrate
to enzyme. The entropy loss arises from the fact that the ES
complex is a highly organized (low-entropy) entity compared to
enzyme and substrate in solution (a disordered, high-entropy
situation). Because ΔS is negative for this process, the term -TΔS
is a positive quantity, and, therefore, the free energy content of
ES complex increases. In other words, entropy reduction raises
the free energy of ES complex that in turn lowers the activation
energy.
11.
How does destabilization of the ES complex occur? How
does it lower the activation energy?
Answer: The destabilization of ES complex occurs by strain,
distortion, desolvation, or other similar effects. The strain or
distortion facilitates the conversion of substrate to the transition
state by weakening critical bonds and by permitting formation of
new weak bonding interactions. The facilitation of additional weak
bonding interactions in the transition state stabilizes it, thereby
lowering the activation energy.
In aqueous solution, most biomolecules (charged groups)
are stabilized by the solvation shell of hydrogen-bonded water
molecules. Upon binding in the active site, enzyme-substrate
interactions replace most or all of these hydrogen bonds,
thereby desolvating and destabilizing them. Besides, there
occurs electrostatic destabilization as the charged groups on
Consortium for Educational Communication
substrate may be forced to interact (unfavorably) with charges
of like sign on active site. The total destabilization energy
(ΔGd) raises the free energy of ES complex, thereby lowering
the activation energy.
12.
How do proximity and orientation effects help in lowering of the activation energy?
Answer: Enzymes take the reactants out of dilute solution and
hold them close to each other or to catalytic residues. This
proximity of reactants is said to raise the “effective” concentration
over that of the substrates in solution, and leads to an increased
reaction rate. Enzymes not only bring substrates and catalytic
groups close together, but they also orient them in a manner
suitable for catalysis as well. Proximity and orientation may also
lead to electrostatic interactions that result in the stabilization of
transition state (electrostatic catalysis).
13.
Name the various mechanisms through which transient
covalent interactions or group transfers lower the activation
energy?
Answer: The various mechanisms that generally involve transient
covalent interaction with a substrate or group transfer to or from
a substrate are: General Acid–base catalysis, Covalent catalysis
and Metal ion catalysis.
14.
How does General Acid–base catalysis result in rate enhancement?
Answer: Transition states can also be stabilized by the transfer of
protons to or from the proton acceptors or donors. Nonenzymatic
reactions involve either the constituents of water (H+ or OH-) alone
or other weak proton donors or acceptors for the proton transfers
to/from transition state. Since the protons are transferred slowly,
Consortium for Educational Communication
the transition state is not effectively stabilized every time it forms,
thus rendering the catalysis slow. However, a number of amino
acid side chains in the active site of an enzyme act as acids or
bases, readily donating or accepting a proton from transition
state, thereby effectively stabilizing it. This results in lowering of
the activation energy and hence rate enhancement.
15.
What do you mean by Covalent catalysis?
Answer: In Covalent catalysis, a powerful nucleophile in the active
site forms a transient covalent bond between the enzyme and
the substrate that results in lowering of the activation energy.
The nucleophilic groups readily attack electrophilic centers
of substrates, forming covalently bonded enzyme-substrate
intermediates which undergo further reaction to give the desired
products.
16.
What is Metal ion catalysis?
Answer: The catalysis by metals, bound to the enzyme, is called
Metal ion catalysis. These metals participate in catalysis in
several ways: by binding to substrates and orienting them, by
mediating oxidation-reduction reactions, by electrostatically or
electrophilically stabilizing or shielding negative charges.
17.
Does a particular enzyme employ just one mechanism
or all of these mechanisms simultaneously during catalysis?
Answer: Whether based on noncovalent interactions (binding
energy), transient covalent interactions or group transfers, these
mechanisms are not mutually exclusive. A given enzyme might
employ a combination of several catalytic strategies in its overall
mechanism of action to bring about a rate enhancement. For most
Consortium for Educational Communication
enzymes, it is difficult to quantify the contribution of any one
catalytic mechanism to the rate and/or specificity of a particular
enzyme-catalyzed reaction. However, binding energy is a major
source of free energy used by enzymes to lower the activation
energies.