Enzymes II

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Enzymes II
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Learning Objectives
Describe how enzymes lower the activation energy
of a reaction (covalent and non-covalent
interactions). Describe how an enzyme active site
is, or becomes, complementary to the transition
state. Describe why enzymes are so
large. Describe enzyme specificity. Describe the
phenomena of induced fit. Describe four specific
types of catalysis.
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Where does the energy come from for the dramatic
lowering of the activation energy for a reaction?
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(1) Rearrangement of covalent bonds during enzyme
catalysis which takes place in the active
site. Catalytic functional groups in the active
site form transient covalent bonds with the
substrate and activate it for the next reaction
step. These provide an alternative, lower-energy
path and lower the activation energy.
(2) Non-covalent interactions between enzyme and
substrate. The formation of an ES complex
involves hydrogen bonding, hydrophobic, and
ionic interactions. These interactions release
free energy which stabilizes the ES complex.
This is called the binding energy.
Binding energy is a major source of free energy
used by enzymes to lower the activation energy of
reactions.
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What happens when S binds to E?
Is the active site complementary to the
substrate? (lock and key hypothesis)
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In order to catalyze a reaction, the active site
of an enzyme must be complementary to the
transition state.
Some weak interactions are formed in the ES
complex, but the full complement of these weak
interactions are realized only when the reaction
has progressed to the transition state. The
transition state is still an unstable
intermediate, but the activation energy is lower,
and the reaction proceeds much faster than the
uncatalyzed process.
Weak bonding interactions between the enzyme and
substrate provide a major driving force for
enzyme catalysis.
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DGB favorable (negative) change in free energy
due to binding
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This requirement for multiple weak interactions
is why enzymes are so large.
The proper three-dimensional arrangement of
catalytic functional groups also requires a
protein large enough to maintain this
three-dimensional arrangement, and yet allow for
movements in the functional groups to complement
the changes in the substrate as the reaction
progresses.
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specificity the ability of an enzyme to
discriminate between its substrate and another
molecule.
Specificity and catalysis arise from the same
phenomena weak interactions between the active
site functional groups and the substrate. The
enzyme active site is designed to lower the
activation energy of one specific,
three-dimensional molecular arrangement in the
transition state. It will not do this with a
different molecule (or it will do it poorly).
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Factors that contribute to the transition state
barrier (the activation energy)
(1) the change in entropy (freedom of motion of
two molecules in solution) (2) the solvation
shell of hydrogen-bonded water that surrounds and
stabilizes molecules in solution. (3) the
distortion of substrates (bond length, angles)
that must occur in many reactions (4) the need
for proper alignment of catalytically important
functional groups in the enzyme active site
Binding energy can be used to overcome these
barriers.
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Enzyme substrate interactions replace the
hydrogen bonds between substrate and water
(desolvation).
Binding energy involving interactions formed only
in the transition state compensate for any
distortion (electron redistribution) that the
substrate must undergo to react.
induced fit changes in the three-dimensional
conformation of the enzyme when the substrate
binds. This brings specific functional groups
into the proper position for catalysis to occur.
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Hexokinase
(transfer of phosphate from ATP to glucose)
The C6 hydroxyl of glucose is similar in
reactivity to H2O, yet hexokinase distinguishes
between glucose and water by a factor of 106.
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In the absence of glucose, hexokinase in an
inactive conformation. The active site is open
and water and ATP can enter, but ATP is not
hydrolyzed (i.e. the phosphate is not transferred
to water).
active site pocket
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When glucose and Mg-ATP bind at the active site,
the binding energy induces a conformational in
the enzyme which results in a catalytically
active form of the enzyme.
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Induced-fit in hexokinase
Hexokinase can discriminate between water and
glucose because of an induced-fit only when
glucose is the substrate.
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Specific types of catalysis
specific acid-base catalysis uses only the H
(H3O) or OH- ions present in water
general acid-base catalysis proton transfers
mediated by other classes of molecules.
covalent catalysis a transient covalent bond is
formed between enzyme and substrate.
metal ion catalysis use of a metal ion, whether
tightly bound to the enzyme or taken up from
solution along with the substrate, to promote
ionic interactions favorable to catalysis.
Charged intermediates can be stabilized by proton
transfers.
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Combination of covalent and general acid-base
catalysis
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Chymotrypsin
Cleaves peptide bonds involving the carboxyl of
aromatic amino acids
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