Lecture13-catalysis - BIOC*2580
Lecture
13:

...

Info iconThis preview shows page 1. Sign up to view the full content.

View Full Document Right Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: BIOC*2580
Lecture
13:

 Basis
of
chemical
and
enzymatic
catalysis
 1 Synopsis:
 Many
 proteins
 are
 able
 to
 bind
 and
 recognize
 specific
 molecules.
 Specific
 binding
 results
 from
 cavities
 and
 regions
 on
 the
 protein
 surface,
 which
 complement
 the
 target
 molecule,
 Enzymes
 speed
 up
 reactions
 by
 a
 variety
 of
 catalytic
 effects,
 including
 proximity
 effect,
 orientation
 effect
 and
 chemical
 catalysis.
 Chemical
 catalysis
 lowers
 the
 activation
 energy
 Ea
 required
for
reaction
by
finding
a
better
chemical
pathway
for
reaction.
This
may
be
 achieved
by
 nucleophilic
catalysis,
electrophilic
catalysis,
general
acid
or
general
base
catalysis
 or
by
transition
state
stabilization.
 
 Reading:
Lehninger
p.
183‐194
(4th
ed
p.196‐202).
 
 
 Enzyme
catalysis
 
 Many
proteins
are
enzymes,
that
is,
they
bind
target
molecules
and
catalyze
a
specific
reaction.

 The
suffix
‐ase
at
the
end
of
a
protein
name
indicates
an
enzyme,
e.g.
ribonuclease,
an
enzyme
 that
 breaks
 down
 RNA,
 ribonucleic
 acid,
 by
 hydrolysis;
 peptidase,
 an
 enzyme
 that
 breaks
 peptide
bonds
by
hydrolysis,
etc.

 
 The
target
molecule
bound
to
and
reacting
on
the
surface
of
the
enzyme
is
called
the
substrate
 of
the
enzyme.
 
 Enzyme
 catalyze
 reactions
 are
 reactions
 that
 might
 otherwise
 occur
 spontaneously,
 but
 at
 a
 very
 slow
 rate;
 enzymes
 are
 not
 magic
 ‐
 the
 reaction
 must
 be
 chemically
 feasible
 in
 the
 first
 place.
Enzymes
may
speed
up
their
reactions
anything
from106
to
1017
fold.
 
 How
is
the
enzyme
so
efficient
when
uncatalysed
reactions
are
slow
?
 Uncatalysed
reactions
may
be
relatively
slow
because
of
the
random
nature
of
the
process.
 
 Molecules
must
first
collide*;
 
 and
if
they
are
in
the
right
orientation
 
 and
if
they
possess
a
critical
threshold
energy,

 
 *collisions
are
important
for
unimolecular
reactions
as
well
as
bimolecular,
since
molecules
can
 exchange
energy
through
collisions.
 
 Page
1
of
4
 BIOC*2580
Lecture
13:

 Basis
of
chemical
and
enzymatic
catalysis
 2 From
simple
chemical
kinetics

 
 
 
 Z
is
the
collision
frequency,

 rate
 = 
p.Z.e ‐(E a RT ) 

 
 p
 is
 a
 probability
 factor,
 which
 has
 a
 lot
 to
 do
 with
 the
 relative
 orientation
 of
 the
 reacting
 molecules.
 
 Ea
is
called
the
activation
energy,
the
minimum
energy
a
molecule
must
possess
to
initiate
the
 € ‐(Ea/RT) reaction.
 
 e 
is
the
 fraction
of
molecules
at
Kelvin
temperature
T
which
possess
 energy
 Ea;
 this
 value
 tends
 to
 zero
 as
 Ea
 increases
 (Ea
 is
 always
 positive),
 so
 Ea
 should
 be
 as
 low
 as
 possible.

 
 We
can
speed
up
a
reaction
if
we
can
increase
p
or
Z,
or
decrease
Ea.
 Enzymes
bind
their
substrates
to
reduce
the
randomness
of
collision
 
 Proximity
 effect:
 enzymes
 bind
 their
 substrates
 so
 their
 reactive
 groups
 are
 brought
 close
 together*
 and
 stay
 together
 long
 enough
 for
 the
 reaction
 to
 proceed.
This
eliminates
randomness
of
collision
in
free
solution
(increases
Z).
 
 *In
the
case
of
apparently
unimolecular
reactions,
it's
a
reaction
between
the
 single
substrate
and
reactive
amino
acid
side
chains
in
the
enzyme:
 
 Orientation
 effect:
 even
 if
 two
 molecules
 manage
 to
 meet
 by
 random
 collision,
 their
 reactive
 groups
 are
not
 necessarily
pointed
in
the
right
direction
 to
 proceed
with
the
reaction.

 
 
 Since
 binding
 of
 substrates
 by
 enzymes
 involves
 very
 specific
 interactions,
 substrates
 of
 enzymes
 are
 precisely
 positioned
 and
 reactive
 groups
 are
 well
 aligned.
 This
 eliminates
 randomness
 of
 substrate
orientation
(increases
p).
 Page
2
of
4
 BIOC*2580
Lecture
13:

 Basis
of
chemical
and
enzymatic
catalysis
 3 Randomness
can
be
represented
by
entropy;
so
the
proximity
effect
and
orientation
effect
both
 reduce
the
activation
entropy
of
the
reaction.
 
 Proximity
 effect
 is
 the
 elimination
 of
 translational
 entropy,
 and
 orientation
 effect
 is
 the
 elimination
 of
 rotational
entropy.
These
entropies
can
be
calculated
at
any
given
temperature,
 and
this
allows
us
to
estimate
that
a
theoretically
perfect
enzyme
could
speed
up
a
reaction
by
 105‐fold
by
the
proximity
effect,
and
by
 105‐fold
by
the
orientation
effect.
Overall
this
is
a
 1010‐ fold
 speed‐up
 for
 the
 combination
 of
 two
 effects.
 These
 two
 effects
 account
 for
 much
 of
 the
 observed
speed
up
in
enzyme
catalysis.
 
 How
enzymes
decrease
Ea:

 
 Chemical
 catalysis
 ‐
 the
 enzyme
 provides
 a
 reaction
 pathway
 that's
 better
 than
 the
 uncatalyzed
 reaction.
 At
 298
 K,
 reducing
 Ea
 by
 5.7
kJ
increases
rate
10‐fold.
 
 For
example,
examine
the
hydrolysis
reaction:
 
 X‐CO‐NH‐Y
+
H2O
X‐CO2‐
+
+NH3‐Y
 
 This
 overall
 equation
 for
 hydrolysis
 shows
 the
 addition
 of
 H2O
 to
 break
 an
 amide
 bond.
 With
 H2O
 alone,
 the
 reaction
 is
 incredibly
 slow,
 because
 the
 :O
 in
 H2O
 is
 a
 poor
 nucleophile
 and
 an
 excessively
weak
acid.
Although
O
has
two
 lone
pairs,
it's
very
electronegative
and
reluctant
to
 share
its
electrons.
The
reaction
is
radically
 speeded
up
by
using
OHˉ,
a
much
better
nucleophile
 due
to
the
excess
negative
charge,
or
H3O+,
an
excellent
proton
donor.
 
 However,
most
biochemical
reactions
happen
close
to
pH
7,
so
strong
acid
or
strong
base
are
 ruled
out.

 (Nor
can
we
raise
the
temperature,
the
chemist's
usual
trick
for
speeding
up
reactions,
reducing
 Ea/RT
by
increasing
T).
 
 Enzymes
speed
up
reactions
at
normal
pH
and
temperature.
 
 Nucleophilic
catalysis:
reaction
is
initiated
by
a
nucleophile
on
the
enzyme,
e.g.
CysSH,
or
His
or
 Asp‐
or
Glu‐,
more
rarely
TyrOH,
SerOH
or
LysNH2.
Nucleophiles
act
by
donating
a
lone
pair
to
an
 electron
deficient
C
atom
in
the
substrate
(e.g.
C=O
groups).
 
 Electrophilic
catalysis:
an
electrophile
is
a
species,
which
reacts
by
attracting
electrons
from
a
 reactant.
 There
 are
 no
 really
 excellent
 electrophiles
 among
 the
 amino
 acids,
 but
 what
 the
 enzyme
 might
do
is
to
recruit
a
non‐amino
acid
helper
molecule
called
a
 prosthetic
group.
The
 prosthetic
 group
 is
 bound
 into
 the
 enzyme's
 active
 site
 like
 the
 substrate.
 The
 metal
 Zn2+
 sometimes
 functions
 in
 this
 way,
 and
 is
 found
 in
 the
 active
 site
 of
 carboxypeptidase
 A,
 an
 enzyme
that
hydrolyzes
a
single
amino
acid
from
the
C‐terminus
of
a
peptide
chain.
 Page
3
of
4
 BIOC*2580
Lecture
13:

 Basis
of
chemical
and
enzymatic
catalysis
 4 General
 Acid
 and
 General
 Base
 catalysis:
 catalysis
 by
 weak
 acid
 or
 weak
 base
 functional
 groups
 that
 donate
 a
 proton
 to
 or
 steal
 a
 proton
 from
 the
 substrate
 (as
 opposed
 to
 specific
 acid
 or
 base
 catalysis,
which
involves
specifically
H3O+
or
OHˉ).

 
 The
enzyme
can
position
an
acidic
or
basic
group
in
 a
 confined
 space
 in
 close
 proximity
 to
 the
 substrate.
If
a
single
H+
donor
is
localized
in
a
small
 volume,
 it
 behaves
 as
 if
 the
 concentration
 of
 the
 reactive
group
is
very
high,
without
altering
the
pH
 of
the
general
environment.
 
 2 Each
of
the
above
effects
can
contribute
about
10 ‐fold
speed
up
factor
to
the
overall
 enzyme
 catalyzed
reaction.
 
 Transition
state
stabilization

 
 Transition
 state
 stabilization:
 all
 reactions
 pass
 through
 a
 transition
 state
 which
 represents
 an
 energy
maximum;
Ea
is
the
energy
needed
to
get
 up
to
the
 transition
 state.
 Enzymes
 can
 reduce
 Ea
 by
 providing
 a
 different
 chemical
 pathway
 through
the
reaction.
 
 By
 shaping
 the
 active
 site
 of
 the
 enzyme
 so
 it
 fits
 the
 transition
 state
 even
 better
 than
 the
 substrate,
Ea
can
be
significantly
lowered.
When
 the
 substrate
binds,
the
enzyme
may
stretch
or
 distort
a
key
bond
and
weaken
it
so
that
less
 activation
energy
is
needed
to
make
the
bond
break
at
the
start
of
the
reaction.
In
many
cases,
 the
 transition
 state
 of
 a
 reaction
 has
 a
 different
 geometry
 at
 the
 key
 atom
 (e.g.
 tetrahedral
 instead
 of
trigonal
planar).
By
optimizing
binding
of
a
tetrahedral
atom,
the
substrate
is
helped
 on
its
way
to
reaction
 
 Page
4
of
4
 ...
View Full Document

{[ snackBarMessage ]}

Ask a homework question - tutors are online