Induced fit model of enzyme catalysis Video Lecture | Biochemistry for MCAT

So today, I'm going to talk
to you about the induced fit
model of enzyme catalysis and
how this concept can tell us
a lot about how enzymes work.
But before we do that,
let's review the idea
that enzymes make
reactions go faster.
And when you look at a
reaction on a reaction
coordinate diagram, you'd see
that the catalyzed reaction
would have a much
smaller activation
energy than the uncatalyzed one.
Also remember that
because of this,
the energy of the catalyzed
reaction's transition state
is far lower than the energy
of the uncatalyzed reaction's
transition state.
So what do enzymes look like?
Well, most enzymes are
proteins, or at least partially
made up of protein.
And substrates are any molecule
that an enzyme will act on.
And often, these substrates
are the reactants
that the enzyme will
ultimately help turn
into products
through a reaction.
Now enzymes also
have what is called
the active site, which is
the location on the enzyme
where substrates bind.
And that's where the
reaction ultimately happens.
And it's important to
recognize that every enzyme has
a unique active
site that will only
bind to certain substrates.
And just to clarify, I've
referred to the active site
here as both of the notches
found on the enzyme, and not
the space in between them.
So here, of the
two substrates I've
drawn, the enzyme will only be
able to bind to substrate 1,
since they fit together
like puzzle pieces.
Whereas the shape
of substrate 2 isn't
going to fit nicely in
the enzyme's active site.
Now since enzymes have
unique active sites,
we say that enzymes are
specific to certain substrates,
and by extension
certain reactions.
But let's dive a
little deeper into what
happens when enzymes and
substrates bind to each other
and how that binding
pattern changes
as a reaction progresses.
So first you'll have
your enzyme here
and your substrate over here.
And I'm just going to label
this with the number 1,
since it'll be the
first thing that
happens in the sequence
of events to come.
And at this stage,
nothing has happened yet.
And the enzyme and the substrate
have yet to come in contact.
So next what will happen
is the enzyme will bind
to the substrate.
But this binding
won't be perfect.
So we'll call this
initial binding,
which is stage 2 of the process.
And what that means is that
the forces holding these two
together are strong, but they're
not at their maximum strength
just yet.
And enzymes and
substrates don't actually
fit together quite
like puzzle pieces.
And they actually
work a little bit more
like two pieces of clay
that will both mold
together so that the
fit is much tighter.
So in our next step, this
is exactly what happens.
The enzyme and the
substrate will both change
shape a little bit and bind
to each other really strongly.
And we call this the induced
fit because both the enzyme
and the substrate have changed
their shape a little bit so
that they bind together
really tightly.
And it's at this point where
the reaction that the enzyme is
catalyzing is at full force.
And this would be stage 3.
So our next stage occurs after
the reaction is completed
and the binding becomes similar
to what it was in stage 2.
But the difference
here is that there
was something different
about the substrate.
So in this reaction, the
enzyme is cutting our substrate
into two parts.
So now, the two parts
have become separated.
And this would occur after
the reaction is finished.
And we'll call this stage 4.
Now in our next and last stage,
the products of the reaction
have been released
from the enzyme.
And our enzyme is
back in the same state
that it was in stage 1.
And we'll call this stage 5.
Now, let's look at this from
a slightly different angle.
I'm going to label the enzyme
as E, the substrate as S,
and our two products
as P1 and P2.
And they're going to represent
this series of events,
these different steps in
the sequence of reactions.
So first we'll have
E and S separate.
And this is stage 1.
And next, E and S will
bind to each other to form
an enzyme substrate complex,
which I have called ES.
And it corresponds to
stage 2 from before.
Now what's really interesting
is that in the next step, where
we had the induced
fit of stage 3,
we're actually at the transition
state of the entire reaction.
And this is the same as that
really high energy point
that we saw at the
beginning of this video.
And it's at the point
of the transition state
where our enzyme is most
tightly bound to its substrate.
Now, I've written the substrate
out here with the letter X.
Because of the reaction's
transition state
our substrate isn't
quite a reactant
and it isn't quite
our product either.
It's somewhere in between.
So that's why I've written
it out as X instead of S.
And I've also written this
double dagger symbol, which
is just a universal symbol
for transition states.
Now in our next stage, which
is after the reaction has
occurred, since it exists
after the transition stage,
we have the enzyme bound to
the two products P1 and P2.
And this was stage
4 from before.
And then finally in our
last stage, stage 5,
we have our enzyme,
which is now separated
from our two
products, P1 and P2.
Now the big M away from this
is that binding between enzyme
and substrate is strongest
at the reaction's transition
state.
And this is because the
enzyme and the substrate
have molded together.
And that's why we call
it the induced fit.
Now, some enzymes
will actually bind
to more than one substrate.
And if we look at a reaction
that might be familiar,
which is lactic
acid fermentation,
we can see that our enzyme,
lactase dehydrogenase,
will have space to bind to
two different substrates
in this reaction, one
space being for NADH
and the other
being for pyruvate.
So enzymes don't necessarily
bind just to one substrate.
Now, sometimes things
will bind to enzymes
at places other than
their active sites.
And we call this
allosteric binding.
So if we have an enzyme
here with it's active site,
a regulating molecule
like an inhibitor
made by the enzyme at
a different location
than the enzyme's active site.
Now when something binds
to an enzyme like this,
it usually has the
effect of changing
the shape of an
enzyme in some way
to affect its ability
to catalyze reactions.
So in this case, when an
inhibitor binds top the enzyme,
it might change the
shape of the active site,
thereby inhibiting
the enzyme, as it's
no longer able to bind to
its intended substrate.
They don't quite fit
together anymore.
So while enzymes bind
to reactive groups
at their active
sites, they can also
bind to regulators at
their allosteric sites.
And allosteric sites just
refer to any binding site
outside of the active site.
And remember allosterically
binding molecules
can either be activators
or inhibitors,
any regulating molecule.
So what did we learn?
Well, first we learned
that enzymes are specific
and that they can each bind
to only specific substrates
to catalyze specific reactions.
Next, we learned about
the induced fit model
and how enzymes bind their
substrates most tightly
in the middle of a reaction
at the reaction's transition
state.
And finally, we learned that
enzymes have both active sites
and allosteric sites, with
active sites being where
the reaction takes place
and allosteric sites being
where regulation takes place.