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BOGDEN FEDELES: Hello
and welcome to 5.07
Biochemistry online.
I'm Dr. Bogden Fedeles.
Despite the staggering
biodiversity we see in nature,
the types of chemical reactions
employed are only but a couple
of handfuls.
And these are used over and
over again very efficiently
and with conserved mechanisms.
As you might recall
from Organic Chemistry,
one of the most
versatile chemical groups
is the carbonyl, C double
bond O. Not surprisingly,
carbonyl chemistry
is well-represented
in biochemistry.
In fact, the carbonyl
chemistry allows formation
of carbon-carbon bonds.
It's one of the very few
ways in which enzymes
can start with small molecules
and put them together
into a macromolecule, or
start with a macromolecule
and break it down into smaller
pieces during metabolism.
This video summarizes
some of the most important
carbonyl reactions you
will encounter in 5.07.
In this video, we're
going to be talking
about carbonyl chemistry.
And as we will see,
carbonyl chemistry
is fundamental for some of the
carbon-carbon bond formation
and cleavage reactions.
As you recall from
organic chemistry,
carbonyl contains a C double
bond O. And all the properties
of the carbonyl derive from its
ability to polarize this bond,
so that we can draw a
resonance structure where
the carbon has a positive
charge and the oxygen
a negative charge.
As you recall, there
are simple carbonyls,
such as aldehydes and ketones.
Also we have acyl derivatives,
compounds in which the carbonyl
is attached to a heteroatom.
x can be oxygen,
nitrogen, sulfur.
So here, respective, we have
esters, amides, thioesters,
and of course, we have an OH
group here, carboxylic acid.
Here is a summary
of the reactions
that we're going to
be talking about.
First, we're going
to be discussing
nucleophilic addition.
Here, the good nucleophile
reacts with the carbonyl,
adding to the carbon that
the carbonyl can generate.
This tetrahedral compound.
Next we're going to be
talking about enolization.
This is the property
of carbonyls
that contain an
alpha hydrogen, which
can rearrange to form enol.
Next we're going to
introduce the aldol reaction.
This is the reaction in which
a carbon-carbon bond is formed
and occurs between a carbonyl
that acts as electrophile
and a enolizable carbonyl,
which acts as a nucleophile.
In the aldol reaction, a bond
is formed between these two
carbons, generating an aldol.
We're also going to see that
the aldols can dehydrate.
The aldols we saw above
can lose a water molecule
to form an alpha,
beta-unsaturated carbonyl.
Now about the acyl
derivatives, we're
going to be talking about
acyl transfer reactions, where
an acyl derivative
can convert into
a different acyl derivative with
the appropriate nucleophile.
A variation of this reaction
is Claisen reaction,
where similarly to
the aldol reaction,
we have an enolizable
carbonyl reacting
with an acyl derivitive
and generating
a beta-keto carbonyl.
This reaction also forms
a carbon-carbon bond,
which is right here.
Let's talk in more detail about
the nucleophilic addition.
The general reaction
scheme is as we saw before.
Here is a carbonyl compound
reacting with a nucleophile
and forming a tetrahedral
intermediate that contains
an alkoxide or an alcohol.
Now let's take a look at
two different reactions.
One is the reaction of alcohols
with carbonyl compounds, where
we form a compound
that looks like this.
This is called a hemiacetal.
Now this reaction is reversible.
And, in fact, it
reaches equilibrium
because delta G naught
is approximately zero.
This reaction can be
acid or base catalyzed.
Let's take a quick
look at that mechanism.
If it's based
catalyzed, the base
will first deprotonate
the alcohol,
which will form the
alkoxide, which is then
a very good nucleophile to
attack the carbonyl, which
forms this alkoxide version
of the hemiacetal, which
can be then protonated.
In acid-catalyzed
mechanism, we have
to activate the carbonyl
first, so the protonation
of the carbonyl
is the first step.
All right, so this
activated carbonyl
can then be attacked
by our alcohol.
Which, this product is just
one proton transfer away
from our hemiacetal.
All right, the second reaction
I want to include here
is the formation of
Schiff bases which
is the reaction of a
carbonyl with an amine.
Similarly to the
hemiacetal formation,
this reaction generates first
a tetrahedral intermediate,
which is, however,
unstable, and loses water
to generate the imine,
with a Schiff base.
Let's take a look
at the mechanism.
As you notice, the reaction--
because the amine group is
a good nucleophile, the
reaction can occur even
in neutral conditions.
We don't need, necessarily,
acid or base catalysis.
The first step, the imine
attacks the carbonyl,
forming this compound
with split charges.
Now proton transfer happens
to generate our intermediate.
Then water is eliminated.
And this is the imine.
You'll notice the
imine nitrogen can also
be protonated, to
generate this iminium ion,
which, as we will see
in other situations,
it's an activated version
of the carbonyl group.
From these two
examples, we can get
some idea of how the
nucleophilic addition occurs.
So let's take a look at
what kind of nucleophiles
we can add to the
carbonyl group.
We have some good nucleophiles.
And here we have things
with negative charges,
such as alkoxide, or hydroxide.
I have the thiolates.
And other things such as amines.
And we also have
some OK nucleophiles.
And here we have alcohols,
even water, and thiols.
As you saw in these
couple of mechanisms,
the OK nucleophiles
don't react very well,
unless they are deprotonated
to form good nucleophiles,
such as the alcohols.
Or the carbonyl gets activated,
either by protonation
in a strong acid,
as we saw here,
or it becomes an activated
carbonyl, for example,
in an iminium ion.
Another important nuclear
force that we're going to see
is the, what we're going
to call, a C minus.
Basically a
carbanion In our case
it's going to be enolates, which
can also add to the carbonyls.
And these will form the
basis for the aldol reaction.
The second reaction we're
going to be talking about
is enolization.
Here, a carbonyl that
contains an alpha hydrogen
can rearrange to form an enol.
We're going to call this
the keto form and this
the enol form.
An equilibrium between
a keto and an enol form
is called tautomerization.
And this is a very
important reaction
in many biochemical systems.
Turns out, the delta G, for
the reaction as written,
it's very high, 30 to
50 kilojoules per mole.
That means that equilibrium
strongly favors the keto form.
However, in certain
cases, the enol
can form and get stabilized.
The mechanism of enolization,
it's very straightforward.
All we need is a
decent base that
can remove the alpha proton.
And it will form this enolate.
Now, enolate is able
to form because it
has resonance stabilization.
We can draw another
resonance structure, as such,
where we see the negative
charge is on the carbon.
So it is in fact a carbanion.
We're going to call it
a disguised carbanion.
As the carbon is not
very electronegative,
having such a high electron
density on the carbon
would make it a very
good nucleophile.
And in fact, this enolate
is the nucleophile
that executes reactions
such as the Aldol reaction
and the Claisen reaction.
Something to keep in
mind, well, how acidic
is this alpha hydrogen?
We can compare it with
a hydrogen in an alkyne.
The pKa of such a
hydrogen is close to 50.
It's extremely hard
to remove a proton.
Now if we look at an alpha
hydrogen next to a carbonyl,
the pKa is 18 to 20.
So it's 30 orders of
magnitude more acidic,
and this is because, as we saw,
when we removed this hydrogen,
we formed the enolate anion,
which is resonance stabilized.
The more extreme case of this,
if we have two carbonyls, alpha
to the same proton, the
pKa drops even further,
around 9 to 11.
This is because we can draw
even more resonance structures
to the enolate that's formed.
This is one.
This is another.
And another.
As we saw before,
the charge here
is delocalized between the
oxygens and the alpha carbon.
So it is this beta keto carbonyl
in its enolate form will
behave as a carbanion and it
can act as a good nucleophile.
The Aldol reaction.
This is a very important
reaction in biochemistry
because it allows formation
of carbon-carbon bonds.
Or, if the reaction
runs in reverse,
cleavage of the
carbon-carbon bonds.
The Aldol reaction
is the reaction
between an enolizable
carbonyl, as we show here,
a carbonyl that has an alpha
hydrogen, and another carbonyl.
And what happens is, a
new carbon-carbon bond
forms between alpha carbon
and the carbonyl carbon.
The product of the
Aldol reaction,
it's called Aldol as a
contraction between aldehyde
and alcohol, as in some
cases this carbonyl
will be an aldehyde and
this would be Aldol.
It's essentially a beta
hydroxy of carbonyl.
Now, this reaction has a
delta G naught close to 0.
That is, it reaches equilibrium.
And it can be catalyzed
by acid or by base.
Let's take a quick
look at the mechanism.
Given the previous
mechanistic insights--
we looked at the nucleophilic
addition, and enol formation,
then the mechanism
of the Aldol reaction
should be fairly
straightforward.
If it's base-catalyzed,
the base is
going to help us form
the enolate, as such.
And as we discussed
previously, the enolate
is a good nucleophile, and can
react via nucleophilic addition
with the other carbonyl.
And one proton transfer to
generate the Aldol product.
The reaction can also
be acid-catalyzed.
Again, formation of the
enol in acid catalysis
involved first protonation
of the carbonyl.
Now this activated
carbonyl, it's
a much better electron sink, and
stabilizes the enol formation.
Now, in the second
step the enol can
react with the other
carbonyl, to generate
a protonated version
of the Aldol, which
is one proton transfer away
from the Aldol product.
In biochemical
systems, the enzyme
that catalyzed the Aldol
reaction is called aldolase.
And there are actually
two kinds of aldolases.
Class one, and class two.
The distinctive feature
of these enzymes
is the way they
catalyze the reaction.
Class one uses an
active site lysine
to form a Schiff base
with the carbonyl, which
activates the carbonyl, and
allows for the enol formation.
Class two uses a metal
ion, such as zinc,
to accomplish the same thing.
So here is how the mechanism
for the class 1 aldolase
would look.
So here is our
enolizable carbonyl,
and here is our
active site lysine.
As we saw before,
an amine reacting
was a carbonyl will
give us a Schiff base.
The reaction goes via a
tetrahedral intermediate,
which we're not
going to draw here,
but what we form is
this iminium ion.
Now the carbonyl
is activated enough
that an active site base
can remove an alpha hydrogen
to form the enol.
Which is now well-positioned
to attack the other carbonyl.
This generates the Aldol
product, in its imine form,
still attached to the enzyme.
And now the hydrolysis of imine
is going to release the Aldol.
Now, class two enzymes
use a zinc ion.
As the ion approaches
the carbonyl,
it's going to draw some of the
electrons from the carbonyl,
and make the proton in the alpha
position a lot more acidic.
So you can imagine,
some of these electrons
get de-localized.
So that a base can remove the
proton and form the enolate.
Which, in the second
step, it reacts
with the carbonyl, which
will generate the Aldol
product in the active
site of the enzyme,
still bound to the zinc, and
now which can dissociate,
and generate the final--
and release the product.
Now, a very important
consideration
for the Aldol reaction
is that it can
occur in the reverse fashion.
For example, to cleave
a carbon-carbon bond.
So the bond that will be
cleaved, as we see here,
is the bond that
got formed, which
is the bond between the
alpha and beta carbons.
The aldolase is one of the
key enzyme in glycolysis,
that allows us to break a
six carbon sugar into two
three-carbon sugars by
cleaving a carbon-carbon bond
via the Aldol reaction.
As the mechanism
catalyzed by the aldolase,
we can see that the
reverse pathway is pretty
straightforward, where the
Aldol binds to the enzyme,
say in class one,
forms an active site,
covalent attraction, a
Schiff base with the lysine,
from which the chemistry
occurs to break
the carbon-carbon bond, and
leads to the release of one
carbonyl molecule,
and then the other one
will be still bound to the
enzyme as a Schiff base
and hydrolyzed.
For the class two, the Aldol
will interact with the enzyme
by forming an interaction
with the zinc,
and this activated carbonyl
allows the chemistry
to occur exactly in the
reverse manner, as shown here.
One other reaction involving
Aldols is Aldol dehydration.
Here's an Aldol, beta
hydroxy carbonyl.
Now, if an Aldol has an
additional alpha hydrogen,
it can lose a water molecule to
form an alpha beta unsaturated
carbonyl.
Now this reaction is
favorable thermodynamically.
The delta G naught
is approximately 0.
And this is a
reaction we're going
to see in a lot of
biochemical pathways,
for example, in the
biosynthesis of fatty acids,
going left to right, or in
the catabolism of fatty acids,
going right to left.
Here's a quick insight
on the mechanism.
Once again, it can be
base- or acid-catalyzed.
This reaction works because
the alpha hydrogen here
is next to a carbonyl, and
therefore can form an enol.
So if a base can remove this
hydrogen to form the enolate,
then we can envision how this
electronic movement will allow
for a water molecule
to be eliminated,
forming our alpha beta
unsaturated carbonyl.
The acid-catalyzed mechanism
goes along the same lines.
As you remember,
in order to form
the enol in an
acid-catalyzed context,
first we have to
protonate the carbonyl.
All right.
Now a base can remove
our alpha hydrogen,
forming the enol, which
can kick off a water
molecule, generating
these pieces, which
is just one proton transfer
away from our final product.
So let's talk now about acyl
derivatives, and acyl transfer.
As we mentioned,
acyl derivatives
have a carbonyl attached
to a header atom.
And this header atom can be
oxygen, nitrogen, sulfur.
As all these header
atoms contain
a lone pair of electrons,
one of the key properties
of the acyl derivatives would
be resonance between the header
atom and the oxygen.
Now the properties of
the acyl derivatives
will be dictated by how easy
or how difficult it is to adopt
this minor resonance structure.
In other words, how likely
is it for the header
atom to participate in
these electron conjugations.
Let's take a look at a
couple of acyl derivatives.
This is a carboxylate.
If the header atom a
nitrogen, we have amide.
If the header atom
is oxygen, we also
have esters, or
carboxylic acids.
And when the header atom is
sulfur, we have thioesters.
The order in which I wrote them
here is not actually random.
It turns out for
the carboxylate,
because it has already a
negative charge, the ability
to adopt this resonance
is greatly increased.
So it's very well
resonance-stabilized.
The ability to form these
resonance structures,
it's also great for amides,
and this dictates the chemistry
and the biochemistry of
the amide bond, which
is explored in greater detail
when we talk about protein.
Esters can also adopt
these resonance structures.
However, thioesters, because the
sulfur is a third-row element,
so the p-orbitals of
sulfur are much bigger,
they don't overlap very
well with the p-orbitals
of the carbon, the
ability to adopt
these resonance structures
is greatly diminished.
Therefore, thioesters
behave a lot more
like ketones, where the
electrons of the carbonyl bond
are localized between the
carbon and oxygen, and not
so much between the
carbon and sulfur.
So therefore, thioesters
are the least resonant.
And this is the trend.
And this trend inversely
correlates with the reactivity.
Carboxylates are least
reactive, whereas thioesters
are the most reactive.
Now, when we talk
about acyl transfer,
we talk about the reaction
between an acyl derivative
with another nucleophile,
which will replace the x header
atom with the y header atom.
So this reaction always occurs
via a tetrahedral intermediate.
When both substituents are
attached to the carbon.
Now from here, this
tetrahedral intermediate
can fall apart by
kicking off the YR
to regenerate the
starting material,
or it can kick off the
XR group, to generate
a new acyl derivative.
Let's now talk about
the Claisen reaction.
This is a very important
reaction in biochemistry,
related to the Aldol reaction,
in which we form or cleave
carbon-carbon bonds.
The Claisen reaction happens
between an enolizable carbonyl
and an acyl derivative.
Let's pick in this
case an ester.
And during this reaction,
a carbon-carbon bond
is formed between
the alpha carbon
of the enolizable carbonyl,
and the keto carbon
of the acyl derivative.
The product of the
Claisen reaction
is a beta keto carbonyl.
Let's look at the mechanism.
As with all carbonyl
reactions, when
we form a carbon-carbon bond,
we need to form an enolate.
So this is the first step.
A base will form,
remove the alpha proton,
and form the
enolate, which is now
poised to add to the acyl
derivative in an acyl transfer
reaction, forming first a
tetrahedral intermediate, which
can spontaneously fall apart
by eliminating the header atom
group, to form our beta
keto carbonyl product.
Now, in biochemistry a preferred
substrate for Claisen reactions
is a thioester.
One of the most
common thioesters
we're going to encounter in
this course is acetyl-CoA.
CoA, or coenzyme-A,
it's a thiol that
can form thioesters
with a lot of acids,
for example, acetic acid here.
Acetyl-CoA can undergo a
Claisen reaction with itself,
and therefore acts both
as an enolizable carbonyl
and as an acyl derivative.
From when we were talking
about thioesters, because
of their limited conjugation
with the carbonyl,
they are very reactive,
and they allow
the formation of the enolate.
Here is the acetyl-CoA
enolate, which
can react with another
acetyl-CoA molecule.
It will generate a
tetrahedral intermediate.
Let's draw this molecule first.
Which can lose one
of the CoA molecules,
to generate this beta keto
thioester, acetoacetyl-CoA.
As we will see
later in the course,
this is a precursor to
formation of ketone bodies, one
of the ways in which acetyl-CoA
can be used to store energy.
Now, what is coenzyme-A,
often abbreviated CoA?
We mentioned it's a thiol.
That means it has an SH
group, which it turns out,
is on a very long linker.
There you go, this
is coenzyme-A.
You might recognize this
part of the molecule
as being adenine bound to a
ribose bound to two phosphates.
It's essentially ADP.
But notice there's another
phosphate in the three
prime position, so it's an ADP
with a three prime phosphate.
This portion of the
molecule, If we squint,
resembles the amino
acid cysteine,
but without the carboxyl group.
And this middle portion
of the molecule,
it's something that looks
very difficult to synthesize.
Notice this carbon that has
two methyl groups attached,
and two other carbons
attached to it.
So it's like a tetravalent--
a carbon attached to it, four
other carbons, that's it.
Fairly rare sight
in biochemistry.
This portion of the molecule
is called pantothenic acid.
Pantothenic acid is
an essential nutrient,
also known as vitamin B5.
In this video we talked
about carbonyl chemistry.
Carbonyl is the C double bond
O, and a lot of its properties
are due to the polarizability of
this bond, where the carbon has
a partial positive
charge, and oxygen
a partial negative charge.
We talked about reactions
to simple carbonyls,
such as nucleophilic addition,
enolization, Aldol reaction,
and the Aldol dehydration.
And acyl derivatives,
where the carbonyl
is next to a header atom, such
as oxygen, nitrogen, or sulfur.
And we mentioned the
acyl transfer reaction,
and the Claisen reaction.
We saw in this video the
nucleophilic addition,
where a nucleophile attacks
the carbon of carbonyl
to add and form a
tetrahedral product.
For example, alcohols
can add to carbonyls
to form a hemiacetals,
and amines
can add to carbonyls to form
imines, or Schiff bases.
And we reviewed that
good nucleophiles
are the ones like alkoxides,
thiolates, amines, or C
minus enolates.
Whereas OK nucleophiles
like alcohols and thiols,
they need to be activated
first to undergo
nucleophilic addition.
We also talked about
enolization, the ability
of a carbonyl with
an alpha hydrogen
to rearrange into a hydroxyl
bound to a double bond, which
we call an enol.
Now this equilibrium,
called tautomerization,
favors strongly the keto form.
However, it does form
to a sufficient extent
to allow chemistry to happen.
For example, when we
remove the alpha hydrogen,
we form an anion
called enolate, which
is a disguised carbanion which
is a very good nucleophile.
Next, we discussed the Aldol
reaction, a very important
carbon-carbon bond formation
or cleavage reaction
in biochemistry.
This reaction happens between
an enolizable carbonyl
and the regular carbonyl,
and a new carbon-carbon bond
is formed between the alpha
carbon and the keto carbon,
as shown here.
The mechanism can be
both base-catalyzed and
acid-catalyzed.
And the enzymes that catalyze
this, called aldolases,
use either a lysine
in the active site
to form first a
Schiff base, or they
use a zinc in the active
site to polarize the carbonyl
and allow for the
enol formation.
We also saw that
Aldol products can
dehydrate to form alpha
beta unsaturated carbonyls.
The mechanism could be both
acid- and base-catalyzed,
and involves in both cases
formation of an enol.
Next, we also talked about acyl
derivatives, and acyl transfer.
As we show here, the resonance
in the acyl derivative
dictates there how
well they react.
Carboxylate and amine are
the most resonant stabilized,
and therefore are
the least reactive,
whereas esters,
especially thioesters,
are the least resonance
stabilized, and therefore
most reactive.
Finally, we discussed the
Claisen reaction, a reaction
similar to the Aldol, between
an enolizable carbonyl
and an acyl derivative, which
generates a beta keto carbonyl.
We introduced the acetyl-CoA,
a very important thioester,
that can undergo Claisen
reaction with itself
to form acetoacetyl-CoA.
And we also introduced
the structure
of CoA, which is
built around vitamin
B5, an essential nutrient.
