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BOGDEN FEDELES: Hello
and welcome to 5.07

00:00:22.920 --> 00:00:25.020
Biochemistry online.

00:00:25.020 --> 00:00:26.170
I'm Dr. Bogden Fedeles.

00:00:29.030 --> 00:00:32.509
Despite the staggering
biodiversity we see in nature,

00:00:32.509 --> 00:00:36.590
the types of chemical reactions
employed are only but a couple

00:00:36.590 --> 00:00:37.880
of handfuls.

00:00:37.880 --> 00:00:41.210
And these are used over and
over again very efficiently

00:00:41.210 --> 00:00:43.970
and with conserved mechanisms.

00:00:43.970 --> 00:00:45.860
As you might recall
from Organic Chemistry,

00:00:45.860 --> 00:00:48.530
one of the most
versatile chemical groups

00:00:48.530 --> 00:00:53.270
is the carbonyl, C double
bond O. Not surprisingly,

00:00:53.270 --> 00:00:55.940
carbonyl chemistry
is well-represented

00:00:55.940 --> 00:00:58.490
in biochemistry.

00:00:58.490 --> 00:01:02.540
In fact, the carbonyl
chemistry allows formation

00:01:02.540 --> 00:01:04.190
of carbon-carbon bonds.

00:01:04.190 --> 00:01:07.250
It's one of the very few
ways in which enzymes

00:01:07.250 --> 00:01:10.670
can start with small molecules
and put them together

00:01:10.670 --> 00:01:14.360
into a macromolecule, or
start with a macromolecule

00:01:14.360 --> 00:01:20.060
and break it down into smaller
pieces during metabolism.

00:01:20.060 --> 00:01:22.130
This video summarizes
some of the most important

00:01:22.130 --> 00:01:25.880
carbonyl reactions you
will encounter in 5.07.

00:01:25.880 --> 00:01:27.680
In this video, we're
going to be talking

00:01:27.680 --> 00:01:29.580
about carbonyl chemistry.

00:01:29.580 --> 00:01:32.240
And as we will see,
carbonyl chemistry

00:01:32.240 --> 00:01:38.210
is fundamental for some of the
carbon-carbon bond formation

00:01:38.210 --> 00:01:41.210
and cleavage reactions.

00:01:41.210 --> 00:01:43.550
As you recall from
organic chemistry,

00:01:43.550 --> 00:01:49.490
carbonyl contains a C double
bond O. And all the properties

00:01:49.490 --> 00:01:56.000
of the carbonyl derive from its
ability to polarize this bond,

00:01:56.000 --> 00:01:59.300
so that we can draw a
resonance structure where

00:01:59.300 --> 00:02:03.200
the carbon has a positive
charge and the oxygen

00:02:03.200 --> 00:02:05.270
a negative charge.

00:02:05.270 --> 00:02:08.080
As you recall, there
are simple carbonyls,

00:02:08.080 --> 00:02:11.550
such as aldehydes and ketones.

00:02:15.890 --> 00:02:22.060
Also we have acyl derivatives,
compounds in which the carbonyl

00:02:22.060 --> 00:02:24.560
is attached to a heteroatom.

00:02:24.560 --> 00:02:28.010
x can be oxygen,
nitrogen, sulfur.

00:02:28.010 --> 00:02:34.760
So here, respective, we have
esters, amides, thioesters,

00:02:34.760 --> 00:02:39.440
and of course, we have an OH
group here, carboxylic acid.

00:02:39.440 --> 00:02:41.620
Here is a summary
of the reactions

00:02:41.620 --> 00:02:43.300
that we're going to
be talking about.

00:02:43.300 --> 00:02:45.110
First, we're going
to be discussing

00:02:45.110 --> 00:02:47.870
nucleophilic addition.

00:02:47.870 --> 00:02:51.920
Here, the good nucleophile
reacts with the carbonyl,

00:02:51.920 --> 00:02:58.170
adding to the carbon that
the carbonyl can generate.

00:02:58.170 --> 00:03:01.970
This tetrahedral compound.

00:03:01.970 --> 00:03:05.160
Next we're going to be
talking about enolization.

00:03:05.160 --> 00:03:07.430
This is the property
of carbonyls

00:03:07.430 --> 00:03:10.940
that contain an
alpha hydrogen, which

00:03:10.940 --> 00:03:12.800
can rearrange to form enol.

00:03:15.580 --> 00:03:19.680
Next we're going to
introduce the aldol reaction.

00:03:19.680 --> 00:03:23.490
This is the reaction in which
a carbon-carbon bond is formed

00:03:23.490 --> 00:03:28.020
and occurs between a carbonyl
that acts as electrophile

00:03:28.020 --> 00:03:32.750
and a enolizable carbonyl,
which acts as a nucleophile.

00:03:32.750 --> 00:03:37.530
In the aldol reaction, a bond
is formed between these two

00:03:37.530 --> 00:03:43.410
carbons, generating an aldol.

00:03:43.410 --> 00:03:47.970
We're also going to see that
the aldols can dehydrate.

00:03:47.970 --> 00:03:53.600
The aldols we saw above
can lose a water molecule

00:03:53.600 --> 00:03:59.160
to form an alpha,
beta-unsaturated carbonyl.

00:03:59.160 --> 00:04:01.320
Now about the acyl
derivatives, we're

00:04:01.320 --> 00:04:06.140
going to be talking about
acyl transfer reactions, where

00:04:06.140 --> 00:04:09.720
an acyl derivative
can convert into

00:04:09.720 --> 00:04:13.881
a different acyl derivative with
the appropriate nucleophile.

00:04:13.881 --> 00:04:19.529
A variation of this reaction
is Claisen reaction,

00:04:19.529 --> 00:04:24.020
where similarly to
the aldol reaction,

00:04:24.020 --> 00:04:29.030
we have an enolizable
carbonyl reacting

00:04:29.030 --> 00:04:33.770
with an acyl derivitive
and generating

00:04:33.770 --> 00:04:37.300
a beta-keto carbonyl.

00:04:37.300 --> 00:04:41.310
This reaction also forms
a carbon-carbon bond,

00:04:41.310 --> 00:04:42.550
which is right here.

00:04:47.400 --> 00:04:52.470
Let's talk in more detail about
the nucleophilic addition.

00:04:52.470 --> 00:04:56.360
The general reaction
scheme is as we saw before.

00:04:56.360 --> 00:05:05.660
Here is a carbonyl compound
reacting with a nucleophile

00:05:05.660 --> 00:05:09.210
and forming a tetrahedral
intermediate that contains

00:05:09.210 --> 00:05:12.970
an alkoxide or an alcohol.

00:05:12.970 --> 00:05:16.570
Now let's take a look at
two different reactions.

00:05:16.570 --> 00:05:22.620
One is the reaction of alcohols
with carbonyl compounds, where

00:05:22.620 --> 00:05:26.950
we form a compound
that looks like this.

00:05:26.950 --> 00:05:30.570
This is called a hemiacetal.

00:05:30.570 --> 00:05:32.850
Now this reaction is reversible.

00:05:32.850 --> 00:05:35.280
And, in fact, it
reaches equilibrium

00:05:35.280 --> 00:05:39.960
because delta G naught
is approximately zero.

00:05:39.960 --> 00:05:43.920
This reaction can be
acid or base catalyzed.

00:05:46.670 --> 00:05:49.960
Let's take a quick
look at that mechanism.

00:05:49.960 --> 00:05:56.190
If it's based
catalyzed, the base

00:05:56.190 --> 00:06:00.850
will first deprotonate
the alcohol,

00:06:00.850 --> 00:06:03.920
which will form the
alkoxide, which is then

00:06:03.920 --> 00:06:09.250
a very good nucleophile to
attack the carbonyl, which

00:06:09.250 --> 00:06:13.840
forms this alkoxide version
of the hemiacetal, which

00:06:13.840 --> 00:06:15.610
can be then protonated.

00:06:21.010 --> 00:06:24.100
In acid-catalyzed
mechanism, we have

00:06:24.100 --> 00:06:26.920
to activate the carbonyl
first, so the protonation

00:06:26.920 --> 00:06:29.260
of the carbonyl
is the first step.

00:06:34.130 --> 00:06:36.160
All right, so this
activated carbonyl

00:06:36.160 --> 00:06:39.370
can then be attacked
by our alcohol.

00:06:47.580 --> 00:06:51.060
Which, this product is just
one proton transfer away

00:06:51.060 --> 00:06:54.300
from our hemiacetal.

00:06:54.300 --> 00:06:57.810
All right, the second reaction
I want to include here

00:06:57.810 --> 00:07:00.120
is the formation of
Schiff bases which

00:07:00.120 --> 00:07:03.320
is the reaction of a
carbonyl with an amine.

00:07:05.940 --> 00:07:08.625
Similarly to the
hemiacetal formation,

00:07:08.625 --> 00:07:14.040
this reaction generates first
a tetrahedral intermediate,

00:07:14.040 --> 00:07:17.160
which is, however,
unstable, and loses water

00:07:17.160 --> 00:07:19.410
to generate the imine,
with a Schiff base.

00:07:23.170 --> 00:07:26.340
Let's take a look
at the mechanism.

00:07:26.340 --> 00:07:31.290
As you notice, the reaction--
because the amine group is

00:07:31.290 --> 00:07:33.510
a good nucleophile, the
reaction can occur even

00:07:33.510 --> 00:07:35.380
in neutral conditions.

00:07:35.380 --> 00:07:38.405
We don't need, necessarily,
acid or base catalysis.

00:07:43.320 --> 00:07:49.600
The first step, the imine
attacks the carbonyl,

00:07:49.600 --> 00:07:51.670
forming this compound
with split charges.

00:07:55.840 --> 00:08:01.950
Now proton transfer happens
to generate our intermediate.

00:08:01.950 --> 00:08:05.345
Then water is eliminated.

00:08:12.140 --> 00:08:13.690
And this is the imine.

00:08:13.690 --> 00:08:16.700
You'll notice the
imine nitrogen can also

00:08:16.700 --> 00:08:24.680
be protonated, to
generate this iminium ion,

00:08:24.680 --> 00:08:29.090
which, as we will see
in other situations,

00:08:29.090 --> 00:08:35.150
it's an activated version
of the carbonyl group.

00:08:35.150 --> 00:08:36.980
From these two
examples, we can get

00:08:36.980 --> 00:08:40.219
some idea of how the
nucleophilic addition occurs.

00:08:40.219 --> 00:08:42.260
So let's take a look at
what kind of nucleophiles

00:08:42.260 --> 00:08:44.030
we can add to the
carbonyl group.

00:08:44.030 --> 00:08:47.450
We have some good nucleophiles.

00:08:47.450 --> 00:08:50.210
And here we have things
with negative charges,

00:08:50.210 --> 00:08:54.080
such as alkoxide, or hydroxide.

00:08:54.080 --> 00:08:57.430
I have the thiolates.

00:08:57.430 --> 00:08:59.870
And other things such as amines.

00:08:59.870 --> 00:09:03.690
And we also have
some OK nucleophiles.

00:09:03.690 --> 00:09:09.530
And here we have alcohols,
even water, and thiols.

00:09:09.530 --> 00:09:11.860
As you saw in these
couple of mechanisms,

00:09:11.860 --> 00:09:14.900
the OK nucleophiles
don't react very well,

00:09:14.900 --> 00:09:18.920
unless they are deprotonated
to form good nucleophiles,

00:09:18.920 --> 00:09:20.180
such as the alcohols.

00:09:20.180 --> 00:09:24.020
Or the carbonyl gets activated,
either by protonation

00:09:24.020 --> 00:09:26.210
in a strong acid,
as we saw here,

00:09:26.210 --> 00:09:29.960
or it becomes an activated
carbonyl, for example,

00:09:29.960 --> 00:09:32.580
in an iminium ion.

00:09:32.580 --> 00:09:37.010
Another important nuclear
force that we're going to see

00:09:37.010 --> 00:09:41.792
is the, what we're going
to call, a C minus.

00:09:41.792 --> 00:09:45.110
Basically a
carbanion In our case

00:09:45.110 --> 00:09:49.820
it's going to be enolates, which
can also add to the carbonyls.

00:09:49.820 --> 00:09:52.560
And these will form the
basis for the aldol reaction.

00:09:56.619 --> 00:09:58.870
The second reaction we're
going to be talking about

00:09:58.870 --> 00:10:01.600
is enolization.

00:10:01.600 --> 00:10:08.320
Here, a carbonyl that
contains an alpha hydrogen

00:10:08.320 --> 00:10:11.530
can rearrange to form an enol.

00:10:11.530 --> 00:10:14.290
We're going to call this
the keto form and this

00:10:14.290 --> 00:10:16.720
the enol form.

00:10:16.720 --> 00:10:19.770
An equilibrium between
a keto and an enol form

00:10:19.770 --> 00:10:22.499
is called tautomerization.

00:10:22.499 --> 00:10:24.040
And this is a very
important reaction

00:10:24.040 --> 00:10:26.260
in many biochemical systems.

00:10:26.260 --> 00:10:30.370
Turns out, the delta G, for
the reaction as written,

00:10:30.370 --> 00:10:35.140
it's very high, 30 to
50 kilojoules per mole.

00:10:35.140 --> 00:10:40.120
That means that equilibrium
strongly favors the keto form.

00:10:40.120 --> 00:10:43.706
However, in certain
cases, the enol

00:10:43.706 --> 00:10:47.260
can form and get stabilized.

00:10:47.260 --> 00:10:51.260
The mechanism of enolization,
it's very straightforward.

00:10:51.260 --> 00:10:53.710
All we need is a
decent base that

00:10:53.710 --> 00:10:56.170
can remove the alpha proton.

00:10:59.510 --> 00:11:03.970
And it will form this enolate.

00:11:03.970 --> 00:11:06.710
Now, enolate is able
to form because it

00:11:06.710 --> 00:11:09.260
has resonance stabilization.

00:11:09.260 --> 00:11:16.170
We can draw another
resonance structure, as such,

00:11:16.170 --> 00:11:19.480
where we see the negative
charge is on the carbon.

00:11:19.480 --> 00:11:21.500
So it is in fact a carbanion.

00:11:21.500 --> 00:11:25.604
We're going to call it
a disguised carbanion.

00:11:25.604 --> 00:11:28.070
As the carbon is not
very electronegative,

00:11:28.070 --> 00:11:31.430
having such a high electron
density on the carbon

00:11:31.430 --> 00:11:35.680
would make it a very
good nucleophile.

00:11:35.680 --> 00:11:38.720
And in fact, this enolate
is the nucleophile

00:11:38.720 --> 00:11:42.050
that executes reactions
such as the Aldol reaction

00:11:42.050 --> 00:11:44.990
and the Claisen reaction.

00:11:44.990 --> 00:11:47.870
Something to keep in
mind, well, how acidic

00:11:47.870 --> 00:11:50.720
is this alpha hydrogen?

00:11:50.720 --> 00:11:56.570
We can compare it with
a hydrogen in an alkyne.

00:11:56.570 --> 00:12:00.530
The pKa of such a
hydrogen is close to 50.

00:12:00.530 --> 00:12:06.830
It's extremely hard
to remove a proton.

00:12:06.830 --> 00:12:09.760
Now if we look at an alpha
hydrogen next to a carbonyl,

00:12:09.760 --> 00:12:12.530
the pKa is 18 to 20.

00:12:12.530 --> 00:12:17.510
So it's 30 orders of
magnitude more acidic,

00:12:17.510 --> 00:12:20.630
and this is because, as we saw,
when we removed this hydrogen,

00:12:20.630 --> 00:12:25.880
we formed the enolate anion,
which is resonance stabilized.

00:12:25.880 --> 00:12:32.710
The more extreme case of this,
if we have two carbonyls, alpha

00:12:32.710 --> 00:12:37.430
to the same proton, the
pKa drops even further,

00:12:37.430 --> 00:12:41.300
around 9 to 11.

00:12:41.300 --> 00:12:45.700
This is because we can draw
even more resonance structures

00:12:45.700 --> 00:12:49.710
to the enolate that's formed.

00:12:49.710 --> 00:12:50.270
This is one.

00:12:54.690 --> 00:12:55.460
This is another.

00:13:00.445 --> 00:13:01.800
And another.

00:13:01.800 --> 00:13:05.140
As we saw before,
the charge here

00:13:05.140 --> 00:13:09.560
is delocalized between the
oxygens and the alpha carbon.

00:13:09.560 --> 00:13:16.300
So it is this beta keto carbonyl
in its enolate form will

00:13:16.300 --> 00:13:21.548
behave as a carbanion and it
can act as a good nucleophile.

00:13:24.830 --> 00:13:28.410
The Aldol reaction.

00:13:28.410 --> 00:13:30.570
This is a very important
reaction in biochemistry

00:13:30.570 --> 00:13:36.120
because it allows formation
of carbon-carbon bonds.

00:13:36.120 --> 00:13:38.190
Or, if the reaction
runs in reverse,

00:13:38.190 --> 00:13:41.430
cleavage of the
carbon-carbon bonds.

00:13:41.430 --> 00:13:44.220
The Aldol reaction
is the reaction

00:13:44.220 --> 00:13:50.210
between an enolizable
carbonyl, as we show here,

00:13:50.210 --> 00:13:55.590
a carbonyl that has an alpha
hydrogen, and another carbonyl.

00:13:55.590 --> 00:13:58.500
And what happens is, a
new carbon-carbon bond

00:13:58.500 --> 00:14:06.260
forms between alpha carbon
and the carbonyl carbon.

00:14:11.270 --> 00:14:13.900
The product of the
Aldol reaction,

00:14:13.900 --> 00:14:17.080
it's called Aldol as a
contraction between aldehyde

00:14:17.080 --> 00:14:20.640
and alcohol, as in some
cases this carbonyl

00:14:20.640 --> 00:14:23.170
will be an aldehyde and
this would be Aldol.

00:14:23.170 --> 00:14:29.400
It's essentially a beta
hydroxy of carbonyl.

00:14:29.400 --> 00:14:34.380
Now, this reaction has a
delta G naught close to 0.

00:14:34.380 --> 00:14:39.610
That is, it reaches equilibrium.

00:14:39.610 --> 00:14:45.490
And it can be catalyzed
by acid or by base.

00:14:45.490 --> 00:14:48.060
Let's take a quick
look at the mechanism.

00:14:48.060 --> 00:14:50.670
Given the previous
mechanistic insights--

00:14:50.670 --> 00:14:54.410
we looked at the nucleophilic
addition, and enol formation,

00:14:54.410 --> 00:14:56.580
then the mechanism
of the Aldol reaction

00:14:56.580 --> 00:14:59.410
should be fairly
straightforward.

00:14:59.410 --> 00:15:02.340
If it's base-catalyzed,
the base is

00:15:02.340 --> 00:15:13.390
going to help us form
the enolate, as such.

00:15:13.390 --> 00:15:17.350
And as we discussed
previously, the enolate

00:15:17.350 --> 00:15:21.910
is a good nucleophile, and can
react via nucleophilic addition

00:15:21.910 --> 00:15:24.540
with the other carbonyl.

00:15:29.720 --> 00:15:35.050
And one proton transfer to
generate the Aldol product.

00:15:39.030 --> 00:15:42.690
The reaction can also
be acid-catalyzed.

00:15:42.690 --> 00:15:46.920
Again, formation of the
enol in acid catalysis

00:15:46.920 --> 00:15:48.750
involved first protonation
of the carbonyl.

00:15:56.590 --> 00:15:57.990
Now this activated
carbonyl, it's

00:15:57.990 --> 00:16:03.370
a much better electron sink, and
stabilizes the enol formation.

00:16:09.140 --> 00:16:10.810
Now, in the second
step the enol can

00:16:10.810 --> 00:16:22.770
react with the other
carbonyl, to generate

00:16:22.770 --> 00:16:26.520
a protonated version
of the Aldol, which

00:16:26.520 --> 00:16:31.280
is one proton transfer away
from the Aldol product.

00:16:33.830 --> 00:16:35.940
In biochemical
systems, the enzyme

00:16:35.940 --> 00:16:40.340
that catalyzed the Aldol
reaction is called aldolase.

00:16:40.340 --> 00:16:43.260
And there are actually
two kinds of aldolases.

00:16:43.260 --> 00:16:46.190
Class one, and class two.

00:16:46.190 --> 00:16:48.270
The distinctive feature
of these enzymes

00:16:48.270 --> 00:16:50.520
is the way they
catalyze the reaction.

00:16:50.520 --> 00:16:54.660
Class one uses an
active site lysine

00:16:54.660 --> 00:16:57.740
to form a Schiff base
with the carbonyl, which

00:16:57.740 --> 00:17:01.590
activates the carbonyl, and
allows for the enol formation.

00:17:01.590 --> 00:17:05.220
Class two uses a metal
ion, such as zinc,

00:17:05.220 --> 00:17:08.670
to accomplish the same thing.

00:17:08.670 --> 00:17:13.340
So here is how the mechanism
for the class 1 aldolase

00:17:13.340 --> 00:17:13.839
would look.

00:17:17.310 --> 00:17:21.560
So here is our
enolizable carbonyl,

00:17:21.560 --> 00:17:26.569
and here is our
active site lysine.

00:17:26.569 --> 00:17:29.090
As we saw before,
an amine reacting

00:17:29.090 --> 00:17:33.020
was a carbonyl will
give us a Schiff base.

00:17:33.020 --> 00:17:36.720
The reaction goes via a
tetrahedral intermediate,

00:17:36.720 --> 00:17:39.960
which we're not
going to draw here,

00:17:39.960 --> 00:17:42.903
but what we form is
this iminium ion.

00:17:46.290 --> 00:17:49.110
Now the carbonyl
is activated enough

00:17:49.110 --> 00:17:53.590
that an active site base
can remove an alpha hydrogen

00:17:53.590 --> 00:17:54.810
to form the enol.

00:17:59.970 --> 00:18:04.670
Which is now well-positioned
to attack the other carbonyl.

00:18:12.720 --> 00:18:17.370
This generates the Aldol
product, in its imine form,

00:18:17.370 --> 00:18:19.210
still attached to the enzyme.

00:18:19.210 --> 00:18:23.720
And now the hydrolysis of imine
is going to release the Aldol.

00:18:27.020 --> 00:18:34.592
Now, class two enzymes
use a zinc ion.

00:18:34.592 --> 00:18:39.300
As the ion approaches
the carbonyl,

00:18:39.300 --> 00:18:44.510
it's going to draw some of the
electrons from the carbonyl,

00:18:44.510 --> 00:18:48.365
and make the proton in the alpha
position a lot more acidic.

00:18:53.200 --> 00:18:55.120
So you can imagine,
some of these electrons

00:18:55.120 --> 00:18:56.200
get de-localized.

00:18:59.900 --> 00:19:05.860
So that a base can remove the
proton and form the enolate.

00:19:09.980 --> 00:19:12.506
Which, in the second
step, it reacts

00:19:12.506 --> 00:19:19.500
with the carbonyl, which
will generate the Aldol

00:19:19.500 --> 00:19:24.870
product in the active
site of the enzyme,

00:19:24.870 --> 00:19:29.340
still bound to the zinc, and
now which can dissociate,

00:19:29.340 --> 00:19:31.770
and generate the final--

00:19:31.770 --> 00:19:34.250
and release the product.

00:19:34.250 --> 00:19:36.690
Now, a very important
consideration

00:19:36.690 --> 00:19:38.410
for the Aldol reaction
is that it can

00:19:38.410 --> 00:19:41.790
occur in the reverse fashion.

00:19:41.790 --> 00:19:46.920
For example, to cleave
a carbon-carbon bond.

00:19:46.920 --> 00:19:50.370
So the bond that will be
cleaved, as we see here,

00:19:50.370 --> 00:19:52.170
is the bond that
got formed, which

00:19:52.170 --> 00:19:58.452
is the bond between the
alpha and beta carbons.

00:19:58.452 --> 00:20:01.440
The aldolase is one of the
key enzyme in glycolysis,

00:20:01.440 --> 00:20:06.090
that allows us to break a
six carbon sugar into two

00:20:06.090 --> 00:20:09.360
three-carbon sugars by
cleaving a carbon-carbon bond

00:20:09.360 --> 00:20:11.910
via the Aldol reaction.

00:20:11.910 --> 00:20:14.630
As the mechanism
catalyzed by the aldolase,

00:20:14.630 --> 00:20:18.270
we can see that the
reverse pathway is pretty

00:20:18.270 --> 00:20:21.370
straightforward, where the
Aldol binds to the enzyme,

00:20:21.370 --> 00:20:24.690
say in class one,
forms an active site,

00:20:24.690 --> 00:20:27.660
covalent attraction, a
Schiff base with the lysine,

00:20:27.660 --> 00:20:29.850
from which the chemistry
occurs to break

00:20:29.850 --> 00:20:33.590
the carbon-carbon bond, and
leads to the release of one

00:20:33.590 --> 00:20:36.180
carbonyl molecule,
and then the other one

00:20:36.180 --> 00:20:39.500
will be still bound to the
enzyme as a Schiff base

00:20:39.500 --> 00:20:41.340
and hydrolyzed.

00:20:41.340 --> 00:20:44.370
For the class two, the Aldol
will interact with the enzyme

00:20:44.370 --> 00:20:48.240
by forming an interaction
with the zinc,

00:20:48.240 --> 00:20:51.300
and this activated carbonyl
allows the chemistry

00:20:51.300 --> 00:20:56.550
to occur exactly in the
reverse manner, as shown here.

00:21:03.510 --> 00:21:07.790
One other reaction involving
Aldols is Aldol dehydration.

00:21:11.740 --> 00:21:15.730
Here's an Aldol, beta
hydroxy carbonyl.

00:21:15.730 --> 00:21:21.970
Now, if an Aldol has an
additional alpha hydrogen,

00:21:21.970 --> 00:21:30.570
it can lose a water molecule to
form an alpha beta unsaturated

00:21:30.570 --> 00:21:32.918
carbonyl.

00:21:32.918 --> 00:21:35.840
Now this reaction is
favorable thermodynamically.

00:21:35.840 --> 00:21:39.280
The delta G naught
is approximately 0.

00:21:39.280 --> 00:21:40.990
And this is a
reaction we're going

00:21:40.990 --> 00:21:45.190
to see in a lot of
biochemical pathways,

00:21:45.190 --> 00:21:49.360
for example, in the
biosynthesis of fatty acids,

00:21:49.360 --> 00:21:53.680
going left to right, or in
the catabolism of fatty acids,

00:21:53.680 --> 00:21:56.530
going right to left.

00:21:56.530 --> 00:21:58.540
Here's a quick insight
on the mechanism.

00:21:58.540 --> 00:22:00.930
Once again, it can be
base- or acid-catalyzed.

00:22:03.920 --> 00:22:08.500
This reaction works because
the alpha hydrogen here

00:22:08.500 --> 00:22:11.220
is next to a carbonyl, and
therefore can form an enol.

00:22:13.930 --> 00:22:20.770
So if a base can remove this
hydrogen to form the enolate,

00:22:20.770 --> 00:22:28.270
then we can envision how this
electronic movement will allow

00:22:28.270 --> 00:22:33.600
for a water molecule
to be eliminated,

00:22:33.600 --> 00:22:38.136
forming our alpha beta
unsaturated carbonyl.

00:22:38.136 --> 00:22:44.610
The acid-catalyzed mechanism
goes along the same lines.

00:22:44.610 --> 00:22:46.160
As you remember,
in order to form

00:22:46.160 --> 00:22:50.524
the enol in an
acid-catalyzed context,

00:22:50.524 --> 00:22:52.190
first we have to
protonate the carbonyl.

00:22:57.145 --> 00:22:58.530
All right.

00:22:58.530 --> 00:23:05.780
Now a base can remove
our alpha hydrogen,

00:23:05.780 --> 00:23:11.500
forming the enol, which
can kick off a water

00:23:11.500 --> 00:23:16.930
molecule, generating
these pieces, which

00:23:16.930 --> 00:23:22.240
is just one proton transfer
away from our final product.

00:23:27.990 --> 00:23:32.085
So let's talk now about acyl
derivatives, and acyl transfer.

00:23:35.340 --> 00:23:37.475
As we mentioned,
acyl derivatives

00:23:37.475 --> 00:23:41.070
have a carbonyl attached
to a header atom.

00:23:43.580 --> 00:23:49.900
And this header atom can be
oxygen, nitrogen, sulfur.

00:23:49.900 --> 00:23:52.030
As all these header
atoms contain

00:23:52.030 --> 00:23:56.290
a lone pair of electrons,
one of the key properties

00:23:56.290 --> 00:24:03.510
of the acyl derivatives would
be resonance between the header

00:24:03.510 --> 00:24:10.860
atom and the oxygen.

00:24:10.860 --> 00:24:13.980
Now the properties of
the acyl derivatives

00:24:13.980 --> 00:24:19.290
will be dictated by how easy
or how difficult it is to adopt

00:24:19.290 --> 00:24:21.172
this minor resonance structure.

00:24:21.172 --> 00:24:23.130
In other words, how likely
is it for the header

00:24:23.130 --> 00:24:30.780
atom to participate in
these electron conjugations.

00:24:30.780 --> 00:24:34.530
Let's take a look at a
couple of acyl derivatives.

00:24:34.530 --> 00:24:37.140
This is a carboxylate.

00:24:37.140 --> 00:24:41.575
If the header atom a
nitrogen, we have amide.

00:24:44.450 --> 00:24:49.160
If the header atom
is oxygen, we also

00:24:49.160 --> 00:24:56.120
have esters, or
carboxylic acids.

00:24:58.640 --> 00:25:04.220
And when the header atom is
sulfur, we have thioesters.

00:25:04.220 --> 00:25:08.300
The order in which I wrote them
here is not actually random.

00:25:08.300 --> 00:25:10.100
It turns out for
the carboxylate,

00:25:10.100 --> 00:25:13.910
because it has already a
negative charge, the ability

00:25:13.910 --> 00:25:18.060
to adopt this resonance
is greatly increased.

00:25:18.060 --> 00:25:22.190
So it's very well
resonance-stabilized.

00:25:22.190 --> 00:25:25.550
The ability to form these
resonance structures,

00:25:25.550 --> 00:25:30.590
it's also great for amides,
and this dictates the chemistry

00:25:30.590 --> 00:25:33.380
and the biochemistry of
the amide bond, which

00:25:33.380 --> 00:25:39.270
is explored in greater detail
when we talk about protein.

00:25:39.270 --> 00:25:46.990
Esters can also adopt
these resonance structures.

00:25:46.990 --> 00:25:51.840
However, thioesters, because the
sulfur is a third-row element,

00:25:51.840 --> 00:25:54.390
so the p-orbitals of
sulfur are much bigger,

00:25:54.390 --> 00:25:56.430
they don't overlap very
well with the p-orbitals

00:25:56.430 --> 00:25:59.605
of the carbon, the
ability to adopt

00:25:59.605 --> 00:26:03.200
these resonance structures
is greatly diminished.

00:26:03.200 --> 00:26:07.410
Therefore, thioesters
behave a lot more

00:26:07.410 --> 00:26:10.250
like ketones, where the
electrons of the carbonyl bond

00:26:10.250 --> 00:26:14.010
are localized between the
carbon and oxygen, and not

00:26:14.010 --> 00:26:17.910
so much between the
carbon and sulfur.

00:26:17.910 --> 00:26:22.125
So therefore, thioesters
are the least resonant.

00:26:25.100 --> 00:26:27.720
And this is the trend.

00:26:27.720 --> 00:26:32.880
And this trend inversely
correlates with the reactivity.

00:26:32.880 --> 00:26:36.805
Carboxylates are least
reactive, whereas thioesters

00:26:36.805 --> 00:26:38.557
are the most reactive.

00:26:42.220 --> 00:26:46.960
Now, when we talk
about acyl transfer,

00:26:46.960 --> 00:26:50.200
we talk about the reaction
between an acyl derivative

00:26:50.200 --> 00:26:57.265
with another nucleophile,
which will replace the x header

00:26:57.265 --> 00:26:59.986
atom with the y header atom.

00:26:59.986 --> 00:27:07.800
So this reaction always occurs
via a tetrahedral intermediate.

00:27:07.800 --> 00:27:13.740
When both substituents are
attached to the carbon.

00:27:13.740 --> 00:27:16.830
Now from here, this
tetrahedral intermediate

00:27:16.830 --> 00:27:20.250
can fall apart by
kicking off the YR

00:27:20.250 --> 00:27:23.010
to regenerate the
starting material,

00:27:23.010 --> 00:27:27.260
or it can kick off the
XR group, to generate

00:27:27.260 --> 00:27:29.472
a new acyl derivative.

00:27:33.410 --> 00:27:37.920
Let's now talk about
the Claisen reaction.

00:27:37.920 --> 00:27:40.490
This is a very important
reaction in biochemistry,

00:27:40.490 --> 00:27:44.600
related to the Aldol reaction,
in which we form or cleave

00:27:44.600 --> 00:27:46.392
carbon-carbon bonds.

00:27:46.392 --> 00:27:52.670
The Claisen reaction happens
between an enolizable carbonyl

00:27:52.670 --> 00:27:55.770
and an acyl derivative.

00:27:55.770 --> 00:28:00.170
Let's pick in this
case an ester.

00:28:00.170 --> 00:28:03.110
And during this reaction,
a carbon-carbon bond

00:28:03.110 --> 00:28:08.173
is formed between
the alpha carbon

00:28:08.173 --> 00:28:11.760
of the enolizable carbonyl,
and the keto carbon

00:28:11.760 --> 00:28:13.910
of the acyl derivative.

00:28:13.910 --> 00:28:16.060
The product of the
Claisen reaction

00:28:16.060 --> 00:28:22.680
is a beta keto carbonyl.

00:28:22.680 --> 00:28:26.240
Let's look at the mechanism.

00:28:26.240 --> 00:28:28.930
As with all carbonyl
reactions, when

00:28:28.930 --> 00:28:33.757
we form a carbon-carbon bond,
we need to form an enolate.

00:28:33.757 --> 00:28:34.840
So this is the first step.

00:28:37.720 --> 00:28:41.460
A base will form,
remove the alpha proton,

00:28:41.460 --> 00:28:45.860
and form the
enolate, which is now

00:28:45.860 --> 00:28:51.140
poised to add to the acyl
derivative in an acyl transfer

00:28:51.140 --> 00:29:01.500
reaction, forming first a
tetrahedral intermediate, which

00:29:01.500 --> 00:29:06.840
can spontaneously fall apart
by eliminating the header atom

00:29:06.840 --> 00:29:11.950
group, to form our beta
keto carbonyl product.

00:29:14.720 --> 00:29:18.990
Now, in biochemistry a preferred
substrate for Claisen reactions

00:29:18.990 --> 00:29:21.611
is a thioester.

00:29:21.611 --> 00:29:22.985
One of the most
common thioesters

00:29:22.985 --> 00:29:27.600
we're going to encounter in
this course is acetyl-CoA.

00:29:27.600 --> 00:29:31.500
CoA, or coenzyme-A,
it's a thiol that

00:29:31.500 --> 00:29:35.790
can form thioesters
with a lot of acids,

00:29:35.790 --> 00:29:38.130
for example, acetic acid here.

00:29:38.130 --> 00:29:42.060
Acetyl-CoA can undergo a
Claisen reaction with itself,

00:29:42.060 --> 00:29:46.260
and therefore acts both
as an enolizable carbonyl

00:29:46.260 --> 00:29:48.720
and as an acyl derivative.

00:29:48.720 --> 00:29:52.140
From when we were talking
about thioesters, because

00:29:52.140 --> 00:29:55.590
of their limited conjugation
with the carbonyl,

00:29:55.590 --> 00:29:59.100
they are very reactive,
and they allow

00:29:59.100 --> 00:30:01.964
the formation of the enolate.

00:30:05.600 --> 00:30:08.310
Here is the acetyl-CoA
enolate, which

00:30:08.310 --> 00:30:14.060
can react with another
acetyl-CoA molecule.

00:30:14.060 --> 00:30:18.370
It will generate a
tetrahedral intermediate.

00:30:18.370 --> 00:30:19.900
Let's draw this molecule first.

00:30:23.180 --> 00:30:26.500
Which can lose one
of the CoA molecules,

00:30:26.500 --> 00:30:33.830
to generate this beta keto
thioester, acetoacetyl-CoA.

00:30:37.970 --> 00:30:40.220
As we will see
later in the course,

00:30:40.220 --> 00:30:46.700
this is a precursor to
formation of ketone bodies, one

00:30:46.700 --> 00:30:52.630
of the ways in which acetyl-CoA
can be used to store energy.

00:30:52.630 --> 00:30:58.465
Now, what is coenzyme-A,
often abbreviated CoA?

00:30:58.465 --> 00:31:03.040
We mentioned it's a thiol.

00:31:03.040 --> 00:31:07.950
That means it has an SH
group, which it turns out,

00:31:07.950 --> 00:31:10.280
is on a very long linker.

00:31:18.070 --> 00:31:21.460
There you go, this
is coenzyme-A.

00:31:21.460 --> 00:31:25.090
You might recognize this
part of the molecule

00:31:25.090 --> 00:31:29.050
as being adenine bound to a
ribose bound to two phosphates.

00:31:29.050 --> 00:31:32.709
It's essentially ADP.

00:31:32.709 --> 00:31:34.750
But notice there's another
phosphate in the three

00:31:34.750 --> 00:31:41.020
prime position, so it's an ADP
with a three prime phosphate.

00:31:41.020 --> 00:31:44.800
This portion of the
molecule, If we squint,

00:31:44.800 --> 00:31:50.020
resembles the amino
acid cysteine,

00:31:50.020 --> 00:31:53.880
but without the carboxyl group.

00:31:53.880 --> 00:31:56.670
And this middle portion
of the molecule,

00:31:56.670 --> 00:32:01.210
it's something that looks
very difficult to synthesize.

00:32:01.210 --> 00:32:05.080
Notice this carbon that has
two methyl groups attached,

00:32:05.080 --> 00:32:07.290
and two other carbons
attached to it.

00:32:07.290 --> 00:32:08.700
So it's like a tetravalent--

00:32:11.990 --> 00:32:15.760
a carbon attached to it, four
other carbons, that's it.

00:32:15.760 --> 00:32:19.070
Fairly rare sight
in biochemistry.

00:32:19.070 --> 00:32:22.500
This portion of the molecule
is called pantothenic acid.

00:32:22.500 --> 00:32:26.560
Pantothenic acid is
an essential nutrient,

00:32:26.560 --> 00:32:27.980
also known as vitamin B5.

00:32:32.490 --> 00:32:36.640
In this video we talked
about carbonyl chemistry.

00:32:36.640 --> 00:32:41.190
Carbonyl is the C double bond
O, and a lot of its properties

00:32:41.190 --> 00:32:46.500
are due to the polarizability of
this bond, where the carbon has

00:32:46.500 --> 00:32:48.300
a partial positive
charge, and oxygen

00:32:48.300 --> 00:32:50.206
a partial negative charge.

00:32:50.206 --> 00:32:52.740
We talked about reactions
to simple carbonyls,

00:32:52.740 --> 00:32:56.660
such as nucleophilic addition,
enolization, Aldol reaction,

00:32:56.660 --> 00:32:59.470
and the Aldol dehydration.

00:32:59.470 --> 00:33:01.300
And acyl derivatives,
where the carbonyl

00:33:01.300 --> 00:33:06.190
is next to a header atom, such
as oxygen, nitrogen, or sulfur.

00:33:06.190 --> 00:33:09.020
And we mentioned the
acyl transfer reaction,

00:33:09.020 --> 00:33:12.210
and the Claisen reaction.

00:33:12.210 --> 00:33:15.150
We saw in this video the
nucleophilic addition,

00:33:15.150 --> 00:33:17.880
where a nucleophile attacks
the carbon of carbonyl

00:33:17.880 --> 00:33:22.590
to add and form a
tetrahedral product.

00:33:22.590 --> 00:33:24.530
For example, alcohols
can add to carbonyls

00:33:24.530 --> 00:33:26.880
to form a hemiacetals,
and amines

00:33:26.880 --> 00:33:31.487
can add to carbonyls to form
imines, or Schiff bases.

00:33:31.487 --> 00:33:33.070
And we reviewed that
good nucleophiles

00:33:33.070 --> 00:33:38.610
are the ones like alkoxides,
thiolates, amines, or C

00:33:38.610 --> 00:33:39.800
minus enolates.

00:33:39.800 --> 00:33:42.960
Whereas OK nucleophiles
like alcohols and thiols,

00:33:42.960 --> 00:33:45.150
they need to be activated
first to undergo

00:33:45.150 --> 00:33:48.440
nucleophilic addition.

00:33:48.440 --> 00:33:51.350
We also talked about
enolization, the ability

00:33:51.350 --> 00:33:54.740
of a carbonyl with
an alpha hydrogen

00:33:54.740 --> 00:34:00.620
to rearrange into a hydroxyl
bound to a double bond, which

00:34:00.620 --> 00:34:01.660
we call an enol.

00:34:01.660 --> 00:34:04.250
Now this equilibrium,
called tautomerization,

00:34:04.250 --> 00:34:06.800
favors strongly the keto form.

00:34:06.800 --> 00:34:10.940
However, it does form
to a sufficient extent

00:34:10.940 --> 00:34:13.050
to allow chemistry to happen.

00:34:13.050 --> 00:34:15.320
For example, when we
remove the alpha hydrogen,

00:34:15.320 --> 00:34:18.230
we form an anion
called enolate, which

00:34:18.230 --> 00:34:22.489
is a disguised carbanion which
is a very good nucleophile.

00:34:22.489 --> 00:34:25.310
Next, we discussed the Aldol
reaction, a very important

00:34:25.310 --> 00:34:28.659
carbon-carbon bond formation
or cleavage reaction

00:34:28.659 --> 00:34:30.889
in biochemistry.

00:34:30.889 --> 00:34:33.500
This reaction happens between
an enolizable carbonyl

00:34:33.500 --> 00:34:37.795
and the regular carbonyl,
and a new carbon-carbon bond

00:34:37.795 --> 00:34:42.639
is formed between the alpha
carbon and the keto carbon,

00:34:42.639 --> 00:34:44.090
as shown here.

00:34:44.090 --> 00:34:46.600
The mechanism can be
both base-catalyzed and

00:34:46.600 --> 00:34:47.840
acid-catalyzed.

00:34:47.840 --> 00:34:51.570
And the enzymes that catalyze
this, called aldolases,

00:34:51.570 --> 00:34:54.110
use either a lysine
in the active site

00:34:54.110 --> 00:34:59.690
to form first a
Schiff base, or they

00:34:59.690 --> 00:35:02.815
use a zinc in the active
site to polarize the carbonyl

00:35:02.815 --> 00:35:04.190
and allow for the
enol formation.

00:35:07.300 --> 00:35:09.550
We also saw that
Aldol products can

00:35:09.550 --> 00:35:12.820
dehydrate to form alpha
beta unsaturated carbonyls.

00:35:12.820 --> 00:35:16.830
The mechanism could be both
acid- and base-catalyzed,

00:35:16.830 --> 00:35:21.352
and involves in both cases
formation of an enol.

00:35:21.352 --> 00:35:25.990
Next, we also talked about acyl
derivatives, and acyl transfer.

00:35:25.990 --> 00:35:32.750
As we show here, the resonance
in the acyl derivative

00:35:32.750 --> 00:35:39.159
dictates there how
well they react.

00:35:39.159 --> 00:35:41.450
Carboxylate and amine are
the most resonant stabilized,

00:35:41.450 --> 00:35:43.390
and therefore are
the least reactive,

00:35:43.390 --> 00:35:45.995
whereas esters,
especially thioesters,

00:35:45.995 --> 00:35:48.190
are the least resonance
stabilized, and therefore

00:35:48.190 --> 00:35:50.290
most reactive.

00:35:50.290 --> 00:35:54.040
Finally, we discussed the
Claisen reaction, a reaction

00:35:54.040 --> 00:35:56.650
similar to the Aldol, between
an enolizable carbonyl

00:35:56.650 --> 00:36:00.260
and an acyl derivative, which
generates a beta keto carbonyl.

00:36:00.260 --> 00:36:04.920
We introduced the acetyl-CoA,
a very important thioester,

00:36:04.920 --> 00:36:06.880
that can undergo Claisen
reaction with itself

00:36:06.880 --> 00:36:08.770
to form acetoacetyl-CoA.

00:36:08.770 --> 00:36:10.390
And we also introduced
the structure

00:36:10.390 --> 00:36:14.840
of CoA, which is
built around vitamin

00:36:14.840 --> 00:36:17.484
B5, an essential nutrient.