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BOGDEN FEDELES: Hello
and welcome to 5.07

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00:00:22,920 --> 00:00:25,020
Biochemistry online.

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00:00:25,020 --> 00:00:26,170
I'm Dr. Bogden Fedeles.

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00:00:29,030 --> 00:00:32,509
Despite the staggering
biodiversity we see in nature,

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00:00:32,509 --> 00:00:36,590
the types of chemical reactions
employed are only but a couple

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00:00:36,590 --> 00:00:37,880
of handfuls.

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00:00:37,880 --> 00:00:41,210
And these are used over and
over again very efficiently

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00:00:41,210 --> 00:00:43,970
and with conserved mechanisms.

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00:00:43,970 --> 00:00:45,860
As you might recall
from Organic Chemistry,

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00:00:45,860 --> 00:00:48,530
one of the most
versatile chemical groups

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00:00:48,530 --> 00:00:53,270
is the carbonyl, C double
bond O. Not surprisingly,

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00:00:53,270 --> 00:00:55,940
carbonyl chemistry
is well-represented

20
00:00:55,940 --> 00:00:58,490
in biochemistry.

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00:00:58,490 --> 00:01:02,540
In fact, the carbonyl
chemistry allows formation

22
00:01:02,540 --> 00:01:04,190
of carbon-carbon bonds.

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00:01:04,190 --> 00:01:07,250
It's one of the very few
ways in which enzymes

24
00:01:07,250 --> 00:01:10,670
can start with small molecules
and put them together

25
00:01:10,670 --> 00:01:14,360
into a macromolecule, or
start with a macromolecule

26
00:01:14,360 --> 00:01:20,060
and break it down into smaller
pieces during metabolism.

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00:01:20,060 --> 00:01:22,130
This video summarizes
some of the most important

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00:01:22,130 --> 00:01:25,880
carbonyl reactions you
will encounter in 5.07.

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00:01:25,880 --> 00:01:27,680
In this video, we're
going to be talking

30
00:01:27,680 --> 00:01:29,580
about carbonyl chemistry.

31
00:01:29,580 --> 00:01:32,240
And as we will see,
carbonyl chemistry

32
00:01:32,240 --> 00:01:38,210
is fundamental for some of the
carbon-carbon bond formation

33
00:01:38,210 --> 00:01:41,210
and cleavage reactions.

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00:01:41,210 --> 00:01:43,550
As you recall from
organic chemistry,

35
00:01:43,550 --> 00:01:49,490
carbonyl contains a C double
bond O. And all the properties

36
00:01:49,490 --> 00:01:56,000
of the carbonyl derive from its
ability to polarize this bond,

37
00:01:56,000 --> 00:01:59,300
so that we can draw a
resonance structure where

38
00:01:59,300 --> 00:02:03,200
the carbon has a positive
charge and the oxygen

39
00:02:03,200 --> 00:02:05,270
a negative charge.

40
00:02:05,270 --> 00:02:08,080
As you recall, there
are simple carbonyls,

41
00:02:08,080 --> 00:02:11,550
such as aldehydes and ketones.

42
00:02:15,890 --> 00:02:22,060
Also we have acyl derivatives,
compounds in which the carbonyl

43
00:02:22,060 --> 00:02:24,560
is attached to a heteroatom.

44
00:02:24,560 --> 00:02:28,010
x can be oxygen,
nitrogen, sulfur.

45
00:02:28,010 --> 00:02:34,760
So here, respective, we have
esters, amides, thioesters,

46
00:02:34,760 --> 00:02:39,440
and of course, we have an OH
group here, carboxylic acid.

47
00:02:39,440 --> 00:02:41,620
Here is a summary
of the reactions

48
00:02:41,620 --> 00:02:43,300
that we're going to
be talking about.

49
00:02:43,300 --> 00:02:45,110
First, we're going
to be discussing

50
00:02:45,110 --> 00:02:47,870
nucleophilic addition.

51
00:02:47,870 --> 00:02:51,920
Here, the good nucleophile
reacts with the carbonyl,

52
00:02:51,920 --> 00:02:58,170
adding to the carbon that
the carbonyl can generate.

53
00:02:58,170 --> 00:03:01,970
This tetrahedral compound.

54
00:03:01,970 --> 00:03:05,160
Next we're going to be
talking about enolization.

55
00:03:05,160 --> 00:03:07,430
This is the property
of carbonyls

56
00:03:07,430 --> 00:03:10,940
that contain an
alpha hydrogen, which

57
00:03:10,940 --> 00:03:12,800
can rearrange to form enol.

58
00:03:15,580 --> 00:03:19,680
Next we're going to
introduce the aldol reaction.

59
00:03:19,680 --> 00:03:23,490
This is the reaction in which
a carbon-carbon bond is formed

60
00:03:23,490 --> 00:03:28,020
and occurs between a carbonyl
that acts as electrophile

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00:03:28,020 --> 00:03:32,750
and a enolizable carbonyl,
which acts as a nucleophile.

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00:03:32,750 --> 00:03:37,530
In the aldol reaction, a bond
is formed between these two

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00:03:37,530 --> 00:03:43,410
carbons, generating an aldol.

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00:03:43,410 --> 00:03:47,970
We're also going to see that
the aldols can dehydrate.

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00:03:47,970 --> 00:03:53,600
The aldols we saw above
can lose a water molecule

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00:03:53,600 --> 00:03:59,160
to form an alpha,
beta-unsaturated carbonyl.

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00:03:59,160 --> 00:04:01,320
Now about the acyl
derivatives, we're

68
00:04:01,320 --> 00:04:06,140
going to be talking about
acyl transfer reactions, where

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00:04:06,140 --> 00:04:09,720
an acyl derivative
can convert into

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00:04:09,720 --> 00:04:13,881
a different acyl derivative with
the appropriate nucleophile.

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00:04:13,881 --> 00:04:19,529
A variation of this reaction
is Claisen reaction,

72
00:04:19,529 --> 00:04:24,020
where similarly to
the aldol reaction,

73
00:04:24,020 --> 00:04:29,030
we have an enolizable
carbonyl reacting

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00:04:29,030 --> 00:04:33,770
with an acyl derivitive
and generating

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00:04:33,770 --> 00:04:37,300
a beta-keto carbonyl.

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00:04:37,300 --> 00:04:41,310
This reaction also forms
a carbon-carbon bond,

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00:04:41,310 --> 00:04:42,550
which is right here.

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00:04:47,400 --> 00:04:52,470
Let's talk in more detail about
the nucleophilic addition.

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00:04:52,470 --> 00:04:56,360
The general reaction
scheme is as we saw before.

80
00:04:56,360 --> 00:05:05,660
Here is a carbonyl compound
reacting with a nucleophile

81
00:05:05,660 --> 00:05:09,210
and forming a tetrahedral
intermediate that contains

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00:05:09,210 --> 00:05:12,970
an alkoxide or an alcohol.

83
00:05:12,970 --> 00:05:16,570
Now let's take a look at
two different reactions.

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00:05:16,570 --> 00:05:22,620
One is the reaction of alcohols
with carbonyl compounds, where

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00:05:22,620 --> 00:05:26,950
we form a compound
that looks like this.

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00:05:26,950 --> 00:05:30,570
This is called a hemiacetal.

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00:05:30,570 --> 00:05:32,850
Now this reaction is reversible.

88
00:05:32,850 --> 00:05:35,280
And, in fact, it
reaches equilibrium

89
00:05:35,280 --> 00:05:39,960
because delta G naught
is approximately zero.

90
00:05:39,960 --> 00:05:43,920
This reaction can be
acid or base catalyzed.

91
00:05:46,670 --> 00:05:49,960
Let's take a quick
look at that mechanism.

92
00:05:49,960 --> 00:05:56,190
If it's based
catalyzed, the base

93
00:05:56,190 --> 00:06:00,850
will first deprotonate
the alcohol,

94
00:06:00,850 --> 00:06:03,920
which will form the
alkoxide, which is then

95
00:06:03,920 --> 00:06:09,250
a very good nucleophile to
attack the carbonyl, which

96
00:06:09,250 --> 00:06:13,840
forms this alkoxide version
of the hemiacetal, which

97
00:06:13,840 --> 00:06:15,610
can be then protonated.

98
00:06:21,010 --> 00:06:24,100
In acid-catalyzed
mechanism, we have

99
00:06:24,100 --> 00:06:26,920
to activate the carbonyl
first, so the protonation

100
00:06:26,920 --> 00:06:29,260
of the carbonyl
is the first step.

101
00:06:34,130 --> 00:06:36,160
All right, so this
activated carbonyl

102
00:06:36,160 --> 00:06:39,370
can then be attacked
by our alcohol.

103
00:06:47,580 --> 00:06:51,060
Which, this product is just
one proton transfer away

104
00:06:51,060 --> 00:06:54,300
from our hemiacetal.

105
00:06:54,300 --> 00:06:57,810
All right, the second reaction
I want to include here

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00:06:57,810 --> 00:07:00,120
is the formation of
Schiff bases which

107
00:07:00,120 --> 00:07:03,320
is the reaction of a
carbonyl with an amine.

108
00:07:05,940 --> 00:07:08,625
Similarly to the
hemiacetal formation,

109
00:07:08,625 --> 00:07:14,040
this reaction generates first
a tetrahedral intermediate,

110
00:07:14,040 --> 00:07:17,160
which is, however,
unstable, and loses water

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00:07:17,160 --> 00:07:19,410
to generate the imine,
with a Schiff base.

112
00:07:23,170 --> 00:07:26,340
Let's take a look
at the mechanism.

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00:07:26,340 --> 00:07:31,290
As you notice, the reaction--
because the amine group is

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00:07:31,290 --> 00:07:33,510
a good nucleophile, the
reaction can occur even

115
00:07:33,510 --> 00:07:35,380
in neutral conditions.

116
00:07:35,380 --> 00:07:38,405
We don't need, necessarily,
acid or base catalysis.

117
00:07:43,320 --> 00:07:49,600
The first step, the imine
attacks the carbonyl,

118
00:07:49,600 --> 00:07:51,670
forming this compound
with split charges.

119
00:07:55,840 --> 00:08:01,950
Now proton transfer happens
to generate our intermediate.

120
00:08:01,950 --> 00:08:05,345
Then water is eliminated.

121
00:08:12,140 --> 00:08:13,690
And this is the imine.

122
00:08:13,690 --> 00:08:16,700
You'll notice the
imine nitrogen can also

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00:08:16,700 --> 00:08:24,680
be protonated, to
generate this iminium ion,

124
00:08:24,680 --> 00:08:29,090
which, as we will see
in other situations,

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00:08:29,090 --> 00:08:35,150
it's an activated version
of the carbonyl group.

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00:08:35,150 --> 00:08:36,980
From these two
examples, we can get

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00:08:36,980 --> 00:08:40,219
some idea of how the
nucleophilic addition occurs.

128
00:08:40,219 --> 00:08:42,260
So let's take a look at
what kind of nucleophiles

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00:08:42,260 --> 00:08:44,030
we can add to the
carbonyl group.

130
00:08:44,030 --> 00:08:47,450
We have some good nucleophiles.

131
00:08:47,450 --> 00:08:50,210
And here we have things
with negative charges,

132
00:08:50,210 --> 00:08:54,080
such as alkoxide, or hydroxide.

133
00:08:54,080 --> 00:08:57,430
I have the thiolates.

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00:08:57,430 --> 00:08:59,870
And other things such as amines.

135
00:08:59,870 --> 00:09:03,690
And we also have
some OK nucleophiles.

136
00:09:03,690 --> 00:09:09,530
And here we have alcohols,
even water, and thiols.

137
00:09:09,530 --> 00:09:11,860
As you saw in these
couple of mechanisms,

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00:09:11,860 --> 00:09:14,900
the OK nucleophiles
don't react very well,

139
00:09:14,900 --> 00:09:18,920
unless they are deprotonated
to form good nucleophiles,

140
00:09:18,920 --> 00:09:20,180
such as the alcohols.

141
00:09:20,180 --> 00:09:24,020
Or the carbonyl gets activated,
either by protonation

142
00:09:24,020 --> 00:09:26,210
in a strong acid,
as we saw here,

143
00:09:26,210 --> 00:09:29,960
or it becomes an activated
carbonyl, for example,

144
00:09:29,960 --> 00:09:32,580
in an iminium ion.

145
00:09:32,580 --> 00:09:37,010
Another important nuclear
force that we're going to see

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00:09:37,010 --> 00:09:41,792
is the, what we're going
to call, a C minus.

147
00:09:41,792 --> 00:09:45,110
Basically a
carbanion In our case

148
00:09:45,110 --> 00:09:49,820
it's going to be enolates, which
can also add to the carbonyls.

149
00:09:49,820 --> 00:09:52,560
And these will form the
basis for the aldol reaction.

150
00:09:56,619 --> 00:09:58,870
The second reaction we're
going to be talking about

151
00:09:58,870 --> 00:10:01,600
is enolization.

152
00:10:01,600 --> 00:10:08,320
Here, a carbonyl that
contains an alpha hydrogen

153
00:10:08,320 --> 00:10:11,530
can rearrange to form an enol.

154
00:10:11,530 --> 00:10:14,290
We're going to call this
the keto form and this

155
00:10:14,290 --> 00:10:16,720
the enol form.

156
00:10:16,720 --> 00:10:19,770
An equilibrium between
a keto and an enol form

157
00:10:19,770 --> 00:10:22,499
is called tautomerization.

158
00:10:22,499 --> 00:10:24,040
And this is a very
important reaction

159
00:10:24,040 --> 00:10:26,260
in many biochemical systems.

160
00:10:26,260 --> 00:10:30,370
Turns out, the delta G, for
the reaction as written,

161
00:10:30,370 --> 00:10:35,140
it's very high, 30 to
50 kilojoules per mole.

162
00:10:35,140 --> 00:10:40,120
That means that equilibrium
strongly favors the keto form.

163
00:10:40,120 --> 00:10:43,706
However, in certain
cases, the enol

164
00:10:43,706 --> 00:10:47,260
can form and get stabilized.

165
00:10:47,260 --> 00:10:51,260
The mechanism of enolization,
it's very straightforward.

166
00:10:51,260 --> 00:10:53,710
All we need is a
decent base that

167
00:10:53,710 --> 00:10:56,170
can remove the alpha proton.

168
00:10:59,510 --> 00:11:03,970
And it will form this enolate.

169
00:11:03,970 --> 00:11:06,710
Now, enolate is able
to form because it

170
00:11:06,710 --> 00:11:09,260
has resonance stabilization.

171
00:11:09,260 --> 00:11:16,170
We can draw another
resonance structure, as such,

172
00:11:16,170 --> 00:11:19,480
where we see the negative
charge is on the carbon.

173
00:11:19,480 --> 00:11:21,500
So it is in fact a carbanion.

174
00:11:21,500 --> 00:11:25,604
We're going to call it
a disguised carbanion.

175
00:11:25,604 --> 00:11:28,070
As the carbon is not
very electronegative,

176
00:11:28,070 --> 00:11:31,430
having such a high electron
density on the carbon

177
00:11:31,430 --> 00:11:35,680
would make it a very
good nucleophile.

178
00:11:35,680 --> 00:11:38,720
And in fact, this enolate
is the nucleophile

179
00:11:38,720 --> 00:11:42,050
that executes reactions
such as the Aldol reaction

180
00:11:42,050 --> 00:11:44,990
and the Claisen reaction.

181
00:11:44,990 --> 00:11:47,870
Something to keep in
mind, well, how acidic

182
00:11:47,870 --> 00:11:50,720
is this alpha hydrogen?

183
00:11:50,720 --> 00:11:56,570
We can compare it with
a hydrogen in an alkyne.

184
00:11:56,570 --> 00:12:00,530
The pKa of such a
hydrogen is close to 50.

185
00:12:00,530 --> 00:12:06,830
It's extremely hard
to remove a proton.

186
00:12:06,830 --> 00:12:09,760
Now if we look at an alpha
hydrogen next to a carbonyl,

187
00:12:09,760 --> 00:12:12,530
the pKa is 18 to 20.

188
00:12:12,530 --> 00:12:17,510
So it's 30 orders of
magnitude more acidic,

189
00:12:17,510 --> 00:12:20,630
and this is because, as we saw,
when we removed this hydrogen,

190
00:12:20,630 --> 00:12:25,880
we formed the enolate anion,
which is resonance stabilized.

191
00:12:25,880 --> 00:12:32,710
The more extreme case of this,
if we have two carbonyls, alpha

192
00:12:32,710 --> 00:12:37,430
to the same proton, the
pKa drops even further,

193
00:12:37,430 --> 00:12:41,300
around 9 to 11.

194
00:12:41,300 --> 00:12:45,700
This is because we can draw
even more resonance structures

195
00:12:45,700 --> 00:12:49,710
to the enolate that's formed.

196
00:12:49,710 --> 00:12:50,270
This is one.

197
00:12:54,690 --> 00:12:55,460
This is another.

198
00:13:00,445 --> 00:13:01,800
And another.

199
00:13:01,800 --> 00:13:05,140
As we saw before,
the charge here

200
00:13:05,140 --> 00:13:09,560
is delocalized between the
oxygens and the alpha carbon.

201
00:13:09,560 --> 00:13:16,300
So it is this beta keto carbonyl
in its enolate form will

202
00:13:16,300 --> 00:13:21,548
behave as a carbanion and it
can act as a good nucleophile.

203
00:13:24,830 --> 00:13:28,410
The Aldol reaction.

204
00:13:28,410 --> 00:13:30,570
This is a very important
reaction in biochemistry

205
00:13:30,570 --> 00:13:36,120
because it allows formation
of carbon-carbon bonds.

206
00:13:36,120 --> 00:13:38,190
Or, if the reaction
runs in reverse,

207
00:13:38,190 --> 00:13:41,430
cleavage of the
carbon-carbon bonds.

208
00:13:41,430 --> 00:13:44,220
The Aldol reaction
is the reaction

209
00:13:44,220 --> 00:13:50,210
between an enolizable
carbonyl, as we show here,

210
00:13:50,210 --> 00:13:55,590
a carbonyl that has an alpha
hydrogen, and another carbonyl.

211
00:13:55,590 --> 00:13:58,500
And what happens is, a
new carbon-carbon bond

212
00:13:58,500 --> 00:14:06,260
forms between alpha carbon
and the carbonyl carbon.

213
00:14:11,270 --> 00:14:13,900
The product of the
Aldol reaction,

214
00:14:13,900 --> 00:14:17,080
it's called Aldol as a
contraction between aldehyde

215
00:14:17,080 --> 00:14:20,640
and alcohol, as in some
cases this carbonyl

216
00:14:20,640 --> 00:14:23,170
will be an aldehyde and
this would be Aldol.

217
00:14:23,170 --> 00:14:29,400
It's essentially a beta
hydroxy of carbonyl.

218
00:14:29,400 --> 00:14:34,380
Now, this reaction has a
delta G naught close to 0.

219
00:14:34,380 --> 00:14:39,610
That is, it reaches equilibrium.

220
00:14:39,610 --> 00:14:45,490
And it can be catalyzed
by acid or by base.

221
00:14:45,490 --> 00:14:48,060
Let's take a quick
look at the mechanism.

222
00:14:48,060 --> 00:14:50,670
Given the previous
mechanistic insights--

223
00:14:50,670 --> 00:14:54,410
we looked at the nucleophilic
addition, and enol formation,

224
00:14:54,410 --> 00:14:56,580
then the mechanism
of the Aldol reaction

225
00:14:56,580 --> 00:14:59,410
should be fairly
straightforward.

226
00:14:59,410 --> 00:15:02,340
If it's base-catalyzed,
the base is

227
00:15:02,340 --> 00:15:13,390
going to help us form
the enolate, as such.

228
00:15:13,390 --> 00:15:17,350
And as we discussed
previously, the enolate

229
00:15:17,350 --> 00:15:21,910
is a good nucleophile, and can
react via nucleophilic addition

230
00:15:21,910 --> 00:15:24,540
with the other carbonyl.

231
00:15:29,720 --> 00:15:35,050
And one proton transfer to
generate the Aldol product.

232
00:15:39,030 --> 00:15:42,690
The reaction can also
be acid-catalyzed.

233
00:15:42,690 --> 00:15:46,920
Again, formation of the
enol in acid catalysis

234
00:15:46,920 --> 00:15:48,750
involved first protonation
of the carbonyl.

235
00:15:56,590 --> 00:15:57,990
Now this activated
carbonyl, it's

236
00:15:57,990 --> 00:16:03,370
a much better electron sink, and
stabilizes the enol formation.

237
00:16:09,140 --> 00:16:10,810
Now, in the second
step the enol can

238
00:16:10,810 --> 00:16:22,770
react with the other
carbonyl, to generate

239
00:16:22,770 --> 00:16:26,520
a protonated version
of the Aldol, which

240
00:16:26,520 --> 00:16:31,280
is one proton transfer away
from the Aldol product.

241
00:16:33,830 --> 00:16:35,940
In biochemical
systems, the enzyme

242
00:16:35,940 --> 00:16:40,340
that catalyzed the Aldol
reaction is called aldolase.

243
00:16:40,340 --> 00:16:43,260
And there are actually
two kinds of aldolases.

244
00:16:43,260 --> 00:16:46,190
Class one, and class two.

245
00:16:46,190 --> 00:16:48,270
The distinctive feature
of these enzymes

246
00:16:48,270 --> 00:16:50,520
is the way they
catalyze the reaction.

247
00:16:50,520 --> 00:16:54,660
Class one uses an
active site lysine

248
00:16:54,660 --> 00:16:57,740
to form a Schiff base
with the carbonyl, which

249
00:16:57,740 --> 00:17:01,590
activates the carbonyl, and
allows for the enol formation.

250
00:17:01,590 --> 00:17:05,220
Class two uses a metal
ion, such as zinc,

251
00:17:05,220 --> 00:17:08,670
to accomplish the same thing.

252
00:17:08,670 --> 00:17:13,340
So here is how the mechanism
for the class 1 aldolase

253
00:17:13,340 --> 00:17:13,839
would look.

254
00:17:17,310 --> 00:17:21,560
So here is our
enolizable carbonyl,

255
00:17:21,560 --> 00:17:26,569
and here is our
active site lysine.

256
00:17:26,569 --> 00:17:29,090
As we saw before,
an amine reacting

257
00:17:29,090 --> 00:17:33,020
was a carbonyl will
give us a Schiff base.

258
00:17:33,020 --> 00:17:36,720
The reaction goes via a
tetrahedral intermediate,

259
00:17:36,720 --> 00:17:39,960
which we're not
going to draw here,

260
00:17:39,960 --> 00:17:42,903
but what we form is
this iminium ion.

261
00:17:46,290 --> 00:17:49,110
Now the carbonyl
is activated enough

262
00:17:49,110 --> 00:17:53,590
that an active site base
can remove an alpha hydrogen

263
00:17:53,590 --> 00:17:54,810
to form the enol.

264
00:17:59,970 --> 00:18:04,670
Which is now well-positioned
to attack the other carbonyl.

265
00:18:12,720 --> 00:18:17,370
This generates the Aldol
product, in its imine form,

266
00:18:17,370 --> 00:18:19,210
still attached to the enzyme.

267
00:18:19,210 --> 00:18:23,720
And now the hydrolysis of imine
is going to release the Aldol.

268
00:18:27,020 --> 00:18:34,592
Now, class two enzymes
use a zinc ion.

269
00:18:34,592 --> 00:18:39,300
As the ion approaches
the carbonyl,

270
00:18:39,300 --> 00:18:44,510
it's going to draw some of the
electrons from the carbonyl,

271
00:18:44,510 --> 00:18:48,365
and make the proton in the alpha
position a lot more acidic.

272
00:18:53,200 --> 00:18:55,120
So you can imagine,
some of these electrons

273
00:18:55,120 --> 00:18:56,200
get de-localized.

274
00:18:59,900 --> 00:19:05,860
So that a base can remove the
proton and form the enolate.

275
00:19:09,980 --> 00:19:12,506
Which, in the second
step, it reacts

276
00:19:12,506 --> 00:19:19,500
with the carbonyl, which
will generate the Aldol

277
00:19:19,500 --> 00:19:24,870
product in the active
site of the enzyme,

278
00:19:24,870 --> 00:19:29,340
still bound to the zinc, and
now which can dissociate,

279
00:19:29,340 --> 00:19:31,770
and generate the final--

280
00:19:31,770 --> 00:19:34,250
and release the product.

281
00:19:34,250 --> 00:19:36,690
Now, a very important
consideration

282
00:19:36,690 --> 00:19:38,410
for the Aldol reaction
is that it can

283
00:19:38,410 --> 00:19:41,790
occur in the reverse fashion.

284
00:19:41,790 --> 00:19:46,920
For example, to cleave
a carbon-carbon bond.

285
00:19:46,920 --> 00:19:50,370
So the bond that will be
cleaved, as we see here,

286
00:19:50,370 --> 00:19:52,170
is the bond that
got formed, which

287
00:19:52,170 --> 00:19:58,452
is the bond between the
alpha and beta carbons.

288
00:19:58,452 --> 00:20:01,440
The aldolase is one of the
key enzyme in glycolysis,

289
00:20:01,440 --> 00:20:06,090
that allows us to break a
six carbon sugar into two

290
00:20:06,090 --> 00:20:09,360
three-carbon sugars by
cleaving a carbon-carbon bond

291
00:20:09,360 --> 00:20:11,910
via the Aldol reaction.

292
00:20:11,910 --> 00:20:14,630
As the mechanism
catalyzed by the aldolase,

293
00:20:14,630 --> 00:20:18,270
we can see that the
reverse pathway is pretty

294
00:20:18,270 --> 00:20:21,370
straightforward, where the
Aldol binds to the enzyme,

295
00:20:21,370 --> 00:20:24,690
say in class one,
forms an active site,

296
00:20:24,690 --> 00:20:27,660
covalent attraction, a
Schiff base with the lysine,

297
00:20:27,660 --> 00:20:29,850
from which the chemistry
occurs to break

298
00:20:29,850 --> 00:20:33,590
the carbon-carbon bond, and
leads to the release of one

299
00:20:33,590 --> 00:20:36,180
carbonyl molecule,
and then the other one

300
00:20:36,180 --> 00:20:39,500
will be still bound to the
enzyme as a Schiff base

301
00:20:39,500 --> 00:20:41,340
and hydrolyzed.

302
00:20:41,340 --> 00:20:44,370
For the class two, the Aldol
will interact with the enzyme

303
00:20:44,370 --> 00:20:48,240
by forming an interaction
with the zinc,

304
00:20:48,240 --> 00:20:51,300
and this activated carbonyl
allows the chemistry

305
00:20:51,300 --> 00:20:56,550
to occur exactly in the
reverse manner, as shown here.

306
00:21:03,510 --> 00:21:07,790
One other reaction involving
Aldols is Aldol dehydration.

307
00:21:11,740 --> 00:21:15,730
Here's an Aldol, beta
hydroxy carbonyl.

308
00:21:15,730 --> 00:21:21,970
Now, if an Aldol has an
additional alpha hydrogen,

309
00:21:21,970 --> 00:21:30,570
it can lose a water molecule to
form an alpha beta unsaturated

310
00:21:30,570 --> 00:21:32,918
carbonyl.

311
00:21:32,918 --> 00:21:35,840
Now this reaction is
favorable thermodynamically.

312
00:21:35,840 --> 00:21:39,280
The delta G naught
is approximately 0.

313
00:21:39,280 --> 00:21:40,990
And this is a
reaction we're going

314
00:21:40,990 --> 00:21:45,190
to see in a lot of
biochemical pathways,

315
00:21:45,190 --> 00:21:49,360
for example, in the
biosynthesis of fatty acids,

316
00:21:49,360 --> 00:21:53,680
going left to right, or in
the catabolism of fatty acids,

317
00:21:53,680 --> 00:21:56,530
going right to left.

318
00:21:56,530 --> 00:21:58,540
Here's a quick insight
on the mechanism.

319
00:21:58,540 --> 00:22:00,930
Once again, it can be
base- or acid-catalyzed.

320
00:22:03,920 --> 00:22:08,500
This reaction works because
the alpha hydrogen here

321
00:22:08,500 --> 00:22:11,220
is next to a carbonyl, and
therefore can form an enol.

322
00:22:13,930 --> 00:22:20,770
So if a base can remove this
hydrogen to form the enolate,

323
00:22:20,770 --> 00:22:28,270
then we can envision how this
electronic movement will allow

324
00:22:28,270 --> 00:22:33,600
for a water molecule
to be eliminated,

325
00:22:33,600 --> 00:22:38,136
forming our alpha beta
unsaturated carbonyl.

326
00:22:38,136 --> 00:22:44,610
The acid-catalyzed mechanism
goes along the same lines.

327
00:22:44,610 --> 00:22:46,160
As you remember,
in order to form

328
00:22:46,160 --> 00:22:50,524
the enol in an
acid-catalyzed context,

329
00:22:50,524 --> 00:22:52,190
first we have to
protonate the carbonyl.

330
00:22:57,145 --> 00:22:58,530
All right.

331
00:22:58,530 --> 00:23:05,780
Now a base can remove
our alpha hydrogen,

332
00:23:05,780 --> 00:23:11,500
forming the enol, which
can kick off a water

333
00:23:11,500 --> 00:23:16,930
molecule, generating
these pieces, which

334
00:23:16,930 --> 00:23:22,240
is just one proton transfer
away from our final product.

335
00:23:27,990 --> 00:23:32,085
So let's talk now about acyl
derivatives, and acyl transfer.

336
00:23:35,340 --> 00:23:37,475
As we mentioned,
acyl derivatives

337
00:23:37,475 --> 00:23:41,070
have a carbonyl attached
to a header atom.

338
00:23:43,580 --> 00:23:49,900
And this header atom can be
oxygen, nitrogen, sulfur.

339
00:23:49,900 --> 00:23:52,030
As all these header
atoms contain

340
00:23:52,030 --> 00:23:56,290
a lone pair of electrons,
one of the key properties

341
00:23:56,290 --> 00:24:03,510
of the acyl derivatives would
be resonance between the header

342
00:24:03,510 --> 00:24:10,860
atom and the oxygen.

343
00:24:10,860 --> 00:24:13,980
Now the properties of
the acyl derivatives

344
00:24:13,980 --> 00:24:19,290
will be dictated by how easy
or how difficult it is to adopt

345
00:24:19,290 --> 00:24:21,172
this minor resonance structure.

346
00:24:21,172 --> 00:24:23,130
In other words, how likely
is it for the header

347
00:24:23,130 --> 00:24:30,780
atom to participate in
these electron conjugations.

348
00:24:30,780 --> 00:24:34,530
Let's take a look at a
couple of acyl derivatives.

349
00:24:34,530 --> 00:24:37,140
This is a carboxylate.

350
00:24:37,140 --> 00:24:41,575
If the header atom a
nitrogen, we have amide.

351
00:24:44,450 --> 00:24:49,160
If the header atom
is oxygen, we also

352
00:24:49,160 --> 00:24:56,120
have esters, or
carboxylic acids.

353
00:24:58,640 --> 00:25:04,220
And when the header atom is
sulfur, we have thioesters.

354
00:25:04,220 --> 00:25:08,300
The order in which I wrote them
here is not actually random.

355
00:25:08,300 --> 00:25:10,100
It turns out for
the carboxylate,

356
00:25:10,100 --> 00:25:13,910
because it has already a
negative charge, the ability

357
00:25:13,910 --> 00:25:18,060
to adopt this resonance
is greatly increased.

358
00:25:18,060 --> 00:25:22,190
So it's very well
resonance-stabilized.

359
00:25:22,190 --> 00:25:25,550
The ability to form these
resonance structures,

360
00:25:25,550 --> 00:25:30,590
it's also great for amides,
and this dictates the chemistry

361
00:25:30,590 --> 00:25:33,380
and the biochemistry of
the amide bond, which

362
00:25:33,380 --> 00:25:39,270
is explored in greater detail
when we talk about protein.

363
00:25:39,270 --> 00:25:46,990
Esters can also adopt
these resonance structures.

364
00:25:46,990 --> 00:25:51,840
However, thioesters, because the
sulfur is a third-row element,

365
00:25:51,840 --> 00:25:54,390
so the p-orbitals of
sulfur are much bigger,

366
00:25:54,390 --> 00:25:56,430
they don't overlap very
well with the p-orbitals

367
00:25:56,430 --> 00:25:59,605
of the carbon, the
ability to adopt

368
00:25:59,605 --> 00:26:03,200
these resonance structures
is greatly diminished.

369
00:26:03,200 --> 00:26:07,410
Therefore, thioesters
behave a lot more

370
00:26:07,410 --> 00:26:10,250
like ketones, where the
electrons of the carbonyl bond

371
00:26:10,250 --> 00:26:14,010
are localized between the
carbon and oxygen, and not

372
00:26:14,010 --> 00:26:17,910
so much between the
carbon and sulfur.

373
00:26:17,910 --> 00:26:22,125
So therefore, thioesters
are the least resonant.

374
00:26:25,100 --> 00:26:27,720
And this is the trend.

375
00:26:27,720 --> 00:26:32,880
And this trend inversely
correlates with the reactivity.

376
00:26:32,880 --> 00:26:36,805
Carboxylates are least
reactive, whereas thioesters

377
00:26:36,805 --> 00:26:38,557
are the most reactive.

378
00:26:42,220 --> 00:26:46,960
Now, when we talk
about acyl transfer,

379
00:26:46,960 --> 00:26:50,200
we talk about the reaction
between an acyl derivative

380
00:26:50,200 --> 00:26:57,265
with another nucleophile,
which will replace the x header

381
00:26:57,265 --> 00:26:59,986
atom with the y header atom.

382
00:26:59,986 --> 00:27:07,800
So this reaction always occurs
via a tetrahedral intermediate.

383
00:27:07,800 --> 00:27:13,740
When both substituents are
attached to the carbon.

384
00:27:13,740 --> 00:27:16,830
Now from here, this
tetrahedral intermediate

385
00:27:16,830 --> 00:27:20,250
can fall apart by
kicking off the YR

386
00:27:20,250 --> 00:27:23,010
to regenerate the
starting material,

387
00:27:23,010 --> 00:27:27,260
or it can kick off the
XR group, to generate

388
00:27:27,260 --> 00:27:29,472
a new acyl derivative.

389
00:27:33,410 --> 00:27:37,920
Let's now talk about
the Claisen reaction.

390
00:27:37,920 --> 00:27:40,490
This is a very important
reaction in biochemistry,

391
00:27:40,490 --> 00:27:44,600
related to the Aldol reaction,
in which we form or cleave

392
00:27:44,600 --> 00:27:46,392
carbon-carbon bonds.

393
00:27:46,392 --> 00:27:52,670
The Claisen reaction happens
between an enolizable carbonyl

394
00:27:52,670 --> 00:27:55,770
and an acyl derivative.

395
00:27:55,770 --> 00:28:00,170
Let's pick in this
case an ester.

396
00:28:00,170 --> 00:28:03,110
And during this reaction,
a carbon-carbon bond

397
00:28:03,110 --> 00:28:08,173
is formed between
the alpha carbon

398
00:28:08,173 --> 00:28:11,760
of the enolizable carbonyl,
and the keto carbon

399
00:28:11,760 --> 00:28:13,910
of the acyl derivative.

400
00:28:13,910 --> 00:28:16,060
The product of the
Claisen reaction

401
00:28:16,060 --> 00:28:22,680
is a beta keto carbonyl.

402
00:28:22,680 --> 00:28:26,240
Let's look at the mechanism.

403
00:28:26,240 --> 00:28:28,930
As with all carbonyl
reactions, when

404
00:28:28,930 --> 00:28:33,757
we form a carbon-carbon bond,
we need to form an enolate.

405
00:28:33,757 --> 00:28:34,840
So this is the first step.

406
00:28:37,720 --> 00:28:41,460
A base will form,
remove the alpha proton,

407
00:28:41,460 --> 00:28:45,860
and form the
enolate, which is now

408
00:28:45,860 --> 00:28:51,140
poised to add to the acyl
derivative in an acyl transfer

409
00:28:51,140 --> 00:29:01,500
reaction, forming first a
tetrahedral intermediate, which

410
00:29:01,500 --> 00:29:06,840
can spontaneously fall apart
by eliminating the header atom

411
00:29:06,840 --> 00:29:11,950
group, to form our beta
keto carbonyl product.

412
00:29:14,720 --> 00:29:18,990
Now, in biochemistry a preferred
substrate for Claisen reactions

413
00:29:18,990 --> 00:29:21,611
is a thioester.

414
00:29:21,611 --> 00:29:22,985
One of the most
common thioesters

415
00:29:22,985 --> 00:29:27,600
we're going to encounter in
this course is acetyl-CoA.

416
00:29:27,600 --> 00:29:31,500
CoA, or coenzyme-A,
it's a thiol that

417
00:29:31,500 --> 00:29:35,790
can form thioesters
with a lot of acids,

418
00:29:35,790 --> 00:29:38,130
for example, acetic acid here.

419
00:29:38,130 --> 00:29:42,060
Acetyl-CoA can undergo a
Claisen reaction with itself,

420
00:29:42,060 --> 00:29:46,260
and therefore acts both
as an enolizable carbonyl

421
00:29:46,260 --> 00:29:48,720
and as an acyl derivative.

422
00:29:48,720 --> 00:29:52,140
From when we were talking
about thioesters, because

423
00:29:52,140 --> 00:29:55,590
of their limited conjugation
with the carbonyl,

424
00:29:55,590 --> 00:29:59,100
they are very reactive,
and they allow

425
00:29:59,100 --> 00:30:01,964
the formation of the enolate.

426
00:30:05,600 --> 00:30:08,310
Here is the acetyl-CoA
enolate, which

427
00:30:08,310 --> 00:30:14,060
can react with another
acetyl-CoA molecule.

428
00:30:14,060 --> 00:30:18,370
It will generate a
tetrahedral intermediate.

429
00:30:18,370 --> 00:30:19,900
Let's draw this molecule first.

430
00:30:23,180 --> 00:30:26,500
Which can lose one
of the CoA molecules,

431
00:30:26,500 --> 00:30:33,830
to generate this beta keto
thioester, acetoacetyl-CoA.

432
00:30:37,970 --> 00:30:40,220
As we will see
later in the course,

433
00:30:40,220 --> 00:30:46,700
this is a precursor to
formation of ketone bodies, one

434
00:30:46,700 --> 00:30:52,630
of the ways in which acetyl-CoA
can be used to store energy.

435
00:30:52,630 --> 00:30:58,465
Now, what is coenzyme-A,
often abbreviated CoA?

436
00:30:58,465 --> 00:31:03,040
We mentioned it's a thiol.

437
00:31:03,040 --> 00:31:07,950
That means it has an SH
group, which it turns out,

438
00:31:07,950 --> 00:31:10,280
is on a very long linker.

439
00:31:18,070 --> 00:31:21,460
There you go, this
is coenzyme-A.

440
00:31:21,460 --> 00:31:25,090
You might recognize this
part of the molecule

441
00:31:25,090 --> 00:31:29,050
as being adenine bound to a
ribose bound to two phosphates.

442
00:31:29,050 --> 00:31:32,709
It's essentially ADP.

443
00:31:32,709 --> 00:31:34,750
But notice there's another
phosphate in the three

444
00:31:34,750 --> 00:31:41,020
prime position, so it's an ADP
with a three prime phosphate.

445
00:31:41,020 --> 00:31:44,800
This portion of the
molecule, If we squint,

446
00:31:44,800 --> 00:31:50,020
resembles the amino
acid cysteine,

447
00:31:50,020 --> 00:31:53,880
but without the carboxyl group.

448
00:31:53,880 --> 00:31:56,670
And this middle portion
of the molecule,

449
00:31:56,670 --> 00:32:01,210
it's something that looks
very difficult to synthesize.

450
00:32:01,210 --> 00:32:05,080
Notice this carbon that has
two methyl groups attached,

451
00:32:05,080 --> 00:32:07,290
and two other carbons
attached to it.

452
00:32:07,290 --> 00:32:08,700
So it's like a tetravalent--

453
00:32:11,990 --> 00:32:15,760
a carbon attached to it, four
other carbons, that's it.

454
00:32:15,760 --> 00:32:19,070
Fairly rare sight
in biochemistry.

455
00:32:19,070 --> 00:32:22,500
This portion of the molecule
is called pantothenic acid.

456
00:32:22,500 --> 00:32:26,560
Pantothenic acid is
an essential nutrient,

457
00:32:26,560 --> 00:32:27,980
also known as vitamin B5.

458
00:32:32,490 --> 00:32:36,640
In this video we talked
about carbonyl chemistry.

459
00:32:36,640 --> 00:32:41,190
Carbonyl is the C double bond
O, and a lot of its properties

460
00:32:41,190 --> 00:32:46,500
are due to the polarizability of
this bond, where the carbon has

461
00:32:46,500 --> 00:32:48,300
a partial positive
charge, and oxygen

462
00:32:48,300 --> 00:32:50,206
a partial negative charge.

463
00:32:50,206 --> 00:32:52,740
We talked about reactions
to simple carbonyls,

464
00:32:52,740 --> 00:32:56,660
such as nucleophilic addition,
enolization, Aldol reaction,

465
00:32:56,660 --> 00:32:59,470
and the Aldol dehydration.

466
00:32:59,470 --> 00:33:01,300
And acyl derivatives,
where the carbonyl

467
00:33:01,300 --> 00:33:06,190
is next to a header atom, such
as oxygen, nitrogen, or sulfur.

468
00:33:06,190 --> 00:33:09,020
And we mentioned the
acyl transfer reaction,

469
00:33:09,020 --> 00:33:12,210
and the Claisen reaction.

470
00:33:12,210 --> 00:33:15,150
We saw in this video the
nucleophilic addition,

471
00:33:15,150 --> 00:33:17,880
where a nucleophile attacks
the carbon of carbonyl

472
00:33:17,880 --> 00:33:22,590
to add and form a
tetrahedral product.

473
00:33:22,590 --> 00:33:24,530
For example, alcohols
can add to carbonyls

474
00:33:24,530 --> 00:33:26,880
to form a hemiacetals,
and amines

475
00:33:26,880 --> 00:33:31,487
can add to carbonyls to form
imines, or Schiff bases.

476
00:33:31,487 --> 00:33:33,070
And we reviewed that
good nucleophiles

477
00:33:33,070 --> 00:33:38,610
are the ones like alkoxides,
thiolates, amines, or C

478
00:33:38,610 --> 00:33:39,800
minus enolates.

479
00:33:39,800 --> 00:33:42,960
Whereas OK nucleophiles
like alcohols and thiols,

480
00:33:42,960 --> 00:33:45,150
they need to be activated
first to undergo

481
00:33:45,150 --> 00:33:48,440
nucleophilic addition.

482
00:33:48,440 --> 00:33:51,350
We also talked about
enolization, the ability

483
00:33:51,350 --> 00:33:54,740
of a carbonyl with
an alpha hydrogen

484
00:33:54,740 --> 00:34:00,620
to rearrange into a hydroxyl
bound to a double bond, which

485
00:34:00,620 --> 00:34:01,660
we call an enol.

486
00:34:01,660 --> 00:34:04,250
Now this equilibrium,
called tautomerization,

487
00:34:04,250 --> 00:34:06,800
favors strongly the keto form.

488
00:34:06,800 --> 00:34:10,940
However, it does form
to a sufficient extent

489
00:34:10,940 --> 00:34:13,050
to allow chemistry to happen.

490
00:34:13,050 --> 00:34:15,320
For example, when we
remove the alpha hydrogen,

491
00:34:15,320 --> 00:34:18,230
we form an anion
called enolate, which

492
00:34:18,230 --> 00:34:22,489
is a disguised carbanion which
is a very good nucleophile.

493
00:34:22,489 --> 00:34:25,310
Next, we discussed the Aldol
reaction, a very important

494
00:34:25,310 --> 00:34:28,659
carbon-carbon bond formation
or cleavage reaction

495
00:34:28,659 --> 00:34:30,889
in biochemistry.

496
00:34:30,889 --> 00:34:33,500
This reaction happens between
an enolizable carbonyl

497
00:34:33,500 --> 00:34:37,795
and the regular carbonyl,
and a new carbon-carbon bond

498
00:34:37,795 --> 00:34:42,639
is formed between the alpha
carbon and the keto carbon,

499
00:34:42,639 --> 00:34:44,090
as shown here.

500
00:34:44,090 --> 00:34:46,600
The mechanism can be
both base-catalyzed and

501
00:34:46,600 --> 00:34:47,840
acid-catalyzed.

502
00:34:47,840 --> 00:34:51,570
And the enzymes that catalyze
this, called aldolases,

503
00:34:51,570 --> 00:34:54,110
use either a lysine
in the active site

504
00:34:54,110 --> 00:34:59,690
to form first a
Schiff base, or they

505
00:34:59,690 --> 00:35:02,815
use a zinc in the active
site to polarize the carbonyl

506
00:35:02,815 --> 00:35:04,190
and allow for the
enol formation.

507
00:35:07,300 --> 00:35:09,550
We also saw that
Aldol products can

508
00:35:09,550 --> 00:35:12,820
dehydrate to form alpha
beta unsaturated carbonyls.

509
00:35:12,820 --> 00:35:16,830
The mechanism could be both
acid- and base-catalyzed,

510
00:35:16,830 --> 00:35:21,352
and involves in both cases
formation of an enol.

511
00:35:21,352 --> 00:35:25,990
Next, we also talked about acyl
derivatives, and acyl transfer.

512
00:35:25,990 --> 00:35:32,750
As we show here, the resonance
in the acyl derivative

513
00:35:32,750 --> 00:35:39,159
dictates there how
well they react.

514
00:35:39,159 --> 00:35:41,450
Carboxylate and amine are
the most resonant stabilized,

515
00:35:41,450 --> 00:35:43,390
and therefore are
the least reactive,

516
00:35:43,390 --> 00:35:45,995
whereas esters,
especially thioesters,

517
00:35:45,995 --> 00:35:48,190
are the least resonance
stabilized, and therefore

518
00:35:48,190 --> 00:35:50,290
most reactive.

519
00:35:50,290 --> 00:35:54,040
Finally, we discussed the
Claisen reaction, a reaction

520
00:35:54,040 --> 00:35:56,650
similar to the Aldol, between
an enolizable carbonyl

521
00:35:56,650 --> 00:36:00,260
and an acyl derivative, which
generates a beta keto carbonyl.

522
00:36:00,260 --> 00:36:04,920
We introduced the acetyl-CoA,
a very important thioester,

523
00:36:04,920 --> 00:36:06,880
that can undergo Claisen
reaction with itself

524
00:36:06,880 --> 00:36:08,770
to form acetoacetyl-CoA.

525
00:36:08,770 --> 00:36:10,390
And we also introduced
the structure

526
00:36:10,390 --> 00:36:14,840
of CoA, which is
built around vitamin

527
00:36:14,840 --> 00:36:17,484
B5, an essential nutrient.