1 00:00:00,090 --> 00:00:02,520 The following content is provided under a Creative 2 00:00:02,520 --> 00:00:04,059 Commons license. 3 00:00:04,059 --> 00:00:06,360 Your support will help MIT OpenCourseWare 4 00:00:06,360 --> 00:00:10,720 continue to offer high quality educational resources for free. 5 00:00:10,720 --> 00:00:13,350 To make a donation or view additional materials 6 00:00:13,350 --> 00:00:17,280 from hundreds of MIT courses, visit MIT OpenCourseWare 7 00:00:17,280 --> 00:00:20,640 at ocw.mit.edu. 8 00:00:20,640 --> 00:00:22,920 BOGDEN FEDELES: Hello and welcome to 5.07 9 00:00:22,920 --> 00:00:25,020 Biochemistry online. 10 00:00:25,020 --> 00:00:26,170 I'm Dr. Bogden Fedeles. 11 00:00:29,030 --> 00:00:32,509 Despite the staggering biodiversity we see in nature, 12 00:00:32,509 --> 00:00:36,590 the types of chemical reactions employed are only but a couple 13 00:00:36,590 --> 00:00:37,880 of handfuls. 14 00:00:37,880 --> 00:00:41,210 And these are used over and over again very efficiently 15 00:00:41,210 --> 00:00:43,970 and with conserved mechanisms. 16 00:00:43,970 --> 00:00:45,860 As you might recall from Organic Chemistry, 17 00:00:45,860 --> 00:00:48,530 one of the most versatile chemical groups 18 00:00:48,530 --> 00:00:53,270 is the carbonyl, C double bond O. Not surprisingly, 19 00:00:53,270 --> 00:00:55,940 carbonyl chemistry is well-represented 20 00:00:55,940 --> 00:00:58,490 in biochemistry. 21 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. 23 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. 27 00:01:20,060 --> 00:01:22,130 This video summarizes some of the most important 28 00:01:22,130 --> 00:01:25,880 carbonyl reactions you will encounter in 5.07. 29 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. 34 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 61 00:03:28,020 --> 00:03:32,750 and a enolizable carbonyl, which acts as a nucleophile. 62 00:03:32,750 --> 00:03:37,530 In the aldol reaction, a bond is formed between these two 63 00:03:37,530 --> 00:03:43,410 carbons, generating an aldol. 64 00:03:43,410 --> 00:03:47,970 We're also going to see that the aldols can dehydrate. 65 00:03:47,970 --> 00:03:53,600 The aldols we saw above can lose a water molecule 66 00:03:53,600 --> 00:03:59,160 to form an alpha, beta-unsaturated carbonyl. 67 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 69 00:04:06,140 --> 00:04:09,720 an acyl derivative can convert into 70 00:04:09,720 --> 00:04:13,881 a different acyl derivative with the appropriate nucleophile. 71 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 74 00:04:29,030 --> 00:04:33,770 with an acyl derivitive and generating 75 00:04:33,770 --> 00:04:37,300 a beta-keto carbonyl. 76 00:04:37,300 --> 00:04:41,310 This reaction also forms a carbon-carbon bond, 77 00:04:41,310 --> 00:04:42,550 which is right here. 78 00:04:47,400 --> 00:04:52,470 Let's talk in more detail about the nucleophilic addition. 79 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 82 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. 84 00:05:16,570 --> 00:05:22,620 One is the reaction of alcohols with carbonyl compounds, where 85 00:05:22,620 --> 00:05:26,950 we form a compound that looks like this. 86 00:05:26,950 --> 00:05:30,570 This is called a hemiacetal. 87 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 106 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 111 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. 113 00:07:26,340 --> 00:07:31,290 As you notice, the reaction-- because the amine group is 114 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 123 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, 125 00:08:29,090 --> 00:08:35,150 it's an activated version of the carbonyl group. 126 00:08:35,150 --> 00:08:36,980 From these two examples, we can get 127 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 129 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. 134 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, 138 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 146 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.