1 00:00:00 --> 00:00:05 OK. Today we're going to get into some stuff where we're kind of 2 00:00:05 --> 00:00:10 peering way back in evolution about how life first learned to make 3 00:00:10 --> 00:00:15 energy. But before we do that I just want to finish up talking a 4 00:00:15 --> 00:00:20 little bit more about enzymes, the biological catalysts that are 5 00:00:20 --> 00:00:25 critical for life to exist and about how energy is stored. 6 00:00:25 --> 00:00:30 I want to clarify a point that clearly confused a couple of you in 7 00:00:30 --> 00:00:35 the last lecture. So the Gibbs free energy that we 8 00:00:35 --> 00:00:40 talked about can tell us that a reaction could go and, 9 00:00:40 --> 00:00:45 in this case, would actually release energy if it occurred, 10 00:00:45 --> 00:00:49 if these reactants were converted to these products. 11 00:00:49 --> 00:00:54 But the problem for most reactions is that in order for the reaction to 12 00:00:54 --> 00:00:59 take place there's a state in the middle, some chemical state known as 13 00:00:59 --> 00:01:04 the transition state which is energetically less favorable than 14 00:01:04 --> 00:01:09 either the reactants or the products. 15 00:01:09 --> 00:01:12 And if A and B are going to convert to C and D they have to probably 16 00:01:12 --> 00:01:16 start coming together in some kind of way, and that becomes 17 00:01:16 --> 00:01:20 energetically unfavorable. And this gives this activation 18 00:01:20 --> 00:01:30 energy -- 19 00:01:30 --> 00:01:34 -- or delta G00. And if the cell wants chemical 20 00:01:34 --> 00:01:39 reactions to take place at 25 degrees Centigrade aqueous solution 21 00:01:39 --> 00:01:43 it has to do something about that, and so it employs biological 22 00:01:43 --> 00:01:48 catalysts. And what a catalyst does, as you've heard in chemistry, 23 00:01:48 --> 00:01:53 is it lowers the activation energy in some way so that the molecules 24 00:01:53 --> 00:01:57 have enough energy just within their normal energy distribution at that 25 00:01:57 --> 00:02:02 temperature to get over the hump. These biological catalysts come in 26 00:02:02 --> 00:02:08 two flavors. As I said there are enzymes which are made of protein 27 00:02:08 --> 00:02:14 with all of those amino acids, the side chains that we talked about 28 00:02:14 --> 00:02:20 when the thing folds up in 3-dimensional space form a little 29 00:02:20 --> 00:02:26 chemical environment that enables that activation energy to be lowered. 30 00:02:26 --> 00:02:31 There are also few -- Not so many. But we now know that 31 00:02:31 --> 00:02:36 there are catalysts made out of RNA. These are called ribozymes. There 32 00:02:36 --> 00:02:41 are not so many of them but they're important. Now, 33 00:02:41 --> 00:02:46 the characteristics of these that are important is the specificity -- 34 00:02:46 --> 00:03:03 Each enzyme or ribozyme is highly 35 00:03:03 --> 00:03:13 specific for a given reaction. So that means the reaction probably 36 00:03:13 --> 00:03:18 will barely go unless that enzyme or, in some cases, 37 00:03:18 --> 00:03:23 ribozyme is present. And so that's really the secret to 38 00:03:23 --> 00:03:28 how cells control all of these many, many, many hundreds or thousands of 39 00:03:28 --> 00:03:34 chemical reactions that take place that are necessary for life. 40 00:03:34 --> 00:03:39 Because what they need to do, and if they want to control whether 41 00:03:39 --> 00:03:45 reaction takes place or not is they control the availability or the 42 00:03:45 --> 00:03:51 activity of an enzyme. And when we talk about gene 43 00:03:51 --> 00:03:57 regulation you'll see, for example, one way a cell might do 44 00:03:57 --> 00:04:03 it is to not even bother to make the enzyme unless it wants a particular 45 00:04:03 --> 00:04:07 reaction to take place. Or it could take an enzyme that's 46 00:04:07 --> 00:04:10 there and put little bells and whistles on it that make it more 47 00:04:10 --> 00:04:14 active or less active. And we'll see an example of that 48 00:04:14 --> 00:04:17 pretty soon. That is the secret to how cells are then able to 49 00:04:17 --> 00:04:25 regulate metabolism. 50 00:04:25 --> 00:04:30 And these biological catalysts use a whole variety of different molecular 51 00:04:30 --> 00:04:35 mechanisms, although all of them follow this principle of what 52 00:04:35 --> 00:04:41 they're trying to do is lower the activation energy. 53 00:04:41 --> 00:04:45 So I'll just give you an example. I showed you of how one particular 54 00:04:45 --> 00:04:49 enzyme does it just in sort of cartoon form. I gave you the 55 00:04:49 --> 00:04:53 example of glutamate being converted to glutamine. Now, 56 00:04:53 --> 00:04:57 both of those are amino acids that are critical for making proteins. 57 00:04:57 --> 00:05:02 The cell has to make both of them. But as I showed you converting 58 00:05:02 --> 00:05:06 glutamate to glutamine is energetically unfavorable. 59 00:05:06 --> 00:05:10 It's got a delta G plus 7. And then I showed you if you had an 60 00:05:10 --> 00:05:14 ATP going to ADP at the same time you could actually drive the whole 61 00:05:14 --> 00:05:18 reaction forward because there was a net gain. But how is that actually 62 00:05:18 --> 00:05:22 accomplished? And it's the enzyme that carries this out. 63 00:05:22 --> 00:05:26 And I'll just show you, as I say, in sort of cartoon form. 64 00:05:26 --> 00:05:30 The way the enzyme works it has one binding pocket for glutamic 65 00:05:30 --> 00:05:35 acid or glutamate. It fits in here. 66 00:05:35 --> 00:05:39 It makes lots of specialized contacts, all those sort of 67 00:05:39 --> 00:05:43 molecular interactions we're talking about. And it also binds this 68 00:05:43 --> 00:05:47 molecule adenine triphosphate or ATP which is an adenine, 69 00:05:47 --> 00:05:51 a ribose and then three phosphates joined together. 70 00:05:51 --> 00:05:55 And it makes interactions along here that enable it to bind very 71 00:05:55 --> 00:05:59 specifically. Now, by providing all this binding energy 72 00:05:59 --> 00:06:03 for ATP and for glutamic acid what the enzyme has done is positioned 73 00:06:03 --> 00:06:07 the carboxyl group of glutamic acid right next to the last 74 00:06:07 --> 00:06:11 phosphate on the ATP. This enables this to form a bond 75 00:06:11 --> 00:06:16 here which liberates ADP and leaves you now with the glutamic acid with 76 00:06:16 --> 00:06:21 a phosphate on. That reaction goes forward because 77 00:06:21 --> 00:06:26 you broke the bond of ATP, but this is still a pretty unhappy 78 00:06:26 --> 00:06:31 molecule. It's got a lot of oxygens at very close proximity. 79 00:06:31 --> 00:06:35 So the enzyme has another binding pocket that's absolutely specific 80 00:06:35 --> 00:06:39 for ammonia. It won't fit water which is very close, 81 00:06:39 --> 00:06:44 which is a good thing because that would just reverse the process. 82 00:06:44 --> 00:06:48 Ammonia gets in there and then it attacks here and liberates the 83 00:06:48 --> 00:06:53 phosphate. And that then gives you glutamine and the inorganic 84 00:06:53 --> 00:06:57 phosphate. So the enzyme has provided this binding surface that 85 00:06:57 --> 00:07:02 makes the reactions go under biological conditions. 86 00:07:02 --> 00:07:06 But it's also managed in the same process to have it go by a mechanism 87 00:07:06 --> 00:07:10 in which it sort of temporarily captured that energy that's in the 88 00:07:10 --> 00:07:14 ATP bond and then used it to drive the rest of the reaction. 89 00:07:14 --> 00:07:19 I mean it's the magic of how all of this developed. 90 00:07:19 --> 00:07:23 It's really amazing but that's how every single biochemical step in 91 00:07:23 --> 00:07:27 your body takes place. Virtually of them require an enzyme 92 00:07:27 --> 00:07:32 that in some way is highly tuned to do just the one single reaction. 93 00:07:32 --> 00:07:36 As I said, the principle of how these enzymes work is they lower the 94 00:07:36 --> 00:07:40 activation energy. And the way they do that in general 95 00:07:40 --> 00:07:44 is they provide a binding pocket that resembles the transition state. 96 00:07:44 --> 00:07:48 So as things approach here then it fits best into the pocket and 97 00:07:48 --> 00:07:52 therefore you get some energy back and kind of lowered the energy hump 98 00:07:52 --> 00:07:56 that's necessary to go over. And here's a reaction I'll be 99 00:07:56 --> 00:08:00 showing you in today's lecture. It's going to involve the transfer 100 00:08:00 --> 00:08:05 of a phosphate to a glucose. And the first thing that happens is 101 00:08:05 --> 00:08:10 this enzyme interacts with ATP and takes one of the phosphates and 102 00:08:10 --> 00:08:15 attaches it to one of its aspartic acid carboxyl groups. 103 00:08:15 --> 00:08:20 So you've got actually a mixed in hydride if you know chemistry. 104 00:08:20 --> 00:08:25 But again it's captured that phosphate. This is a very unstable 105 00:08:25 --> 00:08:30 bond. And so if you break it you will release energy. 106 00:08:30 --> 00:08:34 And what the enzyme does is it allows the hydroxyl of here to come 107 00:08:34 --> 00:08:38 and attack this phosphate, and that then releases the aspartate 108 00:08:38 --> 00:08:42 of the enzyme and you end up affecting the transfer of the 109 00:08:42 --> 00:08:46 phosphate that began life on ATP. And now it ends up on the glucose. 110 00:08:46 --> 00:08:50 But, as you can see here, phosphate interacts with four atoms. 111 00:08:50 --> 00:08:54 But as this hydroxyl comes in it has to attack the phosphate. 112 00:08:54 --> 00:08:58 And somewhere in the middle there's an intermediate where all of these 113 00:08:58 --> 00:09:02 things are interacting. And some crystallographers actually 114 00:09:02 --> 00:09:06 managed to capture that in a crystal structure. And here you can see 115 00:09:06 --> 00:09:10 this is the oxygen coming from the sugar, this is the oxygen of the 116 00:09:10 --> 00:09:14 aspartate and here is the phosphate where it's now, 117 00:09:14 --> 00:09:17 as the attack is taking place the thing is sort of pushed out, 118 00:09:17 --> 00:09:21 and it's caught right at that transition state. 119 00:09:21 --> 00:09:25 And that's what the enzyme is providing a binding pocket for and 120 00:09:25 --> 00:09:29 thereby lowering the activation energy. It's a really beautiful 121 00:09:29 --> 00:09:33 piece of structural work. The second thing then I want to 122 00:09:33 --> 00:09:38 clarify was this molecule ATP which is, as I say, like energy money for 123 00:09:38 --> 00:09:42 the cell. When there's a reaction where it can extract energy it tries 124 00:09:42 --> 00:09:47 to make ATP. And when there's a reaction that doesn't want to go it 125 00:09:47 --> 00:09:52 will somehow figure out a way to spend that energy and make the 126 00:09:52 --> 00:09:57 reaction go forward. And the molecule, just to put it 127 00:09:57 --> 00:10:02 again, because it's a pretty important one in biology. 128 00:10:02 --> 00:10:08 That's adenine which you already saw when we talked about nucleic acids. 129 00:10:08 --> 00:10:14 And it's got three phosphates like this. You can see it's probably a 130 00:10:14 --> 00:10:20 pretty unhappy molecule because it's got all of these oxygens stuck 131 00:10:20 --> 00:10:26 together. And if you break this bond then you release some energy. 132 00:10:26 --> 00:10:33 So you could think of it in this kind of way. 133 00:10:33 --> 00:10:41 That if we have ADP, which is adenosine diphosphate plus 134 00:10:41 --> 00:10:49 inorganic phosphate, and ATP is here. And if you were to 135 00:10:49 --> 00:10:57 break the bond and make it back into ADP and inorganic phosphate then you 136 00:10:57 --> 00:11:05 would have gone energetically downhill. 137 00:11:05 --> 00:11:09 But in order to make this you could think of it as taking an inorganic 138 00:11:09 --> 00:11:13 phosphate ion and this ADP, if you start pushing them together 139 00:11:13 --> 00:11:18 the negative charges are going to repel and you kind of go up an 140 00:11:18 --> 00:11:22 energy hill. But if you ever get them close enough then they start to 141 00:11:22 --> 00:11:26 share electrons and they fall into this sort of energy well. 142 00:11:26 --> 00:11:31 And this is what ATP is. And so it's sort of like taking a 143 00:11:31 --> 00:11:35 spring and pushing it together. And then when you form the bond 144 00:11:35 --> 00:11:40 it's like you put a little hook on it. And now you've got this spring 145 00:11:40 --> 00:11:45 that's compressed. And it's stable, it won't do 146 00:11:45 --> 00:11:49 anything, but there's energy stored in there that you can use. 147 00:11:49 --> 00:11:54 And it's the same principle in terms of how the cell stores energy 148 00:11:54 --> 00:11:59 within ATP. And this energy is stored -- 149 00:11:59 --> 00:12:06 -- if you think of it in bundles of 150 00:12:06 --> 00:12:11 about 12 kilocalories per mole. That's about how much energy is 151 00:12:11 --> 00:12:17 released under physiological conditions when you hydrolyze that 152 00:12:17 --> 00:12:22 bond. So hydrolyzing ATP to give ADP plus inorganic phosphate will 153 00:12:22 --> 00:12:27 have a delta G of minus 12 kilocalories per mole under 154 00:12:27 --> 00:12:32 physiological conditions. Now something in terms of evolution, 155 00:12:32 --> 00:12:36 which I know a number of you said you were interested in, 156 00:12:36 --> 00:12:40 here's a really interesting thing. This is the main energy storage 157 00:12:40 --> 00:12:44 molecule for the cell, but you've heard about it before 158 00:12:44 --> 00:12:48 because adenosine, that's the nucleotide that we find 159 00:12:48 --> 00:12:52 in RNA. And, in fact, ATP is also the precursor, 160 00:12:52 --> 00:12:56 as we'll learn, for making RNA. And one of the things that puzzled 161 00:12:56 --> 00:13:00 scientists for many years is how did life ever get started 162 00:13:00 --> 00:13:04 in the first place? There seemed to be a chicken and an 163 00:13:04 --> 00:13:08 egg issue that proteins did the work and DNA stored the information and 164 00:13:08 --> 00:13:11 RNA was kind of a messenger in between, and we'll talk a lot about 165 00:13:11 --> 00:13:15 that in between. So how could you ever get life 166 00:13:15 --> 00:13:19 started? So the current thinking is that sometime, 167 00:13:19 --> 00:13:22 if you remember in that first lecture, we had about 4. 168 00:13:22 --> 00:13:26 billion years ago the first organism, something like today's 169 00:13:26 --> 00:13:30 bacterium showed up here about maybe 3.8 billion years ago. 170 00:13:30 --> 00:13:34 That somewhere in between there was what people are now thinking of as 171 00:13:34 --> 00:13:38 an “RNA world” where RNA managed to act as a ribosome and catalyzed 172 00:13:38 --> 00:13:42 chemical reactions, but it also had the capacity to 173 00:13:42 --> 00:13:47 store information. But it's sort of intriguing, 174 00:13:47 --> 00:13:51 although no one has proven that. It's just a hypothesis. We also 175 00:13:51 --> 00:13:55 see that the major energy storage molecule found in all living things 176 00:13:55 --> 00:13:59 is also a building block of RNA. It certainly sort of fits with that 177 00:13:59 --> 00:14:03 kind of idea. Now, there's one other kind of 178 00:14:03 --> 00:14:07 reaction I'm going to have to tell you about. Penny will talk quite a 179 00:14:07 --> 00:14:11 bit about this when you're thinking about how organisms make living. 180 00:14:11 --> 00:14:15 But this is a set of reactions known as “redox reactions”. 181 00:14:15 --> 00:14:27 So the loss of one or more 182 00:14:27 --> 00:14:37 electron(s) is called an oxidation. And the gain of one or more 183 00:14:37 --> 00:14:41 electron(s) is called a reduction. If you're going to take away an 184 00:14:41 --> 00:14:46 electron somebody else has to get it. So these things always happen 185 00:14:46 --> 00:14:50 together. And therefore they're given the term redox reactions where 186 00:14:50 --> 00:14:55 electron(s) from somebody goes to somebody else. 187 00:14:55 --> 00:14:59 So somebody gets oxidized and somebody gets reduced in 188 00:14:59 --> 00:15:05 the same reaction. And you can think of them as a 189 00:15:05 --> 00:15:11 transfer of hydrogen atoms, not hydrogon ions. And the most 190 00:15:11 --> 00:15:18 familiar kind of sequence that you will see over and over again in 191 00:15:18 --> 00:15:24 biology is the sequence you go from, let's say, a methyl group to an 192 00:15:24 --> 00:15:30 alcohol with a hydroxyl to an aldehyde or a ketone with the double 193 00:15:30 --> 00:15:37 bond oxygen to a carboxyl group. You go one more step then it's CO2. 194 00:15:37 --> 00:15:43 So going in this direction it's an oxidation. If it's going in that 195 00:15:43 --> 00:15:50 direction the molecules are getting reduced. Just the same way that the 196 00:15:50 --> 00:15:56 cell and life have molecules that store energy in ATP, 197 00:15:56 --> 00:16:03 they also have an important molecule that stores electrons. 198 00:16:03 --> 00:16:14 And that molecule is known as NAD or nicotinamide adenine dinucleotide. 199 00:16:14 --> 00:16:37 NAD+. And its structure is, 200 00:16:37 --> 00:16:46 let's say a ribose, a five carbon sugar. And it's got this entity on 201 00:16:46 --> 00:16:55 it. This is in your book so don't worry if you don't get 202 00:16:55 --> 00:17:03 the structure down. There's a positive charge on the 203 00:17:03 --> 00:17:11 nitrogen here. And it's joined through a 204 00:17:11 --> 00:17:19 diphosphate linkage to, guess what? Another molecule of 205 00:17:19 --> 00:17:27 adenosine. Here we find again a piece of a thing we find in RNA is 206 00:17:27 --> 00:17:35 now part of this system for storing electrons. 207 00:17:35 --> 00:17:45 And the way this works is if you have two hydrogen atoms transferred 208 00:17:45 --> 00:17:55 to here then this entity right here goes to this plus a hydrogen ion. 209 00:17:55 --> 00:18:02 And this we would know is NADH. I left out an oxygen here. 210 00:18:02 --> 00:18:08 Somebody picked it up. [LAUGHTER] Just too excited by the annual 211 00:18:08 --> 00:18:14 Valentine's Day visit here. I wish the rest of you had a song 212 00:18:14 --> 00:18:20 for you, too, but we didn't have time to set that up. 213 00:18:20 --> 00:18:26 So there's an important thing here, too, because actually a lot of 214 00:18:26 --> 00:18:32 energy is stored in there. This is a bundle of energy in this 215 00:18:32 --> 00:18:38 molecule that's actually about 50 kilocalories per mole. 216 00:18:38 --> 00:18:43 And especially when we get to next week's lecture you'll see how cells 217 00:18:43 --> 00:18:48 go about extracting the energy out of that and making that energy into 218 00:18:48 --> 00:18:53 ATP, which is sort of a universal currency the cells can spend. 219 00:18:53 --> 00:18:59 Now, somebody asked about memorizing all of these structures 220 00:18:59 --> 00:19:02 I mean really, As Julia says in her thing, 221 00:19:02 --> 00:19:05 we're trying to get you to focus on the concepts here. 222 00:19:05 --> 00:19:09 You won't have to memorize the structure of everything. 223 00:19:09 --> 00:19:12 It would be helpful if you recognized that glutamine and 224 00:19:12 --> 00:19:15 glutamate are of the 20 amino acids, but we'll give you the structures 225 00:19:15 --> 00:19:19 and we'll give you the structures of something like NADH if you needed to 226 00:19:19 --> 00:19:22 do something with it. But the important thing is to 227 00:19:22 --> 00:19:25 remember that energy is stored in that high energy bond of ATP, 228 00:19:25 --> 00:19:29 that electrons are stored in this NADH, and they can be used in 229 00:19:29 --> 00:19:33 reactions that oxidize or reduce. NAD and NADH can be used in 230 00:19:33 --> 00:19:38 reactions that remove or give electrons to biomolecules. 231 00:19:38 --> 00:19:44 Now, the same thing goes for what I'm about to tell you now because 232 00:19:44 --> 00:19:49 one of the first things that had to happen as life evolved was there had 233 00:19:49 --> 00:19:54 to be some mechanism of getting energy made. And the reaction I'm 234 00:19:54 --> 00:20:00 going to tell you about is called glycolysis. 235 00:20:00 --> 00:20:07 And it's a way of taking a molecule of glucose through a whole series of 236 00:20:07 --> 00:20:15 biochemical transformations and to end up yielding -- 237 00:20:15 --> 00:20:26 -- two molecules of something that's 238 00:20:26 --> 00:20:32 known as pyruvate. And it also makes two molecules of 239 00:20:32 --> 00:20:37 ATP and two molecules of NADH. So it's a way that was invented in 240 00:20:37 --> 00:20:42 evolution of making ATP by carrying out a chemical transformation. 241 00:20:42 --> 00:20:48 And this is basically the same chemical transformation that we've 242 00:20:48 --> 00:20:53 been talking about that Lavoisier and Pasteur studied except that, 243 00:20:53 --> 00:20:58 as I'll show you, you do a little bit to convert it either to lactate 244 00:20:58 --> 00:21:02 or to ethanol. I'll get to that in a few minutes. 245 00:21:02 --> 00:21:06 Remember the point, also just to remind you, the reason I gave you 246 00:21:06 --> 00:21:10 that historical thing is because what it turned out when people 247 00:21:10 --> 00:21:14 started out to study something, was winemaking of great interest to 248 00:21:14 --> 00:21:18 French scientists, was what they actually learned was 249 00:21:18 --> 00:21:22 how cells made energy. And, in fact, here we're looking at 250 00:21:22 --> 00:21:26 a sort of biochemical fossil in a way because this pathway of 251 00:21:26 --> 00:21:30 glycolysis, which you'll see is kind of awkward. 252 00:21:30 --> 00:21:35 It's got ten different biochemical steps, it needs ten different 253 00:21:35 --> 00:21:40 enzymes, and what the cells got out of it is two molecules of ATP. 254 00:21:40 --> 00:21:45 But this system developed apparently way, 255 00:21:45 --> 00:21:50 way back in evolution before life forms got into these various 256 00:21:50 --> 00:21:55 Kingdoms because it's in virtually in every living creature no matter 257 00:21:55 --> 00:22:00 what it is and it's essentially biochemically identical. 258 00:22:00 --> 00:22:03 Now, it's possible we could go back nowadays and devise a better method, 259 00:22:03 --> 00:22:07 but once that something like that gets fixed in evolution, 260 00:22:07 --> 00:22:10 if something mutates to try and change it most of the time it's a 261 00:22:10 --> 00:22:14 disadvantage. And so if something gets locked in, 262 00:22:14 --> 00:22:17 and this is true of many, many of these very complicated 263 00:22:17 --> 00:22:21 biochemical pathways. So you won't have to remember all 264 00:22:21 --> 00:22:24 these structures I'm going to put on the board, but try and stay with me 265 00:22:24 --> 00:22:28 because I want to sort of show you one of these. This is probably the 266 00:22:28 --> 00:22:31 most ancient of these pathways. And it's still in all of us. 267 00:22:31 --> 00:22:35 It's in the bacteria in our guts. It's in the plants in the field. 268 00:22:35 --> 00:22:39 If you go out in the open ocean organisms still can carry out 269 00:22:39 --> 00:22:43 glycolysis. So one thing, though, I want to try and put it in 270 00:22:43 --> 00:22:46 this way, if I came to you and said I've got the greatest idea. 271 00:22:46 --> 00:22:50 This is going to be how we're going to make energy and evolution as part 272 00:22:50 --> 00:22:54 of this entrepreneurship, I think you'd be right to be 273 00:22:54 --> 00:22:58 skeptical so I'll probably sort of tell you in that way. 274 00:22:58 --> 00:23:02 So I've already shown you how to write glucose in a linear form, 275 00:23:02 --> 00:23:07 although I then told you that most of the time in solution it's 276 00:23:07 --> 00:23:12 cyclized into a pyranose ring, a six membered ring. But for the 277 00:23:12 --> 00:23:17 moment we can think of glucose as a stick. And I'll get you to just 278 00:23:17 --> 00:23:22 focus on the one position, the two position and the six 279 00:23:22 --> 00:23:27 position in that linear thing. If you look back at your notes you 280 00:23:27 --> 00:23:32 can see what the full structure of glucose looks like. 281 00:23:32 --> 00:23:39 But this is how the process of glycolysis starts. 282 00:23:39 --> 00:23:47 This is if your body is going to take a molecule of glucose and make 283 00:23:47 --> 00:23:55 energy out of it, this is the first thing it does. 284 00:23:55 --> 00:24:03 It takes an ATP. It converts it to an ADP. It puts the phosphate down 285 00:24:03 --> 00:24:08 here to give glucose-6- phosphate. That's the only thing that changes. 286 00:24:08 --> 00:24:11 Isn't this just like most young entrepreneurs? 287 00:24:11 --> 00:24:14 Give them some venture capital. The first thing they do is spend it, 288 00:24:14 --> 00:24:17 buy a nice potted plant for the company they're building. 289 00:24:17 --> 00:24:21 It doesn't seem to be, if you want to make energy, 290 00:24:21 --> 00:24:24 starting out here spending energy is the first thing that the cell is 291 00:24:24 --> 00:24:27 doing. It's using up an ADP, although the overall goal is to make 292 00:24:27 --> 00:24:32 ADP. It then does a little shuffle, 293 00:24:32 --> 00:24:38 reverses the position of the double bond and the hydroxyl. 294 00:24:38 --> 00:24:44 This is an energetically something without much cost, 295 00:24:44 --> 00:24:51 but this sugar is different because this is now fructose-6-phosphate. 296 00:24:51 --> 00:24:57 It's got a little bit different arrangement of the double bond and 297 00:24:57 --> 00:25:04 the hydroxyl, but energetically it's pretty much the same thing. 298 00:25:04 --> 00:25:10 Then the next thing that happens the cells spends another molecule of ATP. 299 00:25:10 --> 00:25:25 It gives now -- 300 00:25:25 --> 00:25:31 -- fructose-1, , this is the sixth position, 301 00:25:31 --> 00:25:37 the one position to two position, 1,6-diphosphate. 302 00:25:37 --> 00:25:41 It doesn't look like we're on our way to make energy yet. 303 00:25:41 --> 00:25:46 Cells invested two molecules of ATP and what it's done is it's got this 304 00:25:46 --> 00:25:50 glucose transformed to fructose 1, -disphopshate. Well, what happens 305 00:25:50 --> 00:25:55 now then is the cell splits this into two three carbon units. 306 00:25:55 --> 00:26:00 There were six carbons in glucose. Yeah? 307 00:26:00 --> 00:26:10 Well, it's a linear molecule. 308 00:26:10 --> 00:26:14 There's a phosphate here and a separate phosphate down there. 309 00:26:14 --> 00:26:19 They should be. Yeah. I'm probably dropping charges and 310 00:26:19 --> 00:26:23 hydroxyls, OK? But check your book if you notice 311 00:26:23 --> 00:26:28 something like that. So what we get -- 312 00:26:28 --> 00:26:32 What the cell gets out of this then are two three carbon units, 313 00:26:32 --> 00:26:45 one of which is this -- 314 00:26:45 --> 00:26:49 -- known as dihydroxyacetone phosphate. And you can find these 315 00:26:49 --> 00:26:54 names in your book. You don't have to, as I say, 316 00:26:54 --> 00:26:58 remember the structures. What I've done is basically taken 317 00:26:58 --> 00:27:02 this molecule and I've flipped it over so that the phosphate will be 318 00:27:02 --> 00:27:05 down. And you'll see why I've done that in a second. 319 00:27:05 --> 00:27:09 And from the bottom half of the molecule then we get -- 320 00:27:09 --> 00:27:37 This is glycereldahyde-3-phosphate. 321 00:27:37 --> 00:27:41 So this is three carbons. This is three carbons. This was 322 00:27:41 --> 00:27:45 six carbons. So the cell has split it into these three carbon units 323 00:27:45 --> 00:27:49 that are very similarly related except where the double bond is. 324 00:27:49 --> 00:27:53 And there's an enzyme that actually catalyzes the conversion of those 325 00:27:53 --> 00:27:58 two. It's a catalytically perfect enzyme that goes. 326 00:27:58 --> 00:28:01 It's just limited by the rate of diffusion. And it can do something 327 00:28:01 --> 00:28:05 of the order of ten to the eighth molecules a second. 328 00:28:05 --> 00:28:09 It's a really, really efficient catalyst. So what happens then is 329 00:28:09 --> 00:28:13 this, since these are in equilibrium the cell is going to now 330 00:28:13 --> 00:28:24 start to pull these -- 331 00:28:24 --> 00:28:28 This. But these will be converted into that and will be able to get 332 00:28:28 --> 00:28:32 here. So we're going to follow the fait then of these -- 333 00:28:32 --> 00:28:46 -- two glycaraldahyde-3-phosphate 334 00:28:46 --> 00:28:56 molecules. Excuse me. Sorry. OK. Now, at this point the 335 00:28:56 --> 00:29:04 cell is at the aldehyde stage. And it's going to carry out an 336 00:29:04 --> 00:29:08 oxidation reaction. So it's going to take a couple of 337 00:29:08 --> 00:29:13 electrons away from here, and it's going to therefore be 338 00:29:13 --> 00:29:17 carrying out an oxidation. If the molecule is getting oxidized 339 00:29:17 --> 00:29:22 something else has to be reduced. What's going to get reduced is NAD+. 340 00:29:22 --> 00:29:26 We'll need two molecules of that because we've got two molecules of 341 00:29:26 --> 00:29:31 glyceraldehydes phosphate. So we end up with two molecules of 342 00:29:31 --> 00:29:35 NADH plus a hydrogen ion. And this is an energetically 343 00:29:35 --> 00:29:40 favorable reaction. So the cell is able to sneak a 344 00:29:40 --> 00:29:45 phosphate in and make a molecule and still have the reaction go forward, 345 00:29:45 --> 00:29:49 have a molecule that's not very stable, but it can make it because 346 00:29:49 --> 00:30:00 the overall thing goes forward. 347 00:30:00 --> 00:30:04 And there are two of these. And what we have now is 348 00:30:04 --> 00:30:09 1,3-phosphoglycerate. What the cell has basically managed 349 00:30:09 --> 00:30:14 to do is to get two phosphate groups very, very close together. 350 00:30:14 --> 00:30:19 So you're probably getting, hopefully, the concept that if you 351 00:30:19 --> 00:30:24 stick a bunch of negative charges together and hold them together that 352 00:30:24 --> 00:30:29 molecules, if you break one of those bonds are going to go energetically 353 00:30:29 --> 00:30:35 downhill. And you can do work. 354 00:30:35 --> 00:30:41 And the way it does that then is in breaking this bond it uses it to 355 00:30:41 --> 00:30:48 make two molecules of ATP. So you've now got, this is up at 356 00:30:48 --> 00:31:02 the acid level or a carboxyl group. 357 00:31:02 --> 00:31:07 And we've got three phosphoglycerates. 358 00:31:07 --> 00:31:12 So at least from the point of view of this as a plan for making energy, 359 00:31:12 --> 00:31:18 we've now managed to get back those two ATPs we invested. 360 00:31:18 --> 00:31:23 So up until now we've got our, the venture capital money we put in 361 00:31:23 --> 00:31:29 has be recovered, and we've got a couple of molecules 362 00:31:29 --> 00:31:34 of NADH out of it. But what the cell now does is finish, 363 00:31:34 --> 00:31:39 to carry out some more steps that let it make a couple more molecules 364 00:31:39 --> 00:31:44 of ATP. So the first step then is a kind of just a switcheroo between 365 00:31:44 --> 00:31:50 where this hydroxyl is and this phosphate is. So it brings the 366 00:31:50 --> 00:31:55 phosphate up to here. As you might guess this is 367 00:31:55 --> 00:32:04 energetically not much of a change. 368 00:32:04 --> 00:32:10 However, what it does now is it enables the cell to eliminate a 369 00:32:10 --> 00:32:16 molecule of water from here so we get two molecules of water come out 370 00:32:16 --> 00:32:22 because we had all along here we're carrying on two molecules from up 371 00:32:22 --> 00:32:28 there because we have two of these three carbon units. 372 00:32:28 --> 00:32:34 Then the molecule that we then get here -- 373 00:32:34 --> 00:32:44 -- is this molecule which is known 374 00:32:44 --> 00:32:52 as phosphoenolpyruvate. And several of you are saying you 375 00:32:52 --> 00:33:00 don't remember much from chemistry. So this is a keto group, which I 376 00:33:00 --> 00:33:06 know you were introduced to. But it's in an equilibrium with 377 00:33:06 --> 00:33:10 what's termed an enol form where you have an OH here, 378 00:33:10 --> 00:33:15 a double bond like that, and that's known as an enol. 379 00:33:15 --> 00:33:20 Now, this is energetically greatly disfavored. So normally most of the 380 00:33:20 --> 00:33:24 time you find something in a keto form, but occasionally you find it 381 00:33:24 --> 00:33:29 in an enol form. And what's happened here really is 382 00:33:29 --> 00:33:34 the cell has trapped what would like to be a keto at this position in an 383 00:33:34 --> 00:33:38 enol form. Again, this is a very energetically 384 00:33:38 --> 00:33:43 unstable molecule. You've got all these oxygens 385 00:33:43 --> 00:33:48 together, two of these, and so the cell is once again able 386 00:33:48 --> 00:33:53 to take ADP and make two molecules of ATP. And we end up with -- 387 00:33:53 --> 00:34:05 -- two molecules of pyruvate. 388 00:34:05 --> 00:34:13 And extraordinary amount of work. What do we get out of it? Well, 389 00:34:13 --> 00:34:21 we've got a total of four ATPs now plus two NADHs. 390 00:34:21 --> 00:34:29 What did we invest? Two ATPs. So the net yield from 391 00:34:29 --> 00:34:37 this reaction is two ATPs plus two NADHs. 392 00:34:37 --> 00:34:43 So strange as it seems this was one of the first sequences of 393 00:34:43 --> 00:34:49 biochemical steps that were put together in a pathway that we're 394 00:34:49 --> 00:34:55 capable of letting an organism generate molecules of ATP, 395 00:34:55 --> 00:35:01 or sort of form of energy money, but metabolizing something it could 396 00:35:01 --> 00:35:06 find like a molecule of sugar. There are two enzymatic steps. 397 00:35:06 --> 00:35:10 That means that there has to be a separate enzyme for every step in 398 00:35:10 --> 00:35:15 the pathway. Now, the ATPs, as I said, 399 00:35:15 --> 00:35:19 have energy in bundles of about 12 kilocalories per mole. 400 00:35:19 --> 00:35:24 There's a lot of energy here in NADH. And in the next lecture I'm 401 00:35:24 --> 00:35:28 going to talk to you about respiration, which is something 402 00:35:28 --> 00:35:33 you're aware of. You know we respire, 403 00:35:33 --> 00:35:38 but chemically what that we'll see means is basically it's a way of 404 00:35:38 --> 00:35:43 extracting the energy that's in the NADH by transferring electrons to 405 00:35:43 --> 00:35:47 oxygen. And that's a wonderful way to make energy. 406 00:35:47 --> 00:35:52 It's far more efficient than this ancient pathway, 407 00:35:52 --> 00:35:57 but at the time life started there wasn't any oxygen in 408 00:35:57 --> 00:36:02 the environment. And, in fact, it didn't reach, 409 00:36:02 --> 00:36:07 as I said, I think it was something like 20% of today's levels until we 410 00:36:07 --> 00:36:12 were about a half a billion years or so ago in evolution. 411 00:36:12 --> 00:36:18 So organisms had to learn to make energy without oxygen being around. 412 00:36:18 --> 00:36:23 And this was the way that they did it. And it was such a success in 413 00:36:23 --> 00:36:28 evolution that our bodies do, the bacteria in our gut do it and 414 00:36:28 --> 00:36:32 just virtually all living forms. So it's sort of a biochemical fossil 415 00:36:32 --> 00:36:36 but it was so successful it took hold. It's sort of like legs. 416 00:36:36 --> 00:36:40 Those appeared in evolution. And there are all sorts of organisms now 417 00:36:40 --> 00:36:43 that use legs, and they've evolved into wings and 418 00:36:43 --> 00:36:47 everything, but it's all the same basic idea. You could imagine a 419 00:36:47 --> 00:36:51 life form that started with wheels. And maybe if it had been the first 420 00:36:51 --> 00:36:54 thing to do maybe there'd be some sort of organisms with wheels, 421 00:36:54 --> 00:36:58 but legs were such a success at some point that that's what got used and 422 00:36:58 --> 00:37:02 then evolution made various embellishments on it. 423 00:37:02 --> 00:37:07 But there is a problem here. I don't know if anybody can see 424 00:37:07 --> 00:37:12 what it is. If I'm going to be able to use ATP to make energy and I want 425 00:37:12 --> 00:37:18 to keep generating more and more molecules of ATP so I can build 426 00:37:18 --> 00:37:23 stuff, I cannot give those electrons in NADH to oxygen. 427 00:37:23 --> 00:37:29 So what would happen if I just kept running this system? 428 00:37:29 --> 00:37:33 Anybody see what the problem would be? Yeah. You'd run out of NADH, 429 00:37:33 --> 00:37:38 exactly. We need to somehow recycle that NAD so it can take place. 430 00:37:38 --> 00:37:43 If we could give it to oxygen, oxygen as I've told you in 431 00:37:43 --> 00:37:48 respiratory, that would be cool. But organisms didn't have that 432 00:37:48 --> 00:37:52 option. And so they worked out ways of doing things with pyruvate. 433 00:37:52 --> 00:37:57 And this is where you'll see this coming together with what we talked 434 00:37:57 --> 00:38:02 about the other day. So let's take those two molecules of 435 00:38:02 --> 00:38:07 pyruvate. And there are basically two strategies, 436 00:38:07 --> 00:38:12 two major strategies you find in nature. One is to take the two 437 00:38:12 --> 00:38:18 NADHs plus two hydrogen ions and convert it to two molecules of NAD+ 438 00:38:18 --> 00:38:23 so that regenerates it. And what do you get if you do that? 439 00:38:23 --> 00:38:31 You end up with molecule. 440 00:38:31 --> 00:38:35 Two molecules of that which I introduced you to the other day. 441 00:38:35 --> 00:38:40 That's lactic acid or lactate, the organisms that make yogurt carry out. 442 00:38:40 --> 00:38:45 That's what they do. That's why yogurt goes sour. 443 00:38:45 --> 00:38:50 What the organisms are doing when they're making the yogurt that you 444 00:38:50 --> 00:38:55 had for lunch, I love those pictures. 445 00:38:55 --> 00:39:00 I found them on the Web and put them in. 446 00:39:00 --> 00:39:04 What they're doing really is they're getting rid of that NADH so that 447 00:39:04 --> 00:39:08 they can do another cycle and make more energy. Now, 448 00:39:08 --> 00:39:13 I mentioned that this happens to us, too. And this happens in athletic 449 00:39:13 --> 00:39:17 events where you exercise really, really hard, you know, like sprints 450 00:39:17 --> 00:39:22 or speed skating or something like that. Because what happens is 451 00:39:22 --> 00:39:26 you're exercising so hard that you use up the oxygen in your muscles 452 00:39:26 --> 00:39:31 faster than your bloodstream can bring you more. 453 00:39:31 --> 00:39:34 So what you're doing is you're making your muscles go anaerobic. 454 00:39:34 --> 00:39:38 It's like you're going back way, way in evolution when there's was no 455 00:39:38 --> 00:39:41 oxygen around. And your muscles have to keep 456 00:39:41 --> 00:39:45 working, so what they do, since there's no oxygen around, 457 00:39:45 --> 00:39:49 they stick it on pyruvate and you get lactic acid in your muscles. 458 00:39:49 --> 00:39:52 So if you go out for the track team in the spring and you haven't 459 00:39:52 --> 00:39:56 exercised and you run a whole lot of sprints and, God, 460 00:39:56 --> 00:40:00 your muscles are so sore, they're all full of lactic acid. 461 00:40:00 --> 00:40:04 So you don't have to worry about it accumulating in your muscles from 462 00:40:04 --> 00:40:08 eating yogurt, but it does show up in this kind of 463 00:40:08 --> 00:40:12 way. And the other thing then that the way nature has found to recycle 464 00:40:12 --> 00:40:16 these NADHs is to it this way, to carry out a transformation where 465 00:40:16 --> 00:40:20 you get two molecules of carbon dioxide and two molecules 466 00:40:20 --> 00:40:30 of acetaldehyde. 467 00:40:30 --> 00:40:37 And this can be converted to the two molecules of carbon dioxide and two 468 00:40:37 --> 00:40:44 molecules of ethanol. So this is the fermentation that we 469 00:40:44 --> 00:40:51 talked about. And so when those yeasts that we saw growing the other 470 00:40:51 --> 00:40:58 day are busy metabolizing sugar into ethanol and carbon dioxide, 471 00:40:58 --> 00:41:05 the reason they're doing it is they need to get energy to carry out all 472 00:41:05 --> 00:41:13 the biosynthetic reactions that they need to make more biomaterial. 473 00:41:13 --> 00:41:16 But what's happening to the whole system is that you're generating 474 00:41:16 --> 00:41:19 carbon dioxide and making stuff into ethanol. So it doesn't matter if 475 00:41:19 --> 00:41:22 people are making wine or beer or something they're going to distil to 476 00:41:22 --> 00:41:26 make whiskey or brandy or something. It's all the basic thing. The 477 00:41:26 --> 00:41:29 yeast take the sugars, make it into carbon dioxide and to 478 00:41:29 --> 00:41:33 ethanol. But when you're making bread you're 479 00:41:33 --> 00:41:37 only really interested in the carbon dioxide because those little bubbles 480 00:41:37 --> 00:41:41 then expand when you heat it up and that's what makes bread rise. 481 00:41:41 --> 00:41:46 And that was an open fermentation, as you can guess, like in making 482 00:41:46 --> 00:41:50 wine. People like to have a closed system so that, 483 00:41:50 --> 00:41:54 for example, a lactic acid bacteria doesn't get in and turn your whole 484 00:41:54 --> 00:41:59 set of grapes into something that would be sour. Sour wine. 485 00:41:59 --> 00:42:03 So that's where we'll stop today, the most ancient of these 486 00:42:03 --> 00:42:08 energy-producing things. Again, you don't have to memorize 487 00:42:08 --> 00:42:12 all this, but I think, hopefully if you think about, 488 00:42:12 --> 00:42:17 you'll see some really, really important concepts that are critical 489 00:42:17 --> 00:42:21 to understanding how life works. OK? See you on Wednesday. Happy 490 00:42:21 --> 00:42:24 Valentine's Day.