1 00:00:12,930 --> 00:00:15,720 PROFESSOR: OK, well let's move on then, and just talk about 2 00:00:15,720 --> 00:00:18,130 the amino acids. 3 00:00:18,130 --> 00:00:19,380 Amino acids side chains. 4 00:00:23,390 --> 00:00:30,520 And you won't have to memorize these structures. 5 00:00:30,520 --> 00:00:34,210 We will give you a chart if you have a problem. 6 00:00:34,210 --> 00:00:38,680 On the other hand, you need to get very familiar with them, 7 00:00:38,680 --> 00:00:41,640 so they're old friends even if you can't quite remember how 8 00:00:41,640 --> 00:00:44,740 many methylene are in a chain, or something like that. 9 00:00:44,740 --> 00:00:49,980 And you will find that they fall into certain categories. 10 00:00:49,980 --> 00:00:55,100 And I'm just going to try and give you examples of the major 11 00:00:55,100 --> 00:00:56,260 categories. 12 00:00:56,260 --> 00:00:59,420 There are negatively charged side chains. 13 00:01:03,050 --> 00:01:10,560 An example would be amino acids known as aspartate, or 14 00:01:10,560 --> 00:01:15,815 Asp, in which the side chain which corresponds to the R1 or 15 00:01:15,815 --> 00:01:21,840 to the R2 over there, has a methylene group, and then a 16 00:01:21,840 --> 00:01:22,780 carboxyl group. 17 00:01:22,780 --> 00:01:29,300 But at pH sevenish, which is the pH that you find inside a 18 00:01:29,300 --> 00:01:33,340 cell, that carboxyl group would be deprotonated so it 19 00:01:33,340 --> 00:01:36,020 would have a negative charge. 20 00:01:36,020 --> 00:01:40,630 The other negatively charged amino acid is glutamate, which 21 00:01:40,630 --> 00:01:45,380 also, as you'll see has a carboxyl group. 22 00:01:45,380 --> 00:01:52,510 There are positively charged amino acids. 23 00:01:52,510 --> 00:01:58,040 A good one to illustrate this is Lysine, in which there's 24 00:01:58,040 --> 00:02:05,110 four methylene groups, and then an amino 25 00:02:05,110 --> 00:02:06,900 group at the end. 26 00:02:06,900 --> 00:02:14,240 However, again, at pH 7, the kind of pH that you find 27 00:02:14,240 --> 00:02:17,250 inside the cell, that amino group is going to get 28 00:02:17,250 --> 00:02:18,240 protonated. 29 00:02:18,240 --> 00:02:21,400 And so it will have a positive charge on. 30 00:02:21,400 --> 00:02:28,120 If you have a Lysine side chain, and Arginine, and in 31 00:02:28,120 --> 00:02:33,160 most cases, Histidine, are examples of other amino acids 32 00:02:33,160 --> 00:02:37,650 that can have a positively charged group. 33 00:02:37,650 --> 00:02:41,720 And why I'm going through all of this, I hope, will become 34 00:02:41,720 --> 00:02:43,980 apparent in a few minutes. 35 00:02:43,980 --> 00:02:46,590 Some of the side chains are not positive or negative 36 00:02:46,590 --> 00:02:50,210 charged, but rather, they're polar. 37 00:02:50,210 --> 00:02:53,070 And we just talked about polar bonds the last time, where you 38 00:02:53,070 --> 00:02:57,510 have, the more electronegative an atom is, the more greedy it 39 00:02:57,510 --> 00:02:58,680 is for electrons. 40 00:02:58,680 --> 00:03:01,900 And if you recall, if you have a carbon carbon bond or a 41 00:03:01,900 --> 00:03:06,270 hydrogen hydrogen bond that's nonpolar, and the electrons 42 00:03:06,270 --> 00:03:10,290 were distributed equally, the oxygen is greedier for 43 00:03:10,290 --> 00:03:12,170 electrons and so there is a little bit of a negative 44 00:03:12,170 --> 00:03:14,050 charge there and a little bit of positive 45 00:03:14,050 --> 00:03:15,490 charge on the hydrogen. 46 00:03:15,490 --> 00:03:18,560 Well, that same principle applies to 47 00:03:18,560 --> 00:03:20,400 amino acid side chains. 48 00:03:20,400 --> 00:03:25,260 Take, for example, the amino acid Serine, which has a 49 00:03:25,260 --> 00:03:27,230 methylene group and then a hydroxyl group. 50 00:03:27,230 --> 00:03:28,530 Well, here we are. 51 00:03:28,530 --> 00:03:31,390 There's an OH bond, so there will be a little bit of a 52 00:03:31,390 --> 00:03:36,620 negative charge on oxygen with a positive charge on there. 53 00:03:36,620 --> 00:03:41,660 There's another alcohol called threonine, which also has 54 00:03:41,660 --> 00:03:43,230 hydroxyl groups. 55 00:03:43,230 --> 00:03:48,300 And you can make amides of both Aspartate and Glutamate, 56 00:03:48,300 --> 00:03:51,650 to give Asparagine and Glutamine, and both of these 57 00:03:51,650 --> 00:03:53,870 are also polar too. 58 00:03:53,870 --> 00:03:57,380 So what I'm hoping you're beginning to get a sense of, 59 00:03:57,380 --> 00:04:00,150 you can do an awful lot with the properties of a peptide 60 00:04:00,150 --> 00:04:04,500 chain, depending on which amino acids you 61 00:04:04,500 --> 00:04:05,710 dangle off the side. 62 00:04:05,710 --> 00:04:08,900 And ultimately, that order of amino acids is what's going to 63 00:04:08,900 --> 00:04:14,800 be determined by what's in the gene encoding that protein. 64 00:04:14,800 --> 00:04:25,600 Then there are quite a number of amino acids side chains 65 00:04:25,600 --> 00:04:27,990 which are hydrophobic. 66 00:04:27,990 --> 00:04:34,430 They're sort of fearing water, if you will. 67 00:04:34,430 --> 00:04:42,130 The simplest is Alanine, or Ala, which is just a methyl 68 00:04:42,130 --> 00:04:49,770 group, or Leucine, is perhaps, a little more obvious because 69 00:04:49,770 --> 00:04:57,240 that's got this. 70 00:04:57,240 --> 00:04:59,770 And you can see that that's a kind of-- 71 00:05:02,520 --> 00:05:04,540 draw it like that. 72 00:05:04,540 --> 00:05:09,240 This is, very much, a kind of structure that's not going to 73 00:05:09,240 --> 00:05:12,820 want to interact with water. 74 00:05:12,820 --> 00:05:23,060 And then, another example would be Phenylalanine, or 75 00:05:23,060 --> 00:05:30,600 Phe, and that one is a methylene group and, then, a 76 00:05:30,600 --> 00:05:32,830 benzene ring. 77 00:05:32,830 --> 00:05:35,800 So most of you know, have some sense of the properties of 78 00:05:35,800 --> 00:05:40,230 benzene, a very, very organic solvent. 79 00:05:40,230 --> 00:05:43,980 So here you put a side chain like this, it's very much a 80 00:05:43,980 --> 00:05:46,440 residue that doesn't want to interact with water anymore 81 00:05:46,440 --> 00:05:49,920 than Benzene wants to interact with water. 82 00:05:49,920 --> 00:05:52,960 And then there are three special cases. 83 00:05:58,150 --> 00:06:01,070 One of these is Glycine. 84 00:06:06,110 --> 00:06:11,100 In this case, it's just a hydrogen. 85 00:06:11,100 --> 00:06:14,390 One of the consequences of that is that since it's just a 86 00:06:14,390 --> 00:06:18,825 hydrogen, that's going to be a very, very flexible place, if 87 00:06:18,825 --> 00:06:21,270 we have a chain of amino acids and there's a Glycine there, 88 00:06:21,270 --> 00:06:24,320 it's going to be very little of way of constraints 89 00:06:24,320 --> 00:06:27,420 introduced, either by steric constraints or by 90 00:06:27,420 --> 00:06:28,880 interactions. 91 00:06:28,880 --> 00:06:35,230 Another very special one is one called Cystine, Cys. 92 00:06:35,230 --> 00:06:39,490 And it's the same idea as Cyrine, there's an ethylene. 93 00:06:39,490 --> 00:06:46,530 But instead of having an OH, it has an SH group. 94 00:06:46,530 --> 00:06:50,850 And that may not seem to be a great consequence, the sulfur 95 00:06:50,850 --> 00:06:52,620 is a little bit larger. 96 00:06:52,620 --> 00:06:54,530 But sulfurs have-- 97 00:06:54,530 --> 00:06:57,890 a sulfide group here has a sulfhydryl group here has a 98 00:06:57,890 --> 00:07:01,980 very special property, and that is, it can oxidatively 99 00:07:01,980 --> 00:07:04,720 dimerize with another sulfhydryl. 100 00:07:04,720 --> 00:07:09,080 So if you have a side chain, and there's a cystine that has 101 00:07:09,080 --> 00:07:14,320 an SH group, and another, either part of the same chain, 102 00:07:14,320 --> 00:07:17,390 or part of the different polypeptide chain that also 103 00:07:17,390 --> 00:07:22,460 has a cystine, and they're in an oxidizing environment, and 104 00:07:22,460 --> 00:07:28,010 they're also close enough together to interact, they can 105 00:07:28,010 --> 00:07:39,060 form a bond like this, which is known as a disulfide bond, 106 00:07:39,060 --> 00:07:44,050 and it's the only one of the amino acids that's capable of 107 00:07:44,050 --> 00:07:47,860 reaching outside the chain in either hooking to a different 108 00:07:47,860 --> 00:07:51,010 part of the chain or to a completely different protein. 109 00:07:51,010 --> 00:07:54,260 And in fact, proteins that tend to get excreted out into 110 00:07:54,260 --> 00:07:57,860 the media, either by bacteria or other things, often have a 111 00:07:57,860 --> 00:07:59,380 lot of disulfide bonds. 112 00:07:59,380 --> 00:08:02,200 Because when you link the peptide chains together like 113 00:08:02,200 --> 00:08:05,660 that, it tends to make a very tough protein that's hard to 114 00:08:05,660 --> 00:08:09,630 break down and can be very, very robust. 115 00:08:09,630 --> 00:08:18,570 And there is one other special category of, one other special 116 00:08:18,570 --> 00:08:23,550 amino acid that's known as Proline. 117 00:08:23,550 --> 00:08:31,820 You have the alpha carbon atom, the carboxyl group, and 118 00:08:31,820 --> 00:08:34,650 then there's the amino group here. 119 00:08:34,650 --> 00:08:43,770 But this carbon is linked by a little ring with three 120 00:08:43,770 --> 00:08:48,080 methylenes to that amino acid. 121 00:08:48,080 --> 00:08:53,710 Again, this may seem sort of an unnecessary detail or 122 00:08:53,710 --> 00:08:58,400 something, but this is the way life evolved on earth. 123 00:08:58,400 --> 00:09:01,500 This is an amino acid, but because of this ring 124 00:09:01,500 --> 00:09:07,100 structure, this bond is not able to rotate. 125 00:09:07,100 --> 00:09:11,610 So wherever a Proline shows up in the sequence, it puts some 126 00:09:11,610 --> 00:09:16,760 structural constraints on the conformational space that that 127 00:09:16,760 --> 00:09:19,760 chain is capable of getting itself into. 128 00:09:19,760 --> 00:09:26,760 So when we study protein structure, this is at the 129 00:09:26,760 --> 00:09:31,630 heart of how proteins work, we'll spend quite a bit of 130 00:09:31,630 --> 00:09:34,815 time in the ensuing lectures talking about the central 131 00:09:34,815 --> 00:09:41,090 dogma and the idea that the linear order of the amino 132 00:09:41,090 --> 00:09:45,980 acids, in a protein, is determined by the sequence of 133 00:09:45,980 --> 00:09:48,440 the DNA and how that's encoded. 134 00:09:48,440 --> 00:09:52,610 But at the end, what you end up with is a linear sequence 135 00:09:52,610 --> 00:09:57,120 of amino acids, all joined together by peptide bonds. 136 00:09:57,120 --> 00:09:59,590 And there's an incredible number of 137 00:09:59,590 --> 00:10:01,660 conformations possible. 138 00:10:01,660 --> 00:10:04,650 These things could go all over the place in all kinds of 139 00:10:04,650 --> 00:10:05,330 different ways. 140 00:10:05,330 --> 00:10:09,780 Yet, only one form, in general, is the biologically 141 00:10:09,780 --> 00:10:13,256 active conformation or maybe there's a couple of them and 142 00:10:13,256 --> 00:10:16,740 it switches back and forth as part of a machine action, or 143 00:10:16,740 --> 00:10:18,330 are part of what it does. 144 00:10:18,330 --> 00:10:22,000 But by and large, for every protein there'll be one, or 145 00:10:22,000 --> 00:10:24,030 just a couple of conformations. 146 00:10:24,030 --> 00:10:29,140 And so understanding proteins, what many, many people are 147 00:10:29,140 --> 00:10:31,850 interested in is trying to understand how you can get 148 00:10:31,850 --> 00:10:35,010 from that linear sequence and determine the three 149 00:10:35,010 --> 00:10:37,010 dimensional structure. 150 00:10:37,010 --> 00:10:42,240 There are techniques, X-ray crystallography and NMR 151 00:10:42,240 --> 00:10:46,250 techniques now, which enable us to get the structures, 152 00:10:46,250 --> 00:10:47,880 solve the structures of proteins. 153 00:10:47,880 --> 00:10:50,750 In fact, there's the structures of tens of 154 00:10:50,750 --> 00:10:52,960 thousands of them are in a database 155 00:10:52,960 --> 00:10:54,900 called the Protein Database. 156 00:10:54,900 --> 00:10:57,030 And we're going to be talking about a little protein viewer 157 00:10:57,030 --> 00:11:00,020 that you'll be using that, in fact, once you've used it in 158 00:11:00,020 --> 00:11:02,780 your problem set, you could go open the structure of any 159 00:11:02,780 --> 00:11:07,570 protein whose structure has ever has been solved, if you 160 00:11:07,570 --> 00:11:09,000 want to do it. 161 00:11:09,000 --> 00:11:14,820 But what we haven't yet figured out is a reliable way 162 00:11:14,820 --> 00:11:18,590 of saying, here is a protein that consists of a particular 163 00:11:18,590 --> 00:11:21,400 chain of amino acids. 164 00:11:21,400 --> 00:11:24,550 I'm going to predict its three dimensional shape. 165 00:11:24,550 --> 00:11:28,430 So we understand parts of it, but there's 166 00:11:28,430 --> 00:11:29,830 parts we don't know. 167 00:11:29,830 --> 00:11:33,120 And I'm going to take you through the first part of 168 00:11:33,120 --> 00:11:35,900 understanding protein structure. 169 00:11:35,900 --> 00:11:39,760 And before we do that, I want to just talk about the levels 170 00:11:39,760 --> 00:11:47,450 of protein structure and the terms that are used to 171 00:11:47,450 --> 00:11:48,700 describe these. 172 00:11:53,500 --> 00:11:55,800 When people talk about the primary structure of a 173 00:11:55,800 --> 00:12:09,490 protein, what they're talking about is the sequence of amino 174 00:12:09,490 --> 00:12:13,630 acids, and it's possible I'll abbreviate those as AA, at 175 00:12:13,630 --> 00:12:15,260 some point without thinking about it. 176 00:12:15,260 --> 00:12:19,060 So just in case I do, that's a fairly commonly used 177 00:12:19,060 --> 00:12:20,850 abbreviation for amino acids. 178 00:12:20,850 --> 00:12:24,580 So that simply, Phenylalanine joined to a Proline joined to 179 00:12:24,580 --> 00:12:27,490 a Glycine joined to two Cystines joined to something 180 00:12:27,490 --> 00:12:33,190 else, but that's not terribly useful in terms of telling 181 00:12:33,190 --> 00:12:35,170 what the protein does. 182 00:12:35,170 --> 00:12:38,780 Then there's secondary structure. 183 00:12:41,970 --> 00:12:50,350 These are regions of local folding and they're driven by, 184 00:12:50,350 --> 00:12:51,120 guess what? 185 00:12:51,120 --> 00:12:52,960 Hydrogen bonds. 186 00:12:52,960 --> 00:12:55,710 And we'll talk about how that goes in just a moment. 187 00:13:01,880 --> 00:13:05,030 Then the term, tertiary structure, is the term used to 188 00:13:05,030 --> 00:13:09,010 describe the entirety of the folded protein. 189 00:13:09,010 --> 00:13:12,250 If I went in and determined the structure of a protein 190 00:13:12,250 --> 00:13:14,950 using x-ray crystallography, this is what I would see. 191 00:13:14,950 --> 00:13:16,490 It would be the tertiary structure. 192 00:13:16,490 --> 00:13:20,810 And there are other forces that we haven't discussed yet 193 00:13:20,810 --> 00:13:25,540 that contribute to that tertiary structure. 194 00:13:25,540 --> 00:13:32,070 And then, a quaternary structure means that there's 195 00:13:32,070 --> 00:13:42,650 more than one polypeptide chain. 196 00:13:42,650 --> 00:13:45,940 And it could be as simple as an enzyme that's got two 197 00:13:45,940 --> 00:13:48,080 subunits and you've got to have them both there in order 198 00:13:48,080 --> 00:13:50,870 for it to work, or as I think you're beginning to probably 199 00:13:50,870 --> 00:13:53,950 get the sense from my use of the term protein machines, 200 00:13:53,950 --> 00:13:58,590 there are structures that have multiple interacting proteins 201 00:13:58,590 --> 00:14:01,880 and have complexities that rival some of the mechanical 202 00:14:01,880 --> 00:14:05,740 things that we build ourselves. 203 00:14:05,740 --> 00:14:14,030 So the interesting story, a little, bit how the insights 204 00:14:14,030 --> 00:14:21,110 into secondary structure were first arrived. 205 00:14:21,110 --> 00:14:24,970 Some of you may have heard the term Linus Pauling. 206 00:14:29,680 --> 00:14:35,160 He was at Cal Tech, a Nobel Prize winner, very, very 207 00:14:35,160 --> 00:14:39,260 influential scientist, in a variety of ways. 208 00:14:39,260 --> 00:14:43,950 The key insight that Linus Pauling had 209 00:14:43,950 --> 00:14:48,180 came in the late 1940s. 210 00:14:48,180 --> 00:14:52,020 People had been doing X-ray crystallography on minerals 211 00:14:52,020 --> 00:14:55,270 and things like that, and the basic idea was you had a 212 00:14:55,270 --> 00:14:59,490 crystal of some type, you bounced electrons off, you got 213 00:14:59,490 --> 00:15:00,530 a diffraction pattern. 214 00:15:00,530 --> 00:15:03,660 Then you could work backwards and figure out the structure 215 00:15:03,660 --> 00:15:06,300 that was generating the diffraction pattern. 216 00:15:06,300 --> 00:15:09,140 And that had, then, been extended to proteins. 217 00:15:09,140 --> 00:15:11,760 And it was discovered there were certain proteins that 218 00:15:11,760 --> 00:15:15,210 would crystallize and you could bounce electrons off and 219 00:15:15,210 --> 00:15:17,000 get a diffraction pattern. 220 00:15:17,000 --> 00:15:21,860 And at least a category of these proteins, and analysis 221 00:15:21,860 --> 00:15:26,630 of the diffraction pattern suggested it was some kind of 222 00:15:26,630 --> 00:15:33,620 helix, and there was a repeating element of about 5.4 223 00:15:33,620 --> 00:15:35,680 angstroms, roughly. 224 00:15:35,680 --> 00:15:38,400 And so, Linus Pauling was very 225 00:15:38,400 --> 00:15:39,910 interested in protein structure. 226 00:15:39,910 --> 00:15:47,560 And I think it was in late 1948, he was visiting England 227 00:15:47,560 --> 00:15:50,890 and he caught the flu, just like some of 228 00:15:50,890 --> 00:15:52,180 you have been catching. 229 00:15:52,180 --> 00:15:54,663 And he spent a few days reading detective stories and 230 00:15:54,663 --> 00:15:56,120 then he got bored. 231 00:15:56,120 --> 00:15:59,350 And so he tried to take on this-- 232 00:15:59,350 --> 00:16:00,770 think about this problem. 233 00:16:00,770 --> 00:16:02,340 While he was lying in bed. 234 00:16:02,340 --> 00:16:04,710 And he made a simplifying assumption. 235 00:16:04,710 --> 00:16:09,720 He said let's just forget about all the side chains. 236 00:16:09,720 --> 00:16:12,010 Maybe they don't really matter in terms 237 00:16:12,010 --> 00:16:13,600 of this basic property. 238 00:16:13,600 --> 00:16:20,700 Maybe it's determined by the backbone of the peptide chain. 239 00:16:20,700 --> 00:16:25,250 So he took a strip of paper, started pleating it. 240 00:16:25,250 --> 00:16:29,760 And he was a very good chemist, so he knew about this 241 00:16:29,760 --> 00:16:31,250 partial double [? blind ?] 242 00:16:31,250 --> 00:16:36,260 character of the peptide bond and the constraints that it 243 00:16:36,260 --> 00:16:40,950 put on the structures that the protein could take. 244 00:16:40,950 --> 00:16:45,630 And in doing this, he realized that if he folded the thing 245 00:16:45,630 --> 00:16:50,350 into a helix, kind of like this, into a right handed 246 00:16:50,350 --> 00:16:57,820 helix, that things worked out such that the carboxyl group 247 00:16:57,820 --> 00:17:03,960 in the backbone was just beautifully positioned to form 248 00:17:03,960 --> 00:17:08,724 hydrogen bond that was on one of the nitrogens. 249 00:17:08,724 --> 00:17:10,885 He called this an alpha helix. 250 00:17:13,910 --> 00:17:21,369 There were 3.7 amino acids per turn. 251 00:17:21,369 --> 00:17:29,750 And the distance from here to here was 5.4 angstroms. 252 00:17:29,750 --> 00:17:33,900 And if we just-- 253 00:17:33,900 --> 00:17:35,340 sorry, I meant to put that up 254 00:17:35,340 --> 00:17:37,180 earlier, or did I go backwards? 255 00:17:37,180 --> 00:17:38,740 Anyway, there are all the amino acids and 256 00:17:38,740 --> 00:17:40,880 they're in your book. 257 00:17:40,880 --> 00:17:47,830 Here is just the backbone of an alpha helix. 258 00:17:47,830 --> 00:17:53,820 And the orangey yellow colored bonds are the hydrogen bonds. 259 00:17:53,820 --> 00:17:55,860 And I hope you can see how the spiral goes. 260 00:17:55,860 --> 00:17:57,900 And you can also see, as it goes by, you can look right 261 00:17:57,900 --> 00:18:00,800 down the hole down the middle of the helix. 262 00:18:00,800 --> 00:18:04,260 So let's put on some amino acids now. 263 00:18:04,260 --> 00:18:07,920 And again, you'll see, as it goes by, you can look right 264 00:18:07,920 --> 00:18:08,700 down the helix. 265 00:18:08,700 --> 00:18:13,750 But you see how the amino acids stick out onto the side. 266 00:18:13,750 --> 00:18:18,590 And if you look, for example, there is a Phenylalanine and a 267 00:18:18,590 --> 00:18:23,240 Tyrosine, they're aromatic groups that are very 268 00:18:23,240 --> 00:18:24,620 hydrophobic. 269 00:18:24,620 --> 00:18:29,490 And up here there's a Lysine, so that's this side of the 270 00:18:29,490 --> 00:18:31,370 helix is charged. 271 00:18:31,370 --> 00:18:32,380 That's a glutamate. 272 00:18:32,380 --> 00:18:34,270 So there's a couple of charged amino acids on 273 00:18:34,270 --> 00:18:35,620 this side of the helix. 274 00:18:35,620 --> 00:18:39,530 Up here we've got a water hating part and somehow this 275 00:18:39,530 --> 00:18:44,946 is, I think, reminding me that I left something out. 276 00:18:51,140 --> 00:18:52,870 Let me just fix that up while I'm at it. 277 00:18:52,870 --> 00:19:01,340 The other hydrophobic amino acids, I forgot to say those 278 00:19:01,340 --> 00:19:11,450 are Isoleucine, Valine, Methionine, Tyrosine, and 279 00:19:11,450 --> 00:19:12,380 Tryptophan. 280 00:19:12,380 --> 00:19:15,060 Those are in your book. 281 00:19:15,060 --> 00:19:18,320 Those are other examples of hydrophobic amino acids. 282 00:19:18,320 --> 00:19:23,660 But I think, even in this little example of an alpha 283 00:19:23,660 --> 00:19:29,810 helix, you can see, depending on which amino acid was where, 284 00:19:29,810 --> 00:19:34,610 along that little region of alpha helix, it would very 285 00:19:34,610 --> 00:19:37,700 much influence what that part of the protein 286 00:19:37,700 --> 00:19:39,790 was capable of doing. 287 00:19:39,790 --> 00:19:46,150 There's a second region of secondary structure that's 288 00:19:46,150 --> 00:19:47,070 very important. 289 00:19:47,070 --> 00:19:51,080 It's called a beta sheet. 290 00:19:51,080 --> 00:19:55,520 The one I'm showing you is an example of an anti-parallel 291 00:19:55,520 --> 00:19:57,130 beta sheet, although you can have parallel 292 00:19:57,130 --> 00:19:59,000 beta sheets as well. 293 00:19:59,000 --> 00:20:04,010 But what I've done here is to take one strand of a 294 00:20:04,010 --> 00:20:06,560 polypeptide chain and I've written it out this way. 295 00:20:06,560 --> 00:20:10,590 And then I've taken a second-- 296 00:20:10,590 --> 00:20:12,132 what has happened? 297 00:20:12,132 --> 00:20:13,382 Oops. 298 00:20:15,510 --> 00:20:16,680 That's interesting. 299 00:20:16,680 --> 00:20:18,040 The stool just broke. 300 00:20:18,040 --> 00:20:20,070 OK. 301 00:20:20,070 --> 00:20:23,520 Fortunately, I noticed. 302 00:20:23,520 --> 00:20:28,810 So what we have here is that the possibility for hydrogen 303 00:20:28,810 --> 00:20:33,760 bonding between this hydrogen of amino group and this 304 00:20:33,760 --> 00:20:36,720 oxygen, again, so we can get hydrogen 305 00:20:36,720 --> 00:20:42,140 bonds formed like this. 306 00:20:42,140 --> 00:20:46,490 And this makes what are called a beta sheet structure. 307 00:20:46,490 --> 00:20:48,400 And they can build up as well. 308 00:20:48,400 --> 00:20:53,390 This next one gives-- you can see how you can put one beta 309 00:20:53,390 --> 00:20:56,210 sheet on top of another. 310 00:20:56,210 --> 00:21:02,310 And both of these are two major types of secondary 311 00:21:02,310 --> 00:21:09,180 structure and the way an alpha helix is represented is 312 00:21:09,180 --> 00:21:10,430 something like this. 313 00:21:10,430 --> 00:21:14,890 This would be an alpha helix. 314 00:21:14,890 --> 00:21:22,530 And a beta sheet is written as an arrow like that. 315 00:21:22,530 --> 00:21:27,680 And so most proteins tend to have structures that consist 316 00:21:27,680 --> 00:21:32,340 of, for example, an alpha helix, some kind of turn, 317 00:21:32,340 --> 00:21:39,970 maybe a beta sheet, another turn, another beta sheet. 318 00:21:39,970 --> 00:21:42,940 Now maybe a turn, maybe an alpha helix going this way, 319 00:21:42,940 --> 00:21:47,820 some combination of regions of secondary structure. 320 00:21:47,820 --> 00:21:54,880 And I've got just a couple of examples of that. 321 00:21:54,880 --> 00:22:00,670 Here you can see a domain of a protein with some beta sheets 322 00:22:00,670 --> 00:22:05,740 in purple, alpha helix in green. 323 00:22:05,740 --> 00:22:10,550 Where that's a piece of a protein coming from what's 324 00:22:10,550 --> 00:22:13,290 known as the bracket one gene. 325 00:22:13,290 --> 00:22:15,180 Some of you may be aware there's a familial 326 00:22:15,180 --> 00:22:22,050 susceptibility to breast cancer that was discovered. 327 00:22:22,050 --> 00:22:24,090 It's a complex protein. 328 00:22:24,090 --> 00:22:26,830 Part of it, and a very, very important part of it, is this 329 00:22:26,830 --> 00:22:28,660 piece known as the BRCT domain. 330 00:22:28,660 --> 00:22:32,840 It's the bracket one c terminal domain, consists of 331 00:22:32,840 --> 00:22:36,020 beta sheets alpha helix. 332 00:22:36,020 --> 00:22:38,090 Here's a protein I've already shown you the structure of, 333 00:22:38,090 --> 00:22:41,430 but maybe you recognize now, that green fluorescent protein 334 00:22:41,430 --> 00:22:44,810 is mostly beta sheets. 335 00:22:44,810 --> 00:22:46,690 It's the only beta sheets is going down here. 336 00:22:46,690 --> 00:22:49,350 There's a little bit of an alpha helix up there. 337 00:22:49,350 --> 00:22:52,840 And there's a bit of one over here? 338 00:22:52,840 --> 00:22:58,760 Here's an example of a protein that's mostly alpha helix. 339 00:22:58,760 --> 00:22:59,600 What's this one do? 340 00:22:59,600 --> 00:23:02,650 This is a protein we'll talk about when we talk about DNA 341 00:23:02,650 --> 00:23:03,750 replication. 342 00:23:03,750 --> 00:23:07,610 It's involved in recognizing mismatches in DNA, for 343 00:23:07,610 --> 00:23:11,790 example, the G improperly got paired with the T during DNA 344 00:23:11,790 --> 00:23:13,200 replication. 345 00:23:13,200 --> 00:23:16,050 There's a system comes along and repairs those mismatches 346 00:23:16,050 --> 00:23:19,490 gives you another several thousandfold increase in 347 00:23:19,490 --> 00:23:22,630 fidelity, and if you mutate it in that kind of protein in a 348 00:23:22,630 --> 00:23:23,790 human, you have a familial 349 00:23:23,790 --> 00:23:25,630 susceptibility to colon cancer. 350 00:23:25,630 --> 00:23:31,670 So it doesn't matter what their function is, when you 351 00:23:31,670 --> 00:23:34,040 get down to regions of secondary structure, you'll 352 00:23:34,040 --> 00:23:37,540 see these recurring things -- alpha helices, beta sheets. 353 00:23:37,540 --> 00:23:40,140 And if you understand their properties, you begin to 354 00:23:40,140 --> 00:23:44,480 understand some of the basic structure of forces that are 355 00:23:44,480 --> 00:23:47,550 giving the proteins their properties. 356 00:23:47,550 --> 00:23:50,020 That's an enzyme called chymotrypsin. 357 00:23:50,020 --> 00:23:54,180 What it does, it's an enzyme that catalyzes the cleavage of 358 00:23:54,180 --> 00:23:57,050 peptide bonds in other proteins. 359 00:23:57,050 --> 00:23:58,740 But there it is. 360 00:23:58,740 --> 00:24:00,950 Got a lot of alpha helices, beta sheets, turns. 361 00:24:00,950 --> 00:24:03,340 You can go on and on. 362 00:24:03,340 --> 00:24:06,640 I just said, one more up there. 363 00:24:06,640 --> 00:24:08,310 That's the Ras protein. 364 00:24:08,310 --> 00:24:09,310 That's an oncogene. 365 00:24:09,310 --> 00:24:12,890 Mutate that in a particular way, you have a 366 00:24:12,890 --> 00:24:14,980 susceptibility to cancer. 367 00:24:14,980 --> 00:24:17,480 But it doesn't matter, when you get down to the protein 368 00:24:17,480 --> 00:24:22,040 structure, most proteins have beta sheets, alpha helices. 369 00:24:22,040 --> 00:24:24,770 OK. 370 00:24:24,770 --> 00:24:26,240 Go back to that one in a second. 371 00:24:26,240 --> 00:24:31,040 So we have to understand the rest of the 372 00:24:31,040 --> 00:24:33,650 structure of proteins. 373 00:24:33,650 --> 00:24:37,880 We have to be able to talk about the other forces that 374 00:24:37,880 --> 00:24:42,790 are important for making a protein. 375 00:24:42,790 --> 00:24:49,670 And the third force is pretty simple. 376 00:24:49,670 --> 00:24:54,480 That's an ionic bond, and it's just this simple, that if you 377 00:24:54,480 --> 00:25:01,815 had a peptide chain that had, for example, an Aspartate with 378 00:25:01,815 --> 00:25:08,420 a negatively charged amino acid on it, and we had, say, a 379 00:25:08,420 --> 00:25:16,160 Lysine, four Methylenes, and the NH3 plus that was attached 380 00:25:16,160 --> 00:25:20,860 somewhere else on that polypeptide chain, then we can 381 00:25:20,860 --> 00:25:24,640 get an ionic bond, because of the attraction between the 382 00:25:24,640 --> 00:25:28,800 negative charge on here and a positive charge on that. 383 00:25:28,800 --> 00:25:34,380 So that is one of the things that then a force that can 384 00:25:34,380 --> 00:25:37,000 influence the structure of proteins. 385 00:25:37,000 --> 00:25:42,200 The next one is a harder one to understand. 386 00:25:42,200 --> 00:25:47,540 It's known as the van der Waals interaction. 387 00:25:47,540 --> 00:25:50,400 And here's basically what's going on is that a non-polar 388 00:25:50,400 --> 00:26:01,610 bond can have a transient polarity. 389 00:26:04,250 --> 00:26:05,500 Sorry about this. 390 00:26:09,470 --> 00:26:26,000 And it can induce polarity in a nearby non-polar bond, and 391 00:26:26,000 --> 00:26:27,250 that can then give an attraction. 392 00:26:32,900 --> 00:26:43,150 These things need to be very close together, about 0.2 to 393 00:26:43,150 --> 00:26:50,500 0.4 nanometers apart, the two non-polar bonds, in order for 394 00:26:50,500 --> 00:26:51,950 this to happen. 395 00:26:51,950 --> 00:26:57,080 Does anybody remember the length of the covalent bond, 396 00:26:57,080 --> 00:27:01,240 the 0.15 to 0.2 nanometers, so within one or 397 00:27:01,240 --> 00:27:04,090 two covalent bonds. 398 00:27:04,090 --> 00:27:06,060 They have to be that close. 399 00:27:06,060 --> 00:27:13,160 Their strength is about one third, one quarter to one 400 00:27:13,160 --> 00:27:16,670 third, to that of the hydrogen bond. 401 00:27:16,670 --> 00:27:18,880 And if you remember, the hydrogen bond was about one 402 00:27:18,880 --> 00:27:26,550 twentieth of the force of the strength of the hydrogen bond. 403 00:27:26,550 --> 00:27:29,700 But nevertheless, you can have a lot of them because, if you 404 00:27:29,700 --> 00:27:32,930 have an extended surface of a protein that's very close 405 00:27:32,930 --> 00:27:36,650 together, you can get a lot of these van der Waal 406 00:27:36,650 --> 00:27:37,880 interactions. 407 00:27:37,880 --> 00:27:40,230 And I'd always found this a somewhat 408 00:27:40,230 --> 00:27:42,490 esoteric kind of force. 409 00:27:42,490 --> 00:27:48,380 But in fact, we're familiar with these because that's how 410 00:27:48,380 --> 00:27:52,410 a lizard manages to go up a surface. 411 00:27:52,410 --> 00:27:55,780 It uses van der Waals interactions. 412 00:27:55,780 --> 00:27:59,470 And as I'll show you in a minute, the trick is it's got 413 00:27:59,470 --> 00:28:04,120 little hairs on the bottom of its feet that have about a 414 00:28:04,120 --> 00:28:08,640 billion split ends and they're so tiny they're able to make 415 00:28:08,640 --> 00:28:11,650 van der Waals interactions with the surface. 416 00:28:11,650 --> 00:28:15,180 In a minute, I think there's a shot from underneath. 417 00:28:15,180 --> 00:28:19,170 I got these movies from Robert Full at Berkeley, 418 00:28:19,170 --> 00:28:20,530 who's worked on these. 419 00:28:20,530 --> 00:28:24,210 You could see the lizard kind of peeling its foot off. 420 00:28:24,210 --> 00:28:28,302 And here they've made a little robot that can work by van der 421 00:28:28,302 --> 00:28:30,750 Waals forces and it will climb up the wall 422 00:28:30,750 --> 00:28:32,410 kind of like a lizard. 423 00:28:32,410 --> 00:28:35,090 And here's what's going on at the molecular level. 424 00:28:35,090 --> 00:28:39,500 These are the toe pads on a lizard like this. 425 00:28:39,500 --> 00:28:43,390 We're going to be just zooming in now. 426 00:28:43,390 --> 00:28:46,750 And you'll see they're covered with hairs, and you keep 427 00:28:46,750 --> 00:28:49,425 zooming in more, there's more hairs. 428 00:28:49,425 --> 00:28:53,140 And we keep zooming in more, get down to a single hair, 429 00:28:53,140 --> 00:28:55,500 there is a 30,000 fold magnification. 430 00:28:55,500 --> 00:28:59,240 There's 115,000 magnification. 431 00:28:59,240 --> 00:29:02,660 And in the end, a gecko, such as you've got here, has a 432 00:29:02,660 --> 00:29:06,550 billion 0.2 micron tips. 433 00:29:06,550 --> 00:29:12,540 And just to compare it to a human hair, over on the edge, 434 00:29:12,540 --> 00:29:17,510 then you can see what the gecko hair is like. 435 00:29:17,510 --> 00:29:20,182 It's a very, very fine hair and it's able to use van der 436 00:29:20,182 --> 00:29:23,380 Waal interactions to stick to the surface. 437 00:29:23,380 --> 00:29:27,940 Bob actually made a Band-Aid by collecting this little 438 00:29:27,940 --> 00:29:31,180 hairs out of the thing. 439 00:29:31,180 --> 00:29:35,440 And he made a little joke of putting it in a Band-Aid box. 440 00:29:35,440 --> 00:29:36,690 But this is interesting because it 441 00:29:36,690 --> 00:29:37,800 isn't affected by water. 442 00:29:37,800 --> 00:29:39,000 You can peel it off. 443 00:29:39,000 --> 00:29:40,230 You can put it back down. 444 00:29:40,230 --> 00:29:43,000 And he thinks there were commercial possibilities for 445 00:29:43,000 --> 00:29:45,070 using van der Waals interaction. 446 00:29:45,070 --> 00:29:49,100 So, OK, I think we have one more force to go, but I think 447 00:29:49,100 --> 00:29:52,340 we will call it a day right here.