1 00:00:16,750 --> 00:00:17,720 Good morning, class. 2 00:00:17,720 --> 00:00:18,850 Nice to see you again. 3 00:00:18,850 --> 00:00:22,590 Hope you had a great weekend. 4 00:00:22,590 --> 00:00:25,960 If you didn't, it wasn't because of the weather. 5 00:00:25,960 --> 00:00:29,620 So here I am, once again a member of the walking wounded, 6 00:00:29,620 --> 00:00:32,040 and we're talking about carbohydrates today, 7 00:00:32,040 --> 00:00:33,910 as you may recall, or at least we 8 00:00:33,910 --> 00:00:37,840 were at the end of our discussion last time. 9 00:00:37,840 --> 00:00:42,490 And, we made the point that these multiple hydroxyl groups 10 00:00:42,490 --> 00:00:44,490 on the carbohydrates, on the one hand, 11 00:00:44,490 --> 00:00:50,920 determine the identity of various kinds of sugars. 12 00:00:50,920 --> 00:00:53,570 Just the orientation, the three-dimensional orientation 13 00:00:53,570 --> 00:00:57,720 of them, for one thing, and for another 14 00:00:57,720 --> 00:01:01,070 that these multiple hydroxyl groups represent 15 00:01:01,070 --> 00:01:03,810 the opportunity for forming covalent bonds 16 00:01:03,810 --> 00:01:06,280 with other monosaccharides as is indicated here 17 00:01:06,280 --> 00:01:10,710 in these disaccharides, or covalent bonds end-to-end 18 00:01:10,710 --> 00:01:14,450 to create large molecules, which will increasingly 19 00:01:14,450 --> 00:01:17,350 be the theme of our discussion today, i.e. 20 00:01:17,350 --> 00:01:19,130 when I talk about large molecules, 21 00:01:19,130 --> 00:01:23,450 we just used the phrase generically, macromolecules, 22 00:01:23,450 --> 00:01:29,530 since in principle these end to end joinings of molecules which 23 00:01:29,530 --> 00:01:33,770 involve the dehydration and the formation 24 00:01:33,770 --> 00:01:35,960 of these covalent bonds like right here 25 00:01:35,960 --> 00:01:39,030 can create molecules that are hundreds, indeed even 26 00:01:39,030 --> 00:01:41,769 thousands of subunits long. 27 00:01:41,769 --> 00:01:43,560 So, here, if we're talking about a polymer, 28 00:01:43,560 --> 00:01:46,750 we refer to each one of these subunits 29 00:01:46,750 --> 00:01:49,050 of the polymer as being a monomer, 30 00:01:49,050 --> 00:01:53,090 and the aggregate as a whole as being a polymer. 31 00:01:53,090 --> 00:01:57,510 Here, we touched upon the fact toward the end of last lecture, 32 00:01:57,510 --> 00:02:02,530 in fact, at the very end, that one can cross-link 33 00:02:02,530 --> 00:02:05,700 these long, linear chains of carbohydrates. 34 00:02:05,700 --> 00:02:07,440 And here, we see the fact that glycogen, 35 00:02:07,440 --> 00:02:11,420 which is a form of glucose that is stored in our liver 36 00:02:11,420 --> 00:02:13,830 largely, and to a small extent in the muscles 37 00:02:13,830 --> 00:02:17,470 actually is cross-branched. 38 00:02:17,470 --> 00:02:21,450 So, if one draws on a much smaller scale a glycogen 39 00:02:21,450 --> 00:02:25,322 molecule, one might draw a picture that looks like this. 40 00:02:25,322 --> 00:02:27,030 And it looks almost like a Christmas tree 41 00:02:27,030 --> 00:02:28,900 with multiple branches. 42 00:02:28,900 --> 00:02:30,790 And, the purpose of this is actually 43 00:02:30,790 --> 00:02:34,180 to sequester the glucose, to store the glucose 44 00:02:34,180 --> 00:02:38,030 into metabolically inactive form until the time comes 45 00:02:38,030 --> 00:02:40,020 that the organism needs, once again, 46 00:02:40,020 --> 00:02:42,250 the energy that is stored in the glucose 47 00:02:42,250 --> 00:02:45,530 upon which occasion these bonds are rapidly broken down 48 00:02:45,530 --> 00:02:47,610 and the glucose is mobilized and put 49 00:02:47,610 --> 00:02:50,560 into the circulation for eventual disposition 50 00:02:50,560 --> 00:02:53,750 and use in certain, specific tissues. 51 00:02:53,750 --> 00:02:57,820 While it's encumbered in these high molecular weight polymers, 52 00:02:57,820 --> 00:03:00,900 the glucose is essentially metabolically inactive. 53 00:03:00,900 --> 00:03:03,520 The body doesn't realize it's there. 54 00:03:03,520 --> 00:03:06,890 And, we can, as a consequence store large amounts of energy 55 00:03:06,890 --> 00:03:08,770 in these glycogen molecules. 56 00:03:08,770 --> 00:03:12,030 And it can be stored there indefinitely. 57 00:03:12,030 --> 00:03:18,000 Now, the fact is this idea of end-to-end polymerization 58 00:03:18,000 --> 00:03:20,520 that I just mentioned can be extended 59 00:03:20,520 --> 00:03:24,760 to other macromolecules which also become linked end-to-end 60 00:03:24,760 --> 00:03:28,810 in specific kinds of polymers. 61 00:03:28,810 --> 00:03:31,660 And here, we are moving, now, into the notion 62 00:03:31,660 --> 00:03:33,810 of talking about amino acids. 63 00:03:33,810 --> 00:03:36,180 And, we're talking about proteins. 64 00:03:36,180 --> 00:03:38,790 If we look at an amino acid, what we see 65 00:03:38,790 --> 00:03:42,630 is it has an important structure like this. 66 00:03:42,630 --> 00:03:45,270 Here's a central carbon ? 67 00:03:45,270 --> 00:03:48,380 for, in principle, the distinct side 68 00:03:48,380 --> 00:03:51,690 chains where R represents some side chain that 69 00:03:51,690 --> 00:03:54,260 can be any one of, as we'll see shortly, 70 00:03:54,260 --> 00:03:57,290 20 distinct identities. 71 00:03:57,290 --> 00:04:01,090 But, all the amino acids share in common the property 72 00:04:01,090 --> 00:04:03,320 that they have this overall structure. 73 00:04:03,320 --> 00:04:08,110 And, as you may recall from our discussions of last week, 74 00:04:08,110 --> 00:04:12,100 at neutral pH, an amino acid of this sort, whatever 75 00:04:12,100 --> 00:04:14,650 R is, wouldn't look like this at all 76 00:04:14,650 --> 00:04:17,930 because the amine group would attract an extra proton, 77 00:04:17,930 --> 00:04:20,279 causing it to become positively charged. 78 00:04:20,279 --> 00:04:23,730 And, the carboxyl group would release a proton, 79 00:04:23,730 --> 00:04:26,370 causing it to become negatively charged. 80 00:04:26,370 --> 00:04:28,750 And, as you might deduce from this, 81 00:04:28,750 --> 00:04:32,360 at very low pHn due to the greatly increased concentration 82 00:04:32,360 --> 00:04:34,820 of protons, free protons in the solution, 83 00:04:34,820 --> 00:04:37,810 the equilibrium would be driven more in favor 84 00:04:37,810 --> 00:04:41,230 of reattaching a proton to the carboxyl group 85 00:04:41,230 --> 00:04:44,630 just because there are so many of these protons around. 86 00:04:44,630 --> 00:04:49,490 Conversely, at very high pH, where the hydroxyl ions are 87 00:04:49,490 --> 00:04:53,880 in predominance, they obviously tend to scavenge protons, 88 00:04:53,880 --> 00:04:58,220 reducing the level of protons to very low levels in the water. 89 00:04:58,220 --> 00:05:00,250 And, under very high pH conditions, 90 00:05:00,250 --> 00:05:02,770 this proton would be released and pulled away 91 00:05:02,770 --> 00:05:06,620 by the hydroxyl ions causing this amine group once again 92 00:05:06,620 --> 00:05:11,040 to return to its negative charge state. 93 00:05:11,040 --> 00:05:15,890 Now, the fact of the matter is that these amino acids 94 00:05:15,890 --> 00:05:19,190 exist in a very specific three-dimensional 95 00:05:19,190 --> 00:05:20,400 configuration. 96 00:05:20,400 --> 00:05:22,460 And that's illustrated much more nicely here 97 00:05:22,460 --> 00:05:25,950 than I could possibly draw on the board, which in any case 98 00:05:25,950 --> 00:05:27,960 would be hopeless. 99 00:05:27,960 --> 00:05:30,300 And, you can see the principle that once 100 00:05:30,300 --> 00:05:34,400 you have four distinct side groups coming off of carbon, 101 00:05:34,400 --> 00:05:39,800 that there is, in principle, two different ways to create them. 102 00:05:39,800 --> 00:05:42,440 And, this is sometimes called chirality. 103 00:05:42,440 --> 00:05:44,620 Chiral, you see, is the form right here. 104 00:05:44,620 --> 00:05:46,200 The hands are chiral. 105 00:05:46,200 --> 00:05:49,050 If I try, as much as I will, to superimpose 106 00:05:49,050 --> 00:05:50,570 one hand on top of another. 107 00:05:50,570 --> 00:05:53,990 It doesn't work because they are mirror images of one another, 108 00:05:53,990 --> 00:05:55,520 which are asymmetrical. 109 00:05:55,520 --> 00:05:58,300 And, as a consequence, we see a similar kind of relationship 110 00:05:58,300 --> 00:06:05,940 occurring here where we see that these two forms of amino acids 111 00:06:05,940 --> 00:06:07,455 could, in principle, exist. 112 00:06:07,455 --> 00:06:08,830 And, they are not interchangeable 113 00:06:08,830 --> 00:06:12,300 unless one breaks one of the bonds and reforms it. 114 00:06:12,300 --> 00:06:14,340 These two forms are called the L and the D, 115 00:06:14,340 --> 00:06:17,290 and it turns out that the L form is the one that's 116 00:06:17,290 --> 00:06:20,730 used by virtually all life forms on the planet, i.e. 117 00:06:20,730 --> 00:06:23,060 there was an arbitrary choice made 118 00:06:23,060 --> 00:06:26,220 sometime about 3 billion years ago or more to use 119 00:06:26,220 --> 00:06:29,750 one of the three dimensional configurations, 120 00:06:29,750 --> 00:06:31,330 and not to use the other. 121 00:06:31,330 --> 00:06:33,680 The other is found in certain rare exceptions, 122 00:06:33,680 --> 00:06:37,600 but virtually all life forms on this planet use the L form. 123 00:06:37,600 --> 00:06:42,110 That said, by the way, this indicates some of the arbitrary 124 00:06:42,110 --> 00:06:45,800 decisions that were made early during evolution because we 125 00:06:45,800 --> 00:06:49,380 could imagine on another planet if life were to exist there 126 00:06:49,380 --> 00:06:51,940 and it were to depend on amino acids, 127 00:06:51,940 --> 00:06:55,690 and that evolutionary system might have chosen the D form. 128 00:06:55,690 --> 00:06:57,480 So, this is sort of a luck of the draw. 129 00:06:57,480 --> 00:07:01,660 This is actually the way things evolved here. 130 00:07:01,660 --> 00:07:05,120 And, what we begin to see, now, is if we talk about proteins 131 00:07:05,120 --> 00:07:09,020 or if we wanted to be more specific and use the more 132 00:07:09,020 --> 00:07:11,800 biochemical term ?polypeptide,? 133 00:07:11,800 --> 00:07:16,100 we see once again we have an end-to-end joining system which 134 00:07:16,100 --> 00:07:17,910 is a bit different from that which 135 00:07:17,910 --> 00:07:22,970 the monosaccharides employ to create long chains of glycogen 136 00:07:22,970 --> 00:07:26,500 or of starch because here we see once again a dehydration 137 00:07:26,500 --> 00:07:30,810 reaction where an amine group and a carboxyl group 138 00:07:30,810 --> 00:07:35,190 are caused to shed their hydroxyl and the proton, 139 00:07:35,190 --> 00:07:38,820 causing the formation of a peptide bond. 140 00:07:38,820 --> 00:07:40,940 And here, we see this important, very important 141 00:07:40,940 --> 00:07:43,990 biochemical entity, a peptide bond consisting here 142 00:07:43,990 --> 00:07:48,250 of this carbonyl and this nitrogen fused 143 00:07:48,250 --> 00:07:50,170 in this specific way. 144 00:07:50,170 --> 00:07:53,000 And, of course, if you recognize this as being a peptide bond, 145 00:07:53,000 --> 00:07:56,460 then you can understand why proteins are sometimes given 146 00:07:56,460 --> 00:07:59,170 the term ?polypeptide.? 147 00:07:59,170 --> 00:08:03,840 In some cases, if one has very short stretches of amino acids 148 00:08:03,840 --> 00:08:06,760 linked end to end like this, we talk about these being 149 00:08:06,760 --> 00:08:09,270 oligopeptides, where ?oligo? 150 00:08:09,270 --> 00:08:11,390 is the general term used in biology 151 00:08:11,390 --> 00:08:13,310 to refer to a small number of things 152 00:08:13,310 --> 00:08:16,800 rather than a large number of things. 153 00:08:16,800 --> 00:08:19,160 And, once again, we have, here, the possibility 154 00:08:19,160 --> 00:08:20,920 of extending this infinitely. 155 00:08:20,920 --> 00:08:22,810 There are no constraints, in principle, 156 00:08:22,810 --> 00:08:27,490 on making this 500, 1,000, even 2,000 amino acids long, 157 00:08:27,490 --> 00:08:30,400 where each one of these, once again, is an amino acid, 158 00:08:30,400 --> 00:08:33,840 and where once again I'm being very coy about the identities 159 00:08:33,840 --> 00:08:38,049 of R1 and R2, which, as I will indicate very shortly, 160 00:08:38,049 --> 00:08:41,549 can be one of 20 distinct alternatives. 161 00:08:41,549 --> 00:08:43,640 Here, you see that we are continuing 162 00:08:43,640 --> 00:08:47,030 this process of peptide bond formation. 163 00:08:47,030 --> 00:08:50,350 And most importantly here is the realization 164 00:08:50,350 --> 00:08:54,540 that there is a polarity of elongation here. 165 00:08:54,540 --> 00:08:57,210 It doesn't move with equal probability left or right, 166 00:08:57,210 --> 00:08:58,470 or right to left. 167 00:08:58,470 --> 00:09:00,480 We start at the amino end here. 168 00:09:00,480 --> 00:09:03,170 This is the amino end, and this is the carboxyl end. 169 00:09:03,170 --> 00:09:05,220 The amino end and the carboxyl end, 170 00:09:05,220 --> 00:09:07,970 and invariably, again because of the way life 171 00:09:07,970 --> 00:09:11,010 has evolved on this planet, the new amino acid 172 00:09:11,010 --> 00:09:13,600 is added on the carboxyl end. 173 00:09:13,600 --> 00:09:16,830 And so, when one often talks about proteins, 174 00:09:16,830 --> 00:09:22,380 one refers to their N terminal, and to their C terminal 175 00:09:22,380 --> 00:09:27,150 ends, these referring obviously to the amino group 176 00:09:27,150 --> 00:09:30,120 at one end and a carboxyl and at the other end 177 00:09:30,120 --> 00:09:34,020 so that polarity is always a directed synthesis adding it 178 00:09:34,020 --> 00:09:36,260 on C-terminal end, in other words 179 00:09:36,260 --> 00:09:41,150 to use a short-hand notation, we think about proteins 180 00:09:41,150 --> 00:09:44,550 as going with this polarity N toward C. 181 00:09:44,550 --> 00:09:48,300 Things are growing at the C terminal end progressively. 182 00:09:48,300 --> 00:09:52,990 And, each time one can imagine the addition of an amino acid 183 00:09:52,990 --> 00:09:53,700 on the end of it. 184 00:09:53,700 --> 00:09:57,550 So, again, it can be extended, in principle, indefinitely. 185 00:09:57,550 --> 00:10:00,240 Keep in mind as well, something that's implicit in everything 186 00:10:00,240 --> 00:10:03,250 I'm telling you but I won't always mention it explicitly, 187 00:10:03,250 --> 00:10:06,180 and that is virtually every biochemical reaction 188 00:10:06,180 --> 00:10:08,310 is reversible. 189 00:10:08,310 --> 00:10:12,620 And therefore, if one is able to form a peptide bond, 190 00:10:12,620 --> 00:10:16,660 one is able to break it down by biological means as well, i.e. 191 00:10:16,660 --> 00:10:21,460 by introducing a water molecule back in and thereby using 192 00:10:21,460 --> 00:10:25,030 the process of hydrolysis, which is the breakdown 193 00:10:25,030 --> 00:10:27,300 of a bond through the introduction of a water 194 00:10:27,300 --> 00:10:32,630 molecule to destroy the previously created bond. 195 00:10:32,630 --> 00:10:36,210 To use an MIT phrase, the reversibility is intuitively 196 00:10:36,210 --> 00:10:40,840 obvious because if you are able to make a, well, 197 00:10:40,840 --> 00:10:44,080 I don't know if it?s still used, but it was used in the late 198 00:10:44,080 --> 00:10:45,320 Stone Age around here. 199 00:10:45,320 --> 00:10:49,540 Anyhow, any biochemical action must be reversible 200 00:10:49,540 --> 00:10:52,370 because if, for example, this polymerization were 201 00:10:52,370 --> 00:10:55,370 irreversible, then all the protein that was ever 202 00:10:55,370 --> 00:10:57,900 synthesized on the surface of the planet over the last 3 1/2 203 00:10:57,900 --> 00:11:00,100 billion years would accumulate progressively. 204 00:11:00,100 --> 00:11:01,900 And obviously, that doesn't happen. 205 00:11:01,900 --> 00:11:04,550 And therefore, macromolecular synthesis, 206 00:11:04,550 --> 00:11:06,190 to the extent that it proceeds forward, 207 00:11:06,190 --> 00:11:09,820 obviously must go the other direction as well. 208 00:11:09,820 --> 00:11:12,570 And the resulting concentration of a complete protein 209 00:11:12,570 --> 00:11:15,210 is known as its steady state. 210 00:11:15,210 --> 00:11:18,900 So we might make a protein at one rate 211 00:11:18,900 --> 00:11:20,570 and break it down at the same rate. 212 00:11:20,570 --> 00:11:23,160 And its steady-state concentration 213 00:11:23,160 --> 00:11:26,030 represents the compromise between these two, i.e., 214 00:11:26,030 --> 00:11:28,380 the concentration of such a protein 215 00:11:28,380 --> 00:11:31,459 that we might observe at any one point in time. 216 00:11:31,459 --> 00:11:32,750 Indeed, the term ?steady-state? 217 00:11:32,750 --> 00:11:37,000 could be expanded to any process in which there is a synthesis 218 00:11:37,000 --> 00:11:38,820 and there is a breakdown of something. 219 00:11:38,820 --> 00:11:41,160 And the equilibrium concentration 220 00:11:41,160 --> 00:11:45,190 which results is, once again, called the steady-state 221 00:11:45,190 --> 00:11:47,100 of that molecule. 222 00:11:47,100 --> 00:11:49,300 Now, let's get down to the nitty-gritty, 223 00:11:49,300 --> 00:11:52,130 which is obviously something which 224 00:11:52,130 --> 00:11:55,260 we can't avoid for very long, which is to say the R's, i.e. 225 00:11:55,260 --> 00:11:57,280 the side chains. 226 00:11:57,280 --> 00:12:00,610 Once again, here we see an arbitrary artifact 227 00:12:00,610 --> 00:12:03,710 of very early evolution in the biosphere 228 00:12:03,710 --> 00:12:08,070 because there are, in effect, 20 different side chains creating 229 00:12:08,070 --> 00:12:11,460 20 distinct amino acids, which are 230 00:12:11,460 --> 00:12:15,350 used in proteins by all organisms on this planet. 231 00:12:15,350 --> 00:12:17,360 Again, there are rare exceptions, 232 00:12:17,360 --> 00:12:20,230 certain fungi and certain bacteria 233 00:12:20,230 --> 00:12:22,690 are able to make unusual amino acids. 234 00:12:22,690 --> 00:12:24,400 But these are the basic building blocks 235 00:12:24,400 --> 00:12:28,440 of virtually all life forms on the planet. 236 00:12:28,440 --> 00:12:30,440 99.99% of all the protein that is created 237 00:12:30,440 --> 00:12:34,870 is synthesized through the polymerization of these 20 238 00:12:34,870 --> 00:12:36,800 amino acids. 239 00:12:36,800 --> 00:12:40,540 And, by the way, one of the amino acids, glycine, 240 00:12:40,540 --> 00:12:42,940 over here, you see it right here, 241 00:12:42,940 --> 00:12:46,010 violates this rule of chirality. 242 00:12:46,010 --> 00:12:47,990 And, you will recall before I said 243 00:12:47,990 --> 00:12:52,920 that because there are four distinct amino acids, 244 00:12:52,920 --> 00:12:55,730 four distinct side chains around a central carbon 245 00:12:55,730 --> 00:12:57,340 sometimes called the alpha carbon, 246 00:12:57,340 --> 00:13:00,280 you always have a handedness of amino acids. 247 00:13:00,280 --> 00:13:04,560 But this notion cannot be respected in the case 248 00:13:04,560 --> 00:13:09,282 of glycine seen up here simply because we don't have four 249 00:13:09,282 --> 00:13:11,740 distinct, here's the central carbon where I'm pointing with 250 00:13:11,740 --> 00:13:15,881 the red, and here these two hydrogens are equivalent to one 251 00:13:15,881 --> 00:13:16,380 another. 252 00:13:16,380 --> 00:13:17,680 They are not four distinct chains. 253 00:13:17,680 --> 00:13:19,440 There's only three distinct chains here. 254 00:13:19,440 --> 00:13:22,130 So glycine violates this rule of chirality, 255 00:13:22,130 --> 00:13:24,530 of left- and right-handedness. 256 00:13:24,530 --> 00:13:27,010 And here, by the way, the side chain, 257 00:13:27,010 --> 00:13:30,620 which in all of these cases is depicted as extending off 258 00:13:30,620 --> 00:13:33,140 to the right of each amino acid, the side chain 259 00:13:33,140 --> 00:13:38,040 is simply an H, simply a proton, a hydrogen atom. 260 00:13:38,040 --> 00:13:41,870 In fact, what we see about these amino acids 261 00:13:41,870 --> 00:13:44,280 is that the side chains have quite 262 00:13:44,280 --> 00:13:46,900 distinct biochemical properties. 263 00:13:46,900 --> 00:13:50,040 And that begins to impress us with the notion 264 00:13:50,040 --> 00:13:53,250 that proteins and their biochemical attributes 265 00:13:53,250 --> 00:13:57,100 can be dictated by the identities of the amino acids 266 00:13:57,100 --> 00:13:59,220 that are used to construct them. 267 00:13:59,220 --> 00:14:01,830 We can talk about the notion of nonpolar 268 00:14:01,830 --> 00:14:05,960 versus polar amino acids, i.e., amino acids 269 00:14:05,960 --> 00:14:10,010 which have poor affinity for water. 270 00:14:10,010 --> 00:14:14,990 They don't have a separation of plus and minus charges. 271 00:14:14,990 --> 00:14:19,600 And as a consequence, they are a little bit or quite a bit 272 00:14:19,600 --> 00:14:21,402 hydrophobic. 273 00:14:21,402 --> 00:14:23,610 Now, you will say, well, how can they be hydrophobic, 274 00:14:23,610 --> 00:14:25,680 because here this oxygen is charged, 275 00:14:25,680 --> 00:14:28,100 and here this amine group is charged? 276 00:14:28,100 --> 00:14:30,560 That would make it highly hydrophilic. 277 00:14:30,560 --> 00:14:32,390 But keep in mind, when I'm talking 278 00:14:32,390 --> 00:14:35,180 about these amino acids, I'm not talking about them 279 00:14:35,180 --> 00:14:37,460 when they are in a single amino acid form. 280 00:14:37,460 --> 00:14:39,440 I'm talking about their properties 281 00:14:39,440 --> 00:14:43,650 once they have been polymerized into state like this. 282 00:14:43,650 --> 00:14:46,500 And, once they are polymerized into state like this, 283 00:14:46,500 --> 00:14:51,580 the NH2 and CO charging, that is, the charge here 284 00:14:51,580 --> 00:14:53,360 and the charge here become irrelevant 285 00:14:53,360 --> 00:14:55,710 because this oxygen and this amine group 286 00:14:55,710 --> 00:14:58,120 are both tied up in covalent bonds. 287 00:14:58,120 --> 00:15:01,640 And, this acquisition of a proton and this shedding 288 00:15:01,640 --> 00:15:04,670 of a proton over here cannot occur, 289 00:15:04,670 --> 00:15:07,330 because both of these atoms, O and N, 290 00:15:07,330 --> 00:15:09,640 are involved in covalent bonds. 291 00:15:09,640 --> 00:15:14,730 So therefore, when we talk about nonpolar and polar amino acids, 292 00:15:14,730 --> 00:15:18,330 keep in mind we are focusing on the biochemical properties 293 00:15:18,330 --> 00:15:21,990 of the side chain because the central backbone 294 00:15:21,990 --> 00:15:24,930 of the polypeptide and the central backbone 295 00:15:24,930 --> 00:15:26,581 is defined quite clearly here. 296 00:15:26,581 --> 00:15:28,080 Here's the central backbone, and you 297 00:15:28,080 --> 00:15:33,380 see it has a quite repeating structure, N, C, C, N, C, C, N, 298 00:15:33,380 --> 00:15:34,850 C, C, this is invariant. 299 00:15:37,360 --> 00:15:41,790 What changes, and what defines the biochemical attributes 300 00:15:41,790 --> 00:15:45,410 of this oligopeptide, or a polypeptide, 301 00:15:45,410 --> 00:15:47,560 are the identities of these side chains, which 302 00:15:47,560 --> 00:15:50,070 again are plotted on this particular graph. 303 00:15:50,070 --> 00:15:53,710 You have a different version in your book off to the right. 304 00:15:53,710 --> 00:15:56,880 Here, you see, we have a proton, a methyl group, a valine, 305 00:15:56,880 --> 00:16:01,360 a lucine, an isolucine, and the differences 306 00:16:01,360 --> 00:16:08,270 between this suggests these are all quite aliphatic, quite 307 00:16:08,270 --> 00:16:14,160 similar to the propane that we talked about last time, 308 00:16:14,160 --> 00:16:15,210 or the hexane. 309 00:16:15,210 --> 00:16:18,440 That is to say, these are quite hydrophobic side groups. 310 00:16:18,440 --> 00:16:22,730 And, as such, if there were a polypeptide, we can imagine, 311 00:16:22,730 --> 00:16:24,870 and you put the polypeptide in water, 312 00:16:24,870 --> 00:16:28,080 you can imagine that these amino acids would not 313 00:16:28,080 --> 00:16:31,110 like to be directly confronting the water because of the fact 314 00:16:31,110 --> 00:16:33,140 that they are hydrophobic. 315 00:16:33,140 --> 00:16:37,150 Methionine is also a bit hydrophobic. 316 00:16:37,150 --> 00:16:41,130 I'm equivocating there because the S 317 00:16:41,130 --> 00:16:44,590 has a slight degree of hydrophilicity. 318 00:16:44,590 --> 00:16:46,690 It has a slight degree of polarity, 319 00:16:46,690 --> 00:16:48,230 but not really that much. 320 00:16:48,230 --> 00:16:50,600 And, these aromatic side chains here, 321 00:16:50,600 --> 00:16:52,810 because they have these benzene rings, 322 00:16:52,810 --> 00:16:55,340 consequently are called aromatic. 323 00:16:55,340 --> 00:16:58,520 These are quite strongly hydrophobic. 324 00:16:58,520 --> 00:17:02,240 So, they really hate to be in the intimate contact 325 00:17:02,240 --> 00:17:03,690 with water. 326 00:17:03,690 --> 00:17:06,530 Here, on the other hand, let's look at these side chains 327 00:17:06,530 --> 00:17:13,530 because here we have strongly polar molecules, 328 00:17:13,530 --> 00:17:14,970 side chains again. 329 00:17:14,970 --> 00:17:17,380 Keep in mind we are focusing on the side chains. 330 00:17:17,380 --> 00:17:19,470 Here we see serine with the hydroxyl group that 331 00:17:19,470 --> 00:17:22,280 can form hydrogen bonds with the water, threonine, which 332 00:17:22,280 --> 00:17:25,460 has its own hydroxyl group, asparagine, 333 00:17:25,460 --> 00:17:28,800 which has two atoms here, this carbonyl and the NH2, 334 00:17:28,800 --> 00:17:33,220 both of which can form hydrogen bonds with the water, 335 00:17:33,220 --> 00:17:35,520 as can glutamine. 336 00:17:35,520 --> 00:17:37,540 So, these are quite hydrophilic. 337 00:17:37,540 --> 00:17:41,340 They are not as fanatically hydrophilic as these charge 338 00:17:41,340 --> 00:17:43,570 molecules where the side chains are not 339 00:17:43,570 --> 00:17:46,210 just capable of forming hydrogen bonds. 340 00:17:46,210 --> 00:17:48,580 In this lower group here, the side chains 341 00:17:48,580 --> 00:17:50,750 are capable of undergoing ionization. 342 00:17:50,750 --> 00:17:53,150 So they're actually strongly charged. 343 00:17:53,150 --> 00:17:56,820 And here, we see here the carboxyl group, 344 00:17:56,820 --> 00:17:59,390 and our aspartic acid and glutamic acid 345 00:17:59,390 --> 00:18:01,410 has actually discharged its proton, 346 00:18:01,410 --> 00:18:03,630 becoming negatively charged. 347 00:18:03,630 --> 00:18:05,950 These are acidic amino acids, by virtue 348 00:18:05,950 --> 00:18:09,130 of the carboxyl group they have, basic amino acids 349 00:18:09,130 --> 00:18:12,600 here: arginine, lysine, and histidine, 350 00:18:12,600 --> 00:18:15,380 all acquire a positively charged side 351 00:18:15,380 --> 00:18:18,110 chain by virtue of these nitrogen 352 00:18:18,110 --> 00:18:21,100 here which have a strong affinity for pulling away 353 00:18:21,100 --> 00:18:25,760 protons or abstracting protons from the aqueous solvent. 354 00:18:25,760 --> 00:18:30,080 And so, we have a whole gradient of hydrophilicity 355 00:18:30,080 --> 00:18:32,510 down to hydrophobicity. 356 00:18:32,510 --> 00:18:35,260 And here, we have intermediate structures. 357 00:18:35,260 --> 00:18:38,990 We also have some very special idiosyncratic kinds 358 00:18:38,990 --> 00:18:40,310 of amino acids. 359 00:18:40,310 --> 00:18:43,610 Here is tyrosine, and tyrosine is little bit schizophrenic 360 00:18:43,610 --> 00:18:44,230 again. 361 00:18:44,230 --> 00:18:47,340 It has this highly hydrophobic aromatic group here, 362 00:18:47,340 --> 00:18:50,090 the benzene ring, which hates to be in water, 363 00:18:50,090 --> 00:18:53,130 and the hydroxyl group which actually is a friend of water. 364 00:18:53,130 --> 00:18:54,680 So, here, we have something where 365 00:18:54,680 --> 00:18:57,710 its role is quite equivocal. 366 00:18:57,710 --> 00:19:01,090 Here, we have cystine, as indicated here, 367 00:19:01,090 --> 00:19:03,190 and what's interesting about the cystine group 368 00:19:03,190 --> 00:19:06,860 in this case is the SH group, the side chain, the SH 369 00:19:06,860 --> 00:19:12,280 group, because this SH group is able to form bonds with yet 370 00:19:12,280 --> 00:19:15,130 other SH groups from other cystines. 371 00:19:15,130 --> 00:19:18,250 So, let's just look at the cystine here for a moment. 372 00:19:18,250 --> 00:19:21,230 You see there's a CH2, and then there's an SH. 373 00:19:21,230 --> 00:19:23,860 So, let's imagine, I'm not going to draw all the atoms here, 374 00:19:23,860 --> 00:19:25,870 but let's imagine here we have the CH2 group. 375 00:19:25,870 --> 00:19:29,270 I'm not drawing the backbone, SH, over here. 376 00:19:29,270 --> 00:19:31,280 And, we can imagine another protein chain, 377 00:19:31,280 --> 00:19:33,820 another polypeptide chain down here. 378 00:19:33,820 --> 00:19:37,390 Again, I'm not drawing the backbone, 379 00:19:37,390 --> 00:19:40,550 but I'm drawing another SH like this. 380 00:19:40,550 --> 00:19:43,290 And, the fact is, under the conditions of oxidation 381 00:19:43,290 --> 00:19:46,990 and reduction that operate at least in the extracellular 382 00:19:46,990 --> 00:19:50,870 space, one can oxidize this, these two, 383 00:19:50,870 --> 00:19:52,730 resulting in the formation of what 384 00:19:52,730 --> 00:19:55,350 is known as a disulfide bond. 385 00:19:59,820 --> 00:20:02,280 So, here, we have now for the first notion 386 00:20:02,280 --> 00:20:07,060 the idea that the polypeptide chains can be covalently linked 387 00:20:07,060 --> 00:20:11,790 to one another through these cross-links, as indicated here. 388 00:20:11,790 --> 00:20:14,130 Conversely, if you add a reducing agent 389 00:20:14,130 --> 00:20:16,600 that will add protons back to this, 390 00:20:16,600 --> 00:20:20,050 and reduce the oxidation state of the sulfurs, 391 00:20:20,050 --> 00:20:25,400 once again causing the disulfide bond to fall apart. 392 00:20:25,400 --> 00:20:27,880 Now, in principle, these disulfide bonds 393 00:20:27,880 --> 00:20:31,070 could be used to link two proteins together. 394 00:20:31,070 --> 00:20:33,230 But, more often than not, if you look 395 00:20:33,230 --> 00:20:36,760 at the structure of a single protein, 396 00:20:36,760 --> 00:20:38,900 here's the structure of a single protein. 397 00:20:38,900 --> 00:20:44,750 And often, there are intramolecular bonds, 398 00:20:44,750 --> 00:20:49,020 disulfide bonds, i.e., bonds from one domain 399 00:20:49,020 --> 00:20:51,410 of the protein to another, from one part of the protein 400 00:20:51,410 --> 00:20:52,170 to the other. 401 00:20:52,170 --> 00:20:53,710 I'll draw them in right here. 402 00:20:53,710 --> 00:20:55,610 Here might be a disulfide bond. 403 00:20:55,610 --> 00:20:58,130 Here might be a disulfide bond, and I could go on and on. 404 00:20:58,130 --> 00:21:00,100 There might be another one over here. 405 00:21:00,100 --> 00:21:02,860 Why do we have these disulfide bonds? 406 00:21:02,860 --> 00:21:05,410 Because as we will indicate very shortly, 407 00:21:05,410 --> 00:21:07,710 the three-dimensional structure of a protein 408 00:21:07,710 --> 00:21:11,070 is very specifically determined. 409 00:21:11,070 --> 00:21:12,680 A protein can only function when it 410 00:21:12,680 --> 00:21:14,640 assumes a certain three-dimensional 411 00:21:14,640 --> 00:21:18,990 configuration, when it assumes a certain three-dimensional, 412 00:21:18,990 --> 00:21:25,090 stereochemical configuration. 413 00:21:25,090 --> 00:21:27,250 When we talk about stereochemistry, 414 00:21:27,250 --> 00:21:29,790 we are talking about the three-dimensional structures 415 00:21:29,790 --> 00:21:32,040 of molecules, small and large. 416 00:21:32,040 --> 00:21:34,970 And, here, we begin to touch on a theme of how 417 00:21:34,970 --> 00:21:39,470 these complex polypeptide chains are able to create proteins 418 00:21:39,470 --> 00:21:42,340 that have very specific, often very rigid, 419 00:21:42,340 --> 00:21:44,950 structures in three-dimensional space. 420 00:21:44,950 --> 00:21:47,530 Part of this structural rigidity is maintained 421 00:21:47,530 --> 00:21:52,760 by these covalent disulfide bonds, which 422 00:21:52,760 --> 00:21:55,930 tightly link neighboring regions, or even not 423 00:21:55,930 --> 00:22:00,640 so neighboring regions, of a single polypeptide chain, 424 00:22:00,640 --> 00:22:03,290 these intramolecular links. 425 00:22:03,290 --> 00:22:06,310 This doesn't preclude there being intermolecular links 426 00:22:06,310 --> 00:22:08,360 between two polypeptide chains that 427 00:22:08,360 --> 00:22:12,760 are mediated as well by the disulfide bonds. 428 00:22:12,760 --> 00:22:15,190 Here's another very peculiar amino acid 429 00:22:15,190 --> 00:22:19,550 because what you see here is at the side chain, which 430 00:22:19,550 --> 00:22:24,110 is CH2, CH2, CH2, CH2 is hydrogen bonded here 431 00:22:24,110 --> 00:22:26,260 to the amine group. 432 00:22:26,260 --> 00:22:29,790 It's not swinging out in free space. 433 00:22:29,790 --> 00:22:31,280 I misspoke. 434 00:22:31,280 --> 00:22:35,020 What we see here is CH2, CH2 is covalent bonded 435 00:22:35,020 --> 00:22:36,170 to the amine group. 436 00:22:36,170 --> 00:22:38,150 You pick that up, right? 437 00:22:38,150 --> 00:22:40,760 I was just testing you. 438 00:22:40,760 --> 00:22:41,410 Sure I was. 439 00:22:41,410 --> 00:22:44,040 OK, so here we see a five-membered ring 440 00:22:44,040 --> 00:22:45,520 that's created. 441 00:22:45,520 --> 00:22:48,260 So here, this thing is not swinging out in free space. 442 00:22:48,260 --> 00:22:51,900 It creates a five-membered ring where the end of the side chain 443 00:22:51,900 --> 00:22:54,830 is actually covalently linked to the amino group. 444 00:22:54,830 --> 00:22:57,920 And, that also has implications for the structure of proteins 445 00:22:57,920 --> 00:23:00,580 because this particular amino acid, whenever 446 00:23:00,580 --> 00:23:03,500 it occurs within a polypeptide chain, 447 00:23:03,500 --> 00:23:06,760 doesn't have the flexibility of assuming certain configurations 448 00:23:06,760 --> 00:23:10,630 that the other ones have whose four side chains are not 449 00:23:10,630 --> 00:23:12,490 so encumbered. 450 00:23:12,490 --> 00:23:14,150 None of them has total flexibility, 451 00:23:14,150 --> 00:23:16,380 but this one is far more encumbered 452 00:23:16,380 --> 00:23:19,160 in the kinds of three-dimensional structures 453 00:23:19,160 --> 00:23:21,520 that it can assume. 454 00:23:21,520 --> 00:23:26,050 And, with that in mind, we begin to ask questions 455 00:23:26,050 --> 00:23:29,510 about how polypeptide chains assume 456 00:23:29,510 --> 00:23:31,500 three-dimensional structure. 457 00:23:31,500 --> 00:23:36,570 If we talk about a polypeptide chain, in our minds, 458 00:23:36,570 --> 00:23:41,285 hopefully, there's only 28 combinations. 459 00:23:44,400 --> 00:23:46,410 Oh, am I good or what? 460 00:23:46,410 --> 00:23:50,340 Anyhow, all right, so, look here. 461 00:23:50,340 --> 00:23:55,170 And here, you see, this is a typical polypeptide chain. 462 00:23:55,170 --> 00:23:57,570 Here, we have a three letter code. 463 00:23:57,570 --> 00:23:59,990 In truth, there is a single letter code 464 00:23:59,990 --> 00:24:02,480 which was introduced around 1965. 465 00:24:02,480 --> 00:24:07,090 So, each of the 20 amino acids has its own single letter code. 466 00:24:07,090 --> 00:24:13,020 And, to make a frank and depressing admission, 35 years, 467 00:24:13,020 --> 00:24:15,430 40 years after the single amino acid letter 468 00:24:15,430 --> 00:24:18,845 code was instituted, I still haven't learned it. 469 00:24:18,845 --> 00:24:20,720 But, we could learn these three letter codes, 470 00:24:20,720 --> 00:24:23,760 which fortunately are present here. 471 00:24:23,760 --> 00:24:25,820 In the single letter code L is lucine, 472 00:24:25,820 --> 00:24:31,580 and A is alanine, see, they know it. 473 00:24:31,580 --> 00:24:33,130 This is another example of not being 474 00:24:33,130 --> 00:24:35,860 able to teach old dogs new tricks. 475 00:24:35,860 --> 00:24:39,710 Anyhow, so here we see the way, one way 476 00:24:39,710 --> 00:24:44,060 by which one might depict an amino acid chain, 477 00:24:44,060 --> 00:24:45,250 a polypeptide chain. 478 00:24:45,250 --> 00:24:49,490 And keep in mind, this can go on indefinitely. 479 00:24:49,490 --> 00:24:52,140 As we begin to wrestle with the three-dimensional structure 480 00:24:52,140 --> 00:24:54,700 of the chain, we begin to realize the following, 481 00:24:54,700 --> 00:24:58,700 and that is that after the chain is initially synthesized, 482 00:24:58,700 --> 00:25:00,720 it's initially chaotic. 483 00:25:00,720 --> 00:25:03,330 And, as it extends, it increasingly 484 00:25:03,330 --> 00:25:09,110 begins to assume a very specific three-dimensional molecular 485 00:25:09,110 --> 00:25:11,440 configuration which is indicated down here. 486 00:25:11,440 --> 00:25:14,910 So, the chaos that operates initially 487 00:25:14,910 --> 00:25:19,570 will eventually result in a native configuration over here, 488 00:25:19,570 --> 00:25:22,610 which in many respects often represents the lowest 489 00:25:22,610 --> 00:25:24,810 free energy state. 490 00:25:24,810 --> 00:25:28,250 Since for the last 40 years, people have been trying 491 00:25:28,250 --> 00:25:31,100 to figure out, if you knew the amino acid sequence of this 492 00:25:31,100 --> 00:25:35,270 primary polypeptide here, if you knew its primary structure, 493 00:25:35,270 --> 00:25:37,320 and when I say, ?primary structure,? 494 00:25:37,320 --> 00:25:39,965 what I mean is the sequence of the amino acids. 495 00:25:39,965 --> 00:25:42,340 So, if you knew the primary structure of the amino acids, 496 00:25:42,340 --> 00:25:45,840 you should, in principle, be able to develop a computer 497 00:25:45,840 --> 00:25:48,310 algorithm that would predict the three-dimensional 498 00:25:48,310 --> 00:25:51,530 configuration, which is shown here in a very schematic way, 499 00:25:51,530 --> 00:25:54,930 and which we will discuss in much greater detail shortly. 500 00:25:54,930 --> 00:25:57,580 And, the fact is, after 40 years of trying, 501 00:25:57,580 --> 00:26:00,480 one still is unable to do that, i.e., 502 00:26:00,480 --> 00:26:04,210 if I were to give the primary amino acid 503 00:26:04,210 --> 00:26:07,330 sequence of the polypeptide to the smartest 504 00:26:07,330 --> 00:26:10,550 biochemists in the world, and there are some very smart ones, 505 00:26:10,550 --> 00:26:12,560 he or she could still not tell me 506 00:26:12,560 --> 00:26:14,110 what the three-dimensional structure 507 00:26:14,110 --> 00:26:18,261 of this protein with total certainty would be. 508 00:26:18,261 --> 00:26:18,760 Why? 509 00:26:18,760 --> 00:26:21,320 Because there's an almost infinite number 510 00:26:21,320 --> 00:26:24,550 of intramolecular interactions that greatly 511 00:26:24,550 --> 00:26:29,760 complicate how the protein assumes the structure. 512 00:26:29,760 --> 00:26:32,530 Moreover, if we talk about this as the native state 513 00:26:32,530 --> 00:26:35,870 of the protein, we can imagine that there?s ways of disrupting 514 00:26:35,870 --> 00:26:38,840 that because much of this native state is created 515 00:26:38,840 --> 00:26:42,360 by intramolecular hydrogen bonds. 516 00:26:42,360 --> 00:26:44,700 Remember, the hydrogen bonds are relatively weak, 517 00:26:44,700 --> 00:26:49,070 and if we heat up the temperature, 518 00:26:49,070 --> 00:26:51,120 then we can break hydrogen bonds. 519 00:26:51,120 --> 00:26:55,650 And therefore, every time we fry an egg, for example, 520 00:26:55,650 --> 00:26:58,300 if we want to get down to Earth, we denature. 521 00:26:58,300 --> 00:27:02,000 We break up the native three-dimensional structure 522 00:27:02,000 --> 00:27:05,360 of the albumin molecules that constitute the egg white. 523 00:27:05,360 --> 00:27:07,640 And so, when everything turns white, what we've done 524 00:27:07,640 --> 00:27:10,880 is to take a native molecule like this, heated it 525 00:27:10,880 --> 00:27:13,700 up to temperatures where the intramolecular 526 00:27:13,700 --> 00:27:16,130 bonds no longer stabilize. 527 00:27:16,130 --> 00:27:17,670 Notably, hydrogen bonds no longer 528 00:27:17,670 --> 00:27:20,130 stabilize this three-dimensional configuration, 529 00:27:20,130 --> 00:27:23,480 and we put it into a denatured state, which 530 00:27:23,480 --> 00:27:26,450 might be all the way up here. 531 00:27:26,450 --> 00:27:30,960 And, therefore, this acquisition of a native configuration, 532 00:27:30,960 --> 00:27:35,350 or a native state, native representing the natural state, 533 00:27:35,350 --> 00:27:38,830 is also reversible in many molecules 534 00:27:38,830 --> 00:27:40,710 simply by heating them up. 535 00:27:40,710 --> 00:27:42,750 There are to be sure yet other molecules which 536 00:27:42,750 --> 00:27:45,290 are different from the egg white from the albumin in egg 537 00:27:45,290 --> 00:27:47,310 white where if you cool them back down, 538 00:27:47,310 --> 00:27:50,960 they will spontaneously reassume their native structure. 539 00:27:50,960 --> 00:27:54,360 Many proteins, most, will not do so. 540 00:27:54,360 --> 00:27:57,450 Well, again, let's go back to this issue of the acquisition 541 00:27:57,450 --> 00:27:59,720 of complex, three-dimensional structure. 542 00:27:59,720 --> 00:28:04,590 And here, we begin to see how some of this structure 543 00:28:04,590 --> 00:28:08,650 is acquired and stabilized through these intramolecular 544 00:28:08,650 --> 00:28:09,810 hydrogen bonds. 545 00:28:09,810 --> 00:28:12,650 And there are many opportunities for these intramolecular 546 00:28:12,650 --> 00:28:15,740 hydrogen bonds because here we see one polypeptide chain here, 547 00:28:15,740 --> 00:28:17,200 here we see another. 548 00:28:17,200 --> 00:28:20,780 And, we see that the NH2 group right here, I'm sorry, 549 00:28:20,780 --> 00:28:24,440 the nitrogen group here with the proton side chain, 550 00:28:24,440 --> 00:28:28,740 and the carbonyl group here with the oxygen are not encumbered. 551 00:28:28,740 --> 00:28:31,860 They are, in principle, available to form hydrogen 552 00:28:31,860 --> 00:28:35,900 bonds with a polypeptide chain somewhere else. 553 00:28:35,900 --> 00:28:37,770 Now, this other polypeptide chain 554 00:28:37,770 --> 00:28:39,790 could once again be from another protein, 555 00:28:39,790 --> 00:28:41,450 from another polypeptide. 556 00:28:41,450 --> 00:28:44,300 But more often than not, we are once again 557 00:28:44,300 --> 00:28:49,090 dealing with intramolecular cross-links. 558 00:28:49,090 --> 00:28:51,330 But in this case, the intramolecular cross-links 559 00:28:51,330 --> 00:28:54,060 are not disulfide bonds which are covalent, 560 00:28:54,060 --> 00:28:58,080 and hard and stable as a rock in the absence of reducing agents. 561 00:28:58,080 --> 00:29:01,090 Here, we're talking about much weaker bonds, hydrogen bonds 562 00:29:01,090 --> 00:29:07,080 which also act between different loops of the protein 563 00:29:07,080 --> 00:29:09,880 and serve, once again, to stabilize 564 00:29:09,880 --> 00:29:12,510 the three-dimensional structure, the native state 565 00:29:12,510 --> 00:29:14,180 of the protein. 566 00:29:14,180 --> 00:29:16,880 And, you can see how these opportunities for forming 567 00:29:16,880 --> 00:29:18,900 multiple hydrogen bonds can create 568 00:29:18,900 --> 00:29:22,840 an enormous degree of stability. 569 00:29:22,840 --> 00:29:25,730 And, here are some examples of what we now 570 00:29:25,730 --> 00:29:29,450 call the secondary structure of the protein. 571 00:29:29,450 --> 00:29:32,510 Just a second ago, or several minutes ago to be honest, 572 00:29:32,510 --> 00:29:35,590 and I'm always honest with you, class, 573 00:29:35,590 --> 00:29:39,000 the primary structure is the amino acid sequence. 574 00:29:39,000 --> 00:29:41,080 The secondary structure represents 575 00:29:41,080 --> 00:29:42,760 configurations like this. 576 00:29:42,760 --> 00:29:46,120 Here is an alpha helix. 577 00:29:46,120 --> 00:29:49,370 Here is a beta pleated sheet. 578 00:29:49,370 --> 00:29:51,250 And, what we see here in this alpha helix 579 00:29:51,250 --> 00:29:55,000 is we have a helical structure where the amine group down 580 00:29:55,000 --> 00:29:58,630 here, the NH group, hydrogen bonds with a residue that is, 581 00:29:58,630 --> 00:30:00,900 I think, three and a half residues upstream, 582 00:30:00,900 --> 00:30:04,680 one, two, there's an amine down there, so, 583 00:30:04,680 --> 00:30:07,420 with the carbonyl group that's three and a half residues 584 00:30:07,420 --> 00:30:08,920 upstream of it. 585 00:30:08,920 --> 00:30:12,230 This one, once again, reaches three and a half residues 586 00:30:12,230 --> 00:30:13,020 upstream. 587 00:30:13,020 --> 00:30:16,150 Not all the hydrogen bonds are shown in the background. 588 00:30:16,150 --> 00:30:18,520 Only the ones on our side of the helix 589 00:30:18,520 --> 00:30:20,410 are shown, on the front side of the helix. 590 00:30:20,410 --> 00:30:23,360 But, you can imagine that this can perpetuate itself. 591 00:30:23,360 --> 00:30:25,390 And, each of these carbonyl's may 592 00:30:25,390 --> 00:30:29,080 associate with a proton, an NH group that's 593 00:30:29,080 --> 00:30:32,280 either above or below that particular residue. 594 00:30:32,280 --> 00:30:35,540 And this, in turn, can create a helical structure. 595 00:30:35,540 --> 00:30:38,670 By the way, proline doesn't fit well. 596 00:30:38,670 --> 00:30:41,750 If you add a proline in here, proline 597 00:30:41,750 --> 00:30:45,411 is known in the trade as a helix breaker. 598 00:30:45,411 --> 00:30:45,910 Why? 599 00:30:45,910 --> 00:30:49,860 Because it cannot twist itself around to form an alpha helix. 600 00:30:49,860 --> 00:30:51,970 And so, if the primary amino acid 601 00:30:51,970 --> 00:30:54,800 were to dictate that a proline would be inserted right 602 00:30:54,800 --> 00:30:57,210 here, for example, then this helix 603 00:30:57,210 --> 00:31:00,070 might exist down below and above, 604 00:31:00,070 --> 00:31:02,680 but it would not be continuous because the presence 605 00:31:02,680 --> 00:31:06,020 of a proline is highly disruptive of the formation 606 00:31:06,020 --> 00:31:09,254 of an alpha helix. 607 00:31:09,254 --> 00:31:10,670 This means that, in principle, you 608 00:31:10,670 --> 00:31:13,410 can make some predictions about the localized 609 00:31:13,410 --> 00:31:16,190 structure of a polypeptide by knowing whether or not 610 00:31:16,190 --> 00:31:18,130 proline is present, for example. 611 00:31:18,130 --> 00:31:19,960 But that still doesn't give you the power 612 00:31:19,960 --> 00:31:22,720 to predict the entire three-dimensional structure 613 00:31:22,720 --> 00:31:25,620 of the finished protein itself. 614 00:31:25,620 --> 00:31:29,060 Now, let's agree that this is the secondary structure 615 00:31:29,060 --> 00:31:32,080 of the protein, i.e., the various domains which often 616 00:31:32,080 --> 00:31:35,740 form alpha helices within a certain segment of the protein 617 00:31:35,740 --> 00:31:37,890 or a certain segment of the protein 618 00:31:37,890 --> 00:31:39,700 will form beta pleated sheets. 619 00:31:39,700 --> 00:31:42,120 And there are several other less common kinds 620 00:31:42,120 --> 00:31:44,890 of secondary structure. 621 00:31:44,890 --> 00:31:48,260 And here, we deal with tertiary structure. 622 00:31:48,260 --> 00:31:50,220 Now we are getting really interesting. 623 00:31:50,220 --> 00:31:51,740 Or, maybe you don't like it. 624 00:31:51,740 --> 00:31:54,120 But some people say it's really interesting 625 00:31:54,120 --> 00:31:57,610 because here are the tertiary structures of some arbitrarily 626 00:31:57,610 --> 00:31:59,930 chosen proteins. 627 00:31:59,930 --> 00:32:04,140 Here, the tertiary structure of this particular protein, 628 00:32:04,140 --> 00:32:08,880 and the identities of these are not given in our textbook. 629 00:32:08,880 --> 00:32:10,766 And, I'm sure if we spent two or three weeks, 630 00:32:10,766 --> 00:32:12,140 we could find out what they were. 631 00:32:12,140 --> 00:32:15,920 But anyhow, here is a protein, a three-dimensional structure 632 00:32:15,920 --> 00:32:20,960 of a protein which is composed of four alpha helices which 633 00:32:20,960 --> 00:32:22,510 go up. 634 00:32:22,510 --> 00:32:26,410 Another alpha helix, alpha helix, alpha helix, alpha 635 00:32:26,410 --> 00:32:28,630 helix, they are depicted here, fortunately, 636 00:32:28,630 --> 00:32:30,580 in four different colors. 637 00:32:30,580 --> 00:32:33,280 And so, we see that what we talk about tertiary structure, 638 00:32:33,280 --> 00:32:36,980 we're talking about how the alpha helices are disposed 639 00:32:36,980 --> 00:32:39,070 with respect to one another. 640 00:32:39,070 --> 00:32:41,070 The primary structure of the amino acid sequence 641 00:32:41,070 --> 00:32:42,410 is not shown here. 642 00:32:42,410 --> 00:32:45,240 The secondary structure represents these individual 643 00:32:45,240 --> 00:32:48,970 alpha helices, and the tertiary structure represents how these 644 00:32:48,970 --> 00:32:51,710 alpha helices are arranged vis-?-vis one another. 645 00:32:51,710 --> 00:32:55,430 Here is a protein which is structured much differently. 646 00:32:58,420 --> 00:33:02,310 It's formed of many beta pleated sheets. 647 00:33:02,310 --> 00:33:05,310 We saw that in the last figure, in the last overhead. 648 00:33:05,310 --> 00:33:08,300 You see it as a quite different overall three-dimensional 649 00:33:08,300 --> 00:33:09,790 structure. 650 00:33:09,790 --> 00:33:12,210 This could be the beginning of an alpha helix down here, 651 00:33:12,210 --> 00:33:14,560 although that's quite equivocal. 652 00:33:14,560 --> 00:33:16,200 And here, we see yet another point. 653 00:33:16,200 --> 00:33:19,230 And that is, as we said before, the tertiary structure 654 00:33:19,230 --> 00:33:23,620 independent of these alpha helices and beta pleated sheets 655 00:33:23,620 --> 00:33:28,420 may be stabilized by these covalent inter-strand 656 00:33:28,420 --> 00:33:31,650 cross-links formed by the cystines. 657 00:33:31,650 --> 00:33:33,800 And in the end, if we put all that together, 658 00:33:33,800 --> 00:33:36,360 then we come to the realization that the three-dimensional 659 00:33:36,360 --> 00:33:40,100 structure of a protein as determined by the art of x-ray 660 00:33:40,100 --> 00:33:47,190 -- There we go. 661 00:33:47,190 --> 00:33:49,940 I'm not actually dyslexic. 662 00:33:49,940 --> 00:33:52,250 I actually have a cousin who I won't mention 663 00:33:52,250 --> 00:33:54,650 whose son was so dyslexic that when he came to stairways 664 00:33:54,650 --> 00:33:56,910 he didn't know whether to put his foot up or down. 665 00:33:56,910 --> 00:33:58,010 Now that's difficulty. 666 00:33:58,010 --> 00:34:00,660 This is not so bad. 667 00:34:00,660 --> 00:34:03,970 OK, anyhow, because I solved it within less than two minutes 668 00:34:03,970 --> 00:34:05,614 time, all right, so here we see this 669 00:34:05,614 --> 00:34:07,780 is what the three-dimensional structure of a protein 670 00:34:07,780 --> 00:34:08,690 looks like. 671 00:34:08,690 --> 00:34:10,610 This is called a space-filling model 672 00:34:10,610 --> 00:34:12,969 because here, one draws in, as determined 673 00:34:12,969 --> 00:34:15,050 by x-ray crystallography what the, 674 00:34:15,050 --> 00:34:16,670 if we could see what a protein looks 675 00:34:16,670 --> 00:34:18,409 like, what it actually must look like, 676 00:34:18,409 --> 00:34:22,760 where each of the atoms including these side chains 677 00:34:22,760 --> 00:34:24,270 is actually depicted. 678 00:34:24,270 --> 00:34:28,832 Before, when we used these far more schematic descriptions 679 00:34:28,832 --> 00:34:31,290 like here, we were just talking about the overall structure 680 00:34:31,290 --> 00:34:31,956 of the backbone. 681 00:34:31,956 --> 00:34:35,739 We weren't really indicating where the side chains were, 682 00:34:35,739 --> 00:34:37,616 and what space they would fill up. 683 00:34:37,616 --> 00:34:39,199 And, if we give them the chance, if we 684 00:34:39,199 --> 00:34:42,190 put in all of the other atoms, the side chains, 685 00:34:42,190 --> 00:34:45,670 and we create a space-filling model where 686 00:34:45,670 --> 00:34:48,320 the actual atoms are shown, this is 687 00:34:48,320 --> 00:34:50,290 what the protein would look like. 688 00:34:50,290 --> 00:34:53,300 And the fact of the matter is that all virtually proteins 689 00:34:53,300 --> 00:34:55,710 have very specific structures. 690 00:34:55,710 --> 00:34:58,670 It's not as if they can shift from one structure to another. 691 00:34:58,670 --> 00:35:01,140 Once they leave their normal native structure 692 00:35:01,140 --> 00:35:07,910 they will lose their ability to do what their normal jobs are. 693 00:35:07,910 --> 00:35:10,980 And, this particular overhead happens 694 00:35:10,980 --> 00:35:12,660 to bring in yet another theme that we're 695 00:35:12,660 --> 00:35:14,720 going to focus on increasingly, which 696 00:35:14,720 --> 00:35:17,440 is, what do proteins do in cells? 697 00:35:17,440 --> 00:35:19,160 I'm glad I asked that question. 698 00:35:19,160 --> 00:35:23,320 One of the things they do is they act as catalysts, i.e. , 699 00:35:23,320 --> 00:35:25,290 as enzymes. 700 00:35:25,290 --> 00:35:27,860 The fact is, as we will discuss later, 701 00:35:27,860 --> 00:35:30,690 virtually all biochemical reactions 702 00:35:30,690 --> 00:35:35,530 require an enzyme catalyst in order to propel them forward. 703 00:35:35,530 --> 00:35:38,590 That is to say, if there's a biochemical reaction to occur, 704 00:35:38,590 --> 00:35:41,860 almost always it will not occur spontaneously 705 00:35:41,860 --> 00:35:44,360 the same way that a hydroxyl ion and a hydrogen 706 00:35:44,360 --> 00:35:46,890 will join together spontaneously in water. 707 00:35:46,890 --> 00:35:50,930 Almost all biochemical reactions require the mediation 708 00:35:50,930 --> 00:35:56,550 of an enzyme which is a biological catalyst in order 709 00:35:56,550 --> 00:35:58,510 to encourage this to happen. 710 00:35:58,510 --> 00:36:05,860 And, almost all catalysts in our cells are proteins. 711 00:36:05,860 --> 00:36:11,820 So, if you have 4,326 distinct biochemical reactions occurring 712 00:36:11,820 --> 00:36:14,110 in the cell, that means that there's probably 713 00:36:14,110 --> 00:36:16,830 almost as many distinct enzymes, each one of which 714 00:36:16,830 --> 00:36:19,800 is assigned to mediate one or another 715 00:36:19,800 --> 00:36:22,790 of those distinct biochemical reactions. 716 00:36:22,790 --> 00:36:24,400 And here, we see the fact that this 717 00:36:24,400 --> 00:36:28,510 is an enzyme which happens to be called hexokinase. 718 00:36:28,510 --> 00:36:31,160 Recall that the -ase suffix at the end 719 00:36:31,160 --> 00:36:34,270 dictates that this is already an enzyme rather 720 00:36:34,270 --> 00:36:35,850 than a carbohydrate. 721 00:36:35,850 --> 00:36:41,200 And, this attaches, in fact, a phosphate group onto glucose. 722 00:36:41,200 --> 00:36:43,800 And, what happens is that the glucose, which 723 00:36:43,800 --> 00:36:47,090 is the substrate, which is acted upon by the catalyst, 724 00:36:47,090 --> 00:36:51,330 is pulled into this site in the protein which 725 00:36:51,330 --> 00:36:56,570 is highly specialized to mediate the enzymatic reaction. 726 00:36:56,570 --> 00:36:59,270 Almost all the business of this complex enzyme 727 00:36:59,270 --> 00:37:01,930 is carried out right here. 728 00:37:01,930 --> 00:37:04,210 And somehow, a lot of the other amino acids 729 00:37:04,210 --> 00:37:06,900 that are located at a distance are doing other things 730 00:37:06,900 --> 00:37:09,670 like regulating the activity of the enzyme. 731 00:37:09,670 --> 00:37:11,700 But the actual business end of the enzyme 732 00:37:11,700 --> 00:37:16,720 is present in what is called a catalytic cleft, an active site 733 00:37:16,720 --> 00:37:19,360 of this enzyme in which the substrates are pulled in 734 00:37:19,360 --> 00:37:22,360 and are manipulated and changed chemically 735 00:37:22,360 --> 00:37:26,470 by the actions of this particular enzyme. 736 00:37:26,470 --> 00:37:31,180 Now, in saying that virtually all catalysts, but not all, are 737 00:37:31,180 --> 00:37:35,050 proteins, I also mean to say that proteins 738 00:37:35,050 --> 00:37:37,810 have a second major function in the body. 739 00:37:37,810 --> 00:37:41,010 The first major function is to act as enzymes in catalysts. 740 00:37:41,010 --> 00:37:45,450 The second major function is to create biochemical structures, 741 00:37:45,450 --> 00:37:49,560 i.e., structures of different cytoskeleton proteins such as I 742 00:37:49,560 --> 00:37:53,580 showed you two lectures ago. 743 00:37:53,580 --> 00:37:55,990 And so, we are going to come repeatedly to the situations 744 00:37:55,990 --> 00:37:59,160 where complex structural entities in the cell 745 00:37:59,160 --> 00:38:02,650 are composed of different structural proteins. 746 00:38:02,650 --> 00:38:04,590 Again, this is just a prelude to talking 747 00:38:04,590 --> 00:38:07,530 about these in greater details, these two major functions 748 00:38:07,530 --> 00:38:09,900 of enzymatic catalysis on the one hand, 749 00:38:09,900 --> 00:38:13,280 and creating structure on the other hand. 750 00:38:13,280 --> 00:38:17,550 And so now, we get to really four hierarchical levels 751 00:38:17,550 --> 00:38:20,590 of protein structure. 752 00:38:20,590 --> 00:38:25,980 The primary structure is the amino acid sequence. 753 00:38:25,980 --> 00:38:29,140 And, if we dwell for second on this amino acid sequence, 754 00:38:29,140 --> 00:38:32,270 let's realize that any single amino acid can 755 00:38:32,270 --> 00:38:34,340 follow any other amino acid. 756 00:38:34,340 --> 00:38:36,870 So, what that means is that if glycine 757 00:38:36,870 --> 00:38:39,360 is the first amino acid, as it happens to be here, 758 00:38:39,360 --> 00:38:42,290 serine is only one of 20 different possible 759 00:38:42,290 --> 00:38:44,300 second amino acids. 760 00:38:44,300 --> 00:38:50,910 Aspartic acid is only one of 20 different third amino acids 761 00:38:50,910 --> 00:38:52,870 as the third residue. 762 00:38:52,870 --> 00:38:54,700 We often call these different residues: 763 00:38:54,700 --> 00:38:57,170 the first residue, second residue, third residue, 764 00:38:57,170 --> 00:38:59,460 fourth residue, and fourth, and so forth. 765 00:38:59,460 --> 00:39:01,410 And, keep in mind, if we think about 766 00:39:01,410 --> 00:39:04,050 the combinatorial implications of that, 767 00:39:04,050 --> 00:39:07,070 the first amino acid residue can have 20 different ones. 768 00:39:07,070 --> 00:39:09,260 The second can have 20 different identities. 769 00:39:09,260 --> 00:39:11,060 The third can have 20 different identities. 770 00:39:11,060 --> 00:39:15,590 That means if we make a tripeptide 771 00:39:15,590 --> 00:39:18,600 - a tripeptide has three amino acids in it. 772 00:39:18,600 --> 00:39:21,980 That means we can make 400 dipeptides, 400 773 00:39:21,980 --> 00:39:26,100 distinct dipeptides, and we can make 774 00:39:26,100 --> 00:39:29,880 8,000 distinct tripeptides. 775 00:39:29,880 --> 00:39:34,620 Now, if you imagine that the average amino acid, 776 00:39:34,620 --> 00:39:36,890 the average protein in the cell is, 777 00:39:36,890 --> 00:39:39,970 let's say, 150 amino acid residues long, 778 00:39:39,970 --> 00:39:45,660 that means that in principle, one could make 20 779 00:39:45,660 --> 00:39:51,960 to the 150th power distinct amino acid sequences because 780 00:39:51,960 --> 00:39:53,580 of these absence of any constraints 781 00:39:53,580 --> 00:39:56,820 of which amino acid will follow which other amino acids. 782 00:39:56,820 --> 00:40:01,820 In other words, if the average polypeptide 783 00:40:01,820 --> 00:40:03,770 has this many residues, this is the number 784 00:40:03,770 --> 00:40:07,260 of distinct 150 amino acid residue long proteins 785 00:40:07,260 --> 00:40:10,131 that one could, in principle, synthesize. 786 00:40:10,131 --> 00:40:11,630 I'm not saying all of them have ever 787 00:40:11,630 --> 00:40:14,390 been synthesized since the formation of life 788 00:40:14,390 --> 00:40:15,400 on this planet. 789 00:40:15,400 --> 00:40:21,260 Indeed, since some amino acid chains are 4, 5, 600, 790 00:40:21,260 --> 00:40:24,970 even 2,000 amino acid residues long, 791 00:40:24,970 --> 00:40:27,450 I think the one that is affecting muscular dystrophy 792 00:40:27,450 --> 00:40:29,490 is more than 2,000 amino acids. 793 00:40:29,490 --> 00:40:30,000 Dystrophin. 794 00:40:30,000 --> 00:40:31,230 Does anybody know here? 795 00:40:31,230 --> 00:40:32,250 It's big. 796 00:40:32,250 --> 00:40:35,360 Anyhow, imagine the number of possibilities. 797 00:40:35,360 --> 00:40:38,350 So, combinatorially, life can make almost 798 00:40:38,350 --> 00:40:42,850 whatever types of amino acids it would like by dictating 799 00:40:42,850 --> 00:40:44,580 the sequence of amino acids. 800 00:40:44,580 --> 00:40:48,390 Now, let's just go and look here again. 801 00:40:48,390 --> 00:40:50,070 There is a secondary structure. 802 00:40:50,070 --> 00:40:51,950 The tertiary structure is the way 803 00:40:51,950 --> 00:40:54,620 in which the different alpha helices here 804 00:40:54,620 --> 00:40:57,450 or beta pleated sheets are disposed three-dimensionally 805 00:40:57,450 --> 00:40:59,290 with respect to one another. 806 00:40:59,290 --> 00:41:02,490 And, the quaternary structure represents 807 00:41:02,490 --> 00:41:07,570 how different polypeptides are associated one with the other. 808 00:41:07,570 --> 00:41:11,330 So, for example, hemoglobin is a tetramer. 809 00:41:11,330 --> 00:41:13,980 Hemoglobin doesn't exist as a monomeric protein. 810 00:41:13,980 --> 00:41:15,760 Its solution exists as a tetramer. 811 00:41:15,760 --> 00:41:18,400 And there's two kinds of globin chains. 812 00:41:18,400 --> 00:41:21,620 There is an alpha kind and a beta kind. 813 00:41:21,620 --> 00:41:24,170 And, if we look in a very rough and schematic way at the way 814 00:41:24,170 --> 00:41:26,750 that a hemoglobin tetramer is arranged, 815 00:41:26,750 --> 00:41:30,460 there are two alpha polypeptide chains and two beta polypeptide 816 00:41:30,460 --> 00:41:31,440 chains. 817 00:41:31,440 --> 00:41:33,979 They are not covalently attached to one another. 818 00:41:33,979 --> 00:41:36,270 They are associated with one another via hydrogen bonds 819 00:41:36,270 --> 00:41:38,310 and hydrophobic interactions. 820 00:41:38,310 --> 00:41:40,960 And, this is the actual native configuration 821 00:41:40,960 --> 00:41:44,210 of globin to alpha and to beta chains. 822 00:41:44,210 --> 00:41:46,750 It doesn't exist as a single amino acid in solution. 823 00:41:46,750 --> 00:41:48,260 It exists as a tetramer. 824 00:41:48,260 --> 00:41:50,620 And, indeed, most, or I shouldn't say most, 825 00:41:50,620 --> 00:41:55,300 but very many proteins exist in these configurations 826 00:41:55,300 --> 00:41:59,280 where the tertiary structure represents 827 00:41:59,280 --> 00:42:01,950 four different amino acid chains. 828 00:42:01,950 --> 00:42:05,010 And each of these has an N and C terminal. 829 00:42:05,010 --> 00:42:06,960 Each of these is chemically distinct. 830 00:42:06,960 --> 00:42:09,890 These four could probably be taken apart from one another 831 00:42:09,890 --> 00:42:12,050 simply by raising the temperature. 832 00:42:12,050 --> 00:42:13,710 And, they associate like this. 833 00:42:13,710 --> 00:42:15,902 And, in the absence of this association, 834 00:42:15,902 --> 00:42:18,360 if you just had one of these alphas, or one of these betas, 835 00:42:18,360 --> 00:42:20,170 it wouldn't function well at all. 836 00:42:20,170 --> 00:42:23,570 In fact, it might be totally dysfunctional. 837 00:42:23,570 --> 00:42:26,350 One other thing that may be implicit to you, 838 00:42:26,350 --> 00:42:29,180 but I haven't said, but that is very important to realize 839 00:42:29,180 --> 00:42:31,947 is the following: Let's imagine that this 840 00:42:31,947 --> 00:42:34,030 is the three-dimensional structure of the protein, 841 00:42:34,030 --> 00:42:36,160 as it may well be. 842 00:42:36,160 --> 00:42:39,880 Let's now think about hydrophobic and hydrophilic 843 00:42:39,880 --> 00:42:41,660 amino acids. 844 00:42:41,660 --> 00:42:44,720 The hydrophobic amino acids hate to be present water. 845 00:42:44,720 --> 00:42:48,940 And therefore, they are, we can imagine this case correctly, 846 00:42:48,940 --> 00:42:53,480 tucked away inside the interstices of the protein 847 00:42:53,480 --> 00:42:56,030 far way from the surface. 848 00:42:56,030 --> 00:42:58,270 They don't have any contact with water. 849 00:42:58,270 --> 00:43:01,940 Conversely, the highly charged hydrophilic amino acids 850 00:43:01,940 --> 00:43:05,230 are actually sticking out at the surface. 851 00:43:05,230 --> 00:43:08,210 And this begins to yield yet another insight 852 00:43:08,210 --> 00:43:11,680 into how the three-dimensional stereochemistry of proteins 853 00:43:11,680 --> 00:43:15,390 is maintained and dictated because the hydrophobic amino 854 00:43:15,390 --> 00:43:17,780 acids, through hydrophobic interactions, 855 00:43:17,780 --> 00:43:20,900 stabilize the inner core of the protein that is well 856 00:43:20,900 --> 00:43:23,760 shielded from the aqueous solvent. 857 00:43:23,760 --> 00:43:26,080 The hydrophilic amino acids are on the outside. 858 00:43:26,080 --> 00:43:29,490 They like to be in intimate contact with the water. 859 00:43:29,490 --> 00:43:31,740 So, we already now have talked about a number 860 00:43:31,740 --> 00:43:35,240 of distinct different interactions that 861 00:43:35,240 --> 00:43:37,870 are responsible for creating the three-dimensional 862 00:43:37,870 --> 00:43:40,280 stereochemistry of the protein. 863 00:43:40,280 --> 00:43:43,760 First of all, there are the disulfide bonds, 864 00:43:43,760 --> 00:43:47,220 which create chain-to-chain covalent interactions. 865 00:43:47,220 --> 00:43:51,630 They are the hydrogen bonds in which different chains 866 00:43:51,630 --> 00:43:53,200 can interact one another. 867 00:43:53,200 --> 00:43:56,370 And there are these hydrophobic and hydrophilic interactions. 868 00:43:56,370 --> 00:43:59,200 And, there are some relatively inconsequential van der Waals 869 00:43:59,200 --> 00:44:00,702 interactions, which are really not 870 00:44:00,702 --> 00:44:02,410 worth discussing although some people get 871 00:44:02,410 --> 00:44:03,620 really excited about them. 872 00:44:03,620 --> 00:44:05,960 But we won't. 873 00:44:05,960 --> 00:44:10,120 So, here we now begin to see that we have really interesting 874 00:44:10,120 --> 00:44:13,060 polypeptides unlike the boring polypeptides that 875 00:44:13,060 --> 00:44:20,350 are ultimately the way one must judge carbohydrates. 876 00:44:20,350 --> 00:44:22,290 Some people think carbohydrate chemistry 877 00:44:22,290 --> 00:44:23,730 is really interesting. 878 00:44:23,730 --> 00:44:26,100 But it really isn't that interesting 879 00:44:26,100 --> 00:44:29,870 because you just have the same monomer in a hundred, 880 00:44:29,870 --> 00:44:31,370 or 500 stretches. 881 00:44:31,370 --> 00:44:33,230 Here, a protein is much more interesting 882 00:44:33,230 --> 00:44:35,770 because of this enormous variability 883 00:44:35,770 --> 00:44:39,570 in amino acid sequence, and the consequent ability 884 00:44:39,570 --> 00:44:45,660 to create all kinds of chemical reactivities and structures 885 00:44:45,660 --> 00:44:48,910 because of these 20 different amino acids. 886 00:44:48,910 --> 00:44:51,140 If we were to imagine life on another planet, 887 00:44:51,140 --> 00:44:53,060 and we imagine that there were, let's say, 888 00:44:53,060 --> 00:44:57,060 amino acid-like molecules that were part of life, 889 00:44:57,060 --> 00:45:00,150 maybe that other life wouldn't have exactly the same 20 890 00:45:00,150 --> 00:45:02,170 amino acids as we do. 891 00:45:02,170 --> 00:45:06,430 It almost certainly would be a water base the way we are. 892 00:45:06,430 --> 00:45:10,100 But, it would also rely on hydrogen bonds 893 00:45:10,100 --> 00:45:14,570 and hydrophilicity, and hydrophobicity interactions 894 00:45:14,570 --> 00:45:17,740 in order to dictate the three-dimensional structure. 895 00:45:17,740 --> 00:45:19,890 In the absence of this very specific 896 00:45:19,890 --> 00:45:22,320 three-dimensional structure I will tell you 897 00:45:22,320 --> 00:45:24,819 that this enzyme could not function. 898 00:45:24,819 --> 00:45:26,360 And, if you were to take this enzyme, 899 00:45:26,360 --> 00:45:29,540 if it were typical enzyme and you were to heat it up briefly, 900 00:45:29,540 --> 00:45:33,400 even often slightly above normal body temperature, 901 00:45:33,400 --> 00:45:36,040 it might denature, i.e., it might 902 00:45:36,040 --> 00:45:40,860 lose its three-dimensional structure irreversibly. 903 00:45:40,860 --> 00:45:46,530 And, once it was denatured, this process of denaturation, 904 00:45:46,530 --> 00:45:49,400 it might not be able to spontaneously reassume 905 00:45:49,400 --> 00:45:51,850 that pre-existing three-dimensional configuration 906 00:45:51,850 --> 00:45:54,690 and therefore would forever be inactive. 907 00:45:54,690 --> 00:45:56,590 That means to say very explicitly 908 00:45:56,590 --> 00:45:58,650 that even though the amino acids that 909 00:45:58,650 --> 00:46:02,850 are creating that active catalytic site remain there. 910 00:46:02,850 --> 00:46:06,810 Their highly specific three-dimensional disposition 911 00:46:06,810 --> 00:46:10,360 is critical for the continued actions of this enzyme. 912 00:46:10,360 --> 00:46:13,840 And, once their three-dimensional dispositions 913 00:46:13,840 --> 00:46:16,770 are shifted around through the process of interactions, 914 00:46:16,770 --> 00:46:20,450 then, we have trouble because the enzyme can no longer 915 00:46:20,450 --> 00:46:22,240 do its assigned task. 916 00:46:22,240 --> 00:46:27,480 We are going to go now to an even higher order of complexity 917 00:46:27,480 --> 00:46:28,890 in one sense. 918 00:46:28,890 --> 00:46:32,180 We are going to go to the royalty of the macromolecules, 919 00:46:32,180 --> 00:46:34,320 which are the nucleic acids. 920 00:46:34,320 --> 00:46:36,490 Of course, protein chemists would take great umbrage 921 00:46:36,490 --> 00:46:39,510 at the very notion that there are 922 00:46:39,510 --> 00:46:41,540 things better than proteins. 923 00:46:41,540 --> 00:46:44,440 But, the fact of the matter is, I 924 00:46:44,440 --> 00:46:46,180 can't show you that overhead because it's 925 00:46:46,180 --> 00:46:49,290 from the other textbook which is copyright, 926 00:46:49,290 --> 00:46:50,724 and we are being filmed. 927 00:46:50,724 --> 00:46:52,140 How many people have had the backs 928 00:46:52,140 --> 00:46:55,230 of their heads immortalized on these videos? 929 00:46:55,230 --> 00:47:00,040 Did you call home and ask anybody to identify you? 930 00:47:00,040 --> 00:47:04,440 I don't know, but soon each of us 931 00:47:04,440 --> 00:47:07,140 has the limelight for 15 minutes a lifetime, right? 932 00:47:07,140 --> 00:47:09,330 So, you'll have your 15 minutes. 933 00:47:09,330 --> 00:47:11,740 Here are some nucleic acids. 934 00:47:11,740 --> 00:47:15,140 And let's look at these nucleic acids and the way 935 00:47:15,140 --> 00:47:16,507 they are put together. 936 00:47:16,507 --> 00:47:19,090 Keep in mind to anticipate what we are going to say next time, 937 00:47:19,090 --> 00:47:21,600 once again, we want to make end-to-end aggregates. 938 00:47:21,600 --> 00:47:25,150 We want to polymerize molecules. 939 00:47:25,150 --> 00:47:29,160 And in this case, we want to do so once again 940 00:47:29,160 --> 00:47:31,807 through a dehydration reaction. 941 00:47:31,807 --> 00:47:33,890 And, moreover, just to look at the building blocks 942 00:47:33,890 --> 00:47:37,432 of nucleic acids, we start again in this case with two pentoses. 943 00:47:37,432 --> 00:47:38,890 Recall that they have fuor carbons: 944 00:47:38,890 --> 00:47:42,530 one, two, three, four, did I say four? 945 00:47:42,530 --> 00:47:45,500 You know I meant five. 946 00:47:45,500 --> 00:47:47,030 One, two, three, four, five. 947 00:47:47,030 --> 00:47:48,530 So, whenever I say four from now on, 948 00:47:48,530 --> 00:47:54,740 I mean, or, whenever I say four I may also mean four. 949 00:47:54,740 --> 00:47:57,540 OK, one, two, three, four five. 950 00:47:57,540 --> 00:48:01,570 And let's look at the two basic kinds of pentose molecules 951 00:48:01,570 --> 00:48:05,510 that are present in nucleic acid because they define 952 00:48:05,510 --> 00:48:09,580 the essential difference between DNA and RNA. 953 00:48:09,580 --> 00:48:12,310 Here's a regular old rather familiar kind 954 00:48:12,310 --> 00:48:14,930 of pentose with five carbons. 955 00:48:14,930 --> 00:48:17,300 And here's an unfamiliar kind of pentose 956 00:48:17,300 --> 00:48:19,430 which we call deoxyribose. 957 00:48:19,430 --> 00:48:20,270 Why? 958 00:48:20,270 --> 00:48:21,830 Because if you look really carefully, 959 00:48:21,830 --> 00:48:23,496 you'll see that the hydroxyl group here, 960 00:48:23,496 --> 00:48:26,590 which should be present in any self-respecting pentose is 961 00:48:26,590 --> 00:48:30,330 missing, and is replaced simply by a hydrogen group, i.e., 962 00:48:30,330 --> 00:48:35,360 it's lost its oxygen, whence cometh the word, ?deoxyribose,? 963 00:48:35,360 --> 00:48:39,770 and ultimately clearly the word, ?deoxyribose nucleic acid.? 964 00:48:39,770 --> 00:48:42,720 And one of the attributes, one of the virtues 965 00:48:42,720 --> 00:48:45,000 of carbohydrates, as we discussed last time, 966 00:48:45,000 --> 00:48:47,730 were these numerous hydroxyl groups, 967 00:48:47,730 --> 00:48:51,970 which represent opportunities for all kinds of dehydration 968 00:48:51,970 --> 00:48:54,690 reactions which can enable one to build 969 00:48:54,690 --> 00:48:56,920 much more complex molecules. 970 00:48:56,920 --> 00:49:00,110 And here, we see the structure of, for example, 971 00:49:00,110 --> 00:49:04,450 a deoxyribonucleotide whose detailed structure 972 00:49:04,450 --> 00:49:06,660 we'll get into next time. 973 00:49:06,660 --> 00:49:08,890 But just, let's look at how these hydroxyl groups 974 00:49:08,890 --> 00:49:09,940 have been used. 975 00:49:09,940 --> 00:49:12,340 The hydroxyl group, in this case in DNA, 976 00:49:12,340 --> 00:49:17,600 and by the way notice that the structure I've shown here, 977 00:49:17,600 --> 00:49:19,960 there's a side chain attached here, 978 00:49:19,960 --> 00:49:21,650 and a side chain attached here. 979 00:49:21,650 --> 00:49:23,900 And neither of those depends on whether or not 980 00:49:23,900 --> 00:49:27,360 there is a hydrogen or a hydroxyl right here. 981 00:49:27,360 --> 00:49:29,090 And look at what's happened here. 982 00:49:29,090 --> 00:49:32,390 Here, we have this hydroxyl over here 983 00:49:32,390 --> 00:49:35,070 to which a base has been attached covalently, 984 00:49:35,070 --> 00:49:37,950 once again, by a dehydration reaction. 985 00:49:37,950 --> 00:49:41,660 And here, we have a situation where actually three phosphate 986 00:49:41,660 --> 00:49:44,050 groups have been attached to the hydroxyl group 987 00:49:44,050 --> 00:49:46,320 in this direction. 988 00:49:46,320 --> 00:49:48,530 And, this represents the basic building blocks 989 00:49:48,530 --> 00:49:50,084 of nucleic acids. 990 00:49:50,084 --> 00:49:52,500 Now, one of the things that's going to be really important 991 00:49:52,500 --> 00:49:54,270 and that you're going to have to memorize, I told you, you 992 00:49:54,270 --> 00:49:56,320 weren't going to have to memorize anything. 993 00:49:56,320 --> 00:49:58,100 But you didn't believe me, did you? 994 00:49:58,100 --> 00:49:58,841 Good. 995 00:49:58,841 --> 00:50:01,090 OK, one of the things you're going to have to memorize 996 00:50:01,090 --> 00:50:03,500 is the numbering system here. 997 00:50:03,500 --> 00:50:07,110 This is number one, two, three, four, five, 998 00:50:07,110 --> 00:50:09,840 or to be totally frank, and you know 999 00:50:09,840 --> 00:50:13,880 I'm always that, one prime, two prime, three prime, four prime, 1000 00:50:13,880 --> 00:50:15,314 five prime. 1001 00:50:15,314 --> 00:50:16,980 And that numbering system, it turns out, 1002 00:50:16,980 --> 00:50:21,080 is going to be very important for our subsequent discussions. 1003 00:50:21,080 --> 00:50:24,150 Notice here that, for example, it's here 1004 00:50:24,150 --> 00:50:27,720 at the two prime position that this deoxyribose is lacking 1005 00:50:27,720 --> 00:50:34,720 the oxygen that is present normally in RNA. 1006 00:50:34,720 --> 00:50:38,650 And, with all this in mind, we will wait in great suspense 1007 00:50:38,650 --> 00:50:41,280 until Wednesday when we actually talk 1008 00:50:41,280 --> 00:50:45,700 about how this is exploited to make highly complex polymers. 1009 00:50:45,700 --> 00:50:46,740 Have a good two days. 1010 00:50:46,740 --> 00:50:48,740 See you Wednesday at 10:00.