WEBVTT 00:00:16.750 --> 00:00:17.720 Good morning, class. 00:00:17.720 --> 00:00:18.850 Nice to see you again. 00:00:18.850 --> 00:00:22.590 Hope you had a great weekend. 00:00:22.590 --> 00:00:25.960 If you didn't, it wasn't because of the weather. 00:00:25.960 --> 00:00:29.620 So here I am, once again a member of the walking wounded, 00:00:29.620 --> 00:00:32.040 and we're talking about carbohydrates today, 00:00:32.040 --> 00:00:33.910 as you may recall, or at least we 00:00:33.910 --> 00:00:37.840 were at the end of our discussion last time. 00:00:37.840 --> 00:00:42.490 And, we made the point that these multiple hydroxyl groups 00:00:42.490 --> 00:00:44.490 on the carbohydrates, on the one hand, 00:00:44.490 --> 00:00:50.920 determine the identity of various kinds of sugars. 00:00:50.920 --> 00:00:53.570 Just the orientation, the three-dimensional orientation 00:00:53.570 --> 00:00:57.720 of them, for one thing, and for another 00:00:57.720 --> 00:01:01.070 that these multiple hydroxyl groups represent 00:01:01.070 --> 00:01:03.810 the opportunity for forming covalent bonds 00:01:03.810 --> 00:01:06.280 with other monosaccharides as is indicated here 00:01:06.280 --> 00:01:10.710 in these disaccharides, or covalent bonds end-to-end 00:01:10.710 --> 00:01:14.450 to create large molecules, which will increasingly 00:01:14.450 --> 00:01:17.350 be the theme of our discussion today, i.e. 00:01:17.350 --> 00:01:19.130 when I talk about large molecules, 00:01:19.130 --> 00:01:23.450 we just used the phrase generically, macromolecules, 00:01:23.450 --> 00:01:29.530 since in principle these end to end joinings of molecules which 00:01:29.530 --> 00:01:33.770 involve the dehydration and the formation 00:01:33.770 --> 00:01:35.960 of these covalent bonds like right here 00:01:35.960 --> 00:01:39.030 can create molecules that are hundreds, indeed even 00:01:39.030 --> 00:01:41.769 thousands of subunits long. 00:01:41.769 --> 00:01:43.560 So, here, if we're talking about a polymer, 00:01:43.560 --> 00:01:46.750 we refer to each one of these subunits 00:01:46.750 --> 00:01:49.050 of the polymer as being a monomer, 00:01:49.050 --> 00:01:53.090 and the aggregate as a whole as being a polymer. 00:01:53.090 --> 00:01:57.510 Here, we touched upon the fact toward the end of last lecture, 00:01:57.510 --> 00:02:02.530 in fact, at the very end, that one can cross-link 00:02:02.530 --> 00:02:05.700 these long, linear chains of carbohydrates. 00:02:05.700 --> 00:02:07.440 And here, we see the fact that glycogen, 00:02:07.440 --> 00:02:11.420 which is a form of glucose that is stored in our liver 00:02:11.420 --> 00:02:13.830 largely, and to a small extent in the muscles 00:02:13.830 --> 00:02:17.470 actually is cross-branched. 00:02:17.470 --> 00:02:21.450 So, if one draws on a much smaller scale a glycogen 00:02:21.450 --> 00:02:25.322 molecule, one might draw a picture that looks like this. 00:02:25.322 --> 00:02:27.030 And it looks almost like a Christmas tree 00:02:27.030 --> 00:02:28.900 with multiple branches. 00:02:28.900 --> 00:02:30.790 And, the purpose of this is actually 00:02:30.790 --> 00:02:34.180 to sequester the glucose, to store the glucose 00:02:34.180 --> 00:02:38.030 into metabolically inactive form until the time comes 00:02:38.030 --> 00:02:40.020 that the organism needs, once again, 00:02:40.020 --> 00:02:42.250 the energy that is stored in the glucose 00:02:42.250 --> 00:02:45.530 upon which occasion these bonds are rapidly broken down 00:02:45.530 --> 00:02:47.610 and the glucose is mobilized and put 00:02:47.610 --> 00:02:50.560 into the circulation for eventual disposition 00:02:50.560 --> 00:02:53.750 and use in certain, specific tissues. 00:02:53.750 --> 00:02:57.820 While it's encumbered in these high molecular weight polymers, 00:02:57.820 --> 00:03:00.900 the glucose is essentially metabolically inactive. 00:03:00.900 --> 00:03:03.520 The body doesn't realize it's there. 00:03:03.520 --> 00:03:06.890 And, we can, as a consequence store large amounts of energy 00:03:06.890 --> 00:03:08.770 in these glycogen molecules. 00:03:08.770 --> 00:03:12.030 And it can be stored there indefinitely. 00:03:12.030 --> 00:03:18.000 Now, the fact is this idea of end-to-end polymerization 00:03:18.000 --> 00:03:20.520 that I just mentioned can be extended 00:03:20.520 --> 00:03:24.760 to other macromolecules which also become linked end-to-end 00:03:24.760 --> 00:03:28.810 in specific kinds of polymers. 00:03:28.810 --> 00:03:31.660 And here, we are moving, now, into the notion 00:03:31.660 --> 00:03:33.810 of talking about amino acids. 00:03:33.810 --> 00:03:36.180 And, we're talking about proteins. 00:03:36.180 --> 00:03:38.790 If we look at an amino acid, what we see 00:03:38.790 --> 00:03:42.630 is it has an important structure like this. 00:03:42.630 --> 00:03:45.270 Here's a central carbon ? 00:03:45.270 --> 00:03:48.380 for, in principle, the distinct side 00:03:48.380 --> 00:03:51.690 chains where R represents some side chain that 00:03:51.690 --> 00:03:54.260 can be any one of, as we'll see shortly, 00:03:54.260 --> 00:03:57.290 20 distinct identities. 00:03:57.290 --> 00:04:01.090 But, all the amino acids share in common the property 00:04:01.090 --> 00:04:03.320 that they have this overall structure. 00:04:03.320 --> 00:04:08.110 And, as you may recall from our discussions of last week, 00:04:08.110 --> 00:04:12.100 at neutral pH, an amino acid of this sort, whatever 00:04:12.100 --> 00:04:14.650 R is, wouldn't look like this at all 00:04:14.650 --> 00:04:17.930 because the amine group would attract an extra proton, 00:04:17.930 --> 00:04:20.279 causing it to become positively charged. 00:04:20.279 --> 00:04:23.730 And, the carboxyl group would release a proton, 00:04:23.730 --> 00:04:26.370 causing it to become negatively charged. 00:04:26.370 --> 00:04:28.750 And, as you might deduce from this, 00:04:28.750 --> 00:04:32.360 at very low pHn due to the greatly increased concentration 00:04:32.360 --> 00:04:34.820 of protons, free protons in the solution, 00:04:34.820 --> 00:04:37.810 the equilibrium would be driven more in favor 00:04:37.810 --> 00:04:41.230 of reattaching a proton to the carboxyl group 00:04:41.230 --> 00:04:44.630 just because there are so many of these protons around. 00:04:44.630 --> 00:04:49.490 Conversely, at very high pH, where the hydroxyl ions are 00:04:49.490 --> 00:04:53.880 in predominance, they obviously tend to scavenge protons, 00:04:53.880 --> 00:04:58.220 reducing the level of protons to very low levels in the water. 00:04:58.220 --> 00:05:00.250 And, under very high pH conditions, 00:05:00.250 --> 00:05:02.770 this proton would be released and pulled away 00:05:02.770 --> 00:05:06.620 by the hydroxyl ions causing this amine group once again 00:05:06.620 --> 00:05:11.040 to return to its negative charge state. 00:05:11.040 --> 00:05:15.890 Now, the fact of the matter is that these amino acids 00:05:15.890 --> 00:05:19.190 exist in a very specific three-dimensional 00:05:19.190 --> 00:05:20.400 configuration. 00:05:20.400 --> 00:05:22.460 And that's illustrated much more nicely here 00:05:22.460 --> 00:05:25.950 than I could possibly draw on the board, which in any case 00:05:25.950 --> 00:05:27.960 would be hopeless. 00:05:27.960 --> 00:05:30.300 And, you can see the principle that once 00:05:30.300 --> 00:05:34.400 you have four distinct side groups coming off of carbon, 00:05:34.400 --> 00:05:39.800 that there is, in principle, two different ways to create them. 00:05:39.800 --> 00:05:42.440 And, this is sometimes called chirality. 00:05:42.440 --> 00:05:44.620 Chiral, you see, is the form right here. 00:05:44.620 --> 00:05:46.200 The hands are chiral. 00:05:46.200 --> 00:05:49.050 If I try, as much as I will, to superimpose 00:05:49.050 --> 00:05:50.570 one hand on top of another. 00:05:50.570 --> 00:05:53.990 It doesn't work because they are mirror images of one another, 00:05:53.990 --> 00:05:55.520 which are asymmetrical. 00:05:55.520 --> 00:05:58.300 And, as a consequence, we see a similar kind of relationship 00:05:58.300 --> 00:06:05.940 occurring here where we see that these two forms of amino acids 00:06:05.940 --> 00:06:07.455 could, in principle, exist. 00:06:07.455 --> 00:06:08.830 And, they are not interchangeable 00:06:08.830 --> 00:06:12.300 unless one breaks one of the bonds and reforms it. 00:06:12.300 --> 00:06:14.340 These two forms are called the L and the D, 00:06:14.340 --> 00:06:17.290 and it turns out that the L form is the one that's 00:06:17.290 --> 00:06:20.730 used by virtually all life forms on the planet, i.e. 00:06:20.730 --> 00:06:23.060 there was an arbitrary choice made 00:06:23.060 --> 00:06:26.220 sometime about 3 billion years ago or more to use 00:06:26.220 --> 00:06:29.750 one of the three dimensional configurations, 00:06:29.750 --> 00:06:31.330 and not to use the other. 00:06:31.330 --> 00:06:33.680 The other is found in certain rare exceptions, 00:06:33.680 --> 00:06:37.600 but virtually all life forms on this planet use the L form. 00:06:37.600 --> 00:06:42.110 That said, by the way, this indicates some of the arbitrary 00:06:42.110 --> 00:06:45.800 decisions that were made early during evolution because we 00:06:45.800 --> 00:06:49.380 could imagine on another planet if life were to exist there 00:06:49.380 --> 00:06:51.940 and it were to depend on amino acids, 00:06:51.940 --> 00:06:55.690 and that evolutionary system might have chosen the D form. 00:06:55.690 --> 00:06:57.480 So, this is sort of a luck of the draw. 00:06:57.480 --> 00:07:01.660 This is actually the way things evolved here. 00:07:01.660 --> 00:07:05.120 And, what we begin to see, now, is if we talk about proteins 00:07:05.120 --> 00:07:09.020 or if we wanted to be more specific and use the more 00:07:09.020 --> 00:07:11.800 biochemical term ?polypeptide,? 00:07:11.800 --> 00:07:16.100 we see once again we have an end-to-end joining system which 00:07:16.100 --> 00:07:17.910 is a bit different from that which 00:07:17.910 --> 00:07:22.970 the monosaccharides employ to create long chains of glycogen 00:07:22.970 --> 00:07:26.500 or of starch because here we see once again a dehydration 00:07:26.500 --> 00:07:30.810 reaction where an amine group and a carboxyl group 00:07:30.810 --> 00:07:35.190 are caused to shed their hydroxyl and the proton, 00:07:35.190 --> 00:07:38.820 causing the formation of a peptide bond. 00:07:38.820 --> 00:07:40.940 And here, we see this important, very important 00:07:40.940 --> 00:07:43.990 biochemical entity, a peptide bond consisting here 00:07:43.990 --> 00:07:48.250 of this carbonyl and this nitrogen fused 00:07:48.250 --> 00:07:50.170 in this specific way. 00:07:50.170 --> 00:07:53.000 And, of course, if you recognize this as being a peptide bond, 00:07:53.000 --> 00:07:56.460 then you can understand why proteins are sometimes given 00:07:56.460 --> 00:07:59.170 the term ?polypeptide.? 00:07:59.170 --> 00:08:03.840 In some cases, if one has very short stretches of amino acids 00:08:03.840 --> 00:08:06.760 linked end to end like this, we talk about these being 00:08:06.760 --> 00:08:09.270 oligopeptides, where ?oligo? 00:08:09.270 --> 00:08:11.390 is the general term used in biology 00:08:11.390 --> 00:08:13.310 to refer to a small number of things 00:08:13.310 --> 00:08:16.800 rather than a large number of things. 00:08:16.800 --> 00:08:19.160 And, once again, we have, here, the possibility 00:08:19.160 --> 00:08:20.920 of extending this infinitely. 00:08:20.920 --> 00:08:22.810 There are no constraints, in principle, 00:08:22.810 --> 00:08:27.490 on making this 500, 1,000, even 2,000 amino acids long, 00:08:27.490 --> 00:08:30.400 where each one of these, once again, is an amino acid, 00:08:30.400 --> 00:08:33.840 and where once again I'm being very coy about the identities 00:08:33.840 --> 00:08:38.049 of R1 and R2, which, as I will indicate very shortly, 00:08:38.049 --> 00:08:41.549 can be one of 20 distinct alternatives. 00:08:41.549 --> 00:08:43.640 Here, you see that we are continuing 00:08:43.640 --> 00:08:47.030 this process of peptide bond formation. 00:08:47.030 --> 00:08:50.350 And most importantly here is the realization 00:08:50.350 --> 00:08:54.540 that there is a polarity of elongation here. 00:08:54.540 --> 00:08:57.210 It doesn't move with equal probability left or right, 00:08:57.210 --> 00:08:58.470 or right to left. 00:08:58.470 --> 00:09:00.480 We start at the amino end here. 00:09:00.480 --> 00:09:03.170 This is the amino end, and this is the carboxyl end. 00:09:03.170 --> 00:09:05.220 The amino end and the carboxyl end, 00:09:05.220 --> 00:09:07.970 and invariably, again because of the way life 00:09:07.970 --> 00:09:11.010 has evolved on this planet, the new amino acid 00:09:11.010 --> 00:09:13.600 is added on the carboxyl end. 00:09:13.600 --> 00:09:16.830 And so, when one often talks about proteins, 00:09:16.830 --> 00:09:22.380 one refers to their N terminal, and to their C terminal 00:09:22.380 --> 00:09:27.150 ends, these referring obviously to the amino group 00:09:27.150 --> 00:09:30.120 at one end and a carboxyl and at the other end 00:09:30.120 --> 00:09:34.020 so that polarity is always a directed synthesis adding it 00:09:34.020 --> 00:09:36.260 on C-terminal end, in other words 00:09:36.260 --> 00:09:41.150 to use a short-hand notation, we think about proteins 00:09:41.150 --> 00:09:44.550 as going with this polarity N toward C. 00:09:44.550 --> 00:09:48.300 Things are growing at the C terminal end progressively. 00:09:48.300 --> 00:09:52.990 And, each time one can imagine the addition of an amino acid 00:09:52.990 --> 00:09:53.700 on the end of it. 00:09:53.700 --> 00:09:57.550 So, again, it can be extended, in principle, indefinitely. 00:09:57.550 --> 00:10:00.240 Keep in mind as well, something that's implicit in everything 00:10:00.240 --> 00:10:03.250 I'm telling you but I won't always mention it explicitly, 00:10:03.250 --> 00:10:06.180 and that is virtually every biochemical reaction 00:10:06.180 --> 00:10:08.310 is reversible. 00:10:08.310 --> 00:10:12.620 And therefore, if one is able to form a peptide bond, 00:10:12.620 --> 00:10:16.660 one is able to break it down by biological means as well, i.e. 00:10:16.660 --> 00:10:21.460 by introducing a water molecule back in and thereby using 00:10:21.460 --> 00:10:25.030 the process of hydrolysis, which is the breakdown 00:10:25.030 --> 00:10:27.300 of a bond through the introduction of a water 00:10:27.300 --> 00:10:32.630 molecule to destroy the previously created bond. 00:10:32.630 --> 00:10:36.210 To use an MIT phrase, the reversibility is intuitively 00:10:36.210 --> 00:10:40.840 obvious because if you are able to make a, well, 00:10:40.840 --> 00:10:44.080 I don't know if it?s still used, but it was used in the late 00:10:44.080 --> 00:10:45.320 Stone Age around here. 00:10:45.320 --> 00:10:49.540 Anyhow, any biochemical action must be reversible 00:10:49.540 --> 00:10:52.370 because if, for example, this polymerization were 00:10:52.370 --> 00:10:55.370 irreversible, then all the protein that was ever 00:10:55.370 --> 00:10:57.900 synthesized on the surface of the planet over the last 3 1/2 00:10:57.900 --> 00:11:00.100 billion years would accumulate progressively. 00:11:00.100 --> 00:11:01.900 And obviously, that doesn't happen. 00:11:01.900 --> 00:11:04.550 And therefore, macromolecular synthesis, 00:11:04.550 --> 00:11:06.190 to the extent that it proceeds forward, 00:11:06.190 --> 00:11:09.820 obviously must go the other direction as well. 00:11:09.820 --> 00:11:12.570 And the resulting concentration of a complete protein 00:11:12.570 --> 00:11:15.210 is known as its steady state. 00:11:15.210 --> 00:11:18.900 So we might make a protein at one rate 00:11:18.900 --> 00:11:20.570 and break it down at the same rate. 00:11:20.570 --> 00:11:23.160 And its steady-state concentration 00:11:23.160 --> 00:11:26.030 represents the compromise between these two, i.e., 00:11:26.030 --> 00:11:28.380 the concentration of such a protein 00:11:28.380 --> 00:11:31.459 that we might observe at any one point in time. 00:11:31.459 --> 00:11:32.750 Indeed, the term ?steady-state? 00:11:32.750 --> 00:11:37.000 could be expanded to any process in which there is a synthesis 00:11:37.000 --> 00:11:38.820 and there is a breakdown of something. 00:11:38.820 --> 00:11:41.160 And the equilibrium concentration 00:11:41.160 --> 00:11:45.190 which results is, once again, called the steady-state 00:11:45.190 --> 00:11:47.100 of that molecule. 00:11:47.100 --> 00:11:49.300 Now, let's get down to the nitty-gritty, 00:11:49.300 --> 00:11:52.130 which is obviously something which 00:11:52.130 --> 00:11:55.260 we can't avoid for very long, which is to say the R's, i.e. 00:11:55.260 --> 00:11:57.280 the side chains. 00:11:57.280 --> 00:12:00.610 Once again, here we see an arbitrary artifact 00:12:00.610 --> 00:12:03.710 of very early evolution in the biosphere 00:12:03.710 --> 00:12:08.070 because there are, in effect, 20 different side chains creating 00:12:08.070 --> 00:12:11.460 20 distinct amino acids, which are 00:12:11.460 --> 00:12:15.350 used in proteins by all organisms on this planet. 00:12:15.350 --> 00:12:17.360 Again, there are rare exceptions, 00:12:17.360 --> 00:12:20.230 certain fungi and certain bacteria 00:12:20.230 --> 00:12:22.690 are able to make unusual amino acids. 00:12:22.690 --> 00:12:24.400 But these are the basic building blocks 00:12:24.400 --> 00:12:28.440 of virtually all life forms on the planet. 00:12:28.440 --> 00:12:30.440 99.99% of all the protein that is created 00:12:30.440 --> 00:12:34.870 is synthesized through the polymerization of these 20 00:12:34.870 --> 00:12:36.800 amino acids. 00:12:36.800 --> 00:12:40.540 And, by the way, one of the amino acids, glycine, 00:12:40.540 --> 00:12:42.940 over here, you see it right here, 00:12:42.940 --> 00:12:46.010 violates this rule of chirality. 00:12:46.010 --> 00:12:47.990 And, you will recall before I said 00:12:47.990 --> 00:12:52.920 that because there are four distinct amino acids, 00:12:52.920 --> 00:12:55.730 four distinct side chains around a central carbon 00:12:55.730 --> 00:12:57.340 sometimes called the alpha carbon, 00:12:57.340 --> 00:13:00.280 you always have a handedness of amino acids. 00:13:00.280 --> 00:13:04.560 But this notion cannot be respected in the case 00:13:04.560 --> 00:13:09.282 of glycine seen up here simply because we don't have four 00:13:09.282 --> 00:13:11.740 distinct, here's the central carbon where I'm pointing with 00:13:11.740 --> 00:13:15.881 the red, and here these two hydrogens are equivalent to one 00:13:15.881 --> 00:13:16.380 another. 00:13:16.380 --> 00:13:17.680 They are not four distinct chains. 00:13:17.680 --> 00:13:19.440 There's only three distinct chains here. 00:13:19.440 --> 00:13:22.130 So glycine violates this rule of chirality, 00:13:22.130 --> 00:13:24.530 of left- and right-handedness. 00:13:24.530 --> 00:13:27.010 And here, by the way, the side chain, 00:13:27.010 --> 00:13:30.620 which in all of these cases is depicted as extending off 00:13:30.620 --> 00:13:33.140 to the right of each amino acid, the side chain 00:13:33.140 --> 00:13:38.040 is simply an H, simply a proton, a hydrogen atom. 00:13:38.040 --> 00:13:41.870 In fact, what we see about these amino acids 00:13:41.870 --> 00:13:44.280 is that the side chains have quite 00:13:44.280 --> 00:13:46.900 distinct biochemical properties. 00:13:46.900 --> 00:13:50.040 And that begins to impress us with the notion 00:13:50.040 --> 00:13:53.250 that proteins and their biochemical attributes 00:13:53.250 --> 00:13:57.100 can be dictated by the identities of the amino acids 00:13:57.100 --> 00:13:59.220 that are used to construct them. 00:13:59.220 --> 00:14:01.830 We can talk about the notion of nonpolar 00:14:01.830 --> 00:14:05.960 versus polar amino acids, i.e., amino acids 00:14:05.960 --> 00:14:10.010 which have poor affinity for water. 00:14:10.010 --> 00:14:14.990 They don't have a separation of plus and minus charges. 00:14:14.990 --> 00:14:19.600 And as a consequence, they are a little bit or quite a bit 00:14:19.600 --> 00:14:21.402 hydrophobic. 00:14:21.402 --> 00:14:23.610 Now, you will say, well, how can they be hydrophobic, 00:14:23.610 --> 00:14:25.680 because here this oxygen is charged, 00:14:25.680 --> 00:14:28.100 and here this amine group is charged? 00:14:28.100 --> 00:14:30.560 That would make it highly hydrophilic. 00:14:30.560 --> 00:14:32.390 But keep in mind, when I'm talking 00:14:32.390 --> 00:14:35.180 about these amino acids, I'm not talking about them 00:14:35.180 --> 00:14:37.460 when they are in a single amino acid form. 00:14:37.460 --> 00:14:39.440 I'm talking about their properties 00:14:39.440 --> 00:14:43.650 once they have been polymerized into state like this. 00:14:43.650 --> 00:14:46.500 And, once they are polymerized into state like this, 00:14:46.500 --> 00:14:51.580 the NH2 and CO charging, that is, the charge here 00:14:51.580 --> 00:14:53.360 and the charge here become irrelevant 00:14:53.360 --> 00:14:55.710 because this oxygen and this amine group 00:14:55.710 --> 00:14:58.120 are both tied up in covalent bonds. 00:14:58.120 --> 00:15:01.640 And, this acquisition of a proton and this shedding 00:15:01.640 --> 00:15:04.670 of a proton over here cannot occur, 00:15:04.670 --> 00:15:07.330 because both of these atoms, O and N, 00:15:07.330 --> 00:15:09.640 are involved in covalent bonds. 00:15:09.640 --> 00:15:14.730 So therefore, when we talk about nonpolar and polar amino acids, 00:15:14.730 --> 00:15:18.330 keep in mind we are focusing on the biochemical properties 00:15:18.330 --> 00:15:21.990 of the side chain because the central backbone 00:15:21.990 --> 00:15:24.930 of the polypeptide and the central backbone 00:15:24.930 --> 00:15:26.581 is defined quite clearly here. 00:15:26.581 --> 00:15:28.080 Here's the central backbone, and you 00:15:28.080 --> 00:15:33.380 see it has a quite repeating structure, N, C, C, N, C, C, N, 00:15:33.380 --> 00:15:34.850 C, C, this is invariant. 00:15:37.360 --> 00:15:41.790 What changes, and what defines the biochemical attributes 00:15:41.790 --> 00:15:45.410 of this oligopeptide, or a polypeptide, 00:15:45.410 --> 00:15:47.560 are the identities of these side chains, which 00:15:47.560 --> 00:15:50.070 again are plotted on this particular graph. 00:15:50.070 --> 00:15:53.710 You have a different version in your book off to the right. 00:15:53.710 --> 00:15:56.880 Here, you see, we have a proton, a methyl group, a valine, 00:15:56.880 --> 00:16:01.360 a lucine, an isolucine, and the differences 00:16:01.360 --> 00:16:08.270 between this suggests these are all quite aliphatic, quite 00:16:08.270 --> 00:16:14.160 similar to the propane that we talked about last time, 00:16:14.160 --> 00:16:15.210 or the hexane. 00:16:15.210 --> 00:16:18.440 That is to say, these are quite hydrophobic side groups. 00:16:18.440 --> 00:16:22.730 And, as such, if there were a polypeptide, we can imagine, 00:16:22.730 --> 00:16:24.870 and you put the polypeptide in water, 00:16:24.870 --> 00:16:28.080 you can imagine that these amino acids would not 00:16:28.080 --> 00:16:31.110 like to be directly confronting the water because of the fact 00:16:31.110 --> 00:16:33.140 that they are hydrophobic. 00:16:33.140 --> 00:16:37.150 Methionine is also a bit hydrophobic. 00:16:37.150 --> 00:16:41.130 I'm equivocating there because the S 00:16:41.130 --> 00:16:44.590 has a slight degree of hydrophilicity. 00:16:44.590 --> 00:16:46.690 It has a slight degree of polarity, 00:16:46.690 --> 00:16:48.230 but not really that much. 00:16:48.230 --> 00:16:50.600 And, these aromatic side chains here, 00:16:50.600 --> 00:16:52.810 because they have these benzene rings, 00:16:52.810 --> 00:16:55.340 consequently are called aromatic. 00:16:55.340 --> 00:16:58.520 These are quite strongly hydrophobic. 00:16:58.520 --> 00:17:02.240 So, they really hate to be in the intimate contact 00:17:02.240 --> 00:17:03.690 with water. 00:17:03.690 --> 00:17:06.530 Here, on the other hand, let's look at these side chains 00:17:06.530 --> 00:17:13.530 because here we have strongly polar molecules, 00:17:13.530 --> 00:17:14.970 side chains again. 00:17:14.970 --> 00:17:17.380 Keep in mind we are focusing on the side chains. 00:17:17.380 --> 00:17:19.470 Here we see serine with the hydroxyl group that 00:17:19.470 --> 00:17:22.280 can form hydrogen bonds with the water, threonine, which 00:17:22.280 --> 00:17:25.460 has its own hydroxyl group, asparagine, 00:17:25.460 --> 00:17:28.800 which has two atoms here, this carbonyl and the NH2, 00:17:28.800 --> 00:17:33.220 both of which can form hydrogen bonds with the water, 00:17:33.220 --> 00:17:35.520 as can glutamine. 00:17:35.520 --> 00:17:37.540 So, these are quite hydrophilic. 00:17:37.540 --> 00:17:41.340 They are not as fanatically hydrophilic as these charge 00:17:41.340 --> 00:17:43.570 molecules where the side chains are not 00:17:43.570 --> 00:17:46.210 just capable of forming hydrogen bonds. 00:17:46.210 --> 00:17:48.580 In this lower group here, the side chains 00:17:48.580 --> 00:17:50.750 are capable of undergoing ionization. 00:17:50.750 --> 00:17:53.150 So they're actually strongly charged. 00:17:53.150 --> 00:17:56.820 And here, we see here the carboxyl group, 00:17:56.820 --> 00:17:59.390 and our aspartic acid and glutamic acid 00:17:59.390 --> 00:18:01.410 has actually discharged its proton, 00:18:01.410 --> 00:18:03.630 becoming negatively charged. 00:18:03.630 --> 00:18:05.950 These are acidic amino acids, by virtue 00:18:05.950 --> 00:18:09.130 of the carboxyl group they have, basic amino acids 00:18:09.130 --> 00:18:12.600 here: arginine, lysine, and histidine, 00:18:12.600 --> 00:18:15.380 all acquire a positively charged side 00:18:15.380 --> 00:18:18.110 chain by virtue of these nitrogen 00:18:18.110 --> 00:18:21.100 here which have a strong affinity for pulling away 00:18:21.100 --> 00:18:25.760 protons or abstracting protons from the aqueous solvent. 00:18:25.760 --> 00:18:30.080 And so, we have a whole gradient of hydrophilicity 00:18:30.080 --> 00:18:32.510 down to hydrophobicity. 00:18:32.510 --> 00:18:35.260 And here, we have intermediate structures. 00:18:35.260 --> 00:18:38.990 We also have some very special idiosyncratic kinds 00:18:38.990 --> 00:18:40.310 of amino acids. 00:18:40.310 --> 00:18:43.610 Here is tyrosine, and tyrosine is little bit schizophrenic 00:18:43.610 --> 00:18:44.230 again. 00:18:44.230 --> 00:18:47.340 It has this highly hydrophobic aromatic group here, 00:18:47.340 --> 00:18:50.090 the benzene ring, which hates to be in water, 00:18:50.090 --> 00:18:53.130 and the hydroxyl group which actually is a friend of water. 00:18:53.130 --> 00:18:54.680 So, here, we have something where 00:18:54.680 --> 00:18:57.710 its role is quite equivocal. 00:18:57.710 --> 00:19:01.090 Here, we have cystine, as indicated here, 00:19:01.090 --> 00:19:03.190 and what's interesting about the cystine group 00:19:03.190 --> 00:19:06.860 in this case is the SH group, the side chain, the SH 00:19:06.860 --> 00:19:12.280 group, because this SH group is able to form bonds with yet 00:19:12.280 --> 00:19:15.130 other SH groups from other cystines. 00:19:15.130 --> 00:19:18.250 So, let's just look at the cystine here for a moment. 00:19:18.250 --> 00:19:21.230 You see there's a CH2, and then there's an SH. 00:19:21.230 --> 00:19:23.860 So, let's imagine, I'm not going to draw all the atoms here, 00:19:23.860 --> 00:19:25.870 but let's imagine here we have the CH2 group. 00:19:25.870 --> 00:19:29.270 I'm not drawing the backbone, SH, over here. 00:19:29.270 --> 00:19:31.280 And, we can imagine another protein chain, 00:19:31.280 --> 00:19:33.820 another polypeptide chain down here. 00:19:33.820 --> 00:19:37.390 Again, I'm not drawing the backbone, 00:19:37.390 --> 00:19:40.550 but I'm drawing another SH like this. 00:19:40.550 --> 00:19:43.290 And, the fact is, under the conditions of oxidation 00:19:43.290 --> 00:19:46.990 and reduction that operate at least in the extracellular 00:19:46.990 --> 00:19:50.870 space, one can oxidize this, these two, 00:19:50.870 --> 00:19:52.730 resulting in the formation of what 00:19:52.730 --> 00:19:55.350 is known as a disulfide bond. 00:19:59.820 --> 00:20:02.280 So, here, we have now for the first notion 00:20:02.280 --> 00:20:07.060 the idea that the polypeptide chains can be covalently linked 00:20:07.060 --> 00:20:11.790 to one another through these cross-links, as indicated here. 00:20:11.790 --> 00:20:14.130 Conversely, if you add a reducing agent 00:20:14.130 --> 00:20:16.600 that will add protons back to this, 00:20:16.600 --> 00:20:20.050 and reduce the oxidation state of the sulfurs, 00:20:20.050 --> 00:20:25.400 once again causing the disulfide bond to fall apart. 00:20:25.400 --> 00:20:27.880 Now, in principle, these disulfide bonds 00:20:27.880 --> 00:20:31.070 could be used to link two proteins together. 00:20:31.070 --> 00:20:33.230 But, more often than not, if you look 00:20:33.230 --> 00:20:36.760 at the structure of a single protein, 00:20:36.760 --> 00:20:38.900 here's the structure of a single protein. 00:20:38.900 --> 00:20:44.750 And often, there are intramolecular bonds, 00:20:44.750 --> 00:20:49.020 disulfide bonds, i.e., bonds from one domain 00:20:49.020 --> 00:20:51.410 of the protein to another, from one part of the protein 00:20:51.410 --> 00:20:52.170 to the other. 00:20:52.170 --> 00:20:53.710 I'll draw them in right here. 00:20:53.710 --> 00:20:55.610 Here might be a disulfide bond. 00:20:55.610 --> 00:20:58.130 Here might be a disulfide bond, and I could go on and on. 00:20:58.130 --> 00:21:00.100 There might be another one over here. 00:21:00.100 --> 00:21:02.860 Why do we have these disulfide bonds? 00:21:02.860 --> 00:21:05.410 Because as we will indicate very shortly, 00:21:05.410 --> 00:21:07.710 the three-dimensional structure of a protein 00:21:07.710 --> 00:21:11.070 is very specifically determined. 00:21:11.070 --> 00:21:12.680 A protein can only function when it 00:21:12.680 --> 00:21:14.640 assumes a certain three-dimensional 00:21:14.640 --> 00:21:18.990 configuration, when it assumes a certain three-dimensional, 00:21:18.990 --> 00:21:25.090 stereochemical configuration. 00:21:25.090 --> 00:21:27.250 When we talk about stereochemistry, 00:21:27.250 --> 00:21:29.790 we are talking about the three-dimensional structures 00:21:29.790 --> 00:21:32.040 of molecules, small and large. 00:21:32.040 --> 00:21:34.970 And, here, we begin to touch on a theme of how 00:21:34.970 --> 00:21:39.470 these complex polypeptide chains are able to create proteins 00:21:39.470 --> 00:21:42.340 that have very specific, often very rigid, 00:21:42.340 --> 00:21:44.950 structures in three-dimensional space. 00:21:44.950 --> 00:21:47.530 Part of this structural rigidity is maintained 00:21:47.530 --> 00:21:52.760 by these covalent disulfide bonds, which 00:21:52.760 --> 00:21:55.930 tightly link neighboring regions, or even not 00:21:55.930 --> 00:22:00.640 so neighboring regions, of a single polypeptide chain, 00:22:00.640 --> 00:22:03.290 these intramolecular links. 00:22:03.290 --> 00:22:06.310 This doesn't preclude there being intermolecular links 00:22:06.310 --> 00:22:08.360 between two polypeptide chains that 00:22:08.360 --> 00:22:12.760 are mediated as well by the disulfide bonds. 00:22:12.760 --> 00:22:15.190 Here's another very peculiar amino acid 00:22:15.190 --> 00:22:19.550 because what you see here is at the side chain, which 00:22:19.550 --> 00:22:24.110 is CH2, CH2, CH2, CH2 is hydrogen bonded here 00:22:24.110 --> 00:22:26.260 to the amine group. 00:22:26.260 --> 00:22:29.790 It's not swinging out in free space. 00:22:29.790 --> 00:22:31.280 I misspoke. 00:22:31.280 --> 00:22:35.020 What we see here is CH2, CH2 is covalent bonded 00:22:35.020 --> 00:22:36.170 to the amine group. 00:22:36.170 --> 00:22:38.150 You pick that up, right? 00:22:38.150 --> 00:22:40.760 I was just testing you. 00:22:40.760 --> 00:22:41.410 Sure I was. 00:22:41.410 --> 00:22:44.040 OK, so here we see a five-membered ring 00:22:44.040 --> 00:22:45.520 that's created. 00:22:45.520 --> 00:22:48.260 So here, this thing is not swinging out in free space. 00:22:48.260 --> 00:22:51.900 It creates a five-membered ring where the end of the side chain 00:22:51.900 --> 00:22:54.830 is actually covalently linked to the amino group. 00:22:54.830 --> 00:22:57.920 And, that also has implications for the structure of proteins 00:22:57.920 --> 00:23:00.580 because this particular amino acid, whenever 00:23:00.580 --> 00:23:03.500 it occurs within a polypeptide chain, 00:23:03.500 --> 00:23:06.760 doesn't have the flexibility of assuming certain configurations 00:23:06.760 --> 00:23:10.630 that the other ones have whose four side chains are not 00:23:10.630 --> 00:23:12.490 so encumbered. 00:23:12.490 --> 00:23:14.150 None of them has total flexibility, 00:23:14.150 --> 00:23:16.380 but this one is far more encumbered 00:23:16.380 --> 00:23:19.160 in the kinds of three-dimensional structures 00:23:19.160 --> 00:23:21.520 that it can assume. 00:23:21.520 --> 00:23:26.050 And, with that in mind, we begin to ask questions 00:23:26.050 --> 00:23:29.510 about how polypeptide chains assume 00:23:29.510 --> 00:23:31.500 three-dimensional structure. 00:23:31.500 --> 00:23:36.570 If we talk about a polypeptide chain, in our minds, 00:23:36.570 --> 00:23:41.285 hopefully, there's only 28 combinations. 00:23:44.400 --> 00:23:46.410 Oh, am I good or what? 00:23:46.410 --> 00:23:50.340 Anyhow, all right, so, look here. 00:23:50.340 --> 00:23:55.170 And here, you see, this is a typical polypeptide chain. 00:23:55.170 --> 00:23:57.570 Here, we have a three letter code. 00:23:57.570 --> 00:23:59.990 In truth, there is a single letter code 00:23:59.990 --> 00:24:02.480 which was introduced around 1965. 00:24:02.480 --> 00:24:07.090 So, each of the 20 amino acids has its own single letter code. 00:24:07.090 --> 00:24:13.020 And, to make a frank and depressing admission, 35 years, 00:24:13.020 --> 00:24:15.430 40 years after the single amino acid letter 00:24:15.430 --> 00:24:18.845 code was instituted, I still haven't learned it. 00:24:18.845 --> 00:24:20.720 But, we could learn these three letter codes, 00:24:20.720 --> 00:24:23.760 which fortunately are present here. 00:24:23.760 --> 00:24:25.820 In the single letter code L is lucine, 00:24:25.820 --> 00:24:31.580 and A is alanine, see, they know it. 00:24:31.580 --> 00:24:33.130 This is another example of not being 00:24:33.130 --> 00:24:35.860 able to teach old dogs new tricks. 00:24:35.860 --> 00:24:39.710 Anyhow, so here we see the way, one way 00:24:39.710 --> 00:24:44.060 by which one might depict an amino acid chain, 00:24:44.060 --> 00:24:45.250 a polypeptide chain. 00:24:45.250 --> 00:24:49.490 And keep in mind, this can go on indefinitely. 00:24:49.490 --> 00:24:52.140 As we begin to wrestle with the three-dimensional structure 00:24:52.140 --> 00:24:54.700 of the chain, we begin to realize the following, 00:24:54.700 --> 00:24:58.700 and that is that after the chain is initially synthesized, 00:24:58.700 --> 00:25:00.720 it's initially chaotic. 00:25:00.720 --> 00:25:03.330 And, as it extends, it increasingly 00:25:03.330 --> 00:25:09.110 begins to assume a very specific three-dimensional molecular 00:25:09.110 --> 00:25:11.440 configuration which is indicated down here. 00:25:11.440 --> 00:25:14.910 So, the chaos that operates initially 00:25:14.910 --> 00:25:19.570 will eventually result in a native configuration over here, 00:25:19.570 --> 00:25:22.610 which in many respects often represents the lowest 00:25:22.610 --> 00:25:24.810 free energy state. 00:25:24.810 --> 00:25:28.250 Since for the last 40 years, people have been trying 00:25:28.250 --> 00:25:31.100 to figure out, if you knew the amino acid sequence of this 00:25:31.100 --> 00:25:35.270 primary polypeptide here, if you knew its primary structure, 00:25:35.270 --> 00:25:37.320 and when I say, ?primary structure,? 00:25:37.320 --> 00:25:39.965 what I mean is the sequence of the amino acids. 00:25:39.965 --> 00:25:42.340 So, if you knew the primary structure of the amino acids, 00:25:42.340 --> 00:25:45.840 you should, in principle, be able to develop a computer 00:25:45.840 --> 00:25:48.310 algorithm that would predict the three-dimensional 00:25:48.310 --> 00:25:51.530 configuration, which is shown here in a very schematic way, 00:25:51.530 --> 00:25:54.930 and which we will discuss in much greater detail shortly. 00:25:54.930 --> 00:25:57.580 And, the fact is, after 40 years of trying, 00:25:57.580 --> 00:26:00.480 one still is unable to do that, i.e., 00:26:00.480 --> 00:26:04.210 if I were to give the primary amino acid 00:26:04.210 --> 00:26:07.330 sequence of the polypeptide to the smartest 00:26:07.330 --> 00:26:10.550 biochemists in the world, and there are some very smart ones, 00:26:10.550 --> 00:26:12.560 he or she could still not tell me 00:26:12.560 --> 00:26:14.110 what the three-dimensional structure 00:26:14.110 --> 00:26:18.261 of this protein with total certainty would be. 00:26:18.261 --> 00:26:18.760 Why? 00:26:18.760 --> 00:26:21.320 Because there's an almost infinite number 00:26:21.320 --> 00:26:24.550 of intramolecular interactions that greatly 00:26:24.550 --> 00:26:29.760 complicate how the protein assumes the structure. 00:26:29.760 --> 00:26:32.530 Moreover, if we talk about this as the native state 00:26:32.530 --> 00:26:35.870 of the protein, we can imagine that there?s ways of disrupting 00:26:35.870 --> 00:26:38.840 that because much of this native state is created 00:26:38.840 --> 00:26:42.360 by intramolecular hydrogen bonds. 00:26:42.360 --> 00:26:44.700 Remember, the hydrogen bonds are relatively weak, 00:26:44.700 --> 00:26:49.070 and if we heat up the temperature, 00:26:49.070 --> 00:26:51.120 then we can break hydrogen bonds. 00:26:51.120 --> 00:26:55.650 And therefore, every time we fry an egg, for example, 00:26:55.650 --> 00:26:58.300 if we want to get down to Earth, we denature. 00:26:58.300 --> 00:27:02.000 We break up the native three-dimensional structure 00:27:02.000 --> 00:27:05.360 of the albumin molecules that constitute the egg white. 00:27:05.360 --> 00:27:07.640 And so, when everything turns white, what we've done 00:27:07.640 --> 00:27:10.880 is to take a native molecule like this, heated it 00:27:10.880 --> 00:27:13.700 up to temperatures where the intramolecular 00:27:13.700 --> 00:27:16.130 bonds no longer stabilize. 00:27:16.130 --> 00:27:17.670 Notably, hydrogen bonds no longer 00:27:17.670 --> 00:27:20.130 stabilize this three-dimensional configuration, 00:27:20.130 --> 00:27:23.480 and we put it into a denatured state, which 00:27:23.480 --> 00:27:26.450 might be all the way up here. 00:27:26.450 --> 00:27:30.960 And, therefore, this acquisition of a native configuration, 00:27:30.960 --> 00:27:35.350 or a native state, native representing the natural state, 00:27:35.350 --> 00:27:38.830 is also reversible in many molecules 00:27:38.830 --> 00:27:40.710 simply by heating them up. 00:27:40.710 --> 00:27:42.750 There are to be sure yet other molecules which 00:27:42.750 --> 00:27:45.290 are different from the egg white from the albumin in egg 00:27:45.290 --> 00:27:47.310 white where if you cool them back down, 00:27:47.310 --> 00:27:50.960 they will spontaneously reassume their native structure. 00:27:50.960 --> 00:27:54.360 Many proteins, most, will not do so. 00:27:54.360 --> 00:27:57.450 Well, again, let's go back to this issue of the acquisition 00:27:57.450 --> 00:27:59.720 of complex, three-dimensional structure. 00:27:59.720 --> 00:28:04.590 And here, we begin to see how some of this structure 00:28:04.590 --> 00:28:08.650 is acquired and stabilized through these intramolecular 00:28:08.650 --> 00:28:09.810 hydrogen bonds. 00:28:09.810 --> 00:28:12.650 And there are many opportunities for these intramolecular 00:28:12.650 --> 00:28:15.740 hydrogen bonds because here we see one polypeptide chain here, 00:28:15.740 --> 00:28:17.200 here we see another. 00:28:17.200 --> 00:28:20.780 And, we see that the NH2 group right here, I'm sorry, 00:28:20.780 --> 00:28:24.440 the nitrogen group here with the proton side chain, 00:28:24.440 --> 00:28:28.740 and the carbonyl group here with the oxygen are not encumbered. 00:28:28.740 --> 00:28:31.860 They are, in principle, available to form hydrogen 00:28:31.860 --> 00:28:35.900 bonds with a polypeptide chain somewhere else. 00:28:35.900 --> 00:28:37.770 Now, this other polypeptide chain 00:28:37.770 --> 00:28:39.790 could once again be from another protein, 00:28:39.790 --> 00:28:41.450 from another polypeptide. 00:28:41.450 --> 00:28:44.300 But more often than not, we are once again 00:28:44.300 --> 00:28:49.090 dealing with intramolecular cross-links. 00:28:49.090 --> 00:28:51.330 But in this case, the intramolecular cross-links 00:28:51.330 --> 00:28:54.060 are not disulfide bonds which are covalent, 00:28:54.060 --> 00:28:58.080 and hard and stable as a rock in the absence of reducing agents. 00:28:58.080 --> 00:29:01.090 Here, we're talking about much weaker bonds, hydrogen bonds 00:29:01.090 --> 00:29:07.080 which also act between different loops of the protein 00:29:07.080 --> 00:29:09.880 and serve, once again, to stabilize 00:29:09.880 --> 00:29:12.510 the three-dimensional structure, the native state 00:29:12.510 --> 00:29:14.180 of the protein. 00:29:14.180 --> 00:29:16.880 And, you can see how these opportunities for forming 00:29:16.880 --> 00:29:18.900 multiple hydrogen bonds can create 00:29:18.900 --> 00:29:22.840 an enormous degree of stability. 00:29:22.840 --> 00:29:25.730 And, here are some examples of what we now 00:29:25.730 --> 00:29:29.450 call the secondary structure of the protein. 00:29:29.450 --> 00:29:32.510 Just a second ago, or several minutes ago to be honest, 00:29:32.510 --> 00:29:35.590 and I'm always honest with you, class, 00:29:35.590 --> 00:29:39.000 the primary structure is the amino acid sequence. 00:29:39.000 --> 00:29:41.080 The secondary structure represents 00:29:41.080 --> 00:29:42.760 configurations like this. 00:29:42.760 --> 00:29:46.120 Here is an alpha helix. 00:29:46.120 --> 00:29:49.370 Here is a beta pleated sheet. 00:29:49.370 --> 00:29:51.250 And, what we see here in this alpha helix 00:29:51.250 --> 00:29:55.000 is we have a helical structure where the amine group down 00:29:55.000 --> 00:29:58.630 here, the NH group, hydrogen bonds with a residue that is, 00:29:58.630 --> 00:30:00.900 I think, three and a half residues upstream, 00:30:00.900 --> 00:30:04.680 one, two, there's an amine down there, so, 00:30:04.680 --> 00:30:07.420 with the carbonyl group that's three and a half residues 00:30:07.420 --> 00:30:08.920 upstream of it. 00:30:08.920 --> 00:30:12.230 This one, once again, reaches three and a half residues 00:30:12.230 --> 00:30:13.020 upstream. 00:30:13.020 --> 00:30:16.150 Not all the hydrogen bonds are shown in the background. 00:30:16.150 --> 00:30:18.520 Only the ones on our side of the helix 00:30:18.520 --> 00:30:20.410 are shown, on the front side of the helix. 00:30:20.410 --> 00:30:23.360 But, you can imagine that this can perpetuate itself. 00:30:23.360 --> 00:30:25.390 And, each of these carbonyl's may 00:30:25.390 --> 00:30:29.080 associate with a proton, an NH group that's 00:30:29.080 --> 00:30:32.280 either above or below that particular residue. 00:30:32.280 --> 00:30:35.540 And this, in turn, can create a helical structure. 00:30:35.540 --> 00:30:38.670 By the way, proline doesn't fit well. 00:30:38.670 --> 00:30:41.750 If you add a proline in here, proline 00:30:41.750 --> 00:30:45.411 is known in the trade as a helix breaker. 00:30:45.411 --> 00:30:45.910 Why? 00:30:45.910 --> 00:30:49.860 Because it cannot twist itself around to form an alpha helix. 00:30:49.860 --> 00:30:51.970 And so, if the primary amino acid 00:30:51.970 --> 00:30:54.800 were to dictate that a proline would be inserted right 00:30:54.800 --> 00:30:57.210 here, for example, then this helix 00:30:57.210 --> 00:31:00.070 might exist down below and above, 00:31:00.070 --> 00:31:02.680 but it would not be continuous because the presence 00:31:02.680 --> 00:31:06.020 of a proline is highly disruptive of the formation 00:31:06.020 --> 00:31:09.254 of an alpha helix. 00:31:09.254 --> 00:31:10.670 This means that, in principle, you 00:31:10.670 --> 00:31:13.410 can make some predictions about the localized 00:31:13.410 --> 00:31:16.190 structure of a polypeptide by knowing whether or not 00:31:16.190 --> 00:31:18.130 proline is present, for example. 00:31:18.130 --> 00:31:19.960 But that still doesn't give you the power 00:31:19.960 --> 00:31:22.720 to predict the entire three-dimensional structure 00:31:22.720 --> 00:31:25.620 of the finished protein itself. 00:31:25.620 --> 00:31:29.060 Now, let's agree that this is the secondary structure 00:31:29.060 --> 00:31:32.080 of the protein, i.e., the various domains which often 00:31:32.080 --> 00:31:35.740 form alpha helices within a certain segment of the protein 00:31:35.740 --> 00:31:37.890 or a certain segment of the protein 00:31:37.890 --> 00:31:39.700 will form beta pleated sheets. 00:31:39.700 --> 00:31:42.120 And there are several other less common kinds 00:31:42.120 --> 00:31:44.890 of secondary structure. 00:31:44.890 --> 00:31:48.260 And here, we deal with tertiary structure. 00:31:48.260 --> 00:31:50.220 Now we are getting really interesting. 00:31:50.220 --> 00:31:51.740 Or, maybe you don't like it. 00:31:51.740 --> 00:31:54.120 But some people say it's really interesting 00:31:54.120 --> 00:31:57.610 because here are the tertiary structures of some arbitrarily 00:31:57.610 --> 00:31:59.930 chosen proteins. 00:31:59.930 --> 00:32:04.140 Here, the tertiary structure of this particular protein, 00:32:04.140 --> 00:32:08.880 and the identities of these are not given in our textbook. 00:32:08.880 --> 00:32:10.766 And, I'm sure if we spent two or three weeks, 00:32:10.766 --> 00:32:12.140 we could find out what they were. 00:32:12.140 --> 00:32:15.920 But anyhow, here is a protein, a three-dimensional structure 00:32:15.920 --> 00:32:20.960 of a protein which is composed of four alpha helices which 00:32:20.960 --> 00:32:22.510 go up. 00:32:22.510 --> 00:32:26.410 Another alpha helix, alpha helix, alpha helix, alpha 00:32:26.410 --> 00:32:28.630 helix, they are depicted here, fortunately, 00:32:28.630 --> 00:32:30.580 in four different colors. 00:32:30.580 --> 00:32:33.280 And so, we see that what we talk about tertiary structure, 00:32:33.280 --> 00:32:36.980 we're talking about how the alpha helices are disposed 00:32:36.980 --> 00:32:39.070 with respect to one another. 00:32:39.070 --> 00:32:41.070 The primary structure of the amino acid sequence 00:32:41.070 --> 00:32:42.410 is not shown here. 00:32:42.410 --> 00:32:45.240 The secondary structure represents these individual 00:32:45.240 --> 00:32:48.970 alpha helices, and the tertiary structure represents how these 00:32:48.970 --> 00:32:51.710 alpha helices are arranged vis-?-vis one another. 00:32:51.710 --> 00:32:55.430 Here is a protein which is structured much differently. 00:32:58.420 --> 00:33:02.310 It's formed of many beta pleated sheets. 00:33:02.310 --> 00:33:05.310 We saw that in the last figure, in the last overhead. 00:33:05.310 --> 00:33:08.300 You see it as a quite different overall three-dimensional 00:33:08.300 --> 00:33:09.790 structure. 00:33:09.790 --> 00:33:12.210 This could be the beginning of an alpha helix down here, 00:33:12.210 --> 00:33:14.560 although that's quite equivocal. 00:33:14.560 --> 00:33:16.200 And here, we see yet another point. 00:33:16.200 --> 00:33:19.230 And that is, as we said before, the tertiary structure 00:33:19.230 --> 00:33:23.620 independent of these alpha helices and beta pleated sheets 00:33:23.620 --> 00:33:28.420 may be stabilized by these covalent inter-strand 00:33:28.420 --> 00:33:31.650 cross-links formed by the cystines. 00:33:31.650 --> 00:33:33.800 And in the end, if we put all that together, 00:33:33.800 --> 00:33:36.360 then we come to the realization that the three-dimensional 00:33:36.360 --> 00:33:40.100 structure of a protein as determined by the art of x-ray 00:33:40.100 --> 00:33:47.190 -- There we go. 00:33:47.190 --> 00:33:49.940 I'm not actually dyslexic. 00:33:49.940 --> 00:33:52.250 I actually have a cousin who I won't mention 00:33:52.250 --> 00:33:54.650 whose son was so dyslexic that when he came to stairways 00:33:54.650 --> 00:33:56.910 he didn't know whether to put his foot up or down. 00:33:56.910 --> 00:33:58.010 Now that's difficulty. 00:33:58.010 --> 00:34:00.660 This is not so bad. 00:34:00.660 --> 00:34:03.970 OK, anyhow, because I solved it within less than two minutes 00:34:03.970 --> 00:34:05.614 time, all right, so here we see this 00:34:05.614 --> 00:34:07.780 is what the three-dimensional structure of a protein 00:34:07.780 --> 00:34:08.690 looks like. 00:34:08.690 --> 00:34:10.610 This is called a space-filling model 00:34:10.610 --> 00:34:12.969 because here, one draws in, as determined 00:34:12.969 --> 00:34:15.050 by x-ray crystallography what the, 00:34:15.050 --> 00:34:16.670 if we could see what a protein looks 00:34:16.670 --> 00:34:18.409 like, what it actually must look like, 00:34:18.409 --> 00:34:22.760 where each of the atoms including these side chains 00:34:22.760 --> 00:34:24.270 is actually depicted. 00:34:24.270 --> 00:34:28.832 Before, when we used these far more schematic descriptions 00:34:28.832 --> 00:34:31.290 like here, we were just talking about the overall structure 00:34:31.290 --> 00:34:31.956 of the backbone. 00:34:31.956 --> 00:34:35.739 We weren't really indicating where the side chains were, 00:34:35.739 --> 00:34:37.616 and what space they would fill up. 00:34:37.616 --> 00:34:39.199 And, if we give them the chance, if we 00:34:39.199 --> 00:34:42.190 put in all of the other atoms, the side chains, 00:34:42.190 --> 00:34:45.670 and we create a space-filling model where 00:34:45.670 --> 00:34:48.320 the actual atoms are shown, this is 00:34:48.320 --> 00:34:50.290 what the protein would look like. 00:34:50.290 --> 00:34:53.300 And the fact of the matter is that all virtually proteins 00:34:53.300 --> 00:34:55.710 have very specific structures. 00:34:55.710 --> 00:34:58.670 It's not as if they can shift from one structure to another. 00:34:58.670 --> 00:35:01.140 Once they leave their normal native structure 00:35:01.140 --> 00:35:07.910 they will lose their ability to do what their normal jobs are. 00:35:07.910 --> 00:35:10.980 And, this particular overhead happens 00:35:10.980 --> 00:35:12.660 to bring in yet another theme that we're 00:35:12.660 --> 00:35:14.720 going to focus on increasingly, which 00:35:14.720 --> 00:35:17.440 is, what do proteins do in cells? 00:35:17.440 --> 00:35:19.160 I'm glad I asked that question. 00:35:19.160 --> 00:35:23.320 One of the things they do is they act as catalysts, i.e. , 00:35:23.320 --> 00:35:25.290 as enzymes. 00:35:25.290 --> 00:35:27.860 The fact is, as we will discuss later, 00:35:27.860 --> 00:35:30.690 virtually all biochemical reactions 00:35:30.690 --> 00:35:35.530 require an enzyme catalyst in order to propel them forward. 00:35:35.530 --> 00:35:38.590 That is to say, if there's a biochemical reaction to occur, 00:35:38.590 --> 00:35:41.860 almost always it will not occur spontaneously 00:35:41.860 --> 00:35:44.360 the same way that a hydroxyl ion and a hydrogen 00:35:44.360 --> 00:35:46.890 will join together spontaneously in water. 00:35:46.890 --> 00:35:50.930 Almost all biochemical reactions require the mediation 00:35:50.930 --> 00:35:56.550 of an enzyme which is a biological catalyst in order 00:35:56.550 --> 00:35:58.510 to encourage this to happen. 00:35:58.510 --> 00:36:05.860 And, almost all catalysts in our cells are proteins. 00:36:05.860 --> 00:36:11.820 So, if you have 4,326 distinct biochemical reactions occurring 00:36:11.820 --> 00:36:14.110 in the cell, that means that there's probably 00:36:14.110 --> 00:36:16.830 almost as many distinct enzymes, each one of which 00:36:16.830 --> 00:36:19.800 is assigned to mediate one or another 00:36:19.800 --> 00:36:22.790 of those distinct biochemical reactions. 00:36:22.790 --> 00:36:24.400 And here, we see the fact that this 00:36:24.400 --> 00:36:28.510 is an enzyme which happens to be called hexokinase. 00:36:28.510 --> 00:36:31.160 Recall that the -ase suffix at the end 00:36:31.160 --> 00:36:34.270 dictates that this is already an enzyme rather 00:36:34.270 --> 00:36:35.850 than a carbohydrate. 00:36:35.850 --> 00:36:41.200 And, this attaches, in fact, a phosphate group onto glucose. 00:36:41.200 --> 00:36:43.800 And, what happens is that the glucose, which 00:36:43.800 --> 00:36:47.090 is the substrate, which is acted upon by the catalyst, 00:36:47.090 --> 00:36:51.330 is pulled into this site in the protein which 00:36:51.330 --> 00:36:56.570 is highly specialized to mediate the enzymatic reaction. 00:36:56.570 --> 00:36:59.270 Almost all the business of this complex enzyme 00:36:59.270 --> 00:37:01.930 is carried out right here. 00:37:01.930 --> 00:37:04.210 And somehow, a lot of the other amino acids 00:37:04.210 --> 00:37:06.900 that are located at a distance are doing other things 00:37:06.900 --> 00:37:09.670 like regulating the activity of the enzyme. 00:37:09.670 --> 00:37:11.700 But the actual business end of the enzyme 00:37:11.700 --> 00:37:16.720 is present in what is called a catalytic cleft, an active site 00:37:16.720 --> 00:37:19.360 of this enzyme in which the substrates are pulled in 00:37:19.360 --> 00:37:22.360 and are manipulated and changed chemically 00:37:22.360 --> 00:37:26.470 by the actions of this particular enzyme. 00:37:26.470 --> 00:37:31.180 Now, in saying that virtually all catalysts, but not all, are 00:37:31.180 --> 00:37:35.050 proteins, I also mean to say that proteins 00:37:35.050 --> 00:37:37.810 have a second major function in the body. 00:37:37.810 --> 00:37:41.010 The first major function is to act as enzymes in catalysts. 00:37:41.010 --> 00:37:45.450 The second major function is to create biochemical structures, 00:37:45.450 --> 00:37:49.560 i.e., structures of different cytoskeleton proteins such as I 00:37:49.560 --> 00:37:53.580 showed you two lectures ago. 00:37:53.580 --> 00:37:55.990 And so, we are going to come repeatedly to the situations 00:37:55.990 --> 00:37:59.160 where complex structural entities in the cell 00:37:59.160 --> 00:38:02.650 are composed of different structural proteins. 00:38:02.650 --> 00:38:04.590 Again, this is just a prelude to talking 00:38:04.590 --> 00:38:07.530 about these in greater details, these two major functions 00:38:07.530 --> 00:38:09.900 of enzymatic catalysis on the one hand, 00:38:09.900 --> 00:38:13.280 and creating structure on the other hand. 00:38:13.280 --> 00:38:17.550 And so now, we get to really four hierarchical levels 00:38:17.550 --> 00:38:20.590 of protein structure. 00:38:20.590 --> 00:38:25.980 The primary structure is the amino acid sequence. 00:38:25.980 --> 00:38:29.140 And, if we dwell for second on this amino acid sequence, 00:38:29.140 --> 00:38:32.270 let's realize that any single amino acid can 00:38:32.270 --> 00:38:34.340 follow any other amino acid. 00:38:34.340 --> 00:38:36.870 So, what that means is that if glycine 00:38:36.870 --> 00:38:39.360 is the first amino acid, as it happens to be here, 00:38:39.360 --> 00:38:42.290 serine is only one of 20 different possible 00:38:42.290 --> 00:38:44.300 second amino acids. 00:38:44.300 --> 00:38:50.910 Aspartic acid is only one of 20 different third amino acids 00:38:50.910 --> 00:38:52.870 as the third residue. 00:38:52.870 --> 00:38:54.700 We often call these different residues: 00:38:54.700 --> 00:38:57.170 the first residue, second residue, third residue, 00:38:57.170 --> 00:38:59.460 fourth residue, and fourth, and so forth. 00:38:59.460 --> 00:39:01.410 And, keep in mind, if we think about 00:39:01.410 --> 00:39:04.050 the combinatorial implications of that, 00:39:04.050 --> 00:39:07.070 the first amino acid residue can have 20 different ones. 00:39:07.070 --> 00:39:09.260 The second can have 20 different identities. 00:39:09.260 --> 00:39:11.060 The third can have 20 different identities. 00:39:11.060 --> 00:39:15.590 That means if we make a tripeptide 00:39:15.590 --> 00:39:18.600 - a tripeptide has three amino acids in it. 00:39:18.600 --> 00:39:21.980 That means we can make 400 dipeptides, 400 00:39:21.980 --> 00:39:26.100 distinct dipeptides, and we can make 00:39:26.100 --> 00:39:29.880 8,000 distinct tripeptides. 00:39:29.880 --> 00:39:34.620 Now, if you imagine that the average amino acid, 00:39:34.620 --> 00:39:36.890 the average protein in the cell is, 00:39:36.890 --> 00:39:39.970 let's say, 150 amino acid residues long, 00:39:39.970 --> 00:39:45.660 that means that in principle, one could make 20 00:39:45.660 --> 00:39:51.960 to the 150th power distinct amino acid sequences because 00:39:51.960 --> 00:39:53.580 of these absence of any constraints 00:39:53.580 --> 00:39:56.820 of which amino acid will follow which other amino acids. 00:39:56.820 --> 00:40:01.820 In other words, if the average polypeptide 00:40:01.820 --> 00:40:03.770 has this many residues, this is the number 00:40:03.770 --> 00:40:07.260 of distinct 150 amino acid residue long proteins 00:40:07.260 --> 00:40:10.131 that one could, in principle, synthesize. 00:40:10.131 --> 00:40:11.630 I'm not saying all of them have ever 00:40:11.630 --> 00:40:14.390 been synthesized since the formation of life 00:40:14.390 --> 00:40:15.400 on this planet. 00:40:15.400 --> 00:40:21.260 Indeed, since some amino acid chains are 4, 5, 600, 00:40:21.260 --> 00:40:24.970 even 2,000 amino acid residues long, 00:40:24.970 --> 00:40:27.450 I think the one that is affecting muscular dystrophy 00:40:27.450 --> 00:40:29.490 is more than 2,000 amino acids. 00:40:29.490 --> 00:40:30.000 Dystrophin. 00:40:30.000 --> 00:40:31.230 Does anybody know here? 00:40:31.230 --> 00:40:32.250 It's big. 00:40:32.250 --> 00:40:35.360 Anyhow, imagine the number of possibilities. 00:40:35.360 --> 00:40:38.350 So, combinatorially, life can make almost 00:40:38.350 --> 00:40:42.850 whatever types of amino acids it would like by dictating 00:40:42.850 --> 00:40:44.580 the sequence of amino acids. 00:40:44.580 --> 00:40:48.390 Now, let's just go and look here again. 00:40:48.390 --> 00:40:50.070 There is a secondary structure. 00:40:50.070 --> 00:40:51.950 The tertiary structure is the way 00:40:51.950 --> 00:40:54.620 in which the different alpha helices here 00:40:54.620 --> 00:40:57.450 or beta pleated sheets are disposed three-dimensionally 00:40:57.450 --> 00:40:59.290 with respect to one another. 00:40:59.290 --> 00:41:02.490 And, the quaternary structure represents 00:41:02.490 --> 00:41:07.570 how different polypeptides are associated one with the other. 00:41:07.570 --> 00:41:11.330 So, for example, hemoglobin is a tetramer. 00:41:11.330 --> 00:41:13.980 Hemoglobin doesn't exist as a monomeric protein. 00:41:13.980 --> 00:41:15.760 Its solution exists as a tetramer. 00:41:15.760 --> 00:41:18.400 And there's two kinds of globin chains. 00:41:18.400 --> 00:41:21.620 There is an alpha kind and a beta kind. 00:41:21.620 --> 00:41:24.170 And, if we look in a very rough and schematic way at the way 00:41:24.170 --> 00:41:26.750 that a hemoglobin tetramer is arranged, 00:41:26.750 --> 00:41:30.460 there are two alpha polypeptide chains and two beta polypeptide 00:41:30.460 --> 00:41:31.440 chains. 00:41:31.440 --> 00:41:33.979 They are not covalently attached to one another. 00:41:33.979 --> 00:41:36.270 They are associated with one another via hydrogen bonds 00:41:36.270 --> 00:41:38.310 and hydrophobic interactions. 00:41:38.310 --> 00:41:40.960 And, this is the actual native configuration 00:41:40.960 --> 00:41:44.210 of globin to alpha and to beta chains. 00:41:44.210 --> 00:41:46.750 It doesn't exist as a single amino acid in solution. 00:41:46.750 --> 00:41:48.260 It exists as a tetramer. 00:41:48.260 --> 00:41:50.620 And, indeed, most, or I shouldn't say most, 00:41:50.620 --> 00:41:55.300 but very many proteins exist in these configurations 00:41:55.300 --> 00:41:59.280 where the tertiary structure represents 00:41:59.280 --> 00:42:01.950 four different amino acid chains. 00:42:01.950 --> 00:42:05.010 And each of these has an N and C terminal. 00:42:05.010 --> 00:42:06.960 Each of these is chemically distinct. 00:42:06.960 --> 00:42:09.890 These four could probably be taken apart from one another 00:42:09.890 --> 00:42:12.050 simply by raising the temperature. 00:42:12.050 --> 00:42:13.710 And, they associate like this. 00:42:13.710 --> 00:42:15.902 And, in the absence of this association, 00:42:15.902 --> 00:42:18.360 if you just had one of these alphas, or one of these betas, 00:42:18.360 --> 00:42:20.170 it wouldn't function well at all. 00:42:20.170 --> 00:42:23.570 In fact, it might be totally dysfunctional. 00:42:23.570 --> 00:42:26.350 One other thing that may be implicit to you, 00:42:26.350 --> 00:42:29.180 but I haven't said, but that is very important to realize 00:42:29.180 --> 00:42:31.947 is the following: Let's imagine that this 00:42:31.947 --> 00:42:34.030 is the three-dimensional structure of the protein, 00:42:34.030 --> 00:42:36.160 as it may well be. 00:42:36.160 --> 00:42:39.880 Let's now think about hydrophobic and hydrophilic 00:42:39.880 --> 00:42:41.660 amino acids. 00:42:41.660 --> 00:42:44.720 The hydrophobic amino acids hate to be present water. 00:42:44.720 --> 00:42:48.940 And therefore, they are, we can imagine this case correctly, 00:42:48.940 --> 00:42:53.480 tucked away inside the interstices of the protein 00:42:53.480 --> 00:42:56.030 far way from the surface. 00:42:56.030 --> 00:42:58.270 They don't have any contact with water. 00:42:58.270 --> 00:43:01.940 Conversely, the highly charged hydrophilic amino acids 00:43:01.940 --> 00:43:05.230 are actually sticking out at the surface. 00:43:05.230 --> 00:43:08.210 And this begins to yield yet another insight 00:43:08.210 --> 00:43:11.680 into how the three-dimensional stereochemistry of proteins 00:43:11.680 --> 00:43:15.390 is maintained and dictated because the hydrophobic amino 00:43:15.390 --> 00:43:17.780 acids, through hydrophobic interactions, 00:43:17.780 --> 00:43:20.900 stabilize the inner core of the protein that is well 00:43:20.900 --> 00:43:23.760 shielded from the aqueous solvent. 00:43:23.760 --> 00:43:26.080 The hydrophilic amino acids are on the outside. 00:43:26.080 --> 00:43:29.490 They like to be in intimate contact with the water. 00:43:29.490 --> 00:43:31.740 So, we already now have talked about a number 00:43:31.740 --> 00:43:35.240 of distinct different interactions that 00:43:35.240 --> 00:43:37.870 are responsible for creating the three-dimensional 00:43:37.870 --> 00:43:40.280 stereochemistry of the protein. 00:43:40.280 --> 00:43:43.760 First of all, there are the disulfide bonds, 00:43:43.760 --> 00:43:47.220 which create chain-to-chain covalent interactions. 00:43:47.220 --> 00:43:51.630 They are the hydrogen bonds in which different chains 00:43:51.630 --> 00:43:53.200 can interact one another. 00:43:53.200 --> 00:43:56.370 And there are these hydrophobic and hydrophilic interactions. 00:43:56.370 --> 00:43:59.200 And, there are some relatively inconsequential van der Waals 00:43:59.200 --> 00:44:00.702 interactions, which are really not 00:44:00.702 --> 00:44:02.410 worth discussing although some people get 00:44:02.410 --> 00:44:03.620 really excited about them. 00:44:03.620 --> 00:44:05.960 But we won't. 00:44:05.960 --> 00:44:10.120 So, here we now begin to see that we have really interesting 00:44:10.120 --> 00:44:13.060 polypeptides unlike the boring polypeptides that 00:44:13.060 --> 00:44:20.350 are ultimately the way one must judge carbohydrates. 00:44:20.350 --> 00:44:22.290 Some people think carbohydrate chemistry 00:44:22.290 --> 00:44:23.730 is really interesting. 00:44:23.730 --> 00:44:26.100 But it really isn't that interesting 00:44:26.100 --> 00:44:29.870 because you just have the same monomer in a hundred, 00:44:29.870 --> 00:44:31.370 or 500 stretches. 00:44:31.370 --> 00:44:33.230 Here, a protein is much more interesting 00:44:33.230 --> 00:44:35.770 because of this enormous variability 00:44:35.770 --> 00:44:39.570 in amino acid sequence, and the consequent ability 00:44:39.570 --> 00:44:45.660 to create all kinds of chemical reactivities and structures 00:44:45.660 --> 00:44:48.910 because of these 20 different amino acids. 00:44:48.910 --> 00:44:51.140 If we were to imagine life on another planet, 00:44:51.140 --> 00:44:53.060 and we imagine that there were, let's say, 00:44:53.060 --> 00:44:57.060 amino acid-like molecules that were part of life, 00:44:57.060 --> 00:45:00.150 maybe that other life wouldn't have exactly the same 20 00:45:00.150 --> 00:45:02.170 amino acids as we do. 00:45:02.170 --> 00:45:06.430 It almost certainly would be a water base the way we are. 00:45:06.430 --> 00:45:10.100 But, it would also rely on hydrogen bonds 00:45:10.100 --> 00:45:14.570 and hydrophilicity, and hydrophobicity interactions 00:45:14.570 --> 00:45:17.740 in order to dictate the three-dimensional structure. 00:45:17.740 --> 00:45:19.890 In the absence of this very specific 00:45:19.890 --> 00:45:22.320 three-dimensional structure I will tell you 00:45:22.320 --> 00:45:24.819 that this enzyme could not function. 00:45:24.819 --> 00:45:26.360 And, if you were to take this enzyme, 00:45:26.360 --> 00:45:29.540 if it were typical enzyme and you were to heat it up briefly, 00:45:29.540 --> 00:45:33.400 even often slightly above normal body temperature, 00:45:33.400 --> 00:45:36.040 it might denature, i.e., it might 00:45:36.040 --> 00:45:40.860 lose its three-dimensional structure irreversibly. 00:45:40.860 --> 00:45:46.530 And, once it was denatured, this process of denaturation, 00:45:46.530 --> 00:45:49.400 it might not be able to spontaneously reassume 00:45:49.400 --> 00:45:51.850 that pre-existing three-dimensional configuration 00:45:51.850 --> 00:45:54.690 and therefore would forever be inactive. 00:45:54.690 --> 00:45:56.590 That means to say very explicitly 00:45:56.590 --> 00:45:58.650 that even though the amino acids that 00:45:58.650 --> 00:46:02.850 are creating that active catalytic site remain there. 00:46:02.850 --> 00:46:06.810 Their highly specific three-dimensional disposition 00:46:06.810 --> 00:46:10.360 is critical for the continued actions of this enzyme. 00:46:10.360 --> 00:46:13.840 And, once their three-dimensional dispositions 00:46:13.840 --> 00:46:16.770 are shifted around through the process of interactions, 00:46:16.770 --> 00:46:20.450 then, we have trouble because the enzyme can no longer 00:46:20.450 --> 00:46:22.240 do its assigned task. 00:46:22.240 --> 00:46:27.480 We are going to go now to an even higher order of complexity 00:46:27.480 --> 00:46:28.890 in one sense. 00:46:28.890 --> 00:46:32.180 We are going to go to the royalty of the macromolecules, 00:46:32.180 --> 00:46:34.320 which are the nucleic acids. 00:46:34.320 --> 00:46:36.490 Of course, protein chemists would take great umbrage 00:46:36.490 --> 00:46:39.510 at the very notion that there are 00:46:39.510 --> 00:46:41.540 things better than proteins. 00:46:41.540 --> 00:46:44.440 But, the fact of the matter is, I 00:46:44.440 --> 00:46:46.180 can't show you that overhead because it's 00:46:46.180 --> 00:46:49.290 from the other textbook which is copyright, 00:46:49.290 --> 00:46:50.724 and we are being filmed. 00:46:50.724 --> 00:46:52.140 How many people have had the backs 00:46:52.140 --> 00:46:55.230 of their heads immortalized on these videos? 00:46:55.230 --> 00:47:00.040 Did you call home and ask anybody to identify you? 00:47:00.040 --> 00:47:04.440 I don't know, but soon each of us 00:47:04.440 --> 00:47:07.140 has the limelight for 15 minutes a lifetime, right? 00:47:07.140 --> 00:47:09.330 So, you'll have your 15 minutes. 00:47:09.330 --> 00:47:11.740 Here are some nucleic acids. 00:47:11.740 --> 00:47:15.140 And let's look at these nucleic acids and the way 00:47:15.140 --> 00:47:16.507 they are put together. 00:47:16.507 --> 00:47:19.090 Keep in mind to anticipate what we are going to say next time, 00:47:19.090 --> 00:47:21.600 once again, we want to make end-to-end aggregates. 00:47:21.600 --> 00:47:25.150 We want to polymerize molecules. 00:47:25.150 --> 00:47:29.160 And in this case, we want to do so once again 00:47:29.160 --> 00:47:31.807 through a dehydration reaction. 00:47:31.807 --> 00:47:33.890 And, moreover, just to look at the building blocks 00:47:33.890 --> 00:47:37.432 of nucleic acids, we start again in this case with two pentoses. 00:47:37.432 --> 00:47:38.890 Recall that they have fuor carbons: 00:47:38.890 --> 00:47:42.530 one, two, three, four, did I say four? 00:47:42.530 --> 00:47:45.500 You know I meant five. 00:47:45.500 --> 00:47:47.030 One, two, three, four, five. 00:47:47.030 --> 00:47:48.530 So, whenever I say four from now on, 00:47:48.530 --> 00:47:54.740 I mean, or, whenever I say four I may also mean four. 00:47:54.740 --> 00:47:57.540 OK, one, two, three, four five. 00:47:57.540 --> 00:48:01.570 And let's look at the two basic kinds of pentose molecules 00:48:01.570 --> 00:48:05.510 that are present in nucleic acid because they define 00:48:05.510 --> 00:48:09.580 the essential difference between DNA and RNA. 00:48:09.580 --> 00:48:12.310 Here's a regular old rather familiar kind 00:48:12.310 --> 00:48:14.930 of pentose with five carbons. 00:48:14.930 --> 00:48:17.300 And here's an unfamiliar kind of pentose 00:48:17.300 --> 00:48:19.430 which we call deoxyribose. 00:48:19.430 --> 00:48:20.270 Why? 00:48:20.270 --> 00:48:21.830 Because if you look really carefully, 00:48:21.830 --> 00:48:23.496 you'll see that the hydroxyl group here, 00:48:23.496 --> 00:48:26.590 which should be present in any self-respecting pentose is 00:48:26.590 --> 00:48:30.330 missing, and is replaced simply by a hydrogen group, i.e., 00:48:30.330 --> 00:48:35.360 it's lost its oxygen, whence cometh the word, ?deoxyribose,? 00:48:35.360 --> 00:48:39.770 and ultimately clearly the word, ?deoxyribose nucleic acid.? 00:48:39.770 --> 00:48:42.720 And one of the attributes, one of the virtues 00:48:42.720 --> 00:48:45.000 of carbohydrates, as we discussed last time, 00:48:45.000 --> 00:48:47.730 were these numerous hydroxyl groups, 00:48:47.730 --> 00:48:51.970 which represent opportunities for all kinds of dehydration 00:48:51.970 --> 00:48:54.690 reactions which can enable one to build 00:48:54.690 --> 00:48:56.920 much more complex molecules. 00:48:56.920 --> 00:49:00.110 And here, we see the structure of, for example, 00:49:00.110 --> 00:49:04.450 a deoxyribonucleotide whose detailed structure 00:49:04.450 --> 00:49:06.660 we'll get into next time. 00:49:06.660 --> 00:49:08.890 But just, let's look at how these hydroxyl groups 00:49:08.890 --> 00:49:09.940 have been used. 00:49:09.940 --> 00:49:12.340 The hydroxyl group, in this case in DNA, 00:49:12.340 --> 00:49:17.600 and by the way notice that the structure I've shown here, 00:49:17.600 --> 00:49:19.960 there's a side chain attached here, 00:49:19.960 --> 00:49:21.650 and a side chain attached here. 00:49:21.650 --> 00:49:23.900 And neither of those depends on whether or not 00:49:23.900 --> 00:49:27.360 there is a hydrogen or a hydroxyl right here. 00:49:27.360 --> 00:49:29.090 And look at what's happened here. 00:49:29.090 --> 00:49:32.390 Here, we have this hydroxyl over here 00:49:32.390 --> 00:49:35.070 to which a base has been attached covalently, 00:49:35.070 --> 00:49:37.950 once again, by a dehydration reaction. 00:49:37.950 --> 00:49:41.660 And here, we have a situation where actually three phosphate 00:49:41.660 --> 00:49:44.050 groups have been attached to the hydroxyl group 00:49:44.050 --> 00:49:46.320 in this direction. 00:49:46.320 --> 00:49:48.530 And, this represents the basic building blocks 00:49:48.530 --> 00:49:50.084 of nucleic acids. 00:49:50.084 --> 00:49:52.500 Now, one of the things that's going to be really important 00:49:52.500 --> 00:49:54.270 and that you're going to have to memorize, I told you, you 00:49:54.270 --> 00:49:56.320 weren't going to have to memorize anything. 00:49:56.320 --> 00:49:58.100 But you didn't believe me, did you? 00:49:58.100 --> 00:49:58.841 Good. 00:49:58.841 --> 00:50:01.090 OK, one of the things you're going to have to memorize 00:50:01.090 --> 00:50:03.500 is the numbering system here. 00:50:03.500 --> 00:50:07.110 This is number one, two, three, four, five, 00:50:07.110 --> 00:50:09.840 or to be totally frank, and you know 00:50:09.840 --> 00:50:13.880 I'm always that, one prime, two prime, three prime, four prime, 00:50:13.880 --> 00:50:15.314 five prime. 00:50:15.314 --> 00:50:16.980 And that numbering system, it turns out, 00:50:16.980 --> 00:50:21.080 is going to be very important for our subsequent discussions. 00:50:21.080 --> 00:50:24.150 Notice here that, for example, it's here 00:50:24.150 --> 00:50:27.720 at the two prime position that this deoxyribose is lacking 00:50:27.720 --> 00:50:34.720 the oxygen that is present normally in RNA. 00:50:34.720 --> 00:50:38.650 And, with all this in mind, we will wait in great suspense 00:50:38.650 --> 00:50:41.280 until Wednesday when we actually talk 00:50:41.280 --> 00:50:45.700 about how this is exploited to make highly complex polymers. 00:50:45.700 --> 00:50:46.740 Have a good two days. 00:50:46.740 --> 00:50:48.740 See you Wednesday at 10:00.