WEBVTT 00:00:15.737 --> 00:00:17.820 PROFESSOR: It's going to be a great lecture today. 00:00:17.820 --> 00:00:18.720 It's about proteins. 00:00:18.720 --> 00:00:20.040 I love proteins. 00:00:20.040 --> 00:00:21.780 Don't forget the handout, yeah. 00:00:21.780 --> 00:00:24.880 OK, so I'm going to briefly wrap up 00:00:24.880 --> 00:00:27.130 the lecture we were doing on Friday because there were 00:00:27.130 --> 00:00:29.520 a couple of things that I wanted to make a note of, 00:00:29.520 --> 00:00:32.430 and then we'll move on to section 2.3 00:00:32.430 --> 00:00:35.280 about amino acids, peptides, and proteins. 00:00:35.280 --> 00:00:37.980 Now, in the last class, I introduced you 00:00:37.980 --> 00:00:41.340 to the lipidic molecules, and you can pick them out 00:00:41.340 --> 00:00:44.430 of a lineup because they are rich in carbon-carbon and 00:00:44.430 --> 00:00:45.970 carbon-hydrogen bonds. 00:00:45.970 --> 00:00:49.350 As you can see here in these line-angled drawings, 00:00:49.350 --> 00:00:51.930 the majority of a lot of these molecules 00:00:51.930 --> 00:00:55.110 is carbon-carbon or carbon-hydrogen hydrogen. 00:00:55.110 --> 00:00:59.280 They are molecules that are mostly hydrophobic, so there 00:00:59.280 --> 00:01:00.820 are some terminologies here. 00:01:00.820 --> 00:01:01.320 Whoops. 00:01:01.320 --> 00:01:05.700 Hydrophobic, which can also be referred to as lipophilic. 00:01:05.700 --> 00:01:11.310 You either-- you can hate water and love fatty acid or fatty 00:01:11.310 --> 00:01:15.000 types of materials, so those both terms are synonymous. 00:01:15.000 --> 00:01:18.380 And some of the lipids are what are known as amphipathic, 00:01:18.380 --> 00:01:21.720 and they include hydrophobic and hydrophobic components. 00:01:21.720 --> 00:01:24.780 There are a couple of tiny terms that I 00:01:24.780 --> 00:01:26.910 didn't mention explicitly, so I just 00:01:26.910 --> 00:01:29.250 want to go ahead and do that now. 00:01:29.250 --> 00:01:33.260 For example, in this phospholipid structure-- 00:01:33.260 --> 00:01:34.560 and we'll talk about these-- 00:01:34.560 --> 00:01:39.510 they have long chain fatty acids attached via esters 00:01:39.510 --> 00:01:41.640 to this glycerol unit, so there's 00:01:41.640 --> 00:01:44.310 one here and the second one here, 00:01:44.310 --> 00:01:47.190 and then what's known as the polar head group. 00:01:47.190 --> 00:01:51.030 In those fatty acids, they could be fully saturated. 00:01:51.030 --> 00:01:54.750 It means they have no double bonds in the structure, 00:01:54.750 --> 00:02:06.080 so that term saturated is equivalent to no double bonds, 00:02:06.080 --> 00:02:08.289 so no carbon-carbon double bonds. 00:02:08.289 --> 00:02:10.810 Or they could be unsaturated, where 00:02:10.810 --> 00:02:16.260 there is a double bond within it, 00:02:16.260 --> 00:02:20.370 so that's one or more double bonds. 00:02:20.370 --> 00:02:23.690 And those double bonds take on a particular shape 00:02:23.690 --> 00:02:27.680 because there's not freedom of rotation around double bonds 00:02:27.680 --> 00:02:30.080 the same way there is around single bonds. 00:02:30.080 --> 00:02:32.330 So those single bonds, you can twist them around 00:02:32.330 --> 00:02:35.780 and twist them around, but the double bond geometry is fixed. 00:02:35.780 --> 00:02:37.760 And so double bonds, we refer to them 00:02:37.760 --> 00:02:41.820 as either trans, where the two groups are on opposite sides, 00:02:41.820 --> 00:02:46.760 leaving the double bond, or we refer to them as cis, 00:02:46.760 --> 00:02:49.100 where the two groups are on the same side. 00:02:49.100 --> 00:02:51.890 And we tend to use that cis and trans 00:02:51.890 --> 00:02:55.380 sort of naming system in a lot of other contexts as well, 00:02:55.380 --> 00:02:57.020 but you almost always want to remember 00:02:57.020 --> 00:02:59.360 that trans is as far away as possible, 00:02:59.360 --> 00:03:02.030 cis is closer than trans. 00:03:02.030 --> 00:03:05.750 All right, so I'm just going to take you forward 00:03:05.750 --> 00:03:08.400 to the phospholipid structure. 00:03:08.400 --> 00:03:21.730 This is a very important semi-permeable membranes 00:03:21.730 --> 00:03:26.320 are made up through the non-covalent, supramolecular 00:03:26.320 --> 00:03:30.340 association of phospholipid monomer units. 00:03:30.340 --> 00:03:32.530 Here's a monomer unit up here. 00:03:32.530 --> 00:03:35.170 You see it has an amphipathic structure, 00:03:35.170 --> 00:03:38.920 with a lot of hydrophobicity but also hydrophilicity, 00:03:38.920 --> 00:03:43.870 and these molecules assemble into supramolecular structures 00:03:43.870 --> 00:03:46.630 that form the boundaries of your cells. 00:03:46.630 --> 00:03:50.080 Saying they are semi-permeable tells us a little bit 00:03:50.080 --> 00:03:52.510 about what can go through them. 00:03:52.510 --> 00:03:55.187 If they were fully permeable, anything could come and go 00:03:55.187 --> 00:03:56.770 and they wouldn't be much use frankly. 00:03:56.770 --> 00:03:58.990 It's like leaving the door open the whole time. 00:03:58.990 --> 00:04:01.300 But because they're semi-permeable, 00:04:01.300 --> 00:04:04.870 only a few things can come and go without extra help, 00:04:04.870 --> 00:04:09.080 and other things need active mechanisms to go through. 00:04:09.080 --> 00:04:12.620 So let's take a look at the boundary here. 00:04:12.620 --> 00:04:15.268 So when you see a membrane bilayer, 00:04:15.268 --> 00:04:17.560 they are-- they're often shown looking like this, where 00:04:17.560 --> 00:04:20.440 every one of these units is a phospholipid, 00:04:20.440 --> 00:04:23.620 and there's water on both sides of the phospholipid, 00:04:23.620 --> 00:04:27.100 because that polar head group is interacting 00:04:27.100 --> 00:04:29.140 with water on both sides. 00:04:29.140 --> 00:04:32.380 So down here could be the inside of the cell. 00:04:32.380 --> 00:04:34.960 Up here could be the outside of the cell. 00:04:34.960 --> 00:04:38.180 And a lot of cells, especially eukaryotic cells, 00:04:38.180 --> 00:04:41.830 the ones that make us up, have a lot of endomembranes, 00:04:41.830 --> 00:04:44.240 membranes within the cells. 00:04:44.240 --> 00:04:47.020 For example, forming the boundary to the nucleus 00:04:47.020 --> 00:04:48.710 or to the mitochondria. 00:04:48.710 --> 00:04:49.544 Yes? 00:04:49.544 --> 00:04:52.210 AUDIENCE: Why is there a [INAUDIBLE] 00:04:52.210 --> 00:04:54.230 PROFESSOR: Oh, this guy must be-- 00:04:54.230 --> 00:04:59.180 so this looks like it's probably a saturated fatty acid. 00:04:59.180 --> 00:05:03.450 So what do you think this one might be, folks? 00:05:03.450 --> 00:05:04.380 Unsaturated. 00:05:04.380 --> 00:05:06.060 And what's the double-bond geometry? 00:05:06.060 --> 00:05:07.170 AUDIENCE: Cis. 00:05:07.170 --> 00:05:08.180 PROFESSOR: Cis. 00:05:08.180 --> 00:05:08.760 Yeah, it is. 00:05:08.760 --> 00:05:12.280 It's like a-- it looks like a ballerina or something. 00:05:12.280 --> 00:05:15.210 OK, so we have a lot of concerns, 00:05:15.210 --> 00:05:18.630 and we'll see later about how things get in and out of cells. 00:05:18.630 --> 00:05:26.050 But most commonly, things like oxygen or water 00:05:26.050 --> 00:05:35.440 and other small hydrophobic molecules 00:05:35.440 --> 00:05:39.400 can pass readily in and out through the semi-permeable 00:05:39.400 --> 00:05:42.340 barrier, but other things, things that are charged, 00:05:42.340 --> 00:05:45.220 things that are big, need a different mechanism 00:05:45.220 --> 00:05:46.120 to get in and out. 00:05:46.120 --> 00:05:49.750 And we will see later on how proteins provide 00:05:49.750 --> 00:05:52.480 the opportunities to cargo things 00:05:52.480 --> 00:05:56.770 into cells or out of cells, even very large entities, 00:05:56.770 --> 00:05:58.810 and there are certain mechanisms whereby 00:05:58.810 --> 00:06:02.650 that happens through a semi-permeable membrane, OK? 00:06:02.650 --> 00:06:05.800 I want to show you the other feature of membranes. 00:06:05.800 --> 00:06:07.137 They are self-healing. 00:06:11.340 --> 00:06:14.250 What this means is if you poke them, 00:06:14.250 --> 00:06:17.700 you poke a hole in a cellular membrane, You? 00:06:17.700 --> 00:06:21.600 Basically push apart those non-covalent forces. 00:06:21.600 --> 00:06:24.150 Once you take the thing away, be it a needle 00:06:24.150 --> 00:06:28.710 or a very fine glass capillary, they seal right back up 00:06:28.710 --> 00:06:31.690 to close to close the hole in the cell wall, 00:06:31.690 --> 00:06:34.950 so that kind of tells us that they're non-covalent forces. 00:06:34.950 --> 00:06:37.500 So this is a really cool video of someone 00:06:37.500 --> 00:06:41.130 doing micro-injection into eukaryotic cells. 00:06:41.130 --> 00:06:44.520 The needle points to the cell, approaches the surface. 00:06:44.520 --> 00:06:46.590 You can drop something into the cell, 00:06:46.590 --> 00:06:49.080 and then the cell closes and maintain-- 00:06:49.080 --> 00:06:52.840 regains its integrity of the barrier, 00:06:52.840 --> 00:06:56.670 so this is a very cool observation. 00:06:56.670 --> 00:06:58.140 People do this. 00:06:58.140 --> 00:07:00.060 They have to not drink too much coffee 00:07:00.060 --> 00:07:02.910 because it's quite complicated to do a lot of micro-injection, 00:07:02.910 --> 00:07:06.750 because you can really cause carnage in your cell population 00:07:06.750 --> 00:07:10.590 if you're not very dexterous with the micro-injection 00:07:10.590 --> 00:07:12.900 but people can be very good at it. 00:07:12.900 --> 00:07:14.830 So I just want to ask a couple of questions 00:07:14.830 --> 00:07:17.550 before, give you a couple of things to think about 00:07:17.550 --> 00:07:19.200 before we close up. 00:07:19.200 --> 00:07:20.200 The lipids. 00:07:20.200 --> 00:07:22.500 So here's a typical lipid bilayer, 00:07:22.500 --> 00:07:25.140 where I've highlighted a single lipid. 00:07:25.140 --> 00:07:27.390 And the colors, those are the head groups, 00:07:27.390 --> 00:07:32.520 and all in white and gray are the hydrophilic components, 00:07:32.520 --> 00:07:35.970 and just one of the phospholipids is highlighted, 00:07:35.970 --> 00:07:38.670 and that would be this molecular structure here. 00:07:38.670 --> 00:07:42.480 So first of all, what do you think the non-covalent forces 00:07:42.480 --> 00:07:45.210 at that membrane interface may be? 00:07:45.210 --> 00:07:48.810 That is, what's going on here at the interface? 00:07:48.810 --> 00:07:50.790 What are the types of interactions 00:07:50.790 --> 00:07:53.760 that you might have there? 00:07:53.760 --> 00:07:55.650 Give you a minute to think about it, 00:07:55.650 --> 00:07:57.960 and I want to show you that I'm actually giving you 00:07:57.960 --> 00:08:01.800 a clue here, because you can see the structure, negative charge, 00:08:01.800 --> 00:08:03.990 positive charge, but also remember 00:08:03.990 --> 00:08:08.130 this is a barrier to water, so there are other things going on 00:08:08.130 --> 00:08:11.160 with the solvent that the membrane is sitting in 00:08:11.160 --> 00:08:14.250 because there's water surrounding that barrier layer. 00:08:14.250 --> 00:08:17.740 Anyone want to tell me what the answer is, and why? 00:08:17.740 --> 00:08:20.168 Yeah, did you-- are you-- yeah. 00:08:20.168 --> 00:08:21.380 AUDIENCE: Hydrogen bonding. 00:08:21.380 --> 00:08:24.596 PROFESSOR: Yeah, between what and what? 00:08:24.596 --> 00:08:37.409 AUDIENCE: Like the oxygen and [INAUDIBLE] 00:08:37.409 --> 00:08:39.230 PROFESSOR: Right, so water. 00:08:39.230 --> 00:08:42.659 Water is a good hydrogen bond donor and acceptor, 00:08:42.659 --> 00:08:44.670 so there will be hydrogen bonding. 00:08:44.670 --> 00:08:46.650 What about amongst all those lipid 00:08:46.650 --> 00:08:48.405 head groups, what's the other major force? 00:08:51.390 --> 00:08:52.300 Yeah? 00:08:52.300 --> 00:08:53.582 AUDIENCE: Electrostatic force. 00:08:53.582 --> 00:08:55.290 PROFESSOR: Between the different charges. 00:08:55.290 --> 00:08:57.600 So the correct answer here is both of them. 00:08:57.600 --> 00:09:00.660 Don't think it's just electrostatic, it's both. 00:09:00.660 --> 00:09:04.380 It's electrostatic amongst the head groups, hydrogen bonding 00:09:04.380 --> 00:09:08.680 between all that sort of dense bunch of charge, and the water. 00:09:08.680 --> 00:09:11.130 And then the other question, what type of molecules 00:09:11.130 --> 00:09:12.010 can get across? 00:09:12.010 --> 00:09:14.520 I've already answered that question to you. 00:09:14.520 --> 00:09:17.730 Salts are going to need ways to get in and out. 00:09:17.730 --> 00:09:21.840 Small proteins are too big to dissolve in that membrane 00:09:21.840 --> 00:09:24.270 through passive mechanisms, so we're 00:09:24.270 --> 00:09:27.150 going to have to figure out how to get proteins 00:09:27.150 --> 00:09:29.160 in and out of cells. 00:09:29.160 --> 00:09:31.560 Neurotransmitters, such as this, this 00:09:31.560 --> 00:09:34.500 is GABA, or gamma aminobutyric acid. 00:09:34.500 --> 00:09:35.550 It's charged. 00:09:35.550 --> 00:09:38.400 It just can't get through without a transporter 00:09:38.400 --> 00:09:41.280 of some kind, and it's actually proteins 00:09:41.280 --> 00:09:44.160 that end up doing the heavy lifting of the transport 00:09:44.160 --> 00:09:45.950 processes that we'll see. 00:09:45.950 --> 00:09:48.990 OK, so moving along. 00:09:48.990 --> 00:09:53.550 This section will be about the building blocks of your protein 00:09:53.550 --> 00:09:55.590 macromolecules, which I want to remind 00:09:55.590 --> 00:09:59.670 you comprise 50% of all of the macromolecules, 00:09:59.670 --> 00:10:02.640 so that suggests it's a pretty important class 00:10:02.640 --> 00:10:06.720 of macromolecules that has a lot of different functions. 00:10:06.720 --> 00:10:08.460 Now, the amino acid building locks-- 00:10:08.460 --> 00:10:10.440 blocks look pretty simple. 00:10:10.440 --> 00:10:13.050 They're called amino acids because they 00:10:13.050 --> 00:10:21.480 have an amine, the carboxylic acid, 00:10:21.480 --> 00:10:24.600 and there's a carbon that is tetrehedral between the 00:10:24.600 --> 00:10:27.450 carboxylic acid and the amine. 00:10:27.450 --> 00:10:32.010 And the simplest of those is when those are both hydrogen, 00:10:32.010 --> 00:10:35.310 but most of the amino acids are differentiated 00:10:35.310 --> 00:10:37.830 from that-- this one I've showed you on the board. 00:10:37.830 --> 00:10:42.690 This amino acid is glycine. 00:10:42.690 --> 00:10:46.920 Usually, when it's just a lonely amino acid in aqueous solution, 00:10:46.920 --> 00:10:51.180 it's in a different charged form, 00:10:51.180 --> 00:10:56.650 just consistent with what we talked about in the last class. 00:10:56.650 --> 00:10:57.890 And I put it here. 00:10:57.890 --> 00:10:59.480 So this is glycine. 00:10:59.480 --> 00:11:07.595 It's one of the 20 encoded amino acids. 00:11:11.420 --> 00:11:14.090 That means the amino acids that are 00:11:14.090 --> 00:11:17.510 made through ribosomal biosynthesis 00:11:17.510 --> 00:11:22.080 through a code that's provided by the messenger RNA, 00:11:22.080 --> 00:11:27.800 so they are encoded by messenger RNA. 00:11:27.800 --> 00:11:30.640 Later on, you'll see all of the beautiful mechanics 00:11:30.640 --> 00:11:32.330 of those processes. 00:11:32.330 --> 00:11:35.270 Now, this table looks pretty complicated, 00:11:35.270 --> 00:11:36.830 so I'm going to deconstruct it a bit. 00:11:36.830 --> 00:11:40.470 But what I first of all want to assure you is that these-- 00:11:40.470 --> 00:11:43.870 you will always get a handout with these structures on them. 00:11:43.870 --> 00:11:46.960 We are not asking you to remember these structures. 00:11:46.960 --> 00:11:49.510 You might become familiar with some of them, 00:11:49.510 --> 00:11:51.790 but you do not have to remember them. 00:11:51.790 --> 00:11:54.670 You'll have a table that shows them, but on that table, 00:11:54.670 --> 00:11:57.880 I won't necessarily give you the information 00:11:57.880 --> 00:12:00.730 on what their properties are, because those are things 00:12:00.730 --> 00:12:04.090 that you should be able to spot by looking at their chemical 00:12:04.090 --> 00:12:05.140 structures, all right? 00:12:05.140 --> 00:12:06.400 So that's important. 00:12:06.400 --> 00:12:09.430 So these are all line-angled drawings, 00:12:09.430 --> 00:12:11.020 so you see the carbon. 00:12:11.020 --> 00:12:13.120 The hydrogens aren't shown in there. 00:12:13.120 --> 00:12:15.850 The charges are shown for what's called the side 00:12:15.850 --> 00:12:29.550 chain, because most of the amino acids have a side chain. 00:12:36.120 --> 00:12:38.290 The amino acids are also chiral, but you'll 00:12:38.290 --> 00:12:41.830 learn more than you ever wanted to know about chirality in 512, 00:12:41.830 --> 00:12:44.780 so I won't weigh you down with any of those properties. 00:12:44.780 --> 00:12:47.320 So there is a side chain that dictates the properties 00:12:47.320 --> 00:12:48.920 of the amino acids. 00:12:48.920 --> 00:12:52.030 One tiny detail, the amino acids that 00:12:52.030 --> 00:12:54.970 are encoded in our proteins are all what 00:12:54.970 --> 00:12:58.120 are known as alpha amino acids. 00:12:58.120 --> 00:12:59.740 There are other amino acids. 00:12:59.740 --> 00:13:02.470 GABA, that I showed you on the previous slide, 00:13:02.470 --> 00:13:04.390 is not an alpha amino acid. 00:13:04.390 --> 00:13:06.820 Actually it's, a gamma amino acid. 00:13:06.820 --> 00:13:11.320 These are called amino acids because the amine group 00:13:11.320 --> 00:13:14.722 is at the alpha position relative to the carboxyl. 00:13:14.722 --> 00:13:16.930 Don't need to know a lot more about that with respect 00:13:16.930 --> 00:13:17.810 to that. 00:13:17.810 --> 00:13:20.830 So let's take a look at this set of amino acids, 00:13:20.830 --> 00:13:24.490 and what you see is amino side chains with rather 00:13:24.490 --> 00:13:26.220 different properties. 00:13:26.220 --> 00:13:29.950 I've amassed-- here's glycine at the very top. 00:13:29.950 --> 00:13:32.140 All amino acids have a three-letter code 00:13:32.140 --> 00:13:33.700 or a one-letter code. 00:13:33.700 --> 00:13:35.950 I particularly enjoy using one letter codes 00:13:35.950 --> 00:13:38.970 and spelling out people's names in peptides and things 00:13:38.970 --> 00:13:39.470 like that. 00:13:39.470 --> 00:13:42.640 I'll let you do that in the privacy of your own room. 00:13:42.640 --> 00:13:46.180 It's kind of amusing to see if your name actually spells out 00:13:46.180 --> 00:13:47.350 a peptide. 00:13:47.350 --> 00:13:50.380 Some of us-- if I get a little stopped stuck with Barbara 00:13:50.380 --> 00:13:54.670 because there are no B amino acid one letters with a B. 00:13:54.670 --> 00:13:58.090 The next most abundant type of amino acid 00:13:58.090 --> 00:14:01.300 have hydrophobic side chains. 00:14:01.300 --> 00:14:03.170 What that means is they have a lot of CHs, 00:14:03.170 --> 00:14:05.710 but not a lot else, right? 00:14:05.710 --> 00:14:07.290 So take a look at them. 00:14:07.290 --> 00:14:13.740 Alanine has a methyl group, for example, where I've shown 00:14:13.740 --> 00:14:17.730 the R, that would be alanine. 00:14:17.730 --> 00:14:19.500 And they get increasingly big. 00:14:19.500 --> 00:14:20.950 They're quite large. 00:14:20.950 --> 00:14:23.670 Some of them have quite extended size chains. 00:14:23.670 --> 00:14:25.740 Other ones have side chains with rings 00:14:25.740 --> 00:14:27.360 with double bonds in them. 00:14:27.360 --> 00:14:30.780 Those are what we would designate in organic chemistry 00:14:30.780 --> 00:14:32.190 as aromatic. 00:14:32.190 --> 00:14:34.320 They show-- they are still hydrophobic, 00:14:34.320 --> 00:14:36.250 but they show different properties 00:14:36.250 --> 00:14:39.210 to this other set of amino acids. 00:14:39.210 --> 00:14:41.340 Some of these amino acids may actually 00:14:41.340 --> 00:14:45.330 have polar groups in them, but their major feature 00:14:45.330 --> 00:14:47.160 is that they're hydrophobic. 00:14:47.160 --> 00:14:49.830 But in an amino acid, such as tyrosine, 00:14:49.830 --> 00:14:53.190 you could not only have hydrophobic interactions 00:14:53.190 --> 00:14:57.660 with that ring system, but also hydrogen bonding with the OH 00:14:57.660 --> 00:15:00.060 on the tyrosine, so some of the amino acids 00:15:00.060 --> 00:15:03.120 can do a few different things. 00:15:03.120 --> 00:15:05.130 The next set of amino acids are those 00:15:05.130 --> 00:15:07.920 that are polar and charged, and I've 00:15:07.920 --> 00:15:12.120 shown you the most common state of all of those amino acids, 00:15:12.120 --> 00:15:14.670 but you already know that the amine of lysine 00:15:14.670 --> 00:15:16.500 is likely to be charged. 00:15:16.500 --> 00:15:19.680 This quanidinium group of arginine, take my word for it, 00:15:19.680 --> 00:15:20.660 it's charged. 00:15:20.660 --> 00:15:22.820 It's a bit more complicated to draw. 00:15:22.820 --> 00:15:26.010 Histidine is also one of those that's annoying to draw, 00:15:26.010 --> 00:15:29.370 but the negatively-charged side chains with a carboxylate 00:15:29.370 --> 00:15:31.590 are both negatively charged, and that's 00:15:31.590 --> 00:15:34.230 something you would remember from the previous class 00:15:34.230 --> 00:15:35.190 hopefully. 00:15:35.190 --> 00:15:36.930 And then finally, there are amino acids 00:15:36.930 --> 00:15:39.360 with polar uncharged side chains, 00:15:39.360 --> 00:15:41.140 such as those shown here. 00:15:41.140 --> 00:15:44.190 Now, this doesn't look like a very exciting set 00:15:44.190 --> 00:15:45.120 of building blocks. 00:15:45.120 --> 00:15:49.800 How can life run on things made of 20 relatively 00:15:49.800 --> 00:15:52.460 simple building blocks with functional groups? 00:15:52.460 --> 00:15:54.870 And it's that the building blocks are not functional 00:15:54.870 --> 00:15:56.110 themselves. 00:15:56.110 --> 00:16:02.680 It is the polymers that are made up of amino acids, 00:16:02.680 --> 00:16:05.830 and I'll always call them AAs because it's easier for me. 00:16:05.830 --> 00:16:09.760 The polymers of amino acids are heteropolymers. 00:16:14.420 --> 00:16:17.660 That means they're made up of a bunch of different monomer 00:16:17.660 --> 00:16:19.760 units when they're called heteropolymers. 00:16:26.710 --> 00:16:29.770 And the other important thing about these polymers 00:16:29.770 --> 00:16:34.600 is that they are of defined sequence. 00:16:38.030 --> 00:16:39.270 What is the sequence? 00:16:39.270 --> 00:16:42.510 It's the order in which the amino acids appear. 00:16:42.510 --> 00:16:46.430 So I'm writing that down, order. 00:16:46.430 --> 00:16:48.100 And all the functions of proteins 00:16:48.100 --> 00:16:51.010 are dictated by the order of the amino acids, 00:16:51.010 --> 00:16:53.630 so let's take a look at the sidebar here. 00:16:53.630 --> 00:16:56.290 So once again, remember a couple of things 00:16:56.290 --> 00:16:59.510 that we will always give you this table to think about. 00:16:59.510 --> 00:17:00.967 Ooh, come back. 00:17:00.967 --> 00:17:03.550 There are a couple of outliers I just want to mention quickly. 00:17:03.550 --> 00:17:05.920 So I talked to you about glycine, 00:17:05.920 --> 00:17:09.819 the simplest amino acid with no elaborate side chain. 00:17:09.819 --> 00:17:13.260 Proline is a little odd because its side chain is kind of 00:17:13.260 --> 00:17:16.210 in a cyclic structure, and towards the end of the class, 00:17:16.210 --> 00:17:19.480 I'll talk to you about collagen, whose structure 00:17:19.480 --> 00:17:23.109 is totally dependent on the involvement of proline 00:17:23.109 --> 00:17:27.160 in the sequence of the amino acids that make up collagen. 00:17:27.160 --> 00:17:31.480 And then the last sorts of unusual amino acid is cysteine. 00:17:31.480 --> 00:17:36.180 It has a thiol, and the one clever thing about cysteine-- 00:17:36.180 --> 00:17:39.890 I'm just going to put a bit of a peptide here. 00:17:39.890 --> 00:17:49.640 One cysteine, and then I'm going to put a second cysteine, 00:17:49.640 --> 00:17:55.120 and these are going to be deemed in a peptidic structure. 00:17:55.120 --> 00:17:58.630 What cysteine can do is it can exist either 00:17:58.630 --> 00:18:03.130 with the thiol side chain, SH, or it 00:18:03.130 --> 00:18:06.280 can be at a different oxidation state 00:18:06.280 --> 00:18:12.290 where the two sulfurs are joined to each other. 00:18:12.290 --> 00:18:16.240 So for the most part, your linear arrangement 00:18:16.240 --> 00:18:20.530 of amino acids that dictates sequence is solely held by-- 00:18:20.530 --> 00:18:24.370 together by the covalent bonds and the peptide backbone 00:18:24.370 --> 00:18:26.360 that we'll talk about in a minute. 00:18:26.360 --> 00:18:28.900 But occasionally, enfolded structures, 00:18:28.900 --> 00:18:31.540 if two cysteines are close to each other 00:18:31.540 --> 00:18:33.430 and the environment is oxidizing, 00:18:33.430 --> 00:18:35.140 they will form a cross-link. 00:18:35.140 --> 00:18:37.240 But they're not what drives folding. 00:18:37.240 --> 00:18:39.490 They kind of fall into place later on, 00:18:39.490 --> 00:18:42.130 but that just sort of sets cysteine apart a little bit 00:18:42.130 --> 00:18:44.830 for its properties, all right? 00:18:44.830 --> 00:18:47.000 OK, so coming down the side here. 00:18:47.000 --> 00:18:50.350 Amino acids are assembled in a unique linear polymer 00:18:50.350 --> 00:18:53.650 of defined order, and we designate that defined 00:18:53.650 --> 00:18:55.855 sequence the primary sequence. 00:19:03.450 --> 00:19:09.850 And proteins can be 1,000 amino acids, 1,500, 100 amino acids. 00:19:09.850 --> 00:19:17.910 They can be various lengths where they, you know, 00:19:17.910 --> 00:19:20.400 we would generally consider the smallest 00:19:20.400 --> 00:19:23.960 protein to be about 400 amino acids, 00:19:23.960 --> 00:19:27.270 and you might go up to thousands of amino acids. 00:19:27.270 --> 00:19:30.390 I'm going to write 2,000 or more here. 00:19:30.390 --> 00:19:33.570 When the proteins are smaller, they 00:19:33.570 --> 00:19:37.400 are not capable of adopting too much ordered structure, 00:19:37.400 --> 00:19:39.240 and we mostly call them peptides. 00:19:39.240 --> 00:19:41.820 Peptides are sort of shorter sequences, 00:19:41.820 --> 00:19:44.260 so peptide sequences. 00:19:44.260 --> 00:19:54.640 So this would be a protein, and peptides, probably two 00:19:54.640 --> 00:19:57.740 to 39 amino acids, but these breakpoints 00:19:57.740 --> 00:19:59.990 are a little bit more vague. 00:19:59.990 --> 00:20:04.077 So the primary sequence will define the structure 00:20:04.077 --> 00:20:05.660 of a protein, and we're going to start 00:20:05.660 --> 00:20:08.600 to talk about the hierarchical structure of proteins 00:20:08.600 --> 00:20:12.320 as put in place, and that's the primary sequence, 00:20:12.320 --> 00:20:15.950 And that primary sequence is kind of a cool thing 00:20:15.950 --> 00:20:18.050 because it's very specific. 00:20:18.050 --> 00:20:21.950 It defines-- it's got encoded into its structure, 00:20:21.950 --> 00:20:25.820 the three-dimensional fold of the protein, OK? 00:20:25.820 --> 00:20:29.630 All the information for the folded, compact, globular 00:20:29.630 --> 00:20:33.320 structure that's functional is encoded 00:20:33.320 --> 00:20:35.240 in that primary sequence. 00:20:35.240 --> 00:20:36.890 It's a cryptic code. 00:20:36.890 --> 00:20:39.830 We may not be able to tell by looking at it 00:20:39.830 --> 00:20:42.800 what it really looks like, but all the information 00:20:42.800 --> 00:20:48.080 is there in order to program the folding into a globular 00:20:48.080 --> 00:20:49.220 structure. 00:20:49.220 --> 00:20:51.950 So the primary sequence determines the fold, 00:20:51.950 --> 00:20:56.060 and it's the fold of the protein that mandates its function. 00:20:56.060 --> 00:20:57.830 It's not the sequence of the protein. 00:20:57.830 --> 00:20:59.930 The sequence defines the fold. 00:20:59.930 --> 00:21:04.730 The fold, the three-dimensional form, defines the function, OK? 00:21:04.730 --> 00:21:05.900 So that's very important. 00:21:05.900 --> 00:21:08.420 And I think it's absolutely amazing 00:21:08.420 --> 00:21:11.510 that with a relatively limited set of building blocks, 00:21:11.510 --> 00:21:15.830 we can define so many different functions of all the proteins 00:21:15.830 --> 00:21:18.290 in our body that may be structural, 00:21:18.290 --> 00:21:20.900 they may be catalysts, they may be things 00:21:20.900 --> 00:21:23.570 that transfer information from the outside 00:21:23.570 --> 00:21:25.130 to the inside of cell. 00:21:25.130 --> 00:21:29.570 All of that is programmed with this rather limited set 00:21:29.570 --> 00:21:32.440 of building blocks, OK? 00:21:32.440 --> 00:21:36.400 Now, let's now talk about peptides 00:21:36.400 --> 00:21:38.500 because one gets a little frustrated 00:21:38.500 --> 00:21:40.450 looking at single amino acids. 00:21:40.450 --> 00:21:44.330 They don't tell us so much about the peptidic structure, 00:21:44.330 --> 00:21:48.620 so I'm going to draw two amino acids, 00:21:48.620 --> 00:21:51.970 and then I'm going to tell you one important thing. 00:21:51.970 --> 00:21:55.870 So let's put R1, and I'm going to draw another amino acid, 00:21:55.870 --> 00:21:58.840 and I'm putting it in a particular orientation. 00:22:01.870 --> 00:22:07.850 R2, because that designates that these 00:22:07.850 --> 00:22:09.990 might be different amino acids. 00:22:09.990 --> 00:22:14.270 For example, if R1 is H, there's an implied hydrogen here, 00:22:14.270 --> 00:22:16.070 that would be glycine. 00:22:16.070 --> 00:22:19.460 If R2 is a methyl group, there's an implied hydrogen there, 00:22:19.460 --> 00:22:21.770 that would be alanine, all right? 00:22:21.770 --> 00:22:26.990 When nature bonds all these amino acids together, 00:22:26.990 --> 00:22:33.940 it carries out a condensation reaction 00:22:33.940 --> 00:22:39.290 to form a peptide bond between these two 00:22:39.290 --> 00:22:42.410 components of the amino acid, the amine 00:22:42.410 --> 00:22:44.275 and the carboxylic acid. 00:22:44.275 --> 00:22:47.840 And now I'm going to draw you the first of the dipeptides 00:22:47.840 --> 00:22:49.880 that you'll meet. 00:22:49.880 --> 00:22:52.720 And there are so many things to tell you 00:22:52.720 --> 00:22:55.120 about these structures, it sort of 00:22:55.120 --> 00:22:57.035 drives me crazy thinking about, oh, I 00:22:57.035 --> 00:22:58.660 must remember to tell them that or I've 00:22:58.660 --> 00:23:01.180 got to remember to tell them that, because the structures 00:23:01.180 --> 00:23:01.720 are cool. 00:23:01.720 --> 00:23:04.150 R1, R2. 00:23:04.150 --> 00:23:11.763 OK, so this is a dipeptide, two amino acids, 00:23:11.763 --> 00:23:13.180 and there are some characteristics 00:23:13.180 --> 00:23:14.740 I want you to remember. 00:23:14.740 --> 00:23:23.570 When we write out peptides, we always write them N to C. 00:23:23.570 --> 00:23:33.200 So in that peptide, this would be the carboxyl terminus, 00:23:33.200 --> 00:23:35.000 and this would be the amino terminus. 00:23:37.890 --> 00:23:40.890 If you don't always remember to write things in this order, 00:23:40.890 --> 00:23:43.980 and you tell your friend, oh, go and get this peptide 00:23:43.980 --> 00:23:45.990 made, and you put it down in the wrong order, 00:23:45.990 --> 00:23:47.910 they'll make the wrong peptide. 00:23:47.910 --> 00:23:51.030 So you always-- there is basically an agreement 00:23:51.030 --> 00:23:54.450 amongst everyone that we always write from left to right, 00:23:54.450 --> 00:23:56.340 the sequence of peptides. 00:23:56.340 --> 00:23:58.500 The next important thing about this structure, 00:23:58.500 --> 00:24:03.660 as you look at it, there are several bonds joining 00:24:03.660 --> 00:24:06.030 the polymeric structure. 00:24:06.030 --> 00:24:10.500 Many of these bonds show free rotations. 00:24:10.500 --> 00:24:12.420 You can twist them around, there's nothing 00:24:12.420 --> 00:24:13.830 stopping that conversion. 00:24:16.370 --> 00:24:18.780 All of these show freedom of rotation. 00:24:18.780 --> 00:24:29.030 But the amide, or peptide bond, is 00:24:29.030 --> 00:24:31.070 unique in that there's restricted 00:24:31.070 --> 00:24:33.180 rotation about that bond. 00:24:33.180 --> 00:24:35.360 So it's as if you've got a linear polymer, 00:24:35.360 --> 00:24:38.780 but every third bond has kind of stuck 00:24:38.780 --> 00:24:41.000 in a particular orientation, which 00:24:41.000 --> 00:24:45.350 starts to define a lot of details about protein tertiary 00:24:45.350 --> 00:24:46.190 structure. 00:24:46.190 --> 00:24:48.647 It's not complete spaghetti. 00:24:48.647 --> 00:24:51.230 It's like spaghetti with little bits that haven't been cooked. 00:24:51.230 --> 00:24:54.040 They're stiffer than the rest of the sequence. 00:24:54.040 --> 00:24:55.640 And the other really important thing 00:24:55.640 --> 00:24:58.370 about the peptide structure is that embedded 00:24:58.370 --> 00:25:05.710 within that structure, there is the amide or peptide functional 00:25:05.710 --> 00:25:15.320 group where, remember, this can be a hydrogen bond acceptor, 00:25:15.320 --> 00:25:18.340 and this can be a hydrogen bond donor. 00:25:18.340 --> 00:25:21.940 Once you know that, the next few slides will make a lot of sense 00:25:21.940 --> 00:25:25.155 as we talk about higher-order structure of proteins. 00:25:25.155 --> 00:25:26.530 So let's just take a look at that 00:25:26.530 --> 00:25:28.870 with a slightly longer peptide. 00:25:28.870 --> 00:25:31.600 By convention, if I'm going to draw a peptide 00:25:31.600 --> 00:25:34.160 that's methionine isoleucine threonine-- 00:25:34.160 --> 00:25:35.500 you can look up that names-- 00:25:35.500 --> 00:25:37.180 those names on the chart-- 00:25:37.180 --> 00:25:39.490 that would be the MIT peptide. 00:25:39.490 --> 00:25:41.740 These are the three amino acids. 00:25:41.740 --> 00:25:45.430 I'm going to condense them into a tripeptide. 00:25:45.430 --> 00:25:47.240 When I condense three amino acids, 00:25:47.240 --> 00:25:49.510 I spit out two molecules of water, 00:25:49.510 --> 00:25:54.430 and I put in place two amide or peptide bonds. 00:25:54.430 --> 00:25:58.420 If I go down this backbone, every third bond 00:25:58.420 --> 00:26:00.440 is going to be fixed, fairly fixed. 00:26:00.440 --> 00:26:02.950 There's not freedom of rotation around it, 00:26:02.950 --> 00:26:06.190 and every third bond is going to have the capacity 00:26:06.190 --> 00:26:09.580 to be involved in hydrogen bonding interactions, 00:26:09.580 --> 00:26:12.610 as I've suggested here, all right? 00:26:12.610 --> 00:26:14.350 What else is there here? 00:26:14.350 --> 00:26:19.090 When I write the MIT peptide, I write M first, 00:26:19.090 --> 00:26:21.730 I second, T third. 00:26:21.730 --> 00:26:25.450 If I wrote TIM, it would be a completely different chemical 00:26:25.450 --> 00:26:27.940 structure with different chemical properties, 00:26:27.940 --> 00:26:31.600 so the directionality is important to understand, 00:26:31.600 --> 00:26:33.290 and there you have it. 00:26:33.290 --> 00:26:35.170 So now you can go home and practice your name 00:26:35.170 --> 00:26:37.840 in amino acids and draw them out. 00:26:37.840 --> 00:26:41.560 If you draw them out fairly sort of sharply, 00:26:41.560 --> 00:26:44.290 then you'll never get confused about what 00:26:44.290 --> 00:26:46.883 end's what and where the substitutes are, 00:26:46.883 --> 00:26:48.550 but it's important to remember as you're 00:26:48.550 --> 00:26:51.640 making a dipeptide-- oops, I forget this doesn't work. 00:26:51.640 --> 00:26:53.770 As you're condensing a dipeptide, 00:26:53.770 --> 00:26:56.110 when you're putting these R groups on, one goes up, 00:26:56.110 --> 00:26:58.300 one goes down, but these are nuances 00:26:58.300 --> 00:27:00.700 of the structure that may be lit for-- good 00:27:00.700 --> 00:27:02.290 for a later discussion. 00:27:02.290 --> 00:27:06.760 So here is now a longer linear peptide, and the suggestion 00:27:06.760 --> 00:27:09.400 of a globular structure that might be found 00:27:09.400 --> 00:27:12.970 if that peptide was folded up. 00:27:12.970 --> 00:27:20.850 And the primary sequence here defines the globular structure, 00:27:20.850 --> 00:27:25.330 and the process whereby you go from the extended primary 00:27:25.330 --> 00:27:29.530 sequence to the folded structure is called protein folding. 00:27:37.130 --> 00:27:39.470 And physical chemists and physicists 00:27:39.470 --> 00:27:42.380 and computational chemists have for years 00:27:42.380 --> 00:27:47.060 tried to understand how we could predict the folded structure 00:27:47.060 --> 00:27:49.190 from the primary sequence. 00:27:49.190 --> 00:27:52.130 It's not simple because what you're doing 00:27:52.130 --> 00:27:55.210 is you're solving a massive energy diagram, 00:27:55.210 --> 00:27:57.170 where as you fold a structure up, 00:27:57.170 --> 00:28:02.090 you're trying to maximize all those non-covalent forces 00:28:02.090 --> 00:28:06.920 for maximum thermodynamic stability, right? 00:28:06.920 --> 00:28:09.950 It's kind of a three-dimensional puzzle where you're 00:28:09.950 --> 00:28:12.510 trying to have as many hydrogen bonds, 00:28:12.510 --> 00:28:15.650 electrostatic interactions, and so on, as you can possibly 00:28:15.650 --> 00:28:16.460 make. 00:28:16.460 --> 00:28:20.090 So when computational chemists try to fold proteins, 00:28:20.090 --> 00:28:22.940 they're basically solving a three-dimensional puzzle 00:28:22.940 --> 00:28:25.720 where they are maximizing interactions. 00:28:25.720 --> 00:28:28.850 And there are a lot of ab initio and molecular dynamics 00:28:28.850 --> 00:28:34.010 programs that are now starting to be able to fold proteins 00:28:34.010 --> 00:28:36.890 into fairly reliable structures, but they don't always 00:28:36.890 --> 00:28:40.370 get them right because they haven't 00:28:40.370 --> 00:28:41.810 gotten all the clues yet. 00:28:41.810 --> 00:28:45.500 And also while they may be able to do ab initio 00:28:45.500 --> 00:28:48.830 or computational folding with small structures, 00:28:48.830 --> 00:28:51.990 the headache gets way bigger the larger the structures get. 00:28:51.990 --> 00:28:55.370 So the predictors aren't very good at predicting 00:28:55.370 --> 00:28:57.620 big structures, they're getting better 00:28:57.620 --> 00:28:59.720 at predicting small structures. 00:28:59.720 --> 00:29:05.870 And so just to reinforce to you, the primary sequence 00:29:05.870 --> 00:29:09.710 is established by covalent bonds, the peptide bonds, 00:29:09.710 --> 00:29:12.200 but the globular tertiary structure 00:29:12.200 --> 00:29:15.920 is based on non-covalent covalent interactions, OK? 00:29:15.920 --> 00:29:17.870 Now, I want to ask you this. 00:29:17.870 --> 00:29:20.390 I love cartoons with science in them, 00:29:20.390 --> 00:29:25.910 but you know, 10%, 20% of the time, they make mistakes, 00:29:25.910 --> 00:29:28.430 and I felt this one was particularly pertinent. 00:29:28.430 --> 00:29:31.490 So a bunch of guys lugging around in a lab and says, 00:29:31.490 --> 00:29:34.700 well, we finished the genome map, 00:29:34.700 --> 00:29:37.147 now we just have to figure out how to fold it. 00:29:37.147 --> 00:29:38.480 What is wrong with that cartoon? 00:29:41.970 --> 00:29:42.470 What fold? 00:29:42.470 --> 00:29:43.072 Yeah? 00:29:43.072 --> 00:29:44.530 AUDIENCE: You want to [INAUDIBLE].. 00:29:44.530 --> 00:29:45.197 PROFESSOR: Yeah. 00:29:45.197 --> 00:29:46.150 AUDIENCE: [INAUDIBLE] 00:29:46.150 --> 00:29:48.180 PROFESSOR: Yeah, the genome doesn't fold. 00:29:48.180 --> 00:29:51.660 It's double helical, duplex DNA or something. 00:29:51.660 --> 00:29:53.260 You're actually folding proteins, 00:29:53.260 --> 00:29:54.960 so the cartoon is not quite right, 00:29:54.960 --> 00:29:56.790 but it's sort of kind of cute. 00:29:56.790 --> 00:30:00.360 All right, now, when we talk about the non-covalent forces 00:30:00.360 --> 00:30:02.490 that hold proteins together, I just 00:30:02.490 --> 00:30:04.440 want you to remember from last time 00:30:04.440 --> 00:30:08.370 this set of non-covalent forces, because if you understand them 00:30:08.370 --> 00:30:11.810 and recognize them, you'll understand how they may occur 00:30:11.810 --> 00:30:14.070 in folded protein structures. 00:30:14.070 --> 00:30:18.190 All right, so here's a peptide sequence. 00:30:18.190 --> 00:30:19.190 Here's a puzzle for you. 00:30:19.190 --> 00:30:21.990 You can go back and figure out what the one-letter code spells 00:30:21.990 --> 00:30:23.280 there. 00:30:23.280 --> 00:30:27.500 Just take out your table with all the amino acids. 00:30:27.500 --> 00:30:29.790 It's appended to the back of your P-set, 00:30:29.790 --> 00:30:33.020 and you'll be able to see what that very large peptide spells. 00:30:33.020 --> 00:30:34.770 All right, I don't want you working it out 00:30:34.770 --> 00:30:35.290 while you're here. 00:30:35.290 --> 00:30:37.270 You've got to listen to me for the time being. 00:30:37.270 --> 00:30:47.050 OK, so the first order, we get it, there's a primary sequence. 00:30:52.210 --> 00:30:54.380 The next thing to think about is what's 00:30:54.380 --> 00:30:56.510 known as secondary structure. 00:30:56.510 --> 00:30:59.780 It's a higher order than just the primary sequence, 00:30:59.780 --> 00:31:05.600 and it's established by non-covalent bonds, 00:31:05.600 --> 00:31:08.810 and it's called secondary-- oof, my writing's horrid today. 00:31:08.810 --> 00:31:10.420 Secondary structure. 00:31:13.740 --> 00:31:26.530 And those are interactions that are put in place exclusively 00:31:26.530 --> 00:31:31.090 by interactions between the peptide bonds of what's 00:31:31.090 --> 00:31:33.220 known as the peptide backbone. 00:31:33.220 --> 00:31:36.490 So if I look at the structure, these are the side chains. 00:31:36.490 --> 00:31:41.320 The peptide backbone is this continuous linear sequence. 00:31:41.320 --> 00:31:43.840 That's what we would call the peptide backbone, 00:31:43.840 --> 00:31:46.450 and the secondary structure is put in place 00:31:46.450 --> 00:31:49.750 by hydrogen bonding between components 00:31:49.750 --> 00:31:51.370 of the peptide backbone. 00:31:51.370 --> 00:31:54.890 So for example, a hydrogen bonds, 00:31:54.890 --> 00:32:02.810 such as that, or a different hydrogen bonding interaction, 00:32:02.810 --> 00:32:03.680 such as that. 00:32:03.680 --> 00:32:08.300 Between the atoms that have lone pairs of electrons 00:32:08.300 --> 00:32:10.640 and the other atoms-- 00:32:10.640 --> 00:32:14.180 heavy atoms that hold a hydrogen that's quite acidic. 00:32:14.180 --> 00:32:18.050 And there are a couple of major forms of secondary structure. 00:32:18.050 --> 00:32:20.300 What I'm showing you here is what's 00:32:20.300 --> 00:32:22.910 known as the alpha helix. 00:32:22.910 --> 00:32:26.660 First deduced by Pauling, in fact, through model building, 00:32:26.660 --> 00:32:30.230 he said, proteins could form these ordered structures, 00:32:30.230 --> 00:32:34.520 and an alpha helix is an ordered structure exclusively made up 00:32:34.520 --> 00:32:36.470 from the hydrogen-bonding interactions 00:32:36.470 --> 00:32:38.130 of the peptide backbone. 00:32:38.130 --> 00:32:40.640 And you can look at this helical structure. 00:32:40.640 --> 00:32:44.060 It's a continuous strand of peptide, 00:32:44.060 --> 00:32:50.510 but there are hydrogen bonds between COs and NHs all the way 00:32:50.510 --> 00:32:54.530 through the backbone, such that this strand of peptide 00:32:54.530 --> 00:32:58.190 can fold up into a cylindrical, helical structure, where 00:32:58.190 --> 00:33:01.655 all those R groups, the side chains of the amino acids, 00:33:01.655 --> 00:33:04.550 are on the perimeter of that helix. 00:33:04.550 --> 00:33:08.930 So this secondary structure is an important one 00:33:08.930 --> 00:33:13.830 because it's very prevalent in a lot of proteins. 00:33:13.830 --> 00:33:17.030 The next secondary structure is also held together 00:33:17.030 --> 00:33:20.180 by hydrogen bonding, and it's interactions 00:33:20.180 --> 00:33:24.140 between stretched out strands of peptides that may not 00:33:24.140 --> 00:33:26.690 be close to each other in the primary sequence, 00:33:26.690 --> 00:33:29.750 but they align in the folded structure. 00:33:29.750 --> 00:33:31.280 And so for example, what I've shown 00:33:31.280 --> 00:33:34.380 you here is what's known as a-- 00:33:34.380 --> 00:33:38.330 this guy is then to say this is an anti-parallel beta sheet. 00:33:38.330 --> 00:33:42.470 And across that sheet, there are continuous opportunities 00:33:42.470 --> 00:33:44.690 for hydrogen bonding interaction. 00:33:44.690 --> 00:33:48.350 If the strands run in opposite directions, it's anti-parallel. 00:33:48.350 --> 00:33:50.930 If they're in the same direction, it's parallel. 00:33:50.930 --> 00:33:57.220 These two secondary structure elements 00:33:57.220 --> 00:34:00.130 make up a lot of the sort of basics 00:34:00.130 --> 00:34:02.050 of how proteins start to fold. 00:34:02.050 --> 00:34:05.830 They're key non-covalent forces, and there are also 00:34:05.830 --> 00:34:07.870 other smaller motifs. 00:34:07.870 --> 00:34:14.739 One is called a beta turn, where the peptide sequence may 00:34:14.739 --> 00:34:18.040 go through a chain reversal, so the sequence 00:34:18.040 --> 00:34:19.030 would look like this. 00:34:19.030 --> 00:34:20.488 I'm going to just draw it, and I'll 00:34:20.488 --> 00:34:24.560 talk to you in a moment about ribbon diagrams. 00:34:24.560 --> 00:34:27.560 And this piece here would be the turn, 00:34:27.560 --> 00:34:30.108 whereas that would be the interactions enforced 00:34:30.108 --> 00:34:30.650 by the sheet. 00:34:30.650 --> 00:34:34.409 These are the ordered elements of secondary structure. 00:34:34.409 --> 00:34:36.840 You don't have to be able to figure them out, 00:34:36.840 --> 00:34:38.659 but you have to be able to pick them out 00:34:38.659 --> 00:34:42.679 in order to understand the structure, OK? 00:34:42.679 --> 00:34:46.159 So even those simple elements still 00:34:46.159 --> 00:34:50.190 it's hard to make big enough structures to have functions. 00:34:50.190 --> 00:34:53.480 So as I mentioned in a continuation of the theme, 00:34:53.480 --> 00:34:56.540 the protein folding is hierarchical, 00:34:56.540 --> 00:35:00.650 you can start to put together elements of secondary structure 00:35:00.650 --> 00:35:02.990 to make things that are a little larger. 00:35:02.990 --> 00:35:05.780 Helix, turn, helix. 00:35:05.780 --> 00:35:08.180 Helix with a different kind of turn, 00:35:08.180 --> 00:35:12.650 maybe put in place by a metal ion or something, or a strand, 00:35:12.650 --> 00:35:15.020 turn, strand, or now something that's 00:35:15.020 --> 00:35:20.180 a composite of these two major types of secondary structure, 00:35:20.180 --> 00:35:21.840 the helix and the turn. 00:35:21.840 --> 00:35:23.960 And these really start to be proteins 00:35:23.960 --> 00:35:27.290 that might be big enough to be able to do something, 00:35:27.290 --> 00:35:29.750 but they're all exclusively held together 00:35:29.750 --> 00:35:34.940 by non-covalent forces between the amides or peptide bonds 00:35:34.940 --> 00:35:37.580 in the backbone of the protein, OK? 00:35:37.580 --> 00:35:40.690 Not very exciting just yet. 00:35:40.690 --> 00:35:43.570 Now, one other little clue that people will-- 00:35:43.570 --> 00:35:45.730 you might see and you might be confused, 00:35:45.730 --> 00:35:47.800 people sometimes, when they're drawing sort 00:35:47.800 --> 00:35:51.520 of a quick picture of a protein, they might draw a helix, 00:35:51.520 --> 00:35:53.890 but instead of really showing it in detail, 00:35:53.890 --> 00:35:55.510 they might show it as a cylinder, 00:35:55.510 --> 00:35:59.910 so you might need to pick that out of a structure. 00:35:59.910 --> 00:36:02.620 And then I want to call your attention to that, 00:36:02.620 --> 00:36:07.370 that in all those motifs, when you join one helix to another, 00:36:07.370 --> 00:36:11.090 you might need to turn a strand to another strand you 00:36:11.090 --> 00:36:12.650 need to turn, and so on. 00:36:12.650 --> 00:36:16.730 OK, so this is like taking your very extended stored 00:36:16.730 --> 00:36:19.850 of polymer, knowing there are different kinks in it, because 00:36:19.850 --> 00:36:22.490 of the backbone bonds, but folding it up 00:36:22.490 --> 00:36:26.510 in a structure that maximizes the opportunity 00:36:26.510 --> 00:36:30.540 for another order of structure, which we'll talk about now. 00:36:30.540 --> 00:36:33.770 All right, so we've seen primary. 00:36:33.770 --> 00:36:35.285 Secondary is just with backbone. 00:36:38.700 --> 00:36:42.660 And things start to get much more interesting 00:36:42.660 --> 00:36:45.240 when we get to tertiary structure, 00:36:45.240 --> 00:36:48.420 because tertiary structure is enabled 00:36:48.420 --> 00:36:52.740 by all these other interactions, electrostatic, hydrogen 00:36:52.740 --> 00:36:55.050 bonding, hydrophobic forces, that 00:36:55.050 --> 00:36:57.780 can be put in place due to the side 00:36:57.780 --> 00:37:01.402 chains of amino acids interacting with each other 00:37:01.402 --> 00:37:02.735 or with the backbone structures. 00:37:02.735 --> 00:37:05.580 So I'm going to walk you through this, so you can sort of get 00:37:05.580 --> 00:37:08.520 a sense of how these three-dimensional puzzles work 00:37:08.520 --> 00:37:10.110 on a very small scale. 00:37:10.110 --> 00:37:13.430 So look here, that's a very small motif. 00:37:13.430 --> 00:37:16.440 And what I'm going to call your attention to 00:37:16.440 --> 00:37:18.630 is when you fold up these motifs, 00:37:18.630 --> 00:37:20.640 when the secondary structure is in place, 00:37:20.640 --> 00:37:23.340 a lot of the side chains are near each other, 00:37:23.340 --> 00:37:26.400 and they can engage in long-distance contacts. 00:37:26.400 --> 00:37:29.190 And so for example, I'm going to show you 00:37:29.190 --> 00:37:31.650 interactions between side chains, 00:37:31.650 --> 00:37:34.260 between side chains and the peptide backbone, 00:37:34.260 --> 00:37:36.030 or side chains and water. 00:37:36.030 --> 00:37:38.280 But what I want to do is take a look at this and see, 00:37:38.280 --> 00:37:41.310 can you put any of those potential interactions 00:37:41.310 --> 00:37:44.250 on the drawing that's on your handout? 00:37:44.250 --> 00:37:46.140 It's pretty obvious where there's 00:37:46.140 --> 00:37:49.782 an electrostatic interaction, right? 00:37:49.782 --> 00:37:50.730 Boop. 00:37:50.730 --> 00:37:53.430 OK, between plus-- get those out of the way, 00:37:53.430 --> 00:37:54.750 those are the easy ones. 00:37:54.750 --> 00:37:58.830 And then interactions between hydrophobic groups, 00:37:58.830 --> 00:38:02.380 where they want to amass that lipophilic structure, 00:38:02.380 --> 00:38:04.380 so it's not exposed as much to water, 00:38:04.380 --> 00:38:06.960 so they cluster, so those are easy. 00:38:06.960 --> 00:38:10.470 And then you can start thinking about what are all of hydrogen 00:38:10.470 --> 00:38:12.270 bonds you could draw. 00:38:12.270 --> 00:38:16.440 Here I've shown one between side chains, 00:38:16.440 --> 00:38:18.270 between side chains and backbone, 00:38:18.270 --> 00:38:21.180 between side chains and water, and those may all 00:38:21.180 --> 00:38:25.110 contribute to the ultimate thermodynamic stability. 00:38:25.110 --> 00:38:27.030 Make sure you get your hydrogen bonds right. 00:38:27.030 --> 00:38:31.240 Remember, two donors don't interact with each other 00:38:31.240 --> 00:38:32.680 into acceptors, don't-- 00:38:32.680 --> 00:38:36.420 so this might describe the folding possibilities 00:38:36.420 --> 00:38:38.190 of that small motif. 00:38:38.190 --> 00:38:40.376 Now what I want to show you-- 00:38:40.376 --> 00:38:41.980 I'm going to-- let me-- 00:38:46.330 --> 00:38:51.260 is an ab-initio simulation of a folding process. 00:38:51.260 --> 00:38:54.350 So let me just get that a little bigger on the screen. 00:38:54.350 --> 00:38:57.190 So this is computing. 00:38:57.190 --> 00:39:01.720 GB1 is a very small protein that holds reversibly 00:39:01.720 --> 00:39:05.380 under appropriate conditions, and what I'm going to do 00:39:05.380 --> 00:39:08.050 is forward you through this video. 00:39:08.050 --> 00:39:09.440 This is a simulation. 00:39:09.440 --> 00:39:10.840 This is all computation. 00:39:10.840 --> 00:39:14.350 It's not looking at anything by spectroscopy or in solution 00:39:14.350 --> 00:39:15.370 or anything like that. 00:39:19.053 --> 00:39:21.220 And what I'm going to do is I'm going to forward you 00:39:21.220 --> 00:39:22.870 through the structure. 00:39:22.870 --> 00:39:24.750 This is multi-scale modeling. 00:39:24.750 --> 00:39:28.110 It's got a lot of details in how it's done, 00:39:28.110 --> 00:39:31.530 but the starting point is a very denatured protein, 00:39:31.530 --> 00:39:33.450 all stretched out, right? 00:39:33.450 --> 00:39:36.570 And what I'm going to do is just show you for a few seconds, 00:39:36.570 --> 00:39:38.100 you know, this thing's like trying 00:39:38.100 --> 00:39:40.540 to find its thermodynamic minimum, 00:39:40.540 --> 00:39:42.360 and it's actually failing pretty badly. 00:39:42.360 --> 00:39:45.390 And it does that for about 30-- 00:39:45.390 --> 00:39:49.200 60 seconds of the simulations, so I made a point to myself 00:39:49.200 --> 00:39:52.260 to take you to about minute one, where things start 00:39:52.260 --> 00:39:53.475 to get fairly interesting. 00:39:53.475 --> 00:39:55.770 And you're saying, well, what's interesting about that? 00:39:55.770 --> 00:39:59.760 You see that nascent helix, in the background, the red 00:39:59.760 --> 00:40:02.430 and the blue, is starting to form strands that 00:40:02.430 --> 00:40:04.170 are a little bit aligned, and it's 00:40:04.170 --> 00:40:07.530 trying to find as many connections as possible 00:40:07.530 --> 00:40:09.660 to satisfy a stable structure. 00:40:09.660 --> 00:40:12.420 At a certain point in the simulation, 00:40:12.420 --> 00:40:15.720 five of the hydrophobic groups are in a little pea. 00:40:15.720 --> 00:40:18.180 They're in a little hydrophobic cluster, 00:40:18.180 --> 00:40:21.370 and that's a breakpoint in the folding process, 00:40:21.370 --> 00:40:24.100 because that gets everything glued together better, 00:40:24.100 --> 00:40:26.310 so that the rest of it now can start 00:40:26.310 --> 00:40:30.270 to really find its final place in the folded structure. 00:40:30.270 --> 00:40:33.360 These early structures are known as molten globules. 00:40:33.360 --> 00:40:36.270 A lot of the interactions are not yet in place, 00:40:36.270 --> 00:40:38.610 but the hydrophobic cluster is critical. 00:40:38.610 --> 00:40:40.710 But then after that, it's almost as 00:40:40.710 --> 00:40:43.110 if you're sliding downhill to get 00:40:43.110 --> 00:40:47.110 all the remaining interactions in place to fold the protein, 00:40:47.110 --> 00:40:47.850 OK? 00:40:47.850 --> 00:40:51.150 So protein folding is a puzzle that 00:40:51.150 --> 00:40:54.390 can be solved computationally by maximizing 00:40:54.390 --> 00:40:56.340 thermodynamic interactions. 00:40:56.340 --> 00:41:00.990 So it's sigma this, sum of this, sum of this, sum of that. 00:41:00.990 --> 00:41:03.720 That's going to get difficult the larger the protein gets, 00:41:03.720 --> 00:41:07.110 but for small proteins, those simulations really 00:41:07.110 --> 00:41:10.020 start to make sense, OK? 00:41:10.020 --> 00:41:12.450 All right, so let's just move on here. 00:41:12.450 --> 00:41:14.478 Lost-- ah, good. 00:41:14.478 --> 00:41:16.020 What did you think of the simulation? 00:41:16.020 --> 00:41:17.250 It's kind of cool, right? 00:41:17.250 --> 00:41:19.480 So you can find the link in the sidebar. 00:41:19.480 --> 00:41:25.030 So just pop these back on now, and that's 00:41:25.030 --> 00:41:26.350 the folded structure. 00:41:26.350 --> 00:41:28.630 All right, so with many proteins, 00:41:28.630 --> 00:41:30.250 they're much more complex than that. 00:41:30.250 --> 00:41:34.640 So for example, here's cyclin A. It's involved in cell cycle, 00:41:34.640 --> 00:41:38.860 and you can see its alpha helix structure dominantly, 00:41:38.860 --> 00:41:41.860 very clearly, all those beautiful alpha helices. 00:41:41.860 --> 00:41:44.800 Next to it is the green fluorescent protein, 00:41:44.800 --> 00:41:47.440 which is a cylindrical structure made up 00:41:47.440 --> 00:41:49.510 of anti-parallel beta sheets. 00:41:49.510 --> 00:41:51.610 What's really cool is when you sort of rotate it, 00:41:51.610 --> 00:41:53.470 you can see all those sheets, but then it 00:41:53.470 --> 00:41:56.590 does this little sort of curtsy to the audience, 00:41:56.590 --> 00:41:59.200 and you can look down into the barrel. 00:41:59.200 --> 00:42:01.560 And then in some cases, proteins may 00:42:01.560 --> 00:42:05.020 be a mixture of a secondary structure elements. 00:42:05.020 --> 00:42:06.580 Here it's a little hard to tell. 00:42:06.580 --> 00:42:08.800 This is triose phosphate isomerase, 00:42:08.800 --> 00:42:11.630 but if you look down it, you can see the helices, 00:42:11.630 --> 00:42:15.890 and there's also a group of beta strands that are held together. 00:42:15.890 --> 00:42:19.390 So in that protein, it's a mixture of alpha helix and beta 00:42:19.390 --> 00:42:20.130 sheet. 00:42:20.130 --> 00:42:23.890 Now, I'm not going to tell you much about pulling up 00:42:23.890 --> 00:42:26.380 Protein Data Bank files right now because I 00:42:26.380 --> 00:42:27.955 want to cover the next topic. 00:42:27.955 --> 00:42:29.830 And then when we have a few minutes later on, 00:42:29.830 --> 00:42:30.850 I'll show you. 00:42:30.850 --> 00:42:33.250 But wherever I show you a structure, 00:42:33.250 --> 00:42:37.190 I'm trying to show you the Protein Data Bank code, 00:42:37.190 --> 00:42:39.220 and in the web site, you can see there 00:42:39.220 --> 00:42:42.250 is a free download of PyMOL, which 00:42:42.250 --> 00:42:45.490 is the program I used to create all these structures 00:42:45.490 --> 00:42:47.740 and movies, so you can really look at things. 00:42:47.740 --> 00:42:49.677 And believe me, it took me about three years 00:42:49.677 --> 00:42:51.010 to learn how to use it properly. 00:42:51.010 --> 00:42:54.530 It'll probably take you about a week or maybe a couple of days. 00:42:54.530 --> 00:42:57.610 So if I can learn it, you can certainly learn it. 00:42:57.610 --> 00:43:01.460 Now, there is one final element of protein structure 00:43:01.460 --> 00:43:03.070 that people get kind of hung up on, 00:43:03.070 --> 00:43:05.760 and it's what's called quaternary structure. 00:43:05.760 --> 00:43:09.250 It's like, aren't we done yet? 00:43:09.250 --> 00:43:13.300 So in addition to all of these, let's say 00:43:13.300 --> 00:43:19.320 I have a folded motif, and there's its structure. 00:43:19.320 --> 00:43:24.480 That would be have primary, secondary, between the strands 00:43:24.480 --> 00:43:27.840 or the helix, and tertiary structure, right? 00:43:27.840 --> 00:43:34.840 But in some cases, proteins hold up to quaternary structure, 00:43:34.840 --> 00:43:43.340 where it's multiple of these units joined together-- 00:43:43.340 --> 00:43:47.860 hoo, I could have picked a simpler fold, 00:43:47.860 --> 00:43:50.740 but that will get you the general gist of it-- 00:43:50.740 --> 00:43:54.190 all right, where these are actually associated 00:43:54.190 --> 00:43:56.200 by non-covalent forces. 00:43:56.200 --> 00:43:59.110 So there's more than one polypeptide chain. 00:43:59.110 --> 00:44:03.550 In fact, here would be four peptide chains coming together 00:44:03.550 --> 00:44:05.290 in a higher-order structure that's 00:44:05.290 --> 00:44:07.540 made up of four of those units. 00:44:07.540 --> 00:44:11.170 The prototypic example of this is the protein 00:44:11.170 --> 00:44:13.720 that carries oxygen around in your blood, which 00:44:13.720 --> 00:44:19.150 is hemoglobin, and it has four primary sequences 00:44:19.150 --> 00:44:24.090 that have come together in a tetrameric quaternary 00:44:24.090 --> 00:44:25.360 structure. 00:44:25.360 --> 00:44:27.230 Hemoglobin is kind of interesting, 00:44:27.230 --> 00:44:31.330 because it's made up of two alpha and two beta subunits. 00:44:31.330 --> 00:44:34.330 If All these subunits were identical, 00:44:34.330 --> 00:44:37.210 they would be called homooligomers, 00:44:37.210 --> 00:44:38.830 all the same pieces. 00:44:38.830 --> 00:44:42.230 If they are different, they are called heterooligomers. 00:44:42.230 --> 00:44:44.080 We'll see a little bit more about this 00:44:44.080 --> 00:44:46.900 when I talk about hemoglobin in the next class, 00:44:46.900 --> 00:44:50.260 because the features of the quaternary structure 00:44:50.260 --> 00:44:53.890 are very, very important for the proper transport of oxygen, 00:44:53.890 --> 00:44:56.800 and single mutations can really mess things up, 00:44:56.800 --> 00:45:01.010 and you'll see more about that in the next class. 00:45:01.010 --> 00:45:04.030 So just wrap that little bit up, proteins 00:45:04.030 --> 00:45:07.460 are condensation polymers of amino acids. 00:45:07.460 --> 00:45:12.370 Each protein sequence is defined by covalent bonding. 00:45:12.370 --> 00:45:13.660 Native proteins. 00:45:13.660 --> 00:45:17.460 Most of them that are not have quite quaternary structure 00:45:17.460 --> 00:45:21.370 are folded through secondary and tertiary interactions, 00:45:21.370 --> 00:45:23.630 these things that we already talked about, 00:45:23.630 --> 00:45:27.790 and folding is defined by how to maximize 00:45:27.790 --> 00:45:29.860 all those non-covalent forces to get 00:45:29.860 --> 00:45:33.100 the maximum thermodynamic stability 00:45:33.100 --> 00:45:35.230 with the maximum number of interactions. 00:45:35.230 --> 00:45:37.930 And subunits may also come together 00:45:37.930 --> 00:45:40.830 through quaternary structure. 00:45:40.830 --> 00:45:44.550 OK, so I'm going to talk to you about several proteins 00:45:44.550 --> 00:45:46.770 throughout the course, but for now, I 00:45:46.770 --> 00:45:49.890 want to focus you in on a structural protein that 00:45:49.890 --> 00:45:53.190 provides mechanical support for tissues. 00:45:53.190 --> 00:45:57.240 In the next class, we'll talk about transporters and enzymes, 00:45:57.240 --> 00:45:59.340 and as we move on to signaling, things 00:45:59.340 --> 00:46:02.680 like receptors and membrane proteins and so on. 00:46:02.680 --> 00:46:05.970 So the protein I'm going to describe to you is collagen. 00:46:05.970 --> 00:46:09.550 It is the most abundant protein in the human body. 00:46:09.550 --> 00:46:10.920 It plays enormous roles. 00:46:10.920 --> 00:46:13.200 It's not an enzyme, it's not a catalyst, 00:46:13.200 --> 00:46:14.550 it's not a transporter. 00:46:14.550 --> 00:46:17.370 It is one of those structural proteins, where 00:46:17.370 --> 00:46:20.010 the structure of collagen has evolved 00:46:20.010 --> 00:46:23.220 to provide a mechanical stability to lots 00:46:23.220 --> 00:46:26.640 of essential components of complex organisms. 00:46:26.640 --> 00:46:28.200 And there are many different types 00:46:28.200 --> 00:46:32.410 of collagens that are found in different parts of the body. 00:46:32.410 --> 00:46:35.940 For example, bone, tendon, cartilage, and so on. 00:46:35.940 --> 00:46:38.560 They are all college and structures, 00:46:38.560 --> 00:46:40.050 but they have subtle differences, 00:46:40.050 --> 00:46:42.390 maybe some have different, slightly different, 00:46:42.390 --> 00:46:45.540 mechanical properties to adapt to the functions 00:46:45.540 --> 00:46:48.860 that they perform, OK? 00:46:48.860 --> 00:46:51.540 And what I'm going to show you is that a single amino acid 00:46:51.540 --> 00:46:55.020 change in the primary sequence of collagen 00:46:55.020 --> 00:46:59.380 can destabilize the structure, so it is no longer viable. 00:46:59.380 --> 00:47:01.440 And the disease type I'm going to talk to you 00:47:01.440 --> 00:47:06.980 about is a set of diseases known as collagenopathies, 00:47:06.980 --> 00:47:10.440 and the particular one is called osteogenesis imperfecta. 00:47:10.440 --> 00:47:13.980 Osteo always refers to bone because college 00:47:13.980 --> 00:47:17.490 and plays a critical role in the structure of bone. 00:47:17.490 --> 00:47:22.410 Bone isn't just bone, it's collagen involved in it. 00:47:22.410 --> 00:47:25.940 And it's also this disease is called brittle bone syndrome. 00:47:25.940 --> 00:47:29.880 And here's the X-ray of a baby born with brittle bones 00:47:29.880 --> 00:47:33.480 syndrome, and you'll see that the long bones in the upper arm 00:47:33.480 --> 00:47:36.750 are all irregular because the bones are brittle, 00:47:36.750 --> 00:47:40.580 and they'll break even in utero. 00:47:40.580 --> 00:47:42.980 A lot of babies with this defect can't even 00:47:42.980 --> 00:47:44.730 be born through the birth canal because it 00:47:44.730 --> 00:47:47.700 would crush the bones, and many of them 00:47:47.700 --> 00:47:49.680 don't survive very long at all. 00:47:49.680 --> 00:47:52.410 Some survive with different kinds of cases, 00:47:52.410 --> 00:47:54.120 but their lives are greatly impacted, 00:47:54.120 --> 00:47:56.400 and they could just sort of hit a table 00:47:56.400 --> 00:47:58.590 and the bones would break, all right? 00:47:58.590 --> 00:48:01.020 There are those sort of serious situations 00:48:01.020 --> 00:48:05.590 where parents are actually accused of abuse to the child, 00:48:05.590 --> 00:48:08.490 but the child actually had brittle bone syndrome, 00:48:08.490 --> 00:48:11.460 and it was just through helping them put their clothes on 00:48:11.460 --> 00:48:15.600 or taking them upstairs, the bones got broken very readily. 00:48:15.600 --> 00:48:18.300 So osteogenesis imperfecta really 00:48:18.300 --> 00:48:21.510 describes a collection of these defects. 00:48:21.510 --> 00:48:26.640 Now the collagen tertiary structure is shown here. 00:48:26.640 --> 00:48:29.290 It's actually made up of a type of helix. 00:48:29.290 --> 00:48:31.060 It's not an alpha helix. 00:48:31.060 --> 00:48:34.740 It's a polyproline helix, where the individual subunits 00:48:34.740 --> 00:48:37.830 in that tertiary in the structure are fairly long 00:48:37.830 --> 00:48:41.070 and extended, and I show you three strands 00:48:41.070 --> 00:48:45.420 in this polymeric structure, a yellow, a red, and a green. 00:48:45.420 --> 00:48:49.290 And these rolled together into a three helix bundle that 00:48:49.290 --> 00:48:52.680 has a fibrillous structure, and then all these structures 00:48:52.680 --> 00:48:56.310 come together to make the macromolecular structure that 00:48:56.310 --> 00:48:57.260 is collagen. 00:48:57.260 --> 00:48:59.400 It's not just one of those fibrils. 00:48:59.400 --> 00:49:04.740 It's bundles of those fibrils in a very organized pattern where 00:49:04.740 --> 00:49:07.770 you could even see that patterning in electron 00:49:07.770 --> 00:49:09.030 microscopy. 00:49:09.030 --> 00:49:11.660 And there are many genetic defects of collagen, 00:49:11.660 --> 00:49:13.710 and what's so important to think about 00:49:13.710 --> 00:49:16.620 is if you have a defect in one strand 00:49:16.620 --> 00:49:20.790 that defect will propagate through every single strand. 00:49:20.790 --> 00:49:26.130 If this is one strand made up of three polypeptide chains, 00:49:26.130 --> 00:49:29.070 it propagates all the way through the structure. 00:49:29.070 --> 00:49:32.700 And I believe I have little time to just show you, 00:49:32.700 --> 00:49:34.980 here's the collagen structure. 00:49:34.980 --> 00:49:37.050 I'm just showing you how it's extended. 00:49:37.050 --> 00:49:39.480 Those are three independent strands, 00:49:39.480 --> 00:49:42.720 and there's a set of magenta residues in the middle, which 00:49:42.720 --> 00:49:45.210 come from a defect in the sequence 00:49:45.210 --> 00:49:49.800 where a glycine has been changed to an alanine. 00:49:49.800 --> 00:49:52.260 So I'm going to show you this movie because it shows 00:49:52.260 --> 00:49:54.990 you right at the center of the structure, there 00:49:54.990 --> 00:49:57.420 are residues painted in pink. 00:49:57.420 --> 00:50:01.260 And what I'm going to do is show you close up of that segment. 00:50:01.260 --> 00:50:03.270 If you look at those cells they're 00:50:03.270 --> 00:50:06.920 all nicely organized, except where that defect is, 00:50:06.920 --> 00:50:09.930 and that defect is caused by the change of a hydrogen 00:50:09.930 --> 00:50:14.640 to a methyl group on three residues that come together, 00:50:14.640 --> 00:50:18.000 and that bulges out that fibrillous structure 00:50:18.000 --> 00:50:20.490 and makes it not as compact and beautiful 00:50:20.490 --> 00:50:24.113 as it should be in the version that's got the glycine there. 00:50:24.113 --> 00:50:25.530 So if you look at it, you can even 00:50:25.530 --> 00:50:29.250 see that helix gets bulged out and it's not 00:50:29.250 --> 00:50:32.970 as well-aligned as the rest of the structure. 00:50:32.970 --> 00:50:35.430 And then that defect gets propagated 00:50:35.430 --> 00:50:39.870 into all the fibrils and results in the weakening of the bones. 00:50:39.870 --> 00:50:42.720 Either the collagen fails to form properly, 00:50:42.720 --> 00:50:44.550 or the collagen, when it forms, it 00:50:44.550 --> 00:50:47.080 has much less mechanical stability. 00:50:47.080 --> 00:50:48.830 So I think that's a good place to stop 00:50:48.830 --> 00:50:53.520 and I'll pick up next time with hemoglobin. 00:50:53.520 --> 00:50:57.190 Oh, one last little thing, a couple of things for you to do. 00:50:57.190 --> 00:51:00.860 There's a great link on the website to the Protein Data 00:51:00.860 --> 00:51:03.490 Bank to see how enzymes work. 00:51:03.490 --> 00:51:05.280 And if you have a little time, it 00:51:05.280 --> 00:51:07.620 would be awesome if you could just 00:51:07.620 --> 00:51:10.590 take a quick flick through those parts of the text. 00:51:10.590 --> 00:51:13.680 These slides are posted with these reading assignments, 00:51:13.680 --> 00:51:17.180 and they're posted in color if you want to look at them again.