0:00:00.191,0:00:02.860 - DNA gets a lot of attention as the store 0:00:02.860,0:00:06.252 of our genetic information, and it deserves that. 0:00:06.252,0:00:07.889 If we didn't have DNA, there would be no way 0:00:07.889,0:00:10.826 of keeping the information that makes us us, 0:00:10.826,0:00:13.322 and other organisms what those organisms are. 0:00:13.322,0:00:16.654 And DNA has some neat properties, it can replicate itself, 0:00:16.654,0:00:19.591 and we go into a lot of depth on that in other videos. 0:00:19.591,0:00:23.516 So DNA producing more DNA, we call that, 0:00:23.516,0:00:26.488 we call that replication, but just being able 0:00:26.488,0:00:28.856 to replicate yourself on its own isn't enough 0:00:28.856,0:00:31.527 to actually produce an organism. 0:00:31.527,0:00:33.059 And to produce an organism, you somehow have to 0:00:33.059,0:00:35.451 take that information in the DNA, and then 0:00:35.451,0:00:39.921 produce things like a structural molecules, 0:00:39.921,0:00:43.218 enzymes, transport molecules, signaling molecules, 0:00:43.218,0:00:48.291 that actually do the work of the organism. 0:00:48.291,0:00:51.054 And that process, the first step, and this is all a review 0:00:51.054,0:00:53.179 that we've seen in other videos. 0:00:53.179,0:00:55.785 The first step is to go from DNA to RNA, 0:00:55.785,0:00:57.774 and in particular, messenger RNA. 0:00:58.824,0:01:02.052 "Messenger RNA," and this process right over here, 0:01:02.052,0:01:04.293 this is called transcription. 0:01:04.293,0:01:06.127 "Transcription," we go into a lot of detail 0:01:06.127,0:01:08.089 on this in other videos. 0:01:08.089,0:01:10.225 And then you wanna go from that messenger RNA, 0:01:10.225,0:01:14.126 it goes to the ribosomes and then tRNA goes and grabs 0:01:14.126,0:01:17.191 amino acids, and they form actual proteins. 0:01:17.191,0:01:21.359 So you go from messenger RNA, and then in conjunction, 0:01:21.359,0:01:24.958 so this is all, this is in conjunction with tRNA 0:01:24.958,0:01:32.888 and amino acids, so let me say "+tRNA," and "amino acids." 0:01:32.888,0:01:35.849 And I'll write "amino acids" in, I'll write it in a brighter 0:01:35.849,0:01:39.123 color, since that's going to be the focus of this video. 0:01:39.123,0:01:45.990 So tRNA and amino acids, you're able to construct proteins. 0:01:45.990,0:01:47.789 You are able to construct proteins, 0:01:47.789,0:01:51.191 which are made up of chains of amino acids, 0:01:51.191,0:01:53.351 and it's the proteins that do 0:01:53.351,0:01:56.392 a lot of the work of the organism. 0:01:56.392,0:01:59.550 Proteins, which are nothing but chains of amino acids, 0:01:59.550,0:02:00.885 or they're made up of, sometimes 0:02:00.885,0:02:02.627 multiple chains of amino acids. 0:02:02.627,0:02:05.924 So you can image, I'm just going to, that's an amino acid. 0:02:05.924,0:02:07.724 That's another amino acid. 0:02:07.724,0:02:10.092 This is an amino acid. 0:02:10.092,0:02:13.041 This is an amino acid, you could keep going. 0:02:13.041,0:02:16.420 So these chains of amino acids, based on 0:02:16.420,0:02:19.554 how these different, based on the properties 0:02:19.554,0:02:21.017 of these different amino acids, 0:02:21.017,0:02:23.049 and how the protein takes shape and how 0:02:23.049,0:02:24.883 it might interact with its surrounding, 0:02:24.883,0:02:27.855 these proteins can serve all sorts of different functions. 0:02:27.855,0:02:30.619 Anything from part of your immune system, 0:02:30.619,0:02:33.324 antibodies, they can serve as enzymes, 0:02:33.324,0:02:38.420 they can serve as signaling hormones, like insulin. 0:02:38.420,0:02:40.986 They're involved in muscle contraction. 0:02:40.986,0:02:42.287 Actin and myosin, we actually have 0:02:42.287,0:02:43.726 a fascinating video on that. 0:02:43.726,0:02:45.491 Transport of oxygen. 0:02:45.491,0:02:46.455 Hemoglobin. 0:02:46.455,0:02:48.719 So proteins, the way at least my brain of it, 0:02:48.719,0:02:50.089 is they do a lot of the work. 0:02:50.089,0:02:54.419 DNA says, well, what contains the information, 0:02:54.419,0:02:57.809 but a lot of the work of organism is actually done, 0:02:57.809,0:03:00.526 is actually done by the proteins. 0:03:00.526,0:03:02.349 And as I just said, the building blocks 0:03:02.349,0:03:05.054 of the proteins are the amino acids. 0:03:05.054,0:03:07.027 So let's focus on that a little bit. 0:03:07.027,0:03:10.859 So up here are some examples of amino acids. 0:03:10.859,0:03:12.786 And there are 20 common amino acids, 0:03:12.786,0:03:17.523 there are a few more depending on what organism you look at, 0:03:17.523,0:03:19.740 and theoretically there could be many more. 0:03:19.740,0:03:21.087 But in most biological systems, 0:03:21.087,0:03:24.826 there are 20 common amino acids that the DNA is coding for, 0:03:24.826,0:03:26.219 and these are two of them. 0:03:26.219,0:03:29.017 So let's just first look at what is common. 0:03:29.017,0:03:33.022 So, we see that both these, and actually all three of this, 0:03:33.022,0:03:36.761 this is just a general form, you have an amino group. 0:03:36.761,0:03:39.059 You have an amino group, and this where, 0:03:39.059,0:03:42.461 this is why we call it an "amino," an amino acid. 0:03:42.461,0:03:44.423 So you have an amino group. 0:03:44.423,0:03:46.258 Amino group right over here. 0:03:46.258,0:03:49.056 Now you might say, "well, it's called an amino acid," 0:03:49.056,0:03:50.960 "so where is the acid?" 0:03:50.960,0:03:55.720 And that comes from this carboxyl group right over here. 0:03:55.720,0:03:57.392 So that's why we call it an acid. 0:03:57.392,0:04:02.384 This carboxyl group is acidic. 0:04:02.384,0:04:04.520 It likes to donate this proton. 0:04:04.520,0:04:06.656 And then in between, we have a carbon, 0:04:06.656,0:04:09.152 and we call that the alpha carbon. 0:04:09.152,0:04:12.020 We call that the alpha carbon. 0:04:12.020,0:04:14.493 Alpha carbon, and that alpha carbon is bonded, 0:04:14.493,0:04:16.594 it has a covalent bond to the amino group, 0:04:16.594,0:04:18.591 covalent bond to the carboxyl group, 0:04:18.591,0:04:20.959 and a covalent bond to a hydrogen. 0:04:20.959,0:04:24.187 Now, from there, that's where you get the variation 0:04:24.187,0:04:26.242 in the different amino acids, and actually, 0:04:26.242,0:04:30.294 there's even some exceptions for how the nitrogen is, 0:04:30.294,0:04:32.825 but for the most part, the variation between 0:04:32.825,0:04:36.018 the amino acids is what this fourth covalent bond 0:04:36.018,0:04:38.189 from the alpha carbon does. 0:04:38.189,0:04:43.321 So you see in serine, you have this, 0:04:43.321,0:04:45.155 what you could call it an alcohol. 0:04:45.155,0:04:47.187 You could have an alcohol side chain. 0:04:47.187,0:04:50.728 In valine right over here, you have a 0:04:50.728,0:04:54.917 fairly pure hydrocarbon, hydrocarbon side chain. 0:04:54.917,0:04:58.158 And so in general, we refer to these side chains 0:04:58.158,0:05:01.154 as an R group, and it's these R groups 0:05:01.154,0:05:05.159 that play a big role in defining the shape of the proteins, 0:05:05.159,0:05:07.051 and how they interact with their environment 0:05:07.051,0:05:08.955 and the types of things they can do. 0:05:08.955,0:05:10.755 And you can even see, just from these examples 0:05:10.755,0:05:13.518 how these different sides chains might behave differently. 0:05:13.518,0:05:16.084 This one has an alcohol side chain, 0:05:16.084,0:05:18.859 and we know that oxygen is electronegative, 0:05:18.859,0:05:21.378 it likes to hog electrons, it's amazing how much 0:05:21.378,0:05:23.979 of chemistry or even biology you can deduce 0:05:23.979,0:05:26.220 from just pure electronegativity. 0:05:26.220,0:05:28.750 So, oxygen likes to hog electrons, so you're gonna have 0:05:28.750,0:05:31.757 a partially-negative charge there. 0:05:31.757,0:05:38.259 Hydrogen has a low electronegativity relative to oxygen, 0:05:38.259,0:05:40.291 so it's gonna have its electrons hogged, 0:05:40.291,0:05:42.822 so you're gonna have a partially positive charge, 0:05:42.822,0:05:46.781 just like that, and so this has a polarity to it, 0:05:46.781,0:05:48.789 and so it's going to be hydrophilic, it's going to, 0:05:48.789,0:05:50.693 at least this part of the molecule is going to 0:05:50.693,0:05:54.153 be able to be attracted and interact with water. 0:05:54.153,0:05:57.288 And that's in comparison to what we have over here, 0:05:57.288,0:06:02.489 this hydrocarbon side chain, this has no polarity over here, 0:06:02.489,0:06:04.683 so this is going to be hydrophobic. 0:06:04.683,0:06:08.015 So this is going to be hydrophobic. 0:06:08.015,0:06:10.523 And so when we start talking about the structures 0:06:10.523,0:06:12.625 of proteins, and how the structures of proteins 0:06:12.625,0:06:14.552 are influenced by its side chains, 0:06:14.552,0:06:17.524 you could image that parts of proteins that have 0:06:17.524,0:06:18.917 hydrophobic side chains, those are gonna 0:06:18.917,0:06:21.460 wanna get onto the inside of the proteins 0:06:21.460,0:06:23.561 if we're in an aqueous solution, 0:06:23.561,0:06:24.722 while the ones that are more hydrophilic 0:06:24.722,0:06:26.255 will wanna go onto the outside, 0:06:26.255,0:06:27.427 and you might have some side chains 0:06:27.427,0:06:29.250 that are all big and bulky, and so they might 0:06:29.250,0:06:32.420 make it hard to tightly pack, and then you might have 0:06:32.420,0:06:34.080 other side chains that are nice and small 0:06:34.080,0:06:36.355 that make it very easy to pack, so these things 0:06:36.355,0:06:39.653 really do help define the shape, 0:06:39.653,0:06:41.487 and we're gonna talk about that a lot more 0:06:41.487,0:06:44.482 when we talk about the structure. 0:06:44.482,0:06:47.861 But how do these things actually connect? 0:06:47.861,0:06:49.324 And we're gonna go into much more detail 0:06:49.324,0:06:51.924 in another video, but if you have... 0:06:51.924,0:06:56.684 If you have serine right over here, and then you have 0:06:56.684,0:07:01.514 valine right over here, they connect through 0:07:01.514,0:07:03.558 what we call peptide bonds, and a peptide 0:07:03.558,0:07:08.515 is the term for two or more amino acids connected together, 0:07:08.515,0:07:10.257 so this would be a dipeptide, and the bond 0:07:10.257,0:07:12.253 isn't this big, I just, actually let me just, 0:07:12.253,0:07:14.692 let me draw it a little bit smaller. 0:07:14.692,0:07:15.585 So... 0:07:15.585,0:07:17.455 That's serine. 0:07:17.455,0:07:20.624 This is valine. 0:07:20.624,0:07:23.654 They can form a peptide bond, and this would be the smallest 0:07:23.654,0:07:27.428 peptide, this would be a dipeptide right over here. 0:07:27.428,0:07:30.052 "Peptide," "peptide bond," or sometimes 0:07:30.052,0:07:32.141 called a peptide linkage. 0:07:32.141,0:07:35.253 And as this chain forms, that polypeptide, 0:07:35.253,0:07:37.610 as you add more and more things to it, 0:07:37.610,0:07:42.660 as you add more and more amino acids, 0:07:42.660,0:07:44.518 this is going to be, this can be a protein 0:07:44.518,0:07:47.687 or can be part of a protein that does all of these things. 0:07:47.687,0:07:50.021 Now one last thing I wanna talk about, 0:07:50.021,0:07:52.888 this is the way, the way these amino acids have been drawn 0:07:52.888,0:07:54.920 is a way you'll often see them in a textbook, 0:07:54.920,0:07:59.193 but at physiological pH's, the pH's inside of your body, 0:07:59.193,0:08:01.956 which is in that, you know, that low sevens range, 0:08:01.956,0:08:08.318 so it's a pH of roughly 7.2 to 7.4. 0:08:08.318,0:08:12.985 What you have is this, the carboxyl group right over here, 0:08:12.985,0:08:15.087 is likely to be deprotonated, it's likely 0:08:15.087,0:08:16.991 to have given away its hydrogen, 0:08:16.991,0:08:19.452 you're gonna find that more likely than when you have... 0:08:19.452,0:08:21.019 It's gonna be higher concentrations having been 0:08:21.019,0:08:23.121 deprotonated than being protonated. 0:08:23.121,0:08:26.894 So, at physiological conditions, it's more likely 0:08:26.894,0:08:33.546 that this oxygen has taken both of those electrons, 0:08:33.546,0:08:35.125 and now has a negative charge, 0:08:35.125,0:08:37.947 so it's given, it's just given away the hydrogen proton 0:08:37.947,0:08:40.153 but took that hydrogen's electron. 0:08:40.153,0:08:43.717 So it might be like this, and then the amino group, 0:08:43.717,0:08:46.689 the amino group at physiological pH's, 0:08:46.689,0:08:49.150 it's likely to actually grab a proton. 0:08:49.150,0:08:52.691 So nitrogen has an extra loan pair, 0:08:52.691,0:08:55.153 so it might use that loan pair to grab a proton, 0:08:55.153,0:08:56.952 in fact it's physiological pH's, 0:08:56.952,0:08:58.752 you'll find a higher concentration of it having 0:08:58.752,0:09:01.457 grabbed a proton than not grabbing a proton. 0:09:01.457,0:09:05.695 So, the nitrogen will have grabbed a proton, 0:09:05.695,0:09:07.587 use its loan pairs to grab a proton, 0:09:07.587,0:09:09.793 and so it is going to have... 0:09:09.793,0:09:11.825 So it is going to have a... 0:09:11.825,0:09:14.321 It is going to have a positive charge. 0:09:14.321,0:09:19.394 And so sometimes you will see amino acids 0:09:19.394,0:09:21.217 described this way, and this is actually more accurate 0:09:21.217,0:09:24.491 for what you're likely to find at physiological conditions, 0:09:24.491,0:09:26.256 and these molecules have an interesting name, 0:09:26.256,0:09:28.752 a molecule that is neutral even though 0:09:28.752,0:09:31.120 parts of it have charge, like this, 0:09:31.120,0:09:33.419 this is called a zwitterion. 0:09:33.419,0:09:35.985 That's a fun, fun word. 0:09:35.985,0:09:39.874 Zwitterion. 0:09:39.874,0:09:41.558 And "zwitter" in German means "hybrid," 0:09:41.558,0:09:44.809 and "ion" obviously means that it's going to have charge, 0:09:44.809,0:09:46.086 and so this has hybrid charge, 0:09:46.086,0:09:47.990 even though it has charges at these ends, 0:09:47.990,0:09:51.293 the charges net out to be neutral.