| 00:15 | Hey folks, uh welcome the um day, the call. And I |
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| 00:25 | um the email I sent out this I had the dates wrong, I |
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| 00:29 | , is it for next week I this week's dates. Anyway, it |
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| 00:35 | messy. So, uh anyway, um next week, you know, |
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| 00:43 | , next Tuesday, next Thursday, just we're, we're gonna start unit |
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| 00:47 | , right? So next Tuesday will uh chapter 20 finishing, finishing 23 |
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| 00:54 | 24 then continuing 24. So the thing here is that this, this |
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| 01:01 | 24 will not be a flip right? Because we have one here |
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| 01:06 | . All right, but this one not be ok. Um And |
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| 01:13 | I'll send out the email. I'm send out an email today anyway, |
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| 01:17 | I want to mention this. I asked to mention this to you |
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| 01:21 | which is this thing you may have this uh around campus very. I |
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| 01:26 | saw it on above the uh water out there. Um So Biology Peer |
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| 01:34 | . Ok. And I think these are due there's a deadline of April |
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| 01:41 | or something, but she said you still submit them after that. |
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| 01:45 | So if it's a painting job, , it's something that is of interest |
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| 01:49 | you, they're looking for, the, basically the lead. Uh |
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| 01:56 | just, if you're in, you've by a one by 02, you |
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| 02:00 | had those recitation sections, right? that's what you would be doing as |
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| 02:05 | facilitator running those in, in It's two of you per section, |
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| 02:10 | lots of sections of those. So not like just looking for a couple |
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| 02:14 | positions. This is looking for a of positions here. OK. So |
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| 02:17 | that's something you might be of it's probably amounts to, well, |
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| 02:21 | says here 10 hours a week. you, you, you would have |
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| 02:25 | recitation sections a week that you run like an hour each time and then |
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| 02:31 | on Fridays, I think is when meet with the, uh, with |
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| 02:35 | faculty person. So anyway, take look at this. I, this |
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| 02:39 | what I'll send out in the email I'll attach the flyer. So, |
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| 02:47 | , but then if you told uh, the lady who runs this |
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| 02:51 | , they'll, they'll accept forms after as well. So, um, |
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| 02:56 | don't know how long, but sooner than later, I'll probably submit your |
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| 03:00 | . Yeah. So anyway, a of $1000 a semester. So, |
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| 03:06 | , I, like I said, worry about writing this all down because |
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| 03:08 | gonna, I'll attach it in the uh after class. Ok. |
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| 03:13 | so what else? Uh So unit opens tomorrow? Um That's the more |
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| 03:21 | . So something like I forget 45 an hour or something, you'll have |
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| 03:27 | another smart work assignment due Monday. then, yeah, so we |
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| 03:34 | what do we got? We're on the sixth. So 123 weeks. |
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| 03:42 | . Um let's begin with uh what talked about last time. Ok, |
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| 03:50 | we finished up um to the Fan and the attenuation mechanism. OK. |
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| 03:58 | Do look at those, I think would find those animations helpful that, |
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| 04:02 | Robert Lax and Trip Operon. Um if you got questions, let me |
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| 04:07 | . OK. Uh But then we of went into examples of some other |
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| 04:12 | of control mechanisms. OK. So at the stringent response which is really |
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| 04:18 | the cell of starving bacterial cell This is one of the effects that |
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| 04:22 | happen. Um The ribosomes are kind stalling at the codons because if |
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| 04:29 | you're, if you're starving, then don't have adequate amount of amino acids |
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| 04:33 | make your charged T R N A which are involved in making a |
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| 04:37 | right? So they, they kind stall at those codons and that brings |
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| 04:42 | this activity that basically says, we gotta shut down protein synthesis or |
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| 04:47 | least severely limited. And the net is just that the um this signing |
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| 04:54 | effects on the elis and their ability really interact with the OPERON for these |
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| 05:00 | R N A s which are involved making a ribosome course and then transfer |
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| 05:05 | N A s also part of OK. Um Phase variation um that's |
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| 05:13 | that manipulation of DNA that control, remember the levels of control. This |
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| 05:18 | the one that's the top of right? The uh control at the |
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| 05:21 | of DNA, right? So we're a DNA and basically flip flopping |
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| 05:29 | And because a promoter is part of , um it then can, when |
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| 05:35 | , when the arrangement occurs, then gene is shut off, it can't |
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| 05:39 | expressed. This is, but this part of the as we'll get into |
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| 05:43 | this section are about to be in in a little bit beautiful four. |
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| 05:47 | is a feature of many packages, ? They'll have multiple um antigens, |
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| 05:52 | example, for a particular feature. this example was two types of flagella |
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| 05:58 | flagellum protein that makes the flagellum switching to another one to kind of |
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| 06:03 | itself from the immune system. So that's a big feature of of |
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| 06:08 | . OK. So we're gonna look two more mechanisms and then that will |
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| 06:14 | out chapter 10. OK. So first of these, and again, |
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| 06:19 | you go through through these, your goes through a lot more different examples |
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| 06:24 | of gene control. We don't cover of these things, of course. |
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| 06:27 | just kind of remember for this entire , right? Beginning with 21 22 |
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| 06:34 | , 10, none of those chapters covered in there entirely, right? |
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| 06:38 | if you're reading the book, make , you know, you we're only |
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| 06:41 | certain parts of each chapter here. . So Sigma factor regulation. So |
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| 06:47 | aware that Sigma Factors right there. are the guys that are, are |
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| 06:52 | of loosely bound to our, our and then guide it to a |
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| 06:57 | right? So Sigma factors are natural to be involved with regulation. Because |
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| 07:06 | right, if you affect a a factor, it can't find a promoter |
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| 07:11 | you can't express that view, So we use Sigma factors that |
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| 07:14 | that's a way to control. We're only looking at one example of |
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| 07:20 | but there's things like anti sigma factors can affect sigma factors and and how |
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| 07:25 | work. So there's other other layers , but we're just gonna look |
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| 07:29 | look at one example of this. . So uh this is I would |
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| 07:35 | this mechanism. A it's based on , it's a temperature sensitive mechanism. |
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| 07:42 | . Uh The temperature affects a OK. So remember the levels of |
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| 07:49 | , right? Conscription control is before ? Transcription control is manipulating the ali |
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| 07:56 | know, let it transcribe or right? But here we're dealing with |
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| 08:01 | fully formed transcript and temperature is affecting it will work. OK? So |
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| 08:07 | a it's a post transcription mechanism because dealing with the made transcript. |
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| 08:14 | So, uh, so it's so temperature, right? So temperature |
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| 08:19 | the kind of the force here if will. And that's a natural fit |
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| 08:25 | what we are controlling here are what call stress response genes, heat stress |
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| 08:31 | . OK. So, and there's types of stress genes that get expressed |
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| 08:37 | various conditions, whether it's higher, P H or what have you |
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| 08:41 | these are ones related to temperature. . So of course, if you |
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| 08:44 | high temp, right, what's that do? It's gonna unravel proteins, |
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| 08:49 | ? Denature proteins, denature the right? But we're primarily focused here |
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| 08:54 | the proteins. And so protein function in the tank right when you get |
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| 08:59 | temperatures because they can't function, OK. So you gotta do something |
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| 09:02 | it with your bacterial cell. And the controller here we're gonna look at |
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| 09:07 | temps. So what we call ambient , not just normal kind of |
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| 09:12 | Um Here they're using 30 degrees as example. So the art the that's |
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| 09:18 | sigma H. So it's it's a factor specific specific for this stress response |
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| 09:25 | I stigma H and so you see transcript, right? So the transcript |
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| 09:29 | formed in that, you know, temperature range, the writers on binding |
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| 09:36 | is hidden, right? There's a on binding site sitting at the start |
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| 09:41 | that transcript. So right here, , right there some binding site. |
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| 09:48 | . And so uh well, no, I'm just gonna be sorry |
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| 09:51 | that. It's actually in here, ? It's in there little loop, |
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| 09:56 | loops, loops. That's where the binding site is. And so in |
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| 10:03 | folded state, it's not accessible. . So you don't really transcribe this |
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| 10:09 | a Sigma factor. Not the sigma are proteins. They're made like any |
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| 10:14 | protein, there's gonna be a transcript it and you're gonna translate that to |
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| 10:17 | factor. OK. So uh but this is hidden, right, we |
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| 10:23 | translate that at normal times, At times not, it's not exposed |
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| 10:28 | be able to translate. OK? The little bit but again, |
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| 10:33 | These things are, are not all one or the other, right? |
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| 10:37 | can be, there's a, there's equilibrium, right? It's mostly in |
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| 10:42 | form, right? But it can out like that, not a |
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| 10:47 | but a tiny amount of time, , it may stretch out, |
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| 10:52 | Most of the time it's folded right? And so you may get |
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| 10:55 | little bit of translation, right? the green, the green blob here |
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| 11:01 | a Sigma factor protein. OK. what you have to control that are |
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| 11:05 | other proteins here? OK. And are a group of proteins of |
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| 11:13 | generally the same kind of functions they at normal temps, they serve the |
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| 11:18 | of at least for the Sigma factor kind of get rid of it because |
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| 11:21 | don't want this around. If it's an elevated tap, that's when it |
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| 11:26 | you. That's when it helps the . When it's an elevated tap, |
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| 11:28 | at 30 degrees here. OK? we don't want that activity. So |
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| 11:33 | proteins kind of, you know, that help degrade. They, they |
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| 11:37 | proteins for degradation. Ok. Uh have similar systems, the proteins that |
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| 11:42 | around either because they don't work you don't function properly or you wanna |
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| 11:47 | rid of them. We have a of proteins that kind of marks them |
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| 11:50 | destruction. OK? And that's what do when these things are present at |
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| 11:55 | little bit that it gets made at degrees for, you know, within |
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| 11:59 | or minus a few degrees. So when el temperature elevates, you |
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| 12:05 | you want the effect of this sigma , right? Because it will lead |
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| 12:10 | the production of the what we call shock genes, these and others. |
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| 12:15 | ? And so you actually get more these made, these guys G R |
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| 12:21 | DNA K made at, at the temp because they serve now their other |
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| 12:27 | is to bind the proteins so that at high temp begin to unravel, |
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| 12:32 | ? DNA don't become non functioning. you want to try to keep it |
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| 12:38 | , keep it, keep that um structure right intact. So it can |
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| 12:43 | , right? And that's what these do. They're called the chaperone |
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| 12:47 | they kind of stick with the protein kind of help it maintain shape. |
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| 12:52 | its particular folded shape. OK. so it, and that happens because |
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| 12:58 | elevated temp 42 you see how, the Sigma factor transcript is now Primoz |
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| 13:05 | binding sites accessible. OK. And can translate it into lots of Sigma |
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| 13:11 | sigma H that will then promote expression those heat shock genes. OK. |
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| 13:18 | again, it's kind of a a , post transcription control. The transcript |
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| 13:23 | affected by the temperature. So it's one that you want to function at |
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| 13:27 | tech because it will allow the cell to survive, right? While those |
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| 13:33 | are, are are kind of then you can form these guys that |
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| 13:37 | come and help keep it folded, ? So it could function at high |
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| 13:41 | and e uh can't, can survive a while at 42 degrees because of |
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| 13:47 | . So it's a, it's kind remarkable in the way because it can |
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| 13:53 | eco can also withstand a, a P H and it can, it |
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| 13:58 | remain like a P H four. for a while as well, because |
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| 14:02 | also has like stress responses for, that. OK. So we can |
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| 14:06 | at 42 degrees, not forever, certainly for several hours uh because of |
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| 14:11 | effect. OK. Uh Any questions that. So, so the last |
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| 14:19 | here for chapter didn't show that the one here for chapter 10 is um |
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| 14:25 | . Regulatory artist. So the, these are present we're looking at, |
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| 14:30 | course, bacteria here, but they're in us as well. They're present |
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| 14:35 | , across the domains. OK? One of the main reasons is because |
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| 14:42 | , they're efficient means of control because don't have to produce a protein, |
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| 14:47 | ? The Arnold product is the OK? Um So the transcription |
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| 14:54 | of one of these, that's, the end product, right? And |
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| 14:58 | they can uh work on uh through complimentary base pair, target other |
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| 15:06 | OK. And so here's an example , so Staph aureus, uh this |
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| 15:13 | is a pathogen. OK. Like pathogens, they tend to have some |
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| 15:18 | expressed early on and other ones expressed in their infection cycle. OK. |
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| 15:26 | so the Staph aureus uh does it which genes are, are shut off |
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| 15:33 | they've kind of progressed past the initial stage? OK. And so R |
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| 15:38 | A three. And so remember R A molecules, right can fold up |
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| 15:43 | structure. OK. And so forming loops is kind of one of the |
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| 15:48 | a A molecules will do. And very often that specific loop. |
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| 15:53 | and it's just a U G C pair, very often the loop itself |
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| 15:58 | , is important to shape it takes terms of its function. OK. |
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| 16:02 | so for this one, it binds target R N A S, |
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| 16:08 | That so basically, these are genes longer need that need to be |
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| 16:11 | So let's get rid of the transcripts they won't be translated. OK. |
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| 16:16 | so they have a specific target sequences it's, it's just all complimentary |
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| 16:21 | OK. And so uh very often these regulatory R N A S, |
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| 16:27 | end result is to block translation, ? So by looking, so S |
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| 16:34 | is the virus on binding site. that shine delgado, that's the viva |
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| 16:38 | binding site. So I'll put RBS as well. So on binding |
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| 16:44 | so if you can cover it right as this is doing here, |
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| 16:50 | here is the, the R A Sequels right there. So complementary base |
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| 16:59 | to the target transcript and in doing covers up that um ribosome binding |
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| 17:06 | OK? And so the ribosome can't , you don't get translation and basically |
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| 17:11 | expression. OK? And very often only does it cause. So this |
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| 17:17 | this is a translational control, Because we're affecting the ribosome is not |
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| 17:23 | to translate, we call it translational . And so um but very often |
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| 17:29 | when this happens, the blocking of won't be able to bind and translate |
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| 17:35 | , then can also involve other molecules will degrade it. OK? As |
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| 17:40 | see here. So basically destroying OK? It may or may not |
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| 17:44 | . But sometimes you see that injunction , with this mechanism where binds blocks |
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| 17:49 | that often it leads to degradation as . OK. So um so this |
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| 17:57 | seen in a lot of different this kind of control. And so |
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| 18:01 | slide here don't memorize it. The of this is that not only can |
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| 18:06 | uh affect expression by stopping expression, , inhibit translation. Like we just |
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| 18:13 | it can also activate, right. it kind of depends on the gene |
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| 18:17 | the target, what's going on. it can um so here you see |
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| 18:22 | transcript is folded such that the ribosome site is covered, right? But |
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| 18:30 | here comes a small R N A R N A that comes in and |
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| 18:34 | that right. So now it's ribosome to bind, right? So it |
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| 18:41 | work both ways. So in some , they inactivate, in some |
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| 18:45 | they activate. OK. Uh Here promoting um the uh stability, |
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| 18:52 | promote R AM R A degradation. here is the small M R N |
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| 18:56 | and now becomes unstable, degrades. , here's the opposite, right? |
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| 19:00 | binds and it becomes stabilized. So point here is it can work in |
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| 19:05 | ways, right? Activating it, , destabilizing, et cetera, |
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| 19:10 | And even affecting protein function. So you have a um a protein, |
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| 19:16 | ? It's bound, right? And here comes this, here comes a |
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| 19:19 | R N A and it binds the up. Now you activate translation. |
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| 19:25 | the point is it's working in lots different ways, very efficient right. |
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| 19:29 | only the, the end product R A is what causes all the effects |
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| 19:33 | . OK. Now, the last of these um is a variation. |
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| 19:42 | one thing, so these key here occur between genes, OK. So |
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| 19:51 | between uh protein coding genes, And as we just saw a variety |
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| 19:57 | different functions, activate, can et cetera, right? All depends |
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| 20:02 | the type and the target. So the last one here is uh |
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| 20:09 | R N A but the we call antisense R A. So these, |
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| 20:12 | are gonna be embedded, they're embedded the gene they control, right? |
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| 20:20 | how they differ from the other OK. So these are very |
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| 20:24 | You can see E coli has 1000 anti sets R N A S. |
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| 20:29 | controlling 1000 different proteins. OK. , um and so I here's an |
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| 20:37 | of what we're talking about, So here is a double strand of |
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| 20:42 | , it's a cultural protein. And within, within the sense |
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| 20:48 | right? Within this one here. right, we see the antisense |
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| 20:55 | So that sequence of the gene is that coding strand. OK. So |
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| 21:02 | this works is, let's say we we just do our usual expression transcription |
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| 21:09 | , right? So we go uh I just, I threw in on |
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| 21:13 | antisense on the template. I put in just for as a, as |
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| 21:16 | reference point here. OK. So do our normal transcription translation, |
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| 21:21 | So we transcribe the antisense template strand an M R N A, |
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| 21:26 | And so this will be, this then of course be translated right into |
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| 21:32 | , right? So how do we it? How does this antisense gene |
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| 21:37 | it? But what happens is it just gets transcribed? OK. So |
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| 21:44 | gonna transcribe now this into an antisense A. OK. So remember anti |
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| 21:54 | sense, whatever is always a minor . OK. And so remembering from |
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| 22:01 | , right, R N A viruses how that works, right? Plus |
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| 22:04 | into a minus, right. So we go. So we copy that |
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| 22:08 | the minus the antisense strand. And going to have the sequence complementary to |
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| 22:16 | target. Now it's gonna be longer four nucleotide. So I'm just making |
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| 22:21 | , I'm simplifying it here but it be 10, probably 10 or 20 |
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| 22:25 | long that is complementary to OK. . But the point is is the |
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| 22:31 | R N A is spec specific for transcript, right? For the transcript |
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| 22:41 | that gene, whatever this protein is this gene is specific for that. |
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| 22:47 | . And again, just complementary base , right? And so it recognizes |
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| 22:52 | the, it recognizes the M R A for that gene and by binding |
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| 22:57 | it, it blocks the ribosome from being able to, to um |
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| 23:04 | . OK. So it's also kind it's a translational control, right? |
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| 23:11 | any questions about that? Yeah. different, different from the previous one |
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| 23:18 | the the actual uh regulatory component is in the gene, it |
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| 23:27 | OK. But the other one, exist between genes and can act on |
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| 23:32 | types of targets. This one is specific. OK. So it's gonna |
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| 23:36 | control expression of this gene in Um but again, in general, |
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| 23:44 | R N A S as a regulation is efficient, right? It doesn't |
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| 23:48 | as much energy, right? Because only have to make the R N |
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| 23:51 | , you don't have to go in make a protein or anything. Um |
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| 23:56 | questions about that. Yeah, only that in this example that he set |
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| 24:10 | is only the, the for Oh, we out. So |
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| 24:21 | each one now this could be. what it was if I think is |
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| 24:38 | we're not, if we remember to that protein, that's a gene we're |
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| 24:46 | the uh the, you know, so by doing that, we're not |
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| 24:55 | any copy that then. All So that's why. But yeah, |
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| 25:11 | control that. There. Each the other one. All right. |
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| 25:23 | um all right. So that's, , we got one question to |
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| 25:27 | So let me pop this up. uh Yeah, good. There we |
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| 25:37 | . 4444444488. All right. Let pause that. See if you can |
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| 25:45 | it. Yes. Yeah. Four and two eights. Ok, let's |
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| 27:01 | down from |
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