| 00:15 | Ok, folks, welcome. Um for the late start. I kind |
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| 00:22 | , I'm uh I think I was for myself in labs this week today |
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| 00:27 | morning. So you may have seen in there a few minutes ago. |
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| 00:33 | . Um All right. So what gonna do today today is going, |
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| 00:37 | have a end point in mind, we're gonna end a little early |
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| 00:42 | Um Sorry to disappoint you. Um a couple of things. So we |
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| 00:51 | well ahead of schedule. Ok? that means of, I hesitate to |
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| 01:01 | this because if I do, I it won't happen, but it's highly |
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| 01:04 | that the last class date of the will be the 25th. Ok. |
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| 01:12 | , so what we're gonna do is gonna, we're actually gonna, uh |
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| 01:15 | finishing early. Today is a little earlier for I have to be elsewhere |
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| 01:19 | campus. Um uh right after So, um at um, at |
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| 01:27 | . So anyway, uh, but the, um starting in at |
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| 01:32 | OK. You see that right Ok. Um Next Tuesday we're gonna |
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| 01:41 | on that. Um, next, , on Thursday. Ok. Uh |
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| 01:46 | got we're gonna have to finish up little bit of chapter 10 yet, |
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| 01:50 | we'll do in the 1st 15, minutes on Thursday. Then we'll get |
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| 01:56 | unit four. I've already opened up four, um, yesterday, so |
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| 02:02 | four stuff, everything is available to . Unit four. Ok, So |
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| 02:08 | , like I said, we'll start , on that after we finish the |
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| 02:11 | stuff. So basically we'll start, , you know, for here and |
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| 02:17 | send out an email. So uh , to remind everybody and start, |
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| 02:22 | know, Should I move that up bit? OK. Start on |
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| 02:29 | OK. So um and so year is really just all about immune uh |
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| 02:37 | microbiology but starting with kind of the defenses um in the immune system, |
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| 02:43 | immune system and then uh I get diseases and things. So um one |
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| 02:50 | , so there is a chapter 26 all about different microbial diseases. So |
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| 02:57 | don't cover all those, but there a list And you see when you |
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| 03:02 | to chapter 26 notes, there's a of, here's the paths to |
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| 03:06 | here's the diseases, Blah, Blah, Blah. OK. I'll |
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| 03:10 | more about it as we get closer that point. Um But that, |
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| 03:15 | , that stuff um you probably wanna in a table and likely it |
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| 03:20 | it's just memorization, right? Because gonna be questions that relate to diseases |
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| 03:25 | the test saying like I said, we get closer to it. |
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| 03:30 | I'll talk more about it. and we'll see some questions in |
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| 03:36 | And so you kind of get a for what, what's to be asked |
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| 03:38 | that. Ok. Uh, the thing is so the unit quiz, |
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| 03:43 | the unit quizzes are a little bit , more comprehensive. And so |
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| 03:47 | this, the unit three, black quiz starts Friday. All |
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| 03:53 | So this Friday through Sunday is one those, through through Monday is one |
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| 03:57 | those unit quizzes. OK? Um think that's it. Uh Of |
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| 04:04 | there's the last, the last smart for this unit is due next |
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| 04:08 | Um Anyway, so as I'm sure aware, we're rapidly approaching the end |
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| 04:14 | . OK? Um But we still some things to do first. So |
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| 04:19 | question anything before we get rolling. . So we're in the middle of |
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| 04:30 | so to back up for a second regulation. OK. So we started |
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| 04:38 | unit with kind of an overview of translation, right? How you have |
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| 04:45 | uh any organism that's out there and whatever it is, right? Um |
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| 04:50 | doing it basically through the functioning of different proteins. Um And yet uh |
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| 04:58 | is being expressed at any given time , right? That person that's sitting |
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| 05:04 | in a pond somewhere. What's they deal with? Well, all the |
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| 05:08 | of other microbes it's interacting with competing um the, if it's a photosynthetic |
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| 05:15 | , what, what, what's the am? Am I my maximum light |
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| 05:20 | depths? Right. And do I stuff to eat? Is there enough |
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| 05:23 | bla bla bla all kinds of You can think of all kinds of |
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| 05:27 | that's affecting it and it's gonna be of those are gonna turn off different |
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| 05:32 | , turn on different other ones to a response, right? A response |
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| 05:36 | will enable it to survival. So, um so getting back, |
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| 05:41 | we're focusing here on the control aspects we're just looking at, you |
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| 05:46 | we're, this is obviously a tip the iceberg right here are just examples |
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| 05:50 | how, you know, you can expression. You know, every um |
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| 05:55 | any, any college student bio student first learns about regulation, you always |
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| 06:02 | with and uh obviously you're hearing it me here, you're gonna hear it |
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| 06:10 | . I'm sure elsewhere as you go the chain, right? Probably in |
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| 06:13 | bio, you cover it, um in biochem one, you cover |
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| 06:18 | So uh in any case, this likely that the last time you'll hear |
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| 06:22 | . But uh hopefully, uh when do hear it again, you'll be |
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| 06:26 | on it, right? So, so that, that's basically what we're |
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| 06:31 | in different aspects of gene regulation. . We're looking at strictly protic |
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| 06:36 | if you get the eukaryotic systems that blow your mind because it can get |
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| 06:42 | layered, super complex. OK? we're more complex creatures than the |
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| 06:49 | right? So actually it's gonna be complicated process. OK? So even |
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| 06:54 | I look at that stuff, it's it blows my mind. So I |
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| 06:58 | , I'm not, I look at that often. I try not |
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| 07:00 | But uh anyway, so let's get to uh Right. So we went |
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| 07:06 | , OK, so you should, gonna see some questions here. So |
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| 07:11 | especially when you get, you started about the control. So you're gonna |
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| 07:16 | those. So you should look at side by side and say OK, |
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| 07:19 | similar? What's how is one different the other blah, blah, |
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| 07:23 | blah. OK. So uh right, the the uh it's |
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| 07:29 | it's all triggered here by the presence absence of sub molecule and the presence |
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| 07:35 | the molecule triggers triggers something to happen the absence of molecule triggers something to |
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| 07:40 | , right? So the la so and foremost, lactose is a sugar |
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| 07:45 | an energy source for the bacteria that ferment lactose, right? Uh A |
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| 07:51 | so um if you wanna, if wanna use it right, then um |
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| 07:57 | have your expression system that handles lactose only work when lactose is present, |
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| 08:05 | ? Inducible, right? The presence lactose, technically, all lactose, |
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| 08:11 | ? Uh that induces the expression, ? So that's the only time to |
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| 08:16 | it on is the black is Makes sense. Why? Right? |
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| 08:20 | would you turn it on there, ? And so um but then there |
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| 08:24 | the other layer, right? The , right? So our glucose is |
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| 08:28 | . OK. Think of it that glucose is present, shuts off lactose |
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| 08:34 | other sugar. That's the table, ? So I saw hinges on the |
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| 08:41 | of cyclic A MP. So I glucose influences, right? So |
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| 08:47 | then you have low levels psychic A , which means very little of this |
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| 08:53 | active complex forms. But we also about the um the uh um that |
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| 09:02 | excludes like a glucose, glucose is . The protein that helps glucose come |
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| 09:07 | kind of affects the lack the lack , right? It doesn't allow lactose |
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| 09:11 | come in in that case. So glucose goes away, lactose present |
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| 09:16 | boom and you get full blown Uh As you see here, first |
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| 09:23 | presence of inducer uh in activating the uh repression protein. It can't find |
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| 09:33 | the operator uh now free to But now because we have a complex |
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| 09:40 | , you get higher, right? it binds the promoter, increasing the |
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| 09:47 | the magnetism if you will of the by theme. So it binds a |
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| 09:52 | with lots of expression. OK. um any questions about la? So |
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| 10:00 | . All right. So then we into opera, correct? So, |
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| 10:07 | , a different uh metabolism like micros is all about in let's process it |
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| 10:16 | weave it and then let's put, it into glycolysis. So it can |
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| 10:20 | used for energy crypto fan opposite. Anna about that making we're making crypto |
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| 10:29 | as a result of the action of expression. O we're making that five |
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| 10:38 | genes involved one continuous transcript. And uh OK. And so Triter |
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| 10:49 | , it, it kind of more less uh self regulates itself. |
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| 10:54 | It's expression. And so, um the thing OK, say, say |
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| 11:06 | an analogy, So say you're working , right? You're a truck driver |
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| 11:10 | Amazon. OK. And you're gonna fill up your truck with packages to |
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| 11:16 | . Ok. And so here are packages, right? And they're on |
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| 11:21 | conveyor belt. Do you, they , here's your, here's your |
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| 11:26 | you gotta put in your truck, ? That truck cool. OK. |
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| 11:32 | right. Put them in the take them away, you got trucks |
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| 11:37 | to keep building up, right? is this ever, are these boxes |
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| 11:43 | accumulating? If you have the truck coming in? Boom. Any given |
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| 11:52 | , if you look here, it's zero because it's being used. It's |
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| 11:57 | , going out for delivery, but have no trucks, piles up boxes |
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| 12:04 | go anywhere, you wanna stop the , right? So that's when the |
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| 12:11 | is now available to act in this , right? Going up there be |
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| 12:18 | co and then form these, which will block expression. So |
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| 12:25 | it's what's going on here right? is what determines which way you're going |
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| 12:33 | pressure or the state inactive and continuous . So, getting away from the |
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| 12:44 | , but for the cell and you ptotic cumulated need, right? You're |
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| 12:49 | not using it. Right? Because you were making it, it would |
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| 12:52 | going somewhere, it would be more to, you know, to, |
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| 12:55 | hook on to a T R N . Right? Um And then being |
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| 12:59 | a protein somewhere, proteins, Triple can be used as a good |
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| 13:04 | other stuff, you know, but protein. But so if it's |
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| 13:09 | if it's, if it's just sitting and it's not being used for |
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| 13:13 | that it's, that's where the growth comes. It's why it's tied to |
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| 13:17 | , right? The cells are growing . It, it wants everything, |
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| 13:22 | ? It's grow multiply, right? produce energy, gotta make proteins, |
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| 13:26 | ? So of course, your is be used right away fast as it's |
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| 13:30 | it. But because there's a demand it when, when the growth then |
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| 13:36 | down, not the same demand, crypto accumulates, don't keep making |
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| 13:42 | You don't need it that much Shut it down. And so it |
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| 13:47 | , that's why it goes this route a pressor. OK? It uh |
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| 13:52 | know, if you, you don't know this, but I mentioned it |
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| 13:55 | . It also actually affects here. binds that enzyme and, and shuts |
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| 13:59 | off there. So you have two going on. OK? So it's |
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| 14:03 | about saving energy, don't waste. ? You know, it's kind of |
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| 14:08 | gotta think of a bacterium in right? It's not by itself in |
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| 14:11 | vacuum, right? It's, it's compete. And so you're gonna not |
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| 14:16 | wasteful things because it, it, can literally carry it. OK. |
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| 14:22 | , all right, that's as far we got with control. OK? |
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| 14:29 | And it makes sense to do it way. It's a biosyn pathway very |
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| 14:33 | to make things now in the course self growing, right? So why |
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| 14:38 | be let the product of the pathway itself, right? You need to |
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| 14:43 | that and this isn't, this isn't an off, on off switch. |
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| 14:47 | not, it's not all or right? It's a it fluctuates, |
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| 14:53 | ? Depending on the needs, the rate in itself, right? Goes |
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| 14:56 | , goes down. It's, it's really well. So I guess in |
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| 15:00 | cases it could be all off. , you know, but it's, |
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| 15:03 | fluctuate, you know, as based the needs of the sell. |
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| 15:07 | Um Is any questions? So we're look, look at some questions |
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| 15:13 | I don't even think these are Clipper . These are just kind of you |
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| 15:18 | me what you got kind of OK. So here's the right. |
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| 15:23 | lac plus Trip plus means it has Operon. OK. So the Lac |
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| 15:28 | has Trip Opera. OK. So growing it in minimal medium with both |
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| 15:34 | and trippin OK, minimal medium. we've plopped in lactose and trippin. |
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| 15:41 | . No glucose. No glucose at . Ok. So what can you |
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| 15:46 | about these cells with respect to these operant? Ok. So lack OPERON |
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| 15:53 | the OPERON expressed? Yes. because lactose is present and glucose is |
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| 16:03 | , right? Um It's a trip on express. Why not? |
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| 16:12 | it's TRIPP fan present. You don't to uh doesn't need to make |
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| 16:14 | it's, it's there to take it and use it. Right. Um |
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| 16:19 | hope I got this coming up, . OK. I do. All |
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| 16:25 | . Um What is the state of black Operon active or inactive? |
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| 16:33 | Uh Right. Because the truth to that's there, you know, uh |
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| 16:43 | it's being supple crypto and they use , of course it does, it |
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| 16:46 | use it all. It's gonna be and free to bind to the um |
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| 16:50 | don't need to synthesize it if it's , right? If you're being feeding |
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| 16:54 | crypto, why make it? You need bind or, or activating |
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| 16:59 | OK. Um How are, how the psychic A P levels affected? |
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| 17:04 | like opera is high or low? Yeah, I can think about that |
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| 17:12 | . Yeah. Um Yeah, because forming that complex, the activator |
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| 17:16 | right? So not, not applicable Trip Opera. OK. So, |
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| 17:22 | right. This now, so this the one that's gonna be kind |
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| 17:27 | you know, pull your hair out there is, there is a, |
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| 17:32 | , a step wise way to think it that should help. So you |
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| 17:38 | have this slide. That's fine. , I inserted it right before |
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| 17:42 | Oops batteries. Oh, I knew should have changed it. OK. |
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| 18:07 | . OK. So put this in class just as a, to, |
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| 18:12 | , to show you what the OK. So um here's the |
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| 18:18 | the actor pressure hasn't bound yet. . So in that state, we're |
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| 18:24 | defense, right? So we already that accumulates, it'll bind the the |
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| 18:31 | a corepressor bind, you have an and we pull it right? So |
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| 18:39 | mechanism, right? The the this if it's not being used and then |
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| 18:48 | over here to bind and then causing to happen, oop causing that to |
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| 18:54 | off expression, right? Um That , I, I wanna say a |
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| 19:00 | but don't hold up to it in of 95%, of the stoppage of |
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| 19:09 | opera occurs by this way, The corepressor binding, the repressor activating |
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| 19:16 | , OK? That controls the majority this expression. OK? But as |
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| 19:22 | know, these bindings, right? not irreversible, right? Yes. |
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| 19:29 | you had a camera and you took snapshot most of the time you're |
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| 19:32 | you'd see it sitting on the but there's gonna be times when it's |
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| 19:36 | , right? Not very long, very often, but it, it |
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| 19:40 | happen. And that's when you get off and you get some expression. |
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| 19:45 | . So this last mechanism, this attenuation mechanism is about this part |
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| 19:53 | it. All right. So one to make a note when you, |
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| 19:59 | when you are expressing the, um trip to Japan often and you're making |
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| 20:07 | big, big continuous transcript just making OK? That this part is always |
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| 20:15 | part of it, the box in , that's the leader sequence. So |
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| 20:20 | always a part of the transcript. ? Now, if you're in a |
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| 20:26 | where you need to make trip, doesn't matter, it's just a part |
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| 20:29 | the transcript, but you don't do with it, right? But when |
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| 20:34 | don't, when you really wanna put clamp down on it, right, |
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| 20:38 | don't want any expression to occur virtually . Like I said, this, |
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| 20:43 | takes care of most of it, some can still be made. So |
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| 20:48 | really wanna put a clamp on this where attenuation comes in and it involves |
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| 20:54 | part of that transcript that so the um trying to think the best way |
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| 21:08 | . All right. So No All right. So here we're zeroed |
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| 21:14 | . Look at the bottom here, zeroed in on the opera front |
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| 21:19 | OK? So here's your promoter, ? And then here's that, here's |
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| 21:25 | trip L trip L is that leader , OK? First part of the |
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| 21:29 | , OK. So the key point is this junction, OK. |
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| 21:36 | There. So remember a plum That's what this little blob is |
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| 21:41 | OK. A plum race, it then go, right. OK. |
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| 21:48 | this point right here is the critical , OK? Because you get into |
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| 21:58 | , that's the structural genes, E and D and C to B |
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| 22:03 | A, right? So if you're beyond here, you're committing to expressing |
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| 22:10 | genes, OK? If you go that, you're committed to expressing those |
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| 22:15 | . And if you're trying to shut down, you don't wanna do |
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| 22:18 | All right, then that's where it involves A A P getting beyond |
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| 22:27 | point, kick it off. So, um that, that's really |
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| 22:34 | this boils down to is, is , is gonna be knocked off and |
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| 22:38 | allowed to keep going or will not interfered with and it can keep |
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| 22:43 | right? That's in a nutshell. as simple as I can explain |
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| 22:48 | So, how do you do OK. How do you do that |
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| 22:53 | a, a transcript? Right. , the kind of idea of how |
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| 22:56 | works seems kind of crazy because it transcription control, right? Because we're |
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| 23:02 | allowing this. It's about, are gonna allow that to, to um |
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| 23:09 | the structural genes or not? So is transcription control, but we're using |
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| 23:13 | ribosome to do it, right? , all right. So again, |
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| 23:21 | , remember this, right? That is the critical junction, you gonna |
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| 23:25 | it go or you're gonna kick it . Yeah, it being on your |
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| 23:30 | . So how does this happen? , the leader sequence itself when it |
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| 23:35 | . So like all R N A um I think all R N A |
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| 23:39 | they can fold, right? They're double, double strand of the |
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| 23:43 | but they can fold, right? all a U G C base |
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| 23:47 | right? And so they can form secondary structures. So leader sequence itself |
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| 23:52 | form multiples of these, right. if you were just, if you |
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| 23:55 | to take this leader sequence and plop in a, in a buffer |
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| 24:01 | right? And you were able to it, it would assume different |
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| 24:06 | it would fold up in 1234 loops and even as well, a |
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| 24:14 | OK, all those would happen and one's form over the other is all |
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| 24:20 | on, right. So um The , the one that's most favored thermo |
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| 24:29 | is actually the 23. OK. so which one forms it, it |
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| 24:36 | be interfered with if you have something this, on this transcript that sits |
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| 24:43 | a certain spot and just sits there a lump, right? It can |
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| 24:49 | some of these loops from forming, ? Just imagine if something were sitting |
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| 24:53 | here in the 12 area, the loop on the floor, we had |
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| 24:56 | boulder sitting on top of it. . So that's, that's kind of |
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| 25:02 | function of the ribosome here, the position on that transcript determines what loop |
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| 25:09 | because it basically just become a physical for certain loops to form or not |
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| 25:15 | . OK. So that's the role the rhizome in this, right? |
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| 25:20 | if a transcript is formed, rhizome gonna plop on there. OK. |
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| 25:24 | start translating. So, um so kind of the next thing here, |
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| 25:29 | ribosome is controlled before based on where positions itself. So how do you |
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| 25:37 | what positions itself? That's where these come in, right? Because remember |
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| 25:44 | um by the transcript and they form site where TT R N A s |
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| 25:48 | in, right? Because remember we're a polypeptide here, but the ply |
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| 25:53 | here with the le sequence is It's, it doesn't really do anything |
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| 25:59 | the cell. It's just part of mechanism of control. OK. But |
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| 26:04 | , it's doing what Ari does, ? Sites for T R N A |
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| 26:08 | to come in, right? Recognizing codons, right? So you |
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| 26:13 | you can alter the positioning of the by the presence or the proportions of |
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| 26:22 | T R A s and uncharged, ? So to remember C R A |
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| 26:30 | A, it's, it's specific amino , right? That corresponds to the |
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| 26:36 | . And so um you can have charges on charge, right? So |
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| 26:42 | do you think in terms of the , what would influence one or the |
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| 26:49 | moment you have probably have a high of uncharged T R AC. |
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| 27:02 | Have a uncharged to our right. bad if you didn't have a charged |
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| 27:22 | R N A, if you had but uncharged Pr N A to |
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| 27:29 | Right. And I'm sitting there waiting a K A R A so you |
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| 27:33 | start linking those amino acids together. . It's not good at times. |
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| 27:42 | came here all the time. All . If you're rock and roll class |
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| 27:51 | , OK? Um Google it good , bad times. Um All |
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| 27:58 | bad times. If you haven't charged N A, you can't make |
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| 28:01 | right? That's this is where the comes in. OK? So The |
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| 28:09 | thing is it relates to these two here. one and 2 a an |
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| 28:14 | crypto, hold on and the So this is what you, you're |
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| 28:22 | with the normal called the, the . That's where the transcript would normally |
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| 28:28 | . There are the drivers only stopped . So, but now they have |
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| 28:33 | other one Which is not a stop . It's just two of these |
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| 28:39 | So um and similarly, I think other amino acid uh uh opera the |
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| 28:48 | for making the other amino acids have similar thing they'll have if it's |
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| 28:52 | they'll have two of those right in front of me. But regardless |
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| 28:56 | specific for it's, it's these two because it's about controlling the trip |
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| 29:03 | OK. So um so the movement the rhizome can be altered if, |
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| 29:09 | would you have lots of uncharged for fan when there's lots of krypto fan |
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| 29:14 | or when there's no crypto fan Yeah, of course, there's nothing |
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| 29:23 | it goes. If there's no, trip. How are you gonna charge |
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| 29:26 | ? Right. So, that's kind the mechanism here, right. There's |
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| 29:32 | lot of around, then you have of these, all right. If |
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| 29:36 | don't, then you likely have mostly uncharged types. OK? So let's |
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| 29:44 | that in your memory bank. Let's at, yes. So we |
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| 29:48 | right? Uh 12 loop, loop, 34 loop, those can |
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| 29:52 | form. OK? So the two be aware of are this one |
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| 29:58 | which is already labeled for you a . That's one, the other one |
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| 30:02 | the 23, all right. Those the two, the 23 is actually |
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| 30:06 | the anti A 10. It's on next line called the anti. So |
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| 30:11 | are two that in this, those loops. OK. So, so |
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| 30:18 | , those two loops and which one depends on where the ribosome positions |
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| 30:25 | OK? So that's really the crux the whole thing, right? And |
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| 30:31 | it positions itself and which loop forms determines whether it allows the polymerase down |
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| 30:39 | to keep going or to knock it . All right. So that's so |
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| 30:43 | leads to the other leads to the leads to the final locker. |
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| 30:47 | So it's all happen stepwise. So let's look at uh high trip |
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| 30:54 | . So again, high trip defend , you're gonna have lots of charge |
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| 30:59 | R A S. OK? so here comes the R zone, |
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| 31:05 | translating right? That leader sequence. it's got these two adjacent drip |
|
| 31:14 | Not a problem. You have plenty crypto, lots of crypto T R |
|
| 31:19 | S boom, boom goes right in keeps on. OK? And |
|
| 31:24 | and then just stops where it naturally at the translation stop code. |
|
| 31:31 | So that sitting that, that, positioning right here, OK? Is |
|
| 31:40 | the 2 3 form. So the 10 can't form because it's if I'm |
|
| 31:47 | 23 loop, I got this boulder the top can form. I was |
|
| 31:51 | on my head. OK? So 34 and it does. OK? |
|
| 31:58 | so the other thing to notice here here is the Barney plum race riding |
|
| 32:03 | ahead, right? So remember this the, this is the junction point |
|
| 32:07 | you knock it off or keep it . OK. So um the um |
|
| 32:14 | so at high levels, you don't to express, you don't need to |
|
| 32:20 | the trip off. You don't need make it, you've got lots of |
|
| 32:22 | to it, right? So so remember on top of this, |
|
| 32:26 | got the, you got the typical mechanism, right? The trip defense |
|
| 32:32 | active repressor right. But then you , you still can have a little |
|
| 32:35 | of transcription that occur and this one gonna put a clamp on it. |
|
| 32:40 | ? And so, uh so note proximity here between the 34 loop and |
|
| 32:47 | PLYM, right, that's really the here. So which loop forms one |
|
| 32:51 | is farther away from the, from a plume that's up ahead, transcribing |
|
| 32:57 | other one's real close to. So this guy can give it the |
|
| 33:03 | . So you see how it's, can contact that plumbers and knock it |
|
| 33:07 | . OK. So that happens and don't express, you'll express. So |
|
| 33:15 | the proximity of that loop, a loop to the clime contact. But |
|
| 33:23 | then relates back to again, it's step watch, right? This happens |
|
| 33:31 | the ribosome is position here blocking the from forming, allowing the 34 to |
|
| 33:37 | this occurred because there's lots of crypto , to make lots of charged crypto |
|
| 33:45 | N A which allows it to stop its natural stopping point. OK? |
|
| 33:50 | it's one to the other back to because there's lots of crypto don't need |
|
| 33:55 | make it. OK? All So in the other scenario, |
|
| 34:02 | So we've got low to different So that means we have uh |
|
| 34:09 | and so we have the uh let's , let's see the fan, the |
|
| 34:15 | , right? Nothing there blank, ? So the to the around to |
|
| 34:21 | these Ok. So it stalls. brown will stall. So it gets |
|
| 34:28 | those trips. There's no trip to move, can't go any further. |
|
| 34:36 | . So now this area, it not bound, it's not boulders at |
|
| 34:42 | top of it in form. So you have, if you have both |
|
| 34:46 | these, so the two and so you have 23 and four available |
|
| 34:52 | the 23 is more favored. And it's the one that forms, even |
|
| 34:57 | the 34 can do that, the is much more uh energetically favorable. |
|
| 35:02 | it forms. And so note the distance like farther away can't interfere |
|
| 35:08 | the PLYM. All right. So keeps going. OK? And you |
|
| 35:14 | , so you go through, you , so you're out, that's what |
|
| 35:18 | want. You got a low you gotta make it this what needs |
|
| 35:22 | to happen. OK? Um So see this thing in action here. |
|
| 35:31 | Yeah. OK. Um OK. that annoying voice. OK. |
|
| 35:44 | so we're gonna see first the usual . So here is your enzymes, |
|
| 35:49 | ? Multis stepp pathway make trippin, uh the core repressor, repressor, |
|
| 35:57 | an active repressor and we have um to the operator, right? No |
|
| 36:05 | . OK. And then, so , that takes care of most of |
|
| 36:11 | repression here. OK, if you have. And so here is um |
|
| 36:17 | magnus all let it go. So it's a little slow here. We |
|
| 36:24 | there, we gonna do your sequence . Right. Before the structural |
|
| 36:28 | Your four different regions in the loop . 2, 3 and OK, |
|
| 36:37 | loop. And the other ones should loop. And then OK. So |
|
| 37:00 | so proximity can knock the plum This is really slow. Let's try |
|
| 37:06 | . Here. There we go. if we look at the scenario of |
|
| 37:19 | just talk codon trip, codons, ? High trip. right? So |
|
| 37:26 | trippen scenario. Yeah. So here to Riz, it'll go right through |
|
| 37:36 | coons because there's no shortage of crypto at the usual stopping place. 34 |
|
| 37:42 | kicks off the plum race. Um Like so, all right. |
|
| 37:50 | in low crypto condition, OK. we go. And it stalls, |
|
| 37:58 | at the two trip coons. And then the proximity farther away can't |
|
| 38:04 | with the polymerase. Ok. So , that's the attenuation mechanism again, |
|
| 38:13 | takes care of a small portion of control. Most of it again is |
|
| 38:17 | the active repressor. But nonetheless, is important. Ok. So let's |
|
| 38:24 | at this. So read this question hold on and uh let me move |
|
| 38:33 | and open it. OK. So through this one, we pause and |
|
| 38:39 | . OK. Go through. Uh with another slide, it's not the |
|
| 38:45 | but it's gonna have like different And then if we have any questions |
|
| 38:51 | address this. Ok. Move Time is on. I need some |
|
| 40:41 | to read it myself. I look it in a while. I'm sure |
|
| 40:43 | need my answer. Oh, in you pick e it's not e |
|
| 40:55 | All right. How many had to their answers? Goodness, goodness gracious |
|
| 41:02 | . All right. Give me a to switch your answer. Of |
|
| 41:11 | So These mechanisms help block expression of chip opera except one. OK. |
|
| 41:27 | we go at that. If you it, be your correct. Um |
|
| 41:42 | question is why are you correct? actually should be? Why is why |
|
| 41:48 | input because you have an abundance or lack of crypto T R N A |
|
| 42:01 | ? Yes. OK. Yeah. yes, you have a lack |
|
| 42:05 | of if you have a lack of T R N A S that means |
|
| 42:09 | have a lack of trippin in which is the signals for oh let's |
|
| 42:13 | crypto. OK? And so that's B B will lead to that, |
|
| 42:19 | ? We're trying to block expression, ? We wanna do that. |
|
| 42:25 | So yeah, this, this A gonna be a produced, you |
|
| 42:30 | regardless, you know, you're you're gonna have delete sequences transcribed because |
|
| 42:34 | a part of, it's part of operon uh transcript um A R |
|
| 42:41 | OK. So the formation of itinerary . Yeah, of course, |
|
| 42:45 | that's what knocks off dili the block , right? So um the higher |
|
| 42:53 | of Ryan, yes, because that to high levels of R A which |
|
| 42:58 | Amazon doesn't stall at the trip stalls at the stop code on which |
|
| 43:03 | air loop to fall. So, yeah, not this. If |
|
| 43:09 | if it said Ari was installed at Translations Stop Codons, then yes. |
|
| 43:17 | right. That would be great. not as written. OK. So |
|
| 43:20 | uh let's look at one more thing . This one OK. Similar to |
|
| 43:27 | previous table. All right. So so under low or high trip |
|
| 43:33 | So low trip levels synthesize crypto, or no. Yes, I levels |
|
| 43:44 | opposite. All right. What would say your levels transcribe operon adversarial |
|
| 43:52 | No. All right. Those seem basic but I, all right. |
|
| 43:58 | trip levels does trip corepressor repressor complex at low levels? No high |
|
| 44:10 | Yes, because it's, if it's , then it's free to bind to |
|
| 44:14 | . Charge trip T R N A P transfer R A is plenty |
|
| 44:19 | No. Yes. Stalls at stop coons. OK? Which triple |
|
| 44:28 | loop forms, right? An itinerary , anterior loop. OK. So |
|
| 44:33 | are kind of things to know, ? So put this beside a table |
|
| 44:37 | the specific to that, right? uh low lactose, no glucose, |
|
| 44:46 | lactose, no glucose, you know various scenarios see if you can fill |
|
| 44:53 | out. OK. Any questions? . Yeah. So what's stopping? |
|
| 45:04 | transcription is basically the formation of the ? So, right. But |
|
| 45:09 | that goes back to let's go back that picture here. OK. So |
|
| 45:14 | has to do with the proximity of loop to the polymerase that's moving |
|
| 45:21 | So this the, the attenuated loop , it's really close to that |
|
| 45:26 | That's right ahead. So it contacts and knocks it off here. It's |
|
| 45:31 | away. Prox. So it can't , doesn't physically interact with the |
|
| 45:37 | So this is free to then keep . So it's just about, it's |
|
| 45:41 | the loop forming and proximity to the , you know. So it's basically |
|
| 45:46 | physical interaction that knocks it off because so close. Yeah, that's |
|
| 45:52 | that's why it's a transcription mechanism even it's kind of weird, you have |
|
| 45:56 | ribosome moving on the transcript, but essence, your, the end goal |
|
| 46:01 | to either knock that thing off or . And that's what a transcription of |
|
| 46:04 | is. Yeah. OK. Any questions? All right. So, |
|
| 46:10 | the animations look at animations too. , they're posted on Blackboard. So |
|
| 46:14 | think you probably find it helpful and can hear the guy's narration if you |
|
| 46:18 | . Um All right. So we this. OK. So again, |
|
| 46:26 | summary. Um And so yeah, there's any questions about Trip Operon, |
|
| 46:35 | um you'll see some questions on the blackboard quiz about this. Uh um |
|
| 46:43 | what we have left? All So now we're gonna go into some |
|
| 46:49 | these other modes of control. We'll through a couple of we're gonna do |
|
| 46:53 | two before we go. Ok, we'll leave those other two. So |
|
| 46:58 | you got here um, we're gonna unit four Thursday. Ok. We're |
|
| 47:05 | finish up 10, we're gonna finish these two Thursday and then go into |
|
| 47:10 | 23. So the unit four stuff all open, all available. |
|
| 47:16 | you know, do, do look , at at least the first part |
|
| 47:19 | chapter 23 Look at that. Can go before Thursday? So, all |
|
| 47:24 | . So these four mechanisms and, your book goes to a lot |
|
| 47:28 | OK. We don't have the time do all, all of them, |
|
| 47:30 | course, but I picked a few kind of represent some differences from what |
|
| 47:35 | seen with the, with the lack trip opera. Um The first one |
|
| 47:39 | is also a transcription control and it of ties into what we saw with |
|
| 47:46 | the, the adjacent Trip Coones and stalling of the live zone stringent |
|
| 47:52 | Uh First, I just wanted to you, right, these levels of |
|
| 47:56 | control, right? DNA, we'll this as an example. This is |
|
| 48:00 | the second one today. The phase is an example of, of DNA |
|
| 48:05 | of control um transcription, right? transcription, right. Uh So |
|
| 48:13 | your post transcription is the main And are you somehow affecting its |
|
| 48:19 | OK. Translational control is about the , right? Um posttranslational protein. |
|
| 48:27 | . Um All right. So we'll at an example of, we've already |
|
| 48:32 | a number of examples of that. look at one of these. Uh |
|
| 48:37 | see, we're not looking at one those, we're looking at a translational |
|
| 48:41 | . So I think those three, think the, I think one of |
|
| 48:44 | anyway, so let's start with stringent . OK. So as mentioned, |
|
| 48:50 | ? The in the trip attenuation one of them was if the ribosome |
|
| 48:57 | two trip codons, right? And you don't have a, you don't |
|
| 49:01 | , you don't have charged T R phones, it stalls. This is |
|
| 49:05 | of the control mechanism for that. aside from that, right, if |
|
| 49:10 | , if a cell is in a condition, right, um then you |
|
| 49:14 | have multiple vital on multiple amino acid operant rather. And that collectively leads |
|
| 49:24 | a condition that is this stringent So obviously in that condition, |
|
| 49:30 | it's obviously under stress, right? now's the time to go into survival |
|
| 49:36 | , right? And to do to do activities that don't waste energy |
|
| 49:42 | much that can serve. And so gonna shut down a lot of |
|
| 49:46 | OK? And so a ribo zone kind of stalling zones are stalling, |
|
| 49:51 | doing so because they're starved, There's, there's not enough nutrients coming |
|
| 49:55 | the cell. And so you have chromosome associated protein called L A, |
|
| 50:03 | ? It hangs around with um the proteins as part of the rhizome. |
|
| 50:09 | . So when they stall, it of triggers the function of that enzyme |
|
| 50:16 | is to produce this tetro phospho guanine using these two substrates A T P |
|
| 50:24 | G T P. OK. This a signaling molecule much like um such |
|
| 50:30 | P can be that way. So is this OK. And it acts |
|
| 50:36 | primarily on opera and you uh rival R N A S and transfer |
|
| 50:44 | So the goal here is to kind really back down curtail ribosome synthesis because |
|
| 50:53 | having lots around means you, you it for lots of lots of protein |
|
| 50:56 | . So cells are actively growing mid cells right? Growing like crazy, |
|
| 51:02 | gonna be full of ribosome because there's high demand for protein synthesis to sustain |
|
| 51:07 | level of growth, right? But of a sudden now they starve, |
|
| 51:12 | ? You, you don't want to doing that, you wanna shut that |
|
| 51:15 | off, right? And that's what signal molecule helps do. It interacts |
|
| 51:20 | . Um it actually interacts with, even know this, but it interacts |
|
| 51:23 | the uh uh beta subunit N A . And that actually um makes it |
|
| 51:33 | able to interact with these promoters for T R N A s and not |
|
| 51:38 | R N A OPERON. OK? again, it's about conserving energy. |
|
| 51:43 | don't have the same demand for protein . If you're starving as you |
|
| 51:47 | if you have lots of nutrients. it's a way to kind of uh |
|
| 51:51 | a survival, uh hopefully, uh its standpoint, uh there's an influx |
|
| 51:56 | nutrients to overcome this. But, know, until then you're gonna have |
|
| 51:59 | , uh you have to conserve. it's kind of a response like |
|
| 52:03 | But it's all, it's all triggered this is triggered by this stalling at |
|
| 52:09 | , at these total. OK. , because we're affecting transcription and it's |
|
| 52:16 | transcription control mechanism. OK. So um that's what we'll talk about today |
|
| 52:25 | the DNA itself as a way to expression. Manipulate DNA. Fact, |
|
| 52:32 | is something that's a phenomenon, the variation of lots of patterns, |
|
| 52:39 | Um We're gonna look at salmonella, causes foodborne illness. Um uh which |
|
| 52:48 | you, you got vaccinated for um . So, my meningitis is one |
|
| 52:52 | can do this in syria, gonorrhea others. OK. Um Feature me |
|
| 53:00 | it enables a pathogen to become hidden one's immune system. OK. By |
|
| 53:05 | this effect, you can become hidden the immune system, which of course |
|
| 53:08 | a key. If you're a right, you try to do that |
|
| 53:11 | then you grow and inside the body cause disease, of course. |
|
| 53:15 | So this is one way to do . That's why they call it immune |
|
| 53:19 | . OK. So this is gonna to any kind of uh protein, |
|
| 53:26 | say usually protein could be glycoprotein that's be on the periphery somewhere because remember |
|
| 53:31 | talk more about this as we get you before your immune system has the |
|
| 53:37 | to see in air, quote, a pathogen. It can only be |
|
| 53:43 | what's on the outside, right? it something on the virus? It's |
|
| 53:49 | that's on the on the membrane of negative on the on the uh light |
|
| 53:54 | layer of a gram positive, These are the things that your body |
|
| 53:58 | because they're on the periphery, So things like LP S layer of |
|
| 54:03 | gram negative, right pia which can on, we gonna be on the |
|
| 54:07 | , right? Uh flagellum. So these are the things that your |
|
| 54:12 | system cells look for. OK. , and you can produce any response |
|
| 54:17 | them. So the pathogen that has has to hide, hide, you |
|
| 54:22 | the from the OK. So this , we're looking at the so semi |
|
| 54:29 | motile and obviously they have a And so the flagellum remember is produced |
|
| 54:37 | flag units monomers that come together in form of flagellum. And so this |
|
| 54:43 | has different uh two different types of , right? So the H actually |
|
| 54:49 | H here refers to through a call way back H antigen H and is |
|
| 54:56 | flagella, right? That's what they this H one H two. So |
|
| 54:59 | can have an H two flagellum made of this particular flagellum protein or an |
|
| 55:04 | one made up of the C type ? One or the other, |
|
| 55:09 | Not both. It has either one the other. OK. So in |
|
| 55:13 | here, here's the uh flagellum right? That makes H two and |
|
| 55:21 | the promoter, right, typical, setup, right, promoter rut |
|
| 55:26 | And it also has a regulatory gene here, R E G Right here |
|
| 55:34 | interacts with the other type of this the H1 type that makes here. |
|
| 55:41 | it blocks expression by sitting that repressor Right in that promoter. OK. |
|
| 55:50 | H one is not express only H . OK. And so um let |
|
| 55:57 | just get this out the way OK. So the repressor of F |
|
| 56:04 | uh called F L J A, guy, right shuts down expression of |
|
| 56:09 | other type of. So this, , this sound cell is only making |
|
| 56:15 | H two types of gel. So how does this mechanism work? |
|
| 56:23 | About once more than 1000, the is about one in 1000 1 in |
|
| 56:30 | . The it spontaneously recombines. So segment that recombines it's what's here. |
|
| 56:39 | . And so um part of it a promoter for H two, |
|
| 56:46 | So here's the H two promoter. , right there. And so it's |
|
| 56:53 | of the sequence in green that So what happens is it comes |
|
| 56:57 | So these uh this H I N this Recombinate type molecule that facilitates the |
|
| 57:06 | . OK. And so you see it basically inverts the sequence. |
|
| 57:11 | So the promoter, let me erase for a sec. The promoter is |
|
| 57:15 | this way as it should because that's the genes are at. Right |
|
| 57:20 | We're flipping it around. So you how owner has gone there. |
|
| 57:29 | Here is the gene that F L , right? This thing, same |
|
| 57:42 | . But now the promoters away, gone over here, right? Not |
|
| 57:46 | front of the G anymore. It be expressed, right? So you |
|
| 57:50 | express this, you don't make this now the H one but um it's |
|
| 57:59 | . OK. So in the salina , you OK. Um At that |
|
| 58:07 | I mentioned they can the next next can form this H1 type, |
|
| 58:14 | So now the body pips with these , OK. So the thing about |
|
| 58:21 | that, so say you get infected satin primarily with one type of the |
|
| 58:27 | . And some of those spontaneously change sequence, we come on and now |
|
| 58:33 | H1 forms and so subsequent generations of satin at the age one. |
|
| 58:39 | honest. Can't respond that quick, ? So yeah, if, if |
|
| 58:46 | seals with the H two, your can eventually detect it, right |
|
| 58:52 | But by that time, the next has formed the having the H one |
|
| 58:57 | , your body can't, your immune doesn't work that fast. So eventually |
|
| 59:03 | will. But by that time, may have, you know, penetrated |
|
| 59:06 | into your body proliferated right now. have full bone food born illness, |
|
| 59:13 | ? So, uh but that's so about buying time, right? It |
|
| 59:18 | make it completely invisible forever by doing , but it doesn't buy time. |
|
| 59:22 | know how fast bacteria can grow. don't need them for a few |
|
| 59:25 | right? They proliferate and invade and that's what enables them to avoid the |
|
| 59:32 | system, right? So it's uh do the same thing. We have |
|
| 59:36 | strategy of, of buying time as . So to speak, fever, |
|
| 59:41 | get a fever that can slow down pathogen growth, right? That buys |
|
| 59:46 | time, that buys you time for immune system to find it and catch |
|
| 59:50 | and find infection, right? So time thing works both ways. |
|
| 59:55 | So uh so this again just showing same kind of the same thing. |
|
| 60:00 | here's your focus on, on right? Here's the promoter for |
|
| 60:05 | for the H- two flagellum. And we get recombination like that, |
|
| 60:11 | So now is transferred over here and can't express that gene anymore. |
|
| 60:20 | So um OK, let's look at question. A any questions about |
|
| 60:27 | OK. Well, let's look at question first and then see if you |
|
| 60:30 | any questions. OK. So this a, let me pop this thing |
|
| 60:37 | , let me open that. So the yes or no question. |
|
| 60:41 | let me pause for a sec. we've got two salmonella. The uh |
|
| 60:51 | anyway, here's a gentle in blue one in red that H twos are |
|
| 60:57 | , H ones are blue. So a, so say you eat uh |
|
| 61:02 | , some food affected with salmonella. . And that food that you ingest |
|
| 61:09 | . Oh, stop, sorry. , has this, I assume it |
|
| 61:14 | what you see on that slide. has 10, 7 level H one |
|
| 61:18 | 10, 72 P in right? it in your gut. Um So |
|
| 61:27 | the long run, uh is is, is what you ingest from |
|
| 61:32 | salmonella's viewpoint? Is that likely to out for it or is it, |
|
| 61:37 | is that a better, a better for you? Right. So will |
|
| 61:41 | strategy of the praise variation with the of the proteins work here? So |
|
| 61:46 | the, so the question to ask about from the perspective of the |
|
| 61:50 | is this the way to do it not? OK. So if you |
|
| 61:55 | yes, it'll work, then you , yes, that's the right |
|
| 61:59 | Some of them should do if you no, you go no, in |
|
| 62:04 | long run, that's not gonna work it. The, the human will |
|
| 62:08 | it. OK. Mhm A Counting . Yeah. OK. That's what |
|
| 62:43 | thought. So who picked? please take me out. Not gonna |
|
| 62:55 | you. Answer all the time. could no? Oh Mess up. |
|
| 63:04 | on. OK. Come on, be brave. I'll give you a |
|
| 63:15 | , you know, you picked All right. So why don't you |
|
| 63:18 | that? Uh, what you're Is it sex and corrupt? |
|
| 63:34 | So think that is playing poker. never play poker. Poker is all |
|
| 63:43 | . I guess any car going technically you have your, you have your |
|
| 63:46 | in front of you, you have hand cards in front of you, |
|
| 63:49 | ? You, when you're seeing you can have whatever strategy or |
|
| 63:53 | you know, it may work. what if you just show your cards |
|
| 63:55 | everybody? Is that a good No, because essentially if H1 and |
|
| 64:01 | is all it has, it's showing all the parts, right? So |
|
| 64:07 | they're both present in equal numbers, body is on the same time frame |
|
| 64:11 | it'll be able to detect both those attack and goodbye. Right. Better |
|
| 64:17 | come in as mostly just one type switch later on in the body, |
|
| 64:24 | ? That's a more effective strategy because not my time. So that's typically |
|
| 64:29 | it works because they're, they're at early stage of infection, there's a |
|
| 64:33 | stage and that's when salmonella can penetrate in the body and it was |
|
| 64:38 | bad stuff happens. So, so to do, but just, you |
|
| 64:42 | , whenever there can be nice, can have five or six or seven |
|
| 64:47 | options that can switch between them. best strategy is to grow mostly as |
|
| 64:52 | type then switch to another type. questions? So we're gonna end it |
|
| 64:59 | a little early and see you all Thursday. |
|
