| 00:22 | Mhm. Ok, you yeah, welcome. So let's see. Um |
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| 01:00 | the stuff I sent you an email but um the, the what bears |
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| 01:07 | is the cost of schedule. So you're, you're set on a set |
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| 01:12 | a particular time, um So it's open tonight. All right, scheduler |
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| 01:17 | exam three opens tonight, uh which guess is 12 AM on Friday |
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| 01:24 | Um Anyway, uh so we're gonna up chapter nine and get into chapter |
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| 01:32 | . Uh No, weekly quiz opens . The weekly quiz covers um stuff |
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| 01:38 | , it's only like seven questions or questions or something. It's covers 78 |
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| 01:44 | nine material, not 10. That will be next week. Uh |
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| 01:53 | , um, what else? So week, uh we'll wrap up the |
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| 01:58 | three, then we'll start the last . Ok, the week after. |
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| 02:04 | , uh the, the game is for a couple of weeks. |
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| 02:06 | um lot of time because uh let's . So any uh particular questions about |
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| 02:16 | , anybody here. So we're gonna into deregulation midway through today. Uh |
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| 02:24 | Operon, we'll start with that. it it, I assume some of |
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| 02:27 | have gone through Lack Operon already. . Black Operon. Black Operon? |
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| 02:33 | . Ok. All right. Um , so if you have, |
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| 02:39 | then you'll get it again. So , maybe you'll learn something different. |
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| 02:44 | , anyway, so a little bit a recap from last time. |
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| 02:51 | So I remember this. Um, talking about in Chapter nine is really |
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| 02:58 | poos, I guess you'd say can genetic variation. OK. So what |
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| 03:06 | look at a back? OK. divided by para those are just direct |
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| 03:11 | of each other. And of we know that's not the case, |
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| 03:16 | ? So, uh even with that of asexuals reproduction, there are of |
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| 03:23 | , thousands of variants of E for example, and other bacterial species |
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| 03:28 | uh those differences occur through mutation. ? Um A what's called a spontaneous |
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| 03:37 | rate, mistakes actually occur during DNA . OK? It happens to you |
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| 03:44 | well. But there are mechanisms to these mistakes. OK. Uh Ours |
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| 03:51 | pretty good. So we have a good repair rate, I guess you'd |
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| 03:55 | it um bacteria. A kea uh an order of magnitude less. |
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| 04:02 | It's about one in a million spontaneous occurs one in a million times. |
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| 04:07 | stick it, it'll, it'll stay is not fixed rather. And so |
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| 04:13 | so that little bit higher sputation, mutation rate coupled with a high reproductive |
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| 04:20 | to multiply quickly, right? Means a colony probably on a plate that |
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| 04:26 | I don't know, 10 million cells something, there will be a small |
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| 04:30 | there that will have mutations. Um So that right. Um plus |
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| 04:39 | the horizontal gene transfer, this mechanism began talking about. So, of |
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| 04:46 | , remember transmission, right? That's you acquired your genus. That's how |
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| 04:51 | daughter cells from the products of battery . That's those cells, you |
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| 04:55 | require the uh acquired genes that of course. Um but horizontal gene |
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| 05:01 | , right? So it's four right? We've talked about two of |
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| 05:05 | uh transformation. So basically just an of DNA from the environment. The |
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| 05:10 | we look at kind of a couple differences uh gram positive gram negative, |
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| 05:15 | of the gram negative had this by , more complex uh process involving cells |
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| 05:23 | competent, right? That then led a then that leading to the formation |
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| 05:29 | the mechanism, the transformer om that physically takes in the DNA. |
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| 05:35 | So, and this was one of cell density dependent processes, right? |
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| 05:42 | cells had to be present to accumulate of these competence factors. If that |
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| 05:47 | , then the process kicked in There are negatives relatively simple that can |
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| 05:52 | this. OK. Basically a pylos plots can grab on to DNA and |
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| 05:57 | it into the cell, you little bit more to it. But |
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| 06:01 | know, basically that's what it those that can do it, not |
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| 06:04 | bacteria can uh or, or, what we call naturally transformable. Uh |
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| 06:11 | are but many aren't as well. . So it's all, it's all |
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| 06:14 | of a species dependent thing. So uh conjugation was the other mechanism |
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| 06:21 | look then, right? So that's little more complicated cell, cell, |
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| 06:25 | cell, two cells coming together, them ma in quotations, mating |
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| 06:30 | OK. F F N F plus F minus. OK. And uh |
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| 06:35 | specific genes involved. So having these and of course, the these are |
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| 06:41 | a plasmin. OK. And so a plasmin is termed F plus containing |
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| 06:48 | genes here that enable it to, call it, we call it, |
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| 06:52 | mobilize the plasmid, move it copy and move it to the |
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| 06:57 | So we look at three variations of , right. So we have the |
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| 07:02 | , the basic F plus uh F uh mating. OK. Um Where |
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| 07:10 | F plus A requires the plasmid becomes plus itself. Um the H F |
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| 07:17 | . So, so the integration of plasma into the genome into the |
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| 07:23 | OK. Um But remember that, that then he the chromosome possessing that |
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| 07:29 | factor. Now basically think of it a gigantic plasma that can be copied |
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| 07:35 | transferred. But we know that um how much information gets passed between the |
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| 07:43 | . It taught me the pinner of When the connection between them occurs, |
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| 07:48 | ? Because that's the, that's how it's passing between the two cells so |
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| 07:52 | longer they're together, the more information be required. And so they have |
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| 07:57 | stay together for a long time, minutes, two hours. And that's |
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| 08:01 | long time when you consider the environment in and likely molecules and other cells |
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| 08:07 | off of them. So those connections be broken. So it's, that's |
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| 08:12 | it's very unlikely if ever will an chromosome be passed through. Right. |
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| 08:17 | , remember because of that, the factor itself is at their very |
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| 08:22 | So if it were to be pretty much, the whole chromosome had |
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| 08:25 | be copied into because that's where it on the last part. So that |
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| 08:29 | happens, which is why the F stays has an F minus. |
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| 08:36 | But it's still acquired, right? some new genes here. OK? |
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| 08:44 | you can pass those on right through need transfer. OK. Now, |
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| 08:51 | uh just for a second, just . So the, the recoin recomb |
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| 08:56 | all these mechanisms, recombination is always a part of it, right? |
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| 09:00 | , to make that uh DNA, it's a fragment, a part of |
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| 09:04 | chromosome, uh plasmin can integrate, , the H F R formation, |
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| 09:09 | is all recombination. Um And then have prime uh feature here, |
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| 09:15 | So this is all relates to that's the nature of our cell, |
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| 09:21 | ? And then this F factor excising it doesn't happen cleanly, right? |
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| 09:28 | kind of skewed if you will. instead of just the red part coming |
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| 09:33 | , it's something like that. So it shifts one way or the |
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| 09:37 | as it comes out, not a rare occurrence, but when it |
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| 09:41 | happen, it then can lead to uh a gene from the chromosome coming |
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| 09:48 | that plasma. OK. And then mate with another cell. And then |
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| 09:52 | when you make, make it a deploy for me, right? |
|
| 09:54 | this goes into a conjugates with a containing an A gene already. And |
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| 10:00 | it has two copies of it. . So um so the F prime |
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| 10:04 | F R um F plus F F meetings. OK. So um you |
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| 10:12 | , as we go, so, we have the two we have left |
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| 10:14 | do are these two transduction transposition. don't think of any four of these |
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| 10:19 | as yeah, oddball obscure kind of once in a blue moon things, |
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| 10:27 | know, if the opportunity is it will do these things and it's |
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| 10:31 | can be very significant, right? we saw an E coli a |
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| 10:34 | almost a quarter of its chromosome is to be due to acquisition of genes |
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| 10:39 | these mechanisms, right? So it's a, a rare or trivial |
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| 10:43 | It's, it's a, it's a definite significant way in which material cells |
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| 10:49 | , can variation. OK. So all right, is there any questions |
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| 10:57 | these two things? OK. So look at um transduction So you think |
|
| 11:04 | , first thing in your head is , right? Virus is the go |
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| 11:10 | . OK. It's the vehicle to the DNA from one cell to |
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| 11:15 | So remember uh lighting viruses and lysogenic . That's really the the that's what |
|
| 11:25 | the two types of transduction. So generalized transduction is due to a |
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| 11:34 | felt the Ticha like cycle basically is you get generalized transduction. The lysogenic |
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| 11:43 | . Remember that lambda age, that's one you can bring that brings about |
|
| 11:47 | specialized transduction. OK. So that's of the way to differentiate these two |
|
| 11:52 | . Um So we already aware of both these cycles work. So here |
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| 11:59 | our cycle. Uh B inserts its and then viral replication begins. And |
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| 12:08 | the host DNA is um it becomes as well fragmented. And so of |
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| 12:15 | , it's when it's just all of of this is is an error in |
|
| 12:20 | , right? So as the viral are assembling, right? It packages |
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| 12:27 | host DNA into the cell. And so what happens then as this |
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| 12:34 | uh assemble and form and then lice cell, those types like this. |
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| 12:41 | guys here will infect a new OK. And so now and so |
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| 12:48 | it it is still infectious, Because it has the part, the |
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| 12:52 | are to recognize the host on the , right? Bin it and then |
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| 12:57 | the DNA. But but this is going to turn into the viral |
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| 13:03 | right? It's not gonna be copied then viral protein because it doesn't contain |
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| 13:07 | it contains DNA from that host, . So it's one of these fragments |
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| 13:16 | that ended up that, that will up into the cell. So they |
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| 13:20 | it generalized because theoretically any gene genes any of these fragments can be |
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| 13:31 | right? So generally, basically any in that previous host can be packaged |
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| 13:36 | sent to another cell. OK. , uh and of course, |
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| 13:40 | again, recombination, right, And so this new host is acquiring |
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| 13:47 | genes or genes from a previous previously host. OK. That's generalized |
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| 13:53 | OK. Specialized transduction again is with isogenic phau, right? Lambda, |
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| 14:00 | saw that one before. So we that it forms a prophage, |
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| 14:04 | integrates its uh chromosome into the host . So, but that insertion is |
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| 14:12 | just randomly anywhere in the E coli , it's a specific site and that |
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| 14:20 | is called att right here, there's att P and B and that's where |
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| 14:27 | inserts itself. OK. And um and so that relates to why |
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| 14:36 | what can be passed on through Very specialized, it's very restricted. |
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| 14:43 | ? Only the genes that are in vicinity. This one, this |
|
| 14:49 | maybe there's something right here or right . OK. That's it. All |
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| 14:55 | . It's not that it's not theoretically to have any gene in that E |
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| 15:00 | trans transferred it this way only what's the vic city of the ends of |
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| 15:06 | pro right? The two red right? And because what happens is |
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| 15:14 | thing will excise, right? It's it comes out, right? So |
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| 15:18 | Lygen phase can come out and then the lighting phase cycle. OK. |
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| 15:24 | when it does that, it's taking this case, the galactose gene, |
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| 15:30 | right. So G A L is galactus glucose is a sugar, |
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| 15:34 | So it's a, it's a, a pathway to break down uh this |
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| 15:38 | sugar. The other one is one biotin synthesis. This is an enzyme |
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| 15:42 | in or co factor involved in Uh in any case that's irrelevant. |
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| 15:47 | the point is um as this prophage itself, it's doing it kind |
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| 15:57 | it's kind of miss shifting as it out, right? So in this |
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| 16:01 | , we're kind of shifted this So instead of the purple sequence coming |
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| 16:06 | is purple minus that. But plus OK? It's kind of like that's |
|
| 16:13 | coming out. OK. So we're behind part of the lambda age |
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| 16:20 | right? But gaining a part of E coli DNA, OK. In |
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| 16:25 | process, it could just as easily have shifted this way and it could |
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| 16:29 | biote galactose but not this example, glutose. OK. And so now |
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| 16:35 | see the galactose gene ends up in lambda phase DNA. And so this |
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| 16:41 | then uh infect the next host. . And then that new E coli |
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| 16:48 | has an extra copy. So that is the that partial bit. |
|
| 16:55 | So, so of course, I you recall, this looks very similar |
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| 17:03 | the um F prime, right F formation. So um that, that's |
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| 17:10 | based on the a weird excision. , where it takes a part of |
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| 17:17 | chromosome with it. OK. So , the only, the only genes |
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| 17:22 | can be transferred here are either biotin or something very close to it. |
|
| 17:29 | . Um Many questions about that, ? So the kind of thing is |
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| 17:36 | do see ending up in bacterial cells are, that are due to transduction |
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| 17:42 | often times. Um We'll see examples this in the end like cholera to |
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| 17:48 | one that's acquired through transduction and some uh toxins um are acquired this |
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| 17:55 | Uh Now, um the last 4th or transposes elements. OK. So |
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| 18:06 | if I had to um estimate which four is probably the more prevalent, |
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| 18:13 | would say it's likely gonna be the transformation conjugation, trans transduction mechanisms, |
|
| 18:20 | transposition. Uh there are a few resistances passed this way. But uh |
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| 18:28 | I think the more three other mechanisms more prevalent in terms of frequency of |
|
| 18:35 | , but nonetheless, um transposes elements present in, I think almost all |
|
| 18:40 | the things we have them as well they are basically small segments of DNA |
|
| 18:48 | uh jump around. They were called genes. It was discovery of |
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| 18:53 | Um And they can affect, uh can insert themselves and affect uh expression |
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| 19:00 | certain genes. They can think they're in regulation of certain genes. Um |
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| 19:06 | can be bad as well causing inserting and mutating genes as well. |
|
| 19:11 | um but, you know, don't of these as like jumping beings that |
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| 19:16 | just continually popping in different places in chromosome. It, it doesn't occur |
|
| 19:21 | frequently. OK? Um It's, a process that solves. So is |
|
| 19:26 | is controlled to a degree because you want that happening. You don't want |
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| 19:31 | sequences jumping here and there and everywhere all kinds of problems. But they |
|
| 19:35 | have do have a role. Um in with bacteria, it's a way |
|
| 19:42 | formula to transfer genes to another OK. So the the um trans |
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| 19:52 | elements. So there's actually two OK? One type is the |
|
| 19:59 | OK. Another type is actually what's an insertion sequence. So these are |
|
| 20:05 | one and this one. OK. one, that's two, those are |
|
| 20:11 | two types of transpose bos what you in the diagram is an assertion |
|
| 20:17 | OK? Because all it contains is we call an inverted repeat in the |
|
| 20:26 | gene. So all transposes elements have in common. OK? Because that's |
|
| 20:34 | enzyme that allows it to cut out then recombine elsewhere. So they all |
|
| 20:39 | that So, and, and I'm repeat is simply just a sequence. |
|
| 20:44 | you look at a A T C A T 53. It's the same |
|
| 20:49 | here, right? Just going in opposite direction. So just inadvertent. |
|
| 20:54 | a repeated sequence that's just inverted. . And so uh of course, |
|
| 20:59 | the middle here is the transpose H , right? So that is |
|
| 21:04 | that's an insertion sequence. The most type of transposes I want. |
|
| 21:09 | The transposon is this but has one more genes in there besides the one |
|
| 21:17 | transposes. OK. So something that be antibiotic resistance gene, what have |
|
| 21:24 | ? But that's the transpo is a bit more complex containing more and more |
|
| 21:28 | besides the transpo. OK? And there's kind of two ways it can |
|
| 21:36 | , it can uh it can be cut and paste or copy and |
|
| 21:40 | OK. So in other words, , the transposon transposes element uh is |
|
| 21:48 | one location, makes a copy and goes to another location. So I |
|
| 21:52 | two, right? That's what we replicate um replicator uh transposition. |
|
| 22:01 | If it's in one spot and then itself out and goes to another spot |
|
| 22:04 | it's no longer there, that's cut paste. So that's non rep. |
|
| 22:09 | ? So both types, the transpo element can be one of those two |
|
| 22:14 | . OK? And so the um so in terms of, of transferring |
|
| 22:22 | like this to a cell. You can have what are called um |
|
| 22:29 | transposon. OK. So they have of course, the transpose a but |
|
| 22:34 | also have the, the elements that it to conjugate, right? Sex |
|
| 22:39 | transfer genes, et cetera. And so how this happens is the |
|
| 22:47 | transposon will um excise and circularize. . And then it will carry out |
|
| 23:01 | process we've seen before. Rolling circle . The the um of course, |
|
| 23:06 | cells coming together rolling circle replication, the plasmid or, or the the |
|
| 23:12 | into the other cell. And then now have two cells, you a |
|
| 23:19 | of that transposon. OK. The is the cells will not remain in |
|
| 23:27 | state. It's only a transient The transposon is meant to integrate. |
|
| 23:32 | it'll go into this form here where integrate into the chromosome. OK. |
|
| 23:39 | again, these are certain types of have disability. OK. Uh Another |
|
| 23:45 | it could happen as well is if have cam a cell that has, |
|
| 23:53 | its chromosome. OK? Has a for that, right? That's an |
|
| 24:00 | plus platinum. OK? Like we've before. All right. And so |
|
| 24:07 | transposon could be sitting in a So T N is short for |
|
| 24:16 | Um And so it could um as copying and pasting or cutting and |
|
| 24:24 | it could just go into the class that. OK? And uh end |
|
| 24:29 | in a F plus plants. So they can just undergo normal conjugation and |
|
| 24:36 | are not gonna be passed that So in the recipient cell, it |
|
| 24:43 | , it could then in this state this cell receives it, OK. |
|
| 24:53 | a chromosome. Now, it's gotten plasmid. It's become F plus. |
|
| 24:59 | the transpo on Nico do that theoretically back in to the crumble. |
|
| 25:05 | So that's possible as well. And been seen too. OK? How |
|
| 25:11 | this mechanism is, I'm not but definitely this has been document and |
|
| 25:16 | worked out. OK? But both these are possible. OK? Just |
|
| 25:22 | on hit or right on something, think of it that way. Um |
|
| 25:30 | any questions? All right. So here should be kind of if you |
|
| 25:35 | , you know the different, the of the different um mechanism that you |
|
| 25:40 | , OK? This is what you with that. This is how it |
|
| 25:42 | with this one and this doesn't happen this cell, those kind of those |
|
| 25:46 | of things. OK? Um All . So let's switch to um chapter |
|
| 25:56 | in regulation. OK. So we of go back to some of the |
|
| 26:00 | seven uh stuff in, in the of OPERON and, and how they |
|
| 26:06 | and that kind of thing. So um all right, let's start |
|
| 26:11 | the questions. So we're gonna have few questions in this section here. |
|
| 26:15 | with an easy one. OK. , so just kind of your answer |
|
| 26:21 | this. So, regulation of right? So remember that super important |
|
| 26:28 | gene expression obviously is important because it , you know, the response occurred |
|
| 26:34 | a situation, but you, you express stuff, express genes all the |
|
| 26:41 | , right? A you hardly ever all those uh large fractions of genes |
|
| 26:46 | ever. OK? Um two, always remember that gene expression, the |
|
| 26:55 | application, these are processes that build , right? These are all gonna |
|
| 26:58 | energy requiring. So you're gonna be , efficient from what one does. |
|
| 27:03 | . And not just um waste So um from that aspect, regulations |
|
| 27:11 | important as expression. OK. It's counted down from 10. |
|
| 27:33 | All right. Delay. Oh There is. It is a delay. |
|
| 27:42 | , I'd be, I'd be shocked it weren't 99%. So yeah, |
|
| 27:46 | course, it's, it's right that does the work for the most |
|
| 27:51 | Um So the um so what are types of stimuli cells gonna respond |
|
| 28:00 | Right. Well, you can probably your own list here. Everything from |
|
| 28:05 | molecules that are out there are the molecules out there? Are there micros |
|
| 28:08 | are toxic out there? Is What's the, what are the oxygen |
|
| 28:12 | ? What's the um what is the P H uh is there something I |
|
| 28:19 | eat out there that's suitable? What's sodium concentration? And am I in |
|
| 28:24 | stress? Uh temperature? Um a of different things, right. So |
|
| 28:31 | got to be some kind of counteraction that either good or bad uh in |
|
| 28:35 | to survive. And so, um have to convert that signal into something |
|
| 28:41 | the cell that will create an right, make proteins. And so |
|
| 28:46 | , there's not always have to be proteins, but that's not, that's |
|
| 28:50 | a a uh that's the most common . So some kind of sensor protein |
|
| 28:55 | interact with the signal to then uh about this is often where you get |
|
| 29:02 | the induction of uh different molecules that turn on things involved in regulation, |
|
| 29:10 | ? We'll talk about things like activators repressors and things. So oftentimes it's |
|
| 29:16 | that are produced that work on those either shut off expression or promote |
|
| 29:22 | OK? Uh Transcription factors, they often a part of this as |
|
| 29:26 | OK. So whatever the whatever, , the signal gets turned into |
|
| 29:31 | you're gonna get gene expression interaction with , right? Promoters and uh producing |
|
| 29:40 | protein typically sometimes the product may be R N A. OK? It |
|
| 29:45 | depends, but very often it is protein. OK. So then uh |
|
| 29:53 | levels of control. So let's look this. So identifying the right term |
|
| 30:01 | the type of control, because remember translation, right? At all those |
|
| 30:06 | , you can control expression and there's , categories of each type. |
|
| 30:12 | So here we have a trip to opera on trying to oper on expression |
|
| 30:17 | be controlled by crypto itself. Inhibiting of the enzymes responsible for its |
|
| 30:24 | That's what the OPERON does. We'll about this at the very end of |
|
| 30:28 | . But the, the structural genes the OPERON code for enzymes that are |
|
| 30:34 | for making crypto. OK. So of the controls there is crypto |
|
| 30:41 | can actually control its own expression. ? And this is, let me |
|
| 30:47 | this again. OK? Well, it. I meant to stop |
|
| 30:50 | but uh go ahead and answer. it's meant to um so you have |
|
| 30:57 | categories uh putting different names and these of control. OK. Yes. |
|
| 31:06 | . So we're counting down from OK? Looks like we had a |
|
| 31:23 | . Mm I think he probably shouldn't changed. Does not see. So |
|
| 31:30 | all right. So looking at different , so translational control, think of |
|
| 31:36 | involved in translation, right? right? That's one way to control |
|
| 31:45 | , affect ribosome function. OK? Control the level of DNA definitely can |
|
| 31:52 | that. Altering nucleotides can even take of a, of a DNA out |
|
| 31:58 | rearrange it and that can affect OK. But the key here is |
|
| 32:03 | crypto itself inhibiting one of the enzymes enzymes are what into the P |
|
| 32:16 | OK? And so proteins are a of posttranslational control. OK? |
|
| 32:26 | you transcribe, you translate, you make a protein, right? So |
|
| 32:31 | comes after translation, posttranslational. So here we see the different |
|
| 32:37 | OK. Um So the answer here post translational. Um So looking at |
|
| 32:47 | different levels here. OK. So mentioned, beating, we start, |
|
| 32:53 | there. OK? Uh We'll look this process uh next week. |
|
| 32:59 | Phase variation that's actually taking a segment DNA or rearranging it and you affect |
|
| 33:07 | expression. OK. Uh nucleotide right? Uh epigenetics, right? |
|
| 33:14 | can alter the uh the DNA nucleotides effect expression that way. Um going |
|
| 33:22 | next step transcription. OK. So can have um I didn't break it |
|
| 33:28 | to all the different levels here. can have transcription of control, which |
|
| 33:33 | not, is not the M R A transcript. It's before then. |
|
| 33:42 | . It's, are you gonna allow to do its job and make the |
|
| 33:47 | ? All right. That's a lot the, and that's a very common |
|
| 33:50 | . Procaryotes control their genes as OK? That's what we see in |
|
| 33:56 | lactose operon, a trip operon. . That's where the interaction with the |
|
| 34:01 | of ex expression, right? So you do have the transcript, what |
|
| 34:08 | you still do? Well, that falls under post transcription. So here |
|
| 34:15 | made the transcript, OK. And um that is, you can affect |
|
| 34:26 | N A stability, right? So R A stability. So in |
|
| 34:31 | M R N A s only gonna on the order of minutes once they're |
|
| 34:35 | . OK? Because you always make if you need to um it's not |
|
| 34:40 | wise to keep M R N A around forever because if they're there, |
|
| 34:44 | be translated and the cell may not those proteins. So that's why M |
|
| 34:48 | N A s kind of have a lifetime if you will. OK, |
|
| 34:52 | get rid of them. Uh if they're there, they're gonna make |
|
| 34:55 | and we believe we may be wasting for something we don't need. So |
|
| 34:59 | so they kind of just degrade uh new cars. They can, |
|
| 35:03 | they're more stable, they can last , not minutes, more like |
|
| 35:08 | sometimes even days or longer, just on the type. But nonetheless, |
|
| 35:13 | can affect, if you affect M A stability, you can affect |
|
| 35:16 | OK? Um Translational control, um ribosome function. So anything to derive |
|
| 35:26 | , whether it's putting a protein in to block its ability to translate um |
|
| 35:34 | a, is a, is a . OK? Then post translation. |
|
| 35:40 | . So um basically, you can a protein, put phosphate on it |
|
| 35:45 | activate or inactivate it. You can just degrade it and get rid of |
|
| 35:51 | all together. OK. So, or you can bind something to the |
|
| 35:58 | to make it inactive, right? kind of how the trip the fan |
|
| 36:02 | its thing. OK. So uh different levels, right? All the |
|
| 36:06 | to transcription translation. OK? And can all occur, all of these |
|
| 36:12 | occur. So, if you're, actually expressing them in particular gene or |
|
| 36:16 | and genes and opera, all of can be combination, these can be |
|
| 36:22 | together, of course. OK. um let's oops gotta mention this. |
|
| 36:30 | ? Because the genes, so where I'm gonna say most genes are under |
|
| 36:38 | kind of control? There is a set. Remember those core genes we |
|
| 36:42 | about, right? Those typically things in DNA DNA replication and protein |
|
| 36:49 | um certain metabolic pathways that like cause cycle, et cetera. These are |
|
| 36:55 | that are always running more or right? So you always need gonna |
|
| 36:59 | the, the proteins for these. so these are what we call constituted |
|
| 37:03 | pretty much always. Um And so look at this one. So here |
|
| 37:10 | gonna get into some of the terminology when talking about um gene regulation. |
|
| 37:21 | ? It's like repressors, activators, depression induction, um like a terms |
|
| 37:31 | are used at um we'll go over . OK. So what, what |
|
| 37:39 | be confusing is the conditions which allow expression. These can be widely |
|
| 37:45 | OK. If you look at the opera Tripen Operon, they basically have |
|
| 37:50 | ways in which they, they get same results. OK. Um In |
|
| 37:57 | part, it relates to the type opera, it is what's what it's |
|
| 38:03 | in metabolism wise. OK. So turn the timer on. OK. |
|
| 38:39 | . By the operator sequence. So that's a major controlled elements in |
|
| 38:47 | So the operator sequence interacting with a . So uh the, the definition |
|
| 38:55 | active repressor um is the same no what kind of opera or system you're |
|
| 39:03 | about, what varies is how it active. That can be very |
|
| 39:09 | OK. But anything involving an active means you're not promoting transcription, you're |
|
| 39:15 | it. OK. Uh Induction relates expression. So if you induce genes |
|
| 39:21 | allowing to express. So it doesn't anything to do with that. Uh |
|
| 39:26 | of course relates to a, Um D repress. So if you're |
|
| 39:33 | something, you're stopping it. If de repressing, you're allowing it to |
|
| 39:38 | . So like the repressor promotes not de repression. OK? But |
|
| 39:46 | it does bind to an operator. . So uh so let's look |
|
| 39:52 | I will use these terms. So here is just a generic example |
|
| 39:58 | a gene. OK? Got your , got your regulatory sequence. All |
|
| 40:04 | . And what we're gonna look at how many bacterial operon work? The |
|
| 40:09 | sequence is an operator. OK. , um so then there's a regulatory |
|
| 40:17 | which are many times called repressors. . So here's a couple of scenarios |
|
| 40:24 | how we're gonna control this thing. . So when we look at |
|
| 40:29 | de repression versus um repression, de repression is genes are turned |
|
| 40:37 | OK? And so here would be scenario where we have a repressor |
|
| 40:42 | OK. So here's induction and you the just approaching itself as, as |
|
| 40:48 | operator or regulatory sequence, OK. that blocks. So right here it |
|
| 40:54 | be a promoter. OK? Sequence be like right here and so |
|
| 41:01 | your plumbers will be sitting there and can't, can't get around there has |
|
| 41:04 | accidents. Can't, can't go any . OK. So to remove the |
|
| 41:09 | , you have what's called an inducer binds, changes the shape proteins, |
|
| 41:15 | molecules, changes shape, right? now we can no longer find the |
|
| 41:20 | , OK? Or operator sequence or the regulatory sequence is. OK. |
|
| 41:25 | it comes off. So we've gone an active repressor on top to an |
|
| 41:31 | one at the bottom. OK? um repression often involves a corepressor. |
|
| 41:41 | ? And this leads to turning gene off. OK. So in d |
|
| 41:49 | , um so we have a repressor plus a corepressor. OK? Comes |
|
| 41:57 | to form the active complex and that the operator or whatever the regulatory sequence |
|
| 42:04 | . When it goes away, then becomes de repressed unbinds, you can |
|
| 42:11 | transcription. OK? So you can there an active repressor here and an |
|
| 42:19 | one down here are very different One has a molecule bound to it |
|
| 42:24 | make it active. The other if it hasn't, might go back |
|
| 42:28 | it, it's inactive, right? inducer thing. This, so 22 |
|
| 42:34 | conditions producing an active or inactive OK? And in a nutshell, |
|
| 42:40 | is basically the LA OPERON. This the trip opera T R P is |
|
| 42:48 | trip. That's how they both We'll look at a little bit more |
|
| 42:52 | the intricacies, but that's in basic how both of those differ. |
|
| 42:58 | So, yeah, and it turns that the, that the corepressor, |
|
| 43:08 | . And here the inducer you might it's lactose, but actually, it's |
|
| 43:13 | , a slightly different version called allo . OK? Is the inducer |
|
| 43:20 | Again, we'll get, we'll we're gonna go through this, all |
|
| 43:24 | , in a little bit. but while we're here, I just |
|
| 43:27 | that. Um so the thing about active active repressor, right? So |
|
| 43:34 | we just saw, so number the definition of an active repressor is |
|
| 43:38 | same no matter what, you know context we're talking about, an active |
|
| 43:45 | binds the regulatory sequence slash operator and transcription, right? A inaccurate repressor |
|
| 43:55 | do that. It, it allows expression transcription to, to occur. |
|
| 43:59 | that, that's always the case. just how it comes about may be |
|
| 44:04 | different. OK. So um all . So another thing, so it's |
|
| 44:11 | thing if you have, if you get expression, it's one thing to |
|
| 44:18 | the inactive form produced, right? that will allow for expression, but |
|
| 44:23 | may not always be enough, You may need to have some other |
|
| 44:27 | out. OK? And that other is often involvement of activators, |
|
| 44:35 | Scriptural activators. And so without uh , the inclusion of the activators, |
|
| 44:45 | only get a real low level from we talked about basal level of |
|
| 44:51 | OK? Um Not really enough to anything for the cell. OK. |
|
| 44:57 | to ramp it up, you involve . And so it's all about and |
|
| 45:01 | all collect, con, congregate typically the promoter. OK? And in |
|
| 45:09 | so greatly increase the attraction of that by the PLI race. OK? |
|
| 45:16 | in doing so increase expression. And it can go from like One |
|
| 45:23 | , one to level 1000. And how, that's how much difference we're |
|
| 45:27 | about here. OK. Um So um any questions so far? So |
|
| 45:38 | gonna look at this, the same in the context of an actual |
|
| 45:42 | right? So these, these things gonna come up again. OK? |
|
| 45:47 | So we're gonna start with La Let's just start with this question |
|
| 45:50 | OK. That OK. All I'm gonna turn the timer on. |
|
| 47:02 | is one correct thing here just in you pick e change it. |
|
| 47:15 | OK. OK. Uh The consensus correct. So it is b |
|
| 47:38 | So first and foremost, OK, you, you can get all bogged |
|
| 47:45 | in all the different aspects of control la Opera and how it works. |
|
| 47:51 | had a question from a student. was in a lecture earlier. She |
|
| 47:56 | waiting outside the lab. So we by and she asked, what does |
|
| 48:02 | LA OPERON actually do? OK. question. After having gone through all |
|
| 48:07 | mechanisms of control, it's you kind get lost in the weeds a little |
|
| 48:12 | . So for E Cola, for , it's, it's a lactose, |
|
| 48:15 | can use lactose. OK. But , the ability to have this pathway |
|
| 48:22 | to have this OPERON, it means can take lactose in A and |
|
| 48:27 | it can begin to metabolize it and it into glycolysis. OK? It |
|
| 48:33 | ferment lactose. OK. So, this operon enables it to use lactose |
|
| 48:40 | a energy source. If it's available the cell, that's bottom line, |
|
| 48:47 | ? All the things you're gonna see here, that's, that's what it |
|
| 48:51 | do, enables the cell to use as an energy source. OK. |
|
| 48:56 | um so, so having said that not about synthesis, right? It's |
|
| 49:02 | metabolism. It's a catalog pathway. ? Um It's an example of a |
|
| 49:11 | control, not post transcription. The an inactive lack repressor um doesn't |
|
| 49:20 | it allows expression. OK. So written B is the uh is |
|
| 49:27 | So lack Y is how it's going be able to find and bringing |
|
| 49:34 | OK. Uh I must have So um so the good news here |
|
| 49:42 | that we don't have to worry about gene. The lack A OK? |
|
| 49:47 | still don't know to this day what actually does. OK? We know |
|
| 49:51 | you can have E coli mutants lacking completely and it can still utilize |
|
| 49:56 | no problems, nothing. OK? you don't need to concern ourselves with |
|
| 50:02 | . Now, the one thing that tend to, you know, make |
|
| 50:06 | scratch their heads is this statement a low level of lack operatic |
|
| 50:14 | That's true. There's a reason for . Now, when I say |
|
| 50:18 | I mean, like super low, one or two molecules worth of stuff |
|
| 50:24 | made. OK? But it's essential that happen. OK. So |
|
| 50:28 | it's, it's, it's a minimal expenditure, but a necessary one. |
|
| 50:35 | . Um Now, the way this is so the lack Y and lax |
|
| 50:43 | are the, of course, the that we need to concern ourselves |
|
| 50:47 | So lack why is the way is transport protein it can bind and import |
|
| 50:54 | if it's present. OK. Uh this in the membrane, it would |
|
| 51:01 | know it could have a million molecules lactose around it. It would never |
|
| 51:05 | if it didn't have the lack why in the membrane somewhere. OK. |
|
| 51:11 | uh that kind of goes to why always has to occur. OK. |
|
| 51:20 | When lactose is present, it comes the cell, it's a disaccharide. |
|
| 51:24 | we're gonna cleave it into the two . First, we're gonna take a |
|
| 51:29 | bit of it and go this way make a, this is actually the |
|
| 51:35 | allo lactose, a kind of chemical of lactose. Um And that occurs |
|
| 51:40 | low levels of lac Z. So the at high levels, we |
|
| 51:49 | get the processing of lactose. So goes right into the glycolysis, galactose |
|
| 51:57 | a couple more steps to do before can go into glyco. But the |
|
| 52:00 | line is these are gonna be going these antibotic pathways. So OK, |
|
| 52:08 | to this statement here. OK. of transcription. So here is our |
|
| 52:15 | , there's our operon And so in condition here, right here is here |
|
| 52:21 | the lack repressor sitting on the OK? It's repressed, right? |
|
| 52:27 | expression. OK. Now, in state, if if it were this |
|
| 52:34 | that you the thing to remember is all these kind of binding is going |
|
| 52:39 | your press or operator. These are irreversible. Obviously, they come off |
|
| 52:44 | on right. Now if you were go down to the level of molecule |
|
| 52:48 | have a camera there and take a of it, OK? I don't |
|
| 52:53 | 99,000 times out of 10, you see a very small portion of |
|
| 53:02 | Scratch that most of the time it's it's in that state you see |
|
| 53:07 | but there's that little every once in while chance why it comes off and |
|
| 53:14 | you get your little bit of OK? And that's what I |
|
| 53:19 | I mean, low, we're only about a couple of molecules worth |
|
| 53:22 | right? And then that thing is on the operator real quick shutting that |
|
| 53:26 | . OK? But you need that this is how it's gonna see that |
|
| 53:33 | the only way, right? And if it is out there lactose comes |
|
| 53:40 | like Y does its thing make some lactose and then can shut off the |
|
| 53:46 | . OK. Inactivate it. And we begin to make glucose and gala |
|
| 53:51 | cleave lactose in the glucose gluc going ? Um and so again, it |
|
| 53:58 | go from 1 to 10,000 or 1000 difference, excuse me, in terms |
|
| 54:05 | expression level. OK. So what were making one or two molecules worth |
|
| 54:10 | can go to thousands, which I can happen very quickly, right? |
|
| 54:17 | the, the low level expression you maybe produces one or two of these |
|
| 54:22 | white molecules. But as you ramp up, then they fill up more |
|
| 54:28 | them get synthesized and now lactose just pouring in. OK? And is |
|
| 54:36 | , right? So use as it except we don't, we don't know |
|
| 54:39 | rest of the story, right? it's all about having these in the |
|
| 54:44 | place like why in the membrane to able to see and bring it |
|
| 54:47 | OK. So um any questions about ? All right. So the uh |
|
| 54:58 | the two, the two mechanisms, ? With or without lactose, |
|
| 55:01 | So a lactose repression. So there's the lack I is what codes for |
|
| 55:09 | repressor. OK. And it actually its own operator sequence. OK? |
|
| 55:15 | the, the active repressor A actually both operator sequences from the LAC operon |
|
| 55:23 | the repressor operon. And so it them together. And basically this is |
|
| 55:30 | that the, the promoter is inaccessible the prelim, right when this |
|
| 55:34 | So there's no expression going on. . And so, but again, |
|
| 55:39 | know that one in a million times it's, you get a little couple |
|
| 55:44 | mole as well, but for all and purposes, it's, it's |
|
| 55:48 | OK? Um You get, you lactose in it converted to lactose, |
|
| 55:55 | it binds and you have an inactive , right? You get expression or |
|
| 56:01 | and active. So that's one level the story. OK? So the |
|
| 56:09 | level is the presence of an OK? And so let's look at |
|
| 56:16 | question, but now what happens is enters the picture. OK? Um |
|
| 56:24 | it will have an influence. Yeah. OK. Let me turn |
|
| 57:24 | timer on. Done. OK. , it's going to be low c |
|
| 58:01 | A MP levels. OK. So do need the absence of glucose. |
|
| 58:07 | ? Um A repressor bound with Yes, that promotes expression. I |
|
| 58:13 | the person a lactose. OK. And a MP and this cyclic A |
|
| 58:23 | receptor protein go hand in hand. , um you need to have high |
|
| 58:31 | . It's like a A MP to the A, a activator bound to |
|
| 58:35 | promoter. OK? And so we'll how glucose influences this. OK. |
|
| 58:41 | here is our uh psychic A MP so psychic A MP uh in many |
|
| 58:48 | not all living things often plays a in as a signaling molecule. |
|
| 58:54 | Um When a certain condition is occurring a cell, you can trigger something |
|
| 58:59 | a MP which then triggers a cascade events and some kind of effect |
|
| 59:04 | So it's kind of almost a universal molecule. And in in this |
|
| 59:10 | it's kind of um hm it make of a sensor of the energy state |
|
| 59:16 | the cell. OK. So you've uh obviously you, you produce a |
|
| 59:21 | P in the process uh as you and make AD P and so this |
|
| 59:27 | OK? Of AD P to AD A T P to AD P, |
|
| 59:32 | kind of an indicator of the state the health of the cell. |
|
| 59:35 | and for typical bacteria is about OK, a little bit more ATP |
|
| 59:40 | ADP and it kind of indicates a cell. OK. And so A |
|
| 59:47 | P can also be a part of . OK. And this can be |
|
| 59:51 | in the S A MP. But but all three is kind of our |
|
| 59:56 | , if you measure the levels of , it can be a measure of |
|
| 59:59 | energy state of the cell and how it is. And so I think |
|
| 60:02 | kind of how psycho A P levels because of this, in particular when |
|
| 60:07 | is present. Ok. And glucose present, you have lower psychic A |
|
| 60:13 | levels because glucose is a it's indicating glucose is present, it's being |
|
| 60:19 | you know, like cause association A P production, et cetera, |
|
| 60:22 | Um Glucose exerts such a big effect other carbohydrate operon, right? Because |
|
| 60:31 | it's not just lactose, there's lots sugars. E coli can use, |
|
| 60:36 | . Glucose is present, it exerts effect because glucose is used most |
|
| 60:42 | right? That's what glycolysis is built glucose, right? Because it goes |
|
| 60:47 | , glucose, six phosphate and off go, right. Any other |
|
| 60:52 | you gotta do a couple of at one or two other steps in order |
|
| 60:56 | make it funneled into the process. ? We saw with lactose, we |
|
| 61:01 | to cleave it first in the Then glucose and the galactose has to |
|
| 61:05 | go through a couple steps before we into the cycle. So um that's |
|
| 61:10 | as efficient as using glucose alone. when glucose is present, it will |
|
| 61:15 | this effect, same effect on the , many of the other carbohydrate uh |
|
| 61:21 | . OK. Glucose use glucose then these other ones. OK. |
|
| 61:28 | so, so it's like like a levels then. So pretty much the |
|
| 61:32 | protein here, there's more or less a constant level. OK? But |
|
| 61:38 | the cyclic A MP S that can . OK. So if we have |
|
| 61:44 | cyclic A MP, then we're gonna a, get a lot of this |
|
| 61:48 | activator complex that forms. OK. it's all about attracting uh lira to |
|
| 61:56 | promoter site, right? So if have the other conditions, we have |
|
| 62:00 | present, right, which will form lactose, we'll get rid of the |
|
| 62:05 | off of the promoter. Right? , let's really wrap up production and |
|
| 62:10 | an active activator sitting there that will enhance polymerase binding and you get lots |
|
| 62:16 | expression. OK. So um this is what they call metabolic repression. |
|
| 62:25 | lactose is a metabolite. It kind refers to these other kind of carbohydrates |
|
| 62:29 | are affected by glucose, the presence glucose, they call it metabolite |
|
| 62:34 | So um so again, cyclic A level, you have, you have |
|
| 62:38 | present low cy A MP, not have lactose operon expressed um low |
|
| 62:46 | then we switch to lactose OK? promote this expression. So when you |
|
| 62:51 | at this in a growth curve, you have both glucose and lactose |
|
| 62:56 | you get this kind of biphasic what call dioxin growth. OK. So |
|
| 63:02 | have glucose utilized first and then there's lag here. So glucose used up |
|
| 63:14 | then growth occurring, growth going up then lactose finally is utilized uh here |
|
| 63:22 | this point. So there's a lag because you have to switch, switch |
|
| 63:27 | , the expression rights going on, over to lactose operon expression takes a |
|
| 63:31 | bit of time then that kicks OK. So glucose then lactose and |
|
| 63:38 | at the molecular level. So recall mechanism here, right? This is |
|
| 63:43 | uh phospho transfer system, right, common way to import various molecules. |
|
| 63:49 | so glucose comes in phosphorated to glucose phosphate, right. This goes into |
|
| 63:57 | , all right. And so uh molecules here are phosphorated and then hand |
|
| 64:07 | off at glucose. OK. So the state where glucose is present, |
|
| 64:13 | are un phosphorated and that can interfere the lack rise specifically this this sub |
|
| 64:21 | . OK. And so lactose can't the cell, right? So that's |
|
| 64:26 | scenario of glucose present and lactose OK. If glucose is absent, |
|
| 64:32 | you don't have the effect because this interfere with lack Y. OK. |
|
| 64:39 | Latu was free to come in. . And this interaction here is really |
|
| 64:44 | , you know, binding to lack and affecting its shape, not able |
|
| 64:48 | bind and bring in lactose. So uh what they call glucose um |
|
| 64:55 | inducer exclusion, sorry inducer being not lactose, but they call it |
|
| 65:04 | . Um so maximum expression lactose present actions. OK. Um All |
|
| 65:13 | So let's look, this is just , basic summary of the process, |
|
| 65:18 | ? Repression induction. Um But needing uh involvement of this activator absence of |
|
| 65:28 | for maximum expression. OK. So so the thing to remember here is |
|
| 65:34 | operon is a canna bolic operon. , it enables the cell to utilize |
|
| 65:40 | as carbon and energy source. So if we flip to Trippin |
|
| 65:46 | it's not that OK? So let's at this one. OK. So |
|
| 65:55 | this um which is true regarding the fan Operon. OK. And |
|
| 66:06 | the kind of the logic of how operates really is about the type of |
|
| 66:12 | . It's OK? Compared to OK. Yeah. OK. Let |
|
| 66:58 | turn the time. Ron. OK. Yes. This is the |
|
| 67:31 | statement here. D OK. So so it's not a can of |
|
| 67:38 | it's synthesis to. OK. So and that, and that fact is |
|
| 67:48 | of why it operates the way it compared to lack of. So which |
|
| 67:52 | a catalog pathway. Um So depression occurs when a trip to fan its |
|
| 67:59 | . OK? Um The, the the absence of corepressor to defend a |
|
| 68:06 | repressor. So if it's um it will be expressed. OK. |
|
| 68:12 | we'll go through this. OK. we're just gonna kind of go through |
|
| 68:16 | first part of it. OK. I'm gonna come back to that |
|
| 68:22 | All right. Crypto fan opera. about it. Which operant could eco |
|
| 68:25 | live without and we'll come back and it. OK. Black or trip |
|
| 68:29 | OPERON. All right. 50% So structural genes you got more here |
|
| 68:35 | lactose operon. We got five. ? Um The leader sequence. So |
|
| 68:42 | of put this in the back of head for now we're going into it |
|
| 68:46 | time. But the leader sequence is a part of the transcript. |
|
| 68:55 | That's involved in kind of another level control, right? We'll talk about |
|
| 68:59 | later. But the point is it's a part of every transcript. |
|
| 69:05 | Um OK. The regulator and so enzymes, the pathway synthesize crypto, |
|
| 69:14 | ? Um The A O repressor. this is the repressor form that's |
|
| 69:21 | OK. It doesn't bind to the . Um And so that scenario occurs |
|
| 69:29 | Ryan is not present. OK. get expression, keep expressing the genes |
|
| 69:36 | make your demand. Um If it present, it then uh combined is |
|
| 69:43 | to bind the repressor, activating And that relate translates into um an |
|
| 69:50 | repressor that blocks expression. OK. um what we call the holo |
|
| 69:58 | the complete repressor bound with corepressor Um So the question is um when |
|
| 70:10 | the family be present? So I'm ask that in this question. I |
|
| 70:14 | of got the questions that the order OK. When would crypto accumulate in |
|
| 70:18 | ? OK. When would these begin accumulate? OK. So would it |
|
| 70:30 | during mid log, are your defense metabolized during late lock phase? So |
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| 70:37 | see the two arrows there indicating mid late? Um or no, the |
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| 70:44 | two, when would accumulate in the if crypto fans accumulating in a |
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| 70:54 | it's not being blanked, you turned wrong and the is not really |
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| 71:22 | So forget about B it's between A C, OK? It's between A |
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| 71:26 | C. OK. OK. So if crypto accumulate, accumulate in the |
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| 71:45 | , that means it's not being which one was the word? |
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| 71:53 | Don't, No, it's a four word begins with you not being |
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| 72:00 | If it's accumulating, it's not being , sitting there. OK. So |
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| 72:03 | not being used. Is that more to occur during Midlock or late that |
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| 72:10 | used late log or mid log late yeah, because the cells are slowing |
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| 72:22 | in growth. There's not the same for crypto depends if you're growing like |
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| 72:26 | in mid two for the 8 to billion cells, right? There's a |
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| 72:32 | demand, there's a lot of protein that's going on. You gotta keep |
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| 72:35 | out the crypto, but at least at least one crypto every protein I |
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| 72:40 | think I'd be shocked if there So there's always gonna be a |
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| 72:44 | you always protein and had crypto or one of the 20 amino acids, |
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| 72:49 | ? So, but that demand slows as growth slows down. So now |
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| 72:54 | of a sudden crypto fans accumulate, need it, right? So what |
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| 72:59 | ? We do? We do right? It it the bins |
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| 73:05 | to the repression of activating it. it self regulates in a way. |
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| 73:11 | ? Um Similarly, you can also here and affect that enzyme and, |
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| 73:18 | affected at that level. OK. um so back to this question. |
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| 73:26 | you. What O R could E live without? Which one could live |
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| 73:38 | it? Can, it can live one of these ecoli mu mutants that |
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| 73:47 | do this, that don't have an one of these, but it lives |
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| 73:53 | fine. OK. OK. Cutting from 65, I am completely, |
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| 74:16 | , absolutely unequivocally shocked with an Uh Why? OK. Who enter |
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| 74:24 | life from? How can it Could it not live without opera? |
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| 74:32 | is like his opera? Absolutely. a million other things. Millions of |
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| 74:40 | sugars, proteins and fats and everything they can eat. Lactose is one |
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| 74:45 | of so many other things you could . OK. Yeah. If we |
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| 74:48 | living in milk, yeah, that would be hard up. Right? |
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| 74:52 | lactose is what's the milk? But , maybe not because you can eat |
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| 74:57 | . There's lots of things you can , but there's only one way to |
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| 75:02 | a crypto fan and you need that make proteins. And so you can't |
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| 75:07 | without this. You can live without . OK. Can't live needed. |
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| 75:20 | , you have to have it Right. So, um that's |
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| 75:25 | folks. We'll pick you up next . Thanks. Glucose and lactose, |
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| 75:40 | think at the same cost. But exactly what like we see right |
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| 75:50 | Yeah. The, it is the that he got here. So the |
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| 76:05 | of is. Oh my goodness. . So what's happening is uh hold |
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| 76:17 | ? Ok, so, |
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