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00:03 | mm hmm. Yeah. Mhm. . Okay folks. Uh Welcome. |
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00:45 | see um mm hmm. So this we get another, so this week |
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00:55 | a unit quiz is do, so a time, there was a little |
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00:59 | comprehensive um It will cover most of three. Um Up through whatever we |
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01:09 | to on Wednesday. Okay. Um week, of course is the |
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01:14 | the 14th 15th. Um Smart work . Uh Chapter 92 on Sunday then |
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01:21 | couple of days later at 10. . And what else thought? So |
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01:26 | other thing is um um I posted midterm grade. So if you saw |
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01:33 | email, explain if you haven't take look at the email explains, you |
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01:38 | how it's basically just just look look page eight of the syllabus. I |
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01:42 | that exactly. Okay, um the grade is um because we don't have |
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01:53 | we have a good number of sessions at the end I I didn't take |
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01:57 | time to kind of Ephesus and things that because I just wanted to get |
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02:00 | post it so you can see It's not that big a deal is |
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02:03 | gonna be that different. Remember the points are only worth 5% of the |
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02:07 | . Great. So um so the grade, you'll see it is a |
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02:11 | good estimate. So whether it's one one point plus or minus not a |
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02:16 | deal. Ok, so umm But , uh so it covers quicker points |
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02:22 | to the 23rd Exam one and 2 up through 14.2. So all of |
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02:29 | unit two homeworks um And um let's all the quizzes of course. So |
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02:37 | to quiz Five and unit quiz So again I'll explain the syllabus in |
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02:42 | email I sent out earlier. Um take a look at it. You |
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02:46 | have so that the droplets until the so you will have a third exam |
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02:51 | add to that. Okay? Um you're wondering about whether you're dropping out |
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02:58 | whatever drop it, you'll have one exam to put in there, okay |
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03:03 | add to it. And I do in the syllabus as well, how |
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03:08 | you figure it? Right, it's simple. Okay I just you just |
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03:11 | to remember that you're not dividing by , right because you don't have all |
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03:15 | grades yet, you still have two exams. So after the third exam |
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03:20 | so the exams are 16.25% each. you're just gonna keep adding that to |
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03:25 | you're gonna divide by a total of think it's for for the by the |
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03:31 | exam it's like a total of 83 something I forget but that's what you |
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03:36 | by. So just again look at email, I explained all of it |
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03:41 | there. Okay so anyways you'll have information uh to use in making a |
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03:46 | if you even need to make a . Okay. Um The other thing |
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03:52 | depending on where you're at The because now as of this this midterm |
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03:58 | it's you know it's uh 3035% of grade is the homeworks and the clickers |
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04:04 | you know all the non exam And so we've taken two exams. |
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04:09 | it's roughly about 33%. Now is 35%. Yeah so it's balanced out |
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04:16 | ? So very quickly this is going go up right? So the exams |
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04:19 | going to take more weight as we forward. Okay so that means that |
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04:26 | great can dramatically change from what from it is now. Okay. Just |
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04:31 | that in mind. Um So but keep maximizing the points on this. |
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04:37 | side. Okay. But certainly if need to improve the dance floor as |
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04:43 | go forward. Okay. Um Alright you're helping any of it. And |
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04:49 | officers email me let me know. . Um All right so today we're |
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04:55 | finish up nine, a couple of left to do there and then uh |
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05:01 | in chapter 10, get through a chunk of that I think. Um |
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05:07 | And so let's uh start here just kind of review. Just the kind |
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05:13 | the stuff we talked about. Um time. So we uh started we |
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05:22 | Chapter eight and then went into Chapter . So it kind of back up |
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05:26 | a second. So nine is um at mechanisms um gene transfer in |
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05:35 | So bacteria can't sexually produce how they variation, Right being types of reproduce |
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05:42 | binary fission basically a xerox machine. have mutations of course arise but so |
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05:49 | they can acquire new genes through these of horizontal gene transfer. Okay uh |
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05:57 | congregation transaction transposition. All mechanisms by they can receive transfer genes with other |
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06:04 | of the population. Ok. Generally related types can do this but so |
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06:11 | can some farther away in terms of um types of things that transfer um |
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06:18 | have a common function and of course transferring a few genes a pathway uh |
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06:24 | this is occurring uh three combinations So uh the the franklin being idiots |
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06:31 | in. Um If it is a fragment will need to be recombined with |
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06:37 | genome right to make that a permanent fragments of DNA floating in a cell |
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06:43 | not normal. And so a cell's think that's something that needs to be |
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06:46 | care of and gotten rid of and is so it's a recombination is |
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06:51 | Okay um so the uh uh So okay so we've gone through a |
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07:02 | uh into conjugation I think we're almost but let's look at that. Okay |
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07:09 | um okay so this begins with of parts to cells that are gonna come |
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07:18 | what we call a donor and recipient don't containing the plasmid with the |
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07:23 | Factor. Remember the f factor is the jeans products of those genes are |
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07:30 | in the process of carrying out Okay. Sex pilots. These what |
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07:35 | call transfer genes all a part of mechanism. And so um so the |
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07:41 | minus cell. Uh so when and what you might call it basic F |
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07:48 | uh if minus congregation the f minus will inherit. Of course this |
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07:57 | Okay then the process becomes an Plus cell. Okay, you can |
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08:04 | uh the not only the these genes the past but also the F. |
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08:09 | which makes it transferable. Okay so F factor that makes it transferable, |
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08:14 | that designate doesn't have plus but that it's transferable but it's also gonna have |
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08:21 | can be many other types of genes here. Okay. Or not |
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08:26 | But you know other types of genes antibiotic resistance genes and metabolic pathway. |
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08:30 | have you write? The fact that also a plus means it can be |
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08:34 | . Okay? Um Now integrating. the the external plasm like this can |
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08:42 | integrate into the chromosome. Okay so your HFR strain. Okay. Um |
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08:47 | then doing so makes the entire chromosome transferrable. Okay so uh but remember |
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08:55 | this kind of conjugation that the f sell rarely if ever becomes F |
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09:02 | Okay and um the uh transfer then much DNA is transferred from here depends |
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09:13 | how long they're connected, right? long they are? Um So again |
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09:20 | F. Plus factor is at the end, Right? It's the last |
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09:24 | that we copied and transferred and because never never happens really, the f |
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09:30 | stays as an f minus, but fine for it because it has inherited |
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09:35 | number of genes here. Okay. um are acquired a number of genes |
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09:42 | I just can't undergo congregation. But of course can pass them to |
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09:48 | transmission. So the last thing we about was the F prime factor. |
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09:58 | the point here is that the plasma integrated? Okay. To make the |
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10:02 | can also come out. Okay, normally what comes out is what went |
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10:08 | right shown in red here. so that can come out all right |
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10:15 | become a plasma again. Okay. all right. And so but the |
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10:24 | the F prime psych reforms when this is shifted to the left or right |
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10:32 | . So not it's just so this not what's coming out, what's coming |
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10:39 | or exercising is maybe like that. , so it's shifted right? And |
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10:48 | , not a frequent occurrence happens every in a million times. Okay. |
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10:52 | when it does it's it's it means it's now a part of this chromosome |
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10:57 | gene here as part of the but then someone that's left behind. |
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11:02 | ? So part goes with it and parts left behind just because of this |
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11:07 | excision. And so and what can is the potentially a partial deployed can |
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11:17 | . Okay. So when this congee with another cell maybe the same in |
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11:23 | same population the same species then maybe that still requires an additional 18 in |
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11:31 | example. So it has to write me a partial deployed. So uh |
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11:36 | those are the kind of the the congregation we looked at any questions about |
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11:42 | . Yeah so the congregation on the , what do we call that? |
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11:46 | I know the middle ones HFR congregation is just uh I just referred to |
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11:54 | an F plus f minus conjugation. if if it's if it's a question |
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11:59 | specifically about HFR it will say HFR another thing on the list um it |
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12:06 | me off for a second because HFR rarely becomes. Yeah I guess that's |
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12:14 | yeah so it's integrated. It will be called H R recipients spell |
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12:21 | It's yeah I would say it's it inherited. It has received a you |
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12:30 | it's it's now this HFR cell is contains an F. Prime factor. |
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12:35 | no longer an HFR because it's not anymore it's just called and uh okay |
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12:44 | . Yeah. Right okay um I a question. Okay so um Alright |
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12:54 | transactions transaction involves the virus viruses to between carrying the segment of DNA from |
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13:02 | cell to another. Okay so equate with so the two types of generalized |
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13:08 | and specialized. So since we've gone viruses already a quick correlate um generalized |
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13:18 | to elliptic fage. Okay correlate specialized to the Lissa genic land of |
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13:27 | Okay so that's gonna be the difference . So generalized transaction. Uh so |
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13:33 | have a favor infecting a cell. what happens is a an error in |
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13:40 | the packaging occurs. And so not in some cases it's viral DNA package |
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13:45 | host DNA is packaged. Remember that DNA in the process of bladder infection |
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13:51 | get uh digested. Right? So see the fragments here. And so |
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13:58 | of these gets packaged into the viral . Okay and so now that stage |
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14:05 | will still have the parts of the right? That it will be able |
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14:12 | infect the cell. Okay so it go infect the cell once it's gone |
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14:16 | the cycle here lights this cell. it comes out. Okay. And |
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14:21 | infect another cell as we see Okay. And so but that's where |
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14:28 | infection end because it won't go through life cycle because this is host |
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14:33 | N. A. Okay right And so that DNA can potentially get |
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14:41 | into uh this cell's chromosome right? you see right here. And so |
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14:50 | but again that source comes from way here. So in this mechanism potentially |
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15:00 | jean or genius can be transferred. because any one of these right can |
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15:10 | come can be incorrectly packaged into the captions. Okay so theoretically any gene |
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15:18 | be transferred this way. Okay so so that's generalized transaction. Okay again |
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15:27 | of politics page in the process of infection during its life cycle and interrupted |
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15:33 | host DNA. And then ends up the new cell. Okay um Now |
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15:39 | transaction. Okay as the name implies um part of this lambda lice region |
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15:50 | . Okay so remember the land of can integrated DNA into the host chromosome |
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15:57 | that profit. Okay and that's what is really about. And so that |
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16:03 | is very specific. Okay and it at this what's called these insertion |
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16:10 | Okay um between the galactose and biotin . So galactose galactose utilization by attend |
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16:21 | sentences of biotin. So here and . Okay and so um so that's |
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16:28 | integrates always integrates in the E. chromosome. Right? So it's a |
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16:33 | kind of a relationship between E. and this land of age. Okay |
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16:37 | so it always integrated there. Now is gonna look very similar to the |
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16:42 | . Prime formation. Okay because as know, lambda phase can also come |
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16:49 | the chromosome right? So it can a profile page but then it can |
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16:53 | out of that chromosome. Okay and when it does again not a rare |
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17:01 | not frequent uh it'll it'll have it'll right when it comes out this is |
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17:08 | what's exercising? Right? Just in purple purple is just the land of |
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17:13 | . D. N. A. what happens is we shift one way |
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17:17 | the other. Okay so in this we see that the galactose. So |
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17:23 | is actually going with it. And so uh so here you see |
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17:32 | june which is part of the you that chromosome is now sitting in the |
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17:35 | . Right? All because of Ah off kilter um excision. |
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17:42 | So um so that stage effects a host. Right? So that was |
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17:48 | this galactose gene in its plasma or its genome and it affects another |
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17:54 | Coli well then potentially that E coli will acquire a second galactose jean. |
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18:01 | . Now with that can happen is partial deployed. Right? So it |
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18:05 | not two copies of that gene. it can now that can other galactose |
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18:11 | can evolve independently. Maybe gain a different function or what have you. |
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18:18 | But uh but the only genes are here are restricted to just these few |
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18:27 | here here. Maybe something that's on next to either side. That's that's |
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18:33 | extent of what gets transferred by. means is theoretically any gene in that |
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18:39 | that E. Coli can be transferred what's at the in the vicinity of |
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18:45 | . Each end here in this area hmm. In this area or in |
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18:53 | area. That's it. Right. specialist transaction. Okay. Um many |
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19:01 | about that. Yeah. Mhm. how is normally supposed. Mm |
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19:08 | This is what you just you should be here. Two here. |
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19:17 | just a purple this example when the of what should be coming out. |
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19:21 | the excision itself is not the It's what's being put into the |
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19:27 | But but that only occurs because the excision. That's right. So instead |
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19:32 | cutting instead of was being cutting here cutting here, it's like cutting here |
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19:39 | cutting on the other side of the . G Okay, so let's let |
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19:44 | erase all this here. So instead our scissors doing that and that |
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19:52 | It's doing mm hmm. Uh see up, Montana's doing like this and |
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20:00 | . Okay. Sure. Okay. a recombination event. It's it's doing |
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20:10 | what you see right there and then cuts. Right. Right. So |
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20:17 | kind of an odd recombination excision Okay. Again, not a not |
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20:22 | common thing at all. It's a event. Um Any other questions? |
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20:33 | , so the last one here is is transposition. So the transpose sins |
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20:47 | I think, you know, almost they're widespread in almost every organism I |
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20:54 | . And they normally reside in the um within cells within the crow |
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21:04 | And when they're copied or they move , they stay within moved to different |
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21:10 | of the chromosome. Okay. Um can though among bacteria, there are |
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21:17 | types of transposing means carrying certain antibiotic genes that are transferred uh to other |
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21:25 | . Okay. And there's a couple ways that that can happen. |
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21:29 | Now in the process of of transposed copying itself and moving this is what |
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21:35 | call transposition. Okay. And so transpose are gonna be very basic, |
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21:41 | can just consist of what's called the is gene which is basically the part |
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21:46 | allows it to exercise and and and certain elsewhere. Um and then these |
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21:53 | sequences on either end. Okay. and so what we call insertions. |
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21:59 | really an insertion sequence is the most transpose on, right uh continue only |
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22:08 | the transpose a gene. And these of sequences you see here which are |
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22:12 | similar to what you see in the enzymes. Right? They those kind |
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22:18 | enzymes recognize these inverted repeats. So they have uh for example, |
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22:25 | A A T C G A And then on this side it's like |
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22:31 | reversed or inverted. Okay, that's of these kind of sequences. And |
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22:35 | the law often have a staggered kind a cut. Like this generating uh |
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22:42 | we call sticky ends. Oftentimes. And so you see it occurring there |
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22:48 | then um the two Types of movements might say, or what we call |
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22:57 | the word document terms cut and paste copy and paste. Okay, so |
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23:01 | replicated is basically just cut itself out insert elsewhere replicated is here's a |
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23:07 | I'll make a copy and then we'll this will stay here. This one |
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23:11 | here. Okay. Um now as mentioned, these are these are found |
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23:18 | all life forms. Um They there they were often called jumping genes |
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23:26 | some cases um They can be more than just being an assertion sequence. |
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23:33 | can be they can have a transposed plus other genes. Okay. They |
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23:39 | to call those complex transpose seasons. they have antibiotic resistance gene one or |
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23:45 | of those or other genes. Um now these things aren't constantly jumping |
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23:51 | our chromosomes. Okay. Because if did that was probably very detrimental. |
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23:56 | there are mechanisms that um kind of this jumping around. Okay. But |
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24:05 | can um Okay. They may have to do with regulation where they jump |
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24:11 | certain areas that are growing regulatory I'm not well versed in transposing means |
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24:16 | in myself. But nonetheless I do do know there are some types that |
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24:21 | carry antibiotic resistance. Okay. And the for the bacteria then to transfer |
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24:29 | to another cell. Okay. Can a couple of mechanisms. One so |
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24:34 | call conjugated transpose season. So they'll the genes to carry out congregation. |
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24:41 | . And so it's kind of a of how this might happen. And |
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24:45 | here's a donor uh self containing a on uh many with the recipients |
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24:52 | Again, because it has those conjugated . It will have the sex pilots |
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24:58 | be able to carry out those that of the conjugation process. So it's |
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25:03 | a combination of transposition and conjugation in way. Okay. And so once |
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25:09 | connection between the soldiers made, then transpose on exercises. Okay. But |
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25:16 | the transposing itself cannot exist like Alright, This is just a temporary |
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25:21 | where um the uh this will be and then go to, sorry, |
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25:30 | to the next cell. Okay, it's doing this rolling circular application makes |
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25:35 | copy and then once that's complete, goes back to integrating into the house |
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25:40 | that's what transposed onto do. Same the recipient sell. Okay. And |
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25:47 | we just transposed on now has ended in both cells is what we call |
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25:51 | . They kind of have the parts congregate correct. Um Another way could |
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25:58 | be which has been seen before is have a cell? Okay. That |
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26:06 | its chromosome. Okay. To transpose . Okay, And TN it's kind |
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26:16 | shorthand for a transpose on. So we have a sequence here and |
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26:20 | that same cell has a plasma conjugated . And so called F. |
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26:25 | Okay. And so it could be the transpose on um jumps or copies |
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26:34 | or just cuts and jumps over into plasma. Okay, so now it's |
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26:39 | here and that plans because it's enough . Can can mate with a |
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26:47 | Meyers. Okay. And then this transferred. Rolling circle replication. |
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26:53 | So here's the F Plus now and is the chromosome. And so um |
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27:06 | the transpose on here. This jumps into the chrome zone. And so |
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27:11 | we have it. Sorry. Like Okay, so again it's just mating |
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27:18 | between the two selves inherits the F with the transpose on and jumps into |
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27:23 | chromosome. That's that's that's been I'm not sure how prevalent that is |
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27:28 | that has been seen. Okay. kind of hitchhiking along in the |
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27:33 | Plus plasma. Okay. Um Any about that? Yeah. So 11 |
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27:43 | on is being put back. Mm mm hmm mm hmm. I think |
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27:50 | like insertion insertion sequences will have certain . So this is like the sequence |
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27:56 | . It will recognize the secrets like in the crow's own. There'll be |
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28:02 | compatibility there. Yeah. Yeah. Alright. So those that those are |
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28:10 | mechanisms mechanisms of horizontal gene transfer. , so again, one of more |
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28:15 | in which can can acquire D. . A. Um for members of |
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28:21 | population, right? Not to vertical transfer. The parent parent child, |
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28:25 | say. Okay, but from other of the population um Alright, so |
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28:34 | uh any questions. Okay, So flip to chapter 10. So um |
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28:42 | here we go through a few questions center some discussion around the questions. |
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28:49 | so in this uh check with 10 will cover over a couple of |
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28:54 | Um Obviously the overriding theme here is controlling gene expression examples of how gene |
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29:02 | is controlled. And the two we look at our lactose opera which |
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29:09 | may have gone through at some at level and tryptophan operas. Okay. |
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29:16 | so um uh both represent common types bacterial control genes. Um and then |
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29:28 | next week we'll look at, well on Wednesday. Well look at um |
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29:37 | little bit some different examples of some types of little control. Okay. |
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29:42 | we'll spend a little time on both lack of chip opera. Okay, |
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29:45 | there's gonna be some some so we're revisit kind of the operating structure again |
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29:50 | well as um some terms we're gonna to go through. Okay, terms |
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29:55 | use when talking about control of gene gene expression. Okay, so here's |
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30:01 | first one kind of the kind of question, I'm sure. And so |
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30:09 | let me get that going here. , so the the internal response turns |
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30:15 | an output action by the cell. to the information and functioning. Of |
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30:21 | ? Okay, so um this this be applied to any any cell and |
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30:28 | our own cells in fact, um it's made using bacterial cells as an |
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30:34 | here ourselves, respond typically to hormones and those hormones interact with ourselves to |
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30:44 | them what to do um all based , you know, what's going on |
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30:49 | . So what's going on inside the . Okay, so but there are |
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30:54 | types of molecules that are does that the work ultimately. Okay. And |
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31:01 | what's being referenced here. Okay. it is yeah, it's certainly it's |
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31:09 | or protein. Some kind of protein gonna be the one to do the |
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31:14 | generally. Okay. And um so can be things like looking at a |
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31:22 | cell. So um what's the what's cells face out in nature of course |
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31:29 | changes all kinds of changes, fluctuations nutrients, temperature changes, ph oxygen |
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31:36 | , uh etcetera. Okay. And based first you have to be able |
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31:41 | sense what's going on and so generally was some kind of a sensor |
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31:48 | Okay, I will take that input do something with it. Okay. |
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31:55 | they're doing something with, it is gonna be let's turn a gene or |
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32:00 | on. Okay. And that will to formation of a protein and that's |
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32:06 | does the actual work catalyzing enzyme reaction what have you. Okay, so |
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32:12 | all about controlling then uh at least bacterial operations but controlling these in different |
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32:22 | . Uh So they only express genes needed at any given time. |
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32:28 | There are some genes that are always for the most part because of course |
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32:33 | going to be critical functions that always to be on. Okay. But |
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32:37 | many functions they don't have to be only and only when required or |
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32:41 | Okay, lactose opera is one of you don't need to have a lactose |
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32:46 | and functioning, expressing anything unless lactose present. Okay um and so many |
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32:53 | kind of fall in that category. so control is very important. |
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32:58 | I know I carpet this a Is that um you can't see that |
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33:03 | takes energy really right to think about little bit but to to um uh |
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33:10 | to make proteins takes energy right? to to to carry out transcription to |
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33:15 | an RNA molecule that takes energy. all takes energy and so necessary to |
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33:23 | control the processor and not waste the needlessly. Okay so um so here's |
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33:30 | question. So this kind of relates the next topic which is about um |
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33:37 | of control in a way. this is why it helps to um |
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33:44 | of a decent grasp of just the of of DNA RNA protein. |
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33:51 | We talked about that before about the of information. Right? And uh |
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33:57 | it's through those different levels or layers we controlled we can control this expression |
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34:05 | it can be controlled at multiple Okay. At the same time in |
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34:12 | effort to really tightly controlled things. . And of course there's terminology to |
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34:21 | these things. Okay, so here tryptophan opera expression can be controlled by |
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34:29 | tryptophan itself inhibiting one of the enzymes for its synthesis. Okay, this |
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34:35 | a kind of a feedback control Okay so um so that will be |
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34:48 | so c is the consensus be Okay this goes into I will answer the |
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34:55 | here in the next slide. so if tryptophan itself is inhibiting one |
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35:00 | the enzymes. Right, So enzymes proteins. Right, so we're inhibiting |
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35:05 | protein responsible for synthesis. Okay. so let's look on this slide |
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35:10 | Okay, so here are the different of of expression. Right, so |
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35:18 | start with D. N. Okay. Um and we can control |
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35:23 | can't actually control gene expression for some at the level of DNA right there |
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35:28 | the very beginning. Okay, so can modify nuclear times that can alter |
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35:34 | uh in humans and other animals. uh beyond animals is epigenetic is kind |
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35:41 | that realm of modifying nuclear tides and can influence gene expression. Um We'll |
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35:48 | at a process called phase variation. . Very common among many pathogen types |
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35:56 | they can actually take a segment of . N. A. Okay. |
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36:01 | again using recombination. Alright, um we combine it in a different |
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36:09 | And then that alters expression as So anything having to do with just |
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36:14 | DNA like that, that's um that be a level of control transcription. |
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36:21 | . That that's often is can be for folks um in terms of |
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36:28 | Right, so transcription control itself is you going to allow an examination to |
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36:37 | a transcript or not? So transcription is not about having the transcript already |
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36:46 | . It's about is it going to made or not? Okay so there |
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36:49 | are of course influencing the RNA Okay. And that has to do |
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36:55 | promote ministering with its ability to get the promoter. Okay to transcribe. |
|
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37:02 | so that's where the operator sequence comes that we'll talk about. Okay we've |
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37:06 | before and so a regulatory protein and often are involved and you know either |
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37:12 | that or not allowing it to Okay now a term that's not your |
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37:17 | not just kind of added it here post transcription control. Okay so that |
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37:23 | deal with. Okay we've got the formed transcript now. Okay so it's |
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37:29 | made. Right so now we're beyond of control because we've made the transcript |
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37:35 | . And so post transcription control can interfering with the stability of the |
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37:40 | D. Um R. N. . Um I mean they already have |
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37:46 | fairly short lifetime in bacteria anyway. can be it makes me slightly more |
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37:53 | . Maybe a little bit longer lasting even shorter by manipulating the transcript. |
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37:59 | You can then doing to translational And so that of course is about |
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38:07 | right zone. Right you can let ribs and translate their what have you |
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38:11 | . So there's ways that that can blocked. Um and then and so |
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38:17 | of you know realistically All three of . Okay. Could fit under this |
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38:26 | of post transcription all it's kind of more all encompassing term and all three |
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38:32 | these can fit underneath there. So . Post translational. Post translational is |
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38:37 | the answer to the previous question. . So um the tryptophan can act |
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38:42 | the enzyme that inhibits the synthesis. ? So it's it's basically affecting a |
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38:48 | . Right? That's then altering Okay. And that would be post |
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38:54 | . Okay, so um so again it at here. Right. Anything |
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39:03 | that is post translational translational. You're in the process of translating right into |
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39:09 | protein. Haven't gotten there yet. once you have you know post translational |
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39:14 | you've got your protein and you can very common is to add a phosphate |
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39:19 | of protein sometimes that can activate Sometimes that can inactivate. It |
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39:24 | So um or you can just simply the protein altogether and get rid of |
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39:29 | . Any one of those modifiers So modifying altering any of these steps |
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39:36 | here here here any of those will alter expression either for the better to |
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39:46 | or to stop it. Okay. and all can be you know done |
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39:52 | at the various times. It's not one thing happens, you know, |
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39:59 | of these can happen at the same . Okay. Um again it's all |
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40:05 | not necessarily always also in fact probably not. It's more often the case |
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40:14 | it's it's a continuum. Okay, it's not necessarily all or nothing with |
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40:21 | . Okay. It can be levels control or expression, Right? Can |
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40:26 | low could be none of that could a lot. That can be somewhere |
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40:30 | a continuum. Right? So don't think of this as well. It's |
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40:34 | always just ever on or just It can be somewhere in between. |
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40:39 | . All depends. Right. Because situation in and around cells can can |
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40:45 | and can change, you know, then bury and so so too will |
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40:49 | expression. Okay, um now constituents that does refer those types that are |
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41:01 | expressed. So things like genes involved uh white collar assists uh cell |
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41:08 | um protein synthesis components. These are that are being done in a |
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41:14 | So generally the genes that code for things are always going to be |
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41:17 | Okay, so these kind of critical . Okay, so we call those |
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41:23 | of genes. Um Okay, so now gets into kind of the realm |
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41:31 | different types of terminology we use. , and repressor um it can be |
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41:40 | , it can be inactive. and that definition just the same. |
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41:46 | matter what the control effect is. , whatever the conditions are that make |
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41:51 | active or inactive, the definition of inactive, Professor is the same because |
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41:56 | going to see that in the lactose situation um versus the trip depending on |
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42:03 | situation that what when the Professor becomes , it occurs under very different conditions |
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42:11 | those two systems. Okay. But what an active pressure means does not |
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42:16 | . Okay, it still means the thing. Okay. Um and so |
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42:22 | terms like um impression uh de repression um these all are things that you |
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42:34 | to be properly. Okay. And it. Right. So you see |
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42:40 | here you see de repressed. These all have specific meanings. |
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42:48 | And they're used uh depending on what conditions are there bringing them out. |
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42:54 | . Um so mm mm mm mm mm mm mm. Okay. |
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43:10 | So um if you answered binds to operator, you are correct. |
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43:20 | So the so an active repressor will promote transcription but will limit or block |
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43:32 | . Okay. After Professor wouldn't require , inducers are required for inducing |
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43:38 | Okay. Uh they wouldn't be allowing customers to carry out this function. |
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43:44 | . De repressed means to be the of repressed. Okay, so an |
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43:49 | repressor, we're buying to an operator in doing so basically limit the rights |
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43:56 | transcribing. Okay. And so the under which it happens can vary. |
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44:02 | . Um so uh so here's kind kind of a basic scenario of what |
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44:09 | how these terms are used. so here we have a gene and |
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44:15 | regulatory sequence that can code for regulatory that can be a what's called a |
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44:22 | protein. Okay. And it will different interactions depending on the system. |
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44:30 | , so induction de repression. That's we have expression. Right inducing |
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44:37 | Uh if it's repressed not expressing it de repressed then you do have |
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44:42 | Okay. Um and so a scenario that can happen is something like |
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44:47 | So you see a repressor protein so can be in whatever the system is |
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44:54 | Professor interacting with it. The pressure going to be in a either active |
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44:59 | inactive state. So the question is makes it active or inactive. |
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45:06 | So here in that scenario the that is the active form. Okay and |
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45:15 | an active re pressure. Don't matter operation you're talking about the active repression |
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45:21 | to an operator and stop expression. and that's what it's doing here. |
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45:26 | when active form it's bound to the . Okay. Or regulatory sequences what |
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45:31 | calling? Just kind of make it here. Okay, so it's bound |
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45:35 | . Okay. And that's gonna block a plane. Right, right, |
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45:39 | that's gonna be running primaries is going bind there's a promoter right upstream and |
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45:45 | when they continue on and transcribe so gonna be blocked from doing that. |
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45:49 | presence of an inducer. Okay, to the operator binds to the |
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45:55 | Excuse me. And then that changes shape. Okay, so now it |
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46:01 | bind the operator sequence or regulatory So now it's inactive. Okay, |
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46:07 | by neighbors inducer and activate your pressure induces expression. Okay, that's essentially |
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46:15 | a nutshell. This is the lactose control. Okay is just like this |
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46:27 | the inducer is not lactose which you think it's actually a variation of it |
|
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46:34 | alot lactose. Okay and when it's is present in the environment um it's |
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46:43 | into the cell, converted some of converted to allow lactose. And that's |
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46:46 | inducer that then turns on the whole toast pathway. Okay don't worry about |
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46:51 | . Now we'll get to that Um Now the other scenario repression Covid |
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46:58 | . Okay so we stop expressions. a co repressor acts with a repressor |
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47:06 | . Okay and so an example of is here so here we have a |
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47:14 | call the current pressure. Okay that the re pressure and that creates the |
|
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47:21 | complex. Okay so you already see this is the opposite of this |
|
|
47:30 | Because in both scenarios are binding the to the Professor. But one instance |
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47:35 | it's um inactivity through pressure. The scenario it activates the repressor. That's |
|
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47:40 | mean you know opposite conditions can create situations and the reason for that has |
|
|
47:47 | do with kind of the the the of pathway metabolic pathway it is being |
|
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47:53 | . We'll get to that later. And so down here then we have |
|
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48:01 | active complex where it binds the covid . Okay And so um inactive form |
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48:09 | here. So when this leaves right molecule exits no longer bound to the |
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48:16 | complex then it becomes inactivated. And you get you get expression in |
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48:24 | form. Okay, you get gene there. Um but not when it's |
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48:32 | active form. Okay, so the difference between active and inactive, |
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48:42 | ? That those definitions don't change, matter what we're talking about, it's |
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48:46 | what are the conditions that bringing about be very different. Check. So |
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48:52 | and so this then is essentially the cent. Yeah. Mhm. This |
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49:03 | actually the PRP is short for So that's the core pressure is actually |
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49:09 | itself. So tractor fan has earlier mentioned can not only buying to the |
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49:18 | , that's one of the enzymes that synthesizes it. Okay. And blocks |
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49:24 | . It can also buy into a and stop it at the level of |
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49:28 | . Right? So so to defend can't control its own synthesis here at |
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49:35 | level of transcription and post translational. multiple, multiple um points of |
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49:44 | Um and so uh it has to with the fact that trip to fans |
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49:48 | amino acid and the operation for trip fancy makes synthesizers trip to France. |
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49:54 | so it's important to me is obviously to make first. Right? So |
|
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50:00 | has a multiple layers of control for reason and we'll we'll get into that |
|
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50:05 | we talk about crypto fans pathway. . Um so all right. Any |
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50:13 | so far? Yeah, this is in the pathway repressor protein stops the |
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50:19 | from activating genes and correct Well, , it's the absence in the absence |
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50:28 | inducer the oppressor is active And the penalty intercepts for the I would say |
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50:39 | inducer does he intercepting? It's their not their pressure wants to wants to |
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50:47 | . Right. So the only reason wouldn't be repressed, it would be |
|
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50:52 | the presence of inducer was. What activate it. Repressor protein will inactivated |
|
|
50:57 | the inducer comes in and intercepts and can change the shape of that protein |
|
|
51:03 | that you cannot repress and then but the repression the repressor protein um it's |
|
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51:13 | only work with and without the Right. And the logic, the |
|
|
51:22 | of both of those will become clearer we actually look at lack of and |
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51:27 | nutshell, I'll tell you the truth an opera on it works that way |
|
|
51:32 | tryptophan is controlling its fate basically. , so that's probably something you want |
|
|
51:38 | the media. Oh, acid. um when would tryptophan not be available |
|
|
51:45 | bite? You can think about Wonderful, correct when there would be |
|
|
51:54 | lack of that amino acid If if the cell we're doing what people can |
|
|
52:01 | tied to growth when cells are growing well. There's something proteins like |
|
|
52:07 | Right. So the amount of amino in that situation is actually that that |
|
|
52:13 | free meal assets in the cellar were very small because they're being used as |
|
|
52:17 | as they're being made. Okay, that means the only time that the |
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|
52:21 | would buy two or three pressers when to France accumulating in the cell, |
|
|
52:26 | was excruciating itself is not being used the same rate. And that's going |
|
|
52:30 | happen when growth with this leveling offers so much. And so in that |
|
|
52:36 | , why would the seller wants to that? Tryptophan? Don't keep making |
|
|
52:40 | if there's no demand for it. that's why people can kind of controls |
|
|
52:43 | own fate. Okay, It It'll by repressive and then shuts the |
|
|
52:47 | off concentration because then it'll show up a repressor. Right? Right. |
|
|
52:55 | so if if the cell also kicks and begins growing again, then that |
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|
53:00 | Richter fan will go away and then will make more of it needs |
|
|
53:05 | Thanks. Yeah, So and the of lactose opera because uh e coli |
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|
53:13 | example, which we can use You can also use 100 other sugars |
|
|
53:20 | they can use proteins and fats and of other things to eat. So |
|
|
53:25 | that is it's just kind of let's not do anything on this lactose |
|
|
53:28 | present. And so it kind of on lactose is what will turn that |
|
|
53:33 | . It's kind of different from because the catalog catholic it was an |
|
|
53:37 | Okay um Any other questions. so um activated? So this is |
|
|
53:46 | another we have oppressors. We have pressers, we're gonna have inducers. |
|
|
53:51 | also have activators. Okay so this can be, oops. Ok way |
|
|
53:59 | here. Let's go back this Okay so this right this with that |
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|
54:05 | that bound or unbound? Right? that's one level. Um We also |
|
|
54:11 | have we can look up at the interaction between RNA polymerase and the and |
|
|
54:18 | promoter right over in that area we look and if we can um enhance |
|
|
54:27 | binding of the primaries to the promoter helps as well. Okay and so |
|
|
54:34 | is where activators can come into play can form a complex as well. |
|
|
54:39 | you see your activator complex and inducer come together to promote her typically to |
|
|
54:46 | high level expression. Okay so we previously about basal level and high |
|
|
54:53 | Right? So basal levels simply just and promoter. If we add some |
|
|
54:58 | components to that to really enhance binding the memories then that can increase |
|
|
55:04 | Okay and that's where activators can come and we'll see that in the lack |
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|
55:09 | Sapporo there was actually activators that that are needed to really get high expression |
|
|
55:16 | of the opera. Okay and so so let's look at this this so |
|
|
55:24 | talk about the black opera next. so let's look at this question |
|
|
55:28 | Uh Let's see. Okay so um when comparing contrasting lactose opera troupe depends |
|
|
55:40 | which you want to be able to . Okay so they're both different in |
|
|
55:45 | of kind of what they're used Okay. Um uh And obviously as |
|
|
55:51 | just saw both have very different um which bring about an active or inactive |
|
|
55:59 | but it really has to deal with type of pathway it is in |
|
|
56:05 | So looking for the true statement Yeah. So also remembering what's what's |
|
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56:22 | negative pressure and it's an active Okay. Mhm. Okay. Um |
|
|
57:10 | if you um answered B. You correct. Okay so um Black Opera |
|
|
57:22 | controls the metabolic pathway for the metabolism lactose. Not synthesis. Okay, |
|
|
57:34 | about breaking down lactose not making the . Okay. Uh This is actually |
|
|
57:40 | example of that we're gonna look at transcription all not post just transcription. |
|
|
57:50 | . Um inactive because we're manipulating whether preliminaries will make the transcript for the |
|
|
57:56 | or not. Okay uh inactive inactive allows not prevents. Okay, so |
|
|
58:06 | is the only true statement here. lack why product is what allows it |
|
|
58:09 | detect if lactose is in the Okay, so we look at the |
|
|
58:15 | . The one thing we don't need worry about is this one the lack |
|
|
58:22 | . Okay So three genes Z. . A. Uh There's a of |
|
|
58:29 | a promoter lack. Oh but then is the lack I repressor and it |
|
|
58:35 | its own operator sequence and of course the repressor. Um the black aces |
|
|
58:42 | galactus side is planning galactus side transit . Um It's still not known the |
|
|
58:50 | of that. You can have e mutants that lack the gene completely does |
|
|
58:54 | at all hinder their ability to taking in ferment lactose or utilize lactose. |
|
|
59:02 | So we don't need to worry about . But the lac Z and Y |
|
|
59:05 | the products that we'll look at And so number one, the first |
|
|
59:11 | to kind of wrap their head around low level of expression always occurs. |
|
|
59:17 | remember low level expression they're called basil is almost almost next to nothing. |
|
|
59:24 | ? We're talking about low, low level of expression. We're talking a |
|
|
59:28 | molecules worth nothing that so can really anything with but it is essential. |
|
|
59:35 | . And so it all really goes to the lack why product. |
|
|
59:42 | that's the only way the soul can if black was even present. And |
|
|
59:47 | you're gonna have to make some of . And by some I mean like |
|
|
59:50 | two molecules right to two of those wise. Okay, at most are |
|
|
59:56 | . Okay, so it's not a huge energy expenditure to do this. |
|
|
60:04 | but necessary because it's the only way silicon detective is out there because lactose |
|
|
60:09 | permits is a transport protein. It bind to any external lactose and bring |
|
|
60:14 | in. Okay, so um the Z. Product. This is what |
|
|
60:23 | the metabolism of lactose. Okay, I should say. Um So lactose |
|
|
60:30 | a dice aka ride two sugars, and glucose. Okay. It will |
|
|
60:36 | some of that. The same enzyme both of these reactions. It will |
|
|
60:40 | some of the lactose and converted to actually the inducer that binds to the |
|
|
60:45 | . Okay um the hi liberal black . Okay so if we have a |
|
|
60:54 | bit of expression which is what we'll initially right a low level that low |
|
|
61:01 | of bakelite societies is what is used convert to make a lactose. Okay |
|
|
61:08 | enough lactose is present then expression can ramp up. Okay and if that's |
|
|
61:15 | case that it will take lactose and it to galactose and glucose. And |
|
|
61:22 | funnels right into black colleges. Okay the lactose takes one or two steps |
|
|
61:32 | do that but they will also fall what causes. Okay so you know |
|
|
61:38 | it's it's a way for the cell use lactose to get energy from |
|
|
61:40 | Okay. Falls into the pathways you about before. Okay um so the |
|
|
61:50 | so let's look at this in a way here slightly. So here is |
|
|
61:56 | are opera like opera telomerase and here's lack of pressure. Okay so one |
|
|
62:05 | the things that I think I've said before is that the binding right of |
|
|
62:09 | of proteins with other proteins, proteins D. N. A. RNA |
|
|
62:13 | have you. Um That binding is if ever. Well sometimes it's but |
|
|
62:19 | not irreversible. Okay. It comes , it comes off okay, at |
|
|
62:24 | certain rate. Um And so uh this state here the binding is mostly |
|
|
62:33 | so the pressure is mostly on that stopping expression. Okay. But you |
|
|
62:40 | , the one in 10,000 times is bound and it's off. That's when |
|
|
62:45 | can get a little bit of Okay. That's why I say there's |
|
|
62:49 | this low level right enough to make couple of molecules worth. Okay? |
|
|
62:55 | when that happens then that one in , I'm just making that number up |
|
|
62:59 | just trying, to you know. frequency that happens and you have the |
|
|
63:03 | to make a transcript and then synthesizes . Okay. But again, necessary |
|
|
63:09 | we need this guy. All that's the only way. It's gonna |
|
|
63:12 | this if it's out there to see lactose. Okay. And so um |
|
|
63:18 | it does it could bind, bring in and then uh black Z will |
|
|
63:24 | that to right? And you there's only a few molecules of lactose |
|
|
63:31 | there, you know, it'll make inducer and then get a little bit |
|
|
63:35 | expression. But it was a lot it out there because there's a lot |
|
|
63:40 | This will wrap up 2000 fold over normal levels. Low levels. But |
|
|
63:47 | point is that you need to have sorta see lactose, okay. And |
|
|
63:53 | it in. So um so there two scenarios here lactose absent. Alright |
|
|
64:02 | gonna have repression. So what happens the lac repressor forms actually a te |
|
|
64:09 | 1234. And they bind them both lac repressor operator and the lac operator |
|
|
64:17 | . And it brings that together in form. Our name. Preliminaries can't |
|
|
64:22 | . Okay. And so the transcription blocked right? When alone. Black |
|
|
64:28 | with the present. Okay then you binding to the plumber raise. I'm |
|
|
64:34 | today you have your oppressor. Okay just off and you get expression. |
|
|
64:39 | so induction pressure active in that scenario present and active in this scenario. |
|
|
64:45 | so that's um that's one layer of . So it's a little more complicated |
|
|
64:51 | that because of uh Let's any questions point. Yeah. It's alright |
|
|
65:00 | Didn't you just say was the one . Yeah. Well yeah what does |
|
|
65:06 | mean to say? Is that this this is repressor inducer. Okay there |
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65:17 | that unbind from the operator. So combined. Do it's late. So |
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65:26 | see. Yeah. Yeah. So what that means. So their pressure |
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65:29 | accurately come off primaries combined. And transcribe. Yeah that's the she is |
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65:36 | excisions right? Uh Not really decision . It's kind of this those that |
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65:42 | tremor is kind of because of tetra . It can span those two regions |
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65:48 | . And bring that. That's those together. So you know the |
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65:53 | N. A. Is kind of of folded up a little bit but |
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65:55 | they're in proximity they can bring those two regions together in essence. This |
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66:01 | is covering up the promoters inside there up. It's not exposed. So |
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66:08 | why you can't get any expression going . Memories. Can't find does it |
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66:13 | that so that it doesn't have to itself. Probably. Yeah probably. |
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66:19 | um so let's look at this um . This kind of relates to what |
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66:27 | do you have to do? What's next layer here? Oops. Sorry |
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66:37 | that. Okay. Okay so high expression. Our transcriptome. Sorry high |
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66:49 | transcription. Black operation requires all of . Except what if something else comes |
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66:57 | play here has a big influence on and expression. Yes. Sure. |
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67:23 | . Mhm. See Yeah if you . See correct. Okay so cyclic |
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67:53 | . And uh this crp and she'd together. Okay. Work together. |
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68:02 | So you do need the absence. glucose is the it's kind of the |
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68:05 | influencer here. Okay um glucose is preferred easiest. This number of steps |
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68:16 | get to metabolites in terms of like and so aspirations um glucose completed to |
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68:23 | its parts for related to glucose six . And off we go. Okay |
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68:28 | mentioned, you know, lactose. split in two glucose and galactose. |
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68:35 | galactose has to be go through a more steps. Things like other sugars |
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68:41 | sucrose, graham knows you know all of sources, you know, these |
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68:47 | all these are all taking a few steps in order to get into the |
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68:52 | . Okay. Which means it's not efficient. So glucose is Number one |
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68:57 | hierarchy. Okay. So if present will camp down the expression of these |
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69:05 | sugar operations until it's used up, those other ones can be utilized. |
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69:12 | ? And so that's what the glucose influences cyclic GMP levels. Okay, |
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69:20 | let's look at that here. so for high level expression you need |
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69:27 | the absence of for low amounts or absence of glucose. Okay. And |
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69:33 | course need the presence of black clothes . Okay. And so second KMp |
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69:38 | acts as kind of the signal for . Um So it's levels fluctuate with |
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69:46 | levels. Okay. Um generally um there's you don't need to know this |
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69:53 | there's a kind of the A. . P. Http ratio. And |
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70:03 | Is kind of the marker of the state of the cell. Okay, |
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70:09 | normal healthy cell has a ratio of two of about 1.5. Okay, |
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70:14 | that becomes less than that, then kind of a signal for the cell |
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70:19 | I need to you know, we to start a tab metabolizing getting making |
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70:22 | more energy here and glucose has an on that number. Okay. Um |
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70:30 | so if glucose levels are low where not really around, it's not really |
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70:35 | then this can trigger the formation of like electric A. Mp. Because |
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70:39 | all kind of part of the same passwords, right? They're all related |
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70:44 | each other. Second A M P D P A M P cyclic |
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70:48 | Uh So when this kind of energy occur, it's kind of sensed in |
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70:53 | way. Okay, So when witnesses second mp levels are actually low. |
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71:00 | . And so the second game is because it combines with the crp |
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71:08 | Right? These former complex. And that complex is what that complex |
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71:17 | what binds. Right? And then will create high level expression. |
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71:24 | so again activator complex forms and that expression binding to the promoter. |
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71:32 | And so um that will greatly increase . So without you know that part |
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71:39 | it, without the activity you get get really low expression. So you |
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71:42 | need to have that as part of process. So again glucose because glucose |
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71:47 | kind of controlling this to a We call it the tablet repression. |
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71:52 | ? So things like black holes and sugars, you know things like that |
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71:56 | be cantab molecules that can be metabolized on metabolites. Okay, so glucose |
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72:04 | kind of affecting the expression of these metabolites. Hence repressing them. |
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72:09 | So until glucose goes away right then other pathways won't be used. And |
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72:17 | if you have glucose and glucose together the medium you see that effect. |
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72:22 | , so here is um glucose and together in the same medium rights are |
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72:31 | growth. And so here because is . So we have initially um low |
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72:40 | kmp brought by higher. Okay, mps, glucose goes away. |
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72:49 | so it shifts that way and then promotes the in this case the expression |
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72:55 | the lactose opera as we go And of course there's a plateau right |
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73:00 | . Right, as we're switching to expression of this other operations, a |
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73:06 | bit of a delay until it begins kick in. Okay, now, |
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73:10 | the molecular level. Okay, friends glucose serves to kind of inhibit that |
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73:17 | from coming in. Um they call inducer exclusion. Lactose technically isn't the |
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73:23 | but it prevents black from coming in this mechanism. We saw this one |
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73:29 | about how glucose gets transported in the . Right? So glucose out here |
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73:35 | modified to glucose six phosphate. And because molecules diffuse independent of each |
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73:42 | , it will keep coming in, , Because it keeps getting modified. |
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73:46 | . And so but it does so being phosphoric acid and it involves these |
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73:51 | here. Okay. And so when is not this guy, the a |
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74:01 | is not foss for that, it with black white. So basically blocks |
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74:08 | of from coming to the south um lactose is absent, of course then |
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74:16 | nothing to phosphor link. So it on to that group. Okay. |
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74:21 | in that state it can't interfere with the lack Y permeates. So lactose |
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74:27 | . Okay so um so what you for a high level expression we need |
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74:34 | black opera, you need lactose you need glucose absent or certainly at |
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74:41 | levels. Um And that of course That scenario, promotes low, I'm |
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74:49 | . Hi 2nd MP. Okay. it promotes a a an inactive |
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74:59 | Think of all the components here. . Um And uh so then you |
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75:06 | to keep that straight in the context a black opera because when we talk |
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75:08 | the trip to fend opera on, changes. Right? So you want |
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75:12 | be able to convert between these two compare and contrast the two systems. |
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75:18 | . Um Any questions about that. , so we'll look at them. |
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75:24 | a couple of animations that that go to glucose, lactose, opteron chaperon |
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75:31 | . Look at those. They they a great deal in looking at those |
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75:35 | and we'll talk about it next to at it next time as well |
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75:38 | The banks will see you all next . |
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