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00:15 Ok, folks, welcome. Um for the late start. I kind

00:22 , I'm uh I think I was for myself in labs this week today

00:27 morning. So you may have seen in there a few minutes ago.

00:33 . Um All right. So what gonna do today today is going,

00:37 have a end point in mind, we're gonna end a little early

00:42 Um Sorry to disappoint you. Um a couple of things. So we

00:51 well ahead of schedule. Ok? that means of, I hesitate to

01:01 this because if I do, I it won't happen, but it's highly

01:04 that the last class date of the will be the 25th. Ok.

01:12 , so what we're gonna do is gonna, we're actually gonna, uh

01:15 finishing early. Today is a little earlier for I have to be elsewhere

01:19 campus. Um uh right after So, um at um, at

01:27 . So anyway, uh, but the, um starting in at

01:32 OK. You see that right Ok. Um Next Tuesday we're gonna

01:41 on that. Um, next, , on Thursday. Ok. Uh

01:46 got we're gonna have to finish up little bit of chapter 10 yet,

01:50 we'll do in the 1st 15, minutes on Thursday. Then we'll get

01:56 unit four. I've already opened up four, um, yesterday, so

02:02 four stuff, everything is available to . Unit four. Ok, So

02:08 , like I said, we'll start , on that after we finish the

02:11 stuff. So basically we'll start, , you know, for here and

02:17 send out an email. So uh , to remind everybody and start,

02:22 know, Should I move that up bit? OK. Start on

02:29 OK. So um and so year is really just all about immune uh

02:37 microbiology but starting with kind of the defenses um in the immune system,

02:43 immune system and then uh I get diseases and things. So um one

02:50 , so there is a chapter 26 all about different microbial diseases. So

02:57 don't cover all those, but there a list And you see when you

03:02 to chapter 26 notes, there's a of, here's the paths to

03:06 here's the diseases, Blah, Blah, Blah. OK. I'll

03:10 more about it as we get closer that point. Um But that,

03:15 , that stuff um you probably wanna in a table and likely it

03:20 it's just memorization, right? Because gonna be questions that relate to diseases

03:25 the test saying like I said, we get closer to it.

03:30 I'll talk more about it. and we'll see some questions in

03:36 And so you kind of get a for what, what's to be asked

03:38 that. Ok. Uh, the thing is so the unit quiz,

03:43 the unit quizzes are a little bit , more comprehensive. And so

03:47 this, the unit three, black quiz starts Friday. All

03:53 So this Friday through Sunday is one those, through through Monday is one

03:57 those unit quizzes. OK? Um think that's it. Uh Of

04:04 there's the last, the last smart for this unit is due next

04:08 Um Anyway, so as I'm sure aware, we're rapidly approaching the end

04:14 . OK? Um But we still some things to do first. So

04:19 question anything before we get rolling. . So we're in the middle of

04:30 so to back up for a second regulation. OK. So we started

04:38 unit with kind of an overview of translation, right? How you have

04:45 uh any organism that's out there and whatever it is, right? Um

04:50 doing it basically through the functioning of different proteins. Um And yet uh

04:58 is being expressed at any given time , right? That person that's sitting

05:04 in a pond somewhere. What's they deal with? Well, all the

05:08 of other microbes it's interacting with competing um the, if it's a photosynthetic

05:15 , what, what, what's the am? Am I my maximum light

05:20 depths? Right. And do I stuff to eat? Is there enough

05:23 bla bla bla all kinds of You can think of all kinds of

05:27 that's affecting it and it's gonna be of those are gonna turn off different

05:32 , turn on different other ones to a response, right? A response

05:36 will enable it to survival. So, um so getting back,

05:41 we're focusing here on the control aspects we're just looking at, you

05:46 we're, this is obviously a tip the iceberg right here are just examples

05:50 how, you know, you can expression. You know, every um

05:55 any, any college student bio student first learns about regulation, you always

06:02 with and uh obviously you're hearing it me here, you're gonna hear it

06:10 . I'm sure elsewhere as you go the chain, right? Probably in

06:13 bio, you cover it, um in biochem one, you cover

06:18 So uh in any case, this likely that the last time you'll hear

06:22 . But uh hopefully, uh when do hear it again, you'll be

06:26 on it, right? So, so that, that's basically what we're

06:31 in different aspects of gene regulation. . We're looking at strictly protic

06:36 if you get the eukaryotic systems that blow your mind because it can get

06:42 layered, super complex. OK? we're more complex creatures than the

06:49 right? So actually it's gonna be complicated process. OK? So even

06:54 I look at that stuff, it's it blows my mind. So I

06:58 , I'm not, I look at that often. I try not

07:00 But uh anyway, so let's get to uh Right. So we went

07:06 , OK, so you should, gonna see some questions here. So

07:11 especially when you get, you started about the control. So you're gonna

07:16 those. So you should look at side by side and say OK,

07:19 similar? What's how is one different the other blah, blah,

07:23 blah. OK. So uh right, the the uh it's

07:29 it's all triggered here by the presence absence of sub molecule and the presence

07:35 the molecule triggers triggers something to happen the absence of molecule triggers something to

07:40 , right? So the la so and foremost, lactose is a sugar

07:45 an energy source for the bacteria that ferment lactose, right? Uh A

07:51 so um if you wanna, if wanna use it right, then um

07:57 have your expression system that handles lactose only work when lactose is present,

08:05 ? Inducible, right? The presence lactose, technically, all lactose,

08:11 ? Uh that induces the expression, ? So that's the only time to

08:16 it on is the black is Makes sense. Why? Right?

08:20 would you turn it on there, ? And so um but then there

08:24 the other layer, right? The , right? So our glucose is

08:28 . OK. Think of it that glucose is present, shuts off lactose

08:34 other sugar. That's the table, ? So I saw hinges on the

08:41 of cyclic A MP. So I glucose influences, right? So

08:47 then you have low levels psychic A , which means very little of this

08:53 active complex forms. But we also about the um the uh um that

09:02 excludes like a glucose, glucose is . The protein that helps glucose come

09:07 kind of affects the lack the lack , right? It doesn't allow lactose

09:11 come in in that case. So glucose goes away, lactose present

09:16 boom and you get full blown Uh As you see here, first

09:23 presence of inducer uh in activating the uh repression protein. It can't find

09:33 the operator uh now free to But now because we have a complex

09:40 , you get higher, right? it binds the promoter, increasing the

09:47 the magnetism if you will of the by theme. So it binds a

09:52 with lots of expression. OK. um any questions about la? So

10:00 . All right. So then we into opera, correct? So,

10:07 , a different uh metabolism like micros is all about in let's process it

10:16 weave it and then let's put, it into glycolysis. So it can

10:20 used for energy crypto fan opposite. Anna about that making we're making crypto

10:29 as a result of the action of expression. O we're making that five

10:38 genes involved one continuous transcript. And uh OK. And so Triter

10:49 , it, it kind of more less uh self regulates itself.

10:54 It's expression. And so, um the thing OK, say, say

11:06 an analogy, So say you're working , right? You're a truck driver

11:10 Amazon. OK. And you're gonna fill up your truck with packages to

11:16 . Ok. And so here are packages, right? And they're on

11:21 conveyor belt. Do you, they , here's your, here's your

11:26 you gotta put in your truck, ? That truck cool. OK.

11:32 right. Put them in the take them away, you got trucks

11:37 to keep building up, right? is this ever, are these boxes

11:43 accumulating? If you have the truck coming in? Boom. Any given

11:52 , if you look here, it's zero because it's being used. It's

11:57 , going out for delivery, but have no trucks, piles up boxes

12:04 go anywhere, you wanna stop the , right? So that's when the

12:11 is now available to act in this , right? Going up there be

12:18 co and then form these, which will block expression. So

12:25 it's what's going on here right? is what determines which way you're going

12:33 pressure or the state inactive and continuous . So, getting away from the

12:44 , but for the cell and you ptotic cumulated need, right? You're

12:49 not using it. Right? Because you were making it, it would

12:52 going somewhere, it would be more to, you know, to,

12:55 hook on to a T R N . Right? Um And then being

12:59 a protein somewhere, proteins, Triple can be used as a good

13:04 other stuff, you know, but protein. But so if it's

13:09 if it's, if it's just sitting and it's not being used for

13:13 that it's, that's where the growth comes. It's why it's tied to

13:17 , right? The cells are growing . It, it wants everything,

13:22 ? It's grow multiply, right? produce energy, gotta make proteins,

13:26 ? So of course, your is be used right away fast as it's

13:30 it. But because there's a demand it when, when the growth then

13:36 down, not the same demand, crypto accumulates, don't keep making

13:42 You don't need it that much Shut it down. And so it

13:47 , that's why it goes this route a pressor. OK? It uh

13:52 know, if you, you don't know this, but I mentioned it

13:55 . It also actually affects here. binds that enzyme and, and shuts

13:59 off there. So you have two going on. OK? So it's

14:03 about saving energy, don't waste. ? You know, it's kind of

14:08 gotta think of a bacterium in right? It's not by itself in

14:11 vacuum, right? It's, it's compete. And so you're gonna not

14:16 wasteful things because it, it, can literally carry it. OK.

14:22 , all right, that's as far we got with control. OK?

14:29 And it makes sense to do it way. It's a biosyn pathway very

14:33 to make things now in the course self growing, right? So why

14:38 be let the product of the pathway itself, right? You need to

14:43 that and this isn't, this isn't an off, on off switch.

14:47 not, it's not all or right? It's a it fluctuates,

14:53 ? Depending on the needs, the rate in itself, right? Goes

14:56 , goes down. It's, it's really well. So I guess in

15:00 cases it could be all off. , you know, but it's,

15:03 fluctuate, you know, as based the needs of the sell.

15:07 Um Is any questions? So we're look, look at some questions

15:13 I don't even think these are Clipper . These are just kind of you

15:18 me what you got kind of OK. So here's the right.

15:23 lac plus Trip plus means it has Operon. OK. So the Lac

15:28 has Trip Opera. OK. So growing it in minimal medium with both

15:34 and trippin OK, minimal medium. we've plopped in lactose and trippin.

15:41 . No glucose. No glucose at . Ok. So what can you

15:46 about these cells with respect to these operant? Ok. So lack OPERON

15:53 the OPERON expressed? Yes. because lactose is present and glucose is

16:03 , right? Um It's a trip on express. Why not?

16:12 it's TRIPP fan present. You don't to uh doesn't need to make

16:14 it's, it's there to take it and use it. Right. Um

16:19 hope I got this coming up, . OK. I do. All

16:25 . Um What is the state of black Operon active or inactive?

16:33 Uh Right. Because the truth to that's there, you know, uh

16:43 it's being supple crypto and they use , of course it does, it

16:46 use it all. It's gonna be and free to bind to the um

16:50 don't need to synthesize it if it's , right? If you're being feeding

16:54 crypto, why make it? You need bind or, or activating

16:59 OK. Um How are, how the psychic A P levels affected?

17:04 like opera is high or low? Yeah, I can think about that

17:12 . Yeah. Um Yeah, because forming that complex, the activator

17:16 right? So not, not applicable Trip Opera. OK. So,

17:22 right. This now, so this the one that's gonna be kind

17:27 you know, pull your hair out there is, there is a,

17:32 , a step wise way to think it that should help. So you

17:38 have this slide. That's fine. , I inserted it right before

17:42 Oops batteries. Oh, I knew should have changed it. OK.

18:07 . OK. So put this in class just as a, to,

18:12 , to show you what the OK. So um here's the

18:18 the actor pressure hasn't bound yet. . So in that state, we're

18:24 defense, right? So we already that accumulates, it'll bind the the

18:31 a corepressor bind, you have an and we pull it right? So

18:39 mechanism, right? The the this if it's not being used and then

18:48 over here to bind and then causing to happen, oop causing that to

18:54 off expression, right? Um That , I, I wanna say a

19:00 but don't hold up to it in of 95%, of the stoppage of

19:09 opera occurs by this way, The corepressor binding, the repressor activating

19:16 , OK? That controls the majority this expression. OK? But as

19:22 know, these bindings, right? not irreversible, right? Yes.

19:29 you had a camera and you took snapshot most of the time you're

19:32 you'd see it sitting on the but there's gonna be times when it's

19:36 , right? Not very long, very often, but it, it

19:40 happen. And that's when you get off and you get some expression.

19:45 . So this last mechanism, this attenuation mechanism is about this part

19:53 it. All right. So one to make a note when you,

19:59 when you are expressing the, um trip to Japan often and you're making

20:07 big, big continuous transcript just making OK? That this part is always

20:15 part of it, the box in , that's the leader sequence. So

20:20 always a part of the transcript. ? Now, if you're in a

20:26 where you need to make trip, doesn't matter, it's just a part

20:29 the transcript, but you don't do with it, right? But when

20:34 don't, when you really wanna put clamp down on it, right,

20:38 don't want any expression to occur virtually . Like I said, this,

20:43 takes care of most of it, some can still be made. So

20:48 really wanna put a clamp on this where attenuation comes in and it involves

20:54 part of that transcript that so the um trying to think the best way

21:08 . All right. So No All right. So here we're zeroed

21:14 . Look at the bottom here, zeroed in on the opera front

21:19 OK? So here's your promoter, ? And then here's that, here's

21:25 trip L trip L is that leader , OK? First part of the

21:29 , OK. So the key point is this junction, OK.

21:36 There. So remember a plum That's what this little blob is

21:41 OK. A plum race, it then go, right. OK.

21:48 this point right here is the critical , OK? Because you get into

21:58 , that's the structural genes, E and D and C to B

22:03 A, right? So if you're beyond here, you're committing to expressing

22:10 genes, OK? If you go that, you're committed to expressing those

22:15 . And if you're trying to shut down, you don't wanna do

22:18 All right, then that's where it involves A A P getting beyond

22:27 point, kick it off. So, um that, that's really

22:34 this boils down to is, is , is gonna be knocked off and

22:38 allowed to keep going or will not interfered with and it can keep

22:43 right? That's in a nutshell. as simple as I can explain

22:48 So, how do you do OK. How do you do that

22:53 a, a transcript? Right. , the kind of idea of how

22:56 works seems kind of crazy because it transcription control, right? Because we're

23:02 allowing this. It's about, are gonna allow that to, to um

23:09 the structural genes or not? So is transcription control, but we're using

23:13 ribosome to do it, right? , all right. So again,

23:21 , remember this, right? That is the critical junction, you gonna

23:25 it go or you're gonna kick it . Yeah, it being on your

23:30 . So how does this happen? , the leader sequence itself when it

23:35 . So like all R N A um I think all R N A

23:39 they can fold, right? They're double, double strand of the

23:43 but they can fold, right? all a U G C base

23:47 right? And so they can form secondary structures. So leader sequence itself

23:52 form multiples of these, right. if you were just, if you

23:55 to take this leader sequence and plop in a, in a buffer

24:01 right? And you were able to it, it would assume different

24:06 it would fold up in 1234 loops and even as well, a

24:14 OK, all those would happen and one's form over the other is all

24:20 on, right. So um The , the one that's most favored thermo

24:29 is actually the 23. OK. so which one forms it, it

24:36 be interfered with if you have something this, on this transcript that sits

24:43 a certain spot and just sits there a lump, right? It can

24:49 some of these loops from forming, ? Just imagine if something were sitting

24:53 here in the 12 area, the loop on the floor, we had

24:56 boulder sitting on top of it. . So that's, that's kind of

25:02 function of the ribosome here, the position on that transcript determines what loop

25:09 because it basically just become a physical for certain loops to form or not

25:15 . OK. So that's the role the rhizome in this, right?

25:20 if a transcript is formed, rhizome gonna plop on there. OK.

25:24 start translating. So, um so kind of the next thing here,

25:29 ribosome is controlled before based on where positions itself. So how do you

25:37 what positions itself? That's where these come in, right? Because remember

25:44 um by the transcript and they form site where TT R N A s

25:48 in, right? Because remember we're a polypeptide here, but the ply

25:53 here with the le sequence is It's, it doesn't really do anything

25:59 the cell. It's just part of mechanism of control. OK. But

26:04 , it's doing what Ari does, ? Sites for T R N A

26:08 to come in, right? Recognizing codons, right? So you

26:13 you can alter the positioning of the by the presence or the proportions of

26:22 T R A s and uncharged, ? So to remember C R A

26:30 A, it's, it's specific amino , right? That corresponds to the

26:36 . And so um you can have charges on charge, right? So

26:42 do you think in terms of the , what would influence one or the

26:49 moment you have probably have a high of uncharged T R AC.

27:02 Have a uncharged to our right. bad if you didn't have a charged

27:22 R N A, if you had but uncharged Pr N A to

27:29 Right. And I'm sitting there waiting a K A R A so you

27:33 start linking those amino acids together. . It's not good at times.

27:42 came here all the time. All . If you're rock and roll class

27:51 , OK? Um Google it good , bad times. Um All

27:58 bad times. If you haven't charged N A, you can't make

28:01 right? That's this is where the comes in. OK? So The

28:09 thing is it relates to these two here. one and 2 a an

28:14 crypto, hold on and the So this is what you, you're

28:22 with the normal called the, the . That's where the transcript would normally

28:28 . There are the drivers only stopped . So, but now they have

28:33 other one Which is not a stop . It's just two of these

28:39 So um and similarly, I think other amino acid uh uh opera the

28:48 for making the other amino acids have similar thing they'll have if it's

28:52 they'll have two of those right in front of me. But regardless

28:56 specific for it's, it's these two because it's about controlling the trip

29:03 OK. So um so the movement the rhizome can be altered if,

29:09 would you have lots of uncharged for fan when there's lots of krypto fan

29:14 or when there's no crypto fan Yeah, of course, there's nothing

29:23 it goes. If there's no, trip. How are you gonna charge

29:26 ? Right. So, that's kind the mechanism here, right. There's

29:32 lot of around, then you have of these, all right. If

29:36 don't, then you likely have mostly uncharged types. OK? So let's

29:44 that in your memory bank. Let's at, yes. So we

29:48 right? Uh 12 loop, loop, 34 loop, those can

29:52 form. OK? So the two be aware of are this one

29:58 which is already labeled for you a . That's one, the other one

30:02 the 23, all right. Those the two, the 23 is actually

30:06 the anti A 10. It's on next line called the anti. So

30:11 are two that in this, those loops. OK. So, so

30:18 , those two loops and which one depends on where the ribosome positions

30:25 OK? So that's really the crux the whole thing, right? And

30:31 it positions itself and which loop forms determines whether it allows the polymerase down

30:39 to keep going or to knock it . All right. So that's so

30:43 leads to the other leads to the leads to the final locker.

30:47 So it's all happen stepwise. So let's look at uh high trip

30:54 . So again, high trip defend , you're gonna have lots of charge

30:59 R A S. OK? so here comes the R zone,

31:05 translating right? That leader sequence. it's got these two adjacent drip

31:14 Not a problem. You have plenty crypto, lots of crypto T R

31:19 S boom, boom goes right in keeps on. OK? And

31:24 and then just stops where it naturally at the translation stop code.

31:31 So that sitting that, that, positioning right here, OK? Is

31:40 the 2 3 form. So the 10 can't form because it's if I'm

31:47 23 loop, I got this boulder the top can form. I was

31:51 on my head. OK? So 34 and it does. OK?

31:58 so the other thing to notice here here is the Barney plum race riding

32:03 ahead, right? So remember this the, this is the junction point

32:07 you knock it off or keep it . OK. So um the um

32:14 so at high levels, you don't to express, you don't need to

32:20 the trip off. You don't need make it, you've got lots of

32:22 to it, right? So so remember on top of this,

32:26 got the, you got the typical mechanism, right? The trip defense

32:32 active repressor right. But then you , you still can have a little

32:35 of transcription that occur and this one gonna put a clamp on it.

32:40 ? And so, uh so note proximity here between the 34 loop and

32:47 PLYM, right, that's really the here. So which loop forms one

32:51 is farther away from the, from a plume that's up ahead, transcribing

32:57 other one's real close to. So this guy can give it the

33:03 . So you see how it's, can contact that plumbers and knock it

33:07 . OK. So that happens and don't express, you'll express. So

33:15 the proximity of that loop, a loop to the clime contact. But

33:23 then relates back to again, it's step watch, right? This happens

33:31 the ribosome is position here blocking the from forming, allowing the 34 to

33:37 this occurred because there's lots of crypto , to make lots of charged crypto

33:45 N A which allows it to stop its natural stopping point. OK?

33:50 it's one to the other back to because there's lots of crypto don't need

33:55 make it. OK? All So in the other scenario,

34:02 So we've got low to different So that means we have uh

34:09 and so we have the uh let's , let's see the fan, the

34:15 , right? Nothing there blank, ? So the to the around to

34:21 these Ok. So it stalls. brown will stall. So it gets

34:28 those trips. There's no trip to move, can't go any further.

34:36 . So now this area, it not bound, it's not boulders at

34:42 top of it in form. So you have, if you have both

34:46 these, so the two and so you have 23 and four available

34:52 the 23 is more favored. And it's the one that forms, even

34:57 the 34 can do that, the is much more uh energetically favorable.

35:02 it forms. And so note the distance like farther away can't interfere

35:08 the PLYM. All right. So keeps going. OK? And you

35:14 , so you go through, you , so you're out, that's what

35:18 want. You got a low you gotta make it this what needs

35:22 to happen. OK? Um So see this thing in action here.

35:31 Yeah. OK. Um OK. that annoying voice. OK.

35:44 so we're gonna see first the usual . So here is your enzymes,

35:49 ? Multis stepp pathway make trippin, uh the core repressor, repressor,

35:57 an active repressor and we have um to the operator, right? No

36:05 . OK. And then, so , that takes care of most of

36:11 repression here. OK, if you have. And so here is um

36:17 magnus all let it go. So it's a little slow here. We

36:24 there, we gonna do your sequence . Right. Before the structural

36:28 Your four different regions in the loop . 2, 3 and OK,

36:37 loop. And the other ones should loop. And then OK. So

37:00 so proximity can knock the plum This is really slow. Let's try

37:06 . Here. There we go. if we look at the scenario of

37:19 just talk codon trip, codons, ? High trip. right? So

37:26 trippen scenario. Yeah. So here to Riz, it'll go right through

37:36 coons because there's no shortage of crypto at the usual stopping place. 34

37:42 kicks off the plum race. Um Like so, all right.

37:50 in low crypto condition, OK. we go. And it stalls,

37:58 at the two trip coons. And then the proximity farther away can't

38:04 with the polymerase. Ok. So , that's the attenuation mechanism again,

38:13 takes care of a small portion of control. Most of it again is

38:17 the active repressor. But nonetheless, is important. Ok. So let's

38:24 at this. So read this question hold on and uh let me move

38:33 and open it. OK. So through this one, we pause and

38:39 . OK. Go through. Uh with another slide, it's not the

38:45 but it's gonna have like different And then if we have any questions

38:51 address this. Ok. Move Time is on. I need some

40:41 to read it myself. I look it in a while. I'm sure

40:43 need my answer. Oh, in you pick e it's not e

40:55 All right. How many had to their answers? Goodness, goodness gracious

41:02 . All right. Give me a to switch your answer. Of

41:11 So These mechanisms help block expression of chip opera except one. OK.

41:27 we go at that. If you it, be your correct. Um

41:42 question is why are you correct? actually should be? Why is why

41:48 input because you have an abundance or lack of crypto T R N A

42:01 ? Yes. OK. Yeah. yes, you have a lack

42:05 of if you have a lack of T R N A S that means

42:09 have a lack of trippin in which is the signals for oh let's

42:13 crypto. OK? And so that's B B will lead to that,

42:19 ? We're trying to block expression, ? We wanna do that.

42:25 So yeah, this, this A gonna be a produced, you

42:30 regardless, you know, you're you're gonna have delete sequences transcribed because

42:34 a part of, it's part of operon uh transcript um A R

42:41 OK. So the formation of itinerary . Yeah, of course,

42:45 that's what knocks off dili the block , right? So um the higher

42:53 of Ryan, yes, because that to high levels of R A which

42:58 Amazon doesn't stall at the trip stalls at the stop code on which

43:03 air loop to fall. So, yeah, not this. If

43:09 if it said Ari was installed at Translations Stop Codons, then yes.

43:17 right. That would be great. not as written. OK. So

43:20 uh let's look at one more thing . This one OK. Similar to

43:27 previous table. All right. So so under low or high trip

43:33 So low trip levels synthesize crypto, or no. Yes, I levels

43:44 opposite. All right. What would say your levels transcribe operon adversarial

43:52 No. All right. Those seem basic but I, all right.

43:58 trip levels does trip corepressor repressor complex at low levels? No high

44:10 Yes, because it's, if it's , then it's free to bind to

44:14 . Charge trip T R N A P transfer R A is plenty

44:19 No. Yes. Stalls at stop coons. OK? Which triple

44:28 loop forms, right? An itinerary , anterior loop. OK. So

44:33 are kind of things to know, ? So put this beside a table

44:37 the specific to that, right? uh low lactose, no glucose,

44:46 lactose, no glucose, you know various scenarios see if you can fill

44:53 out. OK. Any questions? . Yeah. So what's stopping?

45:04 transcription is basically the formation of the ? So, right. But

45:09 that goes back to let's go back that picture here. OK. So

45:14 has to do with the proximity of loop to the polymerase that's moving

45:21 So this the, the attenuated loop , it's really close to that

45:26 That's right ahead. So it contacts and knocks it off here. It's

45:31 away. Prox. So it can't , doesn't physically interact with the

45:37 So this is free to then keep . So it's just about, it's

45:41 the loop forming and proximity to the , you know. So it's basically

45:46 physical interaction that knocks it off because so close. Yeah, that's

45:52 that's why it's a transcription mechanism even it's kind of weird, you have

45:56 ribosome moving on the transcript, but essence, your, the end goal

46:01 to either knock that thing off or . And that's what a transcription of

46:04 is. Yeah. OK. Any questions? All right. So,

46:10 the animations look at animations too. , they're posted on Blackboard. So

46:14 think you probably find it helpful and can hear the guy's narration if you

46:18 . Um All right. So we this. OK. So again,

46:26 summary. Um And so yeah, there's any questions about Trip Operon,

46:35 um you'll see some questions on the blackboard quiz about this. Uh um

46:43 what we have left? All So now we're gonna go into some

46:49 these other modes of control. We'll through a couple of we're gonna do

46:53 two before we go. Ok, we'll leave those other two. So

46:58 you got here um, we're gonna unit four Thursday. Ok. We're

47:05 finish up 10, we're gonna finish these two Thursday and then go into

47:10 23. So the unit four stuff all open, all available.

47:16 you know, do, do look , at at least the first part

47:19 chapter 23 Look at that. Can go before Thursday? So, all

47:24 . So these four mechanisms and, your book goes to a lot

47:28 OK. We don't have the time do all, all of them,

47:30 course, but I picked a few kind of represent some differences from what

47:35 seen with the, with the lack trip opera. Um The first one

47:39 is also a transcription control and it of ties into what we saw with

47:46 the, the adjacent Trip Coones and stalling of the live zone stringent

47:52 Uh First, I just wanted to you, right, these levels of

47:56 control, right? DNA, we'll this as an example. This is

48:00 the second one today. The phase is an example of, of DNA

48:05 of control um transcription, right? transcription, right. Uh So

48:13 your post transcription is the main And are you somehow affecting its

48:19 OK. Translational control is about the , right? Um posttranslational protein.

48:27 . Um All right. So we'll at an example of, we've already

48:32 a number of examples of that. look at one of these. Uh

48:37 see, we're not looking at one those, we're looking at a translational

48:41 . So I think those three, think the, I think one of

48:44 anyway, so let's start with stringent . OK. So as mentioned,

48:50 ? The in the trip attenuation one of them was if the ribosome

48:57 two trip codons, right? And you don't have a, you don't

49:01 , you don't have charged T R phones, it stalls. This is

49:05 of the control mechanism for that. aside from that, right, if

49:10 , if a cell is in a condition, right, um then you

49:14 have multiple vital on multiple amino acid operant rather. And that collectively leads

49:24 a condition that is this stringent So obviously in that condition,

49:30 it's obviously under stress, right? now's the time to go into survival

49:36 , right? And to do to do activities that don't waste energy

49:42 much that can serve. And so gonna shut down a lot of

49:46 OK? And so a ribo zone kind of stalling zones are stalling,

49:51 doing so because they're starved, There's, there's not enough nutrients coming

49:55 the cell. And so you have chromosome associated protein called L A,

50:03 ? It hangs around with um the proteins as part of the rhizome.

50:09 . So when they stall, it of triggers the function of that enzyme

50:16 is to produce this tetro phospho guanine using these two substrates A T P

50:24 G T P. OK. This a signaling molecule much like um such

50:30 P can be that way. So is this OK. And it acts

50:36 primarily on opera and you uh rival R N A S and transfer

50:44 So the goal here is to kind really back down curtail ribosome synthesis because

50:53 having lots around means you, you it for lots of lots of protein

50:56 . So cells are actively growing mid cells right? Growing like crazy,

51:02 gonna be full of ribosome because there's high demand for protein synthesis to sustain

51:07 level of growth, right? But of a sudden now they starve,

51:12 ? You, you don't want to doing that, you wanna shut that

51:15 off, right? And that's what signal molecule helps do. It interacts

51:20 . Um it actually interacts with, even know this, but it interacts

51:23 the uh uh beta subunit N A . And that actually um makes it

51:33 able to interact with these promoters for T R N A s and not

51:38 R N A OPERON. OK? again, it's about conserving energy.

51:43 don't have the same demand for protein . If you're starving as you

51:47 if you have lots of nutrients. it's a way to kind of uh

51:51 a survival, uh hopefully, uh its standpoint, uh there's an influx

51:56 nutrients to overcome this. But, know, until then you're gonna have

51:59 , uh you have to conserve. it's kind of a response like

52:03 But it's all, it's all triggered this is triggered by this stalling at

52:09 , at these total. OK. , because we're affecting transcription and it's

52:16 transcription control mechanism. OK. So um that's what we'll talk about today

52:25 the DNA itself as a way to expression. Manipulate DNA. Fact,

52:32 is something that's a phenomenon, the variation of lots of patterns,

52:39 Um We're gonna look at salmonella, causes foodborne illness. Um uh which

52:48 you, you got vaccinated for um . So, my meningitis is one

52:52 can do this in syria, gonorrhea others. OK. Um Feature me

53:00 it enables a pathogen to become hidden one's immune system. OK. By

53:05 this effect, you can become hidden the immune system, which of course

53:08 a key. If you're a right, you try to do that

53:11 then you grow and inside the body cause disease, of course.

53:15 So this is one way to do . That's why they call it immune

53:19 . OK. So this is gonna to any kind of uh protein,

53:26 say usually protein could be glycoprotein that's be on the periphery somewhere because remember

53:31 talk more about this as we get you before your immune system has the

53:37 to see in air, quote, a pathogen. It can only be

53:43 what's on the outside, right? it something on the virus? It's

53:49 that's on the on the membrane of negative on the on the uh light

53:54 layer of a gram positive, These are the things that your body

53:58 because they're on the periphery, So things like LP S layer of

54:03 gram negative, right pia which can on, we gonna be on the

54:07 , right? Uh flagellum. So these are the things that your

54:12 system cells look for. OK. , and you can produce any response

54:17 them. So the pathogen that has has to hide, hide, you

54:22 the from the OK. So this , we're looking at the so semi

54:29 motile and obviously they have a And so the flagellum remember is produced

54:37 flag units monomers that come together in form of flagellum. And so this

54:43 has different uh two different types of , right? So the H actually

54:49 H here refers to through a call way back H antigen H and is

54:56 flagella, right? That's what they this H one H two. So

54:59 can have an H two flagellum made of this particular flagellum protein or an

55:04 one made up of the C type ? One or the other,

55:09 Not both. It has either one the other. OK. So in

55:13 here, here's the uh flagellum right? That makes H two and

55:21 the promoter, right, typical, setup, right, promoter rut

55:26 And it also has a regulatory gene here, R E G Right here

55:34 interacts with the other type of this the H1 type that makes here.

55:41 it blocks expression by sitting that repressor Right in that promoter. OK.

55:50 H one is not express only H . OK. And so um let

55:57 just get this out the way OK. So the repressor of F

56:04 uh called F L J A, guy, right shuts down expression of

56:09 other type of. So this, , this sound cell is only making

56:15 H two types of gel. So how does this mechanism work?

56:23 About once more than 1000, the is about one in 1000 1 in

56:30 . The it spontaneously recombines. So segment that recombines it's what's here.

56:39 . And so um part of it a promoter for H two,

56:46 So here's the H two promoter. , right there. And so it's

56:53 of the sequence in green that So what happens is it comes

56:57 So these uh this H I N this Recombinate type molecule that facilitates the

57:06 . OK. And so you see it basically inverts the sequence.

57:11 So the promoter, let me erase for a sec. The promoter is

57:15 this way as it should because that's the genes are at. Right

57:20 We're flipping it around. So you how owner has gone there.

57:29 Here is the gene that F L , right? This thing, same

57:42 . But now the promoters away, gone over here, right? Not

57:46 front of the G anymore. It be expressed, right? So you

57:50 express this, you don't make this now the H one but um it's

57:59 . OK. So in the salina , you OK. Um At that

58:07 I mentioned they can the next next can form this H1 type,

58:14 So now the body pips with these , OK. So the thing about

58:21 that, so say you get infected satin primarily with one type of the

58:27 . And some of those spontaneously change sequence, we come on and now

58:33 H1 forms and so subsequent generations of satin at the age one.

58:39 honest. Can't respond that quick, ? So yeah, if, if

58:46 seals with the H two, your can eventually detect it, right

58:52 But by that time, the next has formed the having the H one

58:57 , your body can't, your immune doesn't work that fast. So eventually

59:03 will. But by that time, may have, you know, penetrated

59:06 into your body proliferated right now. have full bone food born illness,

59:13 ? So, uh but that's so about buying time, right? It

59:18 make it completely invisible forever by doing , but it doesn't buy time.

59:22 know how fast bacteria can grow. don't need them for a few

59:25 right? They proliferate and invade and that's what enables them to avoid the

59:32 system, right? So it's uh do the same thing. We have

59:36 strategy of, of buying time as . So to speak, fever,

59:41 get a fever that can slow down pathogen growth, right? That buys

59:46 time, that buys you time for immune system to find it and catch

59:50 and find infection, right? So time thing works both ways.

59:55 So uh so this again just showing same kind of the same thing.

60:00 here's your focus on, on right? Here's the promoter for

60:05 for the H- two flagellum. And we get recombination like that,

60:11 So now is transferred over here and can't express that gene anymore.

60:20 So um OK, let's look at question. A any questions about

60:27 OK. Well, let's look at question first and then see if you

60:30 any questions. OK. So this a, let me pop this thing

60:37 , let me open that. So the yes or no question.

60:41 let me pause for a sec. we've got two salmonella. The uh

60:51 anyway, here's a gentle in blue one in red that H twos are

60:57 , H ones are blue. So a, so say you eat uh

61:02 , some food affected with salmonella. . And that food that you ingest

61:09 . Oh, stop, sorry. , has this, I assume it

61:14 what you see on that slide. has 10, 7 level H one

61:18 10, 72 P in right? it in your gut. Um So

61:27 the long run, uh is is, is what you ingest from

61:32 salmonella's viewpoint? Is that likely to out for it or is it,

61:37 is that a better, a better for you? Right. So will

61:41 strategy of the praise variation with the of the proteins work here? So

61:46 the, so the question to ask about from the perspective of the

61:50 is this the way to do it not? OK. So if you

61:55 yes, it'll work, then you , yes, that's the right

61:59 Some of them should do if you no, you go no, in

62:04 long run, that's not gonna work it. The, the human will

62:08 it. OK. Mhm A Counting . Yeah. OK. That's what

62:43 thought. So who picked? please take me out. Not gonna

62:55 you. Answer all the time. could no? Oh Mess up.

63:04 on. OK. Come on, be brave. I'll give you a

63:15 , you know, you picked All right. So why don't you

63:18 that? Uh, what you're Is it sex and corrupt?

63:34 So think that is playing poker. never play poker. Poker is all

63:43 . I guess any car going technically you have your, you have your

63:46 in front of you, you have hand cards in front of you,

63:49 ? You, when you're seeing you can have whatever strategy or

63:53 you know, it may work. what if you just show your cards

63:55 everybody? Is that a good No, because essentially if H1 and

64:01 is all it has, it's showing all the parts, right? So

64:07 they're both present in equal numbers, body is on the same time frame

64:11 it'll be able to detect both those attack and goodbye. Right. Better

64:17 come in as mostly just one type switch later on in the body,

64:24 ? That's a more effective strategy because not my time. So that's typically

64:29 it works because they're, they're at early stage of infection, there's a

64:33 stage and that's when salmonella can penetrate in the body and it was

64:38 bad stuff happens. So, so to do, but just, you

64:42 , whenever there can be nice, can have five or six or seven

64:47 options that can switch between them. best strategy is to grow mostly as

64:52 type then switch to another type. questions? So we're gonna end it

64:59 a little early and see you all Thursday.

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