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00:03 mm hmm. Yeah. Mhm. . Okay folks. Uh Welcome.

00:45 see um mm hmm. So this we get another, so this week

00:55 a unit quiz is do, so a time, there was a little

00:59 comprehensive um It will cover most of three. Um Up through whatever we

01:09 to on Wednesday. Okay. Um week, of course is the

01:14 the 14th 15th. Um Smart work . Uh Chapter 92 on Sunday then

01:21 couple of days later at 10. . And what else thought? So

01:26 other thing is um um I posted midterm grade. So if you saw

01:33 email, explain if you haven't take look at the email explains, you

01:38 how it's basically just just look look page eight of the syllabus. I

01:42 that exactly. Okay, um the grade is um because we don't have

01:53 we have a good number of sessions at the end I I didn't take

01:57 time to kind of Ephesus and things that because I just wanted to get

02:00 post it so you can see It's not that big a deal is

02:03 gonna be that different. Remember the points are only worth 5% of the

02:07 . Great. So um so the grade, you'll see it is a

02:11 good estimate. So whether it's one one point plus or minus not a

02:16 deal. Ok, so umm But , uh so it covers quicker points

02:22 to the 23rd Exam one and 2 up through 14.2. So all of

02:29 unit two homeworks um And um let's all the quizzes of course. So

02:37 to quiz Five and unit quiz So again I'll explain the syllabus in

02:42 email I sent out earlier. Um take a look at it. You

02:46 have so that the droplets until the so you will have a third exam

02:51 add to that. Okay? Um you're wondering about whether you're dropping out

02:58 whatever drop it, you'll have one exam to put in there, okay

03:03 add to it. And I do in the syllabus as well, how

03:08 you figure it? Right, it's simple. Okay I just you just

03:11 to remember that you're not dividing by , right because you don't have all

03:15 grades yet, you still have two exams. So after the third exam

03:20 so the exams are 16.25% each. you're just gonna keep adding that to

03:25 you're gonna divide by a total of think it's for for the by the

03:31 exam it's like a total of 83 something I forget but that's what you

03:36 by. So just again look at email, I explained all of it

03:41 there. Okay so anyways you'll have information uh to use in making a

03:46 if you even need to make a . Okay. Um The other thing

03:52 depending on where you're at The because now as of this this midterm

03:58 it's you know it's uh 3035% of grade is the homeworks and the clickers

04:04 you know all the non exam And so we've taken two exams.

04:09 it's roughly about 33%. Now is 35%. Yeah so it's balanced out

04:16 ? So very quickly this is going go up right? So the exams

04:19 going to take more weight as we forward. Okay so that means that

04:26 great can dramatically change from what from it is now. Okay. Just

04:31 that in mind. Um So but keep maximizing the points on this.

04:37 side. Okay. But certainly if need to improve the dance floor as

04:43 go forward. Okay. Um Alright you're helping any of it. And

04:49 officers email me let me know. . Um All right so today we're

04:55 finish up nine, a couple of left to do there and then uh

05:01 in chapter 10, get through a chunk of that I think. Um

05:07 And so let's uh start here just kind of review. Just the kind

05:13 the stuff we talked about. Um time. So we uh started we

05:22 Chapter eight and then went into Chapter . So it kind of back up

05:26 a second. So nine is um at mechanisms um gene transfer in

05:35 So bacteria can't sexually produce how they variation, Right being types of reproduce

05:42 binary fission basically a xerox machine. have mutations of course arise but so

05:49 they can acquire new genes through these of horizontal gene transfer. Okay uh

05:57 congregation transaction transposition. All mechanisms by they can receive transfer genes with other

06:04 of the population. Ok. Generally related types can do this but so

06:11 can some farther away in terms of um types of things that transfer um

06:18 have a common function and of course transferring a few genes a pathway uh

06:24 this is occurring uh three combinations So uh the the franklin being idiots

06:31 in. Um If it is a fragment will need to be recombined with

06:37 genome right to make that a permanent fragments of DNA floating in a cell

06:43 not normal. And so a cell's think that's something that needs to be

06:46 care of and gotten rid of and is so it's a recombination is

06:51 Okay um so the uh uh So okay so we've gone through a

07:02 uh into conjugation I think we're almost but let's look at that. Okay

07:09 um okay so this begins with of parts to cells that are gonna come

07:18 what we call a donor and recipient don't containing the plasmid with the

07:23 Factor. Remember the f factor is the jeans products of those genes are

07:30 in the process of carrying out Okay. Sex pilots. These what

07:35 call transfer genes all a part of mechanism. And so um so the

07:41 minus cell. Uh so when and what you might call it basic F

07:48 uh if minus congregation the f minus will inherit. Of course this

07:57 Okay then the process becomes an Plus cell. Okay, you can

08:04 uh the not only the these genes the past but also the F.

08:09 which makes it transferable. Okay so F factor that makes it transferable,

08:14 that designate doesn't have plus but that it's transferable but it's also gonna have

08:21 can be many other types of genes here. Okay. Or not

08:26 But you know other types of genes antibiotic resistance genes and metabolic pathway.

08:30 have you write? The fact that also a plus means it can be

08:34 . Okay? Um Now integrating. the the external plasm like this can

08:42 integrate into the chromosome. Okay so your HFR strain. Okay. Um

08:47 then doing so makes the entire chromosome transferrable. Okay so uh but remember

08:55 this kind of conjugation that the f sell rarely if ever becomes F

09:02 Okay and um the uh transfer then much DNA is transferred from here depends

09:13 how long they're connected, right? long they are? Um So again

09:20 F. Plus factor is at the end, Right? It's the last

09:24 that we copied and transferred and because never never happens really, the f

09:30 stays as an f minus, but fine for it because it has inherited

09:35 number of genes here. Okay. um are acquired a number of genes

09:42 I just can't undergo congregation. But of course can pass them to

09:48 transmission. So the last thing we about was the F prime factor.

09:58 the point here is that the plasma integrated? Okay. To make the

10:02 can also come out. Okay, normally what comes out is what went

10:08 right shown in red here. so that can come out all right

10:15 become a plasma again. Okay. all right. And so but the

10:24 the F prime psych reforms when this is shifted to the left or right

10:32 . So not it's just so this not what's coming out, what's coming

10:39 or exercising is maybe like that. , so it's shifted right? And

10:48 , not a frequent occurrence happens every in a million times. Okay.

10:52 when it does it's it's it means it's now a part of this chromosome

10:57 gene here as part of the but then someone that's left behind.

11:02 ? So part goes with it and parts left behind just because of this

11:07 excision. And so and what can is the potentially a partial deployed can

11:17 . Okay. So when this congee with another cell maybe the same in

11:23 same population the same species then maybe that still requires an additional 18 in

11:31 example. So it has to write me a partial deployed. So uh

11:36 those are the kind of the the congregation we looked at any questions about

11:42 . Yeah so the congregation on the , what do we call that?

11:46 I know the middle ones HFR congregation is just uh I just referred to

11:54 an F plus f minus conjugation. if if it's if it's a question

11:59 specifically about HFR it will say HFR another thing on the list um it

12:06 me off for a second because HFR rarely becomes. Yeah I guess that's

12:14 yeah so it's integrated. It will be called H R recipients spell

12:21 It's yeah I would say it's it inherited. It has received a you

12:30 it's it's now this HFR cell is contains an F. Prime factor.

12:35 no longer an HFR because it's not anymore it's just called and uh okay

12:44 . Yeah. Right okay um I a question. Okay so um Alright

12:54 transactions transaction involves the virus viruses to between carrying the segment of DNA from

13:02 cell to another. Okay so equate with so the two types of generalized

13:08 and specialized. So since we've gone viruses already a quick correlate um generalized

13:18 to elliptic fage. Okay correlate specialized to the Lissa genic land of

13:27 Okay so that's gonna be the difference . So generalized transaction. Uh so

13:33 have a favor infecting a cell. what happens is a an error in

13:40 the packaging occurs. And so not in some cases it's viral DNA package

13:45 host DNA is packaged. Remember that DNA in the process of bladder infection

13:51 get uh digested. Right? So see the fragments here. And so

13:58 of these gets packaged into the viral . Okay and so now that stage

14:05 will still have the parts of the right? That it will be able

14:12 infect the cell. Okay so it go infect the cell once it's gone

14:16 the cycle here lights this cell. it comes out. Okay. And

14:21 infect another cell as we see Okay. And so but that's where

14:28 infection end because it won't go through life cycle because this is host

14:33 N. A. Okay right And so that DNA can potentially get

14:41 into uh this cell's chromosome right? you see right here. And so

14:50 but again that source comes from way here. So in this mechanism potentially

15:00 jean or genius can be transferred. because any one of these right can

15:10 come can be incorrectly packaged into the captions. Okay so theoretically any gene

15:18 be transferred this way. Okay so so that's generalized transaction. Okay again

15:27 of politics page in the process of infection during its life cycle and interrupted

15:33 host DNA. And then ends up the new cell. Okay um Now

15:39 transaction. Okay as the name implies um part of this lambda lice region

15:50 . Okay so remember the land of can integrated DNA into the host chromosome

15:57 that profit. Okay and that's what is really about. And so that

16:03 is very specific. Okay and it at this what's called these insertion

16:10 Okay um between the galactose and biotin . So galactose galactose utilization by attend

16:21 sentences of biotin. So here and . Okay and so um so that's

16:28 integrates always integrates in the E. chromosome. Right? So it's a

16:33 kind of a relationship between E. and this land of age. Okay

16:37 so it always integrated there. Now is gonna look very similar to the

16:42 . Prime formation. Okay because as know, lambda phase can also come

16:49 the chromosome right? So it can a profile page but then it can

16:53 out of that chromosome. Okay and when it does again not a rare

17:01 not frequent uh it'll it'll have it'll right when it comes out this is

17:08 what's exercising? Right? Just in purple purple is just the land of

17:13 . D. N. A. what happens is we shift one way

17:17 the other. Okay so in this we see that the galactose. So

17:23 is actually going with it. And so uh so here you see

17:32 june which is part of the you that chromosome is now sitting in the

17:35 . Right? All because of Ah off kilter um excision.

17:42 So um so that stage effects a host. Right? So that was

17:48 this galactose gene in its plasma or its genome and it affects another

17:54 Coli well then potentially that E coli will acquire a second galactose jean.

18:01 . Now with that can happen is partial deployed. Right? So it

18:05 not two copies of that gene. it can now that can other galactose

18:11 can evolve independently. Maybe gain a different function or what have you.

18:18 But uh but the only genes are here are restricted to just these few

18:27 here here. Maybe something that's on next to either side. That's that's

18:33 extent of what gets transferred by. means is theoretically any gene in that

18:39 that E. Coli can be transferred what's at the in the vicinity of

18:45 . Each end here in this area hmm. In this area or in

18:53 area. That's it. Right. specialist transaction. Okay. Um many

19:01 about that. Yeah. Mhm. how is normally supposed. Mm

19:08 This is what you just you should be here. Two here.

19:17 just a purple this example when the of what should be coming out.

19:21 the excision itself is not the It's what's being put into the

19:27 But but that only occurs because the excision. That's right. So instead

19:32 cutting instead of was being cutting here cutting here, it's like cutting here

19:39 cutting on the other side of the . G Okay, so let's let

19:44 erase all this here. So instead our scissors doing that and that

19:52 It's doing mm hmm. Uh see up, Montana's doing like this and

20:00 . Okay. Sure. Okay. a recombination event. It's it's doing

20:10 what you see right there and then cuts. Right. Right. So

20:17 kind of an odd recombination excision Okay. Again, not a not

20:22 common thing at all. It's a event. Um Any other questions?

20:33 , so the last one here is is transposition. So the transpose sins

20:47 I think, you know, almost they're widespread in almost every organism I

20:54 . And they normally reside in the um within cells within the crow

21:04 And when they're copied or they move , they stay within moved to different

21:10 of the chromosome. Okay. Um can though among bacteria, there are

21:17 types of transposing means carrying certain antibiotic genes that are transferred uh to other

21:25 . Okay. And there's a couple ways that that can happen.

21:29 Now in the process of of transposed copying itself and moving this is what

21:35 call transposition. Okay. And so transpose are gonna be very basic,

21:41 can just consist of what's called the is gene which is basically the part

21:46 allows it to exercise and and and certain elsewhere. Um and then these

21:53 sequences on either end. Okay. and so what we call insertions.

21:59 really an insertion sequence is the most transpose on, right uh continue only

22:08 the transpose a gene. And these of sequences you see here which are

22:12 similar to what you see in the enzymes. Right? They those kind

22:18 enzymes recognize these inverted repeats. So they have uh for example,

22:25 A A T C G A And then on this side it's like

22:31 reversed or inverted. Okay, that's of these kind of sequences. And

22:35 the law often have a staggered kind a cut. Like this generating uh

22:42 we call sticky ends. Oftentimes. And so you see it occurring there

22:48 then um the two Types of movements might say, or what we call

22:57 the word document terms cut and paste copy and paste. Okay, so

23:01 replicated is basically just cut itself out insert elsewhere replicated is here's a

23:07 I'll make a copy and then we'll this will stay here. This one

23:11 here. Okay. Um now as mentioned, these are these are found

23:18 all life forms. Um They there they were often called jumping genes

23:26 some cases um They can be more than just being an assertion sequence.

23:33 can be they can have a transposed plus other genes. Okay. They

23:39 to call those complex transpose seasons. they have antibiotic resistance gene one or

23:45 of those or other genes. Um now these things aren't constantly jumping

23:51 our chromosomes. Okay. Because if did that was probably very detrimental.

23:56 there are mechanisms that um kind of this jumping around. Okay. But

24:05 can um Okay. They may have to do with regulation where they jump

24:11 certain areas that are growing regulatory I'm not well versed in transposing means

24:16 in myself. But nonetheless I do do know there are some types that

24:21 carry antibiotic resistance. Okay. And the for the bacteria then to transfer

24:29 to another cell. Okay. Can a couple of mechanisms. One so

24:34 call conjugated transpose season. So they'll the genes to carry out congregation.

24:41 . And so it's kind of a of how this might happen. And

24:45 here's a donor uh self containing a on uh many with the recipients

24:52 Again, because it has those conjugated . It will have the sex pilots

24:58 be able to carry out those that of the conjugation process. So it's

25:03 a combination of transposition and conjugation in way. Okay. And so once

25:09 connection between the soldiers made, then transpose on exercises. Okay. But

25:16 the transposing itself cannot exist like Alright, This is just a temporary

25:21 where um the uh this will be and then go to, sorry,

25:30 to the next cell. Okay, it's doing this rolling circular application makes

25:35 copy and then once that's complete, goes back to integrating into the house

25:40 that's what transposed onto do. Same the recipient sell. Okay. And

25:47 we just transposed on now has ended in both cells is what we call

25:51 . They kind of have the parts congregate correct. Um Another way could

25:58 be which has been seen before is have a cell? Okay. That

26:06 its chromosome. Okay. To transpose . Okay, And TN it's kind

26:16 shorthand for a transpose on. So we have a sequence here and

26:20 that same cell has a plasma conjugated . And so called F.

26:25 Okay. And so it could be the transpose on um jumps or copies

26:34 or just cuts and jumps over into plasma. Okay, so now it's

26:39 here and that plans because it's enough . Can can mate with a

26:47 Meyers. Okay. And then this transferred. Rolling circle replication.

26:53 So here's the F Plus now and is the chromosome. And so um

27:06 the transpose on here. This jumps into the chrome zone. And so

27:11 we have it. Sorry. Like Okay, so again it's just mating

27:18 between the two selves inherits the F with the transpose on and jumps into

27:23 chromosome. That's that's that's been I'm not sure how prevalent that is

27:28 that has been seen. Okay. kind of hitchhiking along in the

27:33 Plus plasma. Okay. Um Any about that? Yeah. So 11

27:43 on is being put back. Mm mm hmm mm hmm. I think

27:50 like insertion insertion sequences will have certain . So this is like the sequence

27:56 . It will recognize the secrets like in the crow's own. There'll be

28:02 compatibility there. Yeah. Yeah. Alright. So those that those are

28:10 mechanisms mechanisms of horizontal gene transfer. , so again, one of more

28:15 in which can can acquire D. . A. Um for members of

28:21 population, right? Not to vertical transfer. The parent parent child,

28:25 say. Okay, but from other of the population um Alright, so

28:34 uh any questions. Okay, So flip to chapter 10. So um

28:42 here we go through a few questions center some discussion around the questions.

28:49 so in this uh check with 10 will cover over a couple of

28:54 Um Obviously the overriding theme here is controlling gene expression examples of how gene

29:02 is controlled. And the two we look at our lactose opera which

29:09 may have gone through at some at level and tryptophan operas. Okay.

29:16 so um uh both represent common types bacterial control genes. Um and then

29:28 next week we'll look at, well on Wednesday. Well look at um

29:37 little bit some different examples of some types of little control. Okay.

29:42 we'll spend a little time on both lack of chip opera. Okay,

29:45 there's gonna be some some so we're revisit kind of the operating structure again

29:50 well as um some terms we're gonna to go through. Okay, terms

29:55 use when talking about control of gene gene expression. Okay, so here's

30:01 first one kind of the kind of question, I'm sure. And so

30:09 let me get that going here. , so the the internal response turns

30:15 an output action by the cell. to the information and functioning. Of

30:21 ? Okay, so um this this be applied to any any cell and

30:28 our own cells in fact, um it's made using bacterial cells as an

30:34 here ourselves, respond typically to hormones and those hormones interact with ourselves to

30:44 them what to do um all based , you know, what's going on

30:49 . So what's going on inside the . Okay, so but there are

30:54 types of molecules that are does that the work ultimately. Okay. And

31:01 what's being referenced here. Okay. it is yeah, it's certainly it's

31:09 or protein. Some kind of protein gonna be the one to do the

31:14 generally. Okay. And um so can be things like looking at a

31:22 cell. So um what's the what's cells face out in nature of course

31:29 changes all kinds of changes, fluctuations nutrients, temperature changes, ph oxygen

31:36 , uh etcetera. Okay. And based first you have to be able

31:41 sense what's going on and so generally was some kind of a sensor

31:48 Okay, I will take that input do something with it. Okay.

31:55 they're doing something with, it is gonna be let's turn a gene or

32:00 on. Okay. And that will to formation of a protein and that's

32:06 does the actual work catalyzing enzyme reaction what have you. Okay, so

32:12 all about controlling then uh at least bacterial operations but controlling these in different

32:22 . Uh So they only express genes needed at any given time.

32:28 There are some genes that are always for the most part because of course

32:33 going to be critical functions that always to be on. Okay. But

32:37 many functions they don't have to be only and only when required or

32:41 Okay, lactose opera is one of you don't need to have a lactose

32:46 and functioning, expressing anything unless lactose present. Okay um and so many

32:53 kind of fall in that category. so control is very important.

32:58 I know I carpet this a Is that um you can't see that

33:03 takes energy really right to think about little bit but to to um uh

33:10 to make proteins takes energy right? to to to carry out transcription to

33:15 an RNA molecule that takes energy. all takes energy and so necessary to

33:23 control the processor and not waste the needlessly. Okay so um so here's

33:30 question. So this kind of relates the next topic which is about um

33:37 of control in a way. this is why it helps to um

33:44 of a decent grasp of just the of of DNA RNA protein.

33:51 We talked about that before about the of information. Right? And uh

33:57 it's through those different levels or layers we controlled we can control this expression

34:05 it can be controlled at multiple Okay. At the same time in

34:12 effort to really tightly controlled things. . And of course there's terminology to

34:21 these things. Okay, so here tryptophan opera expression can be controlled by

34:29 tryptophan itself inhibiting one of the enzymes for its synthesis. Okay, this

34:35 a kind of a feedback control Okay so um so that will be

34:48 so c is the consensus be Okay this goes into I will answer the

34:55 here in the next slide. so if tryptophan itself is inhibiting one

35:00 the enzymes. Right, So enzymes proteins. Right, so we're inhibiting

35:05 protein responsible for synthesis. Okay. so let's look on this slide

35:10 Okay, so here are the different of of expression. Right, so

35:18 start with D. N. Okay. Um and we can control

35:23 can't actually control gene expression for some at the level of DNA right there

35:28 the very beginning. Okay, so can modify nuclear times that can alter

35:34 uh in humans and other animals. uh beyond animals is epigenetic is kind

35:41 that realm of modifying nuclear tides and can influence gene expression. Um We'll

35:48 at a process called phase variation. . Very common among many pathogen types

35:56 they can actually take a segment of . N. A. Okay.

36:01 again using recombination. Alright, um we combine it in a different

36:09 And then that alters expression as So anything having to do with just

36:14 DNA like that, that's um that be a level of control transcription.

36:21 . That that's often is can be for folks um in terms of

36:28 Right, so transcription control itself is you going to allow an examination to

36:37 a transcript or not? So transcription is not about having the transcript already

36:46 . It's about is it going to made or not? Okay so there

36:49 are of course influencing the RNA Okay. And that has to do

36:55 promote ministering with its ability to get the promoter. Okay to transcribe.

37:02 so that's where the operator sequence comes that we'll talk about. Okay we've

37:06 before and so a regulatory protein and often are involved and you know either

37:12 that or not allowing it to Okay now a term that's not your

37:17 not just kind of added it here post transcription control. Okay so that

37:23 deal with. Okay we've got the formed transcript now. Okay so it's

37:29 made. Right so now we're beyond of control because we've made the transcript

37:35 . And so post transcription control can interfering with the stability of the

37:40 D. Um R. N. . Um I mean they already have

37:46 fairly short lifetime in bacteria anyway. can be it makes me slightly more

37:53 . Maybe a little bit longer lasting even shorter by manipulating the transcript.

37:59 You can then doing to translational And so that of course is about

38:07 right zone. Right you can let ribs and translate their what have you

38:11 . So there's ways that that can blocked. Um and then and so

38:17 of you know realistically All three of . Okay. Could fit under this

38:26 of post transcription all it's kind of more all encompassing term and all three

38:32 these can fit underneath there. So . Post translational. Post translational is

38:37 the answer to the previous question. . So um the tryptophan can act

38:42 the enzyme that inhibits the synthesis. ? So it's it's basically affecting a

38:48 . Right? That's then altering Okay. And that would be post

38:54 . Okay, so um so again it at here. Right. Anything

39:03 that is post translational translational. You're in the process of translating right into

39:09 protein. Haven't gotten there yet. once you have you know post translational

39:14 you've got your protein and you can very common is to add a phosphate

39:19 of protein sometimes that can activate Sometimes that can inactivate. It

39:24 So um or you can just simply the protein altogether and get rid of

39:29 . Any one of those modifiers So modifying altering any of these steps

39:36 here here here any of those will alter expression either for the better to

39:46 or to stop it. Okay. and all can be you know done

39:52 at the various times. It's not one thing happens, you know,

39:59 of these can happen at the same . Okay. Um again it's all

40:05 not necessarily always also in fact probably not. It's more often the case

40:14 it's it's a continuum. Okay, it's not necessarily all or nothing with

40:21 . Okay. It can be levels control or expression, Right? Can

40:26 low could be none of that could a lot. That can be somewhere

40:30 a continuum. Right? So don't think of this as well. It's

40:34 always just ever on or just It can be somewhere in between.

40:39 . All depends. Right. Because situation in and around cells can can

40:45 and can change, you know, then bury and so so too will

40:49 expression. Okay, um now constituents that does refer those types that are

41:01 expressed. So things like genes involved uh white collar assists uh cell

41:08 um protein synthesis components. These are that are being done in a

41:14 So generally the genes that code for things are always going to be

41:17 Okay, so these kind of critical . Okay, so we call those

41:23 of genes. Um Okay, so now gets into kind of the realm

41:31 different types of terminology we use. , and repressor um it can be

41:40 , it can be inactive. and that definition just the same.

41:46 matter what the control effect is. , whatever the conditions are that make

41:51 active or inactive, the definition of inactive, Professor is the same because

41:56 going to see that in the lactose situation um versus the trip depending on

42:03 situation that what when the Professor becomes , it occurs under very different conditions

42:11 those two systems. Okay. But what an active pressure means does not

42:16 . Okay, it still means the thing. Okay. Um and so

42:22 terms like um impression uh de repression um these all are things that you

42:34 to be properly. Okay. And it. Right. So you see

42:40 here you see de repressed. These all have specific meanings.

42:48 And they're used uh depending on what conditions are there bringing them out.

42:54 . Um so mm mm mm mm mm mm mm. Okay.

43:10 So um if you answered binds to operator, you are correct.

43:20 So the so an active repressor will promote transcription but will limit or block

43:32 . Okay. After Professor wouldn't require , inducers are required for inducing

43:38 Okay. Uh they wouldn't be allowing customers to carry out this function.

43:44 . De repressed means to be the of repressed. Okay, so an

43:49 repressor, we're buying to an operator in doing so basically limit the rights

43:56 transcribing. Okay. And so the under which it happens can vary.

44:02 . Um so uh so here's kind kind of a basic scenario of what

44:09 how these terms are used. so here we have a gene and

44:15 regulatory sequence that can code for regulatory that can be a what's called a

44:22 protein. Okay. And it will different interactions depending on the system.

44:30 , so induction de repression. That's we have expression. Right inducing

44:37 Uh if it's repressed not expressing it de repressed then you do have

44:42 Okay. Um and so a scenario that can happen is something like

44:47 So you see a repressor protein so can be in whatever the system is

44:54 Professor interacting with it. The pressure going to be in a either active

44:59 inactive state. So the question is makes it active or inactive.

45:06 So here in that scenario the that is the active form. Okay and

45:15 an active re pressure. Don't matter operation you're talking about the active repression

45:21 to an operator and stop expression. and that's what it's doing here.

45:26 when active form it's bound to the . Okay. Or regulatory sequences what

45:31 calling? Just kind of make it here. Okay, so it's bound

45:35 . Okay. And that's gonna block a plane. Right, right,

45:39 that's gonna be running primaries is going bind there's a promoter right upstream and

45:45 when they continue on and transcribe so gonna be blocked from doing that.

45:49 presence of an inducer. Okay, to the operator binds to the

45:55 Excuse me. And then that changes shape. Okay, so now it

46:01 bind the operator sequence or regulatory So now it's inactive. Okay,

46:07 by neighbors inducer and activate your pressure induces expression. Okay, that's essentially

46:15 a nutshell. This is the lactose control. Okay is just like this

46:27 the inducer is not lactose which you think it's actually a variation of it

46:34 alot lactose. Okay and when it's is present in the environment um it's

46:43 into the cell, converted some of converted to allow lactose. And that's

46:46 inducer that then turns on the whole toast pathway. Okay don't worry about

46:51 . Now we'll get to that Um Now the other scenario repression Covid

46:58 . Okay so we stop expressions. a co repressor acts with a repressor

47:06 . Okay and so an example of is here so here we have a

47:14 call the current pressure. Okay that the re pressure and that creates the

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

47:35 it's um inactivity through pressure. The scenario it activates the repressor. That's

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

47:53 . We'll get to that later. And so down here then we have

48:01 active complex where it binds the covid . Okay And so um inactive form

48:09 here. So when this leaves right molecule exits no longer bound to the

48:16 complex then it becomes inactivated. And you get you get expression in

48:24 form. Okay, you get gene there. Um but not when it's

48:32 active form. Okay, so the difference between active and inactive,

48:42 ? That those definitions don't change, matter what we're talking about, it's

48:46 what are the conditions that bringing about be very different. Check. So

48:52 and so this then is essentially the cent. Yeah. Mhm. This

49:03 actually the PRP is short for So that's the core pressure is actually

49:09 itself. So tractor fan has earlier mentioned can not only buying to the

49:18 , that's one of the enzymes that synthesizes it. Okay. And blocks

49:24 . It can also buy into a and stop it at the level of

49:28 . Right? So so to defend can't control its own synthesis here at

49:35 level of transcription and post translational. multiple, multiple um points of

49:44 Um and so uh it has to with the fact that trip to fans

49:48 amino acid and the operation for trip fancy makes synthesizers trip to France.

49:54 so it's important to me is obviously to make first. Right? So

50:00 has a multiple layers of control for reason and we'll we'll get into that

50:05 we talk about crypto fans pathway. . Um so all right. Any

50:13 so far? Yeah, this is in the pathway repressor protein stops the

50:19 from activating genes and correct Well, , it's the absence in the absence

50:28 inducer the oppressor is active And the penalty intercepts for the I would say

50:39 inducer does he intercepting? It's their not their pressure wants to wants to

50:47 . Right. So the only reason wouldn't be repressed, it would be

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

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

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

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

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

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

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

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

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

65:17 that unbind from the operator. So combined. Do it's late. So

65:26 see. Yeah. Yeah. So what that means. So their pressure

65:29 accurately come off primaries combined. And transcribe. Yeah that's the she is

65:36 excisions right? Uh Not really decision . It's kind of this those that

65:42 tremor is kind of because of tetra . It can span those two regions

65:48 . And bring that. That's those together. So you know the

65:53 N. A. Is kind of of folded up a little bit but

65:55 they're in proximity they can bring those two regions together in essence. This

66:01 is covering up the promoters inside there up. It's not exposed. So

66:08 why you can't get any expression going . Memories. Can't find does it

66:13 that so that it doesn't have to itself. Probably. Yeah probably.

66:19 um so let's look at this um . This kind of relates to what

66:27 do you have to do? What's next layer here? Oops. Sorry

66:37 that. Okay. Okay so high expression. Our transcriptome. Sorry high

66:49 transcription. Black operation requires all of . Except what if something else comes

66:57 play here has a big influence on and expression. Yes. Sure.

67:23 . Mhm. See Yeah if you . See correct. Okay so cyclic

67:53 . And uh this crp and she'd together. Okay. Work together.

68:02 So you do need the absence. glucose is the it's kind of the

68:05 influencer here. Okay um glucose is preferred easiest. This number of steps

68:16 get to metabolites in terms of like and so aspirations um glucose completed to

68:23 its parts for related to glucose six . And off we go. Okay

68:28 mentioned, you know, lactose. split in two glucose and galactose.

68:35 galactose has to be go through a more steps. Things like other sugars

68:41 sucrose, graham knows you know all of sources, you know, these

68:47 all these are all taking a few steps in order to get into the

68:52 . Okay. Which means it's not efficient. So glucose is Number one

68:57 hierarchy. Okay. So if present will camp down the expression of these

69:05 sugar operations until it's used up, those other ones can be utilized.

69:12 ? And so that's what the glucose influences cyclic GMP levels. Okay,

69:20 let's look at that here. so for high level expression you need

69:27 the absence of for low amounts or absence of glucose. Okay. And

69:33 course need the presence of black clothes . Okay. And so second KMp

69:38 acts as kind of the signal for . Um So it's levels fluctuate with

69:46 levels. Okay. Um generally um there's you don't need to know this

69:53 there's a kind of the A. . P. Http ratio. And

70:03 Is kind of the marker of the state of the cell. Okay,

70:09 normal healthy cell has a ratio of two of about 1.5. Okay,

70:14 that becomes less than that, then kind of a signal for the cell

70:19 I need to you know, we to start a tab metabolizing getting making

70:22 more energy here and glucose has an on that number. Okay. Um

70:30 so if glucose levels are low where not really around, it's not really

70:35 then this can trigger the formation of like electric A. Mp. Because

70:39 all kind of part of the same passwords, right? They're all related

70:44 each other. Second A M P D P A M P cyclic

70:48 Uh So when this kind of energy occur, it's kind of sensed in

70:53 way. Okay, So when witnesses second mp levels are actually low.

71:00 . And so the second game is because it combines with the crp

71:08 Right? These former complex. And that complex is what that complex

71:17 what binds. Right? And then will create high level expression.

71:24 so again activator complex forms and that expression binding to the promoter.

71:32 And so um that will greatly increase . So without you know that part

71:39 it, without the activity you get get really low expression. So you

71:42 need to have that as part of process. So again glucose because glucose

71:47 kind of controlling this to a We call it the tablet repression.

71:52 ? So things like black holes and sugars, you know things like that

71:56 be cantab molecules that can be metabolized on metabolites. Okay, so glucose

72:04 kind of affecting the expression of these metabolites. Hence repressing them.

72:09 So until glucose goes away right then other pathways won't be used. And

72:17 if you have glucose and glucose together the medium you see that effect.

72:22 , so here is um glucose and together in the same medium rights are

72:31 growth. And so here because is . So we have initially um low

72:40 kmp brought by higher. Okay, mps, glucose goes away.

72:49 so it shifts that way and then promotes the in this case the expression

72:55 the lactose opera as we go And of course there's a plateau right

73:00 . Right, as we're switching to expression of this other operations, a

73:06 bit of a delay until it begins kick in. Okay, now,

73:10 the molecular level. Okay, friends glucose serves to kind of inhibit that

73:17 from coming in. Um they call inducer exclusion. Lactose technically isn't the

73:23 but it prevents black from coming in this mechanism. We saw this one

73:29 about how glucose gets transported in the . Right? So glucose out here

73:35 modified to glucose six phosphate. And because molecules diffuse independent of each

73:42 , it will keep coming in, , Because it keeps getting modified.

73:46 . And so but it does so being phosphoric acid and it involves these

73:51 here. Okay. And so when is not this guy, the a

74:01 is not foss for that, it with black white. So basically blocks

74:08 of from coming to the south um lactose is absent, of course then

74:16 nothing to phosphor link. So it on to that group. Okay.

74:21 in that state it can't interfere with the lack Y permeates. So lactose

74:27 . Okay so um so what you for a high level expression we need

74:34 black opera, you need lactose you need glucose absent or certainly at

74:41 levels. Um And that of course That scenario, promotes low, I'm

74:49 . Hi 2nd MP. Okay. it promotes a a an inactive

74:59 Think of all the components here. . Um And uh so then you

75:06 to keep that straight in the context a black opera because when we talk

75:08 the trip to fend opera on, changes. Right? So you want

75:12 be able to convert between these two compare and contrast the two systems.

75:18 . Um Any questions about that. , so we'll look at them.

75:24 a couple of animations that that go to glucose, lactose, opteron chaperon

75:31 . Look at those. They they a great deal in looking at those

75:35 and we'll talk about it next to at it next time as well

75:38 The banks will see you all next .

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