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00:01 here we go. It's actually Alright folks welcome. Looks like we

00:26 a a smaller crowd I guess that's be expected day before the exam.

00:34 I'm sure the absentees are diligently studying ? Yes. Ah It's not supposed

00:42 say what uh Probably. Let's Um. Oh yeah. Right.

00:51 quiz. Yeah, that's wrong. . You're right. Uh Okay.

01:00 should be friday through monday. okay. Um Yeah the other

01:08 Right. Okay, correct. Thanks that. So the exam to

01:14 we're going to finish up 21 22 7878 is relatively short. So those

01:22 no means that especially chapter eight, very tiny part of that. Chapter

01:29 . Uh This is kind of some this is probably gonna be review.

01:33 hope for you seven and eight. talked about ah cocoa wrote genomes,

01:42 structure. We begin with the old of information just to kind of get

01:52 get our heads back into that uh that again. Okay. As we

01:56 out of metabolism to degree um I that's everything. So uh here's what

02:05 covered last time except for this is last bit is just mentioning that

02:12 So um the natural cycle or triangle you want to look at it.

02:19 started with a little bit about pretty like wastewater treatment and how environmentally influx

02:28 nutrients can affect probably populations which can you can have an impact on marine

02:37 and do those processes of eutrophication. The reduction of B. O.

02:45 . But then the loss of auction the water to impact marine life.

02:50 uh wastewater treatment and kind of threw . Remember the main things about that

02:58 um microbes are the ones that are the work really of knocking down the

03:04 organic materials and wastewater um promote um activity we're promoting aerobic aerobic hetero trophy

03:15 The by mixing getting oxygen in their promoting respiration to knock down the

03:24 O. D. The organic And then but then the other part

03:28 that is um you want that activity occur obviously but the material coming out

03:36 ? The water coming out of your should be clean drinking water obviously.

03:43 . Right? So we need to these microbes settled. So settling is

03:48 big part of the wastewater treatment before discharge because themselves themselves are bot okay

03:56 we need to make sure they settle . That's what that clarify was all

04:00 . And that's where flagellation right? get those filament types are growing and

04:05 kind of they form this matrix. And so you get a balance of

04:10 types and zones which you can eat swimming types of microbes bacteria. And

04:17 you have settling of this material right have a clear as clear as you

04:23 effluent coming out that you can then . Right? So the end product

04:27 a waste water treatment system and it's course um that can be used for

04:31 water. It was cleaned up enough it can also just be a company

04:36 is has their own treatment process going to get rid of any kind of

04:44 materials in their stream and then to in the nearby river or lake or

04:49 have you. But obviously that discharge be relatively clean. Um All right

04:58 we went to nitrogen cycle and the aspects of that fixation, the notification

05:04 the petrification process is so each side the triangle there and then we're gonna

05:10 with a process this one here Um there was a recent but let's say

05:19 the last 15 years or so it's evident that that process is one that

05:25 actually very significant. Especially in marine . Okay. And so the amount

05:32 photosynthesis occurring in marine environments is Okay. You think of the oceans

05:39 other bodies of water on earth. this process is one that um returns

05:47 to the atmosphere. So it's not not um you don't before these guys

05:55 discovered it was thought the notification is nitrogen that's how nitrogen gets back into

05:59 environment in the atmosphere. Okay. of the animus reaction and those bacteria

06:06 then subsequent seeing that these things are in many different environments. Right?

06:14 that activity is actually very significant. . And let's just flip here.

06:18 what accounts for the majority in marine is 50% of uh into return to

06:29 environment. I mean to the Sorry, the atmosphere so half

06:34 If nitrogen is lost in marine As into through this reaction.

06:39 So just for compared to purposes so reaction is the oxidation of ammonia.

06:48 . And aerobically using night trite. ? That gets reduced ultimately to

06:55 Okay. And in the process of is oxidized. Okay, so just

07:00 comparative purposes, we saw this one in Nitra fication. Right? So

07:05 is oxidized aerobically. Okay. Okay. Oh to reduced water.

07:14 And then ammonia oxidized to nitrite. right. One half of the night

07:20 find reactions. The other one is nitrite to nitrate. But just just

07:24 , just compared to purposes. So money oxidation here with these bacteria

07:29 for a production of this little Right? Using it to break down

07:35 and get energy from it producing it oxidizing it tonight. Right. The

07:39 reaction is also an oxidation of Okay. Um but it is a

07:48 aerobic process. So we're using nitrite terminal except er respiration. Okay,

07:54 anaerobic respiration oxidation of ammonia to end . Okay so again this is obviously

08:01 different process from notification. So this going of course result into the

08:08 So it's not it's not lumped into identification. Okay. Um It's it's

08:17 a it's like a another type of to get rid of nitrate from the

08:24 . They just don't they don't put into the identification category, but it

08:29 is one of the counts for a of nitrogen loss. Okay, so

08:33 , oxidation of pneumonia, anaerobic oxidation produce and to and so these cell

08:43 are actually very they're they're bacterial, are a type of bacteria. He's

08:49 my seeds. Okay. Very Um Typically just spherical cells. Um

08:57 they are gram negative but they have of a weird envelope in many

09:03 And the ones that carry out this have actually specialized structures which are the

09:08 blobs here inside the cell that they an um an amok zones structures that

09:17 specifically carrying carrying out this reaction and find these things are widespread throughout the

09:25 interacting with algae and sponges and things that in the environment. So fairly

09:32 . Um But again, this this for a significant amount of end to

09:37 returned to the atmosphere. So I that closes out, I'm sorry,

09:47 out What we're gonna talk about in of 21, So that's that's

09:52 Okay, so again, um this not on the exam tomorrow.

09:57 so this is all stuff for three. Okay. Any questions before

10:03 . Okay, so as we get just talking about aspects of bacterial genetics

10:11 in terms of precarious. I'm not we're not going through did a replication

10:18 all and all that that entails. , Your Okazaki fragments and leading and

10:23 strand and all the stuff you I'm assuming and buy a one.

10:28 not we're not doing all that. . We're not doing the whole here's

10:34 company synthesis occurs, right? Because assume you know that already.

10:38 um I'm just gonna kind of point some things that are specific to pro

10:43 that you may or may not be of in both of these processes.

10:47 , So, um but I do know to me this is one of

10:53 basic, I shouldn't say basic but of those things as a I know

10:59 not all bio majors, but it's of those things you should know.

11:02 shouldn't leave here not knowing what what flow of information. Right? And

11:07 that means. Okay, and be to explain it to somebody. Doesn't

11:11 to explain it to the degree but you should be able to know

11:15 as a bio person. Okay. like you should know the basics of

11:21 , right? You should know the of metabolism just went through.

11:26 so this is one of those. the first part is probably gonna be

11:30 bit of a review if not, it was forgotten some things and this

11:34 jog your memory. Okay, so one question is make sure this is

11:39 . Yeah, this is my favorite . I've had this. I used

11:41 teach intro bio and this always showed on the exam and it always got

11:47 a 50 50 response although I've changed modified it somewhat. So this will

11:53 you right away if you know the or not. Okay so the process

11:58 transcription and translation is carried out in test tube to the test tube.

12:05 adding stuff from three different animal Right? So from the hippo we

12:11 those three from the fish. We that from a zebra. We got

12:18 stuff. Okay so we're gonna pop into a test tube or flask and

12:24 gonna get some protein made. Some new protein will be made. Okay

12:29 the question is which from which animal is that protein being expressed? Okay

12:37 you've got different combination of answers Take a look see see what makes

13:05 . Mhm. Okay counting down. here we go. 10 9.

13:59 I predict 2/3 will answer correctly. see. Okay I was even

14:11 Alright. Um Alright so we got studying to do on transcription translation.

14:21 . Um You do I don't Okay I when you assume the obvious choice

14:30 everybody picked was be fish you see . N. A. Right?

14:38 So of course it's remembering this Right that so any D.

14:44 A. In there will certainly be translated into protein? So the fish

14:49 will show up. The other one shows up is why the hippo.

14:58 . Yeah so yeah it's the hippo it's deep hippo and fish.

15:04 So we got that and we had . So M. R.

15:10 A. Can ribosomes from the hippo T. R. N.

15:16 S from the hippo. Canned ribosomes plop on the amarna and translate.

15:21 . As they can with the N. A. Okay. So

15:24 we have RNA polymerase. Right? this one goes there to make an

15:33 . RNA and then blah blah And then these involved in their right

15:42 make that. But then also of they can eventually you'll make that from

15:47 . N. A. All there'll fish Amarna. Right. Anyway,

15:51 get the point I'll go through this . I got enough space.

15:54 so hip on fish. Right. the old flow of information um same

16:01 all living things uh depending on if call this a living thing or

16:07 the one exception to this is what what doesn't follow DNA RNA protein.

16:18 virus retroviruses. Right. Retroviruses don't that order. But aside from

16:25 as far as I know everything else . So here's another question again,

16:29 is just for the purposes of terminology kind of how stuff works.

16:34 So we have a certain bacteria found been found that a region of the

16:40 designated X. Comprises a specific sequence . N. A. This sequence

16:46 only be converted into protein can be into protein only when cells are grown

16:51 galactose as a sole carbon source. the flying statements is false regarding this

16:58 . So it was kind of again different way to have you think about

17:05 process and the terminology we use and . Okay. Oh let me open

17:13 . Okay. So the X. is not revealed when cells are grown

17:20 glucose as a carbon source. Um conversion of the DNA sequence into a

17:27 requires a bribe requires ribosomes. Um . Is a gene. Um The

17:39 stage in converting DNA sequence requires synthesizing an RNA copy of the X

17:46 . Just looking for the false See just Amanda eventually requires five.

18:56 . Yeah I pretty much just gave away and everything anyway. Okay.

19:06 . So you didn't I put an word in number and be the conversion

19:10 D. N. A. Sequence a protein eventually requires. Okay.

19:16 . With the false statements. All right, so I got some

19:31 to do. Alright. The Type is not revealed. Well that's

19:36 much says here you have to go on glucose. Okay, so I'm

19:41 galactose. Thank you. Um So phenotype. Right, that term.

19:51 um the phenotype is typically revealed through functioning of one or more of these

20:05 . They have proteins. The proteins those jeans. Okay. Right so

20:12 protein can be an enzyme and then enzyme or enzymes maybe I to ferment

20:18 and then that shows up as a a as a phenotype. Okay,

20:25 conversion of the DNA sequence of the requires Robertson's. Yeah, that's the

20:29 know, it requires it in uh here. Right. Protein. That's

20:40 my ribosomes are needed is at that of the process. Okay. Uh

20:45 first stage X. Is a Well, yeah X is a

20:48 Okay. Um the first stage in the DNA sequence into a protein requires

20:56 , synthesizing RNA copy of the X . That's our. Does that?

21:02 right, so we're talking about this of the process. So that part

21:08 RNA polymerase. Okay. Not So the is the false statement.

21:20 . Um No, that's for Not this. Um Any questions anybody

21:29 I'm insane for picking be Okay. Yeah. Yeah. So yeah.

21:42 you carry out that process occurs Alright, so again, this is

21:52 you've obviously heard these terms genotype and . So that's just kind of to

21:58 just help you re remember these. , so, so here I'm showing

22:04 an E coli here's a blow up micro micro micro graph of an E

22:09 . Okay, so we inoculate lactose we collect and ferment lactose. So

22:15 is one that can't so we see visual visual obviously fermentation. This is

22:21 ph change occurs acidity uh die turns yellowish color. Okay, so of

22:28 there's a phenotype we can see the has this feature being able to ferment

22:34 . Right? So um you can get individual on the plate.

22:39 This could be your in lab. used McConaughey's auger. And so that

22:46 ones would be lactose fermenters. so again another visual. So we're

22:52 taught when you first hear phenotype that see characteristics, you can see observable

23:00 . Right? But remember that it's they're not all necessarily be observable.

23:06 got lots of stuff going on inside body. That's you know, part

23:09 your phenotype that you can't see. but it's the expression of those genes

23:16 proteins that generates the phenotype. so again another type of phenotype.

23:23 ability to um lice blood cells Okay. And so again, one

23:30 of one or more proteins is gives the phenotype. Okay, so um

23:38 of course phenotype and genotype. You if you look at DNA RNA protein

23:43 is of course D. N. . Right? And we convert that

23:46 proteins to give us a phenotype. so one last kind of example here

23:51 kind of tie it together. I . So this is basically a rapid

23:57 kind of test if you're a lab you're doing the unknown. If you

24:02 this you would be done with the project in probably two days. So

24:08 allows you to inoculate a number of at one time and you can test

24:14 of different sugars like a rabbit knows blah blah blah. You have the

24:19 . R. V. P. for that is the VP your real

24:24 assist etcetera. So different compartments. . So what you actually do is

24:33 you need to know this but here a covering. And you can take

24:37 covering off. There's a needle, a there's a wire loop that goes

24:40 the whole thing and you take the off and it reveals a wire

24:45 You flame you touch a colony with . Then you take that loop through

24:50 the compartments and inoculates them all at time. Okay. And incubate.

24:55 . They look for different color Uh So this one we're focusing just

25:00 one test. Right? You re test. Right? So positive test

25:03 is a pink color like that. . So so what does that actually

25:10 ? Right. So that's the phenotype this one. Is your area or

25:14 ea says the enzyme positive. So it's has that enzyme. It

25:21 potentially do this reaction. Okay. is this right here. Right,

25:26 it's a metallic sis to form 02 and ammonium. This is

25:30 Of course it's a color changes based the basic ph occurring. Okay.

25:36 so does that relate to in terms its genome. Okay well that obviously

25:40 has a gene that codes for this in this chromosome uh in order to

25:49 it useful so to speak. We right on your primaries. Transcribe produce

25:55 protein messenger RNA A. Right. so this is our our copy of

26:03 gene. So we make RNA copies genes. So think of the chromosome

26:08 your your book on reserve in the . Right? You can't take it

26:12 you. It's a permanent fixture Right? But if you if you

26:17 um if you want to get information it, you can pick the pages

26:22 want in xerox in right? So of the pages as the genes of

26:26 chromosome. Then you can make copies copies of your M RNA.

26:32 So so again the genome is the fixture. Right? You can make

26:38 of different genes as you see fit produce the transcript. So these are

26:45 of the messenger RNA as the working of your genes. Okay. The

26:51 you actually do stuff with. And these become translated through ribosomes and TR

26:56 A. S to produce a Okay. Probably peptide that then of

27:04 in this case is the enzyme. , so um a big part of

27:13 uh that um it's super important is control element. The control element is

27:21 to the whole process because I've mentioned probably several times a semester. Um

27:27 you can't see from a textbook or diagram is the amount of energy this

27:33 . Right remember we're building something. ? Anabel is um we're making a

27:39 amino acids. It takes a lot energy to do that. This is

27:43 energy requiring process from making the memories making the probably pep type.

27:50 So um it's not a trivial thing express the gene. Okay. So

27:57 important in only expressing genes that are . Right. And there's different categories

28:03 those in terms of importance. You have a set of genes that are

28:10 pretty much on. All right. are gonna be for your critical type

28:13 . There are gonna be many genes are only off and on or on

28:18 different times. Right. And so environmental conditions dictate that which ones are

28:24 or off. Okay. Um Our okay respond to very specific chemical signals

28:34 out by our body typically through hormones the like Okay um and ourselves um

28:43 they have the right receptor for they'll take the signal and then do

28:49 activity like this to produce a specific typically. Okay, that's with ourselves

28:54 to. Right. Are these body ? We put out three home runs

28:59 bacteria um take their cues from what's on in the environment and they can

29:05 various things. Okay, both external . Right. The point now is

29:10 we'll talk about control later. But point now is that you know control

29:14 a big part of this always Okay. And so um and so

29:20 the basics of transcription translation. Uh here is our template DNA. Remember

29:29 sense antisense thing. Right. We about that in the context of

29:33 Right so um the the transcription begins a copy of the anti sense or

29:44 strand. Okay I have explained this on the next slide so just hold

29:48 a second. And so here's our here. Okay both the D.

29:54 . A. And the M. . I. Have elements of uh

30:03 enabled it to be worked on so speak. So the D.

30:08 A. Of course has the um gene has a promoter. Okay so

30:15 are set up in front of Okay these are what guide the RNA

30:20 to the appropriate sites in front of gene. Okay so there's gonna be

30:25 in the D. N. That our regulatory that are a

30:31 That's a constant. Okay um the . RNA will have elements um remember

30:38 start coding stop code in the code in between. Right? The arriba

30:43 binding site. Right so it's gonna these elements that enable it to be

30:50 usable. Okay. Uh And so remember with precarious we have this feature

30:59 being the poly ribose. Um Right you can have multiple as soon as

31:03 ribosome binding site appears. Right, can begin to plop down. Right

31:13 the party. Right I don't think . Multiple time zones can attach to

31:16 transcript and proteins can be synthesized from of those. Okay. Um and

31:23 of course remember this is that's possible there is no separation process. There's

31:28 there's no translation occurs in the Like in ourselves and transcription transcription of

31:34 translation outside. That's how it occurs eukaryotic cells, bacteria don't have that

31:39 division. Okay so basically happens almost . Okay So then of course with

31:46 code on remember that there are there's code book to decipher that. Right

31:54 we have a start code on then count 123. Right? Until we

31:58 to a stop code on. And uh ribosomes are what recognized code ons

32:06 bring the right, you know, to the party. And ribosomes are

32:09 of the the the books typically called Workbench brings everything together at the

32:17 I mean the M. R. . A bound to that site for

32:22 come and attach so all of Okay and and the result, of

32:27 the poly peptide. Okay. Um let's just refigure all through this

32:34 a sense antisense thing. Okay so again as I said and we talked

32:41 viruses RNA viruses. Right, These simply the rules. I'm gonna click

32:48 . Right? So it can be D. N. A.

32:49 N. A. It could be RNA. It can be RNA

32:52 It follows the same terminology. There's sense and antisense strand or plus a

33:00 strand. Okay, coding template all all these alright. Are

33:07 coding plus sense. Antisense template minus all synonymous. Okay, so for

33:14 . N. A. Or we the anti sense strand, That one

33:19 the template. And in doing so basically making right an identical copy.

33:29 the scent strength. Okay, so is a sense strand. If it

33:35 that it's a minus, then the is a plus, which is what

33:41 M. RNA represents. Okay. so if we look line up our

33:48 , right? So here is N. A. Very top

33:53 N. A. At the very right there the same everywhere, there's

33:56 G. C. A. Same in the M. R. Right

34:04 where there's a T. Right? a year or so? All

34:07 so except for that, you it's it's an identical copy of

34:11 N. A. Okay, which makes sense. Right. If

34:16 . N. A. Is the strand containing the coding information that's ultimately

34:21 you want to get a copy Okay. And so that's what the

34:24 . RNA represents. Okay. So then of course, you know,

34:31 you jesus start code on and so . Right? So um since anti

34:38 um now let's look at this Okay, which are these terms includes

34:49 of the others? Uh have you of all of these? Maybe except

34:58 couple which includes all the others mm . So which is the looking for

35:33 one that's all encompassing all encompassing. . Hmm. It's your I might

36:00 it. Okay, counting down 21 . Okay. Uh Yeah. If

36:19 answer genome you are correct. Yeah. Uh Yeah. Wrong.

36:33 answer the right. Good. Um Megillah is probably something you may

36:38 have heard of that's particular to We'll talk about that in a

36:43 So that's and that are specific to genomes. Okay. Um The smallest

36:52 here is the gene. Okay. so let's um so we're gonna go

36:58 precarious genomes and then I'm gonna show only for comparative purposes the eukaryotic

37:07 Um but I'm not going to be you on the particulars of that but

37:12 see what I mean here in a . Okay, so genome transcriptome

37:16 Right. So there is a and called that was gently lISZT to release

37:23 chromosome and uh it may have in to that one or more smaller

37:32 Right? Plasmids. Right. Like . And so that if present also

37:39 part of the chromosome. Okay. genome in us is basically all of

37:44 46 chromosomes that's in our cell. course damage have half that amount.

37:50 in the bacterial cell it's um obviously chromosome but it can also be these

37:56 elements called plasma. It's okay. Transcriptome is the number of transcripts of

38:03 RNA. So it's basically you we're talking here. D.

38:05 A. You can guess R. . A protein. Right. So

38:14 whereas the genome is the permanent Alright. So it's not going to

38:20 in terms of abundance. Okay. the amounts in terms of your transcription

38:25 program can change and fluctuate. R N A. M RNA transcripts

38:32 and go okay um particularly precarious lifetimes RNA molecules are not long. We're

38:39 on the order of minutes. Um Which is fine because you'll just

38:44 more if we need it. proteins uh have a finite finite life

38:50 well. So but again you can produce more through transcription translation.

38:57 so of course it's control gene control will manage all this. Okay,

39:06 in terms of average numbers, in of pro Cariou genomes um E coli

39:12 actually on the upper end about 66 seven million base pairs. Um The

39:20 ones are like we talked about those don't have a cell wall. Michael

39:25 are kind of on that smaller end 500,000. Um And as mentioned they

39:31 possess one or more of these extra elements plasmas. Okay, so um

39:41 organization. All right, so here's I'm going to show you just for

39:46 to purposes the eukaryotic system. so again, in both types you're

39:50 have what are called structural genes. are genes that code for proteins that

39:57 some function. Right. Whether part the metabolic pathway or what have

40:01 Okay, you also have genes that control. Okay. Some of these

40:08 code for anything. They're just a that a protein binds to that then

40:15 expression in some way. Okay. do have you can have genes that

40:20 code for proteins that call for an molecule. Okay. Um but most

40:26 code for proteins. The operation and . So that's that's a feature of

40:33 genomes. The regulation and operation. . A system. So that's kind

40:38 an older name for a gene. you can see it in the context

40:42 mono sis tronic is one gene party Tronic multiple genes. A constant is

40:51 this in terms of gene structure. matter what you're talking about what life

40:57 you're talking about. You're talking about . There's a promoter is a part

41:02 your promoter and you get a gene now. Other things may vary

41:06 but you're always gonna have that. , and so again, the promoter

41:11 important for bringing the primaries to the of that gene. Okay, so

41:20 , I'm not gonna test you on periodic gene structure but just as a

41:25 to show you. Okay, so more complex, there's a lot of

41:31 processing that goes on with you carry genes. Okay, so control again

41:39 , it's gonna be a common feature all genes. And so you're going

41:41 have elements that are very close to promoter uh called proximal elements that can

41:49 far away. Thousands of bases Okay. But these are these will

41:55 how much expression occurs. Okay. but then beyond that in terms of

42:01 internal parts of the gene, It's organized into coding sequences, exxons

42:08 non coding and non coding sequences in . Okay. And then you have

42:14 elements here, what's called a sequence that is translated into part of the

42:22 M. RNA. Okay, so transcription. Okay, we initially bring

42:29 uh this part here from the promoter the start of transcription. Right?

42:35 is basically right here. So this is what is transcribed. Okay.

42:43 all of its transcribed initially. So call the primary transcript. And the

42:47 step we'll get rid of the Okay, so this in itself is

42:53 a translatable transcript. It has to processed into this right where we take

43:01 the entrance, this is what's called . Okay. And so and so

43:06 you're seeing here on the screen is in the nucleus. Okay, so

43:11 transcription and the processing. Okay then have elements of the cap and the

43:18 . These are because remember these have exit the nucleus and the cap and

43:24 helped facilitate that. Um they also facilitate this. The stability of the

43:30 . Any transcripts lacking one or both these cap and tail are pretty much

43:37 fairly quickly. So the cap and enhance stability of transcripts. And eukaryotes

43:44 can last longer in some cases for types of transcripts that can last for

43:51 weeks or months. Okay. Um any case so now this is what

43:57 call mature M. R. A. That's something that can be

44:01 exit and outside the nucleus in the . L. Patrick particular um uh

44:09 in the site is all these will translated. Okay so so you don't

44:15 any of this in bacteria. Either the structure of Exxon in tron

44:23 splicing or any of this stuff. so bacteria have their own unique kind

44:28 system. Now some there are some carry outs that have some instances where

44:35 of their genes are dealt in this . Right. Because we know previously

44:40 archaea do have some features common to that bacteria don't. Right so there

44:46 some similarities for some archaea jeans. but for the most part archaea also

44:52 the same structure as bacteria and that's we're going to look at here.

44:58 so this is the operation structure. . In a nutshell, what it

45:03 means is most appropriate genes are organized that fashion. Okay you do have

45:09 that have the one promoter. One that produces the mono sis tronic

45:17 Okay but most have kind of the you're gonna see here. So it's

45:21 promoter. Um with two or more following it. Okay so multiple genes

45:31 to a single promoter. Okay. you see here in this example,

45:36 again, the promoter is where is a recognizes the promoter binds to it

45:44 it up in front of the gene then you get transcription and the whole

45:49 is transcribed policies, tronic messages, continuous message. Okay, so it

45:57 mean that in that single message, , you have start, stop,

46:07 , stop. So the elements of are there for each one,

46:13 Start, stop. So each start stop coordinates for each gene in that

46:22 . Okay, so it kind of where one gene begins and ends,

46:27 one gene ends, the next one . Okay, so you see

46:31 Okay, so um so that's the part, translation of course will then

46:38 to production of the proteins for each those genes. And it's very typical

46:44 these are part of the same metabolic . Okay, so something like whatever

46:50 look at this in control, uh opera an opera on each of those

46:58 have different metabolisms but they lead to production of a protein. Okay.

47:05 so um so uh the control Okay, so the opera itself is

47:12 you see here. Okay, promoter structural genes. That's the opera.

47:18 , regulatory elements which may be up are not considered part of the

47:23 Okay, so when you see this these two lines, that just means

47:30 there's separation between these two parts. can be way upstream. Okay.

47:36 be hundreds of bases thousands of bases . Okay. And that's where you'll

47:42 very typically regulatory elements. Okay, regulatory gene coding for regulatory protein that

47:50 common is to interact with an element the opera called an operator.

47:57 The operator is it is just a . So the promoter and operator don't

48:02 for anything. Okay. But they sequences recognized either by RNA polymerase promoter

48:10 regulatory proteins or different types if you're operator. Okay. And so by

48:15 here, we're basically physically blocking the of to get beyond there so it

48:23 do anything. Right in that in scenario. Okay, operator is bound

48:29 regulatory protein. So we're not gonna any transcription. Okay. So we're

48:34 controlling expression by doing this. now um the back up here.

48:42 as we go further along into next and talk about this, uh the

48:50 under which this kind of binding occurs different. Different, different environmental um

48:59 internal conditions can determine whether this is or not bound. Right, so

49:06 we get into what's called induce a operations, um repress herbal operations

49:12 Right, so it's all about what the conditions allowing this to happen or

49:16 happen. That's really the crux of . Okay. Um and there's different

49:21 of situations that will occur as we'll later. Okay, also you can

49:28 control through the end product of a . So this could be a control

49:38 that may interact with an enzyme appear block activity. Right? And then

49:46 don't express the protein. Okay. too is control. Right? Control

49:52 doesn't just have to be at N. A. It can be

49:58 in these steps. So control can to all these levels. That's really

50:05 if you're kind of not super confident your knowledge of transcription translation thing for

50:17 , it's that's why it's good to it because we get to controlling

50:21 We're controlling these aspects of transcription That's how we affect gene expression.

50:27 ? Um So what do you know nuts or bolts or the mechanics of

50:32 transcription translation works? No it in context of you know this is why

50:38 we're gonna control you can control it these different levels. Okay. Um

50:46 . See any questions about that? . Yeah. So basically this.

50:56 here. Yeah. Another. Um All right so the regular so

51:07 an opera on is this I just . Okay. And so of course

51:14 can have multiple of the you'll have of these across the chromosome in the

51:21 or archaea. Now if the opera are part of a a common um

51:34 process then they may be controlled Okay then you have what's called a

51:44 . Right So the best example here let me just let me start this

51:48 we'll talk about this at the But signal factors. Okay, so

51:53 just mentioned is binds to a It does so through the presence of

52:02 sigma factor. So sigma factors are of an RNA polymerase structure.

52:08 the sigma factor is actually a piece can kind of come off and

52:11 Okay. The simple fact is not in the actual synthesis of a

52:17 It's more about this is the way can find a promoter. So sigma

52:22 recognizes different promoter sequences. So its is to help the memories get the

52:28 because the sigma factor is the one can recognize the sequence. Okay,

52:34 sigma factors for that reason can be control element. Right? Because if

52:40 doesn't get if it doesn't recognize the or somehow affected to not be able

52:46 interact with the promoter there again you're expression. So sigma factors can be

52:51 point of control as well. Okay so you can control multiple operations

52:58 If they all share that same sigma control element. So you can kind

53:05 control them all together and you collectively all those coordinated co ordinate li controlled

53:14 a regular. Okay and so example is just think of of nitrogen regulation

53:23 there is such a thing as a regular. Okay, so think about

53:27 the ways nitrogen is used in a . Right? Um to make amino

53:33 to make nuclear tides Um uh There's other things it's used for as

53:40 Um So you have processes of nitrogen assimilation taking it in right.

53:48 Maybe it's got like maybe it's a fire and it's doing that reaction or

53:52 it's nitrogen fixation or what have Right. So the point is there's

53:57 roles for nitrogen and multiple metabolisms for . Yeah. Uh There are yeah

54:10 do see the side sigma factors but there's you might think there's a signal

54:16 for every promoter but there's not there's only about 10 or 12 or 88

54:22 10. 12 single factors totally. so um but yeah they do synthesize

54:29 and they will have certain of these controlled together because of that. They'll

54:36 those signal factors in common that are controlled. Studies shown that cells with

54:44 sigma factors are less. They don't more as many proteins. Yeah I'm

54:53 there's some mutants mutants that that they've that. Yeah that that that is

54:57 case. Yeah. Um So if look at nitrogen regularly on then we're

55:05 all hopes are controlling then all the involved in these various nitrogen metabolisms through

55:12 specific um signal factor. Okay. kind of allocate resources. Right,

55:19 comes if a self presented with some of nitrogen, maybe you can use

55:24 and do this or that with it on what it needs it for and

55:27 can control the operations involved in that that particular sigma factor, it's a

55:34 of efficiency, making it efficient and waste energy. Right? Because that's

55:39 really what control is all about is not let's not express everything that makes

55:44 sense only that's express what's needed and the right amounts that's more efficient.

55:51 . Um so one more So it regular. Okay. And we'll see

55:59 regular in the context of transformation that's up next week because transformation can be

56:06 through regular but any time you're involving or more operations that are controlling a

56:14 a common process, you can call irregular. Okay. Many questions about

56:22 . Another regular thing kind of be little confusing but it's just like you

56:26 have multiple genes under one promoter. an operation. You can have multiple

56:32 under the similar control. And that's regular. So it's a level the

56:37 of scope. Right? So if want to really break it down nuclear

56:43 . Right. Gene opteron, regular genome. Okay. We want to

56:51 it down in terms of scale. . Um I think I may have

56:56 one. that's right. Um plasmas. Alright. So plasmids Uh

57:08 originate in bacteria, you know, years ago when we discovered these

57:14 We've since taken them into the lab completely deconstructed them. Synthesize them,

57:20 them for our own purposes. So recall, you know, the techniques

57:25 genetic recombination and cloning genes and these of things all involved using plasmas very

57:31 for that purpose. Right? So that reason alone, we've deconstructed and

57:36 and have constructed these for our own . Okay. And we put different

57:41 in them too to fit our Okay. But the point is these

57:48 actually exist and come from bacteria. . And um we've just taken out

57:55 done our own things with them. of course in bacteria have them,

58:00 ? These are completely autonomous. That of can do their own thing to

58:04 degree and they don't. So the a bacterium typically undergoes replication when the

58:13 gets to a certain size. And then and then before it

58:18 Right? Of course the chromosome And he started so gets a

58:22 And so that's kind of cute for chromosome replication. The plasma doesn't have

58:27 follow those rules. The platform has own Remember that essential element for DNA

58:33 is that story sequence. Right. so because it has its own it

58:38 just replicate on its own. And so the copy number. So

58:44 number of plasmas Purcell can vary as . You have types are called low

58:48 number, plasmas types are called high number. Okay. High copy number

58:53 be 50 per cell. Low copy one or two per cell. Um

59:02 you can also integrate these things into chromosome. Okay, we'll see that

59:06 week. Um The the transferability. conjugation, conjugation. So it's come

59:17 and they transfer things like plasma. between them. So plasmas are obviously

59:24 in scope. They may be contained average. It can be of course

59:29 one gene. But they typically have 5 to 10 is the maybe the

59:34 count. Um I'd say 5 to bases. The average size. But

59:40 see some bigger some smaller um types plasma is based on kind of what

59:48 carrying. Okay, so our factors for resistance contain antibiotic resistance genes.

59:55 There's actually some of those in here recycling. That's tet tetracycline, resistance

60:02 . Okay. Um An example the plant carry will carry a pathway.

60:11 three or four genes. Maybe an on. Okay. For a certain

60:15 . Very common. We mentioned before aromatic metabolism, right? The three

60:21 four genes involved. And that can something that's passed through a plasma.

60:25 we call those cattle bolic plasma. The F factor is can be one

60:31 in addition two an R factor or catatonic pathway. So plans. We

60:38 have multiple things in it. theoretically. I mean you can certainly

60:42 a password to put the and put things in there if you wanted

60:45 But it can be but naturally korean can have multiple of these types of

60:50 in it. And so if it the f factor. That's what makes

60:55 transferable actually F factor will be a just for example, it would be

61:01 portion of class mid and that factor would contain genius specific for enabling it

61:13 conjugate and then pass to another Okay, we'll talk about that process

61:18 week. But if that's what that factor means F is for fertility.

61:24 . Makes it transferable. Um so little bit more replication.

61:32 So by direct remember that's how the replicates. Right. The plasmids can

61:36 that way as well. If the If the Passman is one that is

61:45 of being transferred as an F Okay then when undergoing that transfer it'll

61:57 a different mode of replication. I'll you what, I'll show you what

62:00 mean by that in a second. for bidirectional replication is what That's what

62:04 know. Right? So that's where strands come apart. Right? The

62:09 replication forks become a part of the . We make two copies.

62:14 So that's that's the one we're most with. So, the rolling circle

62:19 , that's typically what precedes the transfer . So two cells will come

62:26 One will will do the rolling circle with its plasma. Okay. And

62:32 does So by by making a So, nick basically means breaking the

62:38 bond within that um poly peptide Right, So you expose a three

62:46 hydroxy in. So, if you right, your replication, the DNA

62:53 looks for this and begins to extend that add nucleotides to that.

62:59 so creating that nick enables that to . And so it will then begin

63:07 synthesize using of course the template. template would be that inner circle,

63:16 ? So it will begin to use a template and copy copy it.

63:20 ? Then the copy would begin to the one with the five prime and

63:27 . And so that will become That's what you see happening here.

63:32 , That's the displaced strand coming off the other one is copying the

63:37 knocking it off. Okay, and it looks kind of that's why they

63:41 it a rolling circle. Right, the dark purple strand, the plus

63:46 here is what has displaced the other . And you see it over here

63:52 envision, you know, this is between there's a relationship between two

63:57 right? There's one here. one here. Okay. And so

64:05 rolling circle replication occurs, that displaced gets shoveled into the recipient.

64:11 so the recipient receives a copy of plasma. Okay, and can eventually

64:20 course take that single strand and copy and make a double stranded molecule.

64:26 , so basically I just showed you congregation. This is this is typically

64:32 rolling circle replication. Oh, doesn't have to be. But typically it's

64:37 you see when cells are coming together one is going to receive a

64:41 They do the rolling circle thing. . And so, um so that's

64:48 something you haven't you haven't seen this type of replication. Okay.

64:55 now uh many questions at that Yeah. Right. Yeah.

65:08 Right. Yes. Right. So gonna be that would involve um if

65:18 recall uh primers get involved in primary all that, that's what would happen

65:23 this, to this one over You have a primer coming in and

65:28 on and so forth. Okazaki, all that kind of stuff. Fun

65:31 . Yeah. Yeah. Right. . Right. All right. Um

65:37 so it can, in terms of orange, you don't even have an

65:40 that's specific for this type and one this type. Okay. It's often

65:46 a transfer or e it's what's used if they're gonna do the ruling circle

65:51 because they're coming together with another Okay. It was just no,

66:01 , there's two different stories within the of the bacteria. So depending on

66:05 it's going to it was transferable or , it may use that story to

66:10 their own circle thing. It may the other or if it's just in

66:14 and just replicating the cell is not any kind of congregation thing. So

66:19 of it as the as this one for this kind of process. Um

66:25 it the usual replication, it's going this congregation process. It may use

66:32 will use the transfer story, let's it that. We'll talk about this

66:36 week. But that's kind of that's what's going on here. Kind of

66:41 which mode of replication we're using are using this one? Because we're conjugating

66:45 the cell or are we not? . Just depends what's going on.

66:51 , um, in terms of the itself and holding on to the

66:57 that's another consideration. A plasma that's is being held onto by the

67:07 Okay, so, again, this back to the energy thing,

67:11 You're holding on to the to this and you're and it's copying it.

67:17 energy being used to copy this extra element. Right. And, you

67:23 , it was going to do There should be a a benefit for

67:28 to have that plasma or else Miles want to expend energy extra energy to

67:33 it. Okay, so that's where comes in. Right? So,

67:38 , very, you know, kind basic example, Let me just show

67:42 come back to this in a So, if you have you collide

67:47 , so that one on top has plasma Um, and it contains 10

67:53 . Okay. One of the bottom doesn't have a plan within its

67:59 Right? The s for sensitive. if you grow to different growth media

68:04 was recycling. Okay, then, , um this one grows because it

68:15 the resistance gene selected that selective pressure keep it if if you're growing it

68:21 tetro cycling. That is the selective . Okay. Um down here without

68:30 . Of course, this one no , right? It's lacking the um

68:37 gene of course, down here without cycling, it will grow. What

68:44 this 1? Of course? And grill, it doesn't matter. It's

68:51 there. So, but what can is okay if you keep this guy

69:00 that medium indefinitely and continue to transfer right? To know tetro cycling growth

69:10 over and over. It can lose plastic because it there's no need for

69:15 to hold on to it. That can happen after, I don't

69:19 , 10 transfers or something maybe, it can eventually lose it. Um

69:27 so, you know, having a pressure on it enables it to then

69:34 on to it. Okay. Because there's a use for it.

69:38 Um So the low versus high copy . Okay. So that can play

69:46 role in as well if you have high copy number plasmid, right?

69:53 even without selective pressure, right? gonna have a higher probability of hanging

69:58 because there's just more of them Right? So if it divides whether

70:03 that plane, that plane there's so in there that It'll it'll be passed

70:09 to the next generation because there's a in there. Okay. vs one

70:13 2 Maybe. Maybe not. So for sometimes to ensure inheritance of

70:22 plans mids, they have this system of like a quasi my topic spindle

70:30 . Okay. It's, it's not . It's just kind of, it

70:32 of looks like that. But what have are these proteins called par for

70:40 and they kind of form on each of the plans man here in here

70:49 then they extend so they're attached to copy and then they begin to plagiarize

70:55 go to opposite poles right in the divides. So kind of as a

71:00 to ensure that the daughter cells receive a copy of that plasma. So

71:05 do see that is kind of pseudo thing, but it ensures that inheritance

71:13 these plans to the next generation. . Um, let's see is

71:21 is okay. Oh, any We got one more thing to

71:28 So we'll just save that for Okay. So we'll see you next

71:37 . Good luck on the exam. being sarcastic when I say that being

71:45 . Good luck on the exam. . When they asked

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