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BIOL 2321_Microbiology for Science Majors - 2321_MW1130_3_28_23_Lecture
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00:03 I see. Right. Yeah, to folks. Welcome. Uh Been
00:28 of a been kind of a unsettling , I guess last week. Uh
00:34 think I was going back to pandemic being on remotely. But uh
00:42 uh I'm glad I'm back up So you are too. Um So
00:51 not gonna say anything about last Uh I, I honestly don't know
00:57 , you know about this. I , I, I know with the
00:59 but I mean, I don't know details and so it's not, I
01:02 even need to go there, but you, it affects people in different
01:06 , obviously. And so, you , I, I, and your
01:11 already reached out, I'm sure to provo et cetera. So with the
01:16 resources available. So certainly um if feel the need, definitely.
01:23 just talk to somebody reach out. . Um So uh let, let's
01:30 back in here uh this course. um April 19th, OK, I
01:37 that up there to remind myself and as well. So we've got um
01:44 the, the, the last day drop for the W 19th. So
01:48 gonna have another exam, right? exams, you're gonna have a third
01:56 to still evaluate. Ok. So exam, right? This a little
02:02 , a little bit just to touch what we did in the first
02:07 Um, but again, you're gonna three exams, you have, you
02:13 the three exam before the, drop date. Ok. So,
02:19 , if you are the first one and two scores have been not
02:24 good, maybe in your estimation kind ugly. Well, you know,
02:30 , you, you mean obviously you the option of just dropping out,
02:34 I would say just throw out whatever doing study wise and just try something
02:40 new because what have you got to ? Right. Worst case scenario just
02:44 the same grade like you did in exams 1 and 2. So if you're in
02:49 kind of group then to make this exam, the opportunity to say,
02:55 know, what the hell with I'm just gonna try something completely
02:59 And, um, because even if end up repeating a course, if
03:04 haven't figured that part out, it's gonna be the same thing over and
03:06 again, be a vicious cycle, ? And, um, so,
03:13 , you know, if, if wondering what to do, just come
03:16 office hours or arrange, if you make office hours, arranges a certain
03:21 . Ok. And not a Ok. So, um,
03:30 but that's, that's the approach I take it, you know, with
03:32 third exam you get, remember right? So, um take the
03:38 to use that as your shot to , OK, I'm gonna try
03:43 let me see if this works. . So, um, anyway,
03:51 , so what we're gonna do, we're in the middle of this section
03:54 relatively short compared to the others. three. So we are at the
04:00 of the day, we're pretty much through it, maybe even a little
04:04 more than that. So, uh the uh but we'll be in four
04:10 the exam. So at least to you some, some time there before
04:13 , before the third exam. So finish up next week, the next
04:19 . OK. Um And uh they the last section which is kind of
04:26 really on medical microbiology, clinical OK. Um The end of it
04:33 be learning different diseases. So, anyway, it's time, time enough
04:38 that. So the other thing is rapidly closing out at the end
04:41 It's uh you know, once we to April, it's not that long
04:45 we're through. So, um let's um so yeah, also arrange
04:53 me if you want to see your . Not a problem. OK.
04:56 uh we can make that happen. . Uh Any questions or anything,
05:03 one. OK. So um All . So let's look at a little
05:09 of a recap. OK. But some of the things we covered so
05:14 . So kind of uh put this into context. OK. So we're
05:19 at uh the first part, that 21, 22 was more kind of an extension
05:26 the unit two material all the So the most, most of the
05:31 here in this unit is really on of aspects of bacterial genetics.
05:36 So last time we looked at um pro structure, OK. I kind
05:44 view of the DNA on a protein flow of information. OK. Um
05:53 uh the, the universality of the of course is how, you know
05:57 living things. That's how the information processed. OK. Yes, there
06:02 be some differences, natural components carrying out somewhat but the process is pretty
06:07 the same. OK? Um the June structure, OK? You
06:15 here um the operon structure, they're efficient because that genes, uh most
06:24 the DNA does code for, for protein, protein genes. Um The
06:29 so the proteins in any, in of that, do the work
06:33 of what that organism is, various and so forth. OK. And
06:38 controlling it, controlling it is also . OK. And that's where uh
06:46 genes and their products, the operator in the period. We learn this
06:54 uh next time and next week uh the control them because that is equally
07:00 important. OK? Um You don't waste energy, you don't want to
07:05 time and energy on things you don't to have. And so being able
07:08 turn it on when you turn it , when you don't need it equally
07:12 . OK? And we'll delve into um next time and next week the
07:19 uh so in terms of the so here again, hopefully a review
07:24 or less of, of the process uh DNA R N A, the
07:30 . And again, I'm not gonna testing you on the fine details of
07:34 . It's more if you see the transcription translation, what's where's where's a
07:42 fit in the process? What it our front of gene, they're,
07:45 are transcribed. OK. Uh and or these are parts of translation.
07:52 uh not much more uh detailed in . OK. So, um because
07:59 is one of those things, everybody at least the science majors should know
08:04 how this operates. OK. Um so, of course, our focus
08:09 is more on pro and so the to them. OK. And so
08:16 is another thing we looked at. . And remember these are, are
08:23 outside the chromosome extrachromosomal. They are course, much less information.
08:29 But they can be transferred and we'll about that today. All right,
08:33 of genetic information on these plasmas of types. OK. This can carry
08:39 resistance, they can carry a metabolic on it. They can uh have
08:45 features and so they can be right? So that's kind of what
08:49 nine is about we'll talk about OK? So um in this mode
08:54 replication, right, this rolling circle you see here that, that we
08:59 in, in the transfer process. we that um and so we just
09:05 look at and actually what we're not covering this. So you gonna put
09:10 line through that. OK? But are co we did cover sigma
09:15 And so for any gene, So a gene is a unit in
09:20 chromosome. Um gene can be sometimes R N A may be the
09:26 but um um the promoter is right? It's what lines up the
09:31 plume right in front of that OK? And so here is,
09:36 , we talked about this last So the sema factor is a portion
09:41 that R N A P limra that a recognition of a promoter,
09:47 And so uh and it also can off, right? So it finds
09:53 guides the R A plumb race to site at the promoter in front of
09:56 gene then comes off and they can ahead and find another R N A
10:02 . OK. So um this is the transcriptions initiated the, so we
10:07 looked at so this term consensus, ? It's a sequence that you find
10:13 common to end number different promoters, ? So the minus 10 minus
10:19 And so it's that region right here the plume is, where the sigma
10:25 is looking for that, right? , and for most uh genes,
10:29 this sigma 70 is common to most as you see here. OK?
10:36 don't need to memorize the sequences you just, you know, you
10:40 need to do that. But uh in these, in these two regions
10:44 from the start site, which is here plus one. Um It's
10:51 it's common among uh lots of different . So the uh the lines of
10:59 allows for you to get transcription of that gene. And so um
11:06 this, we talked a little we ended last time with kind of
11:09 strong versus weak promoter equates to OK. And that's um just to
11:19 a little off. OK. So as we get into um regulation next
11:27 , maybe starting Thursday is um levels expression we call basal level.
11:37 Or maybe background level is the way look at it um below level.
11:42 ? Um Because if you have a , it can certainly bind to it
11:49 and begin to transfer, but generally the involvement of that alone does not
11:56 get you much expression. OK. so that's what we call it
12:02 So this is generally not a level will really do much for itself.
12:08 . So you have to other things to occur for it to like really
12:13 . And that's where things like control , transcription factors activate these types of
12:21 get involved in, in increasing OK. And so is the conditions
12:28 conditions that affect this? Ok. In you, it could be a
12:35 some type of growth factor because your starts dividing that sets into motion and
12:40 number of factors that enable uh to turned on to allow that to
12:46 So, you know, it, it varies. Um the, but
12:51 you do get these things expressed, you can get very high level.
12:56 what does that mean? Ok. , what that means is um lots
13:02 transcripts being formed which equates to then of transcripts being translated right into obviously
13:11 of protein. OK? And so level motion, it is minuscule.
13:18 ? Not much of anything, And so even within that tiny
13:23 you need to have a good amount , of protein product to for the
13:28 do meaningful expression. If you will meaningful um um expression of that
13:35 right? It's an enzyme or OK. So it's a, that's
13:40 control is all about is you may at this level and then how do
13:45 get it to that level? And things bring that about, right,
13:50 , right? Have lactose present, glucose absence actually. OK. That
13:56 you high level expression and it turns activators and other things, OK?
14:01 even if lactose is present and glucose , is uh also present, you
14:08 get the expression that either. So all very from the conditions the particular
14:13 responds to OK? Or in the of proo opera responds to. So
14:18 all about the promoter and control elements , that, that manipulate all
14:23 OK. So, uh and because it's not a trivial thing to
14:29 this, it takes a takes it is a positive delta gene
14:34 OK? It takes lots of And so, so it's aren't gonna
14:37 wasteful, right? Neither are So um and so, and,
14:43 of course, and you carry outs us, it's much more complicated,
14:48 ? Um You can even involve not multiple transcription factors and elements, but
14:55 involving this would actually be the DNA . OK? And it actually will
15:02 on itself when, when certain of molecules come together at the promoter that
15:08 bring about secondary threshold DNA loops over it really enhances expression. And so
15:13 that also means is is increasing, the affinity, right? Of that
15:22 for that promoter, right? The it binds through it, the more
15:27 you get, that's really what that's or how we get all these things
15:31 and why is everything happening? It's happening at the promoter, right?
15:36 so increase the of that promoter for race and then you'll get lots of
15:43 that, that's why if you're really doing that and you know, and
15:46 only relying on the kind of the itself to buy and nothing else is
15:52 that's usually gives you just low OK. So high level and low
15:57 expression, OK. Um All So this will kind of basically summarize
16:04 of this here, I think. , in terms of the bacterial structure
16:08 the gene, right? So, looking at those, remember the the
16:15 strings, right, the coating and template strand, right. So your
16:21 and minus, right. So uh promoter here, OK, minus 35
16:27 10 and their genes, right? operon container promoter and multiple genes associated
16:34 it. OK? And so um this and when it's transcribed, it's
16:40 transcribed, right? One message Polycystic is that old name for a
16:46 So all in the same one continuous of R N A OK M R
16:54 . And so each gene within that its own uh start and stop
17:02 that's for gene A start and stop gene B. And if there were
17:07 four or five other more genes in , then they also have their own
17:10 and stop. That's what determines, know, the the polypeptide. So
17:15 ribosomes, right? So this is right here, translations next,
17:24 So ribosomes also need things to be to recognize and then bind to the
17:31 , right? And that's where this Shindo Garno sequence comes in.
17:36 . And so that's what's shown right . OK. Small sequence. But
17:42 what bosoms recognize. All right. it allows them to bind to
17:47 Uh and they bind to the five end and they begin to translate in
17:50 direction. OK. And so they , um then of course, he
17:57 about here, it's gene a product then gene B product, right?
18:02 both of those and it could be , it could be multiple, average
18:06 of genes per operon 3-5 is typical. . Uh The point here is it's
18:13 one transcript I think is translated. . So um so, I
18:20 so don't, so things to right? Know what goes with
18:25 know, know what goes with right? And so um yeah,
18:30 I said, I can on all details of this but you know,
18:34 least have the basic understanding here. . Um Any questions about that,
18:42 . So let's look at this. yeah, information I heard about
18:46 right? So learned that a few . Um So once this, once
18:52 r on binding site, rum binds then goes right now it's free to
18:58 bound by other ribosome and it moves so it will keep happening. So
19:02 get multiple rhizomes on a transcript. . Um All translating and so lots
19:08 protein are made. Uh So let's at this question because this is one
19:12 had at the beginning right last time didn't get to it the second time
19:17 . So um so we look through points here real quick. Let me
19:23 this. Sorry. OK. And it so you can read.
20:11 Sure. OK. Let's count OK. Time out for 10, 98.
21:02 it to pause. OK. Here go. Let see. OK.
21:15 upper serves as a site for sigma binding. True folks would disagree with
21:26 . Anybody does, does the operator as a site for Sigma factor
21:30 This is the answer promoter, not operator. So, oh yeah.
21:41 . You have a promoter and you an operator, right? Operator.
21:44 haven't really talked about its function. gonna be involved in regulation.
21:49 Um Operon possesses multiple promoters. Um , it's, it's one OPERON,
21:56 mean, it's, it's one multiple genes. OK? So it
22:00 have multiple one. OK. Uh genes have a single operon cliff for
22:08 of same metabolic pass away. Um That's what makes it efficient.
22:18 all, you, you transcribe that , they're all part of the same
22:24 . So that makes more sense than have. Oh This one works
22:27 This one works there. You can control it, right. Um Similar
22:32 bind to the promoter sequence of right? So promoter is promoter is
22:40 and so it's gonna be plum bins you transcribe it into an R N
22:44 , OK. So D is the one here that fits a single operon
22:51 , right? With all the information the structural genes. That's essentially what
22:56 is. All right, that's what is. OK. Um Many questions
23:03 that. OK. So, so mean, promoter, operator,
23:09 translation of what fits, where does go? OK, Sigma Factor,
23:13 cetera. OK. So, um right. So let's look at gene
23:19 mechanism. So chapter nine. So the context for this chapter is so
23:27 pro Caros divide by binary big as all know. So you might get
23:35 that well there, but because of , then E coli should be all
23:43 same. All E coli can be genetically identical if that were the
23:47 right? But of course, you , that's not true, right?
23:52 E coli that causes disease and those don't, for example, OK.
23:58 So devil um Devolution 101, right? on the variation in the population,
24:09 ? If everybody is the same, you either all perish or survive the
24:15 , right? So uh if you're an environment that's very stable and not
24:23 at all that can work, but really not the case. OK?
24:30 it can be in certain words, ? But for most of us,
24:35 , populations have to be able to , right? Survive when things get
24:43 in some way or another, Climate change, right? Has caused
24:46 to occur in population. So, you can only hope to survive if
24:52 had a variation in populations because then subset of that population will presumably have
24:58 optimal combination of genius to enable survival reproduction. Right. That's what it's
25:02 about survive and reproduce, right. , what do bacteria do if all
25:08 can do is buy? Well, have one mechanism that we have as
25:13 , which is spontaneous mutations that A mistake is made. Their replication
25:19 get fixed and, and it can , right? Those generally they may
25:25 a benefit sometimes. OK. So have that but bacteria and a Kia
25:31 have the ability. So, excuse , also the ability to do this
25:36 ? Horizontal gene transfer, right? vertical gene transfer just think of that's
25:42 you acquired your genes, this vertical , parents reproduced uh genes inherited,
25:49 on to you. OK. That's happens in binary fission, right?
25:54 daughter cells are inheriting a copy of parental chromosome, right? If it's
26:01 we're talking about. So um uh that's what happens, you know,
26:08 binary fission. But um you do spontaneous mutation that can create some
26:14 Uh but you also have, they have the ability to do this right
26:17 pass genes between members of the population sometimes in different populations or other uh
26:26 the same species, maybe the E and the salmonella, for example.
26:30 . So that's, that's how big in which bacteria Akea generate variation in
26:36 population. OK. And so the we will look at, we'll look
26:42 , I think we'll get through these today. But transformation conjugation transduction
26:48 OK. And so uh so when look at this is uh the
26:55 not the, it's more blue, blue blob. OK. We call
26:59 pan genome. This is E OK. So we, we,
27:05 been studying E COLI for decades, ? We sequence sequence all kinds of
27:10 coli strains and we've come up with number of all genes we've seen in
27:16 coli. So that's what we call pan genome, right? 10,000, over 10,000 genes
27:25 that we've seen that are, we've in all E coli, OK?
27:29 , it doesn't mean that every, E coli is gonna have all of
27:33 , they'll have a set of OK? And so think of
27:37 think of it a gene pool, ? You're gonna have a, you
27:39 a portion of those genes in the pool. OK. So, uh
27:43 the average E coli in yellow, ? Has about 4800. OK?
27:51 those, you know, 10,000 plus so of those um 2000, what
27:59 call core genes. These are the function genes. Every E Cola has
28:05 have right, involved with DNA replication in certain metabolisms, psychosis.
28:14 uh um uh protein synthesis genes of these are all the things that all
28:20 gotta have. Right? Or I these are poor core genes.
28:26 So then what about on average these other genes? Right. If you
28:32 at K 12, which is like , a, a lab AAA harmless
28:38 K 12. Ok. Oh, step. The chipotle, um,
28:45 , food more important. Well, there's gonna be the difference between those
28:51 , right? Has got to be difference in genes as well, of
28:55 , right? Because there's genes that 0157 has that enable it to cause
29:01 . And of course, the K doesn't have this. OK. So
29:05 is how you get variations within the . OK? And so many of
29:12 genes, OK? We require through of these horizontal gene transfer mechanisms.
29:19 ? So we look at e coli , right? Most of it like
29:23 most procaryotes, mostly protein coding, ? You have some right that code
29:30 the end products R N A. ? Definitely regulation some of that for
29:37 . So that's things like an operative , for example. OK. But
29:42 look at the number here, almost quarter um of the genome acquired from
29:47 microbes. The question is how do find that out? How do you
29:50 with that? OK. I'm just give a real basic example here and
29:56 I'm not gonna test you, but to kind of show you how this
29:59 be OK. And so what we're about are what we call the core
30:03 flexible. So these flexible gene these are the types that can
30:07 you often see being transferred by one those methods. OK? Like antibiotic
30:12 will be in a flexible gene Ok. Um So generally, genes
30:19 that flexible pool are not absolutely necessary have for survival. OK? If
30:26 selective pressure is there to, to it, then, yeah.
30:31 But generally, again, cells are be wasteful. If they, they're
30:34 something they don't need, they generally to get rid of it.
30:39 Um But back to the question of do we know this, how you
30:45 that out? OK. But a way is to look at this parameter
30:52 percent G C. OK. Um your days because I know that the
31:02 C and A DNA, uh he's guy that figured out um that particular
31:11 . Um But uh it's also been uh to kind of as a taxonomic
31:17 kind of compare organisms. OK. not really anymore. But um it
31:24 at one time. And so um organisms have a particular percent G
31:29 We do too. I can't think the top of my head what it
31:31 . But E coli has a value like this. OK. So if
31:36 looking at a, a segment of genome, it should have that
31:43 Right. Again, you're looking at statistically significant numbers, right? You
31:50 come close to 50.8%. OK. telling you, OK. This is
31:55 coli sequence. OK? But then you, you do that, this
31:59 all on, on, on on a computer when you do kind
32:02 the work on the computer. But you go, you're, you're looking
32:06 a sequence and you come upon a , a pretty long segment where they're
32:14 in that range. OK? That's clue that, oh OK, this
32:19 probably a region that it, it through one of these mechanisms of gene
32:24 . OK. And so the 54.8 corresponds to a related species,
32:32 So you can hypothesize it maybe, , this definitely is something that likely
32:38 from something else, maybe that maybe something else. But that's how
32:44 can figure these things out. Because 2500 bases is the average size
32:50 a gene is about 1000 bases. that's significant when you see that this
32:57 for this entire sequence. Then of , right, afterwards, it goes
33:00 down to this value. So that's pretty good idea. But this is
33:03 acquired this way. OK. for e coli almost a quarter of
33:08 genome was, was, was acquired way. OK. So these sequences
33:16 are also, if they're, if part of a common function, which
33:20 typically are, this is what we and don't worry about writing this,
33:25 we're gonna see it on the next . That's what, that's what these
33:28 islands are. OK, genomic So you see that term, I
33:35 on the next slide or a couple slides, uh that's what these
33:39 So they're, they're regions of the believe to have been acquired through horizontal
33:44 transfer, the caring functions, you , not, not a lot,
33:49 you know, for a particular type of feature like say a virulence you
33:53 what are called S right? So means this, this will contain information
33:59 code for some kind of factor. . Um A or a pill or
34:05 I don't know. Um or it be another type of island, but
34:10 what that refers to when we when we get to there. That
34:13 what that's kind of what this OK. So um all right.
34:19 real quick, this is more just of a real quicky overview of each
34:23 , right? And so, and you can recognize it, right?
34:26 transformation probably in terms of how it are the most simplistic or they can
34:31 a little more complicated in terms of mechanism, but basically the uptake of
34:35 DNA. OK? From the of course, um conjugation that's cell
34:40 contact. So transformation doesn't require just a cell taking DNA in basically
34:46 Conjugation a little more complicated, You involve uh what are called recipient
34:51 donor cells coming together very specifically uh pilots and other components involved. But
34:58 know, you're transferring DNA, typically gonna be uh a plas is what's
35:05 here and they can be from the . It's really mostly just fragments that
35:09 out there, they're taken up. if it's conjugation, that's gonna be
35:12 plasma being from one cell to another virus. All right. That's,
35:19 the key is in identifying transform transduction the virus is the intermediate here.
35:26 . And so um the virus uh it packages its DNA, it accidentally
35:33 packages host fragments and then those are carried to another host. OK.
35:40 Transposition. Uh These are through um generally transposon jump around in the,
35:51 the, in the chromosome uh of cell in which it resolves, but
35:57 it can jump out of the cell other cells. And that's involves kind
36:03 a little bit of conjugation there as . But it's, it's a little
36:07 but we'll, we'll talk about but it is a way in which
36:09 antibiotic genes uh resistances are passed. . So basically the three most common
36:18 gonna be these top three. But it does happen with transmission as
36:23 . It just said you're gonna rank . And what probably happens more commonly
36:27 those top three. OK. Um right. So we'll go through in
36:33 little more detail on each, on one of these, OK. Uh
36:38 I mentioned a second ago, the the uh islands, right? So
36:44 are areas just move this out of way. These are areas in a
36:50 , right, that contain AAA segment DNA believed to have been acquired the
36:59 as it mentioned, right? I , it's categorized based on kind of
37:04 function, right. Pathogen is the uh symbiosis island. So we talked
37:10 earlier about um metro fixation, Nitrogen fixation is actually a property you
37:16 in widely different types of bacteria, ? And that's that would be a
37:21 that would have those genes in in genomic island. OK. Um cata
37:27 pathway, think of the a aromatic , aromatic compounds. That's often what
37:33 see in this form as well. . So um so again,
37:38 all these are again, are just in in, in the micro or
37:43 believed to been required of ho OK. And so um so one
37:51 thing before you went to these these different uh mechanisms, OK?
37:58 just the in, in general when is in a cell, OK.
38:04 from the problems, right? So , when extra DNA is called a
38:10 , what can happen to it? . Well, number one, especially
38:15 it's a fragment, right? A fragment that just enters the cell that
38:20 is an alarm bell for the for bacteria because it thinks it's a virus
38:27 . OK. So that's one if it's a plasma d a circular
38:32 of DNA, less likely to be . Right. And so it,
38:40 , but again, it depends but certainly many plasmids can coexist,
38:47 . In the fragments. On the hand, probably have, they have
38:51 less stability they have before they be . OK? Because again, so
38:58 , oh, this is, this something not right. And so it
39:02 use it as food, OK? can eat nucleic acids, that's organic
39:07 . That can be a food It can coexist certainly a plastic can
39:12 out here like this. Um But is often we're gonna see that you
39:21 it in transformation, you see it uh conjugation, you see it in
39:27 , you see it with all three those also transition, you see them
39:29 all four, you see a recombination simply a part of it.
39:35 It's a recombination right? That can a fragment a more a permanent part
39:42 that genome, right? So if recombines, then, then it then
39:48 part of that genome. And so how it can become part of
39:53 So transformation generally that frame when that in will have to recombine or otherwise
40:00 been away with OK. Um plasmas can go either way they can recombine
40:06 be part of the genome they come and be exist as a plasma.
40:11 It's a combination uh there's a multiple involved in this, but the er
40:18 A is the major one. And what it does, it actually uh
40:24 to the donor DNA. And then for, looks for homology with the
40:35 DNA. So there has to be , it can't be completely just
40:39 but it has to be a little of similar. It's all a T
40:43 C base pair is all right. we have a AAA level of that
40:49 the two. Then recombination can OK. And so um you see
40:57 , the um hybrid segment here now will have this will actually, this
41:02 cleave off here and now you'll have hybrid of the parental DNA if you
41:10 and the, and the donor. . So, um but it's
41:15 you know a a, you mistakes and the mu mutants and
41:20 maybe this is a maybe B gene mutated, right? It's not functional
41:25 it goes to recombination with another. a as a result of transformation or
41:31 , it requires new DNA. maybe now it gets a good copy
41:35 that gene and it can repair that now. So that's that, that
41:41 . OK. Um So the point is that recombination is pretty much gonna
41:45 a part of all four of these . OK. Um And, and
41:51 um in many cases, especially in is critical for this to be a
41:57 of it, permanent part of that . OK. So, um so
42:03 we look at transformation, let's look this question first. All right.
42:08 this is, you know, with section, it is kind of one
42:10 the things to, to know is ? What identifies each for each one
42:17 these four mechanisms? What do you to each of these? So you
42:23 what it is? OK. I said transformation compared to the other
42:53 is probably the most basic in many . OK. Counting down.
43:20 Yeah, it's gonna be so cell contact that's conjugation for immediate transduction,
43:27 , pilus, conjugation, plasmid, . But yeah, you need fragments
43:32 the environment for sure. OK. is transposition. So um now having
43:39 said it's kind of the most well, it's all relative. So
43:43 look at gram positive versus gram there can be some differences there.
43:49 ? And in fact, in a positive, it can be a little
43:52 complicated. OK. So um so compare both those. So the gram
44:00 positive. So it's tied to this of sentence bio formation. So this
44:09 is all about um cell density, ? Get to a certain cell
44:15 then things begin to happen. Similarly, for grand positives and how
44:20 conjugate I'm sorry, transform. So uh this thing called a transformer
44:29 , OK. Uh trans locus, hear that term as well. The
44:33 thing, I mean the same thing . And so it becomes actually a
44:39 process in the ground positive to do . OK. Um I'm guessing because
44:45 have the cell wall, a thick wall that covers their, their uh
44:51 , that it has to be kind this way. The gram negatives with
44:55 outer membrane don't, don't have the complication. Uh They can actually take
45:00 up using pie a pill, a . OK. But so with,
45:06 know, with the grand positives, term competence, right? If the
45:09 is competent, it's not ready to up, right? If it's not
45:15 it won't. So it has to to that stage and being competent.
45:19 . Um The uh and there's competence that enable that as we'll see.
45:25 the type a type four pilot is specialized pilot. So there's a sex
45:29 is a specialized type, type four another one so that it can extend
45:34 then bin DNA and then take it . So by comparison, it's a
45:38 more simple mechanism that we will see the gram positive. OK. And
45:45 um just to mention this here, this, of course, if
45:50 if a bacterium can take this up part of its functioning, we call
45:55 natural transformation, right? It does on its own um artificial transformation was
46:03 because we use transformation in the lab it's all a part of the competent
46:09 technology. I use plasmids to put in, right? Then if you
46:14 make that copies of the plants so can make a cell that we have
46:17 show them into the cell and the that's, that's transformation. We're trying
46:23 shove DNA into a cell, We wanna make it, take it
46:27 so we can then copy it. transformation. But it's more man,
46:32 directed transformation. We call art. . So um um and you can
46:38 that um using typically ice conditions and heat shock and chemicals like calcium
46:47 magnesium sulfate, I think. And that kind of opens up the mixed
46:52 in the wall and will it'll take OK? Not very efficient, but
46:57 , it will do it. Nowadays, they use electrical charges kind
47:01 shock it for the same effect, more efficient. OK? But
47:05 artifi transformation is only something one does the lab. OK? Basically forcing
47:11 to take it up. OK? their will. All right. So
47:16 anyway, so if you, if would like if you're in the
47:19 you may like to hear this And uh and I should do some
47:23 this stuff. But uh so let's back on the gram positive.
47:29 So here is a very positive I guess the streptococcus. OK.
47:36 this is the completed structure here once is formed. OK? Once that
47:44 me go back here. Nope, way, once that forms OK,
47:51 the cell is copied but they can in DNA, right? Until it
47:56 it's not OK. So what, induces that? Well, you're gonna
48:02 um a sign. So it's an , right? You see all these
48:09 , all right, we're gonna be together by this Sigma factor,
48:16 So that's remember Regulon, that's called transformation Regulon. OK? Because we're
48:24 multiple OPERON together. OK? And getting, getting them to express different
48:31 of this transformer. OK. well, what makes that happen?
48:37 do we activate that? Well, comes from these things competence factors.
48:44 . So again, this is the sensing thing, biofilm formation. He
48:51 cells emitted chemical signals, right? only if you got enough cells
48:57 did you have enough chemical produced to initiate bio formation? The same thing
49:03 , enough cells are together forming enough these that are throwing off these competence
49:09 , enough cells are together, then reach again a threshold level,
49:13 And this time this is what happens you reach that threshold, right?
49:19 collection of of um competence factors bind , triggering the um formation and activation
49:29 the sigma factor. OK. So , that leads to that.
49:35 And so once you have that sigma , then all the operon to make
49:40 thing transformer zone are turned on, ? You can make that thing making
49:46 cell now competent right now competent you take in DNA. OK. So
49:53 when it does come in, so see the this is double stranded,
49:58 one of those strands is degraded, other one comes in. And so
50:04 course, the next step will have be recombination, right? It's gonna
50:07 to the fragment coming in. We to recombine with the genome in order
50:14 be a hang around to be a of that genome. OK. Um
50:21 the question is OK. Why is time to this this um quorum sensing
50:30 ? OK. So recall, let's back to chapter four, right time
50:40 cell number. OK. So our curve, right? So at as
50:49 begin log phase, so at every around here, right, we have
50:57 proportions of cells right? Dead versus . OK. Those proportions are
51:04 right? As we go up, ? If there's more live cells
51:09 there's also more dead cells there. ? All of slightly more live shows
51:14 they're still growing up, right? in the population, what's the source
51:22 the DNA fragments out there more like I'm ecoli and I have your E
51:32 cells that have been produced, As a result of growth,
51:35 And half of you are dead, ? What's coming out of you mice
51:43 what's pouring out of you proteins, , everything, all your guts are
51:48 out, right? Um That, , and so the likelihood of this
51:54 and being successful is if you have kind of why it's tied to cell
51:59 yes, there's lots of live but there's also more dead cells,
52:03 cells equals lysis and DNA spilling out can be taken up. Ok?
52:10 That's what that is. That's, why they think this is happening.
52:15 right. It's tied to this. . Um Of course, it can
52:20 and the environment will be um uh any other cells out there in the
52:28 that are living with them are dying well, living and dying. And
52:31 they, they could be possible sources DNA as well. OK? Um
52:36 also DNA doesn't live or isn't viable a long time in the environment,
52:41 it gets subjected to the elements and and may become useless. But uh
52:47 they think that tying this to the quorum sensing is, is, is
52:53 lot, it's a greater likelihood of being more successful because of this.
52:58 ? But you can see again, ? Look at all the energy expenditure
53:02 make these things co factors to, express the sigma factor, to turn
53:07 all these genes to, to make , that that's all making stuff,
53:12 of energy. So they tie it , to a, a process that
53:17 kind of help regulate it. So doesn't just waste energy doing all this
53:21 has a greater chance of success. hope that makes sense. Any questions
53:27 that? Yeah, I'll get I, I wanna say yes,
53:36 I'm always hesitate to say all for . But I think for those that
53:40 , it's very similar to us. Yeah. It's typically through this kind
53:50 form sensing mechanism. Yeah. The Yeah. Yeah. Yeah.
54:07 . Um OK. So that's OK. So again, uptake of
54:15 DNA. All right. So conjugation little more involved. OK. So
54:20 cell contact. Um so the F factor, OK. So a plasma
54:30 an F factor, makes it what call conjugating. It can carry out
54:36 process of conjugation. OK. So so remember that an F factor describe
54:47 is any pattern that has an factor it that way it can conjugate.
54:53 that there's other, there can be other genes in there. Besides the
54:58 factor, the F factor is simply a collection of genes that enable the
55:04 , right? The sex pilots gene other components involved in congregation.
55:11 The um but that plastic has room other stuff. You can have antibiotic
55:16 on it. You can have, can be a catalog plastic,
55:20 You can hand these other things but the factor makes the whole entity be
55:26 to be transferred, right? And uh this is all carried out through
55:32 recipients. So you have F plus and F minus cells that don't have
55:38 capability. And so these are what conjugate. OK. And so these
55:42 examples of some, these are the of things you'd see this is what
55:48 it F plus is having these kinds genes. OK. Um So the
55:58 itself is um so uh the sex pilots pick her for this process
56:08 to a receptor on an F minus . Now, F plus cells won't
56:15 this. So you won't have an plus cell conjugating with an F
56:20 It will only be with an F cell. OK. Um The different
56:25 of origin of replication, right? plasma is gonna have different one of
56:33 right plasmid, it'll have one for key for transfer. OK. So
56:40 this is occurring, so you can this connection between these two cells,
56:46 ? That, that in itself is connection, it's not gonna be super
56:53 , right? Um So to enable , you bring the cells together,
56:58 ? So this is kind of the point to latch on to an F
57:02 the cell but then you kind of it to you. OK. So
57:06 is will depolymerize shortening the connection. you see we go down to
57:12 OK? A lot of cells are cool. That's, that's a connection
57:16 can be maintained for a bit. you don't have time to transfer.
57:21 . And um and so these other like a relax, for example,
57:28 this is what forms to kind of bridge the cells and then the rolling
57:33 replication occurs. OK. And so the transfer of that other strand into
57:41 recipient, which then gets copied. you have the components of that replication
57:48 plumb race. Um But then these components that help shovel that DNA into
57:54 recipient. OK. And so the result is that F minus now inherits
58:02 plas but then all the genes on and can express it. And so
58:07 um has an essence become an F though because the plasma, it's inherited
58:12 an F fat. So it, then can conjugate as well. So
58:19 so let's let's look at a this quick, a basic kind of this
58:26 of basic conjugation I call it um . So here would be a F
58:34 cell, OK? A factor in . OK? So you have the
58:40 of the pilots which is basically just or adding pilots units to make it
58:46 and um will attach to the recipient F minus is a little bit slow
58:54 video go on. So there we . So attachment and a little funky
59:07 there we go cross itself toward. now you don't see really much of
59:12 going on here. OK? But happening is the, the um X
59:19 genes are being expressed. OK. so that's kind of what's happening now
59:25 then it, it, it can the plastic copied and then transferred.
59:29 you kind of have the components that part of that process being formed right
59:33 . OK. So then it OK. And then we see the
59:41 of DNA eventually. OK. so the thing to remember here is
59:50 transfer and reception of that plasmid. inherits any of the genes in the
59:57 . And one of the genes on plasmid apparently is one that is uh
60:09 hygiene. OK? Because you see of a sudden it was, it
60:16 , it was bald, then it a bunch of hair. All
60:20 like a chia pet, right? I don't think everybody knows what the
60:25 pet is. I think it's made comeback late. It was this thing
60:29 the seventies, I guess it's made come back here and there. Um
60:34 , so uh again, just you can express whatever genes are on
60:38 past of the course. OK. , so put that in your memory
60:42 because now we're gonna see a Um That's so conjugation will have a
60:49 of variations and we're gonna see that . So, all right. So
60:55 answer this question and one of those is this 1 HFR formation. All
61:00 So um take a look. So , what do you need for
61:07 All right. The formation of H R so requires what? OK.
61:56 . It's cut down from six Mhm All right. Uh Y S
62:08 integrated in the chromosome. OK. let's look at that. So as
62:15 said before, the plasmid can exist the chrome organ insert itself. And
62:22 what's happening with the H F R since we're high frequency recombinant um
62:30 And so a population with these you have a greater proportion of them
62:35 a class inserted in the genome. . Um The process looks like
62:45 OK. So you see the terms I asked, so these, this
62:52 occurs in common areas. So I that's for conser sequence. OK.
63:01 OK. So when it integrates it do so again, it's a
63:09 This is this is recombination occur. . And so uh so hr cell
63:21 into the genome. So it does thing it does by doing this,
63:27 basically makes the entire chromosome now something can be transferred. OK? So
63:33 like that it's now become a giant factor if you will. OK?
63:38 the whole thing can be transferred. ? Now figure number is this is
63:45 part that's boxed in, that's what it conjugated. OK. That's that
63:53 contains the parts to be able to to another set. OK. So
63:59 this gets copied, the copying begins transfer, I should say copying the
64:07 goes in this direction. OK. the, so remember it's two cells
64:18 , then you begin to copy that transfer that genome. OK. The
64:24 part that would be transferred would be this box. OK? So inheriting
64:34 is what makes you an F OK. Inheriting this right here think
64:42 F plus, but the thing is rarely does an H F R by
64:52 F minus conjugation. Does that ever ? Right. The F minus stays
65:03 MS? OK. Because for that , we still have to be together
65:07 so long. And how long that's close to two hours being, being
65:14 for the transfer, the whole chromosome the last bit being this part containing
65:21 thing that makes it an, so why in these kind of congregations,
65:28 recipient stays as an F minus. . Um So let me show you
65:34 here. OK. So it's gonna this one. Uh this one I
65:51 a far conjugation. Yeah. Um Here we go. So um
66:00 let me pull this up here. . So here it is. So
66:15 you have factor integrating, right? integrated into the. So OK.
66:22 you don't see an external pattern. . So then uh conjugation proceeds.
66:29 . Fix pilot. So here we're have the parts being produced and
66:41 So remember hold on out of Yeah. Thank you. OK.
67:12 uh OK. So wrist Partch, that's the new part that contains that
67:22 congregation specific genes, right? So that they won't be together long enough
67:30 that to be transferred to it. ? So that's why this F minus
67:36 gonna stay as it is. But know the other part here is the
67:43 . So, yeah, the F can't, can't now conjugate.
67:49 But you can still, it has new genes. OK? Um And
67:56 reproduce a binary fission and pass it through vertical gene transfer. OK.
68:02 because, and so these connections, , what makes these connections fall
68:07 Well, they call a thing called motion, right? So there's this
68:13 in solution are bombarding the cells, ? And that creates movement,
68:18 And so for them to stay hard two hours, that would be a
68:22 tall task, right? Because just movements just would not really allow
68:27 And so, uh but again, this is the, this is characteristic
68:31 an H F R mating with an minus. OK. So let's um
68:44 here of scenario minus. OK. here we have biosynthesis, right?
68:55 F minus is lacking that. Um then acquires that gene through the mating
69:02 recombination occurs. It becomes part of cell but it stayed. Excuse
69:10 the state doesn't F minus. Because at last the state that's,
69:15 typical. OK. Um Any question that. So there's gonna be one
69:22 variation we're gonna see. OK. that's um that's gonna be this
69:29 OK. So let's uh take a here. So the F prime,
69:36 is our third variation here. They to the F plus and minus F
69:48 , has it plasmid outside the but you have HR or plasmid.
69:57 now we have the F prime. . Let's count down 25.
70:46 OK. OK. So it is one of them is what C H
71:00 R cell and uh excision. and so the excision and so this
71:08 occur. Nope, um the um . The plasma, so the H
71:19 R cell that forms plasma goes in , 999,000 times, 100 and
71:29 If it exc exercises, that's what out. OK? But every one
71:34 a million times or so you'll have , what I call one of these
71:39 guide excisions, it doesn't what, went in is not completely coming
71:44 OK? And that's what you're gonna here. So here's an H F
71:47 cell. So this is what went , right? That and that's what
71:55 have come out if it exc like I said, most of the
71:59 . OK? But once, like said, one of the million times
72:03 you have this, it's what they illegitimate recombination. OK. So what
72:08 see here is we're taking um So focus on the B and the A
72:15 here, right? So A and , so when you have one of
72:21 A bar excisions, they call it the B part, the B gene
72:28 actually going with the plasma now, . You see here. Uh
72:34 I wouldn't have before, right? it should only have what's between the
72:38 and B gene should be going But because it's kind of kind of
72:42 this way, now it has this gene in the plasma, that's what
72:47 call it F prime. OK. so the thing about these types is
72:54 can conjugate, OK? If, the um if the F factor genes
73:01 all present, they can conjugate. . And that's how a cell can
73:07 up an extra copy of a right? Um we call partial
73:13 So, bacteria haro one chromosome, they can acquire, you have this
73:20 way that they can acquire an extra of, right, forming a partial
73:25 . So the thing about that is , you know, whatever B function
73:31 it will do. So OK, in the chromosome but then this other
73:36 can actually evolve independently. And so it requires a mutation or something and
73:43 , makes it a slightly different activity maybe enhances the be activity or
73:49 But regardless it's, it's an extra that you know, can evolve
73:54 maybe uh have, have heavy OK. Beneficial use. So,
74:00 and, and this is one way other ways to form partial diploid.
74:05 And so we can kind of look all these together now. OK.
74:10 this is the, what I call the most basic conjugation, right?
74:14 plus F minus meaning OK, the F R. So it's integration of
74:20 F factors. OK. Then the , the F prime right. F
74:27 relies on the H F R cell then this weird excision, right?
74:32 in this case, the excision is out the aging with it and you
74:37 form a partial deploy. OK? those are all the congregation variations.
74:45 ? I have a question about So we'll pick it up and do
74:52 and transposition. OK. Next
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