| 00:02 | Ok, see. Right that Ok. Um Hey folks. Uh |
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| 00:32 | . Uh So we are um we up uh chapter nine today and get |
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| 00:42 | chapter 10. Um So 10 is , who's, I'm, I'm sure |
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| 00:50 | number of you. I've already done Operon before, at least once. |
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| 00:55 | operant control anybody. No. Ok. Um All right. |
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| 01:02 | then we'll learn to get, so we'll start kind of, we'll |
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| 01:07 | on LA later today, later this . So, um what else? |
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| 01:15 | blackboard quiz opens tomorrow? Ok. It will only, it'll cover stuff |
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| 01:22 | uh 21. No, wait from 78 and nine. Nothing on 10 |
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| 01:28 | 10 is on the quiz. That'll be next week. It'll be |
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| 01:31 | there. Um ok. So, , one thing, so I think |
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| 01:37 | mentioned in the email uh Friday. tomorrow schedule opens. Ok, for |
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| 01:43 | three. So if it's important to a specific time, then it will |
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| 01:49 | open, I guess at midnight Ok. So or yeah. Um |
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| 01:57 | right. So just a little bit recap. So. Ok. Um |
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| 02:07 | in Chapter nine. OK. Um gene transfer. Ok. Basically for |
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| 02:16 | summarize pro right? Generate genetic Ok. Now, those types like |
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| 02:31 | life. Ok. Um, can pass genes on vertically, right. |
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| 02:39 | , if you're a bacterium that's binary , right? Um If it's a |
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| 02:45 | , right, it's, it's um can do it through mitosis. Uh |
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| 02:49 | of course, uh we have AEX , right? So, uh but |
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| 02:54 | still is a vertical gene transfer. with binary fission, as you |
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| 02:58 | that's basically like a xerox machine, ? But as we talked about last |
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| 03:02 | , um the it's not that Population of an E COLI will have |
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| 03:09 | small proportion that will uh they'll OK. And you genes can be |
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| 03:17 | can occur through mutation, of Um But also in bacteria through this |
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| 03:23 | gene transfer, right this way to members of the population, perhaps other |
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| 03:30 | in, in, in the OK. And so uh and |
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| 03:34 | it's, it's, and it is , right? It's not a trivial |
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| 03:38 | . It can uh it can lead a number of genes, can require |
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| 03:43 | number of genes this way. Um saw the E coli where a quarter |
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| 03:48 | the E COLI geno is thought to due to the inheritance of these genes |
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| 03:54 | through horizontal gene transfer. OK. it's not just a kind of a |
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| 03:59 | rare thing that happens on then it's significant in the, in the pro |
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| 04:03 | world. OK. So, um we looked at two of the two |
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| 04:09 | the four. So the four of mechanisms we get transformation. So I |
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| 04:13 | basically uptake of naked DNA. And looked at the gram positive and and |
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| 04:19 | mechanisms of the transformer, right, competence, making it some competent means |
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| 04:25 | can take up DNA. Um And the gram negative by comparison, a |
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| 04:31 | little simpler having a pilot that can and bind DNA and bring it |
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| 04:36 | OK. So the uh remember that , the gram positive model we looked |
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| 04:42 | was an example of a quorum right? At this time to sell |
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| 04:47 | , you have enough cells present enough factors accumulate. Then you trigger the |
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| 04:53 | of forming this transformer zom that can in the DNA. OK. And |
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| 04:59 | we look at uh conjugation right? that involves cell cell contact the number |
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| 05:05 | . So the plus or F Uh what makes it that are this |
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| 05:11 | of genes specific to the process of copy In the form of? |
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| 05:20 | And so we looked at like three um the basic uh F plus. |
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| 05:27 | this is about a donor recipient, ? F plus F minus conjugating. |
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| 05:34 | um the H F R cell Is the transfer integrates into the host |
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| 05:42 | OK. And in, in doing , it basically uh allows the entire |
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| 05:49 | then to be moved and copied and . OK. Remember that doesn't happen |
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| 05:58 | that connection has to be for a time, long time being maybe 90 |
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| 06:03 | , two hours, right, in to pass the whole chromosome and it |
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| 06:05 | doesn't happen um due to physical effects Brownian motion like bouncing off the cell |
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| 06:12 | creating instability. So, um so though maybe the entire chromosome is not |
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| 06:19 | , but certainly a number of genes OK. So, um but then |
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| 06:25 | in all these processes, right, is important, right? The recombination |
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| 06:30 | it to become part of the genome the cell. OK? Combining that |
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| 06:35 | DNA with the genome. OK. so uh then the this F prime |
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| 06:43 | , OK, also relies on a H F R. OK. And |
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| 06:50 | this has to do with the, the plans comes out. So I |
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| 06:55 | know what the but uh numbers are terms of how often it integrates. |
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| 07:02 | uh but it certainly does happen because F R cells form certainly. Um |
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| 07:08 | then usually what happens is when it exercises or comes out that's what comes |
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| 07:13 | . OK? What when it is comes out a clean excision if you |
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| 07:17 | ? OK. But there's a one a million or so times when it |
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| 07:21 | happen that way and it takes one the genes from the chromosome with |
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| 07:26 | So this is what the F prime represents. OK. Taking that chromosome |
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| 07:34 | that would kind of be side, maybe took away. OK. So |
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| 07:41 | that means is this is remember the um partial deployed OK. Cell. |
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| 07:50 | uh contains maybe there's an, there's a gene here, right? Uh |
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| 07:58 | , if it, if it conjugates , this conjugates then with a cell |
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| 08:05 | already containing a on a in its , then it has two copies of |
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| 08:10 | , you have one or more copies a gene in a partial diploid. |
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| 08:15 | . So um so that catches us to today. Any questions? |
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| 08:22 | So we're gonna get two more transduction and transposition. OK. Um |
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| 08:28 | transposition transduction, excuse me is a intermediate. So just go back to |
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| 08:34 | . Uh So there's 22 mechanisms, is called generalized transduction. OK. |
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| 08:43 | other one is called specialized and both relate to the type of stage |
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| 08:49 | So remember your lighting pha right? is a light and then you have |
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| 08:54 | lio phase, right? You can inside the chromosome and then eventually go |
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| 08:59 | a light. But that's really what how these two types of transduction |
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| 09:06 | It's really that OK. So in transduction, this is a mighty p |
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| 09:12 | this a little P is carrying this . So what happens is uh this |
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| 09:19 | this goes through the normal viral life here. OK. And uh so |
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| 09:25 | enters and begins the whole copying the and production of viral proteins, et |
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| 09:32 | , right? We talked about this part of that is uh degradation of |
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| 09:36 | whole genome OK. But then when comes to the assembly, right? |
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| 09:41 | viral particles, um the DNA inserts DNA rather than viral DNA. |
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| 09:49 | And now you produce, as shown these um uh non purple ones right |
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| 09:59 | . These are containing host DNA. . And so, uh as so |
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| 10:05 | cell then uh goes through and it lied and the virus is release and |
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| 10:11 | new cells and then those containing host . OK. This guy. All |
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| 10:19 | . Well, um in fact, it is, it should be |
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| 10:23 | right? It has has the ability recognize the host, right? It |
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| 10:27 | the tail fibers if you will, can recognize, bind, insert |
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| 10:33 | But now the DNA is not it's not a virus, it's |
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| 10:37 | from that previous host. OK. in so they call it generalized because |
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| 10:49 | any gene or genes that are present this host anywhere on this chromosome can |
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| 10:59 | um let's draw it here can be by accident, right? A segment |
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| 11:05 | be inserted. So theoretically any segment the genome can be, you |
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| 11:11 | incorrectly packaged in the age. And when you get, when it undergoes |
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| 11:15 | process of infection, as we see , then that DNA can contain any |
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| 11:22 | the genes that are in that previous chromosome. OK. So that's why |
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| 11:26 | say generalized. It can be any from the previous host can be transferred |
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| 11:29 | way. OK. That's, and , and that's what separates it from |
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| 11:35 | trans function. OK. So it's just an error in packaging as |
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| 11:41 | virus is making new viral particles. . So the other mechanism um is |
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| 11:51 | a lysogenic phase. So we talk lambda phase before, right? And |
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| 11:55 | here it's going to integrate, Because it forms of proof, |
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| 11:59 | So prop is part of its OK. And so the insertion is |
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| 12:06 | is specific, right? It's a point where it inserts, that's kind |
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| 12:10 | where the term specialized transduction comes right? So it's a specific |
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| 12:16 | And so it's at these sites called , right? P and B, |
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| 12:22 | ? So, and that's when land into uh E coli genome as part |
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| 12:28 | its like prophage, that's where it goes into OK is right there. |
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| 12:34 | so here you see the integrated P DNA. And so again, when |
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| 12:40 | exits, OK, it may take of that DNA from the chromosome with |
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| 12:49 | . OK. And it could, this example is showing um uh the |
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| 12:57 | is being taken as part of the is of that P DNA. Um |
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| 13:03 | so here's our lamb phase lambda DNA now and galactose gene didn't have that |
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| 13:09 | it before, right? Because this what's in its genome. OK? |
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| 13:14 | so this um if it infects then cell, another E coli that E |
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| 13:22 | can end up getting an extra, . As you see there again, |
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| 13:29 | diploid, right, partial diploid So uh this looks of course, |
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| 13:34 | resembles what process we came before they having a weird excision, right? |
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| 13:40 | the F prime formation, right? it looks very similar to that. |
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| 13:44 | . So it's all based on the being slightly shifted one way or the |
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| 13:51 | , right? It could just as have been shifted to this side. |
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| 13:55 | I'm sorry to this side and you the, the bio uh biotin GE |
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| 14:00 | it, OK. In this it was more shifted to this |
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| 14:05 | So we had that galactic. So just about this a bar excision, |
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| 14:10 | ? Just like the OK. And it's not a common, um, |
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| 14:17 | and I'm sure it's not a, , it's a relatively rare occurrence but |
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| 14:21 | does happen. Ok. And, , but again, another way to |
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| 14:25 | a partial diplo. OK. um, and so again, having |
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| 14:32 | electric copy of the gene, That thing can evolve independently, |
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| 14:37 | Maybe in different function, maybe it help the cell survive better or something |
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| 14:42 | that. Ok. So, so again, very specific. |
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| 14:47 | so not any gene in a hose be transferred to another E coli. |
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| 14:52 | ? It's only gonna be what's, here on what's flanking either side of |
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| 15:01 | end of the phase genome, So anything that's here or here, |
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| 15:07 | . A few genes, OK. maybe two. That's it, |
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| 15:12 | And it's typically gonna be whatever on the genes are bio here, |
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| 15:18 | there, whatever is here. That's it's restricted to. Right. |
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| 15:23 | you aren't gonna get any gene in genome passed just what's on either |
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| 15:27 | It's all based on it. Excising of incorrectly if you want. |
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| 15:33 | So that's specialized transduction. Um Any about that, right? Ok. |
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| 15:41 | let's look at transformation. OK. transportable elements. So these are, |
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| 15:47 | , um, these are found, think in almost all what he |
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| 15:52 | OK. Um They're sometimes called jumping because they, they typically, they |
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| 16:00 | reside in the cell they're in, ? That's what they do and they |
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| 16:07 | around the genome. OK. So , they have a way to excise |
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| 16:13 | , copy and excise and then go another location, the genome. |
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| 16:18 | Um These were discovered in, in plants. Um And so they |
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| 16:24 | they have different effects, they can gene expression of certain genes. They |
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| 16:30 | can insert themselves called the mutations in genes. Um They can carry other |
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| 16:38 | with them. OK? Um But are ways which you can, which |
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| 16:44 | transpo element can um be shifted to cell and, and will that, |
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| 16:50 | where the, that's our interest right? Because it's a, it's |
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| 16:54 | of the mechanisms of hoon transferring. . Um Now the, you |
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| 17:00 | you don't get the idea that uh , they can jump around from around |
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| 17:05 | chromosome that they're doing is zillions of a minute. OK. It's actually |
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| 17:11 | at a fairly low break. And there are ways to control |
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| 17:16 | It's not really well understood how it's . Uh But because you don't want |
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| 17:21 | like that jumping around over the you know, can create all kinds |
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| 17:23 | mutations and this and that. So is in a kind of a, |
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| 17:28 | controlled manner that this happens. But , OK, the, uh so |
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| 17:34 | transpo element, right? So technically, um there's two types, |
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| 17:42 | ? One's called an insertion sequence. . And that's the most simplest, |
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| 17:46 | of them, no matter what kind is, all of them have a |
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| 17:50 | a right? That's the enzyme that it to um excise itself and then |
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| 17:56 | itself somewhere else, right? That is a part of any transposing |
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| 18:01 | OK? And so here you see and an insertion sequence is a |
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| 18:09 | simplest one because all it has is transpose gene. OK? And it |
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| 18:16 | these inverted repeat sequences. So an repeat is simply just here is a |
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| 18:23 | T C G T and here's the sequence here in reverse. OK. |
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| 18:30 | that's simply all it means that's what inverted repeat sequence is. And |
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| 18:34 | and there's in, in the middle be in this case, a |
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| 18:40 | OK. So that's a number to sequence. And so, so the |
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| 18:45 | transposes element is that OK, which , which is basically what you're seeing |
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| 18:49 | . That's, that's an insertion OK? And um the movement. |
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| 18:58 | the transpose enables it to excise, ? And then recombine uh elsewhere. |
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| 19:07 | ? And now there's two ways it be to use uh word document |
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| 19:14 | right? You can copy and paste you can cut and paste. |
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| 19:17 | And that's the difference between replicated and repli nonreplicating, right? Nonreplicating you |
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| 19:24 | just cutting it out and go non um or sorry, replicated means you're |
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| 19:32 | , it's staying there and you're copying and the copy goes here. So |
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| 19:36 | have two copies now, right? replicated. Nonreplicating, don't it just |
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| 19:42 | excise and goes elsewhere? OK. um so the um transpose on |
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| 19:53 | short for T N is the OK? That's, that's an insertion |
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| 20:00 | . So something like this that would in addition to the transpose other |
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| 20:07 | OK? So just like a it's a bigger version, OK? |
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| 20:12 | now we're pairing other genes with So not only the ability to kind |
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| 20:17 | excise and recombine, but now carry with it. OK? And so |
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| 20:23 | the pro world, those can often antibiotic resistance genes. OK? And |
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| 20:30 | then the question is it's one thing have that in a cell jumping |
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| 20:36 | right? But to get it out the population and that's what it's gonna |
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| 20:41 | to exit the cell. So how can happen is what types we call |
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| 20:47 | transports. OK. So that enables to be transferred to another cell. |
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| 20:53 | so same basic principle as we saw , you know, the F plus |
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| 20:58 | minus conjugation. OK. So the has as part of its genes, |
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| 21:06 | ? The the the genes to enable . OK. And so here's donor |
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| 21:13 | , right? And um the transposon excise itself right to here and then |
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| 21:24 | begins to roll in circle replication and copying and then the the movement of |
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| 21:31 | the uh plasmid or the DNA to recipient cell. But the thing is |
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| 21:37 | can't exist, it won't exist in state where, where it's like a |
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| 21:42 | a plasma state. Hang on cell are meant to integrate. OK? |
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| 21:48 | so it'll go back to this state here. OK? But the thing |
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| 21:53 | now you got that transposon, both spread that uh whatever genes are with |
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| 22:00 | transposon to another cell and then that can do the same to other |
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| 22:06 | So it'll spread can spread through this this way. OK. You |
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| 22:10 | theoretically another way to do this that can happen is just a scenario |
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| 22:18 | So here is a chromosome. And here is a transposon T N |
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| 22:27 | short, right, right there. so say the cell has a |
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| 22:32 | right? It has an F right F plus it could be possible |
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| 22:38 | the transposon just jumps into that and into a AAA plasma that already can |
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| 22:46 | that factor and so that can perpetuate transpo as well. That's been seen |
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| 22:52 | . OK. So the transposon, difference here in this scenario is the |
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| 22:57 | itself is not a complicated type entity this is up here. All |
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| 23:03 | it's simply, it's just a transposon to jump into you and that factor |
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| 23:08 | that the cell has already and then can be passed on that way. |
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| 23:13 | . So um so those mechanisms horizon . OK. So kind of the |
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| 23:20 | here is to see each type, ? Transformation conjuration. Can you identify |
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| 23:30 | , what's, how do you identify one? What's the unique, what |
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| 23:33 | the unique features of each one? kind of the the thing here? |
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| 23:39 | . So um any questions? So let's look at, OK, |
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| 23:48 | gears here. So chapter 10, didn't look at gene expression. |
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| 23:53 | So, well, regulate gene right? So remember the points of |
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| 23:59 | , right? Um Energy, they're to remember the gene expression uses lots |
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| 24:07 | energy to do that. So you're have to control it very tightly and |
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| 24:11 | all based, the control is all on kind of what we know |
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| 24:15 | right? Transcription translation. That's, what I was controlled at those various |
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| 24:22 | . OK. So we'll look at we look at um lactose operon and |
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| 24:30 | are examples of this. OK? there's gonna be terminology that you, |
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| 24:35 | you always use in the context of regulation. OK? Uh repression, |
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| 24:41 | induction, um corepressor, these are of the terms that are used. |
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| 24:46 | we'll go through what all those OK. Um And how you would |
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| 24:51 | them really? So let's start with question here. OK. So um |
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| 24:58 | is a bacterial cell for the internal turns into an output action. So |
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| 25:06 | have external stimulus. OK. Uh cell responds to that in some way |
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| 25:14 | it responds by doing what by producing functioning of various R N A |
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| 25:25 | protein proteins, DNA double helix or . OK. That should be a |
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| 25:34 | easy one. Yeah. Yeah. , Yeah, it's counts down from |
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| 26:11 | , right? So of course, is gonna be functioning of various types |
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| 26:21 | proteins. OK. That's what we're gonna control the expression of. |
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| 26:27 | . So if we um look right? So you can imagine a |
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| 26:36 | cell on the environment surrounded by members its population, other America with other |
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| 26:43 | uh environmental conditions. What are all things that we'll have to respond |
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| 26:47 | You? Probably write your own list this right? Temperature. Phh sodium |
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| 26:52 | , oxygen levels. Um the the movements that are present, right? |
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| 26:59 | , any and all these things. so it's got to respond to in |
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| 27:03 | way, OK, whether it's good bad. And so that of |
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| 27:08 | will evolve. Um The only way can do it is to have some |
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| 27:13 | of way to convert that outside Into an inside action. So very |
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| 27:20 | you're gonna have some kind of sensor that will respond or, or, |
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| 27:25 | convert that response to an internal OK. And so then what's it |
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| 27:31 | be, what's going, it's typically gonna be expression of some kind of |
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| 27:36 | or proteins? OK. Not but most of the time that's the |
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| 27:41 | . And so what does that Well, the regulatory elements we talked |
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| 27:47 | before in terms of the pro for example, OK. And things |
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| 27:54 | a regulatory coaching, an operator right? These are the things that |
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| 27:57 | become, right? Uh Not the thing because we're gonna control on multiple |
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| 28:04 | . OK. And so um the let's look at this question here. |
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| 28:12 | . So the fan, let me about that Crypto Fan Opera expression can |
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| 28:24 | controlled by crypto itself inhibiting one of enzymes responsible for its synthesis. |
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| 28:32 | So the trip operon um those um code for proteins that make crypto. |
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| 28:42 | . So the crypto can be self . So crypto does this by interacting |
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| 28:47 | one of the enzymes that actually makes . OK. And so what kind |
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| 28:53 | control is this? So there's right? Even the names with different |
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| 28:57 | of control. OK. Yeah. OK. It's counted down from |
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| 30:09 | right? Um Who picked your Who picked B as in boy? |
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| 30:22 | you take is that you are How do you do with the |
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| 30:30 | right? Cause enzymes, right? one of the enzymes, right? |
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| 30:36 | or proteins. OK. So that into post translational, right? Translational |
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| 30:50 | is on OK. Transcription. Um be we'll just say in our |
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| 31:02 | there's some variations there control a little , right? So just say |
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| 31:07 | right, DNA. Um so we're a protein, right? By altering |
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| 31:13 | function. OK? And so this gonna be right there. Once you |
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| 31:20 | , once you finish translation, post , you've made a protein, |
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| 31:25 | So that's will always be um a controlling it, right? This is |
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| 31:30 | old allosteric inhibition if you remember OK. So here are the levels |
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| 31:37 | here, right? Um And all occur um together, it can occur |
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| 31:45 | different times, it can occur It doesn't, it doesn't have to |
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| 31:48 | just one. OK. And so DNA controls the level of DNA. |
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| 31:53 | look at that next week. Uh the context of phase variation, we |
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| 32:00 | it OK. So DNA, se are altered such that they affect |
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| 32:07 | OK? Or you can modify nucleotides affect expression. OK. Um Epi |
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| 32:15 | is just that right? You're affecting from DNA, that expression. So |
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| 32:23 | can then go um to transcription, control. And so it's, it's |
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| 32:33 | what you think. In other most people think it has to do |
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| 32:38 | the made transcript. OK? It has to do with the enzyme that |
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| 32:46 | it OK. Are you allowing a to be made or not. That's |
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| 32:51 | control. OK? It's not when already have transcript. OK. Control |
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| 32:58 | very common in bacteria. OK. our IKEA, it's how the whole |
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| 33:05 | at, but a lactose operon it's transcription control. Um whether we're |
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| 33:12 | let our race bind to a promoter make it work or not, that's |
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| 33:18 | of control, right? We get um things like technically this is what |
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| 33:26 | would call a post transcription. So we have made the transcript. |
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| 33:37 | you, can you affect R am A? Stability and different ways? |
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| 33:43 | . Um Most, this is probably of a thing in you Caros because |
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| 33:50 | R N A s can have A N A s in general. Don't |
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| 33:54 | around for a long time once they're , right? They actually be grade |
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| 33:59 | they're made to be degraded and um , but in e period, they |
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| 34:04 | to have, can have a longer . OK. So it may become |
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| 34:09 | to kind of destabilize and to get of them. In some cases, |
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| 34:13 | R N A S exists on the of about maybe a few minutes at |
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| 34:18 | , right? It can be hours days actually for you periodic R N |
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| 34:22 | s depending on the type. But stability is a way to, |
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| 34:25 | get rid of them. And so translational control. OK. So this |
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| 34:32 | the ribosome, right? You gotta it translate or not. OK. |
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| 34:40 | , post translation. That's protein. , um as we just mentioned, |
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| 34:48 | , like feedback inhibition, things like , the protein itself can uh |
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| 34:54 | OK. And so of all what is probably, probably the least |
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| 35:04 | expensive, probably that. All Maybe that, because you don't have |
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| 35:12 | make anything so much as you do other ones, right? You have |
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| 35:16 | make a transcript, you have to the parts that affect transcription, |
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| 35:21 | Um If I had to guess I'd say that. Um but nonetheless, |
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| 35:27 | all all can be a part of control engine expression. Um and art |
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| 35:35 | um of genes. So I've been on, OK, controlling genes, |
|
| 35:42 | genes. Um but there are always right? Genes involved in like p |
|
| 35:48 | aspiration genes involved in uh uh things data replication protein. So, so |
|
| 35:56 | are things that always need to be . So those, those fall into |
|
| 36:01 | category here. OK. Um All . So any questions about that? |
|
| 36:10 | that? So let's look at some the terminology here. OK. So |
|
| 36:15 | look at this question. So an repressor, right? So, repressor |
|
| 36:22 | a control element that affects expression. . Um And there's different conditions that |
|
| 36:32 | make it active or inactive. And fact, when we look at lactose |
|
| 36:38 | conditions are the opposite. Um So what we get here, give you |
|
| 37:33 | hint. It's not two of the I know you like this like |
|
| 37:37 | You're not sure, sorry. It's down. So it is one of |
|
| 37:47 | D or E Yeah. How many had to change their answer when I |
|
| 38:00 | it wasn't true but, ok. down. Hm. All right. |
|
| 38:15 | see. Ok. What is the answer? Um It is e it |
|
| 38:22 | to an operator. So, so an active repressor, I |
|
| 38:29 | even if you're not even sure this kind of the key word here, |
|
| 38:32 | ? Repress or repress. OK? That's not gonna promote transcription. That's |
|
| 38:39 | , that's the purpose of an active is to stop transcription. OK? |
|
| 38:44 | It doesn't require an inducer. It require what's called a corepressor. |
|
| 38:51 | But not in an inducer induces OK? So it's not that it |
|
| 38:59 | , wouldn't be C right? Because essentially what A is. Uh And |
|
| 39:04 | D repress. So that means you're the repression, right? So it's |
|
| 39:11 | doing that either. OK. So only be OK? So we'll look |
|
| 39:15 | these terms inducer uh de repression et cetera. OK. So, |
|
| 39:24 | right. Um So here's just a promoter gene and control elements. |
|
| 39:34 | So um a regulatory protein of some is not always, but most, |
|
| 39:45 | always because sometimes R N A cells can be control elements. We'll |
|
| 39:49 | about that next week. But what focusing on now is those that involve |
|
| 39:55 | proteins. OK? And so it's kind of a generic uh |
|
| 40:00 | but very often the regulatory sequence will the opera, I mean, I'm |
|
| 40:08 | , operator, excuse me would be operator write that. Um And so |
|
| 40:16 | protein interacting with an operator is very the case in OK. So um |
|
| 40:24 | induction de repression. So both of mean we're getting expression, right? |
|
| 40:30 | you see depression occurring or induction it means you're getting expression. |
|
| 40:37 | Um And so here's an example of , let me get this out of |
|
| 40:41 | way. So here, so he to the repressor protein, OK? |
|
| 40:49 | interacting with the operator sequence. So when it's active, it's able |
|
| 40:54 | bind that operator. OK? And doing so, basically, physically blocking |
|
| 41:03 | access of the R A plumbers to OK, to be able to get |
|
| 41:09 | and transcribe. OK? It's not you have the presence of an |
|
| 41:16 | OK? That binds to the So now we've inactivated it. |
|
| 41:22 | We've created an inactive repressor by the of an induction. OK? In |
|
| 41:27 | binds. So the repressor can't it falls off. OK. The |
|
| 41:34 | counter with that is repression slash involving corepressor. That scenario is no |
|
| 41:43 | OK. So basically going between these states, right? Induction, |
|
| 41:52 | uh de de repression, repression, , et cetera. So we're going |
|
| 41:57 | those two states. OK. So depression, we have a repressor protein |
|
| 42:04 | , right? But this time the binds, right? And now we |
|
| 42:10 | the active protein complex. OK. it's the opposite of the previous |
|
| 42:17 | right. So here, the active does not bind anything. And that's |
|
| 42:24 | binds to the operator here. The doesn't bind unless you have this corepressor |
|
| 42:31 | it to make it active completely. opposite of, of here. |
|
| 42:38 | And in a nutshell induction is how operon works. The repression is how |
|
| 42:45 | works. But regardless of this, repressor becomes active or inactive. The |
|
| 42:54 | of that term is the same, , which is an active repressor stops |
|
| 43:02 | . OK? An inactive one allows . So that's, it doesn't |
|
| 43:07 | that's the same no matter what kind opera control you're talking about. |
|
| 43:11 | It's just that the conditions that bring those two states about can be quite |
|
| 43:17 | . But the net result is the either you're allowing or not allowing |
|
| 43:20 | And so that's the thing to Triumph. So um now the other |
|
| 43:27 | to kind of also think about is these bindings, this binding here. |
|
| 43:33 | . These are all um it's not , it goes back and forth. |
|
| 43:43 | . Um Yes, the the binding in the absence, for example, |
|
| 43:48 | in induction, in the absence of inducer, the binding there is very |
|
| 43:54 | but it still comes off, you , every, every so often, |
|
| 43:58 | 11 of the million times it comes , right? So don't think of |
|
| 44:02 | things as permanent bindings, there's like constants to get technical and things. |
|
| 44:07 | they come unbind and unbind and different will enhance or promote that binding. |
|
| 44:14 | the point is because we're gonna see scenario where that's important, even though |
|
| 44:18 | bound, it can come off every in a while. OK. So |
|
| 44:23 | look at some other things, So you can have um a activators |
|
| 44:29 | course, or repressors that can be , inactive uh that can stop |
|
| 44:34 | But then things that promote expression, ? So kind of counter to a |
|
| 44:39 | is an activator, right? A of activators enhance expression. So this |
|
| 44:44 | back to what we talked about last and basal level of expression, |
|
| 44:49 | It involved just a and a promoter you a low level basic expression. |
|
| 44:57 | do you jack that up? that can be done by the presence |
|
| 45:00 | activators. OK. Transcription factors can this as well. They come to |
|
| 45:06 | promoter and enhance the binding of that plumb race for that promoter, greatly |
|
| 45:12 | expression. OK. So that's what help do, right? Like the |
|
| 45:18 | says they activate expression by binding to uh with other molecules typically binding to |
|
| 45:24 | um motor and that complex enhances the of the plume is for that |
|
| 45:30 | greatly increase the expression. So that's you go from basal level to high |
|
| 45:36 | . And that can be a lactose . It can go from 1000 fold |
|
| 45:43 | in expression, right? Um and again, there's also conditions that |
|
| 45:50 | affect when this thing becomes a, that the lactose operon scenario. |
|
| 45:59 | So, um OK, so let's kind of get into the la operon |
|
| 46:08 | with this question. OK. So um um so the basics here |
|
| 46:23 | you know, gene control, depression , similar terms are used, |
|
| 46:35 | we feel that period gene regulation that really be crazy. Very complicated. |
|
| 46:43 | . Those are more complicated to be , right? So it can involve |
|
| 46:49 | layers. OK? Um If I mean, I'm not even sure |
|
| 46:55 | undergraduate, they even expose you to um because it is so crazy. |
|
| 46:59 | uh that's why with um even in in re bio, I think you |
|
| 47:07 | a little bit of this, I . Yes, yes. one of |
|
| 47:42 | is true. You change the answer the end. No one of these |
|
| 47:47 | true. OK. Let's go to time around. OK. Let's |
|
| 48:34 | Oh OK. If you and e . All right. So um this |
|
| 48:48 | B uh it would be an active prevents expression not in active. |
|
| 48:57 | Black Opera is an example of No, it's gonna be um transcription |
|
| 49:02 | , not post. OK. Um operon control is a metabolic pathway for |
|
| 49:11 | break down metabolism of lactose. Uh So B Black Y product, |
|
| 49:19 | . It's the lactose detector you will . So uh so pretty good. |
|
| 49:27 | . So do remember this right? the, expresses the genes that make |
|
| 49:35 | proteins to begin the breakdown of completely opposite of what Crypto Fan Opera |
|
| 49:42 | . OK. So, all So lactose opera, so the good |
|
| 49:49 | is you don't have to worry about . OK. Still not knowing what |
|
| 49:55 | function is that thing. OK? can have a decline mutant lacking that |
|
| 50:02 | together. It doesn't affect its ability use lactone. OK? So don't |
|
| 50:06 | to worry about that. So and y um so of course, |
|
| 50:11 | a repressor that interacts with an OK. The lac repressor itself as |
|
| 50:19 | operator sequence too. OK. So Z black Y should I? So |
|
| 50:27 | right here, right? This point here that goes back to that even |
|
| 50:34 | a repressed state, my repress was bound to the operator. OK? |
|
| 50:46 | That binding isn't permanent. Yes, if you already go down low. |
|
| 50:52 | the level of the cell and have camera there taking pictures of it most |
|
| 50:56 | the time it's gonna be bound to operator, right? But there's many |
|
| 50:59 | a couple of times when it's right. That's when can come in |
|
| 51:03 | make a little bit of transcript. . So that's what happens with this |
|
| 51:08 | , right? Not and we're talking the number amount of protein made it |
|
| 51:13 | one or two molecules work, So miniscule, OK? But nonetheless |
|
| 51:19 | as we'll see, OK. So black line function is basically a transport |
|
| 51:26 | protein for lactose, right? It it and brings it in um inside |
|
| 51:34 | cell. Once lactose gets in it's a disaccharide. So we're gonna |
|
| 51:39 | it into uh well, first we're convert some of it into alo |
|
| 51:45 | OK. This is actually the inducer is not, it's actually this slightly |
|
| 51:50 | version called alo lactose is the OK. Then uh as this is |
|
| 51:55 | out by the lac Z beta galactic All right. So, um so |
|
| 52:02 | is at low levels of black Z , which you would have, |
|
| 52:08 | If we're, if we're in this right here, right? And you |
|
| 52:13 | get a little bit of expression, gonna have a couple of molecules of |
|
| 52:17 | Z uh protein in couple of LA . OK. And so the lack |
|
| 52:23 | Y will do this and sit in membrane, the lac, if there's |
|
| 52:28 | lactose present, we'll convert some of to inducer. OK. Now, |
|
| 52:34 | it ramps up, if it ramps , then it will be converting most |
|
| 52:38 | it to the lactose to these two . All right. And that's what |
|
| 52:44 | they funnel into OK. They fall black get make. OK. |
|
| 52:51 | so the only way for this E , let's say it's E coli there's |
|
| 52:59 | things that can ferment lactose. But , the only way you can see |
|
| 53:04 | is with this being in the membrane the eyeball for lacto, right? |
|
| 53:11 | it's there, it can detect If it's not, it will never |
|
| 53:13 | , it could have a zillion molecules lactose around and never know it unless |
|
| 53:17 | have a lack why protein sitting in membrane. OK. So that's why |
|
| 53:23 | has to be this low level. . Again, I'm talking a couple |
|
| 53:28 | molecules work not a lot. But those one or two lack why |
|
| 53:33 | sit in here and they look and a lack of OK. So uh |
|
| 53:40 | of just to reiterate the point right? This is why we're having |
|
| 53:42 | happen because even in right, this state, right? There's a lack |
|
| 53:49 | pressure bound to the operator blocking But the one that a million times |
|
| 53:58 | not found, then you get a bit of expression. And again, |
|
| 54:03 | literally, I literally mean just one two molecules of these things, |
|
| 54:08 | So um that goes in fine. it's out there, OK? Very |
|
| 54:19 | , it will wrap up expression. ? So lactose comes in and is |
|
| 54:28 | by lay into the code and that bind to the repressor. OK? |
|
| 54:35 | it doesn't take a lot of inducer get the effect and you'll go from |
|
| 54:40 | or two molecules to thousands in right? It'll happen that fast expression |
|
| 54:50 | increase and uh then will come rushing , you get lots, then you |
|
| 54:56 | you'll get lots of these, Like peras and then very quickly it's |
|
| 55:04 | in right process, it use the source to grow, right? We |
|
| 55:09 | about before. So, uh but again, just to reiterate, |
|
| 55:14 | have to have a low level of or else you're not gonna see |
|
| 55:19 | OK. So that's why um it this way. OK. And so |
|
| 55:24 | , the the level will, the is 1000 fold or more, |
|
| 55:29 | Very quickly. OK? And it very quickly shut off, right? |
|
| 55:34 | all the lactose is used up, ? Then you can't make any more |
|
| 55:38 | and then go with that. So so we look at both sides |
|
| 55:44 | right? So here's lactose uh right? In the presence of in |
|
| 55:50 | absence of lactose again, logic, ? Why, why have expression if |
|
| 55:55 | isn't there? And other than I , the amount of this occurring in |
|
| 56:01 | scenario is miniscule. So the the lost for that is not great. |
|
| 56:08 | ? So it's fine for that little to happen. Um The um and |
|
| 56:14 | you see here how it happens is repressor, active repressor kind of brings |
|
| 56:19 | both operators from the regulatory lac eye from the, the uh lactose |
|
| 56:28 | And so this is basically it's inaccessible the clim. You can't, you |
|
| 56:33 | transcribe this. OK. Then in presence of lactose, it comes |
|
| 56:39 | converted all lactose and then binds and this site is free and we can |
|
| 56:46 | them All right. So uh press , pressor active. OK. Um |
|
| 56:54 | that's one part of the story. . Black clubs present black accent, |
|
| 57:02 | ? So the other missing piece here glucose. So glucose exerts an effect |
|
| 57:10 | the other layer here. OK. let's look and see what that effect |
|
| 57:16 | . If you can Figure that one , high level transcription of lactose operon |
|
| 57:25 | all of the following except, I'll open it again. Sorry, |
|
| 57:49 | meant that I get my thumb wasn't enough to turn it off. What's |
|
| 57:53 | , what's going down? All Try again. All right. |
|
| 58:00 | Mhm. And there is an OK. So don't pick Fs. |
|
| 58:28 | . OK. Oops it to the . Hold on. There we |
|
| 58:35 | See. Yes. All right. count down. OK. True. |
|
| 59:10 | see it. OK. Here we . OK. Oh, look at |
|
| 59:21 | . C is correct. OK. um obviously you want lactose present? |
|
| 59:31 | makes sense. Um This right creates , this creates the um inactive repressor |
|
| 59:43 | get expression. So I certainly need . And you need the option to |
|
| 59:47 | glucose and you need this, this these are related to each other. |
|
| 59:56 | . A MP levels. It's like a MP levels. OK. So |
|
| 60:01 | to this phenomenon called metabolite depression, . Uh operates so exerts its effect |
|
| 60:14 | the presence of a number of other , not just lack um lots of |
|
| 60:21 | types of sugars as well. Glucose is kind of the the big |
|
| 60:27 | , right? Um glycolysis, Glucose, you could think of that |
|
| 60:35 | glycolysis is made for glucose, Because glucose goes right in no other |
|
| 60:41 | necessary, right? As it comes , right, it's converted to |
|
| 60:45 | six phosphate and then goes right into process, right? Other sugars and |
|
| 60:51 | require an extra step right, in to, to funnel themselves into the |
|
| 60:56 | . OK. With that, this to efficiency relates to efficiency, |
|
| 61:02 | So um so how does this Well, these other sugar promotors if |
|
| 61:10 | will lactose and the like um rely this receptor protein. OK. And |
|
| 61:18 | levels of cyclic A MP. So A MP is actually in the biological |
|
| 61:26 | in us as well common as a signaling molecule for different phenomena, you |
|
| 61:34 | , in, in us it's it's various things um as a way to |
|
| 61:39 | , OK, if something's happening, need to do something. So the |
|
| 61:42 | molecule kind of has that function. . So in a way it's kind |
|
| 61:47 | a energy in the bacterial. So kind of an energy assessor if you |
|
| 61:54 | . OK. So um so remember kind of the related molecules here A |
|
| 62:00 | P AD P A MP, All related. And so really |
|
| 62:09 | in, I'm sure in ourselves as , the A T P AD P |
|
| 62:14 | are kind of a indicator of kind the end health state of the |
|
| 62:19 | OK. Typically bacterial cells have like 1.5 ratio more, a little more |
|
| 62:23 | T P than AD P is an that they're functioning well that they're |
|
| 62:28 | OK. And so these ratios can affected when you see the presence of |
|
| 62:32 | of a MP level changing. So you don't worry about all that |
|
| 62:38 | . This is kind of the basis for what's like a MP and how |
|
| 62:41 | , how it is affecting things. . So for glucose, um high |
|
| 62:48 | of glucose and P levels drop, . Um Because glucose is the preferred |
|
| 62:54 | if it's there and um the low second A P levels rise. So |
|
| 63:02 | , it's an indicator of the energy's energy state of the cell. |
|
| 63:07 | So in the low glucose uh then the cells are kind of on |
|
| 63:13 | lookout if you will for other other sugars lactose being one of |
|
| 63:18 | OK? And so if present, these high cyclic A MP, these |
|
| 63:25 | A MP molecules in red will then to the receptor. The receptor is |
|
| 63:31 | of at a somewhat positive level, it's the cyclic A MP S that |
|
| 63:36 | go up and down, right? if they're high, then there's plenty |
|
| 63:41 | them to bind, right? And you'll create this active complex activator basically |
|
| 63:48 | what it is. OK? And uh that's when the is or not |
|
| 63:54 | around, right? Second P O high, it binds and we get |
|
| 64:01 | of expression. OK? If Glucosure present, then you have low levels |
|
| 64:05 | it's less likely to form this act complex. OK. So again, |
|
| 64:10 | about buying the promoter, increasing the of the prelimerase for the promoter, |
|
| 64:16 | expression. OK. So you have have not just lactose presence but the |
|
| 64:21 | of glucose. OK. So both those things give you a high levels |
|
| 64:26 | , of expression of the lactose OK. So this is all we |
|
| 64:32 | about depression, right? Um They say lactose operon repression because it it |
|
| 64:40 | multiple types of sugars, right? theta repression, glucose has the same |
|
| 64:44 | on other sugars, right? So give it the name metabolite repression |
|
| 64:48 | OK? The tablets are any kind molecule that can be metabolized. You |
|
| 64:53 | refer to glucose as a metabolite, ? But because it's the one exerting |
|
| 64:57 | effect, we don't call it OK. So when we look at |
|
| 65:02 | and again, it goes back to , right? We saw what you |
|
| 65:06 | to do with lactose, right? lactose comes in, you have to |
|
| 65:09 | it into two sugars, right? lactose and glucose, glucose can go |
|
| 65:12 | ahead. But then the galactose has be go through a step or |
|
| 65:16 | So it's like 12 or three steps lactose can be completely utilized. And |
|
| 65:22 | again, the efficiency and energy to that. Uh And that's why glucose |
|
| 65:27 | a big effect. It does. . So um and so when you |
|
| 65:32 | at these here, have both of in a culture, broth, lactose |
|
| 65:36 | glucose together, right? Then glucose course, is used first. That's |
|
| 65:40 | the that's what's meant by um ox , two curves. So there's two |
|
| 65:50 | here, right? There's one glucose is utilized. There's a little |
|
| 65:54 | , right? So remember that's where now has to switch on these other |
|
| 65:59 | lactose operon, right? So there's bit of a lag, then it |
|
| 66:02 | up again. So this biopic, do they call dioxin growth? |
|
| 66:07 | And so at the molecular level, , we've seen this before, this |
|
| 66:13 | that um group translocation uh mechanism of , right? So glucose comes in |
|
| 66:21 | then is immediately converted to glucose, phosphate, right? So glucose never |
|
| 66:26 | in itself, which is why it coming in, right? That's that |
|
| 66:29 | translocation. So uh one of these then, so these are the guys |
|
| 66:35 | hand off the phosphate groups and one these subunits when it's un phosphorated after |
|
| 66:44 | phosphorated glucose, right? It interacts the lac Y and so it blocks |
|
| 66:50 | basically it can't lactose can't come into cell, right? So that's how |
|
| 66:54 | exerts the effect when it's absence, ? In these phosphorated forms, which |
|
| 67:01 | doing nothing because there's no glucose coming , right? That can't affect, |
|
| 67:06 | no effect on the la wine. it's, it's free to function and |
|
| 67:10 | lactose in it if it's there. . So um glucose, present |
|
| 67:16 | absent maximum expression of black. So um OK. Here again, |
|
| 67:27 | the summary. OK. Um Are any questions about this? So |
|
| 67:35 | we're gonna, I'm gonna go through the beginning of the Trip Opera just |
|
| 67:39 | give you a snapshot of that. uh we'll do questions, you know |
|
| 67:45 | comparing black opera Trip Opera. So all on the same page there. |
|
| 67:50 | . But do there's a couple of that relate to these opera. I |
|
| 67:55 | they'll be helpful looking at them. . Any question at the moment. |
|
| 68:01 | . So let's just for comparison. at the Tripen Opera. OK. |
|
| 68:04 | a question. So remember it's going be different, obviously, both in |
|
| 68:15 | , right? How it's controlled. ? one of these are true. |
|
| 68:57 | one of these are true. A all right. Counting down |
|
| 69:24 | OK? Um No, it And the he is from the |
|
| 69:40 | So let's just look at the basics this. Number one oxy lacto. |
|
| 69:47 | is one that it's a biosyn. an anabolic pathway. It makes crypto |
|
| 69:54 | , right? Amino acid, of . And so it involves um five |
|
| 70:02 | genes. All right, one typical operon structure. We're not gonna |
|
| 70:09 | about it today but make a mental of this sequence. OK? Leader |
|
| 70:16 | . So as it's transcribed, that sequence is a part of every transcript |
|
| 70:27 | . Which will be pretty much this of the transcript. OK. Leader |
|
| 70:32 | sequence. OK. That's a part the control as well. We'll get |
|
| 70:37 | that next time. OK? Um These are the five enzymes that end |
|
| 70:45 | producing crypto. OK. Um So fan, so in that state, |
|
| 70:52 | uh it's obviously the uh derepress it's allowed to express, right? So |
|
| 70:59 | repressor protein shown here. So the O repressor is the call it the |
|
| 71:07 | form. OK? You see there when it's the hole or holo |
|
| 71:15 | that's the active form. OK? in this state, um we're having |
|
| 71:21 | , right? And we get we get activation when the is |
|
| 71:29 | OK? And so it binds, the making the whole oppressor. |
|
| 71:36 | So that then will bind to the blocking expression. OK. So similar |
|
| 71:45 | concept to Laos operon, it's about repressor being active or inactive and in |
|
| 71:50 | inactive state, not binding to the , active state binding. So |
|
| 71:54 | that concept is the same. Which is the conditions are different. |
|
| 71:58 | allow that. OK. So the then is if crypto fans being |
|
| 72:05 | but it's present, it, it's made, right? It's right here |
|
| 72:10 | ? Then, then how is, do we keep getting expression? All |
|
| 72:16 | , how do we keep getting this ? If this is present, anybody |
|
| 72:25 | is being made, it's gonna be or something it's gonna be used for |
|
| 72:31 | give an egg. Ok. That's of what's in turkey to make you |
|
| 72:41 | , right. Crypto, right. is an amino acid, which is |
|
| 72:46 | proteins in turkey, right? In . Right. So certainly every, |
|
| 72:52 | protein in the cell has at least crypto. Right. So it's for |
|
| 72:58 | sense of proteins. Oh, it be these for other things, primarily |
|
| 73:02 | in that. Right. So when it likely that crypto fan is being |
|
| 73:12 | ? When would it begin to Because there's a new trip fan all |
|
| 73:20 | a sudden trip fans here and now building up. It's not going |
|
| 73:23 | It's not being used for anything. protein go. OK. That's gonna |
|
| 73:29 | tied to gross right time cell Is it more likely to be synthesizing |
|
| 73:43 | fan here or here? A B obviously stationary phase you're not growing um |
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| 73:56 | producing a lot of crypto, So it's gonna accumulate. So what |
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| 74:00 | you gonna do? You're gonna shut off, right. That's how Crypto |
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| 74:04 | can self regulate both in this right? But also can also interact |
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| 74:11 | that enzyme. That first question we or one of the first questions we |
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| 74:16 | , we can that enzyme and stop . So both as posttranslational control and |
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| 74:25 | of control, right? So it's uh it's how all amino acid |
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| 74:32 | work like the amino acid, they kind of controls its own destiny if |
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| 74:37 | will, right? Which makes If relative compare Operon to La |
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| 74:44 | which is one E collector probably live , if it had to all |
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| 74:52 | Goodness. Come on. People can without like which one you can live |
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| 75:00 | , which you can live without wits can live without witch. Oh, |
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| 75:07 | goodness. You gotta be capable. have got to be capable and you |
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| 75:16 | it without a tri on or a soft. Of course, you can |
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| 75:23 | a bazillion things on this planet, kinds of stuff. I'm having an |
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| 75:31 | to his Aunt Ron. So what you find Aunt Ron? Is he |
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| 75:35 | live very long? No. Um Can you live without trip |
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| 75:42 | OK, I can't say put a over your head like I did with |
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| 75:45 | Respiration experiment. But, you don't eat any trip to fan, |
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| 75:49 | ? And see what happens, Uh You can live without eating a |
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| 75:53 | toast. All right. So that's , folks. We'll see you next |
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| 5999:59 | |
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