| 00:02 | Thanks. So let me just uh my screen and um we get |
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| 00:10 | So, uh as before, uh me um put this in there, |
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| 00:18 | uh section ID, just in case don't see it, put the clicker |
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| 00:27 | oh four. OK. 4996841. . Um All right. So, |
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| 00:41 | as you did before, if you questions, I'll periodically will um I'll |
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| 00:46 | over at the chat section if you questions. Uh You can also just |
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| 00:50 | uh unmute, unmute yourself and, ask a question. That's fine |
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| 00:55 | So, um I, I'm I don't see your screen. |
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| 00:59 | I haven't shared it yet. Uh So uh let me do that |
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| 01:06 | . Um Three. OK. Yeah. And if you are mute |
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| 01:21 | microphone, if you're out there so um you know, there you |
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| 01:25 | OK. Uh Let me get a here. OK. So uh recall |
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| 01:36 | I sent out the email uh regarding the classroom. So, uh because |
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| 01:45 | in the Agnes Arnold Auditorium, uh won't be subjected to what those that |
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| 01:52 | classes in Agnes part of the hall be. So we are just gonna |
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| 01:56 | normal lab class in class sessions starting . Right. So from Monday to |
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| 02:03 | rest of the semester, we're back as usual. Ok, so just |
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| 02:08 | up in class, uh Tuesday, sorry, next Tuesday. So show |
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| 02:13 | in class next Tuesday as you normally and we carry on. So no |
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| 02:19 | remote uh classes like we're doing this . Ok. So again, just |
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| 02:25 | to class next Tuesday right over in Ane Arnold Auditorium. Um What |
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| 02:31 | Ok. So today we're continuing unit . So chapter seven and eight. |
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| 02:35 | , so also kind of like with 21 22 we covered last time chapter |
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| 02:41 | . Now I really pay attention to . Uh pay attention to this, |
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| 02:45 | ? The what's gonna be covered because don't cover hardly, definitely not in |
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| 02:51 | entirety though I covered seven and So I really do do focus on |
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| 02:55 | what's here. OK. In terms the specifics of those two chapters, |
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| 02:59 | . Uh I don't feel the need go into stuff you've had before in |
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| 03:04 | detail. This is more kind uh my approach here is uh the |
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| 03:10 | that are specific to pro Caros in the context of gene expression. |
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| 03:15 | . So again, just kind of sure you, um stick to what's |
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| 03:19 | and, and certainly don't, you need to know those, these chapters |
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| 03:22 | their entirety. OK. Um All . The uh so of course exam |
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| 03:29 | begins tomorrow uh through Saturday, depending when you're signed up for. |
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| 03:36 | what else? Uh Yeah, I these are flip class. I'll have |
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| 03:40 | number of questions here. But, , you know, uh and we'll |
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| 03:45 | through some things and so I, usually this is kind of, |
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| 03:49 | so today and next week, uh then the week after is kind of |
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| 03:55 | uh an overview of bacterial genetics if will. OK. So today we |
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| 04:00 | of start with um a bit of review really because uh some people are |
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| 04:06 | , it may have been a while you've, you've had this material. |
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| 04:10 | just, it's important to go over of the basics of, of genes |
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| 04:17 | , and gene expression. Uh for of this, it'll be uh more |
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| 04:22 | a review than others. Uh it may kind of just be, |
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| 04:25 | a while since you've got, we've through that, you've gone through |
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| 04:28 | So it's kind of just the first of this is kind of just the |
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| 04:31 | getting you back into the thinking again how the whole process works in terms |
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| 04:35 | gene expression. OK. And uh important to know that uh you |
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| 04:41 | one because you're bio, bio right? Your bio majors for the |
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| 04:45 | part, and it's something you just know as a bio major. But |
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| 04:50 | us, you know, it's as get in the gene regulation coming up |
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| 04:54 | week, if you don't know how process works, then how are you |
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| 04:58 | really understand how it's controlled because they go hand to hand, right. |
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| 05:03 | , so anyway, so we'll do little bit of a review here in |
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| 05:06 | beginning with questions and, and Uh So if you have questions, |
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| 05:09 | me know. Um other than so there will be a weekly quiz |
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| 05:13 | week. Uh Yes, I know have an exam but the weekly quiz |
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| 05:17 | really, it's not that there's maybe questions, just do it on |
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| 05:21 | It's not, it's not gonna be big a deal. Ok? Um |
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| 05:25 | no smart work due for another not the third of April. So don't |
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| 05:30 | to worry about that. Um All . So as I mentioned, stick |
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| 05:34 | this in terms of um what's gonna covered. And so we'll start with |
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| 05:41 | question that pretty much will tell me you kind of know they see this |
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| 05:47 | or not. It's one that uh is a 5050 response. So let's |
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| 05:52 | at the process of transcription and translation carried out in a test tube. |
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| 06:00 | . Two way test tube is So we have components from three different |
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| 06:05 | . OK. So from a we're dumping in M R N A |
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| 06:10 | R N A s and rhizomes from fish. We're dumping in, dating |
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| 06:15 | a zebra. We're dumping in R plume in any other necessary enzymes, |
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| 06:24 | and amino acids. So the question oops question is assume some new protein |
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| 06:36 | made in the test tube. there will be the proteins of which |
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| 06:43 | or animals will be expressed. So those are your choices. So |
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| 06:49 | a look. Let me open the here. So uh pause it for |
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| 06:56 | second. So uh so again, is uh this, this is |
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| 07:08 | this can be done. You can the so called cell free extract. |
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| 07:11 | you basically break up in the cells you can uh add the different components |
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| 07:17 | of the process. And uh I'm sure if this exact experiment has been |
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| 07:24 | , but some, some types like because it's, this process is a |
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| 07:29 | translation that's universal, right? All based life uh carries it out pretty |
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| 07:37 | the same way. All right, count down. OK. Number |
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| 08:08 | Yeah. So that's kind of what thought. Um D and E so |
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| 08:15 | pretty much um well, number So it's all, it's all based |
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| 08:22 | this, of course. Right. here. Central dog. Right. |
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| 08:27 | . See, we started learning that maybe as early as junior high high |
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| 08:32 | , for sure, I'm guessing. nonetheless, um DNA R N A |
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| 08:36 | , right? How the information flows all lives. OK. So, |
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| 08:44 | DNA, right. Certainly. Uh proteins of the fish are certainly gonna |
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| 08:49 | in there. OK? Because DNA , is the template, right? |
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| 08:54 | But remember that M R N A right transcripts. So DNA to R |
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| 09:01 | A, right? So I uh both the hippo and fish proteins are |
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| 09:07 | here. OK? Because DNA is template, right? M R N |
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| 09:11 | is a DNA version of the temp . OK? So even with the |
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| 09:15 | DNA, because you have all the , the DNA will go to R |
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| 09:19 | A to proteins. And the M N A is kind of by bypassing |
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| 09:23 | , the DNA stuff and going from R N A to protein. |
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| 09:25 | hippo and fish are gonna be the that are represented you. OK? |
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| 09:32 | The zebra is not, there's no of template coming from the zebra. |
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| 09:37 | ? So that's why it's not one part of this. OK. So |
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| 09:40 | look at another question. OK. kind of relates to how you talk |
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| 09:47 | genetics, I guess. So this uh for a certain bacterium. It |
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| 09:51 | been found in the region of the designated X. OK. Uh comprises |
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| 09:58 | specific protein coding sequence of DNA OK. Um The sequence, this |
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| 10:09 | X can be converted into protein only the cells are grown on galactose. |
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| 10:18 | a sole carbon source, galactose is type of sugar. OK. So |
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| 10:23 | growing on the lactose, the, X uh X sequence is then converted |
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| 10:30 | a protein when grown on the OK? Which is the following statements |
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| 10:36 | these is true regarding the information about bacteria. So the two above sentences |
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| 10:43 | of these is true. OK. So the X phenotype is revealed is |
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| 10:54 | when cells are grown on glucose as carbon source. B the X sequence |
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| 11:01 | a protein. See the conversion of DNA sequence into a protein starts with |
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| 11:10 | binding to the X sequence of The X sequence is A K E |
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| 11:20 | to the are all true statements. these sentences 1 and 2 above and then click |
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| 11:29 | things, right? And don't make assumptions, just answer what you're giving |
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| 11:47 | . I have one more question and will do some explanation here. Oh |
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| 12:03 | I look at, there's any questions up up there? OK. Can |
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| 12:13 | here? I assume, yeah, assuming everybody can hear me. I |
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| 12:17 | have heard some heard by now. . OK. All right. Let's |
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| 12:35 | down quick here. 15. All . X is a correct. |
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| 12:58 | it, so obviously you'll answer So in any case. So um |
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| 13:04 | X phenotype, so it says you to grow on galactose to see |
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| 13:09 | All right, to see the phenotype sequence is a protein. It's a |
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| 13:13 | sequence of A nucleotides, right? of course makes it A G uh |
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| 13:19 | conversion, the sequence starts with um converting it into a transcript, not |
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| 13:26 | his own binding. OK. So is of course A G. So |
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| 13:30 | do one more, just kind of relating to the terms genotype and |
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| 13:36 | OK, which can sometimes be miss , but uh just quickly go do |
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| 13:56 | . And again, I realize this be kind of basic for some of |
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| 13:59 | all, but some of you may have seen this in a while. |
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| 14:02 | it's worth um worth a shot worth , rehashing it a little bit. |
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| 14:12 | OK, so let's go what we here. So C and E are |
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| 14:22 | . OK. So which is So C is definitely true. The |
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| 14:28 | represents the expression of the, of . That's correct because again, it's |
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| 14:36 | genotype. The phenotype take it as DNA to protein. Uh The |
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| 14:43 | M type is always constant on a type may not be, that's true |
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| 14:50 | well. OK. Um They're not interchangeably. So B and C are |
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| 14:57 | , right? So two of A and C are true, which means |
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| 14:59 | is true. So, um so and B and C are the two |
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| 15:04 | ? OK. So A and genotype , let's just look at this real |
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| 15:11 | here, right? So the phenotype from functioning of proteins, right? |
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| 15:17 | again, in the DNA R N protein genotype is the DNA and pheno |
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| 15:23 | is, is the protein is the . Typically, it's, it's expressed |
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| 15:29 | um phenotype is often defined as the features an organism has, right? |
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| 15:37 | so that translates into the um the uh proteins working at that particular time |
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| 15:50 | produce that particular phenotype. Ok. here's an E coli, right? |
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| 15:56 | E coli can ferment this sugar And there's a test that shows that |
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| 16:02 | when it becomes yellow, acid results lactose. Fermentation. Yellow is positive |
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| 16:07 | growing on lactose, bronze, Something that lactose negative would not, |
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| 16:11 | it would not be able to convert and it would remain as a neutral |
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| 16:16 | solution. And so um that's a , right? You can obviously see |
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| 16:22 | right, a change in the growth uh based on the organ and being |
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| 16:26 | to use that sugar. OK. the plate is another way to express |
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| 16:31 | as well. So you can see the lactose phenotype is shown by the |
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| 16:37 | pinkish colonies. OK? Um So now this statement about genotype is always |
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| 16:45 | . I mean genotype is the the DNA is always there, |
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| 16:48 | It's what you um prior to your dividing the DNA duplicates and those that |
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| 16:55 | is passed on to daughter cells, cetera. Um this molecular inheritance as |
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| 17:00 | all know. So it is a right? You always have it. |
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| 17:04 | um but the phenotype can change uh on what's being expressed. And |
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| 17:10 | and that's where gene regulation comes into , right? Controlling which genes are |
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| 17:18 | expressed. OK? We will learn there are some genes that are pretty |
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| 17:22 | expressed all the time. These are be things you might, you might |
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| 17:27 | critical function type genes that always need be pretty much on all the |
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| 17:31 | Things like genes involving glycolysis and right? Um Some are not always |
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| 17:40 | , need to be expressed. There genes you haven't expressed since you |
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| 17:45 | you know, 10 days old, ? And a developing uh develop from |
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| 17:50 | to a developing fetus, right? lots of genes were being expressed back |
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| 17:55 | and aren't being expressed now because you need them. You're a fully uh |
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| 18:00 | adult, right? You're not in fetal stage anymore. So what genes |
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| 18:04 | on or off will determine which phenotypes being expressed? OK. And that |
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| 18:10 | , especially for cells that can change rapidly depending on environmental conditions of different |
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| 18:20 | , nutrient availability. PH changes 02 levels, kinds of things, right? |
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| 18:27 | can influence um what particular genes need be on or off. OK. |
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| 18:33 | we'll explore more of that later but week, uh but that's why, |
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| 18:37 | know, the G N type is , you know, may not be |
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| 18:41 | . And so the certainly the right? So the genotype um is |
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| 18:48 | into a phenotype through the mechanism of translation. OK. Um So the |
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| 18:58 | so here is another different way to at. So especially for you a |
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| 19:02 | , you know, you're doing this project, although you're not using this |
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| 19:05 | , which is actually a, it's kind of a, a multi test |
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| 19:10 | in one kind of uh uh cassette uh each compartment you see there, |
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| 19:16 | only circled one, the urea or . Um the others are different biochemical |
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| 19:22 | , right? You're doing these in lab with different test tubes, |
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| 19:25 | This is just a different form and all the little compartments are inoculated and |
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| 19:32 | then you wait to see what kind results you get, right? And |
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| 19:36 | are typically always color based where a , if it has a metabolic |
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| 19:42 | it will result in the P H typically. And you see the result |
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| 19:46 | a color change, right? So only focusing on urea, OK. |
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| 19:50 | urea uh test which uh if it's of using it will turn that compartment |
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| 19:59 | . OK. And that indicates positive . OK. Um The, so |
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| 20:06 | does that mean? Right. That's bit. So we can, |
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| 20:09 | that's observable, we can see right? And that's another thing is |
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| 20:12 | phenotypes may not always, certainly be , maybe they be they may be |
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| 20:19 | . OK. Like for example, of all the metabolic reactions going on |
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| 20:22 | your body, right? Those are phenotypes. Um but you're not not |
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| 20:29 | visible to the naked eye, Uh If you can use lactose, |
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| 20:33 | not gonna turn yellow, right? that's, you're, you're, you |
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| 20:36 | , you're having a P change and have a P in the car. |
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| 20:39 | ridiculous. But, but the point that not necessarily everything is absorbed with |
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| 20:43 | naked eye, but you could measure different metabolic activities with um different types |
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| 20:48 | tests, right? That's when you a physical, you get a blood |
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| 20:52 | and those numbers represent your different phenotypes what their, what their levels |
|
| 20:57 | So, one way to look at anyway. So, back to |
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| 21:01 | So here is a, a It's, it's positive for hydrolysis, |
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| 21:06 | called. So what does that actually at the molecular level? Well, |
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| 21:11 | is what the enzyme does. So enzyme is what produces this positive result |
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| 21:17 | it hasn't, right, urea is down into uh decoupage and ammonia forms |
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| 21:23 | that's becomes basic cos the color So then of course, ura enzyme |
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| 21:30 | from a gene, right, the genotype. And so that uri a |
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| 21:36 | , if in order to, to that enzyme, that protein, we |
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| 21:41 | to go through the expression of that transcription, translation, transcription R N |
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| 21:46 | polymerase copying that gene that DNA into R N A form. OK. |
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| 21:53 | R N A messenger R N A . Same thing. OK. Then |
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| 22:00 | the next part, excuse me, transfer R N A S. These |
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| 22:05 | about the translation of that transcript into actual protein. Yeah. And then |
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| 22:13 | will fold, typically folding is involved protein like peptide chain or changes depending |
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| 22:18 | how big it is. And then enzyme protein folds into a shape that |
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| 22:23 | becomes an active enzyme that can participate this reaction. OK. So a |
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| 22:28 | of things, um uh is we're begin to focus more and more on |
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| 22:35 | that for, for simplifications sake, just showing you this way. Uh |
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| 22:41 | reality, you can form lots of . OK? All those transcripts will |
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| 22:47 | lots of protein, right? So a cell, generally 11 transcript producing |
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| 22:56 | protein is not gonna be enough, not meaningful. So it typically you're |
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| 23:00 | produce lots of these things, That's where control comes in because you |
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| 23:04 | to produce them for a period of , you need them, but you |
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| 23:07 | want to rapidly shut it all off well. OK? And that's the |
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| 23:11 | of regulation. OK. So, but regulation occurs at multiple levels. |
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| 23:18 | you can see the multiple levels right? We've got DNA at the |
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| 23:23 | of DNA, right? Um The we have the uh at the level |
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| 23:33 | R N A, right, both transcription translation uh at the level of |
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| 23:37 | protein and all three of these, , all three levels can you control |
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| 23:43 | ? OK. I will see that we go through this unit. |
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| 23:47 | So control is as equally as if not more. So the actual |
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| 23:52 | of producing proteins because one thing that mentioned time and again, that you |
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| 23:59 | get from these diagrams of whether it's replication or whether it's protein synthesis, |
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| 24:07 | energy expenditure required for those processes. ? Remember if you're building a |
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| 24:13 | you're that's analyst that takes energy, ? And so in a highly competitive |
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| 24:21 | that these microbes are in, you want to waste energy, right? |
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| 24:26 | that will put you at a So always being efficient is a big |
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| 24:32 | and controlling your gene expression is a part of that. OK. So |
|
| 24:39 | so just continue on with this. kind of getting to more, more |
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| 24:43 | the molecular level here. So your terms, you should know, |
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| 24:47 | Transcription, translation and what those right? And again, I'm not |
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| 24:52 | for the super detail here. Um You've had that before, I'm |
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| 24:56 | uh I'm not gonna go into the workings of a, of a rhizome |
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| 25:00 | , and all and all the various and stages. OK? It's more |
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| 25:04 | of over them. OK? Um if you see transcription, you |
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| 25:10 | what's the danger for that on a that produces an M R N |
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| 25:14 | a messenger R N A, a , right? That's all part of |
|
| 25:18 | . So if you use an the the DNA is the constant, |
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| 25:23 | ? So it's like the the book reserve in the library, OK? |
|
| 25:28 | can't take it home with you, ? So, but it's always gonna |
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| 25:32 | there. And if you want some from that book, the DNA, |
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| 25:37 | gotta make copies of it, So you take, you copy whatever |
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| 25:40 | you want a xerox machine, that's transcription process, right? The transcription |
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| 25:47 | . So you make copies, And those copies can be used. |
|
| 25:50 | so that's, that's in basic what's going on here as I'm sure |
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| 25:54 | probably know. So the, with that transcript then um you, |
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| 26:02 | that's the, that, that's called the working copy of DNA if you |
|
| 26:06 | , OK. So that, because can always make, you can always |
|
| 26:09 | more M R N A S Of A G always, you can |
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| 26:14 | that as long as you're alive. um but the, the DNA is |
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| 26:18 | permanent thing, right? So R A is come and go DNA is |
|
| 26:22 | . And um uh so with those , then you translate, that's what |
|
| 26:27 | the functional proteins, right? The thing to remember is that although most |
|
| 26:32 | , right? So the gene is core unit in DNA, right? |
|
| 26:36 | contains a sequence to produce a OK? That gene um uh |
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| 26:45 | and most genes are just that protein genes, but there are a number |
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| 26:52 | some that are not protein coding OK? Although they're so-called genes just |
|
| 26:57 | the end product of the gene is R N A, not a |
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| 27:01 | And those are things like Rizo R A molecules transfer R N A |
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| 27:07 | So there are genes for those and genes, the end product is simply |
|
| 27:12 | R N A, not a So just you know, remember that |
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| 27:16 | not, not all genes are protein . Some are simply R N A |
|
| 27:20 | . OK. So uh so the thing to remember here is the |
|
| 27:25 | in right, there's no nuclear So polyribosome poly zone formation can |
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| 27:31 | Transcription translation can occur virtually at the time. OK? Because there's no |
|
| 27:37 | of the process like there is in carry on. OK. So um |
|
| 27:43 | means you get lots of protein sens quickly. OK. So uh so |
|
| 27:49 | main things, right? So we ribosome, there's a ribosome binding |
|
| 27:53 | So the transcript, you see there a specific sequence and so ribosomes read |
|
| 27:59 | you will translate five prime to three . So you see that ribosome is |
|
| 28:05 | well on its way in in the of translation, it has bound the |
|
| 28:09 | binding site and then it up. remember there's punctuation in a, in |
|
| 28:15 | transcript. It's how it's read, how it becomes translated, right? |
|
| 28:19 | you have what are called um start or initiator codons, right? That |
|
| 28:25 | the beginning of the sentence if you uh then the co dots, |
|
| 28:30 | the three base nucleus ties that come after the initial codon, right. |
|
| 28:37 | you each codon has three bases, ? So you, you read it |
|
| 28:40 | that fashion. And so um and, and as you do, |
|
| 28:45 | produce a protein like peptide. So have the parts right, the ribosome |
|
| 28:49 | it brings it all together, it transcript, it provides a site for |
|
| 28:54 | sensors to occur. Uh or T N A S T R N A |
|
| 28:58 | come in and they are bringing a acid with them, right? That |
|
| 29:06 | to a particular codon. OK. I'll elaborate that in a second. |
|
| 29:12 | back to the sense, anti So we mentioned this in the context |
|
| 29:16 | viruses, right? And R N viruses. And so remembering that, |
|
| 29:22 | and so you see mark there on , the sense and anti sense strand |
|
| 29:26 | minus applies as well, right? so let's take a closer look at |
|
| 29:32 | same sequence you're seeing there here. . So the same sequence. And |
|
| 29:40 | uh so again, the, the way you talk about nucleic |
|
| 29:45 | which is a five prime end and three prime end. OK. And |
|
| 29:50 | uh so here's the complementary strands the sense and one is an anti |
|
| 29:54 | . OK. So the sense is a plus and the sense is a |
|
| 29:59 | . OK. So remember when you , you copy a minus, it |
|
| 30:04 | a plus. And as we saw the contact the virus, as you |
|
| 30:08 | plus, you, you, you a minus, you copy it into |
|
| 30:11 | minus strand. So regardless, so point here is that when we |
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| 30:16 | when we're doing transcription, OK, DNA we are making a complimentary copy |
|
| 30:23 | the anti sense strand. OK. this one right here. OK. |
|
| 30:33 | of course, it's a minus right? So, because it is |
|
| 30:37 | copy with make up, that is plus strain. OK. And so |
|
| 30:42 | so, but it's an R N form, it's in the form of |
|
| 30:45 | N A, right? So remember no uh diamine in R N |
|
| 30:50 | they get replaced with Euro cells as see here. So when you compare |
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| 30:54 | M R N A to the, the sense strand, they're identical, |
|
| 30:59 | ? Except for where you see a , right? So, so the |
|
| 31:03 | thymine there's a year or so. ? But except for that, they're |
|
| 31:10 | , right? And that's, that's you want because you're trying the, |
|
| 31:13 | , the, the sense strain of contains the information to make that |
|
| 31:18 | And we make that we get that the R N A form because we're |
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| 31:22 | the antis senses or minus strain of . OK? And so now with |
|
| 31:28 | M R N A, we can . OK. So remember that's where |
|
| 31:34 | gene code table comes in, So uh my crude way to draw |
|
| 31:40 | T R N A. Yeah is like this. OK. So you |
|
| 31:51 | to kind of do it like this here's an amino acid A a amino |
|
| 31:58 | , OK? And then down here we call the anti Cota, |
|
| 32:06 | So the anti codon matches up with code, I can draw it |
|
| 32:12 | This and OK, so they match with the coat on and so in |
|
| 32:23 | so, right. A U G ? Match has a meth, |
|
| 32:27 | So the T R N A for would have the complimentary base to a |
|
| 32:34 | G, right? And then bring with it and it would with the |
|
| 32:38 | T R N A bringing the appropriate acid that corresponds to the code dot |
|
| 32:43 | . So, uh so that's how read a transcript translated rather to produce |
|
| 32:49 | approach. OK. So, you , that's the basics of transcription and |
|
| 32:57 | . OK. Um Let's uh Is I see a couple of people |
|
| 33:09 | able to hear, is anybody else to hear me? OK. All |
|
| 33:19 | , good. All right. All . Then it might be an |
|
| 33:22 | There's a couple of people, it be an issue with the um |
|
| 33:25 | So check that. OK. All . Um Back to here. |
|
| 33:32 | So, uh so again, we'll now get into kind of more |
|
| 33:39 | of specific stuff. This is more less kind of an overview which |
|
| 33:42 | you know, again, if you're very comfortable with this, |
|
| 33:46 | you know, then, then, , good, good. That's |
|
| 33:49 | Uh Hopefully, if you're not kind a little bit, not so |
|
| 33:53 | hopefully this has helped. Um But we're gonna kind of get into how |
|
| 33:57 | gene organization in uh So let's start this question here. OK. So |
|
| 34:06 | of these teams are, which of terms includes all of the others? |
|
| 34:11 | . You open a poll there. , um, so it's gonna be |
|
| 34:16 | some terms you're not familiar with because , there's some differences, of course |
|
| 34:20 | how pro Caros organize their genes versus Kaos. So it's gonna be some |
|
| 34:26 | , um, that you may not heard before. So, and there's |
|
| 34:31 | one, a couple in here you not be familiar with. So that's |
|
| 34:35 | gonna go through that in this next here. OK. Let me put |
|
| 34:54 | timer on. OK. Cut All right. Um Yeah, |
|
| 35:27 | There's gonna be genome, right? , uh if we're gonna rank |
|
| 35:31 | it would be a gene from, smallest to largest, let's say um |
|
| 35:38 | being the smallest. No, of not. Nucleotide is small. Excuse |
|
| 35:43 | , nucleotide, then gene, then , then Regulon, then G dot |
|
| 35:58 | . So um that so small is biggest, right? In terms of |
|
| 36:06 | . OK. So, um so we're gonna do is first talk a |
|
| 36:16 | about getting scope. So genome transcript prote genes transcripts proteins. OK. |
|
| 36:24 | for procaryotes, um for us, genome, of course is our |
|
| 36:31 | OK? Also for bacteria and the , but in addition to their to |
|
| 36:36 | chromosome, they may have one or plass. OK. We'll talk about |
|
| 36:43 | and a little bit. Uh you like extra chromosomal small genetic elements. |
|
| 36:50 | . But it does represent part of genome. OK. Uh The transcriptome |
|
| 36:54 | gonna be whatever transcripts are, are that cell at a given time. |
|
| 37:00 | . And that, and a prote fluctuate, right? Because transcript the |
|
| 37:05 | expression, you know, will determine which tran, which transcripts are available |
|
| 37:10 | a given time. And then that course, determines what proteins will be |
|
| 37:14 | from those transcripts. So the transcription can fluctuate and depending on conditions of |
|
| 37:21 | cell of the cell and what it . Um But the genome of course |
|
| 37:25 | , is, is the constant uh terms of genome sizes. So, |
|
| 37:29 | know, on the larger end, pro of GEOM is on the order |
|
| 37:33 | maybe six million base pairs. Uh coli I think is around four |
|
| 37:39 | Um smallest you one of those uh Michaels, those those ones that lack |
|
| 37:46 | cell wall. Uh those are on smaller end like 500,000. So I |
|
| 37:51 | 1000 to almost uh um nine almost a billion base pairs. Uh |
|
| 38:03 | million. I'm sorry. Uh you know, within that range, |
|
| 38:06 | , probably about one million is what most mature are typically. Uh But |
|
| 38:11 | they can also have so they're, haploid for the most part, although |
|
| 38:14 | are some, some odd balls that fit that mold. But for the |
|
| 38:19 | part, cars are haploid with 11 and again, may have one or |
|
| 38:24 | of, of these plass. Um All right. So let's |
|
| 38:29 | this is gonna be one of those that we're gonna look at now, |
|
| 38:35 | go over the answer, but then gonna see it again at the |
|
| 38:37 | OK? So it's gonna be one those, I guess before and after |
|
| 38:40 | . OK. So let me So you can read this. So |
|
| 38:44 | is gonna be uh really going through the, the different terminology uh that |
|
| 38:49 | associate with prokaryotes and how they organize genes. So, while reading |
|
| 39:25 | so what we're gonna do is I'm show you a diagram of how you |
|
| 39:32 | out the genes are organized and it's for reference purposes just for comparison. |
|
| 39:39 | not going to test you on your pain structure. OK? But |
|
| 39:44 | it's helpful to see that and then how bacterial proc uh genes differ. |
|
| 40:12 | ? OK. I'm gonna start the . OK. OK. So let's |
|
| 40:48 | here. Well, consensus was f believe. OK, most people pick |
|
| 40:59 | we'll revisit that question a little So let's go ahead. All |
|
| 41:06 | So just briefly before I get e cheese. So just to give you |
|
| 41:11 | little bit of comparison here, um structural genes. So the structural |
|
| 41:19 | um are the ones that code for typically. OK. So we're just |
|
| 41:24 | , we're just gonna worry about protein genes which, which comprise the ball |
|
| 41:29 | the genome anyway. Um So uh , protein coding genes, OK? |
|
| 41:35 | control elements. OK. The uh promoters, uh regulatory sequences, these |
|
| 41:43 | all involved in controlling expression. Then we look at operon and what |
|
| 41:48 | Regulon is. OK. So this Cistron, you see there. |
|
| 41:52 | Cistron, I think it's kind of older term. Um It basically just |
|
| 41:57 | a gene, but you're gonna see like mono systems cynic in the context |
|
| 42:02 | a transcript. OK. So a Syron R N A that transcript contains |
|
| 42:08 | for just one gene. We'll see Caros can form polycystic R N A |
|
| 42:14 | and so that transcript will contain information multiple genes in that single transcript. |
|
| 42:22 | . That's unique to uh pro OK. So let's just first take |
|
| 42:29 | look at you carry out a This is how it, this is |
|
| 42:33 | it is in your, in your . OK. So the first zero |
|
| 42:39 | first on the Exxon intron, So this right here. Well, |
|
| 42:45 | start over here. Control elements enhancer . So all that means is are |
|
| 42:51 | close to the structural genes or far ? OK. The proximal elements are |
|
| 42:57 | course close by enhancer elements can be away, thousands of pairs away. |
|
| 43:04 | . Um Now, what's unique about periodic gene structure? And are some |
|
| 43:10 | IKEA have, have some similarities not all um but the E Exxon |
|
| 43:18 | um uh structure. OK. One to point out is that regardless of |
|
| 43:25 | type of organism you are pro you caros, right? In terms |
|
| 43:31 | gene structure, the constants are a . OK? And regulatory health, |
|
| 43:39 | are gonna be common for any, g you're gonna have a promoter, |
|
| 43:43 | gonna have then a a sequence after promoter that codes for the actual to |
|
| 43:50 | information for a protein, right? the promoters will kind of lines it |
|
| 43:56 | . So remember a, a prelimerase what produces the transcript. But you |
|
| 44:00 | get a alim in front of the and the promoter is what facilitates |
|
| 44:05 | OK. So you're not gonna see gene in anything. It doesn't have |
|
| 44:09 | promoter in front of it. Uh The promoter can also be involved |
|
| 44:14 | regulate breaking for regul regulation as OK? But the promoter is a |
|
| 44:21 | . You see that, see that every gene, right? Promoter then |
|
| 44:24 | the information to code for that OK? All right, back to |
|
| 44:31 | gene. So Exxon Enron, so Exxon sequences are those that actually um |
|
| 44:37 | the information to produce a polypeptide. . The enrons come in between say |
|
| 44:43 | , the, the I N is intervening sequences. So enrons come between |
|
| 44:47 | . OK. So when that's when is transcribed into a, what we |
|
| 44:54 | a primary R N A transcript or M R N A sometimes called, |
|
| 45:01 | contains both exons and enrons. So now we have an R A |
|
| 45:06 | containing both exxons and introns. There also other elements. So you see |
|
| 45:10 | , you see a, a a tail is what it's called, |
|
| 45:14 | call it signal um a five prime , right? These are elements we're |
|
| 45:20 | to see. And you see down . So lots of processing occurs of |
|
| 45:24 | N A in New Caros, And the processing is necessary to take |
|
| 45:29 | the enrons and then what we call together the Exxon sequences. So and |
|
| 45:36 | putting on these modifications and what's called five prime tap and a poly a |
|
| 45:41 | . So that's what we call a M R N A. OK. |
|
| 45:46 | an M R N A that can translated. All right, the pre |
|
| 45:49 | R N A cannot be. So what we have to go through this |
|
| 45:52 | . Um the axons, right can we just label these very simply uh |
|
| 46:01 | and three, these can be spliced in different orders. OK? And |
|
| 46:08 | can create slightly different proteins. So what you cars can do. |
|
| 46:13 | And uh and the cap and tail remember that these, these, this |
|
| 46:18 | you're seeing on the screen. Now is what happens in the nucleus, |
|
| 46:22 | ? So then these M R N S have to exit the nucleus outside |
|
| 46:27 | and then the er and the cytosol become translated. OK. So the |
|
| 46:32 | and tail have a couple of functions help, help it get out of |
|
| 46:37 | nucleus, uh maintain stability of the R N A. Um any M |
|
| 46:44 | N A s that don't have the and tail are rapidly degraded. So |
|
| 46:49 | needs those features to exit the nucleus you remain stable for a period of |
|
| 46:53 | and be translated. OK. So of this do you see in |
|
| 47:00 | OK. So um uh of they have control elements. Uh |
|
| 47:07 | and there's a promoter but there's none this already processing or, or Enron |
|
| 47:12 | structure. OK. So let's flip what it does look like in the |
|
| 47:18 | , right? And, and so , those uh this right here that's |
|
| 47:27 | to designate uh genes that may be continuous, they could be far |
|
| 47:36 | far in the other direction away that's what that means. OK. |
|
| 47:41 | So here you see the single a single promoter, single gene structure |
|
| 47:47 | here, right? one promoter and right. Bacteria and archaea can have |
|
| 47:58 | called an opera structure, right? you have one promoter and multiple structural |
|
| 48:05 | . OK. So promoter and then and more structural genes, two or |
|
| 48:12 | sorry, two or more structural genes are, that typically will be |
|
| 48:17 | OK. And so the only accel of course will bind to the motor |
|
| 48:24 | . And here is where you see Polycystic message. So it's one continuous |
|
| 48:31 | A R A, a transcript that the information for all in this |
|
| 48:35 | all three structural genes on one OK. Very efficient. OK. |
|
| 48:43 | so uh of course, they get into the individual proteins very typically |
|
| 48:49 | right? And so they will be of a common metabolic pathway. |
|
| 48:56 | So this enables bacteria to turn on turn off expression of an entire metabolic |
|
| 49:03 | , which is a very efficient way do it. OK? Not just |
|
| 49:07 | it on but very quickly turn it altogether as well. OK. So |
|
| 49:12 | is a the classic operon structure. . So the Aron itself also includes |
|
| 49:19 | operator. So promoter operator, structural , that's, that's the opera. |
|
| 49:28 | . So um so the operator has function, all right, a little |
|
| 49:33 | different function. It's involved in the . OK. Regulation in conjunction with |
|
| 49:39 | regulatory protein. OK. That's produced a regulatory team. OK. So |
|
| 49:46 | protein very often interacts with the operator . OK. And basically producing a |
|
| 49:54 | block, right? Can't get around . The can't get around to |
|
| 49:59 | OK. So that's a mechanism that's common in pro Caros. OK. |
|
| 50:07 | so um now what we'll see is conditions that bring about this regulatory |
|
| 50:18 | operator interaction to affect transcription, to , to affect expression uh will |
|
| 50:27 | right? We're gonna look at the operon and the Tripen operon and they |
|
| 50:34 | turn off expression bye AAA protein binding operator. But the conditions under which |
|
| 50:43 | happens are very different. So, so there's gonna be variations we'll see |
|
| 50:48 | , on this feed. OK? This is also what we call transcription |
|
| 50:56 | . OK? Because we're affecting the of that opera. OK? Any |
|
| 51:03 | you're interfering with R N A plum its ability to do or not do |
|
| 51:07 | job. That's transcription control. This is a transcription of control mechanism |
|
| 51:13 | common in, in uh pro OK. So, uh so that's |
|
| 51:22 | opera structure. OK. So it, it comprises uh the |
|
| 51:26 | Is this all right here? Our motor operators about two can I |
|
| 51:35 | now the Regulon, OK. So is a single opera. OK. |
|
| 51:45 | , there will be processes uh OK. Uh That involve uh more |
|
| 51:55 | one operator. OK? And when involve more than one operator, you |
|
| 52:02 | can have what's called a Regulon. ? Um A very good example of |
|
| 52:08 | is um controlling multiple operon through a factor. So we'll talk about Sigma |
|
| 52:16 | at the end here uh today, a Sigma factor. So you see |
|
| 52:21 | you have Ayra, OK. A of this is a Sigma factor that |
|
| 52:27 | kind of a transient part because the factor will guide the A pli to |
|
| 52:31 | promoter. And then then once it that the Sigma factor falls off and |
|
| 52:37 | it binds to another a eli right? So Sigma factors guide the |
|
| 52:41 | race to various promoters OK. And you have a number of operon in |
|
| 52:50 | those promoters respond to the same sigma , then you can control those operon |
|
| 52:58 | , right? So here would be example in this diagram that this Sigma |
|
| 53:06 | is common to these promoters in these OK. So that's how you can |
|
| 53:17 | control of these various operon. And so why would you do |
|
| 53:23 | Well, because presumably the, the are all a part of a particular |
|
| 53:31 | ? Ok. A good example is , what we call the nitrogen |
|
| 53:36 | Ok. So think of all the pathways in which nitrogen might be |
|
| 53:44 | right? We need nitrogen to form acid nitrogen to produce nucleotides. We |
|
| 53:50 | through um previously a lecture uh about , you know, and it's used |
|
| 53:57 | either in aerobic expiration or as a AAA food source for a little, |
|
| 54:05 | ? So all it represent can different in the same cell. OK. |
|
| 54:11 | nitrogen coming in then will be, know, controlled in terms of where |
|
| 54:16 | goes this pathway and that pathway and other. And for that reason, |
|
| 54:21 | kind of want to control the OPERON that are all involved in these different |
|
| 54:27 | of nitrogen metabolism. OK? That's example. OK. Um And that's |
|
| 54:33 | you do it, you control the together to kind of make sure that |
|
| 54:37 | nitrogen coming in is allocated as it be for, for most efficient |
|
| 54:43 | OK? Um And so that's what Regulon is. It's a way to |
|
| 54:48 | multiple OPERON that are part of a part of a common metabolism, |
|
| 54:53 | That nitrogen be right. Um We'll see it in chapter in chapter |
|
| 54:59 | we see a Regulon that's involved in in grand positive organisms. And uh |
|
| 55:07 | again, because it's, it's using number of OPERON to, to bring |
|
| 55:12 | this, this uh transformation bringing in from the environment. So again, |
|
| 55:18 | are you at? Where, where it's a process involving multiple |
|
| 55:22 | Um You can control those various OPERON a Regulon. And again, it's |
|
| 55:29 | that Sigma factor kind of being common those motors of that particular of that |
|
| 55:34 | Regulon and controlling those opera together. . So that's, that's basically an |
|
| 55:39 | . So a Regulon is AAA control that controls multiple opera at the same |
|
| 55:50 | . OK. Uh Let me just over here. Any questions. |
|
| 55:59 | Um Got it again, feel free chime in on a problem wondering. |
|
| 56:10 | OK. So let's look at this on plasmids. So we're going to |
|
| 56:16 | about plasmids for a second or a minutes. Um So, um so |
|
| 56:26 | are uh we finished today, so talk about OPERON and um then |
|
| 56:35 | we're gonna revisit that again when we to chapter 10 on um regulation, |
|
| 56:44 | ? So, in regulation, of , we're looking at opera and how |
|
| 56:47 | controlled in various ways we look at couple of different examples. Um When |
|
| 56:53 | get, when we get to next in chapter nine, that's more about |
|
| 56:58 | horizontal gene transfer, how bacteria and can uh transfer genes between them. |
|
| 57:08 | . That's separate from, from um through, through replication, right? |
|
| 57:17 | binary fission, a cell splits in , those two daughter cells receive that |
|
| 57:23 | , right? That's one mode of . But there's also another mode where |
|
| 57:26 | can exchange DNA genes with members of population. And that's what like |
|
| 57:33 | transformation transduction transposition is all about. . We'll look at that next |
|
| 57:40 | Um But plasmids are a, are part of that as well. |
|
| 57:45 | So that's, we'll see that you , you can um move, move |
|
| 57:50 | around uh through classmates. OK. let me go ahead and set the |
|
| 58:35 | . OK. You know, OK. Let's see. Um |
|
| 58:50 | Uh C C is the true is correct statement here. OK. Um |
|
| 58:56 | plasmas have this feature of being what call a OK? They don't um |
|
| 59:02 | kind of to a certain extent, things on their own. They're not |
|
| 59:06 | to um replication of the chromosomes. remember the chromosome in a cell replicates |
|
| 59:13 | to cell division, that's kind of it's linked to uh plasmas can kind |
|
| 59:16 | do the wrong thing in that Uh They're not always retained. Uh |
|
| 59:23 | on to a plasmid is, is really dependent on uh is there a |
|
| 59:32 | for the cell to hold on to ? And there's factors that play into |
|
| 59:35 | as we'll talk about. OK. they do have a, they can |
|
| 59:39 | a different way of replicating uh from , for example, our chromosome |
|
| 59:45 | Um So let's talk a little bit plasmids. So again, these are |
|
| 59:51 | chromosome elements. So you see this a, an E coli, I |
|
| 59:54 | that's been gently lic. So you the larger chromosome spilling out right threads |
|
| 60:02 | I've circled the what the actual, actual it's like right here. |
|
| 60:11 | Um Right here. OK. So see how small it is compared to |
|
| 60:20 | larger chromosome. And again, an size of a plasma is typically around |
|
| 60:26 | to 10,000 bases. OK. There be some that are on the larger |
|
| 60:31 | upwards to 50 to 100,000. But the more typical ones are much less |
|
| 60:36 | that. Um They um because they so the elements that make them |
|
| 60:44 | right, the or sequence, This is what this is where uh |
|
| 60:50 | is where replication initiates, right? um the uh OK. So the |
|
| 61:06 | because it has its own orbital it can replicate independent of the larger |
|
| 61:11 | . OK. And this plasmin So plasmas of course originated in with |
|
| 61:17 | . But when they were discovered, are 40 plus years ago by |
|
| 61:23 | um we've taken these plasmas out of and have engineered them for our own |
|
| 61:30 | . So if you may or may know plasmas are a vectors, |
|
| 61:35 | Or plasmas. These are uh really in um in the recoin DNA, |
|
| 61:42 | ? In, in, in uh them to carry various genes and |
|
| 61:46 | So we, we construct them for own purposes. So uh the, |
|
| 61:52 | other terms you see here like the three bam H one um pst |
|
| 62:00 | these are restriction enzyme sites. So can cut plasmids with restriction enzymes. |
|
| 62:05 | then, and then we combine in other genetic elements. That's how you |
|
| 62:10 | manipulate a plasmid and, and, , and construct it for your own |
|
| 62:14 | . OK. And so in this , we see uh a couple of |
|
| 62:18 | , the AMP which is Apollon tetracycline, which is for tetracycline |
|
| 62:25 | So, plasmas um because they're a size, they can kind of be |
|
| 62:30 | transferred between cells by different methods, by a conjugation. And in doing |
|
| 62:37 | , whatever plasmas are transferred, the cell will receive a course of plasma |
|
| 62:43 | the ability to express whatever genes are that plasma. OK. So um |
|
| 62:49 | number that also relates to or and can have, you can actually have |
|
| 62:55 | or in a plasma and one may may be for when it, when |
|
| 63:00 | um conjugating, one may be what , they often will dictate whether |
|
| 63:05 | whether it's high or low. And simply means how many copies are produced |
|
| 63:09 | cell. OK. So high copy can be anything from upwards of around |
|
| 63:14 | per cell. Low copy number OK. And so plasma is varied |
|
| 63:20 | that's typically dictated by the that they , whether it's a high or low |
|
| 63:25 | number. OK. Um We will next week when we talk more about |
|
| 63:32 | and conjugation how they could be transferred the cell to cell that they could |
|
| 63:37 | into the chromosome. So that, is true. OK. And |
|
| 63:41 | of course, by integrating to the that can kind of make them a |
|
| 63:46 | permanent resident of the cell. Uh But they can also, if |
|
| 63:53 | integrate, they can also actually come and exist as a extra chromosomal plasma |
|
| 63:58 | well. So they can go both . OK. Um And transferable. |
|
| 64:03 | are transferrable and so you can transfer cells of the same species, sometimes |
|
| 64:09 | different species. OK. And so we can classify plasmids in different |
|
| 64:15 | uh these are a couple of ways factor F factor cata plasmids based on |
|
| 64:21 | kind of genes they're carrying. So this one, since it has |
|
| 64:27 | resistance and hyper resistance, you might this A an R factor, |
|
| 64:31 | It has genes for antibiotic resistance. an F factor is what makes it |
|
| 64:37 | we call mobile, makes it OK. And so um this could |
|
| 64:43 | this pattern itself could be that way um let me just get this out |
|
| 64:49 | the way here if we um if were to like uh have a, |
|
| 65:00 | a jean in here, right, we call the factor, OK. |
|
| 65:11 | that factor means it has the sets genes needed to make it transferable and |
|
| 65:16 | components that, that are part of process. And so if it has |
|
| 65:21 | , we can say it has the factor and so what can be transferred |
|
| 65:25 | whatever other genes are in there? right. So for example, a |
|
| 65:30 | and tempo resistance. So the fact now we have an F factor in |
|
| 65:34 | , it makes it transferable and those resistances can be passed on as |
|
| 65:38 | OK. Kind of al simply just a 345 genes involved in a particular |
|
| 65:46 | pathway. Very common is like right? We talked about aromatic uh |
|
| 65:51 | of aromatic compounds. So those those often small pathways that can be found |
|
| 65:55 | plasmin. And again, if it that factor, it can be transferable |
|
| 65:59 | other cells. OK. Um So replication. So bidirectional replication is |
|
| 66:08 | you're familiar with. That's what you . Um you know, separate the |
|
| 66:13 | of the right. And then you , you create the two forks, |
|
| 66:17 | ? And then you carry out bidirectional , right, um forming two |
|
| 66:24 | What we saw before now can also by a mechanism called rolling circle |
|
| 66:32 | OK. So how that begins is the formation of a of a niche |
|
| 66:37 | which is basically a a cleavage of covalent bond right in the sugar prostrate |
|
| 66:48 | bone. OK. And in doing , you expose the three prime hydroxyl |
|
| 66:55 | of a nucleotide. So if you , you know kind of deification, |
|
| 66:59 | know that DNA polymerase works by adding to the three prime hydroxyl end, |
|
| 67:07 | ? That's how you synthesize DNA. if you expose that three prime |
|
| 67:10 | the DNA Climara can then begin to from that. Of course, what |
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| 67:14 | copying, it's copying the template Of the of the complementary strand as |
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| 67:19 | doing that. OK. And so happens is, so here's what |
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| 67:24 | we had create Nick, right? is the rep a replicates a enzyme |
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| 67:29 | the one that does this. So create a Nick, right? So |
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| 67:32 | expose that three prime in and from , you can um the plym can |
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| 67:40 | , right? And of course, you, it's copying uh this is |
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| 67:44 | template, it's cocky, right? so as it does, it's displacing |
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| 67:52 | strand. So you see how this here is being displaced, right? |
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| 67:57 | we we're synthesizing new DNA from that , right? So that's being displaced |
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| 68:03 | as it continues, right? So see the dark purple is the new |
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| 68:07 | for creating a copy. Now, this other strand that's been displaced |
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| 68:13 | right? It too can be right? So you have um uh |
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| 68:18 | and then you do the whole copying of that template and uh you create |
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| 68:24 | double stranded copy of that. All . And so that's what we see |
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| 68:29 | conjugation. So, so imagine if had some in conjugation, two cells |
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| 68:36 | coming together, so it could be cell, right? And this would |
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| 68:41 | the other. So OK. And we'll see this process next week, |
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| 68:47 | ? So in one cell as a , every as we're doing a growing |
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| 68:52 | replication, the other strand as is displaced is shoveled into a a cell |
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| 69:00 | mating with. OK. And so this other cell will get a copy |
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| 69:06 | that. Here's the one cell, the other cell. And so in |
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| 69:10 | other cell, it'll make the complementary of that and it too will have |
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| 69:14 | copy of that plasmin. OK. that's how you can transfer plasma plasmas |
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| 69:19 | cells through components that bring bring about connection between the cells. And then |
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| 69:25 | circle replication enables the the recipient cell get a copy of that plasmin. |
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| 69:31 | again, the replication we'll see again the context of conjugation where we're transferring |
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| 69:37 | plasmin text. So as mentioned earlier that question, you know, we |
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| 69:44 | the cells that rep painting, retaining um um plasmin itself, right? |
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| 69:54 | And so what are the factors involved that? And so selective pressure, |
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| 70:00 | is what it's about low copy number high copy number is also a |
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| 70:05 | OK. So think of a cell divided by binary fission. OK? |
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| 70:11 | if you're a low copy number or sorry, a high copy number of |
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| 70:15 | in that cell and that cell begins divide. Well, no matter if |
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| 70:21 | , you know, divides that plane however, right, because there's so |
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| 70:27 | plasmas, you know that at least is gonna end up in the daughter |
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| 70:32 | , right? So um so for copy number plasmids, you know, |
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| 70:37 | not, it can be an But you know, initially it's, |
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| 70:40 | it's it's the likelihood is very high both the daughter cells will receive a |
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| 70:45 | of the plasmin. But what if low copy number, right? If |
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| 70:48 | a low copy number plasmin, you can't just rely on the fact |
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| 70:53 | you know, division will occur such each gets a copy, right? |
|
| 70:57 | So to kind of improve the odds cells have what are called these P |
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| 71:03 | R or par proteins that's short for . OK. And so this, |
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| 71:08 | kind of like a quasi pseudo mitotic if you will, if you recall |
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| 71:13 | from mitosis, uh it's not but it kind of looks something similar |
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| 71:17 | of action as that. So the proteins actually bind to the plasmid as |
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| 71:23 | see there, then they polymerize and as they polymerize, they kind of |
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| 71:29 | um um push each plasmid to opposite of the cell. OK. And |
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| 71:36 | then when the cell divides, then know, each daughter cell receives a |
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| 71:40 | of the plasmin. So that's, kind of a unique situation for those |
|
| 71:44 | have these like one, maybe one two copies in the cell. |
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| 71:48 | And so having this mechanism kind of that, that, that, that |
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| 71:53 | the cell divides each cell gets a of that plasmin, OK. But |
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| 71:58 | know, back to selective pressure. even if you're a high copy number |
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| 72:02 | plasmin, you know, the the cell can actually lose those over |
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| 72:06 | if you don't have selective pressure on . OK. So what does that |
|
| 72:11 | ? Well, that just shows you of paid uh what what this, |
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| 72:15 | happens as the part proteins polymerize the go to poles and the cell would |
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| 72:22 | , right? And then each cell a copy of that. So back |
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| 72:26 | selective pressure. OK. So here's basic example, right? So here's |
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| 72:32 | E coli and it's carrying a plastic tetracycline resistance. OK? There's an |
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| 72:38 | coli that doesn't have that plastic. it's sensitive, it's, it's uh |
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| 72:43 | . OK. So, so if we're gonna uh the E coli |
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| 72:48 | tetracycline sensitivity will not grow on the not grow on this medium with, |
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| 72:55 | tetracycline, right? It's gonna be to it, the tetra resistant one |
|
| 73:00 | course, can OK. So will ecoli grow on both the types? |
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| 73:06 | course, because, you know, though it's resistance, right? |
|
| 73:11 | it's resistance. All right. That's , that's, that's what the superscript |
|
| 73:15 | means. So it will grow on to, on uh on uh tetracycline |
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| 73:22 | medium with tetracycline because it's resistant to . Ok. The um but it |
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| 73:29 | grew on here as well, of , because it's, it doesn't matter |
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| 73:35 | it's has a resistance, there's no in the media. So it'll grow |
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| 73:38 | as well. Now, the thing OK. If you, if you |
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| 73:46 | to grow it on this medium OK. If you continue to grow |
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| 73:51 | on that and then every so every every couple of weeks or so, |
|
| 73:57 | then transfer to fresh media and you doing that over and over, |
|
| 74:01 | You can go from here uh to media, right? Um That will |
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| 74:10 | eventually without tetracycline being present, The cells will lose that plasmid, |
|
| 74:19 | ? Because there's no selective pressure to it right. So again, this |
|
| 74:23 | back to the same thing we keep about is deficiency and energy, |
|
| 74:30 | It takes energy to maintain that OK. Why? Well, you |
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| 74:34 | to replicate it. All right, go through cell division and you have |
|
| 74:37 | replicate the plasmid, that's extra energy . OK? If there's no pressure |
|
| 74:44 | keep that plasma. In other if there's no, if, if |
|
| 74:47 | doesn't provide that cell with a selective , then why hold on to it |
|
| 74:52 | after several, you know, passages medium, it will lose that |
|
| 74:57 | Ok. That's why if you if you have any cholera and you |
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| 75:01 | a plasmid with a certain gene in , you want, and you want |
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| 75:04 | keep, want to hold on to . Well, then you put, |
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| 75:08 | put an antibiotic, resistance gene in and you keep it on medium with |
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| 75:13 | antibiotic that will ensure that that cell hold along that plasmid. OK? |
|
| 75:20 | it's, it's for its own survival do so, right? So the |
|
| 75:25 | there can, so certainly things that , that are on plan genes on |
|
| 75:29 | are not always critical for survival for , for the cell that has |
|
| 75:32 | but it can be in some So if it does have it, |
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| 75:36 | that will cells that possess that plast of course be the ones that survive |
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| 75:40 | they'll pass that plast on to others this population. Ok? But if |
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| 75:45 | selective pressure is not there and and it continues to not be |
|
| 75:50 | then there is a danger that the will be lost, right? Because |
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| 75:54 | , it becomes, it boil down uh efficiency and energy, right? |
|
| 76:00 | You know, is it worth the energy expenditure to hold on to this |
|
| 76:03 | if I'm not eating it? So that's kind of what's going on |
|
| 76:08 | ? Ok. Um Any questions about ? Ok. So, um, |
|
| 76:21 | let, let me um I'll tell what I know we're almost running out |
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| 76:25 | time. But let me uh I'll go through this a little bit about |
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| 76:29 | a plume race and then we'll wrap continue with the can on Monday. |
|
| 76:36 | , OK, so that, so chapter eight, this is the only |
|
| 76:39 | I'm really talking about here is, a and a little bit about |
|
| 76:44 | OK. So with bacteria, Ara there's a part of course that |
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| 76:51 | will um um synthesize the R N from the DNA template, right? |
|
| 76:58 | the, the core R A plume has these four subjects. And this |
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| 77:02 | what brings about the synthesis of the N A. OK. The sigma |
|
| 77:06 | is more transient. In other it will, it certainly will |
|
| 77:10 | right? So it's, it's right , this little red blob, it's |
|
| 77:14 | Sigma factor. And so it's what it to the promoter. OK. |
|
| 77:19 | so by binding uh to the it puts it in front of the |
|
| 77:24 | . And so it kind of acts scanning and looking for these what I |
|
| 77:29 | minus 35 minus 10 region. This is a region that's very common |
|
| 77:35 | pro promoters. OK. So Sigma looks for that and while it's attached |
|
| 77:43 | the ali, it brings it to area and once it does, so |
|
| 77:50 | strand separation occurs and you begin to the gene. OK? And so |
|
| 77:57 | promoter is gonna be set up right front of that gene. So as |
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| 77:59 | begins copying, it's gonna copy that coated sequence. OK? And so |
|
| 78:07 | that begins to happen, then the sigma factor will fall off. |
|
| 78:12 | . But then it can, is to bind another R N A |
|
| 78:14 | bring it to the promoter and, , and initiate the process again. |
|
| 78:19 | . That's what Sigma factor does. that's how, that's, you'll see |
|
| 78:23 | factors in, in you car your ac it works differently. But for |
|
| 78:28 | and art heal polymerase, that's how works with a Sigma factor that guides |
|
| 78:33 | to the pro boder. OK. so the, the minus 35 minus |
|
| 78:38 | sequences. OK. Uh These are we call consensus. In other |
|
| 78:43 | when we looked at numerous but uh from motors, we always see very |
|
| 78:49 | sequences in these two regions. And the minus 35 minus 10 it refers |
|
| 78:54 | upstream from the start side of OK. So either 10 nus upstream |
|
| 79:02 | the 35 upstream from the start in two regions, we see very similar |
|
| 79:08 | . OK. So here it gives example. So Sigma 70 is a |
|
| 79:13 | common sigma factor. OK? And think the 70 relates to how big |
|
| 79:18 | is the mask. Uh So it's very big, well, it's, |
|
| 79:23 | , it's one that's been found in lot of genes in, in uh |
|
| 79:27 | . And so, um so you here in yellow or both minus 35 |
|
| 79:35 | 10, the uh consensus sequences. they're very common among all these different |
|
| 79:42 | promoters of E COLI, for OK. And you can stretch that |
|
| 79:46 | different different bacterial species. They have in, in these, in these |
|
| 79:51 | 35 minus 10 regions to see this commonality in the OK. That's a |
|
| 79:58 | consensus sequence. So here you see start of transcription here right there plus |
|
| 80:06 | . OK. So use minus 10 minus 25 upstream from that. And |
|
| 80:11 | you know, we talk about promoter that really uh is about the level |
|
| 80:17 | expression. That's what that correlates OK is um levels of expression. |
|
| 80:24 | strong promoter will have high levels of compared to a weak promoter. |
|
| 80:30 | And you can manipulate these things, can. So that's what's done oftentimes |
|
| 80:34 | in biotechnology, when you want if you have a particular protein that |
|
| 80:39 | , that a bacteria makes and you want to enhance production of that |
|
| 80:44 | In other words, enhance expression. oftentimes begin by manipulating the factors that |
|
| 80:50 | expression. And a promoter sequence is of those. OK. So you |
|
| 80:54 | , you can alter the, the in within the sequence to maybe increase |
|
| 81:00 | in some cases, maybe it lowers . OK. So that's what down |
|
| 81:03 | up. So an up an up uh change is what increases activity |
|
| 81:10 | one decreases and so that, that bring that bring that about. And |
|
| 81:16 | um the uh so the minus um again, it is very common, |
|
| 81:22 | ? Most genes that's the Sigma factor controls it. OK? And or |
|
| 81:28 | uh Sigma 70 factor is what binds those promoters and it shapes expression. |
|
| 81:34 | ? Um So the minus 25 so minus 25 minus 10 is, is |
|
| 81:38 | common thing also not just for the 70 but also for the uh 32 |
|
| 81:45 | 28 right? These also have that of sequences a little bit different. |
|
| 81:51 | But these other Sigma factors are involved different functions. So things like heat |
|
| 81:56 | , we'll talk about that later. heat motility, uh stress response. |
|
| 82:01 | these have their own particular Sigma factors their particular sequences they respond to and |
|
| 82:07 | a different one here. This is we looked at earlier in the context |
|
| 82:10 | Regulon, right? The N 54 sigma 54 is nitrogen metabolism, |
|
| 82:17 | So that nitrogen Regulon, right is because the OPERON for that, for |
|
| 82:23 | particular Regulon all respond to that particular factor. So that's how you can |
|
| 82:27 | of control those coordinately, right? So uh that's a, that's a |
|
| 82:34 | think a good place to stop. We'll do some of this limited review |
|
| 82:40 | um uh next week. Uh So next Tuesday we're gonna meet in class |
|
| 82:48 | hopefully for the rest of the it will be that way. |
|
| 82:51 | And so, um, and if you, uh, if you |
|
| 82:58 | have any questions, um, then will see you all in person next |
|
| 83:04 | and, uh, we already has of the stuff at the beginning of |
|
| 83:07 | next time. Um Anyway, if no questions, folks, uh we |
|
| 83:13 | see you next week in person. . And, uh, I will |
|
| 83:21 | this recording and so you can review this afternoon or whenever, uh, |
|
| 83:26 | you like. Ok, thanks, |
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