| 00:01 | Mhm. Ok. Not that. , folks. Uh let's get |
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| 00:19 | So. Ok. Um So something this weekend, didn't it? I |
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| 00:32 | going, oh my God, what this all about? Ok. So |
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| 00:37 | that was kudos to uh that was effort. Excellent. I it turned |
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| 00:44 | to be a good game. um anyway, I uh I will |
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| 00:50 | a couple of points for good OK. Um So, but um |
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| 01:02 | just uh be patient on when those up. I, I've got a |
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| 01:07 | right here at two points. I'm not as proficient in canvas as |
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| 01:12 | was in, in the whiteboard. I don't know how to add like |
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| 01:16 | , a column yet of data. kind of funnels through a certain way |
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| 01:20 | canvas. I haven't figured it out . So just know it'll be |
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| 01:25 | it'll show up, just be OK? If I do start getting |
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| 01:30 | about where's my two points? where's my two points, then it |
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| 01:33 | away. All right, so don't that. All right. Um All |
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| 01:38 | . So we are, oh, best part of this sarcastically. I'm |
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| 01:42 | this, the best part of Saturday being one hour in a parking garage |
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| 01:45 | I could get out. Ok, , we could get out. It |
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| 01:48 | a bunch of us went. So was, that was insane. |
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| 01:53 | So, um, ok, usual stuff. So weekly quiz this |
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| 02:00 | , uh we're in into unit obviously, um, which actually really |
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| 02:07 | up at the end of next Ok. So a relatively short uh |
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| 02:14 | , um, even though we finish the second there, the exam is |
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| 02:18 | not yet until a week later. the 10th, but remember that scheduler |
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| 02:24 | up on, uh, Friday. , um, if you wanna be |
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| 02:28 | already when it opens, that's, when it will for exam three. |
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| 02:34 | . Uh, speaking of exams, two is right on target in terms |
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| 02:39 | , you know, 70 average is of what I shoot for. |
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| 02:44 | so, you know, um, , some to email, you |
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| 02:49 | to arrange to see the exam. fine. Ok. Uh, |
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| 02:55 | uh, in addition, coming by office hours, you can't make office |
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| 02:58 | , other times can be arranged. a problem. So, uh, |
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| 03:03 | there's two more exams, obviously, , three and four. So, |
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| 03:08 | , again, if, um, , you need help or you want |
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| 03:14 | or whatever, just arrange a time meet, just email me. That's |
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| 03:19 | . Um, the, uh, you've got basically now at this |
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| 03:26 | uh, it's about equal bet between , weight of exams and weight of |
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| 03:31 | other stuff. Ok. Homeworks and . So, so very quickly, |
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| 03:37 | know, the, the weight of exams will have a bigger influence on |
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| 03:42 | grades. So obviously you wanna um, if you haven't been, |
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| 03:45 | wanna improve that exam scores? So, uh, again, if |
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| 03:50 | need help, just let me know . So, uh, again, |
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| 03:56 | I said it, after the first , this exam two stuff doesn't show |
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| 04:01 | because remember the final is not It's its own thing. Chapters 23 |
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| 04:06 | 26 is exam four. OK. , um anyway, so let's uh |
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| 04:15 | ahead. So this is a little of a recap here like we always |
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| 04:19 | . OK. So, um So we are looking at kind of |
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| 04:25 | of uh bacterial genetics. OK? looked at um how genes are kind |
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| 04:32 | organized in prokaryotes, this operon And so um the uh looking at |
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| 04:42 | chromosome here and so a hypothetical uh of genes. So structural genes |
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| 04:50 | So, so the one promoter, genes associated with it, that's kind |
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| 04:55 | the operon structure. OK. So the promoter operator and structural genes |
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| 05:01 | are that element the opera. So the uh idea here being that |
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| 05:09 | control the entire pathway, right? A B and C in this |
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| 05:14 | would be part of a common metabolic , synthesizing s synthesizing something or maybe |
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| 05:21 | down something, right? Cat bolic anabolic pathway. Um And by doing |
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| 05:27 | this way you can, you of course, control the whole |
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| 05:30 | turn it on, turn it et cetera. OK. So control |
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| 05:35 | uh are regulatory genes somewhere, you , doesn't have, doesn't have to |
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| 05:39 | right beside the opera can be Uh But nonetheless, that regulatory protein |
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| 05:46 | from that gene interacts with the operator . OK. So that's kind |
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| 05:53 | that's what we'll look at next week maybe starting Thursday into next week, |
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| 05:58 | at how this occurs. OK. basically, it's a physical block, |
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| 06:03 | know, to, to prevent OK. And uh as we'll |
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| 06:08 | uh starting Thursday, this is one of control, but a very common |
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| 06:14 | , a common way in bacteria in to control their genes. This is |
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| 06:19 | we call transcriptional control. OK. , um the uh of course, |
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| 06:28 | uh when you, when you have operon that are part of a common |
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| 06:33 | metabolism, let's say we call that Regulon that when you're controlling multiple operon |
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| 06:41 | in a kind of common metabolic feature nitrogen metabolism, for example. |
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| 06:47 | So the reg um entity outside the chromosome, 12,000 nucleotides is kind of |
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| 07:03 | average size, some can be bigger but they have their own origin of |
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| 07:09 | that enables them to replicate themselves separately the chromosome. OK. And so |
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| 07:16 | rolling circle replication is one of those we looked at and so plasmas |
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| 07:21 | of course, replicate like the like the bidirectional pull the strands |
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| 07:26 | copy OK. In pull the strands and copy. And then um but |
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| 07:34 | rolling circle application, we'll see that in the context of conjugation. |
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| 07:40 | So uh basically, we're just creating uh breaking a bond in that uh |
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| 07:47 | phosphate backbone to release the three prime . So we're calling how DNA polymerase |
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| 07:54 | in replication. It looks for this as nucleotides to it. Of |
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| 08:00 | they're adding it based on the template this inner strand. OK. And |
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| 08:05 | it, it grows in length going but displacing, displacing the, the |
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| 08:12 | the uh opposing strand as it goes , right? And this is actually |
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| 08:17 | strand here is what can be funneled a cell that it's mating with through |
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| 08:23 | . For example, it doesn't have , it doesn't have to do this |
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| 08:26 | in association with conjugation. But you , you do see that OK. |
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| 08:31 | so the strand, the strand and can be replicated, copied primers and |
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| 08:37 | preliminary to copy that strand and you two copies. OK. Um The |
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| 08:45 | the uh certain other things you remember , like you remember the selection, |
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| 08:49 | on to a plasmid, like high number, low copy number, select |
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| 08:53 | pressure for, enables the cell to on to the plasmid. OK. |
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| 08:58 | Then in transcription, we just looked kind of the sigma factor feature of |
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| 09:04 | so that their ply uh gets to right spot in front of the gene |
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| 09:09 | the Sigma factor, finding the promoter it and then initiates a transcription. |
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| 09:16 | the minus 35 minus 10 is a consensus sequence. You see in many |
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| 09:22 | promoters that are recognized by Sigma Uh But again, to roll the |
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| 09:26 | factors to find the promoter, um it to bind, initiate transcription, |
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| 09:32 | it basically just falls off and combine another cli race. OK. And |
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| 09:38 | finally, here is kind of, talked about uh expression levels that will |
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| 09:42 | more important. And we get to 10. But uh what we call |
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| 09:48 | expression versus high level, OK is about, you know, the affinity |
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| 09:53 | the promoter um uh for that RN pli. OK. And so we |
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| 09:59 | enhance that. So binding, binding to a promoter means eye |
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| 10:03 | OK. So if we can enhance , we can promote greater expression, |
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| 10:10 | greater expression means more transcripts, which more protein being made. OK. |
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| 10:16 | transcription factors uh activators uh et these collectively uh interact with a promoter |
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| 10:24 | promote this high level expression. Um The same thing, same thing |
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| 10:30 | us, right? You can involve just these factors here binding, but |
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| 10:36 | too can bring the chromosome into play it becomes part of that, making |
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| 10:43 | promoter very um high affinity. So, uh anyway, so that's |
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| 10:50 | of in a nutshell. What we last week. OK. Uh And |
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| 10:55 | the next slide as well is kind the last slide of the chapter 78 |
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| 10:59 | and there's more of a summary. ? OK. Um Is there any |
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| 11:04 | about stuff last week maybe? OK. So, uh so |
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| 11:10 | this is kind of uh this is kind of the last slide I think |
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| 11:13 | that, of that uh chapter And so it's more of a summary |
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| 11:17 | well. So, so we got , here's our DNA, OK. |
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| 11:23 | we're gonna see the relationship between DNA the RN A and the protein, |
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| 11:27 | ? And so here's our promoter. . So remember um it may not |
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| 11:32 | obvious to you but things like a , uh an operator sequence, these |
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| 11:37 | DNA, right? We're talking about here, OK? In front of |
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| 11:42 | plus one is the start of the uh uh area. OK. And |
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| 11:48 | uh we then have, so remember coding and template stra, right, |
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| 11:52 | minus, OK. The um the message you get from copying that |
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| 12:01 | right, sort of the polycysts, ? So we have this, in |
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| 12:04 | example, we have just two right? But uh they are the |
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| 12:09 | for those are part of the same transcript. This is all this |
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| 12:14 | all one continuous transcript. So you the elements here start stop for each |
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| 12:23 | . So each, even though they're one continuous message within that will be |
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| 12:30 | punctuation mark if you will start and , are, are in each section |
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| 12:34 | that transcript. OK. Um The ribosome obviously that's where translation comes |
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| 12:43 | OK. So the 78 ribosome is intact large um complex comprising the 50 |
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| 12:52 | S units. The 30 S is the um um initially binds to the |
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| 12:59 | binding site and then the larger one with it to form the form the |
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| 13:04 | complex. And so this represent Bonnie . That's that Shine Del Garno |
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| 13:09 | So that's just the name of the guys that discovered this. OK. |
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| 13:14 | so um that binding then remember, you get the polyribosome formation. |
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| 13:22 | Ribosome binds, starts to translate another binds and they keep going, |
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| 13:27 | So it gets full of ribosomes each different states of completeness, completeness of |
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| 13:34 | , right? And so of you form uh the protein. So |
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| 13:38 | see ribosome binding site here, And then here as well. |
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| 13:47 | So the whole thing will be full ribosomes that polysome formation. OK. |
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| 13:53 | of protein being made. OK. um any questions about that? |
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| 14:01 | So um let's, so we had question before. This is one of |
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| 14:06 | before and after ones, right? we look at this. So we |
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| 14:09 | this before. So let's look at again and see what we got. |
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| 14:16 | . Mm Right. Yeah. Mm All right. Let's count down from |
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| 15:31 | . OK. Um I think I last time F was like a big |
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| 15:37 | . So D is correct. Um The operator serves as a site |
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| 15:47 | if anything regulatory protein binding to OK. Operon possesses one promoter, |
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| 15:54 | genes of a single operon code for are the same, not different pathways |
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| 15:59 | wouldn't make any sense. It's gonna the same in a path. The |
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| 16:03 | factors bind to the promoter not to sh the shine Dogan is for the |
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| 16:09 | . OK. All right. Um this concludes 78. Remember going to |
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| 16:17 | textbook? It's not a big chunk this. It's not the entire |
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| 16:21 | So just make sure you stick to we're covering now. OK. Um |
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| 16:27 | question that, so here's one, will take us into the next |
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| 16:39 | Mm hm. Mm hm. So remember if you don't think you |
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| 17:36 | a correct answer, you know what pick. So give a second for |
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| 17:44 | to change their answers. OK. we go. Yes. Um It's |
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| 17:58 | OK. So, and we're gonna through each of those blow by |
|
| 18:02 | So just hang on. Um Obviously giveaway for a not being correct game |
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| 18:11 | bacteria have gametes, gonads, nope, not even the manliest of |
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| 18:18 | coli have those. Um OK. transfer. All right. So um |
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| 18:29 | here. So uh um OK, look here, vertical transmission. |
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| 18:36 | So vertical transmission, think of it how you got your genes, |
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| 18:42 | You got yours by vertical transmission, ? Except um, you didn't have |
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| 18:48 | one parent here, right? You two, right? Two genetically dissimilar |
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| 18:55 | , male, female, right? all know the birds and the |
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| 18:58 | So, um, but you obviously that's what you inherited from your |
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| 19:03 | , except from your father instead of , right? So in the pro |
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| 19:07 | world, vertical gene transfer is basically fish. So divides, obviously, |
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| 19:14 | daughter cells receive a copy of the . OK. So that's the counts |
|
| 19:20 | most of the acquisition of genes that receives, put a number on |
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| 19:29 | Uh 80% of the genes uh acquired way. That's, that's how they're |
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| 19:36 | in the bacterial cell, right? this other 20 whatever percentage um is |
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| 19:44 | horizontal gene transfer, right? So is kind of all about. So |
|
| 19:49 | with vertical gene transfer, you're going . Bacteria are basically a xerox |
|
| 19:56 | right? Just put a cell in and how many copies do you |
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| 19:59 | Right. They're all identical like we know that's not the case, |
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| 20:03 | Uh All E coli is in your right now are not even genetically |
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| 20:08 | right? It's gonna be variations between . OK. Um M maybe very |
|
| 20:13 | , but some may be a little , a little bit larger differences. |
|
| 20:18 | . So how does that happen if doing binary fission and copying each |
|
| 20:22 | Just, you know, making copies copies we know that mutations can |
|
| 20:27 | right. Spontaneous mutations occur, mistakes made during replication. Um Sometimes they're |
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| 20:33 | fixed um and they remain OK. that's what contributes to variation. |
|
| 20:40 | Same thing happens in us but just as, at quite the same rate |
|
| 20:44 | it does in bacteria. OK. occurs at e at an even higher |
|
| 20:49 | . Uh So bacteria is like one one in a million. I think |
|
| 20:54 | error is made and it's not And that, I think it's like |
|
| 20:57 | in 10 to the 10th or something that. It's, it's very |
|
| 21:02 | It's good. It's a very high . Uh But for bacteria it's, |
|
| 21:06 | know, it's, it's a higher rate than what we have. |
|
| 21:11 | But it's not crazy. But because grows so fast, right? Even |
|
| 21:15 | a single colony of cells, which a million plus cells, certainly there |
|
| 21:22 | a few in there that um have a mutation and the, the mutation |
|
| 21:26 | have to mean it's now changed into completely different because most, most mutations |
|
| 21:32 | to be kind of just silent. don't do anything good or bad. |
|
| 21:35 | ? Or they're bad. All That's mostly what mutations result in, |
|
| 21:40 | ? Either no effect or a bad . OK? But sometimes it's a |
|
| 21:45 | one. OK. But nonetheless, the point here is that, um |
|
| 21:49 | can see because procurers grow so we can see, you know, |
|
| 21:52 | little mutation can can occur and we see that kind of real time almost |
|
| 21:58 | ? Within, uh uh you a few hours, if not |
|
| 22:02 | Ok. But nonetheless, so horizontal transfer is another way to acquire genes |
|
| 22:08 | they don't reproduce sexually. Right? a way to generate variation, |
|
| 22:12 | So remember why this variation is so , right? It's important to nec |
|
| 22:18 | necessarily be a clone, right? variation in the population, right? |
|
| 22:24 | is evolution 101, right? Um in the population provides uh I like |
|
| 22:30 | refer to it as options, If you're in a big population and |
|
| 22:36 | in an area where some kind of change occurs and now you don't have |
|
| 22:41 | best combination of genes maybe and you survive as well and maybe this group |
|
| 22:45 | here does because they have variations of genes maybe acquire something different. So |
|
| 22:51 | enables them to survive future generations and inherit those genes. So I think |
|
| 22:57 | all know this concept. So that's it's good to have variation, |
|
| 23:01 | If we were all clones, Basically, you everybody would respond the |
|
| 23:06 | way, good or bad. So having variation is really what it's |
|
| 23:11 | about uh across the whole span of . OK. Um And so these |
|
| 23:19 | to acquire variation through horizontal mechanisms, we can't really do. OK? |
|
| 23:26 | bacteria can or Kia can it through four mechanisms? OK. So this |
|
| 23:32 | kind of put this into context So here is a um for the |
|
| 23:36 | blue blob is basically the, basically a gene pool, right? So |
|
| 23:43 | they say pan genome, that means of us, of all E |
|
| 23:47 | we've sequenced and we've done this for and have a huge database is about |
|
| 23:55 | little over 10,000 genes. Uh Different are known to be in among E |
|
| 24:01 | , doesn't mean each E coli has , right? So gene pool, |
|
| 24:06 | ? You don't have all the genes the gene pool, you have a |
|
| 24:08 | of them. Ok. So yellow just that. So yellow is the |
|
| 24:14 | E coli. It has about of 10,000, it will have about |
|
| 24:20 | OK. And so in the core . So that refers to that would |
|
| 24:27 | genes common to all E coli. ? All E coli will have those |
|
| 24:34 | 67. OK. And those are like uh proteins involved in um uh |
|
| 24:44 | replication, protein synthesis, uh certain processes like glycolysis, the like in |
|
| 24:54 | because ribosome genes, these things like are all core functions that the cell |
|
| 25:01 | to have to even live, So that's what we call them core |
|
| 25:05 | genes. OK. Uh The other are things that can enable their survival |
|
| 25:12 | certain conditions. Um We call them genes. The uh and so an |
|
| 25:18 | here, you know, going back the not all new codes are |
|
| 25:21 | Uh, here's an example of two different strains of K 12 is |
|
| 25:25 | you using, lab, um, . Uh, 0157. I call |
|
| 25:31 | Chipotle E coli. Ok. food borne pathogen. Ok. |
|
| 25:37 | and that right there tells you what it different right from, from your |
|
| 25:42 | e coli genes involved in causing right? Various genes. Ok. |
|
| 25:48 | it has a number of those different your average K 12. OK. |
|
| 25:54 | so looking at and this is you know, it says e coli |
|
| 25:58 | , but it's pretty much similar, or less across the board for most |
|
| 26:04 | types. Um is that mostly protein , unlike our genome? OK. |
|
| 26:10 | Only about 2% of virus is protein . So um there's always gonna be |
|
| 26:17 | segments of the genome for regulating right? Because regulation is a |
|
| 26:21 | big, big thing. OK. uh remember that not all genes code |
|
| 26:27 | proteins, right? So we're gonna some of that code for things like |
|
| 26:31 | , right? Different different RN A and uh then the 20% right? |
|
| 26:37 | 20% acquired from other microbes. And so again, as I |
|
| 26:45 | these two kind of uh categories of , right? The core and the |
|
| 26:49 | OK. Core. Again, think it as the informational genes, gene |
|
| 26:56 | or synthesis, et cetera. Now, so with the 20% |
|
| 27:01 | How does one determine that? You look at a genome and go |
|
| 27:06 | . Yeah, this, this this over here that that came from horizontal |
|
| 27:09 | transfer. OK? How, how kind of a basic way that uh |
|
| 27:17 | can look at that this is all computers, you know, just looking |
|
| 27:22 | data, uh crunching numbers, that of thing. And so uh you |
|
| 27:27 | look at an E coli segment of chromosome. OK. And C so |
|
| 27:34 | term GC, so percent GC is guanine sing ratio, right? If |
|
| 27:41 | recall when you learn DNA structure and bio uh who is that guy? |
|
| 27:49 | his name? Char Bob's rule. . That um I don't think I'm |
|
| 27:55 | that right. But that's he's the that came up with. Oh |
|
| 27:59 | Uh the A T ratio and A ratio, right? Um That G |
|
| 28:06 | GC is a uh a number that was used or is used sometimes to |
|
| 28:13 | at um relationships between organisms, They have a similar percentage GC, |
|
| 28:19 | go oh They might be closely OK. So, so um the |
|
| 28:29 | so that parameter was used for quite while to look at relationships until of |
|
| 28:34 | DNA and 16 sr a lot. nonetheless, um the uh so E |
|
| 28:40 | have about that percent of, of GC in their DNA, |
|
| 28:44 | all E coli do. OK. so you can go, OK, |
|
| 28:48 | I'm looking at a stretch of um it should, if it's E |
|
| 28:53 | DNA, it shouldn't have that percent GC. Ok. But you may |
|
| 28:58 | this and, and look, well, here's a continuous stretch and |
|
| 29:02 | gonna be a significant number of bases be statistically accurate, right? You |
|
| 29:07 | come across, say 2500 bases in row that have that. I |
|
| 29:12 | that's a pretty good, uh, number. And so if that has |
|
| 29:17 | 54.8 then that's significantly different. So then you go, OK, |
|
| 29:23 | among that has that kind of, , of GC content? And this |
|
| 29:27 | does and our bacter Ara, it's enteric bacterium like E coli. Um |
|
| 29:34 | so it could have acquired whatever that , it could have acquired that through |
|
| 29:39 | kind of one of these transfer mechanisms that species. OK. Um |
|
| 29:45 | so that's kind of a basic way how you do this. There's other |
|
| 29:48 | this is kind of a kind of first pass kind of a thing just |
|
| 29:52 | kind of see if this is really to look at further. OK. |
|
| 29:57 | you know, it's, it's a method. Uh not necessarily only the |
|
| 30:00 | one, but you corroborate it. uh um but the point is e |
|
| 30:06 | has a lot of genes acquired this as do other pro curios. |
|
| 30:12 | And so what we're gonna look at this section is different ways this can |
|
| 30:16 | . OK. And so this this is really just a basic |
|
| 30:21 | We're going into each of these in little more detail. But um |
|
| 30:26 | I just pull the plug. Come . OK. Come on, |
|
| 30:37 | Hold on. I really just pulled plug on it. My microphone went |
|
| 30:41 | too. Goodness. OK. Ah pulled the uh literally pulled the plug |
|
| 30:50 | has to reboot. OK. There go. Jeez. Sorry. Mm |
|
| 31:11 | me pause |
|
