| 00:04 | Okay. Okay folks. Welcome. let's get started. Oh okay. |
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| 00:31 | um jesus christ mm hmm. Um yeah, come on my computer |
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| 01:01 | the computer died all this stuff So anyway, exam to check so |
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| 01:14 | to I'm starting to put the they posted on blackboard but it's very similar |
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| 01:21 | the first exam. Um So another now which for some is okay. |
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| 01:26 | I stay in course or do I the course? I don't tell you |
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| 01:29 | do that. But what I can , just give you the information to |
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| 01:32 | you make to help you make that whether you want to or not. |
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| 01:36 | . So um a midterm grade will calculated. It will come out sometime |
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| 01:43 | week. Okay. It will include up to this point and just doing |
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| 01:48 | scores Quizzes on blackboard, uh clipper , you know everything. Alright. |
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| 01:55 | it'll be a uh you can use to evaluate. Okay. Uh believe |
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| 02:01 | drop date is April 20th. So um anyway again I don't usually |
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| 02:12 | um my opinion but um you I can only give you information |
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| 02:19 | And so if you make a my eye on this side toward the |
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| 02:24 | of, well you're doing great. got to figure out How to to |
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| 02:31 | because you dropping the tape again, gonna be in the same book. |
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| 02:35 | me, I've seen this over and for 17 years. Okay. So |
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| 02:43 | that's why I say can we stick out and try to improve. Make |
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| 02:47 | her goal to you know do as you can and get help for God's |
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| 02:52 | . Okay If zero people come to hours literally nobody comes to office |
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| 03:00 | Okay so you can leave the house can lead you can lead a horse |
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| 03:02 | water you can't make him drink. so again I'm here for the resource |
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| 03:08 | you need it. Um So okay santa will be available to view uh |
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| 03:17 | tomorrow. Um And uh certainly looking questions let me know. Okay uh |
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| 03:26 | see so today we're gonna continue with three so we'll finish up eight. |
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| 03:31 | into nine, finished with a chunk that and then 10 ft class. |
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| 03:36 | would probably be some more than the Tuesday because 4.2 I'll give you all |
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| 03:44 | 10 1 10 1 is kind of intro. Here's how the basics of |
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| 03:49 | regulation in bacteria and then we'll kind apply that in the next part. |
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| 03:54 | is um uh Ron Ron. If looked that far ahead or not uh |
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| 04:03 | do this week backward quiz. Um will cover uh last week seven and |
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| 04:11 | talking about 7888 789. Okay the says it also includes 10.1 but I'm |
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| 04:21 | gonna do that. It's just gonna 78 and nine on Blackwater quiz. |
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| 04:25 | I'll send out another reminder email thursday To repeat that again. Okay so |
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| 04:34 | there's already like there's like six questions think on the backboard quiz. Um |
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| 04:38 | work that's due next sunday. So 21 22 is an assignment 78 I |
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| 04:46 | both those are kind of rather So um anyway so that's coming |
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| 04:54 | The other thing here is um the er for exam three which is April |
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| 05:04 | That opens on Friday of this week four. Okay so that's when you |
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| 05:11 | first time here for that. Okay um let's see, I think any |
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| 05:22 | . Yeah. Alright so let's go and start with clicker question is going |
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| 05:30 | relate to most of it. The think we talked about all that. |
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| 05:36 | mean I've been super specific on a of these things but uh we're gonna |
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| 05:42 | fish all this up today uh for minutes probably. So someone of a |
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| 05:47 | for some of these. Okay, we're just true. Some gene |
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| 05:54 | Okay so remember the operation structure, , bacteria and what that entails. |
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| 06:05 | And then the have certain elements, of the process, G expression, |
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| 06:15 | factors you may recall. Okay. , anybody, I assume everybody who |
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| 06:33 | the whole Oscars fiasco thing. I that in real time and I said |
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| 06:40 | is a joke or it's just reel it was real when I saw Will |
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| 06:45 | was mountain, I didn't realize how that guy was, I guess how |
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| 07:00 | was Will smith justified? No, yes defending defending the honor of his |
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| 07:08 | . I did laugh at the general know but but in hindsight. Um |
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| 07:19 | don't know if you you know the G. I. Jane Demi moore |
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| 07:24 | you shave your head. Alright. fast. That's my error. That's |
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| 07:30 | your. Alright. Let's see what are. Um um um um um |
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| 07:37 | um um um Somebody did some Okay. Uh Let's see. Is |
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| 07:43 | correct? All the true operator serves the site for sigma factor binding is |
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| 07:51 | mm hmm. Is that true? operator doesn't site for sigma factor about |
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| 07:58 | . For service as a site not operator can I? Uh So that's |
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| 08:05 | false. Okay. An operator possesses promoters. True. One promote as |
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| 08:16 | opera in one promoter, multiple structural . Multiple genes under control of one |
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| 08:22 | structural genes have a single operation. for enzymes of different metabolic pathways. |
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| 08:27 | wouldn't make any sense because an opera all about being efficient. They're gonna |
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| 08:31 | kind of common pathway. So you it Expression of us of the whole |
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| 08:36 | at one time. Um A single transcript will contain information for all structural |
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| 08:44 | of that opera. That is That's that policy. Histrionic message. |
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| 08:49 | . Some of the factors buying to shining del Garneau sequence. So you |
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| 08:52 | not have known that unless you looked . That's Ribas own binding site. |
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| 08:59 | . Not a sigma factor. My . So that's what we'll go through |
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| 09:06 | . So um so d is the answer. Alright. What's your |
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| 09:14 | 13 If you answered. D who it? Who was a deep person |
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| 09:20 | you guess? Or did you know ? You do it stone cold. |
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| 09:25 | . Good. All right. Um so let's look at just as a |
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| 09:32 | of summary of everything here. Okay we talked last time of course about |
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| 09:38 | know our our focus is called pro genomes. And so here's our bacteria |
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| 09:45 | you can actually um slowly uh lice gently and and the and the chromosome |
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| 09:50 | slowly spool out of it like you there. But so thanks to |
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| 09:57 | Right so genome size um half a to five million is about the range |
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| 10:05 | the appropriate genome. They can have chromosomes and the dish. I mean |
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| 10:11 | in addition to the larger chromosome and represents the entire genome, refugee |
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| 10:17 | all of the D. N. . In the organism. And plasmas |
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| 10:21 | certainly contribute to that. Um The so go to the opera again. |
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| 10:29 | . So here is um uh So opera itself is the promoter. Okay |
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| 10:39 | operator structural genes. So this part the opera. Okay so once you've |
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| 10:43 | it all operator works in conjunction, regulatory proteins partly control methods. |
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| 10:49 | We'll go more into that next week thursday. Um Again the product is |
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| 10:56 | to be a transcript of continuing a piece of RNA containing the coding information |
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| 11:04 | three or however many genes that And the opera generally isn't bigger than |
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| 11:15 | . This kind of seven is kind the high range. OK um We'll |
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| 11:22 | about it next week has five genes part of the operation. But again |
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| 11:27 | just it's one continuous message that gets into its subsequent proteins. Typically part |
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| 11:34 | will be part of a common Okay. Um let's see what else |
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| 11:41 | . I mean regular. Excuse me now we're evolving multiple operations and we're |
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| 11:49 | them. Kind of coordinate coordinate way they all are part of a bigger |
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| 11:55 | function. So we use nitrogen metabolism an example last time. So operations |
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| 12:01 | in different aspects of that. The kind of control that so they can |
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| 12:06 | the utilization and allotment of 19 comments we usually many different things makes sense |
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| 12:13 | control all together. So it's not energy being efficient. Um and the |
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| 12:22 | can occur through the sigma factors or sigma factors which will start off with |
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| 12:28 | are how the race that brings about transcription is guided to the front of |
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| 12:35 | genes. So you want to make that commemorates is going here. Okay |
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| 12:42 | don't want to just plop them down . So oriented and signal factors helped |
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| 12:48 | that. So then we finished with about plasmas. Right. And so |
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| 12:55 | plasmas are these autonomous segments of N. A certain piece of |
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| 13:00 | N. A much smaller than chrome are transferable can be transferable among |
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| 13:07 | Um Of course they carry multiple genes involved in different functions. Can be |
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| 13:15 | , tablet, tablet catholic can be resistance. It can be lots of |
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| 13:20 | things. Okay but it's only gonna a few because obviously plasmids are |
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| 13:24 | They're only going to carry a few . Exactly. But the fact that |
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| 13:29 | has the story right, the ori of replication is what enables it to |
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| 13:36 | autonomous. They can replicate itself. then I think that the hand because |
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| 13:41 | uh rolling circle replication, right? it can do the conventional replication type |
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| 13:49 | our chromosomes activity um bi directional replication form and that mechanism. But it |
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| 13:58 | also be rolling circle replication which we'll today in the context of conjugation. |
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| 14:05 | as the chromosome I'm sorry the plasma strand, well we'll create will break |
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| 14:14 | bond living experience and then begin to from that Exposed three prime hydroxy |
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| 14:23 | And then you go around like this that template but then technology the other |
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| 14:31 | and that was trying to get shoveled typically it would be another cell. |
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| 14:36 | it looks something like that cell one to and that so there so now |
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| 14:42 | the recipient self hands up with a of that plastic and whatever genes are |
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| 14:47 | . Okay that's that process. The we'll talk about later. Okay so |
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| 14:53 | kind of the highlights uh from last . Um so what we'll pick up |
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| 15:01 | with. Okay. Only in terms so again, number seven and eight |
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| 15:09 | stuff. Okay. But we're only at a small portion of each chapter |
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| 15:16 | I'm not gonna expect you to be to translate hey transcript using genetic code |
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| 15:22 | and those kind of things you probably . Okay. But this is |
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| 15:27 | here's the overview and here's some things precarious. Okay. And of course |
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| 15:33 | arctic summer I used to think particular it is a benefactor. Okay, |
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| 15:38 | again, just mentioned that that's what molecules so they can do the |
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| 15:46 | Right. Um need to promote A rider zone needs mechanism as well |
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| 15:59 | align it in front of the um to be translated. Okay. They |
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| 16:05 | arrived his own binding site. These a certain effect. Okay. And |
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| 16:12 | um when you look at precarious, was done, done this for years |
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| 16:22 | . Um just saying, okay, line up these promoter sequences from lots |
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| 16:26 | bacteria that we've sequenced. And is anything similar. Okay, let me |
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| 16:32 | flash forward real quick. I'll come to this and so let's look at |
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| 16:37 | bunch of promoter sequences and what they . There's some hm ology Right. |
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| 16:45 | a couple of areas -35 -10. , what that refers to is those |
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| 16:52 | the basic distances upstream from the start transcription, which is plus one mm |
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| 17:02 | . Okay, so that's plus one and then you go minus numbers and |
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| 17:13 | the promoter. So they find that is, you know, a lot |
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| 17:16 | commonality among different promoters factor of motors the -25-10. Okay. And hence |
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| 17:25 | name -35. See that's what sigma sigma seven. Right. So there's |
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| 17:33 | , you might think that there are sisters. About 3000 on average, |
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| 17:40 | to 5000 genes in the but you , okay, there must be 3-5000 |
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| 17:49 | factors in front of the genes. , well no, you have the |
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| 17:56 | model because that means that means you one promoter and multiple genes. So |
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| 18:01 | lowers the number. But even then may still be around, you may |
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| 18:04 | , oh, this is gonna be the hundreds that you have from the |
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| 18:07 | factors but you don't have maybe 8 10, 12, maybe once. |
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| 18:13 | that's it. Okay, so a very common one is Sigmund 70 |
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| 18:22 | 60% or more of jeans utilizes. . Um, and there are others |
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| 18:31 | will briefly mentioned here. And so are what we call consensus sequences. |
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| 18:36 | there is such a commonality homologous between different types of mothers. They are |
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| 18:41 | common in this way, You can the -25 -10. A consensus there |
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| 18:46 | a consensus among all these promoters and have this very similar sequence. Okay |
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| 18:51 | they're often high in 80 base Okay remember goes back to the 18 |
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| 19:04 | bonding is 200 months GCS three. remember where transcription is going to occur |
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| 19:10 | pull the strands apart. So it of makes sense to have maybe a |
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| 19:14 | bit more Concentration of 18 base pairs energy to pull it apart than |
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| 19:20 | Okay. Um now um so you change. And one of the things |
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| 19:28 | in um biotechnology uh we're often trying get engineer bacteria to either uh make |
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| 19:40 | produce the protein of some sort It's a commercial value. Welcome to |
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| 19:44 | lots of a particular protein or Maybe an enzyme that can have some |
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| 19:50 | of catalytic activity you want and you to mass produce it. Uh Force |
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| 19:55 | to make lots of it because when go now from from the academic lab |
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| 20:00 | industrial lab very often we're talking about and quantities of stuff, okay we're |
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| 20:07 | to commercialize the process stuff won't do need buckets of stuff. Okay so |
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| 20:13 | means making bacteria will produce these things they wouldn't normally do. So that's |
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| 20:19 | you have to go in there and with. Okay fiddle with them gross |
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| 20:23 | , prison with them D. A manipulate. Okay and one of |
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| 20:28 | things to do is to tinker with regions. Right? So you can |
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| 20:34 | based changes and erase this. You make basic changes in the promoter and |
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| 20:43 | can lead to either up or So down means a decrease in expression |
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| 20:51 | for. And what has changed is crossed up uh It's called a |
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| 21:01 | Up right increasing expression. Okay. you often do this um if you |
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| 21:08 | out the if you discover the promoter the june you're working with and you |
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| 21:12 | that perfectly mass produced, high quality one of the things you can try |
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| 21:16 | do is fill it with the Make it more making up reputation. |
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| 21:23 | . Um The terms promoter strength. high versus uh weak expression. |
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| 21:33 | Let me let me flip ahead Okay, I'll come back to this |
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| 21:36 | . I'm skipping over. It's not big deal. So it's something about |
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| 21:39 | high and low promoter strength. Or region this week. Okay. |
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| 21:49 | um so your hand will hold what call basil expression. Okay. Which |
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| 21:58 | just means that you see that you a choice and it's that's what you |
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| 22:06 | . Okay. That can in many . Getty was called fatal oppression very |
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| 22:12 | . That's that's insignificant. It doesn't not even enough. So do |
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| 22:17 | Okay. Maybe a handful approaches. . And so what the have to |
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| 22:27 | is okay if it needs the right expression then that's where you involve different |
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| 22:33 | of uh components. Okay, so level expression may require one or more |
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| 22:40 | these. Okay, this is where control elements? That's right. Um |
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| 22:46 | like activators, transcription factors. Different regulatory proteins. So they can |
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| 22:52 | all right at that promote. Alright really right. You can even have |
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| 23:00 | in bacteriophages as well. You can do it as well. Is to |
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| 23:06 | having the D. N. Scan itself loop around and create secondary |
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| 23:12 | at the side of the motor and them bring everything. Okay so you |
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| 23:17 | inform us that we call it a transcription complex. Okay. So when |
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| 23:24 | when all these parts come together, know high level expression. Okay. |
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| 23:30 | times more for more than you get base depression. Okay. And so |
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| 23:36 | a dynamic situation. It's rarely that just all one or the other. |
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| 23:40 | can be you know none to a to maybe somewhere in between. It |
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| 23:47 | depends on what are the collection of bankers you have to bring this about |
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| 23:54 | these can fluctuate in some cases, on Okay. Um that will determine |
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| 24:06 | know the conditions around the cell and the cell to determine you know and |
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| 24:10 | agent so determined the levels of Okay um and so collecting these parts |
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| 24:19 | the promoter. Right. It's about the affinity of the preliminaries for that |
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| 24:29 | . Okay so I can remember is know buying you know you can you |
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| 24:36 | almost write a paper saying biology is about binding things happen in biology because |
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| 24:42 | life. Whether the proteins binding proteins binding substrate proteins binding DNA |
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| 24:50 | That's really what causes everything to Are these bindings right. And but |
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| 24:56 | lot usually universal. They're almost always . Okay. But you know, |
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| 25:06 | you can influence how how much is and how much is off. |
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| 25:11 | And that's kind of what this is . So, if we have all |
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| 25:15 | confusion factors and already there at the high level it happens because now we've |
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| 25:21 | a site but they're very high affinity the generals colonels combined really well now |
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| 25:29 | that equates to kind of drive And create lots of transcripts. Lots |
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| 25:36 | protein. Okay, so it's really influencing that binding to the promoter. |
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| 25:43 | . He's gonna be finding not so on more off less transcription or it's |
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| 25:49 | be more bond less off. Higher transcription. So that's that's what |
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| 25:56 | the idea is here. Okay, . By making that promoter uh really |
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| 26:03 | that are the primaries, so to . Okay. Um and so and |
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| 26:09 | is I know you can't necessarily fathom important this is maybe at this |
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| 26:16 | but it's so hugely important because, know, just thinking in your own |
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| 26:22 | from zero to you know, if born like that whole process, |
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| 26:28 | is all about that. All Turning genes on and off at different |
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| 26:33 | timing. Right? Making sure that sequence occurred properly. So that you |
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| 26:40 | up with two arms here and two here for example. All right. |
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| 26:43 | all indifferently controlled. So um we now to the world of g |
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| 26:52 | It will literally blow your mind because go, oh my God, this |
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| 26:55 | complicated. How can it possibly But it does. But of course |
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| 27:00 | know when things up works are that can be glaringly visible as |
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| 27:05 | Okay. But anyway, so I'm a tangent here but there isn't any |
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| 27:10 | about that. Makes sense? So . Okay, so um like I |
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| 27:17 | , controlling gene expression is probably one the most important things because again, |
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| 27:23 | be wasteful depending with lots of other out there if you're a bacteria. |
|
| 27:29 | let me go back just to um couple things I skipped over. So |
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| 27:34 | This is just to show that all that 60, 70 is what's used |
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| 27:38 | expression of most genius. You do others behind these specialized functions. Um |
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| 27:46 | shock and uh shock and um jeans temperature sensitive. So uh temperature high |
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| 27:57 | can be bad of course. Um Vienna RNA proteins to denature. And |
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| 28:04 | you want to bring expressed proteins that kind of minimize that effect. |
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| 28:10 | So you do have heat specific genes are controlled by a certain factor um |
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| 28:18 | and chemo taxes. Right? And all of that details has as |
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| 28:22 | own singular factor uh stationary phase dress genes. So these are for other |
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| 28:30 | beyond heat that are triggered again. are all kind of survival genes are |
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| 28:36 | on by the search signal factor that activated at that time. And then |
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| 28:41 | talked about the nitrogen regularly on. so it has its own same effect |
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| 28:46 | control. That's a control those nitrogen operations if you will by a common |
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| 28:53 | factor. Okay so um and one to the body. This is just |
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| 29:02 | the same effect as Uh if it's same 70 it recognizes the -25 |
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| 29:09 | And the simple fact there's a transient of the off off its sole purpose |
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| 29:17 | I hope we get to that promoter . Okay and find that sequence. |
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| 29:24 | ? And in doing so then you um transcription. So this comes |
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| 29:30 | Single handed comes off and transcription. they can go and find another. |
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| 29:37 | guiding that. Yeah. Um I think so here. Alright so this |
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| 29:48 | kind of summarize everything I think that been talking about in this chapter |
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| 29:54 | Most of it. So yeah here the uh bacterial structure. Gene |
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| 30:00 | Okay uh here's the D. A. Here is the promoter. |
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| 30:03 | is showing of minus 25 minus Okay so sense strand plus strand, |
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| 30:09 | coding strand in the template strand to operation promoter to structural genes uh |
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| 30:18 | Check so one continuous message. Place a strong message. So within |
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| 30:26 | each second transfer for this gene and gene will have their own elements. |
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| 30:32 | . Start, start stop pulling on one. Right? Um These leader |
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| 30:38 | can be involved in some aspects of . We'll see that later. |
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| 30:43 | This is translatable. And the next that happens is to get the |
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| 30:49 | Alright. The complete My until the s inappropriate to then find its |
|
| 30:57 | Right? So just like a single has its sights suddenly. Okay. |
|
| 31:02 | so that brings in front of the to then this little tape um expression |
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| 31:09 | translation in this program. So. . And so that shine Del |
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| 31:13 | Just named for the for the two that that discovered this. Okay. |
|
| 31:17 | its fur so china gonna site is . N. A. Right single |
|
| 31:24 | binds D. N. A. , so make sure you've got that |
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| 31:29 | your head. So things like the the promoter sequence. This is |
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| 31:33 | N. A. Okay. Um of binding sites are already are |
|
| 31:40 | Okay. Um and then of course already talked about before the information. |
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| 31:49 | , this all occurs, transcription translation virtually simultaneously because there's no separation of |
|
| 31:55 | process and bacteria. Um Alright. questions so I'm gonna roll on to |
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| 32:06 | nine. Okay so here we're gonna at um He may look at A |
|
| 32:17 | we all have the color in our as you may you know, different |
|
| 32:24 | . Happy because we know E. like all the bacteria archaea replicate like |
|
| 32:34 | . All right. Um 100 You would think. Okay they're all |
|
| 32:39 | all the same right? They're all . It's all binary vision binary vision |
|
| 32:44 | genetically identical dollars. That's not the . Might collect and hold as identical |
|
| 32:52 | yours. Okay even within the same then it's not gonna be identical. |
|
| 32:58 | so this variation it was very Okay Yeah evolution 101 variation is what |
|
| 33:10 | accident. Yeah If if everybody in work genetic control genetically identical. Okay |
|
| 33:19 | Any kind of interaction with your Everybody's trying to behave descent because you're |
|
| 33:28 | . Same day that so that can good or bad. It was something |
|
| 33:36 | . And then maybe there's nobody capable surviving because they all have the same |
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| 33:41 | of genius. But if you have in population right now you may have |
|
| 33:47 | there that can survive different conditions. because you have variation built in why |
|
| 33:55 | so important variations. So important. so bacteria are no different. They |
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| 34:00 | have other ways to get this creation the fact they don't replicate reproduce |
|
| 34:07 | Luck for us. That's what gives surprises. Not all of. Alright |
|
| 34:14 | a sexual reproduction but bacteria can generate for sure as well. Okay so |
|
| 34:20 | transmission is passengers currently vertical transmission. how you will hear now what you're |
|
| 34:32 | capable of. I don't think it's transmission. Okay you can't inherit genes |
|
| 34:38 | the person next to you. Because you can't congregate like a |
|
| 34:43 | Okay. But bacteria can do Right? And so members of the |
|
| 34:48 | can transfer genes in certain different mechanisms that's carried out transformation, conjugation, |
|
| 34:57 | deduction and transposition are all mechanisms for . Ok so here is a |
|
| 35:05 | So the big big blue blob. , are all the polite genes. |
|
| 35:12 | are aware of even sequence city collect decades. Okay so we have a |
|
| 35:20 | they have this information, what do call it? So we have to |
|
| 35:25 | date. I'm not sure what data here but we're aware of Almost a |
|
| 35:30 | over 10,000 different ecologies. Yeah kids been found before. So An average |
|
| 35:40 | has about almost 5000 half that. . Um It's like if there are |
|
| 35:50 | genes for a particular human trait in jeans when you ever have You have |
|
| 35:58 | 10. Alright, that too. so you collect will not have no |
|
| 36:12 | called them at all. 10 will their collection of them roughly half. |
|
| 36:18 | then within that equal About four no over 2000 were called for Jeans. |
|
| 36:27 | so these are common to all Alright so these guys here would be |
|
| 36:33 | color has. Okay and what's probably gene that's in that lot of methodology |
|
| 36:44 | black polycystic some inspiration. Genes involved replication of D. N. A |
|
| 36:52 | synthesis. These are all gonna be functions. What every cell has to |
|
| 36:57 | has to replicate that. It's like . So all components are in there |
|
| 37:01 | gonna be of course and all of . Okay. So um and so |
|
| 37:08 | look at E coli K 12 versus . Okay. You see only 57 |
|
| 37:14 | a lot more regimes I called over . All right. Um comfort |
|
| 37:23 | Warm pathogen chair. And so it sense that. Ok. Price. |
|
| 37:29 | lot of genes involved in enabling cause . Okay. Virulence factors. And |
|
| 37:36 | um but they will share of Oh and 57 10-K 12 K 12 |
|
| 37:41 | benign last spring. It's the one is not harmless but so they're gonna |
|
| 37:47 | certainly common. They're gonna share recordings course maybe some others. But we |
|
| 37:53 | a bacterial genomes in general. Not dissimilar. Okay. Is the level |
|
| 38:02 | um D. N. A. correctional programs much higher in humans. |
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| 38:08 | superhumans anybody know? Is it Yeah. 2%. Who says 2% |
|
| 38:22 | . It's love. It's like two something percent. Right. We have |
|
| 38:27 | lot of DNA that's called regulation a of the DNA. That's like just |
|
| 38:32 | D. N. A. We're exactly sure what it's for but only |
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| 38:36 | 2.5% is actually used to build the . Right? Um So much more |
|
| 38:44 | that in bacterial then in preparing this used for coding proteins. Okay there's |
|
| 38:49 | gonna be a portion for regulation. is a big part of control expression |
|
| 38:55 | but of that. Um So the thing to remember of course is not |
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| 39:01 | most genes are all protein killing some because you do go for the the |
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| 39:07 | chronic can be R. N. . That's what represents these guys. |
|
| 39:12 | there are there are gene but gene is a approach. Okay now. |
|
| 39:19 | so when you look at the genome its entirety e coli about 25% of |
|
| 39:24 | genome required from other microbes. Okay this is part of the horizontal gene |
|
| 39:32 | . Okay so how do we find something like that? Okay and so |
|
| 39:38 | on your genes are going to be I mentioned things like those involved in |
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| 39:48 | reputation and protein sentences. Um This gonna be your all right. And |
|
| 39:56 | are generally not things that are transferred because it's still gonna hold on. |
|
| 40:02 | not something you want to do that passed along. So flexible gene tour |
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| 40:06 | that are not so critical function James . Um So back to this question |
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| 40:14 | how do you how do you find been deduced if a second of material |
|
| 40:21 | . T. A. D. . A. Is but as far |
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| 40:23 | horizontally parameters are used to that is called percent G. C. |
|
| 40:30 | Um If you do you remember that charged off rule he was the guy |
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| 40:42 | he's the one that came up with uh knowledge of the percentage of adding |
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| 40:47 | the percentage of bio means right? is equal to a percentage of science |
|
| 40:52 | . So since that time you see is used actually as a way to |
|
| 40:59 | It's about 34 years old. But that changed once we worked out too |
|
| 41:04 | sequenced DNA. And then that became of this but nevertheless there's a lot |
|
| 41:08 | information on descent. So in bacterial will have in particular G. Percent |
|
| 41:16 | . C. Okay you can kind use it as a taxonomic tool for |
|
| 41:20 | purpose but the video provides about 50.8% . C. Okay so with that |
|
| 41:28 | of mind and look at this is of course on computers with Um you |
|
| 41:35 | scan protozoa bacteria and you know using a significant statistically significant segment of |
|
| 41:45 | Right? Uh you should probably value opposed to 50.8% G. C. |
|
| 41:51 | . Okay um And so you see long stretch that deviates from that. |
|
| 41:56 | maybe 2000 bases but that's about the size of the gene. Okay um |
|
| 42:03 | if you see a long stretch that is is within that region significantly |
|
| 42:08 | Okay so for example something like um erogenous which is a relative of Cola |
|
| 42:15 | the GC content of 54. So that you know maybe that segment That |
|
| 42:22 | second at 2500 bases in this example at that range. Again you might |
|
| 42:28 | that it could have been transferred from . It was easy. That's one |
|
| 42:35 | or the easy way really to um at least provide some elements that maybe |
|
| 42:42 | these these jeans I'm seeing I'm studying transferred horizontally. Okay. And so |
|
| 42:47 | you collapse mentioned this this think about of his genome was acquired this |
|
| 42:53 | I mean that's pretty crazy isn't A of his genome. Okay so |
|
| 42:58 | for technology transfer is all right in of again creates variation but the |
|
| 43:07 | Okay, requiring new jeans. Uh so we were talking about these mechanisms |
|
| 43:13 | get the idea. We're talking about whole scale transfer of crows. Um |
|
| 43:20 | we're not talking about segments but there's congregation. Um Trans deduction. These |
|
| 43:30 | small sectors but nevertheless they represent acquisition new in many cases. Okay so |
|
| 43:39 | so this is just kind of a quickie. Um Here's what these steps |
|
| 43:44 | like. Um So transformation. Okay probably easiest to grasp because we're talking |
|
| 43:52 | taking okay because you get all little say that it's not necessarily as simple |
|
| 44:00 | it sounds okay because there are components . Uh congregation is involved several cell |
|
| 44:09 | . Okay. Uh certainly more complicated transformation to two cells coming together |
|
| 44:18 | This is where can asthma transfer occurs the two. Okay. Um trans |
|
| 44:23 | . That's a virus. Okay so viruses in comedian between the two |
|
| 44:28 | Okay, viral infection occurs um in packaging of viral particles. Host |
|
| 44:35 | N. A. Is inserted rather viral. Yeah that's how the DNA |
|
| 44:40 | transfer to another cell when the virus the new cell. So that's that's |
|
| 44:46 | . Okay. Uh service here viral and it affects another cell. Um |
|
| 44:54 | position. Okay so I think I'm small pig already. Things also based |
|
| 45:02 | has has posed as we do. what they do is they remain in |
|
| 45:09 | organism because they jump around the Okay. But occasionally they can jump |
|
| 45:15 | a ride figure out plasma. Or are other mechanisms by which transposes conform |
|
| 45:23 | transfers for them to sell. I'd say of the four. |
|
| 45:29 | transformation. Conjugation transaction probably won't come to transfer. The transmission does occur |
|
| 45:38 | if you uh to the path this in fact. But in terms of |
|
| 45:47 | communication transaction follow my transformation more No. Um Alright. So what |
|
| 46:00 | transferred? So this is another All right. These are in the |
|
| 46:05 | and they're the particularly acquisitions of of through horizontal gene transfer. That chromosome |
|
| 46:17 | uh we call them islands I guess they are a specific function. Okay |
|
| 46:22 | you see the terms pathogenesis the island fitness island. These are segments that |
|
| 46:30 | a pathway and jeanne's properties. Okay capsule gene the gene for the |
|
| 46:40 | Okay these would be in that class pathogenesis possibly transfer. Okay. |
|
| 46:48 | So we talked about nitrogen fixation symbiotic couldn't be exactly this. Okay um |
|
| 46:58 | we talked about the metabolism of aromatic . So that could that could be |
|
| 47:04 | of the pathway you might see here these can be these types of things |
|
| 47:07 | be transferred. Okay and so um so let's so one of the things |
|
| 47:21 | remember because we're gonna go through the of transfer DNA. Passion here and |
|
| 47:27 | and being taken up and this and . Okay remember that uh combination plays |
|
| 47:36 | big part in one of these Okay so you can have um so |
|
| 47:43 | can be ah say uh layer in D. N. A. Can |
|
| 47:49 | taken up to your transformation for example D. N. A. Can |
|
| 47:55 | how how viruses transfer um passed the of circular but both are forms of |
|
| 48:05 | that can be external to the cell end up in a cell. Okay |
|
| 48:10 | from the viewpoint of the you can use as a food source right? |
|
| 48:16 | on the state of health. Okay could crunch up that that music as |
|
| 48:20 | as organic carbon source. Um Generally it's a single strand. Okay like |
|
| 48:29 | guy that is something certainly bacteria itself gonna be very suspicious of. Okay |
|
| 48:39 | that that's likely gonna think it's environment . Crime. Okay it's not normal |
|
| 48:45 | even ourselves to have the single stranded . N. A. Floating around |
|
| 48:49 | . That's not normal. Okay um extraneous fragments like this for. Okay |
|
| 48:59 | uh that really sets off alarm bells it gets quickly degrading. Okay so |
|
| 49:04 | layered piece like that could be two to integrate. That's where recombination comes |
|
| 49:12 | . Okay plasmas can live external. but they too can integrate as |
|
| 49:19 | Okay and so the combination is a immediately part of the recombination is all |
|
| 49:28 | having some level of form ology complete it's all about complementary base part. |
|
| 49:38 | so if you have enough nucleotides and a complementary to the D. |
|
| 49:43 | A. Is integrated into then it happen. Okay and wreck A. |
|
| 49:48 | that there's multiple components involved? But A. For recombination protein A. |
|
| 49:55 | accommodates a. Is is um that player in all material souls that do |
|
| 50:02 | that they carry every combination. Okay so it it helps align homologous regions |
|
| 50:11 | that causes a donor and recipient to combined. Okay you just have to |
|
| 50:19 | and potentially they can then integrate and certainly when when it integrates into the |
|
| 50:27 | . Now we've got something that has that's the permanent life. Okay and |
|
| 50:35 | the classes to to integrate. Uh so let's look at um this |
|
| 50:44 | So first the first stop is So with the transformation congregation trans deduction |
|
| 50:51 | that world. Okay so the trans okay what's the answer. Everybody hurry |
|
| 51:00 | and pick that one violence showing. . Um Okay so transformation. It's |
|
| 51:11 | about cell cell contact, that's congregation , immediate transaction. Sex pilots |
|
| 51:21 | Those are elements of congregation. Transpose A. That's transposition right at |
|
| 51:28 | end. So each process has it's of features so definitely be familiar with |
|
| 51:37 | . Okay so let's move on. correct answer is easy by the |
|
| 51:42 | Okay give me the fragments in the . Okay. Um Alright so transformation |
|
| 51:53 | It seems it's fairly simple but it be more complicated and it can differentiate |
|
| 51:59 | gram negative and gram positive. Okay so the more complicated process is grant |
|
| 52:05 | . Okay uh likely due to that thick peptidoglycan layer, there's components that |
|
| 52:14 | DNA get into the cell. Um what's called transformers own complex. So |
|
| 52:22 | this will evolve as an example of regular right? There is a regular |
|
| 52:26 | in the grand positives and facilitate Okay quorum sensing. So we saw |
|
| 52:33 | in biofilm information. Okay so quorum sensing is one of those cell death |
|
| 52:39 | things. Alright I have to have cells present too. Two because the |
|
| 52:45 | . Okay um so natural versus artificial . Okay so naturally transformed cells of |
|
| 52:56 | are built to do this but they the capability to do this in |
|
| 53:01 | Okay E coli for example cannot lose . Yes it can only be used |
|
| 53:09 | artificially attached on it. Of course coal ideas. What's used is the |
|
| 53:15 | , genetic recombination. Okay. We it to various aspects for gene cloning |
|
| 53:21 | whatnot. And certainly transformation. We collide as a vehicle to replicate |
|
| 53:28 | Okay. And so the only way can do that to get the plants |
|
| 53:32 | any claims to artificially manipulate. Why? Why that? Well because |
|
| 53:37 | know we collect so well we can it very quickly that it's just it's |
|
| 53:41 | historically just become that role. And so we have officially transforming the |
|
| 53:48 | days. He was using um maybe chloride, potassium chloride and ice on |
|
| 53:55 | . Okay. That create pores in membrane. Um You had the |
|
| 54:02 | N. A heat shock it. how many ice and very wide temperature |
|
| 54:08 | ice and heat shock creates pores in cell where the uh the classes can |
|
| 54:14 | in. Then you put it on and then it kind of closes up |
|
| 54:19 | pores. So it's not very But remember that. But because bacteria |
|
| 54:25 | so much so the high density it have to be super efficient. |
|
| 54:31 | But nevertheless uh your away or if needs in my four years is using |
|
| 54:38 | shot, there is the same There are currently more efficient process than |
|
| 54:42 | chemical withhold chemical transformation. Okay. I think if you were in I |
|
| 54:49 | know if they still do the experiment in bio bio one lab to lab |
|
| 54:54 | did that actually I think the transformations there. But anyway so confidence |
|
| 55:01 | These are these are part of the positive transformation process. The whole part |
|
| 55:06 | the form sensing thing as we'll see in a second. But gram negatives |
|
| 55:12 | there's a little less complicated. So back to remember pilots structure um the |
|
| 55:22 | I am in contact or less numerous have more specialized functions without about sex |
|
| 55:29 | and congregation helps facilitate transferring. Una is a bigger pill I typed for |
|
| 55:35 | code that helps it attach to N. A. And bring it |
|
| 55:41 | . I also saw pillai in twitching . Right? So this is a |
|
| 55:45 | of that will bind to DNA fragments bring them in. Okay. So |
|
| 55:49 | not that complicated. Okay. A gram negatives can do this. |
|
| 55:55 | Um Not in himachal listen, Neisseria both um known pathogens so but we're |
|
| 56:07 | focus mostly on more so on the positives. Okay. And they're mechanism |
|
| 56:13 | so we just talked about artificial transformation that using electricity as we called electrical |
|
| 56:20 | create pores using electric shocks. Um now okay so here's the grand |
|
| 56:28 | processes a streptococcus example. And so so you see. All right one |
|
| 56:45 | different operations. Right? Hence common factor that turns all those on and |
|
| 56:54 | synthesize different components of this transforms um called the complex that brings in the |
|
| 57:00 | . N. A. Okay so that though we have the production of |
|
| 57:06 | competence factors. Alright so the term term competence. So if you see |
|
| 57:11 | term okay in this context Congress refers can information. Yeah. So self |
|
| 57:21 | is ready to take up the N. A. Okay. Um |
|
| 57:26 | so the grand positives is in this . Companies factors are synthesized in the |
|
| 57:34 | and but they have to reach a level to initiate this whole process. |
|
| 57:41 | that's where the quorum sensing comes Okay so um if you have enough |
|
| 57:49 | around then we'll initiate this process. the the complex factors accumulate. Okay |
|
| 57:57 | they reach a threshold level then they'll into the sensor protein comedy. Right |
|
| 58:04 | that ultimately leads to production of sigma . Okay. And then that's its |
|
| 58:11 | is what turns on four problems And so the genes for those codes |
|
| 58:17 | different parts of it transforms us Um And so the question I guess |
|
| 58:27 | why is this a density dependent Okay well you think of a thing |
|
| 58:34 | the growth cycle of a of a bacteria? Right. We follow this |
|
| 58:42 | . Okay. There's time and Okay. Alright. Growth. We've |
|
| 58:53 | that before. Alright so you know didn't point along that line you're going |
|
| 58:58 | have you know a proportion of souls live and so they're dead. Okay |
|
| 59:04 | course the proportion gets more and more , right? As we get to |
|
| 59:09 | phase. Okay. So um for . All right. So in the |
|
| 59:26 | one of those when we're gonna see D. N. A. From |
|
| 59:29 | south and the soul, he alright, so advice is that the |
|
| 59:38 | I'm just guessing that it's likely that is a phenomenon because he has to |
|
| 59:42 | more settles, right? You will likely have more rare reports of dead |
|
| 59:48 | are sliced and now you have N. A. That's available to |
|
| 59:51 | taken up what? Okay. Um if there if not then why go |
|
| 60:01 | all this process for the likelihood of may have been incorrect. Okay. |
|
| 60:09 | , you can't see the is going it's it's an energy producing process requiring |
|
| 60:15 | . Okay, So that's not to the idea why it's time to sell |
|
| 60:21 | more so mentally greater likelihood that maybe have more so than dialyzers and their |
|
| 60:27 | is free to be taken off. . Um The the DNA comes in |
|
| 60:35 | so this is part of the function this complex. It was one strand |
|
| 60:40 | in. Okay. Not both. so one strain is degraded. And |
|
| 60:46 | of course that strand then, but was very it was the coolest thing |
|
| 60:51 | sells very recent mind chromosome. And so that's um that's transformation in |
|
| 60:59 | grand positive at least. Okay. for right. Um he crushes. |
|
| 61:15 | . Thank you. Yeah, I . Okay. Singapore the name the |
|
| 61:33 | not surely order. And I just that when you see if you hear |
|
| 61:36 | term see it think about it means itself is it's confident to take A |
|
| 61:44 | . N. A. And that's only thing that's part of it. |
|
| 61:47 | because you have to get program probably to get this transforms them together and |
|
| 61:51 | was all this kind of set did just say to take it? That's |
|
| 61:58 | . That's that's probably one of that the term. Sure. Yeah. |
|
| 62:03 | for the competence factors when they did they form like a concentration |
|
| 62:08 | Yes. Yes exactly. So That much. Like very similar. |
|
| 62:15 | how biofilm formation occurs as well. that will trigger the expressive of operations |
|
| 62:24 | in formation, et cetera. Um so the conjugation. Mhm. Uh |
|
| 62:34 | will uh evolve. So so contact the indefinitely certain parts evolved. |
|
| 62:42 | So sex pilots is what brings the together um F factors. So remember |
|
| 62:50 | plasma transfers and the platforms that are to transfer ability to pay the f |
|
| 62:56 | . And the facts are simply the segment of the past contain those |
|
| 63:05 | That's an eight um taxes. So a gene for a sex pilots for |
|
| 63:11 | . Okay. Um You're also gonna what we call mating pairs. |
|
| 63:17 | We call it F. Plus which the transferable plasma and f minus Celso |
|
| 63:24 | recipient. Okay so again these congregations genes. This is what makes the |
|
| 63:32 | , are those collection of genes which called which include T. R. |
|
| 63:38 | . Trade genes. Transfer genes. sex pilots which included sex pilots relax |
|
| 63:44 | . Uh we're gonna see that's a complex that access liberation from the cells |
|
| 63:49 | facilitates transfer. Uh Rory has been transfer for transfer the plaster. That's |
|
| 63:57 | rolling circle replication mechanism. Okay, uh so a number of parts coming |
|
| 64:04 | . And uh so we see that the the fact that the pilot will |
|
| 64:11 | extend militarized and stand quite a ways it can and then they will latch |
|
| 64:17 | to a f minus. So a in particular receptor on the surface that |
|
| 64:22 | recognized by the pilots. And then it attaches there will be a deep |
|
| 64:28 | . So it shortens, right, can see how we're at this distance |
|
| 64:34 | and we've shrunk to this distance. finally to that. Okay, because |
|
| 64:42 | gonna be kind of a fragile connection transferring A. D. N. |
|
| 64:46 | . Across the quietest weather so far obviously, so you bring them once |
|
| 64:52 | contact you, kind of bring them to enable uh that connection to the |
|
| 64:58 | a little longer. So you can . Okay, so um and |
|
| 65:06 | rolling circle reputations what occurs here. , so we see somebody call this |
|
| 65:11 | the green is kind of this relaxes that bridges and sells rolling circle replication |
|
| 65:21 | . And uh that bridge facilitation, transparently of the plants with Vienna into |
|
| 65:29 | cell and then gets copied into the . Okay. Finally we end up |
|
| 65:35 | the plus, the plus and minus had become Yeah, that's the outcome |
|
| 65:41 | of these. Um we call F if minus is that we create and |
|
| 65:50 | another right there. And then that is able to transfer its password to |
|
| 65:57 | cells. Okay. So it kind increases the number of the population. |
|
| 66:02 | of course, obviously whatever genes around plasma, whatever they may be, |
|
| 66:11 | certainly be expressed about that by this cell that's required this. Okay. |
|
| 66:19 | that's you know that this is the basic kind of congregation. Okay. |
|
| 66:26 | the so let's talk about. So the most basic. Here's here's here's |
|
| 66:31 | next one. Okay, this is H. F. R. |
|
| 66:40 | Okay. HFR. So okay. remember this is going to evolve. |
|
| 66:47 | One step up let's say, let's see what we come up with |
|
| 66:53 | . All right. Hit the No. Mm hmm. Okay. |
|
| 68:00 | survey says yes, um effective integrated the chromosome. Okay, so the |
|
| 68:10 | . F. R. We've got frequency of incompetent strain. Okay. |
|
| 68:19 | occurs when so we will contain the forests are already detained the net |
|
| 68:24 | So initially. Okay. And so age of our forms from that plastic |
|
| 68:31 | into the chromosome. Okay. And typically there's common sites where it |
|
| 68:38 | We see this thing called S. . So called insertion sequence. OK |
|
| 68:45 | there'll be some big beautiful apology that ever for recombination. You gotta have |
|
| 68:49 | little bit of cosmology between the Okay. Um and then it becomes |
|
| 68:55 | HFR cell Jack. Now the thing Marcel is it's it's at plus |
|
| 69:04 | It's just the planets that we Okay now and plus cell. |
|
| 69:11 | Plus something like this. Okay. chromosome. Here's plasma. Right? |
|
| 69:21 | that contains those plus genes. So that guy could congregate right mate |
|
| 69:28 | an F minus. And but now guy looks like this. Okay here's |
|
| 69:36 | chromosome and now the F factors in . Okay. In there. |
|
| 69:46 | So what that means is that now entire chromosome can be mobilized in |
|
| 69:53 | Okay. And so um but that ever happens. Okay. Part of |
|
| 70:02 | gets transferred. And so what you here is that section contains those those |
|
| 70:10 | specific genes. Okay. When it copied, okay it will begin. |
|
| 70:19 | transferring. They're okay? And then in the clockwise direction. Okay so |
|
| 70:27 | transferable genes are here at the So when it's conjugated with f |
|
| 70:33 | So HFR contracts with minus, That begins to get a copy and mobilized |
|
| 70:41 | pushed into the recipient self. Okay um how how much DNA gets transferred |
|
| 70:52 | totally dependent on how long do you . Okay so it will take on |
|
| 71:00 | order of nine of nearly two Nearly two hours to be together. |
|
| 71:07 | entire chrome zone. And that rarely happens. This doesn't happen if you |
|
| 71:12 | think about what the force is causing come apart while other cells bouncing into |
|
| 71:17 | rally and move. It's just molecules the water matrix bouncing off of |
|
| 71:24 | Right? Eventually. It's gonna be much to connection breaks. Okay. |
|
| 71:29 | so for that reason when you have and H. F. R. |
|
| 71:37 | minus congregation. Okay. The F cell stays as hef minus. |
|
| 71:47 | It's only because the last portion that transferred into the F. Plus. |
|
| 71:55 | they rarely if ever are together long for that to occur. So the |
|
| 71:59 | minus. So typically always stays as F minus. This doesn't because they |
|
| 72:04 | stick together long enough to transfer all it. And the last part that |
|
| 72:08 | be transferred are these F plus That's what makes it transfer. |
|
| 72:13 | So, um yeah, so it's a bad thing. All right. |
|
| 72:19 | the has inherited. Okay. It pass those on through vertical transmission. |
|
| 72:26 | . But in itself cannot. that's that's specific for special for this |
|
| 72:36 | . F. R. F Mhm. Okay. We're ahead. |
|
| 72:42 | . Okay. Um, crushing. . Um, I'm not sure. |
|
| 72:51 | gonna end here, but now we'll next time with some animations that show |
|
| 72:55 | process. Okay. Thanks folks? |
|
