| 00:01 | here we go. It's actually Alright folks welcome. Looks like we |
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| 00:26 | a a smaller crowd I guess that's be expected day before the exam. |
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| 00:34 | I'm sure the absentees are diligently studying ? Yes. Ah It's not supposed |
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| 00:42 | say what uh Probably. Let's Um. Oh yeah. Right. |
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| 00:51 | quiz. Yeah, that's wrong. . You're right. Uh Okay. |
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| 01:00 | should be friday through monday. okay. Um Yeah the other |
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| 01:08 | Right. Okay, correct. Thanks that. So the exam to |
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| 01:14 | we're going to finish up 21 22 7878 is relatively short. So those |
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| 01:22 | no means that especially chapter eight, very tiny part of that. Chapter |
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| 01:29 | . Uh This is kind of some this is probably gonna be review. |
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| 01:33 | hope for you seven and eight. talked about ah cocoa wrote genomes, |
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| 01:42 | structure. We begin with the old of information just to kind of get |
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| 01:52 | get our heads back into that uh that again. Okay. As we |
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| 01:56 | out of metabolism to degree um I that's everything. So uh here's what |
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| 02:05 | covered last time except for this is last bit is just mentioning that |
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| 02:12 | So um the natural cycle or triangle you want to look at it. |
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| 02:19 | started with a little bit about pretty like wastewater treatment and how environmentally influx |
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| 02:28 | nutrients can affect probably populations which can you can have an impact on marine |
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| 02:37 | and do those processes of eutrophication. The reduction of B. O. |
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| 02:45 | . But then the loss of auction the water to impact marine life. |
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| 02:50 | uh wastewater treatment and kind of threw . Remember the main things about that |
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| 02:58 | um microbes are the ones that are the work really of knocking down the |
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| 03:04 | organic materials and wastewater um promote um activity we're promoting aerobic aerobic hetero trophy |
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| 03:15 | The by mixing getting oxygen in their promoting respiration to knock down the |
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| 03:24 | O. D. The organic And then but then the other part |
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| 03:28 | that is um you want that activity occur obviously but the material coming out |
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| 03:36 | ? The water coming out of your should be clean drinking water obviously. |
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| 03:43 | . Right? So we need to these microbes settled. So settling is |
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| 03:48 | big part of the wastewater treatment before discharge because themselves themselves are bot okay |
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| 03:56 | we need to make sure they settle . That's what that clarify was all |
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| 04:00 | . And that's where flagellation right? get those filament types are growing and |
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| 04:05 | kind of they form this matrix. And so you get a balance of |
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| 04:10 | types and zones which you can eat swimming types of microbes bacteria. And |
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| 04:17 | you have settling of this material right have a clear as clear as you |
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| 04:23 | effluent coming out that you can then . Right? So the end product |
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| 04:27 | a waste water treatment system and it's course um that can be used for |
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| 04:31 | water. It was cleaned up enough it can also just be a company |
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| 04:36 | is has their own treatment process going to get rid of any kind of |
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| 04:44 | materials in their stream and then to in the nearby river or lake or |
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| 04:49 | have you. But obviously that discharge be relatively clean. Um All right |
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| 04:58 | we went to nitrogen cycle and the aspects of that fixation, the notification |
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| 05:04 | the petrification process is so each side the triangle there and then we're gonna |
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| 05:10 | with a process this one here Um there was a recent but let's say |
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| 05:19 | the last 15 years or so it's evident that that process is one that |
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| 05:25 | actually very significant. Especially in marine . Okay. And so the amount |
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| 05:32 | photosynthesis occurring in marine environments is Okay. You think of the oceans |
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| 05:39 | other bodies of water on earth. this process is one that um returns |
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| 05:47 | to the atmosphere. So it's not not um you don't before these guys |
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| 05:55 | discovered it was thought the notification is nitrogen that's how nitrogen gets back into |
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| 05:59 | environment in the atmosphere. Okay. of the animus reaction and those bacteria |
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| 06:06 | then subsequent seeing that these things are in many different environments. Right? |
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| 06:14 | that activity is actually very significant. . And let's just flip here. |
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| 06:18 | what accounts for the majority in marine is 50% of uh into return to |
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| 06:29 | environment. I mean to the Sorry, the atmosphere so half |
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| 06:34 | If nitrogen is lost in marine As into through this reaction. |
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| 06:39 | So just for compared to purposes so reaction is the oxidation of ammonia. |
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| 06:48 | . And aerobically using night trite. ? That gets reduced ultimately to |
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| 06:55 | Okay. And in the process of is oxidized. Okay, so just |
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| 07:00 | comparative purposes, we saw this one in Nitra fication. Right? So |
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| 07:05 | is oxidized aerobically. Okay. Okay. Oh to reduced water. |
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| 07:14 | And then ammonia oxidized to nitrite. right. One half of the night |
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| 07:20 | find reactions. The other one is nitrite to nitrate. But just just |
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| 07:24 | , just compared to purposes. So money oxidation here with these bacteria |
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| 07:29 | for a production of this little Right? Using it to break down |
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| 07:35 | and get energy from it producing it oxidizing it tonight. Right. The |
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| 07:39 | reaction is also an oxidation of Okay. Um but it is a |
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| 07:48 | aerobic process. So we're using nitrite terminal except er respiration. Okay, |
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| 07:54 | anaerobic respiration oxidation of ammonia to end . Okay so again this is obviously |
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| 08:01 | different process from notification. So this going of course result into the |
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| 08:08 | So it's not it's not lumped into identification. Okay. Um It's it's |
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| 08:17 | a it's like a another type of to get rid of nitrate from the |
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| 08:24 | . They just don't they don't put into the identification category, but it |
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| 08:29 | is one of the counts for a of nitrogen loss. Okay, so |
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| 08:33 | , oxidation of pneumonia, anaerobic oxidation produce and to and so these cell |
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| 08:43 | are actually very they're they're bacterial, are a type of bacteria. He's |
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| 08:49 | my seeds. Okay. Very Um Typically just spherical cells. Um |
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| 08:57 | they are gram negative but they have of a weird envelope in many |
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| 09:03 | And the ones that carry out this have actually specialized structures which are the |
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| 09:08 | blobs here inside the cell that they an um an amok zones structures that |
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| 09:17 | specifically carrying carrying out this reaction and find these things are widespread throughout the |
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| 09:25 | interacting with algae and sponges and things that in the environment. So fairly |
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| 09:32 | . Um But again, this this for a significant amount of end to |
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| 09:37 | returned to the atmosphere. So I that closes out, I'm sorry, |
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| 09:47 | out What we're gonna talk about in of 21, So that's that's |
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| 09:52 | Okay, so again, um this not on the exam tomorrow. |
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| 09:57 | so this is all stuff for three. Okay. Any questions before |
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| 10:03 | . Okay, so as we get just talking about aspects of bacterial genetics |
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| 10:11 | in terms of precarious. I'm not we're not going through did a replication |
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| 10:18 | all and all that that entails. , Your Okazaki fragments and leading and |
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| 10:23 | strand and all the stuff you I'm assuming and buy a one. |
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| 10:28 | not we're not doing all that. . We're not doing the whole here's |
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| 10:34 | company synthesis occurs, right? Because assume you know that already. |
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| 10:38 | um I'm just gonna kind of point some things that are specific to pro |
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| 10:43 | that you may or may not be of in both of these processes. |
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| 10:47 | , So, um but I do know to me this is one of |
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| 10:53 | basic, I shouldn't say basic but of those things as a I know |
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| 10:59 | not all bio majors, but it's of those things you should know. |
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| 11:02 | shouldn't leave here not knowing what what flow of information. Right? And |
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| 11:07 | that means. Okay, and be to explain it to somebody. Doesn't |
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| 11:11 | to explain it to the degree but you should be able to know |
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| 11:15 | as a bio person. Okay. like you should know the basics of |
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| 11:21 | , right? You should know the of metabolism just went through. |
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| 11:26 | so this is one of those. the first part is probably gonna be |
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| 11:30 | bit of a review if not, it was forgotten some things and this |
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| 11:34 | jog your memory. Okay, so one question is make sure this is |
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| 11:39 | . Yeah, this is my favorite . I've had this. I used |
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| 11:41 | teach intro bio and this always showed on the exam and it always got |
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| 11:47 | a 50 50 response although I've changed modified it somewhat. So this will |
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| 11:53 | you right away if you know the or not. Okay so the process |
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| 11:58 | transcription and translation is carried out in test tube to the test tube. |
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| 12:05 | adding stuff from three different animal Right? So from the hippo we |
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| 12:11 | those three from the fish. We that from a zebra. We got |
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| 12:18 | stuff. Okay so we're gonna pop into a test tube or flask and |
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| 12:24 | gonna get some protein made. Some new protein will be made. Okay |
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| 12:29 | the question is which from which animal is that protein being expressed? Okay |
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| 12:37 | you've got different combination of answers Take a look see see what makes |
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| 13:05 | . Mhm. Okay counting down. here we go. 10 9. |
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| 13:59 | I predict 2/3 will answer correctly. see. Okay I was even |
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| 14:11 | Alright. Um Alright so we got studying to do on transcription translation. |
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| 14:21 | . Um You do I don't Okay I when you assume the obvious choice |
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| 14:30 | everybody picked was be fish you see . N. A. Right? |
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| 14:38 | So of course it's remembering this Right that so any D. |
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| 14:44 | A. In there will certainly be translated into protein? So the fish |
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| 14:49 | will show up. The other one shows up is why the hippo. |
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| 14:58 | . Yeah so yeah it's the hippo it's deep hippo and fish. |
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| 15:04 | So we got that and we had . So M. R. |
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| 15:10 | A. Can ribosomes from the hippo T. R. N. |
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| 15:16 | S from the hippo. Canned ribosomes plop on the amarna and translate. |
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| 15:21 | . As they can with the N. A. Okay. So |
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| 15:24 | we have RNA polymerase. Right? this one goes there to make an |
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| 15:33 | . RNA and then blah blah And then these involved in their right |
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| 15:42 | make that. But then also of they can eventually you'll make that from |
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| 15:47 | . N. A. All there'll fish Amarna. Right. Anyway, |
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| 15:51 | get the point I'll go through this . I got enough space. |
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| 15:54 | so hip on fish. Right. the old flow of information um same |
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| 16:01 | all living things uh depending on if call this a living thing or |
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| 16:07 | the one exception to this is what what doesn't follow DNA RNA protein. |
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| 16:18 | virus retroviruses. Right. Retroviruses don't that order. But aside from |
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| 16:25 | as far as I know everything else . So here's another question again, |
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| 16:29 | is just for the purposes of terminology kind of how stuff works. |
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| 16:34 | So we have a certain bacteria found been found that a region of the |
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| 16:40 | designated X. Comprises a specific sequence . N. A. This sequence |
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| 16:46 | only be converted into protein can be into protein only when cells are grown |
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| 16:51 | galactose as a sole carbon source. the flying statements is false regarding this |
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| 16:58 | . So it was kind of again different way to have you think about |
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| 17:05 | process and the terminology we use and . Okay. Oh let me open |
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| 17:13 | . Okay. So the X. is not revealed when cells are grown |
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| 17:20 | glucose as a carbon source. Um conversion of the DNA sequence into a |
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| 17:27 | requires a bribe requires ribosomes. Um . Is a gene. Um The |
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| 17:39 | stage in converting DNA sequence requires synthesizing an RNA copy of the X |
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| 17:46 | . Just looking for the false See just Amanda eventually requires five. |
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| 18:56 | . Yeah I pretty much just gave away and everything anyway. Okay. |
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| 19:06 | . So you didn't I put an word in number and be the conversion |
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| 19:10 | D. N. A. Sequence a protein eventually requires. Okay. |
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| 19:16 | . With the false statements. All right, so I got some |
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| 19:31 | to do. Alright. The Type is not revealed. Well that's |
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| 19:36 | much says here you have to go on glucose. Okay, so I'm |
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| 19:41 | galactose. Thank you. Um So phenotype. Right, that term. |
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| 19:51 | um the phenotype is typically revealed through functioning of one or more of these |
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| 20:05 | . They have proteins. The proteins those jeans. Okay. Right so |
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| 20:12 | protein can be an enzyme and then enzyme or enzymes maybe I to ferment |
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| 20:18 | and then that shows up as a a as a phenotype. Okay, |
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| 20:25 | conversion of the DNA sequence of the requires Robertson's. Yeah, that's the |
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| 20:29 | know, it requires it in uh here. Right. Protein. That's |
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| 20:40 | my ribosomes are needed is at that of the process. Okay. Uh |
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| 20:45 | first stage X. Is a Well, yeah X is a |
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| 20:48 | Okay. Um the first stage in the DNA sequence into a protein requires |
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| 20:56 | , synthesizing RNA copy of the X . That's our. Does that? |
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| 21:02 | right, so we're talking about this of the process. So that part |
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| 21:08 | RNA polymerase. Okay. Not So the is the false statement. |
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| 21:20 | . Um No, that's for Not this. Um Any questions anybody |
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| 21:29 | I'm insane for picking be Okay. Yeah. Yeah. So yeah. |
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| 21:42 | you carry out that process occurs Alright, so again, this is |
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| 21:52 | you've obviously heard these terms genotype and . So that's just kind of to |
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| 21:58 | just help you re remember these. , so, so here I'm showing |
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| 22:04 | an E coli here's a blow up micro micro micro graph of an E |
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| 22:09 | . Okay, so we inoculate lactose we collect and ferment lactose. So |
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| 22:15 | is one that can't so we see visual visual obviously fermentation. This is |
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| 22:21 | ph change occurs acidity uh die turns yellowish color. Okay, so of |
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| 22:28 | there's a phenotype we can see the has this feature being able to ferment |
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| 22:34 | . Right? So um you can get individual on the plate. |
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| 22:39 | This could be your in lab. used McConaughey's auger. And so that |
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| 22:46 | ones would be lactose fermenters. so again another visual. So we're |
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| 22:52 | taught when you first hear phenotype that see characteristics, you can see observable |
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| 23:00 | . Right? But remember that it's they're not all necessarily be observable. |
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| 23:06 | got lots of stuff going on inside body. That's you know, part |
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| 23:09 | your phenotype that you can't see. but it's the expression of those genes |
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| 23:16 | proteins that generates the phenotype. so again another type of phenotype. |
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| 23:23 | ability to um lice blood cells Okay. And so again, one |
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| 23:30 | of one or more proteins is gives the phenotype. Okay, so um |
|
| 23:38 | of course phenotype and genotype. You if you look at DNA RNA protein |
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| 23:43 | is of course D. N. . Right? And we convert that |
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| 23:46 | proteins to give us a phenotype. so one last kind of example here |
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| 23:51 | kind of tie it together. I . So this is basically a rapid |
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| 23:57 | kind of test if you're a lab you're doing the unknown. If you |
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| 24:02 | this you would be done with the project in probably two days. So |
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| 24:08 | allows you to inoculate a number of at one time and you can test |
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| 24:14 | of different sugars like a rabbit knows blah blah blah. You have the |
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| 24:19 | . R. V. P. for that is the VP your real |
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| 24:24 | assist etcetera. So different compartments. . So what you actually do is |
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| 24:33 | you need to know this but here a covering. And you can take |
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| 24:37 | covering off. There's a needle, a there's a wire loop that goes |
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| 24:40 | the whole thing and you take the off and it reveals a wire |
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| 24:45 | You flame you touch a colony with . Then you take that loop through |
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| 24:50 | the compartments and inoculates them all at time. Okay. And incubate. |
|
| 24:55 | . They look for different color Uh So this one we're focusing just |
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| 25:00 | one test. Right? You re test. Right? So positive test |
|
| 25:03 | is a pink color like that. . So so what does that actually |
|
| 25:10 | ? Right. So that's the phenotype this one. Is your area or |
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| 25:14 | ea says the enzyme positive. So it's has that enzyme. It |
|
| 25:21 | potentially do this reaction. Okay. is this right here. Right, |
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| 25:26 | it's a metallic sis to form 02 and ammonium. This is |
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| 25:30 | Of course it's a color changes based the basic ph occurring. Okay. |
|
| 25:36 | so does that relate to in terms its genome. Okay well that obviously |
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| 25:40 | has a gene that codes for this in this chromosome uh in order to |
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| 25:49 | it useful so to speak. We right on your primaries. Transcribe produce |
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| 25:55 | protein messenger RNA A. Right. so this is our our copy of |
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| 26:03 | gene. So we make RNA copies genes. So think of the chromosome |
|
| 26:08 | your your book on reserve in the . Right? You can't take it |
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| 26:12 | you. It's a permanent fixture Right? But if you if you |
|
| 26:17 | um if you want to get information it, you can pick the pages |
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| 26:22 | want in xerox in right? So of the pages as the genes of |
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| 26:26 | chromosome. Then you can make copies copies of your M RNA. |
|
| 26:32 | So so again the genome is the fixture. Right? You can make |
|
| 26:38 | of different genes as you see fit produce the transcript. So these are |
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| 26:45 | of the messenger RNA as the working of your genes. Okay. The |
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| 26:51 | you actually do stuff with. And these become translated through ribosomes and TR |
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| 26:56 | A. S to produce a Okay. Probably peptide that then of |
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| 27:04 | in this case is the enzyme. , so um a big part of |
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| 27:13 | uh that um it's super important is control element. The control element is |
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| 27:21 | to the whole process because I've mentioned probably several times a semester. Um |
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| 27:27 | you can't see from a textbook or diagram is the amount of energy this |
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| 27:33 | . Right remember we're building something. ? Anabel is um we're making a |
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| 27:39 | amino acids. It takes a lot energy to do that. This is |
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| 27:43 | energy requiring process from making the memories making the probably pep type. |
|
| 27:50 | So um it's not a trivial thing express the gene. Okay. So |
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| 27:57 | important in only expressing genes that are . Right. And there's different categories |
|
| 28:03 | those in terms of importance. You have a set of genes that are |
|
| 28:10 | pretty much on. All right. are gonna be for your critical type |
|
| 28:13 | . There are gonna be many genes are only off and on or on |
|
| 28:18 | different times. Right. And so environmental conditions dictate that which ones are |
|
| 28:24 | or off. Okay. Um Our okay respond to very specific chemical signals |
|
| 28:34 | out by our body typically through hormones the like Okay um and ourselves um |
|
| 28:43 | they have the right receptor for they'll take the signal and then do |
|
| 28:49 | activity like this to produce a specific typically. Okay, that's with ourselves |
|
| 28:54 | to. Right. Are these body ? We put out three home runs |
|
| 28:59 | bacteria um take their cues from what's on in the environment and they can |
|
| 29:05 | various things. Okay, both external . Right. The point now is |
|
| 29:10 | we'll talk about control later. But point now is that you know control |
|
| 29:14 | a big part of this always Okay. And so um and so |
|
| 29:20 | the basics of transcription translation. Uh here is our template DNA. Remember |
|
| 29:29 | sense antisense thing. Right. We about that in the context of |
|
| 29:33 | Right so um the the transcription begins a copy of the anti sense or |
|
| 29:44 | strand. Okay I have explained this on the next slide so just hold |
|
| 29:48 | a second. And so here's our here. Okay both the D. |
|
| 29:54 | . A. And the M. . I. Have elements of uh |
|
| 30:03 | enabled it to be worked on so speak. So the D. |
|
| 30:08 | A. Of course has the um gene has a promoter. Okay so |
|
| 30:15 | are set up in front of Okay these are what guide the RNA |
|
| 30:20 | to the appropriate sites in front of gene. Okay so there's gonna be |
|
| 30:25 | in the D. N. That our regulatory that are a |
|
| 30:31 | That's a constant. Okay um the . RNA will have elements um remember |
|
| 30:38 | start coding stop code in the code in between. Right? The arriba |
|
| 30:43 | binding site. Right so it's gonna these elements that enable it to be |
|
| 30:50 | usable. Okay. Uh And so remember with precarious we have this feature |
|
| 30:59 | being the poly ribose. Um Right you can have multiple as soon as |
|
| 31:03 | ribosome binding site appears. Right, can begin to plop down. Right |
|
| 31:13 | the party. Right I don't think . Multiple time zones can attach to |
|
| 31:16 | transcript and proteins can be synthesized from of those. Okay. Um and |
|
| 31:23 | of course remember this is that's possible there is no separation process. There's |
|
| 31:28 | there's no translation occurs in the Like in ourselves and transcription transcription of |
|
| 31:34 | translation outside. That's how it occurs eukaryotic cells, bacteria don't have that |
|
| 31:39 | division. Okay so basically happens almost . Okay So then of course with |
|
| 31:46 | code on remember that there are there's code book to decipher that. Right |
|
| 31:54 | we have a start code on then count 123. Right? Until we |
|
| 31:58 | to a stop code on. And uh ribosomes are what recognized code ons |
|
| 32:06 | bring the right, you know, to the party. And ribosomes are |
|
| 32:09 | of the the the books typically called Workbench brings everything together at the |
|
| 32:17 | I mean the M. R. . A bound to that site for |
|
| 32:22 | come and attach so all of Okay and and the result, of |
|
| 32:27 | the poly peptide. Okay. Um let's just refigure all through this |
|
| 32:34 | a sense antisense thing. Okay so again as I said and we talked |
|
| 32:41 | viruses RNA viruses. Right, These simply the rules. I'm gonna click |
|
| 32:48 | . Right? So it can be D. N. A. |
|
| 32:49 | N. A. It could be RNA. It can be RNA |
|
| 32:52 | It follows the same terminology. There's sense and antisense strand or plus a |
|
| 33:00 | strand. Okay, coding template all all these alright. Are |
|
| 33:07 | coding plus sense. Antisense template minus all synonymous. Okay, so for |
|
| 33:14 | . N. A. Or we the anti sense strand, That one |
|
| 33:19 | the template. And in doing so basically making right an identical copy. |
|
| 33:29 | the scent strength. Okay, so is a sense strand. If it |
|
| 33:35 | that it's a minus, then the is a plus, which is what |
|
| 33:41 | M. RNA represents. Okay. so if we look line up our |
|
| 33:48 | , right? So here is N. A. Very top |
|
| 33:53 | N. A. At the very right there the same everywhere, there's |
|
| 33:56 | G. C. A. Same in the M. R. Right |
|
| 34:04 | where there's a T. Right? a year or so? All |
|
| 34:07 | so except for that, you it's it's an identical copy of |
|
| 34:11 | N. A. Okay, which makes sense. Right. If |
|
| 34:16 | . N. A. Is the strand containing the coding information that's ultimately |
|
| 34:21 | you want to get a copy Okay. And so that's what the |
|
| 34:24 | . RNA represents. Okay. So then of course, you know, |
|
| 34:31 | you jesus start code on and so . Right? So um since anti |
|
| 34:38 | um now let's look at this Okay, which are these terms includes |
|
| 34:49 | of the others? Uh have you of all of these? Maybe except |
|
| 34:58 | couple which includes all the others mm . So which is the looking for |
|
| 35:33 | one that's all encompassing all encompassing. . Hmm. It's your I might |
|
| 36:00 | it. Okay, counting down 21 . Okay. Uh Yeah. If |
|
| 36:19 | answer genome you are correct. Yeah. Uh Yeah. Wrong. |
|
| 36:33 | answer the right. Good. Um Megillah is probably something you may |
|
| 36:38 | have heard of that's particular to We'll talk about that in a |
|
| 36:43 | So that's and that are specific to genomes. Okay. Um The smallest |
|
| 36:52 | here is the gene. Okay. so let's um so we're gonna go |
|
| 36:58 | precarious genomes and then I'm gonna show only for comparative purposes the eukaryotic |
|
| 37:07 | Um but I'm not going to be you on the particulars of that but |
|
| 37:12 | see what I mean here in a . Okay, so genome transcriptome |
|
| 37:16 | Right. So there is a and called that was gently lISZT to release |
|
| 37:23 | chromosome and uh it may have in to that one or more smaller |
|
| 37:32 | Right? Plasmids. Right. Like . And so that if present also |
|
| 37:39 | part of the chromosome. Okay. genome in us is basically all of |
|
| 37:44 | 46 chromosomes that's in our cell. course damage have half that amount. |
|
| 37:50 | in the bacterial cell it's um obviously chromosome but it can also be these |
|
| 37:56 | elements called plasma. It's okay. Transcriptome is the number of transcripts of |
|
| 38:03 | RNA. So it's basically you we're talking here. D. |
|
| 38:05 | A. You can guess R. . A protein. Right. So |
|
| 38:14 | whereas the genome is the permanent Alright. So it's not going to |
|
| 38:20 | in terms of abundance. Okay. the amounts in terms of your transcription |
|
| 38:25 | program can change and fluctuate. R N A. M RNA transcripts |
|
| 38:32 | and go okay um particularly precarious lifetimes RNA molecules are not long. We're |
|
| 38:39 | on the order of minutes. Um Which is fine because you'll just |
|
| 38:44 | more if we need it. proteins uh have a finite finite life |
|
| 38:50 | well. So but again you can produce more through transcription translation. |
|
| 38:57 | so of course it's control gene control will manage all this. Okay, |
|
| 39:06 | in terms of average numbers, in of pro Cariou genomes um E coli |
|
| 39:12 | actually on the upper end about 66 seven million base pairs. Um The |
|
| 39:20 | ones are like we talked about those don't have a cell wall. Michael |
|
| 39:25 | are kind of on that smaller end 500,000. Um And as mentioned they |
|
| 39:31 | possess one or more of these extra elements plasmas. Okay, so um |
|
| 39:41 | organization. All right, so here's I'm going to show you just for |
|
| 39:46 | to purposes the eukaryotic system. so again, in both types you're |
|
| 39:50 | have what are called structural genes. are genes that code for proteins that |
|
| 39:57 | some function. Right. Whether part the metabolic pathway or what have |
|
| 40:01 | Okay, you also have genes that control. Okay. Some of these |
|
| 40:08 | code for anything. They're just a that a protein binds to that then |
|
| 40:15 | expression in some way. Okay. do have you can have genes that |
|
| 40:20 | code for proteins that call for an molecule. Okay. Um but most |
|
| 40:26 | code for proteins. The operation and . So that's that's a feature of |
|
| 40:33 | genomes. The regulation and operation. . A system. So that's kind |
|
| 40:38 | an older name for a gene. you can see it in the context |
|
| 40:42 | mono sis tronic is one gene party Tronic multiple genes. A constant is |
|
| 40:51 | this in terms of gene structure. matter what you're talking about what life |
|
| 40:57 | you're talking about. You're talking about . There's a promoter is a part |
|
| 41:02 | your promoter and you get a gene now. Other things may vary |
|
| 41:06 | but you're always gonna have that. , and so again, the promoter |
|
| 41:11 | important for bringing the primaries to the of that gene. Okay, so |
|
| 41:20 | , I'm not gonna test you on periodic gene structure but just as a |
|
| 41:25 | to show you. Okay, so more complex, there's a lot of |
|
| 41:31 | processing that goes on with you carry genes. Okay, so control again |
|
| 41:39 | , it's gonna be a common feature all genes. And so you're going |
|
| 41:41 | have elements that are very close to promoter uh called proximal elements that can |
|
| 41:49 | far away. Thousands of bases Okay. But these are these will |
|
| 41:55 | how much expression occurs. Okay. but then beyond that in terms of |
|
| 42:01 | internal parts of the gene, It's organized into coding sequences, exxons |
|
| 42:08 | non coding and non coding sequences in . Okay. And then you have |
|
| 42:14 | elements here, what's called a sequence that is translated into part of the |
|
| 42:22 | M. RNA. Okay, so transcription. Okay, we initially bring |
|
| 42:29 | uh this part here from the promoter the start of transcription. Right? |
|
| 42:35 | is basically right here. So this is what is transcribed. Okay. |
|
| 42:43 | all of its transcribed initially. So call the primary transcript. And the |
|
| 42:47 | step we'll get rid of the Okay, so this in itself is |
|
| 42:53 | a translatable transcript. It has to processed into this right where we take |
|
| 43:01 | the entrance, this is what's called . Okay. And so and so |
|
| 43:06 | you're seeing here on the screen is in the nucleus. Okay, so |
|
| 43:11 | transcription and the processing. Okay then have elements of the cap and the |
|
| 43:18 | . These are because remember these have exit the nucleus and the cap and |
|
| 43:24 | helped facilitate that. Um they also facilitate this. The stability of the |
|
| 43:30 | . Any transcripts lacking one or both these cap and tail are pretty much |
|
| 43:37 | fairly quickly. So the cap and enhance stability of transcripts. And eukaryotes |
|
| 43:44 | can last longer in some cases for types of transcripts that can last for |
|
| 43:51 | weeks or months. Okay. Um any case so now this is what |
|
| 43:57 | call mature M. R. A. That's something that can be |
|
| 44:01 | exit and outside the nucleus in the . L. Patrick particular um uh |
|
| 44:09 | in the site is all these will translated. Okay so so you don't |
|
| 44:15 | any of this in bacteria. Either the structure of Exxon in tron |
|
| 44:23 | splicing or any of this stuff. so bacteria have their own unique kind |
|
| 44:28 | system. Now some there are some carry outs that have some instances where |
|
| 44:35 | of their genes are dealt in this . Right. Because we know previously |
|
| 44:40 | archaea do have some features common to that bacteria don't. Right so there |
|
| 44:46 | some similarities for some archaea jeans. but for the most part archaea also |
|
| 44:52 | the same structure as bacteria and that's we're going to look at here. |
|
| 44:58 | so this is the operation structure. . In a nutshell, what it |
|
| 45:03 | means is most appropriate genes are organized that fashion. Okay you do have |
|
| 45:09 | that have the one promoter. One that produces the mono sis tronic |
|
| 45:17 | Okay but most have kind of the you're gonna see here. So it's |
|
| 45:21 | promoter. Um with two or more following it. Okay so multiple genes |
|
| 45:31 | to a single promoter. Okay. you see here in this example, |
|
| 45:36 | again, the promoter is where is a recognizes the promoter binds to it |
|
| 45:44 | it up in front of the gene then you get transcription and the whole |
|
| 45:49 | is transcribed policies, tronic messages, continuous message. Okay, so it |
|
| 45:57 | mean that in that single message, , you have start, stop, |
|
| 46:07 | , stop. So the elements of are there for each one, |
|
| 46:13 | Start, stop. So each start stop coordinates for each gene in that |
|
| 46:22 | . Okay, so it kind of where one gene begins and ends, |
|
| 46:27 | one gene ends, the next one . Okay, so you see |
|
| 46:31 | Okay, so um so that's the part, translation of course will then |
|
| 46:38 | to production of the proteins for each those genes. And it's very typical |
|
| 46:44 | these are part of the same metabolic . Okay, so something like whatever |
|
| 46:50 | look at this in control, uh opera an opera on each of those |
|
| 46:58 | have different metabolisms but they lead to production of a protein. Okay. |
|
| 47:05 | so um so uh the control Okay, so the opera itself is |
|
| 47:12 | you see here. Okay, promoter structural genes. That's the opera. |
|
| 47:18 | , regulatory elements which may be up are not considered part of the |
|
| 47:23 | Okay, so when you see this these two lines, that just means |
|
| 47:30 | there's separation between these two parts. can be way upstream. Okay. |
|
| 47:36 | be hundreds of bases thousands of bases . Okay. And that's where you'll |
|
| 47:42 | very typically regulatory elements. Okay, regulatory gene coding for regulatory protein that |
|
| 47:50 | common is to interact with an element the opera called an operator. |
|
| 47:57 | The operator is it is just a . So the promoter and operator don't |
|
| 48:02 | for anything. Okay. But they sequences recognized either by RNA polymerase promoter |
|
| 48:10 | regulatory proteins or different types if you're operator. Okay. And so by |
|
| 48:15 | here, we're basically physically blocking the of to get beyond there so it |
|
| 48:23 | do anything. Right in that in scenario. Okay, operator is bound |
|
| 48:29 | regulatory protein. So we're not gonna any transcription. Okay. So we're |
|
| 48:34 | controlling expression by doing this. now um the back up here. |
|
| 48:42 | as we go further along into next and talk about this, uh the |
|
| 48:50 | under which this kind of binding occurs different. Different, different environmental um |
|
| 48:59 | internal conditions can determine whether this is or not bound. Right, so |
|
| 49:06 | we get into what's called induce a operations, um repress herbal operations |
|
| 49:12 | Right, so it's all about what the conditions allowing this to happen or |
|
| 49:16 | happen. That's really the crux of . Okay. Um and there's different |
|
| 49:21 | of situations that will occur as we'll later. Okay, also you can |
|
| 49:28 | control through the end product of a . So this could be a control |
|
| 49:38 | that may interact with an enzyme appear block activity. Right? And then |
|
| 49:46 | don't express the protein. Okay. too is control. Right? Control |
|
| 49:52 | doesn't just have to be at N. A. It can be |
|
| 49:58 | in these steps. So control can to all these levels. That's really |
|
| 50:05 | if you're kind of not super confident your knowledge of transcription translation thing for |
|
| 50:17 | , it's that's why it's good to it because we get to controlling |
|
| 50:21 | We're controlling these aspects of transcription That's how we affect gene expression. |
|
| 50:27 | ? Um So what do you know nuts or bolts or the mechanics of |
|
| 50:32 | transcription translation works? No it in context of you know this is why |
|
| 50:38 | we're gonna control you can control it these different levels. Okay. Um |
|
| 50:46 | . See any questions about that? . Yeah. So basically this. |
|
| 50:56 | here. Yeah. Another. Um All right so the regular so |
|
| 51:07 | an opera on is this I just . Okay. And so of course |
|
| 51:14 | can have multiple of the you'll have of these across the chromosome in the |
|
| 51:21 | or archaea. Now if the opera are part of a a common um |
|
| 51:34 | process then they may be controlled Okay then you have what's called a |
|
| 51:44 | . Right So the best example here let me just let me start this |
|
| 51:48 | we'll talk about this at the But signal factors. Okay, so |
|
| 51:53 | just mentioned is binds to a It does so through the presence of |
|
| 52:02 | sigma factor. So sigma factors are of an RNA polymerase structure. |
|
| 52:08 | the sigma factor is actually a piece can kind of come off and |
|
| 52:11 | Okay. The simple fact is not in the actual synthesis of a |
|
| 52:17 | It's more about this is the way can find a promoter. So sigma |
|
| 52:22 | recognizes different promoter sequences. So its is to help the memories get the |
|
| 52:28 | because the sigma factor is the one can recognize the sequence. Okay, |
|
| 52:34 | sigma factors for that reason can be control element. Right? Because if |
|
| 52:40 | doesn't get if it doesn't recognize the or somehow affected to not be able |
|
| 52:46 | interact with the promoter there again you're expression. So sigma factors can be |
|
| 52:51 | point of control as well. Okay so you can control multiple operations |
|
| 52:58 | If they all share that same sigma control element. So you can kind |
|
| 53:05 | control them all together and you collectively all those coordinated co ordinate li controlled |
|
| 53:14 | a regular. Okay and so example is just think of of nitrogen regulation |
|
| 53:23 | there is such a thing as a regular. Okay, so think about |
|
| 53:27 | the ways nitrogen is used in a . Right? Um to make amino |
|
| 53:33 | to make nuclear tides Um uh There's other things it's used for as |
|
| 53:40 | Um So you have processes of nitrogen assimilation taking it in right. |
|
| 53:48 | Maybe it's got like maybe it's a fire and it's doing that reaction or |
|
| 53:52 | it's nitrogen fixation or what have Right. So the point is there's |
|
| 53:57 | roles for nitrogen and multiple metabolisms for . Yeah. Uh There are yeah |
|
| 54:10 | do see the side sigma factors but there's you might think there's a signal |
|
| 54:16 | for every promoter but there's not there's only about 10 or 12 or 88 |
|
| 54:22 | 10. 12 single factors totally. so um but yeah they do synthesize |
|
| 54:29 | and they will have certain of these controlled together because of that. They'll |
|
| 54:36 | those signal factors in common that are controlled. Studies shown that cells with |
|
| 54:44 | sigma factors are less. They don't more as many proteins. Yeah I'm |
|
| 54:53 | there's some mutants mutants that that they've that. Yeah that that that is |
|
| 54:57 | case. Yeah. Um So if look at nitrogen regularly on then we're |
|
| 55:05 | all hopes are controlling then all the involved in these various nitrogen metabolisms through |
|
| 55:12 | specific um signal factor. Okay. kind of allocate resources. Right, |
|
| 55:19 | comes if a self presented with some of nitrogen, maybe you can use |
|
| 55:24 | and do this or that with it on what it needs it for and |
|
| 55:27 | can control the operations involved in that that particular sigma factor, it's a |
|
| 55:34 | of efficiency, making it efficient and waste energy. Right? Because that's |
|
| 55:39 | really what control is all about is not let's not express everything that makes |
|
| 55:44 | sense only that's express what's needed and the right amounts that's more efficient. |
|
| 55:51 | . Um so one more So it regular. Okay. And we'll see |
|
| 55:59 | regular in the context of transformation that's up next week because transformation can be |
|
| 56:06 | through regular but any time you're involving or more operations that are controlling a |
|
| 56:14 | a common process, you can call irregular. Okay. Many questions about |
|
| 56:22 | . Another regular thing kind of be little confusing but it's just like you |
|
| 56:26 | have multiple genes under one promoter. an operation. You can have multiple |
|
| 56:32 | under the similar control. And that's regular. So it's a level the |
|
| 56:37 | of scope. Right? So if want to really break it down nuclear |
|
| 56:43 | . Right. Gene opteron, regular genome. Okay. We want to |
|
| 56:51 | it down in terms of scale. . Um I think I may have |
|
| 56:56 | one. that's right. Um plasmas. Alright. So plasmids Uh |
|
| 57:08 | originate in bacteria, you know, years ago when we discovered these |
|
| 57:14 | We've since taken them into the lab completely deconstructed them. Synthesize them, |
|
| 57:20 | them for our own purposes. So recall, you know, the techniques |
|
| 57:25 | genetic recombination and cloning genes and these of things all involved using plasmas very |
|
| 57:31 | for that purpose. Right? So that reason alone, we've deconstructed and |
|
| 57:36 | and have constructed these for our own . Okay. And we put different |
|
| 57:41 | in them too to fit our Okay. But the point is these |
|
| 57:48 | actually exist and come from bacteria. . And um we've just taken out |
|
| 57:55 | done our own things with them. of course in bacteria have them, |
|
| 58:00 | ? These are completely autonomous. That of can do their own thing to |
|
| 58:04 | degree and they don't. So the a bacterium typically undergoes replication when the |
|
| 58:13 | gets to a certain size. And then and then before it |
|
| 58:18 | Right? Of course the chromosome And he started so gets a |
|
| 58:22 | And so that's kind of cute for chromosome replication. The plasma doesn't have |
|
| 58:27 | follow those rules. The platform has own Remember that essential element for DNA |
|
| 58:33 | is that story sequence. Right. so because it has its own it |
|
| 58:38 | just replicate on its own. And so the copy number. So |
|
| 58:44 | number of plasmas Purcell can vary as . You have types are called low |
|
| 58:48 | number, plasmas types are called high number. Okay. High copy number |
|
| 58:53 | be 50 per cell. Low copy one or two per cell. Um |
|
| 59:02 | you can also integrate these things into chromosome. Okay, we'll see that |
|
| 59:06 | week. Um The the transferability. conjugation, conjugation. So it's come |
|
| 59:17 | and they transfer things like plasma. between them. So plasmas are obviously |
|
| 59:24 | in scope. They may be contained average. It can be of course |
|
| 59:29 | one gene. But they typically have 5 to 10 is the maybe the |
|
| 59:34 | count. Um I'd say 5 to bases. The average size. But |
|
| 59:40 | see some bigger some smaller um types plasma is based on kind of what |
|
| 59:48 | carrying. Okay, so our factors for resistance contain antibiotic resistance genes. |
|
| 59:55 | There's actually some of those in here recycling. That's tet tetracycline, resistance |
|
| 60:02 | . Okay. Um An example the plant carry will carry a pathway. |
|
| 60:11 | three or four genes. Maybe an on. Okay. For a certain |
|
| 60:15 | . Very common. We mentioned before aromatic metabolism, right? The three |
|
| 60:21 | four genes involved. And that can something that's passed through a plasma. |
|
| 60:25 | we call those cattle bolic plasma. The F factor is can be one |
|
| 60:31 | in addition two an R factor or catatonic pathway. So plans. We |
|
| 60:38 | have multiple things in it. theoretically. I mean you can certainly |
|
| 60:42 | a password to put the and put things in there if you wanted |
|
| 60:45 | But it can be but naturally korean can have multiple of these types of |
|
| 60:50 | in it. And so if it the f factor. That's what makes |
|
| 60:55 | transferable actually F factor will be a just for example, it would be |
|
| 61:01 | portion of class mid and that factor would contain genius specific for enabling it |
|
| 61:13 | conjugate and then pass to another Okay, we'll talk about that process |
|
| 61:18 | week. But if that's what that factor means F is for fertility. |
|
| 61:24 | . Makes it transferable. Um so little bit more replication. |
|
| 61:32 | So by direct remember that's how the replicates. Right. The plasmids can |
|
| 61:36 | that way as well. If the If the Passman is one that is |
|
| 61:45 | of being transferred as an F Okay then when undergoing that transfer it'll |
|
| 61:57 | a different mode of replication. I'll you what, I'll show you what |
|
| 62:00 | mean by that in a second. for bidirectional replication is what That's what |
|
| 62:04 | know. Right? So that's where strands come apart. Right? The |
|
| 62:09 | replication forks become a part of the . We make two copies. |
|
| 62:14 | So that's that's the one we're most with. So, the rolling circle |
|
| 62:19 | , that's typically what precedes the transfer . So two cells will come |
|
| 62:26 | One will will do the rolling circle with its plasma. Okay. And |
|
| 62:32 | does So by by making a So, nick basically means breaking the |
|
| 62:38 | bond within that um poly peptide Right, So you expose a three |
|
| 62:46 | hydroxy in. So, if you right, your replication, the DNA |
|
| 62:53 | looks for this and begins to extend that add nucleotides to that. |
|
| 62:59 | so creating that nick enables that to . And so it will then begin |
|
| 63:07 | synthesize using of course the template. template would be that inner circle, |
|
| 63:16 | ? So it will begin to use a template and copy copy it. |
|
| 63:20 | ? Then the copy would begin to the one with the five prime and |
|
| 63:27 | . And so that will become That's what you see happening here. |
|
| 63:32 | , That's the displaced strand coming off the other one is copying the |
|
| 63:37 | knocking it off. Okay, and it looks kind of that's why they |
|
| 63:41 | it a rolling circle. Right, the dark purple strand, the plus |
|
| 63:46 | here is what has displaced the other . And you see it over here |
|
| 63:52 | envision, you know, this is between there's a relationship between two |
|
| 63:57 | right? There's one here. one here. Okay. And so |
|
| 64:05 | rolling circle replication occurs, that displaced gets shoveled into the recipient. |
|
| 64:11 | so the recipient receives a copy of plasma. Okay, and can eventually |
|
| 64:20 | course take that single strand and copy and make a double stranded molecule. |
|
| 64:26 | , so basically I just showed you congregation. This is this is typically |
|
| 64:32 | rolling circle replication. Oh, doesn't have to be. But typically it's |
|
| 64:37 | you see when cells are coming together one is going to receive a |
|
| 64:41 | They do the rolling circle thing. . And so, um so that's |
|
| 64:48 | something you haven't you haven't seen this type of replication. Okay. |
|
| 64:55 | now uh many questions at that Yeah. Right. Yeah. |
|
| 65:08 | Right. Yes. Right. So gonna be that would involve um if |
|
| 65:18 | recall uh primers get involved in primary all that, that's what would happen |
|
| 65:23 | this, to this one over You have a primer coming in and |
|
| 65:28 | on and so forth. Okazaki, all that kind of stuff. Fun |
|
| 65:31 | . Yeah. Yeah. Right. . Right. All right. Um |
|
| 65:37 | so it can, in terms of orange, you don't even have an |
|
| 65:40 | that's specific for this type and one this type. Okay. It's often |
|
| 65:46 | a transfer or e it's what's used if they're gonna do the ruling circle |
|
| 65:51 | because they're coming together with another Okay. It was just no, |
|
| 66:01 | , there's two different stories within the of the bacteria. So depending on |
|
| 66:05 | it's going to it was transferable or , it may use that story to |
|
| 66:10 | their own circle thing. It may the other or if it's just in |
|
| 66:14 | and just replicating the cell is not any kind of congregation thing. So |
|
| 66:19 | of it as the as this one for this kind of process. Um |
|
| 66:25 | it the usual replication, it's going this congregation process. It may use |
|
| 66:32 | will use the transfer story, let's it that. We'll talk about this |
|
| 66:36 | week. But that's kind of that's what's going on here. Kind of |
|
| 66:41 | which mode of replication we're using are using this one? Because we're conjugating |
|
| 66:45 | the cell or are we not? . Just depends what's going on. |
|
| 66:51 | , um, in terms of the itself and holding on to the |
|
| 66:57 | that's another consideration. A plasma that's is being held onto by the |
|
| 67:07 | Okay, so, again, this back to the energy thing, |
|
| 67:11 | You're holding on to the to this and you're and it's copying it. |
|
| 67:17 | energy being used to copy this extra element. Right. And, you |
|
| 67:23 | , it was going to do There should be a a benefit for |
|
| 67:28 | to have that plasma or else Miles want to expend energy extra energy to |
|
| 67:33 | it. Okay, so that's where comes in. Right? So, |
|
| 67:38 | , very, you know, kind basic example, Let me just show |
|
| 67:42 | come back to this in a So, if you have you collide |
|
| 67:47 | , so that one on top has plasma Um, and it contains 10 |
|
| 67:53 | . Okay. One of the bottom doesn't have a plan within its |
|
| 67:59 | Right? The s for sensitive. if you grow to different growth media |
|
| 68:04 | was recycling. Okay, then, , um this one grows because it |
|
| 68:15 | the resistance gene selected that selective pressure keep it if if you're growing it |
|
| 68:21 | tetro cycling. That is the selective . Okay. Um down here without |
|
| 68:30 | . Of course, this one no , right? It's lacking the um |
|
| 68:37 | gene of course, down here without cycling, it will grow. What |
|
| 68:44 | this 1? Of course? And grill, it doesn't matter. It's |
|
| 68:51 | there. So, but what can is okay if you keep this guy |
|
| 69:00 | that medium indefinitely and continue to transfer right? To know tetro cycling growth |
|
| 69:10 | over and over. It can lose plastic because it there's no need for |
|
| 69:15 | to hold on to it. That can happen after, I don't |
|
| 69:19 | , 10 transfers or something maybe, it can eventually lose it. Um |
|
| 69:27 | so, you know, having a pressure on it enables it to then |
|
| 69:34 | on to it. Okay. Because there's a use for it. |
|
| 69:38 | Um So the low versus high copy . Okay. So that can play |
|
| 69:46 | role in as well if you have high copy number plasmid, right? |
|
| 69:53 | even without selective pressure, right? gonna have a higher probability of hanging |
|
| 69:58 | because there's just more of them Right? So if it divides whether |
|
| 70:03 | that plane, that plane there's so in there that It'll it'll be passed |
|
| 70:09 | to the next generation because there's a in there. Okay. vs one |
|
| 70:13 | 2 Maybe. Maybe not. So for sometimes to ensure inheritance of |
|
| 70:22 | plans mids, they have this system of like a quasi my topic spindle |
|
| 70:30 | . Okay. It's, it's not . It's just kind of, it |
|
| 70:32 | of looks like that. But what have are these proteins called par for |
|
| 70:40 | and they kind of form on each of the plans man here in here |
|
| 70:49 | then they extend so they're attached to copy and then they begin to plagiarize |
|
| 70:55 | go to opposite poles right in the divides. So kind of as a |
|
| 71:00 | to ensure that the daughter cells receive a copy of that plasma. So |
|
| 71:05 | do see that is kind of pseudo thing, but it ensures that inheritance |
|
| 71:13 | these plans to the next generation. . Um, let's see is |
|
| 71:21 | is okay. Oh, any We got one more thing to |
|
| 71:28 | So we'll just save that for Okay. So we'll see you next |
|
| 71:37 | . Good luck on the exam. being sarcastic when I say that being |
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| 71:45 | . Good luck on the exam. . When they asked |
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