



S1: go over, like, the exam, like, other information that you guys wanna know you know things like [S2: oh ] that. okay? so like i have other questions but if we don't get to them like we don't get to them cuz last time most of the questions were from your, practice exam anyway. so, um
S2: most time like i don't understand like the questions on the, 
S1: on the practice exam? <SU-F LAUGH>
S2: well i_ not that i don't understand it i just don't know it i guess.
S1: okay. so i probably_ it probably would be more helpful to like, go over main concepts and like lecture notes and things like that you [S3: yeah ] think? [S4: mhm ] okay [S3: definitely ] um, so i have this set <P :04> and i don't remember if this stuff was like we all covered but, we'll look at it. okay. so how do you guys wanna, run this thing? do we wanna do it from [S3: do you want ] lecture notes first or questions first? what do you guys feel like you guys need more help on?
S3: um i didn't have a lot of questions on the ex- uh the practice exam except for the short answer.
S4: mhm 
S1: okay, how 'bout you two? 
S4: i just have questions from lecture notes. 
S1: and
S5: just, whatever, [S1: whatever ] i don't really care <SS LAUGH> i'll ask questions later 
S1: okay did you guys all take the practice exam?
S4: i didn't finish the short answer yet.
S1: you didn't finish? 
S2: i just did the multiple choice.
S1: you just did the mul- 
S5: yeah i just did multiple choice.
S1: okay. and how was the multiple choice for everybody?
S3: it's [S4: yeah ] i i did okay on it. i 
S4: i did okay but not as well as i, 
S3: yeah it was surprising. 
S4: (xx) 
S5: it wasn't great but
S1: it wasn't great? 
S5: i didn't go over, there were a couple questions that like, i s- got the right answer but i still thought like why (couldn't it be something else?)
S4: yeah i guessed [S3: yeah ] well on some, i felt like
S1: you guessed [S3: yeah ] well? okay [S5: yeah ] so [S4: yeah ] why don't we go through 
S5: like if it was worded differently or so- like i didn't feel like, it'll, [S4: i wouldn't have gotten ] (xx) multiple choice (xx)
S1: okay so why don't we do this? why don't we go over the lecture notes and make sure that we covered everything and [S3: okay ] like, things that i feel are important that you guys should like, focus on and things like that and then, we'll go over those questions on your, [S4: okay ] practice exam? 
S3: okay 
S1: that, 
S4: alright 
S1: okay? alright so we started with i remember like the D-N-A <LAUGH> technology one and two, right?
S3: um, are we go- aren't we gonna be be in the, non-cellular world, [S4: yeah ] of viruses and all that? 
S1: oh yeah yeah yeah. okay. after mutation right? 
S3: yeah 
S1: okay 
S4: (xx) <P :04> i think... (xx) kinda like 
S1: i remember we_ us two went over it 
S3: right
S4: yeah i think a lot of the stuff's kind of just, mostly what he said in class. except for, i don't really understand like
<P :04> 
S3: just looking at the first section?
S4: yeah
<P :04> 
S3: (where are) my questions?
S1: what do, you guys have any questions on that first lecture? [S4: yeah (xx) ] on viruses plasmids and prions?
<P :06> 
S3: uh, i tried to match up like um, you know the all the different kinds of viruses viroids plasmids uh trans- posons [S1: posons ] and prions um uh with the different, parts of that diagram like D-N-A replication transcription R-N-A replication [S1: uhuh ] [S4: mhm ] and translation, um so the retrovilus uh virus is the reverse transcription, [S1: right ] R-N-A virus, is just n- deals with R-N-A making R-N-A, [S1: right ] and prions p- proteins making proteins. [S1: right ] or, yeah. and um 
S1: or, yeah. [S4: converting ] affecting proteins or changing proteins in some way.
S3: but, transposons D-N-A virus and the plasmids are all involved in, the_ using D-N-A and going, somewhat (somehow) this direction? 
S1: right plasmids remember is just a circular D-N-A that's inserted. [S3: okay ] okay? so it's goes_ it starts from D-N-A to R-N-A, to proteins. [S3: okay ] okay uh a D-N-A virus yeah it, um, inserts D-N-A, as its material of... um replication. [S3: right ] right? and then, um it'll go on to to um
S3: but it it goes on to make proteins as well 
S1: right it does.
S3: and transposons are sort of mysterious or what?
S1: transposons
S4: yeah i didn't really understand how it moves around the genome (xx) 
S3: yeah and, it's really vague 
S1: wha- i forget what th- what um
S4: the segments of D-N-A that move from one location to another in the genome.
S3: discovered in nineteen forties but not accepted until later.
S4: yeah
S1: i forget what what i forgot what he said that about it 
S4: he said it was like a defective virus, so it can't get into a particle without a protein, i didn't really understand like
S1: i remember when we were talking about there_ remember how we were talking about there're different um phases of like virus tacking if it's um, if it's goes into the lytic cycle or the lysogenic cycle, [S3: right ] right? and like
S4: he didn't really talk about that in class though did he? lytic and lysogenic 
S5: yeah he never men- he never mentioned the lytic or the lysogenic 
S4: or the lysogenic (xx) 
S3: the the terms are mentioned in the lab book but we didn't go over it in class. 
S4: right he never talks about it. 
S1: okay. well uh the one of them is where D-N-A material is being inserted into the, genome, and then um, it can stay dormant, for a while, which means that it never it_ gets expressed, for a long time after several like replications of the cell. so like, this virus, is being replicated along with the rest of the genome as it, you know what i mean like when the cell divides, and forms two, and then, something in the external environment, signals, the cell_ signals that virus to like, start like, producing its own vi- like taking over the cell and like producing its own virus and things like that. right? [S4: mhm ] so like, that's when i_ that's what immediately what i think of when you say like, it jumps from one part of the of the genome to the other part of the genome. [S3: oh ] do you know what i mean? like, that i- maybe it's a sort of like maybe he's like indirectly talking about um, like the lysogenic versus lytic cycle. do you know what i'm saying? like it [S5: i thought ] can go from, [S4: sounds like it ] different parts of the genome. 
S5: but isn't lytic and lysogenic just whether, it dies or not? whether the cell's destroyed after
S1: right. because, in in one condition in one case like, the cell that's gets infected, will explode and like, whatever. right? but like, in another case it could be two or three cells that, after several replications that it does that. 
S5: so what does that mean for the transposons?
S1: what like the thing is that like the transposons it s- it says like it jumps from like, from parts of the genome to other parts of the [S5: right ] genome right? and like what i'm saying is that like, during one of th- either the lytic or the lysogenic cycle, either like, one of the cycles when it um D-N-A's inserted is inserted, the cell automatically dies. right? it [S5: right ] automatically jumps to the viru- virus attacks the cell, makes a cell, produces the virus and like the protein coat and explodes right? but in the other cycle what can what it can do is it can in- insert that information, that information can go into the genome, right? and like the cell will_ like the virus will stay dormant. af- and the um, D-N-A may or may not be replicated during the [S3: oops ] next, couple phases and it could be replicated where like, um 
S5: are you talking ab- when you say the D-N-A do you mean the transposons? 
S1: the the transposon. or the, viral D-N-A. [S5: right ] right this viral D-N-A will like be replicated along with the rest of the genome, and now, two cells have it now. the virus. 
S3: but it hasn't 
S1: and like, it has_ it st- the um virus still hasn't attacked the cell yet. do you see what i'm saying?
S5: so the, so the viral genes haven't been translated, [S1: it,- y- ] you mean? 
S1: yeah. 
S5: but they're there? 
S1: they have_ right they're there. 
S4: they just moved about in the genome. 
S1: they've just moved 
S5: so like this gene isn't expressed yet but it's there. 
S1: it yeah it's it's still there. right. so like okay so cell number one right? [S5: yeah ] this is, let's say it's just a bacteria it has circular D-N-A or whatever right okay it's got that D-N-A. and then, somehow like some virus gets inserted inside, and its D-N-A's like that. okay? and like, in one cycle this D-N-A may take the cell, and like, make more of this D-N-A. you know what i mean like make more of this D-N-A. [S5: mhm ] and, then it'll like, burst. you know what i mean like normal. right? this is like mo- th- th- this is like the case that you guys have been learning like, it like infects the cell, takes over the cell, the cell bursts and like, releases this thing. [S4: mhm ] this virus right? and that's how the virus grows. another case like what it could happen is that the cell, this like viral D-N-A can like insert inself itself into the regular D-N-A. okay? and like when this cell divides, it's gonna form... two of these. right? and like this viral D-N-A still hasn't, like done what it's supposed to do yet. do you know what i mean? like it's still in the genome. it can maybe move round maybe_ you know what i mean? like st- but it's still in the genome. it hasn't been expressed yet. so after like maybe one cycle two cycles, whenever the conditions are right for that cy- virus to like replicate or like, be activated, those genes to be activated, that cell would g- go into here.
S5: you mean this'll lead 
S4: those will be (lystar) 
S1: these will lead into here... but it could be like, two or three like, like stages after that. like this can replicate again. you know what i mean and form like two more, cells that look just like that. you know what i mean? and it you don't know when it's gonna do that that's the 
S5: so you don't know when it's gonna, come out (as a) plasmid? 
S1: you don't know when it's gonna go into yeah, you don't know when it's gonna come out and like attack the cell.
S4: so, why do they say it's like a defective virus? that it can't get into a particle without like a protein? it guess i don't understand that part of it then.
S1: i don't really 
S3: i don't have that in my notes
S4: you don't?
S5: yeah [S1: what ] neither do i. 
S4: he just said it he didn't or- didn't write it on the board. 
S1: it's a defective what?
S4: virus, it can't get it into a particle without a protein.
S1: can't get it into a particle what particle?
S4: i don't know i just wrote it down. i might just have, not 
S3: um, what i have written that mentions proteins is it says it may have, may have evolved from viruses that lost their ability to make the protein ca- capsid. [S4: mhm ] but then
S5: oh so maybe it needs, you're saying that the transposon needs a protein to enter a cell?
S4: (really) it doesn't [S1: oh ] have a capsid i 
S1: it doesn't have a capsid. 
S4: think it doesn't 
S3: oh that's right that makes sense 
S4: have a capsid, 
S3: so wha- how can get in? 
S4: so it like needs to get in the cell, but it can't because it doesn't have a capsid. 
S1: so it doesn't have a way of getting into the cell? 
S4: it's a defective virus just like a little thing, but it can't get in there cuz it doesn't have like a capsid. 
S1: so then how is a trans- b- how 
S4: that's what i don't understand. 
S1: is it like, brought from one place to the other? how does it affect, other [S3: is that, in the ] cells?
S4: see tha- see that right above that i have it's part of the D-N-A is replicated along with the D-N-A so i don't really understand how it's like a 
S1: part of its D-N-A is replicated along with the rest of the D-N-A?
S4: i says it i say it's part of the D-N-A, that's replicated along with the D-N-A, so maybe it's something in the D-N-A that can't, it's in the D-N-A 
S1: maybe it's just something like, it never went through this stage it's always under this stage. [S4: cuz it can't ] and in some cases it, occurs and some cases not. [S4: yeah (xx) something, it said ] that seems more like, [S5: wait what? ] a genetic defect than 
S4: yeah it said it's evolved from viruses.
S1: seems to me more like of a genetic defect doesn't it? [S3: yeah ] that it's innate and that sometimes it happens and sometimes it doesn't you know what i mean like, breast cancer for ex- instance you know what i mean that could caused by some sort of, transposon virus that was like, implanted in like, half of women like, [S4: mhm ] three centuries ago [S3: mhm yeah ] you know what i mean and like, in some certain conditions, this like thing shows up and some it doesn't. 
S4: yeah i think that's more like what it is like it's just something that's always in there, but it can't go and infect the cell or anything (xx) 
S1: it can't, be moved 
S3: but isn't it, in the cell? 
S4: yeah but it can't like, it can't 
S1: okay what 
S4: it's part of the genome but it can't 
S1: she's saying is that it can't it doesn't have a protein, outer coat. so like in your body, you find like, [S3: random transposons ] this virus just floating around. because 
S2: so it needs an outer coat (on it) to infect something?
S4: to originally get on, to go in (xx) 
S5: right but it's already in your cell, [S1: right ] so then, why does it even need the protein?
S1: it doesn't. that's what she's saying it that like long long time ago right? some virus was created. right? and, long long time ago this virus infected a cell. okay? and, somehow maybe it didn't have the correct D-N-A. right? it didn't have the part of the D-N-A that coded for the protein coat. [S5: okay ] so therefore the D-N-A couldn't reproduce and couldn't ex- like be encapsulated in the protein and like explode out. do you know what i mean cuz like, do you see what i_ remember like, um the step before this is like this this and then like this is the picture i remember it was like some like weird shape with [S5: right ] like flags right? and it's got like D-N-A inside. right? and then it like inserts this D-N-A into the cell. but this outside is a protein coat. 
S5: right. no i know i get that so it doesn't have a protein coat but you're saying that it's already in the cell, so, why does it need a prot- 
S4: i mean it's in the genome but it's not like the v- the virus usually just goes in it doesn't like become part of the genome right? it's 
S1: it's never, the virus is also always like an external D-N-A thing. 
S4: it's not really part of the nucleus or anything. 
S1: it's always, it's never part of the cell. 
S4: it's just something that goes into the cell and it's using it's polymerases to make more of it and then it leaves. it's just like using the cell to produce more of [S1: right ] itself and then it leaves. it's not like taking over it's like joining in the circle ever. [S5: right ] but like this one is in the circle. it's not like floating around the cell like [S1: right ] those over there.
S1: but i also think that even though you didn't talk about the lytic and lysogenic cycles that, sometimes it can still insert into the the D-N-A but i don't think you need to know that. 
S5: so what cycle would that be if it's inserting in the D-N-A? 
S1: yeah it's it's like this. right? except it never has this part it's al- the cell always looks like this. [S4: mhm ] and it just k- it keeps going like that through centuries and centuries and centuries and you may have some sort of transposon 
S5: so that would be the lysogenic?
S3: yeah. right?
S5: cuz it's not 
S1: yes. yeah. lysogenic is like the one that stays dormant right? 
S3: right 
S1: yes.
S5: so then if this were to like, burst out that'd be, like 
S1: it wouldn't ever burst out though
<SIMULTANEOUS CONVERSATIONS NEXT :50> <CONVERSATION 1> 
S2: (xx) (how does a) transposon move from one location to the another?
S4: just moving around (xx) 
S2: oh just moving around that like, s-
S4: that's that's your genome that's (xx) 
S2: mm 
S4: it (ori-) it evolved originally from a, a virus (xx) what they're saying is that over time (xx) (just in the genome)
S2: (xx...) so what does it do? 
S4: (i don't know just kind of it all organizes) (xx) it's just part of your genome. 
S2: mm 
S4: i think i'm gonna look it up in the book (xx) 
S2: (xx)
S4: i remember learning about it... (xx) i remember (xx)
S2: (it's gonna be a problem) on the exam (xx)
<CONVERSATION 2> 
S3: but it could get knocked [S1: it could ] into the lytic d- cycle in which case it would. i mean cuz that's the whole point otherwise it wouldn't be destructive right? 
S1: right exactly it would be destructive and somehow but i but if it doesn't have the ability to make a c- protein coat, it may_ you know, there's so many like there's so many things 
S5: (xx) like if it's already in the cell it doesn't need the protein coat to get, in the cell if it's already in the cell. 
S1: right exactly exactly but like, the thing is that like in what viruses do is that, how they take over is the fact is that they can take over a cell. make the cell do what it wants. right? [S5: and then leave ] and like and leave. right? but this doesn't ever leave, almost. [S5: right ] do you know what i mean? cuz it doesn't, like it 
S5: it doesn't have the protein (xx) 
S1: what they mean by, like right it doesn't have the D-N-A that coats for the protein. let's say 
S5: and it can't leave without protein 
S1: to like make it leave, right exactly it can't leave without protein right? so it just keeps, and like i don't know how this transposon, 
S5: how it, gets transferred to other cells 
S1: how like, how it, right exactly how it affects the cells. <END SIMULTANEOUS CONVERSATIONS> do you see what i'm saying? [S5: yeah ] like it's just something, that like they have identified as some sort of virus external thing. right? like, if he doesn't give you any more m- information_ we never studied transposons [S5: right ] when i was in, <LAUGH> bio one-sixty-two so i don't know, really. do you know what i'm saying? so i'm just saying that i- it like, i don't know how it affects cells like, you know what i mean [S4: i think it's just ] it could be some sort of like 
S5: so why would they hav- have even thought it w- came from a virus if it's just like
S1: part of the D-N-A right?
S5: yeah, (xx) 
S4: there's something_ yeah i don't remember why he said that, it may have evolved from viruses.
S5: cuz it just says that all he wrote was on these notes were segments of D-N-A that move from one location to another. 
S4: right that might have evolved from viruses 
S5: and it's present in the D-N-A of all organisms and it may have evolved from viruses. so like
S1: and i- you know the other thing too is that like, how can they name a virus rather than like, just evolution? you know what i mean like why is it 
S4: just part of your genome why isn't it just part of your_ how do they 
S5: yeah, why'd they think that it was a virus? 
S4: well what i'm saying is how did they look at this and be like hey that's probably a virus? why don't they be like that's part of your genome?
S1: yeah exactly like nobody knows like unless like there was like some sort of gap where like one bird had it and one bird didn't you know what i'm saying like and they had to find that exact link
S4: so i understand like i guess i don't [S1: so ] understand like why they think it's not. 
S1: i don't really, i don't really know like does it say anything about it in the book? does it even talk about transposons? 
S4: i- i think it does cuz
S2: use that (xx) 
S3: (xx) 
S1: it doesn't_ i don't_ like, maybe it would help to know like what kind of like diseases that it causes [S3: sure ] or like, you know like something like that that 
S5: what page is that?
S2: three thirty-five.
S4: page three thirty-five.
<P :06> 
S4: oh this (is looking like kinda different) (xx) <P :13> oh it says it can move from like plasmids to the chromosome or, within the chromosome, within plasmids. 
S3: so that's the movement that's happening 
S4: and it can transport genes. moving genes to locations from different plasmids.
S1: oh from plasmids to genome to [S4: mhm ] (xx) that could be a way too. 
S3: isn't a genome (like a plasmid?) 
S1: so then this only happens in, um bacteria.
S4: genome's in the like
S3: that's the_ it's an example from bacteria.
S4: genome's like your chromosomes the plasmids are just like (xx) bacteria (xx) 
S1: well, how do, eukaryotic cells, oh i guess there's like
S4: more than one (xx) 
S1: yeah that's stupid though. <S3 LAUGH> like, 
S4: it's like just their target (site they'll) just move around (they just) move 
S1: there i- it seems like, it seems like transposons are like, like infects like lower life forms. 
S4: it seems like they are just like (xx) particles and they just move around (xx) 
S1: do you know what i'm saying? like we don't_ like in your body you don't have plasmids that go from like cell to cell. you know and like sometimes go into cell some cells and sometimes go into others and you but you hear about it in like, like when you studied like the um spores or the, what ar- what was it that you guys were studying? [S3: the ] like the, the pods things i forgot what that organism's called. but you know how it's like tan black and like [SS: oh yeah ] yeah that thing. you know how like [S4: astrospores ] there's like conjuc- conjunction and like things like that where like, D-N-A is actually being like, um, moved from one to the other or like if you hear about like budding and like when you take o- ho- like hear about like fungi and like mushrooms how like, sometimes there's conjunction between the two or_ you know what i'm saying? [S3: right ] like organisms where like bacteria, bacteria pla- pla- pass plasmids from like parent t- to daughter cells. [S3: mhm ] you know what i mean like, very like early life forms where like, 
S4: yeah, cuz it's says they're moving 
S1: D-N-A is passed rather than D-N-A is being replicated and like, you know what i mean in forming two cells type of thing. you know what i mean? [S4: yeah ] like, i mean it's still being replicated in like bacteria and stuff but like there's still a plasmid that's not being replicated and that's like, being shoved from one to the other. you [S4: mhm ] know what i'm saying? so like, i feel like this doesn't affect higher life forms but it's something_ i i think that you just pretty much need to know that like, [S4: yeah ] it goes from place to place like, know the example of um, bacteria where like it can go from a plasmid to like the genome genome to plasmid you know what i mean and that's how it gets t- 
S4: but when he said like, it says here that it can bring genes from the uh, plasmid, to like a different location on a different plasmid. how you can (move) genes with it or something. it seems kinda strange but, 
S1: yeah it just seems really 
S4: i guess whatever. it's just moving around. 
S2: it goes from one plasmid to a different one? 
S1: yeah. it's moving around. [S4: it's moving around ] from place to [S5: yeah ] place.
S4: (xx) 
S2: it's probably gonna be like one multiple choice question at the worst. 
S1: maybe.
S4: yeah 
S1: i don't know did yo- did you guys talk about it in discussion? was it like emphasized in discussion? 
SS: no 
S4: (xx) 
S1: yeah
S5: so just know that it's a 
S1: then, just know s- it's like [S5: genetic material (xx) plasmids ] some sort of genetic material that moves from place to place. 
S4: okay. so
S3: okay <LAUGH>
S5: when you said like stuff moves from, plasmids to chromos- what did you say about? stuff is like moving from plasmids to 
S1: that it can take like, if you_ in the book it says like it it can take 
S4: one example is that it takes some ampicillin-resistant genes from, one plasmid to a different plasmid or something. i don't really understand that but that's what it says in the book if you wanna
S1: pretty much the main idea is [S4: that it's moving around ] that it's moving from, moving around
S5: okay
S4: it gets_ it makes a target site and it goes there. 
S1: it goes there. yeah. it can bring things along 
S4: which is not a normal part of, chromosomes. 
S1: with it or it can be ampicillin resistant, you [S5: right ] know what i mean you don't, [S5: right ] you don't know. but somehow like the material that it's bringing with it is affecting the cell in some way either positive or negative you don't know. [S5: okay ] uh okay, so i remember that when you were taking about, the block that says D-N-A technology one was more of like, what was it? like D-N-A sequencing things like that um 
S4: yeah cloning and stuff i [S3: mm ] think i feel kind of
S1: finger_ i remember there was like fingerprinting, [S3: yeah ] um, things like that.
S3: yeah 
S4: i was way more like stressed about it last time [S3: right ] (but) 
S5: (xx) which is the (folder?) 
S4: i think it's started to come together now. [S3: what's that? ] just like the next two lectures kind of, [S3: yeah ] yeah Wednesd- it's lecture twenty-two and twenty-three.
S1: okay so that's 
S5: is fingerprinting is that like what southern blotting is?
S1: southern blotting. oh that's when you put the two like mother father pair together 
S5: it's like the combination of the, [S1: of, the two ] nucleic acid hybridization and like finding the R-F-L-P. it's like you, you're finding... [S4: did you write ] you're finding different restriction, um 
S4: did you write down this stuff? or was i just like 
S5: restriction fragments and then like the D-N-A 
S4: (xx) physical map genetic map 
S5: sequences that they contain? 
S1: yes. it's more_ [S3: (D-N-A se-) ] okay um those are (an) L-P 
S5: like what is fingerprinting (xx) 
S4: i feel like i'm not sure if i was supposed to write that down.
S1: okay, this is what i remember from fingerprinting but i think you guys should listen to me to make sure 
S4: yeah, i'm sorry i just was just asking her something. 
S1: that i'm right but, um fingerprinting is where some sort of restriction enzyme is put on some sort of okay uh D-N-A. okay. like some D-N-A from like two different people. [S5: right ] mine and yours. okay? and some restriction enzyme the same restriction enzyme is put into your D-N-A as into my D-N-A, [S5: right ] and it cuts it up. at certain sequences. right? the specific sequences that that restriction enzyme attacks. 
S3: (can i have that?) 
S1: okay [S4: (xx) have a picture of that ] and then after that um, after that like your segments are like put on that like thing where there's a plus and minus [S5: mhm ] and like the larger fragments go this way and like smaller fragments go this way. [S5: oh yeah ] right? 
S5: which_ the larger fragments is that_ what charge is that also attracting to? like what charge (is that out of) [S1: um ] 
S4: it just doesn't move as [S5: it ] far cuz it's bigger 
S1: yeah it just_ it doesn't 
S5: right, but it's also separated by charge, [S4: oh really? ] which i wouldn't think is important but you never know like i just didn't what know charge 
S1: well, okay. i think it's_ isn't it like when you like learn it in physics it's always from negative charge to positive charge? [S5: yeah ] right? [S5: so you think that, positive (xx) ] right so like neg- so it's always [S2: didn't know that ] like, it's gonna be like a negative and then a positive and it's gonna run toward that positive. right is that right? 
S5: yeah i think that
S2: (xx)
S1: charge goes from like the negative to positive side. i think that's how it is.
S5: so the shorter more positive, fragments (are towards that) 
S1: is gonna be towards more the positive side and [S5: right ] then, right. and i think that'll pretty much tell you what side it started from, like, when you draw the_ when they draw the pictures, they'll have like, the ink wells where or like the wells where they loaded it, you know what i mean? [S5: right ] and that's the side that it started from. so everything on like_ and then this is where it ends. right? [S5: mhm ] so like here are the bigger fragments, and those are the smaller [S5: okay ] fragments. you see what i'm saying? um, and then okay so then they run it out, and you get like these big fragments over here longer fragments this way you know things like that. [S5: right ] but my D-N-A is different than your D-N-A. so, 
S5: you can d- detect differences by seeing the different 
S1: my fragments are going to be different right than yours. and so, like if like let's say, there was a crime, okay <LAUGH> and like, [S5: right ] me and you were suspects and like 
S3: is this what you're looking for? 
S5: (we could) test the blood and see okay 
S1: there was blood at the scene of the crime. exactly. so like, if i if i was like, if i was like the whatever the, i don't know if i was guilty right? then my D-N-A would match the D-N-A, 
S3: yours is a different one. 
S1: of, 
S4: (that's what's wrong with it) 
S1: at the scene of the crime. 
S5: right 
S1: and yours wouldn't [S5: right, ] because, your 
S5: you you cuz of the restriction (xx) 
S1: enzymes your yeah, exactly.
S5: so then what are also i don't know if you guys found this because i didn't see it in the reading S-S-L-Ps, as opposed to R-F-L-Ps? 
S4: um i think those are just like more like, if there's an insertion or deletion it's going to be shorter or longer you can detect it when when you do P-C-R, you're gonna get like replications of uh the chromosomes, so say you have like an insertion in yours that i don't have yours are going to be longer than mine, and that would be detected in P-C-R. or yours would be shorter if you had a deletion. i think it just does (like) the length 
S5: isn't P-C-R just when you're replicating, genes outside the 
S4: mhm, in that, in that cycle, thing. 
S1: where you put it in hot and then cold hot and cold and hot and cold 
S4: in that thermal cycler, and that just like but say mine would be longer 
S5: but why but you're not detecting anything with P-C-R... that's just a way to
S4: right but i'm saying that l- you produce 'em in there, and it says detected by P-C-R, that's what he said in class i think didn't he? or what what did you put down (xx) 
S3: um 
S2: maybe it'll be made obvious by P-C-R
S4: that's just kind of what i got out 
S3: detected by P-C-R is what i've got. yeah 
S4: i just kind of think it would be by P-C-R because yours would be longer than mine so when it went_ when we did P-C-R on it you'd end up like, your_ longer fragments than i would mine would be shorter.
S1: so maybe what she's saying is that like yeah you have detected by P-C-R caused by insertions or deletions. okay so pretty much what she's saying is that like you don't p- okay you put your um, D-N-A into, P-C-R to get replicated se- several times [S5: right ] in order for like any of the se- any of these things to be like put on it right? like you want several copies of your genome. 
S4: mm. okay.
S5: right 
S3: does that help? 
S4: yeah 
S1: okay so you make several copies of the genome. let's say that Diana has like insertion of like nine and_ nine like, amino acids or something like that in hers. [S4: mhm ] or no- not amino acids like nucleic acids. [S5: okay ] right in her like genome. and you have like a deletion of like twenty-nine. you know what i mean [S5: uhuh ] so like her's are gonna be longer, and yours are gonna be shorter. do you know what i mean? [S5: right ] so there's no restriction enzymes that's actually going to be put into it. so like the way they would detect it is, that you put your d- put both of your D-N-As into P-C-R. [S5: okay ] and then um, you run 'em along the gel. [S5: okay ] okay like difference between here is that they would actually put in a restriction enzyme before you b- run it on the gel, to look at the length. and so there was actually going to be two only one band. your band, and her band. when you run it. 
S4: yeah there's just gonna be two, we're gonna run our whole thing. 
S1: yeah you don't cut it up you don't do anything with it 
S5: in in S-S-L-P you don't cut it up? 
S1: you're just comparing, yeah you're 
S4: yeah simple sequence 
S1: just comparing [S5: so ] you're just comparing the length of your D-N-A to the length of her D-N-A.
S4: right cuz our D-N-A is gonna be different length because it might have deletions or something and i might have insertions. [S1: or ] it's just comparing a simple way 
S5: oh so S-S-L-P just gives you one, [S4: right ] thing?
S1: yeah you don't 
S5: not, a bunch of different (factors) 
S1: you're just comparing the length of your genome pretty much. [S4: mhm ] or length of certain chromosomes.
S5: okay. so P-C-R detects it, what cuz it just [S1: because ] (xx)
S4: well
S1: because, if you didn't_ because you don't do anything else to it other than P-C-R. you're just replicating your D-N-A over and over over again. [S5: but ] and like, th- you don't have_ th- the difference is in the length so therefore it's detected by P-C-R because, you don't have to do anything else to it it's just how the difference between your D-N-A and her D-N-A. because they're innately different. [S5: okay ] like you don't even really have to do N-P-C P-C or P-C-R. you know what i mean like 
S5: like P-C-R's just replicating it to like have a big sample. 
<SIMULTANEOUS CONVERSATIONS NEXT :20> <CONVERSATION 1> 
S2: (so then,) this o- this one is just like, where you're like, defining, the differences (in within the) type? differences 
S4: right because like, there's gonna be different gaps in (xx) sequences in everybody, [S2: mhm ] (xx) it's gonna cut at all the same places when you run it this one's gonna run a lot, shorter (xx) this one's gonna run a lot farther. [S2: right ] that's all it is. (xx)
<CONVERSATION 2> 
S1: yeah exactly to s- have it a big enough sample for it to show up. [S5: right ] you see what i'm saying like [S5: right ] if you were to just run your chromosome, you wouldn't be able to see it. [S5: right ] you know what i mean like if and her chromosome you wouldn't be able to see it. but masses of your chromosome you're gonna sh- is gonna show as a big dark band. and masses of her chromosome's gonna show us 
S5: oh cuz all the D-N-A will come [S1: exactly ] together and it'll just show this, you'll see one thing but it's cuz you need you need so you need enough, to see it.
S1: yeah right but you need lots of D-N-A in order <END SIMULTANEOUS CONVERSATIONS> for that band to show up. [S5: okay ] and so that's why tha- it shows up, it's detected, by P-C-R. it's not really being detected it's just, it's innate like 
S4: yeah it's not like you run the it's not like you run the P-C-R and it flashes at it's like whoa 
S1: right exactly it's not like 
S5: so P-C-R you just need it in order to, [S1: for it ] make enough, enough copies to, [S1: to show ] run it in a 
S4: right. 
S1: yup 
S4: it's kinda yeah i thought that was kinda weird i was like detected by P-C-R? 
SS: yeah 
S4: but i just kind of blew it off and said it would be okay. <LAUGH>
S5: but that's just like a step in tr- doing it really. 
S1: mhm 
S4: yeah 
S5: okay. 
S1: but it's a step at everything too.
S4: but it's something you didn't need in R-F-L-P.
S1: uh i think you might.
S4: you might...?
S5: yeah cuz either way you're gonna need a lotta samples. 
S1: because either way you need you need like, if you_ i don't know_ think about the size of your chromosome i mean like, frigging like, a- like skin particles that fall off my skin have like millions of c- of cells in them. <S4 LAUGH> like how are you gonna see that on a like [S4: that true ] as a big dark band on like, you know what i mean like some gel [S4: mhm ] that's white and clear? like that's stupid right? like you [S4: right ] need like millions and millions of copies of your D-N-A in order for like, even like one chromosome to show up anything. [S4: right ] so like... i think you need P-C-R for all D-N-A identification like, [S4: right ] things like that.
S4: it's just strange that he'd like point it out like as this [S5: yeah ] like this one he says detected by gel electrophoresis and (this one he go-) this one's detected by P-C-R. like that's the difference between them.
S5: like aren't you_ don't you have to use gel electrophoresis for, S-S-L-Ps too? [S1: i think ] cuz you need to
S4: i didn't think you did but, i may be, [S3: i don't know ] i can't quite remember in class.
S1: i feel like just 
S4: he kind of didn't make a big deal out [S5: right ] about it cuz he just kinda said like this one's detected by P-C-R i think i- just as long as you know which is detected by what and get the general idea of what they're detecting, i don't think it's gonna be like a short answer or or like
S5: yeah 
S1: you guys have a review session though today right? 
S4: yeah 
S1: you could ask that question i guess. [S4: yeah ] like what do you mean by detected by P-C-R?
S2: um, for the, experiment, i don't know this is kinda like, i guess a lecture behind this one but why is it on the plates, you have that like antibiotic resistance or something you know when you like spreading around like i don't understand that part of it. 
S1: okay. um 
S2: some like ampicillin resistant gene [S4: yeah ] [S1: right ] (in like) the plasmid and then there's like i don't understand what that all_ like why do you need, the [S1: right ] resistance or whatever? like 
S5: i get that (sort of)
S1: go ahead.
S5: because the_ you only wanna like_ you're only examining the bacteria that like, might have the, insertion of the restriction (i mean,) or [S1: of the ] the fragment, [S1: fragment that you want ] the fragment you know how [S2: right ] like you're inserting fragments so you only wanna look at like the specific plasmids that might have taken it, and [S2: mhm ] those are have the like amp resistance in them, [S2: mhm ] so anything else that's in there that does- that's not amp resistant'll just die. [S2: right ] [S4: that's why you put the ] so, all that shows up is what you're examinining. examinining? examining. 
S2: so those are like really (like) colonies 
S4: right 
S1: those are different. see okay there's two different things right. but there's plasmids. you have a normal plasmid, [S2: right ] you cut it with a restriction enzyme to add your fragment in there. okay? [S2: mhm ] so your plasmid originally has ampicill- ampicillin resistance. [S2: mhm ] okay? and your fragment tell- like, gives you blue and whatever [S4: white ] white colonies [S3: right ] right? [S2: oh okay ] okay? so, there's two checks. one check is to make sure you have a plasmid in there. th- so and that's ampicill- ampicillin resistant. that plasmid may or may not have that fragment inserted inside. 
S5: but it'll still be amp resistant, (if) it's just out. 
S1: i- but it'll still be amp re- resistant right?
S2: mhm 
S3: as long as plasmid is there. 
S1: as long as the plasmid got into the cell. okay? so then you like, do this to your sample and you get samples that are ampicillin resistant that grow on the on that petri dish. [S2: uhuh ] right? okay so now you know that those cells have your um, plasmid in it. but you don't know if all those plasmids have that fragment in there. [S2: right ] right? so then you put it on some other, like gel, and it gives a color, or someth- like, i don't know what exactly gives it 
S3: (no) you grow it on the ampicillin, on the ampicillin re- resistant 
S1: resistant thing and it, [S3: and it ] it has some sort of color to it. [S3: right ] right? and then, you know that either either your blue colonies you want or's your white colonies you want right? [S4: right ] so like now, now you know that your plasmid, those colonies have both your plasmid in it and that fragment that you want. 
S2: okay 
S1: okay. (so there's) 
S5: so the color has nothing to do with whether it's, 
S4: ampicillin resistant 
S5: am- like the, the fact that your seeing anything means that it's ampici- it_ you have your plasmids. [S1: yeah ] that are amp resistant. 
S4: isn't it that the white have the recombinant plasmid, [S3: right ] [S5: yeah ] and the blue are just the regular plasmid? 
S1: regular plasmid. [S5: yeah ] i don't_ i didn't remember [S4: right ] exactly 
S5: and
S4: cuz the white had the lacZ gene broken, [SS: right ] and lacZ is what encodes for blue, so, if they don't have lacZ together then
S2: so your white [S3: the ] ones are your cloned, D-N-A? 
S4: are the ones you were interested in. [S5: the ones that you, that ] that you got, (xx) 
S5: were able to 
S1: are recombinant which means that has the fragment in it. okay. so, next one?
S5: when you say plasmid like when you're looking at the plas- does that mean that like, those colonies that are colored whatever are they those, cells? what are they? they're like colonies of plasmids?
S3: they're bacteria 
S1: they're colonies of bacteria, that have plasmids.
S4: the little little cells right? 
S5: so the plasmids change the color of the entire bacteria?
S3: the the it's [S1: it ] just 
S4: yeah uh uh (i feel the same) 
S3: a, it's just a genotype it's just what you're s- right? 
S1: yeah it's just, [S4: so it's just ] yeah
S5: but like the [S3: (were not) ] plasmids, [S1: affect (the c-) ] like affect the, whole phenotype of the bacteria? 
S1: yeah
S5: okay. 
S4: cuz part of them like gets transcripted and translated or whatever to make the blue? okay.
S1: yeah. like what she was saying was okay. well let's use this example again. 
S5: cuz plasmids are just circular D-N-A. [S1: yeah ] only in bacteria, right? yeah.
S4: i think so
S3: i think so
S1: (xx) i don't know whatever. okay so you have this thing right? you have this, plasmid, okay? okay. and then you have this plasmid. right? so like step one was to get this this recombinant plasmid. right? and this recombinant plasmid, inserts into the lac- whate- [S4: Z,-gene ] what was it? lacZ gene? that um, [S4: normally makes the ] 
S5: it like knocks out 
S1: that normally makes the cell blue. [S5: right ] okay? so like, any um bacteria that has this one, will be white, [S5: okay ] and anything [S4: no ] that has_ 
S5: i was thinking of like that the plasmids (were always) (xx) 
S1: or, will be blue. i'm sorry. will be blue. 
S4: yeah <SS LAUGH> i'm like no no, don't confuse me 
S1: this is blue, this is white. okay? okay so then like, and this plasmid right here has ampicillin resistance. [S5: right ] okay, so like, you put it into you inject it into your cells and like, your cells like take out these plasmids or they don't take out these plasmids and depending on which one you like [S5: right ] have these [S5: (xx) ] different results. 
S4: okay...
S1: next lecture... 
S4: the twenty-fourth 
S1: D-N-A technology two? <S1 LAUGH> that's how i go by like 
S4: whatever you want [S5: (i'm not quite sure) ] to go by i'm like what are you talking about? <S1 LAUGH>
S5: okay you know how they use like retroviruses to, cuz like to get, um prokaryotic bacteria to replicate, or to translate, eukaryotic D-N-A? [S1: mhm ] cuz like, then it doesn't have to like splice out the introns which it can't do. 
S1: mhm 
S4: i don't, yeah i don't understand that 
S3: i don't unders- yeah could you go over that? [S4: yeah ] what is_ isn't that 
S4: where where was that? oh that's, yeah that was that lecture 
S1: remember our, like we talked about insulin? and how you can make like bacteria produce insulin? [S3: oh yeah ] and like mass production of insulin for like diabetic people? 
S3: oh right here, (xx) 
S4: (xx) no i just don't like 
S1: so what was your question? 
S5: so like
S4: i don't get like [S5: when you're using ] this whole thing he's talking about how you have the M-R-N-A and you lose the introns, [S1: okay ] and then you use v- reverse transcriptase and you somehow get D-N-A i don't see how that's, [S1: okay ] um useful. 
S1: how it's useful?
S4: well just like i guess i don't unders- 
S5: because, (xx) [S1: no but ] i don't know like this is how i understood it, i don't [S4: mhm ] remember, someone explained it to me that in um, like in prokaryotes you know how, they don't have D-N- like splicing, [S4: mhm ] of introns cuz they don't have enough stuff to do it? [S4: right ] so if you just infected normal D-N-A, it encodes for introns as well as exons. [S4: right ] exons? 
S1: extrons 
S5: exons extrons. [S4: right <LAUGH> ] so you need something that's not gonna have the introns and M-R_ once M-R-N-A is made it doesn't_ it like the introns are already spliced out. so if you use R, reverse transcriptinase or [SS: yeah ] whatever, it's making D-N-A off of R-N-A and R-N-A isn't gonna code for introns if they were already spliced out. [S4: okay ] did that make sense? [S4: yeah so ] (xx) 
S1: does that make sense? okay you want to 
S5: so what i don't under- 
S4: okay so then once you have that D-N-A then what do you do with it do get the protein production? 
S1: you can put_ now you can insert that into bacteria and have pr- bacteria, produce that insulin that you need. [S4: okay ] okay? problem is like, like we can't find insulin for diabetic people, we need to mass produce insulin. okay? so what they did was, and you can't just take that, you can't just can't take the D-N-A from a human being. right? the part of the human genome that's that um, these these diabetic people are missing, and like just like, put that in some p- just type of bacteria make it produce insulin. because it has introns and extrons. [S4: okay ] right? does that make sense? 
S4: yeah, i think so.
S5: but why are you putting into bacteria to begin with? just to replicate it? 
S1: to, well okay um, like, number one like when you like_ gene therapy. reason why gene therapy doesn't work. right? you like insert some D-N-A into your cells, you don't even know like just like this case right here, you don't know if your cell's gonna take up w- take up like, the D-N-A [S5: right ] or not. [S4: mhm ] and also like, D-N-A when it once it gets into the body like it's, considered external D-N-A. right? and it it'll work for like a couple replications but after that like, it's gonna attack it and like it's gonna attack that D-N-A and it's gonna like send it right out. you know what i mean like it's [S4: mhm ] not gonna be_ it's not a pro- it's not like a, a prolonged like um prevention of like diabetes or like treatment you know what i mean it can't be the treatment. [S3: mhm ] okay? so what they're saying is that like why don't we just inject insulin into these people, for diabetic people right? like insulin that they don't produce by themselves that we produce elsewhere, you know what i mean so that we can like cure their like, you know like sugar lows and highs and things like that. okay? so like one way of doing this is that like, i remember one way is like you can, get insulin from pigs. <LAUGH> you know what i mean like purify the insulin that's in pig's blood and give it to people. and that works sometimes. but another way_ but like, okay like you're killing all these pigs just for insulin right? but they_ another way that they can do it is through this process of like making these bacteria produce, like, insulin or make rats produce insulin like extra amounts of insulin. [S5: oh, so you ] do you see what i'm saying like 
S5: so the bacteria just does it you don't have to, take it. 
S1: exactly like the bac- just in this case right? like for like for instance like, we wanna take our recombinant D-N-A right here codes for insulin. [S4: okay ] okay, and we wanna insert it into this bacteria, so this bacteria 
S5: will be_ mass-produce it 
S4: so it'll just be ins- it'll just be a plasmid inside the bacteria producing its stuff and sending it out 
S1: just like yeah it's just like a virus it'll mass produce that, exactly like, exactly. 
S5: then you can extract it from bacteria and then use it for 
S1: you want like you wanna use what the virus does. a virus takes over what the, original cell does and pr- does what it wants. right? [S4: okay ] so like, what we're doing it manipulating that virus to produce something that's positive and not negative.
S4: okay 
S5: okay 
S1: does that make sense?
S3: yeah
S4: (xx) 
S5: yeah, so, then when you, cuz like i know it was one of the questions says like why do you use retroviruses in humans? 
S4: oh yeah the human gene therapy using defective retroviruses, is that what you're talking about? in the question?
S1: right because in order you wanted to use retroviruses because okay remember you have, different types of um, infection of of viruses like D-N-A virus, R-N-A virus, like things like that. [S5: right ] right? okay um, D-N-A virus. why can't we use just the D-N-A of insulin that's encoded in your body right now and put it into a cell and make it produce insulin? 
S5: yeah see that's what_ cuz i- the, our cells have stuff to like_ why do you need to use a retrovirus to do that? cuz our cells can 
S1: yeah because we're putting it into a a we're putting it into a prokaryotic, place. not a eukaryotic place.
S5: right but in our body
S4: couldn't we just put it in our cells? 
S5: yeah 
S4: couldn't you just, get that little piece of D-N-A and insert it into your genome? 
S4: yeah [S1: you ] why do we have to have retroviruses in us if we have eukaryotic cells? 
S1: i don't think that like... i don't think that that's the necessarily like the correct way to think of it because sometimes, your D-N-A doesn't, like, your D-N-A sometimes doesn't get put directly into your genome, it may be something that's just floating out that's like, it h- i think it also has to do with context with the question. what exactly 
S5: like okay it says how is a retrovirus used in hu- in human gene therapy? and it's used as a vector to introduce D-N-A into human cells. but, like can't you just use a D-N-A virus to introduce, D-N-A into human cells too? like why does it have to be a retrovirus? [S4: yeah ] (xx)
S1: mhm 
S4: i see that part in my notes, now like what you're talking about. but i don't like, 
S1: what d- what does it_ what do the notes say? 
S4: it was on the lecture on twenty-fourth. just says something about_ and it it was an example of gene therapy, and it says you insert a normal allele into the retrovirus vector, let the retrovirus infect bone marrow cells and viral D-N-A carrying normal alleles inserts into the chromosome. <P :05> [S1: i think that ] i can't make much_ and there's a [S5: like isn't any ] picture of it in our thing too. 
S1: i almost [S2: (what are) you looking at? ] feel like, it's like, it has something to do with like insertion into the D-N-A actually. like sometimes like this D-N-A isn't like, like m- this D-N-A may not be like, treated as normal D-N-A. do you know what i mean? like it's gonna get into the cell like okay like think about D-N-A viruses right? what do D-N-A viruses carry along with it? 
SS: introns (xx) 
S1: no no no i mean like [S3: the virus i'm sorry (xx) ] the virus itself let's look at um, let's look at just regular D-N-A viruses R-N-A viruses right? [S4: mhm ] remember like R-N-A viruses sometimes have to carry with it like um, no it's just isn't it's just D-N-A retroviruses that carry um the, whatchamacallit the
S4: reverse transcriptase. and [S1: reverse transcriptase ] R-N-A viruses carry the their own polymerase. 
S1: yeah, their own polymerase right? because why do they need their own polymerase? 
S4: because there's no R-N-A polymerase like in a normal cell when they infect it. [S1: right ] for it to use, it has to have something for it to duplicate itself.
S1: to duplicate itself right? so it has to carry something along with it. 
S4: it can't just find it in the cell. 
S1: right. okay, 
S5: but D-N-A, viruses can? 
S1: what about what is 
S4: but there is D-N-A polymerase in cells. cuz i 
S5: there's no R-N-A polymerase? isn't there? 
S4: no cuz you ne- we never do R-N-A replication in your cells, you just do D-N-A replication. and then you do transcription translation we don't do R-N-A replication. 
S5: oh you're right. so R-N-A viruses need R-N-A polymerase so it can do R-N-A replication? 
S4: right that's why they carry it_ they have their own R-N-A polymerase they bring in with them. that way when they get in the cells they just, that's why it's faster than D-N-A viruses R-N-A viruses are better cuz they have their own polymerases, (xx) 
S5: R-N-A viruses are better? 
S4: mhm, cuz they're f- much faster. i think that's what he said, in lecture, when he was talking about_ that was like the day of the exam.
S1: okay, and also 
S4: they're more efficient. 
S1: like now if you think about it right, your_ that D-N-A that's being inserted into your cell, right that's viral D-N-A that's being inserted into your cell, [SS: mhm ] is gonna use the D-N-A polymerase from the cell to replicate itself. right? 
S5: mhm 
S1: correct? 
S5: yeah 
S1: okay but what about the protein, coat?
S4: just goes away doesn't it?
S1: doesn't_ wh- i know there's a difference between D-N-A um, viruses and R-N-A viruses that they n- have to also bring in their own like, [S4: w- ] something in order to make that protein coat.
S4: i thought R-N-A viruses just like they only have to undergo translation to make their protein coat, [S1: mhm ] but D-N-A viruses have to undergo [S1: transcription ] transcription, [S3: transcription (xx) ] and translation, 
S1: and translation in order to make that [S4: to make the ] protein coat. 
S2: so R-N-A viruses are just more ef- efficient? is that
S4: right cuz they just go in and they're already R-N-A so they don't have 
S3: right so they don't need to do transcription they don't need 
S4: to do t- they just_ they don't even need to do transcription, they just do translation to make protein coats, and they do replication to make R-N-A.
S2: so what was the thing about the retrovirus- viruses (xx) 
S1: okay the [S4: (we're getting there) ] D-N-A okay when, there's like this big like thing that we're i think, i feel like we're missing. D-N-A to R-N-A an- is um transcription. [S3: mhm ] [S4: right ] trans- uh R-N-A to protein is translation. [S4: right ] <P :05> just so i don't get confused one second. um, okay in order for this to happen, this D-N-A virus, to go, to make that protein coat that it needs, right? it needs to go through transcription and translation. transcription, um in order to make more of its R-N-A right? <:06 PAUSE WHILE WRITING ON BOARD> you need D-N-A D-N-A polymerase right here. [S4: mhm ] right? and here you need, [S4: R-N-A ] R-N-A polymerase... okay. so this is arbi- this is what it has to bring with it. [S4: mhm ] right? and this is already innately in the cell. [S4: okay ] but, isn't R-N-A polymerase also made_ isn't it from D-N-A to R-N-A, you use D_ R-N-A polymerase?
<P :04> 
S4: i don't have my old notes in, in my notebook. 
S3: yeah 
S4: i don't h- 
S3: don't you? in ord- 
S4: i thought you did. i can't remember now. 
S1: in order to do what? to make what? 
S4: when you're doing transcription is there R-N-A polymerase in transcription?
S5: i think so 
S3: in order to_ yeah [S1: yeah ] cuz if you've got [S2: yeah ] [S4: i thought that was just lika a ] D-N-A template and you put a promoter on and then [S5: yeah ] you and you're building R-N-A you have [S1: mhm, you need to have (xx) ] to have R-N-A polymerase in order to make 
S5: in replication [S4: oh yeah ] you just have, primers but in, yeah you need R-N-A polymerase don't you?
S1: well you never
S5: i thought you said there is no R-N-A polymerase in the cell.
S4: yeah that's what i was_ now now that you say it now i'm thinking about it. 
S1: yeah exactly like there's something else [S3: okay ] that we're missing that is like, in the cell that is has to bring with it blah blah blah blah blah. [S4: i don't know ] that's makes R-N-A different than D-N-A um cells. and that is what, is the difference, that makes it like you need the retrovirus. like i think that um
S3: um
S4: it has special R-N-A polymerases is one thing you said that's all.
S1: so it's like a special thing 
S4: it's a special R-N-A polymerase used for duplication. 
S1: because it's, yeah because it's actually going from R-N-A to R-N-A. not, D-N-A to R-N-A 
S4: right and D-N- D-N-A uses polymerase of the host cell. 
S1: right, to make that protein coat 
S4: and R-N-A has special R-N-A polymerase.
S1: right and so therefore wait wait wait 
S4: oh it's special because it uses R-N-A as a template instead of D-N-A.
S1: exactly. that's what i'm saying 
S5: wait, what does?
S4: the polymerase it brings with it the that she circled is special because it [S1: because (in) ] uses R-N-A as a template to 
S5: to make more R-N-A. 
S1: to make R-N-A whereas here it's using D-N-A as a template to make R-N-A. 
S4: to make more R-N-A, instead of using D-N-A. that R-N-A polymerase wouldn't work. cuz it needs to use D-N-A as a template to make R-N-A. 
S1: so like we're gonna call this R-N-A polymerase A and R-N-A polymerase B. R-N-A polymerase 
S5: oh, the special_ oh okay that's 
S1: A uses D-N-A, as the template. [S4: i get it ] okay? 
S4: okay 
S1: okay so now we got that thing down. <S3 LAUGH> right? 
S3: yeah 
S1: okay, but_ we still have the retrovirus thing there's, [S5: this is what ] [S3: okay ] so something that like
S3: look at these two d- diagrams 
S5: there's an example of A-Z-T uses 
S3: this is um viral D-N-A and then here's a retrovirus, viral R-N-A. <P :09> um right here it's this part right here.
S5: it's actually_ you're gonna have, [S3: this is not (xx) ] R-N-A, and then this R-N-A is being translated to D-N-A.
S3: and then that D-N-A goes in here to make more R-N-A?
S5: right, i i think this is the reason why we're here. <S3 LAUGH> like that what's i'm s- 
S1: okay we want, this protein right? lemme just (look) 
S4: look in chapter (eleven point two) 
S1: okay, the whole point of this_ okay we wanna make this protein. [S4: uhuh ] okay? <P :14> see okay number one i don't think that your professor meant to say that. and i don't think that he meant, 
S5: to say what?
S1: to ask what he asked, in that thing, in your exam. because i don't think he was expecting you to know more than you should've. does that make sense? [S4: no ] he wanted you to regurgitate that fact that he said in lecture notes that, R-N-A ret- or retroviruses is are 
S4: right he wanted us to regurgitate (xx) 
S1: is a way of gene therapy. he wanted you to regurgitate that. [S3: okay ] [S5: okay ] does that make sense? but 
S4: cuz we had_ what he asked us for we had like in our notes. but, i didn't get it right either. <LAUGH>
S5: just that our retroviruses were used as gene therapy?
S4: yeah, [S1: yeah ] retroviruses vectors are used in gene therapy.
S5: okay. but do you get what like i don't understa- like i just don't 
S1: i i totally understand, right 
S4: i don't understand why i put a question mark in my notes too 
S5: understand why (it couldn'ta been like a) normal D-N-A virus because, cuz i understand that in bacteria you need retroviruses, cuz you need to have that R-N-A-
S1: but see okay this thing right here, this like D-N-A, [S5: uhuh ] right? that's being inserted into the cell, it goes through transcription to make R-N-A. right? and this R-N-A, won't, i- depending like, this is what i i kind of don't understand right here is that like, okay you have R-N-A, right? you trans- you bring in D-N-A to the cell, the D-N-A um is, translated, or is replicated and trans- or transcripted, [S3: yes ] by your by the cell. [S5: right ] the host cell. right? the replication makes more of the um D-N-A for like more cells, and um you trans- you'd have to do transcription and translation in order to get, um, the protein coats. [S3: right ] right...? if you were to infect the human's genome right, these R-N-A polymerases and D-N-A polymerases are found in your nucleus right? so they have to get into your nucleus somehow. in order to get, to have use of D-N-A polymerase and R-N-A polymerase. [S4: mhm ] right? okay so then, the thing is that like, okay we make this like nice R-N-A molecule in your in your nucleus, it has to be transported out, right? so it needs to have introns and extrons right? like this like the cell won't recognize it as being like foreign D-N-A that doesn't need to, splice out introns and extrons and things like that. so maybe i splice out like, necessary information that like this protein that this um, protein coat needs in order to form. do you see what i'm saying [S4: mhm ] like, if we want to think about it so technically we don't even have the right answers to answer these questions. [S4: yeah i think that we ] do you see what i'm saying? [S4: yeah i think we're (xx) ] like i think that he was [S5: so just ] pretty much just trying to get you to regurgitate the fact that 
S4: to look at an example, [S1: yeah ] that hu- human gene therapy uses defective retroviruses. 
S1: right does that make sense? but the other thing too that i know is that like, if you wanted to infect um, if you wanted to infect um, like bacteria cells, you know with this with the thing for like gene 
S5: then you that's why you would need it. 
S1: therapy or something, you'd_ that's why you'd need retroviruses 
S5: right, that's what i (was so) confused about. 
S1: because they don't have that facility to do introns and extrons. [S5: right ] but like... [S5: okay so just (a) ] one way of gene therapy, is to make bacteria cells you know to produce some sort of protein that everybody needs or that some people are missing. you know what i mean and that's like the only example that i think of is, when i think of like retroviruses being used. um, i think there's another thing, there's another like, i remember saying that like retroviruses are used to_ in human genome. you know what i mean? but i think, it's the fact that like, maybe like when this when this um cell is like reproducing or when like this viral, stuff takes over, you know what i mean like maybe the cell doesn't do normally what it does. maybe the cell does normally what, viruses do, and viruses are like, are thought of as being like, like prokaryotic cell type things you know what i mean? do you do you see what i'm saying like [S4: yeah ] rather than like the cell going through its normal process of like, let me splice this stuff out but like, the cell really w- this like virus really just wants to do is make tons and tons of copies of its own thing, it doesn't matter, w- where if it has introns and extrons because they don't have introns and extrons so like, maybe they wanna just bypass that thing, [S3: hm ] altogether. [S4: i was ] do you see what i'm saying? like we don't know enough about these [S5: right ] cycles in order to like, answer [S5: to analyze, right ] this like correctly. but maybe he like wrote the wrong word, like maybe he just wanted to say gene therapy not gene therapy in human cells. you know what i'm saying? like [S5: well ] gene therapy has a lotta definitions.
S5: okay then also cuz he like mentioned how s- how it like it... the H-I-V virus [S1: mhm ] uses reverse trans- like what type of virus is H-I-V? 
S1: it's a re-
SS: it's a retrovirus
S4: yeah 
S5: they_ so it 
S4: yeah it's a retrovirus cuz they say in human gene therapy you use a defective retrovirus.
S1: right, what they mean by retro- defective retrovirus is that, the D-N-A or the R-N-A that it carries with it, isn't, harmful to your body it's actually helpful to [SS: oh okay ] your body. that R-N-A is something 
S4: the word defective i was like what's wrong with it? 
S1: that you want, like, [S5: so is ] is like insulin. [S4: okay ] just think of insulin. like
S4: (so in the sense of) positive 
S5: so the fact that H-I-V is a retrovirus, does that make it more th- is th- that's just_ does it_ could be... cuz it says like, A-Z-T_ i remember him talk- like something how like, A-Z-T inhibits reverse transcriptinase or something, [S1: uhuh ] in, okay i don't know what i'm getting at.
S4: yeah i don't_ the example of H-I-V all i wrote was that it, doesn't kill the cell it just uses it to reproduce and weakens your cells.
S1: and more of it weakens your cells and things like that 
S4: yeah and more and more you get weaker and 
S5: but there's no like, reason why it's a retrovirus we should know that it's not like it's a retrovirus cuz it, like
S4: no he didn't like get into all that detail [S4: right ] he just kinda said this is a retrovirus
S5: okay 
S1: and i th- i don't wan- i don't wanna tell you [S5: alright ] any more that's just dumb. <LAUGH> 
S5: and whenever_ w- he said it's a vector you_ is a vector just anything that like you kinda like ins- (xx) 
S1: i think so 
S4: it's like a little piece of D-N-A i think 
S1: yeah, a [S3: (xx) ] vector is something that 
S5: it's just something that like can introduce things to other (xx) 
S4: it's a little piece of D-N-A. [S5: okay ] right. 
S1: i wish i could call my boyfriend. because he did, did you guys have to do presentations in bio, [S4: 'm'm ] where like, [S4: oh, yeah ] you guys had to do like a presentation on something that was bio-related or [S1: oh ] something like that? 
S4: no 
S1: no? 
S3: we (xx) in one of our labs 
S1: i don't know. in m- i did it in lab like where_ or discussion or something where like, we all had to do a research like do a presentation on something that had to do with biology in the world today, [S4: really? ] or something like that and he did like how retroviruses can be used in um gene therapy. <S4 LAUGH> and so therefore he would probably know the information. <S3 LAUGH> but i'd like, do you want me to call him right now and figure it out? [S4: i'm not sure ] cuz i will. 
S5: i think that we should try to, 
S3: (just forget it) 
S4: i think we should get moving cuz we're not getting very far. 
S5: get through (xx) cuz i think this is 
S1: get moving? okay. just wanted to know if that's important if it's that important to you guys if you [S3: that's cool ] you guys really really want to know. but i will call at the end if we have time. how 'bout? 
S4: okay 
S1: okay, so then gene regulation, is your next one? [S4: yeah ] this is stuff we haven't talked about. 
S5: okay where
S4: uh lecture twenty-four. a little ways into it.
S1: sorry 
S5: oh. okay
S4: okay 
S1: okay. go.
S3: in prokaryotes 
S4: what did he say_ like the third thing he said was constitutive versus variable expression? 
S3: <LAUGH> i know it's like okay 
S4: i was like what does that mean? [S3: um, constitutive ] i put a question mark right after 
S2: is a gene that is expressed all the time in all the cells is what i have.
S3: where are we? genes, needed for translation
S4: oh i see constitutive means it's not something that's always expressed and variable it's just expressed sometimes.
S3: yeah. i think that's right 
S1: yeah like your hair cells only [S4: oh it's ] express hair things. your eye cells only express eye things. [S4: right ] and like but they all need to express like, [S4: these things all the time ] things like D-N-A polymerase [S5: yeah ] and R-N-A polymerase things like that. 
S5: constitu- [S4: constitutive- ] i think just know that constitu- [S4: is all the time ] are genes that are always expressed.
S1: right 
S4: okay, i just wrote it down didn't know what it means.
S5: um, also in the antisense thing, is that basically just like, [S3: oh. is that ] it comes and this antisense R-N-A base pairs with M-R-N-A so it can't be translated?
S4: right
S3: right you're g- you're jumping back to gene mutation but yeah.
S4: yeah it says that i- yeah 
S5: oh, sorry. 
S3: that's okay. 
S5: i was just looking at this section. cuz it says um... it stops M-R-N-A production, but isn't that wrong? it doesn't really stop production it just inhibits, translation. right? 
S3: yeah i don't think it stops production 
S4: yeah i think it just re- i don't think it stops production. 
S5: cuz it can't you can't stop it's just, making it so it's not 
S4: it think it just disrupts its function [S3: right ] it doesn't let it go any farther 
S5: and what is the purpose of doing that? so like
S4: so like
S3: inhibit that ge- whatever that M-R-N-A was gonna go and make 
S4: say it was gonna, [S3: transcript ] do something that was gonna be bad, [S5: okay ] make you have a third [S5: okay ] leg or (xx) [S5: i get that ] (xx) 
S3: <LAUGH> this is the M-R-A N-A (for a) [S4: <LAUGH> yeah right, ] third leg.
S1: (xx) 
S4: for a third leg 
S1: (xx) whenever they talk about that i always think of like you know like in, the Simpsons where like that fish has [S3: right the three-eyed fish (joke) <LAUGH> ] like three eyes? 
SS: yeah 
S4: okay
S3: alright. so let's, start out with um (xx) prokaryotes and, use operons and you've got re- a repressible operon or an inducible o- operon, right? 
S1: okay so this is where you're talking about the lac operon and, [S4: oh (xx) ] things like that the promoter region blah blah blah blah blah blah blah blah blah [S3: right right right ] okay so let's talk about that. um can you tell me wh- where it is in your book? [S3: um ] by any chance? [S3: yeah ] so i can like
S4: uhuh it's page 
S2: it's the end of chapter eighteen i think.
S3: yeah, three thirty-seven? 
S4: page three thirty-seven? 
S3: yeah 
S4: maybe 
S3: that's right. i think.
S2: so do you think we need to just foc- focus on like, the terms he says in lectures cuz there's like a lot of stuff in the book that he doesn't go in- (into) 
S4: yes, i think we should focus on the lecture (xx)
S3: yeah so i guess he doesn't use 
S2: (xx) 
S1: okay so why don't you tell me tell me what he has in your notes? and and, exac- like read verbatim what he has in your notes and then 
S4: well first he has like operator and repressor and operons for prokaryotic, that's pretty much all he talks about is just the difference between those and he gives two examples one of the, trip operon w- it's on the next page he gives the two examples of the uh, eight- figure eighteen-point-nineteen, and then figure eighteen-point-twenty. 
S1: eighteen-point-twenty? 
S4: eighteen-point-nineteen eighteen-point-twenty
S1: okay 
S3: so it's 
S5: what page is that?
S4: he went over those two things
S3: three thirty-seven, three thirty-nine 
S4: and that's really what he talked about with prokaryotes. it's just those two, different things. [S1: okay ] i didn't have too many problems with that.
S1: (xx) 
S5: i didn't have too many problems with it but actually i do have a question. the um... when_ like i understand how, when like transcription is reduces or increases l- cuz li- there's like glucose or if there's in the lac one of if there's like enough tryptoph- whatever [S4: right ] that doesn't need like it is reduced, but when are the amounts of the repressor proteins_ (but) like are they just always there? do they ever change the amount of repressor proteins? 
S4: oh that's a good question 
S5: cuz i- like in this ques- i remember the question on the exam like, i knew the answer but i didn't, like their listed possibilities of, [S4: yeah ] like, do you want me to read the 
S1: yeah sure. read the question. 
S4: yeah i know what question you're talking about now. 
S5: it says <READING> assume that (eucalide) cells are grown for a period of time in medium containing only lactose. and then glucose is added to the medium so that both lactose and gluco- glucose are now present. what change would occur in these cells following the addition of glucose? </READING> so like because glucose was added obviously they don't need to_ the lac operon doesn't need to be as, speedy cuz there's already glucose there so it like it doesn't need to break down the lactose as much, so the answer is lacZ gene transcription would be reduced but others possibilities are the lac repressor protein would begin to bind to the operator like is it always bound to the operator cuz it's always functioning? 
S3: yeah that doesn't make any kinda sense. <LAUGH> 
S4: yeah some of the answers didn't make sense [S5: right ] to me and then i was like i don't even know what that mean so 
S5: and then i didn't know if like what_ like it cuz it says [S4: i didn't understand ] a lac repressor protein would begin to bind the operator is it always bound since it
S1: okay it will always be bound unless, the um, [S5: allolactose ] it yeah a- allolactose is there. o- uh once_ if you have that then it'll unbind.
S4: right 
S5: so it's always bo- so when it says a lac repressor will begin to bind to the operator it's, already bound 
S4: that, has nothing to really do with that.
S1: it's already bound. yeah. 
S3: right 
S4: yeah 
S5: and then 
S1: if you, don't need that lacZ gene, gene right? is that right? you d- don't need lacZ. you don't need any of that stuff. 
S5: what? 
S4: well the ans- 
S1: you don't need any of that stuff. 
S3: the beta (galactosidase)
S1: yeah the permease this thing, right? [S4: right ] because the lactose is present. right? 
S3: right 
S4: no if lactose is present you need that to break down the lactose.
S5: right. [S1: okay okay ] glucose is present you don't really need to get any more (of it) 
S1: you don't need that right, because you don't need to break down the lactose in order to get the whatever.
S4: mhm
S2: so the [S1: um ] end s- so the end product of the lac operon is, glucose production? is that it? 
S5: and galactose 
S2: and galactose? so if you have a_ if the glucose is present then it somehow, inhibits 
S4: well the thing is that glucose can break down the lactose, so when the lactose is around it's like i need someone to break me down so it makes this and this stuff breaks down the lactose, and then it stops making it. 
S5: right it makes_ the lac operon makes enzymes to break it down so it doesn't [S4: right ] (xx) it doesn't like do it itself.
S4: right it just makes stuff to break down [S5: right ] the lactose so if glucose is around glucose can break down the lactose by itself so it doesn't need to make anything.
S2: oh okay
S5: so, then like another possibility was there would be an increase in the amount, well two of 'em there'd be an increase or decrease in the amount of lac repressor protein but when, [S4: is there a ] is the amount of rep- protein ever, changed? cuz isn't it just always there? 
S4: yeah i didn't know like when it, [S5: yeah ] repressor protein does that like go up or down? or is [S5: yeah ] that an import- i think [S5: it never said (xx) ] that was just kind of put in there. 
S1: it's always gonna be there. that 
S5: so it's never going to go up or down? 
S4: i don't think we need the like 
S1: i don't th- i think that_ okay the way that it has it in this book, is that this thing it goes through or it's the lacI that produces that, repressor protein, [S5: mhm ] right? and it seems like to me there's no regulation for that, [S3: nope ] for that one. [S5: right ] that is actually the regulator for these so like it's always gonna be there. 
S5: it's always gonna be regulated. 
S1: right it's alwa- i mean you're never have like an increase or decrease of that repressor protein., [S5: right ] there. yo- do you know what i'm saying?
S5: right,okay that's what_ i mean th- obviously_ it's [S1: like that's always gonna ] it's it was weird that he would put answers that could never even happen do you know what i mean? 
S4: yeah i was like, what are those? i read that and i was like i don't i mean they all could vary. 
S3: those are like tricky like, [S1: right ] things you throw on there [S4: like make you ] and yeah and it, doesn't make any kind of sense. 
S5: but there's always that, concentration never chan- okay. the mai- i just wanted to make sure. 
S4: there was another 
S1: i think that, yeah that re- that like, the regulator protein never changes [S5: right ] in, like high or low depending 
S5: but there may be more, 
S4: yeah like question seven 
S5: co-repressor_ the co- the concentration in the co-repressors change though. 
S4: what's a co-repressor? 
S5: like in the [S1: yes yes yes yes yes ] tr- in the tri- in the trip one. cuz 
S4: oh 
S1: the_ or it's, either called the inducer depending on what it does. [S5: right ] do you see what i'm saying? [S5: right ] like, 
S4: yeah i didn't understand 
S1: it um, depending on if like, that uh, the in- it's called inducer or corepressor. and inducer means that it has to bind to it in order for it to do something, [S4: mhm ] right? and the corepressor means that it needs to be there in order to like regulate it. [S5: right ] do you know what i mean? so it's just two definitions. that's it. nothing [S5: okay ] nothing big. and inducer means that it induces it to, like
S3: it induces the lac operat- lac operon to be transcripted right? [S1: mhm ] and the repress- inhibits the transcription of the operon 
S1: exactly. exactly. [S4: okay ] so it's called a corepressor because it just repress it by itself it needs that um regulatory protein, also to repress it.
S3: okay 
S4: okay so, you're saying that glucose is a corepressor? no wait what'd you just say is a corepressor?
S2: tryptophan 
S1: the, tryptophan... [S5: tryptophan ] there's two things, okay one where it's always bound i- if it's like, it's always not bound. okay? it's always it's always always always_ in the tryptophan one, um, in the trip operon, that um, re- that um, the regulator, you know, that binds the operator is never there, it's_ that thing's always being expressed, that the trip operon or the trip genes are always being, are always always always being um, [S4: mhm ] uh, whatever transcripted and then translated. right? but um... and then once like tryptophan is there, [S4: mhm ] right? tryptophan is the corepressor. [S4: oh i see ] because tryptophan can't bind to the operator, [S4: oh it binds to the repress- ] but the tryptophan but and the regulatory thing can bind to the, [S4: i get it ] operator. [S4: i understand ] do you see what i'm saying? [S4: mhm ] so they're both called repressors. [S4: okay ] and then in here, in the the lac o- the lac operon, um, it's called an inducer because, once it adds to it, it like takes it off the operon, [S4: oh i see ] and gets translated. [S4: okay ] you know what i mean so in, by adding that um allo- allolactose, right? [S4: mhm ] by_ that induces the transcription of the lac operon. [S4: right ] okay. <P :06> is that, pretty much what's in that um that section? for gene rep- 
S4: for prokaryotic, yeah. [S1: okay ] and then it goes into eukaryotic which is pages, three fifty-one to three fifty-eight.
S5: what about that?
S4: i was just saying it goes into, eukaryotic after that. (xx) 
S5: yeah 
S1: and what is eukaryotic? 
S4: just, pretranscriptional level, transcriptional level, all the different_ he went through all the different levels.
S1: okay so what's in the trans-
S5: how 
S1: go ahead 
S5: like how in detail is he? cuz like in the, in the, prokaryotes there's just like, operons, right? [S3: right ] but in here there's like, like what you said like pretranscriptional transcriptional R-N-A level ju- like how detailed do we have to know about all these levels? 
S1: well you need to know that there are levels, like there are um that they can be grouped into categories. 
S4: and that different things happen 
S1: right like the diff- right diff-
S5: and like what happens in which level? 
S4: mhm 
S5: okay. 
S1: i think that like, um pretty much the thing is that there, there are regulations everywhere in eukaryotic cells and in some cases like some um, regulation will occur at this level and some will occur at this level and some will occur at that level and all of it is a sort of a regulation. do you know what i mean? so like [S5: yeah ] you need to know the different, you need to know that in eukaryotic cells you can t- you can like categorize all the types of um, regulation into, into like, pre you know [S4: right right ] R-N-A like whatever, into those categories and you need to know and be able to define what, um each regulation is.
S4: okay. on that note i have a question about one of the regulations he talked about. 
S1: okay 
S4: um, at the transcriptional level he talked about, um this, and i kinda un- i un- i think i understand that but then he said that the_ because there are no operons and the genes are spread around, pathways need to be on at the same time, so the same segment in front of all those pathways needs to be on or something, it's like the last thing he said on the transcriptional level. i didn't understand that.
S3: um how i understand it is th- that, it's different because there aren't operons in eukaryotes they're not like grouped together all those genes, [S4: mhm ] so that you've got like several different promoters in different places, but they're all gonna be activated by the same thing. right? like it's the same promoter, but it's just in front of that gene, i- where that gene is in different places? or is that, not make any sense?
S4: um
S1: say say it again. 
S4: i guess i don't 
S1: what do you [S4: or ] what is what, what are they saying that this like activator does? 
S4: i don't know if they were talking about, <S3 LAUGH> that activation complex if they're just saying 
S1: or maybe they're talking about_ this is the way i i i kinda think (over) that, is that in like eukaryotic cells like, there's a lotta things that can affect just a production of protein, or like things like that like you m- several genes may code for like your hair color, [S4: right ] and several genes code for like your skin color and like things like that you know what i [S4: mhm ] mean? like it's not just one gene, that like does it. [S4: mhm ] so therefore you need o- one thing can activate all those different genes. does that make_ is that what he was talking about? 
S4: what i- what is he saying? [S3: think so ] what one thing can activate those things? [S1: like um ] i don't get like, he's saying something like, 
S1: okay let's let's think about it this way 
S4: the pa- how do you turn on all the pathways on at the same time? 
S1: okay y- in the summertime you tan your hair gets lighter. [S4: right ] okay that's two different things. right? that happen i- while you're in the sun. okay tha- at least that's what happens to me so i'm just gonna use myself as a as a case right? okay so i go in the sun, and let's say like U-V-A rays or something like affect like, they hit my cells right? and in my skin cells it hits all the different pigments, that make um, it activates all the pigments that give me dark that give me darker pigments. okay? in my hair it gets lighter, right? so like, it activates all the things in my hair color that make it light. do you see what i'm saying? like it'll activate all of them and it's just from one U-V-A ray.
S4: okay 
S3: it's, yeah it's like um, this activator activates one thing for an operon like in in prokaryotes, [S4: mhm ] but i- or on on on one on one strand of D-N-A or whatever right? [S1: mhm ] [S4: right ] or or not one strand but one, [S1: but one segment ] segment of [S5: one sequence ] D- D-N-A but this can i- if you just shoot this one activator at lotsa different D-N-A it's gonna hit it at d- lotsa different [S4: okay ] places and move it all in the same direction. 
S4: so so this is gonna happen at lots of different places?
S3: i think so
S4: okay
S5: um what's the purpose of enhancers? 
S3: hmm 
S5: i get what they are i just don't 
S4: yeah like i understand that diagram 
S5: like this, what're the d- like what's the point? 
S4: i think it just, 
S3: they just have 'em? 
S4: they help, polymerase initiate transcription. <LAUGH>
S1: i think that, um, <S5 LAUGH> [S4: that's all i put ] you need um, [S2: i think it's all your (xx) ] what is like the pr- isn't there like a difference between like, 
S4: we're just basically 
S5: so basically just like in eukaryotic c- like the transcripti- 
S1: (pun-) like the (top box) like, go ahead
S5: so, i- does he just_ like for the transcription level you should just know that, different from prokaryotes eukaryotes have transcriptional factors? 
S1: transcriptional factors?
S4: that's something, different. 
S3: transcription factors 
S1: that's the only thing that's different? yes 
S4: no and they have enhancers. we're talking about this. 
S5: and like enhancers are 
S1: yes yes y- ohh i know what you're talking about transcription factors are the things that bind to it in order for 
S4: right like this 
S5: right 
S1: that like promoter region to like blah blah blah blah blah 
S5: so that's kinda how it regulates it cuz like these transcriptional factors like speed it up and, right so, depending on 
S4: might not be there might be there, and then how it's regulated like, the polymerase going. this [S1: yes yes yes yes yes yes ] [S5: right ] happened (and it helps regulate the) polymerase going.
S1: you_ yeah i remember. you need like transcription of like, you'll learn all of this in biochem when you take it like there's like transcriptional factor like A B G D E F and like, they all bind at different times and blah blah blah blah blah like, real little annoying stuff. <SS LAUGH> but like you don't have that in like, [S5: okay ] a bacteria cell where they're like oh i don't care what the fuck you do like, i mean <S3 LAUGH> i don't care what you do. <SS LAUGH> 
S4: i know. i'm like (Jesus) 
S1: shoot. <SS LAUGH> i did that in like last time. [S5: yeah ] okay i don't care what you do like i just you know what i mean? like [S5: yeah ] it's just circular D-N-A like there's not really like, real big like ah you know what i mean like [S5: right ] regulation with it. it's just one more like step in a [S5: okay ] regulation cycle like 
S5: s- okay and also because what you were saying before is like because it's not like an operon where everything's on top of each other you just know that it still happens like even if like genes for the same things are spread out like they're all [S4: right ] regulated at the same time. [S1: yeah ] [S4: right (just) ] just cuz it [S4: yeah ] happens that way? 
S1: see okay the way that_ like it's so complicated like, think about it. transcription factors right? those are proteins too. they need to be like, transcripted and translated [S5: right ] into those proteins. do you know what i mean? so like in order to get those you need to induce those. you know what i mean? in order for like this one gene to be expressed you need to express all those gen- transcription factors, all those things that like, are regulated in the transcription factors in order to just to get this gene. do you know what i mean? so like, it's so complicated and like things like that like, they don't tell you that like, that transcription factors also need to be, you know what i mean enhanced or to be like regulated. you know what i'm saying? like, cuz in order d- do you see [S5: i get what you're s- yeah ] like it's a big big cycle like, they just want you know that there're transcription factors affect like the expression of a gene. there're enhancers and what do the enhancers do? you know things like that like 
S5: enhancers aren't t- are those transcription factors? are there just_ they need transcription, cuz they need activators in order 
S4: right enhancers are just something that want the transcription factors i think 
S5: enhancers are not_ aren't the (active) 
S1: ma- does it help to bind them or something like that? 
S4: (to help it to make it) something yeah 
S5: they help bind transcription factors? 
S4: yeah i think to the polymerase region
<P :04> 
S1: it helps binding.
S5: okay and the transcription fac- that i- things transcription factors have to bind to enhancer.
S4: mhm
S1: enhancers help the transcription factor to bind to_ or
S5: so activators are transcription factors that bind to enhancers. 
S1: the like polym- you know, remember when you were_ when you guys did like R-N-A polymerase like you needed_ oh you guys didn't get into detail about that i forgot um, [S4: yeah ] in order for that R-N-A polymerase to bind correctly to the D-N-A you need certain transcription factors, [S5: right ] right? and that like helps the R-N-A bind. and like things like that like so like, the enhancer just helps it bind even more. [S5: right ] you know what i mean? like 
S5: just, all in the initiation complex.
S1: yeah 
S5: okay.
S4: okay
<P :05> 
S1: anything else in that? 
S4: i think i was okay with that.
S5: (xx) um, for the post-translational level, [S1: mhm ] (xx) like, cuz he listed folding assembly cleavage chemical modification transfer 
S4: i would just know [S5: just know those words cuz ] like that's like a multiple choice questions like he'll be like, you know which one of these things doesn't cause, gene regulation (xx) 
S5: so just kinda cuz i don't really know i couldn't tell you what cleavage of the post-transitional le- like i wouldn't know what (i just don't know) 
S4: okay well 
S1: okay post-trans- what's post-translational? 
S5: after translation.
S1: after translation what's after translation you get a protein right? [S5: right ] but you get a protein of just straight amino acid chain. [S5: right ] right? but you know that proteins have three-D forms in order for them to be, correct. [S5: right ] right? so they need to have this correct folding, right? [S5: (oh okay) ] number one they need to get correct like, um 
S4: sometimes they have to be cleaved to work
S1: right they need to like
S5: oh like modified after.
S1: or yeah modified after that. right so like you know there's modification 
S4: yeah, or chemically modified. [S5: ohh ] they could get se- they could get transported to the wrong place 
S5: okay, i get it so basically it's just, it's just 
S4: they could get sent to your hair instead of your eyes 
S1: yeah like it needs to g- go to the [S5: oh (xx) ] Golgi apparatus if it's on the if it's on_ remember like [S4: right ] it has to go to the Golgi apparatus in order for it to be on a cell membrane. [S5: right ] so like if it doesn't get there then it's not gonna do the same thing. 
S5: so post-translational level, so basically it's like, that's, what happened_ okay, i get it. so like anything that happens to the made protein to make it like work, [S1: yeah ] after can be inhi- like, [S1: is post. ] leave_ like these are all_ okay, i get it. 
S2: will we just have to do the same thing for translational translational level? like it's, all he said is that 
S4: just like know the things that are (xx) 
S1: pretty much know what is in each category [S4: (xx) ] like why don't we just go through it? what's in pre-translational? what does pre-translational mean?
S3: you mean transcriptional?
S1: or p- pre-transcriptional 
S5: pre-transcription 
S4: before transcription like [S1: right ] in the D-N-A
S1: in the D-N-A itself right? [S5: right ] so those have to do with like what? 
S5: packing 
S4: the packing and methylation 
S3: D-N-A packing and_ yeah 
S1: okay. right. okay. so like those are pre-translational right? [S3: right ] and that has to affect the D-N-A. know that. um, transcriptional level has to do with while it's being transcri- while it's being made into R-N-A. [S4: right ] right? so it has to do with those enhancer things the, [S4: what we were talking about ] transcription factors things like that. okay and after we go, after we have trans- um scription we get an R-N-A, [S4: right so (xx) R-N-A level ] molecule. and the R-N-A molecule what affects_ what happens to the R-N-A molecule? 
S3: um 
S4: splicing 
S3: yeah splicing 
S4: or degradation 
S1: splicing, right, in order to get those introns out, [S5: right ] don't you need like uh an alpha cap or something like that? 
S4: we don't need to know that.
S1: you don't know need to know_ okay well whatever. like things like that that happen to the messenger R-N-A in order for it to be expressed. 
S5: before it leaves the cyto- [S1: right ] the, nucleus, [S1: mhm ] (xx) okay.
S1: and then, once it's in the cytoplasm, now this R-N-A has to be turned into protein right? so now we have transcriptional or translational, <LAUGH> like level, regulations. things like that and then after that. so like know like, how these things fall into the place of like how, you go from D-N-A to protein. and know what like it's very logical when you think [S5: right ] about it you know what i mean? like 
S5: you just know that things can happen at every step 
S1: yeah like D-N-A packing like where else would that happen other than like, in the D-N- when it's in the form of D-N-A and pre- you know what i mean? and things like that. 
S4: right like i don't think he's gonna ask us to list [S5: right. not at all ] the things in translation or anything retarded like_ we'd hope not that'd be [S5: no ] kind of
S1: and th- the other thing is too is like to know what um each thing means like how how does it regulate? or like what does that what does like, D-N-A packing mean? [S3: (xx) ] you know what know what i mean? [S5: yeah ] things like that. that's, pretty much it.
S3: and at the transati- uh translational level um, uh it just has to do with the difference in um translation initi- initiation is that right? or is there more stuff going 
S4: initiation of translation cuz it can be controlled by proteins binding to that five-prime end, [S3: okay ] on the messenger R-N-A. 
S3: alright 
S5: wait what? 
S4: the proteins bind to the five-prime end of the messenger R-N-A, that's how, uh initiation of translation is controlled.
S1: it's just like that, it's just like the um transcription, initiation complex there's also a translation and initiation complex (xx) 
S5: and that's when it, it binds with_ okay.
S1: yeah
S3: okay
S1: so there are two
S4: okay, then we talked about gene development and reg- regulation. [S3: yeah, and it's ] which is kinda just 
S5: it's kinda just common sense.
S4: yeah he was just kinda like going, kinda slowly through that
S1: what i- wh- 
S5: he was kinda just talking 
S4: yeah he was just kind of like why are ce- multi-cellular organisms different? why does 
S5: cuz they express different dream_ 
S4: yeah i know it took him like ten minutes to say that 
S5: genes it's like it's everything that we talk about after.
S4: right, [S1: okay ] and the gene cascade.
S3: right that's that [S4: but that's not ] seemed to be the most important thing, that he he mentioned you know like 
S5: gene cascade is just the fact that things turn on
S3: right 
S4: right, and like what starts the gene cascade he talked about that and that's all. 
S5: isn't that the 
S3: and then his example 
S4: the cytoplasmic determinants.
S5: oh yeah okay that's a good question. the cytoplasmic de- okay the maternal effect genes are those the cytoplasmic determinants or are those the genes that make the cytoplasmic determinants? <S3 LAUGH> 
S4: i don't know, um <S3 LAUGH> 
S1: okay [S3: uhh ] what are maternal effect genes? <SS LAUGH> 
S4: they're the 
S5: maternal effect genes are 
S4: genes that are expressed by the mother, but they're carried by, everyone or something <LAUGH> 
S5: oh they're genes that like are already in the, egg before it's fertilized. 
S3: that's right 
S5: and they, okay i think, [S3: that ] they, those genes encode the cytoplasmic determinants 
S3: they [S4: i don't know ] encode for the proteins and things but i don't (know what the) 
S5: because maternal effect genes, we don't get maternal_ like, the offspring doesn't get the maternal effect genes they get the product of the maternal_ they're affected by the genes but they don't get them. 
S3: um 
S4: do they get them?
S3: they they transcribe the M-R-N-A, 
S4: what was that? 
S3: that that those genes do make 
S4: shit what was the question? 
S5: cuz there was a que- [S3: isn't it ] 
S4: yeah let's look at the question. 
S5: th- this the first question it says what is a maternal effect gene? and like as far as i thought it could be a gene that's only passed from the mother to her offspring, [S4: mhm ] but it's not pa- you don't get you don't get the gene. 
S4: it's not maternal inheritance yeah
S5: it's what?
S4: it's_ that would be maternal inheritance or whatever 
S3: right right, it's different 
S4: that, other thing we learned, that other term (xx) 
S5: it's a gene that's is in_ it's expressed in the mother and influences the fetus so i think it's a gene that trans- trans- translates the, cytoplasmic determinants and then, the offspring get the d- 
S2: what is cytoplasmic determinants? 
S3: i don't
S5: what are they? 
S4: i don't exactly know they're just those little dots in the picture. 
S2: yeah what is, what does that mean? 
S5: yeah. 
S4: yeah 
S5: they make they <S4 LAUGH> get like, like when [S1: where is it (xx) ] 
S4: they're dots instead of circles 
S5: after mitotic divisions like [S3: (one) that's gonna be on the ] you get different amounts of cytoplasmic determinants and basically just a little like so this cell has more cytoplasmic determinants and it'll re- [S3: (fou- four-twenty-eight) ] express more genes than the one. it just, 
S4: right it gives two different cells two different phenotypes 
S5: it just, allows cells to, [S4: be different ] express diff- cuz you get different amounts of cytoplasmic determinants per cell, (and you) express different things. 
S4: i didn't understand that though like well say, say your mom like has (th-) whatever and it makes two cells and one has a lotta cytoplasmic and one has a little and i [S3: right ] put that the two daughter cells, had different genotypes or whatever now? 
S3: is that true? 
S4: no i put question mark i, i didn't quite hear what he said in class. [S3: mm ] i, didn't know what i wrote down. 
S3: i 
S4: i was 
S1: what page is this? 
S4: trying to write_ it was the very end of 
S3: three eighty-eight, something like that 
S4: lecture. twenty-five. yeah (xx...) did you_ what did you write down there?
S3: um, help me out where do you wanna 
S4: like after gene cascade he said something like he was talking about the asymmetric distribution of cytoplasmic determinants in the zygote, [S3: oh yeah ] and then it was like it was one of the last two things he said. it's my second to last statement. <LAUGH>
S3: i'm wondering, if it <P :05> (xx) <P :10> i didn't i didn't write anything down i don't think.
S4: i don't know that's probably wrong i was just curious like what i was supposed to be writing. 
S5: here here's what it [S4: so it, ] says about the term. 
S4: what happens like_ okay i guess my general question is okay there's gonna be two cells one has a lotta cytoplasmic determinants one has fewer what does it what does that mean? what happens to those two cells because one 
S5: what'd you say? 
S3: i think one becomes anterior and one becomes_ you know like that sort of thing that's what 
S4: like there's two cells [S5: mhm ] and one has a lotta determinants and one has a few, what does that mean from there? 
S5: i think that just like th- i- 
S4: it makes 'em different 
S5: the cytoplasmic determinants like turns on certain genes that'll then depict whether [S4: oh i see ] it's the anterior region and
S4: so that starts the gene cascade to like 
S5: yeah [S3: yeah ] that's the first step of the gene cascade. [S4: oh okay ] and here i just_ it says_ okay so, it says that already present in the unfertilized egg, um cytoplasmic determinants are encoded by gen- so cytoplasmic determinants are encoded by genes of the mother and these genes that encode them are maternal effect genes. so we [S3: right ] don't_ offspring doesn't get the maternal effect genes [S3: those ] we get the cytoplasmic determinants that were encoded by the maternal effect genes. 
S4: that's what i think i think you're right. the but the (translations) are ex- they're expressed by the mother 
S5: like why_ i cannot believe he asked a question like that (xx) 
S4: i think it's like important to say that they they're expressed by the mother that's like one important thing 
S5: right they're expressed by the mother which [S4: i don't ] produces cytoplasmic determinants but we don't get these genes. 
S4: but they're like they're given their phenotype yeah they're given to the, to children's phenotypes 
S5: and then it influences the phenotype of the offspring because, [S4: because the th- the- ] i- it uh the cytoplasmic determinants.
S4: right.
S3: that was in the short answer wasn't it? 
S5: i, didn't (xx) 
S4: i didn't do (short answers)
S3: there was something, okay li- yeah listen this isn't [S5: what number? ] th- it's more clear in the in the short answer i think hold on, 
S5: what number? 
S3: now that i've spoken up um it's uh thirty-one-C, um a gene can be tr- transcribed in one cell and its messenger R-N-A [S4: (oop looking at the answer) ] translated in another cell, and he said um that that's i- in our in the example that he was going through dro- drosophilia or whatever it is um the the bicoid gene from the mom, um produces the M-R R-N-A which the zygote then, uses to translate, into, um, whatever.
S5: wait w- say that again? 
S4: what <LAUGH> sorry, there were too many terms close [S3: sorry ] together. sorry. <LAUGH>
S3: alright so in the- in the- these flies, um it gets the bicoid gene from_ that's the maternal effect gene, [S4: right ] and but that gene encodes for an a- an R-N-A right? no? 
S5: (xx) 
S4: that's what i i don't think that, does a gene encode for an R-N-A? a maternal effect gene? i guess it has to it's a gene right? 
S3: it's a gene that makes an a- there's a there's a picture. 
S5: a gene that can be described (xx) 
S3: um, this is the_ see look, 
S4: oh my god (xx) <S2 LAUGH> i can't even look at this (xx) 
S3: the messenger R-N-A, this is unfertilized eggs and then translation of the bicoid, M-R-N-A is i- then in the fertilized egg. right? or happens during fertilization or something... that's what figure twenty-one eleven is 
S5: whoa 
S4: i do not like this short answer question <LAUGH> i would have not gotten this one 
S5: a gene that can be transcribed in one cell but i- translated in another?
S3: yeah 
S1: maternal effect genes, this is the [S4: oh oh (xx) ] okay they affect the orien- like the polarity of the cell and the polarity of the cell tells you where the head or the anterior or the butt is pretty much.
S3: right 
S1: right?
S4: right 
S1: okay so these, um
<P :10> 
S4: gene can be transcribed (xx)
S3: i bet you could see it from this figure.
S4: translated in another set? 
S5: it's tran- i- he said in drosophilia, whatever the bicoid gene is transcribed in cells of the mother, and the M-R-N-A is translated in the fertilized egg.
S3: yeah
S1: okay 
S4: oh, you guys are looking at the answer (xx) i thought you [S3: yeah ] were just making that up [S3: no ] and i was like i don't think that's right okay but if that's the answer then i guess yeah. 
S3: that_ yeah it is the answer
S1: it says it, does he talk about it in, class? 
S5: wait, the bicoid_ is a bicoid a maternal effect gene?
S4: no
S3: you know what i don't_ i think i- i- he showed us this figure though and this figure says that. [SS: okay ] so i think that that's like totally, up for grabs yeah, i think
S5: this figure says 
S1: okay so you have this developing egg, okay, um, first know that maternal effect genes don't they o- do they only control like the polarity of the egg, or do they do other things too? i thought it was polarity of the egg. 
S3: i th- 
S5: maternal effect genes are just, it just says that... they're genes, [S3: i don't know for sure ] that encode cytoplasmic determinants. so yeah, cytoplasmic determinants are just the like the polarity.
S1: right? isn't that_ is that right? 
S5: yeah, cuz they can also be called 
S4: God i don't understand this 
S5: end polarity genes. 
S3: yeah, yeah, [S1: okay, okay ] that's right. see , right up here (that's what it says.) 
S1: right. i just didn't keep reading.
S3: no that's okay.
S1: um... okay so, 
S3: took me a while (figure this out) 
S1: you_ the cell_ okay the mother has, these genes, right? that code in, it's it's in all cells but like it gets expressed in like, where y- in your, wherever, <LAUGH> that makes eggs. <SS LAUGH> i don't know 
S3: in your e- your nest okay <LAUGH>
S1: your, in your, yeah i don't_ i f- i like can't really remember words right now i'm just dumb. [S3: okay <LAUGH> ] okay but like in your like... i_ like this is disgusting like i don't wanna be like right here but like like <LAUGH> you know what i'm saying like 
S5: your ovaries? 
S1: like all_ yeah in your ovaries. okay, 
S4: <LAUGH> (and we're all like what are you talking about?) 
S1: ovaries. like you have eggs in your ovaries right? and like, your ovarian cells right? like, like express maternal effect genes. right? and, [S5: right ] and these maternal effect genes, express um like or they don't express 'em but they make 'em into messenger R-N-A okay? and this messenger R-N-A is stored into like a part of your of your egg. [S4: okay ] okay? in one certain part. okay? 
S4: oh, so all the M-R-N-A being in one side? 
S1: in one side. right? or like, mostly [S4: of the egg? ] concentrated in one side because it's really like 
S5: is that a cytoplasmic determinant? 
S4: yeah, and that's what makes it 
S1: exactly. and that messenger R-N-A [S5: uhuh ] is the cytoplasmic determinants. so you were right when you said we don't get the genes. [S5: right ] like, [S4: you just get little R-N-A ] the um, egg doesn't get the genes but it gets a, product of the genes which is the messenger R-N-A.
S5: oh
S4: it's just little M-R-N-As stuck down on one end of that thing and that [S1: right, and then once the ] determines that that's gonna be the, head. [S1: yeah and once the egg, ] (or the bottom) 
S5: and then then they're translated in the egg.
S4: and then they're translated to make the things. 
S1: and once the egg is fertilized that messenger R-N-A is translat- translated into some proteins that cause that like cause that polarity, [S4: right (xx) ] within the cell. 
S5: so what are cy- are cytoplasmic determinants specifically M-R-N-A? 
S4: i think they're just things that cause, the cell to be different in different regions i don't think it defines it does it?
<P :08> 
S5: oh. they're messenger R-N-A proteins and other substances in organelles. 
S1: messenger R-N-As 
S3: that are unevenly distributed around so that things happen. right...? what's the term again? cytoplasmic 
S4: i thought (xx) 
S5: oh nurse, nurse something, (xx) nurse cells, give the... [S3: mhm ] cytoplasmic determinants they p- they put it into the egg cell or something
<P :13> 
S4: i don't like this short answer question. 
S3: these are really hard short answer questions. 
S4: i would've done not_ i would've done really badly on that short answer [S3: yeah totally ] question. <LAUGH>
S5: well i think all of his short answers are so much harder than the, ones the practice ones too. 
S4: really? 
S5: i i thought that 
S3: well provide an example like can you come up with a m- more horrifying thing to be asked? <LAUGH>
S4: just this one in general like this is like, horrifying to me. <LAUGH>
S1: an exa- and example of what? 
S3: everything everything was like you know here's this can happen a single gene can encode for more than one polypeptide provide an [S4: (xx) ] example. all he wanted us to say was R-N-A um, um can be alternatively spliced. but i mean like provide an e- i_ it's just sort of an awk- sort of scary 
S1: a single gene can encode more than one polypeptide. 
S4: oh that's a good point. i would not have thought of that [S5: what? ] either. the thing about, i was talking about question D the answer he gave for answer D i wouldn't have come up with that. [S3: which one? ] now that he like says it's the answer 
S5: a gene can be tran- oh a single mature M-R-N-A can encode more then one polypeptide. 
S3: yeah i was at a loss for that one like (xx) 
S5: provide an example what's the example?
S4: the example was like in prokaryotes the operons encode more than one pro- polypeptide, when the polymerase comes across it.
S1: that's right.
S4: that's right.
S5: what?
<SIMULTANEOUS CONVERSATIONS NEXT :32> <CONVERSATION 1> 
S4: um in prokaryotes the operons when they go along, the M-R-N-A, they make more than one polypeptide. 
S5: how do they m- how do they make more than one? different ones? how do they make different ones? doesn't it all encode the same thing?
S4: no i think it d- makes more than one in eukaryotes, because of that whole like thing about the operons and the repressors and stuff that made all those different like made the, remember that picture he showed where it made the different, chemicals coming of off it? the different enzymes? remember that in the lactose picture he showed the different 
<CONVERSATION 2> 
S1: isn't question B and D the same things? 
S3: B and D? 
S1: yeah 
S1: a single gene can produce, encode more than one polypeptide. a single mature M-R-N-A can encode more than one polypeptide, oh a mature M-R-N-A. 
S3: right it's a little different. 
S1: so what was the question in this one? 
S3: or what was the question? 
S1: what is_ or what is one changing R-N-A splicing (that doesn't make sense) 
S3: or you have alternate that uh a-alternate R-N, R-N-A 
S1: oh alternate okay okay okay okay.
<END SIMULTANEOUS CONVERSATIONS> 
S5: wait how can 
S3: just little note to yourself <LAUGH>
S5: how can M-R-N-A j- i thought how can it translate to more than one, [S1: in prokaryotes ] in different poly- how? it's the same basi- like how does it, make a different polypeptide? 
S4: see here it's making these different polypeptides, this picture i'm talking about. 
S5: where? 
S4: in this picture it makes like, B-galactosidase and it makes permease and it makes trip acetylase 
S5: how does it make l- but isn't it, how does it all translated from the same things but it's different? 
S1: because it's prokaryotic. [S5: so it'll like skip? so it'll trans- ] [S3: (xx) ] if that's_ i just remembered like prokaryotic you can have several genes on one like poly- on one like messenger R-N-A whereas in eukaryotic it's one messenger R-N-A gives one product. [S3: right ] don't ask me why it's a freak of nature i don't know. like 
S4: (xx) 
S5: in prokar- so in prokar- so what happens when it translate it does it just skip over a couple things so that like it makes it different? 
S1: what are you taking about? i'm sorry.
S5: like i don't understand how after translation, [S1: mhm ] [S3: after, okay ] how can M-R-N-A encode something things that, like, more than one thing if it's
S1: cuz, it's not, it's prokaryotic it's like, it, it, it gives one protein, but 
S5: but in eukaryotic like every M-R-N-A, or e- right. gives the same, particular protein. 
S1: you have to be careful when you say it's the same particular protein because your protein could be different than his but it still functions the same way. but like, do you see what i'm saying [S3: same type ] okay, you just need to know that in tr- in eukaryotics multicellulars organisms_ us like humans, [S5: mhm ] messenger R-N-A gives one protein product. [S5: right ] okay, in eu- 
S5: no matter how many times it's translated it's gonna be the same protein product 
S1: it's all, right. right. [S5: right ] if everything goes the same way. 
S5: but in prokaryotes it can produce more than one
S1: yeah, one messenger R-N-A (can handle) like several different things. 
S5: and should i just not w- that just doesn't make sense how it does it but we just know it. we just have to know it? so 
S1: you_ there are certain parts of like
S5: so is that the only time when a single mature M-R-N-A can encode more than one polypeptide?
S3: i don't think it can happen in eukaryotes can it? 
S5: yeah 
S1: it can't happen in eukaryotes. what did i just do? 
S4: okay... <LAUGH> okay.
S5: sweet.
S4: <LAUGH> so on to the, we still have four more lectures.
S3: yeah let's, sub- just population genetics and all that right?
S4: yeah
S3: that's not too intimidating it's just a matter of being precise about terms i think.
S4: yep. i think you're, i'm 
S1: what's population genetics? 
S4: what page is it on? page uh, four-twenty-eight, in the book.
<P :04> 
S1: i got that right here, i just forgot to look at it. hmm, [S4: (xx) ] whoop sorry.
S5: that's okay
S3: (xx)
<P :05> 
S1: Hardy-Weinberg [S4: i think this is not too ] equilibrium. 
S3: that's right 
S1: this is where he comes into play. okay, this is really really_ i don't think this you guys have problems with this stuff do you? i-
S4: i have a question, but i gotta find it first.
S1: okay. you just need to pretty much uh, [S5: memorize ] [S4: know the terms ] memorize terms 
S5: actually, 
S4: i have a_ okay go ahead. 
S5: (xx) book_ go ahead. go ahead you.
S4: no mine's like way in there it's on the last like the last lecture so, oh second to the last lecture.
S5: mine might be too. is it allopatric [S4: yeah, yeah ] and sympatric? wh- i- like [S1: (xx) ] i don't understand the difference [S4: oh no that's not but ] between allopatric_ wait what's allopatric? isn't that what 
S4: allopatric's like, say all of a sudden w- it can happen in like geology a river it can just change courses [S5: right ] and a river came between like our half of the table and their half of the table [S5: right ] say they were able to like breed, [S5: right ] like they'd have a different, they'd probably produce a different species cuz they have a lot different genes than us. [S5: right ] so we'd end up making our own species, eventually cuz we'd, after, a long time of breeding, [S5: uhuh ] we'd only have a certain gene pool. that [S5: right ] they_ we wouldn't ever be able to look like her so her her she'd become totally different population than we would.
S5: because we could never, 
S4: right cuz they can't mate anymore cuz the river's in the middle. 
S5: j- just cuz of different_ but it'd have to take a while. okay so what's the [S4: (because we're like) ] difference between allopatric 
S3: allopatric is like different different countries allopatric different places, 
S4: like there's something separates them 
S3: physically, locations, and what's the other term? 
S4: sympatric 
S3: the other one's the opposite sympatric, same, similar.
S4: okay 
S5: okay so what's the differen- [S4: i don't understand sym- ] so isn't allopatric a pre-zygote barrier? 
S3: yeah 
S4: yeah 
S5: oh. okay that's why i didn't understand the difference like what's the difference between 
S3: no it's, yeah, you, you can't have the 
S4: i don't understand sympatric speciation. i don't understand like the whole, i just don't [S5: what is it? ] understand it in general. 
S1: which one? 
S3: which? 
S4: sympatric speciation.
S3: oh 
S5: it's not in this book but i remember it. <LAUGH> 
S4: is it on like page like, four-eighty-two? or, [S5: oh ] four eighty-two four eighty-five is it out there? no that's that stuff. how 'bout four-seventy-three? 
S5: yeah autopolyploidy versus allo i don't get that either.
S4: i don't get any of that. i didn't understand it when he talked about it in lecture even. it's not in there is it? 
S5: no 
S4: okay. <P :05> i didn't understand that.
S5: i think that has to do with speciation doesn't it? 
S4: it says figure twenty-four-point-ten. to explain that so 
S3: oh that was in uh just Friday's lecture right? or no. yeah 
S4: ah yeah Friday s- this is the last lecture_ figure twenty-four-point-ten supposedly, (xx) oh he just used that fig- that stupid figure again to explain [S3: alright so it's ] the formation of polyploids.
S3: it's not as common because you're still you're s- [S4: i'm sorry i just kicked you. ] still in the same territory right?
S2: it's alright
S4: i don't i don't understand how it makes a reproductive barrier i know it's something about like haploids not being able, get it on with triploids or 
S3: polypepti- poly- yeah poly- polyploids 
S4: polyploids or i don't
S5: what are polyploids? <LAUGH>
S4: um, [S5: you have, n- ] organisms that have multiple chromosomes.
S3: right so you could 
S5: so then what's an autopolyploid and an allopolyploid?
S3: um 
S4: i don't know_ oh an autopolyploid all the chromosomes are from the same species, and an allopolyploid the chromosomes come from two different species. [S5: but i thought, i thought ] so like the mule has the horse and the donkey, the two different [S3: right ] chromosomes came from two different species, [S5: okay ] but yours like you're an autopolyploid. 
S5: cuz i thought that two different species can't reproduce fertile offspring. 
S1: they can't. the donkey's infertile.
S5: oh. okay so autopolyploidy you, you'll f- that will be found in nonfertile species like
S1: oh [S4: alloploidy ] alloploi- alloplo- ploidy. 
S5: what did i say auto? 
S1: you said auto. 
S5: okay so an allo it's, okay.
S4: they would be not fertile? is that true? [S5: right ] yeah that's probably true. cuz they're different 
S5: cuz if there (completely) different species
S1: well, they can't, [S4: reproduce ] they can't reproduce because they, yeah 
S4: have chromosomes from two species. it says it's more likely for asexual, [S1: mhm ] allopolyploidy's likely (xx)
S1: think of the donkey i always think of the donkey.
S4: yeah
S5: wait autopo- polyploidy's from asexual? 
S4: no allo, is asexual. 
S5: what does that mean? oh you can't reproduce. 
S4: (xx) 
S1: remember allo is the donkey. allo is from two different species like the 
S5: and can't reproduce which makes it i- 
S4: but in autopolyploidy in sexual organisms, they must mate with haploids works best in self-fertile i just don't understand [S5: wait ] like why triploid or this and that? 
S3: hm 
S5: wait 
S4: i just don't understand it. i don't understand the reproductive barrier. it that just that, different species can't mate with one another?
S1: yeah, because i- yeah it's just that they can't like, 
S5: what is a donkey (anyways?) 
S1: they can't s- p- like, <LAUGH> 
S4: (xx) what is a what? 
S1: this is really really disgusting but like the parts just don't fit, right. <S3 LAUGH>
S5: a donkey is a mule and a what? or mule's a donkey and 
S4: a mule the mule and uh, no if a donkey and a horse, 
S5: mate 
S4: they make a mule. 
S5: donkey plus horse 
S1: okay, <SS LAUGH> the thing about
S4: cuz you never see like a herd of mules because that would just be like (xx) 
<SS LAUGH> 
S5: so ah wait, the other thing about that allopolyploidy 
S1: what do you, Don Quixote do you guys remember Don Quixote? [S3: yeah ] he rides a_ [S5: so ] but like the, the other guy rides a mule. that's all i remember.
S5: <LAUGH> (that's right)
S4: oh okay <LAUGH>
S5: so the mule when it says that it's more likely if asexual reproduction is possible does that mean that if a mule can reproduce asexually then you'll have more allopolyploidy? 
S4: cuz if it could reproduce asexually it could just make more of itself, you don't [S5: right ] even have to try to find something that's 
S3: then it doesn't have to, you don't have to worry about homologous [S1: but you but you don't have ] chromosomes or anything like that right? 
S1: yeah you don't, yeah when you do that there's no like, mixing of the s- the you have don't don't have any variation. you don't have 
S5: so then how do you get allopolyploidy? 
S1: any evolution. do you know what i mean? like you don't get anywhere cuz you're always doing the same thing over and over and over again.
S5: but i thought allopolyploidy's when you get two species to make multi- 
S1: right but you're talking about a mule muting (sic) with a mule. 
S3: you're n- talking about the next generation after that. 
S1: yeah 
S5: but i thought they are_ they're not fertile. 
S1: that's the whole point, 
S3: that's what it means 
S1: is that they're more_ asexual means that they can't_ they don't actually_ asexual means like, you have sex with yourself [S5: right ] kind of thing you know like you don't, you mate with yourself you like have_ it's like a cell, [S5: right ] like you know [S5: okay ] going into two cells you know what i mean? it's like all from one cell. do you know what i mean? so like if the mule could like bud another mule off itself, [S5: right ] that would be like asexual reproduction
S3: mhm
S5: and then and then, in that way you'd get more allopolyploidy 
S1: but there's no, yeah but there's no like sexual reproduction [S5: right ] in the fact_ in the sense that you have two different things [S5: right ] mating. which is what you're talking about when you said like how can you have um, how can like two things not mate? you know two species not mate? i don't remember what the term they used it for. 
S4: oh he he talked about like triploids and haploids can't mate or something 
S1: well okay pretty much what he is, 
S4: like, sexually you always have to mate with a haploid i don't know i don't (understand) 
S1: like, two different species, [S4: mhm ] can't mate because, the parts don't fik. mit. fit. [S4: right ] like you can't mate unless you're of the same species like, you, like can't_ i don't know [S5: (xx) ] like a dog can't mate with like a dog can't mate with like a giraffe. you know [S4: right ] like it just doesn't make sense. you know what i mean? two different species don't mate. and like, pr- that's i think that's that's pretty much it i don't think there's... and i think that what he's getting at is that like, okay remember like, um isn't it like uh, birds have um, like are like three-N or something like that? right? and like humans are like [S5: two-N or, yeah ] haploid and like you know what i mean? do you know what i'm saying? like those two just can't mix because like it's a bird and a human but, you know what you know what i'm saying? like 
S4: even if you did it in a lab it (wouldn't) 
S1: he's saying that even if you did it yeah it just wouldn't work out right cuz, the numbers don't fit right.
S5: so sympatric speciation is just, what really? 
S4: y- a reproductive barrier, that doesn't allow things to mate
S5: so then that's a, that's a post-zygote or that's a pre-zygote
S3: pre-zygote you don't have have a zygote right? 
S5: so but like in allopatric it's cuz of like geography it's cuz of, [S4: cuz like ] a geographic barrier but what about in sympatric? what is your barrier? 
S4: sympatric is a reproductive barrier they can't, they can't, they can't physically 
S3: like even if you 
S1: even if they're in the same place 
S3: put them in the same place [S5: okay ] they can't mate 
S1: like even if [S5: so that's (the same) ] you were to put a bird and a human in the same place they still couldn't mate to make like, [S5: okay ] a half-bird half-human.
S5: so what is that picture?
S3: oh [S4: yeah ] i have one of those. <SS LAUGH> 
S2: (xx) 
S4: i have that picture too. <LAUGH> yeah i have like [S5: that's allopatric ] some kind of circle forms inside 
S2: that was the allopatric speciations (were)
S3: this?
S4: yeah this is [S2: mhm ] this is the, this is some kinda geographical barrier comes in between the same species and that makes, and [S1: oh oh oh oh oh i see i see i see ] (and two) (xx) but i don't understand like how some, reproductive barrier (xx) small population and that makes it a different species, i don't understand this one.
S3: how_ where that divergence happens how how how the 
S4: yeah like how like all of a sudden say like we're here together and we're like 
S3: cuz we're talking about, 
S5: wait what? 
S4: for some reason 
S3: how things, how species arise right? 
S4: how new species arise so say right now we can all breed with each other and then something must happen to cause a reproductive barrier, so that part of the table breaks off. 
S3: and and he was saying it was a mutation that made made you from like f- m- m- m- changed change your, uh fr- like from a a di- uh diploid to a polyploid you know [S4: mhm, that's true ] it's a it's a mutation. 
S1: yeah it could also be like 
S4: but can't people with Down_ Down's Syndrome is polyploid right? they can't mate with each other and produce viable offspring? is that true? or i don't know
S3: well, i don't know 
S1: i never heard of that as an example but it could be. 
S4: i know but i was just curious cuz it's polyploid. 
S5: i did not get that picture.
S4: yeah that's_ he put that up and i was like what is going on? 
S3: oh that's right.
S5: what's is that picture? 
S3: he said we don't have to worry about this bottom part but 
S5: well what is this what is this an example of? 
S1: so don't worry about the bottom part? 
S3: right. that's, allo, polyploidy.
S5: allopatric? oh allopolyploidy?
S4: yeah. oh i see 
S1: oh okay okay okay. so he's talking a- w- when he's talking about this he's talking about like like see how this is like the the um, they're different like, this, full set of chromosomes is four and this is six. [S5: mhm ] do you know what i mean? so like when you get here you don't you can't really pair up, so like they just all, [S3: (xx) ] they_ you know what i mean they just all like re-form together, as like a whole. and when you [S5: mhm ] have that like_ okay, so like you have species A and you have species B. [S5: mhm ] okay? and they both live on this desert deserted island. [SS: mhm ] okay? and somehow species A meets with sp- meets_ or mates with species [S5: mhm ] B in some like, i don't know uh like, other dimension or something like that [S4: right ] something happens where [S5: mhm ] species A can um, like mate with species B. and then you get this all of a sudden right? but you can't pair up anything [S5: right ] from here to here because it doesn't_ the numbers don't fit [S5: mhm ] right. right? so because of that let's say, and then a mitotic error, error, error happens where like, you know what i mean you don't split it up right and things like that, [S5: mhm ] right? and you just get a um, like a daughter cell that has all of them in it. so you go from like, an N of four and an N of six and now you get an N of ten because all chromosomes are in that, in that p- in that species and it forms a new species, species C.
S5: so all these just replicated but they didn't split up they all just went to one cell? 
S1: yeah they just they all went to the same cell. 
S4: so that's allopolyploidy?
S5: but they split up here. 
S1: right because this species can mate with like [S4: it's a_ itself ] this is, it's two of these things mating together. [S4: right, so this is like ] [S5: mhm ] do you see what i'm saying? 
S5: two of these? 
S1: okay [S4: (one is saying) ] species A can only mate with species A to produce species A. [S5: right ] species B can produce reproduce with species B to get species B. some ti- one at one time or another species A mated with species [S5: okay ] B, but it didn't form species A or species B, [S5: right ] it formed species C. [S5: okay ] okay? and species C like, um, mated with itself, to get like species B aga- or species C again. do you know what i'm saying? yeah. 
S5: oh then they also split these up and these two mated together to get species C again. 
S1: yeah or like, yeah like it has to like you can't j- you know what i mean? [S5: okay ] like an- like let's another pair of species A and a species meet uh B uh me- mate and they form another species C, now species C can mate with species Cs and still form species Cs. do you see what i mean? cuz the numbers work out right.
S4: okay
S5: okay so that's your exam- that's an example of allopolyploidy.
S4: so then how would autopolyploidy work? wouldn't that just give you the same species? 
S1: this is autopolyploidy.
S4: right that's what i'm saying. i don't 
S5: this was autopolyploidy?
S4: no this is allo. 
S5: okay <LAUGH> 
S4: this is i- in in auto if they're both from the same species wouldn't you just get more of the same species? i don't see how that's 
S2: you said there's a meiotic error or something? 
S1: yeah
S4: oh, something happens to cause to make a new species 
S1: something happens that_ yeah uh something. it's just mutations like she said, [S4: okay ] [S5: so ] something goes wrong, and it forms a new species. 
S4: okay. what figure is that? [S5: so ] right there?
S1: uh figure twenty-four-ten.
S4: oh (xx) 
S5: so autopolyploidy and allopolyploidy are examples of sympatric speciations where something reproductive happened and
S1: a reproductive error i- it could be a reproductive bar- or it could be like a mutation, or an error that occurs during reproduction, that forms a new species. 
S5: okay 
S1: isn't that isn't that what you were saying is that like, somehow in the same place you form a new species right? [S4: right ] [S5: yeah ] [S3: right ] rather than in 
S4: like somehow w- we all stay in this [S1: exactly ] cubicle [S5: okay ] and we somehow make a new species.
S1: yeah.
S5: but like, so allopolyploidy's [S1: and these are just two ways. ] probably so rare right?
S4: unless you're asexual. it'd probably be rare unless it's asexual. [S3: that's ] cuz it'd be rare for like a cat or dog 
S1: it's it's gonna be rare because you never really cuz [S5: you never have s- e- asexual ] species A, doesn't fit the parts of species B [S5: right ] so like, it has to like be in some sort of like, where species A and species B are like the ex- almost the exact same thing like two different species of monkeys mate. do you know what i'm saying? and like, [S4: yeah ] how often do you get two species of [S5: right ] monkeys mating, at the same place at the same time. 
S5: but autopolyploidy is that rare? isn't that just like a mutation?
S1: that's just like a mutation.
S4: yeah that just happens.
S5: and from that mutation then
S1: you form a new species.
S5: just cuz mut- okay.
S1: because like i- and thing of this as being like um, [S5: right ] a mitotic error. 
S4: okay. i think i have one more question.
S1: um, okay, the S-L-C's gonna close, <S3 LAUGH> so do we wanna move to a different place or like what's the deal? 
S4: um, i don't (xx) 
S1: i can stay until seven if you guys want me to.
S4: do other people have questions? or 
S5: i kinda wanna go over the exam. the practice.
S4: yeah i kinda have some more questions on (xx) 
S1: you do have more questions? and 
S3: i wouldn't mind staying. 
S1: okay. i think we should just move to a different place then
S3: okay.
<RECORDING-RELATED CONVERSATION UNTIL END> 
{END OF TRANSCRIPT}

