Crossing Over and Recombinants

Hi in this video, we're gonna be talking about crossing over and we're competence. So we're first going to focus on gamete formation and this is super important because people get really confused with mapping and gametes and what the genotype of the gametes are. And it's crucial because if you don't understand the genotype of the gametes, you're not going to understand anything about mapping. So we're going to go through this very slowly in the beginning. So first we're going to talk about independent assortment. Now, we've talked about this and you've actually seen this before in a different chapter when we talked about independent assortment, but I want to refresh it here so that when we go on and talk about crossing over a mapping, you understand how it's different. So Mendel's law of independent assortment says the alleles of two genes assort independently. So what that looks like is here, we're looking at these two genes A and B. There's two alleles for each of them and they create certain types. So if we were if I were to ask you, what are the genotype, So the gametes, you hopefully hopefully can fill this out because this is normal dandelion, This is inheritance. So take a second, fill out what are the genotype, so the gametes and then you can come back press play again and see if your answers are correct. They should be hopefully. So if we're doing the jena types of the gametes, you're going to take one of each allele. So a big a big A a little A. And you need to repeat it because there are four, Right? And then you make the other combinations with the B. You do Big B. Little B, little B, Big B. And this gets you four gametes. And these are the gina types, right? And eventually when they create an organism, they'll combine with other gametes and then be di hybrid again. But for now they're hype Lloyd are deployed not by hybrid deployed again, but for now they're happy Lloyd because they contain one A leo for each gene A. And B. Now this is independent assortment. So we're saying that these genes assort independently, so they are not on the same chromosome. But what happens if these two A and B genes are on the same chromosome? They're physically linked and they still have to be sorted into gamma. So what do you get? Well first you can see this looks different, right? So each one of these lines is representing a chromosome. Remember they come in pair? So here you have your dominant allele and recessive allele on the different chromosomes and your dominant for B. Now you're never gonna see this like this? Why? Why is this wrong? You know? Right? The reason is because this is not heterocyclic. These are if you write it like this, you're saying that these are two different genes instead? The other allele has to be written over here because this is on its homologous pair. This is not this is a separate gene location on the same chromosome. Homologous repair pairs are written on different chromosomes. So here we have it written like this A and B. Now you'll notice that before. Remember an independent assortment. We wrote it like this. Well, when we know that things are linked, we write it differently. Right? So this is A and B. Dash A and B. And this is representing different homologous chromosomes. This dash. So it's a little different different notation. But you do need to understand this notation. And that's something you can just blow off. Because if you get asked the question and you need to know if it's written like this or like this because this represents two completely different things. This represents independent assortment. And this represents linkage. But the question is now, what are the genotype of the gammas? Okay, so now we're talking about dividing the chromosome. So what we get is we get the first chromosome, I'll write it this way and it has A and B. And we get the second chromosome A and B. Now because these are linked, they're physically linked. What are the other two gametes now? There would be A and B. A and B. This is if no crossing over is occurring, we'll get the crossing over in the next example. Right? So these are very different gametes than what you saw above, Right? Because the genotype are these is this you have to Jenna types and they're just repeated again for the other two. So this is the two genes are on the same chromosome. And the reason that it's like this, right, is because it's the full chromosome that goes into the daughter cell. They don't split and cut up the genes. The entire chromosome has to go. So these two alleles are linked together. They're physically joined. They have to be sorted into these gametes this way. But we know that crossing over occurs and crossing over results in different gametes. And the reason is because homologous chromosomes break and rejoin. So notice here that the genotype and the notation is written exactly the same as above. The only thing that's different is I made this one red and this one blue. So let's follow what happens now if there's crossing over. So crossing over occurs can occur here. Right? And switch these around. So what happens is you get to Jenna types which are normal. You get the A. B. And the A. B. Which is what you're expecting. Right? Actually it's let me write this correctly. You're not gonna care but I don't want to lead you astray. So it's written like that, right? It suggests there are two separate chromosomes but crossing over can occur. And what you get is you get a connected to be and you get a connected with B. And so now you have four Jenna types. You have the A B. Let me write it in black. You have the A. B. You have the uppercase A. And little B. In the lower case A. And Big B. Now this looks similar to independent assortment, right? I mean that looks exactly the same as independent assortment. Right? The genotype are exactly the same. But what's different here is the independent assortment. These are two chromosomes, completely, two different chromosomes where this is the result of crossing over. Now you may ask yourself, okay if I'm just giving given the gammas, I know the genotype but I know nothing else about the problem. How do I tell if it's crossing over or independent assortment? Well, I'm going to explain it but how you know is by your ratios and I'm going to go through the ratio. So normal independent assortment with two genes is gonna have an F two ratio of what remember 9 to 3 to 3 to 1. But you're gonna see is that if it's crossing over it's not gonna be this ratio, it's going to be very different. So with that let's now move on

Okay, So now let's talk about the discovery of crossing over. So I can very easily explain crossing over to you because there's textbooks on this, we know, and we've known for a while that this concept exists. But back way back when they had no idea that this existed. So I want to go through two important experiments that really, um confirmed to the scientific community that crossing over was a thing that happened. And because it's kind of weird, right, You don't expect chromosomes to just kind of like break off a piece of themselves and be like, hey, you can have this part of me and I'll take your part and we'll be all good. Um, that's kind of an unusual thing. So it's actually brilliant how these scientists figured out that this happened. So the first one, the first study I want to talk about is between Mcclintock and Creighton and they studied corn. And so what they did is they had a corn and it was hetero ziggy's for color, which here you can see and starch and starch is dominant. So this is the leo for this. Um, so the chromosomes for this plant were this, you have one chromosome here, you have the second one here, you can see that you have heterocyclic for color and heterocyclic us for Starch, but you can see that the dominant alleles are on different chromosomes. The CIA well, is here the, and the starchy dominant allele is on a different chromosome now, the reason that they did this was in order to be able to look at crossing over. So if they didn't do this, they would not be able to look at crossing over at all. And because it would just look exactly, you wouldn't be able to tell. So they did this so that you could easily tell crossing over now. They also added a very interesting um, component onto these chromosomes. So on the chromosome number one, it had two special markers that had this thing they call the knob, which I'm representing with this circle. And they had a piece of foreign chromosome which they had trans located, meaning that they had just like broken it off and attached it from another chromosome on the other end. And they use these markers to be able to follow crossing over. Right? Because if this segment crosses to this end, it's going to take the knob with it. Whereas if this segment crosses over, it's going to take this board and chromosome with it and they can actually visualize that under a microscope. So what they did is they made it their chromosomes or their organism. This one here with a colorless starchy plant, which is here. So what they found is that the offspring, some of them looked parental. What do I mean by that? Well, it looked like this. So it was, it was hetero is dominant for color and starch, but some of them were competent, which means that it wasn't heterocyclic dominant, it was heterocyclic dominant for color, but homicide is recessive for um, starch and that was very odd. Not necessarily how it was supposed to be. And so we're confident means that is a mixing between the two parents. And you can talk about were competent Jenna types and you can talk about recombinant DNA types. But essentially if you have a red tall plant and you made it with a red short plant, then it's going to be very competent. If you mix those two together, right? If you get short and red, I don't know, Jordan's red. Um, so those were commented genotype or phenotype. Now chromosome markers were able to identify the components because when they had crossed over either the knob or the foreign chromosome, I came with them. So let's look at this. So here this is what we started with, right? This is the cross that we did here we have our knob chromosome and here's our mate. And so this is the offspring down here. And what you can see is that crossing over occurred because now you have a chromosome that has the foreign piece, but no knob and you have a chromosome that has the knob, but no foreign piece. And there also were competent. Right? They don't neither one of these look like the parents. So here you have the here you have a colorless waxy and this one was colored starchy. And here you have colored colorless starchy, which actually did look like this, but this one didn't have the knob and this one did. So it actually looked different from the parental. So these are the competent types here. So this is a really important um study. And you probably will be asked about this study in some way. But the important parts of this study is using these chromosome markers, the knob and the foreign chromosome piece. In order to be able to identify that the chromosomes crossed over. They switched out parts of each other at some point during the development of these gametes. So with that, let's not turn the beach.

Okay. The second major study that identified crossing over and links chromosomes was done by thomas hunt morgan and his student Alfred. Now this is a super super, super important study. You'll all be asked questions about this. So make sure you understand how they set up this experiment? So they studied fruit flies, stress ophelia. Um And these fruit flies had two traits, eye color and wing length. Now will say that the eye color was red. If it has this wild type marker, soapy with a plus sign and it was purple if it was uh pretty much um I have it here as PP. But it's pretty much without the plus sign, right? Because this is a mutant, wild type and mutant. We're dealing with wild type which has the plus sign, a mutant which has zero plus sign. So it's purple, it's red if it has the plus sign, purple. If it doesn't then for wings it was long, if it has V. G. Plus sign. But sure if V. G. Without the plus sign, this is short for vestigial and it just means short wings, essentially the wing type. So what they did is they did crosses. So here's the first cross the parental types were homos, I guess wild type for both eye color and length for one. And they were Hamas agus recessive for both eye color and or mutant. So this was wild type and this was completely mutant. Now you're gonna notice in crossing over. We talk a lot about gametes. So what are the gametes from this cross? Well this parent here, parent number one will say I'll make it colorful. So you can tell the difference provides a wild type P. Because that's all all this parent one has and a wild type V. G. Because that's all this parent has. It's the only thing that can provide. So this is the gamut this one provides. On the other hand, parent number two can only provide the mutant versions right? Can only provide the mutant P. And the mutant Fiji. So this is the gamut. This one provides the only combination that can happen now when these two mate they produce the F. One generation. So the F. One generation is going to be heterocyclic, right? It's going to have the wild type and the mutant and the wild type and the mutant from each of the appropriate parents. Okay so hopefully you're with me now. This is just a normal cross of Homos wild type, Homos mutant crossing together, creating a hetero zegas for both traits. Now what is next is super important. And you're gonna see these crosses a lot. And this is the F. One. So this guy, these two are the same cross through a tester. Remember what a test crosses? Right? It's going to be a cross with a Hamas I guess recessive. Which is what you see here Hamas I guess process it for the money. Now what are the expected? Let me back up now from this cross. What are the expected ratios? So thomas Hunt Miller again and his student Alfred. They were you know just following Mendel's laws. They were just doing crosses and they were like okay what is my expected ratio? What am I expecting to get from this experiment? So they did this just through a punnett square right? And if we're gonna do the branch method hopefully you know how to do this by now but what's the first step right? You do the punnett square for each trait. So in this case we'll start with P. So here from from the F. One we get those two alleles and from the tester we get two recessive. So if we cross these or P. Plus P. P. P. So what we get is we get one half are gonna be red and one half gonna be purple. Now we do the same cross for the V. G. I'm not gonna write it out because it's the exact same result. So you get half with long wings half of vestigial for both. And then you use the product law to calculate what your expected ratio is. So for one half times one half is what it's gonna be 2/4 same here to force. And because we're just doing one half for each thing our ratio is 1 to 1 to 1 to 1. So this is what they were expecting. They were like let's do this cross and this is what we'll get and it'll be great but that's not what happened. So they did the cross and they were like oh we're gonna expect this 1 to 1 to one ratio. But instead what happened is they got this 13 39 11 95. 1 51 1 54. That's their total. This is not at all anywhere near 1 to 1 to 1 to 1. So they were like oh my gosh, what has happened like why is this the case? Um So remember here the genotype is associated with these um that I talked about here, here's the phenotype in case you're confused. And so they were like oh my goodness what is going on? So what they did is they first separated them from parental to re competence. So what does that mean? Well, parental it means it comes from the parent. So our parents here, right? The gametes they could produce were wild type or mutant. They couldn't produce combinations of wild type of mutant, right? Because this one comes from our test cross And this one comes from here. F one. So these are our pretzels, right? Because the phenotype look like them. So if we were to go back up, we would say that this one is red long wing and we'd say that this is purple vestigial which is what you're gonna see here read long wing. Purple vestigial. We don't see any red vestigial or purple long wings in our parental. So we said that these two because they look like the parents are the parental als they look like the parents. And these two are recombination because they're combinations of the parents there. The red vestigial or the purple long wing which it doesn't look like the parent at all. It's just a combination. And they said, okay well obviously something weird is going on with the ratio. So how many were competence do we have? It should be 1 to 1. Right. So if we did purple long wing here's purple here's long wing, 2 to 4. It should be one should be equal numbers but it's not in the same for this. Were competent which is the red vestigial should be one it's not. So what's going on here? What percentage of this? So they calculated the percentage to how you calculated the percentage, you just add each one of these which they did 1 51 plus 1 54 divided by the total which I've given you. And they got 10.7%. Now this is very different than the predicted 50. Right? So these two it should be 50% and this one should be 25 25 because their 1 to 1. So the parental should be 50% and the confidence should be 50% but it's not. Instead what we get is the confidence are 10.7%. And so he was like okay well your 10.7%, what am I gonna do with that? And so they thought about it for a very long time and eventually the student who was an undergraduate at the time sort of ditched all of his homework one night, thought about this the whole night pulled an all nighter and figured it out. I wish my all nighters were ever that productive. But they just weren't, they were coffee written messes of misery. But um his was very productive. Guess. That's why um he's now in our textbooks. But anyways. Um so Alfred figured it out and he said that the reason this is because the two genes were on the same chromosome, right? So if the two genes were on the same chromosome, then what you're going to get is you're going to get a lot of them with this genotype and a lot of them with this phenotype because that's the phenotype of the parents. And instead what to get the re confidence you're going to have to have crossing over occur, right? So you're gonna have to have plus plus B. G. And we're gonna try to write O. P plus PG and crossing over is not a thing that's going to happen as equally as independent assortment. So he said that this there were components are going to be less frequent if they're on the same chromosome. And that says, Okay, well that explains why it's not 50% to 50%. Which would be expected by what, what's that called? Why would we expect these to be 50? Do you remember independent assortment Mendel's walls. This is why we would expect this to be 5050. But it's not because they're on the same chromosome. But why is it 10.7? Why isn't it 12.3 or 15.9 or 36.8? Why is it 10.7? What is that number important for? And so they did more crosses, right. They did different things and they found that for different traits this number is different. So why? What what does this number mean? Well, this number means that it is the area between the two genes the length of the chromosome. So that means that two genes here. So the P and the V. Gene are located 10.7 the length of the entire chromosome. So they're located 10.7% away for the entire chromosome. So they gave them arbitrary units. These are called 10.7 map units apart. So if we were to draw this chromosome now, What we would say is that this distance and this distance are 10.7 map units apart. So that's super important. And I will do we're going to talk about how to actually calculate the recombination frequency in future videos. But this cross is so important because this one was the first one to be able to not only identify that genes could be on the same or that crossing over can occur. Right? Because mcclintock did that before and the experiment that I've already talked about. But this experiment said that, okay, well these genes crossed over. But also there's this number, this frequency that can tell you something about the length of the distance between them. And so that's when we start getting into using crossing over and recombination frequencies to be able to understand distances and napping. So we're gonna talk about that. But first, let's just turn the page.

Okay, so now let's talk about crossing over terminology. So this is super important because when you're reading these word problems or you have questions on tests or whatever, they're going to be using special terminology to talk about which chromosomes and how things are in interacting and crossing over. And you have to be able to understand the terminology to understand what's actually happening. So you're going to have to memorize these words. But hopefully, you know some of them already from previous classes. But crossing over occurs between two chroma tides. Do you remember what a chromatic is? Well, Chroma 10, So T. I. N. Is going to be D. N. A. Plus protein. Chroma tides are essentially just a single copy of one of the chromosomes. Okay, so like I said, it occurs between two chromosomes. Now you have sister chroma tides and non sister chroma tides. And the difference is that sister chroma tides are two copies of the same chromosome. Non sister copies are copies but they're not of the same chromosome there. Of the homologous pair. Right? So if we have two chromosomes here, they are during mitosis, what happens is that they get replicated actually, let me draw these different colors go back. So we have this chromosome and this chromosome and these are called what homologous and they're gonna write it out but they're homologous pairs now during mitosis they get replicated sister chroma tides are these you can tell because they're the same color whereas non sister chroma tides are gonna be these, they're from the same original homologous pair and they're both copies. But there are. But the non sister chroma tides are of the different homologous pairs while the sister chroma tides are the same homologous pair of the same chromosome. So this is this is important. Now crossing over typically occurs in these non sister chromatic kids because they're they're different chromosomes. You know, they're from the same pair but essentially different. But it can happen in sister chromosomes as well. But generally when we're talking about crossing over, we're talking about non sister promises. Now during mitosis Monagas pears lineup and undergo crossing over. Now when I talk about lining up of chromosomes, What I'm talking about is actually the full four chromosomes that I showed before. So the replicated versions they line up like this in the middle. So if I have another pair here line up in the middle of the cell during meta phase, remember sort of refreshing your memory on my Asus mitosis. Yeah, it'll come back. Um, so there's different terms to describe this. So this these four here are called a tech trap die ads or pairs of two chromosomes or two chroma tides. So that could be these two could be a pair of sister or it could be a pair of non sister. These are die ads. And generally it'll refer is it a non sister diet or a sister diane by valent refers to the pair of homologous chromosomes. Right? So remember that these are two copies. So here we have here we have the homologous pair by violent refers to the pair. So here this whole thing when it pairs up, it's called by valent. Again here by violent is the full thing. And then Kai's marta. And this is a structure that forms between two diets. Remember pair of chromosomes during our chromosomes during crossing over, usually between non sister, but can also happen between sister. So although I'm pretty sure this is a different language. Kai's mata are here. So they are written here. Um so you can see that this is a point where crossing over is occurring and here's another one crossing over. So that's Kai's mona. Now this is super important. Here is in another example of crossing over. You start with these chromosomes. Crossing over happens and you get the mixture that shows up. But the knowing these terms super, super, super, super, super important. Now linked genes. Remember genes on the same chromosome. They also have certain terminologies. There's the cyst confirmation and that means the dominant alleles of two genes are on the same chromosome. So if we're writing it like this, it would look like this if we're writing it with the chromosomes, it's going to look like this because the dominant alleles are on the same chromosome. The trans confirmation, you can imagine is exactly opposite means two different leal's or two genes are on the same chromosome. So you can write it like this. Or if I'm writing it, this is going to look. So here you have a dominant and a recessive and these are two different alleles, but they're on the same chromosome. So this is Cis and this is trans. And again, I've mentioned this before, but linked genes are written differently. You can see it here. Um, so instead of writing it like this, be you write it like this and this is because in the same home a log have no punctuation between them. And so you can see this here, A B instead of back up baby, the slash is going to separate home a log. So it's going to look like this B to represent this one up here or if I wanted to do this one, it would be a B a B. Because this slash represents that. They're on different chromosomes. And if linkages unknown, which some of your questions will be right. Like they're gonna ask you, they give you a bunch of information and ask, are these genes linked? They're not going to write it like this because that will tell you for sure that they're linked. So what you're going to see is you're gonna see a lot of this and especially this dot this dot is used a lot to differentiate different genotype if it's unknown if they're linked. So if you're answering your questions are these genes linked? Oftentimes you're gonna see it written like this with this dot, So understand the different ways to write things because you're gonna be given a lot of questions asked, you know, is it linked? Is it not? Is it independent assortment, is it not? You know, is it all these different things or not? And each one of them are written differently And so that not only can impact how you do the problem and understanding, you know, what you're starting with, but it also can impact your answer choice, right? Because if you have an answer choice and one of them is written with linkage and one of them is written with not, if you know, for a fact is linkage, then that can help you figure out that problem. So, um, with that, let's now move on.