DNA Repair and Recombination

Hi in this video we're gonna be talking about DNA repair and recombination. So first let's give an overview of the different types. Let me actually write with a pen types of DNA damage. So the first type is called deep urination. So this is when pureeing basis. So the A. N. G nucleotides are spontaneously lost. Kind of like missing teeth. So here we have an example of this. So we have our A nucleotide here and it's lost. So this is an example of deep urination. Then we have delamination. Delamination is when a base is chemically converted into a different base. So one that you'll probably see in a good example of is sight unseen being changed into a your sl So here we have DNA double helix, we have our side of here and some chemical modification will happen. Turn it into a year or so called Delamination. Now it doesn't have to be cited in the year. So it can be a lot of different combinations that I didn't list here, but it's just a chemical conversion of one base into a different one. Then we have the timing dime er and this actually is caused by UV light. So anytime you go outside you're exposed to the sun's UV rays, timing timers form and what timing timers are, is to adjacent dime dime arise. So here we have UV light usually from the sun and then they cause like a diamond ization of these stymies which you can see here in yellow and it will distort the double helix. It cause lots of problems and this happens, I mean anytime you go outside luckily our body can handle these and repair them very quickly. But they do happen all the time. And then finally you have double strand break and that's when both strands of D. N. A. Are damaged in some way. So before these were connected but there was a break right here and that caused them to separate. And so obviously if D. N. A. Is damaged D. N. A. Is not repaired in some way by the body it causes serious disease. One example of this is Xenon Irma pigmentosa and you may be familiar with this. You know I think there's been movies and things about people with a light allergy. It's not really an allergy at all. It's just the inability to a pair like repair um DNA damage caused from UV lights and things. With those timing timers. So if you can't repair them then any time you're exposed to the sun you get a bunch of DNA damage and it can really cause significant issues to your skin. And you get lots of rashes and burns and it's pretty it's pretty horrible disease. So you have to stay out of the light. But there are many other different types of diseases that result from unrepaired DNA damage. So those are the four types of DNA damage. Now let's turn the page

Okay so now let's talk about the different ways that DNA is repaired. So every type of mutation in the cell is going to be repaired in a different way. So let's go through some of the four main ways. So the first one is mismatch repair. So mismatch repair fixes mismatched or lost spaces. And it usually does this directly after D. N. A replication. So how this is recognized is there's a double helix of DNA. Right? And let's say that somewhere in it there's a mismatch nucleotide. Well this mismatched nucleotide will actually result in some kind of distortion in the double helix and the enzyme can come in recognize that distortion and fix the nucleotide. So mismatched pair is really like figured out by the body from the distortion and the double helix. Then we have basic cision repair. And this is going to remove nucleotides that have been damaged from chemicals. So we call this D. Emanation. Remember so the enzyme responsible for this is D. N. A. Like a soulless. And what happens here is if you have you know um correctly matched nucleotides and there's one that's incorrectly matched DNA. Like oscillates will come in. It'll recognize this nucleotide it will exercise it and then replace it with the correct nucleotide want that to be read. So when it's been replaced with the correct nucleotide then that's great. So usually base excision repair will only cut out and replace the one nucleotide. It can do a segment like a small segment of nuclear times. But typically it does the one then we have a nucleotide excision repair which fixes these bulky lesions, things like timing timers. And so we refer to this one most like a cut and paste method because if you have a bunch of nucleotides that are correctly matched and then you get one that isn't, what happens is that the enzyme comes in and it actually will cut out a large segment. So like this this size here cut out a bunch of nucleotides, most of which are paired correctly. It cuts that segment out and then it comes back in and and it will replace all the correct nuclear times. And then DNA legatus has to come back in and reseal reseal where it cut in the beginning. So you have a cut enzyme that comes in and cuts out a big segment of nucleotides involving the wrong one. And then you have DNA like gays that comes back in and seals it back up once it's been replaced. And then finally you have double strand break repair. And so this is of course when both strands of DNA double helix are damaged. So there's two ways the first is non homologous end joining. So you have two strands of D. N. A. There's a break right here they get cut out so it looks more like this. So in non homologous end joining is that these ends are just joined back together so they come in and are joined directly back together. And then we have not homologous recombination which I'm going to talk a lot more about in other videos. Homologous recombination is when the cell uses undamaged D. N. A. As a template to repair the break instead of just joining it back together, which you can imagine can be pretty damaging to the cell. If it is missing some a big segment or something, it can actually use other DNA sequences to repair. So I'm going to talk about homologous recombination very soon. So with that let's now turn the page.

Hello everyone in this lesson. We are going to be learning about how cells are able to fix double stranded breaks in their D. N. A. And the way that they're able to fix double stranded breaks in their D. N. A. Is they're going to use this process called homologous recombination. You've probably heard of homologous recombination before. That's probably a familiar term. And that is because when we usually learn about homologous nation we're learning about mitosis and the creation of gametes. Because homologous recombination is going to be a major step in mitosis and it's going to create genetically unique gametes. And that is because homologous recombination is going to allow homologous chromosomes to exchange information. But I also wanted you guys to know that homologous recombination has another very very important job. And that is going to be able to fix these very detrimental breaks that happen in DNA. So homologous recombination can also fix double stranded breaks in the DNA. Double stranded breaks are incredibly detrimental for the cell. And the DNA itself the DNA will start to degrade become damaged. If the cell can't fix that break then the cell will probably go into a pot apoptosis. So cells don't want to go into apoptosis if they don't have to. So they do have mechanisms to attempt to fix these double stranded breaks. And we're going to go over how homologous recombination does that in these eight steps. Okay so let's first start off with the very first step. Obviously we're going to have a break in the D. N. A. And I'm going to go through these steps with these figures. So these are going to be homologous chromosomes. Okay, so these are homologous chromosomes and that's why we are going to call it homologous recombination. Because to be able to fix this break that we see here in the D. N. A. We're going to have to recruit that chromosomes homologous chromosome. So we have the red chromosome in the blue chromosome and they are home a logs to one another. So we can see that the cell has recognized that a double stranded break has occurred right here. So what is going to happen that homologous chromosome is going to be recruited And the process of homologous recombination is going to begin. The next thing that I want you guys to know that it's going to happen is you're going to have these indo nuclear bases which are like cutting proteins. These indo nucleus is are going to remove some of the damaged DNA. So let's say that this is an indo nucleus here and then we have an indo nucleus here. And what's going to happen is these indo nuclear bases are going to cut the D. N. A. They're actually going to degrade the DNA. So indo nuclear bases degrade the damaged D. N. A. In the 5 - three prime direction. And they're going to do this because we do need single stranded areas of these chromosomes for this particular process to work. And as you guys can see even though there is a break, there's still double stranded but we want it to be single stranded for this to work properly. And that's where we get these indo nucleus is coming in. And then these indo nucleus is are basically going to eat away some of the damaged D. N. A. And you guys can see the results of that down here. So you guys can see that this whole section of single stranded DNA that we're supposed to be in. Those yellow spots are now gone. And that is because those indo nucleus is or cutting proteins have removed it. So then the next thing that is going to happen is to stabilize this. Now single stranded DNA. The wreck A proteins are going to bind to the single stranded broken D. N. A. And to the single stranded non broken D. N. A. And basically this is just here for stability to ensure that the D. N. A. Itself doesn't begin to degrade because it's very broken right now. And slightly single stranded and D. N. A. Does not like to be that way. So the wreck a protein is there for stability and making sure that it does not degrade. Okay so now let's go on to the next step. What's going to happen is single broken strand and single undamaged strands in interact with their complementary regions. And this is generally going to be called strand invasion. So strand invasion is going to happen. And this is going to be strand invasion into the homologous chromosome that didn't have a break in it or into the blue strand. Okay, so you're gonna have strand invasion is going to begin to happen. And what is that going to look like? Well guys remember we had those single stranded components of our red broken chromosome and those have now invaded into the blue chromosome. So that is the process of strand invasion right there. Strand invasion, it is now beginning to interact with its complementary region in the homologous chromosome. And this is able to happen because these red and blue chromosome should have pretty much the exact same or very very close to the same D. N. A sequence because they are homologous chromosomes. So that single stay stranded piece of the red chromosome should find its complementary match inside of the blue chromosome and it's going to bind with the blue chromosome and that's going to be the process of strand invasion. You guys can kind of see it does invade the blue chromosome space, it kind of sticks itself inside of the blue chromosome and it's going to create this loop structure. So now that invasion has begun. You're going to see the DNA repair actually begin. And this is where the blue chromosome, the undamaged chromosome is being used as a template strand for the damaged chromosome to rebuild that section of the red chromosome that is missing. Okay guys, and I want you guys to know that these structures that you see here these X. Like structures. These are very important. These are called Holliday junctions. They're named after the individual who actually discovered them and worked with them. So that's why they're named Holiday. His last name was Holiday. And they're going to be where these two segments of DNA actually cross one another. So in the first strand invasion there's a single holiday junction. But this particular structure here is called a double Holliday junction because there's two of them. And this is a very characteristic um very unique characteristic to homologous recombination. You're going to see this bubble of D. N. A. And then you're going to see a double holiday structure. So now that the strand has invaded and the Holliday junctions have formed, we're now going to C. D. N. A polymerase come in and begin to build these new segments of DNA. So you guys can see here that the D. N. A. Is building in this direction and they're going to be new DNA bases being built on this red strand that make it complimentary to the blue strand. And once the red strand has been filled with its complementary basis it is going to be done with DNA repair the same things going on up here. The D. N. A strand is being built and all of these new nucleotides are being added to the red strand that are complementary to the blue strand, which is the template strand. I hope that makes sense. I know that this can be kind of hard to wrap your brain around but that's what's happening. The blue strand is being used as a template to build the extension of the broken red strand to fill in the gaps so that the red strand is no longer missing an important DNA sequence. Okay so that is going to be what happens. And then once all of those D. N. A segments have been put together correctly, we're going to see that those segments are going to be litigated together. They're going to be glued together and then they're going to um either cut those Holliday junctions or untwist those Holliday junctions. But just so you guys know branch migration is going to occur whenever the damaged section of D. N. A. Is being elongated. So whenever it's building, you guys can see up here whenever it's building we'll see that the holiday junction is going to move in the direction that it is building. And that's so it can add more and more to the damaged DNA. So the holiday junction will be sliding as that new D. N. A. Is being built. That is called branch migration. I just thought you guys should know what branch migration is in case you guys see it in one of your tests. So once the DNA repair has been completed, those Holliday junctions need to be unformed. They need to go away because we can't have our. Two homologous chromosomes intertwined with one another. That's just not the way it's going to work. So you can either cut the Holliday junctions or you can untwist the Holliday junctions. So just so you guys know whenever the Holliday junctions are not cut, they're simply unraveled. That is called disillusion. This is where the holiday junctions unwind and generally you're gonna have no crossover crossover is going to be when the homologous chromosomes actually exchange genetic material that doesn't have anything to do with the damaged area. It's like exchanging extra genetic material. And whenever disillusion happens, those holidays functions are simply going to unwind from each other and then there's going to be no crossing over occurring. The only thing that is given to the homologous D. N. A. Is going to be, it's going to fill in the damaged area. No extra D. N. A. Okay, now, whenever those Holliday junctions are cut, in particular ways, you can have the process of resolution, resolution is going to be where the holiday junctions are cleaved and what I mean by that is, let me scroll up so you guys can see a holiday junction. What I mean by that is an enzyme is going to come along and it's going to cut the holiday junction. So all of the D. N. A. Above the cut is going to go into the red chromosome and all of the DNA below the cut is going to go into the blue chromosome so commonly with resolution cutting, you're going to have extra genetic material being exchanged and you're generally going to have crossing over occur. But whenever you're just simply unwinding the holiday junction in disillusion, you're not going to have crossover. But if you cut it you generally are going to have crossover. Okay, so let me write that down for you guys. This generally leads to crossover. Not all the time if the cut is perfect but a lot of the time it's going to lead to crossover. So once those Holliday junctions have the two strands that are cleaved. Now the sorry now the D. N. A helix is those two homologous chromosomes are no longer interacting. They are their own independent chromosome. And like I said, this cleavage can result in crossing over causing DNA exchange outside of the break points or the damaged area. And sometimes this means that you can have some problems where non complementary regions between the two he leases are joined and generally this is going to be fixed by base excision repair. So yes, homologous recombination does fix these major double stranded breaks, but it's not perfect. And sometimes you'll have non complementary regions in one of the homologous chromosomes due to homologous recombination and you're going to have basic cision repair come in and fix it. Okay now these are going to be two examples of where those chromosomes that we talked about up there did not cross over or they did cross over. So you guys can see that right here. The only thing that is given to the red one was the area that was damaged. The only thing that was exchanged was enough D. N. A. To fix the damaged area. However over here you guys can see that there's a whole blue strand down here and then some red and some more red. And it's obviously there was a lot exchanged. That was more than just the damaged area and that it's going to be crossover resolution generally leads to crossover and dissolution generally leads to non crossover. I hope that was helpful guys. I know homologous recombination can be a little bit tricky and a little bit difficult to understand. But I just want you guys to know that homologous recombination is where homologous chromosomes interact with one another to repair a double stranded DNA break. Okay, everyone, let's go on to our next topic.

Which of the following is not a type of DNA damage repair?

• A. Mismatch repair
• B. Base Excision repair
• C. Lost nucleotide repair
• D. Double Strand Break repair

Which of the following types of DNA damage occurs when a base is chemically converted into another base?

• A. Depurination
• B. Deaminatino
• C. Thymine Dimer

Which type of DNA repair is responsible for fixing bulky lesions through a 'cut and paste' method?

• A. Base excision repair
• B. Mismatch Repair
• C. Nucleotide Excision Repair
• D. Homologous Recombination

Homologous recombination occurs directly after DNA replication?

• A. True
• B. False