16. Cell Division
DNA Replication
1
concept
Overview
13m
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Hello everyone in this lesson we are going to be talking about an overview of DNA replication. And in our later lessons we're going to go over that process in more detail. But this is just going to be an overview and a refresher. Okay so I know that you have probably talked about DNA replication and previous biology classes but it is a very very very important and crucial mechanism for life on our planet. So we are going to go over it and this is just going to be an over in the background information. Okay so the way that D. N. A replicates is going to be via semi conservative replication and that means that the old strands of D. N. A. Are going to be utilized as templates for the new strands of D. N. A. So everyone of your double helix DNA molecules in your cells has one old strand and one new strand. So it is semi conservative because one old strand is conserved. Now this whole process of DNA replication is going to begin at the replication origins. These are going to be very specific DNA sequences where replication begins. And generally these origin sequences are going to be composed of adding genes and time means and that is because A. S. And T. S. Where they bind together, they're going to have less hydrogen bond between them than Gs and CS, which makes them easier to pull apart. So generally replication origins and transcription origins where the D. N. A. Is commonly pulled apart and those two strands are pulled apart. They're going to be composed of A. S. And T. S. Because they're less hydrogen bonds and it's easier to pull them apart. So what is an origin actually going to look like? Well let's say that this is the D. N. A. And remember to replicate DNA, we have to split those two strands apart so that those two old strands can be utilized as templates for the new strand. And let's say that this is the origin spot. And this is where the machinery is actually going to pull apart these two strands of D. N. A. So what's going to what happened is we're going to form what's called a replication bubble. This replication bubble is going to be where the two strands of D. N. A. Are actually being separated. So here you can see that this area that I'm drawing in right now is still conjoined. But then inside of the bubble these strands have been separated from one another. This is what an origin is going to look like, where the origin of replication begins. Those two strands of DNA must be pulled apart. So you're gonna have these two separate single stranded DNA strands. Now there's some important terms to know here where the D. N. A. Is actively being separated is called a replication fork. So there are two replication forks for each replication bubble. So there's one here that's where those strands are actively being pulled apart and there's one right here, you can kind of think of it as a fork in the road. If you're going down the road and then the road splits into two roads. That's a fork in the road. Same thing happens with the D. N. A. The two strands are connected, then they are split apart, that is a replication fork. And just remember that this is the replication bubble because the two strands of D. N. A. Actually kind of bubble apart and form that bubble like structure. And at these replication forks and in this bubble, the initiation proteins and molecules that begin the process of DNA replication are going to bind here. We will talk more about that machinery in our next lesson, this is just an overview. So we have talked about our replicate forks that are formed at each origin. Now, DNA replication is bi directional due to the fact that each of these DNA strands that are separated above me are going to be utilized for templates. So that means that there are two sets of replication processes happening at the same time for for both template strands. Also, it's important to realize the DNA replication is also bi directional because it's occurring in this direction and it is occurring in this direction. It's going in opposite directions from the origin location at the same time. So it is bi directional in that process as well. Now, what is going to be the protein that is incredibly important for this whole process that's going to be D. N. A polymerase. This is going to be a protein that catalyze is the replication of DNA. Basically. What it's going to do is going to build that new D. N. A strand by connecting the DNA nucleotides together. Now there's kind of say a drawback two D. N. A polymerase because it only adds nucleotides in one direction, It adds nucleotides in the three on the three N three prime end. Excuse me, It only adds nucleotides to the three prime end of the growing D. N. A strand. Remember D. N. A strands have five prime ends and three prime ins and remember they're going to look like this, if this is our D. N. A strand, remember they are anti parallel. So if this is the five prime end and this is the three prime end then the other DNA strand is going to be the opposite. And recall the D. N. A polymerase, can only add new nucleotides to a growing strand on the three prime end. So that is going to cause some issue which we will talk about later when we talk about the lagging strand. So that means it forms a new strand in the 5 to 3 prime direction. This is very very important. This will absolutely be asked of you on your test or your quiz or your homework, which direction does DNA proliferates synthesize D. N. A. And that's from five prime 23 prime direction. So now let's just go over some, just a really quick what this would actually look like. So remember our replication bubble up here. So now let's just take one side of that replication bubble and look at how D. N. A. Is actually replicated in this process. Now, they're going to be two strands that we're going to be talking about in more detail. The leading strand and the lagging strand. This one on top is the leading strand, and the one down here on the bottom is going to be the lagging strand. Excuse me, The leading strand, pretty simple, straightforward in its creation. The lagging strands got to be a little bit more complicated, it's a little bit more annoying to create and it's going to have more steps. So basically what's happening here, remember that this is the replication fork and D N. A. Is being actively separated in this process. So what's going to happen with the leading strand, which is pretty much the easiest one to understand. So let's say that an RNA primer is formed, we'll talk more about this later. But just know that D N. A preliminary scan cannot begin the process of DNA replication without an RNA primer. It can't start from scratch, it has to have something to build off of. So this is the R N. A. Primer. And in the leading strand, this only has to be made once. So the RNA primer is made. And then we're going to have D. N. A polymerase which I'm going to draw here in green. D. N. A polymerase is going to come up and it is going to begin forming the new strands of D. N. A. I'm just gonna write D. N. A. Poly. But this is D. N. A polymerase. So then what it's going to do is it's going to begin creating this new strand of D. N. A. Which I am coloring here in green. So this one is the new strand and is going to continue along in this direction until it reaches the end of the chromosome. And the D. N. A. Preliminary simply falls off. Pretty simple. Right RNA primers placed down D. N. A polymerase then sits on top of the primer and then begins to form the new strands of D. N. A. And here in black, this is the template strand of D. N. A. Or the old strand. And the new strand is going to be made off of that template. And in the leading strand it's pretty simple. Pretty easy. It just the DNA polymerase just continues on until it finishes its process. And the reason that this is so easy is because of the orientation of the new strand. As you can see the new strand is five prime 23 prime. And that's perfect because remember that's exactly how D. N. A polymerase builds new D. N. A. It adds from five prime to three prime. Now, that's an issue with this lagging strand here. Now, for the lagging strand, I'm going to draw it a little bit differently. This diagram was great for the leading strand, but it's not my favorite for the lagging strand. So I'm going to draw it for you guys, so you can know what's happening. Okay, so I'm going to draw this one from scratch. Okay, so let's say that we have our old strand of D. N. A. And this is going to be utilized to build the lagging strand. So basically you can think of it as this black line right here. So what is going to be the orientation of this black line? So we have our three prime and we have our five prime. Now the overall direction of the process of building the lagging strand is going to be the opposite direction of the way the D. N. A polymerase actually works, which is confusing. I know it's going to be kind of annoying for a little bit, but it'll be fine. Okay, so what is going to happen? Well, remember we have to lay down RNA primer first, so we're first going to lay down the RNA primer and we're going to put it right here. So this is our primer and this is going to be what the DNA polymerase is going to build off of. Now, remember the DNA polymerase can only add to the three prime end? It only adds nucleotides in the 5 to 3 prime direction. So what is going to be the orientation of this new strand? Well, this end down here is going to be the five prime. And this end down here is going to be the three prime. So that means that the new D N. A strand can only be created in this direction. That's the only way the D N. A polymerase will move. But overall, the process of building this new strand is actually going to go in the other direction, which is going to make it a little difficult. So first off, the primary is laid down, RNA polymerase comes in and it begins to create this section of D N A. So that's great. So it's going to move in this direction, in the three prime direction. So, for our little strand here, we're going to have the five prime end is going to be down here, and the three prime end is going to be down here. So, now, what's going to happen? Well, overall the movement of this strand creation DNA replication is going to happen in this direction. So what's going to have to happen is a new RNA primer is going to be built and then the D N A polymerase is going to have to jump backwards and place itself on that new primer and then begin forming this other new strand of D N. A. And as you can see this is a little bit more complicated than the leading strand. So you're going to see this happen. The DNA polymerase is going to build a fragment, then jump back, build a fragment, then jump back, build a fragment, Jump back. That's why it's called the lagging strand because it takes a while it lags behind because it's jumping back and it's replacing all these primers and DNA polymerase has to move every single time. It's kind of annoying. Right? So this process is a little bit more annoying and the reason that this diagram isn't the greatest is because appear this black line is representing the direction the D. N. A polymerase adds D. N. A. To the new strands of D. N. A. But overall remember that D. N. A. This D. N. A strand is growing in this direct which can be kind of confusing. I know I completely understand. So now that we've talked about the overview of how this process works, we're going to go on and talk about the replication machinery which is going to be the specific molecules and proteins needed to build these new strands of DNA. Now, if that confused you, I completely understand this is kind of a weird topic to wrap your brain around after you watch this and then after you watch the different names and jobs of the replication machinery, I definitely recommend looking up an animation of this process that always greatly helped me to watch a video of actually the machinery moving around and building this new strand of DNA, especially for the lagging strand, because it can be pretty confusing. Okay, everyone, let's go on to our next topic.
2
concept
DNA Replication Proteins
14m
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Okay everyone in this lesson, we are going to be talking about the specific molecules and proteins that are utilized to build new strands of D. N. A. And these are going to be collectively called replication machinery. Okay, so DNA replication machinery, like I said, it's going to be composed of all of the things needed to build a new strands of D. N. A. During the process of DNA replication. Now, DNA replication is characterized by bidirectional replication which we talked about in our last lesson. Remember that means that two strands of D. N. A. Are being used as templates and two strands of DNA are being created at the same time. Also remember that this is also referring to the fact that DNA replication is continuing in two opposite directions at the same time as well. So bidirectional kind of has two meanings here. Now both strands are replicated at the same time. This is going to include the leading strand and the lagging strand. And they are going to happen at the exact same time, but not in the exact same way. Remember we talked about the main differences between the leading and the lagging strand in our last lesson now remember something very important that D. N. A polymerase can only add new nucleotides onto the three P. End of a new strand of DNA. But also realize the D. N. A preliminary reads the template DNA strand in the 3 to 5 prime direction and synthesizes the new D. N. A strand in the 5 to 3 prime direction. This confused me whenever I was a student and I know that it does confuse many students, so what is this referring to? So let's say that this is going to be our template strand and our template strand is going to be utilized as basically a template to build this new strands of D. N. A. And remember that we're going to have 15 from end and 13 prime end for each strand of D. N. A. Now remember that D. N. A polymerase can only synthesize from the five to three prime direction. So what's going to happen is you're going to have this new strands of D. N. A. Being built in that particular direction and we're going to have DNA preliminaries here, actively building new segments of this D. N. A strand. So this one in green here is new and we're going to see that it's building from the five prime to the three prime end. It's only adding nucleotides to that three prime end of that green strand. But realize that while it is synthesizing from the five prime to three prime direction, which direction is it moving along the template strand or the black strand? It's moving in the 3-5 prime direction, so it reads the template 3-5 and it creates the new strand in the 5-3. I hope that makes sense. I know that can be kind of hard to wrap your brain around, but it is important to know and I have seen this on a lot of different test questions. Okay, so now again, we're going to go over the difference between the leading and the lagging strand because it is very important to know. The leading strand is pretty easy to create, and that's because it is continuously synthesized in the 5-3 prime direction, and that's because it's really easy to synthesize and it just goes in this particular direction. Now the lagging strands got to be a little bit more annoying, a little bit more complicated and it is discontinuous lee synthesized, which I showed you in the last lesson. But again, it is still synthesized in the 5 to 3 prime direction because that's the only way that D. N. A polymerase can move. Now. The cool thing about the lagging strand is that it is compose of many different fragments of DNA as we learned in our last lesson. D. N. A polymerase creates a segment of DNA, then jumps back, creates a segment of DNA and jumps back. What are those segments of DNA called? These are called Okazaki fragments. Now, they're really cool name actually comes from the couple who actually discovered this process of the lagging strand and they gave it their name. So the Okazaki fragments are these small fragments of replicated D. N. A. Now these small fragments of replicated D. N. A. Are going to be bound together because we can't have the lagging strand just be all chopped up into these different fragments. It has to be its own whole DNA strand. So they're going to be bound together. And the way that they're going to be bound together is via the D. N. A. Light. It's protein which I'll talk more about in just a second. So the leading strand is just continuously made, it doesn't have any brakes. The lagging strand is dis continuously made in fragments. Okazaki fragments and then those Okazaki fragments are all joined together to make a continuous new strand of DNA. So now that we have that background information, let's just go over some of the DNA replication machinery. Now this is not all of the DNA replication machinery, just some of it and I'll go into the rest of it in just a second. So remember in our last lesson I talked about the RNA primer, I told you the DNA polymerase cannot begin the process of DNA synthesis on its own. It needs something to bind to first. It basically needs something to build off of. It can't go from scratch. So the RNA primer is you utilized for the jumping off point. The RNA primer is composed of about 10 RNA nucleotides and they are going to be complementary to the template strand of DNA and they're utilized to begin the process of DNA replication. Now RNA primers, there's only going to be one found in the leading strand but they're going to be many, many found in the lagging strand. Now, what creates these RNA primers is going to be this very important protein called Primus. Its name is pretty self explanatory, it makes those primers so it is going to be utilized to build these RNA primers using the template DNA strand. Cool thing about primates is that it doesn't need a primer but D. N. A polymerase does so it fills the job of beginning the process of DNA replication. Now you may be thinking if the lagging strand is full of all of these primers, what do we do because our D. N. A. Is not full of RNA? What happens? Well, there are actually special RNA or their actual special polymer races. DNA polymerase is they come along after the process, it has finished and removes those RNA primers and fill them in with D. N. A. Which is pretty cool. Those are other specialized types of DNA polymerase is not the one we are going to be talking about now, remember I told you that those Okazaki fragments have to be joined together to create a full strand. So once the primers have been removed DNA legs comes in and does its job and it joins those Okazaki fragments together. It basically allows the DNA backbone of these Okazaki fragments to bind together. So now that you know that that's just some of the replication machinery, let's go down and let's look at this picture. I didn't want to overwhelm you with all of the list of DNA replication machinery. So we're just gonna go in chunks. So I talked about the RNA primer and you can see the RNA primer here and it is being built and this is going to be something that D. N. A polymerase can build off of. Now, you can see D. N. A polymerase up here and you can see D. N. A polymerase up here and that's down there. Excuse me. And that's because remember, two strands are being duplicated at the same time. The lag, excuse me? The lagging strand and the leading strand. So the leading strand is continuous. And this process of DNA replication really doesn't hit any roadblocks and it just continues on this process. The lagging strand. Remember has to do all that jumping. And the creation of the Okazaki fragments. So you can see the D. N. A polymerase is are the kind of box looking thing. Now, once the DNA polymerase is done, remember we're going to have the DNA ligas which is here, this little guy here is going to come in to the lagging strand and bind all of those Okazaki fragments together also I forgot to mention, but here is the D. N. A. Primate protein. It is used once in the leading strand and many, many times in the lagging strand. So those are going to be some of the components that you're definitely going to need to know. Okay, so now let's go down because that is definitely not all of the DNA replication machinery and let's go down and talk about some other really cool proteins and molecules that are utilized in this process. Okay. One of my favorites just because it's really cool DNA hella cases hell a cases are going to be the enzymes or proteins that actually cleave or pry apart the two strands of D. N. A. This is going to break apart that double helix, that's going to break the hydrogen bonds between the the basis basis, complimentary lei bind the hydrogen bonding and healing case is just going to come in and push them all apart. So once Healy case does that and it separates the double helix into two single strands. We want to keep it single stranded so that we can duplicate our DNA, but DNA doesn't want to be single stranded, so we're going to have to have some helper proteins that come in and help with that. And these are going to be single stranded DNA binding proteins. They're commonly abbreviated SSB single stranded binding proteins. And these are going to be here to basically just ensure that the double helix does not reform before the process of DNA replication has actually occurred. Now, another really cool named protein that is very important. DNA topo summaries is also very commonly called D N. A. Gi race and we have talked about two boys summaries before this is going to be utilized to ensure that's super coiling does not happen. So D. N. A. Helix case is actually running down the D. N. A. And separating it. But because DNA is a double helix, this is creating a lot of tension on the coils in the helix. And DNA topo summaries is actively cutting the D. N. A. And relieving that pressure. That's super coiling. So this is also very important. Now the sliding clamp in the clamp loader are going to be something that is going to be specific to the D. N. A polymerase. The D. N. A polymerase isn't perfect. Remember it needs a primer, it's also going to need something to hold it onto the D. N. A. So it doesn't fall off. So the sliding clamp or beta clamp or D. N. A polymerase clamp. It has many names actually just holds the DNA polymerase onto the the template strand of DNA. So it can continuously build new strands of D. N. A. Now the sliding clamp actually cannot get onto the D. N. A. On its own. And it is going to utilize the clamp loader which uses a TP to clamp onto the D. N. A. And allow the DNA preliminaries to bind to the D. N. A. Now this is only going to happen once in the leading strand but can happen many many, many times in the lagging strand. This is another reason why the lagging strand takes longer. It's called the lagging strand and is kind of annoying to build. Okay so now let's look at the same picture. Same picture as I showed you before but we're going to go over the different parts just not to overwhelm you. Okay. So he'll a case really cool protein right here. This blue triangle thing. It's basically just cleaving through bulldozing through those hydrogen bonds and splitting the DNA apart into single strands. But because it does this we're going to need the single stranded binding proteins which you can see here in this purple color and they're actively holding the single stranded DNA. And they're holding it in such a way that it can't bind with another strand of DNA. So it keeps it single stranded. Now I'm going to go out of the picture because I'm in the way of the top boy summaries. So this big green guy here in front of the D. N. A hell a case is going to be utilized to relieve that super coiling. You can see that the D. N. A. Is actively coiling here but not here, that's because of this. To buy some price is really actually cutting the backbone of the D. N. A. To ensure that it does not super coil. Now, what else do we talk about? I don't want to forget, oh the sliding clamp and the clamp loader are not actually shown on this particular diagram. But if they were they would be right here kind of holding the D. N. A polymerase onto the D. N. A. And they would be holding that D. N. A. On. And the clamp loader would be waiting for the clamp to disassociate. And then actually it would be utilized to put that clamp back on if a new Okazaki fragment needed to be made. So just you guys know what we're talking about. This is the D. N. A clamp and the clamp loader doesn't actually clamp onto the D. N. A. It is just utilized to help the D. N. A. Clamp get onto the D. N. A. So I know I went over a ton of replication machinery but all these proteins and molecules are very important to understand. I do want you to understand these and I want you guys to be able to look at this diagram without the law and be able to label this particular diagram because I have seen that a lot in homework and quizzes and things like that, you are going to need to know these different machinery pieces, why they're important, what they do and their function in both of the strands because their functions can be a little different and their importance can be a little different in each of these strands. Okay, everyone, let's go on to our next topic
3
concept
Telomeres
14m
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Hello everyone in this lesson we are going to be talking about telomeres. Now remember whenever you have DNA like ours we have linear D. N. A. And the ends of the D. N. A. Are going to be called telomeres. These are going to be very specialized regions of the D. N. A. That are going to help protect those chromosomes. Those linear chromosomes from degradation at their ends. And the whole process of DNA replication that we have talked about is going to occur differently at the ends of the chromosomes. And we're going to talk about how this process works in this lesson. So the reason that DNA replication is going to occur differently at the ends of the chromosomes is going to be because of the way that the leading strand and the lagging strand are going to be replicated. Remember we learned that the process of replication for the leading strand and the lagging strand are actually very different. It's pretty simplified to copy the leading strand but it's a lot more complicated to create the lagging strand. So the leading strand really has no issue replicating the end of the chromosome. But the lagging strand cannot replicate the end of the chromosome because there's no real place to put an RNA primer. So telomeres are going to be utilized to solve this issue and I'll talk more about the specifics of how this works in just a second. So just know that telomeres are going to be the ends of the D. N. A. Linear D. N. A. So what that would look like is if you have a linear chromosome that is not replicated like the stick drawing here, the ends of the chromosome are going to be unique and these are gonna be telomeres. And their job is to protect the coding region of the D. N. A. So this is the coding region in black. And we obviously don't want to lose any of our coding region. We don't want to lose those genes that code for specific proteins and specific molecules that we need to survive. So basically what we do is we put caps on the ends of our linear chromosome called telomeres to protect our coding region from degradation. So telomeres are going to be long repetitive nucleotide sequences at the ends of chromosomes and their non coding sequences and they're highly repetitive. So that means that if they're lost a little bit it doesn't really matter because it's not affecting the coding region of the D. N. A. And in fact in human being, the repetition of nucleotides is the sequence A G G. G T. T. I don't believe that your professor is probably I don't believe they're going to need you to know this. They might I just thought it was interesting that this is going to be the repeated sequence. And in humans I believe um when cells are created the repetition is about 25 100 times. So this sequence of bases is repeated in a telomere 2500 times at the end of your chromosome and that is to protect it from degradation. So if you lose a couple of bases at the ends of your chromosomes, it's not a big deal because it's part of the telomere. It's a non coding repetitive sequence that you don't need to create your proteins and your molecules you need to survive. Now it's very important to understand that there is a specialized protein that actually creates these telomeres and this is going to be called telomerase. Now telomerase is very important because it's a different type of D. N. A polymerase and it is going to be the one that specializes in building those telomeres. Remember we talked about the fact the DNA replication occurs differently at the ends of chromosomes at telomeres. And that replication is going to be done by telomerase, not by D. N. A. It's going to be started by telomerase and then finished by DNA polymerase, which I'll show you in just a second. And the cool thing about telomerase is that within itself it has an RNA template. So it doesn't really need a primer because it has the primer within itself. So that allows it to kind of build from scratch more than DNA polymerase. So telomerase is going to be responsible for adding the short repetitive D. E. And a sequences onto the end of the lagging strand. So that D. N. A polymerase can finish the replication of the lagging strand end. Now I'm going to draw this out for you. So we will come back to this image in just a second. I'm going to talk about it in just a second but we're going to skip down here so I can show you what's going on because I can understand that. It might be a little confusing as to why the leading strand can perfectly create the ends of the chromosomes. But the lagging strand can't what's going on? Why can't the lagging strand actually replicate the ends of the chromosomes? Well I've drawn these two template strands. So imagine that your D. N. A. Has been separated into single strands and now it is going to be replicated. Remember it's going to be replicated so that you have a lagging strand and a leading strand. And down at the bottom we're going to have the leading strand and we're going to add the RNA primer here in blue. So I'm gonna write primer and from the primer. The D. N. A polymerase which I'm gonna draw here in red. So D. N. A. Polly is going to be able to build off of that primer and it's going to build in the five prime to three prime direction and this is going to be the leading strand. So that means that this is going to be the five prime in of the leading strand. And down here is going to be the three prime moment of the leading strand and this works perfectly for D. N. A polymerase because it simply begins to build off of the primer and it begins to build continuously that leading strand all the way until the end of the chromosome. And then DNA polymerase just simply falls off. It's done its job. It doesn't need to do anything else, it just falls off the end of the chromosome. All done. All of those complementary bases have been put into place. Pretty simple. So it's not a big deal. Right? So that's pretty easy. And this is the new D. N. A. Just so you don't get confused. So that's pretty easy. But the leading strand is always pretty easy. The lagging strand is where we get a little complicated and confusing. So we've done the leading strand. So now at the top here we're going to have to do the lagging strand. So this is going to be the lagging strand. Okay, so remember D. N. A polymerase can only build in the 5 to 3 prime directions. So that makes this a little bit more complicated. So what's going to happen is we're going to have our primer put down again in blue. This is our RNA primer which is going to be put down by primates. And then we're going to have the D. N. A polymerase come in and then it is going to move in the five prime 23 prime direction. And it is going to to build this fragment. This Okazaki fragment of DNA. So remember that this is the five fragment of this fragment. This is the three prime end of this fragment. So D. N. A polymerase moves in that direction. So now what happens remember for this process to go through the entire process of the replication of the lagging strand, even though DNA polymerase is going that way, the replication process must proceed this way, the replication of the leading the lagging strand do go in the same direction, but the D. N. A polymerase is don't really go in the same direction, right? They all go 5 to 3 prime, but it kind of looks like they're going in the opposite direction. So what is going to have to happen? Well, another primer is going to be put down 123. Another primer is going to be put down here and I'm gonna read primer, then what's going to have to happen? Well, the D N. A polymerase is gonna have to jump to this new location to build off of this primer. And then it's again going to build in the 5 to 3 prime direction. So here we go, here's our new Okazaki fragments and this is going to be the five prime mint. And this is going to be the three prime mint. Okay, so now, what should happen next? Well, the next thing that should happen is another primer should be put down but we don't have enough room. Look at this, where is this primer going to go? We don't have enough room right here. We don't have enough room to put another primer. And we also don't have enough room to create another Okazaki fragment. So the lagging strand has an issue because a lot of the time there will be the weird overhang where either a primer will fit but not an Okazaki fragment will fit or neither of them will fit. So what happens? What happens to these two base pairs that are hanging off the end here? Well, we can't replicate them in this manner because there's not enough there's not enough template strand left to create a primer and an Okazaki fragment. So they're probably going to end up being lost. They're going to get cut off and they're going to be lost. And that segment of D. N. A. Is going to be lost. And that's really not good if that segment of DNA at the end of the chromosome is utilized to code for a protein or code for RNA molecule that we need. So that's an issue. So this is where telomerase comes in handy because it's going to create repetitive sequences at the end of this lagging strand so that there is enough room for a new RNA primer and a new Okazaki fragment to be added. So I hope that's helpful. Now we're going to go up to the other drawing that I showed you. So remember this segment, this segment here in yellow, that doesn't isn't able to be replicated. That is going to be this segment right here in this image. Okay, so now we're only looking at the lagging strand. So this is the lagging strand and this is the region that we could not replicate. And this is the region that could be lost. Okay. Which is not good. We don't want to lose this coding region. That's very important. So what does telomerase do? It's going to make a non coding region of repetitive sequences called the telomere. So the telomere, is this right here this repetitive sequence right here? And telomerase is actively building this repetitive sequence of D. N. A. Now, what does this grant the lagging strand? Why is this a good thing? Well, now, what can happen is say the primer binds right here. Our primer binds right here. And what can happen is D. N. A polymerase comes in and it will begin replicating the D. N. A. In this direction. And then, let's say it fills in this Okazaki fragment right here. That's awesome, right? Because now that region in yellow is completely replicated and even some of the telomere is replicated. So that region in yellow is completely replicated and none of the coding region is lost. Now, you might be saying, Okay, so what if some of the telomere is lost? Right, we still have the same problem. There's not enough room for another primer on this end to replicate the rest of the telomere, well remember, it doesn't matter if some of the telomere is lost because it's not a coding region. And it's just repetitive sequences of DNA that we don't need. The only thing that the telomere does is protect the coding region from deterioration. And it allows the end of the chromosome on the lagging strand to be completely replicated. As we can see here and it allows it to not be lost. So if some of the telomeres lost, it's not a big deal. That's its job. Right? So the same thing is happening in this image right here. You can see that the RNA primer was put down right here and that the D. N. A polymerase which I'm highlighting in yellow is building this new sequence of D. N. A. It's the exact same thing that I drew up there. So it's building this new sequence of D. N. A. And then it will finish off this sequence of the coding region and all of the coding region will be replicated. Which is great. And the section that is going to be lost will be this little section right here of the telomere which is an eight A really big deal. So telomeres are very very important, as you can see telomeres are utilized to maintain the integrity of the coding region, ensure that the ends of the chromosomes are not lost. And guys if the telomeres are really messed up and they're too short and some of the coding region begins to be lost, that cell might go into apoptosis. And you will also find that errors in t telomeres or problems with telomeres are common to cancer cells as well. So telomeres are very, very important and when they are lost, the cell usually ends up going through apoptosis or something goes wrong, which can be incredibly detrimental to the organism. But just remember the telomeres are the repetitive sequences at the ends of chromosomes to protect the coding region of the chromosomes from deterioration. Okay, everyone, let's go on to our next topic.
4
concept
Proofreading
14m
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Hello everyone in this lesson. We're going to be talking about DNA proof reading and the fixing of errors in D. N. A. And we're going to be talking about how new nucleotides are added onto the end of a growing DNA strand. Okay so we've talked about DNA replication and we've talked about that whole process but we haven't really talked about the fact that nothing is perfect. We make mistakes and so does the D. N. A. Polymerase. These are gonna be things called mutations errors in the genetic code whenever the incorrect base is put down. Now mutations can be made in many ways radiation different mutations. But this is one of the main ways that mutations are created. And that is due to the fact that D. N. A polymerase isn't always perfect and it doesn't always correctly match the correct base pairs. But overall DNA replication is highly accurate. It's extremely accurate. When you think about it, there's really the only one error per 10 million base pairs. Which is pretty good. If you think about it you're like wow only one error per 10 million base pairs. That's pretty great. But realize that inside each cell there are three billion base pairs in the human genome. There are three billion base pairs. So if DNA polymerase makes a mistake, every 10 million base pairs you're kind of likely you're going to get mistake right. So even though it's rare it does happen. So what does D. N. A polymerase do, how does it fix this issue? Well the cell doesn't want mutations. So it has this ability inside of the D. N. A polymerase called proof reading and proof reading is the ability of preliminaries to double check and correct its mismatched bases. And it does this by kind of putting down a base and then looking back back at it and making sure that it's right and then moving on to the next space. Now the D. N. A polymerase that is actively building the new strands of D. N. A. Can do this. There are other mechanisms by other DNA polymerase is that come along after this fact to fix mutations. But we're not really going to talk about that in this lesson right now. We're just going to talk about DNA polymerase is proof reading ability and fixing the mistakes as it's building the new strand of DNA. So like I said, proof reading occurs before the next nucleotide is added. So like I said basically DNA polymerase puts down a base that it believes is complementary to the template strand looks at it and says is this correct? If it is it moves on If it's not it is going to remove that incorrect base and then put the correct one in its place. How does it do this? It has this really neat ability called the eggs on nucleus activity. Specifically the 3 to 5 prime eggs a nucleus activity. Oh I'm sorry I am in the way they're guys let me scroll down a little bit. Okay so the eggs a nucleus activity. If you remember proteins that are eggs, a nucleus is actually remove base pairs at the ends of DNA strands, proteins that are indo nuclear bases actually cut base pairs out of the middle of the DNA strand. But DNA polymerase is also an exotic nucleus, meaning that it can look at the end of the strand that it is creating. And if the last base is incorrect it simply cuts it off and puts a new one in and it's 3-5 prime eggs a nucleus activity. This can kind of be kind of confusing. So let me let me show you real quick. So let's say that this in black is our template strand. Oh sorry about that guys, this is our template strand and this is going to be the three prime end and this is the five prime end of the template Now. What do we know about the process of DNA replication? Remember we learned that a primer is put down and then the new strand of D N A is going to be made and it's gonna be made in this direction. Remember that this direction is the five prime to three prime direction, That is the direction the D N A is created. But which direction would the D N A be removed? It would be the opposite direction. Right, so you create D N A. In the five prime to three prime direction. You remove a base from the end of the strands of D. N. A. In the three prime to five prime direction. And that is because that strand or that base of DNA. That is being removed. Being removed in that direction by the D. N. A. Preliminaries. Okay I hope that makes sense. Just know that the direction in which the D. N. A polymerase removes an incorrect base is the opposite direction in which it adds new bases. So that kind of makes sense? Right? You're adding in one direction and if you mess up you got to take a step back in the backwards direction, that's all that this particular DNA polymerase is doing. But it is given a fancy name called the 3 to 5 prime eggs, a nucleus activity which is also the proof reading activity. Okay but you're probably going to need to know this name. 3 to 5 prime eggs or nucleus activity. I have seen this intestine quizzes. They're going to ask you to know this. They're also going to ask you to know what proof reading means. Okay. Alright so now that we've talked about proof reading. Let's talk about why D. N. A. Can only build in the 5 to 3 prime direction. Why can new nucleotides only be added to the three prime end of the D. N. A. I know that I've told you this over and over and over again. But I haven't really told you why this is the case. So now we're going to go over why this is the process that happens. Okay so we know the D. N. A. Can only be synthesized in the 5 to 3 direction. Now let's learn about why that is and the reason that this happens is going to be dealing with the structure of the nucleotides themselves. So nuclear ties that are utilized to build new strands of DNA are commonly called D. N. T. P. S. Or deoxyribonucleic nucleus side. Try phosphates and deoxyribonucleic is referring to the sugar that is unique to D. N. A nucleoside. Try phosphates basically. That's going to be those new click bases in those nitrogenous bases with phosphate groups added onto them. So think of a base and its sugar with its phosphate. We know what a nuclear tide looks like. But now imagine it with three phosphates and not just one. This is very important. All nucleotides before they are added to a strand of DNA. Have three phosphates. And after they've been added to a strand of DNA, they only have one phosphate. So D. N. T. P. S. Have three phosphate groups attached to the D. N. A nucleus side. Then what's going to happen to of these phosphate groups are kind of ripped off. Now does this make you think of anything else? Let me ask you whenever we learned about A. T. P. What happens, remember a teepee? Adenosine tri phosphate has three phosphate groups. Now how is energy released? You cut off one of those phosphate groups right? And then you have a D. P. Seen di phosphate. So whenever you cut off one of those phosphates you release energy. Think of that same process that's happening here. D. N. T. P. S. Have three phosphate groups. And when they cut off two of them energy is released in this process. This energy that is released from these nuclear sides is going to be the energy to power DNA synthesis. We know that this process is going to take energy but I haven't really told you where it comes from. This is where it comes from. Now. The reason that this can only occur on the three prime end of the new strands of D. N. A. Is going to be because of these phosphate groups. And how they are removed. The three prime end of the growing D. N. A. Strand helps remove two of the phosphate groups. The three prime end and D. N. A polymerase actually remove these two phosphate groups and then put on the new nuclear tied. And that is going to be why new nucleotides can only be added to the three prime end. And we know this because the five prime end will not undergo this reaction. It will not help remove these two phosphate groups. So nothing happens. So the three prime end is the only end that D. N. A polymerase can work with with these D. N. T. P. S. To build the new strand of D. N. A. Okay so I know I talked about a lot in this lesson but I'm just gonna go over it really briefly and we have some pictures because I know that some of these topics can be a little bit complex. So I'm going to talk about or I'm going to show you the picture of the thing that we just talked about, the D. N. T. P. S. So we're gonna start with this picture here. And I'm gonna go out of the picture. So you can see all of this image. Okay so this right here is the growing strand of new D. N. A. So this is the new D. N. A strand that is actively having new nucleotides added to it. Now this guy right here in blue is the D. N. T. P. So D. N. T. P. And that is because it is a. D. Oxy ribose sugar with a base and three phosphate groups. Now look at this, this is going to be the three prime end of the D. N. A. And this is a peer is the five prime end of the D. N. A. Hopefully you remember why this is and that's because this is going to be the three prime carbon of the de oxy ribose sugar. And this new nucleotide is being added to the three prime end the three prime carbon of this growing strands of D. N. A. So we have the three prime end which is actively attacking these phosphate groups. And it will remove two of these phosphate groups with the help of D. N. A. Polymerase. So when those two phosphate groups are removed energy is released. And then we end up with this over here we have our new strand of D. N. A. Which has an added nucleotide. So we have our new nucleotide in blue right here which has been added to the strand of D. N. A. And then we have our two phosphate groups that have been removed. The process of removing these two phosphate groups releases energy and allows this process to happen. So this is what we just talked about in why D. N. A. Can only be elongated on the three prime end. And that is because the three prime end in conjunction with the D. N. A. Polymerase attacks these phosphate groups, removes two of the phosphate groups from the D. N. T. P. S. Releases energy. And then this energy is used by D. N. A. Polymerase to attach the new nuclear tied to the growing strand of D. N. A. I hope this visual is helpful because I know that this process can be a little bit confusing. Okay so now I'm going to come back into the picture because now we're gonna move on to the other topic that we talked about. We're going to talk about proof reading over here. Remember we talked about proof reading in the beginning of this lesson and that's the fact that D. N. A polymerase can correct any mistakes that it has created. So you can see our D. N. A. Polymerase is moving in this direction creating this new strand of of D. N. A. But wait a second. Something happens, something goes wrong. This is an error. Do sees bind with T. S. No. Remember that in D. N. A. A binds with T. And C. Binds with G. So the D. N. A polymerase has created a mistake here. See does not bind with tea. T only binds with A. So this base right here is the error. So it's going to use its proof reading ability. It's going to see that this base is incorrect. And then it's going to use its 3 to 5 prime, three prime to five prime eggs, o nucleus activity to remove this sea bass to remove that Cytisine. So it's going to use that eggs a nucleus activity to pull out that incorrect base. And then what happens? Well the correct base is added. Oh sorry this is the correct base that is added right here. So it has fixed its mistake. And instead of placing a C. There it now has the correct base which is the A. So that is a diagram of how the 3 to 5 prime eggs a nucleus and proof reading activity actually works. The DNA polymerase notices that it has put down the incorrect base, removes it and simply puts down the correct base and then keeps going. So I know we talked about a lot in this lesson. Hopefully it wasn't too terribly confusing and hopefully the diagrams helped. Just remember that proof reading is a very integral part of our DNA synthesis. We don't want to have mutations. So D. N. A polymerase is able to fix some of the errors that it creates. And also remember that D. N. A polymerase only works in one direction and that is going to be due to the structure of the three prime end of the D. N. A. And the structure of the D. N. T. P. S. And their three phosphate groups, which release energy and allow the process of the elongation of a new strand to be created. Okay everyone, let's go on to our next topic.
5
Problem
ProblemDNA replication occurs differently at telomeres.
A
True
B
False
6
Problem
ProblemDNA is replication in which of the following directions?
A
5' to 3'
B
3' to 5'
C
5' to 5'
D
3' to 3'
7
Problem
ProblemWhich of the following proteins are responsible for unwinding the DNA double helix for replication?
A
DNA helicases
B
Single stranded binding proteins
C
DNA Topoisomerases
D
Sliding Clamp
8
Problem
ProblemOnly the lagging strand uses telomerase to replicate the ends of the telomeres?
A
True
B
False