all right so by now you are an expert on the main structure of DNA you already came into this with an idea of its main function now we're going to start looking at um all the processes that DNA engages in starting with replication or making more DNA molecules okay so we already discussed this um in a more General sense when we were learning about cell division because before a cell can divide it of course has got to duplicate its DNA or replicate its DNA because so that each of the daughter cells can have a full genome right so the name of this is replication do you remember exactly when in the cell cycle DNA replication happens reach back into your brain it is interphase more specifically S phase or synthesis phase of interphase so if you remember that good job okay the main idea of this is very simple we have a double-stranded helix we need to separate the strands and then add new nucleotides to each of those old strands to create two new strands and that makes two new molecules all right so looking at this picture it probably looks um like you would expect that process to look you see the old parent molecule unwinding and new nucleotides being added to form a new Strand and that process when it's done creates two daughter molecules that are identical to one another contain the exact same code and contain the same exact coding information as did the parent strand so let's get into it how does this actually happen you will notice in this unit it's a lot of process I'm going to be walking you through a lot of different processes it is really useful to do a few things as we do this just like as a general tip for this whole unit like imagine and visualize these things happening as I talk you through it and then I'm gonna post some videos a lot of these are just really easier to conceptualize or at least to like um solidify your conceptualization and understanding by watching this in motion right because these are actual processes that are happening like they're moving in 3D space and I find that really helpful so please do take the time to look at some of those videos that I'm posting and in the meantime as we're walking through it like imagine this in your brain as I am telling you about it okay so where does it start it's going to start at the origin or the point of origin so technically you can see right here it's in the center that's where this bubble is going to start forming and it actually is called a bubble like a replication bubble that's going to expand as the molecule is separated Unwound and separated the strands are separated in either direction the place the like little like you can see a v-shaped place on either side where the strands are separating and that's going to move right that spot is going to move as the strands continue to separate that is called the replication fork so sometimes you'll see those kind of like tossed around but technically the point of origin is the beginning it's where this starts and the replication fork is going to be this moving spot where the strands are separating another thing to look out for in um oh this entire unit for all these processes is all of the enzymes that are involved there are a lot that we're going to be talking about it's not even all of them by the way but we're going to be talking about a lot of the important enzymes that are doing parts of the job to make this happen and it really is worth your time to get really straight on what these each do because a lot of these will be seeing either the same enzymes or similar enzymes later so if you can kind of like really make sure you're learning as you go that will help you okay so starting with topoisomerase if we are going to you know be getting at the coding area inside of these strands we have to first unwind the Helix so that's the job of topoisomerase followed shortly behind by Gila case which is what the enzyme that actually separates the strands so remember we talked about how we have relatively weak hydrogen bonds that are keeping those strands together so helicase can easily come in and separate those hydrogen bonds separate the strands without damaging the individual strands themselves so Australians like to you know complementary bases want to bind together so it wouldn't work if helicase was coming here or separating the strands and then as soon as it left the area those strands re-annealed or like glued back together so we have these little proteins called single stranded binding proteins or ssbps and they are going to bind the area and sort of like block the um prevent the strands from re-annealing so that we can actually like do the job inside all right so we've separated the strands now we have to add some new bases enzymes whose job it is to is to add new nucleotides onto a growing new strand of DNA or RNA are in general called polymerases there are several different types and we're going to talk about that in general or in a second but I just want you to know in general that if you see an enzyme called a polymerase it's going to be involved in adding nucleotides in this context okay so I told you there are different types there are different types of DNA polymerases but also RNA polymerases those are so named based on what type of nucleotide they add so if the job of the polymerase is to add RNA nucleotides to a strand that would be called an RNA polymerase if the job is to add DNA nucleotides it'd be called a DNA polymerase our our star player here is DNA polymerase three if you see a diagram like the one here on the right that just says DNA polymerase and you see it chugging along adding nucleotides in this type of scene they mean DNA pole three okay if they don't tell you that's who they mean and DNA polymerase is the one that will do most of the adding of new nucleotides to this growing strand the key here though is that DNA polymerase 3 can only add nucleotides to the three prime end of an existing nucleotide that was a mouthful but essentially what that means is if you have separated like a beautiful separated strand it's just ready to have new nucleotides be added to it DNA polymerase 3 cannot come in and add new nucleotides until there's somebody already there it has to have a three prime end to kind of hook onto and start chugging along so because of that there is another enzyme It's actually an RNA polymerase called primase that will sort of set the scene for DNA Paul 3 and create a little sequence of RNA nucleotides called a primer it's basically just creating a little segment with a free three prime end that so that that spot is is like ready to go and DNA Paul 3 can come grab onto it and start doing its job by adding DNA nucleotides so what I want you to do there's just a it's not like it's impossible to understand it's just a lot of information so before you move on like look at this diagram on the right and make sure the parts that I've told you about so far because there's extra stuff on here that I haven't told you about the parts that I've told you about so far make sense you see toporo isomerase doing its job do you know what that job is and does it make it does that part of the picture make sense to you do you see print helicase there does it location and the job it's doing makes sense Etc so look through and make sure that it kind of makes sense before you move on there's another kind of polymerase called DNA polymerase one and it has a couple of different jobs its main job in this context is to remove the RNA primer created by primase and replace it with DNA nucleotides after DNA Paul 3 has already come through and done it's part of the job so you can see in the picture here that DNA Paul 3 has created in this diagram the DNA nucleotides are in red right it's come through and it's all looking good except we do still have that little green RNA segment that needs removing right we don't want to have part of our new strand brna that's not going to work right so we need to make it DNA so DNA polymerase three or one will come by remove the primer and replace it with DNA nucleotides it also has a proofreading function actually all polymerases have proofreading function they can all check for mistakes as they go but um this one will kind of like look out in general for mistakes little gaps stuff like that all right before we go to the next bit if you are not really comfortable with the five Prime to three prime directionality of a single DNA strand and you don't feel really comfortable with the concept of the two strands of double-stranded DNA being anti-parallel to one another I want you to stop here go back and review that until you're comfortable because that is really going to help you understand this next part okay the idea behind this whole slide in this next little bit is that the the new strands that are being constructed on the old strands have to be made slightly differently because the the old strands are pointing in different directions they're anti-parallel to one another remember the DNA polymerase can only add new nucleotides to the three prime end of an existing nucleotide so looking up at the top you can see that the old strand has its three prime end on the right and the New Strand has its five Prime end on the right that makes sense right Angie parallel so that means that if you follow your finger on this new strand the three prime end is over here on the left and you can see DNA polymerase doing its job right there this all makes sense right that's what we were expecting notice that DNA polymerase 3 here in this case is moving in the same direction as the replication fork and what that means is that the new nucleotides on this old strand here are becoming available for pairing um like in the right direction right they're going to be new bases becoming available as this Fork moves left and DNA polymerase is also moving left so we can just like kind of chug along and create a like a smooth New Strand that New Strand is called the leading strand if you look at the bottom it's a little weirder because now because the other strand is pointing in the other direction this DNA polymerase notice by the way there's more than one DNA polymerase three working at this time and that's the case there are multiple molecules of this that are working at the same time down here to go um five to three left to right the three prime end is over on the right so the DNA polymerases are moving in the wrong direction essentially they're moving away from the replication fork right the replication fork is opening to the left and these guys are going to the right so what they end up doing is they make a little segment and then they kind of fall off and then there's a new segment a new like area of single stranded DNA will become available for pairing and so they join there and they make a little segment and then they fall off and then they're like so it's kind of like a little hopscotchy uh movement of creating these like little segments of new DNA those fragments are called okazaki fragments and the Strand that is being formed in that fashion is called the lagging strand again I know there's a ton of information kind of just walk through this and then again we'll be looking at some videos it's really useful to see the kind of this happening in real time here's another cartoon just another view of the same thing you can see heal a case on in this diagram is on the right that means the replication fork is moving to the right and you can see our leading strand is on the top you could tell that this was our leading strand even if that label was not there because our old strand has its three prime end on the left that means our new strand has its five Prime end on the left are three prime end that's where the action is happening right that's on the right so the DNA polymerase 3 is going to be adding new nucleotides to that three prime end of the New Strand and moving right the same direction as Gila case and our replication fork that means of course that the bottom strand is our lagging strand these guys are going in the wrong direction they are going to be making little segments and then falling off and then jumping back and making a little segment and jumping off remember those little segments are called okazaki fragments this is the exact same thing I just what I like about this diagram is it is very simplified with a focus just on the five Prime to three prime sort of relationships that are all happening here so if that part of it of what I just described is feeling really confusing which would be understandable take time to kind of like pause here and make sure you kind of understand the three prime to five Prime to uh five Prime to three prime and all that sort of stuff before we move on now we've made some new strands of uh DNA what happens next we're done with the polymerases so they're going to fall off um we need to glue the backbones so in particular we need to pay attention to the places where the okazaki fragments are not actually connected to one another right there's a special enzyme called DNA ligase that is going to glue the backbones and so it will do this we'll also look for gaps in the leading strand but we already know there are gaps in the lagging strand because we have to basically glue the okazaki fragments together and voila now we have two complete new DNA molecules that are identical to one another and contain the same code of course as the parent molecule important to note that this process is said to be semi-conservative it's probably like the diagram you're looking at at the right it probably feels really obvious now that you walk through the whole the nitty-gritty of how it works but this was not obvious at first and I just want you to notice that it for each of these daughter strands we have conserved one of the old strands and of course included now our new strand that was created just take a little Gander at this make sure you understand how those bottom four molecules became those bottom four molecules uh before moving on and finally errors errors are called mutations and we will Circle back on the idea of the different kinds of mutations um later but I just kind of wanted to introduce the idea and just pick up a few important points about this first of all they are very rare because like I mentioned DNA polymerases do have a proofreading function and they check their work as they go but I also wanted to point out that um not all mutations are bad that's a common misconception um that students have is that any mutation in your DNA is going to like cause a disease or cause cancer um you know kill the organism and that isn't always true um it could have no effect um we'll kind of get into the reasons for that when we get into how DNA makes proteins but you know the same protein could be formed even if there is a change in the DNA or sometimes there will be a phenotypic change as a result of a mutation but it's actually helpful and so this is actually a driver of evolution um you know if everybody was all the same and the entire gene pool was exactly the same then you know we couldn't we couldn't select for beneficial phenotypes so just a little bit to file away for later wonderful job I will see you soon bye