Lecture 1 - DNA Structure & Replication

Añadido: 2026-05-14

[00:00:02]hi everyone welcome to the second half of your biology course um this week we're going to be starting off taking a look at our dna we're going to spend the first four weeks of the course looking at genetics and we're focusing primarily here for the first three weeks on dna structure how we replicate our dna so creating identical copies of it and then how we transcribe how do we take that temporary copy to be able to produce the protein so i know it's been a while but to recap remember dna dna rna these are our nucleic acids and they are one of the four macromolecules found in the human body dna is a macromolecule that houses our genetic code this is the material that is coding for specific proteins that are ultimately going to be produced where do we store all of our dna well that's within the nucleus remember the nucleus is that organelle within each of our cells that acts as that main control center this is where all of the dna is located now in order for our cells to divide we need to create identical copies of our dna and if you recall during the cell cycle replication of dna occurs in the s phase of interphase our main focus for today is going to be looking at dna replication we're going to take a look at during that s phase what actually happens there how do we create those identical copies of our double-stranded dna molecules and then next week we're going to jump into then looking at transcription the process by which we make a temporary working copy of our dna which is known as messenger rna within the nucleus so that it can leave the nucleus to then be translated by the ribosomes in the cytoplasm to create the proteins all right so over the next three weeks we're going to be looking at these different processes today's main focus is on replication next week we move into looking at transcription so creating that messenger rna from our dna and then the following week we'll look at translation how we take that mrna and how do we read it and how do we produce the functional protein from that working copy so if you'll recall dna and rna stand for deoxyribonucleic acid and ribonucleic acid there are some differences between the two remember dna is double-stranded rna is single-stranded now dna and rna all consist of individual monomers that are known as nucleotides remember your dna and rna those are the polymers the macromolecules and all polymers are made up of individual subunits known as the monomers we know there are five different nucleotides in total four specific to dna and then four specific to rna the main difference thymine exists within our dna whereas uracil exists within our rna and each nucleotide consists of three main components so we have the main five carbon sugar and to this point you've just known that it has five carbons what we're going to do today is start to count those carbons and identify them because that determines the polarity of the nucleotide the difference between your dna and rna is also that the dna contains a deoxyribo sugar so this five carbon sugar can either have two hydroxyls bound to the two prime and three prime carbons or in your deoxyribose sugar you have simply a hydrogen bound to that second carbon attach the deoxyribo sugar we have a phosphate group and here at the other side of this sugar we have a nitrogenous base and it's the nitrogenous bases that dictate what type of nucleotide we have okay so the five different types of nitrogenous bases are cytosine guanine thymine adenine and uracil okay so recall in our dna molecule we'll find cytosine guanine thymine and adenine and then in our rna molecule we'll find cytosine guanine adenine and uracil also remember our dna is a double stranded molecule whereas rna is a single stranded molecule all right and dna as it is a double-stranded molecule forms a double helical structure and within this double helical structure we have two separate strands and these strands are going to be attracted to one another through hydrogen bonding right these hydrogen bonds exist between complementary base pairs so remember adenine always binds with thiamine so you pair a with t and cytosine always binds with guanine c with g and you'll notice here between adenine and thymine there are two hydrogen bonds that exist between those nitrogenous bases and between cytosine and guanine there are three hydrogen bonds that exist between those bases some of the other bonds that exist here besides the hydrogen bonds holding the strands together are the phosphodiester bonds that exist to create the sugar phosphate backbone we're going to see today how we can actually create this phosphodiester backbone by adding each nucleotide onto another to create that strand right and then finally we have the glycosidic bonds that attach the one prime carbon to the nitrogenous base now the specific structure of dna and how it is oriented aids in its function you'll notice here that on each of these sugars we have now added numbers okay so this is what is going to identify one side of the sugar from another specifically we're going to be paying attention to the five prime carbon and to the three prime carbon now because the hydrogen bonds exist between the guanine say and the complementary cytosine and the thymine and the complementary adenine hydrogen bonds remember are very weak bonds and so they can be easily broken when we need to separate those two strands to be able to replicate our dna another thing that is unique is because these strands are complementary to one another they're essentially a mirror image so we have two copies of that information that is being stored within our dna molecule and by having two copies we're ensuring that we're going to be passing that on to future generations when we pass on those alleles now a new concept that we haven't covered yet is the idea of the actual structure of the nitrogenous bases now we know that a nucleotide is determined by the nitrogenous base that attaches through the glycosidic bond to that one prime carbon so we have these five different nitrogenous bases and depending on which one is attached that determines the nucleotide now we know that cytosine always binds with guanine and we know that adenine and dna always binds with thymine and then an rna adenine is going to pair with uracil what you'll notice here is that some of these nitrogenous bases have a single ring structure such as cytosine thymine and uracil and others guanine and adenine have a double ring structure okay so we assign different names to those nitrogenous bases based upon their ring structure so those with double ring structures such as guanine and adenine those are known as purines now with the single ring structure nitrogenous bases those are known as pyrimidines so you have cytosine and thymine within our dna and then within our rna we have cytosine and uracil and so you'll notice that the complementary base pairs always pair a pyrimidine with a purine so a single ring structure nitrogenous base with a double ring structure nitrogenous base now i've mentioned this before and let's focus on that now so first off we are looking at the pentose sugar right that five carbon sugar that makes up the the main core of our nucleotide and this pentose sugar is made up of five carbons so when looking at the sugar starting at the right carbon here that would be your one prime carbon and then we continue counterclockwise counting the two prime three prime four prime and finally the five prime and similarly in our deoxyribose sugar one prime carbon which is attached to the nitrogenous base and counting from there we have counterclockwise one prime two prime three prime four prime and five prime carbon okay and in both cases the five prime is what is connected directly to the phosphate group okay so the one prime connects to the nitrogenous base and the five prime connects to the phosphate group so let's take a look here this is our nucleotide right specifically we are looking at adenine and so if we find our sugar the one prime carbon is the carbon that's attached directly to our nitrogenous base so we start there and then we move counterclockwise so one prime carbon two prime three prime four prime five prime and attach the five prime carbon we have the phosphate group the reason that we're getting into numbering these carbons now is because the five prime and the three prime are what are ultimately creating the polarity the direction of our dna molecules now some new terminology that we're going to introduce you to here we have talked about nucleotides you know that nucleotides are made up of a phosphate sugar and a nitrogenous base standalone we have our nitrogenous base here when you have simply a sugar added to that nitrogenous base we have what is known as a nucleus side okay so omitting the phosphate we're looking at a nucleus side when we add the phosphate we refer to that as a nucleotide so another way to describe your nucleotide is to call it a nucleoside monophosphate okay so you have a nitrogenous base add a sugar to that nitrogenous base you have a nucleus side and then add a phosphate to the nucleus side and you end up with your nucleotide now the reason we're going through this is because i want you to notice something here your adenine and your sugar that would be a nucleus side okay so this would be your adenosine nucleoside if you added a single phosphate group that would be your nucleoside monophosphate if you added two phosphates you would have your nucleoside diphosphate and then three nucleoside triphosphate if we're looking specifically at adenine this would be adenosine triphosphate okay that's your atp molecule so i want you to see the similarities here these form high energy molecules within the body that are then also used as our nucleotides that help to build up our dna molecule we haven't talked about gtp okay gtp is just guanine triphosphate okay so you substitute guanine instead of the adenine gtp is also another high energy molecule used throughout the body our main focus so far has been on atp but gtp is also an energy molecule so now if we were to take a look at cleave off two of those phosphate groups we are now left with an adenine nucleotide okay which we can also refer to as adenosine monophosphate as we mentioned before when we eat food we're taking in carbohydrates we're taking in lipids we're taking in proteins we're also taking in nucleic acids and we can break those down into nucleotides and then further into nucleosides so our diet is a main source of these nucleosides we don't use them to produce energy right we can store up energy if we added on some phosphates here creating an adenosine triphosphate and atp molecule but we're not actually by breaking these down we're not getting a lot of energy what we're using them as is the basic building blocks to build our own dna okay for dna replication but also in the process of transcription so any time whether it's animal or plant byproduct you are taking in nucleic acids dna breaking that down and then utilizing the base structure the nucleosides to be able to use the nucleosides to help build up our own dna molecules so here we're looking at a chromosome remember our linear dna is condensed and coiled up into these structures as we head into prophase of mitosis during that s phase when we're replicating our dna it's in this linear form right as that chromatin but then as we go to then want to divide this dna that we've already replicated we condense that into our chromosomes now we have very unique structures located at the ends of our linear dna so if you coil that up you would see these structures at the terminal ends of our chromosomes and these structures are known as telomeres and telomeres are regions of repetitive dna sequences located at the ends these regions are non-coding right so remember what is the whole purpose of all of this dna well it's all coding for different proteins to be expressed right all these different genes along the chromosome along all these segments of our dna those genes are coding for some specific protein these telomeres here act as almost protective mechanisms because they're non-coding and they're protecting our coating regions in the same way at the ends of your shoelaces you have those either metal clamps or they're bound in plastic that's to prevent the shoelaces from fraying and becoming destroyed telomeres are acting in kind of the same way there as the those tips of the shoelaces the telomeres are essentially protecting the chromosome from deterioration one thing that's important for you to remember is that these telomere sequences in humans are repeated sequences tta ggg so you have thymine thymine adenine guanine guanine guanine and you can see down here in this sequence that is repeated over and over anywhere from 5 000 bases to 10 000 bases and the length of the telomere dictates how long that cell is capable of living every single time that a cell divides and we've replicated our dna telomeres shorten ever so slightly and so when looking at the differences between you know average life expectancy of say a hamster which we just got for my daughter over christmas they're about two years whereas for humans say anywhere between 75 80 years average life expectancy so the length of the telomeres telomeres help to protect the coding regions of that dna and that ultimately allows the cell to function now telomeres are anywhere from five to ten kilobases long kilo referring to thousands so that's five to ten thousand nucleotide bases in length so you can appreciate there's quite a bit of protection there protecting the coding regions of our chromosomes from the external environment now once we take a look at dna replication you're going to see how these telomeres can become susceptible to deterioration based on how we replicate our dna now our dna molecules are made up of two strands of dna that form that double helical structure that you're seeing here and you'll notice here that one strand is labeled five prime at the top and if we follow that strand all the way to the bottom you'll see it's three prime at the other end and if we follow the complementary strand it starts up here at three prime and ultimately runs to five prime each dna strand is a mirror image of the other running in opposite directions and we refer to that as anti-parallel now between these two strands as we've seen previously there are hydrogen bonds that are ultimately holding all of the bases together but remember hydrogen bonds are very weak so it's very easy for us to be able to separate these two parent strands here's your five to three prime parent and here's your three to five prime parent when we separate those strands we are then able to create complementary strands to each of those parents and subsequently we have then created two identical copies of our original dna molecule so just as a recap here if we have a five prime to three prime sequence of dna what would be the complementary strand to this dna molecule we have ggta ccagt so what we've done so far getting rid of the five and the three ends to it you would have told me c c a t g g t c a what you have to do now is add on the polarity so if we know that this strand is running five prime to three prime the complementary strand is going to be running three prime to five prime now if you recall prokaryotes have circular dna molecules now this is fantastic for them because they don't have any exposed ends to the environment right their dna is circular and so they do not have any telomeres and as i mentioned before every time dna replicates in humans and other animals that have linear dna every time eukaryotic dna which is linear has to replicate the telomeres shorten ever so slightly but here in prokaryotes they have circular dna with no telomeres so they're able to conserve all of their original dna every time that they replicate the difference here with prokaryotic dna replication is that they have this point of origin from which they then are going to unzip their circular chromosome in opposite directions and be laying down complementary strands to that ultimately creating their two identical copies now here we're taking a bit of a closer look at a template strand of dna here on the right this would be your parent strand and then how we would go about adding nucleotides to create that complementary strand here on the left so you'll notice the new strand is always going to be created in a five prime to three prime direction okay highlight that and if you look at the parent strand we can only do that if we're starting with the three prime running to five prime now recall if we were to number all the carbons here on this deoxyribose sugar you have the one prime carbon here that binds to the nitrogenous base through the glycosidic bond you have the two prime carbon three prime four prime five prime and what you'll notice here is that every time we lay down a new nucleotide and attach it to the existing strand that we're creating it's the phosphate from that five prime carbon that is going to be binding to the three prime carbon of the adjacent nucleotide ultimately creating that phosphodiester linkage and so what we need here is this free hydroxyl group on this three prime carbon okay and that is going to indicate our direction of new chain growth we're always going to add on to the hydroxyl of the three prime carbon and so let's see here what do we have on the parent strand we have a thymine nitrogenous base and so what's going to pair with thymine adenine and so before this becomes a nucleotide we have the high energy adenosine triphosphate okay generally speaking a nucleoside triphosphate and it's the energy that's stored in these high phosphate bonds that will be cleaved and will be given to creating the new bonds that are going to bind this new nucleotide to the existing nucleotide so then to pair a with t we there's a specific enzyme that is going to be responsible for catalyzing this whole reaction we'll get to that in a minute here we're going to have the two phosphate bonds will be broken the energy and the electrons in those bonds is going to be donated to this hydroxyl group which will then form that phosphodiester linkage further extending that sugar phosphate backbone here you can see the two phosphates given off ultimately creating that new phosphodiester linkage and the hydrogen bonds then will attract and hold together the two opposite strands all right so we can continue this process all the way through so next we have guanine so guanine is going to pair with cytosine so we bring in another nucleoside triphosphate remove the two phosphates all of that energy goes into binding with the hydroxyl from the three prime end and then hydrogen bonds will attract the two complementary base pairs to one another all right and then we can continue all the way along so what i'm wanting to show you is here we've just added this whole sequence here is to add one single nucleotide to the sequence and building this up we're going to look at a much more simplified diagram to be able to go through all of the different enzymes that are responsible for doing all of this work okay but this will okay but we will revisit this to again ensure that you understand when you are when we talk about breaking the sugar fat to ensure that you understand when we talk about you know breaking the sugar phosphate backbone while we be cleaving one of those phosphodiester linkages or when we're unzipping these two strands breaking the hydrogen bonds we're breaking these bonds which are attracting opposite strands to one another so we are going from here to here so let's take a look we're looking at in this example here a template strand this is one of the parents okay here's the three prime end here's the five prime of that parent strand there's the template three prime running to five prime if we continued all the way to the end of the molecule here's the other template running five prime to three prime now in order for dna replication to take place we first off have an enzyme known as helicase and helicase is going to be responsible for unzipping the two strands okay and so what is holding these two parent strands together it's going to be the hydrogen bonds that exist between the adjacent nitrogenous bases between those complementary base pairs so helicase is going to unzip in some direction helicase is going to create what is known as a replication fork previously when we looked at prokaryotic dna replication we saw there was one point of origin but there would be two replication forks where you would have helicase unzipping in two directions around the circular chromosome in the eukaryotic cells because we have linear dna we'll have some point of origin and helicase is going to be then unzipping or unwinding the two strands of dna and that creates this replication fork helicase is going to dictate the overall direction of replication so in this case we are moving left to right and so because we are creating this replication fork here moving left to right these are going to be the ends of the dna that are going to be first replicated and so we can see here that the parent strand in this case because we're unzipping left to right the parent strand at the top is running 3 prime to 5 prime and the parent strand at the bottom is running five prime to three prime so remember what i said your dna is always going to be replicated from the parent strand running from the three prime to the five prime direction and so ultimately here the direction of replication for this top strand is going to be from left to right right it's always going to be from the parents 3 prime to 5 prime and then here because this parent strand is running left to right five prime to three prime we need to find this three prime n somewhere here in the replication fork and then our replication is going to take place in a retrograde fashion moving from the parents three prime to five prime now when helicase is unzipping the dna we are now left with very unstable single strands of dna all of the nucleotides here they're all going to be attracted to one another within the strand and that can cause what's known as super coiling and so to prevent super coiling from taking place we have an enzyme known as topoisomerase and topoisomerase can actually make little snips in the sugar phosphate backbone of our dna molecules and single strand binding proteins can then help to stabilize the strand to prevent any kind of super coiling or folding over that might take place naturally all right so helicase unzips topoisomerase is going to be the enzyme that is going to help to ensure that this strand doesn't super coil so it can be replicated effectively now here at this point we have unzipped the dna the single stranding binding proteins are stabilizing both of these single strands and now we're ready to start to replicate so what do we need to do we need to lay down base pairs well unfortunately the enzyme dna polymerase 3 which is responsible for doing all of that laying down all of those new nucleotides it needs somewhere to attach to it needs a three prime hydroxyl group to attach to and in order to do that we need to have some sort of primer put down and we have another enzyme known as primase and primase is the enzyme that's responsible for laying down these rna primers so at the beginning of replication once the dna has been unzipped primase is going to lay down those rna primers and those rna primers are going to give us that three prime hydroxyl end so that dna polymerase 3 can do its job on continuing on with replication now remember rna primers they're made of rna there's going to be a difference here you're gonna have some uracil where you should have thymine so we're gonna have to take care of that eventually but for now if you understand primase is the second ions i'm working here that is going to lay down the primer before we can move forward all right and the key is that when we're replicating our dna the new strands are always going to be laid down in the five prime to three prime direction because remember they are running anti-parallel to the parent strand okay so if you're looking at the parent strand think 3 prime to 5 prime antiparallel to that for the new strand is going to be 5 prime to 3 prime and so you'll notice this top strand because we're running into the replication fork this is known as the leading strand because once this rna primer is laid down dna polymerase is going to be able to just continue moseying on about laying down those nucleotides as helicase unzips it can continue to lay down those nucleotides continuously and so we refer to the strand that is running three prime to five prime in the same direction of helicase that is known as the leading strand now conversely the strand that is running five to three prime in the direction of helicase that is known as the legging strand well because primase as well as dna polymerase three they are both gonna have to work in the opposite direction to how helicase is going to be unzipping our dna molecule so in this case here with the bottom strand we need to find the three prime of our parent so if we're looking at our five prime end we're going to need to move in this direction because on the parent strand we're only going to be able to go from three to five prime so the new nucleotides always have to be laid down five prime to three prime so we're running anti-parallel so this would be your three prime to five prime so primase in this case we'll lay down the primer again and then we'll move into looking at how dna polymerase proceeds so in this case here we had primase lay down the rna primer of our leading strand and then dna polymerase 3 was able to bind to that leading strand and proceed in the same direction as helicase that's why we define this as the leading strand because it's going to be continuous there will be no interruptions unfortunately though the other strand known as the lagging strand we have the rna primer is going to be laid down by primase in the opposite direction and then dna polymerase iii will also be continuing on in the opposite direction to helicase laying down the new nucleotides and still the five prime to three prime direction here's where you can have a true appreciation for what's happening here with the leading and lagging strands helicase continues to move along this dna molecule further unzipping it the leading strand will just continue to be laid down five prime to three prime following helicase there will be no interruptions but if you recall the original replication fork was located here previously that's where we laid down this rna primer then dna polymerase iii began to replicate in the reverse direction towards our point of origin now since helicases continue to unzip in this direction we had all of this new dna to replicate and so primase laid down another primer and then dna polymerase three created a new sequence from that primer in the five prime to three prime direction you can see here though in this lagging strand we end up with these fragments known as okazaki fragments and so not only are we going to have to remove the rna primer but we're also going to have to join these okazaki fragments together once replication has taken place all right so with the leading strand one continuous strand is being replicated whereas with the legging strand you're going to form these okazaki fragments as helicase continues to unzip in one direction and the rna primer and dna polymerase three will lay down in the opposite direction now recall all of these primers that have been laid down to start off the process of replication all of these primers are made of single stranded rna and so remember the differences that exist will have a different sugar and will have uracil in some cases that have been paired with adenines and so these rna primers need to be removed and they need to be replaced by new dna sequences and so we have another dna polymerase enzyme that's not listed in your textbook but it's known as dna polymerase 1 and dna polymerase 1 possesses what's known as exonuclease activity so you can see here we had a primer that originally existed here at this point dna polymerase one would have come in it would have removed the rna primer and replaced it with dna okay so with dna nucleotides once that has been completed remember there's going to be these fragments still that exist and so to bind the two okazaki fragrance together there is an enzyme known as dna ligase that comes in and glues together that sugar phosphate backbone and so all of these rna primers that you see existing here they're all going to need to be removed and then have new sequences placed on so in summary we have helicase which is the unwinding enzyme that's going to be unzipping your dna in one direction separating the hydrogen bonds from parent strands primase is going to lay down the rna primers which give a starting point and then dna polymerase 3 is going to be laying down the complementary nucleotides dna polymerase 1 is going to remove those rna primers and replace them with dna nucleotides and then dna ligase comes along and is going to be responsible for gluing together that sugar phosphate backbone and so ultimately what you're going to be left with are two identical copies of your original dna so before we looked at the s phase and we said here in this s phase we're replicating all of our dna well this is just a snapshot of what is taking place within our cells during this phase now recall as i mentioned before at the ends of all of our dna molecules we have those structures known as telomeres and those telomeres are those tta ggg repeated nucleotide sequences that are there they're non-coding and meant to protect the coding regions of our dna when our dna is finished replication you are going to have the first five prime end primer is going to be removed but there is going to be no three prime hydroxyl that the dna polymerase one is capable of binding to and so for example here on this dna molecule this primer here once it's removed there will be no way that the dna polymerase can bind to a three prime hydroxyl to be able to replace that primer and so the primer will be removed and we will be left with a little region here of single stranded dna and so every replication that takes place you're left with it's almost like split ends of our dna molecules with these leftover single stranded portions of our telomeres they are more subject to degeneration due to environmental conditions and so at the end of replication you're going to have the leading strand will have a primer here at the beginning and your legging strand will have a primer at the very end and both of those primers once removed each dna molecule is going to have that telomere at one end of it that is going to be single stranded so ultimately causing the telomere to shorten every replication and this is what causes our cells to have a specific lifespan right every single replication that takes place the telomeres shorten now there are specific cells in our body that have specific enzymes known as telomerase enzymes we have them in our stem cells which form into all of our somatic cells and our germ cells remember germ cells located in our testes and ovaries that give rise to the gametes these are essentially the immortal cells in our body right they have the capacity to divide throughout our entire lifetime and that's because of this telomerase enzyme now telomerase is capable of going in and replacing those rna primers at those ends of the telomeres and essentially then creating immortality of these specific cells and so you might be thinking hey if we have this enzyme in certain cells why don't we just give that enzyme to all cells well cancer cells also produce that enzyme and this is why cancer cells essentially become immortalized and the only way that they die is if our own immune cells attack them and kill them if we were to provide telomerase as essentially like a fountain of youth drug it would also then be further providing immortality to any cancer cell that develops in your body increasing the development of cancer all right so let's look at an example here together with strand will be the template for the leading strand during replication if the helicase enzyme moves from left to right this is a key concept to understand right now helicase can move in any direction we're looking at these strands running anti-parallel to one another helicase could move left to right or helicase could be unzipping and moving right to left and hopefully you can see here that's going to change which of these strands will be the leading strand and which will be the lagging strand so recall if you're wanting to identify the leading strand first off figure out where helicase is moving helicase is moving left to right so then what you want to do is from the left find out which parent strand has its three prime oriented to where you're starting from because you know the new strands are going to be laid down five to three and we need to pair that with the anti-parallel and so for this top strand here it's running five to three prime and if helicase is moving in this direction and we need to lay down our new material in 5 prime to 3 prime we have to then lay down in the opposite direction to where helicase is moving and so in this instance here this would become the legging strand so if we look at the bottom strand here running three prime to five prime in the same direction as helicase we know that we'll be then laying down our new strand in the five prime to three prime direction and so that would make the bottom strand the leading strand okay and that brings us to the end of looking at dna structure as well as how we replicate our dna so we're going to move into next week looking at how when we can take the temporary copy of our dna through transcription in order to eventually produce the proteins that we need so for this week if you have any questions please feel free to reach out send me a quick email i'll get back to you as soon as possible otherwise i look forward to seeing you all in tutorial take care