Module 5: The Cell Cycle and DNA

Hello, welcome to episode three of the HSC biology podcast to down the podcast We are going to be going through the inquiry question. How important is it for genetic material to be replicated exactly Looking at the processes of mitosis and myosis and then going through the Watson and Crick DNA model including nucleotide composition Pairing and bonding enjoy The probes spin to start to shape Comotids can this as the bumble breaks down. Yeah, I'm talking membrane Matter face romances need at the heart and a face romances up with a pie to the face forming your memory will start Why don't the stars make a mark side of canis is the cyclist who that's my side of plasmus foot up into my All right, so a bit of a different intro today, and that is because that is one of my favorite ways to teach students About the processes of mitosis and myosis. So this is from a YouTube by a guy named Julian Turner or XY cell life And I'll play that whole song at the end of this podcast, but it's just a Apparently a student project he had where he had to Make up some extra credit and so he made this rap and he's a Professor apparently passed him. I don't know how much truth to that there is but that's the story anyway. All right Well, let's get on with it. All right, so as always, it's important to address that inquiry question Which is how important is it for genetic material to be replicated exactly and the answer to that is it's very important But you need to understand the processes first So with the first point it says model the processes involved in cell replication including but not limited to myosis and myosis And then DNA replication using what's in a creek? Now before we understand the processes of mitosis and myosis we probably should go through the cell cycle first So mitosis is the end phase of the cell cycle and you can think about the cell cycle like Everything that your cell does all the time before it replicates and becomes a new cell and then this process goes on So it's all of the components not just the mitotic phase. It's the duplication phase So looking at the cell cycle you can imagine it like a loop and it just continuously goes around as we get new cells And the beginning phase of that loop is the G1 phase or the cell growth phase So here we get the cellular contents being Duplicated like the mitochondria or the ribosomes or the endoplasmic reticulum All the main components that make up your cell are being duplicated apart from the DNA and the chromosomes Okay, so the DNA isn't being replicated in the G1 phase the cell is just preparing everything It's getting bigger in preparation for the S phase which stands for synthesis And this is where the DNA is going to be replicated and we're going to go through the replication process in a minute But for now, let's just remember that this is the second phase of the cell cycle S or synthesis and the chromosomes are now being duplicated. We're making a copy of all of our DNA, okay? Now Now up next we have the G2 phase and so we've had G1 S now G2 and this is the phase where we do our proofreading or error checking and we have enzymes that analyze the new chromosomes that we have now duplicated and they have the ability to terminate the cycle if need be So this is where we have mutations and things that can go wrong And we do have ways to stop that from continuing through in our somatic cells Which is very important so we can stop this process So G1, S and G2 are all part of the cell cycle and then we have mitosis which is next Now G1, S and G2 are also called interface, okay? So when I go through the process of mitosis all of these things happened before mitosis started And these often take quite a bit longer than the mitosis process but they are different in every animal So bacteria sometimes don't have a G2 phase, they don't proof check. They actually want mutations They have a very high proportion of coding genes in their DNA and this is important because they mutate rather than have variability So depending on what you're going to get in the HSC Again, I can see this question being as stimulus where you're provided with a cell cycle of some sort And you're asked to analyze the details and keeping in mind This is the cell cycle for a human and the times and everything can change depending on the animal So just be aware that it's not always going to be these exact phases and to use the stimulus you're provided with All right, let's talk about the next part of the cell cycle which is mitosis And the way that I often teach mitosis is to remember the acronym PMAT PMAT And it's actually easier to chuck an eye on the front of that and have IPMAT Not the best acronym but it does help you remember and the eye remember We just went through starts for interface which includes G1, S and G2 So IPMAT is where we're going to start So with mitosis we have those four main phases which is pro-phase, meta-phase, Ana-phase and telephase and a few things happen that is different at each phase This is most likely and has been in the past a visual stimulus where you're asked to analyze aspects of this process so you really need to get a Process chart or a flow chart or a diagram that you're used to seeing that includes all of the things I'm about to talk about and if they don't you need to draw it on or annotate it somewhere so you understand All right, so during pro-phase the chromosomes condense So a lot of people see chromosomes and they think of that famous X shape But in fact your chromosomes are usually in a less condensed state They are usually found as chromatin which is still wrapped up DNA around these histones And it's semi-condense, but it's not fully condensed When we see those X patterns the familiar chromosome That's actually when it's completely condensed everything is folded up as tightly as it can go And that's where we actually find it a lot easier to take photographs of them And that's why when you hear the word chromosome you think of that X but in reality your chromosomes are actually sort of In long strings for most of the time in your cell while they are being duplicated Now when you have that that final X pattern you've got to remember that each side of that chromosome is called a chromatid And those chromatids are identical the one on the left and the one on the right are identical It means that all the alleles and all the genes on the left are the same as all the alleles and all the genes on the right And keeping in mind that you have one from mum and one from dad So you're going to have two chromosomes both of which have an identical chromatid So the reason we don't call them two separate chromosomes here is because they're joined by a centromere A point at which both chromosomes are connected And that's how we count chromosomes which is important to remember again when we go through the processes of mitosis and myosis Because the number of chromatids change and the number of chromosomes can change Okay, you've really got to get that in your head and work out Which ones are identical because quite often that comes up when we do crossing over in myosis So during pro phase those that chromatin that long stringy stuff starts to condense and we see the famous X pattern takes shape The nuclear pore the place where the Chromosomes exist inside that nucleus starts to break down So we start to see some gaps and some holes appearing usually on the diagram as drawn as the dotted line Now also during pro phase we will quite often see something called a centriol that is drawn And on a diagram you can think about it like a little asterix and there are two of them one at either end of the cell Which is important for the next phase now during the next phase which is metaphase those centriols Again at either end of the cell we'll start to grow these long tubules kind of like Pipes solid strings that are going to attach to the chromosomes and the chromosomes themselves are going to line up across the middle So metaphase middle one of the easier ones to remember One key feature about the middle and the way they line up here is that they line up in a single line Which is very important when I talk about myosis. I will talk about the fact about why that is different But in my toses remember they line up in a single line of chromosomes down the length of the cell And either end are those centriols which are putting out spindles or spindle fibers Which are going to pierce the chromosomes right on the centra mere that point the joins both chromatids together to form the chromosome that spindle fiber is going to pierce or grab onto each one of the chromatids Which brings us to the end of metaphase and starts the next phase which is anaphase Those spindle fibers which are attached to the centra mere are going to pull the chromosomes apart away from each other Towards the new cells that they're going to be made So anaphase A for away they're going to pull those chromosomes away From each other and you're about to have two new cells and during telephase which is the final phase here The chromosomes are going to be pulled to either end completely the spindle fibers will disappear a new nuclear membrane will begin to develop and the process of cytokinesis That final pinching of the cell to separate them will begin So going over the main parts of each phase we have pro phase chromosomes condensed we get that x-pattern the poor breaks down and at either end we have those little asterixes the centriols metaphase m for middle chromosomes line up along the middle the spindle fibers come out of those centriols and pierce the centra mere The middle of those chromosomes then we have anaphase A for away the chromosomes are pulled away from each other It's about to become two new cells and then telephase we have those spindles breaking down We have a new nuclear membrane forming around each cell and then finally we have cytokinesis Which is where the two new cells are pinched across the center and separated into two new identical cells Which is very important mytosis creates two new identical cells All right, we're just going to have a quick look at myosis now which is different to mytosis Myosis is the production of gametes or sex cells sperm eggs and the process is quite complex Now all of the things that occur during myosis comes up later in the syllabus So I am going to leave it for now But just for future reference I'm going to teach you the p-mat one and p-mat two process which is easy to remember All the names are the same but some of the phases where things happen are Slightly different well are significantly different and it will take a while to teach that so we're going to skip over Myosis for now but that will come up later in the podcast all right We're now going to go through the DNA model proposed by Watson and Crick Which includes a nucleotide composition pairing and bonding so quite a bit there Now the story behind Watson and Crick is a very interesting one and quite a sad one in fact If you guys want a really good summary of the backstory check out the secret of photo 51 which goes through The struggles that Rosalyn Franklin had as a female in science and all of her data was used to build this model But she wasn't recognized so it is a bit of a sad one But I think really important for this top point so please go and check that out All right now with the data that Watson and Crick collected They were trying to build a 3d model of the DNA molecule And most of you would have seen a DNA molecule by now in that double helix shape And so if you don't know the double helix shape it is hard for me to describe it to you You probably should just go look it up But that double helix shape was something that actually took quite a while for them to work out They had a triple helix they had bases on the outside They had a lot of mistakes until they got the data from photo 51 which was produced by Franklin So let's go through the structure of DNA that they proposed and all the different and intricate parts We're going to start with the backbone so these are the strings that run down the outside of that helix And then we're going to talk about the middle parts which are the main nucleotides and their composition and their pairing So the backbone is made up of phosphates and sugar molecules And the phosphate you can imagine like a little circle is joined on to a pentagon which is quite often how we draw the sugar And that is a repeating pattern so you can just remember that it is phosphate, sugar, phosphate, sugar, phosphate, sugar And that runs the length of both sides of that backbone The sugar is deoxyribose which is where the name deoxyriboneucleic acid gets part of its name from And these are nucleic acids which is where the remaining part comes from So those phosphates and sugars are bound together and they're in a repetitive pattern over and over again But attached to those sugars so those pentagons we have the bases And there are four main bases and it's amazing to think that our entire Makeup is based on these four particular bases not no pun intended And those are the letters represented by ATG and C which stands for adenine, thymine, guineine and cytosine And each of those can be rearranged in a particular way So with the nucleotide composition which is part of that dot point A nucleotide is one of those phosphates, one of those sugars and one of the bases ATG or C And those three components make up a single nucleotide Now they can be some differences between those bases Some are what we call purines and pyrimidines But for the most part you don't need to know that Just remember that a nucleotide is one phosphate, one sugar connected to one of the bases So with the base pairing rules you need to remember that A always pairs with T A always pairs with T and G always pairs with C Okay, so ATG, C remember that ATG, C, A goes with T, G goes with C Now finally the last point here is bonding And once again this is where it gets a little confusing and you need a diagram Okay, so A and T as we've said bond together, A goes with T, G goes with C In your DNA that is infinite that goes on for every letter and they just rearrange in different combinations A and T are bonded by two hydrogen bonds, two connecting hydrogen weak bonds that bond them together Okay, it combines them, it keeps them close to each other in this weak form Which can be separated, so they have two bonds Now C and G, which go together, have three hydrogen bonds, a triple bond And again it's a weak bond, but C and G have three, A and T have two So it's a good way to remember it, okay, C and G, three, A and T, two So the T for two, it's a nice way to remember the hydrogen bonding rule Okay, so just to reiterate one more time With the nucleotide composition, we have the phosphate, sugar and base The three components that make up a nucleotide The pairing rules, the pairing rules are that A goes with T And G goes with C, they match up all the time when we build a DNA A always goes with T, G always goes with C And then finally we have the bonding rules, okay So remember that C and G have three, three bonds, hydrogen bonds, A and T have two, okay And that is the basic structure of DNA That Watson and Crick proposed Now as they finish their model, they realize that DNA had an amazing way to copy And this is where we're going to talk about DNA replication Before we spoke about the cell cycle and I said that S or synthesis is where we duplicate I'm now going to go through that process DNA replication is making two identical new strands of DNA based on the first one It can be called semi-conservative DNA replication Because one of the strands is always going to be reused, it's going to be an older strand So it's semi-conservative, we're conserving one and we're making a new one Okay, so that's the idea here Now the process involves many enzymes and lots of different parts So once again, I suggest you get a diagram for this one And follow along as I'm speaking, it's much easier to understand Okay So with DNA replication, we need to make two new ones But we need to separate those bonds first We just spoke about the hydrogen bonds We need to now separate them and we do that by unzipping the DNA strand And this is done using an enzyme called helicase Helicase runs down the length of the DNA unzipping it And this can happen at any point along the DNA Not just from the start to the end, there are lots of helicases And there are lots of parts of the DNA that are being replicated at the same time It would be inefficient to do the entire length from start to finish So when helicase begins to unzip that DNA strand Two enzymes called DNA polymerase attach to either end of the unzipping strands We call one of those strands the leading strand And we call one of them the lagging strand We call them this because the leading strand gets copied over and over again in a repetitive fashion This is because DNA polymerase can only work in one direction You know you're beautiful, oh, oh That's what makes you beautiful Sorry about that It can only go from what we call the five prime to the three prime end But don't worry too much about that right now Just imagine that it goes from one direction towards the other But it can't go in reverse, it can't do it in the opposite way But logically if you think about it, the DNA is opposites They are complementary to each other So on the other strand, the lagging strand Things are going to be copied in small fragments Because it needs to move again in one direction But because it's going coming out the other way It has to do it in these chunks which we call okazaki fragments So I imagine that the enzyme DNA polymerase Is attaching to small sections Then moving off the strand Then moving to another section And copying a little bit again And it keeps doing it over and over again Until we get a number of fragments together Then we have a process of the little bits and pieces in between Being removed and the whole DNA strand gets smoothed over by a DNA ligase Ok, so those fragments need to be built in chunks But that's going to leave small gaps everywhere And that's a problem with DNA And so it gets reconnected by this DNA ligase Ok, so just to reiterate The DNA is unzipped by helicase Helicase separates them into what we call a replication fork Where they're going out in leading and lagging strands Then it looks a bit like a fork The leading strand is copied one after another Bases are attached one after another So A matches with T and G matches with C And on the opposing strand, the lagging strand It is copied in small chunks called okazaki fragments Ok, once the okazaki fragments have been built They are then smoothed over by a DNA ligase Now while this process is happening, as I said, it happens at all different points along the chain There are three nucleotides floating around Waiting to join to the new strands that are being built So nucleotides exist around those DNA polymerase molecules They are drawn in and they are attached They are bonded together using those hydrogen bonds we've spoke about before Ok, so A and T have two, G and C have three, C and G have three And those bonds then are connected together Until it is the whole length of the DNA is joined And we have two new complementary strands And that is the end of the S phase synthesis in the cell cycle So once S phase is ended, we have copied our DNA We are ready for the next phase and then for mytosis So that's DNA replication and there are some other bits you can talk about here So if you want to go into more detail, you can look at something like RNA primase Which preps the DNA for replication You can look at exonuclease, which takes out that RNA And the alternate DNA polymerase, which adds the remaining bits and pieces So there is quite a bit more to this if you want to go into it Just make sure you're looking at a diagram that has all of those components But for the most part, that is the process, which is what they're probably going to test Alright, and just to finish off today, I want to go through the difference between DNA chromosomes, genes and alleles, so a new word today So DNA is what we just spoke about, deoxypribonucleic acid And it is made up of that sugar phosphate backbone With nucleotide pairing and bonding rules That structure we've just spoken about Now when that condenses, when that turns into a form where it gets all wrapped up, it becomes a chromosome And so that DNA, if you imagine it like a piece of string It wraps around these proteins called histones And you can think of them like little yoyos And it wraps around one and then it wraps around another and then it wraps around another And those yoyos, those histones, all start to join together They get very close to each other, so this is that condensing And when enough of them condense, we get chromatin So this is the material I was talking about before DNA wrapped around histones, all bunched up together, make chromatin So it's still not super condensed yet Once those coils start to loop around each other, those coils loop and loop and loop We then get the famous chromosome X shape So there's lots of condensing going on And your string of DNA is wrapped up very tightly in the end In those chromosome structures Now you have to remember that you get half a set of chromosomes from mum And half a set of chromosomes from dad, giving you a full set of 46 chromosomes 23 pairs Now because you get pairs from mum and dad, they both code for similar things So if we take chromosome one, for example And chromosome one is the longest, which is why we call it chromosome one And all the way down to 22 is the shortest And then we have the XX or XY chromosomes that we'll talk about a bit later Which define males and females So with our chromosome one, our longest chromosome If we look at a specific section on mum and dad's chromosomes We see that on those chromosomes they have similar regions And those regions are called genes So I'm going to use hair color for example today If we look at the very top of each of those chromosomes, one from mum and one from dad They're going to have the same region for hair color on that chromosome So let's just say the top of chromosome one is full hair color And both mum and dad obviously have a hair color And you're going to get a hair color as well But which hair color you get will be defined by what individual genes they give you So the top section of each chromosome, those gene regions are called genes Or those regions are called genes But because each of them can be different Mum may have blonde hair, dad may have brown hair Those alternate genes are called alleles Alleles are alternate forms of a gene So you have a chromosome from mum and dad The top of each of those chromosomes, codes for hair color, they're the genes But each of those genes can be slightly different Because one may be for brown hair and one may be for blonde hair And when we go into further details later in the syllabus We learn about which hair color you're most likely to have Based on certain rules, dominance and recessive Code dominance, incomplete dominance And a couple others that we can mention a bit later But if you just remember that genes are regions on the chromosomes Which code for the same thing And the alternate forms of those genes are alleles And they can be different, different forms of the gene That will help you to understand a lot throughout the syllabus Okay guys, I hope that was helpful today And you've learned something As I said before, I'm going to play the entire Julian Turner X Y Cell Life song So enjoy It's always the only track The DNA starts with a line The irony is the other side My oceans is the kid of making lines My tosses can't be sizzle about to die If my genes go left unread All my cells are dead If my genes go left unread All my DNA Preferred mic tosses happens in the interface Then we move the probe base Spindle start to shape Cometis can diss As the bubble breaks down Yeah, I'm talking membrane Matter face chromatis need at the heart And a face chromatis are put apart See the face Roman your memory will start While this starts the kids make a mark Side of the kinesis is the cyclist Through that's my side of Plasma's foot up in two My oceans is a lie You said they had this twice And chromatis is a splice Please remember the differences Keep my tosses make some sense The sounds I make above the knees Have moved my six organs They have my sense they have me Yeah, the DNA starts to unwind The RNA reads the other side My oceans is the key to making lies My tosses copy cells are about to die All my cells are dead If my genes go left unread All my cells are dead Yeah, if my genes go left unread All my cells are dead All my cells are dead A pop tosses make sure I don't spread Mutations are results of Jesus' rad Transcription RNA polymerase Initiates elongates the terminate Translate ribosonal units Leave me a meal, I'll ask you just to do it Chroma's all made of genes Plays the colors of our eyes and gives us a will of speed Go, my oceans gives us variations So we're different people My tosses helps us grow and replace us When they get evil She said, I don't know, I don't know How the cells divide and help you grow The DNA starts to unwind The RNA reads the other side My oceans is the key to making lies My tosses copy cells are about to die If my genes go left unread All my cells are dead If my genes go left unread