DIP Episode 57 - Cell Biology Review For The USMLE Step 1 (Part 2)

Okay, welcome. My name is Divine, a PGOI-Wanda Transitional Year resident. This is the 57th episode of the Divine Intervention Podcasts. And in today's episode, we're talking, we're going to continue reviewing our cell biology as relevant to the USML step one. And again, so here we say, oh, Divine, this is low yield. It's not very important for my test. The thing is, if you go through like an entire USML exam, there will probably be like 10 cell biology questions, right? So the thing is, it can hurt you like, I mean, 10 out of what, 280 questions, probably not a huge deal, right? But let's assume your person that's shooting for the very high 260s, 270s, blah, blah, blah. Each question begins to matter a lot, right? And then on the second hand, if you're the person that's not doing so well, score wise, then each question also kind of matters a lot, right? 10 questions, maybe the difference between you scoring below the USML step one average and scoring above that average, right? So again, every point kind of matters. So this is something where I think if you're just putting the time, you can learn it pretty well. These podcasts, I'll imagine that for cell biology, probably shouldn't come out to more than two, two and a half hours at the most, but I think it's something that's pretty high yield. I can help you a lot on your test, right? And the thing is, again, that's what I kind of value with my approach to these podcasts.

I'm not just giving you just like, oh, just teaching you cell biology. No, as you can tell from the other podcasts I've given and from even the first one, I try to integrate a lot of stuff. Like I basically try to answer the question, how they likely test this concept, right? And again, you'll see that in this podcast. So today we're largely going to talk about DNA and how it's made, okay? But again, as we go along, I'll integrate all the higher pieces of information, right? So I guess first thing is and actually one last thing I'll say is that many times cell biology questions, they are like straight recall questions of their place as experimental questions, right? We give you like this weird genetic experiment and then you're supposed to deduce an answer to certain questions, right? So again, I will try to my plan as I go through these podcasts to sort of highlight like, oh, these are ways they could test these are genetics are concepts. So let's begin, right? So if you want to make DNA, right? Obviously, like we said in the first podcast, that process is known as replication, right? And just like we did in the first podcast, right? There is a weird replication. I mean, there are two big kinds of organisms, right? There's like porcaria and then there's us, eukaryotes, right? And you want to sort of want to be able to differentiate between those two spheres of life and how things sort of going those areas, right?

So if you're talking about porcaria and eukaryotes and you're like, oh, in terms of how we make DNA, which is called replication, there's some similarities. Well, there are, right? In porcaria, it's as well as eukaryotes, DNA replication is semi-conservative, right? So let's say you're studying with a mother cell that has like two strands, right? The thing is those two strands are kind of broken apart, right? And then you make one new strand that maries one of the old strands and then another new strand that maries the other old strand. And then the daughter cell has one new strand, so like one from dad and then the new strand you meet and then one from mom and the new strand you meet, right? So that's why it's known as a as a semi-conservative process. And then in DNA replication is a bidirectional process. You'll see this as we go along in this podcast, but basically when you have like a replication fork, it sort of goes in both directions, okay? So it's a bidirectional process. But if you kind of wanted to tease this a little, tease this a part so much, okay? What's true for porcaria? What's specific to eukaryotes, right? In porcaria, it's right, the DNA is circular, right? That's something you probably learned in medical and probably in college as well versus eukaryotes that have like linear DNA, okay?

And the thing is because porcaria has much smaller genomes and they have circular DNA, they have one origin of replication, origin of replication just means where replication starts. Contrast our eukaryotes that have multiple origins of replication. And again, ask yourself, why does this make any sense? The thing is, the eukaryotic genome is huge, right? And if it's that huge, you don't want to spend forever, you don't want to literally spend your entire life on this earth making DNA, right? So it probably makes sense, it should have like multiple spots where the DNA replication happens so that a lot can happen all at the same time, so that you don't spend forever replicating your genome. And then I guess one thing I'll just mention here, this is kind of just USMLE trivia. Each chromosome has like a P and a Q arm, the P arm is like the short arm, so probably remember that the Q arm is the long arm. Just remember P for like a teeth, right? And then Q is the letter that comes after that. Okay, so those are kind of like the big, big, big things that happen with our replication and replication. You make two new strands of DNA, old strand, new strand, old strand, new strand, that each old strand, new strand pair is known as a sister chromatid, right? So it's like, you start with two old strands, mom and dad. And then you make two new strands, right? Those two new strands brings the total number of strands you have to four.

Mom's chromosome pairs with a new strand that's made, that's chromosome pairs with another new strand that's made. Each mom, each parent new strand pair is known as a sister chromatid. Those individual sister chromatids at the end of replication are held together by something known as a central mirror. It so happens that in mitosis, right? At the same from here, you separate those sister chromatid pairs and you then basically have two daughter cells that contain like, oh, moms, genome and the new genome that you made in replication. And then that's genome and the new genome that was made in replication. Those are kind of like weird terms, the subtle confuse medical students, so just make sure that something, you kind of have a lot down at the back of your mind. And then one quick thing I'll just mention relates to telomeres, right? So the thinnest telomeres, I mean, they're part of the genome, they're part of DNA, they're nonencoding, okay? And the thinnest as a cell keeps dividing the length of the telomeres begin to reduce, okay? They begin to reduce. In fact, they could very easily make this an experimental question on step one. They could give you like two DNA sequences, right? From two different cells. They can say, oh, there's DNA sequences from cell A, there's DNA sequences from cell B, right? And then they point out the region that contains the telomeres. And then you see that cell A has like a telomere base per length of like 30.

And cell B has a telomere base per length of like 60, right? And then they could easily ask you like, oh, which of the following, and let's assume you have from the same cell line, right? And then they could say, oh, which of the following cells is like older or younger, right? Obviously, the cell that is older will have a shorter telomere length. Or another one way they could test this is, they could say, between these two cell types, which one is more susceptible to hipoptosis. The cell that will be more susceptible to hipoptosis will be the one with a shorter telomere length because that's indicative of a cell that has lived for a longer period of time, right? And another way they could test this, right? Because if you think about it, there are certain cells in your body that you don't want to like die off at some point, right? I mean, think of it like your germ cells. You want your germ cells to, because they are germ cells, right? They basically create many cell lines for you. You don't want them to die, right? If my beginning to get into troubles like a plastic anemia, blah, blah, blah. So you don't want that to happen. So these are those germ cells. They express very high levels of the enzyme telomeres. They express high levels of telomeres. Your telomere length basically will not reduce, okay? So that those germ cells can persist throughout life. But that's a good thing. But as you know, as with every good thing, there is usually a bad counterpart.

Cancer cells, right? They are mainly cancer cells that actually overexpress telomeres. And by overexpressing telomeres, those cancer cells, they begin to live for longer than they should. That's why cancer cells generally don't die, okay? At least that's one mechanism behind that. Again, very high to know that those are some nifty ways they could test that telomere concept. So let's sort of jump into replication, which is again, how DNA is made. But the thing is, before I think one thing that helps is to be able to differentiate between replication and transcription. My replication is making DNA from DNA. Transcription is making RNA from DNA, right? So again, there are certain commonalities between both processes, right? Basically, the product of each of those processes is a slander that is complementary, a strand, sorry, that is complementary to the strand you're reading from, okay? But that strand is anti-parallel, okay? And again, again, so again, complementary strand anti-parallel to the parent strand. And the thing is the enzyme, the generic name you can use for the enzymes that do replication and do transcription. You can call them polymerases. But in transcription, we call them RNA polymerases. In replication, we call them DNA polymerases, right? And the thing is, the template, the strand that acts as the template for the synthesis of these products, right? Those strands are always, and again, this is mega high to know. And you'll see why as we go along.

These strands, okay, the template strands are always read in a three-prime to five-prime direction, okay? Contrast that with the products that is made in a five-prime to three-prime direction. Again, read by the polymerase in a three-prime five-prime direction synthesized by the polymerase in a five-prime to three-prime direction, okay? So those are the commonalities between both. But now, if you begin to move into the RNA of differences, first things first, if you're replicating DNA, right? The thing is you need someone to say, I sort of think of it this way. Let's assume you're kind of like your polymerase. Polymerase is like, I don't know where to start. If you want to get polymerase going, you need something known as a primer, okay? And a primer, remember, it's made of RNA. That primer is read by an enzyme known as primase, okay? It's made by an enzyme known as primase. And then, after primase lays down the primer, the DNA polymerase has a three-three-prime end that it can sort of extend off of to make the new complementary daughter DNA strand. And again, how can they test this on an exam? They can very easily test this on an exam, but essentially showing you like a DNA strand, and then you see a U in the DNA. And then they can basically like highlight that section of DNA and say, which of the following best describes the sequence of DNA, right? They can give you like some DNA sounding answers, and then they can give you primer as an answer, right?

Again, remember that primer is made of RNA. So it should make sense that they should potentially continue yourself, right? Again, very high yield to know that. Again, these are ways where they take simple concepts and just test it in unusual ways. And if you're contrasting that with, so you primase lays down the primer and then DNA polymerase comes and does its job, it adds like nucleotide, right? With three-fourths feeds. The thing is, in those processes, you get rid of two-fourths feed, you get rid of a pyrophosphate group, and then you basically make the first four, the first four-dice-turbant. Contrast that with transcription, right? Where you do not need a primer, okay? RNA polymer is just steps in and just does its job, right? And then another key difference is, let me say something real quick, let's sort of do a reason experiment here. Think about it. I just said that the template strand is ready in a three-prime to five-prime direction. And then I said that the daughter strand is synthesized in a five-prime to three-prime direction. Walk with me here for a second. Let's assume, as you're synthesizing that daughter strand in the five-prime to three-prime direction, you make a mistake, right? If you make a mistake, it makes sense that DNA has to go back and fix that mistake. That process is known as proof reading. I'll talk about that in a bit. But why do I say that?

The thing is, if you know that, you are synthesizing something in a five-prime to three-prime direction. If you want to fix a mistake you made along the way, you want to go back in the reverse direction, which will be the three-prime to five-prime direction. So, it should then make sense that DNA polymerase, right? And you'll see the specific polymerases as we go along. But it should make sense that DNA polymerase, right? Should have something known as a three-prime to five-prime, exonuclease activities. God, an exonuclease because it's starting from the very end of the DNA strand, okay? So three-prime to five-prime exonuclease activity. And again, you don't have to memorize that if you just understand, it just makes perfect sense, right? Contrast this with transcription and transcription. RNA polymerase, in general, actually does not have any kind of proof reading activity, okay? In fact, RNA polymerase is a lot more error prone than DNA polymerase. I'm like, hmm, do I? Why does this make any sense? Think about it. If you're making DNA, right, you're going to pass that onto daughter cells. You better not screw that process up. So, it should make sense that DNA polymerase has proof reading activity. But there are any polymerase. I mean, RNA, how many? RN As have very short half-lives. They're destroyed and you can just make a brand new one, right? I sort of think of it as like when a country is going through inflation, they just print a ton of money.

If you're like, oh, you lose the money, just print new ones, right? Same thing here. If you lose your RNA, just make brand new ones, right? RN As don't leave long, right? They're kind of like left-fast, die-young kind of business, right? So, it doesn't, you don't need to be like super, super-particular about how nice your RNA looks, okay? So, again, very, very high yield to know these differences. So, now that we understand these things, let us jump into how replication happens. So, let's talk about the steps in replication. So, the first step is obviously DNA is a double strength, right? So, you want to wind that DNA, right? You want that DNA, remember DNA, right? Remember, 82 GC3, as per the first podcast, you have hydrogen bonds between the purines and pyramidines, right? So, you want to cleave those hydrogen bonds first to separate those two DNA strands. That's done by an enzyme known as helicase, okay? Done by an enzyme known as helicase. And the thing is, as helicase is actually on winding those DNA strands, the thing is those DNA strands, they love themselves so much, right? They're like couples that have been married for many years on end, right? So, they don't want to separate, right? So, the thing you'll try to do is we try to keep those things apart by having enzymes that bind to those singular DNA strands. Those enzymes, I guess you could call them proteins, are known as single stranded because they bind to single strands of DNA.

They're known as single stranded binding proteins, okay? Again, they prevent those separated strands from reaniline. And the thing is actually, if you start seeing single stranded DNA in a cell, that's actually like a trigger, usually for the cell to die or for that DNA to be degraded. So, actually, those single stranded binding proteins can serve as protecting groups for the single stranded pieces of DNA so that they're not destroyed. But, another thing, kind of think about it, right? If you think of your DNA as a double strand, you're winding it, think of unwinding two ropes, right? Yes, you are creating space in the region that you're winding, but the regions that have not been on wound, right? You begin to create tension in those regions. That tension is known as a super coil, okay? And it so happens that there is a fancy enzyme known as taupe isomerase that actually helps a lot with removing those super coils and sort of taking care of that tension. And I mean, if there are taupe isomerase in procaria, it should probably make sense that there should be taupe isomerase in eukaryotes as well. So, why am I making all this fuss about taupe isomerase? Tope isomerase is super high-yield for the USML Ds, right? Because there are many thines both from ecology and pathology that it could bring with respect to this concept on an exam, right?

So, think about, for example, a patient that has a cystic fibrosis, in cystic fibrosis, you sort of think of, oh, before 20, the most common cause of pneumonia in that population is staphoreus, but after 20, the most common cause of pneumonia in that population is pseudomonas. The thing is, pseudomonas can be treated with fluoroquino loans, right? Your fluoroquino loans, right? So, like, like siper floxasin, livo floxasin, moxifloxasin, right? Those drugs all cover pseudomonas, right? So, because they all cover pseudomonas, the way they actually work is that they work by inhibiting bacterial, or you can see prokaryotic taupe isomerase. Another mission example for prokaryotic taupe isomerase is adenigirase, okay? So, those bacterial taupe isomerase can be inhibited by your fluoroquino loans, okay? And so, to think of that in the context of a pseudomonas coverage, if you're looking at eukaryotic taupe isomerase, right? If you want to prevent eukaryotic cells from you divided, see for example, in a patient that has cancer, you may want to use a eukaryotic taupe isomerase inhibitor, right? Like, you can give like a taupe isomerase one inhibitor, like irinotica, right? Or you can give a taupe isomerase two inhibitor, like taupe, sorry, like atopocyte. And an easy way to remember that I think I've talked about this in a previous podcast, irinotica, think of it as one rinotica to help you remember that in inhibits topo one.

And then remember atopocyte, it's sounding like e2-poocyte to help you remember that it inhibits topo two, okay? And then if you also remember scleroderma, right? Remember, there is like a limited scleroderma and there is a diffuse scleroderma. In libides scleroderma, right? The auto-antibodies, which you should know for step one and step two and three actually, and known as the anti-sensory antibody, right? In crest scleroderma. Contrast that with the diffuse scleroderma that's actually the anti-bodies against topoisomerase, okay? So that's kind of like another high-yoda factor to remember there. And then after, right? So we said that you won the DNA with helicase, you prevent them from reanilling with the single stranded binding proteins, you relieve the super cause with topoisomerase. The next thing you do is again, we said the DNA polymerase, as I said a few minutes ago, DNA polymerase cannot just start, right? It kind of needs a primer. And that primer again is made of RNA and that primer is made by something known as primates, right? That's a very imaginative name. So the thing is after you lay down the primer, the DNA polymerase begins to synthesize the strands, okay? But again, because there are two templates, right? It then stands to reason that you should make two-doters strands, okay? And basically getting into the realm of something that is occasionally confusing for a met students, but hopefully, in fact, I have a diagram in the slides that I attached.

Hopefully this clears it up for you, nicely, right? So the two-doters strands, one is known as the leading strand, the other one is known as the lagging strand, okay? And again, I will sort of summarize them. I'll explain them two ways so that you like really get this down, right? But there are key differences you want to realize between the leading and the lagging strand. The leading strand is synthesized continuously. There are no breaks, okay? The leading strand actually synthesized in the same direction as the replication fork, so it goes into the replication fork, okay? Versus the lagging strand that's actually synthesized that discontinuously, it's actually made in little fragments, those are known as okazaki fragments. Well, imagine that's a Japanese name. And then it's actually synthesized, these lagging strands are synthesized away from the replication fork, okay? So let's sort of jump to the diagram. I think that was sort of like clear things of free. So you can see the four strands, right? Well, let's start from the top, okay? Let's start from the top. So if you look at the top here, I talk about template one, dot, or one, template two, dot, or two, right? So template one, if you notice, if you look at the left side of the image, you can see the direction of the replication fork is going to the left of the image, okay?

So think about it, I said that DNA polymerase reads the template in the 3.25 prime direction, but it synthesizes the new strand in the 5 prime to 3 prime direction. So if you look at template one, if you notice, if you're going in the direction of the replication fork, where you can see that the template I wrote it down in the 3 prime to 5 prime direction. But the daughter, like I said a few seconds ago, is made in the 5 prime to 3 prime direction. Flows nicely with the replication fork, no problem, no problem, okay? But contrast of template two, template two is the other strand, right? That other strand, that other parent strand, right? Because again, remember DNA on its own, before you won't study any replication is double-stranded antipyral, right? So the other strand is in the 3 prime to 5 prime direction away from the replication fork, okay? So because it's in the other direction, right? And we need to agree with our mantra that all, we're synthesizing the new strand in the 5 prime to 3 prime direction. We basically synthesize distal from the from the replication fork. And then if you open the fork some more, you then make a new DNA strand. You open the replication fork some more, you then make a new DNA strand, okay? And for each of these things that you do, you basically keep adding primers, right? Because you're essentially looking for new, you're essentially trying to get DNA to make like new, DNA polymerase to make like new little, little strands.

And those little strands are known as ocasaki fragments, okay? So again, hopefully this, this diagram sort of clears it up for you. But this is something you definitely need to know. This is easily something they can put a picture on your USM Ls and then you have to deduce which is the leading strand, which is the lagging strand, and key differences between those two, okay? So again, very, very high yield to know this. So let's continue, right? So you leave the tools, you make the two strands, leading lagging blah, blah, blah. And again, I said this is done by DNA polymerase, okay? Key thing you want to know here is that in Prokaryot, the DNA polymerase, you probably want to remember is like DNA polymerase three, okay? It's the big guy that sort of makes the does all the replication. And then in Eukaryot, you want to remember Bosworth's like DNA polymerase alpha and delta, okay? Those are the things that sort of do the whole process of replication in Eukaryot. And then if you sort of think about this, right? So the leading strand, it has no issues, right? But the lagging strand, and I guess the leading strand to an X-thin, right? The leading strand will have like one primer, right? The lagging strand will have like multiple primers. The thing is you want to be able to sort of get rid of those primers, right? Because again, you don't want the DNA you make to include RNA, right? So, RNA is each in Eukaryot actually comes and removes the primers, okay?

Contrast that with Prokaryot, that actually have DNA polymerase one, DNA polymerase one actually removes the primers in, I mean, what do I want to say? Sorry, I give most of these lectures from memory. Yeah, DNA polymerase one removes the primers in Prokaryot's, okay? Versus RNA is each, the removes the primers in Eukaryot's, okay? RNA is each, so you basically, after RNA is each removes the primers, there's like some weird stuff that comes and puts in the new DNA, and then DNA like it sort of joins those of Okazaki fragments and everything together. In Prokaryot's, I said DNA polymerase one removes the primers, DNA polymerase one is also the DNA polymerase actually that comes in and fills in those spaces that are taken away by, that we're initially filled by the primers, and then DNA polymerase one, so again, DNA polymerase one, sorry, I know I'm kind of confusing myself here, DNA polymerase one removes the primers, and then in addition, it also lays down the new, the new DNA in place of the space that was taken away by the primers. Contrast that with Eukaryot's, RNA is each removes the primers, but RNA is each is actually not what puts in the new stuff, the thing that puts in the new stuff is not very high yield to know for step one. Okay, and then again, DNA like this comes and joins up the fragments together, okay?

So, when I was sort of talking about the differences between transcription and replication, I said that in the process of replication, you can make mistakes on the way, as you're synthesizing the DNA in the 5-prim to 3-prim direction, I said you could fix those mistakes, but it's not going backwards in reverse, right? 3-prim to 5-prim direction, no issue. So that means that DNA polymerase should have like something known as a 3-prim to 5-prim exonuclease activity, right? But the thing is that kind of repair is occurring in the S phase, right? While you actually actively synthesizing the new DNA strand, the thing is there are other kinds of repair that happen in different phases of the cell cycle, right? So let's say after you've made the new DNA strand, that's in the S phase, you go to the G2 phase, right? There are other kinds of repair that happen in the G2 phase, and I'll talk about those as we go along. And just as a quick throwback from what we did before, what's that cancer drug that works in the G2 phase of the cell cycle? Well, I hope you're telling me about Brio-Maisin, right? That drug that has a polymerase fibrosis as a side effect. And the thing is these DNA repair things that I'm going to talk about now, right? I mean, if you have mutations in these processes, you can have lots and lots and lots of diseases. In fact, I'll sort of talk about these diseases we've got, right? So let's talk about one repair mechanism, right? Common one.

You've probably seen this on many examples, uh, relates to thining, thining, dimers, right? So let's say you, um, you, uh, step out in the sun, right? The thing is UV radiation, right? Loves to make thymidine dimers, okay? And just real quick, I just want to go ahead and see this, that this thymidine dimers actually finds on the same like single strand of DNA, right? Many people think, oh, it's on double strands, it's actually not. They actually on single strands. So it's kind of high up to know that, okay? So the thing is these thymidine dimers, they're obviously not good because they cause kinks in the DNA structure. So, uh, so these dimer situation is fixed by certain like endonucleases, right? Because it's like the thymidine, thymidine dimers, you can't see that all of your form that the end of DNA because remember, something is, if a problem is at the end of DNA, it makes sense that an exonuclease should fix that problem. But if some, if a problem is inside DNA itself, like in the middle of DNA, somewhere not at the ends, you want to use something that can go in the middle and cut out stuff and endonuclease to fix those problems, right? In fact, you can call those like excision endonucleases. Those excision endonucleases may fix those thymidine dimers. So the thing is if you have mutations in those excision endonucleases, you actually have a disease known as a Xero-dermapigmentosum, okay?

Xp for short, Xero-dermapigmentosum, those people basically don't step out into the sun because the uviradiation causes all these thymidine dimers. Well, they have mutations in the proteins that help them fix those problems, right? So, they get like recurrent skin cancers, they can get like corneal ulcers, they have like freckling of the skin and all that stuff. So those are kind of high yield things you want to remember there. And really this thymidine dimer issue usually occurs like in like regular cells, right? So, it will potentially occur mostly in the G0 G1 phase of the cell cycle. And then the next one, right, is the one I kind of alluded to is like, oh, let's say you've synthesized the DNA, right? DNA synthesis happens in the S phase, you do like a proofreading in that process, no issue, right? With a 3 prime 5 prime Xonu-please activity of DNA polymerase. But the thing is in the G2 phase, after you've gone through DNA synthesis, the thing is DNA polymerase is not perfect. It's not perfect in its proofreading capabilities, right? So the thing that could happen is that your body sort of has like an added layer of protection to sort of fix any errors that may arise. And that added layer of protection is known as mismatch repair, okay? Again, this usually, for the most part occurs in the G2 phase of the cell cycle. And basically, the thing that happens in mismatch repair is that you'll find the DNA mismatches, right?

So let's say, oh, instead of an A binding with a T, you have an A binding with a G, you'll fix that mismatch with enzymes known as mismatch repair enzymes. That's probably about as much as you need to know for step one. But there's some very high yield times with this. In fact, they'll probably go on this field for like two minutes, right? The thing is, there are some very specific mismatch repair enzymes that you've probably learned during your GI block, right? There's like MSH2, there's MLH1. And the way to remember which one goes with a one and which one goes with a two, just remember that L is an earlier letter in the alphabet. So we should go with the one. So MLH1. And then S is a later letter in the alphabet, right? So we should go with the later number. So MSH2, okay, if you may. The thing is, those are mismatch repair enzymes. If you have mutations in those mismatch repair enzymes, you actually have something known as HNPCC. HNPCC, like that's the abbreviation for hereditary non-polarposis colorectal cancer. Some people call it the lynching syndrome as well. Basically, these people, it's a mismatch repair defect. They get like multiple solid cancers in different parts of the body, like colon cancer, breast cancer, ovarian cancer, stuff like that, okay? And you kind of want to be able to contrast this with familial adenomatosis polarposis.

In FAP, you tend to have like a crap ton of polyps in the GI tract versus HNPCC where they have like just a few polyps, not hundreds and thousands of polyps in the GI tract, like what you have in FAP. And I guess let me talk about this because this will sort of be a nice way to talk about this concept. So going on with the same theme of HNPCC, or lynching syndrome, if you notice, the probability rate of this buzzword that oh, there are many pathways for colon cancer, there's like this thing known as the microsatellite instability pathway. Kind of ties into this mismatch repair business. So let's kind of talk about it. So um microsatellites, I mean, let's even define them for starters, right? What's a microsatellite? Basically a microsatellite is a section of DNA, it's um, it doesn't quote for anything, right? So it's like a non-coating section of DNA. And the thing is these non-coating sections of DNA, they're just like sort of rich and like dipep, like die and try nucleotide, like I sort of think of them as just having like these are just like non-coating regions of DNA they have like some die and try nucleotides, okay? The thing is these things don't cause any problems. And the thing is if you compare one cell to the other in the body, in general, the number of the length or numbers of these microsatellites should sort of be the same between most cells in your body, right?

But let's assume that a cell has a mismatch repair defect, for example, in the patient that has a HNPCC, right? Um, if you have problems with mismatch repair, you begin to accumulate mutations in these microsatellites, right? So let's say like once they would have like 50 microsatellites, another cell would have like 60 microsatellites, because you're having a difference in the number of microsatellites between those two cell types, that phenomenon is what is known as microsatellite instability. That's like the pathway involved in HNPCC, also called a link-just syndrome. I just thought I would throw that in there because people would go, oh, what's a microsatellite? Yeah, that's what a microsatellite is, and that's what microsatellite instability sort of goes with. Okay, so again, so to how you know that that's a nice way to integrate the GI with a cell biology. As I said, I'm not going to give you a straight cell biology lecture. I'm going to try to integrate this with other concepts. Okay, and then I will just see this for the benefits of students at Hopkins, because I will imagine some first years I probably listened to this podcast, so you can probably like turn your ear off for the next like one minute, if you prepare for step one, although who knows, maybe this can show up on step one. But basically, if you remember from the first podcast, I said that if you DM in 8 cytosine, right, you'll home your cell, right?

The thing is, some cell, human cell spontaneously, you can just have like a spontaneous DM in 10 of cytosines and DM in. That makes your cell, that's obviously not cool, if you're a DME strand, right? So the thing is, we have like twin enzymes that can sort of help with that process to fix that defect, right? So one enzyme is euro-celled like cocelliz, right? It basically comes and chops off the nitrogen base from the euro-cell. Yeah, it comes and chops off the euro-cell from the sugar, okay? Remember the nitrogen base is on the one prime carbon, right? So you cut it off. And then you then cut out the rest of the, so you remove the nitrogen base to your left with the sugar and phosphate, you cut out that sugar and phosphate, right? So you cut out that phosphate and it's true bond with something known as an AP Remic DEMIC endonuclease, okay? And again, it's an endonuclease because you're going inside in the middle of DNA. And then some DNA polymerase comes in, fills in the new DNA, and then DNA like is sort of like patches things up together, okay? But that's more for people that are taking like the cell physiology exam at Hopkins in the first year, okay? So back to the USMLE world, right? So, the USMLE world, like, this is not your world. This USMLE land, if you may. One of the, I guess, repair mechanism, I guess this is more big picture, but there are some very tons of high-year concepts that will consider to talk about here, right?

But if you think about the different phases of the cell cycle, we'll say that there's the G0 phase for quiescent cells, and then we'll have the G1 phase, and then you go to the S phase, the G2 phase, and then the M phase, right? The thing is, if you have a mutation and the cell is in the G1 phase, right? You don't want to keep that mutation going, right? You don't want it to like go from like the parent to the daughter cell, right? So the thing is that G1 to S phase, they are certain proteins that sort of like slow down that phase to sort of give the cell enough time to fix whatever defects being played, right? Or in some cases, if the defects are just like in, think of them as kind of like irreconcilable or differences, then one of these proteins that I'm going to mention now, sort of causes the cell to just die of in hipoptosis, right? So these proteins that sort of regulate the transition from the G1 to the S phase, they're known as like RB, right? So like the retinoblastomagine and then a P53, right? And why is it important to know these things, right? The thing is these proteins are, they kind of like tumor suppressor genes, if you may, right? They are tumor suppressor genes because they kind of regulate the transition of the cell from the G1 to the S phase, right?

And the thing is, if you have mutations in these proteins, then you have aberrant transitions from the G1 to the S phase, let's assume like a cell, oh, has like a mutation in the G1 phase, if you are RB and your P53 and you treat it, right? Then you won't have a appropriate regulation, you'll go from the G1 to the S phase and then that can cause cancers, right? And you may say, oh, what kinds of cancers can you get with this? And for, let me sort of take this detour and basically like lay out the different ways they could test this simple concept on the USMLE, first thing is retinoblastoma, right? Retinoblastoma, if you have an RB gene mutation, you can have retinoblastoma, the classical we will present on the USML Es and also like a pediatric shelf exam or step two or step three is in the context of a newborn with a white reflex, right? So if you go from those copy exams for a newborn, well, all the best with that, that's not the easiest job in the world. I really respect pediatricians for that, but if you're newborn, you're supposed to have a red reflex, right? If you have a right white reflex, that's not normal, especially on MBM Es on USML Es, that is not normal, right? If you see a white reflex, sometimes they call it lukokoria, okay? If you see that in an exam, think about retinoblastoma, okay?

And don't forget that those kids in the future, they have a very high risk of getting osteosarcomas, remember like the codmines triangle and all that, all that fun stuff that you're supposed to memorize for tests. Okay, next thing is P53, if you have a P53 mutation, right? You can have like multiple kinds of cancers, you can have like a leaf from any syndrome. Don't forget that they are the nomato-corsinoma sequence, right? With with colon cancer, right? Remember like the AK53 nomonic? I believe I've talked about this in a previous sub podcast, when you start with like an APC gene mutation and then you go to a Keras mutation and then you go to a P53 mutation and then you get colon cancer, right? P53 is kind of important in that regard. And then please don't forget, right? If you're sort of going into the realm of some more cancers, right? If you sort of think about the bug that is the biggest risk factor for cervical cancer, right? Like HPV, the human papilloma virus, HPV actually causes P53 mutations, okay? And that's potentially the pathogenesis behind how HPV causes scleromorphic cell croscinomas in the head, neck, and the reproductive system. And then if you're going into the realm of, so that's a nice way they can test cell biology in the context of repro on step one. If you want to be even more, I guess a little more evil than that, you can go into the land of hemon, right?

If you, again, if you remember, if you're going from the G1 to the S phase, RB, P53 helping you with that, there's an end, there's a protein that, if you overexpress this protein, it can actually make that process just keep happening, aberrantly, going from the G1 to the S phase. That protein is known as cycling D1, right? So you can probably, for those of you that have studied pretty well for your example, you can probably see where I'm going with this discussion, right? Cycling D1 is the protein that's overexpressed in mantu cell lymph formats, a kind of non-hodgekinza lymphoma. Basically, if you have a cycling D1 mutation overexpression from the 1114 translocation, those translocations are very high, you to know for your exams. You have the 1114 translocation, you overexpress in cycling D1, you'll basically keep going from the G1 to the S phase, apparently, okay? And the person can get a mantu cell lymphoma so again, that's kind of like a high-yield thing you want to keep in mind. And I guess this is what gone on for all 39 minutes and some change. So I think I'll probably stop here and make another podcast. I apologize for the time ticking to make these podcasts is just with my clinical duties, it's not always easy to find time to make these things.

But I'll just sort of, again, round up with these concepts of high yield, I strongly encourage you to learn them, commit them to memory, make good notes, I am going to attach slides that have pictures to the picture of just the picture of the replication diagram. And I guess I'll sort of mention that I offer private tutoring for the USML exams, like step 1 to step 3, so like step 1, step 2 CK, step 3, also for step 2 CS, and also do application advising for pre-mets that are trying to get into med school and I guess med students that are trying to get into residency have a lot of experience with that, have reviewed lots of med school applications. So if you know anyone that's seeking that I also offer that on a private basis, feel free to reach out anytime, divine intervention podcasts at gmail.com. But I wish you all the best as you're going to a new day, I'm actually making this at 2 a.m. in the morning, have a wonderful day, God bless and I'll see you in the next podcast. Thank you.

Replication makes DNA from a DNA template; Transcription makes RNA from a DNA template.

Topoisomerase (or Gyrase in prokaryotes).

The leading strand is synthesized continuously, moving in the direction of the replication fork. The lagging strand is synthesized discontinuously in short fragments called Okazaki fragments, moving away from the replication fork.

Retinoblastoma (RB gene mutation).

Thymidine dimers, usually caused by UV radiation.

R Nase H.

Origin of Replication (and they typically have only one).

To prevent the separated single strands of DNA from reannealing.

In prokaryotes, DNA Polymerase I removes them; in eukaryotes, R Nase H/FEN1 are key players.

Hereditary Non-Polyposis Colorectal Cancer (HNPCC) / Lynch Syndrome.

Rb and p53. Mutation leads to uncontrolled cell cycle progression and cancer.

Overexpression of Cyclin D1 (often via t(11;14) translocation), forcing G1 $\to$ S transition.

Origin of Replication (and they typically have only one).

To prevent the separated single strands of DNA from reannealing.

In prokaryotes, DNA Polymerase I removes them; in eukaryotes, R Nase H/FEN1 are key players.

Hereditary Non-Polyposis Colorectal Cancer (HNPCC) / Lynch Syndrome.

Rb and p53. Mutation leads to uncontrolled cell cycle progression and cancer.

Overexpression of Cyclin D1 (often via t(11;14) translocation), forcing G1 $\to$ S transition.