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Prokaryotic Classification

Okay, so hopefully this is an easy one, it says. Which of the following is not classified as a pro carry optics. L is it archaea bacteria or you Correo to hopefully you know that see you Correo to has eukaryotic cells and is classified as a you carry out and not a pro carry out. The answer to this question is see that let's move on.

The Tree of Life

Hi in this video we're gonna be talking about evolution of the cell. So evolution is the process that has created all biological organisms that exist today. So how this happened is that all organisms originally came from a single ancestral cell. So that was a single cell that just existed by itself but eventually evolved to become all the organisms present today. So how we know that it came from the single ancestral cell is because although the organisms on earth today are extremely diverse they all contain these very common molecular mechanisms. So things like the genetic code or certain chemical reactions that make up metabolism and various signaling. Um And all of these processes are extremely similar. I mean remarkably similar and suggesting that they had to come from a single source and that source was the ancestral cell. So how did we become how did we transition from the ancestral cell to the diversity present today? Well that occurred through small changes in the D. N. A. Of a cell or organism which is how evolution works. So if we look at this tree of life we can see that there's very much diversity represented on this very tiny um image here. And uh one of the things that you can see is first that there are a bunch of different colors. There's three different colors here. So obviously they're representing something. So what are they representing? Well the diversity of life because it is so diverse can be classified into three domains These domains are called archaea bacteria and eukaryotes to now bacteria can sometimes be referred to you bacteria. So your textbook will um I don't know sometimes say you bacterias that are bacteria but it's the same thing and the same thing for you. Correo to sometimes it's spelled with a C. Or a. K. But it's all the same thing. And so these three colors on this graph represents these three domains. So bacteria which you can see here in blue is you can see is just extraordinarily diverse. Especially if you consider that animals which make up everything from a whale to an aunt and even beyond. Just composed this like such tiny area of diversity. Um So there's extraordinarily amount of diversity present on earth. And so how we present these um how we present this diversity is to fill a genetic trees. So this is an example of one. Um But I'll show you another example of one later. But philo genetic trees are used to prison the relationships and evolution of organisms. So how do we define these relationships? Well how we do it for eukaryotes which I remember you Correo to typically more complex is we actually just do this by looking at them. So to eukaryotic organisms consists of a whale and a turkey. And I don't really need to know much about those organisms to say that they're very different and that there should be classified as such. But for more simple cells including pro carry oats which are both the Rko and the bacteria. This actually requires the D. N. A sequence. We have to know the actual sequence of the genes in order to be able to differentiate them. And so the first person that did this is named carl woes. Now some of you may need to actually know that name. Some of you will be able to forget it. You'll just have to sort of check in with your professor to see whether or not that name something that you should really remember. But what he did is he actually studied um ribosomes RNA sequences and why he chose ribosomes. RNA sequences is first because they're present in every organism on earth. So we can use them to look at relationships between organisms. But then he also chose them because they don't change that much. They're really crucial to life. And so if we can find a change in a ribosome RNA sequence we can say okay these are two very different organisms. And that's extremely important. Especially when looking at pro carry out ICC cells because typically they're single cells and I can't really tell the difference between one single cell and another. And so by looking at the DNA sequences and these ribosomes RNA sequences we can say okay these are actually two different organisms even if they don't necessarily look like it. Now there's this theory that explains how eukaryotic cells evolved from pro carry out itself. So um so how this happened. Just tell you a little story. So how this happened is that very early in earth's history all that was present on earth were pro carrying like cells but there were different sized pro carry attic cells. There were some larger ones and there were some smaller ones and eventually the larger ones just started taking up the smaller ones. Um Now you can imagine that when these smaller cells were taken up by the larger ones that they were pretty much just destroyed, they couldn't survive in the larger cell. So it it broke down but very rarely. But it did happen where these smaller cells were actually able to survive in these larger cells which is kind of extraordinary. And when they did they actually were just like well we like it here. So we were going to stay and so stay, they did. And so throughout history they kept evolving with these larger cells and eventually they became organelles that today you'll be familiar with and you'll know them as mitochondria and chloroplasts. And so this is the endosymbiont theory explains how eukaryotic cells evolved from pro periodic cells. So we're gonna look at a different representation of a philo genetic tree. And what you can see is you can have the three domains bacteria, archaea, you cario to and they all came from a single ancestral cell. Um And so all these domains came from the ancestral cell. Um And I'm going to talk a little bit about these branches now, you don't need to know this. I just think it's really interesting to think about. Um So if you can see here that there are these branches here now, this organism, whatever branched off here was a single organism and this was another one, but eventually it became the entire bacteria domain, the same for this one, there's another branch here. So this organism eventually became the entire RKO domain and this one eventually became the entire eukaryotic domain. And I think that's just so interesting to think of a single cell evolving into these entire domains of organisms. Um So that's it on evolution or evolution of the cell for now. But let's come back and we'll talk we'll continue on to the next concept.

Identifying Evolutionary Mechanisms

Hi in this video we're going to be going over the practice problem that is associated with the evolution of the sale topic. So this problem asked. Which of the following is not an evolutionary mechanism responsible for organism diversity. So the first thing is sexual reproduction. Well sexual reproduction we know causes diversity because an offspring is not in humans is not a clone of either parent but instead of the combination which increases diversity. So is not the answer. The second one is mutations and mutations are changes within the DNA sequence of a gene. Which because it's changing the DNA sequence is making a new kind of D. N. A sequence therefore increasing diversity. Um So it's not the now see is the endosymbiont theory which if you remember, is a mechanism of how pro carry out ICC cells eventually became eukaryotic cells which isn't necessarily a mechanism of diversity but just as a mechanism of evolution. So this is not this is really not doesn't look like the answer. But let's go into D. So D. Is horizontal gene transfer which is actually giving an organism that doesn't have a gene a new gene which of course increases diversity. So D. Is not the answer. And therefore see the endosymbiont theory is not an evolutionary mechanism responsible for organism diversity.

Evolutionary Mechanisms

Okay so we've talked about the tree of life but now I want to focus on some evolutionary mechanisms and why are we focusing on this? Well we're going to focus on it just briefly here to get an idea of some of the different biological mechanisms that allow for the divergence of species. What allows for humans to be different from bacteria for instance or what allows those three trees the bacteria the R. K. And the U. K. To separate. Now we're only going to cover the very surface. I mean like absolute just shallowest part of evolution. Um And just I want to mention I think three different ways that evolution can come about and how this um And all of this has to do with the D. N. A. So the first way that evolution can come about is through sexual reproduction. And now I know you've heard this in so many of your biology classes but sexual reproduction is a main driver of evolution because it takes the D. N. A. From one individual and mixes it with the D. N. A. Of the other. So you get these crazy combinations D. N. A. That can be beneficial to the offspring and then they pass that on to other offspring. And so these the mixing of different D. N. A. Is a huge driver of evolution because that creates these new genetic combinations That can give some sort of advantages to the offspring. So sexual reproduction is a big one. But we're not going to talk about it that much because you probably have already heard about it and you know a lot about sexual reproduction. So the second one I want to talk about is actually horizontal gene transfer. And this might be a term you've never heard before. And essentially what it does is allows for um what we call is lateral um Right here lateral gene transfer between organisms. So what so what does that mean? What does lateral gene transfer mean? Well it pretty much means if you have a bacteria here and it has some D. N. A. In it. Right here's the D. N. A. It can just give it to another bacteria. So this is where that lateral or the horizontal term comes from. And so when we talk about horizontal gene transfer a lateral gene transfer we're really mainly talking about bacteria right? Because I mean if I'm standing next to another human I can't just like give some D. N. A. To them and they take it into their cells. And then we've mixed up our D. N. A. Not really how that works for humans but it were works really well for bacteria like E. Coli. But it also can work sometimes for viruses. So sometimes viruses, even viruses that infect humans viruses have their own D. N. A. And they can give that D. N. A. To us and it becomes sort of ingrained in ourselves. So when we're thinking about horizontal gene transfer we're not thinking mainly about human to human evolution but bacteria which is super important because we all came from these single cells and horizontal gene transfer may have been one of the earliest ways that we could actually exchange genetic material and create the genetic combinations that led to the diversity of life. So when we talk about a coli for instance the bacteria 20% of their genes come from other organisms. A total of 234 gene transfers. So that's like one in five of their genes has been obtained through horizontal gene transfer. And that's a major driver of evolution. And like I said before viruses also have genetic elements D. N. A. R. N. A. That can become integrated into the cell that they're infecting and which is essentially a type of horizontal gene transfer. So here's an example of horizontal gene transfer. So you see we have this bacteria it has some D. N. A. With this like little red fragment here you can see and undergoes horizontal gene transfer into this yellow organism that doesn't have this D. N. A. Here. And you can see it gets copied and transferred into this yellow bacteria. And then when it's done transferring that bacteria now contains this um D. N. A. Fragment. So that's an example of horizontal gene transfer. But obviously if you're transferring D. N. A. You're going to be transferring other things too. So this DNA encodes for a protein. You can see it's this like pink or red protein here and then this organism here doesn't have it. But whenever the D. N. A. Is in there that pro gets made on the surface of the cell. And so those proteins, even though it's the DNA that's driving that evolution that DNA changing from this organism to this one, it's the protein that gets made that changes the organism which you can see here by those proteins on the surface of the cell. So we talked about sexual reproduction. We've talked about horizontal gene transfer. But let's talk about one of the things that you probably think of most when you think of evolution and that is mutations. So mutations are changes in D. N. A. And there's changes in D. N. A. Obviously can promote evolution. It's usually what we typically think of. When we think of something evolving we think of something getting a bunch of mutations that change it to allow it to survive better. Now when we look at genes we can actually compare them between organisms and when we do that we can determine how much evolution a gene has gone through by looking at how conserved it is. So what I mean by that, Well I mean that genes that are what we call highly conserved means that they have very very small amount or a lower rate of mutations. And the reason that they do is not because these genes just don't get mutated. They do. But when they get mutated it actually kills the organism or makes them less likely to reproduce or something happens with the organism that makes them not likely to survive or passed on that gene. So these genes actually undergo mutations the same rate as all the other genes. But when they do it harms the organism or harms the organism's ability to reproduce. So jeans that are highly conserved, we see these genes, we see the same gene and humans as we do in mice, as we do in chimps, as maybe we even do in bacteria, which some genes are very similar between us and bacteria. And we know that these genes are highly conserved, meaning that they have a very low mutation. And if that is true, this means that these genes are very important, right? Because if mutations even the smallest mutation is killing them or killing the organism, then we know that they have an important function. So when we're looking at evolution, we often look at highly conserved genes because we want to identify how similar are these really highly conserved genes between us and bacteria, or us and mice or us and chimps or whoever you're comparing it to. So when we look at mutations, we actually oftentimes want to look at the genes that aren't mutated for evolution, but another type. So when we typically think of mutations, what do we think of? We think of just single nucleotide changes, right? Maybe adami changes to a guanine and that messes up the gene and the protein so on, so forth. There's actually much larger types of mutations that can happen. And I'm not going to talk about all of them. But I do want to mention here gene duplications and it's a major source of genetic variation. And what a gene duplication is is exactly what it sounds like. We have one gene and something happens to it and that creates another copy that can insert either right next to it or somewhere somewhere else in the genome. But now we have two copies of the gene where we previously had. One, it became duplicated. Now this is also a type of mutation. We don't typically think about this because we're so thinking, we're often thinking about single nucleotide mutations. But this is also a form of really important mutations, especially when it comes to evolution. The reason is is because if you have one copy of a gene, even a really important one and it becomes mutated. Well that could harm the organism. It could kill it, make it less likely to reproduce. Right? So mutations usually don't happen in just one single gene. But if you have two copies of the same gene, so that means that one of them can be mutated, but the other one still has the same function, right? Because it wasn't mutated. So when you make gene copies you can mutate one of them to the evolutions desire. You can just keep throwing mutations out and seeing what happens. Well the other one remains the same and it doesn't kill the the cell because you still have that one normal gene sort of chugging out its protein. And um keeping the cell alive. So when you duplicate a gene that creates this huge area where the self can mutated gene, it may not have been able to otherwise and that can really drive for fourth evolution. So this has happened a lot. We have a lot of gene duplications. Pretty much every organism alive has a lot of gene duplications. And so of course we come up with some terms to differentiate the different types of gene duplications that have diverged. So let's go through those vocab words. So first is we have home logs. And so these are two genes that are related by a descent from a common ancestral DNA sequence. So home a log is pretty much just if you had a gene here and it duplicated. Now we have two genes um that are related from descent right? They both originally duplicated for one. Now these genes can undergo lots of mutations right? This one can undergo a couple of mutations. This one may undergo a couple but essentially they derived from the same original sequence. So we call them a home a log a Ortho log is similar but in this case the the two genes that have duplicated and divide ended up in two or more species but they have the same function. So again if we end up with original DNA sequence and it's duplicated and it forms to one of these might end up in mice and one of them might end up in humans but they both have the same function. And so in this case we would call it an Ortho log and then finally we go to para log and this is the same thing, the same gene duplication situation. But in this time it says within a genome meaning that it's the same species but a new different function. So very different from previous. Again if you have a duplication both of these would be both of these would be in mice for instance but they would have different functions. This one would be a protein on the cell surface and this would be a protein on the Golgi. And they have different functions but they're they're similar right? Because they did come from a gene duplication. They just collected some mutations over the way that made this one go to the Golgi and this one go to the cell surface. But if we look at their D. N. A sequence they're going to look fairly similar because they were originally just a duplicated gene. So let's look at this again. So if we have an early gene and a gene duplication occurs we get two genes well labeled alpha and beta. Right. And so in this case these are home a logs. Right? And then if we take the alpha gene and let's say that it collects some different mutations. Um and we can find and we do we sequence a bunch of organisms and we find the alpha genes present in chicken, human and mouse. This would be called an Ortho log. Right? Because it's um the same gene here with but it's a different organism. So it has the same function in the chicken, in the human and in the mouse. So this gene is submerged, right? It originally came from a gene duplication but it has the same function in all three organisms. And that's different from the presence of the alpha gene and the beta gene in the mice. Right? Or in the mouse. This would be called a para log because it's in the same organism. It's in mice but it has a different function. And all of these genes are called home along because they came from this early gene up here. So this is super important. Definitely understand the difference between these terms. You'll definitely see that again, a lot throughout your biology career now, gene so there's obviously gene duplications they duplicate and then we get all these mutations. It can create actually a large number of genes that have been duplicated that have similar sequences, maybe similar functions. And we call them gene gene families which are set of similar genes due to the result of gene duplication. So for instance if we're looking at this one, all of these genes, the chicken gene, the human gene, the mouse one for alpha. And the same for the beta, again, alpha and beta. All of these would be one gene family. Right? Because they came from this early sequence, they have similar sequences, They may have similar functions. Um and so there are gene family and there's lots of gene families in humans. Um And of course throughout the entire living world. So we know about nearly 5,408, known protein coding gene families. So these are gene families obviously not the number of genes but the number of indistinct gene families. So each one of these gene families can have hundreds of genes in them that have originally derived from gene duplication. Um and we can compare these gene families, how many of them are in humans? How many of them are in bacteria? How many of them are in every living organism to look at evolution. So for instance, there are 200 gene families common to the three primary branches. That's archaea bacteria. And you Carlota. So that means that there are 200 gene families that in our genome that bacteria also have that Rko who live in these crazy places in volcanoes and stuff also have. So these 200 gene families are obviously super Important for life and just a whole right. So by looking at those, we can understand a lot about what it means to be living and what genes are important for that. That's really cool. And there are 63 families of these that are found in each examined living organism, meaning that every So these are the three primary branches. Right? So, so not all of the not all of these 200 are found in Arcadia, but they are found in at least one organism in the RKO. But 63 of them comin in every single organism. So like I said before, we share those with bacteria with RKO with plants with anything that's living. Um And so I think that's pretty cool. Right? Think about these 63 gene families and there could be dozens or hundreds of genes in each of those. So just thinking about how many genes we actually share with these organisms that look and act so different from us I think is pretty awesome. Pretty exciting. Okay, so that is evolution Yeah, we're moving on to practice in the next page. So that are some of the three evolution narrow mechanisms. I want to talk about sexual reproduction, horizontal gene transfer and mutations, especially gene duplications. Now, obviously that's not that's just covered the basic service surface of evolution. There's so much more with evolution we can talk about but we won't talk about it in this class. That might be like an evolutionary biology class. So just understand the basics of how evolution works and what we need to know for cell biology. So with that, let's move on to the practice.

Gene Diversion

Okay, so this question says which of the following terms describes two genes that diverged in two or more species. So this right here is the clue to answering this question. Which one is for two or more species is at home, A log is the Ortho log is a para log or meta log. So first meta log isn't even a thing. So we can mark that out as not being true because I just made that term up. So now we have a B and C. Is a home, a log or a log or para log that specifically within two or more species. So the answer to this question is B. The Ortho log is the term that describes two genes that diverged in two or more species. So with that let's move on.

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<p>Which of the following is not an evolutionary mechanism responsible for organismal diversity?</p>

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