Genomes

hi. In this video, we're going to talk about genomes, how they evolve and what they're made of aside from jeans. So the pro carry ah tick genome, for example, is mostly uninterrupted coding sequences, so that's just uninterrupted sequences of DNA that codes for proteins. There's very little space between the genes and very few regulatory sequences mixed in that genome. The Eukaryotic genome, on the other hand, has huge amounts of non coding. DNA, or N C DNA has many repeated sequences, and it's just much larger and has mawr genes than pro carry its meaning. It needs more regulatory sequences to, but if you actually take a look at this graph right here, you'll notice that pro Kerasiotes on the Y axis. We have the number of protein coding genes on the X axis. We have genome size and pro carry outs. The number of genes and the genome size has a linear relationship. You can see the red here, those air, all the points representing pro carry outs, and it basically makes a straight line, meaning as we increase the number of genes, we're going to proportionally increase the size of the genome in a pro Cariou, you carry outs. On the other hand, we gotta make things complicated, right? So for you Kerasiotes, which are marked as thes little green dots. In this graph, you'll notice that there's huge variation between number of genes and the actual size of the genome. I mean, there are green points all the way out here. There's a bunch up here, and also, if you were to draw a line through this, you'd see that it kind of has a curved to it. This is not a linear relationship between number of coding genes and genomes size Now. How do genomes evolve? Well, one of the ways genomes can evolve is through something called lateral gene transfer. Sometimes this is called horizontal gene transfer, and this is just when jeans transfer from one organism to another through a method that's not reproduction. So we've actually learned about one type of lateral gene transfer already, and that's transformation. What bacteria do when they pick up foreign DNA and incorporate it into their genome. That's lateral gene transfer, and you can see that happening right here in our tree of life are file a genetic tree, which we'll talk about Maurin later video. So here we have genes transferring from one branch over here to another branch over here that is lateral gene transfer. Now, lateral gene transfer can also occur in eukaryotes, though its's mostly common. It's most common bacteria that ISS now. Some pieces of DNA are very ancient, and we actually we call these conserved arrangements of DNA in related genomes. We refer to this relationship as sin, tinny, and Centanni is very useful when determining evolutionary relationships between organisms. You look at these conserved arrangements of DNA these conserved sequences, and it allows you to tell how far to species have diverged from each other. How far two very distantly related organisms have diverged from each other. Now, another way that genomes can evolve is through chromosome duplication. And usually when we get the wrong number of chromosomes, this is a really bad thing. It's deleterious. However, there are instances where chromosome duplications have actually led to the evolution of jeans, and we'll talk about this later when we talk about speciation or the formation of new species. Now, another way that genomes can evolve is through Exon shuffling, and this is where literally the Exxon's in a gene get shuffled around, and this can lead to novel proteins to brand new proteins. It can also lead existing proteins to develop new functions. And in addition to Exon, shuffling deletions can do the same thing. Removing pieces of genes can also lead Thio brand new proteins and brand new protein functions, so there are many ways that genomes can evolve. However, it's worth noting that most mutations that occur are not beneficial, right. It's the rare mutation that is actually beneficial and can lead to some increased fitness of an organism that, let's turn the page.

now, even though the you carry out a genome is mostly made of non coding DNA, there's still a bunch of different types of protein encoding genes. First and foremost are single copy genes, which is just a single copy of the unique gene in the genome. And this is probably how you pictured most jeans being in the genome. But actually some genes are tandem clusters and these air clusters of identical copies of genes that are actually transcribed simultaneously. And this is in part to help increase the output of transcription of these genes. So these tend to be genes that are needed in high demand. All once. Now you can see her in this in this picture that there are ton of different types of proteins that are jeans and code for, and among those are things we've seen, like receptors and structural proteins and cell junction proteins. Chaperones to help with folding There's a whole mess of different types of proteins that are genes encode for now. How do tandem clusters form? Well, they formed through process called gene duplication, where an extra copy of a gene is added to the chromosome and this can be due to something called unequal crossover. An unequal crossover is a misalignment of the chromite IDs during crossing over. So if you look at our example right here, we have a crossover that's going to occur. But UPS, they're swapping this sequence out over here. Oh, that's going to lead to unequal crossover, which you see right here. Boom. Now we have duplicated that be Jean. So that is how gene duplication can lead to tandem clusters. In addition, other things. So let's turn the page and take a look at some other examples.

gene duplication can lead Thio multi gene families, which is a set of several similar genes formed through gene duplication. Now, sometimes these can be gene clusters, which are genes that air near each other on the chromosome and part of the same family, and you can see that we have unexamined of a gene cluster right here. This is showing us the formation, and here we have this hybrid gene and it's evolving, and we wind up with a three member gene family with three versions of this Be Jean. Now it's worth noting that sometimes in multi gene families, the genes air not actually in close proximity, and they could be kind of far apart. That happens through other processes. Now, when we're talking about gene clusters, we can not fail to mention the hawks. Genes, which are highly conserved, is ah, highly conserved gene family that determines the body plan of an embryo. And we're going to revisit this idea when we talk about development. But for now, let's think about this as a gene cluster, and you can see here that all of the individual genes in this gene family help define the different parts of the embryos body, and these genes are highly conserved, and they're used by many, many, many different types of organisms. Again, we will be revisiting this idea of hocks genes when we talk about development. So let's flip the page and talk about what all that non coding DNA is for.

at the most basic level. Some non coding DNA is simply there for structural purposes. We call this constitutive hetero crow Madden and its structural DNA That always remains condensed, and we usually find this around the Centrum year of our chromosome. So this DNA is always gonna stay condensed. It's not going. Thio contain genes so it won't need to be opened up in red. We also find constitutive hetero Crow Mountain at three ends of our chromosomes zones around the telomeres. Now you can have it interspersed in the chromosome, but it's mostly found by the Centrum ear and at the ends. Now we've already talked about another type of non coding DNA and these air segmental duplications. We've talked about thes repeated sequences before, so segmental duplication zehr just segments of DNA that share sequence and occur in more than one place in the genome. And you can see an example of that happening right here where we have this particular area and it gets duplicated. So now we have it twice. Now we have also talked about these short tandem repeats these micro satellites, which are again those short, repeated sequences of DNA that vary between wheels and very number between individuals. So repeated sequences actually are very success susceptible to unequal crossing over which produces mawr repeats. So these repeat sequences are actually self propagating. In a way, you can see an example of them right here. So here we actually have a single nucleotide polymorphism unrelated to what we're talking about. But hey, it's there. We've talked about that before. The focus are these short tandem repeats and you see that we have the sequence C t A. And it gets repeated over and over and over again. And in this one individual he has five repeats another individual as six and another seven and so on and so forth. And some individuals can actually have many, many repeats. I mean big numbers much bigger than you might expect. Now, the reason these air so susceptible toe unequal crossing over, is imagine that you are trying to do some crossing over and you see that you have a sequence match here. C t a c t a and oh, hey, look, there's c t a c t a over there. Well have crossing over between those two points. Boom! You have just created Mawr repeats. So unequal crossing over is really susceptible are, uh, repeated sequences that is, are really susceptible toe unequal crossing over because they have just have the same sequence repeated over and over and over again for a really long stretch of DNA makes it hard for the machinery involved in crossing over to match up the right points on the chromosomes. Now let's flip the page and talk about some other types of non coding DNA.

Now, this next type of non coding DNA is a weird one, something called a transpose herbal element. And these air pieces of DNA that actually behave kind of similar to viruses inserting their DNA in various places in the genome. And they come in two flavors. You can have what are called transpose ons and these air transportable elements that use a DNA intermediate to insert their sequence in your genome. You also have retro transpose ons and these air transpose herbal elements that use an RNA intermediate to insert their sequence in your genome. Now a particular type of retro transpose on. I want to talk about something called a long interspersed nuclear element. Align. And this is a transpose herbal element that special because it actually codes for a reverse transcriptase. Now you might remember that that is an enzyme that does the opposite of transcription. Instead of going from DNA toe RNA, it takes RNA and turns it back into DNA, so this line will use its RNA intermediate and then use reverse transcript. Taste to code that sequence back into the genome as DNA, and you can see an example of what a line would look like right here. You have genes for transposition. That's gonna be the genes responsible for moving this around. And then you have these long terminal repeat. It's kind of just the junk DNA on either end. Now included in the non coding DNA of our genome is DNA that once coded for something but is now inactive. It's lost its functionality, possibly for mutation. And we call these pseudo jeans because they're not really jeans anymore. They're inactive. They've lost their functionality. They were once jeans, but now they're just part of the big mass of non coding DNA in our genome. Now we've also talked about micro RNA before, and technically, this is non protein coding DNA. However, it does code for something it codes for micro RNA, which is involved in RNA interference and is a really important mechanism for you Kerasiotes for the control of gene expression of the regulation of gene expression. Now there's also non coding DNA within genes. We call those sections entrance. We've talked about these introns before, too. That is technically non coding DNA. It just finds itself within a protein coding gene, and you can see right here we have unexamined of a pseudo gene. You see, this is the chimpanzee gene right here. And this is the human version of top. And guess what? Because of this insertion and this deletion. Well, now, this human gene no longer functional, it is now a pseudo gene. So many different types of non coding DNA on Lee, a few types of protein coding DNA. And, of course, the Eukaryotic genome mostly made up of that non coding DNA on Lee, a little portion of it is actually protein and coding. That's all I have for this video. I'll see you guys next time.