Genomes - Online Tutor, Practice Problems & Exam Prep

Genomes consist of coding and non-coding DNA, with prokaryotic genomes primarily featuring uninterrupted coding sequences, while eukaryotic genomes contain significant non-coding DNA and complex regulatory sequences. Evolution of genomes occurs through mechanisms like lateral gene transfer, gene duplication, and exon shuffling, leading to diverse gene families and functions. Non-coding DNA serves structural roles, includes transposable elements, and can form pseudogenes. Understanding these concepts is crucial for grasping genetic variation and evolutionary processes.

Genomes and Genome Evolution

Hi. In this video, we're going to talk about genomes, how they evolve, and what they're made of aside from genes. So the prokaryotic genome, for example, is mostly uninterrupted coding sequences. So that's just uninterrupted sequences of DNA that code 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 ncDNA, has many repeated sequences, and it's just much larger and has more genes than prokaryotes. Meaning it needs more regulatory sequences too. And if you actually take a look at this graph right here, you'll notice that prokaryotes, on the y-axis we have the number of protein-coding genes, on the x-axis we have genome size, and prokaryotes the number of genes and the genome size has a linear relationship. You can see the red here, those are all the points representing prokaryotes and it basically makes a straight line. Meaning, as we increase the number of genes, we are going to proportionally increase the size of the genome in a prokaryote.

Eukaryotes on the other hand, we gotta make things complicated. You'll notice that there's huge variation between the 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 curve to it. This is not a linear relationship between the number of coding genes and genome 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 genes 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, our phylogenetic tree which we'll talk about more in a 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 it's mostly common in bacteria. Now, some pieces of DNA are very ancient. And we actually call these conserved arrangements of DNA in related genomes. We refer to this relationship as synteny. And synteny 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 two species have diverged from each other or 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 genes. 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 exons 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 to 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.

Now, with that, let's turn the page.

Protein Encoding Genes

Now, even though the eukaryotic 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 a unique gene in the genome. And this is probably how you pictured most genes being in the genome. But actually, some genes are tandem clusters, and these are clusters of identical copies of genes that are actually transcribed simultaneously. And this is partly to help increase the transcription output of these genes. So these tend to be genes that are needed in high demand all at once. You can see here in this picture that there are tons of different types of proteins that our genes encode for, and among those are things we've seen like receptors, structural proteins, and cell junction proteins, chaperones to help with folding. There is a whole mess of different types of proteins that our genes encode for. Now, how do tandem clusters form? They form through a 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 chromatids during crossing over. So if you look at our example right here, we have a crossover that's going to occur, but, oops, they are swapping, as you can see right here. Boom. Now, we have duplicated that B gene. So, that is how gene duplication can lead to tandem clusters in addition to other things.

So, let's turn the page and take a look at some other examples.

Gene Families

Gene duplication can lead to multi-gene families, which is a set of several similar genes formed through gene duplication. Sometimes these can be gene clusters, which are genes that are near each other on the chromosome and part of the same family. We have an example of a gene cluster here, showing us the formation; here we have this hybrid gene, and it's evolving, and we wind up with a 3-member gene family with 3 versions of this b gene. It's worth noting that sometimes in multi-gene families, the genes are not actually in close proximity and they can be quite far apart. That happens through other processes.

When talking about gene clusters, we cannot fail to mention the hox genes, which are a 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. 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 embryo's body. These genes are highly conserved and they are used by many different types of organisms. Again, we will be revisiting this idea of Hox genes when we talk about development.

So, let's flip the page and talk about what all that non-coding DNA is for.

Noncoding DNA

At the most basic level, some noncoding DNA is simply there for structural purposes. We call this constitutive heterochromatin, and it's structural DNA that always remains condensed. We usually find this around the centromere of our chromosome. This DNA always stays condensed. It does not contain genes, so it won't need to be opened up and read. We also find constitutive heterochromatin at the ends of our chromosomes around the telomeres. You can have it interspersed in the chromosome, but it's mostly found by the centromere and at the ends.

Now, we've already talked about another type of noncoding DNA, and these are segmental duplications. We've talked about these repeated sequences before. 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. We have also talked about these short tandem repeats. These microsatellites, which are again those short repeated sequences of DNA that vary between alleles and vary in number between individuals. So repeated sequences are very susceptible to unequal crossing over, which produces more repeats. These repeat sequences are actually self-propagating in a way. You can see an example of them right here.

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 here is these short tandem repeats, and you see that we have the sequence CTA, and it gets repeated over and over again. In this one individual, he has 5 repeats, another individual has 6, and another 7, and so on and so forth. Some individuals can actually have many, many repeats, much bigger than you might expect.

Now, the reason these are so susceptible to unequal crossing over is, imagine that you are trying to do some crossing over, and you see that you have a sequence match here, CTA CTA, and oh, hey, look. There's CTA CTA over there. Well, have crossing over between those two points, boom. You have just created more repeats. So unequal crossing over is really, or repeated sequences, that is, are really susceptible to unequal crossing over, because they just have the same sequence repeated over and over and over again for a really long stretch of DNA. This 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 noncoding DNA.

Transposable Elements and Pseudogenes

Now, this next type of non-coding DNA is a weird one. It's something called a transposable element, and these are 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 transposons, and these are transposable elements that use a DNA intermediate to insert their sequence into your genome. You also have retrotransposons, and these are transposable elements that use an RNA intermediate to insert their sequence into your genome. Now, a particular type of retrotransposon I want to talk about is something called a long interspersed nuclear element, or LINE. And this is a transposable element that's 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 to RNA, it takes RNA and turns it back into DNA. So, this LINE will use its RNA intermediate and then use reverse transcriptase to code that sequence back into the genome as DNA. You can see an example of what a LINE would look like right here. You have genes for transposition, that's going to be the genes responsible for moving this around, and then you have these long terminal repeats, kind of, just the junk DNA on either end.

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 due to mutation, and we call these pseudogenes because they're not really genes anymore. They're inactive. They've lost their functionality. They were once genes, but now they're just part of a big mass of non-coding DNA in our genome. We've also talked about microRNA before, and technically, this is non-protein-coding DNA. However, it does code for something. It codes for microRNA, which is involved in RNA interference and is a really important mechanism for eukaryotes for the control of gene expression or the regulation of gene expression. Now, there's also non-coding DNA within genes. We call those sections introns. 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 an example of a pseudogene. You can see this is the chimpanzee gene right here, and this is the human version up top, and guess what? Because of this insertion and this deletion, well, now, this human gene is no longer functional. It is now a pseudogene.

So, many different types of non-coding DNA. Only a few types of protein-coding DNA, and of course, the eukaryotic genome, mostly made up of that non-coding DNA. Only a little portion of it is actually protein encoding. That's all I have for this video. I'll see you guys next time.

Here’s what students ask on this topic:

What is the difference between prokaryotic and eukaryotic genomes?

Prokaryotic genomes primarily consist of uninterrupted coding sequences, meaning their DNA mostly codes for proteins with minimal non-coding regions and regulatory sequences. This results in a linear relationship between the number of genes and genome size. In contrast, eukaryotic genomes are much larger and contain significant amounts of non-coding DNA, including repeated sequences and complex regulatory elements. This leads to a non-linear relationship between the number of genes and genome size. Eukaryotic genomes also have more genes and require more regulatory sequences to manage gene expression.

How do genomes evolve through lateral gene transfer?

Lateral gene transfer, also known as horizontal gene transfer, is the process by which genes are transferred from one organism to another without reproduction. This can occur through mechanisms like transformation, where bacteria pick up foreign DNA from their environment and incorporate it into their genome. Lateral gene transfer is most common in bacteria but can also occur in eukaryotes. This process contributes to genetic diversity and can introduce new functions and traits to an organism, aiding in its evolution.

What are tandem clusters and how do they form?

Tandem clusters are groups of identical gene copies that are transcribed simultaneously to increase transcription output. They form through gene duplication, where an extra copy of a gene is added to the chromosome. This can occur due to unequal crossover during meiosis, where chromatids misalign and swap segments unevenly. Tandem clusters are often found in genes that need to be expressed in high quantities, such as those coding for ribosomal RNA or histones.

What roles do non-coding DNA play in the genome?

Non-coding DNA serves several important roles in the genome. Some non-coding DNA, known as constitutive heterochromatin, provides structural support and remains condensed, typically found around centromeres and telomeres. Other non-coding DNA includes transposable elements, which can move within the genome, and pseudogenes, which are inactive remnants of once-functional genes. Additionally, non-coding DNA can regulate gene expression through elements like microRNA and introns within genes. These various functions highlight the complexity and importance of non-coding DNA in genomic architecture and regulation.

What is exon shuffling and how does it contribute to genome evolution?

Exon shuffling is a process where exons, the coding regions of genes, are rearranged within the genome. This can lead to the creation of novel proteins or new functions for existing proteins. Exon shuffling occurs through mechanisms like unequal crossing over during meiosis or transposable elements inserting themselves into new locations. This process contributes to genome evolution by increasing genetic diversity and enabling organisms to adapt to new environments or challenges through the development of new protein functions.