Evolution of the Cell - Online Tutor, Practice Problems & Exam Prep

All biological organisms evolved from a single ancestral cell, leading to the diversity of life today. This evolution is driven by mechanisms such as sexual reproduction, which mixes DNA, and horizontal gene transfer, allowing bacteria to exchange genetic material. Mutations, including gene duplications, create genetic variation, with homologs, orthologs, and paralogs representing different evolutionary relationships. Highly conserved genes indicate essential functions across species. Understanding these concepts is crucial for grasping the principles of evolution and the interconnectedness of life.

The Tree of Life

Hi. In this video, we're going to be talking about the evolution of the cell. So evolution is the process that has created all biological organisms that originally came from a single ancestral cell. It was a single cell that just existed by itself, but eventually evolved to become all the organisms present today. How we know that it came from a single ancestral cell is because, although the organisms on Earth today are extremely diverse, they all contain these very common molecular mechanisms. Things like the genetic code or certain chemical reactions that make up metabolism and various signaling. All of these processes are extremely similar, remarkably so, suggesting that they had to come from a single source, and that source was the ancestral cell.

How did we transition from the ancestral cell to the diversity present today? Well, that occurred through small changes in the DNA of a cell or organism, which is how evolution works. If we look at this tree of life, we can see that there is very much diversity represented on this very tiny image here. One of the things that you can see is that there are three different colors here. Obviously, they're representing something. What are they representing? Well, the diversity of life, because it is so diverse, can be referred to as Eubacteria. So your textbook will sometimes say Eubacteria instead of bacteria, but it's the same thing. The same thing for Eukaryota, sometimes it's spelled with a 'c' or a 'k', but it's all the same thing. These three colors on this graph represent these three domains. Bacteria, which you can see here in blue, is extraordinarily diverse, especially if you consider that animals, which make up everything from a whale to an ant and even beyond, just compose such a tiny area of diversity. There's an extraordinary amount of diversity present on Earth. We present this diversity through phylogenetic trees. This is an example of one, but I will show you another example later. Phylogenetic trees are used to present the relationships and evolution of organisms.

How do we define these relationships? For eukaryotes, which are members of Eukaryota and typically more complex, we actually just do this by looking at them. Two eukaryotic organisms consist of a whale and a turkey. I don't really need to know much about those organisms to say that they're very different and that they should be classified as such. But for more simple cells, including prokaryotes, which are both the Archaea and the Bacteria, this actually requires the DNA sequence. We have to know the actual sequence of the genes in order to be able to differentiate them. The first person that did this is named Carl Woese. Now, some of you may need to actually know that name. Some of you won't be able to forget it. You'll just have to sort of check in with your professor to see whether or not that name is something that you should really remember. But what he did is he actually studied ribosomal RNA sequences. He chose ribosomal RNA sequences first because they're present in every organism on Earth, and so we can use them to look at relationships between organisms. He also chose them because they don't change that much. They're really crucial to life. So if we can find a change in a ribosomal RNA sequence, we can say, okay, these are two very different organisms. That's extremely important, especially when looking at prokaryotic cells because, typically, they're single cells. I can't really tell the difference between one single cell and another. By looking at the DNA sequences and these ribosomal 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 prokaryotic cells. How this happened is a little story. Very early in Earth's history, all that was present on Earth were prokaryotic cells. But they were different sized prokaryotic cells. There were some larger ones and some smaller ones. Eventually, the larger ones just started taking up the smaller ones. You can imagine that when these smaller cells were taken up by the larger ones, they were pretty much just destroyed. They couldn't survive in the larger cell, so they broke down. But, very rarely, but it did happen that these smaller cells were actually able to survive in these larger cells, which is kind of extraordinary. When they did, they were just like, well, we like it here. So we're going to stay. Throughout history, they kept evolving with these larger cells. Eventually, they became organelles that today you'll be familiar with and you'll know them as mitochondria and chloroplasts. This is the endosymbiotic theory that explains how eukaryotic cells evolved from prokaryotic cells.

We're going to look at a different representation of a phylogenetic tree. You can see the three domains, Bacteria, Archaea, Eukaryota, and they all came from a single ancestral cell. All these domains came from the ancestral cell, and I'm going to talk a little bit about these branches. You don't need to know this; I just think it's really interesting to think about it. If you can see here that there are these branches here. 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. This organism eventually became the entire Archaea domain, and this one eventually became the entire Eukaryotic domain. I think that's just so interesting to think of a single cell evolving into these entire domains of organisms. That's it on evolution, or evolution of the cell for now. But let's come back, and we'll continue on to the next concept.

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 archaea, and the eukaryote to separate? Now we're only going to cover the very surface, I mean, the absolute, just shallowest part of evolution. And I want to mention, I think, three different ways that evolution can come about and how all of this has to do with the DNA. So, the first way that evolution can come about is through sexual reproduction. 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 DNA from one individual and mixes it with the DNA of the other individual. You get these crazy combinations of DNA that can be beneficial to the offspring, and then they pass that on to other offspring. The mixing of different DNA is a huge driver of evolution because that creates new genetic combinations that can give 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.

The second mechanism I want to talk about is horizontal gene transfer, which might be a term you've never heard before. It allows for what we call lateral gene transfer between organisms. What does lateral gene transfer mean? Well, it means if you have bacteria here, and it has some DNA in it, right, here's the DNA, it can just give it to another bacteria. So, this is where the lateral or the horizontal term comes from. Horizontal gene transfer is not how it works for humans, but it works really well for bacteria, like E. coli, but it also can work sometimes for viruses. Sometimes viruses, even viruses that infect humans, have their own DNA, and they can transfer that DNA to us, and it becomes ingrained in our cells. So, when we think about horizontal gene transfer, we're thinking mainly about bacteria, which is super important because we all came from these single cells. Horizontal gene transfer may have been one of the earliest ways that we could exchange genetic material and create the genetic combinations that led to the diversity of life. E. coli, for instance, transfers so that's like 1 in 5 of their genes have been obtained through horizontal gene transfer, which is a major driver of evolution. Viruses also have genetic elements, DNA, RNA, that can become integrated into the cell they are infecting, which is essentially a type of horizontal gene transfer. Here's an example of horizontal gene transfer: you see we have this bacteria, it has some DNA with this like little red fragment here you can see, and undergoes horizontal gene transfer into this yellow organism that doesn't have this DNA here. It gets copied and transferred into this yellow bacteria. And then when it's done transferring, that bacteria now contains this DNA fragment. 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 DNA is in there, that protein gets made on the surface of the cell. 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.

We talked about sexual reproduction, we talked about horizontal gene transfer, but let's talk about what you probably think of most when you think of evolution, and that is mutations. Mutations are changes in DNA and those changes in DNA 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, you know, how much evolution a gene has gone through by looking at how conserved it is. What do I mean by that? Well, I mean that genes that are what we call highly conserved means that they have a very low mutation rate. The reason 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 pass on that gene. So, these genes undergo mutations at the same rate as all the other genes, but when they do, it harms the organism. Genes that are highly conserved, we see the same gene in humans as we do in mice, as we do in chimps, as we do in bacteria, which some genes are very similar between us and bacteria. These genes are highly conserved, meaning they have a very low mutation rate, and if that is true, this means that these genes are very important. So when we look at mutations, we typically think of just single nucleotide changes. Right? Maybe adenine changes to a guanine and that messes up the gene and the protein, so on and so forth. There are much larger types of mutations that can happen. Now, I'm not going to talk about all of them, but I do want to mention here gene duplication which is a major source of genetic variation. 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 else in the genome, but now we have two copies of the gene where we previously had one. This is also a type of mutation. We don't typically think about this because we're often thinking about single nucleotide mutations, but this is also a form of important mutations, especially when it comes to evolution. The reason is that 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. But if you have two copies of the same gene, 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 evolution's 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 cell because you still have that one normal gene sort of chugging out its protein and keeping the cell alive. So when you duplicate a gene, that creates this huge area where the cell can mutate a gene. It may not have been able to otherwise, and that can really drive for the evolution. 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, we have homologs, which are two genes that are related by a descent from a common ancestral DNA sequence. Homolog is just if you had a gene and it duplicated, now we have two genes that are related from descent. Right? They both originally duplicated from 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 homolog. An ortholog is similar, but in this case, the two genes that have duplicated and divided ended up in two or more species, but they have the same function. So again, if we end up with the original DNA sequence and it's duplicated and it forms two, one of these might end up in mice and one of them might end up in humans, but they both have the same function. In this case, we would call it an ortholog. And then, finally, we go to a paralog, which is the same thing with the same gene duplication situation, but in this time, it's within a genome, meaning in the same species but a new different function. So, very different from the previous. Again, if we have a duplication, 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. They have different functions, but they are 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 DNA 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. We'll label them alpha and beta. Right? And, so, in this case, these are homologs. Right? And then, if we take the alpha gene and let's say that it collects some different mutations, and we combine, and we sequence a bunch of organisms and we find the alpha genes present in chicken, human, and mouse. This would be called an ortholog. Right? Because it's 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 paralog because it's in the same organism, it's in mice, but it has a different function. And, all of these genes are called homologs because they came from this early gene. 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 duplications. They duplicate genes, and then we get all these mutations. It can create a large number of genes that have been duplicated that have similar sequences, maybe similar functions, and we call them gene families, which are a 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, and so they're a gene family. There's a lot of gene families in humans and throughout the entire living world. So we know there are 5,408,873 known protein-coding gene families. These are gene families, obviously, not the number of genes, but the number of distinct gene families. So each one of these gene families can have hundreds of genes in them that have originally derived from gene duplication. 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 organism to look at evolution? So, for instance, there are 200 gene families common to the three primary branches. That's archaea, bacteria, and eukaryota. So, that means that there are 200 gene families that in our genome that bacteria also have, that archaea who live in these crazy places like volcanoes also have. These 200 gene families are obviously super important for life as 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 single one of these primary branches, right? So not all of these 200 are found in archaea, but they are found in at least one organism in the archaea but 63 of them common in every single organism. So, like I said before, we share those with bacteria, with archaea, with plants, and with anything that's living. 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 on the next page. Those are some of the three evolutionary mechanisms I want to talk about: sexual reproduction, horizontal gene transfer, and mutations, especially gene duplication. Now, obviously, that's just covering the basic surface of evolution. There's so much more with evolution we could 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.

Which of the following is not an evolutionary mechanism responsible for organismal diversity?

• A. Sexual Reproduction
• B. Mutations
• C. Endosymbiont theory
• D. Horizontal Gene Transfer

Which of the following terms describes two genes that diverged in two or more species?

• A. Homolog
• B. Ortholog
• C. Paralog
• D. Metalog

Which of the following is not classified as a Prokaryote?

• A. Archaea
• B. Bacteria
• C. Eukaryota

Here’s what students ask on this topic:

What is the endosymbiotic theory and how does it explain the evolution of eukaryotic cells?

The endosymbiotic theory posits that eukaryotic cells evolved from prokaryotic cells through a symbiotic relationship. Early in Earth's history, larger prokaryotic cells engulfed smaller ones. While most of these smaller cells were digested, some survived and formed a mutualistic relationship with their host. Over time, these internalized cells evolved into organelles such as mitochondria and chloroplasts. This theory is supported by the fact that mitochondria and chloroplasts have their own DNA, similar to bacterial DNA, and replicate independently within the cell. This symbiotic relationship allowed for the development of more complex cellular structures, leading to the diversity of eukaryotic life we see today.

How do phylogenetic trees help in understanding the evolution of the cell?

Phylogenetic trees are diagrams that depict the evolutionary relationships among various biological species based on similarities and differences in their genetic or physical characteristics. These trees help us understand how different organisms are related and how they have evolved from a common ancestor. By analyzing DNA sequences, especially highly conserved genes, scientists can construct these trees to trace the lineage of species. For example, the three domains of life—Bacteria, Archaea, and Eukaryota—are all shown to have evolved from a single ancestral cell. Phylogenetic trees provide a visual representation of these relationships, helping us comprehend the complexity and diversity of life on Earth.

What role do mutations play in the evolution of the cell?

Mutations are changes in the DNA sequence that can lead to genetic variation, which is a key driver of evolution. These changes can occur in various forms, such as single nucleotide changes, insertions, deletions, or gene duplications. Mutations can be beneficial, neutral, or harmful. Beneficial mutations may provide an advantage in survival or reproduction, allowing the organism to pass on these advantageous traits to its offspring. Over time, these beneficial mutations accumulate, leading to the evolution of new species. Highly conserved genes, which have low mutation rates, indicate essential functions that are critical for survival across different species.

What is horizontal gene transfer and how does it contribute to genetic diversity?

Horizontal gene transfer (HGT) is the process by which an organism transfers genetic material to another organism that is not its offspring. This mechanism is common in prokaryotes, such as bacteria, and can occur through transformation, transduction, or conjugation. HGT allows for the rapid acquisition of new genes, which can confer advantages such as antibiotic resistance or new metabolic capabilities. This process contributes to genetic diversity by enabling the exchange of genetic material across different species, leading to new genetic combinations and potentially new traits. HGT is considered a significant driver of evolution, especially in microbial communities.

What are homologs, orthologs, and paralogs in the context of gene duplication?

Homologs are genes that share a common ancestral DNA sequence. They can be further classified into orthologs and paralogs. Orthologs are genes in different species that evolved from a common ancestral gene and retain the same function. For example, a gene in humans and a similar gene in mice that perform the same function are orthologs. Paralogs, on the other hand, are genes within the same species that arose from a gene duplication event and have evolved to perform different functions. Understanding these relationships helps in studying gene evolution and the functional diversification of genes within and across species.