Model Organisms - Online Tutor, Practice Problems & Exam Prep

Model organisms, such as E. coli, yeast, Drosophila melanogaster, and C. elegans, are essential for studying biological processes due to their rapid reproduction and genetic manipulability. These organisms share conserved genes, aiding in understanding human biology and disease. Techniques like cell culture allow for in vitro studies of cellular mechanisms, while viruses can be engineered to introduce genetic material into cells, facilitating research on gene function and disease mechanisms. This integration of model organisms and advanced techniques enhances our grasp of complex biological systems.

Purpose of Model Organisms

Hi. In this video, we're going to be talking about model organisms. Model organisms are organisms that are commonly used to study biology. They typically have certain features that make them exceptionally useful for study. Examples include organisms that divide quickly or organisms that have transparent bodies, allowing us to look in and see different structures inside the body. Some are also easy to genetically manipulate. We use model organisms to examine all organism biology or specifically human biology because every organism is descended from an ancestral cell. We all came from the same original cell, so we have very common features associated with our survival and disease.

There are pros and cons to this approach. The pro is that genome comparisons between organisms can reveal diversity in sizes, but they all have similar genes, referred to as conservation. There are similar genes and gene sequences among different organisms, even though they can differ significantly. The con to the fact that every organism is descended from an ancestral cell is the concept of genetic redundancy. Over time, throughout evolution, multiple gene versions have arisen within an organism. This means that if we have a gene 'a', within any organism, there can be an a1, an a2, or an a3, and they all have similar functions. When we use model organisms to study a particular function and create a mutant in a1 that shows no effect, it could be because a2 took over, complicating our studies. Despite this, we still use them because they are the best tools we have to study biology.

In this image, I want to explain what it means for a gene to be conserved. We're looking at the protein sequence of a histone protein. You can see in a comparison from chimps to rats to humans that this sequence is highly conserved. In the portions where it differs, usually, there are one or two options, showing it is not entirely diverse. This genetic conservation allows us to use model organisms to study human biology, disease biology, or the biology of organisms in general. Now, let's move on to the next concept.

Top Main Model Organisms

So in this video, we're going to just be very quickly going over different model organisms that are used to study biology today. So the first is Escherichia coli, E. coli, and this is used to study prokaryotic biology. The genetics with E. coli are basically the same throughout all organisms. They rapidly divide, which allows them to be studied quickly in labs, and then also scientists can manipulate E. coli to replicate DNA and actually grow proteins for experimental use. So if we wanted to study the function of some protein, we can grow it in E. coli and use it and sort of extract that protein and use it in other experiments. So this is just an example of what E. coli looks like.

Now, if we go to the next page, we can see that yeast, which right here is just the scientific name for it, is used to study basic eukaryotic biology. The reason this is used is that it's a single eukaryotic cell, has a small genome, and it can be grown in a laboratory. They divide quickly about once every 2 hours, and they're really easy to manipulate genetically. So genetic entire genetic screens to look at specific genes that cause certain phenotypes can be done by just mutagenizing the whole thing. So you can pretty much just kind of put any kind of mutagen on here, and this can be a chemical. It could be UV light. There are many different types of ways to mutagenize DNA. And then say, okay, well, which cells are smaller, or which ones have these weird bumpy things in them. And genetic screens are big reasons why yeast is used to study biology.

Now, if we go down and look at another one, this is the next 2 are really common, but we start getting more advanced here. So Drosophila melanogaster, this is a fruit fly, and has been used to study the mechanisms of genetics. These are things like chromosomal biology, patterning during development. They also divide fairly quickly for such a complex organism about 2 weeks; they have a new batch of offspring. And so mainly, fruit flies are used to study genetics, gene identification, and function.

Now if we look at C. elegans, this is actually been used to study cell differentiation and development. These are worms, actually, little transparent worms. I'll show you a picture of them in just a second. But, one of the really cool things about C. elegans, I think this really blows my mind, is that the entire sequence of events is known from the single zygote, organism, to the final 959 cells that make up the worm. So every cell division that happens from his single zygotic cell to 959 cells, all of them are known. We can say, you know, this cell divides into 12, and I know exactly which of the 959 cells cell 1 becomes. And I think that's really neat and really helps us understand the mechanisms involved in development. We can also use C. elegans to look at human development because 70% of human genes are found to have worm counterparts. And then, usually, we create, like the flies, we create mutants in yeast, we create mutants to study them. So here's an example of the fruit fly and here's an example of C. elegans, which is a transparent worm.

So let's continue on with our model organisms. Arabidopsis is used to study plant genetics and development. This is a weed, a little flowering weed here. It can be grown indoors and has tons of offspring. It is here 1 to 8 to 10 weeks. This is fairly quickly for laboratory science. But we can also, I mean, I know we use it to study plant biology, but it does have universal features to all organisms. And it contains about 26,000 genes, which is around the same number as humans who have 25,000. So really comparing how these genes are organized and expressed can help us determine what makes an organism complex if it's not just the same number amount of genes.

Moving on, we are gonna talk about zebrafish and frogs, which are used again to study developmental biology. So zebrafish, here is their scientific name, are actually transparent for the first two weeks of their development. So it's really easy to inject genes into their embryo and really look and see the internal structures that change. And they're very easy to maintain. You can keep a ton of them in an aquarium, and they reproduce rapidly. Frogs are used to study development because they have extremely large eggs, which are single cells. And so, we use frogs and their eggs to study cell division and also, this unique thing called whole-genome duplication, which is exactly what it sounds like, a duplication of the entire genome, which is really common in different frog species. So here's an example of a zebrafish and here's an example of a frog. And you can see that these are 2 separate species that have undergone gene duplication. This one is larger because it had its genome duplicated and this one is smaller.

Now, not quite the final, but we're getting very close, are mice, and these are used to study disease. So why do we use mice? They reproduce quickly. They produce a lot of offspring, but very important is 99% of their protein-coding genes are very similar to that of humans. They also have extremely similar immune systems, and the immune system is what allows our bodies to fight off disease. So they're extremely useful in studying disease. So we can use them to mimic human disease, especially human diseases caused by certain genetic mutations. So we can induce these mutations into the mice and see and watch them develop the disease so that we can study it. So here's an image of a laboratory mouse.

So now, let's move on.

Cell Culture

So far, we've been talking about larger entire organisms to study biology, but now I want to focus on some smaller aspects that we can use to study cell biology. The first is cell culture, which involves growing human or other cells in a plastic or glass dish inside a laboratory. This method is used to study cellular mechanisms like signaling, growth, division, and gene expression. Growing cells in a dish can involve many types of cells. You can't grow everything, but you can grow a lot. Growth in a glass dish is typically called in vitro. Studies in living organisms are called in vivo. I want to have a huge disclaimer here because there's a controversy over whether cell culture classifies as in vitro or in vivo. The reason is that cells are living, so any studies you do on them are technically in vivo because they're living. But they live inside glass or plastic dishes, so it's also in vitro. For me, I like to think of cell culture as in vitro, whereas in living organisms it's in vivo. But your professor probably has their own opinion, so you should ask them to figure out which one they prefer, especially if you think these topics might be on a test. Make sure to double-check which one cell culture is used by your professor.

Cell culture is used because you can treat these cells with nutrients, proteins, or chemicals and observe how they react on a molecular level. This is important because some chemicals can be harmful to organisms, but for cells, it doesn't necessarily matter because cells, we don't consider as important as actual living organisms. Here are cervical cancer cells from a human, called HeLa cells, growing in cell culture. The blue here actually represents the nucleus. Cell culture also provides a way to study particular human cells in a manner that studying other organisms doesn't allow.

Another smaller way to study biology is through viruses. Viruses are used to study cell biology. What is a virus? A virus is a non-living infectious particle composed of a protein casing surrounding genetic material. They are crucial because they can be manipulated to add DNA to cells. The genetic material that the virus has can be replaced with whatever genetic material scientists desire. This is particularly true with retroviruses, which are RNA viruses that can integrate the genetic material they carry into the host cell's chromosomes. This capability is critical for scientists because if we want to see the effect of a particular gene mutation on a cell, we can replace the retrovirus' genetic material with whatever genetic mutant we want, infect a cell with it, and then that genetic material will be integrated into the host's chromosome, replicated, and expressed, where it wouldn't have been before. This is a vital method for studying cell biology. In this image here, you can see an HIV retrovirus and its structure. There's nothing too complex about it, just the virus particle. Now, let's move on.

Which of the following organisms is often used to study developmental biology?

• A. E. coli
• B. Yeast
• C. C. elegans
• D. Retroviruses

Frogs are often used to study development because why?

• A. They have unusual genetic systems
• B. Their eggs are large enough to see with the naked eye
• C. Their embryos are transparent
• D. They contain a small number of chromosomes

Which of the following organisms would be the most difficult to use when performing a genetic screen?

• A. Yeast
• B. E. coli
• C. Zebrafish
• D. Mice

Here’s what students ask on this topic:

What are model organisms and why are they important in biological research?

Model organisms are species that are extensively studied to understand particular biological phenomena. They are chosen because they have certain advantageous traits, such as rapid reproduction, ease of genetic manipulation, and transparent bodies. These organisms, like E. coli, yeast, Drosophila melanogaster, and C. elegans, share conserved genes with humans, making them valuable for studying human biology and disease. By using model organisms, researchers can gain insights into genetic functions, developmental processes, and disease mechanisms, which can be extrapolated to more complex organisms, including humans. This approach accelerates scientific discovery and enhances our understanding of fundamental biological processes.

How is E. coli used in biological research?

E. coli, a type of bacteria, is widely used in biological research to study prokaryotic biology. It has a simple genetic structure that is easy to manipulate, and it divides rapidly, allowing for quick experimental results. Scientists use E. coli to replicate DNA and produce proteins for various experiments. Its genetic simplicity and rapid growth make it an ideal model for understanding basic genetic mechanisms, gene expression, and protein function. Additionally, E. coli can be engineered to produce large quantities of proteins, which are then used in biochemical and structural studies.

What makes C. elegans a valuable model organism for studying development?

C. elegans, a transparent nematode worm, is a valuable model organism for studying development due to its simplicity and well-mapped cell lineage. Researchers know the exact sequence of cell divisions from a single zygote to the 959 cells that make up the adult worm. This transparency and detailed knowledge allow scientists to observe developmental processes in real-time. Additionally, 70% of human genes have counterparts in C. elegans, making it a useful model for studying human development and disease. Its ease of genetic manipulation and rapid life cycle further enhance its utility in developmental biology research.

Why are zebrafish used in developmental biology studies?

Zebrafish are used in developmental biology studies because they are transparent during the first two weeks of development, allowing researchers to observe internal structures and developmental processes in real-time. They are easy to maintain in large numbers and reproduce rapidly, making them convenient for laboratory studies. Zebrafish embryos can be easily injected with genes, enabling the study of gene function and expression during development. Their genetic similarity to humans also makes them a valuable model for understanding human developmental processes and diseases.

What are the advantages of using cell culture in biological research?

Cell culture involves growing human or other cells in a controlled environment, such as a plastic or glass dish, allowing researchers to study cellular mechanisms like signaling, growth, division, and gene expression. The main advantages of cell culture include the ability to manipulate the cellular environment precisely, treat cells with various nutrients, proteins, or chemicals, and observe their reactions at a molecular level. This method is particularly useful for studying the effects of potentially harmful substances without risking the health of whole organisms. Additionally, cell culture provides a platform for studying specific human cells, which can be challenging to achieve with whole-organism models.