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Cell Biology

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22. Techniques in Cell Biology

Studying Proteins



Studying Proteins

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Hi in this video, I'm gonna be talking about studying proteins. So scientists of course have a variety of different techniques that they use to study protein structure and function and just proteins in general. So I'm going to go through a few of those techniques and just briefly describe what they're used for. So the first is the SCS page or probably acrylamide gel electrophoresis. I'm short an SCS page and this is used to detect proteins in a certain sample. And so what you do is you get a protein solution a variety of different ways to do that. And then you have a gel. It's like hard, it's kind of like it's kind of squishy material made out of poly acrylamide and this is just a matrix. So if you were to zoom in real close into it, what it would look like is it would have a bunch of pores in it and you can adjust these pores, you can make them bigger and you can make them smaller. But essentially when proteins flow through those pores, um it's going to be hard, right? They're going to get stuck. Sometimes they won't fit. It's going to be really hard for them to get through. So if the pores are bigger, you know, they migrate easier. But if the pores are smaller they migrate harder or slower. And so essentially what happens is you take these proteins in a protein solution, you incubate them with this thing called SCS. It's a detergent. You'll find it in your dishwashing detergent, your laundry detergent and that s C. S attaches to the protein everywhere And the reason it does this is for a lot of different reasons. But what the purpose of it is is because it masks the proteins charge. The proteins have charges but we don't want to sort these based on charge. We want to sort these based on size. And so the SCS makes all the proteins negatively charged. And that way when you run a charge through it the proteins are all going to head towards the positive charge at the same rate. So when you run that gel you put a protein solution made all the proteins negative by interacting with S. D. S. And then you run that charge through it and they all migrate through the pores in the acrylamide mixture towards the positive charge. Then once you have that gel you transfer that so you take that protein from the gel and you transfer it onto some type of filter or paper. Nitrocellulose paper for instance is an example and you do this again there an electric field but this time the electric field is going from the gel to the paper instead of through the gel. And then eventually you have this piece of paper with your proteins on it and they're separated by size. So then you can take antibodies for a specific protein for instance and you incubate them in a process called immuno blotting. So just sort of putting an antibody solution on this paper and the antibodies will bind to the protein if the protein is there. So then you can look at that and say, well it's my protein here because they're the antibody buying to it. So that's that's one way to look at proteins. Now, there's a second one. It's used less frequently, but it's called two D gel electrophoresis. And this is awesome because you can actually detect up to 2000 proteins on the same membrane. So the negative or the downside to the SCS page is that you have an antibody. You can use one, you can use to but essentially you have to know the protein you're looking for. But the two D gel electrophoresis is actually allows you detect up to 2000 at the same time. And instead of just sorting on charge or separating by charge, they're also sorted based on ph which sort of gives this diversity of separation that allows you to detect so many proteins. So this is what an SCS page looks like. And you can see that I have protein here, protein, a protein B and I've run it on some kind of gel. So the negative charge would be here and the positive charge would be here. So when I put protein right up here and run this electrical current through it, the protein is going to migrate through all the pores. Now, larger proteins are going to run slower. So there go going to travel slower and be higher because they're larger in size. And smaller proteins are going to run faster because they can easily get through those pores or more easily get to the pores than the larger proteins. So they're going to run slower or faster because they're smaller in size. So faster, equal smaller and slower. The migration is slower equals bigger. So this one here is gonna migrate slower because it's bigger and this one will migrate faster because it's smaller. So that's some gel techniques for proteins then um I want to talk about other ways too. So these are things that you're looking at certain you're looking for certain proteins but sometimes you don't know what these proteins are or what they're doing. So mass spectroscopy is a technique used to identify unknown proteins. It does other things too. But generally a lot of people use mass spectroscopy to do that. And so pretty much what you do is you have samples that that are containing proteins or peptides. So short amino acid segments. And so the samples are sorted or the samples contain the peptides and sort them via a mass to charge ratio. And so they get to stand up with this graph, not gonna show you. It looks like a kind of looks like this. Um But they use this data which tells them about you know what the sizes and what the charges to get the sequence of the peptide. And then that those peptide sequences. Once you have them can actually just be put into some software and that software will tell you, oh this is from this protein or um this is from this organism or you know things like that. That's what spectroscopy is used for. Then we have an mm NMR which we'll talk about more in chemistry classes that these can be used to analyze structures of proteins. And then if you want to know if two proteins or interaction or interacting, one of the best ways is the yeast two hybrid system. And so this is able to examine if two proteins interact inside a living organism. So this is a super important part. So there's a lot of techniques to look at interactions outside of a living organism but then you're like oh is that real? Or is it just because they're sitting so close together in a tube. So this actually looks at inside a living organism. So what do you happen is you have to proteins of interest called bait or pray. And then you fuse these two transcription factors that way if the bait and prey proteins are interacting in the cell then the transcription factors will interact and then the transcription factor interaction will actually transcribe a gene. So what this looks like is you have these two proteins. These are the ones you're saying do these interact this case? They are so you have protein one and protein to our bait and prey and they're interacting but they're also fused here to transcription factors. Now these transcription factors interact because the bait and prey interact, then this is going to support the transcription of some kind of reporter gene. So that is these two hybrid system. And it says, you know, if these two proteins are interacting, these two proteins are going to interact and that's going to transcribe this dream. So those are a few techniques used to study proteins. So with that, let's now move on.

Which method would be best to use if you wanted to identify unknown proteins?


Which method would be best to use if you wanted to analyze the structure of a protein?