Enzymes and Protein Binding - Video Tutorials & Practice Problems
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1
concept
Protein Binding
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6m
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Hi in this video, we're gonna be talking about protein binding. So in order to exert their functions on the cells, proteins have to be able to interact with other proteins or other molecules in order to do their function. And so I'm going to talk to you a little bit about protein binding basics. Um and so what I just said is that all proteins have to bind to some other type of molecules. And where does this is generally through a site called the binding site. Um and that's the region where proteins bind to other molecules or other proteins. So let me tell you a few terms and specifics and characteristics about the binding site that you're going to need to know one is that the binding site is highly specific. So usually only binds to one or a couple particles. Second thing is that the thing that's binding the protein at the binding site is called a Liggan, that's going to be a substance that binds the protein. And then the third characteristic is affinity and affinity is actually just a measurement of how strong the ligand and protein are interaction interacting. So high affinity. There's a strong interaction, low affinity. It's a low interaction. Now, the interactions between proteins and other molecules are really held together by non co valent bonds. Um and some of you may see this term called molecular complementarity in your textbook or lecture, if you don't see it, don't worry about it, you don't need to necessarily know it. But if you do see it and are wondering what that actually means molecular complementarity. Just means that there are properties on the leg in and the protein that allow them to interact with each other in a kind of a strong way. So that could be their shapes, could really pair together like a puzzle piece. Or they could have opposite like a positive or negative charge which attracts them together. Or they could be all polar or all non polar and these properties allow them to interact together. But most of the time, molecular complementarity or how well the protein and ligand interact is due to the number of sort of complementary or non covalin bonds that can be formed between the ligand and the protein. So with non violent bonds, another impact. Another factor that's going to really impact the protein ligand binding is going to be the surface confirmation of the protein binding site. And that is because it provides at a certain chemistry. So what do I mean by that? Well, the protein binding site is going to give the protein certain properties that's going to interact with the Liggan and affect what the ligand can do. So, for instance, sometimes proteins have little channels inside of them and those channels is where where the binding sites are. So the ligand goes inside the channel. But once it's in here, the channel is really restricted from things like water or other molecules. So that would prevent, for instance, the formation of hydrogen bonds on the ligand. So that's that would obviously impact what the ligand can do if it can't form hydrogen bonds. Another type is if, say for instance, the binding site is right on the surface of the protein and there's all these polar amino acids around it. Well, that's going to recruit a lot of water to that area and hydrogen bonds are going to be forming a lot. So the surface confirmation of the binding site is really going to affect what the ligand can do. So, if we are looking at this example, what you see here is you see the protein and the ligand. And if we were to choose, say, okay, what if I were to ask where is the binding site? Um just sort of point to it for a second. Right. So the binding site is gonna be right here and the binding site is, it's kind of flat, you know, it meets right without the proteins right on the surface and that is going to have impacts on, you know, what the legion can do or how free it can interact with other things. You can imagine other things can come in on this side and interact with the leg in. Um and so yeah, so this is kind of protein binding to a ligand within a membrane by layer. Now there are a few common forms of how proteins bind with other proteins or other molecules. So I've italicized these because it's very unlikely that you would ever need to know these exact terms surface string or helix helix, but you do kind of need to know how to proteins interact with each other. So I'm going to go through them um just so we get a good idea. So in the surface string model that takes a protein with some kind of large surface on it and usually just another polyp peptide chain and those interact together and kind of think of it, I don't know, as a hot dog or something. Maybe a hot dog will be later. But um the second one is helix helix, so you have to helix is that interact together. 3rd 1 is gonna be surface surface actually highlight that instead of mark through it. And so that's going to take this surface and this surface and interact together. The 4th 1 is a molecular channel. So that's gonna be if a protein is forming kind of a channel and then the ligand goes inside the protein and interacts with it. So maybe that one looks more like a hot dog, I don't know. And generally molecular channels are important for unstable intermediate proteins that would quickly interact with whatever's in the side of salt and therefore they need to be sequestered away from the side of salt so that they don't form toxic things or aggregates or anything that they don't need to form um so molecular channels are really good for sequestering Liggins away from the environment and then finally is going to be the small molecule. And that's if a protein is interacting with a small molecule. So, for instance, in this example, you can see the protein is around here in these alpha helix, sees areas here, and the small molecule is gonna be right here, I just kind of erased it. Let me go back and do that again. Small molecule is gonna be right here, and you can kind of see this red small molecule in the center of this protein. And so that's going to be, you know, how small molecules and proteins interact. So that's kind of the overview of protein binding. Let's now move on.
2
concept
Antibodies
Video duration:
2m
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So in this video we're gonna talk about antibodies. And the reason we're talking about antibodies in the protein binding section is because antibodies are proteins and there are entire function is to bind to the other things for destruction or recognition. So antibodies are proteins that are sometimes they're called immunoglobulin proteins and they're produced by the immune system. Um And so antibodies are really responsible for helping the body defend and respond to foreign molecules, viruses, bacteria, whatever it is. And so they recognize what's known as an antigen, which is kind of any foreign molecule that could be a foreign amino acid for instance, or it could be a foreign protein. Could be a foreign bacteria or cell wall or any of these structures that aren't naturally produced by um by the animal cell. So for human cells when we talk about it and these are really specific. So generally they don't recognize the entire antigen. They recognize a portion of the antigen called an epic tope. So that's going to be a very small specific region that the antibody binds on the antigen. The antibody binds the antigens episode. So antibodies are shaped, we're looking at what the shape of the protein is like a why it has a heavy and light chain segment, you don't need to necessarily know this. Um You will if you ever take immunology but right now we don't need to know about this. Um But generally the regions um that recognize and again are called variable regions. Um And then so there are two kind of segments here, there's a variable region but then there's also a constant region and the constant region is constant among all the groups of antibodies with the variable region changing based on the antigens episode. So antibodies are extremely precise and they actually have the ability to tell the difference between a single amino acid. So there was a single amino acid change that antibody is not going to bind. So these are super super specific. So if we look at what it and two antibody looks like you can see here there's the Y. Shape and you have this antigen binding site here which is gonna be the variable region. And then all of these blue parts down here will be the constant region. And so this is where the antigen binds which you can see this antigen binding here. And you have all these different antigens for instance and each one of them is going to bind a different antibody and they're really really specific. So that's antibody. So now let's move on.
3
concept
Enzymes
Video duration:
1m
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Okay. So in this video we're going to talk about enzymes, We've talked about enzymes a lot, but I'm going to bring them up and mention them again here because enzymes are extremely important examples of protein binding. And so enzymes are proteins that help to catalyze or speed up reactions. And how they do that is they actually bind to what's known as a substrate and this is a substrate is going to be a special Liggan that binds to enzymes. And it also binds to an active site which is very similar to the binding site. It's exactly the same. It's just an enzymes we call it active site on the enzyme. And so once it binds this active site that stabilizes the state that allows the energy to lower and that speeds up the chemical reaction allows the chemical reaction to take place. So many pharmaceutical drugs target this and sort of inhibit enzymes in order to exert their effects because that's going to affect protein binding in some way. And so if we look at enzyme binding, what you can see. So here's a sort of a model here where you have um an enzyme here and it's bound to a substrate and it causes some type of chemical reaction to take place where the where the substrate is released and something and it changes its some type of chemical reaction that changes the substrate. And so here you can see it interacts with it at a binding site, this active site here which is in blue site and that's where the or the enzyme is interacting with its substrate or leg in. So enzymes are a really great example of protein binding. So now let's move on.
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Problem
Problem
Which of the following is not a form of protein binding?
A
Helix-helix
B
Surface-string
C
Surface-surface
D
Surface-helix
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Problem
Problem
The region of a molecule that an antibody binds is called what?
A
Antigen
B
Epitope
C
Ligand
D
Substrate
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Problem
Problem
The binding site of a protein is highly specific for one or a few ligands
