Protein Basics

Hi in this topic, we're gonna be talking about protein basics. So the first basics that we need to know are just some basic vocabulary. So that when we start talking more about complex protein issues, we understand what we're talking about. So first we're going to talk about about protein structures and proteins are made or four of these structures by linking amino acids together. So um the thing that or a polyp peptide chain is formed by peptide bonds between amino acids. So when a bunch of amino acids are linked together, we actually call that a polyp peptide chain Now. A so how does a polyp peptide chain connect with what a protein is? Well, a multi merrick protein. It's gonna have multiple polyp peptide chains. Each one is going to be called a sub unit. And then a mod americ protein is made up a single polyp peptide chain. So if if a protein only contains one polyp peptide chain, that's a mon americ protein, if it contains multiple polyp peptide chains, then it's a multi merrick protein. And each one of those chains are called a sub unit. So the polyp peptide chain is made from a polyp peptide backbone which has a repeating sequence of nitrogen and carbon atoms. So you can see this here in this example down here, let me go away while we talk about this. So for it to follow this we have carbon, nitrogen carbon, nitrogen, carbon nitrogen. So these repeating sequence of nitrogen carbons. Now the interministerial is going to be um the side with the amino group or the NH three group of its in the other end has a C terminus which has a car box cell group at its end. So we're looking at this, this is a three amino acid poly peptide chain. We have 123 amino acids and here we have a car boxing group, C. 00. H. And here we have an N. H. Three right here. And so this is going to be the in terminus and this one's gonna be the c terminus. And so those are the components that make up the basics of a polyp peptide chain. So now let's move on.

So now let's talk about the amino acids themselves. So helicopter chains are made by linking amino acids together. But each amino acid has unique properties. So um all amino acids have a car box, a group, an amino group and a hydrogen around this sort of central carbon. But there is a property called an R. Group which is a side chain on the amino acid. And that differs between amino acids and gives them the unique properties. But I've talked about now this our group um can be polar and charged, which allows for it to form ionic bonds with other charged molecules. It can be polar and uncharged, which can form hydrogen bonds with other molecule, including water. It can be non polar giving the overall protein this sort of make it unable to interact with water. And then there's a final group called the other group. And these are sort of amino acids that don't necessarily fall into any of these other categories. Um And so these groups kind of classify the different types of our groups that they are. And you can see how these differences um in the amino acids gives the overall poly peptide chain or protein unique properties based on how many of which kind of our groups are present. Now another property that we've talked about before. But I just want to mention again is that amino acids exist as stereo I steamers. And so the four groups are asymmetrically arranged around the alpha carbon. So these are called the D. And L. Forms. Um But since we're talking about proteins, just know that only the L form is used in proteins. So the first example that we're going to talk about here is the structure of amino acid. We have our alpha carbon here. We have our amino group here. We have our car boxes here, we have our hydrogen and we have our our group. And remember this is the one that gives it the unique properties. Now the second example here is going to be the 20 amino acid structures. Now Some of you are going to have to memorize all 20 of these. Um some of you will have the option of memorizing all 20 of these for a test. For instance when I took cell biology I had to memorize all of these for extra credit on a test. Um there's not really much I can help you with with this other than um you know he I've shown you all the structures here and that's just going to be a major made a factor of you know, getting some flash cards out and trying to memorize these structures But these the ones that I'm presenting here are organized by the R group and by the properties that they have. So this one up here has um are sort of charged side chains. These are gonna be polar uncharged. These are the three special cases the others and then these ones down here have hydrophobic or are non polar And so here are the 20 amino acids. Um for your use in case you decide that you either need to or just want to learn all of these structures. I will say if you're planning on taking biochemistry knowing the male is going to be really useful in the future if you're um, you know, I just feel like maybe you should go ahead and do it feel free. So with that, let's now move on.

Okay, so now let's talk about sort of some larger protein folding things that you need to know. So proteins form into complex shapes. There's so many different proteins, they all have different functions. So of course they all have to have a different shape. And so some proteins or most of them actually can actually just self assemble. So their amino acids give them certain properties and those properties allow for folding without assistance. Um So like I said, information required is just inherent in the amino acid side chains or there are groups. Um So there's a couple of terms here that we can use to talk about what state the protein is in. So one is denatured, which is when it's in its unfolded state. Um And the self assembling proteins will re nature or reform in proper conditions. Now, can I just fold anywhere into any shape willy nilly whatever they want. No, and that's because the peptide bonds and the polyp peptide backbone restrict movement. So that is a limit on protein folding. So the peptide or the polyp peptide backbone is restrictive. You know, it has these certain bonds that only allow for so much movement. So that really prevents proteins from folding into just any shape that they feel like it and it helps allow the protein to form into its cracked shape. So here's an example of what a denatured protein would look like. So here it's proper form and here it's denatured. Uh And so this took heat for instance, city nature and lots of things can denature unfold proteins including ph um heat. But self assembling proteins can take it upon themselves to sort of go back to their folded form whenever they are in the proper conditions. So we called the proteins folded shape. It's confirmation. I don't know if I've been using that term, but that's what I meant. The approaching confirmation as it's folded shape and it folds to the property of the R group. Now. Um like I've already said, it can't necessarily fold into whatever shape it wants to um Instead it's restricted by the polyp peptide backbone but it's also restricted by gifts. Free energy. So the confirmation that it forms is the one with the lowest gibbs free energy because it doesn't want to take energy to fold this thing. So it just wants to fold without using energy. And so um now you can imagine that there are tons of confirmations protein skin form. But the one with the lowest gibbs free energy is usually the one that it does form. And this is called a negative state. So um there's usually, you know, this small numb confirmations with kind of equal gibbs free energy or close to equal gifts. Free energy. And that's the state that the protein will actually form in. And of course there's thousands of possibilities of what this could be that the native state is generally the one with the lowest free energy. And so the confirmation folded shape is mainly formed through non covalin interactions. So we've talked about some of these and other videos. These include things like hydrogen bonds, ionic bonds, Vander wal's and hydrophobic interactions. So the protein confirmation is held in its complex shape based on non koval a interactions. And but there is a form of covalin interaction called a di sulfide bond. And um this can form between sulfur atoms on to 16 amino acids and this is really a stabilizing bond. That is really important and protein confirmation. So mostly the protein folds using non covalin bonds that can use this covalin di sulfide bond if it needs to. So here we have just a protein you can see here it's folded into this complex shape and um all these little things sticking off here. Um we can just sort of refer to those, these are the amino acids and all of them have these are groups that have different properties that allow the protein to form into this confirmation versus any of the other confirmations that it could have folded into. Now, sometimes the protein can't fold on its own. And so when it can't fold on its own, it requires the use of proteins called chaperone proteins and they can assist in protein folding. So there are two groups the first called molecular chaperones and they're really responsible for sort of stabilizing unfolded or just partially folded proteins and how they do this is they bind to the protein And prevent aggregation of the unfolded or misfolded proteins. So one that you may read about in the book is HSP 70. And so by preventing that this um sort of aggregation it allows the protein to have a little bit more time to fold correctly. Now the second group is chaperones and chaperones chaperones work a little different because instead of just binding to the protein, what they do is they actually create these small chambers within the cell. And that allows for the sequestering or the separation of unfolded proteins from the rest of the south. And so the protein then can refold without influence of water or other molecules that may be present in the side of some. So these formed these cylindrical folding core and the unfolded protein sort of sits in there and um it is separated from the environment and entrance into the chaperone in core is controlled through proteins that act kind of as lids that open and shut when the protein needs to enter and shut. Well it's in there so it re folds and then it can open again and let it out. So an example of this that you might see in your book is HSP 60. So um chaperones can refold proteins. Generally these require energy through a T. P hydraulic sis. So they're not they're not you know energy they require energy to function. And a lot of times these don't necessarily work the way they should and diseases like Parkinson's and alzheimer's which are really diseases of misfolded proteins. So this is what a chaperone in looks like. You can see there's a nice hole here where the unfolded protein goes into um to refold. And here you can see it from another angle with the chamber inside of there. Now, normally there would be some kind of lid here that could open and close, allowing proteins in and out as necessary. So, so that's protein folding basics approaching folding. Let's now move on.

Okay. So now we're going to talk about the four protein model. So you're going to see proteins um shown a lot of different ways by your professor and also buy textbooks that you may have and there are four different ways of presenting proteins. Each kind of showing a different thing. So the first one is going to be the backbone model and this is kind of the overall organization of the poly peptide chain. The 2nd 1 is the ribbon ribbon model which shows polyp Epstein backbone folding. The wire model is going to show the amino acid side chains and the space filling model is going to show a contour map of the protein surface. So let's look at the example and we'll go over which one is which. The first thing you see here is your backbone model and you can kind of see this is the overall organization of the polyp peptide backbone. Then you have the ribbon model here which has the polyp peptide backbone but also its orientation. So you have this orientation here, we're gonna talk about what that is. You have this different orientation here. And so this is the polyp peptide backbone um just the same as this one is. And the backbone model. But you can see that they're showing different different things. Now, the wire model is here and you can see that we started adding in amino acid side chains here. Um so you can see some here, there's here usually wherever this these yellow things are um can kind of be are usually amino acid side chains. Um and so we're getting more complex into what this protein actually looks like. And then finally you have this space filling model, you go down a little and that's the contour map. And you can see that you can kind of see, you know, the surface of the protein where the divots are, where there's raised atoms and follow this kind of along and creating this contour map of what the protein the overall protein shape is. So those are the four models that you're gonna see of proteins in your textbook or in lecture. So let's move on.