tinywow_video_to_text_65330450.txt

So now we're going to talk about the biological macromolecules proper. So we're going to start with proteins and we introduce each of these different classes of biological macromolecules. We're going to start by introducing the monomers that make up these polymers. For proteins that's going to be am...

So now we're going to talk about the biological macromolecules proper. So we're going to start with proteins and we introduce each of these different classes of biological macromolecules. We're going to start by introducing the monomers that make up these polymers. For proteins that's going to be amino acids. So we call them amino acids in the amino side because each group is going to have an amine functional group. And then acids because each amino acid is also going to have a carboxylic acid functional group as well. And these are the monomers and it turns out both the amines and the carboxylic acids aren't going to actually exist largely when we form the polymer. So they're going to be tied up in amide linkages but in free single monomer amino acids here you've got both an amine group and a carboxylic acid. Now one thing to note, so I've got them drawn out here but that's actually not what they're normally going to look like at physiological pH around pH 7. So it turns out that the amine groups being a base typically are going to exist largely in the protonated state and have a positive charge at pH 7. So in the carboxylic acids are going to be an acid, they're going to largely be deprotonated, they're going to protonate water essentially. They're going to exist deprotonated and have a negative charge. And so you've got a positive charge on one end of the free amino acid, a negative charge on the other end and we call this a zwitcher ion. So we're going to file a way in your head. So at physiological pH most amino acids are going to be in their zwitter ionic form is what we say. All right, so other thing we're going to take note of is this alpha carbon right here. So if you might recall from organic chemistry that the alpha carbon is defined as the carbon next to a carbonyl next to a carbon oxygen double bond. So the carbon next door is called that alpha carbon. So and this is what forms the backbone of any amino acid. You're going to have the amine nitrogen, the alpha carbon and then a carbonyl. And we start hooking these back bones together to make a polymer. You're always going to be following those three atoms in the backbone, nitrogen, alpha carbon carbonyl, nitrogen, alpha carbon carbonyl all the way down the chain. Now attached to that alpha carbon, one, you're going to have hydrogen. So but two, you're going to then have some variable group. So and that variable group is going to make the 20 naturally occurring amino acids different from each other. And one thing to note, I say 20 different ones. I know there's a couple about organisms that use a funky amino acid. So we're just going to ignore that. But outside of those couple of exceptions, there are 20 naturally occurring amino acids that all living organisms use to make up their proteins. That's what's different here. And it largely comes down to that side chain right there. So take a look at that alpha carbon there. That alpha carbon is bonded to four different things for 19 out of the 20 amino acids. The only one where it's not is glycine, where that variable R group is a hydrogen. In that case, the alpha carbon is bonded to two hydrants. And glycine is the only amino acid that is not chiral. The other 19, they are all chiral. And one thing to note, so instead of using R and S, so like an organic chemistry class more commonly, we use D and L for a lot of biomacromolecules like protein, the amino acids, as well as in monosaccharides, we'll see in a little bit. And one thing you should know is that for an amino acid, we always use the L amino acid for living systems. They don't use the D amino acids. We'll find out with sugars though. Monomers are D sugars in carbon-deliving systems. But with these chiral lovely amino acids, it turns out all of our enzymes that are going to use these to make proteins and things of a sort or recognize them. They all recognize only L amino acids, not D amino acids. Also, we're filing away in your head. So depending on the variable R group here, you're going to have some different options. Again, there's 20 options. Glycine is just a hydrogen. Allenine would just be like a methyl group down here, CH3. And they get more complicated as you go from there. And we can group them into a number of different classes. We can talk about the non-polar amino acids. And it really all comes down to that side chain right there. So because what we're going to find out is that you might look at this amino acid. So we're going to grab out the really polar molecule, especially if you consider it as a whiterannic form. I mean, this is like textbook polar. Positive at one end, negative at the other. That's what polar means. So, however, we're going to see in a second that again, most of these amine and carboxylic acid groups are going to be tied up into amine linkages in the interior. The only one is at one end we're going to have a free amino group and then the other end we're going to have a free carbox group. But all the rest are tied up as amides. And amides aren't acidic or basic and they're not charged. And so, you know, we can't really say that these proteins, the amino acids in the protein are quite as polar as a free amino acid. So as a result, though, we classify whether or not we consider the amino acids, proler or non-polar or things of this sort, all based on that variable R group. If that variable R group is non-polar, that's a non-polar amino acid. Regardless of the fact that it's, you know, as a free amino acid, a very polar molecule. That's irrelevant when we're classifying these amino acids. So we have non-polar. We're going to have polar and usually we're going to say polar mean but not charged. We're going to have acidic and we'll learn that a physiological page that can be negatively charged. We're going to have basic and a physiological page that can be positively charged. And as a subset, I didn't really outline this on your outlines, but you could talk about aromatic amino acids as well and they follow a couple of different classes as we'll see. So we're going to have the amino acids and start hooking them together, what you're going to find out is you're going to actually have nucleophilic attack by the amine of one attacking the carboxyl group of the other. And that doesn't actually happen this way. This is all catalyzed by ribosomes and stuff. And I realize these aren't even in their zwitterionic forms and stuff. So I'm just going to kind of want you to see where the bonds are being formed. So I'm not showing a complete mechanism here by any stretch. You know, I could show nucleophilic asyl substitution going on and stuff. So not what I want to really accomplish here. So what I do want you to see is that we're going to have a leading group here and then this nitrogen is now going to be attached to this carbon, right? As we see down here and the bond from between them, that is an amide linkage. And we call that in this specific instance between acids a peptide bond. So all peptide bonds are amide linkage, but not all amides are peptide bonds. You can have amides that are completely independent of amino acids. And those are not going to be called peptide bonds in that case. All right. So all peptide bonds are amides, not all amides are peptide bonds. All right. When you're forming that peptide bond, notice not only did you lose the OH here, but you're also lost one of these two H's as well. And that's where you get these water molecules that are formed in the process as well. And because we're forming water molecules, we call this a condensation reaction. And so when you're forming these peptide bonds, condensation produces water. So, but you can also go the reverse reaction and break them. We call that hydrolysis because it uses up or consumes a water molecule. Now, specifically hydrolysis is kind of a generic term. So it can refer to breaking any carboxylic acid derivative using water. So, but in specifically with proteins, we can also call it proteolysis. So, and there are proteolytic enzymes in your body that will cut amino acid in various places, including in your digestive tract. If you look like chymotrypsin and trypsin and things of this sort, they cut proteins following specific amino acids in the process of digestion and stuff like other proteolytic enzymes. Now, one thing to note, we look at a backbone now, and again, emphasize this on the last slide as well, but following the backbone, you've got nitrogen, alpha carbon, carbonyl, nitrogen, alpha carbon, carbonyl, and that's what the backbone's going to look like. Now, coming off that backbone though, you're going to have on the alpha carbon, a hydrogen and then some variable group that's going to be one of those 20 different things that are possible for the 20 different amino acids. And here I've just generated a list of them as R1, R2, R3. They could be three identical amino acids. They could be three different ones. It is, you know, depends on just what protein you happen to be talking about. So, I'm going to take a look at the different, the 20 different amino acids. And you're going to have to kind of organize them in your head by class. And you probably don't have to memorize the structures for the DIT or the OIT, but you probably should know which ones are polar, non-polar, acidic, basic things of that sort. So, here's the non-polar amino acid. You've got glycine, whose variable group is just a hydrogen, alanine, just a methyl group, valine and isopropyl group. So, of particular importance though, this is one that's unique here is proly. And prolyin connects the alpha carbon and the amine nitrogen, so with a five-membered ring. And so, it's the only amino acid that actually the variable R group is connected to the backbone in a ring like that. So, it turns out when you incorporate proly in a protein, because of this ring structure, it actually puts a characteristic kink into the structure of a protein. So, and that means that they're usually going to get incorporated in certain places, but not in other places. All right, we've got leucine, isoleucine, methionine, phenylalanine, tryptophan. So, probably worth knowing the three-letter codes as well. And I put the one-letter codes as well. So, and maybe you saw those in a biochemistry class in a long way, probably not something you need to know for the DIT or the OIT as well. So, but the three-letter codes, knowing that GLY is lysine, totally worth your time, and again, knowing that these are all listed as non-polar amino acids. And again, even if my structure is well, you should look at these and be able to see like, oh, yeah, non-polar, all carbons and hydrants and non-polar, all carbons and hydrants. And the only one that's not all carbons and hydrants, the only two I should say, are a couple here, methionine, which has a sulfur in there, but notice no hydrin bonding, or anything like that. And then also tryptophan. And tryptophan is a little bit tricky, because there is some hydrin bonding there with that NH bond. However, the bulk of this entire side chain is mostly carbons and hydrants, and it's fairly non-polar and gets classified as non-polar. Also note that both phenylalanine and tryptophan are also considered aromatic amino acids. So, we take a look at like chymotrypsin, chymotrypsin happens to cut aromatic amino acids, including after phenylalanine and tryptophan. And again, you don't have to know that. I'm just giving an example of why you might, you know, class something as aromatic. So, now we've got our polar uncharging amino acids. We've got six of them here. We've got serine, threon, cysteine, asparagine, tyrosine, and glutamine. So, if you look at serine and threon, these are both alcohols on the side chain in one way, shape, or form. If you look at phosphorylating and stuff like this, phosphorylation often happens on a serine or threon, right on the alcohol group itself and stuff like this. So, but definitely polar and recognize them as such, because that OH there is capable of hydrogen bonding. So, it's a small group with an OH, definitely highly polar, but, again, not charged, though, either. So, cysteine here, we've got an SH group. We're going to find out that cysteine does something special in forming disulfide bridges as a consequence of having this sulfhydro group. So, and whereas the SH is technically not considered hydrogen bonding, at least not in gen-chomerocam, there are some biochemists and biochemistry textbooks that actually consider the SH bond to participate in some smaller degree of hydrogen bonding. Now, for the purpose of the DHC or the O2, I probably wouldn't consider hydrogen bonding. However, I just want to point out, though, that this is a still a fairly polar group. This SH group, and that's why cysteine is being classed as one of these polar amino acids. If you look at asparagine and glutamine, they're both amides. So, with a fair amount of hydrogen bonding, that's possible. And then tyrosine here. So, with an OH, there is some still, you know, some non-polarness, too, with this whole big bending ring and stuff like that. So, but overall, it's still going to be classified more as a polar uncharging amino acid. Note that, also, tyrosine is also an aromatic amino acid, along with tryptophan and phenylalanine we saw as part of the non-polars. Now, finally, we're talking about the cynic and basic ones, and these are pretty important. So, they're three, they're classified as basic, lysine, arginine, histidine. So, and they're basic, and you might think, something's a little strange about them as being basic. Well, they're basic because in water, they've already acted as a base, which means they're largely in their conjugate acid form, at least that's going to be true for lysine and arginine. And the conjugate acid, they're both amines down here in one way, shape, or form, and the conjugate acid is going to actually be positively charged. And that's going to be the predominant form at pH 7, a physiological pH. Now, I listed the pKa's for both of them here, and I don't expect you to memorize pKa's or anything like this, but I only did that to show that at pH 7, we're more acidic than the pKa, and when the pH is more acidic than the pKa, it will largely exist in the conjugate acid form and solution. And that's why these are largely in the conjugate acid forms and positively charged. And the fact that they're positively charged has unique consequences. One, we'll find out it can play a role in protein folding. So, but also commonly, we'll find out that DNA is negatively charged. We'll find out proteins that associate with DNA, like histone proteins and eukaryotes, often incorporate a lot of lysine and arginine residues to give them a positive charge so that it can interact well and bind to DNA. So, histone over here is often, again, considered also a basic amino acid, though with a pKa of 6, well, at pH 7, we're actually more basic than that number, and it's largely going to exist in its conjugate base form, and its conjugate base form here is neutral. Now, however, we're not that far away, though, from pH 7 with a pKa of 6 in this case anyways. And so, as a result, it means about 10% of the molecules would actually exist in the conjugate acid form and have a positive charge. 90% would look like this, though, and be neutral. But still, if 10% of the molecules of the histine residues, I really should say in a protein, kind of look like positively charged, that still contributes a fair amount of overall positiveness into the structure if 10% of the molecules do or 10% of the residues do. Now, one thing to note, so here I've listed, like, pKa and stuff like that. That's just the free amino acid. It turns out these pKa's, when they're in the context of a larger protein, often get modified a little bit depending on what else is in the area and stuff like that. So, these pKa's are not set in stone. The pKa's are listed just for the free amino acids, but you definitely don't have to memorize them. So, what you should take away here is that lysine-argent histine are basic amino acids, and either often have a full positive charge or at least some partial positive charge in a protein. All right, finally, we've got the acidic amino acids, and the big thing to take away here is that they tend to have a negative charge at pH 7. So, their pKa's are both right around 4 for the variable groups. They're carboxylic acids. So, and with the pKa of 4, well, at pH 7, we're much more basic than that, so they're going to largely exist in their conjugate base forms, which are carboxylates and have a negative charge. And so, we've got aspartic acid and glutamic acid, but the conjugate bases are called aspartate and glutamate, and because of pH 7 at physiological pH, they exist largely in their conjugate base form. You know, it's probably more proper to call them aspartate and glutamate. However, what we're going to find out is we use them pretty interchangeably, whether I say aspartate or aspartic acid and glutamic acid, treat them as synonymous in this context of protein. Also, notice the difference between asparagene and aspartic acid. Aspartic acid or aspartate is a carboxylic acid or a carboxylate, whereas asparagene was an amide instead. So, and these are negatively charged, whereas the amides, without asparagene, they were polar and cable head and bonding, but they weren't charged. Cool. So, these acidic ones are negatively charged at physiological pH, and again, we might find that some of these negatively charged acidic ones might be interacting with one of the basic positively charged ones in protein structure that plus minus interaction and things of this sort. So, knowing which ones are acidic and basic of particular importance here. So, now we're going to talk more about proteins themselves, the polymers. Again, these are going to be chains of amino acids, and typically we could be talking about, you know, dozens, but more likely hundreds or even thousands of amino acids to compose a typical protein. We often think of proteins as enzymes, and all enzymes are proteins, excluding a very small subset of ribosymes, where you've got RNA that can have some enzymatic activity, but largely when we talk about enzymes in a biological context, we're almost talking exclusively about proteins. But not all proteins are enzymes. We've got three other classes we want to group them into, and we're going to talk about structural proteins. So, things like your skin and your hair and stuff like that are built up of proteins, and they're not catalyzing any reactions like an enzyme would. They're just playing a structural role. You can also talk about the proteins of the cytoskeleton that make up like the microtubules and the microfilaments and things of this sort. Proteins that binding, that are responsible for binding, so we've got receptors on like the cell surface or in the nuclear surface and things of this sort. And then you also got things like hemoglobin, which binds oxygen. Motor proteins being the last class we'll talk about, and this is like mice and motors that are walking along the act and things of this sort, and they're transporting organelles and other things around the cell. So, cool, those are the kind of classes. And you might be able to fit an extra cluster and break these up a little differently, but these are kind of pretty standard four classes of proteins you might talk about. And finally, we're going to talk about protein structure, and it turns out we break up protein structure into four, a hierarchy of four classes, if you will. That's primary structure, secondary structure, tertiary structure, quaternary structure. You might see primary labeled this way, secondary like so, tertiary like so, quaternary like so. And we're just going to get kind of more complex and larger as we go up the chain here. And so, turns out a primary structure is just the amino acid sequence, and we'll talk a little more about each of these in a second. But the amino acid sequence simply is the primary structure. Secondary structure is going to be some localized folding of these amino acids, and very small regions of the protein and stuff like this. And we're going to find out that these are all going to be mediated by hydrogen bonding in the backbone. So, the variable R groups are not going to be involved in secondary structure. tertiary structure, this is the overall three-dimensional shape of a single polypeptide. So, we'll find out that not all proteins are made up of a single polypeptide. Some are actually composed of multiple polypeptide chains interacting and stuff like this, but how a single polypeptide folds up into its overall three-dimensional shape, that's called tertiary structure. And it turns out this is really important because we like to say that form determines function for a protein. Exactly the shape that it takes up determines what it can do. And if it doesn't fold in the proper shape, it won't carry out the proper function. And then finally, quaternary structure. And this is a 3D shape of a protein composed of multiple subunits, multiple peptide chains. So, like I hinted to before, so if you've got a protein that's composed of just a single polypeptide, well, it doesn't have quaternary structure. But if you've got a protein that now is composed of multiple subunits, multiple polypeptides, like say hemoglobin, hemoglobin is composed of four separate polypeptide chains. So, and how they interact and come together, that is called quaternary structure. Like I said, we'll talk a little more about each of these here in a sec. And so, we'll start with primary structure. And again, primary structure is just simply that sequence of amino acids, that linear sequence of amino acids in a polypeptide. And it turns out one thing you should know, though, is that all the necessary information for proper protein folding is contained within that primary structure within that amino acid sequence. So, it turns out all the different interactions that when this protein folds up, all the different interactions that are possible, it turns out are totally a function of what that sequence of amino acids is. So, we have lovely modeling programs that can determine what a protein might look like. And they've gotten much, much better at these predictions over time. And the idea is that they're just going to minimize the energy. So, as this protein folds, and ultimately it's going to achieve some sort of energy minimization, that's why it folds into shape it does. And it's all a function of what that amino acid sequence is. Next level of hierarchy in the structure here is the secondary structure. And again, this is all about localized structures, localized elements. And it's all held together by hydrogen bonding in the backbone. Super important. So, again, those variable R groups are not involved in secondary structure at all. So, and the two most important types of secondary structure are going to be the alpha helix and the beta sheet. They're not the only two. They're other things like beta turns and stuff like this. But these are probably the only two you're likely to encounter on the DAT or the OAT. And let's take a look. We're going to find out with the alpha helix. Now, we're going to take a little bit of structure in a second. The hydrogen bonding that takes place again within the backbone is parallel to the principal axis. So, whereas with the beta sheets, we're going to find out that hydrogen bonding is going to be perpendicular to that principal axis. Let's take a look. So, here's an example of the structure of an alpha helix. And when we show them in the context of a broader protein structure, we often show the ribbon as kind of a way of representing proteins and stuff like that. When you see it on a right-handed coil like this, that's an alpha helix. And sometimes they're short, sometimes they're long. They don't have to be super long to be considered an alpha helix. But if you notice, we're holding it together here. So, it's hydrogen bonding within the backbone. So, the carbonyl oxygen of one amino acids interacting with the nitrin, the hydron, the nitrin, the amine nitrin of another amino acid. And that's what actually holds this together. And you can see that those run parallel to the axis of that alpha helix. So, second type here is called the beta sheet. And it turns out these can run one of two ways. And you've got two sheets that are going to line up together. And again, if you were showing this in the broader context of a protein structure, we'd often show like ribbons. So, lined up parallel to each other, hence the name. And it turns out they can either be parallel or anti-parallel. So, it turns out it's just running the same direction off to directions. And it turns out we often can look at a protein based on, so, directionality. And we look at the amino end. And at one end of the protein, there's going to be that free amino acid. It's not part of an amine linkage. So, and at the other end, there's going to be a free carboxylic acid group that's not part of an amine linkage as well. But again, all the others are going to be in the inter parts of peptide bond and amine linkages. Well, we'll often refer to the end that is free. A free amine group is the end terminus. We'll often refer to the other end as the C terminus. And so, in this case, if the two portions of the protein that are interacting with each other here in this parallel fashion, and again with hydrogen bonding going on here. So, if they both run in the same direction in terms of N terminus to C terminus. So, then we call it parallel. But if they run in opposite directions, then we'll call it an anti-parallel. You should just know that both are possible. There's parallel and there's anti-parallel. So, structurally, there's some minor differences that aren't super important. But this is what a beta sheet looks like. And again, if I say secondary structure, the first thing that comes to your mind should be alpha helix and beta sheet. Also, once again, note that if you look at the direction in which these beta sheets run, the hydrogen bonding is more perpendicular than parallel to that. Alright, so now we're going to talk about tertiary structure. And again, tertiary structure is the overall three-dimensional shape taken by a single polypeptide chain. And we've got an example on the board here. So, this is myoglobin. Myoglobin is a single polypeptide. It's responsible for binding oxygen in your muscle tissues. So, and it is this heen portion that actually binds the oxygen directly. And it turns out that itself is not made up of amino acids. It's kind of a prosthetic group to the protein. So, but the protein along with this heen group accomplishes the function. We can see here some alpha helices. We see there are kind of the ribbons going around in that right-handed coil and stuff like this. Not a whole lot for beta sheets going on in myoglobin and stuff like that. So, we just want you to kind of see an overall way we kind of give the shape of a polypeptide here. What you should know as far as enmolecular force and things involved in the folding here. Some important things. You know, like the forces like hydrogen bonding, dipole dipole forces, lemon dispersion forces. Those are all involved. So, but more important than that. So, well, first important is what we call this hydrophobic effect. So, if you look at a globular protein, a globular protein is one that's typically dissolved in the cyzol. So, it's got water all around it. So, ideally, all the non-polar amino acids, you prefer if they weren't actually facing out in interacting with water. What you find is that one of the big principles governing protein folding is to make sure all those non-polar amino acids face towards the interior of the protein and therefore don't have to be on the outside and interact with water. So, it turns out it actually minimizes some entropic unfavorability in the interaction with the solvent. So, not the most important thing. So, however, this idea of trying to sequester all these non-polar residues on the interior of a protein, that is the hydrophobic effect. It's one of the big things that governs how a protein folds up. You also find, like, if you've got proteins that actually span the membrane, well, the interior of the lipid bilayer is non-polar as well. And you find out that usually the amino acids that are lining that area across the membrane are also going to be non-polar so they can interact with the non-polar interior of the membrane. Some other things involved here. One is called a disulfide bridge. And this disulfide bridge goes back to the cysteine residue. So, cysteine residue, if you recall, the variable R group, and I guess I said R here, this is just generic organic chemistry R in this case, my bad. So, but we got some protein that's got a sulfhydroyl group coming off it. That's part of the variable group for cysteine. So, in some other region, you're going to find another one. And many of these are connected in the bigger, broader context of a protein in some way, shape or form. You don't have to be at the beginning and end of the chain or anything like that. So, they're just somewhere in the broader context of a protein. What's going to happen, though, is these can undergo oxidation. And if they undergo oxidation, and again, they're still all connected. So, but now they're also connected by a new bond right here between those sulfur atoms. This is the oxidized form. When they're separate sulfhydro groups, that's the reduced form. So, and this is called a disulfide bridge. And so, now we see that it's not just in molecular forces, but you can actually have a covalent bond playing a role in making sure a protein folds up into its proper shape as well. So, in fact, you know, I haven't had hair in a very long time. So, but back when I was a kid, there was such a thing, it was a little more common as they called a permanent. And people would go to the stylist and they would get a perm or a permanent. And the reason they called it this is that what they would do in this perm or permanent is they would take and add a reducing agent to somebody's hair and keep in mind that hair is made up of protein. And that reducing agent would break all these lovely disulfide bridges. So, and then they would shape a person's hair to the way they want it, and then they would go back and add an oxidizing agent to form new disulfide bridges. And those new, you know, disulfide bridges, those new covalent bonds would then lock the person's hair into this new shape. And they could wash it everything else. As long as they didn't add a reducing agent of some sort, it would stay largely in that shape because of these new disulfide bridges. So, a big thing, though, is that, you know, covalent bonds can also play a role in protein folding in the form of these disulfide bridges. And then finally, we've got salt bridges. And these salt bridges, these are just plus-minus interactions. You might have some basic amino acids, which were positively charged on the side chains, you might recall, and then some negatively charged acidic amino acids that are negatively charged on the side chain, and maybe they're interacting in this plus-minus fashion. And we call that a salt bridge. You might be like, well, why don't we call that ionic bond? Well, again, everything's dissolved in water. So, it's not like we have an ionic bond. You know, usually if you put a pair of, you know, an ionic compound like sodium chloride in water, it dissociates in the sodium ions and chloridines, and they're free to swim around. Well, in this case, it's dissolved in solution. So it's not proper to call it ionic bond, but if you've got in the protein folding, some permanent plus-minus interaction holding this thing together in a localized region, we call that a salt bridge. And so plus-minus interactions can play a role as well. Cool. That's all that's involved in holding the tertiary structure of a protein together. Cool. And then finally, we've got quaternary structure. And again, if you've got a single polypeptide chain, there is no quaternary structure. But if you're a larger protein complex with multiple subunits, and here now I've got hemoglobin, and whereas myoglobin was a single polypeptide, so hemoglobin is composed of four separate polypeptide chains. They all have heme. They can all bind oxygen, and that's why a typical hemoglobin protein combined as many as four oxygen molecules. So then you can see them diagrammed in blue, green, pink, and red here. So there's four separate polypeptide chains. But how those four polypeptide chains interact with each other to form this giant protein complex? That's what we refer to as quaternary structure. And all the same interactions we talked about with tertiary structure can all contribute to that as well. The hydrophobic effect acts sulfide bridges. So between the separate polypeptide chains are possible, salt bridges, and all the, again, like the forces like hydrogen bonding, diaphragm forces, London dispersion forces. And finally, we'll close this discussion of proteins talking really briefly about protein folding. So in the book of protein folding is often unaided and spontaneous. So again, it's a function of just the primary sequence of amino acid, that primary structure. And again, we're just trying to minimize the energy of all the different interactions possible and stuff like that to get the overall shape. But again, folding into the shape is absolutely essential to it carrying out the function it's designed for. If it doesn't fold properly, it's not going to carry out its proper function. Cool, not all of them, though, are going to be unaided. It turns out they're what we call chaperone proteins that often help a good number of proteins fold. And it's going to work in a couple of different ways. Some of them are like barrel-shaped proteins themselves, these chaperone proteins are proteins, and they're often shaped like a barrel. And as a protein is being produced, it's actually one of these barrels. And that barrel is just giving an environment that sequesters it from the rest of the cell that facilitates it folding into its proper shape. And so the idea is that maybe it wouldn't fold up into its proper shape unaided for certain proteins, all by itself in the environment of the cell. But in this barrel-shaped chaperone protein, it might. So that's one form of chaperone protein. So there's some others, though, that oftentimes when a protein folds, there are key characteristics if it mis-folds. So usually one of those key characteristics of a protein mis-folds is that some of those non-polar regions that are supposed to be sequestered on the inside aren't, and they're exposed. And there are other proteins that can recognize that they're exposed. And they might come and bind to it and stretch it out, and then go and let it refold. And then I do this multiple times, giving it a chance to refold. Because if it doesn't fold properly, it can't carry out its function, and what's going to happen is it's just going to get degraded, and those amino acids are going to be recycled. And that's expensive. You just spend a lot of energy making this protein, and then it doesn't work. So we really want to make sure these fold correctly. And so there's other proteins that might carry out this function as well. And again, these are also considered a form of chaperone protein, aiding in protein folded. Now, what if at the end of this again, they don't fold properly? Well, again, usually that's going to mark them for degradation. We're going to get proteolytic enzymes that come in and chew it back up into individual proteins so they can be recycled and make proteins again. But that's not always going to be the case. So it turns out, in the case of, like, say, Alzheimer's disease, so a typical protein involved in the disease itself is called beta-ambuloid. And when it misfolds, at least some of these non-polar regions exposed, and other beta-ambulae proteins take their non-polar regions, and then they interact with each other, and all of a sudden you get big masses, big aggregates of these beta-ambulae proteins coming together that have misfolded forming, plaques, which are consistent with the onset of disease. So protein folding, big deal. Now, what can cause protein misfolding or unfolding? And again, we often call this protein denaturation. So change in pH. Most organisms have an optimal pH range they exist at. For humans, it's right around pH 7.4, right? And if inside your cells and stuff like that, the pH gets too far out of 7.4, you're not going to live very long. And one of the reasons for that, though, is that the proteins inside your body are going to fold properly right around pH 7.4, in most cases. And so get around outside that range, not going to go so well. Now, in your lysosomes, the pH is closer to 5, and so proteins that might be involved inside the lysome are actually designed, if you will, to carry out their function at pH 5. They don't actually fold properly at pH 7.4, but at pH 5 instead. High salt concentrations can cause protein denaturation, organic solvents, high temperatures. So all of these things are important. So there's usually an optimal temperature, which in order to exist as well. And again, this often comes down to its proteins folding properly at that temperature. So for humans, it's a 37 degree Celsius. But there are other, you know, extremely files that might be, you know, highly elevated temperatures. Like we often use the TAC polymerase as part of the PCR. And that TAC polymerase is actually part of an extremophile. And it functions best at 70 degrees Celsius because these extremophiles that comes from the TAC, I don't know what TAC stands for, but these extremophiles often live in hot springs. They exist around 70 degrees Celsius and they go to the sort. So temperature important. Now, again, this can happen, you know, in vivo, but this can also happen in vitro. Oftentimes, if we're doing some sort of protein assay, we actually want a denatro protein first and stuff like this. Like we might be doing, you know, gel electrophoresis or something like this. And so we can manipulate all of these lovely things as well if we want to synthetically kind of denatro protein in a test tube, so to speak. Thank you. Thank you. Thank you. Thank you. Thank you. Thank you. Thank you. Thank you. Thank you.