Understanding Membranes and Protein Structures

working on membrane proteins, right? As well as membrane structure. The whole week, last week, was biological membranes. So what are membranes made of? What are the two main components of membranes? You guys can just unmute and blurt it out or write in the chat like usual, just so we can get a little bit of a review before we get started on today's lesson. Lipids and proteins, good. What... is special about the lipids that make up the biological membranes? Bilayer. So the membranes themselves are bilayers, that is correct. But if we were to look at the individual lipid molecules inside it, what do they look like? The hydrophilic and hydrophobic ones. Yes, that's true. They have hydrophilic and hydrophobic components, which makes them what? What is the term that we talked about? for molecules like that. Amphimatic? Amphipathic, exactly. Now, also, we were to look at the hydrophilic versus the hydrophobic ends. What makes up the hydrophobic end of the lipid membranes? The phosphate? The hydrophobic, please. or hydrophilic the chain long chain of yes the fatty acid chains are what are going to make the hydrophobic piece and how many fatty acid chains in these molecules two two good what has three so yes the fatty acid chains that are in your lipid membranes there are two fatty acid chains per molecule What has three? We did talk about a type of molecule. Yes, triacylglycerols. Those were the ones that had the three chains instead of two. No problem. Now, those three fatty acid chains are linked to a glycerol molecule, right? Just like in the lipid membrane, you have the two fatty acid chains linked to the glycerol. What are triacylglycerols used for? What are they good for? If they are not part of the membranes, what are they primarily used as? Their storage lipids. Exactly. They are going to be your storage lipids. Okay, so now going back to the lipids in the membrane, you have two fatty acid chains that are linked with glycerol. And then what else? What makes them hydrophilic? The phosphate. You have a phosphate on top of it. What else can you have on top of that phosphate or on top of the glycerol? Glucose binding? Not glucose, just glucose, but sugar binding. Hypes of sugars that can bind, yes. What are the lipids called when they have those sugar bindings? Glycol, yeah. Yes, Felix. Perfect. Glycolipids. They are called glycolipids. And then if they have a phosphate, is that all they will have? Or sometimes would they have other things attached to it, to the phosphate group as well? They'll have a polar group on top of the phosphate, right? Exactly. You can have polar groups on top of that as well. Exactly. We talked about the choline molecules being attached to it. We talked about others being attached to it. Good. Now for the protein components, these proteins are going to be in different forms, right? So can you tell me some ways that they can interact with the membranes? So there are two main categories of these proteins, right? Who can tell me what they are? Isn't it extracellular and intercellular? Almost, not quite. No. So you have the extracellular and intracellular side of the membrane. And remember, it is going to be different in the type of lipid composition. But for proteins specifically, let's think about that. Integral and integral. Integral is one of them. Good. What's the other one? Peripheral. Peripheral. Good, Alicia. So yes. So they are going to be integral and peripheral proteins. What's special about the integral proteins? What are they doing? Why are they called integral proteins? Aren't they embedded within the lipid bilayer? Yes, so they are integrated into the lipid bilayer, hence they're integral proteins. Do they have to be in both membranes, both layers of the membranes to be integrated, or could they just be in one? I think they have to be in both. So these were some of the examples we looked at were only integrated on one side of the membrane, right? They don't have to be integrated into both, but they do have to be attached within the membrane. So they are embedded within the membrane either completely trans, you know, if they're passing transmembrane proteins, they're passing both side of the membrane. Versus if they are just integrated to the one side, they're linked either by their hydrophobic area, but then their amino acid sequence, or they may be linked to a fatty acid chain, but they are integrated into the membrane itself in just one side, right? But then peripheral proteins, what about those? How are they different? What are they interacting with? They form temporary bonds with the cell membranes, which allows them to easily detach and attach. So it's, in some cases, they may be a temporary bond. In some cases, it may be that they are attaching to a protein that's already embedded within them, but it's a loose attachment. It's not a complete embedding within the membrane. It's just, you know, more relaxed attachment to those sites. Good. Okay, so we're going to go ahead. and get started on this week's lesson now. And we are going to talk about that. Okay. So next week, next lecture, when we start talking about the function of proteins, we're going to then review some of the function of the membranes as well as we talked about them to kind of make sure that everyone is on the same page on that as well. So I'm going to go ahead and share my screen so we can hear. get started on that. It's sharing, guys? Yes. Yes, perfect. The chat shows up on top of it. Yay. for her. Okay, so today we are going to look at, we're going to start chapter four, and today we're going to focus on protein structure itself. So we're going to look at what makes proteins, how do we build them, and then what different types of structures can be formed from them once you have your amino acid sequence. And then next lesson on First day, we are going to focus on the function of proteins. So that's what you're going to be doing this time. Today is all about shapes and structure of protein. So why do we care about proteins, first of all, right? We care about proteins primarily because they are the worker beads inside ourselves. They are the ones that are doing all the functions associated with What we need to do to survive, to do the work that we need to do, to look the way that we need to look, all the good stuff. There are seven main categories of functions that they perform. You can have enzymes that are going to catalyze all your chemical reactions. We talked a little bit about that earlier as well. Then we have structural proteins that are going to provide support for the cell, right, both intracellularly. with your tubulin and microtubules and actin fibers and then extracellularly. The way they bind to the make the cells bind to the matrix interact with each other the way an organism is maintaining its shape and structure. Then you can have transport proteins that will carry your small molecules both within the cells and then also through the bloodstream. or another way all along the bodies. Then you have motor proteins that are going to help us generate movement both at the cellular level as well as at an organismal level. You can also have storage proteins that are going to store small molecules, receptor proteins that will send signals kind of like what we talked about last time with biological membrane, the proteins that we're binding. receptor proteins that were binding signals from outside and taking them in to perform, to respond to whatever environmental factor they were getting exposed to. And then finally you have transcriptional regulation proteins that regulate transcription of our DNA to regulate how our DNA is going to be expressed and what parts are going to be expressed or not. So all these These are extremely important functions, and that's essentially what's keeping us alive, is all these worker bees of proteins. Now proteins are made up of amino acids. Those are the basic subunits of our proteins. If you look at an amino acid structure at a very basic level, you will see that they will have a carboxyl group on one side, amino group on the other side, right? And then you have your main carbon in the center with the typical hydrogen on there. Now this can change right under different pH so that this carboxyl and amino group can become partially charged. So your carboxyl group will have your partial negative charge and the amino group will be your positive side of this amino acid. This allows for different side chains to be attached as well as for it to interact with multiple amino acids to create that long chain of amino acid that it needs to produce. So in our cell where our pH is close to seven, the amino acids are actually going to be present in this ionized form. So they are ready for binding to other amino acids to create the polypeptide chain that we need to have. Right. So in this case, this methyl group is what you're shown as your side chain. Right. And this is going to be making up this amino acids, but this ionized. amino acid is what's needed to create the polypeptide chain. Now when we look at the amino acids in general, they can be found in two optical isomer forms. So you can have the L versus the D forms. Our body exclusively uses the L amino acids to prepare the proteins. So cells in general, they're going to be using the L form of the amino acids to create proteins inside it. Now when we look at the how these polypeptide chains are going to be made, this is again just review from chapter two, but amino acids are going to be joined together by peptide bonds using those carboxyl and amino groups, right, the ionized carboxyl and amino groups. So here you have an example with a glycine amino acid and an alanine amino acid. When they are forming their bonds, they're going to combine the carboxyl and the amino group. It's a condensation reaction, so you're going to have removal of water molecule from there to create your peptide bond between those two amino acids. So when we are making proteins, we are essentially making proteins with amino acids linked together in a long... polypeptide chain according to the instructions provided by the mRNA. And the main backbone of this polypeptide chain is going to be these carbon and amino and carboxyl groups, right? So this is going to be the main backbone of the polypeptide chain. The side chains are going to kind of hang out to the sides of it on either side, depending upon what they are and what their you know, overall function is, what their overall basis is. So to the gray boxes, these are telling you the main structure of the amino acids, right? That's always gonna be constant. And these colored boxes are your side chains that are going to show differently depending upon their chemically distinct properties, right? So you may have some charged amino acids, which are shown right here in blue. You may have some uncharged but polar groups, side chains like here with a hydroxyl group on one side. You may have some nonpolar groups, right, that are going to be hydrophobic in the green. So depending upon what it is that you're building, you'll have a combination of these amino acids to make up this particular polypeptide chain. At the end of the day, you'll still have that carboxyl terminus on one end, which will have that negative charge and the amino as terminus on the other end, which is called, you know, we typically call this the N terminus and this the C terminus of the polypeptide chain or our final protein. So. That is how you would be building your polypeptide chain. Now, looking at the amino acids that you're going to see inside our typical cells and our bodies, you will find that there are 20 different amino acids that are used to create our polypeptide chains or proteins inside our body. There will be some that are going to be charged. You can have negatively and positively charged side chains that will make those amino acids negatively or positively charged. You can also have uncharged but polar side chains that are still going to be hydrophilic, but they have no charge associated with them. And then you have a range of amino acids that are considered non-polar or hydrophobic. So depending upon the protein where it's going to be residing at the end of the day, what function it's going to perform, what structure it's going to take up. It's going to be a mix of these amino acids in particular sequences to present that inflammation in the right way. The way proteins are typically made, the chain is always presented with the N-terminus first. So when you're going to see polypeptide chain sequences on the test or quizzes or in papers, you're going to see the N-terminus being presented first and the carboxyl group or the C-terminus at the end of that. polypeptide chain. Okay. So this is another just to show the actual structure of these side chains and some other properties that they may also hold because of their charged nature or the other structural nature. So you can see that the negatively and positively charged amino acids will also contain additional properties. So they can be acidic or basic in nature. Then you have polar side chains that are able to form hydrogen bonds because of partial charges on them, but they are not ionic in nature. Otherwise, you have non-polar side chains that are going to be different in the type of interactions that they can perform. So they won't be able to form the typical hydrogen bonds, but they will be able to form other types of bonding structures between them. And the actual amino acid backbone will still have. the negative and the positive end to form hydrogen bindings. So there are three different types of non-covalent bonds that help this long polypeptide chain that forms after translation to create the final protein structure that can actually do work. These non-covalent bindings will include just simple electrostatic attractions because of the negative and the positive charges that are present on these side chains. It could include VanderWaal interactions or hydrogen bonds. Now, all of these by themselves are very, very weak interactions, right? They are not very strong and they're usually transient in some cases. But when you have a bunch of these happening together, it makes up for a strong structure at the end of the day. Now, these can happen both within the side chains as well as with the backbone, the backbones, just within the backbone or back. and the side chain. Any one of those combinations can happen to create the final structure that you need. The two common structures that form because of these type of folding patterns is alpha helices and beta sheets. Both of these are specific types of interactions that happen when you have some kind of a repeated pattern happening inside your amino acid sequence that allows for a a specific type of holding to occur. So in the case of your alpha helices, you are going to have the NH and the CO bonds interacting with each other, usually in a very repeated pattern, in a typical pattern to create that structure to make this alpha helix structure. In beta sheets, you have side chains or the backbones rather that are the backbone is interacting with parallel polypeptide chains. So here, again, you will have some kind of a repeated structure. so that you can have all these backbones interacting with each other. In both cases, the side chains are not involved in this first set of interactions. This is all happening at the backbone level. So just at the internal level, you'll have these hydrogen bondings that are happening between the carboxy and the N-terminal sides of the actual backbone to create these type of alpha-haloses and beta-sheets. So alpha helices, first of all, if we talk about those, they are going to be responsible to create rigid cylindrical structures. They are not always going to look exactly the same. It depends on the pattern that you see, the regular repeated pattern that you're seeing within the backbone for the type of amino acids that are there. So the hydrogen bonds are going to be between every, you know, in one, um, In the typical example between every fourth amino acid linking the carbon oxygen of one to the NH of another, that causes this turn to occur. And depending on which side it is on, the way these interactions happen, it could be either a left-handed helix or a right-handed helix. And the turn would be every about 3.6 amino acid. Now, depending upon how many amino acids are there, in between those typical turns, how many are in this space between that, it could be a more loose alpha helix or a more tight alpha helix. So if there are five amino acids in this space versus if there are three or six or 10, it's going to change how big this alpha helix is in between that space, right? And that's what's shown kind of over here is that how many amino acids are present in between. these bondings to create a more tightly linked alpha helix versus a more loosely linked alpha helix. This is one of the main protein structures that you see when you have proteins that are transmembrane proteins that cross lipid bilayers. It takes about 20 amino acids in this alpha helix to create a more tightly linked alpha helix. create this enough length to pass to completely pass that lipid bilayer. In this case, the hydrophobic amino acid side chains are going to be what's on the outside. And the inside, the backbone is obviously hydrophilic. And that's creating these hydrogen bondings and other, you know, electrostatic interactions to create this alpha helix inside that is going to then create this alpha helix structure. Now if you look at it, it almost seems like there's a channel in there, right? But there is, it's not, there's not enough space in that little helix to have any type of molecules pass through. So it is a very small structure at the end of the day. No ions can pass through it, no molecules can pass through it. You would need multiple helices like these to create a pore to create a structure where molecules or ions could pass. Any questions about alpha helices? Oh, thank you. Okay, so you said that what part of the helix is hydrophilic? So the backbone is hydrophilic, essentially, right? So all these interactions are happening in that hydrophilic backbone, all the hydrogen bondings are there. All the side chains in this particular case where you have this transmembrane protein are going to be hydrophobic. So the hydrophobic amino acid side chains are kind of forced outward towards the outside in this case because the way the helix is turning with interacting just with that hydrophilic backbone in the back. Does that make sense? Yes, thank you. Any other questions? So here you can see that a little bit more clearly, right, in this ball stick model. So these amino acid groups, you know, the side chain groups would be what typically would be your hydrophilic, not hydrophilic, hydrophobic groups in case of a transmembrane protein. And so when the hydrogen bonding occurs in the backbone, so remember, if you look at this all the r groups are excluded from this bonding it's only the backbone interaction so only the those carboxyl and your amino group interactions so as they are making those interactions that causes them to become inverts right as they're creating those hydrogen bonds. And these are groups that are hydrophobic would then tend to stick outside, which is where the lipid membrane would be. So they would be associating with what is energetically favorable for them in that case. Okay. Okay. Any other questions for that before we go to the next one? Okay, so now sometimes that's enough, you create a single structure, and that's good, you're in a area that's hydrophobic, all your amino acids were hydrophobic, and that works. But there are other times that you have a situation where there are multiple areas of these hydrophobic amino acids within that, I mean, you know, that long amino acid chain, the polypeptide chain. In that case, sometimes these multiple alpha helices that form at you know, the first stage at the first level will intertwine with each other in order to maintain those hydrophobic regions within each other, right? And it can be that these particular, in this case, this protein was going to be in the cytosol. So it doesn't want those hydrophobic amino acid side chains to be interacting with the cytosolic aqueous environment. So by creating this intertwined structures, those alpha helices would maintain the hydrophobic structures within that coiled coil conformation, while amino acids that are then going to be towards the outside would tend to be more hydrophilic. And here's an example of how that shows. So the green areas are going to be your hydrophilic and the red stripe are hydrophobic, right? So by coiling against each other you're going to create an environment where you are maintaining the hydrophobic together and the hydrophilic separately another type of basic structure that forms in the secondary layer of structure is called beta again this is also going to look at just hydrogen bonding or electrostatic binding between the site and not the side chains but just the main backbone of the amino acid, the polypeptide chain. In this case, the direction of the arrow is going to show you which way the C-terminal is. So in this case, the C-terminus is going that way, this one will be here, right? So that is going to point towards the C-terminus of the polypeptide chain of that region of that set of amino acids. So in beta sheets, You have, instead of having amino acids that are next to each other doing hydrogen bonding, you have parallel areas, repeated sections of the polypeptide chain that are lying side by side to each other, interact through hydrogen bonding. When that happens, you then create this kind of a very stable, rigid sheet of protein that is going to help you. create a very stable structure. So this kind of interactions are very common in structural proteins and they are also seen in amyloid structures. So kind of what you see in neurodegenerative diseases like Alzheimer's. You can see examples of that even in yeast. These amyloid structures will form that resemble very much those insoluble aggregates you see in the brain in neurodegenerative diseases as well. So these particular beta sheets can go both parallel or anti-parallel to each other, the different segments. So if all the polypeptide chain sections line up so that the carboxy terminus is at the same direction in all cases, as is shown here. So the polypeptide chain is folded in a way that it's always the C terminus is always in the same direction between that interactions. It's called a parallel bit of sheet and if they are lining up so that they are in opposing direction as you see up here, they are going to be what you called anti parallel configuration. So those are the two different types of beta sheets that you should be aware of the parallel versus anti parallel. You should be able to tell that the arrow is pointing towards the C terminus and that it's going to be on the interaction is going to come from. Sheets that are polypeptide sections that are laying side by side, having hydrogen bonding interaction between them. And again, you can see that from here that the R groups, again, are excluded from this interaction. It is solely between the backbone. Right. So, again, the carbon oxygen and the nitrogen hydrogen sections of the backbone that are interacting to create these hydrogen bondings. to create that final beta sheet in the structure. Questions on beta sheet? I'm sorry, does the beta sheet follow the same configuration throughout? Same configuration, meaning what? Like one entire beta sheet is always going to be parallel or anti-parallel. So a section of the beta sheet in one, you know, let's say that there's a protein that has multiple sections of beta sheets. A particular beta sheet would typically follow the same structure, but that would change, that could change potentially in a separate area of that polypeptide chain. So if you had one section. and then you had an alpha helix in between and then there was another section, it doesn't have to follow the same pattern in those two sections. Okay, thank you. Okay, so now we go to other, you know, types of interactions that can happen too and also what exactly are these interactions doing, right? So what is dictating how these proteins chains or polypeptide chains are holding in these particular conformations? So obviously the hydrophobic forces around them, if they're stuck in a hydrophobic environment, or the hydrophobic side chains are going to be part of what dictates where the protein is going to fold and how it's going to be folding up. So when you have these hydrophobic forces, when you have a lot of non-polar side chains together, they are going to tend to form a more compact conformation because they would all tend to kind of get away from that aqueous environment, get inward and create a more compact structure. So they are usually going to get add into a central core or some, they will get embedded within that protein, final protein structure so that the out, the one, the, you know, polypeptide chain, as well as the side chains that are on the outer side of that protein are interacting with the aqueous environment. typically the case inside the cell. The polar side chains can form hydrogen bonds obviously with the water molecules around them as well as themselves between the different side chains as well as in the backbone as well. So the hydrogen bonds are what's going to stabilize that final protein structure. So hydrophobic forces dictate how it's going to start to fold up and the hydrogen bonds then stabilize that structure. through those hydrogen bonding interactions. These interactions, like I said, can occur between two side chains. They can interact from the backbone to the side chain of that molecule, or they could be interacting with the water molecules on the outside as well, right? That's another thing that they can do. And obviously, just like we talked about in your alpha helices and beta sheets, you can have the side chain to side chain interactions, which are the ones that are most common inside. that secondary structure. Now once these proteins are folding, they're essentially folding in a way so that they can be at their lowest energy state within the environment that they are in. And that can change as the pH changes, as their localization change. There could be slight modification to that conformation to that structure if that protein is going to be activated in a particular way, in a different environment. When we isolate proteins from cells, we want to maintain that structure, obviously, if we are going to study their function. However, in some cases, we are just looking at the structure, not structure, but just the amino acid sequence and whether or not the protein was there, in which case it may not be that important, right? We could just extract it without worrying about maintaining its final structure intact. If we expose the... protein to high concentration of urea, which is found in many extraction buffers, you tend to denature the proteins to their back to their primary structure, which is the single long polypeptide chain. However, sometimes if you remove that urea and give them just the right environment, it can spontaneously reform that original confirmation. That tells you that all the information that was needed to mint to create that structure is already present in this polypeptide chain. And you don't really need anything outside of that to maintain its structure, to create that structure. Now, before I talk about some other aspects of this, can you think of some other ways that I can denature a protein? So if I have a protein that I've isolated from a cell, it's intact right now, what are some things I can do? Heat, good. So heat would denature the proteins again by destroying those interactions, right? Those different types of hydrogen bonding, electrostatic interactions, the van der Waals forces, those get broken down by heat and the protein gets destroyed in its structure. pH would also affect the protein exactly. So if a protein is typically found at pH 7 and you suddenly put it at a really basic or really acidic environment, it's going to change that as well. Electric shock can create again some type of a structural destabilization as well. UV wouldn't necessarily directly affect all proteins can affect some of them, but not all of them for sure. Okay, so now we have our proteins, we are looking at how they maintain the structure, right. And so we are going to look at some other ways that they can control it. So each protein, like I said, is going to form a single stable conformation, that's its typical conformation, that may change slightly when they get into a different environment in order for it to become activated or inactive. Now inside the body, inside the cells itself, there, it's a very crowded environment. There is a lot of this protein already folded up there that maybe, right, there are other proteins that are present there. There's, there is a lot going on in, you know, in an isolated environment, in a test tube, it's a different thing. But inside the cell, it's a busy house. So Inside the house, many times you need chaperone proteins to guide the folding of the polypeptide chain so that they can create that final structure in a proper manner and in an efficient manner. So if you let a protein kind of synthesize by itself, it may take longer. It may not be able to fold properly because it may end up getting crowded up by all these other polypeptide chains and form aggregates or get. incorrectly folded. However, with the help of chaperone proteins, they can guide this protein to polypeptide chain to correctly fold into its proper conformation along the most energetically favorable pathway so that it is done in a more efficient, quick manner and work properly. Now, many of these chaperones are going to require ATP binding and hydrolysis to work properly. and that's going to then provide the energy for this process to occur. Now some chaperones will simply bind to the polypeptide chain itself and kind of guide it into the right conformation. Others can act as isolation chambers so they kind of almost work like an enzyme structure where they provide just the right environment they isolate this newly. synthesize partially folded protein into this place, into the right environment where it's by itself and it can fold up properly into its final conformation. And then it's going to release it back out into the cytosol or whatever environment it is in at that time. And that is a somewhat complex process that it can go through. But this allows the prolipeptide chain to form its final structure. without the risk of aggregating with other polypeptide chains or other proteins that are present there. This system will also require input of energy, obviously, in the form of ATP, so that this whole process can occur where the polypeptide chain goes in, the chamber cap is on there, and then gets released out once it is formed properly. Proteins have several levels of... organization starting from your polypeptide chain all the way to its final functional form. The primary structure of a protein and again this is a little bit of a review from before is simply the long polypeptide chain that forms after translation. This is just the amino acid sequence of that particular protein. The secondary structure is that first level of organization through presence of alpha helices and beta sheets. that occur because of interactions with the backbone, right? The hydrogen bonding that happens in the backbone to create structures. The tertiary structure is going to be this 3D conformation that you're looking at after it's been folded appropriately. Now for some proteins, that's it. That's their final functional form. For many of the proteins, however, they still need another level of organization before they can function, before they can actually act properly. And that final structure is called the quaternary structure. In that case, the proteins have to associate either with another polypeptide chain of themselves, you know, kind of like a dimer or... even a more complex structure or tetramer, or with other types of proteins in order to form their final active form. So that in that case, that would be their final quaternary structure. That may include just other proteins just like them, or proteins that are different from them, interacting with them to create the final functional form. Okay, questions through that? before we start talking about how that's going to affect their function? So for that final structure, it's basically they have to interact with another protein to gain their final form. So they themselves have their final form at that point. But in order to be active, to do the work they need to do, they need to interact with another protein, either one, two or multiple, right? So an example of that is hemoglobin molecule, right? You need to have those four molecules together, two alpha and two beta molecules to form that final functional form of hemoglobin, right? Yeah, that makes sense. Okay. And we'll talk more about it actually a lot next time when we start looking at actual functions of proteins. Now, the structure is great, right? We looked at how it is formed and... what dictates how it is going to occur, but what's the use, right? What is the final reason for this function is to provide the protein, the structure it needs to do the function that it needs to perform. So these, all these secondary structures that were created within that polypeptide chain, all that structure that happens in the tertiary structure is, it's one goal to provide it that functional goal that it needs to perform. So within a particular polypeptide chain, within that final protein, you're going to have several functional domains. Some proteins may only have a couple of different functional domains. Others may have several. They may have many, many different forms that occur many, many different directions they do, many functions they perform. So here are, you know, we looked at how last week, actually, when we were looking at biological membrane protein functions, We looked at how many of these alpha helices can kind of hang out together, right? They can cluster together to create a pore so that molecules could go in and out of that structure. You can think about a structure of a final protein enzyme where the way these beta sheets are lined up and the way the alpha helices are structured will create that active site for a particular molecule to come bind to it in order to make it work. right, in order to create an enzymatic reaction, in order to, for a process to occur. Similarly, these beta sheets can also, and we looked at one example of this in bacterial membrane proteins as well, the bacteriorhodopsin, or even the water channels, where these beta sheets were forming a channel or a pore, allowing different types of molecules to go in and out. So the whole final goal of these structures is to create functional domains that can then do work for our cells. Now, another way that our cells or proteins will kind of maintain these conformation, these functional domains, these structures is through another type of interaction. And these are disulfide bonds. This is the only time where you're looking at now an actual covalent bond, right? Because up till now, we've just looked at hydrogen bonding, electrostatic interactions, van der Waal forces, everything that was just kind of transient, not so strong, not fully covalent, non-covalent interactions. But for disulfide bonds, these are going to form between very specific types of side chains. So if you have two cysteine amino acids next to each other, right adjacent to each other, they can create this, they both have this SH group, right, and those can interact with each other where they lose the hydrogen and they form a bond between those sulfides, creating that disulfide bond. It's a strong bond obviously because now it is a covalent bond. It usually is seen only outside the cell. because in the cytoplasmic environment you won't typically see it and the cell the protein is typically going to be found in that normal conformation where the SH groups are separated but in the outside environment if this protein was to go in the extracellular portion of the cell you will see that it will change conformation and create this disulfide bond now when that happens you can imagine that that's going to change that conformation of the protein slightly, the final structure slightly, maybe to create a particular type of binding pocket or activation domain for that protein to occur, right? Now, we talked about how you need to have these structured domains within it. It doesn't mean that the entire polypeptide chain is all made up of structural domains, right? I get all is needed for a function to perform. Typically proteins will have areas of domains that have functional properties associated with them, interspersed with larger areas or, you know, sections of polypeptide chains. That is just the unstructured region for that protein and doesn't really need to be part of any of the actual function involved in there. Now, all of those areas are important in maintaining its structure, but not to the same extent as these little domains are, right? So if there was, for example, a mutation that occurred out here in one of the unstructured regions, sometimes it will go unnoticed and will have absolutely no final consequence on the protein because it doesn't disrupt any of the structured domains and it still allows the overall protein to maintain its final conformation well enough to do the work that it needs to do. However, I think that's a good point. if one of those unstructured regions were to get a mutation in a way that it destroyed that conformation and allowed one of these domains to not be in their proper orientation, then you would obviously see an effect. On contrary, every time you have mutations, you know, within these actual structured domains, they have a higher probability of causing an effect. effect on the functional capabilities of that, right? Now, some of these unstructured regions have, like I said, no real function. Others, they can have actual functional associations too. They are unstructured, but they still have importance in their final confirmation. So in this case, you're seeing a tethering interacting proteins where Your all the structured domains are within the center and then you have these unstructured domains that are maintaining its structure on the outside. And these domains, these unstructured areas can allow for different polypeptide chains to get together in a final conformation. They can allow for the domains to remain in their correct format. So they will still have important importance in their overall activity. So we talked about a little bit misfolded proteins earlier. Well, misfolded proteins, anytime they occur, can have very important consequences, right? It could destroy the function of that one single protein. So if it is an enzyme, it doesn't function anymore, you can't do the work that it needs to do. But it can also lead to disease through other ways. So here is an example with normal prion protein versus an infectious protein. Anytime these proteins are misfolded so that they no longer are structured the way they typically are, you will see that they will create these abnormal aggregates or structures that then cause problems for the host in this case, or in the case of amyloid, when we talked about those amyloid fibrils create these aggregates that could, that essentially destroy the cells because they are going to get stuck within those brain cells and they won't allow for proper signals to get transmitted and they will also destroy the functioning of that cell itself leading to death of the cell eventually and disease in the individual that is having it. Questions? You guys are very quiet today. I did have a question about what exactly entails a domain. Yes, so a domain would be, and we'll actually, for the structural domains, we're going to talk a lot about it last time, next time, not last time, next time. The structured domains are these actual functional regions of the protein. So maybe a particular, for example, if you're looking at a transcriptional regulator, Maybe one of these domains is responsible for binding to the DNA. It contains the amino acids that are going to bind to the specific region in the DNA, which it's going to activate or repress depending on what it does. Another section on the same protein, maybe what is going to be interacting with the receptor on the cell surface or to a molecule outside in the cytosol to become activated. So it's... typically found maybe in the cytoplasm or the membrane, doesn't do much, hangs out until something binds to it. So that would be another functional domain, right? That will be the receptor binding domain or a neural front. smitter binding domain, whatever that function is, which when activated would lead to this protein getting translocated somewhere else, binding to the DNA and then activating its response. It may have a signal section on there, right, to create, to provide instructions on where it needs to be bound, whether it is in the membrane or it is in the nuclear, you know, membrane, or it needs to translocate to the nucleus. Those are all the actual functional domains that are areas of the polypeptide chain that provide the function for that particular protein. Does that make sense? Yes, thank you. Good. And again, we are going to talk a lot about functional domains next time, and we're going to see examples of that and multiple types of proteins as well. So the last thing that we're going to kind of talk about is that quaternary structure that I mentioned, right? So many proteins, you know, there are proteins that function by themselves. It's just one single protein molecule that is needed to perform its function. But many protein molecules actually need multiple copies of themselves or of different types of different versions of themselves or even different proteins in order to make their final functional unit. Right. When you're looking at just polypeptide chains that are just, you know, working as a group, so you need two of them or three of them, they come in two flavors. You can have what we call symmetrical proteins, right, which is shown, one example is shown here in this CAP protein complex. In this case, you have two identical polypeptides of this CAP protein together as one to create a dimer that then performs the function. that it needs to perform. So this would be a symmetrical dimer. Another example is again with some of the enzymes and some of the other proteins which work as homotetramers. So in this case you have four copies of the same polypeptide chain. They all form their same exact tertiary structure but they can't work alone. They have to come together in this particular form, right, and where those four are interacting with each other. And you can see they're always interacting through the same binding region with each other, right? So these different colored areas are the different domains. You can imagine, if you can imagine them. These are different beta sheet areas that are, that may be different functional domains. And they're always interacting between their, there's the blue and the orange colored functional domains, the beta sheet. And in doing so, they're creating this tetramer that's going to be that final functioning molecule at the end of the day, right? So both of these are examples of large proteins that contain more than one polypeptide chain subunit in their final functional form. So you can also, on the other hand, get asymmetrical findings as well, right? You can have... asymmetrical dimers or tetramers or whatever structures as well where you have different isoforms for example the alpha or beta form or different types of proteins entirely coming together to do their work together so at the end of the day proteins can come in a variety of different shapes and sizes and functional forms depending on what it is that they are going to do at the end of the day you can have various forms of these proteins and they may be long fibers or globular or they may be more structural depending on what it is that they are doing. Okay. Identical protein subunits. So this is again, it's going another example of where multiple polypeptide chains of the same type come together to form the final functional unit can form extremely complex structures. So they don't have to just work together towards one function, they can actually form other structures as well, especially in a multicellular organism or inside the cell. So here you are shown two examples where you have identical protein subunits, for example, in the in our body with the actin binding or the microtubulants that can form together to form alpha. helix structures, they can form spherical shells, they can form hollow tubes, they can form filaments, depending upon what their final function is, what their final role is in the upkeep of the cell to do what it needs to do. do. So in these cases, you see that the individual subunits look the same, but they can bind to each other through their binding site to create complex structures. So here's one example of how that may work. In this case, it's more of a lock and key mechanism to create the binding structures to create the helix. Or you can have these similar type of structures to create a ring molecule together. Okay. So actin subunits are the biggest example that you may be familiar with where they come together to create these hollow tubes, right? Or the, or they make filaments rather, and the tubulins would be examples of where you create these hollow tubes to maintain the structure of the cell to do work that they need to do in order to maintain that structure. Okay. So other proteins are just going to be globular where They look, you know, individually, they're just this little structure on their own. But within, embedded within their structure will usually be some type of binding site for a molecule to activate it, inactivate it, to create the enzymatic reaction. If it's an enzyme for it to function as that enzyme product. So they, here you have two examples where the elastase and chymotropin, where, you know, If you look at them, yes, they're both kind of amorphous creatures, but they do have differences in the way they function and obviously the way their structure is also maintained. Another type of shape that you're going to see in proteins is their fibrous shape. Again, structural proteins are many times fibrous in nature. So here you're seeing a short section of a collagen fibro where... you know, if you were to enlarge it and look at it, there are three collagen molecules that are collagen proteins that are kind of coiled coil around each other to create a triple helix structure that is used to maintain that structure in the extracellular matrix in our body. You can also have elastic fibers, right? which you also see many times in your structure as well, and as well as in your muscles, that can stretch and relax as the environment needs according to their functions. These elastic fibers will many times have multiple areas of binding interactions within them to create this kind of a cross-linked structure that can then allow it to contract and relax. Sometimes these are other proteins that are helping it link up with each other, right? So it doesn't have to be the same protein that is interacting at all levels. This week, you're doing this one discussion post where you're looking up a protein of interest and you're looking up a type of a model for it, right? To post as part of your discussion post. Now, you can find the model in any of these forms or even if you have an actual model. maybe electron micrograph of it to show the actual structure of it that's great too but there are different ways that they may be depicting those models you can have a backbone model where it's just basically showing the general structure of that protein it's probably the least informative of them all a little bit harder to notice sometime how that works um the ribbon model for students typically is very easy to see and intuitively look at it will show you all the beta sheets that are present in there, the direction they are going in. It will show you any alpha helices very clearly that are present in there. And then it will show you those kind of unstructured areas of the polypeptide chain as well. A VIR model will show you the backbone along with the amino acid side chains that are present in there. And we'll show you basically how those side chains are kind of interacting with each other or the environment. a little bit better, which is not seen in either the backbone or the ribbon model, obviously because of the way they are created. And then finally, your space filling model is where you kind of see the more globular structure of that final protein. In most of these, you will notice that they will have some type of color confirmation to help you follow the path in which they form, and they'll always have the N and the C terminus marked. in some way. It will be listed on those sites how they are using those. Now, how do we actually determine these structures, right? As scientists, we can use different sophisticated techniques to do that. The ones that are most commonly used are NMR x-rays and cryo-electron microscopy. In an NMR, you have your proteins labeled with some type of molecule so that they can be isolated and looked at. You run them through the NMR machine to look for the spectrum of that protein, but you need some expert analysis in order to predict some type of a structure. structure. That's usually the first level of determining the structure. It's just going to give you an idea on how it is. It needs a lot of expert, you know, information before you can figure out exactly how that works. The other two ways are extra crystallography and cryo electron microscopy. So extra crystallography, you would know from the way DNA structure was also figured out, right? In this case, you create a structure of your crystal, you crystallize your protein, you isolate it, crystallize it, and then you run it through x-rays to form a diffraction pattern off of that crystal. And that will give you an electron density map that you can then create into some kind of a structural model. And you kind of repeat this process until you are able to get a more refined structure. Again, this will require some type of expert analysis to figure out those patterns. However, it is going to give you more information than a simple NMR spectra. And then finally, you have cryo-electron microscopy, which gives you the most detailed structure information. In this case, you actually freeze those crystals, the protein crystals, and then look at them. through electron microscopy to see how those structures are getting maintained and created. Again, you need to either have purified protein or you can actually do that in a specific type of cell structures as well where it is labeled so you can follow it along and see exactly where it is and how it is working. Okay, so this is just a kind of a review of what we did today. We want to understand how the shape of protein is created, dictated. We want to know the various levels of protein structure. So going from the primary long chain of amino acid to the secondary, where you have the alpha helix and beta sheets as common folding patterns formed through interactions within the actual backbone of the polypeptide chain using hydrogen bonding, non-covalent bonding. Thank you. interactions to how the protein is going to fold into its final form to maintain the lowest energy state, and then how these structures are maintained, right? The helices are going to form readily biological structures, but they are going to then be maintained in that environment through that tertiary structure that is maintained around them. Beta sheets are going to form rigid structures at the core of many proteins and they are on, they are going to be based upon hydrogen bonding and non-covalent interactions in the polypeptide chains lying side by side. They come in parallel and anti-parallel form depending on which direction the beta sheet is running. The proteins because of this are going to come in very complicated shapes and structures. Some work alone. some work as homodimers or heterodimers, depending on what different proteins they're interacting with to form their final functional form. If you have misfolded proteins, they can form aggregates that can lead to disease, or they can also lead to just misfunctional proteins or non-functional proteins. Proteins inside our cells are folded with the help of chaperone foods that help maintain the right environment. or isolate them so that they can fold properly without forming aggregates with other polypeptide chains. Okay, right, so other things to remember is that proteins contain a lot of unstructured regions, right? Those unstructured regions can be important in maintaining the proper conformation for the actual structured domains, actual functional domains. or maybe not as useful depending on that polypeptide itself. Many possible polypeptide chains are going to interact with each other in order to form their final function group and those can be classified into families based on that. We will talk a lot more about it next time. Large poly proteins usually contain multiple polypeptide chains of the same type or different types as we talked about. They can assemble together to form filaments, sheets, or spheres that have functional consequences at the end of the day. Some types of proteins, especially structural proteins, are going to have elongated fiber shapes. Extracellular proteins will be examples of those as well, but they are then further stabilized by covalent cross linkages and disulfide bonded bonds like we talked about. Any questions? questions. I'm going to stop the share for a second. Anyone have any questions? I have one kind of about lab tomorrow. Okay. So I have a nine o'clock class, so I won't be able to make that lab Zoom. Yeah, that's fine. Remember, this week's lab is not a required Zoom session, so if you don't come, that doesn't give you anything, you know, any negative penalty. All the information is already online for this week's lab, and there are multiple kind of small activities for you to walk through and go through, and then that discussion post to do. So everything is already present online for you to do. There is no need to... for that i'm just going to be basically going over any questions that people have that's it and i will post that online too just like usual so if you have any questions you can get them answered okay thank you okay i am going to pass

working on membrane proteins, right? As well as membrane structure. The whole week, last week, was biological membranes.

So what are membranes made of? What are the two main components of membranes? You guys can just unmute and blurt it out or write in the chat like usual, just so we can get a little bit of a review before we get started on today's lesson. Lipids and proteins, good. What...

is special about the lipids that make up the biological membranes? Bilayer. So the membranes themselves are bilayers, that is correct.

But if we were to look at the individual lipid molecules inside it, what do they look like? The hydrophilic and hydrophobic ones. Yes, that's true.

They have hydrophilic and hydrophobic components, which makes them what? What is the term that we talked about? for molecules like that. Amphimatic?

Amphipathic, exactly. Now, also, we were to look at the hydrophilic versus the hydrophobic ends. What makes up the hydrophobic end of the lipid membranes?

The phosphate? The hydrophobic, please. or hydrophilic the chain long chain of yes the fatty acid chains are what are going to make the hydrophobic piece and how many fatty acid chains in these molecules two two good what has three so yes the fatty acid chains that are in your lipid membranes there are two fatty acid chains per molecule What has three?

We did talk about a type of molecule. Yes, triacylglycerols. Those were the ones that had the three chains instead of two. No problem. Now, those three fatty acid chains are linked to a glycerol molecule, right?

Just like in the lipid membrane, you have the two fatty acid chains linked to the glycerol. What are triacylglycerols used for? What are they good for?

If they are not part of the membranes, what are they primarily used as? Their storage lipids. Exactly.

They are going to be your storage lipids. Okay, so now going back to the lipids in the membrane, you have two fatty acid chains that are linked with glycerol. And then what else?

What makes them hydrophilic? The phosphate. You have a phosphate on top of it. What else can you have on top of that phosphate or on top of the glycerol?

Glucose binding? Not glucose, just glucose, but sugar binding. Hypes of sugars that can bind, yes. What are the lipids called when they have those sugar bindings? Glycol, yeah.

Yes, Felix. Perfect. Glycolipids.

They are called glycolipids. And then if they have a phosphate, is that all they will have? Or sometimes would they have other things attached to it, to the phosphate group as well? They'll have a polar group on top of the phosphate, right? Exactly.

You can have polar groups on top of that as well. Exactly. We talked about the choline molecules being attached to it. We talked about others being attached to it.

Good. Now for the protein components, these proteins are going to be in different forms, right? So can you tell me some ways that they can interact with the membranes? So there are two main categories of these proteins, right?

Who can tell me what they are? Isn't it extracellular and intercellular? Almost, not quite.

No. So you have the extracellular and intracellular side of the membrane. And remember, it is going to be different in the type of lipid composition. But for proteins specifically, let's think about that.

Integral and integral. Integral is one of them. Good. What's the other one? Peripheral.

Peripheral. Good, Alicia. So yes.

So they are going to be integral and peripheral proteins. What's special about the integral proteins? What are they doing? Why are they called integral proteins?

Aren't they embedded within the lipid bilayer? Yes, so they are integrated into the lipid bilayer, hence they're integral proteins. Do they have to be in both membranes, both layers of the membranes to be integrated, or could they just be in one? I think they have to be in both.

So these were some of the examples we looked at were only integrated on one side of the membrane, right? They don't have to be integrated into both, but they do have to be attached within the membrane. So they are embedded within the membrane either completely trans, you know, if they're passing transmembrane proteins, they're passing both side of the membrane.

Versus if they are just integrated to the one side, they're linked either by their hydrophobic area, but then their amino acid sequence, or they may be linked to a fatty acid chain, but they are integrated into the membrane itself in just one side, right? But then peripheral proteins, what about those? How are they different? What are they interacting with?

They form temporary bonds with the cell membranes, which allows them to easily detach and attach. So it's, in some cases, they may be a temporary bond. In some cases, it may be that they are attaching to a protein that's already embedded within them, but it's a loose attachment.

It's not a complete embedding within the membrane. It's just, you know, more relaxed attachment to those sites. Good.

Okay, so we're going to go ahead. and get started on this week's lesson now. And we are going to talk about that. Okay.

So next week, next lecture, when we start talking about the function of proteins, we're going to then review some of the function of the membranes as well as we talked about them to kind of make sure that everyone is on the same page on that as well. So I'm going to go ahead and share my screen so we can hear. get started on that.

It's sharing, guys? Yes. Yes, perfect.

The chat shows up on top of it. Yay. for her. Okay, so today we are going to look at, we're going to start chapter four, and today we're going to focus on protein structure itself. So we're going to look at what makes proteins, how do we build them, and then what different types of structures can be formed from them once you have your amino acid sequence.

And then next lesson on First day, we are going to focus on the function of proteins. So that's what you're going to be doing this time. Today is all about shapes and structure of protein.

So why do we care about proteins, first of all, right? We care about proteins primarily because they are the worker beads inside ourselves. They are the ones that are doing all the functions associated with What we need to do to survive, to do the work that we need to do, to look the way that we need to look, all the good stuff. There are seven main categories of functions that they perform.

You can have enzymes that are going to catalyze all your chemical reactions. We talked a little bit about that earlier as well. Then we have structural proteins that are going to provide support for the cell, right, both intracellularly. with your tubulin and microtubules and actin fibers and then extracellularly.

The way they bind to the make the cells bind to the matrix interact with each other the way an organism is maintaining its shape and structure. Then you can have transport proteins that will carry your small molecules both within the cells and then also through the bloodstream. or another way all along the bodies. Then you have motor proteins that are going to help us generate movement both at the cellular level as well as at an organismal level. You can also have storage proteins that are going to store small molecules, receptor proteins that will send signals kind of like what we talked about last time with biological membrane, the proteins that we're binding.

receptor proteins that were binding signals from outside and taking them in to perform, to respond to whatever environmental factor they were getting exposed to. And then finally you have transcriptional regulation proteins that regulate transcription of our DNA to regulate how our DNA is going to be expressed and what parts are going to be expressed or not. So all these These are extremely important functions, and that's essentially what's keeping us alive, is all these worker bees of proteins. Now proteins are made up of amino acids. Those are the basic subunits of our proteins.

If you look at an amino acid structure at a very basic level, you will see that they will have a carboxyl group on one side, amino group on the other side, right? And then you have your main carbon in the center with the typical hydrogen on there. Now this can change right under different pH so that this carboxyl and amino group can become partially charged.

So your carboxyl group will have your partial negative charge and the amino group will be your positive side of this amino acid. This allows for different side chains to be attached as well as for it to interact with multiple amino acids to create that long chain of amino acid that it needs to produce. So in our cell where our pH is close to seven, the amino acids are actually going to be present in this ionized form. So they are ready for binding to other amino acids to create the polypeptide chain that we need to have.

Right. So in this case, this methyl group is what you're shown as your side chain. Right. And this is going to be making up this amino acids, but this ionized. amino acid is what's needed to create the polypeptide chain.

Now when we look at the amino acids in general, they can be found in two optical isomer forms. So you can have the L versus the D forms. Our body exclusively uses the L amino acids to prepare the proteins. So cells in general, they're going to be using the L form of the amino acids to create proteins inside it. Now when we look at the how these polypeptide chains are going to be made, this is again just review from chapter two, but amino acids are going to be joined together by peptide bonds using those carboxyl and amino groups, right, the ionized carboxyl and amino groups.

So here you have an example with a glycine amino acid and an alanine amino acid. When they are forming their bonds, they're going to combine the carboxyl and the amino group. It's a condensation reaction, so you're going to have removal of water molecule from there to create your peptide bond between those two amino acids.

So when we are making proteins, we are essentially making proteins with amino acids linked together in a long... polypeptide chain according to the instructions provided by the mRNA. And the main backbone of this polypeptide chain is going to be these carbon and amino and carboxyl groups, right?

So this is going to be the main backbone of the polypeptide chain. The side chains are going to kind of hang out to the sides of it on either side, depending upon what they are and what their you know, overall function is, what their overall basis is. So to the gray boxes, these are telling you the main structure of the amino acids, right? That's always gonna be constant. And these colored boxes are your side chains that are going to show differently depending upon their chemically distinct properties, right?

So you may have some charged amino acids, which are shown right here in blue. You may have some uncharged but polar groups, side chains like here with a hydroxyl group on one side. You may have some nonpolar groups, right, that are going to be hydrophobic in the green. So depending upon what it is that you're building, you'll have a combination of these amino acids to make up this particular polypeptide chain. At the end of the day, you'll still have that carboxyl terminus on one end, which will have that negative charge and the amino as terminus on the other end, which is called, you know, we typically call this the N terminus and this the C terminus of the polypeptide chain or our final protein.

So. That is how you would be building your polypeptide chain. Now, looking at the amino acids that you're going to see inside our typical cells and our bodies, you will find that there are 20 different amino acids that are used to create our polypeptide chains or proteins inside our body. There will be some that are going to be charged. You can have negatively and positively charged side chains that will make those amino acids negatively or positively charged.

You can also have uncharged but polar side chains that are still going to be hydrophilic, but they have no charge associated with them. And then you have a range of amino acids that are considered non-polar or hydrophobic. So depending upon the protein where it's going to be residing at the end of the day, what function it's going to perform, what structure it's going to take up.

It's going to be a mix of these amino acids in particular sequences to present that inflammation in the right way. The way proteins are typically made, the chain is always presented with the N-terminus first. So when you're going to see polypeptide chain sequences on the test or quizzes or in papers, you're going to see the N-terminus being presented first and the carboxyl group or the C-terminus at the end of that. polypeptide chain.

Okay. So this is another just to show the actual structure of these side chains and some other properties that they may also hold because of their charged nature or the other structural nature. So you can see that the negatively and positively charged amino acids will also contain additional properties. So they can be acidic or basic in nature.

Then you have polar side chains that are able to form hydrogen bonds because of partial charges on them, but they are not ionic in nature. Otherwise, you have non-polar side chains that are going to be different in the type of interactions that they can perform. So they won't be able to form the typical hydrogen bonds, but they will be able to form other types of bonding structures between them.

And the actual amino acid backbone will still have. the negative and the positive end to form hydrogen bindings. So there are three different types of non-covalent bonds that help this long polypeptide chain that forms after translation to create the final protein structure that can actually do work. These non-covalent bindings will include just simple electrostatic attractions because of the negative and the positive charges that are present on these side chains. It could include VanderWaal interactions or hydrogen bonds.

Now, all of these by themselves are very, very weak interactions, right? They are not very strong and they're usually transient in some cases. But when you have a bunch of these happening together, it makes up for a strong structure at the end of the day.

Now, these can happen both within the side chains as well as with the backbone, the backbones, just within the backbone or back. and the side chain. Any one of those combinations can happen to create the final structure that you need. The two common structures that form because of these type of folding patterns is alpha helices and beta sheets. Both of these are specific types of interactions that happen when you have some kind of a repeated pattern happening inside your amino acid sequence that allows for a a specific type of holding to occur.

So in the case of your alpha helices, you are going to have the NH and the CO bonds interacting with each other, usually in a very repeated pattern, in a typical pattern to create that structure to make this alpha helix structure. In beta sheets, you have side chains or the backbones rather that are the backbone is interacting with parallel polypeptide chains. So here, again, you will have some kind of a repeated structure.

so that you can have all these backbones interacting with each other. In both cases, the side chains are not involved in this first set of interactions. This is all happening at the backbone level. So just at the internal level, you'll have these hydrogen bondings that are happening between the carboxy and the N-terminal sides of the actual backbone to create these type of alpha-haloses and beta-sheets. So alpha helices, first of all, if we talk about those, they are going to be responsible to create rigid cylindrical structures.

They are not always going to look exactly the same. It depends on the pattern that you see, the regular repeated pattern that you're seeing within the backbone for the type of amino acids that are there. So the hydrogen bonds are going to be between every, you know, in one, um, In the typical example between every fourth amino acid linking the carbon oxygen of one to the NH of another, that causes this turn to occur. And depending on which side it is on, the way these interactions happen, it could be either a left-handed helix or a right-handed helix.

And the turn would be every about 3.6 amino acid. Now, depending upon how many amino acids are there, in between those typical turns, how many are in this space between that, it could be a more loose alpha helix or a more tight alpha helix. So if there are five amino acids in this space versus if there are three or six or 10, it's going to change how big this alpha helix is in between that space, right? And that's what's shown kind of over here is that how many amino acids are present in between. these bondings to create a more tightly linked alpha helix versus a more loosely linked alpha helix.

This is one of the main protein structures that you see when you have proteins that are transmembrane proteins that cross lipid bilayers. It takes about 20 amino acids in this alpha helix to create a more tightly linked alpha helix. create this enough length to pass to completely pass that lipid bilayer.

In this case, the hydrophobic amino acid side chains are going to be what's on the outside. And the inside, the backbone is obviously hydrophilic. And that's creating these hydrogen bondings and other, you know, electrostatic interactions to create this alpha helix inside that is going to then create this alpha helix structure. Now if you look at it, it almost seems like there's a channel in there, right? But there is, it's not, there's not enough space in that little helix to have any type of molecules pass through.

So it is a very small structure at the end of the day. No ions can pass through it, no molecules can pass through it. You would need multiple helices like these to create a pore to create a structure where molecules or ions could pass. Any questions about alpha helices? Oh, thank you.

Okay, so you said that what part of the helix is hydrophilic? So the backbone is hydrophilic, essentially, right? So all these interactions are happening in that hydrophilic backbone, all the hydrogen bondings are there.

All the side chains in this particular case where you have this transmembrane protein are going to be hydrophobic. So the hydrophobic amino acid side chains are kind of forced outward towards the outside in this case because the way the helix is turning with interacting just with that hydrophilic backbone in the back. Does that make sense? Yes, thank you.

Any other questions? So here you can see that a little bit more clearly, right, in this ball stick model. So these amino acid groups, you know, the side chain groups would be what typically would be your hydrophilic, not hydrophilic, hydrophobic groups in case of a transmembrane protein.

And so when the hydrogen bonding occurs in the backbone, so remember, if you look at this all the r groups are excluded from this bonding it's only the backbone interaction so only the those carboxyl and your amino group interactions so as they are making those interactions that causes them to become inverts right as they're creating those hydrogen bonds. And these are groups that are hydrophobic would then tend to stick outside, which is where the lipid membrane would be. So they would be associating with what is energetically favorable for them in that case.

Okay. Okay. Any other questions for that before we go to the next one?

Okay, so now sometimes that's enough, you create a single structure, and that's good, you're in a area that's hydrophobic, all your amino acids were hydrophobic, and that works. But there are other times that you have a situation where there are multiple areas of these hydrophobic amino acids within that, I mean, you know, that long amino acid chain, the polypeptide chain. In that case, sometimes these multiple alpha helices that form at you know, the first stage at the first level will intertwine with each other in order to maintain those hydrophobic regions within each other, right?

And it can be that these particular, in this case, this protein was going to be in the cytosol. So it doesn't want those hydrophobic amino acid side chains to be interacting with the cytosolic aqueous environment. So by creating this intertwined structures, those alpha helices would maintain the hydrophobic structures within that coiled coil conformation, while amino acids that are then going to be towards the outside would tend to be more hydrophilic. And here's an example of how that shows. So the green areas are going to be your hydrophilic and the red stripe are hydrophobic, right?

So by coiling against each other you're going to create an environment where you are maintaining the hydrophobic together and the hydrophilic separately another type of basic structure that forms in the secondary layer of structure is called beta again this is also going to look at just hydrogen bonding or electrostatic binding between the site and not the side chains but just the main backbone of the amino acid, the polypeptide chain. In this case, the direction of the arrow is going to show you which way the C-terminal is. So in this case, the C-terminus is going that way, this one will be here, right?

So that is going to point towards the C-terminus of the polypeptide chain of that region of that set of amino acids. So in beta sheets, You have, instead of having amino acids that are next to each other doing hydrogen bonding, you have parallel areas, repeated sections of the polypeptide chain that are lying side by side to each other, interact through hydrogen bonding. When that happens, you then create this kind of a very stable, rigid sheet of protein that is going to help you. create a very stable structure.

So this kind of interactions are very common in structural proteins and they are also seen in amyloid structures. So kind of what you see in neurodegenerative diseases like Alzheimer's. You can see examples of that even in yeast.

These amyloid structures will form that resemble very much those insoluble aggregates you see in the brain in neurodegenerative diseases as well. So these particular beta sheets can go both parallel or anti-parallel to each other, the different segments. So if all the polypeptide chain sections line up so that the carboxy terminus is at the same direction in all cases, as is shown here. So the polypeptide chain is folded in a way that it's always the C terminus is always in the same direction between that interactions. It's called a parallel bit of sheet and if they are lining up so that they are in opposing direction as you see up here, they are going to be what you called anti parallel configuration.

So those are the two different types of beta sheets that you should be aware of the parallel versus anti parallel. You should be able to tell that the arrow is pointing towards the C terminus and that it's going to be on the interaction is going to come from. Sheets that are polypeptide sections that are laying side by side, having hydrogen bonding interaction between them. And again, you can see that from here that the R groups, again, are excluded from this interaction. It is solely between the backbone.

Right. So, again, the carbon oxygen and the nitrogen hydrogen sections of the backbone that are interacting to create these hydrogen bondings. to create that final beta sheet in the structure.

Questions on beta sheet? I'm sorry, does the beta sheet follow the same configuration throughout? Same configuration, meaning what?

Like one entire beta sheet is always going to be parallel or anti-parallel. So a section of the beta sheet in one, you know, let's say that there's a protein that has multiple sections of beta sheets. A particular beta sheet would typically follow the same structure, but that would change, that could change potentially in a separate area of that polypeptide chain. So if you had one section. and then you had an alpha helix in between and then there was another section, it doesn't have to follow the same pattern in those two sections.

Okay, thank you. Okay, so now we go to other, you know, types of interactions that can happen too and also what exactly are these interactions doing, right? So what is dictating how these proteins chains or polypeptide chains are holding in these particular conformations?

So obviously the hydrophobic forces around them, if they're stuck in a hydrophobic environment, or the hydrophobic side chains are going to be part of what dictates where the protein is going to fold and how it's going to be folding up. So when you have these hydrophobic forces, when you have a lot of non-polar side chains together, they are going to tend to form a more compact conformation because they would all tend to kind of get away from that aqueous environment, get inward and create a more compact structure. So they are usually going to get add into a central core or some, they will get embedded within that protein, final protein structure so that the out, the one, the, you know, polypeptide chain, as well as the side chains that are on the outer side of that protein are interacting with the aqueous environment.

typically the case inside the cell. The polar side chains can form hydrogen bonds obviously with the water molecules around them as well as themselves between the different side chains as well as in the backbone as well. So the hydrogen bonds are what's going to stabilize that final protein structure. So hydrophobic forces dictate how it's going to start to fold up and the hydrogen bonds then stabilize that structure.

through those hydrogen bonding interactions. These interactions, like I said, can occur between two side chains. They can interact from the backbone to the side chain of that molecule, or they could be interacting with the water molecules on the outside as well, right? That's another thing that they can do.

And obviously, just like we talked about in your alpha helices and beta sheets, you can have the side chain to side chain interactions, which are the ones that are most common inside. that secondary structure. Now once these proteins are folding, they're essentially folding in a way so that they can be at their lowest energy state within the environment that they are in.

And that can change as the pH changes, as their localization change. There could be slight modification to that conformation to that structure if that protein is going to be activated in a particular way, in a different environment. When we isolate proteins from cells, we want to maintain that structure, obviously, if we are going to study their function.

However, in some cases, we are just looking at the structure, not structure, but just the amino acid sequence and whether or not the protein was there, in which case it may not be that important, right? We could just extract it without worrying about maintaining its final structure intact. If we expose the... protein to high concentration of urea, which is found in many extraction buffers, you tend to denature the proteins to their back to their primary structure, which is the single long polypeptide chain.

However, sometimes if you remove that urea and give them just the right environment, it can spontaneously reform that original confirmation. That tells you that all the information that was needed to mint to create that structure is already present in this polypeptide chain. And you don't really need anything outside of that to maintain its structure, to create that structure. Now, before I talk about some other aspects of this, can you think of some other ways that I can denature a protein?

So if I have a protein that I've isolated from a cell, it's intact right now, what are some things I can do? Heat, good. So heat would denature the proteins again by destroying those interactions, right?

Those different types of hydrogen bonding, electrostatic interactions, the van der Waals forces, those get broken down by heat and the protein gets destroyed in its structure. pH would also affect the protein exactly. So if a protein is typically found at pH 7 and you suddenly put it at a really basic or really acidic environment, it's going to change that as well.

Electric shock can create again some type of a structural destabilization as well. UV wouldn't necessarily directly affect all proteins can affect some of them, but not all of them for sure. Okay, so now we have our proteins, we are looking at how they maintain the structure, right.

And so we are going to look at some other ways that they can control it. So each protein, like I said, is going to form a single stable conformation, that's its typical conformation, that may change slightly when they get into a different environment in order for it to become activated or inactive. Now inside the body, inside the cells itself, there, it's a very crowded environment.

There is a lot of this protein already folded up there that maybe, right, there are other proteins that are present there. There's, there is a lot going on in, you know, in an isolated environment, in a test tube, it's a different thing. But inside the cell, it's a busy house.

So Inside the house, many times you need chaperone proteins to guide the folding of the polypeptide chain so that they can create that final structure in a proper manner and in an efficient manner. So if you let a protein kind of synthesize by itself, it may take longer. It may not be able to fold properly because it may end up getting crowded up by all these other polypeptide chains and form aggregates or get. incorrectly folded.

However, with the help of chaperone proteins, they can guide this protein to polypeptide chain to correctly fold into its proper conformation along the most energetically favorable pathway so that it is done in a more efficient, quick manner and work properly. Now, many of these chaperones are going to require ATP binding and hydrolysis to work properly. and that's going to then provide the energy for this process to occur. Now some chaperones will simply bind to the polypeptide chain itself and kind of guide it into the right conformation. Others can act as isolation chambers so they kind of almost work like an enzyme structure where they provide just the right environment they isolate this newly.

synthesize partially folded protein into this place, into the right environment where it's by itself and it can fold up properly into its final conformation. And then it's going to release it back out into the cytosol or whatever environment it is in at that time. And that is a somewhat complex process that it can go through.

But this allows the prolipeptide chain to form its final structure. without the risk of aggregating with other polypeptide chains or other proteins that are present there. This system will also require input of energy, obviously, in the form of ATP, so that this whole process can occur where the polypeptide chain goes in, the chamber cap is on there, and then gets released out once it is formed properly. Proteins have several levels of... organization starting from your polypeptide chain all the way to its final functional form.

The primary structure of a protein and again this is a little bit of a review from before is simply the long polypeptide chain that forms after translation. This is just the amino acid sequence of that particular protein. The secondary structure is that first level of organization through presence of alpha helices and beta sheets. that occur because of interactions with the backbone, right? The hydrogen bonding that happens in the backbone to create structures.

The tertiary structure is going to be this 3D conformation that you're looking at after it's been folded appropriately. Now for some proteins, that's it. That's their final functional form.

For many of the proteins, however, they still need another level of organization before they can function, before they can actually act properly. And that final structure is called the quaternary structure. In that case, the proteins have to associate either with another polypeptide chain of themselves, you know, kind of like a dimer or... even a more complex structure or tetramer, or with other types of proteins in order to form their final active form.

So that in that case, that would be their final quaternary structure. That may include just other proteins just like them, or proteins that are different from them, interacting with them to create the final functional form. Okay, questions through that?

before we start talking about how that's going to affect their function? So for that final structure, it's basically they have to interact with another protein to gain their final form. So they themselves have their final form at that point.

But in order to be active, to do the work they need to do, they need to interact with another protein, either one, two or multiple, right? So an example of that is hemoglobin molecule, right? You need to have those four molecules together, two alpha and two beta molecules to form that final functional form of hemoglobin, right?

Yeah, that makes sense. Okay. And we'll talk more about it actually a lot next time when we start looking at actual functions of proteins.

Now, the structure is great, right? We looked at how it is formed and... what dictates how it is going to occur, but what's the use, right?

What is the final reason for this function is to provide the protein, the structure it needs to do the function that it needs to perform. So these, all these secondary structures that were created within that polypeptide chain, all that structure that happens in the tertiary structure is, it's one goal to provide it that functional goal that it needs to perform. So within a particular polypeptide chain, within that final protein, you're going to have several functional domains.

Some proteins may only have a couple of different functional domains. Others may have several. They may have many, many different forms that occur many, many different directions they do, many functions they perform.

So here are, you know, we looked at how last week, actually, when we were looking at biological membrane protein functions, We looked at how many of these alpha helices can kind of hang out together, right? They can cluster together to create a pore so that molecules could go in and out of that structure. You can think about a structure of a final protein enzyme where the way these beta sheets are lined up and the way the alpha helices are structured will create that active site for a particular molecule to come bind to it in order to make it work. right, in order to create an enzymatic reaction, in order to, for a process to occur.

Similarly, these beta sheets can also, and we looked at one example of this in bacterial membrane proteins as well, the bacteriorhodopsin, or even the water channels, where these beta sheets were forming a channel or a pore, allowing different types of molecules to go in and out. So the whole final goal of these structures is to create functional domains that can then do work for our cells. Now, another way that our cells or proteins will kind of maintain these conformation, these functional domains, these structures is through another type of interaction.

And these are disulfide bonds. This is the only time where you're looking at now an actual covalent bond, right? Because up till now, we've just looked at hydrogen bonding, electrostatic interactions, van der Waal forces, everything that was just kind of transient, not so strong, not fully covalent, non-covalent interactions.

But for disulfide bonds, these are going to form between very specific types of side chains. So if you have two cysteine amino acids next to each other, right adjacent to each other, they can create this, they both have this SH group, right, and those can interact with each other where they lose the hydrogen and they form a bond between those sulfides, creating that disulfide bond. It's a strong bond obviously because now it is a covalent bond.

It usually is seen only outside the cell. because in the cytoplasmic environment you won't typically see it and the cell the protein is typically going to be found in that normal conformation where the SH groups are separated but in the outside environment if this protein was to go in the extracellular portion of the cell you will see that it will change conformation and create this disulfide bond now when that happens you can imagine that that's going to change that conformation of the protein slightly, the final structure slightly, maybe to create a particular type of binding pocket or activation domain for that protein to occur, right? Now, we talked about how you need to have these structured domains within it.

It doesn't mean that the entire polypeptide chain is all made up of structural domains, right? I get all is needed for a function to perform. Typically proteins will have areas of domains that have functional properties associated with them, interspersed with larger areas or, you know, sections of polypeptide chains.

That is just the unstructured region for that protein and doesn't really need to be part of any of the actual function involved in there. Now, all of those areas are important in maintaining its structure, but not to the same extent as these little domains are, right? So if there was, for example, a mutation that occurred out here in one of the unstructured regions, sometimes it will go unnoticed and will have absolutely no final consequence on the protein because it doesn't disrupt any of the structured domains and it still allows the overall protein to maintain its final conformation well enough to do the work that it needs to do. However, I think that's a good point.

if one of those unstructured regions were to get a mutation in a way that it destroyed that conformation and allowed one of these domains to not be in their proper orientation, then you would obviously see an effect. On contrary, every time you have mutations, you know, within these actual structured domains, they have a higher probability of causing an effect. effect on the functional capabilities of that, right? Now, some of these unstructured regions have, like I said, no real function.

Others, they can have actual functional associations too. They are unstructured, but they still have importance in their final confirmation. So in this case, you're seeing a tethering interacting proteins where Your all the structured domains are within the center and then you have these unstructured domains that are maintaining its structure on the outside. And these domains, these unstructured areas can allow for different polypeptide chains to get together in a final conformation. They can allow for the domains to remain in their correct format.

So they will still have important importance in their overall activity. So we talked about a little bit misfolded proteins earlier. Well, misfolded proteins, anytime they occur, can have very important consequences, right?

It could destroy the function of that one single protein. So if it is an enzyme, it doesn't function anymore, you can't do the work that it needs to do. But it can also lead to disease through other ways. So here is an example with normal prion protein versus an infectious protein.

Anytime these proteins are misfolded so that they no longer are structured the way they typically are, you will see that they will create these abnormal aggregates or structures that then cause problems for the host in this case, or in the case of amyloid, when we talked about those amyloid fibrils create these aggregates that could, that essentially destroy the cells because they are going to get stuck within those brain cells and they won't allow for proper signals to get transmitted and they will also destroy the functioning of that cell itself leading to death of the cell eventually and disease in the individual that is having it. Questions? You guys are very quiet today. I did have a question about what exactly entails a domain.

Yes, so a domain would be, and we'll actually, for the structural domains, we're going to talk a lot about it last time, next time, not last time, next time. The structured domains are these actual functional regions of the protein. So maybe a particular, for example, if you're looking at a transcriptional regulator, Maybe one of these domains is responsible for binding to the DNA. It contains the amino acids that are going to bind to the specific region in the DNA, which it's going to activate or repress depending on what it does.

Another section on the same protein, maybe what is going to be interacting with the receptor on the cell surface or to a molecule outside in the cytosol to become activated. So it's... typically found maybe in the cytoplasm or the membrane, doesn't do much, hangs out until something binds to it. So that would be another functional domain, right? That will be the receptor binding domain or a neural front.

smitter binding domain, whatever that function is, which when activated would lead to this protein getting translocated somewhere else, binding to the DNA and then activating its response. It may have a signal section on there, right, to create, to provide instructions on where it needs to be bound, whether it is in the membrane or it is in the nuclear, you know, membrane, or it needs to translocate to the nucleus. Those are all the actual functional domains that are areas of the polypeptide chain that provide the function for that particular protein.

Does that make sense? Yes, thank you. Good.

And again, we are going to talk a lot about functional domains next time, and we're going to see examples of that and multiple types of proteins as well. So the last thing that we're going to kind of talk about is that quaternary structure that I mentioned, right? So many proteins, you know, there are proteins that function by themselves. It's just one single protein molecule that is needed to perform its function. But many protein molecules actually need multiple copies of themselves or of different types of different versions of themselves or even different proteins in order to make their final functional unit.

Right. When you're looking at just polypeptide chains that are just, you know, working as a group, so you need two of them or three of them, they come in two flavors. You can have what we call symmetrical proteins, right, which is shown, one example is shown here in this CAP protein complex.

In this case, you have two identical polypeptides of this CAP protein together as one to create a dimer that then performs the function. that it needs to perform. So this would be a symmetrical dimer.

Another example is again with some of the enzymes and some of the other proteins which work as homotetramers. So in this case you have four copies of the same polypeptide chain. They all form their same exact tertiary structure but they can't work alone. They have to come together in this particular form, right, and where those four are interacting with each other. And you can see they're always interacting through the same binding region with each other, right?

So these different colored areas are the different domains. You can imagine, if you can imagine them. These are different beta sheet areas that are, that may be different functional domains.

And they're always interacting between their, there's the blue and the orange colored functional domains, the beta sheet. And in doing so, they're creating this tetramer that's going to be that final functioning molecule at the end of the day, right? So both of these are examples of large proteins that contain more than one polypeptide chain subunit in their final functional form.

So you can also, on the other hand, get asymmetrical findings as well, right? You can have... asymmetrical dimers or tetramers or whatever structures as well where you have different isoforms for example the alpha or beta form or different types of proteins entirely coming together to do their work together so at the end of the day proteins can come in a variety of different shapes and sizes and functional forms depending on what it is that they are going to do at the end of the day you can have various forms of these proteins and they may be long fibers or globular or they may be more structural depending on what it is that they are doing. Okay.

Identical protein subunits. So this is again, it's going another example of where multiple polypeptide chains of the same type come together to form the final functional unit can form extremely complex structures. So they don't have to just work together towards one function, they can actually form other structures as well, especially in a multicellular organism or inside the cell.

So here you are shown two examples where you have identical protein subunits, for example, in the in our body with the actin binding or the microtubulants that can form together to form alpha. helix structures, they can form spherical shells, they can form hollow tubes, they can form filaments, depending upon what their final function is, what their final role is in the upkeep of the cell to do what it needs to do. do.

So in these cases, you see that the individual subunits look the same, but they can bind to each other through their binding site to create complex structures. So here's one example of how that may work. In this case, it's more of a lock and key mechanism to create the binding structures to create the helix. Or you can have these similar type of structures to create a ring molecule together.

Okay. So actin subunits are the biggest example that you may be familiar with where they come together to create these hollow tubes, right? Or the, or they make filaments rather, and the tubulins would be examples of where you create these hollow tubes to maintain the structure of the cell to do work that they need to do in order to maintain that structure.

Okay. So other proteins are just going to be globular where They look, you know, individually, they're just this little structure on their own. But within, embedded within their structure will usually be some type of binding site for a molecule to activate it, inactivate it, to create the enzymatic reaction. If it's an enzyme for it to function as that enzyme product. So they, here you have two examples where the elastase and chymotropin, where, you know, If you look at them, yes, they're both kind of amorphous creatures, but they do have differences in the way they function and obviously the way their structure is also maintained.

Another type of shape that you're going to see in proteins is their fibrous shape. Again, structural proteins are many times fibrous in nature. So here you're seeing a short section of a collagen fibro where... you know, if you were to enlarge it and look at it, there are three collagen molecules that are collagen proteins that are kind of coiled coil around each other to create a triple helix structure that is used to maintain that structure in the extracellular matrix in our body.

You can also have elastic fibers, right? which you also see many times in your structure as well, and as well as in your muscles, that can stretch and relax as the environment needs according to their functions. These elastic fibers will many times have multiple areas of binding interactions within them to create this kind of a cross-linked structure that can then allow it to contract and relax.

Sometimes these are other proteins that are helping it link up with each other, right? So it doesn't have to be the same protein that is interacting at all levels. This week, you're doing this one discussion post where you're looking up a protein of interest and you're looking up a type of a model for it, right?

To post as part of your discussion post. Now, you can find the model in any of these forms or even if you have an actual model. maybe electron micrograph of it to show the actual structure of it that's great too but there are different ways that they may be depicting those models you can have a backbone model where it's just basically showing the general structure of that protein it's probably the least informative of them all a little bit harder to notice sometime how that works um the ribbon model for students typically is very easy to see and intuitively look at it will show you all the beta sheets that are present in there, the direction they are going in. It will show you any alpha helices very clearly that are present in there.

And then it will show you those kind of unstructured areas of the polypeptide chain as well. A VIR model will show you the backbone along with the amino acid side chains that are present in there. And we'll show you basically how those side chains are kind of interacting with each other or the environment.

a little bit better, which is not seen in either the backbone or the ribbon model, obviously because of the way they are created. And then finally, your space filling model is where you kind of see the more globular structure of that final protein. In most of these, you will notice that they will have some type of color confirmation to help you follow the path in which they form, and they'll always have the N and the C terminus marked. in some way.

It will be listed on those sites how they are using those. Now, how do we actually determine these structures, right? As scientists, we can use different sophisticated techniques to do that. The ones that are most commonly used are NMR x-rays and cryo-electron microscopy.

In an NMR, you have your proteins labeled with some type of molecule so that they can be isolated and looked at. You run them through the NMR machine to look for the spectrum of that protein, but you need some expert analysis in order to predict some type of a structure. structure. That's usually the first level of determining the structure. It's just going to give you an idea on how it is.

It needs a lot of expert, you know, information before you can figure out exactly how that works. The other two ways are extra crystallography and cryo electron microscopy. So extra crystallography, you would know from the way DNA structure was also figured out, right?

In this case, you create a structure of your crystal, you crystallize your protein, you isolate it, crystallize it, and then you run it through x-rays to form a diffraction pattern off of that crystal. And that will give you an electron density map that you can then create into some kind of a structural model. And you kind of repeat this process until you are able to get a more refined structure.

Again, this will require some type of expert analysis to figure out those patterns. However, it is going to give you more information than a simple NMR spectra. And then finally, you have cryo-electron microscopy, which gives you the most detailed structure information.

In this case, you actually freeze those crystals, the protein crystals, and then look at them. through electron microscopy to see how those structures are getting maintained and created. Again, you need to either have purified protein or you can actually do that in a specific type of cell structures as well where it is labeled so you can follow it along and see exactly where it is and how it is working. Okay, so this is just a kind of a review of what we did today. We want to understand how the shape of protein is created, dictated.

We want to know the various levels of protein structure. So going from the primary long chain of amino acid to the secondary, where you have the alpha helix and beta sheets as common folding patterns formed through interactions within the actual backbone of the polypeptide chain using hydrogen bonding, non-covalent bonding. Thank you.

interactions to how the protein is going to fold into its final form to maintain the lowest energy state, and then how these structures are maintained, right? The helices are going to form readily biological structures, but they are going to then be maintained in that environment through that tertiary structure that is maintained around them. Beta sheets are going to form rigid structures at the core of many proteins and they are on, they are going to be based upon hydrogen bonding and non-covalent interactions in the polypeptide chains lying side by side.

They come in parallel and anti-parallel form depending on which direction the beta sheet is running. The proteins because of this are going to come in very complicated shapes and structures. Some work alone.

some work as homodimers or heterodimers, depending on what different proteins they're interacting with to form their final functional form. If you have misfolded proteins, they can form aggregates that can lead to disease, or they can also lead to just misfunctional proteins or non-functional proteins. Proteins inside our cells are folded with the help of chaperone foods that help maintain the right environment. or isolate them so that they can fold properly without forming aggregates with other polypeptide chains.

Okay, right, so other things to remember is that proteins contain a lot of unstructured regions, right? Those unstructured regions can be important in maintaining the proper conformation for the actual structured domains, actual functional domains. or maybe not as useful depending on that polypeptide itself.

Many possible polypeptide chains are going to interact with each other in order to form their final function group and those can be classified into families based on that. We will talk a lot more about it next time. Large poly proteins usually contain multiple polypeptide chains of the same type or different types as we talked about.

They can assemble together to form filaments, sheets, or spheres that have functional consequences at the end of the day. Some types of proteins, especially structural proteins, are going to have elongated fiber shapes. Extracellular proteins will be examples of those as well, but they are then further stabilized by covalent cross linkages and disulfide bonded bonds like we talked about. Any questions? questions.

I'm going to stop the share for a second. Anyone have any questions? I have one kind of about lab tomorrow. Okay. So I have a nine o'clock class, so I won't be able to make that lab Zoom.

Yeah, that's fine. Remember, this week's lab is not a required Zoom session, so if you don't come, that doesn't give you anything, you know, any negative penalty. All the information is already online for this week's lab, and there are multiple kind of small activities for you to walk through and go through, and then that discussion post to do. So everything is already present online for you to do.

There is no need to... for that i'm just going to be basically going over any questions that people have that's it and i will post that online too just like usual so if you have any questions you can get them answered okay thank you okay i am going to pass

Transcript for:Understanding Membranes and Protein Structures

Transcript for:
Understanding Membranes and Protein Structures