Notes for biochem .docx

• Hello. We're going to move on to Chapter 6 now. This is the last chapter in Unit 1. And in Chapter 6, we're going to talk about lipids, and particularly lipids that are involved in making up the biological membranes. The rough outline for this is we'll talk a little bit about what membranes do. We'll talk about the lipids that we find in membranes. Then we'll talk about the protein component of membranes because membranes, biological membranes, include lipids and a protein component. And then we'll talk about how materials move back and forth across biological membranes. So this is a really big chapter. There's a lot of pretty meaty information in it. We're going to divide it into four different short lectures, parts one, two, three, and four. So what do membranes do? Biological membranes have a lot of different roles, and their roles change over time or under different circumstances. Probably the first thing you think of if you think about biological membranes is their role in compartmentalization, basically serving as barriers to keep things that are inside the cell in and things that are outside the cell out. And in the case of eukaryotes, eukaryotic cells, which have lots of internal membrane-bound structures called organelles. Membranes even subdivide the inside of the cell into small, discrete domains, each with a particular functionality. And certainly this compartmentalization function of biological membranes is very important. But membranes do lots of other things as well. And these roles we'll kind of delve more deeply into as we move throughout the semester. But they play a very important role in receiving information from outside the cell. The receptors that receive outside information are found in the plasma membrane, in the cell membrane. Membranes have to have systems to regulate what goes in and what comes out of the cell. And so we'll touch a little bit on that in the last part of this chapter. And then importantly, because cells are they're moving they're changing shape they're not rigid either their structure or their form membranes have to have the capacity to change their shape and their structure as well they have to be able to move and expand and contract as the needs of the cell change in And so this puts some constraints on membrane structure that we'll dive a little bit more deeply into here now. So the main component of biological membranes are lipids. And lipids make up the fourth and final class of biological macromolecules that we're looking at in this unit. Lipids are defined not by their chemical structure, but rather by their solubility. So a lipid is classified as a lipid because it has a large hydrocarbon region. So here we're looking at two different types of lipids, the isoprenes and the fatty acids. Notice these long hydrocarbon regions here, hydrocarbon just meaning regions where there's lots of hydrogen and carbon. In these hydrocarbon regions, there are only non-polar covalent bonds. So in these hydrocarbon rich domains, there are no polar bond, no polar covalent bonds, no areas of partial negative, partial positive charge. And that means that lipids are extremely hydrophobic. They do not interact very well at all with water. Now, some lipids, including the fatty acids, might have a really small hydrophilic region on one end where you've got some polar covalent bonds, and that'll become important here when we talk about the types of lipids that are involved in making biological membranes. One of the most common types of lipids that we find inside of cells are the fats. And fats are composed of three different fatty acids. They don't have to be different, but three individual fatty acids. So remember, here's a fatty acid. It looks like this. And those fatty acids are attached, each one, to a different hydroxyl group on a glycerol molecule. So here's the structure of glycerol. It's a three-carbon sugar alcohol. To make a fat, you attach a fatty acid to this hydroxyl group. You attach a fatty acid to that hydroxyl group.
• you attach a fatty acid to that hydroxyl group, so now you have three fatty acids hanging off of that common glycerol scaffold. This attachment of these fatty acids to glycerol is, in fact, another example of a condensation reaction. But fats are not considered biological polymers in the same way that proteins and polysaccharides and nucleic acids are. And the reason for that is you're not attaching one fatty acid to another. You're not attaching one monomer to the next monomer in the chain, but you're attaching three different monomers, in this case three different fatty acids, to a common scaffold, in this case glycerol. So fats are not polymers, but there are a few parallels with what we've talked about earlier. This particular fat that we're looking at over here is a very common fat found inside of cells called triglyceride. If you've ever had blood work done, you know that one of the things they analyze is the triglyceride content in your blood. Now, if you take a fat and you remove one of the fatty acid chains, and instead on that last carbon of the glycerol, you add a phosphate group and then some kind of a polar or charged head group, you've made a phospholipid. Phospholipids are the main constituent of biological membranes. They're not the only constituent. We'll talk about sterols as well. And there are some things that look like phospholipids but aren't technically phospholipids, glycolipids, sphingolipids. They look very similar to this. But phospholipids are the largest lipid component of biological membranes. And if you'll notice, and this will come back to be important here in just a minute, the one end of this phospholipid is polar. We've got the phosphate group and this head group up here. And then the other end is nonpolar or hydrophobic. So you've got one end that's hydrophilic and it interacts with water, one end that's not. That's going to be very important in how membranes form in just a second. Another class of lipids that we find in biological membranes are the sterols. This particular sterol is cholesterol. You've all heard of cholesterol before. But the sterols are hydrocarbons, have a large hydrocarbon region, but a good chunk of that hydrocarbon region is a hydrocarbon ring. So these are hydrocarbon rings. Each point in the ring is a carbon. They're not showing all the hydrogens coming off, but you know carbon has a valence of four. So this particular carbon right here, it would have two hydrogens coming off of it because it's fine making bonds to two other carbons it's got a valence of four it's going to hold on to two hydrogens the um the predominant sterol that we find in animal tissues or animal membranes is cholesterol plants use something phytosterol, which is similar but not exactly the same. And again, these sterols are primarily hydrophobic because in these hydrocarbon regions, they've got all non-polar covalent bonds. But they do have, kind of sticking off of one end, a very small polar region. In this case, for cholesterol, it it's a single hydroxyl group but because that O is more electronegative than that H or that carbon you'll have a partial negative here partial positive on hydrogen and the potential for some hydrogen bonding with that hydroxyl group at the end of that cholesterol and what this kind of is really getting at, or this, let me phrase it differently, this polarity that we see in phospholipids and that we see in the sterols, we have a name for that. We say that these lipids that we find in biological membranes are amphipathic, okay? So amphi means dual, like amphibians live part of their life on land, part of their life in the water. Pathic, loving. So these amphipathic lipids can interact with water on one end, but they're hydrophobic on the other end. And that is very important because it determines how these lipids behave when they're put into an aqueous environment. So if you take an amphipathic lipid and you put it into water, it will arrange itself spontaneously into one of two shapes. In both cases, the shape is minimizing the exposure of the hydrophobic domain in the lipid to the water and trying to get that hydrophilic region facing the water and the hydrophobic region facing the interior. In some case, if the lipids are fairly short and fairly small, they will form what's called a lipid micelle. So here are the hydrophobic regions,
• Hydrocarbon regions point into the middle, and the polar regions point on the outside and interact with the water. In other cases, if the lipids are a little bit longer, a little bit bulkier, they will form what we call a lipid bilayer, where you have two flat sheets of lipids that come together. The hydrophobic domains of the lipids in those two sheets interact, So you have a large hydrophobic core region, and then the polar head groups face out and interact with the aqueous environment on either side. And this, in fact, is the basic structure of biological membranes. Biological membranes are lipid bilayers. We sometimes call them phospholipid bilayers because they contain a lot of phospholipids, but there are other lipids as well, sterols, for example. Lipid micelles we typically find in the blood or inside of cells as sort of fat or lipid storage droplets, if you will. So these are not really involved in membrane structure, so we won't really talk about micelles anymore. it's more kind of an internal cellular way of storing lipids temporarily now what we what membrane biologists study or want to study is how varying the composition of lipids that we find in a lipid bilayer alters the behavior of that bilayer. So we can begin to understand how biological membranes with different lipids, why they exhibit different properties. And so to study the effect of lipid composition on lipid bilayer structure, we oftentimes make artificial membranes in a couple of different ways. So you can add your phospholipids or your other amphipathic lipids to water, agitate, and you'll get the formation of what are called liposomes. So liposome is really, you can kind of think of it as a little cell. So you've got a circular phospholipid bilayer encapsulating an aqueous environment on the inside, and then of course the water on the outside. And you can make liposomes with different membrane compositions and study how those different membrane compositions or those different lipid compositions I should say alter the behavior of that lipid bilayer. Liposomes are also used in the pharmaceutical industry and in the cosmetics industry. A lot of the kind of emollient creams that you can buy either for delivering drugs topically to the skin or for delivering cosmetics to the skin are actually liposomes containing the drug or the cosmetic on the inside. And then the idea is that the lipids of the liposome fuse with the lipids in the skin and you deliver that way. Another type of artificial membrane that's used to study the function of lipid bilayers is called a planar bilayer. And in a planar bilayer, you have two chambers in a glass vessel. and there's a wall, a glass wall, with a little tiny hole. And you can deposit amphipathic lipids across that hole so that you end up with a very small, flat lipid bilayer, and then add things to one side or the other and see how they move, for example, that kind of thing. And these planar bilayers are very, very useful for studying membrane permeability. Permeability simply means how quickly do different classes of molecules move across a lipid bilayer if they move at all. Some don't move at all across a lipid bilayer. And a lot of what we've learned about membrane permeability, we've learned from using these sort of planar bilayer systems. So we're going to build on this idea of membrane permeability and look at how that is a function of what we call membrane fluidity in the next lecture for this chapter.

All right, we're going to move on to part two of chapter six, and in this section we're going to focus on permeability of membranes, what things can get across the membrane more easily than others, and we're going to look at also what affects membrane permeability, and what we'll see is that the permeability of a membrane is a function of its fluidity, and that fluidity in turn is a function of the types of lipids that the membrane is composed of. Okay, so let's look at membrane permeability. So this figure here shows different categories of molecules from really small charged molecules like ions all the way to some small polar molecules, or I'm sorry, some large polar molecules, some small polar molecules, and then some small non-polar molecules. And kind of the size of the arrows indicates how readily molecules of this category can cross from one side of a lipid bilayer to another. And what you can see here is that things that are nonpolar, for example, oxygen gas, things that are small and polar, like water or glycerol, they can get across biological membranes relatively easily. There's some difficulty getting these small polar molecules across the membrane because of the large hydrophobic domain here, but there's enough permeability that water can, for example, make its way across from one side of the membrane to another. But anything that's large and polar, or certainly anything that's charged, even if it's really small, is simply not going to get across the lipid bilayer at any meaningful rate without some help okay and so we say that membranes have selective permeability or phospholipid bilayers have selective permeability they let some things across they keep some things from getting across the permeability of a membrane, how quickly things like water, for example, can get from one side to the next, is a function of the fluidity of that membrane. And what this means, or what this refers to, is the fact that the lipids in a membrane are not fixed and locked into place, but rather they can move around within the plane of the specific leaflet of the bilayer they're part of. So this is our lipid bilayer. It has two halves. Each half is referred to as a leaflet. And a lipid can move quite readily within the plane of the leaflet that it's part of. So this lipid in purple, it might kind of drift over this way, it might drift back that way, it can move around quite readily. What it's not going to do very often and without some help is jump from one leaflet to the next. That's energetically very difficult to do because you have to take this polar head group and bring it through this large hydrophobic domain, and that's not something that's thermodynamically very likely to happen. There are circumstances, though, where cells can make that happen, but that's a story for a different day. So these lipids are kind of moving around within the plane of the bilayer, and the faster they're moving, the more, the faster they're moving, the more likely you are to get little temporary gaps in that bilayer. And as you get those little temporary gaps, that increases, and you get more of those little temporary gaps, those little temporary openings, that increases the permeability of the membrane. So the more fluid the membrane is, the faster the lipids are moving around, the more permeable that membrane is going to be, and the faster things like water, for example, will move from one side of the membrane to the next. Cells have to maintain membrane fluidity kind of in a sweet spot. So they need their membranes to be fluid enough that they're permeable enough that things that need to get in can get in, but they don't want them to be so fluid that they just become super leaky and let everything get across without any kind of regulation. So cells actually work very hard to maintain fluidity within a very narrow range. Turns out that the fluidity of a membrane is in turn a function of the degree of van der Waals interactions between the lipids in the membrane. So we've alluded to van der Waals interactions, which are a type of London dispersion force, if you remember that term for chemistry. We've alluded to van der Waals interactions a little bit when we talked about certain hydrophobic amino acids back in chapter three, but we haven't really gone into them in any detail.

So van der Waals interactions are very weak, attractive forces that come into play when nonpolar, that become particularly important, I should say, when nonpolar molecules get very close together. So in this large hydrophobic core of the membrane, where you've got the fatty acid tails from the phospholipids projecting towards the midline here, you can have, this is where you have your van der Waals interactions occurring. And you can have van der Waals interactions between the two different fatty acids on the same lip, on the same phospholipid. You can have them between, van der Waals interactions between fatty acids on different phospholipids, even phospholipids in opposing leaflets. So the greater the extent of van der Waals interactions, the more strongly those lipids are kind of sticking together, and therefore the less fluid they're going to be. So more van der Waals interactions means a stiffer, less fluid membrane that's not going to be as permeable as a membrane that has fewer van der Waals interactions and is therefore looser and more fluid. So cells can regulate the, let me phrase that differently, by regulating the types of lipids found in their membranes, cells can alter, either increase or decrease, the degree of Van der Waals interactions between the lipids in the membrane, and that in turn regulates fluidity. Now, environmental factors certainly can also affect membrane fluidity by impacting the degree of Van der Waals interactions. The obvious one of that is temperature. So as the temperature drops, as things get cooler, molecules stop moving as quickly and as those fatty acid tails stop moving, they pack closer and closer together. Now they can have more Van der Waals interactions and you get a stiffer, more rigid membrane. You bring the temperature up, the fatty acid tails start moving more, they spend less time close to each other, so you have fewer van der Waals interactions and therefore a more fluid membrane. Pressure works in a similar way. The higher the pressure, the more constrained those lipids are in their ability to move, and therefore the more van der Waals interactions they'll exhibit with each other and they'll become less fluid, more rigid. Lower pressure, less constraint on the movement of those lipids, and you have a more fluid membrane. For the most part, cells can't really alter, though, these environmental conditions. They really can't do much to alter their temperature. They certainly can't do anything to alter the pressure of the environment around them. So if a cell needs to alter membrane fluidity, it has to do that by altering the types of lipids that it's putting into its membrane. So down here, these are kind of the three lipid properties that dictate the degree of Van der Waals interactions between lipids and the membrane, and therefore determine how fluid and how permeable that membrane is going to be. So the first thing we're going to consider is the length of the fatty acid chains in the phospholipids of that membrane. So here I pulled out a couple of phospholipids from a membrane and these phospholipids have relatively long chain fatty tails so you have a long a large region where there are van der waals interactions possible contrast that to shorter chain phospholipids where you simply because you've got a shorter hydrocarbon chain you don't have as many opportunities for van der wa's interactions so membranes that contain lots of short chain fatty acids will tend to be more fluid or less stiff okay that's what's shown here membranes with longer chain with phospholipids phospholipids that have longer chain fatty acids tend to be um stiffer and less fluid because longer fatty acid tails, more opportunities for VanderWaal's interactions, and you have a less fluid, stiffer membrane. The second property of phospholipids that impacts membrane fluidity is whether or not the fatty acid chains in the phospholipids are saturated or unsaturated. And we haven't really introduced this concept yet, so let's talk about what that means. So this is one of many examples, I think, where the naming of something is a little bit confusing, because when you think saturated, oftentimes you think water-holding, and that's not at all what this is referring to. So you'll notice here that in this particular fatty acid, instead of every carbon in the hydrocarbon chain being attached to two hydrogens, you've got a point where you have

two carbons making a double bond. And because they're making a double bond and because carbon has a valence of four, each of these carbons can only hold on to one hydrogen. So we refer to this as an unsaturated fatty acid. It's unsaturated in the sense that there are not as many hydrogens in this fatty acid chain as in theory there could be because of this double bond here between these two carbons. Now, the consequence of this is that any time you have a double bond between two atoms, those two atoms cannot rotate relative to each other around that double bond. They can rotate relative to other atoms if they're attached by a single bond, but if they're attached by a double bond, those atoms are locked into place. And the effect of this, having a double bond in the middle of this fatty acid chain, is it puts a kink in that fatty acid chain. So if that fatty acid chain is part of a phospholipid, that fatty acid has a little bend in it like this. So if you have a membrane that is rich in unsaturated fatty acids, meaning it has a lot of phospholipids with unsaturated fatty acids, then these rigid kinks in the chain prevent these phospholipids from packing very tightly together. That's important because van der Waals interactions only work over a very short distance. So this distance from here to here is really too big for any productive van der Waals interactions to occur. You can have van der Waals interactions here, you can have van der Waals interactions here and here, but you don't have any van der Waals here. Because of that kink, these lipids simply can't be, these fossil lipids simply can't pack together closely enough to maximize the extent of VanderWals interactions. Whereas lipids with saturated fatty acid chains don't have those kinks in them, so they can back together tightly and you can have a lot more opportunity for vanderwaals interactions so again the the more double bonds in the fatty acid chains the more unsaturated the fatty acid is the more fluid or less stiff that membrane is because there are fewer vanderwaals interactions so if we take these two ideas together membranes that contain lots of short unsaturated phospholipids are going to exhibit higher fluidity and therefore higher permeability than will membranes that contain lots of long saturated fatty phospholipids, which will have lower permeability and lower fluidity because they have a lot more extensive Van der Waals interactions occurring. So one way that cells can alter their permeability and the fluidity of their membranes is by replacing short, unsaturated phospholipids with long, saturated phospholipids or vice versa. Now, back in the last lecture, we talked about how sterols like cholesterol are another important lipid component of biological membranes. What's the effect of sterols on membrane fluidity and permeability? Well, in general, sterols tend to decrease the permeability and therefore the fluidity of the membrane. And we can demonstrate that experimentally using an artificial membrane system like a liposome. We talked about how to make liposomes in the last handout, in the last lecture, excuse me. But if you make a liposome that contains, or if you make liposomes that contain different amounts of cholesterol in them, then you can study how those different amounts of cholesterol impact the permeability of the liposome to a small polar molecule like glycerol. And when those experiments are done, what we find is that the greater the percentage of cholesterol in the membrane, the lower the permeability of that membrane is, meaning that the membrane is less fluid. The cholesterol is tending to make the membrane stiffer and less fluid, therefore less permeable. There's a bit of a temperature effect to this. I'm not going to get into that in this class. Your book mentions it a little bit, but just know that the general rule that as you add, as the relative amount of sterols in a membrane increases, permeability and fluidity of that membrane go down. Why is that? So it has to do with the structure of sterols. Remember, sterols are composed of hydrocarbon rings, and because these are rings, they're very stiff and they're very rigid. This sterol can't really move around very well. It's too rigid. So if you start adding more and more sterols into the membrane, you're basically adding a

bunch of rigid immovable lipids into an environment where the other lipids are moving around just fine. So it's kind of like imagine a dance floor and everyone's dancing around and you start adding you know a bunch of trash cans or something into the room that's going to constrain the ability of those dancers to move. The same things here as you add more sterols to the membrane the sterols can't really move they're kind of locked into place you add more of them, that constrains the ability of the other lipids, the fossil lipids, to move around, and that tends to make the membrane less fluid and therefore less permeable. Okay, so that's a quick overview of how membrane emission affects the fluidity and therefore less permeable. Okay, so that's a quick overview of how lipid composition affects the fluidity and therefore the permeability of the membranes. Just remember this idea that fluidity is a function of van der Waals interactions. As van der Waals interactions go up within the hydrophobic domain of a membrane, fluidity goes down. As fluidity goes down, permeability goes down because the lipids are not moving around as much and you don't get those little temporary gaps where things can sneak across. Okay? So we're going to now kind of shift gears in the next two lectures for this chapter and look at how... All right, so in this third part for chapter six, we're going to do just a very quick introduction to membrane proteins. So as we talked about in the first lecture for this chapter, biological membranes are composed of amphipathic lipids like phospholipids and sterols and proteins. But we haven't really talked about what kinds of proteins we find in biological membranes and what they do. So we'll do just kind of a quick overview of that because it plays an important role in the next two sections. So membranes, membrane proteins can be classified in a couple of different ways. So one way we can think about membrane proteins is by classifying them on based on function. And if we do that, then we end up with something like this. So some membrane proteins are involved in the transport of materials from one side of the membrane to the next. Some membrane proteins help the cell to anchor to its environment, so they'll bind to some environmental factor on the outside of the cell and bind to some internal structure on the inside of the cell to help keep the cell in place. Some membrane proteins serve as receptors on the surface of the cell and bind to signals and then transmit that information inside the cell. And then some membrane proteins are actually enzymes, catalyze biochemical reactions that need to take place either just outside the cell or just under the cell membrane. So there's one way we can classify membrane proteins on what's the role of that protein. For our purposes right now, we're going to classify membrane proteins in a little bit different way. We're going to focus on their structure, okay, and specifically how does the protein interact with the membrane or associate with the membrane. And in that context, there are kind of two main categories that we're going to look at. There's actually more than two categories, but we'll save some of those others for your upper-level courses. So one category of membrane proteins are what are called the integral membrane proteins. And these are proteins that physically span the lipid bilayer, meaning one end of the protein is on one side of the bilayer, the other end of the protein is on another side of the bilayer. And so these integral membrane proteins are sometimes also called transmembrane proteins because they go across the membrane. Trans means across. They span one side of the membrane to the next. The other major category of membrane proteins that we're going to look at are what are called peripheral membrane proteins. Peripheral membrane proteins associate with either the outer surface of the membrane or they associate with the inner surface of the membrane, but they don't actually insert into the lipid bilayer and they don't cross from one face of the membrane to the next. So these peripheral membrane proteins, they are interacting typically with the polar head groups of the phospholipids or they're interacting with integral membrane proteins, the part of an integral membrane protein that's either sticking out or sticking into the cell. So in this example here, we have two different

peripheral membrane proteins. One is interacting with the inner surface of the cell. One is interacting with the outer surface of the cell. But neither of these proteins are physically inserted into the lipid bilayer. That's why they're called peripheral membrane proteins. Now obviously, maybe not obviously, but it's not surprising that integral membrane proteins and peripheral membrane proteins will have different structural characteristics, and that's what allows them to associate with the membranes the way that they do. Integral membrane proteins in particular, oh I got ahead of myself here, if we, sorry back up a little bit, so if we look at integral membrane proteins and peripheral membrane proteins and we focus on the proteins that are on the surface of the cell either peripheral membrane proteins on the surface of the cell or the domain of an integral membrane protein that's on the surface of the cell. Remember that those proteins are glycosylated. They have little sugar groups added to them and we talked about this back in chapter 5. This contributes to the formation of that glycocalyx that we mentioned in Chapter 5. And we can use this as a tool as biochemists if we have isolated a membrane protein and we're interested what part of that protein is on the surface versus inside the cell. We can look to see what regions of the protein are glycosylated or not, and that will give us a pretty good indication. Okay, now back to where I jumped ahead earlier. So integral membrane proteins and peripheral membrane proteins are going to have some structural differences from each other that will account for the different ways that those proteins interact with the membrane. Integral membrane proteins in particular, Because they physically cross the lipid bilayer. They have to have a region of the protein that is hydrophobic enough to interact with all of these lipids in that membrane and But then they have to have a region that's hydrophilic and interacts with the aqua is environment inside or outside of the cell. So another way of saying that is that integral membrane proteins are amphipathic, just like the lipids that make up biological membranes are amphipathic. They have a hydrophilic region or regions, and they have a hydrophobic region. In the case of the hydrophobic region, if you go back to chapter three and you look at your table of amino acids, what you'll see is that these yellow amino acids are the nonpolar amino acids, where the R group is nonpolar, no exposed polar covalent bonds at the ends of the R group, so the components of the R group are a kind of hydrogen bond. So these nonpolar amino acids, if they're arranged in the right order, they will fold up and you'll make a hydrophobic alpha helix, a region of alpha helical secondary structure composed of largely hydrophobic amino acids with those hydrophobic R groups pointing away from the helix and interacting through Vanderbilt's interactions with the hydrocarbon domains of the lipids. And so these hydrophobic alpha helices are what help to keep integral membrane proteins stably stuck in the membrane. And it's cut off here, but this particular protein would have a hydrophilic region out here and a hydrophilic region down here, and the hydrophobic alpha helix makes up the membrane-spanning domain. Because integral membrane proteins have these hydrophobic alpha helices that are stuck in the lipid bilayer and interacting with the lipids through Van der Waals interactions, the only way to extract an integral membrane protein from the membrane is to basically break the membrane apart. And we do that biochemically, or as biochemists, we would do that with detergents. So detergents are small amphipathic molecules. They have a little polar head group and a little hydrocarbon tail, a little nonpolar tail. And if you add a large excess number of detergent molecules, those amphipathic detergents will sort of out-compete the lipids for interacting with each other, and they'll coat the hydrophobic region of the detergent, will coat the hydrophobic regions of the lipids, keep the lipids from interacting with each other, and that effectively kind of dissolves or dissociates the lipid bilayer, and now you can pull your integral membrane protein out and analyze it. So sometimes as scientists, if we've identified a new protein and we know it's associated with the membrane, but we're not sure if it's an integral membrane protein or a peripheral membrane protein, one way we can get a quick and dirty test of that is to see whether or not we need detergents to pull that protein away from the membrane. If we do, then we know that was an integral membrane protein and we needed the detergents to blow the membrane up so we could pull the protein out. But if we can

extract the protein from the membrane just by changing salt concentration or changing pH, then odds are that was a peripheral membrane protein that was just interacting with the polar head groups on the surface of the membrane and not actually physically inserted into the lipid bilayer. Okay, so that's a quick overview of membrane proteins. Not a lot of detail, and that's okay, because what we're really more interested in now are the functional aspects of different membrane proteins and we'll look at in more detail, we'll look at a category of membrane proteins, proteins involved in membrane transport as we work through the last two lectures for this chapter. Hello, we're going to begin our home stretch here for chapter six and these next two lectures are going to look at the transport of materials across membranes. We'll begin with an introduction to membrane transport in this lecture and then we'll finish with a longer lecture, a little bit more detailed, looking at some specific examples of membrane transport events and how and why they occur. So there are two primary factors that you have to keep in mind when considering whether something is going to move from one side of the membrane to the other, and if so, how it's going to move. And the first of these is you need to know whether or not the membrane is permeable to that particular type of solute. So remember in the last lecture we talked about, or two lectures ago, we talked about membrane permeability and how anything that's charged or anything that's large and polar is going to simply be too hydrophilic to get across this large hydrophobic core of the lipid bilayer. Whereas anything that's uncharged, nonpolar, or polar but really small, those can move with varying degrees of speed from one side of the membrane to the next, depending on how permeable, how fluid the membrane is. But anything down here is going to need some help to get from one side of the membrane to the next. And by help, I mean need specific membrane proteins to help create a path for these charged or large polar solutes to move across the membrane. So keep that in mind, and we'll touch more on that here in a little bit. The other factor that you have to consider when thinking about membrane transport is whether or not the solute is moving in the thermodynamically favored direction. Are the energetics of that movement in that direction favored or not? And so let's kind of do kind of a quick and dirty overview of how to think about kind of the thermodynamics of membrane transport. And it has to do, it really comes down to entropy again. Remember, entropy is a measure of the randomness or the disorder in a system. And you've got maximum, if you've got two compartments, here we're using these planar bilayer artificial membrane systems just to make a simple illustration of these concepts we're talking about. But we have a very high entropy state, maximum entropy, if there's no difference between these two sides. It's everything, the concentration of the solutes, the same on both sides of this membrane here. This is kind of our maximum entropy state. There's no order. There's no structure. Everything's just kind of random. Over here, where we have a concentration difference on one side of the membrane versus the other, this is a lower entropy state. There's some order. There's some structure in this system. You've got one side that's very different than the other. And so thermodynamically, anything that brings these two compartments closer to the same concentration is going to be bringing the system to a higher entropy state and therefore will be thermodynamically favored. And that's what I've tried to illustrate with these arrows down here. Now, there are two different thermodynamically driven processes that will work to try and equalize concentration differences across a membrane, diffusion and osmosis. Diffusion is when the membrane is permeable to the solute. I just realized I wrote substrate here. That should say solute. Sorry about that. If the membrane is permeable to the solute, then that means that the thermodynamics will favor that solute moving from high to low concentration, bringing the system towards maximum entropy. And that's what's being illustrated down here. So here we have two different solutes, purple and white. I have no idea what they're representing, but just imagine that they're two different types of dissolved molecules separated by our planar bilayer system here. The

In this case, both of these solutes are, or the membrane is permeable to both of these solutes, so over time, without adding any energy to the system, you'll have the purple solute going back and forth but moving in a greater rate or a greater frequency to the right, the white solute going back and forth but moving with greater frequency toward the left until eventually you end up with the maximum entropy state and equal concentrations of our solutes on both sides of the membrane. So for diffusion to occur, the membrane must be permeable to the solute. Osmosis is another thermodynamically driven process that will tend to equalize concentration differences across a membrane. But osmosis occurs when the membrane is impermeable to the solute. The solute can't move from high to low concentration. So instead, water will tend to move from the low solute side to the high solute side in order to bring about an equalization in concentration. So in other words, if you think about concentration changes, you can change the solute or you can change the volume. If you change the volume, you're going to affect the concentration. So in this case here, we have some other dissolved solute, this green. Who knows what green is? But let's imagine that it's an ion, which is charged, and so isn't going to get across this lipid bilayer. So you've got a concentration difference in these two systems, on these two sides of the membrane. The solute can't move, so the rate of water movement back and forth will favor more movement from the low solute side to the high solute side. That decreases the volume on the low solute side, increases the volume on the high solute side, and therefore tends to bring those two concentrations closer to one another and bring the system closer to maximum entropy. So there is some terminology we use to describe the directionality of water movement during osmosis. We say that water moves from the hypotonic side of the membrane to the hypertonic side of the membrane. Hypo means under, hypodermic needle, needle you shoot under your skin. Hyper means over, okay, hyperactive, overactive. So the hypotonic side of the membrane is the side of the membrane with the lower solute concentration. The hypertonic side of the membrane is the side of the membrane with the higher solute concentration. So osmosis occurs when the solute can't move to equalize the concentration difference. So water moves from the hypotonic side to the hypertonic side, changing the volumes on the two sides of the membrane and bringing the system closer to the concentrations of both sides of the membrane closer to one another. Osmosis can have real consequences for cells and this figure illustrates why. So let's consider first a situation where the inside of the cell is hypotonic relative to the outside, or the outside of the cell is hypertonic relative to the inside. That means the same thing. So again, water moves from the hypotonic side to the hypertonic side. So under these conditions, water will move from the inside of the cell away to the outside, and that will cause that cell to shrink and shrivel up. If you reverse it, now we have a cell where the inside is hypertonic relative to the outside, or the outside is hypotonic relative to the inside. Water moves from hypotonic to hypertonic, so in this case the water moves into the cell, and that causes the cell to swell and potentially even burst. Two solutions are isotonic if they have the same concentration of dissolved solutes. So in this case, their water is going back and forth, but there's no net difference in the directionality of the movement of that water, so there's no change in the volume of the cell. If you ever work in a hospital and you hang a saline bag or something for an IV drip, the concentration of the salts in that IV drip are isotonic to the normal solute concentration of the blood. Otherwise, you could run into these problems over here. All right. So again, two factors to consider when thinking about the movement of solutes across the membrane. Is the membrane permeable to the solute or not? Will the solute get across the membrane, across the hydrophobic core of the membrane without help? And then is the movement in the thermodynamically favored direction or not? Now, if the solute is charged, we have to consider more than just

the concentration gradient of that solvent. And here is why. So most cells, let me phrase that differently, under most conditions, cells maintain a net charge difference across their cell membrane, such that the inside of the cell has a higher concentration of negative ions, a lower concentration of positive ions, and therefore is a net negative environment compared to the outside of the cell, which tends to have a greater concentration of positive ions, a lower concentration of negative ions, and therefore tends to be a net positive environment. So there is actually an electrical gradient across the cell membrane. So if the solute is charged, in addition to thinking about whether the solute is moving from high to low concentration or low to high concentration, you have to think about whether the solute is moving, is bringing that electrical gradient across the membrane closer to zero, closer to no difference at all, or is it accentuating, making bigger the electrical gradient across that membrane? And so there's some terms we use to describe that. So delta G sub C is the change in free energy associated with the movement of a solute relative to its concentration gradient. The delta G sub M is the change in free energy in the system associated with the movement of a charged solute relative to the electrical gradient across the membrane. The total delta G, the total change in free energy associated with the movement of that solute, then is the sum of delta G sub C and delta G sub M. We're not going to worry about how to calculate these in this class. We'll save that for cell structure and function down the road. But I just want you to bear in mind that if your solute's charged, thermodynamically you have to take into account not just the concentration gradient, but also the electrical gradient before you can predict what's the thermodynamically favored direction of movement of that solute. Okay, so let's come back to our two factors again. So is the membrane permeable to the solute, and is the solute moving in the thermodynamically favored direction? If the answer to both these questions is yes, then the solute moves by just diffusion, or what we sometimes call simple diffusion, and we've talked about that already. The answer to the first question is no, but the answer to the second question is yes. In other words, the solute is moving in the thermodynamically favored direction, but the membrane is impermeable to that solute. Then that is a process called facilitated diffusion to represent that there's going to have to be some system in the membrane to create a pathway for that solute to go through since the membrane is not permeable to it. Now, if the answer to both of these questions is no, meaning the membrane is impermeable to the solute and the solute is moving in a thermodynamically unfavored direction, then that type of movement is called active transport. And active transport occurs when the delta G, the changing framerate associated with the movement of that solute across the membrane is greater than zero. It is an endergonic reaction. You need an input of energy in order to move that solute in that direction. So diffusion, facilitated diffusion, active transport, these are kind of the three main mechanisms by which solutes will move across the membrane. And I kind of created a little cheat sheet here to give you a sense of how they differ from one another. So we will kind of pick up from this point and now look at, in the last lecture for this chapter, look at some specific examples of facilitated diffusion, some specific examples of active transport, so that you can kind of compare and contrast those and see how they differ from one another. All right, home stretch. This is the last lecture for chapter six, and we're now going to take a little bit deeper dive into the topic that we introduced in the previous lecture, which was membrane transport. So as a quick reminder of where we left off, we talked about the two factors that determine how and if a solute will move across a membrane. The first is whether or not the membrane is permeable to that solute. The second is whether or not the solute is moving in a thermodynamically favored direction. And the answer to both those questions is yes, then the solute can move by a process called diffusion. If the answer to the first question is no, but the second question is yes, then that solute's going to need some protein in the membrane to provide a pathway for it to move. That's called

facilitated diffusion and if the answer to both these questions is no then this is active transport meaning that the movement the direction of movement of the solute is thermodynamically unfavorable therefore the uh there has to be energy added to the system in some way in order for that transport process to take place. And graphically, we can kind of illustrate these differences as I've done here. So we have diffusion on the left where there's no membrane proteins needed to assist movement and the solutes moving in the thermodynamically favored direction. We have active transport on the right, which is when you do need a membrane protein to help to move the solute, and that membrane protein is providing energy in some way to move the solute in the thermodynamically unfavored direction. And in the middle, we have facilitated diffusion, where the movement is still occurring in the thermodynamically favored direction but because the membrane is not permeable to the solute you need some membrane protein to help create a pathway or an avenue for that solute to move. So now we're going to dive a little bit more deeply into all each of these examples and we'll start with facilitated diffusion and we'll begin with looking at how facilitated diffusion occurs through a class of proteins called channel proteins. So channel proteins get their name, quite simply, because they make a conduit, a channel, a pathway through the membrane through which specific solutes can move. And most frequently, not always, but most frequently, channel proteins allow the movement of ions. So what we're looking at here is a sodium ion channel. And we're kind of looking down at the top of this now. So this membrane protein, the arrangement of the protein is such that it kind of creates a core, or a pore, I should say, in the middle that is hydrophilic. And then you get all these hydrophobic amino acids on the outside, because this is obviously an integral membrane protein. And the sodium can move through this pore from high to low concentration down its electrochemical gradient. Sodium is charged, so we have to consider the electrical gradient as well. And it's doing so through this channel protein. So the important part here is the channel protein is not determining the directionality of the sodium movement. The sodium ion is moving in the thermodynamically favored direction. The channel is just providing the conduit, the pathway, for that movement to occur. So this is why we call it facilitated diffusion. It's still diffusion because it's moving in the thermodynamically favored direction, but it's being facilitated, that diffusion is being facilitated by a membrane protein. Now, most channels are highly selective, meaning that they only allow one type of solute or a very small subset of solutes to move from one side to the other. And this is kind of a fun example of this. This is actually a channel protein called aquaporin that is a channel protein for water. So water can move across membranes, but relatively slowly. Sometimes cells need to move water much more quickly from one side of the membrane to the next. And that's where this aquaporin protein comes in. So aquaporins create their channel proteins, and this channel is configured such that water molecules can move from one side of the membrane to the other. But even things that are smaller than water, like dissolved ions, cannot. They don't fit in that channel. So this channel is highly selective for, in this case, water molecules. Most channel proteins are also gated. Gated simply means that they can be opened and closed, much like a gate in a fence as circumstances dictate. And the example of a gated channel that you may be familiar with from your previous biology classes are the voltage gated ion channels. Ion channels that open and close in response to changes in the voltage across the membrane. And these are very, very important in the propagation of action potentials along a neuron, for example. So under one membrane voltage, the channel is closed. In a different membrane voltage, the channel opens up. So the channel plug in this case is sensing the change in voltage across the membrane, altering its structure accordingly to either open or close and allow ions to flow or keep them from flowing. Now ion channels are, or channel proteins are not the only type of membrane protein that is involved in facilitating diffusion. We also have what are called carrier proteins

or sometimes called transporters. And these work in a little bit of a different way. So what we're looking at here is a type of a carrier protein called GLUT1. And GLUT1 is involved in the movement of glucose from high to low concentration across membranes. And the way that this carrier protein works, GLUT1, is it sort of acts like a ratchet so it starts out in a configuration so that it's open to one side of the membrane the glucose comes in and binds that causes it to close and open to the other side and then the glucose falls out and the again the just like with the channel, these carrier proteins are not determining the directionality of movement. The solute's moving in the thermodynamically favored direction. The carrier protein is just providing the pathway for that movement to occur. So in this particular example, in this case, the concentration of glucose outside the cell is higher than inside, so the glucose is moving through glute 1 from outside to inside. But if circumstances were to change and suddenly the inside of the cell had the higher glucose concentration, now glucose would move in the reverse direction through this exact same protein. So again, in facilitated diffusion, the membrane protein is not determining the directionality of movement. It's just providing the pathway for the movement to occur. The directionality is determined by thermodynamics. Active transport, remember, is when the solute is moving in an energetically unfavorable direction. So the thermodynamics of that movement are not favorable. The delta G of movement is much greater than zero. And so there's energy needed to drive that transport process. And there are two categories of active transport, primary and secondary. In primary active transport, the energy to drive the active transport process comes from the hydrolysis of ATP. And we've looked at ATP before, but remember ATP is a nucleotide that has three phosphate groups, and these two phosphate groups at the end are attached by very high energy bonds. So if this bond is broken, that energy is released and can be used by the cell to do something. And this case, during primary active transport, the hydrolysis of ATP releases energy that's used to drive the endergonic active transport process. Secondary active transport, or also called indirect active transport, is when the energetically unfavorable transport process is coupled to an energetically favorable transport process. So in secondary active transport, two different solutes are moving simultaneously, either in the same direction or in opposite directions. It just depends on the example. The key is that one of these solutes is moving in its thermodynamically favored direction, which is exergonic, releasing energy. The other solute is moving in its thermodynamically unfavored direction, which is endergonic, and so that second solute uses the energy from the first solute moving to help the second solute move in the thermodynamically unfavored direction. So the best studied example of active transport, and unfortunately it is certainly not the simplest example of active transport, so it's kind of unfortunate that it's the one we're going to begin with, but it's such an important example to know for biology that we're kind of stuck with jumping into a more complicated example right away. And this is the movement of sodium ions out of the cell and potassium ions into the cell using a membrane protein called the sodium potassium pump or the sodium potassium ATPase. Okay, so this is an example of primary or direct active transport. We're going to get to produce energy from the hydrolysis of ATP to move these ions in a thermodynamically unfavorable way. So here's how the process begins. So here's our sodium potassium ATPase, and the process begins with three sodium ions binding to pockets inside of the sodium potassium ATPase. That triggers a shape change in this protein, which now allows it to bind to ATP and hydrolyze that ATP. Break this high energy bond here. When that happens, oops, sorry, wrong bond, break this high energy bond right here. When that happens, this phosphate group gets stuck onto the ATPase and that causes the

that plus the energy released from the breaking of that bond causes this protein to change its shape such that it opens up to the outside and releases those sodiums. Once the sodiums have fallen out, two potassiums can come in and bind to some potassium ion binding sites on the inside of this ATPase. That then triggers a potassium binding, triggers the phosphate that was added to be released, and the ATPase then goes back to its original configuration and releases those potassium ions into the cell. So we have sodium moving out of the cell, potassium ions moving into the cell. So we have we have sodium moving out of the cell potassium ions moving into the cell. Okay, so I've created a cheat sheet for you here that kind of summarizes the types of membrane transport we've looked at osmosis, simple diffusion, facilitated diffusion, active transport and kind of organizes these ideas by whether or not an energy input is needed, whether or not membrane proteins are needed. By the time you're done with your study, you should be very familiar with the details in this table before you move on. And what I want to end with, looking very briefly at an actual sort of physiological example of coordinated membrane transport. And what I mean by that is nothing is moving across membranes in isolation. Lots of different solutes are moving back and forth across cell membranes, and that movement has to be coordinated in some way. And that's going to differ depending on what kind of cell it is and what its context is, what kind of tissue is a part of that sort of thing. So what we're going to look at here is the movement of sodium ions and glucose from the intestinal lumen into the blood after a meal. So after a, if you've eaten, you've gotten, your stomach's broken down, your food and you've now got a flush of glucose in the intestines, you've got some sodium in the intestines, and now it's time to move that into the cells that line the intestine, and then from there, pass it into the blood. So we have three compartments here. So here's the lumen of the intestine, inside of the intestine. Here's one of the cells lining that intestine. And then here is the bloodstream on the outside there. So we've got to get the glucose and the sodium from the inside of the lumen of the intestine through the cells that line the intestine and out the other side so it can get into the blood. Okay, so let's look at how this process begins. So the process begins with a protein called the sodium glucose symporter. Symport just means movement of two things in the same direction, okay? And this, it turns out, is an example of secondary or indirect active transport. The reason for that is that the concentration of glucose inside the cell is higher than the concentration of glucose in the lumen of your gut. Even if you ate a dozen Snickers bars, the volume of your gut is so big that the concentration of glucose would still be higher in the cells lining the gut than it would be in the lumen. So this glucose is moving in a thermodynamically unfavored direction. Sodium, however, the movement of sodium into a cell is thermodynamically favored because the sodium is moving from high to low concentration and from a more positive environment to a more negative environment. So this is an example of indirect or secondary active transport. The sodium moves through this importer in a thermodynamically favored direction. That's exergonic, and that energy is then used to move the glucose from low to high concentration into the cell. So that endergonic movement of glucose is possible because of the exergonic movement of the sodium ions. All right, so now I've got the sodium and the glucose inside the cell. Because the concentration of glucose in the cell is higher than it is on the outside, the glucose can now move by facilitated diffusion through one of these glute carrier proteins and into the bloodstream. So that's just facilitated diffusion, just like we got done looking at. The sodium, however, needs to get back out the other side of the cell. And in that case, again, you're going to be moving the sodium from a more negative environment to a positive environment and from a low concentration site to a high concentration site. So that's not going to be energetically favored and that's where our sodium potassium ATPase that we just got done looking at comes in. So the sodium potassium ATPase hydrolyzes ATP which is direct active transport or primary active transport.

uses that energy to move sodium from inside the cell outside so it gets to the blood and then potassium moves in the opposite direction. So here we have three different membrane transport systems. This is sodium glucose importer, the sodium potassium ATPase, and one of these glu carrier proteins working together to move sodium and glucose in a directional way from the lumen of the gut through the cells that line the gut and into the blood. And physiology is going to be filled with lots and lots of examples just like this, a coordinated movement of solutes from one side of a membrane to another. Okay, so that's all I have for chapter six. Please look over these notes carefully and be sure that you kind of understand the transitions from one subsection of this chapter to the next so you see the big picture and how it all relates to each other.

All right, welcome to Chapter 7. Chapter 7 is an overview of the structure of cells, the internal structure of cells. And we'll begin with a kind of quick overview of prokaryotic cell structure, focusing mostly on the bacteria. And then we'll move on in the rest of the chapter and focus more on what's going on inside of eukaryotic cells. So if you remember our tree of life from earlier, there are three domains, bacteria, archaea, and eukaryotes. The bacteria and the archaea collectively are called the prokaryotes because they lack a membrane-bound nucleus. So all life on earth as we know it uses DNA as its genetic material, but they package that DNA differently. In eukaryotes, the genome is contained within a membrane-bound organelle called the nucleus inside of cells, and prokaryotes is not the case. Now, there are lots of other differences between prokaryotes and eukaryotes that are maybe a little bit more variable in terms of how definitive they are, either a prokaryotic characteristic or a eukaryotic characteristic. The archaea are kind of, as indicated by their place on the phylogenetic tree, the archaea are kind of in the middle. They share more things in common structurally with prokaryotes than they do eukaryotes, but they do share a number of characteristics with eukaryotes, particularly the way that, or particularly some of their metabolic pathways are more similar to what we see in eukaryotes and prokaryotes. But for this part of chapter seven, we're really going to focus just on, or primarily at least on the prokaryotes. All right. Now, if you look on the left here, this is a, just kind of a cartoon of a typical, if there is such a thing, a typical prokaryotic cell. And it's really hard to use the phrase typical prokaryotic cell with a straight face because there is just tremendous diversity in the prokaryotes, their morphology and their structure. But what we're going to look at are sort of characteristics that most or all bacteria, for the most part, share. In a few cases, there will be some exceptions, and I'll tell you a little bit about those. Now, one of the things that's most apparent is there are no internal membrane-bound structures. And this is true for many, but not all of the prokaryotes. There are some prokaryotes that have internal membrane-bound structures that allow them to carry out photosynthesis. There are certain bacteria that are photosynthetic, and they certainly have their photosynthetic structures encapsulated in an internal membrane. But for the most part, we don't see internal membrane-bound structures inside of prokaryotic cells. And this is in contrast to what we'll see later on with eukaryotes, where eukaryotes have lots of internal membrane-bound structures. Those internal membrane-bound structures, in a eukaryote, we would call an organelle. So organelle is a localized site of specific function, okay, that is separated from the environment by a membrane. And eukaryotes have to have many internal membrane bound structures because they're much larger than prokaryotes. And so relying on simple diffusion to bring the right things together in the right combination to carry out various functions in a eukaryote would be tremendously inefficient. So by packaging, subdividing a eukaryotic cell into smaller pieces, it allows for the more efficient specialization of function in different regions. Prokaryotes are much smaller than eukaryotic cell into smaller pieces it allows for the more efficient specialization of function in different regions prokaryotes are much smaller than eukaryotes and so it's there's not that same sort of demand or pressure on them to have as many internal compartments now that doesn't mean however that the inside of a prokaryotic cell that the uh is is just a big bag of fluid any nothing would be further from the truth. So this over here is a cartoon, but it is a scientifically accurate, drawn-to-scale cartoon. It's based on some real images, electron microscopy images of a bacterial cell. And just to orient you, here's the cell membrane. Here's the cell wall. Here is the genetic material, the DNA inside that bacterial cell. But look, there's tons of stuff packed in here. There's lots of proteins and large complex structures like ribozo.

and there are long filamentous proteins that make up the cytoskeleton. We'll talk about that later. But I just show you this to kind of give you the, or to dissuade you of this mental image that prokaryotes are basically big bags of fluid with some DNA floating around in it. There's nothing further from the truth. There's a lot of stuff packed in here. All right, now nearly all prokaryotes, archaea and bacteria alike, have a cell wall on the outside of their plasma membrane. Okay, so their plasma membrane, their cell membrane, is a phospholipid bilayer, just like we would see in eukaryotes, but most prokaryotes also have have a cell wall and we talked about the cell wall of bacteria a little bit back in chapter 5 in carbohydrates when we talked about peptidoglycan. Archaea don't really use peptidoglycan for their cell wall they use something different but structurally it's similar and this cell wall is quite thick you can see that here so here is membrane. This is kind of a cross-section through the edge of a bacterial cell. Here's the plasma membrane, the phospholipid bilayer. You can see how thin that is. And then look how thick the cell wall is on the outside. The cell wall is primarily there to serve as a protective function. And not only does it help protect the bacteria from getting beat around in its environment, but it also helps to protect the bacteria from bursting and swelling because of osmotic pressure. The cytoplasm of bacteria or of all cells is fairly high salt concentration. The bacteria in the environment oftentimes find themselves in solutions or in areas where there's not nearly as much dissolved salt. So they often find themselves in a hypotonic environment. And as we learned back in chapter six, if you put a hypertonic cell into a hypotonic environment, water will try to rush from the environment into the cell, cause it to swell up and burst. And so the cell wall of bacteria helps to provide some resistance to that so that it doesn't happen. Now, if we look at the DNA, the genetic material of a bacterial cell, it's a little bit amazing, I think, or perplexing as to just how much DNA can be packaged inside such a little cell. So their DNA in prokaryotic cells comes in two forms. One form is the chromosome of the cell. And that chromosome is a very large circular molecule of DNA. And if we were to unspool that large circular molecule of DNA that's shown over here, look how large, if we were to stretch it all out, that circular chromosome is compared to this E. coli bacterial cell. It's really amazing. There are other smaller circular fragments of DNA in bacteria called plasmids. And plasmids do carry very important genes, genes that the cell uses for various functions. And plasmids can be exchanged between bacteria of similar types. And that's through a process called conjugation, you'll learn about it if you take a microbiology course. But it's sort of the closest thing bacteria have to sex. It's not true sex, but it's the closest thing they have to sex. Now, what allows this really huge, large chromosome to be packaged into a very small cell in a very specific region of the bacterial cell that we call the nucleoid. The nucleoid is the region of the cytoplasm in a bacterial cell where the circular chromosome is found. What allows for that is a phenomenon called supercoiling. So if you take a circular molecule like the circular DNA that makes up a bacterial chromosome, and if that circular molecule is twisted, remember DNA is a double helix with a twist, then that is going to automatically cause that molecule to kind of wrap up. If it was linear, it could relax that tension, but it's not. It's circular. It's tied together at the top, kind of like now rubber bands will snarl up in a drawer if you leave them in there for too long. And so this supercoiling of DNA allows it to occupy a really small volume compared to what you'd get if it was a linear molecule. And that allows for a relatively large chromosome to be packaged into a very small region of the prokaryotic cell. All right. Now, all cells, prokaryotic cells,

and eukaryotic contain structures called ribosomes. And ribosomes, we talked a little bit about these back in chapter four. And we'll talk a lot more about them in the fourth unit in this course. But ribosomes are what cells use to make new proteins. And ribosomes, they're kind of large macromolecular machines in a sense. And they have two subunits, a small subunit and a large subunit. And then each of these small and large subunits is in turn composed of lots of different individual pieces. Some of those pieces are proteins and smaller proteins, and some of those pieces are small RNAs. So both prokaryotes and eukaryotes have a very kind of similar overall shape and structure to their ribosomes, but they differ in terms of the specific components that those ribosomes are made of, and that's represented here. So this chart shows the types of RNAs found in the large and the small subunits of both prokaryotic and eukaryotic ribosomes, the types of proteins, just the protein names are abbreviated here. The point of this is just to illustrate that even though at the macro level, eukaryotic and prokaryotic ribosomes look similar, structurally they're different. And we can exploit these differences to our advantage in terms of designing antibiotics. So certain classes of antibiotics, the aminoglycosides, the tetracyclines, the chloramphenicol, are worked by specifically targeting some component of the bacterial ribosome that is not found in eukaryotic ribosomes. We can also use the differences in ribosome composition between prokaryotic and eukaryotic cells as a diagnostic feature if we're studying some new cell and we're not sure if that cell is prokaryotic or eukaryotic yet. We can look in particular at the types of RNAs that make up those ribosomes and those are very diagnostic for saying yes this is definitely a prokaryotic ribosome or no this is definitely a eukaryotic ribosome. Now prokaryotes have projections or protrusions from their surface, and these appendages, if you will, kind of fall into two groups, two broad groups. Some of these appendages are really long and motile, meaning that they can move, okay? And we call these flagella in plural, or flagella in singular. So this particular bacterial cell has one, two, three flagella, it looks like. And these flagella are, if we go back to here, these flagella are large, complex, multisubunit proteins that span the bilayer and the cell lipid bilayer and the cell wall of the bacteria. So here's what the cytoplasmic component of that flagellum looks like. Here's the flagellum sticking out in the environment. And they're kind of like boat motors. So this structure here spins around and that spins this flagellum. so kind of like a propeller on a boat that helps that bacteria to move around in its environment okay and they don't certain types of eukaryotic cells also have structures that we call flagella but they look and work very differently okay we may get to that here in a little bit. Another type of protrusion from prokaryotic cells are these long spiky looking things. These are called finbrae. These are really more anchoring structures. They kind of stick out and they allow adjacent cells to stick to each other or cells to stick to their environment so that they can sort of anchor down rather than just being constantly moving around in the environment that they're in. Now, in the next part of Chapter 7, we're going to look in detail at the structure of eukaryotic cells. And when we're done with that, you're going to come back and do a little bit of comparison and contrast, I hope. And you'll see something, and if you do that, you'll end up with something like this table here. So prokaryotic cells are typically one to two orders of magnitude smaller than eukaryotic cells, but there are exceptions. There are some really large prokaryotic cells that are over 10 microns in size, and there are some very small eukaryotic cells that are below 10 microns in size. But for the most part, prokaryotes tend to be much larger than eukaryotes. Prokaryotes don't have any, don't have a membrane bound nucleus. Eukaryotes

Prokaryotes do. Prokaryotes generally, as I mentioned before, don't have any other membrane-bound organelles, but there are exceptions, and certainly the largest of those exceptions are those bacteria that are photosynthetic, that have the ability to take energy from sunlight and use that to make sugar. And in those bacteria, the photosynthetic apparatus is, in fact, encapsulated in an internal membrane structure. You'll also see in eukaryotes that eukaryotic chromosomes are not circular like they are in prokaryotes, or most prokaryotes anyway, but rather eukaryotes have multiple strands of DNA that make up their chromosomes, and each of these strands are linear, not circular. Again, now there are exceptions. There are some prokaryotes that have multiple small linear chromosomes, and there are some eukaryotes that at least at certain times have their chromosomes adopt a circular sort of structure. So again, this is not a 100% difference between prokaryotes and eukaryotes, but a pretty good distinction characteristic. And then, of course, again, we'll see the eukaryotes that we saw already, but we'll see again that their ribosomes are a little bit bigger. They're a little bit more complex in terms of the number of subunits they're composed of and the types of subunits they're composed of. And in fact, in many ways, again, that's our best diagnostic tool when we're looking at a cell to figure out quickly if it's a prokaryotic or eukaryotic cell, look at the structure of the ribosomes. Okay, so that is it for this. And I said it would be a very quick overview of prokaryotic cell structure, and it was. Now we're going to move on. In the rest of this chapter, we're going to focus on eukaryotic cell structure. We'll begin with a very quick overview looking at the major organelles and some of the other major structural elements in eukaryotic cells. And then we'll talk about, in part three, we'll look at protein trafficking, which is basically looking at how do eukaryotic cells get the correct proteins to the right organelles so that they can function properly. And then we'll end with the discussion of the cytoskeleton, focusing mostly on eukaryotes, but then coming back and comparing that to what we see in prokaryotes at the very end. Okay, so that's the plan for the rest of the chapter. I'll see you in part two. All right, welcome to part two of chapter seven. In part one, we did an overview of the structural aspects of prokaryotic cells, and now we'll do the same thing for eukaryotes. When we talk about eukaryotes, we are, of course, talking about all the plants, all the animals, algae, et cetera. And the way I've got this structured is we'll look at some of the – first we'll look at the aspects of eukaryotic cell structure that are similar between plant and animal cells, and then we'll look at a few differences. All right. And let me just clarify some terms here. These are a couple terms that sometimes get used sloppily, admittedly, sometimes even by me, and those are cytosol versus cytoplasm, okay? So the cytosol refers to the fluid component, the watery component and the stuff dissolved in that water inside of cells. Cytoplasm refers to anything, it's kind of a catch-all term used for anything inside the cell membrane. So the cell membrane encapsulates the cytoplasm. The cytoplasm is composed of cytosol plus various membrane-bound organelles and the things that are floating around in that cytosol. And again, remember that an organelle, at least in the definition that we're going to use here, is a small membrane-bound structure inside of a cell that contains the proteins, et cetera, necessary for a very particular function. So organelles have their own structure, and they are typically dedicated to a small subset of functions, and this allows for more efficient activities inside of eukaryotic cells, which tend to be much bigger volume-wise than prokaryotes. So here we look at a very kind of animal cell. Obviously the largest organelle is the nucleus, and the nucleus contains the genetic material, it contains the chromosomes for that cell. And then there's a variety of organelles branching off of the nucleus and then floating around in the periphery. Many of the same organelles that we saw in the animal cell we'll find in the plant cell. In fact, most of the organelles are the same, but there are a few differences, and we'll highlight what some of those differences are as we get towards the latter half of this particular lecture. Now, this

This is a little bit similar to a picture that we looked at in part one for prokaryotes. And this, again, is just a blow-up of a section of a eukaryotic cell sort of starting from the cell membrane on one side and going all the way to the nucleus on the other. And it's color-coded so that yellow represents lipids, green represents carbohydrates, red represents nucleic acids, RNA and DNA, and blue represents proteins. And again, the purpose of this is just to give you a visual sense that even, you know, we may look under the microscope and think there's a lot of empty space inside of the eukaryotic cell. In reality, if we had better resolution and we could see with our naked eye, we would see that that cytoplasm is just packed full of stuff, lots of proteins and ribosomes and organelles, et cetera. So there's a lot of material packed inside of a eukaryotic cell. It's not just kind of a bag of fluid with a few organelles floating around in it. All right, so the largest organelle, and certainly the one that, the only organelle that we can easily identify using a standard light microscope, is the nucleus, okay? And this is, again, the defining difference between prokaryotic and eukaryotic cells, is the presence of this nucleus. The nucleus in eukaryotic cells is actually a double membrane structure. So you can kind of see that here. There are the nuclear membrane is actually a double phospholipid bilayer and then there are points where those two membranes come together to make a little passageways in and out of the nucleus that we call the nuclear pores and we'll look at that in part three of this chapter. If we zoom inside of the nucleus, what we would find are the chromosomes of the eukaryotic cell. And these chromosomes are linear strands of DNA, not circular like in prokaryotes. And there are almost always more than one chromosome per inside the nucleus. Karyotes have more than one chromosome. The precise number of chromosomes depends on the species of eukaryote you're looking at, and we'll talk a little bit more about that when we get to genetics in unit three. Now, if we zoom in even closer inside the nucleus, we'll find certain areas of the nucleus where there's a higher density of material, and it stains a little bit more darkly when we use some of the stains for electron microscopy. And this darker region of the nucleus is referred to as the nucleolus, and it is a very easily distinguishable location inside of the nucleus. And this is where there's a lot of ribosomal RNA being produced. And we'll talk more about, we've talked a little bit about ribosome structure in this chapter. We'll look at that again here in just a little bit. Okay. The kind of outside the nucleus and kind of floating around in the cell are these football-shaped structures called mitochondria, okay, or mitochondria, plural, mitochondrion, singular. And if we zoom in and we look at a single mitochondrion, again, we see that it's a double-membrane structure. There's actually two phospholipid bilayers that delineate this mitochondrion, but the inner layer has these large inward folds that are called cristae, okay? And what this does is it increases the surface area of that inner mitochondrial membrane, and that's helpful because that's where a lot of the really important components of the mitochondria are found. So the role of the mitochondria is to produce ATP. So mitochondria are very, very important in a process called, say, the respiration that we'll look at in a lot of detail in Chapter 9. And the last part of the respiration takes place inside the mitochondria, and part of that takes place in proteins that are found in the inner mitochondrial membrane. So by having these large infoldings, these large cristae from the inner mitochondrial membrane, that increases the surface area and allows a lot more ATP to be made in that volume of the mitochondria. The fluid-filled space in between the cristae is referred to as the mitochondrial matrix and that's another another very important subcompartment of the mitochondria that we'll talk about more when we get to Chapter 9. The number of mitochondria in a cell is highly variable. So cells that require a lot of ATP, like muscle cells, that muscle contraction is a very ATP... I'm sorry to say wasteful. that's not the right term, it requires a lot of ATP. So muscle tissue has a lot more cell, a lot more mitochondria per volume than some other tissues that maybe don't have quite the same energy expenditures, okay? In addition,

Even though in textbooks these mitochondria are usually shown as individual little football-shaped structures kind of distributed evenly in the cell, that's usually not the case. There is a pattern to where the mitochondria are found. That pattern changes what cell you're looking at and what kind of point in the life of that cell. And we also know that these mitochondria are very dynamic. They move around inside the cell and sometimes they come together and fuse with each other and they break apart again. And we're just now really beginning to develop the tools to study those mitochondrial behaviors inside of the cell and appreciate just how important they are. Mitochondria are also unique from other organelles, at least in animal cells, in that they also have DNA inside of them. So the mitochondria has its own little genome. And this is a reflection of the fact that mitochondria most likely started out as a prokaryotic cell that got involved by some other cell. And then later on, over the course of evolution, the human organelle dedicated that cell. What? Shit. What's funny? Whatelles that contain DNA other than the nucleus and the mitochondria. In plants, however, and in algae, which do have mitochondria and do have a nucleus, they also have chloroplasts, the photosynthetic organelles, and those also contain their own DNA. And we'll talk about that when we get a little bit further in this unit. All right. Peroxisomes are very small, spherical organelles found kind of right at the cell periphery. Typically, they are, again, highly variable in number from cell type to cell type. It really depends on the type of cell you're looking at. And we are just now beginning to appreciate the fact that not all paroxysomes are the same. In fact, what we've classified as one organelle and called them paroxysomes probably are multiple subtypes of organelles that just look alike, and so we kind of lump them together into one category. The precise functions of peroxisomes to some degree is cell-type dependent. However, there is one peroxisome function that we find in all different kinds of cells, and that is that the peroxisomes are sites where hydrogen peroxide is sequestered, sort of contained, and then degraded in a controlled fashion through an enzyme called catalase. So hydrogen peroxide H2O2, this is that stuff in a brown bottle that your mom or dad might have put on cuts when you were little to keep them from getting infected. And if you just allow hydrogen peroxide to break down in an aqueous environment on its own, it generates some oxygen, that's why it bubbles, but it also generates a lot of free radicals. And remember we talked about free radicals back in Chapter 2. Free radicals are sort of transient high-energy molecules that when they interact with other things, they strip electrons from them and damage them in the process. Unfortunately, hydrogen peroxide is a byproduct of a number of different metabolic reactions inside of cells. So, and if that hydrogen peroxide was just allowed to degrade on its own in the cytosol, there would be free radical generation, and those free radicals would damage proteins and lipids, et cetera, and cause problems for the cell. So what cells have done, what eukaryotic cells have done, is they, if you look inside their peroxisomes, the peroxisomes are full of an enzyme called catalase, and catalase breaks hydrogen peroxide down in a controlled fashion to generate water and oxygen without generating any free radicals along the way. And a lot of the metabolic processes that generate hydrogen peroxide as a byproduct also take place inside of peroxisomes, so that when that hydrogen peroxide is generated, catalase can break it down in a controlled fashion, and you don't have that free radical problem. So one example of this is fatty acids, which we looked at in Chapter 6, are good sources of fuel for cells. The initial breakdown of fatty acids is a process that does generate some hydrogen peroxide, and so that initial breakdown of fatty acids into smaller pieces takes place in peroxisomes where the hydrogen peroxide that's generated can be eliminated in a controlled fashion. And then those fatty acid fragments are exported from the peroxisome outside into the cytosol and they can be broken down.

Okay. These aren't really organelles, but certainly we find lots of ribosomes inside of eukaryotic cells. And we've talked about ribosomes already. And I remember ribosomes are the macromolecular machines that cells use to make new proteins. Ribosomes are composed of a large and a small subunit, and then each of those is in turn composed of lots of smaller proteins and some associating RNAs. In eukaryotes, we find ribosomes in two places. So some ribosomes, I'm not sure how well you can see this, you have to zoom in, some ribosomes are just kind of floating around in the cytosol, okay? Not really localized or anchored in any location. But other ribosomes are anchored on the surface of a organelle whose membrane kind of comes out of the outer nuclear membrane. And that organelle is called the rough endoplasmic reticulum, okay? So the rough endoplasmic reticulum, or the rough ER, is an outgrowth of the outer nuclear membrane. And the reason it's called the rough ER is under the microscope it looks rough, and the reason it looks rough is it is just covered with ribosomes. And so you can see that in an electron micrograph cross-section down here. And so that gives us a hint about the function of the rough ER. It's going to be involved in protein synthesis in some way. Specifically, proteins that are destined for the cell membrane or destined to be secreted from the cell or destined for specific organelles in the cell are made first by the ribosomes that are associated with the rough ER. So not all proteins are made by these ribosomes, but certain subcategories of proteins are made by ribosomes on the rough ER. And we'll look in much more detail on how that process works in part three of this chapter. The proteins that are made by the ribosomes in the rough ER, well, sorry, I'm getting ahead of myself there. So if we look kind of off to the side of the rough ER, we see sort of an extension of the rough ER, but it's no longer rough because it doesn't have any proteins attached to it. And this we call the smooth endoplasmic reticulum or the smooth ER. And the smooth ER's function is primarily new lipid synthesis. So most of the lipids that a cell make, eukaryotic cell makes, are made at least in part in the smooth ER. The smooth ER is also in certain cell types the organelle that accumulates and detoxifies certain types of toxins, particularly hydrophobic toxins. Some of the same enzymes that are involved in glyphic synthesis can modify hydrophobic toxins to make them less dangerous to the cell. So if you look, for example, in a liver cell, the liver is, I'm sure you remember from high school, is an organ that has several functions. One of those functions is in detoxifying the blood. And if you look inside certain types of cells in the liver, you will find very extensive networks of smooth ER to help the liver cells carry out that function. In chapter 11, we'll see that the ER also has another, smooth ER specifically, excuse me, also has another purpose, and that is it stores calcium ions, Ca2+. There's a much higher concentration of calcium in the smooth ER than there is in the cytosol, and that calcium can be released into the cytosol in response to certain stimuli and then trigger various responses in the cell, and that's very important when we talk about cell signaling in a later chapter. All right. A little bit, so very close to the rough ER is a flattened network of membranes called the Golgi apparatus or the Golgi body. And the Golgi apparatus receives vesicles containing proteins made in the rough ER. And it receives those vesicles on what's referred to as the cis face of the Golgi.. So the cispace would be the side of the Golgi that's closest to the rumpi arm. And then those vesicles…

All right, welcome to Chapter 7. Chapter 7 is an overview of the structure of cells, the internal structure of cells. And we'll begin with a kind of quick overview of prokaryotic cell structure, focusing mostly on the bacteria. And then we'll move on in the rest of the chapter and focus more on what's going on inside of eukaryotic cells. So if you remember our tree of life from earlier, there are three domains, bacteria, archaea, and eukaryotes. The bacteria and the archaea collectively are called the prokaryotes because they lack a membrane-bound nucleus. So all life on Earth as we know it uses DNA as its genetic material, but they package that DNA differently. And eukaryotes... The genome is contained within a membrane-bound organelle called the nucleus inside of cells, and prokaryotes is not the case. Now, there are lots of other differences between prokaryotes and eukaryotes that are maybe a little bit more variable in terms of how definitive they are, either a prokaryotic characteristic or a eukaryotic characteristic. The archaea are... Kind of as, you know, indicated by their place on the, you know, phylogenetic tree, the archaea are kind of in the middle. They share more things in common structurally with prokaryotes than they do eukaryotes, but they do share a number of characteristics with eukaryotes, particularly the way that, or particularly some of their metabolic pathways are more similar to what we see in eukaryotes and prokaryotes. But for this part of Chapter 7, we're really going to focus just on, or primarily at least on, the prokaryotes, okay? All right. Now, if you look on the left here, this is a, just kind of a cartoon of a typical, if there is such a thing, a typical prokaryotic cell. And it's really hard to use the word, use the phrase typical prokaryotic cell with a straight face, because there is just tremendous diversity in the prokaryotes, in their morphology, in their structure. And what we're going to look at are sort of characteristics that most, or all bacteria, for the most part, share. In a few cases, there will be some exceptions, and I'll tell you a little bit about those. Now, one of the things that's most apparent is there are no internal membrane-bound structures, okay? And this is true for many, but not all of the prokaryotes. There are some prokaryotes that have internal membrane-bound structures. There are certain bacteria that are photosynthetic, and they certainly have their photosynthetic structures encapsulated in an internal membrane. But for the most part, we don't see internal membrane-bound structures inside of prokaryotic cells. And this is in contrast to what we'll see later on with eukaryotes, where eukaryotes have lots of internal membrane-bound structures. Those internal membrane-bound structures, we would, in a eukaryote, we would see them in a prokaryotic cell. In a prokaryote, we would call an organelle. So an organelle is a localized site of specific function, okay, that is separated from the environment by a membrane. And eukaryotes have to have many internal membrane-bound structures because they're much larger than prokaryotes. And so relying on simple diffusion to bring the right things together in the right combination to carry out various functions in a eukaryote, would be tremendously inefficient. So by packaging, sort of subdividing a eukaryotic cell into smaller pieces, it allows for the more efficient specialization of function in different regions. Prokaryotes are much smaller than eukaryotes, and so there's not that same sort of demand or pressure on them to have as many internal compartments. Now that doesn't mean, however, that the inside of a prokaryotic cell is just a big bag of fluid. Nothing would be further from the truth. So this over here is a cartoon, but it is a scientifically accurate, drawn-to-scale cartoon. It's based on some real images, electron microscopy images of a bacterial cell. And just to orient you, here's the cell membrane, okay? Here's the cell wall. Here is the genetic material, the DNA, inside that bacterial cell. But look, there's tons of stuff packed in here. There's lots. There's lots of proteins and large, complex structures like ribosomes.

are long filamentous proteins that make up the cytoskeleton. We'll talk about that later. But I just show you this to kind of give you the, or to dissuade you of this mental image that prokaryotes are basically big bags of fluid with some DNA floating around in it. There's nothing further from the truth. There's a lot of stuff packed in here. All right. Now, nearly all prokaryotes, archaea and bacteria alike, have a cell wall on the outside of their plasma membrane. So their plasma membrane, their cell membrane, is a phospholipid bilayer, just like we would see in eukaryotes. But most prokaryotes also have a cell wall. And we talked about the cell wall of bacteria a little bit back in Chapter 5 in carbohydrates when we talked about peptidoglycan. Archaea don't really use peptidoglycan for their cell wall. They use peptidoglycan for their cell wall. They use something different, but structurally it's similar. And this cell wall is quite thick. You can see that here. So here is the plasma membrane. This is kind of a cross-section through the edge of a bacterial cell. Here's the plasma membrane, the phospholipid bilayer. You can see how thin that is. And then look how thick the cell wall is on the outside. The cell wall is primarily there to serve as a protective function. And not only does it help protect the bacteria, from, you know, getting beat around in its environment, but it also helps to protect the bacteria from bursting and swelling because of osmotic pressure. The cytoplasm of bacteria or of all cells is fairly high salt concentration. The bacteria in the environment oftentimes find themselves in solutions or in areas where there's not nearly as much dissolved salt. So they often find themselves in a hypotonic environment. And as we learned back in Chapter 6, if you put a hypertonic cell into a hypotonic environment, water will try to rush from the environment into the cell, cause it to swell up and burst. And so the cell wall of bacteria helps to provide some resistance to that so that it doesn't happen. Now, if we look at the DNA, the genetic material of a bacterial cell, it's a little bit amazing, I think, or perplexing, as to just how much DNA can be packaged inside such a little cell. So their DNA in prokaryotic cells comes in two forms. One form is the chromosome of the cell. And that chromosome is a very large circular molecule of DNA. And if we were to unspool that large circular molecule of DNA that's shown over here, look how much, look how large, if we were to stretch it all out, that circular chromosome is compared to this E. coli bacterial cell. It's really amazing. There are other smaller circular fragments of DNA in bacteria called plasmids, okay? And plasmids do carry very important genes, genes that the cell uses for various functions. And plasmids can be exchanged between bacteria of similar types. And so. And that's through a process called conjugation. You'll learn about it if you take a microbiology course. But it's sort of the closest thing bacteria have to sex. It's not true sex, but it's the closest thing they have to sex. Now, what allows this really huge, large chromosome to be packaged into a very small cell in a very specific region of the bacterial cell that we call the nucleoid, the nucleoid is the region of the cytoplasm in a bacterial cell, where the nucleoid is the region of the cytoplasm. And that's where the circular chromosome is found. Oops, sorry, I went the wrong way. What allows for that is a phenomenon called supercoiling. So if you take a circular molecule like the circular DNA that makes up the bacterial chromosome, and if that circular molecule is twisted, remember DNA is a double helix with a twist, then that is going to automatically cause that molecule to kind of wrap up. If it was linear, it could relax that tension, but it's not. It's circular. It's tied together at the top. Kind of like now rubber bands will snarl up in a drawer if you leave them in there for too long. And so this supercoiling of DNA allows it to occupy a really small volume compared to what you'd get if it was a linear molecule, and that allows for a relatively large chromosome to be packaged into a very small region of the cell. Prokaryotic cell. All right. Now, all cells, prokaryotic and eukaryotic,

contain structures called ribosomes and ribosomes we talked a little bit about these back in chapter four and we'll talk a lot more about them in the fourth unit in this course but ribosomes are what cells use to make new proteins okay and ribosomes they're kind of large macromolecular machines in a sense and they have two subunits a small subunit and a large subunit and then each of these small and large subunits is in turn composed of lots of different individual pieces some of those pieces are proteins and smaller proteins and some of those pieces are small RNAs so both prokaryotes and eukaryotes have a very kind of similar overall shape and structure to their ribosomes but they differ in terms of the specific components that those ribosomes are made of and that's represented here so this chart shows the types of RNAs found in the large and the small subunits of both prokaryotic and eukaryotic ribosomes the types of proteins just the protein names are abbreviated here the point of this is just to illustrate that even though at the macro level eukaryotic and prokaryotic ribosomes look similar structurally they're different and we can exploit these differences to our advantage in terms of designing antibiotics so certain classes of antibiotics the immunoglycosides the tetracyclines the chloramphenicol are work by specifically targeting some component of the bacterial ribosome that is not found in eukaryotic ribosomes we can also use the differences in ribosome composition between prokaryotic and eukaryotic cells these differences in ribosomes are known in the подiagnostic feature if we're studying some new cell and we're not sure if that cell is prokaryotic or eukaryotic yet we can look in particular at the types of RNAs that make up those ribosomes and those are very diagnostic for saying yes this is definitely a prokaryotic ribosome or no this is definitely a eukaryotic ribosome now prokaryotes have projections or protrusions from their surface they're particularly very much in the eukaryotic type of cell ال-boc. so they're more likely to cause these changes compared to the eukaryotic ribosomes because in comparison to the monoclonal ribosomes the monoclonal ribosomes they actually have a different type of cell like eukaryotic ribosomes but they're not virtually the same as prokaryotic ribosomes projections or protrusions from their surface, and these appendages, if you will, kind of fall into two groups, two broad groups. Some of these appendages are really long and motile, meaning that they can move, okay? And we call these flagella, in plural, or flagellum singular. So this particular bacterial cell has one, two, three flagella, it looks like. And these flagella are, if we go back to here, these flagella are large, complex, multi-subunit proteins that span the bilayer and the cell, lipid bilayer and the cell wall of the bacteria. So here's what the cytoplasmic component of that, of a flagellum looks like, and here's the flagellum sticking out in the environment. And they're kind of like boat motors. So this structure here spins around, and that spins this flagellum, so kind of like a propeller on a boat, that helps that bacteria to move around in its environment, okay? And they don't, certain types of eukaryotic cells also have structures that we call flagella, but they look and work very differently, okay? And we may get to that here in a little bit. Okay. Another type of protrusion from prokaryotic cells are these long, spiky-looking things. These are called fimbriae, and these are really more anchoring structures. So they kind of stick out, and they allow adjacent cells to stick to each other, or cells to stick to their environment so that they can sort of anchor down, rather than just being constantly moving around in the environment that they're in. Okay. Now, um, in the next part of chapter seven, we're going to see, we're going to look in detail at the structure of eukaryotic cells. And when we're done with that, you're going to come back and do a little bit of comparison and contrast, I hope. And you'll see something, and if you do that, you'll end up with something like this table here. So prokaryotic cells are typically one to two orders of magnitude smaller than eukaryotic cells, but there are exceptions. There are some really large prokaryotic cells that are over 10 microns in size, and there are some very small eukaryotic cells that are over 10 microns in size. And there are some very small eukaryotic cells that are below 10 microns in size. But for the most part, prokaryotes tend to be much larger than eukaryotes. Prokaryotes don't have a membrane-bound nucleus. Eukaryotes do.

Prokaryotes generally, as I mentioned before, don't have any other membrane-bound organelles. But there are exceptions, and certainly the largest of those exceptions are those bacteria that are photosynthetic, that have the ability to take energy from sunlight and use that to make sugar. And in those bacteria, the photosynthetic apparatus is, in fact, encapsulated in an internal membrane structure. You'll also see in eukaryotes that eukaryotic chromosomes are not circular like they are in prokaryotes, or most prokaryotes anyway, but rather eukaryotes have multiple strands of DNA that make up their chromosomes, and each of these strands are linear, not circular. Again, now there are exceptions. There are some prokaryotes that have multiple small linear chromosomes, and there are some eukaryotes that at least at certain times, have their chromosomes adopt a circular sort of structure. So again, this is not a 100% difference between prokaryotes and eukaryotes, but a pretty good distinguishing characteristic. And then of course, again, we'll see the eukaryotes that we saw already, but we'll see again that their ribosomes are a little bit bigger, they're a little bit more complex in terms of the number of subunits they're composed of, and the types of subunits they're composed of. And in fact, in many ways, again, that's our best diagnostic tool when we're looking at a cell, to figure out quickly if it's a prokaryotic or eukaryotic cell, look at the structure of the ribosome. Okay, so that is it for this, and I said it would be a very quick overview of prokaryotic cell structure, and it was. Now we're going to move on to the rest of this chapter. We're going to focus on eukaryotic cell structure. We'll begin with a very quick overview, looking at the major organelles and some of the other major structural elements in eukaryotic cells, and then we'll talk about in part three, we'll look at protein trafficking, which is how, basically looking at how do eukaryotic cells get the correct proteins to the right organelles so that they can function properly, and then we'll end with the discussion of the cytoskeleton, focusing mostly on eukaryotes, but then coming back and comparing that to what we see in prokaryotes at the very end. Okay, so that's the plan for the rest of the chapter. I'll see you in part two.

All right, welcome to part two of chapter seven. In part one, we did an overview of the structural aspects of prokaryotic cells, and now we'll do the same thing for eukaryotes. When we talk about eukaryotes, we are, of course, talking about all the plants, all the animals, algae, etc. And we'll kind of, the way I've got this structured is we'll look at some of the, first we'll look at the aspects of eukaryotic cell structure that are similar between plant and animal cells, and then we'll look at a few differences. All right, and let me just clarify some terms here. These are a couple terms that sometimes get used sloppily, admittedly, sometimes even by me, and those are cytosol versus cytoplasm, okay? So the cytosol refers to the fluid component, the watery component and the stuff dissolved in that water inside of cells. Cytoplasm refers to anything, it's kind of a catch-all term we use for anything inside of a cell. So it's a term that we use for anything inside of a cell. So it's a term that we use for anything inside of a cell membrane, okay? So the cell membrane encapsulates the cytoplasm, the cytoplasm is composed of cytosol plus various membrane-bound organelles and the things that are floating around in that cytosol. And again, remember that an organelle, at least in the definition that we're going to use here, is a small membrane-bound structure inside of a cell that contains the proteins, etc., necessary for a very particular function, okay? So organelles have their own structure, and they are typically dedicated to a small subset of functions, and this allows for more efficient activities inside of eukaryotic cells, which tend to be much bigger volume-wise than prokaryotes. So here we look at a very kind of generalized or typical animal cell. Obviously, the largest organelle is the nucleus, and the nucleus contains the genetic material, it contains the chromosomes for that cell, and then there's a variety of organelles kind of branching off of the nucleus and then floating around in the periphery. Many of the same organelles that we saw in the animal cell we'll find in the plant cell. In fact, most of the organelles are the same, but there are a few differences, and we'll highlight what some of those differences are as we get towards the latter half of this particular lecture. Now, this is a little bit similar to a picture that we looked at in part one for prokaryotes, and this, again, is just a blow-up of a section of a eukaryotic cell sort of starting from the cell membrane on one side and going all the way to the nucleus on the other, and it's color-coded so that yellow represents lipids, green represents carbohydrates, red represents nucleic acids, RNA and DNA, and blue represents proteins, okay? And again, the purpose of this is just to give you a visual sense that even, you know, we may look under the microscope and think there's a lot of empty space inside of the eukaryotic cell. In reality, if we had better resolution and we could see with our naked eye, we would see that that cytoplasm is just packed full of stuff, lots of proteins and ribosomes and organelles, etc. So there's a lot of material packed inside of a eukaryotic cell. It's not just kind of a bag of fluid with a few organelles floating around in it. All right, so the largest organelle and certainly the one that the only organelle that we can easily identify using a standard light microscope is the nucleus, and this is, again, the defining difference between prokaryotic and eukaryotic cells is the presence of the nucleus. The nucleus in eukaryotic cells is actually a double membrane structure, so you can kind of see that here. There are, the nuclear membrane is actually a double phospholipid bilayer, and then there are points where those two membranes come together to make a little passageways in and out of the nucleus that we call the nuclear pores. So we're going to look at that in part three of this chapter. If we zoom inside of the nucleus, what we would find are the chromosomes of the eukaryotic cell, and these chromosomes are linear strands of DNA, not circular like in prokaryotes, and there are almost always more than one chromosome per inside the nucleus. So most eukaryotes have more than one chromosome. The precise number of chromosomes depends on the species of eukaryote you're looking at, and we'll talk a little bit more about that when we get to genetics in unit three. Now, if we zoom in even closer and inside the nucleus, we'll find certain areas of the nucleus where there's a higher density of material, and it kind of stains a little bit more darkly when we use some of the stains for electron microscopy. And this darker region of the nucleus is referred to as the nucleolus, and it is a very easily distinguishable location inside of the nucleus. And this is where there's a lot of ribosomal RNA being produced, and we'll talk a little bit about ribosome structure in this chapter. And we'll look at that again here in just a little bit. The outside the nucleus and floating around in the cell are these football shaped structures called mitochondria, or mitochondria plural, mitochondrion singular. And if we zoom in and we look at a single mitochondria, again, we see that it's a double membrane structure. There's actually two phospholipid bilayers that delineate this mitochondrion. But the inner layer has these large inward folds that are called cristae. Okay. And what this does is it increases the surface area of that inner mitochondrial membrane,

helpful because that's where a lot of the really important components of the mitochondria are found. So the role of the mitochondria is to produce ATP. So mitochondria are very, very important in a process called cellular respiration that we'll look at in a lot of detail in chapter nine. And the last part of the respiration takes place inside the mitochondria, and part of that takes place in proteins that are found in the inner mitochondrial membrane. So by having these large infoldings, these large cristae from the inner mitochondrial membrane that increases the surface area and allows a lot more ATP to be made in that volume of the mitochondria. The fluid-filled space in between the cristae is referred to as the mitochondrial matrix, and that's another very important subcompartment of the mitochondria that we'll talk about more when we get to chapter nine. The number of mitochondria in a cell is highly variable. So cells that require a lot of ATP, like muscle cells, that muscle contraction is a very ATP, I sort of say wasteful, that's not the right term, requires a lot of ATP. So muscle tissue has... a lot more mitochondria per volume than some other tissues that maybe don't have quite the same energy expenditures, okay? In addition, even though in textbooks these mitochondria are usually shown as individual little football-shaped structures kind of distributed evenly in the cell, that's usually not the case. There is a pattern to where the mitochondria are found, that pattern changes depending on what cell you're looking at and what kind of point in the life of that cell. And we also know that these mitochondria are very dynamic. They move around inside the cell and sometimes they come together and fuse with each other, then they break apart again, and they're not as nervous, or they don't move at all. These mitochondria are very dynamic, they come together andывают into an extra form of body structure, and we're just now really beginning to develop the tools to study those mitochondrial behaviors inside of the cell, and appreciate just how important they are. Mitochondria are also unique from other organelles at least in animal cells in that they also have DNA inside of them, so the mitochondria has its own little genome, and this is a reflection of the fact that mitochondria most likely started out as course of evolution um he became an organelle dedicated to that cell and the um the dna that's found inside the mitochondria is a very small circular chromosome reminiscent of a prokaryotic chromosome not all of the proteins that we find in mitochondria are coded by mitochondrial genome genes but many are okay um there's there are no other organelles and eukaryotic cells besides the nucleus in the mitochondria that contain dna in i'm sorry i said eukaryotic in animal cells there's no other organelles that contain dna other than the nucleus and the mitochondrion in plants however in an algae um which do have mitochondria and do have a nucleus they also have chloroplasts the photosynthetic organelles and those also contain their own dna and we'll talk about that when we get a little bit further in this in this uh view all right um peroxisomes are very small spherical organelles found kind of right at the cell periphery typically they are um again highly variable in number from cell type to cell type it really depends on the type of cell you're looking at and we are just now beginning to appreciate the fact that organ that not all peroxisomes are there the same in fact what we what we've classified as one organelle and called them peroxisomes probably are multiple subtypes of organelles um they just look alike and so we kind of lump them together into one category the precise functions of peroxisomes to some degree is cell type dependent however there is one peroxisome function that we find in all different kinds of cells and that is that the peroxisomes are sites where hydrogen peroxide is sequestered sort of contained and then degraded in a controlled fashion through an enzyme called catalase okay so hydrogen peroxide h202 this is that stuff in a brown bottle that your you know mom or dad might have put on cuts when you were little keep them from getting infected and um if you just allow hydrogen peroxide to break down in an awkward environment on its own it generates uh some oxygen that's why it bubbles but it also generates a lot of free radicals and remember we talked about free radicals back in chapter two free radicals are sort of transient high energy molecules that when they interact with other things they strip electrons from them and damage them in the process unfortunately hydrogen peroxide is a byproduct of a number of different metabolic reactions inside of cells so um and if that hydrogen peroxide was just allowed to degrade on its own in the cytosol there would be free radical generation and those free radicals would damage um proteins and lipids etc uh and and cause problems for the cell so what cells have done what eukaryotic cells have done is they if you look inside the peroxisomes the peroxisomes are full of an enzyme called catalase and catalase breaks hydrogen peroxide down in a controlled fashion to generate water and oxygen without generating any free radicals along the way of the metabolic processes that generate hydrogen peroxide as a byproduct are also take place inside of peroxisomes so that when that hydrogen peroxide is generated catalase can break it down in a controlled fashion and you don't have that free radical problem so a very one example of this is fatty acids which we looked at chapter six are good sources of fuel for cells the initial breakdown of fatty acids is a process that does generate some hydrogen peroxide and so that initial breakdown of fatty acids into smaller pieces takes place in peroxisomes where the hydrogen peroxide is generated can be eliminated in a controlled fashion

and then those fatty acid fragments are exported from the peroxisome outside into the cytosol and then they can be broken down further. Okay, these aren't really organelles, but certainly we find lots of ribosomes inside of eukaryotic cells, and we've talked about ribosomes already. Remember, ribosomes are the macromolecular machines that cells use to make new proteins. Ribosomes are composed of a large and a small subunit, and then each of those is in turn composed of lots of smaller proteins and some associating RNAs. In eukaryotes, we find ribosomes in two places. Okay, so some ribosomes, I'm not sure how well you can see this, get them to zoom in, some ribosomes are just kind of floating around in the cytosol, okay, not really localized or anchored in any location, but other ribosomes are anchored on the surface of a organelle whose membrane kind of comes out of the outer nuclear membrane, and that organelle is called the rough endoplasmic reticulum. Okay. So the rough endoplasmic reticulum, or the rough ER, is an outgrowth of the outer nuclear membrane, and the reason it's called the rough ER is under the microscope it looks rough, and the reason it looks rough is it is just covered with ribosomes, okay, and so you can see that in an electron micrograph cross-section down here, and so that gives us a hint about the function of the rough ER. It's going to be involved in protein synthesis in some way, specifically proteins that are destined for the cell membrane or destined to be secreted from the cell or destined for the cell membrane. So you can see the typical organelles in the cell are made first by the ribosomes that are associated with the rough ER, okay. So not all proteins are made by these ribosomes, but certain subcategories of proteins are made by ribosomes on the rough ER, and we'll look in much more detail on how that process works in part three of this chapter. The proteins that are made by the ribosomes in the rough ER, well, sorry, I'm getting ahead of myself there. So if we look kind of off to the side of the rough ER, we see sort of an extension of the rough ER, but the ribosomes are made by the ribosomes. But it's no longer rough because it doesn't have any proteins attached to it. And this we call the smooth endoplasmic reticulum or the smooth ER. And the smooth ER's function is primarily new lipid synthesis. So most of the lipids that a cell make, eukaryotic cell makes, are made at least in part in the smooth ER, okay. The smooth ER is also in certain cell types the organelle that accumulates and detoxifies certain types of toxins, particularly hydrophobic toxins. And the same enzymes that are involved in lipid synthesis can modify hydrophobic toxins to make them less dangerous to the cell. So if you look, for example, in a liver cell, the liver is, I'm sure you remember from high school, is an organelle, or it's an organ that has several functions. One of those functions is in detoxifying the blood. And if you look inside certain types of cells in the liver, you will find very extensive networks of smooth ER to help the liver cells carry out that function. In chapter 11, we'll see that the ER also has another smooth ER specific function, and that's the lipid synthesis. So if you look at the lipid synthesis, you'll see that the lipid synthesis is very similar to the smooth ER, okay. So if you look at the lipid synthesis, you'll see that the lipid synthesis is very similar to the smooth ER, okay. But specifically, excuse me, also has another purpose, and that is it stores calcium ions, Ca2+. There's a much higher concentration of calcium in the smooth ER than there is in the cytosol. And that calcium can be released into the cytosol in response to certain stimuli, and then trigger various responses in the cell. And that's very important when we talk about cell signaling in a later chapter. All right, a little bit, so very close to the rough ER is a flattened network of membranes. So I'm going to show you that. It's called the Golgi apparatus, or the Golgi body. And the Golgi apparatus receives vesicles containing proteins made in the ruffiar. And it receives those vesicles on what's referred to as the cis face of the Golgi. So the cis face would be the side of the Golgi that's closest to the ruffiar. And then those vesicles fuse with this cisternae, or membranous sac. And the proteins get modified, and then they get passed from one stack to the next until they get to the last stack in the Golgi that's referred to as the trans face of the Golgi. And here they get packaged in the new vesicles and then delivered to certain specific locations depending on where they need to go. So there's a lot of exchange of material between the ruffiar and the Golgi apparatus, and that'll become very important in part three of this chapter. All right, so those things that we've talked about so far, the organelles, the nucleus, the mitochondria, the ruffiars, the Golgi apparatus, and then, of course, ribosomes, those are found in all eukaryotic cells, plants, bacteria, animal cells. Now we're going to look at some organelles. We're going to look at some organelles that are a little bit more restrictive. And the first of these are lysosomes. So lysosomes look a lot like peroxisomes visually, but they have a very different function. So they are spherical organelles found usually fairly close to the cell membrane, kind of just in the periphery of the cell, but only in animal cells. So we don't find lysosomes in plant cells. And lysosomes basically act as the cell's recycling center. And so they take in large cellular macromolecules, and then they break those down into smaller pieces, export those pieces into the cell, and then they can get reused and recycled. What allows us to do this is we can do this in a way

lysosomes to do this is they are packed full of a category of enzymes called acid hydrolysis. So hydrolase is an enzyme that carries out hydrolysis reactions. If you remember back from Unit 1, all of the biological macromolecules in a cell are made via condensation reactions and then broken down via hydrolysis reactions. So you break down proteins into amino acids by a hydrolysis reaction. You break down nucleic acids and nucleotides by a hydrolysis reaction. You break down polysaccharides and monosaccharides by a hydrolysis reaction. So hydrolases are the enzymes that help to carry out hydrolysis reactions. Acid hydrolases are hydrolases that only fold and work properly in an acidic environment. And that is in fact what the lysosome is. So the pH of the lysosome is around four or five compared to seven to seven and a half in the cytosol. So remember the pH scale from Chapter 2, that's a couple of orders of magnitude difference in acidity inside the lysosome compared to the outside. And so it's very important to remember that the pH of the lysosome is very important to be made. The materials that need to get broken down by a lysosome get delivered to the lysosome. We'll look at how that works in just a minute. They get broken down in that acidic environment by these acid hydrolases, and then they those fragments get exported back out to transport of proteins into the cytosol so they can be reused. The acidic environment of a lysosome is important in a couple of ways. First of all, hydrolysis reactions are more efficient in an acidic environment. So by keeping the pH low in the lysosome, that makes it easier for hydrolysis reactions to occur even without those acid hydrolases. But the other advantage of this is it sort of acts as a fail-safe or a safety program for the cell in the sense that because these hydrolases, which are very damaging enzymes, right? So a nuclease degrades nucleic acids, a protease degrades proteins, a lipase degrades lipids. So these enzymes, if they were just let loose in the cytosol, in theory could do a lot of damage. But because these are acid hydrolases and they only work in an acidic environment, they work inside the lysosome. But if the lysosome were to break and those hydrolases were to leak out in that neutral environment of the cytosol, they're not going to hold properly and they're not going to damage anything. So that's another way that kind of keeping this function contained in a small organelle with a unique, in this case, acidic environment, it sort of helps to protect the cell from accidental damage. How is the acidic environment inside a lysosome maintained? It's maintained through proton pumps. So ATPases that, like we talked about in Chapter 6, that hydrolyze ATP and use that energy to move. Protons from a low to high concentration gradient, which by itself would be a very energetically unfavorable process. So they have to hydrolyze ATP to do that. It's an example of active transport, like we talked about back in Chapter 6. All right. Now, how do materials get delivered to the lysosome? Okay, there are three primary ways, and this slide from your textbook, this figure from your textbook, it's kind of goofily numbered. So what it's numbering is one and two is really just number one. This is all one process. Okay. And then three and four is really one. One process, and then five is a process, and then six is just the endpoint of all of those. So there's really three different processes that allow materials to get delivered to a lysosome for degradation. So the first of those is what's called receptor mediated endocytosis. So endocytosis is the forming of a vesicle from the cell surface, so a piece of the membrane will pinch inward and bring something into the cell from the outside. Receptor mediated endocytosis just means that this is not a random process. So there will be a cluster of receptors in the cell membrane that binds some particular type of molecule. When enough of that molecule is bound to the receptor, then this vesicle pinches inward to bring that material into the cell in this new vesicle that we call an endocytic vesicle. And that endocytic vesicle is then acidified. So vesicles from the Golgi apparatus carrying these proton pumps get brought to this endocytic vesicle. And start to lower the pH of that endocytic vesicle. More the acid hydrolases get delivered to the endosome, and then you basically turn that endosome into a lysosome over a period of time, and then all the stuff that was brought in gets degraded. In some cases, the receptors, as this endosome is maturing into a lysosome, the receptors pinch off and go back to the cell surface so they can be reused again. Receptor mediated endocytosis is a really important function in cells. It's, for example, how cells bring in cholesterol from the outside so they can use it for their membranes. They have receptors in the cell membrane that binds the cholesterol particles and bring them in. And there's lots and lots of examples of receptor mediated endocytosis, different types of receptors binding to different types of macromolecules outside the cell and helping to bring those inward. Interestingly, certain types of viruses, and we'll see this at the very end of the semester, certain types of viruses hijack this receptor mediated endocytosis pathway as a way of getting into a cell in order to infect it. So they basically trick the cell, certain viruses can bind to receptors, and they can't get into the cell. So they have to go back on the cell surface, trick that cell to bring those viruses in and make an endocytic vesicle, and then before that endocytic vesicle matures,

into a lysosome, the viruses escape. So it's kind of an interesting backdoor, if you will, for viral entry into cells. And we'll look at an example of that when we get to the end of the semester. So receptor-mediated endocytosis, that's one mechanism for bringing materials to a lysosome for degradation. And in this case, these are materials from outside of the cell. Another way to bring materials to a lysosome is through phagocytosis. And phagocytosis is similar to receptor-mediated endocytosis, but it's on a much larger scale. So in this case, this cell is encountered some large structure in its exercise environment. This looks to me like a bacteria, in fact. And it's now going to bring that material in, kind of pinch it off to make a new structure called a phagosome. And then the phagosome gets either delivered to or turned into a lysosome in order to be degraded. Not all cells in your body are particularly good at phagocytosis. Some are much better than others, particularly certain cells of the immune system. Things like macrophages, neutrophils, cells that are specialized to cruise around, look for invading bacteria or viruses, or fragments of cells that are infected by bacteria and viruses. Those kinds of cells are really good at phagocytosis, but other types of cells are not so good. Okay, now both receptor-mediated endocytosis and phagocytosis bring materials that started from outside of the cell into the cell so that they can be degraded by a lysosome. In contrast, down here is autophagy or autophagy, depending on if you want to pronounce it the British way or not. Autophagy is a way of taking internal materials and delivering them to a lysosome. And this can happen on a large scale or a small scale. The example that's shown here is a fairly large scale. So in this case, we have some damaged organelle, which happens to be a mitochondrion. And it's old enough and damaged enough that it's just not functioning properly. So the cell can build a new membrane around it to turn it into what we call an autophagosome. And then that autophagosome gets delivered to a lysosome, and the materials of the lysosome can degrade. This damaged organelle and those pieces can be reused again. Autophagy is going on all of the time in all of your cells right now. It's a very important normal process of homeostasis, a way of getting rid of and reusing materials that the cell no longer needs or that are no longer functioning properly. I shouldn't say get rid of, recycling materials that the cell no longer needs or that are no longer functioning properly. Interestingly, cancer cells tend to rely more heavily on autophagy than normal cells. Doesn't mean normal cells don't do autophagy, they do, but cancer cells do autophagy at a really high level. And that's for a couple of reasons. One, they tend to have a, they're so metabolically active, they tend to have a faster rate of damage to some of their organelles like mitochondria, so they have more things to recycle. But also, when, as a tumor grows, and the cells in the center of that tumor get further away from the blood vessels outside that are delivering the nutrients, those cells can switch, can upregulate autophagy at higher levels, and basically persist for a longer period of time until new blood vessels are established. By just recycling, constantly recycling their own internal components. So they can't do it forever, obviously, but they can, it allows them to live longer in a low nutrient environment until the tumor can trigger new blood vessels to grow in and deliver nutrients. Okay, so we don't see lysosomes in animal, excuse me, in plant cells. In plants, the structure that's most similar, but it's actually not similar at all, it's very different, to a lysosome is called the vacuole. Okay. And vacuoles are, can be really large, so, and they're really easy to see because, you know, they don't have a lot of internal structure. They just look like big bags of fluid. And certainly, they do contain a lot of fluid, but they contain some other stuff as well. Not all vacuoles are the same. Some plants have more than one vacuole. Most plants only have, plant cells only have one vacuole. But in general, again, if we kind of look at this in the aggregate, there are three functions of plant, of the vacuoles and plant cells. So the first is storage. So a lot of the pigments that give plants their colors are stored inside of vacuoles. They, they can temporarily store excess waste. Waste materials, salts, minerals, even sometimes excess nutrients, kind of a place to store those nutrients if the cell needs them. And then certain toxins are also found in, in vacuoles. Garlic, the flavor, the, or the chemical that gives garlic its unique flavor is stored inside the, it's called allicin, is stored inside of vacuoles. Rubber, from a rubber tree, that chemical that we, that we extract to make rubber is, is stored inside of the vacuole in those rubber plants. So that's, that's one function of vacuoles. Another function is recycling. There are some hydrolases inside of lysosomes, and those hydrolases can break down materials that are brought to the vacuole, okay? They're not acid hydrolases. It doesn't work in exactly the same way as a lysosome, but it's a little bit similar. And then finally, the last function for plant vacuoles is a structural one. So the vacuole, as it swells and fills with water, it creates a high pressure inside of that cell. And remember, we'll look at this in just a second. Okay. Okay. Okay. Okay. Okay. Okay. Okay. Okay. Okay. Okay. Okay. Okay. Okay. Okay.

wall okay and so um it sort of helps to maintain a really high internal pressure in the cell pushing hard against that cell wall and collectively in all the cells of a tissue in a plant that helps to contribute to the rigidity this overall structural stability of that plant all right so vacuoles are unique to plants another organelle that is unique to plants and algae are the chloroplasts chloroplasts are the sites of photosynthesis so these are the organelles that capture energy from sunlight bring in co2 from the environment and use that sunlight energy and sunlight to turn the carbon dioxide into sugar we'll have a whole chapter devoted to that in chapter 10. if we look inside the chloroplast not all plant cells will have chloroplasts just the ones that are exposed to the sun so the stem and the uh not all the stem but sometimes the stem but always the leaves but the plant cells that have chloroplasts usually have multiple chloroplasts per cell the chloroplast is a double membrane structure similar to the mitochondria and then there are these additional stacks of membranes inside the chloroplast um called bilocoids these bilocoids um again are have a lot of surface area so this is where the photosynthetic um machinery is going to be localized that we'll see in chapter 10 so you can get a lot of photosynthesis activity from a single chloroplast the um fluid-filled environment in and around the phylocoids is referred to as stroma so that'd be similar to the mitochondrial matrix okay and then a place where you have a stack of phylocoids right on top of each other that's called a grana okay um chloroplasts like mitochondria have their own genome and again it's a small circular genome that looks similar to the genome in some bacteria so the hypothesis is that plants and algae evolve the ability to photosynthesize by actually bringing in a photosynthetic bacterium and that photosynthetic bacterium over evolutionary time became the chloroplast and a new organelle for that cell okay and then uh not an organelle but certainly an important structural feature of plant cells is their plant cell wall okay and we've talked about the cell wall of plants back in chapter uh five when we talked about um cellulose but um it's very important for plants that they have a plant cell wall because plants don't have their own internal skeleton they don't have a bony skeleton like like vertebrates do um and they so they rely on the stiff rigid cell wall to help provide that structural rigidity to the plant and it also allows two adjacent plant cells to stick together in more or less a permanent way and that's what you can see in the zoom up here so here is one plant cell here's the other plant cell here's where their cell walls are coming and where they they're they're effectively kind of growing together so there's really this uh point of direct physical connection all the way between their cell walls to keep those two cells effectively glued to one another all right all right now it is important to remember or at least to consider that even in the same organism not all cells will have the exact same amounts of every organelle okay so for example if we look at three different tissues from the same animal okay a pancreatic exocrine cell a cell that exports digestive enzymes into the digestive tract a testy cell so this animal is a male and cardiac muscle makes up the heartbeat these are all cells from the same animal but they don't have the exact same number and distribution of the various organelles those that it reflects the function the different functions of these cells so for example these pancreatic cells secrete a lot of proteins they secrete a lot of digestive enzymes so they have a lot of rough er because proteins that are bound for secretion are made by ribosomes on the rough er and then um inserted into the rough er and then they move on their way off the cell we'll talk about that later the um these particular cells in the testes are cells that make the testosterone the primary male hormone and this is a cholesterol derived hormone so these cells basically have to make a lot of cholesterol that they then turn into testosterone cholesterol is a lipid so these cells have a lot of smoothie are okay so they'll have some rough er because they have to do some of this but they have a lot of smoothie art because they make a lot of cholesterol cardiac muscle as i mentioned before all muscle is going to have a ton of mitochondria because muscle contraction is a very energetically demanding process requires a lot of atp okay so all three of these cells will have lysosomes and rough er and smoothie are mitochondria etc but they're going to have different amounts and different distributions of those various organelles depending on what their function is okay likewise if we look at a plant cell if we look at a cell that's in the leaf then it's going to have a lot of chloroplasts because it's exposing the environment it's going to carry out photosynthesis if we were to contrast that with it i don't have a picture of this but with a plant cell from the root of a plant that's underground that plant cell from that same plant won't have any chloroplasts because it's not exposed to the sun why uh why bother making chloroplasts okay so not all cells necessarily have the exact same kind of amount and distribution of organelles um that in turn really instead really reflects the specific function of the cell okay so that's it for uh this section of chapter seven we're gonna now uh move on to the next part of chapter seven where we're gonna look at how in eukaryotes how do proteins that function

inside of a particular organelle, how do they get to that organelle in the first place so they can do whatever it is they need to do. All right, so I'll see you in the next section.

Hello. We're going to move on to Chapter 5 now. Chapter 5 covers carbohydrates, which are our third major category of biological macromolecules. Carbohydrates include monosaccharides, kind of simple sugars, and polysaccharides, which are polymers of the monosaccharides. And that's really how we've broken this chapter down in terms of the lecture. So the first lecture video will cover monosaccharide structure function, and the second we'll talk about how monosaccharides assemble into polysaccharides and what are some of the functions of different polysaccharides in cells. Now, carbohydrates are characterized by having this chemical formula, CH2O to the N, where N typically is 3, 4, 5, or 6 carbons. So most of the biological monosaccharides that we'll be talking about are 3, 4, 5, or 6 carbon structures. And we'll look at some examples of that now. So monosaccharides can vary from one another in a number of different ways. So one way that monosaccharides can vary from each other is where is the carbonyl group in that monosaccharide located. So remember that a carbonyl group is a C double bond O. So here's a carbonyl group. Here's a carbonyl group. These are one of the functional groups that I asked to memorize back in chapter two. And all monosaccharides, at least in their linear form, and I'll talk about what that means here in just a minute, will have a carbonyl group. And that carbonyl group can either be at the end of the chain or it can be in the middle of the chain. If the carbonyl group is at the beginning of the chain, then we say that that monosaccharide is an albens. If the carbonyl group is in the middle of the chain, then we say that that monosaccharide is an aldose. If the carbonyl group is in the middle of the chain, then we say that that monosaccharide is a ketose. So ketose and aldose are two categories of monosaccharides that differ in the position of the carbonyl group. So if you look at both of these examples here, these two monosaccharides have both have the same chemical formula c3h603 but because they're ones an aldose and ones a ketose they're not structural identical so these would be structural isomers of each other same chemical formula different chemical structures another way that monosaccharides can differ from one another is in the number of carbons in the monosaccharide. And most of the time in this class, with maybe one exception in Chapter 10, we'll be looking at either three-carbon monosaccharides, the trioses, five-carbon monosaccharides, the pentoses, or six-carbon monosaccharides, the hexoses. And some examples of trioses and pentoses and hexoses are shown here. Some of these are aldoses in the top row, and then the bottom row are some ketoses. So monosaccharides can vary in how many carbons do they have, is it an aldose or a ketose. And then finally, or not finally, but in addition, they can vary in, even if those two things are the same, monosaccharides can vary in the orientation of some of the other hydroxyl groups on the other carbons in the chain besides the carbon that's in the carbonyl group. So here we're looking at two very important monosaccharides from a biological perspective, glucose andactose both glucose and galactose are six carbon sugars so their chemical formula is c6h12o6 so they have the same chemical formula they are both aldoses so they both have their carbonyl group on the beginning of the chain and everything is the same except here at carbon 4. So in glucose, this hydroxyl group coming off of carbon 4 is pointing below the plane of the molecule. And you can tell that in this kind of representation because this little line is really thin and this little line is heavier. The heavier line means this is pointing at you and the thin line means this is pointing away from you. So in glucose, the hydroxyl group on carbon 4 is pointing away from us or below the plane of the molecule. But for galactose, that hydroxyl group is pointing towards us or above the plane of the molecule. So again, these are structural isomers of each other. Exact same chemical formula, but different chemical structures. Now, imagine, though, that you can have that same kind of variation on all of these other carbons. Okay, so you can have variation in where is the carbonyl group, you can have variation in the number of carbons in the monosaccharide, and then

in the orientation of the various hydroxyl groups off of the non carbonyl carbons in the molecule as well now in solution in aqueous solution monosaccharides bigger than five carbons in length so for us the pentoses and the hexoses primarily can form rings okay that's what's shown here. So this is the linear form of glucose. And notice that all of these bonds linking these different carbons together, these are single covalent bonds. And remember that two atoms can rotate around a single covalent bond. So this molecule is kind of wiggling around. And if it wiggles around such that the carbonyl group on carbon 1 comes into contact with the hydroxyl group on carbon 5, which is shown here, then we can get a new bond forming, a new covalent bond forming, linking this oxygen from the hydroxyl on carbon 5 onto the carbonyl carbon on carbon 1. And then this, we do that, then this double bond O becomes an OH, and we end up with a ring structure. Now notice that there are two different ring structures shown here, something called alpha glucose and something called beta glucose. This is a really important distinction. So what this reflects, so let's look at the difference between alpha and beta glucose, and then we'll talk about how that difference came about. So in alpha glucose, the hydroxyl group on carbon one, after it's gone into its ring form, is pointing below the plane of the molecule. And we're going to use carbon six here in its orientation to indicate up, if you will, above the plane of the molecule. And in the hydroxyl group here in carbon 1 in the alpha glucose is pointing in the opposite direction. So we would say that's pointing below the plane of the molecule. And you kind of see that over here. So here's that hydroxyl group off of carbon 1 pointing in the opposite direction of carbon 6. In beta glucose, the hydroxyl group off of carbon 1 is pointing in the same direction as carbon 6, as both are above the plane of the molecule. Both alpha and beta glucose are derived from the same linear form of glucose, and there's a 50-50 chance of this linear glucose making either the alpha glucose or the beta glucose. Or I should say there's a 50% chance it'll make alpha glucose and a 50% chance it'll make beta glucose. The way that works is, so this carbonyl oxygen here, or this carbonyl group here, I should say, is rotating relative to this bond. So these two carbons, because that's a single covalent bond, this carbonyl group is spinning around this bond kind of like a propeller. And it will stop spinning as soon as it links up to this oxygen here and turns into a ring. If that happens at a time when the carbonyl oxygen was pointing down, then you end up with the alpha form of glucose. But if this carbonyl oxygen had been pointing up when this ring was formed, then you would end up with beta glucose. So this is a stochastic or random chance whether it'll make alpha or beta glucose. Alpha and beta glucose are not functionally identical in the cell, and we'll talk about that in the next lecture video more than in this one, but alpha glucose is used for certain things in the cell, beta glucose is used for different things, even though their structural difference appears to be relatively minor. So, put together these organic chemistry stick figures to try to illustrate this for you. Okay, so here is my glucose molecule. Get out of the way so you can see. So again, remember, black is carbon, red is oxygen, white is hydrogen. So here's carbon one, and here's carbon five. Here's that oxygen group linking carbon one to carbon five. Okay. And turn sideways now. So here's carbon six. So here this is a hydroxyl group on carbon six pointing above the plane. And in this particular example, here's carbon one and the hydroxyl group on carbon one is pointing below the, or in the opposite direction of the hydroxyl group on carbon 6. So this would be the alpha form of glucose. Here's another stick figure, same thing, here's the oxygen linking, oops, here's the oxygen linking carbon 1 to carbon 5, here's carbon 6 with this hydroxyl group pointed up. And notice here the hydroxyl group on carbon 1. Here's carbon 1. The hydroxyl group on carbon 1 is pointing above the plane in the same direction as carbon 6. So this

would be glucose in the beta form. I put these next to each other. Really hard to do this without getting in the way. Well, hang on. So if I put these next to each other, and I kind of point the carbons one at you, so here's carbon one in the alpha form with the glucose pointing below the plane of the molecule, and then over here is the carbon one of glucose in the beta form with the hydroxyl group pointing above the plane of the molecule. Okay, now please look over this last part carefully. Be sure you understand the difference between the alpha and the beta forms of monosaccharides. So again, this terminology applies to monosaccharides in their ring form and describes the orientation of the hydroxyl group on carbon 1. Is that carbon 1 hydroxyl below the plane of the molecule, in which case it's the alpha form, or is it above the plane of the molecule, in which case it's the beta form? Be sure you understand that terminology, those structural differences, because that's going to come into play in a very important way in the second lecture video for this chapter. Well, we're going to finish up chapter five now and take what we've learned about monosaccharides and use that to discuss how we hook monosaccharides together to polysaccharides and then talk about some of the different functions that carbohydrates have in cells. So polysaccharides are polymers of monosaccharides. So this is our third example of a biological polymer. We talked about proteins, which are polymers of amino acids. We talked about nucleic acids, which are polymers of nucleotides. Now we're going to talk about polysaccharides, which are polymers of monosaccharides. And here we're looking at the beginning to form a polysaccharide. In this case, we're going to look at a very simple polysaccharide, really a disaccharide, di means two, maltose, which is composed of two molecules of alpha glucose. And in blue here, highlighted, are the parts of these two glucose monomers that are going to interact to make the new covalent bond that's going to link these monomers together. So notice that one of the products of this reaction is a water molecule. So this is another example of a condensation reaction. And notice that we're going to begin with, in this example, our glucose is in the alpha form. So the hydroxyl groups on carbon one are pointing down. Okay. So remember alpha beta refers specifically to the orientation of the hydroxyl group on carbon one. So in both these cases, the hydroxyl carbon one is pointing below the plane. So these are alpha glucose molecules. All right, so to link these together, the hydroxyl group on carbon 1 of the first alpha glucose is going to interact with the hydroxyl group on carbon 4 of the second alpha glucose and make what we call a glycosidic linkage. So the glycosidic linkage is linking this carbon one and this carbon four through an oxygen molecule derived from one of the hydroxyls over there, and then it generates water as a byproduct. So these glycosidic linkages would be analogous to a peptide bond in a protein or a phosphodiester bond in a nucleic acid in the sense that it is a covalent linkage formed as a result of condensation reaction, in this case to make polysaccharides. Now, not all glycosidic linkages are the same, and by that I mean that if the orientation of the hydroxyl group on carbon 1 is in the alpha form, like we just saw, then you make the glycosidic bond a little bit differently than if the hydroxyl group on carbon 1 is in the beta form. And so let's look at that over here. So here we're going to look at the formation of a glycosidic linkage between beta galactose and beta glucose. And this results in the formation of a disaccharide called lactose, which is the primary sugar found in milk. Okay. So here we know this is beta galactose because the hydroxyl group on carbon one is pointing above the plane, same direction as carbon six. Likewise, we know this is beta glucose because the hydroxyl group on carbon 1 is pointing above the plane. Now, you'll notice that the hydroxyl group on carbon 4 for the beta glucose is still pointing below the plane. Alpha versus beta just refers to the orientation of hydroxyl.

hydroxyl on carbon one. So the hydroxyl group on carbon four is still below the plane. The hydroxyl on carbon one for the beta galactose is above the plane. The only way for these two hydroxyl groups to interact is if this beta glucose flips upside down. So look at carbon six here versus here, okay? This whole molecule had to flip upside down to bring this hydroxyl group into the same plane as that hydroxyl group and allow for the formation of that glycosidic linkage. To represent that making this glycosidic linkage meant the monomer, the second monomer had to flip upside down, we call this a beta 1,4-glycosidic linkage. And it turns out that alpha 1,4-linked polysaccharides and beta 1,4-linked polysaccharides are used for different purposes in the cell, and we'll talk more about that and why that is here in a little bit. So let me just try to bring out my tinker toy models here and try to illustrate that for you. So here is glucose in the beta form. So here's the carbon one with a hydroxyl group pointing above the plane. So here's carbon six. So this hydroxyl group is pointing in the same orientation as carbon six. That's above the plane. Here is my other monosaccharide that I'm going to add. So here's carbon four with a hydroxyl group pointing down. So for this hydroxyl group and this hydroxyl group to interact, the second monosaccharide has to flip upside down. Now these two hydroxyl groups can come together and interact, and we can make our beta glycosidic linkage. So in beta 1,4-linked polysaccharides, every other monomer is flipped upside down in order to facilitate the formation of that beta glycosidic linkage. Okay, so what do carbohydrates do? Probably the first role that pops to mind, if I ask that question, is carbohydrates' role in energy storage. And that is certainly, if not the primary role of carbohydrates, right up there. So carbohydrates are very good storage forms for chemical energy in the sense that they have all these carbon-hydrogen and carbon-carbon bonds, which are nonpolar covalent bonds, and therefore contain a lot of potential energy, have a low bond dissociation energy, so cells can break these carbon-carbon bonds, break these carbon-hydrogen bonds, get a lot of energy out, and use that energy to do other things. Interestingly, fats are an even richer source of stored potential energy because fats have a very similar structure to carbohydrates, except instead of having a hydroxyl group off of each carbon, they have a second hydrogen. So there are even more nonpolar covalent bonds, high potential energy bonds, in fats than there are carbohydrates, which is why fats are so good at storing or are so energy rich. This role of carbohydrates as energy storage molecules is so important that later on in Unit 2, we'll actually devote two entire chapters to these processes. We'll talk in Chapter 10 about how plants and algae and photosynthetic bacteria take energy and sunlight and use that to turn CO2 into carbohydrate. And then in Chapter 9, we'll talk about how all cells use carbohydrates as energy sources, break them down, and use that energy to make ATP. And we'll go into a lot more detail on this when we get to those chapters, but let me just kind of give you a preview of what we're going to learn there. So here we're looking at a representation of photosynthesis. So in photosynthesis, plants, algae, photosynthetic bacteria, they'll take in carbon dioxide where the carbon is in an oxidized form. So think back to chapter two. This carbon dioxide, the carbon is making four polar covalent bonds with oxygen. So this is not a very reactive molecule. These are very low potential energy bonds. It means this carbon is not very reactive. Photosynthetic organisms capture CO2, use energy from sunlight to reduce these carbons and hook them together to make sugars, to make carbohydrates. And so you have a much more energy-rich molecule with these nonpolar carbon-hydrogen and carbon-carbon bonds in the carbohydrate compared to the CO2. During cellular respiration, which all living organisms carry out, cells will take those nonpolar covalent bonds in carbohydrates, and they will break those bonds and oxidize the carbon back to co2 okay so it's kind of the reverse of photosynthesis the difference is photosynthesis is an endergonic process has a high positive Delta G you need a lot of energy

that energy comes from sunlight cellular respiration is a strongly exergonic process you have a large negative delta g this process releases a lot of energy and that energy is used by the cell then to do other things but we'll fill in some of the details on this when we get to unit two now sometimes cells need to store monosaccharides temporarily that it's going to eventually use as an energy source. And for that, it'll make what we call storage polysaccharides. So storage polysaccharides would be glycogen in animal tissues and the starches in plants. Glycogen is found primarily in the liver and in muscle cells. and other tissues in the plant. These storage polysaccharides, what they have in common is that they are composed of alpha glucose linked by alpha 1,4-glycosidic bonds. These alpha glycosidic bonds are relatively easy for cells to break down, so they can assemble a bunch of alpha glucose together in an alpha-1-glorphine-4 glycosidic bond when it has an excess of glucose. And then when it runs short of glucose and it needs to free these up to use as energy source, it breaks these alpha glycosidic bonds quickly and uses those for energy. I do want you to notice that there are, in a few of these storage polysaccharides, like glycogen and like amylopectin, which is a type of starch, there are branch points. So you'll have like a long chain of alpha-1,4-linked glucose and another chain of alpha-1,4-linked glucose, and then those two chains are linked together at one point. That linkage is actually an alpha-1,6 glycosidic linkage. So carbon 1 at the end of one chain linked to carbon 6 at the end of a different chain. So within a chain, for the storage polysaccharides, it's alpha-1,4. Two chains linked together at a branch point, that alpha 1 6. Other polysaccharides play more of a structural role in the organism. So they're not just temporary storage forms of monosaccharides that the cell's going to break down for energy, but they're actually making a structural contribution to cells and tissues. And these structural polysaccharides, these would be like cellulose implants, titans and insects and crustaceans, peptidoglycans, which they put up the cell wall in bacteria. These are all structural polysaccharides, and what they have in common is they are composed of beta 1,4-linked polysaccharides, and these beta 1,4-linked poly most familiar with. It's the primary component of plant cell walls and it's what gives plant tissues their strong rigid structure. That's why trees can grow so tall and wood is such a good construction material. Cellulose is composed of long fibers laid down in layers and each layer is at a different angle to the layer below and above it, so that you get these layers on top of each other running in different angles, so you get a very strong, mechanically sound tissue. If we look within a single cellulose fiber, this is what we'll see over here. Cellulose is composed of beta glucose, so glucose in the beta orientation, two beta glucoses linked by beta 1,4-glyphosate bonds. That makes up a single strand. And then multiple strands associated by hydrogen bonding, shown here. These yellow dashes indicate hydrogen bonds. So you have long beta 1,4-linked strands, multiple strands associated by hydrogen bonding to give you these strong cellulose fibers. And, you know, hydrogen bonds, an individual hydrogen bond isn't all that strong, but a lot of hydrogen bonds over a large area gives a lot of strength of adhesion. So these cellulose fibers are very strong, very, very stable. Chitin is another type of structural polysaccharide. It makes up the cuticle layer of the exoskeleton in insects. It makes up the exoskeleton, the crunchy outer shell of many crustaceans. And then in some fungi, chitin actually is a component of their cell wall. Chitin has a similar structure to cellulose, but what's different is in the nature of the monosaccharidecharide so in chitin the monosaccharide is called n-acetylglucosamine which is a beta form six carbon sugar and the two n-acetylglucosamines are linked by beta one four glycosidic bonds you continue that

down the chain and then different chains associate with one another by hydrogen bonding just like we saw with cellulose so again you have a long chain of beta 1 4 linked monosaccharides adjacent chains associated with one another by hydrogen hydrogen bonding excuse me peptidoglycan is a little bit different so peptidoglycan is the primary component of bacterial cell walls. And we haven't really talked about bacterial cell walls yet. We don't get to that until Chapter 7. So I just wanted to give you a few pictures here. But here is an electron micrograph looking at the border, kind of the edge of a bacterial cell. So here's the cytoplasm of that bacterial cell. Here's the outside of that bacterial cell. This really dark layer here is the cell membrane. And then this gray hazy layer here, this is the cell wall. And this cell wall is primarily, not exclusively, but primarily composed of peptidoglycan. And here you see these individual peptidoglycan strands here. Peptidoglycan has an interesting structure. So it contains two different monosaccharides. Here. Off of one of its carbons here, it has a short chain of four amino acids, each amino acid connected to the next by a peptide bond. So N-acetylmeramic acid has a little short peptide attached to one of its carbons, and that's represented by green here. Why is that interesting? Well, the reason that's interesting is that you begin, peptidoglycan looks like cellulose and chitin initially in the sense of you have your monomers linked by beta-1,4 glycosidic bonds. But now adjacent strands, if they're positioned such that the peptide chain for one acetylmuramic acid overlaps the peptide chain on an acetylmuramic acid from the chain above it, an enzyme can come in called transpeptidase and make a covalent linkage between these two clusters of amino acids. That's what that little dash is in between the two green bars there. And that covalent linkage is much stronger than the hydrogen bond would be. So the association between strands in peptidoglycan is even stronger than the association between strands in cellulose and in chitin. Some of the antibiotics that we use, for example, penicillin and the derivatives of penicillin, work by inhibiting this process. So that enzyme transpeptidase that links these amino acid groups together on the two different strands, that enzyme transpeptidase is inhibited by penicillin and some of the penicillin-derived drugs. So you prevent these covalent bonds linking the strands together. That greatly weakens the cell wall and makes the bacteria susceptible to being more readily cleared by the body. Okay, so what else do carbohydrates do? So we talked about their role in energy storage. We talked about their role in structural molecules in the case of beta-1,4-linked polysaccharides. Polysaccharides also play important roles in cell-cell recognition. And the reason for that is if you look at the surface of a cell, so here's the cell membrane, here's a protein embedded in the cell membrane, and all of these little orange hexagons here represent short-chain polysaccharides, oligosaccharides, oligo just means short or few, short-chain polysaccharides, oligosaccharides, on the surface of membrane proteins, or in some cases, even attached to the surface of the membrane itself. And there are so many of these on the surface of the cell that, in essence, the cell actually has a little bit of a sugar coating to it, a little bit of a carbohydrate coating to it. It's not very strong, but it's there. We call that the glycocalyx. And the glycocalyx is so extensive, and I really like this picture. So this is an electron micrograph of cells in two different layers of tissue coming together and interacting. So here's a cell, here's a cell, this gray fuzzy area here is the glycocalyx. And you'll see that when these cells are coming together it's their glycocalyces that actually interact first. And so this, each cell will have a different sort of set of oligosaccharides on its surface so it'll have a little bit different kind of carbohydrate address if you will that it's displaying to its neighbors. And the example of this that you've all heard of, but maybe not put this way before, is in the ABO blood typing system in red blood cells. So A blood, B blood, O blood, the difference has to do, in those three types of blood, has to do with a

what particular type of oligosaccharide is attached to a very specific protein on the surface of red blood cells. And if you have A blood, your immune system is used to seeing that form of the oligosaccharide. If you get a transfusion from someone with B blood, your immune system doesn't recognize those B form oligosaccharides, and so it thinks it's foreign and mounts a response against it. And we'll come back and talk a little bit more about the role of carbohydrates in cell-cell recognition in a later chapter. And then finally, the last kind of major role for carbohydrates is in, they serve as the building blocks, either directly or indirectly, for a lot of other biological macromolecules. What's being shown here, and there's a lot of detail in this slide. Don't worry about this detail. I just wanted the image to kind of give you a general sense of what's going on. But this slide is showing the breakdown of glucose, so the process of breaking glucose down and extracting the stored chemical energy in that glucose molecule. Well, a lot of the byproducts in this glucose breakdown can be pulled out of this pathway and used as a starting point to make other types of biological macromolecules. So fats and nucleotides and amino acids, a lot of those begin by taking breakdown products of carbohydrates like glucose, pulling them out of that breakdown pathway, and then using those as precursors to start making other things. We'll talk a little bit more about this when we get to the cellular respiration chapter, but really this role for carbohydrates, I'll save that for when you take your upper level biochemistry classes. And believe me, you'll spend an entire semester pretty much fleshing out the details on this one slide here. Okay, so that's the end of chapter five. It kind of wraps up our quick overview of carbohydrates. We'll hit carbohydrates again throughout the semester in some other roles, but I just wanted to kind of give you a preview of carbohydrate structure function so that when we get to those other examples, they make a little bit more sense. We'll now move on to chapter six and talk about our fourth category of biological molecules, lipids, and how lipids assemble to make biological membranes.

Hello. We're going to move on to Chapter 4 now. And in Chapter 4, we're going to be discussing our second major class of biological macromolecules, and those would be the nucleic acids. So nucleic acids are DNA and RNA. And they also, that term nucleic acid also includes the precursors to DNA and RNA, which are called nucleotides. Nucleotides have a kind of a three-part structure as shown here. So the central part of the nucleotide is a five-carbon sugar. And this, we haven't really talked talked about sugars yet so there's some aspects of the structure of this that are maybe not as clear at the moment that's okay don't worry about it but in the nucleotides that we see today there those sugars can come in two forms so the nucleotides that are used to make RNA are shown down here I'm'm sorry, the nucleotides that form RNA, the structure of their sugar is shown down here, and this type of sugar is called a ribose. The nucleotides that make DNA, they use a different type of sugar called deoxyribose, and the difference is here at carbon 2. So in deoxyribose, the hydroxyl group that's present on carbon 2 in ribose is instead replaced with a hydrogen, hence the term deoxyribose. And we'll talk a little bit later in the chapter about why that matters and why it helps to impart some functional differences between RNA and DNA. All right. Now, attached to this 5-carbon sugar, either ribose or deoxyribose, on carbon 1 is a nitrogenous base, and there are five different types of nitrogenous bases that we find in the nucleotides. The three of these are found in both RNA and DNA, cytosine, guanine, and adenine. And then two of these, uracil and thymine, are found only in RNA in the case of uracil or only in DNA in the case of thymine. Notice that there are kind of two categories of nitrogen spaces. So cytosine, uracil, and thymine are composed of a single hydrocarbon ring we call those bases or we call that group of bases the primitines and then guanine and adenine have a double hydrocarbon ring and these are the purines okay and then the last component of nucleotide is on carbon 5 of that 5-carbon sugar there will be one or more phosphate groups added so here's what a phosphate group looks like PO4 okay obviously this is a charged group and there can be depending on the form of the nucleotide there can be a single phosphate group two phosphate groups or three phosphate groups and we'll look at examples of those here in a little bit. So kind of like we did back in Chapter 3, when we were talking about proteins, we wanted to kind of think about what are some of the ways in which the precursors of proteins, amino acids, could have arisen through chemical evolution. And in that case, remember, we learned that it turns out it's relatively easy to make amino acids in experiments that simulate conditions on the prebiotic Earth. And we can even detect amino acids on the surface of high-carbon meteorites and on coming from those hydrocarbon plumes that come out of those deep-sea hydrothermal vents. So it's not very difficult from a chemical evolution standpoint to imagine that there would have been amino acids available as building blocks as life was beginning to begin. That's not really quite true, at least in the current state of thinking, for the nucleotides. And there's a couple of different reasons for this. First is what some people call the ribose problem, and that is all nucleotides today use ribose as their sugar, either, or a derivative of ribose, like deoxyribose as their sugar and that's a five carbon sugar in experiments that mimic conditions or what we think were conditions on the prebiotic earth however it turns out most of the sugars that we form in those experiments are either six carbon sugars like hexoses or four carbon sugars called threoses it's turns out it's fairly difficult to get five-carbon sugars like ribose to form in any kind of abundance in those kinds of experiments. However, some recent studies focusing more on the surface metabolism model of chemical evolution, if you remember back

in Chapter 2, rather than the prebiotic soup model of chemical evolution. Some of those more recent experiments trying to mimic the surface metabolism model have had better luck generating some 5-carbon sugars, and so it's possible that we're kind of working through this ribose problem. Down here, the primidine problem, this one's a little bit trickier. What this reflects is under most experimental conditions that try to, again, mimic conditions that we think were prevalent on the prebiotic earth, it's much easier to find purines arising in those experiments than it is pyrimidines. And we can tweak the experimental conditions a little bit and get pyrimidines forming, but then we don't get pyrimidines forming, at least not in the same type of abundance. So we still don't have a great chemical understanding yet of how all of the components of nucleotides likely formed during that prebiotic period when chemical evolution was underway. All right, now nucleic acids are polymers of nucleotides, just like proteins are polymers of amino acids. And just as we talked about in Chapter 3, any anytime you make a biological polymer, that involves a condensation reaction. And in this case, the condensation reaction occurs when a hydroxyl group on the 5 prime phosphate of the next nucleotide that's about to be added to the chain interacts with the hydroxyl group on the 3 prime carbon of the last nucleotide in the chain. So that pulls off a water molecule and it makes a new covalent bond between this oxygen and this phosphate group. And that new covalent bond is called a phosphodiester bond or a phosphodiester linkage. So phosphodiester bonds would be analogous to peptide bonds and proteins. They are the covalent bonds that form as a result of a condensation reaction linking the monomers together in a polymer, in this case linking nucleotides together to make a nucleic acid. Pay a lot of attention to structurally what's going on here. This turns out it's really important. The fact that it's the phosphate on the 5' carbon that interacts with the hydroxyl group on the 3' carbon of the last nucleotide, that's where that phosphodiester linkage occurs. Now, making that phosphodiester linkage is a non-spontaneous reaction. It has a very high delta G, and so there has to be some energy invested into the system from somewhere in order to make those phosphodiester bonds. And where that energy comes from is actually the nucleotide that's about to be added. And that's because the nucleotide that's about to be added is in what is sometimes referred to as its activated form, which simply means that instead of a single phosphate group, it has three phosphate groups attached in a string. And these bonds, we'll talk more about these in later chapters, but these bonds that link these phosphate groups together have a very high potential energy. When you break those bonds, you get a lot of energy out. So immediately prior, oops, sorry, I carried away there. So immediately prior to this reaction occurring that we're seeing here, this nucleotide that was about to be added was actually in the triphosphate form, okay? And there's a particular enzyme in the cell that will break this bond here, releasing a lot of energy, and that energy then is used to help make this new phosphodiester bond. And we will look at that particular process in much more detail when we get into the cell cycle and cell replication chapter in a little bit later in the semester. Now to study nucleic acids, one of the first things we have to be able to do is we have to be able to purify them. And what I mean by that is if you break open a cell and you extract all of the nucleic acids, all the DNA and the RNA, et cetera, that are in that cell, you get a mix of nucleic acids of different lengths and different sizes, et cetera. And so one of the first steps in working with that is to kind of figure out a way to sort through that population and just identify the specific nucleic acids that you're interested in and one tool that makes that possible is called gel electrophoresis and you'll be doing this in the bio 206 labs later in the semester so in gel electrophoresis you're going to take advantage of the fact that DNA has a

strong negative charge. And the reason that DNA has a strong negative charge is because of these phosphate groups on the nucleotides in DNA. These phosphate groups are negatively charged. So if you have a bunch of nucleotides hooked together, you've got a molecule that has a strong negative charge. And if you put a molecule that's negatively charged into an electrical field, that molecule will migrate towards the positive end of that electrical field. And that's what we do in gel electrophoresis. So you make a gel, could be made of agarose, could be made of agar, could be made of acrylamide. There's different materials you can use. You cut little holes in the gel, load your sample of mixed nucleic acids in those holes, put the gel in the electric field, let it run for a while, and then those nucleic acids, those mixtures of nucleic acids will separate out into individual bands, each band representing a nucleic acid of a specific size. The smaller the nucleic acid, the faster it can move through the gel. It can wiggle its way through the nooks and crannies of that gel faster. The longer the nucleic acid, the slower it moves because it has a harder time maneuvering through the pores in the gel. And so very quickly, you can go from a mixed nucleic acid population to populations where you still may have different nucleic acids in this band, but at least they're all the same size. So you can cut this band out, isolate those nucleic acids, and if that's the size you're looking for, now you've got a mixture that's enriched for that particular nucleic acid. Okay, so that's kind of a quick introduction to nucleotides and how nucleotides assemble to make nucleic acids. Now we're going to move on and talk about the structure of DNA and RNA as the second and the last section for Chapter 4. Okay, so we are going to move into the second part of Chapter 4, where we're going to talk about the two major categories of nucleic acids, DNA and RNA. We'll talk a little bit about the structure of both of those, how they're different from one another, even though they're both derived from nucleotides. And then we'll talk about how the structural differences give DNA and RNA kind of different sets of functions in the cell as well. And we'll start by talking about DNA. And over here on the left, these are kind of the key players in the discovery of DNA structure. And this discovery of DNA structure was such a critical event in the development of modern biology that these are experiments that you really do need to know, and not just kind of the outcome of the experiment, but who did them and roughly the timeframe. So we're gonna begin kind of in roughly in chronological order. But as a reminder, DNA is a polymer of nucleotides. And in this case, the nucleotides that we find in DNA have deoxyribose as their sugar okay and for the pyrimidines they have cytosine and thymine not uracil uracil is only found in rna and then for the purines of course they have guanine and adenine so there's four types of nucleotides cytosine thymine guanine and adenine that we find in dna and those nucleotides all have deoxyribose as their sugar. Okay. Now, DNA's primary structure is a single linear strand, just like the primary structure of a protein is the linear sequence of amino acids in the protein, primary structure of nucleic acid is the linear linear sequence of nucleotides in that nucleic acid and so that's been shown here. So here we have a single strand of DNA Each nucleotide is connected to the next nucleotide by phosphodiester bonds. Remember those phosphodiester bonds link the 5' phosphate of the 3' hydroxyl group of one nucleotide to the 5' phosphate of the next nucleotide. If we look at this strand, this strand has a polarity. One end is different than the other. Just like proteins have a polarity, one end has an amino group, one end has a carboxyl group. Similarly, same kind of thing happening with the primary structure of DNA as well. So this end of the DNA molecule has a phosphate group on its 5' carbon of that nucleotide that isn't attached to anything else. So we refer to that as the 5 prime end of the DNA strand. The end of the DNA molecule still has a hydroxyl group on the 3 prime carbon of that nucleotide that isn't attached to anything else, and we refer to that as the 3 prime end of the

DNA strand. So DNA has a polarity, a five prime end and a three prime end, and that'll become very important when we get into the structure of DNA here a little bit more deeply. Okay, so starting chronologically, we'll talk a little bit about Erwin Chargaff. He was working in kind of the late 1940s, mid to late 1940s primarily. And he was what today we would call a biochemist and interested in how the composition of nucleotides varied from species to species. So the isolated DNA from a wide range of species representing a wide range taxonomically of different groups of living organisms, bacteria, fungi, plants, vertebrates, non-vertebrates, etc. And for all of these, he quantified how much adenine was in their DNA, how much guanine, how much thymine, how much cytosine. And then he just played with those numbers to see if he'd find any patterns. And here's what he discovered. So first of all, he discovered that in every species, the ratio of purines to pyrimidines was one, or very close to one. And more specifically, in every species, the ratio of adenine to thymine was one, and the ratio of guanine to cytosine was one. So two different species might have different amounts of adenine, but in both species, their ratio of adenine to thymine was one. And so this suggested that there was some kind of relationship between certain subsets of the bases found in DNA. There must be some relationship between adenine and thymine and some relationship between guanine and cytosine to explain why they were always found in equal amounts in the DNA for many given species. Following up on the heels of that, Rosalind Franklin, working with Maurice Wilkins, was more interested in the overall structure of a DNA molecule, and she used a technique called X-ray crystallography, which is explained in Bioskills 11 in your textbook. Basically, in extra crystallography, you crystallize the molecule you're interested in, and that essentially involves dissolving that molecule at high concentrations in a solvent like water, and then evaporating the water away and crystallizing the molecule. Then you put that in the path of an x-ray beam here. The x-rays go through the crystallized molecule. The pattern of crystals diffracts those x-rays. You can then detect that refraction pattern on a screen. And then using mathematical tools, you can work backwards from this diffraction pattern to what the original structure of the crystal must have looked like. And from that, Franklin discovered that DNA is a helical molecule, meaning it's shaped like a helix, like a spiral staircase, and she was able to work out the width of the DNA molecule and the approximate length of one turn in that helix. And then finally along came James Watson and Francis Crick and they were really more organic chemists than anything else and they took the work that Chargaff had done and they took the work that rosalind franklin had done and they began to try to build models that um of dna structure that captured both of the work of shargaff and the work of rosalind franklin and kind of one of the key things they realized as they were doing this was that if the um if you had two strands of DNA that had purines opposite one another, the purines are so big that you, and they knew the width of the DNA molecule from Rosalind Franklin, the purines are so big they won't fit within that width. If you have two pyrimidines opposite each other, they fit just fine within that width, but this distance is so big that there's no type of interaction that could stabilize this association. This is too far for any kind of intermolecular interaction. Or intermolecular interaction, excuse me. But if you had a purine opposite a primidine, that fits nicely within the width constraint that Rosen-Franklin had predicted, and this distance, it turns out, is perfect for hydrogen bonding. And that's, in fact, exactly what happened. So they realized that if you put a guanine and a cytosine opposite one another, that those bases will make three hydrogen bonds with one another. If you put an adenine and a thymine opposite one another, they can make two hydrogen bonds to stabilize that association. But this only works if the two DNA strands are running in opposite directions.

Okay, so in this case, 5' is up, 3' is down. Over here, 5' is down, 3' is up. And the proper way of saying this is we say if the two strands are anti-parallel in direction, then a cytosine and a guanine will be positioned to interact with each other very nicely, and an adenine and a thymine in those two strands will be positioned to interact together very nicely. So taking this information, they then were able to develop a more detailed model, kind of the high points of which are shown here. So here is our anti-parallel double-stranded DNA molecule where we have our base pairing. That's what this relationship between guanine and cytosine and thymine and adenine is called called that base pairing or complementary base pairing so you see the base pairing between the strands to stabilize those two strands association with one another here we're just kind of looking at a linear representation of that so you can see that this is that the two strands are anti-parallel so five prime is is here, three prime is down. On the opposite strand, five prime is up, or down, excuse me, three prime is up. Notice that within a single strand, the sugar phosphates all line up kind of one on top of one another. We call this the sugar phosphate backbone of that strand. And that, of course, is where the phosphodiester bonds are, linking one nucleotide to the next. The hydrogen bonding is occurring between the bases on the opposite strands. So you've got kind of one single-stranded polymer here, one single-stranded polymer here. If they're anti-parallel and their sequences match up, then you can get this kind of base pairing to stabilize the association of those two DNA strands. Just a little bit different representation of that, but you'll notice then when you take this anti-parallel molecule and you twist it to make a helix, it looks like this, and you kind of have two faces on the helix. One face is kind of narrow. That's referred to as the minor groove. One face is wider. That's referred to as the major groove. And that major-minor groove distinction will become important later in the semester when we talk about proteins that bind to DNA and help DNA carry out its functions. Proteins that bind to DNA in a non-specific way, meaning they'll bind to any DNA molecule, tend to bind to the minor group because they're accessing the sugar phosphate backbone, which you see in red here. Proteins that bind to DNA in a sequence-specific way, meaning they only bind to specific sequences of bases, those proteins fit into the major group because that's where they have the most access to a particular subset of bases. And just to kind of give you a better, oops, sorry I'm going the wrong direction here. Got carried away. So to give you a better view of that, we have a model here and I'll try to get out of the way. So here we have a DNA molecule. I'm just kind of spinning it around. So here is our minor groove. So you can see in the minor groove, we've got the sugar phosphate backbone in gray, red, and yellow is kind of most accessible in the minor groove. And if I twist it so you can see the major groove better, the major groove is wider, and so you've got proteins have more access to the bases, the nucleotide bases, in that particular section of the helix. And Crick realized immediately when they were developing this model for DNA structure is that the complementarity of the two opposing strands in a DNA molecule allows for DNA to serve as a template for its own copying. In other words, if you break that double-stranded molecule apart, then each original single strand can serve as a template to assemble a new complementary strand, and you then end up with two copies identical to what you began with. And in fact, when we get to chapter 15, you'll see this is exactly how DNA replication occurs. Okay, so let's shift gears and talk about RNA now. In RNA, we use different kinds of nucleotides. So the 5-carbon sugar is ribose instead of deoxyribose. That has an extra hydroxyl group here. And that helps to make RNA a little bit more reactive than DNA. This extra hydroxyl group here is kind of introducing some extra polar covalent bonds in the sugar, which allows it to interact by hydrogen bonding with a wider variety of things.

than deoxyribose can. So it helps make RNA a little bit more of a reactive molecule and adopt a wider range of shapes. And we'll see why that is here in a minute. In terms of the nucleotide bases for the pyrimidines in RNA, we use cytosine and uracil. We don't use thymine. So we use uracil instead of thymine. And then we still use, of course, the same purines. So there are four bases, four nucleotides in RNA, all use the same ribose sugar. And then you have cytosine, uracil, guanine, and thymine as your options for the bases. Note that if you compare the structure of thymine to uracil, the bases involved in hydrogen bonding with adenine are the same. So uracil can hydrogen bond with adenine just as well as thymine can, and that'll become important here in just a minute. So like DNA, the primary structure of RNA is a long single strand, and again, the nucleotides in this strand are connected by phosphodiester bonds. Just like we saw in DNA, you've got your sugar phosphate backbone here. The only difference is the sugar is ribose instead of deoxyribose. And again, this primary structure has a polarity. So there's a 5' end in this RNA strand, and there's a 3' end in this RNA strand. The key difference between RNA and DNA is most RNAs are not double-stranded. So because this molecule, once it's synthesized, stays single-stranded, it's flexible. It can move around. And that means that if you have regions in that single RNA molecule that are self-complementary, where you have the ability for complementary base pairing, then this RNA molecule can fold up and make what we call a stem loop or a hairpin structure. So you have this, kind of sort of the five-parameter molecule here, you kind of roll in. Here, in the stem region, this is where you have some intramolecular complementarity, guanines binding to cytos anadines bonding the thymines and then here in the loop there's no complementarity so this the molecule remains single stranded there and this flexibility in RNA this ability to kind of fold up in this way allows for RNA to adopt some higher level secondary and tertiary structures that we just don't see in DNA. And in fact, there is a tremendous range structurally in RNA. As a family, RNA is the second most diverse molecule from a structural standpoint compared to proteins of the four major biological macromolecules. Just like with proteins, if you've got RNAs as a family have a wide variety of structures that they can adopt, which means RNAs can carry out a wide variety of functions. So because as a class of molecules, RNAs have a wide variety of structures, that also means that as a class, RNAs carry out a wide variety of functions in the cell. And there's lots of different types of RNAs. Some of these you heard about in high school, messenger RNAs, ribosomal RNAs. Some of them you probably didn't hear about in high school, long non-coding RNAs, pico RNAs, et cetera. Some of these RNAs are information carriers and serve as intermediaries going from genetic information to form a DNA to final protein structure. We'll talk more about that later. Some of these RNAs are structural, meaning they fold up into a shape and that molecule then carries out some structural role in the cell. And some RNAs are catalytic. We haven't really talked about a catalyst, but a catalyst is something that speeds up the rate of a reaction by lowering what's called the activation energy of the reaction. And don't worry about that yet. I'll have a whole chapter devoted to that later. There are some biological macromolecules that can serve as catalysts. So a class of proteins called enzymes serve as catalysts for certain biochemical reactions, and some RNAs can also fold up into a shape that allows them to serve as catalysts for specific biochemical reactions. And in that case, we refer to those types of enzymes as ribozymes. So a ribozyme is an RNA that can catalyze a specific kind of biochemical reaction and make that reaction happen faster. And Sidney Altman and Tom Cech won the Nobel Prize in the late 1980s for the first discovery and characterization

the first ribozyme. Now, like DNA, RNA can serve as a template for its own synthesis, but there's an extra step, okay, because RNA is a single-stranded molecule. So in order for RNA to serve as a template for its own synthesis, you have to first make a complementary copy of the original RNA, and then you separate those two strands, and you take the complementary copy, and you make a complementary copy of that, and that will now be identical to what you started with in the original RNA. So you kind of follow that logic through as you go through here. So because RNA, again, can serve as a template for its own synthesis, and because at least some RNAs are catalytic, this led scientists to wonder, well, is it possible that there are self-replicating RNAs? And if so, that would make RNA the first example of what we call a living molecule. And that's kind of a weird term. I'm not sure I really like it. But a living molecule is a molecule that has the capability of copying itself. And kind of the short version of a very long story is we've not identified any self-replicating RNAs in nature, but we can generate self-replicating RNAs artificially in the lab using some kind of directed evolution types of experiments in a laboratory setting. And the classic paper from 2001 from Johnston and Bartle is shown here which was one of the first demonstrations of this. So not only is at least in theory possible that we could find that there could have been self replicating RNAs but today we actually need RNAs catalytic activity in order to make proteins. What we're looking at here is an interior view of a ribosome. A ribosome is the macromolecular structure in a cell that's responsible for making proteins. We'll talk a lot more about ribosome structure function later. Ribosomes are composed of small proteins and small ribosomal RNAs. In this view over here, the protein component of the ribosome is shown in orange. The RNA component is shown in silver, I guess that is. And the starburst in the middle here indicates the site in the ribosome that's responsible for catalyzing the formation of a peptide bond between two amino acids in a newly forming protein. And you'll notice that this catalytic region in the ribosome is where the ribosomal RNAs are located, not where the ribosomal proteins are located. So RNA is a requirement for making protein even today. So if you take all these facts that are all these different ideas that RNA as a family of molecules has a wide variety of shapes and structures and can carry out a wide variety of functions, that RNA can in theory serve as a template for its own replication, then some RNAs are catalytic and they can catalyze reactions that are important even today. These kind of collectively led to, many years ago, led to what's been referred to as the RNA world hypothesis, which is basically an idea that in the transition from chemical evolution to the first true living organisms, that maybe there was an intermediate period kind of dominated by RNA, that you had some RNAs arising through chemical evolution that were then able to catalyze other types of reactions, including formation of other macromolecules or replication themselves, so that you could then begin to accumulate more and more of these until finally you had really the precursors for that transition into life as we know it today. And this RNA world hypothesis has undergone a lot of changes over the years in how we view it and how we think about it. I've added to your module an extra reading I'd like you to take a look at, which kind of summarizes the modern thinking and some of the controversies still within this RNA world hypothesis. Okay, so that's it for Chapter 4. We're going to move on now and go to Chapter 5, which will be our third class of biological macromolecules, the carbohydrates.

Hello. So we're going to move on to Chapter 3 now, but before we do that, just a reminder of what we talked about in Chapter 2. So in Chapter 2, we did kind of a whirlwind introduction to some fundamental concepts in chemistry. The structure of atoms, how atoms combine to make molecules, to make ionic bonds, covalent bonds, types of covalent bonds, the implications of polar versus non-polar covalent bonds. We talked about the structure of water, water's ability to hydrogen bond because it's a polar molecule, some of the unique properties that gives water. And then we ended up with a discussion of chemical reactions, the energetics of chemical reactions, and then kind of introduction to chemical evolution, and how the earliest kind of precursors to the biological macromolecules necessary for life today could have arisen on a prebiotic Earth. So what we're going to do now for the rest of this unit, chapters 3, 4, 5, and 6, is we're going to take these fundamental principles that we learned in chapter 2, and we're going to apply them to a deeper discussion of the four major categories of biological macromolecules which are shown here proteins nucleic acids carbohydrates and lipids and for each of these we're going to talk about their basic structure how they're made in some cases where they made, in some cases we'll save the where they're made for later on, and then their function and how the structures of the molecule give them their particular functions. As you're going through these chapters, obviously you have to learn each chapter individually, but then when you go back and review, think about it in terms of compare and contrast. How are proteins different than nucleic acids? How are nucleic acids different than carbohydrates, et cetera? Okay? All right, so on to Chapter 3. So in Chapter 3, we're going to discuss proteins. And proteins are the most abundant, and they're the most versatile type of biological macromolecule. Versatile in the sense that they can adopt the widest range of shapes. And in molecular biology, biochemistry, shape or structure equals function. So the function of a molecule is very much a consequence of the particular shape of that molecule. So proteins as a class of molecules can adopt a wide range of shapes, which means that as a class, they can adopt or they can carry out a wide range of functions. So we'll begin, there's two parts to this chapter, two lecture parts in this chapter. The first part, we'll talk about amino acids, which are the building blocks of proteins. And then in the second lecture for this chapter, we'll talk about how amino acids combine to make proteins and how proteins fold up into their final form. So this is the structure of an amino acid. So amino acids have a central carbon, sometimes referred to as the alpha carbon. And remember, carbon has a valence of four, so carbon can make four covalent bonds. For the amino acids, one of those covalent bonds off that central carbon is with a hydrogen. One is with an amino group. That's one of the functional groups I asked you to memorize at the end of Chapter 2. One covalent bond is with a carboxyl group. Another one of those functional groups I asked you to memorize at the end of Chapter 2. And then finally, the fourth covalent bond that this central carbon makes is what we call the R group or the side chain of the amino acid. And in all the different amino acids, that's the only thing that's different. So all amino acids have that central carbon attached to an amino group, a hydrogen, a carboxyl group. Where they differ is in what kind of side chain or what kind of R group do they have. And we'll look at some examples of that in just a minute. Now, in aqueous solution, which of course is the environment that we're concerned with, and at or about neutral pH, which is the typical pH inside of a cell, usually this amino group is going to pick up an extra proton and so have a positive charge. And this carboxyl group is going to lose a proton to the solution and have a negative charge. Okay. And we refer to this as the ionized form of the amino acid. Now, it's important to note that when amino acids are in their ionized form, that doesn't necessarily mean they're charged because this positive charge and this negative charge cancel each other out. So whether or not an amino acid is charged depends on whether the R group of that amino acid has a charge or not, not whether or not the amino or carboxyl groups are in their ionized form, because if they're in their ionized form, their charges will cancel. All right, so we categorize amino acids based on the overall chemical structure of their R group. And so in doing that, there's a couple of different categories.

The first are what we refer to as the nonpolar amino acids. And these are amino acids, and the R groups for all of these are highlighted in green. These are amino acids whose R groups are nonpolar, meaning that there are not any polar covalent bonds kind of exposed at the ends of the R groups so that partial positive or partial negative charges would be able to hydrogen bond with water. So for example, if you look at phenylalanine here, so there's a hydrocarbon ring and a CH2, but there's nothing electronegative in this R group at all, no oxygen, no nitrogen, et cetera. So there's no polar covalent bonds, there's no partial positive or partial negative charges to interact with water. A couple of these, like tryptophan, for example, does have an amino or a nitrogen kind of in the middle of this ring here. And so there is going to be some polar bonds, but they're kind of in the middle of the molecule. They're not sort of exposed really to the periphery very much. So their ability for hydrogen bonding between, for example example this hydrogen and water is going to be fairly limited okay so the overall molecule behaves more as a nonpolar molecule and remember from chapter two that nonpolar molecules molecules that don't have sort of exposed partial positive partial negative charges on their surface don't interact with water. So these nonpolar amino acids are not going to hydrogen bond with water very readily, if at all. Now, they can. Their R groups can interact with each other through what are called van der Waals interactions, and we'll talk more about that in a little bit. Next category of amino acids are the polar amino acids. So these are amino acids whose R groups are not charged, but do have some electronegative atom in there or atoms in kind of the periphery of the R group. So you have some polar bonds out there at the end where you have partial positive and partial negative charges. So for example, greening, there's a hydroxyl group here, so there will be a partial negative charge on that oxygen, partial positive charge on that hydrogen. That oxygen and that hydrogen are kind of at the outside of the molecule, able to interact with water molecules, and they'll hydrogen bond and be solubilized, therefore, by water quite readily. So polar amino acids interact strongly with water through hydrogen bonding. And the last category of amino acids are amino acids that are charged. And the charged amino acids, again, we're not looking at the amino group or the carboxyl group off the central carbon. That just means the amino acids in its ionized form. Those charges cancel. What we're looking at is the R group. And in this case, the R groups of these amino acids have either a negative charge, and in the case of the acidic amino acids, or a positive charge in the case of the basic amino acids. Why do we call this an acidic amino acid if it has a negative charge? Because remember, acids are chemicals that give up a proton to solution. So how do you get a negative charge? You gave up a proton. You lost a positive charge, you're left with an excess negative charge. So the acidic amino acids have given up a proton to solution, they're left with a negative charge. The basic amino acids are the opposite. They have pulled a proton from solution, so they have a positive charge. Now, for our purposes in general biology, I'm not going to ask you to memorize the structures of all the different amino acids or even the names of all the different amino acids. But here is what I want you to know. I want you to know the basic structure of an amino acid in its non-ionized and ionized form. I want you to be able to identify the R group of an amino acid if I show you a picture. And I want you to be able to look at that R group and predict, is it going to be non-polar, polar, acidic, or basic? So really not memorizing names, not memorizing structures, but knowing enough about the categories and applying what we learned in Chapter 2 to tell me if that R group is going to be a non-polar R group, a polar R group, or an acidic or basic one. Okay? All right. Now, we can take this, all these different amino acids, and I should have mentioned earlier, there are 20 different amino acids that we find in living organisms today. There is some variation there in the sense of certain cell types or certain types of organisms can take one of these 20 and modify them to make a few other different kinds, but we'll just focus on kind of the core set of 20 different amino acids, okay? So we can take these 20 amino acids and we can rank them from how non-polar they are, meaning they're going to be highly hydrophobic, not interact with water at all, to how polar they are, how hydrophilic they are, how strongly will they interact with water. And not surprisingly, your nonpolar amino acids fall on the more hydrophobic end, your charged amino acids fall on the most hydrophilic end, and your

polar amino acids kind of fall in the middle there. Okay? All right. Now, proteins are composed of amino acids, and therefore, if we want to understand how living organisms evolved to use protein to rely so heavily on proteins as one of their biological macromolecules, we need to be able to explain how amino acids might have arisen through chemical evolution on a prebiotic Earth. Turns out that's actually pretty straightforward. In, for example, the kinds of experiments that Stanley Miller did that we talked about back in Chapter 2, one of the most predominant types of organic molecules that he found in these experiments were amino acids. He made a number of different amino acids in these very simple recreation experiments, recreating the atmosphere of the early Earth. We can also find amino acids in samples taken from the plumes coming out of deep sea hydrothermal vents where there's a lot of heat and a lot of pressure, which are good ingredients for chemical reactions. Lots of organic synthesis of organic molecules taking place here and we can find even some amino acids there. And in fact, on the surface of some meteorites that have entered the atmosphere at the Earth, we can find amino acids forming simply from the carbon compounds in the meteorite being heated to such high extremes by air friction as they went through the atmosphere. So it turns out it's really not that difficult to envision scenarios where amino acids would have been prevalent and even abundant on the prebiotic earth and therefore available as precursors for cells to, as cells were evolving, precursors to make proteins. Now, there is one, however, part of the chemical evolution story as it applies to amino acids that we don't fully understand yet, and that has to do with the fact that 19 of the 20 amino acids are chiral, meaning that they can be found in mirror images of one another. So quick review of some terminology. An isomer or isomers are two molecules with the same chemical formula but different chemical structures. Optical isomers are two molecules that are mirror images of each other, another way of saying that, two molecules that are chiral. And chirality is pretty simple to understand. Our left and our right hands are optoglycemers or are chiral to one another. So there is no way that I can line up my hands, my left and my right hand, so that my fingers point in the same direction without flipping my hand around so that my palm and the back of my hand are facing in opposite directions. So you can't line. If I put my fingers together perfectly, now my palms are facing opposite directions. If I put the palms in the same direction, now my fingers are pointing in the opposite one another. So your hands are mirror images of each other. They're chiral. You can think of them as optical isomers. Same thing is true for 19 of the 20 mirror acids. So to illustrate that, I hope you can see these okay. So to illustrate that, I made some simple ball and stick molecules of amino acids, okay? So in all these ball and stick molecules, black is carbon, red is oxygen, white is hydrogen, and blue, and unfortunately it's a dark blue in this one, so it's hard to see. Hopefully against my shirt you can tell. Blue is nitrogen. So here is the central carbon of our amino acid. Here's the carboxyl group. I'm missing a proton here because it fell off on my way up to the studio. So there should be a proton off of this. Here's my amino group here. Oh, I'm sorry. I'll just say it's in the ionized form. So we've lost the proton and we've gained a hydrogen here, as I first said. Here's the hydrogen that's off of that central carbon. And if I flip it around, orange, here's my R group. We'll use orange to indicate a variable group like the R group. So here is one amino acid, and here is another. So these two amino acids, let's imagine that these R groups are identical to one another. These two amino acids are identical except for the fact that their R groups are pointing in opposite directions. So in this case, one is pointing to the left and one is pointing to the right. Okay. So, and there's no way, I can't flip these around. These are true, but trim around so the R groups line up. Now the carboxyl groups are are pointing the wrong direction. Okay, so these are true optical isomers of each other. These molecules are chiral. All right, so why are we talking about this? Well, it turns out that in terms of the synthesis of amino acids,

through the kind of processes that we think would have been taking place during chemical evolution, it is equally likely that you will get this form of the amino acid or this form of the amino acid, okay? So the left or the right-handed forms will arise equally with equal frequency. However, living organisms today only use the left-handed form of amino acids to make proteins. That we can't quite explain yet. Why, if both forms of amino acids are equally easy to make, why was only one form used to make proteins? There are some hypotheses that are interesting, but it's still an open question. Now, however, nature doesn't like to waste, and there are some organisms that use right-handed amino acids to do other things besides making proteins. And you'll have a little accessory reading in the textbook, or accessory reading in blue line, excuse me, to look at that. Now, one thing I do want to mention is I said that 19 of the 20 amino acids are chiral, meaning that they can form in the left or the right-handed form. The one that doesn't is glycine, and the reason for that is glycine's R group is a proton. So this is what glycine looks like. So because the R group is the same as the hydrogen coming out of the central carbon, this molecule doesn't have an optical isomer because these two things are the same. But all the other amino acids do have optical isomers. Okay, so as I mentioned before, the living cells today, or living organisms today, use left-hand amino acids to make their proteins. We can't fully explain why that is. why didn't Leif and Rice use right-handed amino acids or use both. But that doesn't mean that the right-handed amino acids aren't important. There are some really interesting uses of right-handed amino acids in nature. Some of the neurotransmitters that you may have heard of in the past are derived from right-handed amino acids. Some venoms, some toxins in organisms that produce poisons are derived from right-handed amino acids. So I've got a little short reading, additional reading posted in blue line for this chapter for you to take a look at to get a little bit more background there. Okay? All Alright, so that's a quick introduction to amino acids. In the next and the final lecture for chapter two're going to talk about how amino acids assemble to make proteins. Now, proteins are our first example of a biological polymer. Polymers are long chain molecules that are composed of repeated subunits. So in the case of proteins, the subunits are amino acids. As we'll see in later chapters, proteins are not the only type of biological polymer. Nucleic acids are a biological polymer. Polysaccharides are a biological polymer. So we're going to, this story about till here will seem, will be repeated in some of those later chapters. Okay, now when biological polymers are made, they're made through a reaction, a type of reaction called a condensation reaction. Okay, so condensation reactions are reactions that generate water as a byproduct. Okay, and in the case of the making of biological polymers like proteins, a hydroxyl group on the next monomer that's about to be added, so in our case the next amino acid, interacts with a hydrogen sticking off the end of the chain. Those two groups pull off to make a water molecule, and a new covalent bond is formed to attach the next monomer to the end of the chain. To break biological polymers down, essentially the opposite has to happen. We call that a hydrolysis reaction. A hydrolysis reaction is when water is used to split something. So in a hydrolysis reaction, a water molecule interacts with this bond here. That bond gets broken and releases the last monomer in the chain. So biological polymers are made through condensation reactions. They're broken down through hydrolysis reactions.

and see what that looks like in more detail as it relates to the formation of proteins. So here we have two amino acids, okay? And these two amino acids are about to undergo a condensation reaction and make a new covalent bond linking them together. So two protons from the, or excuse me, two hydrogens from the amino group, the next amino acid that's about to be added to the end of the chain to interact with an oxygen microboxyl group of the last amino acid on the chain pulls off a water molecule and a new bond is formed between this carboxyl carbon and this amino nitrogen okay and that new bond that new covalent bond we give it a name we call it a peptide bond okay so a peptide bond is what we call the covalent bond that links two amino acids together in a chain okay and so peptide bonds are made by condensation reactions now there's some interesting chemistry here that we won't really go into in very much detail in this class but i just want to mention it. And that is this peptide bond most of the time acts as a single bond, but sometimes can act as a double bond. And the reason for that is one of the electron pairs in this carboxyl oxygen up here can jump down and be shared between this carbon and this nitrogen briefly. So this peptide bond spends most of its time as a single-level bond, but sometimes acts more like a double-trivial bond. All right. Now, when we start hooking amino acids up together double before we would usually, before we would correctly call it a protein. So let's look at a small peptide here. So this is kind of a very simplified version. Here's the more complicated version here. Notice that all groups are projecting away from this central backbone, where the peptide bonds are. You should be able to find all the peptide bonds in here pretty easily by now, okay? And what I want you to notice is that the first amino acid in the peptide still has a full amino group, okay? The last amino acid in the peptide still has a free carboxyl group. So we call the first amino acid in the chain, we call that the N-terminus or the amino terminus of the peptide or of the protein. And the last amino acid in the chain, we call the C-terminus or the carboxyl terminus of the peptide or the protein. And this is a, what this indicates is that peptides and therefore proteins have a polarity. Remember, polarity in a biological context simply means one end is different than the other. In our case, or in this case, the polarity means that there's a free amino group at one end and a free carboxyl group at the other. And we number the amino acids in a peptide or the amino acids in a protein starting at the amino terminus. So the first amino acid that was added is the internal amino acid. We number that amino acid one. The next one is number two, et cetera, until we get to the last amino acid in the chain at the carboxy terminals. Now, once we've kind of assembled our long chain of amino acids, that long peptide chain doesn't typically, if it's long enough, doesn't stay in that linear form for very long. It will fold up into some shape. And this is where kind of the magic of proteins happens. So the range of shapes found within proteins as a family is tremendous, and that's what gives proteins their functional diversity as well. The reason why this folding is possible is that most or all of the bonds in the peptide backbone here are single covalent bonds, and two atoms can rotate freely around single covalent bonds. So this allows a lot of movement of this chain. But because occasionally those peptide bonds have a little bit of a double bond character,

that means that they don't just kind of kind of you know flop around all the time they have a little bit of restriction a little bit of rigidity to them and that helps to kind of limit the randomness within the randomness with which that peptide will move around so that more productive movements leading towards proper folding can happen now protein folding is a gradual process, kind of represented here, and I've got a big styrofoam noodle to kind of represent that. And the point that I want you to remember with this is that protein folding doesn't happen all at one time and it doesn't happen perfectly every time. Okay, so this is our peptide, our chain of amino acids connected by peptide bonds and we'll use blue to indicate our amino terminus, we'll use red to indicate our carboxylterminus. So this is moving around in aqueous solution as a lot of molecules are moving and things are bumping into it, et cetera. And in order for a particular folate conformation to become stabilized, regions of the peptide capable of interacting with each other have to come into contact. So let's say that this region and this region can interact in some way. So if they happen to bump into each other, that stabilizes that interaction. And now this part is folding, and let's say this part and this part have the ability to interact with each other. So if it happens that those two regions come together, now we've stabilized this level of folding. And now let's imagine that this part and this part can interact with each other. See if I can do this. Okay. So if it happens to bump into each other now, now we're beginning to get a structure. Okay. And this process of protein folding takes time. It can go backwards. So if the environmental conditions change, the temperature goes up, the pH changes, et cetera, and you disrupt those interactions that stabilize a folded shape, the protein will unfold. We'll talk more about that in a little bit. So let's look in a little bit more detail at this process of protein folding. And it is helpful to think of, and in fact this is actually what happens, but think of protein folding as occurring in a series of stages. And we begin with the linear structure of amino acids in that peptide. And we call that the primary structure of the protein. And that sets the stage for everything else. If you change the primary structure of the protein, there's a good chance that you will change the final, change what that protein looks like in its final folded form. And there are some really, really good examples of that in the medical literature. A classic one is sickle cell anemia or sickle cell disease. So this is caused by a single amino acid change in one gene that results in a protein that's found in red blood cells, folding it correctly. That misfolded protein changes the shape of the red blood cell, and in this elongated sickle shape, the red blood cell gets stuck in the little capillaries and blood flow gets restricted and it's a very debilitating and sometimes ultimately fatal disease. And all of these consequences of this disease can be traced back to a single change in the primary structure of the protein. The next phase in protein folding is when proteins adopt what we call their secondary structure. And in this case, what we'll see is that the secondary structures of proteins are stabilized by hydrogen bonding between the carboxyl oxygen and an amino hydrogen of different amino acids. So this protein is going to fold up, and this O and this will hydrate among each other and this O and this H will hydrate among each other and that will stabilize that folded shape. Here are the two most common types of secondary structures that we see in proteins, alpha helices and beta pleated sheets. So here's an alpha helix on the left and here a beta-pleated sheet on the right. So in the alpha helix, the protein kind of coils around, and this helical structure is stabilized, again, by this hydrogen bonding. So here's this carbonyl oxygen, hydrogen bonding with an amino nitrogen over here. We'll repeat that over there. Beta-pleated sheets are kind of like an accordion almost. It's looped around on itself. So you kind of have this kind of little region here that's bent like an accordion and then a little loop and then another region that's bent up like an accordion and those regions interact with each other again through that hydrogen bond. These two tie

types of secondary structural elements, or sometimes referred to as secondary structural motifs, appear so commonly in proteins that we use a shorthand to represent where in a protein these types of secondary structures are found. So if you see something that looks like this in a protein, that's an alpha helix. If you see something that looks like this, two arrows running in opposite directions, that's a beta-pleated cheat. The next stage of protein folding is when proteins adopt their tertiary structure. So the tertiary structure is when regions of different secondary structure interact with each other. So to try to kind of represent that, get my noodle into shape here. So here I've got a protein that has adopted some secondary structures. So here's a short alpha helical region. Here's a short beta pleated sheet region. Now this protein is going to continue to move around, and if something here can interact with something there, when these two regions come together, now you can stabilize that next level of folding. Now we say the protein has a tertiary structure. There are lots of different types of interactions between amino acids that can help to stabilize the tertiary structures of proteins. And some of those are shown here. So we have the potential for hydrogen bonding between the R groups of different polar amino acids or between the amino group of one amino acid and a carboxyl group or an R group of another. In some cases, we might have ionic bonds. So if you have an acidic amino acid and a basic amino acid that come into, where those R groups come into contact as a result of a particular folded shape, you can get an ionic bond here to help stabilize that interaction. If non-polar amino acids come into contact with one another, there are groups can interact through what are called van der Waals interactions. We haven't really talked about van der Waals interactions yet. They're a type of London dispersion force, if you learned that terminology back in chemistry, that are very, very weak attractive forces that primarily play a role in interaction between hydrophobic molecules. They're so weak that their impact on polar charged molecules is minimal. But in non-polar molecules that don't make ionic bonds and don't make hydrogen bonds, Van der Waals interactions become important. So we can have non-polar amino acids, the R groups of non-polar amino acids interacting with Vander Waals interactions. We can have hydrogen bonding, we can have ionic bonds. All of these different types of interactions can help to stabilize the tertiary structure of a protein. Down here is a special case called a disulfide bond. And if you remember back in the first part of chapter two, there's an amino acid called cysteine that has a sulfhydryl group, SH, at the end of it. Well, if two cysteines, if the sulfhydryl groups on two different cysteines come into contact with one another, and if that protein is in the correct chemical environment within the cell, then a covalent bond can form linking the sulfur groups of those cysteines together, and we call that a disulfide bond. And because this is a covalent bond, it's very strong. So proteins that have disulfide bonds tend to have pretty stable tertiary structures because they've got these occasional covalent bonds helping to stabilize that tertiary structure of the protein. And again, tertiary structures are where we really start to see tremendous diversity from one protein to the next. But the tertiary structure of a protein is going to be contingent on its secondary structure, which, of course, is contingent on its primary structure. Now, for some proteins, that is it. That's as far as they will fold. However, there are some proteins where the final functional form of the protein is composed of two different peptides that folded up independently into tertiary structures and then came together. And when that happens, we say that protein has quaternary structure. And there's two examples of that here. We'll just look at one of these because it's the one you're probably most familiar with. So over here on the right, this is a ribbon diagram of a protein called hemoglobin. Hemoglobin, as you know, is the protein that's most responsible for carrying oxygen in the blood. Hemoglobin is an example of a protein with quaternary structure. So there are four, one, two, three, four, five, six, seven, eight, nine, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 42, 43, 42, 43, 44, 44, 45, 46, 47, 48, 49, 41, 42, 42, 45, 48, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49, 42, 49

three, four separate peptides that folded up individually into their own tertiary structures, and then those came together to make hemoglobin, the final functional form of the protein. So all proteins will have primary, secondary, tertiary structure. Some proteins will also have quaternary structure if they're composed of more than one subpar. So this table just kind of summarizes what we've talked about so far in terms of protein structure. So make sure you're familiar with the information in this table as you go back through your notes here. Now, it is absolutely critical for proteins to fold correctly in order for those proteins to carry out their proper function in the cell. And the reason for this is a phenomenon called molecular complementarity. This is a fairly simple concept, just this idea that for two molecules to interact with each other other they have to have shapes that have complementary shapes where this protein and this protein can fit together nicely. Those associations can be stabilized by hydrogen bonding and ionic bonding between them. So these proteins can come together, interact for some period of time. Here we have two other proteins whose shapes are not quite as good a fits for one another, and so they don't interact as strongly. They're not likely to, in a productive way, come together and make a stable compound. If proteins don't fold correctly, they're not going to be able to interact with their correct targets, and therefore they won't be able to carry out their functions. And so this is, again, an example of this idea that structure equals function. If the proteins don't fold correctly, they won't have the right structure. If they don't have the right structure, they're not going to be able to interact with the things that they need to interact with in order to carry out their appropriate function in the cell. Proteins can unfold if the environmental conditions change. We call this denaturation. So what are some things that might cause proteins to unfold? Well, there could be the introduction of some chemical that promotes denaturation, and that's just being represented here. So here's a protein called ribonuclease in its correct folded form. If you add it, there's a lot of disulfide bonds in ribonuclease stabilizing this tertiary structure you had a chemical breaks with disulfide bonds now this protein kind of unfolds and it's denatured form it doesn't have the proper function. But there are other more kind of environmental factors that can cause protein denaturation as well. One is simply increasing the temperature. So as the temperature goes up, there's more thermal movement, the molecules are moving faster, and you're more likely to break apart those interactions that are stabilizing that tertiary, folded form of the protein from the protein denature. Likewise, if you alter the pH, you alter the strength and the frequency of ionic bond formation and hydrogen bond formation, and you can denature proteins that way. Well, denatured proteins will eat and it will be cracked. The clear egg white turns white. Well, that's the result of the protein in the egg white. It's called albumin. When you heat it up, the albumin unfolds. In a denatured state, The albumin scatters light instead of transmitting light, and that's why the egg white goes from clear to opaque. What drives protein folding? So there's no magic hand that comes in, grabs a protein, and folds it correctly. It is a stochastic or kind of random process in the sense that the protein, the peptide is moving around and regions have to come together to interact in a productive way to help to stabilize that kind of beginning of that folded shape.

And then you just repeat that over and over again. We think that one of the early events in protein folding is what's sometimes referred to as the oil drop model of protein folding. We think that one of the early events of protein folding is all of the hydrophobic amino acids, the non-polar amino acids that don't interact with water, they can't hydrombot with water, so they're not very stable on the outside of the protein, but they can make van der Waals interactions with each other. And so we think one of the early drivers of protein folding are the non-polar amino acids sort of moving, folding around and moving into the middle of the molecule, so manually the non-polar amino acids here, where they can interact with can interact with each other by general sources and not be bothered by all this water that's out there and now the rest of the protein in this case that has more polar side chains the charge side chains that can interact with the water will continue to fold on its own so this is referred to as kind of the oil drop model is driven by the dynamics of getting these molecules away from that office environment. Many proteins, in fact, maybe we should say most proteins, don't necessarily fold into their final form immediately once they are made. Rather, they have to interact with something in the cell first, and then when they've done that, then they finish their folding. A good example of this is a protein called calmodulin. I think we talked about calmodulin in Bio 201 in the physiology section. Calmodulin is a protein that is important for muscle contractions and things like that. Calmodulin, when it's made, doesn't have a very stable form. It's what we call a disordered protein. But once it encounters calcium, that calcium binds to several sites on the calmodulin molecule, stabilizes some folding around those sites, and then that then allows the rest of the protein to finish folding correctly. Okay, so this is an example of a calmodulin, therefore it's an example of a protein that doesn't adopt its final stable folded form until it's encountered something else in the cell first. And as we looked harder and more carefully at more and more examples of protein folding, we're finding that there are lots of proteins that kind of work this way, that they are relatively disordered, partially unfolded, not in a really stable shape until they encounter something, and then that kind of anchors them, them and the rest of the protein can fold correctly after that. There are systems inside of cells to facilitate the folding of proteins and these systems are called chaperones and chaperonins. And these are protein complexes that help other proteins fold correctly. And we'll talk a little bit more about chaperones in a later chapter. I don't want to spend a lot of time on this, but just give you the, and there's a lot of details in this slide because I pulled it from an upper-level textbook. Don't worry about all these details. But in a nutshell, so chaperones grab onto proteins as they're being synthesized from the ribosome, which we'll talk about that in a later chapter, and they kind of physically move that protein around to help facilitate its folding. Chaperonins create like a small barrel structure so that unfolded, newly formed proteins go into the chaperonins create like a small barrel structure so that unfolded newly formed proteins go into the chaperonin and in that barrel structure it's a more confined environment that limits kind of the randomness with which that new protein will move around and in that more confined environment it's more likely that the protein will be able to make some secondary and tertiary structures in a productive way. So not all proteins need chaperones or chaperonias to fold correctly, but some proteins do. And we'll come back and look at this topic of chaperones at least a little bit more in a later chapter. Now, the last thing I want to mention, again, is this idea that if proteins don't hold correctly, they won't carry out their proper function. And in some cases, the misfolded protein doesn't have any negative effect on the cell other than it can't carry out what it's supposed to do. It can't do what it's supposed to do. But in other cases, the misfolded protein itself causes additional problems because the misfolded protein does things that the properly folded protein would not. And diseases that are associated with this function

phenomenon are called proteinopathies or proteopathies, okay, diseases where misfolded proteins do something that they wouldn't normally do and that something is detrimental to the cell. And there's a lot of examples of proteinopathies that you're familiar with, so Alzheimer's disease, Parkinson's disease, mad cow disease, okay, these are all examples of proteinopathies, diseases caused by misfolded proteins doing things that they wouldn't normally do in the cell. On the picture here, we're looking at one subcategory of proteinopathies, and these are the prion diseases. So mad cow disease, Krebsfeld-Jakob disease, etc. So the prion diseases are diseases that arise when a type of protein called a prion misfolds. What I'm doing here, I keep hitting the wrong button. Here we go. When these prion proteins misfold, And what makes these prion diseases particularly nasty is the misfolded form of the protein will bind to the correctly folded form of another prion protein and cause it to misfold as well. And so you kind of get this cascade or snowball effect where one misfolded prion causes other prions to misfold, and they cause other prions to misfold, and very rapidly you get these big clusters of misfolded prion proteins that make these aggregates or these plaques inside of cells and ultimately will damage or kill the cell that they're in. And so in this sense, prions are infectious. If you ingest a misfolded prion protein, that ingested misfolded protein can cause your own properly folded preons to misfold as well. So they're a particularly nasty example of a proteinopathy. Okay, so that's a little bit about protein structure and how proteins fold up to adopt their final structure. Keep this information in mind as we move through the rest of the semester and we start talking about lots and lots of specific examples of proteins. Each time we talk about a different protein, just remember, this protein that we're talking about because it has this particular function, it has that function because it was able to fold up in a certain way. Okay? All right, so that's the end of Chapter 3. We'll move on next to Chapter 4 and talk about the next category of biological macromolecules, the nucleic acids.