Transcript for:
Exploring Organic Macromolecules and Their Functions

Class well welcome to chapter 5 This is the macro molecules or the biomolecules chapter Probably one of my most fun chapters to go through in the entire book This chapter is going to be broken up into two parts. I've got a part A and a part B, and it's going to cover all of the organic macromolecules that we started talking about in the last chapter. Remember, these are the proteins, the carbohydrates, the lipids, and the nucleic acids. And I just really love going over this chapter just because it really is a lot of fun. It really brings you back to the real world because everybody's always concerned about their diet and health and eating too many carbs or making sure they get enough protein, etc. So it just is a really good chapter just because you can kind of get to the molecular level of what proteins really are and what carbohydrates are and what fats are and why fats have more energy and things like that. So it's just a really, really great chapter. All right. So starting off, we're going to consider these the chemical building blocks of life because these are the macromolecules with these ginormous binds. or biomolecules, whatever you want to call them. And they're all going to be organic, right? So they're all carbon based. So before we get started, I just wanted to kind of figure out like what you already know. So we're going to look at how these molecules, like primarily today, we're going to look at how the molecules are constructed. So what they're made up of, what they're composed of, and how they function within cells. So there's going to be a hierarchy to how they're built. So I want to go over and just kind of construct a table. If we were in class, I would have you on the screen. do this as part of a group work, but I want to construct a table of how these things are all put together. So we're going to use all of these terms and we are going to make a table here that I have the first page of your follow along guide. All right. So before we look at this though, I know this will be a little bit more helpful if we just kind of go over what the basis of structure is for these macromolecules. And then we're going to return and we'll do that table in one second. So to build and... run living organisms, small molecules are organized into really large complex molecules called macromolecules. And we discussed this in our chemistry chapter about the hierarchy, right? We've got little atoms like carbon, hydrogen, oxygen, nitrogen, et cetera. Those come together to form molecules. So like water, carbon dioxide, oxygen gas, et cetera. And then those molecules build really, really large molecules that can have hundreds, thousands of molecules or atoms within those. So those are the three things that we've discussed. the macromolecules. Macromolecules for our organic ones, they're going to be mostly built from smaller identical building blocks called monomers. So I like to think about it as like a monomer is like a little Lego, like a building block. And then you can use those little Lego building blocks to build really, really large complexes with those Legos, right? You can build like the Death Star or whatever, like all these Star Wars structures, right? And those would all come from the individual monomers, okay? So once you build those monomers into those macromolecules, those can also also be considered a polymer. So a polymer is like a complex of all these monomers put together. So mono is single, poly is multiple. The type of bonds that build these monomers into polymers are going to be covalent in our cells because remember we don't want them to be built by ionic bonds because ionic bonds are going to be able to be broken down in water and we are mostly all water. So we want them to be really, really strong covalent bonds. And they're going to be immensely diverse, right, of how they're built. You're going to see all different structures and all different functions. classes of macromolecules or even polymers, if you want to think about it, are proteins, nucleic acids, lipids, and carbohydrates. Okay. So proteins, nucleic acids, lipids, and carbs. So proteins, we know what those are. Nucleic acids are, for example, like DNA and RNA. Lipids, for example, are going to be your fats and then carbohydrates are going to be your sugars, right? So those are the four types of macromolecules. Okay. So let's go ahead and we'll fill out the table, um, on your follow along based on these terms. Okay, so what do we know? Use the following terms to complete the table below. Alright, so let's first go through this. If you even want to take a second to pause and try to figure out what you know before this, and that's great. You can just pause the video and try to do that and then come back and see if you got it correct. Okay, so our four polymers are going to be obviously our macromolecules. So these are going to be, for example, here we have polypeptides and I wrote them a little bit different. So I'll actually give you some other names for these. These polypeptides are also called proteins. So we can put proteins here. Okay, and we'll just go through and we'll highlight or underline these as we go through this. So proteins are going to be our one. Our next one could be considered our nucleic acids. And I'm going to do this in order of how we're going to go through the PowerPoint, in like the order of these things. So nucleic acids is going to be our second one. And then we will look at lipids. lipids and I think I have lipids here as triacylglycerol. So these are going to be our lipids. And I wrote them a little bit different here because these are going to be more of the polymer form when we go through these. But for this one, that's okay. I can just kind of shorthand it. lipids and then I've got polysaccharides which are going to be our carbohydrates and you'll see once we get through here why I decided to do it this way instead okay so those are going to be our I'll just write that here so those are going to be our polymers okay so what are are the monomers that link into becoming these polymers, right? What are the individual building blocks of a little Legos that make these polymers? All right. So proteins, if you didn't know that, those are going to be made up of amino acids. Amino acids make up proteins. That's going to be this guy. Okay, and then what makes nucleic acids? These are called nucleotides. So nucleotides. Okay, and then what makes up lipids? Lipids are going to be mostly made up of fatty acids. So fats, fatty acids, fats, and you're actually going to see that lipids are going to be the one class here that are not really made up of distinct monomers. They're kind of an exception to the rule. And so you'll see that as we go through. And then monosaccharides are going to be what build up carbohydrates. So monosaccharides. And that's why I had originally like the polysaccharides here because it just made more sense. Okay, awesome. All right. So then what is the bond name? The bond type of all of these are going to be covalents. Covalent, and I'll just copy this. And we'll just paste that on all of these. And remember, that's the bond type that's going to link all of these because that is going to be the strongest type of bond. And then the bond name is going to be the remaining things here. So amino acids. are built into proteins using peptide bonds. Okay, so peptide bonds. And like I said, I'm not expecting anybody to really know this right off the bat because this is like a little bit more in detail science that you've probably learned before. But we're going to go through all of it. Okay, so the nucleotides are built into nucleic acids using phosphodiester bonds. Some phosphodiester bonds. Okay, and then fatty acids are built into lipids using ester bonds or ester linkages. That's an ester linkage. And then monosaccharides are built into polysaccharides or carbohydrates using glycosidic linkages. Glycosidic linkages or glycosidic bonds. Okay, so there we go. go. All right, so good thing to probably just make some note cards for all of this. And then we can give an example of an amino acid into protein, or an example of this could be, for example, like an enzyme. Enzymes are types of proteins. An example of nucleotides that build nucleic. acids. What about DNA and RNA? Fatty acids, we can say fats. What about cholesterol? Those are all different examples of lipids. And then monosaccharides would just be sugars, for example, glucose. Okay, cool. All right. So hopefully that was a nice little introduction for you guys for all the macromolecules we're going to look over now. And then we've already went through a couple of these questions, so we can jot these down here on our follow-along guide as well. So what are the macromolecules? macromolecules macromolecules are we will say giants carbon based carbon based molecules that build that builds and run life. Okay, and then what are our four organic macromolecules that build and run life? We have proteins, nucleic. acids, lipids, and carbohydrates. Okay, and then what are monomers? Monomers are the individual building blocks. blocks of macromolecules example legos say and then polymers Polymers are the complex macromolecules. And then those are built from monomers. Built. Built from monomers. And we can say example of protein. Okay. And then providing an example of each, you have those examples up there. So we'll skip that. All right. So now we're going to go into this. We're going to break this down. All right. So question. here for you polymers are made up of connected monomer subunits that are joined by what type of bonds we said those have to be covalent covalent because remember those are going to be really really strong so they're not going to be broken up by water so we don't want it to be ionic talked about another type of bond, which was called hydrogen bonds. Hydrogen bonds are obviously not going to be strong enough, right? Because we said individually, they're really weak. So they're not going to be strong enough to hold together all of these polymers. So they are going to have to be covalent bonds. All right. So we're going to start with proteins. Then we're going to move into nucleic acids. And then part B, we'll go into carbohydrates and lipids. All right. So we start with proteins because proteins, I think to me, are going to be the most complex. They're also one of the most important macromolecule. They are so extremely diverse. If you want to take a minute, you know, before we kind of go through this and just kind of think about like what you know already about proteins. So what are proteins made up of? What are some functions of proteins within cells? Proteins are going to be the most diverse of any of the macromolecules. So they're pretty much instrumental in every single aspect of a living organism and of a living cell. They build living cells. They're involved in chemical reactions, structural. They just, they do everything. So they're going to be extremely diverse. I have some examples of what proteins function in the cell, and these are going to be examples that will move throughout the entire semester. So we've got eight different examples of how proteins function within a cell. So, for example, proteins will function as your hormones. So, for example, insulin. Insulin is a type of protein. We've, I think, mentioned insulin in the past already. Insulin is the protein that regulates your blood sugar. So it is what helps bring glucose. within the cell. So like if you eat a big meal and you digest and you break down all these sugars and they go through your blood, the glucose starts flooding your bloodstream. Insulin is what regulates that uptake of glucose into the cell, because you're going to see in a chapter coming up very soon that we break down glucose to harvest energy from. So it's going to be really important to get that glucose into the cell. So this is one of the functions of protein, example insulin. Proteins also function as receptors on our cell surface. We're going to spend one of the next upcoming chapters here talking about the phospholipid bilayer, which is our membrane, the plasma membrane of cell. And in addition to being like a lipid, right, our phospholipid of our membrane, there's also proteins that are embedded all throughout our membrane and they act as receptors. So they receive signals. They receive signals throughout our protein. They receive the signals on our proteins of our membrane. They also act as our motor protein and our contractural proteins that are involved in muscle contraction and relaxation. So if you guys go on and take your anatomy physiology class, you'll spend a lot of time learning about the structure and the function of muscle. So there's two different types of proteins in our muscle that I'm showing here, actin and also myosin. So actin is going to be a protein that kind of lines our muscle cells like this. And myosin is like kind of like a motor protein. And these are going to be like the structure of this is involved in how our muscles contract and relax. Okay. So functional. um, contractual and motor proteins. We also have types of proteins that are structural proteins. So for example, collagen, we've all heard of collagen. It's in our connective tissue and it's what provides our connective tissue with that like tensile strength. Cause you can see here, the structure of collagen, it's kind of like this rope like structure. So it prevents our, um, cells from tearing and our tissue from tearing. So it's a really, really strong type of protein, um, muscle and collagen. These guys have, especially muscle, they have some of the strongest and most common. complex proteins because they have to help prevent from tissue tearing and muscle tearing. All right. And then next examples, we've got enzymes. So primarily all enzymes are going to be proteins. We are going to look at an exception to this later on down the road that RNA can also act as an enzyme. But from what we know now, mostly all enzymes are going to be proteins and enzymes are molecules that help speed up a reaction. catalysts. They're biological catalysts, so they help speed up a reaction. So here I'm showing you this little purple enzyme, and this enzyme is helping to break down this molecule. So, you know, reactions can proceed without enzymes, but enzymes are just going to help speed them up. Okay, we also have defensive proteins. So, for example, antibodies. Antibodies are proteins, and antibodies are proteins that our white blood cells secrete out, they shoot out, and then they help to, you know, fight off any kind of pathogen. So they help to identify anything foreign in our body. So like viruses, bacteria, etc. And then they will kind of lead the crowd to come and destroy those pathogens. So defensive proteins and then storage proteins are another big one too. So for example, ovobumen. Oval bumen is the protein that is an egg and that feeds like an egg white and that feeds amino acids to the nourishing baby. And then transport proteins. So transport proteins we can think of as kind of like those receptor proteins that are in the surface of our membranes. receptors are used, you know, the receptor proteins are used to receive information. Transport proteins are also embedded within the membrane and they're involved in getting like molecules and signals through the cell membrane. Let's say that you have to get to the nucleus of a cell to tell it something, right? to give it some kind of information that can go through a transport protein. So you can see such diversity within proteins. And then I wrote here just some examples of different types of proteins. So proteins are what make up hair, keratin, feather, skin, blood clot. So fibrin is the protein that is involved in clotting our blood. So our blood doesn't come out when we get a cut or something we don't bleed out. And then spider silk is also... So a protein we'll look at here in a minute as well. So proteins you're going to see make up about 50% of the mass of most cells. So they're just really, really important macromolecules for our cells. All right, so all the following contain amino acids except what? So we know that amino acids build proteins. So which of these is not going to be an example of a protein? So hemoglobin is. This is a protein that carries oxygen on our red blood cells. Antibodies are. We just looked at that. Enzymes we just looked at. and insulin, right? So the one here that is not made of amino acid, not a protein, is going to be cholesterol. And cholesterol is going to be a type of lipid. So it's a type of fat that we'll look at here in a little bit. All right. So proteins are going to be the most diverse of all macromolecules. What are some functions of proteins? So we said enzymes. We had storage. We had receptors, right? So any of those ones that you want to jot down. We had structure, right? We had all those different ones. that we're going to show on the table. All right. So now let's look and see how we make proteins. Proteins are one of my, I think it's one of the most fun here of all the, of all the macromolecules. All right. So what are the monomers that build proteins? We already said this amino acids. So amino acids are the monomers that build proteins. Okay. How many amino acids are there that build proteins? There are 20. So just like we've got the letters of the alphabet and they come together to form words and stories and books. poems, right? There are 20 amino acids that come together to build proteins. Okay. So we're going to look now at what the basic structure of an amino acid is, and you're going to have to be able to recognize a basic amino acid. So all amino acids have the same core backbone, and I will show you that now. And they are going to have the same core background, which is composed of a carbon, a carboxyl group, an amino group, and a hydrogen. So we've already looked at these. Remember the functional groups that we said we're going to come back to quite a bit. So hopefully you remember what a carboxyl looks like in an amino. And then they differ by their R group. It's like one variable group that they all have, and that's what makes them all different. Okay. So looking here at an amino acid, we said that we've got the central carbon. Okay. So all amino acids are going to have a central carbon. All amino acids have this hydrogen. All amino acids have an amino acid, an amino, sorry, an amino group. have a carboxyl group. So this is that central kind of like core backbone that all amino acids have. And this is why an amino acid is called an amino acid because it has an amino group and it has a carboxyl group. And if you remember, a carboxyl group is an acid because it can easily lose this H and kick it out. And that O, remember, can become ionized to O minus because that hydrogen, the electron is stolen by the oxygen and then it kicks out the proton. So it can easily become O minus and become ionized. So sometimes you'll see an ionized version of an amino acid. Okay, so that's the basic core backbone of all amino acids. And then this R group is going to differ. And so you'll see the 20 different ones. Now they all differ by this little R group. And then carbon, remember, needs four bonds. So that's why it has all these different things. So it's bond to an R group, it's bond to the hydrogen, it's bond to an amino group, and it's bond to a carboxyl group. Okay, so if we were in class, I definitely want you to take a second, if you want to pause the video here, and try to draw... out glycine. Glycine is the simplest amino acid. And as it's our group, it only has a hydrogen. So take a second to pause this and draw this out. Cause like I said, you're going to have to be able to recognize this on quizzes and for exams. So drawing this out is going to be really helpful. So we've got, remember the carbon central carbon, we've got a hydrogen or sorry, hydrogen. We've got some kind of our group and with glycine, which is the simplest one, it's just a hydrogen. And then you have an amino group and then you have the carboxyl group. Okay, so take a second to do that. And then we can go ahead when you're done with that, we can go ahead and jot down the follow-along guide. So what monomers build proteins? These are our amino acids. And then how many amino acids build proteins? 20. and then draw out the simplest amino acid glycine, and then what are the main components of an amino acid, how do they differ? So we've got one, a central carbon. Two, there's a hydrogen atom. Three, a carboxyl. 4 in a media group. And then how do they differ? 5 differed by their R group. And R just stands for variable. Okay. All right. So hopefully that's pretty easy to be able to recognize just a basic. amino acid and then let's look at the differences in the R group. So differences in the R group are the ones things that produce the different 20 amino acids. R groups can be as simple as hydrogen which you just saw and glycine or they can be complex with various functional groups. R group you're going to see is what gives the amino acid its diverse properties. Because if we just look basically at a regular amino acid, these are all going to be the same, right? So they're not really going to give any diversity. So what's going to give diversity is what consists in the R group, okay? So amino acids can then be organized in various ways based on those R groups. And then what do you think some of these properties can be? So think about it when we're thinking about any chemical, right, or any molecule, we can have different properties based on the atoms that are involved, right? So you can have... polar, non-polar amino acids, basic, acidic, right? So this is what we're talking about when we think about properties. So we're going to look at four different groups of amino acids. So the first one we're looking at is non-polar hydrophobic, so water-hating non-polar. And the key is here, if we look at, remember the backbone is going to be the exact same thing for all of these amino acids. Same thing. We've got the central carbon, we have the carboxyl group, we have the amino group. We have a hydrogen and then we have some kind of R group. So that R group, the vario group is what's highlighted here. So we're looking at nonpolar hydrophobic. The key here is, let me highlight. Yeah, okay, cool. So the key here is we're looking at nonpolar atoms and molecules that are built here. Most of these are not going to have any kind of oxygen, nothing like no, nothing that's going to be able to steal, nothing like electronegative. It's going to be able to steal electrons from other atoms. because you don't want to generate those ions. So these are mostly all going to be built from non-polar bonds. So if you see here, mostly all of this is like carbon, hydrocarbons, carbon, hydrocarbons, hydrocarbons, hydrocarbons, hydrocarbons. Even if you look here, remember this is like those benzene rings. You saw this back in chapter four, I believe it was. Remember all of these are just carbon. It's just every one of these, this little hexagon here, each one of these little points represents a carbon, and then it would bond, be bound to just hydrogens. So they're just not showing you. It's kind of like this, right? It would be drawn out like this, but here they just simplified it, and they just haven't included the carbons. So this is all carbon. So for purposes of the quiz and exam, et cetera, I want you to be able to recognize definitely a basic amino acid, and then I want you to be able to recognize the property based on the R group. So you don't have to memorize all 20 of these. If you go on to an undergrad in biology or biochem, you might have to do this. If you go to grad school, you will definitely have to do this. you to be able to recognize a basic amino acid and then what the property of the R group is. So if I show you, for example, alanine, you would know that that would be nonpolar. And you'll see how that differs here in a second from a polar amino acid or like an acidic or a basic amino acid. Okay. If we think about it also, just one more note on this, that the backbone of an amino acid is neutral. Because if we remember back from chapter four, carboxyl is an acid. Remember, acids are represented by the negative because they have we will assume this is an ionized amino acid. So we will assume here that this had that hydrogen, right? And it kicked out that H plus, stole the electron and then kicked out the H plus. Because remember a hydrogen atom is just... A hydrogen is just a positive proton and then a negative electron, right? So we would have assumed here that that oxygen, because it's really electronegative, stole that negative and then kicked out the proton. And remember, when we're kicking out protons, we make the environment more acidic. So that's why the carboxyl group is an acid. Okay. And then the amino group, remember, was originally just NH2, but it picked up that extra hydrogen, H+, and became NH3+. And remember, anything that reduces that H+, in the environment, is a base. So this is a base. group is a base and the carboxyl group is an acid so they counteract each other so this whole part of the amino acid is neutral so we have to look at the R group to determine what the property is if it's an acid if it's a base if it's polar or non-polar so like I'm saying these are all non-polar because we're just looking at the R group and these have no polarity. There's no oxygen or anything, right? No electronegative atoms, mostly just hydrocarbons. Okay. So then if we look at a polar hydrophilic R group, these we're going to look at will mostly have oxygens, right? Or some kind of other electronegative atom like sulfur, like S or nitrogen N. Okay. So that's how we're going to represent a polar hydrophilic R group. We've got oxygen, oxygen, oxygen, like hydroxyl groups, OH groups, oxygen. And then this is the nitrogen for an amino group here. And this is a hydro group, which are electronegative atoms. So those can help create polarity. All right, so those are polar uncharged. And then how do we recognize acidic and basic? Well, we're going to recognize acidic and basic amino acids by if they have a carboxyl or if they have an amino group, because those are the two fung... functional groups in the R group. So not what's on the backbone. So if you look here at the acidic amino acids, those have carboxyl groups in the R group, right? And we just looked at this, how a carboxyl group has a negative. And anytime we see negative, we assume it's an acid, right? Because it kicked out, like I showed you before, it kicked out that proton and stole that electron, right? And so if it's kicking out a proton, it's making the environment more acidic. So this is an acid. So that's how we recognize those. And then the basic amino acids would be ones that are positively charged, right? So we've got positively charged amino groups because they were assuming that they picked up the proton, right? Lessened it from the environment. And that's why these are going to be the bases. Okay. So again, just be able to recognize it based on what the R group properties are. So for example, some nonpolar amino acids, glycine, alanine, valine, leucine, isoleucine. methionine, phenylalanine, tryptophan, proline. These mostly all have hydrocarbons in their R group, just carbon, carbon, carbon. And the polar amino acids, serine, threonine, cysteine, tyrosine, asparagine, glutamine. These have some kind of polar amino acid, polar atoms in their R group. So oxygen, these hydroxyl groups, right, the OH, OH, sulfhydryl, or the amino group down here. Okay. and then we have the acidic and basic amino acids and so the acidic amino acid we're looking for that carboxyl group in the R group so aspartic acid and glutamic acid and then basic would be lysine arginine histamine and that we're looking at the ionized amino group in the R group okay cool all right so definitely take some time to spend on looking at those so six asks why are these amino acids nonpolar so we saw those and we can say that because they contain hydrocarbons and hydrocarbons in the R group and hydrocarbons HCs are nonpolar Hopefully you remember that too, just based on like how, um, if you have a CH4 molecule, for example, that's built all from a non-polar covalent bond. Because if you remember back from chapter two, carbon and hydrogen have a very similar electronegativity. So when you're building a CH4, for example, CH4, when you're building that molecule that has all, um, non-polar covalent bonds amongst it, right? Cause it's the carbon and hydrogen have very similar electronegativity. So those are nonpolar. And then why are these uncharged polar? Because they have oxygen. Oxygen or another electro. negative electronegative atom in their R group. Okay, and then why are these amino acids charge acidic or basic? So acids have the carboxyl. in their R group and they are negatively charged and basic have and amino in their R group and they are positively charged. Okay, awesome. So hopefully that, again, wasn't too difficult to look at the differences between polar, nonpolar, acidic, and basic. And then another just side note here, what is the difference between essential amino acids and non-essential amino acids? And I know you guys have probably heard of this too, especially with like dietary considerations. So Essential amino acids are amino acids that we don't make in our bodies, in our cells. So these are the amino acids that we need to actually consume in a diet. That's why they're considered essential amino acids. So some examples of those are histamine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. And like I said, these are going to be ones that we're going to have to consume within our diet because we don't create them. So that's why they're called essential. So we'll get this from eating like different types of meats. and other proteins and things like that that are going to be in other organisms that we eat, other organic matter. And then non-essential amino acids are amino acids that we do create within our own bodies and our own cells. So we don't have to consume those within a diet because we're going to get those. All right. So then you don't have to memorize what these are, just know the difference between essential and non-essential amino acids. So essential amino acids we don't create. and need to get from our diet. Okay. All right. So now that we know what makes up a protein, and those are the amino acids, and we looked at the different types of amino acids, now we're going to look at how amino acids come together to form a protein. Okay. So we already looked and we said that the type of bond that amino acids link to make a protein, they're called peptide bonds, and we know that they're covalent. So the bond... between amino acids are called peptide bonds and they are covalent types of bonds and then that's why they're called and I had on that other table that's why they're called polypeptides proteins another word for polypeptide another word for protein is polypeptide because proteins are built from all of these peptide bonds so they're called polypeptides all right so let's see if you're able to draw out a reaction or like a linkage between two glycine and amino acids. So if you want to take a second to pause and try to draw out two glycines, and then we'll see how they link in the next picture. So this is showing you how two amino acids come together to form a protein. And they link through something called dehydration synthesis or dehydration reactions. So we're going to see here in a second as well. And actually, let me skip ahead to this real quick before we look at this amino acid one. So all the monomers that we're going to look at today. they all leak into polymers via dehydration so dehydration is the loss of water right when you're dehydrated in whose water so when you're linking monomers into a polymer that all comes from dehydration so this is going to be the same thing when we link lipids here now like fatty acids into lipids when we're linking monosaccharides with little sugars into polysaccharide carbohydrates when we're linking nucleotides into nucleic acids like DNA RNA and then also when we're linking amino acids into proteins. This is all going to be by dehydration synthesis. Okay, so you're going to see that we're going to remove a hydroxyl group from one monomer and a hydrogen group from another monomer. That's going to lose the water and then they're going to come together. So this is dehydration synthesis. Now the opposite of that, how do we break apart a polymer into the individual monomers? So this is something called catabolism, like breakdown reactions, which we'll talk about in a minute. talk about in future chapters. This is called anabolism when we start to build things. So anabolic reactions are building, right? So the opposite of that is catabolic. So how do we break something down? Well, if dehydration, the loss of water links monomer into polymer, well then obviously if we add back water, we can break a polymer into individual monomers. And this is called hydrolysis or hydrolysis. It's using water to lyse something. Lysing is like to break up. so hydrolysis or hydrolysis will break it up okay so hopefully you kind of picked up on that um and then i have that let's go back to the follow-along guide real quick before we do the peptide bond so what type of reactions joins monomers into polymers and that is dehydration dehydration reactions and what type of reaction breaks polymers into monomers that's hydrolysis okay all right so let's take a look at how we are building that peptide bond okay so if we have one amino acid here and one amino acid here. Hopefully you can recognize that, right? Because again, this is an amino acid. So we've got that central carbon. We've got a carboxyl group. We have an amino group. We have a hydrogen and then an R group, right? And this is the same thing. Amino group. group, carboxyl, carbon, central carbon, hydrogen, and another R group. So this is just two different amino acids. So how they're going to come together to form a peptide bond, they are going to have a dehydration reaction. So we're going to lose a hydroxyl, an OH group from a carboxyl group. So losing the OH from a carboxyl and the hydrogen from an amino, and that is going to take out a water and that's going to bring this carbon, this carbon and this nitrogen together. And that's a peptide bond. bond. Okay. And that's just going to keep happening over and over and over and over and over and over and over again until you have something called a polypeptide. Polypeptide is just a protein, another name for protein that just has all of these peptide bonds throughout it. Okay. And if we look here, we're always going to have a free, like a carbon, like a free C end, which is going to end up being called our C terminus, our carboxyl terminus, because that's a free carboxyl group. And then we have a free N terminus, which is our amino group. the free amino group. So when these all come together, this is when we're ultimately going to get a protein and proteins can have, you know, a few amino acids or they can have hundreds of thousands of amino acids. So this is where we're going to see like the differences in the protein structure. Okay. So then what type of bond is depicted in the image below? Obviously, because the only type of bond we've looked at so far is going to be a peptide bond. And so again, we're looking here, the loss of a hydroxyl through the carboxyl and the fibrin. hydrogen through the amino, take out that water, which is H2O, right? And we lose that water. So it's a type of peptide bond. Okay. So if you want to take a second to, you know, pause the video and then go ahead and draw out, um, what type of bond links it to draw up a peptide bond between two glycine amino acids. So what type of bonds, this is called a peptide bond. peptide bonds and draw out a peptide bond which into glycines and then what is meant by the C terminus and the N terminus of a protein so the C terminus is going to be this the carboxyl and the N terminus going to be this one so that's just the free C and the free N okay and then we said what type of bond we already did that we already did this okay cool so very interesting question here if maltose if maltose is a disaccharide okay so two and this is like we're talking about sugar i mean i just put this example here now even though we're talking about amino acids right now we're still just talking about the general reactions that link monomers into polymers so let's say that we're talking about sugars instead maltose is a disaccharide which means it's composed of two sugars formed by joining two glucose molecules glucoses are single monosaccharides or single monomers what would be the molecular formula of maltose Well, if you remember, we've talked about this a little bit so far, the molecular formula for glucose is C6H12O6. Okay. So if we have two of these and they come together to form maltose, what would be our molecular formula? So everybody like right off the bat, they think, okay, well we'll just double it. So it'll be C12H24O12. Okay. But that's not correct because remember when we link monomers into polymers, we have to take out water. So the answer is actually B because we have C times 2, which is 12, and then we have H times 2, which is 24, but we have to remove the minus and H2O. Okay, so then that would be H22 because we took out two hydrogens from the 24, and then O would be 12. because we doubled that, but we took out one oxygen. So our answer will be B. All right. So that was an old test question. You may see it again. So just make sure that, um, you are understanding that one. Okay. And then let's look over lastly, our protein folding. And then I'm going to show you guys a cool video on proteins and how all this folding works and the combination. So now that we have built a, um, We built a polypeptide chain, which is this, right? So we talked about how, I mean, what the amino acids are, what the different properties are, how we can link two amino acids via peptide bonds, and how we can keep linking those all together to form a polypeptide. Now let's look at the hierarchy of folding of a protein, like all of this fun stuff. Like how do we get from just a simple amino acid to this crazy complex protein? So proteins, once they form, they are going to be able to take four different... levels of folding, four different levels of structure. Okay. And so proteins undergo complex folding as they produce, um, as they're produced, what guides the protein folding. If you think about it, it's going to be the R groups because the R groups are going to be the variable groups. So if a amino acid has a lot of like polar amino acids or non-polar amino acids, those are going to all kind of like facilitate how a protein folds. Because remember like protein non-polar, non-polar has to. associate. Polar to polar has to associate. You can't have non-polar and polar associating, right? Because they don't mix. It's like oil and water, right? So that R group is going to be what facilitates that folding. And there's four different levels of folding we're going to look at. So primary, secondary, tertiary, and quaternary, okay? Primary, secondary, and tertiary all have to do with how a... single polypeptide fold. So think about a polypeptide as kind of like a ribbon, right? It's how we're going to like start to visualize this. And if we were in class, I would show you, like I'd bring a ribbon or something and show you how the whole, the folding works. So think about this as a whole ribbon, like something. we wrap a present with. Okay. So the primary, secondary, and tertiary are all going to be how we fold an individual polypeptide. An individual polypeptide can be thought of as like one of these little ribbons. And the quaternary structure, that fourth type, is when we have two or more ribbons, individual ribbons or individual polypeptides come together. Okay. So let's look and see how these folds all work. Okay. So primary, secondary, tertiary, and quaternary. So our primary structure is... is our basic structure of a protein. And this is essentially just a polypeptide chain. It's just a chain of amino acids, all that were linked together by the peptide bonds. So that's just the primary structure, just a sequence of amino acids. Okay. And like we said before, based on the R groups, those are going to facilitate and like influence how this whole thing folds in the end based on those different properties of what R groups are involved. Okay. So that's our primary structure. Okay. So we did this one and we... We already answered this question too, so this would be C12H22O11. All right, and then what are the four levels of protein folding? We're going to look at that now. So we've got primary, secondary, tertiary. Okay, so let's look through all of these and we'll go through all the different levels. Alright, so what determines the... Okay, maybe we can go back and answer these questions at the end. Yeah, we'll wait. that one to the table first okay so let's look at the primary structure so we already said primary structure is just a chain of amino acids okay so with that information in mind what type of bonds then are involved in the primary structure well what links amino acids into that polypeptide. That is peptide bonds. So those are the type of bonds that are involved here. And then what structures are formed? Just a single polypeptide gene. And then we can say an example, we'll just say a single chain, single chain protein. So I remember a protein can be very diverse. So like a protein could just be one of these single chains that you're looking at here, or it could be like a whole complex ribbon structure with multiple chains attached. Okay, so that's our primary structure. Simple enough. Now, where does the primary structure come from? And this is kind of like getting a little bit ahead of ourselves, but we'll spend a lot of time later on in the chapter, later on chapters about this. Our primary structure. structure of proteins where that information comes from, comes from our genes, our genome. So we're going to spend lots of time on the flow of information. Remember that DNA goes to RNA and RNA goes to protein, right? We talked about that in chapter one, that was the process of transcription and then translation. So how do we know what kind of protein to create? How do we know what kind of amino acids we have to incorporate? Well, that all comes from our genes, right? Because remember, proteins are going to be like what carries out all of our genetic information. Like our genetic information, like our library. I got letters. And then from those genes, we're going to write stories and books, etc. And that's how our bodies are going to run. That's how our cells are going to run. So our DNA is in the nucleus, and that makes a copy of RNA. And then RNA comes out to the ribosome, and the ribosome then translates. that information to make protein. So that's where that information comes from. So it's all determined from our DNA. Okay. And then primary structure and protein structure is going to be very sensitive to any kind of errors. So this is... is a crazy example here, that even a single amino acid change, right? So let's say that we've got this whole sequence of amino acids that are building the protein. If we change one of these little amino acids, it could have a disastrous effect. And I know you guys are like, what? How can that be? It is very true. So we can have single mutations, which are single changes in the DNA that affect even one amino acid, and that can have a disastrous effect. So a crazy example of that. That is with sickle cell anemia. Sickle cell is a disease that distorts our red blood cells. And it's because the hemoglobin, which is the protein that carries oxygen within our red blood cells, becomes slightly deformed from one single amino acid change. And look at what happens where you get these sickled red blood cells versus our normal red blood cells that appear like this. And this has disastrous effects because these red blood cells, because they're structured differently, they can't move around the body the same. They can't come. kind of squeeze through blood vessels, et cetera. And they give a whole array of crazy symptoms from this. And that's all from one single change. So that's why it's so important to make sure that when we're decoding our DNA to make RNA and RNA is being decoded to make protein, that it is like imperative that we are doing this correctly. Okay. So that is our primary structure. And then moving beyond our primary structure, which is our chain of amino acids, how do we get even more folded beyond that? So next... is our secondary structure and our secondary structure is built through hydrogen bonds that appear at regular intervals along the polypeptide chain so here you can see where the hydrogen bonds are forming so for example this is a hydrogen bond remember it's like dash dash dash if you have like the little dashes that represents hydrogen bonds so here you've got a hydrogen bond that appears between an amino group and a carboxyl group an amino group or carboxyl group for example example here we have an amino group and a carboxyl group so this is going to happen amongst the backbone right so not those are groups this is going to be between those carboxyl and amino group on the backbone of an amino acid and from this you get two different structures that can form based on how they interact or how those hydrogen bonds are formed so you can either have a helix formed something called an alpha helix like this it's kind of like a helical structure like a twisted ribbon or you can have have a sheet-like structure where they form these little kinks. It's kind of like a little accordion or like if you fold up a piece of paper and then like unravel it, it forms this little kink structure. So you got alpha helix or beta sheet are two different types of secondary structure. Okay. So secondary structure, the type of bonds, these are going to be hydrogen. Hydrogen bonds. And then what are the types of structures that are formed? They can either be an alpha helix or a beta pleated sheet. Okay. And then, for example, we can say even though this is like, I mean, we'll just say an alpha helix. Alpha helix, similar to DNA double helix or DNA helix, right? Even though DNA is a different type of monomer polymer, it's made of nucleotides and nucleic acids, we can still kind of think about it as like that little helical structure. And hydrogen bonds build these. So hydrogen bonds build secondary structure. And remember, we talked about hydrogen bonds individually being very, very weak. But... cumulatively they are super strong so what's crazy about this is spider silk which i should use an example before about that are built from proteins spider silk is a protein that spiders secrete and it is a secondary structure of proteins and it's built from those hydrogen bonds so it is super super strong uh they even say that spider silk is obviously like stronger than steel it's like one of the stronger substances that we've discovered on the planet um they even like have created like um like kevlar like um uh suiting out of this material because it's just really really strong bulletproof etc so it's just a really really strong substance because it's built from those hydrogen bonds All right, so that is our secondary structure where we start to form the alpha helix and beta pleat sheets. And then our tertiary structure is when we're just getting even more folded down. And that is going to now be between the R groups of the amino acids. So tertiary is between the R groups. Remember, primary is just the peptide bonds. Secondary is hydrogen bonds between the backbone. And now we're going to make bonds between the R groups of the amino acids. So because the R groups are so diverse, remember we've got polar, non-polar, acidic, basic R groups, they can build a whole array of different types of bonds in a tertiary structure. So we can have hydrogen bonding, we can have ionic bonding, we can have hydrophobic or non-polar interactions. So we can have all different kinds. We can even have those disulfide bonds build between the sulfhydryl groups. Remember we talked about that back in the macromolecule chapter, when we're looking at the different types of R groups and functional groups and how sulfide... hydra, the SH group, remember it builds those SS bonds which are involved in stabilizing proteins. So that's where we would see that type of bond here. So tertiary can build all different types of bonds based on the R group interactions. So if we're looking here at a tertiary structure, so this whole ribbon here would be just the peptides, the peptide bonds of the amino acids. Then that folds on itself to make secondary structures. We've got helixes here. V-List ECR, V-List ECR, and then a beta sheet. And then tertiary is when it just kind of all collapses and like holds on itself. So that would be tertiary structure. Okay, so let's go ahead and do our thing. So tertiary structure, what types of bonds are involved, all types between the R groups. R groups. amino acid. Okay and then what structures are formed? We have all types of 3D structures. An example we can even say like 3D globular proteins. So now let's look at quaternary structures. So the next type is quaternary. And quaternary is when we have two or more polypeptides associating, so two or more chains associating. So we have two examples here. I've shown you collagen. So collagen is... formed from three helices, which are the secondary structure coming together to form collagen. So we have a triple helix, but that would be a quaternary structure because we have two or more chains associating. And then hemoglobin is a globular protein. and this is built from four different subunits. Okay, so four different subunits come together, so that's a globular protein. So you can see that these are both quaternary because we have more than two chains associating. And it's interesting to also note that the final shape determines its function. So we said before that the R group is going to determine how it will ultimately fold on itself based on those different properties of the R group, polar, nonpolar, acidic, basic, but the final shape is going to determine how it functions. So for example, think about how collagen functions. So collagen, we said, is a protein that makes up the connective tissue, right? Which is out front of our cells. It's something called the extracellular matrix. And collagen is involved in preventing our skin, our tissue from ripping, right? So it makes sense that it kind of has this rope-like structure to resist that pulling. Hemoglobin, on the other hand, hemoglobin is the protein that carries oxygen on our red blood cells. And that has to squeeze down right on our red blood cells as our blood. It goes to the body for the vessels and everything. So that has to have, obviously, a globular shape like this, right? It makes more sense as opposed to having a shape like this. So that's where the final shape determines the function. And so here we've got a quaternary structure where it's just kind of all folding on itself. And even though it's only showing, it looks like it may only be showing one chain here, or maybe this is the second chain. I don't know, but it has to be two or more chains that are associating. And then we have the four different levels of protein. structure right there. Okay, all right, so let's fill out our table. So our quaternary structure here is going to be what type of bonds are involved here. These are going to be interactions. interactions between two or more polypeptide chains. Okay, and what types of structures are formed? Two plus. chain structures and so for example here I had collagen example is a triple helix And then there was a couple other questions we had here. What determines the primary structure of a protein? And that was from our DNA. Remember, because the DNA is what tells us what amino acids are going to be incorporated in that primary structure. So primary structure is going to be our DNA. And then what level of protein folding determines the final confirmation of a protein? This is going to be our primary. And if we think about that, what level of protein folding determines the final confirmation? this is our primary structure because remember the primary structure is the sequence of amino acids so based on the properties of those amino acids it's going to tell that protein how to ultimately fold in the end right and then what level of protein folding determines the final function of a protein that is going to be the last level last or the highest level for example the quaternary ...structure. Okay, and then you've got review here. Alright, cool. And I think I have a couple questions here. Alright, so sickle cell disease is caused by a mutation in the hemoglobin gene that changes the charged amino acid, glutamic acid. which is a charged acidic amino acid, to valine, which is a hydrophobic or non-polar amino acid, where in the protein would you expect to find glutamic acid? So glutamic acid is a polar acidic amino acid. So where would we want to find it? find that. So normally, I know I haven't mentioned this to you guys, but normally we are going to want to find any type of polar acid, basic, et cetera, amino acid. We're going to want to find those on the surface of a protein because they're going to interact with the water that's in the environment. And we're mostly going to find non-polar amino acids, hydrophobic amino acids embedded within a protein because those are going to want to avoid contact with water. So that's where we would find that one. And then one more question here, what would be the consequence of... changing one amino acid and a protein containing or consisting of 325 amino acids. So if we just changed one amino acid, what would be the effect of that? Okay. So I've got here, I believe it's all A, B, and C are correct. And the reason is because look at these answers. So the primary structure of a protein would be changed. That is definitely true because if we change one amino acid, we're changing the primary structure. Primary structure is just a sequence of amino acids. So that changes. The tertiary... structure of a protein might be changed. So that's also true because remember the tertiary is like that last level of folding on the one chain. So I'm saying here that it might change. And the reason that it might change, because we've got to think about what type of amino acid it's changing to. So what about if it's a polar amino acid and it changes to another polar amino acid, those polar amino acids are still going to react the same way with the environment. So that may not have a drastic effect. But if you change like a polar amino acid to a non polar amino acid, that's mostly going to have like a more significant effect on the overall structure of the protein. So that's why it might change it. Okay. And then the biological activity or function of the protein might be altered. And that's the same kind of thing we can think about in answer B. Because again, if that amino acid changes in drastic, like let's say like, let's check it out, right? Let's go back up here and let's say that we changed the amino acid and let's say that it was glycine. And then. then it somehow changed to alanine. Well, both of these are nonpolar amino acids and they just have one little R group different. But overall, remember we said that the R group leads to how these amino acids function. So mostly these are going to function the same exact way. So that may not have an effect on the protein if we change it from alanine, from glycine to alanine. But what about if we change it from glycine now to aspartic acid, right? Which is an acidic group. This is definitely has a totally different property. So that's mostly going to change the type of protein that... like is created from this mutation. And that's going to have like a different effect, um, on how it interacts in the environment. So that's why I said here that it may alter, it may alter the biological activity. Okay. All right. And then the last part of protein, before we move into nucleic acids is what is protein denaturation. So proteins are very sensitive to their environment. Um, so they can be easily denatured if they come into an environment that they're not accustomed to being in. So very, very sensitive. So for example, temperature extremes, like if an environment is really too hot or too cold, or if the environment is too acidic or too basic, the protein can fall apart. And this is called denaturation. And denaturation is the falling apart of a protein and it falls apart from the highest level of conformation. So if it has a quaternary structure, that's going to unravel. And then the tertiary structure, think about like a bow or... ribbon that you've tied around a present. Right? You're going to unravel, you're going to take out the bow, and then you're going to like try to stretch out the little kinks that you've made in it, right? So that is what denaturation is. It's like you're breaking up a protein from the highest level. So quaternary comes first. and then tertiary would be broken down or kind of unraveled and secondary would unravel you just kind of unraveling all those um folds that you've created the primary structure is not going to be affected by denaturation right how are we going to break up primary structure, you're going to have to do hydrolysis. Remember hydrolysis is how we break up amino acids. We add back in water. So that's how we would actually break up a primary structure of a protein. Okay. So with that in mind, this is another old test question. A good question. I like your egg whites consists primarily of a protein called ovobumen or albumin. When you heat an egg and the proteins are denatured and the egg white turns from clear to white, which is what happens. happens when we eat egg, right? Which level of protein structure do you expect to be least affected by protein denaturation? And that's what we just looked at. So the least affected would be your primary structure, right? Because you're going to unravel in the quaternary and you'll unravel tertiary and secondary. And then primary structure would be the one that is least affected by all this. Okay. So what is protein denaturation? So protein denaturation is unraveling. Unraveling. protein from the highest level down to basic level and then primary structure is not affected and would need hydrolysis to break down Primary. Okay. And then what are chaperone proteins and what are x-ray crystallography? I'm going to get to that in a second. And then what level of protein structure is least affected? We said primary. Primary. Okay. And we will see this quite a bit throughout the semester, how we'll talk about, we're actually going to do like a lab based on this, about denaturing proteins. Like if we take a different type of enzyme or proteins and we put them in boiling water or ice, are they going to function the same way as they should? should under normal circumstances like room temperature or body temperature. So these last two things that I had on here, just real briefly, I don't want to really get into this really right now because we're going to talk about this in one of the later chapters. So this is chaperone protein. Polyproteins are other proteins that can help fold a protein. If it's become denatured, you can see that you can put the polypeptide chain in there and it can help correct it folds. These are called chaperone proteins. So chaperone proteins are proteins that help other proteins fold, or they can even help them unfold or they can keep them unfolded. So that's what a chaperone protein is. There's a process called x-ray crystallography or x-ray diffraction. It's basically taking x-rays. You can crystallize a protein. protein that you've extracted from cells and then you can run x-rays and then that's how you're able to see the structure of proteins based on their x-rays so this is called x-ray crystallography and that's how we have been able to image different types of proteins within cells so this is showing you here like an antibody protein and then protein from the flu virus they were actually just doing this with coronavirus and saw quite a few of these x-ray crystallography images of the proteins that make up the spikes on the coronavirus and the surface of the coronavirus that help it attach onto the human cells. And that's the same kind of thing you'd be like almost looking at here, like if we're looking at a flu virus and they're talking about proteins and how that would interact with an antibody. Remember, antibodies are things, proteins that our body produces to fight it off. So it's kind of like this lock and key mechanism where they have to be able to bind to each other. So that's something that you'd be able to see by doing these x-rays of proteins. Okay, and then the prion. I added in here too, because I know I took it out of chapter one and told you we're going to come back to it. So prions are interesting. And if we were in class, I would have, um, usually have one of the groups do their group project on prions. So prions were a discovery, um, of an infectious type of protein and they cause some diseases that you may have heard of, uh, like the transmissible spongy form encephalopathy diseases, like scrapey, mad cow disease, Q-Ru, cretz-vom-yuck-a, and these are infectious proteins. And this is pretty wild because we normally don't think about proteins being able to be infectious. When you think about something that's able to be infectious, we think about a virus or a bacteria or a fungi or something like that, right? We don't think about, you know, proteins being able to be infectious because proteins has no genetic material, right? It can't replicate on its own. Where do we get a protein from that comes from the genetic information? Transcription translation. You have DNA. It makes a protein, right? Protein should not be able to replicate. But it was discovered that proteins, these prions, which are infectious proteins, they are able, like actually able to replicate. So what happens is somehow in the body, you either like spontaneously produce this abnormal protein or you get it by ingesting something that's how people were getting it from like eating um infected mad cow disease or kuru um was found in some like aborigine tribes where they were like eating their cannibals and they were eating the brains of people and they were getting this disease. So this comes from you're either consuming it or it's just spontaneously being created in the body. And it's when you have a normal protein, this protein called PRPC, and it converts to this protein called PRPSC, stands for scrapy protein. And this is an abnormal protein. And what's wild about this is this protein is able to attach to other proteins and convert them from being a normal version to an abnormal version. So you end up getting these aggregates of abnormal protein, like these lesions in the brain from abnormal accumulations of these PRP proteins. And that's how these people who get these, they kind of get these plaques and they kind of go crazy. They get dementia from this. It's like almost like Alzheimer's or dementia where you end up getting these like lesions in the brain that, you know, make you kind of go crazy. It affects your memory. So it's pretty wild because like I said, you know, protein should not be able to transform other proteins to become. abnormal, right? Because proteins are all created from the DNA. So this is like defying like the hierarchy or the central dogma of molecular biology. So it's just pretty wild how prions work as an infectious agent. Okay. So that is everything about proteins. All right. So let's watch this little video on protein structure and proteins in general, and then we will move on to our next macromolecule, which is nucleic acids. All right. So here's the seven. minute video on proteins. We all have things that challenge us and for me it is folding. Sheets, towels, shirts. Let's just say I invest a lot in anti wrinkle laundry spray. Amazing invention. My issue with folding extends to paper too. I know foldables in the classroom can be a powerful way to organize concepts but for me it was the actual folding part that I tended to get stuck on. You may think of folding as a convenience of a way to take something and make it more organized. or condensed so it doesn't have to take up so much space. This is true. But in biology, folding can actually have a lot to do with function. We've mentioned how amazing proteins are. They can play so many roles. They can make up channels, be part of a structure, serve as enzymes for important biological processes, be involved in protecting the body, just to name a few. We've also mentioned that you are making proteins all the time in a process known as protein synthesis. But But the conclusion of producing a long chain of amino acids doesn't necessarily equal a functional protein. There are modifications to a protein that often need to happen in order for it to be functional. By modifications, we can mean many things. It might be adding certain chemical groups, such as phosphorylation, something to definitely explore. But another important event to make a functional protein is, believe it or not, folding. But before we get into protein folding, let's talk about shape and why it should be done. shape is so important. Shape and function in biology frequently go hand in hand. In our cell signaling video, we mentioned how protein receptors and the signal molecules that bind them can fit together so perfectly to start some type of cellular response. Or in our enzyme video, we talk about how enzymes, which are frequently proteins, have a very specific shape for the substrates if they build up or break down. When we talk about the way proteins are folded, we need to understand that the way proteins are folded is very important. the different levels of protein structure because there are different ways of folding that can happen in the different structural levels. The first level of protein structure is primary structure. This is the sequence of amino acids that make up a protein. Amino acids are the monomer, which means the building block, of a protein. They are held together by peptide bonds. In protein synthesis, amino acids are added to form a polypeptide chain and proteins are made of one more of these polypeptide chains. Genes, which are made of DNA, determine the order and number of these amino acids. That sequence is critical to the protein's structure and function. In our mutations video, we talk about how one amino acid can be changed in sickle cell disease. Even a single change of an amino acid has the potential to affect a protein's function. We do want to point out each amino acid has a carboxyl group, an amino group, and an R group. And our group is also called a side chain. So even though we have them drawn here like a chain of circles, realize that each of these circles we're drawing is an amino acid like this. Next we move on to secondary structure. Folding is really going to start to happen. In secondary structure, the sequence of amino acids that we mentioned in primary structure can fold in different ways. The most common ways are the alpha helix and the beta pleated sheet. And which one of those foldings the protein does depends on the amino acid arrangement it has. Both of these shapes shapes are due largely in part to hydrogen bonds. Those hydrogen bonds can occur at specific areas of the protein's amino acids. Specifically, these are hydrogen bonds involving the backbone of the amino acid structure. On to tertiary structure. This is looking at more folding that occurs in the 3D shape of a functional protein. And a lot of this is due to something we haven't mentioned much, the R groups, also called side chains. See, the amino group and the carboxyl group are generally standard parts of an amino acid. acid, although the R group found in amino acids can vary among different amino acids. That means the R group can define the amino acid and can make amino acids behave a certain way. For example, some R groups are hydrophilic. They like water. Some R groups are hydrophobic. They don't. And remember that proteins contain many amino acids, which can contain different R groups, and so different areas of the protein can therefore be impacted based on those R groups. When protein is going on, amino acids with hydrophilic R groups may hang out on the outside, while hydrophobic R groups, where are they? They might hang out at the inside part of the protein. The 3D shape is due to other interactions besides hydrophobic interactions. Ionic bonds, van der Waals interactions, disulfide bonds, and hydrogen bonds, all involving the R groups, can influence the folding occurring in tertiary structure. Something to explore. Now when we've been talking about a protein, we've been talking about about a polypeptide chain that has been folded into a functional protein. But proteins can be made of one or more polypeptide chains. And in quaternary structure, you are looking at a protein consisting of more than one polypeptide chain. Each of these polypeptide chains can be a subunit and interactions between them, such as hydrogen bonds or disulfide bonds, can keep them together. Going back to folding, I know what you might be thinking. Who's doing this folding anyway? Are the proteins just folding themselves? Well, the interactions mentioned, like hydrogen bonds and R-group interactions, are occurring depending on the protein's own amino acids, one reason why amino acid sequences are very important for protein function. But folding is far more complex than that, and there can be intermediate steps involved when a protein is folding. In fact, there's a phrase you can search called the protein folding problem to learn more about the questions scientists continue to explore regarding protein folding. And the research has shown that proteins often have help in the folding process. Chaperonins, for example, are proteins that can help with the folding process. They have almost a barrel shape. Proteins go into them and the chaperonin tends to have an environment that is ideal for the proteins folding and this can help the protein be folded correctly so it's functional. Just wish I had something like that for my towels. All of these interactions we mentioned in primary, secondary, tertiary, and quaternary structure are paramount for a mature protein to have its correct shape so it can carry out its function. And that's very relevant. There are many diseases that are related to protein misfoldings. Check out some of our further reading suggestions in the description about that. One last thing we haven't mentioned. Each protein has an ideal environment for functioning, which might include a certain temperature or pH range. If the protein is exposed to something outside of its ideal temperature or pH range, exposed to high heat, for example, you can disrupt the interactions that we had talked about taking place. place at the different structural levels. This can denature the protein, which disrupts its shape. This prevents it from functioning correctly, and depending on what caused it to be denatured, sometimes you are interfering with many levels of protein structure. Sometimes it's just one or two levels. Sometimes denaturing a protein may be reversible, but in many other cases, it's not. The environment that a protein is in definitely matters for its functioning. Well, So that's it for the Amino Sisters and we remind you to stay curious. Awesome. All right. Fun video. Okay. So hopefully that was helpful to review everything we learned about proteins so far and what they're made up of, the amino acids and how they come together and all the different levels of folding and why that is so essential. All right. So moving on to our next type of mapper molecule. this is going to be nucleic acids. So what do we know about nucleic acids? If you want to take a second to consider what you know about nucleic acids, what they are built up from, or how they function in the cell. So first let's look at the functions of nucleic acids. So function of nucleic acids, they function as storage and genetic transfer. So genetic storage and genetic transfer. And this is what is going to ultimately lead us to how we build our proteins because remember like we said that the dna is like our bible or library right it contains all of our genes for making proteins and then proteins are going to come together to build our life and run our life etc run ourselves so it's all going to to be like stored in that genetic information as is DNA. All right. So what is the function of DNA? Genetic storage and genetic transfer. And there's different types of nucleic acids. We have DNA and RNA, for example, and the DNA is going to be the genetic storage and the genetic transfer is going to be in forms of like RNA and also tRNA. Okay. So onto nucleic acid, what are the functions of nucleic acids? Genetic. storage and genetic transfer. All right, so let's look at the different types of nucleic acids and what they're built up of. So there are two types of nucleic acids, and they are DNA and RNA. They stand for deoxyribonucleic acid and ribonucleic acid. So those are two different types. deoxyribonucleic acid DNA and ribonucleic acid RNA. So two types of nucleic acids, DNA and RNA. All right. So what are the monomers that build nucleic acids? These are are called nucleotides. So nucleotides are the little building blocks that build nucleic acids. So just like amino acids with the little monomers that came together to build proteins, nucleotides build nucleic acids. Okay, so what is our monomer? These are called nucleotides. So what are nucleotides built up of? Just like we looked at what an amino acid is built up and have the carboxyl, the amino group, the central carbon, the hydrogen, and the R group. Um, you know, um, nucleotides are also built up of different components. So nucleotide is built up of three different components. We have a nitrogenous base. This is like ATCG, which I'm sure you've heard of. We've got a sugar. The sugar specifically is a pentose or a five carbon sugar and it's either ribose or deoxyribose. That's where we get deoxyribo or ribo. And then we've got a phosphate group. So those are the three different components of a nucleotide. So what monomers build up nucleotides what are the three components of a nucleotide they are a phosphate group phosphate group we have a nitrogenous nitrogenous base so that's either a t a t c g or u and we've got a sugar pentose pentose is five so pentose is five and anything that ends in ose is going to be a sugar you'll see that as we move through the semester. So pentose sugar, and that could either be deoxyribose or ribose. Okay. And then take a second, if you want to pause this and try to draw out the structure of a nucleotide, or at least take a look at it down here. Here's the structure of a nucleotide. You want to be able to draw that out just like you drew out the amino acid. All right. So now looking at the different components of a nucleotide, like we said, the pentose sugar. can either be ribose, which is an RNA, or deoxyribose. And I'm going to show you how to recognize the difference between deoxyribose and ribose. And the nitrogenous bases can be either the purines, which are going to be double ringed. They have nitrogen and carbon bases, and they're either going to be purines, which are adenine and guanine, or pyrimidines, which have one single ring, and that's cytosine, thymine, or uracil. We only find thymine in DNA, and we find uracil in RNA. RNA. And we'll look at the base pairing rules here in a second. Okay. So let's take a look here. This is going to be really, really important stuff. I'm looking at this. This is going to be a really important slide. Take a look at this nucleotides. So here's our nucleotide. That's our little monomer that builds up a nucleic acid polymer. So this is a polynucleotide, just like we looked at like polypeptides that built amino acids into protein. This is a polynucleotide. Nucleotide. all come together to form the polymer nucleic acid. So a nucleotide is built up of those three things that we just looked at. First is a phosphate group. The phosphate group is going to be the same whether it's any kind of nucleic acid. Okay, so phosphate group is all the same. And this is that same phosphate group that you saw as a functional group back in the chapter four, previous chapter, it's one of those functional groups. So it's a phosphorus in the middle and then has those four oxygens and then two negative charges. So PO4 minus two. Okay, then you can have a pinto sugar And the pentose sugar is either going to be a deoxyribose if it's in DNA or a ribose in RNA. And how we're going to look at the difference is deoxyribose is missing an oxygen group. That's why it's called deoxy. And we count the carbons on a sugar from this first carbon on the right that's attached to the base. So if we look here at this pentose, right, this is a five-carbon sugar. That's what these things are here, this and this. This carbon here. is the first carbon. It's the one that's attached to the base. So one, two, three, four, five. This is an oxygen group here. So the fifth carbon is off of the ring. So one, two, three, four, five. And to identify if it's a deoxyribose or a ribose, DNA is deoxyribose. It's missing one oxygen. So you look at the two carbon. If it doesn't have an oxygen there and just has a hydrogen as opposed to the hydroxyl group, it's deoxyribose. And if it has that oxygen here, it's ribose. Okay, so you find ribose in RNA and deoxyribose in DNA. That's how you identify the sugar. And the base is this orange or yellow looking thing over here. And then we've got two different types of bases. So the base is a nitrogenous base. It's very heavy with carbon and nitrogen all around the ring. And you can have double ringed bases or single ringed bases. The double ringed bases are called purines. And that will make up anemine and guanine. And the single ringed bases are called purines. called pyrimidines and it's a cytosine thymine or uracil and they're not a single ring um and we find dna will have thymine in it and rna has uracil so normally a pairs with t in dna but a would pair with u in rna and g and c always pair together so that's how we're looking at that so nucleotides a pairs with t or u if it's rna and gc pairs with g and we'll look at that um based on the base frame of like how you the double helix and then um the one other thing i wanted to show you how do you remember this there's a saying here called pure as gold and that's how we'll remember that the purines are adenine purines are adenine and guanine okay i'm taking off the i'm taking off the underlining so purines are adenine and guanine pure as gold so that's how you can remember um the difference between those two all right so let's look at here we'll fill out our components of our nucleotide. So what are our different types of bases? We can have adenine, A. We can have thymine, thymine, T. We can have guanine, G. We can have cytosine, and we can have uracil. Okay, and now are they purines or permidines? So remember the purines are the doubler. So adenine and guanine, pure as gold. So adenine is a purine, and then guanine is a purine. And then thymine is a pyrimidine. Pyrimidine. Cytosine is a pyrimidine. And uracil is a pyrimidine. Okay, and then do we find it in DNA, RNA, or both? So adenine, we find it in both. Thymine, we only find in DNA. Guanine, we find it in both. Cytosine, we find it in both. uracil we only find it in RNA. And then the sugars we said can either be deoxyribose or ribose. and deoxyribose we find in DNA and ribose we find in RNA and this remember is missing that two prime oxygen okay and then the phosphate group is just that p group and then it's the same same in DNA and RNA okay cool so definitely spend some time on the structure of the nucleotides hopefully that all makes sense easy enough again not hard just memorization right there's lots of information to memorize okay now let's take a look at some other aspects of the DNA and RNA molecules and then we'll move on to our next types of macromolecules okay so how are nucleotides built into nucleic acids so DNA you're going to see takes a double helix structure so it's always a double helix and RNA is just a single helix just one single strand now some reasons of that is thought to be it's either like the DNA or RNA, which came first, it's like the chicken or the egg. So that's a whole nother area of dispute. Um, But either way it is thought that you know the DNA remains in the nucleus of ourselves and that is like our Bible right? It holds all of our genes and genetic information So it's important that we have DNA is like a double strand because it acts as like a backup because you know that if you Have one strand that reads for example AAA, you know, the other strand is gonna read It's going to read TTT, right? So you know it's kind of like a backup because like if you know there's a mutation in one strand and all of a sudden that now reads like C-A-A-A, you knew it was supposed to read TTT and not C-A-A-A. gttt right so you know it like acts as a backup um rna is single stranded because rna does not need to replicate it's not it's just a transitory molecule so it's made off of our dna for going for purposes of making proteins, right? Like the messenger RNA, and then that goes in, it ends up being translated in the process of translation of the ribosome. So it's not as essential because if there's any kind of mutation or error made, it will either be destroyed as a piece of RNA in that process of like proofreading and assessing if that's all correct, or when the protein is produced and there's a malfunction in the protein, then it can also be destroyed. So it's more important that we make sure that our DNA remains intact and we don't have any mutations. Okay, so DNA... DNA is organized as double helix, RNA is organized as single helix, and then both types of RNA are connected in the same fashion. So remember when we looked at amino acids and those come together to form peptide bonds? DNA is constructed by nucleotides in something called a 5'to 3'fashion. So how this works is the 3'carbon of one sugar of a nucleotide is connected to the 5'carbon of the next sugar through a phosphate group. And the base is going to be attached. the one cut one prime carbon of the sugar and these are called phosphodiester bonds and they're covalent type of bonds so let's take a look at how that works okay so like we just said we're going to have this five prime to three prime association so if you see here this is a base this is a sugar and this is a phosphate group we know that this is dna first of all because it says like how do we know what type of nucleic acid is first it has t so we know that has to be dna because because RNA would have U, and it also is missing that oxygen here. So we know that this is a DNA molecule. Okay, so when we're looking at how they're connected, this is how they connect to the backbone. This is called a phosphodiester bond. And we've got the 3'attaching to a 5'through a phosphate. 3'to 5'through a phosphate, 3'to 5'through a phosphate. Do we see that? Right, so we're going to call carbon 1 here, so the one that's attached to the base. So 1, 2, 3, 4, 5. carbon is off the ring that is an oxygen group so this is a pentose so we've got the three prime attaching to the five prime through a phosphate three prime attaching to the five prime through a phosphate okay so that's a five prime to three prime connection when we look at the other strand let me kind of jump ahead here if we've got one strand that runs three prime to five prime to five prime to three prime because remember that DNA has two different strands we've got this one three prime prime, 3 prime to 5 prime, 3 prime to 5 prime. You see that the 3 prime carbon here is attached to the 5 carbon here through the phosphate group and the other strand you can see runs the other direction so the sugars are flipped so the sugars point upward in this strand and they point downward in the other strand. So here you would have the 3 prime here, or sorry the 5 prime here attached to the 3 prime here, 5 prime attached to the 3 prime, 5 prime attached to the 3 prime. So you're gonna have one going one direction and the other going the other direction. So one strand we say runs 5 to 3 and the other strand runs 3 to 5. So they're anti-parallel. One strand runs 5 to 3, one runs 3 to 5. And we know that this is a 5 prime end and this is a 3 prime end because you're just looking to see what end, what carbon is not attached. So here that's the 5 carbon, right? That's pointing upwards, that's the 5 end. And then here's the 3 end. Because remember we're numbering it like 1, 2, 3, 4, 5. those carbons. This fifth carbon is, that's just an oxygen, so the fifth carbon is off the ring. So that's the five end, that's the three end. If we look here, that's the three end, the three carbon, and that's the five carbon. So one is five to three, one is three to five. Okay, so that's how we structure our DNA molecule. So that's what we're looking at here. And then what are the base pairing rules? So we've got A pairs with T and G pairs with C. And there's two hydrogen bonds that connect between... between A and T and three hydrogen bonds that connect with G and C. That's gonna be important down the road when we talk about DNA replication, but we'll get to that later on. So if we look here, this is gonna be also an amazing, I'm gonna. Star this one because this is a really good structure to pay attention to One strand one strand we said double helix. We showed how the phosphodiester were connected in the backbone Now let's look at the sugars. So our not the sugar the bases the bases protrude inside strands inside the helix and we have A pairs with T and C pairs with G. G is C, A to T, right? So that is the base pairing rules. Now if we had RNA, RNA would pair A to U because there's no finding. we've got those hydrogen bondings in the middle. And the hydrogen bonds are in the middle because it's going to help rip this molecule apart and break it apart when the molecule has to replicate. We want to keep these as those strong covalent phosphodiester bonds. So this is how DNA replicates. DNA replicates in a semi-conservative manner, which we'll spend a whole chapter on. This is our original parent DNA molecule. The molecule separates by breaking the hydrogen bonds in the center and then new molecules come in and are created off of the old. strands that's why it's called semi-conservative because it's semi like the new strands are semi-conservative half old and half new so let's see if we have for reading our old strand and it says you know C C A G T T right we just match the new bases so new strand would be G and G and T and C and A and A etc so that's how DNA replicates okay all right and then I got a pick up line here I wish I was an adenine so I can get paired with you if you watch that show um big bang definitely hear wallow saying that all right so that is the base pairing rules and then just um to kind of jump ahead too i was going to show you here this is going to be something we'll look at with a experiment that watson and crick did in the 1950s and watson and crick if you have heard of them they're kind of like as famous as like gregor mendel and punnett squares and pea plants and genetics well watson and crick are the scientific team of scientists that went ahead and kind of described the whole structure of DNA and how DNA is structured and how DNA replicates. And part of the analysis that they did with some other scientists, they did some x-ray crystallography and x-rays of the DNA molecule. And they determined that the helix is two nanometers in width diameter. And to accommodate that, this proved the base pairing rules that A pairs of T and G pairs of C. Because if we remember back that adenine and guanine are double rings. and cytosine and thymine are the single rings. So to fit in a two nanometer double helix, you can only have a purine and a pyrimidine because two pyrimidines will be too small and two purines will be too big. So that was just a cool experiment. We'll get into that a little bit more in one of the later chapters with that to help prove the whole base pairing rules. All right, so that's that. We looked at DNA replication myths and then a couple of questions here and then we'll do the follow along. So a plant growing in phosphorus deficient soil would have a difficult time synthesizing what molecule. well obviously we're talking about nucleic acids so it would be nucleic acids and we also know that because the phosphate group so the only other type of macromolecule that we looked at was amino acids and hopefully you recognize that there is no phosphorus in any of the R groups definitely not in the backbone because that's just a carboxylin and amino group and there was no phosphate groups in any of the R groups of amino acids so they don't have phosphates but it is very important in DNA and RNA because we have that phosphate in the back backbone. Okay and then you arrive late to class, no and as you enter the room you hear me referring to 5 prime and 3 prime end of a molecule, immediately you know that I'm referring to what? And obviously we are talking about DNA so it would have to either be DNA or RNA in this case so it would be DNA and that is referring to 5 prime and 3 prime of how that backbone is connected. Alright so let's take a look I think that was it for the PowerPoint so let's look at follow along guide. out a double helix and indicate the following so if you want to just take a couple minutes and pause this lecture and just go ahead and try to draw out a phosphodiester bonds of a double helix of DNA or RNA and just identify all of these or if you want to even just try to identify them on here this let me see if I can actually See if I can move this up at least because I'm saying that I can even just kind of like go ahead and draw these out for you or like identify them. All right so the phosphodiester covalent bonds are going to be these so those are the phosphodiester bonds because they're facilitated through the phosphate group the five prime end and the three prime end so this is going to be a three prime this is going to be a three prime end because that's a three prime carbon and then this is going to be a five prime end because that's the five prime carbon right there a phosphate group hopefully you're following this is going to get messy a phosphate group is this thing right here a deoxyribose sugar is going to be that thing there's no ribose here because this is on DNA and not RNA and we know that because it's missing that little oxygen. It also has thymine and it's double-stranded. Okay, a purine is going to be the adenine and guanine. So this, for example, would be a purine. That would also be a purine and the pyrimidine would be a single ring. So that would be, no, let's see if that's a purine. This would be a... pyrimidine could be for example fine down there and then the hydrogen bonds are these things in the middle so that would be those hydrogen bonds right there all right so that's just really really ugly but hopefully you got the gist of that all right so those are all the different of the nucleic acids and then what are the base pairing rules we already said that so that is a to T and I'll do two little hydrogen bonds between that and then or to you and then And G will be 1, 1, 2, 3. G to C. My double bonds got ruined there. 1, 2. Okay. So there's the base pairing rules, and then you can explain how I did the Watson-Crick explanation of that. And then go ahead and label this activity here. So I'll let you guys go ahead and do that as well. Deoxyribose sugar. I'm going to avoid doing those lines again because it just gets really messy, but I'll help you point these out. So deoxyribose. Oxyribose sugar would be one of these. Phosphate group would be this. Nitrogenous base would be the ones in the middle. Hydrogen bonds would be the ones in the middle. Phosphodiester bond would be these bonds back here. This would be a five prime end. That would be a three prime end. Circle and label and nucleotide. This is one nucleotide right here that has a base, a sugar and a phosphate, and then fill in the remaining bases. So A to T, G to C, C to G. A to T. Okay. So then I would try, I would say to try that on your own and then listen to how I just described that. And then how does DNA replicate? It replicates by this semi-conservative molecule and then just kind of sketch that out. So it was saying that how the old strands separate, old strands separate and are used as templates to create. Okay, perfect. All right, guys. Well, hopefully you enjoyed that. Like I said, I love this chapter. It's very fun to go through all the different types of macromolecules. All right, so stay tuned. I'm going to end this one here, and then I'm going to jump back on to do the second part of this chapter five, and we will go through the lipids and the carbohydrates. All right, I will talk to you soon. Thank you.