She felt that she is looking at how you can get all right for the last time in this room. >> Good afternoon. All semester long, I've been harping on the idea that if we got to this point and the class average is greater than 70%, I'd be happy. 72% is greater than 70%. I'm happy if you want to get an idea of how you stand, add up your F5 exam scores, that should give you a number out of 400. You can either calculate it as a percentage or you can go to the grading scheme on the syllabus which gives your numbers out of 800 C. And want to get a rough idea of how you stand, just double that number out of 400 and then see where you fall on the scheme out of 800. Of course, in the long run, we will be adding in your final exam score, your lab grade, all of that. But you do have information in the syllabus to help you figure out things like that. And as always, the answers are posted on my bulletin board. If you want to go see Rhea, major mistakes, we recommend that. So to finish up the semester, what I want to mostly do today is talk about how extensions of some of the organic compounds we've been talking about so far play a role in biochemistry. For those of you who face a biochemistry course at some point in your future, sort of pick up where we left off last time. Last time we had been talking about how you can make so from a fat or oil by cleaving the ester linkages in there and making a material that looks something like this that constitutes a soap myself. So my cells are large clusters of molecules, not to be confused with large molecules themselves. Commonly called polymers that we've touched on polymers off and on in the course of the semester. Polymers are sometimes called macro molecules, which simply means that they are very large molecules at very high molecular weights. And typically they are made by linking together much smaller molecules. And there are fundamentally two ways to do that. One kind of polymers, referred to as an addition polymers. Now we talked before about the fact that alkenes, an alkyne tend to do addition reactions. You break down the pi bonds, but you leave the sigma bonds in tact and you attach other things at the carbon atoms that used to be part of the double or triple bond. >> Suffice it to say this. >> There is a way to do this using simple alkenes where once you attach to the alkene is more of the alkene. >> In other words, here's about as simple as an alkene gets. >> This is ethene or ethylene, if you will. And I've just drawn a few more molecules of it here. But the point is, what would happen if we could break that pi bond and use those electrons to form a new bond to the next molecule. Except that would require breaking it's pi bond to avoid putting five bonds on carbon and form a bond to the next molecule and so on and so on. But the point is, if you do that, you cause a whole bunch of ethylene molecules to link up through the process known as polymerization. And you get a great big long polymer like this. And the point is the little dots at each end indicate that by no means are the process in here. What you wind up with is a very long chain of carbon atoms, each having two hydrogens attached. That is what we mean by polymer linking together a whole bunch of smaller molecules called monomers to make the much larger polymer. And naming these things is generally pretty straightforward. You, the name of the original molecule is ethylene. The polymer derived from it is poly ethylene. Has anybody ever heard of this stuff before and have any idea what it's used for? Polyethylene? Sound familiar at all? Well, I'll make this suggestion for future reference next time you look at a container, something like a food packaging, that as well a little recycle symbols on it that looks something like this. Look at the code below that recycle symbol. >> The code usually mean something. >> For example, if you look at a plastic milk jug, you'll probably see a code on there that says HDPE for high-density polyethylene. Polyethylene is basically a plastic, and many of these things are plastics in some way, shape, or form. Two examples that we mentioned earlier this semester. If we start with, if not Ethylene, but tetrafluoride, ethylene, and which we replaced all four hydrogens and ethylene with fluorine atoms and then link them up with a polymer that we make is polytetrafluoroethylene And we get the name Teflon from to trust law or row at the lean, as were the ten. And the flow in the n come from tough lot, of course, is the non-stick coating on pots and pans that we discussed earlier. A two-part product that has become a bit infamous lately. And if we replace one of the hydrogens in ethylene with chlorine, we have a monomer called vinyl chloride, that the polymer made from it is called polyvinyl chloride. This is a much stronger, more durable plastic, a harder plastic that's used to conduct water through people's houses. We still refer to it as plumbing because the pipes that are used to transport water used to be made from lead. Civil Pb for lead comes from its Latin, mean plump them. But pretty much lead piping has been phased out. Everybody's houses now they use polyvinyl chloride or PVC pipe for short. If you check out the plastic pipes in your house that are used to transport water. You'll probably see PVC written on them someplace. So one way of making polymers is by getting alkene molecules to link up as shown. That's called an addition polymer. The other way to do it, the other general classification of polymers is to refer to them as condensation polymers. And the idea here is to bring together two molecules with two functional groups each link them together. The condensation part comes from the fact that when you do, you usually lose some small molecule like water and form some new functional group at the process. For example, let's consider this reaction. What functional groups do we have in each of these molecules? What's the functional group that we have to have in the molecule on the left. Anybody recognize us when? Yep. Or oxalic acid. What functional group do we have in the molecule on the right? >> Yes, that's the mean. >> Now we talked before about reactions in which you can mix things together and essentially lose a water molecule. I'm going to try this because I brought in some of each of these compounds. But the point is, if we can make these things lose a molecule of water by getting rid of h from the amine and OH, on the carboxylic acid as shown. And we can link them together as shown and form a new functional group in the middle here, which we'll say more about in a few moments. But the advantage to having two functional groups at each molecule that allows us to keep the process going even after we linked together with a carboxylic acid and the amine to form this functional group. We have a free carboxylic acid piece at this end that can react with another molecule of the mean, we have a free amine piece at this end. >> The can react with another molecule and a carboxylic acid. >> And so the process continues. The point is you can throw in N molecules, where N is a very large number, and get something that looks kinda like this. And this is called nylon 66. Nylon is another DuPont product, and the reason it's called nylon 66, It's made from a six carbon di, carboxylic acid and a six carbon di me. And let me just show you what I brought in. Maybe about 15 mystery for how well this is going to work, but we'll try it. >> I bought into solutions. >> The orangey stuff is an aqueous solution of the die. I mean, the kind of cloudy white stuff is an aqueous solution of the di carboxylic acid or hopefully a more reactive derivative of it. But we'll see how it goes. The fall. But over here it's not water, but is in fact hexane. And you know what hexane is, hopefully at this point. Now, water is the solvent over here. Polar or non-polar? >> Water is what? Poleward? >> Yep. Hexane is a hydrocarbon, which is the solvent over here. Polar or nonpolar? Most hydrocarbons are nonpolar. Yep. So what's going to happen if I mix these two together? Are we going to get one smooth, homogeneous mixture? Are we going to get two separate layers? Do you separate layers? Remember, like dissolves, like from the very first lecture of the semester. Polar things tend to dissolve and polar things, nonpolar things that the dissolve and nonpolar things. But in general, polar things and nonpolar things don't mix together all that well. That's the part that I'm sure is going to work. >> So we'll do that much to everybody watching at home. >> Hello one last time. >> I'm going to mix these guys together. >> Just as you can see, I'm going to mix them together slowly and I can bring it now you can see this equality layer on top of the emperor layer here. >> So the point is, if these two things don't really dissolve in each other, if there is a reaction taking place, the only place that reaction can occur at the interface of those two players. What I'm going to try to do is even inefficient outlet interface shape where it looks like this, where you can pull out will strand of this and wrap it around. The other is a plastic piece of glass tubing here. And then if I simply rotate it and I expose fresh interface. It can make more of this definition, hopefully give you some idea of how long these molecules, we sometimes call this the nylon rope trick because we keep on rotating piece of glass tubing and we keep on making more nylon as we know. And this is obviously not just one molecule of nylon, but this gives you some idea how long these molecules, and this is basically how nylon was made at the DuPont company for many years, except it's all automated. They don't have people standing around with a student. >> I think you get the idea. >> So I'm gonna leave this here. >> And if anybody wants to try to spin their own after class, you can try that. So here's the point about condensation polymers like nylon. In the course of linking these two things together, what functional group did we make right here? Anybody? What functional group is that? Somebody's going to have a notes open in front of them, which is that with a D. >> That's correct. >> The point is this is an image, that functional group right here. But when we repeat what's in parentheses n times, that means we have a big long strand of atoms at every so often there's an amid functional group in there. That's why nylon is referred to as a poly amid. And the point is it's based on reactions like the one you just saw that allows us to make polymers that looked like that. Let me just show you one other example of this kind of reaction, because I suspect this might ring a bell. Also, the key point is you can do this with any combat or any pair of compounds as long as each compound has two functional groups. And as long as the functional groups and combat a react with the functional groups and compound B. We saw before that this is a dicarboxylic acid. This is a different dicarboxylic acid. What functional group do we have to have in this molecule? >> Who knows the answer? Yeah. Yep. >> This is 8x dy, alcohol does as a dicarboxylic acid. >> Ok? >> The point is, if you mix these two together, you're going to get the same thing taking place. We're going to lose OH, on the carboxylic acid H from the alcohol, linked them together and make a new functional group. And the point is that we do that n times, we're going to get a polymer that looks something like this. Let me move this up on the screen so people can see it. Now, in the process of doing that, what functional group that we created in, of, in this molecule? We already figured out what functional group this is. So do you have signed up to take a class with me again next semester? >> So I'm just going to say one thing faster. >> You'll answer that you get at a glance. >> That's gotta be true next semester two. >> So what's the functional group that is an ester? >> And here's the significance of that answer. If nylon is a poly, a myth, because it's how you make a compound called dacron dash. >> Ron is a what? >> Nylon is a poly amend that. Garan is a polyester. Probably most people have heard the word polyester before. What most people don't realize it, it means it's a big long molecule that has an ester functional group every so often. Nylon and dacron are both use as synthetic fabrics. Dacron is also used as a material in vascular surgery to repair blood vessels. Let's talk for a moment about amino acids, which I'm sure will come up in some future biochemistry course. You might find yourself in. The basic structure of an amino acid is shown here. >> And let me show you some specific examples. >> The point is that the R to the left here simply refers to the rest of the molecule. And the rest of the molecule can be as simple as a hydrogen atom or a methyl group, or it can be a bit more complicated as you can see from some of these other examples that are shown here. >> Main point though, take a look at what's up here. >> Or if you prefer, you could look at one of these pictures. >> What two functional groups do we have in an amino acid daily? >> But ask a mean, but okay, yes, that's, that's one. What's the other one? Club oxalic acid. And this is where the term amino acid comes from. It's a carboxylic acid, but is also me. Now, amino acids are interesting compounds in and of themselves are. The reason for that is that the carboxylic acid is an acid. And the mean, which is a derivative of ammonia, is a base. And what do acids do? They give up protons and form their conjugate bases? And what do you basis? Do they accept protons and form their conjugate acids? The so-called, As with her, I in form of the amino acid is usually the most common form in which it exists at a relatively neutral pH. But the point is, this is an ionic compound, and many of the properties of amino acids are similar to the properties of Ionic compounds, they generally tend to have very high melting points, certainly higher than most other organic compounds. They tend to be good. Electrolyte CPU dissolve an amino acid in water, you get a solution, conducts electricity. That's not true for most organic compounds, et cetera. Here's another interesting aspect of amino acids. Let's look for example, at this compound for a moment. This is the amino acid known as alanine. Now focus on the central carbon atom for a moment. What's the hybridization of the central carbon atom in alanine, or for that matter, any other amino acid. Four single bonds on that carbon means what kind of hybridization, what kind of molecular geometry? >> Sp3. >> So what kind of molecular geometry? Tetrahedral. Okay, now here's the other thing to notice. Attached to that central sp3 hybridized carbon atom, we have four different things. Methyl hydrogen, the amine piece, and the carboxylic acid piece. All right, let me just show you something. Here's a molecular model. >> We can get away with glam life. >> Funny colored background here. Yes, I did. Well, let's do it this way. Alright, Here's a molecular model where we have a central tetrahedral carbon atom with four different colored things, blue, red, white, and green attached to it. So when a crude sense, this could represent a model of alanine or some other amino acid. >> And so could this take a look at those two? >> Are they the same thing? >> Big? >> So I'm seeing some people? Yes. Some people, no. Okay. Well, if they were the same thing, we shouldn't be able to superimpose them on each other so that each of the colors lines up. And we can see here that the weights and the blue line up, but the reds and the greens do not. And no amount of turning this one is going to allow you to line it up with the other one. >> So actually they are not the same thing. >> Although I think you could also see that if we held up a mirror to one of these, what would result in the mirror would be the image of the other one. In short, these two molecules are related to each other, like your right hand and your left hand to related to each other. A left-hand and right-hand are not the same thing. They are mirror images of each other. They're certainly similar in that sense, but mirror images that are not identical to each other. And one interesting aspect of organic chemistry that we will talk about in the fall. For those of you who are going to be a board for that ride. An object is chiral if it is not able to be super impose on its mirror image such that every part of the original lines up with every part of the other. So in fact, what I just showed you is to models that are chiral and more importantly, since they are essentially, well, we talked about isomers versus stereo isomers before. They are isomers in the sense that they are different molecules with the same formula. But more importantly, they are also stereo isomers in the sense that the only difference between them is the arrangement of the atoms in three-dimensional space. If we add two, all of that the criteria that they are mirror images of each other. The fancy word that is used to describe that situation is to say that they are enantiomers of each other. To put it a bit more succinctly, amino acids have a left-handed form and a right handed form. And it turns out that the left-handed form, the one enantiomer of the amino acids it has in some sense have different properties from the right-handed form. Now it turns out that primarily what amino acids are used for when most people think of, when they think of amino acids is they are the so-called building blocks for such interesting molecules as proteins, enzymes, things like that. For example, if you do like we did in the nylon demonstration, let me just get a little bit more of this on screen. In a nylon demonstration, we were able to link together the carboxylic acid part of one molecule with the amine part of another molecule to make a mid. >> Okay? >> If we do the same thing here, except now we're using two amino acids. This is the amino acid known as glycine, is the amino acid known as alanine. Linked them together, get rid of a water molecule. Now here's how you know whether you're talking to a chemist or a biologist. If you're talking to a chemist, they're going to look at that and say, OK, that's an amid. So we link these two things together and made an image just like we did with Nivea. If you're talking to a biologist and say, no, you silly person, that's a peptide bond. Because when you link two amino acids together, the whole point is to try to make peptides. So this thing is referred to as a peptide bond. And since we link together glycine and alanine to make this, this is commonly known as Gly Ala. The point is Gly Ala is an example of a dye peptide because we linked to amino acids together to make it. We still have a carboxylic acid part here that could react with another amine part from another amino acid. We still have an amine part here that could react with another carboxylic acid from another amino acid. So it's possible to link 345 and a whole bunch of amino acids together. If we link together two amino acids, we get a dye peptide. If he linked together, three amino acids may get a tri peptide. You'd be link four amino acids together, we get a tetra peptide. We call it when you eat a whole bunch of amino acids together. Now, not a mono peptide was the prefix that means many, ALI, Yeah, a polypeptide, which you may have heard of, is a whole bunch of amino acids linked together and essentially what proteins are our polypeptide. So let me show you this picture. Proteins, as you may know, adopt a so-called helical structure looking something like this. If you look carefully at this picture, for example, starting here, here's the basic carbon atom of the amino acid. Here's the mid linkage to the next amino acid. And as you go around and around the spiral, you kept, keep on going and finding more and more amino acids linked together. But what holds the whole thing in this helical framework is hydrogen bonding between oxygen atoms in the carbonyl groups and hydrogen atoms attached to nitrogen atoms up something about three or four amino acid linkages away. And these vertical Bayes kind of things here show you the hydrogen bonding, which is an intermolecular attractive force. So we talked about earlier that basically hold the whole thing into this particular shape that it normally occupies. Since I know I'm talking to nutrition majors here. We talked about lipids, which include fats Last time we were just talking about proteins a few moments ago. And the third major food group, carbohydrates. Carbohydrates are called carbohydrates because you can write the formula of a carbohydrate something like this, CN H2O and parentheses m. For example, what's the formula for glucose? How many carbons? 70 hydrogen, 70 oxygen? >> Yes. I was pointing to her, but that's okay. >> C6h12o6. >> In other words, six carbon atoms and also H2O six. >> Glucose is an example of a so-called monosaccharide or simple sugar. You can tell that because the number of oxygen atoms is the same as the number of carbon atoms. Fructose is another example, which also has the formula C6H12O6. But once you start linking monosaccharides or simple sugars together, you get polysaccharides. And the reason that n and m are not the same anymore is that when you do that, you start losing molecules of water, which means you're losing oxygen atoms. Polysaccharides are the more complex carbohydrates that include things such as starch and cellulose. Let me just show you a few pictures that might make this a tad more interesting. And again, there are aspects of all of this that you will become Familiar with as you go out and take courses and organic and or biochemistry. >> Okay? >> Glucose here is one way to draw the structure of glucose. >> And I'll simply point out right now that here we have an aldehyde functional group and alcohol functional groups all over the rest of the molecule. Now the reason they draw on these two little arrows here, it is possible to cause the alcohol functional group at carbon number five in glucose to react with the aldehyde functional group at carbon number one. And when this happens, we close up a ring. And here is one ring, the form of glucose. Here's the other one. And there's only one difference between those two structures. Look right here at carbon number one. When you form this new bond, what was the original carbon? Oxygen is now going to be another alcohol functional group. But the question is of the alcohol functional group stick down as shown here or up as shown here. It turns out that makes a big difference in the down position. This is referred to as alpha glucose. >> In the up position, this is referred to as beta glucose. >> Now, when you start linking these things together to make them more complex carbohydrates. >> Okay, here's a picture of what starch looks like. >> And the point is, notice that the oxygen at carbon number one is sticking down on each of those. That's why this is called an alpha linkage because oxygen in the down position is referred to as alpha. But down here structure for cellulose. >> Now you can see that on some of these, it's sticking up at number one and the up linkage is referred to as beta. Now here's the significance of this. >> In fact, this is probably an accurate statement right now because we're sneaking up on 1pm. >> Suppose you're hungry. Suppose I bring out two plates. >> Ones got starch, which is this. One's got cellulose, which is this. >> Which one are you going to eat? >> I would think starch. Starch includes things like red potatoes, et cetera, et cetera, stuff that the human body can actually digest. Because we have the enzymes that we need to break down those alpha linkages. Cellulose consists of things like wood, paper, things that we don't recommend that you eat because among other reasons, we don't have the enzymes that we need to break down the Beethoven. Therefore, that wouldn't accomplish very much. So as simple a thing as oxygen down or oxygen up make the old big difference if you're hungry. By the way, we were mentioning before that carbohydrates are basically sugars. The compound that we normally call sugar, also known as sucrose, is a dye. Saccharide made by linking together one molecule of glucose and one molecule of fructose. >> And the leakage is both alpha and beta. >> But we'll let you speculate as to how that might be. And if anybody wants to see the structure, I'll draw it out for you at some point. And then finally, in the last 15 minutes of the course, again, this is all just an introduction to topics that you will see in more detail in some future biochemistry course. Let's talk for a few moments about nucleic acids. >> What does DNA stand for? >> And failing that, what does RNA stand for? I hope at least the NA part is obvious. Yes, DNA is deoxyribose nucleic acid. >> What is RNA? >> Ribonucleic acid. >> The difference is de oxy. De oxy means lose an oxygen atom. Let me show you a picture. As it turns out, ribose is a five-carbon sugar as opposed to glucose, which is a six carbon simple sugar. Here is the cyclic form of not ribose, but deoxyribose. If this were ribose, this hydrogen right here would be an OH instead. >> So when we say deoxy, that just means we've lost an oxygen for what ribose should be. >> But the point is, this thing in blue here is a deoxyribose, and this picture is a whole, shows you what one nucleotide of DNA might look like. Now from high school biology, what three things do you need to make a nuclear die? >> I'm sure this was something they pounded into your head, made you memorize their big hints on the screen in case they did. Yeah, phosphate, sugar add a feeling. >> Now, here's what I don't understand. >> Here's the phosphate part, here's the simple sugar part. >> Everybody says nitrogenous base. Why don't we just call it what it is. >> It's an amine, much shorter word. I don't know why. >> Tenth grade biology teachers pound nitrogenous base into everybody's head. >> And they could just say amine and accomplish the same thing with tie-in with amino acids to but anyway, phosphate sugar part. >> And this piece up here is a unit of a particular, I mean, taken all together, these things make what's called an ad mean unit. >> Now, as you're probably aware, there are four different nucleotides, adenine, thymine, cytosine, and guanine, ATC and G. >> All right. That sounds familiar. >> Okay. >> Here's how it all links together. Here's one piece ribose or deoxyribose part with whatever I mean attached to it. And then here's the phosphate Bs hanging down, but the phosphate piece is used to connect it to the next molecule. >> So here's one nucleotide. >> Connect it to the next nucleotide. Connected to the next nucleotide by these phosphate pieces that are used to link it together. And the phosphate pieces just arrived from phosphoric acid, which is H3PO4. The point is, once you link together a whole bunch of nucleotides, you get a poly nucleotide. And that's essentially what any nucleic acid is. Dna is made from deoxyribose. Put an extra oxygen atom right there, and you're making it from ribose. That's what RNA is. And of course, this is the fundamental genetic material which determines what all of us look like. Everybody's familiar, of course, with the double helix structure for DNA discovered by two guys named Watson and Crick back in the 19 fifties. They won a Nobel Prize in 1962 for this work. Now here's something else they probably pounded into your head at high school biology, a pairs with T and G pairs with C. Why do we have two lines between a and T and three lines between G and C. >> Does anybody know has to do with the number of hydrogen bonds? >> If you actually look at what those molecules actually look like, you will see that thiamine and add me when they get together, can form two hydrogen bonds. But cytosine and guanine, When they bind together, can form three hydrogen bonds. We kind of started this semester talking about intermolecular forces of attraction such as hydrogen bonding. Seems to be that talking about hydrogen bonding right here at the end of the semester is a good way to bring the entire four month long conversation full circle, make sense? Ok, so the take home lesson here you can talk about your basic mono saccharide piece. You can talk about your basic phosphate piece, but do not in my presence ever again call it a nitrogenous base. It's an I mean, for crying out loud, to sum up, I would like to thank you folks for being a good group to work with this semester. I have enjoyed the experience. I'm sure that you guys may not have enjoyed it quite as much as I did, but you've done well and that's good. I will say this for the folks that are watching the video tapes, this has been one of the quietest classes I've ever taught. There is nothing wrong with your screen. >> They just weren't saying anything, but doesn't matter as long as we're standing. What's going on? >> Three quick questions before I send you on your way. Where and when is the final exam room? Not this one. Round Lab 206 is the room right next door to this one. >> So don't come to this room. >> And what day and what time is your final exam? Tuesday, 330 right here. Brown Lab 206, which is the room next door to this one. >> Okay. >> I will be shortly sending out an email to let you know and my office hours are during finals week and you can always contact me via email. >> We'll see you at the final exam if we don't see you sooner. >> Question yes, why should this variable, or this obviously was our last class you have for the regrade request. >> You can bring them with you right now. >> This isn't review. You want to turn that into remind us, I think Yeah, you're welcome. Okay. Yeah. Peter. Actually, she shouldn't. Okay.
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From Dana Chatellier October 11, 2018
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