 Welcome back everybody. Every other video in this collection of videos is going to be for chapter 16 and chapter 16 is going to talk about protein molecules. Before I get to protein molecules and before I get to any more chemistry, this is a thought exercise that might be a little bit relevant in a little bit. Usually I show this to my own ground students and I say here's two stacks of Legos and I try to get in an argument with people and I say are these two stacks of Legos identical to each other? Usually the students say no, which is the correct answer, but I try to argue about it and I say no they're the same thing because you've got red, green, white, yellow, you've got red, green, white, yellow, so they must be identical to each other. Obviously that's not true and the reason it's not true is because there's a difference between the top of the stack and the bottom. If you have ever used Legos and maybe you have, maybe you haven't, but you can see the top part of the molecule has these little knobs that point out of the block and the bottom doesn't. The bottom actually has little indentations that point into the block. The point I'm trying to make is that it's not just the order of the colors, right? The order of the colors is the same, red, green, white, yellow, red, green, white, yellow. It's the order of the colors and who's on the top and who's on the bottom? Who's on the left side and who's on the right side? Because the left side, this side here and the right side, they aren't the same thing. One has little knobs that point out and one has little indentations that point in. So it matters where you start and where you end up as far as the colors are concerned. Now this obviously doesn't really have to do with proteins, but I'm going to try to make it relevant to protein molecules in a little bit. So keep this in the back of your mind. This chapter is on protein molecules, but before we get to protein molecules we have to talk about a kind of molecule called an amino acid. This is a generic amino acid molecule and all of the amino acid molecules that I'm going to talk about in these lectures have these features in common. They have this part here, this part if you remember from a couple of weeks ago is called an amine functional group. They also have this part here. If you remember from a few weeks ago this part here is called a carboxylic acid functional group and those two functional groups are why amino acids are called amino acids because they have an amine and they have an acid functional group. With the amino acids that I'm going to talk about every single time the amine and the carboxylic acid are connected to each other by a carbon atom in the middle. This carbon atom here has a special name. It's called an alpha carbon. This is the Greek letter alpha. I don't expect you to know that but I may say alpha carbon in some of the videos so it's just fair warning. So every amino acid molecule that I'm going to talk about like I said has this functional group, this functional group, carbon in between the two. This carbon, the alpha carbon always has a hydrogen attached to it as well and it has r attached to it. So what I'd like you to do now is pause the video and tell me what element r is. If you unpause the video and you actually spent some time doing this you're going to be upset because there is no element with a symbol of r so hopefully you didn't spend too much time looking at the periodic table. What r means when you see it in a chemical structure like this it means some other crap goes here. It's like a placeholder. What this means, what r means is there will be, there are many different amino acids and what makes them different from each other is the atoms that go in place of r. Sometimes you can have very simple replacement for whatever r for r or you can have really complicated replacements and every different kind of replacement gives you a different kind of amino acid molecule and I'm going to show you some examples of different amino acid molecules. Just to emphasize all of the amino acid molecules that I am going to show you they have this part that I'm putting in this red shape they all have that part in common. All of the amino acids that I'm going to show you they all have whatever goes here different from each other. Like I said there are many different things that can take the place of r. What's taking the place of r here you can pause the video and think about it on pausing the video. Well it's the simplest replacement that you can have it's a hydrogen atom because that's the simplest atom that we have as well. This particular amino acid molecule has a name it's called glycine I do not expect you to know that I do not expect you to memorize what glycine looks like I'm just telling you what's got a name and this is what's taking place of r. There's a different amino acid I'm just going to show you a different one again these are the parts this is the part that it has in common with all of the other amino acids and this part here is what's taking place of r this is a little more complicated right you have carbon atom with some hydrogens and you have an alcohol at the end so this is certainly more this molecule here is certainly more complicated than glycine. This amino acid here is called serine you don't need to know that again I'm just telling you it's got a name this is a little bit complicated for what's replacing r you can have really complicated stuff too this is an amino acid molecule called tryptophan and all of this stuff here is taking the place of r so that's a relatively complicated amino acid molecule I think this is the stuff that they say makes you sleepy when you eat too much of it at Thanksgiving I don't know if that's really true at least that's what some people say so these are three different amino acid molecules there are there are many others these are not the only three different amino acid molecules that exist in fact there are 17 more amino acid molecules that are called universal amino acids there's 17 more plus these three so what that means is there are 20 universal amino acid molecules what universal means is that as far as we can tell every single organism that we have looked at has 20 different amino acid molecules and they are these three plus another 17 and we find them in all living organisms and we think we're pretty sure they are in all living organisms there are more than 20 amino acids there are more than 20 different kinds of amino acids but 20 of them as far as we know are found in all living organisms now there's a couple of phrases or words that I want to point out here the atoms that are taking the place of whatever r is they have they're usually referred to in a couple of special ways sometimes people will call the atoms that are taking the place of r they will call them the r group of the amino acid and that just means the group of atoms that's taking place of r so if I said what's the r group for glycine you'd say oh the r group is very simple for glycine it's just a hydrogen if I said what's the r group for serine you'd say ah it's a little more complicated it's a ch2 connected to an alcohol something like that there is another phrase that is also used to describe the atoms that are taking place of r in an amino acid those atoms are sometimes called the side chain for the amino acid molecule side chain just means the chain of atoms that's coming out of the side of the amino acid molecule so if I said if I said what's the side chain of glycine it's the same thing as me saying what's the r group for glycine I said what's the side chain for glycine I'd say oh it's a hydrogen what's the side chain for serine it's a ch2 connected to an alcohol same kind of thing and I want you to know those two phrases because they they might get used if I say r group for an amino acid you're going to know oh those are the atoms in the amino acid molecule taking taking the place of r if I say what's the side chain of this amino acid molecule same question now we're actually going to talk about some chemical reactions suppose that this molecule this amino acid and this amino acid molecule are bouncing around next to each other in one of yourselves and for whatever reason your cell wants to connect these two molecules together one of the most common ways that it can do this is it can rip out the OH here and it can rip out one of the hydrogens here so you can see there are two hydrogens there you can rip out one of them so I'm going to just turn it to an H and if I do that if I take out an OH and an H do you remember what I make right that makes water if I do that this carbon atom is now missing an attachment if I rip out the OH and the H and this nitrogen is also missing an attachment but what what I can do then to make them both happy again is I can connect the carbon to the nitrogen and if I do that they end up connected I made a bigger molecule if you remember from last week we already caught we already talked about this kind of reaction this kind of reaction is called dehydration synthesis it's called dehydration because we ripped out pieces of water from the two molecules it's called synthesis synthesis basically means you you make something but here they kind of mean we made something bigger this is the most common way that living organisms connect different amino acid molecules to each other it doesn't just have to be between glycine and serine we could have also connected serine to tryptophan the same way we could rip out this OH rip out one of those hydrogens connect this carbon to that nitrogen etc etc so the way what you should do is you should think of this the way that amino acid molecules are connected to each other now I know I'm not really explaining what this chemistry is for and any of that that will come but there's a lot of information to cover now I am going to show you these two molecules once they are connected to each other by the reaction that I just showed you those two molecules are down or the one molecule is down here once I take the glycine and connect it to the serine I make this molecule this carbon here is this carbon there this oxygen is this oxygen this nitrogen is this one and this connection here is the one that got made when I connected the two little molecules to each other to make this bigger molecule there are a bunch of things that I want you to know about this I want you to know how this reaction takes place I want you to also know may recognize this functional group from a couple of weeks ago this is called an amide functional group or amide or amide however you want to say it in a couple of weeks ago I said hey if you notice the amide functional group looks a little bit like the carboxylic acid it looks a little bit like the amine and I said that's not a coincidence because a lot of times that's how you make an amide group or an amide functional group and that's just what we did here we took a carboxylic acid we took an amine and we fused them together and we made an amide functional group there's another word that I want you to know unfortunately there's a lot that I want you to know here this bond the connection that got made this single bond here has a special name it is called a peptide bond don't worry about where the name peptide comes from it is a very old name and it's just kind of stuck with us but I want you to know if I show you two amino acids connected to each other and I point to this particular bond the actual bond that connected them to each other you should know that that's called a peptide bond now another thing that I want to point out a couple of minutes ago I connected glycine to serine by ripping out this OH ripping out one of those hydrogens but what if I did it in reverse in other words what if I took the serine and I moved it over here and I wanted to connect them in the opposite way and that's shown here what you notice here is that I have flipped around the serine and the glycine molecules this time the serine is on the left but let's say that I want to connect them this way I can do this as well I can rip out this OH I can rip out one of these hydrogens I make water with the stuff that I ripped out this carbon is missing an attachment I can connect it to the nitrogen like that but this time the serine is on the left and the glycine is on the right side and I'm going to show you that once you make the connection you make this molecule here so this is serine connected to glycine over here this is glycine connected to serine same kind of chemical reaction except different things on the left side in each case the question I want to ask and you can pause the video and think about this is are these two molecules is this molecule here and this one here are they identical to each other if you unpause a video the answer is no for some pretty hopefully pretty obvious reasons this is the side chain for glycine and it's close to this amine group in this molecule on the left but over here in this molecule this is the side chain for glycine and it's way far away from this amine group so these two molecules can't be the same thing because the atoms are in different spots so these are isomers of each other they don't really have a special name they're not cis and trans they're not stereo isomers or anything like that even though they look a little bit like stereo isomers they are not but this is getting back to the legos if you remember I said these two stacks of legos were not identical because the left side of the stack and the right side of the stack were not the same same thing here right the left side of this molecule has an amine functional group the right side has a carboxylic acid functional group and here this hydrogen which is this one is close to the amine here the same hydrogen is far away so if they're in different spots they have to be they have to be different molecules and the reason is basically the same as the reason why the lego stacks are different the left side of this molecule and the right side of this molecule are not the same thing so it matters what order you connect the amino acids in this again I know it sounds ridiculous but at least it's important in chemistry and biology may not be important to you but I'll talk about this in a little more detail on the next slide so here's the three amino acids that we've been talking about let's say I want to connect all three to each other I can rip out this OH I can rip out one of the hydrogens there and I can connect the carbon to the nitrogen if I want to connect now this is a bigger molecule if I want to connect this bigger molecule to the tryptophan I can rip out this OH you can rip out one of the hydrogens I make another water molecule and I can connect this carbon to that nitrogen once I do that I've made a pretty big molecule from three little amino acid molecules it would look like this here's my bigger molecule once all of the connections are made this is a peptide bond that's also a peptide bond now these peptide bonds are stretched out just to show you for emphasis where they are they're not really stretched out in real life but this is how you connect a bunch of amino acid molecules to each other if you wanted to and your cell does this all the time see these three little dots here that what that is trying to tell you is that you don't have to stop at three amino acids I could connect a hundred or I could connect a thousand amino acid molecules to each other by doing the same procedure over and over again rip out the pieces of water connect the carbon to a nitrogen rip out the pieces of water connect another carbon to a nitrogen on another amino acid molecule I could go on for a really long time in this direction in a sense I could go in the other direction as well another thing that I want to point out when I made these connections right when I connected the glycine to the serine to the tryptophan this used to be a carboxylic acid functional group but I destroyed it because I ripped out the OH this used to be an amine but I also kind of destroyed it and I connected the carbon to the nitrogen same thing I destroyed this carboxylic acid destroyed that amine now you should look at the molecule that we made down here is there any place where an amine functional group did not get destroyed you can pause the video and think about that you can also ask yourself is there any place where a carboxylic acid functional group did not get destroyed you think about that as well if you unpause the video over here on the left side that's the only place where an amine functional group did not get destroyed over here on the other side this is the only place where the carboxylic acid didn't get destroyed because we stopped at three so when one end of this molecule has an amine functional group that is still intact the other end of the molecule has a carboxylic acid functional group that is still intact there is a special name for the ends of this kind of molecule this end here has a special name it is called the aminoterminus terminus just means end it's just a fancy word for end amino just means amine functional group so what they're saying if I call this the aminoterminus that's the end that has the amine functional group sometimes chemists and biologists can get lazy they don't want to say this mouthful so sometimes they just call it the n terminus that's the end of the molecule that has a nitrogen there that's what n terminus means the other end again you might not be able to guess specifically what it's called but that end is called the carboxy terminus so again terminus means end carboxy just means the end that has the carboxylic acid functional group and again if you are lazy like most chemists and biologists are you can call that end the c terminus because that end has a carbon there so I want you to know that the left end of these molecules when you connect amino acid molecules to each other is not the same as the right end one of the ends will be called the end terminus or the aminoterminus the other end will be called the c terminus or the carboxy terminus now you can look at this molecule and this is relatively small compared to what your cell can make with a bunch of amino acid molecules but you can probably appreciate that it is a pain in the ass to draw that out to draw all of the atoms out like that so a lot of times people don't do that and instead they just list the names but if you're going to list the names you probably should tell them which end is the end terminus and which end is the c terminus and a lot of times it's written like this so if I wanted to tell people that I was talking about this molecule here but I didn't want to draw every single atom out you could just write n that's this end here and I could write the names of the molecules glycine connected to serine connected to tryptophan and I could write a c at the very end that's a little bit easier it was probably a lot of it easier than drawing every single atom like this what you're going to see is there are improvements on this there are simpler ways of writing amino acids connected to each other as well and again just to emphasize if I connected these amino acid molecules to each other in reverse order if the tryptophan this one was way over here on the left and I would write it like this right because the tryptophan now is near the end terminus and the glycine if this glycine was moved over here then the glycine would be the near the c terminus so here's a summary slide amino acid molecules are attached to each other and I've just shown you how that's done by dehydration synthesis there are 20 universal amino acids found in living organisms I have shown you three I will show you the other 17 soon your body attaches amino acids to each other by what everybody by dehydration synthesis when you do the dehydration synthesis to connect amino acid molecules to each other you make an amide functional group and the connection that actually gets made is called a peptide bond if you attach enough amino acid molecules to each other by this process which we have been talking about you make many peptide bonds and if you make many peptide bonds the molecule that you make is a lot of times called a polypeptide poly means many and peptide just means the kind of bond that we've been talking about so a polypeptide is a big molecule that's made of a bunch of those amino acid molecules connected to each other by the peptide bonds that I showed you finally a lot of times polypeptide molecules are just called protein molecules so protein so this chapter is on protein molecules protein molecules are just collections of amino acid molecules connected to each other by peptide bonds it took us 20 minutes to get here but the reason that I started talking about amino acid molecules is because amino acid molecules are used to make protein molecules so the punchline here and this is the end of this video is yourself use amino acid molecules to make protein molecules and you should understand the chemistry of how that works see you in the next video