we're going to start chapter 5 by looking at amino acids remember that amino acids are our monomer units that are going to come together to make peptides and then to form proteins in a living system so let's look at the structure of amino acids and the different types of amino acids that we have okay so some properties first of amino acids first they have a capacity to polymerize which is how they can make these longer structures such as proteins and PES they do have some really interesting acidbase properties and we touched on that in our last lecture video and they because of the uh side group on amino acids they have a lot of different structures and chemical functionality and one of the most important things is that they are chyro molecules so remember a chyro molecule is going to be one that is nons superimposable upon its mere image all right let's look at our basic amino acid structure all right so as we're looking at this basic amino acid structure and by basic I mean simple not acid base uh this carbon here in the center is called our Alpha carbon it's actually not considered the first carbon of the molecule um the carbon that would be numbered carbon one is going to be part of our carboxy group so this would be carbon 1 Carbon 2 is going to be our Alpha carbon our Alpha carbon is going to have on it the amino group it's going to have on it a hydrogen and it's going to have a side chain if you have a side chain that is neutral so an uncharged amino acid uh then your Zer iion is going to be when you have lost your hydrogen on your carboxilic acid but you still have your hydrogen on your amine and we looked at that in our last lecture video so this would be the zwitter ion of most amino acids but not all all right because we have four groups around this atom so a carboxilic acid an amine a hydrogen and a side chain we are going to have a chyal molecule so here we see our tetrahedral with our Center Alpha carbon our R Group carboxilate our amino group and our hydrogen here we have just a just a general reminder that this is going to be our zwitter ion and that negative charge is not localized on one oxygen but spread out among both oxygens in our structure so this is just another representation of this so all three of these are representing the exact same thing all right let's look at the fact that they are an antier they're non superimposable upon its mere image so here we've got two ball and stick structures of alanine so we've got our Alpha carbon here and here we've got our amino group with the nitrogen shown in blue down here we've got our carboxilate with our oxygen shown in red these are our hydrogens and in this case because it's alanine this is a methyl group on either side so this would be our fisser projection structures of these so amino group on top carboxilate on bottom hydrogen to the right and our methyl group to the left so when we have our methyl group to the left this would be our L alanine given that our nitrogen would be on top and our carboxilate on bottom if our um hydrogen group is to the left and our methyl group is to the right this would be our D or our dextr rotary so D would be dextr rotary and L would be level rotary so this is just talking about how they're going to polarize plain light which is the distinguishing factor in amino acids in biological systems we only use and only make the L versions of amino acids but if you were to make alanine in the lab you would get an enantiomeric um mixture of both L and alanine and deanine all right I really like this image to be able to distinguish them so if you imagine your two hands um if you've got your Alpha carbon in the middle and you've got your carboxilic acid where your fingers are and your ammonia going down below and your AR your hydrogen is going to the left that's going to be your Lev rotary if you've got your carboxilic acid on top and your ammonia on bottom and your hydrogen is going to the right that's going to be your dextra rotary so it's just another way of showing the mirror image nature of these groups all right we have 20 that uh biological amino acids and they can be grouped into these five different categories we can have what's called aliphatic aliphatic just means it's got a lot of carbon hydrogen groups on it or aromatic so remember aromatic is going to have those alternating double Rings um double bonds within rings so these are considered our hydrophobic side chains so they are not going to be ones that are going to dissolve well with water then we'll have our polar side chains that are uncharged our polar side chains that are basic which would be positively charged side chains are polar side chains that are acidic which would make be negatively charged side change side chains and all of these are going to be hydrophilic as they are all POS or polar um amino acid side chains so we're just going to go down the list and look at these amino acids so this is just a figure from your text and it does a really great job of just showing you um with the groupings the different amino acids uh the GR green Parts here those are the side chains everything else about the amino acids for the most part stays the same so they're all going to have the amino group the carboxilate group this is our Alpha carbon and this is our hydrogen and they're showing all of these in the L form all right so our aliphatic amino acids these are hydrophobic ones so Proline um and for each amino acid I'm going to be giving its threel abbreviation and its on letter abbreviation because you can see um either of these so um Pro would be the threel abbreviation for Prine and P would be the on letter abbreviation for Proline so Proline is an interesting amino acid because it's actually the only cyclic amino acid so instead of having it NH3 Plus on the nitrogen side instead there is a three carbon chain so forming a five membered ring between the Alpac carbon and the nitrogen so it's got a very interesting side chain so this um because of the ring shape it actually makes Proline really good for doing what's called hair pin turns so making quick turns in your protein structure so this um three considered to be Amino nitrogen glycine is interesting because it's actually the only non- chyal amino acid so the alpha carbon has two hydrogens on it because its side chain is a hydrogen so it does not have a non-s superimposable mirror image all right alanine we've seen this structure in the previous slide it has a methyl group for its side chain veine is going to have this isopropyl and so I think it looks like an upside down V with when you're looking at the shape of the carbon so I think V for veine as we're looking at Lucine it will have this Beal group on it so there are four carbons 1 2 3 and four and then the arrangement of these carbons is going to be in an ISO group when we're looking at isoline it has uh four four carbon chain they're all in a row 1 2 3 4 but we're connected to the second carbon so this would be a second butal group what's interesting about isoline is it also has a second chyo carbon so remember the alpha carbon is your first chyo carbon but this carbon here is also going to be a chyro carbon because it has four unique groups hydrogen methyl ethyl and then the rest of your amino acid structure and then our last aliphatic amino acid is going to be methionine this is actually known as the start amino acid because the start uh to encode for a protein is going to be always going to be um making athine so all of our protein structures are going to start with athine amino acid so it will have a sulfur on it uh with a methyl group all right so those are aliphatic amino acids now let's look at our um aromatic amino acids so we have three different ones we've got our phenyalanine which we see here tyrosine and tryptophan so the cool thing because these have aromatic groups in them they're going to absorb light in the UV region at 280 NM which means if we're using a UV viz instrument we will be able to measure the concentration of our our protein by looking at the absorption in the UV at 280 nanm another thing that is important to keep in mind when we're looking at our aromatic amino acids is that tyrosine has this o on it now this o is actually a little bit more acidic than a typical oxygen um a typical alcohol would be because it is attached to this aromatic rink so it has a pka of 10.5 so that is actually going to be uh similar to what this um protonated amine is and so you'll need to look at the relative pka of those two groups when you are doing a titration of that Amino acid all right now let's look at some of our polar um amino acids so these are ones that are going to have uncharged side chains so they're going to be hydrophilic and they can form hydrogen bonds because most of uh most of them have a an this the ability to have a partial negative or partial sorry a partial negative charge on their oxygen nitrogen or in the last case sulfur all right so Serene looks just like alanine but one of the hydrogens has been replaced with an alcohol then three anine is going to have two carbon chain and then we'll have an O on that uh first carbon in the side chain asparagine is the amine form of aspartic acid which we'll get to aspartic acid in just a second um but it's going to be the amid form and then our glutamine is going to be the amid form of glutamic acid so we'll get to these when we look at our acidic amino acids um but they're just the amid forms of those acidic amino acids and then cysteine has an sh and this sh is actually really important for disulfide linkages which is where two sulfides can come together and make what's called Ault dulfi Bridge our basic amino acids we've got three we've got histadine lysine and Arginine because they're basic um they are able to have a positive charge um in um the the side chain form so our histadine is actually the only amino acid that can function as a buffer in physiological uh pH ranges uh because of this um these nitrogens here in the side chain our lysine is a diamino group so we've got these two NH3 plus groups and we can proteinate this second nitrogen at a ph of 7 and then this is a guanidinium group here and this guanidinium hydrogen is almost always proteinated and it's our most basic amino acid I mentioned our two acidic amino acids previously uh so they are aspartic acid and glutamic acid you could also see them called aspartate uh because of the fact that these carboxilic acids are going to be deprotonated at physiological phes so this would be aspartate and glutamate um if they are proteinated because we have added acid they would be aspartic acid and glutamic acid so these carboxilic acids are really good nucleophiles so remember nucleophiles are going to be um donating electrons in many enomatic reactions all right so let's just refresh ourselves again on our titration curves since we're now incorporating these side chains into our amino acids so we'll look first at alanine alanine just has a methyl group so all we have in terms of ionizable side groups are going to be our amino acid and and our car sorry our amine group and our carboxilic acid group so remember at our lowest pH before had any equivalent of Base everything is going to be protonated so here we've got our proteinated amine group and our protonated carboxilic acid group as we add a half equivalent a base we get to our first PKA which again remember if we're looking at our PKA our carboxilic acid has a much lower PKA than our amino group and so our carboxilic acid is going to be that that hydrogen will be lost first so this equilibrium is showing that this hydrogen is leaving as we're going this Direction this will get us to our zwitter ion form remember that's where we've got a neutral compound but we have a positive charge and a negative charge in the same compound so our amino group is protonated but our carboxilate is deprotonated so to find that where we predominantly have that switer ion that is going to be our pii so for the pi of alanine we will average the pka of our carboxilic acid and the pka of our amino group to give us a pi value of 6.15 so at a pH of 6.15 we will mainly have our ZT iion form and that's where we've haded added half or sorry one equivalent of Base so we have deprotonated all of our carboxilic acid but not have not deprotonated any of our amino group yet as we continue to add more base we'll reach our second PKA that's where we'll have 50% uh proteinated and 50% deprotonated amine and as we continue to add our full two equivalents of base now we will get to our completely deprotonated form uh where we've got a negative charge on our carboxilate and a neutral charge on our amine so again we start fully deprotonated after one equivalent of Base we'll get to our Zer ion form and after a second equivalent of Base we'll get to our fully deprotonated annion form of alanine all right so now let's look at something that has an ionizable side chain so I'm going to look at glutamic Acid as the our first example so glutamic acid has a carboxilic acid for a side chain so we've got now three ionizable groups the first one is so this is our Alpha carbon this is our carboxilic acid here's our amino group our hydrogen and then this is our side chain and our side chain has an amino acid on it so this first amino acid is going to have a lower PKA it has a pka of 2.2 our side chain amino acid has a pka of 4.1 and then our amino group has a pka of 9.7 when we are at zero equivalents of Base added everything is going to be proteinated so our am's proteinated and both of our amino acids are proteinated as we add one equivalent of Base it's going to remove our most acidic hydrogen first our most acidic hydrogen is the one with the lower PKA value so we're going to deprotonate our side chain or not our side chain our carboxilic acid group first our carox carboxilic acid will become a carboxilate this form here is our zwitter iion we've got a negative charge and a positive charge and it is otherwise neutral so our next form the thing we're going to deprotonate next is going to be this side chain carboxy acid so this has a pka of 4.1 so we will get 50% proteinated 50% deprotonated on the side chain at a pH of 4.1 and then when we add a third equivalent of Base that's when we will deprotonate our amino group and that will give us a glutamic acid that has a 2 minus charge so glutamic acid here or glutamate as the case may be has a Nega one charge cuz we've got two negatives and a positive which would add up to give you a 1 okay so our PI for this is going to be the pka of the side chains that we would remove in order to be able to give us this neutral zwitter ion so we first have to remove the hydrogen um from our amino acid which would give us the co minus and then the next hydrogen that would be removed would be the side chain so that means that the removing of this hydrogen and removing of this hydrogen are the two PKA that we would need to average to get to our PI so our PI would be 2.2 um sorry this should be a 4.1 here and then divided by two to give a 3.3 approximate pi value so our zerion occurs at an acidic pH of 3.3 now let's look at a basic amino acid so when we're in complete complet acidic conditions and we've added no base everything is going to be proteinated so our carboxilic acid is proteinated our amino group is proteinated and our R Group is pronated this R Group has a pka of 10.5 our R group is around nine and our car sorry our amino group is around 9 and our carboxilic acid is around 2.2 when we add our first equivalent of Base that is going to remove our most acidic hydrogen first which is our carboxilic acid giving us this carboxilate now our charge is going to be a negative 1 positive 1 positive 1 so overall a + one so we're not neutral yet even though we've removed one hydrogen when we remove our next hydrogen it's going to go to the next most acidic hydrogen which is our amino group with a PK of 9 so this is now going to be um a neutral on our amino group our carboxilate is a Nega 1 and our side chain is a positive one this is going to be the Zer iion form of lysine so its s iion form isn't going to occur until we have a pH of almost 10 when we add our third equivalent of Base that will finally be able to remove the hydrogen on our side chain as it's the most basic at 10.5 so we can see we've got our three different PKA with our Zer ion occurring between removing the hydrogen on our amino group and removing the hydrogen on our side chain so those would be the two PKA we would average to give a pi value of about 9.8 just to give you an idea of some PKA for different R groups and amino acids aspartate and glutamate are going to have a PKA on their carboxilic acids of about four histadine will be about six um because that is within one pH unit of neutral that is why histadine side chain can be used as a buffer in biological systems uh cine so that's the s H side chain has a PK of around 8.4 tyrosine remember that was the alcohol and the aromatic ring has a PK of about 10.5 lysine we just saw is around 10.5 and Arginine that most basic amino acid is going to have a PKA on its side chain of 122