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Amino Acids and Proteins: How to draw Alpha Amino Acids and Primary Structure of Proteins

Amino Acids and Proteins: How to draw Alpha Amino Acids and Primary Structure of Proteins


Hi guys this is Maverick Puah the Chemistry Guru. Now in this video we want to talk about alpha amino acids in proteins and how to draw the primary structure of proteins. So let’s take a look Now in proteins we have about 20 alpha amino acids. Now why are they called alpha amino acids is because the reference functional group is my acid functional group and the first carbon attached to my acid will be the alpha carbon and I have an amine group attached to my alpha carbon so this amine group will be called my alpha amino group. So this entire guy will just be my alpha amino acid. Now remembering alpha amino acids is fairly easy, you just need to remember these 3 positions. Now position one is my amine group, my NH2 group. Then my position two is the carbon with my R group. And my position three is my acid group. Now the only difference between one amino acid and another amino acid is in the R group so we need to be able to identify my positions one, two and three and I need to be able to look at my second carbon and identify the R group that is sticking to the second carbon because I need to make use of this R group to identify that particular amino acid. Ok let’s have some examples. Now in this case I have 3 amino acids Asp, the short form notation of this amino acid is Asp, Ser and Val. Now the format that is being presented here is a bit different from what we’ve talked about, but if I know that they are alpha amino acids that I can find in proteins then I can easily find my position one my amine group, my position two the carbon with the R group and position three which is my acid group so we do that first to identify the R group sticking out of my second carbon so my Asp, my amine is here this is my position one then my carbon is here this is my position two, then this is my position three. so this is my position one, two and three: amine, carbon with a R group and my acid group and the R group in this case will just be this group here and I can write down this R group which is a CH2COOH now next for Ser, it is essentially the same. Position one is my amine group, position two is the carbon with the R group, then number three is my acid group so now my R group is this that is sticking out of the second carbon this is my CH2OH so again I can put this down my R group is a CH2OH then the last guy Val, position one is my amine position two is the carbon with the R group, position three is my acid group and then I have this group that is sticking out of the second carbon this one is a CH(CH3)2 so this group that we are highlighting here will be my R group so I can also write this down this is a CH group then attached to two methyl groups Now once we have the R group what we can literally do is I can draw back my amino acid. So let me show you what we mean in this case if I want to draw back my Asp and then I know that my R group is a CH2COOH then basically what I do is I just make use of the format that we just memorised earlier my position one is a amine group, position two is a carbon with a R group and position three is an acid group. So for Asp I will draw it something like this: I write my position one which is my NH2, I write my position two which is a carbon with a H and a R group, later I’ll put it in. Usually I would put my R group later because the R group is the one what we need to refer to the question. Then position three is my acid group so it’ll look something like this. So you notice in this case again this is my number one my amine, number two is the carbon with R group then position three is my acid group. So the R group in this case is here and I know that for Asp the R group is a CH2COOH then I just need to write this out this is my CH2COOH and then this will be our Asp so if I were to highlight the R group, then this will be our Asp So similarly for Ser what we can do is I just write down my position one my amine group, then my position two which is a carbon with a H and a R group and position three which is our acid group and my R group which is a CH2OH will just be sticking out of my second carbon so this is my CH2OH. So this will be my Ser and then the final example for Val the R group is a CH(CH3)2, again I write down this format my amine group my position one, my carbon with a H and a R group which is my position two my acid group which is my position three and then the R group in this case is a CH(CH3)2 so I can put it here CH(CH3)2 so this will be my Val now primary structure of proteins is the unique sequence of amino acids joined together by polypeptide bonds to form one continuous chain so essentially all these amino acids will join together and then they will link up with each other forming peptide bonds or amide bonds and then it’ll form one very long chain and this long chain we call it the primary structure of proteins. Now the only difference between one protein and another protein is the sequence of my amino acids. So maybe for example we have a particular protein where the sequence is Asp-Ser-Val, I have another protein where the sequence of this amino acids maybe can be Ser-Val-Asp and then all these different sequences will give the proteins its different properties and different functions Now because my primary structure of proteins is just made of amino acids joined together and all my amino acids follow a fixed format, so what this means is my primary structure will also follow a fixed format and the template is here so what we have is my position one is my amine my N my position two is a carbon with a R group and position three is my acid group and then this will be part of this continuous chain and again the only difference between one part of this chain and another part of this chain is in my R group. So maybe let’s try to draw this part of my primary structure. Maybe we want to draw this Asp-Ser-Val So these are the 3 amino acids that we have talked about earlier so again it is shown here. Now the R group for my Asp is CH2COOH the R group for my Ser CH2OH, the R group for my Val is CH(CH3)2. Now when I want to draw my Asp-Ser-Val what I can do is I can duplicate this chain, that means I write this standard format three times and then I put in the R group subsequently. So let me show you what I mean in this case I want to draw Asp-Ser-Val so therefore I know that I have 3 amino acids joined together so what I’ll do is I’ll just duplicate this chain 1-2-3 three times so I’ll have position one, NCC this is position 1-2-3, then I do this a second time, this is the second set 1-2-3, and then this is the third set this is my NCC so this is the third set. After that what I do is put in the groups, remember my position one is the N, amine group, position two is the C with the R group position three is the acid group. Then what I’ll do is I’ll fill in all the groups first so what we have here is my position one is a amine, position two is a C with an R group, usually R group we will leave it later because again it’s easier for us to write the continuous chain first then after that we fill in the R group later. So position three is my acid group so this is one set, then I duplicate this set. Position one is a amine position two is a C with a H and a R group, position three is a acid group. Then I duplicate this again position one is a amine position two is a H and R group then position three is my acid group. So this structure is fixed. That means for any protein as long as it is a tripeptide that means three amino acids join together for any protein that you can find, this sequence is exactly the same. The only difference is in the sequence of my R group so what’s my first R group, then what’s my second R group, then what’s my third R group. So we already have the R groups, so we’ll just need to put in the R groups. So the first R group my Asp the R group is a CH2COOH so I know that this guy is just a CH2COOH I can put it in CH2COOH then the second guy is my Ser the R group is a CH2OH so I can put in the second group CH2OH this will be the second R group then the third one Val, the R group is a CH(CH3)2 so I can also put this in CH(CH3)2 so I can very easily draw this sequence of my primary structure by duplicating this format position one is a amine group, position two is a C with a R group and then position three is a acid group alright I hope you find this video useful, please like this video and subscribe to my YouTube Channel. If you have any burning questions involving H2 chemistry that you want me to clarify, please leave your questions at the comment section below and I’ll try to address them in future videos. Thanks for watching guys I’ll see you next time

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