this is the video for the standard level portion of b1.2 on proteins proteins are generally long chains made of monomers called amino acids and there are 20 different types of amino acids but they all have a general structure that you should know how to draw so let's do that together these are all going to involve a central carbon atom so I usually draw that first attached to a carboxy group so a carboxy group is a dou bonded oxygen and then this hydroxy group so again I can just kind of label that here as a caroal group okay and then on the other end I have what is called an amine group an amine group is going to be a nitrogen and two hydrogens here so this is my amine end attached to the central carbon atom we have a hydrogen atom and then what we call a functional group and there is no chemical element that um starts with r so that's why we kind of use this and this is my functional group all right and all of the 20 different amino acids are going to be identical so this part will be the same for all of them what makes each of the 20 different amino acids unique is a different R Group and some of them will be very simple some of them will be very complex we'll take a look at those later it's also important to remember that amino acids are three-dimensional molecules so I can look at it like this but I should also be able to recognize it if it's flipped upside down and that our group is pointing downwards or a mirror image all of it is the same they're three-dimensional to form a polypeptide which will eventually fold into a protein I need to be able to connect many amino acids so I'd first start by connecting two amino acids and that's going to form what's called a dipeptide d meaning two so two amino acids hooked together here's an example if I then hook a bunch of them together Bond a bunch of them together that's how I get a polypeptide or many amino acids and that is all going to be done using these condensation reactions so again these cond condensation reactions are going to remove water and it's going going to bond them together now when you learned about um condensation reactions between monosaccharides that formed what was called a glycosidic bond when I am bonding together two amino acids I'm going to get a very special type of bond called a peptide bond so a peptide bond and we can see that right here okay um is that bond between two amino acids and it's very special so it's good to put in your mental tool kit here and it's also the way that we get these words like dipeptide polypeptide are in reference to this peptide bond between the amino acids now here's a better look at all 20 amino acids and as you can see they have the same basic structure what differs is their R group or their functional group okay so all 20 of them plants are amazing and they can manufacture all 20 different amino acids very cool humans can only manufacture nine out of that 20 yet we need all 20 in order to make all the various proteins in our cells so we need all 20 but we can only make nine that means we have to eat the other 11 in our diet and we call those essential amino acids acids so essential are the other 11 they must be consumed in our diet because we cannot manufacture them different organisms will have different metabolisms and they can make different amino acids but the word essential means the same thing in all organisms whichever ones must be consumed because they cannot be manufactured and there's some big implications there for our diet so I don't want to just eat one protein Source like I don't maybe want to eat chicken all the time and that's because chicken might not have all of the essential amino acids or at least all of them in balanced proportions um a lot of animal proteins do have all of the essential amino acids particularly eggs okay but if we want to follow a vegan or plant-based diet we may have to be very purposeful and mindful about what protein sources we're choosing some of them are going to have have some of the essential amino acids but maybe not others and so it's important to a know which essential amino acids are in our diet and B make sure that we get lots of variety there so that we can include them um properly in our diet now let's assume I've done a good job of including all of those different sources of amino acids in my diet and I've manufactured nine of them on my own what are we going to do with them well we use them to make polypeptides and that is of course the kind of like end result um of this protein synthesis pathway here so DNA contains the codes for these polypeptides RNA serves as like a temporary uh messenger of that code so this gives us um not only our our genome which is what's in our DNA but also our protome so protome is the set of proteins that we can make um in an organism and there's just like an endless possibility there right so I have only 20 amino acids to kind of play with but I can put them together in different patterns or make those proteins of different lengths and I just get this huge and infinite really um number of possibilities for different polypeptides that I can make okay and again they're all coded for by our DNA and there's some examples of proteins that are kind of important to know so like insulin Amal Titan those are all polypeptides um with very different structures and very different functions just because they're the genes that code for them um code for a different sequence of amino acids to go into that polypeptide chain a polypeptide is that sequence of amino acids and it's not quite the same thing as a protein a polypeptide becomes a protein when it folds into its specific shape and protein make such a great topic for this theme of Form and Function because a protein function is very specific to its shape now that shape is determined by lots of different kinds of bonds and interactions which we'll talk about um a little bit later but if that shape changes it can often signal a permanent change in the structure of the protein and of course then the function and we call that process denaturation this is a permanent change in the structure of a protein right so it kind of looks like this okay and that permanent change you can see how it causes such a drastically different shape that this normal functional protein won't be able to do its regular job and again that is normally going to be um a permanent change so we won't be able to turn that back into its shape this often involves a protein that used to be soluble becoming insoluble we'll look at this with things like blood clotting and some other stuff now there's two things that I want to keep an eye on that can cause denaturation of these proteins let's say I have a protein that's responsible for catalyzing a reaction well I'm going to notice that as temperatures increase that that reaction rate goes up that protein is becoming more and more active but at a certain temperature that reaction rate is going to fall very drastic ically and that's because at a certain temperature okay I have reached this denaturation point okay and that's the point at which that protein is going to start to kind of like unravel and change its shape and it won't be functional anymore that can vary from protein to protein but all proteins have a denaturation point and the way that heat um and those high temperatures are going to cause that is it breaks makes certain bonds between amino acids now let's say I have the same protein and it's responsible for catalyzing a reaction what I'm going to notice about this protein is that at its optimal pH it has a very high reaction rate that that protein is able to do its job really well but when I expose it to lower or higher pH ranges it's really going to decrease the reaction rate because the functionality of my protein has been decreased because it has been denatured so every protein has an optimal pH it's not the same for every protein it might be seven it might be two it might be 10 who knows but what I do know is that either higher or lower pH values causes um interactions between those amino acids or those bonds to either like break or be disrupted again unfolding that functional shape in my protein and so again great example here um when I change the form the function is also going to change or you can think about this as something's function is very dependent on its form and no better example than here with proteins