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Current time:0:00Total duration:9:59

Video transcript

we've already spent a couple of videos talking about enzymes and what I want to do in this video is dig a little bit deeper and focus on some actors that actually help enzymes and just as a reminder enzymes are around to help reactions to proceed to lower their activation energies to make the the reactions happen more frequently or to happen faster now we've already seen examples of enzymes and just to frame things in our brain properly sometimes in a textbook you'll see an enzyme like this you'll see a drawing like this and you'll say and people will call this the enzyme the call this the enzyme and then they'll call they'll call this right they'll they'll say okay and it's acting on some type of a substrate right over here it's going to do something to that and this is nice for a very abstract textbook idea of a substrate locking into an enzyme like this but this isn't actually what it looks like in a biological system we have to remind ourselves when people talk about enzymes they're talking about proteins now there are these kind of RNA enzymes called ribozymes but the great majority when we're talking about enzymes we tend to be talking about proteins and we spend a lot of time talking about how proteins are these structures there's polypeptides and all the side chains of the various amino acids fold the proteins in all sorts of different ways so if I were a better drawing for something like this you know it would be this this protein that's all folded in different ways maybe have some alpha helixes here maybe it has some beta sheets right over here it's all this kind of crazy stuff right over there and then the substrate might be some type of a molecule that is it gets embedded gets embedded in the protein and you see some examples right over here this is actually a hexokinase model and you see the at least you can see a little bit of the ATP right over there and it's a little harder to see the glucose that's going to be phosphorylated and this reaction is being facilitated by this big protein structure the hexokinase now what we're going to focus on in this video is that when we talk about an enzyme we're talking about proteins we're talking about a chain of amino acids but there's often other parts of the enzyme that aren't officially proteins and we even saw that when we talked about hexokinase when we talked about the phosphorylation of glucose we said hey the rate the way that it lowers the activation energy is you have these positive magnesium ions these positive magnesium ions that can keep the electrons and the phosphate groups a little bit busy draw them away so that the so that this hydroxyl group right over here can bond with this phosphate and not be interfered with these electrons well these these magnesium ions right over here they aren't officially part of the protein these are what we call cofactors so you might have a cofactor right over there that gets that latches on to the broader protein to become part of the enzyme and you actually need that for the reaction to proceed it plays a crucial role here so another drawing in the textbook you'll see something like this or even you know they'll draw they'll say okay in order for this reaction to proceed yes you need the substrate but you also need the cofactor the cofactor and once again it sounds like a fancy word but all it means is the non protein part of an enzyme it's another molecule or ion or atom that is involved in letting the enzyme perform its function that it's not formally it's not formally and part of an amino acid or part of a sidechain or part of the protein but it's another thing that needs to be there to help catalyze the reaction we saw that with hexokinase you had magnesium ions that the the that the that the complex picks up and this is why you know when people talk about your vitamins and minerals a lot of the vitamins and minerals that you need they actually act as cofactors for for enzymes and so you can even see it in this drawing over here at least based on what I read these are the magnesium ions in green right over here and these are Co factors these are cofactors so cofactor non protein part of your actual enzyme now we can subdivide cofactors even more we can divide them into organic cofactors and non org or inorganic cofactors so if you have cofactors you have cofactors we've seen an inorganic cofactor a lot of these ions you'll see magnesium ion's you'll see sodium ions you'll see calcium ions you'll see all sorts of things acting as cofactors oftentimes to distract electrons so that or to keep them busy so that electrons can proceed but you can also have organic ones you can also have organic molecules remember organic molecules these are just they'll involve carbon they have chains of carbons and other things and cofactors that are organic organic molecules we call them coenzymes coenzymes and there's a bunch of examples of coenzymes this right over here is the enzyme lactate dehydrogenase and it has the coenzyme and this coenzyme you are going to see a lot in your biological careers and a nad right over here notice this isn't just an ion it is an entire molecule it has carbon in it that's why we call it organic and it is not formally protein it's not it's not part of the the amino acids that make up the protein so that's what makes it a cofactor and since it's since it's an entire organic molecule we call this a coenzyme Co coenzyme but like any cofactor it plays a role and actually allowing the enzyme to do its function to facilitate reaction and this particular coenzyme nad which you're going to see a lot it helps facilitate the transfer of hydride ions hydride ions never or very seldom exist by themselves but it's a hydrogen with an extra electron so it has a negative so it has a negative charge so it allows to the transfer of this group or from from from a substrate or to a substrate and that's because nad nad can accept a hydride anion right over here and become NADH and if you want to see its broader structure it's actually quite fascinating I'll probably do a whole video on nad because in so many textbooks growing up I just saw you know nad and NADH and I'm like what is this thing and it's a fascinating molecule so what it can do is it can actually pick up the hydride anion right over here at this carbon you can actually form another bond with the hydrogen I'll do that in a future video I'll show the mechanism for it but it's a pretty cool molecule and I like to actually look at this molecule remember we're the whole focus of this is Koen Symes but we see these patterns throughout biology because the name nicotinamide adenine dinucleotide exactly describes what it is nicotinamide nicotinamide right down here that is that is this piece of the molecule and this is the part that can accept a hydride or let go of a hydride so you could say this is the active part of the molecule adenine are good old friends we've we've seen adenine in DNA and RNA in ATP so this is our good old friend adenine right over here and it says dinucleotide because we actually have two nucleotides paired together their phosphate groups are tied together and there's a couple cool ways to think about this you have an adenine right over here you have a ribose you have a phosphate group if you just looked at if you just looked at this piece right over here if you looked at this right over here this is your building block this this is your building block of our or this could be a building block of RNA if you have an adenine right over there and if you include if you include let me undo this if you include all of this this right over here this is adp but the reason why it's called dinucleotides you can also divide it the other way you can say all right you have one nucleotide that has Nikitina mead right over here so that's one of the nucleotides and then the new other nucleotide is right over here the one that involves the one that involves adenine that's what's called dinucleotide so hopefully this makes nad a less of a mysterious molecule we'll see it in the future but I like to look at it because it's it's got all these patterns it's got all these components that you see over and over again and you see it in ATP you see it in RNA over and over again but d this isn't the only this isn't the only cofactor or coenzyme there are many many others in fact when people say take your vitamins and your minerals that tends to be because they are cofactors vitamin c is a very important cofactor to be involved in enzymes that well i won't go into all of the different things that it can do these are two different views of vitamin c a space-filling model and this is a ball-and-stick model right over here vitamin C folic acid once again two different views but these are all coenzymes they all work they all work you know if you have a protein right over here that you know it's all this really complex structure maybe you have some substrates but to help facilitate let me do the substrates in a different color in a different color so maybe you have some substrates so these are the things that the enzymes trying to catalyze the reactions for but then you could have some ions which would you know you could kind of view these as you would view these you would view the ions as cofactors and you could have organic cofactors like your the vitamin C or other things that we talked about that are also involved in help facilitating the mechanism or help facilitate the reaction once again sometimes it might be to help stabilize some charge sometimes it might be to be an electron acceptor or donor or a whole series of things they can they can actually act as part of the reaction mechanism
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