[Music] [Music] hello my name is chris harris and i'm from alley chemistry and welcome to this video on amino acids proteins and dna now this video is dedicated to the aqa specification so if you are studying a level chemistry and your example is aqa then this is perfect for you so it's not like um maybe that you might have seen other resources other videos where they may be quite generic and this one is actually dedicated to aqa so it is designed around the specification in fact there's loads of um these types of videos these are the revision videos loads of types of these videos for year one and year two so it's the full range all in all chemistry um youtube channel there's also some whiteboard tutorials for some generic information some general information on there and there's also some exam paper um through videos as well we'll go through some variety of different types of exam papers so they're all on alley chemistry they're all for free all that i ask is that you hit the 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right so like i say that this is dedicated to the um aqa specification and so therefore it meets the specification points as it's stated on there so first of all we're going to look at amino acids and we're then going to look at um proteins then we're going to look at enzymes we're going to look at dna and then the last bit is looking at anti-cancer drugs so things like cisplatin so that's the um that's the running order for uh for this video okay so let's start with amino acids first okay um so amino acids have an amino group which is nh2 and you might have seen the amines topic already i've done a video on amines and the carboxyl group which is coh and i've also done a video on carboxylic acid and derivatives so um so if you're not too sure on them then i recommend you go and have a look at them there and there isn't a massive amount you need to know um regarding the the actual um you know the intricacies of amines and carboxylic acids but you do need to know that one's basic one's acidic and you need to know them little bits there so might be helpful if you watch them videos first but um this video let's say is going to look at amino acids in particular it's going to look at these functional groups so you've got our carboxyl group and we've got an amino group as well so an amino acid is basically structured in that way and we also have um we also have an r group as well depending on what the what the amino acid is will depend on what this r group is going to be but the basic structure is looking a little bit like this and actually amino acids are amphoteric they're a bit strange they have basic and acidic properties so it gives us this versatility in terms of the reactions that they we can undergo with them now amino acids have an organic side chain like saying it's represented by the r value and that's with the exception of glycine where r is actually a hydrogen in this case but any any other amino acid apart from glycine this would be um a different uh group that's attached to it so it's always this structure this is called an alpha amino acid because the amine and carboxyl group are actually attached to the same carbon don't need to worry too much about that okay so amino acids except for glycine they are all chiral and they're all chiral molecules they have four different groups as you can see and surrounding that central metal line so they will actually rotate plane polarized light and i have done a video on that as well as as you would expect because the full range is on there um where we look at chirality and we look at optical isomerism and and look at how we can detect that and if you've seen that video then you'll know that we use plane polarized light to detect um chiral molecules okay so amino acids are actually named into uh in two different ways they have a common name and they have a systematic name and this is using the iupac rules that you are fully familiar with and by naming other molecules okay so you'll see it name two but what we need to be able to do the exam was expecting you to name it using the iupac rules as well so for example um you've seen the word there before which is glycine that's the common name but the systematic name is actually is actually different so we're going to have a look at an amino acid here now and we're going to look at how we name it so the first thing we need to do this is alanine that's its common name and so the first thing we need to do is find the longest carbon chain so in this example you can see the longest carbon chain's all highlighted in red here this is um this is um three carbons so this is propanoic acid so remember if you've seen the carboxylic acid video uh carboxylic acid derivatives video that we always number from carbon one so this one here is carbon one that's always from the carboxylic acid group okay so that's one two three so there's three carbons there so this is propanoic acid that's the first one and then the second step is then we need to number them carbons like we said before they go one two three so we always name from number from the carboxyl group and then what we need to do is then note where the amine group is this is the nh2 group so what carbon is that on now you can see there that that's on carbon two okay so we call that amino when we're naming the amino acid okay so we say it's on it's an amino group and so then we need to name any other groups that may be attached to it as well so um so these are anything apart from um um the amine group that we've obviously taken into account of so anything such as um oh which would be hydroxy for an example so we had an oh group on there and then finally we just name it so the name of this is two amino propanoic acid so propanoic acid obviously this is the this has priority we just put propanoic acid and we just need to know where the other groups are so two amino so for example if there's a hydroxy group on there um you know and that could be you would put some the number hydroxy two amino propanoic acid okay so you would always um all the other way around so you always do it um in alphabetical order so amino is a so hydroxy would come in between there so no difference there you can see the nomenclature of amino acids is not too traumatic you're just following the standard rules that you're that you'll be familiar with through doing um you know naming molecules all the way through a level okay so amino acids like we said before when the early on that they're actually amphiteric and so therefore they and they act as acids and bases now amino acids can also exist as something called vitarines which is somewhere along the line of them being amphoteric so as vitrine is just a molecule with both positive and negative ions so zvita ions only exist at the amino acids isoelectric point okay so it's vit orion um it's actually mean double a double iron so two ions okay so it comes from the german um it comes from germany a lot like a lot of the naming and names you'll see in chemistry they come from german and so as vitrion just means two so two ions okay so if you study german you'll be you'll be familiar with that so the isoelectric point is the ph at which the average overall charge is zero okay so that's the isoelectric point and this is dependent on the r group that we've seen before okay so let's have a look at an example of a sphiturine so here's his vitarine here so it's likely to be formed um at a ph at the isoelectric point okay um and both the carboxyl and amino groups ionized so you can see here this is as bitter iron because we've got two ions there a positive ion and we've got a negative ion so this is likely to be at the isoelectric point whatever ph that is don't assume that this is always at say ph seven because different amino acids have different isoelectric points okay so just it really just depend on that okay so let's assume if we so at low ph what happens to this ion at low ph in other words an acidic solution so what actually happens is the um if we add up we put this into acidic solution we have a high concentration of h plus ions now the h plus ions is now going to react with the o minus on the carboxyl group there so it's going to react with that and so therefore we have oh now we have our full carboxylic acid that's um that's put that's put on the air so this is if the ph is lower than the isoelectric point this is what we get so at a higher ph so in other words we put it in alkaline solution then what actually happens is the um hydrogen from the um nh3 group you can see here there it is okay so the hydrogen from here drops off um and we form nh2 again but obviously we still have our negative charge on our carboxyl group okay so this is if the ph is higher than the isoelectric point okay so you don't really need to know a lot about that other than the fact that do exist is vitamins you do need to be aware of um you know if it's if it's above or below the um the isoelectric point you know what products would you form so just be prepared to be able to draw the formulas of them okay so that's fine okay so we know a little bit a little bit about the properties of amino acids we know how to name them we know what they look like um so we know all that parts and now what we've got to be able to do is practically we've got to be able to maybe identify and separate amino acids so we know what type of amino acids we have so one of the ways in which we can do that is using thin layer chromatography or tlc um so it's a very loving um form of chromatography tlc um so thin layer chromatography allows us to separate okay and identify amino acids um as they have different solubilities okay so that's quite important because amino acids are actually um colorless and we'll look at how we can detect them later using other methods but we need to separate them and then identify it now this could be useful in terms of um identifying um amino acids say proteins in and say urine samples for medical reasons or it might be even if um mainly in urine samples but it could even be in blood samples etc uh it may even be in hair samples you know for for criminology etc so there's a lot of use for this so this is how very csi this so this is how we're going to identify amino acids using a technique called tlc so tlc basically uses a stationary phase of silica or or alumina which is this bit here so this is your plate here okay so this is um this is your stationary phase so this is not moving and then what we do this um this stationary phase is actually mounted onto a glass or metal plate which is backed on there to give it some some rigidity and then what we do is you put a pencil line is drawn as you can see on the on the plate there so there's your pencil line and then we put our drops of our amino acid mixtures on that pencil line there the case is very similar to what you've seen a standard chromatography method that you that you may have done using filter paper so what we're going to do is place the plate in a solvent now the baseline must be above the solvent level that is absolutely vital if that solvent level is above the spots that you put on then they'll just dissolve in the solvent and you won't get any um chromatogram so you must make sure that the solvent level is below that below that line okay so we're going to leave that and i'll be leave that until the solvent has moved up near the top of the plate and then what we need to do is mark the solvent front um after time so you'll see that what will happen is this um this solvent as you can see here will then migrate up there and it will stop somewhere near the top of the line well once it gets to the near top line you whip it out you whip the chromatography and play it out and then we analyze it okay so it works really by the amino acid spots dissolving in the solvent okay but some of them amino acids may not be very soluble it will actually spend a little bit more time um or have a stronger adherence to the stationary phase so what you'll find is you'll get um you'll get a few dots that's migrating up so you might get a dot here a dot here and one dot here so the ones higher up the chroma the chromatogram are the ones which are the most soluble in the solvent the ones which are um lower down on the chromatogram are the ones which are the least soluble in the solvent and have actually kind of stuck or spent more time on the actual um chromatogram okay um so we have our chromatogram at the end and then what we need to do is basically um mark up where these amino acids are and we use the positions on the chromatogram to help identify what the amino acids are and actually we're going to look at um you know the the method basically we're going to take this out and look at how we can actually interpret our chromatogram to identify an amino acid so let's have a look okay so amino acids like i say these are colorless compounds however they can be seen using um iodine or nine hydrogen solution or fluorescent dye and uv light so what you'll see when it actually rises up you'll not actually see any it looks as though nothing has moved on your chromatogram so we need to be able to um effectively spray a die on them so we can highlight the spots and then we can use that to measure um the um measure the rf value which we'll look at later in the next next slide um and then we use the rf value to to work out what the amino acid is but we'll go through that later so one way in which we can identify these amino acids is using a fluorescent dye and uv light so if we add a fluorescent dye to the um silica plate okay we can actually see this using a uv lamp okay so it's all very high tech and so the colorless spots on that chromatogram and they will block any glow from the fluorescent dye okay so let's have a look so it looks a little bit like this so we spray our chromatogram and you can see it there and the whole chromatogram will be the color of the um will be the color of the dye okay um and then the spots underneath won't actually absorb any of that any of that fluorescent dye so we shine a uv light on there and we can see the spots that appear on our chromatogram so that's one way in which we can see these are our amino acid spots that you can see on the chromatogram there so that's one way in which we can do it another way which you may have used um may have used in school or college is iodine or a chemical called ninhydrin so these this is um a slightly different technique you've got to be really careful um you know with nin hydra in particular it must be used in a fume cupboard so if you have used it you would have used gloves um it's not very pleasant chemical to handle at all but what we do is we place that chromatogram in a sealed jar with a few iodine crystals for the iodine reaction okay and basically what happens um with the iodine um is the iodine vapor starts to stick to the chemicals on the plate and it's dying at purple now this can be um as you can see here let's pull up the picture so the iodine and vapor is known as the locating agent however what we can do instead of this instead of putting it into a jar is we can spray we can hang this on a bit like a washing line in a in a fume cupboard and we can spray it in hydrogen solution onto the chromatogram and we get the same effect so we don't need to put it into a jar for this but you can see that instead of doing it this way where the whole chromatogram is dyed and the the eye the amino acid spots are quite colorless um you can see here with this one it's just highlighting the amino acid spots and again we get the same outcome but there's two different methods of doing it okay right so now we've identified where our amino acid spots are and how far they've migrated up that chromatogram we can now use um a little bit of maths to actually work out the um the amino acids that are present and we can do that using rf values so rf values um are is basically a um a ratio of um how far the solvent has migrated up the um chromatogram against the how far the spots traveled up so this is how we can actually identify our amino acids so you can see the number of spots just before we go into the actual calculation because this is where we're analyzing the chromatogram now but the number of spots on that plate tells you how many amino acids have made up that mixture so in other words if we get on the same we put one spot on that line and if that separates into three separate spots then we know that that amino acid mixture is made up of three different amino acids okay so the number of spots tells us how many amino acids there are and the amino acids like i say they can be identified by calculating the rf value and we compare that to a known library of rf values so here's our chromatogram we pulled it up here and we've just um color coded it so you can see everything what's going on so you can see here that we've got our baseline um which is here there's our baseline okay and we've got a spot we've just simplified this and so you've got a spot here one spot there and we've got the solvent frontage there so that's how far the solvent has actually migrated up that and you can see we've measured the distance traveled by the spot and we've measured the distance traveled by the solvent so the rf value is basically the distance traveled by the spot in red divided by the distance traveled by the solvent in purple okay and if we put them figures in then we work out our rf value and what we do with the rf value um is we obviously measure that against um a known library of sources and we can do that because it's fixed for each amino acid so um every amino acid has a unique rf value however that is only true if we're comparing it against um like for like sources so for example they must have been conducted at the same temperature the solvent must be the same and the makeup of that tlc plate must also be the same as well um that also has an impact in the rf value so you've got to be certain in that data book you've got to know what conditions did they actually conduct the um you know the chromatogram in and as long as yours are in the same condition then you can actually make that comparison and hence use that to um work out your amino acid okay so it's all very csi like i say right okay so this is where we're going to get into obviously there's a bit of biology there all of this is like the biology topic like biochemistry and so now we're going to enter into um so if you study biology you'll probably find this very straightforward um so we're going to enter into a new realm now so moving from amino acids into something called proteins okay now if you've seen the polymers topic you'll know that you need to know about three different types of polymer so um well three different types of condensation polymer should i say so the first type um was polyamide second is polyester and the third one um polypeptides which are known as proteins so this topic really goes through um this part of um the polymers topic so proteins are polymers like i say and they're actually made up of amino acid monomer units and obviously we've seen some amino acids so we know what they are um and this is actually like i say is a type of condensation polymerization and so proteins are actually amino acids joined together and we they're joined together with what we call a peptide link so remember it's that link when we're joining the two monomer units together okay so like say if you've seen the other video on uh polymerization or polymers and then you'll you'll be familiar with this but um like with other condensation polymers the chain can be broken through hydrolysis so we can break that down and remember that's breaking using water so hydro meaning water lysis meaning to break so when we join two amino acids together we form a dipeptide molecule okay so remember um we had a polyesters polyamides and these are polypeptide molecules especially basically a protein so let's have a look so we've got two amino acids here it doesn't really matter what they are it's just a generic example so we've got amino acid one and amino acid two and so what we're gonna do is join these together and we're going to form our dipeptide here and we form a peptide link so peptide link is your nh as you can see here uh reacting with your carbonyl group and this is on an amino acid um joining together okay now because it's a condensation reaction we actually have water being eliminated so just like the condensation reactions you may have seen in the previous video on polymers so let's have a look so these um effectively um break away and it forms a molecule of water and the bonds that are left behind are then used to um i used to then form that peptide link that you can see on there now going forward is a condensation reaction and going backwards is hydrolysis so remember um remember you've seen um you may have seen in the previous video that um condensation we call it condensation because water's been eliminated but hydrolysis is effectively just the reverse of polymerization okay i strongly urge you to go and see that video if you haven't seen it already because it will it'll help with this topic okay so so bringing this back again so the dipeptide has a um carboxyl and amine group you see at either end for further reactions and this obviously can then be used to make a polymer chain exactly the same as any other condensation um and polymerization reaction so these groups here can then be um broken off and then you can join more and more um links on the side there so the protein and can be broken down into amino acids so we can go backwards so this is hydrolysis remember but it requires really severe conditions okay so we need six mole per dm cubed of hydrochloric acid which is pretty strong stuff you want to be really careful with that um six molar hydrochloric acid 110 degrees celsius and we need to reflux it for 48 hours so it takes quite a it takes a lot of severe conditions to break down proteins or protein structures they're quite robust polymers and so to determine the amino acids used to make the protein and we break the bond in the middle of that peptide link so you can see here there's our peptide link there and all we have to do is if we're working backwards is we break it there we cleave it there and we put a hydrogen on the end here to form nh2 and an oh here to form your c and your carboxylic acid okay so we break right down the middle of that peptide link okay so and of course obviously we add oh to each of the amino acid units to reform our polymers sorry our monomer units that we can see here so again this is no different to what you've seen in the um in the other video to do with polymerization if indeed you have you have seen it okay so we've looked at the structure proteins and we know how we make a protein but proteins are incredibly complex molecules they don't just exist in one form okay they actually actually exist in multiple forms so they are um they're actually structured into four different levels and we have primary structures secondary structures tertiary structures and quaternary thankfully you don't need to know all of them of course if you're doing biology i'm not a biologist but i assume you probably need to know all of them um but for chemistry you only need to know the first three okay so we're going to look at the primary structure of proteins first okay so the primary structure um is shows the individual sequence of the amino acids that make up that protein so remember we said that a protein is a polymer and it's made up of loads of monomer units which are amino acids so a primary structure looks a little bit like this so you can see these blocks represent an amino acid and they're joined together in a very very long chain as you can see there okay so you've got your different groups on the side and we have our free carboxyl carboxyl group as you can see there so this is then free to join up with another amino acid and obviously we have a free amine group as well on the end here and this is free to join up again further so this is just showing you the primary structure shows you the individual amino acids that make up that protein that protein molecule so a protein chain is also known as a polypeptide chain remember so each of them black lines on there represent a peptide link okay so they're linking these amino acids together and that's how we describe a primary structure for proteins okay so secondary so we just imagine that secondary is like we're zooming out a little bit so we'll start at that molecular level okay looking at a new amino acid we're then zooming out a little bit further and we can join them amino acids together into a big long chain and we call that a primary structure so a secondary structure is zooming out a little bit further and what happens the secondary structure is actually the height is looking at the zooming out a little bit further we're going to look at the interactions within that so hydrogen bonds exist between them peptide links in that polymer chain and this pulls that straight chain that we've seen there relatively straight into a coiled or pleated structure okay so they look a little bit like this okay so them them amino acid chains that we've seen there can then be twisted into a nice little pretty shape so we've got a helix here as you can see there or we've got this pleated sheet um effect here so we call this an alpha helix chain and a beta pleated sheet that's the name that we give to these um structures of proteins okay so we're just zooming out a little bit further and now we can say right okay so we've seen what makes up that protein and we now can see the shape of these proteins here okay so we're going to zoom out even further and yet i told you these were complex molecules aren't they absolutely massive um right so now we're going to look at a tertiary structure and so um a tertiary structure is basically um where we have them coil chains are then themselves twisted up um and form into different shapes you can see here we've got an example of what some of the coils but the coil itself is then twisted into knots as well it's a bit like spaghetti in a ball to be honest so you can see here we're just zooming out even further so it has this unique shape of this protein this is known as a tertiary protein structure and the additional bonds um hold that long coiled chain together okay so it holds this particular structure so you can see we've literally started it's a bit like looking at it in an individual then zooming out to look at the the town that you live in then zooming out to look at the country then zooming out to look at the earth so it's a little bit like we're going bigger and bigger and bigger and so this is what proteins look like okay so like i say you've seen there proteins have really specific shapes and they're held together by hydrogen bonds and disulfide bonds okay so this is what proteins are not although it looks a bit of a mess proteins do have an ordered structure okay they're shaped in a particular way and they're held together by these bonds so we can see here if we've got our amino acid chain in black so we've just taken out all the individual amino acids okay so we can see here this is our amino acid chain they're all structured together like this okay and now what holds this shape together this is your secondary structure okay your secondary and tertiary for that matter but this is just showing a secondary structure then what happens is we have um um we have interactions between some of these molecules that may hang off the amino acids as you can see there okay um and so they have this fixed 3d shape which is essential for enzymes which are going to look at later um but enzymes obviously allow our body to react or undergo chemical reactions with enzymes okay so we wouldn't be alive if we didn't have enzymes basically so for example breaking down food is a class example so there's two types of bonds that hold this protein shape together so the first one is the purple one there these are disulfide bonds and so this is actually created from um so for example um cysteine is an example of an amino acid it has a thiol group in there which is s h so anything with thigh is to do with sulfur i know um so you've got thial group which is sh and they can lose the hydrogen atom and the sulfur atoms that are remaining can form this disulfide bond so this ss bond that you can see on there and the other type of bonding which you'd be more familiar with are hydrogen bonding so this exists when you have electronegative elements such as oxygen nitrogen so you remember that from year one chemistry yeah so um highly electronegative elements oxygen nitrogen when they bond with hydrogen that will be on the amino acid groups you probably have oh groups on your amino acid um and also nh2 groups will work as well because you've got nitrogen so nitrogen will work there so you have hydrogen bonding between some of the molecules that hang off there so this as you can see holds this structure um into a particular shape okay now if any of these bonds are broken then the protein structure starts to break down okay so um the temperature and ph uh change the shape of proteins as well like i say by affecting the bonding and the formation of disulfide bonds as well so and you might see it um so proteins and structures like this um you'll notice it in things like hair for example so if you're straightening hair hair forms a very specific shape hair is protein forms a specific shape when you um when you put so if you put hair straighteners in so um anything like that i seem to talk a lot about hair to say i don't have much myself um but it does work so you can see your hair shape the shape your hair changes when you apply heat to it you're effectively altering or realigning that protein shape there okay so there's an example in real life okay so remember we we said that these proteins actually have a specific 3d shape and that's useful in enzymes which help catalyze reactions okay so we're going to look at them enzymes in a little bit more detail okay so enzymes or proteins and are biological catalysts that speed up a chemical reaction okay so they're essential especially in the body and but they can also be used in chemical processes such as washing powder so you might have um biological wash and powder you can get non-bio and bio washing powder so your biological washing powder contains enzymes in there non-biological and non-bioid doesn't contain enzymes it uses a chemical instead and some people biological is generally a little bit cheaper than non-bio but some people are allergic to the enzymes in biological wash and powder and cause irritation so um some people would prefer to use non-bio instead because it doesn't cause that reaction but so there's the difference um but i bet you probably didn't know that but anyway and so enzymes catalyze metabolic reactions within living organisms and so they play a vital role in life so you can see here we've got a picture of an enzyme okay um an enzyme's got a little bit cut out um and we're going to look at what why that is in them in a minute so all enzymes are proteins um however some have non-protein elements as well okay so we've seen what proteins are so this is looking at an example of how these proteins can form to make something like an enzyme so substrates okay which is this green bit here so these are molecules that enzymes interact with to help speed up the reaction so the substrate could be a molecule that you want to try and break down it could be um for example um it could be glucose molecule and from the food that you've eaten broken breaking it down into um one though it'll be a sugar sorry a sugar molecule so a large sugar molecule like a carbohydrate breaking it down into glucose into smaller molecules which can then be absorbed into the blood so that could be an example of a substrate so enzymes have a 3d active site which is part of the tertiary protein structure so remember that big big structure there that we'd seen before and actually this is where the chemical reactions actually occur within the active site of the enzyme so that's that bit right in the middle there you can see there so the substrate would fall into into this here and that allows it to then and catalyze the um the reaction regarding the the substrate so enzymes will only work though with them substrates um if they actually fit okay so the active site has a fixed shape and this is why you can't just have one enzyme because one enzyme will not do everything you need a variety of different enzymes within your body and that enzyme is a is specialized it does a particular job okay and so when we say it's specialized it means it has a very fixed shape that shape that we've seen there so if the substrate doesn't fit in that shape then it doesn't work as well as it should do so you can see that enzymes work by receiving the correct shaped substrate into the active site and they must match for them to be catalyzed because if they don't then um the reaction won't happen but the enzymes have chival centers so remember what a chiral center is it's a it's a carbon atom with four different groups around it and you can detect them by shining plain polarized light and overtake that light okay so this is because they're chiral because they contain amino acids and remember we said that the vast majority of amino acids are chiral okay so you would expect the enzyme to have chiral centers as well so this means that actually only one enantiomer in the substrate will actually fit that active site okay so they are actually stereo specific okay this is really important because actually when we're designing drugs we want um drugs to fit particular cells properly we need a drug so your enzymes may break that down the drug first as you as you may well know and then the substance the the actual the product of that is then used to then treat whatever it is okay that's affects what an enzyme does um if um you don't have if for example you've got an enantiomer in there in a drug which doesn't fit that active site then you're going to be in trouble because it won't break it down and it may not be any good in your body or it may work the other way where actually it breaks down that um that molecule and it forms a really um you know um bad molecule which goes around your body and that can have a adverse effect as well so it can work both ways but let's have a look at the mechanism anyway just need to know that it's stereo specific so you can see we've got our active site we've got our enzyme and we've got our substrate now the substrate is then going to approach the enzyme and so the enzymes then going to lock into the enzyme and we call this a lock and k model but i'll come on to that in a minute so this one fits perfectly so that's fine so once it fits in it then reactions can actually occur so we split that into two different uh products we call this a lock and key method because it's um it fits in a bit like a the lock is like the enzyme and the key is like the substrate fits in perfectly it splits into the two new products and that then your body can do whatever it wants with that okay so pretty straightforward so you shouldn't be too um you know it shouldn't be too tricky but i think the key thing here is the is the bit about the enhancement and being stereo specific make sure you alert to that and you're aware of that and when they ask a question just make sure you're aware that not all molecules can be and can fit into the enzyme it must be it must fit in perfectly but also they are chiral as well okay right so the rate of reaction can be slowed down by using inhibitors okay to block the active site from a substrate so for example um if we don't want um if we don't want a drug to be effectively released very quickly we want to be a slow release one and what we can do is we can create these inhibitors which block some of the enzymes and that slows the rate of reaction down so an inhibitor is basically a substance that's a similar shape to the active site of the enzyme um but you can see so you can see there there's our substrate there so this is in green and there's our inhibitor here but you see the inhibitor actually has a slightly different shape as you can see here now what the inhibitor is doing is it's actually blocking the active site here from that substrate to enter okay and so the more of these that we've got the more active sites will be blocked and therefore the rate of reaction will then decrease so it really does depend on the amount of these inhibitors that we've got and that we've got sitting within our active site of our enzyme so another factor as well to consider is how strongly that actually binds to that active site so if it binds really poorly then the rate of reaction won't be reduced as much so it is about the um you know the adhesive power is supposed to sit within that active site that is really very much dependent if it just falls out then you've now got an active site that's vacant and that substrate can then um enter at that point okay so you can see that's quite common sense it's kind of blocked it's a little bit like don't get it confused with this though a bit like poisoning so catalytic poisoning so we're blocking the site from from from um allowing a reaction to occur so some drugs like antibiotics these work as inhibitors okay so very very important this actually because antibiotics are um only be used and you may know this as well but antibiotics should only be used if you've got a bacterial infection so they won't work for viral infections um mainly because of the you know the virus and the bacteria is very very different so antibiotics only work if you think you've got a bacterial infection so some antibiotics work as inhibitors and what they do is they block the active site of the enzyme that is responsible for making the cell wall of a bacteria cell okay so remember from a bacteria it has a cell wall um it's the cell what all cells do they have a cell wall and and if the cell wall can't be made then the bacteria cell will burst and die so a lot of these enzymes is basically preventing the production um you know the tools needed to to make the house it's a bit like say if you've got a house um and it's gonna be built from scratch then it's a bit like um telling the builders that you're not gonna get any bricks they can't build house can they so um they can't work if they don't need bricks if they've got everything else that's fine there's no good if you don't have the out the outer shell um so as active sites are stereo specific it can be really difficult to find drugs that fit into that active site so if the drug's chiral then only one of the enantiomers will work and that's what i was talking about before and sometimes the other enantiomer may actually have a negative effect um you know on your body you've got to be you've got to be careful with that and so when developing new drugs it requires it requires a trial and error method and scientists will try different inhibitors to see which which will work and refine the molecule on the ones that that don't okay so we're basically trying it testing it trialling it again and testing it and so you'll know that with any form of drug drugs must go through a trial phase okay so you manufacture the drug to make sure it actually works then you trial it on in humans to to make sure to see the impact are there any side effects um to the drug does it actually cure the disease so there's a long long trial process with any development of any drug and it is fundamental that any drugs that are given to patients um are safe to use and actually are effective they do work but we need to know how much of this drug do we need does it need to be a big tablet or just a tiny one does it need to be intravenous or does it all kind of be taken um orally you know through through through your gut and so to speed up the drug development um scientists use computer modeling okay to design new drugs to act as inhibitors to fit stereo-specific active sites okay and the computer models allow us to test how a drug will respond without actually making the drug and this is brilliant because scientists to make a drug make a drug and then trial it and if it doesn't work then you think right okay i'll have to make another drug and to make another one it could take absolutely ages so using computer modeling we can design a molecule specifically to fit into that site then get it out to manufacture then get it into clinical trials okay so it says um it is quite an important process and you can see there that enzymes play an important role in medicine okay so we're now going to kind of zoom out a little bit further okay so we've well we've looked at enzymes and we've looked at proteins and we'll look to how they work so now we're going to look at something called dna which i'm sure you would have heard of and dna stands for deoxyribonucleic acid okay so dna it's a polymer that's made up of monomers called nucleotides okay so it's another example of a polymer okay so dna is is effectively what makes it's the instruction manual to make us to make new cells to make new um you know new tissues new you know new people effectively you know so and dna is absolutely vital um now a nucleotide is made up of three components remember dna is made up of chain of these nucleotides okay so we're going to look at the monomer unit which is the nucleotide and that itself is made up of a phosphate a sugar and a base okay so let's look at a phosphate group so a phosphate looks like that okay so it's phosphorus in the middle with two hydroxy groups as you can see there two hydroxy groups and you've got your oxygen groups as well we've got no minus on there as well that will come into use later so a pentose sugar is an example of a sugar so it looks like that so that's pentose or two deoxyribose and then we have bases okay so our bases are um adenine which is a cytosine which is c we have uh we have thymine which is t and we have guanine which is g okay and so the nitrogen's circles you see on there is where the base bonds with the deoxyribose molecule okay which is your pentose sugar so you can see here these are the nitrogens that are responsible so we have four different bases we have one type of sugar one type of phosphate group but we have four different bases to choose from here okay so you don't need to remember the structures of these you will be given the structures of these molecules here so don't panic don't worry too much about this but you do need to know how they interact within the dna molecule okay so using them three components that we've seen in that previous slide what we can do is we can come up with four nucleotides okay so the first one is an adenine nucleotide so you can see here just to show you on that molecule remember we said where the nitrogen that nitrogen was circled on the previous slide so that means that this is actually bonding with the pentose sugar which is here and then obviously onto the the phosphate which is at the top here so that there as you can see is a nucleotide okay so that's one of the monomers that make up dna okay but there's some other ones as well as you've seen so another one is cytosine nucleotide and you can see here that the nitrogen here um there it is that was the one that was circled that's the one that's bonding to the pentose sugar and then thymine nucleotide again there's the bonding nitrogen and then guanine nucleotide there's the bonding nitrogen so you can see they're all the same they've all got this pencil sugar and phosphate and same here and but this one is obviously um obviously it's the base that's changing here so these are the four monomer units effectively that make up dna and you need to be able to draw the structure of these but remember they will give you what they are they'll show you the formula of them you just need to be able to put that together okay so these molecules are complicated and thankfully because it's chemistry or biology or whatever it is biochemistry and we can actually simplify this using a diagram so let's have a look so we're going to use it looks like something from first school doesn't it so um or primary school so you've got phosphates which can be symbolized using a circle for in this example it doesn't really matter what shape they are just pick these shapes so phosphate circle um we've got our sugar which is a pentose um and our base is given a rectangle i've just color coded them so we can see the difference but we can symbolize them as that so it saves us a lot of time as you can see drawing a pentagon is a lot better than drawing a pentose sugar so actually what we can then do is we can join them all together so we can have our adenine cytosine thymine guanine and that actually builds up and you can see here there's our um our phosphate which is the um there we go which is the red and then we've got our pentose sugar which is here and you see these join all together and these form a sugar phosphate backbone with your bases sticking out you see on there and so these are obviously this is our polynucleotide chain this is what this is um and so the phosphates on one of the nucleotide is covalently bonded with the sugar one another and this creates this sugar phosphate backbone so this is fixed what changes is the bases or the bases that actually come off the top there okay and so this you'll now recognize this within a dna molecule which we're going to which we're going to look at here okay so remember that sugar phosphate backbone in dna is formed via condensation polymerization using nucleotides as the monomer units okay so we're going to use them nucleotides to form this sugar phosphate backbone so let's have a look so you can see here we've got our um two um nucleotides here okay so we've got two different bases here and we're going to react them together so remember we need to try and create that sugar phosphate backbone that we've seen before so what happens you can see here is that the um these will join together these two here these two nucleotides will join together to form this and this is your sugar phosphate backbone as you can say as you've seen before with all the different shapes and what happens is this is a condensation polymerization so what happens is the water is eliminated from it as with any other polymer and water is produced here as you can see here and then as a result we then form this phosphodiester bond okay which is this link here because water has been eliminated from the reaction so the oh groups on the phosphate and the sugar which are these two okay they can react further to extend the polymer chain so effectively and this o h here can react with with um another um another molecule and so can this one as well okay so it just joins on so you can see it's just a type of polymerization it's a little bit more complicated than the other polymers that you've seen but dna is just a polymer and you just need to be aware that it's a condensation once remember you're removing the water there so you've just seen it there in that example that's all you're looking at don't worry about the rest of the molecule okay okay so dna looking at that structures we've seen what the um what the sugar phosphate backbone looks like and we've seen how it's created through condensation polymerization and we've seen all the bases that are coming off each of them nucleotides there's a lot of keywords here so we're going to put all that together to make sense of it all okay so dna is actually formed from two polynucleotide strands okay so remember that okay they're twisted together to form this double helix and this is your classic shape of your um of your dna molecule now you can see we've got our different just observations on the diagram you can see that we've got different colors here so we've got yellow green and we've got like a like a reddish red pink color and purple okay and you can see these colors represent the bases and these lines here are your nucleotide strands your sugar so your sugar phosphate backbone and each of them sugar phosphate back ones you've got bases coming off it so remember in that previous slide where we showed the diagram and we showed where these bases were coming from we had our sugar phosphate backboard at the bottom there now what we've done is taken a long chain of that and twisted it into this dna structure that we see here okay so the polynucleotide strands okay so these are held together by hydrogen bonds between the bases so remember the bass is sticking out they actually start to interact with opposing basses on the either side okay now there's a particular order okay some uh one bass will only interact with another bass um so they it's effectively best friends okay so remember this so a a adenine bonds with thymine which is 80 i remember it as 18 okay um so the a-team if you don't know that then go and google it um so remember is the a team so adenine with thymine is a t and cytosine bonds with guanine which is c and g they're the only two which will pair up c will not bond with t it doesn't want to be near t okay a and t will only bond together and c and g will only bond together so they're very very they're a bit fussy they only want to bond in that order okay so both strands in the dna as a result are complementary which means where there's an adenine on one strand it will align with thymine and cytosine will align with guanine so you can see here that the yellow is matching with the green so adenine with with thymine so a t okay and then c and g cytosine guanine so cytosine and guanine so they they they pair up very specifically and you must remember what pairs with what okay really really important so there is a particular order so it's not just are they bonds they just bond however they please that isn't the case they are a little bit fussy okay so the bases are paired up in specific ways so we've seen them bases that are formed as you can see within our dna and they're joined together using hydrogen bonding okay so as we've seen before the a bonds with t and g bonds with c um um and the arrangement of atoms and they're arranged in a particular way and it allows them to actually form a hydrogen bond so let's have a look so here's our um two different bases here so we're just ignoring the sugar phosphate backbone we're literally zooming in on them two colored bases that are joining together okay so we've got a and t so let's have a look at that one first so you can see there we are so the hydrogen bonds form when we've got our delta positive hydrogen which is here on the amine molecule which is there that interacts with an electronegative element um so the hydrogen there interacts with the oxygen on the thymine molecule which is here which has got the lone pair and vice versa nitrogen on the adenine molecule has lone pair of electrons and that reacts with the um hydrogen you can see on the nh on the thymine molecule so you can see here they align perfectly this is though it's been specifically designed this is sticking out here and this isn't so it's perfectly designed and this means they've got this little interaction here and that holds then bonds together between the two strands in dna and so we can also do um the same for um also here we go so that the a and t uh form hydrogen bonds as there's two like i say there's two atoms to form hydrogen bonds and likewise in g and c we've got three here so we've got one here one here and one here so remember what we what criteria we need for hydrogen bonds so we need nitrogen oxygen or fluorine bonding with a hydrogen so that's from here one chemistry so as long as you're aware of that then i'm sure you'll be able to find where the hydrogen bonds are in between these two bases okay so no other base pairings can happen as the partially charged atoms would be too close to each other and repel um or did not get close enough to um for a hydrogen bond to form so this is why they don't just pair wherever they want and they are very picky and so a and t will only bond and g and c and will only bond because they are lined perfectly to form these interactions okay so um dna is a twisted double helix um and so to allow the bases to align perfectly um to form them to form them bonds so it's twisted for a reason because it allows these bases to really kind of align perfectly and it holds the structure of that dna double helix that we've seen before okay so there's a lot of information in there the key thing is just make sure okay run through this video again and go through it and look at them keywords there's a lot of different keywords and this is quite tough um obviously if you do biology it might be a little bit easier but there's a lot of people who don't do biology and study chemistry so what i'd recommend particularly for you for those people is you just go through this video again run through it and just familiarize yourself with all this new terminology okay um right so let's look at the last uh towards the the last part of the video and this is where we're going to look at cis platinum okay so remember we're talking about anti-cancer drugs i mean you might have seen this in the transition metals video that i've done as well and where we looked at cis platinum in particular because it's got platinum in there which is a transition metal so cis platinum is an anti-cancer drug which has that square planar complex remember um and it has a platinum metal line in the middle two ammonia ligands and two chloride iron ligands surrounding it so if you've seen that video you'll be familiar with this and you can see that in cis platinum cis means the same side trans as opposites it's not transplant and this is cis platinum so this means that our chloride ions as you can see there are um next door to each other adjacent to each other and our two ammonia molecules are also adjacent to each other so we call this cis so we have this um very specific shape here cisplatin um is an anti-cancer drug transplant doesn't okay transplant if we had their molecules opposite each other then it wouldn't be an anti-cancer drug so it's really important it must be structured that way okay so cancer what is cancer so cancer is is is made up of cells that multiply in an uncontrollable fashion we call that a tumor and they do this by replicating its dna so cancer is basically your own cells it's your own cells which have copied wrongly so i imagine it a little bit like imagine you've got a um let's say you've got a um a textbook let's say okay a textbook has a 150 page let's say it's got 100 pages in that textbook is like your dna it has all the information that you need to understand whatever that textbook is telling you about okay so every day day to day your body has to make brands new cells all the time especially skin cells blood cells you know loads of different types of cells that you that you need to replicate um now to replicate these cells we need to make an exact copy of an existing one so it's a bit like you taking that book and photocopying every page in that book now if you photocopy every single page you've got an identical copy to your original and that's fine but sometimes because these are happening so often sometimes there's a mistake and sometimes you might copy all the pages but you might forget to copy page 42 in which case there's a bit of information missing and so you have a cell that looks it looks like a cell but there's a there's a deformity in that now if that if that cell if you then say right i've copied that and then you then take that dodgy copy and copy that one you're then going to make multiples of these dodgy copies and so it's a bit like your body does the same thing it's it replicates a cell but this cell's got a slight fault in it and if that is then copied and copied and copies uncontrollably so in other words it's just not stopping then you form um a lump a growth and that's a tumor now cancer is dangerous if it spreads okay so if these cells start moving away from the location where it was then it starts replicating and spreading then you've got issues because it effectively needs a blood supply it's a cell so it'll take nutrients and and the blood supply and it may push against other organs which may cause a lot of pain and you know so it's really really serious and it's difficult to treat because your body as far as your body is concerned it's your own cell so um it needs um help to destroy or either mark these cells in some way or destroy them so cis platinum binds to dna in these cancer cells so it seeks out these cancer cells chemically so it's a chemical drug um and it binds to the dna in these cells and so as the complexes attach the dna what it does is it prevents that cell from reproducing through the normal cell division that you would that you would see so remember if you do biology here's the biology bit so um this would be mitosis okay so um mitosis is where you get the the division of cells and it stops that from happening the cell dies because it's unable to repair itself so it blocks the spreading of this cancer okay so it's quite useful as you can see so the how it works the chloride ions in the complex are really easy to displace okay and they can detach themselves from this complex fairly easily and so the platinum so this bit here in the middle can then bind to the nitrogen atoms and the guanine base within the cancer cells dna okay so this can bond quite quite nicely these can break off fairly easily they're quite weak bonds remember they're coordinate bonds so another guanine base can do the same with the second chlorine in the cisplatin as well okay so we've got another another base that's in there so it's a a guanine based styme and so the cis platinum bonds to the dna it creates a distortion in that strand so it creates a bit of a kink in that strand and it means that it can't unwind itself so remember uh when you again if you do biology you'll know about rna messenger rna et cetera and the dna to replicate itself it must unzip itself okay and it must replicate the bases to form another strand okay which is your rna and then that is then raveled back up again with another strand to form a new dna so if there's a big if there's a big block it's a bit like um having a book okay um and um somebody has put your want to copy that book okay and somebody has put um somebody's put a hand say you you turn to the pages you're copying it somebody's put the hand in the place of one of the pages it's stopping you from copying all of that or let's say they rip out that page so it's a little bit like this so cisplatin is acting as that person putting the hand on that book stopping you from actually copying it okay copying the full amount so that is effectively what dna what cisplatin does it really binds on a molecular level to that dna the problem is though as you may be aware with cancer is that cis platinum will also prevent healthy cells from reproducing it's not as specific as we like it to be and this is the reason why you still see even though we can cure the vast majority of cancers if they're caught early enough we can and but this is why research still needs to go on because we develop drugs this is chemotherapy and you see the effects you know if anybody's seen somebody going through chemotherapy you see the effects of um you know receiving drugs like this can people can lose the hair for example because it kills off the hair cells they can lose a lot of weight they lose their appetite their their vomiting you know it has a really there's some nasty side effects with it but you know the you know the the the advantage i suppose is that hopefully it will kill off the cancer and you won't have it anymore so you know that outweighs it's that short-term pain for long-term gain as they say so it that's the downside so it affects like say the blood supply so the immune system is suppressed so if you've got if you're going through chemotherapy you're probably likely to catch infections where you wouldn't normally carry it because because your immune system is down um obviously you can risk kidney damage as well and hair cells regeneration like i say you can lose your hair so you know if you're under um chemotherapy you'll be monitored your body you know you have an mot regularly to make sure that your body is functioning the right way blood tests to make sure that your organs are not shutting down because of this um because of the chemotherapy so like i say um the effects are the side effects of cis platinum can be reduced though by giving lower doses and using a more targeted delivery um of the drug to reduce the attack on on healthy cells okay so um we use a combination this is why hospitals use a combination of chemotherapy which is chemical therapy and radiotherapy which is using radiation to shrink the tumor to a much more manageable size and also you can operate as well you can remove physically remove the tumor if it's if it's causing problems you can physically remove it but there may still be some cancer cells in there so it's about trying to blend it with variety of different techniques to reduce the amount of chemotherapy or the length of time you have to have chemotherapy obviously it depends on how aggressive the cancer is but like i say despite the short-term side effects cisplatin's still used as chemotherapy treatments and because the long-term benefits obviously outweigh the short-term pain that you may get because in the hope that it could eliminate the cancer completely and clearly that's that's more of a um you know an advantage is despite the side effects you know hopefully you'd be cancer-free um okay so that's it so that's the whole video on amino acids proteins and dna there's a lot in there especially if you're not um okay with biology you don't study biology i recommend you just run through that again and just familiarize yourself with the keywords there is a full range of aqa videos in year one and year two there's also whiteboard tutorials and past paper walkthroughs it's all an ally chemistry youtube channel um it's all for free all i ask is that you hit the subscribe button that'll be absolutely fantastic that show your support um and also um it'll you'll get the notifications as well you get keeping up to date with any new videos that i'm putting on and also if you want to copy these click on the description box the link in the description box and you'll be able to get ahold of that absolutely great value for money right that's it okay bye bye