Hey everyone and welcome to this entire topic one video for AQA Alevel biology. And if you didn't know, you can actually download for free a workbook that you can use alongside this video so you can fill in the gaps, create your own notes as you go. So check that out in the description. Plus, if you want even more help than that, getting those top grades, then check out my flashcards and my A4 notes, which are mark scheme specific. I update them every single year to make sure it stays bang on with that mark scheme. But for now, that's it. Enjoy the video. AQA biology topic 1. And we start with 3.1.1 monomers and polymers with two very simple definitions that are here for you to learn. Monomer, which is the smaller units from which larger ones are made. The way to remember this is mono means one. So you've got these single smaller units. Poly means many, but the literal definition that they'd want for AQA is polymers are molecules made from a large number of monomers joined together. These are the definitions as they appear in the specification which means that is what they'd want on the mark scheme. So the monomers and polymers that you need to know for AQA a level biology are the monossaccharides for example glucose and we'll look at all of the other monossaccharides that you need to know amino acids and nucleotides. The polymers are starch, cellulose and glycogen which I've put within this row because those are carbohydrates. then the polymer protein made up of amino acid monomers and then DNA and RNA polymers which are made up of the monomer nucleotides. Now there are two key chemical reactions that you'll see come up throughout this topic because condensation reactions are the ones that join molecules together. Hydraysis reactions are the ones that split molecules apart. But in terms of an exam style answer, here are your bullet points of exactly what you would need to say to get full marks on a question that asks you to define a condensation reaction. It joins two molecules together. It forms a chemical bond and it involves the elimination of a water molecule. Hydrarolysis is the opposite. It breaks a chemical bond between two molecules, meaning it's going to split them apart, and involves the use of a water molecule. Now, these are your generic definitions. If you were asked in an exam question to describe how a protein forms or how a disaccharide forms, they would want you to give the definition of a condensation reaction. But in terms of proteins, you'd be saying two amino acids together forming a peptide bond. So basically, if it's an applied example, you have to name the two molecules and name the bond. Same with a hydraysis reaction. If it was applied example, you should be naming the chemical bonds that's broken and naming the molecule that's been split apart and what are the two molecules it's been split into. More on that later throughout this video when we see these applied examples. So that takes us on to 3.1.2 carbohydrates. And here's just a general overview of the different carbohydrates that you need to know for AQA biology. The monossaccharides are the monomers and it's these three here. Glucose, fructose, and galactose. Disaccharides are made up of two monossaccharides. And you need to know about sucrose, moltos, and lactose. And then the polysaccharides, these are made up of multiple monossaccharides bonded together. And you need to know about starch, cellulose, and glycogen. Looking at the prefixes here, we've got mono, that means one. Di means two. Poly means many. So bear that in mind for all of these. Monossaccharides are one sugar unit. Disaccharides are two. Poly means multiple joined together. So let's have a look at each of these in the level of detail that you need to know. Starting with the monossaccharides, we have glucose, fructose, and galactose. Like we just said, these are the monossaccharides. And a monossaccharide is the generic term for the monomers from which larger carbohydrates are made. And to turn those monossaccharides or monomers into the polymers, which are polysaccharides or even into disaccharides, you would have a condensation reaction between two monossaccharides. And the name of the bond is a glycosidic bond. So in carbohydrates the bonds that you need to learn for how you join multiple monossaccharides together is a glyosidic bond. Now you need to know the structure and the chemical formula for glucose. You don't need to know it for fructose and galactose but you do need to know it for glucose. So chemical formula as you learned at GCSE six carbons 12 hydrogens and six oxygen atoms. This is the level of detail that you need to know the diagram to show how those atoms are structurally arranged. So you don't literally have to show where all of the carbons are, all of the hydrogen's and all of the oxygens. They just want you to see the ones that are going to be of relevant information when we come to the bonding. But just as a bit of information inside of this ring, this hexagonal ring, we have got these corners, let's call them. And wherever you've got these corners, that is representing where carbon would be. So this would be carbon and we actually call it carbon 1. This is carbon 2, carbon 3, carbon 4, carbon 5, and the sixth carbon branch is off the top there. But you wouldn't be asked to do that. You just need to know you've got a hexagon. You've got a branch coming off here. Oxygen is at this position in your hexagon. And then on carbon one and carbon 4, it's symmetrical. a hydrogen atom on top, a hydroxal group on the bottom. So you do need to know that that is called a hydroxal group. Now this is actually called alphaglucose and that's because there are two isomers of glucose that you learn. And for those of you that don't take chemistry, you might be thinking what is an isomer? Isomers are when you have the same molecular formula. So C6 H1206, but those atoms are arranged in a different structure. So structurally it's different but it contains the same atoms. So we've got alpha glucose here on the left that we just talked about. Beta glucose is here on the right. And the only difference between them is carbon one we have flipped the hydrogen to be at the bottom. Hydroxil to be at the top. Now so for alpha glucose it's pretty much symmetrical with the exception of the branch there and the oxygen. But in terms of what's on carbon one and four, it's symmetrical. Whereas on beta glucose, they've flipped around and that has relevance to the final shape that polysaccharides have when lots of these bond together. So I'll come back to that when we get to the polysaccharides. But first, it's the disaccharides. We've covered now everything that you need to know for the monossaccharides. Dysaccharides are formed by a condensation reaction or the condensation of two monossaccharides. We have a chemical bond which is a glycosidic bond that occurs. And these are the disaccharides that you need to know. We said moltos, lactose and sucrose. But here are the word equations. Glucose and glucose is moltos plus water. Glucose plus galactose is lactose plus water. Glucose plus fructose will make sucrose and water. So ways to try and make this a bit easier to remember is first of all all of them contain at least one glucose molecule which is why I've put those glucose in bold. Moltos has got two glucose. So that's what you need to remember for moltos. Lactose is made up of glucose and galactose. That one's probably an easier one to remember because galactose has lactose within the name. And then sucrose is glucose plus fructose. Other thing I've put in bold here is something else that's the same for all of them. One of the products for all of these is water. And that's because they are joined by a condensation reaction which we said is the joining together of two molecules forming a chemical bond with the elimination of water. So that is why water is one of the products each time. So those could be a good thing to put on a flash card just to test yourself until you can remember those word equations. So just to show you these condensation reactions, we can see here we've got two monossaccharides. We've shown some of the atoms within them, but the ones of interest are on carbon one and carbon 4, the hydroxal group at the bottom here. And this is where the water is going to be removed from. So I've highlighted in blue the two hydrogens and the oxygen make up the H2O that gets removed. Now it doesn't have to be the O of carbon 4 and the H of carbon 1. It could be the O of carbon 1 and the H of carbon 4. I'd have to have highlighted these. But the main thing is it's from the two hydroxal groups that the water is removed. That leaves you one oxygen atom behind. And that's where we get this glycosidic bond. The carbon to the oxygen to the carbon. And this is actually called a one to four glycosidic bond because it's forming between carbon 1 and carbon 4. A hydraysis reaction. So the opposite of this, it's through the addition of water, a chemical bond is broken. So that' be breaking this glycosidic bond and that then splits those two molecules apart back to their original monossaccharides. And we can see here the water has been reinserted as our hydroxil and hydrogen to make up that other hydroxal group. So last in the carbohydrates then is the polysaccharides which are created by condensation reactions between many glucose monomers and you learn about starch, cellulose and glycogen. Starch is found in plants as is cellulose. Glycogen is found in animals. And the overall function of these are starch is a store of glucose. Cellulose provide structural strength to the cell walls. And glycogen is also a store of glucose. But we can have a look at all of those in more detail. This is your summary table of everything you need to know for the polysaccharide. So take a screenshot or pause or if you have downloaded the booklets that you can get for free in the link in the description then pause at this stage and fill in this table in your booklets. So the monomers is one thing that you need to know. Starch has alpha glucose as does glycogen. Cellulose is beta glucose. Now as we go through this table you will notice that everything we say for starch it's very very similar to what we say for glycogen. And that's because these two molecules are structurally very similar. And that's because they both perform the same function. It's just starch performs this function of being a glucose store in plants whereas glycogen it's a glucose store in animals. So there are a lot of similarities between these two. Cellulose has got a completely different structure because it's got a completely different function. So bear that in mind as we go through. So starch alphaglucose is the monomer. It's glycosidic bonds, but we talked about a one to four glycosidic bond when we saw that very basic animation showing a condensation reaction, but you can actually also get one to six glycosidic bonds. And carbon 6 is the one that branches off the top of the hexagon. So if you get a bond between carbon one of one monossaccharide and carbon 6 of another that creates a branching point in the structure. So we get 1 to4 and 1 to six glycidic bonds here. Function we've talked about store of glucose found in plants in particular get a lot in the chloroplasts. And then the structure. Although I've talked about amaloes and amalo pectex in here, I haven't actually seen those two terms come up on the new spec yet in a mark scheme, but I'm keeping it in just in case and so that you've got the full understanding. So amalo this is one of the polymers in starch which is made up of only one to four glycosidic bonds between the alphaglucose and that results in this long unbranched chain which then coils up to make a helix. Amalopectin is another of the polymers in starch and this one has got 1 to four and 1 to six glycosidic bonds. So that means you end up with these straight chains with branches coming off them. Now the advantage of these two structures linking to the function of being an energy storage is if it can coil up into a helix because it's a coil that means you can then compact it down to fit a lot of glucose in a small space. the branch structure on the amalop pectin that provides a greater surface area of exposed ends of the chains. So if you did need to hydrayze the starch back into glucose for respiration, then having more branches and therefore more exposed ends means that hydraysis of starch back into glucose happens more rapidly which is needed for glucose for respiration. And I actually paused and typed that in here cuz I remember they've got really picky on you saying that in the mark scheme in the last couple of years. So you would have to say rapid hydraysis into glucose for respiration to get that mark. So highlight that in this table as you write it out. Now it's also a really large molecule which means it's insoluble and therefore it's not going to dissolve and affect the water potential and therefore have any impact on osmosis. I'm going to jump to glycogen next cuz that's so similar. Alpha glucose again 1 to 4 and 1 six glycic bonds store of glucose but this time it's found in animals mainly the muscle and liver cells. It's a highly branched molecule. So this actually has a higher proportion of the 1 to six glycosidic bonds compared to starch. And this means we have even more branches and you get an even more rapid hydraysis of glycogen back into glucose for respiration. The advantage here is glycogen is the store of glucose in animals and animals move. They might have to run from a predator and for that you need muscle contraction which requires ATP from respiration. So animals need to be able to hydrayze their glucose store more rapidly for respiration because they might need to run or fight to protect themselves. Plants don't have that. That's why they don't have as many 1 to six glycosidic bonds. But in terms of the structure linking to the function, exactly the same as it was for starch. Branch structure increases the surface area for more rapid hydrarolysis back to glucose respiration. Insoluble, so it's not going to affect the water potential. you don't actually get this coiled structure. Um, so I'd go for these two if I was asked to give marking points for that one. Then cellulose, this one's completely different. It's beta glucose. We have one to four glycosidic bonds and this time we have the function of it provides structural strength to the plant cell walls. Now for the structure here you have long straight chains of betalucose and that's because the one to four glycosidic bonds form directly next to each other which we saw in that animation when we looked at where the bond forms. So you end up with this long straight chain. The chains are held in parallel. So you have multiple long straight chains held in parallel by hydrogen bonds to make a structure known as a fibral. And one hydrogen bond is not strong. But because there are so many hydrogen bonds collectively they provide the structural strength to the plant cell wall is also insoluble. So it's not going to affect the water potential. One extra point just to add here about the structure that you'll see is every other beta glucose in these long straight chains is inverted 180° C which basically means it's flipped upside down. So we can see here the CH2O is at the bottom then it's at the top then it's at the bottom then it's at the top. So that has to happen in order for you to get this continual chain of one to four glycosidic bonds and these long straight chains. So that's often work worth a marking point as well. So how do we test for these biological molecules then? So the test for starch is you add iodine solution. A positive test observation would be that it goes from this orangey brown color to bluey black. The test for reducing sugars, you add Benedict's reagent and heat. You need to name the reagent and you have to say heat to get this mark. And we can see here Benedict's reagent is this blue color. A positive observation would be that that blue color turns. And there's actually a range of different colors it can turn depending on the concentration of sugar present. So you can go from green to yellow to orange or brick red. And the more red it is, the higher the concentration of sugar present. So this one here is orange. That's quite a high concentration of reducing sugar present. The non-reducing sugars which is only sucrose. The reducing sugars is all of the monossaccharides, all of the disaccharides except sucrose. You don't need to learn about why that is the case. You just need to know that sucrose is the only sugar that you learn that is non reducing which basically means it can't reduce the copper sulfate in Benedict's reagent. So for the non-reducing sugars test, this would be a longer question because there's more stages. First of all, you have to do a reducing sugars test. And if you get a negative test result for that, meaning it remains blue, that tells you you don't have a reducing sugar. So the next step is then to see, well, maybe it is still a sugar, but it's non-reducing. And the way to test for this is by splitting sucrose our non-reducing sugar back into its monossaccharides to confirm that it is sucrose. Now to do this we have to hydrayze sucrose back into the monossaccharides. And this is done by something called acid hydraysis. But the marking point would be add acid and boil or boil an acid. You don't have to name which type of acid. You would then cool the solution and add an alkali to neutralize it or in fact it goes beyond neutraliz and it makes it slightly alkaline because that is the pH that Benedict's reagent works best in. Then you would have to say add Benedict's reagent and heat. And yes, you do have to say step four. Sometimes students miss that one out cuz I think well I've already talked about that in step one. But this is actually now starting again after you've done the acid hydrarolysis. And because we cooled it down, you have to heat it up again. So don't miss this mark. Add bendix reagent and heat. And this time the positive test observation, it will go from that blue to probably orange or brick red. You don't usually get the yellows or greens for this. And this is often an application question. And it's because you should have quite a high concentration of sugar. Now, because if you started with sucrose, lots of sucrose molecules, which are disaccharides, and then you hydrayzeed that into monossaccharides, you've now doubled your sugar concentration because you might have gone from, let's just make this simple and say 10 sucrose molecules. After we hydrayzeed that, that now made 20 monossaccharides. So, you have a higher sugar concentration. That's why you should get orange or brick red as your positive test result. 3.1.3 is lipids. So the two lipids that you need to learn about are triglycerides and phospholipids. Triglycerides are formed by a condensation reaction and the molecules that you're joining together are one molecule of glycerol gets three fatty acid molecules attached to it. So you actually have three condensation reactions happening here, one for each of those fatty acid chains. In a phosphoipid, you still have a glycerol molecule. You still have fatty acid chains, but you don't have three, you have two because one of the fatty acid chains is swapped for a phosphate group instead. And we'll have a look at some images of this as well. So, the condensation reaction is occurring between the glycerol molecule and the fatty acid for both of these. And the bond that is created is called an esther bond. We talk about R groups with the lipids and the R groupoup is linked to the fatty acid and with your fatty acid the R groupoup can either be saturated or unsaturated which we'll come back to but this is just visualizing what we were saying in terms of the structure. So this one here is a triglyceride tri meaning three and we have three fatty acid chains. So you have glycerol at the top here. You might be shown it from a different angle, but basically you have a glycerol backbone with three fatty acid chains attached to it, which would have been three condensation reactions and therefore three esther bonds for the phosphoipid. One of those fatty acid chains is not present and instead we have a phosphate group. So it would have been two condensation reactions, two esther bonds. And this is just showing you a bit more detail about the condensation reaction between the one molecule of glycerol and the three fatty acid chains. So here is glycerol. You don't need to learn the chemical structure of it. But we do have glycerol with the hydrogens on this side, fatty acid chains which end in a caroxile group C double bond O. And the water is removed from that hydroxal group and that hydrogen. And we can see the esester bond then is a carbon to the oxygen to the carbon but with that double bond O and the H and H there. So that forms an esther bond and they've got that written here our um esester bond. So this is just showing you once more just to make sure we're all clear on this because sometimes they do ask you to circle where the water's removed from where the esester bond would form. So here's glycerol. Here's one of the three fatty acids. Here's where we're removing the water from. And that is where the water is going to be removed. There is our esester bond that is made or the three esester bonds. And that means three molecules of water have been made because of those three condensation reactions. Now we talked about the fact that there are fatty acid chains and the R group can be either saturated or unsaturated. So R group generally means a variable group, the bit that's different every time. So for all fatty acids, they all start with a caroxile group, which is the name for this C double bond O. And then you have this hydrocarbon R group, meaning it's just made up of hydrogens and carbons. And it can either be saturated or unsaturated. Saturated is when you only have single bonds between all of the carbons in the chain. and therefore you have the maximum number of hydrogens bonding to it. So it's saturated. But to get the mark you would have to say only single bonds between those carbon atoms. When you have an unsaturated fatty acid you have at least one. We've only got one in this picture but you could have multiple. So at least one double bond between the carbon atoms. And because of that double bond there, that now means we've got a bond used up here, which would have been used to bond a hydrogen. So it is now unsaturated because it's not bonded to the maximum number of hydrogen's possible because the bond is used up in that carbon carbon double bond in set. But for biology, the definition is the parts highlighted in yellow. So you need to know the properties of these different lipids. So triglycerides they are an energy storage molecule and the way that the structure links the function is the energy storage parts is the idea that there's a large ratio of these energy storing carbon to hydrogen bonds compared to the number of carbon atoms present and that in terms of the chemistry behind this provides a lot of energy storage. You don't need to know the ins and outs of why you just need to know that's the fact. There's also a high ratio of hydrogen to oxygen atoms and they can act as a metabolic water source. Basically meaning that triglycerides can release water if they are oxidized. And that's essential for animals in deserts. So for example camels, their hump is made up of triglycerides, not of water, but they can then break down those triglycerides um to get this metabolic water source. Triglycerides do not affect water potentials because they are insoluble in water. Therefore, has no impact on osmosis. And that's good because we don't want lots of water moving in or out causing cells to burst or shrivel. Now, that is because they're very, very large, but they're also hydrophobic. Now, this isn't a term we've come across yet, but hydro means water. Phobic literally means fearing, but in terms of biology, it means to repel. So, water repelling. and that's what makes them insoluble in water. Lipids also have a relatively low mass and that means you can store a lot of these lipids without it increasing the mass as much as let's say muscle tissue would and therefore it's not going to impact mobility as much. So phosphoipids in contrast these have a very different function. This is just showing us the structure again. We've got the glycerol molecule, two fatty acid chains and the phosphate group. Now, although this picture is showing one saturated and one unsaturated fatty acid chain, that is not always the case. It's just what this picture is happening to show. So, we've got two condensation reactions would have occurred to make two esther bonds. And the key difference here is the properties that this phosphate group provides on what we call the head of this structure. And the head is basically the red circle that we've drawn around the phosphate group and the glycerol molecule. That part is known as the head and it's described as being hydrophilic. Hydro meaning water. Filic literally means loving. But that's not what we mean in biology. Hydrophilic means that it can interact with water. It's not going to be repelled. Instead, it can interact. And that is because of this charge on that oxygen in the phosphate group that makes it polar, meaning it's got a charge. And therefore, it's going to be able to interact with water, but polar molecules repel fats or lipids. So, we've got this hydrophilic head that can interact with water, but repel lipids. The tails are known as hydrophobic tails. They don't have any charges on them, so they are nonpolar. And hydrophobic tail means it repels water but it interacts with fats. Now it's that hydrophilic head and hydrophobic tail that link to the main function which is the fact that phosphoipids form cell membranes. They create this phospholipid blayer. Two layers of phosphoipids and that makes all cell membranes whether it's cell surface membrane or the membranes on organels. So in aquous environments because of that liquid that water the phospholipids will arrange like this. The hydrophilic heads face outwards towards the water because they can interact with it but they're repelled by the lipids. Whereas the hydrophobic tails are repelled by water on the outside. So they spin inwards and they can interact with the um fatty acids on the other side. So that's why it forms this billayer in this structure. Now the test for lipids in terms of the biochemical test is you would need to take your sample that you're testing, mix it or shake it with ethanol, then you add distilled water and a positive test result is white in color and we describe this consistency as an emulsion. For this one, it's really important that you don't say add ethanol and water and mix. You have to add the ethanol first. And then you add the distilled water. And in terms of in the mark scheme, they often accept you saying mix and shake at 0.1 and at point2. Whenever I've done this experiment in the lab, I always do it in this order. And you can see you do get that um test result there. 3.14 is proteins. So amino acids are the monomers from which proteins are made. And proteins have loads of different functions because there's so many different proteins that can be made. And what's different about all of them is their final 3D shape. And that is what determines the function of a protein. You need to know the general structure of the monomers, the amino acids. So here we have what's known as the central carbon. And coming off that you have the amine group NH2, a caroxile group C. You have an R group which is this variable group meaning it's different every time. And because there's 20 different amino acids, there's 20 different options of what that R group could be. And then there's always a hydrogen atom as well. You do need to draw the amine group on the left, the caroxile group on the right. But it doesn't matter if you have the H or the R on top or on bottom. So the best way that I find to remember this is always draw your central carbon first, which means the carbon in the middle and then four branches coming off it. And then it's just trying to remember amining group NH2 on the left, caroxile group, CO on the right, R and H top and bottom. So as I said there's 20 different amino acids and what is different each time is which side chain they have which is that variable R group to form a dieptide which means two di means two two amino acids bonded together. It is another condensation reaction. So we can see we've got the hydroxal group removed from the caroxile group of one amino acid and the hydrogen removed from one amine group of the other amino acid. That is where the water is being removed from. The two molecules being joined together are two amino acids and the bond that is formed is a peptide bond. So that is how we make a deptide. A polyeptide means many amino acids joined together via many condensation reactions and many peptide bonds would form. Now when you do have your polyeptide chain that is then arranged into four levels of structural arrangement the final finished protein is either tertiary or cturnary in um structure. Primary is the first structure that's made but it has to be processed, folded and packaged. So the first stage is making it a secondary then a tertiary. Sometimes it's a quarterary. So let's go through what each of these terms mean. The primary structure is the order or sequence of the amino acids in a polyeptide chain and those amino acids are held by peptide bonds. This used to always come up as a one mark question. It just be that first bullet point. Now since about 2023, I've seen it come up as two marks and they wanted you to say as your second mark held by peptide bonds. So let's add that in. And as a key point, they will underline the word order or sequence. You have to say that to get the mark because the order that the amino acids form is going to determine the 3D shape that we see in the tertiary structure. So that's the first level of arrangement that then will go to the GGI body or GGI apparatus and gets processed further into our secondary structure which will either be an alpha helix or a beta pleated sheet. That's the name for these two shapes. And what happens is that sequence of amino acids that we saw in the primary structure that goes and gets coiled or folded into these two shapes. And the key thing is knowing those are held in those shapes by many hydrogen bonds. So your key marking points for this one would be stating alpha helix and betle sheet held by hydrogen bonds for your two marks. And you could be asked where do the hydrogen bonds form? So it is between different amino acids and it is between the oxygen and hydrogen. the oxygen in the C double bond O of a caroxile group and the hydrogen in an amine group. So that's what I'm showing you here. These pink dash lines are representing hydrogen bonds forming between different amino acids between the oxygen of the caroxile group and the hydrogen of an amine group. Then we get the tertiary structure. So this is often a three mark definition. It's the further folding of that secondary structure. So again, this is happening in the GG body where you process and package proteins that forms this unique 3D shape. It doesn't look a lot there because it's just a load of squiggly lines, but that is folding on top of folding to create a 3D shape. And then the third mark, you have to name the different bonds that hold that 3D shape in place. So you have ionic bonds, more hydrogen bonds, and sometimes you get a dulfide bond. Dulfide bonds means two. Di meaning two sulfide the element sulfur. So if you happen to have an R group that contains sulfur and you have two of those in your chain then you can get a dulfide bond as well. But you don't always get them because you only get those dulfide bonds. Um if you do have two R groupoups that have sulfur. Just to point out here, I've noticed I've used different spelling. It used to be dulfide was the British spelling with a PH. Dulfide with an F was US spelling. They have now just used the F spelling universally. Um, so PH isn't actually used. F is. You wouldn't get penalized in biology, but that's just what I've got that disparity there. Okay. Lastly then, cernary structure. This is when you have a protein made up of more than one polyeptide chain. And in this example, I've picked four because that links to an example that you learn later on in the course for hemoglobin. Each of those polyeptide chains is still folded up into a tertiary structure though. So this is still going to be a unique 3D shape. It's just you've got more than one polyeptide chain doing that. So the importance of the primary structure here which was our first one that unique sequence of amino acids held by peptide bonds is even one amino acid being in a different position or different sequence will mean that the bonds that would form in the tertiary structure so those ionic hydrogen dulfide bonds would be in a different location and that's because these bonds ionic bonds dulfide bonds they occur between the R groups. So if you're moving the amino acids in the chain, you're moving where the bonds are going to form between the R groups. And if you have bonds in a different place, that causes a different folding shape. And that's why you end up with a different 3D shape. So this comes up a bit later more synoptically when you learn about mutations in topic four and topic 8 because the sequence of amino acids in the primary structure is coded for by the sequence of bases in DNA. So if your DNA mutates and you get a different base sequence, you might code for a different amino acid sequence, therefore these bonds occur in different locations. You get a different 3D shape. And if that happens to an enzyme, for example, and you get a different 3D shape, that now means you've got an enzyme with a different shaped active site, and it's not going to function. And that's what we're just showing here. If it was carrier proteins though or channel proteins that you have embedded in the cell surface membrane, if they change shape then the molecule that they transport might no longer be complimementaryary and it can't be transported across the membrane anymore. So that bit I've actually already said mutations could cause this. So test for proteins then is this bright blue solution by your and it turns purple. No heat is needed. But the key thing to remember here is the spelling. Everyone that takes chemistry, you are familiar with a bureet that you use in titrations. One common mistake here is writing bureet instead of by uret. They will accept if you've spelled it incorrectly, but phonetically it sounds the same. But I just split it up here to try and help you remember. By don't say boret, you're going to lose the mark. Okay? Enzymes. This is still within the proteins topic. This is one of the key examples that you need to learn about. Enzymes are proteins that have a tertiary structure and their role is to catalyze reactions and they do this by lowering the activation energy. Meaning the amount of energy needed to start the reaction. And whilst enzymes are pretty big proteins, it's only the active site, that small part here, that is of importance importance. That's where the substrate binds. So the active site is specific and unique in shape and that is because of everything we just talked about there in protein structure. That unique sequence of amino acids determining the exact location of the tertiary structure bonds like the ionic and dulfide and hydrogen bonds causes a particular 3D folding in the tertiary structure to create that unique shape active site. And due to this specific active site, enzymes can only bind to a particular substrate and therefore they only catalyze one particular reaction and they will create this enzyme substrate complex. Key marking term that enzyme substrate complex and once you get that complex that is what lowers the activation energy. Now there's two models of enzyme action to explain how the enzymes lower this activation energy. You learn the lock and key model at GCSE. You now learn the induced fit model at Alevel as well. And this is the accepted model. Now the induced fit one, but you need to have an awareness the lock and key used to be the accepted one. So lock and key just briefly this is the idea that the enzyme is like the lock substrate is like the key and they fit due to being perfectly complimentary in shape. The enzyme never changes shape. So the enzyme active site is a fixed shape. Due to random collisions we would get the substrate binding you get an enzyme substrate complex. And once the enzyme substrate complex is formed, the charge groups within the active site are thought to distort the substrate and therefore lower the activation energy and then the products are released. The enzyme active site is empty and the enzyme can be reused. It's not used up in the reaction. The induced fit model is the current accepted model. And in this model, the enzyme is more like a glove and the substrate is like your hand. So when you've got an empty glove, it's not exactly complimentary in shape to your hand. But when you put your hand inside of it, it enables a glove to mold around your fingers and then it becomes completely complimentary in shape to your hand. That is what is happening in this model of how we think enzymes work. The active site is not actually completely complimentary in shape to the substrate until it collides and binds. because when it does that the active site molds around the substrate and then it does become completely complimentary but because it's molding around it when it's in this enzyme substrate complex that is going to be putting strain and tension on the bonds and therefore less energy is needed to break them. So that is the accepted model. Now we have more of an awareness that proteins aren't completely rigid. there is some flexibility to their structure and it better explains how the activation energy is lowered. So factors that affect enzymes then are temperature, pH, substrate concentration, enzyme concentration and also inhibitors. So we're going to go through each of these. Temperature then if you have too lower temperature then the enzyme and the substrate don't have enough kinetic energy to be able to move fast enough and have successful collisions. meaning they bind and you get those enzyme substrate complexes. And that's why we can see at the lower temperatures there's a lower rate of reaction. But as you increase the temperature, the rate increases because more kinetic energy is gained and therefore more successful collisions, more enzyme substrate complexes. So at that point, temperature is the limiting factor, meaning it's limiting the rate and as you increase the temperature, the rate increases. We then have our optimum temperature which means the temperature at which the reaction happens the fastest. Beyond the optimum there is now so much kinetic energy that the tertiary structure bonds will break. So the ionic bonds hydrogen bonds will start to break. And if you break those bonds in the tertiary structure, the tertiary structure protein is then going to unfold and you lose that unique 3D shape and therefore the active sites a different shape. The substrate can't bind. You don't get enzyme substrate complexes and the rate of reaction decreases with pH. too high meaning too alkali or too low meaning too acidic a pH interferes with the charges in the amino acid and in particular of relevance is the amino acids in the active site and this again causes a break in the bonds. So, if you've got too high a pH, that means you've got too many O minus ions, too lower pH, which is more acidic, you've got too many H+ ions. And because you've got two lots of ions there, whichever it is, those ions interfere with those charges, causing the bonds to break, the ionic bonds to break there that are holding the tertiary structure in place. So same idea again the bonds break that means the tertiary structure unfolds and you lose that unique 3D shape. We describe that as the enzymes denatured, fewer enzyme substrate complexes form and that's why the rate of reaction decreases either side of the optimum pH. Optimum pH meaning the pH which the rate of reaction is fastest and the optimum pH is different for different enzymes because some enzymes are going to be working in locations that are very acidic. So for example, the stomach has stomach acid which is very acidic. So enzymes that work there such as proteases are going to have an optimum closer to one or two but the enzyme amalayise has an optimum closer to 8 because the pH of the small intestines is slightly alkaline substrate and enzyme concentration then if there is insufficient substrate then the reaction will be lower. So we can see that here at lower substrate concentrations rate of reaction is lower. And that's because if you have less substrate present, you're just less likely to have substrate present to collide with the enzyme active site and therefore fewer enzyme substrate complexes, lower rate of reaction. So as you add more and more substrate, rate of reaction increases. You're going to have more successful collisions. So at this point with the low substrate concentration, substrate is a limiting factor. But then we get this plateau in the rate of reaction and therefore substrate concentration is no longer the limiting factor and it must be something else. And in this case it's going to be the enzyme concentration is now limiting because if you add more and more substrate eventually all of the enzymes are going to be saturated or in use. Every active site will have a substrate already bound to it. So that's why it levels off. for enzyme concentration. Some similar concepts here because at the low enzyme concentrations, you just don't have enough enzyme there to collide and bind with the substrate. So you have fewer enzyme substrate complexes. So at the lower enzyme concentrations, enzyme concentration is limiting the rate of reaction. But as you add more and more enzymes, then eventually you end up with enzymes with empty active sites because unless you also add more substrate, then you're going to end up running out substrate because that has been broken down or been turned into the product and you just have more and more enzymes that are not in use. So it doesn't have any impact on the rate of reaction. Enzyme inhibitors then are molecules that can inhibit or prevent an enzyme from working. And you have competitive and non-competitive inhibitors. A competitive inhibitor has a very similar shape to the substrate. And because it's similar in shape to the substrate, that means it's almost complimentary to the active site and it can bind to the active site to form an enzyme inhibitor complex and prevent enzyme substrate complexes. And in this way, it reduces the rate of reaction. But if you add enough substrate to the reaction, that can actually knock out the inhibitor and then the substrate can bind again. So that's why this one's known as competitive inhibitors cuz they're both competing for the active site. Non-competitive inhibitors bind to the enzyme at a point that is not the active site, which is technically called an aloststeric site, but you don't have to know that term to get the mark. You just need to know that it's a point that is not the active site. But when the inhibitor binds to that point, the alisteric site or not the active site section, it causes a change in the shape of the protein. So a slight change to the tertiary structure. And because we've slightly changed the tertiary structure, meaning that unique 3D shape, the active site changes shape and therefore the substrate is no longer complimentary and it cannot bind. So you still have this enzyme inhibitor complex and you cannot form enzyme substrate complexes and no matter how much extra substrate you add that isn't going to reverse this. So this can be demonstrated with this graph here. We've got rate of reaction against substrate concentration. The blue line is showing us if there was no inhibitor. And that links what we talked about previously with low substrate concentration, fewer collisions, but then it plateaus because you don't have enough enzymes. But in this one, we've now can see with both a competitive and non-competitive inhibitor, the rate of reaction is lower at almost all points until this bit here. And we can see that cuz the curve has shifted to the right. Now, the competitive inhibitor when you get to the high substrate concentrations, it does actually have the same maximum rate of reaction when you have a high enough substrate concentration. And that's because the high concentration of substrate will knock the competitive inhibitors out of the active site. Enzymes can then all start working again and therefore you get the same maximum rate of reaction. Whereas a non-competitive inhibitor, it doesn't matter how much extra substrate you add, it's going to be plateauing at a much lower rate of reaction because as that non-competitive inhibitor binds to the alisteric site, changes the shape of the active site and therefore the enzymes can't work any faster because the active site isn't going to be in use. So this might be some of the enzymes haven't actually got a non-competitive inhibitor bound to them. That's why you get some rate of reaction still rather than zero. Next then 3.1.5 nucleic acids. So deoxxyribboucleic acid or DNA and ribboucleic acid RNA are important information carrying molecules. These two molecules will have the same function in any living cell that they're found in. DNA holds the genetic information whereas RNA transfers the genetic information. Ribosomes are formed from RNA and proteins. That's such a small spec point that sometimes gets forgotten, but it's come up a couple of times now as a one mark question. So just remember that fact. And both DNA and RNA are polymers made up of the monomer nucleotides. So here we see a generic nucleotide. It has a phosphate group, a pento sugar and a nitrogen containing organic base. But for DNA you need to know that that pento sugar is deoxyibbos and that the options for the nitrogen containing organic base are adinine, guanine, cytosine and thymine. For RNA the pento sugar is ribos and you still have adinine, guanine and cytosine but instead of thamine you have the base uricil. So those are the two differences between the nucleotides which pento sugar it is and thamine in DNA versus uricil in RNA. The polyucleotides then both DNA and RNA form polyucleotides which means a polymer made up of those nucleotides and the way that they form is exactly the same as well. It's a series of condensation reactions and you get a phosphodiester bond. That is the name of the bonds that forms and it's between the pento sugar and the phosphate group. So for DNA it's between the deoxyibbos and the phosphate group. For RNA it's between the ribos and the phosphate group. And this is a very strong covealent bond which is important because we do not want this polyucleotide to break down because the sequence of these bases is what is going to code for the sequence of amino acids when we come to creating proteins. So a few more things about this molecule. Then a DNA molecule. So we're just focusing on DNA. Now this is actually made up of two polyucleotide chains and they join together by hydrogen bonds to form this shape here which is a double helix and you have complimentary base pairs opposite each other which is where the hydrogen bonds form. In contrast an RNA polyucleotide molecule that is just single stranded and they are much shorter compared to the length of a DNA polyucleotide molecule. So let's have a look then at this complimentary base pairing. Paying close attention as well to the complimentary spelled with an e not an I. This type of complimentary means like opposites attracting. Complimentary with an I means saying something nice to someone. So we have our complimentary bases here. Cytosine and guanine are complimentary base pairs. Meaning if they align opposite each other hydrogen bonds can form. Adinine and thymine are the complimentary bases as well in DNA. Adinine and thymine can form two hydrogen bonds whereas guanine and cyen sightseene can form three. So this complimentary base pairing is really important because it helps to maintain the order of the sequences of bases when DNA replicates and also when mRNA is being created to help ensure that the correct base sequence is maintained so that it codes for the correct amino acid sequence. So how the structure relates to the function then? So it's a very stable structure due to the phosphodic bonds in the double helix. This is talking about DNA. The double strand means that when DNA replication occurs, both strands can act as a template. The hydrogen bonds between the two strands are quite weak, which is actually beneficial because it means they can be easily broken. So again, the two strands can separate and both act as a template during DNA replication. It's a large molecule, so it carries lots of genetic information. And those complimentary base pairs enable identical copies of DNA to be made. Which takes us on to DNA replication. So before any cell divides or replicates whether that's by mitosis or meiosis all the DNA in the cell must double or replicate first of all so that when the cell divides each new cell has its own copy of DNA. This process of DNA replication is described as being semicconservative replication. What that means is in the daughter DNA, which means the new molecule that's made, one strand is from the parental DNA, which means the original DNA molecule, and one strand is newly synthesized. So, if we have a look here, this top bit is showing us the parental DNA. And we can see that we're going to make two new copies. And each of those has one strand of the original parental DNA. and one strand is going to be newly synthesized. That's what we mean by semi conservative replication. So some key things then before we go through the exact process. This is dependent on complimentary base pairing. So again just a reminder it's adinine and thymine cytosine and guanine and there's two enzymes involved DNA helilicase DNA pymerase both of which you're commonly assessed on knowing what those enzymes do. So that's a key thing to make a note of here. Starting with DNA helilicase. This is the enzyme that breaks the hydrogen bonds between complimentary bases in the poly or between those two polyucleotide strands and that then causes the two strands to separate and also the double helix to unwind. Then within the nucleus cuz this whole process happens in the nucleus there are free floating DNA nucleotides that are attracted and align opposite to their complimentary base pairs. Then DNA polymerase can catalyze the joining together of these adjacent nucleotides. So DNA polymerase is catalyzing the condensation reaction and the forming of the phosphodiester bond to create that new DNA polyucleotide chain. Now the evidence for semiconservative replication is linked to first of all Watson and Crick who discovered the structure of DNA in 1953 but they were helped significantly by Rosen Franklin's research on X-ray defraction and then they hypothesized that DNA must replicate either conservatively or semicconservatively and it was Miselson and Style who then conducted experiments to determine it is semiconservative replication not conservative. Now, these experiments I'm not actually going to explain in detail in this video because this actually comes up on the specs saying as application questions you need to be able to understand and explain it. But I do have a full video on this which I'll link here. But just search miss and style and I've got a full explanation in detail of this experiment if you've come across questions on this you weren't sure on. Right next 3.1.6 Six ATP. ATP is a nucleotide derivative and it is made up of an adinine base. So it's only got one nitrogenous base and it's always adinine. It has a pento sugar but it's ribos and it has three phosphate groups. And its role is it's an immediate source of energy in metabolic processes. And all cells must have a constant steady supply of ATP so they can perform their metabolic processes. So let's go through some of the key details. Then ATP hydraysis meaning the splitting apart of ATP which breaks off an inorganic phosphate and releases energy that is catalyzed by the enzyme ATP hydraise very similar to the word hydrarolysis. So that reaction breaks ATP or hydrayes ATP into a DP meaning diphosphate, T means triphosphate and PI which is inorganic phosphate. The energy released can actually be coupled to energy requiring reactions in cells or that inorganic phosphate that's been broken off can be added to another compound which is known as phosphorilation and that then makes that new molecule more reactive. That happens at the start of respiration. Glucose gets phosphorolated and you'll learn about that in topic five. ATP can also be reynthesized which is when ADP and PI join by a condensation reaction. It's also an example of phosphorilation cuz you're adding an inorganic phosphate onto this molecule. So this reynthesis is catalyzed by ATP synthes and that happens in both photosynthesis and respiration both which come up in topic five. So here is our word equation. ATP plus water goes to ADP and PI. Energy is released. So, it's not actually a product that you'd write in there because you can't produce or use up energy. 3.1.7 is water. And water is a polar molecule. One water molecule, so H2O, has unevenly distributed charge due to the fact that the oxygen is slightly negative and the hydrogen is slightly positive. So this symbol means delta. So delta negative delta positive which means slightly negative slightly positive. And because of that hydrogen bonds can form between the oxygen and hydrogen of different water molecules. And that concept underpins pretty much all of the properties we're about to see in water. So hydrogen bonds form between those different water molecules like we just said. And there are five key properties of water that you need to know for AQA. I've put them here highlighted in yellow and what each one means. So it's a metabolite which means it's used in many reactions. In this video alone, we've already seen it multiple times in condensation and hydrarolysis reactions. In an exam, I would state that as well. Although it's in brackets here, I would say for example, condensation and hydrarolysis reactions. Number two, it's an important solvent, meaning you can dissolve solutes in it. And that is really important because metabolic reactions happen in solution. Then we've got it's got a high heat capacity, which means it takes a lot of energy to raise the temperature of water, and that's because of these hydrogen bonds. But in terms of in the exam, they just want you to say that means it buffers, temperature changes. Number four, it has a large latent heat of vaporization. You do have to get this the right way round. High heat, large latent. You can't say high latent. So, think of the L's together. Large latent heat of vaporization. That means it takes a lot of energy to convert water in its liquid state to its gaseous state. And again, that's because of these hydrogen bonds. You'd have to have energy to break the bonds to then convert it from liquid to gas. So that means when you sweat, water provides a cooling effect because it takes a lot of energy to evaporate the water from your skin and that energy comes from the heat in your skin. So it provides a cooling effect. And number five, it has strong cohesion between water molecules and that is because of the hydrogen bonds. Cohesion meaning like sticking together with those hydrogen bonds. So because water molecules form these hydrogen bonds between each other, they all stick together and you can get these continuous columns of water inside of plants inside of the xyllem which comes up in the cohesion tension theory of topic three. And also it provides surface tension where water meets air. Meaning that you can actually balance some items on top of water and that provides a habitat for organisms. Last bit of topic one is 3.1.8 inorganic ions. Inorganic ions are found in solution in the cytoplasm and in other body fluids. They're present in the body in varying concentrations depending on different ions which they are. Each ion has a specific role and most of these come up throughout the A level in different places. We've briefly talked about in this video the role of hydrogen ions because we talked about that in terms of enzymes and how lots of H+ means that you have a more acidic solution or lower pH. So hydrogen ions affect pH. Iron ions comes up more in topic three when you learn about hemoglobin because hemoglobin contains iron ions and is actually the part of hemoglobin that oxygen binds to. So it's involved in oxygen transport. Sodium ions come up in multiple places in the A level. The first one you're going to see is in topic two for co- transansport and then again in topic three because you have co-ansport in absorption of digestive molecules. So glucose and amino acids are transported from the illium into the blood by coransport. Phosphate ions has come up in this video. They're components in DNA, RNA, and also ATP. So that takes us to the end of topic one. Hopefully you found it helpful. And if you do want readymade alleible notes or flashcards that are mark scheme specific created by me, a teacher of over 15 years, then the link is in the description. But that is it for this video. Hopefully you found it helpful and I'll see you in a video very soon.