biology i hope that you are doing well what we're going to do is finish our last bit of content this weekend so that when we come in next week we're focusing primarily on review games review practice questions and familiarize or familiarizing ourselves with the mechanics of uh the ap test that we'll be taking so what i want to do is just continue our conversation on macromolecules so if you pause this video for one second you should be able to come up with the four major macromolecules so they are carbohydrates lipids proteins nucleic acids okay so here's what i want to do is um we talked a bit about the structure of these macromolecules we also talked about uh the food sources or the places that they might come from now what i want to do is focus on this idea this is really important you want to make sure this is in your notes it's a very common ap biology question the idea is that structure determines function meaning how the particular macromolecules are oriented in three-dimensional space how they're arranged determines their function how they work now if you're familiar with engineering that should make a lot of sense right so we design the way that things look the way that they work because of the ultimate function that they that we hope to get out of them right okay so let's start with carbohydrates so if you recall carbohydrates are composed of monosaccharides monosaccharides are the monomer units the main or more most common one is glucose we also have fructose and galactose so when those monomers come together through dehydration reactions meaning a water is removed in a covalent bond is formed we form a disaccharide and then you can continue to add on more and more uh monosaccharides until you have something known as a polysaccharide it's in essence a chain of sugar uh monomers in a row now let's think it uh through this so we have uh tons of sugar and polymers how white might we arrange them based upon the particular function that we're interested in well the main ways that we can line them up are linear or branched so let's think this through so here what we're going to do is we are going to focus in on cellulose first now the question i have is do you think plants have tons of readily available glucose or are they scarce as it pertains to glucose now the answer is that it's abundant because they are photosynthesizers they produce lots of glucose so not only do they store it for energy but they also use it for protection with their cells they make cells called cell walls and one of these structures uh is cellulose so what is cellulose um well if you take a string of uh your glucose molecules and then you create bonds adjacent to the next string and so on you can create these really strong durable sheets of sugar now you're not going to generally use those sheets for energy um the the structure would be different it would look something like these here which we'll look at in a second but we're not going to use them for energy instead we're going to use them for protection so we can see this this sturdy layer that it's going to provide for each of the cells um that proves to be very important when we later talk about transpiration and and things like that okay but some of the the glucose uh is going to be used for storage so here is one way that we can store the glucose we can coil it up in a molecule called amylose so this is found in plants or we can store it in amylopectin which is kind of this interesting branch structure here in either case what you should see is that amylose and amylopectin are organized in such a way that we are able to store more glucose in a given area why is that significant because starch more broadly is basically uh stored right so the structure determines the function what is the function well we want to hold on to sugar so we can use it when we need it how do we best compact it in a given area or we can coil it or we can branch it similarly when we're looking at glycogen which is the animal storage for glucose we have glycogen it's going to have this branched dense network as well again the whole goal there is to fit as much glucose in one area as you can so the structure the way that you organize them determines the function what about proteins so um this whole structure determines function thing holds up for all the macromolecules uh what about proteins well first um hopefully you recall uh that we talked about the the monomer being an amino acid so we'll look at an image of that in a second there are 20 amino acids uh that are potential for constructing proteins in the human body and they too are going to come together through dehydration reactions so you get two of those monomers or amino acids together a dehydration reaction will um occur where water pops out and then what you will see is the formation of something called a peptide bond so proteins at the most basic level are held together by peptide bonds so here's the amino acid structure that should be familiar remember this is the amino group and this is the carboxyl group notice that these will be electronegative um we'll get into that in a little bit more detail later but nitrogen and hydrogen are fairly different in terms of electronegativity so what will happen is the electrons will pull towards the nitrogen and produce a partial negative charge and these hydrogen will be positive similarly and the carboxyl group will be uh negatively charged the oxygen parts of it will because uh the oxygen is very electronegative so it's going to for instance pull the electrons away from the carbon towards the oxygen this will be partially negative as well that'll uh come into play uh in a moment here now the thing i want to highlight is this r group so there's 20 different amino acids all of them have an amino group all of them have a hydrogen group all of them have carboxyl group they all have an r group but the r group is variable or variant depending on which of the 20 amino acids you look at so let's take a look here um if we look here uh they're all 20 that are arranged a good chunk of them are non-polar if you remember your functional groups things that are nonpolar generally have mostly carbon and hydrogen if you look through this this mostly holds true there's a couple anomalies there there's a little bit of sulfur here a little bit of nitrogen there um but these are going to be relatively non-polar meaning they are going to be hydrophobic or repel away from water um we have some polar groups notice the commonality lots of oxygens uh through here uh whether it's in a hydroxyl group or whether it's in a carbonyl and then we have some charge there's some positively charged groups some negatively charged groups now again each of the r groups will be different and what r group is present determines which amino acid you are dealing with okay so why is this important well it's important because um the r group actually becomes very significant for the actual uh structure of the protein so um when we come to proteins proteins have a more complex structure compared to the other macromolecules that actually have four structural levels four ways that the amino acids will orient themselves so that you have this final protein product so if you would like you can pause and write this down here i am going to actually just work through each of these by showing you examples but here is kind of an overview definition of each of the structural levels is primary secondary tertiary and quaternary what is the primary so the primary is going to be the actual covalent bonds between each of the monomers each of the amino acids that results from the dehydration reaction remember those covalent bonds that are formed are called peptide bonds so this here is amino acid one we have a carboxyl group that's here um so we usually call this the c uh part of it because of the carbon and then um we have the ammonia sorry amino group here that's the n and then we'll have a water that's going to leave so that the ammonia group or amino group binds with the carboxyl group a water pops off and a peptide bond uh forms okay so moving on to a little bit more detail here um what we can do is we can actually continue to build a series of amino acids when we do that that is called a polymer so our polymer is first and foremost at the primary structure level a a chain of amino acids now one thing i want to highlight is the very top part um is what we call the n-terminus of our protein it's called the n-terminus because this amino group the tail end is called the c-terminus so when we are adding on new amino acids we are going to add the amino acid to the c terminus okay so this amino acid here will be added onto the c terminus this is the c terminus of the growing polypeptide chain another way of saying that is this is going to grow in this direction that way okay so we can see a water is going to leave because this is a dehydration reaction and a new peptide is formed peptide bond is formed so the peptide bond there a peptide bond there now here's something interesting that will be relevant in a moment these are r groups that are sticking out so these r groups will play into the tertiary structure when we get to it but for now the uh primary structure is just the individual amino acids linked together through those peptide bonds so you can kind of think of them as like beads on a necklace or something like that okay um another thing that i want to highlight really quickly because this becomes relevant for our secondary structure in a second these carbonyls sticking down and these hydrogens sticking up off of the nitrogen those are going to play a role in the secondary structure so we'll get to that okay so to summarize the primary structure is just the covalently bonded uh individual amino acids they're covalently bonded through the dehydration reactions and those dehydration reactions you know pull out water right um we're always going to go from the n prime end and grow it in the direction of the c prime n so this would be the c prime and here are c terminus so if we wanted to add a new one on we're going to add it right there okay what's the secondary structure well i had mentioned before that the carbonyl and the hydrogen on the nitrogen is going to be significant okay why is that so this here is a carbonyl we have a carbon there an oxygen there what's going to happen is the oxygen is a lot more electronegative and so it's going to pull electrons towards itself and become partially negative this will become partially positive um interestingly the nitrogen so this is the nitrogen here with the hydrogen on it that's that there the nitrogen is more electronegative so it's going to pull electrons towards itself so the hydrogen here is going to become partially positive the nitrogen will become partially negative okay so here's what ends up happening when we have a ton of monomers in a row they start to kind of loop back in on themselves so imagine this is kind of a long chain here so it's going like this direction and then it will kind of fold in on itself and then it will actually fold in on itself again and it will continue to do so when it folds back in on itself remember we have these carbonyls and the hydrogens off the nitrogen that are sticking out so it turns out um that they will actually line up with the the carbonyls and hydrogens on the nitrogen from the next layer up as it loops back around when it does that it forms hydrogen bonds so remember the hydrogens sticking up are partially positive uh the oxygens now sticking down are going to be partially negative and so that's going to attract uh they're going to attract each other and that forms a weak interaction that kind of holds things together this is a hydrogen bond here so that should look familiar like all of the hydrogen bonds you saw in the water molecule um so what's going to happen is the secondary structure will either loop like this or it's going to coil like this and the reason it does that is because the amino acids will hydrogen bond across from each other so we can see this a little bit more clearly here here is an alpha helix so it is an actual coil right there so these oxygen and hydrogen um will connect with each other as you coil this thing up here and this is going to form a hydrogen bond again remember the oxygen is partially negative pointing off the carbonyl the hydrogen is partially positive pointing off the nitrogen and so you're going to see all of these interactions across in the alpha helix uh you can hear it in the name it's a helix or coil so that's the way to remember it um what about the beta pleated sheet so the beta pleated sheet is going to do long loops like this it'll just continue to fold backward and forward that's what we saw on the last slide there so let me show you here now we'll have these formations across these will be hydrogen bonds here and these are going to hold the the secondary structure together there okay well we have our primary structure we have our secondary structure what we have remaining is our tertiary structure so remember we had all those r groups sticking off some of them are polar some of them are non-polar some of them are positively charged some of them are negatively charged so we see tons of interactions happen remember those r groups are just sticking off so as you're kind of folding all these amino acids up what will happen is one r group will come in contact with another r group and there's a few different things that can happen first there's hydrophobic interactions so this is where uh two hydrophobic r groups meaning two non-polar r groups come in contact with each other and are drawn towards each other they usually come together in the center um you can also have things like ionic bonds so that is when a fully positive or a fully negative charge comes in contact with the other and creates an ionic bond there um there is one type of r group that will covalently bond with itself so cysteines will bond with himself when they do they're considered a disulfide bridge this is a very strong part of the tertiary structure that will hold it together and then there's also hydrogen bonds so sometimes we'll have like a partially positive hydrogen sticking out partially negative oxygen sticking out and they'll form hydrogen bonds so basically we see like all kinds of chemistry happening on this level as the r groups are pointing out we can see hydrophobic interactions uh ionic bonds disulfide bridges which is covalent bonds and hydrogen bonds we see it all so there's tons of things holding together the tertiary structure at the final level is the quaternary structure so quaternary structure is where you have multiple tertiary structures held together in some way um so hemoglobin is a great example hemoglobin has like these four subunits that come together um and they actually have iron in them as well that's gonna help bond the oxygen but all of this comes together just so that you can hold oxygen and shuttle it through your blood um so this would be a quaternary structure made up of you can see kind of this tertiary structure that's one of them this tertiary structure that's another and then you have three and four so there's four uh units coming together here okay so if you want to pause this video you can kind of look and visualize all of them together primary structure is sequence of amino acids the secondary structure is the structure that emerges from all the hydrogen bonding that's the helices and the folded sheets the beta pleated sheets the tertiary structures all the r group interactions the covalent bonding the ionic bonding the hydrophobic interactions the hydrogen bonding and the coronary structure from time to time we see more complex proteins uh you're holding multiple subunits together from that are tertiary structures okay now coming back to the structure determining the function um here's just one example of that so um many but not all proteins are enzymes enzymes generally will take a chemical and break it down or take two chemicals and put them together so enzymes facilitate chemical reactions so here's just uh one example maybe we have a substrate come in uh it enters the octave site this is the actual site of the protein that binds the substrate coming from chemistry we can think of a substrate as a reactant and then let's say it breaks it down into two products uh that looks something like this two triangles right so the substrate goes in or the reactant goes in the active site breaks down and it releases those products the two little triangles here now let's say that something happens that messes up the active site and our substrate can no longer bind um the enzyme reaction that that's the reaction that's being catalyzed by the enzyme will not move forward why because the structure of the enzymes change if the structure changes the function which is to break down this substrate into two parts two products will no longer be able to occur uh the main reason is because this uniquely binds to this reactant or substrate and now it won't be able to bind because of the change in shape okay uh this the next two will go a little bit faster we have nucleic acids so nucleic acids are dna and rna the major monomer is the nucleotide and nucleotides are going to be made up of a five carbon sugar that five carbon sugar is ribose um and then we'll see it's it's modified in dna we've removed part of that ribose um to make it deoxyribose um there's a phosphate group that should sound familiar that was one of those functional groups it's got a pro a phosphorus with four oxygen around it and then it has a nitrogenous base you should remember this from biology before adenine thymine guanine cytosine or uracil um dna nucleotides are gonna be slightly different than rna nucleotides so we'll see what the differences are uh now okay i keep having to move my face it keeps getting in the way let's take a look at the dna nucleotide just to get a baseline so here's the phosphate group remember that is the uh so it's the phosphate group it's the one with phosphorus and the oxygens bound to it um some of them are double bonded and some of them are charged i'm just drawing the basic outline so hopefully that recalls your memory from that functional group slide then you have a ribose sugar now this is called deoxyribose why because over here in the rna nucleotide there's an oxygen for our pentose sugar deoxyribose the oxygen has been removed and then here's the nitrogenous bases for um our particular um nucleotide of interest it's going to have amine cytosine guanine thymine okay so this is the monomer for a dna nucleotide it's very similar for an rna nucleotide couple tweaks here um so here is one of the tweaks one of the tweaks is that it has that oxygen here which makes it arrive with sugar the other tweak is that it will have uracil instead of thymine so see how thymine is here that thymine is replaced with uracil here so those are the major differences so when you're making an mrna you're using these type of nucleotides when you're making a dna you're using this type of nucleotides to create that um polymer there okay so when we're looking at nucleic acids nucleic acids are going to have a five prime end um and they're gonna move in the direction towards the three prime end meaning you're always going to add on the three prime end so this is the growing side over here you're going to continue to add your nucleotides on that direction so just so we can see the five prime end is called a five prime because it's built off of the fifth carbon in the ribose so the five prime end always has a phosphate on the top and it's going to move in this direction this is the three prime end here uh because it's the third sugar or sorry third carbon on the sugar and so what will happen is you will take a nucleotide and you're going to attach the phosphate to the three prime end notice here that a water is going to pop off as you form that bond it's called a phosphodiester linkage you don't really need to know that but it's similar to that peptide bond it's just the new covalent bond forming to hold this new nucleotide together let's say you want to add another one where you're going to add it you're going to add it here on the three parameters so you add your nucleotide there and it will just continue to grow in that direction there okay coming back to structure determining function this is dna dna is double sided or double-stranded the reason why is it gives it a lot more durability so we keep it double-stranded to prevent mutations we keep it double-stranded to prevent uh it from unraveling or degrading the reason why is dna encodes all of the information in your body and so you don't want to lose any of that information or have it degrade so it is stable in this double stranded configuration but let's say we want to make a protein what we do is first we transcribe it into m rna or messenger rna maybe you remember that from biology mrna is single stranded why is it single stranded well it's going to degrade uh in essence and so we just need it to last long enough to to translate it into a protein so the information it encodes for the protein is all we need it for and then once we've made that protein this is going to naturally degrade so it's choose the single stranded route because it's less stable and it is kind of transient it will disappear over time okay um just a couple last things on nucleic acids if you recall um there is a base pair rule so uh you'll have the double stranded dna on one side will be an adenine let's say and on the other side it has to bond to a thymine so an adenine and a thymine always bind together a guanine and a cytosine always bind together the reason why is because of the underlying chemistry but these are called the the base pair rules so when the adenine and the thymine bond together they bond with two hydrogen bonds when the cytosine and the guanine bond together they bind with three hydrogen bonds so you can probably predict um which is the strongest hell base pair it's going to be the cytosine and guanine here because there's more hydrogen bonds holding that pair together the other thing to note is that um when you're looking at dna one side runs five prime to three prime like this the other strand is actually going to run in the opposite direction it will be five prime uh to three prime so if you wanna grow the strand on this side of the dna you're gonna need to add it here if you wanna grow on this strand of the dna you're gonna need out here so that's what we call antiparallel they move in opposite directions they run five prime to three prime in the opposite um just so you can visualize that uh hopefully we can see that here if we look at this strand this is the five prime end this is the three prime end if we want to grow this dna strand um we're going to go in that direction on this side this is five prime uh to three prime if we want to grow this side we're going to go in that direction out there notice an adenine is always bound to a thymine coming across it's going to have two hydrogen bonds there a guanine will always be bound to a cytosine across we have three hydrogen bonds there if they're not bound to their partner but bound to another base uh pair then it actually means that there's some sort of mutation or error that happened um and so we're going to have some corruption of our information and dna which is pretty problematic because like i had mentioned the dna and rna encode information for our genetics so it's extremely vital that that code is preserved so just so you can see here um this is a sequence for a gene in the the body it's important for cell signaling um and you can see it's just a series here of a t's g's and c so this encodes information in the same way that uh computers will store information in ones and zeros so the combinations of one and zeros will encode information this is what's known as digital information so our dna and rna are encoded in digital information but instead of using ones and zeros so two digits we have four a g t and c like we've been discussing so all of the information for the whole body is encoded in dna and it's encoded in the series the specific sequence or series of a's g's t cs okay lipids so lipids are um the only macromolecule that are primarily nonpolar all the other ones that we've looked at they have phosphate groups and carbonyls and nitrogens and all that sort of stuff and so they're generally polar and will dissolve pretty well in water there may be some exceptions but lipids are the opposite so they're generally got these very long non-polar regions now the ones that we're interested in are known as phospholipids those are the ones that play a huge role in cell membrane so phospholipids are going to have a hydrophobic region and they're going to have a hydrophilic region and i'll show you how that is uh the case so with the phospholipid if you remember it has a phospholipid head the phospholipid head is going to have oxygens and phosphorus in it so it becomes partially negative and then what we'll end up seeing here is uh there's tons of carbons and hydrogens here and so this is going to be non-polar so the head will be polar because there's some carbons and oxygens that are going to unship or share those electrons unequally so it'll produce partial negative on the oxygens partial positive on the carbons so this part of it will dissolve really well in water because of those partial charges on the head but the tails they're all carbon and hydrogen so this is going to be non-polar so what ends up happening is we will see arrangements where let's say this is a cell membrane here there's water on the outside here so all of these polar heads are going to orient themselves towards the water on the top there's also water inside the cell known as the cytosol they can orient themselves towards the water on the inside itself and in this middle range all of those hydrophobic nonpolar parts those tails are going to tuck themselves away so that they're never exposed to the water there's some other interesting configurations the liposome does something similar you can think of it as like a cell membrane but just a lot smaller and then you might actually store some things in this centerpiece um my shell is similar as well except that you can see all the tails are coming together at a single focal point so they don't have any polar heads in the center okay so those are different arrangements and these structures are kind of just determined based upon functions so if you want to ship things you can make little vacuoles or containers that look like this and put the stuff in the middle here if we want to for instance create a membrane for the whole cell we're going to do that here this will become more important we'll see later because this controls what can come in and what cannot come in so we'll get into a little bit more detail with function in the next unit for these okay this is kind of the last quick concept so um we talked about lipids they have those long fatty acid chains those fatty acid chains are the non-polar part of the lipid well it turns out that those fatty acid chains can be one of two things they can be saturated or they can be unsaturated society saturated fatty acids are going to be more rigid unsaturated fatty acids are going to be more fluid or flexible and so if we take a look here this is more fluid meaning that the membrane has more flex why is that happening it's because of structure because of these tails here so you can see all of these tails moving through these tails are going to be giving a uh added layer of fluidity or rigidity so this is really going to be important um in certain species that live in very very cold water uh you want these uh kinks in the membrane so that you don't end up having the membrane freeze over and basically fracture or break uh in contrast we have viscous uh membranes viscous means it's fluid or sorry viscous means it's it's not moving the reason why is because of all of these saturated fatty acids so it's easier for the membrane to shear here if it gets too cold so the hydrocarbon tails add some level of stability and that is it so thanks for sitting through this hopefully again as you wrap up and are thinking about this remember structure determines function the the structure of the macromolecules will determine their function within the cell and we'll get into that in a bit more detail as we get into unit two but hopefully that's helpful and uh now you guys are officially done with the content for this