All right, hello everyone. So as I most probably said during my lecture, I have recorded this chapter because of course Monday there was a public holiday and Wednesday there was no universities because of the public concerns that we're having. So I decided to actually record this whole lecture and to try to be as, you know, explanatory as I can because I thought it would be a bit unfair if I brought everyone on a Saturday, you know, Saturday's supposed to have fun.
I don't want to bring anyone on Saturday. just for this chapter. I thought I could actually, you know, record it and then on your own you can basically on your free time choose whenever to go over this chapter. So most probably on Friday I did speak about this but I'm gonna go again straight from the beginning to the end.
Okay, so chapter three is called the chemical building blocks of life and if you guys remember one of the concepts of biology is that as diverse that we are as organisms like I am diverse to a bird, to a fly, to a... fish you know how much diversity there is as basically unified we are and one of the biggest unifying properties is chemistry the chemical building blocks of life so these macromolecules that we today we'll be speaking a lot about so in chapter two we learned a lot about elements and we learned that these elements they love to you know fulfill this octet rule so they create these bonds with other elements which create you know molecules and compounds and then these compounds or molecules start to basically also start to bind together and create these bigger structures that we call macromolecules and that's what they are and then humans are basically on all organisms we have four main types of chemical building blocks so these big four polymers or macromolecules that we like to call them which are proteins lipids for uh nucleic acids and fats and i'll be definitely going into a lot of these ones sorry not fats but lipids lipids is basically the uh micromolecule here but before we go into the main characteristics of them let's first start with the simplest thing of like what these uh micromolecules are made of they're actually made up consisting primarily made up of carbon and basically anything that's made out of carbon we call them organic molecules so let's take a look at you know carbon so if you look at take a look at carbon right here carbon has six electrons two go in the k energy level so two basically in this orbital then the other the other four will go into the l energy level uh and the l energy uh orbit uh or shell and basically you know there'll be four of them so it gives you four valence electrons that means that carbon can bind to four other uh molecule basically molecules or elements to create the molecule so that gives it such a nice characteristic of carbon that it can actually bind to four different things and usually macromolecules are consisting of carbon and this carbon skeleton which is composed either of one two three or can go up to 40 and more carbons so you have basically this massive skeleton of carbons and basically you usually have a lot of hydrogen together remember this carbon and hydrogen have a very similar electronegativity meaning that they once they actually form a bond they will share that electron quite nicely so you don't have any polarity happening here so basically you get a lot of these non-polar properties so that's the main structure of micromolecules but what happens sometimes is that of course that some of them will only have hydrocarbons so they're basically only carbon and hydrogen and these are non-polar and this is all you see them a lot in lipids but in other micromolecules the hydrogen is replaced either by oxygen nitrogen sulfur or phosphorus and the addition of these different elements you get different properties coming up because now oxygen for example has a different electronegativity so you get different things uh different properties so now polarity starts to come into place sulfur by itself is a very special molecule that likes to link with other sulfur so if you have one compound of sulfur and the other one with a sulfur they will find they will form something called the disulfide bridge so again it's giving these uh macromolecules different properties depending on what they have if they have hydrogen they're mostly non-polar they have oxygen nitrogen sulfur they'll become start to give actually more polarities and whatnot so what we can actually add to these basically car skeleton carbon skeletons are functional groups and there are many different types for example we have this oh which we like to call hydroxyl we have carbonyl which is the co or carboxyl which is cooh amino nh2 so uh sulfahydro which is sh phosphate groups or methyl groups and the nice thing about these functional groups is when you add them basically to this carbon skeleton you know you really do change a whole lot these um the properties then of this whole compound because for example you know uh if we have methyl group for example this h3 this is very what they call it non-polar it's all just carbon and hydrogen so you're not really messing around a lot with the properties it's just purely you know giving it a nice um non-polar properties but for example if you add carboxyl which is an oh it's very polar oxygen is very polar as we learned this so you're giving actually these kind of compounds some functions. So if I look for example at the chemical structure, the first thing I'll do is look at the functional groups. Okay, there's the carbon skeleton and then I'll look at basically the functional groups. Okay, this has a hydroxyl group.
Okay, this is quite a polar substance. If I see for example this sulfahydryl group, this SH, like okay, this is prone to create these sulfide bridges, meaning that if it sees another sulfide, it's just gonna bind with it so well. So I can start guessing already the properties by looking. at the functional groups. So now that we saw basically what these big macromolecules consist of, one thing that is very important with macromolecules is the term that we call isomers.
So isomers are molecules with the same molecular or empirical formula, meaning that they have the same molecular empirical formula but these guys are not the same, these are not the same compounds. So before we go into details, let's first of all give you a definition about molecular and empirical formula. So molecular formula It's a formula that gives you both the number and the type of atom that makes up a molecule.
For example, it's glucose. Glucose is made of six carbons, 12 hydrogens, and six oxygens. So you write it as is. The empirical is different because here you only show the simplest ratio of these elements.
So let's take, again, glucose. So this is the molecular formula. The empirical formula will be the simplest ratio.
So here we see that the simplest thing today, or the highest number, so we can divide all of these guys is by six so this becomes one this becomes two and this becomes one so the empirical formula is ch2o let's take a look at example of water and hydrogen peroxide so water has two hydrogens and one oxygen so molecular formula is h2o the empirical formula would be the simplest ratio but because here you know you cannot divide one by anything it stays the same but hydro peroxide has two h two h's so h2 and two o's so o2 so h2o2 So that's the molecular formula. Then the empirical would be then dividing this by complete two. So it gives you HO.
So the simplest ratio. So isomers, again, have exactly the same empirical or molecular formulas, but they differ. And depending on how they differ, we call them certain things.
So if we look at, for example, here, glucose and fructose, they have the exact same empirical and molecular formula. But let's have a look at their carbon skeleton. Here, suddenly, you have the carboxyl group, which is shown here, the carbonyl group, which at the beginning.
Then this one is actually at the second one. So it's changed. So the carbon skeleton is changed, but again same molecular and empirical formula, but different carbon skeleton.
So that means they're structural isomers. The structure of the carbon skeleton is differing. Let's take a look here now, glucose and galactose. Same carbon skeleton, but look at this OH here. This one is more to basically the right and this is more to the left.
So this is called stereoisomers. So this differs on how the groups are attached. So these can be completely different.
You know, they look similar, but they're very different. So stereoisomers, we can also call them enantumers. So there are different types of stereoisomers or a subtype.
Sorry, that's the correct word. So a subtype of stereoisomers are enantumers. These are basically, again, isomers that are mirror images of each other. So let's use this example.
So let's imagine you have your left and your right palm. They face each other. These guys are mirror images of each other. Because when you put them on top of each other, they are asymmetrical.
They do not superimpose. So hence, they're asymmetrical. That's what an enantiomer is.
So if you take a look at here, stereoisomers like glucose and galactose, these guys are not enantiomers. Remember this, because when you put these guys on top of each other, they are symmetrical. If you flip them together, they become symmetrical.
So that's one thing you have to remember, that not all stereoisomers are enantiomers, but all enantiomers are stereoisomers. they're a subtype of stereosomers and one property of enantiomers is chirality chirality means that the carbon is actually has different groups so as we said we have different functional groups and in enantiomers oh sorry in chiral carbons they have different ones so if we look at alanine we have this metal group this amino group this uh hydrogen group and basically this carb uh this carboxylic acid group basically here's the o so these are basically what it means so you have this l9 l-analyte and d-alanine So L means level which means left and D is dextro which means right. So this depends all on the nitrogen group. So as you can clearly see the nitrogen is on the left So we call this L-Alonine and this nitrogen is on the right. So we call this D-Alonine So these guys might look so similar to each other but guys Super different.
We only have L-Alonine in our bodies. Basically, all our amino acids are L-Alonine. amino acids like the l9 we are not able to actually recognize them our enzymes are not able to use them as building blocks or anything so when you anyone who goes to the gym and takes amino acids or any kind of supplement to enhance you know their growth anyhow if you have a look at your protein shakes and you see oh these are supplemented with the amino acid that's just crap sorry to say because that they're you're gonna be you're gonna excrete them you're not gonna use them your body doesn't use it they don't recognize it they only recognize l-alanine so this is where how important this chirality this basically you know uh these chiral atoms can be you know how their um their spatial arrangement uh can matter so now let's talk about micro molecules molecules are basically can consist of polymers so polymer is big structures which are built by linking monomers so monomers are small similar chemical subunits so you what you're doing is you use monomers so these small subunits that come together and they create one big polymer. So polymer is just the addition of multiple monomers together. So I'll give you an example.
So we have the four main types, like one of the first ones carbohydrates and the polymer is starch. The starch is a repeating monomers of a monosaccharide that we call glucose. So it's multiple glucose coming together to create this big structure as polymer. DNA is a polymer because it's repeating basically monomers.
So they're repeating nucleotides. that are bound together. Same thing goes with proteins. Basically, we have a polypeptide, which is the polymer, which are made of this one monomer, which is the amino acid.
So we have multiple amino acids connected together to create this polypeptide. Lipid. Lipid is a macromolecule, but it's not a polymer because polymer are made of simple monomers. Well, basically here, this guy is a big macromolecule, but it's not a polymer. and this is because the monomer is not the same it's actually made of two different monomers the triglyceride is actually made of a glycerol and three fatty acids so it's a bit different so it's still a macromolecule but not a polymer because the monomer is not the same so keep that in mind so we're going to go into details about each one but before let's first see how do these monomers you know join together to create polymers and how they can break also to create again from polymer to a monomer because that's very important so imagine you have two monomers here but what's going to happen is the hydrogen from this monomer and the oh group from this monomer will join together to create water and by basically now suddenly this carbon needs an actual electron and this guy also needs an electron electron so they basically then form together and this is how they're connected so this process called dehydration because you're losing water to break this you use a hydrolysis reaction Hydro is water, laxative is breaking.
Because what you're doing is you're breaking water to break this bond and basically give back the monomerase hydrogen group and the OH group back again. So basically it literally is the reverse. This is a whole reverse reaction and you use water so dehydration you create water, in hydrolysis you break water to break the monomers apart.
So this is how you assemble and disassemble polymers and we'll definitely be seeing examples here. So let's start with carbohydrates. Carbohydrates are very simple. definition.
These are molecules with a 1 to 2 to 1 molar ratio of carbon, hydrogen, and oxygen. So you'd write the empirical formula as such, C, H2, and O, where the N is the number of carbons. So these are hydrated carbons. So basically, let's imagine that you have five carbons.
So this would be five. So this would be C5, H10, O5. That's how you would read it. And carbohydrates, these guys are... big macromolecules, so there's polymers that are very good at actually storing energy, but also are very good in structural support.
Two very different functions, right? Energy and support. How can this be? Well, it's all depending on these isomers, basically.
So you have basically, for example, the simplest sugars, which are monosaccharides. So these monosaccharides are obviously simple sugars, and they can exist as... three carbon sugars, five carbon sugars, or six carbon sugars.
These guys are not that used that much. These are mostly used in basically actually in fatty acids. this guy was mostly used actually in um nucleic acids and this is mostly used in carbohydrates so we'll stick for now to these six carbon sugars and let's take an example glucose glucose has the following formula and what it does so usually it's actually linear but sometimes what can happen is that they can actually form a ring in aqueous solutions so what occurs is that here the oxygen this hydrogen bond is broken so the oxygen now creates another bond with C and this H is transferred here so you can really see this is what you get so now oxygen is this is gone it connects to the carbon this bubble bond is also gone and the hydrogen moves to the oxygen to all fulfill the octet rules so you get the formation of a hydroxyl group how this hydroxyl group which is the OH how it's actually kind of facing is it if it's facing down you have alpha glucose if it's facing up you have beta glucose and this really can differ in a lot of stuff because alpha glucose is the glucose that we can recognize in our body beta glucose not really this cannot be recognized so this is very important this is why you get two different functions i'll explain this a bit later but keep this in mind about alpha and beta glucose so you have glucose and you have two different actually isomers of glucose you have fructose which is a structural isomer because look at this this is basically another carbonyl group is at the beginning now this is the second So the whole carbon structure is changed, hence it's a structural isomer. So this is fructose. Galactose is a sterile isomer because the OH at the carbon 4 here is completely flipped.
So it's a sterile isomer. It's not in an antifumor because it's not a mirror image of each other. So keep that in mind.
So and this really can differ because glucose and fructose might seem very similar but they're not because fructose is actually our taste buds will see it as more Sweet actually because of this change so this is how small changes in the structure can really give different properties so we have something called disaccharides because one thing is that when you put glucose through your blood or basically People also glue a glucose fructose or galactose when you go when they go through the blood They can actually easily be cut because there are many enzymes in your blood and all around your body That's gonna cut them so to prevent that to to actually help them transport to the body to certain tissues that need them we put them in a disaccharide so basically we combine them together so we can actually either have glucose and fructose together that gives you sucrose or you have glucose and galactose gives you lactose maltose glucose and glucose and again so if you look at here this is the alpha glucose and this is fructose so here literally this is how it happens that the h here and the oh here so from the carbon one and carbon here on five they basically they actually combine and you get water So this is basically again dehydration and this is what allows this oxygen to bind together here. So we're basically creating this nice disaccharide. So sucrose, this guy over here, which is made of glucose and fructose, these are actually made mostly found in sugar, in table sugar, and lactose is mostly found basically which is glucose and lactose in milk.
And what these actually do, when you have the sucrose or maltose or lactose, this bond over here is not broken down easily. the enzymes that break this down are not found in your blood they're found in specific tissues where the sucrose or maltose or sucrose will basically go so that's why they're you they're basically the disaccharides can easily go to the blood because the enzyme that breaks them down is not in the blood it's in specific tissues that they will go so now you have polysaccharides so polysaccharides is a long chain of monosaccharides it's more than two because two is disaccharide more than two when you have much more polysaccharides and as i said they have two different functions energy and structural support. So let's start with energy.
With energy, basically we're going to have a look at starch. Starch is a long chain of alpha glucoses which are joined by this one to four glycosidic linkages. So what that means is that the carbon number one will bind to the carbon number four of the next monomer.
So that's what it means. So this is carbon number one binding to carbon number four. of the other monomer and same thing your carbon number one to carbon number four and it goes on and on so this creates a nice straight chain but what can also happen is that this carbon number one can bind to carbon number six which is basically found here and what you do get here is you get actually a branch and this is what happens in starch starch you have amylose which are basically long chains of alpha glucoses bind by this one to four amylopectin is the same but it has also this one to six linkages so you have basically this you know very straight structure but also that has branching and that's called amylopectin so amylose is unbranched amylopectin is branched so the starch is actually made of 20 of amylose and 80 of this amylopectin glycogen is very similar like to amylopectin but glycogen is basically made also from alpha glucose and also this one fourth uh branches sorry that's basically a linear straight basically binding but also has a lot of this alpha 1 6 linkages And the main difference between glycogen and amylopectin is that glycogen is much, much more branched. So amylopectin is branched every 20 subunits.
This is branched every 10. So hence, there's much more branching. So that's the main difference. Starch is mostly found in actually plants. Glycogen is mostly in animals.
So we actually have glycogen, which is mostly found in our muscles and liver. Cellulose, very similar to glycogen or starch, but they do not use glucose alpha glucose they use beta glucose so basically the hydroxyl the hydroxyl group the oh is facing up so go here so this guy is facing up so different always because the side the alpha glucose because the oh is facing down beta is up so that gives a completely different structure even though they're very similar because they're actually bounding by the same kind of link which is the one four so carbon number one to carbon number four but they use beta glucose And as I said before, beta glucose is not recognized by our enzymes, so we cannot break them down. So they can create a really nice tight structure, which are actually found in a lot of bacteria, in fungi, and different other basically organisms.
Because it actually makes them quite strong. So this is how they can differ. So now, nucleic acids. Nucleic acids are basically polymers that are made, so basically, which are...
RNA and DNA, so these are the polymers, and they're made of monomers of a nucleotide. So again, RNA and DNA are just repeating units of nucleotides that are bound together. So let's first of all look at what a nucleotide is.
So a nucleotide is first of all formed by this five-ring sugar, which I was explaining before. So in this sugar, basically, in RNA you have a rival sugar, meaning that in carbon number two it has an OH group. In DNA...
this is a deoxy ribose sugar deoxy meaning less oxygen so hence there's one oxygen less here and this is what it means in dna it stands for deoxy while rna the r starts for ribose so that's where the difference comes so and also basically in carbon number five you have a phosphate group and basically in carbon number one you have a nitrogenous base so in both rna and dna this doesn't change what changes is this guy over here the nitrogenous base and in humans we have five We have adenine, guanine, cytosine, thymine, and uracil. And as humans that we are, we are very lazy sometimes that we like to cut these short. So we call adenine A, we call guanine G, cytosine C, thymine T, and uracil U.
So DNA and RNA all have A, G, and C, but only DNA has T and RNA has U. The difference between T and U, if you look at them, they look quite similar, is the methyl group. Here you don't have any methyl group in U, in the T you have a methyl group.
So that's the difference really between them. But we can also divide these guys depending on how many rings they have. If they have two rings like A and G they're called purines.
If they actually have only one ring they're pyrimidines as you can see here. So how do these monomers then get together? It's very simple.
The phosphate of the one nucleotide will bind to the three prime carbon through the OH. basically this OH group through hydrolysis. So basically you have water coming out to allow the phosphate basically to bind to the carbon number three.
So this is what you get this five and it's called a phosphodiester bond basically. So this is where the linkage starts to occur. So basically here you actually get to have polarity.
You actually have a five prime top and a three prime bottom because the five prime is this phosphate group which is quite polar and you also have a three prime end which is just facing the OH which is also polar. So when someone tells you 5'end of DNA it means the one that basically the phosphate is sticking out. If they're saying the 3'end is basically where the OH is sticking out so that's what it means. And in DNA it's actually made of two strands.
So we can have a look here they're made of two strands and they're anti-parallel meaning that this strand starts with a 5'end and the other one to 3'end. So they're going anti-parallel to each other and how these guys are connected to each other is through hydrogen bonds and this is all because of the nitrogenous bases like a and t a will only bind to t It's only comfortable to bind to T and this is called complementary. They're complementary to each other.
C will only bind to G and because A will only create these double bonds with T and C will only create these triple hydrogen bonds with G. And this is how these two anti-parallel strands are connected with each other, through these hydrogen bonds that are between the A and T or the C and G. So they're through the nitrogenous bases. That's how they're connected.
And again, because I know this is complementary, if I know the sequence here, so if I know this is composed of A, C, T, G, for example, I know the other ones are going to be composed of T, G, A, and C, because I know the complementary of it. So in RNA, it's very similar. As we saw, the only thing that differs in the nucleotides mostly is on two things, which is basically the sugar, that is ribose.
and of course that uh thymine doesn't exist it only has uracil so that's the biggest difference but in structure very similar i mean in the binding of it it's very similar so you get again the phosphate binding basically to the carbon number three and it's repeating and again this is all through hydrolysis suicide not hydrolysis through dehydration dehydration is what's causing all of this so dna basically here now as you can see is all bound together uh in terms of two strands RNA is not RNA is one strand so one thing that DNA and RNA have very in common with each other is the function of they encode or they have the genetic material of proteins they encode what a protein is so for example insulin insulin has been certain amino acid sequence has a certain sequence that is encoded by DNA and RNA so they have they actually stored genetic information because of the combination of the nucleotides So if you have like A, G, C, T, C, C, G, D, this combination, it stands for, actually, it's a recipe for the protein insulin, for example. So this is what it means. But because RNA is single-stranded, it has more functions than DNA. DNA is most, its main function is, you know, storing of genetic material, so is RNA.
But RNA can also be found in these ribosomes. It can also be found in tRNAs. So these are basically, you know, enzymes that help translation.
so they can be part of enzymes also and have different functions so keep that in mind because RNA is single-stranded so it's more malleable compared to DNA. So we have other nucleotides like ATP and Nalazenfad. ATP it stands for adenosine triphosphate so very similar to euclidite, carbon sugar basically the nitrogenous base which is adenine in this case and is made of a triphosphate so hence triphosphate and this bond between the phosphorus and oxygen is very very high in energy.
So this is why we use ATP as a source of energy, because when we break this, it will give us energy. So if you want to run, what happens is we get ATP and we stop breaking these basically bonds here. And this will give us a lot of energy to do our work. So we have this nicotinamide adenine dinucleotide and flavin adenine dinucleotide, these are mostly used for cellular reactions like photosynthesis or cellular respiration.
We will definitely go. more in details in chapter 7, I guess. So proteins. Proteins is a quite a very complex macromolecule, quite complex than the rest, because you have multiple different types of proteins and they have a lot of functions.
And these are just examples of their functions. These guys can, these proteins can be enzymes, meaning these can be basically kind of these proteins that will help breaking and forming of bonds. They can actually help us in defense. So a lot of immune cells actually express certain proteins.
that help us combat bacteria viruses or other microorganisms or even cancer and i actually study this a lot i study a lot of these different proteins and i actually use them to create new therapies so you can also for transport some proteins can help us transport certain ions from one place to the other they can also help us in support to create kind of these really nice structures that we need to do with the for example itself to give us some support basically uh we also have motion they can also help us in motion like actin they can basically you know help us in moving they can also help us in regulating they can be basically of course hormones that help us in regulating certain things like the amount of water or certain other chemicals in our body and they can also help us to store like calcium ions some proteins can help us store calcium ions so let's start off proteins proteins as i said are polymers and they're basically made of amino acids don't which are not all the bottomers so let's look at the amino acid The structure is the following. It has an amino group, a carboxylic acid here, a carboxyl group. and a single hydrogen and an R. This R is a variable group meaning that it changes between amino acids and there are 20 amino acids in humans and they all differ in this R here.
So you have multiple R's but one thing that you actually do notice is that this carbon has four different groups right so they're chiral so that's why you have the always D and an L form. because you either basically depending on the RF is obviously in the amino sorry amino group if it's in the left side on the right side you know if it's L or D because these are chiral the only non-chiral amino acid that exists in human is called glycine because this R is simply an H atom so suddenly now you have two H atoms so this rule of chirality is gone because you have um same groups so and then basically chirals are carbons that have four different groups so glycine is the only one so it's basically the type of r group that gives certain properties to amino acids so let's take an example here so we have these guys like alanine valine isoleucine leucine and glycine so you can clearly see that their r groups are mostly made of hydrogen or carbon and hydrogen groups so these guys are quite actually non-polar so their r group is so non-polar that they give their property of this amino acid to be non-polar but you can also have for example here uh r groups that have oxygen and that gives polarity so hands here Here you actually give them basically certain charges like this, like Arginine has now this amino group with a positive charge or here you have an oxygen with a negative charge. So basically giving them charges.
You can also give them an aromatic ring. So these are basically these ring structures that we call them aromatics and these ring structures can be composed simply of C and carbon and hydrogen, carbon and hydrogen so they're non-polar or this basically aromatic and actually have an oxygen which gives us this polarity. or they can also have a charge so you also have special r groups like here that you have a sulfide and again the sulfide as i told you they love to bind to other sulfur screens with disulfide so giving them extra properties here and again this is another one system here you have this aromatic with also another uh positive stroling so what i'm trying to show here is that i don't want you guys to memorize these amino acids no what i'm trying to understand you is look at the arc groups and based on the R groups you can clearly see is this guy polar is this guy aromatic does this guy have a special function and etc this is what I'm trying for you guys to look at so have a look at this and really repeat or see what I'm trying to say so the peptide bond how do these basically amino acids bind together so when you have amino acids two amino acids what happens when they're in physiological pH so basically in our blood so pH of 7.2 you they become ionized meaning that the carbon the carboxyl group becomes negative and the amino group becomes positive so what happens here is that the oxygen in the carboxyl group from one amino acid will bind to the hydrogens here in the amino group creating water so again this is dehydration so water being lost and now basically now you get the formation here of a dipeptide now this carbon can bind to this nitrogen so one thing one when you guys will do is when you guys read this chapter In the chapter, they'll tell you that this bond right here is kind of has a characteristic of a double bond. Even though it's not, it has a characteristic because the oxygen here, this double bond, the electrons actually start to come around here.
And this gives it a kind of a pseudo, like a fake double bond. It gives you very similar character, but it's not. And this is what makes this actually quite inflexible, this bond.
This will not, you know, move around. So this is what it means. So basically there's a difference between polypeptide, a peptide, and a protein.
So peptide is simply a primary structure, meaning the sequence of amino acids. That's what a peptide is. It's simply the sequence.
Once that polypeptide is basically folding and has a function, it becomes a protein. That's the main difference. So polypeptide are just...
bunch of amino acids stuck together and once they start to actually fold and have a function they become a protein that's the difference between a protein and a polypeptide so as i said these polypeptides have to of course fold so they have basically different structures the first is the primary structure which is the sequence of amino acids you just look at the sequence but then these amino acids can interact with each other because they have all these different polar groups they can then start to fold with each other because the polar groups will attract each other and they start to create these secondary structures so they can actually fold in this kind of nice helix kind of formation which is a coil spiral or they can actually go into this planar structure which is like a sheet we call them beta sheets or in this we call it an alpha helix and this is all because of the hydrogen uh bonds that's creating among the different amino acid groups and this is what a secondary structure is and once they start to basically kind of fold into either this alpha helix or this beta sheets what happens is that because now a certain amino acid are coming closer to each other so in a 3d kind of way they're coming closer they start to form form other bonds because now amino acids that were further from each other that now are closer because of the secondary structure they start to actually make new bonds because suddenly what happens is that some amino acids that one is more positive one is positive one negative down far but now when their secondary structures are folding they're getting close to each other and then suddenly the positive negative will start to bind with each other so folding it even more so these can be of course ionic bonds this could be van der waals forces this could be other hydrogen forces this could be disulfide bridges so different R groups that have sulfur will bind to each other and further you know really push this into a tertiary structure so that's what the difference is between secondary and tertiary. For thorny structure is that some proteins are made of different peptides so they can be made of four for example peptides and what happens is that then becomes the interaction of one peptide with the other peptides so let me give you an example here so primary structure is simply the amino acids amino acids just the sequence and you see these are groups will start to kind of you know interact with each other because of polarities or non-polar basically a polarity sorry it actually this is mostly because of polarity so the hydrogen bonding is going to happen and you're going to have these beta sheets shown here or you're going to have this alpha alpha helix but have a look here now so and this amino acid for example so this amino acid and this amino acid are quite you know very far from each other if you put them in a planer but when they're basically kind of folded they are much more in contact with each other and they start creating these other extra bonds these could be of course extra hydrogen bonds ionic bonds this could be under valves this could be disulfide bridges and whatnot and same thing here because of this basically now uh these structures that are forming because of this secondary structure you get these amino acids are more closely with each other and you further push more other bonds that we created and you get this tertiary structure so this is one pro one big polypeptide and for example here this is one protein that consists of four polypeptides so the quaternary structure is basically how this polypeptide interacts with the other polypeptide and how they're folded within each other that's the proton structure so one thing that we also have started to see within proteins so as i was saying before Sequencing DNA is super easy, but sequencing amino acids is super hard. It's really hard to actually sequence amino acids.
And to see the structure is even harder. So that is, you need to use something called crystallography, and that is a very hard technique. It's not easy. So one thing that we started to realize is that, of course, protein, depending on the DNA sequence, the DNA sequence encodes for the protein. So we started to see in the DNA sequencing, basically these kind of repeats.
So of course from the DNA sequence we can get the protein sequence and we start to see in the protein sequence, oh they are repeating protein sequences and they're giving very similar structures and these structures are found on different other proteins and these are called motifs. So they're repeats. So motifs, if you want to define what a motif is, this is actually taken from art. It's this repeat of this kind of theme or thematic in basically in music. or in uh or in arts or in theater sorry that's what a motif is it's basically a repeat so you have basically repeat of amino acids that are giving specific structure like for example here you have repeats of these amino acids that are giving you this beta sheet and then this alpha and this beta or here you have this this helix then you have a turn another helix and we started to see that oh damn this motif is actually this repeat of amino acids was also found on a different protein and it's giving you different structures That's where motifs are.
So if you want to put them, for example, like amino acids as letters, they're repeating words or phrases that are found in different proteins and giving you different, sorry, similar structures. So they're the same amino acid sequences that are found in different proteins that give you similar structures. That's what motifs are.
Domains, it's a bit different. Domain is a functional unit within a larger structure. So let's imagine this is a whole protein. We have this one domain. 1, 2, and 3. This domain by itself is carrying one function.
This is carrying a second function, and this is carrying a third function. This protein has three... functions and this is because one domain which is basically here a functional unit with a larger structure this one whole unit is able to carry out one responsibility so within that domain you have a specific of course motif that's helping it because for example here this motif this helix turn helix as you can see has kind of looks like kind of a two fingers together this is really great in my dna because dna is again um double stranded so having these kind of two helixes helps so for example here when you have this kind of this domain number one this is really helping this domain is helping it to bind to dna so much probably this whole domain is basically binding um to the dna its function is to bind to dna and it's helped because of this motif so this whole domain if you want to put it again if motifs are repeating phrases a domain is the whole paragraph in a whole essay for example you have a whole essay the domain would be this one paragraph so it's one whole unit that has a function and this function is mostly carried out by certain motifs that it has.
So that's the difference between motif and a domain. So one thing that we started to realize is that okay do these proteins are these proteins actually do they fold on their own or do you need the help of anyone else? So at the beginning we started things like no most probably these proteins fold on their own they do this kind of trial and error multiple times and it gets it to its proper folding.
But then we start to realize like, hmm, this would take a long time. And then through this trial and errors, what happens is these nonpolar groups in the proteins will be exposed to other nonpolar molecules in different proteins. And nonpolar and non, with other nonpolar, they become like glue. They're very sticky with each other.
So this would create a complete mess. And then we start to actually discover chaperones, which are basically proteins that help proteins form correctly. So these guys will come and help you. fold in a protein this is very important because you also have to remember if the protein does not fall to its proper structure the function is not done again structure is function remember this in chapter one so if these guys are not actually properly folded to its proper structure their function is gone an example here cystic fibrosis cystic fibrosis is actually a mutation in the chloride chloride ion channel which is found in your lung and it's one amino acid that is actually removed, that's actually changed, and it fails to fold properly.
So this is this kind of chloride ions do not function. So chloride is not being removed. And this really, you need this to actually remove mucus from your lungs.
So now that these chlorines are not being able to remove, mucus is not removed from your lungs. So these patients really need to go actually to a lot of physiotherapy to actually really kind of massage out the mucus from the lungs. So this is quite a nasty disease. to how important actually proteins need to actually fold properly and i'll give you an example how sometimes this can happen like this folding so these are there's a family that's called the groe family of chaperones this is a family of proteins that have very similar function and they basically they are very barrel shaped chaperonin so you have here basically this misfolded protein it comes inside here into this barrel then you have atp that comes in cap comes in it closes and because atp as we said when you break ATP into ADP, so when you break this kind of this oxygen and phosphorus bond, you give a lot of energy. So this energy is going to be transferred here to fold the protein.
That's why you need ATP. Once this is folded, the cap is gone and the protein is not corrected. So that's, for example, how these protein shappens can actually work.
So one thing about protein, sometimes protein can lose its structure and function when it actually becomes unfolded. So for folded to unfolded protein is called denaturation for example you see here this is a whole protein that's folded properly once you get once it's denatured meaning it's basically the protein is unfolded and that can actually remove its structure and its function so again as you remove this structure its structure function is gone and there are conditions that actually can push this denaturation like temperature ph or on the concentration of solution when you increase temperature you can unfold it completely when you increase pH, ionic concentration, you can also do this. So one thing, actually, you can think about this.
Back in the day, when we didn't have fridges, actually, food used to go bad because you'd have microorganisms like bacteria growing. So one way to stop this, you would actually put your food in high ionic concentration of solutions like salt or vinegar to increase pH. And what this would do, it would actually denature the proteins of bacteria so bacteria would not be able to replicate so that's how what we want to wait to stop actually you know the growth of bacteria through this so one thing that i want you to see is that once it's denaturing this denaturing can be completely irreversible or could also be reversible and basically let's imagine this you have basically this really nice folded protein and there's a hypothesis the 3d structure of a protein is the thermodynamically stable structure it depends only on the primary structure of the protein and the solution conditions prediction if a protein is denatured and allowed to re-nature under native conditions, it will refold into the native structure. So you test this.
You take basically this guy over here, you put reducing agents that will basically break down these disulfide bridges, and you basically put heating, and what you see is basically now this unfolding. So now if you remove basically these heating conditions and reducing agents, if this is correct hypothesis, this should be able to go back. So the result is denatured ribonuclease refolds properly under non-denaturing conditions so the hypothesis is correct so the information of the primary structure is sufficient to refold to occur so basically meaning that when it's unfolded so basically with the nature it can be actually go back and this is called this is called renaturing not dnh re-naturing so they're basically going from this unfolded state to the folded state and this all consists of the primary structure because folding is consisting primarily on the primary structure on the sequence of amino acids and that is by itself will tell the protein how to fold properly. So now let's move on to our last macromolecule, lipids. Lipids are not polymers.
Remember that because their monomers are not simple. So if you want to define lipids, it's quite hard to define lipids. But one main characteristic of lipids is that they heat water. They're insoluble in water, meaning that they are hydrophobic.
They're afraid of water. And this is because lipids have a lot of CH bonds and this high proportion of non-polar CH bond is what makes it hydrophobic. And lipids can come in different forms.
They can come in fats, oils, waxes and even vitamins like vitamin A, B, E and K. So don't always think that lipids are a bad thing. Not really. Because sometimes you need these fats to survive.
So let's start up with fats, the first one, which are triglycerides. So triglyceride is a big macromolecule that's consisting of one glycerol and three fatty acids. So this is your basically glycerol, which is basically these three carbon, carbon skeleton, which has three hydroxyl groups. And this is basically this long fatty acid, which is this long hydrocarbon chain. So all of these are carbon hydrogens and you have a carboxylic acid at the end.
That's why it's called the fatty acid because it's carboxylic acid. So acid acid coming from carboxylic acid. and this is basically the long hydrocarbon chain and basically these guys will start to bind so you get to have three of these guys binding here to one glycerol so you clearly see here in the oh groups you have basically again this dehydration reaction that allows basically this oxygen to bind to basically here the fatty acid chains so three of them so what happens is that sometimes in these fatty acid chains You can clearly see here all of these guys are single bonded. Here you start to have different double bonds. This is called saturated fats, meaning that they do not have any double bonds.
Here you have double bonds and these are called unsaturated fats and these give different properties. So saturated fats are basically have a higher melting points and are more from animal origins, so like butter. And because of these no double bonds, they mostly like to be in kind of a solid form in room temperature unsaturated fats have a lower melting point and a plant origin so these guys in room temperature they're liquid so in unsaturated fats when you create these double bonds so when you have these double bonds what happens is that basically the bonds here basically can actually flip so basically the groups can flip around if it stays if basically this double bond is formed and there's no flipping it's called cis If there's a flipping, it's called trans.
So that's where trans fats comes from. And this is actually something that we do a lot. This is more like kind of produced industrially because we create, we try to put a lot of these kinds of saturated, this double bonds and you create these trans fats. And these guys are actually very nasty because they can increase LDL, which is a very bad type of cholesterol. And these are the ones that are associated with high cardiovascular disease.
risks. So that's the difference between saturated and unsaturated fats. So there are other types of lipids like terpenes which are like found here and these are mostly found you know through like pigments and chlorophyll and retinol. There are also steroids these guys are made up of one of four basically kind of rings shown here and these are very important in creating a lot of hormones and also what's it called membranes. So one type of basically lipid that I really want you guys to talk about is phospholipids because these guys are actually what our cell membranes are made of.
and they're very similar to triglycerides meaning that they have one glycerol but they have two fatty acids because in the other three uh third carbon you have a phosphate group and inside that phosphate group you have a choline which is basically an organic molecule so this is what how it looks like you have the glycerol here so this is basically your glycerol these two oxygens are now creating with two really big uh fatty acids and then the other one is creating with this phosphate which has a choline so that's what a phospholipid is so These guys here are all polar because you see a lot of oxygen, oxygen, nitrogen. These are very polar. But these tails, which can consist of more than 20 hydrocarbons, are very non-polar because the majority is purely carbon and hydrogen.
So these guys are very non-polar. So these tails, well, the head is basically very polar. So tail non-polar, head very polar. And this is what gives you a very specific...
kind of structure. So what happens is that when you throw these basically let's say, let's say these kind of phospholipids out, what you get is you get this basically mesel. Mesel is basically this structure in where these tails are all you know getting together so this because of hydrophobic exclusion they're going inside together and hiding from the water and the polar groups are facing the water so you get this actually so inside there's no water actually and it's protecting these tails from the water while the heads love water and they're basically contacting with water and that's what a mesal is and this is actually what you see in soap detergents they're basically mesals so what happens is that of course when you have let's say a dirty plate that's covered in fat fat hates when you put water water is just going to slide through it doesn't want to interact with it and mesal what's going to do so basically this detergent is going to go and put the fat inside here so now it becomes soluble inside here and then basically the other outside is still solid in water and that's how you remove fats That's how whole detergent works. So phospholipid bilayers, so this is basically seen in cell structures, they're the same but made up of two layers.
So what happens is you get, for example, here the water, sorry, the phosphate heads are sticking out in water, and then you create this basically kind of structure around here composed of tails. So the hydrophobic, hydrophilic heads, so we say the loving water heads are out, and hydrophobic tails are basically, hydrophobic tails are inside. what you create basically a cell membrane and we will be talking a lot about this actually quite soon so guys this is the end of the lecture i hope that this is enough uh please please please if this is understandable great if you don't understand it please send me an email we can of course meet in my office hours outside office hours we can have a zoom meeting but if i see so many people not understanding this then i will actually create one session where we can actually i'll talk about this thank you so much guys i hope this has been useful