Lecture on Carbohydrates and Membrane Structure

okay great now let's dive into the material today so today's topic is carbohydrates as well as an introduction to membrane structure and from the very first class i believe professor yaffi talked to you about the four main classes of biological molecules so proteins and amino acids you've spent a lot of time talking about that nucleic acids is coming up and the other two are carbohydrates or sugars and lipids today we're really going to focus most of the lecture on carbohydrates what they are structure something about nomenclature and then at the end we're going to talk a little bit about lipids and basic membrane structure now carbohydrates and lipids are really critical energy storage molecules for cells and when we talk about metabolism the most interesting part of this course after spring break we're going to delve into this in a lot more detail but sugars are also very important to understand nucleic acid structure turns out membranes are essential for signal transduction those are the two major topics that professor gaffy is going to talk about for the rest of his time and so this year we're going to try something different and have me introduce at least some of these topics now which will deal with some redundancies that otherwise might have existed and maybe set it up better for him to uh to to discuss some of the lectures coming up now today's lecture is unfortunately topically a little bit disjointed but it still has important information about biochemistry and it will help us all speak the same language both for the upcoming lectures on from uh from professor yaffi as well as things that i will start off with when i come back and it's a nice way to sort of ease back in after the exam okay so what is a carbohydrate or a sugar so let's break this down and so it's carbo hydrate okay so a carbohydrate is effectively carbon in some ratio with water so all carbohydrates have the same chemical formula cnh2on and so there are some deviations from this in biology sometimes you can introduce a heteroatom phosphate sulfur nitrogen etc technically these are not carbohydrates although they're often lumped together with carbohydrates and why would nature do this because it changes some of the chemical properties that can be useful for either structural or signaling reasons you may encounter these later um certainly in other classes but we're not going to talk much more about that today we're really just going to focus on the base carbohydrate cnh2n structure now carbohydrates come in different forms and so they can come as single units with that structure these are so called monocyte or these single units can come together to form various polymers and those polymers could be two units so-called disaccharides so two sugars stuck together or many units and so sometimes those are referred to as oligosaccharides or polysaccharides and there's really no clear distinction between you know a few chains together oligosaccharides many polysaccharides they're somewhat used interchangeably now you guys have almost certainly heard of many of these things so what's a monosaccharide so a good example of that is glucose so glucose is of course the main sugar that exists in your blood what's a disaccharide so common one is sucrose so sucrose is a disaccharide so two sugars stuck together glucose plus fructose you've probably heard of both of those things before sucrose is of course table sugar it's what you would have mixed into your coffee if you had that this morning and an example of a polysaccharide is starch so what's in a potato all right now clearly these are all sugars they're all relevant to a human diet you would never confuse you've probably not knowingly tasted glucose it's not particularly sweet sucrose is much sweeter and a potato is not necessarily sweet at all yet this really points out that how these sugars are built the different structures matter a lot they matter for things like how you taste them in your diet and how carbohydrates are built also matters a lot for all kinds of aspects of biology which is why it's somewhat important to at least understand some of what we're talking about a common language about how to describe these molecules okay so the simplest biological sugars have three carbons that are least commonly used these are referred to as trioses and if we take the general formula c3 h2o 3 okay and we say what are two ways that we can satisfy that formula there's two main ways we can do it one is like this okay so if you add up count all the carbons hydrogens and oxygens you will see that that is c3 h2o o3 this molecule is called glyceraldehyde and the other way we can do this is like this okay again three carbons three waters if you add up all the atoms this molecule is called dihydroxy acetone and these are sugars same chemical formula different chemical structure that has a term that's called an isomer and it turns out that we can chemically interconvert these molecules in the following way and so if we carry out this chemistry okay we will get this intermediate okay and that will allow you to interconvert glyceraldehyde this aldehyde with this ketone dihydroxyacetone and the enzyme class that carries this out is a class of enzymes called isomerases and this is exactly the chemistry that that enzyme would use to interconvert these two forms of this trials this three carbon sugar molecule all right now if we look at dihydroxyacetone there's no stereocenter here what do i mean by a stereocenter that's a carbon that has reminder from 512 carbon that has four different subs non-equivalent substituents around it however if you look at glyceraldehyde that carbon in the middle is a stereocenter okay four non-equivalent groups around it and so there's two ways that i can draw glyceraldehyde i can draw it like this okay or i could draw it like this all right so two different ways so the one on the left here is d glyceraldehyde and the one on the right is l glyceraldehyde okay and i know that this is review some people are good at seeing these things some people are not i brought a couple models here here's like just you know the blue and the brown are two stereocenters with four different constituents on them no way you can twist these around to make them identical molecules why does this matter well enzyme active sites are going to fit this molecule different than this molecule and this is why these stereoisomers matter so much for biology it's also something that's really hard to accomplish if you think about how do you actually generate stereoisomers if you were in an organic chemistry lab really hard but biology does this all the time and the real reason is is because it's enzymes that ultimately catalyze these inner conversions and different stereoisomers will fit differently into enzyme active sites now the way that i've been drawing these sugars is a convention called a fissure projection and when drawn in this way the convention is is that so you put the carbonyl towards the top if the o h group the alcohol is pointing to the right that's d if it's pointing to the left that's l and so d pointing to the right l pointing to the left like amino acids biology has chosen one stereo chemistry for most biological sugars because of course enzymes act on them and so in biology it's d sugars this is in contrast to l amino acids and so if you can remember that sugars are d you know that amino acids are the opposite or if you remember that amino acids are l you can remember that sugars are the opposite okay all right so dihydroxyacetone is really the only sugar with three or more carbons that doesn't have a chiral center everything else will and so if i go to a four carbon sugar draw a couple of them here so okay so here's c4h2o4 drawn with a ketone if you look at this this is a chiral center oh group is pointing to the right this is a d sugar if i had drawn it with the o h group on this side it would be an l sugar all right if i draw this sugar as a different isomer this time with an aldehyde okay now we encounter a bit of an issue because now i have one two stereocenters okay so if there's two stereocenters that means there's two to the n ways that i can draw this as a stereoisomer and so you can see that this could get really complicated very quickly now this sugar obviously is a d because i drew both o h groups two pointing to the right but you can imagine i could draw one this way or one that way and so how do you know if it's a d or an l sugar and so the convention is is that whether or not a sugar is designated as d or l refers to the stereocenter that is furthest away from the carbonyl and so this is the relevant stereocenter that says it's a d sugar so what do i mean i can draw and then any other sugar would have a different name and so what do i mean by that let me draw this a few different ways and so the sugar that i've drawn here is referred to as d erythrose all right if i draw it now i have the oh group on the carbon furthest from the carbonyl pointing to the left so this would be l erythros and if i draw it differently by altering the stereochemistry of this carbon now it has a different name and so this carbon is d or this sugar is d threose all right makes sense if i flip the oh group to this side it would be l throws all right so lots of possibilities turns out nature only uses a subset of these stereoisomers and makes them relevant for biology for example d erythros is something that you will encounter when we talk about metabolism later in the course d3os as far as i know is not used in biology i would never say it's never used in biology never bet against biology it can do absolutely everything there's always an exception somewhere but in general d3os is not something that really exists at least commonly in nature all right so if we go through and you look at all of these different sugars that i've drawn you can see that they either have an aldehyde or they have a ketone somewhere in the molecule all right so if you have an aldehyde these sugars are generically referred to as aldoses all right and if you have a ketone an internal carbonyl these are generically referred to as ketosis now you might say as you start getting to longer and longer sugars you could put the ketone anywhere along the sugar and there would be a ton of different possibilities but it turns out ketosis always have the carbonyl as the second carbon in from the end the reason for that is is because biology as you will see when we talk about metabolism interconverts these via isomerase reactions and so you can't use an isomerase reaction to interconvert a ketose and an aldose unless the ketone is one carbon away from the end of the sugar and so this fact really limits some of the diversity of ketosis that can actually exist in nature now most important biological sugars at least the most common ones end up having six carbons or five carbons and these are referred to as hexoses or aldos or pentoses sorry so much nomenclature okay so six carbon sugars are hexoses five carbon sugars are pentoses and if we just talk about the hexoses you're very familiar with a couple of them okay and so one that we mentioned earlier blood sugar glucose looks like this okay so this molecule is d glucose it's a d sugar because the stereocenter here furthest from the carbonyl points o h group points to the right so it's a d sugar it's an aldose because it has an aldehyde all right and it's a hexose because it has one two three four five six carbons and what makes it glucose is the stereochemistry of these other sites that end up being this is the molecule glucose now if i carry out that isomerase reaction that i showed you earlier okay so it'll give me this intermediate i'm going to draw the whole thing then i interconvert that aldose now it becomes a ketose okay this is d fructose another common sugar that certainly is in the news a lot d sugar because the stereocenter furthest from the carbonyl points to the right makes it a d sugar it's a ketose it's a hexose this organization of other stereocenters is what makes it d fructose all right now if we go through and we count these there's four stereocenters in glucose three stereocenters in fructose that means two to the end there are 16 ways i can make a ketose aldose eight ways i can make a ketose i'm sorry an aldos hexose eight ways i can make a ketose hexose among those that's even 12 different ways that i can have d hexoses that are a ketocernal dose could be very very complicated but it turns out fructose is the only d hexose ketose that really is relevant for nature there's only two other molecules related to glucose only two other hexose aldoses that are sugars used in nature you've probably heard of these as well i'll draw them to illustrate a different point okay so this molecule is galactose important sugar found in milk all right if i draw glucose next to it again glucose so these two sugars differ here okay the stereochemistry there okay so there are i guess isomers of each other there's a special name for it we'll get to a second so that's how galactose is related to glucose the other major aldos hexose is this one okay this is d-mannose okay this differs from glucose here that carbon at that carbon by the way by convention the way that you number carbons in sugars is you start with the end that's closest to the carbonyl either the aldehyde or the carbon one up from the ketone so this would be carbon one two three four five six so galactose differs from glucose at carbon four glucose differs from mannose at carbon two these have names these isomers have names in relation to each other and so two sugars that differ by one part of stereochemistry so galactose to glucose or glucose to mannose are called epimers and these can be interconverted by enzymes called epimerases we'll talk about how these work later in the course and so glucose is an epimer of galactose glucose is an epimer of manos manos is not an epimer of galactose because mannose and galactose differ at both carbon two and carbon four their stereochemistry okay why is that relevant because if you're going to interconvert galactose and mannose you would have to do it in two steps two different epimerase reactions to interconvert those two sugars all right great so we've discussed now all of the major hexoses that nature uses we've discussed all the major trioses that nature uses the other major length of sugars that ends up being important in biochemistry is the five carbon sugars the pentoses and so i want to mention a couple pentoses and do so in a way that will allow me to basically solidify some of the nomenclature that i've gone through and of course one of the five carbon sugars ribose is really critical to nucleic acid structure which is one of the reasons why we're talking about this at this point in the course okay so this is a pentose one two three four five carbon sugar okay d ribose all right it's a d sugar because the stereocenter furthest from the carbonyl points to the right it's an aldose because it has an aldehyde group i can act on this with an isomerase not going to draw out the isomerase reaction again it's exactly what i drew before if i did this now i turn this into a ketose okay pentose because it's five carbons ketos because it has a ketone d sugar because the stereocenter furthers from the carbonyl points to the right this has the name of d ribulose all right and it turns out that there's an important epimer of d ribulose that's found in nature the epimer changes the stereochemistry at carbon three carbon one two three four five that's carbon three and so if this was acted on by an epimerase that did that you get this sugar also a pentose also a ketose a d sugar but an epimer of ribulose it's called d xyulose okay it's an epimer because of xylose and ribulose are epimers because they differ by stereochemistry only at one position i'll just say right off the bat you should not memorize names of sugars in their structures these are things you can look up in books the point of going through all this is just to expose you to some of the nomenclature remind you about stereochemistry i realize these are basic things many of you have already encountered this some of you find this very easy some people find these sort of spatial things more difficult this is very well reviewed though in textbooks or other places online if you need to to to a look it up but the key thing is just to remember this nomenclature because it'll make it easier for us to talk about sugars um later in the course all right let's take a short break so i can get some board space back and then we'll build off of some of these concepts in a minute i've been drawing all of these sugars as straight chains but you probably know from high school or from looking at dna or rna that the ribose there is not a straight chain but instead forms a ring and in fact in solution particular aqueous solution sugars particularly five carbons and longer almost always exist as rings and there is a very clear reason for this and you probably remember from 512 organic chemistry that alcohols will react with aldehydes and ketones in solution okay and so here i have a model of glucose and fructose if you want to come and play with them and so if you look at this and you just look at the model you see that this oxygen right here this alcohol in space is very close or can be moved to be very close to this aldehyde here on the end of the molecule or the same thing here with fructose right here's a you know here's a alcohol very close in space with this ketone all right so what happens in this situation well if you have this is review of organic chemistry okay so here's any generic aldehyde here's some alcohol okay so if those things react you end up with this so-called hemi acetol or the same thing if i do it with a ketone and an alcohol now you get this hemi ketal okay now given that you have an alcohol reacting with a carbonyl an aldehyde or a ketone on the same molecule well what happens is you effectively get a ring with oxygen being one of the components of the ring and so if we draw this for glucose okay so this is d glucose all right and so if the alcohol here on carbon one two three four five interacts with the aldehyde on carbon one okay you can play with the model and see that that is the one that's close in space you now end up getting this okay this where you get a ring between carbons one and five okay we can number the rest of them two three four five six all right or if i turn this molecule so that you can now draw it in a slightly more chemically proper way okay now you basically have this is carbon one two three four five six okay so carbon five oxygen from carbon five now bound to carbon one gives you this six membered ring structure the six-membered ring structure is reminiscent of an organic molecule called a looks like that called pyran and so the six-membered ring in a sugar is also referred to as a pyranose all right so that's the first thing the second thing is that this whole business can be very tedious to draw in fact it's very tedious drawing sugars in general as i'm sure you are would agree with me if you're taking notes during this lecture and so oftentimes these pyranoses like glucose are drawn with shorthand and the shorthand is as follows okay where i basically represent the oh groups as simply lines and so this is another shorthand to draw that pyranose form of glucose again carbon one two three four five six okay now the last thing is you can see i didn't draw the o h group there on carbon one and that's because by making this pyranose ring if you look at carbon one i have now generated a new stereocenter okay and so carbon one now has four non-equivalent groups on it which means i could draw the oh group at carbon one in two different ways and so this is carbon one i could draw it such that the oh group points down or i could draw it such that the oh group points up and those are two different molecules and so there's a naming convention for this too and so if the oh group points down using this way of drawing the molecule it's called alpha if the o h group points up it's called beta all right and so this alpha versus beta ends up being structurally different because it puts the basically that that oh group pointing in a very different position in space okay so if i make a ring here with glucose all right and the oh group is pointing here versus there very different position in space and this has implications for how you build bonds for disaccharides and polysaccharides that make structural differences and we'll cover this a lot when we get to metabolism but it should be very clear now that glucose if you just take a solution of glucose and put it in water it is not one thing there's actually multiple different forms it can have it could be as i drew it up here with the oh group pointing down this would be alpha d gluco because it's glucose pyranose because it's in the pyrinos ring form i could have drawn it with the oh group pointing up different molecule that would be beta d gluco pyrinos or it could just be the open chain d glucose i was drawing earlier all right all of those are perfectly legitimate ways for glucose to exist in solution all right now it turns out that in reality about a third of it in solution is this two-thirds is that and a trace amount is this okay and that's uh you know has to do with just what is more favorable forms or not okay but which form it's in actually matters um for structural reasons as we'll see later in the course now the final complexity is is that this ring is not flat okay so if i actually take glucose here and make a form of it okay so here's my glucose molecule there's no way for me to make this completely flat say like benzene and so there's really two different pyranose conformations that can be formed i'll try to draw them but they're harder to draw here's a overhead that you can look at it's easier but basically you can have it form this so-called boat form okay or this so-called chair form so there's the boat versus the chair conformation glucose turns out prefers the chair conformation and there's sort of an interesting thing that comes from this because if you take beta d glucopyranose all right it turns out of all the hexoses that exist in possible hexoses that exist the form of of a hexose aldose that best spreads out all the hydroxyl groups is beta-d glucopyranose right the more common one in solution why is this matter well because if this has this reactive aldehyde bound up in this stable ring structure it's less likely to react with other aldehydes in the cell and so this is likely why nature chose d-glucose as the most common storage sugar why it's sugar in your blood because it's the most stable hexose that's out there all right and it's not just a random reason that nature picked this one but actually because of real chemical stability issues for why it's there all right now i want to mention that ketosis also can form rings and i'm going to use this as an example to show you that a keto so here's fructose okay so this is d fructose and so turns out this can form two possible rings it can form a five-membered ring or a six-membered ring so how do i form a five-membered ring some colors okay so if i take the carbon here from carbon one two three four five the hydroxyl from carbon five form a ring there all right now i get this molecule okay let's number these one two three four five six okay or if i now turn this so that i draw it in the way you're probably more used to seeing it i'm going to use the shorthand here so this here would be carbon 1 2 3 4 five six hydroxyl from carbon five forming a bond to carbon two that creates a new stereocenter at carbon two oh group is pointing up so this is a beta sugar okay aoh group pointing up so this here as i drew it would be beta d fructo and this is a furanose why is that because the organic molecule that's a five-membered ring with an oxygen in it is a furan and so the five-membered ring is referred to as a furanose beta d fructofyranos if i drawn it with the oh group putting down it would be alpha d fructophironos okay there's another possible ring i can do instead i take the hydroxyl from carbon 6 and do that form a ring now i'm going to form a six membered ring okay we have carbon one two three four five six so if i now turn this okay so this here now i drew the o h group pointing down so it's an alpha if i drew it up it would be beta so this is alpha d fructo pyranose six membered ring version of fructose five-membered ring version of fructose so lots of non-equivalent ways i can draw fructose and it turns out these actually matter and they matter for real things that probably matter to you and so i brought with me here two different sweeteners okay this is corn syrup this is honey has anyone ever i'm sure most of you have had honey has anyone ever tasted corn syrup come on someone's tasted corn syrup is it sweet which one's sweeter honey by far much much much sweeter i used to have it so you guys could come up and taste them but i couldn't come up with a way to do that in a sanitary way so i gave up on it but nonetheless much sweeter than that it turns out these are not pure fructose they're a combination of sugars but their composition is actually from a chemical standpoint similar amounts of fructose in each one and it turns out that honey is beta d fructopyranose whereas corn syrup is beta defructophyranos all right so same sugar different structure one's a fair nose one's a pyranose tastes very differently to you one being much more sweet one being much less sweet okay now of course i also want to talk about ribose because it's the thing that you guys are going to talk about the most next because it's in nucleic acids and so just as a reminder here's ribose it's a aldose and a pentose okay so this is d-ribose ribose as you know from high school forms five-membered rings that's because it links alcohol on carbon four to the aldehyde on carbon one and that gives you this ring structure okay okay now number carbons one two three four alcohol and carbon four forming a ring to the aldehyde on carbon one this is carbon five all right and the way i drew it oh group pointing up so this is beta d ribo firanos will be the proper way to have it and so when you guys talk about this in dna well the base is going to be linked to carbon 1. it's going to replace that ox the hydroxyl group the beta form of the hydroxyl group with the nitrogen and you're going to talk about bonds being from the 5 prime or the 3 prime end those are those hydroxyl groups that's where five prime and three prime comes from because those are the five in the three position on ribose great perfect all right so we will return to carbohydrates in great detail we'll discuss how we combine different carbohydrates different monosaccharides to make disaccharides and polysaccharides how these different structural properties end up mattering for things like energy storage as well as to produce various structural molecules that can be important for different cells and organisms but for the remaining you know part of the class today i really want to shift topics to now discuss a completely different class of biomolecules and that's lipids so as i said earlier the reason we're going to do this is because coming up for professor yaffi's lectures lipids end up being really important molecules for various aspects of cell signaling they're also very important for energy transduction which is why i'm talking about them as well we will spend a lot of time later talking about lipids in great detail but really what i want to focus on today is how lipids are used to create membranes that is barriers that really separate the outside world from the inside of cells things that make compartments within cells and these things also end up being surfaces where you can have key things happen so you reduce spatial complexity if you go to a 2d surface versus a 3d surface which is part of why they're so important in signal transduction but to talk about these i have to introduce first of all what is a lipid okay so lipids are a class of molecules you think of them as fats that's sort of how they fit in the nutritional standpoint of what we'll talk about but first i want to give a general definition of what a lipid is now there's lots of different classes of lipids and we'll cover these later in the course but in general at the highest level almost all lipids consist of two pieces consists of something called a fatty acid that's esterified to an alcohol okay so what is a fatty acid well a fatty acid is really any molecule that has a carboxylic acid group okay so there's a carboxylic acid and then hooked up to that carboxylic acid is a whole bunch of saturated hydrocarbons alkyl chains okay oftentimes fatty acid would be drawn like this right because of all the different saturated chains okay so acid group on one end really greasy alkyl chain on the other and it turns out that this can be esterified to an alcohol so here's just a generic alcohol and as you certainly remember from organic chemistry if i form i can use an alcohol and an acid to form an ester okay and so then that would be okay so now i have basically this ester bond and this esterification between some lipid species and a fatty acid in general is the general thing that leads to class of molecules known as lipids now why this is particularly useful for biology is that this long greasy alkyl chain is not water soluble all right so if you take oil from your cabinet canola oil or olive oil or whatever and you pour it in water what happens it doesn't mix together you get these globs of oil floating in the water okay and so if you want to form a barrier between two aqueous compartments a way to do this is to have basically a hydrophobic layer a membrane basically separate the two aqueous compartments okay the inside and the outside of the cell now if i take a lipid and the lipid i form this ester and it doesn't have a charged group anywhere on the molecule this is sometimes referred to is a neutral lipid so what do i mean by neutral lipid it's basically taking this which is intrinsically a fatty acid is intrinsically a polar molecule it has this carboxylic acid on the end of it okay but if i form an ester linkage to an alcohol and the alcohol has no charge on it now it's just this really greasy molecule and it turns out that's exactly what is in your olive oil or in your canola oil in your cabinet it's basically a bunch of fatty acids long ankle chains esterified to non-charged alcohols which makes this neutral lipid this greasy molecule which is great for energy storage in plants something we'll talk about but if you want to mix it together with water it doesn't do very well okay so if you go to make salad dressing and you pour your oil in with your vinegar the aqueous thing you get a bunch of droplets you don't get a solution and if you think about it that's not very good at generating an interface between two compartments right you just get a bunch of droplets you actually don't get an interface between two compartments so if you want to make an interface you have to do something different you need to have a charge group like on this fatty acid that's going to be happy sticking towards the aqueous side and then a hydrophobic portion that's going to be happy sticking to form a barrier okay effectively that's what soap is all right so if you want to wash your hands and use canola oil it doesn't work very well right okay but what happens if you have a bunch of greasy stuff in the water and you take a drop of dawn dish detergent and drop it in the water you get this immediate barrier that forms across the top as you get this film where you basically align up all these charged hydrophilic parts to the aqueous pieces and all of the greasy parts to the to the hydrophobic side okay so you end up having this you know nice charged molecule with this long hydrophobic part so you have a hydrophilic end and a hydrophobic end and that ends up being very useful as a way to form an aqueous um um uh hydrophobic interface and this is exactly how soap works as i'm sure you've learned in other classes as an aside you know how you make soap you basically boil the neutral lipids in lye okay so boiling it in base if you remember from organic chemistry will break the ester linkage and now you have these molecules and that's how you make soap all right now the way biology does this is they actually assemble lipids that effectively have that same property okay where basically they have a head group from the alcohol that's charged with the hydrophobic group contributed from these fatty acids and this is what allows things to assemble into membranes and so membranes are largely made up of and certainly for the purposes of the upcoming lectures so-called phospholipids so what is a phospholipid well on a phospholipid the alcohol part of the lipid is derived from a molecule called glycerol all right so glycerol looks like this okay so this is glycerol all right three carbon molecule three alcohols actually very similar if you look back in your notes to dihydroxyacetone the difference between glycerol and dihydroxyacetone is carbon two is an alcohol here before it was a ketone turns out that's where glycerol comes from dihydroxyacetone getting turned into to glycerol and basically what a phospholipid is is that you esterify a fatty acid to two of the alcohols and another phosphate and charged alcohol to the other hydroxyl group so what do i mean by that so like this so here's ester linkage number one i'll draw it this way just for ease this is to carbon two here's ester linkage number two okay so that's a fatty acid a sterified two two and three and then you now make an ester to a phosphate okay so there's a phosphate at carbon one and then you make another ester linkage to another alcohol where r equals alcohol and that alcohol also turns out to be charged and so the most common phospholipid membrane lipid is a molecule called phos the tidal choline which is that structure with the r group being this alcohol okay so this is choline okay and so phosphatidylcholine is basically that structure okay so this is phosphatidylcholine drawn out in all of this glory so you have this hydro philic end here you have a hydrophobic end okay that's good this can point towards the aqueous side this can point towards the greasy side and make a nice interface and so another common word for phosphatidylcholine an old word for it is a molecule called lecipine anyone read the labels on the side of your food ever in fact i think there's an old commercial that makes fun of this soy lecithin what's that i don't want that in my ice cream okay well what is lecithin it's phosphatidylcholine it's basically why is this done well it's commonly added to ice cream because what is ice cream and it's an emulsion between fat the cream and sugar which is pretty aqueous soluble as you might guess from looking at what we drew earlier today and so by putting phosphatidylcholine in your ice cream you basically stabilize this emulsion between the aqueous and the fat face so this is why it's added to lots of food and in fact it says soy lecithin an emulsifier that's why it's added you can do this yourself this is a common trick that many cooks know so if you make salad dressing you put a little mayonnaise in your salad dressing okay why do you do that well mayonnaise has eggs in it eggs have a lot of phosphatidylcholine that mayonnaise that you add into your salad dressing basically stabilizes that emulsion between the oil and the vinegar and helps it be more stable and distribute better across your your lettuce i think my favorite example of this is who's made chocolate chip cookies everyone's done this right okay so how do you make chocolate chip cookies so you take butter and sugar all right fat and something is very non very polar aqueous soluble sugar and you try to mix them together you have to cream it right and that takes forever it's a pain in the butt it doesn't come together very well and so you get lazy and you put the egg in there and then it all comes together really really easily right so why is that the egg is the emulsifier that actually brings it together whereas trying to get the butter and sugar to make your sure your cookies nice and fluffy is a lot harder because you're really trying to get these two things to come together and it's basically this exact chemistry that's taking place when you're doing that active cooking all right now phosphatidylcholine is not the only phospholipid found in membranes but i'll just quickly mention what a couple of the other ones are so it turns out you have two other major phospholipids by abundance and then another phospholipid that's really important for signaling so i'll list them here first so there's phosphatidyl serine phosphatidyl ethanolamine these it turns out phosphatidylcholine phospital serine phosphatidyl ethanolamine is what makes up the majority of the phospholipids in cell membranes and then there's a much more minor phospholipid that's important for signaling which is phosphatidyl inositol so what are these so serine ethanoline and inositol are just like choline different alcohols that can be esterified to the phosphate in exactly the same way i did for phosphatidylcholine and so what's phosphatidylserine so if you remember this is okay so this here is the amino acid serine okay i'm sure you remember that if we esterify that alcohol to the phosphate okay there's phosphatidyl serine okay what's ethanolamine look like so ethanolamine is this alcohol okay so that's ethanolamine okay sterify the alcohol the phosphate esterify that phosphate to glycerol okay phosphatidyl ethanol amine and the last one is inositol so what is inositol well inositol is a six-membered hydrocarbon ring where all of the carbons have an alcohol on them and so if i esterify one of these alcohols on inositol of course there's a if i sterify one of those alcohols to the phosphate to make phosphatidyl and acetol turns out that that ends up being a really useful lipid to make for signaling and you'll hear a lot from this about this in a couple of contexts i believe from professor yaffi later in the course all right so this having these general membrane structure this general phospholipid structure where you have this hydrophobic part of the molecule and the hydrophilic part of the molecule is really what allows these lipids to come together to form these membrane bilayers that are often drawn like this okay and so when i'm drawing it like this basically what those two wavy lines represent those are the hydrophobic fatty acid parts and this is the hydrophilic so-called head group okay that's the charged alcohol stuck on to the end of the and to to to to the phosphate on on the glycerol all right and these of course assemble such that all of the hydrophilic head groups face an aqueous compartment on either side okay and then you have this nice hydrophobic portion that is a membrane and that is what can create a barrier between two different compartments in cells okay now just to put this into context for the protein structure stuff that you learned about okay so when you learn about all the different ways that you have protein structure of course you have amino acids that are hydrophilic amino acids that are hydrophobic if you have a protein that's floating in solution it has all the hydrophilic parts on the outside and the hydrophobic parts in the middle all right but you can imagine that you can also have proteins that assemble to sit such that they span the membrane so hydrophobic parts that interact with the hydrophobic part the inner part of the membrane hydrophilic parts on either side these can form channels these can form all kinds of ways to move stuff across membranes or you might think that you might have a protein that does something like that hydrophobic part on one end hydrophilic part on the other and really floats on the surface of a membrane and you will see that the way cell signaling works is is that you basically have lots of protein complexes that will assemble that membranes two-dimensional space those membranes as well as some of the membrane lipids can then act as messengers that allow cells to carry out various signals and i will leave that to professor yaffi to talk about all right so i will also come back and discuss membranes in a very different context in the context of metabolism during the second half of the course because it turns out a lot of energy transduction and the way cells really store energy also ends up being really important with respect to membranes all right you guys are lucky you get out a little bit early today this is the first time that we've done the lectures this way so i don't have my timing quite right but i will see you guys again for uh metabolism after spring break you

okay great now let&#39;s dive into the material today so today&#39;s topic is carbohydrates as well as an introduction to membrane structure and from the very first class i believe professor yaffi talked to you about the four main classes of biological molecules so proteins and amino acids you&#39;ve spent a lot of time talking about that nucleic acids is coming up and the other two are carbohydrates or sugars and lipids today we&#39;re really going to focus most of the lecture on carbohydrates what they are structure something about nomenclature and then at the end we&#39;re going to talk a little bit about lipids and basic membrane structure now carbohydrates and lipids are really critical energy storage molecules for cells and when we talk about metabolism the most interesting part of this course after spring break we&#39;re going to delve into this in a lot more detail but sugars are also very important to understand nucleic acid structure turns out membranes are essential for signal transduction those are the two major topics that professor gaffy is going to talk about for the rest of his time and so this year we&#39;re going to try something different and have me introduce at least some of these topics now which will deal with some redundancies that otherwise might have existed and maybe set it up better for him to uh to to discuss some of the lectures coming up now today&#39;s lecture is unfortunately topically a little bit disjointed but it still has important information about biochemistry and it will help us all speak the same language both for the upcoming lectures on from uh from professor yaffi as well as things that i will start off with when i come back and it&#39;s a nice way to sort of ease back in after the exam okay so what is a carbohydrate or a sugar so let&#39;s break this down and so it&#39;s carbo hydrate okay so a carbohydrate is effectively carbon in some ratio with water so all carbohydrates have the same chemical formula cnh2on and so there are some deviations from this in biology sometimes you can introduce a heteroatom phosphate sulfur nitrogen etc technically these are not carbohydrates although they&#39;re often lumped together with carbohydrates and why would nature do this because it changes some of the chemical properties that can be useful for either structural or signaling reasons you may encounter these later um certainly in other classes but we&#39;re not going to talk much more about that today we&#39;re really just going to focus on the base carbohydrate cnh2n structure now carbohydrates come in different forms and so they can come as single units with that structure these are so called monocyte or these single units can come together to form various polymers and those polymers could be two units so-called disaccharides so two sugars stuck together or many units and so sometimes those are referred to as oligosaccharides or polysaccharides and there&#39;s really no clear distinction between you know a few chains together oligosaccharides many polysaccharides they&#39;re somewhat used interchangeably now you guys have almost certainly heard of many of these things so what&#39;s a monosaccharide so a good example of that is glucose so glucose is of course the main sugar that exists in your blood what&#39;s a disaccharide so common one is sucrose so sucrose is a disaccharide so two sugars stuck together glucose plus fructose you&#39;ve probably heard of both of those things before sucrose is of course table sugar it&#39;s what you would have mixed into your coffee if you had that this morning and an example of a polysaccharide is starch so what&#39;s in a potato all right now clearly these are all sugars they&#39;re all relevant to a human diet you would never confuse you&#39;ve probably not knowingly tasted glucose it&#39;s not particularly sweet sucrose is much sweeter and a potato is not necessarily sweet at all yet this really points out that how these sugars are built the different structures matter a lot they matter for things like how you taste them in your diet and how carbohydrates are built also matters a lot for all kinds of aspects of biology which is why it&#39;s somewhat important to at least understand some of what we&#39;re talking about a common language about how to describe these molecules okay so the simplest biological sugars have three carbons that are least commonly used these are referred to as trioses and if we take the general formula c3 h2o 3 okay and we say what are two ways that we can satisfy that formula there&#39;s two main ways we can do it one is like this okay so if you add up count all the carbons hydrogens and oxygens you will see that that is c3 h2o o3 this molecule is called glyceraldehyde and the other way we can do this is like this okay again three carbons three waters if you add up all the atoms this molecule is called dihydroxy acetone and these are sugars same chemical formula different chemical structure that has a term that&#39;s called an isomer and it turns out that we can chemically interconvert these molecules in the following way and so if we carry out this chemistry okay we will get this intermediate okay and that will allow you to interconvert glyceraldehyde this aldehyde with this ketone dihydroxyacetone and the enzyme class that carries this out is a class of enzymes called isomerases and this is exactly the chemistry that that enzyme would use to interconvert these two forms of this trials this three carbon sugar molecule all right now if we look at dihydroxyacetone there&#39;s no stereocenter here what do i mean by a stereocenter that&#39;s a carbon that has reminder from 512 carbon that has four different subs non-equivalent substituents around it however if you look at glyceraldehyde that carbon in the middle is a stereocenter okay four non-equivalent groups around it and so there&#39;s two ways that i can draw glyceraldehyde i can draw it like this okay or i could draw it like this all right so two different ways so the one on the left here is d glyceraldehyde and the one on the right is l glyceraldehyde okay and i know that this is review some people are good at seeing these things some people are not i brought a couple models here here&#39;s like just you know the blue and the brown are two stereocenters with four different constituents on them no way you can twist these around to make them identical molecules why does this matter well enzyme active sites are going to fit this molecule different than this molecule and this is why these stereoisomers matter so much for biology it&#39;s also something that&#39;s really hard to accomplish if you think about how do you actually generate stereoisomers if you were in an organic chemistry lab really hard but biology does this all the time and the real reason is is because it&#39;s enzymes that ultimately catalyze these inner conversions and different stereoisomers will fit differently into enzyme active sites now the way that i&#39;ve been drawing these sugars is a convention called a fissure projection and when drawn in this way the convention is is that so you put the carbonyl towards the top if the o h group the alcohol is pointing to the right that&#39;s d if it&#39;s pointing to the left that&#39;s l and so d pointing to the right l pointing to the left like amino acids biology has chosen one stereo chemistry for most biological sugars because of course enzymes act on them and so in biology it&#39;s d sugars this is in contrast to l amino acids and so if you can remember that sugars are d you know that amino acids are the opposite or if you remember that amino acids are l you can remember that sugars are the opposite okay all right so dihydroxyacetone is really the only sugar with three or more carbons that doesn&#39;t have a chiral center everything else will and so if i go to a four carbon sugar draw a couple of them here so okay so here&#39;s c4h2o4 drawn with a ketone if you look at this this is a chiral center oh group is pointing to the right this is a d sugar if i had drawn it with the o h group on this side it would be an l sugar all right if i draw this sugar as a different isomer this time with an aldehyde okay now we encounter a bit of an issue because now i have one two stereocenters okay so if there&#39;s two stereocenters that means there&#39;s two to the n ways that i can draw this as a stereoisomer and so you can see that this could get really complicated very quickly now this sugar obviously is a d because i drew both o h groups two pointing to the right but you can imagine i could draw one this way or one that way and so how do you know if it&#39;s a d or an l sugar and so the convention is is that whether or not a sugar is designated as d or l refers to the stereocenter that is furthest away from the carbonyl and so this is the relevant stereocenter that says it&#39;s a d sugar so what do i mean i can draw and then any other sugar would have a different name and so what do i mean by that let me draw this a few different ways and so the sugar that i&#39;ve drawn here is referred to as d erythrose all right if i draw it now i have the oh group on the carbon furthest from the carbonyl pointing to the left so this would be l erythros and if i draw it differently by altering the stereochemistry of this carbon now it has a different name and so this carbon is d or this sugar is d threose all right makes sense if i flip the oh group to this side it would be l throws all right so lots of possibilities turns out nature only uses a subset of these stereoisomers and makes them relevant for biology for example d erythros is something that you will encounter when we talk about metabolism later in the course d3os as far as i know is not used in biology i would never say it&#39;s never used in biology never bet against biology it can do absolutely everything there&#39;s always an exception somewhere but in general d3os is not something that really exists at least commonly in nature all right so if we go through and you look at all of these different sugars that i&#39;ve drawn you can see that they either have an aldehyde or they have a ketone somewhere in the molecule all right so if you have an aldehyde these sugars are generically referred to as aldoses all right and if you have a ketone an internal carbonyl these are generically referred to as ketosis now you might say as you start getting to longer and longer sugars you could put the ketone anywhere along the sugar and there would be a ton of different possibilities but it turns out ketosis always have the carbonyl as the second carbon in from the end the reason for that is is because biology as you will see when we talk about metabolism interconverts these via isomerase reactions and so you can&#39;t use an isomerase reaction to interconvert a ketose and an aldose unless the ketone is one carbon away from the end of the sugar and so this fact really limits some of the diversity of ketosis that can actually exist in nature now most important biological sugars at least the most common ones end up having six carbons or five carbons and these are referred to as hexoses or aldos or pentoses sorry so much nomenclature okay so six carbon sugars are hexoses five carbon sugars are pentoses and if we just talk about the hexoses you&#39;re very familiar with a couple of them okay and so one that we mentioned earlier blood sugar glucose looks like this okay so this molecule is d glucose it&#39;s a d sugar because the stereocenter here furthest from the carbonyl points o h group points to the right so it&#39;s a d sugar it&#39;s an aldose because it has an aldehyde all right and it&#39;s a hexose because it has one two three four five six carbons and what makes it glucose is the stereochemistry of these other sites that end up being this is the molecule glucose now if i carry out that isomerase reaction that i showed you earlier okay so it&#39;ll give me this intermediate i&#39;m going to draw the whole thing then i interconvert that aldose now it becomes a ketose okay this is d fructose another common sugar that certainly is in the news a lot d sugar because the stereocenter furthest from the carbonyl points to the right makes it a d sugar it&#39;s a ketose it&#39;s a hexose this organization of other stereocenters is what makes it d fructose all right now if we go through and we count these there&#39;s four stereocenters in glucose three stereocenters in fructose that means two to the end there are 16 ways i can make a ketose aldose eight ways i can make a ketose i&#39;m sorry an aldos hexose eight ways i can make a ketose hexose among those that&#39;s even 12 different ways that i can have d hexoses that are a ketocernal dose could be very very complicated but it turns out fructose is the only d hexose ketose that really is relevant for nature there&#39;s only two other molecules related to glucose only two other hexose aldoses that are sugars used in nature you&#39;ve probably heard of these as well i&#39;ll draw them to illustrate a different point okay so this molecule is galactose important sugar found in milk all right if i draw glucose next to it again glucose so these two sugars differ here okay the stereochemistry there okay so there are i guess isomers of each other there&#39;s a special name for it we&#39;ll get to a second so that&#39;s how galactose is related to glucose the other major aldos hexose is this one okay this is d-mannose okay this differs from glucose here that carbon at that carbon by the way by convention the way that you number carbons in sugars is you start with the end that&#39;s closest to the carbonyl either the aldehyde or the carbon one up from the ketone so this would be carbon one two three four five six so galactose differs from glucose at carbon four glucose differs from mannose at carbon two these have names these isomers have names in relation to each other and so two sugars that differ by one part of stereochemistry so galactose to glucose or glucose to mannose are called epimers and these can be interconverted by enzymes called epimerases we&#39;ll talk about how these work later in the course and so glucose is an epimer of galactose glucose is an epimer of manos manos is not an epimer of galactose because mannose and galactose differ at both carbon two and carbon four their stereochemistry okay why is that relevant because if you&#39;re going to interconvert galactose and mannose you would have to do it in two steps two different epimerase reactions to interconvert those two sugars all right great so we&#39;ve discussed now all of the major hexoses that nature uses we&#39;ve discussed all the major trioses that nature uses the other major length of sugars that ends up being important in biochemistry is the five carbon sugars the pentoses and so i want to mention a couple pentoses and do so in a way that will allow me to basically solidify some of the nomenclature that i&#39;ve gone through and of course one of the five carbon sugars ribose is really critical to nucleic acid structure which is one of the reasons why we&#39;re talking about this at this point in the course okay so this is a pentose one two three four five carbon sugar okay d ribose all right it&#39;s a d sugar because the stereocenter furthest from the carbonyl points to the right it&#39;s an aldose because it has an aldehyde group i can act on this with an isomerase not going to draw out the isomerase reaction again it&#39;s exactly what i drew before if i did this now i turn this into a ketose okay pentose because it&#39;s five carbons ketos because it has a ketone d sugar because the stereocenter furthers from the carbonyl points to the right this has the name of d ribulose all right and it turns out that there&#39;s an important epimer of d ribulose that&#39;s found in nature the epimer changes the stereochemistry at carbon three carbon one two three four five that&#39;s carbon three and so if this was acted on by an epimerase that did that you get this sugar also a pentose also a ketose a d sugar but an epimer of ribulose it&#39;s called d xyulose okay it&#39;s an epimer because of xylose and ribulose are epimers because they differ by stereochemistry only at one position i&#39;ll just say right off the bat you should not memorize names of sugars in their structures these are things you can look up in books the point of going through all this is just to expose you to some of the nomenclature remind you about stereochemistry i realize these are basic things many of you have already encountered this some of you find this very easy some people find these sort of spatial things more difficult this is very well reviewed though in textbooks or other places online if you need to to to a look it up but the key thing is just to remember this nomenclature because it&#39;ll make it easier for us to talk about sugars um later in the course all right let&#39;s take a short break so i can get some board space back and then we&#39;ll build off of some of these concepts in a minute i&#39;ve been drawing all of these sugars as straight chains but you probably know from high school or from looking at dna or rna that the ribose there is not a straight chain but instead forms a ring and in fact in solution particular aqueous solution sugars particularly five carbons and longer almost always exist as rings and there is a very clear reason for this and you probably remember from 512 organic chemistry that alcohols will react with aldehydes and ketones in solution okay and so here i have a model of glucose and fructose if you want to come and play with them and so if you look at this and you just look at the model you see that this oxygen right here this alcohol in space is very close or can be moved to be very close to this aldehyde here on the end of the molecule or the same thing here with fructose right here&#39;s a you know here&#39;s a alcohol very close in space with this ketone all right so what happens in this situation well if you have this is review of organic chemistry okay so here&#39;s any generic aldehyde here&#39;s some alcohol okay so if those things react you end up with this so-called hemi acetol or the same thing if i do it with a ketone and an alcohol now you get this hemi ketal okay now given that you have an alcohol reacting with a carbonyl an aldehyde or a ketone on the same molecule well what happens is you effectively get a ring with oxygen being one of the components of the ring and so if we draw this for glucose okay so this is d glucose all right and so if the alcohol here on carbon one two three four five interacts with the aldehyde on carbon one okay you can play with the model and see that that is the one that&#39;s close in space you now end up getting this okay this where you get a ring between carbons one and five okay we can number the rest of them two three four five six all right or if i turn this molecule so that you can now draw it in a slightly more chemically proper way okay now you basically have this is carbon one two three four five six okay so carbon five oxygen from carbon five now bound to carbon one gives you this six membered ring structure the six-membered ring structure is reminiscent of an organic molecule called a looks like that called pyran and so the six-membered ring in a sugar is also referred to as a pyranose all right so that&#39;s the first thing the second thing is that this whole business can be very tedious to draw in fact it&#39;s very tedious drawing sugars in general as i&#39;m sure you are would agree with me if you&#39;re taking notes during this lecture and so oftentimes these pyranoses like glucose are drawn with shorthand and the shorthand is as follows okay where i basically represent the oh groups as simply lines and so this is another shorthand to draw that pyranose form of glucose again carbon one two three four five six okay now the last thing is you can see i didn&#39;t draw the o h group there on carbon one and that&#39;s because by making this pyranose ring if you look at carbon one i have now generated a new stereocenter okay and so carbon one now has four non-equivalent groups on it which means i could draw the oh group at carbon one in two different ways and so this is carbon one i could draw it such that the oh group points down or i could draw it such that the oh group points up and those are two different molecules and so there&#39;s a naming convention for this too and so if the oh group points down using this way of drawing the molecule it&#39;s called alpha if the o h group points up it&#39;s called beta all right and so this alpha versus beta ends up being structurally different because it puts the basically that that oh group pointing in a very different position in space okay so if i make a ring here with glucose all right and the oh group is pointing here versus there very different position in space and this has implications for how you build bonds for disaccharides and polysaccharides that make structural differences and we&#39;ll cover this a lot when we get to metabolism but it should be very clear now that glucose if you just take a solution of glucose and put it in water it is not one thing there&#39;s actually multiple different forms it can have it could be as i drew it up here with the oh group pointing down this would be alpha d gluco because it&#39;s glucose pyranose because it&#39;s in the pyrinos ring form i could have drawn it with the oh group pointing up different molecule that would be beta d gluco pyrinos or it could just be the open chain d glucose i was drawing earlier all right all of those are perfectly legitimate ways for glucose to exist in solution all right now it turns out that in reality about a third of it in solution is this two-thirds is that and a trace amount is this okay and that&#39;s uh you know has to do with just what is more favorable forms or not okay but which form it&#39;s in actually matters um for structural reasons as we&#39;ll see later in the course now the final complexity is is that this ring is not flat okay so if i actually take glucose here and make a form of it okay so here&#39;s my glucose molecule there&#39;s no way for me to make this completely flat say like benzene and so there&#39;s really two different pyranose conformations that can be formed i&#39;ll try to draw them but they&#39;re harder to draw here&#39;s a overhead that you can look at it&#39;s easier but basically you can have it form this so-called boat form okay or this so-called chair form so there&#39;s the boat versus the chair conformation glucose turns out prefers the chair conformation and there&#39;s sort of an interesting thing that comes from this because if you take beta d glucopyranose all right it turns out of all the hexoses that exist in possible hexoses that exist the form of of a hexose aldose that best spreads out all the hydroxyl groups is beta-d glucopyranose right the more common one in solution why is this matter well because if this has this reactive aldehyde bound up in this stable ring structure it&#39;s less likely to react with other aldehydes in the cell and so this is likely why nature chose d-glucose as the most common storage sugar why it&#39;s sugar in your blood because it&#39;s the most stable hexose that&#39;s out there all right and it&#39;s not just a random reason that nature picked this one but actually because of real chemical stability issues for why it&#39;s there all right now i want to mention that ketosis also can form rings and i&#39;m going to use this as an example to show you that a keto so here&#39;s fructose okay so this is d fructose and so turns out this can form two possible rings it can form a five-membered ring or a six-membered ring so how do i form a five-membered ring some colors okay so if i take the carbon here from carbon one two three four five the hydroxyl from carbon five form a ring there all right now i get this molecule okay let&#39;s number these one two three four five six okay or if i now turn this so that i draw it in the way you&#39;re probably more used to seeing it i&#39;m going to use the shorthand here so this here would be carbon 1 2 3 4 five six hydroxyl from carbon five forming a bond to carbon two that creates a new stereocenter at carbon two oh group is pointing up so this is a beta sugar okay aoh group pointing up so this here as i drew it would be beta d fructo and this is a furanose why is that because the organic molecule that&#39;s a five-membered ring with an oxygen in it is a furan and so the five-membered ring is referred to as a furanose beta d fructofyranos if i drawn it with the oh group putting down it would be alpha d fructophironos okay there&#39;s another possible ring i can do instead i take the hydroxyl from carbon 6 and do that form a ring now i&#39;m going to form a six membered ring okay we have carbon one two three four five six so if i now turn this okay so this here now i drew the o h group pointing down so it&#39;s an alpha if i drew it up it would be beta so this is alpha d fructo pyranose six membered ring version of fructose five-membered ring version of fructose so lots of non-equivalent ways i can draw fructose and it turns out these actually matter and they matter for real things that probably matter to you and so i brought with me here two different sweeteners okay this is corn syrup this is honey has anyone ever i&#39;m sure most of you have had honey has anyone ever tasted corn syrup come on someone&#39;s tasted corn syrup is it sweet which one&#39;s sweeter honey by far much much much sweeter i used to have it so you guys could come up and taste them but i couldn&#39;t come up with a way to do that in a sanitary way so i gave up on it but nonetheless much sweeter than that it turns out these are not pure fructose they&#39;re a combination of sugars but their composition is actually from a chemical standpoint similar amounts of fructose in each one and it turns out that honey is beta d fructopyranose whereas corn syrup is beta defructophyranos all right so same sugar different structure one&#39;s a fair nose one&#39;s a pyranose tastes very differently to you one being much more sweet one being much less sweet okay now of course i also want to talk about ribose because it&#39;s the thing that you guys are going to talk about the most next because it&#39;s in nucleic acids and so just as a reminder here&#39;s ribose it&#39;s a aldose and a pentose okay so this is d-ribose ribose as you know from high school forms five-membered rings that&#39;s because it links alcohol on carbon four to the aldehyde on carbon one and that gives you this ring structure okay okay now number carbons one two three four alcohol and carbon four forming a ring to the aldehyde on carbon one this is carbon five all right and the way i drew it oh group pointing up so this is beta d ribo firanos will be the proper way to have it and so when you guys talk about this in dna well the base is going to be linked to carbon 1. it&#39;s going to replace that ox the hydroxyl group the beta form of the hydroxyl group with the nitrogen and you&#39;re going to talk about bonds being from the 5 prime or the 3 prime end those are those hydroxyl groups that&#39;s where five prime and three prime comes from because those are the five in the three position on ribose great perfect all right so we will return to carbohydrates in great detail we&#39;ll discuss how we combine different carbohydrates different monosaccharides to make disaccharides and polysaccharides how these different structural properties end up mattering for things like energy storage as well as to produce various structural molecules that can be important for different cells and organisms but for the remaining you know part of the class today i really want to shift topics to now discuss a completely different class of biomolecules and that&#39;s lipids so as i said earlier the reason we&#39;re going to do this is because coming up for professor yaffi&#39;s lectures lipids end up being really important molecules for various aspects of cell signaling they&#39;re also very important for energy transduction which is why i&#39;m talking about them as well we will spend a lot of time later talking about lipids in great detail but really what i want to focus on today is how lipids are used to create membranes that is barriers that really separate the outside world from the inside of cells things that make compartments within cells and these things also end up being surfaces where you can have key things happen so you reduce spatial complexity if you go to a 2d surface versus a 3d surface which is part of why they&#39;re so important in signal transduction but to talk about these i have to introduce first of all what is a lipid okay so lipids are a class of molecules you think of them as fats that&#39;s sort of how they fit in the nutritional standpoint of what we&#39;ll talk about but first i want to give a general definition of what a lipid is now there&#39;s lots of different classes of lipids and we&#39;ll cover these later in the course but in general at the highest level almost all lipids consist of two pieces consists of something called a fatty acid that&#39;s esterified to an alcohol okay so what is a fatty acid well a fatty acid is really any molecule that has a carboxylic acid group okay so there&#39;s a carboxylic acid and then hooked up to that carboxylic acid is a whole bunch of saturated hydrocarbons alkyl chains okay oftentimes fatty acid would be drawn like this right because of all the different saturated chains okay so acid group on one end really greasy alkyl chain on the other and it turns out that this can be esterified to an alcohol so here&#39;s just a generic alcohol and as you certainly remember from organic chemistry if i form i can use an alcohol and an acid to form an ester okay and so then that would be okay so now i have basically this ester bond and this esterification between some lipid species and a fatty acid in general is the general thing that leads to class of molecules known as lipids now why this is particularly useful for biology is that this long greasy alkyl chain is not water soluble all right so if you take oil from your cabinet canola oil or olive oil or whatever and you pour it in water what happens it doesn&#39;t mix together you get these globs of oil floating in the water okay and so if you want to form a barrier between two aqueous compartments a way to do this is to have basically a hydrophobic layer a membrane basically separate the two aqueous compartments okay the inside and the outside of the cell now if i take a lipid and the lipid i form this ester and it doesn&#39;t have a charged group anywhere on the molecule this is sometimes referred to is a neutral lipid so what do i mean by neutral lipid it&#39;s basically taking this which is intrinsically a fatty acid is intrinsically a polar molecule it has this carboxylic acid on the end of it okay but if i form an ester linkage to an alcohol and the alcohol has no charge on it now it&#39;s just this really greasy molecule and it turns out that&#39;s exactly what is in your olive oil or in your canola oil in your cabinet it&#39;s basically a bunch of fatty acids long ankle chains esterified to non-charged alcohols which makes this neutral lipid this greasy molecule which is great for energy storage in plants something we&#39;ll talk about but if you want to mix it together with water it doesn&#39;t do very well okay so if you go to make salad dressing and you pour your oil in with your vinegar the aqueous thing you get a bunch of droplets you don&#39;t get a solution and if you think about it that&#39;s not very good at generating an interface between two compartments right you just get a bunch of droplets you actually don&#39;t get an interface between two compartments so if you want to make an interface you have to do something different you need to have a charge group like on this fatty acid that&#39;s going to be happy sticking towards the aqueous side and then a hydrophobic portion that&#39;s going to be happy sticking to form a barrier okay effectively that&#39;s what soap is all right so if you want to wash your hands and use canola oil it doesn&#39;t work very well right okay but what happens if you have a bunch of greasy stuff in the water and you take a drop of dawn dish detergent and drop it in the water you get this immediate barrier that forms across the top as you get this film where you basically align up all these charged hydrophilic parts to the aqueous pieces and all of the greasy parts to the to the hydrophobic side okay so you end up having this you know nice charged molecule with this long hydrophobic part so you have a hydrophilic end and a hydrophobic end and that ends up being very useful as a way to form an aqueous um um uh hydrophobic interface and this is exactly how soap works as i&#39;m sure you&#39;ve learned in other classes as an aside you know how you make soap you basically boil the neutral lipids in lye okay so boiling it in base if you remember from organic chemistry will break the ester linkage and now you have these molecules and that&#39;s how you make soap all right now the way biology does this is they actually assemble lipids that effectively have that same property okay where basically they have a head group from the alcohol that&#39;s charged with the hydrophobic group contributed from these fatty acids and this is what allows things to assemble into membranes and so membranes are largely made up of and certainly for the purposes of the upcoming lectures so-called phospholipids so what is a phospholipid well on a phospholipid the alcohol part of the lipid is derived from a molecule called glycerol all right so glycerol looks like this okay so this is glycerol all right three carbon molecule three alcohols actually very similar if you look back in your notes to dihydroxyacetone the difference between glycerol and dihydroxyacetone is carbon two is an alcohol here before it was a ketone turns out that&#39;s where glycerol comes from dihydroxyacetone getting turned into to glycerol and basically what a phospholipid is is that you esterify a fatty acid to two of the alcohols and another phosphate and charged alcohol to the other hydroxyl group so what do i mean by that so like this so here&#39;s ester linkage number one i&#39;ll draw it this way just for ease this is to carbon two here&#39;s ester linkage number two okay so that&#39;s a fatty acid a sterified two two and three and then you now make an ester to a phosphate okay so there&#39;s a phosphate at carbon one and then you make another ester linkage to another alcohol where r equals alcohol and that alcohol also turns out to be charged and so the most common phospholipid membrane lipid is a molecule called phos the tidal choline which is that structure with the r group being this alcohol okay so this is choline okay and so phosphatidylcholine is basically that structure okay so this is phosphatidylcholine drawn out in all of this glory so you have this hydro philic end here you have a hydrophobic end okay that&#39;s good this can point towards the aqueous side this can point towards the greasy side and make a nice interface and so another common word for phosphatidylcholine an old word for it is a molecule called lecipine anyone read the labels on the side of your food ever in fact i think there&#39;s an old commercial that makes fun of this soy lecithin what&#39;s that i don&#39;t want that in my ice cream okay well what is lecithin it&#39;s phosphatidylcholine it&#39;s basically why is this done well it&#39;s commonly added to ice cream because what is ice cream and it&#39;s an emulsion between fat the cream and sugar which is pretty aqueous soluble as you might guess from looking at what we drew earlier today and so by putting phosphatidylcholine in your ice cream you basically stabilize this emulsion between the aqueous and the fat face so this is why it&#39;s added to lots of food and in fact it says soy lecithin an emulsifier that&#39;s why it&#39;s added you can do this yourself this is a common trick that many cooks know so if you make salad dressing you put a little mayonnaise in your salad dressing okay why do you do that well mayonnaise has eggs in it eggs have a lot of phosphatidylcholine that mayonnaise that you add into your salad dressing basically stabilizes that emulsion between the oil and the vinegar and helps it be more stable and distribute better across your your lettuce i think my favorite example of this is who&#39;s made chocolate chip cookies everyone&#39;s done this right okay so how do you make chocolate chip cookies so you take butter and sugar all right fat and something is very non very polar aqueous soluble sugar and you try to mix them together you have to cream it right and that takes forever it&#39;s a pain in the butt it doesn&#39;t come together very well and so you get lazy and you put the egg in there and then it all comes together really really easily right so why is that the egg is the emulsifier that actually brings it together whereas trying to get the butter and sugar to make your sure your cookies nice and fluffy is a lot harder because you&#39;re really trying to get these two things to come together and it&#39;s basically this exact chemistry that&#39;s taking place when you&#39;re doing that active cooking all right now phosphatidylcholine is not the only phospholipid found in membranes but i&#39;ll just quickly mention what a couple of the other ones are so it turns out you have two other major phospholipids by abundance and then another phospholipid that&#39;s really important for signaling so i&#39;ll list them here first so there&#39;s phosphatidyl serine phosphatidyl ethanolamine these it turns out phosphatidylcholine phospital serine phosphatidyl ethanolamine is what makes up the majority of the phospholipids in cell membranes and then there&#39;s a much more minor phospholipid that&#39;s important for signaling which is phosphatidyl inositol so what are these so serine ethanoline and inositol are just like choline different alcohols that can be esterified to the phosphate in exactly the same way i did for phosphatidylcholine and so what&#39;s phosphatidylserine so if you remember this is okay so this here is the amino acid serine okay i&#39;m sure you remember that if we esterify that alcohol to the phosphate okay there&#39;s phosphatidyl serine okay what&#39;s ethanolamine look like so ethanolamine is this alcohol okay so that&#39;s ethanolamine okay sterify the alcohol the phosphate esterify that phosphate to glycerol okay phosphatidyl ethanol amine and the last one is inositol so what is inositol well inositol is a six-membered hydrocarbon ring where all of the carbons have an alcohol on them and so if i esterify one of these alcohols on inositol of course there&#39;s a if i sterify one of those alcohols to the phosphate to make phosphatidyl and acetol turns out that that ends up being a really useful lipid to make for signaling and you&#39;ll hear a lot from this about this in a couple of contexts i believe from professor yaffi later in the course all right so this having these general membrane structure this general phospholipid structure where you have this hydrophobic part of the molecule and the hydrophilic part of the molecule is really what allows these lipids to come together to form these membrane bilayers that are often drawn like this okay and so when i&#39;m drawing it like this basically what those two wavy lines represent those are the hydrophobic fatty acid parts and this is the hydrophilic so-called head group okay that&#39;s the charged alcohol stuck on to the end of the and to to to to the phosphate on on the glycerol all right and these of course assemble such that all of the hydrophilic head groups face an aqueous compartment on either side okay and then you have this nice hydrophobic portion that is a membrane and that is what can create a barrier between two different compartments in cells okay now just to put this into context for the protein structure stuff that you learned about okay so when you learn about all the different ways that you have protein structure of course you have amino acids that are hydrophilic amino acids that are hydrophobic if you have a protein that&#39;s floating in solution it has all the hydrophilic parts on the outside and the hydrophobic parts in the middle all right but you can imagine that you can also have proteins that assemble to sit such that they span the membrane so hydrophobic parts that interact with the hydrophobic part the inner part of the membrane hydrophilic parts on either side these can form channels these can form all kinds of ways to move stuff across membranes or you might think that you might have a protein that does something like that hydrophobic part on one end hydrophilic part on the other and really floats on the surface of a membrane and you will see that the way cell signaling works is is that you basically have lots of protein complexes that will assemble that membranes two-dimensional space those membranes as well as some of the membrane lipids can then act as messengers that allow cells to carry out various signals and i will leave that to professor yaffi to talk about all right so i will also come back and discuss membranes in a very different context in the context of metabolism during the second half of the course because it turns out a lot of energy transduction and the way cells really store energy also ends up being really important with respect to membranes all right you guys are lucky you get out a little bit early today this is the first time that we&#39;ve done the lectures this way so i don&#39;t have my timing quite right but i will see you guys again for uh metabolism after spring break you

Transcript for:Lecture on Carbohydrates and Membrane Structure

Transcript for:
Lecture on Carbohydrates and Membrane Structure