okay so welcome back everybody to uh 705. i know this has been a really challenging semester for all of us i want to particularly acknowledge for the seniors out there the the tragedy of missing the end of your senior year hopefully us mit can somehow make it up to you i can say for my part we will do our best to teach you biochemistry remotely and just as a couple logistics a reminder i'm matt vanderheiden i'm going to be covering the remaining part of of 705 for the rest of the semester we get to focus on biochemistry of metabolism we're going to learn what metabolism is why it's important and basically this is can be quite a polarizing topic in my experience people tend to really love or really hate metabolism it's interesting because there are some people out there who pretend to hate it but actually deep down really love it hopefully i will inspire you over the rest of the semester to at least have some appreciation for why metabolism is important and regardless for those of you who want to go to med school this is a favorite topic of mcat exams and also you will see that it will come up in many different areas of biology regardless of whether you go to med school or not so if you do anything further in biology hopefully you'll find this material somewhat useful okay so getting into what metabolism is so i think it's good to start with a textbook definition of metabolism and so metabolism is the chemical reactions that all cells and organisms use to do two things one extract energy from the environment and two synthesize the macromolecules that make up all life so really what metabolism is then is the chemistry that makes life possible and so understanding metabolism is really something that will help you better understand your food there's lots of material out there in the popular press about what's healthy and what's not at least this will allow you to form some of your own opinions about those claims and how they relate to what really goes on in our cells and bodies there's lots of implications for medicine very relevant to agriculture the energy sector biofuels come from and so metabolism really matters to tackle many of the challenges that face us in society now as a topic this can be very daunting as shown here on this image we have um hundreds this is a typical oops this is a typical metabolic pathway chart that is hanging in the walls of my office many other laboratories and academic places around the world if you look at this chart it's filled with hundreds of enzymes complex pathways our goal here is not to memorize this chart you can always look up details of any pathway or reaction that you want the goal here really is to see beyond this complexity i want you to appreciate why metabolism works the way it does why this chart is organized as it is because what we will find is that this chart is really variations on relatively few reactions it basically is life repurposing similar chemistry to do many different things i think there is a beauty in how life can use these reactions to get such a diversity of macromolecules and enable cells to solve all kinds of different problems you'll see that all of the pathways really follow common principles these are shared across all species and all forms of life and so at the chemical level all life is really related and this is why it's so relevant to understanding many of the challenges in medicine understanding ecology evolution and for you mit students you'll see it's also very critical for using engineering approaches based on biology to solve various problems in the world okay so now let's start getting into this a bit more now the first topic that we're going to cover over the next several lectures really relates to coming back to sugars and carbohydrates which i talked about and introduced in my previous lecture and we're going to do this because sugars and carbohydrates are key energy transduction molecules and cells and it really facilitates a discussion of the principles for how metabolism works now our goal here isn't to memorize pathways we could you know read about the glycolytic pathway in a couple in an hour or i could draw it up here in a very short period of time many of you have probably already done this in high school our goal is instead to understand this pathway at a deeper level really see why the breakdown of sugars works the way it does how cells use this to release energy and how that can be used to support other cell functions and so before we get to that i want to start by introducing just a couple high-level concepts about metabolism and so really based on our definition before metabolism is really about two things it's about making stuff and we have a fancy term for that that is called anabolism it's about breaking stuff down and the term for that is called catabolism and anabolism building stuff that is producing biomass growing all of the material that's out there anabolic steroids help you grow this is anabolism to build stuff that is one side of metabolism the other side is breaking stuff down catabolism that is breaking down our food eating food digesting our food as a way to get energy now of course to reproduce life has to build more cells you need more stuff you can't create something from nothing and so that requires energy input anabolism typically requires energy input whereas that energy has to come from somewhere and that's where catabolism comes from we have to break down food and ultimately that is catabolism is the source for biological energy for many different um systems now some of this is actually somewhat intuitive we all learned as little kids that we need to eat food if we're gonna grow up and be big and strong you also know that if you're gonna run a race you gotta eat a bunch of food you need that energy to fuel your activity but maybe what's less intuitive to many of you is we also need energy to sustain life even if we're doing absolutely nothing okay adults sit on the couch all day hopefully they're not growing but they'll still starve if they don't constantly eat some food even if they're inactive and so why is that the case well hopefully some of you recall the second law of thermodynamics so what is the second law of thermodynamics it's in effect the entropy of the universe is increasing okay that life care the universe continually tends towards disorder life is exactly the opposite of this life is actually maintaining extreme order in the face of the second law and so all life must constantly battle entropy and many have described life at the very highest level as being a really the ability to main order to fight entropy which of course requires constant energy input and metabolism is the process that all cells use to do this now for humans i think we all know we need to eat and breathe in order to stay alive for you future mds out there what happens if your heart stops or you start stop breathing well of course you die in a matter of several minutes why is that well that's because every cell in your body has to do constant catabolism in order to derive energy in order to remain viable this means they need constant food and particularly oxygen delivery and if you don't get those things metabolism can no longer work and the cells die and so energy is sort of this mystical com concept that we like to talk about and so before we delve a little bit deeper into what i mean by biological energy what it is why we have to constantly do catabolism to maintain it i want to go back and say just a little bit more about carbohydrates and finish our discussion there and talk about carbohydrates and sugar polymers polysaccharides because this has some additional properties i didn't have time to cover in my prior lecture that is important to understand how it allows these molecules to store energy in a very efficient way and it'll also enable us to talk a little bit about how carbohydrates can also be used as structural molecules for lots of different organisms all right so a little diversion to discuss carbohydrates and polysaccharides and so if you recall from my prior lecture sugars that are greater than four to five carbons can exist either in open chain or ring forms okay furanose or pyranose rings i'll just remind you by redrawing up here glucose so this is d glucose drawn in the open chain form remember this can form a ring okay so it's a reminder carbon one two three four five six if we have this hydroxyl group from carbon five form a hemiacetal bond with the aldehyde at carbon one you get this ring structure this would be alpha or beta depending on whether the hydroxyl group here at carbon one is pointing up or pointing down d glucose so this is review of what we already talked about last time now what i want to talk about is that if we form a disaccharide or a polysaccharide that is begin to make sugar bonds and if we do that in a way that ties up this hemiacetal or hemiketal bond this then prevents the ring from opening and gaining access to that carbonyl that aldehyde carbonyl as this moves between the open chain and the ring form and so a good example of this is the disaccharide sucrose so sucrose is a disaccharide of glucose plus galactose okay and here is what this disaccharide looks like okay so you have here glucose in the um alpha d pyranose form here's fructose in the beta because the oh group is pointing out fructo furanos form and so the formal name for this molecule sucrose would be alpha d gluco pirano seal one two because we're going from carbon one of glucose to carbon two there's one two three four five six of fructose beta d fructo firanos sucrose or alpha d gluco pyranoseal one two beta d fructo furanos okay so this disaccharide forms a bond between carbon one and carbon two that would be the aldehyde in glucose or the ketone tied up in the hemiacetal or the hemi ketal bond of these two molecules and so there's no way that either of these sugars can access the open chain form without breaking this oak like acidic bond and that's one reason why sucrose is a very good storage molecule for carbohydrates because without breaking that bond you prevent access to gaining these reactive aldehyde or ketone bonds that could react with some other molecule in the cell now i mentioned this because whether or not a particular sugar is enabled to get access to this reactive aldehyde or ketone really forms the basis for a classic sugar detection lab test and this is relevant to discuss this lab test because it explains some nomenclature that is still used and in fact we will continue to use a bit as we discuss some aspects of sugar metabolism so what this test is is basically is that if you heat the sugar with copper okay which is blue and that copper can gain access to a free carbonyl that is if the sugar can access the open chain form to expose the aldehyde or keystone that copper can then become reduced to copper plus that changes the color from blue to red and so if you reduce the copper you oxidize the bond there and this test turns positive if there is a reducing sugar is what it's called so a sugar that reduces the copper from the blue two plus state to the red plus state is a positive test and so basically a reducing sugar is any sugar with an ability to access open chain form because that will provide the free aldehyde or ketone to reduce the copper in this test so this term reducing sugar obviously applies to all monosaccharides because every single one of them has an aldehyde or a ketone and can access the open chain form but it'll only apply to some disaccharides or polysaccharides so look come back to sucrose up there so is sucrose or reducing sugar no it's not because there is no way that you can access a free aldehyde or ketone in sucrose because it's tied up in that oak like acidic bond between carbon one of glucose and carbon two of fructose and so you need to break that bond to give the monosaccharide subunits in order to access the open chain form however let's give an example of a disaccharide that can be a reducing that is a reducing sugar and that's the disaccharide maltose so maltose is basically two glucose molecules and those two glucose molecules are like this okay so this has a o glycosidic bond between carbon one of this glucose and carbon four of that glucose and so formally this would be alpha d gluco puranoseal 1 4 alpha or beta pointing down alpha pointing up as beta d gluco pyranose so maltose or alpha-d glucopranosyl one for alpha or beta glucopuranos is a reducing sugar because this sugar could access the open chain form you could open up this carbonyl and expose the free aldehyde at position one now we could also refer to this sugar as having two different ends we can refer to this end as being the non-reducing end and this end as being the reducing end because of course this bond this aldehyde on the first glucose is tied up in this o glycosidic bond whereas the one on this one is not so this end is non-reducing and this end is reducing now this becomes much more relevant if we start talking about polymers and so what starch is so starch what potatoes are made out of is basically a polymer of maltose of maltose molecules so basically or glucose with 1-4 linkages uh okay so i could draw that end the reducing end of the polymer in the alpha or beta but this here being the non-reducing end every other subunit is tied up in this one for o glycosidic bond and so starch is really a polymer of glucose molecules with bonds between the one and the four position of each subunit now we will see later that we build and break down starch polymers from only one end from the non-reducing end and so having these terms reducing and non-reducing provides a term to specify different ends of a polymer reducing and non-reducing ends turns out also be important for naming conventions for disaccharides or polysaccharides and this becomes relevant if we consider the disaccharide lactose so lactose is also a polymer of glucose plus galactose except this polymer of glucose galactose unlike sucrose is different because it has a different linkage between the glucose sorry glucose i apologize sucrose is a disaccharide of glucose plus fructose fructose i wrote the name correctly but lactose is a disaccharide between glucose and galactose and so i'll draw it here do okay so this is lactose this is galactose here on the non-reducing end so the formal name for this would be beta because there's a beta linkage here between carbon 1 and carbon carbon one of this galactose and carbon four of this glucose so b beta d galacto piranha seal 1 4 this is glucose in the alpha or beta d glucose pyranose lactose or beta d galacto pyranosel14 alpha or beta depending if i drew down alpha of beta d glucopyranose now this also has non-reducing and reducing ends and by convention you would name the sugar from the non-reducing end to the reducing end hence i put galacto pyranoseal one for alpha d-gluco pyranose um named them in that order now you'll note that lactose unlike starch unlike maltose unlike sucrose links these disaccharides with a beta linkage between this sugar and that sugar where the other ones had alpha linkages and structurally this is very different and i just want to point that out so this here is basically um alpha d-gluco pyranose and so alpha this would be this is carbon one this is the hydroxyl pointing down that's why it's alpha if i make an o glycosidic bond to another sugar you can see that it points and creates this kinked structure now if i were to make this beta this hydroxyl rather than being here would be at this position on carbon one you can see that that now creates a very different very different geometry now you have a flat molecule as opposed to a kinked molecule now this has consequences of course for the enzymes that break down these sugars obviously it's going to be a very different enzyme that breaks a bond in this orientation versus a bond in that orientation this has basically implications for what enzymes we have and so lactose of course is milk sugar all mammals make milk so make lactose and break it down when we're babies um but most mammals tend to lose expression of the enzyme lactase that's able to break this one for beta linkage um as we age and this is basically what accounts for lactose intolerance now if you think about it in the world much of the world has issues with varying degrees of lactose intolerance in adulthood the exception to this is often people of european ancestry why is this well europeans historically drank milk well into adulthood and so this selected for continuous lactose or lactase the enzyme that would break that beta 1 4 linkage expression as um people move into adulthood and so it's an example of how cultural um things drinking milk into adult adulthood really affected evolution um such that that subpopulation of people people with that genetics to increase lacto lactase expression um um don't become lactose intolerant um as they age now this alpha versus beta linkage that is whether or not you have this more kinked versus more flat structure also has a major effect on the structure of a polymer as well and so if we look here at this starch polymer it's basically this series of glucose molecules stuck together with alpha one four linkages so that's going to create a kinked structure this is best shown here on this slide so you can see this kink structure and so when you build this polymer you're going to end up more with this helical structure in 3d space that's a very efficient way to store glucose monomers in much less space than you would otherwise get with beta linkages now it turns out that nature takes us a step further and in addition to just having this starch polymer it turns out sometimes you can add branches to the starch polymer to further increase the efficiency of energy storage okay so if you have here a starch polymer so i just draw here a couple subunits okay so this here is a starch polymer glucose polymer with alpha 1 4 linkages that i can put an additional branch on this by adding a linkage up here on the top with an alpha one six linkage so the one position of here to the sixth position of here which has the effect of creating branches on this long polymer such that you have a single reducing n and lots of non-reducing ends each of these non-reducing ends has a polymer of alpha 1 4 linkages that would be stuck to the main chain polymer via this alpha 1 6 linkage and this has a couple implications for storage the first is by only having one reducing end it reduces maximally the exposure to a free aldehyde and so that makes it a good storage sugar and also as we will see we're going to break down these sugar polymers biologically from the non-reducing ends and so there's and build from those ends and so there's lots of hooks or lots of places to either add or remove sugars from which allows you to access um carbohydrates quickly as needed that's shown nicely here on this slide better than i can draw it so up here you have your non-reducing end across a polymer so this here would be starch with the alpha 1 4 linkages on the polymer or reducing end on one side non-reducing end on the other you can then add branch points to that by making an oak like acidic bond between carbon one down to carbon six creating a branch and so you can see this helical branch structure will then form that is both very efficient to pack lots of glucose into one place and give lots of non-reducing ends with which to build and remove sugars from for biology to either store or quickly access sugar molecules as needed now in plants of course potatoes use starch in a straight chain we know that however plants also use this branched structure this is a molecule called amylopectin amylopectin is better known in the food industry is sure gel it's the material that allows you to make jelly it's the gelling agent and jelly and effectively this has every every 24 to 30 units there would be a branch with one of these alpha 1 6 linkages to give you this multi-branch structure now animals don't make starch animals don't make amylopectin but amyl animals make another molecule called glycogen glycogen also a sugar polymer exactly like amylopectin alpha 1 4 linkages with these alpha 1 6 to create branch points just like amylopectin except glycogen has even more branches with a branch every 8 to 12 glucose units and so this is a very complex structure for both plants and animals to quickly store and quickly release glucose molecules when they're needed now this is in contrast to a glucose polymer that can be done that has a very different 3d structure so what if we take starch and rather than have these alpha 1 4 linkages but instead replace these with beta 1 4 linkages okay so now beta linkages looks simple enough but this changing the geometry from the alpha to the beta bond removes the kink now it's much more of a flat structure turns out this is here's a shown on an image here so here's a beta linkage and so now you have this flat structure this is the same polymer as starch chemically but has a different linkage the beta 1 4 linkage and that polymer with the beta 1 4 linkage is cellulose and cellulose is of course what wood is made out of and so wood in potatoes cellulose and starch exactly the same polymer same number of calories if you could access the glucose units but the alpha and beta bonds make them very different obviously wood and cellulose is a very good structural polymer for plants we build houses out of it we don't build houses out of potatoes but we eat a lot of potatoes so equally good molecule for plants to store lots of food for energy turns out wood is a great source of energy too you just need to have an enzyme that can break the beta 1 4 bond termites have symbiotic microbes that allow them to do this and this is why termites can eat wood a lot of energy tied up in wood now we lack the time to go into the details about how this relates to other structural carbohydrates but in general structural carbohydrate or carbohydrate-like molecules form polymers of sugar or related molecules also with these beta linkages and a good example is chitin so the material in insect shells is basically a sugar-like molecule that's a polymer with a beta linkage in it same thing of cartilage in humans and animals and you can look up the details of what these things look like of course if you're interested chitin and and cartilage aren't made of true polysaccharide polymers but they're very related to polysaccharides and they really illustrate how nature can take carbohydrate chemistry and repurpose it to basically act as an energy source but also build all kinds of structural molecules that are really useful in biology okay all right now i want to go back to here's ways that one can store and use carbohydrates in interesting ways but now i want to come back to them as energy sources and assuming you can access the glucose and whatever polymer it's present in how can you actually metabolize it to provide energy in a way that sustains life and this means we're going to turn to another topic a topic that's typically referred to as bioenergetics bioenergetics which is really the discussion of how energy is transduced in biological systems i'm going to introduce this topic today we're going to revisit it throughout the course but it's really important to ask this question we really want to consider what do we mean when we say biological energy what is biological energy well someone probably made you memorize in high school and often you're thinking oh it's just atp and certainly atp adenosine triphosphate is a very important molecule for biological energy transduction but i want to actually explore why atp is actually useful and if atp is energy why don't we just eat all kinds of atp i can say for a fact that absolutely none of you had atp today for breakfast no one sells atp as an energy booster and so if atp is such a great energy source why don't we just eat it and to really understand atp how it works what biological energy really is we really need to revisit some very basic topics in thermodynamics now thermodynamics strikes fear into the hearts of students everywhere you can get details of thermodynamics and the theory around these things and other courses that's not really what we're going to try to accomplish here in 705 our goal here is really a practical understanding of how thermodynamics applies to biology and metabolism and we need to go into this because it's key to understanding why we store energy go through all this trouble to store energy is these carbohydrate polymers to begin with why we eat potatoes and not atp as well as why atp is actually useful to cells and so let's take a step back and just think about it let's think about wood i just told you wood is a polymer of glucose molecules with beta 1 4 linkages how can we just as forget as organisms as cells but how can you release energy from wood to do other kinds of work well we can burn it and so what's the chemistry of burning wood well it's a carbohydrate polymer so it has this cn h2n um uh formula if we combine that carbohydrate with oxygen it releases co2 in water plus some light plus heat this light and heat is energy we can use it to do work boil water turn a turbine make electricity whatever use the warm ourselves by the fire give ourselves um use the light to do some other things okay and so this burning of wood is certainly release of energy now we lack the enzymes to do this reaction and wood because we can't break that beta 1 4 linkage but we certainly can break that alpha 1 4 linkage in starch from potatoes and we use the exact same chemistry to burn that glucose and release energy except the difference is is that if i burn wood i do this all in one step but life is a much better engineer than that it basically rather than releasing all of that energy in one step it really releases it step wise in a manner that's actually useful to cells but it's exactly the same release of energy and so what life is or extracting biological energy is is it's really the ability to do stepwise oxidation of glucose or other carbon i'll write glucose for now to get energy okay so we burn wood that's favorable it releases energy if we do stepwise oxidation we also can release energy as well same reaction also releases energy how much energy do we get from releasing us burning glucose as you do when burning it in a fire well it has to be exactly the same amount because it's exactly the same reaction so we burn wood we get light and heat cells burn glucose it releases the exact same amount of energy it just does so in a way that allows the cells to do biologically useful things what are those well it could be heat all of us maintain temperature so heat is a conversion of energy that of course is useful to biology but it can do other things too it can allow cells to move it can allow them to do any reaction to fight that entropy that allows life to exist and so all things including ourselves have to follow the same laws of thermodynamics okay life is not special in that regard and so burning wood is favorable because it increases the entropy of the universe right you're breaking up this polymer into a bunch of monomers that's going to be spontaneous that is in accordance with the second law of thermodynamics if cells burn it as well but remember the second law says that net entropy of the use of the universe must always increase and so if we're going to do something that's not energetically favorable like build a glucose polymer we obviously have to put energy into it okay and to do so the energy that's released must be greater than the energy that we actually store and so this is actually a really key point because anything that we do that requires energy input for a cell to carry out that process requires a source of energy release somewhere else that is equivalent or greater than what is actually put in and so cells need energy because they do lots of thermodynamically unfavorable things fighting that entropy of the universe and all of those processes must come from the release of energy elsewhere like the burning of carbohydrate and so that constant energy input is at the very highest level why we need to do constant metabolism in order to maintain order and survive as organisms now this of course comes from things like burning of of uh of carbohydrate but of course that carbohydrate has to come from somewhere and so ultimately you have to have an external source that external source is of course the sun photosynthetic organisms can use light energy from the sun to do exactly these same things build those excess polymers and it's why we as animals or anything that eats other animals as a way to live is ultimately depending on eating photosynthetic organisms because photosynthetic organisms do this by harvesting energy of the sun now that's all very high level but i want to come back to the specifics of metabolism ultimately and understand those as how they relate to enzymes reactions and pathways that is how do you get that complex series of reactions that make life possible and ultimately still be guided by these exact same principles in other words how do we couple the energy releasing reactions like burning glucose in a way that obeys the laws of thermodynamics and operates under biologically acceptable conditions in order to do things that are biologically unfavorable that's really what bioenergetics is and so the next thing we want to consider then if we want to understand this is really let's ask the question what determines if a specific reaction occurs that is what determines if something like burning wood actually spontaneously if you light wood on fire it will burn it does so every single time everyone has had that experience but no one has ever seen co2 and water spontaneously come together and form a tree that doesn't happen so what determines whether you burn wood and that is favorable versus why it is that co2 and water don't come together and spontaneously form a tree do not say or do not think that this is determined entirely by enzymes enzymes are catalysts enzymes are the spark that makes the burning of wood possible but remember enzymes cannot change thermodynamics enzymes only change the rate at which a reaction happens it does not change the equilibrium that tree wants to if given the catalyst forms co2 in water that reaction is spontaneous because it is thermodynamically favorable that tree will not take co2 and water and spontaneously reform a tree and there's no amount of enzyme that will make that happen all by itself and so remember that if you have any reaction between a and b there is some equilibrium as defined by the chemical properties of a and b such that the equilibrium lies far to one side or the other and that equilibrium is determined by thermodynamics it is not determined by enzymes i don't care how much enzyme i add if the thermody if the equilibrium lies towards a as i draw it the more i can add all the enzyme i want and i can never create more b and so this is super important and is actually a point that has gotten wrong by lots of biologists they think oh this enzyme is expressed therefore this pathway must be happening or this reaction must be happening faster you need an enzyme to catalyze a reaction so a reaction may not occur your wood may not burn unless you give it a spark a catalyst to actually make it happen but you cannot add a catalyst to fight thermodynamics you cannot take that co2 in water and turn it back into a tree and the same thing is true you can add all the enzyme in the world you want and all it will do is help a and b establish the equilibrium that is defined by the thermodynamics of the relationship between a and b now what determines the equilibrium between any two species that's a topic for another class why a species is favored to be one side or another however a useful tool to think about this in biochemistry and quantify this for any pair of reactions is something you've probably learned about before it's something called the gibbs free energy gibbs free energy or delta g delta g is related to the way we'll talk about the equilibrium constant and it's basically a term that we can use to specify if a reaction is favorable or not and so hopefully you learned in an introductory class that if delta g is less than zero our reaction is spontaneous if delta g equals zero a reaction is at equilibrium if delta g is greater than zero our reaction is not spontaneous right if we take our log and ask what is delta g to turn that log into co2 plus water it is less than zero because it is very spontaneous if we take a pile of ashes and ask what delta g is to recreate the log it's greater than zero because it ain't gonna happen and if it's at some equilibrium delta g is equal to zero now delta g depends entirely on conditions all right as we will see in a minute and because of that this means that there can be conditions where absolutely any reaction can be favorable if the conditions are right and we'll see that this becomes very relevant to understand how metabolism works and so let's go back and just now consider some generic reaction a and b so at equilibrium what happens so at equilibrium the concentration of a and the concentration of b are not changing okay delta g equals zero these two things are at equilibrium whatever that equilibrium is a and b are not changing in concentration now if i come and i add more a to this side of the equation what does that mean well you know from le chatelier's principle that that's going to favor production of b we have shifted things now out of equilibrium so if i add a that leads the production of b to re-establish this equilibrium that means that delta g from a to b is less than zero until i've reestablished equilibrium and now delta g is back to zero again now what happens if i add b well if i had b now i'm going to produce some a all right so add b okay that leads the production of a until i reestablish that equilibrium all right so delta g in that case to go from b back to a the reverse reaction is less than zero or i could also say that delta g to go to a to b here because that's not going to happen i just added more b i'm not going to suddenly create more a more b from a so here now delta g is greater than zero all right now note when i did this i don't actually have to specify how much a or how much b i've added the equilibrium depends on the ratio of b to a okay not the absolute concentration of either species and so having a way to think about this equilibrium it turns out is also useful for biological systems to define some delta g that is helpful to relate to this equilibrium constant and that is this concept of delta g naught prime a standard free energy which for biological systems is what the relates to the equilibrium constant at 25 degrees with a ph of 7 and 1 atmosphere pretty typical biological conditions and this here is basically related to the equilibrium constant and we can calculate the actual delta g by the following formula delta g equals delta g naught prime plus rt times the log of the products over the reactants so this would be drawn for the reaction a to b so the reaction a to b is related to delta g not prime which is related to the equilibrium constant i'll tell you that how in a second plus r is the gas constant t is the temperature in kelvin times the natural log of the ratio of products b over reactants a all right this tells you whether or not at specific concentrations of bna that is a specific ratio of dna whether it is favorable to go from a to b delta g less than zero or whether it is favorable go do from b to a delta g greater than zero and so this should begin to make it clear that whether or not a specific reaction occurs is affected by the actual conditions present and you can calculate that based on this relationship and so if i specify concentrations of a and b as well as delta g not prime i can know at those concentrations which direction of the reaction is favored now of course my drawing a to b is entirely arbitrary i could equally draw it b to a and if i did that okay so this is delta g not prime a to b all i do is flip the signs so delta g equals delta g not prime the negative of a to b is equal to the positive of delta g naught prime from b to a okay because the direction is arbitrary plus rt log in this case now i have a is my product and b is my reactant if i just flip the sign flip the that ratio is just going to change the sign of my product and give me exactly the same result with the opposite sign which makes sense what's favorable in one direction is not favorable in the other direction and vice versa now i can also set delta g equals zero that's equilibrium if i do that then delta g naught prime equals negative rt so this would be for a to b i'll use the top example so delta g equals zero then i have delta g not prime equals rt times the log b over a so if i know two things are at equilibrium i can calculate delta g naught prime and know what the equilibrium constant is and so it follows from this then that if delta g naught prime is negative that means b is favored over a at equilibrium okay and if delta g naught prime is positive that means a is favored over b at equilibrium all right and so delta g naught prime really is a convenient way to look at a reaction and know which direction the equilibrium rot lies so a and b delta g not prime is negative equilibrium lies to be between a and b if if delta g not prime is positive the equilibrium lies towards a but the key concept is is that for any specific reaction any specific conditions of a and b whether or not a is converted to b will be defined by the equilibrium constant but it will also be defined about what delta g is under those conditions so to be clear delta g will depend on conditions okay because i'll write it again delta g equals delta g naught prime plus rt times the log of for the reaction a goes to b so products over reactants and so whether or not a is converted to b will be a property of the equilibrium constant plus the concentration of b in the concentration of a that ratio of concentrations at the conditions present and if in that calculation delta g is less than zero that reaction is spontaneous if delta g is greater than zero that reaction is not spontaneous or to put it another way if delta g is less than zero under those conditions energy is released or if delta g is greater than zero that reaction will not occur without energy input okay if i burn wood energy is released but there's no way i can reassemble that log without some kind of energy input and really getting this concept is central to understanding metabolism as well as what biological energy means and hopefully what is now apparent based on what i just said is that what really determines delta g is two things of course it's the equilibrium constant but in essence delta g for any reaction is proportional to the ratio of the reactants over the products and that i can come up at least in theory with any relationship any ratio of reactants to products to make this favorable at some tiny tiny concentration if i have nothing but co2 in water and infinite time and infinite catalysis a tiny bit of wood could spontaneously form and so life really creates the conditions that allow that and select for that to happen and of course add energy input so it can actually happen more and so this should be very clear to you that absolutely no reaction is irreversible i don't care what your textbook says lots of sources will discuss irreversible reactions i'll talk about irreversible reactions later in the course but what we mean when we say the word irreversible reaction is these are under conditions that are found in cells and in nature and i stress this because if we want to understand the energetics for how pathways work we have to appreciate that life can create conditions to do unfavorable things because that's the only way the pathways can work all right what do i mean by that well suppose again we'll come back to our reaction a goes to b all right suppose i need to build a pathway where i need to convert a to b because b is actually useful for some purpose that i need to do in a cell however what if this is at least by equilibrium unfavorable what if the equilibrium lies towards a that means delta g not prime is positive is greater than zero for a to b what does that mean delta g not prime greater than zero for the reaction a to b that means the equilibrium lies towards a and so there is no amount of enzyme i can add that will allow me to net convert a to b because the equilibrium lies far towards a however whether or not a cell is able to build a pathway where it converts a to b depends on delta g not the equilibrium constant for that specific reaction so how can i turn a into b well i could turn a into b if i keep the concentration of b low enough that delta g not delta g not prime that's the equilibrium constant but delta g favors a to b conversion that is delta g for a to b is less than zero how can i do that well remember delta g equals delta g not prime plus rt log of b over a all right so this term is positive because i told you the equilibrium lies towards a all right so i need a concentration a ratio of b to a such that b is low enough that this term is more negative than that term is positive and if that's the case delta g will be less than zero and i can net move that forward so how can i do that how can i keep the concentration of b low well i can build a pathway that consumes b in a way to keep it low which favors a to b conversion in other words i can build a pathway a goes to b goes to c okay so even here where delta g naught prime is greater than zero if delta g naught prime for this reaction b to a is much less than zero such that equilibrium strongly follow strongly favors c that means my unfavorable equilibrium here can be overcome by the very favorable equilibrium of b to c in essence i can use b to c to pull a to b such that it actually happens produce this intermediate that's useful on the path to making c this strategy is used in lots of metabolic pathways and it's useful to generate lots of chemically useful intermediates now note that this only will work if conversion of a to c is favorable that is if delta g not prime is less than zero i can only pull this reaction if delta g not prime is less than zero that is if equilibrium favors a to c i can build a pathway this way to do something unfavorable on the way to making c this brings up another key point and that everything that we discuss relationship between any two metabolites in any single reaction also must be true for entire pathways so i have a three-step pathway from a to c whether i turn a into c in one step or turn a into c in multiple steps the free energy is exactly the same if i burn wood by lighting it on fire it releases the same amount of energy then if a termite has an enzyme that breaks that beta 1 4 linkage in the wood and can burn that glucose stepwise through metabolism the exact same amount of energy is released glucose on one side co2 and water on the other side exactly the same amount of energy released whether i do it in one step or i do it in multiple steps the equilibrium constant between those has to be the same and the delta g has to be the same between all of it and so it should become apparent then that a to c has to be favorable if i'm going to use this trick of keeping product low in order to pull an otherwise unfavorable reaction forward in other words there's no way for me to keep b low and net convert a to b all on its own that will not work and it's these unfavorable reactions that ultimately then require energy input and this is where atp now starts becoming useful for cells okay so now i want to talk a little bit about how atp provides energy that allows otherwise unfavorable reactions to occur and atp is useful because delta g applies to sets of reactions in the same way it applies to single reactions that is applies to whole systems all reactions are a series of reactions whether they happen alone or coupled together all have to follow the same rules so now let's make our reaction more complicated let's say a plus b goes to c plus d where this is really two reactions coupled together a being turned into c and b being turned in to d all right so will this reaction happen can i turn a plus b into c plus d well how do i know well it's going to be got to calculate delta g and so it's going to be delta g not prime for a going to c plus delta g not prime for b going to d so those will relate to what's the equilibrium constant the equilibrium relationship between a and c and b and d okay if it's less than zero equilibrium will favor to the right if it's greater than zero equilibrium will favor to the left of a and c and b and d add them together that gives me my overall delta g not prime for those two reactions plus rt times the log of the products so that's c and d over a and b products over the reactants okay so if i take an unfavorable reaction say a to c if delta g naught prime is greater than zero okay so would favor a and i couple it to another reaction b to d that's very favorable because i add these two terms together i can now take something that where the equilibrium would be unfavorable and make it favorable however whether or not this actually happens still depends on this ratio of products to reactants so it still depends on the ratio of c to a and d to b in our hypothetical thing here so to know if a specific reaction will actually occur we have to take into account both the sum of the delta g not primes related to equilibrium constants and the actual ratios that are present in cells and so the net effect is is that i can couple more favorable reactions to make otherwise unfavorable reactions now become favorable that is have energy input but it still depends on conditions and so let's think a little bit about the polymer synthesis that we learned from professor yaffi and so in that process what did we do we made several polymers and you learned about the chemistry to do this we made dna we made rna and we made protein these are polymers of nucleic acids protein is a polymer of amino acids all of these fight entropy right we're building polymers not breaking them down and all of them were synthesized using reactions that hydrolyze atp in fact those reactions actually hydrolyzed atp in the following way in every single one of those cases if you look back what you will see is that they all had steps where atp was taken to amp plus two inorganic phosphates this reaction is very favorable in fact it's two reactions it's really atp goes to amp plus pyrophosphate and then that pyrophosphate goes to two inorganic phosphates it turns out delta g not prime is less than zero for both of these reactions okay that means the equilibrium lies towards amp plus pyrophosphate and here the equilibrium lies towards two inorganic phosphates and so there's actually two tricks here by metabolism one is it's two very favorable reactions that were coupled to do something unfavorable build a polymer and it used the trick of keeping pyrophosphate low by coupling it to a downstream very favorable reaction which even further pulls this reaction and is a way why you can actually get good um why atp hydrolysis here becomes so useful as a way to build these polymers let's just go quickly and add a few numbers to show exactly what i mean by how atp hydrolysis can be useful in this setting and so let's do something a little simpler let's go to atp plus adp plus to inorganic phosphate all right so let's give this some numbers delta g not prime in this case is equal to negative 7.5 k cals per mole all right what does this mean delta g not prime is related to the equilibrium constant it's less than zero which means the equilibrium lies towards adp plus phosphate okay now let's see how this actually helps by considering what the first step in glucose metabolism by cells is so the first step cells do in glucose metabolism is add an inorganic phosphate group to glucose so it's this reaction glucose plus inorganic phosphate goes to glucose phosphate just a quick note on shorthand that i will use in this course so pi of course is inorganic phosphate that is this po4 three minus group all right when it forms a phosphodiester bond like to an alcohol in one of the glucose molecules i'll draw this in a future lecture i'll oftentimes indicate it by putting a circle around the phosphate and so adding this phosphate to glucose is a step that traps that glucose in cells for now let's just consider this reaction and so delta g naught prime of this reaction is positive 3.3 k cals per mole what does that mean delta g naught prime relates to the equilibrium constant it says the equilibrium constant lies here to the left to the glucose plus phosphate side so if we want to net trap glucose phosphate in cells well it's not going to happen spontaneously you need some kind of energy input that can come from atp and so if we couple those two reactions as follows so we now have glucose plus atp goes to glucose phosphate plus adp all right now let's draw this out what is will this happen so we can calculate delta g delta g equals delta g not prime so there's two reactions happening here glucose to glucose phosphate and atp to adp we know what delta g naught prime is by adding those together so it's 3.3 plus negative 7.5 that equals negative 4.2 what does that tell us that says now we've created conditions where the equilibrium constant lies towards the right towards the glucose phosphate plus adp side but how much of this occurs or whether it occurs isn't just the property of the equilibrium constant it's also how much is there and so that's rt times the log of the products glucose phosphate and adp over glucose and atp and so if this term is less than 4.2 that is if the ratio of glucose phosphate to glucose and adp to atp in this term ends up being less than positive 4.2 this reaction is spontaneous it is favored lots of conditions where that would be the case although if this term is 4.2 or greater now it will no longer occur how much atp is needed well it's hard to answer this question in absolute terms because if there's a lot of adp around you need a lot more atp for the adp to be useful and this is the problem with equating atp with energy the energy here is in the ratio of atp to adp or atp to atp and this is something that we will come back to in the next lecture because in the end this is what will determine if a reaction is happens it is not the absolute concentration of atp it's the fact that atp hydrolysis is favorable but how favorable that is depends on the relevant concentrations of atp or adp and relative concentrations are all that matters in thermodynamics it is not absolute concentrations it is the atp adp ratio that is the correct way to think about energy and this is true for any reaction with respect to energetics if an atp adp ratio exists such that when coupled to a reaction delta g is less than zero then it becomes spontaneous and this is how atp provides energy and we will come back to this more in the next lecture thank you you