Transcript for:
Fundamentals of Reactions and Enzymes

now i can keep track of your comments okay so today we are going to um start a new chapter and this is actually going back to the beginning of the book and talking about um just like basics of how reactions happen how enzymes work how they help catalyze different reactions and how macromolecules are built inside our body cells so you know it's placed in the beginning of the book but i didn't really want to talk about it in the beginning of the semester until we had some relationship with these you know cell components first and we understood why it is important to learn about this stuff i felt it would be better placed later after we had kind of talked about the general way the cells work and kind of you know how signaling pathways work why atp is important why enzymes are important and now that we know their importance we can kind of go back and think about how they work and how they're built so uh the chapter talks about three different kind of divided into three different parts the first one is talk part is talking about how energy is utilized by cells and how cells are organized um in their environment the second one talks uh focuses more on free energy and catalysis by enzyme so it's focused on enzymes in general and then the final portion is talking about activated carriers and biosynthesis and that's where they talk a lot about atp and its used in uh metabolism in different reaction pathways as macromolecules are built and destroyed um to create energy so uh that's gonna be our overview for that so um the whole actually last set of lectures uh we're gonna be focusing on three different chapters all three of them are going to be focused on metabolism essentially and metabolic reaction processes so if you go back and think about that pathway analysis assignment you're doing for the lab you're looking at the pathways at a more kind of global level right you're looking at the overview just different enzymes or different proteins that are involved in a process you're not looking at a very molecular level where you look at um individual steps and see how individual steps are organized and you know what's phosphorylating what and how that process is happening so now in this set of lectures we're going to start looking at that yes so that we know the steps we know this protein is getting activated and that's leading to this response how does that get activated and exactly what happens inside um okay so going back to um what we're going to be talking about for a lot of today's lectures is enzymes and enzyme kinetics so enzymes are proteins typically and they accelerate chemical reactions and they are responsible for many many many many much of other chemical reactions that happen inside our body simply because while those ex you know while those chemical reactions are favorable they cannot normally occur at the temperature that our body is maintained at and instead require a higher temperature input before that reaction can spontaneously occur so enzymes kind of help provide a environment where those um reactions can still occur at the physiological temperature and they just speed up the rate of the cellular reaction so that we aren't all looking like slots or acting like slots rather now enzyme catalyzed reactions that usually are never done in isolation they are usually part of a signaling pathway or part of a metabolic pathway where there are several steps in the process going from the first you know full molecule that they're working with to the last products that they are getting um and they are usually combined in a series of catalytic reactions that all require individual enzymes to process um the products at each point um these enzymes are highly specific they can only work with um that one specific substrate or a very small subset of substrates and not um you know based on their binding site their active site and we'll talk about that soon as well uh so enzymes are basically what control our meta metabolism and all the reactions that make up our metabolism so at the end of the day when we look at metabolism our metabolism is controlled by basically the rate of reactions that are happening inside our cells and um you know these are all the reactions that are needed for us to survive and grow basically all the reactions that we need in order to utilize energy from food uh to create energy uh for our other reactions that are happening that are needed for us to grow and survive and reproduce um and it is a total sum of all the reactions that are happening both catabolic and anabolic so uh just a review and this should be a review from chemistry um the catabolic uh reactions are going to be uh reactions or pathways where we are breaking down molecules uh while we are generating energy as a response so when we break these bonds we release energy that can then be utilized by other reactions in our cells um on the other hand anabolic pathways or antibiotic reactions are usually biosynthetic pathways where we are combining macro or you know monomers or different molecules together to form a macromolecule or to form another product um and in the process we are not going to be releasing but yeah rather requiring energy to be used this energy that we use in anabolic pathways is the same one that was released by the catabolic pathways so we utilize the energy that is released by catabolic uh reactions in our anabolic reactions so the overall um metabolism is gonna be uh looking at the sum of these two sets of reactions so sound like a cell metabolism at the end of the day like i said um is a combination i don't know why it's doing in this way is a combination is the sum of those catabolic and anabolic reactions uh in general you can think about the food that we take in um as it is broken down that is going to be catabolic pathways because that's going to release energy uh some energy and it's going to release some heat that can then be utilized to create other molecules inside our cells similarly the food that is broken down gives rise to a lot of these building blocks that can be used as reactants within those anabolic pathways as well to make those new molecules that we need inside our cells that are different than the original ones that we started with um so this slide talked about you know how living things anytime that you have a living organism or a living thing in nature it's usually going to be highly ordered and it's going to continue to maintain that order but if we go back and think about the laws of physics that we look at we know that typically um things tend to go towards this order so how is it that living things can maintain and generate that order and maintain that within their system if overall living you know overall all things are supposed to go towards entropy well they do that by um using the environment as their external you know space that they can um utilize to create that disorder while maintaining their own order so reminding you of the laws of physics the first law of physics uh there are two parts that energy cannot be created or destroyed and however this energy can be transferred and changed in forms so we can while we cannot destroy or create external energy with the extra energy inside our body we can take it from outside and then utilize it or we can transfer it outside and utilize it in that way as well the second law of thermodynamics is where we talk about how entropy is continuously increases overall in a closed system right so overall you would expect the more and more disorder to occur over time and no energy transfer that we create um is going to be 100 efficient so some of it will get lost in the process however when it gets lost it has to get lost somewhere um and so it could be as heat that is helped to maintain our body temperatures or it could be dissipated outside as well released outside into the environment as well so this i loved the example that they showed that a spontaneous reaction is which is going to increase disorder and entropy because it involves breaking down of the molecules or it involves um more and more disorder to be formed it's basically breaking down those orderly molecules into smaller components on the other hand any time that you're trying to organize these systems and anytime you're trying to build these molecules back up you're going to require some energy input so you will need actual input of energy before you can create order in the system that order that we need to maintain as living organisms is taken um is you know basically maintained through that those metabolic pathways through the heat or through the energy that is produced by the catabolic pathways inside our systems so cells um like i said remain orderly because that's part of living things however they do that this don't defy the second law of thermodynamics they still do that by then as a result doing one of two things one they will create energy or heat they will release heat as they input energy into a system and that heat when it is released is going to be what our body uses to maintain our body temperature but also can be used to do work in our environmental system and secondly overall what we end up doing is create entropy within the environment that we are surviving it so while we are maintaining order inside we are creating disorder outside um for plants especially that are taking in energy from the environment it works a little bit differently right because they can take this uh you know energy from the environment from the photons of sunlight from inorganic molecules and they can use all that energy to create those chemical bonds needed to build the macromolecules to survives to make the glucose to make uh the actual food for themselves so they can then break it down again and then get the energy from there so by doing that uh especially our plants right they are converting energy from one form to another again similar to how uh we would look at the first law of thermodynamics now um when we do that in a plant setting right you're taking the electromagnetic light energy that is then getting utilized by chlorophyll molecule kind of acting like a solar energy cell um to then use that energy to create those macromolecules and uh run photosynthesis um in our normal body systems which are you know in animal systems you are still converting energy from one form to another all the time right except um usually in our case it is going to be in the form of atp that is then broken down uh for energy used to create bonds it would be in the form of heat energy that is produced from breaking down chemical bonds so uh in our case we are using it as well to convert energy from one form to another in order to utilize it for our daily needs so these are possible ways that you can convert energy from one way to another again a lot of this should be um you know review from physics or chemistry well most of this is physics so one of them uh was using our potential energy that we have inside our body stored in our body um and convert it into kinetic energy or to heat energy so the example of this would be if you raise a brick up and then as the brick is thrown and falls it is converted to kinetic energy if it hits the floor or hits some place or you rub it against the surface you in the process produce heat energy um so energy can be again converted to multiple different ways the one that we use in our body the most are this um type of the energy conversion that is shown in b where you have chemical bond energy and as those chemical bonds are broken they are um that energy is released in the form of heat that is then dispersed in the surroundings to maintain our metabolism and the second one is for plants specifically the electromagnetic light energy that is converted into chemical bond energy as you use it to build the bonds to make glucose so that you can use it for food um so this is just looking at that process a little bit more in detail and we'll talk about this process how these are just two flip side of the coins um later on as well that in the process of photosynthesis in the first part in the first uh step you are capturing the sunlight um or capturing the photons from uh the sun to create light and to use that light energy um and then we are taking in water that is then broken down to make the molecules that we need to make um in the process as these bonds are broken down you're releasing the oxygen um and then you are creating um activated molecules of atp and nadph that can then create that can then take those extra energy to manufacture bonds uh to create your glucose molecules in that second step so at each step you are going to have carriers of energy in the form of carrier molecules in our body which are your nadh um atp your fad all of those and those will carry that energy to be used in um as chemical bond energy that can then be utilized to create our sugar molecules um so at the end of the day one of the things that we will notice about living things is that all living things require carbon in some form or another and these carbon atoms are constantly cycling through various phases of life and various phases of um energy cycle um in the biosphere so you take the carbon dioxide from atmosphere to uh you know in the form of again the plants to use in the photosynthesis so that it can be made into food and those macromolecules all contain carbon molecules that are then broken down to create energy for the various systems that we are various pathways that we are reactions that are occurring inside our cells um so again in photosynthesis um you are taking your carbon dioxide and water from the air to make oxygen and sugars breaking it you know come recombining it it's not even so much as broken down but rather recombining it to create your glucose and oxygen that is released into the atmosphere and in cell respiration you take those same components that you have just made in photosynthesis and this time you re organize them and break them down and reorganize them to release carbon dioxide and water so here the input was your energy of sunlight and here you are getting the energy from the chemical bonds that you're breaking down any questions so far our students have become quieter and quieter as the semester has progressed ryan is back okay okay so um next we'll talk about how that energy transfer occurs um and so energy transfer a lot of time occurs through transfer of electrons and so there are going to be uh basically one molecule in each case that's going to be losing the electrons and the second one that's going to be gaining the electrons so a lot of the reaction the metabolic reactions in our body at the end of the day are oxidation and reduction um or involve oxidation and reductions in the oxidation um a molecule that is getting oxidized is going to be the one that loses electrons and in reduction you have a gain of electron where the molecule is gaining the electrons as a result of this process um so here you have an example of two charge you know two atoms that are going to form together combined together in a polar covalent bond um when you form a co polar covalent bond one of the atoms is going to kind of hog the electrons more for a longer time than the other maybe because of the sides usually because of a larger size because they has more electrons more protons more neutrons that can pull the electrons more towards themselves so the uh atom that has the partial negative charge in the final molecule is going to be the reduced um you know atom and the second one is the one that is getting stripped of the electrons is going to be the oxidized um side of that molecule so in our natural reactions like i said we talked about how we have carbon compounds um so a lot of these carbon compounds have carbon hydrogen bonds and so at each step of this oxidization process one of these hydrogen is essentially getting taken and replaced with either an uh oxygen alone or an oxygen and hydrogen together so here you have a simple methane molecule uh considering a single carbon with four hydrogens as it is oxidized more and more each time uh you're essentially adding an oxygen bond to it so in a methanol there is a single oxygen bond um it's a hydroxyl in formaldehyde there are two oxygen you know double oxygen bond um you know formic acid there's a double oxygen bond um and then a hydroxyl so each time you're replacing one of the hydrogen with an oxygen bond and then a carbon dioxide it's going to be a two double bonds with two oxygens so uh reduction is essentially occurring as um you are increasing the number of hydrogens in this in that molecule and oxidation is occurring as you're adding more and more oxygens to that molecule and stripping away those hydrogens so just to review this first part um so um we have biological we maintain biological order in our systems because we can release the extra heat uh into the environment and cause disorder in the environment instead of disorder inside um cells are able to convert energy from one form to another the most common forms of energy conversion that we have inside our cellular system not as an organism but as a cellular system uh at a molecular level is either converting um our chemical bond energy into actual heat energy or converting our photo electric energy or photomagnetic energy rather from sunlight into a chemical bond energy uh photosynthetic synthetic organisms are the ones that use this light as a way for energy input and synthesize it for organic molecule um you know building in the form of glucose and cells obtain energy basically by breaking down or oxidizing organic molecules each time as they do that they are releasing heat energy as well as electrons that are bound to carrier molecules for energy input into other reactions oxidation and reduction involve electron transfers between those two molecules or atoms that are combining together or that are separating in the reaction together any questions uh excuse me professor just like i have a concern about like the drinks that they claim they are antioxidant what they do and why they are beneficiary you're talking about antioxidants yes since like we you just show us the oxidation process the more oxygen bound we will have like what this is this something related to it the antioxidant or no kind of sort of so um we'll talk more about that actually uh maybe next week uh i don't know why in one of the other chapters uh but in a reactive in a antioch not antioxidant but in a reactive oxygen species basically what you are getting are these um you know because of these uh oxidative oxidized and oxidation and reduction reactions you're getting these um ions essentially that are or you're getting um compounds broken down from other molecules that have highly negative charge or highly positive charge right and those highly especially those highly negative charged molecules that usually contain oxygen in them which is what will be the basic kind of point of reactive oxygen species are harmful to our body because they are highly um they are able to interact with a lot of different uh molecules in our system and break down bonds and destroy them and so the antioxidants work by kind of destroying that negative charge right they work by breaking those down in a way so that they are no longer reactive which they are in their ionic state oh so are those uh oxy oxidative like free are those like the free radicals yes the one okay yeah got it now yes thank you yeah so usually you know like these are usually coupled reactions so you're not going to get these to be present all the time but many of our reactions in our body just normal living reactions do create reactive oxygen species some more than others and those are the ones that you are trying to destroy by taking antioxidants okay okay got it thank you okay so um let's talk about now how enzymes specifically work now um i know like you know back in the day when you a lot of this again was done back in the day when you did gb1 as well and maybe even later but uh we always talk about how um enzymes help uh move the reaction the rate of reaction and make it um you know quicker but in in some way by lowering that activation energy um and that can sometimes make you think that well it's gonna help a reaction proceed even if it is not favorable right even if it is um not going to be normally occurring but that's actually not true an enzyme can only help a reaction that would have occurred spontaneously had it been provided the right environment or temperature it cannot help proceed a reaction that wouldn't have occurred spontaneously um so that is an important point to remember about enzyme kinetics that enzymes can only help those reactions that are energetically favorable but they just needed a little push in their current setting to help them over that hump so that they could create that product so enzymes do that by reducing the amount of activation energy that is needed by that um reaction so that the reactants can be converted into products a little bit easier and um at a in a more favorable manner and for that to in order to do that they usually need to provide those uh reactants or that reactant with just that right environment where in a mini setting which they create through their activation site so that they can hold on to the reactant in the correct conformation so they can provide a mini environment where the ph is lower maybe or the environment is favorable for that reaction to spontaneously occur and create the products um so in this case uh you know as the chemical reaction is proceeding uh you will still have loss of free energy just like you would have in any other reaction as a result of the formation of products as well now enzymes have to still obey the same law of physics that normal bodies do and other atoms do so enzymes will increase the rate of those favorable reactions but they can only do that for spontaneous reactions and they will still create disorder because they will be releasing a free energy as a result into the environment in this case inside the body to maintain the metabolic state of the body and our enzymes can not force a reaction that wouldn't have normally occurred given the right environment so any reaction that requires actual energy input is an a reaction that is non-spontaneous and cannot be fueled or cannot be helped by an enzyme alone that still requires atp input or uh gtp input whatever form of energy they need in order to create that um you know in order to use that energy to create those bonds so an enzyme alone won't make that reaction happen without input of energy if that was the need for that reaction does that make sense guys yes yes it does thank you okay so um what the enzyme can do is provide that environment like i said to lower the activation energy so that there is a higher probability that a reaction can occur um in the system that they are in so molecules generally will need a you know you will need usually a certain number a threshold of molecules to be there before the reaction can occur or a certain temperature to be there um before the reaction can occur and by providing that smaller mini space for that reaction it helps to lower that activation energy and that allows the reaction to move a little bit easier so in a typical setting you will require a lot more energy input in a per molecule in order for the reaction to occur and it actually shows you right here um in this graph uh that you require a certain amount of energy input to undergo um a catalyzed reaction however if you have higher energy input then you can lower that activation energy or if you have the right environment you can lower that activation energy so that those reactions can go and flow at a higher rate in their current setting in the process uh the enzyme itself is not changed in any way shape or form so it's not like atp which will give off that phosphate and then be converted to adp instead the enzyme remains completely unchanged it's only a holder or only a uh providing that little room for that enzyme for that reactant to bind to convert into product and then be released um and it does so by having an active site that the molecule binds to um and we've talked about how that active site helps to hold that molecule in place um and how they are able to uh process that system now in that process um the same again laws of physics apply so the free energy change will determine whether a reaction can occur or not for a spontaneous reaction to occur the free energies of that change of that system should be uh you know the free energy in that system is going to be uh usually negative to make sure that the energy is an energetically favorable reaction um so the free energy is essentially whatever energy the system has to use in order to make that uh reaction occur in the case of a spontaneous reaction you don't need input of that free energy you're rather going to be releasing the energy back into the system in a non-spontaneous reaction or in an energetically unfavorable reaction you are going to be using some of that uh free energy and not releasing it back into the environment right so in a spontaneous reaction the change in energy is going to be less than zero and in a um non-spontaneous reaction the change in um free energy is going to be positive because you're using more energy than you started in a body setting the only way a unfavorable reaction can occur is if you have it coupled with an energetically favorable reaction because you're gonna take this energy that you take from the first one and put it into the second one in order to have that occur otherwise these reactions will not happen uh on their own and so typically you will notice that in your cascade of a in a signaling pathway or in a metabolic pathway you will have an enzyme coupled reaction um you will have several enzyme coupled reactions where one of them is giving off energy and then the second process the one that comes after it uses that energy to create the final product so by doing this reaction coupling you can help to move those unfavorable reactions and have them happen inside the body even though you cannot take in more energy from outside or raise the temperature or do any of those things that would not allow you to survive in the environmental setting so in this case you had one reaction um x2y that was driven by a positive change in energy in free energy because it released energy this released energy was then used by the second uh reaction chain uh from c to d where you had uh to use energy some of this energy in order for this reaction to occur so this one had a change of negative delta g because you took away some of that free energy in order for this reaction to occur so the free energy and whether when it's positive and when it's negative is clear i got a little bit confused okay we said when it's negative it's a spontaneously occurring one and it's spontaneously oh so free energy is basically what's outside right so if a reaction is spontaneously occurring it's going to throw more free energy into the system right because it's going to release energy so the change in the overall system the delta g in the environment would be more energy so you had one unit of free energy outside a spontaneous reaction occurred and it threw another one unit outside so now there are two units outside so it will be a positive change in free energy energy that is not you know kind of held up in chemical bonds or in uh some other way okay yeah yeah got it now and then when you release uh when you use that energy right when you go through a non-spontaneous reaction you take some of that energy in so you took away one of those units so that you can catalyze your reaction then that would lead to a negative change in free energy and they say like it's unfavorable because like our body does not like to lose energy well so unfavorable it's not our body but generally a reaction is unfavorable if it is going to require energy input nobody likes to do work including apparently atoms so if they have to input any work into it or any energy into a system they don't want to do it if it can be freebie if it can just happen on its own that's great so a favorable reaction is one that can just happen spontaneously and doesn't need any energy input if anything it's gonna give me some more energy to play with and an unfavorable reaction is one where you require work you require energy input you're required to put some effort before that thing can happen and you are not getting anything back from it as such in the form of energy right yes it's clear now thank you okay um so um in our body systems because our body is you know a semi-closed system in this way uh you will eventually for every single molecule that you are or every single chain of these reactions that you are uh going through your body will have some sort of an equilibrium reached at some point where um there is no net change in the you know in your two products and they it's the point where the change in your free energy is essentially zero so going from step one to step four the overall change at that point is going to be just no net change of energy and that's gonna be where uh chemical uh equilibrium is reached between those reactions so um we can look at this in a equilibrium you know in an equation form where we can look at whether our energy shift is positive or negative a change in energy is positive or negative and relate it to whether the reaction will occur spontaneously or not right um and so here you have these two reactions you have the a plus b and it's coupled with a second you know c plus d products that you're getting produced as a result um so your you know uh the free energy change is going to be the total change that you are getting between your reactants and the products that are getting produced and that's what you're going to look at and we'll talk about actually this equilibrium constant later on uh so we'll talk about that in a minute where it will become a little bit more clearer to you how to look at that um so the changes in free energy uh of your reaction are sequential so uh are added so if you have six reactions in a row that are all coupled to each other the total change that you're going to look at is the change of free energy is going to be an additive effect so you're going to take all those uh numbers that you get for individual change in energy and or rather right here you will take the individual changes uh in free energy from each part of your coupled reaction chain and you will add all of those up to get your final answer and for an equilibrium constant to be our equilibrium point to be occurring all that net change should be zero okay so um for each mini reaction you have an equilibrium point for that reaction however when they are coupled then the equilibrium point is different right so individually these may have very different equilibrium point where the change delta change in free energy or change in free energy is zero but when you couple them together it's going to be related to the overall change in energy of all the various products that are there does that make sense guys or no yes no yes okay okay so um let's look at an example of this one so here we have coupled reactions uh which share a couple reactions are basically ones where you have at least one um intermediate step which is shared by both the reactions that are present within that chain of metabolic pathway um so individually the single reactions will produce a certain amount of free energy so let's look at the first one in the single reaction you have a glucose and fructose molecule coming together um to give you sucrose and the delta g is plus 23 kilojoules per mole is that a spontaneous or non-spontaneous reaction non-spontaneous it is a non-spontaneous reaction exactly net result would be that this will not happen on its own right because the free energy change is positive now um let's look at one where you have atp and it is broken down to release the phosphate and your net delta g or net energy change is negative 30.5 kilojoules per mole was that going to happen spontaneously given the right environment yes it will so in a couple reaction you would not look at these individually but you would rather combine all those steps together and get an overall sum to get the final answer regarding whether this will happen or not so a delta g of a coupled reaction where you have a glucose molecule that has uh you know that gets a phosphate added to it and then it is combined with a fructose to create sucrose you will take the energy uh from the first reaction you know for the single reaction and you will add that delta g to the second reaction standard g to get a final answer which in this case is negative 7.5 kilojoules per mole so would this coupled reaction work so individually this one would not single reaction would not have normally occurred right but when you couple it with this atp driven uh hydrolysis essentially what do what happens does this happen now yes right so it takes the energy that is gotten from all this energy that is released through hydrolysis of atp and that energy is then used to drive that second unfavorable reaction so on the test you should be able to given a set of reactions and provided their information you know given a metabolic chain and provided delta g for individual steps you should be able to figure out if it is a favorable or an unfavorable metabolic chain okay um so the equilibrium constant um that i showed you earlier in the equation and we'll see that equation again later is basically a constant that measures whether the reaction is going to be moving forward or not um so for a reaction to occur uh you want the equilibrium constant around one so it can or in a positive direction so it can occur right so in a particular setting when the all when the delta g is zero and there is no net change in energy the equilibrium constant would be one right and then when the delta g changes it's going to then move towards the positive or the uh above one or below one um and the equilibrium constant is taken by taking the ratio of change from the uh from the products over the reactants so here let's look at that a little bit more in detail you have um your actual two reactants in this case that are going to combine together to make our product so the association rate is going to be dependent upon an association rate constant which uh you will know from uh reactions and then from enzyme kinetics and then you will have a certain uh it will be dependent on the concentration of each one of the reactants that are present there so the association rate is going to be a product of these three numbers a dissociation rate is going to be basically similarly but in this case you will have again a constant for the dissociation for this particular product and then you will look at just the concentration of the product and how easily it can get broken off so at equilibrium these two should be equal that's why it's going to be your equilibrium constant would be one at that point so your association rate of building those products should be equal to the dissociation rate at that point does that make sense yes no maybe okay i have no answers and i don't know if people are writing in the chat yes okay thank you thank you okay so here are some examples for this um so if you have a thousand molecules of a and it has a molecules of b and you're provided with um the constant you should be able to again uh calculate the overall uh dissociation rate or the association rate right so in this case um we are told that at equilibrium you would have um a certain number of your molecules each one of your reactants and a certain amount of product now what you will notice that just slight changes in those uh num uh you know equilibrium constants will have a really big effect or a slight change in concentration of your molecules will have a really big effect at the end of the day on how well they can bind and where that equilibrium constant occurs so in the second one it's talking about how the in this case uh the reaction has a weaker interaction and so it has a lower uh equilibrium constant and what you end up with is a lot more product uh a lot more reactants than product so here this reaction was favorable however in the second one the reaction doesn't look like it is um that favorable at all and it moves at a very slow rate and so um this would be an example of how the reaction works probably under enzyme with enzyme catalysis versus um an example of something that is allowed to just happen on its own it's gonna go at a much slower rate in that case now it makes sense for me i got it now when you like explain the example okay i am glad so yeah this was an example of something different but it also shows you how enzymes um help provide that environment so that those bonds can occur better and allow that reaction to occur easier and get more product from that reaction so in our body in general we have to have certain amount of thermal energy or heat energy in order for molecules to be mobile enough so that they can interact with each other and they can find their substrate and they can do the work that they need to do if you were to lower the temperature the metabolic rate goes down way down because those molecules are not as well in motion they are not able to interact with other molecules in their space and find the substrates that they need to in order to have the reaction occur um so if you had a reaction that was only you know that was possible that was best most efficient under 37 degrees celsius or physiological temperature if you move it to room temperature you would expect that rate of reaction to go down way down right another thing is that enzymes while they can help move the reaction rate forward they cannot change the equilibrium point of the reaction beyond a certain point right so if your uncatalyzed reaction at equilibrium has a particular rate the same rate is going to happen after enzyme catalyzed reaction as well it's going to make that go faster but it won't change that overall equilibrium rate so that constant remains the same regardless of enzymes being present there does that make sense yes no maybe yes it does okay so the enzymes performance basically depends on how quickly it can help the reactants get together to create the product or get in the right conformation to create the product in general the higher the substrate concentration the quicker the enzyme rate the rate of reaction will increase as the concentration of substrate increases until it um reaches a point where basically all the enzyme is saturated with your substrate and at that point um you would eventually flatten out the curve and slow down that process so the rate of reaction um for a substrate for our for any reaction uh as the concentration increases of the substrate you're increasing the amount of uh product that is getting paid the reaction is getting made at half of uh we max is basically the point which is reaching the maximum rate of that reaction and that goes back to your reaction constant that is maintained regardless of whether or not the reaction is going to occur right or whether or not the enzyme is there so as you get close to that equilibrium state that k constant you are going to sorry i wanted to you're going to start to slow down that rate of reaction eventually leading to a maximum state where it can no longer affect no matter how much more substrate you add it won't change that rate of reaction any further and that's the point at which uh it will be maximized so the michaelis-menten kinetics basically look for this exact point the amount that oh uh the v max where there is no where the reaction plateaus off and no matter how much more substrate you add you're not gonna get any more product and also it looks at the optimum point of amount of optimum concentration of substrate where you will get the maximum effect of your rate of reaction from your enzyme so the km is um the substrate concentration at which you get the highest rate of reaction um within or about the highest you know a rate of reaction um in your uh subs with your enzyme kinetics uh so it's half the maximum velocity but that's where that's the point where it's going to start to plateau off essentially and at the high substrate concentrations you know there's going to be a point where no matter how much more substrate i provided it just the enzymes are saturated they cannot take any more and it's going to that's what they're going to be the maximum rate of reaction for that uh particular compound or that sorry can you go back yes i'm still trying to figure out what exactly that so at km that's like i guess the ideal substrate concentration yes so the michaelis-menten constant is basically yes if you can think about it the ideal substrate concentration so until then if you notice it kind of increases and the rate of reaction is increasing uh kind of you know exponentially it's going in a very linear way and this point the km where you reach the half velocity half of the maximum velocity is the point where the increase starts to plateau off so it starts to you know kind of lose its the same kind of momentum that it was getting so this is the concentration that typically we run for we look for the km in an enzyme kinetics to uh look at the optimum rate of reaction within a situation for that for that particular set of reactions the reactants and products does that make sense yeah so basically that's like the most efficient at that concentration that's the most efficient point exactly and after that while it's still increasing it's increasing at a slower rate and then once you uh you know there'll come a point when as you get close to the maximum rate of reaction that it will just plateau off it never quite reaches that anyway um and that's the point where no matter how much more substrate you add at that point everything in your enzymes are saturated they cannot function they have a partic they have the requirement for they need two minutes to you know make this reaction go there's nothing more they can do they can't make it uh faster than that okay thank you so basically you know the velocity or how long uh the process takes is not dependent on substrate concentration it has to take whatever amount of time it takes it can't do it any faster okay so um again you know like some of you may have done these experiments in biochemistry or in gv1 where we add more and more you know we add double the substrate or quadruple the substrate or half the substrate and see how the reaction moves forward and what you will notice is that the increasing substrate concentration typically will lead to increasing products until a particular point at which point it just plateaus off and it doesn't matter how much more you add um so the initial rate of substrate consumption if you plot that against your substrate concentration you can calculate the uh v max and your michaelis menten constant as well so this is the equation for that so the velocity or the rate of your substrate consumption how long it takes for the reaction to occur is um you know a pro or you can calculate that by looking at the v max for that particular substrate divided by um the michaelis constant plus the concentration of substrate so how much substrate is present uh what is the most efficient point on that curve and then um that is um you know looked at in relation to the maximum rate of reaction that can possibly happen for that particular equation okay yes no maybe okay sounds good yes i thought i heard a question no yes it's clear not you somebody else had a question okay so now in some activity doesn't mean that you cannot control enzyme activity right you can still control it through a few ways you can control it partly by substrate concentration that is one way to control the rate of reaction you can also control it by having inhibitors of the pathway and you can have two different types you can have competitive inhibitors and you can have inhibitors that are not going to bind to the exact same site and we'll talk about a little bit of both so if you have a substrate by itself it's going to have the rate of reaction that it does typically when you add some type of an inhibitor to that reaction it will lower your overall rate of reaction and make it go at a slower rate because now it will still go uh but it will work a different way now it does matter what type of uh inhibitor you have if it is a reversible inhibitor or uh you know or irreversible one one that binds and never lets go so that's going to affect this line so sometimes it can inhibit the reaction a lot more than just a marginal um inhibition so chemical reactions will proceed um in the direction where they are there's loss of free energy so into the environment right so there's release of free energy um and enzymes reduce that energy needed to initiate those spontaneous reactions by providing it the right environment the free energy change for a reaction determines whether it will occur or not so whether the free energy is increasing is a positive which will mean a spontaneous reaction or whether it is decreasing or getting consumed by the reaction which would mean that it is a non-spontaneous reaction enzymes can only uh power the spontaneous reactions and then they can use that energy in a coupled format to power the non-spontaneous reactions um the free energy change always tries to proceed towards an equilibrium where the overall free energy change from the chain of reactions is zero at which point your constant is going to be one uh so the standard free energy change is what we compare to look at the energetics of different reactions how much total energy is getting uh produced or absorbed into the reaction the in equilibrium constant that we get is going to be directly proportional to delta g or change in that free energy so if it is spontaneous you will see a higher equilibrium constant also if you have complex reactions the overall change of energy is additive so you take the energy from all of them and combine it together for sequential reactions to calculate the overall change in free energy and similarly in those the comp the equilibrium constant is going to be maintained by looking at all of the reactions as a whole not individual reactions uh by themselves because those that are energy energetically favorable will be able to power the ones that are unfavorable typically um the in equilibrium constant also indicates how strong the bindings are so a higher equilibrium constant will indicate weaker binding and a lower equilibrium constant will indicate quicker movement uh into our higher rate of reaction um and then you have many types of non-covalent interactions that allow the enzymes to bind each other to form those connections and those are powered by just thermal energy that allows the molecules to move so typically when you lower the temperature you are also going to lower the rate of reactions any questions about this part before we go into biosynthesis so let me see we're gonna we have about 10 minutes so we can get through at least some of it i was trying to i know i was going a little bit faster than usual today yeah we'll be able to go through most of it so we may you know like do a mini review next time before we get started okay so um let's talk about now how these reactions um combine together to help us in our actual cell in our metabolic pathways so inside our bodies many times many of these reactions are usually combined together in these type of metabolic chains that help us um you know get the energy that we need from the food as it's broken down as well as make macromolecules that are needed to build our body systems um and so activated carriers of energy in the form of atp gtp fad nadh all of those are required to take energy that is produced from catabolism of food as it's broken down and those um you know energy molecules are released from the chemical bond breaking and they take them to they transfer that energy to these activated carriers that can then power those anabolic pathways or anabolic reactions where we have these small building blocks that are then combined together to make new molecule molecules needed for the cells and um as normally these would be energetically unfavorable reactions and wouldn't occur without the help of this energy input and then that leads to inactivated carrier molecules that can then go on and cycle back to get more energy from the catabolic um reactions the most common and most widely used of these activated carrier is our atp which is why it's called the currency of our cells and that is um basically uh adenine and a ribose so it is a nucleotide that is combined with three phosphate groups uh so it has these two phosphate bonds that can be broken down um and those though uh bonds as they are broken down release energy that can then be used to um catalyze your anabolic reactions so in a plant or in a in the case of a plant which is taking energy from sunlight or in the case of animals which are breaking down food molecules they are taking that energy and they are using that energy to create these atp molecules by con combining this highly energetic third phosphate on this adenosine adenine diphosphate uh molecule now as at this means that it is going to be a positive energy change because you are taking um that energy in there and then when you break it down you will release that energy or uh that will then power the energetic uh the anabolic reactions where energy is required as an input now there are two things that i want to clarify here because i want to you to know the difference between delta g and the standard of free energy i don't think i've clarified that well enough so delta g is the change in um free energy in the environment alone right and that one is going to be positive if the energy is released into the environment and negative if the energy is consumed by the environment right however the standard free energy which is uh the delta g naught the standard free energy change is the opposite of that so the standard free energy is going to be greater than zero or a positive as you build the bonds and negative as you release the bonds so that's looking at the actual reaction side so the delta g itself looks at the free energy inside in the environment and the delta g knot you can think about that as the energy that is inside the reaction or inside the reactants and products uh themselves does that clarify that uh difference between delta g and delta g not it does but like delta g not if it's like bigger than zero it's like favorable at that time when like the binding happening between the phosphates yeah because no energy there is more energy inside the molecule than before so it's the same idea but delta g is looking at free energy that is in the environment and delta g not is looking at the standard change in energy which is inside the pathway or the actual reactants and products so like the cell will be happier to have more energy inside it this time well it's happier say it again uh i meant like the sale uh that process is more favorable like to have to build the atp because it will be more energy with delta g not no see so the thing is this requires energy input so it's still an unfavorable reaction over right it's an unfavorable reaction because delta g is below zero it's negative it required energy in the form of a phosphate taken in from the food energy or from sunlight to the input inside okay i see yes right so it is it's just talking about the state of the actual reactants versus state of the environment okay yes got it thank you okay so yeah uh so this one we did so atp hydrolysis is often tied to this portion because otherwise this won't happen right so i you have to tie it with another kind of reaction either taking an energy from the sunlight to make atp or taking in energy from food to prepare atp and then that atp as it is broken down is going to release a lot of energy that is then tied to for either phosphorylation of another product um because you take that phosphate group and you put it on something else right um to move another reaction forward in that way whether it is a signaling pathway to activate a protein or whether it is a metabolic reaction to uh help create a new molecule that can then be broken down for more energy or for use in a different system uh so this third bond is a phospho ester bond right in this case when it's broken down because it's usually combined to a carbon molecule or to a another organic molecule um as it is moved over from uh the atp where it was combined to a oxygen from the second phosphate rice uh so energetically unfavorable reactions are that's how they are driven they are driven by this atp hydrolysis where the atp is converted to adp that phosphate that is uh taken off is then used on your reactants are on your products to create the new step and so the activation step is where the phosphate is added and then to your reactant and then the condensation step is where then that activated uh you know reactant is then combined with whatever else it needs to be the next macromolec the next monomer to create your uh product and in the process that phosphate is then let go and usually it leads to uh some condensation step as an intermediate um so the activation is taking the atp changing it to adp and creating a intermediate uh product from your reactant that is then used to create the final product in the second step okay yes i can't tell yes thank you i like to have some some type of answer from you guys given that i can't really see you um other carrier molecules that can also carry energy are nadh and nadph um and these are going to be carriers for electrons uh and not necessarily phosphate the same way that we have atp right um so you have nadph which is a reduced electron carrier and nadp plus which is an oxidized electron carrier so both of them can be electron carrier but in different ways uh nadh is used in a lot of catabolic reactions and nadph on the other hand is used when you're building molecules so it's one of those intermediate steps where you are using it as an intermediary to build macromolecules uh in our system including as we build for example dna or another macromolecule okay so nadph is an activated care of electrons uh it goes through oxidation reduction process um to make nadp plus which is the oxidized electron carrier and then when it is reduced it turns to nadph um acetyl coa is another activated carrier in this case uh again if you look at this molecule it is overall a very stable molecule but it has this carboxy group at the or rather an acetyl group sorry at the end of its chain uh that's bound to a sulfur that is a very high energy bro um energy bond and that bond when broken can provide a lot of energy for use in a macromolecule building synthesis of any type of macromolecule whether it is a polysaccharide chain or our dna and rna are proteins all of those require a lot of energy input and those are usually filled through one of these methods and a lot of them are fueled through energy from some type of nucleoside triphosphate hydrolysis um many of these bonds if you remember actually not just include a single bond getting broken but two bonds two phosphate groups getting broken uh from that triphosphate chain hydrolysis either gtp or atp so that you get amp molecules at the end of the day um to make those bonds to create the final macromolecule chains that we get so here is an example of exactly that in um when we are building many of these macromolecule what you get in atp hydrolysis is not just a single phosphate group getting taken off but rather a pyrophosphate formation where two phosphates are broken down together and then those the the two phosphates are then broken down further to even create more um energy uh production and so both of these require a water molecule to break down first the bond between um the two phosphate uh on one side and the adenosine monophosphate on the other and then these uh this pyrophosphate molecule is further broken down by breaking that at the oxygen bond between them uh again within second water molecule and so this leads to um release of two phosphate molecules that can then be used to fuel reactions um so this is something that we've seen in synthesis of nucleic acid as well as when we made rna molecules when we were transcribing and translating dna that these required that pyrophosphate not just a monophosphate but a paraphosphate from the atp and that pyrophosphate was then used to fuel the um extension of those dna and mrna chains so nucleic acid is a multi-step process driven by this type of atp hydrolysis and with the high energy need that it has it uses a lot of energy a lot of atp is used in a single round of transcription or translation of individual mrna molecules so the activated carriers and biosynthesis here is a review of that the formation of an activated carrier is usually done is usually coupled to er to energetically favorable reactions so that these activated carriers can take the electrons or phosphates or energy from these molecules that we are breaking down and releasing energy from atp is the most widely used activated carrier that is um broken down to release phosphates and those atp phosphates are then used to join molecules together or to activate them other forms of carriers include nadh and nadph those two are both carriers of electrons and are used to foil uh to fuel oxidation and reduction reactions not phosphate transfers nadph and nadh have very different roles in the cells and we'll talk more about them in the next chapter cells also make use of many other types of activated carriers including acetyl coa and other molecules and the synthesis of biological polymers like nucleic acids and polysaccharides and fatty ace chains require an input of energy that is um taken from hydrolysis of atp to create paraphosphate in many ways uh which is two phosphates coming off of it instead of one leaving behind an amp or adenosine monophosphate and then that is those two fire of two phosphates in the form of pyrophosphate are further broken down for more energy release so um that was chapter three now next week we are gonna start to look at how cells obtain energy from food and we will be looking at breakdown on utilization of sugars and fats and how they are used to regulate our metabolism so that's all for this week