Transcript for:
Understanding Microbial Metabolism Fundamentals

hi welcome to my presentation of chapter 3 microbial metabolism so this chapter is all about metabolism which is the sum total of all the chemical reactions inside of a cell broadly you can break metabolism into two parts catabolism and anabolism catabolism means breaking larger molecules down to smaller molecules anabolism means taking smaller molecules and building them up into bigger molecules in catabolism uh energy is generally released when you're breaking larger things down into smaller things and some of that energy is going to be captured by cells and stored mostly as atp anabolism on the other hand requires energy so the energy that cells have stored in atp will be used to fuel anabolic reactions that they use to build the large molecules that they need and a lot of the time you'll have a series of reactions that all happen in sequence one after the other and that's called a metabolic pathway the general purpose of metabolism is to allow the cell to grow and reproduce although for microbial cell growth and reproduction are basically the same thing it also allows cells to maintain homeostasis which is just maintaining the internal conditions they need to live in a stable state metabolism is always carried out by enzymes for almost every reaction you have in the cell you have an enzyme that is designed to make that reaction go faster an enzyme is defined as a protein catalyst a catalyst is something that helps a reaction go faster but does not participate in the reaction as a reactant or a product so it's not actually a part of the reaction it doesn't get changed in the reaction but it does make the reaction go faster so if you have a catalyst that is a protein that's an enzyme something to remember about enzymes is that their name will always end with ace so anytime you see the word of some protein and it ends in ace you know that's an enzyme a lot of enzymes also need cofactors which is just a molecule uh that that has to be there present with the enzyme in order for the enzyme to be able to function properly so in general with metabolism you're starting by taking in nutrients from the environment and then you have to break those nutrients down in catabolism after you've broken those nutrients down you're going to extract well in that process you're going to extract some energy from them and store it as atp and you're going to be left over with tiny pieces of those nutrients which are frequently precursor molecules or precursor metabolites you can stick those precursors together to make building blocks that will be used to build the macromolecules for the cell when you link the building blocks together you actually are building those macromolecules and then you assemble the macromolecules into the structures of the cell finally once the cell has twice as much stuff and twice as many structures as it has started out with it's ready to divide into two cells so the first part of this breaking down your nutrients to precursor molecules that's catabolism it generates energy that would be stored as atp and the rest of this putting those precursor molecules together to make building blocks and putting the builder building blocks together to make macromolecules and even assembling those macromolecules into cellular structures all of that is anabolism building bigger things so that's all going to require energy usually in the form of atp and all of those steps are going to require enzymes so first we'll go over what types of nutrients microbes need to bring in from the environment and how they do that um so cells are mostly water 75 of the weight weight wet weight of a cell is just water and almost the rest of it is all consisting of macromolecules which are the really large molecules in the cell um so if we're talking about a cell's dry weight that means the water has been removed wet weight means the water is still in the cell you have four basic types of macromolecules in cells proteins lipids nucleotides and polysaccharides for proteins the building blocks are amino acids for lipids you have various building blocks actually but a common one is a fatty acid for polysaccharides the building blocks are sugars and for nucleotide sorry for nucleic acids the building blocks are nucleotides to build all those things you're going to need the macronutrients macronutrients are any any element or compound that is needed by the cell in large amounts the two biggest macronutrients are carbon and hydrogen an organic molecule is defined as a molecule based on carbon so cells of course need a lot of carbon and all molecules that have carbon in them have a lot of hydrogen in them as well so every organic molecule in the cell is going to need carbon and hydrogen so the cell has to have those things or in order to build those molecules then the cells also need a lot of oxygen and nitrogen oxygen is used for nucleotides amino acids and sugars so three of the building blocks for three of the macromolecules are going to need oxygen in them nitrogen is also very commonly needed is needed to build nucleotides and amino acids so without oxygen and nitrogen you can't make the building blocks that you need for most of your macromolecules then you also need a good amount of phosphorus that would be used in nucleotides also also some lipids require phosphorus and some proteins need it as well then you have some other macronutrients that are not needed in quite as large amounts those would be sulfur potassium magnesium selenium sodium and calcium most of those are needed as vitamins or cofactors by certain enzymes the exception is sulfur that is needed as a cofactor by some enzymes but it's also needed to build two of the amino acids um so out of those macronutrients the ones the cells need the most of are the carbon the hydrogen the oxygen nitrogen and phosphorus the rest they need in smaller amounts but it's still overall a large amount enough for it to be considered a macromolecule then apart from the macronutrients cells also need micronutrients that's just anything they need but they only need a little bit of it there's a lot of different micronutrients needed by cells and different species are going to have different micronutrients that they require so we won't go over specific micronutrients so we'll talk about some where some of those major macronutrients are coming from for organisms for carbon since that's a really important macronutrient you need it to build every organic molecule in the cell we have special names for organisms depending on where they get their carbon from organisms can be heterotrophs or autotrophs heterotrophs are organisms that get their carbon from organic molecules that usually means that it's coming from another organism and autotrophs are organisms that get their carbon from inorganic molecules which generally means co2 or carbon dioxide so most microbes are heterotrophs animals are heterotrophs some microbes and plants are autotrophs uh in general microbes that are heterotrophs or organisms that are heterotrophs would also be getting their energy from this or uh from the other organisms that they're getting carbon from and in general autotrophs would be getting energy from um well from light frequently most commonly actually from light and photosynthesis uh there are exceptions to that so we commonly think about autotrophs as being producers in a food chain and heterotrophs as being consumers which would mean that autotrophs are producing energy from light by photosynthesis and heterotrophs are consuming it um but that's not always accurate the words technically just mean where you're getting carbon from not where you're getting energy from so even though most autotrophs get energy from light and photosynthesis the actual name autotroph just means they're getting carbon from inorganic molecules like carbon dioxide heterotrophs usually get energy from organisms that they eat but the word heterotroph just means that they're getting carbon from organic molecules which would have to come from some other organism um and then i guess i'll just mention that in general wherever organisms would be getting their carbon from they're getting their hydrogen from there as well [Music] if they're heterotrophs organisms also need sources for nitrogen nitrogen in the environment is found in three major formats uh you have ammonia or nh3 you have nitrate or no3 minus and you have molecular nitrogen into which is found in the atmosphere uh so most of the gas in the atmosphere is nitrogen actually and it's in the form into in the soil and the water that's where you have your nitrate and your ammonia and for ammonia nh3 that can also exist as the ammonium ion in h4 plus whether your ammonia is ammonia or ammonium depends on the ph of the soil or the liquid where it is um most microbes are able to get nitrogen from ammonia and a lot of microbes can also get nitrogen from nitrate very few of them can get nitrogen from molecular nitrogen microbes that can use molecular nitrogen as a nitrogen source are very special we call them nitrogen fixers they're going to take in nitrogen as molecular nitrogen from the air and they're going to put it out as ammonia in general um which is a format that can be used by a lot of different organisms not just microbes um so that means they're taking nitrogen from an unusable format molecular nitrogen and putting it into a usable format like ammonia usable for other organisms of course the nitrogen fixtures themselves can use molecular nitrogen you also have some microbes that get nitrogen from organic molecules as we mentioned nucleotides and amino acids need nitrogen so they also have nitrogen and they can be used as nitrogen sources so this diagram is showing um the nitrogen cycle or how nitrogen is moving through the environment or through the air in the soil um on a very basic level so you have a lot of nitrogen in the atmosphere as molecular nitrogen that is going to kind of diffuse into the soil and you have nitrogen fixing bacteria that are able to use it some of them would be associated with the roots of plants and they're going to take up that molecular nitrogen and convert it into a format that's useful for the plant um you also have some nitrogen fixing bacteria that just live free in the soil so they're all taking up this molecular nitrogen and using it as their nitrogen source the in the process of doing that they're also converting it to a different format and releasing some of it as a waste product um for them a waste product so the major waste product for these guys would be ammonia or ammonium depending on the ph so you end up with a lot of this ammonia in the soil you're going to have other bacteria in the soil that are able to take up that ammonia and use it as a nitrogen source they're going to convert it themselves into another format in this case nitrate or nitrite and release that as a waste product which will be taken up by other bacteria and used by them as a nitrogen source so you also have plants that are able to use the nitrates and the ammonia so they would also be taking up some of that nitrogen from the soil and then finally you also have some bacteria that are using nitrates as their nitrogen source so they're taking in nitrates and they're also changing its format and they're actually converting it back some of it they're converting it back to n2 or molecular nitrogen and releasing that as a waste product and it's a gas so it goes back up into the atmosphere um for micronutrients you have two basic categories for micronutrients trace metals and growth factors trace metals are inorganic they're metals generally usually those are needed by enzymes as cofactors out of all of them the most important one is iron but there's also a lot of them and which one is the most important does depend on which species we're talking about exactly then you have growth factors those are organic micronutrients that would include all the vitamins usually vitamins are being used as cofactors by enzymes also but some of them are doing different things it's just anything that the cell has to have that's an organic molecule that the cell cannot make that has to be brought in as an organic mitral nutrient or growth factor so depending on the species of course you're going to need a different combination of growth factors some species can make most things themselves and they don't need a lot of growth factors some species cannot make a lot on their own and they do need a lot of growth factors so in addition to growth factors being vitamins they can also be other things anything the cell needs that it can't make so for instance you have some microbes that are not able to make every amino acid in that case those amino acids that the cell cannot make would be a growth factor that the cell needs to get from the environment in order to live but we wouldn't count that as a vitamin because it's an amino acid so those are the things that cells need basically um then they have to get those things from the environment into the cell so there's well you probably remember from uh general biology that there is a number of ways that cells can transport things across the membrane um microbes are going to be using a lot of active transport to get nutrients into the cell so active transport is the opposite of passive transport and passive transport you're not using any energy to move the thing into the cell and things are moving uh down their concentration gradient always by diffusion in active transport it's the opposite you're moving something up its concentration gradient and that requires energy um so a lot of the time nutrients need to be kind of concentrated inside the cell but they're not that concentrated in the environment so then in order to get the nutrient from the environment into the cell you have to use active transport to pump it up its concentration gradient or else it would never enter the cell there's three types of active transport that microorganisms use commonly you have simple transport group translocation and abc transporter systems in simple transport it's simple you just have one protein that is inserted through the membrane and the nutrient will travel through the pore formed by that protein the protein will use atp um in one way or another to to move the nutrient through it into the cell then in group translocation uh you're using multiple proteins not just one and each protein in the system has its job to do it has to be at least two uh proteins in a group translocation system but it could be more one of them is going to be the protein that is actually transporting the nutrient across the membrane and the rest of them will be modifying the nutrients so it can get in more easily then finally you have abc transporter systems those always use the same three proteins one of them grabs the substrate or the nutrient that's being brought in one of them is actually transporting it across the cell membrane and the last one is providing energy by hydrolyzing atp into adp and a free phosphate group so here's a diagram showing those three forms of transport of active transport for microbes at the top you have simple transport where one protein is involved in bringing the nutrient into the cell this particular simple transporter is not using atp for energy it's using the proton motive force so it's allowing a proton to go down its concentration gradient into the cell and it uses the energy of that proton moving to transport the nutrient into the cell also up its concentration gradient next we have the group translocation example here you have one protein that is actually moving the nutrient into the cell and then you have another protein right here the r that is modifying the nutrient once it gets inside the cell by adding a phosphate group to it the point of doing that would be to prevent it from getting back outside the cell then finally you have your ap abc transporter system at the bottom for the system you have one protein that is outside the cell in the periplasm that's going to grab the nutrient initially and bring it to the transporter protein which actually transports it inside of the cell and then you have a third protein that is providing atp energy to power that process so for simple transport the energy is going to be generally coming from the proton motive force so this applies only to microbes of course because uh non-microbial organisms don't use the proton motive force in the in uh transport that's driven by the proton motive force you always have the transporter allowing protons to move down their concentration gradients they're going to do that spontaneously just by diffusion and when they do that the energy of their movement can be used to pump the substance that you're trying to move across the membrane so so far we've been talking about nutrients being brought into the cell but you could actually use this also for waste products that you need to get out of the cell if you needed to pump them against a concentration gradient to get them out you have two basic types of sim uh simple transporters symporters and anti-porters in symporters the uh the proton that's going down its concentration gradient and the substance that's being transported are both moving in the same direction [Music] so in and in in an anti-porter system the proton and the substance are moving in opposite directions so here you have a diagram showing those types of transporters first you have an anti-porter here so you have this proton flowing down its concentration gradient into the cell and in exchange for that a sodium ion is being pumped out of the cell so this is being used this antiporter system is being used to get a waste product out of the cell not to bring a nutrient in next to it you have a symporter where your proton is moving down its concentration gradient into the cell and a nutrient lactose is also being pumped into the cell using the energy from that protons movement so in both cases you're always going to have the proton moving into the cell because if it's providing the energy then it needs to be moving from where you have a lot of it to where you have a little of it and you always have a lot of protons outside the cell and only a little bit inside the cell because the cell is generating that proton motive force which is just the concentration gradient of protons across the membrane with a lot of them outside and a little bit only a little bit of them inside the cell so your proton will always be moving into the cell um if your substance being transported is moving out then that's the opposite direction that's an antiporter if the substance being transported is moving in that's the same direction that's a sim porter and in general biology we went over active transport but we really only talked about basic active transport and co-transport or secondary active transport so simple transport for microbes is actually a type of secondary active transport where you're using atp indirectly to set up the proton motive force and then and then you're exploiting that concentration gradient to uh to move a substance against it's against its concentration gradient okay now we have group translocation um for group translocation the energy to power the transport of the substance is always coming from an organic molecule of some kind um so there's a lot of different organic molecules that can be used for this it just has to be something that has a lot of energy in its bonds so glucose is an example of a organic compound with a lot of energy in its bonds and later in this chapter we're going to go over actually how you break down glucose and catabolism to get energy from it but the first process in breaking down glucose for energy is glycolysis in glycolysis you're converting glucose into different types of sugars and so an intermediate one of those intermediate sugars in glycolysis is also going to have a lot of energy in its bonds because it's coming just from glucose so you can use most of those intermediates from glycolysis as energy sources for group translocation and the other characteristic of group translocation is that you're modifying the substance somehow during the transport which is going to require at least one but maybe more than one protein to do so in this diagram here this is showing an example of a group translocation system they can have multiple proteins uh multiple different proteins in them and they're pretty diverse so this is just an example um not even yeah they don't all look like this that's what i'm trying to say um so here you have your actual transporter you're always going to have a transporter protein in group translocation that's taking this this nutrient glucose and moving it into the cell once the glucose gets inside the cell it's going to be modified by adding a phosphate group to it to make glucose 6-phosphate um that process of adding that phosphate is going to require all these other proton uh proteins so we've got like four different proteins here that are all involved in modifying this glucose what they're doing is taking a phosphate group that is from an intermediate from glycolysis and transferring it ultimately across all these different proteins to the glucose so the phosphate is coming from a glycolysis intermediate and it's going to the glucose this bonds between the glyco the glycolysis intermediate and the phosphate group has a lot of energy in it so when you break that bond you release the energy and that energy is being handed off from protein to protein here until ultimately it's added um to the glucose with the phosphate group and that keeps the glucose inside of the cell finally we have the ap avc transporter systems abc here stands for atp binding cassette that's because the protein in this system that is hydrolyzing atp has an abc domain an atp binding cassette so it's basically just part of the protein that is binding atp any protein that is hydrolyzing atp has to be able to bind atp and is going to have an atp binding cassette and this whole system has been named after after the fact that one of the proteins in it has an atp binding cassette um it's more common to find abc systems in gram negative bacteria because they have a you know a periplasm but you could also find it in gram-positive bacteria and an archaea is just less common so in general you're going to have a substrate binding protein that's found in the periplasm it's going to bind the nutrient that you're bringing into the cell then that nutrient is going to be transported into the cell through the transporter protein and then you're going to have another protein inside the cell that is hydrolyzing atp that has the atp binding cassette that is providing energy to transport this nutrient into the cell um these this paraplasmic binding protein or the substrate binding protein is important um because because it has a really high affinity for the substrate which is the nutrient that's being transported which means that it binds the substrate really strongly and it means that even if you only have a little bit of the substrate there it's going to get bound so this can be used for transporting things that are really rare into the cell basically it's easy for this nutrient or the substrate to find this substrate binding protein and then once it finds that protein is going to bind to it very strongly and the protein will bring it to to the transporter okay so that's the basics of how cells are getting their nutrients and what nutrients they need now we'll look at how they are conducting catabolism to get energy from those nutrients but before we get into the specifics of the catabolism we're going to need to talk about some more background information about metabolism and about energy yeah some background information first so first off we'll talk about energy conservation the textbook talks a lot about energy conservation which you might know from physics um that energy conservation basically just means that energy cannot be created or destroyed it can only change form when we're talking about energy conservation in biology and especially with regard to metabolism what we're actually talking about is how organisms capture the energy that flows through their hands basically right so if you have nutrients coming into the cell and you're breaking them down into smaller molecules you're releasing energy and that energy is going to be released in one way or another it could be released as chemical energy that goes into the bonds of another chemical it could be released as heat energy which is kind of wasted energy um those are the main ways that it would be released but regardless of how it's released the cell's challenge is to capture that energy somehow uh so the cell is usually trying to get the energy released as chemical energy that's going to be captured in some compound that the cell is going to keep around and use for energy later on if you don't have the ability to store the energy in atp you might be breaking down glucose and that does release energy and you could use it to make atp but if you are not actually making atp then that energy is just flowing through your fingers and it goes right out back out to the environment and you haven't actually benefited from it because you haven't captured it so energy conservation for organisms means capturing and storing the energy that they're releasing through catabolic reactions so this is similar to how we generate power any power generator no matter what what it's getting energy from exactly has the challenge of capturing that energy so you're going to have some source that is releasing energy uh like burning fuel or water water that's falling for a dam for a hydro generator or wind blowing in a in a windmill that's all energy being released and the the point of the power generator is to capture that energy and store it somehow capture it as electricity and then store it by transmitting it to the electrical grid so in this image you have an example this is a type of power generator that's kind of in development now that's trying to capture the power of waves so waves have energy in them and in this setup the waves are coming into this uh kind of chamber and you have air filling this chamber the top of it and the bottom is filled by the water so when the waves come in they're going to be pushing up into the chamber and the air that's in here is going to get compressed then that compressed air is ultimately going to move this turbine and the turbine has a magnet on it and once a magnet is spinning that generates electricity that electricity is going to be added to the grid so this whole system is designed to capture the energy that's in these waves and store it as electricity so this is an energy conservation system and kind of the biochemical sense i guess where you are capturing energy and storing it so organisms can be classified based on where they're get where they get their carbon they can also be classified based on where they get their energy so organisms are either going to be chemotrophs or phototrophs chemotrophs are organisms that get energy from chemicals phototrophs get their energy from light so most of the organisms that we're familiar with are chemotropes they get their energy from some type of chemical which means that they are going to release the energy from the bonds of that chemical capture it in the bonds of a different chemical and ultimately store it in the form of atp you have two types of chemotrophs chemo organotrophs and chemolithotrophs chemo organotrophs get their energy from organic compounds such as glucose so that would include us it also includes most most microbes um that we are familiar with and have been cultured in the lab but you also have some chemolithotrophs um which are organisms that get their energy from inorganic compounds like molecular hydrogen or hydrogen sulfide or ammonium or iron a lot of different options actually that they have um lith literally means stone so chemolithotrophs get their energy from something like stone of course molecular hydrogen is not not stone um all those things aren't stone but they are all inorganic compounds and in that sense are like stone so there's not that many chemolithotrophs compared to the chemo organo chemo organotropes which are very common a lot of archaea are chemolithotrophs and you also have specific groups of bacteria that are chemolithotrophs like the sulfur bacteria iron bacteria nitrifying bacteria those guys are all chemolithotrophs um then you have the phototropes which get their energy from light meaning that first they convert light energy to chemical energy then they capture it and store it within the bonds of atp you have two basic types of phototrophs oxygenic phototrophs and an oxygenic phototrophs oxygenic phototrophs use normal photosynthesis that the type that is used by plants so that includes the plants but it also includes cyanobacteria algae and other photosynthetic microbes that use photosynthesis that produces oxygen all right so normal photosynthesis um produces oxygen you're taking in carbon dioxide and giving out glucose and oxygen but that's not the first type of photosynthesis that evolved before you had oxygenic photosynthesis you had an oxygenic photosynthesis so you have some organisms that still do an oxygenic photosynthesis today and they are an oxygenic phototrophs so they use the type of photosys synthesis that does not that does not produce oxygen it does produce glucose or organic molecules like that but it doesn't produce oxygen so all of the microbes that that are an oxygenic phototrophs are bacteria uh all organisms that are an oxygenic phototrophs are bacteria specific groups of bacteria um right so those are the sources for energy for uh for organisms usually they're going to be storing that energy as atp but sometimes they might use a different molecule like for instance gtp which is real closely related to atp basically almost the same thing but a little bit different so there's a variety of molecules that they can use other than atp to store that energy but they usually use atp and here you have your diagram breaking down organisms based on where they get their energy so you're either getting energy from chemicals or for light or from light if you're getting energy from chemicals and it's organic chemicals that probably came from some other organism then you're a chemo organotroph if you're getting energy from some inorganic compound that did not come from another organism that is a chemolithotrophe um and then if you're getting energy from light or a phototroph if you're using normal photosynthesis you're an oxygenic phototroph if you're using the early type of photosynthesis that does not make oxygen you're an an oxygenic phototroph so you can actually combine the name for organisms based on their energy source and the name for them based on their carbon source to get even more complicated words um if you're a chemo organotroph then you are a heterotroph so if you're getting your energy from an organic compound then you're also getting your com your carbon from that organic compound as well all right so glucose has energy in it but it also has a lot of carbon in it so it's good uh as a source for both of those of those requirements um so if you are that then you are a chemo organo heterotroph and that would be like us and most cultured bacteria getting our carbon from organic molecules and getting our energy from organic molecules as well if you're a chemolithotrophe or a phototroph you're usually an autotroph but not always an autotroph remember is an organism that gets its carbon from an inorganic source generally carbon dioxide so if you're a chemolithotroph and you're getting your energy from an inorganic compound you're usually getting your carbon also from an inorganic compound if you are a phototroph and you get your energy from light you usually get your carbon from an inorganic compound for organisms that do normal photosynthesis they're using carbon dioxide as part of that so they're using the photosynthesis to generate energy from light they're also using it to generate glucose from carbon dioxide so those guys would be photo autotrophs photo autotrophs would be organisms that get energy from light and get carbon from carbon dioxide both of those through the process of photosynthesis then you also have chemolithoautotrophs which would be organisms that get their energy and their carbon both from inorganic compounds so you have some exceptions to this you have some chemolithotrophs that get their carbon from an organic compound even though their energy comes from an inorganic compound and you also have some exceptions of phototrophs that are not autotrophs but usually it holds true that a chemolithotroph and a phototroph are both going to be autotrophs which is why autotrophs are known as producers and that usually holds true so this diagram is showing the breakdown of all that big old classification system so first you can divide organisms based on where their energy comes from from chemicals and their chemotropes or from light in their phototrophs if their energy is coming from chemicals and their chemotrophs then you can look at where their carbon is coming from if it's coming from carbon dioxide the inorganic carbon source then they are chemoautotrophs um which would probably mean that they're chemolithotropes and they're getting their energy from some inorganic compound like hydrogen or sulfur or iron they could also be chemoheterotrophs if their carbon source is organic compounds which should be chemo organoheterotrophs technically if their energy and comp and carbon are both coming from organic compounds and the full word would be chemo organoheterotrophs but a lot of the time they shorten the word because it's just a real long word then technically you could be using oxygen or not using oxygen to make your energy so we'll go through this bit of the diagram later later in this chapter on the other side if your energy is coming from light you're a phototroph um if your carbon is coming from carbon dioxide then you are a photoautotroph performing normal photosynthesis um and then you could either be performing photosynthesis that produces oxygen or photosynthesis that does not produce oxygen um if your carbon source is organic compounds even though you're a phototroph then you are a photoheterotroph and there are a few examples of bacteria that use light for energy but still get carbon from an organic molecule okay so now we'll talk about free energy and we'll get into a little bit of the physics behind this um so energy and physics is defined as the ability to do work and we have a concept called free energy which is abbreviated as g after gives the guy who discovered it um free energy is defined as energy that's available to do work so some energy that is in a compound is going to be kind of tied up and you can't do anything with it so that is part of the energy of the compound but it's not part of the free energy of the compound since it's not available to do work right now we measure free energy in joules which is just a unit of energy any time you have a reaction you're going to have a change in the free energy between the reactants and the products so we call that the delta g the change in free energy is delta g and you're always comparing the reactants to the products when you're figuring out the delta g how much free energy did the reactants have versus how much free energy do the products have um you also have another term which is delta g um not prime so in this in this um abbreviation here the triangle is actually the greek letter delta which means change the capital g is for free energy this zero is technically called not and the apostrophe is called prime so that's delta g not prime the not and the prime there mean standard conditions so the delta g not prime is the change in free energy at standard conditions during the reaction at standard conditions so that would mean ph seven or neutral the temperature is 25 degrees celsius or room temperature pressure is one atmosphere which is sea level pressure and the concentration of all reactants and products is one molar which is one mole of that compound per per liter of solution um so usually reactions that are occurring in real life or kind of out in the environment out in the world are not at they're not at standard conditions but in the lab it's more common for them to be at standard conditions and we use delta g at standard conditions as kind of a way to compare the delta g of different reactions um without the specific temperature and reactant concentration and stuff affecting the numbers based on their free energy change or their delta g you can divide reactions into um endergonic or exergonic categories exergonic reactions are reactions that release energy so this graph here shows the free energy during an exergonic reaction so you start out with this amount of free energy in the reactants and then you go through the reaction and you end up with this much free energy in the products which is less than how much you had in the reactants so the delta g is going to be negative for exergonic reactions because um the reactants had more energy the products had less so when you subtract the energy of the reactants from the products you get a negative number um that amount of energy the delta g that is energy that has been released during the course of this reaction so if cells are conserving energy that means that once this energy from the reaction is released the cell is going to capture it somehow and store it in in some compound usually atp exergonic reactions are generally also spontaneous meaning that they'll happen by themselves without you doing anything to start them theoretically endergonic reactions are the opposite the delta g during the reaction is positive so here you have a graph for an endergonic reaction the reactants start off with low free energy and the products end up with high free energy so when you subtract the free energy of the reactants from the products you get a positive number and delta g is positive whenever delta g is positive in a reaction that means that the products have gained energy the only way that can happen is if the energy came from somewhere else so that means that endergonic reactions require energy in order to go forward and they are reactions that require energy so you would have to put energy into the system in order for the reactants to react to form the products otherwise there's no way for the products to get more energy than what the reactants had so when organisms need to do an endergonic reaction they will usually use atp to power the reactions you're gonna they're gonna take some of that energy that is stored in atp and use it to put into that reaction so the products can end up with more energy than the reactants we also have a concept called free energy of formation which is abbreviated gf not that is the energy that is absorbed or released when a compound is being formed so it's related to the delta g of a reaction but instead of specifying the reaction you only specify the compound itself rules about delta rules about the free energy of formation are that elements that are pure and neutral so not charged have energy of formation of zero so that means that molecular nitrogen that's just two nitrogens so it's pure no other elements are in that compound and it also does not have a charge so molecular nitrogen does not have an energy of formation it causes zero to form to form match to form molecular nitrogen and the same thing for molecular hydrogen molecular oxygen but any compound that has a charge plus or minus or that has multiple elements inside of it is going to have some value for the free energy of formation that is not zero um if the value for free energy of formation of a compound is less than zero then that means that they're formed by an exergonic reaction so uh that reaction would release energy it would be spontaneous um and they're gonna have less free energy than whatever had formed them um but the reaction to form compounds that have a negative free energy of formation even though it's spontaneous because it's exergonic it could still be pretty slow it might still take a very long time um on the other hand if the compound has a free energy of formation that is above zero or positive then they are formed by an endergonic reaction that requires energy and is not spontaneous so for those compounds with a positive free energy of formation you have to put energy in to the system for that thing to be formed that thing has more energy than whatever it was formed from also if any if a compound has a positive free energy of formation that means that um they'll actually decay spontaneously over time so if you have that compound um sitting around and you just wait eventually it'll start turning back into whatever it was formed from because the reverse reaction in that case would be exergonic and you would release energy um but a lot of the time it takes uh you know that decay happens very slowly um so just because a reaction is spontaneous doesn't mean it'll happen quickly it might be very slow just because a reaction is non-spontaneous and therefore the products will decay doesn't mean they're going to decay quickly it could also take a very long time for that to happen there's also another type of energy that's important for reactions in biology which is activation energy the activation energy is the energy you have to put into a reaction to make it go even if it's a spontaneous reaction where energy is released overall um so whenever you have a graph of the free energy in a reaction you have the reactants at some level of free energy the products at some other level of free energy and you're always going to have a hump in the middle of the reaction this hump however big it is that's the activation energy um and this is related to the energy of what's called the transition state so the transition state is sort of it's sort of like a frankenstein compound that's composed of the reactants merging with the products so you have bonds in the reactants that are breaking you have bonds in the products that are forming but the bonds are not really broken or really formed yet in the transition state so in this reaction here in the diagram you have as your reactants a and b c and your products are a b and c so the b atom needs to transfer from from bc to a to form a b so in the transition state you have this bond between bc and the reactant breaking at the same time the new bond between a b and the products it's forming so that's the transition state bonds are breaking and forming the transition state only lasts for like an instant so we haven't actually observed it it it does not last long enough to observe really but we know that it exists because of of the energy that it has um so you have to put in the activation energy to get enough energy into the reactants so they can form the transition state and then move to the products the transition state has a lot of energy associated with it because the bonds are under a lot of stress and they're very long so in general the longer a bond is the more energy it has and when you're in the transition state and bronze bonds are kind of breaking and forming um but not really broken or really formed they're very long there so they have a lot of energy and it's just very unstable also the more unstable something is the more energy it's going to have so conversely because the transition state has so much energy it's very unstable you have to add enough energy to the reactants so they're able to form the transition state and that is the activation energy so once you've gotten the reactants up to actually to actually form the transition state then the reaction doesn't need more energy it'll proceed and form the products very very quickly if it's an exergonic reaction then the reactants have more free energy than the products have so you add in the activation energy to reach the transition state and then when you complete the reaction and form the products you're releasing all of the energy um all the activation energy that have been used to form the transition state and also some additional energy so everything you put in you're releasing plus some and that ends up with the products having less free energy than what the reactants did so every spontaneous reaction needs the activation energy to occur non-spontaneous reactions still also have activation energy so every reaction needs the activation energy to be put in before the reaction can proceed so this is the reason why even though your reaction is spontaneous it might take a real long time to happen because it's waiting for activation energy also if you have a non-spontaneous reaction and the products would spontaneously decay back to their reactants that might take a very long time because again you need the activation energy for that uh unstable product to actually decay in general for reactions that are occurring just kind of in the environment the energy for the activation energy is coming from heat right so heat means well i guess it just means the movement of molecules and we measure that using temperature but that's just an average of the speed with which all the molecules are moving in whatever object you're measuring the temperature of so when objects are moving around very quickly when molecules are moving around very quickly they have a lot of energy and that creates a lot of heat or you uh you sense that as a lot of heat when those molecules collide with each other some of the force that they have is going to be released and that can provide activation energy for a reaction to occur but not only do the molecules have to collide with enough force to equal the activation energy but also they have to collide in the right orientation so for this reaction here between a and bc you're going to end up having b attached to a in the products for a to make a b that means that if you're having a and bc just kind of floating around uh in a liquid or in the air and they're going to collide with each other to make this reaction happen they have to collide with the b end of bc hitting a right a has to hit b if the orientation is reversed and a hits c instead that doesn't help you because a doesn't need to react with c a needs to react with b so it has to hit b and it has to hit b with enough energy um or enough force that the activation energy is released and you can form the transition state so it's kind of hard to get to the transition state when you don't have something else to help when you're just relying on random collisions between molecules being in the right orientation and having enough force to release enough energy to stay uh to reach that transition state enzymes are basically solving that problem for organisms enzymes work by lowering the activation energy and they do that by stabilizing the transition state so instead of needing to put in this much activation energy to make a spontaneous reaction proceed with an enzyme you might only need a tiny fraction of that amount only a little bit of activation energy is needed and then the reaction can proceed so that means the reaction is going to happen way way faster with the enzyme if you didn't have enzymes most of the reactions that we rely on that are spontaneous would not happen quickly enough for our purposes some of those would take days some of them would take years but even if it's something that would only take days to occur spontaneously without an enzyme you can't wait around for days to break down glucose to get energy out of it out of it has to happen quickly you need things to happen generally on the scale of milliseconds reactions in the body and in a cell have to occur so quickly that you're measuring it in milliseconds otherwise you're not producing enough product quickly enough to actually meet the cell's needs and the cell is going to die an example of that is the biosynthesis of heme heme is the uh it's the chemical group in hemoglobin that actually binds oxygen and hemoglobin is the protein in red blood cells that carries oxygen around right so your red blood cells are full of this protein called hemoglobin that binds oxygen to carry it around your body and within hemoglobin it's a specific chemical group called heme that is actually binding the oxygen so here you have some precursors to heme the body has to make heme um so it starts with this precursor uroporphirinogen 3 and it's going to perform a reaction on that to convert it to copro porphyrinogen 3 and the only difference there is replace replacing this acetyl group with a methyl group replacing the ch2coo minus with just a ch3 in the methyl group this is actually a spontaneous reaction so it will occur by itself you technically might not need an enzyme to make it happen but we measured how long it would take for it to occur we measure that in half and the half-life for this reaction is 2.3 billion years so if you had what that means is if you had one gram of europorphinogen 3 and you waited 2.3 billion years you would have half a gram of coproporefrontage in three and half a gram left of your reactant so you cannot afford to wait for billions of years to make heme you need it today and that's why you need an enzyme to catalyze that reaction to lower the activation energy for the reaction to make it go much much faster so enzymes have a variety of ways that they can work a variety of strategies that they use to lower activation energy uh one thing that they can do is just hold the reactants near each other and in the right orientation so instead of you having to randomly wait for the molecules to hit each other in the right orientation the enzyme will actually hold them in the right orientation right next to each other and that makes it easier for them to react lowers the activation energy you can also have enzymes changing the shape of the reactant so for instance they might bend a reactant to put stress on a bond uh that means when the bond is stressed it's more likely to break or it's easier to break it um so if you need to take something off one reactant and add it to another then you could do something like that to lower the activation energy and make the reaction occur more quickly another thing enzymes can do is change the local chemical conditions so for instance some reactions will go quickly at a low ph but not at a high ph some reactions will go quickly if water is there some reactions will go quickly if water is not there but in the body you always have water and ph is 7. in a cell you have water around 75 percent of the weight is water and you have ph 7 neutral ph so if you have a reaction that goes fast at a ph of 2 but you only have ph 7 in the cell in order to make that reaction happen quickly an enzyme can make basically a little pocket with a ph 2 for that reaction to occur and it kind of sticks the reactants into that little pocket and that lowers the activation energy makes the reaction happen much more quickly also unknown stuff so we know enzymes can lower activation energy by holding reactants in the right orientation close together by changing the shape of reactants by stressing bonds and by altering local chemical conditions but there's also other ways that they lower activation energy and we do not know what they are um so here's some basic vocab words that are related to enzymes first you have a substrate which you're probably familiar with we you're probably familiar with these from general biology actually but we'll just go back over them just in case so a substrate is the reactant that the enzyme is actually going to bind to and catalyze a reaction with either catalyzing the substrate to react with another reactant or catalyzing the substrate to be broken down into smaller bits every enzyme has an active site which is the part of the enzyme that is actually doing catalysis so the substrate is always going to bind the enzyme at the active site and then the enzyme will do will perform the catalysis right there so in the enzyme the amino acids that are at the active site are the most important ones if you change those it's very likely that the enzyme will lose its function some enzymes have cofactors which is just a molecule the enzyme needs in order to function correctly you can have inorganic cofactors which would be like the trace metals you could also have organic cofactors which are usually classed as vitamins um and they also have a special name which is coenzyme so an organic cofactor is a coenzyme an inorganic cofactor is not a coenzyme some enzymes will also have a prosthetic group which is a group of atoms that is attached to the enzyme generally covalently and it's this attachment is not an amino acid so it's not actually part of the protein right so cofactor is usually going to have kind of a loose association with the enzyme a prosthetic group is going to be more permanently attached to the enzyme usually using covalent bonds there's a lot of different prosthetic groups that can be added to enzymes it could be a sugar could be a phosphate group and a lot of other things as well the phosphate group itself is very common to add to enzymes so you can have enzymes that are phosphorylated or not phosphorylated usually that's used as kind of an on off switch so that the enzyme is not active but then you add a phosphate group to it and now it is active so in this image here this is an enzyme this is an enzyme that breaks down protein this is a substrate for that enzyme so this is the reactant that the enzyme is going to break down and the substrate binds to the enzyme right here at the active site and these three colored amino acids in the enzyme are the active site amino acids that are actually doing the catalysis then this enzyme might also have a cofactor somewhere or a prosthetic group attached to it that's not shown in the diagram so here's a diagram of basically how enzymes uh how enzymes work so here you have an enzyme with its active site right here this is its substrate um this substrate is a polysaccharide actually so this substrate is going to bind to the enzyme at the active site then the enzyme is going to change the shape of the reactant in this case stressing this bond between these two sugars in the polysaccharide by bending it once the bond is stressed it's very easy for the bond to break then so the activation energy is lowered because this bond has been put under a lot of stress and it is going to break and then you have these two individual sugars that are gonna that are the product of the reaction that will then leave the enzyme and the enzyme is then ready for a new polysaccharide to bind so it can catalyze another reaction so enzymes are also crucial for capturing energy from exergonic reactions and storing it um as atp so in order to capture exergonic reaction energy and store it what enzymes have to do is couple the exergonic reaction that releases energy to an endergonic reaction that will absorb that energy so in the first exergonic reaction you're releasing your energy that energy is used to make the second the endergonic reaction proceed and one of the products of that endergonic reaction is going to be atp so the energy released in the first reaction powers the second reaction and ends up in one of the products usually atp atp here's atp atp is synthesized from adp and a free phosphate group so when you have this adp and a free phosphate group if you put in energy you can attach that free phosphate group to adp that gives you atp and then you can use the atp breaking off that last phosphate group to release energy and that gives you back your adp and your free phosphate so right here where you're putting in energy to attach the free phosphate to the adp and get atp this energy is going to come from some exergonic reaction an enzyme is going to ultimately transfer that in energy from the exergonic reaction to atp atp has it has a lot of energy in its bonds especially the ones between the phosphate groups and it takes a lot of energy to attach that free phosphate to adp and make the atp you get a lot of energy out when you break that bond so you have to put a lot of energy in in order to make that bond in order to get that much energy you usually have to use a particular kind of reaction called a redox reaction redox is short for reduction reduction oxidation um reduction means gaining an electron and oxidation means losing an electron so reduction oxidation reaction or redox reaction is one where an electron is transferred from one compound to another one of those compounds has gained the electron and is reduced the other compound lost the electron and is oxidized so redox reactions are actually really common just any time an electron moves it's a redox reaction a lot of the time they involve oxygen and when they were first discovered the only ones that we knew about involved oxygen so that's why it's called oxidation but now we know they don't they don't have to involve oxygen um and i'll just note that in chemistry the definition of redox is more complicated than this but we don't we don't need the complicated definition we just need our definition um so for our purposes reduction is gaining an electron that's called reduction because the charge goes down when you gain an electron so it's reducing charge and oxidation is losing an electron [Music] if you say that a molecule has been reduced that means that it gained an electron any molecule that is going to be reduced by gaining an electron is called the electron acceptor and a molecule that has been oxidized has lost an electron and we call that molecule the electron donor so you're going to have an electron going from the electron donor to the electron acceptor in a in a redox reaction the one of them becomes oxidized the other becomes reduced when the electron is transferred you always have reduction in oxidation occurring together right if an electron is going to leave from one compound it's going to have to go to another compound so you can't have just one without the other [Music] a great ammonite for redox reactions is oil rig oxidation is losing reduction is gaining so oil rig stands for oxidation is losing reduction is gaining personally i always have to use oil rig to remember which is which it gets confusing sometimes but just remember oil rig and that that'll help you keep straight what what is what what's reduction what's oxidation what's reduced what's oxidized um and finally i'll note that a lot of the time um it might not look like an electron is being transferred in a reaction but a hydrogen is being transferred if a hydrogen atom is being transferred in a reaction that means an electron is transferred as well because every hydrogen atom is nothing but one proton and one electron a lot of the time you may see redox couples used to write compounds that are reduced or oxidized in a reaction in a redox couple you just write the oxidized form of that substance and then a slash and then the reduced form with the oxidized form always first so for an example you have the reaction to form water from hydrogen and oxygen which is also actually classed as a redox reaction um because the electrons end up not being equally shared between hydrogen and oxygen in water the oxygen is kind of hogging the electrons so it's like it's stealing them from hydrogen in a way so in order to form water you're going to combine two hydrogens with one oxygen which they always write that as half of molecular oxygen because oxygen does not ever exist just as a single oxygen in nature it always exists as part of some other compound if nothing else it exists as molecular oxygen o2 so half of an o2 plus a molecular hydrogen equals a water what's actually happening here is that oxygen is thieving some electrons from hydrogen because oxygen attracts electrons to itself very strongly and hydrogen does not so you're actually having one electron from each of these hydrogens kind of leave the hydrogen and go to the oxygen so when the electrons leave hydrogen that means that hydrogen is being oxidized it loses its electrons oxygen is gaining the electrons so it's being reduced um so that leaves you with once the hydrogen has left it has lost the electrons that leaves you with uh h plus a hydrogen minus an electron is a proton or h plus and this oxygen once it has picked the electrons up it gains a charge so it goes from being just o to o2 minus once it's taken up two electrons from each of these one from each of these hydrogens and you put those together and you get water where the electrons are mostly on the oxygen and not very much by the hydrogen so if we were to write this the situation kind of for the hydrogen and the oxygen in this reaction as redox couples you would write 2h plus slash h2 for hydrogen so the oxidized form is first once once hydrogen has lost its electrons it is oxidized so its oxidized form is 2h plus h plus because they're a 2h plus because there's two hydrogens there and the reduced form is h2 or molecular hydrogen for oxygen um again you're always writing the oxidized form first the oxidized form is actually where oxygen starts off at one half o2 and then it ends up oxidized in water as h2o sorry it ends up reduced after gaining those electrons from hydrogen as h2o and water we can measure um the potential of a compound to be oxidized or reduced in a redox reaction using the reduction potential which is abbreviated as e or e naught prime at standard conditions so reduction potential is the tendency of a substance to be an electron donor or an electron acceptor as measured in volts and e naught prime is the reduction potential at standard conditions so ph 7 temperature 25 degrees celsius atmosphere 1 atmosphere of pressure and all reactants and products at 1 molar concentration when reduction potential goes up and is a bigger number that means the substance is better as an electron acceptor so it's easier for it to take electrons if a substance is good at accepting electrons that means it's a strong oxidizer it's going to take the electrons from something else and gain them for itself in the process oxidizing whatever had its electrons stolen another word for the reduction potential is the electron transfer potential uh so anytime you're going to have two substances reacting together as a in a redox reaction you have to compare the reduction potential to see who will be reduced and who will be oxidized the substance that has the smaller reduction potential is going to give electrons to the to the substance with the larger reduction potential so the substance with the smaller reduction potential will be oxidized the substance with the larger reduction potential will be reduced by gaining electrons so if you look at hydrogen and oxygen um those redox couples the reduction potential for the hydrogen redox for the hydrogen redox couple is negative 0.42 volts the redox potential of the oxygen redox couple is 0.82 volts um so negative 0.42 volts if you look on the scale there is pretty positive it's not the most positive but it's pretty far up on the positive end or it's we use the concept of reduction potential to measure how likely a substance is to accept or donate electrons in a redox reaction that's measured using volts so e is the abbreviation for reduction potential and e naught prime is the reduction potential at standard conditions in general if you have a bigger reduction potential or a bigger e value that means the substance is better at accepting electrons and is likely to oxidize other substances by stealing their electrons if the substance has a smaller e value that means it is better at donating electrons it is likely to be oxidized and to reduce something else by giving electrons to it and another name for the reduction potential is the electron transfer potential so you might see it called electron transfer potential if you're looking at some other source so whenever two substances are coming together for a redox reaction in order to know who is going to be reduced and who is going to be oxidized you have to compare the reduction potentials for those two substances right so the the substance with the smaller e value is going to give electrons to the substance with the larger e value so the smaller uh the substance with the smaller e value um that is donating electrons is going to be oxidized and the substance with the larger e value that is receiving electrons is going to be reduced if you look at hydrogen and oxygen um substances are always written as redox couples when you're writing their reduction potential so for hydrogen the redox couple is 2h plus slash h2 and that has a reduction potential of negative 0.42 volts whereas oxygen has a reduction potential of positive 0.82 volts so if you look at those where those values are on um on this diagram showing different uh reduction potentials for different redox couples you'll see that hydrogen is pretty close to the top with negative 0.42 which means that it's a very good donator of electrons that's a very small value for reduction potential so it's very easy for hydrogen to donate electrons to something and to be oxidized by losing its electrons oxygen on the other hand is very close to the bottom of this diagram with a positive reduction potential of 0.82 that's a very positive reduction potential there's not much that has a reduction potential more positive than oxygen has so that means that oxygen is very good at accepting electrons it's very likely that oxygen will oxidize something by stealing electrons from it actually there are better electron acceptors than oxygen but none that are relevant in biology so in organisms oxygen is the best electron acceptor that you can possibly use it's the strongest electron acceptor that can be used if you have two substances that are going to have a redox reaction together um and they're very close to each other in their e values that means that in general you're not going to have a lot of energy exchanged between those two substances during the reaction and there's not going to be a big change in free energy so there's going to be a small delta g if the substances have e values that are close together if the substances have e values that are very far apart from each other they're going to be there's going to be a lot of energy transferred in that reaction and you're going to have a very big delta g in general so you can use e to actually estimate delta g um so in general when electron carriers are used in a reaction um you're gonna start let's see let me get my pointer you're gonna start here with nad plus that does not have electrons on it um [Music] that is going to be used by an enzyme as a cofactor um that enzyme is going to load the nad plus with electrons and it gives you nadh so you start with nad plus load with electrons and then you have nadh that nadh is going to travel to a different enzyme and bind that enzyme as a cofactor um and that enzyme is also going to have another reactant associated with it which is something that's going to pick up that electron or those electrons from the nadh um and so you're going to have this enzyme transferring electrons from from the nadh to the uh substrate that is going to pick up the electrons and at the end nad plus is released again it's ready to be recharged with more electrons next we'll talk in a little bit more detail about atp or adenosine triphosphate which is the main molecule that cells use to store energy they don't use it to store energy in the long term only in the short term um so most atp is used pretty quickly after it's made if cells are going to store energy for uh for the long term they're going to use other molecules to do it generally polysaccharides like starch or glycogen would be used there's also other ones that microbes use there's a lot of different ones that microbes use to store energy but always polymers are used to store energy and usually they're polysaccharides but they could also be lipids in addition to using atp for energy cells for short-term energy cells can also use other things like gtp or coenzyme a which is abbreviated coa um gtp is closely related to addition to atp or adenosine triphosphate um so adenosine triphosphate is an adenosine with three phosphate groups added to it it's very similar to a nucleotide so this part of the atp well here's the whole atp molecule this part here is the adenosine it's a sugar and a nitrogenous base and then you also have three phosphate groups attached to that so that's atp tp for triphosphate [Music] when you hydrolyze atp you are breaking off one of these phosphate groups the bonds between these phosphate groups have a lot of energy in them so when you break these bonds a lot of energy is released [Music] and you usually use water to do that which is why it's called atp hydrolysis so if you combine atp with water the water can remove that last phosphate group and you'll be left with adp and a free phosphate adp is adenosine diphosphate because it has two two phosphates on it uh and that is exergonic so if you're going to use atp to get energy out you remove one of those phosphates in atp hydrolysis energy comes out as well when you break the bond between that phosphate and the rest of the molecule and you're left with the free phosphate and with adp that has two phosphates on it um then in your catabolic reactions you're going to be taking energy in from nutrients and using it ultimately through redox reactions to attach a free phosphate to the adp which gives you back atp okay so now we'll get into the specifics of how atp is generated through catabolism we're only going to be focusing on carbohydrate catabolism today you can also catabolize proteins and lipids to make atp and we won't really talk too much about that but the process for lipids and for proteins is related to the process for cover for carbohydrates so you have three big processes that go on in carbohydrate catabolism glycolysis fermentation and respiration so you're always starting with glycolysis no matter what else you do in glycolysis you convert glucose to pyruvate and you also generate a small amount of atp since glycolysis is always the first step you do no matter what else you're going to do sometimes glycolysis is also counted as a part of the other processes fermentation and respiration so fermentation is can be defined in a variety of ways but a good definition for fermentation is using carbs for energy without oxidative phosphorylation which is a process within respiration so it's basically using carbohydrates to make energy without using respiration fermentation requires pyruvate from glycolysis so you have to do glycolysis before you do fermentation um a benefit of fermentation is that it doesn't require oxygen the way that respiration does or a substitute for oxygen um a limitation of fermentation is that it actually does not make atp the benefit of fermentation is that it lets you do glycolysis again and glycolysis makes atp so we'll talk about uh how how those processes are related to each other more presently and then after we go through that we'll get into respiration which is using pyruvate from glycolysis to make a lot of atp it also requires oxygen or something to substitute for oxygen um you have three other processes that are a part of respiration they are pyruvate oxidation the krebs cycle also called the citric acid cycle and then oxidative phosphorylation at the end where you're making most of your atp you have two basic types of respiration aerobic and anaerobic aerobic respiration is respiration that requires oxygen and anaerobic respiration is respiration that uses something else to substitute for the oxygen so in this diagram here this is giving you a basic summary of carbohydrate catabolism you always start with glycolysis in which glucose is converted to pyruvate then you can either do fermentation or respiration if you're doing fermentation um then you're basically you're basically taking the pyruvate converting it to something else it could be any of a number of things and you are regenerating your nadh to nad plus so that you can do glycolysis again and make a little bit of atp but fermentation itself does not make atp fermentation just lets you do glycolysis again um if you're doing respiration then the pyruvate from glycolysis is going to go into pyruvate oxidation which would be on the diagram right here even though it's not labeled um after that you're going to go into the krebs cycle also called the citric acid cycle and after that you go into oxidative phosphorylation which is this part of the diagram down here where you're making most of your atp okay so first we'll look a little bit more at glycolysis which occurs in the cytosol um glycolysis all the reactions in glycolysis are shown in this diagram here so as you can see it's pretty complicated there's like 10 different reactions in there you do not need to know all that stuff at all ultimately what's happening here is you're starting with glucose you are splitting glucose into two so glucose has six carbons in in it when you split it into two you get two molecules that each have three carbons in them and then you're continuing to convert those molecules until they end up as pyruvate at the end so you're basically taking one glucose and converting it into two pyruvates in that process you use atp at the beginning you have to transfer phosphate groups to glucose in order for this to proceed and those phosphate groups are coming from adp or from atp sorry um then once glucose has been split into two then you uh get into the reactions that actually yield atp and you transfer those phosphate groups back to a to adp to make atp so that ultimately you're making twice as much atp as what you had to use so in the first part of glycolysis you use atp in the second part of glycolysis you make atp overall you're making two atp you have to use two and you make four which means that overall you make two another thing that you make here is nadh from nad plus so nad plus is going to be required in one of these steps um you're going to transfer electrons from the from this glycolysis intermediate to nad plus which gives you nadh this is a really important step if you don't have nad plus then you can't continue with glycolysis you have to have nad plus and glycolysis gives you nadh so once you've done glycolysis and you have nadh you have to do something with that nadh to get it back to nad plus you have to use those electrons somehow so you can get back the oxidized form in plus and do glycolysis again if you can't do that glycolysis will stop and you will not be making more atp so this idea that once you've reduced nadh to innate sorry once you've reduced nad plus to nadh that you need to oxidize it back to nad plus that's redox balance so the textbook talks about that as redox balance just basically when you oxidize something you need to reduce it to continue using it or when you reduce something you need to oxidize it again to continue using it so overall what we're getting out of glycolysis is our pyruvates two of them for each glucose two atps and two nadhs you can also have other sugars that are not glucose do glycolysis in order to have some other sugar interglycolysis you have to make it look like glucose or like one of the intermediate products for glycolysis so the simplest thing you can do after doing glycolysis is fermentation which also occurs in the cytosol in fermentation you're taking the products of glycolysis and using them in a way that gives you back nad plus from nadh it can be just one reaction or it could be multiple reactions but it's always going to be much simpler than the alternative respiration because it's just one process instead of like three in one um it also does not require oxygen so as long as you have enough stuff to do glycolysis and you have some enzymes you can do fermentation you don't need extra things so it's easier to do if you're in an environment that doesn't have a lot to offer you uh but fermentation doesn't make any atp in general there's a lot of different reactions that count as fermentation actually and a few of them do make atp but almost all of them do not so the main benefit of fermentation is just that it's letting you do glycolysis again fermentation is requiring the pyruvate from glycolysis and the nadh from glycolysis and it's giving you back the nad plus so in this diagram here the first half is glycolysis in which you are converting glucose to pyruvate you're also making atp and you're making nadh from nadplus the second half is fermentation where you're regenerating nad plus from the ending from the nadh so you take the pyruvate from glycolysis you're going to convert it to something else in this case lactate but it could be a lot of different things and you're also using the nadh that you made in glycolysis you're taking the electrons off of the nadh and putting it onto whatever fermentation product this is and that means that you're left with nad plus then nad plus goes back to glycolysis to participate in glycolysis by picking up electrons again so fermentation is basically a way to let you cycle nadh back to nad plus so you can continue doing glycolysis that is the benefit of fermentation so that allows the salt to maintain redox balance basically meaning that for every nadh you make from nad plus you also make nad plus back again right so you if you convert nad plus to nadh you convert it back to nad plus um so as i mentioned fermentation is pretty diverse there's a lot of different reactions that count as fermentation uh because fermentation is so broadly defined as just using carbohydrates to make energy but without doing respiration or without doing oxidative phosphorylation that means a lot of different things will count as fermentation what all the different fermentation reactions have in common is that they all use pyruvate pyruvate from glycolysis and they all use nadh to get nadplus back again most of them don't make atp there are a few exceptions to that and each of them is going to make some fermentation product which is generally going to be a waste product for the cell that makes it there's a lot of different things you can make you can make ethanol lactate or lactic acid you can make vinegar you can make a lot of different things some of the things that can be made in fermentation are useful for us some of them are harmful it probably depends on the context so if you're trying to make wine then it's not beneficial for you to have vinegar in there of course if you're trying to make vinegar it's beneficial to have vinegar so we use fermentation in industry a lot to make some of the different products that that we enjoy like like cheese and stuff and alcohol those are all made through fermentation there are different types of fermentation products every organism is able to ferment actually but a lot of organisms don't ferment very frequently you have a lot of organisms that can do respiration and fermentation and if you're able to do respiration you're always going to do that over over fermentation because it makes a lot more atp like a lot more atp so fermentation is pretty inefficient it does not make a lot of atp basically unless you do glycolysis again and glycolysis lets you get a little bit of atp if you're able to do respiration then you can make a whole bunch of atp very quickly so if organisms have the option to do respiration they will do that instead but if you run out of oxygen then you can't do respiration anymore and then it's useful to have fermentation it's something you can fall back on whenever you run out of the things you need for respiration so a lot of organisms that well for instance like yeast that makes ethanol or that makes a alcohol through fermentation yeast can respire also so if you're trying to have yeast ferment grain to beer you have to make sure that they're not allowed access to air if they have access to oxygen they're not going to do fermentation they're going to do respiration so you have to restrict their air access so they have no choice but to do fermentation and make ethanol okay so now we'll go through respiration starting with the first process which is pyruvate oxidation uh that occurs in the cytosol for prokaryotes but in eukaryotes it occurs in the mitochondrial matrix which is the innermost part of the mitochondria you can also call this process the bridge stage or the bridge step because it is linking glycolysis with the next process which is krebs or the citric acid cycle um so it's like it's pretty simple it's only one reaction so it's a lot simpler than these other processes which would be why it can be called the bridge stage sometimes basically with pyruvate oxidation you're taking the pyruvate from glycolysis and converting it to acetyl coa so and again the coa stands for coenzyme coenzyme a so this is coenzyme a with an acetyl group on it which has these two carbons so you take your pyruvate you combine it with coenzyme a and you get acetyl coa but pyruvate has three carbons in it and acetyl coa only has two in the acetyl group so that means you have one carbon that's left over that carbon is going to leave as carbon dioxide which is a waste product so you're technically splitting a carbon off of the pyruvate that leaves as a waste product as co2 and you're combining the remaining two carbons with coenzyme a to make acetyl coa this process also will uh load electrons on an nad plus to give you nadh so overall what you're making here is two acetyl coa for every glucose since every glucose makes two pyruvates you do pyruvate oxidation twice for every glucose so two acetyl coa is for every glucose and two nadhs for every glucose also for our carbon tracking we had six carbons and glucose then in glycolysis we split that in two so you ended up with two uh pyruvates each with three carbons uh now in pyruvate oxidation we're splitting it again one of the carbons from each pyruvate goes to co2 which means that from our original glucose two of the carbons are going to go as co2 in pyruvate oxidation and the remaining four two from each remaining pyruvate will end up as acetyl coa and then we go into the krebs cycle also called the citric acid cycle also called the tricarboxylic acid cycle i like to call it krebs because that's one syllable instead of uh you know a bunch but the book is referring it to to it as a citric acid cycle which is abbreviated cac this is occurring in the cytosol for prokaryotes and also in the mitochondrial matrix for eukaryotes the inner most part of the mitochondrion the krebs cycle is a much more complex series of reactions than pyruvate oxidation uh even more complex than glycolysis actually and it's a circular set of reactions where your initial reactant is regenerated as a product at the end so you're starting with this four carbon molecule oxaloacetate and you're going to add the carbons from acetyl coa to it that gives you a three carbon molecule citrate which is also citric acid so that's why this is called the citric acid cycle citrate or citric acid is the first product that you form and then that citrate is going to go through a lot of different steps actually more than what's shown here this is just a summary there's a lot of steps in here and eventually at the end it ends up as oxaloacetate again in some of these steps you're going to be taking carbons off of citrate citrate has six carbons two of those carbons are from the acetyl-coa ultimately from glucose each of those carbons is going to be removed as a co2 and leave as a carbon dioxide so by the end you're left with your four carbons again in oxaloacetate another thing you're doing here in the krebs cycle is making atp a little bit actually technically you're not making atp you're making gtp but they're real real similar um is basically guanosine instead of adenosine so so we generally will frequently use the terms uh interchangeably so you don't need to know that the krebs cycle or the citric acid cycle makes gtp specifically atp is good enough and finally what the krebs cycle is doing is making a bunch of electron carriers or i should say reducing a bunch of electron carriers all right so you have nad plus here here and here so nad plus is being reduced to nadh at three different points in the krebs cycle and you also have an fad being reduced to fadh2 so this is the first time we're seeing an electron carrier other than nadplus play a role here um in in catabolism overall for the krebs cycle uh you are converting those carbons from acetyl-coa into carbon dioxide and you are making electron carriers um for every glucose you're going to be making six nadhs and two fadh2s and two atps and having um ultimately for every glucose for co2 released then we go into the final process of respiration which is oxidative phosphorylation oxygen phosphorylation means using an electron transport chain to make atp for prokaryotes this is happening in the cell membrane in eukaryotes it's happening in the inner mitochondrial membrane which is the membrane that bounds the mitochondrial matrix first we'll look at the electron transport chain and then we'll look at how that's used to make atp the electron transport chain requires all of those electron carriers that we reduced in the previous steps of respiration and in glycolysis so all the nadhs we made and the fadh2 that we made they're all coming here to the electron transport chain and what they're doing is dropping their electrons off at the electron transport chain the electrons are moving along the chain they're used to pump hydrogen ions across the membrane which is protons across the membrane and at the end the electrons are added to the final electron acceptor which is oxygen so this is a diagram of oxidative phosphorylation actually the whole thing this diagram is for eukaryotes so this is the inner mitochondrial membrane this is the outer mitochondrial membrane the mitochondrial matrix would be in here and this is the little space between the membranes of the mitochondria um these big protein complexes that are embedded in the inner membrane are the protein complexes of the electron transport chain so you're going to have your electron carriers nadh and fadh2 come in and drop their electrons off at the electron transport chain those electrons will be transferred from complex to complex to complex along the electron transport chain at the end they are added to oxygen which is the final electron acceptor or the terminal electron acceptor and at each stage of the journey as the electrons travel on the electron transport chain they are used to pump hydrogen ions or protons across the membrane for eukaryotes that means these hydrogen ions or these protons end up in the intermembrane space between the two mitochondrial membranes but for prokaryotes that means that the the protons are ending up outside of the cell um which means that they're creating the proton motive force then you're going to use that proton motive force to make atp this enzyme here is actually using the proton motor force to make atp at the end so the whole point of this electron transport chain is just to pump these protons and make a concentration gradient for protons across a membrane um right then at the end after the electrons have been dropped off on the electron transport chain the electron carriers are now oxidized again so you have nad plus again and fad again and those are ready to go back to the previous stages of respiration anti-glycolysis so that you're maintaining redox balance and the whole thing can keep going so looking in more detail at the electron transport chain um you have generally four different uh protein complexes that are part of the electron transport chain it actually varies from organism to organism especially for microbes you can have strange electron transport chains the different complexes can be different you can be missing one even and the components of each complex can be different from organism to organism then in addition to those uh protein complexes you're going to have cofactors that are carrying electrons along the electron transport chain so in general each one of these complexes is going to have one or more cofactors inside of it that is actually going to accept the electron from the electron carrier and then transfer it to its next location some of those cofactors like this one here q that's ubiquinone they're actually going to travel through the membrane to the next complex uh carrying electrons to the next complex in the electron transport chain then the electrons would hop from cofactor to cofactor on that complex until they get to the next transporting cofactor then at the very end the electrons are added to oxygen when you add those electrons to oxygen you're making water so some of those cofactors are called are classed as flavins some of them are classed as cytochromes and then you also have ubiquinone or quinones in general those those cofactors are always going to have different redox potentials and the redox potential is always going to go up as you're moving along the electron transport chain so that as you go each cofactor is better and better and better at accepting electrons until you get to oxygen which is the best at accepting electrons some of those electron carry or some of those cofactors are able to carry hydrogens so they're carrying electrons as hydrogens with an electron and a proton some of them are only able to carry electrons not the protons if your electrons are coming from nadh they're going to enter the electron transport chain at protein complex 1 if they're coming from fadh2 they enter at protein complex two depending on where they enter they're going to travel further on the chain all right so the electrons the interim complex two don't have as far to go they're skipping complex one um and that means that you're not going to have as many opportunities to use these electrons from fadh2 to pump protons so the electrons that are coming from nadh pump the most protons the electrons that come from fadh2 pump less protons and contribute less to the proton motive force that you're generating once your electrons have made it onto a complex one or complex two depending on if they come from nadh or from fadh2 they're going to be transferred ultimately to ebiquinone and ubiquinone is going to diffuse through the membrane carrying the electrons with it to complex to complex three and it drops them off there um from complex three another cofactor cytochrome c is going to be carrying the electrons to complex four then complex four uh is able to add those electrons to oxygen to make water that's actually a little complicated because in order to do that you have to take molecular oxygen o2 and split it in half so complex 4 is actually splitting electron splitting oxygen in half and then adding electrons to it to make water you're also having some protons come in from from the cytosol or from the mitochondrial matrix depending on if this is a eukaryote or a prokaryote so half of an oxygen plus two protons plus two electrons that's water because one hydrogen uh is one proton and one electron um at certain stages here you're pumping uh your pumping electrons so complex 1 pumps electrons complex 4 also pumps electrons and then ubiquinone is also able to pump electrons so it picks up electrons as hydrogens it picks up an electron and then a proton as a hydrogen and then when it drops it off it only drops the electron off at complex three the extra proton it drops off on the other side of the membrane so at these three points you are pumping hydrogen across or hydrogen ions which are protons across the membrane and establishing the proton motive force um different organisms to have can have different combinations of these complexes but almost every organism is going to have complex three it's the most conserved complex so the most the the one that changes the least and is most commonly found as these electrons move along the electron transport chain they are losing some of their energy and the energy is being converted to the proton motive force so on this graph we have the free energy of the electrons on whichever carrier they're on at them at whichever point we're talking about on the electron transport chain um so they're starting off here if they're coming from nadh they're starting off on complex one and they have a lot of energy if they're coming from fadh2 then they come then they start off on complex two then they get transferred to uvequinone that takes them to complex three they hop from carrier or cofactor to cofactor on complex three every time they hop they're losing a little bit of energy the free energy of those electrons on the cofactor is going down a little bit and a little bit in a little bit then they're carried on cytochrome c to complex four they continue losing energy and at the end they are added to the final electron acceptor or the terminal electron acceptor which in this case is oxygen for regular uh aerobic respiration so as as they proceed they lose energy that energy is used to pump protons and therefore the energy is being converted into the proton motive force uh in order to make this work the organism is exploiting the different redox potentials or the different reduction potentials of of the different cofactors and carriers that are being used to transport the electrons so when you start off on the electron transport chain the cofactors that are carrying electrons have lower reduction potentials and if you have a low reduction potential then it's hard it's hard for you to accept an electron but it's good it's easy for you to donate an electron so it's not very easy for these carriers at the start of the electron transport chain to accept the electrons that are being added to them but they are able to accept the electrons because the electrons have a lot of energy as you go electrons lose energy and the reduction potential of each next uh carrier gets a little bit higher and a little bit higher and a little bit higher until you end up at oxygen which has like the highest uh reduction potential of any uh compound that's relevant in biology um so that means that as you go along the electron transport chain the carriers are getting better and better at accepting electrons the electrons have less energy which means it's hard to accept those electrons when they don't have a lot of energy but since these carriers have a very high reduction potential and a very high ability to accept electrons they are able to accept them and oxygen is the most efficient thing the best thing you can use as the final electron acceptor because it has the highest reduction potential of any compound that's relevant in biology so you can use something else to accept the electrons at the end um if it's able to accept them but you're not going to be able to extract the maximum amount of energy from the electrons unless you're adding them to oxygen so here's another summary of the electron transport chain this one is shown for prokaryotes so here you have the outside of the cell and here you have the cytosol of the cell and here you have your complex one so nadh is going to come in and drop its electrons off at complex one that gives you back nad plus um those electrons are going to hop to ubiquinone which carries them to complex three if your electrons are coming from fadh2 then they're going to enter onto complex two and also be added to ubiquinone which carries them to complex 3. complex 1 is pumping hydrogen ions or protons outside of the cell ubiquinone is also dropping off protons outside of the cell then the electrons are going to travel from complex 3 on cytochrome c to complex 4 where they're going to be added to the final electron acceptor which is oxygen and that makes water then complex 4 is also pumping protons across the membrane as you go here the reduction potential of each uh complex and carrier is getting higher and higher so we start out with negative numbers and we end up with positive numbers at the end and then of course oxygen has the most positive number of all now for the second part of oxidative phosphorylation the part where you actually make the atp that's done by an enzyme called atp synthase atp synthase allows protons to cross the membrane down their concentration gradient and uses the energy of their passage to make atp so this is super similar to how the flagellar motors work they also let hydrogen ions flow down across the across the membrane down their concentration gradient and it uses the energy to rotate the motor atp synthase also has a component that rotates when hydrogen ions are crossing the membrane through it so here you have the structure of the atp synthase at the bottom here the part that's embedded in the membrane is the f naught unit and the top part is the f1 unit the f naught unit is the unit that's allowing protons to cross the membrane and then the f1 unit is the unit that's actually making atp so when these protons cross the membrane through the f through the f naught unit um then these proteins that are part of that unit called the c proteins are going to start rotating similar to the motor and the flagella that rotation is going to be transmitted through these gamma and epsilon proteins up to the f1 unit and then once that rotation is transmitted to the f1 unit the beta subunits here are going to start undergoing conformational changes so changing their shape a little bit so they're able to bind adp and the free phosphate and then when the motor rotates again and they change back to their initial confirmation they're going to synthesize atp from the adv a from the adp and the free phosphate so protons are flowing down their concentration gradient through the f naught unit that causes it to rotate the rotation is transmitted to the f1 unit then the f1 unit uses that rotation to make atp so this whole process is able to make quite a lot of atp um in general you're gonna have between three and four hydrogen ions pumped across the membrane for every atp that you make right so it takes um about three to four hydrogen ions flowing through atp synthase to make a single atp for prokaryotes how much it takes exactly depends on the organism the specific organism and it's also different for eukaryotes when you consider how many hydrogens you're able to pump for every electron on the electron transport chain you end up making about 34 atps for every glucose that you originally used for glycolysis it does depend on whether the electrons are coming from nadh or fadh2 because they enter at different points of the electron transport chain um but overall you're making about 34 atp ideally under like the most perfect conditions actually in real life you usually don't make all of those 34 atp um because some of those hydrogen ions and the proton motive force are being used for something else not for making atp right so you can use the proton motor force to operate flagella and if you're doing that then you're not using it to make atp if you're a eukaryote then you have a lot of different structures in the cell that all you know you have to transport things between them um and specifically some of the reactions to make atp are occurring in the mitochondria and some of them are occurring in the cytosol so right you have glycolysis on pyruvate oxidation in the cytosol you have uh sorry just like yeah both of those in the cytosol you have to take the products of those reactions and pump them into the mitochondria uh to do the krebs cycle which is inside the mitochondrial inner matrix uh and that takes atp and then also depending on what exactly you have in your electron transport chain that's going to affect how much atp you're able to make out of it so 34 atp per glucose is like an ideal value that a cell usually wouldn't reach but it would hopefully get like pretty close up to there in any case glycolysis makes two atp for each glucose if you're doing fermentation then that's all you're getting if you're doing respiration then you get not only those two atp but also the 34 atp from respiration um um well from oxidative phosphorylation and and a couple more actually from the krebs cycle so that's quite a lot of atp if you're doing if you're doing respiration versus fermentation and a final point i'll add here is that the atp synthase can run backwards if it runs backwards then it's going to pump hydrogen ions out of the cell instead of allowing them to flow in and it's not going to make atp if it's running backwards um but then it can be used to create the proton motor force so some organisms that don't do respiration are still going to have an atp synthase so it can help them make the proton motive force okay here's your overall summary for for respiration so you start with glucose this is shown in a eukaryote because it has the mitochondrion so you start with glucose that enters glycolysis and glycolysis is going to be converted to pyruvate pyruvate is then going to enter pyruvate oxidation and be converted into acetyl-coa acetyl-coa will enter the krebs cycle or the citric acid cycle the carbons that are in the acetyl-coa that had come from glucose are going to leave as carbon dioxide you also had a carbon leaf as carbon dioxide and pyruvate oxidation and the main benefit of the krebs cycle is that you're getting a lot of electron carriers you also make electron carriers in glycolysis and in pyruvate oxidation but you make a whole lot in the krebs cycle then all those electron carriers are going to enter oxidative phosphorylation they drop their electrons off at the electron transport chain those electrons hop from complex to complex along the chain they're used to pump hydrogen ions across the membrane and ultimately the electrons are added to oxygen to make water then all those uh all of those hydrogen ions or protons that have been pumped across the membrane are going to be contributing to the proton motive force and they'll be used by atp synthase to make atp so you have some different options for how organisms can do respiration we just talked about aerobic respiration which is the main kind of respiration that you have but you also have anaerobic respiration that some organisms can do it's basically the same process but you're using something other than oxygen for the final electron acceptor or the terminal electron acceptor different organisms can use different things you could use nitrate you could use iron you could use sulfate and a lot more options as well [Music] all of those options are going to have a less positive reduction potential than what oxygen has which means they're not as good at accepting electrons which means they do not make as much atp so in order to make the maximum amount of atp you have to use oxygen if you're not using oxygen you're going to make less but the benefit is you don't need oxygen which sometimes is not around the diagram here is an example of an electron transport chain for anaerobic respiration in which the final electron acceptor is nitrate instead of oxygen and that has electrons added to it to make nitrite and water uh the typical organisms we're used to thinking about are chemo organoheterotrophs which means they're getting carbon and energy from organic compounds so those types of organisms are going to use an organic compound as the ultimate electron source for respiration usually they're going to be using glucose but they could also use something else so that means that all the electrons that are ultimately added to oxygen have come from glucose originally right they're added to those electron carriers and those electron carriers drop them off at the electronic transport chain but ultimately they came from glucose uh you also have chemolithotropes that use inorganic compounds to donate electrons as their energy source um so they would not be using glucose to do glycolysis they're going to have a completely different process where they're starting not with glucose but with something like hydrogen sulfide or iron or ammonia or molecular hydrogen and then they're using that to take electrons uh for their electron transport chain so respiration for those types of organisms is going to look very different from respiration for um for heterotrophic organisms that are using an organic compound a lot of the time chemolithotrophs can live happily in community with chemo organoheterotrophs especially the ones that are doing anaerobic respiration because the products of anaerobic respiration can then be the electron donors needed by the chemolithotrophs so uh as an example if you are a a chemorganoheterotroph who's doing anaerobic respiration and you're using sulfate as your final electron acceptor that means when you're adding electrons to that sulfate you make hydrogen sulfide while some chemolithotrophs use hydrogen sulfide as an energy source to donate electrons in the first place for their electron transport chain so that chemolithotroph would basically use the waste product from this anaerobic respire as an energy source so they can live well in communities together here you have the overall summary for carbohydrate catabolism you always start with glycolysis no matter what glycolysis makes a little bit of atp and it makes nadh you can then do fermentation you're taking the pyruvate from glycolysis and converting it to a fermentation product there's a lot of different ones you are not making atp most likely but what you are doing is using the electrons from nadh which gives you back nad plus which means you can do another round of glycolysis and make a little bit of atp you can also go the other route and do respiration after doing glycolysis in that case you're taking the pyruvate from glycolysis you're converting it to acetyl acetyl-coa in pyruvate oxidation in that step you're also losing one carbon that had been in glucose as carbon dioxide the other two carbons from the pyruvate um that had been in glucose are going to end up in acetyl coa and you're also generating nagh and pyruvate oxidation the acetyl coa from pyruvate oxidation is going into the krebs cycle or the citric acid cycle both of the carbons in the acetyl group are going to end up leaving as carbon dioxide and at that point all of the carbons in glucose will have been oxidized fully to carbon dioxide meaning all the all of their electrons that could be stripped have been stripped away and you're left with just the carbon dioxide you're also making a little bit of atp from the krebs cycle and you're making a lot of electron carriers all those electron carriers from glycolysis from pyruvate oxidation and from the krebs cycle are then going to enter oxidative phosphorylation they're going to drop their electrons off at the electron transport chain those electrons are going to travel on the electron transport chain losing energy at each hop until they're added to the final electron acceptor at the end which is oxygen for aerobic aerobic respiration or not oxygen for anaerobic respiration um in the process of being moved on the electron transport chain the electrons are going to be used to pump protons across a membrane either the mitochondrial membrane or the cell membrane uh and then those pumps um hydrogen ions or protons are setting up the proton motive force or proton gradient concentration gradient then atp synthase is going to let those hydrogen ions flow down their concentration gradient back across the membrane and use the energy of their transport to make atp then the final note is that the electron carriers that drop their electrons off at the electron transport chain are now oxidized back to nad plus and fad they're going to go back to glycolysis to pyruvate oxidation and to the krebs cycle so those processes can repeat again then this diagram is showing you how energy is changing as carbons and electrons that had been in glucose are moving into other molecules through the process of respiration so you start with glucose um which is here defined as free energy of zero it does not have a free energy of formation of zero but all these changes are being graphed as relative to glucose so that's why glucose is set as zero so first you have glycolysis in the initial steps of glycolysis you're using atp which means you're adding energy into this molecule uh that you're converting glucose from or two then in the later stages of glycolysis you are extracting energy out of that intermediate molecule some of the energy is going as electrons on nadh some of it is going into the bonds of atp so now you have less energy in pyruvate at the end of glycolysis than what you had in glucose some of the energy went into nadh as an electron some went into atp then you enter pyruvate oxidation or pyruvate processing as it's called here in which the pyruvate is converted to acetyl coa and you also have one carbon that had been in glucose leave as carbon dioxide so in this process you're losing a lot of energy the electrons from pyruvate are some of the electrons from pyruvate are being added to nadh so some of the energy that pyruvate had is leaving in this nadh then you're left with co2 that is basically completely stripped of energy fully oxidized and then you have acetyl coa which still has energy left in it but a lot less than what glucose has had as you see that acetyl-coa is going to move into krebs cycle or the citric acid cycle and it's going to ultimately lose a lot of energy throughout the citric acid cycle every time you have electrons being added to nadh energy is leaving the the original acetyl coa and going into the electron carrier you also have some energy entering atp and at the end you're left with both carbons and this acetyl-coa that had come from glucose leaving as carbon dioxide so when they leave as carbon dioxide they have been fully stripped of all of the energy that you can take from them and basically they are fully oxidized which means all the electrons that they had available to take you have taken and added to an electron carrier so next we'll briefly consider anabolism which is building bigger molecules from smaller um one of the most basic anabolic reactions or pathways that cells have is gluconeogenesis gluconeogenesis can be defined as making glucose from something that is not a carbohydrate so if you have a sugar of any type it's not too hard to convert it to glucose i mean it does depend on what type of sugar it is actually some are easier to convert than others but you can generally convert sugars to different form for to different sugars um in gluconeogenesis you're using something that is not a sugar to make glucose could be an amino acid it could be fatty acids or glycerol both of those the fatty acids and the glycerol come from fats in order to do this you have to take that source the amino acid the fatty acid or the glycerol you have to make it look like an intermediate of glycolysis or you have to make it look like oxaloacetate and then gluconeogenesis is basically glycolysis but backwards so if you're starting with glucose and going forward through the steps of glycolysis to end up pyruvate that is glycolysis if you're starting with something else like pyruvate or oxaloacetate and you're going backwards through the steps of glycolysis to get glucose out at the end that is not glycolysis that is gluconeogenesis um you have different react uh sorry different enzymes if you're going to do glycolysis you have one set of enzymes you need if you're going to do gluconeogenesis you have a completely different set of enzymes that you need to make it go backwards the other difference is that you need atp it doesn't make atp overall it uses atp overall in general if you have an amino acid or glycerol or something and you've converted it to make it look like an intermediate of glycolysis that means that it could enter glycolysis or it could enter gluconeogenesis depending on what enzymes the cell has available at the time if the cell has enzymes for glycolysis it's going to go into glycolysis if the cell has enzymes for gluconeogenesis it's going to go into gluconeogenesis mostly it would be determined by what the cell needs at that moment so if the cell needs atp then it's going to use that glycerol converted to an intermediate in glycolysis to make atp if the cell needs triggers to build its structures then it's going to send the glycerol into gluconeogenesis instead another important pathway for making sugars is the pentose phosphate pathway this is used to make five carbon sugars whereas glucose is a six carbon sugar the most important five carbon sugar is ribose you need ribose for nucleotides which means you also need ribose for electron carriers and for atp in the pentose phosphate pathway you're taking you're taking an intermediate from glycolysis glucose 6-phosphate and you are basically removing a carbon from it as as carbon dioxide and that gives you a five carbon sugar which is called ribulose 5-phosphate because it still has the phosphate from that glycolytic intermediate and then this ribulous biphosphate which is the actual product of penta of the pintos phosphate pathway can be used to make different uh five carbon sugars so it can make it can be used to make ribose but it could also be used to make other uh five carbon sugars that the cell would need but the main thing it needs it for is to make nucleotides for dna and rna this is also the first process that we've looked at that uses nadph so in the pentose phosphate pathway one thing that you do is take some electrons from the glucose 6-phosphate and add them to nadp plus which gives you nadph you're going to need that nadph for other processes that the cell does you need it to make fatty acids you're also going to need it once you have ribose to make deoxyribose for dna those are some of the main places that you need nadph but it's also used in other places and it also depends on what organism we're talking about uh photosynthetic organisms also need nadph for photosynthesis um for making amino acids you have a lot of different reactions that are used because every amino acid is going to need a different set of reactions to make it different organisms are able to make different amino acids any amino acid that an organism can't make is something that that organism has to get from its environment as a micronutrient for most amino acids uh the precursor metabolite to make the amino acid is an intermediate from glycolysis or from the krebs cycle or citric acid cycle um so oxaloacetate for instance is a precursor metabolite for several amino acids which means that in order to build that amino acid you're going to take the bulk of the molecule from that intermediate from glycolysis or from the krebs cycle so the carbons the carbon skeleton for the molecule is going to come from that intermediate then you have to add the amine group to it or the amino group which is the nh2 uh it's actually coming from ammonia though though from nh3 so from nh3 you're taking the n and two of those h's and adding them on to uh the precursor metabolite to make your final amino acid um so that's called amination so in the diagram here it shows a couple ways that that can happen either you have your precursor like oxaloacetate and you add the amine group to it in this case to make aspartic acid one of the amino acids that would be regular amination um but you could also do transamination in which you're stealing basically the amino group or stealing the amine group from another amino acid and adding it to your precursor metabolite to make your final amino acid so you can do it either way then for nucleotide anabolism we're not going to talk about it very much well not that we talked about amino acid anabolism very much but nucleotide anabolism is even more complicated than amino acid anabolism basically every nucleotide has your three parts the ribose the phosphate and the nitrogenous base um there's four different nitrogenous bases well five different nitrogenous bases actually you have purines some of them are purine some of them are pyrimidines so some of those bases have two rings in them and are classified as purines some of them have one ring in them and they're classified as pyrimidines and there's five different bases total for a g t c and u uh four for dna and four for rna so the ribose for the nucleotide is always coming from the pintos phosphate pathway the phosphate is always coming from atp and those bases are coming from different sources from a lot of different sources actually they can come from amino acids from intermediates from the krebs cycle from folic acid from carbon dioxide from ammonia and from other sources as well so in these diagrams here um you can see basic skeletons for each of these types of bases the purine base that has two rings and the pyrimidine base that has one ring and you have different parts of that molecule highlighted with different colors every color indicates a different source for that part of the molecule so for this uh basic skeleton of a purine base you can see that you have like five different sources for the molecules that are part of those two rings the sources would be different amino acids from folate this one here is from carbon dioxide so it gets quite complicated how to make those then we have fat anabolism um not lipid anabolism but fat anabolism so a fat is a type of lipid there's a lot of different lipids all the only thing they have in common to be defined as a lipid is just that they are not water soluble they are they are organic molecules that are not water soluble so that covers a lot of ground but we commonly think about fats of fat is a glycerol with three fatty acids attached to it and it can be made in this general way so first you would make the fatty acids they're going to be made by a protein called acell carrier protein or acp one acp is going to form kind of the basis for your fatty acid and then you're going to be adding additional little bits to it that are coming from additional acps um and the fatty acid is just a long chain of basically carbons and hydrogens with a carboxyl group in it somewhere so depending on how many acps you add that determines how long your fatty acid is going to be in this diagram here here you have your initial acetylacp that's forming the basis for your fatty acid and then you're going to take other acps and add a compound called melanate to them which has three carbons in it and then you're going to start adding that to the base acp in two carbon chunks so two of these carbons from the melonyl acp are going to end up on your growing fatty acid then you're going to repeat that cycle and add another two carbons to make it even a little bit longer and you just continue repeating that cycle and it gets longer every time until it's as long as you need it to be then you would combine that with three of those with your glycerol glycerol itself is going to be made from an intermediate of glycolysis and then that gives you a fat but for making other lipids you're going to use different pathways and remember this is more applicable to bacteria because bacteria use fatty acids for their membranes but archaea do not do that they use hydrocarbons instead and their lipids are made in a different way and finally we'll talk about how anabolism and catabolism are integrated with each other so a lot of these metabolic pathways that we're talking about are amphibolic pathways which means they can go both directions so a good example of that is glycolysis gluconeogenesis if it goes forwards that's glycolysis and that's catabolic if it goes backwards that's gluconeogenesis and that's anabolic so most of these pathways can go both ways and they're amphibolic the major exception would be electron transport chains they can only go one way never both ways everything else can go both ways so you can go forwards through the path in order to make atp or you can go backwards through the path in order to make glucose or other components that you need other macromolecules you need for the cell and the cell is always controlling whether the pathways it has go forwards or go backwards it depends a lot on the enzymes that are available you always are going to need one set of enzymes to go one direction and a different set of enzymes to go the other direction so if you only have enzymes available to do glycolysis then you cannot do gluconeogenesis if the cell starts making the gluconeogenesis enzymes and it stops making the glycolysis enzymes you're going to end up doing gluconeogenesis instead of glycolysis