|  
         Biology 
        C2005 Lecture 8 
         
           
         ::Free energy, 
        delta G and delta Go:: 
        We now have some idea of how the rate of chemical 
        reactions in the cell are speeded up so that they can occur in time frames 
        consistent with cell growth. But what about this problem of DIRECTION, 
        a problem the catalysts cannot address. Are all the 
        chemical transformations in these biosynthetic paths, for example, exergonic, 
        so that the direction of carbon flow from glucose is a spontaneous reaction? 
        The answer is no, quite the opposite. Most of the chemical transformations 
        needed in a biosynthetic pathway are by themselves endergonic, and will 
        not go from left to right unless something is done about it. Thus 
        the building of a new E. coli cell must deal with this energy problem, 
        and much of the cell machinery has indeed been devoted to the solution. 
        To understand the problem, we must discuss it in some more quantitative 
        detail, and for this purpose, the use of the concept of FREE ENERGY CHANGE 
        associated with a chemical reaction is very useful. 
         
          We can define a unit of 
        energy such that it is tied to the directionality of a chemical reaction 
        as follows: 
         
           
         
        For the model reaction A + B <--> C + D, written in the left-to-right 
        direction indicated: 
         
        IF Delta G IS <0 THEN A AND B WILL TEND TO PRODUCE C AND D. 
         
        IF Delta G IS >0 THEN C AND D WILL TEND TO PRODUCE A AND B. 
         
        IF Delta G IS 0 THEN THE REACTION WILL BE AT EQUILIBRIUM: NOT TENDING 
        TO GO IN EITHER DIRECTION IN A NET WAY. 
         
          In an energy diagram: 
         
        Note that the Delta G is independent of the route between the starting 
        reactants and the final products (say, 3 kcal/mole, for all 4 routes shown 
        here). 
         
        Free energy is that part of the energy change associated 
        with a chemical reaction that can be harnessed to perform work. 
         
         We can measure Delta G according to the following 
        equation [must take this on faith here]: 
         
        Delta G = Delta Go + RTln([C][D]/[A][B]) 
         
        where A, B, C and D are the concentrations of the reactants and the products 
        AT THE MOMENT BEING CONSIDERED. 
         
        This ratio is sometimes called Q (so Delta G = Delta 
        Go + RTlnQ).. Q is NOT the equilibrium constant, though it looks 
        like it...: 
         
         Here are the terms: 
         
        R = UNIVERSAL GAS CONSTANT = 1.98 CAL / DEG K MOLE 
        T = ABSOLUTE TEMP. (0o C = 273o K; Room temp = 22o 
        C = 298o K) 
        ln = NATURAL LOG 
        Delta Go = A constant, a QUANTITY RELATED TO THE INTRINSIC 
        PROPERTIES OF A, B, C, AND D. {Q&A} 
         
        The first term, delta Go, relates to the QUALITY of the reactants and products, and the second term, 
        RTlnQ, relates to the QUANTITY of the reactants 
        and products, how much of each is present. 
         
         What is this Delta Go? It is called 
        the: STANDARD FREE ENERGY CHANGE of a reaction. 
         
        One useful way to define of it is to consider the special case when all 
        the reactants and all the products are present at 1 unit concentration. 
        The change in free energy of this reaction is: 
         
        Delta G = Delta Go + RTln(1), or Delta G = Delta Go 
        +RT x 0, 
         
        or delta G = delta Go (a special case when all participants are at 1M) 
         
         So Delta Go is 
        the free energy change that occurs when all participants in the chemical 
        reaction are at unit concentration. What is unit concentration? 1 M, for 
        most reactants and products (water and hydrogen ions are treated differently, 
        as we'll see. ) 
         
         One way to think of this delta Go 
        is to picture 1000 moles of A, B, C and D in 1000 liters of solution. 
        So all components are at 1M. One mole of A + B is now converted to C +D. 
        The energy absorbed is the standard free energy 
        change. Note that the concentration of reactants has not appreciably changed 
        in this hypothetical condition. 
         
          Why make such a fanciful and arbitrary situation? 
        By defining the conditions for a STANDARD 
        free energy change, all reactions can be compared to one another, regardless 
        of the particular conditions; it puts them all on an equal footing. The 
        Delta Go reflects the nature of 
        the reactants and products without regard to their concentration. Note 
        that the actual free energy change of a reaction 
        does depend on these concentrations, and the 
        SECOND TERM of the equation for delta G takes these into account. {Q&A} 
         
        Please note from the above explanation that delta G and delta Go 
        are not the same thing. That distinction is important. 
         
        ::Equilibrium:: 
        Delta Go can be calculated, although not accurately, from tables 
        of free energies of formation from simple atoms or molecules, comparing 
        these values for the reactants and the products. But it is most easily 
        and accurately determined experimentally, by measuring the concentration 
        of the reactants and products at equilibrium. For at equilibrium, Delta 
        G = 0 and 
         
        Q = Keq, (a special case). So: Delta Go = -RTlnKeq. 
         
        If we measure A, B, C and D at equilibrium, let's say we get: [C]eq[D]eq/[A]eq[B]eq 
        =  
        2.5 x 10-3 
         
         Note very little C and D are formed from A 
        and B in this case. 
         
        Then Delta Go = -2 x 300 x ln (0.0025) = -600 x -6 = 3600 
         
        So the calculated Delta Go is +3600 cal/mole, or +3.6 kcal/mole. 
        So 3.6 kcal will be absorbed when 1 mole of A + B goes to C + D. Energy 
        is absorbed rather than released, confirming the lack of a tendency of 
        C and D to be formed from A and B. 
         
         That is, since the standard free energy change 
        is positive, this reaction does not tend to go to the right, but rather 
        to the left. That is, if we start with 1M A, B, C and D, then C + D --> 
        A + B. So A and B will build up at the expense of C + D. 
         
        Note: 
        If we write A + B --> C + D, Delta Go = +3.6 kcal/mole, then 
        we can also write: 
        C + D --> A + B , Delta Go = -3.6 kcal/mole (the equilibrium 
        constant for this C+D --> 
        A+B reaction is just 1/2.5 x10-3, or 400) 
         
        Note also, that if the reactants combine in ratios other than 1:1, we 
        can write: 
        aA + bB <--> cC + dD, Delta G = Delta Go + RT ln [C]c[D]d 
                      
                      
                     
                              
                    [A]a[B]b 
         
         ::Summary 
        of free energy changes:: 
        And to reiterate: the free energy change of an overall reaction is independent 
        of the route taken by the reactants, it could be direct or indirect [see 
        energy diagram with routes that go up or down to intermediates]. 
         
        The reaction will go to the right if delta G is <0 and to the left if 
        delta G is >0. At delta G = 0 the reaction is at equilibrium, and under 
        this special condition (delta G = 0) Q is equal to the Keq. 
         
         We stated that delta 
        Go is called the STANDARD free energy change and represents 
        the free energy change when these reactants and products are observed 
        to react with each being at a concentration of 1M, which is the standard 
        condition, by definition. However, biochemists make 2 exceptions to the 
        definition of these STANDARD CONDITIONS in the cases of water and hydrogen 
        ion concentration. Since these two components in a reaction are usually 
        constant in a biological reaction, they are defined 
        to be equal to 1 for the purpose of Delta Go calculation when 
        [H2O]=55M (pure water) and [H+] = 10-7 M (i.e., 
        pH7, or neutrality). Strictly speaking, one should acknowledge this use 
        of these 2 exceptions by designating the free energy change as delta Go' 
        rather than delta Go, but we will not bother to do that here. 
         
          All 
        chemical reactions have a Delta Go associated with them, a 
        value which can be written down in a book. Thus any two reactions can 
        be compared under the standard condition of unit concentration. 
         
        The equilibrium constant of a reaction can be easily measured by measuring 
        the concentration of all reactants and products after the reaction has 
        reached equilibrium. From the equilibrium constant, one can calculate 
        the Delta Go of the reaction, since at equilibrium, delta G 
        = 0, and so Delta Go = -RTlnKeq. 
         
         Whereas the first 
        term in the equation for delta G takes into account the nature of the 
        reactants, the second term deals with the amounts of the reactants and 
        products in the situation under consideration. Thus if you know what you 
        have and how much of each, you can predict the direction in which the 
        net reaction will go. 
         
          ::ATP 
        hydrolysis:: 
        To start our consideration of the free energy changes that are associated 
        with biochemical reactions, let's consider one of the most important and 
        fundamental energy-related biochemical reaction, the hydrolysis of adenosine 
        triphosphate, or ATP. Hydrolysis means the breakage of bonds by the addition 
        of water. Here: 
         
          
         
        where A = adenine (a base); R = ribose, a 5C sugar; joined to 3 phosphate 
        groups, which are themselves joined together. See [Purves6ed 
        6.8]. 
         
        The Delta Go of this reaction is about -7 kcal/mole. 
         
          ::"High 
        energy" bonds ("~"):: 
        Most HYDROLYSIS reactions in the cell do release 
        free energy, but usually less than 5 kcal/mole. The few, like ATP hydrolysis, 
        that release more than 5 kcal/mole, are important, because this amount 
        of energy can be harnessed for useful work, as we'll see. The bonds whose 
        HYDROLYSIS IS 7 KCAL/MOLE OR MORE ARE CALLED "HIGH 
        ENERGY BONDS" for this reason. These bonds are not stronger than 
        other bonds, so this is somewhat of a misnomer, but it turns out to be 
        a convenient term. It is denoted by a SQUIGGLE when we are talking about 
        it: AR-P-P~P. Looking at the structure of ATP we can rationalize the high 
        energy release by seeing that the addition of water relieves the electrical 
        repulsion between the negatively charged (acidic) phosphate groups. By 
        such reasoning we would predict that the bond between the first and second 
        phosphates should also be a high energy bond, and indeed it is, so: 
         
          
        AR-P~P~P. That is, hydrolyzing between P atoms 1 and 2 also releases about 
        7 kcal/mole (i.e., delta Go = -7kcal/mole) 
         
        On the other hand the bond between the ribose and the first phosphate 
        is not a high energy bond. 
         
          
        Given the Delta Go, one can calculate the equilibrium constant, 
        which turns out to be about 10+5. 
         
        (-7 = RT x 2.3 log K = 0.6 x 2.3 log K; K =10(-7/-1.4)= 105). 
         
        You should practice these types of calculations by doing the problems 
        in Problem Set 4. 
         
          
        (In doing these problems, note that the universal gas constant is usually 
        given as 1.98 cal/deg-mole, whereas Delta Go and delta G are 
        usually expressed in kilocalories, so you usually have to divide the RT 
        term by 1000 to get an answer in kcal.) 
         
        I will just note that the concentration of WATER is 
        not taken into account, as it is present at 
        55 M in aqueous solution and does not CHANGE in aqueous reactions, and 
        by convention is defined as 1. (We can make such arbitrary definitions 
        because we are only considering changes here 
        [concentration changes, free energy changes], not absolute values.) 
         
          
        So if we start with 1M ATP we will end up with only about 10-5 
        M ATP remaining at equilibrium. 
         
        Yet a 1 ml. solution of ATP will last for days on this bench top. We still 
        must add a catalyst to get this reaction to go in a reasonable time. 
         
        So we add an enzyme, say a pure preparation of ATP-ase 
        (note nomenclature). 
         
          
        Now all the ATP is hydrolyzed in a few minutes. The reaction has been 
        allowed to reach its equilibrium and has gone far to the right, because 
        of the very favorable (large and negative) delta G. 
         
        And 7 kcal of energy, free energy, is released. Free energy, so it could 
        be used for useful work, but what work did it do here? Nothing? Energy 
        had to go somewhere. It is released as HEAT. The test tube solution warmed 
        by about 7oC, by my calculation [since 1 ml of solution here, 
        at 1 M]. 
         
          
        This hydrolysis of ATP is in fact the most common reaction the cell uses 
        to produce usable energy. The trick is to harness this energy chemically, 
        to put it to useful chemical work. Keep in mind the overall problem, to 
        make a new E. coli cell that requires many endergonic transformations. 
         
          ::Coupled 
        reactions:: 
        So let's take an example of one of these endergonic energy-requiring reactions: 
        One such reaction is the very first transformation that a glucose molecule 
        undergoes upon entering an E. coli cell: 
         
           
         
        + Pi --> glucose-6-P + H2O; Delta Go 
        = +3.6 kcal/mole. 
        (Note that Pi is used as an abbreviation for PO4---) 
         
        So the Delta Go is unfavorable in the very first reaction in 
        the utilization of glucose in the cell. 
         
          
        How bad is the situation? 
         
        G + Pi --> G-6-P, Keq = [G6P]/[G][Pi] 
         
        If [G] and [Pi] are ~ 0.01M (typical) and Keq (from 
        Delta Go of +3.6) = 2.5 X 10-3 then [G6P] = 2.5 x 10-7, which is even 
        below the Km's of most enzymes (for example, for the next reaction taking 
        G6P further). Now let's consider putting the two reactions we've talked 
        about together: ATP + H2O --> ADP + Pi Delta Go 
        = -7 kcal/mole 
        Glucose + Pi --> G6P + H2O Delta Go = +3.6 kcal/mole 
        ----------------------------------------------------------------------------- 
        Glucose + ATP --> G6P + ADP Delta Go = -3.4 kcal/mole overall 
        = net sum of the two considered reactions 
         
          
        So let's mix the reactants together and hope for the best.... I guess 
        we should add a couple of enzymes to catalyze these 2 reactions: say: 
        "glucose phosphorylase" and "phosphatase".... But under these conditions 
        the 7 kcal/mole produced by the hydrolysis of ATP is lost mainly to heating 
        the surroundings (H2O). And besides, in mammals, where E. coli 
        lives, the temperature is kept constant, so we cannot influence reactions 
        by heat. The problem is solved by an enzyme, hexokinase. 
        This enzyme binds both ATP AND glucose. The 
        very phosphate from the ATP is transferred 
        to the glucose molecule. So the overall reaction written here on the bottom 
        line is not merely the net sum of the two reactions written above it, 
        rather, it IS the reaction catalyzed by hexokinase. 
        The phosphorylation of glucose has been COUPLED 
        to the hydrolysis of ATP. {Q&A} 
         
          
        What about the G6P produced? Does it now contain the high energy phosphate 
        bond? Well, what is the Delta Go for G6P hydrolysis? Easy: 
        -3.6 kcal/mole, since reverse reaction (second line) is +3.6. But -3.6 
        falls short of the -5 needed to qualify for a high energy bond, so no 
        squiggle here. Remember, if you write a reaction backwards, you just reverse 
        the sign of the Delta Go. 
         
          
        This coupling to ATP hydrolysis 
        is a very common way the cell uses to drive otherwise endergonic reactions. 
        [Purves6ed 
        6.9] Since the ATP is so often used to "pay for" the energy cost of 
        these chemical transformations, ATP is called the energy 
        "CURRENCY" of the cell. Coupling to ATP is one of two ways the 
        cell manages to run endergonic reactions; we will discuss the second way 
        a little later. 
         
          
         
          
        So is this the solution for E. coli growing on minimal medium? Far from 
        it; we have just passed the buck. Where's this ATP coming from? Not from 
        the medium, where glucose is the only carbon source. ATP must be synthesized 
        from glucose just like all other small molecules. And that itself takes 
        energy. But, once we have some ATP, most of the molecule can be used over 
        and over again to provide energy for coupled reactions, as long as we 
        can re-phosphorylate ADP back to ATP. The problem has thus shifted to 
        this reaction: ADP + Pi --> ATP (Delta Go = +7 kcal/mole). 
        If we could find a way to do that, we would have solved our energy problem. 
         
          
        Here is where we have some divergence in the unity 
        of biochemistry: The world is divided mainly into two types of organisms, 
        those who can run this reaction using the energy derived from sunlight, 
        the photosynthetic organisms, like plants; and the rest of us, E. coli, 
        humans, butterflies, who make ATP from ADP by using the energy derived 
        from the breakdown (catabolism) of carbon 
        compounds like glucose. Plants are actually also included in this latter 
        category, since when it's dark they derive energy from glucose catabolism, 
        as the rest of us do. We will consider this process of glucose-based energy 
        metabolism in some detail, and not really consider PHOTOSYNTHESIS, for 
        lack of time. Obviously, photosynthesis is the more basic and essential 
        process for the planet, since there would be no glucose if it were not 
        for the plants and their ability to harness solar energy. But photosynthesis 
        is a bit more complex, so it is not a good place to start. 
         
          
        So, ATP by way of glucose: 
         
        The overall plan is (for E. coli growing in air [dissolved oxygen]): 
        glucose + O2 --> CO2 + H2O, and: ADP 
        + Pi --> ATP 
         
        First, an overview: 3 parts: In each of these 3 parts 
        we will be concerned with our goal: to produce ATP's for use in reactions 
        that require energy. 
         
        1) GLYCOLYSIS: in which the 6C glucose is broken down to a 3C compound, 
        pyruvic acid [glucose (6C) --> pyruvate (3C)]. 
         
        2) THE KREBS CYCLE, in which the pyruvate is broken down to CO2 
        [pyruvate --> CO2] 
         
        3) The ELECTRON TRANSPORT CHAIN, in which oxygen is taken up and water 
        is produced in a separate series of reactions [utilization of O2] 
         
          
        I am now going to discuss GLYCOLYSIS in some 
        detail, for two reasons: 
         
        1) It will illustrate the problems and the solutions of energy requirements, 
        so one aim is to understand energy metabolism. 
         
        2) It is a real life detailed example of a typical metabolic pathway,such 
        as we have been alluding to with all these arrows leading to A's and B's 
        and C's. (The pathway will be characterized by a series of small changes 
        between substrate and product at each step) 
         
        ::Glycolysis:: 
        I'll show the first few reactions with the sugar in open chain form, because 
        I think it is easier to see what's going on. 
         
         1. 
        a phosphorylation (kinase enzyme) 
         
        2. an isomerization 
         
        3. phosphorylation 
        again... note that we have now used 2 ATPs: 
        rather than generating energy, we are consuming it, so far. 
         
        4. hydrolysis 
         
          
        5. isomerization 
        of dihydroxyacetone phosphate (as we saw in step 2, but in reverse, transforming 
        the ketone into the aldehyde; and swing it upside down when done: you 
        have another molecule of glyceraldehyde-3-phosphate): note now we have 
        2 of everything for each glucose molecule that entered the pathway, this 
        will be true from this point on. 
         
        So, so far, through rxn 5, we've produced 2 molecules of glyceraldehyde-3-phosphate 
        (GAL-3-P) for each molecule of glucose we used. AND it so far has COST 
        us 2 ATP's This ATP debt is a loose end that we will have to deal 
        with sooner or later..... 
         
        6. 
        Step 6 is an oxidation, GAL-3P and another phosphate to 1,3 diphosphoglyceric 
        acid, (or 1,3-diPGA). 
         
           
         
          
        OXIDATION, the loss of ELECTRONS. 
        We saw it before in the formation of the disulfide bond - there the loss 
        of two electrons was in the two hydrogen atoms that were taken away. Here, 
        in reaction 6, we have 2 electrons to be lost from the reactants, GAL-3-P 
        and phosphate: 
         
        ::NAD:: 
        Two electrons have been lost. The protons are not important in oxidation, 
        they are sometimes there with the electrons, and sometimes not. {Q&A}. 
        These electrons must go somewhere. They are taken up by the OXIDIZING 
        AGENT which itself will get reduced. As you can see from the NAD 
        handout, this is a compound called NAD, 
        or NICOTINAMIDE ADENINE DINUCLEOTIDE [Purves6ed 
        7.3]: 
         
        The nicotinamide part is also the vtramin niacin. Niacin sounds less ominous. 
         
           
         
          
        In getting reduced, NAD can accept two electrons, but only one proton. 
        The other proton goes into solution as a hydrogen ion. But it is the electrons 
        that are important in oxidations. 
         
        Instead of writing the reduction of NAD as NAD+ --> 
        NADH + H+, we will simply write: NAD --> NADH2, referring to 
        the two H's that came from glyceraldehyde-3-phosphate, despite the fact 
        that both proton did not end up on NAD. {Q&A} 
         
          
        This rxn 6 is rather complicated, involving a phosphorylation as well 
        as an oxidation. The phosphorylation did not require an ATP, but it did 
        require an NAD.... so now have a new loose end 
        analogous to the ATP/ADP situation, we have to worry about restoring NADs 
        from NADH2's as well as ATP's from ADP's. 
         
        But at least we have something of value here, a high 
        energy phosphate, as you can see the squiggle at the top of 1,3-di-PGA 
        on your glycolysis 
        handout. That means that enough energy can be released from the hydrolysis 
        of this phosphate even to drive the phosphorylation of ADP in a coupled 
        reaction. 
         
          
        Let's take the money and run... this high energy bond is cashed in the 
        next reaction, rxn 7. 
      7. 
        Note that the top carbon is now a carboxylic acid in 3-PGA, whereas it 
        had been an aldehyde in GAL-3-P. This change is the result of the oxidation 
        that took place in reaction 6. {Q&A}. 
         
        So we've now paid off one of the 2 ATPs the debt we ran up at the start. 
        Wait a minute, actually, we're all paid up (since we have two di-PGA's 
        for every mole of glucose that started down the glycolytic pathway). 
         
        Continuing along: 
         
          
        8. Isomerization 
        of 3-PGA to 2-PGA.  
      9. 
        Dehydration, water removed. The result is an unstable compound, phospho-enol 
        pyruvic acid (PEP), one whose hydrolysis can result in the release of 
        a large packet of free energy. 
         
            [2-PGA, as well as PEP, is at a higher energy 
        level than pyruvate, but the shift in atoms allows 
            cash-in of ATP along the way, since the phosphate 
        bond is a high energy bond in PEP.]  
      10. 
        Transfer of the phosphate to ADP (X2), resulting in PYRUVIC 
        ACID (pyruvate), which can be considered the end point of glycolysis. 
        [Purves6ed 
        7.7a], [Purves6ed 
        7.7b], [Purves6ed 
        7.7c]. 
         
          
        So after the 10 steps of glycolysis we have 4 ATPs produced and 2 invested, 
        for a net gain of 2 ATPs produced from ADP. 
        So glycolysis does produce energy in the form 
        of ATP. And the overall reaction will run far to the right, as the Delta 
        Go from glucose to 2 pyruvates is -18 kcal/mole (even taking 
        coupled reactions producing the 2 net ATP into account). That is, 
         
        1 glucose + 2 ADP + 2 Pi + 2 NAD <--> 2 pyruvate + 2 ATP + 2 NADH2 
         
        Delta Go = -18 kcal/mole 
         
        The diagram below shows Delta Go's for 
        the individual steps in glycolysis. 
         
        (For a different way of looking at it, see the chart of Delta G's drawn 
        by Purves [Purves6ed 
        7.6]) 
         
           
         
          
        Although the pathway overall is quite favorable, some individual reactions 
        are quite unfavorable, the most extreme being reaction #4. The energy-requiring 
        reactions in this case are being pushed by the build-up of reactants by 
        the more favorable reactions before them, and they are being pulled by 
        the withdrawal of products by the more exergonic reactions further downstream. 
        The actual Delta G's will be influenced by the drain of products, so that 
        the second term in the equation for Delta G is being brought into play 
        here. 
         
        Delta G = Delta Go + RTln([products]/[reactants]), 
        where RT~0.6 (in kcal/deg-mole) 
         
        For instance, if the products are drained such that the ratio of P/R reaches 
        down to 0.00001, this produces ~ 7 kcal/mole of negative Delta G , enough 
        to balance out the unfavorable Delta Go of +6.8 for rxn 4. 
         
          
        This indirect affect on the Delta G is the second 
        method the cell utilizes to carry out an individual reaction that 
        has an unfavorable Delta Go. 
         
        So we have 2 methods: 
         
        1.) DIRECT COUPLING of the unfavorable reaction 
        to an energetically favorable one to produce a new coupled reaction with 
        a net negative (favorable) Delta Go (as in the hexokinase reaction 
        #1). 
         
         2.) INDIRECTLY, via the WITHDRAWAL 
        OF PRODUCTS or buildup of substrates 
         
        SO, we have our overall negative Delta Go , and we have generated 
        net ATP, so we should feel pretty good, except for one thing: we have 
        an important loose end to tie up. We borrowed an NAD to oxidize Gal-3-PO4. 
        That was a key reaction in the path, as oxidations are usually accompanied 
        by large changes in free energy. We were able to get a PO4 
        added to our 3-carbon compound, and this phosphate was the one that was 
        used to phosphorylate ADP in the very next step (#7). We used NAD, and 
        it became reduced to NADH2. So now we must consider how we are going to 
        repay that debt. Otherwise the small stores of NAD in the cell would very 
        soon all be converted to NADH2 and glycolysis would quickly 
        grind to a halt. 
         
        We need an oxidizing agent to oxidize NADH2. A great one abounds: 
        O2. 
         
        It readily takes up electrons, for instance from Fe++ to make it Fe+++ 
        as steel goes to rust. 
         
          ::Anaerobiosis:: 
        Does E. coli have access to oxygen? In the lab, yes. We vigorously and 
        constantly shake the E. coli cultures on mechanical shakers to get air 
        dissolved in the culture medium to provide a constant source of oxygen, 
        called an AEROBIC state. In the gut, sometimes yes, sometimes no (crowded). 
        Do our own cells have access to oxygen? Sure, through the lungs via the 
        blood vessels to all tissues. But when you are running across campus to 
        class so as not to miss the first golden words here, your muscles may 
        need ATP faster than you can deliver oxygen to them for NADH2 
        oxidation, your muscles will be in an AN-AEROBIC 
        state. And are many organisms that live in naturally anaerobic environments, 
        in mud at the bottom of rivers, e.g. So let's first consider the anaerobic 
        case when no oxygen is available for the oxidation of NADH2. 
        Under these circumstances the cell must make do with what it has available, 
        which is mainly: 2 pyruvates. Fortunately, pyruvate itself is able to 
        act as an oxidizing agent, as seen in rxn 11, where it accepts electrons 
        into its C=O bond, adding two hydrogens as well, to form lactate, or LACTIC 
        ACID. It gets the electrons from our NADH2 molecule, 
        which is really NADH and H+, so it is recapturing one proton (an H+ ion) 
        from the aqueous pool. Even the Delta Go is favorable, and we get our 
        NAD regenerated from NADH2. The NAD shuttles back and forth 
        then, getting reduced in rxn 6 and reoxidized in rxn 11 over and over 
        and over again, while glucose runs down to lactate, and ADP's are converted 
        to ATPs to power cell division for E. coli or running up stairs for humans 
        even in the case of insufficient oxygen. 
         
        I think it's the build-up of lactic acid that makes your muscles hurt 
        if they are doing anaerobic glycolysis too long. 
         
          ::Fermentation:: 
        So pyruvate is a crossroads: If no oxygen, then if you are E. coli or 
        humans, you carry out a lactic acid fermentation... 
        [Purves6ed 
        7.5b], [Purves6ed 
        7.15]. 
         
        If you are yeast, there is a variation on this theme, you break down pyruvate 
        first to acetaldehyde and CO2, which is not an oxidation, but 
        then use the acetaldehyde as an oxidizing agent for NADH2, 
        with the product here being the 2 carbon alcohol, ethanol (rxns 12 and 
        13). Beer drinkers appreciate this variation, as lactic acid beer would 
        be pretty bad, and probably not even produce those psycho-pharmacological 
        effects for which ethanol is famous. {Q&A}. 
         
          
        Just as in the case of ATP, the NAD - NADH2 case is one of re-generation, 
        not generation. Once a little NAD is made, it can shuttle back and forth 
        millions of times getting alternately reduced and oxidized: 
         
        Consider the efficiency 
        of fermentation: 
         
        For: glucose--> 2 lactates, without considering 
        the couplings for the formation of ATP's: Delta Go = -45 kcal/mole. 
        {Q&A}. 
         
        Out of this comes 2 ATPs, worth 14 kcal/mol. So the efficiency is about 
        14/45 = 30%, which is not bad, about what a gasoline engine can do. 
         
          
        Where did the other 31 kcal get to? They are released as heat, which is 
        why, after you've run fast to class, in addition to the lactic acid PAIN 
        in your legs, you are also SWEATING. 
         
        Now taking the ATPs into account, the overall Delta Go is about 
        45 - 14 = 31 kcal/mole, so the lactic acid fermentation runs essentially 
        completely to the right (or clockwise) as written. 
         
          ::Energy 
        yield:: 
        The efficiency is pretty good, but on the other hand the YIELD 
        is poor. What do I mean by YIELD? Well, glucose has a lot more chemical 
        energy in it than we are tapping here. For example, if we BURN glucose 
        (i.e., react it with oxygen) and measure the calories of heat given off, 
        we get no less than 686 kcal/mole. Compare that to the measly 45 kcal/mole 
        we got from converting glucose to two lactates. The lactic acid that we 
        are throwing away at the end could be used for more energy, but in the 
        absence of oxygen there is no way to use it. 
         
          (C) 
        Copyright 2001  Lawrence Chasin and Deborah Mowshowitz   Department 
        of Biological Sciences   Columbia University   New York, NY 
        Clickable pictures are from Purves, et. al., Life, 5th Edition, 
        Sinauer-Freeman's Images of Life 5.0.  A 
        production of the Columbia 
        Center for New Media Teaching and Learning 
      |