• Metabolism and Energy
    • Definitions and diagrams
      • phototrophs and heterotrophs
      • catabolism and anabolism: Catabolism is the set of reactions involved in breaking down molecules for the production of building blocks and energy. Anabolism is the process of using those building blocks and energy to make macromolecules, structures, and ultimately, cells
        • exergonic -energy yielding reactions
        • endergonic -reactions that require energy
      • Energy
        • radiant (light)
        • chemical from oxidations
        • thermal (heat)
    • Chemical energy currencies
      • phosphorylation potential
        • ATP as "high-energy phosphate" compound
        • coupled reactions involving ATP
        • ways of making ATP
          • photophosphorylation
          • substrate level phosphorylation
          • oxidative phosphorylation
      • protonmotive force
      • oxidations provide the chemical energy to create both of the above currencies
    • Redox reaction
      • definitions
        • oxidation-loss of electrons; and reduction-gain of electrons
          • an oxidation : Ared->Aox + e-, e.g., H2->2H+ plus 2e-
          • oxidation liberates energy (reduction requires energy)
        • standard reduction potentials
          • half reactions and coupled redox reactions. molecules that can undergo redox reactions can be ranked. The convention is to order redox half reactions on a scale in which reductants at the negative end can donate electrons to oxidants at the more positive end of the scale.
          • to put it another way, molecules that have electrons to give away are called reductants, and molecules that would rather accept electrons are called oxidants.
          • keep in mind, however, that redox half-reactions are for notation only. An oxidation cannot occur by itself. There must be an accompanying reduction. (the electrons have to go somewhere.)
      • the value of standard reduction potentials
        • ie, what does it tell you that NAD->NADH has a reduction potl. of -320 mV, whereas oxygen ->H2O has a redox potential of +815mV?
        • first of all: since the redox half reaction NAD->NADH is more negative, this means that NADH (the reductant of the more negative half-reaction) will donate electrons to oxygen (the oxidant of the more positive half reaction).
        • it also gives you the energy payoff. The overall reaction NADH + oxygen->NAD + water has a change in reduction potential of 320 + 815 = 1135 mV or approx. 1.1 volts. The magnitude of the change in reduction potential is a direct indication of the amout of energy released (and therefore available to do work).
        • so.. you tell me: which reaction provides a bigger energy payoff, NADH + oxygen ->NAD + water, or NADH plus nitrate ->NAD plus nitrite? And: if a bacterium has both nitrate and oxygen available as terminal electron acceptor, which will it use first?
    • Enzymes
      • protein or RNA catalysts
      • substrates and products
      • metabolic reactions are series of enzyme-catalyzed reactions
      • lower energy of activation by stabilizing transition state
  • Overview of catabolism of a chemoheterotroph growing on glucose
    • aerobic respiration
      • glycolysis: glucose to pyruvate
      • TCA (tricarboxylic acid) cycle, or citric acid cycle, or Krebs cycle: the complete oxidation of pyruvate to carbon dioxide
      • oxidative phosphorylation: major energy payoff (or currency exchange, if you prefer), where NADH or FADH2 are "exchanged" for ATP at a quite favorable exchange rate.
    • fermentation
      • glycolysis
      • reduction of pyruvate to generate NAD+, with no major energy payoff
  • Details of glycolysis
    • Glucose>>>fructose bisphosphate stage involves a series of isomerizations and kinase reactions that actually use energy ( in the form of two high energy phosphate compounds). In bacteria, the first reaction is a transport process that uses one PEP molecule to import glucose and simultaneously convert it to glucose-6-phosphate.
    • fructose bisphosphate is split into two molecules (DHAP and Gly-3-P) that each have 3 carbons. The subsequent reactions of glycolysis only involve Gly-3-P, so that the equilibrium is forced in the direction of Gly-3-P by mass action.
    • the next two reactions of glycolysis are major ones
      • the aldehyde (glycerALDEHYDE-3-P) is oxidized eventually to an acid (3-phosphoglyceric ACID): a process that releases energy. Where does the energy go? First to the production of NADH in an oxidation reaction that is combined with the phosphorylation reaction producing 1,3 bisPGA, a high energy phosphate molecule.
      • then, the energy of 1,3 bisPGA is used to drive the next, substrate level phosphorylation reaction, producing ATP and 3 PGA
    • there is another SLP reaction in glycolysis:PEP + ADP > pyruvate + ATP
      • thus, the total payoff is 2 ATP and 2 NADH
        • glucose to fruc diphosphate -2ATP
        • FDP->2 (note the 2!) pyruvate +4 ATP and +2 NADH
        • (we double everything after the split of fructose bisphosphate)
      • what happens to those 2 NADH molecules depends on the metabolic capacity of the bacterium, and the environment
  • Aerobic respiration (if the bacterium can do it, and if there is oxygen present)
    • TCA cycle
      • in general
        • provides for the complete oxidation of acetylCoA to CO2
        • produces mucho reduced coenzymes
      • details
        • in between glycolysis and TCA is a linker reaction that converts pyruvate into AcetylCoA and CO2, reducing NAD to NADH in the process
        • then, the two carbons of AcetylCoA are oxidized to 2 CO2, in a series of reactions that includes 4 oxidations and 1 substrate level phosphorylation
        • the net is 3 NADH, 1 FADH2, and 1 ~P (ATP or GTP) per Acetyl CoA oxidized
    • electron transport chain
      • respiratory organisms (like bacteria and you) can "trade in" their NADHs and FADH2 for ATP, using a set of mechanisms collectively referred to as oxidative phosphorylation. Like substrate level phosphorlyation, oxidative phosphorylation is a way of converting redox energy into ATP, but unlike SLP, (which was well-characterized and agreed upon by the 50s), ox/phos was a major source of argument as to the details. It still is, actually, and the argument has resulted in, by my tally, 3 Nobel prizes to some of the arguers.
      • What's agreed upon is that, in our mitochondria and in some bacteria, a series of membrane-bound complexes serve as "coupling sites" for the synthesis of ATP. Coupling sites I, III, and IV each can make one ATP. NADH donates electrons and protons to Complex I, and the electrons travel all the way through complex IV, thus you get a total of 3 ATP per NADH. FADH2 feeds into complex III, however, so you miss one ATP and only get 2 total. The actual site of ATP synthesis is called complex V, or ATP synthase. More on that later.
      • The clash of egos came over the details: how exactly do these complexes account for the synthesis of ATP, i.e., how is the movement of electrons from NADH to O2, through the respiratory chain, coupled to the synthesis of ATP.
        • chemical hypothesis, based on analogy with SLP. Problems: ox/phos required intact membranes, and ox/phos was blocked by "uncouplers". Major problem: high-energy chemical intermediate was never found.
        • chemiosmotic hypothesis and Peter Mitchell (one of the Nobel laureates)
          • the protonmotive force
          • respiration as a great big complicated proton pump
          • uncouplers explained
        • mitochondrial chain in detail
        • bacterial aerobic respiration
      • ATP synthase (F1FO-ATPase) is a reversible enzyme that uses the protonmotive force to drive the synthesis of ATP
        • comprised of a hydrophilic portion called F1 (where ATP is made or hydrolyzed), and a hydrophobic FO that conducts protons across the membrane
        • current concept is that protons moving across the membrane (down their concentration gradient) cause the F1 to rotate, and in so doing release ATP. This was worked out biochemically by Paul Boyer (last year's Nobel laureate) and structurally by John Walker (ditto).
  • Anaerobic respiration and chemolithotrophy
    • anaerobic respiration involves electron acceptors other than oxygen
      • nitrate
      • ferric iron
      • sulfate
      • carbonate
      • fumarate
    • chemolithotrophs use inorganic reductants in place of NADH or FADH2
  • Fermentation (non respiratory bacteria, or facultative bacteria when there is no oxygen or other terminal electron acceptor
    • lactate fermentations
    • ethanol fermentations
    • acetate/butyrate fermentations