- 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
- 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
- substrate level phosphorylation
- oxidative phosphorylation
- protonmotive force
- oxidations provide the chemical energy to create both of the above
- Redox reaction
- 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
- 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
- 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?
- 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.
- 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
- 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
- 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
- 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
- ferric iron
- 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