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Microbes as Energy Transducers
The Metabolic Menu
 Metabolic Strategies
 Respiration & Fermentation
 Chemolithotrophy
 Photoautotrophy
 Biogeochemical Cycles
 Metabolism in Primitive Organisms

The tendency of a molecule (B) to accept an electron from
another molecule is given by its electrode potential (E), a.k.a
the reduction potential.
E0 is the electrode potential under standard conditions.
Eh is the actual electrode potential.
E0’ is the electrode potential at pH 7 (under biological
conditions).
Molecules with more negative Eh or E0’ values are better
electron donors.
Electrons flow spontaneously to molecules with more
positive Eh or E0’ values.
The total free energy change occurring in these two half
reactions can be calculated by the following equation:
DGo’ = (-nF)(DEh)
where Eh is the free energy change under standard
biological conditions, n is the number of electrons
transferred, and F is the faraday constant (-96.48 kJ/V)
DEh = Eo’(oxidized partner) - Eo’(reduced partner)
Oxidation and Reduction are Coupled Reactions
Negative E0’
A becomes oxidized,
losing electrons
Positive E0’
B becomes reduced,
gaining electrons
Redox Rxns:
Eo’= -0.42 V
Eo’= +0.82 V
DGo’ for the formation of water:
Eo’of electron donor once oxidized
DEh = (+0.82) – (-0.42)
Eo’of electron donor when reduced
DGo’ = (-2)(96.48)(1.24) = -239.27 kJ
Other final electron acceptor
O2 as final electron acceptor
Metabolic Menu
For Chemotrophs
a.k.a
chemolithotrophs,
chemoautotrophs
a.k.a
chemoorganotrophs,
chemoheterotrophs
Electrons in redox
reactions are carried from
the primary electron donor
to the terminal electron
donor.
Electrons are not freely
diffusible in the cell.
They are carried by
electron carriers.
Electron carriers
1. Freely diffusible (coenzymes/cofactors) –
move electrons from one enzyme to another to
take part in reactions (like batteries or
electron taxis)
-NAD/NADH: catabolic, energygenerating reactions, transfers hydride
ion (2 e- + 1 H+)
-NADP/NADPH: anabolic, biosynthetic
reactions
2. Fixed carriers, where carrier is a prosthetic
group firmly attached to enzyme in the
cytoplasmic membrane (electron transport
chain)… like a power line or stops on the city bus
line
Then, need to store energy…
Energy currencies for cells are usually
compounds whose DG0’ is greater than 30 kJ/mol.
Anhydride bonds
Energy contained in glucose
used to convert low-energy
phosphoryl groups to highenergy bonds:
1,3 bisphosphoglycerate
Phosphoenolpyruvate
Acetyl-CoA
Succinyl-CoA
2 stages:
1. Splitting glucose (C6) into
two phosphoglyceraldehydes
(C3)
2. Oxidizing
phosphoglyceraldehyde to
pyruvate
Two Ways to Make ATP:
Quick & Dirty
Fermentation
or Turbo-Charged
Aerobic and Anaerobic Respiration
Fermentation:
Balances the reduction of
NAD+ with a subsequent
oxidation of NADH.
Restores electrical balance.
Net yield: 2ATP and
“waste” products that are
derived from the original
electron donor.
ATP Synthase
Structure & Function
F1 subunits:
3 a, 3 b, 1 g, 1 d, and 1 e.
b subunits = site of ATP
hydrolysis/synthesis
F0 subunits: proton
channel
Torque
generated
rotor
stator
F1 Subunit Topview
ATP Synthase acts as
a rotary motor turning
in 120 degree steps.
3 or 4 protons flowing through turns c proteins enough
to change conformation of b protein  1 ATP
Conformation of active sites on b subunits is constantly
changing… like watching The Wave at a Mariners game.
Loose
Open: substrate binding
Tight: product
release from highaffinity site,
actually requires
more energy than
ATP synthesis
The force that powers ATP
Bidirectional:
synthase is the proton motive
force, or Dp.
Major route of H+ into cell,
but protons can get pumped
out, too.
ATP synthase reaction is
close to equilibrium; direction
depends on Dp
One site for ATP hydrolysis
and synthesis
(Protons can also be pushed
back out by reverse e- flow,
usually in chemolithotrophs
R-
+
K+
K+ R-
K+ K+
K+
+
+
- K - K K+ K+
K+ R
K+ K+
+
K
valinomycin
+
K+
+
K K
K+
K+ K+
K+ R
R-
Uncouplers are ionophores
that collapse the Dp. They
inhibit ATP synthesis that is
coupled to e- transport.
Other cations could run
ATP synthase too…
Judicious choice of
ionophores (small lipidsoluble, cation-carrying,
ion gradient-thwarting
molecules) show that
you can run ATPase with
a K+ gradient.
Valinomycin, added to
cells loaded with K+,
uncouples Dp by carrying
out K+ and creating a
temporary diffusion
potential.
Net gain
…in the rich world of the gut where E. coli lives!
Bacteria
e- source
Archaea
e- sink
A theory on a uniting feature of the Archaea:
energetically stressed lifestyle.
Archaea are adapted to energy-poor extremes, but
Bacteria outcompete them in “easy” environment.
Success in Stress:
Marine sedimentary record of large radiation of
tetraether-based, isoprene membranes in an anoxic
period during the mid-Cretacean, perhaps driven by
competition for ammonia (e- donor) utilization?
Doesn’t prefer life of luxury:
Low extant diversity (89 genera vs. 1,400 bacterial
genera) due to inability to radiate in replete
environments
Energetic stress:
Halophilic lifestyle (must prevent excess Na+ from entering cell)
Thermophilic lifestyle (must keep from melting/denaturing)
Nitrifiers (low N, low O2 in open ocean)
Anaerobic methanogens (always Archaea) (not a good living: one methane
produced can gain as little as one cation (1/3 to ¼ ATP)
Aerobic methanotrophs
Acidophilic lifestyle
Alkaliphilic lifestyle – think what this does to one’s Dp!!
-Na+ powered flagellae and ATP synthase
-local H+ gradients (proton pump next to ATPase?
-S-layers, membrane properties retain H+
Archaea are good at
maintaining cells.
Bacteria prefer the
“growth” lifestyle.
Few or no Archaeal
pathogens because
living in a host is not
adapted to a lowenergy ecosystem
Archaea survive heat, low pH; Bacteria prefer cool and neutral
D.L. Valentine, 2007, Nature Reviews Microbiology 5: 316
Membranes:
Stable to temperature, pH
Less permeable to ions so
less leakage/uncoupling;
better maintenance of
chemiosmotic potential
D.L. Valentine, 2007, Nature Reviews Microbiology 5: 316
Speaking of stress…
Fermentation, a very stressful situation
O2 is not highly soluble in water
Many environments easily become anoxic
Decomposition of organic material must continue anaerobically
If alternate e- acceptors (SO4-2, NO3-, Fe3+) are not available, then…
Fermentation!
~3 ATP per glucose now, not 38 as in aerobic respiration.
Respiration vs. Fermentation
ADP + Pi
½ O2
NADH + H+
B
NADH + H+
FADH2
FAD
H2O
NAD+
ATP
NAD+
BH2O
Fermentation – Key Features
(1) Always anaerobic (if O2 around, can’t be used)
(2) No externally supplied terminal electron acceptor.
(3) Substrate-level phosphorylation is the rule*.
Many types.... 2 major themes
(1) NADH+H+ gets oxidized to NAD+
(2) Electron acceptor is usually Pyruvate or its derivative.
*Rules are always meant to be broken!
Pasteur Effect: ~20X more biomass when aerated
Redox balance
The short list
Fermentation as a diagnostic tool:
end products are a metabolic fingerprint
Escherichia, Salmonella, Proteus, Aeromonas:
Ferment glucose to a number of organic acids. Produce H2 and CO2:
enzyme called formic hydrogenlyase splits formic acid to make these.
Enterobacter makes neutral fermentation products.
Fermentation as a diagnostic tool:
end products are a metabolic fingerprint
Enteric bacteria:
g-proteobacteria, G- rods, nonsporulating, facultative anaerobes,
oxidase-negative, fermentative
Enterobacter:
negative
Escherichia,
Salmonella,
Proteus,
Aeromonas:
positive
Methyl Red Test:
Red if pH < 5.0
Escherichia,
Salmonella,
Proteus,
Aeromonas:
negative
Voges-Proskauer Test:
pink = butanediol produced
Enterobacter:
positive
Clostridium spp: endospore-forming, anaerobic rods
Ferment amino acids, purines, aromatic compounds/antibiotics
Pyruvate
Tricarboxylic acid (TCA) cycle: used in aerobic
respiration, anaerobic respiration, and even fermentation!
Don’t want NADH or FADH2
Still need precursors for amino
acids etc.
Convert from oxidative pathway to
reductive pathway (incomplete
CAC)
Blocked between a-ketoglutarate
and succinyl-CoA, cannot operate
in oxidative direction
Runs in reverse from OAA to
Succinyl CoA
Fumarate
dehydrogenase instead
of succinate
dehydrogenase
Reverse arrows for NADH and
FADH2
Propionic Acid Fermentation: incomplete citric acid cycle
Pyruvate
OAA
Lactate
Mal
Variations in
many
fermentative
microbes
Fum
Succ
Succ CoA
Prop CoA
MethylMalonyl CoA
The unusual fermentation of succinate
Sodium ATPase:
Uses Na+ gradient
…DG0’ so small (-20.5 kJ) that cannot even do substrate-level
phosphorylation! Coupled to sodium transport; slowly build up
“equity” in form of Na+ gradient (Dp)
The unusual fermentation of oxalate
H+ ATPase:
Uses proton gradient
…DG0’ so small (-26.7 kJ) that cannot even do substrate-level
phosphorylation! Oxalate consumes protons in cytoplasm during
conversion to formate. Slowly boosts Dp by making cytoplasm
more basic.