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III. Fermentation and Respiration Overview
An emphasis on the flow of carbon and other
elements in fermentation and respiration
• 3.8 Glycolysis
• 3.9 Fermentative Diversity and the Respiratory
Option
• 3.10 Respiration: Electron Carriers
• 3.11 Respiration: The Proton Motive Force
• 3.12 Respiration: Citric Acid and Glyoxylate Cycle
• 3.13 Catabolic Diversity
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III. Fermentation and Respiration Overview
• Two key metabolic pathways
• Complementary
• Overlapping
• Definition depends on context-industrial, medical,
biochemical
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Fermentation
• In food science fermentation can refer to the
production of foods such as yogurt
• In chemical engineering it can refer to the
production of ethanol as an additive for gasoline
• In microbiology it refers to the breakdown of
carbon compounds (eg glucose) to smaller
compounds with a limited harvest of energy
through substrate level phosphorylation and no
oxygen used
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Respiration
• In medicine or exercise science respiration refers
to breathing
• In microbiology respiration refers to the removal of
electrons from a substance and their transfer to a
terminal acceptor with a significant harvest of
energy through oxidative phosphorylation (redox
reactions). Oxygen may be used as the terminal
acceptor (aerobic respiration) or not (anaerobic
respiration).
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• Fermentation: substrate-level phosphorylation;
ATP is directly synthesized from an energy-rich
intermediate
• Respiration: oxidative phosphorylation; ATP is
produced from proton motive force formed by
transport of electrons
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Fermentation
• A basic and important process for microorganisms
• A sugar is the starting material and the end
product depends on the species
• Three Stages (I) Preparation, (II) Energy
Harvesting, (III) Reboot
• Reboot stage is very diverse!
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3.8 Glycolysis
• Stage I and Stage II (Figure 3.14) called Glycolysis
(Embden–Meyerhof-Parnas or EMP pathway): a
common pathway for catabolism of glucose
• End product of glycolysis is pyruvate (pyruvic acid)
• In fermentation pyruvate is processed through
Stage III
• It accepts electrons so is reduced
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Fermentation with lactic acid produced
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Figure 3.14
3.9 Fermentative Diversity and the Respiratory
Option
• Fermentations may be classified by products
formed (See Sec.13.12) in Stage III
• Ethanol
• Lactic acid (homolactic vs heterolactic)
• Propionic acid
• “Mixed acids”
• Butyric acid (extra ATP generated)
• Butanol
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3.9 Fermentative Diversity and the Respiratory
Option
• Fermentations may be classified by substrate
fermented (See Sec.13.12)
• Usually NOT glucose
• Amino acids
• Purines and pyrimidines
• Aromatic compounds
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3.9 Fermentative Diversity and the Respiratory
Option
• Fermentation
• Helps detoxify and eliminate waste products
• Provides metabolites for other microbes in the
environment
• May help to recover additional ATP
• Maintains redox balance (page 87 and Fig. 3.14) of
NAD and NADH.
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3.9 Fermentative Diversity and the Respiratory
Option
• Fermentation
• Helps detoxify and eliminate waste products
• Provides metabolites for other microbes in the
environment
• May help to recover additional ATP
• Maintains redox balance (page 87 and Fig. 3.14)
• AND…….
• Helps to generate precursor metabolites for
anabolism
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Broad Overview of Metabolism
Prokaryotes will not make something if they can import it
There are only a few key precursor molecules (but lots of ways
to make them)
Energy sources vary
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3.9 Fermentative Diversity and the Respiratory
Option
• Pentose Phosphate Pathway (Shunt)
• “Alternate” pathway
• Runs “parallel” to glycolysis
• Different reactions thus different intermediates
• Generates different precursor metabolites
• Generates reducing power
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3.12 Respiration: Citric Acid and Glyoxylate
Cycle
• Citric acid cycle (CAC): pathway through which
pyruvate is completely oxidized to CO2 (Figure
3.22a) (aka Krebs or TCA cycle)
• Initial steps (glucose to pyruvate) same as glycolysis
• Subsequently 6 CO2 molecules released and NADH and
FADH generated
• Plays a key role in both catabolism AND
anabolism…why?
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Figure 3.22a
3.12 Respiration: Citric Acid and Glyoxylate
Cycle
• The citric acid cycle generates many compounds
available for biosynthetic purposes
• - α-Ketoglutarate and oxaloacetate (OAA): precursors of
several amino acids; OAA also converted to
phosphoenolpyruvate, a precursor
of glucose
• Succinyl-CoA: required for synthesis of cytochromes,
chlorophyll, and other tetrapyrrole compounds
• Acetyl-CoA: necessary for fatty acid biosynthesis
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In other words-the citric acid cycle
generates key precursor metabolites
As well as
harvesting energy
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3.12 Respiration: Citric Acid and Glyoxylate
Cycle
The Citric Acid Cycle is also a key collection point
and entry point for metabolites
• C4-C6 citric acid cycle intermediates (e.g., citrate, malate,
fumarate, and succinate) are common natural plant and
fermentation products and can be readily catabolized
through the citric acid cycle alone
• Fatty acids metabolized via Acetyl-CoA
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3.12 Respiration: Citric Acid and Glyoxylate
Cycle
• Glyoxylate cycle
• A variation of the citric acid cycle with glyoxylate as a
key intermediate
• Shares enzymes with citric acid cycle
• Allows utilization of C2-C3 organic acids if larger
molecules not available (Figure 3.23)
• Isocitrate to glyoxylate and succinate
• For anabolism or catabolism
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Figure 3.23
3.10 Respiration: Electron Carriers
Important electron carriers embedded in membranes
include:
• NADH dehydrogenases
• Flavoproteins
• Cytochromes (heme)
• Iron-sulfur proteins
• Quinones
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• Respiration is much more productive than
fermentation
• Aerobic respiration is the most productive of all
Figure 3.22b
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13.5 Autotrophic Pathways (pp 390-391)
• Carbon fixation is reduction of CO2 to
carbohydrate-a key feature of autotrophy
• At least 6 pathways exist in various Archaea and
Bacteria
• But the Calvin cycle (Figure 13.16, 13.17) is the
most important
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13.5 Autotrophic Pathways (pp 390-391)
• Named for its discoverer, Melvin Calvin
• Fixes CO2 into cellular material for autotrophic
growth
• Requires NADPH, ATP, CO2 and special
enzymes e.g. ribulose bisphophate
carboxylase (RubisCO),
• 6 molecules of CO2 are required to make 1
molecule of glucose (Figure 13.17)
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Figure 13.17
13.5 Autotrophic Pathways: RUBISCO
• Responsible for most carbon fixation on planet
• Unusual enzyme-”weak”- when CO2 is low
• easily inhibited by oxygen
• Often found sequestered in carboxysomes to
increase CO2 and lower O2
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3.13 Catabolic Diversity
• Chemolithotrophy
• Uses inorganic chemicals as electron donors
• Examples include hydrogen sulfide (H2S), hydrogen gas
(H2), ferrous iron (Fe2+), ammonia (NH3)
• Begins with oxidation of inorganic electron donor
• Uses an electron transport chain and transmembrane
ion gradient
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• Dissimilative Iron Oxidizers are chemolithotrophs
(13.9 and 14.15)
• Oxidize Fe2+ to Fe3+
• Very widely distributed in many environments
where Fe2+ is available
• Autotrophic or heterotrophic
• Aerobic or anaerobic
• Archaea or Bacteria
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• Acidithiobacillus ferrooxidans is a representative
iron oxidizer
• Acidophile at pH 2-3
• Acid environments with Fe2+
• Fe2+ -> Fe3+ -> FeOH3
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Out
(pH 2)
Outer
membrane
cyt c
Electron transport
generates proton
motive force.
Rusticyanin
e–
Periplasm
Reverse e– flow
NAD+
Q cyt bc1
e–
cyt c
cyt aa3
In
(pH 6)
+ ATP
NADH
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Cell material
ADP
ATP
Figure 13.24
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Figure 13.23
3.17 Nitrogen Fixation (Sec 3.17 also pp 438439)
• Living systems require nitrogen in the form of NH3
or R-NH2
• “Fixed” or “reduced” nitrogen, not N2
• Only some prokaryotes can fix atmospheric
nitrogen: diazotrophs
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3.17 Nitrogen Fixation
• Some nitrogen fixers are free-living, and others
are symbiotic
• Cyanobacteria are free-living
nitrogen fixers
• Soybean root nodules contain
endosymbiotic
Bradyrhizobium japonicum
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3.17 Nitrogen Fixation
• Energetically expensive (8 ATP per N atom)
• Requires electron donor, often pyruvate
• Reaction is catalyzed by nitrogenase
• Sensitive to the presence of oxygen
• Fe plus various metal cofactors
• Can catalyze a variety of reactions
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