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II. Energetics, Enzymes and Redox
• 3.3 Energy/Carbon Source Classes of
Microorganisms
• 3.4 Bioenergetics
• 3.6 Electron Donors and Electron Acceptors
• 3.7 Energy-Rich Compounds
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3.3 Energy Classes of Microorganisms
• Metabolism
• The sum total of all of the chemical reactions that occur
in a cell
• Catabolic reactions (catabolism)
• Energy-releasing metabolic reactions
• Anabolic reactions (anabolism)
• Biosynthetic metabolic reactions
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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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3.3 Energy/Carbon Source Classes of
Microorganisms
• Microorganisms have a variety of ways to conduct
their metabolism
• Grouped into carbon source classes
• Heterotrophs rely on reduced carbon
• Autotrophs fix CO2 or reduce CO2
• Grouped into energy source classes
• Chemotrophs use chemical energy
• Chemolithotrophs use inorganic compounds
• Chemoorganotrophs use carbon compounds
• Phototrophs use light energy
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3.3 Energy Classes of Microorganisms
• Autotrophs may be chemotrophs or phototrophs
with respect to energy source
• Phototrophic autotrophs (photoautotrophs) are
familiar
• Cyanobacteria (Sec.14.3)
• Photosynthesize using chlorophyll a
• Fix CO2 to carbohydrate using Calvin Cycle
• Chemotrophic autotrophs (chemoautotrophs) are
less familiar
• Methanogens (Sec.13.20) = Archaea; sediments,
animals
• Reduce CO2 to CH4 with unusual enzymes for energy
• Utilize methanol or acetate from CH4 for carbon
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3.3 Energy Classes of Microorganisms
• Heterotrophs may be chemotrophs or phototrophs
with respect to energy source
• Chemotrophic heterotrophs (chemoheterotrophs)
are very common
• Phototrophic heterotrophs (photoheterotrophs)
also exist
• Heliobacter (Sec. 14.8) a gram + rod
• Carries out photosynthesis using bacteriochlorophyll g
• Relies on pyruvate, lactate, butyrate, acetate for carbon
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3.4 Bioenergetics
• In any chemical reaction, some energy is lost
as heat but some energy (Free energy = G):
energy released that is available to do work
• The change in free energy during a reaction at
standard conditions is referred to as ΔG0′
• ΔG: free energy that occurs under actual
conditions in a cell
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3.6 Electron Donors and Electron Acceptors
• Energy from oxidation–reduction (redox) reactions
is used in synthesis of energy-rich compounds
(e.g., ATP)
• Redox reactions occur in pairs (two half
reactions; Figure 3.8)
• Electron donor: the substance oxidized in a
redox reaction (loses electrons)
• Electron acceptor: the substance reduced in a
redox reaction (gains electrons)
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3.6 Electron Donors and Electron Acceptors
Half reaction
donating e–
Half reaction
accepting e–
Electron
donor
Formation
of water
Electron
acceptor
Net reaction
Energy from oxidation–reduction (redox) reactions is used in
synthesis of energy-rich compounds (e.g., ATP)
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Figure 3.8
3.6 Electron Donors and Electron Acceptors
• Reduction potential (E0′): measurement of energy
transfer in redox reactions or tendency to donate
electrons
• Expressed as volts (V)
• Half reactions with highly positive reduction
potentials occur easily
• Reduced substance with a more negative E0′
donates electrons to the oxidized substance with a
more positive E0′
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3.6 Electron Donors and Electron Acceptors
• The redox tower represents the range of possible
reduction potentials (Figure 3.9)
• The reduced substance at the top of the tower
donates electrons
• The oxidized substance at the bottom of the tower
accepts electrons
• The farther the electrons "drop," the greater the
amount of energy released
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Figure 3.9
3.6 Electron Donors and Electron Acceptors
• Redox reactions usually involve reactions between
intermediates (carriers)
• Electron carriers are divided into two classes
• Prosthetic groups (attached to enzymes)
• Example: heme
• Coenzymes (diffusible)
• Examples: NAD+, NADP
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3.7 Energy-Rich Compounds
• Chemical energy released in redox reactions is
primarily stored in certain phosphorylated
compounds (Figure 3.12)
• ATP; the prime energy currency
• Phosphoenolpyruvate
• Glucose 6-phosphate
• Chemical energy also stored in coenzyme A, a
high energy sulfur compound
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Anhydride bonds Ester bond
Ester bond
Anhydride bond
Phosphoenolpyruvate
Adenosine triphosphate (ATP)
Glucose 6-phosphate
Compound
Thioester
bond
Acetyl
Anhydride bond
Coenzyme A
Acetyl-CoA
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Acetyl phosphate
G0′kJ/mol
ΔG0′< 30kJ
Phosphoenolpyruvate
1,3-Bisphosphoglycerate
Acetyl phosphate
ATP
ADP
Acetyl-CoA
–51.6
–52.0
–44.8
–31.8
–31.8
–35.7
ΔG0′< 30kJ
AMP
Glucose 6-phosphate
–14.2
–13.8
Figure 3.12
3.7 Energy-Rich Compounds
• Long-term energy storage involves insoluble
polymers that can be oxidized to generate ATP
• Examples in prokaryotes
• Glycogen
• Poly-β-hydroxybutyrate and other
polyhydroxyalkanoates
• Elemental sulfur
• Examples in eukaryotes
• Starch
• Lipids (simple fats)
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3.7 Energy-Rich Compounds
• An energy rich compound that also serves as an
electron carrier
• Reduced NAD carries high energy electrons
• Provides “reducing power” for biosynthesis
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Modes of ATP Synthesis
• Substrate level phosphorylation
• Transmembrane gradient (eg proton gradient or
pmf)
• Respiration
• Aerobic
• Anaerobic
• Photosynthesis
• Anoxygenic
• Oxygenic
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• Direct transfer of high energy phosphate
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• Example: pyruvate kinase reaction
• Part of catabolic pathway called glycolysis or EMP
pathway
• PEP is a product of another reaction
Substrate level phosphorylations are common in all organisms
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Metabolic pathways that use a gradient to make ATP
• Respiration
• Aerobic-use oxygen as final electron acceptor
• Anaerobic-use something other than oxygen as final
acceptor
• Photosynthesis
• Anoxygenic-use something other than water as original
electron donor
• Oxygenic-use water as original electron donor
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Transmembrane gradient
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Figure 3.20
• Transmembrane gradient
• Fig. 3.20 shows NADH as the electron donor
• And oxygen as the electron acceptor
• But………….
• MICROBES CAN USE MANY OTHER
SUBSTANCES AS DONORS OR
ACCEPTORS!!!!!!
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• ATP Synthase aka
F1F0 Synthase or
ATPase
• Controlled entry of
protons drives ATP
synthesis
• 3-4 protons/ATP
• Can work in reverse
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• Anaerobic respiration
• Nitrate (NO3–), ferric iron (Fe3+), sulfate (SO42–),
carbonate (CO32–), fumarate, DMSO are examples
of acceptors
• Less energy released compared to aerobic
respiration
• “Primitive” form of respiration?
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Figure 13.39
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Figure 13.39
Nitrate Reduction is a Good Example of
Anaerobic Respiration (Ch.13.16 and 13.17)
• Nitrate Reduction = use of nitrate as electron
acceptor in anaerobic respiration (nitrate to nitrite)
• A dissimilative process
• Conversion of nitrate to more reduced substances
such as N2O or N2 = denitrification
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Nitrate reductase
Nitrate
reduction
(Escherichia
coli)
Nitrite reductase
Nitric oxide reductase
Denitrification
(Pseudomonas
stutzeri)
Gases
Nitrous oxide reductase
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Figure 13.40
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Figure 13.41
• Lithotroph: type of chemotroph that uses
inorganic substance (e.g. a mineral) as a source of
energy: in other words as an electron donor.
• Anaerobic respiration: process in which electrons
are transferred to a final acceptor that is not
oxygen-can be organic or inorganic
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Photosynthesis
• Uses light energy to remove an electron from an
electron donor and boost it to a high energy level
• Photons captured by pigment molecules
• Chlorophylls, bacteriochlorophylls, accessory
pigments such as carotenoids
• Absorb different wavelengths
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Photosynthesis-Anoxygenic
• Anoxygenic photosynthesis uses an electron
donor other than water
• H2S is a common donor
• Green sulfur bacteria, purple bacteria, Heliobacter,
some Archaea
• Use a transmembrane gradient to generate ATP
via cyclic photophosphorylation
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Photosynthesis-Oxygenic
• Oxygenic photosynthesis uses water as electron
donor
• Cyanobacteria
• 2 Photosystems linked by electron carriers
• Use a transmembrane gradient to generate ATP
via either cyclic photophosphorylation or
noncyclic photophosphorylation
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Makes reducing power in the form of NADPH
When reducing power is not needed-cyclic
photophosphorylation
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III. Fermentation and Respiration Overview
• 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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