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Microbial Metabolism
§  All cells need to accomplish two fundamental tasks
•  Synthesize new parts
•  Cell walls, membranes, ribosomes, nucleic acids
•  Harvest energy to power reactions
•  Sum total of these is called metabolism
•  Human implications
• 
• 
• 
• 
• 
Used to make biofuels
Used to produce food
Important in laboratory
Invaluable models for study
Unique pathways potential
drug targets
6.1. Principles of Metabolism
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§  Can separate metabolism into
two parts
CATABOLISM
ANABOLISM
Energy source
(glucose)
Cell structures
(cell wall, membrane,
ribosomes, surface
structures)
•  Catabolism
•  Processes that degrade
compounds to release energy
•  Cells capture to make ATP
Energy
Macromolecules
(proteins, nucleic acids,
polysaccharides, lipids)
Energy
•  Anabolism
Subunits
(amino acids,
nucleotides, sugars,
fatty acids)
•  Biosynthetic processes
•  Assemble subunits of
macromolecules
•  Use ATP to drive reactions
•  Processes intimately linked
Energy
Precursor
metabolites
Waste products
Nutrients
(acids, carbon
dioxide)
(source of nitrogen,
sulfur, etc.)
Catabolic processes harvest
the energy released during the
breakdown of compounds and
use it to make ATP. The
processes also produce
precursor metabolites used in
biosynthesis.
Anabolic processes (biosynthesis)
synthesize and assemble subunits
of macromolecules that make up
the cell structures. The processes
use the ATP and precursor
metabolites produced in
catabolism.
Harvesting Energy
§  Free energy is energy available to do work
•  E.g., energy released when chemical bond is broken
•  Compare free energy of reactants, products
•  Exergonic reactions: reactants have more free energy
•  Energy is released in reaction
•  Endergonic reactions: products have more free energy
•  Reaction requires input of energy
•  Change in free energy is same regardless of number of
steps involved (e.g., converting glucose to CO2 + H2O)
•  Cells use multiple steps when degrading compounds
•  Energy released from exergonic reactions powers
endergonic reactions
1
Fig. 6.4
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Intermediatea
Starting compound
Intermediateb
End product
Intermediateb1
End product1
Intermediateb2
End product2
(a) Linear metabolic pathway
Starting compound
Intermediatea
(b) Branched metabolic pathway
Starting compound
Intermediated
End product
Intermediatea
Intermediatec
Intermediateb
(c) Cyclical metabolic pathway
Fig. 6.9
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Glucose molecules
To:
Lipid
synthesis
To:
Amino acid
synthesis
To:
Carbohydrate
synthesis
To:
Nucleic acid
synthesis
CO2 molecules + energy
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Terminal
electron
acceptors
Energy
sources
Energy
released
Organic
carbon
compounds
Organic
carbon
compounds
H 2S
CO2
SO4
S0
FeOOH
Fe2+
NH4+
NO2– ( to form NH4+)
NO3– ( to form NH4+)
Mn2+
MnO2
Relative tendency to give up electrons
Relative tendency to give up electrons
H2
NO3– ( to form NH2)
O2
(a) Energy is released when electrons are moved from an energy source with a
low affinity for electrons to a terminal electron acceptor with a higher affinity.
Terminal
electron
acceptors
Inorganic
energy
sources
H2
Pyruvate
NO3–
(to form
NH4+)
O2
(b) Three examples of
chemoorganotrophic
metabolism
Relative tendency to give up electrons
Glucose
Terminal
electron
acceptors
H 2S
CO2
Relative tendency to give up electrons
Glucose
as an
energy source
Relative tendency to give up electrons
Fig. 6.7
Fe2+
O2
(c) Three examples of
chemolithotrophic metabolism
2
Components of Metabolic Pathways
§  Role of the Chemical Energy Source and the
Terminal Electron Acceptor
§  Some atoms, molecules more electronegative than
others
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Energy
release
Organic
carbon
compounds
H2
Organic
carbon
compounds
H 2S
CO2
SO4
S0
FeOOH
Fe2+
NH4+
NO2– ( to form NH4+)
NO3– ( to form NH4+)
Mn2+
MnO2
Relative tendency to give up electrons
•  (E.g., glucose to O2)
Terminal
electron
acceptors
Energy
sources
Relative tendency to give up electrons
•  Greater affinity for electrons
•  Energy released when
electrons move from low
affinity molecule to high
affinity molecule
NO3– ( to form NH2)
O2
(a) Energy is released when electrons are moved from an energy source with a
low affinity for electrons to a terminal electron acceptor with a higher affinity.
Components of Metabolic Pathways
§  Role of the Chemical Energy Source and the
Terminal Electron Acceptor (continued…)
§  More energy released when
difference in electronegativity
is greater
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•  Acceptor:
•  Terminal electron acceptor
Glucose
Pyruvate
NO3–
(to form
NH4–)
O2
(b) Three examples of
chemoorganotrophic
metabolism
Terminal
electron
acceptors
H2
H 2S
CO2
Fe2+
Relative tendency to give up electrons
•  Energy source
Inorganic
energy
sources
Relative tendency to give up electrons
•  Electron donor:
Relative tendency to give up electrons
Glucose
Terminal
as an
electron
energy source acceptors
O2
(c) Three examples of
chemolithotrophic metabolism
Components of Metabolic Pathways
§  Role of Electron Carriers
•  Energy harvested in stepwise process
•  Electrons transferred to electron carriers, which represent
reducing power (easily transfer electrons to molecules)
–  Raise energy level of recipient molecule
•  NAD+/NADH, NADP+/NADPH, and FAD/FADH2
3
Components of Metabolic Pathways
§  Role of ATP
•  Adenosine triphospate (ATP) is energy currency
• 
• 
• 
• 
Composed of ribose, adenine, three phosphate groups
Adenosine diphospate (ADP) acceptor of free energy
Cells produce ATP by adding Pi to ADP using energy
Release energy from ATP to yield ADP and Pi
§  Three processes to generate ATP
•  Substrate-level phosphorylation
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Unstable (high-energy) bonds
•  Exergonic reaction powers
•  Oxidative phosphorylation
•  Proton motive force drives
•  Photophosphorylation
•  Sunlight used to create proton
motive force to drive
P ~ P~ P
ATP
Pi
Pi
Energy used
The energy comes
from catabolic
reactions.
Energy released
The energy drives
anabolic reactions.
P~ P
ADP
6.3. The Central Metabolic Pathways
§  ATP
§  Reducing power: NADH, FADH2, NADPH
§  Precursor metabolites
•  Glucose molecules can have
different fates
•  Can be completely oxidized
to CO2 for maximum ATP
•  Can be siphoned off as
precursor metabolite for
use in biosynthesis
Precursor Metabolites
§  Precursor metabolites are intermediates of
catabolism that can be used in anabolism
•  Serve as carbon skeletons for building macromolecules
•  E.g., pyruvate can be converted into amino acids alanine,
leucine, or valine
4
Components of Metabolic Pathways
§  Prokaryotes remarkably diverse in using energy
sources and terminal electron acceptors
•  Organic, inorganic compounds used as energy source
•  O2, other molecules used as terminal electron acceptor
•  Electrons removed through series of oxidation-reduction
reactions or redox reactions
•  Substance that loses electrons is oxidized
•  Substance that gains electrons is reduced
•  Electron-proton pair, or
Transfer of electrons
hydrogen, actually moves
e
•  Dehydrogenation = oxidation Compound + Compound
X
Y
•  Hydrogenation = reduction
X loses electron(s).
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–
e–
Compound X + Compound Y
(reduced)
(oxidized)
Y gains electron(s).
X is the reducing agent.
Y is the oxidizing agent.
X is oxidized by the reaction.
Y is reduced by the reaction.
Overview of Catabolism
§  Three central metabolic pathways
•  Oxidize glucose to CO2
•  Catabolic, but precursor metabolites and reducing power
can be diverted for use in biosynthesis
•  Termed amphibolic to reflect dual role
•  Glycolysis
•  Splits glucose (6C) to two pyruvates (3C)
•  Generates modest ATP, reducing power, precursors
•  Pentose phosphate pathway
•  Primary role is production precursor metabolites, NADPH
•  Tricarboxylic acid cycle
•  Oxidizes pyruvates from glycolysis
•  Generates reducing power, precursor metabolites, ATP
Overview of Catabolism
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GLUCOSE
§  Central metabolic
pathways
•  Glycolysis
•  Pentose phosphate
pathway
•  Tricarboxylic acid cycle
§  Key outcomes
•  ATP
•  Reducing power
•  Precursor metabolites
2
Pentose phosphate
pathway
Starts the oxidation of glucose
Glycolysis
Oxidizes glucose to pyruvate
1
Yields
~
~
+
Reducing
power
ATP
by substrate-level
phosphorylation
Yields
Reducing
power
Biosynthesis
5
3a
Fermentation
Reduces pyruvate
or a derivative
Acids, alcohols, and gases
Pyruvate
Pyruvate
Transition step
CO2
CO2
Yields
Reducing
power
AcetylCoA
AcetylCoA
X2
CO2
CO2
3b
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
Yields
ATP
by substrate-level
phosphorylation
~
~
+
Reducing
power
4
Respiration
Uses the electron transport
chain to convert reducing
power to proton motive force
Yields
~
~
ATP
by oxidative
phosphorylation
5
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Glycolysis
Pentose phosphate
pathway
Glucose 6-phosphate
Lipopolysaccharide
(polysaccharide)
Fructose 6-phosphate
Ribose 5-phosphate
Nucleotides
amino acids
(histidine)
Erythrose 5-phosphate
Peptidoglycan
Dihydroxyacetone
phosphate
Amino acids
(phenylalanine,
tryptophan,
tyrosine)
Lipids
(glycerol
component)
3-phosphoglycerate
Amino acids
(cysteine,
glycine, serine)
Phosphoenolpyruvate
Amino acids
(phenylalanine,
tryptophan, tyrosine)
Anabolic
Pathways—
Synthesizing
Subunits from
Precursor
Molecules
Pyruvate
Pyruvate
Acetyl-CoA
Acetyl-CoA
Amino acids
(alanine,
leucine, valine)
Lipids
(fatty acids)
Oxaloacetate
Amino acids
(aspartate, asparagine,
isoleucine, lysine,
methionine, threonine)
α- ketoglutarate
X2
Amino acids
(arginine, glutamate,
glutamine, proline)
TCA cycle
6.3. The Central Metabolic Pathways
§  Pentose Phosphate Pathway
•  Also breaks down glucose
•  Important in biosynthesis of precursor metabolites
•  Ribose 5-phosphate, erythrose 4-phosphate
•  Also generates reducing power: NADPH
•  Yields vary depending upon alternative taken
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GLUCOSE
2
Pentose phosphate
pathway
Starts the oxidation of glucose
Glycolysis
Oxidizes glucose to pyruvate
1
Yields
~
~
+
Reducing
power
ATP
by substrate-level
phosphorylation
Yields
Reducing
power
Biosynthesis
5
3a
Fermentation
Reduces pyruvate
or a derivative
Acids, alcohols, and gases
Pyruvate
Pyruvate
Transition step
CO2
CO2
Yields
Reducing
power
AcetylCoA
AcetylCoA
X2
CO2
CO2
3b
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
Yields
~
ATP
by substrate-level
phosphorylation
~
+
Reducing
power
4
Respiration
Uses the electron transport
chain to convert reducing
power to proton motive force
Yields
~
~
ATP
by oxidative
phosphorylation
6
6.3. The Central Metabolic Pathways
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GLUCOSE
Pentose phosphate
pathway
Starts the oxidation of glucose
2
Yields
Glycolysis
Oxidizes glucose to pyruvate
1
P~ P~ P +
Reducing
power
ATP
by substrate-level
phosphorylation
§  Glycolysis
Yields
Reducing
power
Biosynthesis
5
Fermentation
Reduces pyruvate
or a derivative
Acids, alcohols, and gases
3a
Glucose
Transition step
CO2
CO2
Yields
•  Converts 1 glucose
to 2 pyruvates; yields
net 2 ATP, 2 NADH
•  Investment phase:
Reducing
power
Pyruvate
Pyruvate
x2
CO2
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
Yields
P~ P ~ P +
~
ADP
Reducing
power
ATP
by substrate-level
phosphorylation
1 ATP is expended to add a phosphate group.
~ ~
ATP
CO2
3b
Respiration
Uses the electron transport
Chain to convert reducing
power to proton motive force
4
Yields
Glucose
6-phosphate
P~ P~ P
ATP
by oxidative
phosphorylation
2
A chemical rearrangement occurs.
Fructose
6-phosphate
~ ~
ATP
ATP is expended to add a phosphate group.
4
The 6-carbon molecule is split into two 3-carbon
molecules.
~
ADP
•  2 phosphate groups
added
•  Glucose split to two
3-carbon molecules
3
Fructose
1,6-bisphosphate
Dihydroxyacetone
phosphate
A chemical rearrangement of one of the
molecules occurs.
5
Glyceraldehyde
3-phosphate
NAD+
NAD+
NADH + H+
1,3-bisphosphoglycerate
•  Pay-off phase:
ADP
~
~
The addition of a phosphate
group is coupled to a redox
reaction, generating NADH and
a high-energy phosphate bond.
~
~
ATP
•  3-carbon molecules
converted to pyruvate
•  Generates 4 ATP,
2 NADH total
6
NADH + H+
ATP is produced by
substrate-level
phosphorylation.
7
~ ~
~ ~
3-phosphoglycerate
8
2-phosphoglycerate
A chemical rearrangement occurs.
9
H 2O
H 2O
Phosphoenolpyruvate
ADP
~
~
ATP
Water is removed, causing the
phosphate bond to become
high-energy.
10
ATP is produced by
substrate-level
phosphorylation.
~ ~
~ ~
Pyruvate
6.3. The Central Metabolic Pathways
§  Transition Step
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GLUCOSE
•  CO2 is removed
from pyruvate
•  Electrons reduce
NAD+ to
NADH + H+
•  2-carbon acetyl
group joined to
coenzyme A to form
acetyl-CoA
•  Takes place in
mitochondria in
eukaryotes
2
Pentose phosphate
pathway
Starts the oxidation of glucose
Yields
Glycolysis
Oxidizes glucose to pyruvate
1
~
~
+
Reducing
power
ATP
by substrate-level
phosphorylation
Pyruvate
Yields
CO2
Reducing
power
Biosynthesis
Pyruvate
CO2
NAD+
Acids, alcohols, and gases
CoA
Transition step
Yields
Transition step:
CO2 is removed, a redox reaction generates
NADH, and coenzyme A is added.
Fermentation
Reduces pyruvate
or a derivative
5
Pyruvate
3a
CO2
Reducing
power
AcetylCoA
AcetylCoA
NADH + H+
x2
CO2
CoA
CO2
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
3b
Acetyl-CoA
1 The acetyl group is transferred
to oxaloacetate to start a new
round of the cycle.
Yields
~
~
+
Reducing
power
ATP
by substrate-level
phosphorylation
CoA
Respiration
Uses the electron transport
chain to convert reducing
power to proton motive force
4
Yields
~
~
ATP
by oxidative
phosphorylation
NADH + H+
A redox reaction
generates NADH.
8
Oxaloacetate
2 A chemical
rearrangement occurs.
Citrate
NAD+
Isocitrate
NAD+
Malate
Water is added.
7
3 A redox reaction
generates NADH
and CO2 is
removed.
NADH + H+
H 2O
CO2
Fumarate
α-ketoglutarate
NAD+
4
FADH2
6
CoA
A redox reaction
generates FADH2-
NADH + H+
FAD
5 The energy released
during CoA removal is
harvested to produce ATP.
CoA
Succinyl-CoA
Succinate
CoA
A redox reaction
generates NADH,
CO2 is removed,
and coenzyme A
is added.
CO2
~ + Pi
~ ~
ATP
ADP
6.3. The Central Metabolic Pathways
§  Tricarboxylic
Acid (TCA)
Cycle
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GLUCOSE
2
Pentose phosphate
pathway
Starts the oxidation of glucose
2 CO2
2 ATP
6 NADH
2 FADH2
Precursor
metabolites
~
+
Reducing
power
Pyruvate
CO2
Reducing
power
Biosynthesis
3a
Pyruvate
CO2
NAD+
Acids, alcohols, and gases
CoA
Transition step
Yields
Transition step:
CO2 is removed, a redox reaction generates
NADH, and coenzyme A is added.
Fermentation
Reduces pyruvate
or a derivative
5
Pyruvate
•  Completes
oxidation of
glucose
• 
• 
• 
• 
• 
~
ATP
by substrate-level
phosphorylation
Yields
CO2
Reducing
power
AcetylCoA
AcetylCoA
§  Produces
Yields
Glycolysis
Oxidizes glucose to pyruvate
1
NADH + H+
x2
CO2
CoA
CO2
3b
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
Acetyl-CoA
1 The acetyl group is transferred
to oxaloacetate to start a new
round of the cycle.
Yields
~
~
+
Reducing
power
ATP
by substrate-level
phosphorylation
CoA
Respiration
Uses the electron transport
chain to convert reducing
power to proton motive force
4
Yields
~
~
ATP
by oxidative
phosphorylation
A redox reaction
generates NADH.
8
NADH +
H+
Oxaloacetate
2 A chemical
rearrangement occurs.
Citrate
NAD+
Isocitrate
NAD+
Malate
Water is added.
7
3 A redox reaction
generates NADH
and CO2 is
removed.
NADH + H+
H 2O
CO2
Fumarate
α-ketoglutarate
NAD+
4
FADH2
6
CoA
A redox reaction
generates FADH2-
NADH + H+
FAD
5 The energy released
during CoA removal is
harvested to produce ATP.
CoA
Succinyl-CoA
Succinate
CoA
CO2
~ + Pi
~ ~
ATP
A redox reaction
generates NADH,
CO2 is removed,
and coenzyme A
is added.
ADP
7
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NH2
NH3 (ammonia)
α-ketoglutarate
Glutamate is
synthesized
by adding ammonia
to the precursor
metabolite
α-ketoglutarate.
Aspartate
NH2
Oxaloacetate
Glutamate
The amino group (NH2) of glutamate can be
transferred to other carbon compounds to
produce other amino acids.
Fig. 6.30
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From glycolysis
Phenylalanine
Branch
point II
Compound
a
3-C
Branch
point I
7-C
compound
+
Tyrosine
4-C
Compound
b
Tryptophan
From pentose
phosphate pathway
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
GLUCOSE
2
Pentose phosphate
pathway
Starts the oxidation of glucose
Glycolysis
Oxidizes glucose to pyruvate
1
Yields
~
~
+
Reducing
power
ATP
by substrate-level
phosphorylation
Yields
Reducing
power
Biosynthesis
5
3a
Fermentation
Reduces pyruvate
or a derivative
Acids, alcohols, and gases
Pyruvate
Pyruvate
Transition step
CO2
CO2
Yields
Reducing
power
AcetylCoA
AcetylCoA
X2
CO2
CO2
3b
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
Yields
~
ATP
by substrate-level
phosphorylation
~
+
Reducing
power
4
Respiration
Uses the electron transport
chain to convert reducing
power to proton motive force
Yields
~
~
ATP
by oxidative
phosphorylation
8
Table 6.1
Overview of Catabolism
§  Respiration transfers electrons from glucose to
electron transport chain
•  Electron transport chain generates proton motive force
•  Harvested to make ATP via oxidative phosphorylation
•  Aerobic respiration
–  O2 is terminal electron acceptor
•  Anaerobic respiration
–  Molecule other than O2 as terminal electron acceptor
–  Also use modified version of TCA cycle
6.4. Respiration
§  Uses reducing power (NADH, FADH2) generated
by glycolysis, transition step, and TCA cycle to
synthesize ATP
•  Electron transport chain generates proton motive force
•  Drives synthesis of ATP by ATP synthase
•  Process proposed by British scientist Peter Mitchell in
1961
•  Initially widely dismissed
•  Mitchell conducted years of self-funded research
•  Received a Nobel Prize in 1978
•  Now called chemiosmotic theory
9
Table 6.3
The Electron Transport Chain—Generating Proton
Motive Force
§  Electron transport chain is membrane-embedded
electron carriers
• 
• 
• 
• 
• 
Pass electrons sequentially, eject protons in process
Prokaryotes: in cytoplasmic membrane
Eukaryotes: in inner mitochondrial membrane
Energy gradually released
Release coupled to ejection
of protons
•  Creates electrochemical
gradient
•  Used to synthesize ATP
•  Prokaryotes can also power
transporters, flagella
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Electrons from the
energy source 2 e–
Energy released is
used to generate a
proton motive force.
High energy
Low energy
Electrons donated
to the terminal
electron acceptor.
2
1/
2
H+
O2
H 2O
The Electron Transport Chain—Generating Proton
Motive Force
§  Components of an Electron Transport Chain
•  Most carriers grouped into large protein complexes
•  Serve as proton pumps
•  Three general groups are notable
•  Quinones
•  Lipid-soluble molecules
•  Move freely, can transfer electrons between complexes
•  Cytochromes
•  Contain heme, molecule with iron atom at center
•  Several types
•  Flavoproteins
•  Proteins to which a flavin is attached
•  FAD, other flavins synthesized from riboflavin
10
The Electron Transport Chain of Mitochondria
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GLUCOSE
2
Pentose phosphate
pathway
Starts the oxidation of glucose
Yields
Glycolysis
Oxidizes glucose to pyruvate
1
P ~ P ~P +
Reducing
power
ATP
by substrate-level
phosphorylation
Yields
Reducing
power
Biosynthesis
5
Pyruvate
Pyruvate
Eukaryotic cell
Fermentation
Reduces pyruvate
or a derivative
Acids, alcohols, and gases
3a Transition step
CO2
Yields
CO2
Reducing
power
AcetylCoA
AcetylCoA
x2
CO2
CO2
3b
TCA cycle
Incorporates an acetyl
group and releases CO2
Inner
mitochondrial
membrane
(TCA cycles twice)
Yields
Reducing
power
ATP
by substrate-level
phosphorylation
4
Respiration
Uses the electron transport
chain to convert reducing
power to proton motive force
Yields
P
P P
ATP
by oxidative
phosphorylation
4
Use of Proton Motive Force
Electron Transport Chain
Complex III
Complex I
H+
4
H+
Ubiquinone
2
H+
10
1/
2
2 H+
Intermembrane
space
Mitochondrial
matrix
O2
Terminal
electron acceptor
H 2O
NAD+
H+
H+
2 e–
Complex II
+
ATP synthase
(ATP synthesis)
Cytochrome c
Path of
electrons
NADH
Proton motive force
is used to drive:
Complex IV
3 ATP
+ 3 Pi
3 ADP
Fig. 6.20
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Prokaryotic cell
Cytoplasmic
membrane
Electron Transport Chain
NADH dehydrogenase
Uses of Proton Motive Force
Ubiquinol
veoxidase
force
rive:
H+ (0 or 4)
ATP synthase
(ATP synthesis)
H+ (2 or 4)
Ubiquinone
Path of
electrons
10
Active transport
(one mechanism)
H+
Rotation of a flagella
H+
H+
Proton motive force
is used to drive:
Transported
molecule
Outside of
cytoplasmic
membrane
2 e– –
Cytoplasm
Succinate
dehydrogenase
NADH
+
H+
NAD+
2 H+
1/
2
H 2O
O2
Terminal
electron acceptor
3 ATP
+ 3 Pi
3 ADP
The Electron Transport Chain—Generating Proton
Motive Force
§  General Mechanisms of Proton Ejection
•  Some carriers accept only hydrogen atoms (protonelectron pairs), others only electrons
•  Spatial arrangement in membrane shuttles protons to
outside of membrane
•  When hydrogen carrier accepts electron from electron
carrier, it picks up proton from inside cell
–  or mitochondrial matrix
•  When hydrogen carrier passes electrons to electron
carrier, protons released to outside of cell
–  or intermembrane space of mitochondria
•  Net effect is movement of protons across membrane
•  Establishes concentration gradient
•  Driven by energy released during electron transfer
11
The Electron Transport Chain—Generating Proton
Motive Force
§  Electron Transport Chain of Mitochondria
•  Complex I (NADH dehydrogenase complex)
•  Accepts electrons from NADH, transfers to ubiquinone
•  Pumps 4 protons
•  Complex II (succinate dehydrogenase complex)
•  Accepts electrons from TCA cycle via FADH2, “downstream” of
those carried by NADH
•  Transfers electrons to ubiquinone
•  Complex III (cytochrome bc1 complex)
•  Accepts electrons from ubiquinone from Complex I or II
•  4 protons pumped; electrons transferred to cytochrome c
•  Complex IV (cytochrome c oxidase complex)
•  Accepts electrons from cytochrome c, pumps 2 protons
•  Terminal oxidoreductase, meaning transfers electrons to
terminal electron acceptor (O2)
The Electron Transport Chain—Generating Proton
Motive Force
§  Electron Transport Chain of Prokaryotes
•  Tremendous variation: even single species can have
several alternate carriers
•  E. coli serves as example of versatility of prokaryotes
•  Aerobic respiration in E. coli
•  Can use 2 different NADH dehydrogenases
–  Proton pump equivalent to complex I of mitochondria
•  Succinate dehydrogenase equivalent to complex II of
mitochondria
•  Can produce several alternatives to optimally use
different energy sources, including H2
•  Lack equivalents of complex III or cytochrome c
–  Quinones shuttle electrons directly to ubiquinol
oxidase, a terminal oxidoreductase
–  Two versions for high or low O2 concentrations
The Electron Transport Chain—Generating Proton
Motive Force
§  Electron Transport Chain of Prokaryotes (cont…)
•  Anaerobic respiration in E. coli
•  Harvests less energy than aerobic respiration
–  Lower electron affinities of terminal electron acceptors
•  Some components different
•  Can synthesize terminal oxidoreductase that uses nitrate
as terminal electron acceptor
–  Produces nitrite
–  E. coli converts to less toxic ammonia
•  Sulfate-reducers use sulfate (SO42–) as terminal
electron acceptor
•  Produce hydrogen sulfide as end product
12
The Electron Transport Chain—Generating Proton
Motive Force
§  ATP Synthase—Harvesting the Proton Motive
Force to Synthesize ATP
•  Energy required to establish gradient
•  Released when gradient is eased
•  ATP synthase allows protons to flow down gradient in
controlled manner
•  Uses energy to add phosphate group to ADP
•  1 ATP formed from entry of ~3 protons
•  Calculating yields
•  Based on experiments on rat mitochondria:
~2.5 ATP made per electron pair from NADH
~1.5 ATP made per electron pair from FADH2
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
GLUCOSE
Pentose phosphate
2
pathway
Starts the oxidation of glucose
Yields
Glycolysis
1 Oxidizes glucose to pyruvate
Yields
Reducing
power
ATP
by substrate-level
phosphorylation
Reducing
power
Biosynthesis
5
Pyruvate
Pyruvate
Fermentation
Reduces pyruvate
or a derivative
GLUCOSE
Glycolysis
Oxidizes glucose to pyruvate
~~
2 ATP
net gain = 0
~~
2 ATP
Acids, alcohols, and gases
3a Transition step
Yield
CO2
CO2
Reducing
power
AcetylCoA
AcetylCoA
x2
CO2
CO2
TCA cycle
3b Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
Yields
ATP
by substrate-level
phosphorylation
Reducing
power
Respiration
4 Uses the electron transport
chain to convert reducing
power to proton motive force
Yields
ATP
by oxidative
phosphorylation
2 NADH
Oxidative
phosphorylation
Substrate-level
phosphorylation
Pyruvate
Pyruvate
AcetylCoA
AcetylCoA
2 NADH
~~
6 ATP
6 NADH
~~
18 ATP
~~
4 ATP
Oxidative
phosphorylation
x2
CO2
Oxidative
phosphorylation
2 FADH2
CO2
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
~~
6 ATP
~~
2 ATP
Oxidative
phosphorylation
Substrate-level
phosphorylation
~~
2 ATP
The Electron Transport Chain—Generating Proton
Motive Force
§  Calculating theoretical maximum yields
•  In prokaryotes:
• 
• 
• 
• 
Glycolysis: 2 NADHà 6 ATP
Transition step: 2 NADH à 6 ATP
TCA Cycle: 6 NADH à 18 ATP; 2 FADH2 à 4 ATP
Total maximum oxidative phosphorylation yield = 34 ATP
•  Slightly less in eukaryotic cells
•  NADH from glycolysis in cytoplasm transported across
mitochondrial membrane to enter electron transport chain
–  Requires ~1 ATP per NADH generated
13
The Electron Transport Chain—Generating Proton
Motive Force
§  ATP Yield of Aerobic Respiration in Prokaryotes
•  Substrate-level phosphorylation:
•  2 ATP (from glycolysis; net gain)
•  2 ATP (from the TCA cycle)
•  4 ATP (total)
•  Oxidative phosphorylation:
• 
• 
• 
• 
6 ATP (from reducing power gained in glycolysis)
6 ATP (from reducing power gained in transition step)
22 ATP (from reducing power gained in TCA cycle)
34 (total)
•  Total ATP gain (theoretical maximum) = 38
Overview of Catabolism
§  Fermentation
•  If cells cannot respire, will run out of carriers available to
accept electrons
•  Glycolysis will stop
•  Fermentation uses pyruvate or derivative as terminal
electron acceptor to regenerate NAD+
•  Glycolysis can continue
6.5. Fermentation
§  Fermentation used when respiration not an option
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
•  E. coli is facultative anaerobe
•  Aerobic respiration, anaerobic
respiration, and fermentation
GLUCOSE
Pentose phosphate
pathway
Starts the oxidation of glucose
2
Yields
Glycolysis
Oxidizes glucose to pyruvate
1
P ~
P
~P +
Reducing
power
ATP
by substrate-level
phosphorylation
Yields
Reducing
power
Biosynthesis
Fermentation
Reduces pyruvate
or a derivative
5
Pyruvate
Pyruvate
3a
Acids, alcohols, and gases
Transition step
CO2
CO2
Yields
Reducing
power
AcetylCoA
AcetylCoA
•  Streptococcus pneumoniae
lacks electron transport chain
x
CO2
2
CO2
3b
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
Yields
P ~
P ~
Reducing
power
P
ATP
by substrate-level
phosphorylation
+
4
•  Fermentation only option
P ~
P
~
P
ATP
by oxidative
phosphorylation
•  ATP-generating reactions are
only those of glycolysis
•  Additional steps consume
excess reducing power
–  Regenerate NAD+
Respiration
Uses the electron transport
chain to convert reducing
power to proton motive force
Yields
NADH + H+ NAD+
H 3C
O
O
C
C
O–
H 3C
OH
O
C
C
O–
H
Lactate
Pyruvate
(a) Lactic acid fermentation
CO2
H 3C
O
O
C
C
O–
Pyruvate
NADH+ H+
O
H 3C
C
H
Acetaldehyde
NAD+
OH
H 3C
C
H
H
Ethanol
(b) Ethanol fermentation
14
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
GLUCOSE
Pentose phosphate
pathway
Starts the oxidation of glucose
2
Yields
Glycolysis
Oxidizes glucose to pyruvate
1
P
~
P
~
Reducing
power
+
P
ATP
by substrate-level
phosphorylation
Yields
Reducing
power
Biosynthesis
Fermentation
Reduces pyruvate
or a derivative
5
Pyruvate
Pyruvate
Acids, alcohols, and gases
3a
Transition step
CO2
CO2
Yields
Reducing
power
AcetylCoA
AcetylCoA
x
CO2
2
CO2
3b
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
Yields
P
ATP
by substrate-level
phosphorylation
~
P
~
Reducing
power
P
+
4
Respiration
Uses the electron transport
chain to convert reducing
power to proton motive force
Yields
P
~
P
~
P
ATP
by oxidative
phosphorylation
NADH +
H 3C
O
O
C
C
NAD+
H+
O–
OH
O
C
C
H 3C
O–
H
Lactate
Pyruvate
(a) Lactic acid fermentation
CO2
O
H 3C
C
+
NADH
O
H+
NAD+
O
O–
C
Pyruvate
H 3C
OH
C
H 3C
H
C
H
H
Ethanol
Acetaldehyde
(b) Ethanol fermentation
6.5. Fermentation
§  Fermentation end products varied; helpful in
identification, commercially useful
•  Ethanol
•  Butyric acid
•  Propionic acid
•  2,3-Butanediol
•  Mixed acids
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Pyruvate
Fermentation
pathway
Microorganisms
End products
Lactic acid
Ethanol
Butyric acid
Propionic acid
Mixed acids
2,3-Butanediol
Streptococcus
Lactobacillus
Saccharomyces
Clostridium
Propionibacterium
E. coli
Enterobacter
Lactic acid
Ethanol
CO2
Butyric acid
Butanol
Acetone
Isopropanol
CO2
H2
Propionic acid
Acetic acid
CO2
Acetic acid
Lactic acid
Succinic acid
Ethanol
CO2
H2
CO2
H2
(yogurt, dairy, pickle), b (wine, beer), (acetone): © Brian Moeskau/McGraw- Hill; (cheese): © Photodisc/McGraw-Hill; (Voges-Proskauer Test), (Methyl-Red Test): © The McGraw-Hill Companies, Inc./Auburn University Photographic Services
6.6. Catabolism of Organic Compounds Other
than Glucose
§  Microbes can use variety of compounds
•  Excrete hydrolytic enzymes; transport subunits into cell
•  Degrade further to appropriate precursor metabolites
•  Polysaccharides and disaccharides
•  Amylases digest starch; cellulases digest cellulose
•  Disaccharides hydrolyzed by specific disaccharidases
•  Lipids
•  Fats hydrolyzed by lipases; glycerol converted to
dihydroxyacetone phosphate, enters glycolysis
•  Fatty acids degraded by β-oxidation to enter TCA cycle
•  Proteins
•  Hydrolyzed by proteases; amino group deaminated
•  Carbon skeletons converted into precursor molecules
15
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Fig. 6.24
POLYSACCHARIDES
Starch
Cellulose
amylases
cellulases
DISACCHARIDES
Lactose Maltose
Sucrose
LIPIDS (fats)
proteases
Amino acids
+
monosaccharides
(simple sugars)
Pentose phosphate
pathway
PROTEINS
lipases
glycerol
disaccharidases
GLUCOSE
deamination
fatty acids
NH3
Glycolysis
Applies to
both branches
In glycolysis
Pyruvate
Pyruvate
AcetylCoA
AcetylCoA
ß-oxidation
removes
2-carbon units.
x2
TCA cycle
6.7. Chemolithotrophs
§  Prokaryotes unique in ability to use reduced
inorganic compounds as sources of energy
•  E.g., hydrogen sulfide (H2S), ammonia (NH3)
•  Produced by anaerobic respiration from inorganic molecules
(sulfate, nitrate) serving as terminal electron acceptors
•  Important example of nutrient cycling
•  Four general groups
6.10. Anabolic Pathways—Synthesizing Subunits from
Precursor Molecules
§  Prokaryotes remarkably similar in biosynthesis
•  Synthesize subunits using central metabolic pathways
•  If enzymes lacking, end product must be supplied
•  Fastidious bacteria require many growth factors
•  Lipid synthesis requires fatty acids, glycerol
•  Fatty acids: 2-carbon units added to acetyl group from
acetyl-CoA
•  Glycerol: dihydroxyacetone phosphate from glycolysis
•  Nucleotide synthesis
• 
• 
• 
• 
DNA, RNA initially synthesized as ribonucleotides
Purines: atoms added to ribose 5-phosphate to form ring
Pyrimidines: ring made, then attached to ribose 5-phosphate
Can be converted to other nucleobases of same type
16