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Chapter 9
Metabolism: Energy
Release and Conservation
1
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Sources of energy
•most microorganisms use
one of three energy sources
•the sun
•reduced organic
compounds
•reduced inorganic
compounds
•the chemical energy
obtained can be used to do
work
Figure 9.1
2
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Chemoorganotrophic fueling
processess
Figure 9.2
3
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Chemoorganic fueling
processes-respiration
• most respiration involves use of an electron
transport chain
• aerobic respiration
• final electron acceptor is oxygen
• anaerobic respiration
– final electron acceptor is different exogenous
acceptor such as NO3-, SO42-, CO2, Fe3+ or SeO42-.
– organic acceptors may also be used
• as electrons pass through the electron transport
chain to the final electron acceptor, a proton
motive force (PMF) is generated and used to
synthesize ATP
4
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Chemoorganic fueling
processes - fermentation
• uses an endogenous electron acceptor
– usually an intermediate of the pathway used
to oxidize the organic energy source e.g.,
pyruvate
• does not involve the use of an electron
transport chain nor the generation of a
proton motive force
• ATP synthesized only by substrate-level
phosphorylation
5
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Overview of aerobic
catabolism
• three-stage process
– large molecules (polymers)  small
molecules (monomers)
– initial oxidation and degradation to
pyruvate
– oxidation and degradation of pyruvate
by the tricarboxylic acid cycle (TCA
cycle)
6
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many
different
energy
sources
are
funneled
into
common
degradative
pathways
Figure 9.3
7
ATP made
primarily
by
oxidative
phosphorylation
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Amphibolic Pathways
• function both as
catabolic and
anabolic pathways
• important ones
– Embden-Meyerhof
pathway
– pentose phosphate
pathway
– tricarboxylic acid
(TCA) cycle
Figure 9.4
8
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The Breakdown of Glucose
to Pyruvate
• Three common routes
– Embden-Meyerhof pathway
– pentose phosphate pathway
– Entner-Doudoroff pathway
9
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The Embden-Meyerhof
Pathway
• occurs in cytoplasmic matrix of both
procaryotes and eucaryotes
• the most common pathway for
glucose degradation to pyruvate in
stage two of aerobic respiration
10
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addition of phosphates
“primes the pump”
oxidation step –
generates NADH
high-energy molecules –
used to synthesize ATP
by substrate-level
phosphorylation
Figure 9.5
11
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Summary of glycolysis
glucose + 2ADP + 2Pi + 2NAD+

2 pyruvate + 2ATP + 2NADH + 2H+
12
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The Pentose Phosphate
Pathway
• also called hexose monophosphate
pathway
• can operate at same time as glycolytic
pathway or Entner-Doudoroff pathway
• can operate aerobically or anaerobically
• an amphibolic pathway
13
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oxidation
steps
produce
NADPH,
which is
needed for
biosynthesis
Figure 9.6
14
sugar
transformation
reactions
produce
sugars
needed
for
biosynthesis
sugars can
also be
further
degraded
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Figure 9.7
15
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Summary of pentose
phosphate pathway
glucose-6-P + 12NADP+ + 7H2O

6CO2 + 12NADPH + 12H+ Pi
16
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The Entner-Doudoroff
Pathway
reactions of
pentose
phosphate
pathway
• yield per
glucose
molecule:
– 1 ATP
– 1 NADPH
– 1 NADH
Figure 9.8
17
reactions of
glycolytic
pathway
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The Tricarboxylic Acid
Cycle
• also called citric acid cycle and
Kreb’s cycle
• common in aerobic bacteria, freeliving protozoa, most algae, and
fungi
• major role is as a source of carbon
skeletons for use in biosynthesis
18
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Figure 9.9
19
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Summary
• for each acetyl-CoA molecule
oxidized, TCA cycle generates:
– 2 molecules of CO2
– 3 molecules of NADH
– one FADH2
– one GTP
20
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Electron Transport and
Oxidative Phosphorylation
• only 4 ATP molecules synthesized
directly from oxidation of glucose to
CO2
• most ATP made when NADH and
FADH2 (formed as glucose
degraded) are oxidized in electron
transport chain (ETC)
21
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The Electron Transport
Chain
• series of electron carriers that
operate together to transfer electrons
from NADH and FADH2 to a
terminal electron acceptor
• electrons flow from carriers with
more negative E0 to carriers with
more positive E0
22
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Electron transport chain…
• as electrons transferred, energy
released
• in eucaryotes the electron transport
chain carriers are within the inner
mitochrondrial membrane
23
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Mitochondrial ETC
Figure 9.11
24
electron transfer accompanied by
proton movement across inner
mitochondrial membrane
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Procaryotic ETCs
• located in plasma membrane
• some resemble mitochondrial ETC,
but many are different
– different electron carriers
– may be branched
– may be shorter
– may have lower P/O ratio
25
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Electron Transport Chain of E. coli
branched pathway
upper branch –
stationary phase and
low aeration
lower branch – log
phase and high
aeration
Figure 9.12
26
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Oxidative Phosphorylation
• Process by which ATP is synthesized
as the result of electron transport
driven by the oxidation of a chemical
energy source
27
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Chemiosmotic hypothesis
• is the most widely accepted hypothesis to
explain oxidative phosphorylation
– electron transport chain organized so protons move
outward from the mitochondrial matrix as electrons
are transported down the chain
– proton expulsion during electron transport results in
the formation of a concentration gradient of protons
and a charge gradient
– The combined chemical and electrical potential
difference make up the proton motive force (PMF)
28
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PMF drives ATP synthesis
• diffusion of protons back across
membrane (down gradient) drives
formation of ATP
• ATP synthase
– enzyme that uses PMF down gradient
to catalyze ATP synthesis
29
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Inhibitors of ATP synthesis
• blockers
– inhibit flow of electrons through ETC
• uncouplers
– allow electron flow, but disconnect it from
oxidative phosphorylation
– many allow movement of ions, including
protons, across membrane without
activating ATP synthase
• destroys pH and ion gradients
– some may bind ATP synthase and inhibit its
activity directly
30
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ATP Yield During Aerobic
Respiration
• maximum ATP yield can be calculated
– includes P/O ratios of NADH and FADH2
– ATP produced by substrate level
phosphorylation
• the theoretical maximum total yield of
ATP during aerobic respiration is 38
– the actual number closer to 30 than 38
31
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Maximum Theoretic ATP Yield
from Aerobic Respiration
Figure 9.15
32
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Theoretical vs. Actual Yield of
ATP
• amount of ATP produced during
aerobic respiration varies depending
on growth conditions and nature of
ETC
• under anaerobic conditions,
glycolysis only yields 2 ATP
molecules
33
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Anaerobic Respiration
• uses electron
carriers other
than O2
• generally yields
less energy
because E0 of
electron acceptor
is less positive
than E0 of O2
Table 9.1
34
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Microbial Fermentations
• oxidation of NADH produced by
glycolysis
• pyruvate or derivative used as
endogenous electron acceptor
• substrate only partially oxidized
• oxygen not needed
• oxidative phosphorylation does not occur
– ATP formed by substrate-level
phosphorylation
35
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Fermentations
Figure 9.17
36
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homolactic
fermenters
heterolactic
fermenters
food
spoilage
yogurt,
sauerkraut,
pickles, etc.
Figure 9.18
37
alcoholic
fermentation
alcoholic
beverages,
bread, etc.
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Table 9.2
38
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Fermentations of amino
acids
• Stickland
reaction
– oxidation of
one amino acid
with use of
second amino
acid as electron
acceptor
– carried out by
some
Clostridium
spp.
Figure 9.19
39
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Catabolism of
Carbohydrates and
Intracellular Reserves
• many different carbohydrates can
serve as energy source
• carbohydrates can be supplied
externally or internally (from
internal reserves)
40
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Carbohydrates
• monosaccharides
– converted to other
sugars that enter
glycolytic
pathway
• disaccharides and
polysaccharides
– cleaved by
hydrolases or
phosphorylases
Figure 9.20
41
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Reserve Polymers
• used as energy sources in absence of
external nutrients
– e.g., glycogen and starch
• cleaved by phosphorylases
(glucose)n + Pi  (glucose)n-1 + glucose-1-P
• glucose-1-P enters glycolytic pathway
– e.g., PHB
PHB    acetyl-CoA
• acetyl-CoA enters TCA cycle
42
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Lipid Catabolism
• triglycerides
– common energy sources
– hydrolyzed to glycerol
and fatty acids by
lipases
• glycerol degraded via
glycolytic pathway
• fatty acids often oxidized
via β-oxidation pathway
Figure 9.21
43
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β-oxidation pathway
Figure 9.22
44
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Protein and Amino Acid
Catabolism
• protease
– hydrolyzes protein to amino acids
• deamination
– removal of amino group from amino acid
– resulting organic acids converted to
pyruvate, acetyl-CoA, or TCA cycle
intermediate
• can be oxidized via TCA cycle
• can be used for biosynthesis
45
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deamination often occurs by transamination
Figure 9.23
46
transfer of amino group
from one amino acid to α-keto acid
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Chemolithotrophy
• carried out by chemolithotrophs
• electrons released from energy source
which is an inorganic molecule
– transferred to terminal electron acceptor
(usually O2 ) by ETC
• ATP synthesized by oxidative
phosphorylation
47
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Figure 9.24
48
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Table 9.3
49
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Table 9.4
50
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Nitrifying bacteria
oxidize ammonia to nitrate
Figure 9.25
51
NH3  NO2  NO3
requires 2 different genera
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Sulfur-oxidizing bacteria
ATP can be
synthesized by
both oxidative
phosphorylation
and substratelevel
phosphorylation
Figure 9.26
52
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Autotrophic growth by
chemolithotrophs
• Calvin cycle requires NADH as
electron source for fixing CO2
– many energy sources used by
chemolithotrophs have E0 more
positive than NAD/NADH
• use reverse electron flow to generate
NADH
53
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Metabolic flexibility of
chemolithotrophs
• many switch from chemolithotrophic
metabolism to chemoorganotrophic
metabolism
• many switch from autotrophic
metabolism (via Calvin cycle) to
heterotrophic metabolism
54
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Phototrophy
• photosynthesis
– energy from light trapped and converted to
chemical energy
– a two part process
• light reactions in which light energy is trapped
and converted to chemical energy
• dark reactions in which the energy produced in
the light reactions is used to reduce CO2 and
synthesize cell constituents
55
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Table 9.5
oxygenic photosynthesis – eucaryotes and cyanobacteria
anoxygenic photosynthesis – all other bacteria
56
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Figure 9.27
57
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The Light Reaction in
Oxygenic Photosynthesis
• chlorophylls
– major light-absorbing pigments
• accessory pigments
– transfer light energy to chlorophylls
– e.g., carotenoids and phycobiliproteins
58
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different
chlorophylls
have different
absorption
peaks
Figure 9.28
59
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Accessory pigments absorb different wavelengths of light than
chlorophylls
Figure 9.29
60
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Organization of pigments
• antennas
– highly organized arrays of chlorophylls and
accessory pigments
– captured light transferred to special
reaction-center chlorophyll
• directly involved in photosynthetic electron
transport
• photosystems
– antenna and its associated reaction-center
chlorophyll
61
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Green plant photosynthesis
noncyclic
electron flow –
ATP + NADPH
made (noncyclic
photophosphorylation)
cyclic electron
flow – ATP
made (cyclic
photophosphorylation)
Figure 9.30
62
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electron flow  PMF  ATP
Figure 9.31
63
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The Light Reaction in Anoxygenic
Photosynthesis
• H2O not used as an electron source;
therefore O2 is not produced
• only one photosystem involved
• uses different pigments and mechanisms to
generate reducing power
• carried out by phototrophic green bacteria,
phototrophic purple bacteria and
heliobacteria
64
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A Photosynthetic Reaction Chain
Figure 9.32
65
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Purple nonsulfur bacteria
electron source for
generation of NADH
by reverse electron
flow
Figure 9.33
66
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Green sulfur bacteria
Figure 9.34
67
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Bacteriorhodopsin-Based Phototrophy
• Some archaea use a type of phototrophy
that involves bacteriorhodopsin, a
membrane protein which functions as a
light-driven proton pump
• a proton motive force is generated
• an electron transport chain is not
involved
68