chapter 21 metabolic diversity: catabolism of organic compounds
TRANSCRIPT
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Chapter 21
Metabolic Diversity: Catabolism of Organic Compounds
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I. Fermentations
21.1 Fermentations: Energetic and Redox
Considerations
21.2 Fermentative Diversity: Lactic and Mixed-Acid
Fermentations
21.3 Fermentative Diversity: Clostridial and Propionic
Acid Fermentations
21.4 Fermentations without Substrate-Level
Phosphorylation
21.5 Syntrophy
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21.1 Fermentations: Energetic and Redox Considerations
Two mechanisms for catabolism of organic
compounds
Respiration
Exogenous electron acceptors are present to accept
electrons generated from the oxidation of electron donors
- Aerobic and anaerobic respiration
Fermentation
Electron donor and acceptor are the same compound
Relatively little energy yield
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In the absence of external electron acceptors, compounds
can be catabolized anaerobically by fermentation
ATP is usually synthesized by substrate-level
phosphorylation
Energy-rich phosphate bonds from phosphorylated organic
intermediates transferred directly to ADP
Redox balance is achieved by production and secretion of
fermentation products
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The Essentials of Fermentation
Figure 21.1
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A requirement for most fermentations is that organic
intermediates can be generated that contain an
energy-rich phosphate bond or a molecule of
coenzyme-A
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Energy-Rich Compounds Involved in SLP
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Anaerobic Breakdown of Major Fermentable Substrates
Figure 21.2
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In many fermentations, redox balance is maintained by
the production of molecular hydrogen (H2)
H2 production involves
transfer of electrons from
ferredoxin to H+ by
a hydrogenase
Pyruvate-ferredoxin oxidoreductase
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21.2 Lactic and Mixed-Acid Fermentations
Fermentations are classified by either the substrate
fermented or the productions formed
A wide variety of organic compounds can be fermented
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Common Bacterial Fermentations
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Some Unusual Bacterial Fermentations
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Lactic Acid Fermentations
Lactic acid fermentation can occur by
homofermentative and heterofermentative pathways
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Glucose Fermentation by Homofermentations
Figure 21.4
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Glucose Fermentation by Heterofermentations
Figure 21.4
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The Entner-Doudoroff Pathway
A variant of the glycolytic pathway (e.g. Pseudomonas)
A widespread pathway for sugar catabolism in bacteria
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Entner-Doudoroff Pathway
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Mixed-Acid Fermentations
Mixed-Acid Fermentations
Generate acids
Acetic, lactic, and succinic acids
Sometimes also generate neutral products
e.g., butanediol
Characteristic of enteric bacteria
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Butanediol Production in Mixed-Acid Fermentations
Figure 21.5
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21.3 Clostridial and Propionic Acid Fermentations
Clostridium species ferment sugars, producing
butyric acid
Butanol and acetone can also be byproducts
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The Butyric Acid and Butanol/Acetone Fermentation
Figure 21.6
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Some Clostridium species ferment amino acids using a
complex biochemical pathway known as the Stickland
reaction
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The Stickland Reaction
Figure 21.7
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Secondary Fermentations
Secondary Fermentation
The fermentation of fermentation products
C. kluyveri
- Ethanol + Acetate → Caproate + Butyrate
Propionibacterium
- Lactate → Propionate + Acetate
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The Propionic Acid Fermentation of Propionibacterium
Figure 21.8
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21.4 Non-Substrate-Level Phosphorylation Fermentations
Fermentations of certain compounds do not yield
sufficient energy to synthesize ATP
Catabolism of the compound can then be linked to ion
pumps that establish a proton or sodium motive force
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Succinate Fermentation by Propionigenium modestum
Figure 21.9a
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Oxalate Fermentation by Oxalobacter formigenes
Figure 21.9b
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21.5 Syntrophy
Syntrophy
A process whereby two or more microbes cooperate to degrade a
substance neither can degrade alone
Most syntrophic reactions are secondary fermentations
Most reactions are based on interspecies hydrogen transfer
H2 production by one partner is linked to H2 consumption by the
other
Syntrophic reactions are important for the anoxic portion of
the carbon cycle
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Syntrophy: Interspecies H2 Transfer
Figure 21.10
H2 consumption affects the energetics of the reaction carried out by the H2 producer, allowing the reaction to be exothermic.
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Figure 21.10
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Energetics of Growth of Syntrophomonas
Figure 21.11a
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Energetics of Growth of Syntrophomonas
Figure 21.11b
Disproportionation of crotonate
(anaerobic respiration with crotonate as an electron acceptor)
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II. Anaerobic Respiration
21.6 Anaerobic Respiration: General Principles
21.7 Nitrate Reduction and Denitrification
21.8 Sulfate and Sulfur Reduction
21.9 Acetogenesis
21.10 Methanogenesis
21.11 Proton Reduction
21.12 Other Electron Acceptors
21.13 Anoxic Hydrocarbon Oxidation Linked to Anaerobic
Respiration
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21.6 Anaerobic Respiration: General Principles
In anaerobic respiration electron acceptors other than O2
are used
Anaerobic and aerobic respiratory systems are similar
But anaerobic respiration yields less energy than aerobic
respiration
Energy released from redox reactions can be determined
by comparing reduction potentials of each electron
acceptor
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Major Forms of Anaerobic Respiration
Figure 21.12
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■ Assimilative metabolism of an inorganic compound
(e.g., NO3-, SO4
2-, CO2)
- The reduced compounds are used in biosynthesis
■ Dissimilative metabolism of inorganic compounds
- During anaerobic respiration, the reduced products
are excreted
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21.7 Nitrate Reduction and Denitrification
Inorganic nitrogen compounds are the most common
electron acceptors in anaerobic respiration
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Most products of nitrate reduction (denitrification)
are gaseous (NO, N2O or N2)
- Some are NO2- and NH4
+
Denitrification is the main biological source of
gaseous N2
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Steps in the Dissimilative Reduction of Nitrate
Figure 21.13
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The biochemical pathway for dissimilative nitrate
reduction has been well-studied
Enzymes of the pathway are repressed by oxygen
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Respiration and Anaerobic Respiration (E. coli)
Figure 21.14a
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Respiration and Anaerobic Respiration (P. stutzeri)
Figure 21.14c
Periplasmic proteins
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21.8 Sulfate and Sulfur Reduction
Several inorganic sulfur compounds can be used as electron acceptors in anaerobic respiration
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The reduction of SO42- to
H2S proceeds through
several intermediates and
requires activation of
sulfate by ATP
Activated sulfates
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Schemes of Assimilative and Dissimilative Sulfate Reduction
Figure 21.15b
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Many different compounds can serve as electron
donors in sulfate reduction
e.g., H2, organic compounds, phosphite
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Electron Transport and Energy Conservation during Sulfate Reduction
Figure 21.16
Membrane-associated propotein complex
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Some sulfur-reducing bacteria can gain additional
energy through disproportionation of sulfur
compounds
- S2O32- + H2O → SO4
2- + H2S
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21.9 Acetogenesis
Acetogens and methanogens use CO2 as an
electron acceptor in anaerobic respiration
H2 is the major electron donor for both groups of
organisms
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The Processes of Methanogenesis and Acetogenesis
Figure 21.17
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Acetogens (homo acetogens)
Reduce CO2 to acetate by the acetyl-CoA pathway, a
pathway widely distributed in obligate anaerobes
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Reactions of the Acetyl-CoA Pathway
Figure 21.18
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Organisms Employing the Acetyl-CoA Pathway
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21.10 Methanogenesis
Methanogenesis
Involves a complex series of biochemical reactions that
use novel coenzymes
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Coenzymes of Methanogenesis (Methanofuran)
Figure 21.19a
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Coenzymes of Methanogenesis (Methanopterin)
Figure 21.19b
Resembles folic acid
Playes a role analogus to THF
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Coenzymes of Methanogenesis (Coenzyme M)
Figure 21.19c
Required for the terminal step of methanogenesis
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Coenzymes of Methanogenesis (Coenzyme F430)
Figure 21.19d
Contains nickel and required for the terminal step of methanogenesis
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Coenzymes of Methanogenesis (Coenzyme F420)
Figure 21.19e
A redox coenzyme structurally resembling FMN
Oxidized form absorbs light at 420 nm and fluoresces blue-green
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The autofluorescence of coenzyme F420 can be
used to identify methanogens microscopically
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Fluorescence Due to the Methanogenic Coenzyme F420
Figure 21.20
Autofluourescence in Cells of the Methanogen Methanosarcina barkeri
F420 fluorescence in Cells of the Methanogen Methanobacterium formicicum
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Coenzymes of Methanogenesis (Coenzyem B)
Figure 21.19f
7-Mercaptoheptanoylthreonine phosphate
Required for the terminal step of methanogenesis catalyzed by the methyl reductase enzyme complex
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H2 is the major electron donor for methanogenesis
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Methanogenesis from CO2 plus H2
Figure 21.21
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Additional electron donors exist
e.g., formate, CO, organic compounds
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Methanogenesis from Methanol
Figure 21.22a
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Corrin ring Vitamin B12 (cyanocobalamin)
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Methanogenesis from Acetate
Figure 21.22b
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Autotrophy in methanogenes occurs via the acetyl-
CoA pathway
Energy conservation in methanogenesis is linked to
both proton and sodium motive forces
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Energy Conservation in Methanogenesis
Figure 21.23
Methanophenazine
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21.11 Proton Reduction
Pyrococcus furiosus Member of the Archaea
Grows optimally at 100°C on sugars and small peptides as electron donors
May have the simplest of all anaerobic respiratory mechanisms
This organism ferments glucose by reducing protons in an anerobic respiration linked to ATPase activity
- Electron transport chain is not involved
- But protons are the net electron acceptor
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Modified Glycolysis and Proton Reduction in P. furiosus
Fdox/red = ~ -0.42 V
2H+/H2 = ~ -0.42 V
No substrate-level phosphorylation
Figure 21.24
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21.12 Other Electron Acceptors
Fe3+, Mn4+, ClO3-, and various organic compounds
can serve as electron acceptors for bacteria
Fe3+ is abundant in nature and its reduction is a
major form of anaerobic respiration
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Alternative Electron Acceptors for Anaerobic Respirations
Figure 21.25
toxic
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Biomineralization During Arsenate Reduction
Figure 21.26
The reduction of arsenate by sulfate-reducing bacteria has been employed for clean-up of toxic wastes and groundwater
- Spontaneous production of As2S3 during reduction of arsenate to arsenite along with the reduction of sulfate to sulfide
After inoculation Biominerlization after 2 weeks
Synthetic As2S3
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Halogenated compounds can also serve as
electron acceptors via a process called reductive
dechlorination (dehalorespiration)
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Characteristics of Genera of Reductive Dechlorinators
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21.13 Anoxic Hydrocarbon Oxidation
Aliphatic and aromatic hydrocarbons can be oxidized
anaerobically
Hydrocarbons are oxidized to intermediates that can
be catabolized via the citric acid cycle
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Anoxic Catabolism of the Aliphatic Hydrocarbon Hexane
Figure 21.27
The first step in degradation is the addition of oxygen to the molecule through the incorporation of fumarate
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Anoxic Degradation of Aromatic Hydrocarbon Benzoate
Figure 21.28
Aromatic hydrocarbons are catabolized by ring reduction and cleavage
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Anoxic Oxidation of Methane
Methane
The simplest hydrocarbon
Can be oxidized under anoxic conditions by a consortia
containing sulfate-reducing bacteria and
methanotrophic archaea
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Figure 21.29a
Methane-oxidizing cell aggregates
Possible mechanism of the cooperative degradation of methane
(or some other carriers of reducing power)
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III. Aerobic Chemoorganotrophic Processes
21.14 Molecular Oxygen as a Reactant in Biochemical
Processes
21.15 Aerobic Hydrocarbon Oxidation
21.16 Methylotrophy and Methanotrophy
21.17 Hexose, Pentose, and Polysaccharide Metabolism
21.18 Organic Acid Metabolism
21.19 Lipid Metabolism
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21.14 Molecular Oxygen as a Reactant
Oxygen plays an important role as a direct reactant
in certain biochemical reactions
Oxygenases
Enzymes that catalyze the incorporation of atoms of
oxygen from O2 into organic compounds
Two major classes
Monooxygenases: incorporate one oxygen atom
Dioxygenases: incorporate both oxygen atoms
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Monooxygenase Activity
Figure 21.30
= Hydroxylase
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21.15 Aerobic Hydrocarbon Oxidation
Many bacteria and eukaryotic microbes can use
aliphatic and aromatic hydrocarbons as electron
donors when growing aerobically
Oxygenases are central enzymes in these biochemical
reactions
Aerobic aromatic compound degradation involves ring
oxidation
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Hydroxylation of Benzene to Catechol by a Monooxygenase
Figure 21.31a
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Cleavage of Catechol by an Intradiol Ring-Cleavage Dioxygenase
Figure 21.31b
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Sequential Reaction of Dioxygenases
Figure 21.31c
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21.16 Methylotrophy and Methanotrophy
Methylotrophs use compounds that lack C-C bonds
as electron donors and carbon sources
Methanotrophs are methylotrophs that use CH4
The initial step in methanotrophy requires methane
monooxygenase (MMO)
- Soluble MMO (sMMO)
- Membrane-bound MMO (particulate MMO, pMMO)
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Oxidation of Methane by Methanotrophic Bacteria
Figure 21.32
Methanol dehydrogenase: periplasmic enzyme
Membrane-associated
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Methanotrophs are classified into two physiological
groups that differ in the pathways invoked for
assimilation of carbon into cell material
Type I: Ribulose Monophosphate Pathway
- Assimilates formaldehyde
Type II: Serine Pathway
- Assimilates formaldehyde and CO2
Methylosinus sp. (type II)
Methylococcus capsulatus (type I)
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Some Characteristics of Methanotrophic Bacteria
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The Ribulose Monophosphate Pathway
Figure 21.34
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The Serine Pathway
Figure 21.33
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21.17 Hexose, Pentose, and Polysaccharide Metabolism
Sugars and polysaccharides are common
substrates for chemoorganotrophs
Polysaccharides such as cellulose and starch are
common in nature
Their breakdown yields hexoses and pentoses that are
readily catabolized by microbes
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Naturally Occurring Polysaccharides Yielding Sugars
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Starch is fairly soluble and readily degraded by
many fungi and bacteria employing amylases
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Hydrolysis of Starch by Bacillus subtilis
Figure 21.37
Purple-black color of the starch-iodine complex
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Cellulose is fairly insoluble and its degradation typically
involves attachment of microbes to cellulose fibrils and
production of cellulases
Cellulose degradation is restricted to relatively few
bacteria groups, including the gliding bacteria
Sporocytophaga and Cytophaga
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Cellulose Digestion
Figure 21.35
(Sporocytophaga myxococcoides)
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Cytophaga hutchinsonii Colonies on a Cellulose-Agar Plate
Figure 21.36
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Pentoses are required for the synthesis of nucleic acids
If pentoses are not readily available from the environment, organisms must synthesis themselves
The major pathway for pentose production is the pentose phosphate pathway (= hexulose monophosphate pathway)
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The Pentose Phosphate Pathway
Figure 21.39
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21.18 Organic Acid Metabolism
Organic acids can be metabolized as electron donors
and carbon sources by many microbes
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
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Catabolism of C2-C3 organic acids typically involves
production of oxalacetate through the glyoxylate
cycle
Glyoxylate cycle
- Most TCA cycle reactions + isocitrate lyase &
malate synthase
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The Glyoxylate Cycle
Figure 21.40
CHO
COOH
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Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
111
TCA and Glyoxylate cycles
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21.19 Lipid Metabolism
Lipids are abundant in nature and readily degraded by
many microbes
Catabolism of fats by microbes is initiated by hydrolysis
of the ester bond, yielding fatty acids and glycerol, by
extracellular lipases
Phospholipases are a class of lipases that attack
phospholipids
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Phospholipase Activity
Figure 21.41
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Lipases
Figure 21.42
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Fatty acids are oxidized by beta-oxidation
A series of reactions in which the compounds are first
activated by coenzyme A
Then two carbons of the fatty acid are successively
removed, generating acetyl-CoA
Acetyl-CoA is then catabolized through the citric
acid cycle
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Beta-Oxidation
Figure 21.43
CoA-SH