Chapter 21
Metabolic Diversity:
Catabolism of Organic
Compounds
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
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
21.1 Fermentations: Energetic and Redox Considerations
 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
The Essentials of Fermentation
Figure 21.1
21.1 Fermentations: Energetic and Redox Considerations
 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
Energy-Rich Compounds Involved in SLP
Anaerobic Breakdown of Major Fermentable Substrates
Figure 21.2
21.1 Fermentations: Energetic and Redox Considerations
 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
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
Common Bacterial Fermentations
Some Unusual Bacterial Fermentations
Lactic Acid Fermentations
 Lactic acid fermentation can occur by
homofermentative and heterofermentative pathways
Glucose Fermentation by Homofermentations
Figure 21.4
Glucose Fermentation by Heterofermentations
Figure 21.4
21.2 Lactic and Mixed-Acid Fermentations
 The Entner-Doudoroff Pathway
 A variant of the glycolytic pathway (e.g. Pseudomonas)
 A widespread pathway for sugar catabolism in bacteria
Entner-Doudoroff Pathway
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
Butanediol Production in Mixed-Acid Fermentations
Figure 21.5
21.3 Clostridial and Propionic Acid Fermentations
 Clostridium species ferment sugars, producing
butyric acid
 Butanol and acetone can also be byproducts
The Butyric Acid and Butanol/Acetone Fermentation
Figure 21.6
21.3 Clostridial and Propionic Acid Fermentations
 Some Clostridium species ferment amino acids using a
complex biochemical pathway known as the Strickland
reaction
The Strickland Reaction
Figure 21.7
Secondary Fermentations
 Secondary Fermentation
 The fermentation of fermentation products
 C. kluyveri
- Ethanol + Acetate → Caproate + Butyrate
 Propionibacterium
- Lactate → Prpionate + Acetate
The Propionic Acid Fermentation of Propionibacterium
Figure 21.8
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
Succinate Fermentation by Propionigenium modestum
Figure 21.9a
Oxalate Fermentation by Oxalobacter formigenes
Figure 21.9b
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
Syntrophy: Interspecies H2 Transfer
H2 consumption affects the energetics of the reaction carried out by
the H2 producer, allowing the reaction to be exothermic.
Figure 21.10
Syntrophy: Interspecies H2 Transfer
Figure 21.10
Energetics of Growth of Syntrophomonas
Figure 21.11a
Energetics of Growth of Syntrophomonas
Disproportionation of crotonate
Figure 21.11b
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
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
Animation: Electon Transport: Aerobic & Anaerobic Conditions
Major Forms of Anaerobic Respiration
Figure 21.12
21.6 Anaerobic Respiration: General Principles
■
Assimilative metabolism of an inorganic compound
(e.g., NO3-, SO42-, CO2)
- The reduced compounds are used in biosynthesis
■
Dissimilative metabolism of inorganic compounds
- During anaerobic respiration, the reduced products
are excreted
21.7 Nitrate Reduction and Denitrification
 Inorganic nitrogen compounds are the most common
electron acceptors in anaerobic respiration
21.7 Nitrate Reduction and Denitrification
 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
Steps in the Dissimilative Reduction of Nitrate
Figure 21.13
21.7 Nitrate Reduction and Denitrification
 The biochemical pathway for dissimilative nitrate
reduction has been well-studied
 Enzymes of the pathway are repressed by oxygen
Respiration and Anaerobic Respiration (E. coli)
Figure 21.14a
Respiration and Anaerobic Respiration (P. stutzeri)
Periplasmic proteins
Figure 21.14c
21.8 Sulfate and Sulfur Reduction
 Several inorganic
sulfur compounds can
be used as electron
acceptors in anaerobic
respiration
21.8 Sulfate and Sulfur Reduction
 The reduction of SO42- to
H2S proceeds through
several intermediates and
requires activation of
sulfate by ATP
Activated sulfates
Schemes of Assimilative and Dissimilative Sulfate Reduction
Figure 21.15b
21.8 Sulfate and Sulfur Reduction
 Many different compounds can serve as electron
donors in sulfate reduction
 e.g., H2, organic compounds, phosphite
Electron Transport and Energy Conservation during Sulfate Reduction
Membrane-associated
propotein complex
Figure 21.16
21.8 Sulfate and Sulfur Reduction
 Some sulfur-reducing bacteria can gain additional
energy through disproportionation of sulfur
compounds
- S2O32- + H2O → SO42- + H2S
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
The Processes of Methanogenesis and Acetogenesis
Figure 21.17
21.9 Acetogenesis
 Acetogens (homo acetogens)
 Reduce CO2 to acetate by the acetyl-CoA pathway, a
pathway widely distributed in obligate anaerobes
Reactions of the Acetyl-CoA Pathway
Figure 21.18
Organisms Employing the Acetyl-CoA Pathway
Organisms Employing the Acetyl-CoA Pathway
21.10 Methanogenesis
 Methanogenesis
 Involves a complex series of biochemical reactions that
use novel coenzymes
Coenzymes of Methanogenesis (Methanofuran)
Figure 21.19a
Coenzymes of Methanogenesis (Methanopterin)
Playes a role analogus to THF
Resembles folic acid
Figure 21.19b
Coenzymes of Methanogenesis (Coenzyme M)
Required for the terminal step of methanogenesis
Figure 21.19c
Coenzymes of Methanogenesis (Coenzyme F430)
Contains nickel and required for the terminal step of
methanogenesis
Figure 21.19d
Coenzymes of Methanogenesis (Coenzyme F420)
A redox coenzyme structurally
resembling FMN
Oxidized form absorbs light at 420 nm
and fluoresces blue-green
Figure 21.19e
21.10 Methanogenesis
 The autofluorescence of coenzyme F420 can be
used to identify methanogens microscopically
Fluorescence Due to the Methanogenic Coenzyme F420
Autofluourescence in Cells of the
Methanogen Methanosarcina barkeri
F420 fluorescence in Cells of the
Methanogen Methanobacterium
formicicum
Figure 21.20
Coenzymes of Methanogenesis (Coenzyem B)
7-Mercaptoheptanoylthreonine phosphate
Required for the terminal step of methanogenesis catalyzed by the methyl reductase
enzyme complex
Figure 21.19f
21.10 Methanogenesis
 H2 is the major electron donor for methanogenesis
Methanogenesis from CO2 plus H2
Figure 21.21
21.10 Methanogenesis
 Additional electron donors exist
 e.g., formate, CO, organic compounds
Methanogenesis from Methanol
Figure 21.22a
Methanogenesis from Acetate
Figure 21.22b
21.10 Methanogenesis
 Autotrophy in methanogenes occurs via the acetylCoA pathway
 Energy conservation in methanogenesis is linked to
both proton and sodium motive forces
Energy Conservation in Methanogenesis
Methanophenazine
Figure 21.23
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
Modified Glycolysis and Proton Reduction in P. furiosus
Fdox/red = ~ -0.42 V
2H+/H2 = ~ -0.42 V
Figure 21.24
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
Alternative Electron Acceptors for Anaerobic Respirations
Figure 21.25
Biomineralization During Arsenate Reduction
 The reduction of arsenate by sulfate-reducing bacteria has been
employed for clean-up of toxic wastes and groundwater
After inoculation
Synthetic As2S3
Biominerlization of
As2S3 after 2 weeks
Figure 21.26
21.12 Other Electron Acceptors
 Halogenated compounds can also serve as
electron acceptors via a process called reductive
dechlorination (dehalorespiration)
Characteristics of Genera of Reductive Dechlorinators
21.13 Anoxic Hydrocarbon Oxidation
 Aliphatic and aromatic hydrocarbons (organic
compounds containing only carbon and hydrogen) can
be oxidized anaerobically
 Hydrocarbons are oxidized to intermediates that can
be catabolized via the citric acid cycle
Anoxic Catabolism of the Aliphatic Hydrocarbon Hexane
The first step in degradation is the addition of oxygen to the molecule through the
incorporation of fumarate
Figure 21.27
Anoxic Degradation of Aromatic Hydrocarbon Benzoate
Aromatic hydrocarbons are catabolized by ring reduction and cleavage
Figure 21.28
Anoxic Oxidation of Methane
 Methane
 The simplest hydrocarbon
 Can be oxidized under anoxic conditions by a consortia
containing sulfate-reducing bacteria and
methanotrophic archaea
Anoxic Methane Oxidation
Methane-oxidizing cell aggregates
(carriers of reducing power)
Possible mechanism of the cooperative degradation of methane
Figure 21.29a
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
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
Monooxygenase Activity
Hydroxylase
Figure 21.30
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
Hydroxylation of Benzene to Catechol by a Monooxygenase
Figure 21.31a
Cleavage of Catechol by an Intradiol Ring-Cleavage Dioxygenase
Figure 21.31b
Sequential Reaction of Dioxygenases
Figure 21.31c
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)
Oxidation of Methane by Methanotrophic Bacteria
Methanol dehydrogenase: periplasmic enzyme
Figure 21.32
21.16 Methylotrophy and Methanotrophy
 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
Some Characteristics of Methanotrophic Bacteria
The Ribulose Monophosphate Pathway
Figure 21.34
The Serine Pathway
Figure 21.33
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
Naturally Occurring Polysaccharides Yielding Sugars
21.17 Hexose, Pentose, and Polysaccharide Metabolism
 Starch is fairly soluble and readily degraded by
many fungi and bacteria employing amylases
Hydrolysis of Starch by Bacillus subtilis
Purple-black color of the
starch-iodine complex
Figure 21.37
21.17 Hexose, Pentose, and Polysaccharide Metabolism
 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
Cellulose Digestion
(Sporocytophaga myxococcoides)
Figure 21.35
Cytophaga hutchinsonii Colonies on a Cellulose-Agar Plate
Figure 21.36
21.17 Hexose, Pentose, and Polysaccharide Metabolism
 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
The Pentose Phosphate Pathway
Figure 21.39
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
21.18 Organic Acid Metabolism
 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
The Glyoxylate Cycle
Figure 21.40
TCA and Glyoxylate cycles
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110
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
Phospholipase Activity
Figure 21.41
Lipases
Figure 21.42
21.19 Lipid Metabolism
 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
Beta-Oxidation
Figure 21.43