Catabolism of Organic Compounds - Marmara Üniversitesimebig.marmara.edu.tr/Enve303/Chapter14.pdf · 2013-11-19 · •14.7 Nitrate Reduction and Denitrification •14.8 Sulfate and

11/19/2012

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LECTURE PRESENTATIONS

For BROCK BIOLOGY OF MICROORGANISMS, THIRTEENTH EDITION

Michael T. Madigan, John M. Martinko, David A. Stahl, David P. Clark

Lectures by

John Zamora

Middle Tennessee State University

© 2012 Pearson Education, Inc.

Catabolism of

Organic Compounds

Chapter 14

I. Fermentation

• 14.1 Energetic and Redox Considerations

• 14.2 Lactic and Mixed-Acid Fermentations

• 14.3 Clostridial and Propionic Acid

Fermentations

• 14.4 Fermentations Lacking Substrate-Level

Phosphorylation

• 14.5 Syntrophy

© 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI

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14.1 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

– Fermentation

• Electron donor and acceptor are the same

compound

• Relatively little energy yield


14.1 Energetic and Redox Considerations

• In the absence of external electron acceptors,

organic compounds can be catabolized

anaerobically only by fermentation (Figure 14.1)

– ATP is usually synthesized by substrate-level

phosphorylation

• Energy-rich phosphate bonds from

phosphorylated organic intermediates

transferred to ADP

• Redox balance is achieved by production of

fermentation products


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Figure 14.1 The essentials of fermentation


14.2 Lactic and Mixed-Acid Fermentations

• Fermentations are classified by either the

substrate fermented or the products formed

• A wide variety of organic compounds can be

fermented – Lactic acid bacteria produce lactic acid

– Lactic acid fermentation can occur by • homofermentative and

• heterofermentative pathways


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• Mixed-acid fermentations – Generate acids

• Acetic, lactic, and succinic

– Sometimes also generate neutral products • Example: butanediol

– Characteristic of enteric bacteria


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14.3 Clostridial and Propionic Acid

Fermentations

• Clostridium species ferment sugars,

producing butyric acid

– Butanol and acetone can also be by-products



Fermentations

• Some Clostridium species ferment amino acids

using a complex biochemical pathway known as

the Strickland reaction


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Fermentations

• Secondary fermentation – The fermentation of fermentation products

– Fermentation of ethanol plus acetate by

Clostridium kluyveri

• Propionic acid fermentation

– Propionibacterium and related prokaryotes

produce propionic acid as a major

fermentation product


3 Lactate

Acetate CO2

2 Propionate

3 Pyruvate

2 Oxalacetate

2 Malate

2 Fumarate

2 Succinate

CoA transfer

2 Propionyl CoA

2 Succinyl CoA 2 Methylmalonyl CoA

Overall: 3 Lactate 2 propionate acetate CO2 H2O

G0 171 kJ (3 ATP)

14.4 Fermentations Lacking Substrate-

Level Phosphorylation

• 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

– Propionigenium modestum catabolizes

succinate under strictly anoxic conditions • Establishes a sodium motive force

• Sodium motive force forms ATP


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14.4 Fermentations Lacking

Substrate-Level Phosphorylation

• Oxalobacter formigenes catabolizes oxalate

and produces formate

– Formate is excreted from the cell

• Export of formate from the cell establishes a

proton motive force

• Proton motive force forms ATP


14.5 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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Figure 14.9 Syntrophy: Interspecies H2 transfer.


Ethanol fermentation:

Methanogenesis:

Coupled reaction:

G0 19.4 kJ/reaction

G0 130.7 kJ/reaction

G0 111.3 kJ/reaction

Reactions

Syntrophic transfer of H2

Ethanol fermenter Methanogen

2 Ethanol

2 Acetate

Interspecies hydrogen transfer

14.5 Syntrophy

• Syntrophy (cont’d)

– H2 consumption affects the energetics of the

reaction carried out by the H2 producer,

allowing the reaction to be exothermic


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II. Anaerobic Respiration

• 14.6 Anaerobic Respiration: General Principles

• 14.7 Nitrate Reduction and Denitrification

• 14.8 Sulfate and Sulfur Reduction

• 14.9 Acetogenesis

• 14.10 Methanogenesis

• 14.11 Proton Reduction

• 14.12 Other Electron Acceptors

• 14.13 Anoxic Hydrocarbon Oxidation Linked to

Anaerobic Respiration


14.6 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

© 2012 Pearson Education, Inc.

Animation: Electron Transport: Aerobic & Anaerobic Conditions

Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI

electron.html

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14.6 Anaerobic Respiration: General

Principles

• In the assimilative metabolism of an inorganic

compound (e.g., NO3, SO4

2, CO2) the

reduced compounds are used in biosynthesis

• During anaerobic respiration, the reduction of

inorganic compounds is called dissimilative

metabolism because the reduced products

are excreted


14.7 Nitrate Reduction and Denitrification

• Inorganic nitrogen compounds are the most

common electron acceptors in anaerobic

respiration

• All products of nitrate reduction

(denitrification) are gaseous (Figure 14.12)

• Denitrification is the main biological source of

gaseous N2


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Figure 14.12 Steps in the dissimilative reduction of nitrate


Nitrate

Nitrite

Nitric oxide

Nitrous oxide

Dinitrogen

Gases

Nitratereduction (Escherichiacoli)

Denitrification (Pseudomonasstutzeri)

NO3

NO2

NO

N2O

N2

Nitrate reductase

Nitrite reductase

Nitric oxide reductase

Nitrous oxide reductase

14.7 Nitrate Reduction and Denitrification

• The biochemical pathway for dissimilative

nitrate reduction has been well studied

• Enzymes of the pathway are repressed by

oxygen


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14.8 Sulfate and Sulfur Reduction

• Inorganic sulfur compounds can be used as

electron acceptors in anaerobic respiration

• Reduction of SO42 to H2S proceeds through

several intermediates and requires activation

of sulfate by ATP.




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• Many different compounds can serve as electron

donors in sulfate reduction

– Examples: H2, organic compounds, phosphite

4H2 + SO42- + H+

HS- + 4H2O ∆G0’ = -152 kJ

CH3COO- + SO42- + 3H+

CO2 + H2S + 2H2O

∆G0’ = -57.5 kJ

4HPO3+ SO42- + H+

4HPO42- + HS- ∆G0’ = -364 kJ


14.9 Acetogenesis

• Acetogens and methanogens use CO2 as an

electron acceptor in anaerobic respiration

– H2 is the major electron donor for both groups of

organisms (Figure 14.16)

• Acetogens carry out the reaction

4H2 + H+ + 2HCO3-CH3COO- + 4H2O ∆G0’ = -105 kJ


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Figure 14.16 The contrasting processes of methanogenesis and acetogenesis


Proton or sodium

motive force (plus

substrate-level

phosphorylation for

acetogens)Methanogenesis

( G0 136 kJ)Acetogenesis( G0 105 kJ)

14.10 Methanogenesis

• Methanogenesis

– Biological production of methane

– Carried out by a group of strictly anaerobic

Archaea called the methanogens

– Involves a complex series of biochemical reactions

that use novel coenzymes


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• The autofluorescence of coenzyme F420 can

be used to identify methanogens

microscopically (Figure 14.19)


Figure 14.19 Fluorescence due to the methanogenic coenzyme F420 . The organisms

were made visible by excitation with blue light in a fluorescence microscope

Methanosarcina barkeri Methanobacterium formicicum


• H2 is the major electron donor for

methanogenesis (Figure 14.20)

• Additional electron donors exist

– Examples: formate, CO, organic compounds


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14.11 Proton Reduction

• Pyrococcus furiosus

– Member of the Archaea

– Grows optimally at 100C on sugars and

small peptides as electron donors

– May have the simplest anaerobic respiration

mechanism (Figure 14.23)

– Organism uses modified glycolysis and

protons in anaerobic respiration linked to

ATPase activity


14.12 Other Electron Acceptors

• Fe3+, Mn4+, ClO3, and various organic

compounds can serve as electron acceptors for

bacteria (Figure 14.24)

• Fe3+ is abundant in nature and its reduction is a

major form of anaerobic respiration


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Figure 14.24 Some alternative electron acceptors for anaerobic respirations


Couple Reaction E0

0.03

0.13

0.14

0.16

0.20

0.48

0.80

1.00

Fumarate/Succinate

Trimethylamine-N-oxide (TMAO)/Trimethylamine (TMA)

Arsenate/Arsenite

Dimethyl sulfoxide (DMSO)/Dimethyl sulfide (DMS)

Ferric ion/Ferrous ion

Selenate/Selenite

Manganic ion/Manganous ion

Chlorate/Chloride

14.12 Other Electron Acceptors

• The reduction of arsenate has been

employed for cleanup of toxic wastes and

groundwater (Figure 14.25)

• Halogenated compounds can also serve as

electron acceptors via a process called

reductive dechlorination (dehalorespiration)


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Figure 14.25 Biomineralization during arsenate reduction by the sulfate-reducing bacterium

Desulfotomaculum auripigmentum


Appearance of

culture bottle after

inoculation

Following growth for 2 weeks

and biomineralization of

arsenic trisulfide, As2S3

Synthetic sample

of As2S3

Desulfotomaculum can reduce AsO43- to AsO3

3-, along with sulfate

(SO42-) to sulfide (HS-)

14.13 Anoxic Hydrocarbon Oxidation

• Aliphatic and aromatic hydrocarbons and organic

compounds containing only carbon and hydrogen

can be oxidized anaerobically

• The first step in degradation is the addition of

oxygen to the molecule through the incorporation

of fumarate

• Hydrocarbons are oxidized to intermediates that

can be catabolized via the citric acid cycle


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• Aliphatic hydrocarbons are straight-chain

saturated or unsaturated compounds

• Many of them are substrates for denitrifying

and sulfate-reducing bacteria

• Aromatic hydrocarbons are catabolized by

ring reduction and cleavage

• Can be degraded by some denitrifying, ferric

iron-reducing, and sulfate-reducing bacteria



• Methane

– The simplest hydrocarbon

– Can be oxidized under anoxic conditions by a

consortia containing sulfate-reducing bacteria

and methanotrophic archaea

CH4 + SO42- + H+

CO2 + HS- + 2H2O ∆G0’ = -18 kJ


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Figure 14.28 Anoxic methane oxidation


Methanotrophic Archaea(ANME-types)

Sulfate-reducing Bacteria

Organiccompounds

Mechanism for cooperative

degradation of CH4.

An organic compound or

some other carrier of reducing

power transfers electrons

from methanotroph to SRB.

III. Aerobic Chemoorganotrophic

Processes

• 14.14 Molecular Oxygen as a Reactant and

Aerobic Hydrocarbon Oxidation

• 14.15 Methylotrophy and Methanotrophy

• 14.16 Sugar and Polysaccharide Metabolism

• 14.17 Organic Acid Metabolism

• 14.18 Lipid Metabolism


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14.14 Oxygen as a Reactant and

Hydrocarbon Oxidation

• Oxygen used as a direct reactant in certain

biochemical reactions

• Oxygenases

– Enzymes that catalyze the incorporation of atoms

of oxygen from O2 into organic compounds

– Two classes:

• Monooxygenases: incorporate one oxygen atom

• Dioxygenases: incorporate both oxygen atoms


14.14 Oxygen as a Reactant and

Hydrocarbon Oxidation

• Many microbes can use aliphatic and aromatic

hydrocarbons as electron donors when growing

aerobically

• Oxygenases are central enzymes in these

biochemical reactions

• Aerobic degradation of aromatic compounds

involves ring oxidation


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14.15 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)

– In the MMO reaction, CH4 is converted to CH3OH

and H2O

– Other oxidation steps convert CH3OH to CO2

– The steps in CH4 oxidation to CO2

CH4CH3OH CH2O HCOO-CO2


14.16 Sugar 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

• Starch is fairly soluble and readily degraded by

many fungi and bacteria employing amylases


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Metabolism

• Cellulose is fairly insoluble and its

degradation typically involves attachment of

microbes to cellulose fibrils and production of

cellulases (Figure 14.34)

• Cellulose degradation is restricted to

relatively few bacteria groups, including the

gliding bacteria Sporocytophaga and

Cytophaga (Figure 14.35)


Figure 14.34 Cellulose digestion.


BacteriaCellulose

fiber

Transmission electron micrograph showing attachment of the cellulose-

digesting bacterium Sporocytophaga myxococcoides to cellulose fibers.

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Figure 14.35 Cytophaga hutchinsonii colonies on a cellulose–agar plate


Cellulosedigestion

Areas where cellulose has been hydrolyzed are more translucent


Metabolism

• Pentoses are required for the synthesis of

nucleic acids

• If pentoses are not readily available from the

environment, organisms must synthesize them

• The major pathway for pentose production is the

pentose phosphate pathway


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14.17 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

• Catabolism of C2 and C3 organic acids

typically involves production of oxalacetate

through the glyoxylate cycle


14.18 Lipid Metabolism

• Lipids are abundant in nature and readily

degraded by many microbes

• Catabolism of fats is initiated by hydrolysis of the

ester bond, yielding fatty acids and glycerol, by

extracellular lipases (Figure 14.41)

– Phospholipases are a class of lipases that attack

phospholipids

• Fatty acids are oxidized by beta-oxidation to

acetyl-CoA, which is then oxidized to CO2 by

citric acid cycle


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Figure 14.41 Lipases


Glycerol

Fatty acid

Fatty acid

Fatty acid

Lipase

Fatty acid

Fatty acid

Phospholipase B

Phospholipase A

Phospholipase C

Phospholipase D

Activity of lipases on a fat

Phospholipase

activity on

phospholipid

Documents

Catabolism of Organic Compounds - Marmara Üniversitesimebig.marmara.edu.tr/Enve303/Chapter14.pdf · 2013-11-19 · •14.7 Nitrate Reduction and Denitrification •14.8 Sulfate and