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Chapter 5
Microbial
Metabolism
Lectures prepared by Christine L. Case
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Catabolic and Anabolic Reactions
 Metabolism: The sum of the chemical reactions in
an organism
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Catabolic and Anabolic Reactions
 Catabolism: Provides energy and building blocks for
anabolism.
 Anabolism: Uses energy and building blocks to
build large molecules
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Role of ATP in Coupling Reactions
Figure 5.1
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Catabolic and Anabolic Reactions
 A metabolic pathway is a sequence of
enzymatically catalyzed chemical reactions in a cell
 Metabolic pathways are determined by enzymes
 Enzymes are encoded by genes
ANIMATION Metabolism: Overview
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Collision Theory
 The collision theory states that chemical reactions
can occur when atoms, ions, and molecules collide
 Activation energy is needed to disrupt electronic
configurations
 Reaction rate is the frequency of collisions with
enough energy to bring about a reaction.
 Reaction rate can be increased by enzymes or by
increasing temperature or pressure
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Energy Requirements of a Chemical
Reaction
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Figure 5.2
Enzyme Components
 Biological catalysts
 Specific for a chemical reaction; not used up in that
reaction
 Apoenzyme: Protein
 Cofactor: Nonprotein component
 Coenzyme: Organic cofactor
 Holoenzyme: Apoenzyme plus cofactor
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Components of a Holoenzyme
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Figure 5.3
Important Coenzymes




NAD+
NADP+
FAD
Coenzyme A
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Enzyme Specificity and Efficiency
 The turnover number is generally 1 to 10,000
molecules per second
ANIMATION Enzymes: Overview
ANIMATION Enzymes: Steps in a Reaction
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The Mechanism of Enzymatic Action
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Figure 5.4a
The Mechanism of Enzymatic Action
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Figure 5.4b
Enzyme Classification

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
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Oxidoreductase: Oxidation-reduction reactions
Transferase: Transfer functional groups
Hydrolase: Hydrolysis
Lyase: Removal of atoms without hydrolysis
Isomerase: Rearrangement of atoms
Ligase: Joining of molecules, uses ATP
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Factors Influencing Enzyme Activity




Temperature
pH
Substrate concentration
Inhibitors
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Factors Influencing Enzyme Activity
 Temperature and pH denature proteins
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Figure 5.6
Effect of Temperature on Enzyme
Activity
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Figure 5.5a
Effect of pH on Enzyme Activity
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Figure 5.5b
Effect of Substrate Concentration on
Enzyme Activity
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Figure 5.5c
Enzyme Inhibitors: Competitive
Inhibition
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Figure 5.7a–b
Enzyme Inhibitors: Competitive
Inhibition
ANIMATION Competitive Inhibition
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Enzyme Inhibitors: Noncompetitive
Inhibition
ANIMATION Non-competitive Inhibition
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Figure 5.7a, c
Enzyme Inhibitors: Feedback Inhibition
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Figure 5.8
Ribozymes
 RNA that cuts and splices RNA
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Oxidation-Reduction Reactions
 Oxidation: Removal of electrons
 Reduction: Gain of electrons
 Redox reaction: An oxidation reaction paired with a
reduction reaction
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Oxidation-Reduction
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Figure 5.9
Oxidation-Reduction Reactions
 In biological systems, the electrons are often
associated with hydrogen atoms. Biological
oxidations are often dehydrogenations.
ANIMATION Oxidation-Reduction Reactions
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Representative Biological Oxidation
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Figure 5.10
The Generation of ATP
 ATP is generated by the phosphorylation of ADP
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Substrate-Level Phosphorylation
 Energy from the transfer of a high-energy PO4– to
ADP generates ATP
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Oxidative Phosphorylation
 Energy released from transfer of electrons
(oxidation) of one compound to another (reduction)
is used to generate ATP in the electron transport
chain
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Photophosphorylation
 Light causes chlorophyll to give up electrons. Energy
released from transfer of electrons (oxidation) of
chlorophyll through a system of carrier molecules is
used to generate ATP.
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Metabolic Pathways of Energy
Production
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Carbohydrate Catabolism
 The breakdown of carbohydrates to release energy
 Glycolysis
 Krebs cycle
 Electron transport chain
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Glycolysis
 The oxidation of glucose to pyruvic acid produces
ATP and NADH
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Figure 5.11
Preparatory Stage of Glycolysis
 2 ATP are used
 Glucose is split to form 2 glucose-3-phosphate
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Figure 5.12, steps 1–5
Energy-Conserving Stage of Glycolysis
 2 glucose-3-phosphate oxidized to 2 pyruvic acid
 4 ATP produced
 2 NADH produced
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Figure 5.12, steps 6–10
Glycolysis
 Glucose + 2 ATP + 2 ADP + 2 PO4– + 2 NAD+  2
pyruvic acid + 4 ATP + 2 NADH + 2H+
ANIMATION Glycolysis: Overview
ANIMATION Glycolysis: Steps
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Alternatives to Glycolysis
 Pentose phosphate pathway
 Uses pentoses and NADPH
 Operates with glycolysis
 Entner-Doudoroff pathway
 Produces NADPH and ATP
 Does not involve glycolysis
 Pseudomonas, Rhizobium, Agrobacterium
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Cellular Respiration
 Oxidation of molecules liberates electrons for an
electron transport chain
 ATP is generated by oxidative phosphorylation
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Intermediate Step
 Pyruvic acid (from glycolysis) is oxidized and
decarboyxlated
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Figure 5.13
The Krebs Cycle
 Oxidation of acetyl CoA produces NADH and FADH2
ANIMATION Krebs Cycle: Overview
ANIMATION Krebs Cycle: Steps
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The Krebs Cycle
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Figure 5.13
The Electron Transport Chain
 A series of carrier molecules that are, in turn,
oxidized and reduced as electrons are passed down
the chain
 Energy released can be used to produce ATP by
chemiosmosis
ANIMATION Electron Transport Chain: Overview
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Overview of Respiration and
Fermentation
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Figure 5.11
Chemiosmotic Generation of ATP
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Figure 5.16
An Overview of Chemiosmosis
ANIMATION Electron Transport Chain: The Process
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Figure 5.15
A Summary of Respiration
 Aerobic respiration: The final electron acceptor in
the electron transport chain is molecular oxygen
(O2).
 Anaerobic respiration: The final electron acceptor
in the electron transport chain is not O2. Yields less
energy than aerobic respiration because only part of
the Krebs cycles operates under anaerobic
conditions.
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Respiration
ANIMATION Electron Transport Chain: Factors Affecting ATP Yield
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Figure 5.16
Anaerobic Respiration
Electron Acceptor
Products
NO3–
NO2–, N2 + H2O
SO4–
H2S + H2O
CO32 –
CH4 + H2O
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Carbohydrate Catabolism
Pathway
Eukaryote
Prokaryote
Glycolysis
Cytoplasm
Cytoplasm
Intermediate step
Cytoplasm
Cytoplasm
Krebs cycle
Mitochondrial matrix
Cytoplasm
ETC
Mitochondrial inner membrane Plasma membrane
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Carbohydrate Catabolism
 Energy produced from complete oxidation of one
glucose using aerobic respiration
ATP Produced
NADH
Produced
FADH2
Produced
Glycolysis
2
2
0
Intermediate step
0
2
Krebs cycle
2
6
2
Total
4
10
2
Pathway
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Carbohydrate Catabolism
 ATP produced from complete oxidation of one
glucose using aerobic respiration
Pathway
By Substrate-Level
Phosphorylation
By Oxidative Phosphorylation
From NADH
From FADH
0
Glycolysis
2
6
Intermediate step
0
6
Krebs cycle
2
18
4
Total
4
30
4
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Carbohydrate Catabolism
 36 ATPs are produced in eukaryotes
Pathway
By Substrate-Level
Phosphorylation
By Oxidative Phosphorylation
From NADH
From FADH
0
Glycolysis
2
6
Intermediate step
0
6
Krebs cycle
2
18
4
Total
4
30
4
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Fermentation
 Any spoilage of food by microorganisms (general
use)
 Any process that produces alcoholic beverages or
acidic dairy products (general use)
 Any large-scale microbial process occurring with or
without air (common definition used in industry)
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Fermentation
 Scientific definition:
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Releases energy from oxidation of organic molecules
Does not require oxygen
Does not use the Krebs cycle or ETC
Uses an organic molecule as the final electron acceptor
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An Overview of Fermentation
ANIMATION Fermentation
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Figure 5.18a
End-Products of Fermentation
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Figure 5.18b
Fermentation
 Alcohol fermentation: Produces ethanol + CO2
 Lactic acid fermentation: Produces lactic acid
 Homolactic fermentation: Produces lactic acid only
 Heterolactic fermentation: Produces lactic acid and other
compounds
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Types of Fermentation
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Figure 5.19
A Fermentation Test
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Figure 5.23
Types of Fermentation
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Table 5.4
Types of Fermentation
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Table 5.4
Lipid Catabolism
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Figure 5.20
Catabolism of Organic Food Molecules
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Figure 5.21
Protein Catabolism
Protein
Extracellular proteases
Deamination, decarboxylation,
dehydrogenation, desulfurylation
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Amino acids
Organic acid
Krebs cycle
Protein Catabolism
Decarboxylation
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Figure 5.22
Protein Catabolism
Desulfurylation
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Figure 5.24
Protein Catabolism
Urea
Urease
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NH3 + CO2
Clinical Focus Figure B
Biochemical Tests
 Used to identify bacteria.
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Clinical Focus Figure A
Photosynthesis
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Figure 4.15
Photosynthesis
 Photo: Conversion of light energy into chemical
energy (ATP)
 Light-dependent (light) reactions
 Synthesis:
 Carbon fixation: Fixing carbon into organic molecules
 Light-independent (dark) reaction: Calvin-Benson cycle
ANIMATION Photosynthesis: Overview
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Photosynthesis
 Oxygenic:
6 CO2 + 12 H2O + Light energy 
C6H12O6 + 6 H2O + 6 O2
 Anoxygenic:
6 CO2 + 12 H2S + Light energy 
C6H12O6 + 6 H2O + 12 S
ANIMATION: Photosynthesis: Comparing Prokaryotes and Eukaryotes
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Cyclic Photophosphorylation
ANIMATION Photosynthesis: Light Reaction: Cyclic Photophosphorylation
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Figure 5.25a
Noncyclic Photophosphorylation
ANIMATION Photosynthesis: Light Reaction: Noncyclic
Photophosphorylation
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Figure 5.25b
Calvin-Benson Cycle
ANIMATION Photosynthesis: Light Independent Reactions
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Figure 5.26
Photosynthesis Compared
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Table 5.6
Chemotrophs
 Use energy from chemicals
 Chemoheterotroph
Glucose
NAD+
ETC
Pyruvic acid
NADH
 Energy is used in anabolism
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ADP + P
ATP
Chemotrophs
 Use energy from chemicals
 Chemoautotroph, Thiobacillus ferrooxidans
2Fe2+
NAD+
ETC
2Fe3+
NADH
ADP + P
ATP
2 H+
 Energy used in the Calvin-Benson cycle to fix CO2
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Phototrophs
 Use light energy
Chlorophyll
ETC
Chlorophyll
oxidized
ADP + P
ATP
 Photoautotrophs use energy in the Calvin-Benson
cycle to fix CO2
 Photoheterotrophs use energy
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Requirements of ATP Production
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Figure 5.27
A Nutritional Classification of
Organisms
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Figure 5.28
A Nutritional Classification of
Organisms
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Figure 5.28
A Nutritional Classification of
Organisms
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Figure 5.28
Metabolic Diversity among Organisms
Nutritional Type
Energy Source
Carbon Source
Example
Photoautotroph
Light
CO2
Oxygenic: Cyanobacteria
plants
Anoxygenic: Green,
purple bacteria
Photoheterotroph
Light
Organic
compounds
Green, purple nonsulfur
bacteria
Chemoautotroph
Chemical
CO2
Iron-oxidizing bacteria
Chemoheterotroph
Chemical
Organic
compounds
Fermentative bacteria
Animals, protozoa,
fungi, bacteria.
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Polysaccharide Biosynthesis
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Figure 5.29
Lipid Biosynthesis
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Figure 5.30
Pathways of Amino Acid Biosynthesis
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Figure 5.31a
Amino Acid Biosynthesis
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Figure 5.31b
Purine and Pyrimidine Biosynthesis
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Figure 5.32
The Integration of Metabolism
 Amphibolic pathways: Metabolic pathways that
have both catabolic and anabolic functions
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Amphibolic Pathways
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Figure 5.33
Amphibolic Pathways
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Figure 5.33