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Chapter 5
Microbial
Metabolism
Lectures prepared by Christine L. Case
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Q&A
 All E. coli look alike
through a
microscope; so how
can E. coli O157 be
differentiated?
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Learning Objectives
After completing this chapter, you should be able to:
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Distinguish catabolism from anabolism and how they interact during metabolism
Identify the role of ATP
Identify the components of an enzyme
Describe the mechanism of an enzymatic reaction
List factors that influence enzyme activity
Distinguish between competitive and noncompetitive inhibition
Explain oxidation, reduction, and redox
Discuss why enzymatic reactions are important
Explain the overall function of metabolic pathways
List the steps involved in aerobic carbohydrate catabolism and identify major products of each step
List the steps involved in anaerobic respiration and identify major products of each step
List some of the major products of fermentation
List the steps involved in photosynthesis
Compare and contrast the light-dependent reactions versus the light-independent reactions of
photosynthesis
Categorize the various nutritional patterns among organisms according to carbon source and mechanisms
of carbohydrate catabolism and ATP generation
Describe the major types of anabolism and their relationship to catabolism
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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
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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.
 This is the number of substrate molecules that are
converted every 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
Enzyme Classification
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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
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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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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
(cristae)
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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
 Really, 38 are produced, but 2 were required for glycolysis, so net gain is 36
ATPs
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.
Chemolithotroph
Inorganic chemicals
CO2
Sulfur oxidizing bacteria, Nitrifying
bacteria, Iron bacteria, Hydrogen
bacteria
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Check Your Understanding
Check Your Understanding
 Almost all medically important microbes belong to
which of the aforementioned groups? 5-23
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Metabolic Pathways of Energy Use
Learning Objective
5-24 Describe the major types of anabolism and their
relationship to catabolism.
ANIMATION Metabolism: The Big Picture
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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