MICROBIOLOGY
Chapter 5
Microbial Metabolism
Dr. Abdelraouf A. Elmanama
Ph. D Microbiology
Medical Technology Department, Faculty of Science, Islamic University-Gaza
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Microbial Metabolism
• Metabolism is the sum of the chemical
reactions in an organism.
• Catabolism is the energy-releasing processes.
• Anabolism is the energy-using processes.
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Microbial Metabolism
• Catabolism provides the building blocks and energy for
anabolism.
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Figure 5.1
• 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.
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• 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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Enzymes
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Figure 5.2
Enzymes
• Biological catalysts
• Specific for a chemical reaction; not used up in that
reaction
• Apoenzyme: protein
• Cofactor: Non-protein component
• Coenzyme: Organic cofactor
• Holoenzyme: Apoenzyme + cofactor
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Enzymes
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Figure 5.3
Important Coenzymes
• NAD+
• NADP+
• FAD
• Coenzyme A
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Enzymes
• The turnover number is generally 1-10,000 molecules
per second.
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Figure 5.4
Enzyme Classification
• 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
• Enzymes can be denatured by temperature and pH
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Figure 5.6
Factors Influencing Enzyme Activity
• Temperature
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Figure 5.5a
Factors Influencing Enzyme Activity
• pH
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Figure 5.5b
Factors Influencing Enzyme Activity
• Substrate concentration
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Figure 5.5c
Factors Influencing Enzyme Activity
• Competitive inhibition
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Figure 5.7a, b
Factors Influencing Enzyme Activity
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Competitive inhibition
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Factors Influencing Enzyme Activity
• Noncompetitive inhibition
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Figure 5.7a, c
Factors Influencing Enzyme Activity
• Feedback
inhibition
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Figure 5.8
Ribozymes
• RNA that cuts and splices RNA
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Oxidation-Reduction
• Oxidation is the removal of electrons.
• Reduction is the gain of electrons.
• Redox reaction is an oxidation reaction paired with a
reduction reaction.
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Figure 5.9
Oxidation-Reduction
• In biological systems, the electrons are often
associated with hydrogen atoms. Biological oxidations
are often dehydrogenations.
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Figure 5.10
The Generation of ATP
• ATP is generated by the phosphorylation of ADP.
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The Generation of ATP
• Substrate-level phosphorylation is the transfer of a
high-energy PO4- to ADP.
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The Generation of ATP
• Energy released from the transfer of electrons
(oxidation) of one compound to another (reduction) is
used to generate ATP by chemiosmosis.
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The Generation of ATP
• Light causes chlorophyll to give up electrons. Energy
released from the transfer of electrons (oxidation) of
chlorophyll through a system of carrier molecules is
used to generate ATP.
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Metabolic Pathways
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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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Preparatory Stage
Preparatory
Stage
Glucose
• 2 ATPs are used
1
• Glucose is split to
form 2 Glucose-3phosphate
Glucose
6-phosphate
2
Fructose
6-phosphate
3
4
Fructose
1,6-diphosphate
5
Dihydroxyacetone
phosphate (DHAP)
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Glyceraldehyde
3-phosphate
(GP)
Energy-Conserving Stage
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1,3-diphosphoglyceric acid
• 2 Glucose-3phosphate oxidized
to 2 Pyruvic acid
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3-phosphoglyceric acid
8
• 4 ATP produced
• 2 NADH produced
2-phosphoglyceric acid
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Phosphoenolpyruvic acid
(PEP)
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Pyruvic acid
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Glycolysis
• Glucose + 2 ATP + 2 ADP + 2 PO4– + 2 NAD+ 
2 pyruvic acid + 4 ATP + 2 NADH + 2H+
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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 generated by oxidative phosphorylation
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Intermediate Step
• Pyruvic acid (from
glycolysis) is oxidized
and decarboyxlated
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Figure 5.13.1
Krebs Cycle
• Oxidation of acetyl CoA produces NADH and FADH2
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Krebs Cycle
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Figure 5.13.2
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.
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Figure 5.14
Chemiosmosis
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Figure 5.15
Chemiosmosis
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Figure 5.16.2
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 operations under anaerobic
conditions.
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Anaerobic respiration
Electron acceptor
Products
NO3–
NO2–, N2 + H2O
SO4–
H2S + H2O
CO32 –
CH4 + H2O
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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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• Energy produced from complete oxidation of 1 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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• ATP produced from complete oxidation of 1 glucose
using aerobic respiration
Pathway
By substratelevel
phosphorylation
By oxidative
phosphorylation
From
From
NADH
FADH
Glycolysis
2
6
Intermediate step
0
6
Krebs cycle
2
18
4
Total
4
30
4
• 36 ATPs are produced in eukaryotes.
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0
Fermentation
• 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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Fermentation
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Figure 5.18b
Fermentation
• Alcohol fermentation. Produces ethyl alcohol + 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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Fermentation
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Figure 5.19
Fermentation
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Figure 5.23
Lipid Catabolism
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Figure 5.20
Protein Catabolism
Protein
Extracellular proteases
Deamination, decarboxylation, dehydrogenation
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Amino acids
Organic acid
Krebs cycle
Protein Catabolism
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Figure 5.22
Biochemical tests
• Used to identify
bacteria.
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Figure 10.8
Photosynthesis
• Photo: Conversion of light energy into chemical energy
(ATP)
• Light-dependent (light) reactions
• Synthesis: Fixing carbon into organic molecules
• Light-independent (dark) reaction, Calvin-Benson
cycle
• Oxygenic:
6 CO2 + 12 H2O + Light energy  C6H12O6 + 6 O2 + 6 H2O
• Anoxygenic:
CO2 + 2 H2S + Light energy  [CH2O] + 2 A + H2O
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Cyclic Photophosphorylation
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Figure 5.24a
Noncyclic Photophosphorylation
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Figure 5.24b
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Figure 5.25
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Table 5.6
• Halobacterium uses
bacteriorhodopsin,
not chlorophyll, to
generate electrons
for a chemiosmotic
proton pump.
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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 ferroxidans
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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Metabolic Diversity Among Organisms
Nutritional type
Energy source
Carbon source
Example
Photoautotroph
Light
CO2
Photoheterotroph
Light
Organic
compounds
Chemoautotroph
Chemical
CO
Iron-oxidizing
bacteria.
Chemoheterotroph
Chemical
Organic
compounds
Fermentative bacteria.
Animals, protozoa,
fungi, bacteria.
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Oxygenic:
Cyanobacteria plants.
Anoxygenic: Green,
purple bacteria.
Green, purple
nonsulfur bacteria.
Metabolic Pathways of Energy Use
• Polysaccharide Biosynthesis
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Figure 5.28
Metabolic Pathways of Energy Use
• Lipid Biosynthesis
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Figure 5.29
Metabolic Pathways of Energy Use
• Amino Acid and Protein Biosynthesis
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Figure 5.30a
Metabolic Pathways of Energy Use
• Amino Acid and Protein Biosynthesis
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Figure 5.30b
Metabolic Pathways of Energy Use
• Purine and
Pyrimidine
Biosynthesis
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Figure 5.31
Amphibolic pathways
• Are metabolic pathways that have both catabolic and
anabolic functions.
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Figure 5.32.1
Amphibolic pathways
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Figure 5.32.2