Chapter 8
Microbial Metabolism
Topics
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Metabolism
Energy
Pathways
Biosynthesis
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Metabolism
• Catabolism
• Anabolism
• Enzymes
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• Metabolism
– Collection of controlled biochemical
reactions that take place within a microbe
– Ultimate function of metabolism is to
reproduce the organism
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• Catabolism and Anabolism
– Two major classes of metabolic reactions
– Catabolic pathways
• Break larger molecules into smaller products
• Exergonic
– Anabolic pathways
• Synthesize large molecules from the products
of catabolism
• Endergonic
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Catabolism
• Enzymes are involved in the breakdown
of complex organic molecules in order
to extract energy and form simpler end
products
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Anabolism
• Enzymes are involved in the use of
energy from catabolism in order to
synthesize macromolecules and cell
structures from precursors (simpler
products)
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The relationship between catabolism and anabolism.
Fig. 8.1 Simplified model of metabolism
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Enzymes
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Function
Structure
Enzyme-substrate interaction
Cofactors
Action
Regulation
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Function
• Catalysts for chemical reactions
• Lower the energy of activation
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Structure
• Simple enzyme
– protein alone
• Conjugated enzyme
– protein and nonprotein
• Three-dimensional features
– Enable specificity
• Active site or catalytic site
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Conjugated enzymes contain a metallic cofactor, coenzyme, or
both in order for it to function as a catalyst.
Fig. 8.2 Conjugated enzyme structure
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12
Specific active sites (amino acids) arise due to the folding of the
protein (enzyme).
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Fig. 8.3 How the active site and specificity of the apoenzyme arise.
Enzyme-substrate interactions
• Substrates specifically bind to the active
sites on the enzyme
– “lock-and-key”
– Induced fit
• Once the reaction is complete, the
product is released and the enzyme
reused
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An example of the “lock-and-key” model, and the induced fit
model.
Fig. 8.4 Enzyme-substrate reactions
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Cofactors
• Bind to and activate the enzyme
• Ex. Metallic cofactors
– Iron, copper, magnesium
• Coenzymes
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Coenzyme
• Transient carrier - alter a substrate by
removing a chemical group from one
substrate and adding it to another
substrate
• Ex. vitamins
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An example of how a coenzyme transfers chemical groups from
one substrate to another.
Fig. 8.5 The carrier
functions of coenzymes
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Action
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Exoenzymes
Endoenzymes
Constitutive
Induction or repression
Types of reactions
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Exoenzymes are inactive while inside the cell, but upon release
from the cell they become active. In contrast, endoenzymes
remain in the cell and are active.
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Fig. 8.6 Types of enzymes, as described by their location of action.
Constitutive enzymes are present in constant amounts, while
regulated enzymes are either induced or repressed.
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Fig. 8.7 Constitutive and regulated enzymes
Types of Reaction
• Condensation
• Hydrolysis
• Transfer reactions
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Condensation reactions are associated with anabolic reactions,
and hydrolysis reactions are associated with catabolic reactions.
Fig. 8.8 Examples of enzyme-catalyzed synthesis
and hydrolysis reactions
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Transfer reactions
• Transfer of electrons from one substrate
to another
– Oxidation and reduction
• Oxidoreductase
• Transfer of functional groups from one
molecule to another
– Transferases
• Aminotransferases
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Examples of oxidoreductase, transferase, and hydrolytic
enzymes.
Table 8.A A sampling of enzymes, their substrates, and their
reactions
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Regulation
• Metabolic pathways
• Direct control
• Genetic control
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The different metabolic pathways are regulated by the enzymes
that catalyze the reactions.
Fig.8.9 Patterns of
metabolism
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Competitive inhibition and noncompetitive inhibition are examples
of direct control (regulation) of the action of the enzymes.
Fig. 8.10 Examples of two common control mechanisms
for enzymes.
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Genetic control
• Repression
• Induction
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Repression is when end products can stop the expression of
genes that encode for proteins (enzymes) which are responsible
for metabolic reactions.
Fig. 8.11 One type of genetic control of enzyme synthesis
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Summary of major enzyme characteristics.
Table 8.1 Checklist of enzyme characteristics
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Energy
• Cell energetics
– Exergonic
– Endergonic
• Redox reaction
• Electron carrier
• Adenosine Triphosphate (ATP)
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The general scheme associated with metabolism of organic
molecules, the redox reaction, and the capture of energy in the
form of ATP.
Fig. 8.12 A simplified model that summarizes the cell’s
energy machine.
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Redox reaction
• Reduction and oxidation reaction
• Electron carriers transfer electrons and
hydrogens
– Electron donor
– Electron acceptor
• Energy is also transferred and captured
by the phosphate in form of ATP
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Figure 5.2 Oxidation-reduction, or redox, reactions
Reduction
Electron
donor
Oxidized
donor
Electron
acceptor
Reduced
acceptor
Oxidation
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Electron carriers
• Coenzymes
– Nicotinamide adenine dinucleotide (NAD)
• Respiratory chain carriers
– Cytochromes (protein)
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Electron carriers, such as NAD, accept electrons and hydrogens
from the substrate (organic molecule).
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Fig. 8.13 Details of NAD reduction
Adenosine Triphosphate
(ATP)
• Temporary energy repository
• Breaking of phosphates bonds will
release free energy
• Three part molecule
– Nitrogen base
– 5-carbon sugar (ribose)
– Chain of phosphates
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The phosphates capture the energy and becomes part of the ATP
molecule.
Fig. 8.14 The structure of adenosine triphosphate and its
partner compounds, ADP and AMP.
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ATP can be used to phosphorylate an organic molecule such as
glucose during catabolism.
Fig. 8.15 An example of phosphorylation of glucose by ATP
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ATP can be synthesized by substrate-level phosphorylation.
Fig. 8.16 ATP formation by substrate-level phosphorylation
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• Carbohydrate Catabolism
– Many organisms oxidize carbohydrates as
primary energy source for anabolic
reactions
– Glucose most common carbohydrate used
– Glucose catabolized by two processes:
cellular respiration and fermentation
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Pathways
• Catabolism
– Embden-Meyerhof-Parnas (EMP) pathway
or glycolysis
– Tricarboxylic acid cycle (TCA)
– Respiratory chain
• Aerobic
• Anaerobic
– Alternate pathways
– Fermentation
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A summary of the metabolism of glucose and the synthesis of
energy.
Fig. 8.17 Overview of
the flow, location, and
products of
Pathways in aerobic
respiration.
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Aerobic respiration
• Glycolysis
• Tricarboxylic acid (TCA)
• Electron transport
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Glycolysis
• Oxidation of glucose
• Phosphorylation of some intermediates
(Uses two ATPs)
• Splits a 6 carbon sugar into two 3
carbon molecules
• Coenzyme NAD is reduced to NADH
• Substrate-level-phosphorylation (Four
ATPs are synthesized)
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Glycolysis continued
• Water is generated
• Net yield of 2 ATPs
• Final intermediates are two Pyruvic acid
molecules
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The glycolytic steps associated with the metabolism of glucose to
pyruvic acid (pyruvate).
Fig. 8.18 Summary
of glycolysis
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TCA cycle
• Each pyruvic acid is processed to enter the
TCA cycle (two complete cycles)
• CO2 is generated
• Coenzymes NAD and FAD are reduced to
NADH and FADH2
• Net yield of two ATPs
• Critical intermediates are synthesized
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The steps associated with TCA cycle.
Fig. 8.20 The
reaction of a single
turn of the TCA
cycle
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Electron transport
• NADH and FADH2 donate electrons to
the electron carriers
• Membrane bound carriers transfer
electrons (redox reactions)
• The final electron acceptor completes
the terminal step (ex. Oxygen)
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Electron transport continued
• Chemiosmosis
• Proton motive force (PMF)
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Chemiosmosis entails the electron transport and formation of a
proton gradient (proton motive force).
Fig. 8.22 The electron transport system and oxidative
phosphorylation
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Figure 5.17 An electron transport chain
Respiration
Fermentation
Path of
electrons
Reduced
FMN
Oxidized
Oxidized
FeS
2
Reduced
Reduced
CoQ
Oxidized
Oxidized
Cyt
2
Reduced
Reduced
Cyt
Oxidized
2
Oxidized
Cyt
2
Reduced
Final electron
acceptor
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Figure 5.18
One possible arrangement of an electron transport chain
Bacterium
Mitochondrion
Intermembrane
space
Matrix
Exterior
Cytoplasmic
membrane
Cytoplasm
Exterior of prokaryote
or intermembrane space
of mitochondrion
FMN
Ubiquinone
Cyt b
Phospholipid
membrane
NADH
from glycolysis,
Krebs cycle,
pentose phosphate
pathway, and
Entner-Doudoroff
pathway
Cyt c
Cyt a3
Cyt a
Cyt c2
FADH2
from
Krebs cycle
ATP synthase
Cytoplasm of prokaryote
or matrix of mitochondrion
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Electron transport chain
• Mitochondria
– eucaryotes
• Cytoplasmic membrane
– procaryotes
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Total yield of ATP for one glucose molecule from aerobic
respiration.
Table 8.4 Summary of aerobic respiration for
one glucose molecule
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Anaerobic respiration
• Similar to aerobic respiration, except
nitrate or nitrite is the final electron
acceptor
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• Fermentation
– Sometimes cells cannot completely oxidize
glucose by cellular respiration
– Cells require constant source of NAD+
• Cannot be obtained simply using glycolysis and
Krebs cycle
– Fermentation pathways provide cells with
source of NAD+
• Partial oxidation of sugar or other metabolites to
release energy
• Uses organic molecule within cell as final electron
acceptor
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Fermentation
• Glycolysis only
• NADH from glycolysis is used to reduce the
organic products
• Organic compounds as the final electron
acceptors
• ATP yields are small (per glucose molecule),
compared to respiration
• Must metabolize large amounts of glucose to
produce equivalent respiratory ATPs
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The fermentation of ethyl alcohol and lactic acid.
Fig. 8.24 The
chemistry of
fermentation
systems
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Types of fermenters
• Facultative anaerobes
– Fermentation in the absence of oxygen
– Respiration in the presence of oxygen
– Ex. Escherichia coli
• Strict fermenters
– No respiration
– Ex. yeast
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Products of fermentation
• Alcoholic fermentation
• Acidic fermentation
• Mixed acid fermentation
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An example of mixed acid fermentation and the diverse products
synthesized.
Fig. 8.25 Miscellaneous products of pyruvate
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Figure 5.22 Representative fermentation products and the organisms that produce them
Glucose
Pyruvic acid
Organisms
Propionibacterium
Aspergillus
Lactobacillus
Streptococcus
Saccharomyces
Clostridium
Fermentation
CO2, propionic acid
Lactic acid
CO2, ethanol
Acetone, isopropanol
Wine, beer
Nail polis remover,
rubbing alcohol
Fermentation
products
Swiss cheese
Cheddar cheese,
yogurt, soy sauce
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Biosynthesis
• Anabolism
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Amphibolic
Gluconeogenesis
Beta oxidation
Amination
Transamination
Deamination
Macromolecules
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Amphibolic
• Integration of the catabolic and anabolic
pathways
• Intermediates serve multiple purposes
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Intermediates can serve to synthesize amino acids, carbohydrates
and lipids.
Fig. 8.26 An amphibolic view of metabolism
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Gluconeogenesis
• Pyruvate (intermediate) is converted to
glucose
• Occurs when the glucose supply is low
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Beta oxidation
• Metabolism of fats into acetyl, which
can then enter the TCA cycle as acetyl
CoA.
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Examples of amination, transamination, and deamination.
Fig. 8.27 Reactions that produce and convert amino acids
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Macromolecules
• Cellular building blocks
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Monosaccharides
Amino acids
Fatty acids
Nitrogen bases
Vitamins
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