Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Microbial
Metabolism:
The Chemical
Crossroads
of Life
Chapter 8
Copyright © The McGraw-Hill Companies, Inc) Permission required for reproduction or display.
Metabolism
Nutrients from
outside or from
internal pathways
Pyruvate
Acetyl CoA
Glyceraldehyde-3-P
Amino acids
Sugars
Nucleotides
Fatty acids
Proteins
Peptidoglycan
RNA + DNA
Complex lipids
Relative complexity of molecules
Glycolysis
Krebs cycle
Respiratory chain
Fermentation
Macromolecules
Building
blocks
Glucose
Precursor
molecules
+
ATP
NADH
Yields energy
Chapter 8, pages 198 to 231
Uses energy
Uses energy
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
8.1 The Metabolism of Microbes
• Metabolism: All chemical reactions and physical
workings of the cell
• Functions of metabolism
• Assembles smaller molecules into larger
macromolecules needed for the cell
• Degrades macromolecules and yields energy
• Energy is conserved in the form of ATP or heat
Metabolism
• Anabolism (biosynthesis):
process that results in
synthesis of cell molecules
and structures
• Catabolism: breakdown
of bonds of larger
molecules into smaller
molecules
• usually requires energy input
• often release energy
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Enzymes
• Enzymes are catalysts
• Catalysts - chemicals that increase
the rate of a chemical reaction
without becoming part of the products
or being consumed in the reaction
How do Enzymes Work?
• Energy of activation:
the amount of energy
which must be
overcome for a reaction
to proceed.
• Act as a physical site
where the reactant
molecules (substrates)
can be positioned for
various interactions
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Enzyme Structure
• Most are protein
• Can be classified as simple or conjugated
• Simple enzymes- consist of protein alone
• Conjugated enzymes (haloenzyme) - contain
protein and nonprotein molecules
• Protein (now called the apoenzyme) and
one or more cofactors
• Cofactors are either organic molecules
(coenzymes) or inorganic elements
(metal ions)
Conjugated Enzyme Structure
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Apoenzymes: Specificity and the Active
Site
• Exhibits levels of molecular complexity called the primary,
secondary, tertiary, and quaternary organization
• The actual site where the substrate binds is a crevice or
groove called the active site or catalytic site
Enzyme-Substrate Interactions
• For a reaction to take place, a temporary enzymesubstrate union must occur at the active site
• “Lock-and-key” fit
• The bonds are weak and easily reversible
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Cofactors: Supporting the Work of
Enzymes
• Metallic cofactors
• Include Fe, Cu, Mg, Mn, Zn, Co, Se
• Activate enzymes, help bring the active site and
substrate close together, and participate directly in
chemical reactions with the enzyme-substrate
complex
• Coenzymes
• Organic compounds that work in conjunction with an
apoenzyme to perform a necessary alteration of a
substrate
• Removes a chemical group from one substrate
molecule and adds it to another substrate
• Vitamins: one of the most important components of
coenzymes
Classification of Enzyme Functions
• Site of action
• Type of action
• Substrate
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Location and Regularity of Enzyme
Action
• Either inside or outside
of the cell
• Exoenzymes break
down molecules
outside of the cell
• Endoenzymes break
down molecules inside
of the cell
Rate of Enzyme Production
• Constitutive enzymes:
always present and in
relatively constant
amounts
• Regulated enzymes:
production is either
induced or repressed in
response to a change in
concentration of the
substrate
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Synthesis and Hydrolysis Reactions
Transfer Reactions by Enzymes
• Oxidation-reduction reactions
• A compound loses electrons (oxidized)
• A compound receives electrons (reduced)
• Other enzymes that play a role in necessary
molecular conversions by directing the transfer of
functional groups:
• Aminotransferases
• Phosphotransferases
• Methyltranferases
• Decarboxylases
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
The Role of Microbial Enzymes in
Disease
• Many pathogens secrete unique exoenzymes
• Help them avoid host defenses or promote
multiplication in tissues
• These exoenzymes are called virulence factors
or toxins
The Sensitivity of Enzymes to Their
Environment
• Enzyme activity is highly influenced by the cell’s
environment
• Enzymes generally operate only under the natural
temperature, pH, and osmotic pressure of an
organism’s habitat
• When enzymes subjected to changes in normal
conditions, they become chemically unstable (labile)
• Denaturation: the weak bonds that maintain the
native shape of the apoenzyme are broken
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Direct Controls on the Action of
Enzymes
• Competitive inhibition: The cell supplies a
molecule that resembles the enzyme’s normal
substrate, which then occupies and blocks the
enzyme’s active site
• Noncompetitive inhibition: The enzyme has
two binding sites- the active site and the
regulatory site; a regulator molecule binds to the
regulatory site providing a negative feedback
mechanism
Control Mechanisms for Enzymes
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Controls on Enzyme Synthesis
• Enzyme repression: decrease enzyme expression
• Enzyme induction: increase enzyme expression
8.2 The Pursuit and Utilization of
Energy
• Energy in Cells
• Exergonic reaction: a reaction that releases
energy as it goes forward
• Endergonic reaction: a reaction that is driven
forward with the addition of energy
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Cell Energy Production
A Closer Look at Biological Oxidation
and Reduction
• Biological systems often extract energy through
redox reactions
• Redox reactions always occur in pairs- an electron
donor paired with an electron acceptor
• Electron donor (reduced) + electron acceptor
(oxidized)  Electron donor (oxidized) + electron
acceptor (reduced)
• The energy in the electron acceptor can be captured
to phosphorylate ADP or some other compound,
storing the energy in a high-energy molecule like
ATP
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Oxidation/Reduction
• Oxidation is losing electrons
• Reduction is gaining electrons
• Oxidation is always linked to reduction
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
1
Na
281
Reducing agent
gives up electrons.
Cl
287
Oxidizing agent
accepts electrons.
Na
Oxidized
cation
28
2
Cl
288
Reduced
anion
Electron Carriers
• Repeatedly accept and
release electrons and
hydrogens
• Most carriers are
coenzymes that transfer
both electrons and
hydrogens
• Some transfer electrons
only
• Most common carrierNAD (nicotinamide
adenine dinucleotide)
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Adenosine Triphosphate
The Metabolic Role of ATP
• When used in a chemical reaction, must be replaced
• Ongoing cycle
• Adding a phosphate to ADP replenishes ATP but it
requires an input of energy
• In heterotrophs, this energy comes from certain
steps of catabolic pathways
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Substrate Level Phosphorylation
• ATP can be used to drive reactions
Glucose + ATP  Glucose-6-phosphate + ADP
• Some compounds can be used to make ATP
Phosphoenolpyruvate + ADP  pyruvate +
ATP
• This is called substrate level phosphorylation
8.3 The Pathways
• Metabolism uses enzymes to catalyze reactions
that break down (catabolize) organic molecules
to materials that cells can then use to build
(anabolize) larger, more complex molecules.
• Reducing power and energy are needed in large
quantities for the anabolic parts of metabolism;
they are produced during the catabolic part of
metabolism.
• Pathway- a series of biochemical reactions
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Catabolism: Getting Materials and
Energy
• Glucose is often the nutrient catabolized
• Three major pathways
• Aerobic respiration: series of reactions that
convert glucose to CO2 and allows the cell to
recover significant amounts of energy;
requires oxygen
• Fermentation: Use only glycolysis to
incompletely oxidize glucose
• Anaerobic respiration: Does not use
molecular oxygen as the final electron
acceptor
Glucose Metabolism
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Aerobic Respiration
• Series of enzyme-catalyzed reactions
• Electrons are transferred from fuel molecules to
oxygen as a final electron acceptor
• Principal energy-yielding scheme for aerobic
heterotrophs
• Provides both ATP and metabolic intermediates
for many other pathways in the cell
• Glucose is the starting compound
• Glycolysis enzymatically converts glucose
through several steps into pyruvic acid
Glycolysis
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
AEROBIC RESPIRATION ANAEROBIC RESPIRATION FERMENTATION
Glycolysis
Glycolysis
Glycolysis
Glucose
Glucose
ATP
ATP
NADH
NADH
CO2
CO2
CO2
Acetyl CoA
C
Fermentation
Acetyl CoA
C C C
C
C
Glucose
FADH 2
FADH2
Krebs
CO2
NADH
Krebs
CO2
Acetaldeh yd e
Lactic acid
NADH
ATP
First phosphorylation
Ethanol
ATP
ATP
1
ADP
Or other alcohols,
acids, gases
Electrons
Electrons
Electron transport
Electron transport
O2 is final electron
acceptor.
ATP produced
38
No oxygen electron acceptors
(examples: SO4 2-, NO3-, CO32-)
ATP produced
2 to 36
An organic molecule is final
electron acceptor (pyruvate,
acetaldehyd e, etc.).
ATP produced
PO4
C
C C C
C C
C
C C C
C
C C
C
2
Second phosphorylation
Glucose-6-phosphate
PO4
2
Fructose-6-phosphate
C
ATP
3
ADP
PO4
PO4
C
4
Dihydroxyacetone
phosphate
(DHAP)
Fructose-1,6-diphosphate
(F-1,6-P)
C
Split of F-1,6-P; subsequent
reactions in duplicate
PO4
C
C
C
C
Glyceraldehyde-3
phosphate
C C PO4
C
C PO4
C C C
5
6
To electron transport
NAD
Glyceraldehyde-3-P
(G-3-P)
PO4
NAD
NADH
NADH
PO4 C C C
Diphosphoglyceric
acid
Substrate-level
phosphorylation
PO4
ADP
ATP
C C C
PO4 C C
PO4
C C C
PO4
ADP
ATP
3-phosphoglyceric
acid
PO4
C
To electron transport
C
C
7
PO4
PO4
C C C
2-phosphoglycericacid
C
C C
8
PO4
C
C
Phosphoenolyruvicacid
C
C C
C
C
C
Substrate-level
phosphorylation
9
ATP
C
ATP
C C
Goes to
Krebs cycle or fermentation
Chapter 8, pages 198 to 231
PO4
Pyruvicacid
C
Goes to
Krebs cycle or fermentation
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Pyruvic Acid- A Central Metabolite
• Pyruvic acid from glycolysis serves an important position
in several pathways
• Different organisms handle it in different ways
• In strictly aerobic organisms and some anaerobes,
pyruvic acid enters the Krebs cycle
The Krebs Cycle: A Carbon and Energy
Wheel
• Pyruvic acid is energy-rich, but its hydrogens
need to be transferred to oxygen
• Takes place in the cytoplasm of bacteria and in
the mitochondrial matrix in eukaryotes
• Produces reduced coenzymes NADH and
FADH2, 2 ATPs for each glucose molecule
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Krebs Cycle
The Respiratory Chain: Electron
Transport and Oxidative Phosphorylation
• The final “processing mill” for electrons and
hydrogen ions
• The major generator of ATP
• A chain of special redox carriers that receives
electrons from reduced carriers (NADH and
FADH2) and passes them in a sequential and
orderly fashion from one redox molecule to the
next.
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Electron Transport System
• NADH oxidized
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
• Electrons pass
through membrane
carriers
• Carriers are called
“cytochromes”
Cell wall
H
H
H
H
H
H
H
H
• Protons pumped out
H
H
H
Cytochromes
H
H
H
H
H
• Protons pass through
ATP synthase to form
ATP
Cytoplasm
ATP synthase
Cell membrane
with ETS
ADP
H
H
H
ATP
H
The Terminal Step
• Oxygen accepts the electrons
• Catalyzed by cytochrome aa3 (cytochrome
oxidase)
• 2 H+ + 2 e- + 1/2O2  H2O
• Most eukaryotic aerobes have a fully functioning
cytochrome system
• Bacteria exhibit wide-ranging variations which
can be used to differentiate among certain
genera of bacteria
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
ATP Yield from Aerobic Respiration
Anaerobic Respiration
• Functions like the aerobic cytochrome system
except it utilizes oxygen-containing ions rather
than free oxygen as the final electron acceptor
• The nitrate and nitrite reduction systems are best
known, using the enzyme nitrate reductase
• Denitrification: when enzymes can further
reduce nitrite to nitric oxide, nitrous oxide, and
nitrogen gas- important in recycling nitrogen in
the biosphere
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Fermentation
• The incomplete oxidation of glucose or other
carbohydrates in the absence of oxygen
• Uses organic compounds as the terminal electron
acceptors and yields a small amount of ATP
• Many bacteria can grow as fast using fermentation
as they would in the presence of oxygen
• This is made possible by an increase in the rate of
glycolysis
• Permits independence from molecular oxygen
Products of Fermentation in
Microorganisms
• Products of Fermentation in Microorganisms
• Alcoholic beverages
• Organic acids
• Dairy products
• Vitamins, antibiotics, and even hormones
• Two general categories
• Alcoholic fermentation
• Acidic fermentation
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Fermentation Pathways
Alcoholic Fermentation Products
• Occurs in yeast or bacterial species that have
metabolic pathways for converting pyruvic acid to
ethanol
• Products: ethanol and CO2
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Acidic Fermentation Products
• Extremely varied pathways
• Lactic acid bacteria ferment pyruvate and reduce
it to lactic acid
• Heterolactic fermentation- when glucose is
fermented to a mixture of lactic acid, acetic acid,
and carbon dioxide
• Mixed acid fermentation- produces a
combination of acetic, lactic, succinic, and formic
acids and lowers the pH of a medium to about
4.0
8.4 Biosynthesis and the Crossing
Pathways of Metabolism
• The Frugality of the Cell- Waste Not, Want Not
• Most catabolic pathways contain strategic
molecular intermediates (metabolites) that can be
diverted into anabolic pathways
• Amphibolism: the property of a system to
integrate catabolic and anabolic pathways to
improve cell efficiency
• Principal sites of amphibolic interaction occur
during glycolysis and the Krebs cycle
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Amphibolic Metabolism
Amphibolic Sources of Cellular Building
Blocks
• Pyruvate also provides intermediates for amino acids and can serve
as the starting point in glucose synthesis from metabolic
intermediates (gluconeogenesis)
• The acetyl group that starts the Krebs cycle can be fed into a number
of synthetic pathways
• Fats can be degraded to acetyl through beta oxidation
• Two metabolites of carbohydrate catabolism that the Krebs cycle
produces are essential intermediates in the synthesis of amino acids
• Oxaloacetic acid
• Α-ketoglutaric acid
• Occurs through amination
• Amino acids and carbohydrates can be interchanged through
transamination
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Amino Acid Formation
Anabolism: Formation of
Macromolecules
• Monosaccharides, amino acids, fatty acids, nitrogen
bases, and vitamins come from two possible sources
• Enter the cell from outside as nutrients
• Can be synthesized through various cellular pathways
• Carbohydrate Biosynthesis
• Several alternative pathways
• Amino Acids, Protein Synthesis, and Nucleic Acid
Synthesis
• Some organisms can synthesize all 20 amino acids
• Other organisms (especially animals) must acquire the
essential ones from their diets
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Assembly of the Cell
• When anabolism produces enough
macromolecules to serve two cells
• When DNA replication produces duplicate copies
of the cell’s genetic material
• Then the cell undergoes binary fission
8.5 It All Starts with Light
• Photosynthesis
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
• Proceeds in two
phases
• Light-dependent
reactions
• Lightindependent
reactions
Glucose
H2O
ATP
2H + e–
NADPH
O2
Chloroplast
Chapter 8, pages 198 to 231
CO2
27
Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Light-Dependent Reactions
• Solar energy delivered in discrete energy packets called
photons
• Light strikes photosynthetic pigments
• Some wavelengths are absorbed
• Some pass through
• Some are reflected
• Light is absorbed through photosynthetic pigments
• Chlorophylls (green)
• Carotenoids (yellow, orange, or red)
• Phycobilins (red or blue-green)
Light-Dependent Reactions
• Bacterial chlorophylls
• Contain a photocenter- a magnesium atom held in the
center of a complex ringed molecule called a
porphyrin
• Harvest the energy of photons and converts it to
electron energy
• Accessory photosynthetic pigments trap light energy and
shuttle it to chlorophyll
Chapter 8, pages 198 to 231
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Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Photosynthesis
Light-Independent Reactions
• Occur in the chloroplast stroma or the cytoplasm
of cyanobacteria
• Use energy produced by the light phase to
synthesize glucose by means of the Calvin cycle
Chapter 8, pages 198 to 231
29
Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Calvin Cycle
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
CO2
• Fix carbon dioxide
• Reverse of glycolysis
Splitting
6-carbon
intermediate
P
• Autotrophs
P
P
3-phosphoglyceric
acid
P
Ribulose-1,5-bisphosphate
5-carbon
ADP
Calvin Cycle
ATP × 2
P
P
P
P
ADP
ATP
• 6 CO2  Glucose
P
Seriesof7-carbon
and5-carbon
Intermediates
P
1,3-bisphosphoglyceric acid
P
H
P
H
P
NADPH × 2
NADP+
P
Glyceraldehyde-3phosphate
Glucose
Fructoseintermediates
Other Mechanisms of
Photosynthesis
• Oxygenic (oxygen-releasing) photosynthesis that occurs
in plants, algae, and cyanobacteria- dominant type on
earth
• Other photosynthesizers such as green and purple
bacteria
• Possess bacteriochlorophyll
• More versatile in capturing light
• Only have a cyclic photosystem I
• These bacteria use H2, H2S, or elemental sulfur rather
than H2O as a source of electrons and reducing power
• They are anoxygenic (non-oxygen-producing); many
are strict anaerobes
Chapter 8, pages 198 to 231
30