Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 1
Microbial
Metabolism:
The Chemical
Crossroads
of Life
Chapter 8
Copyright © The McGraw-Hill Companies, Inc) Permission required for reproduction or display.
Metabolism
Glucose
Rela
tiv
e c
om
ple
xit
y o
f m
ole
cu
les
+
Macromolecules
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
Glycolysis
Krebs cycle
Respiratory chain
Fermentation
Yields energy
Building
blocks
Precursor
molecules
ATP
NADH
Uses energy Uses energy
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 2
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
• usually requires energy input
• Catabolism: breakdown
of bonds of larger
molecules into smaller
molecules
• often release energy
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 3
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 4
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 5
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 enzyme-
substrate union must occur at the active site
• “Lock-and-key” fit
• The bonds are weak and easily reversible
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 6
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 7
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 8
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 9
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 10
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 11
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 12
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 13
Oxidation/Reduction
• Oxidation is losing electrons
• Reduction is gaining electrons
• Oxidation is always linked to reduction
2 8 1 2 8 2 8 7 2 8 8
1 2
Reduced
anion
Cl Na Cl Na
Reducing agent
gives up electrons.
Oxidizing agent
accepts electrons.
Oxidized
cation
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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 carrier-
NAD (nicotinamide
adenine dinucleotide)
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 14
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 15
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 16
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 17
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
Second phosphorylation
Dihydroxyacetone
phosphate
(DHAP)
NAD
Glucose
Glyceraldehyde-3
phosphate
Diphosphoglyceric
acid
Split of F-1,6-P; subsequent
reactions in duplicate
Substrate-level
phosphorylation
3-phosphoglyceric
acid
2-phosphoglycericacid
Substrate-level
phosphorylation
Phosphoenolyruvicacid
Pyruvicacid
ATP
Glyceraldehyde-3-P
(G-3-P)
To
ele
ctro
n tra
ns
po
rt
First phosphorylation
To
ele
ctr
on
tra
ns
po
rt
NAD
NADH
Goes to Goes to
Krebs cycle or fermentation Krebs cycle or fermentation
Fructose-6-phosphate
Glucose-6-phosphate
Fructose-1,6-diphosphate
(F-1,6-P)
ATP
ADP
ATP
ADP
ATP
ADP
ATP
ADP
AEROBIC RESPIRATION ANAEROBIC RESPIRATION FERMENTATION
Glycolysis Glycolysis Glycolysis
Glucose Glucose
CO2 CO2 CO2
ATP
NADH NADH
ATP
Acetyl CoA Acetyl CoA Fermentation
FADH2 FADH2
Lactic acid Acetaldehyde
Ethanol
Krebs Krebs
NADH NADH
ATP ATP
CO2 CO2
Electrons Electrons Or other alcohols,
acids, gases
An organic molecule is final
electron acceptor (pyruvate,
acetaldehyde, etc.).
ATP produced � 2 ATP produced � 2 to 36 ATP produced �
38
No oxygen electron acceptors
(examples: SO4 2-, NO3
-, CO32-)
O2 is final electron
acceptor.
Electron transport
Electron transport
ATP
PO4
PO4
PO4 PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4 PO4
PO4
PO4
PO4 PO4
PO4
PO4
C C C C C C
C C C C C C
C C C C C C
C C C C C C
C C C C C C
C C C C C C
C C C C C C
C C C C C C
NADH
C C C C C C
C C C C C C
C C C C C C
1
2
3
4
5
6
7
8
9
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 18
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 19
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.
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 20
Electron Transport System
H
H
H H
H
H H
H
H
H
H
H
H
H H
H
H
H
H
H
Cell wall
Cytochromes
Cytoplasm
Cell membrane
with ETS
ATP
ADP
ATP synthase
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
• NADH oxidized
• Electrons pass
through membrane
carriers
• Carriers are called
“cytochromes”
• Protons pumped out
• Protons pass through
ATP synthase to form
ATP
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 21
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 22
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 23
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 24
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 25
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 26
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 27
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
• Proceeds in two
phases
• Light-dependent
reactions
• Light-
independent
reactions
Glucose
NADPH
ATP
Chloroplast
H2O
O2
CO2
2H + e–
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Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 28
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 29
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
Microbial Metabolism: The Chemical Crossroads of Life
Microbiology: A Systems Approach
Chapter 8, pages 198 to 231 30
Calvin Cycle
• Fix carbon dioxide
• Autotrophs
• Reverse of glycolysis
• 6 CO2 Glucose
P P
P P
P P
P P
P P
P
P
P
P
H
H
3-phosphoglyceric
acid
Splitting
ATP × 2
ADP
1,3-bisphosphoglyceric acid
NADPH × 2
NADP+
Glyceraldehyde-3-
phosphate
Glucose
ADP
ATP
Seriesof7-carbon
and5-carbon
Intermediates
Ribulose-1,5-bisphosphate
5-carbon
Fructoseintermediates
6-carbon
intermediate
Calvin Cycle
CO2
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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