Chapter 5: Microbial Metabolism

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Chapter 5Microbial Metabolism
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Microbial Metabolism

• Metabolism the sum of the chemical reactions in
  an organism
• Catabolism energy-releasing processes
• Breakdown of complex organic compounds
• Exergonic reactions
• Coupled to ATP synthesis
• Anabolism energy-requiring processes
• Building of complex organic compounds from
  simpler ones
• Endergonic reactions
• Coupled to ATP hydrolysis/breakdown

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Catabolism provides the building blocks and
energy for anabolism
ATP
Catabolic Reactions (ATP energy extracted and
stored)
Anabolic Reactions (ATP energy utilized)
ADP Pi
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Microbial MetabolismMetabolic Pathways

• Metabolic pathway 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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Metabolic Reactions

• Chemical reactions occur when bonds are formed or
  broken
• Chemical reactions may occur when atoms, ions,
  and molecules collide
• Activation energy minimum amount of energy
  needed to disrupt electronic configurations so
  that electrons can be rearranged

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Activation Energy
Figure 5.2
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Metabolic Reactions

• Reaction rate the frequency of collisions with
  enough energy to cause a reaction
• Can be increased by
• Increasing temperature (velocity, collision freq,
  energy of molecules)
• Increasing pressure ( distance between
  molecules)
• Increasing reactant concentration
• Enzymes

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Enzymes

• Enzymes are proteins
• Names usually end in -ase
• Some enzymes require cofactors
• Cofactor Nonprotein component of active enzyme
• Examples NAD, FAD

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Enzymes

• Biological catalysts speed up chemical reactions
• Specific for its designated chemical reaction
• Specificity conferred by the 3D shape of the
  enzyme (especially its active site) and substrate
• Induced fit of the substrate into the active
  site pocket
• Not changed or used up in that reaction

E-S complex
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EnzymesMechanism of action

• Orient the substrate(s) into a position that
  increases the probability of a favorable
  collision (a reaction)
• E-S complex transient binding enables more
  effective collisions and lowers the Ea of a
  reaction
• Substrate binds to the enzymes active site
• Can increase the reaction rate up to 10 bil times
  higher
• Turnover number 1-10,000 molecules per second

Figure 5.4
(Enzyme is unchanged)
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Activation Energy

• Enzymes increase the rate of a reaction by
  decreasing the activation energy

Figure 5.2
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Enzyme Activity

• Factors influencing enzyme activity
• Temperature
• pH
• Substrate concentration
• Inhibitors (competitive and noncompetitive)

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Factors Influencing Enzyme ActivityDenaturation

• Enzymes can be denatured by temperature and pH
  changes
• Denaturation loss of 3-D conformation
• Denaturation due to breakage of H-bonds and ionic
  bonds
• Disruption of active site?loss of enzymatic
  function

(Nonfunctional)
Figure 5.6
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Factors Influencing Enzyme ActivityTemperature

• Temperature

Optimal temperature
Figure 5.5a
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Factors Influencing Enzyme ActivitypH

• pH

Optimal pH
Figure 5.5b
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Factors Influencing Enzyme ActivitySubstrate
Concentration

• Substrate concentration

Figure 5.5c
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Factors Influencing Enzyme ActivityInhibitors

• Competitive inhibition
• Inhibitor blocks substrate access to active site
• Reversible or irreversible

Figure 5.7a, b
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Factors Influencing Enzyme ActivityCompetitive
Inhibitors
Enzyme substrate
(Sulfa drug)
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Factors Influencing Enzyme ActivityNoncompetitiv
e Inhibitors

• Noncompetitive inhibition the inhibitor does
  not compete with the substrate for the active
  site
• Inhibitor interacts with another area of enzyme
  (allosteric site)
• Causes a change in the shape of enzymes active
  site
• Reversible or irreversible

Figure 5.7a, c
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Summary of Energy Production Mechanisms
Figure 5.26
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Metabolic reactionsOxidation-Reduction

• Oxidation the loss of electrons
• Reduction the gain of electrons
• Redox reaction an oxidation reaction paired with
  a reduction reaction

Figure 5.9
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Metabolic ReactionsEnergy Production

• Most of the energy released in catabolic
  reactions is trapped in the cell by the formation
  of ATP
• ATP energy currency (readily usable energy)
• Unstable (high-energy) bonds ()
• Generated by the phosphorylation of ADP
• Phosphorylationaddition of a phosphate group

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The Generation of ATP

• Oxidative phosphorylation Generation of ATP by
  chemiosmosis
• Occurs as a result of the electron transport
  chain during aerobic and anaerobic cellular
  respiration
• Also substrate-level phosphorylation and
  photophosphorylation (photosynthesis)

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Carbohydrate CatabolismNAD and FAD Cofactors

• NAD and FAD are electron carriers
• Electrons have energy-generation potential
• Electrons are sequentially plucked off of glucose
  and delivered to the ETC (or another final
  electron acceptor)
• During redox reactions, protons (H) usually
  travel with electrons
• NAD 2e- NADH H
• FAD 2e- FADH2

2H
2H
(Reduced cofactors)
(Oxidized cofactors)
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Carbohydrate Catabolism

• The breakdown of carbohydrates to release energy
• Stepwise oxidation of glucose

Fermentation -Glycolysis (or
alternatives) -Fermentation
Cellular Respiration -Glycolysis -Krebs
cycle -ETC/ chemiosmosis
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Glycolysis

• The oxidation of glucose to pyruvic acid,
  produces ATP and NADH
• i.e. the splitting of 6C glucose into two 3C
  pyruvic acids

NAD
ATP
NADH
2
2
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Cellular Respiration

• Sequential oxidation of molecules frees electrons
  which are delivered to the electron transport
  chain
• Electrons are carried by NADH and FADH2
• Final electron acceptor is an inorganic molecule
  at the end of the ETC
• O2 (aerobic)
• NO3- or SO42- (anaerobic)
• Most ATP is generated by oxidative
  phosphorylation (ETC/Chemiosmosis)

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Cellular RespirationKrebs Cycle

• Oxidation of acetyl CoA produces 3 NADH and 1
  FADH2
• Decarboxylations release of CO2 as waste
• 6 CO2 per glucose
• Oxidation-reduction reactions
• NAD is reduced to NADH
• FAD is reduced to FADH2
• NADH and FADH2 contain most of the energy
  originally contained in glucose
• Proceed to ETC

Figure 5.13.2
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Cellular RespirationThe Electron Transport Chain

• A series of electron transfer molecules that are
  sequentially reduced and oxidized as electrons
  are passed down the chain
• Electrons are delivered here by NADH and FADH2
• Electrons reach their final electron acceptor at
  the end of the ETC
• Energy released is used to set up the proton
  gradient that drives chemiosmosis (ATP
  production)
• Located in the plasma membrane (prokaryotes) or
  the inner mitochondrial membrane (eukaryotes)

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Cellular RespirationThe Electron Transport Chain
Figure 5.14

• Aerobic cellular respiration O2 (the final
  electron acceptor) becomes negatively charged and
  picks up protons from its surroundings to form H2O

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Cellular RespirationChemiosmosis

• Three members of the ETC, actively transport H
  across the membrane
• Buildup of H on one side of the membrane
• Electrochemical gradient
• Protons travel down the electrochemical gradient
  through a specialized protein channel (ATP
  synthase)
• Energy is released and used by ATP synthase to
  form ATP

Figure 5.15
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Cellular RespirationChemiosmosis
Figure 5.16.2
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Cellular RespirationSummary

• Majority of ATP generation from glucose oxidation
  takes place at the ETC
• ETC regenerates NAD and FAD
• Can be used in the next round of glycolysis and
  Krebs cycle

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Cellular Respiration

• Aerobic respiration The final electron acceptor
  in the ETC is molecular oxygen (O2)
• Anaerobic respiration The final electron
  acceptor in the ETC is an inorganic molecule
  other than O2
• NO3-, SO42-, CO2 etc.
• Yields less energy than aerobic respiration
  because only part of the Krebs cycle operations
  and ETC are used

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Fermentation

• Releases energy from (incomplete) 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
• Produces small amounts of ATP
• Most of the energy of the starting material is
  still contained in chemical bonds of the organic
  end-product
• Regenerates NAD for next round of glycolysis
• Glycolysis-only source of ATP generation

Figure 5.18
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Fermentation

• Fermentation end-products depend upon the
  microorganism, substrate, and enzymes
  present/active

Figure 5.18b
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Fermentation
Bread rises
Food production Food spoilage
Alcoholic beverages
Figure 5.19
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Lipid and Protein Catabolism
Extracellular proteases
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Biochemical tests

• Used to identify bacteria

Figure 10.8
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Photosynthesis

• Photo Conversion of light energy into chemical
  energy (ATP)
• Light-dependent (light) reactions
• Synthesis Fixing carbon into organic molecules
  (sugars)
• Anabolism
• Light-independent (dark) reaction, Calvin-Benson
  cycle
• Electron donors photosynthetic pigment (i.e.
  chlorophyll)

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Photosynthesis

• Sun energy is captured by phototrophs and
  converted to chemical energy (ATP) used to build
  organic molecules (i.e. glucose)

Photosynthesis
Glucose
O2
CO2 H2O
Glycolysis Cellular Respiration
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PhotosynthesisThe big picture

• Synthesis of complex, reduced organic molecules
  (sugars) from simple inorganic substances (CO2)
• Carbon fixation synthesis of sugars from carbon
  in CO2 gas
• Electrons are incorporated into energy-rich
  sugars
• Oxygenic (plants, algae, cyanobacteria) 6 CO2
  12 H2O Light energy ? C6H12O6 6 O2 6 H2O
• Anoxygenic (purple sulfur green sulfur
  bacteria) CO2 2 H2S Light energy ? CH2O
  2 S H2O

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Summary of Energy Production Mechanisms
Figure 5.26
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Metabolic Diversity Among Organisms

• Classifications based on energy and carbon
  sources of organisms
• Principal energy source
• Phototrophs light
• Chemotrophs chemicals
• Principal carbon source
• Autotrophs CO2 (inorganic)
• Heterotrophs organic compounds

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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 Animals, protozoa, fungi, bacteria Fermentative bacteria
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Metabolic Pathways of Energy Use

• Glucose metabolism is considered efficient, but
  45 of energy from glucose is lost as heat!
• Remaining energy is stored in the chemical bonds
  of ATP
• Most ATP is used in the production of new
  cellular components (ANABOLISM!)

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