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Title: What is the title of this lecture?
Speaker: Amit Dhingra
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online.wsu.edu
Title: Microbial Metabolism
Instructor: Consetta Helmick
Microbial Metabolism
• Microbial Metabolism
– Aerobic Cellular Respiration or in bacteria called the Embden-Meyerhof Pathway
– Alternate Pathway
• Pentose Phosphate Pathway
• Entner-Doudoroff Pathway
• Biologists had noticed that in vats of grape juice, alcohol and CO2 are produced while yeast cells increase in number– In 1850s, Louis Pasteur set out to prove
• Simplified setup: clear solution of sugar, ammonia, mineral salts, trace elements
• Added a few yeast cells—as they grew, sugar decreased, alcohol level increased
• Strongly supported idea, but Pasteur failed to extract something from inside the cells that would convert sugar
– In 1897, Eduard Buchner, a German chemist, showed that crushed yeast cells could convert sugar to ethanol and CO2; awarded Nobel Prize in 1907
A Glimpse of History
• All cells need to accomplish two fundamental tasks
– Synthesize new parts
• Cell walls, membranes, ribosomes, nucleic acids
– Harvest energy to power reactions
– Sum total of these is called metabolism
– Human implications
• Used to make biofuels
• Used to produce food
• Important in laboratory
• Invaluable models for study
• Unique pathways potentialdrug targets
Microbial Metabolism
• Can separate metabolism into two parts– Catabolism
• Processes that degrade compounds to release energy
• Cells capture to make ATP
– Anabolism• Biosynthetic processes
• Assemble subunits of macromolecules
• Use ATP to drive reactions
– Processes intimately linked
Principles of Metabolism
Macromolecules
(proteins, nucleic acids,
polysaccharides, lipids)
Subunits
(amino acids,
nucleotides, sugars,
fatty acids)
Catabolic processes harvest
the energy released during the
breakdown of compounds and
use it to make ATP. The
processes also produce
precursor metabolites used in
biosynthesis.
Anabolic processes (biosynthesis)
synthesize and assemble subunits
of macromolecules that make up
the cell structures. The processes
use the ATP and precursor
metabolites produced in
catabolism.
ANABOLISMCATABOLISM
Energy source
(glucose)
(source of nitrogen,
sulfur, etc.)
(acids, carbon
dioxide)
Waste products Nutrients
Energy
Precursor
metabolites
Cell structures
(cell wall, membrane,
ribosomes, surface
structures)
Energy
Energy
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• Energy is the capacity to do work
• Two types of energy
– Potential: stored energy (e.g., chemical bonds, rock on hill, water behind dam)
– Kinetic: energy of movement (e.g., moving water)
– Energy in universe cannot becreated or destroyed, but it canbe converted between forms
Energy
• Photosynthetic organisms harvest energy in sunlight– Power synthesis of organic
compounds from CO2
– Convert kinetic energy of photons to potential energy of chemical bonds
• Chemoorganotrophs obtain energy from organic compounds– Depend on activities of
photosynthetic organisms
Harvesting Energy
Radiant energy
(sunlight)Photosynthetic organisms harvest the energy
of sunlight and use it to power the synthesis
of organic compounds from CO2. This
converts radiant energy to chemical energy.
Chemoorganotrophs degrade organic
compounds, harvesting chemical energy.Chemical energy
(organic compounds)
(top): © Photodisc Vol. Series 74, photo by Robert Glusie;
(bottom): © Digital Vision/PunchStock
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• Metabolic pathways
– Series of chemical reactions that convert starting compound end product
• May be linear, branched, cyclical
Components of Metabolic Pathways
Starting compound Intermediatea Intermediateb End product
End product1
End product2
Intermediateb
(c) Cyclical metabolic pathway
End product
Intermediated
Starting compound
Intermediatec
Intermediatea
(a) Linear metabolic pathway
(b) Branched metabolic pathway
Intermediatea
Intermediateb2
Intermediateb1
Starting compound
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Three types of Glucose metabolism
• Aerobic Respiration Cellular Respiration
• Anaerobic Respiration
• Fermentation
Overview of Metabolism in Bacteria
• Central metabolic pathways
– Glycolysis
– Pentose phosphate pathway
– Tricarboxylic acid cycle
• Key outcomes
– ATP
– Reducing power
– Precursor metabolites~ ~
~ ~
+
+
21
5
4
GLUCOSE
Pentose phosphate
pathway
Starts the oxidation of glucose
Glycolysis
Oxidizes glucose to pyruvateReducing
power
ATP
by substrate-level
phosphorylation
Fermentation
Reduces pyruvate
or a derivative
Biosynthesis
Transition step
Acetyl-
CoAAcetyl-
CoA
Respiration
Uses the electron transport
chain to convert reducing
power to proton motive force
ATP
by oxidative
phosphorylation
ATP
by substrate-level
phosphorylation
Reducing
power
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
CO2 CO2
3a
X 2CO2
CO2
3b
Yields
Yields
Yields
Yields
Yields Reducing
power
Reducing
power
~ ~
Acids, alcohols, and gasesPyruvate Pyruvate
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• Role of Enzymes
– Biological catalysts: accelerate conversion of substrate into product by lowering activation energy
• Highly specific: one at each step
• Reactions would occur without, but extremely slowly
Components of Metabolic PathwaysR
ela
tive e
nerg
y
Activation
energy
without an
enzyme
End productEnzyme cEnzyme b
IntermediatebIntermediatea
Enzyme a
(b)
Starting compound
(a)
Energy of
products
Activation
energy
with an
enzyme
Energy of
reactants
Progress of reaction
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• Adenosine triphosphate (ATP)
– Energy currency of cell
– Three negatively charged phosphate groups repel
• Bonds inherently unstable, easily broken
• Releases energy to drive cellular processes
• High energy phosphate bonds denoted by ~
• ATP ADP + Pi
Energy Molecule
O
O
O–
PO O
O
O–
P
O
OO–
PO–
N
N N
N
Adenosine
Phosphate groups
High-energy
bonds
Ribose
OHOH
Adenine
CH2
NH2
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• Role of ATP– Adenosine triphospate (ATP) is energy currency
• Composed of ribose, adenine, three phosphate groups• Adenosine diphospate (ADP) acceptor of free energy• Cells produce ATP by adding Pi to ADP using energy• Release energy from ATP to yield ADP and Pi
• Three processes to generate ATP– Substrate-level phosphorylation
• Exergonic reaction powers
– Oxidative phosphorylation• Proton motive force drives
– Photophosphorylation• Sunlight used to create proton
motive force to drive
PPP
PP
~
~
~
Unstable (high-energy) bonds
Energy used
The energy comes
from catabolic
reactions.
Energy released
The energy drives
anabolic reactions.
ADP
PiPi
ATP
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• Role of Electron Carriers
– Energy harvested in stepwise process
• Electrons transferred to electron carriers, which represent reducing power (easily transfer electrons to molecules)– Raise energy level of recipient molecule
• NAD+/NADH, NADP+/NADPH, and FAD/FADH2
– Serve as carbon skeletons for building macromolecules
Aerobic cellular respiration Bacteria produce Precursor Metabolites
Overview of Metabolism in Bacteria
• Central metabolic pathways
– Glycolysis
– Pentose phosphate pathway
– Tricarboxylic acid cycle
• Key outcomes
– ATP
– Reducing power
– Precursor metabolites~ ~
~ ~
+
+
21
5
4
GLUCOSE
Pentose phosphate
pathway
Starts the oxidation of glucose
Glycolysis
Oxidizes glucose to pyruvateReducing
power
ATP
by substrate-level
phosphorylation
Fermentation
Reduces pyruvate
or a derivative
Biosynthesis
Transition step
Acetyl-
CoAAcetyl-
CoA
Respiration
Uses the electron transport
chain to convert reducing
power to proton motive force
ATP
by oxidative
phosphorylation
ATP
by substrate-level
phosphorylation
Reducing
power
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
CO2 CO2
3a
X 2CO2
CO2
3b
Yields
Yields
Yields
Yields
Yields Reducing
power
Reducing
power
~ ~
Acids, alcohols, and gasesPyruvate Pyruvate
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Aerobic Cellular Respiration or Embden-Meyerhof Pathway in bacteria
• Requires oxygen as the final electron acceptor
• Produces 38 ATP’s in Bacterial and 36 ATP’s in Eukaryotic cells
• Prokaryotic cells produce precursor metabolites which become cellular components or macromolecules
• Glycolysis
– Converts 1 glucose to 2 pyruvates; yields net 2 ATP, 2 NADH
– Investment phase:
• 2 phosphate groups added
• Glucose split to two 3-carbon molecules
– Pay-off phase:
• 3-carbon molecules converted to pyruvate
• Generates 4 ATP, 2 NADH total
~ ~
~
~ ~
~
~
~ ~
~
~ ~
~
~ ~
~
~ ~
+
+
x2
PPP
PPP
PPP2
1
5
4
3b
~ ~
~ ~
~
GLUCOSE
Yields
Fermentation
Reduces pyruvate
or a derivative
PyruvatePyruvate
Reducing
power
Yields
Biosynthesis
Transition step3a
YieldsReducing
power
CO2
CO2
CO2CO2
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
ATP
by substrate-level
phosphorylation
Reducing
power
Respiration
Uses the electron transport
Chain to convert reducing
power to proton motive force
Yields
ATP
by oxidative
phosphorylation
~
1
2
3
8
4
5
6
9
7
H2O
ATP is expended to add a phosphate group.
A chemical rearrangement occurs.
ATP is expended to add a phosphate group.
The 6-carbon molecule is split into two 3-carbon
molecules.
A chemical rearrangement of one of the
molecules occurs.
The addition of a phosphate
group is coupled to a redox
reaction, generating NADH and
a high-energy phosphate bond.
ATP is produced by
substrate-level
phosphorylation.
A chemical rearrangement occurs.
Water is removed, causing the
phosphate bond to become
high-energy.
ATP is produced by
substrate-level
phosphorylation.
Pyruvate
ATP
ADP
Phospho-
enolpyruvate
2-phospho-
glycerate
3-phospho-
glycerate
ATP
ADP
1,3-bisphospho-
glycerate
Glyceraldehyde
3-phosphate
Dihydroxyacetone
phosphate
Fructose
1,6-bisphosphate
ADP
ATP
Fructose
6-phosphate
Glucose
6-phosphate
10
H2O
NADH + H+
NAD+
Glucose
ATP
ADP
NADH + H+
NAD+
Pentose phosphate
pathway
Starts the oxidation of glucose
Glycolysis
Oxidizes glucose to pyruvateReducing
power
ATP
by substrate-level
phosphorylation
Acids, alcohols, and gases
Yields
~ ~
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Bacterial Alternative Pathway
Pentose Phosphate Pathway– Also breaks down glucose– Important in biosynthesis of precursor metabolites
• Ribose 5-phosphate, erythrose 4-phosphate
– Also generates reducing power: NADPH
• Precursor metabolites– Glucose molecules can have
different fates– Can be completely oxidized
to CO2 for maximum ATP– Can be siphoned off as
precursor metabolite foruse in biosynthesis
6.10. Anabolic Pathways—Synthesizing Subunits from Precursor Molecules
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Pentose phosphate
pathway
Ribose 5-phosphate
Erythrose 5-phosphate
Nucleotides
amino acids
(histidine)
Amino acids
(phenylalanine,
tryptophan,
tyrosine)
Lipids
(glycerol
component)
Amino acids
(cysteine,
glycine, serine)
Amino acids
(phenylalanine,
tryptophan, tyrosine)
Amino acids
(aspartate, asparagine,
isoleucine, lysine,
methionine, threonine)
TCA cycle
Amino acids
(arginine, glutamate,
glutamine, proline)
Lipids
(fatty acids)
Amino acids
(alanine,
leucine, valine)
Peptidoglycan
Lipopolysaccharide
(polysaccharide)
Glucose 6-phosphate
Fructose 6-phosphate
Dihydroxyacetone
phosphate
3-phosphoglycerate
Phosphoenolpyruvate
Pyruvate
Acetyl-CoAAcetyl-CoA
Pyruvate
Oxaloacetate
- ketoglutarate
Glycolysis
X 2
• Transition Step
– CO2 is removedfrom pyruvate
– Electrons reduce NAD+
toNADH + H+
– 2-carbon acetyl group joined to coenzyme A to form acetyl-CoA
– Takes place in mitochondria in eukaryotes
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~~ ~ + Pi
H2O
1
2
8
7
6
5
3
4
A redox reaction
generates NADH.
Water is added.
A redox reaction
generates FADH2-
The energy released
during CoA removal is
harvested to produce ATP.ADPATP
CoA
A redox reaction
generates NADH,
CO2 is removed,
and coenzyme A
is added.
A redox reaction
generates NADH
and CO2 is
removed.
A chemical
rearrangement occurs.
The acetyl group is transferred
to oxaloacetate to start a new
round of the cycle.
Transition step:
CO2 is removed, a redox reaction generates
NADH, and coenzyme A is added.
NADH + H+
Acetyl-CoA
CoA
CoA
NADH + H+ Oxaloacetate
NAD+
Malate
Fumarate
FADH2
FAD Succinate Succinyl-CoA
CoA
CoA
CO2
NAD+
-ketoglutarate
Isocitrate
Citrate
CoA
NAD+
CO2
Pyruvate
NAD+
CO2
NADH + H+
NADH + H+
+
+
x 2
21
5
4
~ ~
~ ~
~ ~
GLUCOSE
Respiration
Uses the electron transport
chain to convert reducing
power to proton motive force
ATP
by oxidative
phosphorylation
Yields
ATP
by substrate-level
phosphorylation
Reducing
power
Yields
CO2
CO2
Pyruvate Pyruvate
3a Transition step
YieldsReducing
power
Acetyl-
CoA
Acetyl-
CoA
Biosynthesis
YieldsReducing
power
Pentose phosphate
pathway
Starts the oxidation of glucose
Glycolysis
Oxidizes glucose to pyruvate
YieldsReducing
power
ATP
by substrate-level
phosphorylation
Acids, alcohols, and gases
CO2CO2
Fermentation
Reduces pyruvate
or a derivative
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
3b
• Tricarboxylic Acid (TCA) Cycle– Completes
oxidation of glucose
• Produces– 2 CO2
– 2 ATP– 6 NADH– 2 FADH2
– Precursor metabolites
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~~ ~ + Pi
H2O
1
2
8
7
6
5
3
4
A redox reaction
generates NADH.
Water is added.
A redox reaction
generates FADH2-
The energy released
during CoA removal is
harvested to produce ATP.ADPATP
CoA
A redox reaction
generates NADH,
CO2 is removed,
and coenzyme A
is added.
A redox reaction
generates NADH
and CO2 is
removed.
A chemical
rearrangement occurs.
The acetyl group is transferred
to oxaloacetate to start a new
round of the cycle.
Transition step:
CO2 is removed, a redox reaction generates
NADH, and coenzyme A is added.
NADH + H+
Acetyl-CoA
CoA
CoA
NADH + H+ Oxaloacetate
NAD+
Malate
Fumarate
FADH2
FAD Succinate Succinyl-CoA
CoA
CoA
CO2
NAD+
-ketoglutarate
Isocitrate
Citrate
CoA
NAD+
CO2
Pyruvate
NAD+
CO2
NADH + H+
NADH + H+
+
+
x 2
21
5
4
~ ~
~ ~
~ ~
GLUCOSE
Respiration
Uses the electron transport
chain to convert reducing
power to proton motive force
ATP
by oxidative
phosphorylation
Yields
ATP
by substrate-level
phosphorylation
Reducing
power
Yields
CO2
CO2
Pyruvate Pyruvate
3a Transition step
YieldsReducing
power
Acetyl-
CoA
Acetyl-
CoA
Biosynthesis
YieldsReducing
power
Pentose phosphate
pathway
Starts the oxidation of glucose
Glycolysis
Oxidizes glucose to pyruvate
YieldsReducing
power
ATP
by substrate-level
phosphorylation
Acids, alcohols, and gases
CO2CO2
Fermentation
Reduces pyruvate
or a derivative
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
3b
ETC located in MitochondriaCopyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
21
5
4
Pentose phosphate
pathway
Starts the oxidation of glucose
GLUCOSE
Glycolysis
Oxidizes glucose to pyruvate
YieldsReducing
power
ATP
by substrate-level
phosphorylation
Fermentation
Reduces pyruvate
or a derivative
Acids, alcohols, and gasesPyruvatePyruvate
Reducing
power
Yields
Biosynthesis
Transition step3a
YieldsReducing
power
CO2CO2
Acetyl-
CoA
Acetyl-
CoA
CO2
CO2
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
Yields
ATP
by substrate-level
phosphorylation
Reducing
power
Respiration
Uses the electron transport
chain to convert reducing
power to proton motive force
Yields
ATP
by oxidative
phosphorylation
x 2
3b
+PPP ~ ~
PPP
+
4 4 2 H+ 10 H+
+ 3 Pi
H2O
O22
e–
Eukaryotic cell
Inner
mitochondrial
membrane
Electron Transport Chain
Complex I
Ubiquinone
Complex III
NADHComplex II
3 ADP
3 ATP
Mitochondrial
matrix
Intermembrane
space
Use of Proton Motive Force
ATP synthase
(ATP synthesis)Complex IV
Proton motive force
is used to drive:
Terminal
electron acceptor
Cytochrome c
NAD+
H+H+
H+
H+ 1/2
Path of
electrons
2
The Electron Transport Chain—
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ve forcerive:
+
H+ H+
Terminal
electron acceptor
–
O2
Prokaryotic cell
Cytoplasmic
membrane
Electron Transport Chain
NADH dehydrogenase
H+ (0 or 4)
Uses of Proton Motive Force
Rotation of a flagella
Outside of
cytoplasmic
membrane
Transported
molecule
NADH
Cytoplasm
3 ADP
3 ATP
+ 3 Pi
NAD+
H+
Succinate
dehydrogenase
Path of
electrons
Ubiquinone
Active transport
(one mechanism)
ATP synthase
(ATP synthesis)Ubiquinol oxidase
H+ (2 or 4) 10 H+
H2O
2 H+
Proton motive force
is used to drive:
2 e–
1/2
The Electron Transport Chain• Electron transport chain is membrane-embedded
electron carriers– Pass electrons sequentially, eject protons in process
– Prokaryotes: in cytoplasmic membrane
– Eukaryotes: in inner mitochondrial membrane
– Energy gradually released
– Release coupled to ejection
of protons
– Creates electrochemicalgradient
– Used to synthesize ATP
– Prokaryotes can also powertransporters, flagella
2
1/2
e–
O22 H+
Energy released is
used to generate a
proton motive force.
Electrons from the
energy source
High energy
Low energy Electrons donated
to the terminal
electron acceptor.
H2O
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The Electron Transport Chain
• ATP Yield of Aerobic Respiration in Prokaryotes
– Substrate-level phosphorylation:
• 2 ATP (from glycolysis; net gain)
• 2 ATP (from the TCA cycle)
• 4 ATP (total)
– Oxidative phosphorylation:
• 6 ATP (from reducing power gained in glycolysis)
• 6 ATP (from reducing power gained in transition step)
• 22 ATP (from reducing power gained in TCA cycle)
• 34 (total)
– Total ATP gain (theoretical maximum) = 38
ATP Yield of Aerobic Respiration in ProkaryotesCopyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
~ ~
~ ~
~ ~
~ ~
~ ~
~ ~
~ ~
~ ~
Substrate-level
phosphorylation2 ATP
4 ATP
18 ATP
6 ATPOxidative
phosphorylation
Oxidative
phosphorylation
Oxidative
phosphorylation
2 NADH
6 NADH
2 FADH2
2 ATP
6 ATP
Substrate-level
phosphorylation
Oxidative
phosphorylation
2 NADH
2 ATP
net gain = 0
2 ATP
GLUCOSE
Glycolysis
Oxidizes glucose to pyruvate
x 2 CO2
CO2
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
21
5
4
Pentose phosphate
pathway
Starts the oxidation of glucose
GLUCOSE
Glycolysis
Oxidizes glucose to pyruvate
Yields
Reducing
power
ATP
by substrate-level
phosphorylation
Fermentation
Reduces pyruvate
or a derivative
Acids, alcohols, and gasesPyruvatePyruvate
Reducing
power
Yields
Biosynthesis
Transition step3a
YieldReducing
power
CO2CO2
Acetyl-
CoAAcetyl-
CoA
CO2
CO2
TCA cycle
Incorporates an acetyl
group and releases CO2
(TCA cycles twice)
Yields
ATP
by substrate-level
phosphorylation
Reducing
power
Respiration
Uses the electron transport
chain to convert reducing
power to proton motive force
Yields
ATP
by oxidative
phosphorylation
x 2
3b
Pyruvate Pyruvate
Acetyl-
CoA
Acetyl-
CoA
Anaerobic environments
• Prokaryotes unique in ability to use reduced inorganic compounds as sources of energy
– E.g., hydrogen sulfide (H2S), ammonia (NH3)
• Produced by anaerobic respiration from inorganic molecules (sulfate, nitrate) serving as terminal electron acceptors
• Important example of nutrient cycling
• Four general groups
The Electron Transport Chain
– Anaerobic respiration in E. coli
• Harvests less energy than aerobic respiration– Lower electron affinities of terminal electron acceptors
• Some components different
• Can synthesize terminal oxidoreductase that uses nitrate as terminal electron acceptor – Produces nitrite
– E. coli converts to less toxic ammonia
– Sulfate-reducers use sulfate (SO42–) as terminal
electron acceptor
• Produce hydrogen sulfide as end product
Fermentation• Fermentation end products varied; helpful in
identification, commercially useful– Ethanol
– Butyric acid
– Propionic acid
• 2,3-Butanediol
• Mixed acids
H2
Fermentation
pathway
Microorganisms
Lactic acid
Streptococcus
Lactobacillus
Ethanol Butyric acid Propionic acid Mixed acids 2,3-Butanediol
EnterobacterE. coliPropionibacteriumSaccharomyces
End products Lactic acid Ethanol
CO2
Butyric acid
Butanol
Acetone
IsopropanolCO2
CO2
Propionic acid
Acetic acid
Acetic acid
Lactic acid
Succinic acid
EthanolCO2
H2
CO2H2
Clostridium
Pyruvate
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(yogurt, dairy, pickle), b (wine, beer), (acetone): © Brian Moeskau/McGraw- Hill; (cheese): © Photodisc/McGraw-Hill; (Voges-Proskauer Test), (Methyl-Red Test): © The McGraw-Hill Companies, Inc./Auburn University Photographic Services
Aerobic Cellular Respiration (ACR) in Bacteria summary
Glycolysis Glucose to pyruvateProduces: 2 NADH, 2ATP’s and 6 precursor metabolites
Acetyl Co A or Transitional stepProduces: 2 NADH, 2 CO2 and 1 precursor metabolite
TCA or Krebs cycleProduces: 6 NADH, 2 FADH, 2 ATP’s, 4 CO2, and 2 precursor metabolites
Electron Transport ChainProduces: 38 ATP’s
Oxygen requiredExamples of Bacteria: E. Coil and Staph species
Summary
• Aerobic Cellular Respiration (ACR)
– Or Embden-Meyerhoff Pathway in bacteria
• Pentose Phosphate Pathway
• Entener-Doudoroff Pathway
Pentose Phosphate Pathway Summary
• Glucose to pyruvate
– Produces:
• 5 carbon sugar to intermediate products
• Nucleic acids, nucleotides and amino acids
• 1 ATP
• 2 NADPH (Calvin cycle) Photosynthetic bacteria
• Products go ACR, Anaerobic respiration and Fermentation
• Example of bacteria are E. Coli and Bacillus Sp.
Entner-Doudoroff Pathway summary
• Glucose – pyruvate
• Produces:– 1 ATP
– 1 NADH
– 1 NADPH (Calvin cycle)
– Products can go to ACR, Anaerobic respiration or Fermentation
– Can process Glucose independent• EX Pseudomonas Sp, E. Coli, Bacteroides Sp.
• Only Gram negative can use