Download Microbial metabolism

Energy is the capacity to do work
• Potential energy:
stored energy
• Kinetic energy: energy
of motion
Metabolism
• Metabolism is the
sum total of ALL
chemical reactions
within a cell
– Catabolic
– Anabolic /
Biosynthetic
A metabolic pathway is a series
of sequential, interconnected,
enzyme-catalyzed biochemical
reactions by which a living cell
converts a starting product
(substrate) into an end product.
Metabolism
• Catabolism: “destructive
metabolism”
– Breakdown of substrate:
end product is less complex
than the starting product
– Catabolic pathways
generate energy and
precursor metabolites
– Catabolic pathways are
linked to either respiration
or fermentation
• Anabolism = biosynthesis:
“constructive metabolism”
– Synthesis of new
biomolecules: end product
is more complex than the
starting product
– Anabolic pathways use
energy and precursor
metabolites to synthesize
subunits of macromolecules
Adenosine triphosphate: ATP
• The main energy currency of the cell
• Ribose + adenine + 3 phosphate groups
• Phosphate bonds = high energy bonds: energy is used to form
the bonds and released when the bonds are broken
• Addition of a phosphate group to ADP to generate ATP is
accomplished during metabolism via either substrate level
phosphorylation or oxidative phosphorylation
And microorganisms too!
ATP is made in catabolic
reactions and used in anabolic
reactions
Ways cells make ATP
• Substrate level phosphorylation – used by
all organisms; for fermenters, this is the
only option
• Oxidative phosphorylation – aerobic and
anaerobic respiration
• Photophosphorylation – photosynthesizers
only
Products of Anabolic Metabolism
(Biosynthesis)
• Fatty acids
• Glycerol
– Fatty acids + glycerol
= lipids
(where do you find lipid
in a bacterial cell?)
• Amino acids
– Building blocks for
proteins
• Nucleotides
– Building blocks for
DNA, RNA
The critical components of
metabolic pathways are:
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•
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Enzymes
Adenosine triphosphate (ATP)
Chemical energy source
Terminal electron acceptor
Electron carriers
Oxidation-Reduction Rections
(redox reactions)
• Same principal in biological systems as
inorganic systems:
– Substance that gives up (loses) electron(s) =
oxidized
– Substance that gains electron(s) = reduced
• When electrons move, protons (H+) follow
Oxidation/reduction reactions
Biological Oxidation
Enzymes
• All enzymes are proteins
• Active site = binding site: highly substrate-specific
• Binding of the substrate induces a conformational change
in the enzyme
– This forms the temporary enzyme-substrate complex
– Formation of this complex changes the position of bonds on the
substrate, destabilizing them and thereby lowering the activation
energy of the reaction
• When the changed substrate is released, the enzyme returns
to the native conformation and is ready to bind another
substrate – the enzyme is chemically unchanged by the
reaction.
Enzymes
• Active site: site that binds the substrate
• Allosteric sites: binding site at a location separate from the active
site
– binding to the allosteric site can induce a conformational change in the active
site
• Allosteric regulation: binding of a molecule to the allosteric site to
either allow or block binding of the substrate
– This allows the cell to regulate pathways based on the quantity of the end
product available, so they only make what they need
• Coenzymes: organic cofactors that assist in the transfer of
molecules or electrons
• Environmental factors that influence enzymatic function/activity:
–
temperature, pH, salt concentration
Factors that influence an enzyme: Temperature
• What happens as
temperature increases?
• What is the optimum
temperature?
Factors that influence an enzyme: pH
• What pH do most
enzymes function
optimally?
Enzymes bind substrate and generate a
product
Some enzymes require a cofactor to bind
substrate
Coenzymes carry electrons
Enzyme inhibitors
• Inhibit the binding of the substrate to the
active site
– Competitive inhibition
– Non-Competitive Inhibition
Competitive Inhibition
Non-competitive Inhibition
Electron carriers
• Special types of coenzymes that transfer electrons (and protons)
between molecules
• NAD+/NADH: nicotinamide adenine dinucleotide
• NADP+/NADPH: nicotinamide adenine dinucleotide phosphate
• FAD/FADH2: flavin adenine dinucleotide
Electron Transport Chain &
Proton Motive Force
• The ETC is an association of
electron carriers located within
a cell membrane.
• As electrons pass between
electron carriers in the ETC
they move from higher to lower
affinity carriers, releasing
energy in the process.
• Movement of electrons is paired
with the movement of protons
across the membrane to
generate an electrical gradient
• This electrical gradient = the
proton motive force.
• It consists of a positive charge
at the outside surface of the
membrane and a negative
charge at the inner surface
• The electrical potential energy
of the proton motive force can
be converted to chemical
energy = production of ATP
The Electron Transport Chain and the Proton
Motive Force: Prokaryotic vs eukaryotic cells
• Prokaryotic cells:
– Electron transport chain is located
in the cytoplasmic membrane
– Electrical gradient of the proton
motive force is across the cell
membrane (inside vs outside cell)
– Proton motive force can be used to
generate ATP, or to directly power
flagella or transport molecules
against the concentration gradient
(active transport)
• These latter 2 processes can
also be fueled by ATP
generated via the proton
motive force
• Eukaryotic cells:
– ETC is located in the inner
mitochondrial membrane
– Electrical gradient of proton
motive force is between the matrix
and the region between the inner
and outer membranes
– Only function of the proton motive
force is generation of ATP
Central metabolic pathways:
catabolic pathways
• Glycolysis: primary
pathway for most
organisms
• Substrate = glucose
• End product =
pyruvate
• The other pathways
are the pentose
phosphate pathway
and the tricarboxylic
acid pathway – these
are linked by a
“transition step”
Types of Bacterial Metabolism
• Fermentation
• Respiration
– Aerobic Respiration
– Anaerobic Respiration
• Photosynthesis
Comparison of three types of
metabolism
make a new slide to replace this = a table summarizing what I want them to know = name of the process, pathways used, terminal
electron accentor and “energy yield” – substrate level + phosphorylation and oxidative phosphorylation – need a slide summarizing the
difference between these two – also a note on this slide saying I just want them to know that for both SLP and OP the energy yielod is
greatest for aerobic respiration, lowest for fermentation and intermediate for anaerobic respiration; and also that in fermentation there is
ONLY substrate level phosphorylation, not oxidative phosphorylation
Cellular Respiration
• The series of steps by which cells produce
energy through oxidation of organic
substances
• At a cellular level, this can be linked to
catabolism – electrons extracted in the
metabolism of glucose (or other substrates)
are transferred to the electron transport
chain to generate ATP via oxidative
phosphorylation
Respiration
• Aerobic respiration:
– Uses ETC
– Oxygen is the terminal
electron acceptor
– ATP is generated by
both substrate level and
oxidative
phosphorylation
– Higher energy yield than
anaerobic respiration or
fermentation
• Anaerobic respiration:
– Uses ETC
– Terminal electron
acceptor = various
molecules other than
O2, ie nitrate, nitrite,
sulfate
– ATP is generated by
both substrate level and
oxidative
phosphorylation
Aerobic Respiration
• The COMPLETE breakdown of glucose to
CO2 and H2O with an inorganic compound
serving as the final electron acceptor
Remember the pathways in
aerobic respiration are…
• Glycolysis
– Some use Pentose Phosphate Pathway instead
• TCA cycle
• Electron transport chain
Fermentation
• The incomplete breakdown of glucose with an
organic compound serving as the final electron
acceptor
• Generates less energy than aerobic or anerobic
respiration
• Only central metabolic pathway operating is
glycolysis
• Question: if fermentation is so inefficient, why do
cells use this pathway?
Fermentation products can vary
Fermentation
Saccharomyces produces ethanol
Lactic Acid Bacteria
Precursor metabolites
• There are many important precursor metabolites
formed during the central metabolic pathways
which are used in biosynthetic (anabolic)
pathways.
– Fructose 6-phosphate
• Generated during glycolysis
• Used in the synthesis of peptidoglycan
– Glucose 6-phosphate
• Generated during glycolysis
• Used in the synthesis of lipopolysaccharide
Carbon fixation
• Organism that are able to use CO2 as a
carbon source =
• Pathways utilized include Calvin Cycle and
reverse TCA cycle
• Some bacteria are able to break down CO2
to yield carbon
Chemoorganotrophs depend on
Photosynthetic organisms
What is made as a result of the
TCA cycle?
• ATP
• Reducing power
• Precursor metabolites made from alphaketoglutarate and oxaloacetate
Electron Transport Chain
• Found in the cytoplasmic membrane
• Contains electron carriers
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–
–
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Flavoproteins
Iron-sulfur proteins
Quinones
Cytochromes
Model for energy release in ETC
ETC in eukaryotes
ETC in prokaryotes
ATP yield from aerobic respiration
Remember we are focusing on
catabolic reactions
• Generate ATP for later use by cell
• Generate precursors for other pathways
• Need to re-oxidize coenzymes for continual
use