Lecture 12 - metabolism, energetics, catabolic pathways Flashcards
Catabolism
Breakdown of complex organic molecules
Anabolism
Biosynthetic reactions to build cell mass
How does catabolism support anabolism?
- supply energy to drive anabolic processes
- provide precursor molecules for biosynthesis
Organotrophy
Organic compounds are electron donors
Types of organtrophy
- fermentation
- organic respiration
Lithotrophy
Inorganic compounds donate electrons
Types of litotrophy
- lithotrophy/chemoautotrophy
- methanogenesis
Is organotrophy aerobic or anaerobic?
- fermentation is anaerobic
- respiration can be aerobic or anaerobic
Types of energy storage molecules
- ATP
- NAD+ (carries twice the energy of ATP)
How are ATP and NAD used as energy sources?
- ATP –> ADP via removal of phosphate group releases energy
- NADH –> NAD+ (oxidation) releases lots of energy
Fermentation
Partial breakdown of organic compounds without net e- transfer to an inorganic terminal electron acceptor
Respiration
Complete breakdown of organic molecules with electron transfer to a terminal electron acceptor such as O2
Examples of things that bacteria can break down that we can’t
Fats, cellulose, acidic sugars, lignin, man-made toxic chemicals
Why does NAD+ need to be regenerated?
Used as an electron and proton acceptor for later transfer
How is NAD+ regenerated?
Reduction of pyruvate or other compounds to form partially oxidized products
How is ATP generated in most fermentation pathways?
Substrate-level phosphorylation; less efficient energy production
What is the TCA cycle used for?
More efficient energy production
- carbon is sent through the cycle to produce NADH
- carbon is oxidized to CO2 and its electrons are transferred to NADH
How is glucose catabolism connected to the TCA cycle
Decarboxylation of pyruvate to acetyl-CoA
Where does the TCA cycle occur in prokaryotes
Cytoplasm
What is the electron transport system (ETS)?
Series of membrane-localized electron carriers that transfer electrons from a reduced electron donor to an oxidized electron acceptor during aerobic respiration
How does the electron transport system power the production of ATP?
Electron transport powers pumping of protons into the cytoplasm. These protons are later pumped back in through ATP synthase
Examples of terminal electron acceptors
O2 and oxidized minerals (ex: Fe3+, NO3-)
What values of gibbs free energy indicate a favorable, spontaneous reaction
Negative
Reduction potential (E)
Measure of the tendency of a molecule to accept electrons
- negative values are poor electron acceptors (repel e-); good electron donors
- positive values are good electron acceptors (attract e-)
General trend of electron transfer in terms of reduction potential
Electrons flow from more negative to more positive reduction potentials
How to tell if a molecule is highly oxidized
Lots of oxygen atoms
How to tell if a molecule is highly reduced
Lots of H+
What is the quinone pool?
Bacterial ETS that shuttles electrons between membrane-bound complexes in aerobic NADH oxidation
What kinds of organisms can use anaerobic respiration?
Unique to prokaryotes that can use alternative electron donors and acceptors
Denitrification
Using nitrate (NO3-) as an electron acceptor
- nitrate is successively reduced to nitrogen gas by multiple bacterial species
How can sulfate be used as an electron acceptor?
Sulfate (SO4 2-) is successively reduced to hydrogen sulfide (H2S)
What happens in environments where O2 is depleted?
Alternate, less efficient, electron acceptors are used as the optimal materials are used up
Is sulfate a good electron acceptor?
No, only used when there are no better options
What kinds of electron donors and acceptors does respiration use?
- Organic electron donors
- Inorganic or organic electron acceptors
What kinds of electron donors and acceptors does lithotrophy use?
- Inorganic electron donors
- Inorganic or organic acceptors
Phototrophy
Involves light capture by chlorophyll, usually coupled to splitting of H2S or H2O or organic molecules
Nitrification
- aka nitrogen oxidation
- takes ammonium and gradually oxidizes it to HNO3 to fix it into the soil
Sulfur and metal oxidation example
H2S oxidized to H2SO4
What are the components that drive proton motive force
- Electrical potential: from separation of charge between cytoplasm and extracellular solution
- pH difference: ratio of external to internal chemical concentration of H+
Proton motive force
Electrochemical gradient of protons generated by transfer of H+ through a proton pump
What is the proton motive force used for?
- ATP synthesis
- rotation of flagella
- uptake of nutrients and efflux of toxic compounds and antibiotics (secondary active transport)
