micrb 265 lec 7
What is fermentation mainly used for?
Fermentation is mainly used to reoxidize NADH back to NAD+ when cells do not use or cannot use an electron transport chain.
How is ATP made during fermentation?
ATP is made only by glycolysis through substrate-level phosphorylation.
What is the final electron acceptor in fermentation?
The final electron acceptor in fermentation is an organic molecule, usually derived from pyruvate.
Why is fermentation necessary if there is no ETC?
Without an ETC, NADH would build up and NAD+ would run out, so glycolysis would stop.
What is the main purpose of converting pyruvate to lactate?
It regenerates NAD+ so glycolysis can continue.
What is the net ATP yield of lactic acid fermentation per glucose?
2 ATP.
Why can organisms still grow by fermentation even though it makes less ATP than respiration?
If sugar is abundant, repeated glycolysis can still provide enough ATP for growth.
What is alcoholic fermentation used for biologically and industrially?
It produces ethanol and CO2 and is important in yeast, alcoholic beverages, and bread making.
What does homolactic fermentation produce?
Mostly lactate.
What does heterolactic fermentation produce?
A mixture including lactate, ethanol, and CO2.
What kind of metabolism can E. coli use when oxygen is present?
Aerobic respiration.
What kind of metabolism can E. coli use when oxygen is absent but nitrate is present?
Anaerobic respiration.
What kind of metabolism can E. coli use when both oxygen and nitrate are absent?
Fermentation.
Why is oxygen the best final electron acceptor?
Reducing O2 to H2O gives the greatest Gibbs free energy release.
What is the main difference between aerobic and anaerobic respiration?
The terminal electron acceptor is different; aerobic uses oxygen and anaerobic uses another inorganic acceptor such as nitrate.
Does anaerobic respiration mean oxygen is always toxic?
No. It means the organism is using a terminal electron acceptor other than oxygen, not necessarily that oxygen is toxic.
Can fermentation use an ETC?
No. Fermentation does not use an electron transport chain.
Can fermentation generate proton motive force?
No. Fermentation does not make PMF by an ETC.
What is chemolithotrophy?
It is metabolism where inorganic molecules are used as electron donors.
Why can chemolithotrophs not do fermentation?
They rely on inorganic electron donors and generally use electron transport rather than organic fermentation pathways.
What are examples of inorganic electron donors used by chemolithotrophs?
H2, H2S, Fe2+, NH4+, and NO2- depending on the organism.
What are electrically conductive pili used for?
They transfer electrons outside the cell to extracellular electron acceptors such as iron-containing minerals.
Why does Geobacter need electrically conductive pili?
Its final electron acceptor can be outside the cell and insoluble, so electrons must be transferred outward.
What is phototrophy?
Phototrophy is the use of light to make chemical energy such as ATP and often reducing power.
What is oxygenic photosynthesis?
It uses light for energy, uses water as the electron donor, and produces oxygen.
What organisms commonly do oxygenic photosynthesis?
Cyanobacteria and eukaryotic phototrophs.
What is anoxygenic photosynthesis?
It uses light for energy but does not use water as the electron donor and does not produce oxygen.
What electron donor is commonly used in anoxygenic photosynthesis?
Hydrogen sulfide.
What is the difference between oxygenic and anoxygenic photosynthesis?
Oxygenic uses H2O and makes O2; anoxygenic usually uses H2S or another donor and does not make O2.
What are non-photosynthetic phototrophs?
They use light to generate energy without a full photosynthetic ETC.
How do some archaea generate PMF without a photosynthetic ETC?
They use bacteriorhodopsin, a light-driven proton pump.
What is bacteriorhodopsin?
A membrane protein that uses light energy to pump protons across the membrane.
Does bacteriorhodopsin require an electron transport chain?
No. It directly generates PMF without an ETC.
What molecule inside bacteriorhodopsin absorbs light?
Retinal.
What happens to retinal when it absorbs light?
It isomerizes, changing shape and triggering protein conformational changes.
How does bacteriorhodopsin create proton motive force?
Light causes retinal to change shape, which drives proton transfer through the protein and pumps H+ out of the cell.
What is the net result of one photon absorbed by bacteriorhodopsin?
One proton is pumped out of the cell.
What is the major light-capturing molecule in photosynthesis discussed here?
Bacteriochlorophyll.
How is bacteriochlorophyll structurally similar to heme?
It is similar in ring structure but uses Mg instead of Fe.
Why are accessory pigments important?
They absorb wavelengths of light that chlorophylls do not absorb well and transfer that energy to chlorophyll.
What are examples of accessory pigments?
Carotenoids and phycobiliproteins.
What happens in the purple bacterial photosynthetic ETC?
Light excites electrons, electrons move through carriers, protons are moved across the membrane, and ATP is made from PMF.
Why do electrons return to the reaction center in purple bacteria?
This is cyclic electron flow, which helps generate PMF and ATP.
What is anabolism?
Anabolism is the building of macromolecules from smaller precursor molecules.
What does anabolism require?
Carbon source, inorganic nutrients, vitamins or micronutrients, energy, and reducing power.
What electron carrier is most associated with anabolism?
NADPH.
Why is anabolism energy-intensive?
Building large molecules from smaller ones requires energy input and reducing power.
Why is there a lot of turnover in cells?
Cells constantly replace damaged molecules and remodel components for changing environments.
What does heterotroph mean in terms of carbon source?
It uses organic carbon.
What does autotroph mean in terms of carbon source?
It uses inorganic carbon, usually CO2.
What does phototroph mean in terms of energy source?
It uses light.
What does chemotroph mean in terms of energy source?
It uses chemical compounds.
What does organotroph mean in terms of electron source?
It uses organic electron donors.
What does lithotroph mean in terms of electron source?
It uses inorganic electron donors.
What is carbon fixation?
Carbon fixation is the incorporation of CO2 into organic molecules.
What are two major CO2 fixation pathways emphasized here?
The Calvin cycle and the reductive TCA cycle.
What is another name for the Calvin cycle?
The reductive pentose phosphate pathway.
What is the main purpose of the Calvin cycle?
To fix CO2 into organic carbon that can be used to build cellular molecules.
What molecule accepts CO2 in the Calvin cycle?
Ribulose-1,5-bisphosphate.
What enzyme adds CO2 to ribulose-1,5-bisphosphate?
RuBisCO.
What is the first stable product formed after CO2 fixation by RuBisCO?
3-phosphoglycerate.
What energy and reducing power are used in the Calvin cycle?
ATP and NADPH.
What useful product comes out of the Calvin cycle for biosynthesis?
Glyceraldehyde-3-phosphate.
Why must ribulose-1,5-bisphosphate be regenerated?
It is the CO2 acceptor, so the cycle must regenerate it to continue fixing carbon.
Where does the Calvin cycle occur in some bacteria?
In carboxysomes.
What is the role of carbonic anhydrase in carboxysomes?
It helps generate CO2 for RuBisCO.
What is assimilation?
Assimilation is incorporation of inorganic molecules into organic molecules.
Why is nitrogen assimilation important?
Nitrogen is needed for proteins, nucleic acids, coenzymes, and many other cell components.
What are major environmental sources of nitrogen for microbes?
Ammonia, nitrate, and nitrogen gas.
Why is ammonia the easiest nitrogen source to assimilate?
It is already relatively reduced, so less energy is needed to incorporate it.
What does glutamate dehydrogenase do?
It incorporates ammonia into alpha-ketoglutarate to make glutamate.
What does glutamine synthase do?
It adds ammonia to glutamate to make glutamine, using energy.
What is the role of transaminases?
They transfer amino groups between molecules.
What is nitrogen fixation?
Nitrogen fixation is the conversion of atmospheric N2 into ammonia.
What enzyme carries out nitrogen fixation?
Nitrogenase.
Who has nitrogenase?
Only certain bacteria and archaea.
Why is nitrogen fixation energetically expensive?
Breaking the N≡N bond is very difficult and requires a lot of ATP and electrons.
About how much ATP is required for nitrogen fixation in the reaction shown?
16 ATP per N2 fixed.
Why is nitrogenase sensitive to oxygen?
Oxygen damages or inactivates the enzyme.
How can bacteria protect nitrogenase from oxygen?
By using a thick glycocalyx or forming heterocysts.
What is a heterocyst?
A thick-walled specialized cell that protects nitrogenase and does not perform aerobic respiration.
What is phosphate assimilation like compared with nitrogen fixation?
It is generally much easier because phosphate is common and readily incorporated.
Why is sulfur assimilation important?
Sulfur is needed for certain amino acids and cofactors.
What four major classes of biomolecules must bacteria build?
Proteins, nucleic acids, lipids, and carbohydrates.
How can bacteria make glucose when they are not growing on sugars?
By gluconeogenesis.
What pathway makes ribose-5-phosphate for nucleotide synthesis?
The pentose phosphate pathway.
Where do most amino acid carbon skeletons come from?
Glycolysis and the TCA cycle.
Which amino acid classically comes from the pentose phosphate pathway rather than directly from glycolysis or TCA cycle?
Histidine.