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MICRO section 3
| Question | Answer |
|---|---|
| metabolism | all the chemical reactions in a cell |
| catabolism | breaks down molecules and releases energy |
| anabolism | builds complex molecules and requires energy, aka biosynthesis |
| catabolism/anabolism connection | catabolism supplies ATP to reduce power for smaller molecules that anabolism uses to build biomolecules |
| stages of aerobic respiration | glycolysis, TCA cycle, ETC |
| aerobic respiration purpose | to completely oxidize glucose, transfer its energy to electron carriers, and generate ATP |
| respiration energy carriers | ATP, NADH, FADH2 |
| ADP | lower energy form of ATP |
| energized/reduced NAD | NADH |
| non-energized/oxidized NAD | NAD+, accepts two electrons and a proton to become NADH |
| energized/reduced FAD | FADH2 |
| non-energized/oxidized FAD | FAD, accepts two electrons and two protons |
| NADPH use | providing reduced power (high-energy electrons) for biosynthesis |
| oxidation | loss of electrons, doesn't need oxygen |
| reduction | gain of electrons |
| NADH to NAD+ | NADH oxidized and loses electrons |
| NAD+ to NADH | NAD+ is reduced and gains electrons |
| glycolysis | breaks one glucose into two pyruvate molecules, aka EMP pathway |
| glycolysis location | cytoplasm, doesn't need oxygen |
| glycolysis reactions | 10 reactions divided into 2 stages |
| glycolysis stages | glucose activation (energy investment) and energy-yielding stage |
| glucose activation | glucose is phosphorylated using two ATP and converted into fructose-1, 6-biophosphate |
| rate-limiting enzyme of glycolysis | PFK, phosphofructokinase |
| PFK reaction | fructose-6-phosphate to fructose-1,6-biphosphate using ATP |
| aldolase | enzyme that splits fructose-1,6-biphosphate, produces DHAP and G3P |
| energy-yielding stage of glycolysis | G3P is converted into pyruvate, making 4 ATP and 2 NADH per glucose |
| glycolysis inputs | glucose, ADP+Pi, NAD+ |
| glycolysis outputs | 2 pyruvate, 2 net ATP, 2 NADH (2 ATP used) |
| substrate-level phosphorylation | ATP production by directly transferring a phosphate group from a phosphorylated substrate to ADP, occurs during glycolysis and TCA |
| pyruvate during aerobic respiration | converted into acetyl-CoA before entering TCA cycle |
| glucose breakdown pathways | EMP, ED, PPP, EMP most common |
| entner-doudoroff pathway | alternative pathway that breaks glucose into pyruvate and produces energy carriers |
| ED pathway classifications | in the cytoplasm of certain bacteria and arches, ex. pseudomonas and e.coli |
| ED pathway in E.coli | E.coli can catabolize gluconate from intestinal mucus |
| ED pathway products | per glucose: 2 pyruvate, 1 net ATP, 1 NADH, 1 NADPPH |
| pentose phosphate pathway | alternative pathway that produces NADPH and sugar phosphates needed for biosynthesis |
| PPP products | NADPH, ribose-5-phosphate, other sugar phosphate intermediates |
| PPP NADPH use | reducing power for biosynthesis |
| ribose-5-phosphate use | makes nucleotides for DNA and RNA |
| ribulose-5-phosphate | pentose metabolism and the production of precursors involved in carbon fixation and biosynthesis |
| intermediates produced by PPP | glyceraldehyde-3-phosphate, erythrose-4-phosphate, sedoheptulose-7-phosphate |
| PPP main purpose | biosynthetic precursors |
| ED main purpose | alternative glucose breakdown |
| EMP | glucose breakdown |
| fermentation | glucose catabolism without an ETC where electrons from NADH are transferred to organic molecules to regenerate NAD+ |
| fermentation main purpose | regenerate NAD+ so glycolysis can continue, doesn't require oxygen or ETC |
| homolactate fermentation | pyruvate is reduced to lactate while NADH is oxidized to NAD+, often performed by lactobacilli |
| ethanolic fermentation | pyruvate is converted into ethanol and CO2 while NAD+ is regenerated, often performed by yeast |
| pasteur effect | the decrease in fermentation and glucose consumption when oxygen becomes available |
| yeast metabolism with no oxygen | yeast performs ethanolic fermentation and produces ethanol and CO2 |
| yeast metabolism with oxygen | yeast can perform complete aerobic respiration and produces CO2 and H2O |
| how does PFK regulate the Pasteur effect | ATP and citrate inhibit PFK, ADP stimulates PFK, oxygen allows more ATP production and slows glycolysis. without oxygen, ADP increases and glycolysis speeds up |
| allosteric regulation | regulation of an enzyme by molecules binding somewhere other than its active site |
| TCA cycle | tricarboxylic acid cycle, aka Krebs or citric acid cycle |
| TCA cycle location | prokaryotes: cytoplasm, eukaryotes: mitochondria |
| step before TCA cycle | pyruvate is converted into acetyl-coA and releases CO2 and produces NADH |
| products of one TCA cycle | 3 NADH, 1 FADH2, 1 ATP, 2 CO2 |
| products TCA cycle per glucose | 6 NADH, 2 FADH2, 2 ATP, 4 CO2 |
| TCA products per pyruvate oxidized | 4 NADH, 1 FADH2, 1 ATP, 3 CO2 |
| decarboxylation | removal of a carboxyl group that releases CO2 |
| energy-carrying product of TCA | NADH |
| NADH and FADH2 after TCA | donate electrons to the ETC to help produce ATP |
| oxidative phosphorylation | ATP synthesis powered by the proton gradient generated by the ETC |
| ETC | series of membrane-associated proteins and carriers that transfer electrons from donors to terminal electron acceptors |
| ETC purpose | generate a potion motive force (PMF) used to synthesize ATP |
| components of ETC | electron donor, initial substrate oxidoreductase, mobile electron carrier, terminal oxidase, terminal electron acceptor |
| initial substrate oxidoreductase purpose | accepts electrons from an electron donor and transfers them into the ETC |
| initial oxidoreductase example | NADH dehydrogenase |
| mobile electron carrier purpose | transfers electrons between ETC protein complexes. Ex: quinone |
| quinone reduction | accepts two electrons and two protons and makes QH2 |
| terminal oxidase purpose | transfers electrons to the terminal electron acceptor |
| terminal electron acceptor in aerobic respiration | O2 is reduced to water |
| why does ETC need to be in a membrane | to separate protons and establish an electrochemical gradient |
| ETC location in bacteria | cytoplasmic membrane |
| standard reduction potential (E°′) | a measure of a substances tendency to accept electrons and become reduced |
| positive E°′ | substance is a good electron acceptor and is easily reduced |
| negative E°′ | substance is a good electron donor and is easily oxidized |
| what direction do electrons flow in ETC | from more negative E°′ to more positive E°′ |
| ETC pecking order | the arrangement of electron carriers according to their reduction potentials |
| why is oxygen a strong terminal electron acceptor | it has a highly positive reduction potential |
| how does difference in E°′ affect energy production | a larger difference between electron donor and acceptor releases more energy |
| proton motive force, PMF, Δp | stored electrochemical energy produced by differences in proton concentration and electrical charge across a membrane |
| components of PMF | Δψ: electrical potential difference, ΔpH: proton concentration difference |
| how does ETC generate PMF | electron transfer releases energy used to move H+ across the membrane |
| proton location during bacterial respiration | outside the cytoplasmic membrane |
| F0F1 ATP synthase | a membrane-associated enzyme complex that uses proton movement to synthesize ATP |
| F0 component | membrane-embedded proton channel and rotary motor |
| F1 component | catalytic portion that produces ATP from ADP and Pi |
| F0 and F1 location | F0: embedded in membrane, F1 faces the cytoplasm |
| energy transformation during ATP synthesis | electrochemical potential energy to mechanical rotation to chemical energy in ATP |
| ATP synthase in reverse | hydrolyzes ATP to pump protons across the membrane and maintain PMF |
| PMF power besides ATP synthesis | flagellar rotation and membrane transport |
| ATP from aerobic respiration | up to 38 per glucose, 2 from glycolysis, 2 from TCA, 34 from oxidative phosphorylation |
| aerobic respiration | uses O2 as the terminal electron acceptor |
| anaerobic respiration | uses a different terminal electron acceptor such as nitrate, sulfate, or oxidized metals, but still uses ETC |
| nitrate reduction | NO₃⁻ → NO₂⁻ → NO → N₂O → N₂ Nitrate → Nitrite → Nitric oxide → Nitrous oxide → Nitrogen gas |
| is nitrate oxidized or reduced when converted into nitrite | reduced because it gains electrons |
| sulfate reduction | SO₄²⁻ → SO₃²⁻ → S₂O₃²⁻ → S⁰ → H₂S Sulfate → Sulfite → Thiosulfate → Elemental sulfur → Hydrogen sulfide. |
| why do different microorganisms use different terminal electron acceptors in a deep lake | oxygen is at the surface, deeper anaerobic environments have alternative acceptors |
| nitrogen fixation | reduction of atmospheric nitrogen N2 into ammonia/ammonium |
| nitrogen fixation enzyme | nitrogenase |
| nitrogen fixation sequence | N₂ → NH₃ → NH₄⁺ Nitrogen gas → Ammonia → Ammonium. |
| why does nitrogenase need to be protected from oxygen | its oxygen-sensitive and needs anaerobic conditions |
| nitrogenase cofactors | iron, sulfur, molybdenum, Fe-S and Fe-Mo clusters |
| nitrogen fixation location | heterocyst of certain cyanobacteria and root nodules containing nitrogen-fixing bacteria such as Rhizobium |
| ammonium after nitrogen fixation | can be assimilated into amino acids and other nitrogen-containing biomolecules |
| anammox | anaerobic ammonium oxidation where ammonium reacts with nitrite to form nitrogen gas |
| anammox equation | NH₄⁺ + NO₂⁻ → N₂ + 2H₂O |
| anammox importance | returns nitrogen to the atmosphere and is used in wastewater treatment to remove ammonia |
| organotrophy | uses organic electron donors such as O₂, NO₃⁻, or Fe³⁺ |
| lithotrophy | uses inorganic electron donors such as CO₂ |
| nitrification | oxidation of reduced nitrogen compounds, such as ammonium, into nitrite and nitrate |
| nitrogen oxidation sequence | NH₄⁺ → NH₂OH → HNO₂ → HNO₃ Ammonium → Hydroxylamine → Nitrous acid → Nitric acid. |
| nitrification significance | converts reduced nitrogen into nitrates/nitrites that may leach into groundwater |
| sulfur oxidation sequence | H₂S → S⁰ → S₂O₃²⁻ → H₂SO₄ Hydrogen sulfide → Sulfur → Thiosulfate → Sulfuric acid |
| why can microbial sulfur oxidation cause environmental damage | sulfuric acid production causes acidification and corrosion |
| hydrogenotrophy | uses H2 as an electron donor |
| dehalorespiration | a form of respiration where electrons from H2 are used to reduce halogenated organic compounds, helping with bioremediation |
| methanogenesis | the production of methane by reducing CO2 or other single-carbon compounds, performed by methanogenic archea |
| methanogenesis equation | CO₂ + 4H₂ → CH₄ + 2H₂O |
| methanogenesis location | anaerobic environments such as sewage systems and deep lake sediments |
| methanotrophs | microorganisms that oxidize methane for energy, using electron acceptors such as O2, nitrate or sulfate |
| phototrophy | the use of light energy to support cellular energy production and growth |
| bacteriorhodopsin | a light-driven proton pump found in certain halophilic arches , Directly pumps H⁺ using light |
| How does bacteriorhodopsin generate ATP | Light changes the configuration of retinal, causing H⁺ pumping. The resulting proton gradient powers ATP synthase |
| chlorophyll | Absorbs light to excite electrons for photosynthetic electron transport, primarily absorbs red and blue-violet light |
| antenna complex | captures light and transfers excitation energy |
| reaction center | uses energy from antenna complex to initiate electron transfer |
| accessory pigments importance | They absorb wavelengths of light that chlorophyll may not absorb efficiently |
| bacteriochlorophyll | can absorb far-red and other wavelengths, including ranges missed by chlorophyll |
| oxygenic z pathway | uses two photosystems to transfer electrons from water to NADP⁺. |
| oxygenic z pathway process | Water is split, supplying electrons and releasing O₂. Light excites electrons in PSII; electron transport helps establish PMF. Light re-excites electrons in PSI. Electrons reduce NADP⁺ to NADPH. |
| oxygenic z pathway products | 3 ATP and 2 NADPH per 2 H2O photolyze |
| Gibbs free energy | energy available to drive a reaction. ΔG = ΔH − TΔS |
| negative ΔG°′ | reaction is energetically favorable and can proceed spontaneously under standard biochemical conditions |
| What does a positive ΔG°′ | The reaction is energetically unfavorable in the forward direction under standard biochemical conditions |
| reaction coupling | Combining an unfavorable reaction with a favorable reaction so the total free energy change becomes negative |
| Calvin cycle | carbon fixation pathway that uses ATP and NADPH to convert CO₂ into organic carbon compounds |
| inputs Calvin cycle | CO2, ATP, NADPH |
| outputs Calvin cycle | organic carbohydrates, ADP, NADP+ |
| RuBisCO | Ribulose-1,5-bisphosphate carboxylase/oxygenase. It catalyzes the fixation of CO₂ by combining it with ribulose-1,5-bisphosphate (RuBP) |
| RuBisCO reaction | One CO₂ combines with a five-carbon RuBP molecule, forming an unstable six-carbon intermediate that splits into two three-carbon compounds |
| carboxysomes | Structures in certain prokaryotes, including cyanobacteria, that contain RuBisCO and help concentrate CO₂ for carbon fixation |
| Calvin cycle location | Plants: Chloroplast stroma. Cyanobacteria: CO₂ fixation in carboxysomes; other Calvin cycle reactions in the cytoplasm. Other photosynthetic bacteria: Cytoplasm |
| How do the light-dependent reactions support the Calvin cycle | They produce ATP for energy and NADPH for reducing power, both needed to fix CO₂ into organic compounds |
| acetyl-CoA and fatty acid synthesis | Acetyl-CoA provides two-carbon building blocks for fatty acid synthesis and connects fatty acid metabolism with respiration |
| fatty acid synthesis enzyme | Fatty acid synthase |
| How are fatty acids synthesized | By repeatedly adding two-carbon units to a growing chain, using NADPH for reduction |
| Why do many fatty acids contain an even number of carbons | They are built by adding two-carbon units |
| glycolysis/TCA intermediates and amino acid synthesis | Intermediates provide carbon skeletons that can be converted into amino acids by incorporating nitrogen |
| transamination | Transfer of an amino group from one molecule to a carbon skeleton, producing an amino acid |
| amino acid formed from 2-oxoglutarate | Glutamate, through assimilation of ammonium |
| examples of amino acid precursors | Pyruvate → Alanine and valine Acetyl-CoA → Leucine Oxaloacetate → Aspartate (the lecture also groups glutamate here) Phosphoenolpyruvate (PEP) → Tryptophan and tyrosine |
| PPP and biosynthesis | supplies: - NADPH for reducing power. - Ribose-5-phosphate for nucleotide synthesis. - Other sugar phosphate intermediates for biosynthetic pathways. |
| purines and pyrimidines | form nitrogenous bases in nucleotides used to build DNA and RNA, purines AG, pyrimidines CTU |
Created by:
odetteschnell7