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Microbial Metabolism
| Question | Answer |
|---|---|
| Metabolism: | all biochemical reactions needed for life. Includes catabolism and anabolism. Replies on electron donors directing electrons to electron acceptors. |
| Law of Conservation of Energy: | energy is neither created nor destroyed. Cells conserve energy by conservation into a form that can do work. Generate adenosine triphosphate (ATP). |
| Catabolism: | goes from reactants to products (ADP + Pi to ATP). |
| Anabolism: | goes from precursors to cellular materials (ATP to ADP + Pi). |
| Reducing Power: | ability to donate electrons during electron transfer reactions (redox reactions). Redox reactions include two half reactions. |
| Electron Donor: | transfers electrons (oxidized) |
| Electron Acceptor: | adds electrons (reduced) |
| Reducing Power Shown in the Aerobic Respiration of Glucose: | C6H12O6 is an electron donor that gets oxidized to CO2. O2 is an electron acceptor that gets reduced to H2O. |
| Energy Source (Classification of Organisms): | if the energy source is sunlight, then the prefix is photo. If the energy source is preformed molecules, the prefix is chemo. |
| Electron Donor (Classification of Organisms): | if the electron donor is an organic compound, the middle word will be organo. If the electron donor is an inorganic compound, the middle word will be litho. |
| Carbon Source (Classification of Organisms): | if the carbon source is an organic compound, the final word will be hetero. If the carbon source is carbon dioxide, the final word will be auto. |
| Important Note About Classification of Organisms: | it’s important to remember that after all three of the words, troph will always follow. |
| Thiobacillus denitrificans oxidizes ammonia (NH3) for energy to conserve ATP and fixes CO2: | chemolithoautotroph. |
| Thiosulfate (S2O3) oxidizing bacteria obtain energy via the oxidation of thiosulfate. Many of these organisms required pyruvate for growth. | Chemolithoheterotroph. |
| Organisms in the genus Roseobacter can obtain energy via aerobic anoxygenic photosynthesis and they require glucose for growth. | Photoorganoheterotroph. |
| What does catabolism depend on? | Electron flow from electron donor to electron acceptor. |
| What is an electron donor? | Substance that gives up electrons (gets oxidized). Examples: glucose, ammonia. |
| What is an electron acceptor? | Substance that receives electrons (gets reduced). Examples: O₂, nitrate. |
| What is reduction potential? | Measure of a substance's affinity for electrons (in volts). |
| What do positive vs negative reduction potentials mean? | Positive = strong electron acceptor; Negative = strong electron donor. |
| Can electrons exist freely in solution? | No, they react immediately with available compounds. Must be transferred directly to redox reactions. |
| How are electrons transferred in redox reactions? | Directly from donor to acceptor via carrier molecules (no free electrons). |
| What is a redox couple? | Oxidized and reduced forms of the same compound (e.g., NAD⁺/NADH). |
| What are NAD⁺/NADH? | Coenzymes that act as electron carriers in metabolic reactions. |
| How do coenzymes like NAD⁺/NADH work? | They allow many different electron donors and acceptors to interact. |
| What is NADP⁺/NADPH used for? | Electron shuttle in anabolic biosynthetic reactions. |
| What's the difference between NAD⁺/NADH and NADP⁺/NADPH? | NAD⁺/NADH: catabolic reactions; NADP⁺/NADPH: anabolic reactions. |
| What is the overall NAD⁺/NADH reaction? | NAD⁺ + 2e⁻ + 2H⁺ → NADH + H⁺ |
| What is ATP's role in metabolism? | Energy currency that stores and transfers energy for cellular work. |
| What is substrate-level phosphorylation? | Direct ATP synthesis from energy-rich intermediates (e.g., in fermentation). |
| What is oxidative phosphorylation? | ATP synthesis using proton motive force across membranes. |
| What is fermentation? | Glucose breakdown using substrate-level phosphorylation with organic electron acceptors. Some products that are useful for humans include beer, wine, yogurt, cheese, and the effect of microbiome on health. |
| What happens to pyruvate in fermentation? | Reduced to organic products (ethanol, lactate) and excreted as waste. |
| What is respiration? | Electrons transferred from donors to external acceptors (like O₂). |
| Where does electron transport occur? | In the cytoplasmic membrane. |
| What creates the proton motive force? | Electrochemical gradient (usually protons) formed during electron transport. |
| What is phototrophy? | Using light energy to generate proton motive force for ATP synthesis. |
| What's the difference between oxygenic and anoxygenic photosynthesis? | Oxygenic produces O₂ (plants, cyanobacteria); anoxygenic doesn't (many bacteria). |
| What are key features of anoxygenic phototrophs? | First phototrophs on Earth; use organic/inorganic electron donors; live in anoxic light environments. |
| What are the characteristics of purple sulfur bacteria? | Use H₂S/S⁰ as electron donors; anaerobic anoxygenic; have bacteriochlorophylls a and b; use Photosystem II. |
| What are the characteristics of purple nonsulfur bacteria? | Use organic substrates; anaerobic anoxygenic; also chemotrophic; have bacteriochlorophylls a and b; use Photosystem II. |
| What are the characteristics of green sulfur bacteria? | Use H₂S/S⁰ as electron donors; anaerobic anoxygenic; have bacteriochlorophylls c, d, and e; use Photosystem I. |
| What are the characteristics of green nonsulfur bacteria? | Use organic substrates; facultative aerobic; can also perform chemotrophy; have bacteriochlorophyll c; use Photosystem II. |
| What's the difference between aerobic and anaerobic respiration in E. coli? | Aerobic uses O₂ as final electron acceptor; anaerobic uses nitrate (NO₃⁻) as final electron acceptor. |
| CHONPS: | carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur → the major elements that the body needs to survive. |
| Can any organisms survive on just glycolysis? | No. |
| Can any organisms solely ferment? | Yes, but it’s difficult because there’s 0 ATP produced during fermentation. It only serves to reproduce NAD+. |
| Is fermentation respiration? | No. |
| Glycolysis: | first step of cellular respiration. Equation is Glucose + 2NAD + 2ADP → 2 Pyruvate + 2 ATP + 2 NADH + 2 H2O |
| Primary Products of Glycolysis: | pyruvate, ATP, NADH, and H2O |
| Location of Glycolysis: | cytosol of all living cells. |
| Does Glycolysis Use Substrate or Oxidiative Level Phosphorylation? | Substrate |
| Does Glycolysis Require Oxygen? | No, glycolysis can occur under both aerobic and anaerobic conditions |
| First Step of Glycolysis (Energy Investment): | Hexokinase uses 1 molecule of ATP to convert glucose into glucose 6-phosphate. |
| Second Step of Glycolysis (Energy Payoff): | PFK uses an ATP molecule to convert fructose 6-phosphate to fructose 1,6-biphosphate. Important step to regulating glycolysis. |
| What happens when ATP is high in glycolysis? | When ATP is high, PFK will prevent glycolysis from occurring. |
| What happens when ATP is low in glycolysis? | When ATP is low, PFK will be used in abundance to produce more ATP. |
| What are key regulatory enzymes in glycolysis? | Hexokinase (glucose → G6P), phosphofructokinase (F6P → F1,6BP), pyruvate kinase (PEP → pyruvate). |
| What is Glycolysis’s Net Production: | 2 ATP are used in the two steps but four are produced, giving it a net production of 2. |
| Pyruvate Decarboxylation (occurs right after glycolysis): | pyruvate is converted to Acetyl CoA, producing 1 NADH & 1 CO2 (net reaction forms 2 of each). Catalyzed by pyruvate dehydrogenase complex (PDC), takes place in the mitochondrial matrix. |
| Net Outcome of Pyruvate Decarboxylation: | 2 Acetyl-CoA molecules, 2 molecules of NADH, 2 molecules of CO2 |
| Citric Acid Cycle (Krebs Cycle): | produces ATP via substrate level phosphorylation. |
| Citric Acid Cycle (Krebs Cycle) Location: | mitochondrial matrix |
| Does the Citric Acid Cycle Use Substrate or Oxidative Level Phosphorylation? | Substrate Level. |
| Steps of Krebs Cycle: | Acetyl CoA enters the cycle and merges with oxaloacetate to form citrate. Then that citrate goes through seven more steps, forming different intermediates. At the end, the oxaloacetate is reformed and the cycle begins again. |
| How many Times Does the Krebs Cycle Turn? | There are two molecules of acetyl CoA per glucose, so the Citric Acid cycle must be turned twice. |
| Primary Goal of the Krebs Cycle: | generating NADH and FADH2 |
| How does pyruvate enter the Krebs cycle? | Pyruvate → acetyl-CoA via pyruvate dehydrogenase, producing NADH and CO₂. |
| What does one turn of Krebs cycle produce? | 3 NADH, 1 FADH₂, 1 ATP (or GTP), 2 CO₂. |
| What's the total yield per glucose (2 acetyl-CoA)? | 6 NADH, 2 FADH₂, 2 ATP, 4 CO₂ |
| What electron carriers are produced in the citric acid cycle? | NADH and FADH₂ from NAD+ and FAD respectively(which must be reoxidized during electron transport). |
| What is the electron transport chain? | Series of protein complexes embedded in the inner membrane of the mitochondria that transfer electrons from NADH/FADH₂ to O₂, pumping protons to create gradient. |
| How do NADH and FADH2 turn back into NAD+ and FAD? | In the ETC, electrons are removed from NADH and FADH2 and passed to the electron carrier proteins embedded in the membrane. These molecules are oxidized by the ETC. They go back to the citric acid cycle to pick up more electrons, cycle repeats. |
| Main Idea of ETC: | as electrons pass through the proteins and into the mitochondrial matrix, protons are pumped across the inner mitochondrial membrane and into the intermembrane space. |
| Electro-Chemical Gradient: | as high energy electrons pass through each of the proteins, H+ ions continue to accumulate in the intermembrane space. This establishes an electro-chemical gradient. |
| Complex I: | NADH → NAD+ |
| Complex II: | FADH2 → FAD |
| Final Step of ETC: | electrons and transferred from complex to oxygen. Oxygen is the final electron acceptor. O2, protons, and the electrons combine to form water. |
| Final Electron Acceptor: | O2 |
| Final ETC Product: | H2O |
| ATP Synthase: | ATP is formed from ADP through the help of ATP synthase. ETC produces ATP via oxidative phosphorylation. |
| Does ETC use Oxidative Phosphorylation of Substrate Phosphorylation? | Oxidative phosphorylation. |
| Chemiosmosis: | movement of ions down a concentration gradient across a semipermeable membrane. H+ ions have accumulated. |
| ETC Overview: | energy released from e moving through complexes pumps protons from the mitochondrial matrix into the intermembrane space, creating an electro gradient. Protons then flow back into the matrix through ATP synthase, powers the production of ATP from ADP |
| Anaerobic Respiration | not the same as fermentation. Cellular respiration that occurs with molecules other than O2 as an acceptor; you can use SO2, NO3, S, etc. |
| Fermentation | no ETC or Krebs cycle, but does include glycolysis. Generates significantly less ATP than respiration. Includes alcohol fermentation and lactic acid fermentation. |
| Where Does Fermentation Occur | in the cytoplasm of the cell without any specialized location |
| Alcohol Fermentation | pyruvate → acetaldehyde + CO2. Then acetaldehyde + NADH → ethanol + NAD+, replenishing NAD+ to reuse for glycolysis. Acetaldehyde acts as a final electron acceptor. |
| Lactic Acid Fermentation | takes place in human muscle cells, fungi, and bacteria. Pyruvate + NADH → lactate + NAD+, replenishing NAD+ to use for glycolysis. Lactate is transported to the liver where it is transformed back to glucose. |
| Prokaryotic Respiration | yields 38 ATP molecules, ETC takes place across cellular membrane, no ATP cost for transporting intermediates from cytosol to mitochondrial membrane |
| Alcohol Fermentation Final Product | produces ethanol |
| Lactic Acid Fermentation Final Product | produces lactate |
| Flasks A and B, both containing yeast. One of the lids is open enough to allow oxygen \ while the other is taped. Which flask will have 1) lower pH, 2) more growth, and 3) alcohol? Lastly, what would happen if you took the lid of B? | B would have lower pH because fermentation creates acid. A would have more growth because aerobic conditions allow it to use oxygen to produce ATP and grow swiftly. If you took the lid off B, it would revert from fermentation to aerobic respiration. |
| Sourdough Example | over-kneading introduces too much oxygen, inhibiting fermentation and resulting in harder bread. Stretch and folds are preferred to incorporate some oxygen, but not too much. |
| Yeast cannot undergo anaerobic respiration | it can only undergo aerobic respiration in the presence of oxygen and fermentation where there’s no oxygen. But since it’s an eukaryote, it won’t start anaerobic respiration. |
| ATP Production From Fermentation Only: | 0 ATP (separate process from glycolysis, not a continuation) |
| Respiration Vs. Fermentation Energy Production: | up to 38 ATP in respiration and 2 ATP in fermentation (only from initial glycolysis). Therefore, respiration is always more energy efficient. |
| If respiration does not require oxygen, why might an organism undergo fermentation? | Because they cannot carry out anaerobic fermentation. |
| What is the electron acceptor in fermentation? | Glucose |
| What do microbes need to grow? | Carbon source “nutrients,” H2O, proper temperature, proper pH, oxygen or no oxygen, sunlight. |
| Why do cells perform fermentation? | To regenerate NAD⁺ from NADH when O₂ is unavailable, allowing glycolysis to continue. |
| What is photosynthesis? | Light energy converts CO₂ + H₂O → glucose + O₂. Has light reactions and Calvin cycle. |
| Where do light reactions occur? | Thylakoid membranes of chloroplasts |
| Photosystem I and II: | used in the light-dependent reactions. Photosystem II absorbs light at 680 nm and I absorbs at 700 nm. |
| Best Light Ranges for Photosynthesis: | blue and red are the best because they absorb the most light, while green light is usually just reflected. |
| Non-Cylic Phosphorylation (Photosystem II – happens first): | photons from sunlight excite electrons, get passed to primary electron acceptor, then pass through ETC, and get catalyzed by ATP synthase. |
| Photolysis: | the splitting of water by light during photosynthesis. |
| Non-Cyclic Photophosphorylation (Photosystem I — happens next): | electrons arrive at Photosystem I, get excited to a higher energy level, passed to e acceptor, travels down ETC, NADPH is formed. |
| Cyclic Photophosphorylation: | Only Photosystem I is used, e in excited state are recycled back to first ETC, more ATP is made instead of NADPH. Replenishes the ATP that the Calvin cycle uses. |
| Does the Calvin Cycle directly require light? | Does not require light, but does require the products of light-independent reactions. |
| What is the Calvin cycle? | CO₂ fixation cycle that uses ATP and NADPH to produce glucose. Occurs in chloroplast stroma. |
| What are the 3 phases of the Calvin cycle? | 1) CO₂ fixation (RuBP + CO₂), 2) Reduction (using ATP/NADPH), 3) Regeneration (of RuBP). |
| What does the Calvin cycle produce per 6 CO₂? | 1 glucose, consuming 18 ATP and 12 NADPH. |
| Main Purpose of Dark Reactions: | uses products from light reaction to fix CO2 and eventually make sugars. |
Created by:
smurtab