Exam 2 – Microbiology – Flashcards
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| Examples of high energy compounds? |
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| ATP, UTP, GTP, CTP |
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| How is energy stored in cells? |
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| ATP |
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| What is the difference between fermentation and respiration? |
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| The Fate of Pyruvate. Respiration: completely oxidized to CO2 and Water: most energetically favorable. Frementaton: it is fermented into an acid or alcohol |
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| Three Possible mechanisms for cells to form ATP? |
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| Substrate level phosphorylation Respiration linked phosphorylation Photo-phosphorylation |
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| Substrate level phosphorylation |
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| direct transfer of high energy phosphate from phosphoralized organic compound ADP->ATP |
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| Respiration linked phosphorylation |
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| oxidation of electron donator coupled with reduction of electron acceptor |
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| Photophosphorylation |
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| Use of light to create a proton motor force. |
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| What is the purpose of each stage of Glycolsis |
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| phosphorlating everything: preparation redox stages: energy recovery and production of NADH |
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| What is Gibb's free energy? |
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| It is the enthalpy of the system-the product of temp(entropy) |
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| How do you determine if a reaction will be favorable or not? |
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| If delta G is negative the reaction if favorable |
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| What is the role of electron carrier NAD |
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| it is involved in energy generating catabolic reactions |
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| What is the role of the electron carrier NADP |
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| it is involved in biosynthesis and anabolic reactions |
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| What is reduction potential |
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| it is the likelihood that a species will be reduced. |
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| How is reduction potential related to free energy |
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| The amount of free energy released in a redox reaction is the difference in the redox potential between electron donor and acceptor. |
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| why are Oxiduction-Reduction reactions always coupled |
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| They can not occur alone |
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| What sort of work can energized membranes (PMF membranes) preform? |
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| -ATP synthesis -rotating flagellum -active membrane transport |
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| What are the 3 characteristics that all electron transport chains must possess? |
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| -have redox carriers -create PMF (have alternating electron only and proton carriers) -they have to be linked to an intact membrane |
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| What is the structure and function of ATP synthase F1 and F0 subunits |
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| F1 rotates and goes through membrane to inside F0 sets in the membrane like a pore |
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| Describe the possible fates for energy stored in a photon |
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| -captured by antenna complex -transferred to the reaction center -captured by the reaction center |
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| relation between substrate level phosphorylation and glycolsis |
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| SLP is a STEP in gylcolsis |
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| What are examples of light gathering systems? |
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| -Different types of antenna systems -COMPOSTION OF ANTENNA (ex caratnoids) -organization of intracellular membrane complexes -chlorosomes - thylicoids |
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| What are dark reactions? |
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| do not require light.. synthesis processes (ex. Calvin cycle) |
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| What are light reactions? |
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| Light reactions create ATP |
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| Five types of photosynthetic bacteria compare and contrast |
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| A: Have ETC Non-Purple bacteria Purple Sulfur bacteria Green sulfur bacteria cyanobacteria heliobacteria *B: Use Rodopsiin * Heliobacteria C: Anoxygenic (cyclic photophosphor) Green Sulfur bacteria Purple Sulfur Bacteria Non Purple bacteria *D: Oxygenic (Z-Scheme) * Cyanobacteria *E: Can't use sulfur *Non purple bacteria F: Can use sulfur Purple and Green Sulfur bacteria *G: Can reduce NADPH *Green sulfur bacteria *H: Can not reduce NADPH (use reverse ETC) *Purple sulfur bacteria |
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| What are the key enzymes in Krebs cycle |
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| rubisco |
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| Key enzyme in Woods pathway |
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| carbonmonoxide dehydrogenase |
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| Key enezyme in reverse TCA cycle |
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| forwards: succinate dehydrogenate backwards: fumerate reductase |
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| Why is nitrogen fixation so oxygen sensitive? |
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| it has cofactors that fall apart in presence of oxygen |
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| relationship between ETC and PMF |
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| ETC produces PMF |
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| what can make a membrane energized? |
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| -pumping protons out -ATPase (ATP synthesis backwards) |
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| How does fermentation make ATP |
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| -through substrate level phosphorylation (do NOT make PMF) -can make energized membrane with ATPase |
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| How does respiration make ATP |
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| chemiosmosis |
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| Bacteria with rodopsin do NOT use antenna structure |
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| Distinguishing enzyme ED |
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| KDPG aldolase |
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| Distinguishing enzyme Hexose Monophosphate Shunt |
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| 6-phosphogluconate dehydrogenase |
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| distinguishing enzyme of Calvin cycle |
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| rubisco |
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| Wood Pathway |
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| carbonmonoxide dehydrogogenase |
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| anaplueric pathways |
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| replinishes intermediates |
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| What kind of molecules serve as electron acceptors? |
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| They are molecule or atom that can be reduced by gained an electron from something else. (they have the most positive reduction potentials) |
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| What kind of molecules are electron donors? |
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| An electron donor is a molecule or atom that can be oxidized by giving an electron to something else. They have the most negative reduction potentials. |
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| What determines their role as a donor or acceptor? |
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| Their relative reduction potentials. The more positive of the two will be the acceptor. |
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| What are electron transport chains? |
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| ETC's use PMF and are series of electron acceptors and donors that transfer electrons from an electron carrier to a terminal acceptor. |
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| Cofactors associated with the ETC |
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| NADH: electron carriers Flavoprotenin: electron and proton carriers Iron sulfur proteins: electron carriers Cytochromes: electron carrier Quinones: carry protons and go to cytochromes |
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| What is the chemiosmotic theory and who proposed it? |
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| Peter Mitchell proposed the chemiosmotic theory which said that the proton motor force generated by electron transport is employed to drive ATP synthase (enzyme makes ATP from ADP +P) |
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| What are light reactions? |
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| those that harvest light energy to generate a proton motive force and ATP |
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| What are the four major classes of macromolecules in the bacterial or archaeal cells? |
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| Proteins, Lipids, Carbohydrates, Nucleic Acids |
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| What is the purpose of precursor metabolites? |
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| Precursor metabolites are the compounds from which all constituents of the cell can be synthesized. |
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| Precursor molecules of EM Pathway |
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| glucose-6-phosphate fructose-6-phosphate glyceraldehyde-3-phosphate 3-phosphoglycerate phosphoenolpyruvate pyruvate acetyl-CoA |
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| Precursor molecules of the HMS |
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| Glucose-6-phosphate ribose-5-phosphate erythrose-4-phosphate glyveraldehyde-3-phosphate pyruvate acetyl-CoA |
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| Precursor molecules of ED |
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| glucose-6-phosphate glyceraldehyde-3-phosphate pyruvate acetyl-coA |
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| Precursor molecules of the TCA cycle |
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| oxaloacetate alpha-ketogluterate succinyl-CoA |
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| How are intermediates of the TCA cycle replenished? |
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| It is an anaplerotic reaction. through carnoxylation of pyruvate to form oxaloacetate. |
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| What are the other major pathways for CO2 fixation |
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| Calvin Cycle Reductive Citric Acid Pathway Hydeoxypropionate Pathway Reductive Acetyl-CoA Pathway |
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| What are the molecules that contain nitrogen and what are the relative ease of making biomass from each? |
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| NO3, NH4, Amino Acids, Organic nitrogen, N2 N2 is used at last resort |
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| What are the two types of nitrate reduction |
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| Denitroficicaton assimularoty nitrate reduction pathway |
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| Why is nitrogen fixation a critical microbial process? |
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| It is because it is essential for all living organisms survival and only microbes can fix N2 gas to a usable form |
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| WHat are the two components of nitrogenase |
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| FeS FeMoCo |
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| How much energy is required for nitrogen fixation? |
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| 16 ATP per N2 |
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| How can an organism synthesize all of its cell structures from glucose? |
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| It can because glucose can be used to form all of the precursor molecules which can be used to synthesize any cellular component. |
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| What are the main structural arrangements of proteins |
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| Primary Structure: Amino Acids are joined by peptide bonds Secondary Structure: Alpha helix Beta Sheet Tertiary structure: many secondary structures together Quaternary structure: multiple subunits into a wad |
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| What is the structure and function of the cytoplasmic membrane |
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| It serves as a primary boundary for the cell's cytoplasm. It is composed of a phospholipid bi layer with proteins inside |
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| How is cell structure and function studied by cell fractionation and separation of components? |
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| are separated using a centrifuge giving you different layers each with a different cell organelle. the organelle specific layer could be removed and examined more closely giving the scientist the opportunity to understand the purpose and function of the organelle. |
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| How do the position of enexymes and quinones in electron transport chains relate to reduction potential. |
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| The more negative (higher up) pass to the more positive and the change is the reduction potential. |
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| EM ED and HMS differences |
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| HMS: produces sugars needed for biosynthesis ED: only 1 APT produced EM: uses substrate level phosphorlation more ATP then ED |
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| How is the bacterial cell wall assembled? |
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| UDP-NAM is synthesized inside the cell and 5 amino acids are added sequentially to form a pentapeptide side chain. Special enzyes are used to add the side chains so tRNA and ribosomes are not involved. It is non UDP-NAM pentapeptide.UDP-NAM is synthesized inside the cell and 5 amino acids are added sequentially to form a pentapeptide side chain. Special enzyes are used to add the side chains so tRNA and ribsobomes are not involved. It is non UDP-NAM pentapeptide.pentapeptide precursor. The completed NAMNAG precursor is transfered across the membrane b the bactoprenol the disachharide pentapeptide is then transfered to the growing end of the peptidoglycan chain outsid the cell. The bactoprenol then reterns inside and loses a phosphate and is ready to repeart the transfer process. The peptide side chains are then linked to eachother using peptide bonds forming crosslinking. |
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| How are flagellae and pili assembled? |
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| Falgellae: Assembly begins with synthesis of the MS-ring at the cytoplasm surface. Followed by insertion of proteins composing the basal body including motor shaft proteins and the hook. The addition of motor stator proteins (MOT A and B), The Motor switch protiens and buildup of the filament (FilC subunits). The secretion of proteins across the membrane is done through type III secretion. FilC subunits are transferred through the hollow core of the basal body shaft. hook and growing filament where they self assemble into a helically wound structure. Pili: The pilus is assembled from subunits secreted into the periplasm. PapC is assembled first and subunits that are at the tip are assembled first while the ones closest to the cell are assembled last. PapD is a periplasmic chaperone prevents misfolding and premature aggregation of the major and minor subunits of the filaments. |
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| How does bacterial motility function? |
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| flagella are powered by proton motor force. The energy is used by mot proteins which act as a motor and drives flagellar rotation. |
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| What are the purposes of photosystems I and II in cyanobacteria? |
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| Photosystem II occurs first and is the sight of photolysis which allows an electron to be boosted to a higher energy level. The passage of this electron to photosystem I drives synthesis of ATP. Photosystem I: is responsible for reducing NADP+ or providing a reductant that can reduce NADP. |
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| Why does an organism degrade a compound? |
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| to get energy/food |
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| How does an organism degrade a compound? |
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| through enzymes |
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| How do we find out if the organism degrades a compound? |
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| you can use tests for the disappearance of compounds |
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| Why don’t all organisms degrade the compound? |
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| They don't have the specific enzyme for degradation of that compound. |
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| Van Niel's postulates |
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| Microbes are present which utilize every constituent part/product as a source of carbon or energy Microbes are present in every niche |
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| What is an end product of fermentation? |
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| Acetate |
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| If a microbe lacked a sufficient iron source, which stage of respiration would be most affected? |
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| Electron Transport Chain |
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| Which of the following components of the electron chain are freely diffusible in the membrane? |
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| quinones |
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| According to the chemiosmotic mechanism, ATP is generated when |
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| protons flow through ATPase. |
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| Which of the following would prevent chemiosmosis from generating ATP? |
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| All of the Above |
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| Glycolysis has a net yield of _______ molecules of ATP per molecule of glucose consumed. |
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| 2 |
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| The usual sequence of redox reactions in aerobic respiration is |
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| NADH > flavoprotein > nonheme iron protein > CoQ > cytochromes. |
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| The generation of a proton motive force requires |
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| a closed membrane compartment that is impermeable to protons. |
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| In addition to their ability to harvest light in the 400 to 500 nm range, carotenoids also... |
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| intercept toxic single-state oxygen. |
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| Photosynthetic halophiles use bacteriorhodopsin... |
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| to trap light energy and eject protons. |
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| In cyclic phosphorylation, ATP is formed when |
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| sufficient protons are driven outside the membrane by the cytochrome bc1 complex. |
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| Which of the following can be used as a source of electrons in anoxic photosynthesis? |
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| both A and B |
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| Antenna pigments can be an advantage to photosynthetic microorganisms because they can |
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| absorb energy from light of different wavelengths, funneling energy of excitation to reaction centers. |
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| Incorrect All photosynthetic microorganisms possess all of the following features except |
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| a capacity for substrate-level phosphorylation. |
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| The characterization of the bacteriorhodopsin system in Halobacterium lent support to |
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| the chemiosmotic theory of ATP generation. |
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| The thylakoid is a photosynthetic structure characteristic of |
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| cyanobacteria. |
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| In noncyclic electron flow in nonsulfur purple bacteria, electrons leaving the Q pool |
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| are used to reduce NAD+. |
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| During cyclic photosynthesis in nonsulfur purple bacteria, which of the following molecules or components acts as both the initial electron donor and the final electron acceptor? |
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| Bchl 870 |
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| There are ______ precursor metabolites that autotrophic bacteria must be able to make from their central metabolic pathways. |
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| 12 |
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| In addition to precursor metabolites, what is also produced during the TCA cycle? |
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| 2 CO2, 3 NADHs, 1 FADH2, 1 GTP |
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| Which of these reactions are used to replenish intermediates in central metabolic cycles? |
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| anaplerotic |
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| The most abundant enzyme on Earth is probably ______. |
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| rubisco |
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| Acetogenic bacteria produce acetate from ______ by using a key enzyme, acetyl-Co A synthetase/CO dehydrogenase. |
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| H2 & CO2 |
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| The enzyme, GOGAT, is used to replenish ______ when NH4+ is limiting. |
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| glutamate |
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| For every N2 that is fixed to 2NH3, ______ ATPs are used. |
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| 16 |
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| A malonyl-CoA is used per cycle during the biosynthesis of a fatty acid. This adds ______ per cycle. |
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| 2 carbons and releases 1 CO2 |
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| Define PMF |
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| Proton motive force (pmf) is the sum of the membrane electrical potential and the corresponding pH gradient. |
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| What is fermentation? |
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| Fermentation is defined as the sum of the anaerobic catabolic reactions that provide for the growth of microorganisms when energy is derived solely by substrate-level phosphorylation. |
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| How does photosynthesis with bactrorodopsin pigment differ from that due to chlorophyll? |
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| Bacteriorhodopsin can absorb light energy and employ this excitation to carry protons from the cytoplasm to the outer surface of the cell, creating a proton motive force. and is a caratnoid structure |
