1. Assimilatory and Dissimilatory pathways for nitrogen and sulfur (general) + oxidative pathways
    • Assimiltatory pathways: inorganic molecules are reduced and incoprorated into organic materials
    • N and S into Amino Acids and Nucleotides
    • Dissimilatory pathways: Molecules used as final electron acceptors during anaerobic respiration
    • Reduced products excreted as waste
    • Facultative anaerobes use nitrate -> NH3 or N2(g)
    • Obligate anaerobes use sulfate -> H2S
    • Oxidative pathways: inorganic molecules oxidized to produce energy (source of e- and energy)
    • H2, NH3, NO2-, S, H2S
    • Used by lithotrophs
  2. What are the four processes of the nitrogen cycle?
    • Ammonifcation
    • Nitrate assimilation
    • Nitrate dissimilation
    • Nitrogen fixation
  3. Describe nitrate assimilation into amino acids (detail)
    • Occurs under aerobic OR anaerobic conditions
    • Nitrate reducted to nitrite which is reduced to ammonia (nitrate reductase)
    • Ammonia is incorporated into glutamine -> purines, pyrimidines, amino sugars
    • Gultamine converted to glutamate -> amino acids (histidine, tryptophan, alanine)
  4. Describe assimilation of sulfate (detail)
    • Sufate reduced to H2S (anaerobic respiration)
    • H2S incorporated into cysteine (req ATP) -> other organic molecules (methionine, Coenzyme A, Acyl protein carriers)
  5. Describe nitrogen fixation (detail) (not the pathway)
    • Remove N2(g) from the air and convert it to a form usable by organisms
    • Ammonia is the primary product (NH4+ in solution)
    • Occurs ONLY under anaerobic or microaerophilic conditions
    • Nitrogenase performes nitrogen fixation (sensative to O2, gene is laterally transferred)
    • Widespread in bacteria, some archaea
    • soil: Azobacter, Azospirillum, Clostridium
    • water: Cyanobacterium (anabaena, Nostoc)
    • Symbiotes: Rhizobium
    • Infects root nodules
    • Fix nitrogen for legumes
    • Legume supplies nutrients and protection
  6. Describe process of infection of a root hair by Rhizobium
    • Senses chemicals in root hair of legume
    • Interaction between lectin on root hair cell and attachment site of bacterial cell
    • Bacteria moves into plant via infection thread
    • Change in root hair morphology (nodule formation where fixation occurs)
  7. The nitrogen fixation pathway
    • Nitrogenase: the enzyme that carries out nitrogen fixation
    • Two components
    • 1. MoFe protein (tetramer)
    • 2. Fe protein (dimer)
    • nif genes: involved in N2 fixation
    • 21 genes
    • Expression repressed by nitrogen sources (NH4+, NO3-, AA, urea)
    • Nitrogenase reaction: Ferredoxin serves as main carrier of electrons
    • Fd passes 2 e- to Fe protein
    • Fe protein passes 2 e- to MoFe protein
    • 2 e- and 2 H+ reduce N2 -> NH3
  8. Describe strategies for protecting nitrogenase
    • Nitrogenases are inactivated by O2
    • Strategies to protect developed by aerobes
    • Active respiratory system in azobacter: rapid use lowers the cellular O2 levels
    • protective proteins (redox enzymes)
    • Root nodule formation: protected by leghemoglobins
    • Binds O2
    • Part made by plant, part by bacterium
    • Heterocysts in aerobic cyanobacteria: Nostoc and Anabeana
    • Differentiate vegetative cells into nitrogen-fixing cells (HETEROCYSTS) which are formed when the concentration of nitrogen decreases
  9. Describe heterocysts in detail
    • Non-dividing cells with thick walls
    • Houses nitrogenase: protected by...
    • thick cell wall (allows for N2 fixation to occur)
    • High rate of respiration (low O2 concentration internally)
    • Have only PSI for photosynthesis (no O2 produced)
    • Does not fix carbon (no PSII - inactive calvin cycle)
    • Supplies glutamine
    • Receives carbohydrates
  10. Describe dissimilation pathways (general)
    • Inorganic molecules other than O2 is used as final electron acceptor (anaerobic respiration)
    • Nitrate -> NH3 or N2(g)
    • Sulfate -> H2S
    • CO2, Fe3+, Mn4+
    • Reduced products are excreted as waste
  11. Describe dissimilatory nitrate reduction (detail)
    • Occurs in facultative anaerobes when O2 levels are low
    • Occurs in membrane (ETC) and membrane potential is generated
    • Denitrification: occurs under AEROBIC conditions
    • Nitrate used as final electon acceptor -> N2(g)
    • Important for biodegredation of organic molecules
    • Soil bacteria: conversion of nitrate to N2(g), nitric oxide (g), or Nitrous oxide (g)
    • Drains nitrate and removes from soil (bad for farmers)
    • Alcaligenes, Pseudomonas,¬†Paracoccus
  12. Describe dissimaltory sulfate reduction (detail)
    • Restricted to obligate anaerobes
    • Sulfate reducers: found in anaerobic mud or anaerobic aquatic environments
    • Carry out anaerobic respiration (sulfate is final e- acceptor -> H2S)
    • Include gram+ and gram- bacteria and archaea
    • Two physiological groups of reducers...
    • Group I: Cannon oxidize acetyl CoA-> CO2.
    • Produces acetate when growing on certain carbon sources
    • Group II: Via two pathways
    • 1. Reductive citric acid pathway
    • 2. Acetyl CoA pathway
  13. Describe Oxidative pathways (detail)
    • Inorganic molecules oxidized to produce energy (source of electrons and energy)
    • H2, NH3, NO2-, S, H2S
    • Lithotrophs: organisms that derive energy from oxidation of inorganic molecules
    • Nitrification: soil and water bacteria
    • Conversion of NH3 to NO3-
    • Occurs in the presence of O2
    • Nitrifiers oxidize NH3 as source of energy
    • Two step process...
    • 1. NH4+ -> NO2- (Nitrosomonas, Nitrosococcus)
    • 2. NO2- -> NO3- (Nitrobacter, Nitrococcus)
    • Nitrate is assimilated into cell material or used as a source of oxygen
    • Sulfur-oxidizing prokaryotes: found in sulfur mines, hot springs, sulfur mines, coal mines
    • Mostly bacteria (thiobacillus) associated with sulfur cycle
    • Forms of sulfur used as source of energy and e-: S, H2S, SO4-, S2O32- (thiosulfate)
    • Plants/microbes ASSIMILATE sulfur
    • Animals obtain sulfur from AA
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