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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
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What are the four processes of the nitrogen cycle?
- Ammonifcation
- Nitrate assimilation
- Nitrate dissimilation
- Nitrogen fixation
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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)
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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)
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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)
- ONLY PERFORMED BY PROKARYOTES
- 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
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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)
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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
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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
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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
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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
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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
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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
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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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