FINAL Week 7 Metabolic Diversity

Question 1

Anaerobic Respiration

Answer 1

On anoxic to oxic scale:
> Obligate anaerobes (-0.42 to -0.22): proton reduction, carbonate/S/C/Sulfate/Fe respiration, reductive dechlorination
> Facultative aerobes (-0.22 to 0.82): fumerate respiration, reductive dechlorination, Fe/nitrate respiration/denitrification
> Obligate aerobes: aerobic respiration
* Anaerobic respiratory chains often contain e- transport components (cytochromes, quinone, etc) with terminal reductases/acceptors

Question 2

Microbial Environmental Redox Ladder

Answer 2

1. Oxic: aerobes (O2)
2. Sub-oxic (anaerobic): denitrifiers (NO3), MnO2 reducers, Fe(0H)3 reducers
3. Sulfidic: SO4 reducers, methanogens (CO2)
4. Methanic
   * *As going down ladder, E0 of e- acceptors are more negative, lower energy yield, more + deltaG

Question 3

O2 vs NO3 Respiration in E. coli

Answer 3

Aerobic (O2): 2 more protons
Anaerobic (NO3): nitrate reductase
> Gene encoding enzymes for AnRes are repressed by O2 (only activated by presence of e- acceptor)
> Denitrification: reduction of fixed NO3 to N2 (gas)

Question 4

Metal Reduction

Answer 4

1. can be e- acceptors

2. Mineral solubilization and bioremediation (sometimes to prevent further transport through the environment)

Question 5

Sulfur Respiration/Reduction (anaerobic)

Answer 5

Bacteria and archaea
> e- donors for SRB are in small organic acids or H2
> SO4 (Activated to APS for a more positive e- acceptor) –> H2S (1 ATP)
> Dissimilative: SO4 –(ATP sulfurylase) –> APS –(Reductase)–> SO3 –> H2S (Excretion)
> Assimilative: SO4 –> APS –> PAPS –> SO3 –> H2S (organic cysteine, methionine, etc)

Question 6

Methanogenesis: Dissimilative CO2 Reduction (anaerobic)

Answer 6

Archaea only; CO2 e- acceptor
> Some use H2/acetate/lactate as e- donor
> Does not yield much energy due to e0 proximity of e- acceptors and donors, despite their abundance

Question 7

Electron Acceptors (all + e0)

Answer 7

1. Organics:
> TMAO/TMA: rotten fish
> DMSO/DMS, fumerate/succinate
2. Metals:
> Ferric/ferrous ion
> Selenate/selenite
> Manganic/manganous ion
> Chlorate/chloride
> Arsenate/arsenite
3. Halogenated compounds (dichloromethane) --> microial bioremediation

Question 8

Fermentation: no usable external e- acceptors

anaerobic

Answer 8

does NOT use proton motive force (PMF) for ATP generation
> Can occur via glycolysis
> Organic –> energy rich compound (Substrate-level phos) –> oxidized compound –> fermentation product (waste)
> Substrate fermented: both e- acceptor and donor
> Energetically weak (no OxPhos)
> Can utilize many substrates (NOT FA since they are too reduced)
> Examples; formate, butyrate, acetate
> Common processes: alcoholic (hexose –> ethanol), homo/heterolactic (hexose –> lactate + (ethanol), Mixed acid, butanol (hexose –> butanol + acetone)

Question 9

Syntrophy (anoxic)

Answer 9

Inter-species H2 transfer (From ethanol fermenter to methanogen)
> Small available energy
> Mutually beneficial (coupling of unfavorable and favorable reactions)

Question 10

Anoxic Decomposition

Answer 10

One microbe’s junk = another’s main source
> Freshwater: SO4/SRB activity is minimal
> Trophic cascades

Question 11

Phototrophy: Photosynthesis and facultative nutritional mode

Answer 11

1. Photosynthesis: CO2 –> organic sugars
   > Oxy: H2O as donor, 2 photosystems, chlorophyll, non-cyclic photophosphorylation
   > e- from H2O –> PMF + NADPH reducing power; PSI –> NADPH –> cyclic e- flow –> more ATP
   > Anoxy: multiple donors (S0/H2S), 1 photosystem, bacteriochlorophyll, cyclic photophosphorylation
   > P870 –> P870* via light activation
2. Green/purple nonsulfurs, halophiles (bacteriorhodopsins), marine bacteria (PR)

Question 12

Accessory Pigments

Answer 12

1. Carotenoids:
   > Carotenes and xanthophylls
   > Photoprotection, prevent ROS damage, isoprenoid chains, absorbs blue light
2. Phycobiliproteins:
   > Cyanobacteria, 3 pigments types, increases in content when light intensity decreases

Question 13

Photosynthetic Membranes

Answer 13

1. Bacterias do not have chloroplasts, but their reaction centers are integrated into internal membrane systems
   > Thylakoid membranes (cyanobacteria), cytoplasmic membrane invagination (purple), chlorosome (Green)

Question 14

Autotrophy: Multiple CO2 Fixation Pathways

Answer 14

Calvin-Benson Cycle

1. Cyanobacteria, green plants, algae, archaea
2. RuBisCO as inclusion bodies
3. Light energy and CO2 substrate –> macromolecules (needs a lot of ATP/NADPH)

Question 15

Chemolithotrophy Diversity

Answer 15

1. Diverse inorganic e- donors:
> H2, H2S, S0, NH4, NO2, Fe
2. Diverse e- acceptors:
> Aerobic: O2
> Anaerob: NO3, SO4, metals, organics
**Energy production via PMF and ATPase, reducing powers from inorganic donors/reverse e- flow

Question 16

Reduced Sulfur Compounds Oxidation

Answer 16

1. e- from S oxidation –> ETC
2. Reverse e- flow needed for NADPH synthesis (e- donors are more positive than NAD+)
3. CO2 fixation proceeds via Calvin or reverse TCA

Question 17

Iron Oxidation (Fe2+ –> Fe3+)

Answer 17

1. pH is very important: stable spontaneous at ~7 but stable at sub-3 pH (high redox couple = 0.76)
2. Natural proton gradient: e- from Fe2+ oxidation + protons from ATPase –> Water
3. Cells must oxidize a lot of Fe2+ due to very short ETC