Metabolic Diversity
Spend more time talking about phototrophs, anoxygenic and oxygenic phototrophs, chemolithotrophs and anaerobic respiration.
Phototrophs - eukaryotic and prokaryotic microorganisms.
Chlorophyll - heterocyclic compound with a Mg atom in the middle. Chlorophyll a is the common chlorophyll of higher plants. It absorbs red (680 nm) and blue (430 nm) light wavelengths and reflects green - Why plants are green! Other chlorophylls have different absorption spectra - absorb different wavelengths of light.
Bacteriochlorophyll - analogous to higher plants chlorophyll but have a absorption maximum in the neighborhood of 700 nm and greater. Different phototrophs with different bacteriochlorophylls can coexist since they are not competing for the same light wavelengths - increase biodiversity.
Bacteriochlorophyll located in (1) invaginations of the cytoplasmic membrane, (2) the cytoplasmic membrane, or (3) the cytoplasmic membrane and chlorosomes. Recall in eukaryotic phototrophs the chlorophyll is found in the thylakoid membranes inside the chloroplasts. In these membranes there are special chlorophyll molecules called reaction centers associated with other light-harvesting chlorophyll molecules whose purpose is to harvest quanta of light and transfer their energy to the reaction center.
Purple bacteria
Invagination of cytoplasmic membrane called chromatophores. Contains reaction center, light-harvesting I and light-harvesting II components plus bc1 complex which is common to the respiratory electron transport chain. The function of light harvesting I and II also referred to as B870 and B800-850 respectively, is to channel absorbed light energy to the reaction center.
Electron flow ( Figure 13.10) - Light harvesting antennae bacteriochlorophyll a molecules funnel their energy to the reaction center bacteriochlorophyll a molecules - the special pair. The special pair becomes excited and is converted to a good electron donor with sufficiently low E_o' (-1000 mVolts) to reduce a very electronegative acceptor molecule - bacteriopheophytin. Solar energy has now been converted to chemical energy.
Bacteriopheophytin reduces quinones in the reaction center which reduce quinones in the quinone pool before the electrons flow to Cyt bc1 to iron sulfur proteins, through Cyt c2 back to P870 of the reaction center.
How does this drive ATP synthesis?
The quinones move electrons down the electron transport chain but also move protons from inside the cell to outside the cytoplasmic membrane thus establishing a PMF which can be used to drive ATP synthesis via photophosphorylation - cyclic photophosphorylation since the electrons flow in a circular fashion.
How are reducing equivalents (NADPH) generated? NADPH is used to reduce CO₂ to organic carbon used by the cell- auxotrophy!
Need a source of electrons since in cyclic photophosphorylation there is no net gain or loss of electrons from the transporters. The ultimate souce of electrons for the reduction of NADP⁺ is a reduced inorganic molecule like H₂S, elemenal sulfur, thiosulfate, H₂ or organic acids like butyrate or malate.
Two ways to reduce NADP⁺ to NADPH.
Direct reduction if the reducing agent has a redox potential more negative than NADP⁺. H₂ has a redox potential of -420 mVolts and NADP⁺ is -320 mVolts.
Reverse electron flow - reduced compounds that have a more positive redox potential than NADP⁺. The membrane potential is used to push electrons from the quinone pool to NADP+ - where the quinones have a more positive redox potential than NADP+.
Anoxygenic phototrophs - by definition these are organisms that obtain their energy from the sun by converting solar energy to chemical energy and do not produce oxygen during photosynthesis as higher plants and some eukaryotic and prokaryotic microorganisms do.
Compare Figure 13.9 with 13.13
We have been talking about energy but what about carbon? How do autotrophs obtain their carbon if not from organic sources?
Calvin cycle or reductive pentose cycle (see 13.18)
Ribulose bisphosphate carboxylase is the enzyme responsible for the first reaction in the cycle involving CO2 and ribulose bisphosphate - a 5 carbon sugar. The product is 2 molecules of phosphoglyceric acid.
Phosphoglycerate is phosphorylated and reduced by NADPH to 3-phosphoglyceraldehyde.

Steps:
6 molecules of ribulose bisphosphate accepts 6 molecules of CO2 for a total of 36 carbons among 12 3-carbon molecules (phosphoglyceric acid). These 12 molecules are than rearranged to make 6 5-carbon molecules (ribulose bisphosphate) and 1 6-carbon (hexose) molecule. A total of 12 NADPHs and 18 ATPs are used during the reduction of 6 CO2s to hexose.
Chemolithotrophs - obtain their energy from the oxidation of reduced inorganic molecules. ATP generated from oxidation of inorganic molecules like chemoorganotrophs (aerobic respiration process) and reducing power (NAD(P)H) is generated either directly if the inorganic molecule has a redox potential sufficiently low or by reverse electron transport reactions. Recall the greater the difference between the redox potentials of two reactions, the greater the amount of energy released.
Hydrogen oxidizing bacteria - most are facultative chemolithotrophs capable of growing either chemoorganotrophically or chemolithotrophically.
Chemolithotrophic growth - hydrogenase enzyme oxidizes H2 and the electrons are transfered to quinones in the electron transport chain ultimately moving to oxygen as the terminal electron acceptor. A PMF is generated by the movement of the electrons and ATP is made via membrane bound ATPases.
Reducing equivalents in the form of NADPH
some species reduce NADP+ directly
most species use the reverse electron transport mechanism discussed earlier
Carbon fixation - use the Calvin cycle but organic carbon will repress the synthesis of key enzymes of the Calvin cycle.

H2 --------> 2H+ 2e (-0.420 V)
1/2O2 +2H+ +2e ----------> H2O (+0.820 V)
H2 + 1/2 O2 ------->H2O
[Delta]G^o = -nF[Delta]E_o´
= -2 (96.5kJ/V) (0.820 -(-)0.420)
= -240 kJ/reaction

Sulfur oxidizing bacteria - These were some of the first chemolithotrophs described by Winogradsky. Use reduced sulfur such as H²S, S^o, and S₂O₃^2-(thiosulfate).
ATP formation - Electrons enter the electron transport chain at various points depending on the redox potential of the source. Electrons flow to oxygen as the terminal electron acceptor and generate a PMF which is used to drive ATP synthesis.
Reducing equivalents - NADPH is formed by the reverse electron transport mechanism.
Carbon fixation - Calvin cycle
Note: they grow poorly on elemental sulfur or thiosulfate since these compounds have a relatively high redox potential.

HS^- ---------> S^o + 2e + H⁺ (-0.270 V)
1/2O₂ +2H+ +2e ----------> H2O (+0.820 V)
HS^- + 1/2O₂ + H⁺ -----> S^o + H₂O
= -2 (96.5 kJ/V) (0.82 -(-)0.270)
= -210.37 kJ/reaction
S^o + 4H₂O----------> SO₄^2- + 6e + 8H⁺ (-0.180 V)
3/2O₂ +6H⁺ +6e ----------> 3H₂O (+0.820 V)
S^o + H₂O +3/2O₂ -------> SO₄^2- + 2H⁺
=-6 (96.5 kJ/V) (0.82 -(-)0.180)
=-587.1 kJ/reaction

Note:H+ is generated which means that this is an acidifying reaction - sulfuric acid is generated. Some sulfur-oxidizing bacteria can live at pHs in the 1-2 range.
Iron-oxidizing bacteria - Ferrous iron, Fe+2, is oxidized to ferric iron, Fe+3. Iron has an interesting chemistry about it: Ferrous iron rapidly oxidizes to ferric iron in air at neutral pH - stable in anoxic conditions. At acidic conditions, ferrous iron is stable. Best known iron-oxidizing bacteria is Thiobacillus ferroxidans. Found in acid polluted waters like coal mining dumps.
Energy production - ATP formation
Very little difference between the redox potential of Fe+3/Fe+2 and 1/2O2/H2O compare +0.77 V at pH 3 for the former to +820 V for the latter. The redox potential of Fe+3/Fe+2 is too positive to reduce NAD+, FAD, and many of the electron transport chain.
Unique ecology allows these bacteria to take advantage of the natural pH gradient in which they live. The live in acidic environments such that the pH outside the cell might be 2 and inside the cell the pH is around 6 - this difference is a preformed PMF. To maintain a constant pH inside the cell, the oxidation of Fe+2 to Fe+3 is a proton consuming reaction - 2Fe⁺³ + 1/2O₂ +2H⁺ -----> 2Fe⁺³ + H₂O.
Carbon fixation - Calvin cycle as usual. Generate NADPH by the reverse electron transport process using the PMF to drive electrons uphill. Because of the very positive redox potential of Fe+3 / Fe+2 the reverse electron process requires a lot of energy, therefore there is very little biomass generated by these organisms in the habitat but there is lots of ferric iron precipitates.
There is some iron oxidation occuring near neutral pH specifically at the oxic and anoxic interfaces in nature. Recall that at neutral pH ferrous iron is rapidly oxidized to ferric iron in the presence of oxygen.
Neat phenomenon - large deposits of ferric iron have been found in ancient sediments which were originally thought to be the result of abiotic oxidation of ferrous iron where the oxygen came from oxygenic photosynthesis. Perhaps these deposits were formed by anoxygenic phototrophs oxidizing ferric iron in anoxic environments.
Ammonium and nitrite-oxidizing bacteria - referred to as the nitrifying bacteria. They use ammonia and nitrite as their energy source - electron source. Nitrosomonas oxidize ammonia and Nitrobacter oxidize nitrite. These bacteria are widespread in soils.
Growth yields from the oxidation of NH₃ or NO₂^- are very small since there is very little energy available from the oxidation of these two compounds. The redox potentials of ammonia to nitrite is 0 volts and nitrite to nitrate is +0.43 Volts and therefore they donate electrons to the electron transport chain at relatively high redox potential electron carriers.
Carbon fixation - Calvin cycle
Summary - chemolithotrophs growing autotrophically require ATP and NADH. NADH generated either by the direct reduction of NAD⁺ by H₂ for the hydrogen oxidizing bacteria or the energy driven reverse electron flow for the other chemolithotrophs.
ATP production - the chemolithotrophs contain cytochromes and quinones like the chemoorganotrophs. With the exception of the hydrogen oxidizing bacteria, the other chemolithotrophs cannot feed electrons into the electron transport chain at NADH level but instead at some intermediate level between NADH and oxygen.
Mixotrophy - chemolithotrophs that can grow on organic carbon as heterotrophs.
Anaerobic respiration - uses an electron acceptor other than oxygen - could be organic or inorganic in nature.
facultative aerobes - are aerobes that can use either oxygen or another electron acceptor such as nitrate.
obligate anaerobes - are anaerobes unable to use oxygen.
Nitrate reduction and denitrification - nitrate as an electron acceptor and reduced to nitrous oxide or dinitrogen gas. This process is called denitrification which is detrimental to agriculture since it represents a loss of nitrogen from the ecosystem.
Enzyme is nitrate reductase which is synthesized under anoxic conditions only. Produces nitrite which is reduced using nitrite reductase.
Nitrite may be reduced to ammonia or reduced to nitrous oxide or dinitrogen gas. (See figure 13.29).
See figure 13.30 for comparison of nitrate reduction with aerobic respiration. The point is less energy from nitrate reduction than aerobic respiration.
Common denitrifiers include species of pseudomonads such as P. fluorescens and P. aeruginosa.

Sulfate - reducing bacteria - sulfate is reduced to hydrogen sulfide. An organic molecules including organic acids, fatty acids, alcohols and H₂ as an electron source = source of energy. H2 produced during the oxidation of lactate diffuses out of the cell and is subsequently oxidized by a hydrogenase leaving the protons outside the cell and transporting the electrons to sulfate. This generates the PMF which can be used to make ATP. There are other types of sulfate reducing bacteria that we will not get into.
Methanogenesis - methane formers. These use carbon dioxide as an electron acceptor