Metabolism I: autotrophs and heterotrophs Flashcards
Autotrophs
What do each of these use as energy source and electron donor?
Thiobacillus thioparus
Thiocapsa roseopersicina
Acidithiobacillus ferrooxidans
Hydrogenophilus thermoluteolus
The ‘anammox’ Bacteria
- autotrophs use CO2(or DIC) a s their source of C. They MUST HAVE a source of energy (energy source) AND a source of reducing power (electron donor) to grow.
- Thiobacillus thioparus uses thiosulfate as both energy source and electron donor. O2is the terminal electron acceptor. Product of respiration is H2O.
[Thiobacillaceae < Nitrosomonadales < Betaproteobacteria < Pseudomonadota] - Thiocapsa roseopersicina uses sulfide as electron donor and electromagnetic radiation as energy source. No terminal electron acceptor as cyclic photophosphorylation used. Product of respiration is S8.
[Chromatiaceae < Chromatiales < Gammaproteobacteria < Pseudomonadota] - Acidithiobacillus ferrooxidans uses ferrous iron (Fe2+) as energy source and electron donor. O2 is terminal electron acceptor. Product of respiration is H2O.
[Acidithiobacillaceae < Acidithiobacillales < Acidithiobacillia < Pseudomonadota] - Hydrogenophilus thermoluteolus uses molecular hydrogen (H2) as energy source and electron donor. O2 is terminal electron acceptor. Product of respiration is H2O
[Hydrogenophilaceae < Hydrogenophilales < Hydrogenophilia < Pseudomonadota] - The ‘anammox’ Bacteria use ammonium (NH4+) as both energy source and electron donor. Nitrite (NO2-) is the terminal electron acceptor. Product of respiration is N2.
[mostly Ca. Brocadiaceae < Ca. Brocadiales < Ca. Brocadiia < Planktomycetota]
More on autotrophs and heterotrophs
heterotrophs
heterotrophs use organo-C compounds as their source of C-and-E. There are specialist functional guilds thereof:
* methanotrophs use methane or methanol(the most reduced C compound) as their C-and-E source. examples:
Methylococcus capsulatus TexasT (if they begin with methano they are archaea) [Methylococcaecae < Methylococcales < Gammaproteobacteria <seudomonadota]
Crenothrix polyspora (uncultivated)
[Crenotrichaceae < Sphingobacteriales < Sphingobacteriia < Bacteroidota]
NB: above is probably really in Gammaproteobacteria!
Methylosinus trichosporium OB3bT [Methylocystaceae < Hyphomicrobiales < Alphaproteobacteria < Pseudomonadota]
* methylotrophs use C1 compounds other than methane as their C-and-E source. A C1compound = compound with no C-C bonds. It can be multi-C though, like trimethylamine ((CH3)3N).
examples: Methylorubrum extorquens AM1 and Methylorubrum podarium FM4T
[Methylobacteriaceae < Hyphomicrobiales <Alphaproteobacteria < Pseudomonadota]
Hyphomicrobium sulfonivorans S1T
[Hyphomicrobiaceae < Hyphomicrobiales < Alphaproteobacteria < Pseudomonadota]
* diazotrophs use N2 gas as their N source but a wide-range of C-and-E compounds.
example: Azotobacter chroococcum DSM 2286T
[Azotobacteriaceae < Pseudomonadales < Gammaproteobacteria < Pseudomonadota]
* fermenters use fermentation rather than respiration – I’m only including here for completeness.
example: Clostridium acetobutylicum WT
[Clostridiaceae < Eubacteriales < Clostridia < Bacillota]
autotrophs have energetic issues
- all of the NADH and succinate entering the respiratory chain of heterotrophs is from the glycolytic pathways (Embden-Meyerhoff pathway in most Eukarya and many Bacteria; Entner-Doudoroff pathway in the Viridiplantae
and many Bacteria; oxidative pentose-phosphate pathway in many Bacteria) and from Krebs’ cycle. - not all heterotrophs have these.
- autotrophs don’t have either. Their C-assimilation does not use these pathways. Their electron donor/energy source dissimilation is usually very direct and uses only short pathways in which NAD+is not reduced to NADH.
- NADH is required to make NADPH, which is needed for all biomass formation.
- as such, autotrophs have to be able to make NADH – they use reverse electron transport.
- Following slides show forward and then reverse electron transport in Thiobacillus thioparus from the Betaproteobacteria.
autotrophs have further energetic issues
How do they get their electrons?
- SO forward electron transport translocates protons into the periplasmic space and builds Δp (proton-motive force) and thus ATP can be made.
- BUT reverse electron transport does the reverse and lowers Δp thus if you need to make NAD(P)H at any given time, you can make less ATP as a result.
- Life is a constant balancing act for them!
- how do they gain their electrons? We will look at one key example – the Lu-Kelly cycle in Paracoccus versutus A2T part of the Alphaproteobacteria. There are other variations of it in other organisms – we don’t care about them! You may see it called “the sox cycle” or “the
Kelly-Friedrich cycle” but Wei-Ping Lu discovered it with Kelly in the early 1980s and deserves credit. All Friedrich’s group did was discovered the genes decades later
[Paracoccus < Paracoccaceae < Rhodobacterales < Alphaproteobacteria < Pseudomonadota] - encoded by the sox operon, so each polypeptide has a name like SoxA, and if e.g. SoxA and SoxX form a protein, it is SoxAX.
- I will show it to you firstly all written out with proper equations and balancing and then drawn as a cycle to show how it all fits.
autotrophs don’t make NADH directly however they use their electron donors very directly so they are coupled to respiratory chain instead of making a pool of NADH, they still though need NADH to make NADPH. So they make NADH by reverse electron transport.
energy conservation in Paracoccus spp. using thiosulfate
Thiosulfate as the energy source:
Thiosulfate (S2O32-) is a chemical compound that serves as an energy source for certain biological processes.
Oxidation of thiosulfate to sulfate:
Thiosulfate is oxidized (loses electrons) to form sulfate (SO42-). This oxidation process also involves the consumption of water.
During this process, 8 electrons are conserved and transferred to cytochrome c (cyt c), which is a protein involved in electron transport.
Thiosulfate binding and initial reaction:
Thiosulfate binds to a protein complex called SoxZY, specifically to the thiosulfate-binding protein.
Within SoxZY, there’s a protein called SoxY which has a cysteine residue with a sulfur-hydrogen group (-SH) on its side chain. Let’s denote this as “SoxZY-SH” and underline the sulfur (S) to remember it later.
The reaction is catalyzed by another protein called SoxAX, which acts as an enzyme with the name L-cysteine S-thiosulfotransferase (EC 2.8.5.2).
The reaction can be represented as follows:
S2O32- + SoxZY-SH + 2 cyt cox → SoxZY-S-S-SO3- + 2 cyt c red + H+
Oxidation of sulfonate group to sulfate:
The terminal sulfonate group (-SO3-) in SoxZY-S-S-SO3- is oxidized (loses electrons) to form sulfate (SO42-).
This oxidation reaction is catalyzed by an enzyme called SoxB, which is known as S-sulfosulfanyl-L-cysteine sulfohydrolase (EC 3.1.6.20).
The sulfate produced is then released from the cell. What remains is the sulfane group (-S-), a part of the thiosulfate molecule.
The reaction can be represented as:
SoxZY-S-S-SO3- + H2O → SoxZY-S-S- + SO42- + 2H+
Oxidation of Sulfane Moiety to Sulfonate:
The pendent sulfane moiety of thiosulfate is oxidized to sulfonate by an enzyme called SoxCD, which is S-sulfanyl-L-cysteine oxidoreductase (EC 1.8.2.6).
The reaction can be represented as:
SoxZY-S-S- + 6 cyt cox + 3 H2O → SoxZY-S-SO3- + 6 cyt cred + 6 H+
Oxidation of Sulfonate Group to Sulfate:
The terminal sulfonate group (-SO3-) is further oxidized into sulfate (SO42-) and liberated by the enzyme SoxB, which is S-sulfosulfanyl-L-cysteine sulfohydrolase (EC 3.1.6.20).
The sulfate formed is then extruded from the cell.
The reaction is similar to step 2, except only one H+ is produced because the other H from the water reacts with the remaining -S group from the original cysteine residue, restoring it.
The reaction can be represented as:
SoxZY-S-SO3- + H2O → SoxZY-SH + SO42- + H+
This is because there is alway 2 sulfates made
paracoccus versutus
can go autotrophically and heterotrophically
Respiration electron transport chain step by step
NADH Dehydrogenase (Complex I):
Located in the inner mitochondrial membrane, Complex I is the first complex in the electron transport chain.
It accepts electrons from NADH generated in previous stages of cellular respiration, such as glycolysis and the citric acid cycle.
Simultaneously, Complex I catalyzes the conversion of NADH to NAD+ and pumps protons (H+) from the mitochondrial matrix into the intermembrane space.
This proton pumping contributes to the formation of a proton gradient across the inner mitochondrial membrane, which is crucial for ATP synthesis.
Succinate Dehydrogenase (Complex II):
Succinate donates its electrons to Complex II.
It is primarily involved in the citric acid cycle, where it catalyzes the conversion of succinate to fumarate.
During this process, electrons from succinate are transferred to FAD (Flavin Adenine Dinucleotide), forming FADH2.
Electrons from Complex II also enter the quinone pool, where quinones become quinols.
Complex II does not directly contribute to proton pumping.
Quinone Pool:
Electrons from both Complex I and II are deposited into the quinone pool.
This process opens gates in Complex I and II, allowing protons to cross the membrane, contributing to the generation of the proton motive force (PMF).
Cytochrome bc1 Complex (Complex III):
Electrons from the quinone pool are transferred to Complex III.
Complex III pumps additional protons across the inner mitochondrial membrane, further contributing to the PMF.
Cytochrome c and Cytochrome c Oxidase (Complex IV):
Electrons are transferred from Complex III to cytochrome c.
Cytochrome c transports electrons to Complex IV.
At Complex IV, electrons are transferred to molecular oxygen, which combines with protons to form water.
The reduction of oxygen at Complex IV is the final step in the electron transport chain.
Proton Motive Force and ATP Synthesis:
The pumping of protons by Complexes I, III, and IV generates the proton motive force (PMF) across the inner mitochondrial membrane.
The proton gradient established by the PMF drives the synthesis of ATP by ATP synthase, which couples the flow of protons back into the mitochondrial matrix to the phosphorylation of ADP to ATP.
This process, known as oxidative phosphorylation, results in the formation of ATP from ADP and inorganic phosphate.
In summary, the electron transport chain consists of a series of protein complexes that facilitate the transfer of electrons from NADH and FADH2 to molecular oxygen, ultimately leading to the production of ATP via oxidative phosphorylation. This process ensures the efficient production of ATP, the energy currency of the cell, to support various cellular activities.
What are the translocation numbers (protons transferred)
4–>2–>4 for most eukarya
