Chapter 14 - Metabolic diversity of Microorganisms

Which organisms use PMF

All mechanisms (except fermentation) use the proton motive force for the synthesis of ATP (oxidative and photo-phosphorylation)

oxygenic vs anoxygenic photosynthesis

Oxygenic:

• Electron donor: water

• Produces: oxygen

• Your average photosynthesis reaction

• Uses both photosystems

Anoxygenic:

• Electron donor: not water, other substances such as hydrogen sulfide, hydrogen, iron. (Chemotrophy)

• Produces: not oxygen, other things such as elemental sulfur

• uses only one photosystem

What cells do photosynthesis?

• Phototrophs

• AND a lot of bacteria

What colors are phototrophs

They come in all colors

• People assume they are only green because of chlorophyll but this is not true

Does photosynthesis only produce oxygen?

There is also lots of anoxygenic photosynthesis

• anoxygenic photosynthesis is a type of photosynthesis that does not produce oxygen. It’s carried out by certain bacteria (like purple sulfur bacteria) using molecules other than water (like hydrogen sulfide) as electron donors:

  CO₂ + 2H₂S + light → CH₂O + H₂O + 2S

Problem with Oxygen in atmosphere

Creation of ozone upon uv light

Is photosynthesis well characterized?

Yes but there are many uncharacterized phototrophs in oceans

Two types of organisms doing photosynthesis

Oxygenic photosynthesis

• Electron source: Water (H₂O) — they split water molecules by oxidation releasing electrons, releasing O₂

• These electrons flow to a metabolic pathway that can fix CO₂

• Since CO₂ fixation is expensive, light is used to turn ADP into ATP and this ATP also helps with CO₂ fixation.

  • This ATP is ALSO used for water splitting

Anoxygenic photosynthesis

• An electron donor like H₂S is used and is oxidized to SO₄^2- to release electrons that go towards carbon fixation

• Here too, light is used to turn ADP into ATP, this energy is used for carbon fixation.

  • Here the ATP is not needed to help with water splitting because H₂S is a much better electron donor.

Why is water used as an electron donor if it is a poor donor?

Is is available, very abundant

Name of scheme in oxygenic photosynthesis

Z-scheme

Z-scheme pathway (oxygenic photosynthesis)

• Electrons are accepted in photosystem II, these electrons come from water splitting. These are accepted by P680 which is a really good electron acceptor.

• The electron in the photosystem is now excited by light and goes up in energy to an excited state. This causes P680 to become a really good electron donor.

• The electron goes through the electron transport chain (proton motive force!!) and slowly goes down in energy and moves into photosystem I. (P700)

• In photosystem I it is excited again by light and eventually the electron moves into NAD(P)H

Photosystem I vs II

Photosystem I:

• Produces NAD(P)H

• Has P700 which absorbs light

• Is second in the light dependent reactions

Photosystem II:

• Splits water to generate:

  • Electrons (for the chain)

  • Protons (for ATP synthesis)

  • Oxygen (by product)

• Has P680 to absorb light

• First in the chain.

What happens if there are too many NADH molecules in oxygenic photosynthesis (so too many electrons)

• Organisms will shut down photosystem II

• Instead they create a proton motive force

• So photosystem I still excites the electrons, then the electron falls down and releases energy which is used to create ATP.

• This also means there is no oxygen formed because that only happens in photosystem II.

Heterocyst’s and photosynthesis

• In the heterocyst’s photosystem II is switched off.

• They only have photosystem I

• Photosystem II produces oxygen and we don’t want that for the nitrogenase.

How are the electrons accepted in the photosystem?

By chlorophyll which love to receive oxygen

Electron flow in Anoxygenic photosynthesis

• Pretty much only found in prokaryotes not eukaryotes

• Contains bacteriochlorophyll a (instead of just chlorophyll)

• Red or infrared light excites the pigment (P870)

• The cyclic electron flow generates proton motive force.

• Found in purple-sulfur bacteria

Reduction of NAD in anoxygenic photosynthesis

• Even though electrons are cycling around, they cannot be used to reduce NAD (low reduction power) which is necessary for CO₂ fixation in autotrophs.

• Therefore reverse electron transport is used.

• This allows reduction of NAD to NADH which is then used for CO2 fixation.

Through what process is CO2 reduced

The Calvin cycle

What is the most abundant enzyme on the planet?

• RubisCO

• Pretty inefficient → therefore you require a lot

• ¼ enzymes go wrong

• The enzyme does not need to get better, no evolutionary pressure

• Instead of making 3-P-glycerate it makes 2-P-glycolate

Calvin cycle general steps

1. Carboxylation 6CO₂ molecules are turned into 12 C3 molecules with phosphate. This is done by rubisco.

2. ATP & NADPH is invested producing Ribulose 1,5 biphosphate

3. 2 C3 molecules are lost so we are left with 10 C3 molecules

4. With ATP the 10 C3 molecules are turned into 6 C5 molecules.

chemoorganotrophy vs chemolithotrophy

Chemoorganotrophy:

• Uses organic compounds are an electron donor

• Uses carbon from substrate for cell material.

• Does fermentation

Chemolithotrophy:

• Uses an inorganic electron donor

• Fix carbon from CO2

Hetero vs. Autotrophs

Hetero: carbon source is organic molecules

Auto: carbon source is carbon dioxide

The problem with chemolithotrophy

• Chemolithotrophs use inorganic compounds as electron donors (energy source)

• For that reason they are often autotrophic, and get their C from CO2.

• The problem is that to do this you need another electron donor. (NADPH)

• To be able to form NADPH from NADP, an electron donor is needed with a sufficiently negative potential.

• For example H2 meets this requirement (above NADH in redox tower) but H2S does not (below NADH in redox tower)

Solutions for weak electron donors in chemolithotrophy

1. Coupling to ATP hydrolysis

2. Reversed electron transport

3. Electron bifurcation (mostly used in anaerobes)

Hydrogen oxidizing bacteria

• organisms that combine hydrogen and oxygen → creates lots of energy

• Have very fast growth

• Many different species

• Are chemolitho-autotrophs

• Growth at low oxygen concentrations, because the hydrogenases are oxygen sensitive

• Calvin-cycle for carbon fixation

• Hydrogen is almost entirely derived from fermentative conversions

Electron transport scheme of hydrogen oxidizing bacteria

• Hydrogen is used to generate proton motive force

• Hydrogen is split up, protons are dumped out. Electrons are used to further the chain

• Electrons go through the chain.

• Proton motive force is created and can be used to create ATP

• Additionally hydrogen is used to create NADH, this NADH is used to fix CO2

Oxidation of sulfur compounds

• Sulfur can be an electron donor in this case

• Sulfite (H₂S) can be taken apart and be converted into sulfate (SO₄^2-)

• Can have sulfur globules for later use.

• Many sulfur oxidizers are acid tolerant because they are producing sulfuric acid.

Sulfur reducing bacteria

• They are often found in seawater where there is a lot of sulfate

• Black sand on the beach is from sulfur reducing bacteria

Iron bacteria

• Use iron as their electron donor.

• Use Fe²⁺ and some oxygen to make Fe⁺³ , water and ATP

• Very slow growth

• This is because iron is a poor electron donor.

• When Fe³⁺ reacts with water, it forms insoluble iron. This is a thermodynamic advantage.

• Usually live in acidic environments

Iron bacteria without oxygen

Some can use nitrate as their electron acceptor

Electron transport chain with iron bacteria

• Fe²⁺ is converted to Fe³⁺ this happens on the outside of the cell to prevent insoluble iron inside the cell.

• Electrons are used to generate energy.

Nitrifying bacteria

• Are widespread in soil, water and biofilters

• They oxidize ammonia: NH₃ → NO₂^-

• And then oxidize nitrite: NO₂^- → NO₃^-

• Then there are separate organisms that can take nitrite (which still has some electrons), put the electrons on oxygen to make nitrate and some ATP.

• These two reactions often occur in two separate organisms because nitrite is a very toxic molecule. However recently it was discovered that there are organisms who can do both reactions. (Called Nitrospira)

Electron transport chain with nitrifying bacteria

• Ammonia is oxidized

• Electrons flow via cytochromes

• The cytochromes are linked to oxygen, protons are pumped out

• Protons go back in and produce ATP

Why do Nitrifying bacteria have a low growth rate and yield

• They make a toxic intermediate (nitrite, NO₂^- )

• The energy drop in the redox tower is not very high.

• They are autotrophs so lots of energy goes to CO2 fixation.

• Because NO₂^-/NH₃ is below NADH in the redox tower, reverse electron transport is needed to build the NADH/NADPH pool which is needed for CO2 fixation.

How does the ANAMMOX process work in the absence of oxygen?

• With nitrite.

• Is done by ANAMMOX bacteria

• Reaction: NH₃ + NO₂^- → N₂ + 2H₂O + xATP

• So NH₃ is the electron donor and NO₂^- the electron acceptor.

• Has a large vacuole called the anammoxosome, separate compartment for toxic intermediate.

Anammoxosome

• Large vacuole found in bacteria that do not use oxygen.

• Has a special membrane that protects cell against toxic intermediate H₂N=NH₂ (Hydrazine)

• Hydrazine is used by rockets as fuel.

Special role of NO₂^- in creation of hydrazine

• NO₂^- acts as electron acceptor for the oxidation of NH₃

• And as electron donor for the reduction of CO₂

Two types of sulfate-reducing bacteria

• Dissimilatory sulfate reduction: use of sulfate for respiration; production of lots of H₂S

• Assimilatory sulfate reduction: incorporation of sulfate for biosynthesis (synthesis of cysteine, methionine and other organic sulfur compounds)

Halorespiration

• Respiration with all kinds of chloride compounds

• Are often discovered in polluted sites

Other electron acceptors

• Fe³⁺

• Mn⁴⁺

• AsO₄^3-

Organisms that use CO2 as their electron acceptor

• Very abundant but not very good.

  • Often occurs in places where there are not many other electron acceptors available.

• Methanogens do this: Makes methane from CO2 (strictly anaerobic)

• Acetogenesis: makes acetic acid (vinegar)

Assimilatory metabolism

• Reductions to make cell material (amino acids)

• Small amounts

• No excretion

• Costs energy

Dissimilatory metabolism

• Reductions meant for obtaining energy (ATP)

• Large amounts

• Excretion of the reduced compounds.

What kind of bacteria that do something with nitrogen are out there?