2. Bacterial Energetic

Anaerobic Respiration in Bacteria

While bacteria can produce ATP and recycle NAD+ through fermentation, they are also capable of generating a great deal of ATP through a process called anaerobic respiration.

Before going forward, be warned that he assumes a lot of stuff covered in later lectures, namely The Citric Acid Cycle and proton gradients. Do not despair, just plan on re-visiting this lecture once you learn those topics.

Cellular Respiration

  • Glycolysis and Citric Acid Cycle
  • Oxygen is the final electron acceptor

Fermentation

  • Increased glycolysis and alt pathways to regenerate NAD+
  • Oxygen not used

Anaerobic Respiration

  • Occurs in anaerobic organisms that grow without oxygen
  • Glycolysis and the Citric Acid Cycle occur, but oxygen is not the electron acceptor; the final acceptors are inorganic molecules.
  • ATP synthesis here still relies on a proton gradient (a topic covered in great detail later).

Anaerobic Bacteria

Bacteria that grow in the absence of oxygen. Classified by the type of final electron acceptor.

Type | Acceptor | Final Product | Free Energy (kJ/2e-)
Denitrifier | nitrate (NO3) or nitrite (NO2) | dinitrogen (N2) |  -209.46
Metal Reducer | Fe(III), Mn (IV), Co(III), etc. | Fe(II) | -206.12
Sulfidogen | sulfate (SO42−)or sulfur | HS- | -20.24
Methanogen | CO2 | methane (CH4) | -14.58

Compare with Aerobic: 1/2 O2 -> H20 | -219.07

So the most exergonic respirations occur in denitrifiers. If all materials were in equal abundance, denitrifies would flourish, producing the most ATP. But they don’t dominate because in most environments, metal ions are more abundant. Thus, metal reducers typically dominate.

The focus in this lecture, however, is on denitrifies.

Definition of Denitrification (more on this shortly). Note that it produces water.
2NO3 + 12 H+ + 10e ===> N2 + 6H2O

Economic Impact of Denitrifiers

Since denitrifiers use nitrate as a final electron acceptor, which is converted to dinitrogen, their presence in soil results in a loss of nitrate in farmlands. This means farmers need to invest in fertilizers to replenish the lost nitrate–nitrate is a critical nutrient for plants.

Unfortunately, this fertilizer is often washed away, accumulating in rivers and lakes, which then needs to be removed in water treatment plants, incurring most cost. Water treatment is necessary because excess nitrate in drinking water can lead to health issues, especially in babies. Specifically, nitrate oxidizes hemoglobin (see earlier lecture on this) putting its bound-iron in the ferric 3+ state. This creates methemoglobin,  which is unable to bind to oxygen and can lead to hypoxia and death.

Secondary impact of fertilizer in water is that nitrate accumulation stimulates the growth of phytoplankton. As phytoplankton flourishes, it begins consuming large amounts of oxygen, which in turn oxygen-starves (and eventually kills) other aerobic organisms–fish!

The steps of denitrification

The process of Denitrification is a step-wise reduction process:
NO3 ===> NO2
NO2 ===> N2O
N2O  ===> N2

Final outcome:
2NO3 + 12 H+ + 10e ===> N2 + 6H2O

But each step requires electrons. The rest of the lecture focuses on the mechanics of this process.

Enzymes and Co-factors Involved in Denitrification

Start by looking at both Gram Positive and Gram Negative Bacteria.

image by Graevemoore at Wikipedia
image by Graevemoore at Wikipedia

Both types of bacteria have a cell membrane that separate the periplasm from the cytoplasm. Electron acceptors are embedded in the walls of this membrane.

The first acceptor is the hydrophobic Coenzyme Q, which accepts protons and electrons from a variety of sources, notably NADH. When so reduced, it’s called ubiquonol.

Ubiquonol diffuses within the membrane of the cell to transfer its electrons to enzymes. In particular, it interacts with Nitrate Reductase as shown below. This in turn releases protons from Coenzyme Q into the periplasm, which helps create a proton gradient.

Nitrate Reductase
copyright HarvardX, taken from MCB63X lecture slide.

The proton gradient is further amplified by the consumption of the two protons that are converted into H2O during the reduction of nitrate. Nitrite are able to escape the cytoplasm by the nitrite transport. A second transport protein allows for the import into the cytoplasm of nitrate. Together they limit the accumulation of nitrate inside the cell.

The remaining reduction steps occur in the periplasm:

2H+ + Nitrite —(Nitrite reductase)—> NO + H2O
2NO + 2H+ –> N2O + H2O : occurs quickly to limit the toxicity of NO
N2O + H2O —(Nitrous oxide reductase)—> N2 + H2O

The final dinitrogen then diffuses out of the bacteria as a gas to accumulate in the environment.

As with the first reduction, the last three reductions require electrons.

In the first reaction, the electrons were provided to the reductase by ubiquonol. But ubiquonol is too hydrophobic to deliver electrons to the enzymes in the periplasm. Instead, ubiquonol transports its electrons to a membrane-bound complex called Complex III. First, the electrons in Complex III are transported to the periplasm side of the complex. Then they’re transferred to a molecule periplasm-friendly called cytochrome c.

Reduced cytochrome c interacts with the various reductase in the periplasm. Thus it serves as an electron shuttle.

Nitrate Reduction
copyright HarvardX, taken from MCB63X lecture slide.

Note that the Complex III also transports protons from the cytoplasm to the periplasm, again increasing the proton gradient. In the end, there’s enough of a protein gradient to drive ATP synthesis. This mechanism of synthesis will be discussed in greater detail later.

In the end this lecture demonstrates that anaerobic organisms are capable of generating plenty of energy on their own.

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