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  • Energy that can be acquired by the organism's respiration reaction

    • 　Now you are asked to calculate the "total difference in standard Gibbs energy before and after the chemical reaction". This is a long word, and it is 100% up to you again. Let's get used to it by solving the example questions.

      　First, let's consider the standard Gibbs energy of formation for carbon dioxide (CO2), a familiar compound in biological metabolism: the elements that make up CO2 are carbon (C) and oxygen (O). The stable states of each element on its own are carbon (C) and oxygen molecules (O2), and the Gibbs energy required to produce one mole of CO2 from C and O2 is -394.4 (kJ/mol) as the standard Gibbs energy of formation of CO2 (gas). This is reported as an experimental value and can be found in the Chemistry Handbook and other publications.

      Fig. 1


      (Why the minus sign? Because from the point of view of the system (CO2 formation reaction), it is in the direction of losing energy, just as combining C and O2 (burning black coal) produces heat.)

    • 　Organisms use oxygen to oxidize organic matter to obtain energy (respiration). The figure below shows the reaction of oxidation of organic matter by respiration, assuming formaldehyde as the simplest organic matter. Below each substance is the standard Gibbs energy of formation for each substance. The total energy of the chemical reaction in its product form (right side) minus the total energy of the original form (left side) (⊿∑Gf0) is the energy that the organism can acquire. The reason why the energy difference has a negative value is because, from the point of view of the reaction system, the organism is losing energy, which it can gain.

      Fig. 2

      ※　The standard Gibbs energy of formation of O2 in its standard state is 0 (kJ/mol), but dissolving it in water produces energy (16.3 kJ/mol). Assuming respiration in water, we used O2(aq) as above. Also, the energy used in the calculation changes depending on whether the organisms in the water take in CO2 as CO2(aq) or as H2CO3 or HCO3-. In this course, I have dealt with this issue in an appropriate manner. Please forgive me.

      　As in this example, the standard Gibbs energy of formation for each substance is noted below the reaction equation, and the total difference (⊿∑Gf0) is calculated before and after the reaction (left side: original form, right side: product form). The standard Gibbs energy of formation (Gf0) for each substance is an important thermodynamic constant and is summarized in the table below.

      Fig. 3

    • 圖示 資料夾
      Table of Standard Gibbs Energy of Formation (download) 資料夾

      Use it as you will learn in this course. When using it in your research, double-check the values with the original references in the citation.



    • 　Next, in the absence of oxygen, organisms appear that use nitric acid as an oxidant to respire. They are known as nitrate-reducing bacteria.

      Fig. 4


      　Although nitrate respiration appears to provide slightly less energy than oxygen respiration, nitrate reduction actually occurs in two stages. Nitrate-reducing bacteria respire NO3- and exhale NO2-, then nitrite-reducing bacteria respire NO2- and exhale N2. If divided into two stages, it would be much less efficient than oxygen respiration.


      　Assume an environment where there is little oxygen and nitric acid, but lots of manganese oxide (MnO2) and organic matter. The environment would be like a pool of water where manganese oxide minerals are exposed and organic matter has accumulated.

      Fig. 5


      　Some organisms (prokaryotes) have this specific form of respiration. Some organisms respire iron hydroxide as an oxidant.

      Fig. 6

      The energy gained is also much less, 110 kJ.

       

      　Oxygen and even nitric acid are gone, and without oxidized minerals such as manganese oxide and iron hydroxide, organisms that use sulfuric acid as an oxidizing agent will show their faces.

      Fig. 7


      　Of the dissolved sulfur compounds in the aqueous environment, sulfuric acid is the most energy-intensive to synthesize from its constituent elements (S and O). Stripping oxygen from such a stable compound requires a great deal of energy, and the energy available from organic matter is used to do so. This reduces the energy available to the organism, which is quite inefficient. It is precisely because of this harsh situation that bacteria with the special ability to reduce sulfuric acid dominate here and there.


      　When sulfuric acid reduction occurs, hydrogen sulfide (H2S) is produced as a reaction product. Hydrogen sulfide is what gives off the smell of rotting in a ditch river (often described as the smell of rotten eggs).　Sulfuric acid reduction occurs in places where large amounts of organic matter accumulate for long periods of time. However, the sulfuric acid ions that are the source of the sulfuric acid must be present.

       

      　A natural environment with lots of organic matter and an abundance of sulfate ions is marine sediments. When marine sediments are sampled, you can sometimes smell hydrogen sulfide (because seawater is rich in dissolved sulfuric acid). If sulfate reduction occurs in marine sediments and there is zero oxygen in the bottom water, hydrogen sulfide leaches out of the sediments and accumulates in the bottom water. Because hydrogen sulfide is highly poisonous, it can cause extreme degradation of the bottom layer environment. When this hydrogen sulfide meets oxygen, it reacts quickly to form S and water (H2O). S is solid and colloidal. When bottom waters rise to the surface for some reason, the S colloids give the ocean surface a bluish-white color. This is called a blue tide. Solid S also reacts directly with oxygen to form SO42-. Water in which blue tides occur is hypoxic, which is a matter of life and death for surface organisms. By the way, blue tides do not occur in eutrophic lakes (not to be confused with blue-green algae). This is because freshwater contains few sulfate ions.

      ※The chemistry of sediments is explained in the course on the chemistry of sediments in "Marine Chemistry" (OOKI in charge).