Chapter 6 Capturing and storing energy: photosynthesis
Chapter summary:
- Living organisms have found ways to capture sun light energy and store it in the form of high energy electrons on carbon atoms, thus becoming organic carbon
- This requires electrons themselves and energy to ‘attach’ electrons on organic carbon.
- Photosynthesis has found a set of magical molecules, chlorophylls, capable of capturing photonic energy to steal electrons from the oxygen atom by breaking the \(H_2O\) molecule, releasing \(O_2\)
- Chlorophyll then manages to energize the electron stolen from oxygen and ‘ship’ them onto the NADP electron transfer molecule
- Photosynthesis uses the same energy currency ATP to ‘attach’ electrons on organic carbon, and uses the same Proton Motive Force to synthesize ATP
- The capture of electrons and the synthesis of ATP need light and are refered to the light reactions
- The ‘attachments’ of electrons onto carbon occurs in the Calvin cycle (C3 plants), do not require light and are referred to as the dark reactions
- C4 and CAM plants have found strategies to avoid photorespiration or the parasitic effect of \(O_2\) during the dark reactions
In the previous chapter, we have seen the way life has found to release the energy stored in high energy electrons on organic molecules. The secret is that in an aerobic environment with the atoms of oxygen in the dioxygen molecule being so eager to capture electrons, the electrons can freely and will naturally transfer from the organic molecules to oxygen. This electron transfer releases energy. We have seen that in the case of methane combustion, the electron transfer is direct, leading to the release of ephemeral heat and light, resulting in a large and sudden increase of entropy. But this type of energy release is just not sustainable for organisms which must find ways to minimize the energy release in the form of heat, and have a way to release the energy exactly where it is needed.
It does need an intermediate and ubiquitous storage of energy. The secret is the phosphoanhydride bond of the ATP molecule, which can temporarily store lots of energy without the involvement of direct electron transfer. In the case of the oxidative phosphorylation, the formation of the phosphoanhydride bonds is thought to be mechanically induced between ADP and a phosphoryl group during the rotation of the ATPase, itself powered by a proton flow maintained between compartments. In the end the electron transfer only indirectly leads to the formation of ATP, by powering the proton pumps. It is thus fascinating that the release of the energy chemically stored onto high energy electrons on organic molecules involves many small steps, which essentially prevent the direct transfer from the electron donor to the acceptor, which would lead to combustion…
The entire machinery works, in the long run, if somehow the source of organic molecules (= the source of electrons) is replenished, otherwise with a finite amount of organic molecules, the respiration process would eventually deplete all organic molecules on earth. So the corollary to the energy release in respiration, is the capture and storage of energy in a chemical form. And this is where it is very useful to be on a planet close enough to its star such that it receives enough but not too much energy. One of life’s secret has been to be able to capture this allochthonous source of energy, i.e., sunlight, and store it, and now you know in what form: in the form of high energy electrons onto organic molecules, and specifically on the carbon atoms as a first step. This chapter provides enough of the details of photosynthesis processes that lead to the formation of carbohydrates.
6.1 Requirements to store energy on organic molecules
The famous “for dust thou art, and unto dust shalt thou return” from Genesis (3:19; first book of the Hebrew Bible), is the oldest known description of what inorganic and organic molecules are: inorganic molecules correspond to the ‘dust’ in the quote, while organic molecules exist only as a temporary reprieve time on planet earth. Indeed, the widespread occurrence of dioxygen on planet earth imposes that in the presence of \(O_2\), the stable state of CHNSP atoms be the fully oxidized state. By now, we know that the fully oxidized state of these 5 atoms corresponds \(H_2O\), \(CO_2\) (or \(CO_3^{2-}\) or conjugated acids in water; Figure 2.6), \(NO_3^-\), \(SO_4^{2-}\), and \(PO_4^{3-}\) (and conjugated acids in water; Figure 2.7). In other words, the normal stable state of CHNSP on our planet is really ‘dust’ where CHNSP have ‘no’ available energy stored on them. Remember, it is the molecules with the -ate suffix: carbonate, nitrate, sulfate, and phosphate.
What about this incredible life on our planet then? Yes, the big difference is that among CHNSP, the C, N, and S atoms have gained high energy electrons and have managed to keep the ‘electron kleptomaniac’ oxygen atom away enough from them. We know that in organic molecules, the C, N, and S atoms are present in some reduced form, while the P atom always stays oxidized in the phosphate or phosphoryl form. Hydrogen atoms, are always on an oxidized state, i.e., that they lose their electron to all other atoms. The N and S atoms always are fully reduced (disulfide bridge in proteins being an exception), i.e., that they each have 8 electrons for themselves and therefore have oxidation state of \(5-8 = -3\) for nitrogen and \(6-8 = -2\) for sulfur. The carbon atom is the one that behaves as the adjustment variable, as it can have from 1 to 7 electrons for itself for oxidation states or \(4-1 = +3\) to \(4-7 = -3\) (Table 2.1).
In the end, life has managed to store electrons on only C, N, and S atoms. But on which atom does it happen first? Or does it happen in all three at the same time? Theoretically, it could really happen on all three atoms. An ideal atom for storing energy is an atom that is not scarce in the environment, for which a minimum of energy would be required to store high energy electrons, and that would be stable enough even when having oxygen bonded to it in addition to other atoms. Well, there is actually only one atom among C, N, and S able to do all that, and that atom is the carbon atom. This is not to say that N and S cannot eventually store electrons. They absolutely do, eventually. It is to say that the entry point for electron storage in life is the carbon atom.
If the stable state of carbon in the aerobic environment of planet earth is carbon dioxide or carbonates where the carbon atom’s electrons have been stripped away, then there must be a mechanism to ‘beat’ the ambient thermodynamics. Specifically, there must be a source of electrons, a mechanism for energizing the electrons, to ‘attach’ them on the carbon atoms, and prevent the electrons to automatically be stripped away by \(O_2\). The source of electrons is the oxygen atom of water, and the mechanism is called photosynthesis. No, there is no error. Although we have said that oxygen, because of its electronegativity, does not donate electrons to CHNSP, under enough allochthonous energy, it can and will. In photosynthesis, this energy is light, and this energy is strong enough to strip electrons from the oxygen atom of the \(H_2O\) molecule in a reaction that we call photolysis.
In summary, the entry point for electron storage in life requires these primary conditions:
- a source of electrons
- a mechanism to strip these electrons from their source
- a mechanism to energize these electrons
- the energy to ‘attach’ these electrons onto the \(C\) of \(CO_2\)
- a mechanism to ‘attach’ these electrons onto \(C\) of \(CO_2\)
These five conditions listed above occur during two major phases referred to as the light reactions (conditions 1 to 4 included), which occur in the presence of light, and the carbon reactions or dark reactions (conditions 4 and 5), which do not require light to occur.