This chapter is about respiration. Yes, plants have mitochondria in all living cells and those mitochondria carry out the usual steps of respiration. A common misconception is that plants do not do respiration. I hope you will remember that plant cells have mitochondria and do normal respiration. It is the only way to get energy for plant survival when the sunlight is insufficient to drive photosynthesis (such as at night or on an overcast day). Plant roots get their energy exclusively from respiration. Flowers and fruits depend on respiration as well since chlorophyll is not abundant in most maturing flowers or fruits (and certainly is insufficient to meet their vast energy needs).
I really like this chapter because it shows you right up front (Fig 6.1 page 113) that respiration is not just about glucose being burned as a fuel. There are many compounds that may serve as the fuel. There are several ways to get sugars, amino acids, lipids, and even nitrogenous bases into this pathway as fuel. The intermediates of the pathway can be taken out, so the respiration pathway can also be a source of molecules for synthetic processes as well (notice the double-heads on many of the arrows). If you have never heard of respiration using multiple fuels or being the basis for biosynthesis before, I hope this concept will be a major lesson for you.
In addition to the two pyruvate, glycolysis generates two ATP and 2 NADH + H+. These yields represent a tiny fraction of the total energy found in a glucose molecule. The remaining energy will come out later in the pathway. Your book makes one real mis-statement in my opinion on page 117:"The synthesis of ATP from the energy of pyruvic acid occurs in the second phase of respiration, the Krebs cycle." As you will see, there is very little ATP generated in the Krebs cycle...most of it comes out even later in the pathway.
Before the Krebs cycle can begin, the pyruvate must be taken into the mitochondrion (Fig 6.5). In doing that, one of the three carbon atoms of pyruvate is removed as CO2 and the corresponding hydrogens are attached to NAD+. The remaining two carbons are attached to Coenzyme A.
One enzyme of note, succinate dehydrogenase, is not a solute in the matrix; it is attached to the inner membrane of the mitochondrion (the endosymbiont cell membrane). For this reason, we can homogenize cauliflower in a blender and spin down "mitochondria" (maybe some are whole, but many are "vesicles" = fractions of mitochondria) and this enzyme into a pellet. The pellet can then be brought back into solution and used in the respiration assay you used in Cell and Molecular Biology (BIO 221). Obviously you could not do this with other enzymes in the path. Why not?
While the Krebs cycle gives off the remaining two carbons of pyruvate as CO2, the more important product of these steps is the attachment of the hydrogen atoms to NAD+. For every glucose metabolized, eight NADH + H+ are made. These will yield tremendous energy (ATP) in the next part of the pathway. The Krebs cycle also yields a small amount of substrate-level ATP...two...big deal. Another interesting compound is ubiquinol. Your old-fashioned texts probably told you "FADH2" which does participate but is not a mobile trap for H+ and e-. Instead the protons and electrons are transferred from FADH2 to ubiquinone, which becomes ubiquinol (Fig 6.7 pg 119). Maybe your concept of respiration is modernized here?! Remember some of what you read in books is "factoid" and therefore subject to change. It keeps our discipline of biology constantly upgrading and dynamic. As scientists, we love that part of it!
The carriers are mostly membrane proteins that contain heme. Most are cytochromes (Fig 6.10). Heme contains an iron atom that, due to its two valence states (Fe2+ and Fe3+), is responsible for holding and releasing the electrons being passed. Cyanide blocks this part of respiration by "chelating" (= removing) the iron from the heme of cytochromes. Ubiquinol is a quinone that works differently: the electrons and protons are held in the conversion of carbonyl oxygen to a hydroxyl group (Fig 6.7). This quinone conversion is precisely what you observed in studying the potato enzyme, polyphenoloxidase, in Principles of Biology. In that case, catechol was the polyphenol reactant and the product, o-quinone, was converted to a red-brown color. Ubiquinone is one of the carriers that actually transport H+ across the inner membrane.
With all of this in mind, why do you think evolution resulted in succinate dehydrogenase being membrane-bound? (Hint: compare Figs 6.6 and 6.8)
The accumulation of H+ in the intermembrane space (between the inner and outer membranes = between the endosymbiont cell membrane and the vesicle membrane) represents a conservation of potential energy as a gradient of protons is achieved. The protons (H+) leak back into the matrix through a transport protein called ATP synthase (Fig 6.12) and the collapse of the proton gradient releases the potential energy held in the gradient. This energy is used to make ATP. The system can generate about 3 ATP for every NADH + H+. Because of the large number of NADH + H+ made in previous steps, this synthesis of ATP is massive. Most of the ATP in respiration is made here.
The protons and electrons passed in this sytem ultimately are attached to an oxygen atom (making a molecule of water). This explains our human need for oxygen. It also helps explain why cyanide is so toxic to us.
To me, the cyanide-resistant pathway is interesting, because it provides a way for a plant to use cyanide as a pesticide. Many plant species place cyanide in their seeds and then protect those seeds with heavy pit walls. Any animal persistent enough to penetrate the pit wall will be rewarded with a poisonous meal. The cyanide of peach pits was likely the chemotherapeutic ingredient of Laetrile (a controversial cancer therapy drug never approved for use in the US).
Assuming that this strategy works, the next problem is how to get your seeds to sprout since they contain cyanide. Obviously the embryos have to use a cyanide-resistant respiration pathway (Fig 6.16). This provides substrate-level ATP for growth until the cyanide is diluted or metabolized away.
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