THE ELECTRON FLOW PATHWAYS

Little is known about the electron flow pathways when Chloroflexus oxidizes to S° and fixes CO2, but it seems reasonable to suppose that NAD is reduced by reverse electron flow from the MQ pool in analogy to the mechanism used by the purple sulfur bacteria (Chapter 9). 

The use of generic electron sources and sinks and generic electron flow pathways makes the similarities and interrelationships of the major reactions in organic chemistry become obvious. The electron flow pathways become the building blocks of even complex organic reaction mechanisms, so all the mechanisms seem to flow from first principles. 

Until you have the principles of mechanistic organic chemistry thoroughly mastered, it is best to restrict your mechanistic proposals to simple combinations of the electron flow pathways, shown in Chapter 7. You may see a shortcut that with several arrows would allow you to transform the lines and dots of the Lewis structure of the reactant into the lines and dots of the product, but that is not the point of it. What you are trying to do with arrows is guess what is actually going on in the reaction, and for that you should use... 

As a start toward this, the Appendix gathers together important tools a p/fa chart, a bond-strength table, a list of sources and sinks, the electron flow pathways, trends, general rules, and other useful items. Continue to customize your toolbox with any valuable tools that you need. 

Although it is tempting to get the problem over with by using a burst of arrows and as few steps as possible, our objective is to write a reasonable hypothesis, not necessarily the shortest one. Construct your mechanistic sentences with known, tested words, the electron flow pathways. Mechanistic steps that you invent as a beginner may not be reasonable. Selecting from known pathways turns an apparent open-ended question into a simpler multiple-choice question. 

Armed with the tools that we have learned in the previous chapters, we can predict where the lowest-energy path may go. The electron flow pathways are the trails to guide us in this wilderness of an unfamiliar energy surface. Some trails may dead-end in high valleys that have no reasonable exit other than the one we came in. Others may lead us to a low point (side product) on the energy surface but not the lowest accessible point (major product). The reacting partners are also exploring these dead ends, and very few reactions produce only one product. 

Fig. 1. The electron flow pathways of non-cyclic- and cyclic photophosphorylation in the plant kingdom and the cyanobacteria. Electron flow in non-cyclic photophosphorylation extends from HjO to NADP and involves PSI and PSIl, whereas that in cyclic photophospho lation (shown within the heavy dashed rectangle involves only PSI and follows a cyclic path. This cyclic path is composed of the P700->Fd and hc-complex- P700 (which also occur in non-cyclic photophosphorylation) plus the Fd->bc-complex section (shown with a dashed arrow) that links them Fd = ferredoxin Pheo = pheo-phytin (PQ) = plastoquinone, mobile in the lipid bilayer and exchanging with PQ at the Pg site PC = plastocyanin.

Fig.4. The electron flow pathway of non-cyclic photophosphorylation in green sulfur bacteria. P840 = P840 at the ground state energy level P840 = P840 at its excited S, energy ievel after absorbing a photon of iight (hv) of the appropriate wavelength BChl = bacteriochlorophyll a Bpheo = bacteriopheophytin a Fd = ferredoxin [Q] = probably menaquinone.

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