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B1. General Oxidizing Agents

Oxidizing agents are required to oxidize organic molecules. In organic lab, you never used dioxygen as an oxidizing agent. It is difficult to limit the extent of oxidation using dioxygen. In addition, side reactions are likely given the nature of the reactive oxygen reduction products. (The mechanisms of combustion reactions of organic molecules with dioxygen to produce carbon dioxide and water are very complicated.)

Figure: mechanisms of combustion reactions


CH4 --> CH3. + H .
O2 --> 2 O.


CH4 + H . --> CH3. + H2
CH4 + HO . --> CH3. + H2O
CH3. + O . --> CH2O + H.

CH2O + HO . -> CHO. + H2O

CH2O + H . -> CHO. + H2
CHO. --> CO + H.
CO + HO . -> CO2 + H.


H. + O2 --> HO. + O.


H . + R. + M-> RH + M*

after Chemistry, 5th ed. Zumdahl. pg 1097

 In organic lab, other oxidizing agents are often used, including permanganate and chromate.

Figure: permanganate

Figure: chromate

Oxygen can often be inserted into a molecule in a nonoxidative process by hydration of an alkene to an alcohol (a readily reversible reaction), which could then be oxidized to either an aldehyde/ketone or carboxylic acid using an appropriate oxidizing agent.

Most biological oxidation reactions (such as those found in glycolysis, Kreb Cycle, and fatty acid oxidation) do not use dioxygen as the immediate oxidizing agent. Rather they use nicotinamide adeninine dinucleotide (NAD+) or flavin adenine dinucleotide (FAD) as oxidizing agents, which get reduced. Enzymes that uses these oxidizing agents are usally called dehydrogenases. Dioxygen can also be used to introduce oxygen atoms into biological molecules in oxidative reactions. Enzymes that introduce one oxygen atom of dioxygen into a molecule (and the other oxygen into water) are called monooxygenases. (Note: some monooxygenase that hydroxylate biomolecules are called hydroxylases.) Those that introduce both atoms of dioxygen into a substrate are called dioxygenases. These oxygenases are not usually used to oxidize organic molecules for energy production. Rather they introduce O atoms for other reasons, including increasing the solubility of nonpolar aromatics to facilitate secretion, and to produce new molecular species which have different biological activities. Finally, biological molecules can be oxidized by dioxygen in which no atoms of oxygen are added to the substrate. Rather, electrons lost from the oxidized substrate are passed via intermediate electron carriers to dioxygen , which get reduced to superoxide (if one electron is added), hydrogen peroxide (if two electrons are added) or water (if 4 electrons are added). These enzymes are called oxidases. (Note: The letters oxi- or oxygen- are used in all the enzymes that use dioxygen as the oxidizing agent.)

In this chapter section, we will discuss biological oxidation reactions. Most introductory biochemistry texts don't approach oxidation reactions in one cohesive chapter. Probably because of that, when I was learning biochemistry, I found the presentation of these different enzymes involved in redox reactions to be very confusing. Hopefully this section will alleviate that problem. First the chemistry of NAD+ and FAD will be discussed. Then the enzymes using dioxygen in oxidative reactions (monooxygenases, dioxygenases, and oxidases) will be explored.