11.11: Biological Reactions

Biological Substitution Reactions

Both S_N1 and S_N2 reactions are common in biological chemistry, particularly in the pathways for biosynthesis of the many thousands of plant-derived substances called terpenoids, which we saw briefly in Chapter 8 Chemistry Matters and will discuss in CHEM 232. Unlike what typically happens in the laboratory, however, the substrate in a biological substitution reaction is usually an organodiphosphate rather than an alkyl halide. Thus, the leaving group is the diphosphate ion, abbreviated PP_i, rather than a halide ion. In fact, it’s useful to think of the diphosphate group as the “biological equivalent” of a halide. The dissociation of an organodiphosphate in a biological reaction is typically assisted by complexation to a divalent metal cation such as Mg²⁺ to help neutralize charge and make the diphosphate a better leaving group.

As an example, two S_N1 reactions occur during the biosynthesis of geraniol, a fragrant alcohol found in roses and used in perfumery. Geraniol biosynthesis begins with dissociation of dimethylallyl diphosphate to give an allylic carbocation, which reacts with isopentenyl diphosphate (Figure \(\PageIndex{1}\)). From the viewpoint of isopentenyl diphosphate, the reaction is an electrophilic alkene addition, but from the viewpoint of dimethylallyl diphosphate, the process is an S_N1 reaction in which the carbocation intermediate reacts with a double bond as the nucleophile.

Following this initial S_N1 reaction, loss of the pro-R hydrogen gives geranyl diphosphate, itself an allylic diphosphate that dissociates a second time. Reaction of the geranyl carbocation with water in a second S_N1 reaction, followed by loss of a proton, then yields geraniol.

As another example, S_N2 reactions are involved in almost all biological methylations, which transfer a –CH₃ group from an electrophilic donor to a nucleophile. The donor is S-adenosylmethionine (abbreviated SAM), which contains a positively charged sulfur (a sulfonium ion, Section 5.12), and the leaving group is the neutral S-adenosylhomocysteine molecule. In the biosynthesis of epinephrine (adrenaline) from norepinephrine, for instance, the nucleophilic nitrogen atom of norepinephrine attacks the electrophilic methyl carbon atom of S-adenosylmethionine in an S_N2 reaction, displacing S-adenosylhomocysteine (Figure \(\PageIndex{2}\)). In effect, S-adenosylmethionine is simply a biological equivalent of CH₃Cl.

Biological Elimination Reactions

All three elimination reactions—E2, E1, and E1cB—occur in biological pathways, but the E1cB mechanism is particularly common. The substrate is usually an alcohol rather than an alkyl halide, and the H atom removed is usually adjacent to a carbonyl group, just as in laboratory reactions. Thus, 3-hydroxy carbonyl compounds are frequently converted to unsaturated carbonyl compounds by elimination reactions. A typical example occurs during the biosynthesis of fats and oils when a 3-hydroxybutyryl thioester is dehydrated to the corresponding unsaturated (crotonyl) thioester. The base in this reaction is a histidine amino acid in the enzyme, and the loss of the –OH group is assisted by simultaneous protonation.