Biological pathways

Fig. 1. Biological pathways and processes iavolved ia the nitrogen cycle.

Radical reactions are not as common as polar reactions but are nevertheless important in some industrial processes and in numerous biological pathways. Let s see briefly how they occur. 

In biological pathways, dehydrations rarely occur with isolated alcohols but instead normally take place on substrates in which the -OH is positioned two carbons away from a carbonyl group. In the biosynthesis of fats, for instance, /3-hydroxybutyry) ACP is converted by dehydration to tram-crotonyl ACP, where ACP is an abbreviation for acyl carrier protein. We ll see the reason for this requirement in Section 11.10. 

Acid-catalyzed hydration of isolated double bonds is also uncommon in biological pathways. More frequently, biological hydrations require that the double bond be adjacent to a carbonyl group for reaction to proceed. Fumarate, for instance, is hydrated to give malate as one step in the citric acid cycle of food metabolism. Note that the requirement for an adjacent carbonyl group in the addition of water is the same as that we saw in Section 7.1 for the elimination of water. We ll see the reason for the requirement in Section 19.13, but might note for now that the reaction is not an electrophilic addition but instead occurs... 

Nucleophilic substitution and base-induced elimination are two of the most widely occurring and versatile reaction types in organic chemistry, both in the laboratory and in biological pathways. We ll look at them closely in this chapter to see how they occur, what their characteristics are, and how they can be used. 

All three elimination reactions--E2, El, and ElcB—occur in biological pathways, but the ElcB mechanism is particularly common. The substrate is usually an alcohol, 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 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 loss of the OH group is assisted by simultaneous protonation. 

The S il reaction occurs when the substrate spontaneously dissociates to a carbocation in a slow rate-limiting step, followed by a rapid reaction with the nucleophile. As a result, SN1 reactions are kinetically first-order and take place with racemization of configuration at the carbon atom. They are most favored for tertiary substrates. Both S l and S 2 reactions occur in biological pathways, although the leaving group is typically a diphosphate ion rather than a halide. 

Direct hydroxylation of an aromatic ring to yield a hydroxybenzene (a phenol) is difficult and rarely done in the laboratory., but occurs much more frequently in biological pathways. An example is the hydroxylation of p-hydroxyphenyl acetate to give 3,4-dihydroxyphenyl acetate. The reaction is catalyzed by p-hydroxyphenylacctate-3-hydroxylase and requires molecular oxygen plus the coenzyme reduced flavin adenine dinucleotide, abbreviated FADH2. 

Aromatic alkylations occur in numerous biological pathways, although there is of course no MCI3 present in living systems to catalyze the reaction. Instead, the carbocation electrophile is usually formed by dissociation of an organodiphosphate, as we saw in Section 11.6. The dissociation is typically assisted by complexation to a divalent metal cation such as Mg2+ to help neutralize charge. 

A third important reaction of alcohols, both in the laboratory and in biological pathways, is their dehydration to give alkenes. The C-0 bond and a neighboring C—H are broken, and an alkene tt bond is formed. 

Much of organic chemistry is simply the chemistry of carbonyl compounds. Aldehydes and ketones, in particular, are intermediates in the synthesis of many pharmaceutical agents, in almost all biological pathways, and in numerous industrial processes, so an understanding of their properties and reactions is essential. We ll look in this chapter at some of their most important reactions. 

A third method of aldehyde synthesis is one that we ll mention here just briefly and then return to in Section 21.6. Certain carboxylic acid derivatives can be partially reduced to yield aldehydes. The partial reduction of an ester by dhsobutylaluminum hydride (DIBAH), for instance, is an important laboratory-scale method of aldehyde synthesis, and mechanistically related processes also occur in biological pathways. The reaction is normally carried out at —78 °C (dry-ice temperature) in toluene solution. 

Water can add reversibly to o ,/3-unsalurated aldehydes and ketones to yield /3-hydroxy aldehydes and ketones, although the position of the equilibrium generally favors unsaturated reactant rather than saturated adduct. A related addition to an c /S-unsaturated carboxylic acid occurs in numerous biological pathways, such as the citric acid cycle of food metabolism where ds-aconitate is converted into isocitrate by conjugate addition of water to a double bond. 

One of the biological pathways by which an amine is converted to a ketone involves two steps (1) oxidation of the amine by N.AD+ to give an imine, and (2) hydrolysis of the imine to give a ketone plus ammonia. Glutamate, for instance, is converted by this process into a-ketoglutarate. Show the structure of the imine intermediate, and propose mechanisms for both steps. 

Carboxylic acids, RC02H, occupy a central place among carbonyl compounds. Not only are they valuable in themselves, they also serve as starting materials for preparing numerous acyl derivatives such as acid chlorides, esters, amides, and thioesters. In addition, carboxylic acids are present in the majority of biological pathways. We ll look both at acids and at their close relatives, nitriles (RC=N), in this chapter and at acyl derivatives in the next chapter. 

Carboxylic acid derivatives are among the most widespread of all molecules, both in laboratory chemistry and in biological pathways. Thus, a study of them and their primary reaction—nucleophilic acyl substitution—is fundamental to understanding organic chemistry. We ll begin this chapter by first learning about carboxylic acid derivatives, and then we ll explore the chemistry of acyl substitution reactions. 

The aldehyde intermediate can be isolated if 1 equivalent of diisobutvl-aluminum hydride (D1BAH) is used as the reducing agent instead of LiAlH4. The reaction has to be carried out at -78 °C to avoid further reduction to the alcohol. Such partial reductions of carboxylic acid derivatives to aldehydes also occur in numerous biological pathways, although the substrate is either a thioester or acyl phosphate rather than an ester. 

There are two advantages to the enaroine-Michael reaction versus the enolate-ion-Michael that make enamines so useful in biological pathways. First, an enamine is neutral, easily prepared, and easily handled, while an enolate ion is charged, sometimes difficult to prepare, and must be handled with care. 

Aldol reactions occur in many biological pathways, but are particularly important in carbohydrate metabolism, where enzymes called aldolases catalyze the addition of a ketone enolate ion to an aldehvde. Aldolases occur in all organisms and are of two types. Type 1 aldolases occur primarily in animals and higher plants type II aldolases occur primarily in fungi and bacteria. Both types catalyze the same kind of reaction, but type 1 aldolases operate place through an enamine, while type II aldolases require a metal ion (usually 7n2+) as Lewis acid and operate through an enolate ion. 

Reductive animations also occur in various biological pathways, fn the biosynthesis of the amino acid proline, for instance, glutamate 5-semjaldehyde undergoes internal imine formation to give 1-pyrrolinium 5-carboxylate, which is then reduced by nucleophilic addition of hydride ion to the C=N bond. 

One of the steps in the biological pathway for carbohydrate metabolism is the conversion of fructose 1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. Propose a mechanism for the transformation. 

Waters KM, Shankaran H, Wiley HS, Resat H, Thrall BD. Integration of microarray and proteomics data for biological pathway analysis and network modeling of epidermal growth factor signaling in human mammary epithelial cells. Keystone Symposia, 2005. 

Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet 2002 31 19-20. 

Chemical biology/chemical genetics is the use of a chemical compound as a tool or probe to learn something about a biology pathway [20]. The chemical compound is used in the same sense as a mouse knockout experiment or an SiRNA... 

Despite the complexity of the experiments and the enormous data manipulation necessary, complex biological pathways, as well as new drug targets are being identified by this method. Examples include screens for compounds that arrest cells in mitosis, that block cell migration, and that block the secretory pathway [50], or assays with primary T cells from PLP TCR transgenic mice for their inhibitory activity on the proliferation and secretion of proinflammatory cytokines in PLP-reactive T cells [51], and identification of small-molecule inhibitors of histone acetyltransferase activity [52]. 

It was postulated (169) that these amides are 8,8a-secobenzophenanthridine alkaloids produced by oxidative cleavage of ring B of the corresponding benzophenanthridines. The success of Baeyer-Villiger-type oxidations of the immonium bond of benzophenanthridine skeletons (168,171,172,175) indicates that this type of oxidation could be a real biological pathway. 

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