Nucleotide amides

Nucleotide imidazolides react with amino components to produce the corresponding nucleotide amides ... 

Introduction of the cobalt atom into the corrin ring is preceeded by conversion of hydrogenobyrinic acid to the diamide (34). The resultant cobalt(II) complex (35) is reduced to the cobalt(I) complex (36) prior to adenosylation to adenosylcobyrinic acid i7,i -diamide (37). Four of the six remaining carboxyhc acids are converted to primary amides (adenosylcobyric acid) (38) and the other amidated with (R)-l-amino-2-propanol to provide adenosylcobinamide (39). Completion of the nucleotide loop involves conversion to the monophosphate followed by reaction with guanosyl triphosphate to give diphosphate (40). Reaction with a-ribazole 5 -phosphate, derived biosyntheticaHy in several steps from riboflavin, and dephosphorylation completes the synthesis. 

Pantothenic acid, sometimes called vitamin B3, is a vitamin that makes up one part of a complex coenzyme called coenzyme A (CoA) (Figure 18.23). Pantothenic acid is also a constituent of acyl carrier proteins. Coenzyme A consists of 3, 5 -adenosine bisphosphate joined to 4-phosphopantetheine in a phosphoric anhydride linkage. Phosphopantetheine in turn consists of three parts /3-mercaptoethylamine linked to /3-alanine, which makes an amide bond with a branched-chain dihydroxy acid. As was the case for the nicotinamide and flavin coenzymes, the adenine nucleotide moiety of CoA acts as a recognition site, increasing the affinity and specificity of CoA binding to its enzymes. 

A great many protective groups have been developed for the amino group, including carbamates (>NC02R), used for the protection of amino acids in peptide and protein syntheses, and amides (>NCOR), used more vv idely in syntheses of alkaloids and for the protection of the nitrogen bases adenine, cytosine, and guanine in nucleotide syntheses. 

One of the reactions used in determining the sequence ot nucleotides in a strand of DNA is reaction with hydrazine. Propose a mechanism for the following reaction, which occurs by an initial conjugate addition followed by internal amide formation. 

Figure 17.38 A simple diagram illustrating the two roles of glutamine (i) generation of ATP, via glutaminolysis, (ii) formation of purine and pyrimidine nucleotides, for the synthesis of nucleic acids in proliferating cells (Chapter 20). ( represents the carbon atoms of glutamine, one of which is released as CO2 and the others are converted to aspartate, via part of the Krebs cycle (Chapter 9). (N) represents the amide nitrogen of glutamine.

Figure 20.9 The positions in the pathway for de novo pyrimidine nucleotide synthesis where GLUCOSE provides the ribose molecule and GLUTAMINE provides nitrogen atoms. Glucose forms ribose 5-phosphate, via the pentose phosphate pathway (see chapter 6), which enters the pathway, after phosphorylation, as 5-phospho-ribosyl 1-pyrophosphate. Glutamine provides the nitrogen atom to synthesise carbamoylphos-phate (with formation of glutamate), and also to form cytidine triphosphate (CTP) from uridine triphosphate (UTP), catalysed by the enzyme CTP synthetase. It is the amide nitrogen of glutamine that is the nitrogen atom that is provided in these reactions.

Glutamine also supplies an amino function to start off purine nucleotide biosynthesis. This complex little reaction is again an Sn2 reaction on PRPP, but only an amino group from the amide of glutamine is transferred. The product of the enzymic reaction is thus 5-phosphoribosylamine. 

The search for RNAs with new catalytic functions has been aided by the development of a method that rapidly searches pools of random polymers of RNA and extracts those with particular activities SELEX is nothing less than accelerated evolution in a test tube (Box 26-3). It has been used to generate RNA molecules that bind to amino acids, organic dyes, nucleotides, cyano-cobalamin, and other molecules. Researchers have isolated ribozymes that catalyze ester and amide bond formation, Sn2 reactions, metallation of (addition of metal ions to) porphyrins, and carbon-carbon bond formation. The evolution of enzymatic cofactors with nucleotide handles that facilitate their binding to ribozymes might have further expanded the repertoire of chemical processes available to primitive metabolic systems. 

A common source of DNA damage is the spontaneous loss of the amine group on cytosine and the formation of an amide. This occurs at a rate of about 100 times a day. Fortunately, the body produces enzymes able to detect and repair such degraded cytosines. Given this information, suggest why DNA differs from RNA in possessing the nucleotide thymine rather than uracil. 

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