Pyrimidine Thymine

Avery s paper prompted other biochemists to rethink their ideas about DNA One of them Erwin Chargaff of Columbia University soon discovered that the distribution of adenine thymine cytosine and guanine differed from species to species but was the same within a species and within all the cells of a species Perhaps DNA did have the capacity to carry genetic information after all Chargaff also found that regardless of the source of the DNA half the bases were purines and the other half were pyrimidines Significantly the ratio of the purine adenine (A) to the pyrimidine thymine (T) was always close to 1 1 Likewise the ratio of the purine guanine (G) to the pyrimidine cyto sine (C) was also close to 1 1 For human DNA the values are... 

The primary stmcture of DNA is based on repeating nucleotide units, where each nucleotide is made up of the sugar, ie, 2 -deoxyribose, a phosphate, and a heterocycHc base, N. The most common DNA bases are the purines, adenine (A) and guanine (G), and the pyrimidines, thymine (T) and cytosine (C) (Fig. 1). The base, N, is bound at the I -position of the ribose unit through a heterocycHc nitrogen. 

As indicated in Chapter 11, the base pairing in DNA is very specific the purine adenine pairs with the pyrimidine thymine the purine guanine pairs with the pyrimidine cytosine. Further, the A T pair and G C pair have virtually identical dimensions (Figure 12.10). Watson and Crick realized that units of such similarity could serve as spatially invariant substructures to build a polymer whose exterior dimensions would be uniform along its length, regardless of the sequence of bases. 

A with T the purine adenine (A) always pairs with the pyrimidine thymine (T)... 

There are instances in which toxicants have chemical or structural similarities to endogenous chemicals that rely on these special transport mechanisms for normal physiological uptake and can thus utilize the same system for membrane transport. Useful examples of drugs known to be transported by this mechanism include levodopa, which is used in treating Parkinson s disease, and fluorouracil, a cytotoxic drug. Levodopa is taken up by the carrier that normally transports phenylalanine, and fluorouracil is transported by the system that carries the natural pyrimidines, thymine, and uracil. Iron is absorbed by a specific carrier in the mucosal cells of the jejunum, and calcium by a vitamin D-dependent carrier system. Lead may be more quickly moved by a transport system that is normally involved in the uptake of calcium. 

Firstly the sizes and non-covalent interactions that could be used to discriminate between the bases are very similar, indeed, there are almost no detectable differences between the dimensions or hydrogen bonding requirements of the purines, adenine and guanine, or between the pyrimidines, thymine, cytosine and uracil. The second problem is one of manufacture how can nanopores with reproducible dimensions be formed and linked to a reporting mechanism These problems have been answered to some degree by Bashir and co-workers, as seen in Fig. 8.8 [22],... 

The major bases found in nucleic acids are adenine and guanine (purines) and uracil, cytosine, and thymine (pyrimidines). Thymine is found primarily in DNA, uracil in RNA, and the others in both DNA and RNA. Their structures, along with their chemical parent compounds, purine and pyrimidine, are shown in Figure 10.1, which also indicates other biologically important purines that are not components of nucleic acids. Hypoxanthine, orotic acid, and xanthine are biosynthetic and/or degradation intermediates of purine and pyrimidine bases, whereas xanthine derivatives—caffeine, theophylline, and theobromine—are alkaloids from plant sources. Caffeine is a component of coffee beans and tea, and its effects on metabolism are mentioned in Chapter 16. Theophylline is found in tea and is used therapeutically in asthma, because it is a smooth muscle relaxant. Theobromine is found in chocolate. It is a diuretic, heart stimulant, and vasodilator. 

Becker RS, Kogan G (1980) Photophysical properties of nucleic acid components. 1. The pyrimidines Thymine, uracil, N,N-dimethyl derivatives, and thymidine. Photochemistry and Photobiology 31 5-13. 

Addition and elimination reactions of RS radicals derived from cysteamine and 2-mercaptoethanol involving C5-C6 double bond in various pyrimidines (thymine, uracil, and cytosine) were studied by the pulse radiolysis technique in aqueous solutions.For this purpose the kinetic parameters, i.e. the rate constants of the addition and elimination reactions, were determined using two chemical-monitoring systems. 

Classic Watson-Crick base pairs are formed by unique hydrogen-bonding interactions between the nitrogenous bases of DNA and RNA. The purine adenine associates specifically with the pyrimidine thymine in DNA (or the related unmethylated analog, macil, in RNA), and the pmine guanine interacts with the pyrimidine cytosine. These complementarity rules. 

Base A nitrogen-containing building block of DNA the two types are the purines adenine (A) and guanine (G), and the pyrimidines thymine (T) and cytosine (C). 

Photodimerization of adjacent pyrimidines (thymines in this example) results from the absorption of ultraviolet light. 

The reducing property of ascorbic acid also assists another vitamin, folic acid (Figure 5.18). This is an essential co-factor in various one-carbon transfers for example the methyl group originating from the essential amino acid methionine is required in the formation of a wide variety of compounds including purines, the pyrimidine thymine, the amino acid serine, choline, carnitine, creatine, adrenalin, and many others. In its functional state, folic acid must be in its most reduced tetrahydrofolate form and this is brought about and/or maintained by ascorbic acid. 

As an aside, it is of interest to note that deoxyribonucleic acid, or DNA, which has been called the molecule of heredity, consists of a repeated backbone with a collection of side chain groups, the sequence of which is different in different species (and in individuals within the same species) and contains the genetic information. The side chains on the DNA backbone consist of only four types of bases, the two purines adenine (A) and guanine (G), and the two pyrimidines thymine (T) and cytosine (C). What is commonly referred to as the genetic code is a long sequence of the four letters A, G, T, and C in the order in which these bases appear on the DNA chain. ... 

Figure 1 illustrates two nucleotides, in which the phosphate is attached to the (ribose) sugar at either the 5 -carbon (5 -AMP) or the 3 -carbon (3 -TMP). The numbering systems for both purine (guanine shown here) and pyrimidine (thymine shown here) compounds are given, in addition to that for the sugar (ribose or deoxyribose). Note that the linkage between the... 

DNA vs RNA DNA uses deoxyribose, RNA uses ribose DNA uses the pyrimidine thymine, RNA uses uracil... 

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