Nitrogenous Bases

8 Key excerpts on "Nitrogenous Bases"

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  The Molecular Fabric of Cells

  • BIOTOL, B C Currell, R C E Dam-Mieras(Authors)
  • 2013(Publication Date)
  • Butterworth-Heinemann

    (Publisher)

  These are: • a nitrogenous base; pyrimidines, thymine, cytosine, uracil • a sugar; • a phosphoric acid. 4.2.1 Nitrogenous Bases The Nitrogenous Bases found in nucleic acids fall into 2 categories. They are either pyrimidines or purines. Pyrimidines (Figure 4.2) are structurally related to the heterocyclic compound pyrimidine. Three are commonly found in nucleic acids: reverse 74 Chapter 4 thymine and cytosine are found in DNA, whereas in RNA thymine is replaced by uracil. In order to avoid ambiguity in describing which atoms are involved in bonds, there is a convention involving the numbering of the atoms. This is shown for the compound pyrimidine in Figure 4.2. H Ns sCH I II HC2 6CH pyrimidine b) O II HN C -I II 0 = C CH H thymine c) d) CH 3 NH 2 1 1 .c '/ N CH 1 II =C CH N N / H 0 0 II C / HN CH 1 II =C CH N N ' H cytosine uracil Figure 4.2 Pyrimidines. Pyrimidines found in nucleic acids are derivations of pyrimidine. The numbering system used to identify atoms within the heterocyclic ring is shown in structure a). Thymine b), cytosine c) and uracil d) are found in nucleic acids. purines: Purines (Figure 4.3) are derivatives of the fused ring compound purine. Only two are adenine, routinely found in nucleic acids: these are adenine and guanine. The numbering system guanine ugec j w ^ purines is illustrated within Figure 4.3. a) b) H Q 1 II sCH N N / NH 2 1 N / / C VN 1 II HC N s C^N N N H CH c) O II HN / / C VN N V II CH H 2 N-C V C v N ' purine adenine N' H guanine Figure 4.3 Purines. The fused ring Nitrogenous Bases found in nucleic acids are a) derivatives of purine, b) adenine and c) guanine occur in nucleic acids. The numbering of atoms in the purine ring is shown in structure a). Note that unusual bases are sometimes found in nucleic acids, particularly in transfer methylation RNA; these will be briefly discussed in Section 4.6.2. Methylation of bases also occurs as a defence mechanism in bacteria to prevent hydrolysis of DNA by restriction enzymes.

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  Applications

  • Z. Deyl(Author)
  • 2000(Publication Date)
  • Elsevier Science

    (Publisher)

  341 Chapter 14 NUCLEOTIDES, NUCLEOSIDES, NITROGENOUS CONSTITUENTS OF NUCLEIC A C I D S s. ZADRA~IL GENERAL ASPECTS Heterocyclic Nitrogenous Bases derived from purines and pyrimidines - adenine, guanine o r cytosine, u r a c i l and thymine, and t h e corresponding nucleosides and nucleotides - a r e t h e only, though decisive, c e l l c o n s t i t u e n t s i n l i v i n g organisms bound t o n u c l e i c acids. I n a d d i t i o n t h e r e a r e t h e i r polyphosphate d e r i v a t i v e s (immediate precursors o f n u c l e i c a c i d biosynthesis and n a t u r a l sources o f energy) 01 igonucleotides and modified nucleosides (mostly methylated d e r i v a t i v e s a r i s i n g 4 a t the l e v e l o f macromolecules) c a t a b o l i c processes o f nucleic acids i n t h e c e l l , o r nucleotide coenzymes and a n t i b i o t i c s d e r i v a t i v e s and analogues of t h e n u c l e i c a c i d constituents r e s u l t from i n v i t r o synthetic a c t i v i t y i n organic chemistry l a b o r a t o r i e s where, i n a d d i t i o n t o t h e i n c r e a s i n g l y used nucleotides and 01 igonucleotides6, i n biochemistry and mole- c u l a r b i o l o g y ( s y n t h e t i c l i n k e r s , primers, genes and t h e i r p o r t i o n s ) t h e number o f analogues and antimetabol i t e s 7 , which have been synthesized, t e s t e d and used as p o t e n t i a l and r e a l v i r o s t a t i c s , b a c t e r i o s t a t i c s , c y t o s t a t i c s , c a r c i n o s t a t i c s o r o t h e r therapeutics i s extended.

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  Essentials of Organic Chemistry

  For Students of Pharmacy, Medicinal Chemistry and Biological Chemistry

  • Paul M. Dewick(Author)
  • 2013(Publication Date)
  • Wiley

    (Publisher)

  14

  Nucleosides, nucleotides and nucleic acids

  14.1 Nucleosides and nucleotides

  The nucleic acids DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are the molecules that play a fundamental role in the storage of genetic information, and the subsequent manipulation of this information. They are polymers whose building blocks are nucleotides, which are themselves combinations of three parts: a heterocyclic base, a sugar, and phosphate. The most significant difference in the nucleotides comprising DNA and RNA is the sugar unit, which is deoxyribose in DNA and ribose in RNA. The term nucleoside is used to represent a nucleotide lacking the phosphate group, i.e. the base-sugar combination. The general structure of nucleotides and nucleosides is shown below.

  Before we analyse nucleotide structure in detail, it is perhaps best that we consider the nature of the various component parts. In nucleic acid structures, there are five different bases and two different sugars.

  The bases are monocyclic pyrimidines (see Box 11.5 ) or bicyclic purines (see Section 11.9.1), and all are aromatic. The two purine bases are adenine (A) and guanine (G), and the three pyrimidines are cytosine (C), thymine (T) and uracil (U). Uracil is found only in RNA, and thymine is found only in DNA. The other three bases are common to both DNA and RNA. The heterocyclic bases are capable of existing in more than one tautomeric form (see Sections 11.6.2 and 11.9.1). The forms shown here are found to predominate in nucleic acids. Thus, the oxygen substituents are in keto form, and the nitrogen substituents exist as amino groups.

  The two sugars are pentoses, D -ribose in RNA and 2-deoxy-D -ribose in DNA. In all cases, the sugar is present in five-membered acetal ring form, i.e. a furanoside (see Section 12.4). The base is combined with the sugar through an N

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  Principles of Nucleic Acid Structure

  • Stephen Neidle(Author)
  • 2010(Publication Date)
  • Academic Press

    (Publisher)

  2

  The Building-Blocks of DNA and RNA

  Publisher Summary

  Nucleic acid is composed of individual acid units termed nucleotides. Each repeating unit in a nucleic acid polymer comprises three units linked together—a phosphate group, a sugar, and one of the four bases. The bases are planar aromatic heterocyclic molecules and are divided into two groups—the pyrimidine bases thymine and cytosine and the purine bases adenine and guanine. Thymine is replaced by uracil in ribonucleic acids, which also have an extra hydroxyl group at the 2’ position of their (ribose) sugar groups. Individual nucleoside units are joined together in a nucleic acid in a linear manner, through phosphate groups attached to the 3’ and 5’positions of the sugars. Hence the full repeating unit in a nucleic acid is a 3’, 5’-nucleotide. Nucleic acid and oligonucleotide sequences use single-letter codes for the fiveunit nucleotides—A, T, G, C, and U. The two classes of bases can be abbreviated as Y (pyrimidine) and R (purine). Phosphate groups are usually designated as p.

  2.1 Introduction

  Chemical degradation studies in the early years of the twenty-first century on material extracted from cell nuclei established that the high molecular-weight “nucleic acid” was actually composed of individual acid units, termed nucleotides. Four distinct types were isolated – guanylic, adenylic, cytidylic and thymidylic acids. These could be further cleaved to phosphate groups and four distinct nucleosides. The latter were subsequently identified as consisting of a deoxypentose sugar and one of four nitrogen-containing heterocyclic bases. Thus, each repeating unit in a nucleic acid polymer comprises these three units linked together – a phosphate group, a sugar, and one of the four bases.

  The bases are planar aromatic heterocyclic molecules and are divided into two groups – the pyrimidine bases thymine and cytosine and the purine bases adenine and guanine. Their major tautomeric forms are shown in Fig. 2.1 . Thymine is replaced by uracil in ribonucleic acids, which also have an extra hydroxyl group at the 2′ position of their (ribose) sugar groups. The standard nomenclature for the atoms in nucleic acids, as approved by the International Union of Biochemistry, is shown in Figs. 2.1 . and 2.2 . Accurate bond length and angle geometries for all bases, nucleosides and nucleotides have been well established by X-ray crystallographic analyses. Structural surveys (

  Clowney et al ., 1996

  ;

  Gelbin et al ., 1996

  ) have calculated mean values for these parameters (which define their equilibrium values) from the most reliable structures in the Cambridge and Nucleic Acid Databases. These have been incorporated in several implementations of the AMBER and CHARMM force fields widely used in molecular mechanics and dynamics modelling, and in a number of computer packages for both crystallographic and NMR structural analyses (

  Parkinson et al ., 1996

  ). Accurate crystallographic analyses, at very high resolution, can also directly yield quantitative information on the electron-density distribution in a molecule, and hence on individual partial atomic charges. These charges for nucleosides have hitherto been obtained by ab initio quantum mechanical calculations, but are also available experimentally for all four DNA nucleosides (Pearlman and Kim, 1990

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  Textbook of Biochemistry with Clinical Correlations

  • Thomas M. Devlin(Author)
  • 2015(Publication Date)
  • Wiley-Liss

    (Publisher)

  The capacity of nucleic acids to maintain and transmit the archived information efficiently arises directly from their chemical structure. 2.2 • STRUCTURAL COMPONENTS OF NUCLEIC ACIDS: NUCLEOBASES, NUCLEOSIDES, AND NUCLEOTIDES Nucleic acids are linear polymers of nucleotide units. Each nucleotide consists of a phos- phate ester, a pentose sugar, and a heterocyclic nucleobase. In RNA, the sugar is D-ribose; in DNA, it is the closely related sugar, 2-deoxy-D-ribose. In either case, the base is attached to the 1-position of the sugar through a -N-glycosidic bond. Two classes of major nucleo- bases are found in nucleic acids: purines and pyrimidines (Figure 2.2). The major purines are guanine and adenine, which occur in both DNA and RNA and are attached to the sugar at N-9. The three major pyrimidine nucleobases are cytosine, uracil, and thymine. Cytosine is present in both DNA and RNA. However, uracil is generally found only in RNA, and thymine is generally found only in DNA. Each pyrimidine is linked to the sugar through the N1-position. A nucleobase glycosylated with either pentose sugar is a nucleo- side. Nucleosides that contain ribose are ribonucleosides (Figure 2.3) whereas those with deoxyribose are deoxyribonucleosides (Figure 2.4). Four ribonucleosides are commonly found in RNA—adenosine (A), guanosine (G), cytidine (C), and uridine (U)—and four deoxyribonucleosides in DNA—deoxyadenosine (dA), deoxyguanosine (dG), deoxycyti- dine (dC), and deoxythymidine (dT). In addition, more than 80 minor nucleosides have been found in naturally occurring nucleic acids. Nucleotides are phosphate esters of nucleosides (Figure 2.5). Any of the hydroxyl groups on their sugars can be phosphorylated, but the bases are not. Nucleotides that con- tain a phosphate monoester are nucleoside monophosphates. For example, the 5-nucleotide of deoxycytidine is deoxycytidine 5-monophosphate (5-dCMP).

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  Recombinant DNA Principles and Methodologies

  • James Greene(Author)
  • 2021(Publication Date)
  • CRC Press

    (Publisher)

  2

  Biochemistry of Nucleic Acids

  Paul S. Miller Johns Hopkins University, Baltimore, Maryland

  I. CHEMICAL STRUCTURE AND PROPERTIES OF NUCLEIC ACIDS

  A. Chemical Structure

  Nucleic acids are high molecular weight macromolecules that form the genetic material of all living organisms. Two types of nucleic acids are generally encountered: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA serves as the repository for genetic information for both procaryotes and eucaryotes. RNA serves a functional role in the conversion of genetic information into cellular proteins, and in the case of certain viruses it serves as the genetic material as well.

  The nucleic acids can be considered as polymers of deoxyribo- or ribonucleotides. The basic structures of DNA or RNA in their single-stranded forms and the numbering system used to designate the various atoms are shown in Figure 1 . Each nucleotide unit is composed of a nitrogenous heterocyclic base, a sugar residue, and a phosphate group. The heterocyclic bases are either six-membered pyrimidine rings or nine-membered purine rings. Two types of purines and two types of pyrimidines are found in nucleic acids. Both DNA and RNA contain the purines adenine and guanine. DNA contains the pyrimidines cytosine and thymine, whereas RNA contains the pyrimidines cytosine and uracil. In addition to the four common bases, RNA also contains a number of unusual bases such as 4-thiouracil, thymine, 7-methylguanine, 6, 6-dimethyladenine, and hypoxanthine. These unusual bases are generally found in transfer RNA (tRNA) and in mRNA. With the exception of 5-methylcytosine, DNA contains almost exclusively the four common heterocyclic bases.

  The heterocyclic bases are linked to the sugar via an N-glycosyl bond. The resulting compound is called a nucleoside. Nucleosides found in DNA contain D-2′-deoxyribose sugars in the furanose form, whereas those in RNA contain D-ribose sugars in the furanose form. In order to distinguish between atoms in the heterocyclic base and atoms in the sugar, the sugar atoms are given numbers with primes (Figure 1

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  Molecular Biology

  Structure and Dynamics of Genomes and Proteomes

  • Jordanka Zlatanova(Author)
  • 2023(Publication Date)
  • Garland Science

    (Publisher)

  Figure 4.2 )—as well as a nitrogenous base and phosphate group(s). The base and sugar together form a nucleoside; depending on the number of phosphate groups attached to a nucleoside, it may be designated a nucleoside mono-, di-, or triphosphate. Nucleic acids are made of nucleoside monophosphates, shaded in blue, which contain Nitrogenous Bases that are derivatives of either pyrimidine or purine.

  The bases are all derived from either purine or pyrimidine, shown in Figure 4.1 . The kinds of bases found in nucleic acids are shown in

  Figure 4.2A

  . The basic groups contained in nucleic acids are always attached to the 1′-carbon of the sugar. Four different kinds are found in DNA: adenine (A), guanine (G), cytosine (C), and thymine (T). RNA contains the same bases except that uracil (U) substitutes for thymine. A ribose or deoxyribose with a base attached is called a nucleoside (

  Figure 4.2B

  ). When a phosphate group is attached to the 5′-carbon of the sugar, a nucleotide, also called a nucleoside 5′-phosphate, is obtained (see Figure 4.1 ).

  Figure 4.2

  Nucleosides in RNA and DNA. (A) Chemical formulas of pyrimidines and purines. Uracil, shown in the box, is present only in RNA. (B) Differences between the nucleosides in DNA and RNA are highlighted in red. The table shows the nomenclature of nucleosides formed by the addition of each base to the respective pentose.

  As depicted in

  Figure 4.3A

  , the sugar moiety of nucleic acids is in the ring or β-furanose form. To a first approximation, we may say that four of the five atoms of the ring lie in the same plane; the position of the fifth atom, either C-2′ or C-3′, with respect to the plane determines whether the conformation is that of an endo nucleoside, with the fifth atom on the same side of the plane as the C-5′ atom, or an exo nucleoside, with the fifth atom on the opposite side of the plane. Actually the situation is more complex, with a variety of slightly different sugar conformations found. Nucleosides also have two conformations determined by the non-free rotation around the glycosidic bond (

  Figure 4.3B

  ). The preferred conformation in nucleic acids is the anti conformation, in which the base and the sugar ring are as far away from each other as possible. As an example,

  Figure 4.3C

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  Engström-Finean Biological Ultrastructure

  • J. B. Finean(Author)
  • 2013(Publication Date)
  • Academic Press

    (Publisher)

  C H A P T E R V Role of Nucleic Acids Although proteins may be the foundation stones of biological ultra-structure they owe their design and construction to the nucleic acids which are the ultimate source of the codes of life. Nucleic acids were identified by Miescher in 1871, but it was not until about 1930 that they began to attract any scientific attention. Developments of recent years have been spectacular, and the story of the form in which these mole-cules hold their secrets and of how they perpetuate them and apply them in the construction and maintenance of living systems provides one of the most fascinating chapters of molecular biology. A. The Structure of Nucleic Acids and Nucleoproteins The nucleic acids are polymers of the general form ^ I Base—Sugar—Phosphate I Base—Sugar—Phosphate Nucleotide The monomer (nucleotide) consists of a base, a sugar, and a phosphate. 1. THE SUGAR COMPONENT In practically all nucleic acids analyzed thus far, the sugar component has been found to be either D-ribose or 2-deoxy-D-ribose (Fig. V.l) and this has led to the differentiation of two main types of nucleic acid, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). From some points of view it may be preferable to use the generic terms pentose nucleic acid (PNA) and deoxypentose nucleic acid (DNA). 193 194 V. Role of Nucleic Acids CH 2 OH OH OH OH H (a) (b) FIG. V.l. Structural formulas of (a) D-ribose and (b) 2-deoxy-r>ribose. 2. THE HETEROCYCLIC BASES, PURINES AND PYRIMIDINES The structural formulas of four of the main purines and pyrimidines found in nucleic acids are given in Fig. V.2. Crystallographic studies of these molecules in isolation have indicated that the ring structures are approximately planar and that there are small variations in the C—N and C—C bond lengths associated with differences in the double bond character arising in particular from the keto and amido groups attached to the rings.

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