Nucleotides

10 Key excerpts on "Nucleotides"

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  Voet's Principles of Biochemistry

  • Donald Voet, Judith G. Voet, Charlotte W. Pratt(Authors)
  • 2018(Publication Date)
  • Wiley

    (Publisher)

  By identifying the genes in samples of DNA, researchers can focus on the genetic features that have a common purpose or provide some unique function to an organism. Jizeng Jia et al., Nature, 496, 91–95 (04 April 2013), doi:10.10138/nature/2028 1,031 1,441 2,980 8,443 1,635 278 Brachypodium 26,552 22,405 Rice 39,049 25,489 Sorghum 34,496 26,722 Barley fl-cDNA 23,585 17,345 Ae. tauschii 32,660 23,705 a 304 766 303 447 234 88 332 95 38 414 85 37 812 136 59 587 276 208 68 212 839 234 293 348 179 42 43 Section 1 Nucleotides we consider some of the techniques used in manipulating DNA in the laboratory. In later chapters, we will examine in greater detail the participation of Nucleotides and nucleic acids in metabolic processes. Chapter 24 includes additional informa- tion about nucleic acid structures, DNA’s interactions with proteins, and DNA packaging in cells, as a prelude to several chapters discussing the roles of nucleic acids in the storage and expression of genetic information. 1 Nucleotides KEY IDEAS • The nitrogenous bases of Nucleotides include two types of purines and three types of pyrimidines. • A nucleotide consists of a nitrogenous base, a ribose or deoxyribose sugar, and one or more phosphate groups. • DNA contains adenine, guanine, cytosine, and thymine deoxyriboNucleotides, whereas RNA contains adenine, guanine, cytosine, and uracil riboNucleotides. Nucleotides are ubiquitous molecules with considerable structural diversity. There are eight common varieties of Nucleotides, each composed of a nitrogenous base linked to a sugar to which at least one phosphate group is also attached. The bases of Nucleotides are planar, aromatic, heterocyclic molecules that are structural derivatives of either purine or pyrimidine (although they are not synthesized in vivo from either of these organic compounds).

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  Fundamentals of Biochemistry

  Life at the Molecular Level

  • Donald Voet, Judith G. Voet, Charlotte W. Pratt(Authors)
  • 2016(Publication Date)
  • Wiley

    (Publisher)

  tauschii 32,660 23,705 a 304 766 303 447 234 88 332 95 38 414 85 37 812 136 59 587 276 208 68 212 839 234 293 348 179 Jizeng Jia et al., Nature, 496, 91–95 (04 April 2013), doi:10.10138/nature/2028 43 Section 1 Nucleotides we consider some of the techniques used in manipulating DNA in the laboratory. In later chapters, we will examine in greater detail the participation of Nucleotides and nucleic acids in metabolic processes. Chapter 24 includes additional informa- tion about nucleic acid structures, DNA’s interactions with proteins, and DNA packaging in cells, as a prelude to several chapters discussing the roles of nucleic acids in the storage and expression of genetic information. 1 Nucleotides KEY CONCEPTS • The nitrogenous bases of Nucleotides include two types of purines and three types of pyrimidines. • A nucleotide consists of a nitrogenous base, a ribose or deoxyribose sugar, and one or more phosphate groups. • DNA contains adenine, guanine, cytosine, and thymine deoxyriboNucleotides, whereas RNA contains adenine, guanine, cytosine, and uracil riboNucleotides. Nucleotides are ubiquitous molecules with considerable structural diversity. There are eight common varieties of Nucleotides, each composed of a nitrogenous base linked to a sugar to which at least one phosphate group is also attached. The bases of Nucleotides are planar, aromatic, heterocyclic molecules that are structural derivatives of either purine or pyrimidine (although they are not synthesized in vivo from either of these organic compounds). N N N H N 6 7 8 9 5 1 4 3 2 N 4 5 3 6 1 2 N Purine Pyrimidine O H H H H OH Ribose OH CH 2 HO OH HO OH 4′ 5′ 3′ 2′ 1′ O H H H H OH H CH 2 4′ 5′ 3′ 2′ 1′ Deoxyribose The most common purines are adenine (A) and guanine (G), and the major pyrimidines are cytosine (C), uracil (U), and thymine (T). The purines form bonds to a five-carbon sugar (a pentose) via their N9 atoms, whereas pyrimidines do so through their N1 atoms (Table 3-1).

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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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  Organophosphorus Chemistry

  Volume 44

  • David W Allen, David Loakes, John C Tebby(Authors)
  • 2015(Publication Date)
  • Royal Society of Chemistry

    (Publisher)

  Nucleotides and oligoNucleotides: monoNucleotides Raman Narukulla a and Yao-Zhong Xu * b DOI: 10.1039/9781782622765-00170 The 60th anniversary of DNA’s discovery marks the conclusion of our first hour of discovery. Each of tick of the year builds on our understanding; to think how differently we viewed things in 1953, and how much progress we have made since then. This chapter is to discuss some selected research work published in the year 2013 on the chemical synthesis of Nucleotides and oligoNucleotides with an interest in medicinal appli-cations. Due to limited space, it would not be possible to include all relevant articles in it. Nucleotides are the building blocks of nucleic acids which play vital roles in many biological processes. Chemically, a nucleotide is made of a nucleoside (base and sugar) and a phosphate group. Therefore a molecule similar to these compounds could be used as a potential therapeutic agent. Indeed, chemically modified nucleosides and Nucleotides have been used for such a purpose. For instance, the first anti-cancer drug methotrexate acted on both thymidylate synthase and on de novo purine synthesis. The importance of these moieties has created great interest and resulted in the formation of a new field of chemistry of nucleic acid components, i.e ., modified Nucleotides and oligoNucleotides. Relevant research articles on this subject will be discussed in the sections below. 1 Nucleoside monophosphates Nucleoside monophosphates, also called monoNucleotides or simply Nucleotides, are moieties consisting of one (occasionally two) nucleosides and a single phosphate. They are generally prepared from mono-phosphorylation of nucleosides. 1.1 Modified nucleoside monophosphates There are a limited number of naturally occurring Nucleotides, however, synthetic methods are now offering an unlimited number of modified nucleoside monophosphates for biological studies or medicinal exploit-ations.

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  Asymmetric Synthesis of Natural Products

  • Ari M. P. Koskinen(Author)
  • 2022(Publication Date)
  • Wiley

    (Publisher)

  6 Nucleosides, Nucleotides, and Nucleic Acids It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material. J.D. Watson, F.H.C. Crick, 1953 Nucleic acids deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) play important roles in life. The former is the carrier of the cellular and organism’s hereditary information, and the latter function as signal transduction molecules for the synthesis of proteins. The information embedded in DNA is read and transcribed into RNA within the nucleus of the cell, and this information is then passed on to other parts of the cell where the sequence information in the messenger RNA is translated into a protein sequence. In this chapter we shall not study the genetic functions of DNA or RNA, fascinating as they are in their chemistry, but these are left to the realm of biochemistry and molecular biology. Many biologically active natural compounds and pharmaceuticals derived from them interact directly with DNA or RNA. It is therefore important to familiarise ourselves with the structural features of these biological macromolecules in order to understand their interactions with small molecules at molecular level. We shall briefly inspect the structural features of the heterocyclic nucleobases and their naturally occurring relatives, as well as molecules structurally related to the nucleic acid constituents with medicinal importance. In eukaryotic cells, the hereditary information is stored in the cell nucleus in the supercoiled duplex form of DNA, which is further arranged in supramolecular structures with histone proteins to form nucleosomes. The human genome consists of approximately 3.1 billion base pairs, which encode approximately 20 000 proteins (Table 6.1). It is interesting to note that the length of the DNA does not correlate with a number of proteins coded.

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  Introduction to Organic Chemistry

  • William H. Brown, Thomas Poon(Authors)
  • 2016(Publication Date)
  • Wiley

    (Publisher)

  648 THE ORGANIZATION, MAINTENANCE, and regulation of cellular function require a tre- mendous amount of information, all of which must be processed each time a cell is replicated. With very few exceptions, genetic information is stored and transmitted from one generation to the next in the form of deoxyribonucleic acids (DNA). Genes, the hereditary units of chro- mosomes, are long stretches of double‐stranded DNA. If the DNA in a human chromosome in a single cell were uncoiled, it would be approximately 1.8 meters long! Genetic information is expressed in two stages: transcription from DNA to ribonucleic acids (RNA) and then translation through the synthesis of proteins: DNA transcription RNA translation proteins Thus, DNA is an enormous molecule that stores our genetic information, whereas RNA serves in the transcription and translation of this information, which is then expressed through the synthesis of proteins. In this chapter, we will first examine the DNA molecule in detail to gain an understanding of its structure and function. We start by examining the structure of nucleosides and Nucleotides and the manner in which these monomers are covalently bonded to form nucleic acids. Then we explore how genetic information is encoded on molecules of DNA, the function of the three types of ribonucleic acids, and, finally, how the primary structure of a DNA molecule is determined. 20.1 What Are Nucleosides and Nucleotides? Controlled hydrolysis of nucleic acids yields three types of simpler building blocks: hetero- cyclic aromatic amine bases, the monosaccharide d‐ribose or 2‐deoxy‐d‐ribose (Section 17.3), and phosphate ions. Figure 20.1 shows the five heterocyclic aromatic amine bases most Nucleic acid A biopolymer containing three types of monomer units: heterocyclic aromatic amine bases derived from purine and pyrimidine, the monosaccharides D‐ribose or 2‐deoxy‐ D‐ribose, and phosphate.

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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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  The Molecular Fabric of Cells

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

    (Publisher)

  71 Nucleic acids 4.1 Introduction 72 4.2 Components of nucleic acids 73 4.3 Nucleosides 77 4.4 Nucleotides 78 4.5 DNA 86 4.6 RNA 104 4.7 Genetic engineering -an outline 115 4.8 Hybridisation in molecular biology and biotechnology 121 Summary and objectives 126 72 Chapter 4 Nucleic acids 4.1 Introduction Nucleic acids include two types of macromolecules with crucial roles within cells. These are deoxyribonucleic acid, DNA, which contains the genetic information of most organisms and ribonucleic acid, RNA, which is involved in the expression of the information contained in DNA. Both DNA and RNA are linear, unbranched polymers of monoNucleotides. MonoNucleotides, such as adenosine-triphosphate, ATP, and diNucleotides such as nicotinamide adenine dinucleotide, NAD + , also have important roles in the metabolism of cells. 4.1.1 Information transfer and roles: the central dogma Before discussing the structure of nucleic acids, we will summarise their roles by reference to the so-called 'Central Dogma of Molecular Biology' (Figure 4.1). DNA < > RNA ^ protein X v transcription translation replication Figure 4.1 The central dogma of molecular biology. Arrows represent the flow of information between the various types of molecules. This describes the flow of information from DNA through RNA to proteins. The central dogma describes three major processes in which information transfer occurs in cells. replication Replication, in which the DNA molecule is copied, with its information content being preserved. This occurs prior to cell division so that each 'daughter' cell receives an exact copy of the DNA present in the original cell. The sequence of the Nucleotides (bases) in the DNA represents the information store. This specifies the order of the amino acids in proteins, ie the primary structure of proteins.

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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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  Biomolecules

  From Genes to Proteins

  • Shikha Kaushik, Anju Singh(Authors)
  • 2023(Publication Date)
  • De Gruyter

    (Publisher)

  Chapter 5  Nucleic Acids

  The versatility and elegant simplicity of DNA (deoxyribonucleic acid) double helix dictate life. Although, nucleic acid was first identified as ‘nuclein’ by Friedrich Miescher, a Swiss physician and biologist in 1869, yet it took more than 70 years to demonstrate that it is the molecule that carries genetic information. DNA of a single cell contains all genetic information necessary for processes of life. The double-helical structure of DNA was discovered by James D. Watson and Francis H. C. Crick in 1953, using the X-ray diffraction data of Rosalind Franklin, and this marvelous discovery proved to be the significant turning point that paved the way to the development of biomedical science and modern biology. Structurally, DNA is a flexible molecule which can adopt numerous unusual structures depending on the solution conditions. To understand the structure of B-form of DNA (natural/native form), it is important to understand the individual components of DNA. Nucleic acids (DNA and RNA (ribonucleic acid)) are long linear polymers which are made up of monomer units called Nucleotides. All Nucleotides are made up of three components: a nitrogen heterocyclic base, a pentose sugar, and a phosphate group. They are termed as nucleic acids because they are found in nucleus and comprise phosphoric acid (phosphate) as one of its components. The two types of nucleic acids that occur in cells are DNA and RNA. DNA acts as a carrier of genetic information and is found in the nucleus of the cell, whereas RNA is present in both the nucleus and cytoplasm.

  5.1  Components of Nucleic Acids

  Both DNA and RNA are biopolymers, which are made up of monomer units called nucleotide. Nucleotide is the building block of nucleic acids which consists of three components:

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