DNA Structure
The DNA structure refers to the double helix shape formed by two strands of nucleotides, which are composed of a sugar, a phosphate group, and a nitrogenous base. The nitrogenous bases adenine, thymine, cytosine, and guanine form complementary base pairs, with adenine pairing with thymine and cytosine pairing with guanine. This structure allows DNA to store and transmit genetic information.
8 Key excerpts on "DNA Structure"
eBook - ePub- Dorian J. Pritchard, Bruce R. Korf(Authors)
- 2013(Publication Date)
- Wiley-Blackwell(Publisher)
...19 DNA s tructure Overview The chromosomes are composed essentially of DNA, which contains coded instructions for synthesis of every protein in the body. DNA consists of millions of nucleotides within two interlinked, coiled chains. Each nucleotide contains one of four bases and it is the sequence of these bases that contains the coded instructions (see Chapter 24). Each base on one chain is matched by a complementary partner on the other, and each sequence provides a template for synthesis of a copy of the other. Synthesis of new DNA is called replication (see Chapter 20). The unit of length of DNA is the base pair (bp) with 1000 bp in a kilobase (kb) and one million base pairs in a megabase (Mb). A typical human body cell contains nearly 7000 Mb of DNA. The s tructure of DNA We can visualize DNA as an extremely long, flexible ladder that has been twisted right-handed (like a corkscrew) by coiling around a telegraph pole. Each ‘upright’ of the ladder is a series of deoxyribose sugar molecules linked together by phosphate groups attached to their 3′ (‘three prime’) and 5′ (‘five prime’) carbon atoms. At the bottom of one upright is a 3′ carbon atom carrying a free hydroxyl (−OH) group and at the top, a 5′ carbon carrying a free phosphate group. On the other upright this orientation is reversed. The ‘rungs’ of the ladder are pairs of nitrogenous bases of two types, purines and pyrimidines. The purines are adenine (A) and guanine (G) and the pyrimidines are cytosine (C) and thymine (T). The bases are attached to the 1′ carbon of each sugar. Each unit of purine or pyrimidine base together with one attached sugar and one phosphate group constitute a nucleotide. A section of double-stranded DNA is therefore essentially two linked, coiled chains of nucleotides. This double helix has a major groove corresponding to the gap between adjacent sections of the sugar–phosphate chains and a minor groove along the row of bases...
eBook - ePub- Hugh Fletcher, Ivor Hickey(Authors)
- 2012(Publication Date)
- Garland Science(Publisher)
...A1 DNA Structure Key Notes Nucleotides DNA is a polymer containing chains of nucleotide monomers. Each nucleotide contains a sugar, a base, and a phosphate group. The sugar is 2′-deoxyribose which has five carbons named 1′ (one-prime) 2′, etc. There are four types of base: adenine and guanine have two carbon-nitrogen rings and are purines; thymine and cytosine have a single ring and are pyrimidines. The bases are attached to the 1′ carbon of the deoxyribose. A sugar plus a base is termed a nucleoside. A nucleotide has one, two or three phosphate groups attached to the 5′ carbon of the sugar. Nucleotides occur as individual molecules or polymerized as DNA or RNA. DNA polynucleotides Nucleotide triphosphates of the four bases are joined to form DNA polynucleotide chains. Two phosphates are lost during polymerization and the nucleotides are joined by the remaining phosphate. A phosphodiester bond forms between the 5′ phosphate of one nucleotide and the 3′ hydroxyl of the next nucleotide. The polynucleotide has a free 5′ phosphate at one end (5′ end) and a free 3′ OH (3′ end) at the other end. The sequence of bases encodes the genetic information. It is read 5′→3′. Polynucleotides are extremely long. It is possible to have 4 n different sequences. The double helix DNA molecules are composed of two polynucleotide strands wrapped around each other to form a double helix. The sugar-phosphate part of the molecule forms a backbone. The bases face inwards and are stacked on top of each other. The two polynucleotide chains run in opposite directions (antiparallel). The double helix is right-handed and executes a turn every 10 bases. The helix has a major groove which interacts with proteins and a minor grove. Variant DNA Structures have been identified including Z DNA which has a left-handed helix. Complementary base pairing Hydrogen bonds between bases on the two DNA strands stabilize the double helix...
eBook - ePub- Harri Lönnberg(Author)
- 2020(Publication Date)
- De Gruyter(Publisher)
...7 Nucleic acids 7.1 Structure of DNA The commonly known structure of DNA is a double helix composed of two polydeoxyribonucleotides. These two strands run in opposite directions and are H-bonded to each other forming AT and CG base pairs (Figure 7.1A). The NH groups of nucleic acid bases serve as H-bond donors and the lone electron pairs of carbonyl oxygens and ring nitrogens are H-bond acceptors. The strength of one hydrogen bond varies from 8 to 12 kJ mol –1. The CG base pair is considerably more stable than the AT pair, since it is formed by three H-bonds instead of two present in the AT pair. One should, however, bear in mind that H-bonding is not the only interaction responsible for the double helical structure. In fact, the vertical stacking interactions (cf. Section 1.9) between the H-bonded base pairs stabilize the double helical structure even more than the horizontal H-bonding [ 1 ]. Figure 7.1: (A) Primary structure of double-stranded DNA and (B) Watson–Crick base pairs. DNA is polyanionic under physiological conditions; the p K a values of the internucleosidic phosphodiester linkages are around 1. The multiple negative charges are largely neutralized by a dynamic cloud of monovalent cations that moves along the nucleic acid chain. Within single strands, the base moieties are up to one order of magnitude more basic than in nucleosides [ 2 ]. With double-stranded nucleic acids, the situation is less clear, but there are indications that protonated base pairs, in particular CG pairs, may exist even in pH range 6–7. The base pairs normally present in double helical nucleic acids are called Watson–Crick base pairs. The base pair is approximately planar and perpendicular to the axis of the double helix. The pairs are isomorphous. This means that the distance between the N and O atoms is invariably 2.8 Å, the anomeric carbons are 10.6 ± 0.2 Å apart and the N-glycosidic bonds form a 55° angle with the line connecting the anomeric carbons...
eBook - ePubAdvanced Molecular Biology
A Concise Reference
- Richard Twyman(Author)
- 2018(Publication Date)
- Garland Science(Publisher)
...Chapter 16 Nucleic Acid Structure Fundamental concepts and definitions DNA and RNA are nucleic acids, polymers composed of nucleotide subunits. Each nucleotide comprises a nitrogenous base linked to a phosphorylated sugar. The sugar residues are covalently joined by 5′→3′ phosphodiester bonds, forming a polarized but invariant backbone with projecting bases. The nature and order of the bases along the polymer comprises the genetic information carried by nucleic acids. The projecting bases interact specifically with other bases to form complementary pairs, allowing nucleic acids to form duplexes, act as templates and recognize homology, three processes which underpin the essential biological processes of replication, recombination and gene expression (q.v.). Duplex nucleic acids adopt different conformations depending on the base sequence, topological constraints, environmental conditions and interaction with proteins. Such conformational polymorphism is as important for the function of nucleic acids as the base sequence itself. DNA is the genetic material of cells and exists primarily in a double-stranded form — this makes it particularly suitable as a repository of genetic information, a blueprint, because it can preserve its integrity by acting as a template for its own repair (see Mutagenesis and DNA Repair). Cellular RNA is transcribed from the DNA and exists predominantly in a single-stranded form, although it usually folds to form complex secondary and tertiary structures. There are several classes of RNA which have distinct functions, mostly concerning the expression of genetic information (Table 16.1). Viral genomes can be composed of either DNA or RNA (see Viruses). 16.1 Nucleic acid primary structure Nucleotide structure. Nucleotides are the basic repeating units of nucleic acids and are constructed from three components: a base, a sugar and a phosphate residue. Nucleotides also have many other functions in the cell, e.g...
eBook - ePub- David P. Clark(Author)
- 2009(Publication Date)
- Academic Cell(Publisher)
...3.10). Consequently, the number of adenines in DNA is equal to the number of thymines, and similarly the numbers of guanine and cytosine are equal. Note that the nucleic acid bases have amino or oxygen side-groups attached to the ring. It is these chemical groups, along with the nitrogen atoms that are part of the rings themselves, that allow the formation of hydrogen bonds. The hydrogen bonding in DNA base pairs involves either oxygen or nitrogen as the atoms that carry the hydrogen, giving three alternative arrangements: O–H–O, N–H–N and O–H–N. Figure 3.09 Double Helix—50th Anniversary Coin A £2 coin commemorating the discovery of the double helix was issued in 2003 by Great Britain. Figure 3.10 Base Pairing by Hydrogen Bond Formation Purines (adenine and guanine) pair with pyrimidines (thymine and cytosine) by hydrogen bonding (colored regions). When the purines and pyrimidines first come together, they form the bonds indicated by the dotted lines. antiparallel Parallel, but running in opposite directions base pair Two bases held together by hydrogen bonds double helix Structure formed by twisting two strands of DNA spirally around each other hydrogen bond Bond resulting from the attraction of a positive hydrogen atom to both of two other atoms with negative charges right-handed helix In a right-handed helix, as the observer looks down the helix axis (in either direction), each strand turns clockwise as it moves away from the observer Working in Cambridge, England, James Watson and Francis Crick based their model of the double helix partly on the interpretation of data from X-ray crystallography by Rosalind Franklin and Maurice Wilkins, which suggested a helical molecule. Chemical analysis by Erwin Chargaff showed that DNA contained equimolar amounts of A and T and also of G and C. This, and chemical modeling, led Watson and Crick to propose that DNA was double stranded and that A in one strand is always paired with T in the other...
eBook - ePub- Raymond S. Ochs(Author)
- 2021(Publication Date)
- CRC Press(Publisher)
...Another alternative is to indicate the 5' and 3' ends explicitly with numbers: 5'-GTTCACG-3' 16.2 Structure of the Double Helix DNA has two strands joined by noncovalent forces. Figure 16.3 shows the sugar-phosphate backbones of the two strands in a ladder-like structure in which the “rungs” consist of a nucleotide base contributed by each strand. Each rung has a purine and pyrimidine hydrogen-bonded together so that they are all of uniform length. Invariably, a T always appears opposite an A, and a G always appears opposite a C. Edwin Chargraff discovered this rule prior to the discovery of the DNA Structure: the total number of A bases equals that of T bases, and the total number of G bases equals that of C bases. Thus, the rungs consist of either AT pairs or GC pairs. Note that there are two hydrogen bonds in the AT pair and three in the GC pair. Because of this rule of complementarity, the same information is present in each half of the double helix. That is, once the sequence of one strand is known, the other can be readily predicted. It also suggests a mechanism for replication: if the two strands separate, each can serve as a new daughter strand template. FIGURE 16.3 Two-dimensional view of DNA base pairing. There is further detail to the DNA Structure. The base pairs in the center, due to their alignment and formation of hydrogen bonds, are planar and hydrophobic. They stack on top of each other – somewhat offset – in three dimensions, as if they were flat rungs in a spiral ladder, while the sugar-phosphate strands form the “sides” of the ladder, wrapped in a helix (Figure 16.4). The helix has features in common with the protein α-helix introduced previously in this text. The two are compared in Figure 16.5. In each case, an inner hydrophobic core is internally hydrogen-bonded and cannot form hydrogen bonds to water. The exterior of the α-helix can be hydrophilic or hydrophobic depending on the R groups of the individual amino acids...
eBook - ePubBiochemistry Explained
A Practical Guide to Learning Biochemistry
- Thomas Millar(Author)
- 2018(Publication Date)
- CRC Press(Publisher)
...13 The Structures and Functions of DNA and RNA In this chapter you will learn: the general structure of DNA specific forms A-DNA, B-DNA and Z-DNA DNA topology chromosome structure about the breakdown of polynucleotides – the different nucleases about restriction enzymes the difference between blunt and sticky ends the structure of RNA and how it differs from DNA the different types of RNA and their functions the basic steps in DNA replication the basic steps in protein synthesis about codons the mechanisms of transcription and translation the structure of transfer RNAs The purpose of this section is to give an overview of the structure and the function of nucleic acids. Details about DNA synthesis, protein synthesis, laboratory manipulation of genetic material, differences between bacterial viral and other genetic material has now developed into a subject in its own right, molecular biology, and is beyond the scope of this book. Whole texts are devoted to this subject and these are commended to you. The structure of DNA The basis of a DNA molecule is a polymer of deoxynucleotides linked together by phosphodiester bonds. These occur by forming phosphoester bonds between de-oxyribose groups of adjacent molecules. At physiological pH, the chain of phosphate groups is negatively charged and hence very water-soluble. The charge is stabilised with Mg 2+ or DNA binding proteins. In actual fact, deoxytriphosphonucleosides are used to build the polymer rather than monophosphonucleosides as illustrated, and pyrophosphate (two phosphates joined together by an acid anhydride bond) is cleaved during polymerisation. Its cleavage provides the energy for the condensation of the phosphonucleosides. The enzymes, which catalyse the polymerisation of DNA, are called DNA polymerases. DNA polymerase requires all 4 deoxyribonucleoside 5' triphosphates and Mg 2+ to be present for it to be active...
eBook - ePub- Alexander McLennan, Andy Bates, Phil Turner, Michael White(Authors)
- 2012(Publication Date)
- Taylor & Francis(Publisher)
...Long DNA molecules are susceptible to cleavage by shearing in solution – this process can be used to generate DNA of a specific average length. Buoyant density DNA has a density of around 1.7 g cm −3, and can be analyzed and purified by its ability to equilibrate at its buoyant density in a cesium chloride density gradient formed in a centrifuge. The exact density of DNA is a function of its G+C content, and this technique may be used to analyze DNAs of different composition. Related topics (A2) Nucleic acid structure and function (B2) Spectroscopic and thermal properties of nucleic acids Stability of nucleic acids At first sight, it might seem that the double helices of DNA and RNA secondary structure are stabilized by the hydrogen bonding between base pairs. In fact, this is not the case. As in proteins (Section A3), the presence of H-bonds within a structure does not normally confer stability. This is because one must consider the difference in energy between, in the case of DNA, the single-stranded random coil state, and the double-stranded conformation. H-bonds between base pairs in double-stranded DNA (dsDNA) merely replace what would be equally strong and energetically favorable H-bonds with water molecules in free solution, if the DNA were single-stranded (ssDNA). Hydrogen bonding, along with the shapes of the bases, contributes to the specificity required for base pairing in a double helix (dsDNA will only form if the strands are complementary; Section A2), but it does not contribute to the overall stability of that helix. The root of this stability lies elsewhere, in the stacking interactions between the base pairs (Section A2, Figure 5b). The flat surfaces of the aromatic bases cannot hydrogen-bond to water when they are in free solution, in other words they are hydrophobic...
