Determination of the double-helical structure of DNA has illuminated molecular biology for more than half a century. Fig. 9-CO, p.215

Nucleic Acids: How Structure Conveys Information What Is the Structure of DNA? What Are the Levels of Structure in Nucleic Acids? 3. What Is the Covalent Structure of Polynucleotides? 4. Knowing the types & general features of B- DNA. 5. How Does the Denaturation of DNA Take Place?

DNA structure DNA is the largest macromolecule in the cell. In eukaryotic cells, 99% of the cell DNA is present in linear form folded on itself several times to occupy small space within the chromosomes of the nucleus . Each chromosome contains single DNA molecule. Small amounts of DNA (about 1%) are circular shape present inside the mitochondria.

The DNA can be described as a polymer of nucleotides (Polynucleotide) The DNA can be described as a polymer of nucleotides (Polynucleotide).That is a long chain of repeating nucleotide units connected together strongly (by covalent bonds). Therefore, nucleotide is the unit of DNA structure that has complex structure made of 3 different components: 1 .Nitrogen base 2. Pentose sugar 3. Phosphate groups.

Without phosphate groups, the combination of nitrogen base and sugar is called a nucleoside. The nitrogen bases are heterocyclic (combination of carbon and nitrogen atoms) present in the cell with 5 different types. Two purines : adenine and guanine (with 9 atoms of 4 nitrogens and 5 carbons arranged in two rings) and Three pyrimidine: Cytosine, Thymine and Uracil having 6 atoms ring including 2 nitrogens and 4 carbons

In the nucleotide structure, the pentose sugar connects to nitrogen base at carbon one from one direction and to phosphate group at carbon 5 of the other side

There are 4 different types of nitrogen bases present in each nucleic acid. Adenine, Guanine and cytosine are present in both DNA and RNA .However only RNA contains Uracil and only DNA contains Thymine nitrogen bases. Also RNA nucleotides have ribose while DNA has deoxyribose as pentose sugars.

FIGURE 9. 1 Structures of the common nucleobases FIGURE 9.1 Structures of the common nucleobases. The structures of pyrimidine and purine are shown for comparison. Fig. 9-1, p.216

The difference is - 2'-OH in ribo and 2'-H in deoxyribose The difference is - 2'-OH in ribose and 2'-H in deoxyribose

In single polynucleotide chain of DNA(and similarly for RNA structure) the chain is made from covalent linkage of sugar phosphate backbone .In this arrangement the nitrogen bases are exposed freely to the inside of the backbone structure.

In DNA structure two polynucleotides are twisted around each others in double helical arrangement so that bases of opposite polyncleotides are specifically connected by weak hydrogen bonds.

Opposite direction of DNA polynucleotide chains The two strands have their 3’ and 5’ terminals at opposite ends ( antiparallel ) 5’ terminal: at one end of each DNA strand is a phosphate group linked to carbon atom 5 of deoxyribose 3’ terminal: at one end of each DNA is a hydroxyl group attached to carbon atom 3 of deoxyribose.

FIGURE 9.5 A fragment of an RNA chain. Fig. 9-5, p.219

Has polarity Has a Hydroplilic side Has a Hydrophobic side FIGURE 9.6 A portion of a DNA chain. Fig. 9-6, p.219

James Watson and Francis Crick, 1959 won the 1962 Nobel Prize in Medicine for their discovery of the structure of DNA. This was one of the most significant scientific discoveries of the 20th century

ROSALIND FRANKLIN 1920-58 Gave an idea that the structure of DNA is a helical structure. Physical Chemistry & X-ray crystallography expert Died of ovarian cancer

The 3-dimensional double helix structure of DNA, correctly elucidated by James Watson and Francis Crick. Complementary bases are held together as a pair by hydrogen bonds FIGURE 9.7 The double helix. A complete turn of the helix spans ten base pairs, covering a distance of 34 Å (3.4 nm). The individual base pairs are spaced 34 Å (3.4 nm) apart. The places where the strands cross hide base pairs that extend perpendicular to the viewer. The inside diameter is 11 Å (1.1 nm), and the outside diameter is 20 Å (2.0 nm). Within the cylindrical outline of the double helix are two grooves, a small one and a large one. Both are large enough to accommodate polypeptide chains. The minus signs alongside the strands represent the many negatively charged phosphate groups along the entire length of each strand. Fig. 9-7, p.221

FIGURE 9.8 Base pairing. The adenine–thymine (A–T) base pair has two hydrogen bonds, whereas the guanine–cytoside (G–C) base pair has three hydrogen bonds. Fig. 9-8a, p.222

FIGURE 9.8 Base pairing. The adenine–thymine (A–T) base pair has two hydrogen bonds, whereas the guanine–cytoside (G–C) base pair has three hydrogen bonds. Fig. 9-8b, p.222

Less Common Nucleobases FIGURE 9.2 Structures of some of the less common nucleobases. When hypoxanthine is bonded to a sugar, the corresponding compound is called inosine. Fig. 9-2a, p.216

Hypoxanthine + Sugar = Inosine FIGURE 9.2 Structures of some of the less common nucleobases. When hypoxanthine is bonded to a sugar, the corresponding compound is called inosine. Fig. 9-2c, p.216

5 FIGURE 9.2 Structures of some of the less common nucleobases. When hypoxanthine is bonded to a sugar, the corresponding compound is called inosine. Fig. 9-2b, p.216

FIGURE 9.3 A comparison of the structures of a ribonucleoside and a deoxyribonucleoside. (A nucleoside does not have a phosphate group in its structure.) Fig. 9-3, p.217

Commonly Occurring Nucleotides FIGURE 9.4 The structures and names of the commonly occurring nucleotides. Each nucleotide has a phosphate group in its structure. All structures are shown in the forms that exist at pH 7. (a) Ribonucleotides. (b) Deoxyribonucleotides. Fig. 9-4a, p.218

FIGURE 9.4 The structures and names of the commonly occurring nucleotides. Each nucleotide has a phosphate group in its structure. All structures are shown in the forms that exist at pH 7. (a) Ribonucleotides. (b) Deoxyribonucleotides. Fig. 9-4b, p.218

commonly occurring nucleotides FIGURE 9.4 The structures and names of the commonly occurring nucleotides. Each nucleotide has a phosphate group in its structure. All structures are shown in the forms that exist at pH 7. (a) Ribonucleotides. (b) Deoxyribonucleotides. Fig. 9-4c, p.218

FIGURE 9.4 The structures and names of the commonly occurring nucleotides. Each nucleotide has a phosphate group in its structure. All structures are shown in the forms that exist at pH 7. (a) Ribonucleotides. (b) Deoxyribonucleotides. Fig. 9-4d, p.218

Three different conformations of the DNA double helix Three different conformations of the DNA double helix. (A) A-DNA is a short, wide, right-handed helix. (B) B-DNA, the structure proposed by Watson and Crick, is the most common conformation in most living cells. (C) Z-DNA,  is a left-handed helix unlike A- and B-DNA, is a left-handed helix.

FIGURE 9.10 Right- and left-handed helices are related to each other in the same way as right and left hands. Fig. 9-10, p.224

FIGURE 9.11 A Z-DNA section can form in the middle of a section of B-DNA by rotation of the base pairs, as indicated by the curved arrows. Fig. 9-11, p.225

FIGURE 9.12 Two base pairs with 32° of righthanded helical twist; the minor-groove edges are drawn with heavy shading. Fig. 9-12, p.225

FIGURE 9. 14 Supercoiled DNA topology FIGURE 9.14 Supercoiled DNA topology. The DNA double helix can be approximated as a two-stranded, right-handed coiled rope. If one end of the rope is rotated counterclockwise, the strands begin to separate (negative supercoiling). If the rope is twisted clockwise (in a right-handed fashion), the rope becomes overwound (positive supercoiling). Get a piece of right-handed multistrand rope, and carry out these operations to convince yourself. Fig. 9-14a, p.227

FIGURE 9. 14 Supercoiled DNA topology FIGURE 9.14 Supercoiled DNA topology. The DNA double helix can be approximated as a two-stranded, right-handed coiled rope. If one end of the rope is rotated counterclockwise, the strands begin to separate (negative supercoiling). If the rope is twisted clockwise (in a right-handed fashion), the rope becomes overwound (positive supercoiling). Get a piece of right-handed multistrand rope, and carry out these operations to convince yourself. Fig. 9-14b, p.227

FIGURE 9.15 A model for the action of bacterial DNA gyrase (topoisomerase II). Fig. 9-15, p.228

Chromatin is comprised of histones and DNA: 147 base pairs of DNA  wraps around the 8 core histones to form the basic chromatin unit, the nucleosome The function of chromatin is to efficiently package DNA into a small volume to fit into the nucleus of a cell and protect the DNA structure and sequence FIGURE 9.16 The structure of chromatin. DNA is associated with histones in an arrangement that gives the appearance of beads on a string. The “string” is DNA, and each of the “beads” (nucleosomes) consists of DNA wrapped around a protein core of eight histone molecules. Further coiling of the DNA spacer regions produces the compact form of chromatin found in the cell. Fig. 9-16, p.229

FIGURE 9. 17 The experimental determination of DNA denaturation FIGURE 9.17 The experimental determination of DNA denaturation. This is a typical melting-curve profile of DNA, depicting the hyperchromic effect observed on heating. The transition (melting) temperature, Tm, increases as the guanine and cytosine (the G–C content) increase. The entire curve would be shifted to the right for a DNA with higher G–C content and to the left for a DNA with lower G–C content. Fig. 9-17, p.229

FIGURE 9.18 The double helix unwinds when DNA is denatured, with eventual separation of the strands. The double helix is re-formed on renaturation with slow cooling and annealing. Fig. 9-18, p.231

END