Dna Nature

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DNA NatureGraduation Research ( 2009 )

DNA Nature .. By / M. Hosny

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Alexandria University Faculty of Science Biochemistry Department

DNA NatureGraduation Research ( 2009 )

By / Mohamed Hosny Abu-samraChemistry / Biochemistry department

Supervised byProf. Dr. / Mahmoud Mohamed Balbaa

DNA Nature .. By / M. Hosny

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CONTENTS TitlesIntroduction DNA structure Chromosome structure DNA Replication Gene Mutation Genomics Cloning References 4 4 6 9 16 17 22 25

BoxesBox 1 Box 2 Box 3 Box 4 Box 5 Box 6 Box 7 6 7 13 14 17 18 19

TablesTable 1 Table 2 Table 3 Table 4 5 8 13 14

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IntroductionThe discovery that genetic information is coded along the length of a polymeric molecule composed of only four types of monomeric units was one of the major scientific achievements of the twentieth century. This polymeric molecule, DNA, is the chemical basis of heredity and is organized into genes, the fundamental units of genetic information . Every organism possesses a genome that contains the biological information needed to maintain the life of that organism . Most genomes , including the human genome and those of all other cellular life forms , are made of DNA but a few viruses have RNA genomes . DNA is found inside a special area of the cell called the nucleus. Because the cell is very small, and because organisms have many DNA molecules per cell, each DNA molecule must be tightly packaged. This packaged form of the DNA is called a chromosome. DNA spends a lot of time in its chromosome form. But during cell division, DNA unwinds so it can be copied and the copies transferred to new cells. DNA also unwinds so that its instructions can be used to make proteins and for other biological processes.

Researchers refer to DNA found in the cell's nucleus as nuclear DNA. An organism's complete set of nuclear DNA is called its genome. Besides the DNA located in the nucleus, humans and other complex organisms also have a small amount of DNA in cell structures known as mitochondria. Mitochondria generate the energy the cell needs to function properly. In sexual reproduction, organisms inherit half of their nuclear DNA from the male parent and half from the female parent. However, organisms inherit all of their mitochondrial DNA from the female parent. This occurs because only egg cells, and not sperm cells, keep their mitochondria during fertilization. 6

1. DNA structureDNA consists of two polynucleotide strands wound around each other to form a right-handed double helix . The structure of DNA is so distinctive that this molecule is often referred to as the double helix. Each nucleotide monomer in DNA is composed of a nitrogenous base (either a purine or a pyrimidine), a deoxyribose sugar, and phosphate. The mononucleotides are linked to each other by 3',5'-phosphodiester bonds.These bonds join the 5'-hydroxyl group of the deoxyribose of one nucleotide to the 3'-hydroxyl group of the sugar unit of another nucleotide through a phosphate group.The antiparallel orientation of the two polynucleotide strands allows hydrogen bonds to form between the nitrogenous bases that are oriented toward the helix interior. There are two types of base pairs (bp) in DNA: A) adenine (a purine) pairs with thymine (a pyrimidine), and B) guanine (a purine) pairs with cytosine (a pyrimidine) . 5 Several types of noncovalent bonding contribute to the stability of its helical structure: 1. Hydrophobic interactions : The base ring n cloud of electrons between stacked purine and pyrimidine bases is relatively nonpolar. The clustering of the base components of nucleotides within the double helix is a stabilizing factor in the three-dimensional macromolecule because it minimizes their interactions with water, thereby increasing entropy. 2. Hydrogen bonds : The base pairs, on close approach, form a preferred set of hydrogen bonds, three between GC pairs and two between AT pairs. The cumulative "zippering" effect of these hydrogen bonds keeps the strands in correct complementary orientation.

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A diagrammatic representation of the Watson and Crick model of the double-helical structure of the B form of DNA. The horizontal arrow indicates the width of the double helix (20 A), and the vertical arrow indicates the distance spanned by one complete turn of the double helix (34 A). One turn of B-DNA includes ten base pairs (bp), so the rise is 3.4 A per bp. The central axis of the double helix is indicated by the vertical rod. The short arrows designate the polarity of the antiparallel strands. The major and minor grooves are depicted. (A, adenine; C, cytosine; G, guanine; T, thymine; P, phosphate; S, sugar 3 [deoxyribose].)

3. Base stacking : Once the antiparallel polynucleotide strands have been brought together by base pairing, the parallel stacking of the nearly planar heterocyclic bases stabilizes the molecule because of the cumulative effect of weak van der Waals forces. 4. Electrostatic interactions : DNA's external surface, referred to as the sugar- phosphate backbone, possesses negatively charged phosphate groups. Repulsion between nearby phosphate groups, a potentially destabilizing force, is minimized by the shielding effects of divalent cations such as Mg2+ and polycationic molecules such as the polyamines and histones . A , B & Z DNA : The structure discovered by Watson and Crick, referred to as B-DNA, represents the sodium salt of DNA under highly humid conditions. DNA can assume different conformations because deoxyribose is flexible and the C1-N-glycosidic linkage rotates. When DNA becomes partially dehydrated, it assumes the A form . In A-DNA , the base pairs are no longer at right angles to the helical axis . Instead, they tilt 20 away from the horizontal. In addition, the distance between adjacent base pairs is slightly reduced, with 11 bp per helical turn instead of the 10.4 bp found in the B form. Each turn of the double helix occurs in 2.5 nm, instead of 3.4 nm, and the molecule's diameter swells to approximately 2.6 nm from the 2.4 nm observed in B-DNA. The A form of DNA is observed when it is extracted with solvents such as ethanol. The Z form of DNA (named for its "zigzag" conformation) radically departs from the B form. ZDNA (D = 1.8 nm), which is considerably slimmer than B-DNA (D = 2.4 nm), is twisted into a left-handed spiral with 12 bp per turn. Each turn of Z-DNA occurs in 4.5 nm, compared with 3.4 nm for B-DNA. DNA segments with alternating purine and pyrimidine bases (especially CGCGCG) are most likely to adopt a Z configuration. 5 Table 1. Selected Structural Properties of B , A , and Z-DNA B-DNA (Watson-Crick Structure) 2.4 nm 10.4 3.4 nm Right-handed A-DNA 2.6 nm 11 2.5 nm Right-handed Z-DNA 1.8 nm 12 4.5 nm Left-handed

Helix diameter bp per helical turn Rotation per bp Helix rotation

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A-DNA, B-DNA, and Z-DNA. Because DNA is a flexible molecule, it can assume different conformation forms depending on its base pair sequence and/or isolation conditions. Each molecular form in the figure possesses the same number of base pairs. 5

The Denaturation (Melting) of DNA: The double-stranded structure of DNA can be separated into two component strands (melted) in solution by increasing the temperature or decreasing the salt concentration. Not only do the two stacks of bases pull apart but the bases themselves unstack while still connected in the polymer by the phosphodiester backbone. The strands of a given molecule of DNA separate over a temperature range. The midpoint is called the melting temperature, or Tm. The Tm is influenced by the base composition of the DNA and by the salt concentration of the solution. DNA rich in GC pairs, which have three hydrogen bonds, melts at a higher temperature than that rich in AT pairs, which have two hydrogen bonds. Box 1. The human mitochondrial genome The complete sequence of the human mitochondrial genome has been known for over 20 years . At just 16569 bp , it is much smaller than nuclear genome , and it contains just 37 genes . Thirteen of these genes code for proteins involved in the respiratory complex , the main biochemical component of the energy-generating mitochondria ; the other 24 specify non-coding RNA molecules that are required for expression of the mitochondrial genome . The genes in this genome are much more closely packed than in the nuclear genome and they do not contain introns . In many respects , the human mitochondrial genome is typical of the mitochondrial genomes of other animals . 2

2. The Structure of ChromosomesThe term chromosome is used to refer to a nucleic acid molecule that is the repository of genetic information in a virus, a bacterium, an eukaryotic cell, or an organelle. It also refers to the densely colored bodies seen in the nuclei of dye-stained eukaryotic cells, as visualized using a light microscope.

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Chromatin Consists of DNA and Proteins The eukaryotic cell cycle produces remarkable changes in the structure of chromosomes . In nondividing eukaryotic cells (in G0) and those in interphase (G1, S, and G2), the chromosomal material, chromatin, is amorphous and appears to be randomly dispersed in certain parts of the nucleus. In the S phase of interphase the DNA in this amorphous state replicates, each chromosome producing two sister chromosomes (called sister chromatids) that remain associated with each other after replication is complete. The chromosomes become much more condensed during prophase of mitosis, taking the form of a speciesspecific number of well-defined pairs of sister chromatids . Chromatin consists of fibers containing protein and DNA in approximately equal masses, along with a small amount of RNA . The DNA in the chr