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Structure of DNA Chemical Nature of DNA: - DNA monomers are Deoxyadenylate A, Deoxygyanylate G, Deoxycytidilate C and Deoxythymidilate T. - They are held together in a polymeric form By 3" to 5" phosphodiester bonds forming single strand (Figure 5). - The information content of DNA (the genetic code) resides in the sequences in which these monomers are ordered. - The polymer of one strand posses two ends; 5'- phosphate terminus and 3'- hydroxyl terminus so that it runs in the 5' to 3' direction and called coding strand (fig. 5). - The other strand runs anti-parallel to the first one i.e in the 3' to 5' direction and called non –coding strand (template strand) that used for synthesis of mRNA during transcription process. - The two strands are paired to each other through purines and pyrimidines on the opposites strands where adenosine(A) is linked to thymine (M) by two hydrogen bonds while guanine (G) is linked to cytosine (C) by three hydrogen bonds (fig. 6). - The concentration of deoxyadenosine (A) nucleotides equals that of thymidine (T) nucleotides while the concentration of the deoxycytidine (C) nucleotides equals that of deoxyguanosine (G) nucleotides. TYPES OF DNA - DNA exists in 6 double- helical structures ; A,B,C,D,E and Z which differ in: 1. The number of base pairs found in each turn of the helix. 2. The pitch or the angle between each base pair. 3. The helical diameter of the molecule. 4. The handedness (right or left) of the double helix direction. - Inter-conversion of one type to another might happen of in vivo depending on salt concentration and hydration conditions. - As shown in the Fig 7 ,the B form is the dominant form of DNA under physiological conditions (low salt and high degree of hydration ) and has a pitch of 3,4 nm per turn. - Minor and major grooves are found to which specific proteins interact with exposed atoms of nucleotides. - Each single turn contains 10 base pairs (bp). - Z-DNA is a left –handed double helix in which the phosphodiester backbone zigzags along the molecule. - Z-DNA is the least twisted (12bp/turn ) and has only one type of groove that may not bind to proteins that bind in the minor and major grooves of B form ,thus exert regulatory effects. - Z-DNA contains some 5'-methylated deoxycytidine nucleotides, loss of which lead to the reversion of Z form to B form thus affecting gene activity. - Denaturation (Melting) is the separation of the two strands of DNA and can be made by increasing temperature or decreasing salt concentration. - This denaturation occurs by breakdown of hydrogen bonds. FUNCTION OF DNA The genetic information is stored in the nucleotide sequence (arrangement) of DNA and serves for two purposes. 1. It provides the information inherited by daughter cells by the replication of the genetic information into daughter DNA molecules (fig. 8). 2. It is the source of informations for the syntheses of all protein molecules of the cell by acting as a template for the transcription into RNA. REPLICATION OF DNA - Replication of DNA molecules occurs in a semi- conservative manner ( fig.9) - Thus when each strand of the double stranded parental DNA molecules separates from its complement during replication, each one serves as template on which a new complementary strand is synthesized. - The two newly formed double stranded daughter DNA are then sorted between the two daughter. THE PROCESS OF DNA REPLICATION DNA replication must be completed and carried out with high fidelity to maintain genetic stability within the organism and the species. This is a function of DNA polymerase1 that was found to ensure fidelity and repair of DNA replication in E.coli which occurs in a rate of 1000 nucleotide per second. This required also the four different deoxynucleotide triphosphates (dNTP) and DNA as a template for replication. DNA replication in prokaryotes and euokaryotes occurs on both strands simultaneously (fig.10A). Unpairing of the two strands occurs by unwinding proteins at the replication forks forming replication bubbles (fig 10B). The same enzyme replicates at the same time. The enzyme replicates one strand( leading strand or template strand) in a continuous manner in the 5'to 3' direction and replicates the other strand (lagging strand) Discontinuously (fig.10C). DNA synthesis initiated by priming of short length RNA (RNA primers) of about 10-200 bp long on the lagging strand (coding strand). These newly synthesized fragments of DNA attached to RNA primers are called Okazaki fragments (Figure 11A). In mammals, RNA primers are removed by the replication complex then the gaps are filled by the proper base-pairing and sealed by DNA ligase (11B). In mammals, polymerase alpha is present in nucleus and responsible for chromosome replication in rate of 100 nucleotide per second. Lower molecular weight polymerase beta in mammalian nuclei may function in DNA repair. Mitochondrial DNA polymerase gamma is responsible for replication of Mitochondrial genome (another circular DNA). DNA topoisomerases are enzymes responsible for nicking of supercolied DNA to allow unwinding process. These enzymes are also responsible for quick resealing of the nicks.