Saturday, February 29, 2020
An Introduction To DNA
An Introduction To DNA DNA (deoxyribonucleic acid) is the genetic material of eve living organisms including some viruses. It is a dimer consists of two strands that immerse upon each other and appear as a double helix that are linked together covalently with each other. Each strand is made up of similar repeating units called nucleotides. Each nucleotide composed of three different moieties,a 2-deoxyribose sugar,a phosphate group and a nitrogenous base. 1.1.1 2-Deoxyribose sugar The 2-deoxyribose sugar, a major structural component of DNA is a cyclic molecule .The sugars are joined together by phosphate groups that form phosphodiester bonds between third and fifth carbon atoms of adjacent sugar rings.The 5Ã¢â¬ ² carbon of deoxyribose sugar is attached to the 3Ã¢â¬ ² carbon of the next, and make a network of 3Ã¢â¬ ² carbon and 5Ã¢â¬ ² carbon.5Ã¢â¬â¢end of a DNA molecule is characterized by a free phosphate (P) group and the 3Ã¢â¬ ² end is characterized by a free hydroxyl (OH) group. It lacks an hyd roxyl group at the 2 position as in a ribose therefore a sugar moiety is a 2-deoxyribose. Two free hydroxyl groups are also located on the 5 carbon and 3-carbon of 2-deoxyribose sugar.These hydroxyl groups give a DNA oligomer its designation of 5 and the 3 end(usually accent as Ã¢â¬Å"three prime endÃ¢â¬ and Ã¢â¬Å"five prime endÃ¢â¬ ). 1.1.2 Sugar-Phosphate backbone The 2-deoxyribose sugar and a phosphate group forms the backbone in the DNA which are highly polar and defines directionality of the molecule. The polar hydrophilic back- bone is surrounded by a core of hydrophobic bases and is important for the stability and structure of DNA. The phosphate groups have a negative charge that gives a concentra- tion of negative charge on the backbone of DNA and also makes DNA,a negatively charge 5 1 Fundamentals molecule. The charge is also neutralised by DNA-binding proteins that contain the pos- itively charged amino acids lysine and arginine, which are attracted to the negatively charged phosphate backbone. See Fig. 1.1. Figure 1.1: DNA backbone 1.1.3 Nucleic acid bases DNA contain four different nitrogenous bases that make monomer of one nucleotide different from other. These bases are adenine (A), thymine (T), cytosine (C), and gua- nine(G). The bases come in two categories pyrimidines and purines. Larger nucleic acids adenine and guanine are members of a class of doubly ringed structures called purines while the smaller nucleic acids cytosine and thymine are members of a class of singly- ringed chemical structures called pyrimidines .A six-membered ring with two-nitrogen molecule formed a pyrimidine structure whereas purine is produced by a nine-membered, ring with four- nitrogen molecule. Each unit of the ring constructing the base is numbered to for specific identification. They are arranged in a particular order along the backbone of DNA to make a long chain of varying sequence that contains the code for proteins.The sequence specifies the exact genet ic instructions required to create a particular organism with its own unique traits. 6 1 Fundamentals 1.1.4 Base Pairing in DNA The nitrogenous bases are responsible to form double-strand of DNA in consequence of weak hydrogen bonds and have specific shapes and hydrogen bond properties. The three hydrogen bonds form between guanine and cytosine and then denoted as G.C or C.G,depending on which is associated with the first strand. Similarly adenine and thymine also bond exclusively by pairing of two hydrogen bonds and then denoted as A.T or T.A. This coupling up of nitrogen bases termed as complementarity.,A hydrogen bond donor need an equivalent hydrogen bond acceptor to form a hydrogen bond in the base across from it. Purines are only complementary with pyrimidines because molecules in pyrimidine-pyrimidine pairings are very far from each other that doesnÃ¢â¬â¢t makes the hydrogen bonding to be established. Purine-purine pairing are energetically unfavourable because the molecule s are too close and create an electrostatic repulsion. The only possible pairings are GT and AC. Primary and secondary amine groups or hydroxyl groups are common hydrogen bond donar while carbonyl and tertiary amines are common hydrogen bond acceptor groups. There are two hydrogen bonds between an A:T base pair. One hydrogen bond lie between the 6Ã¢â¬ ² primary amine of adenine and the 4Ã¢â¬ ² carbonyl of thymine. The other hydrogen bond form between the 1Ã¢â¬ ² tertiary amine of adenine and the 2Ã¢â¬ ² secondary amine of thymine. On the other hand,G:C base pair has three hydrogen bonds. One hydrogen bond lie between guanine with its 6Ã¢â¬ ² hydrogen bond accepting carbonyl and cytosine having 4Ã¢â¬ ² hydrogen bond accepting primary amine. The second hydrogen bond also formed between guanine on 1Ã¢â¬ ² secondary amine and cytosine 3Ã¢â¬ ² tertiary amine and the third formed between the 2Ã¢â¬ ² primary amine on guanine and the 2Ã¢â¬ ² carbonyl on cytosine.