nucleic acid.pdf

Dr. Mohammed Molecular Geneticstawfiq Lecture 2 Dr.Sanaa Jassim Nucleic acids Naturally occurring chemical compound that is capable of being broken down to yield phosphoric acid, sugars, and a mixture of organic bases (purines and pyrimidines). Nuc...

Dr. Mohammed Molecular Geneticstawfiq Lecture 2 Dr.Sanaa Jassim Nucleic acids Naturally occurring chemical compound that is capable of being broken down to yield phosphoric acid, sugars, and a mixture of organic bases (purines and pyrimidines). Nucleic acids are the main information- carrying molecules of the cell, and, by directing the process of protein synthesis, they determine the inherited characteristics of every living thing. The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids were first isolated by Friedrich Miescher (1869) from pus cells.They were named nuclein. Hertwig (1884) proposed nuclein to be the carrier of hereditary traits. Because of their acidic nature they were named nucleinic acids and then nucleic acids (Altmann, 1899). DNA structure DNA Nucleotides: The building blocks of nucleic acids are nucleotides. Nucleotides that compose DNA are called deoxyribonucleotides. The three components of a deoxyribonucleotide are a five-carbon sugar called deoxyribose, a phosphate group, and a nitrogenous base, a nitrogen-containing ring structure that is responsible for complementary base pairing between nucleic acid strands (Figure 1). The carbon atoms of the five-carbon deoxyribose are numbered 1ʹ, 2ʹ, 3ʹ, 4ʹ, and 5ʹ (1ʹ is read as “one prime”). A nucleoside comprises the five-carbon sugar and nitrogenous base. Page 1 Molecular Genetics Lecture 2 Dr.Sanaa Jassim Figure 1. (a) Each deoxyribonucleotide is made up of a sugar called deoxyribose, a phosphate group, and a nitrogenous base—in this case, adenine. (b) The five carbons within deoxyribose are designated as 1ʹ, 2ʹ, 3ʹ, 4ʹ, and 5ʹ. The deoxyribonucleotide is named according to the nitrogenous bases (Figure 2). The nitrogenous bases adenine (A) and guanine (G) are the purines; they have a double-ring structure with a six-carbon ring fused to a five-carbon ring. The pyrimidines, cytosine (C) and thymine (T), are smaller nitrogenous bases that have only a six-carbon ring structure. Figure 2. Nitrogenous bases within DNA are categorized into the two-ringed purines adenine and guanine and the single-ringed pyrimidines cytosine and thymine. Thymine is unique to DNA. Page 2 Molecular Genetics Lecture 2 Dr.Sanaa Jassim Individual nucleoside triphosphates combine with each other by covalent bonds known as 5ʹ-3ʹ phosphodiester bonds, or linkages whereby the phosphate group attached to the 5ʹ carbon of the sugar of one nucleotide bonds to the hydroxyl group of the 3ʹ carbon of the sugar of the next nucleotide. Phosphodiester bonding between nucleotides forms the sugar- phosphate backbone, the alternating sugar-phosphate structure composing the framework of a nucleic acid strand (Figure 3). During the polymerization process, deoxynucleotide triphosphates (dNTP) are used. To construct the sugar-phosphate backbone, the two terminal phosphates are released from the dNTP as a pyrophosphate. The resulting strand of nucleic acid has a free phosphate group at the 5ʹ carbon end and a free hydroxyl group at the 3ʹ carbon end. The two unused phosphate groups from the nucleotide triphosphate are released as pyrophosphate during phosphodiester bond formation. Pyrophosphate is subsequently hydrolyzed, releasing the energy used to drive nucleotide polymerization. Figure 3. Phosphodiester bonds form between the phosphate group attached to the 5ʹ carbon of one nucleotide and the hydroxyl group of the 3ʹ carbon in the next nucleotide, bringing about polymerization of nucleotides in to nucleic acid strands. Note the 5ʹ and 3ʹ ends of this nucleic acid strand. Page 3 Molecular Genetics Lecture 2 Dr.Sanaa Jassim Discovering the Double Helix: By the early 1950s, considerable evidence had accumulated indicating that DNA was the genetic material of cells, and now the race was on to discover its three-dimensional structure. Around this time, Austrian biochemist Erwin Chargaff (1905–2002) examined the content of DNA in different species and discovered that adenine, thymine, guanine, and cytosine were not found in equal quantities, and that it varied from species to species, but not between individuals of the same species. are also known as Chargaff’s rules. Chargaff’s Rules: Chargaff (1950) made observations on the bases and other components of DNA. These observations or generalizations are called Chargaff’s base equivalence rule. (i) Purine and pyrimidine base pairs are in equal amount, that is, adenine + guanine = thymine + cytosine. [A + G] = [T + C], i.e., [A+G] / [T+C] = 1 (ii) Molar amount of adenine is always equal to the molar amount of thymine. Similarly, molar concentration of guanine is equalled by molar concentration of cytosine. [A] = [T], i.e., [A] / [T] = 1; [G] = [C], i.e., [G] / [C] = 1 (iii) Sugar deoxyribose and phosphate occur in equimolar proportions. (iv) A-T base pairs are rarely equal to С—G base pairs. (v) The ratio of [A+T] / [G+C] is variable but constant for a species It can be used to identify the source of DNA. The ratio is low in primitive organisms and higher in advanced ones. Page 4 Molecular Genetics Lecture 2 Dr.Sanaa Jassim Analysis of the diffraction patterns of DNA has determined that there are approximately 10 bases per turn in DNA. The asymmetrical spacing of the sugar-phosphate backbones generates major grooves (where the backbone is far apart) and minor grooves (where the backbone is close together). These grooves are locations where proteins can bind to DNA. The binding of these proteins can alter the structure of DNA, regulate replication, or regulate transcription of DNA into RNA. Other scientists were also actively exploring this field during the mid- 20th century. In 1952, American scientist Linus Pauling (1901–1994) was the world’s leading structural chemist and odds-on favorite to solve the structure of DNA. Pauling had earlier discovered the structure of protein α helices, using X-ray diffraction, and, based upon X-ray diffraction images of DNA made in his laboratory, he proposed a triple-stranded model of DNA.At the same time, British researchers Rosalind Franklin (1920–1958) and her graduate student R.G. Gosling were also using X-ray diffraction to understand the structure of DNA. It was Franklin’s scientific expertise that resulted in the production of more well-defined X-ray diffraction images of DNA that would clearly show the overall double-helix structure of DNA. Watson and Crick proposed that DNA is made up of two strands that are twisted around each other to form a right-handed helix. The two DNA strands are antiparallel, such that the 3ʹ end of one strand faces the 5ʹ end of the other (Figure 4). The 3ʹ end of each strand has a free hydroxyl group, while the 5ʹ end of each strand has a free phosphate group. The sugar and phosphate of the polymerized nucleotides form the backbone of the structure, whereas the nitrogenous bases are stacked inside. These nitrogenous bases on the interior of the molecule interact with each other, base pairing. Page 5 Molecular Genetics Lecture 2 Dr.Sanaa Jassim Figure 4 Watson and Crick proposed the double helix model for DNA. (a) The sugar- phosphate backbones are on the outside of the double helix and purines and pyrimidines form the “rungs” of the DNA helix ladder. (b) The two DNA strands are antiparallel to each other. (c) The direction of each strand is identified by numbering the carbons (1 through 5) in each sugar molecule. The 5ʹ end is the one where carbon #5 is not bound to another nucleotide; the 3ʹ end is the one where carbon #3 is not bound to another nucleotide. Base pairing takes place between a purine and pyrimidine. In DNA, adenine (A) and thymine (T) are complementary base pairs, and cytosine (C) and guanine (G) are also complementary base pairs, explaining Chargaff’s rules ( Figure 5 ). The base pairs are stabilized by hydrogen bonds; adenine and thymine form two hydrogen bonds between them, whereas cytosine and guanine form three hydrogen bonds between them. Page 6 Molecular Genetics Lecture 2 Dr.Sanaa Jassim Figure 5. Hydrogen bonds form between complementary nitrogenous bases on the interior of DNA. Page 7