BCH 201 General Biochemistry 1 (Nucleic Acids) Lecture Notes PDF

DEPARTMENT OF BIOCHEMISTRY & MOLECULAR BIOLOGY FEDERAL UNIVERSITY DUTSIN-MA COURSE CODE: BCH 201 COURSE TITLE: General Biochemistry 1 (Chemistry of Nucleic Acids) NUMBER OF UNITS: 3 Units COURSE DURATION: Two hours per week COURSE LCTURER: Dr. Nura Lawal Definition: Nucleic aci...

DEPARTMENT OF BIOCHEMISTRY & MOLECULAR BIOLOGY FEDERAL UNIVERSITY DUTSIN-MA COURSE CODE: BCH 201 COURSE TITLE: General Biochemistry 1 (Chemistry of Nucleic Acids) NUMBER OF UNITS: 3 Units COURSE DURATION: Two hours per week COURSE LCTURER: Dr. Nura Lawal Definition: Nucleic acids are long-chain polymeric molecules, the monomer (the repeating unit) is known as the nucleotides and hence sometimes nucleic acids are referred to as polynucleotides. There are prominently two types of nucleic acids known to us. Deoxyribonucleic Acid (DNA) Chemically, DNA is composed of a pentose sugar, phosphoric acid and some cyclic bases containing nitrogen. The sugar moiety present in DNA molecules is β-D-2-deoxyribose. The cyclic bases that have nitrogen in them are adenine (A), guanine (G), cytosine(C) and thymine (T). These bases and their arrangement in the molecules of DNA play an important role in the storage of information from one generation to the next one. DNA has a double-strand helical structure in which the strands are complementary to each other. Ribonucleic Acid (RNA) RNA molecule is also composed of phosphoric acid, a pentose sugar and some cyclic bases containing nitrogen. RNA has β-D-ribose in it as the sugar moiety. The heterocyclic bases present in RNA are adenine (A), guanine (G), cytosine(C) and uracil (U). In RNA the fourth base is different from that of a DNA. The RNA generally consists of a single strand which sometimes folds back; that results in a double helix structure. Functions of Nucleic Acids 1. Nucleic Acid is responsible for synthesis of protein in our body 2. RNA is a vital component for protein synthesis. 3. Loss of DNA content is linked to many diseases. 4. DNA is an essential component required for transferring genes from parents to offspring. 5. All the information of a cell is stored in DNA. 1  6. DNA fingerprinting is a method used by forensic experts to determine paternity. It is also used for identification of criminals. Components of Nucleic acid: 1) Nitrogenous bases: Purines and pyrimidines are both organic compounds that take part in the synthesis of DNA and RNA; therefore they are called as the building blocks of the genetic materials. Purines Pyrimidines Purine is a heterocyclic aromatic organic Pyrimidine is a heterocyclic aromatic compound composed of a pyrimidine ring organic compound that is composed of fused with imidazole ring. carbon and hydrogen. It comprises adenine and guanine as It comprises Cytosine, thymine, uracil as Nucleobases Nucleobases It consists of two hydrogen-carbon rings It consists of one hydrogen-carbon ring and and four nitrogen atoms two nitrogen atoms The melting point of purine is 214 °C The melting point of pyrimidine is 20-22 °C Structures: 2 2) Sugar: Five carbon sugars are called pentoses. RNA contains the pentose D-Ribose, while 2- deoxy D-ribose is found in DNA. In both cases, the pentose is in the five membered ring form known as furanose: D-ribofuranose for RNA and 2-deoxy D-ribose for DNA. When these ribofuranoses are found in nucleotides, their atoms numbered as 1’, 2’, and 3’ and so on, to distinguish them from the ring atoms of the nitrogenous bases. An important property of the pentoses is their capacity to form esters with phosphoric acid. In this reaction, the OH- groups of the pentose, especially those at C3 and C5 are involved forming a 3’, 5’-phosphodiester bond between adjacent pentose residues. 3) Phosphoric acid residue: The molecular formula of phosphoric acid is H3PO4. It contains three monovalent hydroxyl groups and divalent oxygen atom, all linked to a pentavalent phosphorus atoms. Through 3’, 5’ phosphodiester bond, nucleotides linked in Nucleic acids. 3 Nucleosides and Nucleotides: Nucleosides: Nucleosides are compounds formed when a base is linked to a sugar via glycosidic bond. In nucleosides, the bond is an N-glycosidic because it connects the anomeric C’1 to N-1 of pyrimidine or to N-9 of a purine. The conformation of N-glycosidic bond is beta in purines and pyrimidines. Nucleosides are named by adding the ending –idine to the root name of a pyrimidine or –osine to the root name of purine. The nucleoside adenosine (A) is formed in this way from adenine and ribose, for example. The corresponding derivatives of the other bases are called guanosine (G), uridine (U), thymidine (T) and cytidine (C). When the sugar component is 2-deoxyribose, the product is a deoxyribonucleoside e.g., 2-deoxyadenosine. Mainly nucleosides serve as component parts of nucleotides. In exception, adenosine functions as an autocoid or local hormone. Adenosine acts locally on specific cells to cause blood vessels dilation, smooth muscle contraction, neuronal discharge, neurotransmitter release and influence fat metabolism. Adenosine is also implicated in sleep regulation. Increased levels of adenosine in brain cells promote sleepiness. Caffeine promotes wakefulness by blocking the interaction of extracellular adenosine with its neuronal receptors. Recently two nucleoside analogues 3’- azidodeoxythymidine and 2’, 3’-dideoxycytidine have been therapeutically used for the treatment of AIDS (Acquired immune deficiency syndrome) patients. They inhibit DNA synthesis in HIV by causing premature chain termination due to its analogues nature to dTTP and dCTP. Nucleotides: Nucleotides result when phosphoric acid is esterified to a sugar hydroxyl group of a nucleoside. Ribose sugar has three hydroxyl groups at C-2’, C-3’ and C-5’ where as deoxysugar has two hydroxyl groups at C-3’ and C-5’. The vast majority of monomeric nucleotides in the cell are ribonucleotides or deoxyribonucleotides having 5’-phosphate groups. Nucleotides have acidic properties because; they are referred by names like adenylic acid, guanylic acid etc. Structures of Nucleosides of RNA 4 Structures of Nucleosides of DNA Structures of Nucleotides of DNA Structures of Nucleotides of RNA 5 Partial structure of Polynucleotide of DNA Partial structure of Polynucleotide of RNA The monomeric deoxvnucleotides in DNA are held The monomeric deoxvnucleotides in together by 3', 5'-phosphodiester bridges. RNA are held together by 3', 5'- phosphodiester bridges. 6 Cyclic nucleotides Nucleoside monophosphates in which the phosphoric acid is esterified to two of the available ribose hydroxyl groups are found in all cells. Formation of two ester linkages with one phosphate results in cyclic structure example: cAMP and cGMP, they are act as secondary messenger which in turn act as important regulators of cellular metabolism. 7 Watson – Crick Model: In 1953, J.D. Watson (an American biologist) and F.H.C. Crick (a British Physicist) proposed the three dimensional model of physiological DNA. For this Watson, Crick and Wilkins got Nobel Prize in medicine in 1962. Term DNA was given by Zaccharis. The important features of Watson – Crick Model or double helix model of DNA are as follows: 1. The DNA molecule consists of two polynucleotide chains or strands that spirally twisted around each other and coiled around a common axis to form a right-handed double-helix. 2. The two strands are antiparallel i.e. they ran in opposite directions so that the 3′ end of one chain facing the 5′ end of the other. 3. The sugar-phosphate backbones remain on the outside, while the core of the helix contains the purine and pyrimidine bases. 4. The two strands are held together by hydrogen bonds between the purine and pyrimidine bases of the opposite strands. 5. Adenine (A) always pairs with thymine (T) by two hydrogen bonds and guanine (G) always pairs with cytosine (C) by three hydrogen bonds. This complimentarily is known as the base pairing rule. Thus, the two stands are complementary to one another. 6. The base sequence along a polynucleotide chain is variable and a specific sequence of bases carries the genetic information. 7. The base compositions of DNA obey Chargaff s rules. According to which A=T and G=C; as a corollary purines (A+G) = pyrimidines (C+T); also (A+C) = (G+T). It also states that ratio of (A+T) and (G+C) is constant for a species. 8. The diameter of DNA is 2 nm (20 A). Adjacent bases are separated 0.34nm (3.4 A) along the axis. The length of a complete turn of helix is 3.4nm (34 A) i.e. there are 10 base pairs per turn. 9. The DNA helix has a shallow groove called minor groove and a deep groove called major groove across. 8 Biological importance of DNA: 1. Hereditary material: The genetic information stored in the nucleotide sequence of DNA helps in synthesis of specific proteins or polypeptides and transmit the information to daughter cells or offspring’s. 2. Autocatalytic role DNA: DNA undergoes replication (self-duplication) in the S-phase of cell cycle. During the process each DNA strand of a double helix can act as template for the synthesis of daughter strand. 3. Hetero catalytic role: During transcription any one strand of DNA acts as template for the synthesis of RNA. This is called the hetero catalytic role of RNA. 4. Variations: DNA undergoes recombination its meiosis and occasional mutation (changes in nucleotide sequences) which creates variations in population and ultimately contributes to evolution. 5. DNA controls cellular metabolism, growth, and differentiation. 6. DNA finger printing (-DNA typing or profiling): This technique is used to identify criminals, determine paternity, verification of immigrant etc. 7. Recombinant DNA technology (Genetic engineering): It involves the artificial cleaving and rejoining DNA sequences from two or more organisms to create recombinant DNA. This technology is employed for production of genetically modified organisms (GMOs), genetically modified foods (GMFs), vaccines, hormones, enzymes, clones etc. Ribonucleic acid: RNA is a polymer of ribonucleotides held together by 3',5'-phosphodiester bridges. Although RNA has certain similarities with DNA structure, they have specific differences 1. Pentose: The sugar in RNA is ribose in contrast to deoxyribose in DNA. 2. Pyrimidine: RNA contains the pyrimidine uracil in place of thymine (in DNA). 9 3. Single strand: RNA is usually a single stranded polynucleotide. However, this strand may fold at certain places to give a double stranded structure, if complementary base pairs are in close proximity. 4. Chargaff's rule-not obeyed: Due to the single-stranded nature, there is no specific relation between purine and pyrimidine contents. Thus the guanine content is not equal to cytosine (as is the case in DNA). 5. Susceptibility to alkali hydrolysis: Alkali can hydrolyse RNA to 2',3'-cyclic dieters. This is possible due to the presence of a hydroxyl group at 2' position. DNA cannot be subjected to alkali hydrolysis due to lack of this group. TYPES OF RNA: The four major types of RNAs with respect to their cellular composition given below 1. Messenger RNA (mRNA): (5-1O %) functions as a carrier of genetic information from the DNA in the cell nucleus to the site of protein synthesis in the cytoplasm. mRNA has a short lifetime (usually less than one hour); it is synthesized as it is needed, then rapidly degraded to the constituent nucleotides. 2. Ribosomal RNA (rRNA): (80-85 %) the main component of ribosomes that are the site of protein synthesis. rRNA accounts for 80-85% of the total RNA of the cell. rRNA accounts for 65% of a ribosome’s structure (the remaining 35% is protein). 3. Transfer RNA (tRNA): (10-20%) delivers individual amino acids to the site of protein synthesis. tRNA is specific to one type of amino acid; cells contain at least one specific type of tRNA for each of the 20 common amino acids. tRNA is the smallest of the nucleic acids, with 73-93 nucleotides per chain. Central dogma of molecular biology: The central dogma of molecular biology states that “genetic information contained in the DNA is transferred to RNA molecules and then expressed in the structure of synthesized proteins”. 10 There are two steps in the flow of genetic information: Transcription: in eukaryotes, the DNA containing the stored information is in the nucleus of the cell, and protein synthesis occurs in the cytoplasm. The information stored in the DNA must be carried out of the nucleus by mRNA. Translation: mRNA serves as a template on which amino acids are assembled in the sequence necessary to produce the correct protein. The code carried by mRNA is translated into an amino acid sequence by tRNA. The communicative relationship between mRNA nucleotides and amino acids in a protein is called the genetic code. REFERENCES Horton, R.H., Laurence A.M., Scrimgeour, K.G., Marc, D. P., Rawn, J.D. (2006). Principles of Biochemistry. David, L.N., Michael, M.C. (2008). L e h n i n g e r Principles of Biochemistry. 4th edition. W.H. Freeman and Company New York. 11