Lect-10-Chemistry of Nucleotides PDF

Chemistry of Nucleotides 1 Intruduction Nucleotides are precursors of the nucleic acids: 1- deoxy-ribonucleic acid (DNA) 2- ribonucleic acid (RNA) The nucleic acids are concerned with the storage and transfer of genetic information. 3- The universal currency of energy, namely ATP, is a nucleotid...

Chemistry of Nucleotides 1 Intruduction Nucleotides are precursors of the nucleic acids: 1- deoxy-ribonucleic acid (DNA) 2- ribonucleic acid (RNA) The nucleic acids are concerned with the storage and transfer of genetic information. 3- The universal currency of energy, namely ATP, is a nucleotide derivative. 4- Nucleotides are also components of important co-enzymes like NAD+ and FAD, and metabolic regulators such as cAMP and cGMP. 2 Composition of Nucleotides A nucleotide is made up of 3 components: a. Nitrogenous base, (a purine or a pyrimidine) b. Pentose sugar, either ribose or deoxyribose 3 c. Phosphate groups esterified to the sugar. When a base combines with a pentose sugar, a nucleoside is formed. When the nucleoside is esterified to a phosphate group, it is called a nucleotide or nucleoside mono-phosphate. When a second phosphate gets esterified to the existing phosphate group, a nucleoside diphosphate is generated. The attachment of a 3rd phosphate group results in the formation of a nucleoside triphosphate. The nucleic acids (DNA and RNA) are polymers of nucleoside monophosphates. 4 Bases Present in the Nucleic Acids Two types of nitrogenous bases; the purines and pyrimidines are present in nucleic acids 1. Purine Bases The purine bases present in RNA and DNA are the same; adenine and guanine. Adenine is 6-amino purine and guanine is 2-amino, 6-oxypurine. 5 The numbering of the purine ring with the structure of adenine and guanine 2. Pyrimidine Bases The pyrimidine bases present in nucleic acids are cytosine, thymine and uracil. Cytosine is present in both DNA and RNA. Thymine is present in DNA and uracil in RNA 6 Nucleosides i. Nucleosides are formed when bases are attached to the pentose sugar, D-ribose or 2- deoxy D-ribose . ii. All the bases are attached to the corresponding pentose sugar by a beta-N-glycosidic bond between the 1st carbon of the pentose sugar and N9 of a purine or N1 of a pyrimidine. 7 iii. The deoxy nucleosides are denoted by adding the prefix d- before the nucleoside. iv. The carbon atoms of the pentose sugar are denoted by using a prime number to avoid confusion with the carbon atoms of the purine or pyrimidine ring . v. Nucleosides with purine bases have the suffix -sine, while pyrimidine nucleosides end with -dine. Adenine + ribose → Adenosine Guanine + ribose → Guanosine Uracil + ribose → Uridine Cytosine + ribose → Cytidine Thymine + ribose → Thymidine Adenine + deoxyribose → Deoxyadenosine vi. Uracil combines with ribose only; and thymine with deoxy ribose only . Name Examples Nucleosides in DNA* • Deoxyadenosine, deoxyguanosine, deoxycytidine, deoxythymidine Nucleosides in RNA† • Adenosine, guanosine, cytidine, uridine Other nucleosides • Pseudouridine, thymidine, S-adenosyl methionine, 5-deoxyadenosyl cobalamin 8 Nucleotides i. These are phosphate esters of nucleosides. Base plus pentose sugar plus phosphoric acid is a nucleotide. ii. The esterification occurs at the 5th or 3rd hydroxyl group of the pentose sugar. Most of the nucleoside phosphates involved in biological function are 5'-phosphates . iii. Since 5'-nucleotides are more often seen, they are simply written without any prefix. For example, 5'-AMP is abbreviated as AMP; but 3' variety is always written as 3'-AMP. iv. Moreover, a base can combine with either ribose or deoxy ribose, which in turn can be phosphorylated at 3' or 5' positions. One purine and one pyrimidine derivative are given as examples v. Many co-enzymes are derivatives of adenosine monophosphate. Examples are NAD+, NADP, FAD and Co-enzyme A. 9 vi. Nucleotides and nucleic acids absorb light at a wavelength of 260 nm; this aspect is used to quantitate them. As nucleic acids absorb ultraviolet light, chemical modifications are produced leading to mutation and carcinogenesis Nucleoside triphosphates i. Corresponding nucleoside di- and tri- phosphates are formed by esterification of further phosphate groups to the existing ones. In general, any nucleoside triphosphate is abbreviated as NTP or d-NTP . ii. Nucleoside diphosphate contains one high energy bond and triphosphates have 2 high energy bonds. ATP is the universal energy currency . It is formed during oxidative processes by trapping the released energy in the high energy phosphate bond. iii. A phosphodiester linkage may be formed between the 3' and 5' positions of ribose group. Such compounds are called cyclic nucleotides. 3', 5'-cyclic AMP or cAMP is a major metabolic regulator. Cyclic GMP also behaves similarly. These are second messengers in mediating the action of several hormones. iv. Deoxy ribonucleotides are used for synthesis of DNA and ribonucleotides for RNA. In pseudouridylic acid (found in tRNA) uridine is attached to ribose phosphate in a C-C bond instead of C-N bond in UMP. v. active methionine, amino acid adenylates, active sulfate etc are higher energy compounds containing adenosine monophosphate 10 Examples and functions of nucleotides 1- Adenosine, guanosine triphosphate (ATP), (GTP) • High-energy compounds 2- Cyclic adenosine, guanosine monophosphate (cAMP) (cGMP) 3- Nicotinamide adenine dinucleotide (NAD) (NADP) 4- Uridine diphosphate (UDP)-glucose 5- UDP-glucuronic acid • Second messenger • Coenzymes • Glycogen and UDP-glucuronic acid synthesis • Detoxification 6- Cytidine diphosphate (CDP)-choline • Synthesis of lecithin and sphingomyelin 7- 3’-phosphoadenosine-5’-phosphosulfate (PAPS) • Sulfate donor Watson-Crick model of DNA i. In 1953, Watson and Crick proposed the DNA structure . ii. DNA consists of two polydeoxyribonucleotide strands coiled around the same axis to form a right-handed helix. DNA is composed of 11 deoxyribonucleotides (deoxyribose + phosphate in diester linkage + bases like A, T, C, G). iii. Polydeoxyribonucleotide strand is formed by phosphodiester bond between 3’-OH group of one sugar and 5'-OH group of another sugar. iv. One strand is oriented in 5’ to 3’ direction; the other is oriented in 3’ to 5’ direction (antiparallel). v. The two strands are complementary to each other and are held together by hydrogen bonds between the bases. vi. Each strand acts as a template for synthesis of daughter DNA strand. vii. Base pairing rule: Adenine pairs with thymine by two hydrogen bonds; guanine pairs with cytosine by three hydrogen bonds. Four deoxyribonucleotides are deoxyadenylate, deoxyguanylate, deoxycytidylate and thymidylate. 12 The structure and functions of different types of RNAs. Ribonucleic acid (RNA) is a single-stranded polymer of ribonucleotides linked by phosphodiester bond between 3’-OH of a preceding nucleotide 13 and 5’-OH of next nucleotide. Ribonucleotides contain three major components: i. Ribose sugar. ii. Nitrogenous bases—purines (adenine and guanine) or pyrimidines (cytosine and uracil). iii. Phosphate. Types of RNA 1-Messenger RNA • Single-stranded polyribonucleotide strand formed by transcription. It carries genetic information from DNA for protein synthesis . • The mRNAs differ in size and sequences depending upon the protein that has to be synthesized • The coding region of mRNA is sandwiched between initiator codon (AUG) and terminator codons (UGA, UAA, UAG) • Poly(A) tail: 3’ terminal contains a polymer of adenylate residues, which stabilizes the mRNA • The mRNA is complementary to template strand of DNA. 14 2- Transfer RNA i. Transfer RNA (tRNA) functions as an adapter, which brings a specific amino acid from cytosol to the site of protein synthesis. ii. It is small in size (75 nucleotides). iii. Although there are 20 amino acids, around 32 tRNAs are found in humans. iv. Intrastrand hydrogen bonds present in tRNA gives it a clover leaf shape. v. A highly conserved sequence CCA is present towards the 3’ end (acceptor arm). The last nucleotide, adenine at the 3’ end is involved in binding covalently to a specific amino acid. vi. Three loops present in tRNA are: 15 • D arm: Formed by 2 or 3 dihydrouridine residues • Anticodon arm: It has a triplet codon (complementary to the codon on mRNA molecule) that specifically interacts with the codon on mRNA • TΨC arm: T, Ψ and C stands for thymine, pseudouridine and cytosine. 3- Ribosomal RNA i. Ribosomal RNAs (rRNAs) are the most abundant forms of RNA, which are associated with ribosomes. ii. They have catalytic activity (like enzymes). They have a role in translation 16 Differences between DNA and RNA DNA RNA Found in nucleus Found in nucleus and cytoplasm Bases are A, T, G and C Bases are A, U, G and C Deoxyribose is the sugar Ribose is the sugar component Double stranded Single stranded (usually) END OF THE LECTUER 17 Reference 1- TEXTBOOK OF BIOCHEMISTRY Sixth Edition For Medical Students DM VASUDEVAN MBBS MD FAMS FRCPath Distinguished Professor of Biochemistry College of Medicine, Amrita Institute of Medical Sciences, Cochin, Kerala (Formerly Principal, Colle ge of Medicine, Amrita, Kerala) (Formerly, Dean, Sikkim Manipal Institute of Medical Sciences, Gangtok, Sikkim) E-mail: [email protected] SREEKUMARI S MBBS MD Professor, Department of Biochemistry Sree Gokulam Medical College and Research Foundation Thiruvananthapuram, Kerala E-mail: [email protected] KANNAN VAIDYANATHAN MBBS MD Clinical Associate Professor, Department of Biochemistry and Head, Metabolic Disorders Laboratory Amrita Institute of Medical Sciences, Kochi, Kerala Email: [email protected] 2- orabys illustrated reviews of medical biochemistry ( part 1 )by said oraby Egypt 3- Quick Review of Biochemistry for Undergraduates Krishnananda Prabhu md Associate Professor Department of Biochemistry Kasturba Medical College Manipal University Manipal, Karnataka, India Jeevan K Shetty md Associate Professor Department of Biochemistry RAK College of Medical Sciences Ras Al Khaimah, UAE-SAS 18