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Chemistry of nucleic acids
Nucleic acids are polymers of nucleotides linked by phosphodiester bonds. There are two types: DNA and RNA. DNA contains the genetic information and directs protein synthesis. It exists as a double helix with nucleotides paired through hydrogen bonds between complementary bases (A-T and G-C). RNA is single-stranded and also involved in protein synthesis.
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Overview of nucleic acids, types (DNA, RNA) and their functions in genetics and heredity.
Structure of nucleic acids, basic components, nucleotides, and functions including energy currency.
Details of purine and pyrimidine bases, their structures, and biologically important derivatives.
Purine and pyrimidine bases in plants, analogs, and minor bases present in nucleic acids.
Structure, polymorphism, conformations, and Chargaff's rule for DNA with details on double helix.
Denaturation, melting temperature, and organization of DNA in prokaryotic and eukaryotic cells.
Structure of RNA, types (mRNA, tRNA, rRNA), their functions in protein synthesis and other roles.
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Chemistry of nucleic acids
- 1. CHEMISTRY OF DR. AREEBAGHAYAS TUTOR
- 2. WHAT ARE NUCLEICACIDS? Nucleic acids are polymers of a specific sequence of monomeric units called nucleotides, which are linked together through 3’, 5’ phosphodiester bonds.
- 4. There aretwo type of nucleic acids: • Deoxyribonucleic acid (DNA) • Ribonucleic acid (RNA) Nucleic acids serve as repositories and transmitters of genetic information.
- 5. FUNCTIONS OF NUCLEICACIDS DNA is the chemical basis of heredity. Reserve bank of genetic information. Responsible for maintaining the identity of different species of organisms over millions of years. Cellular function is under the control of DNA. The basic information pathway. DNA directs the synthesis of RNA, which in turn directs protein synthesis.
- 6. BASIC NUCLEIC ACIDSTRUCTURE POLYMERS of NUCLEOTIDES ↓ Held by 5’ and 3’ SUGAR PHOSPHATE BRIDGES
- 7. COMPOSITION OF NUCLEICACIDS (5-carbon)
- 8. NUCLEOTIDES Nucleotides arethe building blocks of nucleic acid. A nucleotide consists of three parts: 1. Heterocyclic base 2. Sugar 3. Phosphate
- 9. NUCLEOSIDE The moleculeswithout phosphate group is called nucleoside. The nitrogenous bases of nucleic acids are derivatives of two parents compounds Purines and Pyrimidines. The nitrogenous base of nucleotide is linked covantly to pentose sugar by β-N-glycosidic bond, almost always to N-1 of a pyrimidine or to N-9 of a purine.
- 10. FUNCTIONS OF NUCLEOTIDES Activated precursors of DNA & RNA. ATP – Universal currency of energy. GTP-involved in protein biosynthesis as source of energy. Activation of metabolic intermediates in many biosynthetic pathway-e.g.UDP-glucose & CDP-diacylglycerol. Carrier of methyl group: e.g., SAM (S-adenosylmethionine). Components of coenzymes: NAD, FAD & CoA. Metabolic regulators & chemical messengers e.g. cAMP, cGMP.
- 11. SUGAR in nucleotide Nucleic acid have two kinds of PENTOSES. Ribonucleotides of RNA contain β-D-ribose. Deoxyribonucleotides of DNA contain β-2’-deoxy-D- ribose. The prefix deoxy - means “without oxygen” . Nucleotides can be hydrolyzed to yield nucleosides and phosphoric acid.
- 14. PURINE BASES Twoprinciple purines bases are present in both DNA and RNA- 1. ADENINE (A) 2. GUANINE (G)
- 15. PYRIMIDINE BASES Themajor pyrimidine bases are- 1. Cytosine (C) 2. Uracil (U) 3. Thymine (T)
- 16. PURINES AND PYRIMIDINES Purines and pyrimidines are AROMATIC HETEROCYCLIC COMPOUNDS contain both carbon and other elements (hetero atoms).
- 17. BIOLOGICALLY IMPORTANT BASES URICACID is another purine base. It is the end product of purine nucleotide catabolism. Other Purine bases are HYPOXANTHINE & XANTHINE. They are intermediates in the formation of ADENINE & GUANINE nucleotides.
- 19. PURINES Purine basesare nine membered ring structures consisting of pyrimidine ring fused to imidazole ring. The atoms of purine ring are numbered in the anticlockwise manner.
- 20. • Adenine hasan amino group (-NH2) on the C6 position of the ring. • Guanine has an amino group at the C2 position and carbonyl group at the C6 position.
- 21. Minor Purines PresentNucleic Acids Several minor & unusual bases are often found in DNA & RNA. These include 5-methylcytosine, N4-acetylcytosine, N6 methyladenine, N6 dimethyl adenine N7 methylguanine. Importance: The unusual bases in nucleic acids help in the recognition of specific enzymes.
- 22. Purine Bases OfPlants Plants contain certain methylated purines. Caffeine in coffee. It acts as a stimulant. Theophylline in tea leaves. It acts as a bronchial smooth muscle relaxant. Theobromine in cocoa It acts as vasodilator ,lower blood pressure
- 23. PURINE ANALOG Theyhave structural similarities but inhibit the enzymes involved in the metabolism of purine nucleotides. 1. ALLOPURINOL: • Inhibits xanthine oxidase & used in the treatment of hyperuricemia (gout). 2. 6-MERCAPTOPURINE: • It inhibits purine nucleotide synthesis & used as an anticancer drug. 3. METABOLIC INTERMEDIATES: • These are formed during metabolism of nucleotides • E.g. hypoxanthine, xanthine & uric acid.
- 24. PYRIMIDINE BASES Pyrimidinescontain six membered nitrogenous ring. The atoms in pyrimidine ring are numbered in clockwise direction.
- 25. • Thymine containsa methyl group at C5 position with carbonyl groups at C4 and C2 positions. • Cytosine contains a carbonyl group at C2 position an amino group at C4.
- 26. Minor (Unusual) Pyrimidines Methylcytosine present in DNA Dihydrouracil present in tRNA. PYRIMIDINE ANALOGS: They have structural similarities but act as inhibitors of enzymes or interact with nucleic acids. 1. 5-fluorouracil: • It inhibits the enzyme thymidylate synthase. • It is used in the treatment of cancer.
- 27. Minor/Unusual Bases SpecificDNA and RNA contains small quantities of Minor/modified bases also. These modifications includes- • Methylation • Hydroxymethylation • Glycosylation • Alteration of atoms
- 28. Minor/Unusual base Modificationof Adenine: N-methyladenine, N6N6- dimethyladenine Modification of Guanine: 7-methylguanine Modification of Cytosine: 5-methylcytosine 5-hydroxymethylcytosine Modification of Uracil: Dihydroxyuracil
- 29. STRUCTURE OF DNA DNA is a polymer of deoxyribonucleotides. The monomeric units held together by 3’5’-phosphodiester bonds as back bone. DNA is very flexible molecule and has the ability to exist in various forms based on environmental conditions, a features known as structure polymorphism.
- 30. Conformations of DNAdouble helix The double helical structure of DNA exists in 6 forms A, B, C, D, E and Z form. Among these B, A & Z forms are important. B-form is most predominant form under physiological conditions. A-from is right-handed helix. It contains 11 base pairs. A-form DNA is tilted from the central axis.
- 31. Z-form isa left –handed helix and contains 12 base pairs per turn. The polynucleotide strands of DNA move in a zig- zag fashion called as Z-DNA. DNA also exists in certain unusual structures. These structure are important for molecular recognition of DNA by proteins & enzymes.
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- 34. CHARGAFF’S RULE DNAhas equal numbers of adenine & thymine residues (A=T) and equal number of guanine & cytosine residues (G=C). This is called as Chargaff’s rule of molar equivalence of between purines & pyramidines in DNA structure. RNAs which are usually single stranded, do not obey Chargaff’s rule.
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- 37. DNA double helix Double helical structure was proposed by Watson & Crick in 1953. The DNA is a right handed double helix. It consists of two polydeoxyribonucleotide chains twisted around each other on a common axis of symmetry. The chains are paired in an antiparallel manner, the 5'-end of one strand is paired with the 3'-end of the other strand.
- 38. One strandruns in the 5 ' to 3 ' direction while the other runs in 3' to 5 ' direction. The width (or diameter) of a double helix is 20Å (2nm). Each turn of helix is 34Å (3.4nm) with 10 pairs of nucleotides, each pair placed at a distance of about 3.4 Å. The hydrophilic deoxyribose-phosphate backbone of each chain is on the outside of the molecule, whereas the hydrophobic bases are stacked inside.
- 39. The polynucleotidechains are not identical but complementary to each other due to base pairing. The two strands are held together by hydrogen bonds between a purine & pyrimidine.(A = T, G = C) The spatial relationship between the two strands in the helix creates a major (wide) groove and a minor (narrow) groove.
- 40. These groovesprovide access for the binding of regulatory proteins to their specific recognition sequences along the DNA chain. DNA helix proves Chargaff’s rule. The genetic information resides on template strand or sense strand. The opposite strand is antisense strand.
- 41. COMPLEMENTARY STRANDS Thetwo strands of DNA are not identical but two strands are complementary to each other. Adenine pairs with thymine through two hydrogen bonds. Guanine pairs with cytosine through three hydrogen bonds.
- 42. G-C basepairs are more stable than A-T base pairs. Complementary base sequence accounts for chargaff’s rule. It also accounts for each DNA strand acting as a template for the synthesis of its complementary strand during DNA replication.
- 43. SIZE OF THEDNA MOLECULE Huge in size B-DNA with a thickness of 0.34nm Molecular weight of 660 daltons Length is expressed in base pairs(bp) A kilobase pair 103bp, a megabase pair(Mb) is 106bp & gigabase pair (Gp) is109 1kb=1000bp 1Mb=1000kb=1,000,000bp 1Gb=1000Mb=1,000,000,000bp Length varies from species to species
- 44. DENATURATION OF DNA The two strands of DNA are held together by hydrogen bonds Disruption of hydrogen bonds (by change in pH or increase in temperature) results in separation of strands The phenomenon of loss of helical structure of DNA is known as DENATURATION. Phosphodiester bonds are not broken by denaturation. It is measured by absorbance at 260nm.
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- 46. MELTING TEMPERATURE (TM) •It is defined as the temperature at which half of the helical structure of DNA is lost. • G-C base pairs are more stable than A-T base pair. • Tm is greater for DNAs with high content of G-C base pair. • Formamide destabilizes hydrogen bonds of base pairs. • This is used in rDNA technology. • RENATURATION (REANNEALING): • It is a process in which the separated complementary DNA strands can form a double helix.
- 47. ORGANIZATION OF DNAIN CELL PROKARYOTIC DNA: • The DNA is organized as a single chromosome in the form of double stranded circle. • Packed in the form of nucleoids. EUKARYOTIC DNA: • DNA is associated with various proteins to form chromatin which then organized into compact structures chromosomes.
- 48. Organization of DNAin cell
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- 50. Structure of RNA RNA is a polyribonucleotide It is single stranded polynucleotide. Phosphodiester bond links the nucleotides. Formed between 3-OH group of one pentose sugar & 5- OH group of another pentose sugar of ribonucleotide. Nucleotides found in RNA are : - AMP, GMP, CMP, UMP Thymine base absent in RNA. Minor methylated thymine & dihydrouracil also present.
- 51. Due tosingle–stranded nature, there is no specific relation between purines & pyramidine content. It will not obey the chargaff’s rule. • ALKALI HYDROLYSIS: Alkali can hydrolyse RNA to 2’3’-cyclic diesters. This is due to presence of OH group at 2’position. • Orcinol colour reaction: • RNAs can be identified by orcinol colour reaction due to presence of ribose.
- 52. Structures of DNA& RNA
- 53. Types of RNA Three major types: • Messenger RNA:5-10% • Transfer RNA:10-20% • Ribosomal RNA:50-80% RNAs are synthesized from DNA Involved in protein synthesis.
- 54. Messenger RNA (mRNA): •It carries genetic information from DNA for protein synthesis. • Precursor form is heterogeneous nuclear RNA(hnRNA) Structure: It contains • Cap: is an inverted 7-methyl GTP attached to 5'end. • 5'UTR: (5’untranslated region) is at the 5'end. • Coding region contains 3 types of codons: 1. Initiating codon-is always for AUG for methionine. 2. Specific codon-for different amino acids 3. Terminating codons-which are UGA, UAA & UAG.
- 55. • 3'UTR (3'untranslatedregion) at 3' end. • Polyadenylate tail (poly A tail): Consists of 200- 300 adenylate residues at the 3' end. mRNA accounts for 5 to 10% of total RNA. Function: It is required for protein biosynthesis
- 56. Transfer RNA (tRNA) Transfer RNA (soluble RNA) contains 71-80 nucleotides. Molecular weight-25,000. At least 20 species of tRNAs, corresponding to 20 Amino acids. Required for protein biosynthesis. It contains many unusual bases & nucleosides. Unusual bases present in t RNA are thymine, dihydrouracil, hypoxanthine,1-methyladenine & 2-N dimethyl guanine
- 57. Structure of tRNA Darm T ΨC arm Extra arm
- 58. • Pseudouridine isan unusual nucleoside found in t- RNA. Structure: • Clover leaf structure & it has five arms. • CCA arm: Cytosine-Cytosine-Adenine (CCA- arm) present at 3'end. It is an acceptor arm for the attachment of amino acids to form amino acyl tRNA. • D arm: contains dihydrouracil. • T¥C arm: (thymidine-pseudouridine-cytosine arm)
- 59. • Anticodon arm:contains of sequence of three bases that are complementary to codon mRNA. tRNA is also called adapter tRNA because it carries specific amino acids on its 3’ end along with anticodon at its anticodon arm. • Extra arm: also called variable arm. Based on length of extra arm-tRNA is classified into • Class-1 tRNA: Contain short arm (3-5 base pairs) • Class-2t RNA: Contain long arm (13-20base pairs)
- 60. • tRNA accountsfor 15-30% of total cellular RNAs. • tRNA is smaller in size. • tRNA is synthesized as precursor tRNA. • Mature form is formed by post transcriptional modifications. FUNCTIONS: • tRNA is required for protein synthesis. • It is required for the transfer of specific amino acids to the site of protein synthesis. • Also required for incorporation of specific amino acids to the growing polypeptide chain.
- 61. Ribosomal RNA r-RNAis found in ribosomes. Eukaryotic ribosomes are factories of protein synthesis. Composed of two major nucleoprotein complexes-60s subunit & 40s subunit 60s subunit contains- 28s rRNA, 5s rRNA & 5.8s rRNA 40s subunit contains- 18s rRNA
- 62. Cellular RNA &their functions
- 63. Synthetic Analogues ofNucleotides • Allopurinol: used in the treatment of hyperuricemia and gout. • 5-fluorouracil,6-mercaptopurine,8-guanine, 3- deoxyuridine,5- or 6-azauridine,5- or 6-azacytidine & 5-idouracil are used in treatment of cancer. Azathioprine is used to suppress immunological rejection during transplantation.
- 64. Arabinosyladenine isused for treatment of neurological diseases, viral encephalitis. Arabinosylcytosine is used in cancer therapy as it interferes with DNA replication. Zidovudine or AZT are sugar modified synthetic nucleotide analogs, used in the treatment of AIDS.