Structure of DNA and RNA, Nucleotides Nucleosides.pptx

structure of DNA and RNA

1. Structure of DNA and RNA

2. NUCLEOTIDE Composition of Nucleotides A nucleotide is made up of 3 components: Nitrogenous base (a purine or a pyrimidine) Pentose sugar , either ribose or deoxyribose Phosphate groups esterified to the sugar. When a base combines with a pentose sugar, a nucleoside is formed.

3. NUCLEOSIDE NUCLEOTIDE

4. When the nucleoside is esterified to a phosphate group, it is called a nucleotide or nucleoside monophosphate . 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 .

5. Nitrogenous Bases of RNA and DNA Two classes of nitrogenous bases namely purines and pyrimidines are present in RNA and DNA . Purine Bases Two principal purine bases found in DNAs, as well as RNAs Adenine (A) Guanine (G).

6. Pyrimidine Bases Three major pyrimidine bases are: Cytosine ( C) Uracil ( U) Thymine (T )

7. Cytosine and uracil are found in RNAs and cytosine and thymine in DNA. Both DNA and RNA contain the pyrimidine cytosine but they differ in their second pyrimidine base. DNA contains thymine whereas RNA contains uracil .

8. All the pyrimidine bases can exist in lactam form and Lactim form. If the group is –HN–CO–, it is called the Lactam type ( keto ), while the same if isomerises to – N = C – OH, it is called Lactim form ( enol ). At the physiological pH, the lactam ( keto ) forms are predominant.

9. Minor bases seen in nucleic acids

10. You read 3' or 5' as "3-prime" or "5-prime". (Ribose is the sugar in the backbone of RNA, ribonucleic acid.)

11. A phosphate group is attached to the sugar molecule in place of the -OH group on the 5' carbon. Nitrogenous bases attach in place of the -OH group on the 1' carbon atom in the sugar ring. Nucleotide The phosphate group on one nucleotide links to the 3' carbon atom on the sugar of another one forming 3’,5’ phosphodiester bridges

12. Sources of carbon and nitrogen in purine ring N1 of purine is derived from amino group of aspartate C2 and C8 arise from formate of N10 formyl THF N3 and N9 are obtained from amide group of glutamate C4,C5 and C7 are contributed by glycine C6 directly from CO2

13. Different major bases with their corresponding nucleosides and nucleotides Base Ribonucleoside Ribonucleotide Adenine (A) Adenosine Adenosine monophosphate (AMP) Guanine (G) Guanosine Guanosine monophosphate (GMP) Uracil (U) Uridine Uridine monophosphate (UMP) Cytosine (C) Cytidine Cytidine monophosphate (CMP)

14. Base Deoxyribonucleoside Deoxyribonucleotide Adenine Deoxyadenosine Deoxyadenosine monophosphate ( dAMP ) Guanine Deoxyguanosine Deoxyguanosine monophosphate ( dGMP ) Cytosine Deoxycytidine Deoxycytidine monophosphate ( dCMP ) Thymine Deoxythymidine Deoxythymidine monophosphate ( dTMP )

15. Structure of ATP and its components

16. BIOLOGICALLY IMPORTANT NUCLEOTIDES Adenosine nucleotides : ATP, ADP, AMP and Cyclic AMP . Guanosine nucleotides: GTP, GDP, GMP and cyclic GMP . Uridine nucleotides : UTP, UDP, UMP, UDP-G. Cytidine nucleotides : CTP, CDP, CMP and certain deoxy CDP derivatives of glucose, choline, ethanolamine

17. ATP ATP serves as the main biological source of energy in the cell. ATP is required as a source of energy in several metabolic pathways, e.g. fatty acid synthesis, glycolysis, cholesterol synthesis, protein synthesis, gluconeogenesis, etc. and in physiologic functions such as muscle contraction, nerve impulse transmission, etc.

18. AMP AMP is the component of many coenzymes such as NAD+, NADP+, FAD, coenzyme A, etc. These coenzymes are essential for the metabolism of carbohydrate, lipid and protein.

19. C-AMP (Cyclic adenosine 3', 5'-monophosphate ) c-AMP is formed from ATP by the action of adenylate cyclase . c-AMP acts as a second messenger for many hormones, e.g. epinephrine, glucagon, etc.

20. GDP and GTP These guanosine nucleotides participate in the conversion of succinyl -CoA to succinate. GTP is required for activation of adenylate cyclase by some hormones. GTP serves as an energy source for protein synthesis.

21. C-GMP (Cyclic guanosine 3', 5’-monophosphate ) c-GMP is formed from GTP by guanylyl cyclase . c-GMP is an intracellular signal or second messenger that can act antagonistically to c-AMP. c-GMP is involved in relaxation of smooth muscle and vasodilation

22. UDP ( Uridine diphosphate ) UDP participates in glycogenesis. UDP-glucose and UDP- galactose take part in galactose metabolism and required for synthesis of lactose and cerebrosides . UDP- glucuronic acid is required in detoxification processes and for biosynthesis of mucopolysaccharides such as heparin, hyaluronic acid, etc.

23. CTP ( Cytidine triphosphate) and CDP ( Cytidine diphosphate ) CTP and CDP are required for the biosynthesis of some phospholipids. CDP-choline is involved in the synthesis of sphingomyelin .

24. PURINE , PYRIMTDTNE AND NUCLEOTIDE ANALOGS Allopurinol is used in the treatment of hyperuricemia and gout 6 – thio -guanine and 6 – Mercaptopurine : In both of these naturally occurring purines, –OH groups are replaced by “ thiol ” (–SH) group at 6 – position of purine, widely used in clinical medicine. Azathioprine (which gets degraded to 6-mercaptopurine) is used to suppress immunological rejection during transplantation. Arabinosyladenine is used for the treatment of neurological disease.

25. DNA STRUCTURE AND FUNCTION

26. DNA is a polymer of deoxyribonucleotides ( or simply deoxynucleotides ) Deoxyribonucleotide is composed of a nitrogenous base, a sugar and phosphate group. The bases of DNA molecule carry genetic information, whereas their sugar and phosphate groups perform a structural role

27. The sugar in a deoxyribonucleotide is deoxyribose . The purine bases in DNA are adenine (A), and guanine (G). Pyrimidine bases are thymine (T) and cytosine (C ). The 3′-hydroxyl of one sugar is linked to the 5′-hydroxyl of another sugar through a phosphate group. Polarity of DNA molecule In the case of DNA, the base sequence is always written from the 5′ end to the 3′ end. This is called the polarity of the DNA chain.

28. Watson-Crick Model of DNA Structure A diagrammatic representation of the Watson and Crick model of the double-helical structure of the B form of DNA

29. Base pairing rule. Base pairing of A with T and G with C. Hydrogen bonds between bases

30. Features of DNA double helix are The DNA is right handed double helix . It consists of 2 polydeoxyribonucleotide chains ( strands ) twisted around each other on a common axis. The 2 strands are antiparallel i.e. one strand runs in 5’ to 3’ direaction and other in 3’ to 5’ direaction . The width/diameter of double helix is 20 angstrom( 2nm )

31. Each turn of the helix is 34 angstrom ( 3.4 nm ) with 10 pairs of nucleotides, each pair placed at a distance of 3.4 angstrom Each strand of DNA has a hydrophilic deoxyribose phosphate backbone on outside or periphery and hydrophobic bases at inside or core of the molecule. The 2 strands are not identical but complementary to each other due to base pairing.

32. The 2 strands are held together by hydrogen bonds formed by complementary base pairs . The A-T pair is double bond and G-C pair is triple bond. The hydrogen bonds are formed between a purine and a pyrimidine only . If 2 purines face each other they would not fit in the allowable space and 2 pyrimidine would be too far away to form bonds . Hence the possible spatial arrangements are A-T,T-A,G-C and C-G.

33. The complementary base pairing proves Chargaff’s rule . The amount of adenine = t hymine and g uanine = cytosine. One strand has genetic information and is known as sense strand or coding strand and the opposite strand is known as antisense strand. The double helix as wide/major grooves and narrow/minor grooves . Proteins can interact with DNA at these grooves without distrupting the base pairs.

34. Chargaff’s Rule Erwin Chargaff ( 1940 ) observed that in all species, The overall base composition of an organism is invariant. It can not be changed by changing environmental conditions, age or nutrition.    The base composition of one species is different from another species.  The base composition is the same in all the tissues of an organism. Also, the total sum of the purines is equal to the total sum of pyrimidines (A + G = T + C).  Chargaff’s rule: The number of adenine is always equal to the number of thymine and the number of cytosines are always equal to the number of guanines and the sum of the total purines are equal to the sum of the total pyrimidines

35. Types of DNA The double helical structure exists in atleast 6 different forms A to E and Z based on variation in conformation of nucleotides B-DNA ( described by Watson and Crick ) is most predominant under physiological conditions. The Z-form is left handed and arranged in “ zig zag ” fashion.

36. Triple-stranded DNA Triple-stranded DNA formation occur due to additional hydrogen bonds between the bases. Thus, a thymine can selectively form two Hoogsteen hydrogen bonds to the adenine of A-T pair to form T-A-T Likewise, a protonated cytosine can also form two hydrogen bonds with guanine of G-C pairs that results in C-G-C. Triple-helical structure is less stable than double helix. This is due to three negatively charged backbone strands in triple helix results in an increased electrostatic repulsion.

37. Four-stranded DNA Polynucleotides with very high contents of guanine can form a novel tetrameric structure. called G-quartets. These structures are planar and are connected by Hoogsteen hydrogen bonds. Antiparallel four-stranded DNA structures, referred to as G- tetraplexes have also been reported. The ends of eukaryotic chromosomes namely telomeres are rich in guanine, and therefore form G- tetraplexes .

38. DNA Denaturation Separation of double-stranded DNA into 2 single strands by breaking of hydrogen bonds between the bases is known as DNA denaturation It can be done by change in pH or increasing temperature or use of chemical agents ( Formamide ) Loss in helical structure can be measured by increase in absorbance at 260 nm in spectrophotometer. Tm ( Melting temperature ) – The temperature at which half of DNA has denatured

39. Above Tm DNA is single strands and below Tm DNA is double strand G-C base pairs ( 3 hydrogen bonds ) are stronger than A-T base pairs ( double bond ) so DNA with more G-C content have greater Tm. Renaturation ( reannealing ) – is process by which the seperated complementary DNA strands can form double helix

40. Organization of DNA DNA is a long structure . i.e In a Diploid Human cell , the DNA size is 6.0 x 10 9 bp and contour length 2 meter . Such a long DNA has to be packed in a nucleus of about 10um size. In prokaryotes DNA is organized as a single chromosome in form of a double stranded circle

41. Organization in Eukaryotes DNA double helix wrap around a core of eight histone proteins . The DNA-histone complex is called chromatin . The double helix of DNA is highly negatively charged due to all the negatively charged phosphates in the backbone. Histones are positively charged proteins due to being rich in arginine and lysine amino acids so histones bind with DNA very tightly. Core histones are H2A, H2B, H3, and H4

42. Two each of the histones (H2A, H2B, H3, and H4) come together to form a histone octamer which binds and wraps approximately 2 turns of DNA, or about 150 base pairs . This complex is known as nucleosome . Two adjacent nucleosomes are connected by linker DNA to which H1 histone is attached . These Nucleosome chain gives a ‘ beads on string ’ appearance and length of DNA is now condensed to 10 nm fibre

43. which gets further condensed and coiled to produce a solenoid of 30 nm diameter. This solenoid structure undergoes further coiling to produce a chromatid of 700 nm. Chromatin is held over a scaffold of non-histone chromosomal or NHC proteins .

44. chromatin is densely packed to form darkly staining heterochromatin. At other places, chromatin is loosely packed to form euchromatin which is lightly stained . Euchromatin is transcriptionally active chromatin whereas heterochromatin is transcriptionally inactive During the course of mitosis the loops are further coil becomes highly compacted into chromosomes that become visible under light microscope ( during metaphase

45. DNA wraps twice around histone octamer to form one nucleosome

46. Ribonucleic acid (RNA) DNA is double stranded, while RNA single stranded

47. RNA is a polymer of ribonucleotides held together by 3',5'-phosphodiester bridges. Although RNA has certain similarities with DNA structure, they have specific difference

48. Pentose : The sugar in RNA is ribose in contrast to deoxyribose in DNA. Pyrimidine : RNA contains the pyrimidine uracil in place of thymine (in DNA). Single strand : RNA is usually a single stranded polynucleotide. 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

49. Susceptibility to alkali hydrolysis : Alkali can hydrolyse RNA to 2',3'-cyclic diesters . 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.

50. Types of RNA The 3 major types of RNA are Messenger RNA (mRNA) Transfrer RNA ( tRNA ) Ribosomal RNA ( rRNA ) All of these are involved in the process of protein biosynthesis. Each differs from the others by size and function.

51. Messenger RNA (mRNA): The gene present in DNA is transcribed into mRNA. This constitutes about 2–5% of total RNA in the cell. They are generally degraded quickly. Ribosomal RNA ( rRNA ): This constitutes about 80% of all RNA in the cell. 28S, 18S and 5S are the major varieties. They are involved in protein biosynthesis and are very stable.

52. Transfer RNA ( tRNA ): There are about 60 different species present. They constitute about 15% of the total RNA in the cell. They are very stable . Micro RNA ( miRNA ): They alter the function of mRNA. They are moderately stable.

53. Small RNA: They constitute about 1–2% of total RNA in the cell. There are about 30 different varieties. They are very stable. Small Nuclear RNAs ( SnRNAs ) are a subgroup of small RNA. Some important species of SnRNAs are U1 (165 nucleotides), U2 (188 nucleotides), U3 (216), U4 (139), U5 (118), U6 (106). They are involved in mRNA splicing

54. Structure of mRNA mRNA is synthesized in the nucleus as heterogenous RNA ( hnRNA ), which are processed into functional mRNA. The mRNA carries the genetic information in the form of codons. Codons are a group of three adjacent nucleotides that code for the amino acids of protein.

55. In eukaryotes mRNAs have some unique characteristics , e.g. the 5' end of mRNA is “capped” by a 7- methyl- guanosine triphosphate. The cap is involved in the recognition of mRNA in protein biosynthesis and it helps to stabilize the mRNA by preventing attack of 5'-exonucleases.

56. A poly (A) “tail” is attached to the other 3'-end of mRNA. This tail consists of series of adenylate residues, 20-250 nucleotides in length joined by 3' to 5' phosphodiester bonds.

57. Function of mRNA mRNAs serve as template for protein biosynthesis and transfer genetic information from DNA to protein synthesizing machinery . If the mRNA codes for only one peptide, the mRNA is monocistronic . If it codes for two or more different polypeptides, the mRNA is polycistronic . In eukaryotes most mRNA are monocistronic .

58. Transfer RNA ( tRNA ) All single stranded transfer RNA molecules get folded into a structure that appears like a clover leaf. They contain a significant proportion of unusual bases . These include dihydrouracil (DHU ), pseudouridine ( Ψ ) and hypoxanthine . Moreover, many bases are methylated.

59. Three unusual (modified) nucleosides present in tRNA

60. All t-RNAs contain four main arms : The acceptor arm. The D arm The anticodon arm The TψC arm.

61. Structure of clover leaf transfer RNA

62. The acceptor arm : This arm is capped with a sequence CCA (5'to 3'). The amino acid is attached to the acceptor arm. The anticodon arm : This arm, with the three specific nucleotide bases (anticodon), is responsible for the recognition of triplet codon of mRNA. The codon and anticodon are complementary to each other. The D arm : lt is so named due to the presence of dihydrouridine .

63. The T ψ C arm contains both ribothymidine (T) and pseudouridine ( ψ, psi ). The extra arm is also known as variable arm because it varies in size, is found between the anticodon and TψC arms.

64. Ribosomal RNA ( rRNA ) The ribosomes are the factories of protein synthesis. The eukaryotic ribosomes are composed of two major nucleoprotein complexes-60S subunit and 40S subunit. The 60S subunit contains 28S rRNA , 5S rRNA and 5.8S rRNA . while the 40S subunit contains 18S rRNA .