Structure and forms of dna&rna


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Structure and forms of dna&rna

  1. 1. Rashmi Vijay
  2. 2.  A pentose sugar – deoxy riobose sugar Nucleotides – A,T,G,C a phosphate
  3. 3.  Deoxyribose sugar  4 C atoms and oxygen molecule forms the ring  5th C atom is outside the, part of CH2 group  3 OH groups at positions 1,3,5
  4. 4. Purines are double ring compounds with 5 membered imidazole ring joined topyrimidine ring at positions 4’ and 5’Pyrimidines are single ring compounds with nitrogenous bases at positions 1,3 of a 6membered benzene ring
  5. 5.  Alternate with deoxyribose sugars joined by 3’-C atom of one deoxyribose to 5’-C atom of the other
  6. 6.  Nucleotide = a nitrogenous (nitrogen- containing) base + a pentose + a phosphate Nucleoside = a nitrogenous (nitrogen- containing) base + a pentose
  7. 7. Nucleotide Base Pairing
  8. 8. Formation ofPhosphodiester bondsto make apolynucleotide strand
  9. 9.  The discovery of the structure of DNA by Watson and Crick in 1953 was a momentous event in science, an event that gave rise to entirely new disciplines and influenced the course of many established ones. Won Nobel Prize
  10. 10. 1. Right handed double helix, wound around central axis with plectonemic coiling.2. Two polynucloetide strands run antiparallel3. The offset pairing of the two strands creates a major groove and minor groove on the surface of the duplex4. Phosphate and dRibose forms the back bone of each polynucloetide strand5. Nitrogen bases are projected inward6. Two polynucloetide strands held together by H- bonds , AT and GC7. Each base pair tilts 360 and hence has 3600, and each of this turn has 10 nucleotide base pair8. Bases are place at a distance of 3.4 A09. Diameter of the helix 20 A010. Molecular weight / unit length = 2x10 6/ micrometr
  11. 11.  To shed more light on the structure of DNA, Rosalind Franklin and Maurice Wilkins used the powerful method of x-ray diffraction to analyze DNA fibers. They showed in the early 1950s that DNA produces a characteristic x-ray diffraction pattern. In 1953 Watson and Crick postulated a three dimensional model of DNA structure that accounted for all the available data.
  12. 12.  Erwin Chargaff developed a chemical technique to measure the amount of each base present in DNA. Chargaff also observed certain regular relationships among the molar concentrations of the different bases. These relationships are now called Chargaff’s rules
  13. 13. Chargaff’s rules  He found that the base composition of the DNA, defined as the percent G+C, differs among species but is constant in all cells of an organism and within a species.
  14. 14.  The biochemical investigation of DNA began with Friedrich Miescher, who in the year 1868 isolated a phosphorus- containing substance, which he called “nuclein,” from the nuclei of pus cells (leukocytes) obtained from discarded surgical bandages. Miescher and many others suspected this substance is in some way with cell inheritance, but the first direct evidence that DNA is the bearer of genetic information came in 1944 through a discovery made by Oswald T. Avery, Colin MacLeod, and Maclyn McCarty.
  15. 15.  These investigators found that DNA extracted from a virulent (disease-causing) strain of the bacterium Streptococcus pneumoniae, also known as pneumococcus, genetically transformed a nonvirulent strain of this organism into a virulent form.
  16. 16.  When injected into mice, the encapsulated strain of pneumococcus is lethal, whereas the nonencapsulated strain, like the heat-killed encapsulated strain, is harmless. Earlier research by the bacteriologist Frederick Griffith had shown that adding heat-killed virulent bacteria (harmless to mice) to a live nonvirulent strain permanently transformed the latter into lethal, virulent, encapsulated bacteria. Avery and his colleagues extracted the DNA from heat-killed virulent pneumococci, removing the protein as completely as possible, and added this DNA to non-virulent bacteria. The DNA gained entrance into the non-virulent bacteria, which were permanently transformed into a virulent strain. Avery and his colleagues concluded that the DNA extracted from the virulent strain carried the inheritable genetic message for virulence.
  17. 17.  A second important experiment provided independent evidence that DNA carries genetic information. In 1952 Alfred D. Hershey and Martha Chase used radioactive phosphorus (32P) and radioactive sulfur (35S) tracers to show that when the bacterial virus (bacteriophage) T2 infects its host cell, Escherichia coli, it is the phosphorus-containing DNA of the viral particle, not the sulfur-containing protein of the viral coat, that enters the host cell and furnishes the genetic information for viral replication
  18. 18.  DNA is a remarkably flexible molecule. Many significant deviations from the Watson- Crick DNA structure are found in cellular DNA, some or all of which may play important roles in DNA metabolism. These structural variations generally do not affect the key properties of DNA defined by Watson and Crick: strand complementarity, antiparallel strands, and the requirement for A=T and G C base pairs.
  19. 19.  Structural variation in DNA reflects three things:  the different possible conformations of the deoxyribose,  rotation about the contiguous bonds that make up the phosphodeoxyribose backbone, and  Free rotation about the C-1–N- glycosyl bond
  20. 20. Comparison of A, B, and Z forms of DNA.Each structure shown here has 36 base pairs.The bases are shown in gray, thephosphate atoms in yellow, and the ribosesand phosphate oxygens in blue. Blue is thecolor used to represent DNA strands in laterchapters.
  21. 21.  The Watson-Crick structure is  Whether A-DNA occurs in also referred to as B-form cells is uncertain, but there is DNA, or B-DNA, which is evidence for some short the most stable structure for stretches (tracts) of Z-DNA in a random-sequence DNA both prokaryotes and molecule under physiological eukaryotes. conditions and is therefore the standard point of  These Z-DNA tracts may play reference in any study of the a role (as yet undefined) in properties of DNA. regulating the expression of some genes or in genetic Two structural variants that recombination. have been well characterized in crystal structures are the A and Z forms.
  22. 22.  Single stranded polymer of nucleotide monomers made of Ribose sugar, Nitrogenous bases and Phosphate group The structure of RNA is similar to, but not identical with, that of DNA. There is a difference in the sugar (RNA contains the sugar ribose instead of deoxyribose), RNA is usually single-stranded (not a duplex), and RNA contains the base uracil (U) instead of thymine (T), which is present in DNA.
  23. 23.  Serves as genetic material in some Viruses Present in 3 predominant forms rRNA, tRNA and mRNA Normally doesnt replicate or transcribe Made of fewer nucleotides (max 12000) Chain starts with adenine or guanine Contents expressed in terms of sedimentation coefficients ‘S’ – Svedberg constant
  24. 24.  rRNA = forms 80% total cellular RNA tRNA = 10-20% total cellular RNA mRNA = 3-5% total cellular RNA
  25. 25.  Found in Ribosomes most abundant RNA in cells (75%) most stable RNA in cells
  26. 26.  four species rRNA in eukaryotes  28S rRNA (large subunit)  5.8S rRNA (large subunit)  5S rRNA (large subunit)  18S rRNA (small subunit) 28, 18 & 5.8S rRNA are synthesized as a single transcript, then processed -DNA has one promoter, one termination sequence for all three pieces of rRNA -DNA has multiple copies of the whole transcription unit.  cut into pieces yielding four spacers & 3 rRNAs.  spacers are broken down to nucleotides.  rRNA pieces bind ribosomal proteins and begin to self assemble into ribosomal subunits 5S rRNA transcribed from another gene as a separate transcription unit three species of rRNA in prokaryotes 23S in large subunit, 5S in the large subunit and 16S in the small subunit
  27. 27. Types of rRNA
  28. 28.  Made up of nucleotides twisted around itself at some region forming helical structure The strand assumes a shape of rod, coil or extended strand depending on ionic strength, temp, pH. In helical region, most of the bases are complementary and are joined by H – bonds The unpaired/unfolded single strand will have bases, and are not complementary, hence don’t show purine-pyrimidine equality rRNA strand unfold upon heating and refold on cooling
  29. 29. Secondary structures of rRNA
  30. 30. Secondary structures of rRNA
  31. 31.  Jacob and Monod coined the term mRNA least abundant (about 5%) of cellular RNAs mRNA may be mono or poly cistronic. bacterial mRNA is not processed eukaryotic mRNA is processed initial eukaryotic transcripts are quite large  allows for posttranscriptional regulation of gene expression  introns, exons and splicing (1) eukaryotic mRNAs contain "introns“ (2) introns = intervening sequences (3) exons = expressed sequences (4) introns must be excised from mRNA before translation (5) RNA splicing = process of excising introns from mRNA and splicing the mRNA back together
  32. 32.  Single stranded linear molecule without any base pairing (base pairing destroys its nature) They have complementary sequence to the segment of DNA on which they are transcribed
  33. 33.  Cap: region at 5’ end. Important for protein synthesis, otherwise mRNA binds poorly to ribosomes. cap protects mRNA from 5-endonucleases Non coding region - I (leader): region next to cap with 10-100 nucleotides. Rich in A & U residues and doesnt translate into proteins Initiation codon: region next NC-I. Common in both Prokaryotes and Eukaryotes The coding region: consists an average of 1500 nucleotides, which translates in to amino acids Termination Codon: do not code for any amino acids and thus brings termination of translation Non coding region – II (trailer): consists about 50-150 nucleotides. doesnt translate into proteins. Contains AAUAA in all sequenced examples Poly ‘A’ sequence: present at 3’ end. Contains about 200-250 nucleotides, which become shorter with age of the organism. Poly ‘A’ is added in nucleus before m-RNA reaches the cytoplasm from nucleus.
  34. 34. mRNA has rapid turnover. rRNA & tRNA are stable (days, months) - rRNA deeply buried in structure of ribosomes both rRNA and tRNA have many modified bases -modified bases help protect against nuclease attack mRNA turns over fast  bacterial mRNA half life = minutes  eukaryotic mRNA half life = hours
  35. 35.  nucleotide composition of mRNA : mRNA base composition like total genomic DNA base sequence complementarity of mRNA: measure complementarity by doing RNA-DNA hybridization size heterogeneity: mRNA varies greatly in size relative to rRNA & tRNA. mRNA varies in size depending on protein for which it codes gene amplification: one gene (DNA) gives rise to many transcripts (mRNA). each transcript can be translated to many proteins. get more proteins faster
  36. 36.  2nd most abundant (20%) RNA in cells synthesized in precursor form and then processed 16 nucleotide leader sequence removed from 5 end and terminal UU is removed from 3 end ,UU replaced by CCA CCA found at the 3 end of all functional tRNAs intron "loop" is removed many bases methylated many bases modified –  uracil converted to dihydrouracil, ribothymine or pseudouridine  adenine converted to inosine Transfer RNAs vary in length from 73 to 93 nucleotides.
  37. 37. Nucleotide sequence of yeast tRNA Ala.This structure was deduced in 1965 by Robert W.Holley and his colleagues;it is shown in the cloverleaf conformation inwhich intrastrand base pairing is maximal.The following symbols are used for the modifiednucleotides (shaded pink): , Ψ, pseudouridine; I, inosine; T, ribothymidine; D, 5,6-dihydrouridine; mI I, 1-methylinosine; m1G, 1-methylguanosine; m2G, N2-dimethylguanosineBlue lines between parallel sections indicateWatson-Crick base pairs.The anticodon can recognize three codons foralanine (GCA, GCU, and GCC).Note the presence of two G=U base pairs,signified by a blue dot to indicate non-Watson-Crickpairing.In RNAs, guanosine is often basepaired withuridine, although the G=U pair is not as stable as theWatson- Crick G=C pair
  38. 38. Extra nucleotides occur in the extra arm or inthe D arm.Two of the arms of a tRNA are critical for itsadaptor function.The amino acid arm can carry a specificamino acid esterified by its carboxyl group tothe 2- or 3-hydroxyl group of the amino acidresidue at the 3 end of the tRNA.The anticodon arm contains the anticodon.The other major arms are the D arm (DHUarm), which contains the unusual nucleotidedihydrouridine (D), and the T Ψ C arm, whichcontains ribothymidine (T), not usually presentin RNAs, and pseudouridine (Ψ), which has anunusual carbon–carbon bond between the baseand ribose.The D and T Ψ C arms contribute importantinteractions for the overall folding of tRNAmolecules,and the T Ψ C arm interacts with the large-subunit rRNA.