PowerPoint PresentationSlide 2Slide 3Slide 4Slide 5Slide 6Slide 7Slide 8Slide 9Slide 10Slide 11Slide 12Slide 13 The polymeric structure of nucleic acidsSlide 15Slide 16Slide 17Slide 18Conventions in writing DNA/RNA sequencesChargaff’s Rules (1951-’52)Slide 21Slide 22Slide 23Slide 24Slide 25Slide 26Slide 27Slide 28Slide 29Slide 30Slide 31Slide 32Slide 33Slide 34Slide 35Slide 36DNA Melting CurvesSlide 38Slide 39Slide 40Slide 41Slide 42Slide 43Slide 44Slide 45Slide 46Slide 47Slide 48Slide 49Slide 50Slide 51Lecture 21 (Chapter 33)Nucleotides and Nucleic AcidsLecture 21 (Chapter 33)Nucleotides and Nucleic Acids“We have discovered the secret of life.”Francis Crick, to patrons of The Eagle, a pub in Cambridge, England (1953)Francis Crick (right) and James Watson (left) point out features of their model for the structure of DNA.OutlineOutline• Central Dogma review• Differences between DNA and RNA• Nitrogenous bases• Nucleotides• Nucleic acids (DNA) -Composition of DNA (Chargaff’s Rule)-The DNA double helix (Watson-Crick)-Secondary structure of DNA (A, B, Z DNA)-Denaturation and Renaturation of DNA- Higher order packing of DNA in cells (chromosomes and histones)• Nucleic acids (RNA) secondary and tertiary structures of RNA• Central Dogma review• Differences between DNA and RNA• Nitrogenous bases• Nucleotides• Nucleic acids (DNA) -Composition of DNA (Chargaff’s Rule)-The DNA double helix (Watson-Crick)-Secondary structure of DNA (A, B, Z DNA)-Denaturation and Renaturation of DNA- Higher order packing of DNA in cells (chromosomes and histones)• Nucleic acids (RNA) secondary and tertiary structures of RNACentral DogmaCentral DogmaDNA and RNA differ in the sugar component and one of the bases DNA and RNA differ in the sugar component and one of the bases BaseBaseBaseBaseAlpha or Beta ?Alpha or Beta ?Nucleoside=Base + sugarNucleoside=Base + sugarDNA and RNA differ in the sugar component and one of the bases DNA and RNA differ in the sugar component and one of the bases BaseBaseBaseBasePPPPNucleotide=Base+sugar+phosphateNucleotide=Base+sugar+phosphateDNADNABackbones of DNA and RNABackbones of DNA and RNAPhosphodiester bridgesPhosphodiester bridgesRNARNA3’ -><- 5’Nitrogenous Bases: Pyrimidines-StructureNitrogenous Bases: Pyrimidines-StructureFound in both RNA and DNA*Found in RNA only The pyrimidine ringThe pyrimidine ringFound in DNA onlyNitrogenous Bases: Purines-StructureNitrogenous Bases: Purines-StructureBoth are found in both RNA and DNABoth are found in both RNA and DNAThe purine ring systemThe purine ring systemN-glycosidic bond links N1 of pyrimidines to C1 of deoxyribose" N9 of purines "The DeoxyribonucleotidesThe DeoxyribonucleotidesBases:AdenineAdenineGuanineGuanineThymineThymineCytosineCytosineN-glycosidic bond links N1 of pyrimidines to C1 of ribose" N9 of purines "The RibonucleotidesThe RibonucleotidesBases:AdenineAdenineGuanineGuanineUracylUracylCytosineCytosineNucleotidesNucleotides“High-energy” phosphoanhydride bonds“Low-energy” phosphomonoester bondCyclic NucleotidesCyclic Nucleotides- The phosphoric acid moiety is esterified to two of the available OH groups on the ribose ring- The phosphoric acid moiety is esterified to two of the available OH groups on the ribose ring(cAMP)(cAMP)The polymeric structure of nucleic acids The polymeric structure of nucleic acids5’3’RNA/DNA axisRNA/DNA axis5’--OH--3’-OHSense StrandSense StrandAntisense StrandAntisense StrandSense StrandSense StrandAntisense StrandAntisense StrandChemical Properties of purines and pyramidinesChemical Properties of purines and pyramidines1. UV light absorbance: important for measuring DNA concentration2. Nucleotides are polyprotic acids1. UV light absorbance: important for measuring DNA concentration2. Nucleotides are polyprotic acidsPurines and Pyrimidines- Absorption of UV lightPurines and Pyrimidines- Absorption of UV lightPyrimidines and Purines typically strongly absorb at UV at 260 nmPyrimidines and Purines typically strongly absorb at UV at 260 nmAt pH 7: A monomeric nucleotide (nucleoside monophosphate) has net charge of -2At pH 7: A monomeric nucleotide (nucleoside monophosphate) has net charge of -2Nucleic acids (polymers of nucleotides) derive their name due to the acidic nature of the phosphate groups of their component nucleotidesNucleic acids (polymers of nucleotides) derive their name due to the acidic nature of the phosphate groups of their component nucleotidesNucleotides (ribo and 2ʹ-deoxyribo) are polyprotic acids Nucleotides (ribo and 2ʹ-deoxyribo) are polyprotic acidsRNARNA5′-P end 3′-OH endReading direction5’-ACGU- 3’5’-p-ACGU- 3’5’-pApCpGpU- 3’5’-ACGU- 3’5’-p-ACGU- 3’5’-pApCpGpU- 3’Nucleic acids have directionalityNucleic acids have directionality-OHConventions in writing DNA/RNA sequencesConventions in writing DNA/RNA sequencesComplement to top strand (the bottom strand) can be written as:5’ - ATGTCG - 3’ 3’ - TACAGC – 5’Usually if you write a duplex sequence the top strand is 5’-3’ left to right.Usually if you write a duplex sequence the top strand is 5’-3’ left to right.5’- CGACAT-3’ or 3’TACAGC-5’(forward)(backward)Chargaff’s Rules (1951-’52)The % GC or AT varies between organisms but always A=T and G=C.(ds) [Purines] = [Pyrimidines]The Double Helix (Watson-Crick)The Double Helix (Watson-Crick)Based on Chargaff’s rule of DNA base composition, X-ray diffraction data obtained by Rosalind Franklin and Maurice WilkinsBased on Chargaff’s rule of DNA base composition, X-ray diffraction data obtained by Rosalind Franklin and Maurice WilkinsJames Watson and Francis Crick concluded that:James Watson and Francis Crick concluded that:DNA is a complementary Double HelixDNA is a complementary Double HelixDouble HelixDouble HelixNote that the strands are antiparallelNote that the strands are antiparallelphosphatephosphatedeoxyribosedeoxyriboseWatson and Crick base-pairsWatson and Crick base-pairsH-bondsH-bondsDouble Helix – B-form Double Helix – B-form ~ 10.4 nucleotides per turn~ 10.4 nucleotides per turnAxial view, looking down the helix axisAxial view, looking down the helix axisDouble HelixDouble HelixThe Major and Minor Grooves are lined sequence-specific hydrogen-bonding groupsThe Major and Minor Grooves are lined sequence-specific hydrogen-bonding groupsSSSSSSSSWatson and Crick base-pairsWatson and Crick base-pairsS =
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