2. Nucleosides & Nucleotides Nucleotides: 1. Nitrogenous base 2. Pentose 3. Phosphate Nucleosides: 1. Nitrogenous base 2. Pentose

3. Nucleotides & Nucleic Acids Nitrogenous bases are either pyrimidines or purines

4. Nucleotides & Nucleic Acids Nitrogenous bases are either pyrimidines or purines

7. Properties of Nucleotides/Bases CompoundMol. WeightMelt Pt (˚C) Uracil 112.09 338 Cytosine 111.10 320-5 Thymine 126.11 326 Adenine 135.11 360-5 Guanine 151.15 365 Deoxycytidine 5’-phosphate 321.24 187 Thymidine 5’-phosphate 322.21 Deoxyadenosine 5’-phosphate 331.22 142 Deoxyguanosine 5’-phosphate 347.23 360 (salt)

9. Naturally Occurring Modified Bases in tRNA Adenine 1-methyladenosine N 6 -methyladenosine Inosine (deaminated adenosine) 1-methylinosine Guanine 1-methylguanosine N 2 -methylguanosine N 2, N 2 -dimethylguanosine 7-methylguanosine Cytosine 3-methylcytidine 5-methylcytidine 2-thiocytidine N 4 -acetylcytidine Uracil Ribosylthymine (5-methyluridine) 5-methoxyuridine 5,6-dihydrouridine 4-thiouridine 5-methyl-2-thiouridine Pseudouridine (uracil attached to ribose at C5)

10. DNA Methylation Natural DNA contains:5-methylcytosine N 6 -methyladenine N 4 -methylcytosine 5-hydroxymethyluracil Sequence-specific methylation after DNA synthesis 0% to 100% methylation 5-methylcytosine (favors Z-DNA in CG sequences) Bacteria: methylation distinguishes self from foreign DNA (methylation after synthesis) base-base mismatch repair (nonmethylated strand scanned) Higher Eukaryotes: 5-methylcytosine is only methylated form found predominately at CpG role in gene expression (undermethylated  increase in transcription)

12. Nucleotides & Nucleic Acids Ribose sugars can be either 2’-deoxy (DNA)

13. Nucleotides & Nucleic Acids Ribose sugars... or have a 2’-OH (RNA)

18. H H H H H H H H TAUTOMERS

24. HOOGSTEEN

30. Nucleotides & Nucleic Acids

31. Hydrogen bonding patterns in RNA and DNA Involve ring N, carbonyls, amino groups Permits complementary association of 2 strands of nucleic acid (structure of DNA by Watson & Crick) Uridine (RNA)

32. Nucleotides & Nucleic Acids Chargaff’s rules 1940s 1. Base composition of DNA varies from one species to another 2. DNA from different tissues of same species have same base composition 3. Base composition of DNA in given species does not change with age, nutritional state, environment 4. In all cellular DNAs, regardless of species, the number of adenosine residues is equal to the number of thymidine residues (A=T), and the number of guanosines = cytidines (G=C) A + G (purines) = C + T (pyrimidines)

33. pKa values in nucleosides/tides Base Nucleoside3’-Nucleotide5’-Nucleotide (site of protonation) Adenine (N1) 3.523.703.88 Cytosine (N3) 4.174.434.56 Guanine(N7) 3.3(3.5)(3.6) Guanine (N1) 9.429.8410.00 Thymine (N3) 9.93-10.47 Uracil (N3) 9.389.9610.06 Data relate to 20 ˚C and zero salt concentration They correspond to loss of a proton for pKa > 9 and capture of a proton for pKa < 5

37. Nucleotides & Nucleic Acids Properties of RNA and DNA Bases hydrophobic at neutral pH, hydrophobic stacking interactions Stabilize 3D structure of nucleic acids

38. Nucleotides & Nucleic Acids Properties of RNA and DNA Nitrogenous rings are mostly planar Resonance in cyclic rings allow nucleotide bases to absorb UV light