Nucleosides Nucleotides 1 Nitrogenous base 2 Pentose 3
Nucleosides & Nucleotides: 1. Nitrogenous base 2. Pentose 3. Phosphate Nucleosides: 1. Nitrogenous base 2. Pentose
Nucleotides & Nucleic Acids Nitrogenous bases are either pyrimidines or purines
Nucleotides & Nucleic Acids Nitrogenous bases are either pyrimidines or purines
Properties of Nucleotides/Bases Compound Uracil Cytosine Thymine Adenine Guanine Deoxycytidine 5’-phosphate Thymidine 5’-phosphate Deoxyadenosine 5’-phosphate Deoxyguanosine 5’-phosphate Mol. Weight 112. 09 111. 10 126. 11 135. 11 151. 15 321. 24 322. 21 331. 22 347. 23 Melt Pt (˚C) 338 320 -5 326 360 -5 365 187 142 360 (salt)
Naturally Occurring Modified Bases in t. RNA Adenine 1 -methyladenosine N 6 -methyladenosine Inosine (deaminated adenosine) 1 -methylinosine Guanine 1 -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 C 5)
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 Cp. G role in gene expression (undermethylated increase in transcription)
Nucleotides & Nucleic Acids Ribose sugars can be either 2’-deoxy (DNA)
Nucleotides & Nucleic Acids Ribose sugars. . . or have a 2’-OH (RNA)
TAUTOMERS H H H
HOOGSTEEN
Nucleotides & Nucleic Acids
Nucleotides & Nucleic Acids 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)
Nucleotides & Nucleic Acids Chargaff’s rules 1940 s 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)
p. Ka values in nucleosides/tides Base (site of protonation) Adenine (N 1) Cytosine (N 3) Guanine (N 7) Guanine (N 1) Thymine (N 3) Uracil (N 3) Nucleoside 3. 52 4. 17 3. 3 9. 42 9. 93 9. 38 3’-Nucleotide 5’-Nucleotide 3. 70 4. 43 (3. 5) 9. 84 9. 96 3. 88 4. 56 (3. 6) 10. 00 10. 47 10. 06 Data relate to 20 ˚C and zero salt concentration They correspond to loss of a proton for p. Ka > 9 and capture of a proton for p. Ka < 5
Nucleotides & Nucleic Acids Properties of RNA and DNA Bases hydrophobic at neutral p. H, hydrophobic stacking interactions Stabilize 3 D structure of nucleic acids
Nucleotides & Nucleic Acids Properties of RNA and DNA Nitrogenous rings are mostly planar Resonance in cyclic rings allow nucleotide bases to absorb UV light
- Slides: 42