2. Nucleosides & 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
Compound Mol. Weight Melt Pt (˚C)
Uracil
Cytosine
Thymine
Adenine
Guanine
Deoxycytidine 5’-phosphate
Thymidine 5’-phosphate
Deoxyadenosine 5’-phosphate
Deoxyguanosine 5’-phosphate (salt)

9. Naturally Occurring Modified Bases in tRNA
Adenine
1-methyladenosine
N6-methyladenosine
Inosine (deaminated adenosine)
1-methylinosine
Guanine
1-methylguanosine
N2-methylguanosine
N2, N2 -dimethylguanosine
7-methylguanosine
Cytosine
3-methylcytidine
5-methylcytidine
2-thiocytidine
N4-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
N6-methyladenine
N4-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. TAUTOMERS H H

24. HOOGSTEEN

30. Nucleotides & Nucleic Acids

31. 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)

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 Nucleoside 3’-Nucleotide 5’-Nucleotide
(site of protonation)
Adenine (N1)
Cytosine (N3)
Guanine (N7) (3.5) (3.6)
Guanine (N1)
Thymine (N3)
Uracil (N3)
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