1. Chapter 2
Nucleic Acids

2. Nucleic Acids Are Essential For Information Transfer in Cells
Information encoded in a DNA molecule is transcribed via synthesis of an RNA molecule
The sequence of the RNA molecule is "read" and is translated into the sequence of amino acids in a protein.

3. Central Dogma of Biology

4. Nucleic Acids First discovered in 1869 by Miescher.
Found as a precipitate that formed when extracts from nuclei were treated with acid.
Compound contained C, N, O, and high amount of P.
Was an acid compound found in nuclei therefore named nucleic acid

5. Nucleic Acids
1944 Oswald, Avery, MacLeod and McCarty demonstrated that DNA is the molecule that carrier genetic information.
1953 Watson and Crick proposed the double helix model for the structure of DNA

6. Nucleic Acids Nucleic acids are long polymers of nucleotides.
Nucleotides contain a 5 carbon sugar, a weakly basic nitrogenous compound (base), one or more phosphate groups.
Nucleosides are similar to nucleotides but have no phosphate groups.

7. Pentoses of Nucleotides
D-ribose (in RNA)
2-deoxy-D-ribose (in DNA)
The difference - 2'-OH vs 2'-H
This difference affects secondary structure and stability

8. Nitrogenous Bases

9. Bases are attached by b-N-glycosidic linkages to 1 carbon of pentose sugar – (Nucleoside)

10. Nucleosides Base is linked via a b-N-glycosidic bond
The carbon of the glycosidic bond is anomeric
Named by adding -idine to the root name of a pyrimidine or -osine to the root name of a purine
Conformation can be syn or anti
Sugars make nucleosides more water-soluble than free bases

12. Anti- conformation predominates in nucleic acid polymers

13. Nucleotides
Phosphate ester of nucleosides

14. The plane of the base is oriented perpendicular to the plane of the pentose group

15. Other Functions of Nucleotides
Nucleoside 5'-triphosphates are carriers of energy
Bases serve as recognition units
Cyclic nucleotides are signal molecules and regulators of cellular metabolism and reproduction
ATP is central to energy metabolism
GTP drives protein synthesis
CTP drives lipid synthesis
UTP drives carbohydrate metabolism

16. Nucleotide monomers are joined by 3’-5’ phosphodiester linkages to form nucleic acid (polynucleotide) polymers

17. Nucleic Acids Nucleic acid backbone takes on extended conformation.
Nucleotide residues are all oriented in the same direction (5’ to 3’) giving the polymer directionality.
The sequence of DNA molecules is always read in the 5’ to 3’ direction

18. Bases from two adjacent DNA strands can hydrogen bond
Guanine pairs with cytosine
Adenine pairs with thymine

19. Base pairing evident in DNA compositions

20. H-bonding of adjacent antiparallel DNA strands form double helix structure

21. Properties of DNA Double Helix
Distance between the 2 sugar-phosphate backbones is always the same, give DNA molecule a regular shape.
Plane of bases are oriented perpendicular to backbone
Hydrophillic sugar phosphate backbone winds around outside of helix
Noncovalent interactions between upper and lower surfaces of base-pairs (stacking) forms a closely packed hydrophobic interior.
Hydrophobic environment makes H-bonding between bases stronger (no competition with water)
Cause the sugar-phosphate backbone to twist.

22. View down the Double Helix
Hydrophobic
Interior with base pair stacking
Sugar-phosphate
backbone

23. Structure of DNA Double Helix
Right handed helix
Rise = 0.33 nm/nucleotide
Pitch = 3.4 nm / turn
10.4 nucleotides per turn
Two groves – major and minor

24. Within groves, functional groups on the edge of base pairs exposed to exterior
involved in interaction with proteins.

25. Factors stabilizing DNA double Helix
Hydrophobic interactions – burying hydrophobic purine and pyrimidine rings in interior
Stacking interactions – van der Waals interactions between stacked bases.
Hydrogen Bonding – H-bonding between bases
Charge-Charge Interactions – Electrostatic repulsions of negatively charged phosphate groups are minimized by interaction with cations (e.g. Mg2+)