1. Chapter 27 Nucleosides, Nucleotides, and Nucleic Acids I Irene Lee Case Western Reserve University Cleveland, OH ©2004, Prentice Hall Organic Chemistry 4 th Edition Paula Yurkanis Bruice

2. Nucleic Acids

3. In nucleic acid, the phosphate group is phosphodiester

4. The Bases in Nucleic Acids Adenine, guanine, cytosine, and thymine are found in DNA Adenine, guanine, cytosine, and uracil are found in RNA

5. Nucleosides = Base + Sugar

6. Nucleotides = Base + Sugar + Phosphate

8. Different Forms of Nucleotides

9. The energy released from ATP hydrolysis is used to drive the phosphorylation of D-gluose (coupled reactions) ATP as a Chemical Energy Source

10. Breakage of the Phosphoanhydride Bond in ATP

11. Without ATP, the OH – group cannot be displaced

12. This reaction does not occur without ATP because of the poor leaving group

13. Phosphoryl Transfer Reaction Mechanism I

14. Phosphoryl Transfer Reaction Mechanism II

15. Phosphoryl Transfer Mechanism III

16. Pyrophosphate can be further hydrolyzed to phosphate

17. Why is the hydrolysis of a phosphoanhydride bond so exergonic?

18. 1. Greater electrostatic repulsion in ATP 2. More solvation in the products 3. Greater resonance stabilization in the products

19. The interactions between ATP, Mg 2+, and arginine and lysine residues at the active site of an enzyme Since all the negative charges in ATP are neutralized, ATP is readily approached by nucleophiles

20. Other Important Nucleotides Cyclic AMP serves as a link between several hormones and certain enzymes that regulate cellular function

21. The Nucleic Acids Biosynthesis of DNA occurs in the 5’ 3’ direction

22. Complementary Base Pairing in DNA

24. The sugar–phosphate is on the outside, and the bases are on the inside

25. The DNA Double Helix

26. Hydrolysis of RNA

27. The Three Helical Forms of DNA Hydrogen bonding and base stacking interactions hold the DNA helix together

29. Replication of DNA

30. Transcription of DNA A stretch of bases representing a portion of a gene is called an exon A stretch of bases that contain no genetic information is called an intron mRNA is spliced prior to leaving the nucleus

31. A Transfer RNA

32. The Proposed Mechanism for Aminoacyl-tRNA Synthetase

33. The Substrate-Binding Site for tRNA His

34. A protein is synthesized from its N-terminal end to its C-terminal end Each amino acid is specified by a three-base sequence known as the genetic code

35. Translation

37. Why does DNA contain thymine instead of uracil? The synthesis of thymine is energetically expensive

38. Because cytosine can be converted to uracil …. Having T’s in place of U’s in DNA allows the U’s that are found in DNA to be recognized as mistakes

39. DNA Sequencing

41. Laboratory Synthesis of DNA

43. Oligonucleotide Synthesis with Phosphoramidites

44. The amino groups of the bases must be protected

45. Removal of the Protecting Group by Ammonia

46. Utilization of H-phosphate monomer to synthesize DNA strand

49. Hoogsteen Base Pairing