1. Biochemistry Lecture 6

2. Functions of Nucleotides and Nucleic Acids Nucleotide Functions: –Energy for metabolism (ATP) –Enzyme cofactors (NAD + ) –Signal transduction (cAMP) Nucleic Acid Functions: –Storage of genetic info (DNA) –Transmission of genetic info (mRNA) –Processing of genetic information (ribozymes) –Protein synthesis (tRNA and rRNA)

3. NucleotideNucleosideNucleobase

7. Pyrimidine Nucleobases

8. Purine Nucleobases

11. UV Absorption of Nucleobases

13.  -D-ribofuranose in RNA  -2’-deoxy-D-ribofuranose in DNA

14.  N-Glycosidic Bond

15. Polynucleotides

16. Hydrolysis of RNA

17. Hydrogen Bonding!

18. Discovery of DNA Structure One of the most important discoveries in biology Why is this important – " This structure has novel features which are of considerable biological interest “ --- Watson and Crick, Nature, 1953 Good illustration of science in action: –Missteps in the path to a discovery –Value of knowledge –Value of collaboration –Cost of sharing your data too early

19. Covalent Structure of DNA (1868-1935) Friedrich Miescher isolates “nuclein” from cell nuclei Hydrolysis of nuclein: –phosphate –pentose –and a nucleobase Chemical analysis: –phosphodiester linkages –pentose is ribofuranoside Structure of DNA: 1929 (Levene and London) Structure of DNA: 1935 (Levene and Tipson)

21. Road to the Double Helix Franklin and Wilkins: –“Cross” means helix –“Diamonds” mean that the phosphate- sugar backbone is outside – Calculated helical parameters Watson and Crick: – Missing layer means alternating pattern (major & minor groove) – Hydrogen bonding: A pairs with T G pairs with C Double helix fits the data! Watson, Crick, and Wilkins shared 1962 Nobel Prize Franklin died in 1958

25. Other forms of DNA

26. The Central Dogma

27. DNA Replication “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material” Watson and Crick, in their Nature paper,1953

31. Using DNA Structure

33. Thermal Denaturation

34. Molecular Mechanisms of Spontaneous Mutagenesis Deamination Very slow reactions Large number of residues The net effect is significant: 100 C  U events /day in a mammalian cell Depurination N-glycosidic bond is hydrolyzed Significant for purines: 10,000 purines lost/day in a mammalian cell Cells have mechanisms to correct most of these modifications.

37. DNA Technologies

39. DNA Cloning

42. Restriction Enzymes

46. Antibiotic Selection Antibiotics, such as penicillin and ampicillin, kill bacteria Plasmids can carry genes that give host bacterium a resistance against antibiotics Allows growth (selection) of bacteria that have taken up the plasmid

49. PCR Polymerase Chain Reaction

51. Site-Directed Mutagenesis

52. DNA Electrophoresis

53. DNA Sequencing

55. Shotgun Sequencing

58. DNA Fingerprinting

59. Expression of Cloned Genes

60. Protein Purification

61. Eukaryotic Gene Expression in Bacteria An eukaryotic gene from the eukaryotic genome will not express correctly in the bacterium Eukaryotic genes have –Exons: coding regions –Introns: noncoding regions Introns in eukaryouric gene pose problems Bacteria cannot splice introns out mRNA is intron-free genetic material

63. cDNA

64. DNA Microarrays: Applications DNA Microarrays allow simultaneous screening of many thousands of genes: high-throughput screening genome wide genotyping –Which genes are present in this individual? tissue-specific gene expression –Which genes are used to make proteins? mutational analysis –Which genes have been mutated?

65. DNA Microarrays: Design Two fundamental approaches One-color array –Patented and commerialized by Affymetrix –Photolitographic synthesis of probe DNA on the chip –Targets are biotin labeled –Bound targets detected using streptavidin-fluorofore complex –Widely used in industry Two-color array –Developed by Stanford University, 1996 –Probes sometimes pipetted on the chip –Targets linked to either green or red fluorescent labels –Used often in academia