1. CHMI 2227 - E.R. Gauthier, Ph.D. 1 CHMI 2227E Biochemistry I Nucleic acids: - structure - physico-chemical properties

2. CHMI 2227 - E.R. Gauthier, Ph.D.2 Nucleic acids

3. CHMI 2227 - E.R. Gauthier, Ph.D.3 Hershey and Chase The Waring blender experiment… 32 P in nucleic acids only 35 S in proteins only (Met/Cys)

4. CHMI 2227 - E.R. Gauthier, Ph.D.4 Nature of nucleic acids 1. nitrogenated bases

5. CHMI 2227 - E.R. Gauthier, Ph.D.5 Nature of nucleic acids 2. sugars

6. CHMI 2227 - E.R. Gauthier, Ph.D.6 Nature of nucleic acids 3. nucleosides H Deoxyadenosine Glycosidic bond 1’1’ 9 1 1’1’ Cytidine H

7. CHMI 2227 - E.R. Gauthier, Ph.D.7 Purines BaseDNARNA AdenineDeoxyadenosineAdenosine GuanineDeoxyguanosineGuanosine Nature of nucleic acids 3. nucleosides Pyrimidines BaseDNARNA Cytosine DeoxycytidineCytidine ThymineDeoxythymidine- Uracil-Uridine

8. CHMI 2227 - E.R. Gauthier, Ph.D.8 Nature of nucleic acids 3. nucleosides

9. CHMI 2227 - E.R. Gauthier, Ph.D.9 Nature of nucleic acids 4. nucleotides Guanosine 5’monophosphate Deoxythymidine 5’triphosphate Alpha  Beta  Gamma 

10. CHMI 2227 - E.R. Gauthier, Ph.D.10 Number of phosphate groups Deoxynucleotide/Nucleotide 1Deoxyadenosine-5’-monophosphate 2Deoxyguanosine-5’-diphosphate 3Adenosine-5’-triphosphate Nature of nucleic acids 4. nucleotides

11. CHMI 2227 - E.R. Gauthier, Ph.D.11 Nature of nucleic acids 5. polynucleotides

12. CHMI 2227 - E.R. Gauthier, Ph.D.12 Nature of nucleic acids 5. phosphodiester bond http://www.mbi.ufl.edu/facilities/msg/bch4024m/lecture45.pdf  

13. CHMI 2227 - E.R. Gauthier, Ph.D.13 Nature of nucleic acids 6. Chargaff’s rules

14. CHMI 2227 - E.R. Gauthier, Ph.D.14 Structure of nucleic acids 1. DNA bases Sugar/phosphate backbone

15. CHMI 2227 - E.R. Gauthier, Ph.D.15 Structure of nucleic acids 1. DNA 1 Å (Ångstrom) = 0.1 nm = 1 x 10 -10 m

16. CHMI 2227 - E.R. Gauthier, Ph.D.16 Structure of nucleic acids 1. DNA

17. CHMI 2227 - E.R. Gauthier, Ph.D.17 Structure of nucleic acids 2. DNA/RNA hybrids and RNA duplexes

18. CHMI 2227 - E.R. Gauthier, Ph.D.18 Structure of nucleic acids 2. DNA/RNA hybrids and RNA duplexes

19. CHMI 2227 - E.R. Gauthier, Ph.D.19 Structure of nucleic acids Java applets:  http://www.moleculesinmotion.com/

20. CHMI 2227 - E.R. Gauthier, Ph.D.20 DNA absorbance

21. CHMI 2227 - E.R. Gauthier, Ph.D.21 DNA denaturation

22. CHMI 2227 - E.R. Gauthier, Ph.D.22 DNA denaturation Hyperchromic shift DNA#1 DNA#2

23. CHMI 2227 - E.R. Gauthier, Ph.D.23 DNA denaturation A+T-rich G+C-rich

24. CHMI 2227 - E.R. Gauthier, Ph.D.24 Hybridization

25. CHMI 2227 - E.R. Gauthier, Ph.D.25 Agarose gel electrophoresis +- Power Scanning Electron Micrograph of Agarose Gel (1×1 µm)  Polymerized agarose is porous, allowing for the movement of DNA DNA

26. CHMI 2227 - E.R. Gauthier, Ph.D.26 Agarose gel electrophoresis DNA molecules of known length Standard curve: Log length vs distance migrated Staining with ethidium bromide Ethidium bromide fluoresces red only when it intercalates between base pairs.

27. CHMI 2227 - E.R. Gauthier, Ph.D.27 Southern blot and Northern blot 32 P-labeled nucleic acid probe is complementary to one of the DNA molecules on the gel Annealing

28. CHMI 2227 - E.R. Gauthier, Ph.D.28 Southern blot Genomic DNA cut with restriction enzyme Different allele?

29. CHMI 2227 - E.R. Gauthier, Ph.D.29 FISH Fluorescent in-situ hybridization

30. CHMI 2227 - E.R. Gauthier, Ph.D.30 Microarrays aka DNA chips RNA labeling 1000’s of genes

31. CHMI 2227 - E.R. Gauthier, Ph.D.31 DNA denaturation

32. CHMI 2227 - E.R. Gauthier, Ph.D.32 DNA denaturation

33. CHMI 2227 - E.R. Gauthier, Ph.D.33 The «C value» paradox

34. CHMI 2227 - E.R. Gauthier, Ph.D.34 The «C value» paradox The mountain grasshopper Podisma pedestris The fruit fly Drosophila melanogaster 18,000 Mb180 Mb kbp

35. CHMI 2227 - E.R. Gauthier, Ph.D.35 The «C value» paradox Single copy Moderately repeated Highly repeated

36. CHMI 2227 - E.R. Gauthier, Ph.D.36 Human genome 3000 Mb Genes and other related sequences 900 Mb Extra-genic DNA 2100 Mb Coding DNA 90 Mb Non-coding DNA 810 Mb Repeated DNA 420 Mb Single/low copy number DNA 1680 Mb PseudogenesGene fragments Introns, etc Tandem repeats Interspersed repeats Satellite DNA Minisatellite DNA Microsatellite DNA LTR elementsSINE elements LINE elementsTransposons

37. CHMI 2227 - E.R. Gauthier, Ph.D.37 Human genome