1. Week #1CHEM 3511 - Summer 20081 SURVEY OF BIOCHEMISTRY Nucleic Acids

2. Week #1CHEM 3511 - Summer 20082 PRS Question Which statement is INCORRECT? 1.B-DNA is double helical 2.In DNA, two H-bonds form between adenine and thymine 3.In DNA, molar amounts of A+T = molar amounts of G+C 4.DNA strands run antiparallel to each other

3. Week #1CHEM 3511 - Summer 20083 PRS Question Which is not found in DNA? 1.Thymine 2.2’-OH on pentose 3.3’-OH on pentose 4.Phosphodiester bond

4. Week #1CHEM 3511 - Summer 20084 PRS Question The link between the adenine base and the ribose sugar occurs: 1.From N1 of A to the C1’ of ribose 2.From N3 of A to the C1’ of ribose 3.From N7 of A to the C1’ of ribose 4.From N9 of A to the C1’ of ribose

5. Week #1CHEM 3511 - Summer 20085 Nucleic Acids Basics of Nucleic Acid Structure Supercoiling & Topoisomerases RNA Structure Recombinant DNA Technology

6. Week #1CHEM 3511 - Summer 20086 Limitations to DNA Flexibility Glycosidic Bond Sugar Pucker Sugar-Phosphate Backbone What is a torsion angle and how does it play a role in biomolecular structure?

7. Week #1CHEM 3511 - Summer 20087 Rotational Degrees of Freedom Glycosidic Bond Only 2 permissible conformations of base: syn or anti

8. Week #1CHEM 3511 - Summer 20088 Glycosidic Bond Conformations “Anti” conformation is most stable in B-DNA and A-DNA

9. Week #1CHEM 3511 - Summer 20089 Sugar Pucker B-DNA has a C2’-endo conformation…

10. Week #1CHEM 3511 - Summer 200810 Sugar Pucker A-DNA has a C3’-endo conformation…

11. Week #1CHEM 3511 - Summer 200811 DNA Supercoiling Increasing supercoiling

12. Week #1CHEM 3511 - Summer 200812 DNA Supercoiling L = T + W Linking Number (L) Number of times one strand crosses another strand Here the red strand of DNA crosses the blue strand of DNA 10 times L = 10

13. Week #1CHEM 3511 - Summer 200813 DNA Supercoiling L = T + W Twist (T) Number of times one strand makes a complete revolution about the helical axis. Here the red strand of DNA makes 10 revolutions about the helical axis T = 10

14. Week #1CHEM 3511 - Summer 200814 DNA Supercoiling L = T + W Writhe (W) Number of times a duplex makes a complete revolution about itself. Counterclockwise turns are negative Clockwise turns are positive W = 0

15. Week #1CHEM 3511 - Summer 200815 Where do we observe supercoiling of DNA?

16. Week #1CHEM 3511 - Summer 200816 Topoisomerases Topoisomerases are enzymes that cleave DNA, thereby relieving supercoiling tension. –Type 1A: ss breaks –Type 1B: ss breaks –Type 2: ds breaks

17. Week #1CHEM 3511 - Summer 200817 Types of RNA Messenger RNA - carries genetic information for protein synthesis Transfer RNA - covalently binds amino acids corresponding to its anticodon sequence Ribosomal RNA - RNA molecules that play a role in protein synthesis in conjugate with ribosomal proteins

18. Week #1CHEM 3511 - Summer 200818 Transfer RNA Structures Carnegie Mellon U. NIH

19. Week #1CHEM 3511 - Summer 200819 Ribosomal RNA Structures Frog 5S rRNA Subunit

20. Week #1CHEM 3511 - Summer 200820 Recombinant DNA Technology Goal: Introduce foreign gene into a host organism –Reproduction of the gene or gene product –Function of the new gene product on the host –Players: Gene insert, host, vector used to carry gene into host

21. Week #1CHEM 3511 - Summer 200821 Gene Insert Genomic DNA – All of the DNA carrying genetic information for normal functioning of an organism cDNA – DNA copied from mRNA PCR – DNA that has been copied from a template in a polymerase chain reaction

22. Week #1CHEM 3511 - Summer 200822 What is Polymerase Chain Reaction (PCR)? In vitro DNA synthesis –Components include: Heat-stable DNA polymerase (Taq polymerase) Two Primers (DNA oligonucleotides) Deoxynucleotides –dATP, dTTP, dCTP, dGTP DNA template Mg ++, buffer components, and water

23. Week #1CHEM 3511 - Summer 200823 How does PCR work? One PCR Cycle: