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SURVEY OF BIOCHEMISTRY Nucleic Acids

SURVEY OF BIOCHEMISTRY Nucleic Acids. PRS Question. Which statement is INCORRECT? B-DNA is double helical In DNA, two H-bonds form between adenine and thymine In DNA, molar amounts of A+T = molar amounts of G+C DNA strands run antiparallel to each other. PRS Question.

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SURVEY OF BIOCHEMISTRY Nucleic Acids

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  1. SURVEY OF BIOCHEMISTRYNucleic Acids

  2. PRS Question • Which statement is INCORRECT? • B-DNA is double helical • In DNA, two H-bonds form between adenine and thymine • In DNA, molar amounts of A+T = molar amounts of G+C • DNA strands run antiparallel to each other

  3. PRS Question • Which is not found in DNA? • Thymine • 2’-OH on pentose • 3’-OH on pentose • Phosphodiester bond

  4. PRS Question • The link between the adenine base and the ribose sugar occurs: • From N1 of A to the C1’ of ribose • From N3 of A to the C1’ of ribose • From N7 of A to the C1’ of ribose • From N9 of A to the C1’ of ribose

  5. Nucleic Acids • Basics of Nucleic Acid Structure • Supercoiling & Topoisomerases • RNA Structure • Recombinant DNA Technology

  6. 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. Glycosidic Bond Rotational Degrees of Freedom Only 2 permissible conformations of base:syn or anti

  8. Glycosidic Bond Conformations “Anti” conformation is most stablein B-DNA and A-DNA

  9. Sugar Pucker B-DNA has a C2’-endo conformation…

  10. Sugar Pucker A-DNA has a C3’-endo conformation…

  11. DNA Supercoiling Increasing supercoiling

  12. DNA Supercoiling L = T + W Linking Number (L) Number of times one strand crosses another strand Here the red strand of DNA crossesthe blue strand of DNA 10 times L = 10

  13. 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. DNA Supercoiling L = T + W Writhe (W) Number of times a duplex makes a complete revolution about itself. Counterclockwise turns are negativeClockwise turns are positive W = 0

  15. Where do we observe supercoiling of DNA?

  16. Topoisomerases • Topoisomerases are enzymes that cleave DNA, thereby relieving supercoiling tension. • Type 1A: ss breaks • Type 1B: ss breaks • Type 2: ds breaks

  17. 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. Transfer RNA Structures Carnegie Mellon U. NIH

  19. Ribosomal RNA Structures Frog5S rRNASubunit

  20. 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. 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. 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. How does PCR work? One PCR Cycle:

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