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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 BIOCHEMISTRYNucleic Acids CHEM 3511 - Summer 2008
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 CHEM 3511 - Summer 2008
PRS Question • Which is not found in DNA? • Thymine • 2’-OH on pentose • 3’-OH on pentose • Phosphodiester bond CHEM 3511 - Summer 2008
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 CHEM 3511 - Summer 2008
Nucleic Acids • Basics of Nucleic Acid Structure • Supercoiling & Topoisomerases • RNA Structure • Recombinant DNA Technology CHEM 3511 - Summer 2008
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? CHEM 3511 - Summer 2008
Glycosidic Bond Rotational Degrees of Freedom Only 2 permissible conformations of base:syn or anti CHEM 3511 - Summer 2008
Glycosidic Bond Conformations “Anti” conformation is most stablein B-DNA and A-DNA CHEM 3511 - Summer 2008
Sugar Pucker B-DNA has a C2’-endo conformation… CHEM 3511 - Summer 2008
Sugar Pucker A-DNA has a C3’-endo conformation… CHEM 3511 - Summer 2008
DNA Supercoiling Increasing supercoiling CHEM 3511 - Summer 2008
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 CHEM 3511 - Summer 2008
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 CHEM 3511 - Summer 2008
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 CHEM 3511 - Summer 2008
Where do we observe supercoiling of DNA? CHEM 3511 - Summer 2008
Topoisomerases • Topoisomerases are enzymes that cleave DNA, thereby relieving supercoiling tension. • Type 1A: ss breaks • Type 1B: ss breaks • Type 2: ds breaks CHEM 3511 - Summer 2008
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 CHEM 3511 - Summer 2008
Transfer RNA Structures Carnegie Mellon U. NIH CHEM 3511 - Summer 2008
Ribosomal RNA Structures Frog5S rRNASubunit CHEM 3511 - Summer 2008
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 CHEM 3511 - Summer 2008
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 CHEM 3511 - Summer 2008
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 CHEM 3511 - Summer 2008
How does PCR work? One PCR Cycle: CHEM 3511 - Summer 2008
