Lecture 14.docx

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University of California - Irvine
Biological Sciences
Alexander Mc Pherson

Pg.1 Lecture 14 Ionization of the nucleotides 1. Though the pKas of the nucleotides are far from the normal conditions, they are critical for Viruses that survive in those low-pH environments 2. Thus those pKas may have a physiological significance in that context Tautomeric Equilibria 1. Sometimes the double bonds of the nucleotide bases have different tautomeric forms a. Memorize these forms 2. We don’t know if these tautomers exist in-vivo, but it is possible; and the implications could be mutations because the base pairings would not be the same. a. Watson and Crick were lucky in choosing the correct base pairing because they did not know about ionization or tautomerization DNA 1. DNA can exist as A & B & Z forms 2. The bases can rotate around the glycosidic bond a. This alters the hydrogen bonding 3. Then, even the sugar can also have different confirmations a. This alters the confirmation of the glycosidic bond 4. The pyrimidine also can have different forms : with the Keto over the sugar, which is the Syn RNA 1. Don’t have to memorize all the different RNA bases 2. Can be modified extensively 3. We don’t find these modifications in mRNA or rRNA but mostly in tRNA a. Dihydrouridine: commonly found in tRNA i. ** The ring is fully saturated with no double bonds ii. This breaks the planar and is no longer aromatic iii. Does not H-bond the same way as uridine and does not stack like other bases b. Pesudouridine: i. No longer a glycosidic bond, but still planar ii. Not bound to the N-C ATP & GTP 1. Readily break down because of the highly-unfavorable (-4) charges 2. 7kcal per phosphate for Gamma & Beta (alpha is not) a. 13kcal/mol for each ATP DNA does not have polarity because double stranded run anti-parallel 1. How is it synthesized? 2. 5’ to 3’ direction 3. Technically we would have 3 phosphates at the 5’ end, but those are easily hydrolyzed 4. At the 3’ end we see OH for DNA a. But at RNA we see a 2’ and 3’ OH b. Doesn’t matter if we incorporate RNA on the 2’ because the bond can just migrate 5. Oxygen on the DNA/RNA 3’ will attack one of the phosphates of the next nucleotide a. This reaction requires energy (which comes from the release of pyrophosphate) b. A new bond requires 7kcal/mol c. In a later reaction the pyrophosphates are further hydrolyzed (releasing another 7kcal) i. Totaling 15kcal d. Can we think of this reaction
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