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Aromatic Heterocycles and DNA Structure Unraveled: From Pyridine to Protein Synthesis

Explore the world of heterocycles, from 5-membered rings like pyrrole to DNA structures and protein synthesis. Learn about the aromaticity criteria, electrophilic reactions on carbon, nucleophilic substitutions, and the Polymerase Chain Reaction (PCR). Discover the essential role of DNA bases, nucleotides, ribosides, and the intricate processes of transcription and translation. Unravel the genetic information encoded in the double helix of DNA and the fascinating mechanisms involved in DNA and RNA synthesis.

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Aromatic Heterocycles and DNA Structure Unraveled: From Pyridine to Protein Synthesis

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  1. Heterocycles (McM chapt 28) • Monocyclic or fused rings • Cont. one ore more ring atom ≠ C (normally O; N; S) • Aromatic, partly saturated or saturated ring(s) 5-Membered rings (Heteroatom N, O, S)

  2. Criteria for Aromaticity (Hückel) (Monocyclic) ring Planar No of p-electrons in conjugation 4n+2 (n: 0, 1, 2,....)

  3. 5-membered rings - electron rich - reactive i E-fil. Ar subst. React. in a-position generally preferred Selectivity not always good React.: Pyrrole > thiophene > furan

  4. 6-Membered rings (Heteroatom N)

  5. Pyridine as a base pKa: 5.2 sp2 N less basic than sp3

  6. Electrophilic Reaction on Carbon: E-phil. Ar. Subs. 6-membered rings - electron deficient -  reactivity • Both C and N may react • 3/5 pos. most reactive C • Diazines less reactive • Sulfonation, Nitration, halogenatil • Not FC react. Benzo ring most reactive Much slower react. than naphthalene

  7. Nucleophilic Aromatic Substitution • SNAr • SN1: Via arylic cation • Benzyne • SRN1: Involves radicals • VNS: Vicarious nucl. Subst. 6-membered rings - electron deficient - reactive in Nu-fil. Ar subst. 2 / 4 Pos. reactive; electron def. C, neg. charge partly on N in intermed 3 / 5-Pos. much less reactive (benzenoid pos.)

  8. Nucleosides, Nucleotides, Nucleic acids (DNA; RNA) DNA bases RNA bases DNA Nucleosides RNA Nucleosides Ribosides 2-Deoxyribosides

  9. Nucleotides A-T and G-C Base pairs Double a-helix (DNA)

  10. Nucleotide sequence in DNA - genetic information

  11. DNA helicases: Unwinding DNA binding proteins: Prevents winding back DNA primase: formation of DNA/RNA primer (from free nucleosides in cell) DNA polymerase: Catalyse elongation of new strand (5’ - 3’) Lagging strand: DNA ligase: Connects Okasaki fragments

  12. Transcription: DNA - RNA

  13. Translation: RNA - Protein 3 RNA bases coding for one AA (see Table 28.1) Protein synthesis occurs at ribosomes

  14. DNA / RNA Synthesis: Protecting groups and activating groups (cf. peptide synth)

  15. The Polymerase Chain Reaction (PCR, 1986) technique for quickly "cloning”(make many copies of) a particular piece of DNA in the test tube (rather than in living cells like E. coli). primers: short oligonucleotides (ca 20 nucleotides) precisely complementary to the sequence at the 3' end of each strand of the DNA Tac DNA polymerase: Heat stable enzyme from Thermus aquaticus (bacteria) in hot springs Yellowstone Nat. Park

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