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Organic Chemistry 4th Edition Paula Yurkanis Bruice Chapter 27 Nucleosides, Nucleotides, and Nucleic Acids I Irene Lee Case Western Reserve University Cleveland, OH ©2004, Prentice Hall Nucleic Acids In nucleic acid, the phosphate group is phosphodiester The Bases in Nucleic Acids Adenine, guanine, cytosine, and thymine are found in DNA Adenine, guanine, cytosine, and uracil are found in RNA Nucleosides = Base + Sugar Nucleotides = Base + Sugar + Phosphate Different Forms of Nucleotides ATP as a Chemical Energy Source The energy released from ATP hydrolysis is used to drive the phosphorylation of D-gluose (coupled reactions) Breakage of the Phosphoanhydride Bond in ATP Without ATP, the OH– group cannot be displaced This reaction does not occur without ATP because of the poor leaving group Phosphoryl Transfer Reaction Mechanism I Phosphoryl Transfer Reaction Mechanism II Phosphoryl Transfer Mechanism III Pyrophosphate can be further hydrolyzed to phosphate O P O P OO -O OO- + H2O 2 -O O P O- OH Why is the hydrolysis of a phosphoanhydride bond so exergonic? 1. Greater electrostatic repulsion in ATP 2. More solvation in the products 3. Greater resonance stabilization in the products O O P P O -O OO- O P -O O- O + P -O OH O- The interactions between ATP, Mg2+, and arginine and lysine residues at the active site of an enzyme Since all the negative charges in ATP are neutralized, ATP is readily approached by nucleophiles Other Important Nucleotides Cyclic AMP serves as a link between several hormones and certain enzymes that regulate cellular function The Nucleic Acids Biosynthesis of DNA occurs in the 5’ 3’ direction Complementary Base Pairing in DNA The sugar–phosphate is on the outside, and the bases are on the inside The DNA Double Helix Hydrolysis of RNA The Three Helical Forms of DNA Hydrogen bonding and base stacking interactions hold the DNA helix together Replication of DNA Transcription of DNA • A stretch of bases representing a portion of a gene is called an exon • A stretch of bases that contain no genetic information is called an intron • mRNA is spliced prior to leaving the nucleus A Transfer RNA The Proposed Mechanism for Aminoacyl-tRNA Synthetase The Substrate-Binding Site for tRNAHis A protein is synthesized from its N-terminal end to its C-terminal end Each amino acid is specified by a three-base sequence known as the genetic code Translation Why does DNA contain thymine instead of uracil? The synthesis of thymine is energetically expensive Because cytosine can be converted to uracil …. Having T’s in place of U’s in DNA allows the U’s that are found in DNA to be recognized as mistakes DNA Sequencing Laboratory Synthesis of DNA Oligonucleotide Synthesis with Phosphoramidites The amino groups of the bases must be protected Removal of the Protecting Group by Ammonia Utilization of H-phosphate monomer to synthesize DNA strand Hoogsteen Base Pairing