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Introduction to Organic Chemistry 2 ed William H. Brown

Introduction to Organic Chemistry 2 ed William H. Brown. Nucleic Acids. Chapter 19. Nucleic Acids. Nucleic acid : a biopolymer containing three types of monomer units heterocyclic aromatic amine bases derived from purine and pyrimidine the monosaccharides D-ribose or 2-deoxy-D-ribose

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Introduction to Organic Chemistry 2 ed William H. Brown

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  1. Introduction to Organic Chemistry2 edWilliam H. Brown

  2. NucleicAcids Chapter 19

  3. Nucleic Acids • Nucleic acid: a biopolymer containing three types of monomer units • heterocyclic aromatic amine bases derived from purine and pyrimidine • the monosaccharides D-ribose or 2-deoxy-D-ribose • phosphoric acid • Following are names and one-letter abbreviations for the heterocyclic aromatic amine bases most common to nucleic acids

  4. Purine/Pyrimidine Bases

  5. Nucleosides • Nucleoside: a building block of nucleic acids, consisting of D-ribose or 2-deoxy-D-ribose bonded to a heterocyclic aromatic amine base by a b-N-glycoside bond

  6. Nucleosides • Uridine

  7. Nucleotides • Nucleotide: a nucleoside in which a molecule of phosphoric acid is esterified with an -OH of the monosaccharide, most commonly either the 3’-OH or the 5’-OH

  8. Nucleotides • Adenosine 5’-monophosphate (AMP)

  9. Nucleotides • Deoxythymidine 3’-monophosphate (3’dTMP)

  10. Acyclovir & AZT

  11. DNA - 1° Structure • Deoxyribonucleic acids (DNA): a biopolymer that consists of a backbone of alternating units of 2-deoxy-D-ribose and phosphate in which the 3’-OH of one 2-deoxy-D-ribose is joined by a phosphodiester bond to the 5’-OH of another 2-deoxy-D-ribose unit • Primary Structure: the sequence of bases along the pentose-phosphodiester backbone of a DNA molecule (or an RNA molecule) read from the 5’ end to the 3’ end

  12. DNA - 1° Structure; TG

  13. DNA - 2° Structure • Secondary structure: the ordered arrangement of nucleic acid strands • Double helix: a type of 2° structure of DNA molecules in which two antiparallel polynucleotide strands are coiled in a right-handed manner about the same axis • the double helix model of DNA 2° structure was proposed by James Watson and Francis Crick in 1953

  14. T-A Base Pairing • a major factor stabilizing the double helix is base pairing between T-A and between C-G

  15. T-A Base Pairing

  16. C-G Base Pairing

  17. C-G Base Pairing

  18. Forms of DNA • B-DNA • the predominant form in dilute aqueous solution • a right-handed helix • 34 Å per 10 base pairs; 20 Å thick • minor groove of 12 Å and major groove of 22 Å • A-DNA • a right-handed helix, but thicker than B-DNA • 29 Å per 10 base pairs

  19. DNA - 3° Structure • Tertiary structure: the three-dimensional arrangement of all atoms of nucleic acid, commonly referred as supercoiling • Circular DNA: a type of double-stranded DNA in which the 5’ and 3’ ends of each stand are joined by phosphodiester bonds (Fig 19.10) • Chromatin:consists of DNA molecules wound around particles of histones in a beadlike structure

  20. Ribonucleic Acids (RNA) • RNA are similar to DNA in that they, too, consist of long, unbranched chains of nucleotides joined by phosphodiester groups between the 3’-OH of one pentose and the 5’-OH of the next. However, • the pentose unit in RNA is b-D-ribose rather than b-2-deoxy-D-ribose • the pyimidine bases in RNA are uracil and cytosine rather than thymine and cytosine • RNA is single stranded rather than double stranded

  21. RNA • RNA molecules are classified according to their structure and function • Ribosomal RNA (rRNA): a ribonucleic acid found in ribosomes, the site of protein synthesis

  22. RNA • Transfer RNA (tRNA): a ribonucleic acid that carries a specific amino acid to the site of protein synthesis on ribosomes

  23. RNA • Messenger RNA (mRNA): a ribonucleic acid that carries coded genetic information from DNA to the ribosomes for the synthesis of proteins • present in cells in relatively small amounts and very short-lived • single stranded • its synthesis is directed by information encoded on DNA • a complementary strand of mRNA is synthesized along one strand of an unwound DNA, starting from the 3’ end

  24. RNA • Transcription: the synthesis of mRNA from DNA

  25. The Genetic Code • Codon: a triplet of nucleotides on mRNA that directs incorporation of a specific amino acid into a polypeptide sequence

  26. The Genetic Code • Properties of the Code • only 61 triplets code for amino acids; the remaining 3 (UAA, UAG, and UGA) signal chain termination • the code is degenerate, which means that several amino acids are coded for by more than one triplet. Leu, Ser, and Arg, for example, are each coded for by six triplets • for the 15 amino acids coded for by 2, 3, or 4 triplets, it is only the third letter of the codon that varies. Gly, for example, is coded for by GGA, GGG, GGC, and GGU • there is no ambiguity in the code; each triplet codes for one and only one amino acid

  27. Sequencing DNA • Restriction endonuclease: an enzyme that catalyzes hydrolysis of a particular phosphodiester bond within a DNA strand • over 1000 endonucleases have been isolated and their specificities determined • typically they recognize a set sequence of nucleotides and cleave the DNA at or near that particular sequence • EcoRI from E. coli, for example, cleaves as shown

  28. Sequencing DNA • examples of endonucleases

  29. Sequencing DNA • Polyacrylamide gel electrophoresis: a technique so sensitive that it is possible to separate nucleic acid fragments differing from one another in only a single nucleotide • Chain termination or dideoxy method: a method developed by Frederick Sanger for sequencing DNA molecules

  30. DNA Replication • the sequence of nucleotides on one strand is copied as a complementary strand to form the second strand of double-stranded DNA • this synthesis is catalyzed by the enzyme DNA polymerase • DNA polymerase will carry of this synthesis in vitro using single-stranded DNA as a template, provided the four dNTPs and a primer are present • because the new DNA strand grows from the 5’ to 3’ end, the primer must have a free 3’-OH group to which the first nucleotide of the growing chain is added

  31. Chain Termin. Method • The key is addition of a 2’,3’-dideoxynucleoside triphosphate (ddNTP) to the synthesizing medium • synthesis terminates at any point where a ddNTP becomes incorporated

  32. Chain Termin. Method • a single-stranded DNA of unknown sequence is mixed with primer and divided into four separate reaction mixtures • to each mixture is added all four dNTPs, one of which is labeled in its 5’- phosphoryl group with P-32 • also added are DNA polymerase and one of the four ddNTPs • when polyacrylamide gel electrophoresis of each reaction mixture is completed, a piece of x-ray film is placed over the gel to detect gamma radiation from the decay of P-32 • the base sequence of the complement to the original single-stranded template is read directly from the bottom to top of the developed film

  33. Nucleic Acids End Chapter 19

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