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Organic Chemistry. William H. Brown & Christopher S. Foote. Nucleic Acids. Chapter 28. 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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Organic chemistry

Organic Chemistry

William H. Brown &

Christopher S. Foote

Nucleic acids


Chapter 28

Nucleic acids1
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


  • 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-glycosidic bond


  • Nucleotide: a nucleoside in which a molecule of phosphoric acid is esterified with an -OH of the monosaccharide,


Example 28.1 identify these nucleotides

Dna 1 structure
DNA - 1° Structure

  • Deoxyribonucleic acids (DNA)

    • 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

Dna 2 structure
DNA - 2° Structure

  • Secondary structure: the ordered arrangement of nucleic acid strands

  • The double helix model of DNA 2° structure was proposed by James Watson and Francis Crick in 1953

  • 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

T a base pairing
T-A Base Pairing

  • A major factor stabilizing the double helix

Forms of dna
Forms of DNA

  • B-DNA

    • the predominant form in dilute aqueous solution

    • a right-handed helix

    • 2000 pm thick with 3400 pm per ten base pairs

    • minor groove of 1200pm and major groove of 2200 pm

  • A-DNA

    • a right-handed helix, but thicker than B-DNA

    • 2900 pm per 10 base pairs

  • Z-DNA

    • a left-handed double helix

Dna 3 structure
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 28.10)

  • Histone: a protein, particularly rich in the basic amino acids lysine and arginine, that is found associated with DNA molecules

Dna 3 structure1
DNA - 3° Structure

  • Chromatin: consists of DNA molecules wound around particles of histones in a beadlike structure

    • further coiling produces the dense chromatin found in nuclei of plant and animal cells

Ribonucleic acids rna
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 -D-ribose rather than -2-deoxy-D-ribose

    • the pyrimidine bases in RNA are uracil and cytosine rather than thymine and cytosine

    • RNA is single stranded rather than double stranded


  • RNA molecules are classified according to their structure and function

  • Ribosomal RNA (rRNA): a ribonucleic acid found in ribosomes, the site of protein synthesis


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


  • 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

    • their 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


  • the synthesis of mRNA from DNA is called transcription

The genetic code1
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

Sequencing dna
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

Sequencing dna1
Sequencing DNA

  • following are several more examples of endonucleases and their specificities

Sequencing dna2
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

    • Maxam-Gilbert method: a method developed by Allan Maxam and Walter Gilbert; depends on base-specific chemical cleavage

    • Dideoxy chain termination method: developed by Frederick Sanger

    • Gilbert and Sanger shared the 1980 Nobel prize for biochemistry for their “development of chemical and biochemical analysis of DNA structure.”

Replication in vitro
Replication in Vitro

  • During replication, the sequence of nucleotides in one strand is copied as a complementary strand to form the second strand of a double-stranded DNA

  • Synthesis is catalyzed by DNA polymerase

  • DNA polymerase will catalyze synthesis in vitro using single-stranded DNA as a template, provided that (1) the four deoxynucleotide triphosphate (dNTP) monomers and (2) a primer are present

  • Primer: an oligonucleotide capable of forming a short section of double-stranded DNA (dsDNA) by base-pairing with its complement on a single-stranded DNA (ssDNA)

Replication in vitro1
Replication in Vitro

  • Because a new DNA strand grows from its 5' to 3' end, the primer must have a free 3'-OH group to which the first nucleotide of the growing chain is added

Dideoxy chain termination
Dideoxy Chain Termination

  • the key to the chain termination method is addition to the synthesizing medium of a 2’,3’-dideoxynucleotide triphosphate (ddNTP)

  • because a ddNTP has no 3’-OH, chain synthesis is terminated where a ddNTP becomes incorporated

Dideoxy chain termination1
Dideoxy Chain Termination

In this method, the following are mixed

  • single-stranded DNA of unknown sequence and primer; then divided into four reaction mixtures

  • To each reaction mixture is then added

    • the four dNTP, one of which is labeled in the 5’ end with phosphorus-32

    • DNA polymerase

    • one of the four ddNTPs

  • Dideoxy chain termination2
    Dideoxy Chain Termination

    after gel electrophoresis of each reaction mixture

    • a piece of film is placed over the gel

    • gamma rays released by P-32 darken the film and create a pattern of the resolved oligonucleotide

    • the base sequence of the complement to the original strand is read directly from bottom to top of the developed film

    Prob 28 8
    Prob 28.8

    Draw structural formulas for the enethiol (the sulfur equivalent of an enol) forms of each antimetabolite used in the treatment of certain types of cancer.

    Prob 28 9
    Prob 28.9

    Draw two additional tautomers for cytosine and three additional tautomers for thymine.

    Nucleic Acids

    End Chapter 28