BRING YOUR MOLECULAR MODEL KIT!

Chapter 25 Nucleosides, Nucleotides, and Nucleic Acids

I.  Nucleoside:  A base bonded to the anomeric carbon of D-ribose or to 2'-deoxy-D-ribose.
    A.  Adenine is base; Adenosine is the nucleoside, Guanine is the base; Guanosine is the nucleoside, Cytosine is the base; Cytidine is the nucleoside, Thymine is the base; Thymidine is the nucleoside, Uracil is the base; Uridine is the nucleoside.
    B.  Uracil attaches only to D-ribose
    C.  Thymine attaches only to 2'deoxy-D-ribose

II.  Nucleotide:  A nucleoside with either the 5'- or 3'-OH group bonded in an ester linkage to phosphoric acid.
    A.  A nucleotides with a D-ribose sugar is called  a ribonucleotide
    B.  A nucleotides with a 2' deoxy-D-ribose sugar is called a deoxyribonucleotide

III.  Phosphoric Acid
    A.  Phosphoric acid is converted to pyrophosphoric acid and triphosphoric acid when heated with P2O5.
    B.  Nucleotides can exist as monophosphate, diphosphate, and triphosphate

IV.  ATP:  The Carrier of Chemical Energy
    A.  Couple reactions:  2 reactions in which the energy of one is used to drive the other.
        1.  Hydrolysis of ATP is highly exorthermic (-7.3 kcal/mole)
        2.  Phosphoryl Transfer Reaction
            a.  glucose reacts with ATP in a one step nucleophilic reaction SN2
                1.  breaking an anhydride bond
                2.  in-line displacement
            b.  phosphorylation is said to be driven by the hydrolysis of ATP

    B.  Mechanism of Phosphoryl Transfer Reaction:  Illustrated by a nucleophilic acyl substitution reaction.
        1.  Nucleophilic attack by the carboxylate ion on the gamma phosphorus group with subsequent nucleophilic acyl substitution with a thiol to form the thioester.
            a.    forms an acyl phosphate and ADP in step 1
            b.  forms a thioester and a phosphate in step 2
        2.  Nucleophilic attack by the carboxylate ion on the Beta phosphorus group with subsequent nucleophilic acyl substitution with a thiol to form the thioester.
            a.  forms an acyl pyrophosphate and AMP in step 1
            b.  forms a thioester and pyrophosphate in step 2
        3.  Nucleophilic attack by the carboxylate ion on the alpha phosphorus group with subsequent nucleophilic acyl substitution with a thiol to form the thioester.
            a.  forms an acyl adenylate and pyrophosphate in step 1
            b.  forms a thioester and AMP in step 2
        4.  If pyrophosphate is formed, it is immediately hydrolyzed to 2 phosphate ions, ensuring irreversibility.

    C.  High Energy Phosphoanhydride Bonds
        1.  More electrostatic repulsions are present in ATP than ADP or phosphate
        2.  The product has an overall greater negative charge and therefore better solvated
        3.  Greater resonance stabilization in the products

    D.  Kinetic stability of ATP in the cell
        1.  the negative charges of ATP makes it unreactive to nucleophiles
        2.  When ATP is bound in the active site of the enzyme, the charges are decreased by Mg2+ and the positively charged groups of amino acids.

II.  Other important nucleotides
    A.  GTP
    B.  Dinucleotides:  NADH, NADPH, FADH2 and FMNH2
    C.  Cyclic AMP

III.  Nucleic Acids:  long strands of nucleotides linked by phosphodiester bonds (from the 3'-OH group of one nucleotide to the 5'-OH group of the next nucleotide
    A.  DNA and RNA are polynucleotides
        1.  Formed by the nucleophilic attack by a 3'-OH group of one nucleotide triphosphate on the alpha-phosphorus of another nucleotide triphosphate, breaking a phosphoanhydride bond and eliminating pyrophosphate
        2.  Synthesized in the 5' to 3' direction.
    B.  Primary Structure of a nucleic acid is the sequence of bases in the strand.
    C.  DNA consists of two strands of nucleic acids with the sugar-phosphate backbone on the outside and the bases on the inside.

More to come!