Download DNA Lecture 2

The amino and keto forms represent the most
stable forms of the bases, i.e., the equilibria lie far to
the left.
Note that the tautomeric forms of each base have
different H-bonding characteristics-
As indicated above, N-1 of adenine is a H-bond
acceptor in the amino form, but a H-bond donor in the
imino form.
Likewise, the keto oxygen on C-4 of thymine can
only act as a H-bond acceptor while the enol form can
act as a H-bond donor.
As we will see later the complementary pairing of
bases in double stranded DNA normally involves Hbonding of amino and keto forms as follows-
Since the imino form of A (adenine) can’t form
H-bonds to the keto form of T (thymine) in the same
manner, tautomeric forms have been proposed to
contribute to spontaneous mutations that result from
the formation of abnormal base pairs such as-
Compounds formed from replacement of the
OH group of D-ribose or 2-deoxy-D-ribose by a base
to form an N-glycosidic bond are called nucleosides.
Note that replacement of the OH group by the
base, changes the hemiacetal structure of C-1 to an
acetal type structure-
Fig 21-3(b) shows the structures of the
deoxyribonucleosides corresponding to the bases
found in DNA.
Observe that the N-glycosidic linkage involves C1' of the sugar and N-9 of the purine or N-1 of the
pyrimidine.
The complete structures, names and abbreviations
of the four nucleotides found in DNA
(Fig 22-3) are-
Observe that the phosphate group is bound to the
sugar in the form of an ester linkage, i.e., a phosphate
ester of phosphoric acid and an alcohol.
Now let's consider the manner in which the
nucleotides are linked together to form a linear
polymer.
The nucleotides are linked by 5'-3' phosphodiester
bonds (Fig 22-4) as follows-
In the polymer, the terminal nucleotide at one end
will have a free 5'-phosphate group whereas the
terminal nucleotide at the other end will have a free 3'OH group.
The direction of the chain is defined as 5'→3'.
Note that when the phosphate group forms a
diester linkage there is only one ionizable oxygen that
is usually represented in the ionized (charged) form.
Consider why the phosphodiester is in the ionized
form. Recall that phosphoric acid itself has three acidionization equilibria-
The ionization of the phosphodiester group found
in a nucleic acid corresponds to-
Based on the pKa, we would expect that the
unionized (acid) form of such a polymer of nucleotides
should be a strong acid, hence the name nucleic acid.
We should also recognize that the ionized (basic)
form with the negative charge on the phosphate
oxygen exists almost exclusively at pH 7.0.
We can show this by calculating the ratio of the
basic to acidic forms at pH 7.0-