Chemistry Reference
In-Depth Information
such as Rnase H remove the RNA primer strand from the RNA
DNA hybrid in Okasaki fragments during DNA
replication, yet they do not cleave either double-stranded DNA or RNA. DNA and RNA polymerases, even without
their elaborate proofreading function, insert the wrong nucleotide only every 10
3
e
10
4
bases, despite the relatively
e
small free energy difference of only
Crick and mismatched base pairs.
Nucleic acid metabolism is dominated by phosphoryl transfer reactions (
Figure 10.13
). These include the
reactions involved in DNA and RNA biosynthesis, catalysed by DNA and RNA polymerases. In these reactions,
2 kcal/mol between Watson
w
e
FIGURE 10.13
Phosphoryl transfer reactions. The figure shows (a) nucleotide polymerisation, (b) nucleic acid hydrolysis, (c) first cleavage
of an exon
e
intron junction by group I ribozyme (d) and by a group II ribozyme, (e) strand transfer during transposition, and (f) exon ligation
during RNA splicing.
(Adapted from
Yang et al., 2006
.
)
the hydroxyl group at the 3
0
end of an RNA or DNA strand attacks the
-phosphate of an incoming (deoxy)
ribonucleotide triphosphate [d]NTP to form a new phosphodiester bond, releasing a molecule of pyrophosphate
(
Figure 10.13
(a)). A similar phosphoryl transfer occurs in DNA and RNA cleavage, except that the phosphate
being attacked is the backbone of a nucleic acid, and the nucleophile is either a water molecule or a sugar
hydroxyl. When a water molecule is the nucleophile, the cleavage products are a 5
0
phosphate and a 3
0
hydroxyl
(
Figure 10.13
(
b)). When the 2
0
or 3
0
hydroxyl group of a ribonucleotide is the nucleophile, as in RNA splicing,
catalysed by the group I and group II self-splicing ribozymes, the 5
0
end product is covalently linked to the
ribonucleotide (
Figures 10.13
(
c) and (d)). If the nucleophile is the terminal 3
0
hydroxyl of a DNA or RNA strand,
a
