Nucleic Acids in Chemistry and Biology

RNA Structure and Function 265

O Base

O OH

P

O

O O

O Base

O OH

O

5'

O Base

O OH

P

O

O

O Base

O OH

O

O

O

Nuc

H

O Base

OH OH

P

O

O

O Base

O OH

O

O

Nuc

O

Nuc O

H

3' 3'

5' 5'

3'

‡

Figure 7.17 Reaction mechanism for the spliceosome, group II introns, group I introns, and RNase P. During
spliceosomal and group II intron splicing, the nucleophile (Nuc-OH) is the 2
-OH of a specific bulged
adenosine within the spliced intron. For group I intron splicing, the nucleophile is the 3
-OH of a
guanosine moiety. For RNase P, and for alternative reactions by group II introns, the nucleophile is water

Figure 7.16 The structure of a eukaryotic precursor mRNA. The untranslated regions (UTRs) are shown as
stem-loop structures and the 5
-cap is a diamond. Exons are black, introns are pink, and an edited exon
(undergoing a C→U transversion) is shown in red. The poly-A tail is indicated at the 3
-end

functions. Remarkably, in higher eukaryotes the exons are very short (
200 nt) while the introns can be
very long (1000 nucleotides) (see Section 6.1).

7.2.2.1 Nuclear pre-mRNA Splicing. Before an mRNA can be functional and provide a proper tem-

plate, obviously the introns must be removed and the exons stitched together so that the processed mRNA
contains a coherent coding sequence that is specific for a particular protein. Thus, mature mRNA is much
shorter than the precursor transcript. This pre-mRNA splicingis carried out by the spliceosome, which is
a dynamic ribonucleoprotein (RNP) machine that specifically recognizes the sequences at exon/intron
boundaries (splice sites), and carries out the chemical reactions for cutting and pasting the exons together.^33
The spliceosome is composed of five highly conserved RNA molecules (the small nuclear RNAs or
snRNAs U1, U2, U4, U5, and U6) and a host of specialized proteins that bind RNA or remodel it through
the consumption of ATP. Splicing proceeds through two sequential trans-esterification reactions, each of
which involves an SN2 reaction at phosphorus (Figure 7.17). The nucleophile during the first step of spli-
cing is the 2
-hydroxyl group of an adenosine within the intron (the branch-point A), which attacks a spe-
cific sequence at the 5
-splice site and releases a 3
-hydroxyl leaving group. During the second step of
splicing, this 3
-OH group attacks the 3
-splice site, thereby ligating the exons and releasing an intron lar-
iat molecule (Figure 7.18).
Most pre-mRNA transcripts from mammals contain numerous exons, with ten being an approximate
average (Section 6.1). Depending on the tissue and developmental stage of the organism, these exons can