Chap. 8 Problem 1
Mechanisms of post-transcriptional
gene control of protein coding genes
are shown in Fig. 8.1. The most
commonly used mechanism is the
regulation of alternative pre-mRNA
splicing. However, other methods
such as regulation of mRNA decay
and translation inhibition by miRNA
can play important regulatory roles,
depending on the gene.
Chap. 8 Problem 3
The sequences in a pre-mRNA that dictate where splicing occurs are located
at the exon/intron boundaries of the message (Fig. 8.7 below). These
sequences are bound by the snRNA components of the snRNPs that make up
spliceosomes (Fig. 8.9). Thus, the intron sequences ultimately tell the splicing
machinery where to process the mRNA. The branch point A residue of the
intron carries out the first transesterification reaction in which the
phosphodiester bond between the upstream exon and the intron is broken (Fig.
8.8). The 2’ OH group of the A residue is free to carry out this reaction.
The 3’ OH group of the A residue is linked in a phosphodiester bond.
Chap. 8 Problem 4
Heterogeneous nuclear RNAs (hnRNA) include several different types of RNA
found in the nucleus, including pre-mRNAs and processing intermediates. Small
nuclear RNAs (snRNA) participate in splicing reactions. The structures and
functions of the U1 and U2 snRNAs are shown in Fig. 8.9. Micro RNAs
(miRNAs) and short interfering RNAs (siRNAs) are involved in posttranscriptional gene silencing. miRNAs inhibit translation of mRNA, while siRNAs
cause mRNA degradation (Fig. 8.25).
Chap. 8 Problem 5
Both group II intron self-splicing and spliceosome-mediated splicing occur by
similar transesterification reactions and produce similar products (Fig. 8.14). In
group II intron splicing all of the reactions are carried out by the folded intron
itself; in spliceosome-mediated splicing, protein and snRNA components assemble to
create the functional enzymatic structure. Evidence supporting the idea that
introns in pre-mRNAs evolved from group II self-splicing introns comes from
experiments showing that group II self-splicing can be reconstituted using a
combination of separate intron fragments, and does not require an intact intron
per se.
Chap. 8 Problem 6
The results suggest that the fifth intron is not efficiently spliced out of the
pre-mRNA transcript for this gene in most tissues. This results in truncation
of the transcript at the cleavage and polyadenylation site in the fifth intron.
However, the splicing of the fifth intron is efficient in muscle cells. This
removes the cleavage and polyadenylation signal and results in a longer spliced
mRNA containing all 10 exons. A muscle-specific splicing factor may be
responsible for removal of the fifth intron in these cells. This factor may
participate in the assembly of cross-exon recognition complexes bound to the
fifth and sixth exons (Fig. 8.13).
Chap. 8 Problem 10
The function of a gene can be knocked down (inhibited) by the
technique of RNA interference (RNAi). In this method a doublestranded siRNA of 21-23 nucleotides, in which the two bases at
each 3’ end are single-stranded, is introduced into a cell. There, it
forms a complex with the RISC (Fig. 8.26) which base-pairs it to
its target mRNA. Because base-pairing is exact, the mRNA is
cleaved by the Argonaute protein of the RISC (Fig. 8.25). The
fragments of the cleavage event then are rapidly degraded by the
cell, and the mRNA is not translated.