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872 Nucleic Acid Synthesis

are released from the transcription complex before Pol II
leaves the promoter and carries out chain elongation. In-
terestingly, the same general transcription factors, includ-
ing TFIID, bind to the TATA-less promoter, even though
TATA binding by TBP is not available.
There is an important contrast in the assembly of RNA
polymerase complexes in eukaryotes and prokaryotes.
E. coli RNA polymerase binds to the promoter as a com-
plex with the σ-factor, providing the specificity for initi-
ation but not elongation. Eukaryotic Pol II, on the other
hand, goes through a much more complex choreography
because of the prerequisite for binding to the promoter
by other transcription factors. This dichotomy reflects the
complex structural organization of the eukaryotic genome
and the presence of a much larger number of genes with FIGURE 8 A schematic representation of RNA splicing. The cod-
ing sequence in metazoan genomes is usually present in seg-
their complex regulation. Such regulation is not only de-
ments (exons; indicated by boxes) interspersed between noncod-
pendent on the environment, but also on the stage of de- ing introns. After synthesis of the primary RNA transcript (called
velopment and differentiation, at least in the metazoans. heterogeneous nuclear RNA or hnRNA), the intron sequences
4. A unique difference between prokaryotic and eu- are removed by precise cleavage and rejoining is mediated by the
karyotictranscriptionisthatinprokaryotesasinglemRNA spliceosome complex, so that the resulting mature mRNA con-
tains a correctly juxtaposed coding sequence for the polypeptide.
containing many genes can be transcribed from the DNA

The mRNA is also “capped” by 5 -5 linkage with GMP, and a tail
template as a single transcription unit, coupled with their of poly(A) is added at the 3 terminus to increase the stability of

direct translation on ribosomes into discrete polypeptides. mRNA and to enhance its efficiency in directing protein synthesis
This process reflects the fact that genes which encode en- when the mRNA is transported from the nucleus to the cytoplasm.
zymes in a given pathway are often clustered in an operon
and are co-ordinately regulated.
In contrast to the synthesis of polycistronic mRNA in ing the coding sequence. The primary gene transcripts of
E. coli and other bacteria, eukaryotic transcription units nuclear genomes, called heterogeneous nuclear RNA
usually consists of single genes. This characteristic (hnRNAs), are present in a form of protein-bound particles
may also reflect uncoupled transcription and translation (ribonucleoprotein particles, or hnRNP). RNA splicing
in these organisms. Thus, heterogeneous nuclear RNA is the process of excising introns from hnRNAs, and con-
(hnRNA) is synthesized in the nucleus and then trans- tiguous exons are then joined to form mature mRNAs,
ported to the cytoplasm along with its processing into ma- which are subsequently translocated to cytoplasm and are
ture mRNA including splicing, addition of poly(A) tail at used as templates for translation (Fig. 8). The cleavage

the 3 end, and capping at the 5 end. Subsequently, the and rejoining occur at specific junctions between exons
RNA is translated on ribosomes (endoplasmic reticulum). and introns, so that there are no errors in mature mRNA.
Thus, synthesis and utilization of mRNA are temporally First,twoadjacentexonsarealigned,whiletheintervening
and spatially separated. intronisextruded,formingaloop(“lariat”)structure.Then
the upstream exon is cleaved and joined to the downstream
exon via a transesterification reaction. In most cases, two
factors are essential for this process. One, the cis-elements
D. RNA Splicing in Metazoans
in introns and exons, is the signaling sequences for the
The central dogma of molecular biology that the informa- exact junction sites. The other is the splicing machin-
tion flow from DNA to RNA to protein involves colinearity ery, consisting of several small ribonucleoprotein parti-
of the sequences of the monomer units is somewhat vio- cles (snRNP; U1, U2, and U4–U6), each of which con-
lated in metazoans because of the presence of interrupted tains small RNA molecules and proteins. The U1 and U2
or fragmented genes (Fig. 8). Thus, while the polypep- snRNPs contain RNA complementary to the intron cis-
tide sequence is colinear with the codons of the coding element and catalyze the formation of the intron lariat,
sequence in the mRNA, the RNA itself is not collinear while two adjacent exons are aligned together. With other
with the gene from which it is transcribed. In other words, snRNPs forming an intermediate complex (spliceosome),
the gene contains additional intervening sequences called U6 catalyzes the transesterfication. It should be noted
introns, which are transcribed but whose RNA sequence that introns in RNA of some lower eukaryotic species are
is subsequently removed from the final mRNA contain- autospliced and therefore do not require snRNPs.