Molecular Biology: General theory
Molecular Biology:
General Theory
Author: Dr Darshana Morar
Licensed under a Creative Commons Attribution license.
TRANSCRIPTION
Transcription is the synthesis of RNA under the direction of DNA. Messenger RNA (mRNA) is
synthesized by transcription or copying of DNA, a process similar to DNA replication. The DNA sequence
is copied by RNA polymerase to produce a complementary RNA strand, called messenger RNA
(mRNA), because it carries a genetic message from the DNA to the protein-synthesizing machinery of the
cell. Other types of transcribed RNA, such as transfer RNA, ribosomal RNA, and small nuclear RNA are
not necessarily translated into an amino acid sequence.
Unlike DNA replication, transcription does not need a primer to start. RNA polymerase simply binds to the
DNA and, along with other cofactors, unwinds the DNA to create an initiation bubble and the bases on the
two strands are exposed. But how does the RNA polymerase know where to begin? The starting point of
a gene is marked by a certain base sequence which is called a promoter site. In prokaryotes,
transcription begins with the binding of RNA polymerase to the promoter on the DNA molecule. At the
start of initiation, the RNA polymerase is associated with a sigma factor that aids in finding the
appropriate additional “signaling” base pairs downstream of the promoter sequences. Transcription
initiation is far more complex in eukaryotes, the main difference being that eukaryotic RNA polymerases
do not directly recognize their promoter sequences. In eukaryotes, a collection of proteins called
transcription factors mediate the binding of RNA polymerase and the initiation of transcription.
As in DNA replication, RNA is synthesized in the 5' to 3' direction (from the point of view of the growing
RNA transcript). Only one of the two DNA strands is transcribed into mRNA (remember that RNA is a
single-stranded molecule), unlike DNA replication, where both strands are copied. The DNA strand that is
transcribed is called the template strand (also known as the antisense strand), while its complement is
called the informational strand (also called the coding or sense strand).
Since the template strand and the informational strand are complementary, and since the template strand
and the mRNA molecule are also complementary, it follows that the messenger RNA molecule produced
during transcription is a copy of the DNA informational strand. Unlike DNA replication, mRNA transcription
can involve multiple RNA polymerases on a single DNA template and multiple rounds of transcription
resulting in amplification of a particular mRNA, i.e. many mRNA molecules can be produced from a single
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Molecular Biology: General theory
copy of a gene. This step also involves a proofreading mechanism that can replace incorrectly
incorporated bases.
In bacteria, just as there is a sigma factor to help signal the beginning of a gene, another factor called
"rho" aids in terminating the process of transcription. When the end of the gene is near, the rho factor
binds to the mRNA, destabilizing the interaction between the template and the mRNA. This releases the
newly synthesized mRNA from the elongation complex, thus stopping transcription. An alternative
strategy for transcription termination in bacteria is known as rho-independent transcription termination.
RNA transcription stops when the newly synthesized RNA molecule forms a G-C rich hairpin loop,
followed by a run of Us, which makes it detach from the DNA template. Transcription termination in
eukaryotes is less well understood. It involves cleavage of the new transcript, followed by templateindependent addition of As at its new 3' end, in a process called polyadenylation.
The stretch of DNA that is transcribed into an RNA molecule is called a transcription unit. A transcription
unit that is translated into protein contains sequences that direct and regulate protein synthesis in addition
to coding the sequence that is translated into protein. The regulatory sequence that is before, or 5', of the
coding sequence is called the 5' untranslated region (5’UTR), and the sequence found following, or 3', of
the coding sequence is called the 3' untranslated region (3’UTR). Transcription has a lower copying
fidelity than DNA replication since, although there are some proofreading mechanisms, they are fewer
and less effective than the controls for copying DNA.
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Molecular Biology: General theory
Figure 9 Transcription of RNA from DNA
(Adapted from: http://biologysemester58.wikispaces.com/Molecular+Genetics )
Prokaryotes
Prokaryotic transcription occurs in the cytoplasm alongside translation. Prokaryotes do not have exons
and introns and an RNA molecule corresponding to the DNA molecule is produced by RNA transcription.
In prokaryotes, mRNA is not modified.
Eukaryotes
Eukaryotic transcription occurs in the nucleus, where it is separated from the cytoplasm by the nuclear
membrane. The mRNA transcript is then transported into the cytoplasm where translation occurs.
Eukaryotic DNA is wound around histones to form nucleosomes and packaged as chromatin. Chromatin
has a strong influence on the accessibility of the DNA to transcription factors and the transcriptional
machinery including RNA polymerase.
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Molecular Biology: General theory
In most mammalian cells, only 1% of the DNA sequence is copied into a functional RNA (mRNA).
Eukaryotic mRNA is modified through RNA splicing, 5' end capping, and the addition of a polyA tail. One
of the most important stages in RNA processing is RNA splicing. In many genes, the DNA sequence
coding for proteins, or "exons", may be interrupted by stretches of non-coding DNA, called "introns". In
the cell nucleus, the DNA that includes all the exons and introns of the gene is first transcribed into a
complementary RNA copy called "nuclear RNA," or nRNA. In a second step, introns are removed from
nRNA by a process called RNA splicing. The edited sequence is called "messenger RNA," or mRNA.
Only one part of the DNA is transcribed to produce nuclear RNA, and only a minor portion of the nuclear
RNA survives the RNA processing steps.
The mRNA leaves the nucleus and travels to the cytoplasm, where it encounters cellular bodies called
ribosomes. The mRNA, which carries the gene's instructions, dictates the production of proteins by the
ribosomes in a process known as translation.
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