How Cells Read the Genome:
from DNA to RNA (BOOK)
Chapter 6 pp 299-320, 324-327
The DNA genomes does not direct protein synthesis itself but uses RNA as an intermediary. The
nucleotide sequence of the appropriate portion for the protein is copied into RNA (transcription) and
these copies are used as templates to direct the synthesis of the protein (translation).
The RNA transcripts in eukaryotic cells should first go to a couple of processes before they can exit
the nucleus.
From DNA to RNA
The name given to producing RNA molecules on DNA is transcription. RNA is a linear polymer just
like DNA but there are two big differences. The first is that the nucleotides in RNA are
ribonucleotides instead of deoxyribonucleotides, they contain the sugar ribose instead of
deoxyribose. The second difference is that RNA contains the base uracil (U) instead of thymine (T).
Another difference can be found in the physical structure, where DNA always occur in cells as a
double-helix, RNA is single stranded.
As mentioned before, the RNA in a cell is made by DNA transcription. Transcription begins with the
opening and unwinding of a small portion of the DNA double helix to expose the bases on both
strands, one of the strands will then function as a template strand. The nucleotide sequence of the
RNA chain is determined by the complementary base-pairing between incoming nucleotides and the
DNA template, just like in DNA replication. The incoming ribonucleotide is covantely linked to the
growing RNA chain which is called the transcript.
In contrast to DNA replication, the RNA strand does not remain hydrogen-bonded to the DNA
template strand, the DNA helix reforms just behind the region where the ribonucleotides are being
added.
RNA polymerase
RNA polymerase is the enzym that perform transcription. The RNA polymerase moves stepwise
along the DNA, unwinding the DNA helix just ahead of the active side.
The almost immediate release of the RNA from the DNA means that many RNA copies can be made
from the same gene in a short time.
Although RNA polymerase catalyse essentially the same chemical reaction as DNA polymerase, there
are some important differences:
- RNA polymerase catalyzes the linkage of ribonucleotides instead of deoxyribonucleotides
- RNA polymerase can start an RNA chain without a primer
- RNA polymerase that begins an RNA molecules must finish it without dissociating from the
DNA template
Although RNA polymerases are not as accurate as DNA polymerase, RNA polymerase nonetheless
have a proofreading system.
, Categories of RNA molecules
RNA molecules that direct the synthesis of proteins are called messenger RNAs (mRNA). The product
of other genes can be the RNA molecule itself, these are known as noncoding RNAs because they do
not code for a protein.
Initiation of transcription in prokaryotes
The bacterial RNA polymerase core enzyme is a multi subunit that uses the DNA template as a guide.
An additional subunit called the sigma (σ) factor associates with the core enzyme and assists it in
reading the signals in the DNA that tell where to begin transcribing. The σ factor and core enzyme are
known as the RNA polymerase holoenzyme. When the RNA polymerase holoenzyme slides into a
sequence of nucleotides indicating a starting point (called a promotor) the polymerase binds tightly.
At a promotor, the RNA polymerase holoenzyme opens up the double helix. The region of unpaired
DNA is called the transcription bubble and it is stabilised by the binding of σ factor to the unpaired
bases on one of the exposed strands. The other strand acts as a template.
The first ten or so nucleotides of RNA are synthesised using a scrunching mechanism in which RNA
polymerase remains bound to the promotor and pulls the DNA into its active site, thereby expanding
the transcription bubble. This is called abortive initiation. From then on, the polymerase moves
along the DNA and the transcription bubble extends at the front, and contracts at its rear. This
continues until the enzyme encounters a terminator where the polymerase halts and release both
the RNA molecule and the DNA template.
Transcription start and stop signals
A comparison of many different bacterial promotors reveal a lot of variations but they al contain
related sequences. These common features are often summarised in the form of a consensus
sequence. A consensus nucleotide sequence is derived by comparing many sequences with the same
function an tallying up the most common nucleotides found at each position. A more accurate way of
displaying is through the use of a sequence logo which reveals the relative frequencies of each
nucleotide at each position.
from DNA to RNA (BOOK)
Chapter 6 pp 299-320, 324-327
The DNA genomes does not direct protein synthesis itself but uses RNA as an intermediary. The
nucleotide sequence of the appropriate portion for the protein is copied into RNA (transcription) and
these copies are used as templates to direct the synthesis of the protein (translation).
The RNA transcripts in eukaryotic cells should first go to a couple of processes before they can exit
the nucleus.
From DNA to RNA
The name given to producing RNA molecules on DNA is transcription. RNA is a linear polymer just
like DNA but there are two big differences. The first is that the nucleotides in RNA are
ribonucleotides instead of deoxyribonucleotides, they contain the sugar ribose instead of
deoxyribose. The second difference is that RNA contains the base uracil (U) instead of thymine (T).
Another difference can be found in the physical structure, where DNA always occur in cells as a
double-helix, RNA is single stranded.
As mentioned before, the RNA in a cell is made by DNA transcription. Transcription begins with the
opening and unwinding of a small portion of the DNA double helix to expose the bases on both
strands, one of the strands will then function as a template strand. The nucleotide sequence of the
RNA chain is determined by the complementary base-pairing between incoming nucleotides and the
DNA template, just like in DNA replication. The incoming ribonucleotide is covantely linked to the
growing RNA chain which is called the transcript.
In contrast to DNA replication, the RNA strand does not remain hydrogen-bonded to the DNA
template strand, the DNA helix reforms just behind the region where the ribonucleotides are being
added.
RNA polymerase
RNA polymerase is the enzym that perform transcription. The RNA polymerase moves stepwise
along the DNA, unwinding the DNA helix just ahead of the active side.
The almost immediate release of the RNA from the DNA means that many RNA copies can be made
from the same gene in a short time.
Although RNA polymerase catalyse essentially the same chemical reaction as DNA polymerase, there
are some important differences:
- RNA polymerase catalyzes the linkage of ribonucleotides instead of deoxyribonucleotides
- RNA polymerase can start an RNA chain without a primer
- RNA polymerase that begins an RNA molecules must finish it without dissociating from the
DNA template
Although RNA polymerases are not as accurate as DNA polymerase, RNA polymerase nonetheless
have a proofreading system.
, Categories of RNA molecules
RNA molecules that direct the synthesis of proteins are called messenger RNAs (mRNA). The product
of other genes can be the RNA molecule itself, these are known as noncoding RNAs because they do
not code for a protein.
Initiation of transcription in prokaryotes
The bacterial RNA polymerase core enzyme is a multi subunit that uses the DNA template as a guide.
An additional subunit called the sigma (σ) factor associates with the core enzyme and assists it in
reading the signals in the DNA that tell where to begin transcribing. The σ factor and core enzyme are
known as the RNA polymerase holoenzyme. When the RNA polymerase holoenzyme slides into a
sequence of nucleotides indicating a starting point (called a promotor) the polymerase binds tightly.
At a promotor, the RNA polymerase holoenzyme opens up the double helix. The region of unpaired
DNA is called the transcription bubble and it is stabilised by the binding of σ factor to the unpaired
bases on one of the exposed strands. The other strand acts as a template.
The first ten or so nucleotides of RNA are synthesised using a scrunching mechanism in which RNA
polymerase remains bound to the promotor and pulls the DNA into its active site, thereby expanding
the transcription bubble. This is called abortive initiation. From then on, the polymerase moves
along the DNA and the transcription bubble extends at the front, and contracts at its rear. This
continues until the enzyme encounters a terminator where the polymerase halts and release both
the RNA molecule and the DNA template.
Transcription start and stop signals
A comparison of many different bacterial promotors reveal a lot of variations but they al contain
related sequences. These common features are often summarised in the form of a consensus
sequence. A consensus nucleotide sequence is derived by comparing many sequences with the same
function an tallying up the most common nucleotides found at each position. A more accurate way of
displaying is through the use of a sequence logo which reveals the relative frequencies of each
nucleotide at each position.
