Chapter 12: Gene Transcription and
RNA Modification (processing)
The primary function of genetic material (DNA) = to store the
information necessary to create a living organism. The
information is contained within units called genes.
Gene = segment of DNA that is used to make a functional
product, either a RNA molecule or a polypeptide. Region (you
get the RNA from) that is being transcribed (exons).
To access the information within a gene the first step is called
transcription (= process of making a copy = process of
synthesizing RNA from a DNA template). DNA structure is not
altered as a result of transcription, it has only been accessed to
make a copy in the form of RNA. Therefore, the same DNA can
continue to store information. DNA replication, provides a
mechanism for copying that information so that it can be
transmitted to new daughter cells and form parent to offspring.
Protein-encoding genes (structural genes) carry the information
for the amino acid sequence of a polypeptide. When a structural gene is described the first product is
messenger RNA (mRNA). During polypeptide synthesis (=translation), the sequence of nucleotides within the
mRNA determines the sequence of amino acids in a polypeptide. One or more polypeptides then assemble
into a functional protein. The structures and functions of proteins largely determine an organism’s traits.
Central dogma of genetics = Once (sequential) information has
passed into protein it cannot get out again (on paper it can).
The flow of genetic information occurs from DNA to mRNA to
polypeptide.
Key concepts regarding transcription:
, - Specifi
c base
sequences determine where transcription starts and ends, there are also regulatory sites (DNA
sequences) that influence whether a gene is turned on or off.
- Proteins play an important part. DNA sequences, in and of themselves, just exist. For genes to be
actively transcribed, proteins must recognize particular DNA sequences and act on them.
Gene expression = the overall process by which the information within a gene is used to produce a
functional product (such as a polypeptide). Gene expression requires base sequences that perform different
functional roles. Promoter = provides a site for beginning transcription. Terminator = specifies the end of
transcription. These two base sequences cause RNA synthesis to occur within a defined location.
The base sequence in the RNA transcript is complementary to the template strand (non-coding/ antisense
strand) of DNA. The opposite strand of DNA is the nontemplate strand also called the coding/sense strand
because its sequence is the same as the transcribed mRNA (excepts T is U).
Transcription factors (proteins) control the rate of transcription. Some bind directly to the promotor others
recognise regulatory sequences/elements (short stretches of DNA involved in regulation of transcription).
Some regulatory sequences inhibit others increase the rate of transcription.
mRNA are used during translation process. In bacteria a short sequence within the mRNA = ribosome-
binding site (Shine-Dalgarno sequence) provides a location for a ribosome to bind and begin translation. It
recognizes this site because its complementary to a sequence in ribosomal RNA.
Each mRNA contains a series of codons (3 nucleotides) which contain information for polypeptide’s
sequence. First codon = start codon, is close to the ribosome-binding site. Followed by many codons and
finally the stop codon that signals the end of translation. If a mutation changed the start codon into a stop
codon, the mutation would not affect the length of the RNA, because it would not terminate transcription.
However the encoded polypeptide would be shorter.
The three stages of transcription are initiation, elongation (synthesis of the RNA transcript), and
termination. These steps involve protein-DNA interactions in which such as RNA polymerase (enzyme that
synthesizes RNA) interact with DNA sequences.
Initiation = recognition step the sequence of bases within the promoter is recognizes by one or more
transcription factors. The binding of specific transcription factors to the promotor identifies the starting site
, for transcription. Transcription factor(s) and RNA polymerase first bind to the promotor when the DNA is in
the form of a double helix. But for transcription to occur the DNA strands must be separated. Synthesis occur
as RNA polymerase slides along the DNA, forming bubble-like structure know as the open promotor complex
(=open complex). Eventually RNA polymerase reaches a terminator,
which causes both RNA polymerase and the newly made RNA to
dissociate from the DNA.
Transcription in Bacteria
Much of our knowledge comes from studies of E.coli.
A promotor is a short sequence of DNA that is necessary to initiate
transcription. This sequence of bases directs the exact location for the
initiation of transcription. Most of the promotors are located just ahead
(upstream from) transcriptional starts site (=located at +1 site and is
where the first base is used as a template for transcription). The bases in
a promotor sequence are numbered in relation to this site. This site is the
first nucleotide used as template for transcription and is denoted +1.
Preceding this site the bases are numbered in negative direction. No base
is numbered zero. Although promotor may encompass a lot of
nucleotides. Short sequences are necessary for a promotor to be
functional. One is called the Pribnow box (5’-TATAAT-3’) and the other one is
5’-TTGACA-3’. The most commonly occurring bases within a specific type of
sequence is called the consensus sequence = for a group of related
sequences, the consensus sequence consists of the most common base found
at each location within that group of sequences.
Bacterial transcription is initiated when RNA polymerase holoenzyme binds at
a promotor. In E.coli the RNA polymerase holoenzyme is composed: core
enzyme of five subunits (α2ββ’ω = α: assembly of the holoenzyme and
binding to DNA, β β’: binding and catalytic synthesis of RNA, ω: assembly of
the core enzyme) + sigma factor (6th unit: recognize the promotor). The
different subunits play distinct functional roles. Proteins such as sigma factor
that influence the function of RNA polymerase are types of transcription
factors. When the holoenzyme protein encounters a promotor, sigma factor
recognizes both -35 and -10 sequences. The sigma-factor contains a structure
called a helix-turn-helix motif that can bind tightly to these sequences. Alpha
helices within the protein fit into the major groove of the DNA double helix
and form hydrogen bonds with the bases. Parts of sigma-factor must fit into
the major groove so that it can recognize a promoter and form hydrogen
bonds with its bases. When it binds it forms a closed complex.
For transcription to begin, the double-stranded DNA must be unwound into
an open complex. The unwinding begins at the TATAAT sequence in the -10
site. A-T base pairs form only two hydrogen bonds, therefore DNA in an AT-
rich region is more easily separated. A short strand of RNA is made within the
open complex, and then the sigma factor is released from the core enzyme.
RNA Modification (processing)
The primary function of genetic material (DNA) = to store the
information necessary to create a living organism. The
information is contained within units called genes.
Gene = segment of DNA that is used to make a functional
product, either a RNA molecule or a polypeptide. Region (you
get the RNA from) that is being transcribed (exons).
To access the information within a gene the first step is called
transcription (= process of making a copy = process of
synthesizing RNA from a DNA template). DNA structure is not
altered as a result of transcription, it has only been accessed to
make a copy in the form of RNA. Therefore, the same DNA can
continue to store information. DNA replication, provides a
mechanism for copying that information so that it can be
transmitted to new daughter cells and form parent to offspring.
Protein-encoding genes (structural genes) carry the information
for the amino acid sequence of a polypeptide. When a structural gene is described the first product is
messenger RNA (mRNA). During polypeptide synthesis (=translation), the sequence of nucleotides within the
mRNA determines the sequence of amino acids in a polypeptide. One or more polypeptides then assemble
into a functional protein. The structures and functions of proteins largely determine an organism’s traits.
Central dogma of genetics = Once (sequential) information has
passed into protein it cannot get out again (on paper it can).
The flow of genetic information occurs from DNA to mRNA to
polypeptide.
Key concepts regarding transcription:
, - Specifi
c base
sequences determine where transcription starts and ends, there are also regulatory sites (DNA
sequences) that influence whether a gene is turned on or off.
- Proteins play an important part. DNA sequences, in and of themselves, just exist. For genes to be
actively transcribed, proteins must recognize particular DNA sequences and act on them.
Gene expression = the overall process by which the information within a gene is used to produce a
functional product (such as a polypeptide). Gene expression requires base sequences that perform different
functional roles. Promoter = provides a site for beginning transcription. Terminator = specifies the end of
transcription. These two base sequences cause RNA synthesis to occur within a defined location.
The base sequence in the RNA transcript is complementary to the template strand (non-coding/ antisense
strand) of DNA. The opposite strand of DNA is the nontemplate strand also called the coding/sense strand
because its sequence is the same as the transcribed mRNA (excepts T is U).
Transcription factors (proteins) control the rate of transcription. Some bind directly to the promotor others
recognise regulatory sequences/elements (short stretches of DNA involved in regulation of transcription).
Some regulatory sequences inhibit others increase the rate of transcription.
mRNA are used during translation process. In bacteria a short sequence within the mRNA = ribosome-
binding site (Shine-Dalgarno sequence) provides a location for a ribosome to bind and begin translation. It
recognizes this site because its complementary to a sequence in ribosomal RNA.
Each mRNA contains a series of codons (3 nucleotides) which contain information for polypeptide’s
sequence. First codon = start codon, is close to the ribosome-binding site. Followed by many codons and
finally the stop codon that signals the end of translation. If a mutation changed the start codon into a stop
codon, the mutation would not affect the length of the RNA, because it would not terminate transcription.
However the encoded polypeptide would be shorter.
The three stages of transcription are initiation, elongation (synthesis of the RNA transcript), and
termination. These steps involve protein-DNA interactions in which such as RNA polymerase (enzyme that
synthesizes RNA) interact with DNA sequences.
Initiation = recognition step the sequence of bases within the promoter is recognizes by one or more
transcription factors. The binding of specific transcription factors to the promotor identifies the starting site
, for transcription. Transcription factor(s) and RNA polymerase first bind to the promotor when the DNA is in
the form of a double helix. But for transcription to occur the DNA strands must be separated. Synthesis occur
as RNA polymerase slides along the DNA, forming bubble-like structure know as the open promotor complex
(=open complex). Eventually RNA polymerase reaches a terminator,
which causes both RNA polymerase and the newly made RNA to
dissociate from the DNA.
Transcription in Bacteria
Much of our knowledge comes from studies of E.coli.
A promotor is a short sequence of DNA that is necessary to initiate
transcription. This sequence of bases directs the exact location for the
initiation of transcription. Most of the promotors are located just ahead
(upstream from) transcriptional starts site (=located at +1 site and is
where the first base is used as a template for transcription). The bases in
a promotor sequence are numbered in relation to this site. This site is the
first nucleotide used as template for transcription and is denoted +1.
Preceding this site the bases are numbered in negative direction. No base
is numbered zero. Although promotor may encompass a lot of
nucleotides. Short sequences are necessary for a promotor to be
functional. One is called the Pribnow box (5’-TATAAT-3’) and the other one is
5’-TTGACA-3’. The most commonly occurring bases within a specific type of
sequence is called the consensus sequence = for a group of related
sequences, the consensus sequence consists of the most common base found
at each location within that group of sequences.
Bacterial transcription is initiated when RNA polymerase holoenzyme binds at
a promotor. In E.coli the RNA polymerase holoenzyme is composed: core
enzyme of five subunits (α2ββ’ω = α: assembly of the holoenzyme and
binding to DNA, β β’: binding and catalytic synthesis of RNA, ω: assembly of
the core enzyme) + sigma factor (6th unit: recognize the promotor). The
different subunits play distinct functional roles. Proteins such as sigma factor
that influence the function of RNA polymerase are types of transcription
factors. When the holoenzyme protein encounters a promotor, sigma factor
recognizes both -35 and -10 sequences. The sigma-factor contains a structure
called a helix-turn-helix motif that can bind tightly to these sequences. Alpha
helices within the protein fit into the major groove of the DNA double helix
and form hydrogen bonds with the bases. Parts of sigma-factor must fit into
the major groove so that it can recognize a promoter and form hydrogen
bonds with its bases. When it binds it forms a closed complex.
For transcription to begin, the double-stranded DNA must be unwound into
an open complex. The unwinding begins at the TATAAT sequence in the -10
site. A-T base pairs form only two hydrogen bonds, therefore DNA in an AT-
rich region is more easily separated. A short strand of RNA is made within the
open complex, and then the sigma factor is released from the core enzyme.
