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Genetics summary chapter 12 VU Amsterdam
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This summary covers complete chaper 12 of genetics at the Vrije Universiteit Amsterdam.
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Chapter 12 summary GENE TRANSCRIPTIONThe primary function of genetic material, which is DNA, is to store the information that is necessary
to create a living organism. The information is contained within unites called genes. At the molecular
level, a gene is defined as a segment of DNA that is used to make a functional product, either an RNA
molecule or a polypeptide. The first step in this process is called the transcription, which means the
act/process of making a copy. In genetics, this term means the process of synthesizing RNA from a
DNA template.
Protein-encoding genes (structural genes) carry the information for the amino acid sequence of a
polypeptide. When a protein-encoding gene is transcribed, the first product is an RNA molecule
known as messenger RNA (mRNA). During polypeptide synthesis – a process called 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.
- Central dogma of genetics: explains the flow of genetics information: DNA -> mRNA ->
polypeptide.
Gene expression requires base sequences that perform different functional roles. Gene expression is
the overall process by which the information within a gene is used to produce a functional product,
such as a polypeptide. The molecular expression of genes determines the organisms’ traits.
The promotor and terminator are base sequences used during gene transcription. The promotor
provides a site for beginning transcription and the terminator specifies the end of transcription.
These two base sequences cause RNA synthesis to occur within a defined location. The base
sequence of RNA is complementary to the template strand of DNA. The opposite strand of the DNA
is the nontemplate strand. For protein-encoding genes, the nontemplate strand is also called the
coding strand, or sense strand, because its sequence is the same as the transcribed mRNA that
encodes a polypeptide, except the DNA has thymine whereas the mRNA has uracil. The template
strand is also called the non-coding strand or antisense strand.
A category of proteins called the transcription factors controls the rate of transcription. Some bind
directly to the promotor and facilitate transcription. Other transcription factors recognize regulatory
sequences (regulatory elements) – short stretches of DNA involved in the regulation of transcription.
Certain transcription factors bind to the regulatory sequences and thereby increase the rate of the
transcription, whereas others inhibit transcription.
In bacteria, a short sequence within the mRNA, the ribosome-binding site (also known as the Shine-
Dalgarno sequence), provides a location for the ribosome to bind and begin translation. The bacterial
ribosome recognizes this site, because it is complementary to a sequence in ribosomal RNA. In
addition, each mRNA contains series of codons, group of 3 nucleotides, which contain information
for the polypeptide’s sequence. The first codon, which is very close to the ribosomal-binding site, is
the start codon. This is followed by the many more codons that dictate the sequence of amino acids
within the synthesizes polypeptide. Finally, a stop codon signals the end of translation.
Transcription occurs in 3 stages:
1. Initiation: the promotor functions as a recognition site for transcription factors. The
transcription factors enable RNA polymerase to bind to the promotor. After the binding, the
DNA is denaturated into a bubble known as the open complex.
2. Elongation : RNA polymerase slides along the DNA in an open complex to synthesize RNA.
3. Termination : A terminator is reached that causes RNA polymerase and the RNA transcript to
dissociate from the DNA.
RNA polymerase is the enzyme that synthesizes RNA and interacts with the DNA sequences. Elliot
Volkin and Lazarus Astrachan exposed E.coli cells to T2 bacteriophage. They observed that the RNA
made after the infection has a base composition that was different from the RNA made prior the
, Chapter 12 summary GENE TRANSCRIPTION
infection. Furthermore, the base composition after the infection was almost similar to that of the
DNA, except thymine was uracil in the RNA. These results were consistent with the idea thar
bacteriophage DNA is used as a template for the RNA synthesis. In 1960, Matthew Meselson and
Jacob found that proteins are synthesized on ribosomes. Later, Jacob proposed that a certain type of
RNA acts as a genetic messenger (from DNA to the ribosomes) to provide the information for protein
synthesis. This type of RNA was called the messenger RNA (mRNA). They hypnotized that this
messenger RNA was transcribed from the base sequences of DNA and then directs the synthesis of
polypeptides.
A promotor is a short sequence of DNA that is necessary to initiate transcription. The site on the DNA
from which the first RNA nucleotides is transcribed is called the transcriptional start site and is
denoted as +1. The bases preceding this site are numbered in a negative direction. No base is
numbered zero. Therefore, most of the promotor is labelled with negative numbers such as -35
sequences and -10 sequences (promotor). Short sequences are necessary for promotor recognition.
Researchers have found out that certain base sequences are necessary for the functioning of the
promotor. A few important promotor sequences are:
- 5’ – TTGAC -3’
- 5’ – TATAAT-3’ -> this one is called the Pribnow box after Pribnow discovered it in 1975.
These promotor sequences are called the consensus sequences, because they occur the
most within a promotor.
Sequences found in DNA, such as those found in promotors or regulatory elements, vary among
different genes.
Transcription is initiated when RNA polymerase (enzyme that catalyzes the RNA synthesis)
holoenzyme binds to the promotor. E.coli RNA polymerase core enzyme consists of 5 subunits: α α β
β’ and ω. The associated of the sixth subunit, the sigma factor (σ) creates what is referred to as the
RNA polymerase holoenzyme. A sigma factor is a protein needed for the initiation of transcription in
bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA
polymerase (RNAP) to gene promotors.
- α2: are important in the proper assembly of the holoenzyme and in the process of binding
DNA.
- β/β’ : are important for the binding of DNA and they carry out the catalytic synthesis of RNA.
- ω: is important for the proper assembly of the core enzyme.
- σ: is important for the recognition of the promotor.
After the six subunits bind to each other, the RNA polymerase binds to the DNA and slides down. The
σ-factor recognizes the -35 and -10 sequences of the promotor. The structure of the σ-factor is called
the helix-turn-helix motif that can bind tightly to these sequences. The σ-factor contains two α
helices that fit into the major groove of the DNA double helix and the amino acids in the α helices
form hydrogen bonds with the bases. Hydrogen bonding occurs between the nucleotides in the -35
and -10 sequences.
The process of transcription is initiated when a σ factor within the holoenzyme (RNA polymerase
holoenzyme) binds to the promotor to form a closed complex. For transcription to begin, the double-
stranded DNA must be unwound into an open complex. This unwinding begins at the TATAAT
sequence in the -10 site, which only contains A/T base pairs. Since AT only form two hydrogen bonds
and GC three, this AT-rich region is easily separated because fewer hydrogen bonds must be broken.
A short strand of RNA is made within the open complex, and the σ factor is released from the core
enzyme (RNA polymerase). This release marks the transition to the elongation phase. The core
enzyme may now slide along the DNA to synthesize a strand of RNA.
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