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Prokaryotic Protein Synthesis

BY: Zandro Cabaral | Category: Bioinformatics | Submitted: 2011-01-30 04:15:15
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Article Summary: "A summary of the protein synthesis in prokaryotes or single celled organisms. Each type of amino acid is activated by joining to Adenosine Triphosphate using a specific aminoacyl - transfer RNA synthetase. This process is called the Activation with ATP. .."

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Each type of amino acid is activated by joining to Adenosine Triphosphate using a specific aminoacyl - transfer RNA synthetase. This process is called the Activation with ATP. The specific aminoacyl - transfer RNA synthetase is also responsible for binding each type of amino acid to its correct transfer RNA. The amino acid-monophosphate - transfer RNA is called a charged transfer RNA. The energy to drive these reactions comes from Adenosine Triphosphate being cleaved to Adenosine Monophosphate and 2 inorganic phosphates, the Pi + Pi.

In Initiation, a 70S ribosome complex is made of 30S and 50S ribosomal subunits; the ribosome contains amino and peptide binding sites. An Initiation Factor 3 binds to the 30S ribosomal subunit and causes it to dissociate from the 50S subunit. Then, messenger RNA and initiation factor-1 bind to the small 30S ribosomal subunit. The 5' end of each messenger RNA has a Shine - Dalgarno sequence which 5'-AGGAGGA-3', about 7 bases before the first codon. The 16S ribosomal RNA of the small ribosomal subunit has a sequence complementary to the Shine - Dalgarno sequence which binds to it. The ribosome looks for the first AUG messenger RNA codon that it comes to. The first messenger RNA codon always codes for the amino acid methionine. Methionine binds to a specific initiator transfer RNA. After binding to initiator transfer RNA methionine receives a formyl group. "N10-formyltetrahydrofolate" is the formyl group donor in a reaction catalyzed by methionine transformylase. Initiation Factor -2 then binds to the initiator transfer RNA - formyl methionine and they bind to the 30S subunit as the large 50S ribosomal subunit re-associates with the small 30S subunit forming a complete ribosome and the initiation factors are released. Release of the initiation factors uses energy from Guanosine Triphosphate being cleaved to GDP + Pi. The initiation complex has now been assembled. It includes the complete ribosome which is 30S and 50S ribosomal subunits bound to messenger RNA at the Shine - Dalgarno sequence.

The initiator - transfer RNA - formylmethionine, with its anticodon base paired to the messenger RNA's codon , held in the ribosome's peptide site with the ribosome's amino site is vacant. Eukaryotes have several Eukaryotic Initiation Factors. The initial formylmethionine amino acid can later be removed from the polypeptide.

The next step is called Elongation. A messenger RNA at the amino site contains the next codon. When another charged transfer RNA - phospho amino acid moves into the vacant amino site, its anticodon will base pair with the messenger RNA codon and binds to the ribosome's amino site. This process consumes Guanosine Triphosphate and requires the elongation factor. Peptidyl transferase, an enzyme that is part of the 50S subunit, catalyzes a reaction that forms a peptide bond between the carboxyl group on the amino acid at the phosphate site and the amino group of the amino acid at the amino site. The polypeptide grows from the amino side or the N-terminal to the carboxyl side or the C-terminal. Formation of the peptide bond is driven by the hydrolysis of the phosphate bond from the phosphate site amino acid. This result in an uncharged phosphate site transfer RNA no longer bound to an amino acid, and the amino site transfer RNA being bound to 2 amino acids. The whole process may be repeated. Eukaryotes also have termination factors that will end synthesis.

The next process is called Translocation. In this process translocation transfer RNA - peptide complex from the amino site to the Pphosphate site. The ribosome moves 3 nucleotides down toward the messenger RNA's 3' end. The uncharged transfer RNA is released. A new transfer RNA phosphate amino acid binds to the amino site consuming another molecule of Guanosine Triphosphate and requiring the Elongation Factor and elongation is repeated and uses 2 GTP's for every peptide bond. Diphtheria toxin alters Elongation Factor 2 and stops elongation and can't translocate.
The last step of protein synthesis is the Termination. When one of the messenger RNA stop codons reaches the amino site, releasing factors cause the messenger RNA and the new polypeptide to be released.

The general concept of protein synthesis is summarized in this statement: the activation of amino acids; messenger RNA initiation factors, join with ribosomal subunits; then,GTP, elongation factors, join with aminoacyl - transfer RNA which forms the peptide bonds, Peptidyl - transfer RNA is then translocated.

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