Transcription and Open Reading Frame

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Transcription The expression of genetic information stored in the DNA sequence starts with synthesis of the RNA copy of the gene in a process called transcription. The RNA copy of the gene is called messenger RNA (mRNA). A special enzyme, RNA polymerase, recognizes a sequence, called promoter, on the DNA double helix upstream from the protein coding sequence. RNA polymerase binds to the promoter and opens it up: separates the complementary strands at about 12-nt-long region of the promoter. Then the enzyme starts the mRNA synthesis using all 4 NTPs. The DNA strand, which is used as a template by RNA polymerase, is called the template or antisense strand. The opposite strand of the gene, which sequence is identical to the sequence of mRNA (except the substitution T U, of course), is called the coding or sense strand. There is also a special sequence after the end of the gene, which signals to RNA polymerase to terminate the mRNA synthesis. Thus synthesized mRNA molecule, which includes the protein coding region flanked by short unrelated sequences from both sides, is either translated by the ribosome into the protein molecule at the spot (in case of prokaryotes) or is transported from the nucleus to the cytoplasm (in case of eukaryotes) and there it is translated by the ribosome. Open Reading Frame (ORF) Since the genetic code is triplet, three reading frames are possible for the same mRNA molecule. For instance, the sequence: …..AUUGCCUAACCCUUAGGG…. can be separated into triplets by three possible ways: ….AUUGCCUAACCCUUAGGG…. ….AUUGCCUAACCCUUAGGG…. ….AUUGCCUAACCCUUAGGG…. The frame, in which no stop codons are encountered, is called the Open Reading Frame (ORF). Since there are three stop codons, UAG, UAA and UGA, in the above example only the last frame, out of 3 possible, is ORF (stop codons in 2 other reading frames are emboldened). The ORF concept is so important because only the ORF can correspond the correct frame at which the mRNA sequence is translated via the Genetic Code. Any other frame cannot be the correct frame since it would not result in the full-length protein. ================================================================================== Comments: 1.Which promoter is recognized by RNA polymerase depends on numerous proteins participating in the regulation of transcription, which is the central issue for the gene expression mechanism. These are transcription factors, repressors and other elements. 2.Since the ORF concept is usually applied to a small internal region of the protein coding sequence, the initiation (or start) codon is not expected to belong to the sequence (the initiation codon must be far upstream of the sequence under consideration). Therefore, the definition of ORF on Wiki http://en.wikipedia.org/wiki/Open_reading_frame is incorrect. Note that their definition contradicts to their own example, in which there is no initiation codon. Again, the only requirement for ORF is the absence of stop codons, nothing else. .

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