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  Biosynthesis of RNA

Biosynthesis of RNA (Transcription):

The biosynthesis of RNA is extremely identical to that of DNA, apart from that in RNA it is differed through comprising dissimilar RNA types (mRNA, tRNA, rRNA), and the nitrogen base uracil in place of thymine. Such that DNA, polymerization of 4 nucleoside triphosphates (that are ATP, CTP, GTP and UTP) in the existence of Mg2+ or Mn2+ ion is catalysed via the enzyme RNA polymerase and one strand of DNA works like template.

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Mechanism:

Transcription includes 3 stages

1. Initiation:

In E. coli, all genes are transcribed through a single large RNA polymerase. This complex enzyme, known as the holoenzyme is required to initiate transcription because the σ factor is necessary for detection of the promoter. It is general for prokaryotes to have various σ factors which recognize dissimilar types of promoter (in E. coli, the very much common σ factor is σ 70).

The holoenzyme binds to a promoter region approximately 40-60 bp in size and after that initiates transcription a short distance downstream (that is 3' to the promoter). Inside the promoter lie two 6 bp sequences which are specifically significant for promoter function and that are hence highly conserved among the species. By using the convention of calling the first nucleotide of a transcribed sequence like +1, there 2 promoter elements be positioned at -10 and -35, i.e. about 10 and 35 bp correspondingly, downstream of where transcription will start.

2. Elongation:

Later than the transcription initiation, the σ factor is released from the transcriptional complex to left the core enzyme (α2 ββ' ω) that carries on elongation of the RNA (Ribonucleic Acid) transcript. So, the core enzyme consists of the catalytic site for polymerisation, possibly in the subunit. The 1st nucleotide in the RNA (Ribonucleic Acid) transcript is generally PPPG or PPPA. After that the RNA (RIBONUCLEIC ACID) polymerase synthesises the RNA (Ribonucleic Acid) in the 5' → 3' direction, by using the 4 ribonucleotide 5' triphosphates  (ATP, CTP, GTP, UTP), like precursors.

The 3'-OH group at the end of the growing RNA (Ribonucleic Acid) chain connects to a phosphate group of the incoming ribonucleotide 5' triphosphate to create a 3',5' phosphodiester bond. The complex of RNA (RIBONUCLEIC ACID) polymerase, DNA (Deoxyribonucleic Acid) template and new RNA (Ribonucleic Acid) transcript is known as a teRNA (ribonucleic acid)ry complex (that is three components) and the region of unwound DNA which is going through transcription is known as transcription bubble. The RNA) transcript creates a transient RNA-DNA  hybrid helix along with its template strand but then peels away from the DNA (Deoxyribonucleic Acid) when transcription proceeds. The DNA (Deoxyribonucleic Acid) is unwound ahead of the transcription bubble and after the transcription complex has passed, the DNA (Deoxyribonucleic Acid) rewinds.

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                                                      Diagram: Transcription by RNA polymerase

In every step the incoming ribonucleotide selected is that which can base pair along with the next base of the DNA template strand. In the figure, the incoming nucleotide is UTP to base pair along with the A residue of the template DNA. A 3', 5' phosphodiester bond is created, extending the RNA chain via one nucleotide, and pyrophosphate is released. Finally the RNA molecule is grown in a 5' to 3' direction.

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                                                                   Diagram: A transcription bubble

The DNA double helix is unwound and RNA polymerase after that synthesizes an RNA copy of the DNA template strand. The nascent RNA transiently creates an RNA-DNA hybrid helix but after that peels away from the DNA which is subsequently rewound into a helix once more.

3. Termination:

Transcription carries on until a termination sequence is reached. The very much common termination signal is a G ≡ C rich region is a palindrome, followed via an A = T rich sequence. The RNA made from the DNA (Deoxyribonucleic Acid) palindrome is self complementary and thus base pairs internally to create a hairpin structure rich in GC base pairs followed via four or more U residues. Though, not all termination sites base this hairpin structure. Those that lack such type of a structure need an additional protein, known as rho protein (ρ) to assist recognize the termination site and stop transcription.

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         Diagram:  A typical hairpin structure formed by the 3' end of the RNA molecule during termination of transcription

Post Transcriptional Modification:

Post-transcriptional modifications are not required for prokaryotic mRNAs. The creation of functionally active RNA molecule carries on after transcription is completed in eukoryotes. The product of transcription in eukarryotes is known as primary transcripts and they go through modification through a process that is known as post transcriptional modification.

 

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