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Transcription or RNA Synthesis

RNA synthesis in bacteria, Initiation, Elongation, Termination, Transcription in eukaryotes
A strand of RNA, also called an RNA transcript, is formed during transcription from the genetic information encoded in a DNA sequence. A single strand of the RNA molecule is made up of bases adenine (A), guanine (G), cytosine (C), and uracil (U) and serves as a mobile molecular copy of the DNA sequence. A portion of the DNA double helix must partially unwind during transcription in prokaryotes and eukaryotes. These regions are known collectively as transcription bubbles. The antisense strand, which functions as a template for gene transcription, always comes first. There is almost no difference between the RNA product and the template strand of DNA and its counterpart, the sense strand. All the T nucleotides in RNA are replaced with U nucleotides because the U is incorporated when the complementarity antisense strand contains an A.

RNA synthesis in bacteria

All of a bacteria's genes are transcribed by the same RNA polymerase. Like DNA polymerase, RNA polymerase continuously branches the growing nucleotide chain's 3′-OH group. There is a crucial difference in how DNA polymerase and RNA polymerase add nucleotides to their ends: DNA polymerase requires 3'-OH groups, while RNA polymerase does not. Dehydration synthesis creates a covalent phosphodiester bond between a new nucleotide and the latest one added during transcription. DNA template strand and the new nucleotide are complementary. The polymerase is composed of six polypeptide subunits, five of which make up the polymerase core enzyme responsible for adding nucleotides to an RNA strand as it grows. Sigma (σ) corresponds to the sixth subunit. A specific promoter is bound by the σ factor, allowing RNA polymerase to transcribe various genes. Many σ factors allow various genes to be transcribed.

Initiation

Initiation of transcription begins with a promoter, a sequence of DNA that the transcription machinery binds to, and begins transcription. A transcription initiation site corresponds to the DNA double helix nucleotide pair responsible for transcribing the first 5′ RNA nucleotide. Upstream nucleotides are referred to as "upstream" nucleotides, while downstream nucleotides are known as "downstream." Most genes have promoters located directly upstream of the genes they regulate. Some promoter sequences are conserved among bacterial genomes, despite differences in promoter sequences. At –10 and –35 positions before the initiation site (designated +1), DNA contains two promoter consensus sequences (regions common to all promoters and bacterial species). There is a consensus sequence called TATAAT in the –10 region. And the σ can recognize and bind the –35 sequence.

Elongation

While the polymerase dissociates from its σ subunit in the transcription phase, the core enzyme is capable of synthesizing complementary RNA in the 5'-to-3' direction at approximately 40 nucleotides per second. During elongation, DNA is continually unwound before and rewound behind the core enzyme.



Termination

The DNA template must be dissociated from the bacterial polymerase once the gene is transcribed, allowing the newly created RNA to be released. Termination of transcription is known as this. After nucleotide strands in the DNA template act as termination signals, RNA polymerase stalls and releases from the DNA template.

Transcription in eukaryotes

Eukaryotes and prokaryotes similarly perform transcription, but with some significant differences. RNA polymerases I, II, and III are used by eukaryotes and differ structurally from bacterial RNA polymerases. These polymerases transcribe different sets of genes. An interesting fact is that archaea possess a polymerase more closely related to eukaryotic than bacterial RNA polymerase II. Eukaryotic mRNAs usually encode one polypeptide each, while bacterial and archaeal mRNAs are usually polycistronic, meaning that each encodes more than one polypeptide.

Eukaryotes have membrane-bound nuclei, and this influences how easy it is to synthesize proteins with RNA molecules. RNA molecules that encode proteins must be transported from the nucleus to the cytoplasm for the eukaryotic cell to function. RNA polymerase direct synthesizes primary transcripts, which encode proteins, that must be protected during their transfer from the nucleus to the cytoplasm and translation. A typical prokaryotic mRNA lasts about 5 seconds, whereas eukaryotic mRNAs last for several hours.

Primary transcripts (also called pre-mRNA) are protected from degradation while they are processed and exported from the nucleus by RNA-stabilizing proteins. The first type of processing takes place during the synthesis of the primary transcript; a special nucleotide, 7-methylguanosine, is added to the 5' end. Along with preventing degradation, the cap facilitates ribosome translation by recognizing factors involved in subsequent protein synthesis. A second enzyme will then add approximately 200 adenine nucleotides to the 3′ end of the poly-A tail, completing the elongation process. Upon completion of this modification, the pre-mRNA is further protected from degradation, and cellular factors are alerted to the need to export it to the cytoplasm.

A polypeptide gene in eukaryotic cells is made up of coding sequences called exons (ex-ons denote the expression of these sequences) and intervening sequences called introns (int-rons refer to their role). Introns are not encoded by the transcribed RNA sequences and are therefore removed from pre-mRNA during processing. In the case of pre-mRNA, all the RNA sequences encoded by the introns must be accurately removed before protein synthesis, to properly assemble exon-encoded RNA sequences that encode for a functional polypeptide. A single nucleotide error could shift the sequences of the re-joined exons, rendering the polypeptide ineffective.

A spliceosome containing small nuclear ribonucleoproteins (snRNPs) facilitates RNA splicing by removing intron-encoded RNA sequences and connecting those encoded by exons. A nucleus-bound pre-mRNA is stripped of intron-encoded RNA sequences. In addition to regulating gene expression and transporting mRNA, introns may also play other roles that are not translated. In the cytoplasm, the mature transcript, the mRNA which encodes a polypeptide, is transported after completing these modifications. Exons can be included or excluded from the final mRNA product based on the way introns are spliced. Alternative splicing occurs during this process. It is possible to generate various forms of mRNA transcripts by alternative splicing from the same DNA sequence. Several archaeal species have also been demonstrated to be able to splice their pre-mRNA.
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Ankur Choudhary is India's first professional pharmaceutical blogger, author and founder of pharmaguideline.com, a widely-read pharmaceutical blog since 2008. Sign-up for the free email updates for your daily dose of pharmaceutical tips.
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