post transcriptional modification

Post Transcriptional Modification:

Primary transcript made by RNA polymerase normally undergo further alteration, called post transcriptional processing or modification.

Prokaryotes: mRNA transcribed directly from DNA template  and used immediately in protein synthesis.

Eukaryotes: Primary transcript(hnRNA) must be processed to produce the mRNA(active form). It occurs in nucleus of cell.

Post transcriptional modifications of RNA accomplish three things:

1. Modifications help the RNA molecule to be recognized by molecules that mediate RNA translation into proteins. 
2. During post transcriptional processing, portions of the RNA chain that are not supposed to be translated into proteins are cut out of the sequence. In this way, post transcriptional processing helps increase the efficiency of protein synthesis by allowing only specific protein coding RNA to go on to be translated.
3. Without post transcriptional processing, protein synthesis could be significantly slowed, since it would take longer for translation machinery to recognize RNA molecules and significantly more RNA would have to be unnecessarily translated.

Terms used in Post Transcriptional Modification

• 3' Splice site- One of the conserved sequence of an intron contains an adenine next to a guanine base at the 3' end of an intron.
• 5' Capping- One post transcriptional modification made in the cell nucleus. The addition of a GTP molecule to the 5' end of a primary RNA transcript forming a 5'-5' linkage between the two.
• 5' Splice site- One of the conserved sequences of an intron contains an gaunine next to a uracil base at the 5' end of an intron.
• Exon- Sequences that are preserved in primary RNA transcript splicing that will be translated into proteins in the cell cytoplasm. 
• Intron- Non-protein coding sequences of a primary RNA transcript splicing.
• Guaninyl transferase- The enzyme responsible for catalyzing the reaction that produces the 5' cap through the addition of a GTP molecule to the 5' end of a primary RNA transcript.
• Poly A tail- One post transcriptional modification made in the cell nucleus. A string of up to 500 adenines added to the 3' end of primary RNA transcripts. Addition catalyzed by the enzyme poly A polymerase that recognizes the sequences AAUAAA.
• RNA splicing- A two step reaction in which introns are removed from a primary RNA transcript and exons are joined together to form mature mRNA.

Post transcriptional modification mainly includes

1. 5' capping
2. Addition of poly A tail
3. Splicing

5' End Capping:

At the end of transcription, the 5' end of the RNA transcript contains a free tri phosphate group since it was the first incorporated nucleotide in the chain. The capping process replaces the tri phosphate group with another structure called the " cap ". The cap is added by the enzyme guanyl transferase. This enzyme catalyzes the reaction between the 5' end of the RNA transcript and a guanine tri phosphate(GTP) molecule.

In the reaction, the beta phosphate of the RNA transcript displaces a pyrophosphate group at the 5' position of the GTP molecule. The cap is formed through a 5'-5' linkage between the two substrates. Capping protects the 5' from enzymatic degradation in the nucleus and assists in export to the cytosol. Eukaryotic mRNA lacking the cap are not efficiently translated.

Addition of poly A tail:

Post transcriptional RNA processing at the opposite end of the transcript comes in the form of a string of adenine bases attached to the end of the synthesized RNA chain. The addition of the adenines is catalyzed by the enzyme poly (A) polymerase. The mRNA is first cleaved about 20 nucleotides downstream from an AAUAA recognition sequence. Another enzyme, poly (A) polymerase, adds a poly (A) tail which is subsequently extended to as many as 200 A residues. The poly (A) tail appears to protect the 3' end of mRNA from 3'-5' exonuclease attack. 

Histone and interferons mRNAs lack poly A tail. After the mRNA enters the cytosol, the poly A tail is gradually shortened.

Splicing:

• Removal of introns from RNA transcript is known as splicingi
• Introns or intervening sequences are the RNA sequences which do not code for the proteins.
• These introns are removed from the primary transcript in the nucleus, exons(coding sequences) are ligated to form the mRNA molecule, and the mRNA molecule is transported to the cytoplasm.
• The molecular machine that accomplishes the task of splicing is known as the spliceosomes.
• Small nuclear RNA molecules that recognize splice sites in the pre mRNA sequences.
• The excised intron is released as a " lariat" structure, which is degraded.

 Alternative Splicing:

• Alternative patterns of RNA splicing is adapted for the synthesis of tissue-specific proteins(antibodies).
• The pre mRNA molecules from some genes can be spliced in two or more alternative ways in different tissues.
• This produces multiple variations of the mRNA and thus diverse set of proteins can be synthesized from a given set of genes.
• Introns are removed from the primary transcript in the nucleus, exons( coding sequences) are ligated to form the mRNA molecule.( After removal of all the introns, the mature mRNA molecules leave the nucleus by passing into the cytosol through pores in to the nuclear membrane)

Alternative splicing accomplishes this two ways:

1. By splicing together exons from two different primary RNA transcripts in a process called trans-splicing
2. By splicing out entire exons.