Messenger RNA (mRNA)

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Introduction

Ribonucleic acid or RNAs are the working copies of DNA. The information present in DNA is expressed in the form of these working copies. Three major types of RNA are found in all the living cells; messenger RNA, ribosomal RNA, and transfer RNA. 

The messenger RNA (mRNA) carries the message of DNA from the nucleus to the cytoplasm. This message is used by the ribosomes to make proteins. In this article, we will discuss the synthesis of mRNA, its processing, and its role in protein synthesis. We will also see the differences between eukaryotic and prokaryotic mRNA.

Structure

A molecule of messenger RNA is a linear chain of ribonucleotides. The nucleotides are arranged in the form of triplets called codons. All the codons are collectively called genetic code. 

Genetic Code

mrna-molecule

Genetic code is a dictionary through which the sequence of nucleotides in mRNA is translated into the sequence of amino acids in a protein. The genetic code is composed of words called codons. A codon is a sequence of three nucleotides that codes for one specific amino acid in proteins. 

Different codons are represented by the first letter of the base present in the nucleotide. Recall that four different bases could be present in the ribonucleotide of mRNA; adenine (A), guanine (G), cytosine (C), and uracil (U). Using these four bases, 64 different combinations have been made, with each combination taking three bases at a time. These 64 codons code for the 20 amino acids mostly present in proteins. 

  • 61 codons code for the 20 amino acids. One of these codons is always present at the beginning of the mRNA molecule called initiation codon. The initiation codon (AUG) always codes for methionine amino acid.
  • The other 3 codons do not code for any amino acid. They are called stop codons or termination codons. They are usually present at the end of the mRNA molecule. These codons signal to stop the process of protein synthesis. 

The genetic code on mRNA is already read in 5’ to 3’ direction. There is no break or punctuation between different codons i.e. they are read continuously. This is the reason why the addition or deletion of one nucleotide changes the entire reading frame.  

There are 61 codons for 20 amino acids. This shows that more than one codon may code for the same amino acids. However, one codon codes for only one amino acid.

With a few exceptions, the genetic code is universal. The individual codons code for the same amino acids in all the organisms. Therefore, this genetic code is applicable in the case of any living organism.

Synthesis 

Like the other types of RNA, messenger RNA is also made from DNA by the process of transcription. This process involves the making of working copies of DNA in the form of mRNA. 

Recall that mRNA carries the message of a gene. The process of transcription involves copying the sequence of nucleotides in a gene into the nucleotide sequence of mRNA. As the DNA molecule is double-stranded, one of the gene’s strand acts as a template strand for making mRNA. The other strand is called the non-template strand. the nucleotide sequence in mRNA is complementary to the template strand while it is identical to the non-template strand. 

RNA polymerase

It is the enzyme that constructs the mRNA chain using the template strand of the gene. The enzyme attaches to the template strand and adds nucleotides to make mRNA. The synthesis of mRNA always takes place in 5’ to 3’ direction. The 5’ end is called head while the 3’ end is called the tail of mRNA.

Steps in Transcription

The process of transcription involves three steps; initiation, elongation, and termination. 

Initiation

The synthesis begins with the recognition of the gene by RNA polymerase. It identifies and attached to the specific sequences present at the beginning of the template strand. Such sequences are called consensus sequences. They are different in eukaryotes and prokaryotes.

The recognition and binding of consensus sequence by RNA polymerase in eukaryotes are facilitated by specific factors called transcription factors. 

Elongation

The RNA polymerase travels down the gene until it reaches the initiation site. Here it begins making the RNA strand complementary to the template strand. The ribonucleoside triphosphate molecules are used as precursors for adding nucleotides in the mRNA chain. 

The elongation process continues until a termination sequence is reached. Here, transcription stops. 

The process of elongation is facilitated by some factors in eukaryotes, called elongation factors. 

Termination

Once the RNA polymerase reaches the termination sequence, it halts, and no more elongation takes place. The newly formed molecule of mRNA is released from the transcription complex in either of the two ways;

  • A hairpin loop is formed in mRNA that pulls the mRNA from RNA polymerase
  • A protein called rho-protein uses ATP to break the bonds and release mRNA from the complex

The DNA double helix unwinds during the process of transcription generating supercoils. These supercoils are removed by special enzymes called topoisomerases. These enzymes are different in eukaryotes and prokaryotes.

Site of Synthesis

The site of mRNA synthesis is different in eukaryotes and prokaryotes. Recall that eukaryotic cells have their entire DNA in the nucleus while prokaryotes lack any nucleus in their cells. The synthesis of mRNA in eukaryotes occurs within the nuclei of the cells. On the other hand, prokaryo6tic mRNA is made within the cytoplasm. 

Post-transcriptional Modifications

The process of transcription in eukaryotes results in a collection of transcripts collectively known as heterogeneous nuclear RNA (hnRNA). It undergoes several modifications before becoming fully functional.

As mentioned earlier that eukaryotic mRNA is made within the nucleus. It must move outside the nucleus into the cytoplasm so that it can perform its function. The post-transcriptional modifications also assist in this movement of mRNA. 

Capping

A cap is added to the 5’ end of pre-mRNA in this process. This cap is made up of 6-methylguanosine. It is attached to the 5’ end of mRNA via 5’-5’ triphosphate linkage. It is an unusual linkage formed in the following steps;

  • The terminal phosphate is removed from the nucleotide at the 5’ end of pre-mRNA
  • A molecule of GMP provided by GTP) is added to the 5’ end by guanylyltransferase enzyme
  • The terminal guanine is then methylated by a cytosolic enzyme that adds a methyl residue at its 7’ nitrogen

The 7’methylguanosine cap thus formed has two functions;

  1. It stabilizes the mRNA molecule against the 5’ exonucleases
  2. It allows efficient initiation of protein synthesis as eukaryotic ribosomes identify mRNA through its cap

Addition of Tail

Just like a cap at the 5’ end, a tail is added at the 5’ end of pre-mRNA. The tail is made up of 20 to 50 adenine nucleotides and is called a poly-A tail. These nucleotides are not transcribed from DNA. Rather, they are added after the process of transcription by a nuclear enzyme called polyadenylate polymerase. 

This enzyme identifies a specific sequence present at the 3’ end of pre-mRNA, called the polyadenylation sequence. The enzyme cleaves the pre-mRNA downstream this sequence and starts making poly-A tail using ATP molecules as precursors.

 This poly-A tail serves the following functions;

  • Helps in exits of mRNA from the nucleus
  • Stabilizes mRNA against 3’ exonucleases
  • Assists in the process of translation

Removal of Introns

The primary transcript also contains RNA sequences that do not code for proteins. These sequences are present in between the coding sequences and are called the intervening sequence or introns. The other coding sequences are called exons (expressed sequences). 

The maturation of mRNA in eukaryotes involves the removal of these intervening sequences or introns by a process called splicing. 

 The process of splicing is carried out by complexes called small nuclear RNA particles (snRNPs) also called ‘snurps’. These particles are formed by small nuclear RNA (snRNA) along with multiple proteins.

Specific sequences are present at the beginning and the end of each intron called splice sites. The snRNPs bind to these splice sites and cause a transesterification reaction between the two ends. The introns are thus removed leaving behind the coding sequences of mRNA or exons. 

The pre-mRNA can undergo splicing in alternative ways generating multiple variants of mRNA. This results in the synthesis of multiple protein products. This process of alternative splicing helps in the synthesis of a large and diverse set of proteins from a limited number of genes. 

After these modifications, the mRNA molecule is ready to perform its role in protein synthesis. 

Role in Protein Synthesis

the only purpose of making mRNA is to transmit and decode the instructions present in the gene. The mRNA molecule forwards the message in the gene to the protein-making machinery i.e. ribosomes. 

Recall that the information for protein synthesis is present in mRNA in the form of codons that code for amino acids. During the process of protein synthesis, ribosomes bind to the mRNA molecule in such a way that one codon is exposed at one time. This codon is decoded by the anti-codon loop of tRNA. The anti-codon loop has a nucleotide sequence complementary to one specific codon. It recognizes the codon exposed on the ribosome and hybridizes it via hydrogen bonding. The same tRNA molecule also carries an amino acid at its 3’ end. The decoding of the exposed codon results in the addition of this amino acid into the polypeptide chain. 

The process continues and the entire information present in mRNA is decoded in the form of amino acids being added to the polypeptide chain. When a termination codon is reached, the decoding process stops, and the polypeptide thus formed is released from the ribosomes. 

Eukaryotic and Prokaryotic mRNA

Although mRNA serves the same functions in both prokaryotes and eukaryotes, some differences do exist. Here are the differences between the mRNA of two organisms.

  • The eukaryotic mRNA is made in the nucleus while prokaryotes make their mRNA in the cytoplasm
  • The eukaryotic mRNA is monocistronic i.e. codes for only one protein while the prokaryotic mRNA is polycistronic i.e. codes for multiple proteins
  • mRNA in eukaryotes contains a cap and a tail while they are absent in prokaryotic mRNA
  • The process of transcription and translation are coupled in prokaryotes while this is not the case in eukaryotes
  • Prokaryotic mRNA has a very short life while eukaryotic mRNA is more stable
  • Ribosomes identify prokaryotic mRNA via the Shine-Dalgarno sequence while eukaryotic mRNA is identified by its cap

Summary

Messenger RNA carries the message present in the gene to the protein-making machinery of the cells. 

It is composed of ribonucleotides that are arranged in the form of codons. One codon is made up of three nucleotides. all the codons in the molecule of mRNA are read in a series without any space, starting from its 5’ end. 

Messenger RNA is made from the gene in a process called transcription. This process is carried out by RNA polymerases that identify and bind to the gene at a consensus sequence. The process of transcription includes three steps;

  1. Identification and binding to the gene by RNA polymerase
  2. Reading of the gene and making of mRNA chain by combining ribonucleotides
  3. Breaking of the DNA-RNA hybrid and release of mRNA from the complex

The mRNA formed as a result of transcription is premature RNA (pre-RNA). It undergoes several modifications in eukaryotes before becoming functional. These changes are as follows;

  • Addition of a cap at the 5’ end so that it becomes stable and can be identified by the ribosomes 
  • Addition of poly-A tail at the 3’ end to stabilize this end and exist of mRNA from the nucleus
  • Removal of the non-coding intervening sequences (introns) by the process of splicing

The mature RNA is identified and bound by the ribosomes in the cytoplasm. The message in mRNA is translated in the form of an amino acid sequence in the polypeptide chain by the assistance of transfer RNA. 

Several differences exist between the messenger RNA found in eukaryotes and prokaryotes. Most of these differences are due to the absence of a nucleus in prokaryotes. 

References

  1. Denise R. Ferrier, Lippincott Illustrated Reviews, Biochemistry, Ed. 6th
  2. Rodwell, Kennelly, Harper’s Illustrated Biochemistry, Ed. 30th
  3. https://en.wikipedia.org/wiki/File:MRNA-interaction.png
  4. https://en.wikipedia.org/wiki/File:5iy8.jpg