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Formation and Characteristics of tRNA, rRNA and mRNA
The Ribonucleic acid (RNA) exists as three forms in a cell. They are transfer RNA or tRNA, Ribosomal RNA or rRNA and Messenger RNA or mRNA. The messenger RNA as the name implies is carrier of information from DNA to the protein factory of the cell called as the ribosome. In ribosome, the information carried by the mRNA is read by rRNA and they participate in the conversion of the received information into proteins through a process called translation with the help of the tRNA.

Transfer RNA (tRNA): tRNAs are tiny in nature and acts as a tool in translation of mRNA into proteins by linking the base pairs of mRNA and amino acid sequence on a polypeptide. Transfer RNAs are amino acid specific and it scans and detects the parts of mRNA coding the type of aminoacid and enables the exact placement of the aminoacid in the polypeptide chain. The physique of the tRNA molecule resembles that of a clover leaf with several extended loops. They are acceptor arm, Dihydrouracil arm, anticodon arm and TⱷC arm each having a special function.

The acceptor arm as the name indicates acts as the site for aminoacid attachment and the anticodon arm detects the codons in mRNA and aids in their binding. RNA polymerase III is the active enzyme in the process of tRNA synthesis which involves transcription of genes corresponding to tRNA. The sequential array of the nucleotides in tRNA is susceptible to modification by chemical groups which contribute to methylation, saturation of double bond, deletion of amino group, replacement by sulfur group and so on.

Ribosomal RNA (rRNA): rRNAs are the native RNAs of the cell organelle Ribosome (protein factory) and hence the name Ribosomal RNA. They signify their presence by deriving the information from mRNA and participating in protein synthesis. The cell relies on ribosomes for all its protein requirement and the amount of protein synthesized in a cell is directly proportional to the number of ribosome molecules present in the cell. S value denotes the size of the ribosome and they exist as 70s in prokaryotes and 80s in eukaryotes. 70s ribosome is the combination of 50s subunit and 30s subunit. The 50s subunit of prokaryotes has 2 rRNAs and the 30s subunit has 1 rRNA. Whereas the 60s subunit in eukaryotes possess 3 rRNAs and 40s subunit has 1 rRNA.

The occurrence of inter RNA molecule base pairing and intra molecular base pairing stabilizes the structure of the rRNA molecule. The functional proteins are found attached to the rRNAs in ribosomes. Few RNAs possess the characteristics of an enzyme and are called as ribozymes.
The process of formation of rRNA is complex involving several steps before the final product of mature rRNA. In prokaryotes, the RNA polymerase mediated transcription of rRNA genes results in the formation of pre-rRNA. The pre-rRNA exists in folded form and base pairing occurs resulting in the formation of stem-loop structure. This is followed by binding of ribosomal proteins to the folded pre-rRNA and modification of bases by methylation and action of RNAse III on specific points on rRNA causing cleavage and finally trimming the 5′and 3′of the rRNA by the M5, M16 and M23 ribonucleases resulting in the formation of mature rRNA. In eukaryotes, the steps involved in the formation of mature rRNA are similar to prokaryotes except for the additional step of ribonuclease activated trimming in prokaryotes.

Messenger RNA (mRNA): The carriers of information from DNA to the ribosome and poses as the template for synthesis of proteins. RNA polymerase II activated transcription of genes addressing proteins in nucleus results in the formation of mRNA. The format of coding regions separated by the non coding region exists in eukaryotes. The coding regions are called as Exons and the non-coding regions are called as Introns. Like the other two RNAs, mRNA formation is also initiated by the formation of pre-mRNA by transcription of both the coding and non-coding regions present as such. This is followed by a process called as splicing which removes the introns allowing the continuity of the Exons, making it an exact template for protein synthesis. Capping and polyadenylation occurs post splicing. Capping process protects the 5′ end of mRNA from the action of exonucleases and polyadenylation protects the 3′ end of the mRNA. All this described processes are skipped by the prokaryotes as the information is translated much earlier even before the completion of the transcription itself.

The transfer RNA and ribosomal RNA are considered stable whereas the life span of the messenger RNA is short.
Other RNA types

SnRNA – small nuclear RNA

These are short RNA molecules (around 150 nucleotides in length) found in the nucleus of eukaryotic cells. They were actually discovered by accident in the 1960s while doing some experiments with gel electrophoresis, and several functions have been connected with them up to now. The most important one is the processing of pre-mRNA, but they also help in the stability of telomeres and regulation of RNA polymerase II and some transcription factors. Subtype of snRNAs are snoRNAs (small nucleolar RNA), found in the nucleolus, and they are responsible for the synthesis and modification of rRNAs, tRNAs and snRNAs themselves.

The main function of the snRNA, processing of the pre-mRNA, is actually performed along with SM proteins (Sec1/Munc18-like proteins). Together, they form the complexes known as snRNPs (small nuclear ribonucleoproteins). More snRNPs join together to form the spliceosome – complex which actually process the primary transcript of RNA into mature messenger RNA. SnRNAs involved in the processing of pre-mRNA are U1, U2, U4, U5 and U6.

Splicing of pre-mRNA

Spliceosome basically removes the introns (non-coding parts of the DNA/RNA) and ligates the exons (coding parts) back together. It performs this by recognizing specific sequences on the transcript. These are 5’ end splice, 3’ end splice, branch point and polypyrimidine tract.

U1 snRNA attaches the first to the GU nucleotide sequence at the 5’ end splice site, following by U2, which attaches to the branch point. After the U4 and U6 attach, U1 gets removed. U5 also attaches a bit more upstream. U4, U5, and U6 together form the lariant (loop) form of the intron, and they cut it out acting as nuclease.

Alternative splicing

During the splicing of pre-mRNA, alternative splicing also occurs, which basically refers to the arranging of DNA exons in different ways (or completely omitting some) in order to get different mRNAs (and different proteins) from the same gene.
Other RNA types

MiRNA – micro RNA

These are small non-coding RNA molecules (usually about 22 nucleotides long), and their main function is transcriptional and post-transcriptional regulation of gene expression. They were discovered during the 1990s, but their function was well defined one decade later, when they were grouped separately from other RNA molecules.

They are not found in prokaryotes – only in eukaryotes and some viruses whose genetic material consists out of DNA (viruses can also have only RNA). There is difference between animal and plant miRNAs, though. Animal miRNAs are complementary with target mRNA in only 6-8 nucleotides at the 5’ end; this region is called the seed region. Plant miRNAs, on the other hand, bind completely or almost completely to the target mRNAs, and they are not region-specific; they can bind to both 5’ and 3’ UTRs (untranslated regions) as well as to the coding region.

Once they are transcribed, they basically prevent the expression of a certain gene by binding to the specific mRNA that is awaiting translation. This complex of mRNA-miRNA is then degraded by cell’s mechanisms. Some 1000 miRNAs in humans are complementary to around 60% of our genes, so more than half of our genes can be regulated with this mechanism.

Even though the mechanism is well conserved among the species, micro RNAs themselves are not 100% specific. One micro RNA can bind to and silence more messenger RNAs. For example, studies have shown that on average, one miRNA targets around 7 mRNAs, but the number can go as high as 200 mRNAs, which means that one miRNA could affect the expression of hundreds of proteins. Also, one mRNA can be regulated by more micro RNAs.

The mechanism of silencing by micro RNA molecules is very interesting and it provides a lot of ground for manipulation, making research about it absolutely necessary, especially since a lot of diseases are connected to miRNAs, like heart and nervous diseases, obesity, etc.
Other RNA types

SiRNA – small interfering RNA

Small interfering RNA molecules are another type of short RNA molecules that can silence some genes by targeting them for degradation. SiRNAs were discovered at the end of the 20th century by the group of scientists in England. These newly discovered molecules were similar in length to micro RNA molecules (around 22 nucleotides), and their last two nucleotides (at 3’ end) were found overhanging. The 5’ end of small interfering RNA molecules is phosphorylated, while the 3’ end is hydroxylated.

Small interfering RNAs are produced in the cell by the enzyme dicer which cleaves long double stranded mRNA molecules and short hairpin RNAs (it also cleaves pre-micro RNA molecules into miRNAs). Another way for siRNA to be present in the cell is by introducing it inside using transfection. This is very important since scientists are able to make synthetic small interfering RNA molecules. Now, it is only necessary to make siRNAs complementary to the gene we want to silence (post-translational silencing), and insert it into the cell. This mechanism opens a lot of room for genetic experiments, especially those concerning drugs and confirmation of gene function.

The main difference between siRNA and miRNA is in their way of action. While micro RNAs don’t necessarily bind to the target mRNA with great precision, siRNA binds completely (every nucleotide establishes connection with the binding site on the target mRNA). This is due to the fact that micro RNAs are “universal”, meaning that they can bind to more mRNA molecules, while small interfering RNAs bind only to one mRNA from which they have been expressed. Moreover, micro RNAs only inhibit the translation of target mRNA (which goes to p-bodies where it is either stored or degraded), while small interfering RNA cleave the target mRNA themselves.

Their ability to degrade mRNA gives them additional possible functions related to the RNA interference pathways, like the antiviral mechanism or shaping of the chromatin structure.

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Formation and Characteristics of tRNA, rRNA and mRNA00