RNA Processing

Once the RNA is transcribed, does it undergo translation right away? In eukaryotes, the mRNA (the product of transcription) goes through several more steps before being translated into protein. And it’s not just mRNA: tRNA and rRNA also undergo processing, so they can play their part in the protein synthesis machinery.

RNA Processing RNA Processing

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Table of contents

    Here, we will discuss RNA processing: what it is, what types of RNA are involved, and how it takes place.

    Types Of RNA Involved In RNA Processing

    Let's start by looking at the definition of RNA.

    Ribonucleic acid (RNA) is an organic molecule that plays a vital role in protein synthesis. It is composed of a single chain of alternating ribose (5-carbon) sugar and phosphate groups with nitrogenous bases attached to it. RNA has four bases: adenine (A), uracil (U), guanine (G), and cytosine (C).

    In this article, we will tackle three types of RNA that are involved in RNA processing:

    • Messenger RNA (mRNA): produced during transcription, this molecule contains the protein information of the gene that was encoded in DNA and will be used as a template in translation.

    • Transfer RNA (tRNA): decodes mRNA into a protein during translation.

    • Ribosomal RNA (rRNA): makes up the core of the ribosome, the organelle in which protein synthesis takes place.

    What is RNA Processing?

    RNA processing prepares the transcript (the product of transcription) so it can function in translation or protein synthesis. As such, it takes place after transcription and before translation.

    When it is newly formed and unprocessed, “pre-” is attached to the name of the transcript: pre-mRNA, pre-tRNA, and pre-rRNA. After processing, the transcript is said to become “mature”, meaning it is ready for protein synthesis.

    Before we proceed, let’s do a brief recap on transcription and translation.

    Transcription: Process Of Making RNA from DNA

    Transcription is where a gene's DNA sequence is copied and written into mRNA. Transcription has three basic steps: initiation, elongation, and termination. Transcription can be summed up as follows:

    1. Initiation: an enzyme called RNA polymerase binds to the promoter, a site on the DNA strand that signifies the start of the gene. This causes the DNA to unwind.

    2. Elongation: The RNA polymerase travels through the strand from 3′ → 5’. As it travels through the strand, it “copies” the strand by adding complementary base pairs from 5′ → 3′. Thymine (T) in DNA is encoded as uracil (U) in mRNA.

    3. Termination: The RNA comes across a termination sequence in the gene which signals the end of transcription. Hydrogen bonds that join DNA with the newly formed mRNA break, releasing the mRNA molecule.

      • Whereas prokaryotic transcription ends here, eukaryotic pre-mRNA undergoes further processing: capping, polyadenylation, and splicing, all of which we will elaborate on later.

    Translation: Process of Making Proteins from RNA

    Translation is the process of “reading” the information contained in the mRNA and converting it into an amino acid sequence. Like transcription, translation takes place in three steps: initiation, elongation, and termination.

    1. Initiation: the small ribosomal subunit binds to the charged initiator tRNA molecule (tRNAi) and together these traverse the mRNA strand up to the start codon “AUG”. The anticodon on the tRNAi binds to the start codon through base pairing.

    2. Elongation: the ribosome continues to translate codons and add amino acids to the growing amino acid chain.

    3. Termination: translation ends when nonsense or stop codon (UAA, UAG, or UGA) is encountered. Release factors call for the tRNA and the polypeptide chain to be hydrolyzed, releasing the newly formed protein.

    Codon: A codon consists of three nucleotide bases in an mRNA, and each codon specifies an amino acid.

    Anticodon: a codon in the tRNA that is complementary to a codon in the mRNA.

    Steps in RNA Processing

    In the following section, we will discuss mRNA processing that takes place in eukaryotic cells. We will also discuss tRNA and rRNA processing that takes place in both prokaryotic and eukaryotic cells.

    Messenger RNA (mRNA) Processing in Eukaryotes

    In eukaryotic cells, the newly transcribed pre-mRNAs must undergo further processing before they can be moved from the nucleus to the cytoplasm and then translated into a protein. These additional steps give the eukaryotic mRNA a longer half-life compared to prokaryotic mRNA.

    Pre-mRNAs undergo three additional steps before translation: 5’ capping, polyadenylation, and pre-mRNA splicing. Let’s go over each of these steps.

    5’ capping in messenger RNA processing: description & diagram

    While the pre-mRNA is being synthesized, the 5’ end of the pre-mRNA transcript will be covered with a functional group 7-methylguanosine cap through a triphosphate linkage. The functional group stabilizes it, preventing it from breaking down while it is being processed and transported out of the nucleus. Additionally, factors involved in protein synthesis can detect the cap and help initiate translation.

    The process of 5’ capping is simplified in the diagram below (Fig. 1).

    Polyadenylation in messenger RNA processing: description & diagram

    After the elongation step in transcription, an enzyme called endonuclease creates a break between an AAUAAA sequence and a GU-rich sequence in the pre-mRNA. This leaves the AAUAAA on the pre-mRNA.

    Then, a poly-A tail (a chain of around 200 adenine residues) will attach to the pre-mRNA. The poly-A tail will provide added protection and will signal the need for the pre-mRNA to be transported to the cytoplasm.

    The process of polyadenylation is simplified in the diagram below (Fig. 2).

    Splicing in messenger RNA processing: description & diagram

    Splicing is the process of removing introns from pre-mRNA and then joining the exons. This is done by a complex of approximately 200 proteins and RNA molecules called spliceosomes.

    Introns are intervening sequences, while exons are protein-coding sequences; both are found in eukaryotic genes. Splicing occurs while the pre-mRNA is still in the nucleus.

    You can recall the difference between exons and introns by taking note of the first syllable:

    Exons are expressed while introns intervene.

    Introns in mRNA do not encode functional proteins; hence, it is important that they are removed from the pre-mRNA prior to protein synthesis to ensure that the exons are joined correctly for the encoding of amino acids.

    Note that introns can be over 70 bases long and each of these has to undergo splicing to generate an mRNA molecule that can be properly translated. If there is a mistake in the splicing process (even by one nucleotide), the rejoined exons would shift and be read incorrectly. As a result, the protein to be encoded would be dysfunctional.

    The process of pre-mRNA splicing is simplified in the diagram below (Fig. 3).

    Transport RNA (tRNA) and Ribosomal RNA (rRNA) Processing

    In addition to eukaryotic mRNAs, tRNAs and rRNAs that are found in both eukaryotes and prokaryotes also undergo processing before taking part in protein synthesis.

    • Pre-tRNA is transcribed and processed in the nucleus before moving into the cytoplasm where it is attached to free amino acids for translation.

    • Pre-rRNA is transcribed, processed, and combined to form ribosomes in the nucleolus.

    Most prokaryotic and eukaryotic tRNAs and rRNAs are transcribed as a long precursor molecule made up of several tRNAs or rRNAs. Enzymes cut this precursor into subunits of tRNA or rRNA. Some pre-rRNAs are linked to a methyl functional group to stabilize them. Additionally, as with mRNAs, eukaryotic pre-tRNAs and pre-rRNAs undergo splicing.

    Mature rRNAs account for almost half of each ribosome. Some RNA molecules in a ribosome are solely structural, while others include catalytic or binding activity. Through intramolecular hydrogen bonding, mature tRNAs develop a three-dimensional structure with the amino acid binding site at one end and the anticodon at the other. The anticodon is a codon in the tRNA that is complementary to a codon in the mRNA.

    It is important to note that while these molecules participate in translation, they are not themselves translated.

    RNA Processing - Key takeaways

    • RNA processing prepares the transcript (the product of transcription) so it can function in translation or protein synthesis. Pre-mRNAs undergo three steps before translation: 5' Capping, polyadenylation, and splicing.
    • 5' Capping: the 5’ end of the pre-mRNA transcript will be covered with a functional group 7-methylguanosine cap. This stabilizes it and helps translation factors initiate translation.
    • Polyadenylation: a poly-A tail (a chain of around 200 adenine residues) attaches to the pre-mRNA. The poly-A tail will provide added protection and will signal the need for the pre-mRNA to be transported to the cytoplasm.
    • Splicing: removing introns (intervening sequences) from pre-mRNA and then joining the exons (protein-coding sequences).
    • Pre-tRNAs and pre-rRNAs also undergo processing: most are transcribed as long precursor molecules which are cut by enzymes. Some are attached to functional groups to stabilize them. Pre-tRNAs and pre-rRNAs also undergo splicing.

    References

    1. Zedalis, Julianne, et al. Advanced Placement Biology for AP Courses Textbook. Texas Education Agency.
    2. Ahern, Kevin, and Indira Rajagopal. Book: Biochemistry Free & Easy (Ahern and Rajagopal). Oregon State University, 6 Mar. 2021, https://bio.libretexts.org/@go/page/1640.
    3. “RNA.” Encyclopædia Britannica, Encyclopædia Britannica, Inc., https://www.britannica.com/science/RNA
    4. Cvitkovic, Ivan, and Melissa S Jurica. “Spliceosome Database: A Tool for Tracking Components of the Spliceosome.” Nucleic Acids Research, Oxford University Press, Jan. 2013, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531166/.
    Frequently Asked Questions about RNA Processing

    What are the steps of RNA processing?

    In eukaryotes, messenger RNA processing takes place in three steps: 5' capping, polyadenylation, and splicing.

    What is the process of making RNA from DNA?

    The process of making RNA from DNA is transcription.

    What is the function of a spliceosome?

    The function of spliceosomes is to remove introns from pre-mRNA and then join the exons.

    How many proteins are in the spliceosome?

    There are approximately 200 proteins in a spliceosome.

    What does RNA processing do?

    RNA processing prepares the transcript for translation.

    Test your knowledge with multiple choice flashcards

    The mRNA of what type of cells undergo processing after termination?

    What steps constitute eukaryotic mRNA processing?

    When does RNA processing take place?

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