Divyan Bavan
Ribonucleic acid (RNA) is a nucleic acid polymer made of ribonucleotides—a subunit made of a ribose sugar, phosphate group, and nitrogenous base. This makes it very similar to DNA; the main differences are that RNA uses ribose and uracil instead of deoxyribose and thymine. However, the structures and functions of RNA diverge greatly from DNA, which is relatively incumbent. RNA can form hairpins, be double or single stranded, catalyze reactions, and perform many other tasks. These functions are critical for the existence of life. Without RNA, cells would cease to exist; its diversity is what allows it to take on various functions within the cell. To organize this diverse system, scientists have created different classes of RNA within eukaryotic cells. Although there is still a lot to explore within this space, it is easy to understand how RNA, specifically in eukaryotes, expresses, processes, and regulates the genetic message encoded by DNA.
To express this message, three core RNAs are needed: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). To start this process in eukaryotes, RNA polymerase II must first transcribe a gene. On binding of the general transcription factors to DNA, RNA polymerase II starts the continuous synthesis of RNA in the 5’ to 3’ direction, 30 nucleotides from the TATA promotor box (Alberts et al., 2022). This forms a single-stranded, RNA-based copy of the 3’ to 5’ DNA strand (coding strand). RNA is important to cells because it can mobilize information from the genome and allow it to be expressed in the cell. If the gene’s fate is to produce protein, the RNA is classified as pre-mRNA. This long molecule then undergoes several processing steps to convert it to mature mRNA: addition of a 7-methylguanosine cap at the 5’ end, addition of a 3’ polyA tail, and the splicing of introns (Alberts et al., 2022). The cap and tail of the mRNA protect it from degradation and signal proper transcription, while splicing is an important step which will be discussed later in this essay. The final product of this process is an RNA molecule containing a cap, 5’ untranslated region, coding sequence, 3’ untranslated region, and 3’ polyA tail (Alberts et al, 2022).
As mature mRNAs leave the nucleus, they must have their coding sequence—which consists of triplet codons—translated into a polypeptide chain. The recognition of these codons is done by tRNAs: single-stranded RNAs which are expressed in tRNA-specific genes (Alberts et al., 2022). Unlike mRNA, however, tRNA does not have a linear structure. It has intramolecular base-pairing; that is, bases on the RNA form pairs with other bases on the same strand. This creates a distinct clover-leaf structure, which include the 3’ acceptor stem and anticodon arm (Wang et al, 2023). The latter contains a three-base anticodon, which determines the tRNA’s respective mRNA-codon through base complementarity. This association is functionalized through the addition of amino acid to a conserved CCA motif on the 3’ acceptor stem, catalyzed by a specific aminoacyl-tRNA synthetase (Giegé et al, 2000-2013). This creates the final tRNA molecule, primed for recognition and translation of mRNA through its anticodon and amino acid, respectively.
To catalyze this continual process of tRNA-based codon recognition and polypeptide synthesis, the cell contains about 10 million ribosomes. These are protein factories made up of ribosomal proteins and 3 types of rRNA—18S, 5.8S, and 28S—which are assembled in the nucleolus (Alberts et al, 2022). These rRNAs form three important sites in the ribosome: the A, P, and E sites. They are responsible for coordinating the binding of an aminoacyl-tRNA, positioning of two adjacent amino acids, and release of the unpaired tRNA, respectively (Wang et al., 2023). The formation of the peptide bond is also catalyzed by rRNA, as crystal structures show that the closest ribosomal protein is too far away for catalysis. The ribosome is a key example of how RNA can facilitate reactions, showing how diverse and capable they are (Alberts et al., 2022).
As mentioned earlier, RNA has to undergo several processing steps to reach its mature form. One of these steps is splicing, which removes introns—stretches of unneeded DNA between coding segments (exons)—from the original transcript and joins the exons together. This is facilitated by the spliceosome: a complex of proteins and small nuclear RNAs (snRNAs). snRNA can be split into 5 groups—U1, U2, U4, U5, and U6—which are all critical for the proper functioning of the spliceosome. U1 is especially important for recognizing the 5’ splice junction through base pairing, which leads to the recruitment of other proteins and snRNAs (Alberts et al, 2022). An example of this is found in tropomyosin, where U1 binds to a 9 nt sequence at the 5’ splice site (Gooding et al, 2008). The result of this is the formation of a lariat, which causes excision of the intron from the pre-mRNA. While this process does take energy, introns play several roles within the cell. For example, one function of introns is to provide a starting point for the creation of small nucleolar RNAs (snoRNAs). Many snoRNAs originate from introns spliced out of ribosomal proteins and play a distinct role in the processing of pre-rRNA transcripts (Alberts et al., 2022). This happens through the base-pairing of snoRNA to the pre-rRNA transcript, which facilitates the recruitment of RNA-modifying enzymes. These enzymes perform transformations such as methylation of 2’ -OH positions on nucleotide sugars and isomerizations of uridine to pseudouridine (Alberts et al., 2022). These transformations are thought to play a key role in ribosome assembly.
To control this complex system of RNAs, DNA, and proteins, the cell has evolved several mechanisms to regulate RNA expression. While this can be done before transcription initiates through enhancers and repressors, RNA can also control several aspects of gene expression. Two examples of this are miRNA and siRNA. These classes of RNA—which are single stranded—silence genes by altering or destroying their respective mRNA to inhibit translation (Alberts et al., 2022). This is facilitated by the RNA-induced silencing complex (RISC). After processing by Dicer and other enzymes, miRNA or siRNA complex with RISC, which then binds to mRNA. If there is partial complementarity between the mRNA and miRNA, several proteins are recruited to inhibit the translation of the mRNA. A similar process occurs for siRNA, except siRNA relies on all bases to be complementary and directly cleaves the mRNA (Alberts et al., 2022). This makes miRNAs broader regulators which can control multiple genes, while siRNAs are gene-specific, only inducing the silencing of one gene. Each form has its advantages in organisms, however, and this area will continue to evolve as we understand more about them.
Of course, there are many other important types of RNA which can be mentioned—telomerase RNA, RNAse P RNA, SRP RNA, lncRNA, piRNA—but the classes discussed in this essay play the largest roles within the cell. Our understand of these diverse molecules have enabled many advances not just in our understanding of life, but to therapeutics and new methods for discovery. The COVID-19 vaccine is based on the application of mRNA to the immune system, and siRNA has enabled us to rapidly study the functions of specific genes by easily silencing them. It is because of our understanding of how RNA functions that these advances were able to flourish. However, there is still a lot we don’t understand about RNA. With more discoveries being made every day, it is only a matter of time before we uncover new ideas and innovations that change the world.
Works Cited
Alberts, Bruce, et al. Molecular Biology of the Cell. 7th ed., New York, Garland, 2022.
Giegé, Richard, and Magali Frugier. Transfer RNA Structure and Identity. Www.ncbi.nlm.nih.gov, Landes Bioscience, 2013, www.ncbi.nlm.nih.gov/books/NBK6236/.
Gooding, Clare, and Christopher W. J. Smith. “Tropomyosin Exons as Models for Alternative Splicing.” Advances in Experimental Medicine and Biology, vol. 644, 1 Jan. 2008, pp. 27–42, https://doi.org/10.1007/978-0-387-85766-4_3.
Voet, Donald, and Judith G Voet. Biochemistry. 4th ed., Hoboken, N.J., John Wiley And Sons, 2011.
Wang, David, and Aisha Farhana. “Biochemistry, RNA Structure.” PubMed, StatPearls Publishing, 2023, www.ncbi.nlm.nih.gov/books/NBK558999/.