Ribonucleic acid (RNA) is the nucleic acid present in almost all organisms (except some viruses) that are responsible for carrying instructions from the genetic material (DNA) to code or synthesize proteins. RNA is usually a single-stranded structure exception being some viruses like the rotaviruses. In some viruses, RNA acts as the genetic material. In general understanding, the RNA is mainly of 3 types; mRNA (messenger RNA), tRNA (transfer RNA), and rRNA (ribosomal RNA), based on their functions and locations. But there are also other types of RNA with their locations, functions, and structure are explained below.
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General Structure of RNA
Before discussing the types of RNA, understanding the general structure is essential. RNA is a linear structure made up of four different nucleotides. Each nucleotide is made up of five-carbon sugar; ribose, a phosphate group, and one of the four bases; uracil (U), cytosine (C), guanine (G), and adenosine (A). So, the linear structure of RNA is repeating chains of phosphate and ribose groups with one of the four bases attached to every ribose.
Unlike DNA, RNA is not a double-stranded structure but a single short chain with a three-dimensional structure due to base pairing and tertiary interactions within molecules of RNA. The bases C pairs with G and A pairs with U. RNA generally attach to the ribonucleoprotein (RNP) complex inside a cell.
Types of RNA
Broadly, the RNA is classified into coding RNA (cRNA) and non-coding RNA (ncRNA). mRNA is the example of cRNA and tRNA, and rRNA are some examples of ncRNA.
- cRNA: As the name suggests, the cRNA codes amino acids, the building blocks of protein.
- ncRNA: These do not code amino acids but help in protein synthesis in some ways. The ncRNAs are of two types; housekeeping ncRNA (tRNA and rRNA) and regulatory ncRNA. The regulatory ncRNA is further classified into long ncRNA (lncRNA) and short ncRNA (sncRNA).
- lncRNA is at least 200 nucleotides long.
- sncRNA contains less than 200 nucleotides and is again classified into five more types; micro RNA (miRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), PIWI-interacting RNA (piRNA), and small-interfering RNA (siRNA).
| Type of RNA | Functions |
| mRNA (messenger RNA) | Acts as a template for protein synthesis |
| tRNA (transfer RNA) | Transports amino acids to the ribosome |
| rRNA (ribosomal RNA) | Assembles mRNA, tRNA, and translation factors for peptide bond formation |
| miRNA (micro RNA) | Antisense RNA involved in gene regulation |
| snRNA (small nuclear RNA) | Component of splicesome and helps in splicing RNA (removal of introns and joining of flanking exons) |
| snoRNA (small nucleolar RNA) | Specification sites of modified nucleoside components |
| piRNA (PIWI-interacting RNA) | Have a central role in gametogenesis, silencing transposons, fighting viruses and regulating endogenous genes |
| siRNA (small-interacting RNA) | Mediates inactivation or degradation of complementary messenger or viral RNA |
The Three Main Types of RNA
mRNA
Messenger RNA or mRNA is the first RNA synthesized for protein production. It carries the message from the DNA for protein synthesis site (ribosomes) hence named messenger RNA or mRNA. It makes up 2-5% of the total RNA. These are typically found near the nuclear membrane inside the cell’s cytoplasm.
- Size of mRNA: The size of the mRNA varies vastly. Since many proteins form with at least 100 amino acids, mRNA must be at least 300 nucleotides long based on the triplet code.
Structure of mRNA
It is always single-stranded with the bases A, U, C, and G. Although there is some coiling, the bases do not pair as it functions as a template for coding amino acids; the pairing alters its motive. Its base sequence is complementary to that of DNA, and the types of mRNA are equal to the number of genes. mRNA can be monocistronic when a single gene (cistron) codes for the mRNA or polycistronic if multiple genes code the same mRNA. The structural components of mRNA are as follows:
- Cap: The 5′ end of mRNA consists of a methylated structure called a cap. The cap determines the rate of protein synthesis as mRNA without a cap binds poorly to the ribosomes.
- Noncoding region: The cap is followed by 10-100 nucleotides rich in A and U nucleotides and does not translate any protein.
- Initiation codon: AUG is the initiation codon in prokaryotes and eukaryotes to start coding for amino acids.
- Coding region: The coding region comprises approximately 300-1,500 nucleotides.
tRNA
Transfer RNA or tRNA is the cell’s second most common RNA (about 10-20% of the total RNA). It is too small to be precipitated by ultracentrifugation, also called soluble RNA.
Size of tRNA: It is a small RNA with a molecular weight of about 25,000 to 30,000, and mature eukaryotic tRNA has a sedimentation coefficient of 3.8S. These are approximately 70-90 nucleotides long.
Structure of tRNA
Although several models for tRNA structure have been proposed, the cloverleaf structure is widely accepted. tRNA has three common structures:
Primary structure
- The primary structure of tRNA is formed by a small single-stranded RNA molecule that folds into the desired form. Four different regions of double-stranded RNA are formed due to the folding.
- The modification in the bases gives rise to three arms; anticodon arm, D arm, and TΨC arm.
- A loop at the end of the anticodon arm is for the single-stranded anticodon to bind. It may contain residues of either inosine, lysidine, or pseudouridine.
- The D arm contains Dihydrouridyine residue and is the recognition site for the enzyme aminoacyl tRNA synthetase.
- The TΨC arm has residue of ribothymidine (T), pseudouridine (Ψ), and cytidylate (C) in a particular order and serves as the binding site for ribosomes.
- The two ends of the shape form the acceptor stem region for the attachment of amino acids.
Secondary structure (cloverleaf shaped)
- The secondary structure of tRNA has distinctive folds with three hairpin loops which form the cloverleaf structure.
- Like the primary structure, it has three arms (anticodon arm, D arm, and TΨC arm) and an acceptor region.
- The arms form a loop due to the unpaired base pairing. The loops are DHU loop or D loop, TΨC loop, and anticodon loop. Each hairpin loop denotes one of the three types.
- The DHU or D loop recognizes amino acid activating enzyme (aminoacyl tRNA synthetase).
- The TΨC loop helps tRNA to bind to ribosomes for protein synthesis.
- The anticodon loop has a complementary codon for mRNA binding.
- An extra loop or variable loop is present between the anticodon loop and the TΨC loop to maintain the tRNA’s stability.
Tertiary structure (L-shaped):
- The secondary structure of tRNA converts into a three-dimensional L-shaped structure.
- The TΨC arm and acceptor region stack together on one side, and the D arm and anticodon stack on another, forming two extended helices.
- These two helices then align at a right angle forming an L-shape. It is the most stable and is an essential structure for the synthesis of protein.
rRNA
Ribosomal RNA or rRNA is found on ribosomes. It makes up to 80% of the RNA of the cell. The base sequence of rRNA is complementary to the region of the DNA that sizes it mainly helps form ribosomes for protein synthesis.
Size of rRNA
- The ribosome is a complex molecule consisting of several types of rRNA and proteins.
- The eukaryotic ribosomes have one copy of 5s rRNA (approx. 120 nucleotides), 28S rRNA (approx 4718 nucleotides), and 5.8S rRNA (approx. 160 nucleotides) in the larger sub-units (60S ribosomes) and 18SRNA (approx. 550 nucleotide) in smaller subunits (40S ribosomes).
- But the prokaryotic ribosomes lack the 5.8S rRNA and have 23S rRNA (approx. 2900 nucleotides) instead of 28S rRNA in larger subunits (50S ribosome), and the smaller subunit (30S ribosome) has 16S rRNA (approx 1540 nucleotides).
Did you know? “S” is sedimentation or density unit which describes the results of ultracentrifugation.
Structure of rRNA
- It has a single-strand with some folded/twisted regions forming helical regions. In the helical regions, the base pairs are mostly complementary. In contrast, the unfolded region has no complement.
- It has the typical four bases found in all the RNA, A, U, C, and G, with some degree of methylation.
- The proportion of the bases varies vastly among species.
- The rRNA molecules are unbranched and flexible polynucleotides that behave like a random coil in low ionic strength. But as the iconic strength increases, it starts showing helical regions formed by base pairing A with U and C with G. Heating unfolds the rRNA, and cooling down refolds it.
References
- Encyclopedia Britannica. n.d. RNA | Definition, Structure, Types, & Functions. [online] Available at: https://www.britannica.com/science/RNA.
- Eagri.org. n.d. [online] Available at: http://eagri.org/eagri50/GBPR111/lec16.pdf.
- Gray, M., & Beyer, A. (2014). Ribonucleic acid (RNA). Accessscience.com. Retrieved 4 July 2022, from https://www.accessscience.com/media/EST/media/589000PV0001.pdf.
- Brimacombe, R., & Stiege, W. (1985). Structure and function of ribosomal RNA. Biochemical Journal, 229(1), 1-17. https://doi.org/10.1042/bj2290001
- tRNA / transfer RNA | Learn Science at Scitable. Nature.com. Retrieved 4 July 2022, from https://www.nature.com/scitable/definition/trna-transfer-rna-256/.
