Types of RNA: Structure and Functions

DNA holds the instructions for life, but it does not build anything by itself. That work is done by RNA. RNA is the active, working copy of genetic information: it carries the message out of the DNA, brings the building blocks to where proteins are made, and forms the machine that assembles them. Without RNA, the information in DNA could never be turned into a living, functioning cell.

There is not just one kind of RNA. Different types do different jobs. Three of them do the main work of making proteins: messenger RNA carries the instructions, transfer RNA delivers the amino acids, and ribosomal RNA forms the core of the ribosome where proteins are assembled. Several other RNAs help control which genes are switched on and off. This article explains the structure and function of each type, starting with the three main ones.

Ribonucleic acid (RNA) is the nucleic acid present in almost all organisms (except some viruses) that is responsible for carrying instructions from the genetic material (DNA) to code or synthesize proteins.

RNA is usually single-stranded, with some exceptions such as rotaviruses, which have double-stranded RNA. 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. Other types of RNA also exist, and their locations, functions, and structures are explained below.

The three main types of RNA at a glance

Although cells contain several kinds of RNA, three do the central job of protein synthesis. It helps to hold the whole picture before the detail:

These three work as a team during translation. The mRNA is the instruction sheet, the tRNAs are the delivery trucks bringing amino acids, and the rRNA is the workbench (the ribosome) where the protein is actually built. The other RNAs described later mostly help regulate genes rather than build proteins directly.

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 adenine (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 pair C with G and A with U. RNA often associates with proteins to form ribonucleoprotein (RNP) complexes inside the cell.

Two features separate RNA from DNA. First, RNA uses the sugar ribose, while DNA uses deoxyribose (which has one less oxygen). Second, RNA uses the base uracil (U) where DNA uses thymine (T). RNA is also usually single-stranded, whereas DNA is double-stranded. Being single-stranded lets an RNA molecule fold back on itself into loops and shapes, and these shapes are what allow different RNAs to do very different jobs.

Figure: Types of RNA

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.

1. cRNA: As the name suggests, the cRNA codes amino acids, the building blocks of protein.
2. 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).

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.

An mRNA can be monocistronic, carrying the code for a single protein (usual in eukaryotes), or polycistronic, carrying the codes for several proteins on one mRNA molecule (common in prokaryotes). The structural components of mRNA are as follows:

1. 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.
2. 5′ untranslated region (5′ UTR): After the cap comes a stretch that is not translated into protein. It helps the ribosome recognize and bind the mRNA before the coding region begins.
3. Initiation codon: AUG is the initiation codon in prokaryotes and eukaryotes to start coding for amino acids.
4. Coding region: The coding region comprises approximately 300-1,500 nucleotides.
5. Tail: The 3′ end of eukaryotic mRNA usually has a chain of adenine nucleotides called the poly-A tail, which protects the mRNA and helps it be translated.

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.

Figure: Secondary structure of tRNA (cloverleaf shape)

Size of tRNA: It is a small RNA with a molecular weight of about 25,000 to 30,000 daltons 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 folding and internal base pairing give rise to three arms: the anticodon arm, the D arm, and the 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 dihydrouridine residues 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 (rRNA) is the most abundant RNA in the cell, making up about 80% of the total RNA. It is the main building material of the ribosome, the machine that makes proteins. rRNA is not just structural, though. It also carries out the central chemical step of protein synthesis, which makes it one of the most important molecules in biology.

Function of rRNA

rRNA has two roles that matter:

1. It forms the structure of the ribosome. Together with ribosomal proteins, rRNA folds into the two subunits that make up a ribosome. It provides the framework that holds the mRNA and tRNAs in the correct positions during translation.
2. It catalyzes peptide bond formation. The chemical joining of two amino acids into a protein is carried out by the rRNA itself, not by a protein enzyme. Because an RNA is doing the catalysis, rRNA is called a ribozyme (an RNA that acts like an enzyme). This peptidyl transferase activity is the single most important reason rRNA matters: the ribosome is, at its core, an RNA machine.

Structure of rRNA

rRNA is a single strand that folds back on itself. Where the folded strand runs alongside a complementary stretch, the bases pair (A with U, G with C) to form short double-stranded helical regions. Between these helices are unpaired loops. This mix of paired stems and unpaired loops gives rRNA a complex, compact three-dimensional shape, which is what lets it hold the ribosome together and position the other molecules correctly.

rRNA contains the usual four RNA bases (A, U, G, C), with some of them chemically modified (for example, by methylation). The exact base proportions vary between species.

Sizes of rRNA (the S values)

rRNA molecules are named by their sedimentation coefficient, measured in Svedberg units (S), which reflects how fast they settle during ultracentrifugation. The values do not add up in simple arithmetic, which is a common point of confusion (see below).

In prokaryotes (70S ribosome):

• Large subunit (50S): 23S rRNA (about 2,900 nucleotides) and 5S rRNA (about 120 nucleotides)
• Small subunit (30S): 16S rRNA (about 1,540 nucleotides)

In eukaryotes (80S ribosome):

• Large subunit (60S): 28S rRNA (about 4,700 nucleotides), 5.8S rRNA (about 160 nucleotides), and 5S rRNA (about 120 nucleotides)
• Small subunit (40S): 18S rRNA (about 1,900 nucleotides)

The 16S rRNA (in prokaryotes) is especially important in microbiology. Its sequence is used to identify and classify bacteria, because it changes slowly over evolution and differs enough between species to tell them apart. This is the basis of 16S rRNA sequencing, a standard method in bacterial identification.

How to Remember

The three main types by their names. The names tell you the jobs. mRNA is the messenger (carries the message). tRNA is the transfer RNA (transfers amino acids). rRNA is the ribosomal RNA (builds the ribosome). If you remember what each letter stands for, you remember the job.

The team, as a kitchen. Picture making a dish from a recipe. The mRNA is the recipe card (the instructions). The tRNAs are the shoppers bringing each ingredient (amino acid). The rRNA is the kitchen counter and the cook combined (the ribosome, where it all comes together). This keeps the three roles straight.

rRNA is a ribozyme. The most testable fact about rRNA: it does not just sit there as structure, it does the chemistry. rRNA catalyzes the peptide bond. "The ribosome is an RNA machine" captures why this matters.

tRNA shapes: clover then L. In two dimensions, tRNA looks like a cloverleaf. In three dimensions, it folds into an L-shape. "Cloverleaf on paper, L in real life."

The S values do not add up. A 50S and a 30S subunit make a 70S ribosome, not 80S. S units measure how fast something settles, not its mass, so they cannot simply be added. Do not try to make the numbers add.

Key exam facts in one table

Where Students Get Confused

The S values do not add up (50S + 30S = 70S). Svedberg units measure how fast a molecule sediments in a centrifuge, which depends on both size and shape, not on mass alone. So subunit S values cannot be added like weights. A 50S and 30S subunit combine into a 70S ribosome, and 60S plus 40S make 80S. The arithmetic looks wrong only because S units are not additive.

rRNA is not just structural, it is the catalyst. A common assumption is that proteins do all the enzyme work and RNA is passive. In the ribosome it is the opposite: the rRNA catalyzes the peptide bond. rRNA is a ribozyme.

mRNA, tRNA, rRNA all take part in translation, but in different roles. mRNA is the message, tRNA delivers amino acids, rRNA is the machine. They are not alternatives; they work together in the same process.

Uracil replaces thymine in RNA. RNA has no thymine. Wherever DNA would use T, RNA uses U. This is one of the two main chemical differences from DNA (the other is the ribose sugar).

Monocistronic versus polycistronic. A monocistronic mRNA codes for one protein; a polycistronic mRNA codes for several. Prokaryotes often use polycistronic mRNAs; eukaryotic mRNAs are usually monocistronic. "Poly = many proteins on one message."

References

• Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R. Molecular Biology of the Gene. 7th ed. Pearson; 2013.
• Nelson DL, Cox MM. Lehninger Principles of Biochemistry. 8th ed. W.H. Freeman; 2021.
• Alberts B, Heald R, Johnson A, et al. Molecular Biology of the Cell. 7th ed. W.W. Norton; 2022.
• Madigan MT, Bender KS, Buckley DH, Sattley WM, Stahl DA. Brock Biology of Microorganisms. 16th ed. Pearson; 2021.