Sechenov School
Home › Biochemistry › RNA Structure

RNA Structure

*Acidum ribonucleicum*

For medical students2 min readUpdated 2026-10-10

Ribonucleic acid is a vital single-stranded macromolecule whose spatial configuration ensures the proper functioning of the cellular apparatus. Three main types of this acid are distinguished in living cells, each playing an indispensable role in the multi-step process of protein biosynthesis.

Main TypesThree functional types: rRNA, tRNA, and mRNA
ComplementarityAdenine — Uracil (A-U) and Guanine — Cytosine (G-C) pairs
OrganizationAlternation of helical stems (hairpins) and unpaired loops

Main Types of Ribonucleic Acids

For complete protein synthesis inside the cell, the coordinated work of several specialized Acidum ribonucleicum molecules is required. According to classical biochemical concepts, the cellular pool is represented by three main types:

  1. Ribosomal RNA (rRNA) — participates in forming the structure of ribosomes.
  2. Transfer RNA (tRNA) — necessary for delivering amino acids.
  3. Messenger RNA (mRNA) — serves as the direct template for translation.

All listed molecules are functionally united by a common global task—ensuring protein biosynthesis; however, their spatial configurations can differ significantly.

Secondary Structure: Hairpins and Loops

Despite the fact that any RNA molecule is initially single-stranded, it does not exist as a straight thread. In the aqueous environment of the cell, the chain bends spontaneously, forming a complex secondary structure.

The main mechanism of this folding is the formation of hydrogen bonds between nitrogenous bases that happen to be close to each other within the same polynucleotide chain. The interaction obeys the strict rule of complementarity:

Due to these hydrogen bridges, double-stranded helical regions form, traditionally called hairpins in biochemistry. The architecture of the secondary structure is not uniform: rigid helical fragments regularly alternate with flexible unpaired regions. It is these bond-free regions that form characteristic loops, giving the molecule its recognizable shape.

Tertiary Structure and Compaction

The secondary structure is only an intermediate stage of spatial organization. For full functionality, the molecule must acquire its final, even denser form—the tertiary structure.

The mechanism of its formation is based on the creation of additional hydrogen bonds. The following actively participate in this process:

The main physiological function of the tertiary structure is to ensure reliable compaction of the long single-stranded molecule. The formation of this complex three-dimensional network of hydrogen bonds and protein interactions guarantees maximum stabilization of the RNA spatial structure, which is critically important for protecting the molecule from degradation and ensuring its precise operation during protein biosynthesis.

Mnemonic

To remember RNA base pairing, think of AU (Adenine-Uracil) and GC (Guanine-Cytosine).

Frequently asked questions

What characteristic shape does the secondary structure of transfer RNA (tRNA) have?

The secondary structure of transfer RNA (tRNA) has a characteristic 'cloverleaf' shape. This configuration is formed through complementary interactions within the single-stranded molecule and includes the following elements:

  • Acceptor stem — containing the 3'-end and 5'-end.
  • TΨC loop (T-loop).
  • D-loop.
  • Anticodon loop — contains the anticodon, a triplet of nucleotides complementary to the mRNA codon.

The acceptor 3'-end features the CCA sequence, which serves for amino acid attachment.

Which modified nitrogenous bases are part of tRNA loops?

The tRNA molecule contains modified nitrogenous bases, accounting for 10–15% of its composition. Examples of such minor bases include:

  • Dihydrouridine (D) — a chemically modified base.
  • Ribothymidine (T) — a chemically modified base.
  • Pseudouridine ($\Psi$) — a chemically modified base.

They are formed during post-transcriptional modifications of pre-tRNA. While sources do not specify the exact localization of these bases within particular loops, they mention the presence of the D-loop and T-loop in the secondary structure.

What is the main difference in RNA composition compared to DNA during secondary structure formation?

Instead of thymine, uracil participates in forming complementary hydrogen bonds with adenine (forming the A — U pair).

What are 'hairpins' in the context of ribonucleic acid?

These are double-stranded helical fragments that form within a single chain due to hydrogen bonds between complementary bases.

How is the tertiary structure formed and stabilized?

Through additional hydrogen bonds between unpaired regions, rRNA/mRNA chains, and through interaction with specific proteins.

Go deeper

More topics in Biochemistry

Absorptive and Postabsorptive StatesProtein Denaturation and RenaturationDNA StructureCarbohydrate Structure, Digestion, and AbsorptionHyperthyroidism and HypothyroidismEnzyme Activity MeasurementTransmembrane Glucose TransportHyperammonemiaQuaternary Protein StructureEnzyme Reaction KineticsGlycogen Synthesis (Glycogenogenesis)Amino Acid SynthesisBiochemistry →