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RNA gene

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An RNA gene is any gene that encodes RNA that functions without being translated into a protein. Commonly-used synonyms of "RNA gene" are noncoding RNA (ncRNA) and small RNA (sRNA). Less-frequently used synonyms are non-messenger RNA (nmRNA), small non-messenger RNA (snmRNA), and functional RNA (fRNA).

The most prominent examples of RNA genes are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of translation. However, since the late 1990s, many new RNA genes have been found, and thus RNA genes may play a much more significant role than previously thought. Even so, they are probably not as significant or numerous as the protein-coding genes.

Table of contents

Types of RNA genes

Transfer RNA

Transfer RNA plays a critical role in the process of translation. tRNA is the "adaptor" molecule hypothesized by Francis Crick, which mediates recognition of the codon sequence in mRNA and allows its translation into the appropriate amino acid.

Important features of tRNA include:

  1. anticodon - This is the triplet sequence complementary to the codon for a particular amino acid. For example, the codon for lysine is UUU; the anticodon is AAA. By matching a lysine-charged tRNA with the anticodon AAA to the codon UUU, proper translation is achieved.
  2. amino acid - Each tRNA is covalently attached to an appropriate amino acid by a dedicated enzyme called amino-acyl tRNA synthase. In the example above, a tRNA with the anticodon AAA would be coupled to the amino acid lysine.
  3. base modification - tRNA contains several bases that are not "canonical" bases, i.e. that are modified forms of the standard adenine, guanine, cytosine, and uracil bases.
  4. CCA tail - The sequence CCA is added to the 3' end of the tRNA molecule. This sequence is important for the recognition of tRNA by enzymes critical in translation.
  5. three-dimensional structure - All tRNAs have a similar L-shaped structure that allows them to fit into the P and A sites of the ribosome.

Each amino acid (of which there are 20) has a unique tRNA. Before translation, each tRNA is "charged" by an amino-acyl tRNA synthetase enzyme. Each amino acid, but 'not' each codon, has a different aminoacyl tRNA synthetase. Recognition is not mediated primarily by the anticodon, which would require 64 separate tRNA synthetases, but rather by other sites in the tRNA, especially critical sequences near the 3' end of the molecule.

The synthetase hydrolyzes ATP to bind the appropriate amino acid to the 3' hydroxyl of the tRNA molecule. It also mediates a proofreading reaction to ensure high fidelity of tRNA charging; if the tRNA is found to be improperly charged, the amino acid-tRNA bond is hydrolyzed.

See translation for more on the role of tRNA.

Ribosomal RNA

Ribosomal RNA (rRNA) is the primary constituent of ribosomes. Ribosomes are the protein-manufacturing organelles of cells and exist in the cytoplasm. rRNA is transcribed from DNA, like all RNA, and in eukaryotes it is processed in the nucleolus before being transported through the nuclear membrane. This type of RNA makes up the vast majority of RNA found in a typical cell (~95%).

Small nuclear RNA

Small nuclear RNA (snRNA) is a class of small RNA molecules that are found within the nucleus of eukaryotic cells. They are involved in a variety of important processes such as RNA splicing (removal of introns from hnRNA) and maintaining the telomeres. They are always associated with specific proteins, and the complexes are referred to as small nuclear ribonucleoproteins[?] (snRNP) or sometimes as snurps.

Small nucleolar RNA

Small nucleolar RNA (snoRNA) is a class of small RNA molecules that are involved in chemical modifications of ribosomal RNAs (rRNAs) and other RNA genes, for example by methylation. snoRNAs are a component in the small nucleolar ribonucleoprotein (snoRNP), which contains snoRNA and proteins. The snoRNA guides the snoRNP complex to the modification site of the target RNA gene via sequences in the snoRNA that hybridize to the target site. The proteins then catalyze modification of the RNA gene.

microRNA

microRNA (also miRNA) are RNA genes that bind another gene's mRNA transcript and may inhibit the expression of the target gene.

See miRNA.

gRNAs

gRNAs (for guide RNA) are RNA genes that function in RNA editing. Thus far, RNA editing has been found only in the mitochondria of kinetoplastids, in which mRNAs are edited by inserting or deleting stretches of uridylates (Us). The gRNA forms part of the editosome and contains sequences that hybridize to matching sequences in the mRNA, to guide the mRNA modifications.

The term "guide RNA" is also sometimes used generically to mean any RNA gene that guides an RNA/protein complex via hybridization of matching sequences.

Signal recognition particle RNA

The signal recognition particle[?] (SRP) is an RNA-protein complex present in the cytoplasm of cells that binds to the mRNA of proteins that are destined for secretion from the cell. The RNA component of the SRP in eukaryotes is called 4.5S RNA.



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