Transfer RNA

Transfer RNA (abbreviated tRNA) is a small RNA chain (74-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has sites for amino-acid attachment and codon (a particular sequence of 3 bases) recognition. The codon recognition is different for each tRNA and is determined by the anticodon region, which contains the complementary bases to the ones encountered on the mRNA. Each tRNA molecule binds only one type of amino acid, but because the genetic code is degenerate, more than one codon exists for each amino acid.

Transfer RNA 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.

Structure of tRNA

tRNA has primary structure (the order of nucleotides from 5' to 3'), secondary structure (usually visualized as the cloverleaf structure), and tertiary structure (all tRNAs have a similar L-shaped 3D structure that allows them to fit into the P and A sites of the ribosome). The primary structure was reported in 1969 by Robert W. Holley. The secondary and tertiary structures were derived from X-ray crystallographic studies reported independently in 1974 by American and British research groups headed, respectively, by Alexander Rich and Aaron Klug.


Structure of tRNA

Features

1. The 5'-terminal phosphate.
2. The acceptor stem (also called the amino acid stem) is a 7-bp stem that incudes the 5'-terminal nucleotide and the 3'-terminal nucleotide with the 3'-terminal OH group (which can bind the amino acid). The acceptor stem may contain non-Watson-Crick base pairs.
3. The CCA tail is a CCA sequence added to the 3' end of the tRNA molecule. This sequence is important for the recognition of tRNA by enzymes critical in translation.
4. The D arm is a 4 bp stem ending in a loop that often contains dihydrouridine.
5. The anticodon arm is a 5-bp stem containing the anticodon.
6. The T arm is a 5 bp stem containing the sequence TΨC.
7. Modified bases are bases contained in tRNA that are not "canonical" bases, i.e. modified forms of the standard adenine, guanine, cytosine, and uracil bases.

Anticodon

An anticodon is a unit made up of three nucleotides which play an important role in various DNA cycles, including RNA translation. Each tRNA contains a specific anticodon triplet sequence that can base-pair to one or more codons for an amino acid. For example, one codon for lysine is AAA; the anticodon of a lysine tRNA might be UUU (some anticodons can pair with more than one codon due to a phenomenon known as degeneracy or wobble). Frequently, the third nucleotide of the anticodon is one of two not found on mRNA: inosine and pseudouridine. Consequently, the link between an anticodon and an mRNA codon is less strict than those links in DNA and RNA-DNA hybrids.

Aminoacylation

Aminoacylation is the process of adding an aminoacyl group to a compound.

Each tRNA is aminoacylated (or charged) with a specific amino acid by an aminoacyl tRNA synthetase. There is often just one aminoacyl tRNA synthetase for each amino acid, despite the fact that there can be more than one tRNA, and more than one anticodon, for an amino acid. Recognition of the appropriate tRNA by the synthetases in not mediated solely by the anticodon, and the acceptor stem often plays a prominent role.

Reaction:
1. amino acid + ATP --> aminoacyl-AMP + PPi
2. aminoacyl-AMP + tRNA --> aminoacyl-tRNA + AMP

tRNA genes

There are 497 nuclear human genes encoding cytoplasmic tRNA molecules + 22 mitochondrial tRNA genes. 324 tRNA-derived putative pseudogenes are revealed.

Cytoplasmic tRNA genes can be grouped into 49 families according to their anticodon features. These genes are found on all chromosomes, except 22 and Y chromosome. High clustering on 6p is observed (140 tRNA genes), as well on 1 chromosome.

tRNA molecules are transcribed (in eukaryotic cells) by RNA polymerase III, unlike messenger RNA which is transcribed by RNA polymerase II.

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