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 a site for amino acid attachment and a three-base region called the anticodon that recognizes the corresponding three-base codon region on mRNA via complementary base pairing. Each type of tRNA molecule can be attached to only one type of amino acid, but because the genetic code is degenerate - that is, it contains multiple codons that specify the same amino acid - multiple types of tRNA molecules bearing different anticodons may carry the same 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.

Features

 * 1) The 5'-terminal phosphate group.
 * 2) The acceptor stem (also called the amino acid stem) is a 7-bp stem that includes the 5'-terminal nucleotide and the 3'-terminal nucleotide with the 3'-terminal OH group (which is used to attach the amino acid). The acceptor stem may contain non-Watson-Crick base pairs.
 * 3) The CCA tail is a CCA sequence at the 3' end of the tRNA molecule. This sequence is important for the recognition of tRNA by enzymes critical in translation. In prokaryotes, the CCA sequence is transcribed.  In eukaryotes, the CCA sequence is added during processing and therefore does not appear in the tRNA gene.
 * 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 whose loop contains the anticodon.
 * 6) The T arm is a 5 bp stem containing the sequence TΨC where Ψ is a pseudouridine.
 * 7) Bases that have been modified, especially by methylation, occur in several positions outside the anticodon. The first anticodon base is sometimes modified to inosine (derived from adenine) or pseudouridine (derived from uracil).

Anticodon
An anticodon (sometimes called nodoc from the reversed letters of the word codon) is a unit made up of three nucleotides that correspond to the three bases of the codon on the mRNA. 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 wobble base pairing. Frequently, the first nucleotide of the anticodon is one of two not found on mRNA: inosine and pseudouridine, which can hydrogen bond to more than one base in the corresponding codon position. In the genetic code, it is common for a single amino acid to occupy all four third-position possibilities; for example, the amino acid glycine is coded for by the codon sequences GGU, GGC, GGA, and GGG.

To provide a one-to-one correspondence between tRNA molecules and codons that specify amino acids, 61 tRNA molecules would be required per cell. However, many cells contain fewer than 61 types of tRNAs because the wobble base is capable of binding to several, though not necessarily all, of the codons that specify a particular amino acid.

Aminoacylation
Aminoacylation is the process of adding an aminoacyl group to a compound. It produces tRNA molecules with their CCA 3' ends covalently linked to an amino acid.

Each tRNA is aminoacylated (or charged) with a specific amino acid by an aminoacyl tRNA synthetase. There is normally a single 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 is not mediated solely by the anticodon, and the acceptor stem often plays a prominent role. Reaction:
 * 1) amino acid + ATP &rarr; aminoacyl-AMP + PPi
 * 2) aminoacyl-AMP + tRNA &rarr; aminoacyl-tRNA + AMP

tRNA genes
Organisms vary in the number of tRNA genes in their genome. The nematode worm C. elegans, a commonly used model organism in genetics studies, has 19,000 genes in its nuclear genome, of which 659 code for tRNA. In the human genome, which according to current estimates has about 30,000 genes in total, there are about 2000 non-coding RNA genes, which include tRNA genes. There are 22 mitochondrial tRNA genes; 497 nuclear genes encoding cytoplasmic tRNA molecules and there are 324 tRNA-derived putative pseudogenes.

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.