tRNA

Transfer RNAs (tRNA) are small chains of nucleotides (74-93) that transport code specified amino acids to growing peptide, polypeptide and protein chains at the ribosomes on cytoplasmic rough endoplasmic reticulum. Thus, tRNAs participate in translation of the genetic code.

There exist more than 20 different tRNAs, which are similar across species. Among these are two tRNAs that can be charged with methionine. One Met-charged tRNA is used exclusively in initiation of polypeptide polymerization. Transfer RNAs possess 4 arms and 3 loops, though some tRNA molecules have an extra or variable loop (left).

The body of the tRNA is transcribed from a tRNA gene, and the acceptor stem is added after the body is synthesized. The acceptor stem is the same for all tRNA molecules and is replaced often during lifetime of a tRNA molecule. Post-transcriptional modification is responsible for the presence of non-standard nucleotides in tRNAs.

The parts of a tRNA molecule (often depicted as a simple clover leaf):
1. 3' terminal OH group of the CCA acceptor tail of 2. the acceptor arm (the 5' terminal phosphate is at tip of adjacent arm). The CCA sequence is important for recognition of the tRNA by enzymes critical in translation. The CCA sequence is transcribed in prokaryotes, but is added during processing in eukaryotes. The terminal A of the CCA sequence on the acceptor arm carries the specific amino acid, becoming an aminoacyl-tRNA. The transfered amino acid is added, during translation, to the growing polypeptide chain at the ribosome
3. T pseudouridine (Ψ) C arm (TΨC) and 4. T pseudouridine (Ψ) C loop. Thymidylate, pseudouridylate, cytidylate, and guanylate are almost always present in the TΨC loop.
5. (variable loop in some tRNAs)
6. anticodon arm and 7. anticodon loop with triplet anticodon at tip, to which the specific coded amino acid is attached by an Aminoacyl-tRNA synthetase. The anticodon reads the information in a mRNA sequence by base pairing. Frequently the first nucleotide at the 5' end of the tRNA anticodon triplet, or the third nucleotide at the 3' end of the mRNA triple codon is non-standard (inosine, pseudouridine) and is degenerate. That is, the degenerate nucleotide is capable of non-standard base pairing, as described in Crick's wobble hypothesis.
8. DHU or D loop and 9. D arm which often contains dihydrouridine.
10. cross-stabilization of the loops by base-pairs (some are non-standard).

The molecule is folded into an L-shaped tertiary structure with the acceptor stem and the anticodon loop at opposite ends, and with the D and TΨC loops in contact.
detailed explanation of structure

Different tRNAs that may carry the same amino acid are called isoaccepting tRNAs, and some isoaccepting tRNAs respond to different groups of codons specifying the amino acid. The number of isoaccepting tRNA species varies with organism. However, organisms with minimal genomes possess only one tRNA for each amino acid.

Largest Computational Biology Simulation Mimics Life's Most Essential Nanomachine: "The simulations also reveal that the essential translating molecule, transfer RNA, must be flexible in two places for decoding to occur, furthering the growing belief that transfer RNA is a major player in the machine-like movement of the ribosome. The simulation also sets the stage for future biochemical research into decoding by identifying 20 universally conserved ribosomal bases important for accommodation, as well as a new structural gate, which may act as a control mechanism during transfer RNA selection."

The original news release can be found here. : Voxel simulation image : Image 2 : Image 3 : Image 4 : Image 5 : High res movie : Low res movie : See an image of the Q machine at http:/​/​www.lanl.gov/​asci/​.