RNA

RNAs

The messenger RNA (mRNA) serves as an intermediate between DNA and protein. Parts of the DNA are "transcribed" into transcripts (single-stranded RNA molecules) that are processed to mRNA. In prokaryotes the transcript generally does not need to be processed, and can serve as mRNA right away. Transcription starts at a specific site on the DNA called a promoter. Each gene or operon has its own promoter(s). Transcription ends at a terminator sequence on the DNA. The transcripts usually are 300-50,000 nucleotides long, and contain the information to make protein. In eukaryotes (organisms with cells containing a nucleus; in fact, any higher organism) generally the transcripts needs to be processed before they can serve as a blueprint for a protein. The processing involves the removal of intervening sequences (introns) in the gene. The introns may be anywhere between 50 and 10,000 nucleotides in length. The coding regions of the mRNA are called exons. There may be up to 100 introns in a single gene. The introns are spliced out by small ribonucleoprotein particles (consisting of RNA and protein), which appear to pull the two ends of the intron together. However, there are also introns that splice out without the need of a protein: the RNA sequence itself appears to contain sufficient information to know where to splice out the intron. In addition to the removal of introns, a poly-A sequence is added to the 3’ end of the transcript. The processed transcript is the mRNA, and the information in the mRNA can be used to be "translated" into a protein of specific sequence. However, in prokaryotes introns are rare and mRNA generally does not get processed before translation.

The intron splicing process provides an opportunity to increase the amount of usable genetic information without increasing the genome size of the organism: Alternative splicing of a particular transcript can occur. Alternative splicing means that introns may be recognized in different ways in different molecules of the same primary transcript, and the result is that one gene can give rise to different mRNAs and thereby to different proteins. Note that this process is largely limited to eukaryotes as introns in prokaryotes are rare.

Ribosomal RNAs (rRNAs) are essential components of an important part of the protein synthesis machinery: the ribosomes. In addition to rRNA, there are some 70 different proteins in a ribosome. There are hundreds of copies of rRNA genes per genome, thus making the production of lots of rRNA possible. There are four different rRNAs, each with a different size. Each ribosome contains one molecule of each of the four rRNA types. In prokaryotes, ribosomes bind to the mRNA close to the translation start site. This ribosome binding site is referred to as the Shine-Dalgarno sequence or as the ribosome recognition element. In eukaryotes, ribosomes bind at the 5' end of the mRNA and scan down the mRNA until they encounter a suitable start codon.

Transfer RNA (tRNA) carries amino acids to the ribosomes, to enable the ribosomes to put this amino acid on the protein that is being synthesized as an elongating chain of amino acid residues, using the information on the mRNA to "know" which amino acid should be put on next. For each kind of amino acid, there is a specific tRNA that will recognize the amino acid and transport it to the protein that is being synthesized, and tag it on to the protein once the information on the mRNA calls for it.

All tRNAs have the same general shape, sort of resembling a clover leaf. Parts of the molecule fold back in characteristic loops, which are held in shape by nucleotide-pairing between different areas of the molecule. There are two parts of the tRNA that are of particular importance: the aminoacyl attachment site and the anticodon. The aminoacyl attachment site is the site at which the amino acid is attached to the tRNA molecule. Each type of tRNA specifically binds only one type of amino acid. The anticodon (three bases) of the tRNA base-pairs with the appropriate mRNA codon at the mRNA-ribosome complex. This temporarily binds the tRNA to the mRNA, allowing the amino acid carried by the tRNA to be incorporated into the polypeptide in its proper place. Thus, the sequence of the codon (three bases) in the mRNA dictates the amino acid to be put in in the protein at a specific site. The "dictionary" of codons coding for amino acids is called the genetic code. A summary of the amino acids that the 64 possible codons encode can be found at The three codons for which there is no matching tRNA (UAA, UGA, and UAG) serve as "stop-translation" signals at which the ribosome falls off.