RNA

Ribonucleic acid (RNA) is a nucleic acid, consisting of a string of nucleotides. It is biochemically distinguished from DNA by the presence of an additional hydroxyl group, attached to each pentose ring; as well as by the use of uracil, instead of thymine. RNA transmits genetic information from DNA (via transcription) into proteins (by translation).

Table of contents

1 Chemical structure
2 Messenger RNA

2.1 Untranslated Regions
2.2 Anti-sense mRNA

3 RNA genes
4 RNA as genetic material
5 Double-stranded RNA
6 Related articles

Chemical structure

RNA has 4 different bases: adenine, guanine, cytosine, and uracil. The first 3 bases are the same as those found in DNA, but uracil replaces thymine as the base complementary to adenine. This may be because uracil is energetically less expensive to produce, although it easily degenerates into cytosine. Thus, uracil is appropriate for RNA, where quantity is important but lifespan is not, whereas thymine is appropriate for DNA.

Structurally, RNA is indistinguishable from DNA except for the critical presence (noted above) of an additional hydroxyl group attached to the pentose ring in the 2' position. This additional group gives the molecule far greater catalytic versatility and allows it to perform reactions that DNA is incapable of performing.

The other major difference between RNA and DNA is that RNA is almost exclusively found in the single-stranded form (an exception being the genetic material of some kinds of viruses). RNA molecules often fold into more complex structures by making use of complementary internal sequences; that is, one part of a single RNA molecule is the nucleic acid complement of another part of the same molecule (for exampls, 5'-ACUCGA-3' and 5'-UCGAGU-3'), so that the two strands bind together. This allows the formation of hairpin loops, coils, etc., which then direct the formation of higher-order structures.

The first life on earth may have been RNA-based, due to RNA's ability both to carry genetic information like DNA and also to catalyze biochemical reactions like enzymes. This possiblity is termed the RNA world hypothesis. Even today, some viruseses, such as retroviruses, use RNA as their sole genetic material. RNA is less stable than DNA, however, and is also a less efficient catalyst than most protein enzymes. These facts may have led to selection for reduced use of RNA in cells, and greater use of DNA and proteins.

RNA plays several roles in biology:

Messenger RNA, abbreviated mRNA, is transcribed directly from a gene's DNA and is used to encode proteins.
RNA genes are genes that encode functional RNA molecules; in contrast to mRNA, these RNA do not code for proteins. The best-known examples of RNA genes are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which participate in the process of translation. But many others exist.
RNA forms the genetic material (genomes) of some kinds of viruses.
Double-stranded RNA (dsRNA) is used as the genetic material of some RNA viruses and is involved in some cellular processes, such as RNA interference.

Messenger RNA

mRNA runs through several steps during its usually brief existence: During transcription, an enzyme called RNA polymerase makes a copy of a gene from the DNA to mRNA as needed. In prokaryotes, no further processing of mRNA occurs (except in rare cases), and often translation of the mRNA into protein occurs even while transcription is going on. In eukaryotes, transcription and translation occur in different parts of the cell (transcription in the nucleus, where DNA is kept, and translation in the cytoplasm, where ribosomes reside). Also in eukaryotes, mRNA undergoes several processing steps before it is ready to be translated:

addition of a 5' cap - A modified guanine nucleotide is added to the "front" of the message. This is critical for recognition and proper attachment of the ribosome.
splicing - The pre-mRNA is modified to remove certain stretches of non-coding sequences called introns; the stretches that remain include protein-coding sequences and are called exons. Sometimes one pre-mRNA message may be spliced in several different ways, allowing 1 gene to encode multiple functions. Most RNA splicing is performed by enzymes, but some RNA molecules are also capable of catalyzing their own splicing (see ribozymes).
polyadenylation - A sequence (often several hundred) of adenine nucleotides is added to the 3' end of the pre-mRNA. This helps increase the half-life of the message, so that the transcript lasts longer in the cell and consequently is translated more and produces more protein.

After the mRNA has been processed, it is exported from the nucleus into the cytoplasm, where it is bound to ribosomes and translated into protein. After a certain amount of time the message degrades into its component nucleotides, usually with the assistance of RNAses.

Messenger RNA that has been processed and is ready for transcription is called a "mature transcript" or "mature mRNA" or sometimes simply "mRNA". Unprocessed or partially-processed messenger RNA is called "pre-mRNA" or "hnRNA" (for heteronucleic RNA)

Untranslated Regions

There are sections of the RNA before and after its start and stop sequences that are not translated. These come from the template DNA strand that the RNA was transcribed from. These regions, known as the 5'UTR and 3'UTR (five-prime and three-prime untranslated regions, respectively, due to the fact that DNA and RNA run from 5' to 3' and this region is on the end of the RNA sequence) code for no protein sequences. However, their importance lies is the belief that the sequence of the 5'UTR and 3'UTR may, by their varying affinity for certain RNase enzymes, promote or inhibit the relative stability of the RNA molecule. Certain UTRs may allow the RNA to survive longer in the cytoplasm before being degraded, thus allowing them to produce more protein, while others may be degraded sooner, thus lasting a shorter time and producing a smaller relative amount of protein.

Also, there is evidence that certain complexes within the UTRs may not only affect the stability of the molecule, but that they may promote translational efficiency or even cause inhibition of translation altogether, depending on the sequences in the UTRs.

Anti-sense mRNA

Anti-sense mRNA can inhibit gene translation in many eukaryotes, when the anti-sense RNA's sequence is complementary to that of the mRNA of the gene. This means a gene is not expressed as protein if a matching anti-sense mRNA is present in the cell. This may be a defense mechanism against retroposons (transposons that use

dsRNA as an intermediate state) or viruses, because both can use double-stranded mRNA as an intermediate. In biochemical research, this effect has been used to study gene function, simply shutting down the studied gene by adding its anti-sense mRNA transcript. Such studies have been done on the worm C. elegans.

Compare RNA interference.

Double-stranded RNA (or dsRNA) is RNA with 2 complementary strands, similar to the DNA found in all "higher" cells. dsRNA forms the genetic material of some viruses (see virus). In eukaryotes, it may play a role in the process of RNA interference and in microRNAs.