RNA

RNA (ribonucleic acid) is one of the two principal nucleic acids in biology, and is fundamental to life as we know it. RNA is composed of a chain of nucleotides covalently bound to each other by phosphodiester bonds. The nucleotide sequence contains information encoding information for creating the means to achieve all cellular processes - a "blueprint", as it were, for life. This sequence is copied verbatim from a DNA template (stored in the cell's nucleus), and is used for one of two major processes: protein synthesis or transcriptional regulation.

Architecture
Unlike DNA, which is normally double-stranded, RNA typically exists in a single-stranded configuration, and therefore does not form a macromolecule. This, however, does not mean base-pairing does not occur. In fact, RNA frequently adopts complex patterns of base-pairing between nucleotides within the same molecule, due to formation of the thermodynamically favorable hydrogen bonds between purines and pyrimidines. This is referred to as RNA secondary structure, and is a crucial component of its functions.

Processing
RNA that is destined to be translated into protein is known as messenger RNA (mRNA), as each mRNA molecule carries the "message" that directs synthesis of a unique polypeptide. But the product of transcription, pre-mRNA, must first be processed into mRNA before it can be translated into protein.

Splicing
Before the RNA message can be interpreted, the pre-mRNA must be spliced in such a way that removes portions of sequence known as introns. Introns are designed to provide support to pre-mRNA secondary structure during its synthesis and transport, but do not themselves contain codes, aside from a special subset of RNAs that mediate transcriptional regulation (see microRNA). Instead, exons exist for this purpose, which are preserved in the mRNA molceule by specialized machinery that recognizes specific sequences at intron/exon boundaries.

Modifications
Capping is the process of protecting the mRNA molceule from attack by single-stranded nucleases, and conditioning it for recognition by splicing and translation machinery. The 5' end of the mRNA is capped by a covalently modified form of guanosine, 7-methylguanosine (m7G), while the 3' end is polyadenylated and bound by specific proteins which recognize this modification.

Translation
Translation is the process of converting the message contained in the mRNA sequence into a protein of defined sequence. The nucleotides in the mRNA molecule must be translated into amino acids. This is done by partitioning the nucleotide sequence into triplets, called codons. Each codon encodes a particular amino acid, as governed by the genetic code.

Mechanism
Translation is intitiated when a ribosome encounters an mRNA molecule. This is a very specific interaction, mediated by small RNA molecules within the ribosome that recognize certain sequences on the mRNA template. Because the mRNA is interpreted by reading codons (triplets of nucleotides), the ribosome contains three unique "pockets" through which the mRNA transcript progresses. These pockets are catalytic domains within ribosomal enzymes that allow for formation of the peptide bonds that create the protein. Each pocket fits a codon and its corresponding tRNA, to which is attached an amino acid. As the mRNA "slides" through the ribosome, and each amino acid-tRNA hybrid passes through, another amino acid is added to the growing polypeptide, whose sequence is governed by the relative of positioning of codons within the mRNA.

Location
Translation occurs in the cytoplasm, which is the location of the rough endoplasmic reticulum (RER). The "roughness" of RER comes fomr the fact that it is coated with ribosomes, the translational machinery. Historically, it was considered that transcription and translation were temporally distinct processes, but evidence has shown that the two processes occur in tandem, reliant on cooperativity between the nuclear and cytoplasmic compartments.

Transcriptional Regulation
The other key function performed by RNA is transcriptional regulation. Not all RNA molecules are translated into protein. Some are incorporated directly into complexes that mediate various processes in gene expression.

tRNA
Transfer RNA is so named because it enacts the transfer of an amino acid to a growing polypeptide chain during translation. The amino acid is covalently attached to the tRNA, which is of a specific sequence, and consequently adopts a peculiar secondary structure. This structure is capable of binding to only one amino acid, and of recognizing only certain codons in the mRNA transcript, thus ensuring the placement of the proper amino acid in the sequence.

snRNA
Small Nuclear RNA (snRNA) is a special class of RNA that exists in the nucleus. They are components of complexes called spliceosomes whose function is splicing pre-mRNA transcripts before they are exported for translation.

miRNA
MicroRNA (miRNA) is RNA transcribed from introns whose function is to inhibit translation of mRNA. This is a particularly useful mechanism for transcriptional regulation that involves base-pairing between the miRNA and the mRNA transript, which fit into an enzyme complex (RISC) that degrades or inhibits translation of the mRNA into protein.

siRNA
Small Inhibitory RNA (siRNA) is a subclass of miRNAs that are synthetically generated by researchers for the purpose of knocking down expression of a particular gene in a model organism. They mimic the action of miRNAs by utilizing the RISC complex.