RNA is the acronym for ribonucleic acid. RNA is present in the cell in several forms including messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). 3-bases in an mRNA sequence each encode an amino acids, which when synthesis in tandem with other 3-base codes or triplets can form proteins.
RNA with its nitrogenous bases to the left and DNA to the right.
RNA is a polymer with a ribose and phosphate backbone and four different bases: adenine, guanine, cytosine, and uracil. The first three are the same as those found in DNA, but in RNA thymine is replaced by uracil as the base complementary to adenine. This base is also a pyrimidine and is very similar to thymine. Uracil is energetically less expensive to produce than thymine, which may account for its use in RNA. In DNA, however, uracil is readily produced by chemical degradation of cytosine, so having thymine as the normal base makes detection and repair of such incipient mutations more efficient. Thus, uracil is appropriate for RNA, where quantity is important but lifespan is not, whereas thymine is appropriate for DNA where maintaining sequence with high fidelity is more critical.
However, there are also numerous modified bases and sugars found in RNA that serve many different roles. Pseudouridine (Ψ) and the DNA nucleoside thymidine are found in various places (most notably in the TΨC loop of every tRNA). Thus, it is not strictly correct to say that uracil is found in RNA in place of thymine. Another notable modified base is hypoxanthine (a deaminated Guanine base whose nucleotide is called Inosine). Inosine plays a key role in the Wobble Hypothesis of the Genetic Code. There are nearly 100 other naturally occurring modified bases, of which pseudouridine and 2'-O-methylribose are by far the most common. The specific roles of many of these modifications in RNA are not fully understood. However, it is notable that in ribosomal RNA, many of the post-translational modifications occur in highly functional regions, such as the peptidyl transferase center and the subunit interface, inferring that they are important for normal function.
One in a series of interactive artworks demonstrating principles of molecular dynamics created by Zack Booth Simpson & Mine-Control in 2006. Participants forcibly unfolded a simulated RNA molecule and watched it spontaneously refold by base pairing.
The most important structural feature of RNA, indeed the only consistent difference between the two nucleic acids, that distinguishes it from DNA is the presence of a hydroxyl group at the 2'-position of the ribose sugar. The presence of this functional group enforces the C3'-endo sugar conformation (as opposed to the C2'-endo conformation of the deoxyribose sugar in DNA) that causes the helix to adopt the A-form geometry rather than the B-form most commonly observed in DNA. This result in a very deep and narrow major groove and a shallow and wide minor groove. A second consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule (that is, not involved in formation of a double helix), it can chemically attack the adjacent phosphodiester bond to cleave the backbone.
Comparison with DNA
Unlike DNA, RNA is almost always a single-stranded molecule and has a much shorter chain of nucleotides. RNA contains ribose, rather than the deoxyribose found in DNA (there is no hydroxyl group attached to the pentose ring in the 2' position whereas RNA has two hydroxyl groups). These hydroxyl groups make RNA less stable than DNA because it is more prone to hydrolysis. Several types of RNA (tRNA, rRNA) contain a great deal of secondary structure, which help promote stability.
Like DNA, most biologically active RNAs including tRNA, rRNA, snRNAs and other non-coding RNAs (such as the SRP RNAs) are extensively base paired to form double stranded helices. Structural analysis of these RNAs have revealed that they are not, "single-stranded" but rather highly structured. Unlike DNA, this structure is not just limited to long double-stranded helices but rather collections of short helices packed together into structures akin to proteins. In this fashion, RNAs can achieve chemical catalysis, like enzymes. For instance, determination of the structure of the ribosome in 2000 revealed that the active site of this enzyme that catalyzes peptide bond formation is composed entirely of RNA.
Synthesis of RNA is usually catalyzed by an enzyme - RNA polymerase, using DNA as a template. Initiation of synthesis begins with the binding of the enzyme to a promoter sequence in the DNA (usually found "upstream" of a gene). The DNA double helix is unwound by the helicase activity of the enzyme. The enzyme then progresses along the template strand in the 3’ -> 5’ direction, synthesizing a complementary RNA molecule with elongation occurring in the 5’ -> 3’ direction. The DNA sequence also dictates where termination of RNA synthesis will occur.
There are also a number of RNA-dependant RNA polymerases as well that use RNA as their template for synthesis of a new strand of RNA. For instance, a number of RNA viruses (such as poliovirus) use this type of enzyme to replicate their genetic material. Also, it is known that RNA-dependent RNA polymerases are required for the RNA interference pathway in many organisms.
Messenger RNA is RNA that carries information from DNA to the ribosome sites of protein synthesis in the cell. Once mRNA has been transcribed from DNA, it is exported from the nucleus into the cytoplasm (in eukaryotes mRNA is "processed" before being exported), where it is bound to ribosomes and translated into its corresponding protein form with the help of tRNA. After a certain amount of time the message degrades into its component nucleotides, usually with the assistance of RNA polymerases.
Ribosomal RNA is a component of the ribosomes, the protein synthetic factories in the cell. Eukaryotic ribosomes contain four different rRNA molecules: 18S, 5.8S, 28S, and 5S rRNA. Three of the rRNA molecules are synthesized in the nucleolus, and one is synthesized elsewhere. rRNA molecules are extremely abundant and make up at least 80% of the RNA molecules found in a typical eukaryotic cell.
In the cytoplasm, ribsomal RNA and protein combine to form a nucleoprotein called a ribosome. The ribosome binds mRNA and carries out protein synthesis. Several ribosomes may be attached to a single mRNA at any time.
RNA genes (sometimes referred to as non-coding RNA or small RNA) are genes that encode RNA that is not translated into a protein. The most prominent examples of RNA genes are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of translation. However, since the late 1990s, many new RNA genes have been found, and thus RNA genes may play a much more significant role than previously thought.
In the late 1990s and early 2000, there has been persistent evidence of more complex transcription occurring in mammalian cells (and possibly others). This could point towards a more widespread use of RNA in biology, particularly in gene regulation. A particular class of non-coding RNA, micro RNA, has been found in many metazoans (from Caenorhabditis elegans to Homo sapiens) and clearly plays an important role in regulating other genes.
First proposed in 2004 by Rassoulzadegan and published in Nature 2006 , RNA is implicated as being part of the germline. If confirmed, this result would significantly alter the present understanding of genetics and lead to many question on DNA-RNA roles and interactions.
Although RNA contains only four bases, in comparison to the twenty amino acids commonly found in proteins, some RNAs are still able to catalyse chemical reactions. These include cutting and ligating other RNA molecules and also the catalysis of peptide bond formation in the ribosome.
Double-stranded RNA (or dsRNA) is RNA with two complementary strands, similar to the DNA found in all "higher" cells. dsRNA forms the genetic material of some viruses. In eukaryotes, it acts as a trigger to initiate the process of RNA interference and is present as an intermediate step in the formation of siRNAs (small interfering RNAs). siRNAs are often confused with miRNAs; siRNAs are double-stranded, whereas miRNAs are single-stranded. Although initially single stranded there are regions of intra-molecular association causing hairpin structures in pre-miRNAs; immature miRNAs. Very recently, dsRNA has been found to induce gene expression at transcriptional level, a phenomenon named "small RNA induced gene activation RNAa". Such dsRNA is called "small activating RNA (saRNA)".
RNA world hypothesis
Main article: RNA world hypothesis
The RNA world hypothesis proposes that the earliest forms of life relied on RNA both to carry genetic information (like DNA does now) and to catalyze biochemical reactions like an enzyme. According to this hypothesis, descendants of these early lifeforms gradually integrated DNA and proteins into their metabolism.
RNA secondary structures
The functional form of single stranded RNA molecules (like proteins) frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements which are hydrogen bonds within the molecule. This leads to several recognizable "domains" of secondary structure like hairpin loops, bulges and internal loops. The secondary structure of RNA molecules can be predicted computationally by calculating the minimum free energies (MFE) structure for all different combinations of hydrogen bondings and domains. There has been a significant amount of research directed at the RNA structure prediction problem.
Online tools for MFE structure prediction from single sequences are provided by MFOLD and RNAfold.
Comparative studies of conserved RNA structures are significantly more accurate and provide evolutionary information. Computationally reasonable and accurate online tools for alignment folding are provided by KNetFold, RNAalifold and Pfold.
A package of RNA structure prediction programs is also available for Windows: RNAstructure.
A database of RNA sequences and secondary structures is available from Rfam, analyses and links to RNA analysis tools are available from Wikiomics.
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