RNA

From Wikipedia, the free encyclopedia

For other uses, see RNA (disambiguation).
A hairpin loop from a pre-mRNA. Notice its nitrogen-rich (blue) bases and oxygen-rich (red) backbone.
A hairpin loop from a pre-mRNA. Notice its nitrogen-rich (blue) bases and oxygen-rich (red) backbone.

Ribonucleic acid or RNA is a nucleic acid made from a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA is very similar to DNA, but differs in a few important structural details: in the cell RNA is usually single stranded, while DNA is usually double stranded. RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom), and RNA has the nucleotide uracil rather than thymine which is present in DNA.

RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes. Some of these RNA-processing enzymes contain RNA as part of their structures. RNA is also central to the translation of some RNAs into proteins. In this process, a type of RNA called messenger RNA carries information from DNA to structures called ribosomes. These ribosomes are made from proteins and ribosomal RNAs, which come together to form a molecular machine that can read messenger RNAs and translate the information they carry into proteins. It has also been known since the 1990s that several types of RNA regulate which genes are active.

Contents

[edit] Structure

Watson-Crick base pairs in a siRNA (hydrogen atoms are not shown)
Watson-Crick base pairs in a siRNA (hydrogen atoms are not shown)

Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, generally adenine (A), cytosine (C), guanine (G) or uracil (U). Adenine and guanine are purines, cytosine and uracil are pyrimidines. A phosphate group is attached to the 3' position of one ribose and the 5' position of the next. The phosphate groups have a negative charge each at physiological pH, making RNA a charged molecule (polyanion). The bases may form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil.[1] However other interactions are possible, such as a group of adenine bases binding to each other in a bulge,[2] or the GNRA tetraloop that has a guanine–adenine base-pair.[1]

Chemical structure of RNA
Chemical structure of RNA

An important structural feature of RNA 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 causes the helix to adopt the A-form geometry rather than the B-form most commonly observed in DNA.[3] This results in a very deep and narrow major groove and a shallow and wide minor groove.[4] 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.[5]

RNA is transcribed with only four bases (adenine, cytosine, guanine and uracil),[6] but there are numerous modified bases and sugars in mature RNAs. Pseudouridine (Ψ), in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, and ribothymidine (T), are found in various places (most notably in the TΨC loop of tRNA).[7] Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine. Inosine plays a key role in the wobble hypothesis of the genetic code.[8] There are nearly 100 other naturally occurring modified nucleosides,[9] of which pseudouridine and nucleosides with 2'-O-methylribose are the most common.[10] 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-transcriptional modifications occur in highly functional regions, such as the peptidyl transferase center and the subunit interface, implying that they are important for normal function.[11]

Secondary structure of a telomerase RNA
Secondary structure of a telomerase RNA

The functional form of single stranded RNA molecules, just 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.[12] There has been a significant amount of research directed at RNA structure prediction.

[edit] Comparison with DNA

RNA and DNA differ in three main ways. First, unlike DNA which is double-stranded, RNA is a single-stranded molecule in most of its biological roles and has a much shorter chain of nucleotides. Second, while DNA contains deoxyribose, RNA contains ribose, (there is no hydroxyl group attached to the pentose ring in the 2' position in DNA). These hydroxyl groups make RNA less stable than DNA because it is more prone to hydrolysis. Third, the complementary nucleotide to adenine is not thymine, as it is in DNA, but rather uracil, which is an unmethylated form of thymine.[13]

The 50S ribosomal subunit. RNA is in orange, protein in blue. The active site is in the middle (red).
The 50S ribosomal subunit. RNA is in orange, protein in blue. The active site is in the middle (red).

Like DNA, most biologically active RNAs including tRNA, rRNA, snRNAs and other, non-coding, RNAs are extensively base paired to form double stranded helices. Structural analysis of these RNAs have revealed that they are highly structured. Unlike DNA, this structure is not 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.[14] For instance, determination of the structure of the ribosome—an enzyme that catalyzes peptide bond formation—revealed that its active site is composed entirely of RNA.[15]

[edit] Synthesis

Synthesis of RNA is usually catalyzed by an enzyme—RNA polymerase—using DNA as a template, a process known as transcription. Initiation of transcription 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’ to 5’ direction, synthesizing a complementary RNA molecule with elongation occurring in the 5’ to 3’ direction. The DNA sequence also dictates where termination of RNA synthesis will occur.[16]

RNAs are often modified by enzymes after transcription. For example, a poly(A) tail and a 5' cap are added to eukaryotic pre-mRNA.

There are also a number of RNA-dependent 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.[17] Also, it is known that RNA-dependent RNA polymerases are required for the RNA interference pathway in many organisms.[18]

[edit] Types of RNA

See also: List of RNAs

[edit] Overview

Structure of a hammerhead ribozyme, a ribozyme that cuts RNA
Structure of a hammerhead ribozyme, a ribozyme that cuts RNA

Messenger RNA (mRNA) is the RNA that carries information from DNA to the ribosome, the sites of protein synthesis (translation) in the cell. The coding sequence of the mRNA determines the amino acid sequence in the protein that is produced.[19] Many RNAs do not code for protein however. These non-coding RNAs can be encoded by their own genes (RNA genes), but can also derive from mRNA introns.[20] The most prominent examples of non-coding RNAs are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of translation.[13] There are also non-coding RNAs involved in gene regulation, RNA processing and other roles. Certain RNAs are able to catalyse chemical reactions such as cutting and ligating other RNA molecules,[21] and the catalysis of peptide bond formation in the ribosome;[15] these are known as ribozymes.

[edit] In translation

Messenger RNA (mRNA) carries information about a protein sequence to the ribosomes, the protein synthesis factories in the cell. It is coded so that every three nucleotides (a codon) correspond to one amino acid. In eukaryotic cells, once precursor mRNA (pre-mRNA) has been transcribed from DNA, it is processed to mature mRNA. This removes its introns—non-coding sections of the pre-mRNA. The mRNA is then exported from the nucleus to the cytoplasm, where it is bound to ribosomes and translated into its corresponding protein form with the help of tRNA. In prokaryotic cells, which do not have nucleus and cytoplasm compartments, mRNA can bind to ribosomes while it is being transcribed from DNA. After a certain amount of time the message degrades into its component nucleotides with the assistance of ribonucleases.[19]

Transfer RNA (tRNA) is a small RNA chain of about 80 nucleotides that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has sites for amino acid attachment and an anticodon region for codon recognition that binds to a specific sequence on the messenger RNA chain through hydrogen bonding.[20]

Ribosomal RNA (rRNA) is the catalytic component of the ribosomes. 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. In the cytoplasm, ribosomal 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.[19] rRNA is extremely abundant and makes up 80% of the 10 mg/ml RNA found in a typical eukaryotic cytoplasm.[22]

Transfer-messenger RNA (tmRNA) is found in many bacteria and plastids. It tags proteins encoded by mRNAs that lack stop codons for degradation and prevents the ribosome from stalling.[23]

[edit] In gene regulation

Several types of RNA can downregulate gene expression by being complementary to a part of an mRNA or gene. MicroRNAs (miRNA; 21-22 nt) are found in eukaryotes and act through RNA interference (RNAi), where an effector complex of miRNA and enzymes can break down mRNA which the miRNA is complementary to, block the mRNA from being translated, or cause a promoter to be methylated which generally downregulates its gene.[24] Some miRNAs upregulate genes instead (RNA activation).[25] While small interfering RNAs (siRNA; 20-25 nt) are often produced by breakdown of viral RNA, there are also endogenous sources of siRNAs in plants.[26] siRNAs act through RNA interference in a fashion similar to miRNAs, including RNA activation.[27] Animals have Piwi-interacting RNAs (piRNA; 29-30 nt) which are active in germline cells and are thought to be a defense against transposons and play a role in gametogenesis.[28][29] Antisense RNAs are widespread among bacteria; most downregulate a gene, but a few are activators of transcription.[30] Antisense RNA acts by binding to an mRNA, forming double-stranded RNA that is degraded by enzymes.[31] There are many mRNA-like large non-coding RNAs that regulate genes in eukaryotes,[32] one such RNA is Xist which coats one X chromosome in female mammals and inactivates it.[33]

An mRNA may contain regulatory elements itself, such as riboswitches, in the 5' UTR or 3' UTR; these cis-regulatory elements regulate the activity of that mRNA.[34]

[edit] In RNA processing

Uridine to pseudouridine is a common RNA modification.
Uridine to pseudouridine is a common RNA modification.

Many RNAs are involved in modifying other RNAs. Introns are spliced out of pre-mRNA by spliceosomes, which contain several small nuclear RNAs (snRNA),[13] or the introns can be ribozymes that are spliced by themselves.[35] RNA can also be altered by having its nucleotides modified to other nucleotides than A, C, G and U. In eukaryotes, modifications of RNA nucleotides are generally directed by small nucleolar RNAs (snoRNA; 60-300 nt),[20] found in the nucleolus and cajal bodies. snoRNAs associate with enzymes and guide them to a spot on an RNA by basepairing to that RNA. These enzymes then perform the nucleotide modification. rRNAs and tRNAs are extensively modified, but snRNAs and mRNAs can also be the target of base modification.[36][37]

[edit] RNA genomes

Like DNA, RNA can be an information carrier. RNA viruses have genomes composed of RNA, plus a variety of proteins encoded by that genome. The viral genome is replicated by some of those proteins, while other proteins protect the genome as the virus particle moves to a new host cell. Viroids are another group of pathogens, but they consist only of RNA, do not encode any protein and are replicated by a host plant cell's polymerase.[38]

[edit] In reverse transcription

Reverse transcribing viruses replicate their genomes by reverse transcribing DNA copies from their RNA; these DNA copies are then transcribed to new RNA. Retrotransposons also spread by copying DNA and RNA from one another,[39] and telomerase contains an RNA that is used as template for building the ends of eukaryotic chromosomes.[40]

[edit] Double-stranded RNA

Double-stranded RNA (dsRNA) is RNA with two complementary strands, similar to the DNA found in all cells. dsRNA forms the genetic material of some viruses (double-stranded RNA viruses). Double-stranded RNA such as viral RNA or siRNA can trigger RNA interference in eukaryotes, as well as interferon response in vertebrates.[41][42][43]

[edit] Discovery

Nucleic acids were discovered in 1868 by Friedrich Miescher, who called the material 'nuclein' since it was found in the nucleus.[44] It was later discovered that prokaryotic cells, which do not have a nucleus, also contain nucleic acids. The role of RNA in protein synthesis was suspected already in 1939.[45] Severo Ochoa won the 1959 Nobel Prize in Medicine after he discovered how RNA is synthesized.[46] The sequence of the 77 nucleotides of a yeast tRNA was found by Robert W. Holley in 1965,[47] winning Holley the 1968 Nobel Prize in Medicine. Carl Woese realised RNA can be catalytic in 1967 and proposed that the earliest forms of life relied on RNA both to carry genetic information and to catalyze biochemical reactions—an RNA world.[48][49] In 1976, Walter Fiers and his team determined the first complete nucleotide sequence of an RNA virus genome, that of bacteriophage MS2.[50] In 1990 it was found that introduced genes can silence homologous endogenous genes in plants,[51] now known to be a result of RNA interference.[52] At about the same time, 22 nt long RNAs, now called microRNAs, were found to have a role in the development of C. elegans.[53] The discovery of gene regulatory RNAs has led to attempts to develop drugs made of RNA, like siRNA, to silence genes.[54]

[edit] See also

[edit] References

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[edit] External links

v • d • e
Types of nucleic acids
Nucleobases
Nucleosides
Nucleotides
monophosphates (AMP, GMP, UMP, CMP) | diphosphates (ADP, GDP, UDP, CDP) | triphosphates (ATP, GTP, UTP, CTP) | cyclic (cAMP, cGMP, cADPR)
Deoxynucleotides
monophosphates (dAMP, dGMP, TMP, dCMP) | diphosphates (dADP, dGDP, TDP, dCDP) | triphosphates (dATP, dGTP, TTP, dCTP)
Ribonucleic acids
Deoxyribonucleic acids
Nucleic acid analogues
Cloning vectors
Major families of biochemicals
Peptides | Amino acids | Nucleic acids | Carbohydrates | Nucleotide sugars | Lipids | Terpenes | Carotenoids | Tetrapyrroles | Enzyme cofactors | Steroids | Flavonoids | Alkaloids | Polyketides | Glycosides