Difference between revisions of "RNA" - New World Encyclopedia

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'''Ribonucleic acid''' ('''RNA''') is a [[nucleic acid]] polymer consisting of [[nucleotide]] monomers. RNA nucleotides contain [[ribose]] rings and [[uracil]] unlike deoxyribonucleic acid ([[DNA]]), which contains [[deoxyribose]] and [[thymine]]. It is transcribed (synthesized) from DNA by [[enzymes]] called RNA polymerases and further processed by other enzymes.  RNA serves as the template for translation of genes into [[protein]]s, transferring [[amino acid]]s to the [[ribosome]] to form proteins, and also translating the transcript into proteins.
 
  
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== History ==
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[[Image:Pre-mRNA-1ysv.JPG|thumb|200px|A hairpin loop from a pre-mRNA. Notice the single strand and its nitrogen-rich (blue) bases and oxygen-rich (red) backbone.]]
 +
'''Ribonucleic acid''' or '''RNA''' is a [[nucleic acid]], consisting of many [[nucleotide]]s that form a [[polymer]]. Each nucleotide consists of a [[nucleobase|nitrogenous base]], a [[ribose]] sugar, and a [[phosphate]]. RNA plays several important roles in the processes of translating genetic information from deoxyribonucleic acid ([[DNA]]) into [[protein]]s. One type of RNA acts as a messenger between DNA and the protein synthesis complexes known as [[ribosome]]s, others form vital portions of the structure of ribosomes, act as essential carrier molecules for [[amino acid]]s to be used in protein synthesis, or change which genes are active.
  
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Nucleic acids were discovered in 1868 (some sources indicate 1869) by [[Johann Friedrich Miescher]] (1844-1895), who called the material 'nuclein' since it was found in the nucleus.  It was later discovered that prokaryotic cells, which do not have a nucleus, also contain nucleic acids. The role of RNA in protein synthesis had been suspected since 1939, based on experiments carried out by [[Torbjörn Oskar Caspersson|Torbjörn Caspersson]], [[Jean Brachet]] and [[Jack Schultz]]. [[Hubert Chantrenne]] elucidated the messenger role played by RNA in the synthesis of [[Protein|proteins]] in [[Ribosomes|ribosome]]. The sequence of the 77 nucleotides of a yeast RNA was found by [[Robert W. Holley]] in 1964, winning Holley the 1968 [[Nobel Prize for Medicine]]. In 1976, [[Walter Fiers]] and his team at the [[University of Ghent]] determine the complete nucleotide-sequence of [[Bacteriophage MS2|bacteriophage MS2]]-RNA<ref>Fiers W et al., Complete nucleotide-sequence of bacteriophage MS2-RNA - primary and secondary structure of replicase gene, Nature, 260, 500-507, 1976</ref>
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RNA is very similar to DNA, but differs in a few important structural details: 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 uses the nucleotide [[uracil]] in its composition, instead of [[thymine]] which is present in DNA. RNA is [[Transcription (genetics)|transcribed]] from DNA by [[enzymes]] called [[RNA polymerase]]s and is generally further processed by other enzymes, some of them guided by [[non-coding RNA]]s.
  
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== Chemical and Stereochemical structure ==
+
==Overview==
 +
A '''nucleic acid''' is a complex, high-molecular-weight macromolecule composed of [[nucleotide]] chains whose sequence of bases conveys [[gene|genetic information]]. The connectedness of [[life|living organisms]] can be seen in the fact that nucleic acids are found in all living [[cell (biology)|cells]] and in [[virus]]es, and the flow of genetic information is essentially the same in all organisms.
  
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[[Image:NA-comparedto-DNA_thymineAndUracilCorrected.png|thumb|290px|RNA with its nitrogenous bases to the left and [[DNA]] to the right.]]
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The most common nucleic acids are '''[[DNA|deoxyribonucleic acid]]''' (DNA) and '''[[RNA|ribonucleic acid]]''' (RNA). The main role of DNA is the long-term storage of genetic information. DNA is often compared to a blueprint, since it contains instructions for constructing other components of the cell, such as [[protein]]s and RNA molecules. The DNA segments that carry genetic information are called ''[[gene]]s'', but other DNA sequences have structural purposes or are involved in regulating the expression of genetic information.  
  
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RNA is primarily made up of 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.  
+
Although RNA may serve as a genetic blueprint for certain [[virus]]es, it plays a diversity of roles. RNA may be thought of as the intermediate between the DNA blueprint and the actual workings of the cell, serving as the template for the synthesis of proteins from the genetic information stored in DNA. Some RNA molecules (called ribozymes) are also involved in the catalysis of biochemical reactions.
  
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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]]).  Another notable modified base is [[Inosine]] (a deaminated Guanine base), which allows a "wobble codon" sequence in [[tRNA]].  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.
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Nucleic acids are '''polymers''' of repeating units (called '''monomers'''). Specifically, they consist of long chains of [[nucleotide]] monomers connected by [[covalent chemical bond]]*s. RNA molecules may contain as few as 75 nucleotides or more than 5,000 nucleotides, while a DNA molecule may be composed of more than 1,000,000 nucleotide units.
  
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Single stranded RNA exhibits a right handed stacking pattern that is stabilized by base [[Stacking (chemistry)|stacking]].
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A '''nucleotide''' is a chemical compound with three components: a [[nitrogen]]-containing base, a pentose (five-carbon) [[sugar]], and one or more phosphate groups. The nitrogen-containing base of a nucleotide (also called the '''nucleobase''') is typically a derivative of either [[purine]] or [[pyrimidine]]. The most common nucleotide bases are the purines [[adenine]] and [[guanine]] and the pyrimidines [[cytosine]] and [[thymine]] (or [[uracil]] in RNA).
  
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The most 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 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.
+
The sugar component is either deoxyribose or ribose. (“Deoxy” simply indicates that the sugar lacks an [[oxygen]] [[atom]] present in ribose, the parent compound.)
  
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== Comparison with DNA ==
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There are two major compositional differences between RNA and DNA:
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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 [[nucleic acid nomenclature|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.
 
  
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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.
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#The sugar units in RNA molecules are riboses, while DNA is built of nucleotides with a deoxyribose sugar.
 +
#One of the four major nucleobases in RNA is uracil (U) instead of thymine (T).
  
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== Synthesis ==
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RNA is usually single-stranded, but it may contain double-helical regions where a given strand has folded back on itself.
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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.
 
  
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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 known that RNA-dependent RNA polymerases are required for the RNA interference pathway in many organisms.
 
  
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== Biological roles ==
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==Chemical and Stereochemical structure==
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[[Image:Piwi-siRNA-basepairing.png|thumb|265px|right|Base-pairing in a [[siRNA]] segment, a double-stranded type of RNA. Hydrogen atoms are not shown.]]
  
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=== Messenger RNA (mRNA) ===
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RNA is a polymer with a ribose and [[phosphate]] backbone and four different nucleotide 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 [[complementarity (molecular biology)|complementary]] to adenine. This base is also a pyrimidine and is very similar to thymine. 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.
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{{main|Messenger RNA}}
+
 
 +
There are also numerous modified bases and sugars found in RNA that serve many different roles. [[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]]). Another notable modified base is hypoxanthine (a deaminated guanine base whose nucleoside is called [[inosine]]). Inosine plays a key role in the [[Wobble Hypothesis]] of the [[genetic code]]. There are nearly 100 other naturally occurring modified nucleosides, of which pseudouridine and nucleosides with 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, implying that they are important for normal function.
  
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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 [[eukaryote]]s mRNA is "processed" before being exported), where it is bound to [[ribosome]]s 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 polymerase]]s.
+
The most 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 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 results 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.
  
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=== Transfer RNA (tRNA) ===
+
==Comparison with DNA==
−
{{main|Transfer RNA}}
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[[Image:NA-comparedto-DNA thymineAndUracilCorrected.png|thumb|350px|'''Left:''' An RNA strand, with its nitrogenous bases. '''Right:''' Double-stranded [[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. Secondly, while DNA contains ''deoxyribose'', RNA contains ''ribose'', (there is no hydroxyl group attached to the pentose ring in the [[nucleic acid nomenclature|2']] position in DNA, whereas RNA has two hydroxyl groups). These hydroxyl groups make RNA less stable than DNA because it is more prone to [[hydrolysis]].  Thirdly, the complementary nucleotide to [[adenine]] is not [[thymine]], as it is in DNA, but rather [[uracil]], which is an [[methylation|unmethylated]] form of thymine.
  
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Transfer RNA is a small RNA chain of about 74-95 [[nucleotide]]s that transfers a specific [[amino acid]] to a growing [[polypeptide]] chain at the [[ribosome|ribosomal]] site of protein synthesis during [[translation (biology)|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.  It is a type of [[non-coding RNA]].
+
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 &mdash; an enzyme that catalyzes peptide bond formation &mdash; revealed that its active site is composed entirely of RNA.
  
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=== Ribosomal RNA (rRNA) ===
+
==Synthesis==
−
{{main|Ribosomal 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.<ref>{{cite journal | author=Evgeny Nudler, Max E. Gottesman| title=Transcription termination and anti-termination in
 +
E. coli | journal=Genes to Cells| year=2002| volume=7| pages=755-768}}[http://www.genestocellsonline.org/cgi/reprint/7/8/755]</ref>
  
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'''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.
+
There are also a number of [[RNA-dependent RNA polymerase]]s 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.<ref>{{cite journal | author=Jeffrey L Hansen, Alexander M Long, Steve C Schultz| title=Structure of the RNA-dependent RNA polymerase of poliovirus | journal=Structure| year=1997| volume=5| issue=8| pages=1109-1122 | url=http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VSR-4CP0VB1-2&_user=10&_coverDate=08%2F15%2F1997&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=87e7735482144c1d32b14c87166b4d79}}</ref> Also, it is known that RNA-dependent RNA polymerases are required for the RNA interference pathway in many organisms.<ref>{{cite journal | author=Paul Ahlquist| title=RNA-Dependent RNA Polymerases, Viruses, and RNA Silencing | journal=Science| year=2002| volume=296| issue=5571| pages=1270-1273}}</ref>
  
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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.
+
==Biological roles==
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===Messenger RNA (mRNA)===
 +
{{main|Messenger RNA}}
 +
Messenger RNA is RNA that carries information from [[DNA]] to the [[ribosome]] sites of protein synthesis in the cell. In eukaryotic cells, once mRNA has been transcribed from DNA, it is "processed" before being exported from the nucleus into the cytoplasm, where it is bound to [[ribosome]]s and [[Translation (biology)|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, usually with the assistance of [[ribonuclease]]s.
  
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=== Non-coding RNA or "RNA genes" ===
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===Non-coding RNA===
 
{{main|Non-coding RNA}}
 
{{main|Non-coding RNA}}
  
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RNA genes (sometimes referred to as non-coding RNA or small RNA) are genes that encode RNA that is not [[translation (biology)|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.
+
RNA genes (also known as non-coding RNA or small RNA) are genes that encode RNA which is not [[translation (biology)|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. Two other groups of non-coding RNA are [[microRNA]]s (miRNA) which regulate the expression of genes through a process called [[RNA interference]] (RNAi), and [[small nuclear RNA]]s (snRNA), a diverse class that includes for example the RNAs that form [[spliceosome]]s that excise [[intron]]s from [[pre-mRNA]].<ref>{{cite book |last= Berg |first=JM |coauthors= JL Tymoczko, L Stryer |title= Biochemistry | edition=5th Edition |pages =781-808 | publisher= WH Freeman and Company |year=2002 |isbn= 0-7167-4684-0}}</ref>
 +
 
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====Ribosomal RNA (rRNA)====
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{{main|Ribosomal RNA}}
  
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In the late 1990s and early 2000, there has been persistent evidence of more complex transcription occurring in [[mammal]]ian 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.
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Ribosomal RNA is the catalytic component of the [[ribosomes]], the protein synthesis 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.
  
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First proposed in 2004 by Rassoulzadegan and published in Nature 2006 <ref>Rassoulzadegan M., et al. Nature, doi:10.1038/nature04674 , 2006</ref>, 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.
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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.
  
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=== Catalytic RNA ===
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====Transfer RNA (tRNA)====
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{{main|Transfer RNA}}
 +
 
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Transfer RNA is a small RNA chain of about 74-95 [[nucleotide]]s that transfers a specific [[amino acid]] to a growing [[polypeptide]] chain at the [[ribosome|ribosomal]] site of [[protein]] synthesis, during [[translation (biology)|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. It is a type of [[non-coding RNA]].
 +
 
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====Catalytic RNA====
 
{{main|Ribozyme}}
 
{{main|Ribozyme}}
  
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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 [[ligase|ligating]] other RNA molecules and also the catalysis of [[peptide bond]] formation in the [[ribosome]].
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Although RNA contains only four bases, in comparison to the twenty-odd amino acids commonly found in proteins, certain RNAs are still able to catalyse chemical reactions. These include cutting and [[ligase|ligating]] other RNA molecules, and also the catalysis of [[peptide bond]] formation in the [[ribosome]].
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 +
===Double-stranded RNA===<!-- This section is linked from [[Interferon]] —>
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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 [[virus]]es called [[dsRNA virus]]es. In [[eukaryote]]s, long RNA such as viral RNA can trigger [[RNA interference]], where short dsRNA molecules called [[siRNA]]s (small interfering RNAs) can cause enzymes to break down specific mRNAs or [[gene silencing|silence]] the expression of genes. siRNA can also increase the transcription of a gene, a process called [[RNAa|RNA activation]].<ref>{{cite journal | author=Doran G| title=RNAi – Is one suffix sufficient? | journal=Journal of RNAi and Gene Silencing | year=2007| volume=3| issue=1| pages=217-219 | url=http://libpubmedia.co.uk/RNAiJ-Issues/Issue-5/Doran.htm|}}</ref> siRNA is often confused with [[miRNA]]; siRNAs are double-stranded, whereas miRNAs are single-stranded.
  
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=== Double-stranded RNA ===
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==RNA world hypothesis==
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{{main|RNA world hypothesis}}
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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 [[ribozyme|like an enzyme]]. According to this hypothesis, descendants of these early lifeforms gradually integrated DNA and proteins into their metabolism.
  
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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 [[virus]]es. 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 [[siRNA]]s (small interfering RNAs). [[siRNA]]s are often confused with [[miRNA]]s; [[siRNA]]s are double-stranded, whereas [[miRNA]]s are single-stranded. 
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==RNA secondary structures==
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Although initially single stranded there are regions of intra-molecular association causing hairpin structures in pre-miRNAs; immature miRNAs.
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[[Image:Ciliate telomerase RNA.JPG|thumb|250px|Secondary structure of an RNA from a [[telomerase]].]]
 +
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 loop]]s, 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.<ref>{{cite journal | author=Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH| title=Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure| journal=Proc. Natl. Acad. Sci. U. S. A.| year=2004| volume=101| issue=19| pages=7287-7292| url=http://www.pnas.org/cgi/reprint/101/19/7287.pdf}}</ref> There has been a significant amount of research directed at the [[RNA structure]] prediction problem.
  
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== RNA world hypothesis == 
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Online tools for MFE structure prediction from single sequences are provided by [http://frontend.bioinfo.rpi.edu/applications/mfold/ MFOLD] and [http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi RNAfold].
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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 [[ribozyme|like an enzyme]].  According to this hypothesis, descendants of these early lifeforms gradually integrated DNA and proteins into their metabolism.
 
  
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== RNA secondary structures == 
+
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 [http://knetfold.abcc.ncifcrf.gov KNetFold], [http://rna.tbi.univie.ac.at/cgi-bin/alifold.cgi RNAalifold] and [http://www.daimi.au.dk/~compbio/rnafold/ Pfold].
  
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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.
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A package of RNA structure prediction programs is also available for Windows: [http://rna.urmc.rochester.edu/rnastructure.html RNAstructure].
  
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Online tools for MFE structure prediction from single sequences are provided by [http://www.bioinfo.rpi.edu/applications/mfold/ MFOLD] and [http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi RNAfold].  
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A database of RNA sequences and secondary structures is available from [http://www.sanger.ac.uk/Software/Rfam/index.shtml Rfam], analyses and links to RNA analysis tools are available from [http://wikiomics.org/wiki/List_of_articles#RNA Wikiomics].
  
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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 [http://knetfold.abcc.ncifcrf.gov KNetFold], [http://rna.tbi.univie.ac.at/cgi-bin/alifold.cgi RNAalifold] and [http://www.daimi.au.dk/~compbio/rnafold/ Pfold].
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==List of RNA types==
 +
{| class="wikitable"
 +
|-
 +
! Type !! Function !! Distribution
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|-
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| [[mRNA]] || Codes for protein || All cells
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|-
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| [[rRNA]] || Translation || All cells
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|-
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| [[tRNA]] || Translation || All cells
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|-
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| [[snRNA]] || RNA modification || All cells
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|-
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| [[snoRNA]] || RNA modification || All cells
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|-
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| [[miRNA]] || Gene regulation || Eukaryotes
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|-
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| [[piRNA]] || Gene regulation || Animal [[germline]] cells
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|-
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| [[siRNA]] || Gene regulation || Eukaryotes
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|-
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| [[Antisense mRNA]] || Preventing translation || Bacteria
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|-
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| [[tmRNA]] || Terminating translation || Bacteria
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|-
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| [[7SL RNA|SRP RNA]] || mRNA tagging for export || All cells
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|-
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| [[Ribozyme]] || Catalysis || All cells
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|-
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| [[Transposon]] || Self-propagating || All cells
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|-
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| [[Viroid]] || Self-propagating || Infected plants
 +
|-
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|}
  
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A package of RNA structure prediction programs is also available for Windows: [http://rna.urmc.rochester.edu/rnastructure.html RNAstructure].
+
In addition, the genome of many types of viruses consists of RNA, namely:
 +
*[[Double-stranded RNA viruses]]
 +
*[[Positive-sense ssRNA virus|Positive-sense RNA virus]]es
 +
*[[Negative-sense ssRNA virus|Negative-sense RNA virus]]es
 +
*[[Retrovirus]]es
 +
*[[Satellite virus]]es
  
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A database of RNA sequences and secondary structures is available from [http://www.sanger.ac.uk/Software/Rfam/index.shtml Rfam], analyses and links to RNA analysis tools are available from [http://wikiomics.org/wiki/List_of_articles#RNA Wikiomics].
+
==History==
 +
Nucleic acids were discovered in 1868 by [[Johann Friedrich Miescher]] (1844-1895), who called the material 'nuclein' since it was found in the nucleus. It was later discovered that prokaryotic cells, which do not have a nucleus, also contain nucleic acids. The role of RNA in protein synthesis had been suspected since 1939, based on experiments carried out by [[Torbjörn Oskar Caspersson|Torbjörn Caspersson]], [[Jean Brachet]] and [[Jack Schultz]]. [[Hubert Chantrenne]] elucidated the messenger role played by RNA in the synthesis of [[protein]]s in [[Ribosomes|ribosome]]. Finally, [[Severo Ochoa]] discovered the RNA, winning Ochoa the 1959 [[Nobel Prize for Medicine]]. The sequence of the 77 nucleotides of a [[yeast]] RNA was found by [[Robert W. Holley]] in 1964, winning Holley the 1968 [[Nobel Prize for Medicine]]. In [[1976]], [[Walter Fiers]] and his team at the [[University of Ghent]] determined the complete nucleotide sequence of [[bacteriophage MS2]]-RNA.<ref>Fiers W et al., Complete nucleotide-sequence of bacteriophage MS2-RNA - primary and secondary structure of replicase gene, Nature, 260, 500-507, 1976</ref>
  
 
==References==
 
==References==
−
<references/>
+
{{reflist}}
  
 
==External links==
 
==External links==
−
* [http://miracle.igib.res.in/ RNA@IGIB]group at the Institute of Genomics and Integrative Biology working on RNA biology
+
* [http://www.imb-jena.de/RNA.html RNA World website]
 +
* [http://ndbserver.rutgers.edu/atlas/xray/ Nucleic Acid Database] Images of DNA, RNA and complexes.
 +
* [http://rnajunction.abcc.ncifcrf.gov/ RNAJunction Database]: Extracted atomic models of RNA junction and kissing loop structures.
  
 +
== See also==
 +
<div style="-moz-column-count:3; column-count:3;">
 +
* [[Antisense mRNA]]
 +
* [[Genetics]]
 +
* [[Molecular biology]]
 +
* [[Phosphoramidite]]
 +
* [[Quantification of nucleic acids]]
 +
* [[RNA interference]] (RNAi)
 +
* [[RNA Ontology Consortium]]
 +
* [[Sequence profiling tool]]
 +
* [[Double-stranded RNA viruses]]
 +
</div>
 +
{{Nucleic acids}}
  
−
== See also ==
 
−
*[[Antisense mRNA]]
 
−
*[[Genetics]]
 
−
*[[Molecular biology]]
 
−
*[[RNAi]]
 
−
*[[RNA Ontology Consortium]]
 
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*[[RNA world hypothesis]]
 
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*[[Severo Ochoa]]
 
−
*[[Sequence profiling tool]]
 
−
{{Nucleic acids}}
 
  
 
[[Category:Life sciences]]
 
[[Category:Life sciences]]
−
{{credit|104879363}}
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{{credit|RNA|176394201}}

Revision as of 22:13, 7 December 2007


File:Pre-mRNA-1ysv.JPG
A hairpin loop from a pre-mRNA. Notice the single strand and its nitrogen-rich (blue) bases and oxygen-rich (red) backbone.

Ribonucleic acid or RNA is a nucleic acid, consisting of many nucleotides that form a polymer. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA plays several important roles in the processes of translating genetic information from deoxyribonucleic acid (DNA) into proteins. One type of RNA acts as a messenger between DNA and the protein synthesis complexes known as ribosomes, others form vital portions of the structure of ribosomes, act as essential carrier molecules for amino acids to be used in protein synthesis, or change which genes are active.

RNA is very similar to DNA, but differs in a few important structural details: 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 uses the nucleotide uracil in its composition, instead of 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 them guided by non-coding RNAs.

Overview

A nucleic acid is a complex, high-molecular-weight macromolecule composed of nucleotide chains whose sequence of bases conveys genetic information. The connectedness of living organisms can be seen in the fact that nucleic acids are found in all living cells and in viruses, and the flow of genetic information is essentially the same in all organisms.

The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The main role of DNA is the long-term storage of genetic information. DNA is often compared to a blueprint, since it contains instructions for constructing other components of the cell, such as proteins and RNA molecules. The DNA segments that carry genetic information are called genes, but other DNA sequences have structural purposes or are involved in regulating the expression of genetic information.

Although RNA may serve as a genetic blueprint for certain viruses, it plays a diversity of roles. RNA may be thought of as the intermediate between the DNA blueprint and the actual workings of the cell, serving as the template for the synthesis of proteins from the genetic information stored in DNA. Some RNA molecules (called ribozymes) are also involved in the catalysis of biochemical reactions.

Nucleic acids are polymers of repeating units (called monomers). Specifically, they consist of long chains of nucleotide monomers connected by covalent chemical bonds. RNA molecules may contain as few as 75 nucleotides or more than 5,000 nucleotides, while a DNA molecule may be composed of more than 1,000,000 nucleotide units.

A nucleotide is a chemical compound with three components: a nitrogen-containing base, a pentose (five-carbon) sugar, and one or more phosphate groups. The nitrogen-containing base of a nucleotide (also called the nucleobase) is typically a derivative of either purine or pyrimidine. The most common nucleotide bases are the purines adenine and guanine and the pyrimidines cytosine and thymine (or uracil in RNA).

The sugar component is either deoxyribose or ribose. (“Deoxy” simply indicates that the sugar lacks an oxygen atom present in ribose, the parent compound.)

There are two major compositional differences between RNA and DNA:

  1. The sugar units in RNA molecules are riboses, while DNA is built of nucleotides with a deoxyribose sugar.
  2. One of the four major nucleobases in RNA is uracil (U) instead of thymine (T).

RNA is usually single-stranded, but it may contain double-helical regions where a given strand has folded back on itself.


Chemical and Stereochemical structure

Base-pairing in a siRNA segment, a double-stranded type of RNA. Hydrogen atoms are not shown.

RNA is a polymer with a ribose and phosphate backbone and four different nucleotide 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. 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.

There are also numerous modified bases and sugars found in RNA that serve many different roles. 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). Another notable modified base is hypoxanthine (a deaminated guanine base whose nucleoside is called inosine). Inosine plays a key role in the Wobble Hypothesis of the genetic code. There are nearly 100 other naturally occurring modified nucleosides, of which pseudouridine and nucleosides with 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, implying that they are important for normal function.

The most 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 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 results 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

Left: An RNA strand, with its nitrogenous bases. Right: Double-stranded 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. Secondly, while DNA contains deoxyribose, RNA contains ribose, (there is no hydroxyl group attached to the pentose ring in the 2' position in DNA, whereas RNA has two hydroxyl groups). These hydroxyl groups make RNA less stable than DNA because it is more prone to hydrolysis. Thirdly, the complementary nucleotide to adenine is not thymine, as it is in DNA, but rather uracil, which is an unmethylated form of thymine.

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 — an enzyme that catalyzes peptide bond formation — revealed that its active site is composed entirely of RNA.

Synthesis

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.[1]

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.[2] Also, it is known that RNA-dependent RNA polymerases are required for the RNA interference pathway in many organisms.[3]

Biological roles

Messenger RNA (mRNA)

Main article: Messenger RNA

Messenger RNA is RNA that carries information from DNA to the ribosome sites of protein synthesis in the cell. In eukaryotic cells, once mRNA has been transcribed from DNA, it is "processed" before being exported from the nucleus into 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, usually with the assistance of ribonucleases.

Non-coding RNA

RNA genes (also known as non-coding RNA or small RNA) are genes that encode RNA which 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. Two other groups of non-coding RNA are microRNAs (miRNA) which regulate the expression of genes through a process called RNA interference (RNAi), and small nuclear RNAs (snRNA), a diverse class that includes for example the RNAs that form spliceosomes that excise introns from pre-mRNA.[4]

Ribosomal RNA (rRNA)

Main article: Ribosomal RNA

Ribosomal RNA is the catalytic component of the ribosomes, the protein synthesis 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, 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.

Transfer RNA (tRNA)

Main article: Transfer RNA

Transfer RNA is a small RNA chain of about 74-95 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. It is a type of non-coding RNA.

Catalytic RNA

Main article: Ribozyme

Although RNA contains only four bases, in comparison to the twenty-odd amino acids commonly found in proteins, certain 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

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 called dsRNA viruses. In eukaryotes, long RNA such as viral RNA can trigger RNA interference, where short dsRNA molecules called siRNAs (small interfering RNAs) can cause enzymes to break down specific mRNAs or silence the expression of genes. siRNA can also increase the transcription of a gene, a process called RNA activation.[5] siRNA is often confused with miRNA; siRNAs are double-stranded, whereas miRNAs are single-stranded.

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

Secondary structure of an RNA from a telomerase.

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. 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.[6] 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.

List of RNA types

Type Function Distribution
mRNA Codes for protein All cells
rRNA Translation All cells
tRNA Translation All cells
snRNA RNA modification All cells
snoRNA RNA modification All cells
miRNA Gene regulation Eukaryotes
piRNA Gene regulation Animal germline cells
siRNA Gene regulation Eukaryotes
Antisense mRNA Preventing translation Bacteria
tmRNA Terminating translation Bacteria
SRP RNA mRNA tagging for export All cells
Ribozyme Catalysis All cells
Transposon Self-propagating All cells
Viroid Self-propagating Infected plants

In addition, the genome of many types of viruses consists of RNA, namely:

  • Double-stranded RNA viruses
  • Positive-sense RNA viruses
  • Negative-sense RNA viruses
  • Retroviruses
  • Satellite viruses

History

Nucleic acids were discovered in 1868 by Johann Friedrich Miescher (1844-1895), who called the material 'nuclein' since it was found in the nucleus. It was later discovered that prokaryotic cells, which do not have a nucleus, also contain nucleic acids. The role of RNA in protein synthesis had been suspected since 1939, based on experiments carried out by Torbjörn Caspersson, Jean Brachet and Jack Schultz. Hubert Chantrenne elucidated the messenger role played by RNA in the synthesis of proteins in ribosome. Finally, Severo Ochoa discovered the RNA, winning Ochoa the 1959 Nobel Prize for Medicine. The sequence of the 77 nucleotides of a yeast RNA was found by Robert W. Holley in 1964, winning Holley the 1968 Nobel Prize for Medicine. In 1976, Walter Fiers and his team at the University of Ghent determined the complete nucleotide sequence of bacteriophage MS2-RNA.[7]

References
ISBN links support NWE through referral fees

  1. ↑ Evgeny Nudler, Max E. Gottesman (2002). Transcription termination and anti-termination in E. coli. Genes to Cells 7: 755-768.[1]
  2. ↑ Jeffrey L Hansen, Alexander M Long, Steve C Schultz (1997). Structure of the RNA-dependent RNA polymerase of poliovirus. Structure 5 (8): 1109-1122.
  3. ↑ Paul Ahlquist (2002). RNA-Dependent RNA Polymerases, Viruses, and RNA Silencing. Science 296 (5571): 1270-1273.
  4. ↑ Berg, JM and JL Tymoczko, L Stryer (2002). Biochemistry, 5th Edition, WH Freeman and Company, 781-808. ISBN 0-7167-4684-0. 
  5. ↑ Doran G (2007). RNAi – Is one suffix sufficient?. Journal of RNAi and Gene Silencing 3 (1): 217-219.
  6. ↑ Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH (2004). Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. U. S. A. 101 (19): 7287-7292.
  7. ↑ Fiers W et al., Complete nucleotide-sequence of bacteriophage MS2-RNA - primary and secondary structure of replicase gene, Nature, 260, 500-507, 1976

External links

See also

  • Antisense mRNA
  • Genetics
  • Molecular biology
  • Phosphoramidite
  • Quantification of nucleic acids
  • RNA interference (RNAi)
  • RNA Ontology Consortium
  • Sequence profiling tool
  • Double-stranded RNA viruses
Nucleic acids edit
Nucleobases: Adenine - Thymine - Uracil - Guanine - Cytosine - Purine - Pyrimidine
Nucleosides: Adenosine - Uridine - Guanosine - Cytidine - Deoxyadenosine - Thymidine - Deoxyguanosine - Deoxycytidine
Nucleotides: AMP - UMP - GMP - CMP - ADP - UDP - GDP - CDP - ATP - UTP - GTP - CTP - cAMP - cGMP
Deoxynucleotides: dAMP - dTMP - dUMP - dGMP - dCMP - dADP - dTDP - dUDP - dGDP - dCDP - dATP - dTTP - dUTP - dGTP - dCTP
Nucleic acids: DNA - RNA - LNA - PNA - mRNA - ncRNA - miRNA - rRNA - siRNA - tRNA - mtDNA - Oligonucleotide

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