RNA

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For other uses, see RNA (disambiguation).

A hairpin loop from a pre-mRNA. Highlighted are the nucleobases (green and the ribose-phosphate backbone (blue . Note that this is a single strand of RNA that folds back upon itself.

Ribonucleic acid (RNA is a ubi!uitous family of large biological molecules that perform multiple "ital roles in the coding, decoding, regulation, and e#pression of genes. $ogether %ith &NA, RNA comprises the nucleic acids, %hich, along %ith proteins, constitute the three ma'or macromolecules essential for all kno%n forms of life. (ike &NA, RNA is assembled as a chain of nucleotides, but is usually single-stranded. )ellular organisms usemessenger RNA (mRNA to con"ey genetic information (often notated using the letters *, A, +, and ) for the nucleotides guanine, adenine, uracil and cytosine that directs synthesis of specific proteins, %hile many "iruses encode their genetic information using an RNAgenome. ,ome RNA molecules play an acti"e role %ithin cells by cataly-ing biological reactions, controlling gene e#pression, or sensing and communicating responses to cellular signals. .ne of these acti"e processes is protein synthesis, a uni"ersal function %hereby mRNA molecules direct the

assembly of proteins on ribosomes. $his process uses transfer RNA(tRNA molecules to deli"er amino acids to the ribosome, %here ribosomal RNA (rRNA links amino acids together to form proteins.
Contents
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o o o o o o o

1 )omparison %ith &NA 2 ,tructure 3 ,ynthesis 4 $ypes of RNA 4.1 ."er"ie% 4.2 5n translation 4.3 Regulatory RNAs 4.4 5n RNA processing 4.6 RNA genomes 4.7 5n re"erse transcription 4.8 &ouble-stranded RNA 6 9ey disco"eries in RNA biology 7 ,ee also 8 References : ;#ternal links

Comparison with DNA[edit]

$hree-dimensional representation of the6<, ribosomal subunit. RNA is in ochre, protein in blue. $he acti"e site is in the middle (red .

$he chemical structure of RNA is "ery similar to that of &NA, but differs in three main %ays=

+nlike double-stranded &NA, RNA is a single-stranded molecule in many of its biological roles and has a much shorter chain of nucleotides. Ho%e"er, RNA can, by complementary base pairing, form intrastrand double heli#es, as in tRNA.

While &NA contains deoxyribose, RNA contains ribose (in deo#yribose there is no hydro#yl group attached to the pentose ring in the 2> position . $hese hydro#yl groups make RNA less stable than &NA because it is more prone to hydrolysis.

$he complementary base to adenine is not thymine, as it is in &NA, but rather uracil, %hich is an unmethylated form of thymine./10

(ike &NA, most biologically acti"e RNAs, including mRNA, tRNA, rRNA, snRNAs, and other noncoding RNAs, contain self-complementary se!uences that allo% parts of the RNA to fold /20 and pair %ith itself to form double helices. Analysis of these RNAs has re"ealed that they are highly structured. +nlike &NA, their structures do not consist of long double helices but rather collections of short helices packed together into structures akin to proteins. 5n this fashion, RNAs can achie"e chemical catalysis, like en-ymes./30 For instance, determination of the structure of the ribosome?an en-yme that cataly-es peptide bond formation?re"ealed that its acti"e site is composed entirely of RNA. /40

Structure[edit]

Watson-)rick base pairs in a siRNA(hydrogen atoms are not sho%n

;ach nucleotide in RNA contains a ribose sugar, %ith carbons numbered 1> through 6>. A base is attached to the 1> position, in general, adenine (A , cytosine () , guanine (* , oruracil (+ . Adenine and guanine are purines, cytosine, and uracil are pyrimidines. Aphosphate group is attached to the 3> position of one ribose and the 6> position of the ne#t. $he phosphate groups ha"e a negati"e charge each at physiological pH, making RNA a charged molecule (polyanion . $he bases form hydrogen bonds bet%een cytosine and guanine, bet%een adenine and uracil and bet%een guanine and uracil.
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Ho%e"er, other interactions are possible, such as a group of adenine bases binding to each other in

a bulge,/70 or the *NRA tetraloop that has a guanine@adenine base-pair./60

)hemical structure of RNA

An important structural feature of RNA that distinguishes it from &NA is the presence of ahydro#yl group at the 2> position of the ribose sugar. $he presence of this functional group causes the heli# to adopt the A-form geometry rather than the A-form most commonly obser"ed in &NA./80 $his results in a "ery deep and narro% ma'or groo"e and a shallo% and %ide minor groo"e. /:0 A second conse!uence of the presence of the 2>-hydro#yl group is that in conformationally fle#ible regions of an RNA molecule (that is, not in"ol"ed in formation of a double heli# , it can chemically attack the ad'acent phosphodiester bond to clea"e the backbone./B0

,econdary structure of a telomerase RNA.

RNA is transcribed %ith only four bases (adenine, cytosine, guanine and uracil , /1<0 but these bases and attached sugars can be modified in numerous %ays as the RNAs mature. Cseudouridine (D , in %hich the linkage bet%een uracil and ribose is changed from a )@N bond to a )@) bond, and ribothymidine ($ are found in "arious places (the most notable ones being in the $D) loop of tRNA ./110 Another notable modified base is hypo#anthine, a deaminated adenine base %hose nucleoside is called inosine (5 . 5nosine plays a key role in the %obble hypothesis of the genetic code./120 $here are more than 1<< other naturally occurring modified nucleosides, /130 $he greatest structural di"ersity of modifications can be found in tRNA,/140 %hile pseudouridine and nucleosides %ith 2>-.-

methylribose often present in rRNA are the most common./160 $he specific roles of many of these modifications in RNA are not fully understood. Ho%e"er, 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. /170 $he functional form of single-stranded RNA molecules, 'ust like proteins, fre!uently re!uires a specific tertiary structure. $he scaffold for this structure is pro"ided by secondary structural elements that are hydrogen bonds %ithin the molecule. $his leads to se"eral recogni-able EdomainsE of secondary structure like hairpin loops, bulges, and internal loops./180 ,ince RNA is charged, metal ions such as Fg2G are needed to stabilise many secondary and tertiary structures./1:0

Synthesis[edit]
,ynthesis of RNA is usually cataly-ed by an en-yme?RNA polymerase?using &NA as a template, a process kno%n astranscription. 5nitiation of transcription begins %ith the binding of the en-yme to a promoter se!uence in the &NA (usually found EupstreamE of a gene . $he &NA double heli# is un%ound by the helicase acti"ity of the en-yme. $he en-yme then progresses along the template strand in the 3H to 6H direction, synthesi-ing a complementary RNA molecule %ith elongation occurring in the 6H to 3H direction. $he &NA se!uence also dictates %here termination of RNA synthesis %ill occur./1B0 Crimary transcript RNAs are often modified by en-ymes after transcription. For e#ample, a poly(A tail and a 6> cap are added to eukaryotic pre-mRNA and introns are remo"ed by the spliceosome. $here are also a number of RNA-dependent RNA polymerases that use RNA as their template for synthesis of a ne% strand of RNA. For instance, a number of RNA "iruses (such as polio"irus use this type of en-yme to replicate their genetic material./2<0 Also, RNA-dependent RNA polymerase is part of the RNA interference path%ay in many organisms./210

Types of RNA[edit]
See also: List of RNAs

Overview[edit]

,tructure of a hammerhead ribo-yme, a ribo-yme that cuts RNA

Fessenger RNA (mRNA is the RNA that carries information from &NA to the ribosome, the sites of protein synthesis (translation in the cell. $he coding se!uence of the mRNA determines the amino acid se!uence in the protein that is produced./220 Fany RNAs do not code for protein ho%e"er (about B8I of the transcriptional output is non-protein-coding in eukaryotes
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$hese so-called non-coding RNAs (EncRNAE can be encoded by their o%n genes (RNA genes , but can also deri"e from mRNA introns./280 $he most prominent e#amples of non-coding RNAs are transfer RNA (tRNA and ribosomal RNA (rRNA , both of %hich are in"ol"ed in the process of translation.
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$here are also non-coding RNAs in"ol"ed in gene regulation, RNA processing and other roles.

)ertain RNAs are able to catalyse chemical reactions such as cutting and ligating other RNA molecules,/2:0 and the catalysis of peptide bond formation in the ribosomeJ/40 these are kno%n as ribo-ymes.

n translation[edit]
Fessenger RNA (mRNA carries information about a protein se!uence to the ribosomes, the protein synthesis factories in the cell. 5t is coded so that e"ery three nucleotides (a codon correspond to one amino acid. 5n eukaryotic cells, once precursor mRNA (pre-mRNA has been transcribed from &NA, it is processed to mature mRNA. $his remo"es itsintrons?non-coding sections of the pre-mRNA. $he mRNA is then e#ported from the nucleus to the cytoplasm, %here it is bound to ribosomes

and translated into its corresponding protein form %ith the help of tRNA. 5n prokaryotic cells, %hich do not ha"e nucleus and cytoplasm compartments, mRNA can bind to ribosomes %hile it is being transcribed from &NA. After a certain amount of time the message degrades into its component nucleotides %ith the assistance of ribonucleases./220 $ransfer RNA (tRNA is a small RNA chain of about :< nucleotides that transfers a specific amino acid to a gro%ing polypeptide chain at the ribosomal site of protein synthesis during translation. 5t has sites for amino acid attachment and an anticodon region for codonrecognition that binds to a specific se!uence on the messenger RNA chain through hydrogen bonding. /280 Ribosomal RNA (rRNA is the catalytic component of the ribosomes. ;ukaryotic ribosomes contain four different rRNA molecules= 1:,, 6.:,, 2:, and 6, rRNA. $hree of the rRNA molecules are synthesi-ed in the nucleolus, and one is synthesi-ed else%here. 5n the cytoplasm, ribosomal RNA and protein combine to form a nucleoprotein called a ribosome. $he ribosome binds mRNA and carries out protein synthesis. ,e"eral ribosomes may be attached to a single mRNA at any time. /220 Nearly all the RNA found in a typical eukaryotic cell is rRNA. $ransfer-messenger RNA (tmRNA is found in many bacteria and plastids. 5t tags proteins encoded by mRNAs that lack stop codons for degradation and pre"ents the ribosome from stalling. /2B0

Re!ulatory RNAs[edit]
,e"eral types of RNA can do%nregulate gene e#pression by being complementary to a part of an mRNA or a gene>s &NA. FicroRNAs(miRNAJ 21-22 nt are found in eukaryotes and act through RNA interference (RNAi , %here an effector comple# of miRNA and en-ymes can clea"e complementary mRNA, block the mRNA from being translated, or accelerate its degradation. /3<0/310 While small interfering RNAs (siRNAJ 2<-26 nt are often produced by breakdo%n of "iral RNA, there are also endogenous sources of siRNAs. /320/330 siRNAs act through RNA interference in a fashion similar to miRNAs. ,ome miRNAs and siRNAs can cause genes they target to be methylated, thereby decreasing or increasing transcription of those genes./340/360/370 Animals ha"e Ci%i-interacting RNAs (piRNAJ 2B-3< nt that are acti"e in germline cells and are thought to be a defense against transposons and play a role ingametogenesis./380/3:0 Fany prokaryotes ha"e )R5,CR RNAs, a regulatory system similar to RNA interference. /3B0 Antisense RNAs are %idespreadJ most do%nregulate a gene, but a fe% are acti"ators of transcription. /4<0 .ne %ay antisense RNA can act is by binding to an mRNA, forming double-stranded RNA that is en-ymatically degraded./410 $here are many long noncoding RNAs that regulate genes in eukaryotes, /420one such RNA is Kist, %hich coats one K chromosome in female mammals and inacti"ates it./430

An mRNA may contain regulatory elements itself, such as ribos%itches, in the 6> untranslated region or 3> untranslated regionJ thesecis-regulatory elements regulate the acti"ity of that mRNA.
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$he untranslated regions can also contain elements that regulate other genes. /460

n RNA processin![edit]

+ridine to pseudouridine is a common RNA modification.

Fany RNAs are in"ol"ed in modifying other RNAs. 5ntrons are spliced out of premRNA byspliceosomes, %hich contain se"eral small nuclear RNAs (snRNA ,/10 or the introns can be ribo-ymes that are spliced by themsel"es./470 RNA can also be altered by ha"ing its nucleotides modified to other nucleotides than A, ), * and +. 5n eukaryotes, modifications of RNA nucleotides are in general directed by small nucleolar RNAs (snoRNAJ 7<-3<< nt ,/280 found in the nucleolus and ca'al bodies. snoRNAs associate %ith en-ymes and guide them to a spot on an RNA by basepairing to that RNA. $hese en-ymes then perform the nucleotide modification. rRNAs and tRNAs are e#tensi"ely modified, but snRNAs and mRNAs can also be the target of base modification. /480/4:0 RNA can also be