Difference between revisions of "RNA"

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A '''Ribonucleic acid''' (RNA) is a molecule found in all cells, comprised of many individual units of [[nucleic acid]].  It differs from DNA ([[deoxyribonucleic acid]]) in that it only contains a single, not double strand, and substitutes [[uracil]] for [[thymine]]. The sugar backbone of RNA is also composed of ribose (DNA contains deoxyribose). RNAs fall into several different categories, depending on function.
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'''Ribonucleic acid''' (RNA) is a family of biomolecules which perform several essential functions within all cells.  As a type of nucleic acid, RNA is structurally and chemically very similar to [[DNA]]; the two largest differences being that the RNA backbone contains ribose instead of 2'-deoxyribose and uses [[uracil]] instead of [[thymine]] as one of its four bases.<ref>Nelson & Cox. (2008). ''Principles of biochemistry''.</ref>
  
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The primary role of mRNA in is to transfer a copy of the information coded in DNA to a [[ribosome]] to be expressed as a protein, using a form of RNA known as messenger RNA ([[mRNA]]).  mRNA in eukaryotes undergoes spicing after transcription from DNA to remove [[introns]] or to use alternative splicing to create a different gene product. Alternatively-spliced transcripts can also express the same protein, but at different levels, due to the removal or addition of regulatory sequences.
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Unlike DNA, which is primarily used as a template for [[transcription]], RNA molecules perform a diverse set of functions within the cell.  Subsets of RNA are generally classified by their function, which can range from acting as the template for [[Translation (biology)|protein synthesis]] ("messenger RNA" or "[[mRNA]]") to performing [[ribozyme|enzymatic functions]]. Additionally, many viruses use RNA instead of DNA as their genetic material (e.g. [[retrovirus]]es).
  
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The main role of [[tRNA]], or transfer RNA is to carry an amino acid to the mRNA (while the mRNA is in the ribosome) during translation of the mRNA into a protein.
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As with DNA, RNAs can exist in single-stranded (annotated "ssRNA") or double-stranded ("dsRNA") forms; however, the vast majority of cellular RNAs are single-stranded.  dsRNAs generally function in post-transcriptional [[gene regulation]] or as viral genetic material.  Targeted degradation of dsRNAs is a major intracellular defence mechanism against viruses.<ref>Alberts et al. (2008). ''Molecular biology of the cell''.</ref><ref>Weaver, Robert F. ''Molecular Biology''. 4th ed. Boston: McGraw-Hill, 2008.</ref>
  
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The main role of [[rRNA]] or ribosomal RNA is to form the [[ribosome]].  RNA that has catalytic properties (such as the ribosome) is referred to as a [[ribozyme]].
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==Structure==
  
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Purification of RNA is problematic as enzymes that degrade RNA ([[RNases]]) are ubiquitous.  Successful RNA purification depends on degradation of the DNA template used via DNase and avoidance of RNase using sterile technique.
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Every nucleotide of RNA consists of a ribose molecule with a nitrogenous base attached to its 1' carbon and a phosphate group attached to its 5' carbon.  Individual RNA nucleotides are linked by a [[phosphodiester bond]] between the 3' carbon of one nucleotide's ribose and the 5' carbon on the next.
  
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The polio virus is an example of an organism which contains only RNA to carry its genetic information. Some [[protists]] such as ''Paramecium'' carry similar RNA genes in structures called micronuclei. These are involved in mating and replicate independently from the main cell nucleus.
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The four nitrogenous bases used in RNA are [[adenine]], [[guanine]], [[cytosine]], and [[uracil]].  Adenine and guanine are the ''purine'' bases, cytosine and uracil are the ''pyrimidine'' bases.  Like in DNA, these bases can hybridize through [[hydrogen bond]]s; adenine hybridizes with uracil and guanine hybridizes cytosine.
  
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==Prebiotic RNA Polymerization==
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Hybridization of nucleotides within RNA molecules allows for the formation of ''secondary structures'' such as RNA hairpins, these secondary structures give RNA molecules an overall ''tertiary structure'' which is often essential for the RNA to perform its function.  Additionally, RNAs can hybridize through base pairing with other RNAs or with complementary DNA sequences.
  
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===From Primordial Soup===
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==Function==
  
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John Sutherland from the University of Manchester, UK, have found the correct combination of primordial conditions for producing RNA. These findings may lead to a refinement of scientific theories related to the transition of natural nonbiotic molecules into the first elements of biological life.
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RNA performs a wide variety of functions within the cell.  Types of RNA are specified by the functions that they perform. More than 21 functional classes of RNA have been identified, the most common types are described below.
  
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From the paper entitle "Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions" in the peer-reviewed ''Nature'' journal, the authors document their methodologies. The scientists were able to repeatably create RNA structures from a joint precursors solution (pairing the bases and sugars in the molecule), a good blast of UV light, and 5 ingredients thought to be in abundance on the pre-biotic earth.
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===mRNA===
  
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This advancement may prove that the synthesis of the earliest life was far more simple than previously though.
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''Messenger RNAs'' ([[mRNA]]) are the template molecules which are ''translated'' into [[protein]]s by [[ribosome]]s.  They are generally synthesized by [[transcription]] of a DNA template (a [[gene]]) by [[RNA polymerase]], although some viral mRNAs are directly transcribed from an RNA template.
  
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<ref>http://www.newscientist.com/article/mg20227084.200-molecule-of-life-emerges-from-laboratory-slime.html</ref><ref>http://www.chemistry.manchester.ac.uk/aboutus/staff/showprofile.php?id=390</ref><ref>http://www.nature.com/nature/journal/v459/n7244/full/nature08013.html</ref>
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In [[eukaryote]]s, nascent RNA transcripts must generally be processed from ''pre-mRNA'' into mature mRNA, via ''RNA processing'', before they are exported from the nucleus to be translated into proteins.
  
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===From Clays===
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===rRNA===
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Research from Rensselaer Polytechnic Institute suggests that the formation of long strands of RNA may have been catalyzed by clays such as montmorillonite.  The charged clay surface attracts the nucleotides and the increased local concentration of nucleotides causes bond formation between nucleotides, forming a polymer of RNA.<ref>http://www.rpi.edu/dept/chem/chem_faculty/profiles/pdfs/ferris/Royal_Soc..pdf</ref><ref>http://www.rpi.edu/dept/chem/chem_faculty/profiles/pdfs/ferris/Alders.Mass_Spec.pdf</ref><ref>http://www.rpi.edu/dept/chem/chem_faculty/profiles/pdfs/ferris/Huang_MS_JACS_2006%203.pdf</ref>
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===From Ice===
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''Ribosomal RNAs'' ([[rRNA]]) are the RNA molecules that form a major component of the [[ribosome]]s.  There are three rRNAs in [[prokaryote]]s and four rRNAs in [[eukaryote]]s and [[archaea]]ns.
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Strands of RNA have been shown to form in salty ice water. David Deamer's lab at the University of California at Santa Cruz has found that the process of freezing a dilute solution of RNA nucleotides causes the nucleotides to become concentrated as ice crystals form, eventually resulting in the formation of strands of RNA. <ref>J. P. Dworkin, D. W. Deamer, S. A. Sandford, and L. J. Allamandola. 2001. Self-assembling amphiphilic molecules: Synthesis in simulated interstellar/precometary ices. Proc. Natl. Acad. Sci. USA 98:815-819.</ref>
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The genes encoding rRNAs are among the most highly conserved (low level of sequence variance between individuals and species) genes in any genome.  As such, rRNA sequences are often used to generate very precise phylogenetic trees.
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The 28S rRNA (23S rRNA in prokaryotes) is a [[ribozyme]], and is responsible for the aminoacyltransferase (polypeptide-lengthening) activity of the ribosome.
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===tRNA===
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''Transfer RNAs'' ([[tRNA]]) are the ''adapter molecules'' that recognize ''codons'' during translation and bring specific [[amino acids]] to the [[ribosome]] to be added to the growing [[protein|polypeptide]] chain.
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The "cloverleaf" tertiary structure of tRNAs is a common textbook example of the link between RNA structure and function.
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===microRNA===
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''Micro RNAs'' ([[microRNA]])are short RNA molecules involved in post-transcriptional [[gene regulation]].  microRNAs work by binding to complementary sequences on target mRNAs; thus targeting the mRNA for degradation via the [[RISC|RNA-induced silencing complex]] or, less commonly, blocking translation of the mRNA by [[steric hindrance|steric]] (mechanical) hindrance.
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In their mature, functional form, microRNA molecules are 20 to 24 nucleotides long. This length allows for microRNAs to have a very high degree of target specificity (some microRNAs may only have a single target mRNA).
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Because the mechanics of [[RNA polymerase]] require a minimum transcript length of about 50-100 nucleotides, precursor microRNAs are at least 80 nucleotides long (most are longer). As such, several different microRNAs are usually derived from a single precursor transcript.
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Together with siRNAs, microRNAs are a major component of ''gene regulatory networks'', which allow the cell to rapidly and efficiently respond to environmental stimuli.
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===siRNA===
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''Short interfering RNAs'' ([[siRNA]]) are short (~21 base pairs), double-stranded RNA molecules which function in a manner similar to microRNAs (described above).
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siRNAs are commonly used in research for targeted gene knockdown (blocking the expression of a specific gene) and they are also used in several gene therapies.
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===snRNA===
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''Small nuclear RNAs'' ([[snRNA]]) are involved in several different processes that occur within the nucleus, notably [[RNA splicing]] and the regulation of certain [[transcription factor]]s. They generally function in complexes with specific proteins; these snRNA and protein complexes are called ''small nuclear ribonucleoproteins'' ("snRNPs", colloquially pronounced "snurps").
  
 
==References==
 
==References==
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[[Category:Genetics]]
 
[[Category:Genetics]]
 
[[Category:Biochemistry]]
 
[[Category:Biochemistry]]
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[[Category:Biology]]

Latest revision as of 17:32, February 11, 2017

Ribonucleic acid (RNA) is a family of biomolecules which perform several essential functions within all cells. As a type of nucleic acid, RNA is structurally and chemically very similar to DNA; the two largest differences being that the RNA backbone contains ribose instead of 2'-deoxyribose and uses uracil instead of thymine as one of its four bases.[1]

Unlike DNA, which is primarily used as a template for transcription, RNA molecules perform a diverse set of functions within the cell. Subsets of RNA are generally classified by their function, which can range from acting as the template for protein synthesis ("messenger RNA" or "mRNA") to performing enzymatic functions. Additionally, many viruses use RNA instead of DNA as their genetic material (e.g. retroviruses).

As with DNA, RNAs can exist in single-stranded (annotated "ssRNA") or double-stranded ("dsRNA") forms; however, the vast majority of cellular RNAs are single-stranded. dsRNAs generally function in post-transcriptional gene regulation or as viral genetic material. Targeted degradation of dsRNAs is a major intracellular defence mechanism against viruses.[2][3]

Structure

Every nucleotide of RNA consists of a ribose molecule with a nitrogenous base attached to its 1' carbon and a phosphate group attached to its 5' carbon. Individual RNA nucleotides are linked by a phosphodiester bond between the 3' carbon of one nucleotide's ribose and the 5' carbon on the next.

The four nitrogenous bases used in RNA are adenine, guanine, cytosine, and uracil. Adenine and guanine are the purine bases, cytosine and uracil are the pyrimidine bases. Like in DNA, these bases can hybridize through hydrogen bonds; adenine hybridizes with uracil and guanine hybridizes cytosine.

Hybridization of nucleotides within RNA molecules allows for the formation of secondary structures such as RNA hairpins, these secondary structures give RNA molecules an overall tertiary structure which is often essential for the RNA to perform its function. Additionally, RNAs can hybridize through base pairing with other RNAs or with complementary DNA sequences.

Function

RNA performs a wide variety of functions within the cell. Types of RNA are specified by the functions that they perform. More than 21 functional classes of RNA have been identified, the most common types are described below.

mRNA

Messenger RNAs (mRNA) are the template molecules which are translated into proteins by ribosomes. They are generally synthesized by transcription of a DNA template (a gene) by RNA polymerase, although some viral mRNAs are directly transcribed from an RNA template.

In eukaryotes, nascent RNA transcripts must generally be processed from pre-mRNA into mature mRNA, via RNA processing, before they are exported from the nucleus to be translated into proteins.

rRNA

Ribosomal RNAs (rRNA) are the RNA molecules that form a major component of the ribosomes. There are three rRNAs in prokaryotes and four rRNAs in eukaryotes and archaeans.

The genes encoding rRNAs are among the most highly conserved (low level of sequence variance between individuals and species) genes in any genome. As such, rRNA sequences are often used to generate very precise phylogenetic trees.

The 28S rRNA (23S rRNA in prokaryotes) is a ribozyme, and is responsible for the aminoacyltransferase (polypeptide-lengthening) activity of the ribosome.

tRNA

Transfer RNAs (tRNA) are the adapter molecules that recognize codons during translation and bring specific amino acids to the ribosome to be added to the growing polypeptide chain.

The "cloverleaf" tertiary structure of tRNAs is a common textbook example of the link between RNA structure and function.

microRNA

Micro RNAs (microRNA)are short RNA molecules involved in post-transcriptional gene regulation. microRNAs work by binding to complementary sequences on target mRNAs; thus targeting the mRNA for degradation via the RNA-induced silencing complex or, less commonly, blocking translation of the mRNA by steric (mechanical) hindrance.

In their mature, functional form, microRNA molecules are 20 to 24 nucleotides long. This length allows for microRNAs to have a very high degree of target specificity (some microRNAs may only have a single target mRNA).

Because the mechanics of RNA polymerase require a minimum transcript length of about 50-100 nucleotides, precursor microRNAs are at least 80 nucleotides long (most are longer). As such, several different microRNAs are usually derived from a single precursor transcript.

Together with siRNAs, microRNAs are a major component of gene regulatory networks, which allow the cell to rapidly and efficiently respond to environmental stimuli.

siRNA

Short interfering RNAs (siRNA) are short (~21 base pairs), double-stranded RNA molecules which function in a manner similar to microRNAs (described above).

siRNAs are commonly used in research for targeted gene knockdown (blocking the expression of a specific gene) and they are also used in several gene therapies.

snRNA

Small nuclear RNAs (snRNA) are involved in several different processes that occur within the nucleus, notably RNA splicing and the regulation of certain transcription factors. They generally function in complexes with specific proteins; these snRNA and protein complexes are called small nuclear ribonucleoproteins ("snRNPs", colloquially pronounced "snurps").

References

  1. ↑ Nelson & Cox. (2008). Principles of biochemistry.
  2. ↑ Alberts et al. (2008). Molecular biology of the cell.
  3. ↑ Weaver, Robert F. Molecular Biology. 4th ed. Boston: McGraw-Hill, 2008.
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