Difference between revisions of "Ribosomal RNA" - New World Encyclopedia

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A ribosome can be thought of as a giant [[enzyme]] that builds proteins. Its enzymatic activity derives from the presence of the ribosomal RNA (rRNA), which performs the catalytic processes for the synthesis. Meanwhile, the protein portions of the ribosome support the function of the rRNA. More than half the weight of a ribosome is RNA (Alberts et al. 1989).
 
A ribosome can be thought of as a giant [[enzyme]] that builds proteins. Its enzymatic activity derives from the presence of the ribosomal RNA (rRNA), which performs the catalytic processes for the synthesis. Meanwhile, the protein portions of the ribosome support the function of the rRNA. More than half the weight of a ribosome is RNA (Alberts et al. 1989).
  
There are numerous ribosomes in cells—as many as 10 million in a single mammalian cell. Such a cell would need to construct ten million copies of each type of ribosomal RNA molecule. While proteins are rapidly constructed, because each of the many mRNA molecules transcribed from the gene may be translated into as many as 10 protein molecules per minute, and 10,000 protein molecules per mRAN molecule in each cell generation, synthesis of rRNA is not so amplified since these molecules are the final gene product (Alberts et al. 1989). However, adequate rRNA is produced because cells contain multiple copies of the genes that code for rRNA (rRNA genes) (Alberts et al. 1989). Human cells contain about 200 rRNA genes per haploid genome (Alberts et al. 1989).   
+
There are numerous ribosomes in cells—as many as 10 million in a single mammalian cell. Such a cell would need to construct ten million copies of each type of ribosomal RNA molecule. While proteins are rapidly constructed, because each of the many mRNA molecules transcribed from the gene may be translated into as many as 10 protein molecules per minute, and 10,000 protein molecules per mRAN molecule in each cell generation, synthesis of rRNA is not so amplified since these molecules are the final gene product (Alberts et al. 1989). However, adequate rRNA is produced because cells contain multiple copies of the genes that code for rRNA (rRNA genes) (Alberts et al. 1989). Human cells contain more than 200 rRNA genes per haploid genome.   
  
 
Ribosomes are composed of two subunits, named for how rapidly they sediment when subjected to [[centrifugation]]. tRNA is sandwiched between the small and large subunits and the ribosome catalyzes the formation of a peptide bond between the two amino acids that are contained in the tRNA.  
 
Ribosomes are composed of two subunits, named for how rapidly they sediment when subjected to [[centrifugation]]. tRNA is sandwiched between the small and large subunits and the ribosome catalyzes the formation of a peptide bond between the two amino acids that are contained in the tRNA.  
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Prokaryote ribosomes are comparatively smaller than eukaryote ribosomes, with a sedimentation coefficient of 70 Svedberg units (abbreviated as 70S), while eukaryote ribosomes have a sedimentation coefficient of 80 Svedberg units (80S).
 
Prokaryote ribosomes are comparatively smaller than eukaryote ribosomes, with a sedimentation coefficient of 70 Svedberg units (abbreviated as 70S), while eukaryote ribosomes have a sedimentation coefficient of 80 Svedberg units (80S).
  
Both [[prokaryotic]] and [[eukaryotic]] ribosomes can be broken down into two subunits, with one subunit larger in size and with a dome-like shape and one subunit smaller and located above the larger one, forming a cap-like structure. Each 70S ribosome of prokaryots has a small subunit of 30S and a large subunit of 50S, while each 80S ribosome comprises a small subunit of 40S and a large subunit of 60S. Note that Svedberg measures are not additive because sedimentation rate depends on both mass and surface area.
+
Both [[prokaryotic]] and [[eukaryotic]] ribosomes can be broken down into two subunits, with one subunit larger in size and with a dome-like shape and one subunit smaller and located above the larger one, forming a cap-like structure. Each 70S ribosome of prokaryots has a small subunit of 30S and a large subunit of 50S, while each 80S ribosome comprises a small subunit of 40S and a large subunit of 60S. Note that Svedberg measures are not additive because sedimentation rate depends on both mass and surface area.  
  
 
While the ribosomal subunits are quite similar between prokaryotes and eukaryotes, the 70S ribosomes contain proportionally more RNA than protein, while the 80S ribosomes are composed of less RNA than protein. For example, pea seedlines ribosomes have about 40 percent rRNA and 60 percent protein, while ''E. coli'' ribosomes contain 63 percent rRNA and 37 percent protein. In comparing the two subunits themselves, the proportions of rRNA and protein are approximately equal.
 
While the ribosomal subunits are quite similar between prokaryotes and eukaryotes, the 70S ribosomes contain proportionally more RNA than protein, while the 80S ribosomes are composed of less RNA than protein. For example, pea seedlines ribosomes have about 40 percent rRNA and 60 percent protein, while ''E. coli'' ribosomes contain 63 percent rRNA and 37 percent protein. In comparing the two subunits themselves, the proportions of rRNA and protein are approximately equal.
  
The 70S ribosomes have three different types of rRNA: 23S rRNA, 16S rRNA, and 5S r RNA. There are four different types of rRNA in 80s ribosomes: 28s rRNA (but 25-26S rRNA in plants, [[fungi]], and [[protozoan]]s), '''18S rRNA, 5S rRNA, and 5.8S rRNA. These are organized as follows:
+
The 70S ribosomes have three different types of rRNA: 23S rRNA, 16S rRNA, and 5S r RNA. There are four different types of rRNA in 80s ribosomes: 28s rRNA (but 25-26S rRNA in plants, [[fungi]], and [[protozoan]]s), 18S rRNA, 5S rRNA, and 5.8S rRNA. These are organized as follows:
  
 
{| class="wikitable"
 
{| class="wikitable"
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  | eukaryotic || 80S || [[60S]] ([[5S ribosomal RNA|5S]], [[5.8S ribosomal RNA|5.8S]], 28S) || 40S (18S)  
 
  | eukaryotic || 80S || [[60S]] ([[5S ribosomal RNA|5S]], [[5.8S ribosomal RNA|5.8S]], 28S) || 40S (18S)  
 
|}
 
|}
 
 
===Prokaryotes===
 
In [[prokaryotes]] a small 30S ribosomal subunit contains the [[16S ribosomal RNA|16S]] rRNA.
 
 
The large 50S ribosomal subunit contains two rRNA species (the 5S and [[23S ribosomal RNA|23S]] rRNAs).
 
 
Bacterial [[16S ribosomal RNA|16S]], [[23S ribosomal RNA|23S]], and 5S rRNA genes are typically organized as a co-transcribed [[operon]].
 
 
There may be one or more copies of the [[operon]] dispersed in the [[genome]] (for example, ''[[Escherichia coli]]'' has seven).
 
 
[[Archaea]] contains either a single rDNA [[operon]] or multiple copies of the operon.
 
  
 
The 3' end of the [[16S ribosomal RNA|16S]] rRNA (in a ribosome) binds to a sequence on the 5' end of mRNA called the [[Shine-Dalgarno sequence]].
 
The 3' end of the [[16S ribosomal RNA|16S]] rRNA (in a ribosome) binds to a sequence on the 5' end of mRNA called the [[Shine-Dalgarno sequence]].
 
===Eukaryotes===
 
[[Image:RF00177.jpg|thumb|right|120px|Small subunit ribosomal RNA, 5' domain taken from the [[Rfam]] database. This example is [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00177 RF00177] ]]
 
In contrast, [[eukaryotes]] generally have many copies of the rRNA genes organized in tandem repeats; in humans approximately 300–400 rDNA repeats are present in five clusters (on [[chromosomes]] 13, 14, 15, 21 and 22). 
 
  
 
The [[18S ribosomal RNA|18S]] rRNA in most eukaryotes is in the small ribosomal subunit, and the large subunit contains three rRNA species (the [[5S ribosomal RNA|5S]], [[5.8S ribosomal RNA|5.8S]] and [[28S ribosomal RNA|28S]] rRNAs).
 
The [[18S ribosomal RNA|18S]] rRNA in most eukaryotes is in the small ribosomal subunit, and the large subunit contains three rRNA species (the [[5S ribosomal RNA|5S]], [[5.8S ribosomal RNA|5.8S]] and [[28S ribosomal RNA|28S]] rRNAs).
  
Mammalian cells have 2 mitochondrial ([[12S ribosomal RNA|12S]] and 16S) rRNA molecules and 4 types of cytoplasmic rRNA (28S, 5.8S, 5S (large ribosome subunit) and 18S (small subunit). 28S, 5.8S, and 18S rRNAs are encoded by a single transcription unit (45S) separated by 2 Internally transcribed spacer (ITS). The 45S rDNA organized into 5 clusters (each has 30-40 repeats) on chromosomes 13, 14, 15, 21, and 22. These are transcribed by [[RNA polymerase I]]. 5S occurs in [[Tandemly arrayed genes|tandem arrays]] (~200-300 true 5S genes and many dispersed pseudogenes), the largest one on the chromosome 1q41-42. 5S rRNA is transcribed by [[RNA polymerase III]].
+
The bacterial [[16S ribosomal RNA|16S]], [[23S ribosomal RNA|23S]], and 5S rRNA genes are typically organized as a co-transcribed [[operon]]. There may be one or more copies of the [[operon]] dispersed in the [[genome]] (for example, ''[[Escherichia coli]]'' has seven). [[Archaea]] contains either a single rDNA [[operon]] or multiple copies of the operon. In contrast, eukaryotes generally have many copies of the rRNA genes organized in tandem repeats; in humans, approximately 300–400 rDNA repeats are present in five clusters (on [[chromosomes]] 13, 14, 15, 21, and 22).
  
 +
Mammalian cells have two mitochondrial ([[12S ribosomal RNA|12S]] and 16S) rRNA molecules and four types of cytoplasmic rRNA (28S, 5.8S, 5S (large ribosome subunit) and 18S (small subunit). The 28S, 5.8S, and 18S rRNAs are encoded by a single transcription unit (45S) separated by two internally transcribed spacers (ITS). The 45S rDNA is organized into 5 clusters (each has 30-40 repeats) on chromosomes 13, 14, 15, 21, and 22. These are transcribed by [[RNA polymerase I]]. 5S occurs in [[Tandemly arrayed genes|tandem arrays]] (~200-300 true 5S genes and many dispersed pseudogenes), the largest one on the chromosome 1q41-42. 5S rRNA is transcribed by [[RNA polymerase III]].
  
The tertiary structure of the small subunit ribosomal RNA (SSU rRNA) has been resolved by X-ray crystallography <ref name="pmid11283358">{{cite journal | author = Yusupov MM, Yusupova GZ, Baucom A, ''et al'' | title = Crystal structure of the ribosome at 5.5 A resolution | journal = Science | volume = 292 | issue = 5518 | pages = 883–96 | year = 2001 | pmid = 11283358 | doi = 10.1126/science.1060089 }}</ref>. The secondary structure of SSU rRNA contains 4 distinct domains &mdash; the 5', central, 3' major and 3' minor domains. A model of the secondary structure for the 5' domain (500-800 nucleotides) is shown.
+
The tertiary structure of the small subunit ribosomal RNA (SSU rRNA) has been resolved by X-ray crystallography (Yusupov et al. 2001). The secondary structure of SSU rRNA contains 4 distinct domains&mdash;the 5', central, 3' major and 3' minor domains. A model of the secondary structure for the 5' domain (500-800 nucleotides) is shown.
  
 
==Translation==
 
==Translation==
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* [[MRPS1]], [[MRPS2]], [[MRPS3]], [[MRPS4]], [[MRPS5]], [[MRPS6]], [[MRPS7]], [[MRPS8]], [[MRPS9]], [[MRPS10]], [[MRPS11]], [[MRPS12]], [[MRPS13]], [[MRPS14]], [[MRPS15]], [[MRPS16]], [[MRPS17]], [[MRPS18]], [[MRPS19]], [[MRPS20]], [[MRPS21]], [[MRPS22]], [[MRPS23]], [[MRPS24]], [[MRPS25]], [[MRPS26]], [[MRPS27]], [[MRPS28]], [[MRPS29]], [[MRPS30]], [[MRPS31]], [[MRPS32]], [[MRPS33]], [[MRPS34]], [[MRPS35]]
 
* [[MRPS1]], [[MRPS2]], [[MRPS3]], [[MRPS4]], [[MRPS5]], [[MRPS6]], [[MRPS7]], [[MRPS8]], [[MRPS9]], [[MRPS10]], [[MRPS11]], [[MRPS12]], [[MRPS13]], [[MRPS14]], [[MRPS15]], [[MRPS16]], [[MRPS17]], [[MRPS18]], [[MRPS19]], [[MRPS20]], [[MRPS21]], [[MRPS22]], [[MRPS23]], [[MRPS24]], [[MRPS25]], [[MRPS26]], [[MRPS27]], [[MRPS28]], [[MRPS29]], [[MRPS30]], [[MRPS31]], [[MRPS32]], [[MRPS33]], [[MRPS34]], [[MRPS35]]
  
==See also==
+
 
*[[Ribotyping]]
 
  
 
==References ==
 
==References ==
{{reflist}}
+
<ref name="pmid11283358">{{cite journal | author = Yusupov MM, Yusupova GZ, Baucom A, ''et al'' | title = Crystal structure of the ribosome at 5.5 A resolution | journal = Science | volume = 292 | issue = 5518 | pages = 883–96 | year = 2001 | pmid = 11283358 | doi = 10.1126/science.1060089 }}</ref>.
 +
 
 +
Alberts
 +
 
 +
Alberts
  
 
==External links==
 
==External links==

Revision as of 21:56, 4 October 2008

Ribosomal RNA (rRNA) is a type of non-coding ribonucleic acid (RNA) that is a primary and permanent component of ribosomes, the small, cellular particles that form the site of protein synthesis in all living cells. As non-coding RNA, rRNA itself is not translated into a protein, but it does provide a mechanism for decoding messenger RNA (mRNA) into amino acids and interacting with the transfer RNAs (tRNAs) during translation by providing peptidyl transferase activity.


Overview

The protein manufacturing unit of all living cells, the ribosome, is composed of ribosomal RNA and protein. It is at the site of the ribosome that messenger RNA's (mRNA) code for linking amino acids together to form new proteins and where transfer RNAs (tRNA) transfer specific amino acids to the growing polypeptide chain during the translation of the mRNA into a protein. The chemical blueprint for the protein product is provided by the mRNA, derived from the DNA genes.

A ribosome can be thought of as a giant enzyme that builds proteins. Its enzymatic activity derives from the presence of the ribosomal RNA (rRNA), which performs the catalytic processes for the synthesis. Meanwhile, the protein portions of the ribosome support the function of the rRNA. More than half the weight of a ribosome is RNA (Alberts et al. 1989).

There are numerous ribosomes in cells—as many as 10 million in a single mammalian cell. Such a cell would need to construct ten million copies of each type of ribosomal RNA molecule. While proteins are rapidly constructed, because each of the many mRNA molecules transcribed from the gene may be translated into as many as 10 protein molecules per minute, and 10,000 protein molecules per mRAN molecule in each cell generation, synthesis of rRNA is not so amplified since these molecules are the final gene product (Alberts et al. 1989). However, adequate rRNA is produced because cells contain multiple copies of the genes that code for rRNA (rRNA genes) (Alberts et al. 1989). Human cells contain more than 200 rRNA genes per haploid genome.

Ribosomes are composed of two subunits, named for how rapidly they sediment when subjected to centrifugation. tRNA is sandwiched between the small and large subunits and the ribosome catalyzes the formation of a peptide bond between the two amino acids that are contained in the tRNA.

A ribosome also has 3 binding sites called A, P, and E.

  • The A site in the ribosome binds to an aminoacyl-tRNA (a tRNA bound to an amino acid).
  • The NH2 group of the aminoacyl-tRNA which contains the new amino acid attacks the carboxyl group of peptidyl-tRNA (contained within the P site), which contains the last amino acid of the growing chain called peptidyl transferase reaction.
  • The tRNA that was holding on the last amino acid is moved to the E site, and what used to be the aminoacyl-tRNA is now the peptidyl-tRNA.

A single mRNA can be translated simultaneously by multiple ribosomes.

Prokaryote versus eukaryote ribosomes and rRNA

Prokaryote ribosomes are comparatively smaller than eukaryote ribosomes, with a sedimentation coefficient of 70 Svedberg units (abbreviated as 70S), while eukaryote ribosomes have a sedimentation coefficient of 80 Svedberg units (80S).

Both prokaryotic and eukaryotic ribosomes can be broken down into two subunits, with one subunit larger in size and with a dome-like shape and one subunit smaller and located above the larger one, forming a cap-like structure. Each 70S ribosome of prokaryots has a small subunit of 30S and a large subunit of 50S, while each 80S ribosome comprises a small subunit of 40S and a large subunit of 60S. Note that Svedberg measures are not additive because sedimentation rate depends on both mass and surface area.

While the ribosomal subunits are quite similar between prokaryotes and eukaryotes, the 70S ribosomes contain proportionally more RNA than protein, while the 80S ribosomes are composed of less RNA than protein. For example, pea seedlines ribosomes have about 40 percent rRNA and 60 percent protein, while E. coli ribosomes contain 63 percent rRNA and 37 percent protein. In comparing the two subunits themselves, the proportions of rRNA and protein are approximately equal.

The 70S ribosomes have three different types of rRNA: 23S rRNA, 16S rRNA, and 5S r RNA. There are four different types of rRNA in 80s ribosomes: 28s rRNA (but 25-26S rRNA in plants, fungi, and protozoans), 18S rRNA, 5S rRNA, and 5.8S rRNA. These are organized as follows:

Type Size Large subunit Small subunit
prokaryotic 70S 50S (5S, 23S) 30S (16S)
eukaryotic 80S 60S (5S, 5.8S, 28S) 40S (18S)

The 3' end of the 16S rRNA (in a ribosome) binds to a sequence on the 5' end of mRNA called the Shine-Dalgarno sequence.

The 18S rRNA in most eukaryotes is in the small ribosomal subunit, and the large subunit contains three rRNA species (the 5S, 5.8S and 28S rRNAs).

The bacterial 16S, 23S, and 5S rRNA genes are typically organized as a co-transcribed operon. There may be one or more copies of the operon dispersed in the genome (for example, Escherichia coli has seven). Archaea contains either a single rDNA operon or multiple copies of the operon. In contrast, eukaryotes generally have many copies of the rRNA genes organized in tandem repeats; in humans, approximately 300–400 rDNA repeats are present in five clusters (on chromosomes 13, 14, 15, 21, and 22).

Mammalian cells have two mitochondrial (12S and 16S) rRNA molecules and four types of cytoplasmic rRNA (28S, 5.8S, 5S (large ribosome subunit) and 18S (small subunit). The 28S, 5.8S, and 18S rRNAs are encoded by a single transcription unit (45S) separated by two internally transcribed spacers (ITS). The 45S rDNA is organized into 5 clusters (each has 30-40 repeats) on chromosomes 13, 14, 15, 21, and 22. These are transcribed by RNA polymerase I. 5S occurs in tandem arrays (~200-300 true 5S genes and many dispersed pseudogenes), the largest one on the chromosome 1q41-42. 5S rRNA is transcribed by RNA polymerase III.

The tertiary structure of the small subunit ribosomal RNA (SSU rRNA) has been resolved by X-ray crystallography (Yusupov et al. 2001). The secondary structure of SSU rRNA contains 4 distinct domains—the 5', central, 3' major and 3' minor domains. A model of the secondary structure for the 5' domain (500-800 nucleotides) is shown.

Translation

Translation is the net effect of proteins being synthesized by ribosomes, from a copy (mRNA) of the DNA template in the nucleus. One of the components of the ribosome (16s rRNA) base pairs complementary to a sequence upstream of the start codon in mRNA.

Importance of rRNA

Ribosomal RNA characteristics are important in medicine and in evolution.

  • rRNA is the target of several clinically relevant antibiotics: chloramphenicol, erythromycin, kasugamycin, micrococcin, paromomycin, ricin, sarcin, spectinomycin, streptomycin, and thiostrepton.
  • rRNA is the most conserved (least variable) gene in all cells.[1] For this reason, genes that encode the rRNA (rDNA) are sequenced to identify an organism's taxonomic group, calculate related groups, and estimate rates of species divergence. For this reason many thousands of rRNA sequences are known and stored in specialized databases such as RDP-II[2] and the European SSU database.[3]

Genes

  • RPL1, RPL2, RPL3, RPL4, RPL5, RPL6, RPL7, RPL8, RPL9, RPL10, RPL11, RPL12, RPL13, RPL14, RPL15, RPL16, RPL17, RPL18, RPL19, RPL20, RPL21, RPL22, RPL23, RPL24, RPL25, RPL26, RPL27, RPL28, RPL29, RPL30, RPL31, RPL32, RPL33, RPL34, RPL35, RPL36, RPL37, RPL38, RPL39, RPL40, RPL41
  • MRPL1, MRPL2, MRPL3, MRPL4, MRPL5, MRPL6, MRPL7, MRPL8, MRPL9, MRPL10, MRPL11, MRPL12, MRPL13, MRPL14, MRPL15, MRPL16, MRPL17, MRPL18, MRPL19, MRPL20, MRPL21, MRPL22, MRPL23, MRPL24, MRPL25, MRPL26, MRPL27, MRPL28, MRPL29, MRPL30, MRPL31, MRPL32, MRPL33, MRPL34, MRPL35, MRPL36, MRPL37, MRPL38, MRPL39, MRPL40, MRPL41, MRPL42
  • RPS1, RPS2, RPS3, RPS4, RPS5, RPS6, RPS7, RPS8, RPS9, RPS10, RPS11, RPS12, RPS13, RPS14, RPS15, RPS16, RPS17, RPS18, RPS19, RPS20, RPS21, RPS22, RPS23, RPS24, RPS25, RPS26, RPS27, RPS28, RPS29
  • MRPS1, MRPS2, MRPS3, MRPS4, MRPS5, MRPS6, MRPS7, MRPS8, MRPS9, MRPS10, MRPS11, MRPS12, MRPS13, MRPS14, MRPS15, MRPS16, MRPS17, MRPS18, MRPS19, MRPS20, MRPS21, MRPS22, MRPS23, MRPS24, MRPS25, MRPS26, MRPS27, MRPS28, MRPS29, MRPS30, MRPS31, MRPS32, MRPS33, MRPS34, MRPS35


References
ISBN links support NWE through referral fees

[4].

Alberts

Alberts

External links

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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  1. Smit S, Widmann J, Knight R (2007). Evolutionary rates vary among rRNA structural elements. Nucleic Acids Res 35 (10): 3339–3354.
  2. Cole, JR and Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM (2003). The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31: 442–443.
  3. Wuyts, J and Van de Peer Y, Winkelmans T, De Wachter R (2002). The European database on small subunit ribosomal RNA. Nucleic Acids Res 30: 183–185.
  4. Yusupov MM, Yusupova GZ, Baucom A, et al (2001). Crystal structure of the ribosome at 5.5 A resolution. Science 292 (5518): 883–96.