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20-September-2008 09:29:09 - Ribosomal RNA Ribosomal RNA rRNA is the central component of the ribosome, the protein manufacturing machinery of all living cells. The function of the rRNA is to provide a mechanism for decoding mRNA into amino acids and to interact with the tRNAs during translation by providing peptidyl transferase activity. Contents 1 Inside the ribosome 2 Prokaryotes vs. Eukaryotes 2.1 Prokaryotes 2.2 Eukaryotes 3 Translation 4 Importance of rRNA 5 Genes 6 See also 7 References 8 External links Inside the ribosome The ribosome is composed of two subunits, named for how rapidly they sediment when subject to centrifugation. tRNA is sandwiched between the small and large subunits and the ribosome catalyzes the formation of a peptide bond between the 2 amino acids that are contained in the tRNA. The 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. Prokaryotes vs. Eukaryotes Both prokaryotic and eukaryotic can be broken down into two subunits the S in 16S represents Svedberg units: Type Size Large subunit Small subunit prokaryotic 70S 50S 5S, 23S 30S 16S eukaryotic 80S 60S 5S, 5.8S, 28S 40S 18S Note that the S units of the subunits cannot simply be added because they represent measures of sedimentation rate rather than of mass. The sedimentation rate of each subunit is affected by its shape, as well as by its mass. Prokaryotes In prokaryotes a small 30S ribosomal subunit contains the 16S rRNA. The large 50S ribosomal subunit contains two rRNA species the 5S and 23S rRNAs. 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. 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. Eukaryotes Small subunit ribosomal RNA, 5' domain taken from the Rfam database. This example is RF00177 Small subunit ribosomal RNA, 5' domain taken from the Rfam database. This example is 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 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. Mammalian cells have 2 mitochondrial 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 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 1. 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.2 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-II3 and the European SSU database.4 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 See also Ribotyping References ^ Yusupov MM, Yusupova GZ, Baucom A, et al 2001. Crystal structure of the ribosome at 5.5 A resolution. Science 292 5518: 883-96. doi:10.1126/science.1060089. PMID 11283358. ^ Smit S, Widmann J, Knight R 2007. Evolutionary rates vary among rRNA structural elements. Nucleic Acids Res 35 10: 3339-3354. doi:10.1093/nar/gkm101. PMID 17468501. ^ Cole, JR; 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. doi:10.1093/nar/gkg039. PMID 12520046. ^ Wuyts, J; Van de Peer Y, Winkelmans T, De Wachter R 2002. The European database on small subunit ribosomal RNA. Nucleic Acids Res 30: 183-185. doi:10.1093/nar/30.1.183. PMID 11752288. External links Ribosomal RNA by Denis LJ Lafontaine and David Tollervey SILVA rRNA Database Project also includes Eukaryotes 18S and LSU 23S/28S European database on small subunit ribosomal RNA Ribosomal Database Project II 16S rRNA, BioMineWiki Rfam page for Small subunit ribosomal RNA, 5' domain MeSH Ribosomal+RNA v d e Types of nucleic acids Constituents Nucleobases | Nucleosides | Nucleotides | Deoxynucleotides Ribonucleic acids RNA | mRNA pre-mRNA/hnRNA | tRNA | rRNA | aRNA | gRNA | miRNA | ncRNA | piRNA | shRNA | siRNA | snRNA | snoRNA | stRNA | ta-siRNA | tmRNA Deoxyribonucleic acids DNA | cDNA | gDNA | msDNA | mtDNA Nucleic acid analogues GNA | LNA | PNA | TNA | morpholino Cloning vectors phagemid | plasmid | lambda phage | cosmid | P1 phage | fosmid | BAC | YAC | HAC Major families of biochemicals Saccharides | Carbohydrates | Glycosides | | Amino acids | Peptides | Proteins | Glycoproteins | | Lipids | Terpenes | Steroids | Carotenoids Alkaloids | Nucleobases | Nucleic acids | | Enzyme cofactors | Flavonoids | Polyketides | Tetrapyrroles v d e Ribosomal RNA / ribosome subunits Prokaryotes 70S Large: 50S 5S, 23S Small: 30S 16S Eukaryotes 80S Large: 60S 5S, 5.8S, 28S Small: 40S 18S Retrieved from http://en..org/wiki/Ribosomal_RNA Categories: Protein biosynthesis | RNA | Non-coding RNA | Ribosomal RNA | Ribozymes Views Article Discussion this page History Personal tools Log in / create account Navigation Main page Contents Featured content Current events Random article Search Go Search Interaction Community portal Recent changes Contact Donate to Help Toolbox What links here Related changes Upload file Special pages Printable version Permanent link Cite this page Languages العربية Brezhoneg Català Česky Dansk Deutsch Ελληνικά Esperanto Español Français í•œêµì–´ Italiano עברית Latina Nederlands 日本語 Occitan Polski Português РуÑ?Ñ?кий SlovenÄ?ina Svenska Türkçe ä¸æ–‡ This page was last modified on 21 July 2008, at 15:04
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