Ribosomal RNA

Ribosomal ribonucleic acid (rRNA) is the RNA component of the ribosome, the enzyme that is the site of protein synthesis in all living cells. Ribosomal RNA provides a mechanism for decoding mRNA into amino acids and interacts with tRNAs during translation by providing peptidyl transferase activity. The tRNAs bring the necessary amino acids corresponding to the appropriate mRNA codon.

Inside the ribosome
The ribosomal RNAs form two subunits, the large subunit (LSU) and small subunit (SSU). mRNA 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 rRNA.

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 amino (NH2) group of the aminoacyl-tRNA, which contains the new amino acid, attacks the ester linkage of peptidyl-tRNA (contained within the P site), which contains the last amino acid of the growing chain, forming a new peptide bond. This reaction is catalyzed by peptidyl transferase.
 * 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 the peptidyl-tRNA.

A single mRNA can be translated simultaneously by multiple ribosomes.

Prokaryotes vs. Eukaryotes
Both prokaryotic and eukaryotic ribosomes can be broken down into two subunits (the S in 16S represents Svedberg units):

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
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 (the 28S, 5.8S, 18S, and 5S subunits). The 28S, 5.8S, and 18S rRNAs are encoded by a single transcription unit (45S) separated by 2 internally transcribed spacers. 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. 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 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 one of the only gene products present in all cells. 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 and SILVA.

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, RPL28, 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

These denote genes encoding for the proteins of the ribosome and are transcribed as mRNA, not rRNA.