rRNA

Ribosomal RNA (rRNA): is a component of the ribosomes, the protein synthetic factories in the cell. Eukaryotic ribosomes contain four different rRNA molecules: 18 s, 5.8 s, 28 s, and 5 s rRNA. Three of the rRNA molecules are synthesized in the nucleolus, and one is synthesized elsewhere. rRNA molecules are extremely abundant. They make up at least 80% of the RNA molecules found in a typical eukaryotic cell.
Synthesis of the three nucleolar rRNA molecules is unusual because they are made on one primary transcript that is chopped up into three mature rRNA molecules. These rRNA molecules and the 5 s rRNA combine with the ribosomal proteins in the nucleolus to form pre 40 s and pre 60 s ribosomal subunits. These pre-subunits are exported to the nucleus where they mature and assume their role in protein synthesis.
The rRNA molecules have several roles in protein synthesis. First, the 28 s rRNA has a catalytic role, it forms part of the peptidyl transferrase activity of the 60 s subunit. Second, 18s rRNA has a recognition role, involved in correct positioning of the mRNA and the peptidyl tRNA. Finally, the rRNA molecules have a structural role. They fold into three-dimensional shapes that form the scaffold on which the ribosomal proteins assemble. The model on the left shows a the three dimensional structure that the 5 s rRNA from the African frog, Xenopus laevis is thought to adopt.
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 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: 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.
Eukaryotes: 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).
The tertiary structure of the small subunit ribosomal RNA (SSU rRNA) has been resolved by xray crystallography. 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.