Ribosome
From Proteopedia
IntroductionThe ribosome is a complex composed of RNA and protein that adds up to several million daltons in size and plays a critical role in the process of decoding the genetic information stored in the genome into protein as outlined in what is now known as the Central Dogma of Molecular Biology. Specifically, the ribosome carries out the process of translation, decoding the genetic information encoded in messenger RNA, one amino acid at a time, into newly synthesized polypeptide chains. Nobel Prize Winners and Other ContributorsVenkatraman Ramakrishnan of the M.R.C. Laboratory of Molecular Biology in Cambridge, England; Thomas A. Steitz of Yale University; and Ada E. Yonath of the Weizmann Institute of Science in Rehovot, Israel have been awarded the the 2009 Nobel Prize in Chemistry[1] for their landmark work revealing the atomic details of the molecular machine that make proteins in all cells, the ribosome. Their findings are the gloriously enlightening culmination of years of work[2], first heralded by Ada Yonath's report of crystals in 1980[3]. Others made significant contributions to the detailed structure of this machine, as poignantly summarized by Jeremy Berg, current Director of National Institute of General Medical Sciences, in his announcement The Nobel committee has the daunting challenge of limiting itself to up to three laureates for each prize. Several other long-time NIGMS grantees who also contributed greatly to our understanding of the structure and function of the ribosome include Peter Moore, Harry Noller and Joachim Frank. The American Society for Biochemistry and Molecular Biology posted an announcement of the prize echoing this sentiment as well. Impact of Ribosome StructureThe ribosome ranks among the known structures with highest impact. Imagine the wonder and thrill at suddenly knowing how tens of proteins and large and small RNAs fit together into the elegant machines that serve as the protein factories in every cell and organelle of every organism on the planet. The immense size of the ribosome and each of the two individual ribosomal subunits that come together to form the complete ribosome that is active in translation made for a daunting task in structure determination. These structures were at the time they were first determined, and remain (in 2009), the largest asymmetric molecules solved crystallographically. In addition to providing us immense insight into the general molecular and atomic details of protein synthesis in every organism on earth, the development of new antibiotics are likely to rely on this ground-breaking work. Ribosome Components
The small subunit of the prokaryotic ribosome sediments at 30S[4]. It is composed of a 16S chain of RNA about 1,500 bases long (~500 kDa), plus about 20 protein chains. The proteins in the first small subunit determined range from about 3 kDa to 29 kDa. The large subunit of the prokaryotic ribosome sediments at 50S. It is composed of two chains of RNA, a 23S chain (~3000 bases long, 946 kDa) and a 5S chain (~120 bases long, 39 kDa). Assembled with the RNA are about 30 protein chains. The proteins in the first large subunit determined range from 6 kDa to 37 kDa. See also Large Ribosomal Subunit of Haloarcula. The large subunit contains several Kink-turn motifs. The mitochindrial ribosome or mitoribosome is smaller than the the cytoplasmic ribosome with a small subunit which sediments at 28S and a large subunit which sediments at 39S. The whole mitoribosome sediments at 55S. Other macromolecules in a functioning ribosome include three transfer RNA molecules, messenger RNA, and the nascent protein chain. Thus, a complete functioning prokaryotic ribosome contains 7 RNA chains (including three tRNA's and one mRNA), 47 ribosomal protein chains, and one nascent protein chain. The total molecular mass is several million daltons. The cytoplasmic ribosomes of eukaryotes are larger with more RNA and proteins. Eukaryotic cytoplasmic ribosomes also have an additional RNA in the large subunit, the 5.8S rRNA, that is about 150 nts and related to the 5' end of prokaryotic rRNA. In regards to the size, the ribosomal subunits of budding yeast and humans sediment at 40S and 60S; the complete ribosome sediments at 80S and it is generally about another million daltons larger than the prokaryotic one. The Peptidyl Transferase Is A RibozymeThe small subunit of the ribosome is the main site of decoding, directing the interaction of the messenger RNA codon with the anticodon stem-loops of the proper transfer RNA. The formation of peptide bonds occurs in the large subunit where the acceptor-stems of the tRNAs are docked. However, it is important to keep in mind that in the active ribosome the two subunits are in contact via bridges, and the actions in one subunit affect the other as the process of translation advances through the stages of initiation, elongation, and termination. The initial determination of the atomic resolution structures of the subunits surprisingly revealed that RNA, but not protein, contributes directly to forming the site of both decoding and catalysis of peptide bond synthesis, with the ribosomal proteins only acting in an ancillary role, see ribozyme. (Examine the structural data concerning peptide bond synthesis here.) During the elongation stage of translation, new peptides are added to the carboxy-terminus of the growing nascent chain that is linked to the acceptor-end of the tRNA in the peptidyl or P site. As the nascent chain grows, it advances into a tunnel that passes through the large subunit, called the polypeptide exit tunnel. Several factors can interact at the site of extrusion of the nascent polypeptide chain to ensure proper folding or transport across a membrane. Additionally, during protein synthesis, many additional factors such as elongation factors (EF-Tu and EF-G) interact with the ribosome to elicit decoding and peptide bond synthesis accurately and efficiently. Structures of several of these factors in complex with the ribosome, as well as intermediate states in the process, are being observed now, building upon the first atomic structures. First Atomic-Resolution Ribosome StructuresThe particular structures for which the Nobel prize was awarded were published in 2000 and were subsequently refined or improved upon. All these structures were determined using proteins from extremophiles. Here are the links to the Proteopedia entries:
The Thermus thermophilus small ribosomal subunit is composed of a 16S chain of RNA about 1,522 bases long (494 kDa), plus 20 protein chains (S2-S20, THX). The protein chains range from 26 (THX, 3 kDa) to 256 amino acids (S2, 29 kDa).
Proteopedia Topic Pages Covering the Ribosome and Subunits
Ribosome 3D structuresSee Also
References
Additional Literature and Resources
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Wayne Decatur, Michal Harel, Jaime Prilusky, Eric Martz, Alexander Berchansky, Joel L. Sussman, Eran Hodis, David Canner, Margaret Franzen
