Ribosome

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Ribosome

A ribosome is an organelle composed of ribosomal RNA and ribosomal proteins (known as a Ribonucleoprotein or RNP). It translates Messenger RNA (mRNA) into a polypeptide chain (e.g., a protein). It can be thought of as a factory that builds a protein from a set of genetic instructions. Ribosomes can float freely in the cytoplasm (the internal fluid of the cell) or bind to the endoplasmic reticulum, or to the nuclear envelope. Since ribosomes are ribozymes, it is thought that they might be remnants of the RNA world.

The structure and function of the ribosomes and associated molecules, known as the translational apparatus, has been of research interest since the mid 20^th century and is a very active field of study today.

Overview

Ribosomes consist of two subunits (Figure 1) that fit together (Figure 2) and work as one to translate the mRNA into a polypeptide chain during protein synthesis (Figure 3). Prokaryotic subunits consist of one or two and eukaryotic of one or three very large RNA molecules (known as ribosomal RNA or rRNA) and multiple smaller protein molecules. Crystallographic work has shown that there are no ribosomal proteins close to the reaction site for polypeptide synthesis. This suggests that the protein components of ribosomes act as a scaffold that may enhance the ability of rRNA to synthesise protein rather than directly participating in catalysis. (See: Ribozyme)

Ribosome locations

Free ribosomes

Free ribosomes occur in all cells, and also in mitochondria and chloroplasts of eukaryotic cells. Free ribosomes usually produce proteins used in the cytosol or organelle in which they occur. As the name implies, they are free in solution and not bound to anything within the cell.

Membrane bound ribosomes

When certain proteins are synthesized by a ribosome they can become "membrane-bound". The newly produced polypeptide chains are inserted directly into the endoplasmic reticulum by the ribosome and are then transported to their destinations. Bound ribosomes usually produce proteins that are used within the cell membrane or are expelled from the cell via exocytosis.

Structure and function

The ribosomal subunits of prokaryotes and eukaryotes are quite similar. However, prokaryotes have 70S ribosomes, each consisting of a (small) 30S and a (large) 50S subunit, whereas eukaryotes have 80S ribosomes, each consisting of a (small) 40S and a bound (large) 60S subunit. However, the ribosomes found in chloroplasts and mitochondria of eukaryotes are 70S, this being but one of the observations supporting the endosymbiotic theory. The unit "S" means Svedberg units, a measure of the rate of sedimentation of a particle in a centrifuge, where the sedimentation rate is associated with the size of the particle. It is important to note that Svedberg units are not additive - two subunits together can have Svedberg values that do not add up to that of the entire ribosome. This is resulting from the loss of surface area when the two subunits are bound. In addition, the ungainly shape of the fully assembled ribosome has different aquadynamic properties from the two unbound sununits.

The differences between the prokaryotic and eukaryotic ribosomes are exploited by humans since the 70S ribosomes are vulnerable to some antibiotics that the 80S ribosomes are not. This helps create drugs that can destroy a bacterial infection without harming the animal/human host's cells. Even though human mitochondria possess 70S ribosomes, mitochondria are not effected by these antibiotics because the mitochondria is covered by a double membrane that does not admit these antibiotics into the organelle.

In Figure 3, both ribosomal subunits (small and large) assemble at the start codon (the 5' end of the mRNA). The ribosome uses tRNA (transfer RNAs which are RNA molecules that carry an amino acid and present the matching anti-codon, according to the genetic code, to the ribosome) which matches the current codon (triplet) on the mRNA to append an amino acid to the polypeptide chain. This is done for each triplet on the mRNA, while the ribosome moves towards the 3' end of the mRNA. Usually in bacterial cells, several ribosomes are working parallel on a single mRNA, forming what we call a polyribosome or polysome.

Atomic structure

The general molecular structure of the ribosome has been known for several decades, but recently its structure has been achieved at novel resolutions, in the order of a few angstroms.

The atomic structure of the 50S large subunit ribosome from the archeal, Haloarcula marismortui was published in Science on August 11, 2000 by N. Ban, et al.Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science. 2000 Aug 11;289(5481):905-20.. PMID 10937989

Soon after the structure of the 30S from Thermus thermophilus was published in Cell on September 1, 2000, by F. Schluenzen et. al..Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A. Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution. Cell. 2000 Sep 1;102(5):615-23. PMID 11007480 Shortly after a more detailed structure was published in Nature on September 21, 2000 by B. T. Wimberly, et al..Wimberly BT, Brodersen DE, Clemons WM Jr, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature. 2000 Sep 21;407(6802):327-39. PMID 11014182

Using these coordinates, M. M. Yusupov, et al.Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF. Crystal structure of the ribosome at 5.5 A resolution. Science. 2001 May 4;292(5518):883-96. Epub 2001 Mar 29. PMID 11283358 were able to reconstruct the entire Thermus thermophilus 70S particle at low resolution, which was published in Science on May 4 2001.

More recently the structure of the E. coli 70S ribosome was determined at 3.5 angstroms by Schuwirth et al. (Science, 2005)Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH. Structures of the bacterial ribosome at 3.5 A resolution. Science. 2005 Nov 4;310(5749):827-34. PMID 16272117. Also an EM structure was recently published by Mitra et al. (Nature, 2005)Mitra K, Schaffitzel C, Shaikh T, Tama F, Jenni S, Brooks CL 3rd, Ban N, Frank J. Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature. 2005 Nov 17;438(7066):318-24. PMID 16292303 which depicts a ribosome at 11-15 angstroms in the act of passing a newly synthesized protein strand into a translocation channel.

References

External links

70S Ribosome Architecture - Animation of a working Ribosome. Requires the Chime browser plugin from http://www.mdl.com/products/framework/chime/ where registration is required.
Lab computer simulates ribosome in motion

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