Ribosome

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Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). Side and front view.
(1) Head. (2) Platform. (3) Base. (4) Ridge. (5) Central protuberance. (6) Back. (7) Stalk. (8) Front.

A ribosome is an organelle in cells that assembles proteins. Ribosomes are 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.

Ribosomes were first observed in the mid-1950s by cell biologist George Palade in the electron microscope as dense particles or granules^[1] for which he would win the Nobel Prize. The term ribosome was proposed by scientist Richard B. Roberts in 1958:

During the course of the symposium a semantic difficulty became apparent. To some of the participants, microsomes mean the ribonucleoprotein particles of the microsome fraction contaminated by other protein and lipid material; to others, the microsomes consist of protein and lipid contaminated by particles. The phrase “microsomal particles” does not seem adequate, and “ribonucleoprotein particles of the microsome fraction” is much too awkward. During the meeting the word “ribosome” was suggested; this seems a very satisfactory name, and it has a pleasant sound. The present confusion would be eliminated if “ribosome” were adopted to designate ribonucleoprotein particles in the size range 20 to 100S.

—Roberts, R. B., Microsomal Particles and Protein Synthesis^[2]

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.

[edit] 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)

Figure 2 : Large (1) and small (2) subunit fit together (note this figure mislabels angstroms as nanometers)

[edit] Ribosome locations

[edit] Free ribosomes

Free ribosomes are "free" to move about anywhere in the cytoplasm (within the cell membrane). Proteins made by free ribosomes are used within the cell.

[edit] 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.

Free and membrane-bound ribosomes differ only in their spatial distribution; they are identical in structure and function. Whether the ribosome exists in a free or membrane-bound state depends on the presence of a ER-targeting signal sequence on the protein being synthesized.

[edit] Structure

The ribosomal subunits of prokaryotes and eukaryotes are quite similar^[3]

Prokaryotes have 70S ribosomes, each consisting of a (small) 30S and a (large) 50S subunit. Their 50S subunit is composed of a 5S RNA subunit with 120 nucleotides, a 23S RNA subunit with 2900 nucleotides, and 34 proteins. The 30S subunit has a 1540 nucleotide RNA subunit and 21 proteins ^[3].

Eukaryotes have 80S ribosomes, each consisting of a (small) 40S and (large) 60S subunit. Their 60S subunit is composed of a 5S RNA subunit with 120 nucleotides, a 28S RNA subunit with 4700 nucleotides, a 5.8S RNA subunit with 160 nucleotides, and ~49 proteins. The 40S subunit has a 1900 nucleotide RNA subunit and ~33 proteins ^[3].

The ribosomes found in chloroplasts and mitochondria of eukaryotes also consist of large and small subunits bound together with proteins into one 55S particle^[3]. These organelles are decendents of bacteria, so their ribosomes are still essentially bacterial^[4].

The various ribosome share a core structure which is quite similar despite the large differences in size. The extra RNA in the larger ribosomes is in several long continuous insertions, such that they form loops out of the core structure without disrupting or changing it^[3].

All of the catalytic activity of the ribosome is carried out by the RNA. The proteins reside on the surface and seem to function to stabilize the structure^[3].

The differences between the prokaryotic and eukaryotic ribosomes are exploited by pharmaceutical chemists to create antibiotics that can destroy a bacterial infection without harming the cells of the infected person. Due to the differences in their structures, the bacterial 70S ribosomes are vulnerable to these antibiotics while the eukaryotic 80S ribosomes are not. Even though mitochondria possess ribosomes decended from and similar to bacterial ribosomes, mitochondria are not affected by these antibiotics because they are surrounded by a double membrane that does not easily admit these antibiotics into the organelle^[5].

[edit] Atomic structure

Atomic structure of the 50S Subunit

The general molecular structure of the ribosome has been known since the early 1970s. in the early 2000s the structure has been achieved at high resolutions, in the order of a few angstroms.

The first papers giving the structure of the ribosome at atomic resolution, were published in rapid succession in late 2000 . First, the 50S large subunit ribosome from the archeal, Haloarcula marismortui was published^[6]. Soon after the structure of the 30S subunit from Thermus thermophilus was published.^[7] Shortly thereafter a more detailed structure was published.^[8] Early the next year (May 2001) these coordinates were used to reconstruct the entire T. thermophilus 70S particle at 5.5 Å resolution'^[9].

Two papers were published in November 2005 with high resolution structures of the Escherichia coli 70 S ribosome. First the structure was determined at 3.5 Å resolution using [x-ray cyrstallography]] ^[10]. Then two weeks later a structure based on cyro-electron microsopy was published^[11] which depicts the ribosome at 11-15 Å in the act of passing a newly synthesized protein strand into the protein-conducting channel.

[edit] Function

Ribosomes are the workhorses of protein biosynthesis, the process of translating messenger RNA (mRNA) into protein. The mRNA comprises a series of codons that dictate to the ribosome the sequence of the amino acids needed to make the protein. Using the mRNA as a template, the ribosome traverses each codon of the mRNA, pairing it with the appropriate amino acid. This is done using molecules of transfer RNA (tRNA) containing a complementary anticodon on one end and the appropriate amino acid on the other.

Protein synthesis begins at a start codon near the 5' end of the mRNA. The small ribosomal subunit, typically bound to a tRNA containing the amino acid methionine, binds to an AUG codon on the mRNA and recruits the large ribosomal subunit. The large ribosomal subunit contains three tRNA binding sites, designated A, P, and E. The A site binds an aminoacyl-tRNA (a tRNA bound to an amino acid); the P site binds a peptidyl-tRNA (a tRNA bound to the peptide being synthesized); and the E site binds a free tRNA before it exits the ribosomes butt.

Figure 3 : Translation of mRNA (1) by a ribosome (2) into a polypeptide chain (3). The mRNA begins with a start codon (AUG) and ends with a stop codon (UAG).

In Figure 3, both ribosomal subunits (small and large) assemble at the start codon (towards the 5' end of the mRNA). The ribosome uses tRNA 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.

[edit] References

1. ^ G.E. Palade. (1955) "A small particulate component of the cytoplasm." J Biophys Biochem Cytol. Jan;1(1): pages 59-68. PMID 14381428
2. ^ Roberts, R. B., editor. (1958) "Introduction" in Microsomal Particles and Protein Synthesis. New York: Pergamon Press, Inc.
3. ^ ^{a b c d e f} The Molecular Biology of the Cell, fourth eddition. Brusce Alberts, et al. Garland Science (2002) pg. 342 ISBN 0-8153-3218-1
4. ^ The Molecular Biology of the Cell, fourth eddition. Brusce Alberts, et al. Garland Science (2002) pg. 808 ISBN 0-8153-3218-1
5. ^ O'Brien, T.W., The General Occurrence of 55S Ribosomes in Mammalian Liver Mitochondria. J. Biol. Chem., 245:3409 (1971).
6. ^ 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
7. ^ 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
8. ^ 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
9. ^ Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF. Crystal structure of the ribosome at 5.5 Å resolution. Science. 2001 May 4;292(5518):883-96. Epub 2001 Mar 29. PMID 11283358
10. ^ Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH. Structures of the bacterial ribosome at 3.5 Å resolution. Science. 2005 Nov 4;310(5749):827-34. PMID 16272117
11. ^ 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

[edit] See also

[edit] External links

• 70S Ribosome Architecture Animation of a working ribosome. Requires the Chime browser plugin from this site (where registration is required).
• Lab computer simulates ribosome in motion
• Information on ribosomes

This article contains material from the Science Primer published by the NCBI, which, as a US government publication, is in the public domain.