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A 'ribosome' is a small, dense, functional structure found in all known cells that assembles proteins.

Contents

Description

Biogenesis

Ribosome locations

Free ribosomes

Membrane-bound ribosomes

Structure

Atomic structure

Function

References

See also

External links

Description

'Ribosomes' are about 20nm in diameter and are composed of 65% ribosomal RNA and 35% ribosomal proteins (known as a Ribonucleoprotein or RNP). It translates messenger RNA (mRNA) to build a polypeptide chain (e.g., a protein) using amino acids delivered by Transfer RNA (tRNA). It can be thought of as a giant enzyme but, although it contains proteins, its active site is made of RNA, so ribosomes are now classified as "ribozymes".^[1]
Ribosomes build proteins from the genetic instructions held within a messenger RNA. Free ribosomes are suspended in the cytosol (the semi-fluid portion of the cytoplasm) or bound to the rough endoplasmic reticulum, or to the nuclear envelope. Since ribosomes are ribozymes, it is thought that they might be remnants of the RNA world.^[2] While catalysis of the peptide bond involves the C2' hydroxyl of tRNA's P-site adenosine in a sort of proton shuttle mechanism, the full function (ie, translocation) of the ribosome is reliant on changes in protein conformations.
Occasionally ''ribosomes'' are referred to as organelle, but the use of the term organelle is contested.
Ribosomes are an important structure in the cell. Ribosomes were first observed in the mid-1950s by Romanian cell biologist George Palade in the electron microscope as dense particles or granules^[3] for which he would win the Nobel Prize. The term ''ribosome'' was proposed by scientist Richard B. Roberts in 1958:
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.

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 synthesize protein rather than directly participating in catalysis (See: Ribozyme).

Biogenesis

Main articles: Ribosome biogenesis

In prokaryotic cells, ribosomes are synthesized in the cytoplasm with the transcription of many ribosome gene operons. In eukaryotes, the process takes place both in the cell cytoplasm and in the nucleolus of eukaryotic cells. It involves the coordinated function of over 200 proteins in the synthesis and processing of the four rRNAs, as well as assembly of those rRNAs with the ribosomal proteins.

Ribosome locations

Ribosomes are classified as being either "free" or "membrane-bound".

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. Proteins containing disulfide bonds using cysteine amino acids cannot be produced outside of the lumen of the endoplasmic reticulum.

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.

Structure

The ribosomal subunits of prokaryotes and eukaryotes are quite similar. The Molecular Biology of the Cell, fourth eddition. Brusce Alberts, et al. Garland Science (2002) pg. 342 ISBN 0-8153-3218-1
Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S) subunit. Their large subunit is composed of a 5S RNA subunit (consisting of 120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 34 proteins. The 30S subunit has a 1540 nucleotide RNA subunit bound to 21 proteins.
Eukaryotes have 80S ribosomes, each consisting of a small (40S) and large (60S) subunit. Their large subunit is composed of a 5S RNA (120 nucleotides), a 28S RNA (4700 nucleotides), a 5.8S subunit (160 nucleotides) and ~49 proteins. The 40S subunit has a 1900 nucleotide (18S) RNA and ~33 proteins.
The ribosomes found in chloroplasts and mitochondria of eukaryotes also consist of large and small subunits bound together with proteins into one 70S particle. These organelles are believed to be descendants of bacteria (see Endosymbiotic theory) and as such their ribosomes are similar to those of prokaryotes.^[4]
The various ribosomes 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. All of the catalytic activity of the ribosome is carried out by the RNA, the proteins reside on the surface and seem to stabilize the structure.
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. Basis for prokaryotic specificity of action of aminoglycoside antibiotics, Recht MI, Douthwaite S, Puglisi JD, , , EMBO J, 1999 Even though mitochondria possess ribosomes similar to the bacterial ones, 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]

Atomic structure

Atomic structure of the 50S Subunit from ''Haloarcula marismortui''. Proteins are shown in blue and the two RNA strands in orange and yellow. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution, Ban N, Nissen P, Hansen J, Moore P, Steitz T, , , Science, 2000 The small patch of green in the center of the subunit is the active site.

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 prokaryotic) subunit from the archea, ''Haloarcula marismortui'' was published. Soon after the structure of the 30S subunit from ''Thermus thermophilus'' was published. Shortly thereafter a more detailed structure was published.^[6] Early the next year (May 2001) these coordinates were used to reconstruct the entire ''T. thermophilus'' 70S particle at 5.5 Å resolution.^[7]
Two papers were published in November 2005 with structures of the ''Escherichia coli'' 70S ribosome. The structures of vacant ribosome were determined at 3.5 Å resolution using x-ray crystallography.^[8] Then, two weeks later, a structure based on cryo-electron microsopy was published,^[9] which depicts the ribosome at 11-15 Å in the act of passing a newly synthesized protein strand into the protein-conducting channel.
First atomic structures of the ribosome complexed with tRNA and mRNA molecules were solved by using X-ray crystallography by two groups independently, at 2.8 Å ^[10] and at 3.7 Å.^[11] These structures allow to see the details of interactions of the ''Thermus thermophilus'' ribosome with mRNA and with tRNAs bound at classical ribosomal sites. Interactions of the ribosome with long mRNAs containing Shine-Dalgarno sequences were visualized soon after that at 4.5 to 5.5-Å resolution.^[12]

Function

Main articles: Translation (biology)

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 ribosome.

'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''.

References

1. How ribosomes make peptide bonds, Rodnina MV, Beringer M, Wintermeyer W, , , Trends Biochem. Sci., 2007
2. Structural biology. The ribosome is a ribozyme, Cech T, , , Science, 2000
3. G.E. Palade. (1955) "A small particulate component of the cytoplasm." ''J Biophys Biochem Cytol.'' Jan;1(1): pages 59-68. PMID 14381428
4. The Molecular Biology of the Cell, fourth edition. 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. 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
7. 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
8. 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
9. 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
10. Selmer, M., Dunham, C.M., Murphy, F.V IV, Weixlbaumer, A., Petry S., Kelley, A.C., Weir, J.R. and Ramakrishnan, V. (2006). Structure of the 70S ribosome complexed with mRNA and tRNA. Science , 313, 1935-1942
11. Korostelev A, Trakhanov S, Laurberg M, Noller HF. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell. 2006 Sep 22;126(6):1065-77
12. Yusupova G, Jenner L, Rees B, Moras D, Yusupov M. Structural basis for messenger RNA movement on the ribosome. Nature. 2006 Nov 16;444(7117):391-4

See also

★ Translation

★ Prokaryotic translation

★ Eukaryotic translation

★ Organelle

★ Nucleolus

★ wobble base pair

★ rRNA

★ endoplasmic reticulum

★ posttranslational modification

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

★ Molecule of the Month © RCSB Protein Data Bank:

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★ Ribosome

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★ Elongation Factors