A minute round particle composed of RNA and protein that is found in the cytoplasm of living cells and serves as the site of assembly for polypeptides encoded by messenger RNA.
[RIBO(NUCLEIC ACID) + –SOME3.]
ribosomal ri'bo·so'mal (-sō'məl) adj.
ribosome
Dictionary:
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Ribosomes are the cellular organelles that carry out protein synthesis, through a process called translation. They are found in both prokaryotes and eukaryotes, these molecular machines are responsible for accurately translating the linear genetic code, via the messenger RNA, into a linear sequence of amino acids to produce a protein. All cells contain ribosomes because growth requires the continued synthesis of new proteins. Ribosomes can exist in great numbers, ranging from thousands in a bacterial cell to hundreds of thousands in some human cells and hundreds of millions in a frog ovum. Ribosomes are also found in mitochondria and chloroplasts.
Structure
The ribosome is a large ribonucleoprotein (RNA-protein) complex, roughly 20 to 30 nanometers in diameter. It is formed from two unequally sized subunits, referred to as the small subunit and the large subunit. The two subunits of the ribosome must join together to become active in protein synthesis. However, they have distinguishable functions. The small subunit is involved in decoding the genetic information, while the large subunit has the catalytic activity responsible for peptide bond formation (that is, the joining of new amino acids to the growing protein chain).
In prokaryotes, the small subunit contains one RNA molecule and about twenty different proteins, while the large subunit contains two different RNAs and about thirty different proteins. Eukaryotic ribosomes are even more complex: the small subunit contains one RNA and over thirty proteins, while the large subunit is formed from three RNAs and about fifty proteins. Mitochondrial and chloroplast ribosomes are similar to prokaryotic ribosomes.
In spite of its complex composition, the architecture of the ribosome is very precise. Even more remarkable, ribosomes from all organisms, ranging from bacteria to humans, are very similar in their form and function. Recent breakthroughs in studies of ribosome structure, using techniques such as scanning, cryo-electron microscopy, and X-ray crystallography, have provided scientists with highly refined structures of this complex organelle. One particularly exciting conclusion from studies of the large subunit is that it is ribosomal RNA (rRNA), and not protein, that provides the catalytic activity for peptide bond formation. That is, it forms the chemical linkage between the amino acids of the growing protein molecule.
Synthesis
The synthesis of ribosomes is itself a very complex process, requiring the coordinated output from dozens of genes encoding ribosomal proteins and rRNAs. Ribosomes are assembled from their many component parts in an orderly pathway. In eukaryotes, rRNA synthesis and most of the assembly steps occur in a structure within the nucleus called the nucleolus. Eukaryotic ribosome synthesis is especially complicated, because the ribosomal proteins themselves are made by ribosomes in the cytoplasm (that is, outside of the nucleus), so they then must be imported into the nucleolus for assembly onto the nucleolus-derived rRNA. Once assembled, the nearly complete ribosomal subunits are then exported out of the nucleus and back into the cytoplasm for the final steps of assembly.
The exact details of the in vivo ribosome assembly pathway (the process of ribosome assembly within the living cell) are still under investigation. Assembly in eukaryotic cells involves not only the components of the mature particles, but also dozens of auxiliary factors that promote the efficient and accurate construction of the ribosome during its assembly. However, bacterial ribosomes can be constructed in vitro using purified ribosomal proteins and rRNAs. These ribosomes appear to function normally in in vitro translation reactions.
Ribosome Function
Translation of messenger RNA (mRNA) by ribosomes occurs in the cytoplasm. In bacterial cells, ribosomes are scattered throughout the cytoplasm. In eukaryotic cells, they can be found both as free ribosomes and as bound ribosomes, their location depending on the function of the cell. Free ribosomes are found in the cytosol, which is the fluid portion of the cytoplasm, and are responsible for manufacturing proteins that will function as soluble proteins within the cytoplasm or form structural elements, including the cytoskeleton, that are found within the cytosol.
Bound ribosomes are attached to the outside of a membranous network called the endoplasmic reticulum to form what is termed the "rough" endoplasmic reticulum. Proteins made by bound ribosomes are intended to be incorporated into membranes, or packaged for storage, or exported outside of the cell. Ribosomes exist either as a single ribosome (that is, one ribosome translating an mRNA) or as polysomes (two or more ribosomes sequentially translating the same mRNA in order to make multiple copies of the same protein).
Ribosomes have the critical role of mediating the transfer of genetic information from DNA to protein. Ribosomes translate this code using an intermediary, the messenger RNA, which is a copy of the DNA that can be interpreted by ribosomes. To begin translation, the small subunit first identifies, with the help of other protein factors, the precise point in the RNA sequence where it should begin linking amino acids, the building blocks of protein. The small subunit, once bound to the mRNA, is then joined by the large subunit and translation begins. The amino acid chain continues to grow until the ribosome reaches a signal that instructs it to stop.
Many of the antibiotics used in humans and other animals to treat bacterial infections specifically inhibit ribosome activity in the disease-causing bacteria, without affecting ribosome function in the host-animal's cells. These antibiotics work by binding to a protein or RNA target in the bacterial ribosome and inhibiting translation. In recent years, the misuse of antibiotics has resulted in the natural selection of bacteria that are resistant to many of these antibiotics, either because they have mutations in the antibiotic's target in the ribosome or because they have acquired a mechanism for excluding or inactivating the antibiotic.
Bibliography
Frank, Joachim. "How the Ribosome Works." American Scientist 86 (1998): 428-439
Garrett, Robert A., et al, eds. The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions. Washington, DC: ASM Press, 2000
Karp, Gerald. Cell and Molecular Biology: Concepts and Experiments, 3rd ed. New York: John Wiley & Sons, 2002.
—Janice Zengel
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Ribonucleoprotein particles concerned with protein synthesis; they consist of two, one large and one small, reversibly dissociable units (called also 50S and 30S subunits) that are found either bound to cell membranes, particularly rough endoplasmic reticulum, or free in the cytoplasm. They may occur singly or in clusters, called polyribosomes or polysomes, which are ribosomes linked by mRNA and are actively engaged in protein synthesis.
- r. binding site — a nucleotide sequence near the 5′ terminus of mRNA required for binding of mRNA to the small ribosomal subunit. Called also Shine–Dalgarno sequence.
| Wikipedia: Ribosome |
Organelles:
(1) nucleolus
(2) nucleus
(3) ribosomes (little dots)
(4) vesicle
(5) rough endoplasmic reticulum (ER)
(6) Golgi apparatus
(7) Cytoskeleton
(8) smooth ER
(9) mitochondria
(10) vacuole
(11) cytoplasm
(12) lysosome
(13) centrioles within centrosome
Ribosomes (from ribonucleic acid and "Greek: soma (meaning body)") are complexes of RNA and protein that are found in all cells. Ribosomes from bacteria, archaea and eukaryotes (the three domains of life on Earth), have significantly different structure and RNA. The ribosomes in the mitochondria of eukaryotic cells resemble those in bacteria, reflecting the evolutionary origin of this organelle.[1]
The ribosome functions in the expression of the genetic code from nucleic acid into protein, in a process called translation. Ribosomes do this by catalyzing the assembly of individual amino acids into polypeptide chains; this involves binding a messenger RNA and then using this as a template to join together the correct sequence of amino acids. This reaction uses adapters called transfer RNA molecules, which read the sequence of the messenger RNA and are attached to the amino acids.
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Description
Ribosomes are about 20 nm (200 Ångström) in diameter and are composed of 65% ribosomal RNA and 35% ribosomal proteins (known as a Ribonucleoprotein or RNP). They translate messenger RNA (mRNA) to build polypeptide chains (e.g., proteins) using amino acids delivered by transfer RNA (tRNA). Their active sites are made of RNA, so ribosomes are now classified as "ribozymes".[2]
Ribosomes build proteins from the genetic instructions held within messenger RNA. Free ribosomes are suspended in the cytosol (the semi-fluid portion of the cytoplasm); others are bound to the rough endoplasmic reticulum, giving it the appearance of roughness and thus its name, or to the nuclear envelope. As ribozymes are partly constituted from RNA, it is thought that they might be remnants of the RNA world.[3] Catalysis of the peptide bond involves the C2 hydroxyl of RNA's P-site adenosine in a protein shuttle mechanism. The full function (i.e. translocation) of the ribosome is reliant on changes in protein conformations.
Ribosomes are sometimes referred to as organelles, but the use of the term organelle is often used only in reference to sub-cellular components that include a phospholipid membrane, which ribosomes, being entirely particulate, do not. For this reason, ribosomes may sometimes be described as "non-membranous organelles".
Ribosomes were first observed in the mid-1950s by Romanian cell biologist George Palade using an electron microscope as dense particles or granules[4] 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 sizes ranging from 35 to 100S.
– Roberts, R. B., Microsomal Particles and Protein Synthesis[5]
The structure and function of the ribosomes and associated molecules, known as the translational apparatus, has been of research interest since the mid-twentieth 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). Bacterial 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
In bacterial cells, ribosomes are synthesized in the cytoplasm through the transcription of multiple ribosome gene operons. In eukaryotes and some bacterial cells, 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 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 an ER-targeting signal sequence on the protein being synthesized.
Free ribosomes
Free ribosomes are free to move about anywhere in the cytosol. Proteins that are formed from 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.
Structure
The ribosomal subunits of prokaryotes and eukaryotes are quite similar.[7]
The unit of measurement is the Svedberg unit, a measure of the rate of sedimentation in centrifugation rather than size and accounts for why fragment names do not add up (70s is made of 50s and 30s).
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 (16S) bound to 21 proteins.[7]
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.[7]
The ribosomes found in chloroplasts and mitochondria of eukaryotes also consist of large and small subunits bound together with proteins into one 70S particle.[7] These organelles are believed to be descendants of bacteria (see Endosymbiotic theory) and as such their ribosomes are similar to those of bacteria.[8]
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.[7] 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.[7]
The differences between the bacterial 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.[9] 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.[10]
Atomic structure
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 Ångströms.
The first papers giving the structure of the ribosome at atomic resolution were published in rapid succession in late 2000. First, the 50S (large bacteria) subunit from the archea, Haloarcula marismortui was published.[11] Soon after the structure of the 30S subunit from Thermus thermophilus was published.[6] Shortly thereafter a more detailed structure was published.[12] Early the next year (May 2001) these coordinates were used to reconstruct the entire T. thermophilus 70S particle at 5.5 Ångström resolution.[13]
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 Ångström resolution using x-ray crystallography.[14] Then, two weeks later, a structure based on cryo-electron microsopy was published,[15] which depicts the ribosome at 11-15 Ångström resolution 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 Ångström[16] and at 3.7 Ångström.[17] These structures allow one 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 Ångström resolution.[18]
Function
Ribosomes are the workhorses of protein biosynthesis, the process of translating 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 (3 nucleotides) of the mRNA, pairing it with the appropriate amino acid provided by a tRNA. Molecules of transfer RNA (tRNA) contain a complementary anticodon on one end and the appropriate amino acid on the other. 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 ribosome then contains three RNA 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. Protein synthesis begins at a start codon AUG near the 5' end of the mRNA. mRNA binds to the P site of the ribosome first. The ribosome is able to identify the start codon by use of the Shine-Dalgarno sequence of the mRNA in prokaryotes and Kozak box in eukaryotes.
Figure 3 : Translation of mRNA (1) by a ribosome (2)(shown as small and large subunits) into a polypeptide chain (3). The ribosome begins at the start codon of mRNA (AUG) and ends at the 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 is called a polyribosome or polysome.
References
- ^ Benne R, Sloof P (1987). "Evolution of the mitochondrial protein synthetic machinery". BioSystems 21 (1): 51–68. doi:. PMID 2446672.
- ^ Rodnina MV, Beringer M, Wintermeyer W (2007). "How ribosomes make peptide bonds". Trends Biochem. Sci. 32 (1): 20–6. doi:. PMID 17157507.
- ^ Cech T (2000). "Structural biology. The ribosome is a ribozyme". Science 289 (5481): 878–9. doi:. PMID 10960319.
- ^ G.E. Palade. (1955) "A small particulate component of the cytoplasm". J Biophys Biochem Cytol. Jan;1(1): pages 59-68. PMID 14381428
- ^ Roberts, R. B., editor. (1958) "Introduction" in Microsomal Particles and Protein Synthesis. New York: Pergamon Press, Inc.
- ^ a b Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A (2000). "Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution". Cell 102 (5): 615–23. doi:. PMID 11007480.
- ^ a b c d e f The Molecular Biology of the Cell, fourth eddition. Bruce Alberts, et al. Garland Science (2002) pg. 342 ISBN 0-8153-3218-1
- ^ The Molecular Biology of the Cell, fourth edition. Bruce Alberts, et al. Garland Science (2002) pg. 808 ISBN 0-8153-3218-1
- ^ Recht MI, Douthwaite S, Puglisi JD (1999). "Basis for bacterial specificity of action of aminoglycoside antibiotics". EMBO J 18 (11): 3133–8. doi:. PMID 10357824.
- ^ O'Brien, T.W., The General Occurrence of 55S Ribosomes in Mammalian Liver Mitochondria. J. Biol. Chem., 245:3409 (1971).
- ^ a b Ban N, Nissen P, Hansen J, Moore P, Steitz T (2000). "The complete atomic structure of the large ribosomal subunit at 2.4 A resolution". Science 289 (5481): 905–20. doi:. PMID 10937989.
- ^ 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
- ^ 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
- ^ Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH. Structures of the bacterial ribosome at 3.5 Ångström resolution. Science. 2005 Nov 4;310(5749):827-34. PMID 16272117
- ^ 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
- ^ 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. PMID 16959973
- ^ 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
- ^ 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
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
- Role of the Ribosome, Gwen V. Childs, copied here
- Molecule of the Month © RCSB Protein Data Bank:
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Mentioned in
- polyribosome
- entry site (cell and molecular biology)
- monosome (cell and molecular biology)
- shiga-like toxins
- free ribosome (cell and molecular biology)
- elongation (in protein synthesis)
- signal
- signal-recognition particle (cell and molecular biology)
- tRNA
- Translation
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