Ribosome

The ribosome is the molecular machine inside the cell that makes proteins from amino acids in the process called translation . It binds to a messenger ribonucleic acid (mRNA) and reads the information contained in the nucleotide sequence of the mRNA. Transfer RNAs (tRNAs) containing amino acids enter the ribosome in a special pocket, or binding site, called the acceptor site (A site). Once correctly bound, the ribosome can add the amino acid on the tRNA to the growing protein chain.

Structure

The ribosome is made up of two parts, called subunits. The larger of the two subunits is where the amino acids get added to the growing protein chain. The small subunit is where the mRNA binds and is decoded. Each of the subunits is made up of both protein and ribonucleic acid (RNA) components.

The small ribosomal subunit is made up of one ribosomal RNA (rRNA) and approximately twenty-one proteins in prokaryotes (bacteria) and approximately thirty-three proteins in eukaryotes (mammals). In prokaryotes, the large ribosomal subunit contains two rRNAs—one large one and one small one—and approximately thirty-one proteins. In eukaryotes, the large subunit is composed of three rRNAs—one large one and two different small ones—and approximately forty-nine proteins. In eukaryotic cells, ribosomal subunits are synthesized in the nucleolus and then exported to the cytoplasm before use.

The rRNAs have many regions of self-complementarity, that is, regions within the rRNA that can form base pairs with other regions of the same rRNA, linking them together. This self-complementarity produces highly structured RNA molecules that serve as the core of the ribosome. In fact, rRNAs make up most of the mass of the ribosome. The proteins bind to various parts of the rRNAs to fill in the ribosome's structure.

Researchers have worked for many years to try to determine what the ribosome's structure is at the atomic level. How are all the atoms that make up the ribosome arranged in three-dimensional space? On a gross level, the ribosome looks something like an oyster with one of its shells somewhat smaller than the other. The two subunits are joined to each other by interactions between the rRNAs in one subunit and proteins in the other subunit. There may also be interactions between an RNA on one subunit and an RNA on the other subunit and between proteins on the two subunits.

RNA Movements

tRNAs move through the ribosome during the course of protein synthesis. A tunnel runs through the ribosome, right at the interface between the two subunits, and the tRNAs enter one side of this tunnel and are propelled along it during each step of protein synthesis. The three tRNA binding sites of the ribosome—A (acceptor), P (peptidyl), and E (exit)—appear to be intermediate spots in this tunnel. The mRNA binds to a groove at the bottom of the tRNA tunnel. After each amino acid is added to the growing protein, the tRNAs must be moved from one site to the next, and the mRNA must also be moved over one codon (three bases) so that the next amino acid coded for by the mRNA can be added to the protein.

These movements of the tRNAs and mRNA are made possible by a protein factor, called EF-G in prokaryotes or EF-2 in eukaryotes, which binds to the ribosome and uses the energy stored in the triphosphate group of guanosine triphosphate (GTP) to help propel the tRNAs and mRNA along. It also appears that parts of the ribosome move as the tRNAs and mRNA move. In fact, it is possible that EF-G produces movement of these parts of the ribosome and that these movements in turn produce movement of the tRNAs and mRNAs. Certain antibiotics (drugs that kill bacteria) are known to work by preventing some of the movements of bacterial ribosomes, thus stopping protein synthesis.

The poison ricin, from castor bean seeds, cleaves part of the RNA in the large subunit.

Intriguingly, there are certain mutations of the ribosome (changes to the structure of the rRNA or proteins) that affect its movements during translation and appear to cause a decrease in the accuracy of protein synthesis (for example, the wrong amino acids get put into the protein with increased frequency). Thus, the movements themselves may be directly tied to the mechanism by which the ribosome makes sure that the correct amino acid is being added to the protein at each point along the mRNA.

The growing protein chain exits the ribosome through a second tunnel, this one at the top of the large subunit. When protein synthesis ends, the binding of proteins called release factors is thought to induce the ribosome to release the finished protein into the cytoplasm. Exactly how the ribosome does this is unclear.

For many years it was thought that the rRNAs in the ribosome served merely as a scaffold on which to hang the ribosomal proteins. It was proposed that the proteins did all of the important work in the ribosome, such as catalyzing the formation of peptide bonds and moving the tRNAs and mRNA along during protein synthesis. However, it is now clear that the rRNAs play an active role in protein synthesis and are not merely the frame on which the ribosome is built. As more detailed information about the three-dimensional structure of the ribosome becomes available and as researchers do more experiments to probe the inner workings of this fascinating machine, we will have a better understanding of what the rRNAs do and how they do it.

see also Nucleolus; Protein Synthesis; RNA; Transfer RNA

Jon Lorsch

Bibliography

Cate, Jamie H., et al. "X-ray Crystal Structures of 70S Ribosome Functional Complexes." Science 285 (1999): 2095–2104.

Frank, Joachim. "How the Ribosome Works." American Scientist 86, no. 5 (1998): 428–439.

Hill, Walter E., et al., eds. The Ribosome: Structure, Function & Evolution. Washington, DC: American Society for Microbiology Press, 1990.

Lewin, Benjamin. Genes VI. Oxford: Oxford University Press, 1997.

Puglisi J. D., S. C. Blanchard, and R. Green. "Reviews—Approaching Translation at Atomic Resolution." Nature Structural Biology 7, no. 10 (2000): 855–861.

Ribosome

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.

see also Cell, Eukaryotic; Ribozyme; RNA; Translation.

Janice Zengel

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.

Ribosomes

Ribosomes are organelles that play a key role in the manufacture of proteins. Found throughout the cell, ribosomes are composed of ribosomal ribonucleic acid (rRNA) and proteins. They are the sites of protein synthesis .

Although Robert Hooke first used a light microscope to look at cells in 1665, it was only during the last few decades that the cell's organelles were discovered. This is primarily because light microscopes do not have the magnifying power required to see these tiny structures. Using an electron microscope , scientists have been able to see most of the cells substructures, including the ribosomes.

Ribosomes are composed of a variety of proteins and rRNA. They are organized in two functional subunits that are constructed in the cell's nucleolus. One is a small subunit that has a squashed shape, while another is a large subunit that is spherical in shape. The large subunit is about twice as big as the small unit. The subunits usually exist separately, but join when they are attached to a messenger RNA (mRNA). This initiates protein synthesis.

Production of a protein begins with initiation. In this step, the ribosomal small subunit binds to the mRNA along with the first transfer RNA (tRNA). The next step is elongation, where the ribosome moves along the mRNA and strings together the amino acids one by one. Finally, the ribosome encounters a stop sequence and the two subunits release the mRNA, the polypeptide chain, and the tRNA.

Protein synthesis occurs at specific sites within the ribosome. The P site of a ribosome contains the growing protein chain. The A site holds the tRNA that has the next amino acid. The two sites are held close together and a chemical reaction occurs. When the stop signal is present on the mRNA, protein synthesis halts. The polypeptide chain is released and the ribosome subunits are returned to the pool of ribosome units in the cytoplasm .

Ribosomes are found in two locations in the cell. Free ribosomes are dispersed throughout the cytoplasm. Bound ribosomes are attached to a membranous structure called the endoplasmic reticulum. Most cell proteins are made by the free ribosomes. Bound ribosomes are instrumental in producing proteins that function within or across the cell membrane. Depending on the cell type, there can be as many as a few million ribosomes in a single cell.

Because most cells contain a large number of ribosomes, rRNA is the most abundant type of RNA. rRNA plays an active role in ribosome function. It interacts with both the mRNA and tRNA and helps maintain the necessary structure. Transfer RNA is the molecule that interacts with the mRNA during protein synthesis and is able to read a three amino acid sequence. On the opposite end of the tRNAs, amino acids are bonded on a growing polypeptide chain. Generally, it takes about a minute for a single ribosome to make an average sized protein. However, several ribosomes can work on a single mRNA at the same time. This allows the cell to make many copies of a single protein rapidly. Sometimes these multiple ribosomes, or polysomes, can become so large that they can be seen with a light microscope.

The ribosomes in eukaryotes and prokaryotes are slightly different. Eukaryotic ribosomes are generally larger and are made up of more proteins. Since many diseases are caused by prokaryotes, these slight differences have important medical implications. Drugs have been developed that can inhibit the function of a prokaryotic ribosome, but leave the eukaryotic ribosome unaffected. One example is the antibiotic tetracycline.

See also Protein synthesis

Ribosomes

Ribosomes are protein manufacturers within cells. Huge molecules of DNA, or deoxyribonucleic acid, coiled within the chromosomes of every living organism use a universal language called the genetic code. Employed by all cells in the same fashion, the information encoded in DNA acts as a set of instructions for the synthesis of vital protein molecules. Cells assemble thousands of different kinds of proteins using the information within DNA. To construct an analogy, if a single cell were a kitchen, DNA would be a master cookbook and protein molecules would be the meals prepared using the cookbook. In this cellular kitchen, then, ribosomes are the molecular chefs.

The protein molecules made are not directly constructed from DNA. They are synthesized by ribosomes, which use messenger ribonucleic acid (mRNA) molecules as guides. Constructed by copying portions of DNA in chromosomes, mRNA molecules are able to leave the nucleus of the cell and go to the site of protein synthesis in the cytosol (or cytoplasm). Once in the cytosol, the process of interpreting the recipe of DNA into protein involves two phases. The first is called transcription. Transcription creates the mRNA copy of a gene to be expressed. The process is like creating many photocopies of a portion of DNA that can then be sent elsewhere in the cell.

The second process, called translation, directly involves ribosomes, which interpret the "photocopied" information of mRNA molecules. Like barcode scanners in grocery store check-out registers that interpret the black and white UPC code bars of products, ribosomes "read" nucleotide sequences of mRNA and construct protein molecules from amino acids using the encoded information.

Ribosomes are composed of two parts, a large subunit and a small subunit. Additionally, ribosomes contain a distinct kind of RNA found only in ribosomes, called ribosomal RNA (rRNA). During translation, the two separate subunits of a ribosome clasp around a single mRNA molecule . As the ribosome reads the information, it slides along the length of the mRNA molecule until it reaches the end and drops off, leaving the finished protein product. Messenger RNA molecules that have many ribosomes attached to them simultaneously, called polysomes, are formed when multiple protein products are produced from the same mRNA molecule. Ribosomes are found existing free within the cytosol, or as attached structures of the rough endoplasmic reticulum, the organelle which modifies and refines non-functional proteins into functional ones.

Terry Watkins

ribosome A subcellular granule, 10–20 nm in diameter, composed of RNA and protein, which is found in large numbers in all types of cells and in some subcellular organelles. Ribosomes are the site of protein synthesis: m-RNA attaches to them and there receives t-RNA molecules bearing amino acids. In eukaryotic cells they are synthesized in the nucleolus, but are found predominantly in the cytoplasm, singly or in chains (polysomes or polyribosomes, probably linked by the m-RNA), or attached to the endoplasmic reticulum, which is then termed ‘rough ER’. There are two main types of ribosomes, distinguished by their size: 70S ribosomes occur in prokaryotes and in the matrix of chloroplasts and mitochondria; the slightly larger 80S ribosomes occur in the cytoplasm of eukaryotes. (The ‘S’ refers to the Svedberg unit.)