Ribosomes are cytoplasmic granules composed of RNA and protein, at which protein synthesis takes place. They were first observed by Palade in the electron microscope as dense particles or granules. Upon isolation, they were shown to contain approximately equal amounts of RNA and protein Label. To function actively in protein synthesis, they must be bound into complete ribosomes. We know that ribosomes are but one of the required components necessary for the synthesis of protein. The others are messenger RNA, which carries the genetic message; soluble RNA, which carries amino acids to be synthesized; and guanosine triphosphate, which is the source of energy. A number of ribosomes may be attached to the same messenger, each manufacturing its own chain of polypeptides, called a polysome. Ribosomes are also found in the mitochondria and chloroplasts of eukaryotic cells. They are always smaller than the 80S cytoplasmic ribosomes, and are comparable to prokaryotic ribosomes in both size and sensitivity to antibiotics, although the sedimentation values vary somewhat in different phyla.
Prokaryotic and eukaryotic ribosomes do not differ in any fundamental way; both preform the same functions by the same set of chemical reactions. The genetic code is the same in all living organism, and it has been demonstrated that eukaryotic ribosomes are able to translate bacterial mRNAs correctly. Eukaryotic ribosomes are much larger that prokaryotic ones and most of their proteins are different. Antibiotics such as chloramphenicol inhibit bacterial but not eukaryotic ribosomes. Protein synthesis by eukaryotic ribosomes in inhibited by cycloheximide.
Mitochondrial and chloroplast ribosomes resemble those in bacteria. They are inhibited by chloramphenicol, and hybrid ribosomes containing one bacterial and one chloroplast ribosome subunit, for example, are fully active in protein synthesis. Hybrid eukaryotic ribosomes containing subunits from both plants and mammals are also active in protein synthesis, but are inactive if one of the subunits is derived from bacteria. Some structural resemblance must exist, however, since reconstruction experiments have shown that two proteins from the large subunit of E. coli can replace the homologous proteins in mammalian ribosomes. In summary, there is little structural but considerably functional homology between prokaryotic and eukaryotic ribosomes.
Cells devote considerable effort to the production of these essential organells. For example, an E. coli cell contains approximately 15,000 ribosomes, each one with a molecular weight of about three million daltons. Ribosomes therefore represent twenty-five percent of the total mass of these bacterial cellsLabel.
STRUCTURE:
Ribosomes are tiny particles, about 200 A. It is composed of both proteins and RNA; in fact it has approximately 37 - 62% RNA, and rest are made up of proteins Label. The RNA present in ribosomes are obviously called ribosomal RNA, and they are produced in the nucleolus, which is a prominent globular structure in the nucleus. Thus, the proteins are gene products of themselves, and one ribosome is made up of dozens of genes.
The ribosomes fall into two categories: Those that are free to roam in the cytoplasm , and those that are bound to gigantic, cobwebby organelles made up of membranes, called the endoplasmic reticulum; thus, causing a rough surface. Although, the two kinds of ribosomes play similar roles in translating mRNA to produce proteins, they are very distinct in where its product is located. The ribosomes in the cytoplasm allows its protein to roam about freely, while the bound ribosomes transfer their functional protein into the endoplasmic reticulum. In addition, ribosomes are also located within the mitochondria, and the chloroplast, but are only few in content. Click Here
This spherical particle of 23nm, is composed of two subunits; a large and small Label. In Eukaryotes, the co-efficient of ribosomes are 80s, of which is divided into 60s for the large, and 40s for the small subunit. The 60s contain 28s rRNA, with a small fragment that is attached noncovalently and can be released upon heating; a 5.8s, and a very small - 120 nucleated of 5sRNA. Whereas, the 40s subunit has only a single 18s rRNA Label.
In prokaryotes, however, the large and small subunits are split into 50s and 30s, making a total of 70s respectively. The 50s has two types of rRNA - a 23s and a 5s Label. It also has 32 different proteins. On the other hand, the 30s contains a single 16s rRNA image a, image b, image c plus, 21 different types of proteins Label.
To help better understand what the s stands for in rRNA, let us use the prokaryotes as an example. The 50s and 30s refers to the sedimentation coefficient of the two subunits. This coefficient is a measure of the speed with which the particles sediment through a solution when spun in an ultra centrifuge. Thus, the particles with larger coefficient would centrifuge and settle much faster since it is has more mass than the particle with the smaller coefficient.
50s + 30s =======> 70s
Note that the two subunits above make up the entire ribosomal molecule which is 70s. The reason the coefficients do not add up is because they are not proportional to the particle weight.
During protein synthesis, ribosomes line up along the mRNA and form a polysome, also called the polyribosome. The mRNA is aligned in the gap between the 2 ribosomal subunits. It is possible that the nascent peptide chain grows through a channel or groove in the large ribosomal subunit. This is predicted to be the case since ribosomes protect a segment of 30-40 amino acids from degradation. Speaking of amino acids, up to 30 ribosomes can attach on one strand of mRNA to form amino acid chains thus leading to protein formation. Ribosomes act as the backbone for many molecules during translation. It provides room for many structures to situate itself thus enhancing protein synthesis. For example, mRNA inserts itself between the two subunits; the peptidyl transferase complex - the enzyme that allows for the tRNA to break apart from the amino acid on P-site; this enzyme lays across the molecule, between the subunits. It contains the P and the A-site for tRNA binding. Last but not least, the ribosome molecule allows the growing polypeptide chain, to emerge from the back of the structure, thus it is situated perpendicular to the mRNA chain.
Ribosomes have a tertiary structure.
Ribosomes make up a large part of cells in many species, which leads to protein manufacturing. For example, in E.Coli (bacteria), they make up about 1/4 of the total cell mass. They are intensely basiphilic (having high affinity for bases).
Due to its complex structures, with many proteins and different kinds of RNA, researchers have found it very difficult to study the macro molecular structure of ribosomes, especially for the fact it is quite impossible to observe its crystal using an x-ray diffraction. Thus, scientists have been forced to use other means of study to map the proteins and RNA components in ribosome. Some of these are the cross-linking, immunoelectron microscopy, and low-angle neutron scattering methods. The cross-linking shows the protein arrangement and the types of bonds it forms within itself. The neutron scattering experiments forms horizontal lines that show the entire structure of ribosome, with its two subunits, and shows where the proteins are arranged in the molecule. The empty regions around the proteins is where the rRNA is located. The immunoelectron microscopy, shows the proposed location of the 16s rRNA molecule of the small subunit, in prokaryotes.
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Citation Frank, Joachim, et al. "A model of synthesis based on cryo-electron microscopy of the E. coli ribosome." Nature. 376 (1995): 440-444.
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Function:
The ribosomes plays a very important role in protein synthesis, which is the process by which proteins are made from individual amino acids. Without the ribosomes the message would not be read, thus proteins could not be produced. Therefore, ribosomes play a very important role in role in protein synthesis.
The primary agent in the process of translating the mRNA into a specific amino acid chain is the ribosome, which consists of two subunits. These subunits are made up of a third and extremely abundant type of RNA, ribosomal RNA (rRNA), and together contain up to eighty-two specific proteins assembled in a precise sequence Label. The ribosomes constituents must be put together in an extremely precise position and sequence. This assembled ribosome displays a series of small groves, tunnels, and platforms, where the action of protein synthesis occurs Label. There are the active sites, each dedicated to one of the tasks required for translation of mRNA into protein. Proteins being synthesized for export out of the cell, are made by ribosomes attached to the rough endoplasmic reticulum. In contrast, proteins for use by the cell are generally made in the cytoplasm by free ribosomes. Several of these free ribosomes may attach to a single mRNA molecule, giving rise to the polyribosome or polysome Label.
Protein synthesis takes place on polyribosomes (or polysomes) where 80S ribosomes associate with an mRNA coding for a given protein. The number of ribosomes associated in the polysomal chains depends on the size of the mRNA. This is also associated with the size of the protein that is being synthesized. Outside the polyribosome, the ribosomes are dissociated and form a pool of free subunits. Transfer RNAs are also bound to the ribosome. There are quite a few factors involved in the formation of the initiation complex. These include: GTP, methionine tRNA, an initiation codon in mRNA, 80S ribosomes, and three protein factors Label.
The process of protein synthesis begins with the capture of the tRNA, which is carrying an amino acid, by an initiation factor. This binds to a small ribosomal subunit, which occupies one of the active sites in the ribosomes, the P (protein) site. This initiation complex recognized and binds to the 5' end of an mRNA molecule and slides down to the initiation codon, which is always an AUG sequence of amino acids. The large subunit of the ribosome now joins the complex. A second tRNA is now brought into the ribosome by the elongation factor. If the anticodon of the tRNA pairs with the next codon of the message, the tRNA occupies the A (acceptor) site on the ribosome. This positions the second amino acid adjacent to the initiation methionine. Then an enzyme, peptidyl transferase, which is part of the large ribosomal subunit mediates the separation of the first amino acid from its tRNA and the formation of a peptide bond between the initial methionine and the amino acid is formed. The P site is now occupied by an uncharged tRNA molecule label.
The ribosome will now move down the mRNA by one codon, a process known as translocation. This movement shifts the growing polypeptide chain to the P position, and results in an empty A site, where a new charged tRNA can enter and pair, by forming a hydrogen bond between the codon and the anticodon. This holds the tRNA into place long enough for an even more stable binding to occur Label. The uncharged tRNA that previously occupied the P site is booted out of the ribosome and will be recharged and recycled by the cell. The energy needed for this process is supplied by the hydrolysis of guanosine triphosphate (GTP). The process then continues along the length of the mRNA, until the first stop codon is encountered. At that point the action of a termination factor releases the completed protein from the last tRNA and the ribosome dissociates into its component parts.
Another function of the ribosomes occurs in the relation to the neuron and axons. The cell body of a typical large neuron contains vast numbers of ribosomes. Although dendrites often contain some ribosomes, there are no ribosomes in the axon, and its protein must therefore be provided by the many ribosomes in the cell body.
To see the process of protein synthesis click here
Regulation:
The regulation and control of ribosomes has, for many years, been a questioning concern among biologist. There have been many studies done to try to answer the ribosomes formation. It is known that all living cells use ribosomes to synthesize proteins, but there are two main reasons why it is difficult to reach an understanding and consensus on how ribosome synthesis is controlled Label. One of the reasons is that the amount of components involved is very large and complex. The other being that the energy and matter consumed in making the ribosome is high, and changes in ribosome formation can also have an impact on the synthesis of other constituents of the cell Label.
Yet there is some evidence which has been proposed to explain the control and regulation of ribosomes. It is well studied in bacterial cells of E. coli chromosomes. The regulation of ribosomes is done directly by the regulation of synthesis of ribosomal proteins. It is known by the bacterial cell to avoid overproduction of ribosomal proteins which will cause a loss in energy and information. This requires that ribosomal proteins be synthesized in the amount required for ribosome assembly Label. The coordinated levels of production of nearly all ribosomal proteins are achieved by approximately 16 independent operons, which are scattered throughout the cell genome. The mechanisms which control and coordinate the ribosomal proteins are the repression of translation of protein excess. This means that there is translational feedback control. When there is an overproduction of ribosomal protein, it goes back to repress the operon that is activated and stops further production.
Structure linkage:
Antibiotics are drugs produced by bacteria and fungi. These molecules function as drugs used in the chemotherapy of infectious disease, and follow the principle of selective toxicity. Selective toxicity follows the principle of using drugs that kill the harmful microorganism without damaging the host.
As a result of its toxicity, antibiotics can affect the ribosomal structure, inhibiting protein synthesis. For instance, let us take the 70s ribosome of prokaryotes; antibiotics can target this structure and can adverse the effects on the cells of the host. Among the antibiotics that interfere with protein synthesis are chloramphenicol, erythromyocin, streptomycin, and the tetracycline (fig. 20.4)
This paper will be focused on these four antibioticsand its role played in the effect of the ribosome structure, thus leading to the change in protein synthesis. For instance, the chloramphenicol reacts with the 50s structure of the 70s prokaryote ribosome, by inhibiting the formation of the peptide bonds in the growing polypetide chain. Erythromyocin, the second antibiotic, also reacts with the same structure as chloromphenicol. However, it has a very narrow range of activity, since it affects mostly the gram-positive bacteria.
The other two antibiotics attract the 30s structure of the 70s prokaryotic ribosome. The tetracycline interferes with the attachment of the tRNA, which carries the amino acids, to the ribosome, thus preventing the addition of amino acids to the growing polypeptide chain. One unique aspect of tetracycline is that it cannot penetrate well into the mammalian cells, therefore, it does not interfere with the mammalian ribosomes. Aminoglycoside antibiotics, a type of streptomycin, changes the shape of the 30s structure of the 70s prokaryotic ribosome, thus interfering with the initial stage of protein synthesis. This in turn, causes the misreading of the genetic code on the mRNA.
Function Linkage:
RNA polymerase is the enzyme that directs transcription, which is the process by which the mRNA copy of a gene is synthesized. Transcription follows the same rules of base pairing as DNA replication. This base pattern ensure that an RNA transcript is a faithful copy of the gene.
There are three stages of transcription: initiation, elongation, and termination. During initiation, the enzyme recognizes a promoter region, which lies upstream from the gene. The polymerase binds tightly to the promoter and causes localized melting, or separation of the two DNA strands within the promoter. Then the polymerase starts building the RNA chain. Ribonucleoside triphosphates such as ATP, GTP, CTP and UTP are the building blocks the polymerase uses for this job Label. After the first nucleotide is in place, the polymerase binds the second nucleotide, joining it to the first. This forms the initial phosphodiester bond in the RNA chain.
The second stage is elongation, where the RNA polymerase directs the sequential binding of ribonucleotides to the RNA chain. As it does this, it moves along the DNA template and the melted DNA moves with it. This melted region exposes the bases of the template DNA one-by-one so that they can pair with the bases of the incoming ribonucleotides. As soon as the transcription machinery passes, the two DNA strands wind around each other again, reforming the double helix. Only enough separation will occur so that the polymerase can read the DNA template Label.
The final stage is termination, which allows the termination of transcription. These work in conjunction with RNA polymerase, and is sometimes aided by another protein, to loosen the association between RNA product and DNA template. So the RNA dissociates from the RNA polymerase and DNA, thus terminating transcription.
Transcription is very important in that it is the only step in expression of the genes for rRNAs. It is also important to ribosomes, because it sets up the RNA in a 5' to 3' sequence, which allows the ribosomes to read the message 5' to 3'. Without transcription of a gene, the ribosome would not be able to translate an mRNA, thus not allowing it to be separated into its component parts. If this does not occur, then translation will also not occur, thereby affecting the function and role of ribosomes in translation.
Citations
