Ribosome: Definition, Structure, and Function.

The ribosomes are small, dense, rounded, and granular particles of the ribonucleoprotein. They occur either freely in the matrix of mitochondria, chloroplast and cytoplasm (i.e., cytoplasmic matrix) or remain attached with the membranes of the endoplasmic reticulum and nucleus.

They occur in most prokaryotic and eukaryotic cells and are known to provide a scaffold for the ordered interaction of all the molecules involved in protein synthesis.

History

Ribosomes are remarkable organelles of cell. They were studied before they were discovered. Thus, ribosomes were studied in the early 1930s, discovered and isolated in the early 1940s, scrutinized in 1950s and baptized in 1958.

In 1960s they were dissociated and reconstituted; in 1970s sequenced and studied topographically; and in 1980s they continue to be object of considerable research. Before 1930s, it was the prevailing view that DNA was found only in animal cells and RNA only in plant cells.

In the 1930s various direct studies, employing basic staining techniques that discriminated between DNA and RNA, and spectrophotometric measurements of absorption in different cell regions, confirmed that RNA is present in the cytoplasm of both plant and animal cells and suggested that DNA is found exclusively in the nucleus.

Using quantitative techniques in 1940s, a very significant observation was made regarding the ribosome function. It was reported that cells were rich in RNA when they were active in protein synthesis. For example, secretory cells such as pancreas cells and silk gland cells were noted to be RNA-rich, whereas cells of other types (non-secretory cells such as heart muscle cells which make little new proteins) are relatively RNA-poor.

In 1940s Albert Claude homogenized chick and mammalian embryos and obtained a fraction containing what he called microsomes particles of ribonucleoprotein and lipid visible with the dark field microscope.

He, thus, showed that the cytoplasmic RNA was included in tiny particles of ribonucleoprotein later to be called “ribosomes.” In 1952, G.E. Palade described the ribosome. Their presence in both free and membrane attached form was confirmed by Palade and Siekevitz by the electron microscopy.

In 1950s another technique, namely ultracentrifugal analysis was employed to study the ribosomes. This showed that ribosomes sedimented at discrete peaks in the 40S—70S range. When purified by centrifugation and electrophoresis, they were found to contain half RNA and half protein.

As MgCl2 was known to precipitate RNA, Siekevitz suggested that RNA might somehow be involved in protein synthesis. In 1952, Siekevitz and Zamecnik showed clearly that radioactive amino acids first were incorporated into proteins on ribosomes and then were released to the soluble portions of the cell.

In 1958, the papers presented at a meeting of the Biophysical Society at the Massachusetts Institute of Technology were published in a book form. R.B. Roberts edited this collection of papers and coined the name ribosome in his introductory comments.

The term ribosome is due to rich RNA content of this organelle. Tissieres and Watson (1958) isolated 70S E. coli ribosomes and showed that they consist of two subunits, 50S and 30S. In 1960s ribosomes were subjected to exhaustive electrophoretic and chromatographic procedures, this time not to purify them but to examine their parts.

It soon became clear that ribosomes contain three or four kinds of RNA and scores of proteins. Recently, various workers such as Lake, Nomura, Wittman, Traut , Stoffler, Kurland, etc., have studied the relationship between rRNAs and ribosomal proteins to work out the topology of ribosomes.

Occurrence and Distribution

The ribosomes occur in cells, both prokaryotic and eukaryotic cells. In prokaryotic cells, the ribosomes often occur freely in the cytoplasm. In eukaryotic cells, the ribosomes either occur freely in the cytoplasm or remain attached to the outer surface of the membrane of the endoplasmic reticulum.

The yeast cells, reticulocytes or lymphocytes, meristematic plant tissues, embryonic nerve cells, and cancerous cells contain a large number of ribosomes which often occur freely in the cytoplasmic matrix. In the cells in which active protein synthesis takes place, the ribosomes remain attached to the membranes of the endoplasmic reticulum.

Such cells are the pancreatic cells, plasma cells, hepatic parenchymal cells, Nissls bodies, osteoblasts, serous cells, or the submaxillary gland, chief cells of the glandular stomach, thyroid cells and mammary gland cells.

The cells which synthesize specific proteins for the intracellular utilization and storage often contain large number of free ribosomes. Such cells are the erythroblasts, developing muscle cells, skin and hair.

Types of Ribosomes

Recently according to the size and the sedimentation coefficient (S) two types of ribosomes have been recognized

1. 70S Ribosomes.

The 70S ribosomes are comparatively smaller in size and have a sedimentation coefficient 70S and the molecular weight 2.7× 106 daltons. (Dalton is the unit of molecular weight (MW); one dalton equals the weight of hydrogen atom. For example, a water molecule weighs 18 daltons, see De Robertis et al., 1970).

According to the data of electron microscopy, the dimension of the dry particles of 70S ribosomes is 170 × 170 × 200 Ao. They occur in the prokaryotic cells of the blue-green algae and bacteria and also in mitochondria and chloroplasts of eukaryotic cells.

2. 80S Ribosomes.

The 80S ribosomes have the sedimentation coefficient of 80S and the molecular weight 40 × 106 daltons. The 80S ribosomes occur in eukaryotic cells of the plants and animals. The ribosomes of mitochondria and chloroplasts are always smaller than 80S cytoplasmic ribosomes and are comparable to prokaryotic ribosomes in both size and sensitivity to antibiotics, although their sedimentation values vary in different phyla, e.g., 77S in mitochondria of fungi, 60S in mitochondria of mammals, and 60S in mitochondria of animals in general. The ribosomes of chloroplasts are 70S type.

How many ribosomes are present in the cell?

An E. coli cell contains 10,000 ribosomes, forming 25 % of the total mass of the bacterial cell. In contrast, mammalian cultured cells contain 10 million ribosomes per cell, each of which is about twice as large as a prokaryotic ribosome.

Structure of Ribosomes

The ribosomes are oblate spheroid structures of 150 to 250Ao in diameter. Each ribosome is porous, hydrated and composed of two subunits. One ribosomal subunit is large in size and has a domelike shape, while the other ribosomal subunit is smaller in size and occurring above the larger subunit and forming a cap-like structure.

The 70S ribosome consists of two subunits, viz., 50S and 30S. The 50S ribosomal subunit is larger in size and has the size of 160 Ao to 180 Ao. The 30S ribosomal subunit is smaller in size and occurs above the 50S subunit like a cap.

The 80S ribosome also consists of two subunits, viz., 60S and 40S. The 60S ribosomal subunit is dome-shaped and larger in size. In the ribosomes which remain attached to the membranes of the endoplasmic reticulum and nucleus, etc., the 60S subunit remains attached to the membranes.

The 40S ribosomal subunit is smaller in size and occurs above the 60s subunit forming a cap-like structure. Both the subunits remain separated by a narrow cleft. The two ribosomal subunits remain united with each other due to high concentration of the Mg++(.001M) ions.

When the concentration of Mg++ions reduces in the matrix, both ribosomal subunits get separated. Actually, in bacterial cells, the two subunits are found to occur freely in the cytoplasm and they unite only during the process of protein synthesis.

At high concentration of Mg++ ions in the matrix, the two ribosomes (called monosomes) become associated with each other and known as the dimer. Further, during protein synthesis, many ribosomes are aggregated due to common messenger RNA and form the polyribosomes or polysomes.

Chemical composition

The ribosomes are chemically composed of RNA and proteins as their major constituents; both occurring approximately in equal proportions in smaller as well as larger subunit. However, the 70S ribosomes contain more RNA (60 to 40%) than the proteins (36 to 37%), e.g., the ribosomes of E. coli contain 63% rRNA and 37% protein.

While the 80S ribosomes contain less RNA (40 to 44%) than the proteins (60 to 56%), e.g., yeast ribosomes have 40 to 44% RNA and 60 to 56% proteins; ribosomes of pea seedling contain 40% RNA and 60% proteins. There is no lipid content in ribosomes.

1. Ribosomal RNAs

The 70S ribosomes contain three types of rRNA, viz., 23S rRNA, 16S rRNA, 5S rRNA. The 23S and 5S rRNA occur in the larger 50S ribosomal subunit, while the 16S rRNA occurs in the smaller 30S ribosomal subunit.

Assuming an average molecular weight for one nucleotide to be 330 daltons, one can calculate the total number of each type of rRNA. Thus, the 23S rRNA consists of 3300 nucleotides, 16S rRNA contains 1650 nucleotides and 5S rRNA includes 120 nucleotides in it. The 80S ribosomes contain four types of rRNA, viz., 28S rRNA (or 25-26 rRNA in plants, fungi, and protozoa), 18S rRNA, 5S rRNA, and 5.8S rRNA.

The 28S, 5S, and 5.8S rRNAs occur in the larger 60S ribosomal subunit, while the 18S rRNA occurs in the smaller 40S ribosomal subunit. About 60% of the rRNA is helical (i.e., double-stranded) and contains a paired bases.

These double-stranded regions are due to hairpin loops between complementary regions of the linear molecule. The 28S rRNA has the molecular weight 1.6 × 106 daltons and its molecule is double-stranded and having nitrogen bases in pairs.

The 18S rRNA has a molecular weight of 0.6×106 daltons and consists of 2100 nucleotides. The 18S and 28S ribosomal RNA contain a characteristic number of methyl groups, mostly as 2′-O-methyl ribose. The molecule of 5S rRNA has a cloverleaf shape and a length equal to 120 nucleotides.

The 5.8S rRNA is intimately associated with the 28S rRNA molecule and has, therefore, been referred to as 28S-associated ribosomal RNA (28S-A rRNA). The 55S ribosomes of mammalian mitochondria lack 5S rRNA but contain 21S and 12S rRNAs.

The 21S rRNA occurs in larger or 35S ribosomal subunits, while 12S rRNA occur in smaller or 25S ribosomal subunit. It is thought that each ribosomal subunit contains a highly folded ribonucleic acid filament to which the various proteins adhere.

But as the ribosomes easily bind the basic dyes so it is concluded that RNA is exposed at the surface of the ribosomal subunits, and the protein is assumed to be in the interior in relation to non-helical part of the RNA.

2. Ribosomal Proteins

According to Nomura and Garett and Wittmann (1973) each 70S ribosome of E. coli is composed of about 55 ribosomal proteins. Out of these 55 proteins, about 21 different molecules have been isolated from the 30S ribosomal subunit, and some 32 to 34 proteins from the 50S ribosomal subunit.

The primary structure of several of these proteins has been elucidated. Most of the recent knowledge about the structure of ribosomal proteins has been achieved by dissociation of ribosomal subunits into their component rRNA and protein molecules.

When both 50S and 30S ribosomal subunits are dissociated by centrifuging both of them in a gradient of 5 M cesium chloride, then there are two inactive core particles (40S and 23S, respectively) which contain the RNA and some proteins called core proteins (CP) at the same time several other proteins—the so-called split proteins (SP) are released from each particle.

There are SP50 and SP30 proteins which may reconstitute the functional ribosomal subunit when added to their corresponding core. Some of the split proteins are apparently specific for each ribosomal subunit.

The split proteins have been further fractionated and divided into acidic (A) and basic (B) proteins. Nomura et al., (1968) fractionated at least six different groups of proteins in the ribosome. In all, 21 types of proteins have been isolated in smaller subunit (30S) of ribosome of E. coli. These are designated as S1 to S21.

Similarly, in larger subunit (50S) 34 different proteins designated as L1 to L34, have been isolated. Thus, the 70S ribosome was thought to consist of 55 different proteins. However, it was later shown that protein S20 is identical to L26, thus, the correct number of S proteins is 20.

Likewise, L8 was shown to be an aggregate of proteins L7, L12 and L10; thus, the correct number of L proteins is 33. Thus, the prokaryotic 70S ribosome consists of 53 different proteins (20S + 33L = 53 proteins).

Similar organization of ribosomal proteins and RNA is found in 80S ribosomes Different rRNA molecules evidently play a central role in the catalytic activities of ribosomes in the process of protein synthesis. Various ribosomal proteins have been found to mainly enhance the catalytic function of the rRNA in the ribosomes.

3. Metallic Ions

The most important low molecular weight components of ribosomes are the divalent metallic ions such as Mg++, Ca++ and Mn++

Function of Ribosome

Translation — The process of decoding the information in messenger RNA and forming continuous chains of amino acids to form proteins — is carried out by ribosomes.

Ribosomes consist of two subunits: one subunit (30S in bacteria and archaea, 40S in eukaryotes) decodes the mRNA, reading off the triplets of nucleotide that correspond to each amino acid; the other subunit (50S in bacteria and archaea, and 60S in eukaryotes) forms the peptide bonds.

Each subunit comprises ribosomal RNAs (rRNAs) and ribosomal proteins (r-proteins). The rRNAs seem to be responsible for most enzymatic activities, whereas the r-proteins are proposed to have largely structural roles.

In almost all organisms studied, the mature rRNAs are processed from a polycistronic precursor rRNA. During ribosome synthesis, the mature rRNA regions are covalently modified within the precursor, which is then processed to release the mature rRNAs.

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