Essay @ Ribosome | Cytoplasmic Granules | Cell | Cell Biology

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Essay # 1. Introduction to Ribosome:

Ribosomes are cytoplasmic granules composed of RNA and protein. It is a protein biosynthetic factory that translates the DNA genetic information into an amino acid sequence (the primary structure of proteins). They were first observed by Palade (1955) in the electron microscope as dense particles or granules. In 1958, Richard and Roberts gave the organelles its name ‘Ribosome’.

The ribosomes are the smallest cell organelle measuring 170- 230Å in diameter. Unlike other cell organelles, they are not bound by any unit membrane. The main components of ribosomes are proteins and RNA (rRNA). Fabrication of protein is the primary task of ribosomes. A ribosome may be located in many places within the cell. They occur either freely in the matrix of mitochondria, chloroplast and cytoplasm (i.e., cytoplasmic matrix) or others is bound to cellular membranes.

Membrane-bound ribosomes are re­sponsible for the characteristic roughness of the endoplasmic reticulum when seen under a microscope. The proportion of membrane-bound ribosomes varies considerably. In a liver cell, 75% ribosomes are membrane bound and 25% lie freely in the cytoplasmic matrix. However, in the He La cells only 15% ribosomes are membrane bound.

Protein synthesis requires the assistance of two other RNA molecules in addition to the ribosomal RNA. Messenger RNA (mRNA) provides instructions from the cellular DNA for building a specific protein. Transfer RNA (tRNA) brings the protein building blocks, amino acids, to the ribosome. Once the protein backbone amino acids are polymerized, the ribosome releases the protein and it is transported to the Golgi apparatus. There, the proteins are completed and released inside or outside the cell.

Biogenesis:

Eukaryote ribosomes are produced and assembled in the nucleolus. Three of the four strands are produced there, but one is produced outside the nucleolus and transported inside to com­plete the ribosome assembly. Ribosomal proteins enter the nucleolus and combine with the four strands to create the two subunits, which forms the completed ribosome. The ribosome units leave the nucleus through the nuclear pores and unite once in the cytoplasm. Some ri­bosomes will remain free-floating in the cytoplasm, creating proteins for the cell’s use. Oth­ers will attach to the endoplasmic reticulum and produce the proteins that will be “exported” from the cell.

The scheme for the biosynthesis of ribosomes is as follows:

The RNA cistron of nucleo­lar DNA transcribes 45S precursor RNA in the presence of the enzyme RNA polymerase. The ribose sugar of certain regions of 45S RNA undergoes methylation (addition of methyl groups). In the methylated regions which gives rise to 28S and 18S RNA of the ribosomes. The non-methylated regions have a higher content of guanine and cytosine than the methy­lated regions.

Cleavage at site removes the transcribed spacer sequence from the 5’P end of 45S RNA. Cleavage at site 2 separates 18S rRNA. Cleavage at site 3 results in a large seg­ment containing 28S RNA and 5.8S RNA along with spacer segments. Cleavage 4 results in the final trimming of this segment. 5S RNA is synthesized outside the nucleolus. Ribosomal proteins are synthesized in the cytoplasm and translocated to the nucleus where they become associated with RNA.

Structural core proteins first associate with 45 S RNA to form 80S ribo-nucleoprotein particles. Other proteins are probably bound later. The series of degradations by which 45 S RNA forms 18S, 5.8S and 28S RNA occurs within the ribo-nucleoprotein particles. Ulti­mately the 40S and 60S subunits of the ribosome are formed, containing 18S and 28S+5.8S RNA, respectively. 5S RNA, which is synthesized outside the nucleolus, also becomes asso­ciated with the large 60S subunit.

The two types of subunits pass through pores in the nu­clear membrane to the cytoplasm. The 40S subunit binds to mRNA in the cytoplasm to form a 40S-mRNA complex. The 60S subunit now becomes associated with the 40S-mRNA com­plex to form the 80S ribosome with bound mRNA. In prokaryote cells the subunit RNA pre­cursors are trimmed to form 16 S and 23 S RNA. These become associated with protein to form the 30S and 50S subunits, respectively, of the 70S ribosome.

Essay # 2. Structure of Ribosome:

Composition of ribosomes can be divided into two parts – 2/3 part of r-RNA (ribosomal RNA) and 1/3 part RNP (Ribosomal protein or Ribonucleo protein). RNA performs all activities of ribosome that are catalyst based and the protein that resides over the surface stabilizes the organelle. Polypeptide chain is fabricated by translating mRNA (messenger RNA) with the aid amino acids that tRNA (transfer RNA) delivers. Since ribosomes have their active part composed of sub-structures of RNA, they are also termed ribozymes. Struc­ture of ribosome and its sub units are almost similar for both Eukaryotes and Prokaryotes.

Ribosomes in prokaryotes are 70S, where each ribosome comprises of 30S (small) and 50S (large) subunits. 50S further comprises of 5S subunit of RNA (comprising of almost 120 nucleotides) along with subunits of 23 S RNA (almost 2900 nucleotides) and 34 protein sub- units. 30S subunit of RNA comprises 1540 nucleotide that is bounded through 21 units of protein.

Ribosomes in eukaryotes are 80S, where each ribosome comprises of 40S (small) and 60S (large) subunits. 60S comprises of 5S subunit of RNA (almost 120 nucleotides) along with units of 28S RNA (almost 4700 nucleotides), subunit of 5.8S (close to 160 nucleotides) and ~49 units of protein. 40S has 18S RNA (approximately 1900 nucleotide) and ~33 units of protein.

Ribosomes found in mitochondria and chloroplasts of eukaryotes are closer to prokary­ote ribosome rather than the 80S eukaryote ribosome that supports the endo-symbiotic the­ory. Vertebrate mitochondria for example, contain 55S ribosome, each with a large 40S sub- unit and a small 30S unit. The sedimentation coefficients 80S, 70S and 55D are rounded off values (Fig. 4.43). Actual S values in different organisms may be slightly higher or lower. Mitochondrial ribosomes have been called mitoribosomes to distinguish them from cytoplas­mic ribosomes or cytoribosomes. Mitoribosomes occur in a wide variety of forms, the pre­dominant form in multicellular organisms being the 55S ribosome. Under certain conditions mitoribosomes have been obtained in aggregates of 2-7 ribosomes, forming poly-ribosomes.

The unit “S” means Svedberg units, a measure of the rate of sedimentation of a particle in a centrifuge, where the sedimentation rate is associated with the size of the particle. It is important to note that Svedberg units are not additive – two subunits together can have Sved­berg values that do not add up to that of the entire ribosome. This is resulting from the loss of surface area when the two subunits are bound. In addition, the ungainly shape of the fully assembled ribosome has different aqua-dynamic properties from the two unbound subunits.

Dissimilarities in eukaryotic and prokaryotic ribosomes are useful in antibiotic treat­ments against bacterial infections without causing any harmful effect on the neighboring cells. 70S ribosomes, that of bacterial descendants is susceptible to these antibiotics. Mito­chondria have ribosomes that are similar in nature to 70S of bacteria. However, their double impermeable membrane bounded structure does not permit antibiotics to affect the organelle.

Among the antibiotics that interfere with protein synthesis are chloramphenicol, erythromyocin, streptomycin, and the tetracycline. 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. 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.

Essay # 3. Types of Ribosomes:

1. 70S Ribosomes:

The 70S E. coli ribosomes contain 63% RNA and 37% proteins (almost 2:1). Bacterial ribosomes may constitute up to 40% of the dry weight of the cell and 90% of its RNA. Metal ions, chiefly magnesium ions, play an important role in holding the two sub- units together, and also in maintaining the structure of the two subunits. Below a certain level of Mg²⁺ the two subunits of the ribosome separate. The dissociation of the subunits is reversible and the two subunits can re-associate on raising the Mg²⁺ level. A stabilizing role is also attributed to Ca²⁺, Mn²⁺ and Co²⁺.

The 30S and 50S subunits of the ribosome have different binding properties. In E. coli the 30S subunit binds mRNA to form a 30S -mRNA complex before being attached to the 50S subunit. The 50S subunit, however, cannot bind mRNA if the 30S subunit is not present. The segment of mRNA binding to the 30S subunit is about 27 nucleotides in length.

Each 70S ribosome has two binding sites for tRNA, the amino acyl (A site) or acceptor site and the peptidyl (P site) or donor site. The A site receives the tRNA-amino acid complex and the P site binds the growing poly-peptidyl-tRNA. The A site is in the middle of the protected mRNA fragment. The mRNA passes through a tunnel between the two subunits (Fig. 4.44). Between the two subunits is a groove or channel through which the newly formed polypep­tide chain comes out.

2. 55S Ribosomes:

Mitochondria and chloroplasts which have independent protein synthe­sis machinery also contain ribosomes. These ribosomes were formerly thought to be of the 70S prokaryote type. The sedimentation coefficient of mitochondrial ribosomes has, how­ever, been shown to be about 55S, with a large subunit of 40S and a small subunit of 30S. The large subunit contains 16-17S and 5S RNA and the small subunit 12-13S RNA.

3. 80S Ribosomes:

Eukaryotic ribosomes are called ’80S ribosomes’, although actual S val­ues may be lower or higher than 80S. The sedimentation coefficient is 79S-80S in fungi and 80S in mammals. The small subunit is 40S and the large subunit.60S. The sedimentation coefficient of the large (60S) subunit is 56.3S. It contains one molecule each of 5S, 5.8S and 28S RNA and 49 proteins. RNA constitutes 59.4% of the subunit. The RNA- protein ratio is 1:1.

The ribosome is responsible for manufacturing the proteins. In each living cell, the infor­mation contained in the DNA is “transferred” to a messenger RNA (mRNA). The structure of a ribosome is complex, and it is responsible for making the millions of proteins that are needed by cells.

The mRNA leaves the nucleus and travels to the endoplasmic reticulum (or the cytosol) where the two ribosome subunits assemble around it and start synthesizing proteins. This is done by a process called “translation”, which is basically translating the mRNA information into an amino acid sequence. Cell that requires numerous protein for its proper functioning, require comparatively more ribosomes. To function actively in protein synthesis, they must be bound into complete ribosomes! A number of ribosomes may be attached to the same messenger, each manufacturing its own chain of polypeptides, called a polysome. Prokary­otic and eukaryotic ribosomes do not differ in any fundamental way; both perform the same functions by the same set of chemical reactions.