Ribosomes

Though the amino acid sequence of each protein in the cell is encoded by the DNA in a cell nucleus, the proteins aren't really produced there. A simple experiment shows this: even if a brief beam of the radioactive amino acid is given to a cell, the radiation is directly associated with the new protein, not in the nucleus, but in the cytoplasm. When researchers first conducted these studies, they discovered that protein synthesis is correlated with huge complexes of ribonucleic acid (RNA) proteins called ribosomes.

Ribosomes consist of several molecules of a unique RNA molecule called ribosomal RNA, or rRNA along with a complex of many dozen proteins. Ribosomes are one of the molecular assemblies actually found in cells that are most complex. Ribosomes are very complicated protein and RNA structures.

They are the site of protein synthesis; cytoplasmic ribosomes synthesize proteins intended to remain inside the cell, while plasma membrane ribosomes produce proteins for external transport. The newly established polypeptide folds into its desired shape either as the ribosome synthesizes it or soon after protein synthesis has been completed. The size and shape of each protein depend on its sequence of amino acids. Unique and special proteins called molecular chaperones help the polypeptide to fold in its proper shape.

There are two subunits in each ribosome. The subunits only join in forming a functional ribosome when attached to another type of RNA in the cytoplasm called messenger RNA (mRNA). The ribosome attaches to the mRNA, a transcribed copy of a portion of DNA, to make proteins and uses the information for protein synthesis.

Occurrence of Ribosomes

Ribosomes are distributed universally all throughout the kingdom of animals and plants. They're also found in prokaryotes. The mammalian RBC is the only cell type devoid of ribosomes. For any given type, the density of ribosomes per unit area is rather constant. It is high in active m protein synthesis cells and low in cells where synthesis of protein is low.

Distribution of Ribosomes

The ribosomes frequently occur freely in the cytoplasm in prokaryotic cells. The ribosomes occur freely in the cytoplasm in eukaryotic cells or remain attached to the outer surface of the endoplasmic reticulum (ER) membrane. They are called free ribosomes if they are not attached to the ER. Free ribosomes represent protein synthesis sites needed to maintain the cytoplasmic matrix's enzyme composition.

Number and Concentration of Ribosomes

Ribosomes can be observed in all cells containing endoplasmic reticulum. Nearly 100 ribosomes per μ3 are found in rabbit reticulocytes, which corresponds to 1x105 particles per reticulocyte and approximately. 5% of the total cell mass, or approximately 20,000 to 30,000 cell mass. But, if unfavorable nutritional conditions slow the rate of protein synthesis, the number of ribosomes can drop significantly in protein synthesizing cells and bacteria.

Chemical Composition of Ribosomes

RNA and proteins are the main constituents of ribosomes. The lipids are completely absent or traceable. E. Coli's ribosomes possess almost 60-65% of RNA and 35-40% of their weight protein. Ribosomal RNA differs from tRNA and other RNA classes of most cells in size and base content. In all ribosomes, two types of RNAs are found. They are an essential component and can't be easily removed.

Prokaryotic Ribosomes

• As compared to eukaryotic ribosomes, the prokaryotic ribosomes are smaller. This is attributed to the association of eukaryotic cell ribosomes with the cytoplasmic or endoplasmic reticulum. 

• Prokaryotic ribosomes are called 70S ribosomes and have physical dimensions of approximately 14 to 15 nm by 20 nm, with a molecular weight of roughly 2.7 million, and are made of 50S and 30S subunits. 

• The S stands for Svedberg unit in the measurement of ribosome sedimentation coefficient unit. This is a measure of the velocity of sedimentation in a centrifuge; the faster a particle travels when centrifuged, the higher its Svedberg value or the coefficient of sedimentation. 

• The coefficient of sedimentation is a function of the molecular weight, volume, and shape of a particle. Normally, heavier and more compact particles have greater numbers of Svedberg or faster sediments. 

• There are smaller bacterial ribosomes than eukaryotic ribosomes. A prokaryotic cell usually only has a few thousand ribosomes, while there are several million in a metabolically active eukaryotic cell, such as a human liver cell. 

• Proteins that work in the cytoplasm are produced by free ribosomes that are suspended there, while proteins that are bound within membranes or intended for export from the cell are assembled by ribosomes that are bound to rough ER.

• The large subunit, called the 50S, is spherical in the prokaryotic cell with a prominent "stalk" and a "central protuberance." It contains the center of peptidyltransferase which catalyzes the formation of peptide bonds between the incoming amino acid and the growing chain of peptides. 

• The 50S particle is thick and homogenous. The thin and flexible small subunit of ribosomes in prokaryotes is called the 30S. The 30S houses the decoding center for mRNA and is divided into three domains i.e. head, body, and platform. 

• Each one of these domains includes one of the 16S rRNA's main secondary structure domains, namely the 3' major, 5' and central domains. In 16S rRNA, 3' minor domain forms an extended helix running down the 30S subunit surface's long axis, which interacts with the 50S subunit. 

• All four 30S particle domains join in a relatively narrow region of the neck. The two "active sites'' face each other around the interface of the subunit and are physiologically linked by the molecule's two ends.

Eukaryotic Ribosomes

• The eukaryotic ribosome (i.e., one not found in mitochondria and chloroplasts) is larger than the prokaryotic 70S ribosome. It is a dimer of the 60S and the 40S subunit, about 22 nm in diameter, and has the sedimentation coefficient of 80S and a molecular weight of 4 million. 

• Eukaryotic ribosomes can be either associated with the endoplasmic reticulum or free in the cytoplasmic matrix. When bound to the endoplasmic reticulum to form rough ER, they are attached through their 60S subunits. 

• Both free and ER-bound ribosomes synthesize proteins. Proteins made on the ribosomes of the RER are often secreted or are inserted into the ER membrane as integral membrane proteins. 

• Free ribosomes are the sites of synthesis for non secretory and non membrane proteins. Some proteins synthesized by free ribosomes are inserted into organelles such as the nucleus, mitochondrion, and chloroplast. They also assist the transport of proteins into eukaryotic organelles such as mitochondria

The Nucleolus Manufactures Ribosomal Subunits

• When cells are synthesizing a large number of proteins, they must first make a large number of ribosomes. To facilitate this, hundreds of copies of the portion of the DNA encoding the rRNA are clustered together on the chromosome. 

• By transcribing RNA molecules from this cluster, the cell rapidly generates large numbers of the molecules needed to produce ribosomes. 

• These proteins are associated with dangling rRNA molecules. These areas where ribosomes are being assembled are easily visible within the nucleus as one or more dark-staining regions, called nucleoli. 

• Nucleoli can be seen under the light microscope even when the chromosomes are extended, unlike the rest of the chromosomes, which are visible only when condensed.

Major Differences between Eukaryotic and Prokaryotic Ribosomes

Function of Ribosomes

• The main function of ribosomes is to translate the messenger RNA (mRNA) encoded genetic information into proteins. Ribosomes move along a molecule of mRNA during protein synthesis, reading one codon at a time. 

• The ribosome reading of each codon results in the incorporation of one amino acid into a progressively longer protein chain. The transfer of RNA (tRNA) molecules, which are the adapter molecules in the translation mechanism, brings the amino acids to the ribosome. 

• Each of the 20 protein synthesis amino acids is connected to a specific type of tRNA. Thus, ribosomes can recognize and bind the right word for nucleic acid specified by the tRNA anticodon with its attached amino acid. 

• Once the ribosome finally reaches a stop codon on the mRNA, the translation stops, separating and detaching the ribosomal subunits from the mRNA and releasing the completed protein.

Summary 

• All prokaryotes have 70S ribosomes whereas eukaryotes in their cytosol contain larger 80S ribosomes.

• The 70S ribosome consists of subunits 50S and 30S. In catalyzing two biological processes, ribosomes play a key role in the transfer of peptidyl and hydrolysis of peptidyl.

• The eukaryotic ribosome (i.e., one not found in mitochondria and chloroplasts) is larger than the prokaryotic 70S ribosome. 

• At any given moment, many rRNA molecules dangle from the chromosome at the sites of these clusters of genes that encode rRNA. 

• The ribosome reading of each codon results in the incorporation of one amino acid into a progressively longer protein chain. The transfer of RNA (tRNA) molecules, which are the adapter molecules in the translation mechanism, brings the amino acids to the ribosome.