R Ribosome Kundan Kishor Rajak Department of Zoology, School of Life Sciences, Mahatma Gandhi Central University, Motihar, Bihar, India Definition “Ribosome is a tiny granular cellular organelle that floats freely in cytoplasm as well as attached with the endoplasmic reticulum and performs translation (Protein synthesis).” Introduction The word “ribosome” originates from ribonucleic acid and Greek word soma, which means body (Bakowska-Zywicka and Tyczewska 2009). Albert Claude gave the term “microsome” after his excellent work of cell fractionation in the 1930s. Later, his two students – Philip Siekevitz and George Palade worked on the morphological and biochemical analysis of the secretory process related to the “microsome.” Further, Zamecnik’s group correlated microsome with protein biosynthesis and finally, Richard Brooke Robert in 1958 gave the term “ribosome” (Bakowska-Zywicka and Tyczewska 2009). The ribosome is a cellular structure which helps in protein synthesis. The mystery of life is stored in the genome sequence of their deoxyribonucleic acid (DNA). The genetic information of DNA is made available by transcription of genes to messenger ribonucleic acid (mRNA) that are subsequently translated into the various amino acid sequences, which are the building block of proteins. The ribosome plays a central role in the biogenesis of proteins from mRNA. The biogenesis of ribosome occurs in nucleoli. The nucleoli are nuclear domains, which are specialized in the production of ribosomal subunits (Stepinski 2014). Structure of Ribosome Thomas Steitz started the work on the structure and functions of the ribosome in 1990s and finally, in 2000 obtained a high-resolution structure of ribosome. Afterwards, other researchers were able to study the structure of the different subunits of ribosome as well as molecular interaction between them (Zhao 2011). Ribosomes are composed of RNA and protein. It has two subunits consisting of approximately two-third RNA and one-third protein. Ribosomes from mammalian mitochondria are exception, in which the ratio of protein and RNA is reversed (Sharma et al. 2003). Prokaryotic ribosome (70S) contains a smaller subunit (SSU) 30S and a larger subunit (LSU) 50S. The SSU (30S) is composed of one 16S ribosomal RNA (rRNA) containing around 1600 nucleotides and 20 ribosomal proteins (r-proteins), while the LSU # Springer International Publishing AG 2017 J. Vonk, T.K. Shackelford (eds.), Encyclopedia of Animal Cognition and Behavior, DOI 10.1007/978-3-319-47829-6_191-1 2 Mol. Mass ~ 0.7 ×106Da (30S) Mol. Mass ~ 1.3 ×106Da (50S) Total Mol. Mass ~ 2.0 ×106Da (70S) Ribosome SSU (16S rRNA & 20 r-Protein) SSU (18S rRNA & 32 r-Protein) Mol. Mass ~ 1.2 ×106Da (40S) Mol. Mass ~ 2.0 ×106Da (60S) LSU (23S rRNA, 5S rRNA & 33 r-Protein) LSU (5S rRNA, 5.8S rRNA, 28S rRNA & 47 r-Protein) Prokaryotic Ribosome Eukaryotic Ribosome Total Mol. Mass ~ 3.2 ×106Da (80S) Ribosome, Fig. 1 The simplified structure of prokaryotic and eukaryotic ribosome (50S) contains 23S rRNA sequence of 2900 nucleotides, 5S rRNA sequence with about 120 nucleotide and 33 r-proteins (sum total ~ 4620 nucleotides of rRNA and 53 r-proteins of the bacterial 70S ribosome), where S stands for the Svedberg unit for sedimentation velocity. Compared with the prokaryotes, eukaryotic 80S ribosomes also contain a SSU (40S) and a LSU (60S). The SSU (40S) is composed of one 18S ribosomal rRNA containing about 1753 nucleotides and 32 ribosomal proteins (r-proteins), while a LSU (60S) has 5S rRNA containing sequence with about 120 nucleotides, 5.8S with about 154 nucleotides, and 28S r RNAs with about 3354 nucleotide along with 47 r-protein (sum total ~ 5381 nucleotides of rRNA and 79 r-proteins of the yeast 80S ribosome) (Fig. 1) (Wilson and Daudna Cate 2012; Ramakrishnan 2009). Function of Ribosome The ultrastructure of prokaryotic ribosome revealed that it has three tRNA binding sites namely Aminoacyl-tRNA binding site (A site), Peptidyl-tRNA binding site (P site), and Exit site (E site). In the biosynthesis of protein, aminoacyltRNA bind to A site during elongation process, whereas at P site the tRNA linked to the growing polypeptide chain is bound. Further, E site provides the binding site for tRNA (Fig. 2). In prokaryotes, biosynthesis of protein begins by the establishment of a 30S complex between the 30S subunit, mRNA, initiation factors, and aminoacylated tRNA. The 30S subunit binds to specific sequence of mRNA (Shine-Dalgarno sequence) which is situated upstream to the AUG start codon and its complementary sequence is present on the 16S rRNA of the small subunit. The ribosome then changes its own position in a 30 direction with the mRNA till meeting with the start codon. After that large subunit (50S) binds to the 30S initiation complex to form the 70S initiation complex. In this complex, anticodon of AUG is paired in the P site, and further this initiation complex encounters again with other codons and protein synthesis takes place unless the stop codon is encountered. In eukaryotes the assembly and the protein synthesis process is complex than prokaryotes. Initiation of protein synthesis is basically similar in prokaryotes and eukaryotes except the involvement of initiation factors. Some important differences between the protein biosynthesis of prokaryotes and eukaryotes are the initiating amino acid is methionine in eukaryotes while N-formylmethionine in prokaryotes, eukaryotic mRNA is monocistronic while polycistronic mRNA in prokaryotes. Eukaryotic mRNA does not contain Shine-Dalgarno sequence like prokaryotes therefore initiation codon is recognized by ribosomal scanning of mRNA. Initiation of protein biosynthesis in eukaryotes involves the formation of 48S preinitiation complex between the small subunit (40S), mRNA, initiation factors, and start codon. The ribosome then scans the mRNA to locate the start codon. Further, the large subunit (60S) binds to form complete 80S initiation complex. Further, this initiation complex encounters again with other codons and protein synthesis takes place unless the stop codon encounters like prokaryotes. Ribosome 3 Large ribosomal subunit E site of ribosome E P A Small ribosomal subunit A site of ribosome P site of ribosome Ribosome, Fig. 2 All three RNA- binding sites on a ribosome Summary References The ribosome is a cellular structure which involves in protein synthesis. The transcribed mRNA associate with ribosome and protein synthesis occurs according to the codon of mRNA with the help of tRNA and accessory factors. Thus, in prokaryote, 70S ribosomes and in eukaryotes 80S ribosome play role like proteinmaking machines. Bakowska-Zywicka, K., & Tyczewska, A. (2009). The structure of the ribosome-short history. BIT, 1(84), 14–23. Ramakrishnan, V. (2009). The ribosome: Some hard facts about its structure and hot air about its evolution (Cold Spring Harb Symposia on Quantitative Biology, Vol. LXXIV). Cold Spring Harb Laboratory Press, Long Island, New York, 978-087969870-6. (http://sympo sium.cshlp.org/content/74/25.long). Sharma, M. R., Koc, E. C., Datta, P. P., Booth, T. M., Spermulli, L. L., & Agarwal, R. K. (2003). Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins. Cell, 115, 97–108. Stepinski, D. (2014). Functional ultrastructure of plant nucleolus. Protoplasma, 251, 1285–1306. Wilson, D. N., & Daudna Cate, J. H. (2012). The structure and the function of eukaryotic ribosome. Cold Spring Harbor Perspectives in Biology, 4, a11536. Zhao, P. (2011). The 2009 Nobel Prize in chemistry: Thomas A. Steitz and the structure of ribosome. Journal of Biology and Medicine, 84, 125–129. Cross-References ▶ RNA ▶ Transcription