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RIBOSOME; THE ULTIMATE PROTEIN SYNTHESIZING NANO MACHINE

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CellisabigfactorywheretheinstructionsforallactivitiesarecodedintheDNA.A unitofinstructioncapableofdirectingthesynthesisofapolypeptideorprotein (orRNAslikerRNA,ribozymesetc)istermedasagene.Buttheworkforceisthe proteinswhicharecodedbytheseDNAs,specificallygenes.Themostvitalactivityin thisfactoryisundoubtedlyproteinsynthesis.Thisjobisdonebyanextremenano machinecalledribosomewhichsynthesiseproteinsusingdecodedmRNAinformation (fromDNA)inthecytoplasm.This24x7machineisthemostefficientandperfect machinedesignedforthepurposeofproteinsynthesis.Itsamazingstructuralsimplicity insize(just~23nm,1nm=109M)andcomplexityinitsfunctioniesynthesizing thousandsofproteinsrequiredforthecell,isnoteasytocomprehend.Ithink,Idont havetheknowledgetositeanyknownmachineinsizeorcomplexityasmarvellousas ribosomesandthatisit. Ribosomesaremadeupofseveral rRNAmoleculesandribosomalproteins, simplyanRNAproteincomplex.RibosomalRNAaccountsnearly80%ofallRNAsina cell.AlargenumberofRNAtranscriptsarecontinuouslysynthesisedandtransportedto the cytoplasm from the nucleus for protein synthesis. To meet this high demand of protein synthesising machinery, DNA sequences coding for ribosomal RNA the makes upribosomearenormallyrepeatedhundredsoftimes.

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Ribosome (Fig:1)

Zamecnik discovered beyond doubt that the cellular machines responsible for proteinsynthesisareribosomes.Thisdiscoveryfuelledthesearchfordifferentaspects of ribosomes. Later Masayasu Nomura (1960) succeeded in breaking 70S ribosome into its protein and RNA components and could spontaneously reassemble in vitro to 30S and 50S subunits under appropriate condition. These reassembled subunits resemble the native subunit in its activity and structure. High resolution structures of bacterialribosomalsubunitsrevealedtheexactnatureofRNAandproteincomponents in the ribosomes. In 50S subunit, the 5S and 23S rRNAs form the structural core. Proteinsaresecondarycomponentsinthecomplexasthereisnoproteinwithin18A0of the active site for peptide bond formation. As expected the RNA component in the ribosomehascatalyticactivityandribosomeisaribozyme.

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Each E.coli cells contain ~15000, ribosomes, making up 25% of the dry weight of the cell. In prokaryotes, ribosomes are smaller and made up of two unequal subunits 30S and 50S (Svedberg unit) and combined to form a sedimentation coefficient of 70S (18nm diameter). Whereas, Eukaryotic ribosomes are bigger (23nm) and more complex,80Sandmadeupofsubunits40Sand60S.

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EukaryoticMammalianRibosomecomponentsandSubunits (Fig:2)

Eukaryoticcellscontainmillionsofribosomes.Eukaryoticribosomepossessfour distinctribosomalRNAs,3inthelargesubunit60Sandoneinthesmallsubunit40S.In humans, the large subunit contains 28S, 5.8S and 5S RNA molecule, and the small subunitcontainsan18SRNAmolecule.The28S,18Sand5.8SrRNAmoleculesarefirst formedasaprimarytranscriptcalledprerRNAlatertrimmedbynucleasestofromthe final product. Remember, 28S, 18S and 5.8S rRNA molecules are transcribed by RNA polymerase I located in the nucleolus whereas 5S rRNA is synthesized from genes outside the nucleolus and the enzyme involved is RNA polymerase III. The 5S rRNA after synthesis is transported to the nucleolus where it joins other components to form ribosomalsubunits(Fig:2). The genes coding for ribosomal RNA (rRNA) are called rDNA genes. rDNA genesareseenasclusteredatspecificregions.Inhumans,5rDNAclustersarelocated on five different chromosomes. Think about the function of nucleolus, nucleolus is the sitewhereribosomesubunits(40Sand60S)aresynthesized.Nucleolusisnothing,but the clusters of rDNA that form conspicuous irregularly shaped organisation in the nucleusduringinterphase. SynthesizingtherRNAprecursor. Majority of studies on rRNA transcript synthesis were carried out on amphibian oocyteduetolargesizeupto2.5mmindiameterandlargenumbersofnucleolipresent

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(~100).ElectronmicroscopicstudyrevealedtandemrepeatsofrRNAgenes(rDNA)are situated along the DNA molecule. The selective amplification of rDNA is necessary for production of large number of ribosomes that are required for fertilized egg to synthesize enough proteins for embryonic development. The transcription of rDNA is mediated by RNA polymerase I (an RNA pol I for every 100 bp of DNA). The rRNA precursorisfurtherprocessedbyRNAandproteinstoformfinalrRNAproduct.Adjacent rDNAgenesareseparatedbyspacerDNAwhichisnottranscribed. rRNAprecursorprocessing: TheprerRNAisprocessedbytwoways:1) methylation ofnucleotideresidues by methylase and 2) conversion of uridine residues to pseudouridine residues by pseudouridylase.

a)prerRNAmodificationb)modificationbysnoRNA(Fig:3)

AllthesemodificationsoccurafternucleotideincorporationtothenascentRNA, that is post transcriptionally. These modified residues are located at specific positions andareseenasclusteredtogether.OnlythealterednucleotidestakepartintherRNA formationwhereasunalterednucleotidesarediscardedduringprocessing. Thefunctionofmethylationanduridineconversionisstillunclear.Thepossible functionsmaybetoprotectprerRNAfromenzymaticcleavage,promoterRNAfoldingto final3Dstructure,ortopromoteinteractionsofrRNAswithothermolecule. Firsttheformationof45SprerRNA This45SrRNAistrimmeddowntothe28S,18Sand5.8SrRNAmolecules(Fig:4)

ProcessingofMammalianRibosomalRNA(Fig:4). Circlednumbersaretheprincipal cleavagesites

OthermembersinvolvedinprerRNAprocessing. snoRNAs are small, nucleolar RNAs that are present in large numbers seen associated with particular proteins to form particles called snoRNPs (small, nucleolar ribonucleoproteins) that assist in pre rRNA processing. snoRNAs are divided into two groups based on function 1) box C/D snoRNAs decides the ribose moieties of nucleotide residues to be methylated. 2) box H/ACA snoRNAs determine the uridine residues which is to be converted to psuedouridine. This snoRNAs contain nucleotides (1021 nucleotides), that are complementary to sections of rRNA transcript and this regionbindtoformRNARNAduplex(Fig.3b). ExosomesaredozensofdifferentexonucleasesinvolveinRNAdegradationduringpre rRNAprocessingtofinalrRNA. Many findings and explanations on ribosomes are speculations based on electronmicrograph. As we discussed in the first paragraph, we are still at the shore whileexplainingthiswonderfulnanomachines. Glossary: Sedimentation coefficient: a measure of the rate at which a molecule (protein) suspendedinacolloidalsolutionsedimentsinanultracentrifuge.Itisusuallyexpressed inSvedbergs. Ribozymes: RNA with catalytic activity eg: telomerase, spliceosome, peptidyl transferaseetc Abzymes:antibodieswithcatalyticactivitycatalyticmonoclonalantibody. Additionalpoints: Dyskeratosisisrarefataldiseasecharacterizedbyskinabnormalities,bonemarrow failure and high risk of cancer. This disease is due to the mutation of the enzyme that converturidinetopseudouridineinrRNAs.

Difference between spacer DNA and introns: Introns are intra genic or DNA present within the genes that are not transcribed whereas spacerDNA are intragenic andareuntranscribedregionspresentbetweenthegenes. ImportantQuestionsDiscussed: I. Whatareribosomes? II. Hownucleolusisassociatedwithribosome? III. DefinerDNA? IV. WhatarethemajordifferencesbetweenEukaryoticandprokaryoticribosome? V. WhatarethestepsinvolvedinrRNAprocessing? VI. HowprerRNAisprocessed? VII. Whatarethepossiblefunctionsofmethylationandpseudouridineconversion? VIII. WhataresnoRNAs? IX. Whatareexosomes?
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LABELS: BOX C/D SNORNAS, BOX H/ACA SNORNAS, DYSKERATOSIS, METHYLATION, PRE-RRNA PROCESSING, PSUEDOURIDINE, RDNA GENES, RIBOSOME SYNTHESIS, RRNA, SNORNA, ZAMECNIK

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