Molecular biology - Chapter 19: Ribosomes and transfer RNA

Molecular BiologyFourth EditionChapter 19Ribosomes and Transfer RNALecture PowerPoint to accompanyRobert F. WeaverCopyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.119.1 RibosomesE. coli ribosome is a two-part structure with a sedimentation coefficient of 70STwo subunits of this structure:30S is the small subunit that decodes mRNA50S subunit links amino acids together through peptide bonds2Fine Structure of 70S RibosomeT. thermophilus crystal structure of 70S ribosome in complex with mRNA analog and 3 tRNAs shows:Positions and tertiary structures of all 3 rRNA and most proteins can be determinedShapes and locations of tRNAs in A, P, and E sites are evidentBinding sites for tRNAs in ribosome are composed of rRNA, not proteinAnticodons of tRNAs in A and P sites approach each other closely enough to base-pair with adjacent codons bound to 30S subunit as mRNA kinks 45°3More Structural DetailAcceptor stems of tRNAs in A and P sites also approach each other closely (5 Å) in the peptidyl transferase pocket of 50S subunitConsistent with need for 2 stems to interact during peptide bond formation12 contacts are seen between subunits, most RNA-RNA interactions4E. coli Ribosome StructureCrystal structure of E. coli ribosome contains 2 structures differing from each other by rigid body motions of ribosome domains relative to each otherHead of 30S particle rotates by 612 rotation compared to T. thermophilus ribosomeProbably part of a ratchet action that occurs during translocation5Eukaryotic RibosomesEukaryotic cytoplasmic ribosomes are:LargerMore complexEukaryotic organellar ribosomes are smaller than prokaryotic ones6Ribosome CompositionThe E. coli 30 subunit contains16S rRNA21 proteins (S1 – S21)E. coli 50S subunit contains5S rRNA23S rRNA34 proteins (L1 – L34)Eukaryotic cytoplasmic ribosomes are: Larger Contain more RNAs and proteins7Ribosome AssemblyAssembly of the 30S ribosomal subunit in vitro begins with 16S rRNAProteins join sequentially and cooperativelyProteins added early in the processHelp later proteins to bind to the growing particle8Fine Structure of the 30S SubunitSequence studies of 16S rRNA led to a proposal for secondary structure of the moleculeX-ray crystallography studies have confirmed the conclusions of these studies30S subunit with extensively base-paired 16S rRNA whose shape essentially outlines the whole particleX-ray crystallography studies confirmed locations of most of the 30S ribosomal proteins9Interaction of the 30S Subunit with Antibiotics30S ribosomal subunit plays 2 rolesFacilitates proper decoding between codons and aminoacyl-tRNA anticodonsAlso participates in translocationCrystal structures of 30S subunits with 3 antibiotics interferring with these 2 roles shed light on translocation and decodingSpectinomycin StreptomycinParomomycin 10SpectinomycinSpectinomycin binds to 30S subunit near the neckAt this site, binding interferes with movement of the head Head movement is required for translocation11StreptomycinStreptomycin binds near the A site of 30S subunitBinding stabilizes the ram state of the ribosomesFidelity of translation is reduced: Allowing noncognate aminoacyl-tRNAs to bind easily to the A sitePreventing the shift to the restrictive state that is necessary for proofreading12ParomomycinParomomycin binds in the minor groove of 16S rRNA H44 helix near the A siteThis binding flips out bases A1492 and A1493 to stabilize base pairing between codon and anti-codonFlipping out process normally requires energyParomomycin forces it to occur and keeps the stabilizing bases in placeState of the A site stabilizes codon-anticodon interaction, including interaction between noncognate codons and anticodons with decline in fidelity13Interaction of the 30S Subunit with Initiation FactorsX-ray crystal structure of IF1 bound to the 30S ribosomal subunit shows IF1 binds to the A siteIn that position IF1: Blocks fMet-tRNA from binding to the A siteMay also actively promote fMet-tRNA binding to P site through interaction between IF1 and IF2IF1 also interacts closely with helix H44 of the 30S subunitIF accelerates both association and dissociation of the ribosomal subunits14Fine Structure of the 50S Subunit Crystal structure of the 50S ribosomal subunit has been determined to 2.4 ÅStructure reveals relatively few proteins at interface between ribosomal subunitsNo proteins within 18 Å of peptidyl transferase active center tagged with a transition state analog2’-OH group of tRNA in the P site is very well positioned to form a hydrogen bond to amino group of aminoacyl-tRNA in A site152‘-Hydroxyl Group Role2’-OH group of tRNA in the P site Forms a hydrogen bond to amino group of aminoacyl-tRNA in A siteHelps catalyze peptidyl transferase reactionRemoval of this hydroxyl group eliminates peptidyl transferase activityRemoval of the 2’-OH of A2451 of the 23S rRNA inhibits peptidyl transferase activityMay also participate in catalysis by: Hydrogen bondingHelping to position reactants properly for catalysis1650S Exit TunnelExit tunnel through the 50S subunitJust wide enough to allow a protein a-helix to passWalls of tunnel are made of RNAHydrophobicity is likely to allow exposed hydrophobic side chains of nascent polypeptide to slide through easily17PolysomesMost mRNAs are translated by more than one ribosome at at timeA structure in which many ribosomes translate mRNA in tandem is called a polysomeEukaryotic polysomes are found in the cytoplasmIn prokaryotes, transcription of a gene and translation of the resulting mRNA occur simultaneouslyMany polysomes are found associated with an active gene1819.2 Transfer RNAAn adaptor molecule was proposed that could serve as a mediator between string of nucleotides in DNA or RNA and the string of amino acids in the corresponding proteinThe adaptor contained 2 or 3 nucleotides that could pair with nucleotides in codons19The Discovery of tRNATransfer RNA was discovered as a small species independent of ribosomesThis small species could be charged with an amino acidThat species could then pass the amino acid to a growing polypeptide20tRNA StructureAll tRNAs share a common secondary structure represented by a cloverleafFour base-paired stems define three stem-loopsD loopAnticodon loopT loopThe acceptor stem is the site to which amino acids are added in the charging step21tRNA ShapetRNAs share a common three-dimensional shape resembling an inverted LThis shape maximizes stability by lining up the base pairs: In the D stem with those in the anticodon stemIn the T stem with those in the acceptor stemAnticodon of the tRNA protrudes from the side of the anticodon loopAnticodon is twisted into a shape that base-pairs with corresponding codon in mRNA22Modified Nucleosides in tRNA23Recognition of tRNA Acceptor StemBiochemical and genetic experiments have demonstrated the importance of the acceptor stem in recognition of a tRNA by its cognate aminoacyl-tRNA synthetaseChanging one base pair in the acceptor stem can change the charging specificity24The AnticodonBiochemical and genetic experiments have shown that anticodon, like acceptor stem, is an important element in charging specificitySometimes the anticodon can be the absolute determinant of specificity25Structures of Synthetase-tRNA ComplexesCrystallography has shown that synthetase-tRNA interactions differ between the 2 classes of aminoacyl-tRNA synthetasesClass I synthetasesPockets for acceptor stem and anticodon of their cognate tRNAApproach the tRNAs from the D loop and acceptor stem minor groove sideClass II synthetasesAlso have pockets for acceptor stem and anticodonApproach tRNA from opposite including the variable arm and the major groove of the acceptor stem26Proofreading and EditingAmino acid selectivity of at least some aminoacyl-tRNA synthetases is controlled by a double-sieve mechanism1st sieve is coarse excluding amino acids too bigEnzyme accomplishes this with an active site for activation of amino acids just big enough to accommodate the cognate amino acid, not larger amino acids2nd sieve is fine, degrades too small aminoacyl-AMPs Done with a second active site, the editing site, admits small aminoacyl-AMPs and hydrolyzes themCognate aminoacyl-AMP is too big to fit into the editing siteEnzyme transfers the activated amino acid to its cognate tRNA27