Degenerate Code. Translation. trna. The Code is Degenerate trna / Proofreading Ribosomes Translation Mechanism
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1 Translation The Code is Degenerate trna / Proofreading Ribosomes Translation Mechanism Degenerate Code There are 64 possible codon triplets There are 20 naturally-encoding amino acids Several codons specify more than one amino acid Therefore, an amino acid code cannot predict the precise nucleic acid code. The Genetic Code U C A G UUU UCU UAU UGU UUC Phe UCC UAC Tyr Cys UGC U Ala UUA UCA UAA UGA *** UUG Leu UCG UAG *** UGG Trp CUU CCU CAU CGU CUC CCC CAC His CGC C Leu Thr CUA CCA CAA CGA Arg CUG CCG CAG Gln CGG AUU ACU AAU AGU AUC ACC AAC Asn Ser Ile AGC A Pro AUA ACA AAA AGA AUG Met ACG AAG Lys Arg AGG GUU GCU GAU GGU GUC GCC GAC Asp GGC G Val Ser GUA GCA GAA GGA Gly GUG GCG GAG Glu GGG Reading Frame The reading frame of three nucleotides is chosen at initiation. Any polynucleotide contains three reading frames in one direction. A frame-shift mutation is a 1- or 2-base insertion or deletion, affecting reading frame. trna Proposed by Crick Adaptor Hypothesis Small RNA (70-90 nt) Highly modified - unusual nucleotides altered after transcription Characteristic three-dimensional shape 1
2 How does trna work? It has a Structure sufficient to be covalently linked to a specific amino acid; and an Anticodon sequence complementary to at least one codon representing an amino acid in mrna Anticodon RNA-specific pairings Loop contains three nucleotides (often modified by enzymes) that base-pair with codon RNA-RNA base pairing rules allow additional recognition Shape considerations place less stringency on the third (wobble) position 2
3 Charging reaction trna is covalently coupled with an amino acid by a charging reaction Performed by an aminoacyl trna synthetase Synthetase must recognize both specific trnas and amino acids Couples by acylation using ATP Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Charging All trnas end in CCA-OH 3 (added by enzyme without template) Activated aminoacyl bond contains chemical energy for peptide bond synthesis Aminoacyl trna synthetases also deacylate mis-charged trnas, allowing a proofreading function. 3
4 Ribosomes Composed of two large subunits, one 1.4x10 6 (40S) and 2.8x10 6 (60S). Each subunit contains rrna and a large number of proteins 60S contains 28S rrna (4.7 kb), 5.8S (160 nt) and 5S (120 nt); the 40S contains 18S (1.9 kb). Each subunit also contains--- Ribosome Active Sites Two trna binding sites: A and P. Initiation occurs in the P site, and subsequently, incomplete peptides are also bound to the P site. Any amino acyl-trna (except the initiator) can bind the A site. Mechanism of Translation Initiation begins when a complex of 40S subunit, the initiator aminoacyl-trna (mettrna i ), and initiation factors bind to the cap structure of an mrna First, a complex if formed between eif-2 and GTP eif-2 complexes with GTP Next, the eif-2-gtp complex binds the initiator aminoacyltrna: This forms the Ternary Complex 4
5 Finally, the ternary complex is assembled with the 40S ribosomal subunit: mrna is bound by additional initiation factors. First, CBP binds the cap of the mrna, then eif4a unwinds the first 15 nt of RNA structure near the 5' end. This unwinding requires ATP. eif4b also binds and increased the length of unwound RNA. Binding of the 40S-met-tRNA ternary complex with the mrna requires eif-3. Once bound, the 40S subunit migrates to the initator codon, AUG. Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. The large (60S) subunit is then added, requiring eif5 and releasing eif2 and eif3. We ve now completed initiation, and we re ready for elongation. Elongation involves the binding of a new aminoacyl-trna to the A site on the ribosome, followed by peptide bond formation, loss of the trna from the P site, then translocation of the peptidyltrna from the A to the P sites. Binding aminoacyl-trna to the A site requires eef-1 bound with GTP 5
6 eef-1 When eef-1 is released from the aminoacyl-trna (now bound to the A site), it is complexed with GDP. This eef-1-gdp complex is inactive until it is regenerated to GTP. The peptidyl transferase activity of the Ribosome catalyzes peptide bond formation Peptide bond formation proceeds with the amino group attacking the aminoacyl bond, leaving a 3'OH on the free trna in the P site, and the new peptide-trna in the A site. After peptide bond formation, the new peptide-trna (in the A-site) is translocated to the P-site. This requires a factor (eef2) and GTP hydrolysis. Ratchet-like Mechanism Elongation Cycle Ribosomes can only bind either eef-1 or eef-2 at one time, not both. Therefore, placement of an aminoacyltrna in the A site and translocation of peptidyl-trna from the A to P site reactions are exclusive and must be performed in lock-step. 6
7 GTP Cycling of Elongation Factors Termination Occurs when a termination codon enters the A-site and it is recognized directly by a release factor (erf). GTP is required for erf binding to the A site or its release. This causes hydrolysis of the peptide from the trna in the P-site, and release of all the components. Logic of Translation The growing peptide chain always carries with it (at its COOH end) the source of energy needed to form a peptide bond (the aminoacyl-trna linkage). Nucleotide polymerization depends on the 5' triphosphate of each entering nucleotide for energy. 7
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