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Principles of Biochemistry exam 2 SI notes. Werner Bergen...

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SI NOTES: Session 16

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Wobble base pairing occurs between the 5’ end of tRNA, or the anticodon and the base at the 3’ end of mRNA, or the codon Class I aminoacyl-tRNA synthetases: load amino acid onto 2’-OH Class II aminoacyl-tRNA synthetases: load amino acid onto 3’-OH Second genetic code provides extra proof reading by aminoacyl-tRNA synthetases at 2 levels amino acid tRNA Specificity of tRNA is found in its variable pocket Prokaryotic translation= chain initiation → chain elongation → chain termination Synthesis of a polypeptide chain begins at N terminal tRNAmet and tRNAfmet contain a specific triplet, 3’-UAC-5’ that pairs with 5’-AUG-3’ in the mRNA sequence. The AUG is the start signal Shine-Dalgarno sequence acts as ribosome binding site. 5’-GGAGGU-3’ Three sites on the 50S and 70S subunit of tRNA in chain elongation= P site, A site, E site o Peptidyl, aminoacyl, exit Amino acid activation and aminoacyl-tRNA are both catalyzed by aminoacyl-tRNA synthetase o First step: amino acid forms covalent bond to A nucleotide, producing aminoacyl-AMP (energy from hydrolysis of ATP) o Second step: ester linkage formed between amino acid and 3’-OH or 2’-OH of ribose at 3’ end of tRNA Primary function of aminoacyl-tRNA synthetase: makes sure right amino acid pairs with right tRNA P binds to tRNA that carries peptide chain A binds an incoming aminoacyl-tRNA, which has been added to the growing peptide chain E carries an uncharged tRNA that is about to be released from the ribosome Chain elongation steps: 1. Add second amino acid to 70S initiation complex, second aminoacyl-tRNA binds to A site, triplet of tRNA bases form H bonds with triplet of mRNA bases 2. Need GTP, EF-P,EF-Tu, EF-Ts. GTP hydrolyzed, EF-Tu dissociates, EF-P bound next to P site and E site and catalyzes first peptide bond 3. Peptide bond formed in reaction catalyzed by peptidyl transferase 4. Need EF-G, GTP hydrolyzed to GDP and Pi. uncharged tRNA moves from P to E site where it is released. Peptidyl-tRNA translocated to P site from A site, aka translocation Peptide chain termination requires stop codon, stop signals and release factors (RF1,RF2,RF3) Polysome: more than one amino acid is bound to 1 mRNA 2 posttranscriptional modifications of mRNA: 5’ cap and 3’ poly A tail Eukaryotic chain initiation= eukaryotic initiation factors Eukaryotic chain elongation uses the same mechanism of peptidyl transferase and ribosomal translocation BUT the ribosome only contains A and P site

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Eukaryotic chain elongation has 2 elongation factors (eEf-1 and eEf-2) Suppressor tRNA: permits translocation to continue through a stop codon Protein degradation happens mostly in the lysosome structure called proteasomes Nucleases hydrolyze nucleic acids Le Chatelier’s principle: is stress is applied to a system at equilibrium the system reacts to minimize the effect of stress, so balance Endergonic reactions achieved by reaction coupling...