Recitation_5-handout-Simona

Recitation_5-handout-Simona - 7.05 Section 05 TA: Simona...

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7.05 – Section 05 03/12/2008 TA: Simona Tescu Email: tescu@mit.edu 1/8 RECITATION #5 Covers lectures 12, 13, 14: Translation and the ribosome, The genetic code, Splicing, The Central Dogma The genetic code Properties: - Triplet code: 3 bases encode an amino acid - non-overlapping - no punctuation - One triplet code for only one amino acid; one amino acid can be encoded by several triplet codes o degenerate (64 possible 3-base codons – 20 amino acids) Degeneracy occurs because some tRNA anticodons can recognize multiple codons - START codon: AUG (encodes for Met, M) - STOP codons: UAA, UAG, UGA Blossum 62: scoring matrix that reflects favorable amino acid substitutions (because of similar chemical properties); high positive number suggests that the two amino acids can be easily substituted one with the other; high negative number means very rare substitution Question 1 (Question 3, Problem Set 3-2008) Imagine that you found an organism on Mars that synthesized proteins using the same 20 amino acids as life here on earth, but it had a different triplet code that you already knew, which was non-overlapping and non-punctuated. You made an in vitro translation system from this organism, then set out to determine its code and made the following observations: Poly(AUU) coded for poly-Ala, poly-Asp, and poly-Thr Poly(CUAU) coded for a mixed polymer containing Ala, Phe and Gly What are the new conclusions that you could draw about the code of this Martian organism based on these two observations?
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7.05 – Section 05 03/12/2008 TA: Simona Tescu Email: tescu@mit.edu 2/8 Question 2 (Question 4, Problem Set 3-2008) Translation 1. tRNA charging tRNA is charged with one amino acid by aminoacyl-tRNA synthetase 1 ATP is needed Reaction is driven forward by PPi hydrolysis (by H 2 0) Aminoacyl-tRNA synthetase specificity for tRNA is achieved by: o specific binding of the amino acid in the active site (specific binding pocket) o a neighboring hydrolysis site that cleaves improper amino acid (double sieve mechanism) H 2 0 Amino acid + ATP + tRNA + E E-aminoacyl-tRNA + AMP + PPi 2 Pi
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7.05 – Section 05 03/12/2008 TA: Simona Tescu Email: tescu@mit.edu 3/8 2. Initiation 30S ribosomal subunit is bound by two initiation factors : IF 1 and IF 3 , which prevent the formation of the complete ribosome (70S) in the absence of mRNA IF 2 -GTP + fMet-tRNA assist 30S complex to bind to mRNA (to Shine- Dalgarno sequence in bacteria); IF 3 is released 50S subunit binds to the 30S subunit, while releasing IF 1 and IF 2 , and
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Recitation_5-handout-Simona - 7.05 Section 05 TA: Simona...

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