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Lecture26 (Brandl4).docx

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Department
Biochemistry
Course
Biochemistry 2280A
Professor
Eric Ball
Semester
Fall

Description
Lecture 4 Notes – Brandl A one-letter code with A, G, U, C would provide: 4 codons A two-letter code would provide: 4 x 4 = 16 codons A three-letter code would provide: 4 x 4 x4 = 64 codons The code is:  As there are 20 amino acids, a 3-letter code (64 codons) is sufficient  Universal (found in all organisms)  Non-overlapping  Commaless, no gaps (gaps were removed by splicing)  61 codons for 20 amino acids – therefore redundant  Redundancy – some codord specify the same amino acid o Occurs at the 3 position of the codon (wobble)  3 stop codons: o UAA, UAG, UGA  1 start codon: o AUG Other features of the code:  More common amino acids (found in proteins) have more codons o Met – AUG o Trp – UGG  Related amino acids have similar codons o Asp: GAC, GAU o Glu: GAG, GAA o Gln: CAG, CAA Types of Mutations  Missense Mutation – single base mutation which results in a single amino acid change  Frameshift mutation – could be the insertion of one or two or taking away one or two – insertion or deletion of a base results in a change in reading frame of the protein from the point of the mutation onward  Nonsense mutation – a nonsense mutation results in premature termination of the protein tRNA (transfer):  Vehicle that bring amino acids to the growing polypeptide chain  Function in a codon specific fashion, relying on base pairing rules  All roughly ~80 nucleotides in length and have a cloverleaf secondary structure due to internal base pairing (stems and loops)  The anticodon of the tRNA hybridizes with the codon  The correct amino acid is covalently linked to the 3’ end of the tRNA (3 acceptor site)  Wobble results from the fact that accurate base pairing for some tRNAs only requires matching at the first 2 positions o Anti-codon base pairs with the codon using normal base-pair rules  Non-conventional bases  Modified bases put in afterward  Don’t have clover leaf structure in real life – in 3D looks more like an L structure Molecular Basis for Wobble: 1. Some amino acids have more than one tRNA 2. Accurate base pairing for some tRNAs only requires matching at the first two positions of the codon - Base-pairing interactions for the 2 Phe codons, with the Phe-tRNA - Accurate base pairing at the 3 positions of the codon - Accurate base pairing at only the first two positions of the codon – WOBBLE Amino Acid Activation – Aminoacyl tRNA synthetases:  Using ATP as the energy source, the carboxyl group of a specific amino acid is coupled to the 3’ end of a specific tRNA in a high-energy bond  20 of these enzymes: one for each amino acid  Amino acid activation by aminoacyl t-RNA synthetases (otherwise known as charging of tRNAs) is important for: 1. Providing an energy source for later peptide bond formation – store energy from ATP in a high energy ester linkage 2. Providing specificity by coupling the correct amino acid to the specific tRNA Ribosomes:  Protein synthesis occurs on large multimeric protein RNA complexes called ribosomes  Ribosomes have 2 subunits, large and small o The small and large subunits are composed of both RNA (rRNA) and protein o Large subunit: ~49 proteins + 3RNA molecules - The large subunit catalyzes the formation of peptide bonds o Small subunit: ~33 proteins + 1 RNA molecule - The small subunit matches tRNAs to the codons  Three sites for the binding of tRNAs on the ribosome: o A - aminoacyl tRNA site o P - peptidyl tRNA site o E - exit site  The mRNA is bound in proximity to the A and P sites  The mRNA is decoded in a 5’  3’ direction along the mRNA, one codon at a time The Process of Translation:  Assuming a ribosome is already in the process of translating an mRNA….  A tRNA is joined to the growing polypeptide in the P site  An aminoacyl tRNA is bound in the A site o Requires base pairing between the tRNA and the codon  The energy of the amino acid-tRNA bond (ester bond) in the P site is used to form a new peptide bond between the am
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