1. Chapter 15 The Genetic Code

2. THE CODE IS DEGENERATE Degeneracy: many amino acids are specified by more than one codon. Synonyms: codons that specifies the same amino acid.

4. Perceiving Order in the Makeup of the Code Mutations in the first position  often a similar amino acid. Mutations in the second position  a similar amino acid. Transitions are the most common type of point mutations. Codons with pyrimidines in the second position  hydrophobic a.a. Codons with purines in the second position  polar a.a. Mutations in the third position A transition mutation in this position rarely specify a different a.a. Even a transversion mutation does not change a.a. about half the time.

5. Wobble in the Anticodon Wobble concept: the base at the 5’ end of an anticodon is not as spatially confined as the other two, allowing it to form hydrogen bonds with any of several bases located at the 3’ end of a codon.

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7. 3D structure of tRNA  the first anticodon base is at the end of the stack.

8. Three Codons Direct Chain Termination The chain-terminating codons, UAA, UAG, and UGA, are read by release factors. How the Code Was Cracked 1. Artificial messenger RNAs. 2. Cell-free systems for carrying out protein synthesis.

9. Stimulation of Amino Acid Incorporation by Synthetic mRNAs Polynucleotide phosphorylase can catalyze the formation of 3’  5’ phosphodiester bonds and thus make RNA molecules. Poly-U Codes for Polyphenylalanine A high magnesium concentration circumvents the need for initiation factors and the special initiator fMet-tRNA.

10. Mixed Copolymers Allowed Additional Codon Assignments Poly-AC molecules can contain eight different codons, CCC, CCA, CAC, ACC, CAA, ACA, AAC, and AAA. Their proportions can vary with the copolymer A/C ratio.

11. Transfer RNA Binding to Defined Trinucleotide Codons Specific aminoacyl-tRNA molecules can bind to ribosome-mRNA complexes. The binding of a trinucleotide to a ribosome is sufficient.

12. Codon Assignments from Repeating Copolymers Organic chemical and enzymatic techniques were being used to prepare synthetic polynucleotides with known repeating sequences.

14. THREE RULES GOVERN THE GENETIC CODE 1. Codons are read in a 5’ to 3’ direction. 2. Codons are nonoverlapping and the message contains no gaps. 3. The message is translated in a fixed reading frame. Three Kinds of Point Mutations Alter the Genetic Code 1. A missense mutation: change to a codon specific for another amino acid. 2. A nonsense or stop mutation: change to a chain-termination codon. 3. A frameshift mutation: insertion or deletion of base pairs that cause alteration of the reading frame. Genetic Proof that the Code is Read in Units of Three Three single-base pair insertions scrambled a short stretch of codons, but the encoded protein could tolerate the alteration.

15. SUPPRESSOR MUTATIONS CAN RESIDE IN THE SAME OR A DIFFERENT GENE 1. Reverse (back) mutations change an altered nucleotide sequence back to its original arrangement. 2. Suppressor mutations are the mutations that suppress the change due to the other mutation at different locations. (1) intragenic suppression: the suppressor mutation is at a different site in the same gene. (ex. correct conformation of the protein) (2) intergenic suppression: the suppressor mutation is in other genes. Suppressor genes cause suppression of mutations in other genes:

17. Intergenic Suppression Involves Mutant tRNAs Suppressor genes change the way the mRNA template is read. One of the best known examples is a case of mutant tRNA genes that suppress the effects of nonsense mutations in protein-coding genes. UAG suppressor mutants: insert Ser, Gln, or Tyr How (Ser, Gln, or Tyr) codons are read normally in the presence of suppressor tRNAs? - multiple genes for tRNA Tyr or mutation at the wobble position

18. Nonsense Suppressors also Read Normal Termination Signals Competition between the suppressor tRNA and the release factor UAG is used infrequently as a stop codon. UAA is used frequently and mutant cells producing UAA-suppressing tRNAs grow poorly. Proving the Validity of the Genetic Code The genetic code was shown to be working in the living cells as well as in the cell-free system. The gene for T4 lysozyme harboring a mutually suppressing pair of insertion and deletion mutations  differs by a stretch of five amino acids.

19. THE CODE IS NEARLY UNIVERSAL The code is nearly universal, but there are some exceptions. Mitochondrial genetic code is different from the “universal” code. 1. UGA codes for tryptophan. 2. Internal methionine is encoded by both AUG and AUA. 3. In mammal mitochondria, AGA and AGG are chain-termination codons. 4. In fruit fly mitochondria, AGA and AGG specify serine.

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