Translation Chapter 9

Overview Occurs on ribosomes-large aggregates of rRNA and protein tRNA acts as amino acid carriers Prokaryotes—occurs simultaneously with transcription and mRNA degradation Eukaryotes—occurs in cytoplasm mRNA translated 5’3’ Protein synthesis aminocarboxy

Protein Synthesis Polymerization of amino acids: condensation reaction (dehydration synthesis)

~Universal Genetic Code Codons—sets of 3 nucleotides corresponding to a single amino acid Each codon specifies a single amino acid More than one codon can specify the same amino acid code is said to be degenerate Some aa correspond to a single codon AUG—initiator codon, methionine (Met, M) UGG–Tryoptophan (TrP, W) Often codons encoding the same aa differ onl;y at the 3rd nucleotide Codons—sets of 3 nucleotides corresponding to a single amino acid Each codon specifies a single amino acid More than one codon can specify the same amino acid code is said to be degenerate Some aa correspond to a single codon AUG—initiator codon, methionine (Met, M) UGG–Tryoptophan (TrP, W) Often codons encoding the same aa differ onl;y at the 3rd nucleotide

~Universal Genetic Code The Genetic Code Chart shows aa assignments Non-random Tend to be clustered Reflects similar codons specifying the same aa Spontaneous mutations causing a single base change May not cause an aa change Similar aa are specified by similar codons Greatest similarities in first two nucleotides eg glycine – 4 codons – all GGX Greatest variability in third nucleotide of the triplet QUIZ—Codon for R, K, V, F aa for UCG, CCA, GGG

Why~Universal? Exceptions GUG sometimes used as a start Mammalian mitochondria Ciliated protozoa Selenocysteine NH3+ COO- H-C-CH2SeH GUG sometimes used as a start (bacteria) Mammalian mitochondria- AUA start, other codons different than consensus. EX UGA-Trp (not Stop) AGG, AGA-Stop (not Arg) Ciliated protozoa—Ex UAA and UAG—Gln Selenocysteine An essential amino acid for selenoproteins EX. Glutathione oxidase Uses unique tRNA, initially bound to Ser Anticodon recognizes UGA (Stop) as Sel Signals in 3’ region determine Stop or Sel Incorporation of selenocysteine by the translational machinery occurs via an interesting and unique mechanism. The tRNA for selenocysteine is charged with serine and then enzymatically selenylated to produce the selenocysteinyl-tRNA. The anticodon of selenocysteinyl-tRNA interacts with a stop codon in the mRNA (UGA) instead of a serine codon. The selenocysteinyl-tRNA has a unique structure that is not recognized by the termination machinery and is brought into the ribosome by a dedicated specific elongation factor. An element in the 3' non-translated region (UTR) of selenoprotein mRNAs determines whether UGA is read as a stop codon or as a selenocysteine codon.

Selenocysteine The 21st amino acid? An essential amino acid for selenoproteins EX. Glutathione oxidase Uses unique tRNA, initially bound to Ser Anticodon recognizes UGA (Stop) as Sec Signals in 3’ region determine Stop or Sec Dedicated specific elongation factor The 21st amino acid? An essential amino acid for selenoproteins EX. Glutathione oxidase Uses unique tRNA, initially bound to Ser Anticodon recognizes UGA (Stop) as Sec Signals in 3’ region determine Stop or Sec Incorporation of selenocysteine by the translational machinery occurs via an interesting and unique mechanism. The tRNA for selenocysteine is charged with serine and then enzymatically selenylated to produce the selenocysteinyl-tRNA. The anticodon of selenocysteinyl-tRNA interacts with a stop codon in the mRNA (UGA) instead of a serine codon. The selenocysteinyl-tRNA has a unique structure that is not recognized by the termination machinery and is brought into the ribosome by a dedicated specific elongation factor. An element in the 3' non-translated region (UTR) of selenoprotein mRNAs determines whether UGA is read as a stop codon or as a selenocysteine codon.

Degeneracy—Wobble Hypothesis Explains how some tRNA recognize more than one codons tRNA molecules only need to make strong base pairs with 2 of the three codons in the nucleotide This third loose base pairing interaction is called wobble Note: only certain bases can substitute for others

Wobble Example This UCA codon was read by the tRNA with a UGA anticodon But if this UCA was UCG, it would still have been read by the tRNA with a UGA anticodon