BIO206 Tutorial 3 Worksheet

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BIO206 Fall 2022 / University of Toronto Mississauga 1 BIO206 Tutorial 3 Worksheet Translation Total 1 mark (= 1 % of final grade) Submit to Quercus before 10 pm on the day of your Week 3 Tutorial, unless otherwise noted for your section. 1) What is the 'triplet' property of the Genetic code? Then, name its other six properties. Three nucleotides code for an amino acid in the protein. The other six properties are, code is degenerate, the code does not overlap, the code does not contain commas, the code has polarity, the code has start codons, the code has stop codons. 2) Explain why there are three possible reading frames in a protein coding mRNA. 3) Explain why there are six possible reading frames in a dsDNA. This is due to the fact that three are from the 5’ to 3’ direction and three are from the 3’ to 5’ direction. 4) Not all transcribed RNAs get translated. Sometimes, the RNA molecules themselves already have a function. In this case, would there be any reading frames for these RNA molecules? 5) Find an open reading frame in the protein-coding nucleotide sequence below, assuming that the first methionine is the start codon of this protein. acagcagattctaatgaaggtatctcttcttatggagttggagttggaggagcctaagtaatcg gagccggaatagc 6) Explain genetic code degeneracy using alanine as an example. Then, discuss the following: • If the nucleotide in the third position of the alanine codon was mutated in a protein CDS, how would this affect the protein? • If the nucleotide in the first position of the alanine codon was mutated in a protein CDS, how would this affect the protein? Genetic code degeneracy refers to the number of codons that an amino acid has. Alanine has 4 being GCU, GCC, GCA, GCG. If the nucleotide in the third position was mutated in a protein coding sequence, this would result in the protein being slightly changed although not much would be affected. If the first codon was changed, the protein would be greatly impacted as it would not be alanine any more. 7) Name and describe the different types of mutations which can occur in a nucleotide sequence. Assess the possible impact (severity) of these mutations.

BIO206 Fall 2022 / University of Toronto Mississauga 2 8) Which amino acids’ codon(s), if altered, would most likely lead to premature termination of translation? Give a couple of examples and explain your answer. If the first codon is altered there would be premature termination for some proteins. For example, tryptophan’s codon UGG being altered would result in premature termination as well as cysteine’s codons UGU and UGC. 9) Draw a schematic diagram of tRNA, labelling its major structural components. Label the anticodon positions 1 - 3 on this tRNA molecule and draw the codon positions 1 - 3 during codon- anticodon recognition. 10) One of the tRNA genes for proline has a mutation in its anticodon sequence. What might be the possible consequences of this change? 11) Briefly describe the composition of the prokaryotic ribosome and its subunits, including their names and the types of RNA molecules they contain. Describe the eukaryotic ribosome in a similar way. 12) How does the ribosome read the mRNA and synthesize polypeptides in respect to the polarities of these molecules? 13 ) What would be the effect of truncating the 3’end of the 16S rRNA of a prokaryote? 14) Draw a schematic diagram of a translating ribosome immediately before and after a transpeptidation event. 15) Consider the processes in Panel B, below. What is this process? Arrange the letters in the appropriate chronological order and briefly describe the event that is occurring at each step. 16) Briefly describe the role of these molecules during translation • Aminoacyl-tRNA synthetase • initiator tRNA: • EF-Tu • EF-Ts • EF-G • Release factors

BIO206 Fall 2022 / University of Toronto Mississauga 3 17) What is the largest mechanical difference between a prokaryotic and eukaryotic translation initiation? What is the implication of this difference for prokaryotic vs. eukaryotic protein coding genes? 18) List similarities and differences between prokaryotic and eukaryotic translation. 19) Which of the following mutations would likely have the most severe consequences? Explain your reasoning. • A change in amino acid recognition of an aminoacyl-tRNA synthetase • A frame shift mutation at the end of the protein coding sequence within a gene • A mutation at a splice junction A change in amino acid recognition of aminoacyl-tRNA synthetase would be most likely to have severe consequences since if a different amino acid is accepted, the protein has a higher chance to be altered by the recognition since a different amino acid would mean different codons.

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