Problems and Questions for Chapter 13 Material

From Brooker, pages 356-358

Read and consider (but do not submit answers for) questions S2 and S4.
Answer questions C16, C23, C24, C26, and the additional questions below.

C16. Discuss the significance of modified bases within tRNA molecules.

C23. What are the three stages of translation? Discuss the main events that occur during these three stages.

C24. Describe the sequence in bacterial mRNA that promotes recognition by the 30S subunit.

C26. How does a eukaryotic ribosome select its start codon? Describe the sequences in eukaryotic mRNA that provide an optimal
context for a start codon.

Additional Questions
A1. List the factors, ribosome components, and other nucleic acids necessary for the process of translation. Briefly explain each
piece’s function if it was named in class.

A2. Next to each codon, write or type a complementary anticodon. Apply the wobble rules so that the total number of different
anticodons you use is the minimum number sufficient to cover all of the various codons. There is more than one possible solution.
UUU phe UCU ser UAU tyr UGU cys
UUC phe UCC ser UAC tyr UGC cys
UUA leu UCA ser UAA stop UGA stop
UUG leu UCG ser UAG stop UGG trp
CUU leu CCU pro CAU his CGU arg
CUC leu CCC pro CAC his CGC arg
CUA leu CCA pro CAA gln CGA arg
CUG leu CCG pro CAG gln CGG arg
AUU ile ACU thr AAU asn AGU ser
AUC ile ACC thr AAC asn AGC ser
AUA ile ACA thr AAA lys AGA arg
AUG met ACG thr AAG lys AGG arg
GUU val GCU ala GAU asp GGU gly
GUC val GCC ala GAC asp GGC gly
GUA val GCA ala GAA glu GGA gly
GUG val GCG ala GAG glu GGG gly

A3. The partial mRNA sequence 5’ AAGAUGUUUCUAGUUCAG 3’

would be translated to produce the polypeptide LysMetPheLeuValGln

Write all of the possible anticodons that could be used to translate this sequence. Remember to apply wobble rules.
A4. The reading frame is the way nucleotides are grouped into codons, and it therefore determines the amino acids that are
encoded by an mRNA. Each mRNA sequence has three possible reading frames, but only one is valid; that is, only one is actually
used to produce a polypeptide. This limitation does not apply to non-overlapping reading frames, of which there may be several
along a prokaryotic polycistronic mRNA, as we discussed. Explain what is meant by the statement that the start codon sets the
reading frame.

A5. Create a double-stranded sequence of DNA

• that extends from –40 to +45
• that has all sequences necessary for this gene to be transcribed and to produce a polypeptide of exactly 5 different amino
acids in a prokaryote
• that includes a 20-nucleotide 5’ untranslated region (the nucleotides from the transcription start site to the translation start
site)
• with the amino acid sequence of the polypeptide written below it
• with the template and sense strands and the 5’ and 3’ ends of the DNA labeled
• with conserved sequences underlined or boxed
• with Ns standing in for unconserved nucleotides

A6. Describe how your sequence would be different if it were to encode the same polypeptide in a eukaryotic cell.