Chapter Questions
How does a polypeptide chain resemble and how does it differ from a nucleic acid molecule?
What are the "natural" limits to the structure of an R-group in an amino acid?
Why so many tRNA genes? How, in basic terms, do different tRNAs differ from one another?
How might the concentration of various tRNAs and the frequency of various codons influence the rate of polypeptide synthesis?
What is the minimal number of different tRNA-amino acid synthetases in a cell?
Would you expect a ribosome to make mistakes in amino acid incorporation or polypeptide termination? How are such mistakes similar to and different from mutations?
What do the terms "up-stream" and "down-stream" mean in terms of gene structure.
What effects on polypeptide synthesis arise from neglecting codon bias?
Why doesn't release factor cause the premature termination of translation at non-stop codons?
What might happen if a ribosome starts translating an mRNA at the "wrong" place?
A gene has many introns - provide a model for how it might encode functionally distinct polypeptides.
How can a mutation in splice site sequence influence gene expression and protein function?
How does non-sense mediated decay (NMD) protect against potentially deleterious mutations (alleles)?
Why would a cell want to stop (rather than continue) polypeptide synthesis when it is starving?
Why does it matter that rotation around a peptide bond is constrained?
. How can changing the pH of a solution alter a protein's structure and activity?
Make models of polypeptides all of whose R-groups are hydrophilic or hydrophobic?
How might the presence of a folding/refolding-chaperone mitigate the effects of a mis-sense mutation?
How do assembly-chaperones facilitate the assembly of multi-polypeptide proteins?
Under what conditions might you expect heat shock proteins to be unnecessary for an organism?
. A protein binds an allosteric regulator - what might happen to the protein?
How is the post-translational modification of a protein analogous to allosteric regulation? how is it different?
Assuming that synthesis rate decreases by $50 \%$ what happens to steady state polypeptide concentration? What happens if degradation rate increases by $50 \% ?$ Generate predictive graphs of these (and other) possibilities.
How is the proteolytic processing of a polypeptide like and unlike an allosteric effector or a post-translational modification.
Why do post-translational modifications (and their reversals) require energy?
How might a mutation that alters a signal sequence influence the translation, assembly, localization, and function of a polypeptide (protein)? What the effects of mutation on NLS or NES signals?