Seminar questions Transcription/Translation Molecular Cell Biology 2014
These questions are a mixture of essentials (first ones) and questions that do not have a clear
answer (last one).
1. Transcriptional control is based on the ability of protein molecules to recognize
binding sites in DNA with specificity.
a) Why is the binding of an α-helix in the major groove of DNA the most common
type of interaction between DNA-binding proteins and DNA?
b) The DNA-binding proteins used in transcriptional control are often dimers (or
higher multimers). Which are the three main reasons for this? How is this different in
prokaryotes and eukaryotes?
2. Transcription.
a) Describe the overall architecture of bacterial RNA polymerase and the eukaryotic Pol II.
What is similar and what is different?
b) What is the role of TPB (TATA-box binding protein) in eukaryotic transcription? Describe
its structure and how it induces conformational changes in the DNA double-helix. Why is this
an important step of transcription initiation?
c) The trigger loop and the bridge helix are two important parts of RNA polymerase. Explain
the roles of these two regions and of their conformational transitions.
3. Translation
a) Protein-tRNA recognition is done by aaRSs as well as by EF-Tu.
For each of these, explain what features of the tRNA that the protein needs to
recognize, and in general terms how this is achieved.
b) tRNAs and mRNA move through the ribosome during the elongation cycle. Starting from
an aa-tRNA bound to EF-Tu, which structural changes are important in this process?
c) A few different types of aminoglycosides increase the error-rate of bacterial translation.
Explain the structural mechanism of miscoding induced by paromomycin and streptomycin
respectively.
d) Antibiotic resistance can occur through four basic mechanisms. Which are these? Try to
find examples of how aminoglycoside resistance occurs through all of these.
4. The transcription machinery is all made of proteins, while the translation machinery
consists of RNA as well as protein.
a) Compare the two biopolymers protein and RNA; what similarities and differences between
can you think of? What impacts do these have on the use of the two polymers for binding and
catalysis?
b) Sense codons are read by tRNAs while stop codons are read by proteins. How are these
two processes similar and different? Why do you think evolution has selected to use RNA in
one case and protein in the other?
c) Through in vitro evolution, RNA-based RNA polymerases have been generated (see
below). Can you hypothesize on why nature has not selected this system? What information
would you need to answer this question?