Download Seminar questions Transcription/Translation

Seminar questions Transcription/Translation Molecular Cell Biology 2015
These questions are a mixture of essentials and questions that do not have a clear answer.
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 good for sequence-specific
DNA binding by proteins?
b) The DNA-binding proteins used in transcriptional control are often dimers (or
higher multimers). Which are the main reasons for this?
c) What kinds of interactions are typically used in sequence-specific binding of DNA by
proteins?
d) How are metabolite levels used to control transcription of the lac and trp operons?
2. Transcription.
a) 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?
b) 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) Describe the two ribosomal subunits – where are the main functional centers located?
b) tRNAs and mRNA move through the ribosome during the elongation cycle. Describe the
different steps of translocation.
c) A novel antibiotic is shown to increase the error frequency of bacterial protein synthesis.
Where would you predict it to bind? Can you suggest a possible mode of action?
d) When this new antibiotic is clinically used, resistance could start emerging. Which
different mechanisms of resistance could be relevant?
e) How are mitochondrial ribosomes different from bacterial ribosomes? How does this relate
to their function and to evolution?
4. RNA and proteins
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?