OUR ANSWERS TO PROBLEM SET2

For question 1a
we have three important pieces of information:
I-"cellobiase is only made in high amounts when cellobiose is present";
meaning that the 'cellobiose-metabolizing system' is inducible, and the cellobiose is its inducer

and

II-"a mutation in a gene that encodes a regulatory protein [...]results in the lack of synthesis of cellobiase enzyme;
meaning that either this mutation makes a regulatory protein thatn is unable to bind the DNA and the system is positively regulated,
OR this mutation makes a regulatory protein that never binds the cellobiose (kind of like lacI[s]) and the system is negatively regulated

and

III-the mutant strain can be complemented in trans with the wild type regulatory protein-encoding gene (i.e. we can put in a plasmid that expresses WT regulatory protein and everything works like WT);
meaning that our system must be positively regulated....why?
Because if it was negatively regulated, then the regulatory mutation would have to work like a 'superrepressor', and we know that 'superrepressor' mutants (mutants where the regulatory protein is always bound to the DNA) are typically dominant to the wild type!
In this case the wild type is dominant, so it must be a positively regulated system (and the mutation is a 'lacI- type' mutation).

Question 1 part b:
if the CelI-binding site is mutated, it can't bind to the promoter region and therefore can never activate the expression of the cellobiase!
Clarification: the "CelI binding site" refers to the DNA sequence to which the CelI binds. In general "proteinX-binding site" always refers to the DNA sequence that protein X binds to.
The part of the CelI protein that binds to the DNA would be called 'CelI DNA-binding domain'.

Question 2a:
Since we know that cellobiase is only produced when cellobiose is there, and that the regulatory protein is an ACTIVATOR, then one would expect that binding of the cellobiose to the activator would increase its affinity for the DNA target sequence. (If it decreased it, presence of cellobiose would have either no effect or a negative effect on the production of cellobiase).

Question 2b:
In this case, it would be hard for the cellobiose to bind the CelI protein (kind of like in the case of lactose and the LacI[s] mutation!), and we know that if it is not bound to the cellobiose, the CelI protein has low affinity for its DNA target. Therefore, CelI would not bind the DNA very often, causing the levels of cellobiase to be always low.