TECHNIQUUES

I am expecting a lot of questions about techniques, mainly because most of you have never practically used any of them...
In the meantime, I am trying to put together some potentially useful info:

you can have a look here

(partly under construction, partly up and running)

ANNOUNCEMENT

TUTORIAL T04/T07 TIME CHANGE!

Starting Thursday, June 28th, we will meet from 1.30 to 3.30 pm
(still in Buchanan, room D322)

SOME QUESTIONS THAT CAME UP

Here are some points that came up in the last 2 days...

1) For us, all lacO[c] mutants prevent the LacI repressor from binding.

2) If nothing is mentioned, we assume that there is no glucose or lactose in the medium

3) regarding problems set 2...

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.



Cheers

Pam
PS: practice questions can be found here
or by clicking on 'lac operon stuff' (it's under the 'BIOL335 links' column) and following the instruction.
(sorry about the formatting-I am trying to fix it)

WELCOME TO BIOL335!

As requested, our Summer School BIOL334 blog has now become a 334/335 space. I have added a few links that may be useful/relevant for 335 (more to come) and I will post announcements, notes and practice questions.
Please leave a comment, question or request!

Enjoy your course,

Pam

Review and quant genetics

The handout for quantitative genetics is online on the BIOL334 website:
http://www.zoology.ubc.ca:80/genetics/334-1998/web2004/quant.htm

Review session:
Thursday 2-4 pm, room 2321

Drop-in hours for people who can't make it to Thursday's (or who have last minute questions):
Friday, 8-ish-10am, room 2321

If you have any questions, leave a comment! (The function should be enabled now)

Cheers,

Pam

A few practice questions-up to chapter 15

ON 'GENE INTERACTION'

Practice, practice, practice!
Chapter 6 is full of good questions (try 64and 65). Also, there are a lot of loppins questions that you should be able to do-click on the link and have a look at #1, 2, 3, 4, 6 and 8.

Remember that for this kind of problems you'll sometimes need to use your intuition and/or a trial and error approach...

BACTERIA STUFF

Here are some notes and a practice question on mapping in bacteria. Have fun!

ABOUT TETRADS

Also, you can't do question 27, chapter 4 (it requires the use of the Haldane formula, which we are not doing in the Summer).

Pre-MT review

We'll have a review session tomorrow (Thursday) at 2pm in room 2321.
Come prepared with a list of questions!

A recipe for three points testcrosses

Speaking of pedigrees...

That famous chocolatemia pedigree