ASSEMBLING CONTIGS AND SEQUENCING GENOMES

Post all your questions about genome sequencing and about contigs under this post!

Also note that, on the 335 resource page (link on the right) there are now a couple fo additional questions to practice assembling contigs, and an explanation on how to go about solving the RFLP question with the FCD.

Cheers

Pam

PS: remember that Friday (tomorrow) it's 'spring break'!

PROMOTER AND ENHANCER BASHING

If you have any questions regarding promoter bashing or enhancer bashing (or, how to find an enhancer) please post them here!

A 335 LOPPIN_ADAPTED QUESTION

This is a modified version of a question that was in the previous editions of the book.

The loppin 'ant' gene has been cloned. We know that it is only expressed in the antennae of female loppins.

Propose a strategy/experimental procedure to identify and define the regulatory regions that confer this expression pattern to the gene (that is, the regulatory regions that are necessary and sufficient to make the gene only expressed in females' antennae).

Have fun!

Pam

UP TO THIS POINT...

... remember that there are 2 big parts to 335:

1) Gene structure, organization and regulation (in prokaryotes and in eukaryotes)

2) The techniques, tools and strategies to study gene structure, organization and regulation.

So far, you have learned about:

1) Gene structure, organization and regulation in prokaryotes

--> examples of the lac operon, example of the operon seen in problem set 2

2) A number of techniques to study gene structure and regulation, including:

--> how te see if a gene of interest is expressed (if it produces an enzyme, we can use enzyme assays, like for the B-Gal; in all cases we can also look for presence of RNA corresponding to our gene of interest, e.g. with northern blots). We'll see more methods later.

--> how to clone a gene of interest (you have seen two strategies so far: the first one is to clone a gene through functional complementation, the second is to clone it based on sequence homology). Again, you will learn about other strategies to clone genes later on in the course.

Keep these points in mind!

Cheers

Pam

PS: in response to popular request, step-by-step answers to problem sets 2 and 4, and to the questions on the handouts, will be posted on the 335 resource page (by Wednesday afternoon).

FOR THE WEEKEND...

Make sure you enjoy the sunshine!

If you feel like working on BIOL335, you can start with probelm set #4. You'll have to look up some of the techniques in your book. You may also find some help on the techniques page and on jove. On jove, you'll have to type in the technique you're looking for.

IMPORTANT: MONDAY WE'LL MEET AT 1.45 IN ROOM 2449

How do you get a plasmid into E. coli? Here is a video!

And here is how you get the plasmids out of the cells.

FRIDAY JULY 3RD

On Friday our tutorial will still be at 2.30pm. I'll have two sets of lac operon practice quesitons for you, and we'll briefly go over biosynthetic operons. Also, bring your problem set 4! You'll have enough background to start working on it.

Cheers

Pam

PS: we won't move the tutorial to the morning.

THINGS TO KNOW FOREVER...

Here are a few things that we touched on last Tuesday, and that you should always remember:

- genes have promoters

- transcription does not start at the AUG, and is not stopped by stop codons! (The RNApolymerase does not know the genetic code, it just transcribes until it hits a "transcription termination" signal)

- plasmids can exist as independent "mini-chromosomes" inside bacteria, or they may be integrated into a bacterial chromosome

- plasmids may carry, in addition to all the plasmid genes, some bacterial genes.

FOR THURSDAY AND FRIDAY:

we'll work on prokaryotic gene regulation (two main examples), bring your textbook and problem set#2!

Much more info on prokaryotic gene regulation will be posted in the next couple of days. For more info on the lac operon ...there are links on the right!

Cheers

Pam