Wednesday, 7 November 2012

Operon example from Sanders book

Prokaryotes often cluster the information for proteins involved in the same biochemical pathway all together.  Each protein is encoded by what we call and "ORF" each of which has its own start and stop codon.  The old term for an ORF was a "cistron", and for that reason we call the mRNA that contains several ORFs as "polycistronic mRNA".  It's a long mRNA that a single ribosome will cruise along, creating the various proteins one after the other.

I made a video some years ago that shows this.  It's in a copyright-protected part of my website, so you have to login as "biostudent" and use the password "science".  The URL is . and you can see this process for yourself.

For the purpose of this exercise, you can ignore positive regulation (anything involving the CAP/cAMP complex).  Your task is to figure out whether B-galactosidase and permease (proteins from the lacZ and lacY genes, respectively) are likely to be produced by a cell in an environment where lactose is present or not present.  This question mirrors the one in the Sanders & Bowman Genetic Analysis: an integrated approach (1st edition) chapter 14, question 18.  Sadly, the question at the back of the textbook has an incorrect example.  The one below has been corrected, and I'll explain why this one is correct when I show the answer.

Thanks to my super-amazing daughter, I was able to reproduce this table from the one that we handed out in lecture earlier (she did the typing 'cause my colleague Dr. Bird lost the original file!).  Here's an important note:  my other tutorials take into account the "polar effect", but this one doesn't.  In my other tutorials, having lacZ- means the ribosome falls off before hitting the lacY ORF.  In this case, you can assume that you can express permease even if lacZ isn't synthesized.

Here's the YouTube solution!

Tuesday, 6 November 2012

Draw and number a pentose

Here's an important skill:  you should be able to draw and number a pentose sugar.  The bases are a bit harder to draw - they have all kinds of functional groups and there are two fairly different structures (purines and pyrimidines).

You should for sure recognize a purine and know there are two types in nucleic acids (it's the double-ring structure and consists of A or G).  You should also recognize pyrimidines and know which nucleotides fall into this category (single-ring with C and either T or U, depending on whether it's DNA or RNA).

Each nucleotide has the nitrogenous base attached to the 1' carbon of the pentose sugar.  And you number the carbons sequentially from that starting point.

So here:  I'll leave you with a challenge.  Draw a pentose sugar attached to a purine (don't sweat the purine details too much... just make it distinguishable from a pyrimidine).  Be able to alter your figure to depict a ribose, a deoxyribose, and that really strange entity used for Sanger sequencing: a dideoxyribose.  If you can, depict where the phosphates fit on the structure, and then number the pentose carbons according to standard conventions.

Here's how I'd do it  (quick'n'dirty 3 minute video):