Lecture - Introduction to the course

Today we continued with the introduction we started on Monday.  We talked about some generic information about the structure and function of nucleic acids, the processes of transcription and translation (make sure to know the difference!), mechanisms of control of gene expression, and talked a little about the reaches and developments of recombinant DNA technology.  We even mentioned what the field of genomics and proteomics can do.

Next class: On Monday we will be talking about chromosomes (p. 233-244) and hopefully also about genome evolution (p. 245-260).

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Lab 02 - Restriction Enzyme Digestions (REDs) and analysis of lambda DNA

A micrograph of multiple bacteriopages

Restriction enzymes are one of the most basic and important tools in molecular biology. They evolved in bacteria to attack and cut (cleave) foreign DNA, mostly from bacteriophages (viruses that "eat" bacteria). But hey have been isolated to be used in the lab, and are useful to cut any kind of DNA, not just viral.

Cleaving DNA is the first step in any technique that involves recombinant DNA technology. There are techniques that use special enzymes to paste (ligate) different fragments of DNA. For instance a gene can be ligated into a plasmid that can be inserted into bacteria to make many copies of it via bacterial reproduction (cloning), something we will do in a few weeks.

Today we used lambda DNA (DNA from the common lambda bacteriophage) as the substrate to be cleaved with three different restriction enzymes: EcoRI, HindIII, and PstI.

We then ran our first agarose gel electrophoreses of the quarter (there shall be many more), and here are the results. Click on each pic to get a full size image of each gel:

For the lab report:

• The lab report is due Thursday Dec 11th.
• If you can answer the questions on page 44 of "exercise 3" in the lab manual you'll have a solid discussion of results section. Use them as a guide to get ideas to discuss.
• In one of the four posted pictures the samples are significantly smeared. In your discussion include your thoughts (or findings) on what may have caused this.
  
• Include a picture of your gel. If you turn in the one printed in the lab (on thermal paper) you can label the lanes with an ultrafine point permanent marker (sharpies and the like).
• A pdf file of a semi-log paper page will be e-mailed to you for your convinience.
  

Research questions

• The gels we used were pre-poured for us. They were 1% agarose gels. What does this mean?
• If you want to improve the resolution of the gel (making bands sharper, improving separation of bands of similar size) what can you do different when preparing the gel?

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Lab 01 - Playing with micropipettes

Today we had our first lab meeting of the quarter.  Lab manuals, lab notebooks, "blue books" (for lecture quizzes), and disposable lab coats were distributed.   We talked about how to behave in the lab and went over the first and most simple lab exercise:  getting acquainted (or re-acquainted) with micropipettes.  The report for this lab was handed in at the very end of the lab.

Tomorrow:  Lab 2 ("Exercise 3" in the lab manual), Restriction Enzyme Digests (REDs) and gel electrophoreses.

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Winter 08-09 quarter

Welcome to the Winter 08-09 Intro to Molecular Biology class at ONU...!

This blog is meant to be a tool to improve communication between students and the instructor of the class (Alonso Córdoba) and to keep track of the actual happenings in the class throughout the quarter.  Feel free to browse through old entries (Fall 08 quarter) to get an idea of the kind of information you can get by reading this blog.  

An interesting feature is the fact that you can find questions and answers to old quizzes.  You can use this tool to get used to the quiz format or even to study for upcoming quizzes and exams.

Is there something you would like to see posted on this blog?  Just let me know.  I am open to new ideas, suggestions, and constructive criticism.  Just drop me a line or give me a call (contact info on the column to the right of entries).

I hope you enjoy this quarter...!  (stay warm!)

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Random pics... (a Fall 2008 lab)

A little Ice Man? I clearly didn't give students enough to do that day in lab... I'll have to be a little tougher in the future....

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