BIO 315 Molecular Biology
Integrated Lecture Topics & Lab Exercises*
Schedule for Fall 2010
*Detailed descriptions of lab protocols with appropriate handouts (HO) will be distributed to the I:/drive before each lab session; reading assignments will be displayed on the CRAaP page (see the *Please Note and right-most column below).

All Reading Assignments* are from the texts: Molecular Biology of the Gene (MBG), Watson et. al., 6th ed. Calculations for Molecular Biology and Biotechnology, F.H. Stephenson, 2003, and distributed articles

*Please Note: Reading Assignment code: textbook abbreviation, MBG, CMBB, then the chapter & page numbers in parentheses, e.g., MBG (1:31-35). See the CRAaP page for all reading assignments

Please note: the organization and presentation of this course may be different than other science courses that you may have taken. In particular, note the following 5 points:

1. Lecture and laboratory periods are interchangeable, which means that lecture periods may be used for lab work, and lab time may be used for lecture/discussion work.

2. The lab work is very important and in many respects the lab exercises determine the topics for discussion in the lecture periods; in other words, the lab exercises, which are all part of a larger research project, "drive" the topics that we need to address.

3. I designed the course with topics that oscillate between theory and practice; in other words, in order to understand fully the lab work, you must master the underlying theory, and in order to understand fully the theory, you must apply it in the lab exercises.

4. At all times in this course, constantly ask yourself, "What is the biochemical, molecular, genetic, or biological basis for what I am doing in the lab?" And ask, "What do I need to know in order to understand what I am doing in the lab?"

5. Optional Exercise: In order to answer the last question in part (4), you all will assist me in selecting the reading topics and exact page numbers from the texts for this course.

LAB EXERCISES (the Practice) ‹—› LECTURES (the Theory)
"Have theory, will practice; have practice, will theorize." cf

1. PCR Theory & Practice; 2. Primer Design and Analysis: Unique and degenerate Hox Gene Primers and “universal” unique rRNA Gene Primers; Making Pirmers Exercises for 'imaginary' and 'real' primres; Tm calculations by %GC, salt-adjusted, and nearest neighbor thermodynamics; BioMath Calculators; OligoCalculations ; Homeodomain resource ; (see detailed lab Schedule and Protocols (SaP) sheet/handout)

1. PCR and re-PCR of genomic DNA templates with unique rRNA and degenerateHox gene primers; 2. continuation of Lab#2 exercises: BLAST and in silico PCR; 3. start new Eukaryotic Gene Structure exercises (see detailed lab Schedule and Protocols (SaP) sheet/handout)