BIO 315 Molecular Biology
Integrated Lecture Topics & Lab Exercises*
Schedule for Spring 2017

*Detailed descriptions of lab protocols with appropriate handouts (HO) will be distributed to the I:/drive before each lab session; reading assignments and problems will be displayed prominently on the first slide of relevant slide sets, and on the CRAaP page (see the *Please Note and right-most column below).

Spring 2017
Lab* section: T 1:00-3:30 PM (Olin 228A and 219 - DNA Sequencing Lab)
Lecture* periods: MWF 9:10-10:10
*The lecture and lab periods are interchangeable

All Reading Assignments* are from the text: Molecular Biology (MBpp), Cox et. al., 2n ed., and distributed articles

*Please Note: Reading Assignment code: textbook abbreviation, MB, then the chapter & page numbers in parentheses, e.g., MB (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 affects the topics for discussion in the lecture periods; in other words, the lab exercises, which are all part of a larger research project, "drive" many (but certainly not all) of 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?". And "How is the lab work faciliating my understanding of molecular theory in biology?".

And see: the CRAaP page for all Topics, Reading Assignments, OnePts, and Problems

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

Lab Check-in and introduction to the Lab Research Project and its exercises; organization of lab groups into assigned stations; pipet calibrations with calculations of standard deviations by the Excel program, and % error calculations (see detailed lab Schedule and Protocols (SaP) sheet/handout)



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 and degenerate Hox 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)



1. re-PCR of selected PCRs; 2. continuation of Eukaryotic Gene Structure exercises; start What Is a Homeobox? exercise; finish Tree of Life exercise; start and finish KEGG exercises with questions for HOXA1


Exam #1

1. Introduction to Chimera; 2. Chimera Structural Bioinformatics Exercise on DNA & DNA-protein interactions



1. Cloning PCR products into the pJet vector; 2.Transformation of Cloning Reactions into E.coli
3. Colony Picking and Processing (next day!); (see detailed lab Schedule and Protocols (SaP) sheet/handout)


Spring Break!
Plasmid Isolation, Analysis by Spectroscopy (see SaP sheet)


1. Theory of electrophoresis; 2. AGE and sizing of PCR Products; Plasmid Analysis by AGE & REDs; sizing of inserts
Exam #2


1. Theory of capillary electrophoresis (CE) and Di-deoxy sequencing; 2. DNA cycle sequencing reactions and purifications


DNA Sequencing in the Beckman-Coulter automated sequencer; preliminary analysis of results


Detailed analysis of sequencing data and interpretations; Bioinformatics analysis of sequencing results



Exam 3: Final Exam Period scheduled for May 15th, Monday (or Final Project due May 15th Mon.