BIO 315 Molecular Biology
Integrated Lecture Topics & Lab Exercises*

*Detailed descriptions of lab protocols with appropriate handouts (HO) will be distributed to the Netdrive 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). I will keep you fully informed about topics and reading assignments on a weekly basis in class sessions.

 Spring 2020
Lab* section: R 1:00-3:30 PM (Olin 228A and 219 - DNA Sequencing Lab)
Lecture* periods: MWF 12:30-1:30
*The lecture and lab periods are interchangeable

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

*Please Note: Reading Assignment code: textbook abbreviation, MBpp, then the chapter & page numbers in parentheses, e.g., MBpp (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 (Genome Editing by CRISPR) and its modules and exercises; organization of lab groups into assigned stations; pipet calibrations check; accessing the Netdrive from on and off campus



1. PCR Theory & Practice; 2. Primer Design and Analysis: Unique and degenerate Primers and “universal” unique 18S rRNA Gene Primers; Making Pirmers Exercises for 'imaginary' and 'real' primers (to target editable genes); Tm calculations by %GC, salt-adjusted, and nearest neighbor thermodynamics; BioMath Calculators; OligoCalculations ; (see detailed lab Schedule and Protocols (SaPs) sheet/handout)



1. PCR of genomic DNA templates with unique ADE2 gene 18S rRNA primers; 2. continuation of Lab#2 exercises: BLAST and in silico PCR at UCSC Genome Browser; 3. start new Eukaryotic Gene Structure exercises (see detailed lab Schedule and Protocols (SaP, sheet/handout)



Lab: Agarose Gel Electrophoresis of PCR products from previous lab; determination of PCR product sizes, purity, and yield; Computational: Making Degenerate Primers from amino acid sequences; ADE2 Gene Research Exercise; using NCBI, KEGG and SGD; Eukaryotic Gene Structure cont'd


1. Introduction to Chimera; 2.Visualizing DNA exercise by Chimera; complete ADE2 Gene Research; complete Practice Problem for making degnerate primers; set up SnapGene Viewer and locate primers, targets, and PAM sites for CRISPR
Lab 6: Week of Exam #1 + lab experiment
 Lab 7: Plasmid Isolation, Analysis by Spectroscopy (see SaP sheet)



 Lab 8:


 Spring Break! 
 Lab 9:


Lab 10: Week of Exam #2 + lab experiment
 Lab 11: DNA cycle sequencing reactions in the Beckman-Coulter automated sequencer; preliminary analysis of results: Detailed analyses of sequencing data and interpretations; Bioinformatics of sequencing results
Lab 12:


4/30 Lab 13:


Last Lab






Final Exam Period scheduled for May 9th, Saturday