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WEEK	DAYS	TOPIC	LABORATORY EXERCISES	ASSIGNMENT AND LAB BACKGROUND
1	Aug. 19-21	The basics Lab safety Basic lab techniques	Introduction, Laboratory Safety, Safety Video, Lab Tour Basic techniques How to maintain a lab notebook and how to make a poster Description of main course project and PCR project Start lab 1: basic chemistry, metric system, preparation of solutions, pipetting, and dilutions, practice gel making, practice gel loading, different combs Make up stock solutions Start math problems Chapter 1 and 2	Videos of different techniques use of the autoclave, pH meter, large pipettors, micropipettors Using pipettes
2	Aug 26-28	Lecture on DNA, RNA and protein quantification	Finish lab 1 pH solution Make up DNA loading buffer Lab 2: Quantification of unknown DNA	Pictures on use and balancing of the centrifuge August 28, Quiz 1 : basic chemistry, preparation of solutions and dilutions pH solution directions Making up DNA loading buffer Practice gel making and loading Discussion of what students know about DNA, RNA and protein and model organisms Quantification of DNA background Quantification of DNA assignment
3	Sept. 2-4	No Classes Sept 2, Faculty Development Day	Lab 3: Isolation and quantification of proteins	Isolation of proteins protocol Videos of different techniques DNA and protein electrophoresis
4	Sept 9-11	Lecture on electrophoresis: comparison between DNA/RNA and proteins, loading buffers, staining	Lab 4: Electrophoresis of DNA (Sept. 9) Semilog graph paper Read pages 288-295 in your textbook. You will need to put in your lab notebook a graph made on semilog paper showing how you determined the size of the unknown DNA molecule You need to graph the MW of the standards on the Y axis and the distance migrated on the X axis. Then show, how you can determine the MW of your sample.	Sept. 9 Comparison of DNA and protein electrophoresis Electrophoresis protocol (DNA) DNA Staining pictures Pictures of group gels Sept. 11 Gene therapy 1 Quantification of proteins Quantification of proteins assignment Read pages 259 - 261 in your textbook.
5	Sept 16 - 18		Skills test, Sept. 16 Exam 1, Sept. 18	Overview of lab project More overview Making agar plates I will review how to streak a plate but you will not do this until Sept. 23 Protocol for streaking a plate Review of how to streak a plate
6	Sept 23 - 25	Lecture: isolation of DNA	Lab 5: Protein electrophoresis Streak a LB plate (not an LB + AMP plate) while your gel is running or you will not be able to do the experiment on Thursday. Practice measuring out 1 mL while the gel is running. Perform calculation for transformation lab Begin lab project Lab 6: Transformation	Sept. 23 Electrophoresis protocol (protein) *Example of a stained protein gel (C. elegans* proteins) Protein MW markers for C. elegans proteins Idealized results from protein kit (Salwa) While your gel is running, you need to get a LB agar plate (this will be provided for you and is NOT the one you made) and streak the JM107 bacterial culture on it. I will collect your first notebook on Thursday, Sept. 25. I will give you a grade for each lab. You should have in this notebook labs 1, 2 , 3 and 4. Sept. 25 Transformation protocol Discussion of paper poster**
7	Sept 30 - Oct 2	Lecture on restriction enzymes and their uses	Lab 6 continued, DNA isolation, quantification and electrophoresis	Sept. 30 DNA isolation protocol Abbreviated protocol Longer but still abbreviated protocol Quantification and electrophoresis protocol Oct. 2 Guess speaker Restriction enzyme problems Gene Therapy power points Gene therapy 2
8	Oct. 7 - 9		Paper poster due, Oct. 7 Lab 7: Cleavage of DNA with restriction enzymes	Look at pages 400-407 in your textbook for background on restriction enzymes. Oct. 7 - Restriction enzyme problems Protocol for setting up restriction enzyme digests Oct. 9 - set up restriction digests Uses of restriction enzymes: DNA fingerprinting Useful link DNA fingerprinting problems
		Oct 10: Last day to withdraw and receive a grade of W
9	Oct. 14 - 16		Finish Lab 7 - run gel Lab 8: Gel Purification of DNA	Oct. 14 - Protocol for gel and ethidium bromide staining Quiz on Restriction enzymes, Oct. 14 DNA fingerprinting Power Point Oct. 16 - Begin lab 8 Protocol for restriction digest and cutting DNA out of gel
10	Oct. 21 - 23		Lab 8 continued: gel purification of DNA, ligation, transformation and blue white selection	Oct. 21 DNA extraction from gel protocol Xgal and IPTG protocol Calculation for ligation Oct. 23 Ligation protocol Transformation protocol Lac operon
11	Oct. 28 -Oct. 30	Lecture: PCR and real time PCR , C. elegans	All other labs in other lab notebook Lab 9: start PCR project	Oct. 28 PCR powerpoint PCR protocol part 1 Summary of lysis and PCR condtions October 30 PCR protocol part 2
12	Nov. 4 - 6	Nov. 4 - election day, vote and then come to class	Lab 9 continued Exam 2: November 6	November 4 Set up PCR from samples from Oct. 30 PCR protocol part 3 Calculations for making PCR mastermix- to be discussed in class and shown in this power point Discussion of primers November 6 Run gel from PCR from November 4
13	Nov. 11 - 13	Lecture: Blotting: Western blot, Southern Blot, Northern Blot	Lab 10: Western Blot	Turn in project notebook on Tuesday, November 11 Bring your worksheet with the PCR problems to class Antibodies Western Blot protocol Protein electrophoresis setup (review) Other protein techniques Chromatography pictures Chromatography power point Protein comparisions Southern Blot
14	Nov. 18 - 20	ELISA and other protein techniques Introduction to DNA microarrays	Project poster due, November 18 Correction of syllabus due to timing, additional experiments may be added	November 18 ELISA virtual lab to be performed in class Worksheet to be given out in class Completion of discussion of other protein techniques November 20 Background on DNA microarrays DNA microarray power point Worksheet to be given out in class 2:30 Guess speaker (Dr. Marcus Collins) from the CDC to talk about using molecular techniques in microbiology Read this paper - there will be questions on the final exam based on the paper and the talk. Take home exam questions will be due. This is worth 20 points on the final exam.
15	Nov 25 - 27	No class, Nov. 27, Thanksgiving		Class on November 25 will end at 2:30 DNA microarray protocol
16	Dec. 2- 4		Review for final on Dec. 2 FINAL EXAM - Dec. 4 UC311: 1:25 - 3:25	Notebooks due on Dec. 4: These are the experiments to include: PCR, Western Blot and Microarray (you do not need to put the ELISA worksheet in the notebook) You will need to put the questions and data for the DNA microarray in this notebook Review sheet for final exam;
	Dec. 6-12

This course schedule is very tentative. Due to the speed in which the labs are completed (or not completed), the schedule will be revised. All updates for the schedule will be posted on the course web site.