Genetics Lab Syllabus
Spring 2007
Section A01L: Tues 9:40am – 11:40 am in HS 50; taught by Dorn
Section A02L: Tues 1:20 pm – 3:20 pm in HS 50; taught by Dorn
Section A03L: Thurs 9:40 – 11:40 am in HS 50; taught by Rosemary Shade
OBJECTIVES: Welcome to the laboratory portion of Biology 343. This course is
designed to give you hands-on experience with modern genetics techniques. It is not
designed to coincide very much with your lecture material; in fact, it could be a course of
its own, which is what may happen to it someday. You will be learning molecular lab
techniques that are useful for genetics, learning to debug those techniques, as well as how
to interpret your results and what that means for understanding genes and their function.
These exercises are based on molecular biology concepts you should have learned in 105
and 323. Therefore, we will use some lab time to review those molecular biology
concepts. Despite this courses position as a core course there are only two hours a week
devoted to laboratory. That means that your exercises will stretch out over a period of
weeks. We will help you keep track. It may help if you use this schedule as a checklist.
ORGANIZATION: The course consists of three basic sections or “modules”. Within
each module are a series of exercises designed to teach the topics covered by that module.
The first module Basic Lab Techniques teaches the basic techniques you will need for the
rest of the semester. For some of you with experience in professors’ labs this module
will be very basic at times. Please be patient. Remember this course is a required course
for all biology majors even those who are not pursuing research that requires these
techniques. I will not tolerate arrogance or shirking for any reason, I don’t care if
you won the Nobel prize. Last, some of these exercises are designed to at least partially
fail so do not get discouraged.
GRADING: The lab part of the course is worth 100 points toward your total grade.
Those 100 points are partitioned among four quizzes and six reports as shown in the table
below. You will be given report forms to work with.
Quiz/ Report
Due Date (start of lab period)
Points
14-16 Feb
10
27 Feb – 1 Mar
10
6 – 8 Mar
10
Optimization Quiz
13 – 15 Mar
10
Polymorphisms Quiz
27 – 29 Mar
10
3 – 5 Apr
10
10 – 12 Apr
10
Report 4:T-DNA
24-26 Apr
10
Report 5: Reverse Transcriptase
1 – 4 May
10
Report 6: Gene Families
8 – 10 May
Total points
10
100
Nucleic Acids Quiz
Replication Quiz
Report 1: Electronic PCR
Report 2: Polymorphisms
Report 3: Marker Map
1
7-`9 February
Week 1: Basic Lab Techniques Module: Buffers, Pipetting
1. Lecture: Molarity and pipettors exercise
2. Wet lab:
a. Pipettor exercise
b. Figure out how to make TBE
c. Make TBE
3. Take pretest on nucleic acids in class
4. Review basic molecular biology from 323
5. Quiz: Re-take pre-test on D2L due by the beginning of next lab. (Highest score
counts toward grade). POINTS: 10.
14 -`16 February
Week 2: Basic Lab Techniques Module: Extracting DNA
1. Lecture: Talk about DNA protocol
2. Wet Lab: Extract DNA (long protocol)
3. Computer Lab: None
4. Report: None
20 -`22 February
Week 3: Basic Lab Techniques Module: Quantify DNA
1. Lecture:
a. How to quantify DNA and how to make working solution
b. Discuss DNA replication and PCR
c. Computer applications
2. Wet Lab:
a. Quantify DNA
b. Make working solution,
3. Computer lab: Electronic PCR; provide primer sequences and target sequences
4. Quiz (D2L) On DNA replication due by next lab period (10 pts)
27 February -`1 March
Week4: Basic Lab Techniques Module: Optimization of Polymerase chain reaction &
Electrophoresis
1. Lecture:
a. Electrophoresis
b. Optimization of PCR
2. Wet lab:
a. Set up PCR optimization reaction
b. Pour gel (instructors will run the gels)
3. Report 1: Work on electronic PCR results due by next lab period
2
6 – 8 March
Week 5: Genomics Module: Polymorphism Screen
1. Lecture:
a. Discuss optimization results
b. Talk about polymorphisms
c. Talk about restriction enzymes
2. Wet Lab:
a. Setup polymorphism PCR reactions
b. Instructors digest on Thursday
3. Computer Lab:
a. Predict potential polymorphisms
4. Quiz: On optimization POINTS: 10 (due by beginning of next lab)
5. Report 1 (electronic PCR) : due by start of lab POINTS: 10
13 - 15 March
Week 6: Genomics Module: Polymorphism Screen
1. Lecture:
a. Molecular markers & Mapping
2. Wet Lab:
a. Set up PCR for mapping mutants
b. Pour, load & run the gel for polymorphism screen
c. Measure mapping lines
3. Computer Lab:
a. Finish polymorphism prediction
b. Draw mapping lines gels with polymorphism (for Report 3 Marker Map)
4. Report 2: Work on Report 2 (polymorphism results & predictions)
5. Quiz: polymorphism predictions DUE by beginning of next lab POINTS: 10
20 -`22 March Spring Break NO LAB
27 – 29 March
Week 7: Genomics Module: Mapping Molecular Markers
1. Lecture:
a. Talk about polymorphism results
b. Molecular markers and Mapping
2. Wet Lab:
c. Digest mapping lines
3. Report 2: polymorphism results & predictions DUE by next lab POINTS: 10
3
3 – 5 April
Week 8: Genomics Module: Mapping Mutants
Functional Genomics Module: Dissecting a gene
1. Lecture:
a. Insertional mutagenesis and transposable elements
b. Functional genomics
2. Wet Lab:
a. Pour, load & Run gel with mapping reactions
b. Setup PCR of T-DNA mutants
3. Computer Lab: Predict T-DNA gels without insertion
4. Report 3: Marker map & drawn figures of polymorphisms in recombinants DUE
by beginning of next lab POINTS: 10
10-12 April
Week 9: Functional Genomics Module: Dissecting a gene & Gene Expression
1. Lecture:
a. Reverse Transcription, retroviruses
b. Principles of reverse transcription PCR.
2. Wet Lab:
a. Set up RT part of rt-PCR
b. Pour, load and run T-DNA gel
17 – 19 April
Week 10: Functional Genomics Module: Dissecting a gene & Gene Expression
1. Lecture:
2. Wet Lab:
a. Set up PCR part of rt-PCR reaction
b. Pour a gel for rt-PCR (instructors run gel)
c. Measure T-DNA mutants
3. Computer Lab:
a. Predict if the insertion in their mutant will affect the phenotype.
4. Report 4: T-DNA exercise DUE by the start of next class POINTS: 10
24 – 26 April
Week 11: Functional Genomics Module: Gene Expression
1. Lecture:
a. Talk about results of rt-PCR
b. Non-coding vs. coding regions of a gene
c. Gene families
2. Wet Lab: None
3. Computer Lab: Gene Families
4. Report 5: rt-pcr DUE by start of next class POINTS: 10
4
1 – 4 May
Week 12: Functional Genomics Module: Gene Expression
1. Lecture: Discuss possible outcomes
2. Wet Lab:
3. Computer Lab: Gene Families
4. Report 6: Gene families due by beginning of next class POINTS: 10
8-10 May
Week 13: No lab but last report due
5