Genetics Lab Syllabus
Spring 2008
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 but it will on occassion. 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. Those of you with research experience may find that using your expertise to help less-experienced students a challenge to that expertise. You never know how well you know something until you must teach it (take it from me). 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 105 points toward your total grade.
Those 100 points are partitioned among four quizzes and six reports as shown in the table below. The report forms are found on the lab D2L site.
Quiz/ Report Due Date (start of lab period) Points
Quiz 1: Nucleic Acids Review
Quiz 2: Replication
Report 1 : Electronic PCR
Quiz 3 : Optimization
19 - 21 Feb
04 - 06 Mar
11 - 13 Mar
18 - 20 Mar
10
10
10
10
Quiz 4: Polymorphisms
Report 2: Polymorphisms
Report 3: Marker Map
Quiz 5: Gene Expression
Report 4 : RT-PCr
Report 5 : Gene Families
01 - 03 Apr
08 – 10 Apr
15 – 17 Apr
29 Apr – 01 May
06 – 08 May
13 – 15 May
Total points
10
15
10
10
10
10
105
1

12-14 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 20 mins?
4.
Review basic molecular biology from 323
5.
Report: None
6.
Quiz1: Re-take Nucleic Acids Review on D2L due before the next lab (Highest score counts toward grade).
19 – 21 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
5.
Quiz1: Nucleic Acids Review DUE
26 - 28 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; primer sequences (RGA, Thy-1 and GPA) and target sequences on D2L
4.
Quiz2: DNA replication & quantification available.
04 March - 06 March
Week4 : Basic Lab Techniques Module : Optimization of Polymerase chain reaction &
Electrophoresis
1.
Lecture: a.
Electrophoresis b.
Optimization
2.
Wet lab: a.
Set up pcr optimization reaction b.
Pour gel (instructors will run the gels) Thurs pm
3.
Report1 : Electronic PCR ( due next week )
4.
Quiz2 DNA replication DUE
2

11 – 13 March
Week 5 : Genomics Module : Polymorphism Screen
1.
Lecture: a.
Discuss optimization results b.
Talk about polymorphisms c.
Talk about restriction enzymes (example sickle cell anemia)
2.
Wet Lab: a.
Restriction digest of RGA, GPA and Thy-1 amplicons b.
PCR reaction products provided by instructors.
3.
Computer Lab: a.
For each type of marker b.
Find cut sites c.
Predict potential Col:Ler polymorphisms (part of Report 2:
Polymorphisms)
4.
Report 1: e-PCR DUE
5.
Quiz3: Optimization and PCR available
18 -`20 March
Week 6 : Genomics Module: Polymorphism Screen & Molecular Mapping
1.
Lecture: a.
Molecular markers & Mapping
2.
Wet Lab: a.
Pour, load & run the gel for polymorphism screen b.
Set up PCR for mapping
3.
Computer Lab: a.
Finish polymorphism prediction
4.
Quiz3: Optimization DUE
5.
Quiz4: Polymorphisms available
6.
Report: none
25 – 27 March SPRING BREAK
1 April – 03 April
Week 7: Genomics Module: Mapping still
1.
Lecture: a.
Talk about polymorphism gels b.
Molecular markers and Mapping
2.
Wet Lab: a.
Digest mapping reactions b.
Pour, load & run mapping gels
3.
Computer Lab: a.
Draw banding patterns of recombinants
4.
Report 2: Polymorphisms finish up a.
Includes: i.
gel results of actual polymorphisms ii.
Ler:Col Polymorphism electronic predictions
5.
Quiz4: P olymorphisms DUE
3

8 - 10 April
Week 8: Genomics Module: Mapping Mutants Functional Genomics Module: Gene
Expression
1.
Lecture: a.
Discuss mapping results a.
Gene expression and reverse transcription
2.
Wet Lab: a.
Setup reverse transcription
3.
Computer Lab: none
4.
Report2: Polymorphisms DUE a.
Includes: i.
gel results of actual polymorphisms ii.
Ler:Col Polymorphism electronic predictions
5.
Report3: Marker Map continue working on it a.
Includes: i.
drawn figures of recombinant banding predictions ii.
Actual gel pictures.
15 – 17 April
Week 9: Functional Genomics Module: Gene Expression
1.
Lecture: a.
Reverse Transcription, retroviruses, b.
Principles of reverse transcription PCR.
2.
Wet Lab: a.
Set up PCR part of rt-PCR
3.
Computer Lab: Predict rt PCR results for genomic and cDNA bands.
4.
Report3: Marker map DUE a.
Includes i.
drawn figures of recombinant banding predictions ii.
Actual gel pictures.
22 – 24 April
Week 10: Functional Genomics Module: Gene Expression
1.
Lecture:
2.
Wet Lab: a.
Pour, load & run a gel for rt-PCR reactions
3.
Computer Lab: Predict rt PCR results for genomic and cDNA bands.
4.
Report4 : RT-pcr report work on it.
a.
Includes : i.
Predictions via computer ii.
Gel pictures of actual results
5.
Quiz5: Gene expression available
4

29 April – 1 May
Week 11: Functional Genomics Module: G ene Expression
1.
Lecture: a.
Discuss results of rt-PCR b.
Gene families, splice sites
2.
Wet Lab:
3.
Computer Lab: Gene Families
4.
Report4: Rt-PCR work on it a.
Includes:. i.
Predictions via computer ii.
Gel pictures of actual results
5.
Quiz 5: Gene Expression DUE
6 – 8 May
Week 12: Functional Genomics Module: G ene Expression
1.
Lecture:
2.
Wet Lab:
3.
Computer Lab: Gene Families (will be report 5)
4.
Report 4: RT-PCR DUE a.
Includes: i.
Predictions of banding patterns ii.
Gel pictures
13 – 15 May
Week 13 : No lab but Gene Families Report due
Report 5: Gene Families DUE
5