BIO 340/343 INTRODUCTION TO GENETICS
LECTURER: Dr. Lisa Dorn
Fall 2008
OFFICE: HS 45; LAB: HS 47 PHONE: 424-3064; E-MAIL: dorn@uwosh.edu
OFFICE HRS: Mon 8:15pm to 10:15pm, Thursday 2:00 to 4:00pm
LECTURE HOURS: 1:50 – 2:50 pm in Halsey Science Building; Rm. 260
TEXT: Brooker, Genetics: Analysis & Principles (3rd edition) McGraw Hill.
OBJECTIVES: Genetics and its experimental methods is one of the broadest and most
rapidly evolving fields of science. I cannot possibly cover it all, so my goal is to teach
you how to think like a geneticist, while learning genetics concepts so that you can judge
for yourself the value of emerging genetic technologies and discoveries. This course
covers Mendelian genetics and its complications, the molecular basis of genes and their
affect on phenotypes, the methods of identifying and characterizing the genetic basis of
diseases and other phenotypes as well as population and evolutionary genetics.
The prerequisites for this course are Bio105 and 323, which by extension means you have
taken Chem 105 and 106 as well as Bio111. The laboratory part of this course will
expand on what you have learned in Molecular and Cell Biology (Bio 323). I will
assume you have mastered the Bio323 material and will not waste much time reviewing
this material but there will be some review of 323 materials in lab.
ASSESSMENT: How are you going to earn your grade?
EXAMS: 4 exams each worth 100 points. They will be mostly problems similar
to those in your D2L quizzes. (400 total points).
PROBLEM SOLVING: There will be 8 D2L problem-solving sessions where
you will be required to solve problems that will be available on D2L. Worth 10 points
each (total = 80 points). These problems are presented as quizzes. The problems will
be available 1 week before they are due. During those days, you may discuss potential
solutions with your peers and me but once you submit your answer you cannot change
them. You can only see the answers after the submission deadline.
***IMPORTANT***: D2L was behaving very badly last semester. Do not wait for
the last hour to submit your answers. If D2L crashes while you are submitting your
answers and you subsequently miss the deadline, I can help you on a case-by-case basis
but I will do so only once. To help alleviate this problem I will direct D2L to allow late
submissions but it will flag these submissions. If too many students are late repeatedly, I
will remove this feature. However, I may on occasion extend the deadline for a specific
quiz if there are questions that require last minute lecture material.
EXTRA CREDIT QUIZZES: There will be one extra credit quiz at the end of
the semester worth 5 points. Besides the extra credit, it will be very similar to questions
you will find on the last exam so I highly recommend that you do this. *NOTE: If extra
credit points from this quiz are the only way to pass the course that is acceptable.
HOWEVER, you may have other opportunities for extra credit points that may change
your letter grade but not when EC points are the only way to pass the course.
LABORATORY: Is worth 105 points. The lab syllabus is appended to the end of
this document.
Total Possible points = 400 + 80 + 105 = 585.
92 – 100% = A, 89-91% = AB, 82-88% = B, 79-81% = BC, 72 – 78% = C, 68 – 71% =
CD, 67 – 60% = D, below 60 = F.
Disputing a grade: if you feel your exam has been misgraded, you must submit to me a
request for re-grade within a week of the day I have passed exams back (not the day you
picked it up). That request must be in writing accompanied by a copy of the exam in
question that I will keep.
Students With Disabilities are welcome in this class! If you need special
accommodations please contact me during office hours in the first week of class. This
includes students with diagnosed learning disabilities. If you feel you should be
evaluated for a learning disability, please contact the Project Success office at 920 4241033 or go to their website at http://www.uwosh.edu/organizations/success.
Classroom Etiquette: please silence all pagers, cell phones; or iPODs and do not talk or
whisper unless called upon in turn (but feel free to raise your hand for a question or
comment at ANY time!).
Incomplete Grades may be given in extreme circumstances, such as when a student
becomes too ill to complete the semester's work. Please talk to me if you think your
situation warrants an "I" grade and be prepared to provide documentation.
Make up exams. If you cannot make one exam several alternatives may be available to
you depending on the rest of my teaching obligations at that time. I will do what I can,
given your circumstance. If you know ahead of time that you must miss an exam (for
instance if your job requires that you work that day) please let me know ahead of time.
The schedule of lectures, exams and due dates for problems. There may be minor
changes to this schedule of lectures without notice. I will announce such changes in
class. Exams and quizzes will stay on schedule unless (for quizzes) there are
problems with D2L.
Lec
#
Day
Date
Topics
Book
Week
1
Wed
3-Sep
Mendels Laws; Monohybrids & Dihybrids
Chapter 2
1
2
Friday
5-Sep
Dihybrids & Pedigrees
Chapter 2
1
3
Monday
8-Sep
Pedigrees; Probability
Chapter 2
2
4
Wed
10-Sep
Chi-Square Chromosomes Sex-Linkage
Chapter 3:
2
Thursday
11-Sep
Chapter 3:
2
5
Friday
12-Sep
Sex Determination; Meiosis
6
Monday
15-Sep
Recessive Lethals
Chapter
3/4
3
7
Wed
17-Sep
Pleiotropy; Incomplete Dominance
Chapter 4
3
Thursday
18-Sep
8
Friday
19-Sep
Co-Dominance, Overdominance,
Chapter 4
3
9
Monday
22-Sep
Penetrance, Complementation, Epistasis
Chapter 4
4
10
Wed
24-Sep
Epistasis, Linkage and Recombination
Chapter 4
4
Thursday
25-Sep
Friday
26-Sep
EXAM 1 (covers up to lecture 9)
2, 3 & 4
4
11
Monday
29-Sep
Linkage and Recombination;
Chapter 5
5
12
Wed
1-Oct
Mapping genes: dihybrid crosses
Chapter 5
5
Thursday
2-Oct
13
Friday
3-Oct
Mapping genes: Trihybrid crosses
Chapter 5
5
14
Monday
6-Oct
Intragenic Mapping, bacteriophage
Chapter 6
6
15
Wed
8-Oct
Complementation tests and deletion mapping
Chapter 6
6
Quiz 1 Due
2
3
4
Quiz 2 Due
5
Quiz 3 Due
Thursday
9-Oct
6
16
Friday
10-Oct
Complementation tests and deletion mapping;
Chapter 6
6
17
Monday
13-Oct
Complementation tests and deletion mapping;
Chapter 6
7
18
Wed
15-Oct
Chromosomes: Change in Number
Chapter 8
7
Thursday
16-Oct
Friday
17-Oct
EXAM 2 (covering lectures 10 to 17)
4, 5, 6, 12
7
19
Monday
20-Oct
Chromosomes: Structure; Variation & Mutations
Chapter 8
8
20
Wed
22-Oct
Chromosomes: Polyploidy
Chapter 8
8
Thursday
23-Oct
21
Friday
24-Oct
Gene Mutation
chapter 16
8
22
Monday
27-Oct
Gene Mutation
chapter 16
9
23
Wed
29-Oct
Gene Mutation
chapter 16
9
Thursday
30-Oct
8
Quiz 5 Due
9
Chapter
12
Chapter
12
Chapter
12
24
Friday
31-Oct
Transcription Review
25
Monday
3-Nov
Post-Transcriptional Processing
26
Wed
5-Nov
Post-Transcriptional Processing
Thursday
6-Nov
27
Friday
7-Nov
Transcriptional Regulation in Eukaryotes
28
Monday
10-Nov
Transcriptional Regulation in Eukaryotes
29
Wed
12-Nov
Transcriptional Regulation in Eukaryotes
Thursday
13-Nov
Friday
14-Nov
Non-Mendelian Inheritance: X-inactivation & Imprinting
Monday
17-Nov
'EXAM 3 ( Lectures 18 to 29)
Wed
19-Nov
Non-Mendelian Inheritance: X-inactivation & Imprinting
30
7
Quiz 4 Due
9
10
10
10
Chapter
15
Chapter
15
Chapter
15
10
11
11
11
Quiz 6 Due
chapter 7
11
12
chapter 7
12
Thursday
20-Nov
Non-Mendelian Inheritance: X-inactivation & Imprinting
Friday
21-Nov
Population Genetics
31
Monday
24-Nov
Population Genetics
32
Wed
26-Nov
THANKS GIVING BREAK: NO lecture
13
Thursday
27-Nov
THANKS GIVING BREAK NO lab
13
33
Friday
28-Nov
THANKS GIVING BREAK NO lecture
13
34
Monday
1-Dec
Population Genetics
35
Wed
3-Dec
Population Genetics
Thursday
4-Dec
36
Friday
5-Dec
Population Genetics
Ch 25
14
37
Monday
8-Dec
Population Genetics/ Review
Ch 25
15
Tues
11-Dec
Wed
10-Dec
chapter 7
12
12
Chapter
25
Quiz 7 due
13
Ch 25
14
Ch 25
14
14
Quiz 8 Due
EXAM 4 (Lectures 29-37)
15
15
Genetics Lab Syllabus
Fall 2008
Instructor: Rosemary Shade HS 157; shade@uwosh.edu
Section A01L: Tues 9:40am – 11:40 am in HS 50, Section A02L: Tues 1:20 pm – 3:20
pm in HS 50, Section A03L: Thurs 9:40 – 11:40 am in HS 50
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 occasion. 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 useful exercise. 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 105 points are partitioned among four quizzes and five reports as shown in the
table below. The report forms are found on the lab D2L site.
Quiz/ Report
Quiz 1: Nucleic Acids Review
Quiz 2: Replication
Report 1: Electronic PCR
Quiz 3: Optimization/ Polymorphisms
Report 2: Polymorphisms
Report 3: Marker Map
Quiz 4: Gene Expression
Report 4: RT-PCr
Report 5: Gene Families
Due Date (end of lab period)
16 – 18 Sep
30 Sep - 02 Oct
07 - 09 Oct
28 - 30 Oct
04 – 06 Nov
11 – 13 Nov
25 – 27 Nov
02 – 04 Dec
09 – 11 Dec
Total points
Points
10
10
10
20
15
10
10
10
10
105
9 - 11 September
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. Post basic molecular biology review from 323 on D2L
5. Report: None
6. Quiz1: Re-take Nucleic Acids Review on D2L due before the next lab (Highest
score counts toward grade).
16 – 18 September
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
23 - 25 September
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.
30 September - 02 October
Week4: Basic Lab Techniques Module: Optimization of Polymerase chain reaction
1. Lecture:
a. Electrophoresis
b. Optimization
2. Wet lab:
a. Set up pcr optimization reaction
3. Report1: Electronic PCR (due next week)
4. Quiz2 DNA replication DUE
07 – 09 October
Week 5: Genomics Module: Polymorphism Screen
1. Lecture:
a. Talk about polymorphisms
b. Talk about restriction enzymes (example sickle cell anemia)
2. Wet Lab:
a. Pour and Run gel of optimization reaction
b. Restriction digest of RGA, GPA and Thy-1 amplicons
i. amplicons 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
14 -`16 October
Week 6: Genomics Module: Polymorphism Screen & Molecular Mapping
1. Lecture:
a. Discuss optimization results
b. Molecular Markers & Mapping
2. Wet Lab:
a. Pour, load & run the gel for polymorphism screen
3. Computer Lab:
a. Finish polymorphism prediction
4. Quiz3: Optimization and polymorphisms available
5. Report: none
21 October – 23 October
Week 7: Genomics Module: Mapping still
1. Lecture:
a. Talk about polymorphism gels
b. Molecular Markers and Mapping
2. Wet Lab:
a. None
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. Quiz3: Optimization & Polymorphisms still available
28 - 30 October
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. Quiz 3: Optimization/Polymorphisms DUE
5. Report3: Marker Map continue working on it
a. Includes:
i. drawn figures of recombinant banding predictions
ii. Actual gel pictures.
04 - 06 November
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:
4. Report2: Polymorphisms DUE
a. Includes:
i. gel results of actual polymorphisms
ii. Ler:Col Polymorphism electronic predictions
11 – 13 November
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. Report3: Marker map DUE
a. Includes
i. drawn figures of recombinant banding predictions
ii. Actual gel pictures.
5. Report4 : RT-pcr report work on it.
a. Includes:
i. Predictions via computer
ii. Gel pictures of actual results
6. Quiz5: Gene expression available
18 November – 20 November
Week 11: Functional Genomics Module: Gene Expression
1. Lecture:
a. Discuss results of rt-PCR
b. Discuss Quiz 5’s gel images
c. Gene families, splice sites, Genbank
2. Wet Lab: Examine results of rt-PCR
3. Computer Lab: Gene Families
4. Report4: Rt-PCR work on it
a. Includes:.
i. Predictions via computer
ii. Gel pictures of actual results
25 November – 27 November
THANKS GIVING BREAK NO LABS
QUIZ 5 DUE DURING BREAK!!!!!!!!
2 December – 04 December
Week 12: Functional Genomics Module: Gene 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
09 December – 11 December
Week 13: No lab but Gene Families Report due
Report 5: Gene Families DUE