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    • BIO 340/343 INTRODUCTION TO GENETICS LECTURER: Dr. Lisa Dorn Spring 2009 OFFICE: HS 45; LAB: HS 47/50 PHONE: 424-3064; E-MAIL: dorn@uwosh.edu OFFICE HRS: LECTURE HOURS: 9:10 – 10:10 am in Halsey Science Building; Rm. 268 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 can be temperamental. 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. 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 these EC points cannot be used 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 920 424-1033 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. Le c# Day Date Topics Book Week 1 Monday 2-Feb Mendels Laws; Monohybrids & Dihybrids Chapter 2 1 2 Wed 4-Feb Dihybrids & Pedigrees Chapter 2 1 3 Friday 6-Feb Pedigrees; Probability Chapter 2 1 4 Monday 9-Feb Chi-Square Chromosomes Sex-Linkage Chapter 3: 2 5 Wed 11-Feb Sex Determination; Meiosis Chapter 3: 2 Quiz 1 Thursday 12-Feb Due 2 Chapter 6 Friday 13-Feb Recessive Lethals 3/4 2 7 Monday 16-Feb Pleiotropy; Incomplete Dominance Chapter 4 3 8 Wed 18-Feb Co-Dominance, Overdominance, 3 Thursday 19-Feb 3 9 Friday 20-Feb Penetrance, Complementation, Epistasis Chapter 4 3 10 Monday 23-Feb Epistasis, Linkage and Recombination Chapter 4 4 Tuesday 24-Feb Quiz 2 Due 4 Wed 25-Feb EXAM 1 (covers up to lecture 9) 2, 3 & 4 4 11 Friday 27-Feb Linkage and Recombination; Chapter 4 4 12 Monday 2-Mar Mapping genes: dihybrid crosses Chapter 5 5 13 Wed 4-Mar Mapping genes: Trihybrid crosses Chapter 5 5 Thursday 5-Mar 5 14 Friday 6-Mar Intragenic Mapping, bacteriophage Chapter 5 5 15 Monday 9-Mar Complementation tests and deletion mapping Chapter 6 6
    • Tuesday 10-Mar Quiz 3 Due 16 Wed 11-Mar Complementation tests and deletion mapping; Chapter 6 6 17 Friday 13-Mar Complementation tests and deletion mapping; Chapter 6 6 18 Monday 16-Mar Chromosomes: Change in Number Chapter 8 7 19 Wed 18-Mar Chromosomes: Structure; Variation & Mutations Chapter 8 7 Thursday 19-Mar Quiz 4 Due 7 20 Friday 20-Mar EXAM 2 (covering lectures 10 to 18) 7 Monday 23-Mar Spring Break 8 Wed 25-Mar Spring Break 8 Friday 27-Mar Spring Break 8 21 Monday 30-Mar Chromosomes: Polyploidy Chapter 8 9 22 Wed 1-Apr Chromosomes: Polyploidy Chapter 8 9 23 Friday 3-Apr Gene Mutation chapter 16 9 24 Monday 6-Apr Gene Mutation chapter 16 10 Chapter 25 Wed 8-Apr Transcription Review 12 10 Thursday 9-Apr Quiz 5 Due 10 Chapter 26 Friday 10-Apr Post-Transcriptional Processing 12 10 Chapter 27 Monday 13-Apr Post-Transcriptional Processing 12 11 Chapter 28 Wed 15-Apr Transcriptional Regulation in Eukaryotes 15 11 Thursday 16-Apr 11 Chapter 29 Friday 17-Apr Transcriptional Regulation in Eukaryotes 15 11 Chapter 30 Monday 20-Apr Transcriptional Regulation in Eukaryotes 15 12 31 Wed 22-Apr Non-Mendelian Inheritance: X-inactivation & Imprinting chapter 7 12 Thursday 23-Apr Quiz 6 Due 12
    • 32 Friday 24-Apr 'EXAM 3 ( Lectures 18 to 30) 12 33 Monday 27-Apr Non-Mendelian Inheritance: X-inactivation & Imprinting chapter 7 13 34 Wed 29-Apr Non-Mendelian Inheritance: X-inactivation & Imprinting chapter 7 13 Chapter Thursday 30-Apr Population Genetics 25 13 35 Friday 1-May Population Genetics Ch 25 13 Population Genetics Quiz 7 36 Monday 4-May due Ch 25 14 37 Wed 6-May Population Genetics Ch 25 14 Thursday 7-May 14 38 Friday 8-May Population Genetics Ch 25 14 39 Monday 11-May Population Genetics/ Review 15 Tuesday 12-May Quiz 8 Due 15 Wed 13-May EXAM 4 (Lectures 31-39) 15 Friday 15-May 15
    • Genetics Lab Syllabus Spring 2009 Instructors: Lisa Dorn HS45; dorn@uwosh.edu, 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 learn molecular lab techniques that are useful for genetics, learn 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. There are four quizzes and five reports as shown in the table below. Quiz/ Report Due Date (end of lab period) Points Quiz 1: Nucleic Acids Review 17 – 19 Feb 10 Quiz 2: Replication 03 - 05 Mar 10 Report 1: Electronic PCR 10 - 12 Mar 10 Quiz 3: Optimization/ Polymorphisms 7 – 9 Apr 20 Report 2: Polymorphisms 14 – 16 Apr 15 Report 3: Marker Map 21 – 23 Apr 10 Quiz 4: Gene Expression 28 – 30 Apr 10 Report 4: RT-PCr 05 – 07 May 10 Report 5: Gene Families 12 – 14 May 10 Total points 105
    • 10- 12 February Week 2: 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 4. Post basic molecular biology review from 323 on D2L 5. Report: None 6. Quiz1: Nucleic Acids Review on D2L available (Highest score counts toward grade). 17 – 19 February Week 3: 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 24 - 26 February Week 4: 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. Report: None 5. Quiz2: DNA replication & quantification available. 3 March - 5 March Week5: 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
    • 10 – 12 March Week 6: 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 17 -`19 March Week 7: 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 24 – 26 March Week 8: ***************Spring Break NO LABS************************ 31 March – 2 April Week 9: 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
    • 7 – 9 April Week 10: Genomics Module: Mapping 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. 14 - 16 April Week 11: 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 21 – 23 April Week 12: 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. Quiz4: Gene expression available
    • 28 April – 30 April Week 13: Functional Genomics Module: Gene Expression 1. Lecture: a. Discuss results of rt-PCR b. Discuss Quiz 4’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 3 May – 05 May Week 14: 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 5. Quiz4: Due 10 May – 13 May Week 15: No lab but Gene Families Report due Report 5: Gene Families DUE