Barnard BI 203 Syllabus Fall 09, Page 1 of 11

BI 203: Genetics Course Syllabus Spring 2009

Instructor: Professor Daron Barnard Office hours: Monday 9:30 AM – 10:30 AM Office: ST 310C Tuesday 10:30 AM – 11:30 AM Phone: 508-929-8143 Wednesday 9:30 AM – 10:30 AM E-mail: [email protected] Thursday 9:30 AM – 10:30 AM Other times by appointment Class meeting Normal class meetings will be Tuesday/Thursday from 11 – 12:45 AM in ST 102 Lab will meet: Tuesday or Thursday from 1 - 3:45 PM in ST 319

Course description In this course we will cover the basics of hereditary both in a lecture setting as well as a laboratory setting. We will concentrate on three areas of genetics: Mendelian (or transmission) genetics, molecular genetics, and population/evolutionary genetics. While easily divided into these units, they are by no means independent, each being tied to the others. Major concepts to be covered will include how the genetic material: 1) replicates and is passed on, 2) contains information that results in a phenotype, and 3) can change. Recent discoveries as well as historical concepts will be discussed.

Course philosophy Genetics is a broad field and we cannot cover all relevant material. Instead we will focus on the fundamental principles, and explore examples from the major concepts in depth. The goal will be for students to have a foundation of knowledge and to have developed genetics problem solving skills so when presented with a new theory or data, one would understand the underlying concept and could apply this to the new information, allowing a deeper study of any of the areas. It is my hope that when topics interest you, you will examine and probe them further then we are able to during class. I am always willing to help and encourage this type of independent thought. Through this course I want you to think like a geneticist and a biological scientist. To this end we will strive to go beyond the material itself, to understand how biological knowledge is developed. The most important aspect of this course is your learning, so if you are having trouble with the material, please come see me early and often!

Course Goals 1) Students will understand the concepts of classical, molecular, and population genetics. 2) Students will solve genetics problems. 3) Students will make connections between genetics, their lives and other disciplines.

Learning outcomes: At the completion of this course students should be able to (see end of the syllabus for expanded version and tips on how to reach these learning outcomes): 1) Explain the nature of inheritance, the genetic material and how it results in phenotype, variation in genetics, and relationship between these concepts. 2) Use the concepts of Classical, Molecular and Population genetics to analyze data and solve novel genetics problems. 3) Design and carryout genetics experiments, and participate in the generation and evaluation of genetic knowledge. 4) Interact with others regarding the impact and use of genetics and genetic information on society. Barnard BI 203 Syllabus Fall 09, Page 2 of 11

5) Use knowledge of genetics concepts to develop informed questions about a new genetic related topic. 6) Connect genetics with concepts/knowledge from other courses

Required materials • Genetics: A Conceptual Approach, Third Edition (W.H. Freeman) by Benjamin Pierce ISBN: 978-0-716-77928-5

Another option is to get the “ebook” version. This can be purchased directly from the publisher by going to: http://ebooks.bfwpub.com/pierce3e.php Note that this gives you online access anywhere to the text. You can make notes and highlight materials as you would in a paper text. It is $89.95 for a 365 day online subscription.

The study online materials associated with the text are available electronically for no charge on the Pierce website. Go to http://bcs.whfreeman.com/pierce3e/ and register as a student to access everything online.

• Additional handout material for the class and lab will be available on the course BlackBoard site or will be distributed in class.

• You will need a calculator that is not a phone. You will need to have this available for tests.

Additional resources • The BlackBoard site. Resources from the lecture (i.e. Power Point presentations, some readings) will be available at this site. You will also need to use this site to access the problem sets and class announcements. • If you are particularly interested in a topic and wish for further readings, I have lots of books in my office that may be borrowed for short periods of time. These books are also available if you want a different explanation of a topic. • Finally, there is no end to web sites that deal with genetics, particularly that of individual organisms. Many of these will include photos or movies that might let you see some of the concepts that we are discussing in action. I have included links to some on the Blackboard site, but be sure to search for some on your own, and let me know what you find!

Grading and expectations:

The grading breakdown will be as follows (out of a total of 1000 possible points): Problem sets 100 points (10%) Reflection paper 50 points (5%) Literature Summary 50 points (5%) Tests (3) 300 points (30%, each 10% of total) Final Exam 200 points (20%) Lab 300 points (30%)

• Problem Sets will be posted on the BlackBoard site. They are to be completed by class time on the day that they are due at which point they will become unavailable. There will be 11 of these, each worth 10 points. This means that you can miss one of the sets and still receive full credit, or you can complete all of them and receive extra credit. The only way to really grasp genetics is to work through problems, so I suggest that you take these seriously. Barnard BI 203 Syllabus Fall 09, Page 3 of 11

• Tests and Exam are designed to test understanding of the concepts and ability to apply the concepts to novel problems. You can expect questions that range from multiple-choice to essay. The final exam will cover the material following the last test to the end of the semester, as well as being cumulative. The grade that you receive on the final exam may be used to replace your lowest test grade. In other words, if you get 80% on the final exam, and you have a test grade that was lower than 80% (see attendance policy below) you will get 80% of the points available on the test. Therefore the final will have much more weight as it will still count as the final. This will be done with only one test, and only the final exam can be used as a substitution. See attendance policy below for more information.

• Literature Summary will require students to read an article from the primary literature and then write a short paper. This will be a short (2-3 pages) review of the articles that address the “why” and “how” behind the research. See the handout regarding this assignment.

• Reflection Paper will involve finding a news report that touches on some aspect of the genetics that we have been studying. You will then explain the significance of the report to a non- scientist and then write a brief paper describing and reflection on this experience.

• Lab Portion of the grade will consist of brief lab write-ups, an article summary looking at methods, and a major lab report. See the lab description and policy for more information.

Course Policies

• Attendance: General Attendance. I highly recommend attending all the lectures. You are responsible for any assignments, the material covered, and announcements that are made in class. Students find that this is not the type of course that you can skip the lectures and get what you need to know from the book. Attending lecture is the best way to make sure that you are keeping pace with the class and the work.

In addition the class participation portion of the course grade includes group work during class – if you are not present, you are not participating!

Attendance and Tests and the Exam. There will be NO make-up tests. If you miss a test you will receive a zero. However, you may substitute the grade that you receive on the final exam for a single test, if you have missed the test for a valid reason and have cleared it with me. If you just skip a test with no excuse it will remain a zero. See the information regarding tests, and exams above. There will not be a make up exam unless school is cancelled on the day of the exam. I will only consider a make up exam with a valid excuse (as determined my myself and if necessary the Department Chair).

Attendance and the Laboratory. Your attendance is required at all laboratory meetings and absence will require a valid excuse. Biology is an experimental science and some of the most important learning will go on in the lab. If you know that you will not be able to attend a specific lab please talk to me before hand. If you are sick and miss a lab I will need a doctors note. If there is an emergency come talk to me. Otherwise you will receive a zero for that lab. I cannot offer make up labs on an individual basis. Plan ahead!

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• Questions. I strongly encourage you to ask questions. It is likely that if you have a question about something, others do as well. Stop me during lecture or lab if you have a question. I am happy to answer questions after class as well, during my office hours or you can set up a time that is more convenient. Asking questions keeps you engaged in the learning process.

• Cell phones, pagers and other electronics. These should be turned off, and put away prior to class. If they ring or are used (for instant messaging, e-mail, etc.) during class, you will be asked to leave, even if this is during a test. You do not benefit from being in class if you are not paying attention, so there is no point in staying, and it is distracting and inconsiderate to both your classmates and to me. If you need a calculator, bring one that is not a phone. This policy applies for the lecture and the lab as well – this tends to be particularly hard as sometimes there is time when you are waiting during incubations: use this time to your advantage and not to use your phone!

• Computers. You may use a computer for taking notes for this class, but if I feel that you are using it for anything else I will ask you to leave. This includes (but is not limited to) work for other classes, e-mail, surfing the web, instant messaging, and games. This policy applies for the lecture and lab.

• Assignments. Any course work should be neatly typed with black ink (no handwritten assignments) and handed in by the beginning of class on the due date. . Late work will be docked on a per-day basis (one day late 10 points, and 5 points for each subsequent day) up to 50% of the total. Assignments that are over two weeks late will not be accepted without prior permission from me. Not being able to print you assignment does not constitute a valid excuse for work being late. Plan ahead! The only time that assignments can be submitted electronically (e-mail or through BlackBoard) is when I have asked for them in that format.

• Academic Honesty. All students should read and understand the college’s academic honesty policy found in student handbook or at this link: http://www.worcester.edu/academics/acad_pol_proc.htm#acad_honesty. If there are questions about how these policies affect this class, please see me. If you have a question as to whether or not what you are doing is plagiarism ask me BEFORE you hand in the assignment. If you are caught plagiarizing or cheating in any way, you will receive a failing grade for the course.

• Special needs. If there is any reason that you might require special assistance for any portion of this course I urge you to contact the Office of Disability Services at 929-8733. Please do this as soon as possible so that we can arrange services to meet your needs. I cannot address potential issues if I am not aware of them.

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Genetics Outline

With the exception of the tests, this schedule is tentative – we may have to change things around. Any changes in the course outline will be posted in the announcements section of the course blackboard site. Please examine your semester schedule NOW so that any potential conflicts can be addressed as soon as possible. Readings should be previewed before the class for which they are assigned, and read carefully following the class.

Date Topic Assignments Readings (pp.)

Week 1 Thurs 9/3 Introduction to genetics Chapter 1

Week 2 Tues 9/8 Mendelian Inheritance Ch 2 (43-56) Thurs 9/10 Dihybrid crosses Problem set 1 Ch 2 (57-65)

Week 3 Tues 9/15 Sex Determination & linked characteristics Ch 4 (73-91) Thurs 9/17 Extensions of Mendelian Genetics Problem set 2 Ch 5 (99-114)

Week 4 Tues 9/22 Extensions of Mendelian Genetics Ch 5 (115-125) Thurs 9/24 Pedigrees & Genetic Testing Problem set 3 Ch 6 (134-152)

Week 5 Tues 9/29 Test I (Ch 1-6) Thurs 10/1 Linkage Ch 7 (160-175)

Week 6 Tues 10/6 Linkage Problem set 4 Ch 7 (175-189) Thurs 10/8 Linkage Literature Abstract

Week 7 Tues 10/13 Bacterial Genetics Ch 8 (200-215) Thurs 10/15 Bacterial Genetics Problem set 5 Ch 8 (215-230)

Week 8 Tues 10/20 Chromosome Variation Ch 9 (237-260) Thurs 10/22 Chemical Nature of DNA Problem set 6 Ch 10 (267-81)

Week 9 Tues 10/27 TEST II (Ch 7-10) Thurs 10/29 Chromosome Structure Ch 11 (285-309)

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Date Topic Assignments Readings (pp.)

Week 10 Tues 11/3 DNA replication Literature Summary Ch 12 (315-339) Thurs 11/5 Transcription Problem set 7 Ch 13 (345-363)

Week 11 Tues 11/10 RNA Processing Ch 14 (368-391) Thurs 11/12 Translation Problem set 8 Ch 15 (395-418)

Week 12 Tues 11/17 Bacterial Gene regulation Ch 16 (425-448) Thurs 11/19 Eukaryote gene regulation Problem set 9 Ch 17 (453-470)

Week 13 Tues 11/24 TEST III (Ch 11-17) Thurs 11/26 THANKSGIVING BREAK

Week 14 Tues 12/1 Mutation/DNA repair Ch 18 (471-497) Thurs 12/3 Quantitative Genetics Reflection Paper / Problem set 10 Ch 24 (645-671)

Week 15 Tues 12/8 Population Genetics Problem set 11 Ch 25 (679-701)

FINAL EXAM Tuesday December 15TH at 12:30 PM The final exam is cumulative, but about ½ of the exam will focus on 18, 24, and 25.

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Laboratory portion of the course:

Biology is an experimental science. We will use the lab to explore and expand on some of the concepts that we cover in lecture. The lab and lecture will work together to give students the greatest possible exposure to the concepts, experimental approaches, and techniques of genetics. Therefore you can expect to see material on tests that was covered in the lab to a greater extent that was possible in lecture. I will try to have labs scheduled as close to the time that we cover the relevant material in lecture, however this is not always possible, and will mean that we will skip around in the lab manual a bit. Students should develop basic genetics laboratory skills as well and problem solving and analytical skills.

Attached is an outline of the laboratory schedule. This is a general outline and is subject to change. There are some labs that will require members of the group to come in and do some work outside of the normally scheduled lab meetings, (evenings and weekends) so you will need to be flexible. This is part of the course – if you do not think that you will be able to do this you need to talk to me about your ability to do this course.

Lab policies:

• You must pass the lab portion of the course in order to pass the course.

• Please be on time. I will start the class with any important instructions and safety announcements, and if you are late you will miss these. I will start the lab promptly so that we can try to finish promptly.

• Please have read the lab material in advance. This will make things go much more smoothly for everyone concerned. Labs will be confusing if you are reading one sentence ahead of the task you are doing. The best way to avoid this is to read any lab materials before your lab section, and know what will need to be done. This is particularly important when labs will need to span more than one week or need to have work completed outside of our normal lab meetings. If I feel that the class is coming to lab without having read the instructions then I will start giving pop quizzes. This will cause the lab reports to be worth 100 points (see below) and the lab quizzes will be worth 20 points.

Grading:

The lab is worth 20% of your total grade (200 points). Grading in the course will be divided up into two sections: Short Lab Write-Ups 100 points Formal Drosophila write-up 100 points Formal Genomics write-up 100 points

Formal lab write-up. There will be two formal lab write-ups for the Drosophila experiments and the Drosophila genomics (see descriptions). Instructions on how to write up a lab report can be found in the back of your Intro Biology I (BI 105) lab book, and we will talk about format and content during the labs.

Short Lab write ups. For each lab I will indicate questions and/or problems that I would like you to address. These are to be completed (typed when appropriate) and handed in the following lab meeting at the beginning of lab (as noted on the outline). I will indicate the data that Barnard BI 203 Syllabus Fall 09, Page 8 of 11

you need to include. If you are not in lab you will receive a zero for that particular assignment. If you use the lab on the day that it is due to work on the questions and hand it at the end it will be considered late. Each lab will generally be worth 10 points except the genomics lab which is worth 30 points (with the presentation).

Attendance. I expect that all students will be at every lab meeting (see the attendance policy above). If there are extenuating circumstances you need to talk to me immediately – in advance if possible.

Drosophila Experiments.

Drosophila melanogaster is one of the most extensively studied model organisms for genetics. Its rapid generation time and well-characterized mutations make them ideal for an introduction to genetic analysis. We will be using Drosophila for three different genetic analyses. In the first two we will examine the inheritance pattern of a single trait (monohybrid cross) and subsequently the inheritance pattern of two traits (dihybrid cross). The third analysis will examine the inheritance pattern of three different traits, the genes for which lie on the same chromosome. We will use this data to determine what can be said about the positional relationship between these genes (three point link linkage). These labs will be ongoing in addition to the weekly labs, and your group will be responsible for setting up your crosses and scoring your phenotypes to collect the data. This will mean coming in to lab several times a week in addition to your regularly scheduled lab section to count flies.

Genomics Experiments.

The field of modern genetics is generating data (particularly genomic sequence data) faster than it can be analyzed. Computers are used to make a first pass at annotation of the genomic sequence; that is, indication of the regions of interest – particularly genes. However the computers are prone to mistakes – generally in order to make sure that they do not miss potential genes they predict genes where none exist. We will work as part of a larger research group that is annotating genomic sequence data, looking at the computer predictions and determining if there is sufficient evidence to support the prediction. The annotation that we generate will be subsequently made available to the research community, so is a part of an actual research project. We will be working on a species of fruit fly closely related to Drosophila melanogaster called Drosophila erecta. As the genome for D. melanogaster is sequenced and annotated we have a big advantage – we can compare our data with what is known from the D. melanogaster annotation. We will discuss the details in lab, but you will need to read the Genomics chapters in your textbook.

Your group will work together in and out of lab, to annotate a region of DNA. These labs will be entirely computer based. So while I have designated several lab meetings to work on this project, you may work on the project outside of lab. The class will have time to share experiences (what is working, what is not). There will be a report (individual) and a presentation (group).

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Lab Schedule Fall 2009: BI 203 (All Sections)

Week Lab Assignment Due 9/1-3 NO LAB

9/8-10 Lab safety; Cellular Reproduction: Mitosis/meiosis (Read Pierce Ch. 2, pages16-38) 9/15-17 Mendelian genetics – set up Drosophila monohybrid and Cellular dihybrid crosses (read Pierce pages 84-85) Reproduction 9/22-24 Probability in genetics

9/29-10/1 Statistical analysis of genetic experiments Probability Set up Sordaria crosses 10/6-8 Linkage with Sordaria Statistics

10/13-15 Linkage with Drosophila 3 point crosses Sordaria Linkage

10/20-22 Amplification of DNA polymorphisms (PCR)

10/27-29 DNA digestion PCR analysis 11/3-5 Genomics I PCR

11/10-12 Genomics II DNA Digest

11/17-19 Genomics III Drosophila Lab Report 11/24-26 NO LAB - Thanksgiving

12/1-3 Genomics presentation Genomics Lab Population Genetics 12/8-10 NO LAB Population Genetics

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Learning goals for genetics, how they will be achieved, and assessed.

Course Goals: 1) Students will understand the concepts of classical, molecular, and population genetics. 2) Students will solve genetics problems. 3) Students will make connections between genetics, their lives and other disciplines.

At the completion of this course students should be able to:

Learning outcomes Course Assessment Activities Learning Activities Goal Explain the nature of inheritance, the 1 Tests, problem sets, Readings, lectures, problem genetic material and how it results in solving phenotype, variation in genetics, and relationship between these concepts. Use the concepts of Classical, 1,2 Lab reports, problem Analyze genetic crosses and Molecular and Population genetics to sets, exams predict phenotypic ratios, analyze data and solve novel genetics statistically analyze the results, problems. determine genetic distance and linkage, predict heritability, determine allele frequencies Design and carryout genetics 1,2,3 Lab reports, reflection Lab activities experiments, and participate in the papers Reading genetics articles generation and evaluation of genetic Article summaries knowledge. Interact with others regarding the 1,3 Reflection papers Finding reports on genetics impact and use of genetics and Article summaries findings genetic information on society. Reading genetics articles Use knowledge of genetics concepts 1,2 Design a project Discussions regarding topics; to develop informed questions about a describing a genetics designing learning plan new genetic related topic topic of interest and Reading literature exercise plan to learn about this over the next year Article summaries Connect genetics with 1,3 Article summaries Reading literature exercise concepts/knowledge from other Discussions courses

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How to be successful in genetics:

•Attend all classes and labs (and be mentally present) •Print lecture slides out and bring them to lecture or have you computer with you and take notes on the slides •Do the reading before coming to class •Complete all the problem sets and participate in all problem-solving activities in class - Figure out what went wrong with any problems that you answered incorrectly •Form a study group •Make your own glossary - Back (or front) of your notebook •Copy your notes over (transcription?) - At the minimum on a weekly basis (daily is best) •Study as we go: - Do not cram before an exam - 9-10 hours a week outside of class spent studying •Come see me with questions (as soon as they occur to you!) or help with solving problems