BIO 375 Genetics with Laboratory


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BIO 375 Genetics with Laboratory

  1. 1. Biology 375 Genetics with Lab Fall 2006 Saint Martin’s University Professor Margaret Olney, Ph.D. Office: Old Main 407 (I do not have email access at home, Office phone: 438-4327 so emails sent to me in the evening or on the weekends will be answered on the next school day.) Office Hours: Monday 11am-12:30pm, Wednesday 11am-1pm, Thursdays 9:30-11am, or by appointment Lectures: Monday, Wednesday, and Friday 10-10:50am in Old Main 401. Labs: Tuesday 2:00-3:50pm in Old Main 402. Labs begin 9/5/05. The lecture and the lab are one integrated course worth 4 credits. Lab must be taken and is an essential part of this course. At the end of the semester, one grade will be given for the lecture and lab together. Required Textbook: Concepts of Genetics. Eighth Edition. Klug, Cummings, and Spencer. 2006. Pearson Prentice Hall Publishers. ISBN10: 0131345370. ISBN13: 9780131345379 A Value Package including of the following items in addition to the textbook is available in the Saint Martin’s University bookstore. • Student Handbook and Solutions Manual, 8/E • OneKey CourseCompass Student Access Kit for Klug, 8/E • Concepts of Genetics Student Companion Website Access Card Package, 8/E While it may be possible to order the textbook itself online, I strongly recommend that you purchase the Value Package from the bookstore. The additional items in the Value Package are available only in the SMU bookstore and do not increase the cost of the textbook available there. Genetics is all about working problems, and the student handbook and solutions manual will be crucial to your success in this course. This handbook contains detailed step-by-step solutions or discussions for every problem in the textbook, as well as extra study problems, chapter outlines, vocabulary exercises, and an overview of how to study genetics. We will be using the Course Compass website, and you will want to have access to it (although it is possible to purchase access to it separately online for $30 at <>). The student companion website will be an additional useful study tool, as it contains reviews, summaries, questions, hints, feedback, web tutorials, and media labs Other Required Materials: a three-ring binder for your lab notebook and genetics journal. 1
  2. 2. Student Outcomes: By the completion of this course, you should be able to: • understand mitosis, meiosis, and sexual reproduction; • apply Mendel’s Laws of Segregation and Independent Assortment using probability models; • perform test crosses and monohybrid, dihybrid, and trihybrid crosses using Punnett squares; • statistically analyze the results of genetic crosses using the Chi-Square test; • identify inheritance patterns in human pedigrees; • analyze sex-linked traits in humans; • understand the effects of the environment on gene expression; • construct genetic maps using two-point and three-point crosses and calculate map distances; • understand the effects of chromosome mutations • understand the composition and structure of DNA and RNA and the organization of DNA in chromosomes; • understand semiconservative DNA replication, enzymes involved in DNA synthesis, and DNA recombination; • understand the bases of human genetic diseases and the human genome project; • understand the vertical relationships among DNA, RNA, proteins, and phenotypes, including the processes of transcription and translation; • understand the transposable elements and their consequences; and • understand and work problems in population genetics. In addition, you should improve your skills of: 1. applying quantitative methods to the study of biological problems; 2. understanding and applying the scientific method to solving problems in biological systems; 3. understanding biological issues and their relationship to societal issues; 4. formulating questions in a scientific framework; 5. evaluating and interpreting scientific evidence; and 6. communicating effectively and thinking critically. Working Problems: Genetics is not a subject that can be learned successfully by memorization. It is all about working problems. You will need to fully understand the concepts and principles in order to be able to apply them to new circumstances when working problems, for practice and on quizzes and exams. You cannot be math-phobic if you want to succeed in this course. Class Participation: Studies have shown that learning occurs best in an interactive and active environment, so you should not plan on just sitting back and passively taking notes in this course. This does not mean that you shouldn’t take notes. Instead, you should do MORE than just take notes during class. Plan to actively and enthusiastically participate in class lectures, discussions, projects, and activities. You will be rewarded both in your grade and in your level of learning. In general, the more engaged you are, the more (and more deeply) you will learn. Class time will be devoted to lectures, working problems, activities, discussions, and projects. Lab Attendance: You must complete all labs in order to pass this course. If you must miss a lab for an unavoidable reason, you must make arrangements in advance to make up the lab at another time during the same week. If you must miss a video scheduled during lab time, please make arrangements in advance; your video paper will still be due on the assigned day. 2
  3. 3. Bio375 Grading: Quizzes 25 % Lab assignments 17 % Midterm exam 15 % Video papers 8% Genetics journal 5% Lab participation 5% Final project 5% Lecture participation 5 % Final exam 15 % Grading Scale: A exceptionally high level of competence or knowledge. B above average competence or knowledge. C adequate competency related to course goals. D marginal competency but passing F failure to achieve minimum competency A 93.0 - 100 % C+ 77.0 - 79.99 % A- 90.0 - 92.99 % C 73.0 – 76.99 % B+ 87.0 - 89.99 % C- 70.0 – 72.99 % B 83.0 - 86.99 % D+ 67.0 – 69.99 % B- 80.0 - 82.99 % D 63.0 – 66.99 % Course Evaluation: Quizzes: A number of quizzes will be given at the beginning of class (at 10am sharp) as indicated on the course schedule. If you are late to class and the quiz has already been handed out, you will not be allowed to take the quiz, and a zero will be recorded for your score. Quizzes will be short (approximately 20 minutes) and will cover material from the chapters indicated on the course schedule. Quizzes will include a variety of question types, including problems to work and multiple choice, short answer, and essay questions. Examinations: Students will take one midterm examination and one cumulative final examination to demonstrate their understanding of material from lectures, discussions, activities, and assigned readings. A main focus of the exams will be working problems that are similar to the ones at the ends of the chapters, those handed out in class, in your student handbook, and on the Concepts of Genetics Student Companion Website. In addition to problems to work, there may also be multiple choice, short answer, and essay questions. The midterm examination will be 1 hour 50-minutes long on Tuesday, October 10 (during lab time) and will cover the material found in Chapters 1-5 and presented in class August 28-October 9. The final examination will be 1 hour 50-minutes long on Tuesday, December 12 from 10:15am-12:15pm in our regular classroom. The final exam will be cumulative. Participation: This part of your grade includes your active and enthusiastic participation in class lectures, activities, projects, and discussions; promptness; and attendance. If you come (on time) to every class and ask or answer a couple of questions over the course of the semester, you can expect to earn approximately 80% of the participation grade. In order to score higher, you will want to ask and answer questions during every class period. In lab and in group projects, you must contribute as much as other students in order to score well on participation. The more actively engaged you are, the more you will learn. 3
  4. 4. Genetics Journal: Your journal may be kept in the same 3-ring binder as your lab materials, but it should be in a separate, labeled section of the binder. You may use a spiral notebook or a bound journal if you prefer. The important thing is that your journal is legible and that you keep all your work in one place. You will include in your genetics journal all of the genetics problems you have worked from your textbook and from other sources. Always clearly label the chapter and problem number you are working on. You do not have to work problems in order. While you are not required to work any problems in particular, you are strongly encouraged to work as many problems as possible. Genetics really is learned best by working through problems. You are encouraged to work on problems in groups, but be sure each student writes up the problems individually in her or his own journal. You are encouraged to include comments about how you worked the problems, and questions you may have had, and/or trouble you may have encountered. Please be polite, however :). Your journal will be evaluated on its organization, thoroughness, and on how well you explain what you have done to work the problems you present. You do not have to have the correct answers in order to get a good grade, but you must need to know how to get correct answers if you are to score well on the exams. Your genetics journal will be an excellent place to practice. You will also include in your genetics journal 3 articles from the New York Times. The topics of these articles should be related to the field of genetics. Please type a one-half-page summary and explanation of each article you include in your journal. For each entry, include the article (labeled with its date of publication) and your summary/explanation. Final Project: Your final project will focus on one article from the New York Times (this can be the same as one of your articles in your journal). In groups of two, you will research and explain the genetics/biology behind an article. In your research, you must use at least two research articles from scientific journals and may also use others from textbooks or the popular news media (magazines, newspapers). Be cautious using information you might find on the internet—if you use it, make sure that it comes from reputable sources. The final project has two deadlines. On Monday, October 16, your group will turn in your article, a short description of what you will explain, and a list of at least 4 sources that will be used to gather information. On Tuesdays, November 28 and December 5, each group will orally present a poster explaining the genetics behind its article to the class. Groups will randomly be assigned presentation dates/times. Lab assignments: Lab reports will be written according to guidelines drafted by the St. Martin’s Biology Department. Depending on the kind of experiment and/or study conducted during lab, specific instructions for each lab report will be provided. Lab assignments will be due at the beginning of the lab period one week after data collection has been completed. Student Attendance and Late Policy: It is your responsibility to attend classes, take exams, and hand assignments in on time, so plan ahead accordingly. You are required to attend all lectures. If you must miss a lecture because of extraordinary circumstances, please notify your instructor in advance and make arrangements to get copies of lecture notes from one of your classmates. Several quizzes will be given over the course of the semester (as indicated on the schedule) and will be given at the beginning of class (10am sharp). If you arrive after the quizzes are handed 4
  5. 5. out, you will not be able to take the quiz and you will receive a score of zero. Make-up quizzes will be administered only according to the guidelines explained below for exams. All assignments are due at the beginning of class on the due date (10am sharp). Assignments turned in up to 24 hours late will penalized 50% of the point total. Assignments turned in 1-7 days late will be penalized 75% of the point total. Assignments more than 7 days will not be accepted for credit. Make-up exams will not be given unless: 1) you were very ill at the time of the exam and you have a legitimate written excuse from a nurse, counselor, or physician (for reasons of confidentiality, your written excuse only needs to say that you were unable to attend because of illness) and you notified you instructor before the beginning time of the exam (via phone or email); 2) you had a family emergency and you notified the dean’s office or counselor and you notified your instructor before the beginning time of the exam; or 3) you were on a college- sponsored field trip or event which required your absence and you personally notified your instructor of your absence at least one week before the exam. If you miss an exam for any other reason, you will receive a score of zero. Plagiarism and Cheating Policy All students are expected to uphold the integrity of this academic institution. Academic dishonesty includes, but is not limited to, giving or receiving unauthorized information regarding exams or assignments; copying or allowing copying of any assignment, lab write-up, or test; or plagiarism from any written material (whether copyrighted or not). Depending on the severity of the infringement, violators of this policy will receive a zero on the assignment involved or a failing grade in the course, AND (under all circumstances) will have their name and evidence of cheating submitted to the Vice President of Academic Affairs for further action. Further information about penalties for academic dishonesty can be found in the St. Martin’s University Student Conduct Code (see your Student Handbook). Copying or paraphrasing another person’s lab or paper is considered cheating by both people. Plagiarism is taking the ideas, thoughts, content, or graphics from someone else and representing them as your own. This includes cutting and pasting passages of another person’s work off the internet. When you are using information from another source (whether copyrighted or not, including your textbook, the internet, or another student’s paper), always document it within your paper! If you are directly quoting a source (which you should avoid doing if at all possible), either use quotation marks (for short passages) or indent or single-space the quote (for longer passages). In either case you must also indicate the source. If you are unsure what constitutes plagiarism, please consult your instructor. It is very important that you complete your own original work. Do NOT ignore the cheating policy in this (or any) course. It is a very SERIOUS matter. I have encountered many different forms of cheating in the past and will not be shy about turning in and failing violators. You really don’t want to fail this course or to be expelled from St. Martin’s for cheating or plagiarism. 5
  6. 6. Special Needs: If you need course adaptations or accommodations because of a disability, if you have medical and/or safety concerns to share with me, or if you need special arrangements in case the building must be evacuated, please make an appointment to speak with your instructor as soon as possible. Tips for Success in this Course: Genetics is a difficult course. You will not learn all you need to know during the 150 minutes of lecture each week. Educators have estimated that for every hour of in-class time, you should spend approximately 2-3 hours of time out of class, because you are responsible for your own learning and understanding. I cannot learn the information and understand the concepts for you, and I cannot make you learn and understand simply through lecturing. What can you do to succeed? The following list summarizes some strategies: 1. Work problems. Work problems. Work problems. Work problems. Work through problems at the ends of the chapters in your textbook. Work through problems available on the textbook website. Work through problems in the Student Handbook. Work through as many problems as you can. Check your problems in the answer keys (if they are available). Genetics really is not about memorizing; it is about understanding and applying concepts to new problems. This is why I didn’t breeze through my own undergraduate genetics course in college (it was difficult for me to accept that memorization and recall wasn’t enough!). 2. Read your textbook before coming to class. Read it through once to identify the "big ideas." Don't highlight every line. Select key concepts and definitions. Of course, read the textbook more thoroughly after the topics have been covered in class. 3. Review your lecture notes after each class. Review after class to check your understanding of the material covered. Use your textbook and/or its resources (CD-ROM and website) to fill in any missed details and to answer questions that you have. If a question persists after you have tried to answer it yourself, ask a classmate, tutor, or me. Each class builds on information in preceding classes. If a key concept is missed early on, new information will be confusing. 4. Study using the textbook and its handbook and website. At least one of the questions from online will appear on each of your exams (and on several of your quizzes too). The text website (see your textbook for more information) has many valuable resources, including animations, activities, practice problems, and practice questions. 5. Organize a study group. Ask and answer questions for each another. Work problems as a group. Work problems as a group. Work problems as a group. Work problems as a group. Work problems as a group. Work problems as a group. Work problems as a group. However, make sure that each and every member of your study group is able to work through problems on her or his own in order to be prepared for the quizzes and exams. Support Services If you are having difficulty with the content and concepts presented in this course, please do not hesitate to contact your instructor. Instead, or in addition, you may utilize 6
  7. 7. tutors available in the Learning Center (Old Main 214). Tutoring in genetics (and many other subjects) is available free of charge to all St. Martin’s University students. 7
  8. 8. Bio375 Course Schedule (subject to change) 8/28/06 Reading in Date Topic/Quiz Klug et al. Lab M 8/28 Syllabus review and basic concepts Chapter 1 T 8/29 GATTACA video W 8/30 Cell structure and diploid organisms Ch. 2 F 9/1 Mitosis and the cell cycle Ch. 2 M 9/4 Labor Day, no classes GATTACA video paper due T 9/5 Mitosis lab W 9/6 Meiosis Ch. 2 Gamete development and sexual F 9/8 Ch. 2 last day to add/drop reproduction Chapter 2 practice problems due M 9/11 Chapter 2 Quiz Ch. 3 Mendel and monohybrid crosses Mitosis lab due T 9/12 Mendelian genetics lab I W 9/13 Dihybrid and trihybrid crosses Ch. 3 F 9/15 Chromosomes/modern transmission genetics Ch. 3 M 9/18 Laws of probability Ch. 3 T 9/19 Mendelian genetics lab II W 9/20 Chi-Square analysis Ch. 3 F 9/22 Pedigrees Ch. 3 Chapter 3 practice problems due M 9/25 Chapter 3 Quiz Ch. 4 Extensions of Mendelian genetics Mendelian genetics lab due T9/26 Blood typing lab W9/27 Extensions of Mendelian genetics Ch. 4 F9/29 Extensions of Mendelian genetics Ch. 4 Chapter 4 practice problems due M 10/2 Chapter 4 quiz Ch. 5 Genetic linkage and gene mapping Blood typing lab due T 10/3 Genetic mapping lab W 10/4 Chromosome mapping in eukaryotes Ch. 5 F 10/6 Chromosome mapping in eukaryotes Ch. 5 8
  9. 9. Chromosome mapping in eukaryotes Chapter 5 practice problems due M 10/9 Ch. 5 Chapter 5 Quiz Genetic mapping lab due T 10/10 Midterm Exam during lab W 10/11 Sex determination and life cycles Ch. 7 F 10/13 Fall Break, no classes Sex determination in humans final project initial assignment due: M 10/16 Ch. 7 article, summary of what you will explain, and list of at least 4 sources T 10/17 Chromosome lab W 10/18 The X chromosome Ch. 7 Chromosome mutations: variations in F 10/20 Ch. 8 chromosome number and arrangement Chromosome mutations: variations in M 10/23 Ch. 8 midterm grades due chromosome number and arrangement Chromosome lab due T 10/24 Race for the Double Helix video Chapter 7 and 8 practice problems due W 10/25 Chapters 7 and 8 Quiz Ch. 10 DNA F10/27 DNA Ch. 10 M 10/30 DNA Ch. 10 Double Helix video paper due T 10/31 DNA lab W 11/1 DNA replication Ch. 11 F 11/3 DNA replication Ch. 11 last day to withdraw M 11/6 DNA replication Ch. 11 DNA lab due T 11/7 Molecular biology lab I Chapters 10 and 11 Quiz W 11/8 Ch. 12 DNA organization F 11/10 DNA organization Ch. 12 9
  10. 10. M 11/13 DNA transcription Ch. 13 T 11/14 Molecular biology lab II W 11/15 DNA transcription Ch. 13 F 11/17 DNA transcription Ch. 13 Chapters 12 and 13 Quiz M 11/20 Ch. 14 Translation and proteins Molecular biology lab due T 11/21 Human Genome video W 11/22 Translation and proteins Ch. 14 F 11/24 Thanksgiving Break, no classes M 11/27 Mutations Ch. 15 Human Genome video paper due T 11/28 final project presentations W 11/29 Transposable elements Ch. 15 F 12/1 Population genetics Ch. 25 Chapters 14 and 15 Quiz M 12/4 Ch. 25 Population genetics T 12/5 final project presentations W 12/6 Population genetics Ch. 25 T 12/12 10:15 a.m.-12:15 p.m. FINAL EXAM in our regular classroom 10