GENETICS & MOLECULAR BIOLOGY (BIOL3010)

Transcription

1 GENETICS & MOLECULAR BIOLOGY (BIOL3010) FALL 2012 COURSE DESCRIPTION What makes humans different from fruit flies? Why do you look like your mother? Why does your brain have neurons and not liver cells? The short answer to each of these questions is: It's the genes! And, that's what this course is about. Throughout the semester, we will consider what genes are, both physically and functionally. We will consider their chemical make-up, how they are passed on from generation to generation, how they are expressed and how that expression is regulated, how disruptions in the structure and expression of genes arise and how those disruptions lead to cellular defects and disease. WHY STUDY GENETICS? Ultimately, genetics underlies not only how organisms develop, but also how they respond to and interact with each other and their environments. But, aside from that and any particular curiosity you have about our relationship to fruit flies in the grand scheme of life, why should you care about genetics? Genetics has an enormous impact on modern society. Our increasing understanding of the molecular genetic basis of heritable traits, including disease, prompts difficult health and reproduction-related questions for both individuals and lawmakers. Our growing knowledge of the function and control of our genome is enabling greater opportunities for developing effective gene therapies to treat/cure genetic diseases. Rapidly evolving technical advances are making it possible to gather unprecedented information about our individual genetic profiles (our genetic fates?). This course is designed to help you develop the analytical skills necessary to enhance not only your continuing studies in biology, but also your future contributions to the vigorous societal debates that focus on these genetics issues. COURSE OBJECTIVES The overall goals of this course are that you will (1) develop an understanding of how genes and traits are related, (2) learn how to think like a geneticist for future analyses of complex biological phenomena and (3) use your acquired genetic literacy to become an informed member of society. Specifically, at the end of this course, you will: be able to connect all aspects of the function of genes & genomes with their molecular anatomy. understand the mechanisms by which an organism's genome is passed on to the next generation and be able to assess where during that process structural abnormalities in the genome arise. be able to analyze gene variants, genetic crosses and inheritance patterns to deduce information about genes, alleles and gene functions. be able to analyze and understand how different types of mutations affect genes and their corresponding RNA/protein products. be able to relate genes & gene function to core principles in other major disciplines of biology, such as cell biology, development, biochemistry, and evolution.

2 IMPORTANT COURSE DETAILS Lectures: 1:00-1:50 MWF Chem 402 Semester Tests: 7:00-9:00 PM Mondays (see calendar) Chem 402 Required Discussion Sessions: as scheduled INSTRUCTOR INFORMATION Claire Cronmiller, Professor of Biology. Born in Syracuse, New York, but grew up in New York State, Washington State, Massachusetts and New Jersey. Started out as a German literature major in college, but eventually had to admit to a less than scholarly talent for literary criticism. Took Introductory Biology in college to fulfill a science requirement: The rest, as they say, is history. In the lab, grows fruit flies as an experimental model to study the genetic regulation of development, but at home cares for 18-year-old Pulcino, a Quaker parrot. Office: Gilmer 260 Phone: (office), (home) crc2s@virginia.edu Office Hours: T 10-11, W 2:15-3:15 [Gilmer 227] & by appointment [Gilmer 260] (TEACHING ASSISTANTS) Krista Aschenbach, Erin Kodis, Brittany Sutherland, Rich Smindak addresses, office locations & office hours posted on the course Collab site. TEXTBOOK & ONLINE LEARNING PROGRAM The required textbook is: Genetic Analysis: An Integrated Approach by Sanders and Bowman, 1 st ed., Pearson. This book will be used throughout the semester to provide foundational knowledge, as well as application practice problems; the book is available in both hardcover and loose leaf editions. There is also an associated Student Study Guide and Solutions Manual, which is not required but might be useful (if used effectively: see Cronmiller's Tips for Success in Genetics on Collab). Mastering Genetics is an online learning program that will be used to give you help with problem solving and to provide you with feedback on the depth of your understanding of fundamental concepts; access codes are available either bundled with the textbook or separately. Pre-class quizzes (due by 10:00 AM each class day) and weekly homework assignments (due by 5:00 PM each Sunday) will also be provided through Mastering Genetics. PREREQUISITES BIOL 2010 and at least one semester college chemistry (e.g. CHEM1410/1420/1810/1820). The premise for this course is that you have completed these prerequisites and are familiar with their concepts and principles. IMPORTANT COLLEGE DATES: Last Day to Add: September 11 Last Day to Drop: September 12 Last Day to Withdraw: October 23

3 TO DO YOUR BEST, I'D RECOMMEND: Complete the pre-class assignments. Class time will be used to consider concepts and processes at levels that go beyond simply "define and describe." To participate fully in class time discussions and activities, you will need to come prepared. The reading for each class is listed in the course schedule. By 10:00AM on each class day, complete the short Mastering Genetics quiz that is based on the reading material; this will help you gauge your comprehension of the reading, and it will help me identify particularly difficult material that needs to be clarified during class. Come to class. Class presentations and activities will help you understand extensions, implications and applications of genetic concepts. Case studies and word problems will give you guided practice analyzing genetic scenarios. We will also use iclickers to help you assess your own understanding of these concepts and your ability to apply them to problems and simulations. Use the available resources. Among the Learning Aids under the Resources menu, you will find suggestions for reading your textbook, solving problems, integrating concepts throughout the semester, etc. You will also find Cronmiller's Tips for Success in Genetics, which includes strategies for developing your problem solving skills. Practice, practice, practice! Confucius said: I hear and I forget, I see and I remember, I do and I understand. If listening and reading are as far as you go with your course involvement, you will undoubtedly be dissatisfied with your encounter with genetics this semester. Unfortunately, we cannot offer you the hands-on doing experience that would most effectively lead you to genuine understanding of genetic principles. Instead, we use problem solving to simulate "doing." Typically, we are not born with an instinctive ability to dissect and explain genetic scenarios: That ability needs to be developed. Moreover, cultivating that ability is not a passive activity: It will require significant time and effort on your part. However, since solving practice problems, diligently and honestly (see Cronmiller's Tips for Success in Genetics), is the only reliable way to gauge your understanding of genetics concepts, that time and effort will be well worthwhile. If you need it, get help early and often! Each week we offer you 10 hours of walk-in, open office hours. No standing in line -- just come in and ask questions, get help on problems, or listen to questions asked by others. EVALUATION & GRADING Your learning will be assessed by: 3 problem-based semester tests (35%) online quizzes related to the pre-class reading (~12%) weekly homework problems (15%) discussion activities (~17%) [see Discussion Information & Policies on Collab] final exam (~18%) You will also receive 20 points (~3% of the course grade) for taking 2 short online assessments of your general knowledge of genetics. These multiple choice assessments are closed book and require no advance preparation. Check the Syllabus (for the Class & Assignment Schedule) and Tests & Quizzes links on Collab for information regarding the timed, limited access and deadlines for these assessments (one at the beginning of the semester and one at the end). Although iclicker responses will not contribute to your course points, you should take this class participation seriously and answer all questions thoughtfully: iclicker scores will be considered for cases of borderline final grades.

4 The final letter grades for the course will be assigned according to a distribution that uses the standard deviation to describe the dispersion, variability and spread of scores around the average score. TESTS All tests are comprehensive. Genetics, like science generally, is cumulative. Be careful not to pigeonhole your learning: On every test you will encounter questions/problems that will require you to combine several concepts to synthesize plausible answers. In these cases, just memorizing isolated concepts and examples will not work. You will need to draw on and integrate concepts you saw in Chapter 4, even as you consider problems that you encounter in Chapter 7. [Concept maps can help you re-examine and relate material continuously throughout the entire course!] Moreover, what you understand by the end of the course matters most. Comprehensive tests not only give you multiple chances to show and get credit for your comprehension, but they also put the emphasis for assigning final grades on the knowledge and abilities that you ve developed by the end of the class, rather than on the average of your accomplishments throughout the semester. If, in spite of sincere and conscientious efforts for the 3 semester tests, you perform better on the comprehensive final exam than collectively on the semester tests, your final exam score (x3) will be used as your total tests + final exam score in the calculation of your final grade. All tests are closed book format, and only nonprogrammable calculators may be used during tests! (Tip: Get the calculator now, and use it for all problem solving, so that you're comfortable with it during the test.) For suspected test grading errors, please CC after the test scores & answer keys have been posted on Collab. MAKE-UP TESTS Alternate test times for semester tests may be requested for varsity athletic or legitimate academic reasons; requests must be made and approved at least 5 days in advance. Otherwise, students who miss any one of the 3 semester tests and have an excusable justification (e.g. death in the family or incapacitating illness with hospital/physician verification), may take a single, comprehensive make-up test (Monday, November 26th, 7-9 PM). Except in case of emergency, approval to take the make-up test must be requested before the test that will be missed. ELECTRONIC DEVICES Cell phones and pagers that ring during class are disruptive; please turn them off and put them away before class begins. If there is an emergency situation that requires that you be reached, set your phone/pager to vibrate/mute; if it rings, leave the class to take the call. Laptops/digital notebooks may be used during class only if they are being used for a class activity, such as taking notes. "Multitasking is mostly wishful thinking." So, please do not IM, tweet/facebook, surf the web, play games or prepare/read/send or text messages during class. Students who violate these rules will be asked to leave the classroom. [FYI: Studies show that laptop abuse during class lowers grades (research citation available upon request). So, it is in your best interest to stay focused during class.] No electronic devices, except nonprogrammable calculators, may be used at any time during tests. ACCOMMODATIONS FOR STUDENTS WITH DISABILITIES If you have a disability and need accommodations, please provide the Learning Needs and Evaluation Center (LNEC) with the appropriate paperwork. It is your responsibility to file

5 this paperwork in a timely fashion and to follow-up with me (Professor Cronmiller) about any accommodations required. If you would like to discuss your need for accommodations with me, please contact me to set up an appointment. The LNEC is located in the Department of Student Health and can be contacted at /5181. HELP FOR STUDENTS IN DISTRESS A recent American College Health Survey found that stress, sleep problems, anxiety, depression, interpersonal concerns, death of a significant other, and alcohol use rank among the top ten health impediments to academic performance. Students experiencing personal problems or situational crises during the semester are encouraged to contact Counseling and Psychological Services (CAPS) at Student Health ( ; for assistance, support and advocacy. RECORDING & COPYRIGHT POLICIES University Policy prohibits or limits the recording of classroom lectures, as well as the redistribution of course materials. In this course, recording of lectures/presentations is allowed for personal use only. Students may not post such recording (or any provided course materials) to any internet site. Furthermore, according to the Technology Harmonization and Education Act of 2002, I am required to provide this legal notice that online materials provided for your use in this course could be copyright-protected. Fair Use laws permit me to provide this material for your personal use, but we are all prohibited from unlimited copying and distribution of it. HONOR STATEMENT We trust that every student will comply fully with all provisions of the UVA honor system. We also assume that any student, who observes an incidence of cheating, will contact an Honor Advisor. Any student who is caught (by the instructor/ta) cheating or committing academic fraud will receive a "0" (zero) on the assignment/test, irrespective of any subsequent action taken by the Honor Committee. For all assignments, please pay attention to explicit instructions regarding what resources you may (or may not) use for their completion and whether you may (or may not) collaborate with classmates.

6 CLASS/ASSIGNMENT SCHEDULE (under construction) Class # Date Topics Class Preparation Assignments Assessment Activities Unless otherwise indicated, reading assignments must be completed before the class for which they are listed. (They also need to be completed before the associated Mastering Genetics quiz.) Unless otherwise noted, pre- class quizzes must be completed before 10:00 AM on the day of the class for which they are listed. Weekly homework assignments (HW) must be completed by 5:00 PM on the indicated due date. #1: Genetics is all around us. W Aug. 29 Welcome! The big picture Course learning goals Course format & tools Introductions There are no assignments due before the first class. The following tutorial should be completed before taking Quiz #2. Quiz #1: Beginning Assessment Test (under Tests & Quizzes on Collab) (must be completed before 5:00 PM on Sunday, 9/2/12!) Assignment (MG): Introduction to Mastering Genetics #2: Historical & molecular foundations of modern genetics F Aug. 31 The big picture Chapter 1 Quiz #2: Mastering Genetics Gene- trait connection Course Syllabus Graphic Syllabus #3: What genes are. [DNA structure & replication] M Sept.3 DNA chemistry Chapter 7, pp Quiz #3: Mastering Genetics DNA replication MG: Ch.7 Tutorial #1 HW #1 available (MG): due 9/9 D#1 Bidirectional Replication (animation) DNA Replication "Trombone" (animation) #4: What genes are. [DNA replication, telomeres] W Sept. 5 DNA replication cont d Chapter 7, pp Quiz #4: Mastering Genetics DNA proofreading MG: Ch.7 Tutorial #2 End- of- replication problem Telomeres "A structure for deoxyribose nucleic acid" (Watson & Crick, 1953) Telomere Replication (animation) #5: Molecular analysis of genes. [PCR, Electrophoresis, Sequencing] F Sept. 7 PCR Molecular markers Chapter 7, pp MG: Ch.7 Tutorial #3 Quiz #5: Mastering Genetics

7 PCR amplification (animation) #6: How genes function. [RNAs, Transcription] M Sept. 10 D#2 RNA chemistry Transcription Chapter 8: MG: Ch.8 Tutorial #1 Transcription (animation) Quiz #6: Mastering Genetics HW #2 available (MG): due 9/16 #7: How genes function. [Transcription, RNA processing] W Sept. 12 Transcription, cont'd RNA processing Chapter 8: 8.4 MG: Ch.8 Tutorial #2 Quiz #7: Mastering Genetics RNA Splicing (animation) #8: How genes function. [Protein structure, Translation] F Sept. 14 Proteins The "components" of translation Chapter 9: MG: Ch.9 Tutorial trna (animation) Quiz #8: Mastering Genetics Translation I (animation) Translation II (animation) #9: How genes function. [Ribosomes, trna, Genetic Code] M Sept. 17 D#3 trna, genetic code, wobble Nonsense suppression Chapter 9: Quiz #9: Mastering Genetics HW #3 available (MG): due 9/23 #10: Integrating Gene Structure & Function W Sept. 19 Sickle Cell Disease Chapter 10: complete MG: Ch.10 Tutorial Molecular Visualization: Sickle Cell Hemoglobin Tutorial (molecular models) Quiz #10: Mastering Genetics #11: Integrating Gene Structure & Function F Sept. 21 Application of material Chapter 10: complete Quiz #11: Mastering Genetics #12: Semester Test #1 (7:00-9:00 PM) M Sept. 24 D#4 Chapter 1, 7-10 Quiz #12: Mastering Genetics (random selection from everything so far) HW #4 available (MG): due 9/30 #13: Where Transmission Genetics begins: Meiosis! W Sept. 26 Chromosomes Meiosis Chapter 11: MG: Ch.11 Tutorial Quiz #13: Mastering Genetics Nondisjunction Chapter 3: MG: Ch.3 Tutorial #1 Mitosis (animation) Mitosis (animation) Meiosis (animation) Meiosis (animation)

8 #14: How genes behave. [Mendel monohybrid - segregation, di/trihybrid - independent assortment] F Sept. 28 Mendelian patterns of inheritance Chapter 2: MG: Ch.2 Tutorial #1 Quiz #14: Mastering Genetics Independent Assortment (animation) #15: How genes behave. [sex linkage, pedigrees] D#5 M Oct. 1 Pedigrees X- Y chromosomes Sex linkage Chapter 2: 2.6 Chapter 3: MG: Ch.3 Tutorial #2 Quiz #15: Mastering Genetics HW #5 available (MG): due 10/7 MG: Ch.2 Tutorial #2 #16: [Probability, Chi square] W Oct. 3 Probability Chi square analysis Chapter 2: MG: Ch.2 Tutorial #3 Quiz #16: Mastering Genetics #17: How genes function. [Gene interactions, morphs] F Oct. 5 Gain/Loss- of- function mutations "Muller's morphs" Chapter 4: 4.1 MG: Ch.4 Tutorial #1 Quiz #17: Mastering Genetics M Oct. 8 Fall Break HW #6 available (MG): due 10/14 #18: How genes function. [Gene interactions, dominance, penetrance, variable expressivity] W Oct. 10 Dominance relationships Variable phenotypes Chapter 4: 4.2 MG: Ch.4 Tutorial #2 (end- of- chapter problems for whole chapter Quiz #18: Mastering Genetics #19: How genes function. [Gene interactions, epistasis] F Oct. 12 Intergenic interactions Modified Mendelian ratios Chapter 4: 4.3 MG: Ch.4 Tutorial #3 Quiz #19: Mastering Genetics #20: How genes function. [Gene interactions, complementation] M Oct. 15 D#6 Complementation Chapter 4: 4.4 MG: Ch.4 Tutorial #4 Quiz #20: Mastering Genetics HW #7 available (MG): due 10/21 #21: How genes function. W Oct. 17 (Catch- up) Polygenic inheritance Chapter 4 Chapter 21: pp Quiz #21: Mastering Genetics (cumulative review of all reading so far) #22: How genes behave. [Linkage & recombination] F Oct. 19 Genetic recombination Linkage Genetic maps Chapter 5: MG: Ch.5 Tutorial #1 (activities for the whole chapter) Quiz #22: Mastering Genetics

9 # 23: Semester Test #2 M Oct. 22 D#7 Chapters 1-4, & Chapter 21 (pp ) Quiz #23: Mastering Genetics HW #8 available (MG): due 10/28 #24: How genes behave. [Linkage & recombination] W Oct. 24 Mapping Chapter 5: Quiz #24: Mastering Genetics Mitotic recombination #25: How genes behave. [Linkage & recombination] F Oct. 26 Mapping function Mitotic recombination Chapter 5: , 5.8 (omit: LOD Score Analysis, 5.6 & 5.7) Quiz #25: Mastering Genetics MG: Ch.5 Tutorial #2 (end- of- chapter problems for the whole chapter) #26: University classes cancelled (Hurricane Sandy) M Oct. 29 D#8 (Chapter 12: ) Quiz #26: Mastering Genetics HW #9 available (MG): due 11/4 #27: When things go wrong. [Mutations] W Oct. 31 Mutations Chapter 12: MG: Ch.12 Tutorial #1 Quiz #27: Mastering Genetics #28: Why don't things go wrong more often? [Mutagens, carcinogens] F Nov. 2 Chemical mutagens Chapter 12: 12.4 MG: Ch.12 Tutorial #2 Quiz #28: Mastering Genetics #29: Why don't things go wrong more often? [DNA repair] M Nov. 5 D#8 DNA repair Chapter 12: (omit 12.7 & 12.8) MG: Ch.12 Tutorial #3 MG: Ch.12 Tutorial #4 (end- of- chapter problems for the whole chapter) #30: The whole equals more than the sum. [Genic Balance, number] Quiz #29: Mastering Genetics HW #10 available (MG): due 11/11 W Nov. 7 Euploidy/Aneuploidy Chapter 13: Quiz #30: Mastering Genetics Chromosome number Chapter 3: 3.6 MG: Ch.13 Tutorial #1 #31: Chromosomal changes [dosage] F Nov. 9 Dosage compensation Chapter 13: 13.3 MG: Ch.13 Tutorial #2 Quiz #31: Mastering Genetics

10 #32: Semester Test #3 (7:00-9:00 PM) M Nov. 12 D#9 #33: Chromosomal changes [structure] W Nov. 14 Deletions Duplications #34: Chromosomal changes [structure] F Nov. 16 Inversions Translocations Chapters 1-12 Chapter 13: 13.3 MG: Ch.13 Tutorial #3 Chapter 13: 13.4 MG: Ch.13 Tutorial #4 #35: Chromosomal changes [structure, transposable elements] M Nov. 19 Transposition Chapter 13: MG: Ch.13 Tutorial #5 (end- of- chapter problems for the whole chapter) Nov. 21 Nov. 23 #36: Prokaryotic Gene Regulation [operon] M Nov. 26 D#10 Gene regulation defined The Operon in general Thanksgiving Break Thanksgiving Break Chapter 14: Lac Operon (Animation) Quiz #32: Mastering Genetics ( problematic questions from Chapters 5 & 12) HW #11 available (MG): due 11/18 Quiz #33: Mastering Genetics Quiz #34: Mastering Genetics Quiz #35: Mastering Genetics Quiz #36: Mastering Genetics HW #12 available (MG): due 12/2 #37: Prokaryotic Gene Regulation [mutational dissection] W Nov. 28 lac operon mutants Chapter 14: (up to Arabinose operon) #38: Prokaryotic Gene Regulation [catabolite repression] F Nov. 30 lac operon positive control ara, trp operons Chapter 14: 14.2, 14.3 (plus pp : feedback inhibition) Chapter 14: omit rest of MG: Ch.14 Tutorial #1 MG: Ch.14 Tutorial #2 (end- of- chapter problems for whole chapter) Quiz #37: Mastering Genetics Quiz #38: Mastering Genetics

11 #39: Eukaryotic Gene Regulation [cis & trans acting] D#11 M Dec. 3 Transcriptional regulation Chromatin Chapter 15: MG: Ch.15 Tutorial #1 (includes end- of- chapter problems) Quiz #39: Mastering Genetics HW #13 available (MG): due 12/9 #40: Eukaryotic Gene Regulation [DNA modification] W Dec. 5 Genomic imprinting Chapter 15: 15.3 Quiz #40: Mastering Genetics #41: F Dec. 7 Quiz #41: NOTE!! This final quiz is NOT on MG, but is under Tests & Quizzes on Collab. Ending Assessment Test (under Tests & Quizzes on Collab) (must be completed before 5:00 PM on Sunday, 12/16/12!) Dec. 17 9:00 AM - 12:00 noon Time to tie it all together! Final Exam