Biol 14A: Genetics and Genomics Summer Session II: July 6 – August 7, 2015 Instructor: Dr. Inna Nechipurenko ivn@brandeis.edu Class Meeting Time: Mondays, Tuesdays, and Thursdays 11:00 AM – 1:20 PM Room: TBA Office hours: Wednesdays 9:00 AM – 10:00 AM, SSC 2-­‐09 Fridays 9:30 AM – 11:00 AM, SSC 2-­‐09 (see LATTE for any changes/updates) Course Description: This course will introduce you to the fundamentals of genetics, genomics, molecular biology and biological problem solving. Topics include heredity, meiosis, molecular basis of phenotypic variations in individuals and populations, and an introduction to the tools and techniques used in investigations in molecular biology and genetics. Learning Objectives: After completion of this course, students should: •
•
Understand the molecular mechanisms behind inheritance and phenotypic differences Know how to interpret common types of biological data, such as pedigrees, gels, and microarrays Course Format: We meet in three 2-­‐hour and 20-­‐minute lectures each week. You are expected to attend and participate in lecture. Please be aware that your reading, problem solving, and studying outside of lecture are equally essential to your learning and success in this course. Textbook: Morris: Biology, How Life Works. 1st Edition. Course website: I will post lectures, problem sets, take-­‐home quizzes, and solutions to problems, take-­‐
home quizzes, and exams on LATTE – our on-­‐line course website. To access LATTE, go to http://lts.brandeis.edu/courses/newlatte/ and log in using your UNet ID and password. Check the course website frequently for any updates to the course schedule and assignments. Reading assignments: The readings for each lecture are listed on the syllabus and on the course LATTE site. They are intended to prepare you for class, so you should try to complete each reading assignment before the class meeting, with which it is associated. The textbook will be a very useful reference; however, there will not be an exact correlation between topics covered by the textbook and topics covered in class. Use the textbook as a reference, but use the practice problems and lectures as the defining resources in your studying. Problem sets: Practice problems will be posted on LATTE over the course of the summer session. They will not be graded; however, they are meant to help you with application and deeper understanding of the concepts taught in class. Therefore, it is strongly recommended that you do all the practice problems. 1 Graded assignments: Three short (up to three questions each) take-­‐home quizzes will be posted on the course LATTE site. The quizzes will be due on Mondays and will have to be turned in at the beginning of class. This weekly assignment is meant to serve as your personal checklist for understanding the core concepts taught in class that week. Late quizzes will not be accepted. Exams: There will be three one hour-­‐long midterm exams and a cumulative final exam. The lowest midterm exam grade will be dropped. Midterm exam dates are shown in the course schedule below. All midterm exams will be given during the regular class time. There will be NO make-­‐up midterm exams. If you miss a midterm exam for any reason, you will receive a zero on that exam (which can then be dropped as your lowest midterm exam score). Grades: Description Percentage of Final Grade Midterm Exams (lowest 1 of 3 is dropped) 50% (25% each) Cumulative Final Exam (no substitutions) 35% Take-­‐home quizzes (3) (late quizzes cannot be accepted) 15% (5% each) A note on grades: An exam grade higher than B-­‐ generally means you are doing better than we expected the average student to do. A = Exceptional: mastery of most or all of the material B = Good: student demonstrates understanding of much of the course material C = Satisfactory: student demonstrates understanding of some of the course material D = Unsatisfactory: won’t count toward the biology major, but will give you credits toward graduation E = Fail: does not demonstrate progress on learning goals. No credit. Academic Integrity: You are expected to be familiar with and to follow the University’s policies on academic integrity (see http://www.brandeis.edu/studentlife/sdc/ai). Violations of these policies will not be tolerated and may result in sanctions including but not limited to a failing grade in the course. Cell phones and laptops should be used with discretion. If your use of a phone or laptop is perceived as disruptive by anyone in the room, you will be asked to put it away or to leave. Use of cell phones/laptops/iPads will not be permitted during exams under any circumstances. Disabilities: If you are a student with a documented disability on record at Brandeis University and wish to have a reasonable accommodation made for you in this class, please contact me as soon as possible. Course Schedule: The specific order and content of lectures and readings are subject to change. Date Daily Topic Readings July 6 Introduction – course overview Chapter 1: 1.1 – 1.4 Biological molecules Chapter 2: 2.1 – 2.5 Cellular reproduction: Mitosis and Meiosis Chapter 11: 11.1 – 11.3 Chapter 42: 42.1 – 42.4 Mendelian inheritance (part I) July 7 Mendelian inheritance (part II) Chapter 16: 16.1 – 16.5 Probabilities of inheritance and experimental crosses Pedigree analysis and sex chromosomes Chapter 17: 17.1, 17.2, 17.4 Pierce pp139-­‐43 2 July 9 Complex patterns of inheritance (extension of Mendel’s principles) and gene interactions Last new material on Exam 1 Genetic linkage and recombination (part I) Exam 1 Genetic linkage and recombination (part II) Genetic Mapping Cytoplasmic inheritance The central dogma, DNA, and RNA Transcription Proteins and Translation DNA replication Last new material on Exam 2 Mutations and DNA damage repair Exam 2 Genetic variation Basic DNA Techniques Physical maps: Sanger sequencing and restriction mapping Gene cloning and transgenic organisms Last new material on Exam 3 Regulation of gene expression Pierce pp99-­‐117 Chapter 17: 17.3 Pierce pp174-­‐183 Pierce pp174-­‐183 July 27 Exam 3 Stem cells and cellular differentiation Chapter 20: 20.1 and 20.2 July 28 Genes and Development Chapter 20: 20.3 – 20.5 July 30 Genome sequencing and assembly Genome composition Viruses and viral genomes Chapter 13: 13.1 and 13.2 Chapter 13: 13.3 and 13.4 Chapter 13: 13.5 Aug 3 Aug 4 Gene therapy Microbes and metagenomics Genome-­‐wide association studies and complex traits Cancer Aug 6 Final Exam Case 5; Chapter 26: 26.1 Chapter 18 Case 2; Chapter 11: 11.4 and 11.5 July 13 July 14 July 16 July 20 July 21 July 23 3 Chapter 17: 17.5 Review Chapter 2: 2.1 – 2.5 Chapter 3: 3.1 and 3.2 Chapter 3: 3.3 and 3.4 Chapter 4: 4.1 – 4.3 Chapter 12: 12.1 and 12.2 Chapter 14 Chapter 15: 15.1 – 15.3 Chapter 12: 12.3 Pierce pp519-­‐23; pp541-­‐46 Chapter 12: 12.4 Chapter 19: 19.1 – 19.3 Pierce pp459-­‐65