Biol 14A: Genetics and Genomics Fall 2014 Instructors: Dr. Rachel Woodruff
____Danielle DiTirro, Nicholas Clark, Josiah Herzog, Thomas Rands, Shawn Fayer ____
Class Meeting Time: Mondays, Wednesdays and Thursdays 9:00-9:50 a.m.
Room: Gerstenzang 123
Office hours: Updated schedule available at top of course LATTE page.
Recitation Sections: Mon and Wed evenings. Sign up on LATTE.
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, as well as an introduction to the tools and techniques used by past and current researchers in genetics and genomics.
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 all meet for lecture in three 50-minute lectures each week. You are expected to attend and participate in lecture. In addition, you will be joining a recitation section in which you and your classmates will work through problems and discuss biology in a smaller group setting, under the guidance of your TA. You will get the most out of this class if you come to both lectures and recitations prepared to actively engage in thinking, questioning, and problem solving. Please be aware that your reading, problem-solving, and studying outside of class are also essential to your learning. Individual needs vary, but to start with you should plan on spending at least 6-10 hours each week working on this class outside of the class meetings.
Recitation Sections: In 9weeks of this semester, students will meet in groups of 30 with a graduate student TA to work in smaller groups on problem-solving strategies and difficult concepts, and to discuss readings. A primary goal of these meetings is to give you opportunities to talkwith each other about the biology we are studying, and to critically evaluate your ideas. You will be graded for participation and effort in section meetings. Don’t be afraid to be wrong sometimes in discussions: being wrong sometimes is part of science, and part of learning.
Recitation section meetings will begin the week of September 8. You need to sign up for your recitation section on LATTE on or before Thursday, September 4. Students who do not sign themselves up by the deadline will be assigned to a section. You should attend only the recitation section you are registered for.
Locations: Recitation sections 1,2,5,6,7,10,11 are in Bassine 208; Recitation sections 3,4,8,9 are in Bassine 251.
Office Hours: Dr. Woodruff and every TA will hold weekly office hours. Please come and visitany of us during office hours to ask questions about the course, work through practice problems, or just get to know your instructors better. Times and locations will be announced on LATTE, as will any changes to office hour logistics.
Textbook: Morris: Biology, How Life Works. 1st Edition.
Reading assignments are listed on the syllabus and on the course LATTE site. The textbook will be a very useful reference for you; 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.
Course website: Essential resources are posted for you on LATTE. Check the course website on LATTE frequently for course announcements, lecture notes, assignments, practice problems, and answer keys, as well as updates to the course schedule.
Homework: Readings are intended to prepare you for class, so you should complete each reading assignment before the class meeting with which it is associated. Practice problems, which will be posted on LATTE in 15 problem sets over the course of the semester, will help you with application and deeper understanding of the concepts. You should do your best to work all the practice problems. I recommend spending some time on these every day, rather than trying to do them all at once. These practice problems are very important tools for learning and for keeping track of your own progress in the course. And they can be fun! It is strongly recommended that you do all of them, even though not all are handed in and graded.
Graded Homework: Each time you have a recitation section meeting, the latest problem set will be taken up and graded. Problem sets are due to your TA when your recitation section meets. Late problem sets cannot be accepted.
You will also have occasional written homework in response to specific readings. These assignments will be announced on LATTE and in lecture.
Exams: There will be three cumulative hour-long midterm exams and a final exam. The lowest midterm exam grade will be dropped. Mid-term 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). Students with excused absences from the final exam will be able to take a make-up final exam next semester. Chem11a students: Note that our Exam 3 is scheduled only a few days after a Chemistry exam. Please plan your time accordingly so that you don’t freak out that week!
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 during the first week of class.
Cell phones and laptopsshould be used with discretion. Use common sense, and don’t waste your class time trying to multitask. 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.
AcademicIntegrity: For goodness’ sake do not cheat! It can only harm your education. You are expected to be familiar with and to follow the University’s policies on academic integrity (see ). Faculty may refer any suspected instances of alleged dishonesty to the Office of Student Development and Conduct. Instances of academic dishonesty may result in sanctions including but not limited to failing grades being issued.
Grades:
Description / Percentage of Final GradeMidterm Exams (lowest 1 of 3 is dropped) / 45% (22.5% each)
Final Exam (no substitutions) / 30%
Participation (in recitations and lecture) / 14%
Homework assignments (late problem sets cannot be accepted) / 11%
A note on grades and what they mean: 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.
Course Schedule: The specific order and content of lectures and readings is subject to change.
Grand Topic / Date / Daily Topic / ReadingsGenetics / Aug 28 / Introduction / Case 3, pages C3-2 to C3-4
Chapter 1: 1.1 - 1.4
Chapter 2: 2.1 - 2.5
Sept 1 / No Class: Labor Day
Sept 3 / Cellular reproduction: Mitosis and Meiosis / Chapter 42: pages 42-1 to 42-4
Chapter 11: sections 11.1 through 11.3
Sept 4 / Basic biological inheritance / Chapter 16, all
Sept 8 / Pedigree analysis and sex chromosomes / Chapter 17: 17.1, 17.2, 17.4
Pierce pp139-43
Reminder: practice problems are due in every recitation meeting, starting today!
Sept 10 / Probabilities of inheritance and Experimental Crosses / Review Chapter 16
Pierce pp61-63
Sept 11 / Experimental crosses, model organisms, and statistical analysis / Review Chapter 16
Review Pierce pp 61-63
Model organism blog
Sept 15 / Interpreting complex patterns of inheritance and gene interactions / Pierce p99-117
Sept 17 / Genetic Linkage and Recombination / Chapter 17: 17.3
Sept 18 / Genetic Linkage and Recombination, part II
Last new material on Exam 1 / Pierce pp174-183
Sept 22 / Genetic Mapping,
Cytoplasmic inheritance / Chapter 17: 17.5
Molecular Biology I / Sept 23 Brandeis Thursday / Cytoplasmic Inheritance and Biological Molecules / No new readings
Sept 24 / Exam 1
Sept 25 / No Class
Sept 29 / DNA, Genes, and RNA / Review Chapter 2
Chapter 3: 3.1 and 3.2
Oct 1 / Gene structures, Transcription and RNA processing / Chapter 3: 3.3, 3.4
Oct 2 / Proteins and Translation / Chapter 4: 4.1-4.3
Oct 6 / Translation and DNA replication / Chapter 12: 12.1 & 12.2
Oct 8 / DNA Replication and Mutation / Chapter 14
Oct 9 / No Class
Molecular Biology II: Analysis and Manipulation / Oct 13
Brandeis Thursday / Mutations, DNA repair, and Genetic Variation (types) / Review Chapter 14
Chapter 15: 15.1 and 15.4
Oct 15 / Genetic Variation: Effects / Chater 15: 15.2, 15.4
Chapter 12: 12.3
Oct 16 / No Class
Oct 20 / Basic DNA Techniques: gels, hybridizations, PCR
Last new material on exam 2 / Chapter 12, section 12.3
Oct 22 / Application of DNA techniques to study genetic variation
DNA sequencing: techniques and applications / Review 12.3, 15.3
Chapter 13: 13.1
Oct 23 / Physical maps: Sequencing and Restriction mapping / Chapter 12: 12.4
Oct 27 / Exam 2: Cumulative
Oct 29 / Gene Cloning and Transgenic Organisms / Peirce pp519-23 and pp541-46
Gene Expression and Regulation / Oct 30 / Gene Expression and Cellular Differentiation / Blog: 2 posts on fruitfly research, plus written response assignment
Chapter 19: 19.1, 19.2
Pierce pp459-65
Nov 3 / Regulation of gene expression, I
Reminder: Register for Biol15 for next semester! / Chapter 19: 19.3
Recommended Reading-ahead: Chapter 20!
Nov 5 / Regulation of gene expression, II / Pierce pp442-45
Research paper (on LATTE): Gautam 1996
Optional reading: Strachan pp157-175
Nov 6 / Cellular Differentiation and Development / Chapter 20: 20.1-20.2
Nov 10 / Genetics of Development / Chapter 20: 20.3 - 20.5
Nov 12 / Genetics in Neurobiology
Guest Lecturer: Professor Paradis / Review Gautam article
Genomes and Genomics / Nov 13 / Genome sequencing and assembly;
And Genetic Variation Workshop / Chapter 13: 13.1, 13.2
Chapter 15
Nov 17 / Finish Genetic variation (within species);
Genome comparison and composition / Chapter 13: 13.3, 13.4
Nov 19 / Viruses and Viral genomes / Chapter 13: 13.5
Nov 20 / Gene Therapy
Nov 24 / Exam 3: Cumulative
Nov 26-
Nov 28 / No Class
Dec 1 / Microbes and Metagenomics / Case 5
Chapter 26: 26.1
Dec 3 / GWA studies and complex traits / Chapter 18, all
Chapter 15: 15.3
Dec 4 / Cancer genomes and personalized medicine / Case 2
Chapter 11: 11.4
Dec 8 / Cancer mutations / Chapter 11: 11.5
TBA / Final Exam: Cumulative.
Tentative date:
1