Updated 1-9-17
Biol 14A: Genetics and Genomics Fall 2016
Dr. Rachel Woodruff
with TAs Raul Ramos and Jackie Leonard
Introduction
Think for a moment about inheritance. What did you get from your biological parents? What do you know about your own genome? What makes you biologically different from your cousin, an elephant, or a banana tree?
The fields of genetics, genomics, and molecular biology have been developing rapidly over the last few decades: PCR, gene cloning, anti-retroviral therapy, next-generation DNA sequencing, RNAi, somatic cell nuclear transfer (animal cloning), induction of pluripotent stem cells, CRISPR…to name but a few advances! We can expect these fields to continue to advance, and to affect more and more aspects of our lives. How will doctors use their patient’s genomic information in a few years? What discoveries will alter our fundamental understanding of molecular biology? How will genetic engineering be adapted to cope with global warming?
Thesuper-goal of this course is for you to be able to understand and interpret such new developments and applications, as they affect your own life and career, throughout your life.
The Learning Goals for this course encompass the skills and knowledge that will enable you to interpret past, present, and future findings in genetics. These are the large goals we will work toward all semester:
-You should have a conceptual understanding of the molecular mechanisms that result in phenotypes and biological inheritance. If you have a strong framework of understanding what the key components and processes are, you will be able to use this to interpret new information.
-You should understand many of the common tools and approaches currently used by researchers in genetics, genomics and molecular biology. If you understand how these approaches work, and how they are interpreted, you will be ableto understand how they have been used to reach new conclusions, and you will also be better equipped to figure out experimental approaches that are unknown to you.
-You should know strategies and information sources you can use to make sense of new observations relating to molecular biology or genetics.
When you have met these goals, you will be ready to begin being an informed reader of primary research articles in the field. You will be able to question and discuss experimental results and interpretations. Some of you will go on to use these skills and concepts to become researchers, creating the future of the field; and all of you, I hope, will use them to be better-informed voters and advocates for yourself, your families and your communities.
Course structure
Like any 4-credit course, this should take you about 12 hours per week, including class time (4 hours, in this case) and out-of-class time. Success in this 4 credit hour course is based on the expectation that students will spend a minimum of 9 hours of study time per week in preparation for class (readings, papers, discussion sections, preparation for exams, etc.).
Homeworkshould take about eight hours per week, and includes:
- Readings from the textbookBiology: How Life Works (either edition 1 or 2 is OK), and from other sources (posted on LATTE)
- Self-Tests. These are small quizzes you can take on LATTE to test your understanding as you prepare for class. You may want to do these while you do the readings, or use them for review after reading.
- Practice Problems are typically challenging problems which give you practice in applying course concepts. These will be posted on LATTE. You will generally not hand in your answers, but working through these is an extremely part of your work for the class. If you can successfully do these problems, you are meeting most of the learning goals of the course. I recommend that you work through these as well as you can on your own, and then talk with a study group about them (similarly to how we do the Miniquizzes in Recitation, but more time-consuming).
- Weekly Responses. Reflecting on what you are learning and how you are learning can be very helpful to your learning. We ask you to reflect and answer a few questions each week. Your responses will also be used to guide our use of in-class review time.
- Special Assignments. Unlike all of the above, these are sporadic assignments which do not fit into the above categories. There will be a few over the course of the semester.
On attendance: You should attend every class. I know that everyone has extenuating circumstances sometimes, but if circumstances make you miss class more than 3 times during the semester, you may have overextended yourself, and you should consider dropping the class.
Lecturemeetings are not just for traditional listen-and-take-notes lectures. I will frequently pose questions in lecture, for you to answer through an online response tool. These are intended as opportunities for you to apply what we are learning. Once each week, we will also have a portion of lecture explicitly devoted to Review. Exactly what we review will be up to you: part of your Weekly Response homework will be to describe your current confusions and questions about the material, so that your TAs and I can choose the most helpful things to spend more time on.
Recitation sections meet once per week for 50 minutes in Bassine 251. Each section includes ~25 students led by one TA. Both our TAs are graduate students who have research experience in genetics or related fields. You will use this time to practice, through structured, partly-collaborative Miniquizzes, to review, and to ask questions. It is important that you attend the recitation section you are registered for. You registered for one of these on SAGE when you signed up for the class:
Section 1:Mondays, 5:30 – 6:20 pm with Jackie
Section 2:Mondays, 6:30 – 7:20 pm with Jackie
Section 3:Tuesdays, 6:30 – 7:20 pm with Raul
Section 4:Tuesdays, 7:30 – 8:20 pmwith Raul
Resources:
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, grades, and updates to the course schedule.
Office Hours: Please come! Dr. Woodruff and every TA have weekly office hours listed at the top of the course LATTE page. Even though you have one recitation TA, you may attend any one’s office hours. You are also welcome to set up appointments with us outside of office hours if needed.
Textbook: Morris: Biology, How Life Works. either 2nd or 1st Edition. Reading assignments are listed on the syllabus and on the course LATTE site. It is expensive, but you can use it for BIOL15 and BIOL16 as well! 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, recitation activities, and lectures as the defining resources in your studying.
Online Learning Platform: We will be using a response system for some online assignments and to facilitate active learning and group activities in lecture. You use it from your own device (smartphone, computer, etc). In order to use it, you do have to buy a subscription: details on that to be announced on or before the first day of class. If for any reason you do not plan to subscribe, you must communicate this to me (Dr. Woodruff) so we can make sure you are properly accommodated.
Quizzes and Exams:
Instead of midterm exams, we will haveseveralshorter Quizzes, given in lecture (see dates in schedule below). Quiz dates are given in the course schedule below. There are no make-up quizzes. Your one lowest quiz grade will be dropped.
There will also be one cumulative Final Exam. Students with excused absences from the final exam will be able to take a make-up final exam next semester.
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 laptops should only be used in class when they are part of a classroom activity. Use common sense, and don’t waste your class time or distract your classmates by 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 will only hurt your own learning. 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.
Preliminary Course Schedule: The specific order and content of lectures and readings is subject to change. However, Quiz dates are set! Note: assigned readings should be done before the day of class they are listed with.
Date / Daily Topic / Readings etc to do beforethis meeting
Jan 18 / 1 Introduction / Chapter 1
Jan 19 / 2 Molecular structures and nucleic acids / Chapter 2
Chapter 3: 3.1 and 3.2
Jan 23 / 3 Transcription and RNA processing / Chapter 3: 3.3 and 3.4
and see animation on LATTE
Jan 23/24 / Recitation meeting #1
Jan 25 / 4 Proteins and Translation / Chapter 4
Jan 26 / 5 Proteins and Translation continues / Posted on LATTE
Jan 30 / 6 Cell division processes / Chapter 11
Jan 30/Feb1 / Recitation meeting #2
Feb 1 / 7 DNA replication / Chapter 12: 12.1, 12.2
and see animation on LATTE
Feb 2 / 8 Quiz 1(on material through Jan 30)
Feb 6 / 9 DNA methods overview / Chapter 12: 12.3, 12.4
Feb 6/7 / Recitation meeting #3
Feb 8 / 10 DNA Methods Advanced / Posted on LATTE
Feb 9 / 11 Genome Sequencing and Physical Mapping / Chapter 13: 13.1-13.3
Feb 13 / 12 Genomes, genome Structure, and Viral genomes / Chapter 13: 13.4 - 13.5
Feb 13/14 / Recitation meeting #4
Feb 15 / 13 Viruses and Viral life-cycles / Article posted on LATTE
Feb 16 / 14 Quiz 2 (on material through Feb 13)
Feb 20-24 / No Classes
Feb 27 / 15 Mutation and DNA Repair / Chapter 14
Feb 27/28 / Recitation meeting #5
March 1 / 16 Mutagenesis and Cancer / Posted on LATTE
March 2 / 17 Genetic Variation / Chapter 15
March 6 / 18Mendelian Inheritance: introduction and segregation / Chapter 16, 16.1-16.3
March 6/7 / Recitation meeting #6
March 8 / 19Mendelian Inheritance: introduction and segregation / Chapter 16, 16.1-16.3
March 9 / 20 Quiz 3 (on material through March 6)
March 13 / 21 Mendelian Inheritance: Independent assortment / Chapter 16, 16.4 & 16.5
Mar 13/14 / Recitation meeting #7
Mar 15 / 22 Sex linkage and mitochondrial inheritance / Chapter 17
Mar 16 / 23 Analyzing pedigrees and calculating probabilities / Posted on LATTE
Mar 20 / 24 Genetic Linkage and Recombination / Chapter 17: revisit 17.3
Mar 20/21 / Recitation meeting #8
Mar 22 / 25 Genetic Mapping / Posted on LATTE
Mar 23 / 26 Quiz 4 (on material through March 20)
Mar 27 / 27 Genetic complementation and Interactions between genes; Genetic pathways and epistasis / Posted on LATTE
Mar 27/28 / Recitation meeting #9
March 29 / 28 Using chi-square test to test genetic hypotheses / Posted on LATTE
Mar 30 / 29 Model organisms, Transgenics, and Gene Editing (CRISPR) / Posted on LATTE:
April 3 / 30 Complex Traits / Chapter 18
April 3/4 / Recitation meeting #10
April 5 / 31Genetic and epigenetic regulation in eukaryotes / Chapter 19: 19.1, 19.2
April 6 / 32 Quiz 5 (on material through April 3)
April 10-18 / No Classes
April 19 / 33 Genetic and epigenetic regulation in prokaryotes / Chapter 19: 19.3, 19.4
April 20 / 34 Advanced topics in genetic regulation / Posted on LATTE
April 24 / 35 Genome-wide Association Studies and complex traits / Posted on LATTE
April 24/25 / Recitation meeting #11 / Research articleposted on LATTE
April 26 / 36 Review, catch up, or current research topic / Posted on LATTE
April 27 / 37 Genes and Development I / Chapter 20: 20.1-20.3
May 1 / 38 Genes and Development II / Chapter 20: 20.4-20.5
May 1/3 / Recitation meeting #12
May 3 / 39 Gene Therapy and Precision Medicine / Posted on LATTE
Tentatively
May 10
1:30-4:30pm / Final Exam: Cumulative, 3-hour exam
Grading: Your grades are not determined by competitive comparison with your classmates’ grades. Number grades on Quizzes and Exams are scaled to reflect the difficulty of the specific assignment, but they are scaled relative to our expectations of what a student in each grade level (A,B,C) ought to be able to do, not relative to the average grade for of your class group.
Description / Percentage of Final GradeQuizzes
(your lowest 1 score is dropped: remaining quizzes each contribute equally) / 45%
Final Exam
(no substitutions) / 30%
Graded Homework: You are expected to do at least 18of the ~25 small assignments:
-Weekly Responses
-Self Tests
-Special Assignments / 10 %
In-class work:
Lecture participation: in-class questions and activities during lecture
Miniquizzesand other Recitation activities (lowest 1 score is dropped) / 15%
About the professor, Rachel Woodruff: I grew up in Texas, and got my PhD at MIT. When I was in college, I almost majored in Chemistry and History before choosing “Molecular Biophysics and Biochemistry” halfway through my Junior year. Ironically, I never took genetics as an undergrad! Now, I have been teaching at Brandeis for 4½ years, and have taught genetics here 7 times (not including this semester). I love teaching here. Every semester, I learn more from my students. In addition to teaching, I like to play with my 2 young daughters, ride my bikes (only one at a time), and drink an excessive amount of tea. I hope you will come to my office hours and help me put a face, and a story, to your name this semester.