Biol 14A: Genetics and Genomics Fall 2016

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.

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.

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.