Biol 14A: Genetics and Genomics Spring 2014

Updated: April 14, 2014

Instructor: Dr. Rachel Woodruff [email protected]

TAs: Wei Du, Jackie McDermott, Anna Kazatskaya, David Waterman, Adam Kaplan

Class Meeting Time: Mondays, Wednesdays and Thursdays 9:00-9:50 a.m. Gzang 123

Office hours: are open to everyone! See LATTE for full and up-to-date list!

Recitation Sections: Mon, Tues, Wed, Thurs evenings in Bassine 251. 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 be able to:

 Explain the molecular mechanisms behind inheritance and phenotypic differences

 Interpret common types of biological data, such as pedigrees, gels, and microarrays

 Articulate biological questions and hypotheses

Course Format: The entire class will meet for three 50-minute lectures each week. 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. It is wise to set aside 6-10 hours each week for this work outside of class time.

Recitation Sections: The purpose of recitation sections is to give you opportunities to talk and ask questions about biology, and to work through biological problems with your peers and TAs in a smaller group setting.

Recitations will begin the week of September 9. You need to sign up for your recitation section on LATTE during the first week of class. 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. Your recitation section will meet 9 times over the course of the semester, and there will be quizzes given in most but not all recitation meetings.

Schedule: Recitation sections will meet weekly on Mondays, Tuesdays, Wednesdays and Thursdays (5:30, 6:30 and 7:30pm). They will not meet every week, so watch LATTE for updates on the schedule.

1 Updated: April 14, 2014

Office Hours: Dr. Woodruff and every TA will hold weekly office hours. Please come and visit 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.

Readings will be indicated for each topic. 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 of the course schedule. You will also receive emails through the LATTE course forum (if this is a problem, please let us know).

Homework: All homework will be available on LATTE and/or by email.

Practice problems are a very important part of this course. We will provide you with practice problems throughout the semester. Some will be simplified exercises; others will be more realistic genetics problems. These practice problems are very important tools for learning and practicing, as well as for keeping track of your own progress in the course. And they can be fun! It is up to you to spend as much time on them as you need to in order to learn the material.

There are also graded homework assignments. These will be brief responses to what you are already doing in lecture, readings, and practice problems. They come in two types: 1) Weekend Responses will be simple forms, emailed to you, with a few questions for you to fill out between Thursday evening and 5pm Sunday evening. You can expect one of these to be due almost every week of the semester. 2) Class-based assignments will be given on an irregular. These will be short questions based directly on the activities and discussions we have in lecture, and in each case, will be due on the day they are assigned. Both types of homework assignments will be graded for effort (2 points for full credit, 1 point for partial effort, and 0 points if you fail to return your work on time). We cannot accept late homework, but we will drop your 2 lowest homework grades.

Quizzes: Quizzes will be given during the recitations, and will often involve a component of group work. These will help you practice and keep up with the material, and will help both you and us to assess your learning needs. Quizzes will usually be graded for correctness, but sometimes certain sections are graded for effort. Your lowest quiz grade will be dropped. You can only be graded for quizzes you take in the recitation section you are registered for. There will be exactly one make-up quiz, which you can take during the last week of class if you miss one of your regular quizzes.

Exams: There will be three cumulative hour-long midterm exams and a final exam. The lowest midterm exam grade will be dropped. Mid-term exams will be given on: Feb 5, March 13, and April 7. 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

2 Updated: April 14, 2014 dropped as your lowest score). 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 can be disruptive. Their use will be restricted during class. If you want to use your computer in class, you should sit in either the front row or the back row of the classroom, so as to minimize distraction of your peers.

Academic Integrity: 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 http://www.brandeis.edu/studentlife/sdc/ai ). 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.

Course Schedule: The specific order and content of lectures and readings may be subject to change.

Date Daily Topic Readings

Jan 13 Introduction to genetics, genomics and molecular biology Case 3, pages C3-2 to C3-4

Jan 15 Biological Molecules Chapter 1: 1.1 - 1.4 Chapter 2: 2.1 - 2.5 Jan 16 DNA, RNA and the “central dogma” of molecular biology Chapter 3: 3.1 – 3.3

Jan 20 No Class Quiz1 this week. Jan 22 Snow Day: No Class Jan 23 Transcription, RNA processing and Translation Chapter 3: 3.4 Korf pp12-13

Jan 27 Translation Chapter 4: 4.1 - 4.3 Quiz2 this week. Jan 29 Cellular reproduction, mitosis, meiosis and nondisjunction Chapter 42: p42-1 to 42-4 Chapter 11: p11-1 to 11-5 Chapter 19: pp19-8 to 19-9 Jan 30 Chromosomal abnormalities; and DNA replication Chapter 15: 15.4 (last new material covered on Exam 1) Chapter 12: 12.1 and 12.2 Feb 3 DNA repair and mutagenesis Chapter 14: 14.4 No recitations except Mon Feb 5 SNOW DAY

Feb 6 Exam 1 rescheduled Feb 10 Basic Biological Inheritance Chapter 16: 16.1, 16.2, 16.3, 16.5 All recitations meet this week. Feb 12 Pedigree analysis and sex chromosomes (Chapter 16: 16.5) Chapter 17: 17.1, 17.2, and 17.4 Pierce pp139-143 Feb 13 Probabilities of inheritance and Experimental Crosses Chapter 16: 16.4 (and 16.2, 16.3) Feb 17-21 February Vacation Week

Feb 24 Experimental crosses and (Chapter 16: 16.5) Interpreting complex patterns of inheritance

Feb 26 Epistasis, Complementation, and statistical analysis Pierce pp61-63 and p113 Feb 27 Genetic linkage and Recombination Chapter 17: 17.3 Mar 3 Genetic Linkage and Genetic Maps Korf pp 67-73 and 178-180 Mar 5 Cytoplasmic Inheritance; Begin Mutations Chapter 17: 17.5 Pierce 115-25

Mar 6 Genetic variation 1: Types of Mutations, and their effects Chapter 14 (all) (last new material on Exam 2) Mar 10 Introduction to DNA techniques Chapter 12: 12.3

Mar 12 PCR and Genetic Variation II: Population Chapter 15: 15.1 – 15.2 Mar 13 Exam 2: Cumulative Mar 17 Genetic Variation III: Polymorphisms; (Chapter 12: 12.3) DNA sequencing Sections 13.1 and 15.3 Korf p 84 on NGS

Mar 19 Class canceled due to illness Mar 20 RFLPs, Physical maps, and Genome sequencing Chapter 13: 13.2 - 13.4

Mar 24 Genome comparison, Repetitive sequences, Viruses and Transposons: Viral genomes Pierce p302, pp312-316, and optionally pp303-306

Chapter 13: Section 13.5

Mar 26 Complex Traits and Genome-Wide Association Studies Chapter 18 and Section 15.3

Mar 27 Cancer genetics and personalized medicine Case 2 Chapter 11: 11.4 Mar 31 Cancer mutations Chapter 11: 11.5 (last new material covered on exam 3) April 2 Gene Cloning Chapter 12: 12.4 Pierce pp519-523 Pierce pp541-542 April 3 Regulation of Gene Expression I Chapter 19: 19.1, 19.2 Pierce 463-65 April 7 Exam 3: Cumulative No recitations this week April 9 Regulation of Gene Expression II Chapter 19: 19.3 April 10 Regulation of Gene Expression III No new readings April 14 Cellular Differentiation and Development Chapter 20: 20.1 – 20.5 Apr 15-22 Spring Break! April 23 Genetics of Development Chapter 20: 20.1 – 20.5 April 24 Microbes, metagenomics, and humanity Case 5 Chapter 26: 26.1 April 28 Transgenic organisms and the study of Longevity Pierce pp542-546 Longevity article (on LATTE) TBA Final Exam: Cumulative. Tentative date: May 7

Grades:

Description Percentage of Final Grade

Midterm Exams (the best 2 of the 3 count toward your final grade) 40%

Final Exam (no substitutions) 30%

Quizzes and Recitation Activities (we do not count the lowest one) 15%

Homework assignments (we do not count the lowest three) 15% - Weekend responses - Occasional class-based assignments