Biology 208

Genetics

Spring 2014

Class meeting: MWF 10:25-11:15 in Silfen Auditorium, Bill Hall Laboratory meeting: 313 New London Hall Professors:
Dr. Deborah Eastman Class and lab instructor Office: NLH 421 Phone: x2445 e-mail: daeas Office Hours: M 2-3, T 10-11:30, F 12-1 Or by appointment Dr. Kristine Hardeman Lab instructor Office: Olin 310 Phone: x5479 e-mail: khardema Office Hours: T 9-10, F 9-10 Or by appointment

Course Objectives:
To introduce you to the many exciting areas of genetics. To engage you in the experimental approaches used to study classical, molecular and population genetics. To develop your abilities to design experiments and analyze results. To enhance your critical thinking, writing and presentation skills.

Reading Material: The required textbook for this course is Genetics: Analysis of Genes and
Genomes, 8th edition, by Daniel L. Hartl and Maryellen Ruvolo. Additional readings, laboratory protocol sheets and journal articles will be available on our Moodle site.

Websites, Images and Videos: A Moodle site for the course is available through Course Web
Pages site on the Academics home page. This site will contain information and materials for class and laboratory meetings throughout the semester. A companion website for our textbook can be found at http://biology.jbpub.com/book/genetics/. This site has informative and up-to-date research and references, animated flashcards, an interactive glossary, and crossword puzzles.

Class Participation, Excused Absences and Late Assignment Policies: As a student in

this course, your attendance and contributions are highly valued. In class we will be using the iClicker system as a way to ask questions, solve problems and discuss material. Three clicker points will be available each class. A point will be earned for each correct answer, up to 3 pts/class. Attendance and participation in the laboratory is required. If you will miss any laboratory session for a college scheduled event or because of illness please notify your laboratory instructor prior to the event. Absence without verified notification will cause you to lose 25 points from your total laboratory points. Five points per day will be deducted from class or lab assignments that are turned in late without prior arrangement.

Reading Quizzes: PLEASE READ ASSIGNED PAGES AND VIEW ASSIGNED VIDEOS
BEFORE CLASS!!! In order to encourage you to do the reading/viewing you will be required to take a quiz on Moodle for each class meeting. The quiz will open right after class and will close at 9:00 AM on the next day of class. The quizzes will cover assigned readings/videos that will be discussed on the day the quiz closes. Quizzes are open book and you may work together with classmates. Each reading quiz is worth 2 points.

Weekly Practice Exams: Weekly practice exams will be given on-line through the Workshop
application on our Moodle site. Questions on these exams will be similar to problem solving and essay questions you will find on exams in the course. These questions will require critical thinking, application and synthesis skills- i.e. they will not be memorization-type questions. The practice exams will be closed book and done individually. You will have 30 minutes to complete the exam, which will be open on Moodle on Mon. at 12:00 PM through Tues. at 1:00 PM. These exams will then be anonymously peer-graded, also through Moodle Workshop. You will receive a practice exam from another student in the course and will have 20 minutes to grade the exam using a provided detailed rubric. The peer-review period will be open from Tues. at 1:00 PM until Wed. at 1:00 PM. You will not receive credit for your practice exam if you do not grade a peer exam. Each practice exam is worth 10 points. Make-up practice exams will not be given without a week prior notice or a letter from the dean.

The Connecticut College Honor Code: Academic integrity is of the utmost importance in
maintaining the high standards of scholarship in our community. Academic dishonesty is considered to be a serious offense against the community and represents a significant breach of trust between the professor, the classmates, and the student. There are many forms of academic dishonesty including plagiarism, submitting the same work in two courses without prior approval, unauthorized discussion or distribution of exams or assignments, and offering or receiving unauthorized aid on exams or graded assignments. Students violating the Honor Code may be referred to the college's Honor Council for resolution.

Academic Resource Center: The Academic Resource Center (ARC) offers services to
support your academic work such as study skills workshops, time management, coaching and tutoring. Their offices are located in Main Street West, The Plex. Please visit them or call 860439-5294 for more information or to schedule an appointment.

Writing Center: The Roth Writing Center provides one-to-one peer tutoring (free of charge)
to help student writers of all abilities during all stages of the writing process. To make an appointment, call x2173 or stop by the Writing Center at 214 Blaustein. If you're a confident, experienced writer we can help you to push your ideas and polish your style; if you're a relatively inexperienced and not-so-confident writer we can also help you, by working on grammar or organization or whatever you need. Writing Center tutors are trained to help you to discover what you think through writing. Working with a tutor gives you the opportunity to share your work-in-progress with an actual reader, so that you can get useful feedback on that work before you have to turn it in for a final grade. For further information, visit the Writing Center web page at http://write.conncoll.edu/.

Office of Student Disability: If you have a physical or mental disability, either hidden or

visible, which may require classroom, test-taking, or other reasonable modifications, please see me as soon as possible. If you have not already done so, please be sure to register with the Office of Student Disability Services. You can do so by going to the Office of Student Disability Services which is located in Crozier Williams, Room 221, or by contacting the Office at Campus Extensions 5428 or 5240, or by email to barbara.mcllarky@conncoll.edu or lillian.liebenthal@conncoll.edu.

Tips for Studying in and Making the Most of this Class:

1) Prepare BEFORE Class and Laboratory! a. Spend several hours before class reading and taking notes on the assigned pages. Mark or write down particular vocabulary and/or topics that are confusing to you and make sure to ask about them in class (and/ or visit me and well talk about them!). The reading quizzes will hopefully encourage you to do this. b. Before coming to lab make sure to read the assigned material. You need to have a clear idea of what questions you will be asking and what techniques you will be using. 2) Review Your Notes and Text Soon After Class a. Going over your notes after class will give you a chance to re-digest the material discussed and to make sure youve understood important terms, concepts, techniques and problem solving approaches. b. Get together with your peers and discuss the material. Sometimes thinking about a topic in a different way will help you understand it. c. View any movies or images that have been posted. I also encourage you to search the web for additional sources that may help you understand the concepts we are discussing. If you find something particularly helpful, please share with me and other classmates! 3) Explore the course and textbook websites. Work lots of problems! The more ways you look at and think about the material the more clearly you will understand it! 4) Meet regularly with members of your study group to go over notes from class, discuss problem sets, work problems from the book, and review for exams. 5) Come to office hours and peer mentor sessions! We are here to help you!

Student Evaluation
Grades will be based on the points that you earn from class meeting assignments, laboratory assignments, exams and class participation. A total of 895 points will be available as follows:

Class Activities
Hour Exams Exam I on Feb. 19 Exam II on Apr. 2 Exam III on May 5 Final Exam Cumulative Self-scheduled Final Exam Reading quizzes Concept map Class participation/Clicker responses Weekly Practice Exams

Points
3 @ 100 pts. =300 pts.

1 @ 150 pts. 30 @ 2 pts. 1 @ 10 pts. 30 @ 3 pts. 8 @ 10 pts.

=150 pts. = 60 pts. =10 pts. =90 pts. =80 pts.

Laboratory Activities
Laboratory notebook Notebook check-ups weeks: Feb. 17, Mar. 24, May 5 Laboratory research papers First submission due week of Mar. 3 Peer-review due week of Mar. 31 Final submission due week of Apr. 14 Project Presentation Presentations during week of Apr. 21 Journal article critique/discussion Article 1 week of Feb. 10 Article 2 week of Apr. 7 Lab participation 3 @ 25 pts. =75 pts.

First submission = 30 pts. Peer-review = 15 pts. Final submission = 20 pts. 1 @ 30 pts. = 30 pts. 2 @ 10 pts. =20 pts.

15 pts.

=15 pts.

Total= 895 pts.

Your final grade will be determined by the percentage of points that you earn as follows: 94-100 % 83-86% 73-76% 63-66% A B C D 90-93% 80-82% 70-72% 60-62% ABCD87-89% 77-79% 67-69% < 60% B+ C+ D+ F

Genetics Bio 208

Class Meeting Syllabus Spring 2014
Class Dates: Class Topic Jan. 22 Introduction to Genetics DNA AS THE GENETIC MATERIAL Jan. 24 Jan. 27 The Search for the Genetic Material DNA, Chromosomes and Genomes Ch. 1 p. 1-34 Ch. 2 p. 42-49 Ch. 7 p. 227-238 Readings:

Jan. 29

DNA and Chromosomes during the Cell Cycle Mitosis DNA Replication in vitro DNA replication: PCR Molecular Tools to study and manipulate DNA Separation/ identification of DNA fragments Cloning DNA fragments, DNA libraries Tools to study DNA variation DNA markers DNA sequencing

Ch. 4 p. 117-122 Ch. 6 p. 195-210 Ch. 2 p. 57-62

Jan. 31

Ch. 2 p. 49-57; Ch. 12 p. 440-450 Ch. 2 p. 39-40 Ch. 2 p. 62-70 Ch. 6 p. 210-216; Handout/Video

Feb. 3

MENDELIAN INHERITANCE Feb. 5 Mendelian Genetics Segregation Independent Assortment Mendelian Genetics Pedigrees and probabilities 47 Feb. 10 Extensions of Mendelian Inheritance Gene Interactions: Epistasis Extensions of Mendelian Inheritance Dominance; Multiple allele Ch. 3 107-109

Ch. 3 p. 80-90 Ch. 3 p. 90-93

Feb. 7

Ch. 3 p. 93-104 Ch. 4 p. 140-

Feb. 12

Ch. 3 104-107

Feb. 14

The Chromosomal Theory of Inheritance Chromosome behavior during meiosis X-linked inheritance Chromosomal abnormalities Review EXAM I GENETIC MAPPING

Ch. 4 p. 123-31 Ch. 4 p. 131-134 Ch. 8 p. 268-73

Feb. 17 Feb. 19

Feb. 21 Feb. 24

Genetic Linkage and Recombination Genetic Linkage and Mapping Three-point test cross Mapping Human Genes

Ch. 5 p. 155-170 Ch. 5 p. 170-174

Feb. 26

Ch. 5 p. 174-176; Handout/Video Ch. 5 p. 183-84 Ch. 6 p. 216-221 Ch. 11 p. 426-430 Ch. 8 p. 273-88

Feb. 28

Molecular Biology of Recombination

Mechanisms of Chromosomal Abnormalities Deletions, dups., invers. and translocs. MUTATIONS Mar. 3 Mar. 5 Molecular Mechanisms of Mutation Mutagens Mechanisms of DNA Repair Mismatch and base excision Mechanisms of DNA Repair AP, NER, Photo, SOS Genetic Screens Transgenic Organisms

Ch. 14 p. 521-540 Ch. 14 p. 540-548 Ch. 14 p. 548-552

Mar. 7

Ch. 14 p. 552-55 Handout Ch. 12 p. 463-73 Handout

Mar. 10-21

Spring Break
SEX AND GENETICS

Mar. 24

Sex Linked Inheritance Dosage Compensation

Ch. 4 p. 131-138 Ch. 8 p. 261-268

Mar. 26

Sex Determination

Ch. 4 p. 138-140 Ch. 8 p. 266-268 Handout/Video

MICROBIAL GENETICS Mar. 28 Bacterial genetics Bacteriophage genetics REVIEW EXAM II Ch. 9 p. 303-314 Ch. 9 p. 320-325 Ch. 9 p. 330-339

Mar. 31 Apr. 2

GENE EXPRESSION Apr. 4 Transcription: DNA to RNA- the mechanisms Tools to study RNA Processing of mRNA in eukaryotes Translation: RNA to Protein- the mechanisms Translation Translation Units The standard genetic code Tools to study Proteins REGULATION OF GENE EXPRESSION Apr. 11 Regulation of gene expression Reglation of gene expression in prokaryotes lac operon Regulation of gene expression in prokaryotes: trp operon transcription termination regulation in bacteriophage lambda Handout Ch. 11 388-398 Ch. 10 p. 347-358 Handout/Video Ch. 10 p. 358-364 Ch. 10 p. 364-372

Apr. 7

Apr. 9

Ch. 10 p. 372-374 Ch. 19 p. 374-381 Handout/Video

Apr. 14

Ch. 11 p. 398-405

Apr. 16

Regulation of gene expression in eukaryotes: Transcriptional regulation Regulation of gene expression in eukaryotes: Post-transcriptional regulation

Ch. 11 p. 406-417

Apr. 18

Ch. 11 p. 421-426

FRONTIERS IN MOLECULAR GENETICS Apr. 21 Epigenetics and Developmental Genetics Ch. 11 p. 421-22 Ch. 13 p. 481-486 Ch. 13 p. 495-514 Ch. 12 p. 451-462 Handout/Video

Apr. 23

Genomics and Proteomics

POPULATION GENETICS, EVOLUTION AND COMPLEX TRAITS Apr. 25 Population Genetics and Evolution Ch. 17 p. 631-635 Ch. 17 p. 644-655 Ch. 17 p. 622-630

Apr. 28 Apr. 30

Molecular Evolution Quantitative Genetics Heritability of complex traits Quantitative-trait loci REVIEW EXAM III Wrap-up with concept maps

Ch. 18 p. 663-678 Ch. 18 p. 683-687

May 2 May 5 May 7

Genetics Biology 208

Laboratory Schedule Spring 2014 Week of Laboratory Jan. 27 Genetics Laboratory Introduction and Safety Feb. 3 Feb. 10
Chromosomes during Mitosis ABO Genotyping using PCR-RFLP: DNA isolation and PCR set-up ABO Genotyping using PCR-RFLP: Digestion of PCR product Gene Mapping: Set-up Drosophila F1 crosses Journal Article #1 Discussion ABO Genotyping using PCR-RFLP: Gel electrophoresis Epistasis: Corn dihybrid crosses Gene Mapping: Check on F1 crosses-count offspring Notebook Check-up ABO Genotype using PCR-RFLP: Discussion of results Gene Mapping: Continue counting F2 offspring; Discussion of map distances and linear order; Observe Drosophila mutants UV Mutagenesis in Yeast: Mutagenesis and plating Scientific Paper Due SPRING BREAK SPRING BREAK UV Mutagenesis in Yeast: Count colonies and analyze results Project Design-proposal due Notebook Check-up Projects Peer review of Scientific Paper Due Projects Journal Article #2 Discussion Bioinformatics and Systems Biology Final Submission of Scientific Paper Due Project presentations

Feb. 17

Feb. 24

Mar. 3 Mar. 10 Mar. 17 Mar. 24 Mar. 31 Apr. 7 Apr. 14 Apr. 21

April 28 Population Genetics