Disability Statement: This College abides by section 504 of the Rehabilitation Act of 1973 and the Americans with Disabilities Act that stipulates no student shall be denied access to an education “solely by reason of a handicap.” Disabilities covered by law include, but are not limited to, learning disabilities and hearing, sight or mobility impairments. If you have a documented disability that may have some impact on your work in this class and for which you may require accommodations, please see an administrator at the Center of Disability Services, (843) 953-1431 and me so that such accommodation may be arranged.


What to expect from me:


  1. •At each course meeting I will outline the important points for the day and present you with a set of questions to think about that will guide your thinking about the material.

  2. •Each class will begin with questions and by working a problem relevant to the previous day’s material, we will have about 25 minutes of lecture, then we will talk about genetics stories in the news and finally we will get to the days lecture material.

  3. •Office Hours: I can usually be found in my office/lab most of the day.  When you have a question or concern, just stop by.  My door is always open.  I will be guaranteed to be in my office between 11am-12pm on Mondays and Wednesdays.  Feel free to make an appointment if you want to meet at a specific time outside of office hours.  I can’t help you unless you come and discuss questions you may have with me.


What I expect from you:


  1. •Take a look at the day’s background information before coming to class

  2. •Attend class and ask questions

  3. •After class do the assigned readings and start working the suggested problems.  Don’t save all the problems for the few days prior to an exam.

  4. •Come to me with questions as soon as they arise.  The earlier I can help the better.

  5. •Do the assigned problems sets.  While you can work on them with others, make sure you understand the correct answers.


Genetics is a problem-based class that involves applying general genetic concepts to specific problems. Coming to class regularly is only part of the work required to do well in this class.  You cannot expect to completely understand all of the important concepts at the end of each class period.  A solid understanding of the material, and thus the possibility of a good grade, can only be achieved by following the advice listed above.


Exams and Grading: There will be 4 homework assignments, 3 in-class exams and a final exam.


Take Home assignments: These are graded problem sets that must be handed in before class begins on the date they are due.  Papers handed in after class begins have a 5-point automatic deduction.  A further 5 points will be deducted for each day that it is late. These are extended problems that will ask you to apply what you have learned.

In-class Exams: The four midterm exams are non-cumulative and closed book. The final exam covers the material following the fourth midterm plus a cumulative section.  Exams will test your general knowledge of the material and also ask you to apply the concepts you have learned to longer problems.  Exams consist of multiple choice, short answer questions and problems. There will be one review session before each exam.


Missing Exams: Students must provide a valid and documented excuse from the Undergraduate Dean’s Office for missing Assignments or Exams.  Acceptable excuses include illness, personal tragedy or circumstances beyond the student’s control (This does not include over sleeping on exam day).  Anyone who misses an exam or fails to hand in the take home assignments without an acceptable excuse will receive a grade of zero.



Extra Credit: There will be an opportunity for extra credit during each class period. To get extra credit, bring in an article from scientific magazines (Discover, Scientific American, etc.), the news and views sections of Science or Nature or your local and national newspapers.  Everyday at the class break we will talk about genetics research in the news as highlighted by the articles you hand in.  You can hand in one article for 5 points extra credit. This is the only opportunity for extra credit in the semester.


Course Grade: There is no curve in this class; your grade depends only on your own performance in the class.  Grades will be assigned based on the total points you have accumulated.


Point Breakdown:


  1. •3 exams (100 points each)                                     300

  2. •4 Take Home Assignments (50 points each)          200

  3. •1 Final exam (150 points)                                       150


                                             Total Possible Points:  650


Grading Scale:

A        93-100

A-       90-92

B+      87-89

B        83-86

B-       80-82

C+      77-79

C        73-76

C-       70-72

D+      67-69

D        63-66

D-       60-62

F        <60



Honor Code and Academic Integrity:

Lying, cheating, attempted cheating, and plagiarism are violations of our Honor Code that, when identified, are investigated.  Each instance is examined to determine the degree of deception involved.  Incidents where I believe that a student’s actions are clearly related more to ignorance, miscommunication, or uncertainty, will be addressed by consultation with me.  We will craft a written resolution designed to help prevent future repetition of this error in the future.  This resolution, submitted by form and signed by both the student, and me is forwarded to the Dean of Students and remains on file. 


I will report cases of suspected academic dishonesty directly to the Dean of Students.  A student found responsible for academic dishonesty will receive a XF in the course, indicating failure of the course due to academic dishonesty.  This grade will appear on the student’s transcript for two years after which the student may petition for the X to be expunged.  The student may also be placed on disciplinary probation, suspended (temporary removal) or expelled (permanent removal) from the College by the Honor Board.


It is important for students to remember that unauthorized collaboration--working together without permission-- is a form of cheating.  Unless I specify that you can work together on an assignment and/or test, no collaboration is permitted.   Other forms of cheating include possessing or using an unauthorized study aid (such as a PDA), copying from another’s exam, fabricating data, and giving unauthorized assistance.


You can find a complete version of the Honor Code and all related processes in the Student Handbook at


Genetics 212 Fall 2007 Detailed Syllabus


     The July 1, 2005 issue of Science magazine highlighted 125 unanswered questions in science.  As a way to highlight the role genetics will have in eventually answering some of these questions, each week we will read and talk about a short article from this issue of Science.  Some of them will be related to that week’s material, others are just interesting questions to think about.



August 21-23rd    Course Introduction, DNA: Our Common Genetic Heritage

   

  1. •In Class Movie Clip: Instructions for a Human Being and Getting the Letters Out

  2. •Chapter 1: pp 1-15,

  3. •Chapter 2: pp 17-26, 30-37, and 41-42

  4. •Chapter 11: pp 296-299

  5. •Chapter 19:  pp 573-582

  6. •Integrative Case Study: Phenylketonuria pp 156-158

  7. •Science Magazine Question of the Week: In Praise of Hard Questions, How and Where Did Life

                                                                    on Earth Arise?


August 28-30th    Genetic Variation: Molecular Mechanisms of Mutation

                                

  1. •In Class Movie Clip: Cystic Fibrosis-Finding Cures is Hard

  2. •Chapter 10:  pp 266-283

  3. •Chapter 17: pp 472-500; Base Pairing Handout

  4. •Integrative Case Study: Phenylketonuria pp506-508

  5. •Science Magazine Question of the Week: How Does a Single Somatic Cell Become a Whole    

                                                                     Plant?


Suggested Problems: Ch. 10: 25-27, 33; Ch. 17: 17-24 (Not 23), 26


August 30th-September 4th   Mendelian Genetics: A Review


  1. •Chapter 3: pp 47-69

  2. •Integrative Case Study: Phenylketonuria pp 156-158


Suggested Problems: Ch. 3: 12-20, 21-24, 26-30, 33 and 34


September 6th  Modifications of Mendelian Genetics: From Genotype to 

                          Phenotype

                                        

  1. •In Class Movie Clip: Cystic Fibrosis-Complexity in Proteins

  2. •Chapter 5: pp 101-112, 115 (complementation), 122-124

  3. •Integrative Case Study: Phenylketonuria pp 156-158

  4. •Science Magazine Question of the Week: How Can a Skin Cell Become a Nerve Cell?


Suggested Problems: Ch. 5: 12-14, 16, 17, 19, 22-30, 32


Problem Set 1 Due Before Class Begins on September 11th


September 11th    The Genetics of Sex

                                             

  1. •In Class Movie Clip: Human Sex Determination-Messages in the Genes

  2. •Chapter 4: pp 75-95


Suggested Problems: Ch. 4: 17, 19-23, 27, 28, 30, 32, 34, 37


September 13th   Human Mendelian Traits and Pedigrees


  1. •Chapter 6: pp 132-140

  2. •Integrative Case Study: Phenylketonuria pp 156-158

  3. •Science Magazine Question of the Week: What Controls Organ Regeneration?


Suggested Problems: Ch. 6: 10-13,16-18


September 18th   Exam 1: Material Through Sept 6th

                                          (Introduction to Genetics of Sex)


  1. •Review Sheet on WebCT



September 20th   Linkage and Recombination


  1. •Chapter 7: pp 160-182


Suggested Problems: Ch. 7: 13-26


September 25th Recombination and Mapping, continued


September 27th  Bacterial Genetics

                                  

  1. •In Class Movie Clip: Resistant Tuberculosis

  2. •Chapter 8: pp 197-215


Suggested Problems: Ch. 8: 16-23


Problem Set 2 Due Before Class Begins on October 2nd


October 2nd  Viral Genetics: Bacteriophage

                           

  1. •In Class Movie Clip: Animal Farming and Antibiotic Resistance

  2. •Chapter 8: pp 215-225

  3. •Science Magazine Question of the Week: Is an Effective HIV Vaccine Feasible?


Suggested Problems: Ch. 8: 24-28, 31-32


October 4th   Viral Genetics: Human Immunodeficiency Virus

                                 

  1. •In Class Movie Clip: HIV Evolution and Drug Treatment

  2. •Chapter 8: pp 226-228

  3. •Emerging Infectious Disease by Stuart A. Hill

  4. • “A Case for Evolutionary Thinking: Understanding HIV” Evolutionary Analysis, Chapter 1, by Freeman and Herron, 3rd Edition.  Pp 3-17, 22-30 (on webCT)


October 9th    Exam II: Material Through Sept 27th

                        (Pedigrees to Bacteriophage)


  1. •Review Sheet on WebCT


October 11th    Viral Genetics: Avian Influenza


  1. •Emerging Infectious Disease by Stuart A. Hill

  2. •Chapter 23: pp 697-708

  3. • “Flu Virus Evolution” Evolutionary Analysis, Chapter 13, Pp503-509. (Handed out in class)


If you are interested in Avian Flu: The Nature In Focus Avian Flu Website

 

October 16th Fall Break


October 18th    Transposable Elements and Evolving Genomes


  1. •Chapter 11: pp 299-313

  2. •Chapter 23: pp 708-711

  3. •Molecular Biology of the Cell, pp287-292 (handed out in class)

  4. •Science Magazine Question of the Week: Why Do Humans Have So Few Genes?


Suggested Problems: Ch. 11: 29-31 and 33-39


October 23rd     The Genetics of Model Systems


  1. •Chapter18: pp 534-539

  2. •Chapter 19: pp 572-573 (Genome Wide Mutagenesis)

  3. •Molecular Cell Biology, Pp284-289 (handed out in class)


Problem Set 3 Due Before Class Begins on October 25th


October 25th     Molecular Mechanisms of Chromosomal Variation


  1. •Chapter 9: pp 235-252, Chapter 11: figure 11.19

  2. •Lupski, JR (1998) Genomic Disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. TIG 14: 417-422.

  3. •Science Magazine Question of the Week: What Genetic Changes Made Us Uniquely Human?


Suggested Problems: Ch. 9: 19-21,  23 (not b, c, and g), 24, 33, 34, 37



October 30th     Cancer Genetics

                       

  1. •In Class Movie Clip: Breast Cancer-A Family Disease

  2. •Chapter 21: pp 627-636

  3. •Chapter 10: pp 257-259,

  4. •CSHL Cancer Multimedia Site


Suggested Problems: Ch. 21:30-32


November 1st    Exam III: Material through October 25th

                          (HIV to Chromosomal Variation)


November 6th    Genetics Movie Night:  Race - The Power of an Illusion

                    

  1. •Feldman et al, (2003) A Genetic Melting pot, Nature 424: 374


November 13th    Pharmacogenetics


  1. •NIH Tamoxifen Site

  2. •CSHL Cancer Multimedia Site

  3. •Chapter 19: pp 569-571 (Microarrays)

  4. •Science Magazine Question of the Week: To What Extent Are Genetic Variation and Personal Health Linked?


November 15th    Sequence Variation and Forensic Genetics

                        

  1. •In Class Movie Clip: DNA Databases

  2. •Chapter 18: pp 530-532 (PCR), 543-547 (DNA Fingerprinting)

  3. •Jobling and Gill (2004) Encoded Evidence: DNA in Forensic Analysis. Nat Rev Genetics 5: 739-751

  4. •“Scientists Report Genetic Finding that could Aid Anthrax Inquiry”. NY Times, January 22, 2002. (Handed out in class)


November 20th   Mapping Mendelian Human Diseases I                      


  1. •Mapping human genes handout

  2. •Science Magazine Question of the Week: How Much Can Human Life Be Extended?


Practice Problem on WebCT


November 22nd  Thanksgiving

 

November 27th   Mapping Mendelian Human Diseases II    

                   

  1. •In Class Movie Clip: Iceland-Finding Disease Genes

  2. •D. Drayna. “Founder Mutations” Sci.Am. Oct 2005, pp 78-86.

  3. •Integrative Case Study: Phenylketonuria Pp716-720


Problem Set 4 Due Before Class Begins on November 29th


November 29th  Quantitative Genetics and Human Disease


  1. •Chapter 22: pp 642-651

  2. •Other Readings and Problems to be determined


For the 9:25am-10:40am Section in Room 239:

December 11   Final Exam from 8-11am

                         Exam VI (Cancer Genetics through the end of course)        

                         and Cumulative Section


For the 10:50am-12:05am Section in Room 121:

December 6    Final Exam from 8-11am

                         Exam VI (Cancer Genetics through the end of course)        

                         and Cumulative Section



  1. •Review Sheet on WebCT  

Genetics

Genetics is one of those fields that affects the way we think about everything else in Biology.  Far from being a historical subject, genetics is at the leading edge of modern biological research.  This course will be a rigorous introduction to the fundamentals of genetics.  Along the way, we will explore how modern genetic research is done, the technologies that it has led to, and the big unanswered questions that are still out there.  Finally, science is not done in a vacuum; it is a human endeavor that is pursued within a larger social context.   Throughout the course, we will be thinking about genetics and the ways it is changing the society that we live in.


Course Goals

1. To give you a solid understanding of the principles underlying the field of genetics.

2. To give you an appreciation of the role genetics plays in all areas of the biological sciences.

Required Readings: Both texts are only available at the University Bookstore on King Street.


Genetics, A Conceptual Approach

3rd Edition, by Benjamin Pierce


This is the main text for the course.   All assigned chapter readings will come from this text.


Emerging Infectious Disease

by Stuart A. Hill


Other required readings will be on WebCT or handed out in class as indicated in the syllabus.


Electronic Media: This class will use a variety of electronic media to enhance our understanding of genetics.  There is a webCT site for this course. The course website has a hyperlinked version of the syllabus that allows you to connect directly to the web based media.  The webCT site will contain downloadable versions of the homework assignments, class notes, supplemental readings, further (not required) readings for those that are interested, answers to homework/suggested problems, and sample exam questions.  It will also have the grade book, discussion board, and a books section.  Note: All downloadable files will be in PDF format and can be opened with Adobe Acrobat Reader.