Genetics

Biology 305

 

Genetics 305 Spring 2010 Detailed Syllabus


Time: MWF at 9-9:50, 10-10:50, or 11-11:50 a.m.

Room: New Science Center, Room 138/140

Office Hours: By appointment only


Course policies and grading can be found here


Section 1: Course Introduction, Cell Division and Mutation


January 11th   Course Introduction

  1. •Syllabus (pdf)

  2. •Introduction to Text and iClickers (How to register your iClicker for Genetics)


January 13th   Cell Division: Mitosis and Meiosis

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf)

  3. •Chapter 1: pp 1-15,

  4. •Chapter 2: pp 16-35 (See Lecture notes detailed breakdown of important pages)

  5. •Suggested Problems (pdf): Ch. 2: 20, 26, 31, 36


January 15th    Genetic Variation and Mutation                              

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf)

  3. •Reading: CSHL Your Genes, Your Health: What Causes Cystic Fibrosis?

  4. •Chapter 18:  pp 472-481, Table 18.2, 483, Figure 18.13

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

  6. •In Class Movie Clip: SCA1 Patient

  7. •In Class Movie Clip: Trinucleotide Repeat Expansion

  8. •Suggested Problems (pdf): Ch. 18: 16-23


Section 2: Mendelian Genetics and Probability


January 20th Mendelian Genetics: A Review                             

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf)

  3. •Chapter 3: pp 43-60 (Much of this is review)

  4. •Suggested Problems (pdf): Ch. 3: All the end of chapter problems


January 22nd Probability and Statistics                           

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf)

  3. •Chapter 3: pp 60-64

  4. •In Class Discussion Problem: Dihybrid Crosses and Unexpected Outcomes

  5. •Suggested Problems (pdf): Ch. 3: All the end of chapter problems


Section 3: Genetics of Sex and Pedigrees


January 25th Sex-linked Traits                                                                       

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf)

  3. •In Class Movie Clip: Y Chromosome Evolution

  4. •Chapter 4: pp 73-78, 81-87 (Starting with section 4.2)

  5. •Suggested Problems (pdf): Ch. 4: 17, 22-31, 35-38, 40-41


January 27th Mosaicism and Human Sex Determination

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf)

  3. •Chapter 4: pp 79-81, 87-89 (Dosage Compensation)

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

  5. •In Class Movie Clip: X Inactivation

  6. •HHMI Gender Testing of Female Athletes


Problem Set 1 Due Before Class Begins on January 29th (Problem Set 1.pdf)


January 29th Human Mendelian Traits and Pedigrees                            

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf)

  3. •Chapter 6: pp 134-142

  4. •In Class Discussion Problem: Those Old Kentucky Blues

  5. •Suggested Problems (pdf): Ch. 6: 17-26


Section 4: Modifications of Mendel


February 1st Modifications of Mendelian Genetics Part I: Multiple Alleles                                         

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf)

  3. •Chapter 5: pp 99-105, 112-113 (Complementation), 122-124 (Section 5.8)

  4. •Suggested Problems (pdf): Ch. 5:13-32


February 3rd   Exam 1: Material Through January 27th (Introduction to Sex Determination)

  1. •Review Sheet (pdf)

  2. •Practice Exam Problems (pdf)

  3. •Practice Exam Problems Answers (pdf)


February 5th Modifications of Mendelian Genetics Part II: Epistasis                                        

  1. •No Pre-lecture quiz

  2. •Lecture Notes (pdf)

  3. •Chapter 5: pp 105-113

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

  5. •Suggested Problems (pdf): Ch. 5:13-32


February 8th  Modification of Mendel and Human Pedigrees                              

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf)

  3. •Review Pedigree analysis and Modifications of Mendelian Genetics Part I

  4. •Suggested Problems (pdf): Ch. 6: 17-26


Section 5: Linkage and Recombination


February 10th   Linkage and Recombination

  1. •Pre-lecture quiz

  2. •Lecture Notes for the 10th, 12th, and 15th (pdf)

  3. •Chapter 7: pp 160-168

  4. •Suggested Problems (pdf): Ch. 7: 13-25


February 12th Recombination and Mapping Part I

  1. •Pre-lecture quiz

  2. •Chapter 7: pp 168-174

  3. •Suggested Problems (pdf): Ch. 7: 13-25


February 15th Recombination and Mapping Part II

  1. •Pre-lecture quiz

  2. •Chapter 7: pp 174-183

  3. •Suggested Problems (pdf): Ch. 7: 26-31


Problem Set 2 Due Before Class Begins on February 17th (Problem Set 2.pdf)


Section 6: Bacterial and Viral Genetics


February 17th and 19th  Bacterial Genetics                                  

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf)

  3. •In Class Movie Clip: Nova Science Now-Iraqibacter

  4. •Chapter 8: pp 200-218

  5. •Suggested Problems (pdf): Ch. 8: 15-25


February 22nd  Viral Genetics: Bacteriophage                           

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf)

  3. •Chapter 8: pp 218, Figure 8.24, 223-227 (not transduction)

  4. •Suggested Problems: Ch. 8: 26, 28, 30, 31, 34, 35


February 24th  Exam II: Material Through Feb 15th (Pedigrees to Recombination)

  1. •Review Sheet (pdf)

  2. •Practice Exam Problems (pdf)

  3. •Practice Exam Problems Answers (pdf)


February 26th  Viral Genetics: Avian Influenza

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf)

  3. •Reading 1: CDC avian influenza facts.pdf

  4. •Reading 2: Flu Pandemics Review.pdf

  5. •Reading 3: NIAID Handout (pdf)

  6. •In Class Movie Clip: Influenza Virus Recombination

  7. •If you are interested: NOVAScience Now-Reviving the 1918 flu

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


Section 6: The Dynamic Genome


March 1st Transposable Elements and Evolving Genomes

  1. •No pre-lecture quiz

  2. •Lecture Notes (pdf)

  3. •Chapter 11: pp 297-309

  4. •Suggested Problems (pdf): Ch. 11: 30-33, 35-39


March 3rd   Molecular Mechanisms of Chromosomal Variation

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf)

  3. •Chapter 9: pp 237-254, Chapter 11: Figure 11.19 (Look at this carefully)

  4. •Suggested Problems (pdf): Ch. 9: 19-22, 33, 34, 37


March 5th  Cancer Genetics                     

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf)

  3. •Chapter 23: pp 624-641

  4. •CSHL Cancer Multimedia Site

  5. •Suggested Problems (pdf): Ch 23: 21, 22, 24, 26, 27, 29, 30, 33


March 8-12th Spring Break


Section 7: Sequence Variation and Human Gene Mapping


March 15th Pharmacogenetics

  1. •Lecture Notes (pdf) (ppt)

  2. •NIH Tamoxifen Site

  3. •NIGMS Pharmacogenetics FAQ page


Problem Set 3 Due Before Class Begins on March 17th (Problem Set 3.pdf)


March 17th-19th   Sequence Variation and Forensic Genetics                        

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf) (ppt)

  3. •Reading: Chapter 19, Figure 19.11 (PCR) and associated text

  4. •Video Clip: PCR Animation

  5. •Reading: Jobling and Gill (2004) Encoded Evidence. Nat Rev Genetics 5: 739-751 (pdf)

  6. •Movie Clip: DNA Databases

  7. •Movie Clip: Anthrax Investigation on NOVA Science Now


March 22nd Exam III: Material through March 5th (Bacterial Genetics to Cancer)

  1. •Review Sheet (pdf)

  2. •Practice Exam Problems (pdf)

  3. •Practice Exam Problems Answers (pdf)


March 24th Mapping Mendelian Human Diseases I: Advanced Pedigree Analysis                   

  1. •Pre-lecture quiz

  2. •Lecture Notes: (pdf), (ppt)

  3. •Chapter 7: pp 183-185 and Mapping human genes handout (pdf)

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


March 26th Mapping Mendelian Human Diseases II: LOD Scores                        

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf), (ppt)

  3. •Practice Problems (pdf) and Answers (pdf)


March 29h Mapping Mendelian Human Diseases III: Linkage Disequilibrium                     

  1. •Lecture Notes (pdf), (ppt)

  2. •Reading: D. Drayna. “Founder Mutations” Sci.Am. Oct 2005, pp 78-86. (pdf)

  3. •Reading: Peltonen et al. (2000) Nature Reviews Genetics. pp 182-186. (pdf)


March 31th  Human Multifactorial Traits and Association Studies

  1. •Lecture Notes: (pdf), (ppt)

  2. •Reading: Human Genetics, “Multifactorial Traits” (Handed out in Class)

  3. •Reading: Chapter 6, pp 142-145 (Twin Studies); Chapter 24, pp 663-664 (Limitations of Heritability)

  4. •Reading: Chapter 20, pp 556-557 (SNPs)

  5. •Suggested Problems: Chapter 6: 27 and 28


Problem Set 4 Due Before Class Begins on April 5th (Problem Set 4.pdf) (Answers.pdf)


Section 8: Quantitative Trait Loci Analysis and Informatics Project

Image Analysis Software: NIH Image J

Download Instructions (doc)


April 2nd: Quantitative Traits


April 5th: Introduction to Quantitative Trait Loci Mapping

  1. •Lecture Notes: (ppt)

  2. •Reading: Chapter 24, pp 659-666 (Section 24.3)

  3. •Suggested Problems (pdf): Chapter 24: 9, 10, 16, 27-31, 34


April 7th: Quantitative Trait Loci: Olfactory Bulb and Brain Measurements

  1. •Project Introduction and Brain Measurement Instructions: (QTL Handout 1-Volume.pdf)

  2. •Mouse Brain Library Images (this page has the image files and mouse data file)


April 9th: Exam IV: Material through March 29th (Pharmacogenetics to Human Mapping)

  1. •Review Sheet (pdf)

  2. •Practice Exam Problems (pdf)

  3. •Practice Exam Problems Answers (pdf)

  4. •Exam Answer Key (pdf)


April 12th: Quantitative Trait Loci: Olfactory Bulb and Brain Measurements

  1. •Brain Volume Calculations (pdf)


April 14th: Quantitative Trait Loci: Regression Analysis

  1. •Lecture Notes: (pdf), (ppt)

  2. •Reading: Chapter 24, pp 656 (Regression)


April 16th: Quantitative Trait Loci: QTL analysis and Chromosome Mapping

  1. •WebQTL-GeneNetwork Analysis

  2. •WebQTL Linkage Handout (pdf)


April 19th: Quantitative Trait Loci: Gene Expression and Microarrays

  1. •UCSC Genome Browser

  2. •Candidate Gene and Microarray Handout (pdf)

  3. •Reading: Chapter 20, pp 560-562 (Gene Expression and Microarrays)

  4. •Reading: NIH Primer on Microarrays

  5. •Microarray Animation


April 21st: Quantitative Trait Loci: Gene Expression and the Allen Brain Atlas

  1. •Candidate Gene and Brain Atlas Handout (pdf)

  2. •UCSC Genome Browser

  3. •Allen Brain Atlas


April 23rd: Quantitative Trait Loci: Entrez, Pubmed, and Catch-up Day

  1. •Entrez and PubMed Handout (pdf)

  2. •Entrez Gene and PubMed


April 26th: Quantitative Trait Loci Projects Due


Final Exam: Quantitative Trait Loci Analysis and Project

  1. •Review Sheet (pdf)


Schedule (all exams in the New Science Center, Room 138/140)

  1. •9-9:50am Section: Wednesday, May 5th, 8-11:00am

  2. •10-10:50am Section: Wednesday, April 28th, 8-11:00am

  3. •11-11:50am Section: Friday, April 30th, 12-3:00pm


Important Note: You must take the final on the assigned exam day.  I will not allow students to take the exam earlier or later with a different section.  Travel plans are not an acceptable reason to take the exam early.

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.   Occasionally during 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.

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

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. While you can use an earlier addition of the text if you like, I am not responsible for page number and suggested problem discrepancies with other editions of the text.  We will also be using the iClicker response system in class everyday.  Both the text and the iClicker remote are available at the College bookstore.

Become a Fan of our course Facebook page, College of Charleston Genetics.  I will use the status line to post interesting genetics related news and remind you about upcoming assignment due dates.  You can use the page to organize study groups and problem set parties.  The updates will appear in the news feed of your own page to keep you up to date.