Genetics

Biology 305

 

Genetics 305 Spring 2011 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 10th  Cancelled due to Winter Weather


January 12th  Course Introduction

  1. •Syllabus (pdf)

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


January 14th  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 19th 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: 16-21


Section 2: Mendelian Genetics and Probability


January 21st 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 24th 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 (except binomial expansion/factorial equations)


Section 3: Genetics of Sex and Pedigrees


January 26th 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 28th 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 28th (Problem Set1.pdf) (Answer Key.pdf)


January 31st 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 2nd 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 4th Exam 1: Material Through January 28th (Introduction to Sex Determination)

  1. •Review Sheet (pdf)

  2. •Exam 1 Abstract (pdf)

  3. •Practice Exam Problems (pdf)

  4. •Practice Exam Problems Answers (pdf)


February 7th 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. •NIH Bookshelf: Bombay Phenotype

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


February 9th  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 11th 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 14th Recombination and Mapping Part I

  1. •Pre-lecture quiz

  2. •Chapter 7: pp 168-174

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


Problem Set 2 Due Before Class Begins on February 16th (Problem Set 2.pdf)


February 16th Recombination and Mapping Part II

  1. •Pre-lecture quiz

  2. •Chapter 7: pp 174-183

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


Section 6: Bacterial and Viral Genetics


February 18th  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 (except 210-212)

  5. •Suggested Problems (pdf): Ch. 8: 15,16, 20-24


February 21st  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 23rd  Exam II: Material Through Feb 16th (Pedigrees to Recombination)

  1. •Review Sheet (pdf)

  2. •Exam Abstract (pdf)

  3. •Practice Exam Problems (pdf)

  4. •Practice Exam Problems Answers (pdf)


February 25th  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


February 28th 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 2rd   Molecular Mechanisms of Chromosomal Variation

  1. •Pre-lecture quiz

  2. •Lecture Notes (NEWpdf)

  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 4th 


March 7-11th Spring Break


Section 7: Sequence Variation and Human Gene Mapping


  1. •March 14th Molecular Mechanisms of Chromosomal Variation Continued


Problem Set 3 Due Before Class Begins on March 16th (Problem Set 3 .pdf); (ANS.pdf)


March 16th Cancer Genetics                     

  1. •Pre-lecture quiz

  2. •Lecture Notes (NEWpdf)

  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 18th Pharmacogenetics

  1. •Lecture Notes (pdf)

  2. •NIH Tamoxifen Site

  3. •NIGMS Pharmacogenetics FAQ page


March 21st Sequence Variation and Forensic Genetics                        

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf)

  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 23rd Exam III: Material through March 16th (Bacterial Genetics to Cancer)

  1. •Abstract (pdf)

  2. •Review Sheet (pdf)

  3. •Practice Exam Problems (pdf)

  4. •Practice Exam Problems Answers (pdf)


March 25th Mapping Mendelian Human Diseases I: Advanced Pedigree Analysis                   

  1. •Pre-lecture quiz

  2. •Lecture Notes: (pdf),

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

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


March 28h Mapping Mendelian Human Diseases II: LOD Scores                        

  1. •Pre-lecture quiz

  2. •Lecture Notes (pdf),

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


March 30th Mapping Mendelian Human Diseases III: Linkage Disequilibrium                     

  1. •Lecture Notes (pdf),

  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)


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


April 1st: Human Multifactorial Traits and Association Studies

  1. •Lecture Notes: (pdf),

  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


April 4th: Association Studies Continued


Section 8: Quantitative Trait Loci Analysis and Informatics Project


QTL Project Assignment (pdf)

UCLA Student Pre-Test Link

UCLA Student Post-Test Link

Image Analysis Software: NIH Image J

Download Instructions (doc)


April 6th: Introduction to Quantitative Trait Loci Mapping

  1. •Lecture Notes: (pdf)

  2. •Reading: Chapter 24, Section 24.1 and 24.3

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


April 8th: 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 11th: Exam IV: Material through March 30th (Pharmacogenetics to Linkage Disequilibrium)

  1. •Review Sheet (pdf)

  2. •Practice Exam Problems (pdf)

  3. •Practice Exam Problems Answers (pdf)


April 13th: Quantitative Trait Loci: Olfactory Bulb and Brain Measurements

  1. •Brain Volume Calculations (pdf)


April 15th: Quantitative Trait Loci: Regression Analysis

  1. •Lecture Notes

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


April 18th: Quantitative Trait Loci: QTL analysis and Chromosome Mapping

  1. •WebQTL-GeneNetwork Analysis

  2. •WebQTL Linkage Handout (pdf)


April 20th: 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 22nd: 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 25th: Quantitative Trait Loci Catch-up Day


Quantitative Trait Loci Projects Due on Monday, April 25th


Final Exam: Multifactorial Traits to QTL Analysis/Project and Selected Topics Previous Exams

  1. •Review Sheet (pdf)


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

  1. •9-9:50am Section: Monday, May 2nd, 8-11:00am

  2. •10-10:50am Section: Wednesday, May 4th, 8-11:00am

  3. •11-11:50am Section: Friday, April 29th, 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.