Biology Dept
Kenyon College
KAP   Genes and Development
Fall Section Spring Section 1 Spring Section 2

Spring Semester 2007(Sec. 2)

Last modified 03/23/2007
Latest update always overrides all previous versions (electronic and print).

MWF 10:10-11:00 PM (Period 4)
Higley Auditorium

Dr. Wade Powell

FSH 202, x5396

Office hours:
MW, 11-1; T, 4-5; R, 10-11
and by appointment

This course introduces the mechanisms of heredity, the expression of genetic information, and the genetic control of development. Special emphasis is placed on genetic and biochemical approaches toward delineating fundamental cellular and developmental processes.

Class Resources and Required Reading--color coded in Syllabus

Biological Science 2nd edition, by Scott Freeman, 2005
Biological Science CD, by Scott Freeman, 2005
Webnotes: Articles and problems linked to webnotes, or handed out in class.

Genetics programs: Download herePermission to distribute fromD. K. Schmidel.

  Flowers, Mendelian inheritance of traits

  Plasmid, restriction mapping of a recombinant plasmid

Further reading (optional): Cartoon Guide to Genetics, by Gonick and Wheelis.

Visitors: Please report corrections to course directors.

Linked articles: Only viewed at Kenyon.

How to do well in this course.
  • Attend EVERY class. 100% attendance is expected.
  • Be prepared: Complete all assigned reading by the date on the syllabus (i.e. before class).
  • Participate actively in class discussion. Your silence tells me that your understanding of the topic is complete, and I am moving too slowly through the material. Your questions direct me to revisit difficult concepts. Your insightful comments demonstrate hard work and commitment to learning biology. Thorough preparation and class participation are viewed very favorably in determination of final grades.
  • For additional practice, do the problems and tutorials (found in web notes, text, and text CD) promptly.  These are good preparation for the in-class or take-home quizzes that happen most Fridays.
  • Attend review sessions held before tests. These optional sessions offer you another chance to ask your own questions and review difficult topics.
  • Review your chemistry. This course presumes a thorough knowledge of at least high school-level chemistry. Get comfortable with electrons, hydrogen bonds, and the important functional groups. The aspects of protein structure and function introduced in BIOL 113 also play a heavy role in understanding the material in this course.
  • Stay in contact with your instructor. I read e-mail several times daily. I also send e-mails to the class distribution list. Please feel free to contact me by e-mail, and be sure to read the ones I send you. You are also invited to meet with me personally during my office hours or another scheduled appointment.

Grades.  Grades are based on:

  • 20% on ten (10) Friday Quizzes.
    • Brief quizzes during class or longer, graded homework exercises.
    • Please note: Make-up quizzes will not be possible. However, to accomodate absences due tofamily crisis, athletic contests, performances, field trips, job interviews, academic overloads, illnesses, senioritis, general malaise, or any other imaginable conflict, you are required to submit only eight (8) scores for calculating the quiz average. Choose the quizzes you want to take; I do not require any notification, excuse, or permission for missing quizzes. If you take more than eight quizzes, only the eight highest scores will be used.
  • 70% on Exams:
    • Four exams will be held during the semester.
    • The first three exams (in class) cover material from the immediately preceeding portion of the course; each contributes 15% to the final grade.
    • The fourth exam (25%) will be in two parts. 60% of the questions will address the most recently covered material (Part IV: Developmental Biology). Additional questions will be more comprehensive or integrative in nature, drawing explicitly on material presented in other parts of the course. Exam 4 will take place during the college's final examination period (Monday May 7, 8:30 AM)
  • 10% on class attendance and participation.
    • Attendance will be recorded, and 100% attendance is expected. In addition, active, vocal participation is expected from all members of the class and will be a primary determinant of the class participation grade. To participate fully in class, you must thoughtfully read and annotate the assigned material before each meeting.
    • In accordance with college policy, athletes and others with excused absences related to college-sponsored activities must notify the instructor of any conflicts with the course during the first week of the semester. Please note that it is the responsibility of the individual student--NOT the Dean of Students, team, club, coach, athetlics department or faculty sponsor--to notify the instructor of conflicts and seek a means of resolution. Timely communication averts nearly all potential problems.

Academic Honesty.  Do not lie, cheat, or plagiarize. This class will follow the official Kenyon College position on academic honesty. Please review and observe the official College policy on academic honesty. Specific instructions on take-home quizzes or other unique assignments will be provided.

Special Needs. College policy provides for reasonable accomodations for documented physical, psychological or learning disabilities that may impact your ability to participate fully in the course. Please speak with me and with Erin Salva, Coordinator of Disability Services (PBX 5453; salvae@kenyon.edu). All information and documentation of disability is confidential. Please see the Disability Services web site for more information. Logistical details of any approved accommodation (e.g. extended exam time) must be arranged with the instructor at least 3 days in advance.


DATE TOPIC & WEBNOTES links READING -- Color coded
Part I: Heritability of Genotype and Phenotype
Jan 15
Course introduction; history of genetics; genes and genomes.

Jan 17

Chromosome structure

Ch. 18 pp. 383-386; Ch. 3, p 130 (nucleoid) and p. 133 (nucleus)

Jan 19 Cell Division QUIZ 1 Ch. 11 pp. 227-238; Ch. 12 pp. 248-267; Web tutorials 11.1 and 12.1
Jan 22 Mendelian inheritance Ch. 13 pp. 269-281; Web tutorials 13.1 and 13.2; Dihybrid Cross; Download Flowers Software
Jan 24

Sex linked traits and pedigree analysis

Ch. 13 pp. 281-282, 294-297; Sex-linked inheritance; X and Y

Jan 26

Recombination and gene mapping;
QUIZ 2: Take-home; due on Monday.

Ch. 13 pp 283-287; Linkage
Jan 29
Gene product interactions; non-Mendelian genetics

Ch. 13 pp. 287-293

Jan 31 Genetics Catch up
More practice problems
Feb 2 DNA as the genetic material Ch. 14 pp. 303-307
Feb 5 EXAM 1  
Part II: Genes and Gene Expression
Feb 7 DNA structure;
practice DNA bases
Ch. 4 pp. 74-83; Web tutorial 4.1 Classic papers
Feb 9
DNA replication; Quiz 3
Ch. 14 pp. 307-318; Ch. 7, p. 140 (Box 7.1); Web tutorial 14.1

Feb 12

How Genes Work:  One Gene, One Enzyme; m RNA synthesis
Ch. 4 pp. 83-85; Ch. 15 pp. 325-328, 334-336; Ch. 16 pp. 338-341; Web tutorials 15.1 and 16.1; Beadle and Tatum animation
Feb 14
Genetic Code
Ch. 15 pp. 328-333; Web tutorial 15.2
Feb 16


Ch. 3 pp. 48-56; Ch. 16 pp. 345-355; Web tutorial 16.2
Feb 19 Eukaryotic transcription and splicing
PLOS Biology: choosing splice sites
Ch. 16 pp. 342-345
Splice mechanism: Robinson (2006) PLOS Biology
Feb 21
DNA mutation and repair
Ch. 12 pp. 264-266; Ch. 14 pp. 318-323; Ch. 16 pp. 355-359; Web tutorial 12.2
Feb 23

Applying Central Dogma Concepts I:  Regulation of the eukaryotic cell cycle. QUIZ 5

Ch. 11 pp. 227-232, 238-245; Web tutorial 11.1; Cell cycle game
Feb 26
Ch. 18 pp. 395-398; Smoking and Lung Cancer
Feb 28 Applying Central Dogma Concepts II: Immune System and antibody production Ch. 49 pp. 1124-1132
Mar 2 EXAM 2 -------
Mar 3-18
No Class Meetings
Part III: Regulation of gene expression

Mar 19

Problems and Approaches I:
1. PCR: Making lots of DNA from just a little; 2. How to determine and annotate DNA sequence
Ch. 19 pp. 408-411, Ch. 20 pp. 426-439, Web tutorials 19.2 and 20.1; PCR animation
Mar 21

Problems and Approaches II: Customizing DNA molecules. Recombinant DNA, transgenic organisms, and gene therapy.

Ch. 4 pg. 78; Ch. 19 pp. 401-407, 411-424; Web tutorial 19.1; Restriction enzyme animation; Plasmid cloning animation; Plasmid (downloaded with Flowers); puzzler

Mar 23

Problems and Approaches III: Measuring Gene Expression: northern blots, RT-PCR, western blots, QUIZ 6

Ch. 19 pp. 412-413;

Mar 26
(Dr. S)
cDNA microarrays;
Ch. 20 pp. 439-443; DNA Chip; New Yorker Article.
Mar 28
(Dr. S)

Prokaryotic Gene Expression I:  Operons

Ch. 17 pp. 362-379

Mar 30

Prokaryotic Gene Expression II:  Operon Analysis; Regulons, Promoters QUIZ 7

Ch. 17 pp. 362-379; Web tutorial 17.1

Apr 2
Eukaryotic Gene Expression I:  Transcriptional Activation.
Ch. 18 pp. 382-390
Apr 4 Eukaryotic Gene Expression II:  Classes and functions of transcription factors; Analysis of regulatory motifs Ch. 18 pp. 386-391; Web tutorial 18.1
Apr 6

Eukaryotic Gene Expression III:
Nucleosomes and transcription
post-transcriptional regulation

Ch. 18 pp. 384-386; 392-395
Apr 9 Junk DNA? non-coding RNAs and gene expression
RNAi movie
RNAi and riboswitches: Gibbs (2003) Scientific American article (local access only)
Apr 11
Part IV: Developmental Biology
Apr 13 Overview of Developmental Processes; Gene Expression and Development Ch. 21 pp. 461-467; Ch. 22 pp. 481-484
Apr 16 Microbial development and more microbial development; Heterocysts
Apr 18 Fertilization and Cleavage in animals

Ch. 21 pp. 446-458

Apr 20

Cell Movement and Gastrulation; QUIZ 9
Ch. 8, 159-168; Ch. 21 pp. 458-461; Web tutorials 21.1 and 21.2
Apr 23
Embryonic Stem Cells and Human Cloning;
Ch. 21 pp. 466-467; Ch 22 pp. 484 and 489
Apr 25 Pattern formation in Animals Ch. 21 pp. 461, 463-464; Ch. 22 pp. 469-478; Web tutorial 22.1; Animated tutorial
Apr 27 Gene Duplication and Molecular Evolution: Hox Genes QUIZ 10 Ch. 22 pp. 476-478; Ch. 26 pp. 569-572. C. elegans, Twinned genes
April 30
Cell Differentiation: Neurulation and organogenesis. Ch. 22 pp. 484-489
May 2
Plant embryogenesis; meristems
Pattern Formation in Plants: Arabidopsis flowering
Ch. 21 pp. 452-453, 462-463; Ch. 22 pp. 478-481
May 4 Catch-up; Course Evaluation ------------
May 7 EXAM 4 8:30 AM!