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

Spring Semester 2009 (Sec. 1)


Last modified 4/08/2009
Latest update always overrides all previous versions (electronic and print).

MWF 8:10- 9:00 a.m. (Period 1)
Tomsich 101

Dr. Kathy Gillen

Higley 312 pbx 5395
Office hours:

M, W, F 7:30- 8:00, 9- 11:30 a.m.

Linked articles: Only viewed at Kenyon.
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 OR Biological Science 3rd edition, by Scott Freeman, 2008

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

  Flowers, Mendelian inheritance of traits

  Plasmid, restriction mapping of a recombinant plasmid


How to do well in this class:
  • Responsibilities of each student
  • Check your e-mail daily. Occasionally I may send the class notices via e-mail.

    Stay in contact with the instructor. If you have a question, problem, or are concerned with how you are doing in this course, contact me by e-mail, phone, during office hours or in class. If at any time you feel that you do not have the proper background to understand the material that is being presented, please let me know.

    Attend class. Exams are based on the material we cover in lecture. Lectures will cover some material not contained in the readings. See the attendance policy below.

    Learn the vocabulary. You can not understand complex biological concepts if you are not familiar with the words that are being used. Definitions can be found in the glossary of your textbook.

    Read the textbook assignments before coming to class.

    Review textbook assignments and your notes after each class to consolidate material. Slide shows used in class will be on the moodle web page, usually before class. You can print out an abbreviated format to bring to class to help you with note taking.

  • Other opportunities for help
    Connect with your peers. Students at all levels benefit from group study sessions. If you understand the material, you will gain a deeper understanding of the material by discussing it with your peers. If you are unclear about something, your peers may be able to explain it in a different way than it was presented in the lecture

    Visit the Math and Science Skills Center. Our course specific tutor is Nick Severyn (e-mail: severynn), but many other tutors at the center are also available to help with biology. Nick works at the MSSC on Tuesday evenings, 7-9 p.m.

    The textbook CD and website (www.prenhall.com/freeman) are outstanding resources. Tutorials and self-quizzes are also available to help you review the material.

    Kenyon Biology 114 Web site: The following is a good site to check if you need more help, would like a different perspective from the text, or would like links additional information: http://biology.kenyon.edu/courses/biol114/index.html. Clicking on topic index leads to listing of available modules.

    Look over the old exams and quizzes on the moodle site.

    Sunday night review sessions. In addition to office hours, I will be available most Sunday evenings, 6:30- 7:30 p.m. in FSH 103. I will announce these in class.

    Contact the instructor. In addition to the formal opportunities for help listed above, there are many other mechanisms for accessing help in this course. Please contact me if you have any questions or concerns.

How to contact the instructor: Office hours, the weekly review session, and e-mail are the best ways to make contact with me. Also, you may call me at home before 9:00 p.m.

E-mail. I check my e-mail routinely during the normal working day, and can respond to many questions very quickly. E-mail is also a good first contact to make; we can arrange an in-person meeting if necessary. Please note that I generally will not check my e-mail in the evening, please do not expect rapid responses to e-mails sent in the evening.
Office hours. Come see me during my office hours. Please know that you need not have a very specific question or problem in order to come to office hours. Sometimes the most important visits are ones where we discuss general strategies for doing well in the course.

  • Grades are based on:
    70% - Four fifty-minute exams.
    There will be 4 fifty-minute exams, each covering the material in that section of the course, including what is covered in the lecture just prior to the exam. Although none of the exams is strictly cumulative, you will be held responsible for major themes and fundamental concepts we have already covered in the class. The top three exams count as 20%, the lowest at 10%.

    25% - ten quizzes
    There will be ten pop quizzes given throughout the semester. Some of these will be take home. The two lowest grades will be dropped before computing the final quiz average.
    5% - class attendance and participation
    Attendance is expected, and will be recorded. Excessive unexcused absences will not be allowed. Excused absences will be granted for students on the excused absence list, with sicknesses that can be verified through the health center, and for excused varsity athletic contests. Other reasonable absences may be excused provided that they are cleared by me before hand. Grades may be reduced by a third of a letter grade for each set of 3 unexcused absences.
    Optional cumulative final: During the final period students may choose to take an optional cumulative exam. This can be used to replace one of the other four exam scores. Only the top 4 scores will count towards the final grade and the lowest one will still count 10%.


NOTE ON EXAMS AND QUIZZES: Exams or quizzes missed due to unexcused absences (e.g. my alarm didn't go off) will count as a zero. Exams missed due to an excused absence can be made up. It is the responsibility of the student to make arrangements to do so with the instructor. When an exam conflicts with a scheduled excusable event, the student must contact the instructor one week before the exam is scheduled to arrange for an alternate time. Ordinarily, this will be before the rest of the class takes the exam. Therefore, athletes should check the syllabus and their athletic contest schedules closely and make note of any conflicts.

There will be no make up quizzes. If you miss a quiz due to an excused absence, it will not count as a zero and the two lowest grades of the remaining quizzes will be dropped.


Academic Honesty.  Do not lie, cheat, or plagiarize. This class will follow the official Kenyon College position on academic honesty. It is your responsibility to review and observe the official College policy on academic honesty.

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 accomodation (e.g. extended exam time) must be arranged with the instructor in advance.

If particular pages or a section number follow a chapter you are responsible for just those pages or sections.

DATE TOPIC & WEBNOTES links READING second edition-- Color coded Reading third edition
Jan 12 M
history of genetics; Central Dogma
nucleotides (optional)

The Central Dogma Ch. 15 (section 15.3, pp. 334-336)

The Central Dogma Ch. 15 (pp. 320-322).

Jan 14 W

DNA structure(optional), Chromosomes
practice DNA bases (optional)

Ch. 4 (4.1, 4.2); pg. 130; essay pg. 87
pg 133 (the nucleus)

Ch. 4 (4.1, 4.2); pg. 120-121;
Box 4.1 pg. 75
pg 124 (the nucleus)
Jan 16 F histone code: Gel electrophoresis Ch. 18 (18.2), Box 4.1 pg. 78, box 19.2 pg. 412 Ch. 18 (18.2), Bioskills 7 pg B12-B13, box 19.1 pg. 398
Jan 19 M DNA as the genetic material; centrifugation
transformation, conjugation, transduction
Ch. 14 (303-310), Box 7.1 pg. 140, Box 19.1 pg. 404
Ch. 14 (295-302), Box 7.1 pg. 133, Box 12.2 pg. 256
Jan 21 W DNA replication, telomeres
Paper discussion

Ch. 14 pp. 310-318 tissue engineering paper

Ch. 14 (sections 3 and 4) tissue engineering paper
Jan 23 F

Quiz 2 likely

Ch. 11 through section 11.2 Ch. 11 through section 11.2
Jan 26 M
Meiosis animation optional karyotyping link

Ch. 12 (all except section 12.3), Fig 25.9 pg. 547

Ch. 12 (all except section 12.3), Fig 26.8 pg. 535
Jan 28 W Mendelian inheritance
Ch. 13 pp. 269-281; Optional Dihybrid Cross (#'s 1-10) Ch. 13 pp. 265-276; Bioskills 9 Optional Dihybrid Cross (#'s 1-10)
Jan. 30 F Sex linked traits, recombination
Ch. 13 pp 281-286; Linkage  More Practice Ch. 13 pp 276-281; Linkage  More Practice
Feb 2 M Gene mapping, pedigrees Ch. 13 (sec. 13.6), Ch. 19 (sec. 19.3) Ch. 13 (sec. 13.6), Ch. 19 (sec. 19.4)
Feb 4 W Exam 1
Feb 6 F
Non-Mendelian genetics (optional)
epistasis site
Ch. 13 (sec. 13.5) Download Flowers(optional)
Ch. 13 (sec. 13.5) Download Flowers(optional)

Feb 9 M

How Genes Work E. coli
Nobel Prize for cracking genetic code
Chapter 15, Box 27.1 pg 588
Beadle and Tatum animation- click on test tubes
Chapter 15, Box 28.1 pg 576
Beadle and Tatum animation- click on test tubes
Feb 11 W
RNA, transcription
Ch. 4 (sec. 4.3); Ch 16 pp. 338-341
Ch. 4 (sec. 4.3); Ch 16 pp. 329 and section 16.1
Feb 13 F

Eukaryotic transcription and splicing
PLOS article- Alternate mRNA splicing: control by combination

Ch. 16 (section 16.2); pg. 438-439 (gene # and alternate splicing)
Nobel Prize for split genes
Ch. 16 (section 16.2); pg. 426-427 (Why do humans have so few genes?)
Nobel Prize for split genes
Feb 16 Translation Ch. 16 (sections 16.3, .4, .5) Essay on antiobiotics pg.358-9 Ch. 16 (sections 16.3, .4, .5)
Feb 18
DNA mutation and repair
Quiz 5 in class
Ch. 14 (sec. 14.5, 14.6); Ch. 16 (sec. 16.6); essay pg. 535
Ch. 14 (sec. 14.5); Ch. 16 (sec. 16.6)
Feb 20

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

Ch. 11(sec. 11.3,11.4)Cell cycle game -optional
Ch. 11(sec. 11.3,11.4)Cell cycle game -optional
Feb 23 m
X-inactivation , paper on Wilms' tumor
Ch. 18 (18.6); Smoking and Lung Cancer (optional) essay pg. 322
Ch. 18 (18.6); Smoking and Lung Cancer (optional).
Feb 25 w Applying Central Dogma Concepts II: Immune System and antibody production Ch. 49 (sec 49.2) Ch. 49 (sec 49.2)
Feb 27 f EXAM 2 Bring 8.5 x 11 cheat sheet and cell growth pathway. Code provided May start exam at 8:00 a.m May start exam at 8:00 a.m
Mar 2-13
No Class Meetings
No Class Meetings

Mar 16 m

Approaches I: DNA cloning and restriction enzymes
1. PCR: Making lots of DNA from just a little;

Ch. 19 (intro, sec. 19.1, .2)
Plasmid (downloaded with Flowers)

Techniques page if you're interested (for PCR animation click on techniques, amplifying, PCR).
Ch. 19 (intro, sec. 19.1, .2, .3)
Plasmid (downloaded with Flowers)

Techniques page if you're interested (for PCR animation click on techniques, amplifying, PCR).
Mar 18 w

Approaches II: DNA sequencing PCR

Ch. 20 (Pg. 427, recent technological advances, fig. 20.1)

Summary Table, pg. 406-407.
Mar 20 f

Prokaryotic Gene Expression I:  Operons

Ch. 17 (Intro, sections .1, .2 and .3)

Ch. 17 (Intro, sections .1, .2 and .3)
Mar 23 m
Prokaryotic Gene Expression II
Ch. 17 (section 17.4) operon practice
Ch. 17 (section 17.4) operon practice
Mar 25 w

DNA binding proteins

Ch. 17 (section 17.5) footprinting animation

Ch. 17 (section 17.5) footprinting animation
Mar 27 f

Eukaryotic Gene Expression I:  Transcriptional Activation.

Ch. 18 (pp. 382-383, 18.3, 18.4)

Ch. 18 (pp. 370-371, 18.3, 18.4)

Mar 30 m
Eukaryotic Gene Expression II:  regulating protein expression
Ch. 18 (18.5)
Ch. 18 (18.5)
Apr 1 w Problems and Approaches III: Measuring Gene Expression: Northern blots, RT-PCR, cDNA microarrays; Western blots Box 19.2 pp. 412-413; Ch. 20 pp. 440 DNA microarrays
DNA Chip (optional)
Box 19.1 pp. 398-399;
Ch. 20 (section 20.4)
DNA Chip (optional)
Apr 3 f Special topic: RNAi animation and RNAi Nobel

RNAi and riboswitches: Gibbs (2003) Scientific American article (local access only)

p-body articles on moodle site

RNAi and riboswitches: Gibbs (2003) Scientific American article (local access only)
pp. 381-382
p-body articles on moodle site
Apr 6 m gene therapy
Quiz 8 due in class
Chap 19 (sec. 19.4) zinc finger nuclease article on moodle
knock out mice (optional)
Chap 19 (sec. 19.5) zinc finger nuclease article on moodle
knock out mice (optional)
Apr 8 w
EXAM 3 may bring 8.5 x 11 one sided cheat sheet May start exam at 8:00 a.m. May start exam at 8:00 a.m.
Apr 10 f
Overview of Developmental Processes; Model organisms (click on techniques, then model organisms)
Ch. 21(pp. 446-447); Ch. 22 ( pp. 469-470, sec. 22.3) pg 757 box 33.1, pg. 725 box 32.1
Ch. 21(intro and sections 21.1 and 21.2); pg. 713 box 33.1
Apr 13 m Fertilization and Cleavage in animals (optional) Ch. 21(pp. 447- 458) Ch. 22 (pp. 451- 459)
Apr 15 w

Cell Movement and Gastrulation (optional)

Ch. 21 (pp. 458-461) Gastrulation movies(optional) Ch. 22 (sec. 22.4); pg. 695

Apr 17 f

Pattern formation in Animals

Ch. 21 (pp. 463-466); Ch 22 (sec. 22.1)

Ch. 21 (section 21.3)
Apr 20 m
Illustrated Nobel prize for Hox Genes and early embryogenesis in Drosophila
Ch. 26 (sec. 26.3); Box 22.2 (pg. 482) , Twinned genes  Ch. 21 (section 21.4)
Ch. 27 (pg. 556, 557);
Twinned genes
Apr 22 w

Cell Differentiation: myogenesis

Ch. 22 (section 22.4),
Ch 8 pp 166-168
miRNAs in myogenesis (optional)
Ch. 22 (section 22.5),
Ch 8 (section 8.2)
miRNAs in myogenesis (optional)
Apr 24 f Plant embryogenesis;
Pattern Formation in Plants: Arabidopsis flowering
Ch. 21 pp. (462-463); Ch. 22 (sec. 22.2) Box 29.1 pg. 643. Skim ch 40 (section 40.2 - end). Chapter 23
Box 30.1 pg. 631.
Skim ch 40 (section 40.2 - end).
Apr 27 m
C. elegans
Box 22.4 pg. 486 and animation  Box 21.1 pg. 437 and animation 
Apr 29 w
Embryonic Stem Cells and
Cloning fact sheet
Essay pg. 466, Box 22.3 pg. 484, essay pg.489
Box 21.2 pg. 439
May 1 Make up or special topic ------------  
May 4 Monday Exam 4 at 6:30 p.m. Also optional final Exam 4 in TOM 101 (not optional)
Optional cumulative final
Exam 4 in TOM 101 (not optional)
Optional cumulative final