Biology Dept
Kenyon College
BIOL 116   Information in Living Systems

Fall Semester 2009

UNDER CONSTRUCTION!

Last modified 11/30/2009
Latest update always overrides all previous versions (electronic and print).


MWF 10:10- 11:00 a.m. (Period 3)



Dr. Kathy Gillen

Higley 312 pbx 5395
gillenk@kenyon.edu
Office hours:

M, W, F 7:45- 8:00, 9- 10:00; 11:00-11:45 a.m.
Also by appointment; please e-mail me to schedule.


 

Course outline

How is information generated, transmitted, stored, and maintained in biological systems? The endeavor to understand the flow of biological information represents a fundamental undertaking of the life sciences. This introductory course examines the mechanisms of heredity, the replication and expression of genetic information, and the function of genes in the process of evolution, with an emphasis on the tools of genetics and molecular biology to address research questions in these areas. Majors and nonmajors may enroll. Biology majors should take this class prior to the junior year. Prerequisites: BIOL 115 or permission of instructor.
Class Resources and Required Reading--color coded in Syllabus

Biological Science 3rd edition, by Scott Freeman, 2008 (also used in bio 115). There is a copy of this text on reserve in the library.

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

  Flowers, Mendelian inheritance of traits

  Additional readings will be available via Moodle.

 



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 and participate. Exams are based on the material we cover in lecture. Lectures will cover some material not contained in the readings. Please participate in class discussions if you have something to contribute. Your silence tells me that you understand the topic completely and that I am moving too slowly through the material. Your questions direct me to revisit concepts. I realize that the CDC recommends that those with flu-like symptoms impose self-isolation. If you're ill please stay home, but do send me an e-mail. See the attendance policy below for more information.

    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.

    Get comfortable with chemistry. This course presumes a thorough knowledge of at least high school level chemistry. If needed, review electrons, hydrogen bonds, and important functional groups. The aspects of protein structure and function introduced in BIOL 115 also play a heavy role in understanding the material in this course.

  • 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 lead tutor is Mark Sullivan (sullivanm). His hours are Tuesday evening 8-10, but many other tutors at other hours can also help you with biology.

    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.



    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. I will announce location and time 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, those with flu-like symptoms, (illnesses other than flu that keep you from class should 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.

    H1N1 flu: This flu strain is highly contagious and the CDC recommends that those experiencing flu-like symptoms impose self-isolation. Please stay in your room if you are ill; it is not worth exposing the entire class; you wouldn't like it if someone with the flu came to class and exposed you so please use the Golden Rule here. Fortunately the flu seems to run its course in 5 days so you should not miss more than three lectures. If you have flu-like symptoms send me an e-mail. I will not hold the absences against you and I will give you time to make up any missed work. Try to do what reading you feel up to in your room and we can make arrangements for missed work on a case-by-case basis.

Grading scale 90-100 A range, 79-89 B range, 67-78 C range, 56-66 D range, 55 or below F.

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.

COURSE SCHEDULE
DATE TOPIC & WEBNOTES links READING second edition-- Color coded Reading third edition
Aug. 31 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).

Sep. 2 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)

Sep.4
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
Sep. 7 M

DNA as the genetic material; centrifugation
transformation, conjugation, transduction

Quiz 1

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
Sep. 9
W
DNA replication, telomeres
Paper discussion

Ch. 14 pp. 310-318 tissue engineering paper
Guided reading for paper on Moodle

Ch. 14 (sections 3 and 4) tissue engineering paper
Guided reading for paper on Moodle
Sep.11
F

Mitosis
Quiz 2 take home due Monday

Ch. 11 (start through 11.2)
Also readings on Moodle with guided reading.
Ch. 11 (start through 11.2)
Also readings on Moodle with guided reading.
Sep. 14 M
Meiosis animation optional karyotyping link
Quiz 2 due back

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

Ch. 12 (all except section 12.3), Fig 26.8 pg. 535
Sep. 16 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)
Sep. 18 F Sex linked traits, recombination
Quiz 3 take home due Monday
Ch. 13 pp 281-286; Linkage  More Practice Ch. 13 pp 276-281; Linkage  More Practice
Sep. 21 M Gene mapping, pedigrees Ch. 13 (sec. 13.6), Ch. 19 (sec. 19.3) Ch. 13 (sec. 13.6), Ch. 19 (sec. 19.4)
Sep. 23 W Exam 1
Bring Klinger paper, 8.5 x 11 cheat sheet and calculator. Bring Klinger paper, 8.5 x 11 cheat sheet and calculator.
Sep. 25 F
Non-Mendelian genetics (optional)
epistasis site
Ch. 13 (sec. 13.5) Download Flowers(optional)
Ch. 13 (sec. 13.5) Download Flowers(optional)

Sep. 28 M

How Genes Work
E. coli
as model organism (optional)
Nobel Prize for cracking genetic code (optional)
Chapter 15, Box 27.1 pg 588
Beadle and Tatum animation- click on test tubes (optional)
Chapter 15, Box 28.1 pg 576
Beadle and Tatum animation- click on test tubes
(optional)
Sep. 30 W
RNA, transcription
Ch. 4 (sec. 4.3); Ch 16 pp. 338-341
Ch. 4 (sec. 4.3); Ch 16 (through section 16.1)
Oct. 2
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 (optional)
Ch. 16 (section 16.2); pg. 426-427 (Why do humans have so few genes?)
Nobel Prize for split genes (optional)
Oct. 5 Translation
Quiz 4 due
Ch. 16 (sections 16.3, .4, .5) Essay on antibiotics pg.358-9 Ch. 16 (sections 16.3, .4, .5)
Oct. 7
DNA mutation and repair
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)
If needed review Ch. 3 sec. 3.4 on protein structure.
Oct. 9

DNA sequencing
PCR
Plasmid cloning
Quiz 5 handed out

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).
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).
Oct. 12
No class- reading day
.
Oct. 14 W

Approaches II: DNA sequencing PCR
Quiz 5 due

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

Summary Table, pg. 406-407.

Oct. 16
F

Darwin and evidence for evolution Chapter 1, sec. 1.2
Chapter 23, pg. 494-503
Chapter 1, sec. 1.2
Ch. 24 pg. 481-489
Oct. 19 M
natural selection Chapter 23, pg. 503-end Ch. 24 pg. 490-end
Oct. 21
W
EXAM 2
Bring code with notes on back.
Bring code with notes on back. Also calculator and 8.5 x 11 with notes. Bring code with notes on back. Also calculator and 8.5 x 11 with notes.
Oct. 23 F
natural selection Chapter 23, pg. 503-end Ch. 24 pg. 490-end
Oct. 26
M
Evolutionary Processes Ch. 24(sections 24.1 and 24.3)
Bring a calculator to class.
Ch. 25 (sections 25.1 and 25.3)
Bring a calculator to class.
Oct. 28
W
Evolutionary Processes
Quiz 6 in class
Ch. 24(sections 24.2 to end)
Quiz 6 in class
Ch. 25 (sections 25.2, 25.4, 25.5)
Quiz 6 in class
Oct. 30
F
Evolutionary Processes Ch. 24(sections 24.3 to end) Ch. 25 (sections 25.5, 25.6)
Nov. 2
M
Speciation Ch. 25 Chapter 1 (sec. 1.3)
Ch. 26 (start through 26.2)
Nov. 4
W
Speciation
Quiz 7 handed out
Ch. 25 Ch. 26 (26.3 through end)
Nov. 6
F

Prokaryotic Gene Expression I:  Operons

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

Ch. 17 (Intro, sections .1, .2 and .3)
Nov. 9

M
Prokaryotic Gene Expression II
Quiz 7due
Ch. 17 (section 17.4) operon practice
Ch. 17 (section 17.4) operon practice
Nov. 11

DNA binding proteins

Ch. 17 (section 17.5) footprinting animation

Ch. 17 (section 17.5) footprinting animation
Nov. 13 EXAM 3    
Nov. 16

Eukaryotic Gene Expression I:  Transcriptional Activation.

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

Ch. 18 (pp. 370-371, 18.3, 18.4)
Ch. 21 (section 21.2)

Nov. 18
Eukaryotic Gene Expression II:  regulating protein expression
Ch. 18 (18.5)
Ch. 18 (18.5)
Nov. 20 Approaches:
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)

Quiz 8 in class
Box 19.1 pp. 398-399;
Ch. 20 (section 20.4)
DNA Chip (optional)

Quiz 8 in class
Nov 23-27 Thanksgiving break    
Nov. 30 Approaches continued
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)
NOTE THAT WE ARE AHEAD OF SCHEDULE AND WILL START MATERIAL A DAY EARLIER THAN POSTED.

Nov. 30/ Dec. 2

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

Dec. 2 and 4

gene therapy
changing the information

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)
Dec. 7 Phylogenies Chapter 1, sec. 1.3
Chapter 26
Chapter 1, sec. 1.3
Bioskills 2, Chapter 27
Dec. 9 Phylogenies/evo-devo
Chapter 26 Chapter 27
class evaluations
Dec. 11 evo-devo readings on Moodle
Ch. 22 (sec. 22.1); pg. 714

readings on Moodle
Ch. 21 (sec. 21.3 to end); pg. 703
Chapter 20 (pg. 424-427)


Dec. 14 factors influencing phenotype Quiz 10 due Quiz 10 due
readings on Moodle

 

 

Exam 4 December 18th 1:30 p.m. December 18th 1:30 p.m.