BIOL 113   From Cell to Organism

Spring Semester 2008

Last modified
January 31, 2008


MWF 11:10- 12:00 noon. (Period 4)
Higley Auditorium


Chris Gillen
310 Higley Hall x5399
gillenc@kenyon.edu
Office hours
: TBA


This course covers the study of life from the biochemical to the physiological levels. Much of the focus will be on cellular processes that are vital to life. The course is designed to introduce students to the process of scientific thinking as well as to the principles of biochemistry, cell biology, and physiology. We will discuss current research methods and approaches to unanswered questions. This is one of the courses in Biology at the foundation level, the others are BIOL109, 110, 112 and 114. There are NO prerequisites, and enrollment is open to both majors and non-majors. BIOL 113 provides a background for more advanced courses in cellular and organismal biology.

Students who are comfortable with their high-school biology and chemistry will find this course an appropriate challenge as a first course in biology. Those who are less comfortable may find BIOL 112 more amenable as a first course in biology.

Class Resources and Required Reading--color coded in Syllabus

Biological Science 2nd edition, by Scott Freeman, 2005. If specific page numbers or sections follow a chapter then you are only responsible for those particular pages or sections.

Reserve reading, Articles available on Moodle to on-campus viewers.


How to do well in this class:

Responsibilities of each student

  • Check your e-mail daily. I often 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 available on Moodle. Old exams and quizzes as well as supplemental reading will also be available.

Other opportunities for help

  • Attend review sessions. Review sessions will be scheduled throughout the semester. There is no set format for the reviews; I will be available to respond to student questions.
  • 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
  • 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.
  • 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, review sessions, and e-mail are the best ways to make contact with me.
    • 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. 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.

Grading: Over many years, the range of average grades on exams in this course is around a 79% and the average grade in the course is B-. A "curve" is needed to translate the raw exam grades into appropriate letter grades. The curve in this course will work in the following way. I will set a grade range for the curve before the exam is administered based on the average exam grades from prior years. Thus, you will not be competing among yourselves, but rather against a fixed curve. If everyone performs very well, then many high grades will be assigned. This policy is intended to encourage cooperation among students in the course, rather than competition. I reserve the right to alter the curve in a way that benefits the entire class, but I will not alter the curve to lower grades.

65% - 4 exams.
25% - 5 quizzes and 2 reading responses. Some quizzes may be take-home. The lowest quiz or response score will be dropped.
10% - class attendance and participation

Class attendance and participation: Attendance is expected, and will be recorded. Excessive unexcused absences will not be allowed. I will initiate expulsion proceeding for students acquiring more than 6 unexcused absences. Excused absences will be granted for students on the excused absence list and for varsity athletics. Other reasonable excuses will be considered, so long as they are provided before class. Attendance and class participation will count toward the final grade. Grades may be reduced by a third of a letter grade for each set of 3 unexcused absences.

Exams and quizzes: There will be 4 exams, each covering the material in that section of the course, including what is covered in the lecture just prior to the exam. Exam dates may be moved forward or back. Timing of exams and quizzes will only be changed with at least one week notice. The fourth exam is held during the scheduled final exam period, the other exams are held during the normal class period (or take home). All 4 exams will count equally in computing the final grade. There will also be 5 quizzes and two response papers; some may be take-home assignments. The material in this course is cumulative. Although each exam will focus on the most recent material, you will be held responsible for major themes we have already covered in the class. If you fail to show up for an exam or quiz at the scheduled time without my prior approval (or an absence excused by the deans) then you will get a zero for that exam or quiz. If you have an excused absence that will conflict with an exam or quiz (e.g. varsity athletic event) you must contact me one week before quiz or exam is scheduled to arrange for an alternate time. Ordinarily, this will be before the rest of the class takes the quiz or exam.

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.

COURSE SCHEDULE
DATE TOPIC Required Reading
Pink = Textbook
Blue = Online and/or Moodle
  Section 1: Macromolecules and cell structure  
1/14

What is life?
Cell video - BioVisions at Harvard Univ

Chapter 1 (through section 1.3)
This syllabus

1/16

Atoms, water

Ch. 2 (sec. 2.1, 2.2, 2.5)
Water and extraterrestrial life

1/18 Free energy, redox reactions Ch. 2 (sec. 2.3, 2.4)
1/21 Amino acids, protein structure QUIZ 1
Ch. 3 (sec. 3.1, 3.2, 3.3), Table 2.1 pg. 38
1/23

Catalysis

Ch. 3 (sec. 3.4), Ch. 4 (sec. 4.1)

1/25

Nucleic acids, RNA world

Ch. 4 (sec. 4.2, 4.3, 4.4)
Jump-Starting a Cellular World
1/28
Membranes I

Ch. 6 (sec. 6.1, 6.2, pp116-117)

1/30 Prokaryotic cell, Eukaryotic cell I QUIZ 2

Ch. 7 (sec. 7.1) Ch. 28 ( pp. 615-617, 619)
2/1 Eukaryotic cell II

Ch. 7 (sec 7.2, 7.3)

2/4 Eukaryotic cell III

Ch. 7 (sec 7.4)
Cilium

2/6 EXAM 1
 
  Section 2: Chemical and electrical signaling  
2/8
Viruses, HIV
Ch. 34 (through pg. 792). Essay pg. 335
HIV Resistance in Monkeys

2/11

Cell signaling- overview
Chapter 47 (47.1, 47.4),
Chapter 8 (section 8.3)
2/13
Animal hormones - glucose regulation
Chapter 43 (sec. 43.4)
Diabetes - islet transplant
2/15

Plant light sensing

Ch. 38 (pg 872, 876-878), Ch. 39 (39.1, 39.2)
2/18 Membranes I I - Ion transport
Ch. 6 (6.3, 6.4); Ch. 45 (45.1);
Box 36.3 pg. 845

Sodium-glucose transport
2/20
Neurons QUIZ 3
Ch. 45 (45.2, 45.3)
2/22

Nervous and endocrine system

Ch. 45 (sec 45.4), Ch. 47 (47.2, 47.3)
2/25
Sensory systems Ch. 46 (sec 46.1, 46.4); Essay pg. 101
Dietary fat receptors
2/27

Muscle and Exercise Movie from Vale lab

Ch. 46(sec 46.5)
2/29 EXAM 2
Sample exam questions
 
3/1-3/16
BREAK  
  Section 3: Cell Respiration and photosynthesis  

3/17

Cell respiration overview; carbohydrates, ATP, mitochodria
Ch. 5, Ch. 2 (sec 2.4); Ch. 9 (sec. 9.1), Ch. 28 ( pp. 615-617, 619)
3/19

Metabolic pathways, enzymes, glycolysis

Ch. 3 (sec 3.4), Ch. 9 (9.2)

3/21
Glycolysis and fermentation
Ch. 9 (sec. 9.2, 9.5)
Glycolysis pathway
3/24

Krebs cycle and oxidative phosphorylation QUIZ 4

Ch. 9 (sec. 9.3, 9.4)

3/26

Oxidative phosphorylation

Ch. 27 (pp. 594 metabolic diversity-598).
Ch. 9 (sec 9.6)
ATPase movie

3/28
Photosynthesis overview
Ch. 10 (sec 10.1)
3/31 Light reactions, ATP synthase QUIZ 5 Ch. 10 (sec. 10.2, 10.3)
4/2 Light-independent reactions, C3 and C4 plants Ch. 10 (10.4 to end)
4/4 Plant nutrition, Nitrogen fixation Ch. 37; pg. 586 Nitrogen cycle
nitrogen reduction
4/7 EXAM 3  
  Section 4: Plant and animal function  
4/9 Plant diversity and structure Ch. 29 (pp. 648-650);
Ch. 35 (pp. 804-5, section 35.2)
4/11 Transport in plants

Ch. 36, pp.113-115 osmosis

4/14
Plant strategies for environmental challenges
Boxes 36.1 and 36.2 pp. 832-833
4/16 Temperature regulation Chapter 41 (section 41.3 to end)
4/18
Respiration Chapter 44 (sections 44.1 and 2)
4/21 Special topic: Discontinuous gas exchange
Reading response 1 due (Take-home, assignment on Moodle)
DGC article: Hetz and Bradley
DGC review: Bradley
4/23
Circulation I
Chapter 44 (section 44.3)
4/25
Circulation I I Chapter 44 (section 44.4)
4/28 Water and electrolyte balance Chapter 42 (sections 42.1, 2 and 3)
4/30 The kidney Ch. 42 (sec 42.4), pg. 1084 How are hormones involved in homeostasis.
5/2 Special topic: Aquaporins
Reading response 2 due (Take-home, assignment on Moodle)
Aquaporin review: Nielsen et al.
Aquaporin article: Rojek et al.
5/8 Final EXAM 4 - May 8th, 1:30 PM
(Focuses on material since Exam 3)