Biology Dept
Kenyon College
BIOL 113   From Cell to Organism

Fall Semester 2008 (Sec. 1)

UNDER CONSTRUCTION!

Last modified 12/08/2008
Latest update always overrides all previous versions (electronic and print).


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



Dr. Kathy Gillen

312 Higley Hall x 5395

gillenk@kenyon.edu
Office hours:

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


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 3rd edition, by Scott Freeman, 2008

Moodle: Articles and problems found on class moodle site

 



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 class Moodle site. These slide shows will be available before class. You can print out an abbreviated format to bring to class to help you with note taking. Old exams and quizzes as well as supplemental reading can also be found in the class folder.

  • Other opportunities for help
    Attend weekly review sessions. Review sessions will be held on Sunday evenings, 6:30- 7:30 p.m. in Fischman 103 unless otherwise indicated. There is no set format for these informal, optional review sessions; I will mainly respond to student questions.


    Visit the Math and Science Skills Center. Our course specific tutor is Jay Galbraith, but many other tutors at the center are also available to help with biology.

    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, the weekly review session, and e-mail are the best ways to make contact with me. You may call me at home before 9:00 p.m. I am also usually available before class, either in my office or the classroom.
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.

70% - 4 exams. The top three will count 20% each, the lowest one 10%
20% - 5 quizzes. Some quizzes may be take-home. The lowest quiz score will be dropped.
5% - class attendance and participation
5%- cumulative part of final

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. The last exam will contain a few cumulative questions that will tie together themes we have seen throughout the semester. Exam dates may be moved forward or back. Timing of exams and quizzes will only be changed with at least one week notice and only after consultation with the class. The fourth exam is held during the scheduled final exam period, the other exams are held during the normal class period (or take home). There will also be 5 quizzes; some may be take-home assignments. You will always be held responsible for major themes we have 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. Students with disabilities who will be taking this course and may need academic
accommodations are encouraged to make an appointment to see me as soon as possible.
Also, you are required to register for support services with the Office of Disability
Services in the Old Bank Building. Please contact Erin Salva at 5453 or email
salvae@kenyon.edu. All information and documentation of disability is confidential. Logistical details of any approved accomodation (e.g. extended exam time) must be arranged with the instructor in advance.

Reading listed as on the Moodle page can be found at the class Moodle site. If specific page
numbers or sections follow a chapter then you are only responsible for those particular pages or sections.

COURSE SCHEDULE
DATE TOPIC & WEBNOTES links READING -- Third edition READING - Second edition
8/29 f
What is life?

The pillars of life (moodle)
Chapter 1 (pages 1-4, 6-10)

The pillars of life (moodle)
Chapter 1 (through section 1.3)

9/1
labor day

Prokaryotic cell structure
Classification

 

Ch. 7 (up to page 122)
Ch 28 (pp 566-567 including Table 28.1)
pg. 320 "The Central Dogma"
Bioskills 2 (B 3-5)

Ch. 7 (up to page 131)
Table 27.2 (pg. 593)
Box 28.1 (pg. 614); pg. 334

9/3 Atoms, water Ch. 2 (sec. 2.1, 2.2, 2.4)
Bioskills 4 (B 8-9)
Ch. 2 (sec. 2.1, 2.2, 2.5)
9/5 Free energy Ch. 2 (sec. 2.3) Ch. 2 (sec. 2.3)
9/8 m Origin of life, amino acids QUIZ 1
Interview with Stanley Miller

Ch. 3 (pp. 43-52, 58-60)
pg. 64-65 Was the first living entity a protein?

Ch. 3 (sec. 3.1, 3.2), Table 2.1 pg. 38;
pp. 63-65, pg. 70 Was the first living entity a protein?

9/10

Origin of life, RNA world

Chapter 4 Chapter 4
9/12
Membranes I

Ch. 6 ( pp. 95-109)

Ch. 6 ( pp103-117)

9/15 m Eukaryotic cell I QUIZ 2
Ch. 7 (pp. 122-134), Ch. 29 (603-609) Ch. 7 (pp. 131-142), Ch. 28 (615-619, skip box 28.2)
9/17 Eukaryotic cell II Ch. 7 (sec 7.4) Ch. 7 (sec 7.4)
9/19 Viruses, HIV paper: Novel anti-HIV approach Ch. 35 (through pg. 782) Ch. 34 (through pg. 792). Essay pg. 335
9/22 m EXAM 1
9/24
Protein folding and structure
Last day to choose Pass/D/Fail option
Ch. 3 (sec 3.4), pH pg. 29-30, bioskills 5 B10
pg. 346 (post-translational modifications),
pg. 63-64 enzyme function
Ch. 3 (sec 3.3), pH pg. 41-42; pg. 354,
pg. 68- enzyme function

9/26

Cell signalling- overview
Ch. 47 (pp.1054-1062, sections 47.3 and 47.4), Chapter 8 (section 8.3)
Chapter 47 (1076-1083, 1088-1096),
Chapter 8 (section 8.3)
9/29 m
Protein targeting pulse chase animation (optional)
Ch. 7 (sec. 7.2, 7.3)
Ch. 7 (sec. 7.2, 7.3)
10/1

Animal hormones- glucose regulation

Chapter 43 (sec. 43.4) Chapter 43 (sec. 43.4)
10/3 Plant light sensing QUIZ 3 take home due 10/8 Ch. 39 (pp. 857-865) Ch. 38 (pg 872, 876 phototropins-877 ), Ch. 39 (39.1, 39.2)
10/6 m
Membranes I I
Ch. 6 (review 6.3, pp 110-116); Ch. 45 (45.1);
Box 37.3 pg. 832; box 42.1 pg. 940
Ch. 6 (6.3, pp 118-123); Ch. 45 (45.1);
Box 36.3 pg. 845
10/8

Neurons quiz 3 due

Ch. 45 (45.2, 45.3) Ch. 45 (45.2, 45.3)
10/10
October reading day
10/13 m Nervous system Ch. 45 (sec 45.4) Ch. 45 (sec 45.4)
10/15 Sensory systems Nobel prize for olfactory receptors Ch. 46 (sec 46.1, 46.2, 46.4) Ch. 46 (sec 46.1, 46.2, 46.4); Essay pg. 101
10/17
Muscle click on movies, myosin-based motility
Ch. 46(sec 46.5)
Ch. 46(sec 46.5)

10/20 m

EXAM 2- bring cheat sheet. 8.5 x 11 inches
10/22

Cell respiration overview; carbohydrates, ATP, redox

Ch. 5, Ch. 9 (pp. 170- 179)

Ch. 5, Ch. 2 (sec 2.4); Ch. 9 (sec. 9.1)

10/24

Metabolic pathways, enzymes

Ch. 3 (pg. 60 -63) last day for WP

Ch. 3 (sec 3.4)

10/27 m
Glycolysis and fermentation
Ch. 9 (sec. 9.3, 9.7)
Ch. 9 (sec. 9.2, 9.5)
10/29

Krebs cycles and oxidative phosphorylation

Ch. 9 (sec. 9.4, 9.5, 9.6)

Ch. 9 (sec. 9.3, 9.4)

10/31

Oxidative phosphorylation QUIZ 4

Ch. 28 (pp. 579 metabolic diversity-583).

Ch. 27 (pp. 594 metabolic diversity-598).

11/3 m
Photosynthesis overview
Ch. 10 (pp. 198-201)
Ch. 10 (sec 10.1)
11/5 Light reactions optional animation Ch. 10 (sec. 10.2, 10.3) Ch. 10 (sec. 10.2, 10.3)
11/7 Calvin cycle, C3 and C4 plants Ch. 10 (10.4 to end) Ch. 10 (10.4 to end)
11/10 m Summary of metabolism Ch. 9 (sec 9.8), How do small cells...(pp 571-572)
Integration paper
Ch. 9 (sec 9.6) Integration paper
11/12
EXAM 3- may bring one-sided 8.5 x 11cheat sheet
11/14 Plant nutrition, nitrogen fixation Ch. 38 Ch. 37; pg. 586 Nitrogen cycle
11/17 m Transport in plants Ch. 37 (sections 1, 2 and 4)
review osmosis pg. 106
Ch. 36, pp.113-115 osmosis
11/19 Plant strategies for environmental challenges

Ch. 37 (sec. 37.3, Boxes 37.1 and 37.2)

Boxes 36.1 and 36.2 pp. 832-833

11/21

Viruses, HIV paper: Novel anti-HIV approach Ch. 35 (through pg. 782) Ch. 34 (through pg. 792). Essay pg. 335
11/24-28
Thanksgiving break
12/1 m Temperature regulation
Quiz 5 handed out
Chapter 41 (pp. 913-914, section 41.3 to end) Chapter 41 (section 41.3 to end)
12/3 Respiration Chapter 44 (sections 44.1, 2 and 44.3) Chapter 44 (sections 44.1 and 2)
12/5
Circulation I QUIZ 5 due
Chapter 44 (section 44.4)
Chapter 44 (section 44.3)
12/8 m Circulation I I Chapter 44 (section 44.5) Chapter 44 (section 44.4)
12/10 Water and electrolyte balance Chapter 42 (sections 42.1, 2 and 3) Chapter 42 (sections 42.1, 2 and 3)
12/12 The kidney optional animation
Information on ADH function
Ch. 42 (sec 42.4) Ch. 42 (sec 42.4). pg. 1084 - how are hormones involved in homeostasis.
12/15

EXAM 4 6:30 p.m.

two- sided 8.5 x 11 cheat sheet allowed.

Exam 4 Tomsich 101 6:30 p.m.

Exam 4 - one hour

Cumulative test- one hour