Biology 111
Molecules, Genes, and Cells

Spring 2006, Davidson College

MWF 10:30-11:20 in Chambers 1062
Lab Mon 1:30 or Tues 1:00 in Watson 147
Dr. Karen Hales, Dana 201A
Phone x2324,
email kahales

lab schedule
lecture schedule
Jump to Jan, Feb, Mar, Apr, May

Course objectives: Cellular and molecular biology is a vast discipline that encompasses a number of sub-fields, each of which is growing extremely rapidly. In this course, instead of trying to learn every detail, you will develop an understanding of the unifying principles of life at the molecular and cellular level through exploration of illustrative examples. You will become familiar with how scientists think in the laboratory, and you will learn to design, execute, and analyze experiments. Finally, you will practice communicating biological ideas with clarity and precision in your written and oral laboratory reports.

Textbooks:
Life: the Science of Biology, 7th edition, by Purves, Orians, Heller, and Sadava.
Study Guide and Lab Manual by Campbell, Bernd, Lom, Hales, and Wessner, Spring 2006 version
(in the bookstore).
Web reading mentioned in the study guide can be found at http://www.bio.davidson.edu/bio111 .
Additional handouts and WWW reading to be announced.

Office hours: I will always be in the office Monday 11:30-12:20 AM and Tuesday 10:00-11:00 AM. IN ADDITION, you are welcome to stop by any other time my door is open. Or, if you would like to make an appointment in advance, email me with possible times that fit your schedule (Tues mornings, Thurs afternoons, and Fri afternoons are best), and I'll respond to let you know which time I put on my calendar.

Student TA evening help sessions: Jamila Schwartz '06 will hold weekly help sessions for Bio111 students on Monday nights from 7 PM to 9 PM. Location TBA. No appointment is necessary.

Email: I will regularly send important announcements via email. You are responsible for any information/assignments/instructions I send by email, so check your messages each day.

Grading: Your final grade for the course will be calculated as follows:

Three reviews
One quiz
Lab reports, both written and oral (details)
Final exam
Participation/Daily Preparation
42% (14% each)
8%
25%
20%
5%

%
94-100
90-93.9
87-89.9
83-86.9
80-82.9
77-79.9
73-76.9
70-72.9
66-69.9
60-65.9
0-59.9
Final grade
A
A-
B+
B
B-
C+
C
C-
D+
D
F

Attendance: I will not record attendance in lecture. However, I will notice if you are not there, and it will affect your participation grade. In lab, attendance is mandatory. One unexcused absence from lab will result in a full letter grade deduction on your final course grade. A second unexcused laboratory absence will result in a failing course grade.

Participation: Your participation/daily preparation grade depends upon the extent to which you participate in classroom and laboratory dialogue over the course of the semester as well as upon your responses to verbal and written quizzing at the beginning of each class and lab.

Lectures: Powerpoint files to accompany each lecture will be posted online by the evening before each class. Follow the links directly from the lecture schedule below. Log in using the same username and password as for email, and for the domain name, type davidson. If you wish to print out the file, please download it in powerpoint format, as you can then set the printer options to include multiple slides per page. IMPORTANT NOTES: 1) I use powerpoint to outline topics and illustrate points but not to write out every idea, so viewing a powerpoint file alone will not substitute for attending lecture; 2) I recommend printing the files ahead of each class to facilitate note-taking.

Daily homework: Reading assignments to accompany each lecture are indicated below. The page numbers refer to the Study Guide. Within the Study Guide reading, you will be directed to read particular sections of your textbook. Some textbook reading is designated as "overview reading," meaning you should read for the general ideas and not for all the details. When the textbook reading is "focused reading" you should focus on specifics. Come to class prepared to answer questions on any aspect of the material from the previous couple of lectures.

Reviews: All reviews will be take-home, closed book, and closed notes unless otherwise indicated. The questions will be posted on the web (with links from the appropriate points in the schedule below), and you should view print out the test only when you are ready to start it. You may hand write or type your answers.You must work on your own and complete the review within the time specified (usually a 12 hour period). Each review is designed to be completed in roughly one to two hours. Reviews will include a combination of new questions and questions from past years. I strongly recommend using old reviews (accessible here) as a primary way to study: 2004 Rev#1, Quiz, Rev#2, Rev#3, Final exam ; 2005 Rev#1, Quiz, Rev#2, Rev#3, Final exam.

Honor Code: You are to affirm your respect for and compliance with the Davidson Honor Code on every review and paper by WRITING OUT THE ENTIRE HONOR PLEDGE and signing your name. The full Honor Pledge reads as follows: "On my honor I have neither given nor received unauthorized information regarding this work, I have followed and will continue to observe all regulations regarding it, and I am unaware of any violation of the Honor Code by others." Plagiarism is an Honor Code violation and is defined as representing another person's words and ideas as one's own. Paraphrasing (taking another person's sentences and changing a few words here and there) is NOT equivalent to writing something in your own words, and it is considered plagiarism unless proper citation is made. Please see the Davidson Department of Biology statement on plagiarism for comprehensive information.

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Lecture schedule
Date
Lecture topic
Click title download file for printing. Log in with your username, password, and davidson as the domain.
Each file will be available by the evening before that lecture.
Reading
Page numbers refer to the Study Guide unless otherwise noted. Each reading assignment ends with the study questions on the appropriate page. The reading accompanies the indicated day's lecture. Verbal or written quizzing on that material may occur on the SUBSEQUENT lecture day. Additional reading TBA.
Notes
M 1/9
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Thinking as a biologist does
pp. 1-4
Also, read the whole syllabus. You are responsible for knowing all the information/requirements detailed therein.
.
Special assignment to be fulfilled by Thursday January 19th at 4 PM: everyone must come see me in my office for a least a few minutes. If you want, you can come by in pairs or groups of three, but no more than that. Feel free to make an appointment ahead of time. This visit will be worth 3 points on the first review. The purpose is threefold: to familiarize you with the location of my office, to help me get to know you, and to show that it's not so difficult to come by for office hours.
W 1/11 Introduction to the cell
4-5
.
F 1/13 Unit 1 introduction: Your body's response to fear. What role does the liver play?
6-9
Beginning of Unit 1: Cellular communication
M 1/16 NO CLASS- Martin Luther King, Jr. Birthday . .
W 1/18 How does your liver "know" when you're scared?
9-11
.
F 1/20

Your liver's response to fear (continued)

11-16
.
M 1/23 Why does your heart pound when you're scared?
16-21
.
W 1/25 How does your heart muscle contract?
21-23
.
F 1/27
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How does your brain tell your legs to run away?
23-32
.
M 1/30

Another example of cellular communication-- how does an egg know when it's been fertilized?

32-38
.
W 2/1 Other cellular communication systems; experimental approaches used to examine cells.
38-41; Appendix, pp. AP 5-AP 8
End of Unit 1.
F 2/3 Catch-up day; question and answer session in preparation for test
Take-home review #1 (covering Unit 1 and the appendix) available today.
M 2/6 Unit 2 introduction: genetics
Mitosis and meiosis
42-44
Beginning of Unit 2: Genetics
W 2/8 Mendel and patterns of inheritance
44-48
Take-home review #1 due at class time.
F 2/10 Analyzing patterns of inheritance
44-48 again; also 94-95
.
M 2/13

Dominance and recessiveness at the molecular level; DNA structure, DNA replication

48-51
.
W 2/15 More on DNA replication; genes, chromosomes, and DNA

51-55
.
F 2/17 The genetic code; mutations and diseases
The steps of gene expression: transcription and RNA processing
55-57 (through study questions in second column)
.
M 2/20

The steps of gene expression: translation and beyond

see the translation animation

57-62
Take-home quiz (on material covered up through this morning) available today.
W 2/22 Finding the sickle cell anemia gene, then cystic fibrosis gene mapping: dihybrid crosses
62-64
.
F 2/24
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More on gene mapping: independent assortment and linkage, RFLPs and VNTRs

64-68
Take-home quiz due at class time.
M 2/27 SPRING BREAK
.
.
W 3/1 SPRING BREAK . .
F 3/2 SPRING BREAK
.
.
M 3/6 Inheritance patterns of RFLPs and VNTRs

68-71
(stop at "So, how do you locate..)
.
W 3/8

Side topic: DNA fingerprinting;
Recombination & mapping the CF gene via linkage to RFLPs and VNTRs

71-75
.
F 3/10 Mapping the CF gene via linkage to RFLPs and VNTRs, continued (no ppt)
75-77
.
M 3/13

When you've mapped a disease to a chromosomal region, how do you find the exact gene?

77-81
.
W 3/15 Confirming you've found the right gene; analyzing the defect at the molecular level

81-86
.
F 3/17 Gene therapy for CF and other diseases

86-88
.
M 3/20

Huntington Disease

88-94
End of Unit 2. Take-home review #2 available today.
W 3/22 Unit 3 intro: bioenergetics and energy conversions
Reactions of photosynthesis: why was paraquat sprayed on Mexican marijuana?
96-101


Beginning of Unit 3: Bioenergetics

F 3/24 Energy conversions in chemical reactions; role of enzymes; more on light reactions of photosynthesis
101-106
Take-home review #2 due at class time
M 3/27
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More on light reactions of photosynthesis
no powerpoint today!
   
W 3/29 NO CLASS (Dr. H at a conference)    
F 3/31 NO CLASS (Dr. H at a conference)    
M 4/3 Finishing photosynthesis: synthesizing food via the Calvin Benson cycle
106-109
  
W 4/5 Releasing energy from food: glycolysis, pyruvate oxidation, and the Krebs cycle; also fermentation

110-115
.
F 4/7 Releasing energy from food, continued. Why is cyanide a good poison?
115-119
.
M 4/10 Why update vaccinations after a flood? Anaerobic metabolism: bacteria that cause tetanus and botulism
119-122
.
W 4/12 Nitrogen metabolism: why is tofu a good source of protein?
122-124
End of Unit 3. Take-home review #3 available today. 
F 4/14 Cancer
126-130
 
M 4/17

EASTER BREAK

   
W 4/19

Cancer continued

130-138

Beginning of Unit 4: miscellaneous topics

Take-home review #3 due at class time.

F 4/21 HIV: statistics, viral anatomy, how the virus invades cells
138-145
 
M 4/24

How is HIV infection detected and treated? Could vaccines work?

145-157
W 4/26 Cloning and genetic engineering
158-162
.
F 4/28 Wrap-up; question and answer session   .
M 5/1 NO CLASS    
W 5/3 NO CLASS . .
5/5- 5/10 Self-scheduled final exam . .

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Laboratory schedule
Date
Topic
Lab manual reading
(in which you will also be referred to particular textbook pages)
Jan 9-10 Introduction to lab. Lab safety. How to measure very small volumes with a pipetman.
1-4
Jan 16-17 NO LAB (MLK day)
.
Jan 23-24 Introduction to spectrophotometry
5-15
Jan 30-31 IDH enzyme activity
16-34
Feb 6-7 Varying parameters affect IDH activity: independent experiments
Discussion on writing lab reports. See sample lab report 1, sample lab report 2 (PDF files).
35-54
also read the Biology Department statement on plagiarism
Feb 13-14 Group oral presentations on IDH lab results. Written report on the IDH experiments due at lab time.
What is your genotype? A PCR answer.
55-57 through "D1S80 factoids"
Feb 20-21 PCR results; Using microscopes; Chlamydomonas mating experiments
bottom of 57 to 60
also 61-69
Feb 27-28 SPRING BREAK
.
Mar 6-7 Chlamydomonas flagellar regeneration
70-78
Mar 13-14 Varying parameters affecting Chlamydomonas flagellar regeneration: independent experiments
79-81
Mar 20-21 A beginner's guide to statistics and graphing
**Special note: Bring potential mutagens to lab today!!
82-88
Mar 27-28 Group oral presentations on Chlamydomonas lab results. Written lab report on the Chlamydomonas results due at lab time.
.
Apr 3-4 Ames test/pouring agar plates.
89-97
Apr 10-11 Quantitating a mutagen: Ames test independent experiments.

98-102

Apr 17-18 EASTER BREAK  
Apr 24-25 Group oral presentations on Ames test results. Written report on Ames test results due at lab time. .

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More information on laboratory write-ups and presentations

Written lab reports:
You will be writing GROUP reports. For a given report, within your lab group a different person should be in charge of each of the major sections (intro, materials and methods, results, discussion). Collaborate on the title, abstract, and references. For the three reports during the semester, you must be in charge of a different section each time. At the end of each report, make a chart indicating who was the primary author and who was the primary editor of each section. See pages 34-38 of your lab manual for instructions on the organization and content of your lab reports.

In your reference section, you should cite the lab manual; you must find at least two additional print sources and one additional online source for each report. Proper formatting of citations is described at the Biology Department statement on plagiarism.

Signing the pledge on your lab report signifies (among other things) that everyone in the group has contributed his or her fair share of the work. In addition to the grading criteria listed below, correct spelling, grammar, and syntax are essential. It is in your best interest to focus my attention on the meat of your report instead of on messy mechanics.

Oral presentations:
Each group will have 15 minutes for their oral presentation, with a few additional minutes for questions afterwards. You will have access to all the audiovisual equipment in the lab, including the computer and document camera. Each presentation should be divided into four sections: Introduction, Materials and Methods, Results, and Discussion. Each member of your lab group must speak, with everyone contributing roughly equally. See pages 38-39 of the lab manual for what kinds of information to put into each section.Your classmates will critique your presentations, but their comments will not determine your grade.

Grading:
I will evaluate your written and oral reports based on the following criteria:
1. Clarity and organization of presentation
2. Whether you show an understanding of your experiments and results
3. Completeness, especially in your discussion section
4. Conciseness

Following is how the components of the lab grade are apportioned.

Each oral presentation
IDH lab report
Chlamydomonas lab report
Ames test lab report
Total lab grade
4% (12% total)
3%
4%
6%
25% of course grade

 



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© Copyright 2006 Department of Biology, Davidson College, Davidson NC 28035
last modified December 3, 2006