Biology 111
Molecules, Genes, and Cells

Spring 2014, Davidson College

MWF 9:30-10:20 in Chambers 1003
Lab Mon 1:30 or Tues 1:40 in Watson 147
Dr. Karen Hales
Dana 201A, x2324

lecture schedule
Jump to Jan, Feb, Mar, Apr

Science news web sites:
Science Daily
Scientific American
New Scientist
New York Times Science Times

lab schedule

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.

Life: the Science of Biology, 9th edition, by Sadava, Heller, Orians, Purves, and Hillis.
Study Guide and Lab Manual by Campbell, Lom, Hales, Bernd, Sarafova, and Wessner, Spring 2014 version (in the bookstore).
A Short Guide to Writing About Biology, 8th edition, by Jan Pechenik.
Web reading mentioned in the study guide can be found at
Additional handouts and WWW reading to be announced.

Office hours: Email me in advance to make an appointment for any mutually acceptable time; list three possible dates/times in your email and I'll get back to you. Or, you are welcome to stop by any time my door is open, which is most of the time when I am not in class or other meetings. Generally, right after class or lab, Tuesday mornings, and Wednesday afternoons are good time frames for appointments.

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 short test
Lab reports, both written and oral (details)
Final exam
Participation and daily preparation, both lecture and lab
36% (12% each)

Final grade

: I will not record attendance in lecture. However, I 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 written and verbal quizzing at the beginning of class and lab.

Classroom etiquette: Please do not get up and leave the classroom in the middle of class unless it is a true emergency. Use the restroom before coming to class. Set phones so that they do not vibrate or make any sound, and put them away.

Policy on recording of class: Davidson College policy prohibits audio and video recording of classes by students without permission of the instructor. I will consider permission requests on a case-by-case basis. For students with a disability, permission will always be granted when the accommodations authorized by the Dean of Students Office include recording. Authorized recordings are for the sole use of the individual student and may not be reproduced, sold, posted online, or otherwise distributed.

Laptops: You may not use a laptop in class unless you have requested and received an exception. You must have sufficient justification to receive permission. Continued permission depends on your complete avoidance of email, social media, and other surfing during class.

Lectures: PowerPoint files to accompany each lecture will be posted online by the evening before each class. I use PowerPoint only to provide illustrations and outline topics but not to write out every idea; viewing a PowerPoint file therefore does **not** substitute for attending lecture. Click the link from the lecture schedule below to download the file. Log in using the same information as for email, and for the domain name type davidson. To print the file, please first set printer options to include multiple slides per page.

Daily homework: Reading assignments to complete before 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 only. When the textbook reading is designated as "focused," you should read carefully for detail. Come to class prepared to answer questions on any aspect of the material from the previous lecture. There will be regular quizzes at the beginning of class on the previous day's material; quiz grades make up a portion of the "participation and daily preparation" portion of your grade.

Reviews: Reviews will be take-home, closed book, and closed notes. They will be posted on the web from links on this syllabus, and a review is typically due on the second class meeting after is posted. You may view/print a review only when you are ready to start it. You can choose whether to hand write or type your answers; however, since I sometimes ask for word counts, typing is more efficient. Each review is designed to be completed in roughly one to two hours, but you will have eight waking hours from when you start until when you must finish.The final exam will be offered through the Exam Center in Chambers, and it will be designed to take two to three hours. I strongly recommend using old reviews as a primary way to study. Old reviews are here: Rev#1, Short Test, Rev#2, Rev#3, Final exam.

Penalty for late assignments: Ten percent per day or part thereof. The full ten percent penalty applies starting at the beginning of each day that the assignment is late; for example, an assignment that is one hour late will have a ten percent penalty applied.

Math and Science Center: The Math and Science Center (MSC) offers free assistance to students in all areas of math and science, with a focus on the introductory courses. Trained and highly qualified peers hold one-on-one and small-group tutoring sessions on a drop-in basis or by appointment, as well as timely recap sessions ahead of scheduled reviews. Emphasis is placed on thinking critically, understanding concepts, making connections, and communicating effectively, not just getting correct answers.  In addition, students can start or join a study group and use the MSC as a group or individual study space.  The MSC is located in the Center for Teaching and Learning in the library.  Drop-in hours are Sunday through Thursday, 8-11 PM, and Sunday, Tuesday, Thursday 4-6 PM, beginning Tuesday January 21. Appointments are available at other times. See the website for hours or contact Dr. Mark Barsoum (mabarsoum or 704-894-2796).

Honor Code: You are to affirm your respect for and compliance with the Davidson Honor Code on every review and paper. 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


Lecture topic
Links will become active by the evening before each class.

Click lecture title to download powerpoint file for printing. Use email credentials to log in. You may need to type davidson\username. Please conserve paper by printing double sided, with multiple slides per page.

Page numbers refer to the Study Guide (SG) unless otherwise noted. SG assignments normally end with the study questions on the appropriate page. Reading assignments accompany the indicated day's lecture. Quizzing on that material may occur on the subsequent lecture day. Additional reading TBA.
M 1/13
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Intro to the course; cells; thinking like a biologist

Read the whole syllabus. You are responsible for knowing all the information/requirements detailed therein.

Special assignment to be fulfilled by the afternoon of Thursday January 23rd: everyone must come see me in my office for a least a few minutes. If you want, you may come by in pairs or groups of three, but no more than that. It's best to make an appointment ahead of time, but you are welcome to drop by any time I am in the office. This visit will be worth 3 points on the first review. A visit must take place for me to record your grade on the first review. The purpose is to familiarize you with the location of my office and to help me get to know you.
W 1/15 Unit 1 introduction: Your body's cellular and molecular response to fear. What role does the liver play?
1-5 (Note that all Study Guide readings will refer you to more extensive readings in the textbook)
Beginning of Unit 1: Cellular communication
F 1/17 How does your liver "know" when you're scared?
M 1/20 Dr. Martin Luther King, Jr. holiday--NO CLASS    
W 1/22 Connecting epinephrine to glucose release in the liver: enzyme cascades and second messengers
F 1/24

Why does your heart pound harder when you're scared?

M 1/27 How does your heart muscle contract? 18-20  
W 1/29 How does your brain tell your legs to run away?
F 1/31
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Another example of cellular communication-- how does an egg know when it's been fertilized?
M 2/3 Cellular communication in bacteria Watch the first ~18 minutes of Part 1 of this lecture by Bonnie Bassler and write a paragraph summarizing what you learned. Don't worry if you don't understand all the terminology--just do your best. Note that you can also get this video free through iTunes. End of Unit 1.
W 2/5 Unit 2 introduction: genetics
Mitosis and meiosis
Review #1 available today. Beginning of Unit 2: Genetics
F 2/7 Mendel and his monohybrid crosses
M 2/10 Analyzing patterns of inheritance
41-45 again; also 87-88
Review #1 due at class time.
W 2/12

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

F 2/14 DNA replication    
M 2/17 Genes and chromosomes
The genetic code; mutations and diseases
The steps of gene expression: transcription

48-54 (through study questions in second column)

W 2/19

The steps of gene expression: RNA processing, translation and beyond


also see one translation animation and another translation animation here

F 2/21 Finding the sickle cell anemia gene, then cystic fibrosis gene mapping: dihybrid crosses 55-58 again; also 59-62 Short test available today.
M 2/24 More on gene mapping: independent assortment and linkage, RFLPs and VNTRs 62-66  
W 2/26

Side topic: DNA fingerprinting
Inheritance patterns of RFLPs and VNTRs
66-68 (stop at "So, how do you locate..") Short test due at class time.
F 2/28 Recombination & mapping the CF gene via linkage to RFLPs and VNTRs
M 3/3
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M 3/10

Mapping the CF gene via linkage to RFLPs and VNTRs, continued. We'll do an in-class exercise using this file.

W 3/12 When you've mapped a disease to a chromosomal region, how do you find the exact gene? 74-76  
F 3/14 Confirming you've found the right gene; analyzing the defect at the molecular level 76-81  
M 3/17

Gene therapy for CF and other diseases; Huntington Disease

81-83; skim 83-86  
W 3/19 Catch up day; question and answer session   End of Unit 2.Review #2 available today.
F 3/21 Unit 3 intro: bioenergetics and energy conversions
Reactions of photosynthesis: why was paraquat sprayed on Mexican marijuana?
89-94 Beginning of Unit 3: Bioenergetics
M 3/24 Energy conversions in chemical reactions; role of enzymes; more on light reactions of photosynthesis
photosynthesis light reactions animation

Review #2 due at class time.

W 3/26 No class--Dr. H at a conference    
F 3/28 No class--Dr. H at a conference


M 3/31 More on light reactions of photosynthesis
no powerpoint today!

W 4/2
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Finishing photosynthesis: synthesizing food via the Calvin Benson cycle
F 4/4 Releasing energy from food: glycolysis, pyruvate oxidation, and the Krebs cycle; also fermentation 103-108  
M 4/7 Releasing energy from food, continued. Why is cyanide a good poison?
W 4/9 Why update vaccinations after a flood? Anaerobic metabolism: bacteria that cause tetanus and botulism
F 4/11 Nitrogen metabolism: why is tofu a good source of protein?
115-117 End of Unit 3. Review #3 available today.
M 4/14 Cancer
Beginning of Unit 4: miscellaneous topics
W 4/16

Cancer continued

Review #3 due at class time.
F 4/18 HIV: statistics, viral anatomy, how the virus invades cells 131-139  


W 4/23 How is HIV infection detected and treated? Could vaccines work?

HIV life cycle video is here
F 4/25 No class--Dr. H off campus    
M 4/28 Cloning and genetic engineering
W 4/30 More on cloning and genetic engineering (no new ppt)    
F 5/2 Even more on cloning and genetic engineering; wrap-up; course evaluations    
M 5/5 Optional question and answer session. Directed evolution lab reports due Wednesday. Please email the file. Put your last name at the beginning of the file title (NOT the subject line of the email, but the title of the file you attach).    
5/9- 5/14 Self-scheduled final exam    

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Laboratory schedule

Page numbers refer to the Lab Manual unless otherwise noted. In the Lab Manual, you will also be referred to particular textbook pages.
Jan 13-14

Preliminaries: Introduction to lab. Lab safety. How to measure very small volumes with a pipetman.

Main activity: Introduction to spectrophotometry

Jan 20-21 No lab--Martin Luther King, Jr. holiday  
Jan 27-28

IDH enzyme activity

After experiments are done: TOSLS assessment tool
BRING A LAPTOP/TABLET if you have one.

Feb 3-4 Parameters that affect IDH activity: independent experiments


Also, in Pechenik, read "Introduction and General Rules"

Feb 10-11

Introduction to data presentation

For reference: sample lab report 1, sample lab report 2 (PDF files).

44-48, also Appendices C and D

Read the Pechenik chapter entitled "Preparing Oral Presentations"

Read the Pechenik chapter entitled "Writing Laboratory and other Research Reports"

Read the Biology Department statement on plagiarism

Feb 17-18

Group oral presentations on IDH lab results.
(Written report on the IDH experiments due at lab time.)
What is your genotype? A PCR answer.

PCR animations are here and here.

49-51 through "D1S80 factoids"

Feb 24-25

PCR results; Using microscopes; introduction to Chlamydomonas

51-top of 62
Mar 10-11 Chlamydomonas flagellar regeneration
Mar 17-18 Varying parameters affecting Chlamydomonas flagellar regeneration: independent experiments
Mar 24-25 A beginner's guide to statistics and graphing


Skim the Pechenik chapter entitled "Reading and Writing about Statistical Analyses," focusing on the information related to the lab manual material.

Read the Pechenik chapter on preparing Lab Poster presentations. Poster template file is here.

Mar 31-Apr 1 Group oral presentations on Chlamydomonas lab results.
(Written lab report on the Chlamydomonas experiments due at lab time.
Apr 7-8 Monday lab: We will meet briefly for the last of four oral presentations from last week.
Tuesday lab: No lab--Dr. H at trustee meetings

READ AHEAD so that you are totally prepared for next week:

1. Lab manual file (not included in the bound study guide/lab manual). There are links/directions for further reading within the document.

2. Visual Guide to the Procedure

Apr 14-15 Directed evolution

As indicated last week, the main lab file is here, with additional reading described within.

Study the Visual Guide to the Procedure. Since you will be performing many steps on your own time, you must be completely clear on every aspect of the experiment.

Before lab April 28-29 you must do all the additional reading, answer questions 1-14 from the lab manual (listed under week 2), and email me your answers. Put your last name at the beginning of the Word file.

Apr 21-22 No lab on Mon/Tues for Easter Break, but Wednesday to Saturday you will continue the Directed Evolution lab
Continue with additional reading, and email me your responses to the questions from the lab manual. Put your last name at the beginning of the Word file.
Apr 28-29 Directed evolution final week
Read data analysis portion of lab manual file before coming to lab.
May 5-6

No lab.

Directed evolution lab reports due  Wednesday May 7. Please email the file. Put your last name at the beginning of the file title (NOT the subject line of the email, but the title of the file you attach).

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More information on laboratory write-ups and presentations

Written lab reports:
You will be writing group reports for the first two lab report assignments. For a given report, a different person within your lab group should be in charge of each of the major sections (introduction, materials and methods, results, discussion). Your steps are as follows:
1. Each group member completes a first draft of a particular section.
2. A different group member provides detailed editing feedback for the section. Editing involves more than fixing typos; rework the order of ideas, the language, and the logic to achieve maximal precision, completeness, and clarity.
3. Everyone in the group reads through the whole report and provides further feedback to tie the work together.
4. Everyone works together to construct the title, abstract, references, and chart indicating who who was the primary author and who was the primary editor of each section.

You must be in charge of a different section and must edit a different section for the second lab report.

See the appropriate appendix in your Study Guide & Lab Manual, as well as the appropriate Pechenik chapter, for instructions on the organization and content of your lab reports. Pay special notice to this additional requirement regarding the reference section: you should cite the lab manual, AND you must find at least three additional relevant sources, two of which must be peer reviewed. Proper formatting of citations is described at the Biology Department statement on plagiarism.

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.

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.

Third lab report: At the end of the semester you will prepare an individual write-up on the directed evolution experiments.

Oral presentations:
Oral presentations will accompany the first two lab reports. 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 the appropriate appendix in your Study Guide & 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 rubric for oral presentations:
Organization 5 pts
Clarity 5 pts
Accuracy 5 pts
Introduction 5 pts
Materials and Methods 5 pts
Results 5 pts
Discussion 5 pts
Answering questions at the end 5 pts

Grading rubric for 1st/2nd/3rd written lab reports (each is worth a different total; see below):
Title/authors/affiliation 2/3/4 pts
Abstract 4/5/5 pts
Introduction 7/11/12 pts
Methods 5/8/10 pts
Results 7/10/12 pts
Discussion/conclusions/future directions 7/11/12 pts
References and acknowledgments 3/4/5 pts
Quality/organization of writing 5/8/10 pts

The lab grades are apportioned as follows:

IDH lab report
Chlamydomonas lab report
Directed evolution lab report
Total lab grade
oral component
25% of course grade
written component
7% written report


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last modified May 2, 2014