Chambers 1003: MWF 8:30-9:20am and
Watson 147: M 1:30-4:20 OR T 8:15-10:55
Information about Bio 111: Molecules, Genes and Cells This course is designed to provide the background necessary to tackle the 'big questions' in biology. We will delve into what is currently known about the components of the cell, the methods used to study them, and the vocabulary used to talk about them. From those broad statements you can tell we will be covering a large amount of information. This course is an introduction to topics that are covered in upper level courses. To make this information more manageable the course provides information on a 'need-to-know' basis. Just as you would not read every history book to find out about a single English rebellion--we will not march through the textbook.
Each unit provides unifying questions and the Study Guide, webreadings, text, and study questions are designed to provide the background information necessary for the class to discuss the 'big question'.
Instructor
Office
Office Phone
Email
Office Hours
Dr. Karen Bernd
Watson 289
704-894-2889 kabernd@davidson.edu
W 9:30-11 and XYZ
Contact me electronically or in person. Try to head off mild confusion before it becomes paralyzing panic. Remember that we have three hours a week in lab. Incubation periods or early wrap up are times you should use to ask questions. Use the time wisely and stay on top of the material. If you find you are having trouble, contact me!
Reading material/ Textbooks
1)WWW readings appear as links from the Study Guide Heading Section of the BIO111 homepage ( http://www.bio.davidson.edu/courses/Bio111/Bio111.html
)
2) Additional animations are found on the website that accompanies our text
( http://www.thelifewire.com , Choose edition 9 links)
From the bookstore:
3) Sadava, Orians, Heller, and Purves : Life the Science of Biology. 9th edition (Bat on cover) [e versions also available through thelifewire.com]
4) Davidson Biology Department, Study Guide, and Lab Manual SPRING 2015 version 
 5)
Pechenik, J A short guide to writing about Biology. 6th or 7th edition (this book is considered a reference source for all biology courses, buy it now and keep it)
The sources listed above (including the web ones) all contain required reading. Be sure that you have access to each. The 8th editions of the Sadava et al. text are still 'around'.
They have different page numbers and less up to date content so using them will require more effort on your part. Also Sadava et al. is used for Bio112 and Pechenik is considered

the style and writing guide for all Bio courses, unless told otherwise (like the citation style specified below). Get the books now and keep them for later.
Schedules 
 Class readings and assignments and Lab readings and assignments are found here and in separate files on Moodle (for easy access and printing 
 The due dates listed will not change. Put them on your calendar now and plan time for assignments accordingly.
Information about Bio 111: Molecules, Genes and Cells Bio111 is designed to provide the background necessary to tackle the 'big questions' in biology. We will delve into what is currently known about the components of the cell, the methods used to study them, and the vocabulary used to talk about them. From those broad statements you can tell we will be covering a large amount of information. This course is an introduction to topics that are covered in upper level courses. To make this information more manageable the course provides information on a 'need-to-know' basis. Just as you would not read every history book to find out about a single English rebellion--we will not march through the textbook.
Each unit provides unifying questions and the Study Guide, webreadings, text, and study questions are designed to provide the background information necessary for the class to discuss the 'big question'.
There are two types of reading for this class. Both types of readings include information from the text and from WWWeb sources. Overview Readings : skim through this quickly to get an idea of the overall topic and to provide background information. Focused Readings : readings that should more deeply read and understood. Your Study Guide will serve to bring these readings together and will provide the basis for our class discussions (so the study guide is a focused reading). Prepare responses to Study Guide questions before class. They will form the basis of our discussion We will discuss all of the topics and questions if you ask about them. The more you ask questions the more this class is tailored to you.
Assignments: All assignments emphasize the fact that knowledge is not useful if you cannot convey what you have learned. Class and lab discussions, reviews, and lab articles require that you practice communication skills and apply and synthesize new information. Check the class and laboratory syllabus now for due dates and times and notice that they often occur
outside of class meeting times and are all turned in through Moodle. The assignment
dates will not change. These are the classes’ ‘job interviews’, ‘game days’, or
‘performances’—put them in your schedule now.
And plan for them like you do for other events where the schedule is set. Do not cut it so close that a computer glitch costs you.
Plan to turn in an assignment with time to spare as late assignments are penalized .
Subtract 5% for 1min late and an additional 5% for every 60min after that. (Why? Because the course builds and the goal is that you learn from the assignments and the feedback provided. Late assignments mean that the materials cannot be reviewed, cannot be returned for the whole class so the whole class loses time (very unfair to those who managed their time). 'Later' in your life job and funding applications, patient diagnoses, departmental/divisional reports, etc. require you meet deadlines with more than 'points lost' as consequences.
Developing time management and balancing skills now will be one of the best things you can get out of your
education.)
You are responsible for all assigned reading, class material, and laboratory material. The 3 reviews, 2 quizzes and final exam will cover material assigned during that 'unit'. Like the

questions in the Study Guide, the reviews will require synthesis and application of information. Samples of reviews I have given are available on my course homepage. I strongly encourage you
to look at the 'spots' right now and work through the questions as we work through the unit. All reviews are take-home, closed-book and to be completed by yourself alone under the honor
code. I require answers to be typed and in the form of complete sentences.
Laboratory: Lab groups (of 4) will be set up during the first week of lab and will be maintained through the semester. You may not miss lab. It should go without saying that you
will not schedule other activities during any lab hours. Since you will be working in groups, labs cannot be 'made-up' during another lab period. This is where you get to practice science by forming hypotheses and determining the best way to test the hypotheses' validity. The lab units introduce background and procedures, require that you design experiments to further your understanding of the topic and then conclude with a report of your findings in oral or written form. The laboratory portion of the course grade will come from your work with your lab group (2%), and your writing assignments (4 and 6%) for a total of 12% of your final grade. Be sure to read the grading rubric . It makes sense to know the expectations so you can fulfill them.
Written work
Be certain that you understand the rules and boundaries of group work and source citation. If you have any questions ASK BEFORE HANDING ANYTHING IN.
Plagiarism is wrong and has severe consequences. The Davidson College Biology
Department’s statement on plagiarism is found at: http://www.bio.davidson.edu
/dept/plagiarism.html and is the guide for this course. You are responsible for reading and following the guide.
This course follows the citation style seen in the journal Cell. You must follow both the 'in text' and bibliographic citation style described here http://www.cell.com/authors .
Bibliographic Information taken from The Cell Journal Website
(http://www.cell.com/authors ) NOTE nothing is indented and pages of entire article are given not just the page where the information was. Look at a print copy (Library basement stacks) to see the rules in action.
References should include only articles that are published or in press.
Unpublished data, submitted manuscripts Abstracts, and personal communications should be cited within the text only. Personal communication should be documented by a letter of permission. Submitted articles should be cited as unpublished data, data not shown, or personal communication. Note: "et al." should only be used after 10 authors. Please use the following style for references:
REFERENCE STYLE—note punctuation AND that nothing is indented.
Sondheimer, N., and Lindquist, S. (2000). Rnq1: an epigenetic modifier of protein function in yeast. Mol. Cell 5, 163-172. ( This is the style for an article in a journal whether you accessed it as a pdf file online or held the paper in your hands )
King, S.M. (2003). Dynein motors: Structure, mechanochemistry and regulation. In
Molecular Motors, M. Schliwa, ed. (Weinheim, Germany: Wiley-VCH Verlag GmbH), pp.
45–78. ( This is the style for an article found within a larger book where different people

wrote different chapters and the listed editors compiled and have their names on the cover
Cowan, W.M., Jessell, T.M., and Zipursky, S.L. (1997). Molecular and Cellular Approaches to
Neural Development (New York: Oxford University Press). ( This is the style for an entire book where the names on the cover wrote the whole thing (ex. your Sadava et al. textbook))
A Grading Rubric for lab articles is found on the Moodle site
Additional Resources: I am available for additional help during scheduled lab times if labwork concludes early, during office hours, or by email sent when the question occurs to you. Written assignments require that you do outside research and reading. There are thousands of resources available in the library (you know-- those books and journals on paper) in addition to all of those found online. To help you find the right resources I advise beginning early and remembering that we have great reference librarians in Little Library.
Your lab and classmates are also valuable resources. I strongly encourage study groups where members work together to determine explanations for study guide questions and discuss the reading and lab assignments. These groups work best if they meet regularly. Do not wait until the assignment looms.
The Math & 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. Located in the Center for Teaching & Learning
(CTL) on the first floor of the College Library, drop-in hours are Sunday through Thursday,
8-11 PM, and Sunday, Tuesday, Thursday, 4-6 PM, beginning Tuesday, January 20.
Appointments are available at other times. Visit http://sites.davidson.edu/ctl or contact Dr.
Mark Barsoum (mabarsoum or ext. 2796), or more information, Note: all services are free
Extra Credit Summaries This course has the breadth of an introductory course but it cannot cover every topic. To facilitate exposure to more topics and current findings I offer extra credit for summaries of science departmental seminars (Biology, Chemistry, Physics,
Smith Lecture, Spring Research Symposium). To earn these points you must attend the seminar (most of which last approximately one hour) and within 72hours of the event you must
a) email me a one to two paragraph summary relaying your impressions of the content and presentation of the seminar OR b) ask a question at the seminar and email a summary of your question and how it was answered. Any points earned will be added on to the score you earn on the next review/exam that directly follows the event. You may earn a maximum of 4
extra credit points during the semester however I encourage you to attend as many as you can.
Seminars will be announced in the Biology eNewsletter. There are usually afternoon, evening,
Thurs, Fri, Sun, and Mon opportunities. Some will be during the Tuesday common hour.
Put them on your calendar and attend as many as possible.
Accommodations for Students With Disabilities: I am happy to provide accommodations for students with learning or physical disabilities. If you are a student with

a learning disability documented by Davidson College please identify yourself to me within the first two weeks of class so that arrangements can be made before any deadline is looming.
Students with other disabilities are encouraged to self-identify so that we may discuss if there is any way in which I can make accommodations that will enhance your learning experience.
All such discussions will be fully confidential unless you otherwise stipulate.
Discussions and Groups: Communicating ideas and working with others is not only critical at the cellular level, it is important at the whole individual level. Discussion and in class group work will be a significant component of this course. The shape of our room is not ideal for this work but, because life rarely includes ‘perfect’ settings, that makes it a good place to practice these life skills.
If there are aspects of the way we use this setup that would make it a better learning environment for you (seat near ‘front’, near window, away from door, a group on the edge so not surrounded by others talking, hard to see red marker on board) please let me know so that we can make the space work for all of us.
Accommodations for students with learning or physical disabilities will be made available. If you are a student with a learning disability documented by Davidson College please let me know within the first two weeks of class so that arrangements can be made before any deadline is looming. Students with other disabilities are encouraged to self-identify so that we may discuss how to enhance your learning experience.
Excused Absences and assignments: Religious observances are excused absences.
Should there be a conflict between any class session and a religious holiday or observance, please let me know so we can work to make sure you have the material.
If an assignments deadline conflicts with a religious observance, or a game, meet, performance, etc., that requires off campus travel, the default is to turn in the assignment before the observance begins or you leave campus. Any other accommodations require discussing it with me at least one day before the deadline.
Course grade
3 Reviews (covering lab and 20% ea
lecture material)
2 quizzes 2% ea
Laboratory grade 12%
Final Exam (in two parts) 22%
Participation 2%
Letter Grade conversion
A =4.0 =94-100
A- =3.7 = 90-93
C = 2.0 = 74-76
C- = 1.7 = 70-73
B+ = 3.3 = 87-89 D+ = 1.3 = 67-69
B = 3.0 = 84-86
B- = 2.7 = 80-83
C+ = 2.3 = 77-79
D = 1.0 = 60-66
F = below 60
Your course grade will be determined by converting your numerical score into a letter grade and adjusting the letter grade as much as 1/2 a grade level up or down based on your preparation for and participation in class questions and discussion (the participation grade).
Remember, an 'A' for participation requires above average and consistent preparation and participation in class. (If you turned in a blank test you would expect to get a '0' on it. Not coming to class or coming to class unprepared and never speaking is equivalent not completing this assignment and will be evaluated as such.)

Molecules, Genes and Cells Prof Bernd Lab Syllabus Spring 2015
Jan 12 Introduction to the lab; safety issues; using a Pipetman:
Spectrophotometry and standard curves
COMPLETE LM6 & 7 questions and tables BEFORE lab
Jan 19 No Lab: MLK Jr activities on Monday
Jan 26 Enzymes: What are they? How do we study them? What parameters affect their
function? Isocitrate Dehydrogenase (IDH) as example enzyme
Feb 2 Parameters that Affect a Specific Enzyme’s Activity: Independent Experiments investigating IDH
Feb 9 In lab writing workshop Learn about scientific conventions and then do it: Title,
Abstract, Experimental procedures, and Results (w/ figures) sections
--BRING figure drafts to lab READ Pechenik 6th ed pd 151-198 (ch9),
BRINGPechenik to lab
READ Grading rubric on Moodle
DUE by beginning of class on Wednesday. Title, Abstract, Experimental Procedures
Feb
16 and Results section one per lab team
Discuss Enzyme Investigations
Feb
23
Molecular biology and genetics: Profiling your genome
What is your genotype? PCR: DNA extraction and reactions
Mar2 No Lab: Spring Break
Mar 9 PCR results and analysis
Introduction to Chlamydomonas: Microscopy basics
Mar
16
Cell Biology: Gene expression to function:
Protein production and localization studies: Building a Chlamydomonas Flagella
Mar
23
Mar
30
Building a Flagella: Investigating Parameters that Affect Flagellar Regeneration:
BRING articles appropriate for Introduction (pdf or paper)
Data Analysis (stats) and In lab Writing workshop: Writing an Introduction
ReREAD Pechenik 166-198 READ Pechenik 139-150 (ch 8)
Apr 6 No Lab Easter Break
Apr13 Specific Lab Article Parts Due in lab
Title, Introduction, Results (w/ figures) and Ref sections: See Grading Rubric
Discussion of role of gene expression in building a flagella
Apr20 Wrap up lab unit,
Apr27 Course Eval,

Date Topic
Jan 12: M BEFORE CLASS complete ‘For before 1 st day of class’ assignment on MOODLE
In class Introduction to course: What is a Cell? The Inner Life of a
Cell (http://youtu.be/yKW4F0Nu-UY ) There IS lab this week
W Unit 1: Stress Response and Sugar release (Cellular Communication)
Intro to polymers and basic molecule types (carbohydrates, amino acids, lipids)
F Sugar release: Second messengers and signaling cascades. New molecule type--nucleic acids
Stopping the cascade: reversing and removing to get back to 'normal'
Study
Guide pgs n/a
1-7
7-12
Jan 19: M No Class Monday Martin Luther King Jr Day: Participate in King Day activities
(NO lab this week)
W
F
Using the sugar
Your heart pounds-- Channels, Pumps and Muscle contractions part I
Using the sugar
Your heart pounds-- Muscle contractions part II
Myosin heads are dancin' song: http://www.biosongs.com/br3lyrics/6.html
Jan 26: M Legs don't fail me now-- synapses, membrane potentials and action potentials
W Legs don't fail me now-- from action potentials to chemical signals and back. Synaptic Vesicle release
F -- from action potentials to chemical signals and back. Synaptic Vesicle release
Feb 2: M How does an egg know when it is fertilized? Another way of using 2nd messengers Fast and slow blocks--what are they and why do we need them?
W No Class Meeting (you have a review) Review1 will be have been made available through
Moodle by 1pm Tuesday and will cover pages 1-35 of Study Guide and first 4 weeks of Lab. It is DUE in submitted to Moodle by 5pm Friday .
See syllabus for details of late policy.
12-20
continue
20-25
25- 29 continue
29-35

Date Topic
Feb 6: F Unit II Genetics Inherited diseases: Sickle Cell, Cystic Fibrosis, Huntingtons, Introduced
Feb 9: M Unit II Genetics Inherited diseases: Sickle Cell, Cystic Fibrosis Huntingtons, Mitosis and
Meiosis Review making and interpreting pedigrees,
Meiosis all rapped up http://www.biosongs.com/11.htm
W
F
Inherited diseases: How do we talk about them? Traits vs alleles, genotypes vs. phenotypes, learning the terms and how to use them.
No class (I will be in Princeton)
S G pgs
39-42 continued
42-45
Feb 16
M
Inherited diseases: DNA and an
Cell cycle rap overview of gene expression (transcription and translation) http://www.biosongs.com/10.htm
45-50
1st set of questions
50-54 W
F
Feb 23
M
W
Inherited diseases: The SRY example and the importance of mutations in evolution and the prevalence of silent mutation. Inherited diseases: Gene expression and revising the common definition of mutation
Sickle Cell-- differences in gene leading to differences in protein folding
Mitosis/meoisis/pedigree quiz available at the end of class (On Moodle). Covers through pg 48
Inherited diseases: Gene expression and revising the common definition of mutation
Sickle Cell-- differences in gene leading to differences in protein folding
Inherited Diseases: Intro to Cystic Fibrosis How do you begin searching when there is no
'obvious' protein?
ReIntroduction to Mendel's Laws
Inherited diseases: Cystic Fibrosis: How to we find a gene in all that DNA:
'Classic' Linkage analysis / RFLPs and VNTRs
54-58
58-62
62-67
F Inherited diseases: Cystic fibrosis Continued
Mitosis/meoisis/pedigree quiz DUE before 6pm Friday night
Spring Break Mar 2
Mar 9 M Inherited diseases: Cystic Fibrosis -- A chromosome is 'big'. How do we get closer: recombination
W Inherited diseases: Cystic Fibrosis-- Positional Cloning and Genomic approaches
Do, and check, questions found at this link http://www.bio.davidson.edu/Courses/Bio111/campbell/CF_RFLP/RFLP_CF.html
continued
67-74
74-77
F Inherited diseases: Cystic Fibrosis-- What is the CF mutation?
Mar 16 M Inherited diseases: Cystic Fibrosis-- What is the problem and how can we tell?
W No class meeting (you have a review) Review2 will be made available through Moodle by 1 pm
Tuesday and will cover pages SG 39-83 and LM55-PCR. It is DUE submitted to Moodle by
5pm Friday .
See syllabus for details of late policy.
77-80
80-83

Date Topic
Mar 21 F Unit III: Bioenergetics: Poison Pot and an Introduction to energy
Mar 23 M Poison Pot: Light, Pigments and Energy
How and where do molecules store energy?
Listen to the kinetic and potential energy song http://www.acme.com/jef/science_songs/kinetic_potential-32.mp3
W Poison Pot: The Light Reactions and harvesting energy from photons
Study
Guide pgs
89-93
93-98
98-99
F
Mar 30:
M
W
Poison Pot: Calvin-Benson Cycle and making food
Cyanide and poison grapes: Only plants photosynthesize-- all cells metabolize glucose, how does that work? Cellular respiration (glycolysis/ Citric Acid Cycle and Oxidative
Phosphorylation) webquiz available through Moodle
Pull together
F Cyanide and poison grapes: Citric Acid Cycle and Oxidative Phosphorylation Amino Acid/
Peptide webquiz due by 5pm FRIDAY
Apr 6: M Easter Break
W
F
Cyanide and poison grapes: Citric Acid Cycle and Oxidative Phosphorylation
Why health officials require vaccinations during floods
Apr 13: M Carbon is not enough-- need nitrogen, but how?
W
F
Carbon is not enough
No class today (you have a review) Review 3 will be made available through Moodle by 3pm
Wednesday covers pages SG 88-117 and Flagella regeneration lab It is DUE submitted to
Moodle by 5:00pm Friday .
See syllabus for details of late policy.
99-103
103-107 continue
107-112 continue
112-115
115-117 continue
W
Date
Topic
Apr 20 M Unit IV: Other Interesting Topics : Epidemiology, Communicable diseases including
HIV (note we are skipping a topic) A brief recap of human anatomy
W HIV/AIDs history and info
Prefinal prep questions will be emailed to you
F Viruses and retroviruses
Apr 27 M HIV/AIDs: Treatment approaches
SG pgs no reading
131-136
HIV/AIDs: methods of detection/ diagnosis Wrap up Final Exam will be available on Moodle by 5pm today.
Available in office for questions
Final Exam Due Monday May 11th before Noon SUBMITTED TO MOODLE
No exam envelope, no exam center--> 'take home' like other reviews
136-140
140-147
147-151