Biology 261

REVISED Principles of Cellular and Molecular Biology: Fall 2008  REVISED







About Warm ups (requirements)

About Post quizzes

Course Goals and Objectives


Dr. Weaver

Warm ups on Campus Cruiser

Answers to warm ups

Answers to this week's quiz

Bioinformatics Laboratory

Science Division Seminars


Dr. Frances E. Weaver

Office Kirkbride 423A    Phone: 610 499-4519
Office hours: M 11:00-11:50; T 2:00-2:50; W-F 1:00-1:50 or by appointment


Class Times: MWF 10:00-10:50 and F 12:00-12:50 KH 229


Laboratory Times: T 11:00-1:50 (A) or Th 8:00-10:50 (B) KH 403 or M 1:00-3:50 (C); KH 403


Required texts:

The World of the Cell 7th edition by  Becker, Kleinsmith and Hardin
Benjamin Cummings Publishing Company; San Francisco CA; 2009   (This is a new edition)


Laboratory Manual for Biology 261, F. Weaver, ed., 2008. To be purchased prior to the first lab.

Course Goals: A. To develop literacy in cell biology. Literacy in cell biology will be assessed on lecture examinations and in quizzes. B. To reinforce scientific process skills. Increased scientific process skills will be assessed in laboratory activities.  C. To reinforce skills in oral and written communication.  Skills in written and oral communication will be assessed in two group oral presentations, two laboratory reports and a reflective paper.  D. To cultivate the understanding that the study of cellular and molecular biology is connected to social issues.  Recognition of these connections will be assessed in a group case study presentation and in an individual reflective paper. E. To prepare students for entry into Biology 262, Principles of Modern Genetics. Satisfactory completion of this course is required for admission to Biology 262. For course objectives, follow the link above.

Regarding Office Hours: You are invited to drop in to my office at any time. You are welcome in my laboratory at any time.  I also have standing office hours, the times for which are shown. You are encouraged to bring any and all questions directly to me in person or by phone or email.  If your schedule does not match mine, I will make time for you!

Email and Course Web Page:  Each student is to be familiar with the course web page and Campus Cruiser site.  Many assignments must be submitted electronically, notably the Warm-ups.  Announcements, shared files and other information will appear on the Campus Cruiser site, using either direct postings or links to the syllabus.  With the exception of the syllabus, web page material will not be distributed on paper unless I deem it necessary.  You may use email for all types of questions pertaining to the course, if necessary, please forward your Campus Cruiser email to the account you check daily.

Course Requirements 


  • 3 Lecture Exams @ 100 pts. each  Laboratory material will appear on lecture exams
  • Pre-lecture warm-ups done on-line: 11 @ 10 pts each = 90 pts (drop two lowest grades)
  • Post-lecture quizzes taken in class: 9 @ 15 pts each =  120 pts (drop one lowest grade)
  • Final exam (cumulative) 150 pts.



  • Laboratory Assignments (see lab syllabus): 280
  • Case presentation and case paper (see lab syllabus) = 60


GRAND TOTAL =  1000 points


Academic Integrity: The course instructor and the Science Division strictly enforce the University's policy on Academic Integrity as outlined in the Student Handbook.

The University Policy is that anyone who cheats, attempts to cheat or assists another student to cheat on an exam or quiz fails the courseOther common violations such as submitting collaborative work when not authorized to do so, and plagiarism also result in failure.  All of these violations mean that you expect to be given credit for work that is not your own, and that is clearly academic fraud.   If you would like further clarification, read Standards for Academic Integrity in the student handbook.  If you are uncertain how to proceed in any situation, contact me before you make a costly mistake! If you do violate the University policy, I will not hesitate to fail you in this course, regardless of your academic standing!

Attendance: Consistent, attentive attendance is the key to success in this course. Activities that take place in class cannot be made up!!!

Grading: Your grade is based on the percentage of the 1000 possible points that you earn. Thus 950/1000 = 95%; 750/100 = 75% etc. The +/- system will be used in this course.

Please be advised that I use this scheme to assign grades and all adjustments such as +/- are made at my discretion!! 

A                     95% or above

A-                    90-94%

B- to B+          80-89%

C- to C+          70-79%

D to D+           60-69%

Review sessions:  Group review sessions will usually be held on one or two evenings of the week before an exam. Attendance at review sessions is optional but is strongly encouraged.  

Exams: Missed exams result in a grade of ZERO!
Times: Exams take place during the Friday noon section as listed on the attached schedule, the format varies with each exam.
The final exam is cumulative and will review the semester's work.

Make ups : Make up exams are given only under conditions of documented emergencies. NO OTHER MAKE UPS WILL BE GIVEN !  I reserve the right to schedule make up exams and will do so only after I have received appropriate documentation.  Make-up exams will differ in content and format from scheduled exams.

Early exams: A student may request to take an exam early for personal, athletic or academic reasons. Requests for early exams must be received  IN WRITING (email is acceptable) no later than ONE WEEK BEFORE the scheduled date of the exam. Early exams will differ in content and format from regularly scheduled exams. Exams for those rare individuals with course conflicts are given at MY convenience.

Late exams or late for exams:  No late exams will be given. See make-up policy above. Students late to exams will have the time remaining in the period to finish, period, that's it, no excuses! 

Warm-ups: Warm-ups are distributed electronically and are completed as assignments in Campus Cruiser. Each warm up is due by 6:30 a.m. Monday as each week of class begins. Submission closes at that time. Warm ups must be done without assistance from anyone else in the class or the purpose of the warm-up is defeated. Warm-ups will be used to determine the depth and pace at which we explore cell biology together.  It is essential that you complete every warm up, but to anticipate the unexpected, I will drop the two lowest grades.  Failure to cite your sources will result in a grade of ZERO for any warm up!

Quizzes: Post quizzes take place in the Friday noon section.   These quizzes are worth 15 points.  Expect to devote at least 30 minutes to taking each quiz. You may take a quiz only at the time it is scheduled.  Missed quizzes result in a grade of ZERO! Quizzes may not be taken early. Again, anticipating the unexpected, I will drop the score of one and only one quiz.  Exceptions to these rules are made only for those rare individuals with course conflicts or those celebrating religious holidays.   Alternate quizzes given for these reasons are scheduled at MY convenience.

Cases Presentation and Case Paper: These are real world situations designed to permit you to direct your own learning about various aspects of cellular and molecular biology that we will work with in laboratory time. More information on cases may be found in the laboratory manual.

Science Division Seminars: Biology 261 students are expected to attend the Science Division Seminars sponsored by the Biology Department. An extra credit question on each seminar topic will appear on the exam following each seminar. A copy of the Science Division Seminar schedule is be available on-line.

Useful information:  I am here every weekday. Voice mail, e-mail and the course web sites operate 24 hrs a day.  The bulletin board next to my office door has yet to fall off, but if you are unable to reach me by these means; you may leave a message with the Science Office, KH323, ext. 4003. 

Alternative testing: I can provide alternative testing or extra time for testing to students with documented special needs.  Just ask.

Alternative note taking: You may record lectures and review sessions for your personal use.

Other alternatives are available for students with documented special needs. Just ask.

Special assistance: The following people and organizations are here to help YOU!


The first thing to do is talk to me. I can arrange special assistance, discuss study or note taking skills, introduce you to the reading and academic skills center, answer any and all questions about the course material or requirements, solve problems arising from labs, be your liaison with other faculty, help you find other students with which to form a study group etc.

For additional help including regular, no cost, tutoring I will refer you to the Science Tutoring Center or to Academic Support Services (610) 499-1273. You may also contact them your own. These services provide free support for all areas of academic success.

Your academic advisor will assist you in coordinating your program of study and provide a valuable reference in all areas of academic life.  Advisors in the Biology department do check with me about student progress.

It is our expectation that we will treat one another with courtesy, that we will have fun, and that you will all succeed.


Biology 261       Fall 2008

Lecture Schedule




The World of the Cell

Sept. 5

Cellular chemistry, Macromolecules

set up/modify email

 1, 2

Sept. 8, 10, 12

Cellular chemistry, Macromolecules

Warm-up (due 9/8)


 2, 3, 4

Sept.  15, 17, 19

Cells and Organelles

Warm-up (due 9/15)



Sept. 22, 24, 26

Bioenergetics and Enzymes

Warm-up (due 9/22)


 5, 6

Sept. 29, Oct. 1, 3

Membranes and Transport

Warm-up (due 9/29)

 7  (all but 158-162)


Oct. 6, 8, 10

Transport, Signaling, Junctions



14 pp 392 to 406

17 484-490

Oct. 10 NOON Exam I

EXAM I   (up to Oct 3 or as announced)  (Note: First lab report due in lab this week)

Review and practice


Oct.  13, 15
(Fall Break Oct. 17-20)

Metabolism part I: Glycolysis, Fermentation,

Warm-up (due 10/13)


Oct. 22, 24

Metabolism part II
Krebs's cycle, Electron Transport


 9, 10

Oct. 27,  29,  Nov. 1

Metabolism part III: Photosynthesis

Warm-up (due 10/27)


 11 to page 315

Nov. 3, 5, 7

Complete photosynthesis


Warm-up (due 11/3)

11 as above


Nov 7  NOON  Exam II

EXAM II  (up to Nov 1 or as announced)

Review and practice


Nov. 10, 12, 14

DNA replication,  Cell Cycle and Mitosis (quick review only) 

Warm-up (due 11/10)



20 skip 620-28

20 628-end  read for appropriate labs  

Nov. 17, 19, 21

Meiosis, Gene Expression I

Warm-up (due 11/17)


 20 as above


Nov. 24, 26

Gene Expression continued  (Thanksgiving Nov. 27-28 )



22 to page 697 overview of sorting

Dec. 2, 3, 5

Gene Expression and Regulation of Eukaryotic Gene Expression

Warm-up (due 12/01)


 22 as above

 23 start at page 723

Dec. 5  NOON  Exam III

EXAM III Up to Dec 2  or as announced

(Note: Case study presentations this week in lab)

Review and practice


Dec. 8, 10, 12

Regulation of Gene Expression

Warm up (due 12/08)



Final Exam as scheduled by the registrar during Dec 14-18th


FINAL Up to Dec 12, cumulative

The final exam is cumulative and will also include any new material we touch on after Dec 5th.

Review and practice



I reserve the right to modify the syllabus.  Modifications will be announced in class or on Campus Cruiser, or distributed by email.


Biology 261 Laboratory                                     Fall 2008

This is a component of Biology 261 and carries no credit as a separate course.


Instructor: Dr. Frances E. Weaver, Kirkbride 423A, ext. 4519

Office Hours: As on lecture syllabus


Required text: F. Weaver, ed. Laboratory Manual for Biology 261, 2008 to be purchased from the instructor prior to the first lab.  Laboratory coats are also required


You are expected to have read and understood the lab exercise before coming to the laboratory! 


You are expected to be on time for lab we are going to be very very busy!



You must follow all safety guidelines for each laboratory


You are expected to purchase a lab coat and wear it in the laboratory each and every lab! 

You must wear closed toe shoes.

Safety glasses and gloves will be provided as necessary.

The instructor will demonstrate the location and location and proper use of all safety equipment.

Follow the safe handling and disposal guidelines for all chemicals and biologicals.

Report spills or injuries to the instructor.


Laboratory requirements (included as part of the Biology 261 total)

1.                  Assignments, data sheets and report = 280 pts.

2.                  Case study presentation and Paper = 60 pts


Grading A schedule of assignments and point values is given on the next page. Additional information precedes each week's laboratory.  


ATTENDANCE IS REQUIRED.   You must attend lab in your assigned section, but if a problem arises consult ME BEFORE you miss a lab!  There are ABSOLUTELY no make-ups for any missed lab!!! 


Late work:  Laboratory reports lose 10% of their value for each day late. Example: a lab report worth 30 points is turned in two days late.  30 X 0.1 = 3

3 X 2 days late = 6.  30-6 = 24 maximum possible score.  Other laboratory assignments will receive a zero after the due date. Extensions are given only under extreme circumstances.


Academic integrity: The Widener University Science Division strictly enforces the University's policies on Academic Integrity.


I reserve the right to modify the syllabus Modifications will be announced in lab or in class, or posted on Campus Cruiser or distributed by email.

Biology 261 - Fall 2008

Laboratory Schedule and Requirements




Due from this lab (pts)


No labs, Please purchase your lab manual


9/8, 9/9, 9/11

Introduction to cells and organelles and review of microscope use.

Sketches (10)   

Calculation Questions (10)

9/15, 9/16, 9/18

Macromolecules: DNA isolation and quantification

Gel electrophoresis of muscle proteins

Data sheets (20)

9/22, 9/23, 9/25

Prokaryote unknowns: morphology, culture and metabolic characteristics

Gram stain and preliminary data (10)

9/29, 9/30, 10/2

Diffusion and Osmosis

Prokaryote unknowns: data collection and identification.

Hypothesis and method for diffusion and osmosis. (15)

Identification of unknown. (10)

10/6, 10/7, 10/9

Enzymes I: Basic experiments with tyrosinase

(Note: lecture exam 10/10)

Report on diffusion and osmosis (30)*

Protocol (written at start of lab) (10)

In lab data analysis (20)

10/13, 10/14, 10/16

Enzymes II: Student designed tyrosinase study


Hypothesis and protocol (20), due two days before lab

In lab data analysis (20)

10/20 Fall Break


10/21 and 10/23 only

Oral presentations of the tyrosinase study

Assignment of cases 


Oral presentation (10)


10/27, 10/28, 10/30

Monday lab meet to assign and

discuss case studies only

All other times- work on case


Enzyme Reports ARE due


Written report on enzymes II (30)*


11/3, 11/4, 11/6

Molecular Biology, part I: Bacterial

transformation and streak plates for


Photosynthesis (may be moved around

if we are behind in lecture)

(Note: lecture exam 11/7)

Photosynthesis Questions for Consideration  (20) (may be moved around if we are behind in lecture)

11/10, 11/11, 11/13

Molecular Biology, part II: Plasmid

isolation and restriction enzyme digestion

Conferences with instructor on case studies

Molecular  Biology I data sheet (15)

11/17, 11/18, 11/20

Molecular Biology, part III:  Bioinformatics


Molecular Biology II

data sheet (20)

Bioinformatics data sheets (10)

11/24, 11/25, 11/27



12/1, 12/2, 12/4

CASE STUDY  PRESENTATIONS (Note: lecture exam 12/5)

Group presentation of cases (30)

12/8, 12/9, 12/11

Clean up week, no labs scheduled. 

Finish all rewrites and papers and turn everything in !

Individual reflective papers on cases (30)


* loses 10% of the maximum value for each day late.  Rewrites are possible for both lab reports, consult your lab manual.



Resource links are updated frequently, check back often


Answers to Warm Ups

Quiz and Exam Answers  

Old Exams etc.

Internet Resources

More Internet Resources


Answers to Quiz 1

Old Exam 1 Questions

Dr. Van Bramer’s essay on how to avoid plagiarism

Our favorite cell animation


The longer, narrated

version is here.


Answers to Quiz 2

 Old Exam 2 Questions

Evaluating Web Resources:

 Carboxypeptidase catalytic triad animation


Answers to Quiz 3

 Old Exam 3 Questions

(see your shared files)

Enzyme Problem Set



Answers to Quiz 4


Membrane Tutorial

Glycolysis complex animation, very cool**

TCA animation, similarly


Glycolysis chemical structres (static)




Anwu- 5

Answers to Quiz 5


Interactive animation of photophosphorylation

Calvin Cycle Animation

Wu-6 was cancelled 

Answers to Quiz 6


Non interactive, simplified animation of photophosphorylation



Answers to Quiz 7 


Why 5' to 3' ?



Answers to Quiz 8


Animations on DNA replication, Hershey-Chase, Meselson and Stahl



Answers to Quiz 9



Telomerase animation






 **John Kyrk has an MS in biology from Harvard.  His web site has many other cell bio animations.