BIOLOGY 315:  CELL BIOLOGY

FALL 2004 SYLLABUS

 

 

Dr. David Howard                               

3016 Cowley Hall

785-6455 (office)        

howard.davi@uwlax.edu

 

Lectures:                 M W F   11:00 – 11:55 a.m., 100 Cowley Hall

 

Required Text:      Karp, G. Cell and Molecular Biology, 3rd edition (2002).

                                    *Additional readings will be handed out in class as needed.

 

Lab Manual:          Howard, DR and J Miskowski. Cell Biology Lab Manual (2004)

                                                                       

Desire2Learn (D2L) Site:      

Course supplements, documents and assignments will be posted through the D2L Web site.  Some lab assignments will require you to use D2L.  Therefore, you must learn how to use this simple campus function.

            How to get on D2L:  If you have not used Blackboard for other courses, follow these directions.

1.      Use the internet to access https://uwlax.courses.wisconsin.edu/

2.      Log in using your UW-L e-mail username (mine is howard.davi).

3.      Your D2L password is the same as your email password.  If you used D2L in the past and had a different password, this has been changed.  If you change your email password, your D2L password will automatically change to match.

4.      If you cannot gain access to D2L using the approaches listed above, contact Instructional Technology: 785-8774, or ITSsupport@uwlax.edu

5.      At your D2L homepage, you will see all your current courses that use D2L.  Click on "Cell Biology" to go to our D2L site.  Start using it.

 

Course Objectives: 

· Obtain working knowledge of fundamental information such as:

ü      the nature of different types of molecules

ü      the structure and function(s) of cellular components

ü      the execution and regulation of important cellular processes.

· Become familiar with experimental techniques used in cell biology research.

· Develop an understanding of “the big picture”– how are various cellular processes coordinated and regulated with respect to one another to ensure proper cell function, as well as the health of the entire organism.  

· Strengthen critical and analytical thinking skills both in verbal and written communications.


Expectations:

Cell Biology is designed to be a rigorous course, and it requires a significant amount of work outside of class.  Reading the text is not optional.  I fully expect you to read and comprehend the assigned pages in the text or on handouts which provide the necessary background on a course topic.  This allows us to spend more lecture time discussing experimental techniques, current advances in the field, and the relevance of a topic to our everyday life. 

This course does not emphasize simply memorizing “facts”, and this is reflected in the homework assignments and exams.  Our understanding of Cell Biology, as with most scientific fields, is constantly changing with new technological advances that allow researchers to ask and answer different questions.  Some of the Cell Biology “facts” of today might very well be different from the “facts” taught in 2010.  Therefore, in addition to understanding the cellular processes that we cover in lecture, we stress the importance of interpreting and analyzing new information and applying your knowledge to new situations.  These are skills that are critical to the success of any kind of scientist, and any professional for that matter.  Thus, this course will prove valuable to you even if Cell Biology does not appear to be directly related to your future career.

One example of technological advances dramatically influencing Cell Biology is that the genomes of several different organisms, including humans, have been sequenced.  The vast amount of data that have been generated, and the fact that these data are freely available, has lead to the emergence of bioinformatics, which is the study of the information provided in genomic or protein sequences.    Bioinformatics has permeated the field of Cell Biology, and many other scientific disciplines, changing the types of questions that researchers might ask and enhancing the answers they might obtain.  Therefore, in order to give you a true representation of modern Cell Biology, bioinformatics will be included in this course.

 

Instructional Techniques and Assignment Guidelines:

Although the majority of classes will have a lecture style format, in-class problems will also be employed throughout the semester.  In-class problems are exam-like questions that are posed to the class during the lecture period.  You will have approximately 5-15 minutes to answer the problem either individually or working in a small group.  These problems will be based on the most recent lecture/reading material, and may even cover information discussed just minutes before.  These exercises are extremely useful because they:

·        reinforce the lecture material

·        help you to determine whether or not you understand a topic

·        allow you to teach and learn from your peers

·        give you practice answering exam-like questions

·        help the instructors assess whether you are grasping the information and/or what are the points of confusion. 

Your answers will be handed in and “lightly” graded for one point, so you will get credit for your effort.  Importantly, after you hand in your answer we will work through the problem as a class to make sure that you leave with the correct answer and the explanation behind it.

You might be given various homework assignments throughout the semester.  These exercises will often build upon lecture material, but they may cover information that is deemed important to the class, but was not discussed in lecture.  To obtain full credit, your answers should be in complete sentences, spelled correctly, legible, and submitted on time.  We will not search for the correct answer in a mish-mash of haphazard thoughts that have been jotted down. 

 

Policy on Late Assignments:

·  Assignments handed in after 5 p.m. on the due date will be considered late and marked down one full letter grade.

·  Assignments handed in after a review session covering the assignment will be marked down two letter grades.

·  Absolutely no assignments will be accepted after one week late or after graded assignments are returned to other students.  This point supercedes the second point.

 

Review Paper Assignment:

Each student will be responsible for writing a review paper that interprets a primary literature article in the field of cell biology. See the handout "Cell Biology Primary Literature Review" for the details of what will be expected of you.

 

Paper Deadlines:

Due Date

Points

What Is Due

Sept. 24, F

3

Photocopy of 1st page of paper you chose, including title, citation, and abstract

Nov. 3, W

7

Detailed outline with 2 additional references

Dec. 6, M

50

Final draft of paper and photocopy of original article

 

 

Exams:

The exams will consist primarily of short answer and multiple choice-type questions.  Questions will include problem solving and data interpretation.  At least some of the multiple-choice questions will have multiple answers (e.g. options like A & B, B & C, All of the above).

Exams will take a week to grade because of the time needed to thoroughly review your responses to the short answer questions. 

For the multiple-choice questions, we will be using the Immediate Feedback Assessment Technique, or IF-AT, forms.  These are lottery ticket-style forms where you scratch off your answer, instead of circling it.  The correct answer will show a star, so you know immediately if you are correct and receive full-credit on the problem.  If you are incorrect, you are able to make a second or third, if necessary, selection and partial credit will be allocated for the correct answer on these tries.  This technique has several benefits in that it provides immediate feedback, you can receive partial credit for second and third choices, and you leave the exam knowing the correct answers and how you performed on the multiple choice section of the exam.  For more information on this technique, you are encouraged to visit the web site:  http://enigma.rider.edu/~epstein/ifat/

 

Missed Exam Policy:

If you must miss an exam because of an illness or an officially approved university activity, you need to contact me before the exam.  If an emergency makes this impossible, you must inform me within 24 hours after the exam.  In any case, be prepared with official documentation of the reason that forced you to miss the exam.  Without proper notification and documentation, you will receive a zero on the exam.

Exams scheduled in two or three other courses around the same time as a Cell Biology exam is not a good reason for missing or rescheduling an exam.


Grading and Point Totals:

 

In this course, you are not in competition with anyone for a grade.  Your grade is based on total points earned, meaning that it is theoretically possible for everyone to get an A.  Grades will be based on your performance on the following assignments.

 

GRADES

A   = 91-100%

AB = 88-90%

B   =  81-87%

BC = 78-80%

C   =  68-77%

D   =  58-67%

 
ASSIGNMENT                                             POINTS                                                                     

3 exams X 75 pts each                         = 225                                      

Amino acid quiz                                                =  10

Homework & in-class problems                        =  ~25 (will vary)                     

Review paper (+ topic & abstract, outline)        =  60                                       

Laboratory                                                       =174                                       

Comprehensive Final exam                               =150                                                               

APPROXIMATE TOTAL                               =644 pts (will vary)                             

                       

                                                                                                 

                               

                                                               

Laboratory: 

Attendance in lab is mandatory and will be noted.  Lab assignments and grading are outlined in the lab syllabus.

 

 

Academic Honesty:

There is a student honor code at the University of Wisconsin-La Crosse (pg. 47 in the Undergraduate Catalog) that we expect to be upheld.  Cheating and plagiarism will not be tolerated.  Plagiarism is taking someone else’s ideas, expressions, or productions and passing them off as your own.  Please visit the following Murphy Library web site for more information on plagiarism: http://www.uwlax.edu/murphylibrary/plagiarism.html.  This web site gives you some specific examples of what is and is not plagiarism.  You may be surprised how significantly you need to change the information found in your literature source to avoid plagiarism. 

Because the nature of science is a collaborative one, you will find yourselves working in groups both in the laboratory and lecture.  Although it is quite beneficial to share ideas and brainstorm with colleagues, it is imperative that you formulate your own answers on written assignments both to adhere to the honor code and to make sure that you truly understand the information being covered.   Writing assignments will be spot-checked for plagiarism and violators will be punished.  The consequences will range from receiving an F or zero on that particular assignment to receiving an F in the class and having the incident officially documented at the Dean of Students Office.

 

 

Students With A Disability:

Any student with a documented disability (e.g., physical, learning, psychiatric, vision, or hearing, etc.) who needs to arrange reasonable accommodations must contact the instructor and the Disability Resource Services Office (165 Murphy Library) at the beginning of the semester. The lecture and lab instructors are willing to make reasonable accommodations for students with special needs.

 

Instructor Meeting Times:

As a former student, I understand that this course is challenging to many students.  It is important that you recognize that this course is cumulative in that you must master the information presented early in the course in order to succeed later in the course.  I want to provide as much assistance as possible throughout the semester, and my time is not limited to regularly scheduled office hours.  If none of the scheduled times work for you, please contact me to set up a personal appointment.  I strongly encourage you to take active responsibility for your own learning.

 

 

Note to teacher education students:

Activities in this course can potentially be used for portfolio development.  These activities include written components on exams, the literature review paper, ALP lab report, immunofluorescence poster, and cell growth and division PowerPoint presentation.

 

 

Questions Are Good.

 

Cell Biology

Fall 2004 Lecture Schedule

 

Date

Planned Topic

Assigned Reading

Sept.   8

W

Introduction. Review of cell structure.

 Ch. 1

10

F

Reviews of cell structure and bonding. Biomolecules.

 Ch. 2

13

M

Introduction to proteins.

 Ch.2

15

W

Protein structure and folding.

 Ch. 2

17

F

Ras protein: conformation, mutations, families and bioinformatics.

 Ch.2, p. 651-3

20

M

Amino Acid Quiz (10 pts).  Protein domains and motifs

 Ch.2, p. 712-5, 764-5

22

W

Protein folding and chaperones

 Ch.2

24

F

Introduction to lipids, membranes, and thermodynamics.

DUE: PHOTOCOPY OF PAPER ABSTRACT & TITLE.

p.49-51, 83-92, Ch. 4: 122-150

27

M

Membranes: The fluid-mosaic model.

Ch. 4: 122-150

29

W

Membranes: Proteins--the mosaic part of the model.

Ch. 4: 122-150

Oct.    1

F

Membranes: Thermodynamics & control of fluidity.

 Ch. 4: 150-165 

4

M

EXAM 1

 

6

W

Membranes:  Movement across the fluid barrier.

Ch. 4: 150-165 

8

F

Membranes: Movement across the fluid barrier continued.

Ch. 4: 150-165 

11

M

Membranes: Wrap up

as previously assigned 

13

W

Enzymes and enzyme kinetics.

Ch. 3: 87-103

15

F

Enzymes and kinetics continued

Ch. 3: 87-103

18

M

Metabolism: Glycolysis and its regulation.

Ch. 3:  105-15

20

W

Metabolism: Mitochondria structure and the TCA cycle. 

Ch. 5

22

F

Metabolism: Mitochondrial oxidative phosphorylation.

Ch. 5

25

M

Metabolism: Chloroplasts and Photosynthesis.

Ch. 6

27

W

Introduction to the secretory pathway.

 

29

F

EXAM 2

Ch. 8

Nov. 1  

M

Secretion: Signal Hypothesis & endoplasmic reticulum

Ch. 8

3

W

Secretion: Protein targeting, Golgi, and lysosomes

PAPER OUTLINE DUE

Ch. 8

5

F

Endocytosis.

Ch. 8

8

M

Vesicle formation and SNARE hypothesis.

Ch. 8

10

W

Cytoskeleton:  Intermediate Filaments, Actin, and Microtubules.

Ch. 9

12

F

Motility: Chromatophores as a model

Ch. 9

15

M

Motor proteins: Dynein, Kinesin, Myosin 

Ch. 9

17

W

Cilia and Flagella.  (Microtubule-based motility)

Ch. 9

19

F

Cell locomotion via lamellipodia. (Actin-based motility)

Ch. 9

22

M

EXAM 3

 

24

W

Mitosis and Cytokinesis.

Ch. 14:  590-608

26

F

Thanksgiving Break

Ch. 14: 590-608

29

M

Mitosis: Mechanisms.

Ch. 14: 580-590, 619-623 

Dec.   1

W

Mitosis and the Cell Cycle.

Ch. 14

3

F

Cell cycle: The central control system and checkpoints.

Ch. 14, 681-9

6

M

Cell cycle: Checkpoints continued, and p53.

DUE: FINAL DRAFT OF PAPER TO LAB INSTRUCTOR.

 

8

W

Signal transduction: Receptor tyrosine kinases and cell cycle control.

Ch. 15

10

F

Signal transduction: G-protein coupled receptors and second messengers.

Ch. 15

13

M

Signal transduction.  Apoptosis.

Ch. 15

15

W

Extracellular matrix & cell-cell interactions

Ch. 7

 

 

 

 

17

F

Final Exam, 2:30-4:30