Biology 385 CELL BIOLOGY
Fall 2014
Class Times: Lecture: Monday, Wednesday, 12:00 - 12:50 in FSC 016
Lab: Tuesday FSC 132, 8:30-10:30; 11:00-1:00
Text: Cell and Molecular Biology:  Concepts and Experiments, 7th Edition by Gerald Karp ISBN 978-1118206737

Instructor: Dr. Bill Patrie

Campus Phone: (717) 477-1400

Office: FSC 152

Email: wjpatr@ship.edu

Web Page: http://webspace.ship.edu/wjpatr/

Office Hours: Monday 1-3, Tuesday 1-2, Wednesday 1-2:30, Friday 11-1, by appointment, and by chance.  If not in my office I’m usually in 132 (cell lab), 137 (across from the cell lab), or room 2.

 

General Class Information
The objectives of this course are to become familiar with cell structure and function, to understand some of the current experimental techniques and how to apply them, and to become familiar with some current literature.  Topics will include: the structure and function of biological molecules; the structure, function and biogenesis of membranes and organelles; the relationship between regulation of the cell cycle and cancer; cellular energetics; cell signaling pathways; and genes and gene expression.  The order of presentation will differ from the textbook, with the rationale that I want to start off with the information you are most familiar with from previous courses (Principles of Biology, Genetics) before moving on to more specialized material.


PowerPoint lecture files, lab handouts and assignments, and on-line quizzes will be posted on D2L.  I will also post your grades on D2L.  Please check them periodically to ensure that you are not missing anything and let me know ASAP if there are any discrepancies.


Students who require special accommodations for taking tests or notes should make an appointment to see me so that we can make appropriate arrangements.

The Textbook
Cell and Molecular Biology:  Concepts and Experiments, 7th Edition by Gerald Karp is a readable introductory cell biology text.  It is important to read the book.  Most of the information in the lectures follows the book closely.  The author may initially strike you as wordy or overly detailed.  However, Karp's narrative is providing illustrative descriptions that help provide a context of practical significance (e.g., disease and medical applications) and experimental approaches used to make key discoveries.  The text also has a web site (Karp Student Companion site) that has practice quizzes and case study readings.  I have not done an exhaustive comparison of the 6th and 7th editions, but they seem quite similar.  If you have inherited a 6th edition, you will probably be fine using it.  I do not recommend earlier editions.

The author includes review questions at the end of each chapter section that focus primarily on the key "facts" presented in that section.  These are useful to test how well you understand and assimilate important concepts.  Try to answer these questions as you read the chapters.  Having those questions in front of you can also be helpful when reading the chapters, allowing you to concentrate on the key concepts.  Analytic questions at the end of each chapter tend to be experimental or application oriented.  Some are pretty straight-forward, others can be challenging.  Make a good effort to answer them before resorting to the answer key.  The acts of contemplation and problem solving are crucial to applying concepts and true learning; looking up answers to a question without thinking only answers that one question.  In the sciences, we are always facing new questions and challenges.

Labs
The laboratory portion of this class will provide some hands-on experience with modern cell biological methods.  These will include growth and maintenance of cells in vitro, protein electrophoresis, immunochemical and immunofluorescent detection of specific proteins, and the analysis of nucleic acids.  Labs will be posted on D2L.  Attendance is mandatory.  If you need to miss a lab, get in touch with me and your lab partner ASAP in order to work something out.  Since we meet just one day a week, it can be difficult to make up or reschedule lab time.

GENERAL CLASS POLICIES

Attendance: There is a high correlation between class attendance and class performance (i.e., grade).  I occasionally take attendance and give extra credit points to those present.  Do not miss labs.  Make arrangements in advance if you do need to miss a lab.  Each unexcused absence from a lab will result in a 25 point deduction from your grade. 

Classroom etiquette: Please turn off cell phones, ipads, etc. during lecture.  Please refrain from talking in class.  Ringing cell phones, texting, and talking during class are unnecessary distractions.  If you use a laptop for taking notes, check with me beforehand and sit near the front (it's easy to get distracted with the internet and games just a click away).  Likewise, let me know if personal situations necessitate keeping a cell phone on.  If you want to record lectures, just let me know.  During exams, electronic devices other than a calculator should be off and put away in a bag or backpack. 

Lab periods are less formal and you will obviously need to talk to your lab partners.

Extra Credit: There will be occasional extra credit opportunities tied in to biology or chemistry seminar attendance and subsequent timely writeup.  Students unable to attend will have an alternative assignment available.  You may do up to 3 for 5 points each.  The only opportunities for these extra credit opportunities will be those assigned by me and available to the entire class.  I do not give extra credit points on an individual basis, so please don’t ask.

Grades

Exams (350 points): There will be 3 class exams (100 points each).  The third test will be given during exam week.  The tests are all cumulative in the sense that the latter chapters build on the concepts of the earlier chapters.  For example, techniques used to characterize proteins such as western blots will be described early in the semester, but will be applied in many of the latter chapters characterizing the cell cycle and signaling pathways.  A lab exam (50 points) will be given during the last week of classes that will cover topics related to experiments done in the lab and to journal articles covered in detail during the semester.

Quizzes and Assignments (approximately 150 points): Approximately 12 quizzes and assignments, worth 10- 20 points each, will be given during the semester.  Format will include on-line quizzes via D2L, in-class short answer quizzes, take-home problems, and literature reading assignments. In class quizzes will be announced, and I will let you know the format beforehand.

Lab Reports & Lab Notebooks (150 points): You will be expected to keep a detailed laboratory notebook. The notebook will be periodically checked during the semester for completeness and organization and collected for a final grade (50 points).  There will be two formal laboratory reports worth 25 points each (Immunofluorescence, EGFR gene), two short group reports (15 points each) and two handouts (10 points each).  Details for notebooks and reports will be provided as a separate handout.
The final grade will be based on the percentage of the total (approximately 650) points.  I don't typically grade on a curve.  Final letter grades will be based on the percentage determined by dividing your point total by the total points in the course.

A= 90 and above; B=80-89; C=70-79; D=60-69; F= less than 60.

 

Class and Lab Schedule- Warning! Subject to mutations and rearrangements!  Last Updated 8/24/2014

DATE

TOPIC

CHAPTER

Mon 8/25

Overview of cell structure and function

1

Tues 8/26

Lab/Lecture - biological molecules, Protein Structure and Function

2

Wed 8/27

Protein Structure and Function

2

Mon 9/1

Labor Day - no class

Tues 9/2

Lab # 1    Protein Structure Computer Tutorial Web Link Handout

Wed 9/3

DNA, replication, genes, and gene expression – an overview

Mon 9/8

Bioenergetics-general

3

Tues 9/9

Lab # 2 Protein assay in class Amino acid quiz

18*

Wed 9/10

Protein Methods/Cell Methods

18*

Mon 9/15

Membranes and transport

4

Tues 9/16

Lab # 3 Cell Methods, Cell culture basics

Wed 9/17

Membranes and transport

4

Mon 9/22

Cytoskeleton

9 

Tues 9/23

Lab # 4 Immunofluorescence (Formal report)

Wed 9/24

Cytoskeleton

9 

Mon 9/29

Cellular membrane systems

8

Tues 9/30

Lab # 4 continued

Wed 10/1

Exam 1 Chapters 1-4, 18*, 9

 

Mon 10/6

Cellular membrane systems

8

Tues 10/7

Lab # 5 Cell Fractionation/Western Blot

Immunofluorescence report due

Wed 10/8

Cellular membrane systems – Mitochondria, chloroplasts, peroxisomes

5.1,5.6, 6.1, 8.9

Mon 10/13

Fall Break - no class

Tues 10/14

Fall Break - no lab   

Wed 10/15

Cellular membrane systems - nucleus

12.2

Mon 10/20

Extracellular matrix and cellular interactions

7

Tues 10/21

Lab # 5 Continued

Wed 10/22

Metabolism

3,5

Mon 10/27

Metabolism

3,5

Tues 10/28

Lab # 5 continued

Wed 10/29

DNA, replication, genes, and gene expression – some details

10,11, 12, 13

Mon 11/3

DNA, replication, genes, and gene expression – some details

10,11, 12, 13

Tues 11/4

Lab # 6 Protein and DNA Sequence Analysis Web Link Handout

Wed 11/5

Exam 2 Chapters 8, 3,5, 6.1, 7, 12.2

Mon 11/10

Cell Signaling

15

Tues 11/11

Lab # 7 Detection of EGFR gene by PCR (Formal report)

Wed 11/12

Cell Signaling

15

Mon 11/17

Cell Signaling

15

Tues 11/18

Lab # 7 continued; Lecture: DNA Techniques

18*

Wed 11/19

Cell Cycle Control

14

Mon 11/24

Cell Cycle Control

14

Tues 11/25

TBA

Wed 11/26 Wed-Sun

Happy Thanksgiving!

Mon 12/1

Cancer

16

Tues 12/2

Lab Final

16

Wed 12/3

Cancer                       lab notebooks due

16

Exam week

Final Test Chapters 10-13 (parts) 15, 14, 16 ,18*

*Chapter 18 covers many varied techniques; appropriate sections will be incorporated into specific topics as needed