Biology 493V-001, Spring 2007

Mondays, Wednesdays & Fridays, 10:30-11:20 PM

Rm. 3306 LSB (computer lab)

 

CONTACT INFORMATION

Lecturer:      Dr. Jane Caldwell

Phone:         293-5201 Ext. 31459

Office:         3324-A LSB (3rd floor, at rear of General Biology labs suite)

E-mail:         jcaldwe2@mix.wvu.edu

Office Hrs.:  Tuesday 3:30-5:00 PM, Wednesday 3:30-5:00 PM, Friday 1:00-2:00 PM, or by appointment
Drop in visits are welcome, although I may not always be available immediately.

REQUIRED MATERIALS

Textbook:     Introduction to Protein Structure, 2nd edition; Carl Branden & John Tooze (© 1999, Garland Science)

Software:     Swiss-Protein PDB Viewer (“spdbv” or “DeepView”: freeware for Mac or PC, on your own computer or in LSB computer lab; details will be discussed in class)

Websites:     WVU eCampus (Vista):         https://ecampus.wvu.edu/        (homework submission and files)
MIX:                                     http://mix.wvu.edu                  (email)
Syllabus:                               http://www.as.wvu.edu/~caldwell/493v.htm

CLASS POLICIES

Attendance: Your attendance and active, thoughtful participation will be an important part of each class meeting.  If you must miss a class, you will need to make arrangements with a classmate to borrow notes.  Most hands-on activities done in class cannot be made up, and homework due in class cannot be handed in late.  (If you are a senior and will miss class for job or grad school interviews, please come talk with me so we can agree on a plan for missed work.)

Computers:  You will need access to your MIX and eCampus (a.k.a. WebCT or Vista) accounts.  All class announcements and email will be sent to your MIX account by default; please notify me right away if you must temporarily use another address.  All scores will be posted in eCampus; please check your grade in eCampus frequently and notify me early of any problems.

                    Much of our class will be based around observations and measurements of actual protein structures using specialized software.  This software will be installed on computers in the LSB computer lab; however, hours of access are limited.  If at all possible, I suggest you download and install this free software on your own computer; ask me if you need help.  I will hand out more details in class.

Homework:  Reading assignments on the attached syllabus should be completed before each class;  class discussions will depend heavily on your input and questions.  Some days one or two students will be responsible for leading discussions!

                    Homework problems will be assigned approximately every 1 to 1½ weeks.  I expect you to work through all of these problems, and to bring your answers to class.  Some problems will be discussed (by you and all classmates) in class, and several problems from each assignment will be graded.  Other assignments will be announced as the semester progresses.  These short homework assignments will count for 20% of your grade. 

                    I encourage group work outside of class, as long as each individual is learning all topics thoroughly and doing all parts of each assignment.  If you discuss a homework problem with another person, please cite them at the end of your answer:  “I talked with Kim about this problem,” or “Dave showed me how to do this calculation on the computer,” etc.  Even if you work together, your answers must be thought through and written down independently; identical answers will receive a zero.

Projects:       As we progress through the semester, you will do some “mini-projects” that will let you practice what you have learned.  Most projects will focus on producing diagrams on the computer as well as describing and explaining protein structures, and are more substantial that ordinary homework.  You will be given several days to do each mini-project.  You will generally place those diagrams in PowerPoint and hand them in using eCampus.

                    Near the end of the semester, you will complete a “major project” that lets you apply all you’ve learned to a specific protein.  Choose any protein that interests you, so long as it has a known, experimentally determined structure not already discussed in class or your textbook.  You will write a 10-15 page paper, make your own diagrams and measurements using the software we have mastered in class, and give a 15-20 minute presentation in class. 

                    All these projects together will count for 30% of your grade.  At least half of these points will come from your “main project.”

Tests:           You will have 2 tests (50 pts each), and a final exam (50 pts).  Tests will cover a combination of material from lectures, texts, and homework, and occasional hands-on tasks using the structure-viewing software.

                    Occasional short, unannounced “pop” quizzes will be given to ensure that you are keeping up.  These will generally be worth 5 points.

Absences:     For regular class meetings, you will be responsible for any material or points you miss.  Homework assignments cannot be handed in late, and hands-on activities cannot be made up, unless arrangements are made with me in advance.

                    If you miss an exam, you will receive a zero.  If you have a valid, verifiable excuse,** contact me within 24 hours to schedule a make-up test.  My voice mail is always available—please call rather than sending e-mail!  Your exam will be graded AFTER I verify your excuse.**

**                Only serious, valid excuses will be considered such as funerals of immediate family members, severe illness, injury, or similar serious issues.  I will determine the validity of all excuses.  When possible, please do find a reliable, trustworthy person to confirm that you could not possibly attend the scheduled exam—this does not need to be a doctor or healthcare professional.  Most problems can be resolved by talking with me in person.

                    Athletes and others, take note:  If you are required miss an exam for a scheduled WVU event, please contact me at least a week in advance to arrange a make-up time.

Grading:       Your grade will be based ONLY on the points you earn during the semester; no extra credit will be given to individuals. 

                    Tests & Quizzes                                 50%            Grading Scale¥:   90-100%   =  A

                    Homework                                         20%                                         80-89%   =  B

                    Projects (Major and Mini)                   30%                                         70-79%   =  C

                    Total                                                100%                                         60-69%   =  D

                                                                                                              0-59%               =   F

                    I do assign plusses and minuses to grades, although these do not affect your GPA.

                    To calculate your grade, you will need to know the percentage you have earned so far for each portion of the semester:

                    Grade = 0.3(% Projects) + 0.2(% on Homework) + 0.5 (% on Tests)

Cheating:     Please don’t waste my time and yours by cheating.  I expect all work handed in to be the direct result of your independent thought and effort; any assignments that vary from this expectation will receive a zero.  More than one incidence of cheating on homework or other assignments, or any type of cheating on an exam will result in a grade of F for the course and written notice of academic dishonesty to the Biology Department and the Dean’s Office.

Evacuation:  In the case of a fire drill or actual emergency, collect your belongings and walk calmly to the stairwells at either end of the building.  (The central glass stairwell is not considered a fire exit.)  After descending the stairs and exiting, please cross Campus Drive.  We will convene in front of the Penny Lane Café for a brief head-count.  For your own safety, please avoid the building and parking lots.  Whenever possible, class will continue after the alarm has been turned off.

Social Justice Statement:

West Virginia University is committed to social justice.  I expect to foster a welcoming learning environment based upon open communication, mutual respect and non-discrimination.  Our University does not discriminate on the basis of race, sex, disability, veteran status, religion, sexual orientation, color or national origin.  I will listen very seriously to any of your suggestions for making our classroom a positive, fair and open environment.

Please tell me as soon as possible if you have a disability and need special accommodations.  You will need a letter from Disability Services (293-6700); even if your letter is delayed, please see me at least one week before the first exam.  All information will be kept confidential, and arrangements will be made discreetly.