BIOLOGY 107 - IMMUNOLOGY
COURSE GREEN SHEET
Spring Semester – 2006 San Jose State University
Tues. / Thurs. 9:00-10:15 DH135
Instructor: Ruth Kibler, Ph.D., Duncan Hall 251; Phone - 924-4892 (Office):
Phone - 924-4900 (Biology Office); E Mail Address: firstname.lastname@example.org
Office Hours: Mon. 12:30 – 2:30 Tues. 10:15 – 12:15; Thurs. Other times by appointment.
Catalog course description: Immunology, Concepts and principles. Mechanisms of cellular
cooperation and regulation of immune responses. Practical considerations and applications.
Course description: Biology 107 is a general immunology course designed to provide
information about all areas of immunology. Emphasis is on the basic concepts. The material
presented will provide you with the vocabulary of immunology and a general knowledge of the
subject. The course is designed to give you the basics needed to take advanced courses in
immunology. Biology 107 has one three-hour/week laboratory component that must be taken
with the lecture.
1) BIOLOGY 3 (Cell Biology) WITH A "C OR HIGHER". Grades of a B or higher in upper
division courses such as Bio 135, Bio 116, Bio 124 MAY substitute for the "C or better
requirement" in Bio 3. See me about Bio 3 substitution courses.
2) Completion of both semesters of organic chemistry with a AC@ OR HIGHER. Concurrent
enrollment in the second semester of organic chemistry is acceptable.
3) Micro 101 with a grade of a C or HIGHER is a Prerequisite for Bio 107. Permission from
the instructor is needed to take Micr 101 concurrently with Bio 107. Second bac. and
graduate students without this prerequisite should see the instructor.
4) Completion of Bio 6 or concurrent enrollment in Bio 6 is required.
The textbook for this course is Immunology by R.A. Goldsby, 5th edition, published by W.H.
Freeman and Company, 2002. Read the book to clarify what you do not understand in the
lecture and the Handouts.
• At the beginning of each handout there are questions assigned for the chapters from this book.
The answers to these questions are found in the back of the book. At least 10% of each
exam will be taken directly from these questions.
• Case studies found in the book are assigned by chapters. Questions on the case studies will
appear in the exams.
• You will be held responsible for the material presented in the lecture, the textbook and the
Handouts. You are not responsible for topics in chapters not covered in the lecture. This
means that you can read the textbook chapters selectively.
Handouts and Laboratory Manual
The Handouts can be purchased in class from the Biology Student Association. Bring the
Handouts for each lecture to class with you. I will be referring to figures in the Handouts during
lecture. The text and figures were generated to give you information about the areas that I feel are
important to understand the subject. The Handouts are designed to lead you through the material
for each Lecture. Use These Handouts to Learn the Material.
The laboratory manual can be purchased from the Biology Student Association.
Appendix to the Handouts
• Look in the appendix at the back of the Handouts. You will find: One Scientific American
article with questions to be submitted.
• Worksheet for Handout 4 on flow cytometry to be submitted.
• One Patient Oriented Problem Solving assignment on Tetanus with questions to be submitted.
• Study questions for the four exams
• Questions on the lecture material on antigens to help you study for that part of the exam.
Exams: There will be three midterm exams and a final exam. Make up exams are given only
with a medical excuse or consulting me BEFORE the exam. All make-up exams will be
taken on the same day. This day will be after the 3rd midterm exam. Please notify me as
soon as possible if there is a problem. Approximately 80% of the final exam will cover the
material after the 3rd exam. Approximately 20% will be cumulative.
The material covered in each exam will be announced. In general, questions from material
covered after the previous exam will be emphasized. The subject of immunology builds on the
material presented in each Handout starting at the beginning of the course.
Exam questions can be multiple choice, fill in, true/false, short answer and drawing experimental
conclusions. I try to return all exams within 10 days so that you can go over them during the
laboratory. I keep all exams, so you must return them to me at the end of the laboratory
class period. FAILURE TO RETURN AN EXAM TO ME DURING THE CLASS LABORATORY
PERIOD WILL RESULT IN A SCORE OF A0" FOR THAT EXAM. The exams are available in
my office for you to review at any time.
If you believe an exam has been scored incorrectly, please bring this to my attention immediately
after the exam has been returned to you. Write the questions you wish reviewed on the back
of the exam along with your reasons for asking for the review of the question. I will
periodically total your points, so you will know how you are doing in the course.
If you wish to drop this course, please do so by the stated University Guidelines
www.sjsu.edu/sac/. University and Department guidelines require a serious and compelling
reason to drop a course. A failing grade, alone, does not constitute sufficient reason to
drop a course. You must submit a form to drop a course. My signing of the form is mainly
informational and does not constitute approval of your dropping of the course
What you can expect from me.
• fairness and impartiality in all grading I grade all homework and exams by ID numbers. The only
reason for this is that I do not wish to know whose papers I am grading. This way, I do not have
preconceived ideas about how you should do on the exam.
• prepared handouts for each lecture.
• tests given on the dates announced in the Green Sheet - no surprise changes.
• study questions provided for each exam - some questions on the exam taken from the study questions.
• up to date assessments of how well you are doing in class. Cumulative point scores are calculated
after each exam.
• return of exams within 10 days after the exam
• trying to make the material interesting - incorporation of current information from meetings attended and
• helping you to understand the material and provide resources when requested. Office hours are to be
used by students to obtain help or to go over material. The numbers of students sometimes make this
difficult, but I encourage you to use this opportunity.
What I expect from you.
• timely attendance at lectures - students who attend class usually do better. Although much of the
material is covered in the handouts and the book, material which is added in lecture can appear on
• reading Handout material before class. You do not have to understand everything, but it will help you if
you have some idea of what material will be covered before you come to lecture.
• take exams on time and on announced dates.
• keep track of when homework is due and turn in assignments on time.
• try to learn and understand the material. Most of my satisfaction in teaching comes from observing
students who have an interest in learning.
• try to achieve the highest grade possible. The most discouraging statement that I can hear from a
student is that you are satisfied with a D.
• inform me of personal concerns or emergencies that affect your performance in the class.
Honesty (my policy) See last page for University Policy
Cheating will not be tolerated in this class. You do not learn by cheating. Please think about
this statement, and do not place me in the position that I must bring this subject to your
attention. The penalty for an infraction of the policy can be very severe. Penalties can include a
A0" for an exam and not being allowed to drop the course as well as a report to Judicial Affairs
where the report is kept on file. Repeat offenders will be given a failing grade in the course and
referred to the Judicial Affairs for administrative sanctions which may include expulsion. I will
inform studenst of any action taken against them. An appeal is urged if you feel falsely
Honesty is required on written material. You must do your own work. Your answers using
the same sentences and wording as an article or another student=s answers is known as
plagiarism. It is appropriate in some cases to use the same terminology as the article, but it is
inappropriate to use complete sentences from the article. It is never appropriate to use the
words of another person unless it is used as a quote.
Requirement for the course: Five points on the first exam will be questions on this.
Tutorial on plagiarism: Each of you must go to the following site at our library and
go through the tutorial on plagiarism. http://tutorials.sjlibrary.org/.
Grading and Points for Course
Exam 1 150 points Feb. 21 Tuesday
Will include at least 5 points on the tutorial on plagarism http://tutorials.sjlibrary.org/
Exam 2 200 points March 14 Tuesday
Exam 3 200 points April 18 Tuesday
Final Exam 250 points May 19 Friday 7:15 a.m.
Total Exam Points = 800
Scientific American Reading Questions: 17 points See Appendix to the Handouts.
Clonal Selection - Scientific American 257:62, 1987. Answers to the questions are due on Feb. 7.
Questions on this assignment are included in Exam 1.
Flow Cytometry Worksheet: 10 points See Appendix. Turn in on February 14. Questions on this
assignment are included in Exam 1.
Patient Oriented Problem Solving and Post-Test: See Appendix
Tetanus Problem Solving: A problem solving set on immunity to tetanus is in the Appendix of your
Handout packet. Included in this material are: a) a pre-test with answers, b) four immunologic problems
relating to tetanus, c) a post test without answers. Answers to the post-test will be graded.
Questions from this problem solving will be included in the second exam. It is a more interesting
learning experience if you do this exercise in groups of 2 to 4. If you do this as a group, turn in one post-
test for the group. You will each individually receive the same grade. I recommend that you do it as a
group. The Post-Test on Tetanus is due on March 2. Points = 15
Total Lecture Points = 842
Laboratory There is a lab fee of $25 for this course.
If a laboratory assignment is turned in late, 10% of the grade will be taken off each day it is late.
If you miss a laboratory, you will receive 0 points for that assignment unless you have a medical excuse
AND discuss it with your laboratory instructor. It is possible to make up a missed laboratory in one of the
other sections if you discuss it with your instructor.
Laboratory Exams: Two Lab Exams, 125 points and 125 points = 250
Poster Session: = 50
The last laboratory session of the course will be a presentation of material in a Poster Session. You
will prepare a poster in pairs from one scientific article. For detailed instructions, see Lab Exercise 14
Lab Exercises You are responsible for turning in material = ~114
from various exercises and your flow charts from most of the labs.
Total Laboratory Points = ~414
TOTAL COURSE POINTS = ~1256
BIO 107 GRADING POLICY
The following is my grading policy so that there is no confusion as to how I grade.
All exams are graded by an ID number so that I do not know whose exam I am grading. The
purpose of using this method is so that I do not have any preconceived ideas about how people
should be doing when I grade.
From the beginning of the course, I guarantee that any student with:
90% or above will receive an A or A-.
80 to 89.9 B+, B or B-
70 to 79.9 C+, C or C-
60 to 69.5 D+, D or D-
less than 60 F
This means that if all of you are between 80 and 89.9, all students will receive a B, B+ or B-. I will
NEVER up the percentage necessary for that grade. I really wish that all students in the class
would attain this level or higher.
I go over the scores at the end of the semester. I look at averages of the different exams, trends
in scores over the years that I have taught the class, presence of graduate students in a certain
area of the grade scale.
It is possible that when I look at the scores at the end of the course I may
lower the percentage required in each grade category. This means that 89
or 88 might become an A- or 79 or 78 might become a B-. (Over the last 8
years, the lowest percentage that became an A- was 87%. The other grade
ranges were lowered consistent with that percentage.)
I also try to look at exam scores for you as individuals, particularly if you are on the borderline of
a grade range. I try to take into consideration if one exam was low and all others were high.
A plus or minus grade will have an approximately 1.5% span. Example: C- could be 70 to
71.5%. A C+ could be78.5 to 79.9%.
I do not give extra credit. Homework and laboratory assignments should receive high scores to
increase your score in the course.
Schedule of Lectures - Idealistic
DATE TOPIC HANDOUT CHAPTER
1-26 Introduction 1
Basic Concepts in Immunology 2 1
1 - 31 Basic Concepts in Immunology 2 1
Antibodies, Antigens, Monoclonal Antibodies - An Parts of
Introduction 3 3,4
2-2 Monoclonal Antibodies - An introduction 4
Cell Membranes and Membrane Molecules, Flow
Cytometry 4 6
2-7 Innate Immunity - Complement Pathways
(Turn in answers to questions on Clonal Selection
article, Scientific Amer. 257:62, 1987) 5 13
2-9 Innate Immunity - The cells Video on phagocytic cells 6 1,2
2-14 (Innate Immunity - Continued) 1,2
(Turn in flow cytometry analysis information) 6
2-16 Development of Hematopoietic Cells 7A 2
Organs, Tissues and Cells of the Lymphoid System 7B 2,15
2-21 Exam 1 through Handout 6 150 points
Will include at least 5 points on the tutorial on plagiarism
2-23 Organs, Tissues and Cells of the Lymphoid System 7B 2,15
Antigens and Antigenic Determinants 8 3,18
2-28 Antigens and Antigenic Determinants, Vaccines
Immunoglobulin Structure and Function 8 3,18
3-2 Immunoglobulin Structure and Function (Continued) 9 4
(Turn in answers to Tetanus Problem Solving)
3-7 Immunoglobulins (continued) 9 4
3-9 Antigen-Antibody Interactions 10 6
3-14 Exam 2 through Ag-Ab interactions (Handout 10) 200
3-16 Variable Region Genes 11 5
3-20 Variable Region Genes (con’t) 11 5
3-23 Constant Region Immunoglobulin Genes 12 5
(Lab Exam 1 on March 21, 22, 23 through Lab 6
Spring Break - March 27 through March 31
4-4 Major Histocompatibility Complex 13 7,8
4-6 MHC (continued) 13 7,8
T Cell Receptor, T cells 14 9,10
4-11 T Cell Receptor, T cells (continued) 14 9,10
4-13 Cytokines 15 10,13
4-18 Exam 3 through Handout 14 or 15 200 points
4-20 Cytokines (continued) 15 11
Cell-cell interactions 16
4-25 Cell-cell interactions (continued) 16 11
4-27 Cell mediated Immunity 17 14
5-2 Cell mediated immunity (continued) 17 14
Immunodeficiency (Lab Exam 2 on May 2, 3, 4 125 19 19
5-4 Immunodeficiency 19 19
Allergy 18 16
5-9 Allergy 18 16
HIV (Poster Session - Labs on May 9,10,11) 20 19
5-11 HIV 20 19
Infection and immunity 21 17
5-16 Infection and immunity 21 17
7:15 am Friday, Final Exam (through Handout 21) 250 points
University, College, or Department Policy Information
Academic Integrity Statement
“Your own commitment to learning, as evidenced by your enrollment at San Jose State
University, and University’s Integrity Policy, require you to be honest in all of your academic
course work. Faculty members are required to report all infractions to the office of Judicial
Affairs. The policy on academic integrity can be found at:
Campus policy in compliance with the Americans with Disabilities Act
“If you need course adaptations or accommodations because of a disability, or if you need
special arrangements in case the building must be evacuated, please make an appointment with
me as soon as possible, or see me during office hours. Presidential Directive 97-03 requires that
students with disabilities requesting accommodations must register with DRC to establish a
record of their disability.”
Department Policy on Repeating Classes
Students will be allowed to repeat biology majors= classes ONLY ONCE. This includes repeating
classes for Academic Renewal and repeating them at other institutions. Note that failure to
successfully complete a required major’s class in the second attempt may result in
disqualification from the major.
Department Policy on Late Adds
The Department of Biological Sciences does not approve Late Adds (adding classes after the end
of the add period indicated in the schedule and directory). You are responsible for adding
classes before the last day to add and for confirming via Touchtone that you are in the class.
When your instructor gives you an add code, you should use it as soon as possible to avoid