Instructor:
Dr. Paramjeet S. Bagga
CMB (BIOL 406)
Spring 2016
RAMAPO COLLEGE OF NEW JERSEY
School of Theoretical and Applied Science
Cell and Molecular Biology (CMB) (BIOL 406)
(Lecture+ Lab = 4 Credit Hours)
Spring 2016
Instructor:
Dr. Paramjeet S. Bagga
Professor of Biology
& Convener of Bioinformatics
Office: G-418
(201) 684-7722, pbagga@ramapo.edu
Website: http://pages.ramapo.edu/~pbagga/
Lecture Syllabus
Class Meets:
M/R at 11:00 AM to 12:40 PM
Room ASB-426
Office Hours:
M/R 12:45-1:00 PM & 5:40-6:55 PM
Or by appointment
Course Prerequisites: BIOL 110/112, CHEM 210/211, 212/213 and BIOL 331.
IMPORTANT DATES:
Feb 18
: First Exam
Mar 31 : Second Exam
Apr 8
: Final day to withdraw
May 05 : Final Exam (8:00 AM – 11:20 AM)
Subject Background:
Cell is the basic functional unit of life. Every living creature is either made of cells or itself is a single cell. The
simplest forms of life are solitary cells. Higher organisms, such as ourselves, are made from groups of cells. Cells
perform specialized functions and are linked by intricate systems of communication in multicellular organisms.
We can appreciate the capabilities and limitations of living organisms only by understanding the structure and
function of cells. Modern biologists study them to learn, on the one hand, how they are made from molecules and,
on the other hand, how they interact with each other to allow cooperative construction of multicellular organisms
as complex as a human being.
The more we learn about the structure, function, and development of different organisms, the more we recognize
that all life processes exhibit remarkable similarities. To study the properties of molecules of life and the
innumerable variations on basic themes that are found in different organisms, modern researchers employ
concepts and experimental techniques drawn from biochemistry, molecular biology, genetics, genomics,
proteomics, and cell biology. The resulting discipline of Cell and Molecular Biology investigates how cells
develop, operate, communicate, and control their activities, and on occasions go awry.
Course Description:
This course consists of lecture and lab in which you will acquire the current state of knowledge about cells
and their biology at molecular level. The concept learning process will be aided with many interesting
experiments. It is a challenging course for the students who are new to this field. However, the
overwhelming inventiveness and the beautiful construction of biological systems will intrigue you and
reward your efforts to understand the exciting story of Cell and Molecular Biology.
The structure and function of cells will be discussed in relation to important cellular processes. Subjects to be
covered include: the biology of macromolecules that the cells are made of (review), the technology for
probing cell structure and function, membrane and organelle structure and function, topics on regulation of
gene expression, signal transduction, cell division, cancer, and apoptosis. The experimental approaches that
have lead to the current knowledge of cellular structure and function will be presented whenever possible. In
addition, Bioinformatics, Genomics, and Proteomics which utilize computer science tools to study molecular
biology, will also be introduced.
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Instructor:
Dr. Paramjeet S. Bagga
CMB (BIOL 406)
Spring 2016
Course Goals (Lecture and Lab):
1. Knowledge of fundamental biological processes at cellular and molecular levels.
2. Understanding of the process of scientific inquiry, data analysis, validation, interpretation
and communication of findings.
Course Objectives (Lecture and Lab):
Upon successful completion of the course (Lecture and Laboratory) students should:
1. Be familiar with the structural and functional organization of the living cells (Lec. Exams).
2. Be able to explain how macromolecules store and transmit hereditary information, and build
complex multi-molecular structures of the cell (Lec. exams).
3. Demonstrate understanding of molecular structure/function relationships. Understand the impact
of variation on biological function (Lec. exams, Lab project report).
4. Exhibit familiarity with the major techniques for studying structure and function of cells at
molecular level (Lab. exams and reports).
5. Be capable of making scientific observations, develop appropriate hypotheses and design
experiments to test the hypotheses. Should be able to quantitatively analyze and validate the
results obtained from the experiments, interpret the outcomes and make inferences. Write
logical and cohesive scientific reports (Lab. exams and reports).
6. Be familiar with Bioinformatics, Genomics and Proteomics (Lec. and Lab exams, Lab project report).
7. Be capable of explaining the mechanisms that regulate the levels of RNA and proteins in
eukaryotic cells (Lec. exams).
8. Exhibit understanding of mechanisms by which cells communicate with each other and control
their activities in order to allow cooperative maintenance of multicellular organisms (Lec. exams).
9. Be familiar with latest models of how cells divide and on occasions go awry (Lec. exams).
(Please also see separate syllabus for the lab portion of this course)
Text - Lodish et. al. 2013. Molecular Cell Biology. Seventh Edition. W.H. Freeman and Company.
Recommended Supplemental Reading
In addition to the above assigned textbook, you may find it useful to consult reference or
supplemental texts during this course. I have listed some suggestions below:
Molecular Biology of the Cell (6th Ed). 2014. Alberts et. al. Garland Publishing. An excellent source
for supplemental information.
Lewin's Cells (3rd Ed). 2013. Plopper et.al. Jones and Bartlett Publishers. Emphasis on Cell Biology.
A Genetic Switch. 3rd Edition. 2004. M. Ptashne. Cold Spring Harbor Laboratory Press. Discusses
in quite detail the regulation of gene expression in lambda phage. A well-written classic.
(7th Ed). 2013. G. Karp. John Wiley and Sons, New York. More emphasis on Experimental Cell and
Molecular Biology.
The following Internet based resources may be helpful in preparing you for the CMB course:
http://www.nature.com/scitable/study-center and http://learn.genetics.utah.edu/
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Instructor:
Dr. Paramjeet S. Bagga
CMB (BIOL 406)
Spring 2016
Lecture Sequence*
Topic
Assignment
The Groundwork and Experimental Technology
1.
The Dynamic Cell: An Introduction
Chpt. 1, pp 424--427, Handouts
2.
Macromolecules: Storage and Expression of Genetic Information
pp 116--152, Handouts
3.
Macromolecules: Protein Structure & Function
pp 59-76, 86, Handouts
4.
Tools for Probing Cell Structure and Function
397-415, 419-424, 427-429, Handouts
5.
Tools for Probing…… contd.
pp 93-101,104-106, 184-191, 198-199, Handouts
6.
Bioinformatics, Genomics & Proteomics
pp 101-104, 106-112, 198-202, 252-256, Handouts
Building and Fueling the Cell
7.
Membrane Structure
8.
Intracellular Compartments: Nucleus, ER,
Peroxisomes and "Protein Sorting"
9.
Receptor Mediated Endocytosis
pp 443-461
pp 350, 577-583, 601-602, 612-617, 627-629
Control of Cellular Activity
10.
Eukaryotic pre-mRNA processing
11.
miRNAs and RNAi
pp 654-659, Handouts
pp 345-360, 364-365, Handouts
pp 216-218, 370-374, Handouts
Cellular Signals
12.
Cell to Cell Signaling
Parts of Chpt. 15 and 16
Cell Cycle and its Control
13.
Cell Division and Regulation of Cell Cycle
14.
Programmed Cell Death and Apoptosis
15.
Cancer
pp 873-879
pp 1006-1015, Handouts
pp 1113-1130
*Notes:
1. This is a tentative sequence of topics to be covered. Modifications will be made as and when necessary during
the semester. Modifications, if any, will be announced in the class.
2.
The above order of topics may differ from that of the text-book (as indicative from the assigned chapter and
page numbers against each topic). The assigned text-book covers extensive, in-depth, information on the
subject and is written to serve the needs of students at various academic levels. Above topics have been very
carefully picked by the instructor in order to design a package that suits the academic level and specific needs
expected of the students registering for this course. While average student of this course should easily be able
to understand the taught subject and follow the assigned readings, advanced students can benefit by reading
further from the book.
3.
Since this is a rapidly progressing science and discoveries are made almost everyday, the text needs to be
supplemented by the latest information from time to time. You will be provided handouts, prepared from
latest articles relevant to this course, in order to keep you up to date with the developments in the field.
Whenever possible I will also post on my website (http://pages.ramapo.edu/~pbagga/) or email you relevant
scientific articles, news etc. You should also frequently check out the "Cell & Molec. Biol. Links "on my
website.
4.
Many lectures will be accompanied by detailed class discussion on the subject. The class may be divided into
teams for discussing answers to the questions formulated by the instructor.
5.
Several lectures will be augmented by hands-on activities using classroom computers.
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Instructor:
Dr. Paramjeet S. Bagga
CMB (BIOL 406)
Spring 2016
Important Information and Course Policies

This course has prerequisites (BIOL 110/112, CHEM 210/211, 212/213 and BIOL 331). I expect
that you have a thorough understanding of fundamentals of Biology & Chemistry, Organic
Chemistry and Genetics. If you don't fulfil ALL of the above requirements talk to me immediately.

I expect that you will pay serious attention to the lecture in the class and read the lecture material
before and after the class. Most of my lectures will start with a review of the previous lecture.
During this you will be encouraged to ask me questions. After answering your queries I will also ask
questions to the class.

It is recommended that you bring your textbook to every class. Most lectures will be presented with
the help of overhead-projections, slides or computer presentations. Every now-and-then the
materials presented will not be from the book. In such cases I will provide handouts, announce the
source, reserve it in the library for students, or post it on my Web-site. Please do not start copying
the lecture-outline presented to you on the screen. All the lecture-outlines will be provided as
handouts or posted on my Web-site. You are, however, encouraged to take additional and detailed
class notes to cover details of the lectures and class discussions.

PLEASE ARRIVE ON TIME TO CLASS. Lectures will begin promptly at the designated time. I
will take attendance before most classes. If you come in to the class late (after your name has been
called, or the lecture has already begun), you will be marked absent. However you are still
encouraged to attend the lecture. If you are late, try to enter the class quietly and take a seat close to
the door where you have entered. If you need to, please go to the restroom before coming to the
class or during the designated break. As far as possible, please do not disturb the class for a
restroom visit during the lecture.

You are required to attend All the classes and be present for All the exams and other class
activities. Since on several occasions the information discussed in this class will be from outside the
book, and since the exams are mostly based on materials covered in the class, absences are expected
to result in poor performances in the exams. Each absence could result in 5% penalty for the
lecture grade. Four (two for once a week class) absences could result in ‘F’ grade for the
course.

You are required to turn off the cell phones while in the class. Alternatively, you may switch the
ringer to vibration or quiet mode.

All assignments must be submitted on time and must be legible. Late submission will result in 10%
penalty per day.

In accordance with College policy, I will use your Ramapo College email address
(@ramapo.edu) to communicate with you about all course-related matters. This class requires
that you have an ACTIVE Ramapo e-mail account and have access to the Internet. From time
to time I will also provide information pertinent to the course and post important messages for the
entire class on my Website. You are required to look at the "Bulletin Board" section on my
Website before coming to each class. I will also try my best to notify you about our cancelled or
late classes during rough weather via the Bulletin Board.

If you have any questions or need help, see me at office hours or e-mail me. I will usually be
available outside my office hours as well. Do not hesitate to ask for help / guidance.
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Instructor:
Dr. Paramjeet S. Bagga
CMB (BIOL 406)
Spring 2016
Exams
1. There will be three exams. The first two exams will each cover the material presented in the class (or
otherwise assigned for self-study) up to that day. The last examination will be given during the final
exam period but will include All the material covered during the semester (i.e., the final exam will be
cumulative). NOTE: You are required to bring pencils for all exams.
2. All electronic gadgets should be turned off and left in your bag during the exam. Theses include cell
phones, PDAs, iPods, MP3 players, IM gadgets, electronic watches that can be used to store information,
transmit or receive any kind of signals etc. You are permitted to use your own calculator. You are not
allowed to borrow a calculator from anyone else. Graphics calculators are not permitted during the
exam. If you need an electronic gadget for medical or another essential/special needs, please obtain
permission from your instructor ahead of time.
3. The first two exams will be returned to you promptly in class. The final exam will be kept in your
instructor's office where you may come to review it on a date and time announced in the class during the
final exam. At this time, you will also be able to look at your final calculated grades. Your final grades
will not be emailed to you. Unfortunately, ALL email/voice mail inquiries for finding out the final
grades will have to be ignored by the instructor. You will be able to see your grades online via your
college account after the grading deadline.
4. Your exams will be re-graded if you think an error has been made in grading, but you must submit the
exam and a written description of the error within five business days of the returned graded exams.
5. Make-up exams will not be given (except in rare circumstances of illness accompanied with an
official note from a physician or other valid documentary proof). Make-up exams in these
exceptional cases (if any) will be given during the final exam period. Make-up exams are generally of
higher difficulty level!
Extra-Credit Activities (optional)
You can choose one or more of the following activities to earn a maximum of 2% points towards your
final course average as extra credit. (None of these activities can be double counted for credit in another course).
1. Journal Club Participation: The goal of TAS Journal club is to enhance awareness of the current research
developments in specific scientific disciplines. Journal Club meets on Wednesdays at 4-5 PM in ASB 426.
You can earn 1% point as extra credit towards your final course average for regular, active participation
for the entire semester in this club. You will have to attend all the weekly meetings (attendance will be taken)
AND demonstrate active participation in the discussions to earn this credit.
2. Journal Club Presentation: You can earn 1% point as extra credit towards your final course average by
making a presentation in the Journal Club. For this presentation, you will need to pick a recent (published not
more than 6 months ago) research article related to Cell & Molecular Biology, published in a standard peerreviewed scientific research journal. News articles will not be acceptable. The article has to be a report of
a hard core research project with original data generated, analyzed and interpreted. The Journal club is not
just about presentations. The purpose of presentation is, in fact, to initiate scientific discussions. Open
discussions during and after the presentation are highly encouraged and anticipated. Up to 25 minutes of brief
presentation will generally be followed by 25 minutes of discussion. Presenting student will be expected to
initiate discussions by asking questions to the audience following their talks. In case all the students of this
course cannot be accommodated in the Journal Club, two presentations of 20 minute each followed by 10
minute discussions for each of the respective presentations can be attempted. If this measure is still not
enough to accommodate all students, an election may be held in the class to select the presenting students.
3. Collegiate Level Assessment (CLA) Test: You can earn 1% point as extra credit towards your final course
average via this an approximately hour and a half test. It will be given at the RCNJ testing center within the
first few weeks of semester. This test is not given every semester. The dates, if the test will be given this
semester, will be announced in the class. Only graduating seniors who came to Ramapo as freshmen may
participate in this activity. (In fact, all graduating seniors of this course are REQUIRED to take this test
in the semesters it is given). The Collegiate Learning Assessment (CLA) is a standardized test that examines
students’ general education skills, including written communication and critical thinking. The test is
administered to incoming first-year students in the fall and to native seniors in the spring. The test, which
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Instructor:
Dr. Paramjeet S. Bagga
CMB (BIOL 406)
Spring 2016
takes about an hour and a half to complete, asks students to respond to a prompt designed to simulate a realworld issue. Students use documents and other provided information to construct written responses. The test
also includes a set of close-ended questions. Individual students will receive their own results after the
semester ends. The College will receive aggregated scores for all Ramapo test-takers. Faculty will use this
data to improve student learning in these important skills areas.
Academic Integrity/ Plagiarism /Cheating:
There is a ZERO TOLERANCE policy for Plagiarism
/Cheating or copying. The penalty for plagiarizing in exams, assignments or other class activities is
disqualification from the course and/or other disciplinary action that the college administration decides.
Students are expected to read and understand Ramapo College’s academic integrity policy, which can be
found in the College Catalog. Members of the Ramapo College community are expected to be honest and
forthright in their academic endeavors. Students who are suspected of violating this policy will be referred to
the Office of the Provost.
Course Grading:
Final grade will be based on your performance in lecture exams (60%; 20% each for exam I & II, and the
final exam) and laboratory grade (40%).
Lecture (60%) and Laboratory (40%) grades will be combined and the final letter-grade for the course
will be calculated out of 100% as follows:
A :            
C+:   C    C  D+  D   F: <  
Participation in class discussions, attendance, all other assignments and progress made during the
semester will be taken into consideration IF your grade is borderline.
You MUST pass both the lecture and the lab sections to receive a passing grade for this course.
Outside-Class Preparation: It is highly recommended that you spend a minimum of 2.5 hours outside the
class for each hour spent in the class. Therefore, you should be spending at least 7.5 hours outside the class
every week studying for the lecture part of this course.
Exit Survey: The instructor may ask you to fill out an exit survey towards the end of the
semester for assessment purposes.
If you need course adaptation or accommodations because of a disability that has been documented
with the Office of Specialized Services, please make an appointment with me.
NOTE: I am allergic to most known fragrances. Please be considerate. I will sincerely appreciate if you maintain a safe
distance from me in the class in case you are wearing cologne or a perfume. I will also appreciate if you don’t wear a
fragrance when coming to see me in my office.
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