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CELL AND MOLECULAR BIOLOGY
The purpose of this course is to deepen your understanding of the chemical processes and
structures that occur in the cell and how they are related to the observable characteristics of
cells. We will begin with an overview of the "typical" cell and the structures that are found in it.
We will examine the molecules from which cell structures are assembled. We will discuss the
ways in which cells capture and use energy to produce order. And we will spend a lot of our
time talking about the supermolecular structures in the cell -- what their functions are, and
how function is related to structure. One of the important goals of this course is to enable you
to understand the evidence and reasoning that have led to the current view of the cell, and
provide you with a basis on which to judge evidence and reasoning that will, in the future,
change our view of the cell. In order to accomplish this, you will also be introduced to some of
the techniques that are used in this area.
Other information is found in supporting files.
GRADING
Your grade will be determined as follows:
Three exams
300 points
Lab report first half
20 points
Critiques (2)
25 points each
Lab report second half
40 points
Lab attendance/participation
20 points
Quizzes
Up to 50 points
Grading scale
A
425 points
A-
400 points
B+
375 points
B
350 points
B-
325 points
C+
300 points
C
275 points
and so on
SCHEDULE
We will usually begin at 9:00 daily, although lab work may require you to come in as
early as 8:30. We will be done by 11:15 each morning. We will begin most afternoons
at 12:30 and be done by 3:00. Tests will be in the morning. You are expected to have
read the text material before the lecture. The overall lab schedule is attached to the lab
handout. We will be moving back and forth between lecture and lab often; please do
not dawdle. The text for this course is Cell and Molecular Biology, 6th Ed., by G.
Karp. We will cover chapters 1-6, 8, 11, 13, and perhaps some of 18 of the text.
There will also be a small number of supplementary reading assignments that I will
provide. All necessary materials will be found at the course Moodle site.
THE LAB REPORTS
These reports should be patterned after research articles that appear in scientific
journals. Be sure to read the document on lab reports; it will give you some hints
about writing your report (it will be obvious to me if you haven’t read it). As you will
discover, research articles consist of: 1) an introduction, which lays out the questions
to be answered and considers their significance - use this section to tell why anyone
would be interested in these questions; 2) a section on material and methods which
describes how the work was done - don't include all the detail found in the manual, but
be sure to include the detail not found in the manual (such as gel loads and restriction
enzymes used); 3) a description of how the methods are supposed to work (i.e., why
you did what you did) and the presentation of the results, including (but don't limit
yourself to) figures and tables - be careful in your use of significant figures; and 4)
discussion of the results and conclusions to be drawn. This last section is a chance to
critique your own work. Put the results together into a coherent whole; comment on the
expected as against the actual results. Don't use platitudes (like, "we learned a lot", or
"our poor results were due to human error"). Be specific, not general. Each lab report
is to be no more than 6 pages of normal (10-12 point) typewritten double-spaced text
(excluding figures and tables). The introduction will be worth 20%, the methods
section, 20%, the results, 30% and the discussion, 30%. Remember, plagiarism may
result in a zero for this assignment (see the Compass). The first report (for the first
week) is due on day 10 of the block. For this report, you should prepare only a
methods section and a results section. Save the introduction and the discussion for
the second report. This report should include in the results section a clear explanation
of the method of isolation that we used.
The second report is due the last day of the term. This report should include a clear
explanation of how we isolated organellar DNA, and how we visualized the DNA of
interest in the Southern blot. In both this and the first report, these are not simply
descriptions of what we did, as much as they are descriptions of why we did it, and
what roles the reagents played in the processes.
THE PAPER SUMMARIES
You are required to choose two research articles from scientific journals (no earlier
than 2011) and critique/summarize them. The articles can be in any area of cellular
and/or molecular biology. I suggest that you look through the following journals in
order to find research on a relevant topic: Cell, Developmental Biology, Development,
Journal of Cell Biology, Journal of Biological Chemistry, Journal of Heredity, Nature,
Plant Physiology, Proceedings of the National Academy of Sciences, Science, or
Genetics. You are welcome to consult any other scientific journal to which you have
access. I recommend that you clear the article with me, first, and read the article at
least twice before you decide to use it for your critique. Don’t be intimidated by the
word ‘critique’. Most of what you write will be in the nature of a summary.
The idea of this assignment is to read a research article critically (or deeply); to
discover what question(s) the researchers were attempting to answer, what techniques
they used to obtain the answer(s), and to evaluate how successful they were in
answering the question(s). Choose three or four of the central experiments reported in
the paper and discuss their design and how they do or do not contribute to the
conclusion(s) the authors are attempting to draw
Your first task will be to understand the purpose of the paper. Are the authors testing a
hypothesis or model? If so, what is it? There will be competing or alternative
hypotheses or models that they will try to eliminate. Frequently, these are not clearly
identified. Rather, it is left to the reader to understand them from the experiments and
controls that are done. You should also take this general approach when examining
individual experiments. Why was it done? What alternatives were they trying to
eliminate? Once you have understood these bases for their work, you need to try to
understand and explain their experimental design and methodology. Do they
adequately test the hypothesis and possible alternative explanations (pay special
attention to controls)? Should they have considered other alternative hypotheses?
Some papers are not easily interpreted as hypothesis testing. Frequently, the
researchers are gathering data on which to base a hypothesis. In this case, rather than
beginning with a hypothesis, the authors begin with a set of questions about the
system of interest, questions that have definite, usually quantitative answers. Here,
your job is to critique the significance of their questions, the experimental design and
methodology used to answer them, and whether the results of these experiments gave
or can give useful answers.
Do not comment on whether or not you enjoyed the paper, or found it well written; stick
to an analysis of the science. It may be necessary for you to read related papers
(for instance, references) in order to understand the article. It is not necessary for
you to describe in detail every experiment in the article. However, you must describe
some (3 to 4). Some of them may not be directly related to the main focus of the work.
Some may be more important or central to their point. Concentrate on these. It is
usually best to center your critique on the figures/tables that are most important. It is
not necessary to launch an attack on the authors' work. Sometimes no weakness will
be apparent to you; other times, your criticisms might be very mild. Please avoid direct
quotations from the article. Use your own words and express your own ideas.
Remember that good writing includes a clear and informative introduction and a
coherent conclusion.
When you hand in the critique, attach a copy of the paper being critiqued. The first critique is
due on day 9 of the term. The second is due on day 17. The critiques should not be more
than 3 pages long.
Course Schedule - Lectures
Week
Day
Chapter
1
Monday
1&2
Tuesday
2
Wednesday
2, 18
Thursday
3
Friday
3, 4
Membrane composition and function
Monday
Tuesday
Exam I
4, 5
Mitochondrial structure and function
Wednesday
5&6
Electron transport, ATP synthesis, chloroplasts
Thursday
6 & 11
Light and dark reactions of chloroplasts, genes and
proteins
Friday
11
Transcription in prokaryotes and eukaryotes
Monday
11
Translation
Tuesday
Wednesday
Exam II
13
Thursday
13
DNA repair
Friday
8
Cytoplasmic membranes, endoplasmic reticulum,
Golgi
Monday
8
Lysosomes, proteasomes, endocytosis
2
3
4
Tuesday
Wednesday
Topic
Properties of cells, cell types, small molecules of
cells
Biological macromolecules
Sections 6,7,9,11,12,13 (to page 766) of ch. 18 for
lab
Glycolysis and regulation
DNA replication
Supplementary
Science and society; ethics
readings
Final Exam
Problem assignments: These problems are assigned for your benefit and are not to be handed
in. They are the most useful of the end-of-chapter problems.
Chapter
Problems
2
1,4,7,8,13,14,15,16,18
3
1,2,3,4,7,8,10,12,17,20
4
2,6,9,11,12,13,15,17,19,21
5
2,3,4,5,6,8,10,12,13,14,16
6
3,4,6,7,8,9,10,13,15,17,19
11
1,2,3,4,6,10,12,14,15,18
13
1,3,4,5,6,7,11,12,13
8
1,4,6,7,9,11,14,15,17
Academic honesty:
‘Cornell College expects all members of the Cornell community to act with academic
integrity. An important aspect of academic integrity is respecting the work of others. A
student is expected to explicitly acknowledge ideas, claims, observations, or data of others,
unless generally known. When a piece of work is submitted for credit, a student is
asserting that the submission is her or his work unless there is a citation of a specific
source. If there is no appropriate acknowledgement of sources, whether intended or not,
this may constitute a violation of the College’s requirement for honesty in academic work
and may be treated as a case of academic dishonesty. The procedures regarding how the
College deals with cases of academic dishonesty appear in The Compass, our student
handbook, under the heading “Academic Policies – Honesty in Academic Work.”’
Accommodation for learning disabilities:
‘Students who need accommodations for learning disabilities must provide documentation
from a professional qualified to diagnose learning disabilities. For more information see
cornellcollege.edu/disabilities/documentation/index.shtml
Students requesting services may schedule a meeting with the disabilities services
coordinator as early as possible to discuss their needs and develop an individualized
accommodation plan. Ideally, this meeting would take place well before the start of
classes.
At the beginning of each course, the student must notify the instructor within the first three
days of the term of any accommodations needed for the duration of the course.’
These are official college policies.