Download Advanced Molecular and Cell Biology (Dorn, Holton)

BIO. 372/572 ADVANCED MOLECULAR AND CELL BIOLOGY (3 cr)
LECTURER: Drs. Lisa Dorn and Bea Holton
Spring 2008
OFFICE: LD: HS45, BH: HS42, 142
PHONE: LD: 3064, BH: 7087, 1102
E-MAIL: [email protected]; [email protected].
OFFICE HOURS:
LD:. Mon 1:50pm to 3:50pm, Friday 1:50 to 3:50pm
BH: W 2-4pm, Th 9:40-11:40am, or by appointment. I usually arrive on campus between 8 am and
4:00pm.
LECTURE HOURS: 11:30am-12:30pm MWF in Halsey Science HS212.
TEXT: Lodish, et. al. (2007) Molecular Cell Biology, 6th edition, W.H. Freeman and Company,
OBJECTIVES:
Molecular and cell biology concerns the anatomy, physiology and biochemistry of animal and plant cells.
This course will be theme-based, meaning that we will cover about 5-6 topics of current interest to cell and
molecular biologists. We will use these topics to learn about general processes such as receptor/ligand
interactions, signal transduction, cytoskeleton (and control of its distribution), gene regulation, cell cycle and
protein translocation. For the sections on molecular biology, we will cover topics concerned with the
molecular mechanisms that generate variation at the phenotypic level and the consequences for the evolution
of that phenotype. Throughout this course, we will read and discuss original papers from the literature so
that students will also become familiar with the methods and the logic that scientists use to test their
hypotheses.
Due Dates and Exam Dates
Date
Significant events
Instructor
22 Feb
Writing Assignment Handout#1
Holton
7-March
Hand in 1st writing assignment
Holton
7-March
Holton
22-30 March
EXAM 1
SPRING BREAK
31 March
Switch instructors
Dorn
11 Apr
EXAM 2 Writing Assignment #2 Handout
Holton/Dorn
25 April
Hand in 2nd writing assignment
Holton/Dorn
25 April
Writing Assignment #3 Handout
Dorn
9 May
Hand in 3rd writing assignment
Dorn
16 May
EXAM 3
Dorn
Dates for paper discussions will be subject to minor changes. Each
Outline of Lecture Topics*
CELL BIOLOGY HALF: The chapters listed will serve as useful background to the papers we will
discuss. We will discuss some of the relevant parts of the chapters as we read articles.
Techniques in cell biology – One of the most important parts of being a scientist is to know how we know
what we know! Throughout the semester we will discuss various specific topics and read papers from the
literature so that we will understand how the authors drew the conclusions that they did. To read papers
productively, one has to understand basic techniques in cell biology.
Ch. 9
Memory – Long term potentiation is the process by which neurons “store” information that allows for
memory. What is the cellular/molecular basis of memory?
Ch. 23
Chemotaxis – Many cells, from macrophages to Dictyostelium (a slime mold) to migratory embryonic cells
and neuronal growth cones, must sense concentration gradients and migrate along those gradients. How do
cells sense gradients in their environment? How do cells respond to those gradients so that they can move in
an oriented fashion? How do cells use environmental signals to control the organization of their
cytoskeleton? To answer these questions, we must consider
How cells receive signals
Ch. 15
How cells transduce signals so that cell behavior and gene expression
alter
Ch. 16
How cells integrate signals and gene controls
Ch. 16
How cellular cytoskeleton is formed and integrated with cellular signaling
Ch. 17, 18
Stem Cell Research – This discussion will focus on past papers that show whether there’s potential to use
stem cells to repair damaged or defective tissues and on recent papers showing progress in making
pluripotent human stem cells.
Cancer – This discussion will blend into the molecular biology part of the course.
Ch. 25
MOLECULAR BIOLOGY/GENETICS HALF:
Molecular structure of genes & chromosomes – Gene expression is indirectly driven by the structure of
chromosomes and the distribution of regulatory elements in the sequence of nucleotides. Here we will
briefly review how sequences of nucleotides are arranged in semi-discrete regions (depending on who is
arguing) of the chromosomes to encode the information in a gene that will be expressed.
Ch. 10
Parts of Chapter 9
(I will refer back to chapter 9 several times in the semester to review experimental techniques)
Transcriptional Regulation -- Most gene expression is regulated at the level of production of mRNA. Here
we will study the various mechanisms by which that is accomplished. Here we will begin our discussion of
the techniques that have evolved out of genomics and their implications for investigating disease.
Ch. 11
Post-Transcriptional Regulation -- This is where we will study epigenetic molecular mechanisms of gene
expression: such as hypermethylation, RNA interference and other mechanisms of post-translational gene
silencing.
Ch. 12
Molecular evolution -- Here we will try to bring together what we know about gene expression to the
study of how DNA sequences inside and outside of the gene regions of a chromosome have evolved and to
some extent the influence of gene expression on speciation and phenotypic evolution.
The literature
*This is an advanced class that covers current, interesting topics. If you have topics that YOU would
like to see covered, please give them to us and we will try to work them in.
GRADING: 40% of the grade will be based on three in-class short essay exams (each exam will include
some comprehensive questions), 45% on three short, research-style papers, and 10% will be based on one
oral presentation, 5% participation in paper discussions (student must be prepared to discuss figures from
discussion papers). 92-100% = A, 89-91 = AB, 82-88 = B, 79-81 = BC, 72-78 = C, 68-71 = CD, 60-67 = D,
below 60% = F. Grades will only be “curved”, if necessary and not until the final total has been calculated.
ORAL PRESENTATION: Undergraduate students will work in pairs; graduate students will work as
individuals. Undergraduates will report, in 20 min., the results of one research paper from the literature.
You may choose any topic that interests you as long as it is relevant to cell or molecular biology, and as long
as the paper comes from a journal that reports primary research (do not use Scientific American, Discovery,
Trends in Cell Biology, etc.). Much of your talk will involve explaining the data to the audience so that the
audience can determine the validity of the work. Graduate students must report on 3 papers and may take up
to 25 min.
GRADUATE STUDENTS: Graduate students will be graded by a higher standard than undergraduates.
Graduate students are expected to be proficient in writing. At this point, they should have a good command
of scientific vocabulary and use it appropriately. They should understand commonly used scientific
techniques and knowledgeably discuss data gleaned from such methods. Their data interpretations should
show insight into the larger, more general problems being addressed. Additional assignments: 1) As
mentioned above, graduate students must give an oral presentation by themselves; and 2) they must prepare a
short (2pg) mini-review of the literature surrounding the topic of the presentation (due at the time of the
presentation).
WRITING ASSIGNMENTS:
General Instructions
We will provide students with selected data from the literature that are relevant to theories discussed in class.
Students are to treat the data as though they were their own and as though they wanted to present them to
others in their field. Consequently, you must first capture the interest of the reader by explaining the
significance of the hypothesis tested in your paper; second, explain clearly the results so that the reader
understands their meaning and draws the same conclusions as you and, finally, discuss how your results
expand upon knowledge published to date. Each paper will have:
- Introduction that gives some background information but mostly outlines questions in the field
(that will be addressed by your data) and significance of the work presented. A rationale statement is often
useful.
- Results section that explains the data. What do the data show? (To answer this question, you may
also have to explain a bit about the techniques used and the rationale for doing specific experiments.) Why
were certain controls done?
- Discussion section in which a reasonable hypothesis is formulated from the data.
This sounds like a lot of writing, but, in fact, the maximum page length will be two typewritten, singlespaced page (font no less than 12). The key is to think clearly, write concisely and say exactly what you
mean…no more, no less.
Students may discuss the data (and interpretations of the data) among themselves. However, and they can
ask us questions, preferably in class where all can profit from the questions and answers.