Biology 335: Molecular Biology Spring
2001
Instructor: Sigrid A. Carle
Rosenberg 205, Ext. 3589
E-mail: carle@hws.edu
Office Hours: Tuesdays 1-2 p.m. and Wednesday
11-noon.
Required Material:
Concepts
of Genetics, sixth edition, William Klug and Michael Cummings; 2000
Lab
notebook
Suggested Material:
A Cell Biology textbook
We will also be using Molecular
Biology, Robert Weaver, 1999. I
didn’t order this book, but if you would like to have a copy, go ahead and buy
it.
Objectives:
My
goal is to provide you with a broad understanding of molecular biology. The course is divided into three
sections. The first part of the course
is devoted to understanding DNA structure, mutations, and repair. Once accomplished, we will turn our
attention to the exciting field of biotechnology and its applications. Lastly, we will examine how organisms
control gene expression, particularly in relation to cancer and development.
My
overall goal as an instructor is to get you to think like a scientist. The field of molecular biology is rapidly
evolving and has changed a great deal since I graduated from William Smith.
Most students will not remember the details of molecular biology a year, much
less five years, from now. Some of this
information will be outdated in five years anyway. More importantly, I hope you will carry away an understanding of
how scientists devise experiments, draw conclusions, and build working models
of how genes work. In light of this
goal, lectures and labs are presented from the experimental point of view. Whenever possible, I present the fundamental
experiments that led to the working models we are discussing.
Lecture: Attendance at lectures is mandatory. It is expected that you will come to class
having read the material and that you will take good notes. You may tape record the lecture if you
wish.
Laboratory: Attendance at labs is mandatory. If you miss a lab without making some
arrangement ahead of time, you will automatically fail the course. Labs are scheduled for Wednesday and
Thursday afternoons. If you can't make
your regular lab, tell me by TUESDAY, and you may be able to switch lab
periods. Since all labs will take more
than one lab period to complete, you will not be allowed to switch lab days for
only one week.
Labs meet in room 216 Rosenberg Hall.
Seminars: The
biology department sponsors seminars every semester. As scientists, we keep in touch with the scientific community by
reading journal articles and by attending seminars. To encourage scientific engagement, I am requiring all students
to attend at least two seminars this semester.
The list of seminars and times (if known) are given below.
Speaker Date/time
Dr. Steven Kresovich Sigma Xi Speaker April 11th
Dr. Cory-Slechta Biology Department Speaker April 20th
@3 p.m.
TBA Biology
Department Speaker TBA,
Friday @ 3 p.m.
Biology Honors and independent study students April 27th
or May 4th
Articles: We will be reading several articles this
term that relate to material covered in class and lab. We will read a mix of primary literature, review
and ethical-issues articles. The
readings are intended to give you an overview of a system or enhance your
understanding of how experiments are conducted and how models are developed.
1. Can
the ends justify the means?:Telomeres and the Proc.
Natl. Acad. Sci. USA Feb. 1st
mechanisms of replicative senescence and 95:9078-9081, 1998 (in class)
immortalization in mammalian cells.
2. Transgenic
monkeys produced by retroviral gene transfer Science
201:309-312, 2001 March 21st/22nd
into mature oocytes. (in
lab)
3.
Paramutation and transgene silencing: a common Trends in Plant Science April 5th
Response to invasive DNA? 1:363-402,
1996 (in
class)
4. Oncogene
papers- Student presentations To be determined April 25th/26th
(in lab)
5. Ethical considerations for genetic
engineering Several
short papers May
2nd/3rd
(in lab)
Grading: Your overall grade for the course will be
determined as follows:
Exam
1 15% 200 pts
Exam
2 15% 200 pts.
Final
Exam 30% 300 pts.
Lab
Work 25% 250
pts
*Paper
Presentation 5% 50
pts
*Papers
to be presented the second to the last week of lab.
The
exams will include material from lecture and lab; the final is comprehensive. Exams 1 and 2 are scheduled for March 8th and April 12th. The final exam is scheduled for May 8th, the same day senior
grades are due, we will need to pick a new final exam day.
LECTURE TOPICS Readings
DNA structure, function, and organization Chapt. 2-W;
Chapt. 11,19,20-K
DNA replication Chapt.
20 & 21-W; Chapt. 12
Mutagenesis and DNA repair Chapt.
17 - K
Recombinant DNA and its applications Chapt. 4,5-W; Chapt. 18-K
Mitochondrial and Chloroplast DNA Chapt. 19-K; and other sources
Transcription-prokaryotes Parts
of Chapts. 15; Chapts. 6-9-W
Transcription-eukaryotes Parts
of Chapts.16-K; Chapts.10-13
Control of gene expression-translational Parts of Chapts.
14-19-W; Chapt. 16-K
and
post-translational
Genetics and cancer Chapt.
21–K
Control of Development - If time permits. Chapt. 20
W=
Weaver K=
Klug and Cummings
LABORATORY
SCHEDULE: We will conduct a semester-long project in
lab. The project involves
identification of a region of a clone by Southern blotting, subcloning this
region, sequencing the region, and determining where to insert an antibiotic
gene into the region such that the clone can be used to mutate the wildtype gene. Periodically, I will collect notebooks and
sections of what will be your final lab write-up. At the end of the semester, you will turn in a full lab report.
Lab
purpose Techniques Date(s)
Isolation
of cosmid DNA and pBS RPM
kit 2/7&8
Identification
of ORF7 in 3vt5 clone Restriction
enzyme digestion of cosmid DNA 2/14&15
Gel electrophoresis
*Southern Blotting 2/21&2/22
Isolation
of ORF7 and subcloning Restriction
enzyme digestion of cosmid DNA 2/28&3/1
Gel electrophoresis
Isolation of ORF7 by
gene clean
Gel electrophoresis and
ligation of ORF7 into pBS 3/7&3/8
Transformation of JM109
with plasmid DNA 3/21&22
*Isolation of plasmid DNA and set up for
sequencing 3/28&29
Determination of cloning strategy Analysis of sequence
data using BLAST 4/4&5
Design
projects and subcloning 4/12-4/19
*Will
require ~ 1 hr of work the day before lab.
We will discuss papers
during lab on March 21st/22 and May 2nd/3rd. April 25th/26th we
will hear student paper presentations.
LAB REPORTS:
Notebook checks are due after lab on the due date. Lab reports are due at 5 p.m. on the due date. Late labs will not be accepted for any
reason.
Topic points Due date
1.
Notebook check 25 2/7 or 8
2.
Introduction and methods through Southern
Blotting 50 2/26
3.
Notebook check 50 3/7&8
4.
Final Lab report 125 4/20