BIO 577:Advanced Molecular Biology, Spring 2009
Instructor: Dr. Kathy Szick-Miranda
Office: Science I, 316
Phone: 654-6165
Email: kszick-miranda@csub.edu Web: www.csub.edu/~kszick_miranda
Office hours: T Th 12:20-3:10pm
Lecture and Lab: T Th 3:10-4:25pm; 4:35-7:05pm, Sci I 215
Course Philosophy/Format:
This course in advanced molecular biology is designed as a rigorous introduction to the topics,
terminology, techniques, methodologies and approaches of modern molecular biology that may not have
been covered in an introductory molecular biology (or molecular genetics) course. This course is taught
with the assumption that students have had previous courses in biochemistry, molecular biology and/or
genetics and that many have already had some laboratory experience. We will examine core concepts in
molecular biology including, DNA damage and repair, homologous recombination, transposition,
chromatin remodeling, alternative splicing, posttranscriptional regulation of gene expression and the role
of regulatory RNAs. Additional topics that contribute to our understanding of gene expression will
include recent advances in genomics and proteomics.
This course serves to help students make the transition from lecture-based, text book-oriented courses
common in undergraduate training to independent learning organized around current research papers and
seminars that are the hallmarks of advanced studies.
The topics/concepts we will cover are grouped into two time block clusters. The first time block will
cover the topic in the traditional lecture/powerpoint format, while the second time block will be focused
on analysis and understanding of current scientific papers.
Students will be assigned a discussion paper. As the discussion leader, it will be the students
responsibility to provide an overview, lead the discussion and summarize the assigned paper. Students
are expected to read all of the assigned literature and contribute in a significant and meaningful way to
the group discussion. Discussion leaders for papers that have not been assigned to a specific person, will
be chosen at random the day the paper is to be discussed.
Participation in classroom discussions and student presentations is essential. Consequently, attendance is
mandatory. There is no mechanism for making up discussion material or classes that are missed and no
credit will be given for classes that are missed.
Reading Materials:
Suggested:
•Weaver, R. 2008. Molecular Biology, Fourth Edition. McGraw Hill.
Required:
•Lab Manual Packet - To be distributed in lab and/or will be available via the web.
•Discussion papers - To be distributed in lab and/or will be available via the web.
Assignment Point Values:
Exam I
Exam II
Exam III (final)
Attendance/Participation
Discussion Leader
Research Report
TOTAL
100pts
100pts
100pts
50pts
50pts
75pts
475pts
Academic Policies: It is expected that your work is YOUR work. In the unexpected event of plagiarism
and/or dishonesty during exams or for the research term-paper, the student will receive a zero on that
activity and be referred to the campus administration for disciplinary action. Please refer to the campus
2007-2009 catalog page 81.
Grading: Grades will be based on the percentage of points accumulated in the course (lecture and lab)
using the scale shown below.
A = 94-100
A-= 90-93.9
B+ = 87-89.9
B = 83-86.9
B- = 80-82.9
C+ = 77-79.9
C = 73-76.9
C- = 70-72.9
D+ = 67-69.9
D = 63-66.9
D- = 60-62.9
F = 0-59.9
*Missed lecture exams due to illness or other justified reasons can be made up. If you know in advance
that you must miss an exam, see me and bring documentation to support your anticipated absence.
LECTURE SCHEDULE & READING ASSIGNMENTS
Wk
1
Date
R-Apr 2
Topic
Intro to the course
Reading
2
T-Apr 7
R-Apr 9
Lecture 1- Molecular Tools
Discussion 1
CH 5 84-119
3
T-Apr 14
R-Apr 16
Lecture 2- Genomics, Proteomics, Bioinformatics
Discussion 2
CH 24 797-827
4
T-Apr 21
R-Apr 23
Lecture 3- DNA Damage and Repair
Discussion 3
CH 20 660-682
5
T-Apr 28
R-Apr 30
Exam I
Lecture 4- Homologous Recombination
CH 22 718-738
T-May 5
R-May 7
Discussion 4
Lecture 5- Transposition
CH 23 743-769
T-May 12
R-May 14
Discussion 5
Lecture 6- Chromatin Remodeling
CH 13 368-398
8
T-May 19
R-May 22
Discussion 6
Exam II
9
T-May 26
R-May 28
Lecture 7- Alternative Splicing
Discussion 7
CH 14 422-434
10
T-June 2
R-June 4
Lecture 8- Posttranscriptional Control of Gene Expression
Discussion 8
CH 16 494-500
Lecture 9-Regulatory RNAs
CH 16 501-520
6
7
10 1/2 T-June 9
R-June 11 FINAL 5:00-7:30pm
DISCUSSION SCHEDULE
Wk
1
Date
R-Apr 2
Topic
Intro to Research Component
2
T-Apr 7
R-Apr 9
Sterilize and imbibe seed; prepare plates and top agar
Plate seed (allow to grow for ~10days)
3
T-Apr 14
R-Apr 16
Design primers
Prepare LB plates and liquid media
4
T-Apr 21
R-Apr 23
Harvest seedlings, isolate RNA, set up RT-PCR
Run gel, purify sample, clone into TOPO vector, transform bacteria
5
T-Apr 28
R-Apr 30
Set-up colony PCR, prepare agarose gel
Run gel on colony PCR
6
T-May 5
R-May 7
Plasmid preps, send samples off for sequencing
LR reactions, transform bacteria
7
T-May 12
R-May 14
Set-up colony PCR, prepare agarose gel
Run gel on colony PCR
8
T-May 19
R-May 22
Plasmid preps, send samples off for sequencing
Transform Agrobacterium
9
T-May 26
R-May 28
Set-up colony PCR, prepare agarose gel
Run gel on colony PCR
10
T-June 2
R-June 4
Wiggle-room
Floral Dips
10 1/2 T-June 9
Discussion 9
R-June 11 FINAL 5:00-7:30pm