BIO 430: Molecular Biology, Winter 2011
Instructor: Dr. Kathy Szick-Miranda
Office: Sci I 316
Phone: 654-6165
Email: kszick-miranda@csub.edu
Web: www.csub.edu/~kszick_miranda
Office hours: M W 8:30-9:30; M 1:00-3:00; W 12:20-2:00
Lecture: M W 9:30-10:50am, Sci I 313
Lab: T R 9:30-12:00, Sci I 313
Required Books:
•Weaver, R. 2008. Molecular Biology, Fourth Edition. McGraw Hill.
•Lab Manual Packet - To be distributed in lab and/or will be available via the web.
Course Description:
Evolution and molecular organization of the cell, macromolecules of organisms, and gene expression.
Emphasis placed on recombinant DNA techniques, genetic engineering and biotechnology. Prerequisite:
BIO 304 and 310.
Course Goals:
In this course we will examine the core concepts of molecular biology, including DNA structure,
replication and repair, recombination, gene expression, and the regulation of gene expression. Upon
completion of this course, you are expected to be able to:
•Define and describe the chemical structure of both DNA and RNA at the molecular and macromolecular
level.
•Describe the process of replication including enzymes involved.
•Describe transcription and translation in both prokaryotes and eukaryotes.
•Understand how and why mutations occur, what mechanisms are involved in repair of mutations and
what effect mutations have in the short term and evolutionarily.
•Finally, an emphasis will be placed on the ability to interpret data that is the direct result of recombinant
DNA techniques and procedures.
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
2009-2011 catalog page 82.
Attendance and Participation:
I will not record attendance in lecture however, the lectures will provide a great deal of information that
you may not find in your text. Laboratory sessions are mandatory. Your overall grade in the course will
reflect the extent to which you participate over the course of the quarter.
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
B- = 80-82.9
D+ = 67-69.9
A-= 90-93.9
C+ = 77-79.9
D = 63-66.9
B+ = 87-89.9
C = 73-76.9
D- = 60-62.9
B = 83-86.9
C- = 70-72.9
F = 0-59.9
*All assignments are due at the beginning of class on the date indicated. Any assignment turned in after
that time will be penalized 10% per day.
Assignment Point Values:
Exam I
Exam II
Exam III (Final)
Journal article review
TOTAL
100pts
100pts
100pts
75pts
375pts
Reading and Lab Assignments:
1. For each lecture, the reading will relate to the topic of that day and should be done in advance of
lecture so that you will be familiar with what will be lectured on.
2. There may be additional handouts and/or reading.
3. You must come to lab prepared (by reading the lab assigned PRIOR to the start of the exercise) AND
you must keep a meticulous notebook.
Laboratory Notebook
Each submission in your notebook must contain: date, title, objective(s), the protocol you
followed, raw data collected, interpretations/conclusions. Laboratory notebooks should be used at
all times in the laboratory, nothing should be written on note paper, paper towels, etc. The
laboratory notebook should serve as a daily diary of your efforts in the lab.
Journal Article Review:
Find an article in some area of molecular biology that interests you. Use articles from primary journals
such as: Science; Nature; Cell; Plant Molecular Biology; The Plant Cell; Proceedings of the National
Academy of Sciences, USA; Molecular and General Genetics; EMBO J. (European Molecular Biology
Organization Journal). Once you have selected an article you must get it approved by me. Submit a PDF
file of the complete article to me for approval (see syllabus for deadline). This can be sent by e-mail.
Please send only one article at a time for approval. Once you have received approval, you are to prepare a
review of the primary research article. Be sure to include the following:
1. Title page – this should include all of the information needed for a complete citation. Title of the
paper, title of the journal, volume, page numbers, year, authors and institution(s) and your name.
2. General background – why is this topic of interest and other important information needed to
understand the research.
3. Introduction of the research – Hypothesis and/or specific aims of the research
4. Description of the experiments along with results
5. Conclusions
6. Future directions
Lecture Schedule - BIO 430 Winter 2011
WK
Day
Date
Topic
Reading
1
W
Jan. 5
Intro to course
Ch1 1-11;Ch2 13-15;Ch3 32-50
2
M
W
Jan. 10
Jan. 12
DNA Structure
DNA Structure
Ch2 15-30
3
M
W
Jan. 17
Jan. 19
MLK HOLIDAY
Chromosome Structure
Ch13 359-367; 377-383
4
M
W
Jan. 24
Jan. 26
Transcription Prokaryotes
Transcriptional Reg. (Proks)
Ch6 126-165
Ch7 172-183
5
M
W
Jan. 31
Feb. 2
Transcription Eukaryotes
Transcript Processing
Ch10 250-274; Ch11 281-314
Ch15 444-464
6
M
W
Feb. 7
Feb. 9
Splicing
Alternative Splicing
Ch14 399-443
7
M
W
Feb. 14
Feb. 16
Transcriptional Reg. (Euks)
Translation
Ch12 321-346
Ch19 607-633; Ch17 521-546
8
M
W
Feb. 21
Feb. 23
Translation
The Genetic Code
Ch18 573-599
Ch18 564-571
9
M
W
Feb. 28
Mar. 2
Replication
Replication
Ch20 639-659
Ch21 683-704
10
M
W
Mar. 7
Mar. 9
Biotechnology/Cloning
Genomics and Proteomics
Ch24 770-777
Ch24 778-819
10 1/2
M
Mar. 14
Review
Final
W
Mar. 16
Final Exam 11:00-1:30
Lab Schedule - BIO 430 Winter 2011
WK
Date
Topic
1
R-Jan 6
Intro Techniques
2
T-Jan 11
R-Jan 13
DNA restriction digest
3
T-Jan 18
R-Jan 20
Gel electrophoresis of restriction digest /Primer design
DNA extraction
4
T-Jan 25
R-Jan 27
PCR theory and practice
EXAM I
5
T-Feb 1
R-Feb 3
Nested PCR
Analysis and purification of PCR product
6
T-Feb 8
R-Feb 10
Ligation and transformation
Plasmid minipreps and restriction digests
7
T-Feb 15
R-Feb 17
Analysis of restriction digests and sequencing prep
EXAM II
8
T-Feb 22
R-Feb 24
Wiggle Room
Wiggle Room
9
T-Mar 1
R-Mar 3
Protein Extraction/SDS polyacrylamide gel/Western blot
Analysis of SDS gel/Western blot detection
10
T-Mar 8
R-Mar 10
Bioinformatics
Bioinformatics/Microarray interpretation
10 1/2
T-Mar 15
Study Time!
*Article selections due January 24th, review due Monday March 7th.