Bio 418 Molecular Biology

Spring 2013

Instructor: Dr. William Patrie
Office: FSC 152 Phone: x1400
Web page email:

Office hours: Monday, Wednesday,  Friday 11:00-1:00 and by appointment

Text: Clark and Pazdernik, Molecular Biology, 2nd edition  2013 ISBN 978-0-12-378594-7

Prerequisites: Microbiology (Bio 220),
Genetics (Bio 260), and Modern Organic Chemistry I (Chem 221)

The objectives of this course are to become familiar with the molecular biology of prokaryotic and eukaryotic organisms, to understand current experimental techniques and how to apply them, to read and interpret the current literature, and to utilize on-line resources related to molecular biology. Topics will include: the structure of genes and chromosomes; DNA replication; transcription and the regulation of transcription in prokaryotes and eukaryotes; RNA processing and post-transcriptional regulation; translation; mechanisms of mutation and repair; and genome organization, and molecular evolution.

The text we are using is a very readable survey that covers most of the major concepts of molecular biology. The author favors breadth over depth, and does this at the expense of real experimental data. To compensate, I include numerous examples from the literature, and will assign a number of literature-based assignments.  The second edition of the text includes online access to some journal articles and a short study guide with study questions which you may find useful, but is not required. We will also make use of the many, and growing, resources at NCBI and other web-based molecular databases as well.

Most classes will consist of lecture/discussion.   Some classes will be held in the computer lab or will make use of portable laptops. Selected topics during the last 2-3 weeks of the semester may include aspects of genomics,, epigenetics and the molecular biology of cancer and will make use of current literature.  Use of internet bioinformatics resources will be interspersed throughout the semester.

If anyone in this class has a need for note-taking or test-taking accommodations, please feel free to discuss this with me.


Final grades will be based on the percentage determined by dividing your point total by the total points in the course.

A= 90 and above; B=80-89.9; C=70-79.9; D=60-69.9; F= less than 60. 

      Online (D2L) Quizzes (100 points): There will be approximately 10 online quizzes during the semester, each worth approximately 10 points.

      Problem sets (approx. 200 points): There will be problem sets, literature assignments, and NCBI-based assignments of varying nature, each worth 10-20 points

      Midterm Exam (100 points):  In class and takehome portions.

      Journal article presentations (25 points):  Short presentations of a recent molecular journal article. To be done as pairs (or trios if necessary). 

      Cloning vector brochure and presentation (100 points): small (2-3 students) group project, more details below

      Term Paper (100 points): individual papers, details below.

      Comprehensive take-home final (100 points):  will include problems, literature analysis and NCBI-based problems.

Journal article presentation

These should be brief presentations of background and major results/conclusions of a recent journal article.  15-20 minutes + questions; 2 per class period during the first week of April.

Term Paper

The topic can be a gene, a disease, an organism, a virus, a biotech application, etc., anything with a molecular biology focus- genome structure (epigenome, transposable elements, funky variations) and/or gene regulation (transcription factors, mechanisms, miRNA) and utilizing molecular techniques. Minimum 10 references; 50% review/50% analysis of 2 or 3 recent papers.  You will turn in digital versions of your paper via the D2L/Turn-it-in  dropbox.  

·       Introductory paragraph

·       A more or less chronological review (e.g., initial discovery, observation, or problem through current literature)

·       Analysis of experiments, results and significance of 2 or 3 relevant, recent papers. Figures from the papers that you discuss should be attached as an appendix. 10 pages double spaced, times new roman 12 point plus cited reference list and any attached figures. Focus on key experiments- you do not need to analyze each figure from the paper. Number figures as your own (Figure 1 through....., and cited in the legend). Attach copies of the papers that you analyze if they not readily available online.

·       Conclusions, unresolved issues, future directions

·       List of cited references


Group Project - Advertising Brochure for a Cloning Vector

The goal of this exercise is to understand the general characteristics of cloning vectors and some of the particular features of the many commercially available vectors that have specialized uses.  Some of these specialized uses might include the in vitro transcription of the cloned gene or the expression of high levels of the protein corresponding to the gene product.  Another use might be as a shuttle vector that allows transfer of the gene into another organism.  There are hundreds of vectors currently being marketed.

Each group will be assigned one vector with the purpose of writing a simple advertising brochure for the vector.  The aim is to inform potential customers of the advantages of using this particular vector.  You may want to use the computer, including internet sources, for illustrations, and to use color and special fonts in your brochure; but of greatest importance is the information you provide.

1.  Before class re-read the background information on plasmid and bacteriophage vectors in your texts.  Read the commercial literature and background references for the particular vector.

2. Discuss with your group the main features of the vector you want to emphasize.  All members of the group should understand how the vector is used.  Write down the information that the brochure will contain.

3.  Prepare the brochure.  Use an eye-catching layout with simple, to-the-point phrases and illustrations.  Also use an additional page that includes basic procedures and references to two or three recent publications using the vector.  Be sure to divide the work among group members.

4.  Submit a copy of the finished brochure for grading.  The original will be displayed and each group member will have the opportunity to act as technical representative, describing features of the vector to other class members.

5.  Play the role of company representatives and sell your product!  Be prepared to discuss advantages and limitations, and give some specific advantages over a competitor’s product. You will need to be prepared to answer questions, which means you must have a firm understanding of the uses and features of the vectors.


Molecular Biology Class Schedule

The following schedule is subject to mutation, repair and recombination!

Modified 1/22/2013


Lecture Topic


Special Topic/ Assignmnt

Jan 23,25

Review- Genetics, DNA, RNA, Protein

Ch. 1-3

Central Dogma

Jan 28, 30, Feb 1

Review continued;
Genes, Genomes, DNA

 Ch. 4,9

Journal article- Selenocysteine

Feb 4, 6, 8

NCBI – Basics
Bioinformatics resources


NCBI -Pubmed and BLAST assignments

Feb 11, 13, 15

Molecular Methods - the basics

Portions of Chapters 5-9, 15, 19

Techniques assignments

Feb 18, 20, 22

DNA Replication, Transcription,RNA processing Translation

Ch. 10-13

Journal article- telomeres

Feb 25, 27, Mar 1

DNA Replication, Transcription,RNA processing Translation

Ch. 10-13

Journal article- alternative splicing
NCBI assignment

Mar 4, 6, 8

Midterm Exam
Regulation of Transcription in Prokaryotes

Ch. 16

Journal article- sigma factors

Mar 11, 13, 15

Regulation of Transcription in Eukaryotes

Topic, and a copy of recent article for term paper due before spring break

Ch. 17-18

Journal article- miRNA
Journal article- Epigenome

Chromatin modification

Mar 16 – 24

Spring Break

Mar 25, 27, 29

Advanced Methods

Portions of Chapters 5-9, 15, 19

Journal article-Metagenomics
NCBI assignment

Apr 1, 3, 5

Mutations and Repair, Recombination

Ch 23-24


Journal article- PRDM9

Apr 8, 10, 12

Mobile DNA
Molecular/ genome evolution

Ch. 22,26
Journal article-

NCBI assignment
Journal article- horizontal gene transfer

Apr 15, 17, 19

Journal Article Presentations


Apr 22, 24, 26

Selected topics


Apr 29,
May 1, 3

Selected topics


Exam Week

Term Paper Due; Vector brochure presentations, takehome final due