Biology Dept.


DePauw University Spring 2015
SOC 4020

Instructor: Fornari

BIO 315A

Molecular Biology

Lecture: 10:20 -11:20 MWF in Olin 136
Lab: 9:00-11:20 R; Olin 228A & 219 (DNA Sequencing Lab)

Instructor: Chet Fornari
Olin 232

click here for all resgistration information


Required Texts: Molecular Biology of the Gene (2015 - ISBN:978-0321762436 ) by J. Watson et al; and (not required)
Calculations for Molecular Biology and Biotechnology: a Guide to Mathematics in the Laboratory, (2010, 2nd ed.) by F.H. Stephenson; Academic Press Publishers

(1) "Follow your reason as far as it will take you."

(2) "Do not pretend that conclusions are certain which are not demonstrated or demonstrable."

--T. H. Huxley

"To kill an error is as good a service
as, and sometimes better than,
the establishing of a new
truth or fact."
- Charles Darwin

What is "BIO 315 Molecular Biology"?

A course designed to present the scientific theory of molecular biology and combine it with the experimental laboratory practices of recombinant DNA and genetic engineering. Pre-requisites: BIO 215, or permission of instructor. (NOTE: CHEM 120 is required for BIO 215).

What is Molecular Biology?

William Stansfield’s A Dictionary of Genetics (5th ed., 1997, Oxford University),  defines molecular biology as “a modern branch of biology concerned with explaining biological phenomena in molecular terms. Molecular biologists often use biochemical and physical techniques to investigate genetic problems.”

And please note:

MOLECULAR BIOLOGY is not merely a “set of techniques” as claimed by many non-molecular biologists (witness that of the 21 chapters in the Watson text, only ONE is entitled 'Techniques of Molecular Biology'). Molecular Biology is a coherent set of  principles, concepts, and ideas, which all have strong support from large experimental data sets; the raw data comes from the application of powerful biochemical, genetic, bioinformatics (computational biology), and biophysical techniques to the main conceptual questions and theoretical problems in all areas of biology. One of the larger goals of modern molecular biology is to elucidate the connections between the genotype (the sequence of nucleotide base-pairs in the organism's genome) and the phenotype (observable traits and behaviors) of all organisms in terms of a general and comprehensive  molecular theory. In this sense, modern Systems Biology, which includes molecular biology, tries to understand the so-called Emergent Properties of life, from atoms to ecosystems.

"Details matter if we seek to understand the universe with all its basic structures, architectures, organization, and especially the myriad interactions of its component parts, which leads to wondrous and beautiful poetry."


Description of Course Contents

The lecture portion of the course (see combined lab-lecture syllabus) serves two purposes; note that the second purpose (see below) is dictated by the laboratory experiments and project: 

(1) to present the basic, core principles of molecular biology by way of protein-nucleic acid interactions within the conceptual frame-work of the Central Dogma functions with special emphasis on gene regulation.

Three primary questions to scrutinize and answer are:

  • What are the essential features and properties of nucleic acid and protein structure?

  • What are the essential features and properties of genetic mechanisms for gene expression?

  • How does understanding macromolecular structure and genetic mechanisms inform us about the functional interactions of the "Central Dogma" (replication, transcription, translation, and gene regulation)?

(2) to provide a solid theoretical basis not onlyfor methodology used in the laboratory projects, but also hypothesis construction and testing by proper experimental design (i.e., the scientific method used in molecular biology).

Three primary questions to scrutinize and answer are:

  • What is the molecular, biochemical, and genetic basis for any method or technique used in the lab?

  • How does the molecular, biochemical, and genetic basis for a technique serve to explain its function in a given lab context?

  • How does understanding the molecular, biochemical, and genetic basis of techniques serve to aid in the effective, intelligent design of experiments for testing specific hypotheses?

We will integrate major concepts to show the unity in the various components of molecular biology (physics, chemistry, biochemistry, genetics). Every attempt will be made to collect details into regular, concept-based patterns which form the over-arching themes and principles of molecular biology. Yes, these patterns and themes exist! Reductionism will lead to Holism and increased awareness of how sets of regularly repeating themes and patterns, first observed in macromolecular sequences, combine in myriad ways to generate the wonderful, rich diversity of living organisms. In other words, together we will try to get at least a glimpse of the subtle variations in relatively simple biological structures, and how these variations combine in numerous ways to contribute to a wonderful and exciting biological complexity.

The lecture portion of the course includess the necessary knowledge and understanding needed to pursue cogent experimental projects in the laboratory, including the interpretation of data and results. This approach also ensures that you are maximally engaged in the process of science within the discipline of molecular biology, as opposed to be becoming pre-occupied with only the products of experimental work in molecular biology.

The course should make you fully aware of the central role that molecular biology plays in all areas of biological research. Becoming knowledgeable and proficient in the philosophy and experimental practice of molecular biology will provide you with a solid foundation for pursuing and understanding other major areas of biology such as genetics, cell biology, developmental biology, physiology, nuerobiology, and evolution and ecology.
All areas of biology are touched by molecular biology, and all areas use its experimental methods and approaches.
The lab portion of the course will engage you in both basic and sophisticated techniques and methods of molecular biology. The lab is designed to reflect the process of doing a research project over the course of the entire semester. Please see the lab & lecture syllabus for more information about the lab sessions and exercises.

The lab portion of the course is a semester-long research project. It consists of a series of integrated experiments organized into "modules": 
1. Basic assays and methods for working with DNA.
2. Design of PCR primers, and PCR of selected template DNAs to generate clonable fragments
2. Cloning and sequencing of target DNA fragments from multigene families (rRNA and HOX genes, and other genes involved in development).
3. Bioinformatics of sequenced DNA fragments (all computer-based work with specific programs).
4. Summarizing all results in a formal Lab Report based on the "Expanded Abstract" format.


Grade categories, distributions, scaling, and Exam dates:
3 exams = 80% of final grade {th, 11th; Tues. Final Exam time slot for third exam, 8:30-11:30 AM}
Lab work, reports, (with flow charts) = 20% of final grade (includes an instructor-evaluation of your preparation for each lab, your execution of experiments, and your understanding, analysis, and interpretation of the results).

Please Note: I may assign a series of One Point Assignments during the semester; each assignment, no matter how long, is worth one point if executed properly, and no point if it falls short of my expectations. These points add to your exam scores.

Links to Web Sites (on Web-site syllabus only)

Biology Animation Library
The Biology Project
Yahoo! Science:Biology:Genetics:Cloning
Yahoo! Science:Biology:Genetics:Cloning:Human Cloning
Yahoo! Science:Biology:Genetics:Human Genetics

DreamTech International
OMIM-Genetic Diseases in Humans
Yahoo! Health:Diseases and Conditions:Genetic Disorders

DNALC Home Page
Homo sapiens
(site for human genetic diseases)
Human Genome Project Information
The Biology Project Molecular Biology
The Biology Project Human Biology
Karyotyping Activity
Genome Sequencing
WU Libraries Genetics, Genomics, Molecular Biology, Computational Biology
BioMath Calculators

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