Biology Dept.


DePauw University

 Spring 2020
SOC 4017

Instructor: Fornari

BIO 315A

Molecular Biology

Lecture: 12:30 -1:30 MWF in Olin 136
Lab: 1:00-3:30 R; Olin 228A & 219 (DNA Sequencing Lab)

Instructor: Chet Fornari
Olin 232

click here for all resgistration information


Required Text: Molecular Biology (2015 - ISBN: 9781464126147 ) by M. Cox, J. Doudna, M. O'Donnell; and (not required but very helpful for the laboratory work): Calculations for Molecular Biology and Biotechnology 3e: a Guide to Mathematics in the Laboratory, (2016, 3rd ed., ISBN: 9780128022115) 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

All our science, measured against reality, is primitive
and childlike -- (and yet it is the most
precious thing we have)."
--Albert Einstein

"One of the strengths of scientific inquiry is that it can progress
with any mixture of empiricism, intuition, and formal theory
that suits the convenience of the investigator."
--G.C. Williams

What is "BIO 315 Molecular Biology"?

A course designed to present the scientific theory of molecular biology combined with the experimental laboratory practices of:
(a) recombinant DNA technology (genetic and genomic engineering)
(b) analysis and visualization of DNA and protein structures (Chimera program)
(c) genomic editing and analysis (relevant experimental and web-based tools for CRISPR).

Pre-requisites: Bio 101 and CHEM 120 OR CHEM 240 OR permission of instructor.

What is Molecular Biology?

William Stansfield’s A Dictionary of Genetics 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”. Molecular Biology is a coherent set of principles, concepts, and ideas that 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. Two of the larger goals of modern molecular biology are (1) to elucidate the connections between the genotype (the sequence of nucleotide base-pairs in an organism's genome) and the phenotype (observable traits and behaviors) in terms of a general and comprehensive molecular theory (often represented by the 'Central Dogma' of molecular biology), and (2) to relate macromolecular structure to function and evolution (essentially how Molecular Biology was 'born' after DNA's structure was solved by Watson and Crick). 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 structures, architectures, organization, and especially the myriad interactions of its component parts, from which emerges a dynamic network of connected component parts, the wondrous and beautiful poetry of life."


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.

Four 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 eukaryotic genes?

  • 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 only for 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 that 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 (mainly by way of the Central Dogma) needed to pursue cogent experimental projects in the laboratory, including methods and 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 in Genome Editing. It consists of a series of integrated experiments organized into "modules" (each module has one or more lab sessions): 
1. Basic assays and methods for working with DNA and enzymes for genetic and genomic engineering.
2. Design of PCR primers (theory and practice), and PCR of selected template DNAs to generate clonable fragments and specicalized vectors for use in genome editing.
2. Cloning (includes Gibson cloning strategies and tactics) and gene editing (by the newest methods - CRISPR for example) and sequencing of target DNA fragments.
3. Bioinformatics of cloned, sequenced DNA fragments and genomes (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 {week of March 2nd; week of April 6; May 1st}
Lab work, reports, (with flow charts) = 20% of final grade (includes an instructor-evaluation of your preparation for each lab (with flow charts), your execution of experiments, and your understanding, analysis, and interpretation of the results).

Please Note: I often assign a series of Optional One Point Assignments - 'OOPAs' during the semester; each assignment, no matter how long, is worth at least 'one point' if executed properly, and no point if it falls short of my expectations. These points add directly to your exam scores, and the OOPA questions/problems are often used on the exam (larger assignments become 'MuPAs' or Multiple Point Assignments).

Links to helpful or interesting Web Sites (on Web-site syllabus only)

Biology Animation Library

The Biology Project

OMIM-Genetic Diseases in Humans

DNALC Home Page

Nucleic Acids Database

Homo sapiens
(site for human genetic diseases)

Human Genome Project Information

Homeodomain Resource

The Biology Project Molecular Biology

The Biology Project Human Biology

Karyotyping Activity

Sanger Wellcome Trust Center


European Bioinformatics Institute

Research Collaboratory of Structural Biology

Ensembl Genome Browser

UCSC Genome Browser

BioMath Calculators

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