DePauw University Spring 2013
Lecture:10:30-11:30 MWF in
Instructor: Chet Fornari
Required Texts: Molecular Biology: Principles and Practice (2011) by J. Doudna, M. Cox, M. O'Donnell; and
"To kill an error is as good a service
as, and sometimes better than,
the establishing of a new
truth or fact."
- Charles Darwin
|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).|
William Stansfield’s A Dictionary of
Genetics (5th ed., 1997, Oxford University),
biology as “a modern branch of biology concerned with
explaining biological phenomena in molecular terms. Molecular biologists
often use the biochemical and physical techniques to investigate genetic
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.
In this regard of characterizing molecular biology, keep the following in mind:
"Details matter the most if we seek to understand the living and non-living matter of the universe (i.e., its basic structures, architectures, organization, and the myriad interactions of its component parts); all the rest is beautiful poetry."
Students enrolled in this course may have heard my many references to "structure, function, organization, and evolution." Now add "sequence" to the start of the list, and insert "genomics" before evolution to generate: "sequence, structure, function, organization, genomics, evolution." In this course, we will sort out, discuss, and analyze the relationships and implications of the terms in this new list. Adding "sequence" and "genomics" to the standard list creates a complete Biological focus, and highlights a more recent trend by both molecular biologists and evolutionary biologists to link sequence to evolution.
A Pedagogical Reminder: Our Focus: structure/mechanism; conceptual pattern leading to function; the molecular function within some discrete process, which is part of an overall biologcial phenomena. The Goal is to explain the biological phenomenon with its underlying processe(s) and mechanism(s) in terms of molecular principles and concetps, which are fundamental to understaning biology. These molecular, fundamental principles exist.
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:
(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:
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 an overwhelming amount of 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.
lab portion of the course is a semester-long research project. It
consists of a series of integrated experiments organized
Grade categories, distributions, scaling, and Exam dates:
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 will add to your test scores.
Biology Animation Library
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