Biology Dept. |
BIO 315AMolecular Biology
Lecture: 12:30 -1:30 MWF in
Olin 136
Instructor: Chet Fornari |
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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
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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. |
| 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." |
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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:
(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:
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
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):
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Grade categories, distributions, scaling, and Exam dates: 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). |
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