CHEMICAL BIOLOGY GRADUATE COURSES:
The Chemical Biology Program offers a number of unique courses that are designed to foster interdisciplinary and independent learning. All courses will be taught in the inquiry style, and will focus heavily on examination of the current literature at the interface of Chemistry, Biochemistry and Biology. All courses will be administered by a minimum of two faculty members from different departments involved in the program in an effort to provide complementary viewpoints on a given topic.
The Chemical Biology Program offers graduate courses in the form of both “courses” (which are the formal equivalent of one-half of a full graduate course) and “modules” (which are the formal equivalent of one-quarter of a full graduate course). 600-level half courses are also available for credit, at the M.Sc. level only and with approval from the Program Director, to a maximum of one half course (equivalent to two module credits).
Note that all students outside the program may take the Chemical Biology courses listed below with the permission of the instructor.
CHBY700 Topics in Chemical Biology
CHBY701 Chemical Biology Colloquium A
CHBY702 Chemical Biology Colloquium B
Relevant offerings from affiliated departments:
CHEM6A03 – Advanced Organic Chemistry
CHEM6D03 – Organic Structure and Synthesis
CHEM6DD3 – Mechanistic Biological Chemistry
CHEM6P03 – Advanced Analytical C hemistry
CHEM6Q03 – Advanced Quantum Chemistry
BCHM6E03 – Recombinant DNA Technology and Gene Expression
BCHM6EE3 – Advanced Topics in Gene Expression
BCHM6K03 – Structure and Function of Membranes and Macromolecules
BCHM6Q03 – Biochemical Pharmacology
BCHM6Y03 – Computational Biology
BIOL6B03- Plant Metabolism and Molecular Biology
BIOL6PP3 – Environmental Microbiology
BCHM710 Special Topics in Proteins
Protein Mass Spectrometry and Proteomics. Introductory sessions of the course will describe mass spectrometric methods for protein identification, analyzing protein primary structure and post-translational modifications. The advantages and limitations of various approaches will be discussed. The course will be based on recent review articles and important current papers. The subsequent emphasis of the course will be to have students invest time in inquiry on an aspect of proteomics that is of interest and/or potential future relevance to them and to summarize this in a paper and presentation with an opportunity for critical discussion of the issues.
BCHM711 Special Topics in Molecular Biology
Shape determination and subcellular organization of bacterial cells. Evidence from recent experiments suggests that there is considerable sub-cellular organization in bacterial cells. It appears that specific proteins may determine cellular shape, mediate the directionality of chromosome segregation and cell division and that some of these proteins constitute a bacterial cytoskeleton that is functionally similar to that of eukaryotes. These exciting developments stand in sharp contrast to the “bag of DNA and enzymes” view of bacteria that prevailed a few short years ago. There is however, considerable controversy about some of this data. We will explore this new literature in the context of the bacteria Escherichia coli. Bacillus subtilis, Streptomyces coelicolor and Caulobacter crescentus in detail in this course. Evaluation will be based on oral and written presentations (70%) and on class participation (30%).
BCHM711 Special Topics in Molecular Biology
Recent developments in the cell biology and molecular genetics of cholesterol transport and trafficking will be discussed. Enrollment limited to 10 students. Contact Department for permission.
BCHM713 Enzyme Catalytic Mechanisms
An examination of enzymes’ catalytic strategies, including strategies for promoting catalysis, enzymatic intermediates, co-factors, as well as the methods used to probe mechanism. Examples from the current literature will be used to demonstrate each concept.
BCHM725 Molecular Mechanisms of Membrane Functions
The molecular basis of the biological activity of membranes at an advanced level. Topics include: bioenergetics, transport, membrane biogenesis and turnover, signal transduction, cell surface interactions and membrane disorders.
The structure of proteins, primary to quaternary will be discussed. Topics include: physico-chemical basis of higher orders of structure and techniques of studying proteins.
BIOL775 Current Topics in Molecular Microbiology
Focus of this course will be current research using molecular genetic, biochemical and bioinformatic methods to study microbial biodiversity, microbial cell-cell interactions (biofilms, symbiosis, pathogenesis), laboratory model organisms and microbial biotechnology.
CHEM708 Analytical Separation Science
The principles and applications of modern chromatographic separations, including the interfacing of separations techniques with spectroscopic and mass spectrometric detectors. This course will focus primarily on gas chromatography and liquid chromatography, recognizing that these methods are still the principal separation techniques used today. The course will also discuss recent developments in chromatographic methods. Since the majority of the students who will take this course are non-specialists in this area, the course will focus on practical applications with a lesser emphasis on detailed theoretical aspects of chromatographic processes.
The aim of this module is to introduce some modern statistical methods in chemistry. In many cases, we have masses of data, but the main problem is analysing and understanding it. With spreadsheet programs and other accessible software, it is now possible to do this routinely. Topics to be covered will include data acquisition, experimental design, filtering and fitting data to mathematical models. The approach will be fairly simple and open to students without a lot of sophisticated mathematical background.
CHEM713 Bioanalytical Chemistry and Chemical Sensors
Principles of electrochemical and optical biosensors, protein immobilization methods, bioassay design.
CHEM730 Theory of Crystallography (co-requisite: Chem 736)
The study of single crystals, how they diffract X-rays, and how the diffraction patterns can be analyzed to provide the molecular and crystal structures of organic, organometallic, and inorganic solids.
CHEM734 Applications of Mass Spectrometry in Organic Chemistry
This module is offered in alternating years and it deals with the principles and applications of organic mass spectrometry. Topics include ionization methods (EI,CI,FAB, MALDI, ESI), tandem mass spectrometry (MS/MS/MS), high resolution (HRP) mass spectrometry, tools to study reaction mechanisms and ion structures, and last but not least: a thorough introduction to the interpretation of unknowns both “ab initio” and with the help of databases.
CHEM735 X-ray and Electron Spectroscopy
This module deals with the principles and applications of a range of photon and electron impact based spectroscopies to studies of the electronic and geometric structure of molecules. Synchrotron based techniques will be featured. Techniques to be discussed include photoelectron, electron impact, Auger and X-ray absorption/emission techniques. Practical approaches to spectral interpretation and aspects of instrumentation will be emphasized.
CHEM736 Molecular Structure Determination by Diffraction Methods (co-requisite: Chem 730)
This module will show the student how to determine the structure of an unknown compound (preferably from the student’s own research) using single crystal X-ray diffraction methods, how to prepare a report for publication, and how to critically examine published structures.
CHEM738 Biophysical analytical techniques
This course will cover the use of modern instrumentation for studying various aspects of biological systems, including biomolecule structure, dynamics and interactions. Topics will include separation techniques based on chromatography and electrophoresis, spectrophotometry and applications to biological systems, steady-state and time-resolved fluorescence spectroscopy, vibrational spectroscopy including Raman scattering and FTIR, and circular dichroism spectroscopy for determination of protein and DNA structure. Immunoassays and DNA hybridization assays will also be described.
CHEM739 Advanced Topics in X-ray Crystallography
This advanced X-ray crystallography course will include the following topics: weak diffractors and microcrystals; structure determination from twinned crystals; modeling disordered structures; multiple occupancy refinements; non-molecular versus molecular structures; superstructures; synchrotron X-ray applications; description/discussion of complex structures. Pre-requisites: Chem 730 and 736.
CHEM740 Basic Theory of NMR
An introduction to the concepts and applications of pulsed Fourier transform nuclear magnetic resonance (NMR) spectroscopy. The module begins with a review of the basic NMR experiment and then proceeds to a description of the pulsed NMR technique and the use of Fourier transformation to generate the spectrum. The next section deals with a general description of the pulse NMR spectrometer and the parameters used in data acquisition and processing. The final section covers more traditional topics dealing with 1H and 13C chemical shifts, coupling constants and relaxation times with the emphasis on the structural information these parameters provide. This section will also illustrate some of the essential one-dimensional techniques used in analyzing NMR spectra (T1 measurements, spin decoupling, NOE difference spectra and 13C spectral editing).
CHEM741 Two-dimensional NMR Spectroscopy
A general introduction to the theory and application of modern multi-dimensional NMR techniques. The material in this module begins with a detailed description of the one-dimensional pulse sequences (spin echo and INEPT) from which most of the two-dimensional techniques have evolved. This is followed by a discussion of the most frequently used two-dimensional NMR techniques for establishing 1H – 1H and 1H – 13C connectivities (COSY, TOCSY, HETCOR, HMQC, HMBC etc.). Each method is discussed in terms of how each type of 2-D spectrum is interpreted, what parameters are required for the optimum 2-D spectrum and the advantages and disadvantages of each technique. The final section surveys some of the recent developments in this area.
CHEM748 Principles of Pulse and Two-dimensional NMR
This module gives some of the basic principles of the theory of pulse NMR. For simple systems, it is relatively easy to calculate what COSY and other experiments should look like, and the aim of this module is to bring students to that level. The main tool for this work is the density matrix and its equation of motion. Familiarity with pulse NMR experiments will be useful as a background, but no specific mathematical skills will be needed.
CHEM749 Advanced Structure Determination by NMR
NMR is an important tool for the structure determination of molecules of all sizes. It has long been used for “small” molecules (molecular weight < 2000) in a chemistry environment, but it is also a vital technique for biological macromolecules. Proteins, nucleic acids and large carbohydrates have all had structures determined. Most important is that the structure determination is done in solution, so that the technique is complementary to X-ray crystallography. Most of this work involves advanced multidimensional NMR methods and isotopic labeling. This course will rely on a basic understanding of two-dimensional NMR acquired in the pre-requisite course. A substantial part of the course will be “hands-on” analysis of spectra of real molecules.
CHEM754 Physical Organic Chemistry
An introduction to basic concepts in physical organic chemistry and the study of organic reaction mechanisms: kinetics and thermodynamics; thermochemistry; isotope effects; acid/base catalysis; linear free energy relationships.
CHEM755 Isotopes in Biological and Organic Chemistry
Applications of isotopes in the study of reaction mechanisms in organic and biological chemistry will be investigated. Topics will include the theory of isotope effects including tunneling effects, the use of positional exchange to elucidate reaction mechanisms, abd tracer techniques to elucidate metabolic pathways. Techniques for synthesizing isotopically labeled compounds will be discussed, as well as isotope effect measurement and interpretation.
CHEM757 Advanced Topics in Bio-organic Chemistry
Bioorganic chemistry is an extremely broad, highly dynamic field in which only one theme is constant – the application of chemical principles and practice to biologically relevant problems. In this course, very recent advances in bioorganic chemistry from a chemist’s point of view are examined by surveying the current chemical literature. Recent (2001) advances include the creation of artificial photosynthetic membranes that convert photons to chemical bonds with 10% quantum efficiency, debates on the importance of entropic contributions to catalysis, and the creation of the chemistry and machinery for automated solid-phase oligosaccharide synthesis.
CHEM758 Bio-organic Chemistry
The Chemistry of Natural Products is described with particular emphasis on the biosynthetic pathways used by cells to assemble this large group of organic compounds. The course is offered in two parts, either of which may be taken individually. Students should be aware, however, that both parts should be taken in order to cover the field comprehensively. Students taking a second credit in this course may be evaluated by a modified method from those who take the course for the first credit. The two parts will normally be offered in alternating years. Part A covers an introduction to natural products and their biosynthesis, as well as the techniques used to determine biosynthetic pathways experimentally. Metabolites derived from acetate are then examined. These include the fatty acids, prostaglandins and the arachidonic acid cascade, the polyketides and the terpenoids and steroids. Part B covers the same introductory material and techniques section as for Part A. Metabolites from the shikimic acid pathway, those derived from amino acids including penicillins, the alkaloids, and porphyrins including vitamin B-12 will then be examined.
CHEM759 Nucleic Acids in Chemistry and Biology
This course is intended particularly for students with chemical and biochemical interests who desire to enrich their knowledge of nucleic acids. Topics will include: chemical and structural aspects of nucleic acids; DNA and RNA structures; chemical and biochemical syntheses of nucleic acids; DNA and RNA sequence information transmission; catalysis by ribozymes and deoxyribozymes; evolution of functional biological macromolecules through nucleic acids; interactions of DNA and RNA with various ligands. The primarily course material will be review articles written by leading experts in related areas.
CHEM760 Principles of Organic Synthesis
Introduction to synthesis; definitions, typical reagents, functional group interconversions; simple examples. Carbon-carbon bond forming processes; retrosynthesis and acceptor-donor approach. Examples of syntheses employing different strategies for molecules of medium complexity.
CHEM761 Problems in Organic Chemistry
The main goal of this inquiry-style course is to improve critical thinking skills. Students are given manuscripts to review which, almost always contain one or more critical flaws that render them unsuitable for publication. Students must identify these flaws correctly and, if appropriate, reasonable alternative interpretations must be given. Occasionally, a problem may consist of a short cumulative-style examination containing problems gleaned from the very recent literature or from the departmental seminar program.
CHEM770 Molecular Electronic Structure Theory
In one version of this module, Hartree-Fock theory and the computation of electronic energies and molecular properties are developed after a review of the Born-Oppenheimer approximation and an introduction to potential energy surfaces. Unrestricted and restricted Hartree-Fock approximations are contrasted in the framework of molecular orbital theory. There is some discussion of Gaussian basis sets and configuration interaction, at the level of second order perturbation theory (Moller-Plesset perturbation theory). A second version provides an introduction to the theory of atoms in molecules with emphasis on the topological properties of the electron density. These properties provide the basis for the definition of atoms, bonds, structure and structural stability. The theory is illustrated through its application to current problems in structure and reactivity. Each student has the opportunity of applying the theory to a problem of her/his own choice.
CHEM771 Quantum Mechanics
This module introduces the quantum theory of the interaction of electromagnetic radiation with matter and the theory of line shapes.