Ph.D. in Chemical Biology Curriculum

Chemical Biology trainees follow an interdisciplinary course of preparation not available in most departmental settings. The classroom component of the Chemical Biology curriculum is comprised of several high-level courses and is designed to provide students with rigorous training in modern aspects of chemical biology. First, all students take Chemical Biology 501/502, which is a two-semester course that discusses the structure, function and chemistry of biological macromolecules including proteins, nucleic acids and carbohydrates. Topics include mechanistic enzymology, the interactions of proteins and small molecules with RNA and DNA, macromolecular folding, combinatorial methods including SELEX and gene shuffling, combinatorial organic synthesis, high throughput screening and chemical genetics. All students will also complete Chemical Biology 601/602, which is also a two-semester long course. In this class, students are taught critical thinking and analysis through weekly discussion of the primary research literature.

Based on individual interests, the remaining course requirements of the Program can be fulfilled from a variety of chemistry, biochemistry or biology classes taught on campus. Hence, a major advantage of the Chemical Biology Program is that it allows students maximum flexibility in their training program. A partial listing of additional courses is presented below.

During the first year in the program, students are required to conduct two semester-long research rotations in different laboratories of their choosing. These rotations are important for many reasons: they provide an opportunity for students to meet the faculty and other graduate students; they provide a basis to select a research advisor; they give students the chance to experience different types of research; and they acclimate students to the research environment at the University.

Upon satisfactory completion of course and research rotation requirements, students undertake the Preliminary Qualifying Examination. Upon successful completion of the examination, a student becomes a candidate for the Ph.D. degree and focuses exclusively on thesis research. Once research results are deemed to be suitable for writing a thesis by the advisor and thesis committee, students begin to write a thesis and then defend it. The expected time needed to obtain the Ph.D. degree is approximately five years.

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M.S. in Cancer Chemical Biology Curriculum

The Master of Science in Cancer Chemical Biology program requires the completion of 24 credits over the course of two semesters. All students will complete the core Chemical Biology courses (Chemical Biology 501, 502: 6 credits), Ethics training (Fall term: 1 credit); Protein-protein Interactions in Human Disease (Fall term: 3 credits), Cancer Biology (Winter term: 3 credits), and Critical Analysis in Chemical Biology (Fall and Winter terms, 3 credits total that includes a capstone project in the Winter term).



Additional Courses

Bioinformatics 526: Fundamentals of Bioinformatics.
This course introduces students to the fundamental theories and practices of Bioinformatics via a series of integrated lectures.  These lectures will focus on the basic knowledge required in this field, including the theory and design of databases, access to genome information, sources of data, and tools for data mining.  The course will also cover identification of both lower order and higher order informational pattern in DNA and approaches to linking genome data to information on gene function.  Emphasis will be placed on how to use the databases and tools.

Bioinformatics 527: Introduction to Bioinformatics & Computational Biology
This course introduces students to the fundamental theories and practices of Bioinformatics and Computational Biology via a series of integrated lectures and labs.  These lectures and labs will focus on the basic knowledge required in this field, methods of high-throughput data generation, accessing public genome-related information and data, and tools for data mining and analysis.  The course is divided into four areas:  Basics of Bioinformatics, Computational Phylogeny (includes sequence analysis), Systems Biology and Modeling.

Bioinformatics 545: Data Analysis in Molecular Biology
This course will cover statistical methods used to analyze data in experimental molecular biology, with an emphasis on gene and protein expression array data. Topics: data acquisition, databases, low level processing, normalization, quality control, statistical inference (group comparisons, cyclicity, survival), multiple comparisons, statistical learning algorithms, clustering visualization, and case studies.

Bioinformatics 551 / Biological Chemistry 551: Proteome Informatics.
Introduction to proteomics, from experimental procedures to data organization and analysis.  Basic syllabus: sample preparation and separations, mass spectrometry, database search analysis, de novo sequence analysis, characterizing post translational modifications, medical applications. Further topics may include, e.g.: 2-D gels, protein-protein interactions, protein microarrays. Research literature seminars required.

Biological Chemistry 528 / Chemistry 528 / Medicinal Chemistry 528: Biology & Chemistry of Protein Cofactors.
This course will explore the roles of organic and organometallic cofactors in biology.  Topics covered will be cofactor assembly, cofactors as sensors, and cofactors in enzyme chemistry, with an emphasis on modulation of cofactor reactivity by complexation with the protein.  The lectures will be complemented by assigned reading material from the primary literature and will assume basic familiarity with bioorganic chemistry.

Biological Chemistry 585: Cell Cycle Regulation.
A survey of recent progress in cell cycle regulation in eukaryotes, emphasizing the molecular basis of cell cycle regulation, the ways in which extracellular signals affect the cell cycle, and the roles of cell cycle regulators in oncogenesis.

Biological Chemistry 640: Post-transcriptional Gene Regulation
A discussion based course that will cover the mechanisms and the biological roles of post-transcriptional gene regulation in eukaryotes. Topics will include RNA interference, microRNAs, regulated polyadenylation, subcellular regulation of translation, and others. The class will focus on reading and discussion of the recent literature, but topics will be introduced by short lectures.

Biological Chemistry 650: Mechanism of Eukaryotic Gene Expression.
Topics in this class will cover eukaryotic RNA polymerases, general transcription factors, mechanisms of transcriptional regulation, and chromatin structure and modification/remodeling.  An emphasis will be placed on structural aspects of transcription and polymerase function.  The course will be taught through a combination of lectures and discussions of the current literature.

Biological Chemistry 673: Kinetics & Mechanism of Enzymes.
This course will cover the investigation of enzyme mechanisms with an emphasis on kinetic and thermodynamic methodology, including: ligand binding to macromolecules, transient kinetics, steady-state kinetics, and kinetic isotope effects. The key kinetic and thermodynamic concepts that govern the action of enzymes, and the thought processes required to deduce catalytic and kinetic mechanisms will be explored. Topics will be treated from both a "gut-feeling" and a mathematical perspective, and applications to real systems, including experimental methods, data analysis, and common errors/fallacies/abuses, will be considered in detail. Because computer methods for analyzing and simulating data have taken a prominent place in the field, the use of software from kinetics research will be emphasized through numerous "hands-on" exercises. 

Biophysics 503: Biomolecular NMR.
Principles of multidimensional NMR will be treated, including quantum mechanical methods such as Density Matrices, Product Operators, Propagators and perturbation theory. Biomolecular applications of two-dimensional proton NMR and three-and four-dimensional heteronuclear NMR will be extensively covered. Methods applicable for solution as well as for solid samples will be introduced. Applications center on protein structure determination but nucleic acids NMR and relaxation experiments for the detection of molecular dynamics will be treated as well.

Biophysics 520 / Chemistry 520: Biophysical Chemistry I.
This course is the first or a two-term Biophysical Chemistry series 520/521, but it can be taken as stand-alone course as well. The course offers an overview of protein, nucleic acid, lipid and carbohydrate structures. Intra- and inter-molecular forces, helix-coil transitions and protein folding will be treated in a thermodynamical context. Thermodynamics of solutions, configurational statistics, ligand interactions, multi-site interactions and cooperativity are treated in depth. Kinetics of protein-ligand binding, including electron transfer and ligand diffusion are discussed. Chemistry 520 will introduce and explain the physico-chemical properties of biological macromolecules and their complexes, mostly in solution. Currently, biophysical, biochemical and pharmaco-chemical reserach literature is full with papers interpreting the properties of biological macromolecules on the basis of their three-dimensional structure. This course will expand on that concept by offering a rigorous background in energetics, folding, interactions and dynamics. As such the course is important to any student who has to deal with the concepts of biomolecular function and structure such as biochemists, biophysicists, mathematical biologists, and molecular pharmacologists. This course will also serve as a basis for the graduate student who will be specializing in any of these topics for thesis research. Moleculary dynamics will be introduced.

Biophysics 521 / Chemistry 521: Biophysical Chemistry II.
This course gives background applications of several physical techniques used in Biophysical research.  General principles of spectroscopy will be explained.  Macromolecular structure determination by X-ray diffraction and two-dimensional NMR will be treated in detail.  IR, Raman, CD, EXAFS, EPR and ESEEM will be introduced.

Biophysics 602 / Chemistry 602: Protein Crystallography.
Principles of Macromolecular Crystallography: Fundamental of the methods for determining 3-dimensional structures of large molecules by x-ray crystallography. Aimed at students who expect to use crystallography as a major tool for their research, and at those who want in-depth knowledge of the methods in order to analyze structure data.

Cell and Developmental Biology 530: Cell Biology.
This graduate course is designed to present basic information as well as the most recent developments in key areas of cell biology, including membranes, protein synthesis and folding, vesticular trafficking, epithelial polarity, cytoskeleton, cell-cell and cell-substrate interactions, and signal transduction. Participating faculty are drawn from various campus and medical school departments and provide lectures in areas of their expertise. Lecturers are encouraged to provide a part of the lecture material in the context of actual experiments so that students are exposed to current experimental approaches in cell biology, as well as basic information.

Cell and Developmental Biology 580: Developmental Biology
Covers basic principles of embryonic development; fertilization to organogenesis in model organisms (mouse, chick, fish, Drosophila and Xenopus). Focus is on cellular and molecular mechanisms. Format is combination lectures and student presentations of current literature with written summaries.

Cell and Developmental Biology 710: Stem Cell Biology.
The biology of stem cells, from the most primitive embryonic stem cells to stem cells resident in adult tissues, is the focus of this course

Chemistry 515: Organometallic Chemistry
Systematic consideration of modern aspects of organometallic chemistry including main group and transition metal complexes. The structure and bonding in organometallic compounds are covered. Particular emphasis is placed on applications of homogeneous organometallic catalysis in polymer synthesis, industrial processes, and synthetic organic chemistry.

Chemistry 540: Organic Principles.
Mechanisms of organic chemical reactions, stereochemistry, and conformational analysis. The important types of organic reactions are discussed. Basic principles are emphasized; relatively little attention is paid to the scope and synthetic applications of the reactions.

Chemistry 541: Advanced Organic Chemistry
Synthetic organic chemistry. The scope and limitations of the more important synthetic reactions are discussed within the framework of multistep organic synthesis.

Chemistry 542: Applications of Physical Methods to Organic Chemistry
Applications of infrared, ultraviolet and nuclear magnetic resonance spectroscopy, optical rotary dispersion, mass spectrometry and other physical methods to the study of the structure and reactions of organic compounds.

Chemistry 543: Organic Mechanisms
Students will learn to propose and write reasonable mechanisms for organic reactions, including complex multi-step processes. Knowledge of the details of the fundamental organic reaction processes will also be gained.

Chemistry 673: Kinetics & Mechanism of Enzymes.
Comprehensive treatment of thermodynamic and kinetic aspects of the binding of ligands to macromolecules, the use of rapid reaction techniques in the elucidation of enzyme reaction mechanisms, steady-state catalysis, and isotope effects.

Epidemiology 460: Introduction to Bacterial Pathogenesis
This course covers the basics of the biochemistry, molecular biology, and genetics of chemotaxis and flagella, pili and adhesins, extracellular proteases, bacterial toxins, invasion and intracellular growth, phase and antigenic variation, gene transfer, LPS, iron, M-proteins, capsules, chemotherapy, antibiotic resistance and global regulation of virulence elements.

Epidemiology 560: Mechanisms of Bacterial Pathogenesis
Microbial structures and their relation to basic mechanisms of bacterial pathogenesis; structure, function, and genetics of bacterial toxins; and host resistance and immunity. Discussions of pathogenic organisms of major public health importance, diseases caused, and their epidemiology.

Human Genetics 541: Gene Structure & Regulation.
Molecular Genetics. A combination of classic and current papers in molecular genetics will be selected to accompnay the lecture material (1-2 papers per lecture). The foundations of modern genetics will launch the course, including both the fundementals and current research methods for analysis of gene structure and gene expression. The gene expression component will include positive and negative regulation of transcription and mRNA splicing and turnover. The basics of DNA recombination, repair, and transposition will be covered in relationship to cancer, evolution, and mutagenesis. Strategies for developmental regulation will be presented. Parallels between prokaryotes and eukaryotes will be drawn, and comparisons will be made between the temporal and spatial control of gene expression in vertebrates and invertebrates. Genetic engineering topics will include gene targeting and transgenesis, with applications to understanding tissue specific control of gene expression. The course will include discussion of the Genome Project, identification of disease genes and an introduction to the medical application of molecular genetics including gene therapy.

Human Genetics 630 / Biology 630/ Microbiology 630/ Pharmacology 630: Genetics Short Course
Topic: New Frontiers in Signal Transduction

Medicinal Chemistry 532: Bioorganic Principles of Medicinal Chemistry.
A mechanistic organic chemistry/biochemistry approach to medicinal chemistry, emphasizing macromolecular targets of drug action. The first of four sections focuses on enzymes as drug targets, with emphasis on inhibitors of enzyme action. Section 2 covers nucleic acids as targets for drug action and includes agents that interact with nucleic acids directly and those that inhibit nucleic acid biosynthesis. Section 3 explores metabolic pathways and mechanisms for xenobiotic transformation. Section 4 discusses the rationale behind drug delivery and prodrug approaches as well as design strategies based on routes of bioactivation.

Microbiology and Immunology 553: Cancer Biology.
This course will cover a broad range of subjects relating to cancer biology. Emphasis is on the relationship between basic science and clinical aspects of cancer. Topics to be covered include carcinogenesis, cancer progression, tumor pathology, oncogenes, cellular growth control, tumor suppressor genes, oncogenic viruses, apoptosis, tumor immunology, clinical oncology, and therapeutics.

Microbiology and Immunology 607: Microbial Pathogenesis I
This first module will emphasize functional and ecological aspects of microbial pathogenicity.

Microbiology and Immunology 615: Molecular and Cellular Determinants of Viral Pathogenesis I
Module I - Molecular and Cellular Determinants of Viral P Pathogenesis.  Concepts of viral pathogenesis and controls.

Microbiology and Immunology 619: Special Topics in Microbiology and Immunology
Didactic overview and critical analysis of the literature focused on a specific timely topic in current microbiology and immunology research.  Students will read and discuss the primary literature as well as complete assignments that further explore the topic.

Microbiology and Immunology 640: Molecular and Cellular Immunology I.
Module I - Molecular and Cellular Immunology: B Cell Immunology. This one-credit course covers many of the important areas of research in immunology. It has two goals: (i) to enable the student to think about problems in immunology in an experimental setting and (ii) to enable the student to read and understand the original literature in immunology or attend and understand seminars in immunology. Major topics discussed include structure and function of immunoglobulins, immunoglobulin genes, generation of diversity, differentiation of immunoglobulin-producing cells.

Microbiology and Immunology 641: Molecular and Cellular Immunology II.
Module II - Molecular and Cellular Immunology: T Cell Immunology. This one-credit course is focused on T cell mediated immunity, with emphasis placed on how the cellular immune reponses are regulated in vivo. Specific areas include innate immunity, T cell development, antigen presentation and recognition, T cell activation, cytokine regulation of cellular responses, lymphocyte recirculation, and effector T cell mechanisms.

Microbiology and Immunology 642 / Biophysics 642: Molecular and Cellular Immunology III.
Module III - Molecular and Cellular Immunology: Molecular Recognition in the Immune System. This one credit course will consist of lectures and discussions pertaining to receptor-ligand interactions in the immune system. The goal of the course is to provide students a broad overview of the structural basis of immune function by reviewing recent literature.

Molecular, Cellular, and Developmental Biology 608 / Biophysics 608: Biophysical Principles of Microscopy.
This course covers the physical, mathematical, and instrumental principles behind the major optical microscopy techniques used in modern cell biology and biochemistry. Included are bright field, dark field, phase contrast, differential interference, interference reflection, polarization, fluorescence labeling and detection, total internal reflection, schlieren, confocal, multiphoton, fluorescence resonance energy transfer, fluorescence lifetime, and CCD imaging techniques, as well as photobleaching, fluorescence temporal and spatial correlation spectroscopy and 3D image deconvolution image analysis. A familiarity with complex exponent mathematics to represent waves and some familiarity with basic geometrical and physical optics is highly beneficial. This course emphasizes the theoretical principles and practical applications rather than a "hands-on how-to-do-it" approach.

Molecular, Cellular, and Developmental Biology 680 / Cell and Developmental Biology 680: Organogenesis of Complex Tissues
Organogenesis of Complex Tissues --- Two course modules are offered, one covering an aspect of stem cell biology (embryonic or adult stem cells) and the other focused on a specific organ system (development, maintenance, organ disease, artificial organs).  Course content is different each year.  Current module topics are listed at:

Neuroscience 601 / Molecular, Cellular, and Developmental Biology 610: Principles of Neuroscience I
This course represents the first half of a year long, graduate-level survey of neuroscience. The goals for NEUROSCI 601 and 602 are: 1) To provide our students with a sense of the state of current knowledge in molecular, cellular, developmental, integrative and cognitive neuroscience. Considerable emphasis is put on pulling together information obtained from different types of investigations (anatomical, physiological, behavioral, biochemical, genetic) to gain a balanced view of neuroscience. 2) To provide our students with a sense of how knowledge was obtained, by reading and discussing "classic papers." 3) To provide our students with a sense of where the current frontier is, by reading and discussing very recent papers. Each week this class meets for 3-5 hours, with a mix of lectures and discussion. The major topics treated in NEUROSCI 601 and 602 are: I) Excitable Membranes, II) Molecular Neuropharmacology, and III) Developmental Neurobiology.

Pathology 643: Immunopathologic Mechanism of Disease
This course focuses on major immunopathologic diseases including autoimmunity, virology, parasitology, and allergy/asthma.  Students are given an overniew of the subject to be covered on the first lecture of the disease series and the following two lectures are covered using recent publications and student discussions.  Special emphasis is given to experimental approaches, methodology, and critical review of the literature.

Pharmaceutical Science 734: Pharmacogenomics and Drug Discovery
This course evaluates how modern genomic technologies have impacted the field of pharmaceutics.  Topics to be discussed include chip technologies, cell based assay technology, model organisms, profiling studies, drug target validation, and identification and combinatorial chemistry.  Class discussion will center on the relevance of their research to problems related to drug targeting and delivery, both from an academic and an industrial perspective.

Pharmaceutical Science 753: Current Topics in Biotechnology
A broad spectrum of topics related to biotechnology and biomedical engineering are covered, including the production, isolation, purification, monitoring, and formulation of biotechnologically derived protein and peptide components, as well as the delivery systems and potential application of these biomedical compounds. Many state-of-the-art biotechnology techniques such as recombinant DNA techniques, the ELISA assays, and biosensors also will be discussed. Two hours lecture a week.

Pharmacology 612: Seminar in Antimicrobial and Cancer Pharmacology
This course uses a combination of textbook and literature reference to provide students with an understanding of the different classes of drugs and used to treat infectious diseases and cancer.  The course will focus on the mechanisms of drug action, the basis of selectivity and therapeutic applications.  Traditional as well as novel approaches to therapeutics will be discussed, as well as the role of drug resistance and strategies for its management.

Pharmacology 615: Molecular Neuropharmacology
Pharmacology 615 uses a combination of textbook and literature readings and class discussions to present students with a study of central nervous system molecular neuropharmacology and neurochemistry. Topics will include neurotransmitters in the central nervous system and drugs used therapeutically in the central nervous system. (Cross-listed with Neuroscience 612.)

Pharmacology 616: Seminar in Cardiovascular Pharmacology
This course consists of seminar presentations along with the use of self-instructional, computer assisted learning modules in the Learning Resource Center.  Emphasis will be placed on pharmacologic interventions used in the management of disorders affecting the cardiovascular system.  Major topics of discussion will focus on the following drug categories:  Drugs affecting the Autonomic Nervous System; Vasoactive Substances; Water, Electrolyte Metabolism and Diuretic Drugs, Antihypertensive Drugs; Calcium Channel Blockers, Cardiac Glycosides and other Cardioactive Agents; Antianginal Drugs; Antiarrhythmic Agents.
Pharmacology 759: Autonomic Nervous System Drugs
Pharmacology 759 is a concise introduction to drugs that affect the function of the sympathetic and parasympathetic nervous systems.  Drugs that affect the somatic neuromuscular junction are also discussed.  Adrenergic and cholinergic agonists and antagonists, and cholinesterase inhibitors, are emphasized.  Drug-receptor interactions, subsequent physiological effects, and uses of drugs in therapy, are discussed.  This course is a section of General and Systematic Pharmacology (Pharm 659).  The combination of Pharm 759 and Pharm 760 gives students an excellent overview of the mechanisms of action and therapeutic effects of the major classes of nervous system drugs.

Pharmacology 760: Central Nervous System Drugs
Pharmacology 760 is a concise introduction to drugs that affect the function of the central nervous system.  Narcotic analgesics, benzodiazepines, barbiturates, anticonvulsants, antidepressants, anti-Parkinson drugs, psychomotor stimulants, general anesthetics and ethanol are discussed.  This course is a section of General and Systematic Pharmacology (Pharm 659).  The combination of Pharm 760 and Pharm 759 (Autonomic Nervous System Drugs) will give students an excellent overview of the mechanisms of action and therapeutic effects of the major classes of nervous system drugs.

Physics 511: Quantum Theory and Atomic Structure I
This course will focus on the explanation of fundamental concepts, mathematical structure, and calculation methods of quantum mechanics. The course covers the following topics: fundamental concepts of quantum mechanics and its mathematical structure, exactly solvable quantum systems, symmetries in quantum mechanics, approximation methods, atomic and Molecular structure, scattering theory, quantum many-particle systems, and relativistic wave equations.