Structural Biology/Biophysics Research Track: Courses
2011 Fall Classes
First block
Genetic Engineering
Biochemistry
Faculty Research Seminar
Scientific Ethics & Integrity
Second block
Protein Chemistry
Biophysical Chemistry
2012 Spring Classes
Journal Club/Grant Writing Class
Track Course Selection (2-half semester courses)
Elective Course Selection
(2-half semester courses)
Structural Biology/Biophysics Research Track Courses
1. Structural Methods
2. Molecular Biophysics
3. Optics
in Biology
4. Molecular Modeling
Below is a sample list of past electives taken by BCP first-year students. To see the entire list of electives please click here. Please note: not all elective courses are taught every year.
CHEM 6740 Bioanalytical Chemistry
PH TX 7500 Macromolecular Therapeutics & Drug Delivery
PATH 6410 Molecular Virology
MBIOL 6480 Cell Biology I
PATH 7310 Host Pathogen Interactions
ONCSC 6500 Clinical & Molecular Cancer Biology
Each student may also choose courses from other research tracks as their elective courses. Below is a list of courses listed by research tracks.
Biochemistry Research Track Courses
1. Regulation of Metabolism
2. Advanced Biochemistry (Protein folding, Binding, etc)
3. Nucleic Acid Chemistry
Chemical Biology/Medicinal Chemistry Research Track Courses
1. Fundamentals of Drug Discovery & Design
2. Understanding Therapeutically Relevant Biomolecules
research track Course Descriptions
Regulation of Metabolism: This half-semester course will begin with a review of carbohydrate and lipid metabolic pathways, with an emphasis on an integrated understanding the pathways and what is known about their regulation. The course will progress to an in-depth analysis of current research in specific areas of nutritional sensing and metabolic regulation. Prerequisite: BIOL 3520 or CHEM 3520 or equivalent. Course leader: Janet Lindsley
Advanced Biochemistry: This course will focus on biochemical and biophysical approaches to studying proteins and their functional interactions. Topics covered will include: protein-ligand interactions, cooperativity and allostery, protein folding and design, spectroscopic techniques, analytical ultracentrifugation, calorimetry, biosensors, proteomics approaches, and protein structure prediction. Prerequisite: MBIOL/BLCHM 6410 or equivalent. Course leaders: Michael Kay and Wes Sundquist
Nucleic Acid Chemistry: Three lectures, one discussion per week for 7.5 weeks. Topics include chemical synthesis of DNA and RNA, nucleoside and oligomer analogs, chemistry of DNA damage and repair, nucleic acid-targeted drugs and binding agents. Prerequisite: 2 semesters undergraduate organic chemistry. Course leader: Cynthia Burrows
Fundamentals of Drug Discovery & Design: In this half-semester course, we cover the basics of drug development and evaluation. The principles of pharmacokinetics, ADME and structure-activity relationships are emphasized. Students will leave the class with the ability to discuss major trends in drug discovery and development, understand the structure-activity relationships and mechanisms of action of major drug classes and appreciate the drug discovery and development process from a chemist’s perspective. Course leaders: Amy Barrios and Eric Schmidt
Understanding Therapeutically Relevant Biomolecules: In this half-semester course, we cover several classes of therapeutically relevant biomolecules, including nucleic acids, peptides, carbohydrates, natural products and synthetic molecules. Key aspects of each class of molecules will be discussed, with an emphasis on recent scientific developments in the field. Students will leave the class able to explain the therapeutic relevance of several classes of molecules, analyze the primary literature and design experiments to test key questions at the interface between chemistry and biology. Course leaders: Amy Barrios and Eric Schmidt
Structural Methods: This course provides an integrated approach to the applications of NMR and X-ray crystallography in structural biology. Topics covered include: basic NMR theory, and the application of 2D and 3D NMR methods for the determining protein and RNA structures; methods of macromolecular crystallization and crystal structure determination. Prerequisite: BIOL 3510 or equivalent. Course leaders: Chris Hill and David Goldenberg
Molecular Biophysics: This course is designed to give students an overview of the complexity of microtubule- and actin-based motors. We will discuss established aspects of motor structure, function, and regulation. This course will also introduce students to the types of physics and math problems that arise in research, the measurements and data analysis techniques used to extract useful information, and some of the big open questions in the field. Students with backgrounds in biology, or physics are equally encouraged. Course leader: Saveez Saffarian and Michael Vershinin
Optics in Biology: The use of optics in biology has evolved from the simple light microscope used by Darwin to the complex cryo-electron and live cell high resolution microscopes used today. With all these advances it can now be argued that we stand at the dawn of quantitative biology and optics provides an essential tool in this pursuit. This course is designed to give students a good understanding of physics involved in advanced optics while focusing their attention on the biological problems amenable to these techniques. Students with backgrounds in biology, chemistry or physics are equally encouraged however knowing algebra is a requirement for taking this course. Each section of the course would deal specifically with a special kind of microscopy followed with a case study in a biological problem that is most amenable to the use of the techniques discussed.
Molecular Modeling: This survey course, including a hands-on compnent, will cover computational and simulation methods for understanding the structure, dynamics and interactions of biological molecules with an emphasis on topics relevant to therapeutic design, delivery and disposition. Possible topics will include molecular modeling, atomistic simulation, molecular docking, drug design, ADME, homology modeling, high performace computing, and protein structure prediction. We will first review fundamental principles of molecular interaction and the survey various modeling approaches to highlight their ranges of applicability and limitations. Experience with computers is desirable for the lab component.
Regular Core Course Descriptions
Genetic Engineering: This course covers essential techniques used in genetic engineering. Assuming modest background in biology, the course introduces fundamental aspects of molecular biology including mechanisms for storage of information in DNA and transfer of this information to RNA and protein molecules. Manipulations of DNA molecules to rearrange or remodel genetic information ("cloning") are described from both theoretical and practical viewpoints. Topics covered include the use of restriction endonucleases, amplification of DNA sequences using the polymerase chain reaction (PCR), detection of DNA and RNA using hybridization (Southern and Northern blotting), properties of cloning vectors and their use in constructing genomic and cDNA libraries, DNA sequencing and sequence analysis, creating and detecting mutations in DNA and introducing these mutations into a genome, and expression and characterization of proteins. Course leaders: Dana Carroll and Jared Rutter
Biochemistry: This course covers the structure and function of nucleic acids and proteins, as well as the thermodynamics and kinetics of their interactions with each other and with other biologically important molecules. Course leaders: Brenda Bass, Michael Kay and Amy Barrios
Protein Chemistry: This course focuses on the mechanisms of chemical reactions involving peptides and proteins and methods for their study. Subject matter includes enzyme mechanisms, chemical modification of proteins and cofactor chemistry. Prerequisite: organic chemistry. Course leader: Ken Woycechowsky
Biophysical Chemistry: Topics covered include: basics of thermodynamics and statistical mechanics, with applications in biochemistry; transport phenomena; enzyme kinetics and inhibition; kinetic isotope effects; principles and applications of absorbance, fluorescence, and CD spectroscopies. Course leader: Peter Flynn
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