Course Descriptions
Physical Biochemistry I
Fall I BSCI 5196-01
Credit: 1.5 hours
Kim Orth, PhD
Emphasizing quantitative analysis/reading/discussion of the primary literature, course study provides an advanced look at multiple aspects of biochemistry, including protein analysis, mass spectrometry, equilibria, specificity, cooperativity and regulation of macromolecular interactions, sedimentation velocity and equilibrium analysis, and related topics. These principles will be illustrated by the study of well-characterized examples from the literature.
Molecular Biophysics: Spectroscopy
Fall II MB 5106-01
Credit: 1.5 hours
Elliott Ross, PhD
Covers optical spectroscopy with emphasis on applications in biomedical research. including interaction of light and matter, absorption spectroscopies (UV/vis and infrared), fluorescence, and circular dichroism.
Quantitative Biology I
Spring II MB 5125-0
Credit: 1.5 hours
Elliott Ross, PhD
This course explores the quantitative understanding of biological regulatory networks by considering (1) their experimental analysis, (2) their depiction by creation of explicit physical models, (3) reduction of the physical models of mathematical models, and (4) the use of the mathematical models to provide mechanistic understanding and drive new and more effective experiments.
The course deals mostly with strategy of modeling process and analysis of simple reactions (first- and second-order chemical reactions, diffusion, equilibrium, and steady-state systems) and their combination into small signaling modules, with some underlying techniques for working with quantitative data. This course is a prerequisite for Part II.
Computational Approaches in Protein Science
Spring I MB 5145
Credit: 1.5 hours
Nick Grishin, PhD
The basics of computational methods used to analyze protein sequences and structures. Topics include sequence similarity searches using profile-based tools, functional prediction, structure prediction and threading, homology modeling, energy-based simulations, protein classification, and evolutionary concepts: homology inference and tree reconstruction.
Advanced NMR Spectroscopy
Fall and Spring II MB 5154-01
Credit: 1.5 hours
Jose Rizo-Rey, PhD
Principles of nuclear magnetic resonance (NMR), emphasizing its application to macromolecular structure determination. Topics include multidimensional NMR spectroscopy, including COSY, TOCSY and NOESY experiments, sequential assignments and structural analysis, practical methods, and new developments in the field. Recommended prerequisite: Biophysics Thread in Core Course.
Protein Structure and Folding
Fall II MB 5124-01
Credit: 1.5 hours
Elizabeth Goldsmith, PhD
Overview of the basic principles governing protein structure and folding. Topics include stereochemical mechanisms by which protein secondary and tertiary structures are generated and stabilized, methods of prediction of tertiary structure from amino acid sequence, and the organization of folding motifs into protein structures. Instruction will be based on didactic material, discussion of the primary literature, and student projects utilizing computer graphics.
Practical X-Ray Crystallography
Spring I MB 5157-01
Credit: 1.5 hours
Chad Brautigam, PhD
Practical X-ray Crystallography will mix lectures and hands-on tutorials, with the goal of providing beginners in the discipline the tools to move forward confidently on crystallographic projects of their own. In the tutorial section, students will grow protein crystals, collect and process X-ray diffraction data, solve the phase problem using both molecular replacement and anomalous diffraction, build protein models, refine the model, analyze the model, and learn effective model presentation. Students will be tutored in the use of state-of-the-art crystallographic software. In the lectures, the principles behind the methods will be discussed. Recommended prerequisite: Biophysics Thread in Core Course.
Computational Methods in the Biological Sciences
Credit: 1.5 hours
Alexander Pertsemlidis, PhD
Biocomputing and computational biology are synonyms that describe the use of computers and computational techniques to analyze biological systems, from individual molecules to organisms to higher-order systems. This course will cover the computational techniques used to access, analyze, and interpret the biological information in common types of biological databases and the biological questions that can be addressed by such methods, applicable to the study of the context of genes within the same genome and across different genomes, the study of molecular sequence data for the purpose of inferring the function, interactions, evolution, and structure of biological molecules, and the study of annotation and ontology.
Quantitative Analysis of Genes and Genomes
Fall -BSCI-TBA
Credit: 1.5 hours
Alexander Pertsemlidis, PhD
Advances in biotechnology are making it possible to obtain massive amounts of data about the genetic information contained in living cells, the transmission of this information from parent to child, the changes in the information over evolutionary time, and the manner in which this information influences the chemical activity of cells. This course is an introduction to algorithmic techniques for the acquisition, analysis, and interpretation of such data.
Physical Biochemistry II
Fall II TBA
Credit: 1.5 hours
Jennifer Kohler, PhD
Provides students with a basic understanding of enzyme mechanism and enzyme kinetic analysis. Topics to be covered include basic Michaelis-Menten kinetics, multisubstrate reactions and inhibitor studies, ranging from the methods to analyze simple competitive inhibitors to suicide or tight binding inhibitors. These principles will be illustrated for a series of classic well-characterized enzyme reactions. Emphasis is placed on quantitative analysis through a series of problem sets and through reading and discussion of the primary literature.
Structure and Function of Ion Channels
Fall I NS5164-01
Credit: 1.5 hours
Ilya Bezprozvanny, PhD
The operation of the nervous and muscular systems rests upon the activities of a constellation ion channels, which mediate electrical signaling by action potentials, intracellular communication by electrical and chemical synaptic transmission, transduction of sensory stimuli, and the excitation-contraction coupling. Drawing upon the techniques of biophysics, biochemistry, and molecular biology, students in this course will consider the structures and functions of representative channels.
Bioinformatics and DNA Microarray Data Analysis
Fall IMM5101-01
Credit: 1.5 hours
Richard Scheuermann, PhD
High-throughput methodologies are generating complex experimental data at an incredible rate. As a result, these developments are forcing a paradigm shift in how the result from biological experimentation are interpreted, in which computers are playing an increasingly important role. The increasing use of computers for data storage, data retrieval, and data analysis is leading to the evolution of two biological disciplines: bioinformatics and computational biology.
In this course, we will use the gene expression microarray experimental platform as a model high throughput methodology to examine how bioinformatics, statistics, and computation are being used to support the discovery of new biomedical knowledge. In addition to didactic lectures and discussion, this class will include a series of hands-on workshops focused on the basic steps for microarray data processing.