Course Descriptions

The Molecular Biophysics Program offers students interested in physics, chemistry, and biology the opportunity to train with more than 30 faculty members conducting rigorous and multifaceted research programs. Researchers in the Program are studying a wide variety of fundamental biological problems using a diverse spectrum of experimental approaches, including X-ray crystallography, NMR spectroscopy, electron microscopy, fluorescence microscopy, mass spectrometry, computational modeling, and more. Students enrolled in the Program benefit from the strong tradition of interdisciplinary training at UT Southwestern Medical Center.

The curriculum has recently been redesigned so students complete the core course along with all specialized program coursework during the first year of graduate school (for details, see the degree plan). The coursework continues to focus on the application of principles and techniques of the physical sciences to biomedical research problems.

Core Curriculum – Genes

Fall (1st half)
2 credit hours
Molecular genetics of model organisms; DNA replication, repair and recombination; transcription; RNA catalysis, processing, and interference; translation; protein turnover; developmental biology; and genomics.

Core Curriculum – Proteins

Fall (1st half)
2 credit hours
Energetic basis of protein structure; stability; ligand binding and regulation; enzyme mechanics and kinetics; methods of purification; and analysis by spectroscopic methods.

Protein Structure and Folding

Fall (2nd half)
2 credit hours
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 is based on didactic material, discussion of the primary literature, and student projects utilizing computer graphics.

Quantitative Biology I

Spring (1st half)
1.5 credit hours
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 Quantitative Biology II.

Professionalism, Responsible Conduct of Research, and Ethics I

Fall full semester
1 credit hour
Topics covered through lectures and small group discussions: goals of education in RCR; professionalism; collaboration; teambuilding and professional behaviors; everyday practice of ethical science; mentorship; data management and reproducibility; animal research; genetics and human research.

Professionalism, Responsible Conduct of Research, and Ethics II

Spring full semester
1 credit hour
Topics covered through lectures and small group discussions: codes of ethics and misconduct; building interprofessional teams; conflict of interest; sexual boundaries and professional behavior; applications of genetic testing; technology transfer and intellectual property; plagiarism, authorship, and citation; peer review; image and data manipulation.

Physical Chemistry of Macromolecules

Spring (2nd half)
1.5 credit hours
This course covers diverse aspects of physical chemistry, including general concepts in thermodynamics and kinetics as well as topics more specific to biological macromolecules. All aspects will be presented from the point of view of statistical mechanics to provide a connection from microscopic behavior to macroscopic properties. Specific topics include diverse types of non-bonding interactions, cooperativity, phase transitions, and polymeric behavior.

Recommended

Core Curriculum – Cells

Fall (2nd half)
2 credit hours
Cell structure; membrane biology; intracellular membrane and protein trafficking; energy conversion; signal transduction and second messengers; cytoskeleton; cell cycle; and introductory material in microbiology, immunology, and neurobiology.

Electives

See degree plan (page 2) for specific elective requirements.

Modern Methods in Structural Biology

Spring (1st half)
1.5 credit hours
Much of modern structural biology is based on results obtained with two high-resolution methods (X-ray crystallography, NMR spectroscopy), often complemented by several lower-resolution approaches (EM, scattering, FRET, among others). We assert that the successful union of these general approaches is absolutely critical in modern structural biology, particularly as biophysical methods are applied to larger, multicomponent systems that are often dynamic in their composition. This course provides the foundation for students to understand these techniques, extending the introduction provided in the first year core course. A central focus of the course is discussions of both the theory and application of X-ray crystallography and NMR spectroscopy, with the aim to establish the physical bases of both methods using instruction that covers theory and application. Combined with introductions into the lower-resolution methods, this course provides students with the ability to critically evaluate the relative strengths and weaknesses of each technique and how they can be combined to provide insight into biological systems.

Spectroscopy

Spring (2nd half)
1.5 credit hours
Overview of optical spectroscopic approaches to biological systems, both in vitro and via light microscopy of cells. Begins with discussion of the interaction of light with matter, and extension to absorption spectroscopy, and UV, both visible and IR.  Circular dichroism of proteins and other chromophores. Fluorescence and fluorescence-based techniques. Static and dynamic light scattering. The course intends to develop physical principles to support rigorous biophysical applications and experimental design. 

Computational Approaches in Protein Science

Spring (1st half)
1.5 credit hours
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

Spring (2nd half)
1.5 credit hours
This course is designed to provide a strong background on biomolecular NMR spectroscopy. Topics covered include diverse practical aspects on the application of one-dimensional and multidimensional NMR techniques, protein structure determination, analysis of protein dynamics, product operator formalism, design of pulse sequences and studies of large proteins/systems. Prerequisite for this course: Modern methods in structural biology.

Quantitative Analysis of High Content/High Complexity Data Sets

Spring (2nd half)
1.5 credit hours
The goal of this course is to teach students how high content/high complexity data sets are generated and analyzed to extract information, and how the information is analyzed and integrated to generate knowledge. The course will begin with an overview of the types of high content data sets generated from a variety of discovery platforms (i.e., genomics, proteomics, metabolomics, imaging, structure), the information they include, and their architecture. Additional introductory lectures cover data preprocessing (focusing on quality control and reproducibility) and the basics of high content data set analyses. Once the student has had a solid introduction, specific examples of the types of data and analyses associated with the various discovery platforms will be studied and discussed. The course will conclude with specific approaches to data analysis and integration. During the course, the students will be exposed to programming languages, such as R and its statistical packages, as well as a variety of bioinformatic tools that are available on the internet. The course material will include theoretical, conceptual, practical, and applied presentations.

Physical Biochemistry I

Fall (2nd half)
2 credit hours
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. The course emphasizes quantitative analysis and reading and discussion of the primary literature.

Physical Biochemistry II

Spring (1st half)
1.5 credit hours
This course is designed to provide 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. The course emphasizes quantitative analysis through a series of problem sets and through reading and discussion of the primary literature.

Practical X-Ray Crystallography

Spring (2nd half)
1.5 credit hours
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. Prerequisite for this course: Modern methods in structural biology. Recommended prerequisite: Protein Structure and Folding.

Quantitative Biology II

Spring (2nd half)
1.5 credit hours
Quantitative Biology I is a prerequisite to this course. The course includes approaches to dealing with larger, complex and/or non-linear systems: building complex behaviors from simple components, appearance of non-linear systems and their analysis, some theoretical approaches to complex systems and to parameterizing large, complex and/or non-linear models. This section includes some teleological discussion of the biological (functional and evolutionary) utilities of complex or non-linear systems.