Course Descriptions

Helpful Documents: Degree Plan | Professional Outcomes

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. Program researchers study 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.

Curriculum

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.

Courses

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.

Macromolecules I: Structural Foundations

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.

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.

Macromolecules II: Energetic Foundations

Spring (1st 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

Please review the degree plan (page 2) for specific elective requirements.

Quantitative Biology

Spring (1st half)
1.5 credit hours
Introduction to quantitative approaches to “complex” systems in biology. The course comprises a mixture of didactic lectures that provide a review of basic concepts, theories, and tools of quantitative science, and also a number of case studies in which deep understanding of biological systems has emerged through the application of this approach. An overall theme is to define complexity in a more rigorous way and to learn about strategies to rationally address complexity.

The course begins with the study of linear systems and the rich mathematical foundations for understanding and predicting their behaviors. The course then moves non-linear systems: What makes them complex and difficult, and why is the mathematical treatment of these systems so much harder? We will explore several biological examples of non-linearity in fields ranging from structural biology to evolution, ending ultimately with a general definition of complexity in biology and an operational strategy for studying such systems.

The syllabus includes a combination of analytical and computational exercises to solve as we go through the course; we will use MATLAB as our primary computing platform.

The course is open to all graduate students and postdocs.

Modern Methods in Structural Biology

Spring (2nd 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.

Using Light in Biology

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.

Advanced NMR Spectroscopy

Fall (1st 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: Modern Methods in Structural Biology

Experimental Biophysics

Fall (1st half)
2.0 credit hours
This course is designed to give students a solid theoretical and experiential background in several biophysical techniques that are available at UT Southwestern. The topics covered are dynamic light scattering, analytical ultracentrifugation, isothermal titration calorimetry, circular dichroism spectroscopy, and microscale thermophoresis. Through lectures, students are exposed to the theoretical underpinnings of the methods.

The students also participate in laboratory exercises in which they conduct experiments using instruments available in the Macromolecular Biophysics Resource. After collecting data, the students are then guided through analyzing and presenting their data.

Prerequisite: Modern Methods in Structural Biology

Logic and Persuasion in Scientific Communication

Fall (2nd half)
1.5 credit hours
The course aims to improve participants’ presentation skills by providing structured instructions on how to build strong arguments, both written and oral. By combining original lectures and practical exercises on: (a) formal and informal logic, including detection of logical fallacies in scientific presentations, and (b) elements of critical thinking, students will learn skills and practice constructing arguments, engaging an audience, and recognizing and responding to problems in communication.

Practical X-Ray Crystallography

Fall (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: Modern Methods in Structural Biology. Recommended prerequisite: Protein Structure and Folding