Biochemistry and Molecular Biology Graduate Program BMB Course Descriptions

Information About the Curriculum

  • All first year students participate in the Basic Biomedical Science Curriculum (BBSC). This integrated curriculum includes three foundation courses: Biochemistry, Cell Biology, and Molecular Biology and Genetics. Students complete three to four 8-week rotations in laboratories of their interest and begin taking required BMB courses.

    Students entering the Graduate Program in BMB are required to take six hours of BMB/MBET courses, and an additional 8 credit hours of electives prior to graduation. Elective courses can be taken from any graduate program and are individually tailored for each student to provide the necessary knowledge base for his/her research program. BBSC courses do not count for BMB electives. Students also develop important oral presentation skills through participation in seminar courses.

    PhD Curricular requirements for BMB:
    • — 6 hours/credits of BMB courses (any BMB course, aside from the seminar courses, research or dissertation)
    • — 8 hours of electives from ANY GSBS graduate program, except BBSC courses
    • — BMB 6111 – to be taken in fall and spring of years 1-4
    • — BMB 6195 – to be taken 3 times (spring semesters), with the student presenting their research twice.

    Students take the Qualifying Examination in the Spring term of their second year. The written portion of the exam is an NIH-style proposal based on the student's research project, followed by an oral defense of the proposal.

    All BMB/MBET courses will have mandatory evaluations at the end of each term. In order to receive a grade, students must complete these evaluations within the deadline provided. All responses are confidential and anonymous.

Note: Click on course titles to access the description.

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Fall Term Courses and Descriptions

Spring Courses and Descriptions

Summer Courses and Descriptions

Biochemistry and Molecular Biology Course Descriptions


Teaching Biochemistry (BMB 6102)

In this course, students will learn and practice skills necessary to facilitate small group learning teams. Facilitator Skills Workshops will be imparted by personnel from the School of Medicine Office of Educational Development. At the end of the course, students will: (a) Be able to distinguish between actual content (the concept the small group is working on) and process (how the group works on acquiring and developing knowledge on that concept); (b) Understand the various group member roles related to both content and process; (c) Have practiced methods for effective communication; (d) Have learned effective questioning skills; (e) Have practiced effective listening skills and empathy; (f) Be capable of providing effective feedback; (g) Be capable of maintaining engaging group discussions and (h) Be able to providing constructive evaluations.

Prerequisite: BBSC-6401 (Biochemistry) or any of the Molecular Biophysics classes from the MBET Track
1 Credit Hour
Instructor: Marc Morais
Term offered: Fall
Year offered: Annually
Hours per week: 2 hours, 12 Week Course


Current Concepts in Biochemistry & Molecular Biology (Faculty Seminar) (BMB 6111)

BMB-committed first year BBSC students and BMB students must register for BMB 6111 every fall and spring term through their fourth year. Students will attend faculty seminars offered by the department of Biochemistry & Molecular Biology, KECK Center, or Sealy Center for Structural Biology & Molecular Biophysics.

1 Credit Hour
Prerequisite: None
Instructor: James Lee
Term offered: Fall and Spring
Year offered: Annually
Hours per week: 1 hour per seminar attended


RNA Biology (BMB 6112)

This course will cover the cutting-edge trend of RNA research as well as classic knowledge on RNA. The main objectives will be: 1) to understand the role and mechanism of small regulatory ncRNAs as well as intermediate and long ncRNAs, 2) recognize diverse roles and properties of RNA, and 3) to understand the metabolism of diverse RNAs including mRNAs and ncRNAs. The lecture will consist of three modules (see “course schedule” below). Each module will last two weeks: one week for lecture and the other week for journal reading and discussion.

1 Credit Hour
Prerequisite: Recommended (but not mandatory) Basic biology courses in BBSC (i.e. Molecular Biology and Genetics)
Instructor: Eric Wagner
Term offered: Spring
Year offered: Annually
Hours per week: 3 hours per week - 8 weeks


Seminar (BMB 6195)

Students must register for the Seminar course (BMB 6195) in years 2, 3 and 4 (three consecutive years after they enter into the BMB graduate program). Each student will attend student seminars regularly and, in addition, each student will present one seminar per year in their third and fourth years.

Prerequisite: BBSC Core
1 Credit Hour
Instructor: Kay Choi and Muge Martinez
Term offered: Spring
Year offered: Annually
Hours per week: Seminar 1


Genomics, Proteomics and Bioinformatics (BMB 6208)

Lecturers will select seminal recent papers on principles and novel techniques used in the interpretation of DNA micro arrays, protein arrays and data mining of structural and functional databases. Each student is requested to read all papers, and present one paper with additional background information in a 45-minute lecture. The faculty will provide additional advice on the context of this paper in the literature, might complement the student presentation with comments from his expertise on particular techniques, and will stimulate the discussion on the content of paper.

Prerequisite: Consent of instructor or BBSC core
2 Credit Hours
Instructor: H. Spratt, W. Braun, J. Wiktorowicz
Term offered: Fall
Year offered: Annually
Hours per week: 2, 10 Week Course


Tutorial in DNA Replication, Repair, and Mutagenesis (BMB 6209)

This course, which is in the tutorial format, deals with various aspects of DNA repair and replication, mutagenesis, and environmental toxicology. A particular focus point will be the interrelationships among repair processes and other important cellular functions.

Prerequisite: Consent of instructor or BBSC core
2 Credit Hours
Instructor: S. Prakash, L. Prakash, T. Hazra
Term offered: Fall
Year offered: Annually
Hours per week: 2, 10 Week Course


Practical Algorithms for Bioinformatics and Systems Biology (BMB 6216)

This course is designed to prepare the student to design, write, and modify such software applications. We will cover the data structures and algorithms most useful in modern systems biology. The presented concepts will be illustrated by real-life examples and exercises in analyzing genomic sequences, expression profiles, regulation networks and interaction. We will learn how to generate simulated / randomized data with given statistical properties and use them for Monte-Carlo analysis. Practical techniques will be presented for parsing the output of web-based servers, as well as for creating our own on-line resources. We will also cover the basics of relational databases and visualization of multidimensional scientific data. In most examples of data processing will be using PERL, a versatile high-level programming language that is very popular in bioinformatics and world-wide-web applications, as well as R, a software environment for statistical computing

Prerequisite: None
2 Credit Hours
Instructor: Kudlicki
Term Offered: Spring
Year offered: Annually
Hours per week: 2 hours, 15 Week Course


Molecular, Cellular and Genetic Basis of Aging (BMB 6223) - Odd Years Only

This course encompasses the principles and novel techniques used in understanding the molecular, cellular (physiological) and genetic factors that regulates the rate of aging and longevity. The mechanisms of aging will be clarified by integrating genetic data with molecular, cellular and physiological outcomes and environmental factors. The course discusses how organisms develop the molecular and biochemical characteristics of aging. A major consideration is how environmental factors interact with genetic factors to influence a aging processes

Prerequisite: Consent of instructor or BBSC core
Instructor: John Papaconstantinou
Term offered: Spring
Year offered: Bi-Annually
Hours per week: 2, 10 Week Course


Structural Biology and Biophysical Chemistry (BMB 6224)

This course deals with the role of biophysical methods, including structural biology, solution biophysical and computational approaches, in the study of proteins in the proteomic era. The focus is on conformational changes and macromolecular assembly, the utility of dynamic and static structural data, and the necessity to combine experimental approaches to obtain a full functional description.

Prerequisite: Consent of instructor or BBSC core Consent of instructor or BBSC core
2 Credit Hours
Instructor: W. Yin
Term offered: Spring
Year offered: Annually
Hours per week: 2, 10 Week Course


Inborn Errors of Metabolism (BMB 6227) – Even years only

This course will cover the inherited diseases whose basic metabolic disturbances have been described. Emphasis will be placed on mechanisms contributing to enzymatic blocks. The primary aim is to give an understanding of the basic defects and their effects on metabolism.

Prerequisites: BBSC Core
2 Credit Hours
Instructor: Srivastava
Term offered: Spring
Year offered: Even years
Hours per week: Lecture


The Meaning of Being an Independent Investigator (BMB 6231)

The goal of a graduate training is to develop a student into an independent investigator. The trademarks of an independent investigator are the acquisition of the ability to:

1. Identify a project of significance through critical analysis of the literature;
2. Identify needed information to fill the gap;
3. Identify the best approaches to acquire the needed information;
4. Assimilate data;
5. Present data in writing or verbally.

This course will be offered to the 2nd year students to provide them with the framework for their graduate training.

Prerequisite: None
2 Credit Hours
Instructor: Muge Martinez and James Lee
Term offered: Fall
Year offered: Annually
Hours per week: 3 hours, 15 weeks


Structure-Based Drug Discovery (BMB 6238)

The drug discovery process requires a combination of different disciplines with the ultimate goal of bringing to the marketplace a drug that can treat health problems. However, the current experimental strategy of drug discovery and development is expensive, inefficient, and lengthy. Structure-aided drug discovery constitutes an advantageous strategy to improve the drug discovery process with less investment of money and time. Using didactic lectures and computer-based interactive projects, this course will provide an in-depth introduction to the theoretical and practical aspects of structure-aided drug discovery. At the completion of this course, participants will have become skilled in applying the software, databases, and concepts necessary to independently initiate a computer-based drug discovery project.

Prerequisite: None
2 Credit Hours
Instructor: Stan Watowich
Term offered: Summer
Year offered: Annually
Hours per week: 6 hours, 7 weeks


Biological Fluorescence (BMB 6239)

Course description and objectives :The course addresses major theoretical and practical aspects of fluorescence spectroscopy as encountered in biological research of macromolecular interactions in solution. The subjects include discussions of fluorescence intensity measurements, emission and excitation spectra, inner filter effect, magic angle, fluorescence lifetime, quantum yield determination, dynamic and collisional quenching problems, and Fluorescence resonance energy transfer (FRET) theory. Practical aspects of the course will focus on the experimental design, approaches and applications of measurement of fluorescence, including steady state and time dependent fluorescence anisotropy as applied to macromolecular structure analyses, and quantitative fluorescence titration methodologies in examining energetics of macromolecular interactions

Prerequisite: Undergraduate background in Biochemistry, Biology, Chemistry
2 Credit Hours
Instructor: Wlodek Bujalowski
Term offered: Summer
Year offered: Annually
Hours per week: 4 hours, 8 weeks


Single Molecular Detection (BMB 6265)

Single molecule methods are an important new set of tools that are currently used in many areas of biology. The goal of this course is to provide conceptual framework on single molecule experimental techniques. We will describe novel methods of single molecule manipulation and analysis. Some of the techniques that will be covered are Atomic Force Microscopy, Optical tweezers and single molecule fluorescence. We will discuss the use of these techniques to study polymer elasticity, protein mechanics, motor proteins, protein folding, RNA folding, receptor-ligand interactions, imaging of single molecule and cell mechanics. In each lecture we will discuss two or more key papers.

Prerequisite: None
2 Credit Hours
Instructor: Andres Oberhauser
Term offered: Summer
Year offered: Annually
Hours per week: 2 hours, 15 week


Protein NMR Spectroscopy (BMB 6266) - Odd Years Only

In this course, students will learn advanced NMR methods for biophysical research of proteins and their molecular interactions. Theoretical aspects of protein NMR spectroscopy will be taught using the Mathematica program. Practical issues will be taught using actual NMR data together with the NMR-Pipe and NMR-View programs.

Prerequisite: Students must have taken Molecular Biophysics II (BMB 6334)
Instructor: Junji Iwahara
Term offered: Summer
Year offered: Biennially-Odd Years
Hours per week: 2 hours, 14 weeks


Introduction to Fast Kinetics (BMB 6312) – Even years only

This course is for advanced graduate students provides an introduction to the theoretical and experimental aspects of transient chemical kinetics analysis of biochemical reaction mechanisms. Emphasis will be placed on application of time-dependent and fast kinetic methods of study of the dynamics of biomolecular interactions.

Prerequisite: BBSC Curriculum
Instructor: W.M. Bujalowski
Term offered: Spring
Year offered: Biennially-Even
Hours per week: 3 hours, 15 Week Course


Cell Signaling for Growth, Differentiation, Death (BMB 6316)

An in depth elective course designed to give students an understanding of multiple signal pathways and to analyze the literature of cell signaling in normal and pathological cell growth, differentiation and death.

1. To acquire knowledge about basic principles governing stress response signaling in biological systems at the molecular and cellular level and the approaches that are being attempted
2. To become familiar with assessment of current research literature
3. To become familiar with how to develop a research project
4. To acquire some practice in process of writing a grant
5. To learn how to evaluate a grant and respond to such a critique
6. To learn how to present such evaluations in a group setting

Prerequisite: BBSC Curriculum
3 Credit Hours
Instructor: J.R. Perez-Polo
Term offered: Summer
Year offered: Annually
Hours per week: 3 hours


Pathophysiology of Inflammatory Disorders (BMB 6322)

This will be a 3 hours course in which various Signaling Pathways that contribute to inflammatory disorders such as various forms of cancers including metastasis, diabetes asthma, CoPD, macular degeneration and other visual complications, arthritis, bacterial infections and sepsis will be discussed. A two hour lecture will be presented on Tuesdays and one hour discussion on Thursdays. The class time will be decided based upon the convenience of the students.

Prerequisite: None
3 Credit Hours
Instructor: S. Srivastava
Term offered: Spring
Year offered: Annually
Hours per week: 3 hours, 16 weeks


Probabilistic and Statistical Methods in Bioinformatics (BMB 6326)

Applications of high-throughput technologies to biological samples produce large amounts of data characterizing the current state of samples. Statistical bioinformatics plays important role in planning experiments for testing specific hypotheses, analyzing the results, evaluating statistical significance of the conclusions and in accepting/modifying the original hypothesis. Examples of data processing will be provided from proteomics experiments and standard databases available in R.

Prerequisite: None
3 Credit Hours
Instructor: Rovshan Sadygov
Term offered: Fall
Year offered: Annually
Hours per week: 3 hours, 16 weeks


Bioinformatics II, Systems Biology & Stochastic Modeling (BMB 6330)

Course description and objectives: In this course we will concentrate on some of the key probabilistic, Statistical concepts and computational modeling techniques actively used in modern biomedical data analysis. Examples of data processing will be provided from proteomics experiments and standard databases available in R. The goal is to comprehensively understand development, physiology, metabolic and gene regulatory networks, by looking at many genes, RNA's proteins and metabolites in an organism simultaneously.

Prerequisite: BBSC Curriculum
3 Credit Hours
Instructor: Rovshan Sadygov
Term offered: Spring
Year offered: Annually
Hours per week: 3 hours


Molecular Biophysics I (BMB 6332)

In this course, students learn thermodynamics and kinetics for biological molecules. Both theoretical and experimental aspects are covered. Students also learn the MATLAB software so that they can use it as a tool for their own research.

3 Credit Hours
Instructors: Wlodek M. Bujalowski, Ph.D., Luis Marcelo F. Holthauzen, Ph.D., Junji Iwahara, Ph.D. (Course Director), James C. Lee, Ph.D., Krishna Rajarathnam, Ph.D., Stanley J. Watowich, Ph.D.
Term offered: Fall
Year offered: Annually
Hours per week: 3 hours, 16 weeks


Molecular Biophysics II (BMB 6334)

In this course, students learn thermodynamics and kinetics for biological molecules. Both theoretical and experimental aspects are covered. Students also learn the MATLAB software so that they can use it as a tool for their own research.

3 Credit Hours
Instructors: Wlodek M. Bujalowski, Ph.D., Luis Marcelo F. Holthauzen, Ph.D., Junji Iwahara, Ph.D. (Course Director), James C. Lee, Ph.D., Krishna Rajarathnam, Ph.D., Stanley J. Watowich, Ph.D.
Term offered: Spring
Year offered: Annually
Hours per week: 3 hours, 16 weeks


Macromolecular Structure (BMB 6336)

Introduction to proteins and nucleic acids, with emphasis on physical underpinnings. Topics include primary, secondary, and tertiary structure, sequence analysis, energetics and predictive methods.

3 Credit Hours
Instructors: Wlodek M. Bujalowski, Ph.D., Andres Oberhauser, Ph.D., Stanley J. Watowich, Ph.D.
Term offered: Fall
Year offered: Annually
Hours per week: 3 hours, 16 weeks


Statistical Thermodynamics (BMB 6341) - Even Years Only

This is an advanced elective course in fundamental biophysics. We will explore topics concerning the connection between the microscopic properties of atoms determined by quantum mechanics with the macroscopic properties determined by thermodynamics. We wish to understand the connection between atomic or molecular properties and bulk behavior as happens in solutions or cells. The central objective of the course is how to get from 10^23 variables (like position, velocity, species) to a small number of thermodynamic observables. The tools of statistics and probability theory will be employed to understand the behavior of large numbers of atomic/molecular systems via their mechanical laws and properties to describe solids, liquids and biopolymers. Lectures, online course materials, and homework problems will be used for each class period.

Prerequisite: No graduate course prerequisites. Undergraduate thermodynamics, differential equations, and some quantum mechanics are recommended.
3 Credit Hours
Instructor: B.M. Pettitt
Term offered: Summer
Year offered: Biennially-Even Years
Hours per week: 3 hours, 15 weeks


Biological Electron Microscopy (BMB 6351)

The purpose of this course is for the student to develop an understanding of the principles of electron microscopy as applied to the study of biological macromolecules and tissues. Knowledge of these principles will form a foundation for gaining practical experience and training in biological electron microscopy. At the completion of this course, participants will have become skilled in applying some of the techniques and concepts necessary to independently initiate projects on quantitative protein unfolding/folding, protein-ligand binding, protein size distribution, protein secondary and tertiary structure, or any number of other quantitative biophysics applications.

Prerequisite: BMB 6334-Molecular Biophysics II or permission from instructor.
3 Credit Hours
Instructors: Marc Morais and Michael Sherman
Term offered: Fall
Year offered: Annually
Hours per week: 3 hours, 15 weeks


Thermodynamics of Macromolecular Assembly (BMB 6360)

This course deals with the role of biophysical methods, including structural biology, solution biophysical and computational approaches, in the study of proteins in the proteomic era, particularly the mechanisms of regulation in biology involving macromolecular assembly.

3 Credit Hours
Instructor: James C. Lee, Ph.D.
Term offered: Summer
Year offered: Biennially-Even Years
Hours per week: 3 hours, 15 weeks


Structural Bioinformatics (BMB 6361)

Structural Bioinformatics is driven by the emergence of large amounts of data on gene sequences, three-dimensional (3D) macromolecular structures of genes and proteins and their functional properties. Those data are derived from high-throughput DNA sequencing, as results from the Protein Structure Initiative to generate a comprehensive overview of all 3D protein folds, and mass spectroscopic/proteomics methods to characterize structural modifications of proteins in a living cell environment. The objective of the course is to make students familiar with the basic concepts and practical state-of the art computational tools to search, retrieve and analyze those high-resolution structural data and be able to generate hypotheses on the biological mechanisms of those systems. The course will focus on probability concepts and statistical models of data representations and analysis, algorithms for sampling data, software tools for protein structure prediction, and computational methods for analyzing the energetics, kinetics and dynamics of bio-macromolecules and their interactions by structural simulations.

Prerequisite: Previous attendance of the course BBSC 6223 Bioinformatics is highly recommended.
3 Credit Hours
Instructor: W. Braun, R. Sadygov, B.M. Pettitt
Term offered: Spring
Year offered: Annually
Hours per week: 3 hours week - 16 weeks


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