Structural Biology and Biophysics (SBB) Curriculum

Fall Term

Research
(BCMB 6097; Credit Hours Vary)
Laboratory Rotation (1/3)

Biomolecular Thermodynamics
(BCMB 6113; 1 Credit Hours; Required)
In this 6-week course, students will learn thermodynamics of various biomolecular processes, including conformational changes, molecular association / dissociation, and protein-drug interactions. Both theoretical and experimental aspects are covered. Students will also learn the MATLAB software and use it to solve or understand thermodynamic problems.

• Instructors: Iwahara, Pettitt
• Term Offered: Fall, first half only
• Year Offered: Annually
• Hours per week: 3, 6-week course

Biomolecular Kinetics
(BCMB 6114; 1 Credit Hours; Required)
In this 6-week course, students will learn kinetics of various biomolecular processes, including molecular association, dissociation, conformational changes, enzymatic catalysis, and target search. Both theoretical and experimental aspects are covered. Students will use the MATLAB software to solve or understand various kinetic problems.

• Instructors: Iwahara, Smith, Yin
• Term Offered: Fall, Second half only
• Year Offered: Annually
• Hours per week: 3, 6-week course

Biochemistry
(BBSC 6303; 3 Credit Hours; Required)
The course deals with the fundamental forces that provide the bases for molecular interactions, and the translation of these forces into the structure and function of proteins and nucleic acids. Emphasis will be on the principles that give rise to these forces; on applying the principles to biochemical problems; and on the application of the principles in understanding macromolecular structure and function. The course also provides a survey of techniques relevant to subjects discussed. In addition the course presents the general principles of regulation in metabolism, molecular signaling and synthesis and function of different biomolecules as they apply to developing an understanding of regulatory mechanisms in homeostasis and disease.

• Instructor: Pettitt, Smith
• Term Offered: Fall
• Year Offered: Annually
• Hours per week: 3, 16-week course

Spring Term

Research
(BCMB 6097; Credit Hours Vary)
Laboratory Rotation (2/3)

Diffraction Methods in Structural Biology
(BCMB 6241; 2 Credit Hours; Required)
This course is a series of lectures with in-class exercises and homework assignments that will cover the following topics: 1) the physical and mathematical basis of diffraction; 2) the relationship between the atomic structure of a periodic object and its diffraction pattern; 3) geometric interpretation of diffraction and the reciprocal space; 4) solution of the crystallographic phase problem; 5) refinement and accuracy of atomic models derived from X-ray diffraction data; 6) practical application of obtained knowledge to solving the crystal structure of a protein.

• Instructor: Leiman
• Term Offered: Spring
• Year Offered: Annually
• Hours per week: 2, 16-week course

Statistical Thermodynamics
(BCMB 6341; 3 Credit Hours; Required)

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.

• Instructors: B.M. Pettitt
• Term Offered: Spring
• Year Offered: Annually
• Hours per week: 3, 15 weeks

Biomolecular Dynamics
(BCMB 6115; 1 Credit Hours; Required [Year 1, 2 or 3])
In this 1-credit hour course, students will learn about experimental research on structural dynamics of biomacromolecules. Structural dynamics of various systems such as enzymes, molecular motors, cell surface receptors, chromatin / chromosome, ribosome, and viral particles will be discussed. Covered methods include nuclear magnetic resonance (NMR), crystallography, cryo-electron microscopy, fluorescence imaging, and single-molecule techniques. The primary focus will be on applications rather than on the principles of the methodologies. Students will read highly influential papers on structural dynamics of macromolecules, which are selected by the instructors. Each instructor gives two sessions: in one session, the instructor gives an introductory lecture on methods highly relevant to the papers selected for discussion; in the following session, the instructor leads discussion while the students present the papers.

• Instructors: Gagnon, Iwahara, Nir, Oberhauser, Rajarathnam, Smith
• Term Offered: Spring
• Year Offered: Annually (only with 3 or more enrollees)
• Hours per week: 1.5, 16-week course

Summer Term

Research
(BCMB 6097; Credit Hours Vary)
Laboratory Rotation (3/3)

Structure Based Drug Discovery
(BCMB 6238; 2 Credit Hours)
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.

• Instructor: Watowich
• Term Offered: Summer
• Year Offered: Annually
• Hours per week: 2, 16-week course

Electives (add) 6 additional credit hours prior to graduation

Fall Term

Research
(BCMB 6097; Credit Hours Vary)

Biological Electron Microscopy
(BCMB 6351; 3 Credit Hours; Required)
Transmission electron microscopy (TEM) has emerged as a powerful tool to 1) study tissues at the level of single cells/organelles; 2) image eukaryotic/prokaryotic cells and characterize their interactions and 3) elucidate three-dimensional structures of large biological macromolecules and assemblies. Within the TEM field, cryo-electron microscopy (cryo-EM) allows visualization of intact molecules/complexes under near native conditions. With improvements of data acquisition hardware and image processing software, it is now possible to determine three-dimensional structures of structurally homogeneous biological macromolecules to near-atomic resolution. Further, the development of cryo-electron microscopy tomographic techniques (cryo-ET) has made it possible to image structurally heterogeneous objects such as cells and organelles to nanometer resolution. 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 provide a foundation for gaining practical experience and training in biological transmission electron microscopy. 

• Instructor: Sherman
• Term Offered: Spring
• Year Offered: Annually
• Hours per week: 3, 16-week course

Genomics, Proteomics and Bioinformatics
(BCMB 6208; 2 Credit Hours)
Lecturers will select seminal recent papers on principles and novel techniques used in the interpretation of genomic sequencing data, RNA-seq analysis, and data mining of structural and functional databases of genes and proteins. Each student is requested to read all papers during the course, and present one paper with additional background information in a 45-minute lecture. The faculty will give introductory lecturers to the topics of the course with an emphasis on Genomics and Bioinformatics. They will also provide additional advice on the context of the papers in the literature, and will complement the student presentation with comments from his expertise on particular techniques. The student presentations of the papers will include discussions among students and faculty on the scientific background of the papers.

• Instructors: Braun
• Term Offered: Fall
• Year Offered: Annually
• Hours per week: 2, 16-week course

Electives (add) 6 additional credit hours prior to graduation

Spring Term

Research
(BCMB 6097; Credit Hours Vary)

Seminar
(BCMB 6195; 1 Credit Hour)
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.

• Instructor: TBA
• Term Offered: II
• Year Offered: Annually
• Hours per week:1

Biomolecular Dynamics
(BCMB 6115; 1 Credit Hours; Required [Year 1, 2 or 3])
In this 1-credit hour course, students will learn about experimental research on structural dynamics of biomacromolecules. Structural dynamics of various systems such as enzymes, molecular motors, cell surface receptors, chromatin / chromosome, ribosome, and viral particles will be discussed. Covered methods include nuclear magnetic resonance (NMR), crystallography, cryo-electron microscopy, fluorescence imaging, and single-molecule techniques. The primary focus will be on applications rather than on the principles of the methodologies. Students will read highly influential papers on structural dynamics of macromolecules, which are selected by the instructors. Each instructor gives two sessions: in one session, the instructor gives an introductory lecture on methods highly relevant to the papers selected for discussion; in the following session, the instructor leads discussion while the students present the papers.

• Instructors: Gagnon, Iwahara, Nir, Oberhauser, Rajarathnam, Smith
• Term Offered: Spring
• Year Offered: Annually (only with 3 or more enrollees)
• Hours per week: 1.5, 16-week course
  

Probabilistic and Statistical Methods in Bioinformatics 
(BCMB 6240; 2 Credit Hours)
Biomedical research is rapidly becoming data-intensive and researchers generate and use increasingly large, complex, multidimensional, and diverse datasets. The data sets are often structured, but with non-trivial structure inconsistent with classical experimental designs. The ability to access, process, analyze, understand, extract value from and disseminate data is becoming critical. Multiple skills are required for these purposes. In this course, we will concentrate on some of the key probabilistic, statistical concepts and machine learning 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 grading is based on class participation, homework assignments, midterm and final exams.

• Instructor: Sadygov
• Term Offered: Spring
• Year Offered: Annually
• Hours per week: 2, 16-week course

Seminar
(BCMB 6196; 1 Credit Hour)
Current Concepts in Biochemistry & Molecular Biology (Faculty Seminars), 6 credits required for all students.

Qualifying Examination
See our definition and guidelines of the qualifying examination.

Summer Term

Research/Dissertation
(BCMB 6097/6099; Credit Hours Vary)

Electives (add) 6 additional credit hours prior to graduation

Fall Term

Research/Dissertation
(BCMB 6097/6099; Credit Hours Vary)

Electives (add) 6 additional credit hours prior to graduation

Spring Term

Research/Dissertation
(BCMB 6097/6099; Credit Hours Vary)

Electives (add) 6 additional credit hours prior to graduation

Seminar
(BCMB 6195; 1 Credit Hour)
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.

• Instructor: TBA
• Term Offered: II
• Year Offered: Annually
• Hours per week:1

Seminar
(BCMB 6196; 1 Credit Hour)
Current Concepts in Biochemistry & Molecular Biology (Faculty Seminars), 6 credits required for all students.

Biomolecular Dynamics
(BCMB 6115; 1 Credit Hours; Required [Year 1, 2 or 3])
In this 1-credit hour course, students will learn about experimental research on structural dynamics of biomacromolecules. Structural dynamics of various systems such as enzymes, molecular motors, cell surface receptors, chromatin / chromosome, ribosome, and viral particles will be discussed. Covered methods include nuclear magnetic resonance (NMR), crystallography, cryo-electron microscopy, fluorescence imaging, and single-molecule techniques. The primary focus will be on applications rather than on the principles of the methodologies. Students will read highly influential papers on structural dynamics of macromolecules, which are selected by the instructors. Each instructor gives two sessions: in one session, the instructor gives an introductory lecture on methods highly relevant to the papers selected for discussion; in the following session, the instructor leads discussion while the students present the papers.

• Instructors: Gagnon, Iwahara, Nir, Oberhauser, Rajarathnam, Smith
• Term Offered: Spring
• Year Offered: Annually (only with 3 or more enrollees)
• Hours per week: 1.5, 16-week course

Summer Term

Research/Dissertation
(BCMB 6097/6099; Credit Hours Vary)

Electives (add) 6 additional credit hours prior to graduation

Fall Term

Research/Dissertation
(BCMB 6097/6099; Credit Hours Vary)

Electives (add) 6 additional credit hours prior to graduation

Spring Term

Research/Dissertation
(BCMB 6097/6099; Credit Hours Vary)

Electives (add) 6 additional credit hours prior to graduation

Seminar
(BCMB 6195; 1 Credit Hour)
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.

• Instructor: TBA
• Term Offered: II
• Year Offered: Annually
• Hours per week:1

Seminar
(BCMB 6196; 1 Credit Hour)
Current Concepts in Biochemistry & Molecular Biology (Faculty Seminars), 6 credits required for all students.

Electives (add) 6 additional credit hours prior to graduation

Summer Term

Research/Dissertation
(BCMB 6097/6099; Credit Hours Vary)

Structure Based Drug Discovery
(BCMB 6238)

Electives (add) 6 additional credit hours prior to graduation

Based on their needs and interests, SBB students can take any courses of UTMB Graduate School of Biomedical Sciences (GSBS) as electives. GSBS courses are listed at the GSBS Course Offerings website. For GSBS courses of programs other than the BCMB program, you need approval of the director.

Overview

The qualifying examination is the examination process that all PhD students must overcome. It takes place during the second term of the second year. For many students, once they pass the test, the remainder of the PhD education is spent in the lab doing research and preparing for the final defense of their work. The test is difficult by design, and is paramount to a good graduate education. Comprehensive examinations in the SSB educational track have two facets: the written examination (NIH-style grant proposal); and an oral defense in front of a committee of faculty members. Read below for specific details.

Requirements

Examination Committee

The Examination Committee for Part I of the qualifying examination shall consist of faculty members knowledgeable in the different research areas of each of the students taking the qualifying examination. The Committee will elect a Chairman. The Committee will communicate the results of the examinations to the Evaluation Committee. To provide continuity between Parts I and II of the qualifying examination, each Committee member will also participate in the Oral Examination of the student for whose proposal he/she is primary reviewer.The Examination Committee for Part I of the qualifying examination shall consist of faculty members knowledgeable in the different research areas of each of the students taking the qualifying examination. The Committee will elect a Chairman. The Committee will communicate the results of the examinations to the Evaluation Committee. To provide continuity between Parts I and II of the qualifying examination, each Committee member will also participate in the Oral Examination of the student for whose proposal he/she is primary reviewer.The Examination Committee for Part I of the qualifying examination shall consist of faculty members knowledgeable in the different research areas of each of the students taking the qualifying examination. The Committee will elect a Chairman. The Committee will communicate the results of the examinations to the Evaluation Committee. To provide continuity between Parts I and II of the qualifying examination, each Committee member will also participate in the Oral Examination of the student for whose proposal he/she is primary reviewer.

Comprehensive Examinations

The examination is divided into two parts:

1. Part I of the examination will usually be scheduled during early Term II (Spring term) of the student's second year. Students with advanced placement or direct admission into the Program may schedule their examination earlier, with approval from the Evaluation Committee. Students will submit to the Examination Committee a written research proposal in the format of an abbreviated NIH R01 grant proposal (15 pages in length, not including references). Students will submit this proposal before January 22nd of the year of their qualifying examination. Within 30 days following submission, the Examination Committee will evaluate the proposal and meet with each examinee individually to critique the quality of his/her writing. The Examination Committee is charged to maintain a consistent standard in evaluating the quality of writing in all of the proposals. The committee should address questions such as:

• Is the research hypothesis-driven?
• Is there an identified significance/relevance to human health?
• Is the literature review current?
• Is the background germane to the experimental design & methods?
• Has the student anticipated problematic areas and proposed alternative methods and approaches?

Evaluation

The Examination Committee will communicate the results of the examination to the Evaluation Committee in writing. If weaknesses are detected, the Examination Committee may recommend corrective measures to the Evaluation Committee. Upon successful completion of Part I, students are allowed 30 days to revise their written proposal before submitting it to the Oral Examination Committee for Part II of the qualifying examination.

2. Part II of the qualifying examination will be scheduled to take place within one month after the submission of the revised written proposal to the Oral Examination Committee. This Committee will be formed by the student with the help of the proposed dissertation supervisor, and approved by the Program Director. This committee should be composed of four members of the SBB Graduate Track including the proposed Supervising Professor, who may not serve as the Chairman of this committee, and a faculty member who is not a member of the SBB or BMB Graduate Program. To provide continuity between Parts I and II of the examination, one of the members of the Oral Examination Committee should be the primary reviewer of the student's proposal from Part I of the Qualifying Examination.

The student and the committee members will determine the date of the oral examination. The written proposal must be submitted to each committee member, and to any SBB faculty member who requests it, at least two weeks before the examination. At the oral examination, the student will give a formal presentation of the proposal and then will accept questions on any topic related centrally or peripherally to the proposal. The Oral Examination Committee will conduct a rigorous and in-depth examination of the scientific merits of the proposal, the student's scientific knowledge, and his/her ability to integrate scientific information. The Oral Examination Committee will communicate the results of the examination to the Evaluation Committee in writing.

Final Evaluation

The Evaluation Committee will evaluate the student's complete academic performance and will present its recommendation to the full Faculty regarding the student's advancement to Candidacy. The full Faculty will vote on the recommendation. The Program Director will inform the BMB Graduate Program Director, who will in turn inform the Dean of the Graduate School in writing once the student has performed satisfactorily and, therefore, is eligible for advancement to Candidacy for the PhD degree.

1. Qualifying/Comprehensive Examination
2. Application for Candidacy Submitted (Application form, research proposal)
3. Application for Candidacy Approved by Dean (prerequisite to registering for Dissertation)
4. Request for Final Oral Submitted (Two weeks before final oral)
5. Report of Final Oral Signed and Submitted
6. Schedule Appointment with Sandy Youngblood to obtain final graduation paperwork.
7. Final Copy of Dissertation Checked and Approved by Dean's Office prior to Duplication
8. Submit final unbound copy of dissertation with:
   • Survey of Earned Doctorates
   • Copyright Disclaimer (signed and dated)
   • Microfilm Agreement Form
   • Two copies of title page and abstract
   • Picture
   • Complete Graduate Information Forms
   • Benchmarking Survey - Graduation (an email notification will be sent to you)
9. Exit Interview with Dean (optional)
10. Clear with Registrar's Office
• Graduation Fee Paid
• Diploma Name Card
• Hold on Record