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Course of Study

The First Year

Entering graduate students arrive on campus a week before classes begin in the fall to enroll in classes and attend orientation. During the first year at Stony Brook, graduate students take Graduate Biochemistry, Membrane Biochemistry, Structural Biology and Spectroscopy, and Computational Methods in Biochemistry and Structural Biology. One of the most important courses that the graduate students take during this period is the research oriented Experimental Biochemistry and Structural Biology, where students complete rotations in which they participate in ongoing research in the laboratories of three different faculty members. From these rotations, each graduate student will select a laboratory in which to conduct thesis research and fulfill the requirements for the Ph.D. degree.

The Second Year and Beyond

During the second year the graduate students generally complete their formal course requirements with two elective courses they find to be of most interest. A written qualifying examination is taken in January of the second year between the fall and spring semesters. During the second year, the student’s own research becomes the primary focus, since he or she will have chosen a laboratory and permanent advisor. Under the guidance of the faculty advisor, the student will write a formal research proposal, and choose an advisory committee that includes at least three additional faculty members. Students present their proposals to this advisory committee (and continue to meet with the advisory committee on a yearly basis to discuss their research progress toward the completion of their degree). The student advances to candidacy after satisfactory completion of the research proposal. The student then works virtually full-time on thesis research that culminates in the submission and defense of a written Ph.D. dissertation.

Departmental Seminars and Journal Clubs

Students attend weekly departmental seminars in biochemistry and structural biology. The seminars feature the current research of internationally recognized speakers from outside the University. In addition students attend a BSB journal club/student seminar series each spring.

Teaching

Graduate students are also required to complete two semesters as teaching assistants. This experience provides an opportunity to develop crucial presentation skills and refine teaching techniques that students will need in their future careers. 

Graduate Course Offerings

Current course information is available via the  Graduate Bulletin

Core Lecture Courses

STRUCTURAL BIOLOGY AND SPECTROSCOPY
BSB 512, SPRING

A broad overview of the theoretical principles and experimental methods used in structural studies of proteins and nucleic acids. The course covers the fundamentals and applications of absorption spectroscopy, including both circular and linear dichroism, vibrational spectroscopy, including infrared and Raman, fluorescence spectroscopy, nuclear magnetic resonance spectroscopy, and X-ray diffraction.

COMPUTATIONAL METHODS IN BIOCHEMISTRY AND STRUCTURAL BIOLOGY 
BSB 515, FALL

An introductory course in the computational methods used in biochemistry and structural biology. The course emphasizes the resources available on the World Wide Web for sequence searching and analysis, bioinformatics, the prediction of protein secondary and tertiary structure, and the graphical analysis of proteins and nucleic acids.

BIOMEMBRANES
MCB 517, FALL

This course extends the graduate course in biochemistry to encompass the molecular architecture of membranes and the organization, functions, and assembly of lipids and proteins in biological membranes.

GRADUATE BIOCHEMISTRY 
MCB 520, FALL

Several topics in modern biochemistry are treated at an advanced level. Topics covered include protein structure, methods of peptide and protein analysis and purification, enzyme kinetics and mechanisms, and enzyme regulation.

Plus one of the following two courses:

MOLECULAR GENETICS
MCB 503, FALL

Introduces the classical work and current developments in lower and higher genetic systems. Covers gene structure and regulation in prokaryotic and eukaryotic organisms, mutational analysis and mapping, transposable elements, and biological DNA transfer mechanisms. Bacteriophage as well as lower and higher eukaryotic systems are used to illustrate aspects of molecular genetic structure and function. 

OR

CELL BIOLOGY
MCB 656, SPRING 

Introduction to the structural and functional organization of cells and tissues and to the way structure relates to function. Particular emphasis is placed on nuclear and chromosomal structure, signal transduction, protein translocation, the cytoskeleton and the extracellular matrix. The interaction of cellular structures and components and their regulation is stressed as is the organization and interaction of cells in tissues. The course is comparative and includes examples of cells and tissues from vertebrates, invertebrates, plants, and prokaryotic systems.

Examples of Elective Courses

Not all electives are given every year. 
*Note: Either MCB 503 or MCB 656 must be a core course. The other can be taken as an elective.

  • MCB 503 Molecular Genetics*
  • MCB 656 Cell Biology*
  • BSB 580 Advanced Structural Biology
  • AMS 533 Numerical Methods and Algorithms in Computational Biology
  • AMS 535 Introduction to Computational Structural Biology and Drug Design
  • AMS 536 Molecular Modeling of Biological Molecules Spring
  • AMS 537 Dynamical Models of Gene Regulation and Biological Pattern
  • BME 534 Functional Genomics
  • CHE 541 Biomolecular Structure and Analysis
  • CHE 542 Chemical Biology
  • CHE 543 Chemical Biology
  • CHE 530 Physical Chemistry of Macromolecules
  • CHE 524 Magnetic Resonance
  • CHE 501 Instrumental Methods in Chemistry
  • CHE 603 Special Top in Bioorganic
  • CHE 525 Theoretical Chemistry
  • CSE 549 Computational Biology
  • HBH 632 Molecular Interactions
  • HBY 511 Biophysical Chemistry

Non-Lecture Courses

ADVANCED STRUCTURAL BIOLOGY
BSB 580, Spring

A hands-on, practical training course where students solve protein structures by NMR, X-ray crystallography and/or electron cryo-microscopy.

EXPERIMENTAL BIOCHEMISTRY AND STRUCTURAL BIOLOGY 
BSB 509, 510, FALL AND SPRING

An introduction to current research methods used in biochemistry and structural biology. The student spends a half-semester in the laboratory of each of three different members of the faculty. In each laboratory the student participates in some aspect of the research being pursued by the faculty member.

GRADUATE RESEARCH
BSB 599, FALL AND SPRING

Original investigation undertaken with the supervision of a faculty member.

COLLOQUIUM IN BIOCHEMISTRY AND STRUCTURAL BIOLOGY
BSB 601, 602, FALL AND SPRING

A weekly series of talks and discussions by visiting scientists in which current research and thinking in various aspects of biochemistry and structural biology will be presented. This course is required every semester of all students registered in the Graduate Program in Biochemistry and Structural Biology. Attendance is mandatory. Visitors are welcome.

JOURNAL CLUBS IN BIOCHEMISTRY AND STRUCTURAL BIOLOGY 
BSB 531,532, FALL AND SPRING

Seminars given by graduate students on the progress of their own thesis research. Required every semester of all students registered in the Graduate Program in Biochemistry and Structural Biology. Attendance is mandatory. 
Visitors are welcome.

DISSERTATION RESEARCH 
BSB 699, FALL AND SPRING

Original investigations undertaken as part of the Ph.D. program under supervision of a research committee.

Ethics
GRD 500

Discussions of ethical practices in bioscience research.

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