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Department of Biological Chemistry Logo
Department of
Biological Chemistry
Johns Hopkins University Medicine logo

The training missions of the GPBC are achieved through a four-component curriculum based on research (discovery-driven education) and augmented by outstanding courses, immersive scientific activities, publishing, mentorship, and professional development activities:

Research is the primary activity of GPBC students. Research starts immediately upon matriculation with a series of research rotations, and thereafter continues in their thesis studies.

Courses: Required and elective courses ensure that GPBC students acquire a solid foundation in biomedical research.

Immersive Scientific Activities: Students receive additional training by attending and participating in seminars, journal clubs, symposia, colloquia, and retreats within the Department of Biological Chemistry as well as those offered by other Departments, Centers, Institutes and Schools across the University

Publishing: Students complete their research requirement by publishing their dissertation, peer-reviewed articles, reviews, etc.

Mentorship: GPBC provides multidimensional mentorship from the moment students arrive on campus through and beyond their graduation, with direct support from the student's research advisor(s), co-mentor, Thesis Committee, and GPBC Director.

Professional Development: The GPBC supports the long-term career success of its graduates by providing:

  • Outstanding, mechanistically-oriented research training
  • OPTIONS career training curriculum
  • Full access to all services of the School's Professional Development Office (PDO)

Steps to the Ph.D.

Each student's path to the Ph.D. is unique. Nevertheless, there is a common timeline of student progress:

Steps to PhD.jpg

 

GPBC Activities, By Year

Year 1:

  • Student orientation day (day 1)
  • Biological Chemistry Bootcamp (week 1)
  • Participate in research rotations (3-4 rotations of 2 months-long duration each)
  • Participate in immersive scientific activities (seminars, journal clubs, colloquia, interest groups, etc.), both required and elective
  • Select thesis advisor/home laboratory & initiate thesis research
  • Take and pass required first-year classes:
    • Biophysics
    • Organic Mechanisms in Biology
    • Molecular Biology & Genomics
    • Genetics
    • Cell Structure & Dynamics
    • Pathways & Regulation
    • 3rd Quarter Elective I
    • 3rd Quarter Elective II
    • Rigor, Reproducibility & Experimental Design in Biological Chemistry, Yr I
  • Take and complete first year ethics training
  • Participate in OPTIONS career development curriculum
  • Participate in annual student review with the GPBC Director

Year 2:

  • Thesis research
  • Participate in immersive scientific activities
  • Write a thesis proposal
  • Take and pass the Doctoral Board Orals exam
  • Take and pass the required second-year class:
    • Rigor, Reproducibility & Experimental Design in Biological Chemistry, Yr 2
  • Take and complete second year ethics training
  • Participate in OPTIONS career development curriculum
  • Form a thesis committee and identify a co-mentor
  • With the thesis advisor, draft and sign an individual development plan (IDP)
  • Participate in Thesis Committee meeting & GPBC Director meeting

Years 3, 4, & 5:

  • Thesis research
  • Publish papers
  • Participate in immersive scientific activities
  • Take and pass any remaining elective classes
  • Annually: IDP, Thesis Committee meeting, and GPBC Director meeting
  • Work with mentors to develop/implement a career plan

Year 5+:

  • Thesis research, with an emphasis on prompt graduation
  • Publish the dissertation and peer-reviewed articles
  • Participate in immersive scientific activities
  • Hold Thesis Committee meetings & GPBC Director meetings every 6 months
  • Implement the student's career plan

Foundations of Modern Biology Core Courses

Macromolecular Structure and Analysis

The structure and properties of biological macromolecules will be presented. Experimental and computational methods used to study macromolecular structure including X-ray crystallography, magnetic resonance, spectroscopy, microscopy, and mass spectrometry will also be covered.

Biochemical and Biophysical Principles

The physical and chemical principles underlying biological processes are presented and discussed. Topics include thermodynamics, chemical equilibrium, chemical and enzymatic kinetics, electrochemistry, physical chemistry of solutions, and structure and properties of water. Elementary concepts of statistical thermodynamics will be introduced as a way of correlating macroscopic and microscopic properties.

Molecular Biology and Genomics

This course module covers the Molecular Biology and Genomics of both prokaryotes (using E. coli as the model organism) and eukaryotes, with a focus on "model organisms" including yeast, flies, worms, mice as well as humans. Both the Molecular Biology (reductionist) perspective and the Genomics (systems biology) perspective will be provided on each topic, and there will be heavy emphasis on mechanism and regulation of fundamental processes in biological information transfer DNA->RNA-> protein. This lecture module will cover genes and genomes, transcription and RNA world, replication, chromosome structure and function and genome instability.

Genetics

Genetics covers fundamental principles of genetics, focusing primarily on yeast, the fruit fly, and the mouse. Problem sets are an integral learning tool in this course.

Cell Structure and Dynamics

The objective of this course is to provide the basics of cell biology, including the structure, function and biogenesis of cellular organelles. Also covered are essential concepts on the cytoskeleton, cell-cell and cell-extracellular matrix interactions, cell motility, chaperones, and protein turnover.

Organic Mechanisms in Biology

This course deals with the chemical mechanisms of enzymes. It is intended to illustrate how catalysis in biological systems can be understood using principles derived from organic reaction mechanisms.

Pathways and Regulation

This course will cover the principles of membrane transport, bioenergetics, metabolic pathways, cell cycle and cell death with particular emphasis on regulatory mechanisms including receptor-mediated signaling, small GTPases, lipid molecules, kinases and phosphatases.

Computational Biology and Bioinformatics

This short course is a survey of quantitative methods in modern biology and the computational concepts that are developing to analyze large data sets. Topics range from a review of statistics to problems in sequence analysis to the modeling of complex systems. The goal of the course is to familiarize students with the concepts of computational biology rather than to achieve a deep understanding of any one topic.

Topics in Biological Chemistry

First-year BC students meet with each of the BC faculty members, throughout the year, to discuss current research articles of special interest or importance.

First Year Elective Courses

The core course modules are completed in the first three quarters of the academic year (Sept. - Mar.). In the fourth quarter, first-year students take two short elective courses and begin to focus on a research area of interest.

Oral Examination

This exam will be conducted by five faculty members, two from the student’s department and three from other science departments. It is a two-part process: the student will write a research proposal outside their thesis area and then the committee will ask questions to probe the student's depth and breadth of knowledge at an oral exam based on the research proposal and first year course work.

Thesis Progress Meetings

After passing the oral exam, each student chooses a thesis committee consisting of the advisor and three other faculty members. At the initial meeting, the student presents a thesis proposal in the format of an NIH Fellowship application. Subsequent meetings with the thesis committee are convened at least once a year to review research progress and discuss plans for the next year.

Advanced Elective Courses

Students are required to take two elective courses in their advanced years of training to broaden and deepen their knowledge base. Electives that are offered cover a broad range of topics including cell growth control, macromolecular structure and x-ray crystallography, developmental biology, neuroscience, the biochemistry of membrane carriers, polarity in mammalian cells, molecular mechanisms of signal transduction, membrane biochemistry, immunology, virology and scientific writing. In addition to expanding students' knowledge, these courses promote close interactions between faculty and students.

BC Student Colloquium

Students in the Biological Chemistry gather monthly to present their work in oral form to other graduate students in the department. Lunch is provided.

Seminars in Biological Chemistry

Students in the Graduate Program in Biological Chemistry are required to attend the Biological Chemistry Departmental Seminars every other Tuesday at 11:30 a.m. Additional seminars will take place all over the campus and are open to all students. Specialized journal clubs and research interest goups are also available. Students are also expected to attend weekly lab meetings.

PhD Dissertation and Thesis Seminar

Students continue with their research and usually in year five or six, the student's thesis committee agrees that the student is nearing completion of his/her research and will be ready to write a dissertation. The student's research is typically published in one or more scholarly papers published in a peer-reviewed journal, prior to or shortly after the submission of the dissertation. The student's advisor and one other member of the thesis committee must read and approve the dissertation. The student presents a formal, public seminar describing his/her completed thesis research to an audience composed of members of his/her department.


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