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Department of Biological Chemistry Logo
Department of
Biological Chemistry
Johns Hopkins University Medicine logo
​The objective of this Ph.D. program is to prepare young scientists for independent careers in biomedical research. The curriculum begins with course-work, which includes both formal lecture modules as well as a literature-based discussion course involving the entire BC faculty. Crucial components of the first year are the 2-3 laboratory rotations that introduce the new student to research techniques and approaches in laboratories of his/her choice. ​​​​​​​​​​​​​

Training Overview

First Year Requirements

  • Bootcamp
  • Foundations of Modern Biology Core Course
  • Two fourth quarter Elective Courses
  • Topics in Biological Chemistry
  • Seminars in Biological Chemistry
  • Biological Chemistry Student Colloquium
  • Laboratory Rotations
  • Ethics Training I

Second Year Requirements

  • Oral Examination and thesis proposal
  • First thesis committee meeting
  • Topics in Biological Chemistry
  • Seminars in Biological Chemistry
  • Biological Chemistry Student Colloquium
  • Ethics Training II

Advanced Year and PhD Requirements

After completion of the first and second year course requirements and successful passing of the oral qualifying exam, students continue their training with the following:

  • Elective Courses (4 in total)
  • Annual thesis committee meeting and IDP
  • Seminars in Biological Chemistry
  • Biological Chemistry Student Colloquium
  • PhD Dissertation and Thesis Seminar

Detailed Description of Course Components

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 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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