Biochemistry and Molecular Biophysics Graduate Group

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Curriculum

Overview

General Requirements

BMB courses

Relevant non-BMB courses

Sample Curricula

 

Overview

The curriculum is designed to provide a superior graduate level education with a few core required courses and substantial flexibility in elective courses to tailor the program to each individual student's needs. Students are encouraged to choose electives that will round out their knowledge of biochemistry and molecular biophysics. A central goal is to build on the strengths and interests of each student and to prepare the student for dissertation research. By the end of the spring semester of their second year, each student should have achieved an understanding of biochemistry, molecular biology, and cell biology appropriate for a contemporary biomedical scientist. Substantial assistance in course selection is available to students from the Advising Committee.

General Requirements

  1. Three Laboratory Rotations (BMB 699)
  2. BIOM 600 Cell Biology and Biochemistry - required (fall, first year).
  3. BMB 508 Macromolecular Biophysics: Principles and Methods - required (fall, first year).
  4. BMB 509 Structural and Mechanistic Biochemistry - required (spring, first year)
  5. BMB 705 Candidacy Exam Prep Course (½ credit)- required (spring, second year)

Elective credits: Six (6) additional elective credits are required that may include formal lecture courses and seminars. These may be BMB or non-BMB classes.

 

BMB Courses

For a brief description of all BMB courses, click here

Lecture Courses    
Course No. Title Course Director Credits
BMB 508 Macromolecular Biophysics: Principles and Methods Sharp 1
BMB 509 Structural and Mechanistic Biochemistry Ferguson /Van Duyne 1
BMB 518 Protein Conformational Diseases Argon / Ischiropoulus 1
BMB 560 Methods of Scientific Inquiry Wilson / Domotor 1
BMB 567 Bioinorganic Chemistry Dmochowski 1
BMB 581 Techniques of Magnetic Resonance Imaging Song/Wehrli 1
BMB 585 Wistar Institute Cancer Biology Course: Signaling Pathways in Cancer Skordalakes/Weeraratna 1
BMB 590 Biological Physics Goulian 1
BMB 601 Fundamentals of Magnetic Resonance Reddy ½
BMB 611 Advanced X-ray Diffraction Methods Van Duyne ½
BMB 618 Applications of HIgh Resolution NMR Spectroscopy to Problems in Structural Biology Wand 1
BMB 619 Protein Folding   Axelsen / Englander ½
BMB 622 Mechano-Enzymes Dominguez/ Goldman/ Grishchuk/ Ostap ½
BMB 624 Ion Channels and Pumps Kallen / Lu ½
       
BMB 626 Mass Spectrometry and Proteomics Speicher/Garcia ½
BMB 627 Computer Programming for Biophysicists and Biochemists Sharp / Van Duyne ½
BMB 628 Principles of Scientific Instruments  Liebman ½
BMB 629 Quantitative Problems in Biochemistry and Biophysics Kallen ½
BMB 632

Probing Structure and Function of Complex RNA-Protein Machines

Lynch 1
BMB 700 Selected Topics in Chemistry Petersson 1
     
Non-Lecture Courses    
BMB 650 Current Biochemical Topics (may be taken twice; counts as an elective credit only once) Black / Shorter 1
BMB 699 Lab Rotation Kohli 1
BMB 705 Candidacy Exam Prep Class Lynch/Marmorstein/Nelson ½
BMB 799 Independent Study (Yrs 1-2) Staff ½ - 4

Relevant non-BMB courses

Many of the courses available to BMB students are taught in collaboration with other graduate programs. Topics covered by these courses are diverse. Students can choose from courses offered within Biomedical Graduate Studies, or from courses offered by graduate programs such as in Chemistry, Biology, and Bioengineering. Many of these courses require course director permission to register. You are strongly encouraged to discuss your course selections with the BMB Advising Committee, during formal course advising sessions, or at any time.

Examples of non-BMB courses taken by current and past BMB students are given below. It should be emphasized that this is not an exhaustive listing. A full listing of courses is described in the Course Register.

   
BIOM 502

Molecular Basis of Disease (Sp)
This course is reserved for BGS students only. BIOM 502 introduces students to basic mechanisms of disease and examines ~8 diseases in detail. The specific diseases chosen for discussion may vary year to year. The focus of the course will be on understanding the pathophysiology of the diseases and how research has enhanced not only our knowledge of disease mechanisms but has also led to improved therapy for patients with these diseases. Students will spend 1-2 weeks on each disease. Students will use materials from the medical school curriculum for background information and will use journal articles for class discussion

BIOM 520 Concepts and Methods in Biostatistics (Sum, 0.5 cu)
  This is an intensive 3-week, 0.5 CU summer course that is designed to introduce Biomedical Graduate Studies doctoral students to basic biostatistical methods and analyses. The class meets Monday through Friday morning for 90 minutes and includes both lectures and computer labs. Topics covered in the lectures include basic methods for describing data, the use of estimation and hypothesis testing, issues related to multiple comparisons and false detection, the use of parametric vs. nonparametric statistical methods and regression analysis. The focus of the computer lab will be to work on data analysis exercises using SAS software (or JMP for those who are Mac-based). Students will be able to analyze a small dataset of their own for their presentation.
BIOM 555 Control of Prokaryotic and Eukaryotic Gene Expression (Sp)
Regulation of gene expression including chromatin structure, transcription, DNA modification, RNA processing, translation, control of gene expression via microRNAs and post-translationalprocessing.
BIOL 446 Statistics for Biologists (F)
  This course covers introductory probability theory, principles of statistical methods, problems of estimation and hypothesis testing in biology and related areas.
BIOL 486 Chromosomes and the Cell Cycle (Sp)
Life depends on the propagation of genetic material from one generation to the next through cycles of genome replication and cell division. The genome is copied by the parent, and one exact copy is inherited by each daughter cell. We will treat chromosomes as discrete entities, rather than collections of genes, that are replicated and divided with high fidelity to ensure that the genome remains stable over many generations. By reading selected primary literature covering several decades, we will build an understanding of the cell cycle by focusing on chromosomes and the associated molecular machinery. We will explore mechanisms that underlie replication and division, particularly control mechanisms that maintain genome integrity and are critical to prevent disease. The goal of the course is to develop a picture of the cell cycle by examining some of the key experiments and insights that have led to our current understanding.

Descriptions below are collected from the various programs of CAMB; please refer to the CAMB web site for more details on other courses offered by this graduate group (click on one of the programs listed on this linked page, then on courses). Links to recent course outlines are given below.

CAMB 512 Cancer Genetics and Biology (Sp)
  The course will involve lectures and readings of important papers on cancer genetics, cancer cell growth, metastasis, angiogenesis and experimental therapeutics.
CAMB/BIOL 526 Experimental Principles in Cell and Molecular Biology (F)
The course aims to introduce principles of current experimental techniques used in modern biology
CAMB 530 Seminar in Cell Cycle and Cancer (F)
  This seminar course will focus on molecular events that regulate cell cycle transitions and their relevance to human cancer. Topics will include control of the G1/S and G2/M transitions, relationships between tumor suppressor genes such as p16, Rb, p53 or oncogenes such as cyclin D, cdc25A, MDM2 or c-myc and cell cycle control. Where appropriate, the focus will be on understanding regulation of cell cycle control through transcriptional induction of gene expression, protein associations, posttranslational modifications like phosphorylation or regulation of protein stability like ubiquitin degradation. Although achieving an improved understanding of mammalian cancer is a goal of the course, much of our knowledge of the cell cycle derives from work done in more genetically tractable organisms, such as yeasts, drosophila, and xenopus.
CAMB 532 Human Physiology (F)
  This course will present a survey of the physiology of most of the major organ systems. It will integrate knowledge of cellular and molecular mechanisms into an understanding of function at the tissue, organ and organism levels. It will begin with a brief review of membrane physiology, followed by electrophysiology and signaling in nerve. Then, after a brief outline of neural control systems and their role in homeostasis, it will present motility and muscle, the cardiovascular system, respiration, the renal and gastrointestinal systems, and selected topics from the endocrine system.
CAMB 534 Seminar on Current Genetic Research: Modeling Human Disease in Diverse Genetic Systems (Sp)
  An advanced seminar course emphasizing genetic research in model organisms and how it informs modern medicine. Each week a student will present background on a specific human disease. This is followed by an intense discussion by the entire class of ~2 recent papers in which model organisms have been used to address the disease mechanism and/or treatment. As a final assignment, students will have the opportunity to write, edit, and publish a "News & Views" style article in the journal "Disease Models and Mechanisms".
CAMB 548 Fundamentals in Virology
  Basic course in virology including molecular, cellular, immunological, and in vivo pathological aspects.
   
CAMB/IMUN 609

Vaccines and Immune Therapeutics

The goal of this course is to expand on students’ general understanding of the immune system and to focus this understanding towards the application of vaccination. Furthermore the course will give the student a sense of how these principles are applied to vaccine and immune therapeutic development. The course covers basic science as well as the clinical, ethical & political implications of modern vaccines. Initial lectures review immune mechanisms believed to be responsible for vaccine induced protection from disease. Subsequent lectures build on this background to explore the science of vaccines for diverse pathogens, including agents of bioterrorism as well as vaccines for cancer. An appreciation for the application of laboratory science to the clinical development of vaccines is provided in the next section of the course along with lectures that focus on the ethical implications of vaccines in different situations. The financial implications of specific vaccines and their impact on the global community, is a specific focus of the course.

CAMB 610 Molecular Basis of Gene Therapy
  This is a team-taught, survey course that focuses on the basic science relevant to achieving efficient and effective gene transfer in animal models and humans for the treatment of disease. The course includes a unit devoted to a variety of vectors useful for gene transfer, with the remainder of the course devoted to the study of current gene therapy approaches using specific diseases as models. Prior background in biochemistry, cell biology, and molecular biology is essential. Aspects of organ system anatomy and physiology, virology and immunology that are relevant to the course material are included in the course. Because of the rapid movement in this field, specific topics vary somewhat from year to year. The course is designed for second year graduate students, however first year students may take the course with the course director's approval. Lecture format with discussion hours interspersed. There will be a take-home examination at the end of each of the three sections, each focusing on the material covered in that section.
CAMB 691 Advanced Topics in Cell Biology and Physiology I (Sp, even years)
 

This course, together with its companion CAMB 692, offers an advanced, in depth analysis of selected topics in cell biology and physiology. CAMB 691 and 692 are complementary courses that focus on different aspects of cell biology; these courses are offered on an alternating basis in the spring semester. The courses can be taken in either order, but require BIOM 600 or an equivalent background in basic cell biology. CAMB 691 will focus on key issues at the forefront of research in the areas of (1) channels and transporters, (2) protein trafficking through cellular pathways, and (3) cytoskeletal dynamics and molecular motors. The course format pairs faculty presentations with student-led discussion sessions highlighting important papers from the primary literature.

CAMB 692 Advanced Topics in Cell Biology and Physiology II (Sp, odd years)
 

An in-depth consideration of key topics in cell biology and physiology. This course will focus on three major aspects: (1) signal transduction; (2) cell cycle and apoptosis; and (3) cell division. The course format will include both faculty lectures and student-led discussion sessions focusing on important papers from the primary literature.

CHEM 521 Statistical Mechanics (F)
  Principles of statistical mechanics with applications to systems of chemical interest.
CHEM 523 Quantum Chemistry
  The principles of quantum theory and applications to atomic systems.
CHEM 525 Molecular Spectroscopy
  A modern introduction to the theory of the interaction of radiation and matter and the practice of molecular spectroscopy. Conventional microwave, magnetic resonance, optical, photoelectron, double-resonance, and laser spectroscopic techniques will be included.
CHEM 557 Mechanisms of Biological Catalysis
 

Reaction mechanisms in biological (enzymes, abzymes, ribozymes) and biomimetic systems with emphasis on principles of catalysis, role of coenzymes, kinetics, and allosteric control.

GCB 531 Introduction to Genome Science
  This course serves as an introduction to the main laboratory and theoretical aspects of genomics and computational biology. The main topics discussed center around the analysis of sequences (annotation, alignment, homology, gene finding, variation between sequences, phylogeny reconstruction/estimation), and the functional analysis of genes (expression levels, proteomics, screens for mutants), together with a discussion of gene mapping, linkage disequilibrium, genetics of complex diseases, and integrative genomics.
GCB 535 Introduction to Bioinformatics.
  This course provides a board overview of bioinformatics and computational biology as applied to biomedical research. Course material will be geared towards answering specific biological questions ranging from detailed analysis of a single gene through whole-genome analysis, transcriptional profiling, and systems biology. The relevant principles underlying these methods will be addressed at a level appropriate for biologists without a background in computational sciences. This course should enable students to integrate modern bioinformatics into their research program
IMUN 506 Immune Mechanisms (F)
  This is an introductory graduate course, which surveys most areas of immunology. It is assumed that students have a background in biochemistry and molecular biology, and at least some familiarity with immunological concepts.

 

Sample Curricula (required courses are in bold)
All courses are 1 credit except as noted.

 

SAMPLE 1

YEAR 1

Fall

BIOM 600 Cell Biology
BMB 508 Macromolecular Biophysics: Principles and Methods
BMB 632 Probing Structure and Function of Complex RNA-Protein Machines
BMB 699 Lab Rotation 1

Spring

BMB 509 Structural and Mechanistic Biochemistry
BIOM 502 Molecular Basis of Disease
BMB 627 Computer Programming for Biophysicists & Biochemists (½)
BMB 611 Advanced X-ray Diffraction Methods(½)
BMB 699 Lab Rotation 2

Summer

BMB 699 Lab Rotation 3

YEAR 2

Fall

BMB 518 Protein Conformation Diseases
BMB 585 Wistar Institute Cancer Biology
CAMB 532 Human Physiology
BMB 799 Independent Study

Spring

BMB 705 Candidacy Exam Prep (½)
BMB 799 Independent Study (3½)

Summer

Dissertation Research

 

 

SAMPLE 2

YEAR 1

Summer pre-Year 1

BMB 699 Lab Rotation 1
BMB 799 Independent Study

Fall

BIOM 600 Cell Biology
BMB 508 Macromolecular Biophysics: Principles and Methods

CHEM 441 Organic Mechanisms Structure
BMB 699 Lab Rotation 2

Spring

BMB 509 Structural and Mechanistic Biochemistry
BMB 626 Mass Spectrometry and Proteomics (½)
BMB 628 Principles of Scientific Instrumentation (½)
CHEM 557 Mechanisms of Biological Catalysis
BMB 699 Lab Rotation 3

Summer

BMB 799 Independent Study (2)

YEAR 2

Fall

BMB 590 Biological Physics
BMB 611 Advanced X-ray methods (½)
BMB 630 Advanced Imaging (½)
BMB 799 Independent Study (2)

Spring

BMB 705 Candidacy Exam Prep (½)
BMB 650 Current BIochemical Topics (1)
BMB 799 Independent Study (2½)

Summer

Dissertation Research

 

SAMPLE 3

YEAR 1

Fall

BIOM 600 Cell Biology
BMB 508 Macromolecular Biophysics: Principles and Methods
BMB 633 Cellular Biochemistry and Biophysics
BMB 699 Lab Rotation 1

Spring

BMB 509 Structural and Mechanistic Biochemistry
BMB 560 Methods of Scientific Inquiry
BMB/CHEM 559 Biomolecular Imaging
BMB 699 Lab Rotation 2

Summer

BMB 699 Lab Rotation 3
BIOM 520 Concepts & Methods in Biostatistics (½)
BMB 799 Independent Study (½)

YEAR 2

Fall

BMB 650 Current Biochemical Topics
BMB 619 Protein Folding (½)
CAMB 532 Human Physiology
BMB 799 Independent Study (1 ½)

Spring

BMB 705 Candidacy Exam Prep (½)
BMB 799 Independent Study (3 ½)

Summer

Dissertation Research

 

SAMPLE 4

YEAR 1

Fall

BIOM 600 Cell Biology
BMB 508 Macromolecular Biophysics: Principles and Methods

BIOL 446 Statistics for Biologists
BMB 699 Lab Rotation 1

Spring

BMB 509 Structural and Mechanistic Biochemistry
BMB 567 Bioinorganic Chemistry
BMB 622 Mechano-Enzymes (½)
BMB 624 Ion Channels and Pumps (½)
BMB 699 Lab Rotation 2

Summer

BMB 699 Lab Rotation 3
BMB 799 Independent Study

YEAR 2

Fall

BMB 618 NMR in Structural Biology
CAMB 526 Exp. Principles in Cell & Molecular Biology
BMB 619 Protein Folding (½)
BMB 631 Redox Potentials & Electron Transfer (½)
BMB 799 Independent Study

Spring

BMB 705 Candidacy Exam Prep (½)
BMB 799 Independent Study (3½)

Summer

Dissertation Research