The Committee on Molecular Metabolism and Nutrition -
Molecular Metabolism and Nutrition
The Metabolism Program at the University of Chicago
embodies a unique structure that takes full advantage of the strengths
and character of the University of Chicago. The Committee on
Molecular Metabolism and Nutrition is an interdepartmental,
degree-granting body that draws its faculty from the ranks of basic
science and clinical science. This is possible because all these
disciplines share the same campus and often the same building. This
provides the student with the opportunity to acquire sound basic
training in biochemistry. At the same time, this training is
tempered by constant exposure to the impact of metabolism on human
health and well being. This provides integrated training in the basic
biochemical mechanisms through which foods and nutrients interact to
optimize health, the pathological consequences of malnutrition, and the
interplay of nutrition and human behavior.
The Biomedical Sciences Cluster
The Committee on Molecular Metabolism and Nutrition is
integrated within a cluster of graduate programs from the Committee on
Cancer Biology, the Committee on Immunology, the Committee on
Microbiology, and the Department of Pathology Molecular Pathogenesis
and Molecular Medicine program. The five academic units share a joint
Admissions Committee, several common courses, a seminar series, and
additional common events for students and faculty within the cluster.
The goal of the cluster system is to encourage interdisciplinary
interactions among both trainees and faculty, and to allow students
flexibility in designing their particular course of study.
In addition, students have extensive opportunities for
interaction with the three other clusters within the Biological
Sciences Division: the Molecular Biosciences Cluster; the Darwinian
Sciences Cluster; and the Neurobiology Cluster. These clusters
offer courses and sponsor seminars and symposia open to Metabolism
The philosophy of the program is to provide students
with a wide range of educational opportunities in a research-rich
environment that will stimulate the student to engage in the life-long
pursuit of knowledge through self-learning. Didactic courses
during the first year provide education in the principles of basic
science. In the summer and continuing into the second year,
coursework gives way to interactive training that stresses the
evaluation of literature, effective communication, and hypothesis
testing combined with early exposure to research. This is
enriched by a strong seminar program that exposes the student to the
national leaders in metabolism research and policy.
- * A minimum of one year of college chemistry,
including organic chemistry.
* One year of college physics and a background in calculus.
* A minimum of 4 semester or 5 quarter courses in the biological
sciences, including biochemistry. Accompanying laboratory courses are
- * One course in statistics, including computer-based
* One course in organismic physiology.
Students may be admitted with deficiences, and students
with a deficiency are encouraged to apply. Any such deficiences
should be made up within 20 months of starting graduate study.
A minimum of 9.5 didactic courses are to be selected
from 7.5 required courses plus electives. It is required that
students maintain a minimum overall “B” average in their
coursework. Any Cs must be offset by As to maintain a B average
and a grade of B or better must be achieved in all programmatic courses.
The Programmatic Core in Metabolism (4.5 credits)
Nutrition 1 (MOMN 36500). Students are exposed to a comprehensive review of nutritional physiology and requirements, including the regulated digestion, synthesis and/or metabolism of vitamins, minerals, lipids, proteins and carbohydrates. Various lecturers specialized in specific areas of metabolic research participate throughout the quarter. The course culminates with the students writing a comprehensive paper linking several of the topics covered throughout the quarter. Brady and Staff. Autumn.
Nutrition 2 (MOMN 36600). This course is an extension of Molecular Nutrition 1 and investigates the physiological control of systemic metabolism. Heavy emphasis is placed on the coordinate regulation of glucose and lipid metabolism by skeletal muscle, liver, adipose tissue, pancreas and brain. The format of the course is a combination of lectures and student presentations of primary literature. At the end of the course, students are expected to write a grant application to investigate a current area of metabolism research and then present and defend the proposal to the lecturers and students. Reardon and Staff. Winter.
Writing (MOMN 30910). Students will gain extensive exposure to the grant writing and review processes. Several speakers will lecture on the various funding agencies, types of grants, and general approaches to grant writing. Students will read funded applications from CMMN faculty to learn the proper approaches for successful grant writing, including responding to reviewers’ critiques. Students will be expected to complete a 20-25 page R01 style grant application by the end of the quarter, which will fulfill the mock grant proposal requirement for the CMMN students. The course culminates with a mock grant review panel in which the students read and critique each other’s applications. Brady. (This course will be held Winter 2011).
Health and Disease (MOMN 30200). This course is offered through the Pritzker School of Medicine at the University of Chicago and exposes students to nutritional and metabolic concerns in the primary care of patients. The course is an overview of contemporary and clinically relevant nutrition. The topics include: nutritional requirements, macro and micronutrients, nutrition through the life cycle, pregnancy, lactation and childhood nutrition. Nutritional assessment is introduced in a pre-clinical format. Clinically relevant topics are also emphasized especially those that are commonly seen in a busy practice or those associated with major morbidity. The content areas include obesity, nutrition and coronary heart disease and the important role of nutrition in critical illnesses. At the end of the course, graduate students must complete a 10 page paper further exploring a current area of clinical nutrition. Schwartz. Spring.
Nutrition (MOMN 40200). This course is conducted as a seminar series. Students will broaden their exposure to metabolism related research through bi-weekly faculty and student presentations of research data and primary literature. Additionally, prominent researchers from other institutions are invited to give a seminar and meet alone with the students to discuss their career paths, experiences in running successfully funded labs and use of cutting edge experimental approaches. Attendance is mandatory for first and second year students but all students are strongly to attend. Rhodes. Autumn, Winter, Spring, Summer.
Molecular Basis of Metabolic
Disease (MOMN 30901). This course covers topics in nutrition in which modern molecular and cell biology provide a greater understanding of the regulation of these metabolic pathways. Students are required to extensively read primary literature and give oral presentations to the class and weekly discussion leader. Wicksteed. Autumn.
Transduction and Disease (MPMM 30600). Topics include receptor ligands, membrane receptor tyrosine kinases, G proteins, proto-oncogenes, cytoplasmic protein kinases and phosphatases, transcription factors, receptor-nucleus signaling, development and cancer, genetic dissection of signaling pathways, cell growth and proliferation, cell cycle regulators, cell cycle progression and apoptosis, and sensing of hypoxia and mechanical stimuli. The role of signaling in disease is a theme throughout the course. Dulin. Winter.
Biotechniques (MOMN 30920). The Biotechniques course will focus on familiarizing students with cutting edge experimental techniques used in biomedical research. The course will comprise a combination of lectures, reading and discussion of primary literature and exposure to several core facilities located on campus. Topics to be covered include generation of transgenic animals, biosensors and cell imaging, genomic microarrays, proteonomics, protein overexpression, knockdown and detection. Sun. Spring.
The General Basic Science Core (3 credits)
Students will be required to take 1 course in 3 of the
following 4 areas.
Protein Fundamentals (BCMB 30400). The course covers the
physico chemical phenomena that define protein structure and
function. Topics include: 1) the interactions/forces that
define polypeptide conformation; 2) the principles of protein folding,
structure and design; and 3) the concepts of molecular motion,
molecular recognition, and enzyme catalysis. Prereq: BCMB
30100, which may be taken concurrently, or equivalent. Koide,
Structural Biology (BCMB 30500). This course emphasizes
the basic principles of protein structure determination by X-ray
crystallography and NMR spectroscopy. The underlying physical concepts
of these methods will be introduced and the capabilities of each will
be discussed and compared in context of their uses in de novo structure
determination and protein engineering studies. Kossiakoff,
Koide. Winter. (This course will not be offered in 2008.)
Structure and Function of Membrane Proteins (BCMB 32300).
This course will be an in depth assessment of the structure and
function of biological membranes. In addition to lectures, directed
discussions of papers from the literature will be used. The main topics
of the courses are: (1) Energetic and thermodynamic principles
associated with membrane formation, stability and solute transport (2)
membrane protein structure, (3) lipid-protein interactions, (4)
bioenergetics and transmembrane transportmechanisms, and (5) specific
examples of membrane protein systems and their function (channels,
transporters, pumps, receptors). Emphasis will be placed on biophysical
approaches in these areas. The primary literature will be the main
source of reading. Perozo, Roux. Winter
Cell Biology 1
(MGCB 31600). Lecture/discussion course on fundamentals of
protein translocation, protein and membrane sorting and transport,
organelle biogenesis, and the cytoskeleton. Glick,
Cell Biology 2
(MGCB 31700). This course will cover cell cycle
progression, cell growth, cell death, cytoskeletal polymers and motors,
cell motility, and cell polarity. Glotzer, Kovar. Winter.
Principles of Genetic Analysis (GENE 31400). Coverage of
the fundamental tools of genetic analysis as used to study biological
phenomena. Topics include genetic exchanges in prokaryotes,
eukaryotes, and their viruses and plasmids; principles of
transformation; analysis of gene function. Bishop and
Mechanisms (GENE 31500). Advanced coverage of genetic
mechanisms involved in genome stability and rearrangement. Topics
include genetics of transposons, site-specific recombination, gene
conversion, reciprocal crossing over, and plasmid and chromosome
segregation. Bishop. Winter.
Human Genetics 1:
Human Genetics (HGEN 47000). This course covers classical
and modern approaches to studying cytogenetic, Medelian, and complex
human diseases. Topics include chromosome biology, human gene
discovery for single gene and complex disease, non-Mendelian
inheritance, mouse models of human disease, cancer genetics, and human
population genetics. The format includes lectures and student
presentations. Cox, Ober, Millen. Autumn.
Fundamentals in Molecular Biology
(MGCB 31000). The course covers nucleic acid structure and DNA
topology, recombinant DNA technology, DNA replication, DNA damage,
mutagenesis and repair, transposons and site-specific recombination.
Prokaryotic and eukaryotic transcription and its regulation, RNA
structure, splicing and catalytic RNAs, protein synthesis, and
chromatin. Staley, Storb. Winter.
1 (MGCB 31200). Nucleic acid structure and DNA topology;
methodology; nucleic-acid protein interactions; mechanisms and
regulation of transcription in eubacteria, and of replication in
eubacteria and eukaryotes; mechanisms of genome and plasmid segregation
in eubacteria. Rothman-Denes. Winter.
2 (MGCB 31300). The content of this course will cover the
mechanisms and regulation of eukaryotic gene expression at the
transcriptional and post-transcriptional levels. Our goal is to explore
with you research frontiers and evolving methodologies. Rather than
focusing on the elemental aspects of a topic, the lectures and
discussions will focus on the most significant recent developments,
their implications and future directions. Singh, Staley. Spring.
Electives (2 credits)
The remaining two (or more) courses may be selected
from available courses in the areas listed below. At least one
advanced metabolism course must be selected (denoted by *).
Statistics is recommended. Students who have completed their
academic requirements are encouraged to formally audit additional
Finally, the divisional course on Scientific Integrity and the Ethical
Conduct of Research and is required for all first year students in the
division and held in the spring, where a variety of speakers discuss
ethical issues in scientific research. This course is graded
- . Advanced Biotechniques*
- . Behavioral Aspects of Diet and Nutrition*
- . Cell and General Pathology
- . Introduction to Cancer Biology
- . Molecular Basis of Nutrition*
- . Molecular Defense Mechanisms
- . Molecular Mechanisms of Cancer Biology*
- . Organ Physiology/Endocrinology
- . Scientific Basis of Nutrition*
- . Specialized Topics in Nutrition*
Students may petition the Ph.D. Curriculum Committee
regarding changes in required areas of coursework. Up to two (2)
required areas may be modified to provide a specific focus of study in
metabolism. Specific changes and the justification for those
changes must be submitted in writing.
Reading and Laboratory Rotations
- . Directed Independent Research - MOMN 30100
. Directed Independent Research - MOMN 30100 (Spring)
In the Winter and Spring of their first year, students
are required to perform 10-week, graded rotations through laboratories
of interest. Since the student will choose their thesis lab
during these rotations, it is critical that serious thought and effort
(reading papers, talking to the PI and lab members, etc.) be given
before choosing the labs. Students should contact prospective
laboratories in the preceding quarter to ensure that space/resources
are available. In the following quarter, students will present an
overview of their project and results from their rotation. A
third, optional rotation can be performed during the summer quarter. It
is expected that a student will have chosen their thesis research lab
no later than the end of their first year.
Current Topics in Nutritional Research (0.5 credit)
The Committee holds a seminar series/journal club
biweekly throughout the year. Student attendance and
participation are required Autumn, Winter and Spring quarters of their
first two years. At the end of the second year, students will be
graded pass/fail. Continued student participation in this series is
expected until graduation.
In the Autumn, CMMN faculty members will give research
talks to further expose students to research being conducted by
Committee members. In the Winter through Summer quarters, faculty
presentations will either comprise research talks or presentation of a
high profile, recent journal article related to Metabolism
research. Additionally, prominent outside speakers will be
invited periodically to give research seminars, and students will meet
with the speaker immediately after the talk.
Students are also required to present twice
yearly. In the first year, presentations will be based on the
laboratory rotation performed the previous quarter. Second year
students will present a mock grant proposal in the winter (see below)
and a journal article in the Spring. In subsequent years,
students are required to present on their thesis research project once
a year. The second presentation can either be discussion of a
journal article, or for more advanced students, a second presentation
of their own research.
Students are required to teach as part of their
doctoral training. This requirement may be met by assistant
teaching two courses that meet the Divisional requirement for a full
TA-ship or taking the Divisional TA training course and assistant
teaching one course. The TA requirement should be completed by
the third year of residence. Teaching performance is evaluated by
the course director and filed in the Graduate Affairs Office.
Mock Grant Proposal
In the Winter of the second year, students are required
to complete a mock grant proposal, consisting of a 10 page, NIH-style
grant proposal and a 45-minute oral presentation. The proposal
should define an unaddressed research area in Molecular Metabolism and
Nutritional Biology, propose 2-3 specific aims to explore the problem
and describe experiments that would be conducted over a 5-year
period. Previous proposals will be available to be used as
templates. The topic chosen cannot be directly related to the
student’s thesis research and must be approved by the CMMN Chair.
The student will present and defend their mock grant proposal to the
Metabolismn Committee faculty and students. A committee
comprising of three CMMN faculty members chosen by the CMMN Chair will
evaluate each mock grant proposal and oral presentation. The
student will meet privately with the committee members after the oral
presentation to discuss the proposal and to answer questions. Any
deficiencies in the written proposal, oral presentation and/or
background knowledge of the research area will have to be addressed
before the student is passed. All required revisions must be
completed by the end of the following quarter.
Starting in the Summer/Autumn after the second year, a
student should begin in earnest, research work towards their thesis
project. By Autumn of the third year, the student should form
their thesis committee and submit their thesis proposal.
The thesis committee will comprise of four members: the
student’s advisor, a committee chair (not to be the advisor) and two
other members of the Metabolism Committee. The thesis proposal should
consist of a detailed background of the research area to be studied,
preliminary data demonstrating the feasibility of the proposed
experiments, 2-3 specific aims and a supporting experimental plan to
address the research area. Total length should be approximately
20 pages. The proposal should be given to committee members at least
two weeks before the oral defense of the thesis proposal. The student
will make a public presentation to students and faculty of CMMN, and
then meet with their committee in private to answer questions and
discuss the proposed experiments in detail. Once accepted by the
committee, the student will then formally enter the Ph.D. program.
Each student will be required to complete a
dissertation documenting original research within 6 years of the thesis
proposal defense. However, it is expected that students will
complete their thesis during their fifth year in the program.
The thesis should consist of 2-3 chapters, and it is expected that at
least two of these chapters will result in first author publications in
prominent journals. Students failing to meet these time limits
must apply for readmission to the Ph.D. program.