Molecular Biophysics and Biochemistry
301 Josiah Willard Gibbs Laboratories, 432.5662
M.S., M.Phil., Ph.D.
Chair
Nigel Grindley
Director of Graduate Studies
Mark Solomon (301 JWG, 432.5662, mbb.grad@yale.edu)
Professors
Donald Crothers (Emeritus, Chemistry), Donald Engelman, Joseph
Fruton (Emeritus), Alan Garen, Sankar Ghosh (Immunobiology),
Nigel Grindley, Andrew Hamilton (Chemistry), Mark Hochstrasser,
William Konigsberg, Peter Lengyel (Emeritus), Richard Lifton
(Genetics; Internal Medicine [Nephrology]), Robert Macnab,
I. George Miller (Pediatric Infectious Diseases; Epidemiology),
Simon Mochrie (Physics; Applied Physics), Peter Moore (Chemistry),
Anna Pyle, Charles Radding (Genetics), Lynne Regan, Frederic
Richards (Emeritus), Gaston Schmir (Emeritus), Robert Shulman
(Emeritus), Sofia Simmonds (Emeritus), Michael Snyder (Molecular,
Cellular & Developmental Biology), Dieter Söll, Joan
Steitz, Thomas Steitz, Scott Strobel, Julian Sturtevant (Emeritus),
William Summers (Therapeutic Radiology), Patrick Sung, David
Ward (Genetics), Kenneth Williams (Adjunct, Research), Harold
Wyckoff (Emeritus)
Associate Professors
Susan Baserga, Mark Gerstein, Michael Koelle, Anthony Koleske,
Andrew Miranker, Mark Solomon, Sandra Wolin (Cell Biology)
Assistant Professors
Thomas Biederer, João Cabral, Enrique De La Cruz, Lise
Heginbotham, Vinzenz Unger
Fields of Study
The principal objective of members of the department
is to understand living systems at the molecular level. Areas
of current interest include structure and function of biological
macromolecules as determined by amino acid or nucleotide sequencing,
diffraction, spectroscopic or computational analyses; mechanisms
of enzyme action; bioenergetics, motility, and chemotaxis;
structure and function of membranes, viruses, ribosomes, ribogymes,
nucleosomes, ribonucleoprotein particles, and other macromolecular
assemblies; developmental genetics; animal virology; plant
molecular genetics; metabolic regulation; protein degradation;
DNA transposition replication, recombination, and repair;
regulation of RNA and protein synthesis; cell cycle; molecular
immunology; chromosome segregation; nuclear organization.
Special Admissions Requirements
Courses in introductory biology, general chemistry, organic chemistry, physical chemistry, mathematics through differential equations, and one year of physics with calculus are required for admission. Biochemistry is recommended. Applicants must take the GRE General Test, which is preferred, or the MCAT.
To enter the Ph.D. program, students apply to an interest-based
track within the interdepartmental graduate program in the
Biological and Biomedical Sciences.
Special Requirements for the Ph.D. Degree
All first-year students (except M.D./Ph.D.) take three
laboratory rotations (MB&B 650a and 651b, Lab Rotation
for First-Year Students). All students are required to take,
for credit, seven one-term science courses. To obtain the
desired breadth and depth of education, students are strongly
encouraged to take (or to have taken the equivalent of) the
core graduate courses offered by the department in biochemistry,
molecular genetics, and structural biology. Additional courses,
chosen from within MB&B or from related graduate programs,
should form a coherent background for the general area in
which the student expects to do dissertation research. All
students attend the two departmental seminars: MB&B 675,
Seminar for First-Year Students, and MB&B 676b, Responsible
Conduct of Research. Students with an extensive background
in biochemistry or biophysics are permitted to substitute
advanced courses for the introductory courses. There is no
foreign-language requirement. The student’s research
committee (see below) makes the final decision concerning
the number and selection of courses required of each student.
All students are required to teach two terms during their
graduate careers, usually during the second and third years.
The student selects a research adviser, usually from the department
faculty, by the end of the second term of residence. At that
time two additional faculty members are chosen to form a research
committee. Requirements for admission to candidacy, which
usually takes place after four terms of residence, are: (1)
completion of course requirements; (2) completion of the qualifying
examination; (3) certification of the student’s research
abilities by vote of the faculty upon recommendation from
the student’s research committee; and (4) submission
of a brief prospectus of the proposed thesis research. The
qualifying examination, taken in the fall of the second year,
is an oral defense of two short, written research proposals,
one in the same area as the student’s thesis research
and one in a different area; the three-member oral committee
includes at least one of the two members of the research committee
excluding the thesis adviser, and the remaining one or two
members are selected by the Qualifying Examination Committee.
Once final drafts of the thesis chapters have been approved
by the research committee, the student presents a dissertation
seminar to the entire department, only after which may the
thesis be submitted. Students must have written at least one
first-author paper that is submitted, in press, or published
by the time of the thesis seminar.
Honors Requirement
Students must meet the Graduate
School's Honors requirement by the end of the fourth term
of full-time study.
Master's Degree
M.Phil. See Graduate
School requirements. Awarded only to students admitted
to candidacy who are continuing for the Ph.D. Students are
not admitted for this degree.
M.S. May be awarded to a student who is in good standing
upon completion of at least two terms of graduate study (granted
to students who are not continuing in the Ph.D. program).
Note that a High Pass average is required for obtaining a
master's degree.
M.S. (for industrial affiliates). Scientists working
in industry may attend courses and conduct research projects
leading to the M.S. degree. Information may be obtained from
the director of graduate studies.
Program materials are available upon request to the Director of Admissions, Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven CT 06520-8114.
Courses
MB&B 600au, Principles of Biochemistry I. Donald
Engelman, Mark Solomon. TTh 11.30–12.45
Rigorous introduction to the major concepts of biochemistry
and to the process of discovery in this discipline, with emphasis
on macromolecular conformation and physical processes in biochemistry.
Energy metabolism, hormone signaling, and muscle contraction
as examples of complex biological processes whose underlying
mechanisms can be understood by identifying and analyzing
the molecules responsible for these phenomena.
MB&B 601bu, Principles of Biochemistry II. Scott
Strobel, Joan Steitz. TTh 11.30–12.45
The chemistry and metabolism of nucleic acids, the mechanism
and regulation of protein and nucleic acid synthesis, and
selected topics in macromolecular biochemistry.
MB&B 602a, Molecular Cell Biology. Sandra
Wolin, Thomas Pollard, Graham Warren, et al. MW 1.45–3
A comprehensive introduction to the molecular and mechanistic
aspects of cell biology for graduate students in all programs.
Emphasizes fundamental issues of cellular organization, regulation,
biogenesis, and function at the molecular level. Also
CBIO 602a, MCDB 602a.
MB&B 625au, Basic Concepts of Genetic Analysis. Tian
Xu, Michael Koelle, Richard Lifton, Shirleen Roeder, Michael
Stern. TTh 1–2.15
The universal principles of genetic analysis in eukaryotes
are discussed in lectures. Students also read a small selection
of primary papers illustrating the very best of genetic analysis
and dissect them in detail in the discussion sections. While
other Yale graduate molecular genetics courses emphasize molecular
biology, this course focuses on the concepts and logic underlying
modern genetic analysis. Also GENE 625a, MCDB 625au.
MB&B 642a, Roles of Microorganisms in the Living
World. L. Nicholas Ornston, Diane McMahon-Pratt,
Robert Macnab. TTh 11.30–12.45
A topical course exploring the biology of microorganisms.
Emphasis on mechanisms underlying microbial adaptations and
how they influence biological systems. Prerequisites: biology,
chemistry, biochemistry. Also EMD 642a, GENE 642a, MBIO
642a, MCDB 642a.
MB&B 650a and 651b, Lab Rotation for First-Year
Students. Nigel Grindley.
Required for all first-year graduate students.
[MB&B 658a, Research Topics in Biophysics.]
MB&B 675, Seminar for First-Year Students. Michael
Koelle, Andrew Miranker, and staff. F 4
Required for all first-year graduate students.
MB&B 676b, Responsible Conduct of Research. Vinzenz
Unger and staff. F 4
Designed for students who are beginning to do scientific
research. The course seeks to describe some of the basic features
of life in contemporary research and some of the personal
and professional issues that researchers encounter in their
work. Approximately six sessions during the spring term, run
in a seminar/discussion format. Required for all first-year
graduate students.
MB&B 700bu, Properties of Macromolecules. Lynne
Regan, Enrique De La Cruz. MW 11.30–12.45
Solution properties of macromolecules. Current topics
in biophysics including hydrodynamics, stability, kinetics,
and multiple equilibria. Techniques for the solution characterization
of macromolecules and their interactions, including fluorescence,
circular dichroism, calorimetry, and centrifugation. Prerequisite:
physical chemistry and biochemistry.
MB&B 701b3u, Diffraction Methods. João
Cabral, Vinzenz Unger. TTh 9–10.15
Biological applications of X-ray crystallography, small-angle
X-ray, and neutron scattering and cryoelectron microscopy.
MB&B 701b4u, NMR Methods. Andrew Miranker. TTh 9–10.15
Basic principles of NMR with emphasis on biological applications
in the primary literature. Application areas include structure
determination, drug binding, molecular recognition, protein
folding, and in vivo metabolism. Prerequisites: physical chemistry
and biochemistry.
[MB&B 704au, Structural Biology.]
MB&B 705au, Molecular Genetics of Prokaryotes. Nigel
Grindley, Charles Radding, Joann Sweasy. MW 11.30–12.45
Molecular aspects of the storage, replication, evolution,
and expression of genetic material in prokaryotes. Required:
previous or concurrent introductory courses in genetics and
biochemistry. Also GENE 705a, MCDB 505au.
MB&B 710b4, Electron Cryo-Microscopy for Protein
Structure Determination. Vinzenz Unger, Fred Sigworth.
Understanding cellular function requires structural and
biochemical studies at an ever-increasing level of complexity.
The course is an introduction into the concepts and applications
of high-resolution electron cryo-microscopy. This rapidly
emerging new technique is the only tool known to date that
allows biological macromolecules to be studied at all levels
of resolution ranging from their cellular organization to
near atomic detail. Also C&MP 710b.
MB&B 741au, Structure and Chemistry of Proteins
and Nucleic Acids. Anna Pyle, Dieter Söll,
João Cabral. TTh 11.30–12.45
Selected topics in the structure of proteins and nucleic
acids; sequence dependent interactions between proteins and
nucleic acids; chemical modifications of DNA; chemical studies
of DNA-binding proteins; catalytic RNA. Prerequisite: biochemistry.
MB&B 743bu, Molecular Genetics of Eukaryotes. Anthony
Koleske, Anna Pyle, Patrick Sung. TTh 11.30–12.45
Selected topics in regulation of gene expression, genome
structure and evolution, signal transduction, cellular physiology,
development, and carcinogenesis. Prerequisite: biochemistry
or permission of the instructor.
[MB&B 746a1, Advanced Biochemical Control.]
MB&B 749au, Medical Impact of Basic Science. Joan
Steitz, Patrick Sung, Andrew Miranker, Enrique De La Cruz,
Sankar Ghosh. TTh 1–2.30
Consideration of examples of recent discoveries in basic
science that have elucidated the molecular origins of disease
or that have suggested new therapies for disease. Emphasis
is placed on the fundamental principles on which these advances
rely. Reading is from the primary scientific and medical literature,
with emphasis on developing the ability to read this literature
critically. Aimed primarily at undergraduates. Prerequisite:
MB&B 600au/601bu or permission of the instructor. Also
GENE 749a.
MB&B 750a2, Biological Membranes. Lise
Heginbotham, Vinzenz Unger, Donald Engelman. MW 10–11.15
Biological membranes and their resident proteins are
essential for cellular function; yet comparatively little
is known about their structure and dynamics. This class provides
an introduction to the biochemistry and biophysics of lipids,
lipid bilayers, and lipid-derived second messengers. In addition,
structural as well as functional aspects of the different
classes of membrane proteins are discussed along with an outline
of experimental approaches used to achieve an understanding
of membrane protein structure and function at a molecular
level.
MB&B 752au, Genomics and Bioinformatics. Dieter
Söll, Mark Gerstein. MW 1–2.15
Genomics describes the determination of the nucleotide
sequence and many further analyses to discover functional
and structural information on all the genes of an organism.
Topics include the methods and results of functional and structural
gene analysis on a genome-wide scale as well as a discussion
of the implications of this research. Bioinformatics describes
the computational analysis of genomes and macromolecular structures
on a large scale. Topics include sequence alignment, biological
database design, comparative genomics, geometric analysis
of protein structure, and macromolecular simulation. Prerequisite:
EEB 122b and MATH 115, or permission of the instructor. Also
CPSC 752au, MCDB 752au.
[MB&B 760b4u, Principles of Macromolecular Crystallography.]
MB&B 775b, Advanced Seminar in Genetics.
MB&B 800a, Advanced Topics in Molecular Medicine. Susan
Baserga and staff. M 11–1
This seminar course, which covers topics in the molecular
mechanisms of disease, illustrates timely issues in areas
such as protein chemistry and enzymology, intermediary metabolism,
nucleic acid biochemistry, gene expression, and virology.
A prior course in biochemistry is a prerequisite. This course
accompanies the lectures in MB&B 550a. M.D. and M.D./Ph.D.
students only.
MB&B 900a or 901b, Reading Course in Biophysics.
Directed reading course in biophysics. Term paper required.
By arrangement with faculty.
MB&B 902a or 903b, Reading Course in Molecular Genetics.
Directed reading course in molecular genetics. Term paper
required. By arrangement with faculty.
MB&B 904a or 905b, Reading Course in Biochemistry.
Directed reading course in biochemistry. Term paper required.
By arrangement with faculty.
The following courses are for students in the joint B.S./M.S.
program with Yale College:
MB&B 569b or MB&B 572b, Independent Research
for B.S./M.S. Candidates. Scott Strobel.
MB&B 570a or MB&B 571b, Intensive Research Seminar
for B.S./M.S. Candidates. Scott Strobel, Nigel
Grindley.
Next: Molecular, Cellular, and Developmental Biology
|
