Molecular Biophysics and Biochemistry
301 Josiah Willard Gibbs Laboratories, 432.5662
www.mbb.yale.edu/
M.S., M.Phil., Ph.D.
Chair
Scott Strobel
Director of Graduate Studies
Mark Solomon (301 JWG, 432.5662, nessie.stewart@yale.edu)
Professors
Susan Baserga, Ronald Breaker (Molecular, Cellular & Developmental Biology), Gary Brudvig (Chemistry), Donald Crothers (Emeritus, Chemistry), Donald Engelman, Joseph Fruton (Emeritus), Alan Garen, Mark Gerstein, Sankar Ghosh (Immunobiology), Nigel Grindley, Andrew Hamilton (Chemistry), Mark Hochstrasser, William Konigsberg, Peter Lengyel (Emeritus), Richard Lifton (Genetics; Internal Medicine/Nephrology), I. George Miller (Pediatric Infectious Diseases; Epidemiology & Public Health), Peter Moore (Chemistry), Thomas Pollard (Molecular, Cellular & Developmental Biology), Anna Pyle, Charles Radding (Emeritus, Genetics), Lynne Regan, Frederic Richards (Emeritus), Gaston Schmir (Emeritus), Robert Shulman (Emeritus), Sofia Simmonds (Emeritus), Michael Snyder (Molecular, Cellular & Developmental Biology), Dieter Söll, Mark Solomon, Joan Steitz, Thomas Steitz, Scott Strobel, William Summers (Therapeutic Radiology), Patrick Sung, Kenneth Williams (Adjunct, Research), Sandra Wolin (Cell Biology)
Associate Professors
João Cabral, Enrique De La Cruz, Michael Koelle, Anthony Koleske, Andrew Miranker, Vinzenz Unger
Assistant Professors
Thomas Biederer, Yorgo Modis, Elizabeth Rhoades, Yong Xiong
Fields of Study
The principal objective of members of the department is to understand living systems at the molecular level. Laboratories in MB&B focus on a diverse collection of problems in biology. Some specialize in the study of DNA dynamics, including replication, recombination, transposition, and/or functional genomics. Others focus on transcriptional regulation, from individual transcription factors to the control of lymphocyte activation, the interferon response, and organismal development. Other groups study RNA catalysis, RNA-protein interactions, and ribonucleoproteins including spliceosomes and the ribosome. Additionally there are those that emphasize protein folding and design, transmembrane signaling, and control of the cell cycle. Structural and computational biology is a strong component of many of these research efforts.
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 strongly 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.) perform three laboratory rotations (MB&B 650, 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 (MB&B 705a, 720a, 721b, 730a, 743b). 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 also attend 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 assist in teaching two terms as a TF-2 during their graduate careers, usually during the second and third years. The student selects a research adviser by the end of the second term of residence. At that time two additional faculty members are chosen to form a research committee, with the total committee including at least two members of MB&B. Students are required to meet with this committee in the spring of years 2 and 3, and in both the fall and spring of subsequent years. The qualifying examination, usually 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 examination committee usually includes at least one of the two members of the research committee excluding the thesis adviser. Requirements for admission to candidacy, which usually takes place after four terms of residence, include (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. Completion of the teaching requirement is not required for admission to candidacy. Once final drafts of the thesis chapters have been approved by the research committee, the student presents a dissertation seminar to the entire department, and only afterward 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. Students must also maintain an overall High Pass average. Student progress toward these goals is reviewed at the ends of the first and second
M.D./Ph.D. Students
M.D./Ph.D. students must satisfy the requirements listed above for the Ph.D. with the following modifications: Laboratory rotations are not required but are available. Assisting in teaching is encouraged but not required. With DGS approval, some courses taken toward the M.D. degree can be counted toward the seven courses required for the Ph.D. provided that the course carries a graduate course number, and that the student has registered for it as a graduate course. M.D./Ph.D. students should still take MB&B 720a, 721b, 730a, and 743b. terms.
Master’s Degree
M.Phil. See Degree Requirements. Awarded only to students admitted to candidacy who are continuing for the Ph.D. Students need not have completed their teaching requirement to receive the M.Phil. 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 and who will not continue in the Ph.D. program. A student must receive grades of Pass or higher in at least five courses approved by the DGS as counting toward a graduate degree, exclusive of seminars or research. A student must also meet the Graduate School’s Honors requirement for the Ph.D. program and maintain a High Pass average.
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.
More detailed 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 523a, Biological Physics. Simon Mochrie.
TTh 2.30–3.45
An introduction to the physics of biological systems, including molecular motors, protein folding, membrane self-assembly, ion pumping, and bacterial locomotion. Background concepts in probability and statistical mechanics are introduced as necessary. Also PHYS 523a.
MB&B 600au,Principles of Biochemistry I. Michael Koelle, Thomas Biederer.
TTh 11.35–12.50
Discussion of the physical, structural, and functional properties of proteins, lipids, and carbohydrates, three major classes of molecules in living organisms. 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. Joan Steitz, Scott Strobel.
TTh 11.35–12.50
A continuation of MB&B 600a that considers 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, Mark Solomon, and staff.
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, and staff.
MW 11.35–12.50
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 630b, Biochemical and Biophysical Approaches in Molecular and Cellular Biology. Thomas Pollard, Enrique De La Cruz, and staff.
TTh 2.30–3.45
This graduate course introduces the theory and application of biochemical and biophysical methods to study the structure and function of biological macromolecules. The course considers the basic physical chemistry required in cellular and molecular biology but does not require a previous course in physical chemistry. One class per week is a lecture introducing a topic. The second class is a discussion of one or two research papers utilizing those methods. Also MCDB 630b.
MB&B 635a1u, Mathematical Methods in Biophysics. Yong Xiong, Elizabeth Rhoades.
MW 9–10.15
Applied mathematical methods relevant to analysis and interpretation of biophysical and biochemical data are covered. Students apply these methods (statistics and error analysis, differential equations, linear algebra, and Fourier transforms) to analyze data from research groups in MB&B. Prerequisites: MATH 120 (or equivalent) and MB&B 600a (or equivalent) or permission of instructors.
MB&B 650, Lab Rotation for First-Year Students. Mark Solomon.
Required for all first-year MB&B graduate students. Credit for full year only.
MB&B 676b, Responsible Conduct of Research. Thomas Biederer 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, run in a seminar/discussion format. Required for all first-year MB&B graduate students.
[MB&B 705au,Molecular Genetics of Prokaryotes.]
MB&B 710b4, Electron Cryo-Microscopy for Protein Structure Determination. Fred Sigworth, Vinzenz Unger.
TTh 9–10.15
Understanding cellular function requires structural and biochemical studies at an ever-increasing level of complexity. The course is an introduction to the concepts and applications of high-resolution electron cryo-microscopy. This rapidly emerging new technique is the only method that allows biological macromolecules to be studied at all levels of resolution from cellular organization to near atomic detail. Also C&MP 710b.
MB&B 720au,Macromolecular Structure and Biophysical Analysis. Andrew Miranker, João Cabral, Anna Pyle.
TTh 11.35–12.50
An in-depth analysis of macromolecular structure and its elucidation using modern methods of structural biology and biochemistry. Topics include architectural arrangements of proteins, RNA, and DNA; practical methods in structural analysis; and an introduction to diffraction and NMR. Prerequisites: physical chemistry (may be taken concurrently) and biochemistry.
MB&B 721bu,Macromolecular Interactions and Dynamic Properties. Anna Pyle, Elizabeth Rhoades, Yong Xiong.
MW 11.35–12.50
This course examines dynamic properties of macromolecules, their interactions, catalytic activities, and methods for analyzing their behavior. Topics include macromolecular folding, binding interfaces, ligand interactions, and the properties of membrane proteins, enzymes, ribozymes, and molecular motors. These areas are presented together with modern methods for analysis of macromolecular associations and dynamic properties. Prerequisites: biochemistry, physical chemistry, and MB&B 720a or permission of the instructor.
MB&B 730a, Methods and Logic in Molecular Biology. Mark Solomon, Anthony Koleske, Lynne Regan.
TTh 5–8
This course examines fundamental concepts in molecular biology through intense critical analysis of the primary literature. The objective is to develop primary literature reading and critical thinking skills. Required of and open only to first-year graduate students in MB&B.
MB&B 743bu,Advanced Eukaryotic Molecular Biology. Mark Hochstrasser, Anthony Koleske, Patrick Sung.
TTh 11.35–12.50
Selected topics in transcriptional control, regulation of chromatin structure, mRNA processing, mRNA stability, RNA interference, translation, protein degradation, DNA replication, DNA repair, site-specific DNA recombination, somatic hypermutation. Prerequisite: biochemistry or permission of the instructor. Also GENE 743b, MCDB 743b.
MB&B 749au,Medical Impact of Basic Science. Joan Steitz, Mark Hochstrasser, Andrew Miranker, Lynne Regan, Thomas Steitz, Patrick Sung.
TTh 1–2.15
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: biochemistry or permission of the instructor. Also GENE 749a.
MB&B 750au,Biological Membranes. Thomas Biederer, João Cabral, Donald Engelman.
MW 9–10.15
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. Prerequisite: biochemistry.
MB&B 752bu,Genomics and Bioinformatics. Mark Gerstein, Michael Snyder, Dieter Söll.
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 CB&B 752b, CPSC 752bu,MCDB 752bu.
MB&B 760b3, Principles of Macromolecular Crystallography. Thomas Steitz.
TTh 9–10.15
Rigorous introduction to the principles of macromolecular crystallography, aimed at students who are planning to carry out structural studies involving X-ray crystallography or who want to obtain in-depth knowledge for critical analysis of published crystal structures. Prerequisites: physical chemistry and biochemistry.
MB&B 761b4, X-Ray Crystallography Workshop. Yong Xiong, Yorgo Modis, and staff.
HTBA
This laboratory course provides hands-on training in the practical aspects of macromolecular structure determination by X-ray crystallography. Topics include data collection, data reduction, phasing by multiwavelength anomalous diffraction and molecular replacement, solvent flattening, non-crystallographic symmetry averaging, electron density interpretation, model building, structure refinement, and structure validation. The course includes training in the use of computer programs used to perform these calculations. Prerequisites: MB&B 760b3 and a working exposure to the Unix operating system.
MB&B 765bu,Enzyme Mechanisms. Enrique De La Cruz, Gary Brudvig, and staff.
MW 9–10.15
An advanced course on the structure, function, and reaction mechanisms of protein and nucleic acid enzymes. The course covers the theoretical and practical aspects of steady-state and transient kinetic methods, kinetic isotope effects and transition-state theory, with emphasis on how these methods in combination with high-resolution structures have provided a molecular understanding of the catalytic strategy of enzymes. Topics include mechanisms of the classic metabolic enzymes; molecular motors, polymerases, and machines; electron transfer, redox enzymes, and their higher-order complexes; ribozymes and DNA enzymes; and the design and selection of novel enzymes. Prerequisites: physical chemistry and biochemistry.
MB&B 800a, Advanced Topics in Molecular Medicine. Susan Baserga, William Konigsberg, George Miller, 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. M.D. and M.D./Ph.D. students only. Prerequisite: biochemistry (may be taken concurrently).
MB&B 900a or 901b, Reading Course in Biophysics. Mark Solomon.
Directed reading course in biophysics. Term paper required. By arrangement with faculty. Open only to graduate students in MB&B.
MB&B 902a or 903b, Reading Course in Molecular Genetics. Mark Solomon.
Directed reading course in molecular genetics. Term paper required. By arrangement with faculty. Open only to graduate students in MB&B.
MB&B 904a or 905b, Reading Course in Biochemistry. Mark Solomon.
Directed reading course in biochemistry. Term paper required. By arrangement with faculty. Open only to graduate students in MB&B.
The following course is for students in the joint B.S./M.S. program with Yale College:
MB&B 570a or MB&B 571b, Intensive Research for B.S./M.S. Candidates. Michael Koelle, Mark Solomon.
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