Autumn Quarter Courses
BCMB 30400 – Protein Fundamentals: The course covers the physical‑chemical phenomena that define protein structure and function. Topics include: the principles of protein folding, molecular motion and molecular recognition; protein evolution, design and engineering; enzyme catalysis; regulation of protein function and molecular machines; proteomics and systems biology. Ozkan, Arac, Piccirilli
BCMB 30600 – Nucleic Acid Structure and Function: This course focuses on the biology, biochemistry and biophysics of nucleic acids. Topics include nucleic acid structure, folding, chemistry and interactions with proteins, the mechanisms of CRISPRs and other biotech tools, non-coding RNAs, and the enzymology of key processes such as DNA replication, repair and recombination. Emphasis is placed on primary literature and methodology. Prerequisite: Courses in Biochemistry, molecular biology and organic chemistry. Rice, Fei
BCMB 31400 – Genetic Analysis of Model Organisms (=MGCB 31400): Fundamental principles of genetics discussed in the context of current approaches to mapping and functional characterization of genes. The relative strengths and weaknesses of leading model organisms are emphasized via problem-solving and critical reading of original literature. Bishop
BCMB 31600 – Cell Biology (=MGCB 31600): Eukaryotic protein traffic and related topics, including molecular motors and cytoskeletal dynamics, organelle architecture and biogenesis, protein translocation and sorting, compartmentalization in the secretory pathway, endocytosis and exocytosis, and mechanisms and regulation of membrane fusion. Turkewitz, Glick
BCMB 31800 – Current Seminar Topics in Biochemistry and Molecular Biology: This course will expose students to current research topics in biochemistry and molecular biology by highlighting a selection of speakers from the weekly seminar series. Prior to each highlighted seminar, we will discuss relevant papers and subsequently, we will review the seminar. This is a required ½ credit course for all BMB first year students and will be graded as Pass/Fail. Kossiakoff
BCMB 31900 – Introduction to Faculty Research: Lectures on current research by departmental faculty and other invited speakers. A required course for all first-year graduate students. Staff
BCMB 39800 – Selected Reading Topics in Biochemistry and Molecular Biology: Subject matter for individual tutorial-based study is selected through prior consultation and is given under the guidance of a faculty member. The student and faculty member must indicate at time of registration whether the course will be taken on a letter grade or pass/fail basis. Prerequisite: Consent of Department and Instructor. Staff
BCMB 40100 – Research in Biochemistry and Molecular Biology: The student conducts original investigation under the direction of a faculty member. The research is presented and defended as a dissertation in candidacy for the degree of Doctor of Philosophy. Prerequisite: Completion of course requirements and qualifying examination at the Ph.D. level and approval of Chairman of the Department. Staff
Winter Quarter Courses
BCMB 31100 – Evolution of Biological Molecules: The course connects evolutionary changes imprinted in genes and genomes with the structure, function and behavior of the encoded protein and RNA molecules. Central themes are the mechanisms and dynamics by which molecular structure and function evolve, how protein/ RNA architecture shapes evolutionary trajectories, and how patterns in present-day sequence can be interpreted to reveal the interplay data of evolutionary history and molecular properties. Core concepts in macromolecule biochemistry (folding and stability of proteins and RNA, structure-function relationships, kinetics, catalysis) and molecular evolution (selection, mutation, drift, epistasis, effective population size, phylogenetics) will be taught, and the interplay between them explored. Drummond, Thornton
BCMB 31200 – Molecular Biology I (=MGCB 31200): Nucleic acid structure and DNA topology; methodology; nucleic-acid protein interactions; mechanisms and regulation of transcription, replication and genome stability and dynamics. Rothman-Denes, Bishop
BCMB 31358 – Simulation, Modeling, and Computation in Biophysics: This course will develop skills for modeling biomolecular systems, proteins, membranes, ion channels. Fundamental knowledge will cover basic statistical mechanics, free energy, and kinetic concepts. Tools will include molecular dynamics and Monte Carlo simulations, random walk and diffusion equations, and methods to generate random Gaussian and Poisson distributions. A term project will involve writing a small program that simulates a process. Familiarity with a programming language or Math-lab would be valuable. Prerequisite: BIOS 20200 or consent of instructor. Roux
BCMB 33500 – Fundamentals of Biological Data analysis: The primary goals of this course are to provide first-year trainees in MCB graduate programs with a common grounding in the core tools of modern quantitative data analysis as used in molecular and cellular biology and a shared quantitative mindset and commitment to rigorous reproducible science. Our goal is not to be comprehensive, but to provide students with the conceptual foundations and practical and practical skills they are most like to need, regardless of research area. the expectation is that they will build upon these foundations through advanced courses, workshops, and in-lab training. The course will emphasize building reproducible "data analysis workflows" that go from raw data to insights about biological process and function, and present those insights in rigorous and informative ways. The course will use R as the primary programming language because of its widespread use and suitability for quantitative statistical data visualization and analysis, but most of the skills students learn will be readily transferrable to other programming languages. Key elements will include: (a) data import and manipulation, exploratory data analysis using graphical methods, programming methods for assembling these elements into efficient reproducible workflows, (b) using statistical methods and simple models to describe patterns in data, infer relationships, and assess differences across different conditions, over time, etc., and (c) presenting the results of these analyses in publication quality figures, accompanied by rigorous descriptions of methods, results and conclusions. Again, the goal is not mastery per se, but rather an understanding of how one follows multiple paths from raw data to rigorous biological conclusions in a sequence of reproducible steps, each of which can be mastered with further practice. Munro, Drummond, Rust, Rock
BCMB 39800 – Selected Topics in Biochemistry and Molecular Biology: Subject matter for individual tutorial-based study is selected through prior consultation and is given under the guidance of a faculty member. The student and faculty member must indicate at time of registration whether the course will be taken on a letter grade or pass/fail basis. Prerequisite: Consent of Department and Instructor. Staff
BSDG 40100 – Non-Thesis Research: The student participates in one of the research programs of the Department. Prerequisite: Consent of Department Chairman and individual faculty member. Staff
BCMB 40100 – Research in Biochemistry and Molecular Biology: The student conducts original investigation under the direction of a faculty member. The research is presented and defended as a dissertation in candidacy for the degree of Doctor of Philosophy. Prerequisite: Completion of course requirements and qualifying examination at the Ph.D. level and approval of Chairman of the Department. Staff
Spring Quarter Courses
BCMB 31300 – Molecular Biology II (=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. Enrollment requires the equivalent of an undergraduate molecular biology course or consent from the instructors. Staley, Ruthenburg
BCMB 32200 – Biophysical Properties of Biomolecules: The course will cover the properties of proteins, RNA, DNA and their interactions. Particular emphasis will be on interplay between structure, thermodynamics, folding and function at the molecular level. Topics will include cooperativity, linked equilibrium, hydrogen exchange, electrostatics diffusion and binding. Sosnick
BCMB 32600 - Methods in Structural Biology: This course aims to provide students with the theoretical and applied knowledge on the use of modern structural biology methods, namely x-ray crystallography, cryo-electron microscopy and nuclear magnetic resonance spectroscopy. The course includes lectures and hands-on laboratory sessions, including a data-collection visit to the synchrotron at Argonne National Lab, collection of microscopy images at the Advanced Electron Microscopy Facility at UChicago, and data collection at our local NMR facility. The lectures will include x-ray diffraction theory, strategies to solve the phase problem, principles of electron microscopy and optics, single particle analysis, tomography, various NMR techniques and structure calculations from 3D spectra, model building and validation, and recent advances. The laboratory sessions will take registered students from sample preparation to model refinement and building using state-of-the-art experimental and computational tools. Basic knowledge of protein chemistry (as provided in BCMB 30400) strongly recommended. Meredith, Ozkan, Sachleben, Zhao
BCMB 39800 – Selected Topics in Biochemistry and Molecular Biology: Subject matter for individual tutorial-based study is selected through prior consultation and is given under the guidance of a faculty member. The student and faculty member must indicate at time of registration whether the course will be taken on a letter grade or pass/fail basis. Prerequisite: Consent of Department and Instructor. Staff
BSDG 40100 – Non-Thesis Research – Introduction to Research: The student participates in one of the research programs of the Department. Prerequisite: Consent of Department Chairman and individual faculty member. Staff
BCMB 40100 – Research in Biochemistry and Molecular Biology: The student conducts original investigation under the direction of a faculty member. The research is presented and defended as a dissertation in candidacy for the degree of Doctor of Philosophy. Prerequisite: Completion of course requirements and qualifying examination at the Ph.D. level and approval of Chairman of the Department. Staff
Summer Quarter Courses
Proposal Writing Workshop: The main objective of this workshop is to learn the aspects of writing a proposal, coming up with ideas, creating a draft and writing a proposal. The workshop involves morphing original ideas from individual students into proposal forms through verbal discussions in class for proposals in NIH 6-page format. The workshop will take place during early summer quarter. BMB students complete this workshop in conjunction with the Preliminary Examination process. Pan
BCMB 39800 – Selected Topics in Biochemistry and Molecular Biology: Subject matter for individual tutorial-based study is selected through prior consultation and is given under the guidance of a faculty member. The student and faculty member must indicate at time of registration whether the course will be taken on a letter grade or pass/fail basis. Prerequisite: Consent of Department and Instructor. Staff
BCMB 39900 – Introduction to Research: The student participates in one of the research programs of the Department. Prerequisite: Consent of Department Chairman and individual faculty member. Staff
BCMB 40100 – Research in Biochemistry and Molecular Biology: The student conducts original investigation under the direction of a faculty member. The research is presented and defended as a dissertation in candidacy for the degree of Doctor of Philosophy. Prerequisite: Completion of course requirements and qualifying examination at the Ph.D. level and approval of Chairman of the Department. Staff