BMB Course List

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 30500 – Data Science with R Boot camp:  This boot camp is an addendum to Protein Fundamentals and is required for all BMB students.  This boot camp will introduce students to data analysis, using the R programming language.  It will begin with exploratory data analysis on example datasets.  Students will develop these methods in scripts and programs to illustrate reproducible analysis workflows. Students will then build and compare models to explain trends in data sets.  Finally, students will cover methods for refining our graphical presentation and preparing analysis reports. Rock

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.  Prereq: 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/Moffat

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.  Prereq:  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.  Prereq:  Completion of course requirements and qualifying examination at the Ph.D. level and approval of Chairman of the Department.  Staff

 

Winter Quarter Courses

Molecular Dynamics Workshop:  This 3 week workshop covers the fundamental physical elements and numerical algorithms underlying molecular dynamics simulations, and provides the practical information needed to utilize the programs VMD and NAMD. Each week, there will be a one-hour formal lecture plus a one-hour practical session. The workshop will take place during a period of three weeks during mid winter quarter. Roux                                                             

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 Mathlab would be valuable. Prereq:  BIOS 20200 or consent of instructor. Roux

BCMB 31900 – Introduction to Research: Lectures on current research by departmental faculty and other invited speakers. A required course for all first-year graduate students.  Staff

BCMB 32300 – Structure and Function of Membrane Proteins: 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 course 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 transport mechanisms, 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. Students will be responsible for presentation of each assigned paper and discussions of the significance of the papers. Perozo

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.  Prereq:  Consent of Department and Instructor.  Staff

BSDG 40100 – Non-Thesis Research:  The student participates in one of the research programs of the Department.  Prereq:  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.  Prereq:  Completion of course requirements and qualifying examination at the Ph.D. level and approval of Chairman of the Department.  Staff

 

Spring Quarter Courses

BCMB 30800 – Single Molecule Biochemistry:   This course presents a series of advanced case studies designed to familiarize students with current single molecule research. Topics include: motor proteins and the cytoskeleton, nucleic acid processing enzymes, ion channels, and force spectroscopy and macromolecule folding.  Rock, Bezanilla

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 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/Moffat

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.  Prereq:  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.  Prereq:  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.  Prereq:  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 30300 – Application of Nuclear Magnetic Resonance to Structural Biology Workshop:  The main objectives of the workshop are (i) to learn NMR based structure characterization methods and their applications and (ii) to become familiar with technical underpinnings of these methods so as to be able to critically appraise publications using these methods.  Meredith, Sachleben

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.  Prereq:  Consent of Department and Instructor.  Staff

BCMB 39900 – Introduction to Research:  The student participates in one of the research programs of the Department.  Prereq:  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.  Prereq:  Completion of course requirements and qualifying examination at the Ph.D. level and approval of Chairman of the Department.  Staff