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.
Keenan, Piccirilli, Koide
Workshop on X-ray Crystallography: The workshop is an addendum to Protein Fundamentals and is required for all BCMB students. This one week workshop will provide students with an intensive introduction to protein structure determination by x-ray crystallography. In addition to lectures, an extensive laboratory component will give students the opportunity to carry out protein crystallization, data collection (at Argonne), structure determination, refinement, model building and validation. Keenan, Moffat, Adams, Rice, Crosson

 

BCMB 30600 - Nucleic Acid Structure and Function

This course focuses on the biochemistry of nucleic acids. Topics include nucleic acid structure, folding, and chemistry, protein-nucleic acid interactions, non-coding RNAs, and the enzymology of key processes such as DNA replication, repair and recombination. A special emphasis is placed on primary literature. Prereq: Courses in Biochemistry, molecular biology and organic chemistry. Rice, Pan

 

BCMB 31000 – 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

 

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, Ferguson, Palmer, Malamy.

 

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. Rock

 

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 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. Arac-Ozkan, Perozo
BCMB students taking this course are also required to take the Workshop on X-ray Crystallography This one week workshop will provide students with an intensive introduction to protein structure determination by x-ray crystallography. In addition to lectures, an extensive laboratory component will give students the opportunity to carry out protein crystallization, data collection (at Argonne), structure determination, refinement, model building and validation. Keenan, Moffat, Adams, Rice, Crosson

 

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

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 31000 – 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

 

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 in eubacteria, and of replication in eubacteria and eukaryotes; mechanisms of genome and plasmid segregation in eubacteria. Rothman-Denes

 

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 Faculty 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. Arac-Ozkan, Perozo
BCMB students taking this course are also required to take the Workshop on X-ray Crystallography This one week workshop will provide students with an intensive introduction to protein structure determination by x-ray crystallography. In addition to lectures, an extensive laboratory component will give students the opportunity to carry out protein crystallization, data collection (at Argonne), structure determination, refinement, model building and validation. Keenan, Moffat, Adams, Rice, Crosson

 

BCMB 32700 – Protein Aggregation /"Misfolding" and Protein Design

This course will discuss in depth two major topics in protein science in biomedical sciences, protein misfolding and protein design. The class will examine milestone papers from the primary literature that cover important concepts and techniques for the topics. Koide, Meredith

 

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

 

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 30266 – Molecular Immunology

This course will examine the molecular principles of immune recognition. We will explore the roles of protein modification, protein-protein and protein-DNA interactions in the discrimination between self and non-self, and will study the molecular fundamentals of cell stimulation and signaling. Primary literature focused on molecular research of the immune system will be integrated with lectures on commonly used biochemical, structural and immunological techniques used in the research papers examined. Emphasis is placed on class participation. Prereq: BIOS 20200, BIOS 25256, or consent of instructor. Adams

 

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. 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. Rock

 

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 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

 

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

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

 

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 (see page #). 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. Koide, Sachleben

 

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 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

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. Keenan, Piccirilli, Koide

Workshop on X-ray Crystallography: The workshop is an addendum to Protein Fundamentals and is required for all BCMB students. This one week workshop will provide students with an intensive introduction to protein structure determination by x-ray crystallography. In addition to lectures, an extensive laboratory component will give students the opportunity to carry out protein crystallization, data collection (at Argonne), structure determination, refinement, model building and validation. Keenan, Moffat, Adams, Rice, Crosson

This course focuses on the biochemistry of nucleic acids. Topics include nucleic acid structure, folding, and chemistry, protein-nucleic acid interactions, non-coding RNAs, and the enzymology of key processes such as DNA replication, repair and recombination. A special emphasis is placed on primary literature. Prereq: Courses in Biochemistry, molecular biology and organic chemistry. Rice, Pan

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

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, Ferguson, Palmer, Malamy.

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

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. Rock

Lectures on current research by departmental faculty and other invited speakers. A required course for all first-year graduate students. Staff

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. Arac-Ozkan, Perozo

BCMB students taking this course are also required to take the Workshop on X-ray Crystallography This one week workshop will provide students with an intensive introduction to protein structure determination by x-ray crystallography. In addition to lectures, an extensive laboratory component will give students the opportunity to carry out protein crystallization, data collection (at Argonne), structure determination, refinement, model building and validation. Keenan, Moffat, Adams, Rice, Crosson

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

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

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

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

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

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

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

Lectures on current research by departmental faculty and other invited speakers. A required course for all first-year graduate students. Staff

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. Arac-Ozkan, Perozo

BCMB students taking this course are also required to take the Workshop on X-ray Crystallography This one week workshop will provide students with an intensive introduction to protein structure determination by x-ray crystallography. In addition to lectures, an extensive laboratory component will give students the opportunity to carry out protein crystallization, data collection (at Argonne), structure determination, refinement, model building and validation. Keenan, Moffat, Adams, Rice, Crosson

This course will discuss in depth two major topics in protein science in biomedical sciences, protein misfolding and protein design. The class will examine milestone papers from the primary literature that cover important concepts and techniques for the topics. Koide, Meredith

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

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

The student participates in one of the research programs of the Department. Prereq: Consent of Department Chairman and individual faculty member. Staff

This course will examine the molecular principles of immune recognition. We will explore the roles of protein modification, protein-protein and protein-DNA interactions in the discrimination between self and non-self, and will study the molecular fundamentals of cell stimulation and signaling. Primary literature focused on molecular research of the immune system will be integrated with lectures on commonly used biochemical, structural and immunological techniques used in the research papers examined. Emphasis is placed on class participation. Prereq: BIOS 20200, BIOS 25256, or consent of instructor. Adams

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

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. Staley, Ruthenburg

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. Rock

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

 

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

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

The student participates in one of the research programs of the Department. Prereq: Consent of Department Chairman and individual faculty member. Staff

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 summer quarter. Roux

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

 

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. Koide, Sachleben

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

The student participates in one of the research programs of the Department. Prereq: Consent of Department Chairman and individual faculty member. Staff

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