Course Descriptions

BiolChem 212 Descriptive Biochemistry

(4cr.) Fall
A basic course in biochemistry that includes fundamental organic chemistry, biological information transfer processes, energy conservation metabolism, and special topics such as membrane transport and the biochemistry of vision. Intended for nurses and allied health professionals; open to others with permission of instructor. Lecture and discussion.
Course Director: Dr. Jeanne Stuckey

BiolChem  298 Biochemistry - Undergraduate Research in Biological Chemistry

(1-4cr.) Fall, Winter, Spring/Summer; (1-2) Spring Half, Summer Half
Undergraduate research in Biochemistry - Independent undergraduate research for students with freshman or sophomore standing, and permission of Biological chemistry Faculty Member who will supervise the research. May be repeated for a maximum of 4 credits.
Course Director/Advisor: Dr. Ruthann Nichols & Dr. Mark Saper
Course Administrator: Amanda Howard (amanhowa@umich.edu)

BiolChem 398 Biochemistry - Undergraduate Research in Chemistry, Biological Chemistry, Biology, and Biophysics

(1-4cr.) Fall, Winter, Spring/Summer (1-2) Spring Half, Summer Half
For undergraduates who are in the Biochemistry Concentration Program.
Prerequisites: BIOLCHEM 451/452 and permission of instructor. Undergraduate Research in Biochemistry - Independent undergraduate research in biochemistry for students with junior standing or above, and with permission of the Biological Chemistry professor who will supervise the research. May be repeated for a maximum of 4 credits.
Course Director/Advisor: Dr. Ruthann Nichols & Dr. Mark Saper
Course Administrator: Amanda Howard (amanhowa@umich.edu)

BiolChem 415 Introductory Biochemistry 

(3cr.) Fall & Winter
Course Content:
Biological Chemistry 415 provides a broad introduction to the fascinating field of biochemistry. Students will explore the molecular basis and chemical principles pertinent to living systems, including eukaryotes, bacteria, and viruses. The structures and functions of the four major molecules of life (proteins, lipids, carbohydrates, and nucleic acids) and their biosynthetic pathways will be examined. Students will learn the fundamental biological processes including energetics, metabolism, protein structure and enzyme function. The transmission of information within and between cells will be studied including signal transduction and the genetic processes of replication, transcription, and translation. Students will also learn the biochemical roles of vitamins, enzyme cofactors, hormones, drugs, antibiotics, and toxins. This course is taught by medical school faculty and emphasizes the relevance of biochemistry to health, disease, physiology and medicine. The biochemical basis of several diseases will be explored including cancer, diabetes, neurodegenerative disorders, infectious diseases, and metabolic and genetic syndromes. In all of these topics, we stress the integration of metabolism and the various modes of regulation that are vital to biological processes and physiology. Techniques and technologies used to study biochemistry and their relevance to understanding biology will be illustrated.

Intended Audience:
This course is designed to provide a broad survey of biochemistry in one semester for students with a wide range of backgrounds. Biological Chemistry 415 is an excellent preparation for undergraduate students considering careers in biochemistry, medicine, genetics, dentistry, pharmacy, medicinal chemistry, nutrition, public health, bioengineering, environmental studies, and other healthcare-related fields.

Biological Chemistry 515 is the graduate version of this course that includes a research analysis component. Graduate students are required to register for Biological Chemistry 515 and to write an analysis of a primary research paper to receive graduate level credit. Any graduate student who has incorrectly registered for Biological Chemistry 415 should make the correction in enrollment as soon as possible.

*No credit is granted to students who have completed MCDB 310 or CHEM 351 OR BIOLCHEM 451 or 452.

Class Format:
This is a three credit course with three, one hour lectures per week. To enhance learning, a two hour discussion session is offered each week. Instructors hold weekly office hours throughout the semester. Teaching assistants are available to help students learn the material. Learning is enhanced through multiple activities including lectures, online videos and learning aides, discussions, and active learning exercises. Students are provided with the lecture slides as well as BlueReview audio and video recordings of the lectures. Problem sets and discussions facilitate learning and enhance test-taking skills.

Course Requirements:
Grading is based on midterm exams. For Biological Chemistry 415, students also receive credit for completion of weekly problem sets.

Textbook:
Biochemistry, a Short Course, by Tymoczko, Berg, and Stryer. Third Edition. 2015.

Syllabus:
A current draft of the BiolChem 415 syllabus is available for download at the bottom of this webpage.

Course Directors:  Dr. Alex Ninfa (Fall) and Dr. Ray Trievel (Winter)

BiolChem 451 Advanced Biochemistry I

(4cr.) Fall
A rigorous introduction to biochemistry with a chemical emphasis. Designed for undergraduates in the Biochemistry Concentration Program but open to graduate students with a strong background in chemistry. Prerequisites: Chem 215, Biol. 152 or 195, and Math 115. No credit granted to those who have completed or are enrolled in Biol. 310 or 311 or Biol. Chem. 415. Lecture.
Course Directors: Dr. Neil Marsh and Dr. Nils Walter

BiolChem 452 Advanced Biochemistry II

(4cr.) Winter

A continuation of Biochemistry 451 which is a prerequisite. Advanced Biochemistry: Cellular Processes --- This course focuses on the biochemistry of fundamental cellular processes. Topics include mechanisms for the integration of metabolism in both bacterial cells and in multicellular organisms, the process of gene expression focusing on the biochemistry of gene transcription, and mRNA translation. It generally emphasizes chemistry and enzymology of metabolic transformations, enzyme reaction mechanisms, and protein and nucleic acid structure and function.
Course Director: Dr. Alex Ninfa

BiolChem 501 Chemical Biology I

(3cr.) Fall
This course will provide a high-level overview on the structure, function and chemistry of biological macromolecules including proteins, nucleic acids and carbohydrates. Topics include protein and nucleic acid folding, energetics of macromolecular interactions (kinetics and thermodynamics), and mechanistic enzymology. Using specific examples from the current literature, each topic will stress how chemists have used molecular level tools and probes to help understand the specific systems under study. The over arching theme in this course will be that structure and function are intimately linked. Prerequisites: None.
Course Faculty: Dr. Bruce Palfey

BiolChem 502 Chemical Biology II

(3cr.) Winter
This course is a continuation of Chemical Biology 501. The basic concepts obtained in Chemical Biology 501 will be applied to and demonstrated in three broad areas of interest to both chemists and biologists. The first topic will discuss combinatorial methods including SELEX and gene shuffling, combinatorial organic synthesis, high throughput screening and chemical genetics. The second topic will focus on signal transduction, emphasizing general concepts (at the molecular level) and how small molecules have been used to probe and modulate signal transduction pathways. The final topic will cover protein translation, stressing mechanistic aspects of protein synthesis and folding in vivo. Prerequisites: BIOLCHEM 501 (Chemical Biology I) is recommended.

Course Director: Dr. Zaneta Nikolovska-Coleska & Dr. David Sherman

BiolChem/Micrbiol 504 Cellular Biotechnology

(3cr.) Winter
Cellular Biotechnology. Provides an overview and integration of six disciplinary foci: cell biology and culture ecology and evolution molecular genetics and protein engineering bioseparation and processing biosensing and analysis cellular modeling, prediction, and control.
Course Director:  Andrew Putnum

BiolChem 515 Introductory Biochemistry

(3cr.) Fall & Winter

Course Content:
Biological Chemistry 515 provides a broad introduction to the fascinating field of biochemistry. Students will explore the molecular basis and chemical principles pertinent to living systems, including eukaryotes, bacteria, and viruses. The structures and functions of the four major molecules of life (proteins, lipids, carbohydrates, and nucleic acids) and their biosynthetic pathways will be examined. Students will learn the fundamental biological processes including energetics, metabolism, protein structure and enzyme function. The transmission of information within and between cells will be studied including signal transduction and the genetic processes of replication, transcription, and translation. Students will also learn the biochemical roles of vitamins, enzyme cofactors, hormones, drugs, antibiotics, and toxins. This course is taught by medical school faculty and emphasizes the relevance of biochemistry to health, disease, physiology and medicine. The biochemical basis of several diseases will be explored including cancer, diabetes, neurodegenerative disorders, infectious diseases, and metabolic and genetic syndromes. In all of these topics, we stress the integration of metabolism and the various modes of regulation that are vital to biological processes and physiology. Techniques and technologies used to study biochemistry and their relevance to understanding biology will be illustrated.

Intended Audience:
This course is designed to provide a broad survey of biochemistry in one semester for graduate students with a wide range of backgrounds. Biological Chemistry 515 is an excellent preparation for students considering careers in biochemistry, molecular and cellular biology, medicine, genetics, dentistry, pharmacy, medicinal chemistry, nutrition, public health, bioengineering, environmental studies, and other healthcare-related fields.
Biological Chemistry 515 is the graduate version of Biological Chemistry 415 that includes an additional research analysis component. Graduate students are required to register for Biological Chemistry 515 and to write an analysis of a primary research paper to receive graduate level credit. Any graduate student who has incorrectly registered for Biological Chemistry 415 should make the correction in enrollment as soon as possible.
No credit is granted to students who have completed MCDB 310 or CHEM 351, CHEM451

Class Format:
This is a three credit course with three, one hour lectures per week. To enhance learning, a two hour discussion session is offered each week. Instructors hold weekly office hours throughout the semester. Teaching assistants are available to help students learn the material. Learning is enhanced through multiple activities including lectures, online videos and learning aides, discussions, and active learning exercises. Students are provided with the lecture slides as well as BlueReview audio and video recordings of the lectures. Problem sets and discussions facilitate learning and enhance test-taking skills.

Course Requirements:
Grading is based on midterm exams. Biological Chemistry 515 students also write a research paper for credit.

Textbook:
Biochemistry, a Short Course, by Tymoczko, Berg, and Stryer. Third Edition. 2015.

Syllabus:
A current draft of the BiolChem 515 syllabus is available for download at the bottom of this webpage.

Course Directors: Dr. Alex Ninfa (Fall) and Dr. Ray Trievel (Winter)

BiolChem 528 Biology and Chemistry of Enzymes

(2cr.) Winter (Half Semester - First Half)
This course will cover the chemical and catalytic mechanisms of enzyme-catalyzed reactions, with an emphasis on organic and organometallic cofactors in biology and mechanisms of group transfer reactions, redox reactions, rearrangements, decarboxylations, carboxylations, and methylation. Prerequisites: Biological Chemistry 550, Chemical Biology 501 or their equivalent, and one semester of Organic Chemistry. Lecture.
Course Director: Dr. Neil Marsh

BiolChem 530 Protein-protein and protein-ligand interactions by NMR (Not offered Fall 2016)

(3cr.) Fall
The course focuses on solution NMR spectroscopy. The first 30% provides an intuitive background for techniques such as HSQC and saturation transfer. The subsequent 70% concentrates on the interpretation of chemical shift mapping and SAR by NMR. The advantages, disadvantages and limits of the techniques are discussed.
Course Director: Dr. Eric Zuiderweg

BiolChem 551 Proteomics and Informatics

(3cr.) Fall Term

Introduction to proteomics, mass spectrometry, peptide identification and protein inference, statistical methods and computational algorithms, post-translational modifications, genome annotation and alternative splicing, quantitative proteomics and differential protein expression analysis, protein-protein interaction networks and protein complexes, data mining and analysis of large-scale data sets, clinical applications, related technologies such as metabolomics and protein arrays, data integration and systems biology.

Course Director:  Alexey I. Nesvizhskii

BiolChem 552 Biochemistry for Medical Students (MSTP*)

(3cr.) Fall
Macromolecular Structure and Function. Advanced course focusing on the critical analysis of seminal publications in the field of biochemistry. A discussion format is used to expand on ideas presented in the Medical Scientist (M1) curricula, while also allowing greater depth into areas of biochemistry that match the specific interests of the course faculty and students. Discussion. *Enrollment is limited to members of the Medical Scientist Training Program (MSTP).
Course Directors: Dr. Patrick O'Brien and Dr. Yiorgo Skiniotis

BiolChem 591 Special Topics in Signal Transduction

(2cr.) Fall
A literature based discussion course that will cover both seminal discoveries in signal transduction as well as recent advances in the field. The course will meet once per week for two hours, throughout the semester. Two research papers will be discussed each week. Grading is based on short weekly problem sets and a presentation by each student. Prior course work in biochemistry and cell biology is strongly encouraged. Lecture/Discussion.
Course Director: Dr. Lei Yin

[See downloaded documents at the bottom of this webpage for more detailed information]

BiolChem 597 Critical Analysis

(2cr.) Winter
A course designed to help first-year graduate students in the Ph.D. program improve their skills in reading, analyzing, discussing, and writing about the biochemical literature.
Course Director: Dr. Roland Kwok

BiolChem 600 Introduction to Biochemical Research

(6-8cr.) Fall and Winter
Intensive independent study laboratory course for first-year biochemistry M.S. and Ph.D. students. Laboratory. Permission of Instructor.
Course Directors: Dr. Anne Vojtek and Dr. Mike Uhler

BiolChem/Biophys 602 Protein Crystallography

(3cr.) Winter
Protein Crystallography: Principles of Macromolecular Crystallography --- Fundamental of the methods for determining 3-dimensional structures of large molecules by x-ray crystallography. Aimed at students who expect to use crystallography as a major tool for their research, and at those who want in-depth knowledge of the methods in order to analyze structure data.
Course Directors: Dr John Tesmer

BiolChem 640 Regulatory RNA and Control of Gene Expression

(2cr.) Winter

Course content: RNA-based mechanisms are now recognized as key regulators in biology and disease. Most mammalian genes are regulated by noncoding RNAs (e.g. microRNAs, long noncoding RNAs, piRNAs), and/or RNA-binding proteins. RNA-based mechanisms control protein translation, RNA stability, and transcription. Disruptions of these mechanisms contribute to human diseases, including cancer, neurological disorders, and cardiovascular diseases; RNA-mediated processes also are critical for stem cells and development. RNA-based techniques, such as RNA interference and CRISPR genomic modifications, are widely used as research tools to study gene function and biological processes. BiolChem 640 will cover these and related aspects of RNA-mediated control of gene expression. 

Intended audience: BiolChem 640 is intended for graduate students or advanced undergraduates with a wide range of interests in biochemistry, biology, or medicine. RNA regulation impacts almost every area of biology now, and the material covered in class will include both mechanistic and functional analyses. This class also provides writing and presentation experience, which is valuable preparation for graduate prelims or fellowship writing!

Format: This course is a literature-based discussion; we read and analyze primary research papers each week. Grading is based on short weekly problem sets, class participation, and a short research proposal presented in class at the end of the term.

Course Directors: Dr. David Turner and Dr. Dan Goldman

BiolChem 650 Eukaryotic Gene Transcription

(2cr.) Fall

The course will focus on recent discoveries concerning the regulation of eukaryotic gene transcription, including transcription complex architectures, chromatin organization and modifications, mechanisms of epigenetic inheritance and genome-wide functions of transcription regulatory factors.  The course will be taught through a combination of lectures and discussions of current literature. 

Course Director: Dr. Tom Kerppola

[See downloaded documents at the bottom of this webpage for more detailed information]

BiolChem 660 Molecules of life: Protein structure, function and dynamics

(2cr.) Fall

This is a literature-based course that will introduce select biological systems to illustrate how modern protein biochemistry advances our understanding of biological mechanisms. Topics include protein structure, function and dynamics; protein folding/misfolding and how this relates to disease; and the impact modification, processing, and trafficking has on protein function.

Course Director: Dr. Phil Andrews

[See downloaded documents at the bottom of this webpage for more detailed information]

BiolChem 673 Kinetics and Mechanism

(2cr.) Winter (Half Semester - Second Half)
This course will cover the investigation of enzyme mechanisms with an emphasis on ligand binding to macromolecules, transient kinetics, steady-state kinetics, and inhibition. The kinetic and thermodynamic concepts that govern the action of enzymes will be explored.
Prerequisites: Biological Chemistry 550, Chemical Biology 501,or their equivalent, undergraduate calculus. Physical chemistry is recommended. Lecture.
Course Director: Dr. Bruce Palfey

BiolChem 711 Graduate Seminar

(1cr.) Fall and (1cr.) Winter
Two-term course designed to provide experience in evaluating research in biochemistry by preparation and presentation of a seminar based on the student's critical and in-depth study of an original paper from the literature. The presentation is evaluated by the course staff, expert faculty, and fellow students.
Prerequisites: Permission of instructor. Seminar.
Course Directors: Dr. Uhn-Soo Cho, Dr. Stephen Ragsdale, Dr. Ursula Jakobs (Fall) and Dr. Stefanie Galban (Winter)

BiolChem 712 Biological Chemistry Seminar Series

(1cr.) Fall and (1cr.) Winter
Students participate in a weekly seminar series featuring outside speakers of international reputation.  These seminars, along with special lectureships held throughout the year, highlight a broad spectrum of topics including structural biology, protein biochemistry, enzyme reaction mechanisms, molecular genetics, signal transduction, neurobiology, and cell and developmental biology. 
Prerequisites: Enrollment is limited to graduate students in Biological Chemistry and the Program in Biomedical Sciences (PIBS).  Departmental Consent is required (email egoodwin@umich.edu).
Course Director: Dr. Anne Vojtek

Bioinf 528 Advanced Applications of Bioinformatics 

(3cr.) Fall This course introduces fundamental concepts and methods for bioinformatics and the advanced applications. The topics covered include bioinformatics databases, sequence and structure alignment methods, Monte Carlo simulation methods, protein folding and protein structure prediction methods, and modeling of protein-protein interactions. Emphasis is placed on the understanding of the concepts taught and on their practical utilization, with the objective of helping students use the bioinformatics tools to solve problems in their own research.
Course Director: Yang Zhang

CDB 530 Cell Biology CDB

(3cr.) Fall

This graduate course is designed to present basic information as well as the most recent developments in key areas of cell biology, including membranes, protein synthesis, folding and trafficking, epithelial polarity, cytoskeleton, cell-cell and cell-substrate interactions, and signal transduction. Participating faculty are drawn from various campus and medical school departments and provide lectures in areas of their expertise. Lecturers are encouraged to provide a part of the lecture material in the context of actual experiments so that students are exposed to current experimental approaches in cell biology, as well as basic information. In addition to a highly recommended cell biology textbook, reading lists are provided, and 1-2 papers are generally put on reserve in the library for each lecture. Students will be expected to demonstrate their knowledge of course material by examinations.
Course Director: Dr. Billy Tsai.

HumGen 541 Molecular Genetics 

(3cr.) Fall

This course explores how the information content of the DNA genome is (i) organized, propagated, and altered, and (ii) functionally expressed by regulated transcription into RNA – the core molecular properties and processes of genetic systems that underlie all further investigations of organismal, clinical, and population genetics. As a graduate level course, it is expected that students will enter HG 541 with a basic understanding of the nature of biological systems, DNA, RNA, replication, and transcription. HG 541 will focus on developing an advanced modern understanding of these molecules and reactions. We will explore what experimental research in model organisms and humans has taught us about the molecular encoding of genetic information while simultaneously exposing gaps in our understanding. Throughout, attention will be given to newer genome-wide analysis methods that are dramatically increasing our understanding of the extent of genetic variation and the many modes of gene expression. Also, students will be introduced to recombinant DNA technologies as one important way that molecular genetic insight is reduced to practice in biological research. Upon completion of HG 541, students will appreciate the directions research in molecular genetics is heading and be able to draw on this insight as they pursue further studies and research in diverse areas of genetics and biology.
Course Director: Dr. Thomas E. Wilson