Course Descriptions

(4cr.) Fall, Spring/Summer
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.
Fall Course Director: Dr. Jeanne Stuckey.  

(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 ([email protected])

(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 ([email protected])

(3cr.) Winter

This course provides skill set training and practical experience to prepare for and apply to future careers.  As an upper-level undergraduate course students will work to learn to critically read scientific literature and practice their presentation skills.  In addition, "Skills of a Scientist" includes exercises in writing, such as personal statements, research experience, and resumes for competitive review and successful admissions.  The course size is limited; please contact course director for permission to register.
Course Director:  Dr. Ruthann Nichols   ([email protected])

(4cr.) Fall & Winter
Course Content:
Biological Chemistry 415 provides a broad introduction to the fascinating field of biochemistry. This course is taught by medical school faculty and emphasizes the relevance of biochemistry to health, disease, physiology and medicine.  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. 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 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 four credit course with three, one hour lectures per week and 1 one-hour discussion session. Instructors hold weekly office hours and all instruction, including the Discussion Sessions, will be presented by faculty.   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.

Course Directors:  Dr. Alex Ninfa and Dr. Allison Lamanna

(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 Director: Dr. Neil Marsh

(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. Ray Trievel

(3cr.) Winter

This course provides skill set training and practical experience to prepare for and apply to future careers.  As a graduate course students will work to learn to critically read scientific literature and practice their presentation skills submit written reviews of the scientific literature.  In addition, "Skills of a Scientist" includes exercises in writing, such as personal statements, research experience, and resumes for competitive review and successful admissions.  The course size is limited; please contact course director for permission to register.

Course Director:  Dr. Ruthann Nichols   ([email protected])

(3cr.) Fall
This course will provide a high-level overview on the structure, function and biology of nucleic acids.  After gaining a high-level background in nucleic acid structure and their interactions with proteins, we will study important RNA-based biological processes, including pre-mRNA splicing, translation, RNAI and RNA decay.

We now realize that the human genome contains at least 80,000 non-redundant non-coding (nc)RNA genes, outnumbering protein-coding genes by at least 4-fold, a revolutionary insight that has led some researchers to dub the eukaryotic cell an “RNA machine”.  How exactly these ncRNAs guide every cellular function – from the maintenance and processing to the regulated expression of all genetic information – lies at the leading edge of the modern biosciences, from stem cell to cancer research. This course will provide an equally broad and deep overview of the structure, function and biology of DNA and particularly RNA. We will explore important examples from the current literature and the course content will evolve accordingly.  The class will be taught from a chemical/molecular perspective and will bring modern interdisciplinary concepts from biochemistry, biophysics and molecular biology to the fore.  Handouts and primary literature will be available on the Canvas course web site.

Prerequisites: Biochemistry survey course covering the fundamental principles of proteins and nucleic acids (equivalent to Chem 351, Biolchem 415, or MCDB 310).
Course Director:  Dr. Nils Walter

(4cr.) Fall & Winter
Course Content: 
Biological Chemistry 515 provides a broad introduction to the fascinating field of biochemistry. This course is taught by medical school faculty and emphasizes the relevance of biochemistry to health, disease, physiology and medicine.  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. 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 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 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 four credit course with three, one hour lectures per week and 1 one-hour discussion session.  Instructors hold weekly office hours throughout the semester. 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.

Course Director: Dr. Alex Ninfa

(3cr.) 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: Chemistry 525 or Biolchem 660 or Biolchem 515 or equivalent, and one semester of Organic Chemistry. Lecture.
Course Director: Dr. Neil Marsh

(2cr.) Fall and Winter
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 to the Medical Student (M1) curricula, while also allowing greater depth into areas of biochemistry that match the specific interest of the course faculty and students.   *Enrollment is limited to members of the Medical Scientist Training Program (MSTP).
Course Director: Dr. Patrick O'Brien

(3cr.) Winter
A course designed to help graduate students improve their skills in reading, analyzing, and discussing the biochemical literature.
Course Directors: Dr. Roland Kwok

(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 Director: Dr. Anne Vojtek
For Overrides email Course Administrator:  Beth Goodwin  ([email protected])

(4cr.) Fall

BIOLCHEM 601

This course focuses on learning to critically read and review the peer-reviewed scientific literature and communicate in presentations, applications, and interviews.  It is designed for MS students in the Biological Chemistry Department but welcomes MS students in other programs or upper-level undergraduates with permission of the Course Director.  BIOLCHEM 601 focuses on learning and practicing the tools needed to critically read and discuss, as well as write a review of the scientific literature.  It also covers communication skills relevant to research presentations, and post-graduate applications and interviews.

Format:  This is a discussion-based course in a small group setting, thus the enrollment is limited to 18 students.  Grading is based on class participation and assignments.

Course Director:  Dr. Ruthann Nichols

(3cr.) Winter (next offered Winter 2023)
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 Director: TBD

(1 Cr.) Fall and (3Cr.) Winter

This is an advanced literature analysis course in which each student will focus on an important area of current research, review the literature in that area in depth and then analyze this research thoroughly.  Each student will produce a concise and impactful review of the subject, complete with thoughtful suggestions for future directions, suitable for publication.  In the course of preparing the review, the student will become expert in the literature of the chosen area.

Each course track MS student will choose a member of the Biological Chemistry faculty to work with in the completion of the research review article.  This faculty mentor will also advise the course track student in the preparation of the Biochem 711 seminar and will incorporate the student in activities such as group meetings and seminars relating to the topic of the review article. Typically, the research area of the article will be an area highly related to the research of the faculty member.  Each student should meet weekly with the faculty mentor to identify key papers in the field, discuss the interpretation of specific experiments, understand the methodologies and outline the article.  The student will also meet monthly with either of the Master’s Program Directors to ensure that the written work is progressing in a satisfactory manner.  The final review article must be approved by the individual faculty mentor as well as a program director. A typical course track review article will be 25 double spaced pages, will include 25 references and will contain original intellectual contributions from the student including critical analysis of published experiments as well as originally designed proposed experiments for the future development of the field.

Advisory Prerequisite – Enrollment is intended/limited to course track Master’s students in the Biological Chemistry Department. 

Course Directors:  Dr. Michael Uhler and Dr. Debra Thompson

(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 Director: Dr. David Turner

(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. Ray Trievel and Dr. Dan Bochar

Fall 2021 Course Flier available below for download.

(3cr.) 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.

Advisory Prerequisites: Introductory biochemistry (Biolchem 415/515, 451, or equivalent), significant familiarity with protein structure, or by permission of the course director.
Course Director: Dr. Ryan Baldridge and Dr. Michael Cianfrocco

(3cr.)   Winter
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.
Advisory Prerequisite:  Chemical Biology 501 or its equivalent, undergraduate calculus. Physical chemistry is recommended. Lecture.
Course Director: Dr. Bruce Palfey

(2cr.)   Winter
This course will explore leading edge topics in the biochemistry and cell biology of eukaryotic membranes and organelles, focusing primarily on organelles of the secretory and endocytic pathways and interactions of those with non-secretory organelles such as the nucleus, plasma membrane, mitochondria and peroxisomes.  Brief lectures will provide context for critical reading and discussion of the literature.  Students will be expected to read 1-2 papers and one review per week, and to present and discuss background, experimental approaches, results and conclusions of the papers.  Students will be evaluated on the basis of oral presentations and short writing assignments. 

Advisory Prerequisite: Registration requires prior coursework in biochemistry and cell biology or permission of instructor. Material will be complementary to that covered in Biolchem 660.

This course is intended for graduate students (PhD and MS) but undergraduates with research experience will be considered.  Email [email protected] for an override/permission.

Course Directors: Dr. Roberta Fuller and Dr. Phyllis Hanson

(2cr.) Fall
This course will cover recent developments in biochemistry and molecular biology with relevance to human disease.  Short faculty lectures will be combined with in-depth discussion of research papers.  Planned topics include signaling pathways and oncogenes, biochemical mechanisms of inherited retinal degeneration and neural regeneration, modeling of biochemical mechanisms with human stem cells, and regulation of gene expression by microRNAs and chromatin modifications, among others. 

Intended Audience:  Graduate students or advanced undergraduates (with permission of instructor) with a wide range of interests in biochemistry and medicine.

Format:  This course is a literature based discussion with an emphasis on reading and analyzing primary research papers.  Grading is based on short, weekly problem sets, class participation, and a short in-class presentation at the end of the term.

Course Directors:  Dr. Anne Vojtek and Dr. Uhn-Soo Cho

(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 Director: Dr. Stephen Ragsdale (Fall and Winter)
Course Administrator:  Beth Goodwin ([email protected])

(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). 
Course Director: Dr. Anne Vojtek
Departmental Consent is Required, Email Course Administrator, Beth Goodwin ([email protected])

(1cr.) Fall*

This discussion-based class will explore cutting edge topics in RNA, CRISPR and Genome Editing Technologies via seminars and discussions with leading investigators in the fields. We will explore how interesting and novel combinations of questions, techniques, and systems drive key advances in biological chemistry. Students will participate in seminars, discussions, prepare via selected readings, and provide a short written reflection at the end of the semester. Some seminars and discussions will be in-person, others via Zoom. Check web calendar or Canvas course site for details.

Course Director:  Dr. Yan Zhang and Dr. Nils Walter
Seminars: 12:00 PM – 1:00 PM – Seminars
Discussions: 1:30 PM – 2:30 PM – Discussions

Seminars are open to the university community. Discussions are for registered students only.
*To register, email [email protected] for course permission.

(3cr.) Winter
This course provides an introduction to the principles and practical approaches of bioinformatics as applied to genes and proteins. The overall course content is broken down into sections focusing on foundational information, statistics, and systems biology, respectively. 
Course Director:  Dr. Peter Freddolino

(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: Dr. Yang Zhang

(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.

(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