Courses

Courses

Typically, graduate students in Biochemistry take several classes and two seminar courses each semester of their first year. These core courses are designed to develop the student’s ability to critically read and analyze literature, present literature and analysis orally, demonstrate firm grasp of conceptual foundations of modern biochemistry, and complete written term papers and/or exams.  Students customize their plan of study, with help from faculty advisors and their research mentors, choosing from a broad list of available courses in the biomedical science graduate curriculum. Students should complete a minimum of 24 hours of graded coursework (including a total of 8 units of Research Independent Study), as well as at least 6 hours of ungraded coursework, in the first 2 years of study. Note that students coming into the program from the MSTP or with an MA/MS degree may be exempt from the minimum graded coursework requirement.

 

Fall and Spring semester courses of particular interest to Biochemistry students are listed below.  For a current list of available classes each semester, visit the ACES Website.  

Selected Courses of Interest for Biochemistry Graduate Students:

BIOCHEM 593-01 - Independent Study  (2 units) Graded

Instructor:  DGS-Kuehn

Fall and Spring Semesters

Individual research by graduate students in a field of special interest under the supervision of a faculty member.  At the conclusion of rotation research projects, the student will present an oral report containing analysis and interpretation of a faculty mentor-approved topic. If in a thesis lab, the student will prepare ongoing oral and written analyses of the proposed project and accumulated results and interpretations.

 

BIOCHEM 658 - Structural Biochem I  (2 units) Graded

Instructor:  Beese

1st  ½ Fall Semester

Structure of Macromolecules - Principles of modern structural biology. Protein-nucleic acid recognition, enzymatic reactions, viruses, immunoglobulins, signal transduction, and structure-based drug design described in terms of the atomic properties of biological macromolecules. Discussion of methods of structure determination with particular emphasis on macromolecular X-ray crystallography NMR methods, homology modeling, and bioinformatics. Students use molecular graphics tutorials and Internet databases to view and analyze structures.

 

BIOCHEM 659 - Structural Biochem II  (2 units) Graded

Instructor:  Zhou

2nd ½ Fall Semester

Molecular Biology I - Continuation of BCH 658. Structure/function analysis of proteins as enzymes, kinetics of binding, catalysis and allostery, protein folding, stability and design protein-protein interactions. This is an introductory course to learn how to use quantitative methods to understand biological structure and function.

 

BIOCHEM 681 – Physical Biochemistry  (3 units) Graded

Instructor:  Oas

Fall Semester

A structure-based introduction to the role of thermodynamic driving forces in biology. An overview of experimental sources of structural and dynamic data, and a review of the fundamental concepts of thermodynamics. Both concepts are combined to achieve a structural and quantitative mechanistic understanding of allosteric regulation, and of coupled ligand binding and conformational change. Statistical thermodynamics is used to develop ensemble models of protein and nucleic acid dynamics. This treatment leads into specific examples and general principles of how to interpret structural and dynamic information toward the purposes of other research.

 

BIOCHEM 745S/746S - Biochemistry Seminar  (1 unit) Graded

Instructor:  Brennan

Fall/Spring Semester

Required of all first, second & third year biochemistry graduate students. The primary goal of this course is for students to learn how to orally present the background, data, conclusions and future prospects of their research clearly and concisely. First year students present rotation projects. Second and third year students present their research annually (in the fall or spring term), with students providing peer evaluations of each presenter.

 

BIOCHEM 790S - Seminar (Topics)  (2 units) Graded

Instructor:  Kuehn

Fall Semester

This discussion-based course includes introductory lectures and critical reading of primary literature on selected topics in Biochemistry. Topics and instructors announced each semester.  

 

BIOLOGY 701 – Succeeding in Graduate School in the Biological Sciences  (0.5 units) CR/NC

Instructor:  Noor

1st ½ Fall Semester

Weekly lecture and Q&A on choosing a thesis advisor, the grant proposal and scientific manuscript peer review processes, and other topics related to succeeding in graduate school. 

 

BIOLOGY 702 – Succeeding Beyond Graduate School - Career Options with a PhD in the Biological Sciences  (0.5 units) CR/NC

Instructor:  Noor

2nd ½ Fall Semester

Weekly lecture and Q&A on alternative careers in the biological sciences, preparing job applications, and other topics related to succeeding beyond graduate school. 

 

SBB 546S - Structural Biology and Biophysics Seminar (1 unit) Graded

Instructor:  Oas

Fall and Spring Semester

Each week a student presents a paper on their research. Attendance is open to all graduate students, faculty and postdoctoral students who have an interest in structural biology. Required of all SBB certificate students.

  

BIOCHEM 667 - Biochemical Genetics I  (2 units) Graded

Instructor:  Modrich

1st ½ Spring Semester

DNA and Genome Stability – Chromatin and chromosome structure, replication, repair, genetic recombination, mutation and chromosome rearrangement.

The major emphasis will be on reading and discussing primary research papers in depth.  The idea is to explore how new concepts have been developed in nucleic acids biology and biochemistry and what types of experiments have made advance possible. Each section of the course will consist of background lecture material presented by the faculty member, followed by several sessions to discuss papers selected by the faculty as paradigm papers. The students will present these papers orally using figures from the papers and explanatory background as needed. Students will be asked to prepare an 8-10 page research paper or an oral talk to demonstrate proficiency in the topics.

 

BIOCHEM 668 - Biochemical Genetics II  (2 units) Graded

Instructor:  Greenleaf

2nd ½ Spring Semester

RNA to Protein - Mechanisms of transcription, splicing, catalytic RNA, RNA editing, mRNA stability & translation.  Same format as BIOCHEM 667.

  

BIOCHEM 695 – Understanding NMR Spectroscopy  (4 units) Graded

Instructor:  Al-Hashimi

Spring Semester

Course aimed at graduate students who have some familiarity with high-resolution NMR who wish to deepen their understanding of how NMR experiments actually 'work'. Introduces quantum mechanical tools needed to understand pulse sequences, with emphasis on obtaining good understanding of how experiments actually work. Course also covers advanced biomolecular NMR experiments that enable structural and dynamic characterization of biomolecules. For roughly half of course, students will be expected to follow online lectures that accompany course textbook, with class meetings emphasizing concepts, group discussion, and problem solving.  Instructor consent required.

 

BIOCHEM 696 – Macromolecular crystallography  (4 Units)  

Instructor:  Schumacher and Staff

Spring Semester

Macromolecular structure determination by X-ray Crystallography: principles and practice – Theoretical and practical principles of macromolecular X-ray crystallography. Topics covered include crystal symmetry, space group theory and determination, diffraction theory, a practical understanding of crystallization, X-ray intensity data collection and data processing, phase determination, refinement and model validation

 

BIOCHEM 622 (SBB 622) - Structure of Biological Macromolecules  (3 Units)

Instructor:  Richardson

Spring Semester

How to get the most out of experimental and computational 3D structure: a) 3D Molecular Literacy:  Computer and physical molecular models of proteins and nucleic acids; worksheets and hands-on exploration. b) Data bases and the data itself: gaining familiarity with the PDB (Protein Data Bank) in general, the EDS (Electron Density Server), and the peculiarities, caveats, and reliabilities of different categories of molecular data. c) Computational methods for studying and depicting macromolecules: Model building in structural biology, Molprobity and all-atom contact analysis, and methodologies for multiple conformations, ensembles, and mobility. d) Student Projects: interactive 3D illustration of some scientific point about macromolecules, using kinemages or other molecular graphics programs often with short non-interactive introduction. Reports given at end of semester, progress shown periodically. Once a week in-class presentations, discussion, and hands-on work with physical and computer molecular models.  Homework includes worksheets and individual student projects.

 

BIOCHEM 536 (CHEM 536) - Bioorganic Chemistry  (4 Units) Graded

Instructor: McCafferty

Spring Semester

Basic enzymology, mechanisms of enzymatic reactions, cofactors, oxidoreductases, C1 chemistry, carbon-carbon bond formation, carboxylation/decarboxylation, heme, pyridoxal enzymes, thiamine enzymes.

 

BIOCHEM/CBI 761 (CELLBIO 761) - Cellular Signaling Module I: GPCR Signaling and Disease 

(1 Unit) Graded

Instructor:  Caron

First 1/3 Spring Semester

This module will cover the basic mechanism of signal transduction through G protein coupled receptors (GPCR) and how they control a wide array of biological functions from vison to reproduction and are the largest targets of therapeutic interventions. How new concepts in our understanding of their signal transduction mechanisms is leading to the development of new and improve therapies for various disorders.

 

BIOCHEM/CBI 762 (CELLBIO 762) - Cellular Signaling Module II: Intracellular Signaling and Disease  (1 Unit) Graded

Instructor:  McDonnell

Mid 1/3 Spring Semester

This module will cover how ion channels and intracellular nuclear receptors control cellular functions mediated through transcription or calcium signaling to regulate physiological processes in health and disease.

 

BIOCHEM/CBI 763 (CELLBIO 763) - Cellular Signaling Module III: Growth Factor Pathway in Development and Disease  (1 Unit) Graded

Instructor:  Pendergast

Last 1/3 Spring Semester

The focus of this module is on signaling pathways induced by extracellular factors that regulate growth, survival, and development, and their deregulation in disease including cancer. Among the pathways covered are those regulated by ligand-activated Receptor Tyrosine Kinases, Wnt/beta-catenin signaling, Notch signaling, and Hedgehog signaling.

 

Additional courses of interest offered by departments in the Biomedical Sciences:  A list of courses offered from departments in the Basic Sciences can be found on the School of Medicine Biomedical Graduate Education website and in the BCH Graduate Student Handbook.