Biochemistry Courses

100 Level  |  200 Level  |  300 Level  |  500 Level  |  600 Level  |  700 Level  |  800 Level  |  900 Level


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100 FRESHMAN BIOCHEMISTRY SEMINAR

Fall, Spring; 1 cr. The Freshman Biochemistry Seminar will introduce freshman to the discipline of biochemistry, to the UW Biochemistry Department, to some of the research projects the faculty are pursuing, to the University, and to the career options open to an individual with a biochemistry undergraduate degree. Freshmen only. Lisa Lenertz and Lynne Prost

104 MOLECULAR MECHANISMS, HUMAN HEALTH and YOU

Fall, Spring; 3 cr. Students in the course will be introduced to the fundamentals of genetics and evolution, and with this foundation we will discuss "big-picture issues" in public health and epidemiology. Specifically, we will discuss the building blocks of the cell, how information is processed from DNA into protein, and how cellular processes are regulated. Current and medically relevant topics such as cancer, inflammation, infections, depression and drug addiction will provide the framework for further discussion of topics such as the regulation of gene expression and cellular metabolism. A major goal of this course is for students to learn about their own health and to be able to explore and question science articles they find in the mainstream media. This course is intended for students not majoring in the life sciences.
Richard Amasino and Lisa Lenertz

289 HONORS INDEPENDENT STUDY

Fall, Spring; 1-2 cr. Prerequisites: Enrolled in the CALS Honors Program and Sophomore or Junior standing, Inter-Ag. 288.

299 INDEPENDENT STUDY

Fall, Spring; 1-3 cr. Freshman, Sophomore, and Junior students who have the written consent of the instructor may carry Independent Study (299) for a maximum of 3 cr. per semester in Ag. and Life Sciences only. The student must arrange with the faculty member a study plan, the time and place of periodic meetings, the scope of the project, and the number of credits to be earned. Independent Study credits may not ordinarily be used to satisfy basic course requirements, but may be used to meet elective credits. No more than 6 credits of Independent Study may be counted toward credit for graduation. Prerequisites: Freshman, Sophomore, or Junior standing and written consent of instructor. For more information and Independent Study Agreement Form click here

399 COORDINATIVE INTERNSHIP

Fall, Spring; 1-8 cr. The Coordinative Internship is to be an organized, sequential, primarily off-campus learning experience for students, which follows some instruction on campus. Consult the Associate Dean for Resident Instruction, College of Agricultural and Life Sciences for details. Prerequisites: Sophomore, Junior, or Senior standing and consent of supervising instructor, adviser, and internship program coordinator.

501 INTRODUCTION TO BIOCHEMISTRY

Fall, Spring; 3 cr. Chemistry, nutrition, and metabolism of biological systems. Not accepted toward departmental major for M.S. or Ph.D. degrees. Prerequisites: Chemistry 341 or 343. Available in-class or online. [Sample Syllabus] Richard Amasino, Samuel Butcher, Lisa Lenertz, and Jill Wildonger (teaches fall only)

507 GENERAL BIOCHEMISTRY 1

Fall; 3 cr. Chemistry of biological materials, intermediary metabolism, and protein structure. First semester of a year-long course in Biochemistry; Biochemistry 508 is offered in the spring. The course is designed and recommended for undergraduate Biochemistry majors, but others are welcome. Prerequisite: Chemistry 345. Honors credits available with consent of instructor. [Sample Syllabus] Michael Cox and Aaron Hoskins

508 GENERAL BIOCHEMISTRY 2

Spring; 3 cr. Biosynthesis of biological molecules, signal transduction mechanisms, chemistry and metabolism of nucleic acids, protein synthesis, and molecular and cellular biology. Prerequisite: A grade of BC or higher in Biochem 507, or consent of instructor. Honors credits available with consent of instructor. [Sample Syllabus]  Sebastian Bednarek and David Pagliarini

510 BIOCHEMICAL PRINCIPLES OF HUMAN AND ANIMAL NUTRITION (Also Nutri Sci 510)

Fall, Spring; 3 cr. Lectures in nutrition for students with a substantial background in biochemistry. Emphasis on biochemical and physiological fundamentals of nutrition. Discussion of protein, fat, carbohydrate, energy, minerals, and vitamins and their roles and interrelationships in nutrition and metabolism. Prerequisites: BMC 314 or 504; Biochem 501 or 507; or consent of instructor. [Sample Syllabus] David Eide, Susan Marie Smith (Fall), Roger Sunde (Spring)

550 TOPICS IN MEDICAL BIOCHEMISTRY

Spring; 2 cr. Lectures. Biochemical and molecular analysis of selected human diseases. Topics will include lipid metabolism and atherosclerosis, cell cycle regulation and oncogene function in cancer, and human immunodeficiency virus (HIV) structure, life cycle, and mechanism of acquired immunodeficiency disease syndrome (AIDS).  Prerequisites: Biochem 501, 507, or consent of instructor . [Sample Syllabus] Colleen Hayes

575 BIOLOGY OF VIRUSES

Spring; 2 cr. Lectures and discussions. Broad coverage of animal virology taught at molecular level. Topics include virus structure, viral replication/lifecycle, aspects of pathogenesis and prevention. Prerequisite: Biocore 301/302, or AP score of 4 or 5 and Zoology 151 or 152; or MM&I 301. [Sample Syllabus] Paul Friesen and Andrew Mehle

601 PROTEIN AND ENZYME STRUCTURE AND FUNCTION

Fall; 2 cr. Protein structure and dynamics. Protein folding. Physical organic chemistry of enzymatic catalysis. Analysis of enzyme kinetics and receptor-ligand interactions. Enzymatic reaction mechanisms. Prerequisites: Biochem 501 or equivalent, 1 semester of physical chemistry, 1 year of organic chemistry, and consent of instructor. [Sample Syllabus] Hazel Holden and Ivan Rayment

606 MATHEMATICAL METHODS FOR STRUCTURAL BIOLOGY (Also Math/BMI/BMC 606)

Fall, even years; 3 cr. Intended to provide a rigorous foundation for mathematical modeling of biological structures. Mathematical techniques include ordinary and partial differential equations, 3D Fourier analysis and optimization. Biological applications include protein folding, molecular dynamics, implicit solvent electrostatics, and molecular interactions. Prerequisites: Math 340 or 341; Comp Sci 302; or consent of instructor. Julie Mitchell

609 MATHEMATICAL METHODS FOR SYSTEMS BIOLOGY (Also Math/BMI/BMC 609)

Spring, even years; 3 cr. Intended to provide a rigorous foundation for mathematical modeling of biological systems. Mathematical techniques include dynamical systems and differential equations. Applications to biological pathways, including understanding of bistability within chemical reaction systems, are emphasized. Prerequisites: Math 340 or 341; Math 415; or consent of instructor. Gheorghe Craciun

612 PROKARYOTIC MOLECULAR BIOLOGY (Also Microbio/Genetics 612)

Fall; 3 cr. Molecular basis of bacterial physiology and genetics with emphasis on molecular mechanisms; topics include nucleic acid-protein interactions, transcription, translation, replication, recombination, regulation of gene expression. Prerequisites: Micro 470 or equivalent, and Biochem 501 or equivalent; or consent of instructor. Richard Gourse, James Keck and Robert Landick

619 ADVANCED NUTRITION: INTERMEDIARY METABOLISM OF MACRONUTRIENTS (Also Nutri Sci 619)

Spring; 3 cr. Discuss metabolic control; gastrointestinal physiology; nutrient absorption; molecular, cellular, organismal aspects of glucose transport, metabolism, regulation; fuel sensing; molecular regulation of fatty acid, lipid metabolism; cellular, organismal aspects of protein metabolism; hormonal control of metabolism; experimental approaches for studying metabolism. James Ntambi and Richard Eisenstein

620 EUKARYOTIC MOLECULAR BIOLOGY (Also CRB 620)

Spring; 2 cr. This course focuses on the basic molecular mechanisms that regulate DNA, RNA, and protein metabolism in eukaryotic organisms. The course is intended for advanced undergrads and first year graduate students with a firm knowledge of basic biochemistry. Prerequisites: Biochem 508 or equivalent. [Sample Syllabus] Aseem Ansari and David Wassarman

621 PLANT BIOCHEMISTRY (Also Botany 621)

Spring, odd years; 3 cr. Lectures. Biochemistry of photosynthesis, respiration, cell walls, and other metabolic and biosynthetic processes in plants. Prerequisites: Biochem 501 or 507 or consent of instructor. [Sample Syllabus] Sebastian Bednarek, John Ralph and Hiroshi Maeda

625 COENZYMES AND COFACTORS IN ENZYMOLOGY

Spring; 2 cr. Course will emphasize the importance of coenzyme and cofactors of enzymes in biochemistry. All aspects of the biochemistry of coenzymes will be covered, including their biosynthesis as far as is known, the biochemical reactions they catalyze, their chemical and spectroscopic properties, and the mechanisms by which they facilitate biochemical reactions. Prerequisites: Chemistry 343 and 345 or equivalent, and Biochem 501 or equivalent, and Chemistry 561 or 565 or equivalent (may be taken concurrently). Brian Fox

630 CELLULAR SIGNAL TRANSDUCTION MECHANISMS (Also Phmacol-m/ Zoology 630)

Fall; 3 cr. Lecture-discussion. Comprehensive coverage of human hormones, growth factors and other mediators; emphasis on hormone and growth factor action in cytoplasm and nucleus and biosynthesis. Prerequisites: Introductory biochemistry (Biochem 501 or 507 & 508) and cell biology (Biocore 303 or Zool 570 or Path750) or consent of instructor. [Sample Syllabus] Thomas Martin, Arnold Ruoho, Beth Weaver, Richard Anderson, Shigeki Miyamoto, and Emery Bresnick

651 BIOCHEMICAL METHODS

Fall, Spring, 3 cr. Lab and student seminar. Introduction to modern biochemical laboratory techniques and current biochemical literature. Students will present a seminar based upon scientific literature that parallels experiments they will perform in lab. For advanced undergraduates and non-biochemistry graduate students.  Prerequisite:  Biochem 501 or 507. [Sample Syllabus] Alessandro Senes (Fall), Douglas Weibel (Spring; on sabbatical Spring 2015), and Lynne Prost

660 BIOCHEMICAL TECHNIQUES

Fall; 2 cr. Survey of modern techniques in molecular biology and biochemistry. Prerequisites: 2 semesters of organic chemistry, and intermediate or advanced biochemistry / molecular biology, and consent of instructor. Marvin Wickens and Ann Palmenberg

665 BIOPHYSICAL CHEMISTRY (Also Chem 665)

Fall, Spring odd years; 4 cr. Taught together with the advanced (honors) undergraduate course Chemistry 565, this course develops the principles of solution thermodynamics and chemical kinetics, and applies this quantitative framework to discuss experimental data and analysis of the thermodynamics (driving forces, coupled conformational changes, etc.) and mechanisms of biochemical processes involving proteins, lipids, and nucleic acids in solution. Applications include protein folding, nucleic acid helix formation, micelle formation; ligand binding, cooperative binding and other assembly processes; effects of water, salts, other solutes, temperature and pressure on biochemical processes; protein-nucleic acid interactions and enzyme catalysis. Weekly problem sets develop these applications. Typical Fall semester enrollment is 20 – 25 graduate students and 75 – 85 undergraduate students. Students in this course are expected to have some previous background in physical chemistry as well as the Chem 565 prerequisites. Tom Record (Fall), Silvia Cavagnero or James Weissbaar (Alternating Spring)

681/682 SENIOR HONORS THESIS (For Honors Biochemistry majors only) 

Fall, Spring; 3 cr. Prerequisites: Senior standing and consent of instructor.

691/692 SENIOR THESIS

Fall, Spring; 2 cr. Prerequisites: Senior standing and consent of instructor. 

699 SPECIAL PROBLEMS

Fall, Spring; 1-4 cr. Prerequisites: Senior standing and consent of instructor. For more information and Independent Study Agreement Form click here

701 PROFESSIONAL RESPONSIBILITY (Also BMC 701)

Fall; 1 cr. Training for the practical aspects of being a scientist. Will cover ethics, peer review, grant writing, science communication, career alternatives, paper writing, experimental design, research documentation, science funding, academic-private interface, scientific fraud, and more. Prerequisite: Admission to IPiB or the Biophysics graduate program. [Sample Syllabus] Michael Cox

704 CHEMICAL BIOLOGY (Also Chem 704)

Fall; 2 cr. Structure and function of proteins, nucleic acids and carbohydrates; application of organic chemistry to problems in cell biology, biotechnology, and biomedicine. Prerequisites: Biochem 501 or equivalent, 1 year of organic chemistry and consent of instructor. Laura Kiessling and Ronald Raines

726 REGULATION OF GENE EXPRESSION IN PROKARYOTES (Also Micro 726)

Spring odd-years; 3cr. An intensive examination of a limited number of systems to illustrate the range of molecular mechanisms utilized to control gene expression in bacteria. Prerequisites: Micro/Genetics/Biochem 612 or consent of instructor. Robert Landick

729 ADVANCED TOPICS (Also BMC 901)

Fall, Spring; 1 cr. IPiB Seminar. Fourth and Fifth Year IPiB Students or consent of instructor. Margaret Clagett-Dame and Alessandro Senes; Catherine Fox (alternating years)

729 ADVANCED TOPICS

Fall, Spring; 1 cr. Practicum in Undergraduate Teaching. Prerequisite: consent of instructor. Alessandro Senes (Fall), Douglas Weibel (Spring; on sabbatical Spring 2015) and Lynne Prost

729 ADVANCED TOPICS

Spring; 3 cr. Molecular Control of Metabolism and Metabolic Disease. Mammals go through fast-feed cycles. This requires adjustments in fuel utilization and in the regulation of metabolic pathways. The course examines the various physiological states and how they affect metabolic pathways. We discuss a number of special topics related to the unique roles of various tissues and to metabolic pathways in disease states. Prerequisite: Consent of instructor. Alan Attie, Rozalyn Anderson, Dudley Lamming, Melkam Kebede, and Sushant Bhatnagar

729 ADVANCED TOPICS

Fall; 1 cr. Single Molecule Approaches to Biology. A combination of recent literature and original research presentations relating to the use of single molecule techniques in biochemistry including fluorescence microscopy, tethered particle motion, patch-clamping, cryo-electron microscopy, optical trapping, magnetic tweezers, and super resolution microscopy. Aaron Hoskins and James Weisshaar

799 PRACTICUM IN BIOCHEMISTRY TEACHING

Fall, Spring; 1-3 cr. Training and practice in instruction in biochemistry and molecular biology. Prerequisite: Graduate standing and consent of instructor. Marv Wickens

800 PRACTICAL NUCLEAR MAGNETIC RESONANCE THEORY

Fall; 2 cr. Lectures. Multiple pulse NMR, off-resonance effects, composite and shaped pulses, product operators, coherence transfer, multi-dimensional NMR, phase cycling, multiple quantum coherence, and cross relaxation. Prerequisite: Consent of instructor. [Web site] Milo Westler

801 BIOCHEMICAL APPLICATIONS OF NUCLEAR MAGNETIC RESONANCE

Spring; 2 cr. Lectures. Survey of current solution-state nuclear magnetic resonance techniques used in biochemical research; the emphasis will be on how data are acquired and on practical applications. Prerequisite: Consent of instructor. [Sample Syllabus] John Markley

840 REGULATORY MECHANISMS IN PLANT DEVELOPMENT (Also Botany/Genetics 840)

Fall, even years; 3 cr. Molecular mechanisms whereby endogenous and environmental regulatory factors control development; emphasis on stimulus perception and primary events in the signal chain leading to modulated gene expression and cellular development. Prerequisites: Biochem 501 or 601 and Botany 500; or Biocore 301 and 323. Richard Amasino, Patrick Masson and Donna Fernandez

872 SELECTED TOPICS IN MACROMOLECULAR AND BIOPHYSICAL CHEMISTRY (Also Chem 872)

Fall, Spring; 1 cr. Biochemistry 872 is an advanced graduate topics course (seminar/discussion format) based on recent literature in biophysical sciences. The course focuses on biophysical techniques, including optical microscopy, scanning probe microscopy, and electrophysiology. Students in 872 present and discuss recent examples of biological questions that have been approached using these tools. Prerequisites: Biochem/Chem 665 or consent of instructor. Meyer Jackson

901 SEMINAR - NUTRITION AND METABOLISM (Advanced) (Also Nutri Science 901)

Fall; 1 cr. Presentation of original research results; discussion of recent articles in animal metabolism and nutrition. Prerequisite: Consent of instructor. Alan Attie, Rick Eisenstein, James Ntambi, and David Pagliarini

906 TOPICS IN MODELING FOR BIOCHEMICAL SYSTEMS (Advanced)

Fall; 1 cr. Participants discuss topics relevant to predictive modeling of biochemical systems. Students will present published or in-progress works on quantitative approaches to studying biomolecular systems at various scales. Prerequisite: Consent of instructor. Julie Mitchell and Alessandro Senes

909 SEMINAR - ENZYMOLOGY - STRUCTURE AND FUNCTION (Advanced)

Fall, Spring; 1 cr. Research reports, special topics, and reports from recent literature in enzymology and enzyme mechanisms. Prerequisite: Consent of instructor. Samuel Butcher, Brian Fox, Hazel Holden, and Ivan Rayment

910 SEMINAR - MOLECULAR VIROLOGY (Advanced)

Fall, Spring; 1 cr. Research reports, special topics and reports from recent literature in molecular virology. Prerequisite: Consent of instructor. Paul Ahlquist, Paul Friesen, Robert Kalejta, and Ann Palmenberg

912 SEMINAR - MOLECULAR MECHANISMS OF DEVELOPMENT (Advanced)

Fall; 1 cr. Classical and current papers concerning molecular and genetic mechanisms of eukaryotic development will be presented and discussed. Prerequisite: Consent of instructor. Judith Kimble

913 SEMINAR - RIBOGROUP (Advanced) (Also BMC 913)

Spring; 1 cr. Student-led discussions of RNA-related problems. Prerequisites: Biochem 603, Genetics 466 or equivalent; consent of instructor. David Brow, Marvin Wickens and Samuel Butcher

914 SEMINAR - MOLECULAR BIOSCIENCES (Advanced) (Also Micro/BMC/MM&I 914)

Fall, Spring; 1 cr. During the Fall Semester, Molecular Biosciences trainees in their second year of graduate training will present seminars based primarily on literature related to their projects. During the Spring Semester, Molecular Biosciences trainees in their third year of graduate training will present seminars based primarily on their own research. Prerequisite: None. Christina Hull

915 SEMINAR - COMPUTATION AND INFORMATICS IN BIOLOGY AND MEDICINE (Also BMI/BME/CBE/Comp Sci/Genetics 915)

Spring; 1 cr. Participants and outside speakers will discuss current research in computation and informatics in biology and medicine. Required of all CBIM program trainees. Prerequisite: Consent of instructor. Charles Page, Louise Pape and Jude Shavlik

916 SEMINAR - CELLULAR MECHANISMS OF PROTEIN and MEMBRANE BIOGENESIS AND TRAFFICKING (Advanced)

Spring; 1 cr. Recent literature relating to cellular aspects of the regulation of protein and membrane biogenesis including protein synthesis, folding, modification, degradation, sorting and trafficking, as well as aspects of molecular chaperone function and membrane trafficking, will be presented and discussed. Prerequisite: Grad students only or consent of instructor. Sebastian Bednarek and Thomas Martin

917 SEMINAR - REGULATION OF GENE EXPRESSION (Advanced) (Also Micro 917)

Fall, Spring; 1 cr. Participants will discuss recent literature in topics related to prokaryotic and eukaryotic gene regulation. These topics include but are not limited to regulation of transcription, translation, and genome organization. Robert Landick and Richard Gourse

932 SEMINAR - BIOTECHNOLOGY TRAINING PROGRAM (Also Mirco/CBE 932)

Fall, Spring; 1 cr. Biotechnology Training Program (BTP) trainees will present their research for critical review by audience. Prerequisite: Graduate standing. Required of all BTP trainees. Brian Fox and Katrina Forest

945 SEMINAR - CHEMICAL BIOLOGY (Advanced) (Also Chem 945)

Spring; 1 cr. Recent published research in chemical biology and related areas. Intended for advanced graduate students, and required of all NIH Chemistry-Biology Interface (CBI) trainees. Prerequisite: Consent of instructor. Laura Kiessling, Ronald Raines and Douglas Weibel

990 RESEARCH

Fall, Spring, Summer; 1-12 cr. Prerequisites: Graduate standing and consent of instructor.