Academics
Biochemistry
Advanced biochemistry courses (course numbers 400 and above) require completion of four semesters of chemistry (two of general chemistry and two of organic). A grade of C- or better is required in the prerequisite classes for enrolling in biochemistry courses.
In addition to fulfilling the major requirements of chemistry and biochemistry majors, biochemistry courses are taken by students in a variety of majors and programs, including Biology, Animal and Avian Science, and Nutritional Science.
In the final year of the Biochemistry course, students work an extended first term to begin their research project. You will need to be for 12 weeks in the first term, followed by a two-week break over Christmas. You will then complete your project in the first six weeks of the second term, and then submit your project dissertation and deliver an oral presentation at the beginning of the final term.
In the remaining two weeks of the second term, and throughout the eight weeks of your final term, you will study two further courses that you choose from a list of options. These are assessed at the end of the final term.
The extended terms mean that you will need to budget for higher living costs in the final year, as you will be required to be for longer than the standard terms. The additional work in this final year means that you will graduate with an MBiochem - a master's degree - as well as invaluable research experience that will be excellent preparation for further study or a range of careers.
Structure and content
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. Open to first or second semester freshmen students 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, diabetes, HIV, 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
375 MOLECULAR CONTROL OF METABOLISM AND METABOLIC DISEASE (Fall 2015 only)
Fall; 3 cr. Examination of various physiological states and how they affect metabolic pathways. Discussion of a number of special topics related to the unique roles of various tissues and to metabolic pathways in disease states, including adipocyte biology, beta-cell biology, epigenetics, inflammation, and aging related diseases. Intended for advanced undergraduates and graduate students with introductory biochemistry knowledge. Alan Attie
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: Completion of Chem 341 or 343 or concurrent enrollment; or graduate student. Available in-class or online. 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. 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. 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: Biomolecular Chem 314 or 503 or Biochem 501 or 507. 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 . Colleen Hayes
551 BIOCHEMICAL METHODS (effective spring 2018)
Fall, Spring, 4 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: Previous or concurrent enrollment in Biochem 501 or 507. Alessandro Senes (Fall 2018 on sabbatical), Douglas Weibel (Spring), and Lynne Prost
575 BIOLOGY OF VIRUSES (Also MMI 575)
Spring; 2 cr. The goal of this course is to introduce upper-level undergraduate students and graduate students to the biology and biochemistry of viruses and virus infection. We will address the fundamentals of virus properties, virus multiplication, disease mechanisms, prevention and intervention of infection, and how viruses pose new threats to human and animal health through emergence and evolution. We will focus primarily on viruses that are pathogenic to animals. This course is intended to cover important concepts and themes in virology. We will discuss carefully selected examples of viruses that impact our world and everyday life. Thus, this course will not be a "bug per day" style of class. Prerequisite: Biocore 301/302, or AP score of 4 or 5 and Zoology 151 or 152; or MM&I 301. 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: Chem 345 and Biochem 501 or 507. 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. In order to count toward the minimum graduate course requirement, graduate students will be required to give an oral presentation in Biochem 906 during the last few weeks of class. Prerequisites: Math 234 or 320, and either Comp Sci 301 or 302. 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. In order to count towards the minimum graduate course requirement, graduate students will be required to complete a final project. 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; 3 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. 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. 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 hormones, growth factors and other regulators; emphasis on hormone and growth factor receptors, action in cytoplasm and nucleus, and their biosynthesis. Prerequisites: Introductory biochemistry (Biochem 501 or 507 & 508) and cell biology (Biocore 303 or Zool 570 or Path 750) or consent of instructor. Thomas Martin, Arnold Ruoho, Beth Weaver, Richard Anderson, Shigeki Miyamoto, and Emery Bresnick
651 BIOCHEMICAL METHODS (see 551)
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
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, social media responsibility and more. Prerequisite: Admission to IPiB or the Biophysics graduate program. Required for first-year IPiB graduate students. 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 (Fall 2018 on sabbatical); Catherine Fox (alternating years)
729 ADVANCED TOPICS
Fall, Spring; 1 cr. Practicum in Undergraduate Teaching. Prerequisite: consent of instructor. Alessandro Senes (Fall 2018 on sabbatical), Douglas Weibel (Spring) 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, and Dudley Lamming
729 ADVANCED TOPICS
Fall; 2 cr. Foundations of Biotechnology. An overview of the foundations of the biotechnology industry, technology transfer, the basics on patents and protection of intellectual property, business development cycle, and other topics. Other tools and perspectives for becoming successful researchers in the biotechnology arena include guidance on preparing effective oral, visual and written presentations. The course instructors bring in outside experts from the university and local business community to enhance these discussions. Required of Biotechnology Training Program (BTP) trainees. Prerequisite: Graduate student standing. Brian G. Fox
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
328 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.Milo Westler
801 BIOCHEMICAL APPLICATIONS OF NUCLEAR MAGNETIC RESONANCE
Spring; 2 cr. Lectures. Survey of current nuclear magnetic resonance techniques used in biochemical research; the emphasis will be on how data are acquired and on practical applications. Prerequisite: Undergraduates accepted with consent of instructor.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. In Fall 2018, course meets with the QBio Seminar Series, Wednesdays at 2:00pm in the Room, 3rd Floor.
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. 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
918 SEMINAR - SINGLE MOLECULE APPROACHES TO BIOLOGY (Also Chem 918)
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
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.
