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UW Biological Physics, Structure and Design

Courses

Required Courses

BPSD curricula require one lecture course and three literature review courses. An ongoing research seminar, BPSD 520, is also required every quarter (excluding Summer) until graduation. Required courses are:

  • Protein Structure & Function (BIOC 530) 3 credits – Lectures covering a wide range of topics in protein structure/function. (AUT quarter, first year only)
  • Literature Review Seminar (BPSD 540/541/542) 6 credits total – Critical reading of the published literature, with both written and oral presentations. (Autumn/Winter/Spring quarters, first year only)
  • Research in Seminar (BPSD 520) 1 credit – This course covers the on-going research of basic science students from many disciplines. Students are encouraged to start research projects early in the program and to participate in research  seminars. Starting in their second year, students will make oral presentations describing the BMSD 520 seminar series and their research. (every autumn/winter/spring quarter, every year until graduation)
  • Grant Writing Seminar (BIOC 533) 1 credit
  • Ethics 101 Seminar (BIOC 533) 1 credit
  • Biomedical Research Integrity Series – Students are required to attend the series of three lectures and at least one of the discussion sections. See the BRI Website for details on how to register.

Research Credits

Every quarter, students must register for research credits. The course number depends on the student’s progress in graduate school, the department depends on the student’s affiliated department, and the number of units depends on the quarter.

Course Number

  • Rotation: 599
  • Once an advisor is chosen and until the General Exam is passed: 600
  • Once General Exam is passed until graduation: 800

Department

  • Rotation: BPSD

Once an advisor is chosen, use the code the corresponds with the advisor’s department (see Faculty):

  • Biochemistry: BIOC
  • Bioengineering: BIOEN
  • Biological Structure: B STR
  • Chemistry: CHEM
  • Institute for Systems Biology: BIOC
  • Fred Hutch: BIOC
  • Medicinal Chemistry: MEDCH
  • Pharmacology: PHCOL
  • Physiology & Biophysics: PBIO

Number of Units

Autumn, Winter, Spring Quarters:

  • BPSD 599: 5 credits
  • 600/800: 10 credits

Summer Quarter: 2 credits

Electives

Prior to the General Exam the student must take a total of 12 graded credits distributed between at least three of the four BPSD categories:

  • Biomolecular Structure
  • Techniques in Biomolecular Structure
  • Molecular and Cellular Biology
  • Chemistry

The student will select at least 9 graded elective credits from the list below.

An additional 3 elective graded credits, not necessarily from the elective course list, are required. A student must obtain the approval of their BPSD supervisor for any elective courses not listed below that will constitute the additional 3 credits. Moreover, students may petition the BPSD Steering Committee to substitute other courses for this requirement or to have other courses added to the list of electives.

BPSD Electives Course List

B STR 515 Biological X-Ray Structure Analysis (3) Stenkamp [Tech BS]
Theory of x-ray diffraction, with emphasis on applications to biological systems. Prerequisite: permission of instructor. Offered: W.

B STR 519 Current Problems in Macromolecular Structure (2, max. 10) Hol [Bio Str]
A discussion of macromolecular structures related to specific areas of biological research. Emphasis on discussion of relevant research papers and use of computer graphics to visualize the molecular structures. Offered: AWSpS.

B STR 520 Structure Based Design of Drugs (3) Hol, Verlinde [Bio Str]
Lecture and discussion on research papers illustrating protein structure based design of new drugs. Review of methods and extensive discussion of all known mechanisms of drug resistance. Offered: even years; W.
Instructor Course Description: Christophe Verlinde

B STR 521 Advanced Biomacromolecular Crystallography (3) Hol, Merritt, Stenkamp [Tech BS]
Aspects of protein crystallography ranging from crystal growth, phase determination methods, density averaging to refinement, fiber diffraction of DNA and proteins. Offered: odd years; Sp.

B STR 557 Biomolecular Structure Seminar (1) Hol [Bio Str]
Literature review of key research in Biomolecular Structure in the form of short presentations by participants followed by discussion. Critical evaluation of methods and results regarding properties and protein structure determination. Credit/no credit only. Prerequisite: graduate standing in biological structure or biochemistry and permission of instructor. Offered: AWSp.

BIOEN 423/523: Introduction to Synthetic Biology (3) Klavins

BIOEN 424/524: Advanced Systems and Synthetic Biology (3) Sauro
Web site

BIOEN 425/525: Laboratory Methods in Synthetic Biology (4) Klavins

BIOEN 499 Special Projects (1-6, max. 24)
Individual undergraduate bioengineering projects (research or independent study) under the supervision of an instructor. Credit/no credit only. Offered: AWSpS.
Specific Course Description:
Systems and Synthetic Biology Sauro [MCB]
This course is designed for seniors and/or graduates who have an interest in bioengineering at the cellular network level. Students will be introduced to the field of synthetic biology and it’s applications in systems biology and applied engineering. Emphasis will be placed on understanding the control functions of cellular motifs so that students will, by simple visual inspection of a network structure, be able to make some statements on the network’s possible dynamic behavior. In addition, the importance of single cell studies and stochastic behavior will also be emphasized.

BIOEN 501 Molecular Bioengineering (4) Bryers [Bio Str]
Examines advanced topics in molecular diffusion, reaction kinetics, and convective transport modeling as applied to biological systems. Includes mathematical analysis and numerical simulation techniques applied to: Non-Fickian diffusion, rotational versus translational diffusion, immobilized enzyme kinetics, drug release, and gene delivery. Offered: A. Instructor Course Description: James D Bryers

BIOEN 502 Cellular Bioengineering (4) Giachelli [MCB]
Covers basic principles of cell biology (including cell structure, function, and signaling), recombinant RNA/DNA technology, and specific examples of cellular bioengineering applications including gene delivery, RNA silencing, and tissue engineering. Prerequisite: BIOEN 501. Offered: W.

BIOEN 503 Systems Bioengineering (4) Regnier, Vicini [MCB]
Explores whole-body or organ physiology topics from an engineering perspective. Uses various model systems to elucidate engineering principles such as feedback control and homeostatic regulation. Includes real-world examples, computer modeling, and research design approaches. Prerequisite: BIOEN 502. Offered: Sp.

BIOEN 576 Laboratory Techniques in Protein Engineering (4) Stayton [Tech BS]
Practical introduction to fundamentals of recombinant DNA technology and protein engineering. Gene design, bacterial molecular biology, genetic engineering strategy. Laboratory project focused on making site-directed protein mutations. Techniques include the Polymerase Chain Reaction, DNA sequencing, DNA cutting/splicing, protein expression. Prerequisite: background in biochemistry or molecular biology or consent of instructor.

BIOEN 599 Special Topics in Bioengineering (1-6, max. 15)
Offered at a graduate level periodically by faculty members within the Department of Bioengineering; concerns areas of research activities with current and topical interest to bioengineers. Prerequisite: undergraduate or graduate courses (or equivalent) determined individually for each special topic.
Specific Course Descriptions:
Quantitative Molecular Biomechanics Thomas
This course addresses how biological macromolecules convert chemical to mechanical signals or energy and vice-versa. The goals of this course are both to understand biology and to learn the principles needed to engineer biologically inspired devices or devices that interface with biology. Mechanics at the nanoscale can be conceptually quite different than mechanics at the macroscale, so the first unit of this course presents a quantitative engineering and physical principles for molecular biomechanics. The second unit focuses on applications. This will include (1) motor proteins and other molecules that convert chemical energy to mechanical forces, (2) mechanical force and adhesion, and (3) current research on mechanosensory proteins that convert mechanical signals to chemical cues. In all cases, examples will be taken from a broad range of research areas that may include muscle, other eukaryotic cells, and bacteria.
Computational Protein Design Daggett [Bio Str, Tech BS]
Course covers current methods in protein engineering including molecular visualization, homology modeling, molecular dynamics, and computational protein design. Students will learn how to use these tools through lectures and lab time and will apply them to investigate a problem of their choosing during the second half of the quarter. The course will also introduce students to current research in these areas.

CHEM 465 Computations in Chemistry (3) NW [Chem]
Computer calculations on color graphics workstations applied to problems in chemistry. Numerical methods and algorithms for calculating classical dynamics, quantum wavefunctions, wavepacket propagation, chemical kinetics. Use of computer programs for calculating electronic wavefunctions, molecular conformations, simulations of liquids and solids. Prerequisite: either CHEM 455 or CHEM 475, either of which may be taken concurrently. Offered: W.

CHEM 502 Practical NMR Methods for Biological and Organic Structure Elucidation (4) [Tech BS, Chem]
Theory of NMR (rotating frame formalism, multi-pulse experiments, relaxation phenomena, 2D experiments) as applied to structural and dynamic problems in organic and biological chemistry. Provides basis for experiment selection and spectrum interpretation. A more advanced treatment of NMR than 460. Prerequisite: CHEM 224, CHEM 239, or CHEM 337; recommended: CHEM 460 or equivalent, CHEM 435 or CHEM 455. Offered: W.

CHEM 530 Advanced Organic Chemistry (3) [Chem]
Fundamental aspects of organic structures and transformations. Structure and basicity of carbanions, substitution reactions, elimination reactions, nucleophilic addition and addition/elimination reactions, condensation reactions, structure and rearrangements of carbocations, electrophilic addition, electrophilic substitutions, neighboring group effects. Prerequisite: CHEM 337. Offered: A.

CHEM 531 Advanced Organic Chemistry (3) [Chem]
Synthetic organic chemistry. Discussion of practical methods for the synthesis of complex organic molecules with an emphasis on strategy and the control of stereochemistry. Prerequisite: CHEM 530. Offered: W.

CHEM 532 Advanced Organic Chemistry (3) [Chem]
Chemical Biology. Application of chemical methods to the study of biological processes that occur in cells. Prerequisite: CHEM 530 and CHEM 531. Offered: Sp.

CHEM 536 Chemical Biology (3) NW [Chem]
Mechanistic enzymology and chemical biology. Topics include protein structure and function, how enzymes work as catalysts, kinetic methods, functional assays, and applications to current research. Prerequisite: either CHEM 224, CHEM 239, or CHEM 335; recommended: either BIOC 405 or BIOC 44 Offered: W.

CHEM 550 Introduction to Quantum Chemistry (3) [Chem]
Origins and basic postulates of quantum mechanics, solutions to single-particle problems, angular momentum and hydrogenic wave functions, matrix methods, perturbation theory, variational methods. Prerequisite: CHEM 455. Offered: A.

CHEM 551 Introduction to Quantum Chemistry (3) [Chem]
Electronic structure of many-electron atoms and molecules, vibration and rotation levels of molecules, effects of particle exchange, angular momentum and group theory, spectroscopic selection rules. Prerequisite: CHEM 550. Offered: W.

CHEM 552 Statistical Mechanics (3) [Chem]
General theorems of statistical mechanics, relation of the equilibrium theory to classical thermodynamics, quantum statistics, theory of imperfect gases, lattice statistics and simple cooperative phenomena, lattice dynamics and theory of solids, liquids, solutions, and polymers, time-dependent phenomena and mechanisms of interaction. Prerequisite: CHEM 455 and CHEM 456 (concurrent registration permitted) or equivalent. Offered: Sp.

CONJ 524 Structural Basis of Signal Transduction (1.5) Xu [Bio Str, MCB]
Focuses on the structure-function relationship of key enzymes in signal transduction (protein/lipid kinases; phosphatases etc.) and the structural consequences of protein phophorylation. Teaches students to look into critical structural details using PC or Mac. Prerequisite: undergraduate course in biochemistry and basic cell biology, or permission of instructor. Offered: W.

CONJ 531 Signaling Mechanisms in Excitable Cells (1.5) Hille [MCB]
Membrane electricity. Structure and roles of voltage-gated and ligand-gated ion channels in electrical signaling. Calcium as a second messenger. Exocytosis and its regulation. Phototransduction in photoreceptors. Prerequisite: comprehensive undergraduate course in general biochemistry and molecular biology, or permission of instructor. Offered: A.
Instructor Course Description: Peter B Detwiler, Bertil Hille

CONJ 532 Signal Transduction from the Cell Membrane to the Nucleus (1.5) Beavo, Moon, Storm [MCB]
Intracellular signaling pathways leading from cell membrane receptors to nucleus. Pathways activated by seven transmembrane receptors and G-proteins, insulin/PI3 kinase, nitric oxide and WNTs and mechanisms of signal termination. Cytokine/Jak/Stat signaling and role of subcellular localization in signal transduction. Prerequisite: basic knowledge of biochemistry. Offered: A.

CONJ 533 The Dynamic Chromosome (1.5) Henikoff, Roth [Tech BS, MCB]
The chromosome viewed as the ultimate organelle. How chromosomes are maintained and propagated. Epigenetic regulation of genes. Genetic, biochemical, and cytologic methods for understanding chromosome functions. Prerequisite: cell biology, biochemistry, and genetics. Offered: A.

CONJ 535 RNA Structure and Biological Function (1.5) Ferre-D’Amare, Stoddard [Tech BS, MCB]
Survey of the diversity of cell-biological roles played by RNA with emphasis on structural principles and structure-function relationships. Readings from the current literature to cover both, methods for the study of RNA, and examples of the function of this nucleic acid as part of the machinery for gene expression. Offered: W.

CONJ 536 Developmental Cell Biology (1.5) Wakimoto, Wright, Hille, Cooper [MCB]
Focuses on experimental design in cell biology. A topic of current research interest is covered in depth in order to follow a line of investigation and critically evaluate the strengths and limitations of various experimental strategies. Offered: jointly with BIOL 546; W.
Instructor Course Description: Merrill B Hille, Barbara T Wakimoto

CONJ 537 Mechanism of Transcriptional Regulations (1.5) Tsukiyama [MCB]
Focuses on biochemical mechanisms of gene transcription covering a broad range of transcriptional regulation, including mechanisms of transcriptional initiation, elongation and termination. Discusses regulation of transcription by chromatin. Includes a special lecture regarding regulation of transcription in cell growth and differentiation. Offered: A.

CONJ 538 Genetic Instability and Cancer (1/1.5) Maizels, Monnat [MCB]
Seminar focusing on molecular pathways that maintain genomic stability in all cells and that carry out programmed changes in genomic structure in the immune system. Special attention devoted to understanding how failure in these pathways leads to genomic instability and malignancy. Prerequisite: permission of instructor.
Instructor Course Description: Nancy Maizels, Raymond J Monnat, Peggy A. Mccune

CONJ 539 Biological Basis of Neoplasia (1.5) Kemp, Zarbl [MCB]
Lecture/discussion on cellular and molecular mechanisms underlying phenotypes associated with cancer, including genetic pre-disposition, injury, and instability; alteration in control of cell division and cell death; failure of differentiation; tumor angiogenesis and metastasis. Molecular biology of tractable model systems is emphasized. Prerequisite: introductory biochemistry and cell biology. Offered: S.

CONJ 542 Development (1.5) Raible, Roelink [MCB]
Molecular mechanisms of development; molecules and pathways used for the patterning of developing organisms. Similarities and differences in the making of plants, invertebrates, and vertebrates. Prerequisite: Comprehensive undergraduate courses in Biology, Molecular Biology, or permission of instructor. Offered: W.

CONJ 544 Protein Structure, Modification and Regulation (1.5) Stoddard [Tech BS, MCB]
Overview of general principles of protein structure, including forces that contribute to folding and stabilization, followed by an extended coverage of the means by which protein structure and function are modified and regulated. Examples from recent developments in protein folding, processing, and allosteric regulation. Prerequisite: introductory biochemistry and cell biology. Offered: W.
Instructor Course Description: Barry L. Stoddard

CONJ 545 Molecular Interactions and Medicine (1.5) Verlinde [Bio Str, Tech BS, MCB]
Forces governing molecular interactions in biology; with a focus on medicine. Principles of computer modeling techniques in use for predicting the molecular behavior of proteins, ligands and their complexes. In computro ligand discovery; drug design, and the understanding at the atomic level of some genetic diseases. Two computer lab sessions. Offered: Sp.

CONJ 546 Survey of Technologies for Molecular Biology (1.5) Bumgarner [MCB]
Provides a broad overview of modern technologies used in molecular biology with particular emphasis on DNA sequencing and gene expression. In addition to methods and applications for the technologies, examines the theoretical basis and underlying instrumentation through which these technologies are implemented. Offered: A.

CONJ 548 Modeling Proteins and Proteomes (1.5) Samudrala [Bio Str, Tech BS, MCB]
Provides hands-on experience for modeling protein structures, using the models to predict function, and applying the prediction methods to all proteins encoded by an organismal genome. Provides an overview of protein structure, how it mediates function, and its importance for understanding protein interaction networks. Offered: W.

CONJ 551 Immunity (1.5) Strong [MCB]
Provides an understanding of the central cellular and molecular players in the mammalian immune system at a level appropriate for the non-specializing graduate student. Selected topics include the molecular basis of B and T cell activation and effector functions and the mechanisms of innate immunity. Offered: Sp of even years.
Instructor Course Description: Roland K Strong

GENOME 465 Advanced Human Genetics (4) NW King, Olson [MCB]
Explores genetic analysis of naturally occurring variation in humans; origins and consequences of mutation, as mediated by selection, migration, population structure and drift; approaches to finding human disease genes and characterizing them at the molecular level; relevance of to other species to analysis of human genes. Prerequisite: GENET 371; either GENET 372 or BIOC 440. Offered: W.

GENOME 540 Introduction to Computational Molecular Biology: Genome and Protein Sequence Analysis (4) [Tech BS, MCB]
Algorithmic and probabilistic methods for analysis of DNA and protein analysis. Students must be able to write computer programs for data analysis. Prior coursework in biology and probability highly desirable. Prerequisite: permission of instructor. Offered: jointly with MBT 540; W.

GENOME 541 Introduction to Computational Molecular Biology: Molecular Evolution (3) [Tech BS, MCB]
mputational methods for studying molecular evolution. Students must be able to write computer programs for data analysis. Prior coursework in biology and probability highly desirable Prerequisite: MBT/GENET 540 or permission of instructor. Offered: jointly with MBT 541;Sp.

PATH 516 Molecular Basis of Human Genetic Disease (3) [MCB]
Introduces the underlying mechanisms in human genetic disorders , ranging from the single nucleotide, through genomic instability, and chromosomal rearrangements. Includes tissue and organ specific examples of the manner in which these disorders provide insights into human biology. Offered: Sp.

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