Course: BIOEN 457: Advanced Molecular Bioengineering

Credits: 4

Instructor: Patrick Stayton

Texts and Supplemental Materials: No single textbook required, uses Chapters from “Enzyme Structure and Mechanism” by Fersht, “Physical Chemistry” by Alberty, and from different reaction kinetics textbooks.

UW Catalog Description: Fundamentals of molecular recognition: thermodynamics, forces, kinetics. Manipulation of recognition processes for current molecular bioengineering research and development. Fundamental physical chemistry of molecular recognition in the context of biomedicine. Therapeutics based on cells.

Prerequisites by Course: BIOEN 315 and BIOEN 335

Prerequisites by Topic: Molecular bioengineering, general biochemistry

Required or Elective: Elective

Specific Outcomes: By the end of this course, students will be able to:

  • Define thermodynamic principles in context of biomolecular recognition and stability
  • Define kinetic theory and reaction kinetics in context of biomolecular recognition and stability
  • Define how non-covalent bonding energetics relate to biomolecular recognition and stability
  • Apply biomolecular energetics to biotherapeutic design from a modeling and computational standpoint
  • Apply combinatorial and directed evolution approaches to biotherapeutic design
  • Evaluate engineering systems analysis to receptor trafficking in context of how biological feedback systems affect therapeutic strategies
  • Define molecular design strategies for modifying cells to develop cellular therapeutics

Outcomes Addressed by this Course:

A. An ability to apply knowledge of mathematics, science, and engineering.

C. An ability to design a system, component, r process to meet desired needs within realistic constraints.

G. An ability to communicate effectively.

Topics Covered:

  1. Molecular Recognition Fundamentals 1: thermodynamics of biomolecular interactions, non-covalent forces underlying bioenergetics: hydrogen bonding, van der Waals, hydrophobic effect, water in context of molecular recognition biomolecular stability
  2. Molecular Recognition Fundamentals 2: kinetic theory, reaction kinetics, enzyme energetics
  3. Rational Biotherapeutic Design: molecular modeling, computational approaches to predicting energetics
  4. Directed Evolution for Biotherapeutic Design: random mutagenesis approaches and techniques, phage display and selection techniques, combinatorial approaches and techniques
  5. Cellular Warfare: receptor-mediated recognition in immune system surveillance, macrophage-B-Cell collaboration, T-Cell and natural killer cell function, vaccines

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