Course: BIOEN 315: Biochemical and Molecular Bioengineering

Credits: 3

Instructor: Dan Ratner, Valerie Daggett

Office Hours: By appointment with Professors Ratner and Daggett

Class times/location: MWF 9:30-10:20 in OTB 014

Texts and Supplemental Materials: Lehninger “Principles of Biochemistry” by Nelson and Cox (4th or 5th edition) & instructor will supplement text with electronic handouts provided via the course webpage.

UW Catalog Description: Introduces the requisite organic, physical, and biochemistry for incoming bioengineers to understand biological systems at the molecular level.

Prerequisites by Course: CHEM 223, CHEM 237 or CHEM 335; BIOL 200, which may be taken concurrently.

Required or Elective: Required

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

  • Understand biomolecular structure and function.
  • Solve for free energy in context of molecular structure, chemical reactivity and larger systems as an introduction to thermodynamics.
  • Identify the role of chemical reactive groups in molecular structure and bioconjugation techniques.
  • Learn the energetics of protein adsorption.
  • Apply principles of biomolecular engineering to understand insulin and diabetes.

Course Outcomes and Assessment:  This course presents, through three weekly lectures and TA discussion/recitation sections, an opportunity for students to explore the relationship between chemical and biochemical principles and molecular bioengineering. As such, this course addresses certain ABET outcome criteria at a variety of levels.

Outcomes Addressed by this Course:

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

  • Solve for free energy in context of molecular structure, chemical reactivity and larger systems as an introduction to thermodynamics.

Molecular structure and function will be examined from the perspective of thermodynamics, particularly as they relate to protein structure, function and interactions. Assessment will be conducted during a specialized unit on 3D modeling of protein structure, project/assignment (to be conducted by Prof. Daggett). Students will be assigned a computational modeling project that will be used to evaluate this learning objective.

J. Knowledge of contemporary issues.

  • Understand the significance of diabetes mellitus as a critical public health issue.

Diabetes mellitus represents one of the greatest public health challenges of the 21st century, with critical implications to US healthcare policy and emerging healthcare needs in the developing world. Bioen 315 students will use diabetes as a model disease to apply biochemical and molecular engineering principles addressed in the class, most notably those related to protein biochemistry and POC diagnostics.

K.  An ability to use the techniques, skills, and modern engineering tools necessary for engineering practice (i.e. computer and analytical equipment)

  • Identify the role of chemical reactive groups in molecular structure and bioconjugation techniques.

Helping students develop a familiarity with the role that chemical reactivity plays in biological systems is the central focus for this course.  Students will be assigned weekly problem sets focused on applying their knowledge of chemical principles towards problems relevant to the design of diagnostics and therapeutics to address the molecular pathophysiology associated with Type I and Type II diabetes.  Student ability to identify the role of chemical reactive groups in molecular structure and bioconjugation techniques will be assessed through these weekly problem sets.

L. An understanding of biology and physiology.

  • Learn biomolecular structure and function. Apply principles of biomolecular engineering to understand insulin and diabetes.

Upon completing Bioen 315, students are expected to be versed in the basic building blocks of biological systems (proteins, nucleic acids, carbohydrates and lipids), particularly as it relates to molecular structure and function.  This knowledge will serve as their foundation in biochemical and molecular engineering in the BioE core curriculum, and within Bioen 315 it will be used to develop a detailed understanding of the pathology of type I and type II diabetes at a molecular level.  Student competency in this area will be assessed through the weekly problem sets and the final examination, where the students will be asked to apply their knowledge of biomolecular structure and function to demonstrate their understanding of the biology and physiology of diabetes mellitus.

Relationship of Course to Program Educational Objectives:

In this course, students advance their understanding of biological systems components and establish a foundation of knowledge in the area of biochemical and molecular engineering.  Students explore the relationship between chemical and biochemical principles and molecular bioengineering while learning specialized skills, including computational modeling.  They will investigate contemporary critical healthcare issues, gaining an appreciation for the challenges faced by the U.S. as well as developing countries.  BIOEN 315 familiarizes students with terminology and procedures used in a variety of engineering disciplines and in the medical profession.  Helping students develop a familiarity with the role that chemical reactivity plays in biological systems is a central focus for this course and will help prepare them for further training and/or employment in an expanding range of fields.  Thus, BIOEN 315 contributes to providing students with the tools necessary to reach the following Program Educational Objectives:

  1. Earn advanced degrees and/or obtain employment in bioengineering related fields, such as medicine, device development, or biotechnology.
  2. Advance their careers by obtaining appropriate educational and professional qualifications.
  3. Contribute to responsible development of new technical knowledge.
  4. Take leadership roles in addressing domestic or global bioengineering related issues.

Topics Covered:

  1. Organic functional groups and reactivity
  2. Amino acids and side-chains
  3. Protein structure and function (1°, 2°, 3° and quaternary)
  4. Carbohydrate structure and function (mono-, oligosaccharides and glycoconjugates)
  5. Nucleic acid structure and function
  6. Lipid structure and function
  7. Intro to thermodynamics and free energy in the context of molecular structure
  8. Bioconjugate chemistry
  9. Surface modification and protein adsorption
  10. Diabetes as a model disease (molecular pathophysiology, diagnostics and therapeutics)

Course Grading:

35%     Assignments (7 assignments + additional short writing exercises; a detailed description of each assignment will be posted weekly on the course website)

15%     Class Participation (in-class participation along with participation during TA recitations/review sessions)

30%     Midterm Exams (2 midterm exams will be held; weeks 3 and 8)

Course Schedule:

Week Date Due Topics and Activities Readings Assign
1 Apr. 1 (Ratner) Intro to Biocehmical and Molecular Bioengineering, Diabetes intro
Apr. 3 (Ratner) Organic Chemistry for Bioengineers – ‘SPONCH and stuff’ Assign 1
Apr. 5 (Ratner) Bonding (notation, delocalization)Biochemical functional group chemistry
2 Apr. 8(Ratner) Assignment 1 due Chemical reactivity in biological systems Assign 2
Apr. 10 (Ratner) Acid/bases, pKa, nucleophiles, electrophiles
Apr. 12 (Ratner) Formation and hydrolysis of esters and amides
3 Apr. 15(Ratner) Assignment 2 due
Apr. 17 (Ratner) Central Dogma of Biochemical Systems (Intro and Logic to Bioen 315 approach
Apr. 19 Midterm 1
4 Apr. 22 (Daggett) Physical Chemistry in biology and organic chemistry Assign 3
Apr. 24 (Daggett) Molecular interactions (electrostatic, Van der Waal, hydrogen bonding)Structure of water
Apr. 26 (Daggett) Free energies, energy of systems and energy diagrams
5 Apr. 29 (Daggett) Assignment 3 due Proteins Assign 4
May. 1(Daggett) Protein composition (AAàPeptide)
May. 3(Daggett) Protein structure (1°à2°à3°àquaternary)
6 May. 6 (Daggett) Assignment 4 due Driving forces in biomolecular structure (P-chem) Assign 5
May 8 (Daggett) Functional roles of proteins (Enzymes, structure, drugs and drug targets)
May 10 (Ratner) Intro/refresher to enzymes and enzymology
7 May 13 (Ratner) Assignment 5 due Carbohydrates – structure and Function Assign 6
May 15 (Ratner) Biological roles played by carbohydrates (protein/lipid modification, adhesion)
May 17 (Ratner) Lipids – structure and function (membranes)
8 May 20 (Ratner) Assignment 6 due Biological roles of lipids, cholesterol and lipoconjugates (gpi, LPS, glycolipids)
May 22 (Ratner) Bioconjugate chemistry
May 24 (Ratner) Midterm 2
9 May 27 (Ratner) *** NO CLASS *** Memorial Day
May 29 (Ratner) Chemical modification of DNA and proteins Assign 7
May 31 (Ratner) Chemical modification of carbohydrate and lipids
10 Jun. 3 (Ratner) Biomedical applications for molecular engineering
Jun. 5 (Ratner) Assignment 7 due Bioconjugate drug and vaccine design
Jun. 7 (Ratner) Surface engineering for biomaterials and medical devices
11 Jun. 12 Final Exam, OTB 014, 8:30 – 10:20

 

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