Read Microsoft Word - CHE 347 Course memo '04.doc text version


Course ______ChE 647 ­ Instructor___Erik

Biochemical Engineering______________________ Semester ___Spring 2004________

J. Fernandez_____________________________________________ Phone No. __434-924-1351____ of Virginia; Chemical Engineering; 102 Engineer's Way; P. O. Box 400741;_

Office Address __University _ Chemical

Engineering Bldg. 122; Charlottesville, VA 22904-4741____________________________________

E-Mail Address [email protected]____________________________________________________________________

Textbook(s): (Student to purchase)

M. L. Schuler, F. Kargi, Bioprocess Engineering: Basic Concepts, 2nd Edition, Prentice Hall, 2002, ISBN: 0130819085

Reference(s): (To be put on library reserve) - Limit 4

Lehninger, A. L., Nelson, D. L., and Cox, M. M., Principles of Biochemistry, Worth Publishers, New York (1993) Voet and Voet, Biochemistry, New York (1990) Stryer, L., Biochemistry, W. H. Freeman, New York (1988) J. D. Watson, Molecular Biology of the Gene, 2nd Edition, Benjamin/Cummings, Menlo Park, CA (1987)

Computer Needs: Microcomputer Capability ____________PC for Class Web site_____________________________________________________ Software required? _______________________________________ Provided? _______________________________ Other _________________________________________________________________________________________

Course syllabus and instructor bio are attached.


CHE 347/647 - Biochemical Engineering Principles

Spring 2004 Lecture: Tue/Thu, 3:30 ­ 4:45 PM THN 119 Instructor Erik J. Fernandez 122 Chemical Engineering Bldg. 924-1351 [email protected] Class home page: Description: This course will familiarize advanced undergraduate and graduate students in the life sciences and engineering with practical applications of biotechnology using engineering principles. We will then combine basic concepts in biochemistry, and molecular and cell biology, with chemical engineering principles to design processes to create cellular and biomolecular products. Required Text: M. L. Shuler, F. Kargi, Bioprocess Engineering: Basic Concepts, Second edition, Prentice Hall, 2002. Supplemental Sources (on reserve in the Science and Engineering library): Lehninger, A. L., Nelson, D. L. and Cox, M. M., Principles of Biochemistry, Worth Publishers, New York (1993). Voet and Voet, Biochemistry, Wiley, New York (1990). Stryer, L., Biochemistry, W. H. Freeman, New York (1988). J. D. Watson, Molecular Biology of the Gene, Second edition, Benjamin/Cummings, Menlo Park, CA (1987). J. E. Bailey and D. F. Ollis, Biochemical Engineering Fundamentals, Second edition, McGraw-Hill, New York (1986). H. W. Blanch and D. S. Clark, Biochemical Engineering, Marcel Dekker, 1996. Biotechnology Journals with an Engineering Perspective: Applied and Environmental Biotechnology Bioprocess Engineering Biotechnology and Bioengineering Biotechnology Progress Enzyme and Microbial Technology Nature Biotechnology Trade News: Nature Biotechnology Genetic Engineering News

Grading: There will be homework, two quizzes (the first emphasizing biology, the second emphasizing engineering calculations), and a final exam. In addition, for those taking 347, there will be a pledged review paper assignment. For those taking 647, there will be a research writing exercise. A tentative weighting of the homework, quizzes, and final exam will be Class contributions Homework Quizzes (2) Pledged assignments (447) / Research exercises (647) Final Exam 5% 15% 30% 15% 35%

"Class contributions" will be based on quantity and quality of contributions to discussions during class as well as formal or informal office hours. While the quantity will be noted, quality will be emphasized in grading. Homework The homework assignments will be handed out approximately weekly, and are intended as a way for you to learn the material. The homework will be discussed on the date due and graded. You are encouraged to work together on homework, but you should not consult solutions from prior years. Late homework will not be accepted without prior permission of the instructor. Note on spreadsheets: You are welcome to use them, but make sure you indicate the formulas you used and your reasoning as well. Pledged Assignments (347) Review paper. You will report on a biotechnology topic of interest to you. You will investigate the enabling science, engineering challenges, future prospects, economic and ethical aspects. You will complete this assignment in two person teams of your choosing. Research Exercises (647) Mock introduction / research review paper. To give you practice with research writing, you will write a paper that will be an extended, mock introduction to a research paper. You may do this in an area of your choice; your current research would be fine (and probably useful!). The introduction should include background and motivation on the problem, a discussion of previous work, and the remaining questions to th be addressed in your "paper". A detailed outline will be due on February 26 . I will then review these and provide comments and/or meet individually with students. The final draft is due on April 20.

How will you grade participation? Grading stresses quality of participation, not quantity per se. The key to quality is preparation before class. I expect that average participation will be in the B range. A · · · · · · · · B · · · · · C · · · · · · Shows excellent preparation. Analyzes readings and synthesizes it with other knowledge (from other readings, course material, discussions, experiences, etc.) Makes original points. Synthesizes pieces of discussion to develop new approaches that take the class further. Responds thoughtfully to other students's comments. Builds arguments with other students, but may question majority view. Stays focused on topic. Volunteers regularly but does not dominate. Shows good preparation. Interprets and analyzes course material. Volunteers regularly. Thinks through own points, responds to others's points, questions others in constructive way, may question majority view, raises good questions about readings. Stays on topic. Shows adequate preparation. Understands readings but shows little analysis. Responds moderately when called upon but rarely volunteers, or talks without advancing the discussion. Present. Responds when called on but offers little or distracts the discussion. Absent



Tentative Syllabus The syllabus is changing significantly this year, and the list of topics below is tentative. · · Introduction to biochemical engineering Proteins · Thermodynamics of biological systems · Structure, function, and stability · Sequence analysis Enzymes · Catalytic mechanisms · Selectivity · Rate laws, Michaelis-Menten kinetics · Batch kinetics · Inhibition · Determining rate parameters Immobilized enzymes · Surfaces · Porous materials · Mass transfer vs. Reaction rate limitations Cellular kinetics · Batch growth kinetics · Product formation kinetics · Nutrient limitation · Continuous culture · Modeling approaches Bioreactor design · Batch vs. CSTR · Alternatives to CSTR Immobilized cells Scale-up issues · Oxygenation · Mixing · Sterilization Genetic instability Alternative expression systems · Animal cell culture and their products · Plant cell culture · Transgenics Monoclonal antibodies Protein and antibody engineering Metabolic engineering Vaccines





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Erik J. Fernandez Associate Professor

Ph.D. UC Berkeley (1989) B.S. ChE. Cal Tech (1984)

Honors and Awards

· NSF Career Young Faculty Development Award · Rodman Scholars Award (U. Virginia) for Excellence in Teaching (1999) · University Teaching Fello w (U. Virginia, 1997)

Research Interests

The recent sequencing of the human genome promises to provide numerous new proteins as drug targets and therapeutic agents. We are investigating several obstacles to the efficient commercialization of these delicate molecules. To one degree or another, all projects in our group involve collaborations with other groups at the University of Virginia, other universities, and the biotechnology industry. Structural Analysis of Protein Purification The structure of proteins can be adversely affected during manufacturing, purification, formulation and use in ways that are poorly understood. We are using several biophysical experimental techniques as well as molecular simulation to investigate the structural, kinetic, and thermodynamic factors important during protein purification. Currently we are focusing on the challenging case of hydrophobic interaction chromatography, where many molecular interactions are at play. Aggregation of Protein Biopharmaceuticals and Alzheimer's Disease Misfolding and association ("aggregation") can threaten the stability of proteins as pharmaceutical agents. We are investigating the structural, kinetic, and thermodynamic features of protein aggregates. Our goal in this research is to elucidate the mechanisms of protein aggregation to guide engineering of the solvent environment and protein molecules themselves to improve stability. In a similar way, we are also investigating the aggregation of the amyloid-b peptide, which is an important feature of Alzheimer's disease. Nonideal Flow in Chromatography Suboptimal column packing and nonuniform flow can compromise chromatographic resolution and interfere with rapid process development and FDA product approval. We are using magnetic resonance imaging (MRI) to analyze bed structure inside chromatography columns during packing and operation. Experiments are guiding development of a continuum mechanics model that can describe column packing and guide development of improved and novel column packing procedures.


Microsoft Word - CHE 347 Course memo '04.doc

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