BIOE 330 - Bioreactor Engineering

Spring 2006

 

INSTRUCTOR: Prof. Ariel FERNANDEZ

 

TEXTBOOKS: a) Principles of Biochemistry (fourth Edition) Lehninger;

b) Bioprocess Engineering (2nd Edition), M. Shuler, F. Kargi.

 

WEBPAGE: www.owlnet.rice.edu/~bioe330/

 

SYLLABUS

 

January 12,17. Cellular, Chemical and Physical Foundations of Biochemistry. The cellular contexts. Chemical structures, elementary groups, the hydrogen bond. Thermodynamic principles. Some evolutionary implications. Lehninger, Chapter 1.

 

January 19, 24. Structural and Chemical Analysis of Aqueous Biological Environments. Water structure, water-mediated interactions, water-induced interactions, the intramolecular hydrogen bond in water, acid-base chemistry, pH and buffers. Lehninger, Chapter 2.

 

January 26-February 7. Chemical and Biophysical Properties of Proteins. Aminoacids, peptides and protein chains. Protein composition and chemical properties. Four levels of description of protein structure. Covalent and noncovalent features of protein structure. Mass spectroscopy and other sequence-determination tools. Evolutionary change fingerprinted on the protein sequence. Lehninger, Chapter 3.

 

February 9-February 21. 3-D Structure of Proteins. Description, determination, and functional implications. Degrees of freedom and geometric constraints. Basic folding motifs. Protein folding and dynamics. Lehninger, Chapter 4.

 

February 23, 28. Protein Function and Interaction. Protein-ligand associations, catalytic roles, immunological recognition. Lehninger, Chapter 5.

 

March 2-9. Enzymology (part I). Structural and mechanistic aspects of enzymology. Kinetic models in enzymology. Examples of enzymatic reactions. Shuler, Chapter 3.

 

March 16. Midterm Exam.

 

March 21, 23. Enzymology (part II). Complex enzyme kinetics. Immobilized enzymes, diffusion effects. Porous matrices for enzyme immobilization. Industrial applications. Shuler, Chapter 3.

 

March 28. Carbohydrates. Structural, dynamical and biochemical properties of mono and oligosaccharides. Heteropolysaccharides, glycans, glycoproteins and glycolipids. Functional significance of glycosylation. Lecture notes + Lehninger, Chapter 7.

 

March 30. Lipids. Chemical composition. Cellular localization. Lipid membranes. Membrane structure. Membrane transport and dynamics. Lehninger, Chapters 10,11.

 

April 4, 11. Nucleic Acids and the Flow of Biochemical Information. Nucleic acids as information carriers. Structure of nucleic acids. Transcription and translation. The genetic code. Transcription factors and regulatory mechanisms. Shuler, Chapter 4.

 

April 13, 18. Basic Concepts in Metabolomics. Glycolysis. Citric acid cycle. Lecture notes + Shuler, Chapter 5.

 

April 20-27. Alteration and Manipulation of Biochemical Information.  Mutation, selection and evolution. Molecular basis of disease. Natural mechanisms for gene transfer and gene rearrangement. Genetic engineering. Notions of genomics, proteomics and systems biology. Lecture notes + Shuler, Chapter 8.

 

May 9. Final Cumulative Exam.

 

RULES

 

   There will be nine mandatory problem sets/homeworks distributed on January 19, January 31, February 9, February 21, March 2, March 21, March 30, April 13 and April 25. If a problem set is given on a Thursday, it is due the following Tuesday at the beginning of class, unless that Tuesday happens to be a holiday, in which case it is due the next day of class after the holiday. If a problem set is given on a Tuesday, it is due the following Tuesday, with identical rule applying in the event that Tuesday is a holiday. There is no such thing as a late turned-in homework/problem set. If the test is turned in late, the grade assigned is 0. All tests are individual.

 

Homeworks as well as exams will be graded on a 0-100 scale. Exams are closed book. All tests are individual.

 

Each student will obtain a score determined as follows:

 

[Grade in Midterm] + 2 [Grade in Final Exam] + ½ [Grade averaged over all 9 homeworks/problem sets] = score

 

Maximum possible score: 100 + 200 + 50 = 350.

 

No exam or homework will be made up. If a legitimate excuse is presented, the grade for the missing test will be determined by averaging scores on the other tests. Exams will be given only at the regularly scheduled time.