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Nam Sun Wang
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ENCH482
Biochemical Engineering
Fall 2007
Homework
Class Syllabus
Policy on Academic Integrity
8/29 Syllabus, Terminology, Chemical Engineering vs. Biochemical Engineering Brief History, Applications, Nomenclature, Classification, Kingdom of Protists, Virus, Bacteria, Yeasts, Procaryotes/Eucaryotes
Some internet sites that provide good references (Check them out now and come back later during the semester.)
OneLook Dictionary Search
On-Line Intro Biology Book
Cellular/Molecular Biology Hypertextbook
from MIT -- good supplementary reading
Cell Biology
(Organelles)
Life Sciences Dictionary
National Agriculture Library
; then click "Research and Technology", followed by "Biotechnology"
Biotechnology Information Series from Iowa State
Biosequencing Guide from Harvard
ATCC (American Type Culture Collection)
FDA (Food and Drug Administration)
FDA Center for Biologics Evaluation and Research
FDA Center for Drug Evaluation and Research
DOE's Primer on Molecular Genetics (including a glossary of genetic terms)
Bioinformatics Database (Major sources of gene/protein sequences)
NCBI (National Center for Biotechnology Information)
(GenBank)
NCBI (National Center for Biotechnology Information)
(alternative web address)
Databases for Molecular Biology
(Comutational Molecular Biology at the NIH)
Cyber Science at NIH
ExPASy (Expert Protein Analysis System from Swiss)
European Bioinformatics Institute
Bioinformatics Software
Cn3D (See-in-3-D)
(a 3D rendering program for protein structure)
8/31 Biochemistry (RNA/DNA)
9/05 Biochemistry (Amino Acids, Protein),
Demo (BLAST)
List of Amino Acids
Zwitterion Behavior of Amino Acid
9/07 Biochemistry (Carbohydrates, Lipids)
9/10
Demo (Density Gradient Centrifugation)
, Enzymes
9/12 Michaelis-Menten Kinetics
Michaelis-Menten Rate Expression
, derivation & reduction.
9/14 Michaelis-Menten Kinetics
Integrate ODEs Arising from Enzyme Kinetic Mechanisms
9/17 Enzyme Kinetics: Bioreactor (Batch, CSTR)
9/19 Enzyme Kinetics: Bioreactor (Fed-batch), Inhibition, pH Effect
Symbolic Derivation of Reaction Rate Expression with Enzyme Inhibition (Competitive, Noncompetitive, Uncompetitive)
Symbolic Derivation of Reaction Rate Expression with Substrate Inhibition
pH Effect
Mathcad Trial Version
9/21 Review of Computer Methods
9/24 Substrate/Product Inhibition, Temperature Effects, Enzyme Immobilization, External Mass Transfer Resistance
Surface-Immobilized Enzyme -- Effectiveness Factor & Apparent Reaction Rate
Surface-Immobilized Enzyme -- Steady-State CSTR with Product Inhibition
Surface-Immobilized Enzyme -- Batch Bioreactor
9/26 Enzyme Immobilization, Internal Mass Transfer Resistance
Demo (Catalyst Supports)
9/28 Enzyme Immobilization, Internal Mass Transfer Resistance
Demo (Gel Entrapment)
Enzyme Immobilization in Gel Beads & Strings -- Derivation & Use of Effectiveness Factor
Ditto, /w Variation
Enzyme Immobilization in a Spherical Gel-Bead -- Substrate/Product Profile with Substrate/Product Inhibition
10/01 Central Dogma of Biology: Replication
10/03
Quiz #1
10/05 Central Dogma of Biology: DNA Sequencing, PCR, Gene Chip, Mircoarray
DNA Sequencing Gel Pattern
10/08 Central Dogma of Biology: Transcription, Promoter/Operator, Induction/Repression, Translation,
Demo (with Cards)
Codon Translation Table
Central Dogma of Biology
(Artificial Sequence)
Human Genome Project at DOE
10/10 Genetic Codes from Internet (Insulin),
Human Insulin DNA Sequence (
insulin.seq
) (
Annotated
)
10/12 Insulin Folding, Point Mutation, Intron Removal, Genetic Engineering
10/15 Video: The Rise of a Wonder Drug
10/17 Genetic Engineering, Restriction Enzyme, Ligase, Transformation, Genetic Engineering, Luciferase Example, Gene Theraphy,
A List of Restriction Enzymes from Sigma
Restriction Site Search Program
10/19 Cloning
Common Bacterial Cloning Vectors
pBR322
pUC19
,
pUC19 (alternate)
Cloning Luciferase into pBR322
10/22 Metabolic Pathways (Oxidation/Reduction, NAHD, ATP)
10/24 Metabolic Pathways (Glycolysis & TCA), Energy Efficiency
Biochemical Pathways Wall Chart
Glycolysis
(
annotated
)
TCA Cycle
(
annotated
)
Energy Efficiency
10/26 Stoichiometry
Stoichiometry: Ethanol yield as a function of Respiratory Quotient (RQ)
utilize glucose to produce ethanol
Stoichiometry: Biomass yield as a function of Respiratory Quotient (RQ)
utilize ethanol to produce acetic acid
Biomass Estimation from OUR Measurement
10/29
10/31 Cell Growth Kinetics
Estimate Growth and Yield Parameters from Batch Fermentation Data
Optimial Dilution Rate for Maximum Cell Productivity
11/02 Dynamic Simulation of Bioreactor
Dynamic Simulation of Continuous Fermentor
11/05
Quiz #2
11/07 Video: The Chemical Engineer and Biotechnology
11/09 Guest Lecture: Biofuel Cell
11/12 Steady-State Stability Analysis
Steady-States & Stability Analysis /w Andrew's Substrate Inhibition Model
11/14 Steady-State Stability Analysis
Linearized Stability Analysis of Continuous Fermentor
11/16 Structured Model
Structured Model with Intracellular Substrate, Precursors, and Macromolecules
11/19
Fed-Batch Fermentor, Dynamic Simulation of
Two-Compartmental Model for Incomplete Mixing
, Dynamic Simulation
11/21
Cell Recycle
Biodegradation in a Packed Bed Column
11/23 Holiday (Thanksgiving)
11/26
Segregated Model of Recombinant Cells
Oxygen Mass Transfer, Scale-Up
11/28 Guest Lecture by Ankit Patel of Genentech
11/30
Quiz #3
12/03 Instrumentation, Sensor
12/05 Sterilization, Heat Transfer,
Steam Sterilization
12/07 Purification
12/10 Purification
Demo (Ammonium Sulfate Precipitation, Chromatography, Dialysis, Gel Permeation, etc)
12/19 8am-10am
Final Examination
Return to Prof. Nam Sun Wang's
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Biochemical Engineering
Forward comments to:
Nam Sun Wang
Department of Chemical & Biomolecular Engineering
University of Maryland
College Park, MD 20742-2111
301-405-1910 (voice)
301-314-9126 (FAX)
e-mail:
nsw@umd.edu
©2007 by Nam Sun Wang
