BiotechnologyProcess Engineering

This two course sequence offeredin the Fall and Spring semesfersis desfgned to provide ChemicalEngineering and Biochemistry & MolecularBiology sfudenfs training in engineeringof cellularprocesses. Ihrs course is ideafor sfudenfs interestedin potentiallypursuing careersor graduate studies in biotechnology, bioengineering,or the pharmaceuticalindustry

Gourse1: GhE5928 "lntroduction to BiochemicalEngineering" Taughtby Prof.Susan Roberts (ChE) OfferedFall 2008, Mondays and Wednesdays from 8:45am - 10:00am An introductorylecture course in biochemicalengineering, focusing on the application of chemicalengineering and biochemistry/molecular biology principles to thedesign andoptimization of processesin thefood and pharmaceutical industries. Topics coveredwill include enzyme catalysis, metabolic engineering and regulation, cell and tissueengineering, drug delivery, fermentation, microbial growth, bioreactor design, andproduct recovery and purification. Open to highlymotivated juniors, seniors and graduatestudents in chemicalengineering, biochemistry & molecular biology, chemistryor otherlife sciences disciplines, or by consentof instructor.No prerequisitesare necessary. Note:for Chemical Engineering students, this course will count as a technical electiveand is requiredof studentsto obtainthe Concentration in Biochemical Engineering;for Biochemistry& Molecular Biology students, this course will count as an advancedtechnical elective.

Course2: ChES90A/Biochem 590A "Biotechnology Process Engineering Laboratory" Co-Taughtby Prof.Louis Roberts(BMB) and Prof.Susan Roberts (ChE) OfferedSpring 2009, Tuesdays and Thursdays from 8:30am-12:30 pm A comprehensivelaboratory course in biotechnologyprocess engineering focusing on thelaboratory skills necessary to bringa productto the marketplace.Students will workin interdisciplinaryteams to designa processto supplya high-valueproduct, Molecularbiology tools will be usedto engineercells lines to expressthe protein of interest;cells will be cultivatedin bioreactorswith designed process strategies; the proteinproduct will be recoveredfrom the fermentation broth and purified using a widerange of techniquesincluding filtration, chromatography and crystallization; the finalprotein product will be characterizedin terms of proteinquality and function. State-of-the-arttechn iq ues usi ng high-throughput technolog ies wil I be integrated throughoutthe course.This course will involve interaction with industry and students willbe exposed to goodmanufacturing practices and FDA guidelines. Previous experiencein eitherbiochemistry or biochemicalengineering is required. Note:for Chemical Engineering students, this course will count as the second senior laboratorycourse (substituting for ChE 402) and is recommendedof studentsto obtainthe Concentration in Biochemical Engineering; for Biochemistry & Molecular Biologystudents, this course will serve as a substitutefor Biochem526. Universityof Massachusetts,Amherst Fail 2007

CHE 5928 Introductionto BiochemicalEngineering F all 2007: ProiectedCourse Schedule

II:/;,iI ,: :VYili$il\ lDate Readihs 1 5-Sep Course Overviewof biotechnologyand the ChapterI introduction evolutionof the "biochemical engineer" 2 I 0-Sep Cell biology Cell structureand experimental Chapter2:2.1-2.2 background techniques,molecules of the cell (proteinsand antibodies) 12-Sep Moleculesof the cell continued Chapter2:2.2-2.4 (carbohydratesand nucleic acids), cell/tissueculture, nutrient requirements.medium composition

J I 7-Sep Enzymes Enzymekinetics, determinationof rate Chaoter3:3.1-3.3 parameters,enzyme inhibition 19-Sep Appliedenzyme catalysis and Chapter3:3.4-3.7 immobilizedenzyme systems, transportlimitations A T 24-Sep Metabolic Centraldogma of molecularbiology; Chapter4:4.1-4.8 control metabolicresulation 26-Sep RecombinantDNA Chapter8 technolosv/seneticensineerins 5 l-Oct Metabolic Overviewof cellular metabolism, Chapter5 engineerinp stoichiometrv.material balances Chapter14:14.8 3-Oct Relevantproblems in metabolic Refer to handouts engineering 6 8-Oct ColuunusDav - No Cla.ss 9-Oct* Microbial Introductionto cell growth, Chapter6:6.1-6.2 growth and experimentaltechniques used to product measuregrowth, batch kinetic formation/Cell patterns,yield coefficients culture l0-Oct Ex,q.NrI 7 15-Oct Effect of environmentalconditions on Chapter6:6.2-6.5 cell growth,models for quantifying cell growth, growth inhibitors, continuousculture l7-Oct Bioreactor Choiceof cultivation method, Chanter9:9.1-9.6 designfor cell modificationon batchand continuous cultivation reactors,immobilized cells,diffusion limitations 8 22-Oct Bioreactoroperation, scale-up and Chapter10: 10.1-10.5 control (oxygensupply) 24-Oct Bioprocessesto Plant cell culture,challenges for Chapter13 and supply valuable designof plant bioprocesssystems handouts products *Note that on this Tuesdava Monday classschedule is followed.

September5,2007 CHE 5928 page I University of Massachusetts,Amherst Fall 2007

CHE 5928 Introductionto BiochemicalEngineering Fall2007 ProjectedCourse Schedule(cont.) ' !Veek Reading . 9 29-Oct Taxol@Proiect Refer to handouts 31-Oct Mammalian cell culture, industrial Chapter12 and applicationsand considerations handouts 10 5-Nov "Omics" Proteornics- definitions,challenges, Refer to handouts approachesto approaches,cuffent technologiesand understanding applications cellular metabolism 7-Nov Genomicsand bioinformatics Refer to handouts 1l 12-Nov VntnRnN'sDay - No Ct-l.ss 14-Nov Tissue Definition,challenges, overview of Chapter15 engineering the field t2 19-Nov Currenttechnologies (e.g., cell Refer to handouts encapsulation,bioreactor design, materialsprocessing) and recent advances 21-Nov Ex,q,N,III l3 26-N6v Bioprocess Overview,considerations for special Chapter14:14.1-14.5 design systems(e.g., genetically engineered svstems) 28-Apr Product Insolubleparticles (cells and solid Chapter11: 11.1-11.3 recoveryand particulates)s eparation/cell disruption ouri/ication t+ 3-Dec Separationof solubleproducts Chapterll:11.4 5-Dec Final purification and integrationof Chapterll:11.5-11.7 fermentationand senaration 15 10-Dec Student Studentpresentations I presentations 12-Dec Studentpresentations II

September5, 2007 CHE 5928 page 2 Biochemistry/ChemicalEngineering 590.{ Spring 2008- Updated3-25-08 Tuesda Thursda January29 January31 Inhoductionto the courseand safery;central dogma of . Techniquesof directionalcloning: PCR and primer design, molecularbiology; basiclaboratory skills assessment, r estrictiondigestion, ligation, transform at ion I PCR targetgene from plasmid,plan directionalcloning strate February 5 F'ebruary 7 . Determining the presence and orientation of a DNA insert . Designing of restriction mapping analysis; DNA sequencing . PrepareDNA- digestplasmids, run agarosegel and purify . Colony screeningby PCR and identificationof conectplasmids fragments by agarosegel electrophoresis . Lisate DNA and transformbacteria Februaryl2 February14 Performminipreps from selectedcolonies, assess plasmid . pET expressionsystem; principles of activity assays purity, setup diagnosticrestriction digests; prepare DNA for t Principles offermentation and cell growth I sequencing Studentpresentation and written report format ' TransformTranstbrmhost cells with correctconect exnressionexpression plasmids February 2l No class- Mondav schedulefollowed Group presentationson molecularcloning module (GLl February 26 February28 Smallscale induction experiments (i.e., effect of induction . Considerationsfor runninga controlledfermentationsystem time, inducerconcentration, and addition ofcarbon sourceon . Performactivity assays on smallscale cultures and calculate proteinexpression); collection of samples enzymeactlvltles r Tour of fermentationlaboratorv in GoessmannLab 51 REPORTI (Molecular DUE (GLI March 4 Seebelow Group presentationson induction experimentsand fermentation strategv - discusswith Prof. Roberts2(GL2 March6,7,ll,12, 13 Fermentationoperation; collection of cell pelletsand storageunfil proteinpurification. Seeadditional handout for fermentation scheduleas time will be neededprior to eachfermentation dav for cultureinitiation and medium oreoaration. March 25 March 27 . Cell recoveryand protein purification Identif,ringoptimal cell breakageconditions (detergent lysis, . Group discussionto plan cell breakageexperiments and sonication,freeze-thaw, protease inhibitors, etc.); Small scale purification scheme experimentwith inducedcell pelletsas validated by instructors; activitv assavson crude extracts April I April3 . Lysecells ' Gelfiltration purification; p-gal activity and Bradford assays . Ammoniumsulfate precipitation; B-gal activity and Bradford assays . Preparegel filtration resin REPORT 2 (Induction Experimentand Fermenter Operation)DUE (GL2 April8 April 10 - . Vertexlab tour no lab sessiontoday Affinity columnpurification; B-gal activity and Bradford assays for SDS-PAGE April l5 April lT ' SDS-PAGEon all samples Group presentationson recoveryand purificationresults (GL3) . Beginimmunoblotting analysis . Finishpurification calculations April22 April24 . Finishimmunoblotting analysis . Enzymekinetics and protein characterization . . AnalyzeSDS-PAGE gels and immunoblots Determinesedimentation coefficient for B-gal . Usethrombin to cleavehis-tag from B-gal REPORT 3 (Protein Recovervand Purification DUE L3 April 29 May I . DetermineI(,n, v*o^ and turnover number for nativeB-gal r Furtherkinetics analysis (e.g., pH dependence,T dependence, heattreatment, inhibitor addition, etc. May 6 May8 . Summaryof laboratoryobjectives, accomplishments, etc.; Grouppresentations on p-galcharacterization and kinetic studentevaluations anal L4 May 13 REPORT a (B-galCharacterizationand Kinetic Analysis) DUE (G *italics indicates lecture time; GL = group leader responsible for coordinating related experiments and reports.