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Sharing Lab Exercises and Ideas in Biochemistry & Molecular

Biology Teaching

Ann Aguanno, Associate Professor of Biology, Marymount Manhattan College

Benjamin Caldwell, Professor of Chemistry, Missouri Western State University

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Our collegesOur coursesCourse contentExpectations

AssessingLab skillsImproving lab skillsChoosing lab topicsExamples of lab activitiesOther things to consider about your lab course

Lab manual, materials, etcLimitations/obstaclesLab assistants, mentors

Promega

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Our SchoolsMarymount Manhattan College, NYC

Small liberal arts, urban, diverse academically average student population

Missouri Western State University,Medium sized, rural, open access admission, diverse academically average student population

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Your schools?

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Molecular Biology and Biochemistry Lab courses

Cellular & Molecular Biology (BIOL 240)Sophomore level lecture and labRequired for all Biology majors10-12 students per lab section (1 section)

Biochemistry (CHE 370)Junior/Senior level lecture and labRequired for all Biology & Chemistry majors18 students per lab section (3 sections)

BIOL 240 Cell & Mol Bio Syllabus Lecture Topics

ChapterIntro to Cells and Chemistry 1, 2 Energy, catalysis and biosynthesis 3Protein Structure/Function 4 DNA & Chromosomes 5 DNA Replication, Repair 6DNA to Protein 7Control of Gene Expression 8Manipulating Genes & Cells 10Cell Cycle & Cell Death 18Tissues & Cancer 21

Grading: NY Times Articles, Primary Literature Analysis, 3 Exams

Lecture = 60%, Lab = 40%

Text: Alberts, et.al Essential Cell Biology (2010)

Lab Schedule (Spring 2009)

Intro, Safety and the Lab ReportSeparation of Proteins based on chargeSDS PAGE Analysis of ProteinsEnzyme Extraction and AnalysisNucleosome StructureDNA Sequence Analysis and BioinformaticsGenotype to PhenotypeDNA FingerprintingMicroscopy/Intro to Tissue Culture

Lab Manual – In house

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CHE 370 Biochemistry Syllabus Lecture Topics

ChapterChemistry in Biological Systems 1 Water 2Amino Acids, Peptides & Proteins 3 Protein Structure 4 Enzymes 6 Carbohydrates 7 Nucleotides & Nucleic Acids 8 Lipids & Membranes 10 & 11 Principles of Bioenergetics 13 Intro to Metabolism: Glycolysis, Kreb’s Cycle, Oxidative Phosphorylation 14, 16, 19

Grading: Quizzes, Question of the Day 3-4 Exams + Final Exam, Lecture = 80, Lab = 20%

Text: Lehninger (2008)

Lab Schedule (Spring 2009)

1 Check-in; Pre-Lab Assessment; Pipette Calibration;

2 CMC by Fluorescence 3 pH and Buffers4 Titration of Amino Acids5 Protein Quantification6 Gel Filtration Chromatography7 Bioinformatics8 Mid-term Exam9 Enzyme Kinetics I10 Enzymatic Kinetics II 11 Protein Purification Project12 Protein Purification Project13 Protein Purification Project14 Final Exam

Lab Manual – In house 78/17/2009

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Things to considerExpectations BIOL 240 – Sophomores

Pre-requisite materialMATH, MATH, MATH!!!! ( College Algebra, Stats???)General Chemistry- 2 semestersOrganic Chemistry- Co-requisiteGeneral Biology- 1 or 2 semesters?General Lab skills; safety, note taking, lab reports, data/graphical analysis, time management, handling mass & volume, minor instrumentation..more???

How to assess pre-reqs? Progress Proficiency?Pre tests and post test????????Practica????Observe Lab skillsLab notebooks/reports

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Things to considerExpectations CHE 370 - Juniors/Seniors

Pre-requisite material MATH, MATH, MATH!!!! Level ? – Stats, Coll. Algebra, Calculus?General and Organic Chemistry - 1 or 2 semesters?General Biology - how much? General Lab skills; safety, note taking, lab notebook skills, writing lab reports, handling mass & volume, instrumentation, pipetting, ………………more??

How assess pre-reqs? Progress Proficiency?Pre- & Post tests?PreLab Quizzes??Lab notebooks/reports

MWSU Skills SurveyPre-course personal assessment survey:

Ex: I am able to solve basic mathematical problems that require scientific notation or exponents

Strongly Somewhat No Opinion Somewhat StronglyDisagree Disagree Agree Agree

1 2 3 4 50% 0% 0% 35% 65%

Quantitative Test: 305 x 0.00000547Result: 24% Correct Mid-term Result: 88% Correct

MWSU Skills SurveyPre-course personal survey:

Ex: Given a set of data I could accurately determine the standard deviation.

Strongly Somewhat No Opinion Somewhat StronglyDisagree Disagree Agree Agree

1 2 3 4 56% 0% 6% 47% 41%

Pre-test: 0% correctly determined standard deviationMid-term: 87% correctly determined standard deviation

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MWSU Skills SurveyPre-course personal survey:

Ex: I can determine the accuracy and precision of a micropipettor

Strongly Somewhat No Opinion Somewhat StronglyDisagree Disagree Agree Agree

1 2 3 4 56% 0% 12% 23% 59%

Pre-test: 6% Could correctly determine accuracy/precisionMid-term: 47% could determine accuracy/precision

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What skills do you expect your students to have at the start of the course?

What skills should they have acquired by the end of the course?

How do you measure this?

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Lab SkillsSkills matrix discussion

Skills necessary Theory/background on experimental proceduresData analysisInstrumentation exposure

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Lab skillsReview of matrix and discussion

BMB SKILLS Adapted from BMBEd

Vol. 32, No. 1, pp. 11–16, 2004

WHEN SKILL IS LEARNED AND LEVEL TYPELower Level

Courses Upper Level BMB CoursesQuanti-tativ

e

Quali-

tativeLAB TECHNIQUES Theory Usage Proficiency Theory Usage Competence

Theory

Usage

Competence

Acid/Base chemistry

Affinity techniques

Amino acid analysis

cDNA

Cell Culture-Aseptic/Sterile Techniques

Cell Culture: Adherents vs. suspension

Cell Culture-Bactierial/insects

Cell Culture-Mamallian

Centrifugation-high speed

Centrifugation-separation and ppt

Centrifugation-subcellular fractionation

Centrifugation-ultraspeed

Characterization of carbohydrates

Characterization of lipids

Characterization of proteins

Chromatography-Affinity

Chromatography-ion exchange

Chromatography-size exclusion

Chromatography-HPLC

Cloning and Selection

Dialysis and Desalting

BMB SKILLS Adapted from BMBEd

Vol. 32, No. 1, pp. 11–16, 2004

WHEN SKILL IS LEARNED AND LEVEL TYPE

Lower Level Courses Upper Level BMB Courses Qua

nti-tativ

e

Quali-

tativeLAB TECHNIQUES

Theory

Usage

Proficiency

Theory

Usage

Competence

Theory

Usage

Competence

Acid/Base chemistryC111 C120 C120 C120

C321 C370

C321 C370

C321 C370

C321 C370 X

Affinity techniquesC370 C426 370 C370 C370 X

Amino acid analysis C370 B313 B313 X

cDNA B215 B215 B421 B421 B421B215 B421

B215 B421 B421 X X

Cell Culture-Aseptic/Sterile Techniques B215 B215 B215 B390 B390

B390, B421

B390 B421

B390 B421

B390 B421 B431 X

Cell Culture: Adherents vs. suspension

B205B215

B205 B215

B205 B215

B390 B411 B421

B390 B411B421

B390 B411 B421

B205 B215 B390 B421

B205 B215B390 B421

B390 B421 X X

Cell Culture-Bactierial/insects B215 B215 B390 B390B390 B421

B390 B421

B390 B421

B390 B421 X X

Cell Culture-Mamallian B411 B411 X

Centrifugation-high speed B215 B215 C370 C370 C370 C370 X

Centrifugation-separation and ppt C370 C370 X

Centrifugation-subcellular fractionation B215 B215 C370 C370 C370 C370 X

Centrifugation-ultraspeed C370

Characterization of carbohydrates

Characterization of lipids

Characterization of proteins C370 C370C370 C470 C370 X X

Chromatography-Affinity C370 C370 X

Lab Skills MatrixWhat do you think of the matrix?

Are techniques missing?

Should certain methods be removed?

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How to hone lab skillsPipetting activitySolution making activitySpectrophotometer exerciseUsing a pH meter exerciseMaking a dilution seriesCasting and running gels**Lab Skills Course*** (BIOL 251)

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Resources to hone lab skills

Don’t forget the MATH!!! Explain in words the relationship; V=IR, A=-log10(t)If there are 1 x102 blood cells in a 1 x10-2mL sample, how many blood cells in a 1.0mL sample?If you need 20 g NaCl to make 100 mL of solution Q, how much NaCl do you need for 1.5 L of solution Q?A solution has 5 ug/L of lysozyme. How much lysozyme is in 450 mL?Explain how 1/5, 1/50, 1/250 dilutions of a blood sample are made.How many micrograms of DNA are needed to make 100uL of a 100 ug/mL solution?How do you make a 1.2% solution of sugar in water?

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Things to considerReinforcement or redundancy?

compare syllabicommunication essential

Comparison of Lab ActivitiesCell/Molecular Biology Lab Biochemistry Lab

Pipette CalibrationCMC by Fluorescence pH and BuffersTitration of Amino AcidsProtein QuantificationGel Filtration ChromatographyBioinformaticsEnzyme Kinetics IEnzymatic Kinetics II Protein Purification ProjectProtein Purification ProjectProtein Purification Project

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Intro, Safety and the Lab ReportSeparation of Proteins based on chargeSDS PAGE Analysis of ProteinsEnzyme Extraction and AnalysisNucleosome StructureDNA Sequence Analysis and BioinformaticsGenotype to PhenotypeDNA FingerprintingMicroscopy/Intro to Tissue Culture

Comparison of Lab ActivitiesCell/Molecular Biology Lab Biochemistry Lab

Pipette Calibration;CMC by Fluorescence pH and BuffersTitration of Amino AcidsProtein QuantificationGel Filtration ChromatographyBioinformaticsEnzyme Kinetics IEnzymatic Kinetics IIProtein Purification ProjectProtein Purification ProjectProtein Purification Project

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Intro, Safety and the Lab ReportSeparation of Proteins based on chargeSDS PAGE Analysis of ProteinsEnzyme Extraction and AnalysisNucleosome StructureDNA Sequence Analysis and BioinformaticsGenotype to PhenotypeDNA FingerprintingMicroscopy/Intro to Tissue Culture

Comparison of Lab ActivitiesCell/Molecular Biology Lab Biochemistry Lab

Pipette CalibrationCMC by Fluorescence pH and BuffersTitration of Amino AcidsProtein QuantificationGel Filtration ChromatographyBioinformaticsEnzyme Kinetics IEnzymatic Kinetics II Protein Purification ProjectProtein Purification ProjectProtein Purification Project

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Intro, Safety and the Lab ReportSeparation of Proteins based on chargeSDS PAGE Analysis of ProteinsEnzyme Extraction and AnalysisNucleosome StructureDNA Sequence Analysis and BioinformaticsGenotype to PhenotypeDNA FingerprintingMicroscopy/Intro to Tissue Culture

Did you remember to bring a lab experiment?

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Example of Lab Activities:Biochemistry

Pipette calibration

Protein Assays

Protein Purification Project

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Examples of Lab Activities: Cell and Molecular BiologyAnalysis of nucleosome structure*

DNA sequencing analysis & Bioinformatics**

DNA fingerprinting using PCR**

*Modern Biology, Inc (modernbio.com)**Edvotek, Inc (edvotek.com)

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More things to considerLab manual: buy or make in-house?

Start from scratch, pre-made reagents or kits

Cost: $$$, time, effort

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Other things to considerLimitations/obstacles

Student skillsBreadth vs. depthWaste handling/disposalSafetyResources

Equipment, instrumentation, budgets

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Even more things to considerPeer mentors

Utilize upper level undergraduates as tutors, instructors, advisors

Lab AssistantsTeaching Assistants in the lab

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PromegaIntroduction to Promega Education Kits

DNA Fingerprinting

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Where to Get More InformationAdams, D.; Lab Math, 1st Ed; Cold Spring Harbor Laboratory Press; New York, 2003Seidman, L., Moore. C; Basic Laboratory Methods for Biotechnology, 2nd Ed; Benjamin Cummings: San Francisco, 2009Chapman, C; Basic Chemistry for Biology, 2nd Ed.;McGraw Hill; New York,1999BMBEd http://www3.interscience.wiley.com/journal/122288004/grouphome/home.htmlLab Skills paper: BMBEd 32 (1): 11-16 (2004)Journal of College Science TeachingASBMB recommended curriculum http://www.asbmb.org/CareersAndEducation.aspx?id=432Promega Corporation (Promega.com)Modern Biology, Inc (Modernbio.com)Edvotek, Inc (Edvotek.com)

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Acknowledgements

Dr. Melissa Daggett, MWSU Biology Dept.Devin Columbus , MMC Biology AlumniAshley Brower, MMC Lab SupervisorMichele Arduengo, Promega, CorpPoonam Jassal, Promega, Corp

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Open discussion

Concerns

Typical lab problems

Suggestions