ASBMB Student Centered Education Conference July 2011
Ann Aguanno, Associate Professor of Biology
Marymount Manhattan College
Benjamin Caldwell, Professor of Chemistry
Missouri Western State University

• Introductions
• Two laboratory courses
• Student Lab Skills
– Breakout
• Specific Lab Activities
– Breakout
• Pre and Post-Assessment
– Breakout
• Open Discussion
A

o Small (1700) liberal arts college, urban, diverse, academically average student population
Missouri Western State University o Medium-sized (6,000), open access admission, diverse, academically average student population

• Small liberal arts schools?
• PUI?
• R1?
• HBCU?
• Community Colleges?
• Other?
• Biochem. vs. Mol Biology?
A

Cellular and Molecular Biology (BIOL 240) o Sophomore level course o Required for all Biology majors o 10-12 students per lecture; 10-12 students per lab section
Biochemistry (CHE 370) o Junior/Senior Level course o Required for all Biology & Chemistry majors o 48 students per lecture; 16 students per lab section

Lecture
Intro to Chemistry and Cells
Energy, Catalysis, Biosynthesis
Protein Structure and Function
DNA & Chromosomes
DNA Replication, Repair
DNA to Protein
Analyzing Genes
Control of Gene Expression
Cell Cycle and Cell Death
Tissues & Cancer
Laboratory
Lab Safety and the Lab Report
Separation of Proteins by Charge (protein structure; chromatography; micropipette use)
Separation of Protein by MW (SDS PAGE)
Nucleosome Structure (chromatin structure; DNA electrophoresis)
Karyotyping Human Cells (cytogenetics; Microscopy )
Advanced Microscopy/Cell Culture (sterile Technique; photomicroscopy )
Intro to Bioinformatics: DNA Sequencing (DNA sequencing methods; genomics)
Cloning, Transformation, Phenotype Assay (microbiology; transformation; cloning)
Cell Culture (con’t); Insect Cells
PCR-based DNA Profiling (PCR technology )
Grading: 3 Exams, Primary Literature Analysis, Lab Performance and Reports
Textbook: Essential Cell Biology Alberts, et. al, 3rd
Textbook: Reading the Primary Literature , by Gillen
Lab Manual: In-House

Lecture
Chapter
• Chemistry in Biological Systems 1
• Water 2
• Amino Acids, Peptides & Proteins 3
• Protein Structure 4
•
• Enzymes
Carbohydrates
6
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
Lab Schedule
• Check-in; Pre-Lab Assessment;
Pipette Calibration;
• CMC by Fluorescence (Solutions/Graphing)
• pH and Buffers
• Titration of Amino Acids (reinforce pKa’s)
• Protein Quantification (BCA/Bradford)
• Gel Filtration Chromatography
• Bioinformatics
• Mid-term Exam (data analysis/protocols)
• Protein Purification Project (Ion Ex. chrom )
• Protein Purification Project ( Affinity chrom.
)
• Protein Purification Project (SDS-PAGE)
• Protein Purification Project (Western Blot)
• Enzyme Kinetics (LDH)
• Final Exam
Grading: 3-4 Exams + Final, 5-6 quizzes, Questions of the Day,
Lab Performance and Reports (20%)
Textbook: Biochemistry, Garrett & Grisham, 4 th ed.
Lab Manual: In-House
4/17/2020 7

• What are the Fundamental Skills? (5 essential)
• Skills Required for Your Laboratory Course
– Biochemistry vs. Molecular Biology Courses?
B

2:15

• Courses o MATH, MATH, MATH!!! (Level???) o General Biology (1-2 semesters?) o General Chemistry (2 semesters?) o Organic Chemistry (1-2 semester?; coreq ok) o Writing 1 and 2

• Basic Skills o Time management, writing, reading, collaboration o Safety, note taking, lab reports, data/graphical analysis, unit conversion, standards or references, basic statistics o Handling mass & volume, pipetting, minor instrumentation (e.g. pH, centrifugation, basic spectrophotometry) o Multiple ways to analyze, threshold, sensitivity, stringency
A

• Fundamental Skills?
• Specific Skills Required for Your Course?
– Biochemistry vs. Molecular Biology Courses?
A

2:45

o Communicate and apply fundamentals of cellular & molecular biology o Utilize scientific method, critical thinking skills and problem based-learning techniques o Perform laboratory- based scientific investigations by applying the concepts and techniques learned o Apply concepts and techniques learned to current scientific and medical topics o Present and critique experimental results o Analyze primary cellular and molecular biology literature

o Demonstrate proficiency in basic biochemistry lab techniques o Identify connections between experimental design and data generated from procedures o Differentiate between control and experimental data o Perform mathematic transformations of raw data to useful and meaningful information o Generate data in multiple formats (graphs, charts, observations) o Develop conclusions based on objective and logical analysis, interpretation and evaluation of data and observations o Maintain a laboratory notebook using proper scientific verbage and notation in order to effectively communicate within the scientific community o The laboratory experience should also reinforce topics discussed in lecture

3:00

• 3 methods

• Assess Lab Notebooks
• Assess Lab Reports
• Practica
• Exams
• Regular Observations of Lab Performance
• Oral vs. Written Communication
• Pre and Post Test

Use the following scale, circling the appropriate statement that best matches your feeling about the following laboratory related questions.
Strongly Somewhat
Disagree Disagree
1 2
Neutral/ Somewhat Strongly
No Opinion Agree Agree
3 4 5
1. I am able to solve basic mathematic problems that require scientific notation or exponents.
1 2 3 4 5
3. I can accurately determine the correct number of significant digits in a number.
1 2 3 4 5
79. Complete the following mathematical equation, and give your answer with the proper number of significant digits.
a. 4.0 x 10 5 b. 4.00 x 10 5 c. 4.00367 x 10 5 d. 400,367
545
0 .
.
1 x 21 .
3
029


Sample of pre-course survey at
(Spring 2010 results).
I understand & can Identify dependent variables
I understand the differences between accuracy & precision
I understand basics of chromatography
I can generate a standard curve & determine concentrations of unknowns.
I understand the need for more than 1 type of protein assay
I understand the need for more than 1 type of protein assay
I understand the basic concepts & importance of enzyme kinetics
I understand how electrophoresis is used to separate protein/DNA
13
8
8
8
0
0
0
0
6
56
15
6
40
73
31
33
19
23
44
35
54
27
29
46
27
10
21
23
6
0
21
15
35
2
13
27
0
0
19
6
Sample survey questions & responses (%) are shown (grey)
Results of task related questions (Far right , yellow) displays overall class performance
(% correct).
73
54
56
67
69
48
67
42

Scores represent percentage of students receiving full credit for each question.
Class Q1 Q2 Q3 Q4 Q5 Q6 Q7 Q8 Q9 Q10
Bonus
Q's
Average
Exam
Score (%)
Spring
2010
Spring
2011
92.2
76.3
92.5
75.6
66.7
64.4
68.1
80.4
56.3
81.5
70.4
95.6
68.0
83.5
75.7
73.2
73.5
68.5
81.4
69.7
84.6
65.2
79.2
82.9
However, some areas still requiring improvement (indicated by yellow) include:
• Interpreting graphic data (Q’s 2, 6, 9) – graphical/SDS-PAGE results
• Comprehension of enzyme assays and kinetics (Q’s 5, 9)
• Performing biochemical calculations (Q’s 7, 9)

– Skills necessary
– Theory/background on experimental procedures
– Data analysis
– Instrumentation exposure
22

WHEN SKILL IS LEARNED AND LEVEL
BMB SKILLS
Adapted from BMBEd
Vol. 32, No. 1, pp. 11 –16, 2004
Theory
Lower Level
Usage Proficiency Theory Usage Competence
LAB TECHNIQUES
The ory
BMB Courses
Usa ge
Competenc e
Acid/Base chemistry
Affinity techniques • Review of matrix and discussion 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
TYPE
Qua ntitativ e
Qual itativ e
23
Dialysis and Desalting

BMB SKILLS
Adapted from BMBEd
Vol. 32, No. 1, pp. 11 –16, 2004
WHEN SKILL IS LEARNED AND LEVEL
Lower Level
Courses Upper Level BMB Courses
TYPE
LAB TECHNIQUES
Acid/Base chemistry
Affinity techniques
Amino acid analysis cDNA
Cell Culture-Aseptic/Sterile
Techniques
Cell Culture: Adherents vs. suspension
The ory
C111
C120
Usag e
C120
Proficienc
C120 y
Theor y
C321
C370
C370
C426
C370
B215 B215
B215 B215
B205
B215
B205
B215
Cell Culture-Bactierial/insects
Cell Culture-Mamallian
Centrifugation-high speed
B215 B215
B215 B215
Centrifugation-separation and ppt
Centrifugation-subcellular fractionation B215 B215
Centrifugation-ultraspeed
Characterization of carbohydrates
Characterization of lipids
B215
B205
B215
B421
B390
B390
B411
B421
B390
B411
C370
C370
C370
C370
Usag e
C321
C370
Compete nce
C321
C370
Theor y
C321
C370
Usag e
Compete nce
370
B421
B390
B390
B411
B421
B390
B411
C370
C370
C370
B421
B390,
B421
B390
B411
B421
B390
B421
C370
B313
B215
B421
C370
B313
B215
B421
B390
B421
B205
B215
B390
B421
B390
B421
B390
B421
B205
B215
B390
B421
B390
B421
C370
C370
C370
C370
B421
B390
B421
B431
B390
B421
B390
B421
Characterization of proteins
Chromatography-Affinity
C370
C370
C370
C370
C370
C370
C470
C370
C370
Qua ntitativ e
Quali
tativ e
X
X
X
X
X X
X
X
X
X
X
X
X
X
X
X
X

• Does student arrive on time?
• Does student have all required lab materials?
– Notebook
– Manual
– Lab coat
– Goggles
• Can student answer questions regarding the day’s lab activity?
• Can student perform methods associated with day’s activity?
• Does student set up their experiment independently?
• Does student use time well?
• Does student write in notebook
• Does student ask questions that they should already know the answers to?
• Does student critique/evaluate their results effectively?
• Can student troubleshoot?
• Can the student explain to other students?
• Does the student clean up their bench and store materials correctly?
A
3:30

• How to pour gels vs. precast (time vs. $$)
• Kits vs. preparing solutions/reagents ahead of lab time
• Using TA’s to prep?
• Other
B

• Incorporate into Course (BIOL 240)
– Pipetting Activity, Solution Making
– Spectrophotometry Activity
– pH Exercise
– Casting and Running gels
– Sterile Technique
– Instrumentation Principals
• Lab Skills Course at MMC (BIOL 251)
A

Lab Skills
Course
(BIOL 251)

EVERYDAY CHECKLIST
•
•
•
•
•
•
•
•
GENERAL LAB ITEMS
• Did you make a schedule for when you will be working and in the lab?
• Do you have proper PPE?
• Did you check your email?
Did you check to see if any notes were left for you?
• Did you make a list for yourself of task for day
• Are these tasks in order of importance
TISSUE CULTURE
• Did you check Tissue Culture?
• Did you look at your cells under
Did you have the proper background and readings for task?
Did you prepare all reagents and materials for experiment day before?
microscope ?
• Did you check for contamination in
Did you write out the protocol in your lab book?
Did you write in your lab notebook?
Did you clean up after the experiment
– Cleaned dishes/bench paper/ put away reagents and instruments incubator?
• Did you check the CO
2 tanks?
• Full/leaking/at right PSI
• Did you check the incubator?
Did you print out a copy of results and put in results binder
Did you put results in lab notebook
• Temp/CO
2 input
• Did you check to see if you have all
• Did you restock supplies used
– Pipet tips/ autoclaved deionized water/ pipettes
– If you used the last one did you report it?
• Did you properly label all reagents?
•
• materials under hood/ stocked in TC
Did you do all TC chores
Did you check Tissue Culture before you locked up for night?
• Did you properly store all reagents?
– Rm temp/ 4°/-20°
• Is your work space clean and clear?
• Did you make a list of tasks for the next day?
• Did you prepare all reagents materials and lab notebook for tasks next day?
•
•
• Incubator on at right settings/ no leaks/
UV LIGHT ON?
Are the proper signs on the door for TC
Did you put out the garbage
• Did you put out the lab garbage?
• Did you lock the lab?
• Did you say goodbye?
Acid into water
DNA runs to red A

WORDS OF WISDOM
• Make a schedule and stick to it
• Do not eat in the lab
• Don’t get too comfortable
• Make a list of tasks and arrange them in order of importance
• Do not put off small tasks or they will never get done
• Do TC in the morning when you are bright and awake
• Write out complete protocol in lab notebook day before experiment
• Make sure all reagents are out/prepared the day before experiment
• Unlock doors and return keys
• Do not keep common lab materials in 611
• Clean up before you leave each night
• Haste makes waste (take it slow)
• Make time in week to read primary lit papers
• Go to lab meetings with results printed or ready to be easily displayed
• Go to lab meetings prepared to discuss issues and topics
• Be honest, don’t say you did something when you didn’t
• Be honest when you feel overwhelmed
• It takes time to place orders (make sure you have all materials)
• You know it when you can explain it to someone else
• Explain it in different ways
• mg/ml= ug/ul
• Thawing on ice may take a while; take that into account
• Give yourself a time frame then double it to get something done
A

• Compare Syllabi
• Communicate
B

MMC Cell/Molec Lab (240) Biochemistry (441)
• Lab Safety and the Lab Report
• Separation of Proteins by Charge
• Separation of Protein by MW
• Nucleosome Structure
• Karyotyping Human Cells
• Advanced Microscopy/Cell Culture
• Intro to Bioinformatics: DNA Sequencing
• Cloning, Transformation, Phenotype Assay
• Cell Culture (con’t); Insect Cells
• PCR-based DNA Profiling





A

MWSU Biochemistry Lab (370) Molec Cell Bio Lab (115)
• Pre-Lab Assessment
• Pipette Calibration 
• CMC by Fluorescence
• pH and Buffers
• Titration of Amino Acids
• Protein Quantification (BCA/Bradford)
• Gel Filtration Chromatography
• Bioinformatics
• Protein Purification Project (Ion Ex. chrom)
• Protein Purification Project (Affinity chrom.)
• Protein Purification Project (SDS-PAGE)
• Protein Purification Project (Western Blot)
• Enzyme Kinetics


(Lowry)

B

• Peer Mentors
• Teaching Assistants
• Buy or make Lab Manual?
• How much student prep?
• Kits?
• Cost?
• Waste Handling/Safety
• Resources
A

• www.Drop-box.com
• Share your Lab ideas, experiments, exercises, etc…
• Register, let Ben know – share folder