Transcript Aligning and Using Assessments in Gateway Courses for

Aligning and Using Assessments in
Gateway Courses for Biochemistry
& Molecular Biology Majors
Ellis Bell
University of Richmond
Gateway Disciplinary Concepts I
Central Concepts of Biology
Central Concepts of Chemistry
The Central Dogma
Covalent and Noncovalent Structure of DNA
Evolution
What Makes a Sequence Unique
Protein Structure & Function
Structure of the Cell/Organism
Energy Needs of the Cell/Organism
Concepts of Metabolism
How Enzymes Speed Reactions
Regulation of Protein Structure & Function
Defects in Protein Structure & Function
Ethical Issues in Biology
Coulomb’s Law
Covalent Bonds
Noncovalent Interactions
Energy Diagrams for Reactions and Interactions
Energy Diagrams for Molecular Structure
Concept of Dynamic Structure
Chemical Structure and Reactivity
Energy, Enthalpy and Entropy
Rates & Rate Laws
Equilibria & Equilibrium Constants
The Peptide Bond
Laboratory Safety
Gateway Disciplinary Concepts II
Central Concepts of Physics
Central Concepts of Mathematics
Coulomb’s Law
Energy & Stability
Newton’s Laws of Motion
Friction
Concept of Diffusion
Free Energy, Enthalpy and Entropy
Randomness and Stochastic Processes
Probability
Deriving Equations
Using Equations
Populations, Averages, Normal Distributions and Standard Deviations
Linear Regression & Residuals
Essential Interdisciplinary Concepts: Word Association
Interdisciplinary Foundational
Concepts
Concept
Energy
Change Over Time
Structure/Function
Relationships
Modularity
Stochastic vs.
Deterministic
Processes
Modeling Scientific
Phenomena
Word 1
Word 2
Word 3
Word 4
Interdisciplinary Concepts
Concept
Energy
Biology
Chemistry
Physics
Mathematics
Kinetics, Metabolism,
Thermodynamics, Forms of,
Work, Potential vs Kinetic, Heat,
Calorimetry, Bonds, ATP, Entropy, in
vivo vs in vitro
Conservation, Time Evolution,
Kinetic & Potential, Equilibrium
Conservation, Integral,
Global Behaviour,
Stability
Change Over Time
Evolution/Death, Natural Selection
Reactions, Physical vs Chemical, Rates,
Stoichiometry, Reactions, Kinetics,
Evolution, Cell Signaling, Development
Newtons laws, Conserved
Quantities, Dynamics and
Kinematics concepts,
Trajectories, Stability/Instability
Derivative, Difference
Quotient, Evolution,
Dynamics
Structure/Function
Relationships
Organisms, Molecular form
dictates biological role,
Enzyme/Substrate
(Receptor/Ligand)
Folding, Bonding, Substituent Effects,
Enzymes, Molecules, Enzyme Kinetics,
Protein Folding, Operons, Double Helix
Feedback effects, Structure is
dynamic, Input/Output Signal
Processing
Emergent Properties,
Complexity
Modularity
Communities, Gene Networks,
Protein Domains, Facilitator of
Morphological Change
Systems, Transferability, Codependence, Co-factors, Pathways,
Structure, Protein Structure,
Metabolism Cell Re-engineering
Variable reduction, Choice of
generalized coordinate system,
Degrees of
Freedom(internal/external),
Complexity
Flexibility, Adaptability,
Portability, Robustness
Stochastic vs.
Deterministic
Processes
Probability Models, Random vs
Predestined
Entropy, Endo & Exothermic,
Probability & Statistics,
Reproducibility, Anabolism,
Catabolism, Evolution, Brownian
Motion
Dynamical equilibrium,
Importance of Fluctuations,
Brownian Motion, Stochastic
Signals
Randomness, Existence
and Uniqueness, Initial
Value Problem, Noise
Modeling Scientific
Phenomena
Systems, Simulation
Making reasonable approximations,
Newtonian vs QM, Force, Semiempirical Approaches, Protein-ligand
interactions, Bioinformatics,
Computational Biochemistry, Using
and Fitting Equations, Predictions
Phenomena, History of physics,
Relation between theory and
experiment, Experimentum
crucis
Data, Assumptions,
Equations, Simulation &
Evaluation
Notes
Chemist & Biochemist
The Importance of Mathematical Skills
The equation:
[C] = m.[B]/(K + [B])
describes the equilibrium of a fixed total concentration of A with varying
concentrations of B. Using the accompanying template sketch a graph that
represents the dependency of [C] on the concentration of B for a high
value of K and a low value of K
Practice of Science Skills
• a] You wish to make up 85mL of a solution containing
0.38M Glutamic Acid, C5O4N1H9, How many grams of
Glutamic Acid would you weigh out to dissolve in a
total volume of 85mL of water?
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• b] Once you have made up this solution, you decide
that you also need 50mL of an 0.1M solution of
Glutamic Acid and you are going to make it by diluting
some of the above solution with water. How much of
the above solution would you need to use?
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William is preparing to make Coomassie Brilliant Blue stain. From his high school chemistry and
biology classes, he is familiar with preparing simple solutions, including PPE use, but he has not
made a Coomassie Brilliant Blue solution before. He is provided the following formula:
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Dissolve 1 g of Coomassie Brilliant Blue (Bio-Rad) in 1 liter of the following solution:
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Methanol (50% [v/v])
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Glacial acetic acid (10% [v/v])
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H2O (40%)
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Stir the solution for 3-4 hours and then filter through Whatman filter paper. Store at
room temperature.
Questions:
William has not used Glacial Acetic Acid or Methanol before. What safety information should
he reference first?
Glacial Acetic Acid presents three major safety & health hazards, one of which might not be
obvious. What are those hazards?
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What is the primary physical hazard of Methanol?
What is the primary health hazard of Methanol?
What does the acronym PPE stand for?
What PPE should be used for this procedure?
Where should William prepare this solution, and Why?
Communication Skills
Access & Assess Information Skills
• During a proteomics screen you have identified
the peptide: isakrqlvsgikyil.
• Using bioinformatics approaches what can you
find about the structure and function of the
protein that the peptide was derived from?
• How would you attempt to define, using
bioinformatics approaches, which of the amino
acids in this peptide might be critical for the
biological function of the parent protein?
The Structure of the Curriculum
• Current
A series of unconnected courses from a
variety of departments
• Future
What Do we want students to know
and be able to do so we can teach
relevant, challenging Biochemistry &
Molecular Biology Courses to Juniors
What do we want students to know
and be able to do so they can get
engaged with research early in their
undergraduate careers?
Blended Introductory Courses
• IQS: Integrated Quantitative Science
• SMART Courses
Biology/Chemistry
Biology/Math
Biology/Physics
What are the problems/costs
Are they successful?
Stand Alone Biochemistry and
Molecular Biology Gateway Courses
• Interdisciplinary Concepts as the Gateway
Establish the connections between the
disciplines necessary for Biochemistry &
Molecular Biology
• Encouraging Students to engage in Research
• Sophomore Year
The Importance of Gateway
Assessment
Problems with Most Curricula
• Transfer Students
• Little connection between required courses
• Little connection to the current state of the
discipline
An Ideal Curriculum
Would:
1) Ensure all students enter a sophomore/junior level BMB
Course(s) with appropriate background, Skills and Focus on
Interdisciplinarity
2) Facilitate transfer students access to the major
3) Ensure all graduates have appropriate understanding of
foundational disciplinary and interdisciplinary material
necessary for the next steps in their career- Med School,
Grad School, the workplace etc.
4) Ensure all graduates have the skills- Lab, Workplace, Life- to
succeed in a science oriented careers
5) Excite students and retain them in STEM Oriented Majors
and Careers
An Ideal Curriculum might look like:
• 1st Year Bootcamp courses
Disciplinary Intro vs Blended Courses
Standard vs Advanced- pretest/placement etc
Introduction to Research-Skills, Broad Topic Areas
• 2nd Year BMB Gateway Course
Interdisciplinary Science
Gateway Assessment
• 3rd Year BMB Sequence, Biophysical Chemistry/Physical
Chemistry
Bootcamp as necessary
• 4th Year Capstone Experiences
Research, Internships, seminar, course etc