MODELING PROTEINS, ENZYMES, ANDHOW WATER DRIVES STRUCTURE/FUNCTION
LEARNING OBJECTIVES
Educators attending this workshop will:
➢Utilize tools that support NGSS student learning outcomes of three dimensional lesson design including -
➢Molymods to model basic amino acid structure and build a dipeptide
➢Amino Acid Starter Kit© to simulate protein folding
➢Enzymes in Action © to demonstrate enzymatic specificity and actions
➢Acetylcholinesterase Active Site Cube © to apply knowledge of protein structure/function to an observed environmental phenomenon
➢ Landscapes of David Goodsell © to apply multiple representations to a concept
➢ Learn something new and interesting for your own professional development.
➢HAVE FUN!
LEARNING OBJECTIVES
What NGSS dimensions will be targeted?
SEPs CCCs DCIs
Asking questions PatternsPS1.A: Structure and
properties of matter
Developing and using models Cause and effect PS1.B: Chemical reactions
Constructing explanationsScale, proportion, and
quantityLS1.A: Structure and function
Structure and functionLS2.C: Ecosystem dynamics,
functioning, and resilience
the Mosquito
Protein Structure versus . . .
Engage!https://www.orkin.com/other/mosquitoes/
https://cdn.rcsb.org/pdb101/learn/resources/what-is-a-protein/what-is-a-protein.pdf
Amino Acids:Building Blocks for Proteins
Explore! Explain!
Amino Acids:D and L Forms of Amino Acids
Extend!http://www.phschool.com/science/biology_place/biocoach/bioprop/landd.html
Building a Dipeptide
The Protein Folding Problem
Beware student preconceptions about protein folding!
Amino acid #1
Amino acid #2
http://www.biochem.ucl.ac.uk/~martin/c40/peptide.html
Modeling Protein Structure
Elaborate!
Identify and Sort the R Groups
SortIdentify
Modeling the Primary Structure
➢ 2 cysteine side chains (green).
➢ 2 acidic side chains (red).
➢ 2 basic side chains (blue).
➢ Your favorite 3 hydrophilic amino acids (white).
➢ Your favorite 6 hydrophobic amino acids (yellow).
➢ Randomly distribute them on the TOOBER. (Space them about three inches apart to get an even distribution).
You will need 15 total side chains:
Modeling Tertiary Structure
Fold your protein according to basic principles of chemistry and physics:
➢ In an aqueous environment, where do you expect the hydrophobic side chains to fold? Why?
➢ Likewise, consider where the hydrophilic side chains would fold.
➢What interaction may occur between acidic and basic amino acids?
➢What interaction may occur between cysteineamino acids?
Modeling Secondary Structure
Beta Sheets
Alpha HelicesWhy are secondary structures important to protein structure/function?
Modeling Quaternary Structure
Hemoglobin
Modeling Enzyme Action: Catabolism
Extend!https://www.khanacademy.org/science/biology/energy-and-enzymes/introduction-to-enzymes/a/activation-energy
Modeling Enzyme Action: Anabolism
Extend!
Modeling Enzyme Action: Specificity
Extend!
Competitive Inhibition Noncompetitive Inhibition
Modeling Inhibition
Extend!
the Mosquito
Protein Structure versus . . .
Engage!https://www.orkin.com/other/mosquitoes/
https://cdn.rcsb.org/pdb101/learn/resources/what-is-a-protein/what-is-a-protein.pdf
Neuromuscular SignalingA Landscape from David Goodsell
https://www.education.com/
A Molecular Story:Acetylcholinesterase!
Resources!http://www.rcsb.org
http://pdb101.rcsb.org/
Resources!
THANK YOU!
How Can I Get These Great Models?
Purchase from 3D Molecular Designs
https://www.3dmoleculardesigns.com/Education-Products.htm
using your 20% show special discount: SC19
Borrow from the Model Lending Library:
http://cbm.msoe.edu/lendingLibrary/index.php
THANK YOU!
For more molecular stories. . .
Come visit us at booths 1267 and 1269!
We hope to see you soon!