1. Protein Structure Basics!
Empowering Teachers
Through Modeling
Protein Structure Basics!

2. Learning Objectives Educators attending this workshop will:
Utilize tools that support NGSS student learning outcomes of three dimensional lesson design.
Molymods
Amino Acid Starter Kit©
Learn something new and interesting for your own professional development.
HAVE FUN!

3. What NGSS dimensions will be targeted?
Learning Objectives
What NGSS dimensions will be targeted?
SEPs
CCCs
DCIs
Asking questions
Patterns
PS1.A: Structure and properties of matter
Developing and using models
Cause and effect
PS1.B: Chemical reactions
Constructing explanations
Scale, proportion, and quantity
LS1.A: Structure and function
Structure and function
LS2.C: Ecosystem dynamics, functioning, and resilience

4. Protein Structure versus . . .
the Mosquito
The Phenomenon!

5. Amino Acids:
Building Blocks for Proteins

6. Amino Acids:
D and L Forms of Amino Acids

7. Amino Acids Exist as Zwitterions!

8. Amino Acid Form is Dependent on pH!

9. Building a Dipeptide

10. Beware student preconceptions about protein folding!
The Protein Folding Problem
Beware student preconceptions about protein folding!
Amino
Acid #1 #2

11. Modeling Protein Structure

12. Modeling the Primary Structure
You will need 15 total side chains:
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). 

13. 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, where would the hydrophilic side chains occur?
What interaction may occur between acidic and basic amino acids?
What interaction may occur between cysteine amino acids?

14. Modeling the Primary Structure
Some points to ponder:
Why are all of the folded structures in this room different?
2. If an unlimited number of each of the 20 amino acid sidechains were available
How many different sequences of 15 amino acids are possible?
3. It is estimated that there are 100,000 different proteins in the body. If the average protein is about 300 amino acids long, then there are possibilities! Why are there fewer proteins in the body than possible?

15. Modeling Secondary Structure
Beta Sheets
Why are secondary structures important to protein structure/function?
Alpha Helices

16. Modeling Quaternary Structure
Hemoglobin