Bioengineering and Protein Folding
Bioengineering and Protein Folding
Presenter: Hortense Brice Biotechnology Center of Excellence (BCoE) Lindblom Math & Science Academy
Protein Models
Example A
Example B
Protein Models
Example A
Example B
Ac3vity I Focus (Essen3al) Ques3ons 1. What is ScienDfic Modeling? Does Modeling Relate to this AcDvity? 2. How Do the Chemical ProperDes of Amino Acids Determine the Folding of a Protein into its Final 3-‐D Shape? 3. Why are the Colored Tacks (Amino Acids) Placed in Random Order? 4. Does Protein Folding Illustrate the Biological Theme of Form Fits Func3on?
Ac3vity Materials 1. 2. • • • • • •
One (1) Mini-‐Toober 15 Colored Tacks 2 Blue Tacks 2 Red Tacks 6 Yellow Tacks 3 White Tacks 2 Green Tacks Cell Phone or iPad (for Photos of Models)
Amino Acid (Structural Formula)
Ac3vity Instruc3ons 1. Distribute the Tacks Randomly Along the Toober. Spacing: Place the Tacks 3 Inches Apart. 2. Fold your Protein Following the Principles of Chemistry that Determine Protein Folding. 3. Chemical Principles—Amino Acids May be: • Hydrophobic (non-‐polar): Yellow Tacks • Hydrophilic (polar): White Tacks
• Charged: Blue Tacks, Basic. Red Tacks, Acidic. Cysteine Sidechains: Green Tacks DocumentaDon: Take a Digital Photo of Your Folded Protein. Leave Protein Folded.
Four Levels of Protein Structure
Background Informa3on 1. Proteins are Folded PolypepDdes. 2. PolypepDdes are Polymers of Amino Acids. 3. Amino Acids can be Classified as Non-‐polar, Polar, Acidic (negaDvely charged) or Basic (posiDvely charged). 4. Chemical ProperDes (or ClassificaDon) of Amino Acids are Determined by Sidechains (R Groups).
Background Informa3on (page 2) 5. These Chemical ProperDes Govern Chemical InteracDons among the Amino Acids. 6. Basic Laws of Chemistry Determine the Proper Folding of Proteins into Specific Shapes. 7. Protein Shape determines protein funcDon. 8. Proteins must be folded (correctly) in order to funcDon properly.
Protein Engineering Facts 1. Protein Engineering is an example of bioengineering. 2. Protein Engineering Designs New Proteins Not in Existence. 3. Goal: Design of Protein With A Specific FuncDon. 4. Method: AddiDon and/or DeleDon of Amino Acids.
AcDvity II InstrucDons (Folding VariaDons) 1. Reversible Protein DenaturaDon • Unfold and Then Re-‐Fold Your Protein. • Compare the Re-‐Folded Protein to the Digital Photo. 2. Reverse Engineering • Remove the Tacks from The Toober • Fold the Toober into a Compact, Globular Shape.
AcDvity II : Folding VariaDons
2. Reverse Engineering (ConDnued) • Add Tacks to the Pre-‐Folded Toober: Follow the Laws of Chemistry. • Unfold the Toober Document the Sequence of Tacks. 3. The Effects of MutaDons • Using the Reverse Engineered Toober, Mutate A Yellow Tack into A Blue Tack. • Can This Sequence Be Refolded Into The NaDve Shape?
Protein Folding Mechanism
Chaperone Protein Image
Discussion of AcDvity 1. Teacher Comments/ReacDons to The AcDvity 2. Curriculum ConnecDons? Where Does The AcDvity Fit? Grade Levels, Subject Mafer? 3. How Would You Modify The AcDvity to Fit Your ParDcular Student PopulaDon 4. Sharing: Teacher Who Has Used The AcDvity.
A Protein Inquiry AcDvity • BioinformaDcs: Mapping the B-‐Globin Gene
• Available From: 1. 2.
3D Molecular Designs Carolina Biological Supply
The Biotechnology Connec3on • Genes (DNA) Code for Proteins (in most cases) • Biotechnologists Isolate specific genes and manufacture proteins • For Example, an enzyme has been isolated from bacteria living in extremely cold water • This enzyme has been synthesized and placed in cold-‐water laundry detergent
Recombinant DNA Technology (Method)
Restric3on Enzyme Cut Sites (Palindromes) • EcoRI Enzyme • SmaI Enzyme
Protein Folding Anima3ons 1. hfp://bcs.whfreeman.com/lodish5e/ content/cat_010/03010-‐01.htm? v=chapter&i=03010.01&s=03000&n=00010& o 2. 3-‐D Molecular Designs hfp://cbm.msoe.edu/includes/swf/ 15AminoAcids.swf
A Protein Folding Game!
hKp://fold.it/portal/
References 1. Protein Misfolding & DegeneraDve Diseases hfp://www.nature.com/scitable/topicpage/ protein-‐misfolding-‐and-‐degeneraDve-‐ diseases-‐14434929 2. Protein Data Bank. Chaperones hfp://www.rcsb.org/pdb/101/motm.do? momID=32
Presenter: Hortense Brice Biotechnology Center of Excellence (BCoE) Lindblom Math & Science Academy
Protein Models
Example A
Example B
Protein Models
Example A
Example B
Ac3vity I Focus (Essen3al) Ques3ons 1. What is ScienDfic Modeling? Does Modeling Relate to this AcDvity? 2. How Do the Chemical ProperDes of Amino Acids Determine the Folding of a Protein into its Final 3-‐D Shape? 3. Why are the Colored Tacks (Amino Acids) Placed in Random Order? 4. Does Protein Folding Illustrate the Biological Theme of Form Fits Func3on?
Ac3vity Materials 1. 2. • • • • • •
One (1) Mini-‐Toober 15 Colored Tacks 2 Blue Tacks 2 Red Tacks 6 Yellow Tacks 3 White Tacks 2 Green Tacks Cell Phone or iPad (for Photos of Models)
Amino Acid (Structural Formula)
Ac3vity Instruc3ons 1. Distribute the Tacks Randomly Along the Toober. Spacing: Place the Tacks 3 Inches Apart. 2. Fold your Protein Following the Principles of Chemistry that Determine Protein Folding. 3. Chemical Principles—Amino Acids May be: • Hydrophobic (non-‐polar): Yellow Tacks • Hydrophilic (polar): White Tacks
• Charged: Blue Tacks, Basic. Red Tacks, Acidic. Cysteine Sidechains: Green Tacks DocumentaDon: Take a Digital Photo of Your Folded Protein. Leave Protein Folded.
Four Levels of Protein Structure
Background Informa3on 1. Proteins are Folded PolypepDdes. 2. PolypepDdes are Polymers of Amino Acids. 3. Amino Acids can be Classified as Non-‐polar, Polar, Acidic (negaDvely charged) or Basic (posiDvely charged). 4. Chemical ProperDes (or ClassificaDon) of Amino Acids are Determined by Sidechains (R Groups).
Background Informa3on (page 2) 5. These Chemical ProperDes Govern Chemical InteracDons among the Amino Acids. 6. Basic Laws of Chemistry Determine the Proper Folding of Proteins into Specific Shapes. 7. Protein Shape determines protein funcDon. 8. Proteins must be folded (correctly) in order to funcDon properly.
Protein Engineering Facts 1. Protein Engineering is an example of bioengineering. 2. Protein Engineering Designs New Proteins Not in Existence. 3. Goal: Design of Protein With A Specific FuncDon. 4. Method: AddiDon and/or DeleDon of Amino Acids.
AcDvity II InstrucDons (Folding VariaDons) 1. Reversible Protein DenaturaDon • Unfold and Then Re-‐Fold Your Protein. • Compare the Re-‐Folded Protein to the Digital Photo. 2. Reverse Engineering • Remove the Tacks from The Toober • Fold the Toober into a Compact, Globular Shape.
AcDvity II : Folding VariaDons
2. Reverse Engineering (ConDnued) • Add Tacks to the Pre-‐Folded Toober: Follow the Laws of Chemistry. • Unfold the Toober Document the Sequence of Tacks. 3. The Effects of MutaDons • Using the Reverse Engineered Toober, Mutate A Yellow Tack into A Blue Tack. • Can This Sequence Be Refolded Into The NaDve Shape?
Protein Folding Mechanism
Chaperone Protein Image
Discussion of AcDvity 1. Teacher Comments/ReacDons to The AcDvity 2. Curriculum ConnecDons? Where Does The AcDvity Fit? Grade Levels, Subject Mafer? 3. How Would You Modify The AcDvity to Fit Your ParDcular Student PopulaDon 4. Sharing: Teacher Who Has Used The AcDvity.
A Protein Inquiry AcDvity • BioinformaDcs: Mapping the B-‐Globin Gene
• Available From: 1. 2.
3D Molecular Designs Carolina Biological Supply
The Biotechnology Connec3on • Genes (DNA) Code for Proteins (in most cases) • Biotechnologists Isolate specific genes and manufacture proteins • For Example, an enzyme has been isolated from bacteria living in extremely cold water • This enzyme has been synthesized and placed in cold-‐water laundry detergent
Recombinant DNA Technology (Method)
Restric3on Enzyme Cut Sites (Palindromes) • EcoRI Enzyme • SmaI Enzyme
Protein Folding Anima3ons 1. hfp://bcs.whfreeman.com/lodish5e/ content/cat_010/03010-‐01.htm? v=chapter&i=03010.01&s=03000&n=00010& o 2. 3-‐D Molecular Designs hfp://cbm.msoe.edu/includes/swf/ 15AminoAcids.swf
A Protein Folding Game!
hKp://fold.it/portal/
References 1. Protein Misfolding & DegeneraDve Diseases hfp://www.nature.com/scitable/topicpage/ protein-‐misfolding-‐and-‐degeneraDve-‐ diseases-‐14434929 2. Protein Data Bank. Chaperones hfp://www.rcsb.org/pdb/101/motm.do? momID=32
