Transcript Science Olympiad Protein Modeling Challenge

Science Olympiad Protein Modeling
Challenge: Exploring Protein Structure
through Technology
This program is sponsored by a grant from NIH-NCRR-SEPA and the HHMI Pre-College Science Education Program.
What do we do at the Center for
BioMolecular Modeling?
•Create accurate 3D molecular models
•Professional development programs
•Science education outreach programs
The CBM offers concrete representations of
“invisible” structures.
Mental Image
Textbook Illustration
Computer Generated Image
Physical Image
Protein Models….in 4 Easy Steps
Stl file
x,y,z coordinates
Protein Data Bank
RP-RasMol
Z Corp Printer
The Science Olympiad Mission
To promote and improve student interest in
science and to improve the quality of K12
science education throughout the nation.
Protein Modeling Event
– Identify basic features of protein
structure
– Explore protein structure with a
computer visualization program
– Create physical models using the
flexible modeling media, MiniToobers (or alternative materials)
Protein Modeling Event
Pre-Build (40%)
•pre-built model based on a PDB file
On-Site Build (30%)
•model built on-site during competition
Exam (30%)
•questions relating protein structure and
function
Protein Data Bank
Protein Data Bank
Molecule of the Month
Understanding Protein Biochemistry
Resources can be found online at
cbm.msoe.edu/stupro/so/index.html
Visualizing the Molecule
Resources can be found online at
cbm.msoe.edu/stupro/so/index.html
Marking the Toober
• Once a computer visualization image has been
determined, secondary structure location should be
noted and then marked on the toober.
• Positions of significant amino acids should be marked
on the toober as well.
Folding the Toober
Videos online demonstrate how to mark and fold
the toober to mimic the image created using the
visualization program
Resources can be found online at
cbm.msoe.edu/stupro/so/index.html
Zinc Finger Folding Activity
• Zinc finger proteins bind DNA
• A zinc finger domain contains a short alpha-helix, 2
beta-strands and conserved Cys, His amino acids that
bind a molecule of zinc
Score your model!
Using the rubric provided,
score your neighbors’ model of
a zinc finger. How well did
they do?
What we look for when
scoring the models
•Positioning of the blue/red end caps correctly
•Correct number of helices/sheets
•Correct positioning of helices/sheets (topology)
•Right-handed helices
•Correct tertiary structure (relative position of
helices/sheets to one another)
•Model has correct shape (is it globular, saddle shaped,
etc)
•For prebuild – creative additions to help tell the story
•For onsite build – provided amino acids are positioned
correctly, on the toober, but also in 3D space (pointing
inward or outward)
Common Mistakes
•Blue cap/red cap in wrong position
•N-terminus, or the beginning of the protein, is the BLUE cap
and C-terminus, or the end of the protein, is the RED cap
•Missing secondary structures
•Model has 3 helices, and it should have 4 (or vice versa)
•Left-handed helices
•Tertiary structure is incorrect
•Protein should be globular and it is flat
•Creative additions on the prebuild are inappropriate
•Incorrect sidechains
•Too much information (all of the sidechains)
•Onsite amino acids are positioned incorrectly
•In the wrong spot (position 49 rather than 59)
•Amino acids are pointing in the wrong direction
(should be pointing to the center of the protein and
it is facing outward)
The exam
•The exam is a combination of multiple choice and short answers questions.
•Questions cover
•Basic chemistry questions regarding atoms, bonds and reactions
•Basic protein structure
•Structure/function relationship questions
•Specific protein questions (for 2010 – Influenza Hemagglutinin and
Neuraminidase)
•Application questions (what would happen if…)
•Ties will be broken using specific (labeled)questions
on the exam.
Protein Modeling Event Addresses National
Science Content Standards
• Science and Technology
– Abilities of Technological Design
– Understandings about Science and Technology
• Life Science
– The Cell
• Science as Inquiry
– Abilities Necessary to do Scientific Inquiry
• Physical Science
– Structure and Properties of Matter
– Chemical Reactions
Protein Modeling Event Addresses National
Science Content Standards
• Science and Technology
– Abilities of Technological Design
– Understandings about Science and Technology
• Life Science
– The Cell
• Science as Inquiry
– Abilities Necessary to do Scientific Inquiry
• Physical Science
– Structure and Properties of Matter
– Chemical Reactions
Protein Modeling Event Addresses National
Science Content Standards
• Science and Technology
– Abilities of Technological Design
– Understandings about Science and Technology
• Life Science
– The Cell
• Science as Inquiry
– Abilities Necessary to do Scientific Inquiry
• Physical Science
– Structure and Properties of Matter
– Chemical Reactions
Protein Modeling Event Addresses National
Science Content Standards
• Science and Technology
– Abilities of Technological Design
– Understandings about Science and Technology
• Life Science
– The Cell
• Science as Inquiry
– Abilities Necessary to do Scientific Inquiry
• Physical Science
– Structure and Properties of Matter
– Chemical Reactions
Protein Modeling Supports
Science Olympiad Mission
• Emphasis on teamwork
Protein Modeling Supports
Science Olympiad Mission
• Brings science to life, shows how science works,
emphasizes problem solving aspects and understanding of
concepts
Protein Modeling Supports
Science Olympiad Mission
• Promotes partnerships among community, businesses,
industry, and education
Protein Modeling Supports
Science Olympiad Mission
• Promotes high level of achievement and demonstrates
students can perform at levels approaching practicing
scientists
The CBM works with you to offer this
event within your state!
• Provides curriculum training workshops
and web based distribution of materials
from the MSOE Center for BioMolecular
Modeling web site
(cbm.msoe.edu/stupro/so/index.html)
• We can come to your state to provide a
workshop
Model Lending Library
Professional Development Workshop
Modeling the Molecular World Part I: Tactile Teaching with Physical Models
A $200 workshop fee covers the cost of:
•workshop materials, including hands-on
models and instructional materials to take
back to your classroom
•3 hours special graduate credit*
•breakfast and snacks
•dormitory housing for 1 week including
room, bed linens, towels
•lifetime membership in a community of
innovative teachers making the molecular
world come alive for their students
* These graduate credits are intended for teacher certification
purposes. They do not apply to other advanced degree programs.
http://cbm.msoe.edu/profDev/mmw1/index.html
SMART Teams:
Students Modeling A Research Topic
“SMART Teams become producers of visual artifacts,
written in a tactile, 3D language.”