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Science Olympiad Protein Modeling Challenge: Exploring Protein Structure through Technology

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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 ... – PowerPoint PPT presentation

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Title: Science Olympiad Protein Modeling Challenge: Exploring Protein Structure through Technology


1
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.
2
What do we do at the Center for BioMolecular
Modeling?
  • Create accurate 3D molecular models
  • Professional development programs
  • Science education outreach programs

3
The CBM offers concrete representations of
invisible structures.
Mental Image
Textbook Illustration
Computer Generated Image
Physical Image
4
Protein Models.in 4 Easy Steps
Stl file
x,y,z coordinatesProtein Data Bank
RP-RasMol
Z Corp Printer
5
The Science Olympiad Mission
To promote and improve student interest in
science and to improve the quality of K12 science
education throughout the nation.
6
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, Mini-Toobers (or alternative
    materials)

7
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

8
Protein Data Bank
9
Protein Data Bank Molecule of the Month
10
Understanding Protein Biochemistry
Resources can be found online at
cbm.msoe.edu/stupro/so/index.html
11
Visualizing the Molecule
Resources can be found online at
cbm.msoe.edu/stupro/so/index.html
12
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.

13
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
14
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

15
Score your model!
Using the rubric provided, score your neighbors
model of a zinc finger. How well did they do?
16
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)

17
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)

18
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.

19
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

20
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

21
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

22
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

23
Protein Modeling Supports Science Olympiad Mission
  • Emphasis on teamwork

24
Protein Modeling Supports Science Olympiad
Mission
  • Brings science to life, shows how science works,
    emphasizes problem solving aspects and
    understanding of concepts

25
Protein Modeling Supports Science Olympiad
Mission
  • Promotes partnerships among community,
    businesses, industry, and education

26
Protein Modeling Supports Science Olympiad
Mission
  • Promotes high level of achievement and
    demonstrates students can perform at levels
    approaching practicing scientists

27
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

28
Model Lending Library
29
Professional Development Workshop Modeling the
Molecular World Part I Tactile Teaching with
Physical Models July 25-30th
  • 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
30
SMART Teams Students Modeling A Research Topic
SMART Teams become producers of visual
artifacts, written in a tactile, 3D language.
31
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