School Name
Student #1
Student #2
Student #3
Science Olympiad
2009 Regional Competition
Protein Modeling Event
This event was developed by the MSOE Center for BioMolecular Modeling (CBM). To learn more about
the science education programs of the CBM, please visit our website:
www.rpc.msoe.edu/cbm
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Science Olympiad
2009 Regional Competition
Protein Modeling Event
Part I: RNaseA Pre-build (40% of total score)
The model of the RNaseA is to be impounded at 9am the morning of the competition and then
scored. You may pick up your model of RNaseA at the end of the competition after all models have been
scored.
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Science Olympiad
2009 Regional Competition
Protein Modeling Event
Part II: On-Site Modeling Challenge (30% of total score)
Materials Provided at each workstation:
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98 cm Mini-Toober
4 crosslinkers
2 foam amino acid sidechains
o 1 Histidine
o 1 Lysine
1 Blue End Cap
1 Red End Cap
1 meter stick or ruler
1 marker
Folder with Molecule of the Month, abstract and structure summary pages
RasMol/Jmol Quick Reference Card
Amino acid sidechain chart
Instructions:
1. Using the 98 cm Mini-Toober provided, construct a model of amino acids 1-49 of the pdb file
1RTA.
The scale should be 2cm per amino acid. A meter stick has been provided for you.
2. Your Mini-Toober model of amino acids 1-49 of 1RTA.pdb should include the following:
(A) Two of the three amino acids in the active site of this protein
a. 1 histidine
b. 1 lysine
(B) Blue End Cap, indicating the amino terminus (N-terminal end) of this region (amino
acids 1-49) of the protein
(C) Red End Cap, indicating the carboxy terminus (C-terminal end) of this region (amino
acid 1-49) of the protein
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Science Olympiad
2009 Regional Competition
Part I: Multiple Choice Questions
Directions:
There are 10 questions in this section, each worth 2 points. Clearly print the letter of the one BEST
answer to each question in the blank provided for that question. Illegible answers will be incorrect.
______1. Which covalent interactions help to stabilize RNaseA to prevent degradation of the protein,
even in a hostile environment?
A. The presence of many acidic and basic amino acids
B. The amino acids of the catalytic site of the enzyme
C. The presence of 4 disulfide bonds
D. The 7 beta strands within the protein
______2. Which of the following statements is true?
A. RNaseA is a protein receptor, involved in cell signaling.
B. RNaseA is an enzyme that cleaves proteins.
C. RNaseA is a transport protein, moving ions across the membrane.
D. RNaseA is an enzyme that cleaves ribonucleic acids.
______3. What experimental method was used to determine the structure of 1RTA?
A. X-ray diffraction
B. NMR
C. Circular Dichroism
D. MALDI-TOF
_______4. Which journal published the primary citation describing 1RTA?
A. Journal of Molecular Biology
B. Science
C. Journal of Biological Chemistry
D. Journal of Cellular Biology
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_______5. How many alpha helices are present in the full structure of 1RTA?
A. 1
B. 2
C. 3
D. 4
E. 5
_______6. What is the charge on the sidechain of the amino acid lysine at pH 7?
A. Positive
B. Negative
C. Neutral
_______7. Which one of the following amino acids is involved in disulfide bridges?
A. Lysine
B. Tryptophan
C. Cysteine
D. Isoleucine
E. Methionine
_______8. The Nobel Prize in 1972 was awarded to Christian Anfinsen for his work with ribonucleases.
Which of the following represents the contribution he has made?
A. Biological molecules are made of chemical components that can be assembled
artificially.
B. Proteins fold in such a way to arrange specific amino acids into a spot for catalytic
cleavage.
C. He made the connection between the amino acid sequence and the biologically active
conformation.
D. Crystallography can determine the structure of the protein.
_______9. Ribonuclease A can be classified as which of the following?
A. Exonuclease
B. Endonuclease
C. Exosome
D. Endosome
_______10. Ribonuclease A does not cleave DNA. Which of the following explanations explains why
ribonuclease A cannot cleave DNA?
A. DNA is double stranded and RNA is single stranded. Ribonuclease A cannot cleave
double stranded nucleic acids.
B. DNA is missing 2’-OH on the ribose, which is essential for the reaction mechanism.
C. DNA has thymine and RNA has uracil. Ribonuclease A cannot recognize strands with
thymine.
D. DNA has large purine bases, which do not fit into the active site of ribonuclease A.
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Part II: Short-answer Questions
For each of the following questions, provide a brief answer. You may use the PDB’s Molecule of
Month, the abstract of the primary citation, as well as your personal knowledge regarding protein
structure and function to answer these questions. Point value for each question is given in parentheses at
the end of the question. Tie breaker questions are indicated. The points for the tie-breaker questions will
be included in the final score and may be used to determine team placement in case of a tie.
1.
Ribonuclease A preferentially cleaves the phosphodiester backbone of RNA adjacent to cytidine
and uridine nucleotides. In terms of structure, why does ribonuclease show this preference? (2
pts) (tiebreaker question)
Cytidines and uridines are pyrimidines, and thus smaller than adenine and guanine, which are
purines (1 pts). Due to their smaller size, the pyrimidines can fit into the active site more
readily than the purine bases. (1 pts)
2.
What does it mean to be a member of the “diffusion-limited” enzyme family? (2 pts)
Ribonulcease A is a very efficient enzyme in that it will cleave the substrate (RNA) as fast as
RNA can bind to the enzyme. Therefore, the rate of the reaction is limited only by the rate of
diffusion, or as quickly as the RNA can bind to the enzyme.
3. Look at the picture to the right. This is a picture of a protein represented in
spacefill format. The red spacefill atoms represent hydrophilic amino acids
and yellow represents hydrophobic amino acids.
Would you expect to find this protein in the cytoplasm or cell membrane?
Membrane protein (1 pt)
Explain your answer. (2 pts) (tiebreaker question #1)
In soluble proteins, the hydrophobic amino acids tend to be buried on the inside of the protein,
where they are protected from water. If this were a cytosolic protein, the majority of the yellow
amino acids (hydrophobic) would be buried in the center of the protein (1 pt). In this figure, the
yellow is on the outside, so it must be interacting with hydrophobic materials, such as the
phospholipids of the cell membrane rather than with water. (1 pt)
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4.
Identify the secondary structures highlighted in green in the
figure to the right. (1 pt)
Beta-sheets
5.
For your onsite build, you added two amino acids – a histidine and a lysine. Why are these amino
acids significant to the function of this protein? (2 pts)
His12 and Lys41 are part of the active site for this enzyme – it is their job to cleave the
substrate (RNA)
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