P ROTEIN M ODELING By Lin Wozniewski

What the Student Need to Bring The Pre-build Something to Write With The Test The Test Answers The Pre-build Scoring Rubric The On-Site Build Toobers On-Site Build Scoring Rubric A copy of the types of amino acids found in proteins A copy of shortcuts to the J-Mol Program What MSOE will Provide

W HAT THE EVENT SUPERVISOR NEEDS TO PROVIDE Enough expertise to be able to interpret and apply the rubric. Computers for the Students with one of the 3 options for allowing the students access to the J- Mol program Internet access to the J-Mol Program from MSOE Installation of the J-Mol Program on the computers Access to a CD with the J-Mol Program on it Rulers or meter sticks

W HAT THE STUDENTS NEED TO DO Read the article on the molecule they will be modeling Visit the J-Mol website and determine how many amino acids are in the molecule and their order Learn what the side chains of the various amino acids are and what they do Divide the toober or other material up into approximately 2 cm segments to correspond to the number of amino acids in the protein Label the amino acids on the chain in order. Fold the protein according to the 3-d model at the appropriate places

W HAT THE S TUDENTS N EED TO DO Add creative items to emulate the side chains and form appropriate intramolecular bonds Learn the difference between acid and basic side chains Learn the difference between hydrophobic and hydrophilic side chains Learn about hydrogen bonding and sulfur bonding Learn the difference between primary, secondary, and tertiary protein structure

T HE C OMPETITION Students will bring their pre-built models to the assigned impound Students will sit at a computer and build a portion of the model with the toober provided using the J-Mol program Students will answer questions on a test The test will cover General amino acid structure Protein primary, secondary, and tertiary structure Specifics about the particular protein being studied

Amino Acids There are 20 amino acids that make up the proteins Amino Acids are a backbone of a protein & consist of: Nitrogen atom with 2 Hydrogen atoms (the Amine side) A carbon atom, on which the side chain is hooked Another carbon atom with a double bonded oxygen and a hydroxyl group (The Carboxylic Acid side) Nitrogen Amino Group

Side Chains Side chains are classified as Hydrophobic – water hating or Hydrophilic – water loving depending on what is in the side chains Side Chains that have only carbon and hydrogen atoms are Hydrophobic & tend to be buried inside the protein away from the water when it is folded. They are non-polar Side chains that have hydroxyl, carboxylic acid, or amine groups are Hydrophilic & are generally on the outside of the protein when it is folded. These can be acidic or basic, or just polar

Primary Structure of a Protein The Primary Structure of the Protein is the actual order of the amino acids in the protein. This is the next thing the students must determine after they learn about amino acids & the side chains Ala-Val-Glu-Thr-Thr-Cys-Arg-His-Lys-Asp-Met-Try-Pro-etc

Secondary Structure of a Protein The 2 most common types of secondary structure are the alpha helix and beta pleat The alpha helix ONLY coils right-handed (if you are going up the stairs, your right hand rests on the outside banister going up) The beta pleat should bend back and forth in a zigzag pattern of about 20  at each start of a new amino acid Beta Pleat Alpha Helix

Tertiary Structure of a Protein The tertiary structure of the protein is the final folding that is the result of the molecular interactions formed by the primary and secondary structure. This is determined using the J-Mol program. What a finished pre-build might look like Toober Pipe Cleaner 12 Gauge Wire

Resources MSOE has a lending library available where toobers can be sent for to use for a few days in the classroom J-Mol Program docs/fgij/index.htm docs/fgij/index.htm MSOE