Toobers Overview
Students will use the 3-D molecular modeling kits to explore different aspects of the structures
of proteins and DNA. Once they have an understanding of the structures, they will look at how
these two molecules are related by building a specific protein with a given DNA sequence.
Protein folding, Part 1 (Primary to Tertiary structure): Students begin by looking at the side
chains of the amino acids. They sort all of the amino acids according to their properties (acidic,
basic, hydrophobic, etc..). Then, they randomly place 15 amino acids along the Toober to
represent a hypothetical primary structure of the protein. They try to fold the protein to meet
different chemical properties, such as all of the hydrophobic side chains need to be buried on
the inside to minimize interactions with the polar water molecules. As they continue, they
bend the Toober to meet attempt to meet all of the different requirements. Students may be
required to change the position of the amino acids to meet all of the requirements. Through
this investigation, students see how the sequence of amino acids directs the protein folding via
side chain interactions.
Protein folding, Part 2(Primary to Secondary to Tertiary structure): This time students build an
actual protein to model secondary structures commonly found in proteins. Students follow the
instructions to build the protein. The focus this time is how the secondary structures further
stabilize the proteins.
DNA models: Students investigate the structure of DNA using the information that was
available to Watson and Crick. Using smaller pieces they work together to determine the
correct overall structure. Through this investigation, students are prompted to look at the
different components and how they contribute to the overall stability.
Building a protein with a given DNA structure: The goal of this activity is to make the
connection between the genetic information held in DNA and the functionality of proteins.
Students use a given DNA sequence to transcribe and then translate it into an amino acid
sequence. They build the amino acid sequence using the Toober models and fold it to meet the
chemical requirements. Then, different types of mutations (point, frame shift, etc.) are
introduced, and their effects are observed on the various proteins.