Protein Structure

Article excerpt

In Stanley Miller's classic 1953 experiment, amino acids were among the first molecules to form in solution as a result of the electrification of a reducing atmosphere. The week-long experiment resulted in a four percent amino acid concentration. Since that time, amino acids seem to be on the forefront of prebiotic molecule research, which includes the study of DNA, RNA, proteinoids (Sidney Fox), ribozymes (Thomas Cech & Sidney Airman), and pre-RNA molecules such as peptide nucleic acid (Peter E. Nielsen, University of Copenhagen).

There are many theories describing how the unit of life, the cell, came into existence. Life's structural unit is a phospholipid bilayer with embedded proteins surrounding an enzyme-rich (protein) cytoplasm and amino acid containing DNA molecule(s). The genetic material routinely repairs and governs cell processes through protein synthesis and enzyme formation. Few organic compounds have as important a cellular role as proteins. Because protein function is reflective of structure, a strong foundation in protein structure should be provided in all introductory biology classes. All six cognitive levels found in Bloom's Taxonomy of intellectual behavior in learning are explored in this activity (knowledge, comprehension, application, analysis, synthesis, and evaluation).

Preliminary Topics

Atomic structure, valence electrons, and covalent bonding

Functional groups

Polar/Nonpolar interactions, "like dissolves like"

Proteins are polymers of amino acid monomers

There are 20 essential amino acids.

Supplies per Student

* five Index cards

* reference text for amino acid structure and reactivity (polar or nonpolar), protein shape, and enzyme active site

* tape

* pen

Activity Procedure

1. Each amino acid includes a central carbon atom and each of the following functional groups: hydrogen, amino, and carboxyl. Each student should prepare the index cards in Figure 2. Review the relationship between valence electrons and bonding for each atom with the students.

2. Students will now become an amino acid. Using tape, place the central carbon card on the upper chest, the hydrogen group on the forehead, the amino group on the right forearm, and the carboxyl group on the left forearm. Check that each student has the amino group on his/her right arm.

3. The "R" group characterizes different amino acids. Have students select a specific amino acid and prepare their unique "R GROUP" index card. The students should write the name of the amino acid on their card as well as the reactivity of the amino acid (polar or nonpolar). It is helpful to have several of each type of reactivity in the classroom. It is also helpful to have an even number of cysteines for disulfide bridge formation. Students should place this index card on the stomach. At this point in the activity, it would be appropriate to address questions such as those in Student Assignment 1.

4. Take the students out into the hallway. Have each amino acid undergo dehydration synthesis (condensation reaction) with his/her neighboring amino acid. The amino group loses hydrogen, while the neighboring carboxyl group loses a hydroxide group. The resulting peptide (covalent) bond is represented by hand holding. Make sure an amino acid does not bond to itself. One water molecule should be found on the floor below each peptide bond.

5. The resulting protein is linear. Have the students sequentially state their names to represent the primary structure of the protein. Tell the students, "Never break these peptide bonds." Students should now understand questions such as those posed in Student Assessment 2.

6. Secondary structure occurs when, let's say, Mary's carboxyl group H-bonds to Joe's amino group. The linear protein will fold into a beta sheet, just like skin keratin. Hair keratin forms an alpha helix shape from cysteine-cysteine disulfide bridges. …