Download Name: Pd: _____ Date: Modeling Protein Structure Background

Name: _______________________
Pd: _____
Date: _________________
Modeling Protein Structure
Background:
Proteins are the molecules that carry out most of the cell’s
day-to-day functions. While the DNA in the nucleus is “the boss” and
controls the activities of the cell, it is the proteins that “do the work.”.
Proteins are made from a chain of amino acids (20 different
side chains), the order in which these molecules assemble is dictated
by the DNA code. A chain of amino acids is called a polypeptide
chain and is considered the primary structure of a protein. The
amino and carboxyl groups of the amino acids along the chain will
interact forming the secondary structure. The secondary structure
is usually an alpha helix or beta-pleated sheet. The R groups will also
interact, creating a 3-D shape, known as the tertiary structure. The interactions that occur between R
groups will be based on their properties and the functional groups present. Multiple tertiary structures
can interact to form the quaternary structure, but this does not always occur. Therefore, most proteins
become active after folding into their tertiary structure.
In this activity you will examine the structure of proteins and how their structure is related to
their function.
Pre-activity questions:
1. Amino acids have different properties based on their R-groups. Use the amino acid chart at your
lab table to determine if the following amino acids are nonpolar, polar, negatively charged or
positively charged.
Methionine (Met) = __________________________
Leucine (Leu) = _______________________________
Cysteine (Cys) = ______________________________
Threonine (Thr) = ____________________________
Glutamic Acid (Glu) = ________________________
Histidine (His) = ______________________________
2. Identify the type of bond (hydrogen bond, ionic interaction, hydrophobic interaction, disulfide
bridge) that would form between the following amino acid side chains.
a. Methionine and Leucine ________________________________
b. Glutamic Acid and Threonine __________________________
c. Histidine and Glutamic Acid ____________________________
d. Cysteine and Cysteine ___________________________________
e. Threonine and Threonine _______________________________
Procedure:
Each person in your lab group will do the following:
1. Take a pipe cleaner and beads. Assemble the primary structure (place beads on the pipe
cleaner) outlined below using the key: Met(red), Leu (orange), Cys (yellow), Thr (green), Glu
(blue), His (purple).
Met-Leu-Cys-Thr-Thr-Cys-His-Glu-Leu-Thr-Glu-Leu
2. This primary structure will fold to form the secondary structure, which includes the formation of
hydrogen bonds between the amino group of one amino acid and the carboxyl group of another.
a. Represent these interactions by folding your pipe cleaner into an alpha helix or a betapleated sheet.
b. Take a picture of your protein at this point.
3. The folded pipe cleaner will then gain a 3D shape as the R-groups begin to interact. Create your
3D structure by forming at least 3 R-group interactions (THAT CAN ACTUALLY OCCUR).
a. Take a picture of your protein at this point
As a lab group:
4. Create a protein with quaternary structure by joining your protein chains together. You must find
ways for these chains to interact. You can only work with the R-groups that are not already
interacting to form the tertiary structure.
a. Take a picture of your protein at this point
Analysis Questions: (answer on Google Drive)
1. Upload and label the interactions in your four pictures; make sure that each picture has an
appropriate title and the following labels:
a. Primary structure—label peptide bond
b. Secondary Structure—label hydrogen bond
c. Tertiary Structure—label ionic bond, hydrophobic interaction, disulfide bridge or hydrogen
bond
d. Quarternary Structure—label ionic bond, disulfide bridge, hydrophobic interaction, or
hydrogen bond
2. Some scientists will argue that proteins are the most diverse macromolecules. What evidence is
there for this argument, both structurally and functionally?
3. Imagine we placed your protein in a jar of water. What structural changes would occur (think
about the different types of amino acids and how they interact with water)? Why?
4. Egg white is normally a thick, clear liquid containing protein. When heated, it turns into a white
semi-solid. Explain why and how this happens.
5. What environmental factors (other than temperature) could destroy the quaternary, tertiary, and
secondary structure of a protein? Why?
a. What effect would this change in structure have on the function of the protein?