Protein Structure

What are the levels of protein structure and what role do functional groups play?

Proteins accomplish many cellular tasks such as facilitating chemical reactions, providing structure, and
carrying information from one cell to another. How a protein chain coils up and folds determines its
three-dimensional shape. Its shape will, in turn, determine how it interacts with other molecules and thus
performs its function in the cell.

Model 1- Formation of a Peptide Bond

1. Examine the amino acids in Model 1.

a. Circle an amine group in the diagram. (click the picture and select edit to do
so for this and ALL other drawing questions)
b. Draw a triangle around a carboxylic acid (carboxyl) group.

2. How are the amino acids similar to one another?

3. How are the amino acids different from one another?

4. How many amino acids are involved in the reaction to make a dipeptide?

5. In Model 1 the original amino acids are combined through a condensation reaction to
make the dipeptide.

a. What does R1 represent in the dipeptide?

b. What does R 2 represent in the dipeptide?

6. Put a box around the atoms in the amino acids that become the H2O molecule produced
by the reaction in Model 1.

7. A peptide bond is a covalent bond linking two amino acids together in a peptide.
a. Circle the peptide bond in Model 1.

b. Between which two atoms in the dipeptide is the peptide bond located?

c. Between what two functional groups is the peptide bond located?

8. There are 22 different amino acids found in nature. Two were shown in Model 1.
Additional examples are shown below. With your group, write one or two grammatically
correct sentences to describe how these amino acids are similar and how they are different.
Use the terms R-group, amine group, and carboxyl group in your description.
Model 2 – Protein Structure (Part A)
Primary Structure
Amino acid sequence: Ser – Tyr – Ala – Phe – Val – Cys – Tyr – Asp – Cys – Gly
Peptide structure:
 9. Locate the primary structure of the polypeptide in Model 2.
a. Draw an arrow to two different peptide bonds in the diagram.
b. Circle three separate amino acids that were joined together to make the
polypeptide.

10. The first five amino acids in this polypeptide are serine, tyrosine, alanine,
phenylalanine, and valine, in that order (Ser-Tyr-Ala-Phe-Val). If the amino acids were
changed or rearranged (i.e., to Val-Phe-Ala-Ser-Tyr), the polypeptide would have a
different name and identity. With your group, use this information to write a definition of
the primary structure of a protein.

11. Locate the secondary protein structure in Model 2.

a. What types of bonds are holding the secondary structure in place?

b. What groups on the amino acids are always involved in these bonds?

12. Draw a rectangle around two different R groups on the amino acids in the secondary
structure in Model 2.
13. Is there any interaction between R groups in the secondary structure in Model 2?

14. Secondary protein structure can take the form of an alpha(a)-helix or a beta(b)-pleated
sheet, as illustrated below.
a. Which drawing represents an a-helix, Molecule 1 or Molecule 2? Explain your reasoning.

b. Which drawing represents a b-pleated sheet? Explain your reasoning.

15. With your group, write a grammatically correct sentence that summarizes how the secondary
protein structure is formed from the primary structure.
16. Examine the tertiary structure in Model 3 and note the interactions that hold this level of
struc- ture in place.
a. Four types of bonds or interactions are shown. Label them with the
following terms.

-Disulfide bridge -Hydrogen bond

-Hydrophobic interactions -Ionic bond
b. Describe the part of the amino acid that participates in these interactions.

c. How does your answer in part b differ from the bonds that stabilize the
secondary structure?

17. What type of functional groups or atoms would need to be present in the R-groups for
hydrogen bonding to occur between two amino acids in a protein chain?
18. What type of functional groups or atoms would need to be present in the R-groups for
hydro- phobic interactions to occur between two amino acids in a protein chain?

19. How many polypeptide chains are shown in the tertiary protein structure in Model 3?

20. Many proteins, but not all, have a fourth level of structure termed quaternary structure.
a. How many polypeptide chains are shown in the quaternary
structure of the protein in Model 3?

b. What types of bonds and interactions hold the quaternary structure in place?

21. With your group, using grammatically correct sentences, define the following.
a. Tertiary protein structure.

b. Quaternary protein structure.

22. Imagine a protein chain that includes the following amino acids among several others.

a. Which of the amino acids could form a hydrogen bond with another amino
acid in the chain to stabilize the secondary structure of a b-pleated sheet?

b. Which of the amino acids could form disulfide bonds with another amino acid
in the chain to stabilize the tertiary structure of the protein?

C. Which of the amino acids could participate in hydrophobic interactions with

another amino acid in the chain to stabilize the tertiary structure of the protein?

d. What types of bonds or interactions could asparagine form with another

amino acid in the chain in order to form a quaternary structure with another
protein chain?

23. Fill in the following chart using what you’ve learned from Models 1–3.
 Structure Bond(s) or interactions Short description Number of
holding the structure polypeptide
together chains
involved

Primary 1

Secondary 1

Tertiary 1

Quaternary 2 or more

READ THIS!
Heating and changing pH levels are two ways to disrupt the shape of a protein. High
temperatures or pH levels that vary from the natural environment of the protein will break
hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions. Covalent
bonds will usually remain undisturbed. This process of destroying the shape of a protein is
called denaturing.
24. Which of the four levels of protein structure is maintained after denaturing?
Explain your answer.

25. Proteins carry out a variety of functions, and their function is critically dependent upon
their structure and shape. Enzymes are proteins. What would happen to the structure
and function of an enzyme that was exposed to heat or a drastic change in pH?

26. When people get their hair chemically straightened, one chemical is put on the hair to
break the disulfide bonds that give the hair strands their shape (curled) and a second
chemical is used to reform the disulfide bonds to hold the hair in a new position
(straight).
a. What level(s) of protein structure is/are affected by these processes?

b. Why doesn’t the hair stay straight forever after this treatment?

Extension Questions
27. If a mutation in the DNA of an organism results in the replacement of an amino acid
containing a polar R-group with another amino acid containing a nonpolar R-group, how
might the structure of the protein be affected? Address the impact on all levels of the
protein structure in your answer.
28. Egg whites are primarily composed of the protein albumin. One familiar example of the
denaturing of proteins is the difference between the albumin structure in a raw egg
versus a cooked egg. Using what you know about the levels of structure in proteins,
propose an explanation of changes in albumin (and other proteins) that occur during
cooking.

29. Predict what would happen to the egg white if a raw egg were placed in vinegar. Explain
your thinking.