READING QUIZ 2

Your book states that "The polypeptide backbone is rich in hydrogen-bonding potential." Which of the following are capable of hydrogen bonding? Choose all that apply.

-Amino group -Carbonyl group

View Figure 4.25 in Tymoczko. Both panel A and B depict myoglobin, but they highlight different features of myoglobin. Which panel better highlights the secondary structure of myoglobin?

A

The paradigm in biochemistry is that a particular amino acid sequence leads to a particular 3D protein structure. Which of the following are exceptions to this paradigm? Select all that apply.

-Many proteins have regions that are intrinsically unstructured. -Some proteins can shift from one structure to another. Both structures are functional but in different ways. -Some proteins - like PrP - form two different structures. One works properly, while the other leads to disease.

Choose all of the correct statements about protein structure. Hint: For each level of structure, only one statement is correct.

-Primary structure is due to covalent bonding between amino acids. -Secondary structure is due to hydrogen bonding between amino acids. -Tertiary and quaternary structure is primarily due to the hydrophobic effect, hydrogen bonding, ion-ion interactions, and London dispersion forces.

Which of the following are true comparisons of unfolded vs. folded proteins? Select all that apply.

-The unfolded protein is at a higher energy level than the folded protein. -In the unfolded protein, polar R groups tend to form hydrogen bonds with water molecules, but in the folded protein polar R groups form more hydrogen bonds with each other. -The unfolded protein has greater entropy than the folded protein. NOTE: Do not consider the entropy of the solvent for this choice.

Look at Figure 4.11 in your textbook. Is the following statement true or false: an alpha helix has a pore (empty space) in the middle.

FALSE

What is a key difference between alpha helices and beta sheets?

In an alpha helix hydrogen-bonded amino acids are 4 amino acids apart in the primary sequence, but in a beta sheet hydrogen-bonded amino acids may be many amino acids apart in the primary sequence.

T/F: The following observation partially explains why proteins fold like they do: In water, nonpolar chemical groups cause the water to form cage structures. As a result, the entropy of water decreases. When the nonpolar chemical groups cluster, fewer of them are in contact with water, so the entropy of water increases.

TRUE

According to Table 6.4 from the Appling excerpt (p. 163) ...

The delta G of protein folding is based on both enthalpy and entropy.

Afinson conducted an experiment that demonstrated that amino acid sequence (i.e., primary structure) dictates 3D structure. What step of the experiment provided the most important evidence for this principle?

When the urea was removed the protein refolded into a fully active form.