Chapter 4

Question 1

The variations in the physical characteristics between different proteins are influenced by
the overall amino acid compositions, but even more important is the unique amino acid _______

Answer 1

Sequence

Question 2

β sheets can participate in the formation of amyloid fibers, which are insoluble protein
aggregates. What drives the formation of amyloid fibers?

Answer 2

β-sheet stabilization of abnormally folded proteins

Question 3

Protein structures have several different levels of organization. The primary structure of a
protein is its amino acid sequence. The secondary and tertiary structures are more
complicated.

Consider the definitions below and select the one that best fits the term “protein
domain.

Answer 3

a protein segment that folds independently

Question 4

Proteins bind selectively to small-molecule targets called ligands. The selection of one ligand
out of a mixture of possible ligands depends on the number of weak, noncovalent interactions
in the protein’s ligand-binding site. Where is the binding site typically located in the protein
structure?

Answer 4

inside a cavity on the protein surface

Question 5

The order in which amino acids are linked is unique for each protein and is the most
important factor in determining overall protein structure

Answer 5

True

Question 6

Peptide bonds are planar amide bonds that are central to the polypeptide backbone

Answer 6

True

Question 7

The chemical properties of amino acid side chains include charged, uncharged polar, and
nonpolar

Answer 7

True

Question 8

The relative distribution of polar and nonpolar amino acids in a folded protein is determined
largely by hydrophobic interactions, which favor the clustering of nonpolar side chains in
the interior.

Answer 8

True

Question 9

Knowing that there are 20 different possible amino acids that can be used at each position in a
polypeptide, calculate the number of different polypeptides that could theoretically be
produced for a protein that is 180 amino acids in length

Answer 9

20^180

No, we would not expect all of the
theoretically possible proteins to be made

Natural selection favors the retention of genes that encode
proteins with stable conformations.

Question 10

A newly synthesized protein generally folds up into a __________ conformation

Answer 10

Stable

Question 11

All the
information required to determine a protein’s conformation is contained in its amino acid
__________

Answer 11

Sequence

Question 12

On being heated, a protein molecule will become __________ as a result of
breakage of __________ bonds.

Answer 12

denatured, covalent

Question 13

On removal of urea, an unfolded protein can become
__________.

Answer 13

renatured

Question 14

The final folded conformation adopted by a protein is that of __________
energy.

Answer 14

Lowest

Question 15

Why might high concentrations of urea unfold proteins?

Answer 15

-Urea can squeeze between H bonds, destabilizing protein structures
-H bonded network of water molecules becomes disrupted & molecule falls apart

Question 16

Arrangement of Amino acids in B pleated sheet

Answer 16

Amino acid sequence consists of alternating nonpolar & charged amino acids. Therefore one side polar and the other hydrophobic.

-Hydrophobic side would face protein interior

Question 17

Why don’t cells contain millions of proteins that aren’t in use?

Answer 17

Natural selection provides a strong driving force that eliminates both useless/harmful proteins.

Question 18

What would happen if your hair was treated w/ strong reducing agents that broke all the disulfide bonds

Answer 18

Keratin filaments would separate and individual hairs would become weakened

Question 19

What are the advantages of protein phosphorylation or binding of a nucleotide to regulate protein activity.

Answer 19

-Fast rate at which small nucleotide can diffuse to protein
-Phosphates can be added to many different side chains on a protein, increasing complexity of regulation

Question 20

Do noncovalent bonds influence the three-dimensional shape of macromolecules?

Answer 20

Yes

Question 21

What common features of of a helices and B sheets make them universal building blocks for proteins?

Answer 21

All of N-H and C=O groups are engaged in H bonds. Provides stability

Question 22

Would you expect any fragment of a polypeptide chain would fold the same way as an intact protein?

Answer 22

Yes

Question 23

What happens at the molecular level to a mutant enzyme as the temp increases?

Answer 23

The mutation causes the enzyme to have a less stable structure & therefore gets turned off at higher temps.

Question 24

How is it possible that a change in a single amino acid can destroy protein function?

Answer 24

Small changes in protein core can disrupt protein functioning by altering the conformation at a binding site.