Short Answer Questions

Chapter 4
1. Overview of protein structure
Page: 116
Any given protein is characterized by a unique amino acid sequence (primary
structure) and three-dimensional (tertiary) structure. How are these related?
The three- dimensional structure of a protein is determined by its amino acid
sequence.

2. Overview of protein structure

Pages: 117, 147
Name four factors (bonds or other forces) that contribute to stabilizing the native
structure of a protein, and describe one condition or reagent that interferes with
each type of stabilizing force.
Hydrogen bond
Ionic interaction
Hydrophobic interaction
Van der wasls interaction

3. Overview of protein structure

Page: 119
Draw the resonance structure of a peptide bond, and explain why there is no
rotation around the C—N bond.

Peptide C-N bonds are unable to rotate freely because of their partial double-bond
character.

4. Overview of protein structure

Pauling and Corey showed that in small peptides, six atoms associated with the
peptide bond all lie in a plane. Draw a dipeptide of two amino acids in trans
linkage (side-chains can be shown as —R), and indicate which six atoms are part
of the planar structure of the peptide bond.
5. Protein secondary structure
Page: 120
Describe three of the important features of the α-helical polypeptide structure
predicted by Pauling and Corey. Provide one or two sentences for each feature.

1. The polypeptide backbone is tightly wound around an imaginary axis drawn

longitudinally through the middle of the helix.
2. R groups of the amino acid residues protrude outward from the helical backbone.
3. The helical twist of the α- helix found in all proteins is right-handed

6. Protein secondary structure

Page: 123
Describe three of the important features of a β sheet polypeptide structure.
Provide one or two sentences for each feature.
The backbone of the polypeptide chain is extended into a zigzag
Hydrogen bonds are formed between adjacent segments of polypeptide chain.
The R group of adjacent amino acids protrudes from the zigzag structure in opposite
directions

7. Protein secondary structure

Page: 123
Why are glycine and proline often found within a β turn but not in α-helix?

Gly and Pro residues often occur in β turns, the former because it is small and flexible, the
latter because peptide bonds involving the imino nitrogen of proline readily assume the cis
configuration, a form that is particularly amenable to a tight turn.
8. Protein tertiary and quaternary structures
Page: 129
Why is silk fibroin so strong, but at the same time so soft and flexible?
Silk does not stretch, because the β conformation is already highly extended.
However, the structure is flexible because the sheets are held together by numerous
weak interactions rather than by covalent bonds.

9. Protein tertiary and quaternary structures

Page: 133
What is typically found in the interior of a water-soluble globular protein?
Most of the hydrophobic R groups are in the interior, hidden from exposure to water.

10. Protein tertiary and quaternary structures

Pages: 139.141
Explain what is meant by motifs in protein structure.

stable arrangements of several elements of secondary structure and the connections

between them.

11. Protein tertiary and quaternary structures

Pages: 145.146
Describe briefly the two major types of symmetry found in oligomeric proteins
and give an example of each.

Rotational symmetry:
The subunit pack about the rotational areas to form closed structures, Poliovirus
Helical symmetry:
Tend to form structures that are more open- ended , with subunit added in a spiraling array
Tobacco virus.

12. Protein tertiary and quaternary structures

How many protomers does a protein with D4 symmetry have? Please give one
example.
Protomers: 2n = 8
PtCl42-
13. Protein tertiary and quaternary structures
Page: 146
What is the rationale for many large proteins containing multiple copies of a
polypeptide subunit?

The genetic coding capacity of nucleic acids and the accuracy of the protein
biosynthetic process.

14. Protein denaturation and folding

Page: 147

Each of the following reagents or conditions will denature a protein. For each,
describe in one or two sentences what the reagent/condition does to destroy
native protein structure.

(a) urea
Disrupt the hydrophobic interaction that make up the stable core of globular
protein.
(b) high temperature
Effect the weak interaction in a protein.
(c) detergent
Same of urea.
(d) low pH
Alter the net charge of protein, causing electrostatic repulsion and the disruption of
some hydrogen bonding.

15. Protein denaturation and folding

Page: 147
How can changes in pH alter the conformation of a protein?
Cause electrostatic repulsion and the disruption of some hydrogen bonding.

16. Protein denaturation and folding

Two models are used to describe the folding pathway of protein. What are them
(describe them briefly)?
A simulated folding pathway
Its started with the randomly coiled peptide and 3,000 surrounding water molecules
in a virtual “water box.” The molecular motions of the peptide and the effects of the
water molecules were taken into account in mapping the most likely paths to the final
structure among the countless alternatives.
The thermodynamics of protein folding depicted as a free-energy funnel.
The thermodynamic path down the funnel reduces the number of states present
(decreases entropy), increases the amount of protein in the native conformation, and
decreases the free energy.
17. Protein denaturation and folding
Pages: 151.153
What are two mechanisms by which “chaperone” proteins assist in the correct
folding of polypeptides?