Chapter 4 short answer
Terms in this set (24)
Any given protein is characterized by a unique amino acid sequence (primary structure) and threedimensional
(tertiary) structure. How are these related?
The three-dimensional structure is determined by the amino acid sequence. This means that the
amino acid sequence contains all of the information that is required for the polypeptide chain to fold
up into a discrete three-dimensional shape.
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.
Among forces that stabilize native protein structures are (a) disulfide bonds, (b) hydrogen
bonds, (c) hydrophobic interactions, and (d) ionic interactions. Agents that interfere with these forces
are (a) mercaptoethanol or dithiothreitol, (b) pH extremes, (c) detergents and urea, and (d) changes in
pH or ionic strength, respectively.
When a polypeptide is in its native conformation, there are weak interactions between its R groups.
However, when it is denatured there are similar interactions between the protein groups and water.
What then accounts for the greater stability of the native conformation?
In the unfolded polypeptide, there are ordered solvation shells of water around the protein
groups. The number of water molecules involved in such ordered shells is reduced when the protein
folds, resulting in higher entropy. Hence, the lower free energy of the native conformation.
Draw the resonance structure of a peptide bond, and explain why there is no rotation around the
The intermediate resonance structure imparts a partial double bond characteristic to the C—N
bond, thereby prohibiting rotation.
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.
The N and H of the amino and the C and O of the carbonyl are all in the same plane with the
two Cα atoms, which are diagonally opposite relative to the C—N bond.
Draw the hydrogen bonding typically found between two residues in an α helix.
Hydrogen bonds occur between every carbonyl oxygen in the polypeptide backbone and the
peptide —NH of the fourth amino acid residue toward the amino terminus of the chain.
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.
The α-helical structure of a polypeptide is tightly wound around a long central axis; each turn of
the right-handed helix contains 3.6 residues and stretches 5.4 Å along the axis. The peptide NH is
hydrogen-bonded to the carbonyl oxygen of the fourth amino acid along the sequence toward the
amino terminus. The R groups of the amino acid residues protrude outward from the helical
Describe three of the important features of a β sheet polypeptide structure. Provide one or two
sentences for each feature.
In the β sheet structure, several extended polypeptides, or two regions of the same polypeptide,
lie side by side and are stabilized by hydrogen bonding between adjacent chains. Adjacent chains
may be either parallel (with a repeat distance of about 6.5 Å) or antiparallel (7 Å repeat). The R
groups are often small and alternately protrude from opposite faces of the β sheet.
Why are glycine and proline often found within a β turn?
A β turn results in a tight 180° reversal in the direction of the polypeptide chain. Glycine is the
smallest and thus most flexible amino acid, and proline can readily assume the cis configuration,
which facilitates a tight turn.
In superhelical proteins, such as collagen, several polypeptide helices are intertwined. What is the
function of this superhelical twisting?
The superhelical twisting of multiple polypeptide helices makes the overall structure more
compact and increases its overall strength.
Why is silk fibroin so strong, but at the same time so soft and flexible?
Unlike collagen and keratin, silk fibroin has no covalent crosslinks between adjacent strands, or
between its stacked sheets, making it very flexible. Fibroin's unusual tensile strength derives from
the fact that the peptide backbone of antiparallel β-strands is fully extended, and that the R-groups in
the stacked pleated sheets interdigitate, preventing any longitudinal sliding of the sheets across one
What is typically found in the interior of a water-soluble globular protein?
Hydrophobic amino acid residues cluster away from the surface in globular proteins, so much of
the protein's interior is a tightly packed combination of hydrocarbon and aromatic ring R groups with
very few water molecules.
How does one determine the three-dimensional structure of a protein? Your answer should be more than the name of a technique.
The protein is crystallized, and the crystal structure is determined by x-ray diffraction. The
pattern of diffracted x-rays yields, by Fourier transformation, the three-dimensional distribution of
electron density. By matching electron density with the known sequence of amino acids in the
protein, each region of electron density is identified as a single atom. Sometimes, the threedimensional
structure of a small protein or peptide can be determined in solution by sophisticated
analysis of the NMR spectrum of the polypeptide. This technique can also reveal dynamic aspects of
protein structure such as conformational changes. Computer analysis of two-dimensional NMR
spectra can be used to generate a picture of the three-dimensional structure of a protein.
Describe a reservation about the use of x-ray crystallography in determining the three-dimensional
structures of biological molecules.
To obtain an x-ray picture of a biomolecule, the molecule must be purified and crystallized
under laboratory conditions far different from those encountered by the native molecule.
Biomolecules in the cell also have more flexibility and freedom of motion than can be accommodated
in a rigid crystal structure. Therefore, the static picture obtained from an x-ray analysis of a crystal
may not provide a complete or accurate representation of the biomolecule in vivo.
Explain what is meant by motifs in protein structure.
Motifs are particularly stable arrangements of elements of secondary structure (e.g., α helix and
β conformation), including the connections between them, which are found in a variety of proteins.
Draw a βαβ loop, and describe what is found in the interior of the loop.
Hydrophobic amino acid residues are usually found in the interior of the loop; these help
stabilize the arrangement through hydrophobic interactions.
Describe the quaternary structure of hemoglobin.
Each protein molecule is composed of two copies each of two different subunits α and β. The
two αβ protomers are arranged with C2 symmetry.
Describe briefly the two major types of symmetry found in oligomeric proteins and give an example
1) Rotational: In rotational symmetry, subunits are superimposable after rotation about one or
more of the axes. Some examples are hemoglobin and thepoliovirus capsid. 2) Helical: In helical
symmetry, subunits are superimposable after a helical rotation. Some examples are actin filaments
and the tobacco mosaic virus capsid.
What is the rationale for many large proteins containing multiple copies of a polypeptide subunit?
Each different polypeptide requires a separate gene that must be replicated and transcribed. It is
therefore more efficient to have fewer genes, encoding shorter polypeptides that can be used to
construct many large proteins.
Explain (succinctly) the theoretical and/or experimental arguments in support of this statement: "The
primary sequence of a protein determines its three-dimensional shape and thus its function."
Anfinsen showed that a completely denatured enzyme (ribonuclease) could fold spontaneously
into its native, enzymatically active form with only the primary sequence to guide it.
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.
(b) high temperature
(d) low pH
(a) Urea acts primarily by disrupting hydrophobic interactions. (b) High temperature provides
thermal energy greater than the strength of the weak interactions (hydrogen bonds, electrostatic
interactions, hydrophobic interactions, and van der Waals forces, breaking these interactions. (c)
Detergents bind to hydrophobic regions of the protein, preventing hydrophobic interactions among
several hydrophobic patches on the native protein. (d) Low pH causes protonation of the side chains
of Asp, Glu, and His, preventing electrostatic interactions.
How can changes in pH alter the conformation of a protein?
Changes in pH can influence the extent to which certain amino acid side chains (or the amino
and carboxyl termini) are protonated. The result is a change in net charge on the protein, which can
lead to electrostatic attractions or repulsions between different regions of the protein. The final effect
is a change in the protein's three-dimensional shape or even complete denaturation.
Once a protein has been denatured, how can it be renatured? If renaturation does not occur, what
might be the explanation?
Because a protein may be denatured through the disruption of hydrogen bonds and hydrophobic
interactions by salts or organic solvents, removal of those conditions will reestablish the original
aqueous environment, often permitting the protein to fold once again into its native conformation. If
the protein does not renature, it may be because the denaturing treatment removed a required
prosthetic group, or because the normal folding pathway requires the presence of a polypeptide chain
binding protein or molecular chaperone. The normal folding pathway could also be mediated by a
larger polypeptide, which is then cleaved (e.g., insulin). Denatured insulin would not refold easily.
What are two mechanisms by which "chaperone" proteins assist in the correct folding of
Chaperones protect unfolded polypeptides from aggregation by binding to hydrophobic regions.
They can also provide a microenvironment that promotes correct folding.