Ch4 Adaptive Quiz: The 3D Structure of Proteins Flashcards
A change in ________ changes the spatial arrangement of atoms in a protein, but does not involve the breaking of covalent bonds.
Conformation
A regular secondary structure occurs in a protein chain segment when:
the φ and ψ angles are the same, or nearly so, throughout the segment.
A ________ is a part of a polypeptide chain that is independently stable or could undergo movement as a single entity with respect to the entire protein.
domain
Which statement defines denaturation of a protein?
loss of tertiary structure sufficient for loss of function.
What is TOCSY?
a two‑dimensional NMR technique measuring the coupling of nuclear spins in atoms connected by covalent bonds
What is the effective distance of van der Waals forces as atoms approach each other?
0.3 nm to 0.6 nm
How many turns are there in a typical α helix with a length of 4.86 nm?
9
By definition, quaternary structure is exhibited by proteins that have:
two or more separate, but associating, protein chains.
How do aromatic residues affect the formation of amyloid fibrils?
They stabilize the protein structure such that fibrils form more slowly and disease onset occurs later in life.
What was the accomplishment of John Kendrew’s x‑ray crystallography studies in 1959?
the determination of virtually all the non-hydrogen atoms positions in the myoglobin protein structure
What is the predominant factor in protein stability?
The hydrophobic effect
As predicted by Pauling and Corey, peptide bonds are in the ________ configuration.
planar, trans
Which phenomenon is NOT an example of a van der Waals interaction?
ionic interactions that form a salt bridge
Given that an α helix has 3.6 residues per turn and the rise along the α helix axis is 5.4 Å, approximately how many amino acids would you find in a single contiguous α helix that is 210 Å long?
140
What does it mean for two proteins to be in the same protein family?
The proteins either have similar primary structures and/or similar functions and tertiary structures.
Some mutations can reduce protein stability, but not completely destroy it. In the Siamese cat, a G→R transition, changing glycine to arginine (G302R), makes the tyrosinase enzyme in skin cells sensitive to temperature. This enzyme takes part in the synthesis of melanin, the dark pigment in hair and skin. It is properly folded at low body temperatures but denatured at high body temperatures. What can we then say about the Siamese cat?
The dark areas around its paws, nose, and ears are slightly cooler than the rest of the cat.
What is the first step in an x‑ray crystallography study?
purifying the protein
Which type of chemical interaction contributes the MOST to the stability of most proteins?
hydrophobic interactions
What structural feature distinguishes fibroin from other fibrous proteins?
Its polypeptide chains are predominantly in the β conformation.
Which statement regarding the Hsp70 protein family is FALSE?
These proteins are necessary for the growth of some bacterial viruses. (false because this is chaperonins, not Hsp70)
What is the mechanism of denaturation when ribonuclease A incubates with urea and a reducing agent?
The reducing agent cleaves the disulfide bonds and urea disrupts the hydrophobic effect.
Which statement describes the relationship between absorbance (A) and path length (l) according to the Lambert‑Beer law for an absorbing layer of a particular concentration?
A is directly proportional to l.
Peptide bond formation is an example of a _____ reaction.
condensation
A protein’s electrophoretic mobility is directly related to its:
net charge
What is the purpose of analyzing a protein using a combination of liquid chromatography and tandem mass spectrometry (LC‑MS/MS)?
to separate complex mixtures of digested peptides before analyzing each m/z
What is the concentration of a tryptophan solution when the absorbance at 280 nm is 6 using a 1 cm cuvette and the molar extinction coefficient is 5579 L/mol·cm?
1.1 mM
What type of protein is chymotrypsin, as it only contains amino acids?
simple protein
Researchers add sodium dodecyl sulfate (SDS) during the electrophoresis of proteins to:
separate proteins based exclusively on molecular weight.
Which piece of information does mass spectrometry NOT contribute to the study of protein chemistry?
Protein function
What is the order of protein migration, from shortest to longest, in SDS gel electrophoresis if the original mixture contains protein A (Mr 27,000), protein B (Mr 58,400), protein C (homodimer with protomer Mr 11,300), and protein D (Mr 15,600)?
BACD
Lysine has three pKa values of 2.18, 8.95, and 10.53. Calculate the isoelectric point (pI) of lysine.
9.74
Chemical synthesis of peptides by the Merrifield method:
proceeds from the carboxyl terminus to the amino terminus.
