Biochemistry Ch 4
The computer analyzing NMR data requires several parameters. Which parameter is NOT necessary for generating a 3D protein structure? -van der Waals radii -molecular vibrations -chirality -distance constraints -bond lengths
molecular vibrations
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? -39 -58 -140 -315
140
Estimate the number of amino acids in a typical α helix that is 30 Å long. -5800 -45 -20 -The number of amino acids cannot be estimated because of the irregularity of α helices.
20
How many amino acids are in a 6.2 nm long α helix? 9.3 93 0.41 4.1 41
41
How many amino acids are in a 62 Å long α helix? 223 93 335 11 41
41
What is the difference between a family and a superfamily of proteins? -A family consists of proteins having similar primary structures and/or similar functions and tertiary structures, whereas a superfamily consists of families that do not have similar primary structures but do have similar functions and tertiary structures. -A family has less than 100 proteins with similar primary and tertiary structures, whereas a superfamily has greater than 100 proteins. -A family contains proteins with either similar primary or tertiary structures, whereas a superfamily contains proteins having both primary and tertiary structural similarities. -A family has a definite evolutionary relationship, whereas a superfamily only has a strong possibility of an evolutionary relationship.
A family consists of proteins having similar primary structures and/or similar functions and tertiary structures, whereas a superfamily consists of families that do not have similar primary structures but do have similar functions and tertiary structures.
Which amino acid sequence maximizes ion pairing for the stabilization of α helix formation at pH 7? ADVKLEVRIDV ADVVKLIEVAR DAAARVVVVEV AVISNRPYGGG
ADVVKLIEVAR
Which statement is TRUE regarding the β conformation? -Individual strands in the β sheet must be contained within the same polypeptide chain. -Adjacent polypeptide chains are either parallel or antiparallel regarding their amino‑to‑carboxyl orientations. -The β strands consist of α helices oriented in the same plane. -Natural proteins contain parallel β sheets.
Adjacent polypeptide chains are either parallel or antiparallel regarding their amino‑to‑carboxyl orientations.
Rotation about which bond changes the dihedral angle designated ω? Cα-C Cα-R C-N N-Cα
C-N
How does the solvation layer contribute to protein folding? -A decrease in entropy is the major thermodynamic driving force for the association of hydrophobic groups in aqueous solution. -Clustered hydrophobic groups reduce the water's entropy, decreasing the solvation layer. -Hydrogen bonding within the protein structure increases the solvation layer, thus enhancing solubility. -Intramolecular hydrogen bond formation energy is significantly greater than the hydrogen bond formation energy for polar amino acids and water.
Clustered hydrophobic groups reduce the water's entropy, decreasing the solvation layer.
How does genetic engineering aid the translation of 2D NMR spectra into a 3D protein structure? -Comparing the original spectra to the genetically engineered spectra aids the individual signal assignments. -The rare isotopes generate less complicated spectra than 1H spectra, making it easier to interpret. -Labeled carbon and nitrogen allow identification of α helices. -Genetic engineering aids identification of covalent bonds in the structure.
Comparing the original spectra to the genetically engineered spectra aids the individual signal assignments.
Which statement regarding globular proteins is FALSE? -Polypeptide segments fold back on each other to form globular proteins. -Multiple polypeptide chains fold to form globular proteins. -Fibrous proteins are more compact than globular proteins. -The globular folding pattern provides structural diversity. -Most enzymes are globular proteins.
Fibrous proteins are more compact than globular proteins.
Which statement regarding protein folding is FALSE? -Amino‑terminal domains may fold before large proteins are fully synthesized. -Local structures form before long‑range interactions. -Proteins dominated by close‑range interactions fold faster than proteins with many long‑range interactions. -Ionic interactions form in the final steps of protein folding.
Ionic interactions form in the final steps of protein folding.
Which statement does NOT describe a characteristic of a peptide bond? -It causes resonance stabilization of each backbone bond. =It is a linkage between amino acids in a protein. -It is an amide bond. -It is rigid and planar.
It causes resonance stabilization of each backbone bond.
Which statement regarding structural biology is FALSE? -It aids the determination of evolutionary relationships between proteins. -It enables protein sequence determinations based on protein function. -It elucidates the relationships between the structure and function of proteins. -It describes the molecular basis for enzymatic catalysis and ligand binding.
It enables protein sequence determinations based on protein function
What structural feature distinguishes fibroin from other fibrous proteins? It is made up of α chains instead of α helices. Its polypeptide chains are predominantly in the β conformation. Its quaternary structure involves right‑handed supercoils. Its quaternary structure involves left‑handed supercoils.
Its polypeptide chains are predominantly in the β conformation.
What is the general hierarchy of protein folding? -Local structures form before long‑range interactions. -Hydrogen bonding takes place in the short‑range interactions, whereas the hydrophobic effect participates in the long‑range interactions. -The α helices are the first to form, whereas ionic interactions are the last to form. -Nonpolar amino acid side chain aggregation occurs before secondary structure formation.
Local structures form before long‑range interactions.
Are all denatured proteins able to refold properly when returned to native conditions? -Yes, the amino acid sequence contains all the information required to fold the polypeptide chain into its native, three‑dimensional structure. -Yes, the hydrophobic effect drives the folding process. -No, although small stable proteins refold spontaneously, most proteins require assistance. -No, a denatured protein is "sticky" and aggregates with other proteins prior to precipitating.
No, although small stable proteins refold spontaneously, most proteins require assistance.
Why is the sequence DCVPAIPSQR unlikely to participate in an α helix? -Ion pairing disrupts helix formation when similarly charged amino acids are three residues apart. -Glycine residues have too much conformational flexibility. -Proline residues cause kinks in the helix. -Hydrophobic residues are too close together.
Proline residues cause kinks in the helix
Which statement is TRUE regarding salt bridges? -Ionic interactions enhance the flexibility of a protein. -Salt bridges allow hydrophobic residue interaction with water. -Partially buried salt bridges destabilize proteins. -Salt bridge strength is greater in hydrophobic environments than in polar environments.
Salt bridge strength is greater in hydrophobic environments than in polar environments.
Which statement regarding peptide bonds is FALSE? -The peptide bond is almost always in the trans configuration. -A cis peptide bond has a dihedral angle of 0°. -The peptide bond does not rotate. -The N atom in a peptide bond has a partial positive charge.
The N atom in a peptide bond has a partial positive charge.
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? -A glycine → alanine mutation at position 302 would destabilize the protein further so the cat would be lighter in color over its entire body. -A glycine → alanine mutation at position 302 would destabilize the protein further so the cat would be darker in color over its entire body. -The dark areas around its paws, nose, and ears are slightly cooler than the rest of the cat. -The dark areas around its paws, nose, and ears are slightly higher in temperature than the rest of the cat. -Any mutation at 302 should produce a cat with dark hair all over.
The dark areas around its paws, nose, and ears are slightly cooler than the rest of the cat.
Why does silk not stretch even though it has a flexible structure? -Extensive covalent bonding prevents stretching, whereas β conformations create flexibility. -Extensive covalent bonding prevents stretching, whereas α helices create flexibility. -The extended β conformation prevents stretching, whereas extensive hydrogen bonding and van der Waals forces allow for flexibility. -Extensive hydrogen bonding and van der Waals forces allow for flexibility, despite the already overstretched α chains.
The extended β conformation prevents stretching, whereas extensive hydrogen bonding and van der Waals forces allow for flexibility.
What does a circular dichroism (CD) spectroscopy signal indicate? -A specific type of α helix exists in the solution. -The peptide bond is in a folded environment. -The polypeptide is unfolded. -A specific type of β sheet exists in the solution.
The peptide bond is in a folded environment.
Which statement does NOT explain why the stability of a protein is not simply the sum of the weak interaction free energies? -The primary structure dictates exactly how the protein must fold. -Hydrogen bonds with water must break for intra-protein hydrogen bonds to form. -Ionic interactions may be either stabilizing or destabilizing. -It is possible for the difference in free energies between the folded and unfolded states to be close to zero.
The primary structure dictates exactly how the protein must fold.
Which statement is TRUE regarding the oligomeric protein hemoglobin? -The quaternary structure consists of two α subunits and two β subunits. -The secondary structure consists of two α helices and two β sheets. -The quaternary structure is a tetramer of αβ protomers. -The tertiary structure consists of two polypeptide chains and two heme prosthetic groups with ferrous iron atoms in the middle.
The quaternary structure consists of two α subunits and two β subunits.
What is the mechanism of denaturation when ribonuclease A incubates with urea and a reducing agent? -The reducing agent disrupts hydrogen bonding and urea disrupts the hydrophobic effect. -The reducing agent breaks the peptide bond and urea disrupts hydrogen bonding. -The reducing agent cleaves the disulfide bonds and urea disrupts the hydrophobic effect. -The reducing agent alters the pH and urea disrupts hydrogen bonding.
The reducing agent cleaves the disulfide bonds and urea disrupts the hydrophobic effect.
What is the problem with generating one‑dimensional NMR spectra? -1H is scarce in proteins. -The magnetic dipole has low energy. -The spectrum is too complicated for analysis. -1H NMR is not very sensitive.
The spectrum is too complicated for analysis.
What is a Fourier transform? -a regular array of spots generated by the x‑ray beam hitting a protein crystal -a computer‑generated mathematical technique used in x‑ray crystallography -a representation of protein structure constructed from the x‑ray diffraction patterns -an image of all the electron locations in the protein structure
a computer‑generated mathematical technique used in x‑ray crystallography
Which answer choice describes the quaternary structure of hemoglobin? -a pair of αβ protomers; four heme groups -four myoglobin chains joined by disulfide bonds; four heme groups -a triple bundle of subunits; one heme group -a pair of ββ protomers; two heme groups
a pair of αβ protomers; four heme groups
What is an electron‑density map? -a representation of protein structure constructed from the x‑ray diffraction pattern -a regular array of spots generated by the x‑ray beam hitting a protein crystal -a computer‑generated mathematical technique used in x‑ray crystallography -an image of all the electron locations in the protein structure
a representation of protein structure constructed from the x‑ray diffraction pattern
What is NOESY? -a two‑dimensional NMR technique measuring distance‑dependent coupling of nuclear spins in nearby atoms through space -a two‑dimensional NMR technique measuring the coupling of nuclear spins in atoms connected by covalent bonds -a one‑dimensional NMR technique measuring the electromagnetic energy absorption as nuclei switch to the high‑energy state -a one‑dimensional NMR technique measuring the electromagnetic energy absorption as nuclei switch to the low-energy state
a two‑dimensional NMR technique measuring distance‑dependent coupling of nuclear spins in nearby atoms through space
What structural information does an NMR spectrum provide? -a representation of protein structure constructed from an electron‑density map -an energy absorption spectrum representing nuclei identity and their immediate chemical environment -an image of all the nuclei locations in the protein structure -a two‑dimensional representation of a crystal
an energy absorption spectrum representing nuclei identity and their immediate chemical environment
A change in ________ changes the spatial arrangement of atoms in a protein, but does not involve the breaking of covalent bonds. -primary structure -configuration -stereoisomer -conformation
conformation
If you have a 250 Å protein with four subunits, which method would BEST help you determine how each subunit orients in relation to the others? x‑ray crystallography NMR spectroscopy molecular dynamics simulations cryo‑electron microscopy (cryo‑EM)
cryo‑electron microscopy (cryo‑EM)
Which of these methods does NOT require comparison with the amino acid sequence for protein structure determination? -NMR spectroscopy -cryo‑electron microscopy (cryo‑EM) -molecular dynamics simulations -x‑ray crystallography
cryo‑electron microscopy (cryo‑EM)
Which technique generates the structure of a protein quick‑frozen in non‑crystalline ice? -nuclear magnetic resonance (NMR) -x‑ray diffraction -cryo‑electron microscopy (cryo‑EM) -matrix‑assisted laser -desorption/ionization tandem mass spectrometry (MALDI-MS/MS)
cryo‑electron microscopy (cryo‑EM)
Autophagy of amyloid fibers includes: -degradation by encapsulation followed by docking with a lysosome. -aggregation to form larger insoluble structures. -elongation of the fibers and the formation of additional disulfide bonds. -the action of heat shock proteins to refold the proteins.
degradation by encapsulation followed by docking with a lysosome.
Denaturing followed by renaturing of a protein: -requires breaking and reforming disulfide bonds. -requires heat. -demonstrates that primary structure dictates tertiary structure. -always results in the protein regaining its function.
demonstrates that primary structure dictates tertiary structure.
Circular dichroism (CD) spectroscopy can do all of the following EXCEPT: -estimate the fraction of the protein that is folded in either of the common secondary structures. -determine whether proteins are properly folded. -determine the primary structure of proteins. -monitor transitions between folded and unfolded states.
determine the primary structure
Which amino acids are particularly common in β turns? -glycine and alanine -glycine and proline -serine and threonine -alanine and proline
glycine and proline
Reverse turns are classified as secondary structure because: -they link together β sheets. -they link together α helices. -they are not as important as primary structure. -hydrogen bonds between -backbone amide groups stabilize them. -they only occur at interior protein positions.
hydrogen bonds between backbone amide groups stabilize them.
A good way to predict whether an amino acid side chain is on the outside or inside of a protein is to consider its ________ -molecular weight -three-letter abbreviation -one-letter abbreviation -hydropathy (polarity) -None of these choices are correct.
hydropathy
Which of the chemical interactions does NOT stabilize the native conformation of a protein? -peptide bonds -disulfide bonds -ionic interactions -hydrogen bonds -noncovalent interactions
peptide bonds
Which topic is NOT included in the Protein Data Bank (PDB)? -structure‑to‑function relationship -protein evolutionary paths -protein structure -possible mutations
possible mutations
What did Christian Anfinsen use to break the disulfide bonds in ribonuclease A? strong acid reducing agent urea strong base heat
reducing agent
What role does vitamin C play in the synthesis of collagen? -Vitamin C has no role in the synthesis of collagen. -the hydroxylation of proline and lysine -the formation of disulfide bonds -the assembly of the three‑stranded superhelix
the hydroxylation of proline and lysine
What feature of a disease classifies it as a prion disease? -it affects the central nervous system -it results from protein aggregation -the infectious agent is a protein -the diseases are fatal -None of these choices define prion diseases.
the infectious agent is a protein
Which factor is NOT a constraint for α helix formation? -interactions between amino acid residues at the ends of the helical segment -the bulkiness of adjacent amino acid side chains -the intrinsic propensity of an amino acid residue -the occurrence of histidine and alanine residues -the interactions between amino acid side chains spaced three or four residues apart
the occurrence of histidine and alanine residues
A regular secondary structure occurs in a protein chain segment when: -the segment primarily consists of aromatic amino acids. -the pH is near 7.0. -the φ and ψ angles are the same, or nearly so, throughout the segment. -the dihedral angle ω is near 0°.
the φ and ψ angles are the same, or nearly so, throughout the segment.
What is the role of peptide prolyl cis-trans isomerase (PPI)? -to eliminate improperly folded intermediates that do not have correct disulfide bonds -to protect sensitive proteins that may not fold correctly or that may denature due to high temperatures. -to exchange bond formation until the proper native conformation forms -to catalyze the interconversion of the cis and trans isomers formed by Pro residues
to catalyze the interconversion of the cis and trans isomers formed by Pro residues
Why did Christian Anfinsen incubate ribonuclease A with urea and a reducing agent? -to cleave the disulfide bonds and disrupt the hydrophobic interactions -to cleave the peptide bonds and disrupt the hydrogen bonds -to disrupt the hydrogen bonding and the hydrophobic interactions -to alter the pH and disrupt the weak noncovalent bonds
to cleave the disulfide bonds and disrupt the hydrophobic interactions
What did Christian Anfinsen use to disrupt the stabilizing hydrophobic effect in ribonuclease A? -strong base -strong acid -reducing agent -heat -urea
urea
Which statement is NOT a rule governing the physical and chemical constraints of protein folding? -Where they occur together in a protein, α helices and β sheets are generally found in different structural layers. -Segments adjacent to each other in the amino acid sequence are usually stacked adjacent to each other in the folded structure. -The hydrophobic effect makes a large contribution to the stability of protein structures. -α helices are generally left‑handed. -The β conformation is most stable when the individual segments are twisted slightly in a right‑handed sense.
α helices are generally left‑handed.