Biochem HW 4 and 5 homework
How many amino acids, commonly found in nature, are utilized for protein biosynthesis?
20
What level of protein structure describes the spatial location of every atom in a protein?
3 prime
Given the nature of hair and fingernails, and knowing both have high levels of keratin, which of the following is true A. Keratin in hair has fewer cysteines and therefore fewer disulfide bonds than keratin in fingernails. B. Keratin in hair has more cysteines and therefore more disulfide bonds than keratin in fingernails. C. Keratin in hair has more cysteines and therefore fewer disulfide bonds than keratin in fingernails. D. Keratin in hair has fewer cysteines and therefore more disulfide bonds than keratin in fingernails.
A
If a mutation occurred in which a codon changed to that for proline, what would you expect if the codon were found in a region that formed an α helix? A. The proline would disrupt the α helix. B. The proline would have no effect. C. The proline would cause the α helix to turn into a β sheet. D. The proline would form hydrogen bonds to the residue four amino acids ahead (i + 4).
A
The class of proteins that help other proteins fold is called Choose one: A. chaperones. B. ligases. C. proteases. D. kinases.
A
What is the molecular geometry of the constituents of the peptide plane? A. The amide nitrogen is trigonal planar and the carbonyl carbon is also trigonal planar. B. The amide nitrogen is tetrahedral and the carbonyl carbon is also tetrahedral. C. The amide nitrogen is tetrahedral and the carbonyl carbon is trigonal planar. D. The amide nitrogen is trigonal bipyramidal and the carbonyl carbon is trigonal planar.
A
Sodium dodecylsulfate (SDS) plays an important role in SDS PAGE. Select each correct description of what SDS does in denatured electrophoresis. Choose one or more A. Because SDS is a detergent, it plays a role in denaturing the protein. B. Because SDS is a detergent, it supports the native state by interacting with the nonpolar portions of a protein, stabilizing the three-dimensional structure of a protein. C. SDS is a charged detergent that neutralizes the protein, allowing the protein to migrate through the gel based on size. D. SDS is an amphipathic compound that binds to the hydrophobic portion of the protein, coating the mixture and giving the protein an overall negative charge proportional to the size of the protein.
A and D
You have discovered a small organic compound that you think will cause a significant shift in the peptide loop covering the active site of the enzyme, inhibiting the protein's function. Which approach(es) would be most appropriate to test for this hypothesis? Choose one or more A. X-ray crystallography B. Affinity chromatography C. ELISA D. NMR spectroscopy
A and D
Of all the different bond types found in proteins, which has partial double bond character?
A peptide bond
Which secondary structure elements are stabilized by hydrogen bonds? Choose one or more: A. α helices B. antiparallel β sheets C. parallel β sheets D. random coil
A, B,C
Gel Filtration, Affinity, Ion-Exchange, which one is it? Antibodies are sometimes used to bind target proteins in this chromatography.
Affinity
Gel Filtration, Affinity, Ion-Exchange, which one is it? Metal ions can be fixed to a resin and bind to specific sequences of amino acids such as histidine.
Affinity
Gel Filtration, Affinity, Ion-Exchange, which one is it? Natural or mimicked ligand of the target protein is bound to a solid-phase resin, often a dextran bead.
Affinity
Gel Filtration, Affinity, Ion-Exchange, which one is it? Separates proteins based on specific binding properties of the target protein
Affinity
What protein feature will cause the protein to bind to a metal in chelation affinity chromatography—specifically, a resin with immobilized Ni2+? A. proteins with a negative charge B. recombinant proteins engineered to have six or more histidines at the N or C terminus of the protein C. proteins with antigenic affinity for divalent cations D. proteins that have a heme that can bind divalent cation metals, such as iron or nickel
B
Which of the following is categorized as a charged amino acid? A. Q B. R C. M D. A
B
Which of the following is correct concerning a peptide backbone? Choose one: A. The torsional angle between the amide nitrogen and the Cα is called ψ (psi). B. A Ramachandran plot shows the allowable ϕ and ψ angles for a peptide. C. The torsional angle between the Cα and the R group is called ϕ (phi). D. The peptide bond allows for free rotation due to its single bond character.
B
Which of the following statements best describes the difference between a primary and secondary antibody as used in a Western blot? A. The primary antibody and secondary antibody must be produced in the same animal. B. The primary antibody binds the antigen, whereas the secondary antibody binds the primary antibody and serves to detect the complex with its linked enzyme. C. Primary antibodies are covalently bound to an antigen that the secondary antibody, with its conjugated enzyme, also recognizes. D. Both antibodies bind and recognize antigen proteins; the secondary body is helped by the primary antibody.
B
There are two main methods to get proteins into a gas phase for mass spectroscopy: electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). Place the appropriate description of each ionization method in the appropriate space. ESI, MALDI, Both ESI and MALDI Can be used for proteins or peptides that have been treated with proteases like trypsin
Both
There are two main methods to get proteins into a gas phase for mass spectroscopy: electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). Place the appropriate description of each ionization method in the appropriate space. ESI, MALDI, Both ESI and MALDI Is based on the mass and acceleration though a chamber ending in a detector
Both
There are two main methods to get proteins into a gas phase for mass spectroscopy: electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). Place the appropriate description of each ionization method in the appropriate space. ESI, MALDI, Both ESI and MALDI Uses mass-to-charge (m/z) ratio to determine molecular mass
Both
If the cytoplasm of a cell were to become a much more oxidizing environment, what do you predict would happen to an existing surface-exposed disulfide bond in a typical cytoplasmic protein? Choose one: A. The proteins would be quickly ubiquitinated and degraded since the disulfide bond would be incorrect. B. The disulfide bond would be more quickly reduced than normally. C. There would be no change since the disulfide bond is already oxidized. D. The disulfide bond would further oxidize, forming highly reactive sulfur centers.
C
Which of the following is most likely to be found on the exterior of a protein? Choose one: A. Pro B. Glu C. Ser D. Trp
C
α helices, β strands, and β turns are examples of __________ structure. Choose one: A. tertiary B. primary C. secondary D. quaternary
C
Quaternary structures provide increased functionality to proteins in which of the follow ways? Choose one or more: A.They prevent cooperativity. B.They alter the chemical reaction to tolerate more diverse substrates. C. They increase efficiency of biochemical processes. D. They provide structural properties not present in individual subunits.
C and D
Which amino acids contain sulfur? Choose one or more: A. proline B. arginine C. cysteine D. glutamine E. methionine
C and E
Getting your hair permed must involve which of the following? A. irreversible denaturation of keratin B. oxidation of disulfide bonds, reshaping, and then reduction of disulfide bonds C. proteolytic digestions of keratin D. reduction of disulfide bonds, reshaping, and then oxidation of disulfide bonds
D
It has been observed that in a few cases, the peptide plane is actually bent 4°-5° from being a flat plane. What is the most plausible explanation? A. This is not possible. The apparent skewing of the peptide plane must be due to error in the structural measurement. B. The skewed peptide plane is a result of misformed disulfide bonds, causing the protein to denature. C. The fast, dynamic motions in a protein cause the peptide plane to be non-ideal over the lifetime of the protein. D. Some other restraint is causing the peptide plane to adopt an unfavorable state. The favorable energetics of the other restraint offset the energetic unfavorability of the skewed peptide plane.
D
There are two main methods to get proteins into a gas phase for mass spectroscopy: electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). Place the appropriate description of each ionization method in the appropriate space. ESI, MALDI, Both ESI and MALDI Peptides become fragmented and charged due to laser exposure.
MALDI
There are two main methods to get proteins into a gas phase for mass spectroscopy: electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). Place the appropriate description of each ionization method in the appropriate space. ESI, MALDI, Both ESI and MALDI Proteins or peptides are mixed in a solid matrix rather than a solution.
MALDI
There are several limiting issues when determining the structures of some proteins. X-ray vs NMR Large proteins will reorient slowly in solution, averaging out the signal.
NMR
There are several limiting issues when determining the structures of some proteins. X-ray vs NMR Requires isotopic labeling of elements such as N, C, or H
NMR
There are several limiting issues when determining the structures of some proteins. X-ray vs NMR Smaller proteins are more amenable for this type of structual analysis.
NMR
___________ provides information on the structure of a purified protein based on its nuclear spin properties in a magnetic field, whereas ______________ uses diffraction pattern of proteins in solid phase.
NMR, X-Ray
For the following charged amino acids at pH 7, determine whether the net charge on the amino acid is positive, negative, or neutral. (B) glutamate
Negative
For the following charged amino acids at pH 7, determine whether the net charge on the amino acid is positive, negative, or neutral. (E) methionine
Neutral
For the following charged amino acids at pH 7, determine whether the net charge on the amino acid is positive, negative, or neutral. C) Lysine
Positive
For the following charged amino acids at pH 7, determine whether the net charge on the amino acid is positive, negative, or neutral. D) Arginine
Positive
The amino acid sequence determines the structure and function of a protein. The amino acid sequence is called the _________ structure of the protein.
Primary
A __________ mutation will not lead to a change in the protein product of a gene.
Silent
The first step of protein mass spectrometry is to get the protein (usually peptide fragments) into a gas phase as an ion. Which of the following describes matrix-assisted laser desorption/ionization (MALDI) ionization? A. Liquid chromatography is used for elution into a focused laser beam to fragment each eluted protein. B. Small peptide fragments are released from a small metallic capillary under high voltage that removes the solvent and ionizes the peptides into the gas phase. C. Trypsinized fragments can be exposed directly to the first chamber of a tandem mass spectrometry chamber, where collisions with gas particles cause peptide fragmentation. D. Protein fragments are embedded in a solid mixture that absorbs light, and then a laser flashes on this mixture, leaving fragmented and ionized peptides in the gas phase.
D
The mass-to-charge ratios of denatured proteins are equivalent for different mass proteins. However, the cross-linked nature of the acrylamide media can limit migration through the polymer matrix. Gels with less cross-linked acrylamide (low % SDS gels) will do which of the following? A. separate the smaller proteins based on the percentage gel at the expense of larger proteins B. allow the negative charge contributed by the smaller SDS molecules to more easily migrate through a low-percent acrylamide because of the increase in negative charge C. separate proteins as in size-exclusion chromatography, with the smaller proteins migrating most slowly and the larger proteins migrating farther through the gel D. separate larger proteins at the expense of smaller proteins, which will not resolve well
D
Many diseases, including Alzheimer's disease, are associated with A. buildup of uric acid. B. dietary deficiencies. C. antibodies. D. high ATP levels in the liver. E. protein aggregation.
E
There are two main methods to get proteins into a gas phase for mass spectroscopy: electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). Place the appropriate description of each ionization method in the appropriate space. ESI, MALDI, Both ESI and MALDI Ionization evaporates solvent, leaving peptide in gas phase to travel through the separating mass spectrometer.
ESI
There are two main methods to get proteins into a gas phase for mass spectroscopy: electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). Place the appropriate description of each ionization method in the appropriate space. ESI, MALDI, Both ESI and MALDI Sample becomes ionized due to high voltage.
ESI
There are two main methods to get proteins into a gas phase for mass spectroscopy: electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). Place the appropriate description of each ionization method in the appropriate space.ESI, MALDI, Both ESI and MALDI Degrades and charges the peptide with high voltage
ESI
Fibrous or Globular Collagen
Fibrous
Fibrous or Globular Keratin
Fibrous
Fibrous or Globular Silk fibroin
Fibrous
Gel Filtration, Affinity, Ion-Exchange, which one is it? Can be used to determine the molecular mass of an unknown protein using a set of proteins with known molecular mass
Gel Filtration
Gel Filtration, Affinity, Ion-Exchange, which one is it? Uses a porous bead made of complex carbohydrates that allow proteins to go through or around
Gel Filtration
Gel Filtration, Affinity, Ion-Exchange, which one is it? Small proteins are retained due to a longer pathway through the column.
Gel filtration
Gel Filtration, Affinity, Ion-Exchange, which one is it? Two proteins of the same size but different shape (globular vs fibrous) can be separated by this method.
Gel filtration
Fibrous or Globular Hemoglobin
Globular
Fibrous or Globular Heterotrimeric G protein
Globular
Fibrous or Globular Ras (a low molecular weight G protein)
Globular
Fibrous or Globular Serum albumin
Globular
Which amino acid is the smallest and least chemically active?
Glycine
What is a major consequence of the partial double bond character?
Greatly reduced rotational freedom compared to the φ (phi)/ψ (psi) torsion angles
Gel Filtration, Affinity, Ion-Exchange, which one is it? DEAE is a positive charged resin used in this type of chromatography.
Ion-Exchange
Gel Filtration, Affinity, Ion-Exchange, which one is it? Exploits the charge state of a protein to adhere to a chromatography resin
Ion-Exchange
Gel Filtration, Affinity, Ion-Exchange, which one is it? Proteins are displaced from the resin by changing pH or increasing the ionic strength (salt conc.) of elution buffer.
Ion-Exchange
There are two main methods to get proteins into a gas phase for mass spectroscopy: electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). Place the appropriate description of each ionization method in the appropriate space. ESI, MALDI, Both ESI and MALDI Laser will be absorbed by the peptide containing material releasing the peptide into the gas phase.
MALDI
Congratulations, you have purified your protein of interest (YPOI). You and your research partner have subjected your protein to polyacrylamide electrophoresis. You treated your protein with SDS and a reducing agent (beta-mercapto ethanol) and boiled it. Your partner ran a native gel without the SDS and reducing agent treatment. You both observe one band on each gel, but your protein (denaturing SDS PAGE) migrated as a 23,000-dalton protein, while your research partner's gel showed a band at 92,000 daltons. After some discussion, you feel that your protein is a ____________ and that the SDS and reducing agent have: A)altered the ability of the protein to migrate through acrylamide. B)degraded (hydrolyzed) the protein to smaller peptides. C) folded the protein into a smaller, more compact protein, allowing it to funnel through the acrylamide more easily. D)denatured the protein, which is made of equally sized monomers.
Tetramer, D
When a protein folds, transitioning from denatured to native state, the change in free energy is favorable (ΔG < 0). In general, the entropic change is _______ due to the more limited number of conformations. The enthalpic change is __________ due to the many weak interactions that are formed. With the exception of disulfide bonds, weak interactions include the formation of ______ and numerous___________ in the native state.
Unfavorable, Favorable, Hydrogen, Van der waal
There are several limiting issues when determining the structures of some proteins. X-ray vs NMR Nearly any sized protein can be used for this type of structural analysis
X-Ray
There are several limiting issues when determining the structures of some proteins. X-ray vs NMR Dynamic changes are not easily captured.
X-ray
There are several limiting issues when determining the structures of some proteins. X-ray vs NMR Poorly ordered domains, including disordered domains, will have mulitple arrangements averaging out a signal.
X-ray
Extracting a protein bound to a column is called which of the following? A. elution B. extraction C. dissociation D. isolation
elution
For the following charged amino acids at pH 7, determine whether the net charge on the amino acid is positive, negative, or neutral. (A) aspartate
negative
