Biochem Exam 1
What is the reason for the stability of collagen helix?
steric repulsion of the pyrrolidine rings of the proline and hydroxyproline
Polyclonal antibodies often differ in all of these ways EXCEPT _____.
target antigens
Wool fibers return to their original state after stretching because of:
disulfide bonds
Fluorescence microscopy revealed all of these concerning the mineralocorticoid receptor EXCEPT that it _____.
is located in the cytoplasm in the presence of steroid hormones
Levinthal calculated that if a 100-residue protein with three possible conformations available per residue sampled all conformations, the amount of time it would take the protein to fold would be:
longer than the universe has existed
A mass spectrometer measures the _____ ratio, which is the _____ of each ion divided by its _____.
m/z; mass; charge
In sedimentation equilibrium, the shape of the final concentration gradient is solely dependent on the _____.
mass
You have a protein that is chemically modified by a reagent. To determine which amino acid in the protein is modified, you could use what technique?
mass spectrometry
Centrifugation at 100,000 × g for 1 hour produces what fraction of a cell homogenate in the pellet?
microsomal fraction
Centrifugation at 10,000 × g for 20 minutes produces what fraction of a cell homogenate in the pellet?
mitochondrial fraction
The normal PrP protein has a secondary structure that is:
mostly α-helix
_____ is an aliphatic amino acid, but it differs from others because its side chain is bonded to both the _____ and the _____ of the backbone.
proline; nitrogen; α-carbon
A protein is determined by sedimentation equilibrium to have a mass of 80 kDa. An SDS-PAGE of the protein shows bands migrating at the same rate as proteins with masses of 25 kDa and 15 kDa. The best explanation for the data would be the _____.
protein is tetrameric with two each of two different types of subunits
In isoelectric focusing _____.
proteins migrate to a region of the gel in which the pH = pI
A western blot can detect only _____.
proteins whose epitope is intact in the presence of a reducing agent
To generate monoclonal antibodies, what two types of cells were fused together by Milstein and Köhler?
myeloma cells and spleen cells
A key difference between prion diseases and Alzheimer disease is:
Prion diseases are readily transmissible to other organisms but Alzheimer is not.
In SDS-PAGE experiments, the SDS _____.
denatures the proteins
The modification that converts soluble fibrinogen into insoluble fibrin during blood clotting is:
peptide cleavage
What would be the net charge on the peptide Met-Ala-Glu-His-Lys-Phe at pH 5?
+1
Of the 20 core amino acids, how many of them are chiral?
19 (Glycine is achiral as it has 2 hydrogen atoms linked to the α-carbon.)
The amino acid sequence of insulin was determined in:
1953 by Frederick Sanger.
An α-helix made up of 32 amino acids would be _____ times _____ than a β-strand made up of the same number of amino acids.
2.3; shorter
The coat of human rhinovirus consists of how many total subunits?
240
An α-helix of 19 amino acids can cross the double layer of a typical membrane. What will be the approximate length of the helix?
29
After one round of protein purification, the amount of total protein changes from 1 g to 200 mg. The total activity of the sample changes from 100,000 units to 80,000 units. The values for specific activity, yield, and purification level change as follows: _____.
4-fold increase, 20% decrease, 4-fold increase
The frictional coefficient for a sphere of radius r in an electrophoretic setup would be _____.
6πηr
Which is TRUE about the quaternary structure of proteins?
A protein with quaternary structure must have more than one N-terminus.
Which of the following statements about amino acids is TRUE?
Amino acids in solution at neutral pH are dipolar ions, or zwitterions.
The relationship between the amino acid sequence of a protein and its conformation was shown in the classic experiment by _____ using the protein _____.
Anfinsen; ribonuclease
Which of the following statements is TRUE
Beta sheets can be parallel or antiparallel.
In osteogenesis imperfecta, which amino acid residue normally found in collagen is replaced?
Gly
The difference in a domain and a subunit is:
Domains are part of the same polypeptide chain
Which of the following statements is true for BOTH an α-helix and a β-pleated sheet?
Formation is driven by hydrogen bonds between main-chain C=O and NH groups.
Which amino acid would be neutral at pH 7 but positively charged at pH 5 as a free amino acid?
His
What unusual amino acid is commonly found in collagen?
Hyroxyproline
Which of these is NOT TRUE of differential centrifugation?
It can be used to accurately determine the mass of a protein.
The peptide LMEKCSPH is treated with a chemical and then subjected to trypsin digestion. The mass spectrum shows that the peptide remained intact. Which of the following was likely targeted by the chemical?
K
In keratin's structure, van der Waals interactions between what amino acid, found every seventh residue, are used to hold the superhelix together?
Leu
Which of the following statements is FALSE?
Many hormones can alter the activities of enzymes, but polypeptides cannot function as hormones.
In a fully folded soluble protein, which of the following holds TRUE?
Most Glu and Arg groups would face the exterior of the protein.
Lactate dehydrogenase absorbs UV light at 280 nm. Why would the absorbance at 280 nm not be an effective assay for lactate dehydrogenase?
Other proteins absorb light at this same wavelength.
Which of the following diseases is not caused by a prion?
Parkinson disease
Porin proteins are located in bacterial membranes and have water-filled cavities in the interior. Compared with soluble proteins:
Porins would have more hydrophilic residues on the interior of the protein.
Which amino acid is unable to form a hydrogen bond that is an essential part of an α-helix?
Pro
Which of these is NOT an advantage of recombinant DNA technology?
Proteins can easily be separated by their isoelectric points. This is possible through isoelectric focusing, not through recombinant DNA technology.
The one-letter abbreviation for Glutamine is:
Q
The assay for lactate dehydrogenase measures the absorbance of light at 340 nm over time. Which of these statements is FALSE?
The assay is used to determine the mass of lactate dehydrogenase present.
You have two monoclonal antibodies that both bind to a protein that you are investigating. You carry out western blots simultaneously, using one antibody for each experiment. Your first western blot looks great, and a single band is located on the autoradiogram. Your second western blot shows no bands. Which of the following may be TRUE given these results?
The epitope recognized by the second antibody is noncontiguous; it does not recognize amino acids found sequentially in the primary structure of the protein.
Peptide bonds resist rotation and are essentially planar because:
The peptide bond has partial double-bond character.
Which of the following is TRUE when performing Edman degradation on a protein containing two or more cysteine amino acids?
The protein must be treated with a reducing agent followed by iodoacetate prior to sequencing.
If an α-helix is used to span a membrane, which of the following would be expected?
The residues would all be nonpolar.
Using a time-of-flight analyzer, the mass of ions can be determined. Given two ions of the same charge, which ion will be detected FIRST?
The smaller of the two ions will be detected first because the smaller ion will traverse the chamber more quickly.
Which of the following characteristics is TRUE for both valine and threonine?
They are both neutral at physiological pH (~ pH = 7).
Which of the following is TRUE of intrinsically unstructured proteins?
They are rich in charged and polar amino acids.
Which of the following is FALSE about prions?
They lack hydrogen bonding.
Which of the following statements is true when you compare phenylalanine and tryptophan?
Tryptophan is less hydrophobic than phenylalanine.
Which of the following is TRUE regarding a sandwich ELISA?
Two different antibodies that recognize the antigen are necessary.
An indirect ELISA is attempted, but you add the enzyme-linked antibody, wash, and then add the sample. You then realize your mistake; you have no more sample but you have more of the other reagents. Can you recover, and if so, how?
You can recover by adding the enzyme-linked antibody again, then washing, and then adding substrate.
A sandwich ELISA is attempted, but you add the secondary antibody, wash, and then add the sample. You then realize your mistake. You have no more sample but you have more of the other reagents. Can you recover, and if so, how?
You can recover by adding the secondary antibody again, then washing, and then adding substrate.
Which of the following is required when performing dialysis?
a semipermeable membrane
Which type of modification to an amino acid would produce a more hydrophobic protein?
addition of a fatty acid unit
Which amino acid has a one-letter abbreviation of A?
alanine
A "His tag" is sometimes used on recombinant proteins to _____.
allow for ease of purification
Treatment of a protein with a chemical causes a missed cleavage when the protein is treated by clostripain. The chemical added caused a modification to _____.
arginine
Which amino acid has a one-letter abbreviation of R?
arginine
Intrinsically unstructured proteins:
assume a defined structure when they interact with another protein
Secondary structures are influenced by which type of hydrogen bonding primarily?
between backbone atoms of different amino acids
Protein A has a charge of +1 at pH 7 and a mass of 26 kDa. Protein B has a charge of +4 at pH 7 and a mass of 56 kDa. Which of the following techniques could separate them?
both gel filtration and ion exchange chromatography using negatively charged beads
Which of the following amino acids contains a sulfhydryl group in the side chain?
cysteine
A comparison of sequences of serum albumins from primates was used to _____.
determine the evolutionary relationship of the primates
The pitch of an α-helix is:
equal to 5.4 angstroms
In the absence of an enzyme, hydrolysis of a peptide bond is thermodynamically _____ and kinetically _____.
favorable; slow
You need to isolate 1 mg of a sample of a 52-kDa protein by separating it from a 75-kDa protein. Which of the following techniques would be ideal for this task?
gel-filtration chromatography
Aspartate tends to interfere with α-helix formation because it:
has hydrogen bond acceptors near the backbone
Certain combinations of secondary structures are present in many proteins and frequently exhibit similar functions. An example for such a supersecondary structure or a motif is _____.
helix-turn-helix
You have a dilute solution of a protein that has an affinity for glucose and want to concentrate it. Which of the following techniques would be MOST effective for this?
high-performance liquid chromatography
What maintains the secondary structure of a protein?
hydrogen bonds
Which technique is the basis for a test for HIV infection?
indirect ELISA
A peptide bond is:
intermediate between the length of a C-N and C=N bond
The mobility of proteins in an SDS-PAGE experiment is _____.
inversely proportional to the log of their mass
A feature of hemoglobin that is not found in myoglobin is:
quaternary structure
Sickle-cell anemia and cystic fibrosis are caused by what kind of change in primary structure?
replacement of a single critical amino acid
Which of the following is true of gel-filtration chromatography but not ion-exchange chromatography?
requires porous beads
Hydrogen bonding between the C=O of one residue and the NH three residues later is often found in:
reverse turn
The absence of hydroxyl groups on hyroxyproline is a result of this disease:
scurvy
Anfinsen used dialysis to:
separate ribonuclease from the denaturants
The central region of keratin has imperfect repeats of a series of _____ amino acids.
seven
A high purification level with a low yield would indicate that protein purification led to _____.
small amounts of a pure protein
Adding salt can separate proteins according to their _____.
solubility
Most possible combinations of dihedral (psi, phi) angles are disallowed because of:
steric clashes
The primary structure of a protein describes:
the amino acid sequence
Specific activity is _____.
the ratio of enzyme activity to the amount of protein in the mixture
A Ramachandran diagram of ψ versus θ angles is separated into four quadrants. In which quadrant would you expect to find data descriptive of a β-pleated sheet
top left
If ribonuclease is scrambled with incorrect disulfide bonds, the native structure can be returned by:
treatment with β-mercaptoethanol
Name the amino acid with an indole group.
tryptophan
In a parallel β-sheet, one amino acid hydrogen bonds with:
two nonconsecutive amino acids on a neighboring strand
Keratin's structure is best described as:
two right-handed helices intertwined to form a left-handed superhelix
Which of the following amino acids has the LARGEST side chain?
tyrosine
Which of these is NOT an application of the determination of an amino acid sequence?
using tandem mass spectrometry to identify other proteins