BMB 401 – COMPLETE EXAM WITH QUESTIONS AND
ANSWERS #24
A __________ mutation will not lead to a change in the protein product of a gene. -
correct answer silent
An antigen binds to an antibody at which of the following locations? - correct answer At
the variable domain
Disulfide bonds in proteins are - correct answer important for proteins found in oxidizing
environments.
Disulfide bonds stabilize __________ level of protein structure and above. - correct
answer tertiary
For Anfinsen's studies of rnasea folding, which of the following is not correct? - correct
answer Removal of β-mercaptoethanol, followed by removal of urea, resulted in active
rnasea.
How many ATP molecules are hydrolyzed during a full cycle of groel-groes-aided
protein folding? - correct answer 14
In an α helix, hydrogen bonding occurs between the carbonyl oxygen of residue n and
the H on the nitrogen of the peptide bond of which residue? - correct answer n + 4
In the figure shown below, C is which of the following classes? - correct answer α/β
In the figure shown below, which of the following is labeled "B"? - correct answer
Antiparallel β strands
Rhodopsin is made up of amphipathic α helices and is embedded in the lipid
membrane. __________ amino acids are likely to be found on the interior-facing helical
surface. - correct answer Hydrophilic
The __________ model is NOT a proposed model for the folding of globular proteins. -
correct answer hydrophilic collapse
The type of reaction that forms a peptide bond is - correct answer condensation.
What is the isoelectric point (pi) of lysine, which has pka values of 2.1 for the α-carboxyl
group, 9.7 for the α-amino group, and 10.5 for the side chain amino group? - correct
answer 10.1
Which of the following fibrous proteins contains 4-hydroxyproline as part of its repeating
pattern? - correct answer Collagen
,Which of the following is NOT accurately classified as a motif? - correct answer FERM
domain fold
Which of the following is categorized as a charged amino acid? - correct answer R
Which of the following is correct about protein folding? - correct answer The amino acid
sequence of a protein leads to a limited number of possible folding pathways.
Which of the following is correct concerning a peptide backbone? - correct answer A
Ramachandran plot shows the allowable φ and ψ angles for a peptide.
Which of the following is most likely to be found on the exterior of a protein? - correct
answer Ser
Which of the following protein-folding diseases is a loss-of-function disease? - correct
answer Cystic fibrosis
Indicate whether the amino acids are hydrophilic or hydrophobic by dragging them into
the appropriate categories. - correct answer Hydrophobic: methionine, isoleucine,
valine, and phenylalaine
Hydrophilic: aspartate, and lysine
What is the approximate molecular weight of a protein composed of 70 amino acids?
_________daltons - correct answer 7700
The titration of a base into a solution of aspartate is shown in the figure. Examine the
figure and answer the following questions.
Part 1: From the introductory figure, what is the approximate pi of aspartate?
Part 2: From the introductory figure, at what ph is the charge on aspartate -1? - correct
answer Part 1: 3.0
Part 2: 6.8
Part 1: The approximate pi for aspartate can be calculated from the arithmetic mean of
pk1 and pk2 because these are the two pka values for the ionizable groups that govern
the formation of the neutral species.[pk1 + pk2]/2 or [2.1 + 3.9]/2 = 3.0
Part 2: The relevant pka values are 3.9 and 9.7. Therefore, the average is 6.8 from [3.9
+ 9.7]/2. This is the ph where the -1 charged state predominates.
Part 1: The side chains of some amino acids are charged at physiologic ph. Place the
amino acids that possess a charge on their side chain at physiologic ph into the bin.
Most answer choices will not be used.
,Part 2: The side chains of some amino acids are aromatic. Place the aromatic amino
acids into the bin. Most answer choices will not be used. - correct answer Part 1:
Charged: Aspartate. Glutamate, histidine, arginine, and lysine
Part 2:
Aromatic: Phenylalaine, tyrosine, and tryptophan
Which form of cysteine is oxidized? - correct answer B
Which amino acid is the smallest and least chemically active? - correct answer glycine
Given the graph above, calculate the absorbance at 280 nm (UV280) of one mole of the
following peptide. Trp-Tyr-Asp-Ala-Trp-Gly-Gly-Lys-Pro
Abs 280 = ________ - correct answer 11000
The 280-nm absorbance total comes from two tryptophans and one tyrosine. From the
figure, the total absorbance is then: 2(5,000) + 1,000 = 11,000 M-1 cm-1. Since the
aromatic amino acids of proteins absorb 280 nm of light, this is a non-invasive method
to determine protein concentration.
What is the amino acid sequence of the pictured tripeptide, in order from N terminus to
C terminus? - correct answer 1: asparagine
2: histidine
3: arginine
The various chemical properties of the amino acid side chains determine the chemical
properties and the three-dimensional structures of proteins. What are the four groups
that amino acids can be divided into? - correct answer charged; aromatic; hydrophilic or
polar uncharged; hydrophobic or aliphatic
Of all the different bond types found in proteins, which has partial double bond
character?
What is a major consequence of the partial double bond character? - correct answer A
peptide bond
Greatly reduced rotational freedom compared to the φ (phi)/ψ (psi) torsion angles
For the following charged amino acids at ph 7, determine whether the net charge on the
amino acid is positive, negative, or neutral. - correct answer Aspartate - negative
Glutamate - negative
Lysine - positive
Arginine - positive
Methionine - neutral
, Due to its partial double bond character, the peptide bond restricts rotation, constraining
atoms to lie within the same peptide plane. Rotation in the peptide backbone is around
the two bonds that flank adjacent ___________ atoms, between which a peptide plane
is formed.
What is the molecular geometry of the constituents of the peptide plane?
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? - correct answer Calpha
The amide nitrogen is trigonal planar and the carbonyl carbon is also trigonal planar.
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.
From the partial nucleotide sequence given below, what peptides could be encoded?
5'-GCCUCCAAACCCCUCCA-3' - correct answer A.Leu-Gln-Thr-Pro-Pro
B.Pro-Pro-Asn-Pro-Ser
C.Ala-Ser-Lys-Pro-Leu
Indicate where the protein secondary structures are found on the Ramachandran plot by
dragging each letter to the correct circle in the plot.
From the plot of torsion angles shown, is this protein mostly composed of α helices or β
sheets? - correct answer See Word Doc.
Α helices
What level of protein structure describes the spatial location of every atom in a protein?
Which one of the following images represents tertiary structure? Indicate which one by
dragging it into the bin labeled Tertiary Structure. - correct answer 3°
See Word Doc.
What is the quaternary structure of a hexamer made of three different homodimers?
Another hexamer is composed of two homotrimers. Using the same letter/number
designation as before, indicate its quaternary structure. - correct answer A2B2C2
A3B3
Which secondary structure elements are stabilized by hydrogen bonds?
ANSWERS #24
A __________ mutation will not lead to a change in the protein product of a gene. -
correct answer silent
An antigen binds to an antibody at which of the following locations? - correct answer At
the variable domain
Disulfide bonds in proteins are - correct answer important for proteins found in oxidizing
environments.
Disulfide bonds stabilize __________ level of protein structure and above. - correct
answer tertiary
For Anfinsen's studies of rnasea folding, which of the following is not correct? - correct
answer Removal of β-mercaptoethanol, followed by removal of urea, resulted in active
rnasea.
How many ATP molecules are hydrolyzed during a full cycle of groel-groes-aided
protein folding? - correct answer 14
In an α helix, hydrogen bonding occurs between the carbonyl oxygen of residue n and
the H on the nitrogen of the peptide bond of which residue? - correct answer n + 4
In the figure shown below, C is which of the following classes? - correct answer α/β
In the figure shown below, which of the following is labeled "B"? - correct answer
Antiparallel β strands
Rhodopsin is made up of amphipathic α helices and is embedded in the lipid
membrane. __________ amino acids are likely to be found on the interior-facing helical
surface. - correct answer Hydrophilic
The __________ model is NOT a proposed model for the folding of globular proteins. -
correct answer hydrophilic collapse
The type of reaction that forms a peptide bond is - correct answer condensation.
What is the isoelectric point (pi) of lysine, which has pka values of 2.1 for the α-carboxyl
group, 9.7 for the α-amino group, and 10.5 for the side chain amino group? - correct
answer 10.1
Which of the following fibrous proteins contains 4-hydroxyproline as part of its repeating
pattern? - correct answer Collagen
,Which of the following is NOT accurately classified as a motif? - correct answer FERM
domain fold
Which of the following is categorized as a charged amino acid? - correct answer R
Which of the following is correct about protein folding? - correct answer The amino acid
sequence of a protein leads to a limited number of possible folding pathways.
Which of the following is correct concerning a peptide backbone? - correct answer A
Ramachandran plot shows the allowable φ and ψ angles for a peptide.
Which of the following is most likely to be found on the exterior of a protein? - correct
answer Ser
Which of the following protein-folding diseases is a loss-of-function disease? - correct
answer Cystic fibrosis
Indicate whether the amino acids are hydrophilic or hydrophobic by dragging them into
the appropriate categories. - correct answer Hydrophobic: methionine, isoleucine,
valine, and phenylalaine
Hydrophilic: aspartate, and lysine
What is the approximate molecular weight of a protein composed of 70 amino acids?
_________daltons - correct answer 7700
The titration of a base into a solution of aspartate is shown in the figure. Examine the
figure and answer the following questions.
Part 1: From the introductory figure, what is the approximate pi of aspartate?
Part 2: From the introductory figure, at what ph is the charge on aspartate -1? - correct
answer Part 1: 3.0
Part 2: 6.8
Part 1: The approximate pi for aspartate can be calculated from the arithmetic mean of
pk1 and pk2 because these are the two pka values for the ionizable groups that govern
the formation of the neutral species.[pk1 + pk2]/2 or [2.1 + 3.9]/2 = 3.0
Part 2: The relevant pka values are 3.9 and 9.7. Therefore, the average is 6.8 from [3.9
+ 9.7]/2. This is the ph where the -1 charged state predominates.
Part 1: The side chains of some amino acids are charged at physiologic ph. Place the
amino acids that possess a charge on their side chain at physiologic ph into the bin.
Most answer choices will not be used.
,Part 2: The side chains of some amino acids are aromatic. Place the aromatic amino
acids into the bin. Most answer choices will not be used. - correct answer Part 1:
Charged: Aspartate. Glutamate, histidine, arginine, and lysine
Part 2:
Aromatic: Phenylalaine, tyrosine, and tryptophan
Which form of cysteine is oxidized? - correct answer B
Which amino acid is the smallest and least chemically active? - correct answer glycine
Given the graph above, calculate the absorbance at 280 nm (UV280) of one mole of the
following peptide. Trp-Tyr-Asp-Ala-Trp-Gly-Gly-Lys-Pro
Abs 280 = ________ - correct answer 11000
The 280-nm absorbance total comes from two tryptophans and one tyrosine. From the
figure, the total absorbance is then: 2(5,000) + 1,000 = 11,000 M-1 cm-1. Since the
aromatic amino acids of proteins absorb 280 nm of light, this is a non-invasive method
to determine protein concentration.
What is the amino acid sequence of the pictured tripeptide, in order from N terminus to
C terminus? - correct answer 1: asparagine
2: histidine
3: arginine
The various chemical properties of the amino acid side chains determine the chemical
properties and the three-dimensional structures of proteins. What are the four groups
that amino acids can be divided into? - correct answer charged; aromatic; hydrophilic or
polar uncharged; hydrophobic or aliphatic
Of all the different bond types found in proteins, which has partial double bond
character?
What is a major consequence of the partial double bond character? - correct answer A
peptide bond
Greatly reduced rotational freedom compared to the φ (phi)/ψ (psi) torsion angles
For the following charged amino acids at ph 7, determine whether the net charge on the
amino acid is positive, negative, or neutral. - correct answer Aspartate - negative
Glutamate - negative
Lysine - positive
Arginine - positive
Methionine - neutral
, Due to its partial double bond character, the peptide bond restricts rotation, constraining
atoms to lie within the same peptide plane. Rotation in the peptide backbone is around
the two bonds that flank adjacent ___________ atoms, between which a peptide plane
is formed.
What is the molecular geometry of the constituents of the peptide plane?
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? - correct answer Calpha
The amide nitrogen is trigonal planar and the carbonyl carbon is also trigonal planar.
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.
From the partial nucleotide sequence given below, what peptides could be encoded?
5'-GCCUCCAAACCCCUCCA-3' - correct answer A.Leu-Gln-Thr-Pro-Pro
B.Pro-Pro-Asn-Pro-Ser
C.Ala-Ser-Lys-Pro-Leu
Indicate where the protein secondary structures are found on the Ramachandran plot by
dragging each letter to the correct circle in the plot.
From the plot of torsion angles shown, is this protein mostly composed of α helices or β
sheets? - correct answer See Word Doc.
Α helices
What level of protein structure describes the spatial location of every atom in a protein?
Which one of the following images represents tertiary structure? Indicate which one by
dragging it into the bin labeled Tertiary Structure. - correct answer 3°
See Word Doc.
What is the quaternary structure of a hexamer made of three different homodimers?
Another hexamer is composed of two homotrimers. Using the same letter/number
designation as before, indicate its quaternary structure. - correct answer A2B2C2
A3B3
Which secondary structure elements are stabilized by hydrogen bonds?
