Ch04 - The Three-Dimensional Structure of Proteins Flashcards
Cys-Ala-Gly-Arg-Gln-Met
The amino terminal amino acid is:
a. Arg
b. Cys
c. Gln
d. Met
e. None of these
b. Cys
Cys-Ala-Gly-Arg-Gln-Met
The carboxyl terminal end is:
a. Arg
b. Cys
c. Gln
d. Met
e. None of these
d. Met
Cys-Ala-Gly-Arg-Gln-Met
The overall, net ionic charge on this peptide at pH = 7 would be:
a. +2
b. +1
c. 0
d. −1
e. −2
b. +1
The sequence of monomers in any polymer is this type of structure:
a. primary structure
b. secondary structure
c. tertiary structure
d. quaternary structure
e. All of these
a. primary structure
Hydrogen bonds are most important in this type of structure in proteins:
a. primary structure
b. secondary structure
c. tertiary structure
d. quaternary structure
e. All of these
b. secondary structure
The overall folding of a single protein subunit is called:
a. primary structure
b. secondary structure
c. tertiary structure
d. quaternary structure
c. tertiary structure
The location of prosthetic groups is shown in this level of structure:
a. primary structure
b. secondary structure
c. tertiary structure
d. quaternary structure
e. All of these
c. tertiary structure
Structures which repeat over and over in secondary structure are called:
a. primary structure
b. domain
c. supersecondary structure
d. prosthetic group
e. All of these
c. supersecondary structure
Covalent bonds are important in all these structures, except:
a. primary structure
b. secondary structure
c. tertiary structure
d. quaternary structure
e. All of these
d. quaternary structure
Disulfide bonds are most important in this type of structure:
a. primary structure
b. secondary structure
c. tertiary structure
d. quaternary structure
e. All of these
c. tertiary structure
Which of the following forces are involved in maintaining the primary structure of a protein?
a. covalent bonds
b. hydrogen bonds
c. ionic interactions
d. hydrophobic interactions
a. covalent bonds
Which of the following amino acid substitutions would be least likely to have a deleterious effect on protein function?
a. His changes to Asp
b. Leu changes to Ile
c. Glu changes to Gln
d. Trp changes to Gly
b. Leu changes to Ile
A single amino substitution can give rise to a malfunctioning protein.
a. True
b. False
a. True
Assuming the oligopeptide ALPHAHELICKS forms one continuous α-helix, the carbonyl oxygen of the glutamic acid residue is hydrogen bonded to the amide nitrogen of
a. leucine.
b. isoleucine.
c. cysteine.
d. lysine.
e. serine
c. cysteine.
What happens when a protein is denatured?
a. Its secondary structure is disrupted but its primary structure remains intact.
b. Its primary structure is disrupted but its secondary structure remains intact.
c. It is broken apart into its constituent amino acids.
d. It becomes all α-helix
a. Its secondary structure is disrupted but its primary structure remains intact.
Which of the following best defines a domain?
a. A supersecondary region, often shared by proteins, that has a specific function.
b. A repetitive supersecondary structure.
c. A double-layered arrangement formed so that the polar groups face the aqueous environment, while the
nonpolar regions are kept away from the aqueous environment.
d. An unfolded region of a protein.
a. A supersecondary region, often shared by proteins, that has a specific function.
Which of the following amino acids is unlikely to be found in an α-helix?
a. phenylalanine
b. tryptophan
c. proline
d. lysine
c. proline
Which of the following statements regarding hydrogen bonding in secondary structures is true?
a. Both α-helices and β-sheets only use intrachain hydrogen bonds.
b. Both α-helices and β-sheets only use interchain hydrogen bonds.
c. α-helices only use intrachain hydrogen bonds and β-sheets can use either intrachain or interchain hydrogen bonds.
d. α-helices can use either intrachain or interchain hydrogen bonds and β-sheets only use interchain hydrogen bonds.
c. α-helices only use intrachain hydrogen bonds and β-sheets can use either intrachain or interchain hydrogen bonds.
Which of the following factors tend to destabilize α-helices?
a. clusters of amino acids with bulky R-groups
b. clusters of amino acids with similarly charged R-groups
c. Both of these.
d. Neither of these
c. Both of these.
Which of the following best describes the structure of collagen?
a. It is composed of a single α-helix.
b. It is a double helix.
c. It is a triple helix
d. It is composed primarily of β-sheet.
c. It is a triple helix
Which of the following is true?
a. The peptide bonds in the β-sheet are extended.
b. The peptide bonds in the α-helix coil back on themselves.
c. Both α-helices and β-sheets can be found as part of tertiary structure.
d. All of these
d. All of these
Which of the following is often found connecting the strands of an antiparallel β-sheet?
a. β-bulge
b. reverse turn
c. α-helix
d. prosthetic group
b. reverse turn
Which of the following best describes a motif?
a. a repetitive supersecondary structure
b. a common nonrepetitive irregularity found in antiparallel β-sheets
c. a protein conformation with biological activity
d. a group of atoms other than an amino acid
a. a repetitive supersecondary structure
In the β-pleated sheet conformation
a. there are hydrogen bonds perpendicular to the direction of the polypeptide chain.
b. the polypeptide chain is almost fully extended.
c. the polypeptide chains may be hydrogen bonded together in a parallel or antiparallel orientation.
d. all of these
d. all of these
Which of the following is the most common function for fibrous proteins?
a. enzymes
b. structural roles.
c. carrier molecules.
d. enzymes and carrier molecules.
e. All of these.
b. structural roles.
In the α-helix
a. there are no hydrogen bonds
b. the peptide chain is fully extended
c. the peptide chain bends back on itself
d. there are hydrogen bonds parallel to the helix axis
d. there are hydrogen bonds parallel to the helix axis
Which one is not an example of supersecondary structure?
a. the pyrrole ring
b. the Greek key
c. the β-meander
d. the β-barrel
a. the pyrrole ring
Which of the following is true?
a. The collagen helix and the α-helix are the only types of helices in proteins.
b. Globular proteins tend to be water soluble
c. Globular and fibrous are examples of secondary structure
d. All of these
b. Globular proteins tend to be water soluble
As an animal ages, the amount of cross-linking of collagen in tissue
a. tends to decrease.
b. tends to increase.
c. tends to remain unchanged.
b. tends to increase.
Vitamin C (ascorbic acid) prevents scurvy because
a. it is involved in the formation of the proper β-sheet structure of collagen.
b. it is involved in the metabolism of heme used in hemoglobin.
c. it encourages the formation of disulfide linkages in collagen.
d. it is an unusual amino acid found in the primary structure of collagen.
e. it is used to hydroxylate prolines in the primary structure of collagen.
e. it is used to hydroxylate prolines in the primary structure of collagen.
The following is true about the hydroxyproline in collagen:
a. Hydroxyproline is incorporated into the chain during polymerization of amino acids.
b. Vitamin C is necessary for the synthesis of hydroxyproline.
c. Hydroxyproline is important in holding the 3 strands of collagen together.
d. Hydroxyproline requires Vitamin C for its synthesis and it holds the collagen helix together.
e. All of these.
d. Hydroxyproline requires Vitamin C for its synthesis and it holds the collagen helix together.
Which of the following is true about the alpha helix?
a. the structure is stablized by hydrogen bonds
b. there are 3.6 residues for every turn of the helix
c. the pitch of the helix is 5.4 angsroms
d. all of the choices
d. all of the choices
Fibrous proteins
a. are always composed of helical structures.
b. are always composed of β-sheets.
c. can be composed of either helical or β-sheet structures.
d. are always water solubl
c. can be composed of either helical or β-sheet structures.
Generally speaking, this type of protein is water-soluble:
a. Fibrous.
b. Globular.
c. Both fibrous and globular proteins are usually water-soluble.
d. Neither fibrous nor globular proteins are usually water-soluble.
e. You cannot generalize about the solubility of fibrous or globular proteins.
b. Globular.
Domains are
a. independently folded regions of proteins
b. the α-helical portions of proteins
c. the β-pleated regions of proteins
d. all of the above
a. independently folded regions of proteins
Two amino acids frequently found in reverse turns are
a. tyrosine and tryptophan
b. serine and threonine
c. glycine and proline
d. leucine and isoleucine
c. glycine and proline
Which of the following amino acid residues would most likely be found in the interior of a globular protein?
a. glutamic acid
b. lysine
c. leucine
d. serine
c. leucine
The protein myoglobin
a. contains a high degree of β-pleated sheet structure
b. carries oxygen in the bloodstream
c. contains no histidine
d. contains a heme group
d. contains a heme group
Disulfide bonds in proteins occur between the side chains of which of the following amino acid residues?
a. glutamine
b. lysine
c. cysteine
d. methionine
c. cysteine
Refer to Exhibit 4B. The type of bonding labeled “L” in these figure is:
a. Hydrogen bonding of the peptide backbone
b. Hydrogen bonding involving the R-groups
c. Hydrophobic interactions
d. Metal ion coordination
e. Electrostatic attraction (salt bridge)
e. Electrostatic attraction (salt bridge)
Refer to Exhibit 4B. The type of bonding labeled “O” in these figure is:
a. Hydrogen bonding of the peptide backbone
b. Covalent bonding involving the R-groups
c. Hydrophobic interactions
d. Metal ion coordination
e. Electrostatic attraction
b. Covalent bonding involving the R-groups
Refer to Exhibit 4B. The type of bonding labeled “N” in these figure is:
a. Hydrogen bonding of the peptide backbone
b. Covalent bonding involving the R-groups
c. Hydrophobic interactions
d. Metal ion coordination
e. Electrostatic attraction
a. Hydrogen bonding of the peptide backbone
Refer to Exhibit 4B. Which one shows hydrogen bonding of R-groups?
a. M
b. N
c. P
d. M and N
e. All of these
c. P
Refer to Exhibit 4B. Which one shows hydrogen bonding of the peptide backbone?
a. M
b. N
c. P
d. M and N
e. All of these
d. M and N
Refer to Exhibit 4B. Which one shows covalent bonding of R-groups?
a. K
b. L
c. O
d. K and L
e. All of these
c. O
Refer to Exhibit 4B. Which one shows electrostatic attraction of R-groups?
a. K
b. L
c. O
d. K and L
e. All of these
b. L
X-ray crystallography is used to determine protein structure because
a. it can be done on dilute solutions
b. it requires no calculations
c. the positions of all atoms can be found by this method
d. all of these
c. the positions of all atoms can be found by this method
The structure of myoglobin consists
a. almost entirely of α-helices.
b. almost entirely of β-sheets.
c. of a mixture of α-helices and β-sheets.
d. of a unique secondary motif that is neither α-helix nor β-sheet
a. almost entirely of α-helices.
The tertiary structure of a protein is usually a result of which of the following interactions?
a. intramolecular hydrogen bonding
b. electrostatic interactions
c. hydrophobic interactions
d. all of these
d. all of these
Heme would best be described as a
a. motif.
b. domain.
c. prosthetic group.
d. helix.
c. prosthetic group.
Why does myoglobin have a histidine that prevents both O2 and CO from binding perpendicularly to the heme plane?
a. This increases myoglobin’s affinity for O2.
b. This increases myoglobin’s affinity for CO.
c. This lessens the difference in myoglobin’s affinity for CO versus O2.
d. This prevents the iron of the heme from being oxidized.
c. This lessens the difference in myoglobin’s affinity for CO versus O2.
In what oxidation state must the iron atom be for heme to bind oxygen?
a. 0, Fe(0)
b. 1+, Fe(I)
c. 2+, Fe(II)
d. 3+, Fe(III)
e. There is no required oxidation state for the iron.
c. 2+, Fe(II)
Which of the following is not true?
a. The heme group of myoglobin is held in place only through non-covalent bonding.
b. The F8 histidine is important to the function of myoglobin
c. The E7 histidine is important to the function of myoglobin
d. Myoglobin and hemoglobin differ only in one amino acid
d. Myoglobin and hemoglobin differ only in one amino acid
Which of the following can result in protein denaturation?
a. heat
b. extremes of pH
c. detergents
d. all of the above
d. all of the above
The following bond forces are important in tertiary structure:
a. Disulfide bonds
b. Hydrogen bonds
c. Hydrophobic attraction
d. Both hydrogen bonds and hydrophobic attraction.
e. All of these are important in tertiary structure
e. All of these are important in tertiary structure
Quaternary structure is associated with
a. the overall shape of the polypeptide chain
b. the sum of secondary and tertiary interactions
c. simple proteins with only one subunit
d. the relative orientation of one polypeptide to another polypeptide in a multisubunit protein
d. the relative orientation of one polypeptide to another polypeptide in a multisubunit protein
Which of the following forces are involved in maintaining the quaternary structure of a protein?
a. hydrogen bonds
b. ionic interactions
c. hydrophobic interactions
d. All of these
d. All of these
The following bond forces are important in quaternary structure:
a. Disulfide bonds
b. Hydrogen bonds
c. Hydrophobic attraction
d. Both hydrogen bonds and hydrophobic attraction.
e. All of these are important in quaternary structure.
d. Both hydrogen bonds and hydrophobic attraction.
Under normal circumstances:
a. Adult Hb binds to oxygen more tightly than Mb binds.
b. Fetal Hb binds oxygen more tightly than adult Hb.
c. Adult Hb binds oxygen more tightly than either fetal Hb or Mb binds.
d. Mb has the lowest affinity for oxygen of the 3.
e. More than one of these statements is correct.
b. Fetal Hb binds oxygen more tightly than adult Hb.
Which of the following statements regarding hemoglobin (Hb) and myoglobin (Mb) is true?
a. Mb transports oxygen while Hb stores it.
b. Mb has quaternary structure but Hb does not.
c. Mb displays simple kinetics of binding while Hb displays cooperativity.
d. Mb binds Fe(II) while Hb binds heme.
c. Mb displays simple kinetics of binding while Hb displays cooperativity.
Which of the following is not a characteristic of hemoglobin?
a. It contains two different types of subunits .
b. It contains a prosthetic group.
c. It is an allosteric enzyme.
d. It transports oxygen.
e. All of these statements are true for Hb.
c. It is an allosteric enzyme.
The Bohr effect for oxygen binding states that
a. Mb binds oxygen more tightly than Hb.
b. Hb will bind oxygen very tightly when the CO2 concentration is high.
c. as the pH goes down, Hb binds oxygen less tightly.
d. Hb’s ability to bind oxygen increases with higher oxygen concentration.
c. as the pH goes down, Hb binds oxygen less tightly.
In allosteric interactions
a. proteins that consist of a single polypeptide chain form aggregates.
b. disulfide bonds are broken.
c. changes that take place in one site of a protein cause changes at a distant site.
d. metal ions always bind to the protein
c. changes that take place in one site of a protein cause changes at a distant site.
Hemoglobin differs from myoglobin because
a. it does not have a heme group.
b. it is a tetramer, whereas myoglobin is a single polypeptide chain.
c. it does not contain any helical regions.
d. it contains more β-pleated sheet structure.
b. it is a tetramer, whereas myoglobin is a single polypeptide chain.
Which of the following best describes what happens when hemoglobin binds bisphosphoglyceric acid (BPG)?
a. Binding of BPG leads to tighter binding of oxygen.
b. Binding of BPG allows maternal (adult) Hb to bind oxygen more tightly than fetal Hb.
c. Binding of BPG is important to the allosteric nature of hemoglobin
d. Binding of BPG causes the subunits of hemoglobin to separate.
c. Binding of BPG is important to the allosteric nature of hemoglobin
The binding of oxygen to hemoglobin differs from the oxygen-binding behavior of myoglobin because
a. oxygen binding to hemoglobin is cooperative.
b. oxygen binding to myoglobin is cooperative.
c. hemoglobin is not an allosteric protein.
d. the oxygen-binding curve of hemoglobin is hyperbolic.
a. oxygen binding to hemoglobin is cooperative.
In the Bohr effect the binding of oxygen to hemoglobin
a. is increased by the presence of Na+
b. is increased by the presence of H+ and CO2
c. is decreased by the presence of H+ and CO2
d. is unchanged
c. is decreased by the presence of H+ and CO2
The affinity of fetal hemoglobin for oxygen
a. has not been studied
b. is the same as that of adult hemoglobin
c. is lower than that of maternal hemoglobin
d. is higher than that of maternal hemoglobin
d. is higher than that of maternal hemoglobin
Variations in the structure of hemoglobin
a. do not always have an adverse effect on health
b. can alter the binding of heme to the protein
c. can occur on the surface of the protein
d. all of these
d. all of these
Which of the following is true about sickle cell hemoglobin?
a. it has a single amino acid substitution in the beta chain
b. it causes a disease that is always fatal
c. it is found as a monomer instead of a tetramer in red blood cells
d. it has a leucine at a position where normal hemoglobin has an isoleucine
e. none of the choices
a. it has a single amino acid substitution in the beta chain
What would happen to hemoglobin if the BPG were removed?
a. It would not bind oxygen
b. It would dissociate into monomers
c. its oxygen binding curve would resemble that of myoglobin
d. all of the choices
c. its oxygen binding curve would resemble that of myoglobin
The oxygen binding curve of which of the following is the closest to that of myoglobin?
a. hemoglobin at pH 6.8
b. hemoglobin that lacks BPG
c. maternal hemoglobin
d. fetal hemoglobin
b. hemoglobin that lacks BPG
Adult hemoglobin is half saturated with oxygen at what partial pressure of oxygen?
a. 5 torr
b. 10 torr
c. 25 torr
d. 50 torr
e. 100 torr
c. 25 torr
In sickle-cell anemia hemoglobin
a. the four subunits of hemoglobin dissociate from one another
b. the heme group is lost from all subunits
c. the iron is in the Fe(III) form rather than the normal Fe(II)
d. groups of hemoglobin molecules aggregate with each other
d. groups of hemoglobin molecules aggregate with each other
Hydroxyurea works as a treatment for sickle cell anemia because it
a. causes myoglobin to act like hemoglobin
b. causes the body to produce fetal hemoglobin
c. causes hemoglobin to dissociate into monomers, thereby quadrupline the effective concentration of oxygen
carrying molecules
d. none of the choices
b. causes the body to produce fetal hemoglobin
Which of the following proteins is not homologous with the others?
a. myoglogin
b. α-chain of hemoglobin
c. β-chain of hemoglobin
d. collagen
d. collagen
What is the major force that drives nonpolar substances out of aqueous solution?
a. Increased enthalpy of hydrophobic bonds formed between solute molecules.
b. Decreased entropy of newly organized solute molecules.
c. Increased entropy of newly organized solute molecules.
d. Increased enthalpy of H-bonds in the solvent water.
e. Increased entropy of solvent water molecules.
e. Increased entropy of solvent water molecules.
Hydrophobic interactions may occur between the R groups of which of the following amino acids?
a. tyrosine and glycine
b. arginine and histidine
c. phenylalanine and tryptophan
d. valine and asparagine
c. phenylalanine and tryptophan
The information needed for the structure of a protein is contained in
a. amino acid composition
b. primary structure
c. secondary structure
d. tertiary structure
b. primary structure
Incorrect protein folding resulting in exposure of hydrophobic regions can result in
a. aggregation.
b. homology.
c. liposomes.
d. the Bohr effect
a. aggregation.
Proteins that aid in the correct and timely folding of other proteins are called
a. motifs.
b. chaperones.
c. liposomes.
d. cooperative.
b. chaperones.
Which of the following diseases is based on abnormal protein folding?
a. Alzheimers disease
b. Mad Cow Disease
c. Prion diseases
d. Frontotemporal dementia
e. All of the choices
e. All of the choices
The three-dimensional shapes of proteins with biological activities are called _____.
a. prosthetic groups
b. subunits
c. native conformations
d. domain
c. native conformations
Identify the portion of proteins that does not consist of amino acids.
a. Subunit
b. Prosthetic group
c. Domain
d. Motif
b. Prosthetic group
The order in which the amino acids in a protein are linked by peptide bonds
a. Primary structure
b. Secondary structure
c. Domains
d. Tertiary structure
e. Quaternary structure
a. Primary structure
The arrangement of space of the backbone atoms in a polypeptide chain
a. Primary structure
b. Secondary structure
c. Domains
d. Tertiary structure
e. Quaternary structure
b. Secondary structure
Specific clusters of secondary structural motifs in proteins
a. Primary structure
b. Secondary structure
c. Domains
d. Tertiary structure
e. Quaternary structure
c. Domains
The arrangement in space of all the atoms in a protein
a. Primary structure
b. Secondary structure
c. Domains
d. Tertiary structure
e. Quaternary structure
d. Tertiary structure
The interaction of several polypeptide chains in a multisubunit protein
a. Primary structure
b. Secondary structure
c. Domains
d. Tertiary structure
e. Quaternary structure
e. Quaternary structure
_____ are natural glycoproteins found in the cell membranes of nerve tissues and are known to cause spongiform
encephalopathy in humans
a. Viroids
b. Actin-binding proteins
c. Alpha-fetoproteins
d. Prions
d. Prions
_____ are spherical aggregates of lipids arranged so that the polar head groups are in contact with water and the nonpolar tails are sequestered from water.
a. Liposomes
b. Azotosomes
c. Escheriosomes
d. Chromosomes
a. Liposomes
