Ch04 - The Three-Dimensional Structure of Proteins

Question 1

Cys-Ala-Gly-Arg-Gln-Met

The amino terminal amino acid is:
a. Arg
b. Cys
c. Gln
d. Met
e. None of these

Answer 1

b. Cys

Question 2

Cys-Ala-Gly-Arg-Gln-Met

The carboxyl terminal end is:
a. Arg
b. Cys
c. Gln
d. Met
e. None of these

Answer 2

d. Met

Question 3

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

Answer 3

b. +1

Question 4

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

Answer 4

a. primary structure

Question 5

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

Answer 5

b. secondary structure

Question 6

The overall folding of a single protein subunit is called:

a. primary structure
b. secondary structure
c. tertiary structure
d. quaternary structure

Answer 6

c. tertiary structure

Question 7

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

Answer 7

c. tertiary structure

Question 8

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

Answer 8

c. supersecondary structure

Question 9

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

Answer 9

d. quaternary structure

Question 10

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

Answer 10

c. tertiary structure

Question 11

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

Answer 11

a. covalent bonds

Question 12

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

Answer 12

b. Leu changes to Ile

Question 13

A single amino substitution can give rise to a malfunctioning protein.

a. True
b. False

Answer 13

a. True

Question 14

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

Answer 14

c. cysteine.

Question 15

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

Answer 15

a. Its secondary structure is disrupted but its primary structure remains intact.

Question 16

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.

Answer 16

a. A supersecondary region, often shared by proteins, that has a specific function.

Question 17

Which of the following amino acids is unlikely to be found in an α-helix?

a. phenylalanine
b. tryptophan
c. proline
d. lysine

Answer 17

c. proline

Question 18

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.

Answer 18

c. α-helices only use intrachain hydrogen bonds and β-sheets can use either intrachain or interchain hydrogen bonds.

Question 19

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

Answer 19

c. Both of these.

Question 20

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.

Answer 20

c. It is a triple helix

Question 21

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

Answer 21

d. All of these

Question 22

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

Answer 22

b. reverse turn

Question 23

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

Answer 23

a. a repetitive supersecondary structure

Question 24

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

Answer 24

d. all of these

Question 25

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.

Answer 25

b. structural roles.

Question 26

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

Answer 26

d. there are hydrogen bonds parallel to the helix axis

Question 27

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

Answer 27

a. the pyrrole ring

Question 28

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

Answer 28

b. Globular proteins tend to be water soluble

Question 29

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.

Answer 29

b. tends to increase.

Question 30

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.

Answer 30

e. it is used to hydroxylate prolines in the primary structure of collagen.

Question 31

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.

Answer 31

d. Hydroxyproline requires Vitamin C for its synthesis and it holds the collagen helix together.

Question 32

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

Answer 32

d. all of the choices

Question 33

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

Answer 33

c. can be composed of either helical or β-sheet structures.

Question 34

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.

Answer 34

b. Globular.

Question 35

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

Answer 35

a. independently folded regions of proteins

Question 36

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

Answer 36

c. glycine and proline

Question 37

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

Answer 37

c. leucine

Question 38

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

Answer 38

d. contains a heme group

Question 39

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

Answer 39

c. cysteine

Question 40

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)

Answer 40

e. Electrostatic attraction (salt bridge)

Question 41

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

Answer 41

b. Covalent bonding involving the R-groups

Question 42

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

Answer 42

a. Hydrogen bonding of the peptide backbone

Question 43

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

Answer 43

c. P

Question 44

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

Answer 44

d. M and N

Question 45

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

Answer 45

c. O

Question 46

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

Answer 46

b. L

Question 47

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

Answer 47

c. the positions of all atoms can be found by this method

Question 48

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

Answer 48

a. almost entirely of α-helices.

Question 49

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

Answer 49

d. all of these

Question 50

Heme would best be described as a

a. motif.
b. domain.
c. prosthetic group.
d. helix.

Answer 50

c. prosthetic group.

Question 51

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.

Answer 51

c. This lessens the difference in myoglobin’s affinity for CO versus O2.

Question 52

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.

Answer 52

c. 2+, Fe(II)

Question 53

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

Answer 53

d. Myoglobin and hemoglobin differ only in one amino acid

Question 54

Which of the following can result in protein denaturation?

a. heat
b. extremes of pH
c. detergents
d. all of the above

Answer 54

d. all of the above

Question 55

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

Answer 55

e. All of these are important in tertiary structure

Question 56

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

Answer 56

d. the relative orientation of one polypeptide to another polypeptide in a multisubunit protein

Question 57

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

Answer 57

d. All of these

Question 58

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.

Answer 58

d. Both hydrogen bonds and hydrophobic attraction.

Question 59

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.

Answer 59

b. Fetal Hb binds oxygen more tightly than adult Hb.

Question 60

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.

Answer 60

c. Mb displays simple kinetics of binding while Hb displays cooperativity.

Question 61

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.

Answer 61

c. It is an allosteric enzyme.

Question 62

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.

Answer 62

c. as the pH goes down, Hb binds oxygen less tightly.

Question 63

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

Answer 63

c. changes that take place in one site of a protein cause changes at a distant site.

Question 64

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.

Answer 64

b. it is a tetramer, whereas myoglobin is a single polypeptide chain.

Question 65

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.

Answer 65

c. Binding of BPG is important to the allosteric nature of hemoglobin

Question 66

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.

Answer 66

a. oxygen binding to hemoglobin is cooperative.

Question 67

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

Answer 67

c. is decreased by the presence of H+ and CO2

Question 68

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

Answer 68

d. is higher than that of maternal hemoglobin

Question 69

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

Answer 69

d. all of these

Question 70

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

Answer 70

a. it has a single amino acid substitution in the beta chain

Question 71

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

Answer 71

c. its oxygen binding curve would resemble that of myoglobin

Question 72

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

Answer 72

b. hemoglobin that lacks BPG

Question 73

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

Answer 73

c. 25 torr

Question 74

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

Answer 74

d. groups of hemoglobin molecules aggregate with each other

Question 75

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

Answer 75

b. causes the body to produce fetal hemoglobin

Question 76

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

Answer 76

d. collagen

Question 77

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.

Answer 77

e. Increased entropy of solvent water molecules.

Question 78

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

Answer 78

c. phenylalanine and tryptophan

Question 79

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

Answer 79

b. primary structure

Question 80

Incorrect protein folding resulting in exposure of hydrophobic regions can result in

a. aggregation.
b. homology.
c. liposomes.
d. the Bohr effect

Answer 80

a. aggregation.

Question 81

Proteins that aid in the correct and timely folding of other proteins are called

a. motifs.
b. chaperones.
c. liposomes.
d. cooperative.

Answer 81

b. chaperones.

Question 82

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

Answer 82

e. All of the choices

Question 83

The three-dimensional shapes of proteins with biological activities are called _____.

a. prosthetic groups
b. subunits
c. native conformations
d. domain

Answer 83

c. native conformations

Question 84

Identify the portion of proteins that does not consist of amino acids.

a. Subunit
b. Prosthetic group
c. Domain
d. Motif

Answer 84

b. Prosthetic group

Question 85

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

Answer 85

a. Primary structure

Question 86

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

Answer 86

b. Secondary structure

Question 87

Specific clusters of secondary structural motifs in proteins

a. Primary structure
b. Secondary structure
c. Domains
d. Tertiary structure
e. Quaternary structure

Answer 87

c. Domains

Question 88

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

Answer 88

d. Tertiary structure

Question 89

The interaction of several polypeptide chains in a multisubunit protein

a. Primary structure
b. Secondary structure
c. Domains
d. Tertiary structure
e. Quaternary structure

Answer 89

e. Quaternary structure

Question 90

_____ 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

Answer 90

d. Prions

Question 91

_____ 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

Answer 91

a. Liposomes