Deck 5: Protein Function

Question 1

A monoclonal antibody differs from a polyclonal antibody in that monoclonal antibodies:

A) are labeled with chemicals that can be visualized.
B) are produced by cells from the same organism that produced the antigen.
C) are synthesized by a population of identical, or "cloned," cells.
D) are synthesized only in living organisms.
E) have only a single polypeptide chain that can recognize an antigen.

Answer 1

C

Question 2

A prosthetic group of a protein is a nonprotein structure that is:

A) a ligand of the protein.
B) a part of the secondary structure of the protein.
C) a substrate of the protein.
D) permanently associated with the protein.
E) transiently bound to the protein.

Answer 2

D

Question 3

When oxygen binds to a heme-containing protein, the two open coordination bonds of Fe²⁺ are occupied by:

A) one O atom and one amino acid atom.
B) one O₂ molecule and one amino acid atom.
C) one O₂ molecule and one heme atom.
D) two O atoms.
E) two O₂ molecules.

Answer 3

B

Question 4

In hemoglobin, the transition from T state to R state (low to high affinity) is triggered by:

A) Fe²⁺ binding.
B) heme binding.
C) oxygen binding.
D) subunit association.
E) subunit dissociation.

Question 5

The predominant structural feature in myosin molecules is:

A) a $\beta$ structure.
B) an $\alpha$ helix.
C) the Fab domain.
D) the light chain.
E) the meromyosin domain.

Question 6

Which statement about protein-ligand binding is CORRECT?

A) The K_a is equal to the concentration of ligand when all of the binding sites are occupied.
B) The K_a is independent of such conditions as salt concentration and pH.
C) The larger the K_a (association constant), the weaker the affinity.
D) The larger the K_a, the faster is the binding.
E) The larger the K_a, the smaller the K_d (dissociation constant).

Question 7

Which generalization concerning motor proteins is CORRECT?

A) They convert chemical energy into kinetic energy.
B) They convert chemical energy into potential energy.
C) They convert kinetic energy into chemical energy.
D) They convert kinetic energy into rotational energy.
E) They convert potential energy into chemical energy.

Question 8

Which part of the IgG molecule is NOT involved in binding to an antigen?

A) Fab
B) Fc
C) heavy chain
D) light chain
E) variable domain

Question 9

Patients with chronic hypoxia (low O₂ levels) due to decreased lung function may adapt by increasing their circulating BPG levels. Predict which outcome will be TRUE for such a patient.

A) p₅₀ for O₂ will be decreased.
B) p₅₀ for O₂ will be increased.
C) The R-state of hemoglobin will be favored.
D) O₂ binding to hemoglobin will be hyperbolic.
E) None of the answers is correct.

Question 10

Myoglobin and the subunits of hemoglobin have:

A) no obvious structural relationship.
B) very different primary and tertiary structures.
C) very similar primary and tertiary structures.
D) very similar primary structures, but different tertiary structures.
E) very similar tertiary structures, but different primary structures.

Question 11

The interactions of ligands with proteins:

A) are relatively nonspecific.
B) are relatively rare in biological systems.
C) are usually irreversible.
D) are usually transient.
E) usually result in the inactivation of the proteins.

Question 12

The fundamental cause of sickle-cell disease is a change in the structure of:

A) blood.
B) capillaries.
C) hemoglobin.
D) red cells.
E) the heart.

Question 13

Which statement is NOT correct concerning cooperative binding of a ligand to a protein?

A) It is usually a form of allosteric interaction.
B) It is usually associated with proteins with multiple subunits.
C) It rarely occurs in enzymes.
D) It results in a nonlinear Hill Plot.
E) It results in a sigmoidal binding curve.

Question 14

Neuroglobin is a member of the globin family found in neurons. It is a monomeric protein that helps protect the brain from hypoxia (low O₂). Identify the CORRECT statement(s) about neuroglobin below.

A) a and c
B) a and d
C) b and c
D) b and d
E) None of the statements is correct.

Question 15

In the binding of oxygen to myoglobin, the relationship between the concentration of oxygen and the fraction of binding sites occupied can best be described as:

A) hyperbolic.
B) linear with a negative slope.
C) linear with a positive slope.
D) random.
E) sigmoidal.

Question 16

An allosteric interaction between a ligand and a protein is one in which:

A) binding of a molecule to a binding site affects binding of additional molecules to the same site.
B) binding of a molecule to a binding site affects binding properties of another site on the protein.
C) binding of the ligand to the protein is covalent.
D) multiple molecules of the same ligand can bind to the same binding site.
E) two different ligands can bind to the same binding site.

Question 17

An individual molecular structure within an antigen to which an individual antibody binds is as a(n):

A) antigen.
B) epitope.
C) Fab region.
D) Fc region
E) MHC site.

Question 18

Which statement is NOT correct concerning 2,3-bisphosphoglycerate (BPG)?

A) It binds at a distance from the heme groups of hemoglobin.
B) It binds with lower affinity to fetal hemoglobin than to adult hemoglobin.
C) It increases the affinity of hemoglobin for oxygen.
D) It is an allosteric modulator.
E) It is normally found associated with the hemoglobin extracted from red blood cells.

Question 19

Carbon monoxide (CO) is toxic to humans because it:

A) binds to myoglobin and causes it to denature.
B) is rapidly converted to toxic CO₂.
C) binds to the globin portion of hemoglobin and prevents the binding of O₂.
D) binds to the Fe in hemoglobin and prevents the binding of O₂.
E) binds to the heme portion of hemoglobin and causes heme to unbind from hemoglobin.

Question 20

The amino acid substitution of Val for Glu in Hemoglobin S results in aggregation of the protein because of _____ interactions between molecules.

A) covalent
B) disulfide
C) hydrogen bonding
D) hydrophobic
E) ionic

Question 21

Which statement comparing hemoglobin and myoglobin is NOT correct?

A) Hemoglobin binds to O₂ cooperatively, while myoglobin does not.
B) Hemoglobin is a multisubunit protein, while myoglobin is not.
C) Hemoglobin and myoglobin are both primarily composed of $\alpha$ helices.
D) Hemoglobin has a stronger binding affinity for O₂ than myoglobin does.
E) Hemoglobin and myoglobin both contain the heme prosthetic group.

Question 22

The binding of oxygen to hemoglobin stabilizes the _____ of the protein due to interactions between _____ residues in the center of the multisubunit complex.

A) R state; Thr
B) R state; Glu
C) R state; His
D) T state; Glu
E) T state; His

Question 23

During muscle contraction, hydrolysis of ATP results in a change in the:

A) conformation of actin.
B) conformation of myosin.
C) structure of the myofibrils.
D) structure of the sarcoplasmic reticulum.
E) structure of the Z disk.

Question 24

The energy that is released by the hydrolysis of ATP by actin is used for:

A) actin filament assembly.
B) actin filament disassembly.
C) actin-myosin assembly.
D) actin-myosin disassembly.
E) muscle contraction.

Question 25

The binding site of a protein is complementary to a specific ligand due to which characteristic of the binding site?

A) its size
B) its shape
C) its charge
D) its hydrophobicity
E) All of the answers are correct.

Question 26

Sickle cell anemia is caused by a single mutation in the hemoglobin protein from a Glu to a Val, which results in which alteration in the hemoglobin subunits?

A) more neutral charges and formation of a nucleophilic contact point
B) fewer negative charges and formation of a hydrophobic contact point
C) fewer positive charges and formation of a hydrophobic contact point
D) more negative charges and formation of a hydrophilic contact point
E) more positive charges and formation of a hydrophilic contact point

Question 27

Conversion of CO₂ in the blood into the more soluble form of HCO₃^- is catalyzed by which enzyme?

A) hemoglobinase
B) carbonic anhydrase
C) bicarbonase
D) carbondioxidease
E) carbon hydratase

Question 28

Hemoglobin is involved in the transport of which ion and/or molecule through the blood?

A) CO₂
B) O₂
C) H⁺
D) both CO₂ and O₂
E) CO₂, O₂, and H⁺

Question 29

Which statement about CO binding to hemoglobin is NOT correct?

A) CO binds to hemoglobin better than O₂ does.
B) CO binding to hemoglobin is reversible.
C) The binding of one CO molecule to hemoglobin makes the binding of other CO molecules more efficient.
D) A histidine residue in hemoglobin reduces the affinity of CO binding to heme.
E) The binding of one CO molecule to hemoglobin makes the binding of O₂ molecules more efficient.

Question 30

You are examining the effects of a mutation in the proximal histidine of a heme-containing protein. This mutation has changed the histidine into an alanine. Based on your knowledge of the role of heme in hemoglobin and how it is coordinated in the protein, what is the MOST likely effect of the mutation?

A) Heme will no longer be bound in the protein.
B) The iron in heme will be fully coordinated.
C) The iron in heme will have two uncoordinated bonds.
D) The heme will be able to bind to O₂ more effectively than it will to CO.
E) There will be no effect on the protein due to this mutation.

Question 31

If a developing fetus made beta hemoglobin subunits instead of gamma hemoglobin subunits, what would be MOST likely to occur?

A) The fetus would extract O₂ from its mother's blood more effectively.
B) The fetal hemoglobin would have a higher affinity for 2,3-bisphosphoglycerate.
C) The fetal hemoglobin would have a lower affinity for CO.
D) The fetus would not be able to extract O₂ from its mother's blood as effectively.
E) The fetus would be less susceptible to sickle cell anemia.

Question 32

CO binds more strongly to the heme iron than O₂ does due to which reason?

A) CO binds to the heme iron perpendicular to the porphyrin ring, allowing maximum electron orbital overlap between CO and Fe²⁺.
B) CO weighs less than O₂, therefore binding to the heme iron more easily.
C) CO binds to the heme iron covalently, while O₂ binds via ionic interactions.
D) All of the answers are correct.
E) None of the answers is correct.

Question 33

Two proteins bind to the same ligand, and protein A has half of its binding sites occupied when the ligand concentration is 0.5 mM, while protein B has half of its binding sites occupied when the ligand concentration is at 0.3 mM. Which protein binds the ligand more strongly, and what is the dissociation constant for that protein-ligand interaction?

A) Protein A binds more strongly, and K_d = 0.3 mM.
B) Protein A binds more strongly, and K_d = 0.5 mM.
C) Protein B binds more strongly, and K_d = 0.3 mM.
D) Protein B binds more strongly, and K_d = 0.5 mM.
E) Both proteins bind the ligand with the same affinity, and K_d = 0.4 mM.

Question 34

Sickle cell anemia is often lethal in childhood, yet the gene for sickle cell hemoglobin persists in the human population. Which statement BEST describes why this is the case?

A) Individuals with sickle cell anemia are healthier than are normal individuals.
B) Individuals with sickle cell trait can carry more oxygen in their blood than do normal individuals.
C) Individuals with normal hemoglobin have malaria infections less often than do individuals with sickle cell trait.
D) Individuals with sickle cell trait are protected from malaria infection, while normal individuals are not.
E) Individuals with sickle cell anemia have more hemoglobin in their blood than do normal individuals.

Question 35

Which molecule binds MOST strongly to the heme iron?

A) N₂
B) O₂
C) CO₂
D) CO
E) H₂O

Question 36

Which amino acid in hemoglobin is involved in coordinating iron in addition to the heme prosthetic group?

A) Tyr
B) Glu
C) His
D) Val
E) Cys

Question 37

The coordinated nitrogen atoms in the heme prosthetic group have _____ character, which prevents conversion of the heme iron from the _____ state to the _____ state

A) electron-donating; Fe²⁺; Fe³⁺
B) electron-donating; Fe³⁺; Fe²⁺
C) electron-accepting; Fe²⁺; Fe³⁺
D) electron-accepting; Fe³⁺; Fe²⁺
E) electron-accepting; Fe⁺; Fe⁰

Question 38

A Hill coefficient (n_H) of 2 indicates that:

A) there is positive cooperativity in ligand binding.
B) there are two ligand-binding sites.
C) there is negative cooperativity in ligand binding.
D) there is positive cooperativity in ligand binding and there are two ligand-binding sites.
E) there is negative cooperativity in ligand binding and there are two ligand-binding sites.

Question 39

A significant contribution to the change in hemoglobin affinity for oxygen from pH 7.2 to pH 7.6 is due to a change in the protonation state of which amino acid side chain?

A) Cys
B) His
C) Ser
D) Asp
E) Lys

Question 40

The change in hemoglobin-binding affinity for oxygen due to changing pH and CO₂ concentration in the blood is known as the:

A) Hill hypothesis.
B) Messelson theory.
C) Bohr effect.
D) Higgs observation.
E) Boyle hypothesis.

Question 41

Which type of antibody interacts with basophils and plays a role in the allergic response?

A) IgA
B) IgD
C) IgE
D) IgG
E) IgM

Question 42

Which immune-system cells are responsible for producing antibodies?

A) macrophages
B) B cells
C) helper T cells
D) cytotoxic T cells
E) erythrocytes

Question 43

Small molecules attached to larger protein structures that elicit an immune response are referred to as:

A) antibodies.
B) globins.
C) allergens.
D) haptens.
E) hemes.

Question 44

You are working as a scientist in an antibody-design group at a biologics company. Based on your knowledge of antibodies, which region(s) on which antibody type should you target for your design efforts to develop new antigen-binding capabilities in soluble antibodies?

A) IgG antibodies, variable light and variable heavy chain regions
B) IgE antibodies, constant light and variable heavy chain regions
C) IgG antibodies, variable heavy chain regions only
D) IgD antibodies, variable light and variable heavy chain regions
E) IgA antibodies, constant light and constant heavy chain regions

Question 45

Antigens typically bind to antibodies via which type of interactions?

A) covalent bonding
B) hydrophobic interactions
C) hydrogen bonding
D) both covalent bonding and hydrophobic interactions
E) both hydrophobic interactions and hydrogen bonding

Question 46

Which antibody is secreted as a cross-linked pentamer?

A) IgA
B) IgD
C) IgE
D) IgG
E) IgM

Question 47

Which statement about antibodies is INCORRECT?

A) Antibodies bind to antigens via induced fit.
B) Antibodies typically bind to antigens more strongly than enzymes bind to substrates.
C) Antibodies can be both soluble and membrane-bound.
D) Antibodies never release antigens once they are bound together.
E) More than 100 million different antibodies can be produced in humans.

Question 48

A test where antibodies are used to quantitatively detect the presence of antiviral antibodies in human blood samples is referred to as:

A) Western blot.
B) ELISA.
C) Northern blot.
D) FRET.
E) PCR.

Question 49

Macrophages bind to the _____ region of IgG antibodies, thereby triggering phagocytosis of antibody-antigen complexes.

A) Fab
B) Fc
C) epitope
D) hinge
E) antigen

Question 50

You want to purify a specific soluble protein from a solution of lysed cells so that you can conduct biochemical tests of the protein's function. To best achieve this, which type of antibody would be MOST effective to use in your affinity purification?

A) monoclonal IgE
B) polyclonal IgE
C) monoclonal IgG
D) polyclonal IgG
E) monoclonal IgM

Question 51

Which types of covalent bonds hold antibody structures together?

A) hydrogen bonds
B) disulfide bonds
C) van der Waals interactions
D) London forces
E) ionic bonds

Question 52

IgG antibodies have _____ binding site(s) that is/are made up of the _____ regions of the light and heavy chains.

A) one; variable
B) one; constant
C) two; variable
D) two; constant
E) one; diversity

Question 53

Antibodies against a specific antigen can be injected into a person to provide passive immunity. For which reason is this NOT as effective as the process of vaccination with that antigen?

A) Injection of antibodies does not provide long-lasting immunity.
B) Vaccination with antigens triggers a clonal selection of B cells and cytotoxic T cells.
C) Injection of antibodies may cause allergic reactions, while vaccination never causes allergic reactions.
D) Injection of antibodies does not provide long-lasting immunity, and vaccination with antigens triggers a clonal selection of B cells and cytotoxic T cells.
E) Injection of antibodies does not provide long-lasting immunity and may cause allergic reactions, while vaccination never causes allergic reactions.

Question 54

The covalent bonds that hold antibody structures together are formed from which amino acid side chains?

A) His
B) Thr
C) Cys
D) Met
E) Ser

Question 55

Which statement about antigen-antibody interactions is CORRECT?

A) Antigens bind to antibodies cooperatively.
B) Antigens bind to antibodies through induced fit.
C) Antigens bind to antibodies at both the Fab and Fc parts of the antibody.
D) Molecules with molecular weights of less than 5,000 daltons are exceptionally antigenic and bind to antibodies extremely well.
E) Antigens bind only to antibodies that have a preformed binding site that is perfectly complementary to the antigen.

Question 56

Which antibody is principally found in saliva, tears, and breast milk?

A) IgA
B) IgD
C) IgE
D) IgG
E) IgM

Question 57

Muscle fibers are made up of which protein?

A) myosin
B) actin
C) calcitonin
D) both myosin and actin
E) both myosin and calcitonin

Question 58

The immunoglobulin fold motif in antibodies is composed primarily of which type(s) of secondary structure?

A) $\alpha$ helices
B) $\beta$ strands
C) random coils
D) double helices
E) $\delta$ sheets

Question 59

A person who is HIV-positive asks you why they have reduced immune system function. You tell them that the most likely reason is due to a deficiency of which cells that are targets of HIV viral infections?

A) B cells
B) neutrophils
C) cytotoxic T cells
D) helper T cells
E) erythrocytes

Question 60

The Fab regions of an antibody are made of which protein chain?

A) a light chain containing variable and constant regions
B) a heavy chain containing variable and constant regions
C) a heavy chain containing only constant regions
D) both a light chain and a heavy chain containing variable and constant regions
E) both a light chain containing variable and constant regions and a heavy chain containing only constant regions

Question 61

You are attempting to crystallize the head group of a myosin-like muscle protein from a newly discovered vertebrate organism. Assuming that the protein structure is similar to other vertebrate myosins, which enzymes should you use to remove the myosin-like head group from the rest of the myosin-like protein?

A) trypsin
B) myosinase
C) papain
D) both trypsin and myosinase
E) both trypsin and papain

Question 62

What fraction of ligand binding sites are occupied ( $\theta$ ) when [ligand] = K_d? Show your work.

Question 63

Myosin obtains its high tensile strength due to its composition of:

A) $\alpha$ helices supercoiled around each other in a left-handed coiled coil.
B) $\beta$ strands layered on top of each other.
C) $\alpha$ helices supercoiled around each other in a right-handed coiled coil.
D) $\beta$ strands coiled around each other in a $\beta$ -barrel conformation.
E) $\beta$ helices supercoiled around each other in a right-handed coiled coil.

Question 64

Which protein undergoes a conformational change upon interacting with Ca²⁺, leading to stimulation of muscle contraction?

A) actin
B) myosin
C) troponin
D) hemoglobin
E) immunoglobin

Question 65

You are studying a muscle disorder where an individual's muscles have a higher tendency to be overextended due to a protein mutation. This mutation is likely to be in which protein?

A) troponin
B) nebulin
C) myosin
D) myoglobin
E) desmin

Question 66

Describe the concept of "induced fit" in ligand-protein binding.

Question 67

Explain why most multicellular organisms use an iron-containing protein for oxygen binding rather than free Fe²⁺. Your answer should include an explanation of (a) the role of heme and (b) the role of the protein itself.

Question 68

Tropomyosin and troponin prevent muscle contractions in the absence of Ca²⁺ because they:

A) block the myosin head binding sites on actin filaments.
B) prevent the hydrolysis of ATP by myosin.
C) degrade the actin filaments.
D) increase the release of P_i by myosin.
E) block the "power stroke" conformational change of actin filaments.

Question 69

If myosin head groups were unable to hydrolyze ATP due to an alteration in the protein structure but could still bind and release ADP and inorganic phosphate (P_i), which step in the actin-myosin cycle would NOT take place?

A) dissociation of the myosin head group from the actin filament
B) repositioning of the myosin head group on the actin filament
C) attachment of the myosin head group to the actin filament
D) the "power stroke" conformational change in the myosin head group
E) the conformational change in the myosin head group in the presence of Ca²⁺

Question 70

Myosin moves relative to actin filaments by using energy derived from the hydrolysis of which molecule?

A) GTP
B) ATP
C) NADH
D) coenzyme A
E) ADP

Question 71

Explain briefly why the relative affinity of heme for oxygen and carbon monoxide is changed by the presence of the myoglobin protein.

Question 72

Explain why the structure of myoglobin makes it function well as an oxygen-storage protein, whereas the structure of hemoglobin makes it function well as an oxygen-transport protein.

Question 73

Nerve impulses control muscle contractions by releasing which ion?

A) H⁺
B) Mg²⁺
C) Na⁺
D) Ca²⁺
E) Fe²⁺

Question 74

Describe how you would determine the K_a (association constant) for a ligand and a protein.

Question 75

For the binding of a ligand to a protein, what is the relationship between the K_a (association constant), the K_d (dissociation constant), and the affinity of the protein for the ligand?

Question 76

During muscle contraction, the _____ of myofibrils contract and the _____ move closer together due to the movement of myosin thick filaments along actin thin filaments.

A) Z disks; A bands
B) A bands; M lines
C) I bands; Z disks
D) I bands; M lines
E) M lines; I bands

Question 77

Why is carbon monoxide (CO) toxic to aerobic organisms?

Question 78

Which class of proteins includes the LARGEST polypeptide chains discovered to date in humans?

A) myosins
B) actins
C) titins
D) troponins
E) globins

Question 79

Which event triggers a "power stroke" in myosin?

A) hydrolysis of ATP
B) binding of ATP
C) release of ADP
D) release of P_i
E) degradation of actin

Question 80

Individual contractile units in muscle fibers are called:

A) Z disks.
B) sarcomeres.
C) myofibrils.
D) myomeres.
E) porphyrins.