1.

Given the graph below for the hemoglobin binding to O2 in presence of 2,3-biphosphoglycerate (BPG), the following
conclusions can be outline about BPG:
A) BPG is a negative allosteric effector; B) BPG is a positive allosteric effector
C) BPG is decreasing the affinity of hemoglobin for O2;; E) Both A) and C) are correct

2. Hemoglobin's p50 value is about ______ as great as myoglobin's p50 value.

D) ten times

3. Consider a hypothetical hemoglobin with a Hill coefficient of 1 and the same p50 value as normal hemoglobin. Choose the
statement below that best describes the two proteins.
C) The oxygen binding curve for the hypothetical hemoglobin is hyperbolic, and the curve for normal hemoglobin is sigmoidal.

8. During the T to R conformational shift, Fe(II) drags the F-helix via a bond to the side chain of..
C) His F8

12. Myoglobin and the subunits of hemoglobin have:

A) very similar tertiary structures, but different primary structures.

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

A) binding of a molecule to a binding site affects binding properties of another site on the protein.

16. Identify the correct statements regarding the Bohr effect in hemoglobin.

a) The Bohr effect shifts the fractional O2 saturation curve to the right as pH decreases.
c) The Bohr effect favors O2 release in respiring tissues.
A) a and c

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

1
 B) epitope.

21. Why is the decreased affinity of fetal hemoglobin for BPG advantageous?
B) Decreased BPG binding biases the fetal hemoglobin toward the R state.

23. What is the chemical basis for the specificity of binding of an immunoglobin antibody to a particular antigen?
A) Specific binding results from complementarity between the chemical properties (such as size, charge, and hydrophobicity) of
the antigen and the antigen-binding site of the antibody.
B) The conformations of the antigen and antigen-binding site of the antibody are influenced by each other and change as
binding occurs. These conformational changes increase the chemical complementarity of the sites and result in tighter
binding and more specific binding.
C) A) and B) are correct

24. What fraction of ligand binding sites are occupied () when [ligand] = Kd?
Kd 1
A) = 
Kd + Kd 2

26. The role of an enzyme in an enzyme-catalyzed reaction is to:

A) increase the rate at which substrate is converted into product.

27. Which one of the following statements is true of enzyme catalysts?

A) They lower the activation energy for the conversion of substrate to product.

28. The expression of the Michaelis constant is equal to:

A) (K2 + K3)/K1

Where
K1 = the rate constant for ES formation
K2 = the rate constant for ES dissociation
K3 = the rate constant for product formation

k1 k2
E+S ES E+P
k-1

29. The concept of “induced fit” refers to the fact that:

A) substrate binding may induce a conformational change in the enzyme, which then brings catalytic groups into proper
orientation.

30. Michaelis and Menten assumed that the overall reaction for an enzyme-catalyzed reaction could be written as
k1 k2
E+S ES E + P
k-1
Using this reaction, the rate of breakdown of the enzyme-substrate complex can be described by the expression:

A) k-1 [ES] + k2 [ES].

31. For the simplified representation of an enzyme-catalyzed reaction shown below, the statement “ES is in steady-state”
means that:

k1 k2
E+S ES E+P
k-1 k-2
D) k1[E][S] = k-1[ES] + k2[ES].

2
 32. To calculate the turnover number of an enzyme, you need to know:
A) the enzyme concentration.
B) the initial velocity of the catalyzed reaction at [S] >> Km (i.e. Vmax).
C) both A and B.

33. The number of substrate molecules converted to product in a given unit of time by a single enzyme molecule at
saturation is referred to as the: .
A) turnover number.

36. In competitive inhibition, an inhibitor:

A) binds reversibly at the active site.

37. Which of the following statements about allosteric control of enzymatic activity is false?
A) Heterotropic allosteric effectors compete with substrate for binding sites.

39. NADPH and NADH are coenzymes found in which class of enzymes?
A) Dehydrogenases;

40. The allosteric enzyme ATCase is regulated by CTP, which binds to the T-state of ATCase. CTP is a:
B) negative regulator.

41. The ‘catalytic triad’ in chymotrypsin consists of:

C) three amino acids: SER, HIS, and ASP

44. [S] = KM for a simple enzymatic reaction. When [S] is doubled, the rate becomes _ Vmax.
C) 0.67

45. Find the initial velocity for an enzymatic reaction when Vmax = 6.5 x 10–5 mol•sec–1, [S] = 3.0 x 10–3 M, and KM = 4.5 x 10–3
M.
B) 2.6 x 10–5 mol•sec–1

V0 = Vmax [S]/( Km + [S])

46. The plots shown in the figure below are characterizing different types of enzyme inhibition. Identify the correct type of
inhibition for each a), b) and c) graphs:

A) a=competitive inhibition; b=pure noncompetitive inhibition; c=noncompetitive mixed inhibition

47. Fifteen ug (micrograms) of an enzyme of Mr 30,000 working at Vmax catalyzes the conversion of 60 umol (micromoles) of
substrate into product in 3 min. What is the enzyme’s turnover number?

A) 4 x 10-4 min-1.

48. You measure the initial rate of an enzyme reaction as a function of substrate concentration in the presence and absence of
an inhibitor. The following data are obtained:

[S] V0
-Inhibitor +Inhibitor
0.0001 33 17
0.0002 50 29
0.0005 71 50
0.001 83 67
0.002 91 80
0.005 96 91
0.01 98 95
0.02 99 98
3
 0.05 100 99
0.1 100 100
0.2 100 100

a) What is the Vmax in the absence of inhibitor?

b) What is the Km in the absence of inhibitor?
c) What is the Vmax in the presence of inhibitor?
d) What is the Km in the presence of inhibitor?
e) What kind of inhibitor is it likely to be?
A) a) 100; b) 0.0002; c) 100; d)0.0005; e) competitive.

50. In the following diagram of the first step in the reaction catalyzed by the protease chymotrypsin, the process of general
base catalysis is illustrated by the number____, and the process of covalent catalysis is illustrated by the number___.

A) 1; 2

Midterm 2 exam questions practice

ENZYMES Questions

1. For efficient nucleophilic catalysis, a group such as the sulfhydryl on a cysteine residue must be able to form a good leaving group,
in addition to being a good nucleophile.

2. If an enzyme-catalyzed reaction has a low rate at low pH and high rate at higher pH, this implies that a group on either the enzyme
or the substrate must be deprotonated for an efficient reaction.

3. On a transition state diagram for a multistep reaction, the step with the greatest G is the rate-determining step.

4. On a transition state diagram for a one-step, very spontaneous reaction (large negative G), a large peak (high G°) would imply a
low rate for the reaction.

5. Metal ion cofactors can orient the substrate at the active site, providing catalytic enhancement.

6. Large rate enhancement in enzyme catalysis may occur when the binding of substrate reduces the motion of the reacting groups.

7. Metal ion cofactors with more than one oxidation state may assist in catalysis by the oxidoreductase class of enzymes.

8. Since proteins are limited in their abilities to catalyze oxidation-reduction reactions, enzymes often employ coenzymes to assist
with catalysis.

9. Some serine proteases are believed to have developed by convergent evolution, because the amino acid sequences of some serine
proteases show no resemblance to those of others.

10. Clustering several amino acid residues with favorable pK values at an active site can promote a(n) concerted acid-base catalytic
mechanism.

Multiple Choice

4
11. An uncatalyzed reaction has a rate of 4.2 x 10 –7 sec–1. When an enzyme is added the rate is 3.2 x 10 4 sec–1. Calculate the rate
enhancement caused by the enzyme.
D) 7.62 x 1010

12. Which of these amino acid groups would not make a good nucleophilic catalyst?
D) methyl

13. The imidazole side chain of histidine can function as either a general acid catalyst or a general base catalyst because:
B) in the physiological pH range, the nitrogen in the ring can be easily protonated/deprotonated.

14. Chymotrypsin, a serine protease, preferentially cleaves a peptide bond adjoining a bulky non-polar side chain. This is because
chymotrypsin's specificity pocket:
B) is lined with small hydrophobic side chains, leaving considerable room in the nonpolar pocket.

15. If you add enzyme to a solution containing only the product(s) of a reaction, would you expect any substrate to form?
E) Yes, because the reaction proceeds backwards until equilibrium is reached.

16. Which one of the following is correct?

D) If an enzyme-catalyzed reaction requires a group with a low pK to be deprotonated and a group with a higher pK to be protonated,
the pH vs. velocity curve will have a peak in the middle.

17. Which of the following amino acid residues would not provide a side chain for acid-base catalysis?
A) leucine

18. Which of the following amino acid residues would provide a side chain capable of increasing the hydrophobicity of a binding
site?
C) isoleucine

19. Which of the following is not true about enzymes?

A) Enzymes catalyze reactions in the forward direction only.

20. In affinity labeling, a technique used to study enzyme mechanisms,

A) a compound designed to bind at the active site reacts with and therefore permits the identification of a nearby group.

21. Which of the following is the most general term:

C) cofactor

22. ___ is a serine protease that has a specificity pocket that binds small hydrophobic side chains.
E) elastase

23. Alcohol dehydrogenase catalyzes the conversion of methanol to ____.

B) formaldehyde
C) acetone
D) ethanol
E) methene

24. Since L-glucose cannot be metabolized, it has no caloric value. Why is L-glucose not the perfect diet aid?
D) it does not bind to the receptor for the ‘sweet’ taste

25. Would Glu 35 of lysozyme, which is found in a non-polar environment, be expected to be more or less acidic than an external,
well hydrated Glu residue?
B) less acidic

26. ______ metals are the most common metallic enzyme cofactors.
E) Transition

27. Curved arrows are conventionally used to illustrate the movement of:
A) electron pairs.

5
28. Proton transfer from an acid, lowering the free energy of a reaction’s transition state, is characteristic of:
D) general acid catalysis.

29. Simultaneous stimulation of a reaction by general acid and general base catalysis is defined as:
D) concerted acid/base catalysis.

30. A pH/rate curve with an inflection point at pH~4 suggests the involvement of a(n) ___ in the catalytic step.
B) acidic amino acid

31. The catalytic mechanism of bovine pancreatic RNase A relies upon acid/base catalysis involving the amino acid ____.
C) histidine

32. The formation of a Schiff base in the enzymatically catalyzed decarboxylation of acetoacetate is an example of:
A) covalent catalysis.

33. What type of chemical species can participate in catalysis by binding substrates to orient them properly, by undergoing reversible
changes in oxidation state, and by stabilizing negative charges:
E) transition metal cations

34. Which of the following considerations in the rate of a given reaction can be optimized by enzymatic catalysis:
D) all of the above

35. Enzymes that bind reaction transition states with greater affinity than substrates or products
A) are inhibited by transition-state analogs

36. Lysozyme catalyzes the hydrolysis of:

B) β(1-4) glycosidic linkages.

37. Zymogens are not enzymatically active because

D) their active sites are distorted.

38. Serine proteases use _________ to catalyze the cleavage of a peptide bond.
A) covalent catalysis
B) proximity and orientation catalysis
C) general base catalysis
D) electrostatic catalysis
E) all of the above

40. In the lysozome reaction the subsite D NAM is in the____ conformation.

E) half-chair

5. In the graph reaction rate vs substrate concentration, the reason that the curve reaches a plateau, and does not increase any
further at high substrate concentration is that:

A. the active site is saturated with substrate

6. The graph shows the results of reaction rate vs substrate concentration for a(n):
C) A sigmoidal plot, corresponding to an allosterically regulated enzyme.

6
8. The reaction shown below is catalyzed by which an enzyme from which class:

C) a transferase (phosphoryl group transfer)

1) The minimum amount of energy required to bring about a chemical reaction is called:
A) Activation energy

2) Which of the following is not a property of enzymes?

A) Capable of being regulated
B) Reaction rates high in comparison to uncatalyzed reaction
C) Highly specific
D) Side products of reactions are rare
E) All of the above are true

3) Consider the following reaction diagram. Which letter indicates the transition state?
C
B
A D
E
E

C) C

4) In contrast to inorganic catalysts, enzymes have an intricately shaped surface called the __________.
C) Active site

5) The lock and key model of enzyme activity proposes that each:
D) Enzyme binds a specific substrate because the active site and substrate have complementary structures.

6) The synthesis of enzymes in response to changing metabolic needs is referred to as:

A) Enzyme induction

7) Which of the following is a coenzyme?

A) NADP+

8) Alcohol dehydrogenase without NAD+ is called a _______:

A) Apoenzyme

9) The term synthetase is included in which class of enzymes?

7
A) Ligases

10) Which of the following is not a type of oxidoreductase?

E) Peptidase

11) Which of the following classes of enzymes catalyze reactions involving the cleavage of bonds by the addition of water?
B) Hydrolase

12) Consider the following reaction data.

Alanylanine + water ----- alanine

[alanylanine} [water] Rate

0.1 0.1 1x 10-4

0.2 0.1 2x10-4

0.1 0.2 2x10-4

0.2 0.2 4x10-4

The reaction is ________ order overall.

C) Second

13) The steady state assumption states that if:

K1 = the rate constant for ES formation

K2 = the rate constant for ES dissociation
K3 = the rate constant for product formation

B) The rate of formation of ES is equal to the rate of its degradation over the course of the reaction

15) Specific activity is defined as

C) The number of I.U. per mg of protein

16) In the Lineweaver-Burk double reciprocal plot the slope is equal to _____.
C) Km/Vmax

17) In the Lineweaver-Burke double reciprocal plot the vertical intercept is equal to ____.
D) 1/Vmax

18) In the Lineweaver-Burke double reciprocal plot the horizontal intercept is equal to _________.
E) –1/Km

19) In competitive inhibition, increasing the concentration of substrate:

B) Increases the overall rate of the reaction

20) Which of the following amino acids is capable of acting as a general acid or general base at physiological pH ?
B) Histidine

21) Which of the following amino acids can participate in covalent catalysis?
C) Serine
D) Histidine
E) Both C and D are correct

22) Which of the following is a feature of transition metals that makes them efficient cofactors?
8
A) Have a high concentration of positive charge
B) Can act as a Lewis acid
C) Have directed valences
D) Can exist as a variety of valence states
E) All of the above are correct.

24) Which of the following is not present in the active site of alcohol dehydrogenase?
E) Proline

25) Enzyme control is accomplished in which of the following ways?

A) Genetic control
B) Covalent modification
C) Allosteric regulation
D) Compartamentation
E) All of the above are correct

27) Regulatory enzymes are a feature of what type of enzymatic control?

C) Allosteric regulation

28) Positive cooperativity is a feature of what type of enzymatic control?

C) Allosteric regulation

29) Segregation of biochemical pathways into different organelles in an example of which type of enzymatic regulation?
D) Compartmentation

30) Catalysts are effective because they:

C) Decrease the activation energy of a reaction

31) Enzymes act by _________.

A) Decreasing the energy of activation of a reaction
D) Providing a surface to favorably orient the reactants
E) Both A and D are correct

32) Enzyme studies are best carried out:

D) In the presence of an inert crowding agent
33) Alcohol dehydrogenase is an example of which of the following classes of enzymes?
A) Oxidoreductases

34) Which of the following is not an assumption of the law of mass action?
A) Forward reaction is linear
B) Reverse reaction is linear
C) System is homogenous
D) Interacting molecules move randomly and independently of each other
E) All are assumptions of the law of mass action

35) Metabolons are defined as:

B) Complexes that channel product molecules from one active site to another

36) Metabolic flux is best defined as a:

B) Rate of flow of metabolites from one point to another in a pathway

37) Which of the following molecules can most easily facilitate quantum mechanical tunneling?
A) NADH

38) Which of the following amino acids cannot actively participate in a catalytic site?
D) Lysine

39) In addition to serine and aspartate which of the following amino acids is a member of the serine triad?
9
D) Histidine

40) Which of the following is not an important metal in biological systems

E) Ba++

Protein functions questions:

Myoglobin and Hemoglobin

Matching

1. In the _ T _ form of hemoglobin, the iron ion is out of the plane of the porphyrin ring.

2. The conversion of hemoglobin from the T to the R form involves breaking C-terminal ion pairs

3. An increase in pCO2 causes hemoglobin's affinity for oxygen to decrease.

4. Hemoglobin's subunits bind oxygen in a positively cooperative manner.
5. The absence of 2,3-BPG causes hemoglobin's affinity for oxygen to increase
6. The symmetry model of allosterism requires subunits to change conformation simultaneously.
7. Sickle cell hemoglobin does not form fibers in the R form.
8. When unstable hemoglobins are degraded, the products often cause cell lysis, leading to a condition called hemolytic anemia.
9. When oxygen binds to heme, the oxygen forms a hydrogen bond with His E7.
10. Mutations that favor the oxidation of the heme iron to the +3 oxidation state can cause cyanosis.

11. Which of the following is not a ligand to the porphyrin ring Fe 2+ ion in oxymyoglobin?
A) His E7

13. Which of the following statements does not apply to the K value in the equation for the oxygen binding curve of myoglobin?
D) If Y > K, then myoglobin is less than 50% saturated with oxygen.

15. Myoglobin and a single chain of hemoglobin have similar ______ structures.
C) tertiary

17. The value of n in the Hill equation for hemoglobin is about ______ as great as the value for myoglobin.
C) three times

19. Some abnormal hemoglobins have Hill coefficients that are ______ that of normal hemoglobin, indicating that their ability to bind
oxygen cooperatively has been compromised.
A) less than

22. Myoglobin’s primary physiological role is to facilitate oxygen ________.

E) diffusion

23. If the gene for myoglobin is knocked out in mice, the mice:
D) appear normal, with lighter colored muscle tissue.

24. Carbon monoxide binds to Heme:

A) with a higher affinity than oxygen.

25. The primary structure of mammalian hemoglobin, an 2 2 tetramer, is approximately _____ identical to myoglobin.
B) 18%

29. Hemerythrin and hemocyanin are:

D) oxygen transport proteins found in invertebrates.

31. Max Perutz’ investigation of the structure and function of hemoglobin primarily utilized___.

10
A) X-ray crystallography

33. Hemoglobin S, the variant responsible for the misshapen red blood cells characteristic of the disease sickle-cell anemia, is
potentially advantageous to heterozygotes because it confers some level of resistance to the disease _________.
E) malaria

34. Which of the following is not true for the symmetry model of allosterism:
A) the protein is an oligomer of symmetrically (or pseudosymmetrically) related subunits.
B) the oligomer can exist in two conformational states which are in equilibrium.
C) the ligand can bind to a subunit in either conformation.
D) the molecular symmetry of the protein is conserved during the conformational change.
E) none of the above.

35. BPG stands for:

C) bisphosphoglycerate

37. The reaction of carbonic anhydrase catalyzes:

D) the hydration of carbon dioxide, forming bicarbonate and protons

39. If the binding of O2 to hemoglobin was characterized by a Hill constant of -1:

D) the binding of the first O2 would decrease the affinity of the hemoglobin for O2.

40. ______of the world’s human population carry a variant hemoglobin.

A) 5%

5. Which gas does not bind to the porphyrin ring Fe2+ ion in myoglobin?

C) CO2

7. When the partial pressure of oxygen in venous blood is 30 torr, the YO2 value for myoglobin is ______ while the YO2 value for
hemoglobin is ______.

B) 0.91, 0.55

11. Myoglobin’s secondary structure is primarily composed of ______.

C) alpha-helices

14. In sickle-cell anemia, the negatively charged glutamic acid residue is replaced by the neutral amino acid ____________.
C) valine

17. While the binding of O2 to myoglobin as a function of pO2 is described by a simple _____ curve, the binding to hemoglobin
is described by a more complex ___ curve.

11
B) hyperbolic; sigmoidal

19. Given the graph below, choose the best statement:

B) BPG and CO2 are negative allosteric effectors for stripped Hb.
D) The whole blood Hb has a lower affinity for O2 than the stripped Hb.
E) Both B and D are correct.

20. Given the pictures below, which of the following statements are true about the myofibril contraction:

A) The lengths of the band I and H decrease on contraction, whereas the lengths of thick and thin filaments remain constant.
B) The lengths of the sarcomeres decrease on contraction.
C) The thick and the thin filaments are sliding past each other on contraction.
D) A), B) and C) are correct.

21. The mechanism of force generation is shown in the figure below. Which statement fits the best the description of this
mechanism:

A) The myosin head “walks” up the actin filament through an unidirectional cycle that is driven by ATP hydrolysis to ADP and
Pi.
B) In ATP-bound state, the myosin head has lower affinity for actin.
C) Releasing of the Pi upon ATP hydrolysis induces a conformation change in myosin characterized by a higher affinity for
actin.
12
 D) A), B) and C) are correct.

23. The immunoglobulin fold has specific characteristics. Which of the statements below best describe the Ig fold (analyze
figures 22 and 23):
A) four-stranded antiparallel beta sheets and three-stranded antiparallel beta sheets linked by a disulfide bond.
B) The hypervariable sequences reside in the three loops of the variable domains of both light and heavy chains and their amino acids
determine the Ig binding specificity.
C) There are glycosylation sites located between CH1 and CH2 (C=constant) of each of the two heavy chains, thus the Ig is a
glycoprotein.
E) A, B) and C are correct.

24. Antigen-crosslinking by antibodies hastens the removal of the antigen and triggers the B cell proliferation as shown in
figure below.
Which are the structural and chemical characteristics that enable such an immunological process:
A) most antibodies are divalent molecules that can bind two different antigens simultaneously.
B) Divalent binding allows antibodies to cross-link antigens form an extended lattice.
C) IgM and IgA are multivalent.
E) A), B) and C) are correct.

3. Which of the following increases the affinity of hemoglobin for oxygen:

C) increasing pH.

8. Which of the following molecules is a homotropic modulator of oxygen binding to hemoglobin?

D. Oxygen;

10. Hemoglobin can assist with blood buffering. Which of the following does not contribute to buffering through hemoglobin
and the Bohr Effect?

A. Binding H+ on carbamino-terminal residues of hemoglobin

22. Which of the following parts of the IgG molecule are not involved in binding to an antigen?

B) Fc

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

13
 A) conformation of myosin.

24. What event is the immediate trigger of the "power stroke" in muscle contraction?

E) release of Pi

25. Which of the following structures is the beta-anomer of D-glucose:

CH2 OH
O

B)

26. The structures below can be identified as:

1 2
C) 1=aldose, 2=ketose

27. The figure below shows which type of chemical reaction:

14
C) mutarotation in solution;

28. The figure below shows a redox reaction used to identify glucose. In this reaction:

B) Glucose is oxidized to an aldonic acid;

29.Which one of the following is not true concerning D-glucose?

D.D-glucose is a ketose.

30. The  and  forms of D-glucopyranose can be described as

D. anomers.

31.Which of the following is a glycoside

B)

CH2 OH
O O CH3

32. The structure of an amino-sugar is shown below (amino-glucose). Which is the best nomenclature for the structure below:

B) 2-amino-2-deoxy-alpha-D-glucopyranose
33. The reaction below shows the reaction of the anomeric OH of D-glucose with an alcohol. The arrows are showing which
kind of new covalent bond:
15
; E) C and D are correct.

34. The structure below is a dinucleotide. The arrows are showing the following covalent bond:

C) N-glycosidic;
35. Cellulose is a polymer of glucose in which the monomers are linked through which kind of bond:
; B) beta-1,4-glycosidic bond;

36. The structure below shows which kind of biomolecule:

; C) an O-liked sugar, glycoprotein;

37. The figure below shows which class of biomolecules:

B) transmembrane glycoprotein

16
This figure is used in questions 38-40

38. Which of the sugars shown in the figure are L sugars?

C) C and D

39. Which sugar is the enantiomer of sugar A?

C) D;
40. Which two sugars shown in the figure are epimers?
A) A and B;

41. N-linked oligosaccharides can be covalently linked to proteins at the amino acid
E) asn

42. A saccharide that has free aldehyde group is called a(n) _____________.
; C) reducing sugar

This figure is used in questions 43-45.

43. Which structure(s) represent reducing sugar(s)?

D) A, B, and C;

44. Which structure is a ketohexose?

D) D

17
45. Which is ribose?
A) A

51. Enzymes with a kcat / Km ratio of about 108 M-1s-1 (catalytic turnover) are considered to show optimal catalytic efficiency.
Fumarase, which catalyzes the reversible-dehydration reaction

fumarate + H2O malate

has a ratio of turnover number to the Michaelis-Menten constant, (kcat / Km) of 1.6 x108 for the substrate fumarate and 3.6 x 107
for the substrate malate.

Because the turnover number for both substrates is nearly identical, what factors might be involved that explain the different
ratio for the two substrates?

A) The Km for malate must be much larger than for fumarate.

B) Similar turnover numbers suggest no significant differences in rate of conversion of substrate to product, but the different Km
values could possibly be explained by a stronger binding affinity of the enzyme for fumarate than for malate.
E) A) and C) are correct;

52. When 10 ug of an enzyme of Mr 50,000 is added to a solution containing its substrate at a concentration one hundred times
the Km, it catalyzes the conversion of 75 umol of substrate into product in 3 min. What is the enzyme's turnover number?

Hint: Since the reaction takes place at a substrate concentration 100 x Km, then the recorded velocity of 75 umol/ 3min is the
Vmax for this reaction.
Convert the mass of 10 ug into moles enzyme ([Et]) known that the Mr=50,000 g/mol.
Use formula which relates Vmax to Kcat and [Et].

A) Kcat= 12.5 x 104 min-1

62. The reaction shown below is catalyzed by an enzyme from which class:

C) a transferase (phosphoryl group transfer)

66. If an enzyme-catalyzed reaction has a low rate at low pH and high rate at higher pH, this implies that a group on either
the enzyme or the substrate must be ______ for an efficient reaction.

C) deprotonated

67. Find the initial velocity for an enzymatic reaction when Vmax = 6.5 x 10–5 mol•sec–1,
[S] = 3.0 x 10–3 M, and KM = 4.5 x 10–3 M.

B) 2.6 x 10–5 mol•sec–1

1

V0 = Vmax [S]/( Km + [S])

3. The rearrangement of T-form hemoglobin to the R-form:

18
D) involves the movement of the Fe(II) into the heme plane.

4. The Hill plot shows that the fourth oxygen binds to hemoglobin with ______-fold greater affinity than the first.
D) 100

5. Which of the following forms a hydrogen bond with O , but is not one of the six coordination bonds with heme?
2

C)His E7, the distal His residue

6. 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?
A) The hyperbolic binding of oxygen to the single binding site of myoglobin results in a high affinity even at the relatively low
partial pressures of O2 that occur in tissues.
B) The cooperative (sigmoidal) binding of O2 to the multiple binding sites of hemoglobin results in high affinity at high partial
pressures such as occur in the lungs, but lower affinity in the tissues and thus permits hemoglobin to bind O 2 in the lungs and
release it in the tissues.
E) A) and B) are correct
(see figure for question 1)

7. What is the effect of pH on the binding of oxygen to hemoglobin (the Bohr Effect)?

19
 (A) The affinity decreases with decreasing pH.
(B) The affinity increasing with increasing pH.
(C) At lower pH (i.e., higher H+ concentration), there is increasing protonation of protein residues such as histidine, which
stabilizes the low affinity conformation of the protein subunits.
; E) A, B and C are correct
8. Carbon monoxide (CO) is toxic to humans because:
A) it binds to the Fe in hemoglobin and prevents the binding of O 2.

9. Which of the following statements about protein-ligand binding is correct?

A) The larger the Ka, the smaller the Kd (dissociation constant).

11. Which of the following is not correct concerning 2,3-bisphosphoglycerate (BPG)?

A) It increases the affinity of hemoglobin for oxygen.

12. The most rapid way that erythrocytes adapt to high altitudes is:
C) by increasing the intracellular concentration of BPG;

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

C) p50 for O2 will be increased

15.How the effects of sickle cell disease demonstrate that hemoblobin undergoes a conformational change upon releasing
oxygen.

A) In hemoglobin S, the wild-type glutamate (GLU) at residue 6 of the B-chain is replaced by valine (VAL).
B) When oxygen is bound (R state), both hemoglobin A and hemoglobin S are soluble, but in the deoxy- form (T state),
hemoglobin S (but not hemoglobin A) becomes very insoluble due to exposure of the hydrophobic valine residue. This

20
 exposed “patch” causes aggregation of deoxy-hemoglobin S into long insoluble fibrous aggregates, resulting in distorted
shapes of the red blood cells (and leading to the symptoms of the disease).
C) E) A) and B) are correct.

16. Fetal hemoglobin binds BPG with lower affinity than adult hemoglobin. How does this property facilitate the transfer of
O2 from mother to fetus?

A) Lower affinity for BPG means that fetal hemoglobin will have less BPG bound than the mother’s hemoglobin;
B) The lower affinity for BPG shifts the fetus’ fractional O2 saturation curve to the left (i.e., lower p50) of the mother’s, shifting
the fetus Hb into the R state with respect to the mother’s Hb which is more in the T state at the same fraction saturation; at
low pO2, O2 will dissociate from the maternal hemoglobin and can be bound by the fetal hemoglobin.
C) A) and B) are correct

17. In the figure below the sigmoidal Hb binding curve to O2 in the red blood cells of normal blood, pH 7.6 is shown together
with the binding curves in the presence of two allosteric effectors (curves labeled A and B, respectively).
Please choose the correct answers from the following options:

A) BPG is a negative heterotropic effector (stabilizes T state, so R-T equilibrium shifts toward R state in absence of BPG).
Thus, hemoglobin binds O2 more tightly (lower P50) with less 2,3-BPG bound (curve A).

B) H+ binding stabilizes T state (protons are negative heterotropic effectors), so

higher [H+] (lower pH) shifts R-T equilibrium toward the T state (weaker O2
binding affinity). Weaker binding (higher P50), i.e., hemoglobin binds O2
more tightly at higher pH and more weakly at lower pH.
C) A) and B) are correct;

18. Suppose you had a mutant hemoglobin in which a crucial hydrogen bond between the α1 and β2 (and thus also between the
α2 and β1) subunits is lost. That hydrogen bond is involved in stabilizing the R state of hemoglobin, so loss of the hydrogen
bond results in a shift in the R-T equilibrium toward the T state. Those hydrogen bonds between the protomers also help
stabilize the quaternary structure of the normal tetrameric hemoglobin, so loss of the hydrogen bonds shifts the tetramer-
protomer equilibrium in the direction of dissociation to the αβ protomers.
Which of the statements below best describe the mutant Hb?
A) The Hill coefficient, nH, would be expected to be lower because the quaternary
structure is shifted toward αβ protomers, with resultant loss of communication
between subunits and thus decrease in slope of Hill plot in the direction of 1. A nH of 1 would mean no communication at all
between binding sites.
B) The mutant's R-T equilibrium is shifted toward the T state, weaker O2 binding,
so P50 of mutant is higher than that of normal HbA.
E) a) and b) are correct.
Hint: Hill equation is shown below. You need to remember the significance of Hill coefficient

21
The changes in the conformation of tetrameric Hb upon O2 binding are shown in the figure below.

19. Suppose that a protein can bind either a small molecule inhibitor I or its natural ligand [L]. Results of 2 experiments in
which the fractional saturation was measured as a function of the concentration of the inhibitor [I] and as a function of the
concentration of ligand [L] are plotted on the graph below.
Which statements are best describing the displayed graph?

A) For the binding of a ligand to a protein, the relationship between the K a (association constant), the Kd (dissociation
constant), and the affinity of the protein for the ligand is described by:
Ka = 1/Kd. The larger the Ka (and hence the smaller the Kd), the higher the affinity of the
protein for the ligand.
B) Kd for ligand=10 uM and Kd for inhibitor (I)=2 uM; the inhibitor binds with higher affinity to the protein than the ligand
(L).
C) A) and b) are correct;
20. What is the role of ATP and ATP hydrolysis in the cycle of actin-myosin association and disassociation that leads to
muscle contraction?

A) ATP binding to myosin results in a conformational change that causes dissociation of actin from the myosin.
B) ATP hydrolysis results in a change of orientation of the myosin relative to the actin filament, which allows movement to the
next actin subunit.
C) This is followed initially by release of the phosphate (Pi) as hydrolysis product, strong binding of the myosin to this actin
subunit, and subsequently, release of the ADP hydrolysis product
E) A), B) and C) are correct.

21. Given the diagram of human immunoglobulin G, choose the best statement which describe the structure of IgG:
A) IgG has both tertiary and quaternary structures.
B) IgG quaternary structure can be described using the formula 2L+2H (where L=light chain and H=heavy chain).
C) The antigen-binding site is determined by the hypervariable regions located within the variable domains of the two light and two
heavy chain.
D) A) and B) are correct; E) All are correct.

22
23. What properties of antibodies make them useful biochemical reagents?
A) The important properties are the high specificity of protein recognition, and the high affinity of the antibody-antigen association.
B) The conformations of the antigen and antigen-binding site of the antibody are influenced by each other and change as binding
occurs. These conformational changes increase the chemical complementarity of the sites and result in tighter binding.
C) Specific binding results from complementarity between the chemical properties (such as size, charge, and hydrophobicity) of the
antigen and the antigen-binding site of the antibody.
E) A), B) and C) are correct.

24. Suppose that the equilibrium dissociation constant of a Fab-antigen complex is 5 x 10–7 M at 25 °C. Which statements
below best describe this equilibrium?
[Fab] + [antigen]  [Fab•antigen]
A) Kd = [Fab][antigen]/[Fab•antigen] and Kassoc = [Fab•antigen]/[Fab][antigen] and Kassoc=2 x 10 6 M– 1
C) Go' dissoc = –RTlnKd; G o' assoc = –RTlnKassoc and Go' dissoc = +35.9 kJ/mol; G o'assoc =-35.9 kJ/mol;
D) A) and C) are correct

25. The figure below shows the two forms of HB carrying CO2 and O2, respectively. Which statements below best describe
the binding of CO2 to normal Hb?

A) 15–20% of CO2 is exported in the form of a carbamate on the amino terminal residues of each of the Hb polypeptide
subunits.
B) The formation of a carbamate yields a proton which can contribute to the Bohr Effect.
C) The carbamate forms additional salt bridges stabilizing the T state, lowering the Hb affinity for O2.
E) A), B) and C) are correct.

31. Which of these amino acid groups would not make a good nucleophilic catalyst?
D) isopropyl

32. Zymogens are a feature of what type of enzymatic control?

B) Covalent modification

36. An enzyme is considered to have evolved to its most efficient form if

B) kcat/KM is near the diffusion-controlled limit;

.
39.Which of these statements about enzyme-catalyzed reactions is false?
A) The activation energy for the catalyzed reaction is the same as for the uncatalyzed reaction, but the equilibrium constant is
more favorable in the enzyme-catalyzed reaction.

23
42. An enzyme catalyzes a reaction at a velocity of 20 mol/min when the concentration of substrate (S) is 0.01 M. The Km for
this substrate is 1 x 10-5 M. Assuming that Michaelis-Menten kinetics are followed, what will the reaction velocity be when the
concentration of S is 1 x 10-6 M?

V0 = Vmax [S]/( Km + [S]) (Michaelis Menten equation)

D) 1.8 umol/min

43. A biochemist obtains the following set of data for an enzyme that is known to follow Michaelis-Menten kinetics.

Substrate Initial
concentration velocity
(uM) (umol/min)
————————————— Estimate the Vmax and select the best answer below:
1 49
2 96
8 349
50 621
100 676
1,000 698
5,000 699

D) Vmax=700 um/min and Km= 8 uM.

44. How does the total enzyme concentration affect turnover number and Vmax?

A) The turnover number, kcat, is the number of substrate molecules converted to product in a given time by a single enzyme
molecule, so turnover number is not affected by the total enzyme concentration, [E t].
B) For any given reaction, however, Vmax can change because Vmax is the product of turnover number x the total enzyme
concentration, or Vmax = kcat [Et].
C) [Et]=[E] + [ES]; D) A) and B) are correct; E) A), B) and C) are correct.

45. The turnover number for an enzyme is known to be 5000 min -1. From the following set of data, calculate the Km and the
total amount of enzyme present in these experiments.

Substrate Initial
concentration velocity
(mM) (umol/min)
1 167
2 250
4 334
6 376
100 498
1,000 499

D) Km = 2.0 mM. Total enzyme = _0.1_umol;

49. Chymotrypsin belongs to a group of proteolytic enzymes called the “serine proteases,” many of which have an Asp, His,
and Ser residue that are crucial to the catalytic mechanism. The serine hydroxyl functions as a nucleophile. Which of the
statements below are true?!

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 A) In chymotrypsin, histidine functions as a general base, accepting a proton from the serine hydroxyl, thereby increasing
serine's reactivity as a nucleophile. The negatively charged Asp stabilizes the positive charge that develops on the His.
B) The substantially increase in the electronegativity of the serine oxygen, which makes it a much stronger nucleophile lowers
the activation energy of the covalent catalysis between serine and the carbonyl carbon of the substrate peptide bond.
C) The process of general base catalysis is illustrated by the number ---1-----, and the process of covalent catalysis is illustrated
by the number -----2----.
D) A), B) and C) are correct.

50. The allosteric enzyme ATCase is regulated by CTP, which is a negative allosteric regulator. CTP binds to an allosteric
pocket of ATC-ase and stabilizes:

D) the T state and the binding with lower affinity of its substrate aspartate.

In the figure below secondary structure elements are shown. 1=‘anti-paralllel’ beta-sheets, 2=‘parallel’ beta-sheets

Hydroxylation of proline residues in the collagen is catalyzed by the enzyme prolyl hydroxylase.
Which of the following statements best describe this reaction:
A. The enzyme prolyl hydroxylase requires ascorbic acid (vitamin C), Fe2+ and molecular oxygen.
25
 B. The lack of vitamin C is associated with the “scurvy” disease.
C. The lack of HO-Pro (hydroxy proline) interchain H-bond formation is impaired, as is the formation of a stable triple helix.
D. A, B and C are all correct.

Which one of the following statements concerning the binding of oxygen by hemoglobin is correct?
A. The Bohr effect results in a lower affinity for oxygen at lower pH values.
C. The oxygen affinity of hemoglobin increases as the percentage saturation increases.
E. A and C are both correct.

Which one of the following statements concerning the binding of CO2 (carbon dioxide) by hemoglobin is correct? B. Carbon
dioxide decreases oxygen affinity because it lowers the pH; C. Binding of carbon dioxide to the N-termini stabilizes the taut, deoxy
form. D. Both B and C are correct.

Which one of the following statements concerning the titration curve for a nonpolar amino acid is correct? The letters A
through D designate certain regions on the curve below.
A. Point A represents the region where the amino acid is protonated.
B. Point B represents a region of maximal buffering.
C. Point C represents the region where the net charge on the amino acid is zero (the pI).
E. Answers A, B and C are correct

Which of the following statements are true about the oxyhemoglobin?

A) His E7 (distal) is not a ligand to the porphyrin ring Fe 2+ ion, rather it helps the real ligand, molecular oxygen to coordinate the iron.
B) His F8 (proximal) and the nitrogen atoms in the porphyrin ring are ligands to the porphyrin ring Fe 2+ ion.
C) The oxyhemoglobin has the “R” (relaxed) state in the quaternary structure.
E) A.B and C are correct.

While the binding of O2 to myoglobin as a function of pO2 is described by a simple___-curve, the binding to hemoglobin is
26
described by a more complex ______ curve. hyperbolic; sigmoidal

The graph shows the results of reaction rate vs substrate concentration for a(n): A sigmoidal plot, corresponding to an
allosterically regulated enzyme.

63. The following pictures depict different motifs and domains. Please choose the best match:

1 =beta hairpin 2=beta-alpha-beta motif 3= alpha/alpha motif 4=helix-turn-helix 5=Ca2+ binding domain 6=four helix bundle
7=beta sandwich 8= beta barrel 9=alpha/beta barrel

53. In the figure below identify the level of protein structure and chose the correct answer(s):

27
 A. .
B. The figure displays the tertiary structure of a protein which is stabilized by many non-covalent forces and disulfide bonds.
C. The interactions of the R (side chains) groups of the amino acids from the primary structure give a protein its specific three-
dimensional tertiary structure.
D. The tertiary structure is stabilized by: hydrophobic and hydrophilic interactions, salt bridges. hydrogen bonds, disulfide
bonds and involves interactions and cross-links between different parts of the peptide chain
E. B, C and D are correct.

The salting in of proteins can be explained by: salt counter-ions reducing electrostatic attractions between protein molecules.

Enzymes that hydrolyze the internal peptide bonds (not the peptide bonds of the terminal amino acids) of a protein are:
endopeptidases.

In two homologous proteins, which residue is most likely to replace a Glu residue as a conservative substitution? Asp

Proteins are often constructed from multiple segments of 40-200 amino acid residues, commonly called domains

Although a protein’s primary sequence can be inferred from the nucleotide sequence, modifications such as __ can only be
determined by direct protein sequencing.
A) phosphorylation B) disulfide crosslinks C) the addition of carbohydrate groups D) the addition of acetyl groups E) all of
the above

The Edman degradation is used to: Determine a protein’s N-terminal amino acid

An enzyme-linked immunosorbent assay requires: an antibody that binds the protein of interest.

In a Ramachandran diagram, __ of the area represents allowed conformations of a polypeptide chain. less than 25%

In a protein, the most conformationally restricted amino acid is ___; the least conformationally restricted is __. Pro, Gly

Conformation(s) that has (have) both a favorable hydrogen bonding pattern and  and  values that fall within the allowed
Ramachandran conformational regions is (are) _. A) alpha helix B) collagen helix C) beta sheet D) All of the above

Which one of these characteristics is not true for the alpha helix? There is a requirement for glycine every third amino acid
residue.

Which of these characteristics does not describe the beta sheet? Parallel beta sheets containing fewer than five chains are the most
common.

Which statement below does not describe fibrous proteins? Domains are compact and globular.

Which of the following statements about keratin is false? The classification of keratin as “hard” or “soft” is determined by the
proportion of proline residues.

28
Which of the following statements does not apply to collagen? Hydrogen bonds between the -OH groups of Hyp residues stabilize
the helix.

In the absence of ascorbic acid, prolyl oxidase is unable to oxidize proline residues in collagen to hydroxyproline, resulting in:
the disease scurvy

Of the following, which amino acid is least likely to be found on the surface of a single-subunit protein? Trp

The first step in the folding of disordered polypeptide chains into stable proteins is the formation of: secondary structural
elements

Secondary structural elements are often observed in groupings commonly called___. motifs

The classic experiment demonstrating that reduced and denatured RNase A could refold into the native form demonstrates
that _______. 1° structure can determine 3° structure

The tendency of nonpolar molecules to aggregate in a water medium is called ___. Hydrophobic effect

If the free energy change G for a reaction is –46.11 kJ/mol, the reaction is: exergonic.

In a conjugated protein, a prosthetic group is: E) a part of the protein that is not composed of amino acids. (such as sugar, lipid,
hemes, etc).

Below are depicted the major levels of protein structure. Match the best choices:

1 2

3 4
1=primary, 2=secondary, 3=tertiary, 4=quaternary

The Greek key is associated with which of the following? Antiparallel beta-pleated sheets

29