BCH 5045

GRADUATE SURVEY OF BIOCHEMISTRY

EXAM 1

SPRING, 2005

February 11, 2005

Name:
Yellow means correct answer.
Multiple choice and true/false 2 pts each; circle the letter for the correct answer.
1. Enzymes are potent catalysts because they:
A) are consumed in the reactions they catalyze.
B) are very specific and can prevent the conversion of products back to substrates.
C) drive reactions to completion while other catalysts drive reactions to equilibrium.
D) increase the equilibrium constants for the reactions they catalyze.
E) lower the activation energy for the reactions they catalyze.
2. The role of an enzyme in an enzyme-catalyzed reaction is to:
A)
B)
C)
D)
E)

bind a transition state intermediate, such that it cannot be converted back to substrate.
ensure that all of the substrate is converted to product.
ensure that the product is more stable than the substrate.
increase the rate at which substrate is converted into product.
make the free-energy change for the reaction more favorable.

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

A)
B)
C)
D)
E)

Their catalytic activity is independent of pH.

They are generally equally active on D and L isomers of a given substrate.
They can increase the equilibrium constant for a given reaction by a thousand fold or more.
They can increase the reaction rate for a given reaction by a thousand fold or more.
To be effective, they must be present at the same concentration as their substrate.

4. Enzymes differ from other catalysts in that only enzymes:

A)
B)
C)
D)
E)

are not consumed in the reaction.

display specificity toward a single reactant.
fail to influence the equilibrium point of the reaction.
form an activated complex with the reactants.
lower the activation energy of the reaction catalyzed.

5. The benefit of measuring the initial rate of a reaction V0 is that at the beginning of a reaction:
A)
B)
C)
D)
E)

[ES] can be measured accurately.

changes in [S] are negligible, so [S] can be treated as a constant.
changes in Km are negligible, so Km can be treated as a constant.
V0 = Vmax.
varying [S] has no effect on V0.

6. Which of the following statements about a plot of V0 vs. [S] for an enzyme that follows Michaelis-Menten kinetics is
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false?
A)
B)
C)
D)
E)

As [S] increases, the initial velocity of reaction V0 also increases.

At very high [S], the velocity curve becomes a horizontal line that intersects the y-axis at Km.
Km is the [S] at which V0 = 1/2 Vmax.
The shape of the curve is a hyperbola.
The y-axis is a rate term with units of m/min.

7. Which of these statements about enzyme-catalyzed reactions is false?

A) At saturating levels of substrate, the rate of an enzyme-catalyzed reaction is proportional to the enzyme
concentration.
B) If enough substrate is added, the normal Vmax of a reaction can be attained even in the presence of a competitive
inhibitor.
C) The rate of a reaction decreases steadily with time as substrate is depleted.
D) 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.
E) The Michaelis-Menten constant Km equals the [S] at which V = 1/2 Vmax.
8. The Lineweaver-Burk plot is used to:
A)
B)
C)
D)
E)

determine the equilibrium constant for an enzymatic reaction.

extrapolate for the value of reaction rate at infinite enzyme concentration.
illustrate the effect of temperature on an enzymatic reaction.
solve, graphically, for the rate of an enzymatic reaction at infinite substrate concentration.
solve, graphically, for the ratio of products to reactants for any starting substrate concentration.

9. To calculate the turnover number of an enzyme, you need to know:

A)
B)
C)
D)
E)

the enzyme concentration.

the initial velocity of the catalyzed reaction at [S] >> Km.
the initial velocity of the catalyzed reaction at low [S].
the Km for the substrate.
both A and B.

10. 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)
B)
C)
D)
E)

dissociation constant.
half-saturation constant.
maximum velocity.
Michaelis-Menten number.
turnover number.

11. In a plot of l/V against 1/[S] for an enzyme-catalyzed reaction, the presence of a competitive inhibitor will alter the:
A)
B)
C)
D)
E)

curvature of the plot.

intercept on the l/[S] axis.
intercept on the l/V axis.
pK of the plot.
Vmax.

12. In competitive inhibition, an inhibitor:

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A)
B)
C)
D)
E)

GRADUATE SURVEY OF BIOCHEMISTRY

SPRING, 2005

binds at several different sites on an enzyme.

binds covalently to the enzyme.
binds only to the ES complex.
binds reversibly at the active site.
lowers the characteristic Vmax of the enzyme.

13. (4 pts)

Define the terms cofactor and coenzyme.

Ans: (A cofactor is any chemical component required for enzyme activity; it includes both organic molecules, called
coenzymes, and inorganic ions.) This is the books answer. However, in this class, cofactor means inorganic elements
such as Mg, K, Cl, Mn, Mo, Ca, Zn that are required for enzymatic activity. Coenzyme is an organic compound that may
or may not contain an inorganic component.

14. (4 pts)

For a reaction that can take place with or without catalysis by an enzyme, what would be the effect of the
enzyme on the:

(a) standard free energy change of the reaction?

(b) activation energy of the reaction?
(c) initial velocity of the reaction?
(d) equilibrium constant of the reaction?
15. (4 pts)

no change
decrease
increase
no change

Why does pH affect the activity of an enzyme?

Ans: The state of ionization of several amino acid side chains is affected by pH, and the activity of many enzymes
requires that certain of the amino acid residue side chains be in a specific ionization state. (See Fig 6-20, p. 215.)

16. 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.
17. A prosthetic group of a protein is a non-protein 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.

18. 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:
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A) hyperbolic.
B) linear with a negative slope.
C) linear with a positive slope.
D) random.
E) sigmoidal.
19. (4 pts)

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

Ans: Induced fit refers to the structural adaptations that occur when a ligand binds to a protein. This often involves a
conformational change in the protein that alters the binding site to make it more complementary to the ligand.

20. All of the following are considered weak interactions in proteins, except:
A) hydrogen bonds.
B) hydrophobic interactions.
C) ionic bonds.
D) peptide bonds.
E) van der Waals forces.
21. The most important contribution to the stability of a proteins conformation appears to be the:
A) entropy increase from the decrease in ordered water molecules forming a solvent shell around it.
B) maximum entropy increase from ionic interactions between the ionized amino acids in a protein.
C) sum of free energies of formation of many weak interactions among the hundreds of amino acids in a protein.
D) sum of free energies of formation of many weak interactions between its polar amino acids and surrounding
water.
E) stabilizing effect of hydrogen bonding between the carbonyl group of one peptide bond and the amino group of
another.
22. In an aqueous solution, protein conformation is determined by two major factors. One is the formation of the
maximum number of hydrogen bonds. The other is the:
A) formation of the maximum number of hydrophilic interactions.
B) maximization of ionic interactions.
C) minimization of entropy by the formation of a water solvent shell around the protein.
D) placement of hydrophobic amino acid residues within the interior of the protein.
E) placement of polar amino acid residues around the exterior of the protein.
23. A sequence of amino acids in a certain protein is found to be -Ser-Gly-Pro-Gly-. The sequence is most probably part
of a(n):
A) antiparallel sheet.
B) parallel sheet.
C) helix.
D) sheet.
E) turn.
24. (4 pts)
Any given protein is characterized by a unique amino acid sequence (primary structure) and threedimensional (tertiary) structure. How are these related?
Ans: The three-dimensional structure is determined by the amino acid sequence. This means that the amino acid sequence
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contains all of the information that is required for the polypeptide chain to fold up into a discrete three-dimensional shape.
25. (4 pts)

Name four factors (bonds or other forces) that contribute to stabilizing the native structure of a protein,
and describe one condition or reagent that interferes with each type of stabilizing force.

Ans: Among forces that stabilize native protein structures are (a) disulfide bonds, (b) hydrogen bonds, (c) hydrophobic
interactions, and (d) ionic interactions. Agents that interfere with these forces are (a) mercaptoethanol or dithiothreitol, (b)
pH extremes, (c) detergents and urea, and (d) changes in pH or ionic strength, respectively.
26. (4 pts)

What are four structural characteristics common to all amino acids found in naturally occurring proteins?

Ans: All amino acids found in naturally occurring proteins have an carbon to which are attached a carboxylic acid, an
amine, a hydrogen, and a variable side chain. All the amino acids are also in the L configuration.

27. (4 pts)

Why do amino acids, when dissolved in water, become zwitterions?

Ans: Near pH = 7, the carboxylic acid group (COOH) will dissociate to become a negatively charged COO group,
and the NH2 amino group will attract a proton to become a positively charged NH3+ group.

28. Which of these statements about hydrogen bonds is not true?

A)
B)
C)
D)
E)

Hydrogen bonds account for the anomalously high boiling point of water.
In liquid water, the average water molecule forms hydrogen bonds with three to four other water molecules.
Individual hydrogen bonds are much weaker than covalent bonds.
Individual hydrogen bonds in liquid water exist for many seconds and sometimes for minutes.
The strength of a hydrogen bond depends on the linearity of the three atoms involved in the bond.

29. Hydrophobic interactions make important energetic contributions to:

A)
B)
C)
D)
E)

binding of a hormone to its receptor protein.

enzyme-substrate interactions.
membrane structure.
three-dimensional folding of a polypeptide chain.
all of the above are true.

30. The pH of a solution of 1 M HCl is:

A)
B)
C)
D)
E)

0
0.1
1
10
1

31. Which of the following is true about the properties of aqueous solutions?
A)
B)

A pH change from 5.0 to 6.0 reflects an increase in the hydroxide ion concentration ([OH-]) of 20%.
A pH change from 8.0 to 6.0 reflects a decrease in the proton concentration ([H+]) by a factor of 100.
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C)
D)
E)

GRADUATE SURVEY OF BIOCHEMISTRY

SPRING, 2005

Charged molecules are generally insoluble in water.

Hydrogen bonds form readily in aqueous solutions.
The pH can be calculated by adding 7 to the value of the pOH.

32. Which of the following properties of water does not contribute to the fitness of the aqueous environment for living
organisms?
A) Cohesion of liquid water due to hydrogen bonding.
B) High heat of vaporization.
C) High specific heat.
D) The density of water is greater than the density of ice.
E) The very low molecular weight of water.
33. (4 pts)

Name and briefly define four types of noncovalent interactions that occur between biological molecules.

Ans: (1) Hydrogen bonds: weak electrostatic attractions between one electronegative atom (such as oxygen or nitrogen)
and a hydrogen atom covalently linked to a second electronegative atom; (2) electrostatic interactions: relatively weak
charge-charge interactions (attractions of opposite charges, repulsions of like charges) between two ionized groups; (3)
hydrophobic interactions: the forces that tend to bring two hydrophobic groups together, reducing the total area of the two
groups that is exposed to surrounding molecules of the polar solvent (water); (4) van der Waals interactions: weak
interactions between the electric dipoles that two close-spaced atoms induce in each other.
34. (4 pts)

Explain with an appropriate diagram why amphipathic molecules tend to form micelles in water. What
force drives micelle formation?

Ans: Micelle formation minimizes the area of the hydrophobic part of amphipathic molecules that contacts the polar
solvent, water. Hydrophobic interactions between hydrophobic moieties are the driving force for micelle formation.
When amphipathic molecules form micelles in water, the entropy decrease due to the formation of ordered arrays of water
molecules around the hydrophobic moieties is minimized. (See Fig. 2-7, p. 53.)
35. (4 pts)

Phosphoric acid (H3PO4) has three dissociable protons, with the pKas shown below. Which form of
phosphoric acid predominates in a solution at pH 4? Explain your answer.
Acid
H3PO4

pKa
2.14

6.86

HPO42

12.4

H2PO4

Ans: At pH 4, the first dissociable proton (pKa = 2.14) has been titrated completely,
and the second (pKa = 6.86) has just started to be titrated. The dominant form at pH
4 is therefore H2PO4, the form with one dissociated proton (see Fig. 2-16).

36. Stereoisomers that are nonsuperimposable mirror images of each other are known as:
A) anomers.
B) cis-trans isomers.
C) diastereoisomers.
D) enantiomers.
E) geometric isomers.
37. The enzyme fumarase catalyzes the reversible hydration of fumaric acid to l-malate, but it will not catalyze the
hydration of maleic acid, the cis isomer of fumaric acid. This is an example of:
A) biological activity.
B) chiral activity.
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C) racemization.
D) stereoisomerization.
E) stereospecificity.
38. (4 pts)

Differentiate between configuration and conformation.

Ans: Configuration denotes the spatial arrangement of the atoms of a molecule that is conferred by the presence of either
double bonds, around which there is no freedom of rotation, or chiral centers, which give rise to stereoisomers.
Configurational isomers can only be interconverted by temporarily breaking covalent bonds. Conformation refers to the
spatial arrangement of substituent groups that, without breaking any bonds, are free to assume different positions in space
because of the freedom of bond rotation.
39. (4 pts)

Protein A has a binding site for ligand X with a Kd of 10-6M. Protein B has a binding site for ligand X with a
Kd of 10-9 M. Which protein has a higher affinity for ligand X? Explain your reasoning. Convert Kd into Ka
for both proteins. (This is a question from the recommended problem set).

Ans: Protein B has a higher affinity for ligand X. The lower Kd indicates that protein B will be half-saturated with bound
ligand X at a much lower concentration of X than will protein A. Because Ka = 1/Kd, protein A has a Ka = 106 M-1; protein B
has a Ka = 109 M-1.