Chapter 2 Water, Weak Bonds, and the Generation of Order Out of
Chaos
Matching Questions
Use the following to answer questions 1–10:
Choose the correct answer from the list below. Not all of the answers will be used.
a) ionic bonds or salt bridges
b) Brownian motion
c) hydrophobic
d) hydrogen
e) polar
f) nonpolar
g) van der Waals
h) entropy
i) ion product of water
j) amphipathic
k) positive
l) dielectric constant
m) negative
1.
____________: The type of bond found between an oxygen on one water molecule and
hydrogen on a different water molecule.
2.
Movement of particles due to the random fluctuations of energy content of the environment is
known as ____________.
Ans:
b
Section: 2.1
3.
Electrostatic interactions between atoms with opposite electrical charges are also called
____________.
Ans:
Section: 2.3
4.
Water weakens the electrostatic interaction of ions due to its high ____________.
Ans:
Section: 2.3
5.
The distance when two atoms no longer repulse each other yet have the strongest attraction is
known as the____________ contact distance.
Ans:
g
Section: 2.3
Ans:
d
Chapter 2 Water, Weak Bonds, and the Generation of Order Out of Chaos
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6.
____________: Thermodynamic force that drives hydrophobic interactions.
7.
____________: A molecule with two distinctive chemical properties or characteristics.
Ans:
Section: 2.4
8.
Which type of amino acid is responsible for increasing entropy as a protein folds?
Ans:
Section: 2.4
9.
____________: The charge on acetic acid when the pH is more than one pH unit above the pKa.
Section: 2.5
10.
____________: The charge of an amino group when the pH is one pH unit below the pKa.
Ans:
k
Section: 2.5
Fill–in-the-Blank Questions
11.
Molecules that are readily soluble in water are considered .
Ans: polar Section 2.2
12.
The force that is quantified by Coulomb’s law is called .
Ans: ionic or electrostatic interaction Section 2.3
13.
A solvent with a low dielectric constant would be a solvent for salts.
Ans: poor Section 2.3
14.
The transient force, which while weak, still has a large impact on how macromolecules interact
is the .
Ans: van der Waals interaction Section 2.3
15.
Hydrophobic molecules are driven together by , not because they have an affinity for each
other.
Ans: entropy Section 2.4
16.
Lipids that interact with both the water and the hydrophobic regions of the membrane are
considered .
Ans: amphipathic Section 2.4
17.
An acid ionizes to form a proton and its .
Ans: base or conjugate base Section 2.5
Ans:
h
Section: 2.4
Chapter 2 Water, Weak Bonds, and the Generation of Order Out of Chaos
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18.
When the pH is more than two pH units above the pKa of a carboxyl group, the acid is .
19.
Buffers are critical in maintaining proper levels in biological systems.
Ans: pH Section 2.5
20.
The source of the key buffering component of blood is .
Ans: carbon dioxide Section 2.5
Multiple-Choice Questions
21.
What is the H+ concentration in a urine sample that has a pH of 6?
A) 10−6 M
B) 10−8 M
C) 106 M
D) 10−14 M
E) 8 M
Ans: A Section: 2.5
22.
Which of the following is considered a noncovalent bond?
A) electrostatic interactions
B) hydrogen bonds
C) van der Waals interactions
D) All of the above.
E) None of the above.
Ans: D Section: 2.3
23.
What charged group(s) is/are present in glycine at a pH of 7?
A) –NH3+
B) –COO−
C) –NH2+
D) A and B
E) A, B, and C
Ans: D Section: 2.5
24.
Water can form hydrogen bonds with the ___________ of another molecule.
A) carbonyl groups
B) amine groups
C) aromatic rings
D) alcohol groups
E) A, B, and D
Ans: E Sections: 2.3 & 2.4
Ans: unprotonated Section 2.5
Chapter 2 Water, Weak Bonds, and the Generation of Order Out of Chaos
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25.
What pairs of atoms in nucleotide bases are involved in hydrogen bonds?
A) N–H and C═O
B) N–H and S–H
C) O–H and P–O
D) All of the above.
E) None of the above.
26.
Typical van der Waals energies are about:
A) 4–20 kJ/mol.
B) 2–4 kJ/mol.
C) 200 kJ/mol.
D) All of the above.
E) None of the above.
Ans: B Section: 12.3
27.
What two properties of water are important for biological interactions?
A) the polarity of water
B) the density of water
C) the cohesive properties of water
D) A and C
E) B and C
Ans: D Section: 2.2
28.
List atoms commonly found in biological molecules that are often hydrogen-bond acceptors.
A) carbon
B) oxygen
C) nitrogen
D) B and C
E) All of the above.
Ans: D Section: 2.3
29.
What happens to nonpolar molecules in water?
A) They dissolve independently.
B) They aggregate together.
C) They precipitate.
D) All of the above.
E) None of the above.
Ans: B Section: 2.3
30.
What is the [A−]/[HA] ratio when the weak acid is in a solution one pH unit above its pKa?
A) 1:1
B) 1:10
C) 10:1
D) 2:1
E) None of the above.
Ans: C Section 2.3
Ans: A Section: 2.3
Chapter 2 Water, Weak Bonds, and the Generation of Order Out of Chaos
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31.
What are the primary chemical components present in a phosphate buffer at pH 7.4?
A) H3PO4 and PO4−3
B) H2PO4− and PO4−3
C) HPO4-2 and PO4-3
D) H2PO4− and HPO4−2
E) H3PO4 and HPO4−2
32.
What is the concentration of acetic acid in 250 ml of a 100 mM acetate buffer at pH 4.76?
A) 250 mM
B) 100 mM
C) 50 mM
D) 75 mM
E) There is not enough information to tell.
Ans: C Section 2.5
33.
Climate scientists are concerned with the ongoing decrease in the pH of the Earth’s oceans.
Based on what you know about weak acid/base equilibria, which of the following would
contribute to ocean acidification?
A) An increase in phosphate containing fertilizers from river runoff causes a shift in phosphoric
acid equilibrium.
B) An increase in atmospheric CO2 causes a shift in carbonic acid equilibrium.
C) An increase in atmospheric SO2 emissions causes a shift in sulfuric acid equilibrium.
D) All of the above.
E) None of the above.
Ans: B Section: 2.5
34.
Citric acid is an important intermediate in glucose metabolism and is synthesized in
mitochondrial matrix. The three pKa values for each of the carboxylic acids are 3.1, 4.8, and 6.4.
What would the charge be on a citrate molecule formed in the mitochondrial matrix where the
pH is 7.8?
A) +3
B) +2
C) -3
D) -2
E) None of the above.
Ans: C Section 2.5
Ans: D Section 2.5
Chapter 2 Water, Weak Bonds, and the Generation of Order Out of Chaos
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35.
A student observes that when an unknown molecule is added to water, it forms micelles. What
can this student infer about this phenomenon?
A) The unknown molecule is amphipathic.
B) The micelle formation is driven by the resulting decrease in entropy of water.
C) The unknown molecule forms many van der Waals interactions with water.
D) Micelle formation is driven by the hydrophilic effect.
E) All of the above.
Short-Answer Questions
36.
Using Coulomb’s law, describe how water is an ideal solvent for the ions found in cells?
two ions dissolved in water.
Section: 2.3
37.
What is the significance of hydrogen bonding in biochemical structures such as DNA?
Ans:
The bonds are weak enough to be easily disrupted; yet when many are present in large
numbers, they provide the stabilization necessary for larger structures such as DNA.
Section: 2.3
38.
What is an electrostatic interaction? Give an example.
Section: 2.3
39.
How is water able to be a solvent for so many biological molecules?
act as a donor.
Section: 2.2
40.
What is the net effect of many van der Waals interactions?
substantially affect and stabilize the interaction.
Section: 2.3
41.
How is protein folding driven?
This causes an increase in the entropy of water and thermodynamically drives protein
folding.
Ans: A Section 2.4
Chapter 2 Water, Weak Bonds, and the Generation of Order Out of Chaos
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42.
If noncovalent bonds are so much weaker than covalent bonds, how do they stabilize large
biochemical structures?
43.
What thermodynamic and free-energy changes participate in protein folding?
Ans:
A combination of hydrogen bonds and van der Waals forces affect enthalpy and the
entropy associated with hydrophobic interactions.
Section: 2.4
44.
How do hydrophobic interactions aid in membrane formation?
Section: 2.4
45.
Give examples of key functional groups found in biochemistry.
Ans:
hydrophobic, hydroxyl, aldehyde, keto, carboxyl, amino, phosphoryl, sulfhydryl
Section: 2.5, Table 2.1
46.
Draw a titration curve for the ionization of acetic acid.
Ans:
The curve should look like Figure 2.12.
Section: 2.5
47.
Why are conjugate acid–base pairs so important in biological systems?
little effect on the pH.
Section: 2.5
Ans:
There is stability in numbers.
Section: Introduction
Chapter 2 Water, Weak Bonds, and the Generation of Order Out of Chaos
8
48.
Tris buffers are commonly used in biochemistry labs because they buffer within the
physiological range of 7.1 to 9.1 due to a pKa of 8.1. To demonstrate the buffering capacity of
Tris buffer, your biochemistry lab teaching assistant has given you one liter of a 0.1 M Tris
buffer at pH 7.4. Add 2 mL of 1M HCl to this buffer and calculate what the new pH will be.
New [HA] = 0.083 M + 0.02 M = 0.085M HA
Using the Henderson-Hasselbalch equation, recalculate the new pH.
pH = 8.1 + log (0.015)/0.08 = 7.35
Section: 2.5