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MOLECULAR BIOLOGY OF THE CELL, SIXTH EDITION

CHAPTER 2: CELL CHEMISTRY AND BIOENERGETICS
© Garland Science 2015
1. Which of the following elements is not normally found in cells?

A. Copper
B. Iron C.
Silver D.
Cobalt E.
Zinc
2. A hydrophobic molecule is typically …

A. able to form hydrogen bonds with itself but not with water.
B. able to form hydrogen bonds with water.
C. charged.
D. hard to dissolve in a solvent.
E. incapable of interacting favorably with water.
3. For each of the following pairs, indicate whether they interact via hydrogen bonds (H) or
ionic bonds (I), or do not favorably interact (N). Your answer would be a four-letter string
composed of letters H, I, and N only, e.g. HNNI.
( ) ATP and Mg2+
( ) Urea and water
( ) Glucose and the enzyme hexokinase (which uses glucose as a substrate)
( ) A phospholipid tail and inorganic phosphate
4. Which of the following chemicals do you NOT expect to be readily dissolved in water?
A. Uric acid
B. Hexane
C. Glycerol
D. Ethanol
E. Potassium chloride
5. Weak noncovalent attractions in the cell can be very strong in a nonaqueous environment.
Some of these attractions are as strong as covalent interactions in a vacuum (their bond energy is
approximately 340 kJ/mole), but become more than twenty-five times weaker (their bond energy
becomes approximately 13 kJ/mole) in water. What type of attraction shows this phenomenon?
A. Electrostatic attractions
B. Hydrogen bonds
C. van der Waals attractions
D. Hydrophobic force
E. All of the above
6. The bond energies associated with noncovalent attractions in the cell are too weak to
resist disruption by thermal motion. However, cellular macromolecules can interact specifically
AND strongly with each other (or fold by themselves) merely via such interactions. How is this
possible?
A. The bond energies increase radically when two interacting molecules approach each
other.
B. The interacting molecules also fortify their binding via covalent bonds to keep them
from dissociation.
C. Many weak bonds together in a complementary geometry can afford a strong binding.
D. The cell lowers its internal temperature to reduce thermal motion of molecules and
enhance the weak attractions.
7. What is the pH of a 10–8 M solution of hydrochloric acid? Round the pH value to the
nearest integer, e.g. 10.
A. 8
B. 7
C. 6
D. 5
E. 4
8. The cell can change the pH of its internal compartments using membrane transport
proteins that pump protons into or out of a compartment. How many protons should be pumped
into an endocytic vesicle that is 10–15 liters in volume and has a neutral pH in order to change the
pH to 5? Avogadro‘s number is 6 × 1023. Omit complications such as the membrane potential,
buffers, and other cellular components.
A. 6000
B. 60,000
C. 120,000
D. 600,000
E. 6,000,000
9. Which of the following is true regarding a fatty acid molecule in water?

A. It is positively charged at physiological pH, but can become neutral when the pH is
high enough.
B. It is positively charged at physiological pH, but can become neutral when the pH is
low enough.
C. It is negatively charged at physiological pH, but can become neutral when the pH is
high enough.
D. It is negatively charged at physiological pH, but can become neutral when the pH is
low enough.
E. It is not charged at physiological pH.
10. The amino acid serine has an amino group, a carboxyl group, and a hydroxyl group.
Which of the following better represents the structure of this amino acid at neutral pH?
A B C
H O H O H O
+ – +
H3N C C O 3 C C NH 3
+ C C O–
HN 2 HN
CH3 OH CH2
OH
D H O E H O H O
H3N+ C C H H2N C C N C C H
OH OH H OH
11. The three families of cellular macromolecules are polymerized and depolymerized by a
general mechanism involving water. Each of them has a set of monomers whose polymerization
changes the total free energy of the system. Which of the following statements is true regarding
these macromolecules?
A. Each polymerization step requires free-energy input and proceeds by the consumption
of one water molecule.
B. Each depolymerization step requires free-energy input and proceeds by the
consumption of one water molecule.
C. Each polymerization step requires free-energy input and proceeds by the release of
one water molecule.
D. Each depolymerization step requires free-energy input and proceeds by the release of
one water molecule.
12. Sort the following from a low to a high contribution to the total mass of an E. coli
bacterium. Your answer would be a four-letter string composed of letters A to D only, e.g.
DCBA.
(A) Water
(B) Sugars
(C) Proteins
(D) Nucleic acids
13. Which of the following statements is true regarding cellular metabolism?

A. A living organism decreases the entropy in its surroundings.
B. During catabolism, heat is generated, and the cell uses this heat to perform work
during anabolism.
C. The heat released by an animal cell as part of its metabolic processes comes from the
bond energies in the foodstuffs that are consumed by the animal.
D. Living organisms defy the second law of thermodynamics, but still obey the first law.
14. The folding of proteins can be considered a simple conversion from the unfolded to the
natively folded state. At about 27°C (or 300 K), the free-energy change of folding for a particular
protein is measured to be –40 kJ/mole. If the enthalpy change (ΔH) of folding is –640 kJ/mole,
what is the entropy change (ΔS) of folding for this protein? Write down your answer with the
appropriate sign (+ or –) and in kJ/mole/K, e.g. –1000 kJ/mole/K.
15. Which of the following correctly summarizes the overall process of photosynthesis?
A. CO2 + O2 → H2O + sugars
B. CH2O + CO2 + O2 → H2O + sugars
C. CO2 + H2O → H2 + CO2
D. CO2 + H2O → O2 + sugars
16. Which of the following statements is true regarding reactions involving oxidation and
reduction?
A. The carbon atom is more oxidized in formaldehyde (CH2O) than in methanol
(CH3OH).
B. Oxidation of food in all organisms requires oxygen.
C. A molecule is oxidized if it gains an electron (plus a proton) in a reaction.
D. A dehydrogenation reaction is a reduction.
E. In an organic molecule, the number of C–H bonds increases as a result of oxidation.
17. Enzymes are the cell‘s catalyst crew. They make the life of the cell possible by carrying
out various reactions with astounding performance. Which of the following is NOT true
regarding cellular enzymes?
A. Enzymes lower the activation energy of the reactions that they catalyze.
B. Enzymes can specifically drive substrate along certain reaction pathways.
C. Enzymes can push energetically unfavorable reactions forward by coupling them to
energetically favorable reactions.
D. Enzymes are proteins, but RNA catalysts, called ribozymes, also exist.
E. Enzymes can change the equilibrium point for reactions that they catalyze.
18. In the following diagram showing the reaction pathway for a simple single-substrate
enzymatic reaction, which of the quantities corresponds to the activation energy of the forward
reaction?
a
Total energy
b
c
Reaction pathway
A. (a – b)
B. (a + b)
C. (a – c)
D. (a + c)
E. (b – c)
19. In the following diagram showing the distribution of thermal energy in a population of
substrate molecules, the energy thresholds indicated by numbers represent ...
Number of molecules
1 2
Energy per molecule
A. the activation energy at high and low temperature.

B. the reaction rate at high and low pH.
C. the activation energy with and without an enzyme.
D. the reaction rate at high and low substrate concentrations.
E. the activation energy at high and low substrate concentrations.
20. A cellular enzyme catalyzes the catabolic reaction shown below. Its coenzyme is shown
in the box. Which of the following is correct regarding this reaction?
State 1 State 2
A. The substrate is reduced in this reaction and the coenzyme is converted from state 1 to
state 2.
B. The substrate is oxidized in this reaction and the coenzyme is converted from state 1
to state 2.
C. The substrate is reduced in this reaction and the coenzyme is converted from state 2 to
state 1.
D. The substrate is oxidized in this reaction and the coenzyme is converted from state 2
to state 1.
21. The molecules inside the cell constantly collide with other molecules and diffuse through
the cytoplasm in a random walk. The average net distance traveled by such a molecule after a
certain time period t is proportional to the square root of t, i.e. (t)0.5, as well as to its diffusion
coefficient. If, on average, it takes a molecule 100 milliseconds to travel a net distance of 0.5 µm
from its starting point, how long would it normally take for the same molecule to travel a net
distance of 5 µm from the same starting point?
A. 0.2 second
B. 0.3 second
C. 1 second
D. 10 seconds
E. 0.32 seconds
22. Sort the following molecules from a low to high rate of diffusion inside the cytosol. Your
answer would be a four-letter string composed of letters A to D only, e.g. ADCB.
(A) Myoglobin (a protein)
(B) Glycine (an amino acid)
(C) Ribosome (a protein–RNA complex)
(D) CO2
23. The equilibrium constant for the reaction that breaks down each molecule of substrate A
to one molecule of B and one molecule of C is equal to 0.5. Starting with a mixture containing
only molecules A at 1 M concentration, what will be the concentration of molecule A after reaching
equilibrium under these conditions?
A. 0.5 M B.
0.25 M C.
0.125 M D.
0.333 M E.
0.667 M
24. The free-energy change (ΔG) for a simple reaction, A → B, is 0 kJ/mole at 37°C when
the concentrations of A and B are 10 M and 0.1 M, respectively. What is the free-energy change
for the reaction when the concentrations of A and B are instead 0.01 M and 1 M, respectively?
Recall that ΔG° = –5.9 × log(Keq). Write down your answer as a number with the appropriate
sign (+ or –) and in kJ/mole, e.g. +11.8 kJ/mole.
25. Imagine the reaction A → B with a negative ΔG value under experimental conditions.
Which of the following statements is true about this reaction?
A. The reaction is energetically unfavorable.
B. The reaction proceeds spontaneously and rapidly under these conditions.
C. Increasing the concentration of B molecules would increase the ΔG value (toward
more positive values).
D. The reaction would result in a net decrease in the entropy (disorder) of the universe.
E. The reaction cannot proceed unless it is coupled to another reaction with a positive
value of ΔG.
26. In the first reaction of the glycolytic pathway, the enzyme hexokinase uses ATP to
catalyze the phosphorylation of glucose, yielding glucose 6-phosphate and ADP. The ΔG° value
for this reaction is –17 kJ/mole. The enzyme glucose 6-phosphatase catalyzes a ―reverse‖
reaction, in which glucose 6-phosphate is converted back to glucose, and a phosphate is released.
The ΔG° value for this reaction is –14 kJ/mole. What is the ΔG° value for the following
reaction?
ATP + H2O → ADP + Pi
A. –3 kJ/mole
B. +3 kJ/mole
C. –31 kJ/mole
D. +31 kJ/mole
E. –15.5 kJ/mole
27. The enzyme phosphoglucose isomerase converts glucose 6-phosphate to its isomer
fructose 6-phosphate in the second step of glycolysis. The equilibrium constant for the reaction is
0.36. Evaluating the ΔG° of the reaction (ΔG° = –5.9 × log Keq), decide which of the following
conclusions is true.
A. The ΔG° is negative, therefore the reaction proceeds in the forward direction.
B. The ΔG° is negative, but whether or not the reaction proceeds would depend on ΔG,
not ΔG°.
C. The ΔG° is positive, but in a cell that is active in glycolysis, the reaction can still
proceed in the forward direction.
D. The ΔG° is positive, therefore the reaction proceeds in the reverse direction.
28. Which of the following represents an ―activated‖ carrier molecule?

A. AMP
B. NADH
C. NAD+
D. NADP+
E. CoA
29. ATP is the main energy currency in cells, and it can especially be used to drive
condensation reactions that produce macromolecular polymers. How does ATP normally catalyze
the condensation reaction, which by itself is energetically unfavorable?
A. It transfers its terminal phosphate to an enzyme and is released as ADP.
B. It transfers its two terminal phosphates to an enzyme, and is released as AMP.
C. It covalently attaches to both of the substrates.
D. It transfers either one or two terminal phosphate(s) to one of the substrates and is
released as either ADP or AMP.
E. It covalently attaches to the enzyme, forming an enzyme–AMP adduct.
30. Despite their overall similarity, NADH and NADPH are not used indiscriminately by the
cell. What are the distinctive features of these two carrier molecules?
A. NADPH has an extra phosphate near its nicotinamide ring, giving it distinct electron-
transfer properties.
B. In the cell, NADH is usually in excess over NAD+, but NADP+ is usually in excess
over NADPH.
C. NADH is normally involved in anabolic reactions, whereas NADPH is normally
involved in catabolism.
D. Both NADPH and NADH are recognized by the same enzymes with similar affinities,
since the extra phosphate group in NADPH is not involved in such recognition.
E. In the cell, NADH is found mostly in the form that acts as an oxidizing agent,
whereas NADPH is found mostly in the form that acts as a reducing agent.
31. In an enzymatic reaction involving NADH or NADPH, reduction of a substrate

accompanies the oxidation of these carrier molecules to NAD+ or NADP+, respectively. What
else typically happens in such a reaction?
A. A molecule of water is released to the solution upon completion of the reaction.
B. A proton is released during the oxidation of the carriers.
C. A proton is taken up by the substrate that is being reduced.
D. A proton is taken up by the carrier molecule that is being oxidized.
E. A phosphate group is transferred to the substrate.
32. What is the reaction performed on the molecule labeled as substrate in the following
diagram? What is the name of the activated carrier?
Substrate
Product
A. This is a methylation reaction and the activated carrier is ATP.
B. This is a methylation reaction and the activated carrier is S-adenosylmethionine.

C. This is a carboxylation reaction and the activated carrier is ATP.
D. This is a carboxylation reaction and the activated carrier is carboxylated biotin.
E. This is an acetylation reaction and the activated carrier is acetyl CoA.
33. Under anaerobic conditions, glycolysis provides most of the ATP that the cell needs. In
animal cells, pyruvate, the end product of glycolysis, is converted to lactic acid by lactate
dehydrogenase, as shown below:
CH3(CO)COO– + X →CH3(CHOH)COO– + Y
What is the correct carrier pair (in place of X and Y) in this reaction?
A. X is (ADP + Pi), and Y is (ATP)
B. X is (NADP+), and Y is (NADPH + H+)
C. X is (NAD+), and Y is (NADH + H+)
D. X is (NADH + H+), and Y is (NAD+)
E. X is (NADP++ H+), and Y is (NADPH)
34. Macromolecules in the cell can be made from their monomers using one of two
polymerization schemes. One is called head polymerization, in which the reactive bond required
for polymerization is carried on the end of the growing polymer. In contrast, in tail
polymerization, the reactive bond is carried by each monomer for its own incorporation. In the
figure, indicate the polymerization scheme and the type of macromolecule.
A. Head polymerization of a protein

B. Tail polymerization of a protein
C. Head polymerization of a polysaccharide
D. Head polymerization of a nucleic acid
E. Tail polymerization of a nucleic acid
35. What is the end product of glycolysis in the cytoplasm of eukaryotic cells? How many
carbon atoms does the molecule have?
A. Acetyl CoA; it has two carbon atoms attached to coenzyme A
B. Phosphoenolpyruvate; it has three carbon atoms
C. Glucose 6-phosphate; it has six carbon atoms
D. Pyruvate; it has three carbon atoms
E. Glyceraldehyde 3-phosphate; it has three carbon atoms
36. The substrate for the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase is
glyceraldehyde 3-phosphate (with one phosphate group) while its product is 1,3-
bisphosphoglycerate (with two phosphate groups). Where does the extra phosphate group come
from?
A. From combining two molecules of the substrate
B. ATP
C. Fructose 1,6-bisphosphate
D. Pi
E. NADH
37. Steps 6 and 7 of glycolysis are catalyzed by the enzymes glyceraldehyde 3-phosphate
dehydrogenase and phosphoglycerate kinase, respectively. Together, they ...
A. result in the oxidation of an aldehyde to a carboxylic acid.
B. produce both ATP and NADH.
C. couple the oxidation of a C–H bond to the activation of carrier molecules.
D. catalyze the only glycolytic reactions that create a high-energy phosphate linkage
directly from inorganic phosphate.
E. All of the above.
38. Arsenate is a toxic ion that can interfere with both glycolysis and oxidative
phosphorylation. Arsenate resembles Pi (inorganic phosphate) and can replace it in many enzymatic
reactions. One such reaction is catalyzed by glyceraldehyde 3-phosphate dehydrogenase
in step 6 of glycolysis. Upon completion of the reaction, instead of the normal product, 1,3-
bisphosphoglycerate, the mixed anhydride 1-arsenato-3-phosphoglycerate is formed; this
undergoes rapid spontaneous hydrolysis into arsenate plus 3-phosphoglycerate, the latter being
a normal product of step 7 in glycolysis. What would be the effect of arsenate poisoning in
glycolysis?
A. It results in more ATP and NADH molecules generated for every glucose molecule.
B. It results in fewer ATP molecules generated per glucose molecule, but NADH
generation is not directly affected.
C. It brings glycolysis to an abrupt stop.
D. It results in fewer ATP and NADH molecules generated per glucose molecule.
E. It does not affect the number of ATP or NADH molecules generated per glucose
molecule.
39. Which of the following is true regarding energy production and storage in plants and
animals?
A. Plant and animal cells make starch for long-term energy storage.
B. Most of the ATP in a plant cell has been generated in the chloroplast and transported
to other parts of the cell.
C. Oxidation of one gram of starch releases more energy than oxidation of fat, but since
starch absorbs a lot of water, it is not as efficient as fat in energy storage.
D. Animals, but not plants, can store fats in the form of triacylglycerol (triglyceride).
E. Plant seeds often contain large amounts of fats and starch.
40. What are the molecules that normally supply carbon and oxygen atoms, respectively, for
the citric acid cycle?
A. Oxaloacetate, oxaloacetate
B. Acetyl CoA, O2
C. Oxaloacetate, O2
D. Acetyl CoA, H2O
E. Pyruvate, pyruvate
41. Indicate if each of the following descriptions matches lipids (1), nuc leic acids (2),
polysaccharides (3), or proteins (4). Your answer would be a four-digit number composed of
digits 1 to 4 only, e.g. 1332.
( ) Their monomers contain phosphorus and nitrogen.
( ) They constitute almost half of the cell‘s dry mass.
in
( ) They are the maconstituent of all cellular membranes.
( ) They are largelyhydrophobic and can store ene rgy.
42. Sort the following molecules (A to E) based on the oxidation of the carbon atom, from
higher to lower oxidation states. Your nswer
a would be a five-letter string composed of letters A
to E only, e.g. ADCBE. Put the letter corresponding to the highest oxidation level on the left.
A B C D E
43. Indicate true (T) and false (F) statements below regarding glycolysis. Your answer would
be a four-letter string composed of letters T and F only, e.g. TTTT.
( ) Molecular oxygen is used in glycolysis to oxidize glucose.
( ) Along the glycolytic pathway, ATP is both consumed and generated.
( ) In the course of glycolysis, one molecule of NADH is formed per molecule of
glucose.
( ) Following the production of one molecule of fructose 1,6-bisphosphate, the rest of the
glycolytic pathway generates four molecules of ATP.
44. Fill in the blank in the following paragraph.

―During intense ‗anaerobic‘ physical exercise, the high energy
demand in the muscle cells leads to an accumulation of lactic acid
in these cells and their surrounding tissues. Similarly, the yeast
Saccharomyces cerevisiae can produce ethanol when grown
anaerobically. The lactate or ethanol production takes place in a
process called ...‖
45. Sort the following molecules based on the amount of energy that is released when their
phosphate bond is hydrolyzed as indicated. Your answer would be a four-letter string composed
of letters A to D only, e.g. ADCB. Put the molecule with the highest amount of hydrolysis energy
on the left.
(A) ATP when hydrolyzed to ADP
(B) Glucose 6-phosphate when hydrolyzed to glucose
(C) 1,3-bisphosphoglycerate when hydrolyzed to 3-phosphoglycerate
(D) Phosphoenolpyruvate when hydrolyzed to pyruvate
46. Indicate true (T) and false (F) statements below regarding fatty acid metabolism. Your
answer would be a four-letter string composed of letters T and F only, e.g. TTTT.
( ) Most animals derive their energy from fatty acids between meals.
( ) Fatty acids are converted to acetyl CoA in the cytosol, which is then transported into
mitochondria for further oxidation.
( ) Fatty acids are stored in fat droplets in the form of triacylglycerols.
( ) The breakdown of fatty acids into each acetyl CoA unit requires the hydrolysis of two
ATP molecules.
47. Indicate whether each of the following descriptions matches glycolysis (G) or the Krebs
cycle (K). Your answer would be a four-letter string composed of letters G and K only, e.g. GGGK.
( ) It oxidizes acetyl CoA to CO2.
( ) In eukaryotic cells, it is carried out in the cytosol.
( ) It produces FADH2.
( ) α-Ketoglutarate, one of its intermediates, is used to synthesize the amino acid
glutamic acid.
48. Indicate whether each of the following molecules is an intermediate in glycolysis (G) or
in the tricarboxylic acid cycle (T). Your answer would be a four-letter string composed of letters
G and T only, e.g. GGTT.
( ) Fumarate
( ) Malate
( ) Phosphoenolpyruvate
( ) Succinate
The Citric Acid Cycle: Questions 49-52

The citric acid cycle is summarized in the following figure. Answer the following question(s)
about this cycle.
?
49. In step 1 of the citric acid cycle drawn above, what is the molecule indicated with a
question mark?
A. O2
B. ATP
C. H2O
D. H+
E. Pyruvate
50. In the citric acid cycle shown above, which steps produce CO2 as a by-product? List all
such steps by their number, from the smallest number to the largest. Your answer would be a
number composed of digits 1 to 8 only, e.g. 258.
51. In the citric acid cycle shown above, which steps produce either NADH or FADH2? List
all such steps by their number, from the smallest number to the largest. Your answer would be a
number composed of digits 1 to 8 only, e.g. 258.
52. Aconitase catalyzes an isomerization reaction in the citric acid cycle shown above, in
which H2O is first removed and then added back to the substrate. Which step is catalyzed by this
enzyme? Write down the step number as your answer, e.g. 5.
53. The electron carriers NADH and FADH2 donate their electrons to the electron-transport
chain in the inner mitochondrial membrane, leading to ATP synthesis powered by an H+ gradient
across the membrane. If, on average, the oxidation of each NADH or FADH2 molecule in this
pathway results in the production of 2.5 and 1.5 molecules of ATP, respectively, how many ATP
(and GTP) molecules are produced on average as a result of the complete oxidation of one
molecule of acetyl CoA in the mitochondrion? Consider only the citric acid cycle and oxidative
phosphorylation.
A. 10
B. 12
C. 13.5
D. 14.5
E. 15
54. Indicate true (T) and false (F) statements below regarding the cellular metabolism of
nucleotides and amino acids. Your answer would be a four-letter string composed of letters T and
F only, e.g. TTTT.
( ) Nitrogen fixation occurs in the mitochondria in most animal cells to generate amino
acids.
( ) All 20 natural amino acids must be provided in our diet and are therefore ―essential.‖
( ) There are NO essential nucleotides that must be provided in the diet.
( ) Catabolism of amino acids in our body leads to the production of urea which is
excreted.
Answers
1. Answer: C
Difficulty: 1
Section: The Chemical Components of a Cell
Feedback: Metal ions such as copper, iron, cobalt, and zinc are used as cofactors that are
necessary for the function of some enzymes.
2. Answer: E
Difficulty: 1
Feedback: Hydrophobic molecules usually have no charge and form no or few hydrogen
bonds, and are therefore not favored by the network of hydrogen bonds in liquid water.
They do dissolve in nonpolar organic solvents.
3. Answer: IHHN
Difficulty: 2
Feedback: ATP is negatively charged and can form ionic bonds with magnesium ions. Urea
is highly soluble in water due to its hydrogen-bonding capacity. Similarly, interaction
of a polar molecule like glucose with the active site of an enzyme can be mediated by
hydrogen bonds and other noncovalent (or even covalent) bonds. In contrast, the fatty acid
tails in phospholipids are hydrophobic and do not favorably interact with negatively
charged phosphate molecules.
4. Answer: B
Difficulty: 3
Feedback: Hexane is an alkane hydrocarbon incapable of hydrogen-bonding with water
molecules, which results in an entropically unfavorable state when the two interact. All
the other mentioned chemicals can be readily dissolved in water because they have polar
bonds or can dissociate into ions.
5. Answer: A
Difficulty: 2
Feedback: The probing of the charged ions by water molecules greatly reduces the bond
energy of ionic bonds (electrostatic interactions) in aqueous solutions. Hydrogen bonds
are also weakened in water, but they are not that strong in a vacuum to begin with.
6. Answer: C
Difficulty: 1
Feedback: Although each noncovalent bond is weak, when many of them are formed
simultaneously (in a complementary interface), their energies can sum to produce a tight
binding.
7. Answer: B
Difficulty: 3
Feedback: The concentration of hydronium ions would be the sum of those obtained from
the dissociation of water and the acid: [H3O+] = 10–7 + 10–8 = 1.1 × 10–7. The pH value
will then be calculated as: pH = –log [H3O+] = –log [1.1 × 10–7] = 7 – log (1.1) = 6.96. This
is very close to neutral pH.
8. Answer: A
Difficulty: 3
Section: The Chemical Components of a CellFeedback: The initial number of hydronium
ions would be: [H3O+]1 = 10–15 L × 10–7 mole/L = 10–22 mole. The final number at pH 5
would be: [H3O+]2 = 10–15 L × 10–5 mole/L = 10–20 mole. The difference is: [H3O+]2 –
[H3O+]1 = 9.9 × 10–21 mole. This is equivalent to approximately 6000 protons that need to
be pumped in.
9. Answer: D
Difficulty: 3
Feedback: Due to the presence of the carboxyl group, a fatty acid molecule carries a
negative charge at neutral pH. However, lowering the pH can reverse the ionization of
this group to the neutral (protonated) state.
10. Answer: C
Difficulty: 2
Feedback: The amino and carboxyl groups are common to all amino acids. The serine
side chain contains a hydroxyl group.
11. Answer: C
Difficulty: 2
Feedback: The polymerization reaction generally requires a free-energy input. Also, the
addition of each monomer to the growing polymer is a condensation reaction that is
accompanied by the release of one water molecule. The opposite reaction
(depolymerization) involves hydrolysis and consumes one water molecule.
12. Answer: BDCA
Difficulty: 2
Feedback: Water accounts for about 70% of the total mass in a typical cell. In the remaining
―dry mass,‖ proteins constitute about half, the nucleic acids RNA and DNA are next, and
polysaccharides (and their sugar monomers) are still less abundant.
13. Answer: C
Difficulty: 2
Section: Catalysis and the Use of Energy by Cells
Feedback: For a living animal cell, heat-generating reactions from burning of foodstuffs
are ―coupled‖ to other reactions that increase order inside the cell. Concomitantly, there is
an increase in the overall entropy of the universe (cell plus its environment), with no
violation of the laws of thermodynamics for a spontaneous process.
14. Answer: –2 kJ/mole/K
Difficulty: 3
Feedback: For the folding reaction, the free-energy change can be written as:
ΔG = ΔH – TΔS
Therefore:
ΔS = (ΔH – ΔG)/T = (–640 kJ/mole + 40 kJ/mole) / (300 K) = –2 kJ/mole/K
The negative value of ΔS means a decrease in entropy. This is not unexpected since folding
results in the formation of a single conformation (or a limited set of conformations)
out of an enormous number of possible coils.
15. Answer: D
Difficulty: 2
Feedback: Photosynthesis consumes water and atmospheric CO2 to make simple sugars
and the by-product oxygen.
16. Answer: A
Difficulty: 3
Feedback: Oxidation involves the full or partial removal of electrons from an atom, and
does not necessarily involve oxygen. In the cell, organic molecules usually release a
proton to their surrounding when oxidized in a dehydrogenation reaction, decreasing the
number of C–H bonds in the molecule.
17. Answer: E
Difficulty: 2
Feedback: Enzymes catalyze most cellular reactions by lowering the activation energy,
but they cannot change the equilibrium constant of the reactions that they catalyze; that is,
both forward and reverse reactions are sped up by the same factor. However, they can
selectively drive substrates along one of various cellular metabolic pathways, and can also
couple unfavorable reactions to spontaneous heat-generating reactions.
18. Answer: A
Difficulty: 2
Feedback: The activation energy corresponds to the height of the energy barrier between
the reactant and the product, and is the minimum amount of energy that should be provided
in order for the reaction to proceed.
19. Answer: C
Difficulty: 2
Feedback: In the presence of an enzyme (line 1), the fraction of substrate molecules that
have enough thermal energy to proceed through the reaction is increased compared to that
in the uncatalyzed reaction (line 2).
20. Answer: B
Difficulty: 3
Feedback: This is the reaction catalyzed by the enzyme succinate dehydrogenase in the
citric acid cycle. Succinate is oxidized to fumarate, and the FAD carrier is reduced to
FADH2. By subsequently donating its two electrons to the electron-transport chain, FADH2
will be converted back to FAD for another round of the reaction.
21. Answer: D
Difficulty: 3
Feedback: The net distance of 5 µm is 10 times higher than 0.5 µm, and would on
average take 10 seconds (i.e. 102 × 100 milliseconds) to reach.
22. Answer: CABD
Difficulty: 2
Feedback: In general, larger molecules diffuse more slowly compared to smaller
molecules. Interaction with other molecules (including the solvent) and the shape of the
molecule will also affect the diffusion coefficient.
23. Answer: A
Difficulty: 3
Feedback: The equilibrium constant for this reaction is calculated as:
Keq = 0.5 = [B]eq [C]eq / [A]eq
Since the initial mixture contains only molecule A, it follows that:
[B]eq = [C]eq = 1 M – [A]eq
Combining these equations and solving for [A]eq, we will have:
[A]eq = 0.5 M
which means the molecules B and C will also be present at 0.5 M at equilibrium.
24. Answer: +23.6kJ/mole
Difficulty: 4
Feedback: The free-energy change can be written as:
ΔG = ΔG° + RT ln([B]/[A])
When ΔG is equal to zero, the system is at chemical equilibrium, and
ΔG° = – RT ln([B]eq/[A]eq) = – RT ln(10–2) = –5.9 × log (10–2) = +11.8 kJ/mole
When the concentrations are changed, we have:
ΔG = ΔG° + RT ln([B]/[A]) = ΔG° + RT ln(102) = ΔG° – RT ln(10–2) = 2 ΔG° = +23.6
kJ/mole
25. Answer: C
Difficulty: 3
Feedback: The negative ΔG value indicates that the reaction is favorable under these
conditions and would increase the entropy of the universe. However, unless we know the
steps of the reaction, the ΔG value cannot predict the reaction rate, because the latter
depends on the activation-energy barrier. Finally, the ΔG value changes as the
concentrations of reactants and products change. As the products accumulate, the reaction
will eventually reach an equilibrium, where ΔG is equal to zero.
26. Answer: C
Difficulty: 3
Feedback: The two reactions described in the question can be written as:
ATP + glucose → ADP + glucose 6-phosphate ΔG°= –17 kJ/mole
glucose 6-phosphate + H2O → glucose + Pi ΔG°= –14 kJ/mole
Combining these reactions yields the ATP hydrolysis reaction presented in the question.
Since the free-energy changes are additive, the ΔG° value for this combined reaction is
the sum of the ΔG° values for the two reactions above:
(–17 kJ/mol) + (–14 kJ/mole) = –31 kJ/mole.
27. Answer: C
Difficulty: 3
Feedback: Since the equilibrium constant is less than 1, the log Keq term is negative,
making the ΔG° positive, which means the reaction is unfavorable under standard
conditions. But inside a cell performing glycolysis, a lower concentration of fructose 6-
phosphate than of glucose 6-phosphate can drop ΔG to a negative value. The reaction
thus proceeds in the forward direction, providing a continuous supply of substrate for the
next step in the pathway. Note that due to ―coupling‖ of the reactions in the glycolytic
pathway, and even though some steps can have positive ΔG° values, the overall negative
ΔG° of the pathway can drive the entire chain of reactions in the forward direction, even
under the standard conditions.
28. Answer: B
Difficulty: 1
Feedback: The activated carrier molecules carry chemical groups in high-energy linkages
and can deliver the group or the energy (or both) to metabolic reactions when necessary.
They then need to be activated again. NADH is an activated carrier, while its oxidized form
NAD+ is not.
29. Answer: D
Difficulty: 1
Feedback: By transferring either a phosphate group or a pyrophosphate group to a hydroxyl
group on one of the monomers involved in the polymerization, ATP ―activates‖ the
monomer, making the overall reaction favorable.
30. Answer: E
Difficulty: 3
Feedback: The extra phosphate in NADPH does not affect its electron-transfer properties,
but makes it different enough to be recognized by a different set of enzymes. NADPH
operates chiefly with enzymes that catalyze anabolic reactions, which normally need
reducing power. Accordingly, NADPH is found mostly in its reduced form (i.e. in excess
over NADP+) in the cell. The opposite is true for NADH, which is normally involved in
catabolic reactions.
31. Answer: C
Difficulty: 2
Feedback: In a reduction reaction, NADPH (or NADH) is oxidized, donating a hydride
ion to the substrate. A substrate can also capture a proton from the surroundings, creating
two C–H bonds. The carrier is converted to its oxidized form (NADP+ or NAD+).
32. Answer: D
Difficulty: 2
Feedback: The reaction shown is catalyzed by the enzyme pyruvate carboxylase, which
uses a covalently bound carboxylated biotin to carboxylate pyruvate and produce
oxaloacetate.
33. Answer: D
Difficulty: 3
Feedback: Under anaerobic conditions, NAD+ can be recycled in this reaction (in which
pyruvate is reduced), so that glycolysis can continue in the absence of oxidative
phosphorylation.
34. Answer: E
Difficulty: 2
Feedback: Each nucleotide monomer is activated—at the expense of hydrolysis of two
ATP molecules—into an intermediate carrying a reactive phosphoanhydride bond.
35. Answer: D Difficulty: 1 Section: How Cells Obtain Energy from Food
Feedback: In glycolysis, two pyruvate molecules (each with three carbon atoms) are
produced from each molecule of glucose (with six carbon atoms).
36. Answer: D
Difficulty: 2
Section: How Cells Obtain Energy from Food
Feedback: In step 6 of glycolysis, this enzyme couples the oxidation of the substrate with
the production of NADH, as well as incorporation of inorganic phosphate. The P i is then
transferred to ADP to generate ATP in step 7.
37. Answer: E
Difficulty: 2
Feedback: Please refer to Figure 2–48.
38. Answer: B
Difficulty: 3
Feedback: Since step 7 is bypassed, the ATP molecules that are naturally generated in that
step are no longer produced; however, NADH is still made as before in the first half of step
6. Arsenate also has other effects on cell metabolism that collectively make it a toxic
compound. Please refer to Figure 2–48.
39. Answer: E
Difficulty: 1
Feedback: Compared to the polysaccharides glycogen (in animals) and starch (in plants),
fat is more efficient as a long-term energy storage both per gram and per volume. It can
be stored as triglycerides in both plants and animals, although the types of fatty acids
vary. In plant cells, chloroplasts generate sugars that can be oxidized by the mitochondria
to generate ATP for the cell. The ATP produced in the chloroplast by photosynthesis
cannot be transported out of that organelle.
40. Answer: D
Difficulty: 2
Feedback: One molecule of acetyl CoA enters the cycle by combining with oxaloacetate.
41. Answer: 2411
Difficulty: 2
Feedback: The nucleotides contain one to three phosphate groups and a nitrogen-
containing base, and are polymerized to form long nucleic acid molecules such as DNA.
Proteins are made of amino acids and make up half of the dry mass of the cell, i.e.
approximately 15% of the total cell weight. Lipids have large hydrophobic fatty acid chains
and, in addition to forming bilayer membranes, can store food energy and release it when
necessary.
42. Answer: DAECB
Difficulty: 3
Feedback: As a general rule, in organic molecules, a lower number of C–H bonds
corresponds to more oxidized carbon atoms.
43. Answer: FTFT
Difficulty: 2
Feedback: During the stepwise oxidation of glucose in the course of glycolysis, two
molecules of ATP are used to make fructose 1,6-bisphosphate, which is then cleaved and
eventually converted to two molecules of pyruvate, generating four molecules of ATP and
two molecules of NADH.
44. Answer: fermentation
Difficulty: 1
Feedback: Fermentation is an energy-yielding pathway and is often anaerobic.
45. Answer: DCAB
Difficulty: 2
Feedback: Hydrolysis of phosphoenolpyruvate to pyruvate is the most exergonic (releases
the highest amount of energy). ATP can be generated from ADP upon the hydrolysis of
1,3-bisphosphoglycerate to 3-phosphoglycerate. ATP hydrolysis can be used to drive the
phosphorylation of glucose.
46. Answer: TFTF
Difficulty: 2
Feedback: Between meals, fatty acids stored in the fat droplets in adipocytes in the form
of triacylglycerol are released by hydrolysis and enter the bloodstream. Upon entry into
other cells, they are transported to the mitochondria where they are mostly converted to
acetyl CoA in a step-by-step manner, each step producing one FADH2 and one NADH
molecule.
47. Answer: KGKK
Difficulty: 2
Feedback: In the citric acid cycle (Krebs cycle), which takes place in the mitochondria,
the carbon atoms of acetyl CoA are oxidized and released as CO2, while NADH, FADH2,
and GTP are generated in the process. Many intermediates of the citric acid cycle and
glycolysis are precursors for the biosynthesis of important small molecules in the cell.
48. Answer: TTGT
Difficulty: 2
Feedback: Phosphoenolpyruvate is converted to pyruvate in the last step of glycolysis.
Succinate, fumarate, and malate are three consecutive citric acid cycle intermediates
leading to the regeneration of oxaloacetate.
49. Answer: C
Difficulty: 3
Feedback: In the first step of the citric acid cycle, CoA is hydrolyzed by water after the
formation of a citryl CoA intermediate.
50. Answer: 34
Difficulty: 3
Feedback: Steps 3 and 4 are catalyzed by isocitrate dehydrogenase and the α-ketoglutarate
dehydrogenase complex, respectively, and involve decarboxylation of the substrates and
the release of carbon dioxide.
51. Answer: 3468
Difficulty: 3
Refer to: The Citric Acid Cycle Section: How Cells Obtain Energy from Food
Feedback: Steps 3, 4, and 8 produce NADH, while step 6 produces FADH2.
52. Answer: 2
Difficulty: 2
Feedback: Aconitase converts citrate to isocitrate through an aconitate intermediate
created by dehydration of the substrate.
53. Answer: A
Difficulty: 3
Feedback: The complete oxidation of a molecule of acetyl CoA results in the production
of three NADH molecules plus one FADH2 and one GTP (or ATP) molecule. Therefore,
as a result of oxidative phosphorylation, a total of 10 molecules are generated:
(3 × 2.5) + (1 × 1.5) + 1 = 10
54. Answer: FFTT
Difficulty: 2
Feedback: All known nitrogen-fixing cells are prokaryotic microorganisms. Animals rely
on their dietary intake of protein and nucleic acids as sources of useful nitrogen.
However, only 9 of the 20 amino acids that make up proteins and none of the nucleotides
that make up nucleic acids are essential; the remainder can be synthesized from other
ingredients in the diet. When amino acids in our body are degraded, their nitrogen atoms
eventually appear in urea molecules which are excreted.
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provisions. "By reason whereof," says Sir Walter Raleigh, "our ships being
all pestered and romaging everything out of order, very light for want of
ballast, and that which was most to our disadvantage, the one halfe part of
the men of every shippe being sicke and utterly unserviceable; for in the
Revenge there were ninety diseased: in the Bonaventure not so many in
health as could handle her main-saile. The rest, for the most part, were in
little better state."
The island had shrouded the approach of the Spaniards since they were
first seen, and now the enemy hove in sight again full near, and our ships
had scarce time to weigh their anchors, but some of them were driven to
slip their cables and set sail.
Sir Richard was the last that weighed anchor, for he had waited to
recover his men that were upon the island, who otherwise would have been
lost—"Choosing," says Sir Richard Hawkins, "rather to sacrifice his life,
and to pass all danger whatsoever, than to fail in his obligation, by
gathering together those who were ashore; though with the hazard of his
ship and company."
Raleigh and Hawkins agree in giving this high motive.
Sir William Monson says: "When the Lord Thomas warily, and like a
discreet general, weighed anchor and made signs to the rest of his fleet to
do the like, with a purpose to get the wind of them, Sir Richard Grenville,
being a stubborn man, and imagining this fleet to come from the Indies, and
not to be the Armada of which they had been informed, would by no means
be persuaded by his master, or company, to cut his cable and follow his
admiral; nay, so headlong and rash he was, that he offered violence to those
that advised him so to do. But the old saying, that a wilful man is the cause
of his own woe, could not be more truly verified than in him; for when the
Armada approached, and he beheld the greatness of the ships, he began to
see and repent of his folly, and when it was too late, would have freed
himself of them, but in vain."
Severe criticism like this, imputing low motives, is in most cases

overdone. How does Monson know that Grenville mistook the fleet for
treasure-ships? it is a mere surmise, for which there is no evidence. Again,
where does Sir Richard seem to repent of his folly? We have Sir Walter
Raleigh's statement to the contrary; he says:—
"The Lord Thomas with the rest very hardly recovered the wind, which
Sir Richard not being able to do, was persuaded by the master and others to
cut his main-sail, and cast about, and to trust to the sailing of his ship; for
the squadron of Seville were on his weather-bow. But Sir Richard utterly
refused to turn from the enemie, alledging that he would rather choose to
die, than to dishonour himself, his country and her Majesty's ship:
persuading his company that he would pass through the two squadrons in
spite of them, and enforce those of Seville to give way."
Here we have the true motives in the mind of this proud seaman. First,
he would not, for any fear of Spain, leave his men behind to be tortured by
the Inquisition. Secondly, his pride in his country and his Queen forbade
him to fly, however numerous the foe.
No doubt he was a stubborn man—he meant to do what he thought

right, and also what he thought within his power to accomplish. He did not
foresee the accident which rendered his ship helpless, for boldly he sailed
right into the crowd of Spanish galleys; the foremost of them "sprang their
luff" and fell under his lee. As he sailed in and out, exchanging broadsides
and avoiding collisions, "the great San Felipe, being in the wind of him and
coming towards him, becalmed his sails in such sort that the ship could
neither make way nor feel the helm; so huge and high-carged was the
Spanish ship, being of 1500 tons."
This it was that prevented him from forcing his way through the
Armada. Raleigh says, no doubt the other course—sailing away from the
foe—had been the better: "Notwithstanding, out of the greatness of his
mind, he could not be persuaded." So the San Felipe and some others
closed upon the unmoving Revenge; she could not stir upon the water, being
becalmed. Amongst others that lay close to board her was the admiral of the
Biscayans, a very large and strong ship; she carried three tier of guns on a
side, and eleven pieces in every tier. She shot eight forth right out of her
chase, besides those of her stern ports.
While the Revenge was entangled with this ship, four other vessels tried
to board her, two on her larboard, and two on her starboard side.
The fight began at three in the afternoon and it did not end till dawn
next morning, Grenville and his men fighting as Englishmen have seldom
fought before or since. The great San Felipe received the lower tier of the
Revenge, discharged with cross-bar shot into her bowels. She soon shifted
herself from the Revenge with all diligence, "utterly misliking her first
entertainment."
The Spanish ships were filled with soldiers, from two hundred in the
smaller to eight hundred in the largest; in the Revenge there were only
mariners, a few servants of the officers, and some gentlemen volunteers.
Ever and again attempts were made to board the Revenge, but always
the Spaniards were beaten back in their own ships with yell and blow.
At first the George Noble of London stayed close by under the lee of the
Revenge, having some shot through her. Her captain asked Sir Richard what
orders he had for him, being but one of the victuallers and of small force:
"Go, save thyself and thy crew, friend; leave me, I pray thee, to my
fortune."
As the fight went on hour after hour, ever one ship coming on and going
away hurt, while two others were ready to take its place, many of the crew
of the Revenge were slain or hurt, and towards nightfall one of the great
galleons of the Armada and the admiral of the hulks were both sunk, while
the decks of other vessels were crowded with groaning wounded.
Sir Richard, though sore wounded himself, never forsook the upper
deck. His eyes were everywhere, directing and encouraging and bidding his
men think of the gracious Queen and their homes in fair England: "We are
fighting for honour, lads, and our country and this good ship!"
An hour before midnight, Raleigh tells us, Sir Richard was shot in the
body with a musket as he was dressing; anon he was shot also in the head
shortly after, and withal his chirurgeon was wounded to death, as he
stooped over him.
From three of the clock in the previous afternoon, fifteen several great
galleons had assailed her, as well as many small barques. So ill did they like
their treatment that ere the morning dawned they began to desire some
terms of surrender to be offered. The men in the Revenge, too, as the day
waxed and the light grew stronger, began to mark how their wounded
increased and their fighting men grew scanty. They glanced out over the
bulwarks and saw none but enemies baying them round, save one small
ship, the Pilgrim, commanded by Jacob Whiddon, who hovered round all
night to see what success should fall out; but in the dawning, being seen of
the Spaniards, the Pilgrim was hunted away like a hare from a field of
wheat amongst many ravenous hounds, all giving tongue and sending their
fiery breath towards her; but she was a fast sailer, and by God's blessing
escaped their clutches.
SIR RICHARD GRENVILLE AND THE "REVENGE"
Off Flores there took place the pluckiest fight ever recorded in Naval history. The little
English ship, manned by only a hundred able men, was beset by a powerful Armada
containing many thousands of soldiers; the fight lasted from 3 p.m. until the following
morning, and not until all the powder was gone, every spar shot away, and most of the
crew, including Sir Richard, disabled, did she surrender.
In the beginning of the fight the little Revenge had only one hundred
men free from sickness and able to fight, four-score and ten sick men lay in
the hold upon the ballast. These hundred men had had to sustain the volleys,
boarding, and hand-to-hand encounters for sixteen hours on end, whereas
the Spaniards were well supplied with fresh men brought from every
squadron; arms and powder they had at will, and the comfort of knowing
they had strong friends near. The English saw no hope before them—only
honourable death, if so be; their ship's masts were all beaten overboard, all
her tackle cut asunder, her upper works altogether razed, so that she was
well-nigh brought even with the water, and could not stir except as she was
moved by tide and wave. All her powder was now spent to the last barrel,
all her pikes broken, forty of her best men slain, and most of the rest sorely
hurt. For they had borne eight hundred charges of heavy artillery and
rounds of small shot without number, and at last began to stare at one
another as men desperate who have lost their last chance of life.
The Armada were now floating all round the Revenge, not too near, for
they suspected danger from her still.
Then Sir Richard sent for the master-gunner, whom he knew to be a

most resolute man, and bade him split and sink the ship.
"And Sir Richard cried in his English pride,

'We have fought such a fight for a day and a night
As may never be fought again!
We have won great glory, my men,
And a day less or more, at sea or ashore,—
We die—does it matter when?
Sink me the ship, Master Gunner, sink her, split her in twain!
Fall into the hands of God, not into the hands of Spain!"
—
TENNYSON.
So Sir Richard sought to persuade the company, or as many as he could

induce, to yield themselves unto God, and to the mercy of none else. The
master-gunner readily consented, and so did divers others; but the captain
and the master were of another opinion, and besought Sir Richard to have
care of them, for many of them might live yet to serve their prince and
country. They reminded him that the ship had six foot of water in her hold,
three shot under water, which were so weakly stopped that with the first
working of the sea she must needs sink; and she was, besides, so crushed
and bruised that she could never be removed out of the place.
As the matter was thus in dispute, and as Sir Richard, where he lay, still
refused to hearken to any reason, the master was convoyed aboard the
General Don Alphonso Baçan, who promised that all their lives should be
saved, the crew should be sent to England, and the better sort should pay
such reasonable ransom as their estate would bear, and in the meantime
might be free from galley or prison. The Don agreed to this so much the
rather as he desired to get possession of Sir Richard, whom for his notable
valour he greatly honoured and admired.
On this message being delivered, the crew naturally wished to accept

the terms and drew back from the master-gunner, who, in a frenzy of grief
for his admiral's dishonour, as he thought, drew his sword and would have
slain himself on the spot, had not his friends withheld him from it by force
and locked him into his cabin.
Then Don Alphonso asked Sir Richard to come out of the Revenge, the
ship being marvellous unsavoury, filled with blood and dead bodies and
wounded men, like any slaughter-house. To which Sir Richard replied that
the Spaniard might do with his body what he list, for he esteemed it not. As
they bore him out of the ship, he swooned; when he recovered, he was on
the Spaniard's deck, and looking about him said, "I desire you, gentlemen,
to pray for me."
The Spanish admiral used Sir Richard with all humanity and tended him
well, highly commending his valour and worthiness; but the English hero
died on the third day and was buried at sea with all honour.
As he lay surrounded by Spanish hidalgos, who were trying to comfort

him in his agony, the dying man half raised himself and said:
"Here die I, Richard Grenville, with a joyful and quiet mind, for that I
have ended my life as a good soldier ought to do, who has fought for his
country and his Queen, for honour and religion. Wherefore my soul joyfully
departeth out of this body, leaving behind it an everlasting fame, as a true
soldier who hath done his duty as he was bound to do. But the other of my
company have done as traitors and dogs, for which they shall be reproached
all their lives."
Lord Thomas Howard did not deserve this condemnation, for he wished
to attempt a rescue, but his men refused to follow.
A few days after the fight a great storm from the north-west scattered
the fleet, and fourteen Spanish ships went down, together with the Revenge,
off St. Michael's Isle. It seemed to the English that Heaven was on the side
of the Revenge, for 10,000 Spaniards perished in that storm.
Sir Richard Hawkins, correcting Raleigh's account, wrote that there

were on board the Revenge "above 260 men, as by the pay-book appeareth
—all which may worthily be written in our chronicles in letters of gold, in
memory for all posterities, some to beware, others to imitate, the true valour
of our nation in these ages."
CHAPTER VIII
JOHN DAVIS, THE HERO OF THE ARCTIC
AND PACIFIC
John Davis was born near the Gilberts' home about 1550, on the left
bank of the Dart, not far from Dartmouth. His father was a yeoman owning
a small farm in Sandridge, being part of the parish of Stoke Gabriel. The
little inlet or harbour is called Stoke Creek, at the head of which stands the
old church; in this are kept the records of the marriage of John Davis. The
lordly manor-house of the Pomeroys seemed to look down from its height
upon winding river and grove of oaks—the playing-ground of so many
heroes—the three Gilberts, Davis, and Walter Raleigh. The boys had only to
run down over two pastures and they were at the Cove, overhung with
drooping boughs and trailing with dog-roses and honeysuckle. The village
of Dittisham, with its plum and apple orchards, its drying nets and rocking-
boats, meets the gaze as you look across the lake-like reach of the river....
Greenaway Court, the Gilberts' home, stood up among the woods to the
south, and no doubt Adrian Gilbert and the Carew boys and Raleigh must
often have raced in their skiffs, or listened to seamen's stories of the doings
of John Hawkins in the West Indies. There was another house not far from
Dittisham, where Davis as a boy may well have visited, the home of Sir
John Fulford, who had two sons of the same age as the younger Gilberts,
and four daughters, of whom Faith in after years became the wife of John
Davis. John was of course not socially the equal of the others, but his
exploits and fame levelled all distinctions as he grew older; and when he
was a boy, no doubt he was a brave, modest fellow, good enough to play
with his superiors.
Whether John Davis went to the new grammar-school at Totnes we do

not know, but it is clear that he was sent to sea at an early age, and studied
deeply the science of his profession; for by the time he was twenty-eight he
was known to merchants as a captain of great skill and experience.
John returned home in 1579, passing six years at Sandridge, and no

doubt enjoying many a sail up the river with Miss Faith Fulford and her
sisters.
We can see by the Parish Register that John married Faith on September
29, 1582; they had a pleasant neighbour in Adrian Gilbert, who had married
the widow of Andrew Fulford, and was living in the Pomeroy manor-house.
Adrian was now a doctor of medicine and an able mathematician, deeply
interested in geographical discovery and the science of minerals.
There was a learned geographer, Dr. Dee, living at Mortlake, to whom

Adrian one day introduced John Davis; after that they often met and
discussed the North-west Passage and other problems of the day. One day in
1585 Secretary Walsingham called in and heard their arguments: a route to
the Indies which should be clear of all claims on the part of the Spanish and
Portuguese interested the minister.
Having won Walsingham's interest, the two Devon scientists next tried
to persuade the merchants of London to join them; then they rode all the
way to Exeter and Dartmouth to induce wealthy merchants there to
subscribe. Raleigh was at this time high in Court favour; he had been
knighted the year before, and was growing rich upon the Queen's gifts. He
induced her Majesty to grant a charter to himself, Adrian Gilbert, and John
Davis, "for the search and discovery of the North-west Passage to China."
Raleigh was at this time very busy with his Virginia colony, but he found
time to help his old school-friends.
The expedition, preparing in 1585, consisted of two small ships, the

Sunshine of London of 50 tons, and the Moonshine of Dartmouth of 35
tons. Davis commanded the Sunshine, with a crew of eleven seamen, four
musicians, a carpenter and a boy, and four officers; they sailed out of
Dartmouth harbour on the 7th of June 1585. Davis was now in his thirty-
sixth year, and one of the best seamen of his day. Though only the son of a
yeoman farmer, he had made many valuable friends, such as Dr. Dee, the
Gilberts, Raleigh, Walsingham, the Earl of Warwick, and Mr. Sanderson, a
rich city merchant; the Earl of Cumberland and Lord Lumley had sought his
acquaintance. What is more, Davis was beloved by the men under his
command, for he was ever thoughtful of their welfare both before he sailed
and after he returned home; for his kindness proceeded from the heart.
In these scientific days of Arctic discovery we have learnt what sort of

food and clothing is best for our explorers; in those days all was in the
experimental stage. Their provisions consisted of cod and salt-meat, bread
and grease, butter and cheese and beer.
As they were obliged to anchor for twelve days off the Scilly Isles,
Davis took the opportunity of making a survey of all the islands, the rocks
and havens. When they got out into the Atlantic they had some sport trying
to harpoon porpoises, the flesh of which they thought as good as mutton.
Whales too were seen in much larger numbers than are found now; for like
many other interesting and valuable species, whales have been recklessly
destroyed through the greed of man.
On the 19th of July, in a dense mist, they heard "a mighty great
roaring"; Captain Davis had a boat lowered and rowed to find out the cause
thereof. He found that the ships were close to some pack-ice, the large
fragments of which were grinding together. Next day was clear, and they
saw the snow-clad mountains of Greenland, but could not land for the ice;
here they saw many seals and white birds. They rounded the southern point
of Greenland, and were in the channel that lies between Greenland and
Labrador. Finding a fiord some miles up the coast he named it Gilbert
Sound, after his friend and his first-born child. It was near this spot that
they heard the Eskimos shouting, so Davis took a boat and four musicians,
as it was known the natives loved music. In a short time perfect confidence
was established and they began to barter, kayaks or boats and native
clothing being in some demand. Later they managed to kill a Polar bear,
which came in useful, as the men were clamouring for better food.
They next sailed west, and explored Cumberland Gulf. On landing they
heard dogs barking, and when they came up very gently, "we thought they
came to prey upon us and therefore we shot two; but about the neck of one
of them we found a leathern collar, whereupon we thought them to be tame
dogs." After this a strong north-west wind blew, and as it was near the end
of August they resolved to return to England, and arrived at Dartmouth on
the 30th of September.
Adrian Gilbert gave his friend Davis a warm welcome home, and of
course wife and child made home more homelike. But not many days after
his arrival the explorer wrote to Walsingham, "The North-west Passage is a
matter nothing doubtful, but at any tyme almost to be passed, the sea
navigable, voyd of yse, the ayre tolerable, and the waters very depe."
We notice that the spelling of all words of Latin origin is good; it is the
English word that varies most from our spelling. Anyway, he is far superior
in education to the Earl of Cumberland.
Davis also pointed out in his letter how good an opening there was in
the lands he had discovered for trade in oil and furs.
A hasty visit to London resulted in many merchants subscribing for a

second voyage, and the Mermaid, the Sunshine, Moonshine, and North Star,
a small pinnace, were chartered for it. They sailed from Dartmouth on the
7th of May 1586, and coasted along the south shore of Ireland; then Captain
Pope in the Sunshine, with the North Star as a tender, was despatched to
search for a passage northward between Greenland and Iceland, while
Davis went as far as the southern end of Greenland, But the pack-ice made
it impossible to land, so naming the cape "Farewell" he again entered Davis
Straits. On reaching Gilbert Sound he met so violent a gale that he was
obliged to take shelter among the islands which fringe the shore.
Davis writes: "We sent our boats to search for shoal water, where we
might anchor, and as the boat went sounding and searching, the natives
having espied them, came in their canoes towards them with shouts and
cries; but after they had espied in the boat some of our company that were
the year before here with us, they presently rowed to the boat, took hold on
the oar, and hung about the boat with such comfortable joy as would require
a long discourse to be uttered."
Davis, seeing their confidence, went ashore and distributed twenty

knives: "They offered skins to me for reward, but I made signs that they
were not sold, but given them of courtesie." The next day, as the crew were
setting up a new pinnace, more than a hundred canoes came round, bringing
seal-skins and other furs for barter.
Davis and a party went inland, finding a plateau of grass and moss, and
many ravens and small birds. In July, after more exploring, in which the
natives kept him company, Davis organised athletic games, leaping and
wrestling—"In this we found them strong and nimble, for they cast some of
our men that were good wrestlers."
The people were of good stature, with small hands and feet, broad faces,
small deep-set eyes, wide mouths, and beardless; they wore images and
believed in enchantments. But other failings soon appeared, for they were
"marvellous thievish," began to cut the cables, cut away the Moonshine's
boat from her stern, stole oars, a caliver, a boar-spear and swords. Davis
was for forbearance, but his men were angry, and complained heavily, "said
that my lenitie and friendly using of them gave them stomacke to
mischiefe." Still Davis went on giving presents, but at sundown the
Eskimos began throwing stones into the Moonshine, which caused a pursuit
and some shots. At last they captured one of the thieves, and another
followed with lamentation as far as the ship. "At length the fellow aboard us
spake four or five words unto the other and clapped his two hands upon his
face, whereupon the other doing the like, departed as we supposed with
heavy cheer. We judged the covering of the face with his hands and bowing
of his body down, signified his death." But it was not quite so bad as that,
for they gave the captive a new suit of frieze, of which he was very joyful;
he became sociable, trimmed up his darts and fishing tools, and would set
his hand to a rope's end upon occasion.
They soon came upon a mountain of ice and could not get on; the men
grew sick and feeble and begged Davis to return, so he sailed south-east and
found land free from snow. When they came to lat. 67°, they found numbers
of gulls and mews, and caught a hundred cod in half-an-hour. Landing, they
found a black bear, pheasants, partridges, wild ducks, and geese, and killed
some with bow and arrow.
On the 6th of September Davis sent some young sailors ashore to fetch
fish, but they were suddenly assailed in a wood, two being slain by arrows.
Immediately after, a tremendous storm almost drove them on the rocks
among these "cannibals." "But when hope was past, the mighty mercy of
God gave us succour and sent us a fair lee, so as we recovered our anchor
again and now moored our ship, where we saw that God manifestly
delivered us; for the strains of one of our cables were broken, and we only
rode by an old junk."
They reached home in October, bringing five hundred sealskins and
other furs. The Sunshine and North Star made the east coast of Greenland
by July 7th, but found pack-ice, so they sailed round and north to Gilbert
Sound, where the crews played football with the Eskimos. The North Star
was lost in a gale, and the Sunshine came home alone on the 6th of October.
So they had explored a vast extent of unknown coast, and entered many
fiords. They had not found the Northwest Passage, but had found Hudson
Strait, and concluded correctly that the "north parts of America are all
islands."
Had they taken plenty of salt and fishing-tackle they might have brought
home a large cargo of fish, but they brought home the knowledge that a
great trade was possible in the far North. Though Davis, on going west to
his own county, tried to persuade the merchants that another voyage might
be more successful, he did not succeed in rousing their sympathies so far as
to give more subscriptions.
But on going home he found another little son, Arthur, and with his wife
and old friend, Adrian Gilbert, enjoyed a pleasant autumn.
In the winter the restless adventurer rode up to London with Gilbert, and
they visited the merchant-prince, William Sanderson, who gained for Davis
enough help to fit out a third voyage to the Arctic. In our days rich men
have so much scientific spirit that they—some of them—will consent to
subscribe for Arctic and Antarctic voyages for purely scientific purposes. In
the great Queen's days they looked for some return in hard cash, or furs, or
stones and metal of value. But Davis's old shipmates loved him and were
eager to volunteer again, and some were natives of the villages round Stoke
Gabriel.
On the 19th of May 1587, the Sunshine, Elizabeth, and Ellen started
from Dartmouth, the former to fish and make profit. But when they reached
Gilbert Sound Davis resolved to send the two other ships to the fishery,
while he in the Ellen, a pinnace of 20 tons, went north. In estimating the
exploits of these men, we must remember how ill they were fitted out
compared with modern explorers. At the very first the pilot of the Ellen
came to report a leak, and it was debated whether they should risk their
lives in exploring.
But when Davis addressed his little crew and said, "My boys, it will be
far better that we should end our lives with credit than return in disgrace,"
they one and all agreed to go on with their captain.
They went along the west coast of Greenland, calling it the London
Coast, and by the 30th of June had reached lat. 72'12°, the most northerly
point Davis ever reached. Here an island with a cliff 850 feet high was
named "Sanderson his hope"; along the narrow, dark ledges of this giant
rock nestled myriads of white guillemots, screaming and circling as busily
they fed their young.
The sea was clear of ice, save that the Dreadnoughts of the North,
towering icebergs, reflected the sunshine in strange fantastic ways, and
floated proudly down to warmer waters. Beyond them lay "a great sea, free,
large, very salt and blue, and of an unsearchable depth."
But on the 2nd of July they met "the Middle Pack," a hundred miles
long or more, and eight feet thick. The Ellen tried to find a passage through
in vain, so they drifted west till they sighted the western coast of Davis
Strait. Davis took many observations which were useful to succeeding
explorers; he says in his log: "We fell into a mighty race, where an island of
ice was carried by the force of the current as fast as our bark could sail. We
saw the sea falling down into the gulf with a mighty overfall, roaring, with
divers circular motions like whirlpools."
They were to meet the fishing-vessels off the Labrador coast; but these
had gone home without waiting for Davis; and as they were being sought,
the Ellen ran upon a rock and sprung a leak. This was mended with
difficulty in a gale; then, with little fuel and less water, Davis headed for
home. "Being forsaken and left in this distress," he says, "referring myself
to the merciful providence of God, I shaped my course for England, and
unhoped for of any, God alone relieving me, I arrived at Dartmouth."
The log of his third voyage is the only one that has been left, but we
have no means of knowing if the fishing was successful.
When Davis came home all England was talking of a Spanish invasion,
and the Queen had no time to think of him and his discoveries. On reaching
home he found a third little son awaiting him, named John, after his father.
Though London and Greenwich and Exeter neglected Davis for a time,
yet he had done good work in discovering, or mapping afresh many coasts
and seas; he examined rocks and fiords, made notes on the vegetation and
fauna and on the habits and thoughts of the Eskimo tribes; he also explored
the coast of Labrador and called attention to the lucrative trade in whales,
seal, and fish which might be established.
When the Armada came, John Davis was appointed to the command of
a vessel of 20 tons, the Black Dog, to act as a tender to the Lord Admiral,
with a crew of ten men and an armament of three guns. Here Davis was of
use to the flagship as a pilot, for no one had taken more intelligent interest
in surveying the coast and marking shoals than he. We need not go again
through the events of the long fight, but it was in the fight off the Isle of
Wight that Davis saw the fiercest action, when Admiral Oquendo in his
flagship, of 900 tons, rammed the stern of the English flagship, the Ark
Royal, and unshipped her rudder.
After ten days of severe work Davis returned to Plymouth, and was at
home when his fourth child was born, named Philip! Another memorial of
the Armada times was a work on navigation, written by Davis and
dedicated to Lord Howard of Effingham.
The next employment Davis found was to join the Earl of Cumberland's
squadron in the Drake off the Azores, where he probably met Edward
Wright, an eminent mathematician and cosmographer, who had gone to sea
to observe the practical working of problems in nautical astronomy. Davis
himself had invented an instrument for observing the stars, so these two had
much to discuss in common.
It was on this voyage that the English crews suffered so much from
want of water, which was very scarce on the islands. The natives on
Graciosa, on being asked for water, replied that they would rather give two
tons of wine than one of water. They came home with thirteen prizes, and
the money Davis received as his share enabled him to go on an expedition
more to his taste; for he loved peaceful knowledge better than fighting. His
scheme was to go through Magellan's Straits, to navigate the South Sea, and
discover the North-west Passage from the western side.
Magellan, a Portuguese navigator, had only discovered the strait called

by his name seventy years before; it was in 1520 that Magellan first sailed
in and found very deep water. As he passed along, winding to and fro, he
saw so many fires at night lighting up the woods and rocks on the southern
side of the strait, that he named the land "Tierra del Fuego." A snowy peak
far to the south he named "Campana de Roldan," "Roldan's bell"; they were
short of provisions, and the crew murmured and wished to return, but
Magellan, a stern disciplinarian and feared by his men, swore they should
eat the chafing-mats on the rigging rather than return. After thirty-seven
days of sailing through winding reaches that seemed to lead nowhere, and
that stretched a hundred leagues and more, they came out into the South
Pacific; then boldly striking across the ocean to the islands of the far East,
Magellan met his fate at the hands of ruthless savages.
In 1522 Sebastian del Cano, a Basque born on the shores of the Bay of
Biscay, returned to Seville after having been the first to sail round the
world. In 1525 he sailed again from Corunna and passed through the Straits
of Magellan, but died at sea shortly after.
The Spanish Governor of Chili, de Mendoza, fitted out two vessels in

1557 and sent Ladrilleros to explore the straits; this he did under most
appalling hardships; most of his crew died of hunger and cold, and he
brought his ship back to Chili with only two survivors to help him. There
were Spanish heroes in those days as now. Then came Drake, sailing from
Plymouth in November 1577 in the Golden Hind, and finding Magellan's
account of the straits true as to the good harbours, many islands, and plenty
of fresh water, but meeting many violent gales and storms. He was only
sixteen days in the straits, and then sailed far up the western coast of
America up to the 48th degree, where the hills were covered with snow in
June—he was the second to sail round the globe. From Drake's voyage it
was, perhaps, that Davis believed in the possibility of going northwards till
he found an opening on the north-west coast.
In 1586 Cavendish started with three vessels and passed through the
Straits of Magellan and completed the third navigation of the globe.
Chudleigh, another Devon man, was fired by these exploits to do

likewise, and sailed in 1589 with three ships through the Magellan Straits,
where he died. Prince says: "He did not live long enough to accomplish his
generous designs, dying young; although he lived long enough to exhaust a
vast estate."
All these voyages Davis must have carefully studied with his friends,
Sir Walter Raleigh and Adrian Gilbert; the latter of whom joined with him
in the ownership of a ship, the Dainty, and the former helped by ideas,
plans, and subscriptions.
John Davis did not go on this quest to get riches, but solely to get
knowledge; many men thought him a fool, and jeered when he came back
disappointed, but the best men knew his high ambition to be the worthiest.
Perhaps his wife grudged the large stake which he was risking in this
adventure; she and her boys seemed to come only second in his thoughts.
Cavendish went as general on board the Leicester, and owned the

Desire, the ship in which he had sailed round the world; but Cavendish
cared mostly for rich prizes.
John Jones, an old and beloved shipmate, accompanied Davis in the

Desire, 120 tons, and proved a friend in need. The Dainty was commanded
by Captain Cotton, a friend of the Devon group.
The few weeks that Davis spent at home in the summer of 1591 were
his last happy days at Sandridge; but he cheered up his wife with thoughts
of great discoveries and fame and royal favour.
In February a severe storm separated the fleet off the river Plate and
Buenos Ayres, and as Cavendish had not appointed any spot for meeting,
they were some time before they discovered one another in Port Desire.
When they did meet, Davis found the Roebuck seriously damaged, and
heard that the Dainty, his own ship, had deserted and gone home. This was
the first bitter disappointment, for it was in the Dainty that Davis had
intended to go on with his explorations northward.
There were some who suggested that Cavendish wished to knock on the
head Davis's nonsense about Arctic exploring, and they asserted that
Cavendish had told the crew of the Dainty that he wanted them to go into
the river Plate, but that afterwards they might return home with all his heart.
Cavendish abandoned his ship, the Leicester, because he complained

that "he was matched with the most abject-minded and mutinous company
that ever was carried out of England by man living, for they never ceased to
mutiny against him." So he remained on board the Desire as the guest of
Captain Davis.
Port Desire, a good many miles north of the Straits of Magellan, was a
very dreary spot to rest in; steep white cliffs stained by running water
stretched for two miles across the bay; the soil inland was poor, and water
was scarce. The only thing the sailors could find was a sweet-smelling herb
which protected them from scurvy. Nine miles to the south was Penguin
Island, the home of many seals.
On the 20th of March they started again, and reached the straits on the
8th of April. At first the view is desolate and bare, but as you pass the two
narrows and enter the long reach, which runs north and south for a hundred
miles, the hills become thickly wooded with winter's bark and an evergreen
beech, most of them draped in moss and set deep in arbutus and berberis.
High mountains capped with snow stand up to the south, while humming-
birds skimmed the trailing fuchsias.
As they reached the dark frowning rock called Cape Froward, a wintry
gale met them, snowstorms burst upon them, and their only food was
mussels and limpets; they had to anchor for shelter in a little bay for more
than a month.
Anthony Knivet, one of the crew of the Leicester, thus described the
intense cold: "When I came on board with wet feet and began pulling off
my stockings, the toes came off with them: 'tis true! and a shipmate of
mine, Harris by name, lost his nose entirely; for, as he was going to blow it
with his fingers, he cast it incontinently into the fire."
Cavendish now wanted to go back, but Davis assured him the

snowstorms would end, and all would be well, if only they would persevere.
"Then we will go back to the Brazilian coast," said Cavendish, "and obtain
supplies."
So they sailed back through the straits, Cavendish having returned to his
own ship. At Cape Famine Cavendish landed all the sick from the Leicester,
and left them to starve from damp, cold, and hunger.
For the second time Cavendish disappeared in the night without making
any signal; this time he landed his sick on a hot beach under a tropical sun,
and there abandoned them.
Cavendish sailed for England, but died on the way.
In his will he accused Davis of deserting him; but the facts seem to put
the blame for desertion on his own shoulders; or it is possible that each of
these men was waiting for the other, each believing that the other had
deserted him. And our verdict on Cavendish should be modified by the state
of his health, which was evidently broken by anxiety and fear of mutiny, as
well as by the terrible sufferings caused by rough seasons.
In a letter to his executor, which Cavendish wrote before his death, he

says: "Consider whether a heart made of flesh be able to endure so many
misfortunes, all falling upon me without intermission. I thank my God that,
in ending of me, He hath pleased to rid me of all further trouble and
mishaps."
Davis waited for nine weeks in Port Desire for Cavendish; his own
plight was sorry, for his sails were worn-out, his cables chafed and
untrustworthy, and he had lost a boat and oars. However, he resolved to
send the pinnace in search of Cavendish, but two men on board the Desire,
named Charles Parker and Edward Smith, persuaded the crew that Davis
intended to maroon them; they even formed a plot to murder their captain.
This plot was revealed by the boatswain, and Davis, instead of hanging the

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MOLECULAR BIOLOGY OF THE CELL, SIXTH EDITION

1. Which of the following elements is not normally found in cells?

2. A hydrophobic molecule is typically …

9. Which of the following is true regarding a fatty acid molecule in water?

13. Which of the following statements is true regarding cellular metabolism?

Energy per molecule

A. the activation energy at high and low temperature.

28. Which of the following represents an ―activated‖ carrier molecule?

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A. Head polymerization of a protein

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Raleigh and Hawkins agree in giving this high motive.

Severe criticism like this, imputing low motives, is in most cases

No doubt he was a stubborn man—he meant to do what he thought

Then Sir Richard sent for the master-gunner, whom he knew to be a

"And Sir Richard cried in his English pride,

So Sir Richard sought to persuade the company, or as many as he could

On this message being delivered, the crew naturally wished to accept

As he lay surrounded by Spanish hidalgos, who were trying to comfort

Sir Richard Hawkins, correcting Raleigh's account, wrote that there

Whether John Davis went to the new grammar-school at Totnes we do

John returned home in 1579, passing six years at Sandridge, and no

There was a learned geographer, Dr. Dee, living at Mortlake, to whom

The expedition, preparing in 1585, consisted of two small ships, the

In these scientific days of Arctic discovery we have learnt what sort of

A hasty visit to London resulted in many merchants subscribing for a

Davis, seeing their confidence, went ashore and distributed twenty

Magellan, a Portuguese navigator, had only discovered the strait called

The Spanish Governor of Chili, de Mendoza, fitted out two vessels in

Chudleigh, another Devon man, was fired by these exploits to do

Cavendish went as general on board the Leicester, and owned the

John Jones, an old and beloved shipmate, accompanied Davis in the

Cavendish abandoned his ship, the Leicester, because he complained

Cavendish now wanted to go back, but Davis assured him the

Cavendish sailed for England, but died on the way.

In a letter to his executor, which Cavendish wrote before his death, he

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