Part
III
9
Introduction to Metabolism
MICROBIAL METABOLISM
CHAPTER OVERVIEW
This chapter discusses energy and the laws of thermodynamics. The participation of energy in cellular
metabolic processes and the role of adenosine-5-triphosphate (ATP) as the energy currency of cells are
examined. The chapter concludes with a discussion of enzymes as biological catalysts: how they work, how
they are affected by their environment, and how they are regulated.
CHAPTER OBJECTIVES
After reading this chapter you should be able to:
•
•
•
•
•
•
•
•
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discuss the first and second laws of thermodynamics and show how they apply to biological systems
discuss enthalpy, entropy, and free energy and their application to biological reactions
discuss the use of ATP as the energy currency of the cell and show how it is used to couple energyyielding exergonic reactions with energy-requiring endergonic reactions
discuss reduction potential and its relationship to exergonic and endergonic processes
describe the role of enzymes in the catalysis of biological reactions, and discuss the ways in which
enzymes are influenced by their environment
discuss the need for metabolic regulation
describe metabolic channeling
describe how enzyme activity can be controlled by allosteric regulation and covalent modification
describe how feedback inhibition can be used to control the activity of a metabolic pathway
CHAPTER OUTLINE
I.
II.
Microbial Metabolism and Its Importance
A. Metabolism is the total of all chemical reactions in the cell, including both energy-conserving
reactions (catabolism or breakdown) and energy-requiring reactions (anabolism or synthesis)
B. Interactions among the five major nutritional types of microorganisms are critical for the
functioning of the biosphere and its biogeochemical cycles
C. Living cells carry out three major types of work
1. Chemical work—synthesis of complex molecules
2. Transport work—nutrient uptake, waste elimination, ion balance
3. Mechanical work—internal and external movement
Thermodynamics
A. Energy is the capacity to do work or to cause particular changes
B. The science of thermodynamics analyzes energy changes in a collection of matter called a system;
all other matter in the universe is called the surroundings
C. First law of thermodynamics—energy can be neither created nor destroyed
1. The total energy in the universe remains constant
2. Energy may be redistributed either within a system or between the system and its surroundings
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D.
III.
IV.
V.
VI.
VII.
Second law of thermodynamics—physical and chemical processes proceed in such a way that the
disorder of the universe (entropy) increases to the maximum possible
E. Energy is measured in calories where 1 calorie is the amount of heat energy needed to raise the
temperature of 1 gram of water from 14.5 to 15.5C; one calorie of heat equals about 4.2 joules
Free Energy and Reactions
A. The changes in energy that can occur in chemical reactions are expressed by the equation for free
energy change (ΔG = ΔH − T∙ΔS); free energy change (ΔG) is the amount of energy in a system that
is available to do work
B. The change in free energy of a chemical reaction is directly related to the equilibrium constant of
the reaction
1. The standard free energy change (ΔG 0) is the change in free energy under standard conditions
of concentration, pH, pressure, and temperature
2. When ΔG 0 is negative, the equilibrium constant is greater than one and the reaction goes to
completion as written; the reaction is said to be exergonic and releases energy (spontaneous)
3. When ΔG 0 is positive, the equilibrium constant is less than one and little product will be
formed at equilibrium; the reaction is said to be endergonic and requires energy (not
spontaneous)
ATP
A. ATP is a high-energy molecule used to capture, store, and provide chemical energy; removal of the
terminal phosphate by hydrolysis goes almost to completion with a large negative free energy
change (i.e., the reaction is strongly exergonic); ATP has high phosphate group transfer potential
B. These characteristics make ATP well suited for its role as the energy currency; ATP is formed from
ADP and Pi (inorganic phosphate) by energy-trapping processes; exergonic breakdown of ATP can
be coupled with various endergonic reactions to facilitate their completion
Oxidation-Reduction Reactions
A. The release of energy during metabolic processes normally involves oxidation-reduction reactions
1. Oxidation-reduction (redox) reactions involve the transfer of electrons from an electron donor
to an electron acceptor (conjugate redox pairs)
2. The equilibrium constant for an oxidation-reduction reaction is called the standard reduction
potential (E0) and is a measure of the tendency of the electron donor to lose electrons; the
more negative the reduction potential, the better it is as an electron donor
B. When electrons are transferred from an electron donor to an electron acceptor with a more positive
reduction potential, free energy is released that can be used to form ATP
Electron Transport Chains
A. An electron transport chain (ETC) is a series of electron carriers, each with a different redox
potential
B. Electron transport is important in a variety of metabolic processes (e.g., respiration and
photosynthesis); cells move electrons by using a variety of electron carriers organized into a chain
C. Electron carriers include NAD+, NADP+, flavoproteins (FAD, FMN), quinones, iron-sulfur centers
(ferredoxin), and cytochromes (hemes); these carriers differ in terms of how they carry electrons,
and this impacts how they function in electron transport chains
Enzymes
A. Structure and classification of enzymes
1. Enzymes are protein catalysts with great specificity for the reaction catalyzed and the
molecules acted upon
a. A catalyst is a substance that increases the rate of a reaction without being permanently
altered
b. The reacting molecules are called substrates and the substances formed are products
2. An enzyme may be composed only of protein or it may be a holoenzyme, consisting of a
protein component (apoenzyme) and a nonprotein component (cofactor)
a. Prosthetic group—a cofactor that is firmly attached to the apoenzyme
b. Coenzyme—a cofactor that is loosely attached to the apoenzyme; it may dissociate from
the apoenzyme and carry one or more of the products of the reaction to another enzyme
B. Mechanism of enzyme reactions
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1.
Enzymes increase the rate of a reaction but do not alter the equilibrium constant (or the
standard free energy change) of the reaction
2. Enzymes lower the activation energy required to bring the reacting molecules together
correctly to form the transition-state complex; once the transition state has been reached the
reaction can proceed rapidly
3. Enzymes bring substrates together at the active site to form an enzyme-substrate complex; this
can lower activation energy in several ways:
a. Local concentrations of the substrates are increased at the active (catalytic) site of the
enzyme
b. Molecules at the active site are oriented properly for the reaction to take place
C. Environmental effects on enzyme activity
1. The amount of substrate present affects the reaction rate, which increases as the substrate
concentration increases until all available enzyme molecules are binding substrate (saturated)
and converting it to products as rapidly as possible
a. When no further increase in reaction rate occurs with increases in substrate
concentration, a reaction is said to be proceeding at maximal velocity (Vmax)
b. The Michaelis constant (Km) of an enzyme is the substrate concentration required for the
reaction to reach half maximal velocity; it is used as a measure for the apparent affinity of
an enzyme for its substrate
2. Enzyme activity is affected by alterations in pH and temperature; each enzyme has specific pH
and temperature optima; extremes of pH, temperature, and other factors can cause denaturation
(loss of activity due to disruption of enzyme structure)
D. Enzyme inhibition
1. Competitive inhibition occurs when the inhibitor binds at the active site and thereby competes
with the substrate (if the inhibitor binds, then the substrate cannot, and no reaction occurs); this
type of inhibition can be overcome by adding excess substrate
2. Noncompetitive inhibition occurs when the inhibitor binds to the enzyme at some location
other than the active site and changes the enzyme’s shape so that it is inactive or less active;
this type of inhibition cannot be overcome by the addition of excess substrate
VIII. Ribozymes
A. Catalytic RNA molecules are called ribozymes; often they act on RNA substrate molecules
IX. Regulation of Metabolism
A. Regulation is essential for microorganisms to conserve energy and material and to maintain
metabolic balance despite frequent changes in their environment
B. Metabolic processes can be regulated in three major ways:
1. Metabolic channeling—the localization of metabolites and enzymes in different parts of a cell
2. Increasing or decreasing the number of enzyme molecules present (regulation of gene
expression)
3. Stimulation or inhibition of critical enzymes in a pathway (posttranslational regulation)
C. Metabolic channeling
1. Compartmentation is a common mechanism for metabolic channeling; enzymes and
metabolites are distributed in separate cell structures or organelles
2. Channeling can occur within a compartment
3. Channeling can generate marked variations in metabolite concentrations and therefore directly
affect enzyme activity
X. Posttranslational Regulation of Enzyme Activity
A. Allosteric regulation—regulation of enzyme activity by an effector or modulator, which binds
reversibly and noncovalently to a regulatory site on the enzyme; the regulatory site is distinct from
the catalytic site; the effect can be positive or negative
B. Covalent modification of enzymes—regulation of enzyme activity by the reversible covalent
addition or removal of a chemical group (e.g., phosphate, methyl group, adenylic acid); the effect
can be positive or negative
C. Feedback Inhibition
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1.
2.
3.
Every pathway has at least one pacemaker enzyme that catalyzes the slowest (rate-limiting)
reaction in the pathway; often this is the first reaction in a pathway
In feedback inhibition (end product inhibition), the end product of the pathway inhibits the
pacemaker enzyme
In branched pathways, balance between end products is maintained through the use of
regulatory enzymes at branch points; multiple branched pathways often use isoenzymes, each
under separate and independent control
TERMS AND DEFINITIONS
Place the letter of each term in the space next to the definition or description that best matches it.
____ 1.
____ 2.
____ 3.
____ 4.
____ 5.
____ 6.
____ 7.
____ 8.
____ 9.
____ 10.
____ 11.
____ 12.
____ 13.
____ 14.
____ 15.
____ 16.
____ 17.
During this phenomenon, the breakdown of ATP to
ADP and Pi releases energy to do work for the cell;
other processes trap energy by reforming ATP from
ADP and Pi
The science that analyzes energy changes in a
collection of matter
A law stating that energy can be neither created nor
destroyed
The unit of measurement that describes the amount of
heat needed to raise the temperature of 1 gram of water
from 14.5C to 15.5C
The unit of measurement for the amount of work
capable of being done
A law stating that physical and chemical processes
occur in such a way that randomness (disorder)
increases to a maximum
Describes the randomness or disorder of a system
The heat content of a system; in cells it is about that
same as the total energy of the system
A measure of the energy of a reaction that is available
to do useful work
Occurs when the forward rate of a reaction equals the
reverse rate
A reaction that releases energy (ΔG is negative)
A reaction that requires an input of energy (in addition
to the activation energy) in order to proceed (ΔG is
positive)
Reactions in which there is a transfer of electrons from
an electron donor to an electron acceptor
Protein catalysts with great specificity for the reaction
catalyzed and the molecules acted upon
A substance that increases the rate of a reaction
without being permanently altered by the reaction
The reacting molecules in an enzyme-catalyzed
reaction
The molecules formed by a chemical reaction
activation energy
active site (catalytic site)
allosteric enzymes
ATP
calorie
catalyst
compartmentation
competitive inhibitor
denaturation
effectors (modulators)
endergonic reaction
energy cycle
enthalpy
entropy
enzymes
equilibrium
exergonic reaction
feedback (end product)
inhibition
s.
first law of thermodynamics
t.
free energy change
u. isoenzymes
v. joule
w. maximal velocity (Vmax)
x. metabolic channeling
y. Michaelis constant (Km)
z. noncompetitive inhibitor
aa. oxidation-reduction (redox)
reactions
bb. pacemaker enzyme
cc. products
dd. regulatory enzymes
ee. ribozymes
ff. second law of
thermodynamics
gg. substrates
hh. thermodynamics
ii. transition state complex
____ 19. The energy required to bring reacting
molecules together in the correct way to
reach the transition state
____ 18. A complex formed during a reaction
that is composed of the substrates; it
resembles both the substrates and the
products of the reaction
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a.
b.
c.
d.
e.
f.
g.
h.
i.
j.
k.
l.
m.
n.
o.
p.
q.
r.
____ 20. A special place on the surface of an
enzyme where the substrates are
brought together in the proper
orientation for a reaction to occur
____ 21. The high-energy molecule used by cells
as their energy currency
____ 22. Term that describes the velocity of a
reaction when all available enzyme
molecules are binding substrate and
converting it to product as rapidly as
possible
____ 23. Constant that is equal to the substrate
concentration at which an enzymecatalyzed reaction reaches half maximal
velocity
____ 24. An enzyme inhibitor that binds to an
enzyme at the active site and thereby
prevents the substrate from binding and
reacting
____ 25. An enzyme inhibitor that binds to an
enzyme at some location other than the
active site and alters the enzyme’s
shape so that it is inactive or less active
____ 26. Disruption of an enzyme’s structure
with loss of activity caused by extremes
of pH, temperature, or other factors
____ 27. The phenomenon in which metabolic
pathways are regulated by controlling
the intracellular location of the
metabolites and enzymes involved in
the pathway
____ 28. Differential distribution of enzymes and
metabolites among separate cell
structures or organelles
____ 29. Enzymes whose activity and shape are
altered by noncovalent binding of a
small molecule
____ 30. Small molecules that alter the activity
of allosteric enzymes
____ 31. The enzyme that catalyzes the slowest
or rate-limiting reaction in a pathway
____ 32. The process by which the end product
of a metabolic pathway inhibits the first
enzyme in the pathway
____ 33. Different enzymes that catalyze the
same reaction, but that may be
regulated independently of one another
____ 34. Catalytically active RNA molecules
FILL IN THE BLANK
1.
2.
3.
4.
5.
6.
7.
The flows of carbon and energy in an ecosystem are intimately related. Light energy is trapped by
__________ organisms when they use carbon dioxide and sunlight during
to make
complex organic molecules. Some of this trapped energy is obtained by ____________ organisms when
they use the former as food and degrade the organic molecules. These molecules are often degraded by a
process called
, which releases carbon dioxide.
The science of ____________ analyzes energy changes in a collection of matter called a ____________.
All other matter in the universe is called the ____________.
For any reaction, when ΔG 0 is negative, the equilibrium constant is __________ than one, the reaction is
said to be ____________, and the reaction goes to completion in the way it is written. However, in an
____________ reaction, G 0 is positive, the equilibrium constant is _________ than one, and the reaction
is unfavorable; therefore, little product will be formed at equilibrium under standard conditions.
ATP is ideally suited for its role as energy currency. It is formed in energy-trapping and energygenerating processes such as ______ ______, fermentation, and ____________. In the cell’s economy,
ATP breakdown, an
reaction, can be coupled with various ____________ reactions to
facilitate their completion.
In a redox reaction, electrons are transferred from an
to an
. The
two molecules are referred to as a redox couple.
The equilibrium constant for a redox reaction is called the
, and it is a
measure of the tendency of the electron donor to ____ _____ electrons. The more
this
value, the better it is as an electron donor.
A number of enzymes are pure proteins. However, some enzymes consist of a protein component, the
____________, plus a nonprotein component called a ____________. The two together constitute the
____________. When the nonprotein component is firmly attached to the protein it is referred to as a
; when it is loosely attached, it is referred to as a ____________.
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8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
The
(Km) is equal to the substrate concentration at which an enzyme-catalyzed
reaction reaches half maximal velocity. It is used as a measure of the apparent ____________ of an
enzyme for its substrate. The lower the value of Km, the ____________ the substrate concentration at
which the enzyme catalyzes the reaction.
An inhibitor that binds at the active site and thereby prevents the binding of the substrate is called a
____________ inhibitor; while an inhibitor that binds at a location other than the active site, thus altering
the enzyme’s shape so that it is inactive or less active, is called a ____________ inhibitor.
is the capacity to do work. Living cells carry out three major types of work. The
synthesis of complex molecules is ____________ work; nutrient uptake, waste elimination, and the
maintenance of ion balances is ____________ work; and internal and external movement is
____________ work.
Enzymes bind substrates at their
, forming an
complex.
Enzymes speed reactions by
the activation energy of the reaction.
ATP is a
molecule, and it has a high
, which
means that it readily transfers phosphate to water. ATP is made when a third phosphate is added to
during processes such as photosynthesis, fermentation, or aerobic respiration.
Flavoproteins are proteins bearing the electron carrier
or
.
The phenomenon known as
localizes metabolites and enzymes in different
parts of a cell and in doing so influences the activity of metabolic pathways. In some cases, metabolites
and enzymes are distributed among separate cell structures or organelles. This is called
.
Enzyme activity can be regulated by small molecules known as ____________ or ____________. Such
enzymes are called ____________ enzymes. The small molecules bind by noncovalent forces to a
____________ site that is different from the catalytic site.
Every metabolic pathway has at least one ____________ enzyme that catalyzes the slowest or ratelimiting reaction in the pathway. Since other reactions proceed more rapidly than this reaction, changes in
the activity of the
enzyme directly alter the speed with which a pathway operates.
In
when the end product of a pathway becomes concentrated, it inhibits the
____________ enzyme and slows its own synthesis. As the end product concentration ____________,
pathway activity once again ____________ and more end product is formed.
The regulation of multiply branched pathways often involves _____________ to catalyze the same step.
In this situation, excess of a single end product ___________ but does not completely block pathway
activity because some ________________ are still active.
Aspartate carbamoyl transferase is an
enzyme that is inhibited by noncovalent binding of
CTP and activated by noncovalent binding ATP.
Glycogen phosphorylase can be regulated by reversible attachment of phosphate to the enzyme. This is an
example of
of an enzyme to control its activity.
Energy is made available when electrons are transferred from conjugate redox pairs with more
reduction potentials to those with more
reduction potentials.
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MULTIPLE CHOICE
For each of the questions below select the one best answer.
1.
2.
3.
4.
5.
What is the amount of heat energy needed to
raise the temperature of 1.0 gram of water
from 14.5C to 15.5C called?
a. joule
b. calorie
c. erg
d. thermal unit
What is the equilibrium constant (Keq) for the
reaction A + B → C + D?
a. [A][B]
[C][D]
b. [C][D]
[A][B]
c. [A][D]
[B][C]
d. [B][C]
[A][D]
Living organisms use a variety of electron
carriers to aid in the cycle of energy flow.
Which of the following is used as an electron
carrier?
a. NAD+
b. NADP+
c. ubiquinone
d. All of the above are used as electron
carriers.
Which of the following is true about
enzymes?
a. Enzymes are catalysts, and therefore,
they increase the rate of a reaction
without being permanently altered by
the reaction.
b. Enzymes are proteins that can be
denatured by changes in pH or
temperature.
c. Enzymes are highly specific for the
substrates they bind.
d. All of the above are true about
enzymes.
For a reaction to occur, the reacting
molecules must be brought together in the
correct way to form the transition-state
complex. This requires an input of energy.
What is this energy called?
a. activation energy
b. free energy
c. entropy
d. enthalpy
6.
7.
8.
9.
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Which of the following is NOT a way in
which enzymes lower the activation energy
required for a reaction?
a. bringing the substrates together at the
active site; in effect, concentrating them
b. binding the substrates so that they are
correctly oriented to form the transitionstate complex
c. increasing molecular motion, thereby
providing kinetic energy to drive the
reaction
d. All of the above are ways in which
enzymes lower the activation energy
required for a reaction.
Which of the following is NOT a function of
the transport work done by a cell?
a. uptake of nutrients
b. elimination of waste products
c. maintenance of internal/external ion
balances
d. All of the above are functions of
cellular transport work.
Which of the following is a reason for
metabolic regulation?
a. conservation of material
b. conservation of energy
c. maintaining metabolic balance
d. All of the above are reasons for
metabolic regulation.
A small molecule binds to an allosteric
enzyme and thereby increases the activity of
the enzyme. What is the small molecule
called?
a. positive effector
b. negative effector
c. prosthetic group
d. cofactor
10. Which of the following is NOT true about the
regulation of branched metabolic pathways?
a. There are usually separate regulatory
enzymes for each branch, as well as a
regulatory enzyme that controls the
flow of carbon into the entire set of
possible branches.
b. An excess of one end product will
usually completely inhibit the activity
of the branch responsible for the
synthesis of that particular end product.
c. An excess of one end product will
usually slow the flow of carbon into the
entire set of branched pathways.
d. All of the above are true about the
regulation of branched metabolic
pathways.
11. Which of the following is an expression of
the amount of energy made available for
useful work?
a. ΔG = ΔH + T∙ΔS
b. ΔG = T∙ΔS − ΔH
c. ΔG = ΔH − T∙ΔS
d. none of the above
TRUE/FALSE
____ 1.
____ 2.
____ 3.
____ 4.
____ 5.
____ 6.
____ 7.
____ 8.
____ 9.
____ 10.
____ 11.
____ 12.
____ 13.
____ 14.
A reaction will occur spontaneously if the free energy of the system decreases during the reaction
(i.e., if ΔG is negative).
Since ΔS is a measure of disorder, a decrease in ΔS will lead to a decrease in ΔG, and therefore, the
reaction will proceed spontaneously.
The value of ΔG 0 indicates how fast a reaction will reach equilibrium.
Redox couples that have greater negative reduction potentials will donate electrons to couples that
have higher positive potentials. This is the basis for the functioning of electron transport chains.
Ferredoxin is a nonheme iron protein that is active in photosynthetic electron transport.
Enzymes increase the rate of a reaction but do not alter the equilibrium constants for the reactions
they catalyze.
When the amount of enzyme present is held constant, the rate of a reaction will continue to increase
as long as the substrate concentration increases.
Enzyme activity can be greatly affected by the pH and temperature of the environment in which the
enzyme must function.
The ultimate source of most biological energy is visible sunlight through the process of
photosynthesis.
The standard free energy change is unrelated to the equilibrium constant.
Cytochromes contain iron atoms in heme groups or similar iron-porphyrin rings.
Covalent modification represents a reversible way of controlling enzyme activity because the
modified form has an altered activity (either higher or lower) than the unmodified form.
Usually the last step in a pathway is catalyzed by a pacemaker enzyme.
When a biosynthetic pathway branches to form more than one end product, an excess of one of the
end products will only inhibit the branch of the pathway involved in the synthesis of that particular
product, while an excess of all the end products will usually inhibit the flow of carbon into the entire
pathway.
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CRITICAL THINKING
1.
Consider the following diagram of the energy flow for a particular reaction. Is the reaction exergonic or
endergonic? What does the diagram indicate? How would the use of an enzyme catalyst affect the energy
flow? Indicate this on the diagram, and also indicate the energy of activation and the free energy change
of both the catalyzed and uncatalyzed reactions.
C+D
Energy
A+B
Time
Reaction rate
Each of the following two diagrams indicates the rate of a reaction as a function of substrate
concentration. In each case an inhibitor is present (not the same one) and the substrate concentration is
not saturating the enzyme. Explain the difference between the two situations.
Reaction rate
2.
{Substrate}
{Substrate}
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ANSWER KEY
Terms and Definitions
1. l, 2. hh, 3. s, 4. e, 5. v, 6. ff, 7. n, 8. m, 9. t, 10. p, 11. q, 12. k, 13. aa, 14. o, 15. f, 16. gg, 17. cc, 18. ii, 19. a,
20. b, 21. d, 22. w, 23. y, 24. h, 25. z, 26. i, 27. x, 28. g, 29. c, 30. j, 31. bb, 32. r, 33. u, 34. ee
Fill in the Blank
1. photoautotrophic; photosynthesis; chemoheterotrophic; aerobic respiration 2. thermodynamics; system;
surroundings 3. greater; exergonic; endergonic; less 4. aerobic respiration; photosynthesis; exergonic;
endergonic 5. electron donor; electron acceptor 6. standard reduction potential; give up; negative
7. apoenzyme; cofactor; holoenzyme; prosthetic group; coenzyme 8. Michaelis constant; affinity; lower
9. competitive; noncompetitive 10. Energy; chemical; transport; mechanical; 11. active site; enzyme-substrate
12. decreasing 13. high-energy; phosphate group transfer potential; ADP 14. FAD; FMN; 15. metabolic
channeling; compartmentation 16. effectors; modulators; allosteric; regulatory 17. pacemaker; pacemaker
18. feedback inhibition; pacemaker; decreases; increases 19. isoenzymes; slows; isoenzymes 20. allosteric
21. reversible covalent modification 22. negative; positive
Multiple Choice
1. b, 2. b, 3. d, 4. d, 5. a, 6. c, 7. d, 8. d, 9. a, 10. d, 11. c
True/False
1. T, 2. F, 3. F, 4. T, 5. T, 6. T, 7. F, 8. T, 9. T, 10. F, 11. T, 12. T, 13. F, 14. T
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