CHAPTER 2

CHEMICAL COMPONENTS OF CELLS

2009 Garland Science Publishin
Che!ical "#nds
2-1 Figure Q2-1 depicts the structure of carbon. Use the information in the diagram to choose
the correct atomic number and atomic weight, respectively, for an atom of carbon.
Figure Q2-1
(a !, 12
(b 12, 12
(c !, 1"
(d 12, !
2-2 #n element may have more than a one isotope. $sotopes have different atomic weights,
but e%hibit the same chemical behavior. &arbon-1' is an unstable isotope of carbon that
decays very slowly. &ompared to the common, stable carbon-12 isotope, carbon-1' has
two additional ((((((((((((((.
(a electrons
(b neutrons
(c protons
(d ions
2-3 $f the isotope
)2
* has 1! protons and 1! neutrons, how many protons and how many
neutrons will the isotope
)+
* have,
2-4 #. $f -.+ mole of glucose weighs .- g, what is the molecular weight of glucose,
/. 0hat is the concentration, in grams per liter (g1l, of a -.2+ 2 solution of
glucose,
&. 3ow many molecules are there in 1 mole of glucose,
2-5 0hich of the following elements is least abundant in living organisms,
(a sulfur
(b carbon
(c o%ygen
(d nitrogen
2-6 4our friend learns about #vogadro5s number and thin6s it is so huge that there may not
even be a mole of living cells on 7arth. 4ou have recently heard that there are about +-
trillion (+- 8 1-
12
human cells in each adult human body, so you bet your friend 9+ that
there is more than a mole of cells on 7arth. :nce you learn that each human contains
more bacterial cells (in the digestive system than human cells, you are sure that you have
won the bet. ;he human population is now more than ! billion (! 8 1-
.
. 0hat
calculation can you show your friend to convince him you are right,
2-7 #vogadro5s number, calculated from the atomic weight of hydrogen, tells us how many
atoms or molecules are in mole. ;he resulting base for all calculations of moles and
molarity (how many molecules are present when you weigh out a substance or measure
from a stoc6 solution is the following<
1 g of hydrogen atoms = ! 1-
2)
atoms = 1 mole of hydrogen
*ulfur has a molecular weight of )2. 3ow many moles and atoms are there in 12- grams
of sulfur,
(a ).>+ and ! 8 1-
2)
(b )2 and ! 8 1-
2)
(c 1.>+ and 1.-+ 8 1-
2'
(d ).>+ and 2.2+ 8 1-
2'
2-8 ;he first tas6 you are assigned in your summer laboratory ?ob is to prepare a concentrated
@a:3 stoc6 solution. ;he molecular weight of @a:3 is '-. 3ow many grams of solid
@a:3 will you need to weigh out to obtain a +-- ml solution that has a concentration of
1- 2,
(a "-- g
(b 2-- g
(c '-- g
(d 1!- g
2-9 4ou have a concentrated stoc6 solution of 1- 2 @a:3 and want to use it to produce a
1+- ml solution of ) 2 @a:3. 0hat volume of water and stoc6 solutions will you
measure out to ma6e this new solution,
(a 1)+ ml of water, 1+ ml of @a:3 stoc6
(b 11+ ml of water, )+ ml of @a:3 stoc6
(c 1-- ml of water, +- ml of @a:3 stoc6
(d 1-+ ml of water, '+ ml of @a:3 stoc6
2-10 #n ionic bond between two atoms is formed as a result of the ((((((((((((((.
(a sharing of electrons
(b loss of a neutron from one atom
(c loss of electrons from both atoms
(d loss of a proton from one atom
(e transfer of electrons from one atom to the other
2-11 For each of the following sentences, fill in the blan6s with the best word or phrase
selected from the list below. @ot all words or phrases will be usedA each word or phrase
should be used only once.
0hereas ionic bonds form a(n ((((((((((((((((((, covalent bonds
between atoms form a(n ((((((((((((((((((. ;hese covalent bonds
have a characteristic bond (((((((((((((((((( and become stronger and
more rigid when two electrons are shared in a(n ((((((((((((((((((.
7Bual sharing of electrons yields a(n (((((((((((((((((( covalent
bond. $f one atom participating in the bond has a stronger affinity for the
electron, this produces a partial negative charge on one atom and a partial
positive charge on the other. ;hese (((((((((((((((((( covalent bonds
should not be confused with the wea6er (((((((((((((((((( bonds that
are critical for the three-dimensional structure of biological molecules and
for interactions between these molecules.
charge length polar
covalent molecule salt
double bond noncovalent single bond
ionic nonpolar weight
2-12 $ndicate whether the statements below are true or false. $f a statement is false, e%plain
why it is false.
#. 7lectrons are constantly moving around the nucleus of the atom, but they can
move only in discrete regions.
/. ;here is no limit to the number of electrons that can occupy the fourth electron
shell.
&. #toms with unfilled outer electron shells are especially stable and are therefore
less reactive.
C. &ovalent bonds are formed when electrons are either shared or transferred
between atoms.
2-13 ;able Q2-1) indicates the electrons in the first four atomic electron shells for selected
elements. :n the basis of the information in the chart and what you 6now about atomic
structure, which elements are chemically inert,
;able Q2-1)
(a carbon, sulfur
(b helium, neon
(c sodium, potassium
(d magnesium, calcium
2-14 ;able Q2-1' indicates the electrons in the first four atomic electron shells for selected
elements. :n the basis of the information in the chart and what you 6now about atomic
structure, which elements will form ions with a net charge of D1 in solution,
;able Q2-1'
(a carbon, sulfur
(b helium, neon
(c sodium, potassium
(d magnesium, calcium
2-15 ;able Q2-1+ indicates the electrons in the first four atomic electron shells for selected
elements. :n the basis of the information in the chart and what you 6now about atomic
structure, which elements will form ions with a net charge of D2 in solution,
;able Q2-1+
(a carbon, sulfur
(b helium, neon
(c sodium, potassium
(d magnesium, calcium
2-16 ;able Q2-1! indicates the electrons in the first four atomic electron shells for selected
elements. :n the basis of the information in the chart and what you 6now about atomic
structure, which elements form stable but reactive diatomic gases,
;able Q2-1!
(a nitrogen, o%ygen
(b helium, neon
(c sodium, potassium
(d magnesium, calcium
2-17 #. $n what scientific units is the strength of a chemical bond usually e%pressed,
/. $f -.+ 6ilocalories of energy is reBuired to brea6 ! 8 1-
2)
bonds of a particular
type, what is the strength of this bond,
2-18 ;he p3 of an aBueous solution is an indication of the concentration of available protons.
3owever, you should not e%pect to find lone protons in solutionA rather, the proton is
added to a water molecule to form a(n (((((((((((((( ion.
(a hydro%ide
(b ammonium
(c chloride
(d hydronium
2-19 ;he relative strengths of covalent bonds and van der 0aals interactions remain the same
when tested in a vacuum or in water. 3owever, this is not true of hydrogen bonds or ionic
bonds, whose bond strength is lowered considerably in the presence of water in
comparison with the bond strength observed in a vacuum. 7%plain these observations.
2-20 :%ygen, hydrogen, carbon, and nitrogen atoms are enriched in the cells and tissues of
living organisms. ;he covalent bond geometries for these atoms influence their
biomolecular structures. 2atch the elements on the left with the bond geometries
illustrated on the right. *ome elements assume more than one bond geometry.
#. o%ygen
/. carbon
&. nitrogen
2-21 0hich of the following e%pressions accurately describes the calculation of p3,
(a p3 = Elog1-F3
D
G
(b p3 = log1-F3
D
G
(c p3 = Elog2F3
D
G
(d p3 = Elog1-F:3
E
G
2-22 Harger molecules have hydrogen-bonding networ6s that contribute to specific, highE
affinity binding. *maller molecules such as urea can also form these networ6s. 3ow
many hydrogen bonds can urea (Figure Q2-22 form if dissolved in water,
Figure Q2-22
(a !
(b +
(c )
(d '
2-23 #. *6etch three different ways in which three water molecules could be held together
by hydrogen bonding.
/. :n a s6etch of a single water molecule, indicate the distribution of positive and
negative charge (using the symbols I
D
and I
E
.
&. 3ow many hydrogen bonds can a hydrogen atom in a water molecule form, 3ow
many hydrogen bonds can the o%ygen atom in a water molecule form,
2-24 #. 0hat is the p3 of pure water,
/. 0hat concentration of hydronium ions does a solution of p3 " contain,
&. &omplete the following reaction<
&3
)
&::3 D 3
2
: J ((((((((((.
C. 0ill the reaction in & occur more readily (be driven to the right if the p3 of the
solution is high,
2-25 #romatic carbon compounds such as benKene are planar and very stable. Couble-bond
character e%tends around the entire ring, which is why it is often drawn as a he%agon with
a circle inside. ;his characteristic is caused by electron ((((((((((.
(a resonance
(b pairing
(c partial charge
(d stac6ing
2-26 ;he amino acid histidine is often found in enKymes. Cepending on the p3 of its
environment, sometimes histidine is neutral and at other times it acBuires a proton and
becomes positively charged. &onsider an enKyme with a histidine side chain that is
6nown to have an important role in the function of the enKyme. $t is not clear whether this
histidine is reBuired in its protonated or its unprotonated state. ;o answer this Buestion
you measure enKyme activity over a range of p3, with the results shown in Figure Q2-2!.
0hich form of histidine is necessary for the active enKyme,
Figure Q2-2!
2-27 *ilicon is an element that, li6e carbon, has four vacancies in its outer electron shell and
therefore has the same bonding chemistry as carbon. *ilicon is not found to any
significant degree in the molecules found in living systems, however. Coes this difference
arise because elemental carbon is more abundant than silicon, 0hat other e%planations
are there for the preferential selection of carbon over silicon as the basis for the
molecules of life,
M#lecules in Cells
2-28 ;he variety and arrangement of chemical groups on monomer subunits contribute to the
conformation, reactivity, and surface of the macromolecule into which they become
incorporated. 0hat type of chemical group is circled on the nucleotide shown in Figure
Q2-2",
Figure Q2-2"
(a pyrophosphate
(b phosphoryl
(c carbonyl
(d carbo%yl
2-29 ;he amino acids glutamine and glutamic acid are shown in Figure Q2-2.. ;hey differ
only in the structure of their side chains (circled. #t p3 >, glutamic acid can participate
in molecular interactions that are not possible for glutamine. 0hat types of interaction are
these,
Figure Q2-2.
(a ionic bonds
(b hydrogen bonds
(c van der 0aals interactions
(d covalent bonds
2-30 :ligosaccharides are short sugar polymers that can become covalently lin6ed to proteins
and lipids through condensation reactions. ;hese modified proteins and lipids are called
glycoproteins and glycolipids. 0ithin a protein, which of the amino acids (shown in
Figure Q2-)- is the most probable target for this type of modification,
Figure Q2-)-
(a serine
(b glycine
(c phenylalanine
(d methionine
2-31 0hich of the following are e%amples of isomers,
(a glucose and galactose
(b alanine and glycine
(c adenine and guanine
(d glycogen and cellulose
2-32 #. 3ow many carbon atoms does the molecule represented in Figure Q2-)2 have,
/. 3ow many hydrogen atoms does it have,
&. 0hat type of molecule is it,
Figure Q2-)2
2-33 2ost types of molecule in the cell have asymmetric (chiral carbons. &onseBuently there
is the potential to have two different molecules that loo6 much the same but are mirror
images of each other and therefore not eBuivalent. ;hese special types of isomer are
called stereoisomers. 0hich of the four carbons circled in Figure Q2-)) is the
asymmetric carbon that determines whether the amino acid (threonine in this case is a C-
or an H- stereoisomer,
Figure Q2-))
(a 1
(b 2
(c )
(d '
2-34 $ndicate whether the statements below are true or false. $f a statement is false, e%plain
why it is false.
#. # disaccharide consists of a sugar covalently lin6ed to another molecule such as
an amino acid or a nucleotide.
/. ;he hydro%yl groups on monosaccharides are reaction hotspots and can be
replaced by other functional groups to produce derivatives of the original sugar.
&. ;he presence of double bonds in the hydrocarbon tail of a fatty acid does not
greatly influence its structure.
C. Llycerol is a three-carbon compound that connects the fatty acid tails with the
polar head group in phospholipids.
2-35 :n the phospholipid molecule in Figure Q2-)+ label each numbered line with a correct
term selected from the list below.
Figure Q2-)+
2-36 /iological membranes are composed of specialiKed lipids that form bilayers. 0hich of
the following is formed by unmodified fatty acids,
(a fat droplets
(b bilayers
(c micelles
(d planar lipid patches
2-37 &hoose the answer that best fits the statement. &holesterol is an essential component of
biological membranes. #lthough it is much smaller than the typical phospholipids and
glycoplipids in the membrane, it is a(n ((((((((((((((((( molecule, having both
hydrophilic and hydrophobic regions.
(a polar
(b o%ygen-containing
(c hydrophobic
(d amphipathic
2-38 C@# and M@# are different types of nucleic acid polymer. 0hich of the following is true
of C@# but not true of M@#,
(a $t contains uracil.
(b $t contains thymine.
(c $t is single stranded.
(d $t has +N-to-)N directionality.
2-39 2atch each term related to the structure of nucleic acids (#E$ with one of the
descriptions provided.
#. base
/. glycosidic bond
&. nucleoside
C. nucleotide
7. phosphoanyhydride bond
F. phosphoester bond
L. ribose
3. phosphodiester bond
$. deo%yribose
(((( the lin6age between two nucleotides
(((( the lin6age between the +N sugar hydro%yl and a phosphate group
(((( the nitrogen-containing aromatic ring
(((( five-carbon sugar found in C@#
(((( sugar unit lin6ed to a base
(((( lin6age between the sugar and the base
(((( lin6ages between phosphate groups
(((( sugar lin6ed to a base and a phosphate
(((( five-carbon sugar found in M@#
2-40 #. 0rite out the seBuence of amino acids in the following peptide, using the full
names of the amino acids.
Oro-Pal-;hr-Lly-Hys-&ys-Llu
/. 0rite the same seBuence with the single-letter code for amino acids.
&. #ccording to the conventional way of writing the seBuence of a peptide or a
protein, which is the &-terminal amino acid and which is the @-terminal amino
acid in the above peptide,
2-41 0hich of the following statements about amino acids is true,
(a ;wenty-two amino acids are commonly found in proteins.
(b 2ost of the amino acids used in protein biosynthesis have charged side chains.
(c #mino acids are often lin6ed together to form branched polymers.
(d #ll amino acids contain an @3
2
and a &::3 group
2-42 0hich of the following statements is false,
(a #;O contains high-energy phosphoanhydride bonds.
(b #;O is sometimes called the Quniversal currencyR in the energy economy of cells.
(c #;O can be incorporated into C@#.
(d #;O can be hydrolyKed to release energy to power hundreds of reactions in cells.
(e #;O comprises a sugar, phosphate groups, and a nitrogenous base.
Macr#!#lecules in Cells
2-43 /oth C@# and M@# are synthesiKed by covalently lin6ing a nucleotide triphosphate to
the previous nucleotide, constantly adding to a growing chain. $n the case of C@#, the
new strand becomes part of a stable heli%. ;he two strands are complementary in
seBuence and antiparallel in directionality. 0hat is the principal force that holds these
two strands together,
(a ionic interactions
(b hydrogen bonds
(c covalent bonds
(d van der 0aals interactions
2-44 7ach nucleotide in C@# and M@# has an aromatic base. 0hat is the principal force that
6eeps the bases in a polymer from interacting with water,
(a hydrophobic interactions
(b hydrogen bonds
(c covalent bonds
(d van der 0aals interactions
2-45 /ecause there are four different monomer building bloc6s that can be used to assemble
M@# polymers, the number of possible seBuence combinations that can be created for a
M@# molecule made of 1-- nucleotides is (((((((.
(a 1--
'
(b '
1--
(c ' 8 1--
(d 1--1'
2-46 ;here are 2-
1--
different possible seBuence combinations for a protein chain with 1--
amino acids. $n addition to the amino acid seBuence of protein, what other factors
increase the potential for diversity in these macromolecules,
(a free rotation around single bonds during synthesis
(b noncovalent interactions sampled as protein folds
(c the directionality of amino acids being added
(d the planar nature of the peptide bond
2-47 $ndicate whether the statements below are true or false. $f a statement is false, e%plain
why it is false.
#. Q@onpolar interactionsR is simply another way of saying Qvan der 0aals
attractions.R
/. &ondensation reactions occur in the synthesis of all the macromolecules found in
cells.
&. #ll proteins and M@#s pass through many unstable conformations as they are
folded, finally settling on one single, preferred conformation.
C. 0hen nonpolar molecules are placed in an aBueous solution, the water molecules
surrounding the nonpolar surface become completely disordered.
2-48 2acromolecules in the cell can often interact transiently as a result of noncovalent
interactions. ;hese wea6 interactions also produce stable, highly specific interactions
between molecules. 0hich of the factors below is the most significant in determining
whether the interaction will be transient or stable,
(a the siKe of each molecule
(b the concentration of each molecule
(c the rate of synthesis
(d surface complementarity between molecules
2-49 $n a folded protein, most of the nonpolar amino acids are buried inside the protein fold,
whereas the polar and charged side chains are e%posed to the components in the cytosol.
;his fold is more stable because of the e%pulsion of nonpolar atoms from contact with
water, favoring the interaction of nonpolar atoms with each other. 0hat is this fourth type
of noncovalent interaction called,
(a hydrophobic interaction
(b hydrophilic interaction
(c apolar interaction
(d hydrocarbon interaction
2-50 4ou are trying to ma6e a synthetic copy of a particular protein but accidentally ?oin the
amino acids together in e%actly the reverse order. :ne of your classmates says the two
proteins must be identical, and bets you 92- that your synthetic protein will have e%actly
the same biological activity as the original. #fter having read this chapter, you have no
hesitation in sta6ing your 92- that it won5t. 0hat particular feature of a polypeptide chain
ma6es you sure your 92- is safe and that your pro?ect will have to be redone.
2-51 # protein chain folds into its stable and uniBue three-dimensional structure, or
conformation, by ma6ing many noncovalent bonds between different parts of the chain.
*uch noncovalent bonds are also critical for interactions with other proteins and cellular
molecules. From the list provided, choose the class(es of amino acids that are most
important for the interactions detailed below.
#. forming ionic bonds with negatively charged C@#
/. forming hydrogen bonds to aid solubility in water
&. binding to another water-soluble protein
C. localiKing an Qintegral membraneR protein that spans a lipid bilayer
7. tightly pac6ing the hydrophobic interior core of a globular protein
acidic nonpolar
basic uncharged polar
2-52 $t is now a routine tas6 to determine the e%act order in which individual subunits have
been lin6ed together in polynucleotides (C@# and polypeptides (proteins. 3owever, it
remains difficult to determine the arrangement of monomers in a polysaccharide. 7%plain
why this is the case.
2-53 4our lab director reBuests that you add new growth medium to the mammalian cell
cultures before heading home from the lab on a Friday night. Unfortunately, you need to
ma6e fresh medium because all the pre-mi%ed bottles of medium have been used. :ne of
the ingredients you 6now you need to add is a mi% of the essential amino acids (those that
cannot be made by the cells, but are needed in proteins. :n the shelf of dry chemicals
you find the amino acids you need, and you mi% them into your medium, along with all
the other necessary nutrients and replace the old medium with your new medium. :n
*unday, you come in to the lab ?ust to chec6 on your cells and find that the cells have not
grown. 4ou are sure you made the medium correctly, but on chec6ing you see that
somebody wrote a note on the dry mi%ture of amino acids you used< Q@ote< this mi%ture
contains only C-amino acids.R
#. 0hat is the meaning of the note and how does it e%plain the lac6 of cell growth in
your culture,
/. #re there any organisms that could grow using this mi%ture, Sustify your answer.
2-54 7ucaryotic cells have their C@# molecules inside their nuclei. 3owever, to pac6age the
C@# all into such a small volume reBuires the cell to use specialiKed proteins called
histones. 3istones have amino acid seBuences enriched for lysines and arginines.
#. 0hat problem might a cell face in trying to pac6age C@# into a small volume
without histones, and how do these special pac6aging proteins alleviate the
problem,
/. Hysine side chains are substrates for enKymes called acetylases. # diagram of an
acetylated lysine side chain is shown in Figure Q2-+'. 3ow do you thin6 the
acetylation of lysines in histone proteins will affect the ability of a histone to
perform its role (refer to your answer in part #,
Figure Q2-+'