CHAPTER 5

DNA AND CHROMOSOMES

2009 Garland Science Publishing
The Srucure and !unci"n "# DNA
5-1 Using terms from the list below, fill in the blanks in the following brief description of the
experiment with Streptococcus pneumoniae that identified which biological molecule
carries heritable genetic information. Some terms may be used more than once.
Cell-free extracts from S-strain cells of S. pneumoniae were fractionated
to __________________ D!, "!, protein, and other cell components.
#ach fraction was then mixed with __________________ cells of S.
pneumoniae. $ts ability to change these into cells with
__________________ properties resembling the __________________
cells was tested by in%ecting the mixture into mice. &nly the fraction
containing __________________ was able to __________________ the
__________________ cells to __________________ 'or
__________________ ( cells that could kill mice.
carbohydrate lipid "-strain
D! nonpathogenic "!
identify pathogenic S-strain
label purify transform
5-2 )any of the breakthroughs in modern biology came after *atson and Crick
published their model of D! in +,-.. $n what decade did scientists first identify
chromosomes/
'a( +001s
'b( +,21s
'c( +,31s
'd( +401s
5-3 )itotic chromosomes were first 5isuali6ed in the +001s with the use of 5ery simple tools7
a basic light microscope and some dyes. *hich of the following characteristics of mitotic
chromosomes reflects how they were named/
'a( motion
'b( color
'c( shape
'd( location
5-4 $n a D! double helix, _____________________.
'a( the two D! strands are identical
'b( purines pair with purines
'c( thymine pairs with cytosine
'd( the two D! strands run antiparallel
5-5 $ndicate whether the following statements are true or false. $f a statement is false, explain
why it is false.
!. D! molecules, like proteins, consist of a single, long polymeric chain that is
assembled from small monomeric subunits.
8. 9he polarity of a D! strand results from the polarity of the nucleotide subunits.
C. 9here are fi5e different nucleotides that become incorporated into a D! strand.
D. :ydrogen bonds between each nucleotide hold indi5idual D! strands together.
5-6 Se5eral experiments were re;uired to demonstrate how traits are inherited. *hich
scientist or team of scientists first demonstrated that cells contain some component that
can be transferred to a new population of cells and permanently cause changes in the new
cells/
'a( <riffith
'b( *atson and Crick
'c( !5ery, )ac=eod, and )cCarty
'd( :ershey and Chase
5-7 Se5eral experiments were re;uired to demonstrate how traits are inherited. *hich
scientist or team of scientists obtained definiti5e results demonstrating that D! is the
genetic molecule/
'a( <riffith
'b( *atson
'c( Crick
'd( :ershey and Chase
5-8 *hich of the following chemical groups is not used to construct a D! molecule/
'a( fi5e-carbon sugar
'b( phosphate
'c( nitrogen-containing base
'd( six-carbon sugar
5-9 *hich of the following se;uences can fully base-pair with itself/
'a( ->-!!<CC<!!-.>
'b( ->-!!<CC<99-.>
'c( ->-!!<C<C!!-.>
'd( ->-!!<C<C99-.>
5-10 9he D! from two different species can often be distinguished by a difference in the
______________________.
'a( ratio of ! ? 9 to < ? C
'b( ratio of ! ? < to C ? 9
'c( ratio of sugar to phosphate
'd( presence of bases other than !, <, C, and 9
5-11 @or a better understanding of D! structure, it helps to be able to compare physical
characteristics e5ident from a side 5iew of double-stranded D! with those of indi5idual
base pairs.
!. Use brackets to designate the ma%or and minor groo5es on @igure A--++! and
shade in the surface that will be exposed in the ma%or gro5e in @igure A--++8.
8. $f base pairs were aligned and stacked directly on top of each other, the ma%or and
minor groo5es would be linear depressions all along the D!. #xplain why this is
not the actual conformation of a D! molecule.
@igure A--++
5-12 *hich D! base pair is represented in @igure A--+2/
'a( !-9
'b( 9-!
'c( <-C
'd( C-<
@igure A--+2
5-13 Use the terms listed to fill in the blanks in @igure A--+..
!. !-9 base pair
8. <-C base pair
C. deoxyribose
D. phosphodiester bonds
#. purine base
@. pyrimidine base
@igure A--+.
5-14 9he structures of the four bases in D! are gi5en in @igure A--+3.
@igure A--+3
!. *hich are purines and which are pyrimidines/
8. *hich bases pair with each other in double-stranded D!/
5-15 Using the structures in @igure A--+- as a guide, sketch the hydrogen bonds
between the base pairs in D!. :int7 9he bases in the figure are all drawn with
the B:B that attaches to the sugar at the bottom of the structure.
5-16 8ecause hydrogen bonds hold the two strands of a D! molecule together, the
strands can be separated without breaking any co5alent bonds. #5ery uni;ue D!
molecule CmeltsD at a different temperature. $n this context, Tm, melting
temperature, is the point at which two strands separate, or become denatured.
&rder the D! se;uences listed below according to relati5e melting temperatures
'from lowest Tm to highest Tm(. !ssume that they all begin as stable double-
stranded D! molecules. #xplain your answer.
!. <<C<C!CC
8. 9!99<9C9
C. <!C9CC9<
D. C9!!C9<<
5-17 $ndicate whether the following statements are true or false. $f a statement is false, explain
why it is false.
!. #ach strand of D! contains all the information needed to create a new double-
stranded D! molecule with the same se;uence information.
8. !ll functional D! se;uences inside a cell code for protein products.
C. <ene expression is the process of duplicating genes during D! replication.
D. <ene se;uences correspond exactly to the respecti5e protein se;uences produced
from them.
5-18 9he complete set of information found in a gi5en organismEs D! is called its
____________.
(a( genetic code
'b( coding se;uence
'c( gene
'd( genome
5-19 9he manner in which a gene se;uence is related to its respecti5e protein se;uence
is referred to as the _________ code.
'a( protein
'b( genetic
'c( translational
'd( expression
5-20 <i5en the se;uence of one strand of a D! helix as
->-<C!99C<9<<<9!<-.>,
gi5e the se;uence of the complementary strand and label the -> and .> ends.
5-21 *hen double-stranded D! is heated, the two strands separate into single strands in a
process called melting or denaturation. 9he temperature at which half of the duplex D!
molecules are intact and half ha5e melted is defined as the Tm.
!. Do you think Tm is a constant, or can it depend on other small molecules in the
solution/ Do you think high salt concentrations increase, decrease, or ha5e no
effect on Tm/
8. Under standard conditions, the expected melting temperature in degrees Celsius
can be calculated from the e;uation Tm F -,., ? 1.3+ GH'< ? C(I B GJ4-Klength of
duplexI. Does the Tm increase or decrease if there are more < ? C 'and thus fewer
! ? 9( base pairs/ Does the Tm increase or decrease as the length of D!
increases/ *hy/
C. Calculate the predicted Tm for a stretch of double helix that is +11 nucleotides
long and contains -1H < ? C content.
5-22 Consider the structure of the D! double helix.
!. Lou and a friend want to split a double-stranded D! molecule so you each ha5e
half. $s it better to cut the length of D! in half so each person has a shorter
length, or to separate the strands and each take one strand/ #xplain.
8. $n the original +,-. publication describing the disco5ery of the structure of D!,
*atson and Crick wrote, C$t has not escaped our notice that the specific pairings
we ha5e postulated immediately suggest a possible copying mechanism for the
genetic material.D *hat did they mean/
5-23 !. $n principle, what would be the minimum number of consecuti5e nucleotides
necessary to correspond to a single amino acid to produce a workable genetic
code/ !ssume that each amino acid is encoded by the same number of
nucleotides. #xplain your reasoning.
8. &n a5erage, how often would the nucleotide se;uence C<!99< be expected to
occur in a D! strand 3111 bases long/ #xplain your reasoning.
The Srucure "# Eucar$"ic Chr"%"s"%es
5-24 @or each of the following sentences, fill in the blanks with the best word or phrase
selected from the list below. ot all words or phrases will be usedM each word or phrase
should be used only once.
$n eucaryotic __________________, D! is complexed with proteins to
form __________________. 9he paternal and maternal copies of human
Chromosome + are __________________, whereas the paternal copy of
Chromosome + and the maternal copy of Chromosome . are
__________________. Cytogeneticists can determine large-scale
chromosomal abnormalities by looking at a patientEs
__________________. @luorescent molecules can be used to paint a
chromosome by a techni;ue that employs D! __________________,
and thereby to identify each chromosome by microscopy.
bands extended kinetochore
chromatin homologous nonhomologous
chromosomes hybridi6ation
condensation karyotype
5-25 !. Define a gene.
8. Consider two different species of yeast that ha5e similar genome si6es. $s it likely
that they contain the same number of genes/ ! similar number of chromosomes/
C. @igure --+- in the textbook shows the < ? C content and genes found along a
single chromosome. $s there any relationship between the < ? C content and the
locations of genes/
5-26 9he human genome has enough D! to stretch more than 2 m. :owe5er, this D! is not
contained in a single moleculeM it is di5ided into linear segments and packaged into
structures called chromosomes. *hat is the total number of chromosomes found in each
of the somatic cells in your body/
'a( 22
'b( 2.
'c( 33
'd( 3J
5-27 9he number of cells in an a5erage-si6ed adult human is on the order of +1
+3
. Use
this information, and the estimate that the length of D! contained in each cell is
2 m, to do the following calculations 'look up the necessary distances and show
your working(7
!. &5er how many miles would the total D! from the a5erage human stretch/
8. :ow many times would the total D! from the a5erage human wrap around the
planet #arth at the #;uator/
C. :ow many times would the total D! from the a5erage human stretch from #arth
to the Sun and back/
D. :ow many times would the total D! from the a5erage human stretch from the
#arth to Nluto and back/
5-28 9he process of sorting human chromosomes pairs by si6e and morphology is called
karyotyping. ! modern method employed for karyotyping is called chromosome painting.
:ow are indi5idual chromosomes CpaintedD/
'a( with a laser
'b( using fluorescent antibodies
'c( using fluorescent D! molecules
'd( using green fluorescent protein
5-29 9he human genome comprises 2. pairs of chromosomes found in nearly e5ery cell in the
body. !nswer the ;uantitati5e ;uestions below by choosing one of the numbers in the
following list7
2. J, O211
3J ,2 O+1
,
!. :ow many centromeres are in each cell/ *hat is the main function of the
centromere/
8. :ow many telomeres are in each cell/ *hat is their main function/
C. :ow many replication origins are in each cell/ *hat is their main function/
5-30 #xplain the differences between chromosome painting and the older, more traditional
method of staining chromosomes being prepared for karyotyping. :ighlight the way in
which each method identifies chromosomes by the uni;ue se;uences they contain.
5-31 $ndicate whether the following statements are true or false. $f a statement is false, explain
why it is false.
!. Comparing the relati5e number of chromosome pairs is a good way to determine
whether two species are closely related.
8. Chromosomes exist at different le5els of condensation, depending on the stage of
the cell cycle.
C. #ucaryotic chromosomes contain many different sites where D! replication can
be initiated.
D. 9he telomere is a speciali6ed D! se;uence where microtubules from the mitotic
spindle attach to the chromosome so that duplicate copies mo5e to opposite ends
of the di5iding cell.
5-32 @or each of the following sentences, fill in the blanks with the best word or phrase
selected from the list below. ot all words or phrases will be usedM each word or phrase
should be used only once.
#ach chromosome is a single molecule of __________________ whose
extraordinarily long length can be compacted by as much as
__________________-fold during __________________ and tenfold
more during __________________. 9his is accomplished by binding to
__________________ that help package the D! in an orderly manner so
it can fit in the small space delimited by the __________________. 9he
structure of the D!Bprotein complex, called __________________, is
highly __________________ o5er time.
+1,111 chromosome mitosis
+11 different nuclear en5elope
+111 D! nucleolus
cell cycle dynamic proteins
cell wall interphase similar
chromatin lipids static
5-33 9he images of chromosomes we typically see are isolated from mitotic cells. 9hese
mitotic chromosomes are in the most highly condensed form. $nterphase cells contain
chromosomes that are less densely packed and __________________________.
'a( occupy discrete territories in the nucleus
'b( share the same nuclear territory as their homolog
'c( are restricted to the nucleolus
'd( are completely tangled with other chromosomes
5-34 @igure A--.3 clearly depicts the nucleolus, a nuclear structure that looks like large dark
region when stained. 9he other dark speckled regions in this image are the locations of
particularly compact chromosomal segments called ____________.
'a( euchromatin
'b( heterochromatin
'c( nuclear pores
'd( nucleosomes
@igure A--.3
5-35 )itotic chromosomes are _____ times more compact than a D! molecule in its
extended form.
'a( +1,111
'b( +11,111
'c( +111
'd( +11
5-36 $nterphase chromosomes are about______ times less compact than mitotic chromosomes,
but still are about______ times more compact than a D! molecule in its extended form.
'a( +1M +111
'b( 21M -11
'c( -M 2111
'd( -1M 211
5-37 @or each of the following sentences, choose one of the options enclosed in s;uare
brackets to make a correct statement about nucleosomes.
!. ucleosomes are present in Gprocaryotic/eucaryoticI chromosomes, but not in
Gprocaryotic/eucaryoticI chromosomes.
8. ! nucleosome contains two molecules each of histones GH1 and H2A/H2A and
H2BI as well as of histones :. and :3.
C. ! nucleosome core particle contains a core of histone with D! wrapped around
it approximately Gtwice/three tie!/"our tie!I.
D. ucleosomes are aided in their formation by the high proportion of
Gacidic/#a!ic/po$arI amino acids in histone proteins.
#. ucleosome formation compacts the D! into approximately Gone-third/one-
hundredth/one-thou!andthI of its original length.
5-38 9he classic Cbeads-on-a-stringD structure is the most decondensed chromatin structure
possible and is produced experimentally. *hich chromatin components are not retained
when this structure is generated/
'a( linker histones
'b( linker D!
'c( nucleosome core particles
'd( core histones
5-39 ucleosomes are formed when D! wraps _____ times around the histone octamer in a
______ coil.
'a( 2.1M right-handed
'b( 2.-M left-handed
'c( +.4M left-handed
'd( +..M right-handed
5-40 @or each of the following sentences, fill in the blanks with the best word or phrase
selected from the list below. ot all words or phrases will be usedM each word or phrase
should be used only once.
$nterphase chromosomes contain both darkly staining
__________________ and more lightly staining __________________.
<enes that are being transcribed are thought to be packaged in a
__________________ condensed type of euchromatin. ucleosome core
particles are separated from each other by stretches of
__________________ D!. ! string of nucleosomes coils up with the
help of __________________ to form the more compact structure of the
__________________. ! __________________ model describes the
structure of the .1 nm fiber. 9he .1 nm chromatin fiber is further
compacted by the formation of __________________ that emanate from a
central __________________.
.1 nm fiber heterochromatin linker
acti5e chromatin histone :+ loops
axis histone :. more
beads-on-a-string histone :3 synaptic complex
euchromatin less 6ig6ag
5-41 9he octameric histone core is composed of four different histone proteins, assembled in a
stepwise manner. &nce the core octamer has been formed, D! wraps around it to form
a nucleosome core particle. *hich of the following histone proteins does not form part of
the octameric core/
'a( :3
'b( :2!
'c( :.
'd( :+
5-42 9he core histones are small, basic proteins that ha5e a globular domain at the C-terminus
and a long extended conformation at the -terminus. *hich of the following is not true
of the terminal CtailD of these histones/
'a( $t is sub%ect to co5alent modifications,
'b( $t extends out of the nucleosome core.
'c( $t binds to D! in a se;uence-specific manner.
'd( $t helps D! pack tightly.
5-43 Stepwise condensation of linear D! happens in fi5e different packing processes. *hich
of the following four processes has a direct re;uirement for histone :+/
'a( formation of Cbeads-on-a-stringD
'b( formation of the .1 nm fiber
'c( looping of the .1 nm fiber
'd( packing of loops to form interphase chromosomes
5-44 #5idence suggests that the replication of D! packaged into heterochromatin occurs
later than the replication of other chromosomal D!. *hat is the simplest possible
explanation for this phenomenon/
The Regulai"n "# Chr"%"s"%e Srucure
5-45 !lthough the chromatin structure of interphase and mitotic chromosomes is 5ery
compact, D!-binding proteins and protein complexes must be able to gain access to the
D! molecule. Chromatin-remodeling complexes pro5ide this access by
__________________.
'a( recruiting other en6ymes
'b( modifying the -terminal tails of core histones
'c( using the energy of !9N hydrolysis to mo5e nucleosomes
'd( denaturing the D! by interfering with hydrogen-bonding between base pairs
5-46 Lou are studying a newly identified chromatin-remodeling complex, which you call
$C"C. Lou decide to run an in vitro experiment to characteri6e the acti5ity of the
purified complex. Lour molecular toolbox includes7 '+( a 311-base-pair D! molecule
that has a single recognition site for the restriction endonuclease #co"$, an en6yme that
clea5es internal sites on double-stranded D! 'dsD!(M '2( purified #co"$ en6ymeM '.(
purified Dase $, a D! endonuclease that will clea5e dsD! at nonspecific sites if they
are exposedM and '3( core octamer histones. Lou are able to assemble core nucleosomes
on this D! template and test for $C"C acti5ity. @igure A--3J! illustrates the D!
template used and indicates both the location of the #co"$ clea5age site and the si6e of
the D! fragments that are produced when it cuts. @igure A--3J8 illustrates how the
D! molecules in your experiment looked after separation according to si6e by using gel
electrophoresis. Lour experiment had a total of six samples, each of which was treated
according to the legend below the gel. 9he si6es of the D! fragments obser5ed are
indicated on the left side of the gel.
@igure A--3J
! #xplain the results in lanes +B3 and why it is important to ha5e this information
before you begin to test your remodeling complex.
8. *hat can you conclude about your purified remodeling complex from the results
in lanes - and J/
5-47 9he -terminal tail of histone :. can be extensi5ely modified, and depending on the
number, location, and combination of these modifications, these changes may promote
the formation of heterochromatin. *hat is the result of heterochromatin formation/
'a( increase in gene expression
'b( gene silencing
'c( recruitment of remodeling complexes
'd( displacement of histone :+
5-48 )ethylation and acetylation are common changes made to histone :., and the specific
combination of these changes is sometimes referred to as the Chistone code.D *hich of
the following patterns will probably lead to gene silencing/
'a( lysine , methylation
'b( lysine 3 methylation and lysine , acetylation
'c( lysine +3 acetylation
'd( lysine , acetylation and lysine +3 acetylation
5-49 *hen there is a well-established segment of heterochromatin on an interphase
chromosome, there is usually a special barrier se;uence that pre5ents the heterochromatin
from expanding along the entire chromosome. <ene !, which is normally expressed, has
been mo5ed by D! recombination near an area of heterochromatin. one of the
daughter cells produced after this recombination e5ent express gene !, e5en though its
D! se;uence is unchanged. *hat is this the best way to describe what has happened to
the function of gene ! in these cells/
'a( barrier destruction
'b( heterochromati6ation
'c( epigenetic inheritance
'd( euchromatin depletion
5-50 Lour friend is working in a lab to study how yeast cells adapt to growth on different
carbon sources. :e grew half of his cells in the presence of glucose and the other half in
the presence of galactose. 9hen he har5ested the cells and isolated their D! with a
gentle procedure that lea5es nucleosomes and some higher-order chromatin structures
intact. :e treated the D! briefly with a low concentration of )-nuclease, a special
en6yme that easily degrades protein-free stretches of D!. !fter remo5ing all the
proteins, he separated the resulting D! on the basis of length. @inally, he used a
procedure to 5isuali6e only those D! fragments from a region near a particular gene
called Sweetie or another gene called Salty. 9he separated D! fragments are shown in
@igure A---1. #ach 5ertical column, called a lane, is from a different sample. D! spots
near the top of the figure represent D! molecules that are longer than those near the
bottom. Darker spots contain more D! than fainter spots. 9he lanes are as follows7
+. CmarkerD containing known D! fragments of indicated lengths
2. cells grown in glucose, D! 5isuali6ed near Sweetie gene
.. cells grown in galactose, D! 5isuali6ed near Sweetie gene
3. cells grown in glucose, D! 5isuali6ed near Salty gene
-. cells grown in galactose, D! 5isuali6ed near Salty gene
@igure A---1
!. 9he lowest spot 'as obser5ed in lanes 2, 3, and -( has a length of about +-1
nucleotides. Can you propose what it is and how it arose/
8. *hat are the spots with longer lengths/ *hy is there a ladder of spots/
C. otice the faint spots and extensi5e smearing in lane ., suggesting the D! could
be cut almost anywhere near the Sweetie gene after growth of the cells in
galactose. 9his was not obser5ed in the other lanes. *hat probably happened to
the D! to change the pattern between lanes 2 and ./
D. *hat kinds of en6yme might ha5e been in5ol5ed in changing the chromatin
structure between lanes 2 lane ./
#. Do you think that gene expression of Sweetie is higher, lower, or the same in
galactose compared to glucose/ *hat about Salty/