Studiebot antwoord

Vraag gesteld door: Rina2005 - 1 jaar geleden

Maak een oefenexamen van de volgende tekst: Hereditary information in DNA directs the development of
your biochemical, anatomical, physiological, and, to some
extent, behavioral traits. Your resemblance to your parents has
its basis in the accurate replication of DNA prior to meiosis and
therefore its transmission from your parents generation to
yours. Replication prior to mitosis ensures faithful transmission
of genetic information from a parent cell to two daughter cells.
Of all natures molecules, nucleic acids are unique in their
ability to dictate their own replication from monomers. The
relationship between structure and function is evident in the
double helix: The specific complementary pairing of nitroge
nous bases in DNA has a functional significance. Watson and
Crick ended their classic paper with this statement: It has
not escaped our notice that the specific pairing we have pos
tulated immediately suggests a possible copying mechanism
for the genetic material.1 In this section, you will learn about
the basic principle of DNA replication, the copying of DNA,
as well as some important details of the process.
1
J. D. Watson and F. H. C. Crick, Molecular structure of nucleic acids: a structure
for deoxyribose nucleic acids, Nature 171:737738 (1953).
370
light blue represents newly synthesized DNA.
. Figure 16.10 A model for DNA
replication: the basic concept. In this
simplified illustration, a short segment of DNA
5
3
3
A
C
T
A
G
T
G
A
T
C
5
has been untwisted. Simple shapes symbolize
the four kinds of bases. Dark blue represents
DNA strands present in the parental molecule;
5
3
A
C
T
A
G
T
G
A
Mastering Biology Animation:
DNA Replication: An Overview
5
3
A
C
T
5
A
G
T
T
C
3
(a) The parental molecule has two complemen
tary strands of DNA. Each base is paired by
hydrogen bonding with its specific partner,
A with T and G with C.
(b) First, the two DNA strands are separated.
Each parental strand can now serve as a
template for a new, complementary
strand.
A
G
5
3
A
T
C
C
T
A
G
5
3
3
T
G
A
T
C
5
(c) Nucleotides complementary to the parental
(dark blue) strand are connected to form the
sugar-phosphate backbones of the new
daughter (light blue) strands.
The Basic Principle: Base Pairing
to a Template Strand
In a second paper, Watson and Crick stated their hypothesis for
how DNA replicates: Now our model for deoxyribonucleic acid
is, in effect, a pair of templates, each of which is complementary
to the other. We imagine that prior to duplication the hydrogen
bonds are broken, and the two chains unwind and separate. Each
chain then acts as a template for the formation on to itself of a
new companion chain, so that eventually we shall have two pairs
of chains, where we only had one before. Moreover, the sequence
of the pairs of bases will have been duplicated exactly.2
Figure 16.10 illustrates the basic idea. If you cover a DNA
strand in Figure 16.10a, its linear sequence of nucleotides is
revealed by applying the base-pairing rules to the uncovered
strand. The two strands are complementary; each stores the
information necessary to reconstruct the other. When a cell
copies a DNA molecule, each strand serves as a template for
ordering nucleotides into a new, complementary strand.
Nucleotides line up along the template strand according to the
base-pairing rules and are linked to form the new strands. One
double-stranded DNA molecule becomes two, each an exact
replica of the parental molecule.
This model of DNA replication remained untested for several
years following publication of the DNA structure. The necessary
experiments were simple in concept but difficult to perform.
Watson and Cricks model predicts that when a double helix
replicates, each of the two daughter molecules will have one
old strand, from the parental molecule, and one newly made
strand. This semiconservative model can be distinguished
from a conservative model of replication, in which the two paren
tal strands somehow come back together after the process (that
is, the parental molecule is conserved). In yet a third model,
called the dispersive model, all four strands of DNA following
replication have a mixture of old and new DNA (Figure 16.11).
2
J. D. Watson and F. H. C. Crick, Genetical implications of the structure of
deoxyribonucleic acid, Nature 171:964967 (1953).
. Figure 16.11 DNA replication: three alternative models.
Each short segment of double helix symbolizes the DNA within a
cell. Beginning with a parent cell, we follow the DNA for two more
generations of cellstwo rounds of DNA replication. Parental DNA
is dark blue; newly made DNA is light blue.
Parent cell
First
replication
Second
replication
(a) Conservative model.
The two parental
strands reassociate
after acting as
templates for new
strands, thus
restoring the
parental double
helix.
(b) Semiconservative model.
The two strands
of the parental
molecule separate,
and each functions
as a template for
synthesis of a new,
complementary
strand.
(c) Dispersive model.
Each strand of
both daughter
molecules con
tains a mixture of
old and newly
synthesized DNA.
CHAPTER 16 Nucleic Acids and Inheritance
371
Although mechanisms for conservative or dispersive DNA
replication are not easy to devise, these models remained
possibilities until they could be ruled out. After two years of
preliminary work at the California Institute of Technology in
the late 1950s, Matthew Meselson and Franklin Stahl devised
a clever experiment that distinguished between the three
models, described in Figure 16.12. Their results supported the
semiconservative model of DNA replication, as predicted by
Watson and Crick, and their experiment is widely recognized
among biologists as a classic example of elegant design.
The basic principle of DNA replication is conceptually sim
ple. However, the actual process involves some complicated
biochemical gymnastics, as we will now see.
DNA Replication: A Closer Look
The bacterium E. coli has a single chromosome of about
4.6 million nucleotide pairs. In a favorable environment, an
E. coli cell can copy all of this DNA and divide to form two geneti
cally identical daughter cells in considerably less than an hour.
Each of your somatic cells has 46 DNA molecules in its nucleus,
one long double-helical molecule per chromosome. In all, that
represents about 6 billion nucleotide pairs, or over 1,000 times
more DNA than is found in most bacterial cells. If we were to
print the one-letter symbols for these bases (A, G, C, and T) the
size of the type you are now reading, the 6 billion nucleotide pairs
of information in a diploid human cell would fill about 1,400
biology textbooks. Yet it takes one of your cells just a few hours
to copy all of this DNA during S phase of interphase. This replica
tion of an enormous amount of genetic information is achieved
with very few errorsonly about one per 10 billion nucleotides.
The copying of DNA is remarkable in its speed and accuracy.
More than a dozen enzymes and other proteins participate
in DNA replication. Much more is known about how this
replication machine works in bacteria (such as E. coli) than
in eukaryotes, and we will describe the basic steps of the pro
cess for E. coli, except where otherwise noted. What scientists
have learned about eukaryotic DNA replication suggests,
however, that most of the process is fundamentally similar
for prokaryotes and eukaryotes.
Getting Started
The replication of chromosomal DNA begins at particular sites
called origins of replication, short stretches of DNA that
have a specific sequence of nucleotides. The E. coli chromo
some, like many other bacterial chromosomes, is circular and
has a single origin. Proteins that initiate DNA replication recog
nize this sequence and attach to the DNA, separating the two
strands and opening up a replication bubble (Figure 16.13a).
Replication of DNA then proceeds in both directions until the
entire molecule is copied. In contrast to a bacterial chromosome,
a eukaryotic chromosome may have hundreds or even a few
thousand replication origins. Multiple replication bubbles form
and eventually fuse, thus speeding up the copying of the very
UNIT THREE The Genetic Basis of Life
Figure 16.12 Inquiry
Does DNA replication follow the conservative,
semiconservative, or dispersive model?
Experiment Matthew Meselson and Franklin Stahl cultured
E. coli for several generations in a medium containing nucleo
tide precursors labeled with a heavy isotope of nitrogen, 15N.
They then transferred the bacteria to a medium with only 14N,
a lighter isotope. They took one sample after the first DNA
replication and another after the second replication. They ex
tracted DNA from the bacteria in the samples and then centri
fuged each DNA sample to separate DNA of different densities.
1
Results
Bacteria
cultured in
medium
with 15N
(heavy
isotope)
3
DNA sample
centrifuged
after first
replication
2
Bacteria
transferred
to medium
with 14N
(lighter
isotope)
4 Less
dense
DNA sample
centrifuged
after second
replication
More
dense
Conclusion Meselson and Stahl compared their results to
those predicted by each of the three models in Figure 16.11, as
shown below. The first replication in the 14N medium produced
a band of many molecules of hybrid (15N-14N) DNA. This result
eliminated the conservative model. The second replication pro
duced both light and hybrid DNA, a result that refuted the dis
persive model and supported the semiconservative model. They
therefore concluded that DNA replication is semiconservative.
Predictions:
Conservative
model
Semiconservative
model
First replication
Dispersive
model
Second replication
Data from M. Meselson and F. W. Stahl, The replication of DNA in Escherichia
coli, Proceedings of the National Academy of Sciences USA 44:671682 (1958).
INQUIRY IN ACTION Read and analyze the original paper in
Inquiry in Action: Interpreting Scientific Papers.
Instructors: A related Experimental Inquiry Tutorial can be
assigned in Mastering Biology.
WHAT IF? If Meselson and Stahl had first grown the cells in
14N-containing medium and then moved them into 15N-containing
medium before taking samples, what would have been the result
after each of the two replications?
372
CHAPTER 16 Nucleic Acids and Inheritance 373
long DNA molecules (Figure 16.13b). As in bacteria, eukaryotic
DNA replication proceeds in both directions from each origin.
At each end of a replication bubble is a replication fork,
a Y-shaped region where the parental strands of DNA are being
unwound. Several kinds of proteins participate in the unwind
ing (Figure 16.14). Helicases are enzymes that untwist the
double helix at the replication forks, separating the two paren
tal strands and making them available as template strands.
After the parental strands separate, single-strand binding
proteins bind to the unpaired DNA strands, keeping them
from re-pairing. The untwisting of the double helix causes
tighter twisting and strain ahead of the replication fork.
Topoisomerase is an enzyme that helps relieve this strain by
breaking, swiveling, and rejoining DNA strands.
Synthesizing a New DNA Strand
The unwound sections of parental DNA strands are now
available to serve as templates for the synthesis of new
complementary DNA strands. However, the enzymes that
(a) Origin of replication in an E. coli cell (b) Origins of replication in a eukaryotic cell
Origin of replication Origin of
replication
Double
stranded
DNA molecule
Double-stranded DNA molecule
Two daughter
DNA molecules
Parental (template) strand
Bubble
Parental (template) strand
Replication fork
Replication fork
Replication
bubble
Two daughter DNA molecules
Daughter (new) strand
Daughter (new) strand
In a linear chromosome of a eukaryote, replication bubbles form at
many sites along the giant DNA molecule during S phase of interphase.
The bubbles expand as replication proceeds in both directions (red
arrows). Eventually, the bubbles fuse and synthesis of the daughter
strands is complete. The TEM shows three replication bubbles along the
DNA of a cultured Chinese hamster cell.
The circular chromosome of E. coli and other bacteria has only one
origin of replication. The parental strands separate there, forming
a replication bubble with two forks (red arrows). Replication
proceeds in both directions until the forks meet on the other side,
resulting in two daughter DNA molecules. The TEM shows a
bacterial chromosome with a replication bubble.
0.5 om
0.25 om
. Figure 16.13 Origins of replication in E. coli and eukaryotes. The red arrows indicate the
movement of the replication forks and thus the overall directions of DNA replication within each bubble.
DRAW IT In the TEM, add arrows in the forks of the third bubble.
Mastering Biology BioFlix Animation: The Replication Fork in E. coli
RNA
primer
Replication
fork
Topoisomerase breaks, swivels,
and rejoins the parental DNA
ahead of the replication fork,
relieving the strain caused by
unwinding.
Single-strand binding
proteins stabilize the un
wound parental strands.
Helicase unwinds
and separates
the parental
DNA strands.
Primase synthesizes RNA
primers, using the parental
DNA as a template.
5
3
5
5
3
3
. Figure 16.14 Some of the proteins involved in the
initiation of DNA replication. The same proteins function at both
replication forks in a replication bubble. For simplicity, only the left
hand fork is shown, and the DNA bases are drawn much larger in
relation to the proteins than they are in reality.
. Figure 16.15 Addition of a nucleotide to a DNA strand.
synthesize DNA cannot initiate the synthesis of a poly
nucleotide; they can only add DNA nucleotides to the end
of an already existing chain that is base-paired with the
template strand. An initial nucleotide chain that can be used
as a pre-existing chain is produced during DNA synthesis;
this is actually a short stretch of RNA, not DNA. The RNA
chain is called a primer and is synthesized by the enzyme
primase (see Figure 16.14). Primase starts a complementary
RNA chain with a single RNA nucleotide and adds RNA
nucleotides one at a time, using the parental DNA strand
as a template. The completed primer, generally five to
ten nucleotides long, is thus base-paired to the template
strand. The new DNA strand will start from the 3 end of
the RNA primer.
Enzymes called DNA polymerases catalyze the synthesis
of new DNA by adding nucleotides to the 3 end of a pre
existing chain. In E. coli, there are several DNA polymerases,
but two of them appear to play the major roles in DNA
replication: DNA polymerase III and DNA polymerase I. The
situation in eukaryotes is more complicated, with at least 11
different DNA polymerases discovered so far, although the
general principles are the same.
Most DNA polymerases require a primer and a DNA tem
plate strand, along which complementary DNA nucleotides
are lined up, one by one. In E. coli, DNA polymerase III (abbre
viated DNA pol III) adds a DNA nucleotide to the RNA primer
and then continues adding DNA nucleotides, which are
complementary to the parental DNA template strand, to the
growing end of the new DNA strand. The rate of elongation
is about 500 nucleotides per second in bacteria and 50 per
second in human cells.
Each nucleotide to be added to a growing DNA strand
consists of a sugar attached to a base and to three phosphate
groups. You have already encountered such a moleculeATP
(adenosine triphosphate; see Figure 6.9). The only difference
between the ATP of energy metabolism and dATP, the adenine
nucleotide used to make DNA, is the sugar component, which
is deoxyribose in the building block of DNA but ribose in ATP.
Like ATP, the nucleotides used for DNA synthesis are chemi
cally reactive, partly because their triphosphate tails have an
unstable cluster of negative charge. DNA polymerase catalyzes
the addition of each monomer to the growing end of a DNA
strand by a condensation reaction in which two phosphate
groups are lost as a molecule of pyrophosphate (
P
Pi).
Subsequent hydrolysis of the pyrophosphate to two molecules
of inorganic phosphate (
Pi) is a coupled exergonic reaction
that helps drive the polymerization reaction (Figure 16.15).
Antiparallel Elongation
As we have noted previously, the two ends of a DNA strand
are different, giving each strand directionality, like a one-way
street (see Figure 16.5). In addition, the two strands of DNA
in a double helix are antiparallel, meaning that they are ori
ented in opposite directions to each other, like the two sides
UNIT THREE The Genetic Basis of Life
DNA polymerase catalyzes addition of a nucleotide to the 3 end
of a growing DNA strand, with the release of two phosphates.
New strand Template strand
5 3
Phosphate
Sugar
A T
Base
C G
G C
OH
3
Incoming nucleotide
A
C
5
DNA
poly
merase
P P i
Pyro
phosphate
5
3
A T
C G
G C
T
OH
P
3
2 i
DRAW IT Circle the area where the new bond was made.
Mastering Biology Figure Walkthrough
OH
A
C
5
of a divided street (see Figure 16.15). Therefore, the two new
strands formed during DNA replication must also be antipar
allel to their template strands.
The antiparallel arrangement of the double helix, together
with a constraint on the function of DNA polymerases, has
an important effect on how replication occurs. Because of
their structure, DNA polymerases can add nucleotides only
to the free 3 end of a primer or growing DNA strand, never
to the 5 end (see Figure 16.15). Thus, a new DNA strand can
elongate only in the 5 S 3 direction. With this in mind,
lets examine one of the two replication forks in a bubble
(Figure 16.16). Along one template strand, DNA polymerase
III can synthesize a complementary strand continuously by
elongating the new DNA in the mandatory 5 S 3 direction.
DNA pol III remains in the replication fork on that template
strand and continuously adds nucleotides to the new comple
mentary strand as the fork progresses. The DNA strand made
by this mechanism is called the leading strand. Only one
primer is required for DNA pol III to synthesize the entire
leading strand (see Figure 16.16).
To elongate the other new strand of DNA in the manda
tory 5 S 3 direction, DNA pol III must work along the other
template strand in the direction away from the replication
fork. The DNA strand elongating in this direction is called the
lagging strand. In contrast to the leading strand, which
elongates continuously, the lagging strand is synthesized
discontinuously, as a series of segments. These segments of
the lagging strand are called Okazaki fragments, after Reiji
Okazaki, the Japanese scientist who discovered them. The
fragments are about 1,0002,000 nucleotides long in E. coli
and 100200 nucleotides long in eukaryotes.
P
P
P
T
374
CHAPTER 16 Nucleic Acids and Inheritance 375
RNA primer
Site where
replication begins
Sliding clamp
DNA pol III
Parental DNA
Single-strand binding proteins
Helicase
Origin of replication Overview
Overall directions
of replication
Leading strand
Lagging strand
Lagging strand Template
strand
Leading strand
Primer
After an RNA primer is made,
DNA pol III starts to synthesize
the leading strand.
1
5
3
5
3
3
5
5
3
3
5
The leading strand is
elongated continuously
in the 5: 3 direction
as helicase opens up the
fork further to the left.
2
3
5
3
5
3
5
. Figure 16.16 Synthesis of the leading strand during DNA
replication. This diagram focuses on the left replication fork shown
in the overview box. DNA polymerase III (DNA pol III), shaped like a
cupped hand, is shown closely associated with a protein called the
sliding clamp that encircles the newly synthesized double helix
like a doughnut. The sliding clamp moves DNA pol III along the
DNA template strand.
Mastering Biology BioFlix Animation: Synthesis of the
Leading Strand
Figure 16.17 illustrates the steps in the synthesis of the
lagging strand at one fork. Whereas only one primer is
required on the leading strand, each Okazaki fragment on the
lagging strand must be primed separately (steps 1 and 4).
After DNA pol III forms an Okazaki fragment (steps 2 to 4),
another DNA polymerase, DNA pol I, replaces the RNA nucle
otides of the adjacent primer with DNA nucleotides one at a
time (step 5). But DNA pol I cannot join the final nucleotide
of this replacement DNA segment to the first DNA nucleotide
of the adjacent Okazaki fragment. Another enzyme, DNA
ligase, accomplishes this task, joining the sugar-phosphate
backbones of all the Okazaki fragments into a continuous
DNA strand (step 6).
Mastering Biology BioFlix Animation: Synthesis
of the Lagging Strand
3
1 2
5
3
3
5
Template
strand
Site where
replication
begins
Primer for
leading
strand
RNA primer
for fragment 1
RNA primer
for fragment 2
Okazaki fragment 1
Okazaki
fragment 2
DNA ligase forms
a bond between the
newest DNA and the
DNA of fragment 1.
6
Fragment 2 is primed.
Then DNA pol III adds DNA
nucleotides, detaching when it
reaches the fragment 1 primer.
4
The lagging
strand in this region
is now complete.
7
DNA pol III adds
DNA nucleotides to
the primer, forming
Okazaki fragment 1.
2
After reaching the
next RNA primer to
the right, DNA pol III
detaches.
3
Primase joins RNA
nucleotides into the first
primer for the lagging
strand.
1
Overall direction of replication
1
2
3
5 3
5
1
2
3
5 3
5
3
3
5
5
3 3
3
5
5
5
5
3
3
5
3
3
5
5
5
1
2
1
1
Origin of replication
Overall directions
of replication
Leading strand Lagging strand
Leading strand Template strand
DNA pol I replaces the RNA
with DNA, adding nucleotides
to the 3 end of fragment 1
(and, later, of fragment 2).
5
Overview
. Figure 16.17 Synthesis of the lagging strand.
376 UNIT THREE The Genetic Basis of Life
molecular brake, slowing progress of the replication fork and
coordinating the placement of primers and the rates of repli
cation on the leading and lagging strands. Second, the DNA
replication complex may not move along the DNA; rather,
the DNA may move through the complex during the replica
tion process. In eukaryotic cells, multiple copies of the com
plex, perhaps grouped into factories, may be anchored to
the nuclear matrix, a framework of fibers extending through
the interior of the nucleus.
Some experimental evidence supports a model in which
two DNA polymerase molecules, one on each template
strand, reel in the parental DNA and extrude newly made
daughter DNA molecules. In this so-called trombone model,
the lagging strand is also looped back through the complex
(Figure 16.19). Whether the complex moves along the DNA
or whether the DNA moves through the complex, either
anchored or not, are still open, unresolved questions that are
under active investigation.
Synthesis of the leading strand and synthesis of the lagging
strand occur concurrently and at the same rate. The lagging
strand is so named because its synthesis is delayed slightly
relative to synthesis of the leading strand; each new fragment
of the lagging strand cannot be started until enough template
has been exposed at the replication fork.
Figure 16.18 and Table 16.1 summarize DNA replication.
Please study them carefully before proceeding.
The DNA Replication Complex
It is traditionaland convenientto represent DNA poly
merase molecules as locomotives moving along a DNA rail
road track, but such a model is inaccurate in two important
ways. First, the various proteins that participate in DNA rep
lication actually form a single large complex, a DNA replica
tion machine. Many protein-protein interactions facilitate
the efficiency of this complex. For example, by interacting
with other proteins at the fork, primase apparently acts as a
DNA pol III
Leading strand
Leading strand
template
Lagging strand
template
Lagging strand
DNA pol III
Parental DNA
DNA pol I DNA ligase
Primase Primer
5
5
5
5
3
5
3
5
3
3
3
3
Helicase
unwinds the
parental
double helix.
1
Molecules of single
strand binding protein
stabilize the unwound
template strands.
2
The leading strand is
synthesized continuously
in the 5 to 3 direction
by DNA pol III.
3
6 5
Primase begins synthesis
of the RNA primer for the
fifth Okazaki fragment.
4
DNA ligase joins the
3 end of fragment 2
to the 5 end of
fragment 1.
7
1 2 3
4
5
Origin of replication
Overview
Overall directions
of replication
Leading strand
Lagging strand
Lagging strand
Leading strand
DNA pol III is completing
synthesis of fragment 4. When
it reaches the RNA primer on
fragment 3, it will detach and
begin adding DNA nucleotides
to the 3 end of the fragment 5
primer in the replication fork.
DNA pol I removes the primer
from the 5 end of fragment 2,
replacing it with DNA nucleotides
added one by one to the 3 end of
fragment 3. After the last addition,
the backbone is left with a free
3 end.
. Figure 16.18 A summary of bacterial DNA replication. The detailed diagram shows the left-hand
replication fork of the replication bubble shown in the overview (upper right). Viewing each daughter strand in
its entirety in the overview, you can see that half of it is made continuously as the leading
strand, while the other half (on the other side of the origin) is synthesized in fragments
as the lagging strand.
DRAW IT Draw a diagram
showing the right-hand fork of the
bubble in this figure. Number the
Okazaki fragments, and label all
5 and 3 ends.
Mastering Biology Animation: DNA Replication: A Closer Look
CHAPTER 16 Nucleic Acids and Inheritance 377
Parental DNA
Helicase
Leading strand
Leading strand template
Lagging strand
Connecting protein
DNA pol III
Lagging
strand
template
DNA pol III
5
3
3 5
5 3
5
Overall direction of replication
3
5 3
3 5
. Figure 16.19 The trombone model of the DNA
replication complex. In this proposed model, two molecules
of DNA polymerase III work together in a complex, one on each
strand, with helicase and other proteins. The lagging strand
template DNA loops through the complex, resembling the slide
of a trombone.
DRAW IT Draw a line tracing the lagging strand template in this figure.
Mastering Biology BioFlix Animation: DNA Replication
Table 16.1 Bacterial DNA Replication Proteins and Their
Functions
Protein Function
Helicase
5
5
3
3 Unwinds parental double helix at
replication forks
Single-strand binding
protein 5 3
Binds to and stabilizes single
stranded DNA until it is used as a
template
Topoisomerase
5
3
3
5
Relieves overwinding strain ahead
of replication forks by breaking,
swiveling, and rejoining DNA strands
Primase
5 5
3
3
Synthesizes an RNA primer at 5 end
of leading strand and at 5 end of
each Okazaki fragment of lagging
strand
DNA pol III
3
3 5
5
Using parental DNA as a template,
synthesizes new DNA strand by
adding nucleotides to an RNA
primer or a pre-existing DNA strand
DNA pol I
3 5
3 5
Removes RNA nucleotides of primer
from 5 end and replaces them with
DNA nucleotides added to 3 end of
adjacent fragment
DNA ligase Joins Okazaki fragments of lagging
strand; on leading strand, joins 3
end of DNA that replaces primer to
rest of leading strand DNA
Proofreading and Repairing DNA
We cannot attribute the accuracy of DNA replication solely to
the specificity of base pairing. Initial pairing errors between
incoming nucleotides and those in the template strand
occur at a rate of one in 105 nucleotides. However, errors in
the completed DNA molecule amount to only one in 1010
(10 billion) nucleotides, an error rate that is 100,000 times
lower. This is because during DNA replication, many DNA
polymerases proofread each nucleotide against its template
as soon as it is covalently bonded to the growing strand.
Upon finding an incorrectly paired nucleotide, the poly
merase removes the nucleotide and then resumes synthesis.
(This action is similar to fixing a texting error by deleting the
wrong letter and then entering the correct one.)
Mismatched nucleotides sometimes evade proofreading
by a DNA polymerase. In mismatch repair, other enzymes
remove and replace incorrectly paired nucleotides that have
resulted from replication errors. Researchers highlighted the
importance of such repair enzymes when they found that a
hereditary defect in one of them is associated with a form of
colon cancer. Apparently, this defect allows cancer-causing
errors to accumulate in the DNA faster than normal.
Incorrectly paired or altered nucleotides can also arise
after replication. In fact, maintenance of the genetic
information encoded in DNA requires frequent repair of
various kinds of damage to existing DNA. DNA molecules
are constantly subjected to potentially harmful chemi
cal and physical agents, such as X-rays, as well discuss
in Concept 17.5. In addition, DNA bases may undergo
spontaneous chemical changes under normal cellular
conditions. However, these changes in DNA are usually
corrected before they become permanent changes
mutationsperpetuated through successive replications.
Each cell continuously monitors and repairs its genetic
material. Because repair of damaged DNA is so important
to the survival of an organism, it is no surprise that many
different DNA repair enzymes have evolved. Almost 100
are known in E. coli, and about 170 have been identified
so far in humans.
Most cellular systems for repairing incorrectly paired
nucleotides, whether they are due to DNA damage or to
replication errors, use a mechanism that takes advantage of
the base-paired structure of DNA. In many cases, a segment
of the strand containing the damage is cut out (excised) by
a DNA-cutting enzymea nucleaseand the resulting
gap is then filled in with nucleotides, using the undam
aged strand as a template. The enzymes involved in filling
the gap are a DNA polymerase and DNA ligase. There are
several such DNA repair systems; one is called nucleotide
excision repair.
. Figure 16.20 Nucleotide excision repair of DNA damage.
1
Teams of enzymes detect
and repair damaged DNA,
5
3
3
5
such as this thymine dimer
(often caused by ultraviolet
radiation), which distorts
the DNA molecule.
Nuclease 2
5
3
A nuclease enzyme cuts
the damaged DNA strand at
two points, and the damaged
DNA
polymerase
3
5
5
3
5
3
3
5
DNA
ligase
3
5
section is removed.
3
Repair synthesis by
a DNA polymerase
f
ills in the missing
nucleotides, using the
undamaged strand
as a template.
4
DNA ligase seals the
free end of the new DNA
to the old DNA, making the
strand complete.
An example is shown in Figure 16.20. An important
function of the DNA repair enzymes in our skin cells is to
repair genetic damage caused by the UV rays of sunlight:
For example, adjacent thymine bases on a DNA strand
can become covalently linked into thymine dimers, caus
ing the DNA to buckle and interfere with DNA replication.
The importance of repairing this kind of damage is under
scored by a disorder called xeroderma pigmentosum (XP),
which in most cases is caused by an inherited defect in a
nucleotide excision repair enzyme. Individuals with XP
are hypersensitive to sunlight; mutations in their skin cells
caused by ultraviolet light are left uncorrected, often result
ing in skin cancer. The effects are extreme: Without sun
protection, children who have XP can develop skin cancer
by age 10.
Evolutionary Significance of Altered DNA
Nucleotides
EVOLUTION Faithful replication of the genome and repair
of DNA damage are important for the functioning of the
organism and for passing on a complete, accurate genome
to the next generation. The error rate after proofreading and
repair is extremely low, but rare mistakes do slip through.
Once a mismatched nucleotide pair is replicated, the
sequence change is permanent in the daughter molecule that
has the incorrect nucleotide as well as in any subsequent
UNIT THREE The Genetic Basis of Life
copies. As we mentioned earlier, a permanent change in the
DNA sequence is called a mutation.
Mutations can change the phenotype of an organism (see
Concept 17.5). And if they occur in germ cells, which give
rise to gametes, mutations can be passed on from generation
to generation. The vast majority of such changes either have
no effect or are harmful, but a very small percentage can be
beneficial. In either case, mutations are the original source
of the variation on which natural selection operates during
evolution and are ultimately responsible for the appearance
of new species. (Youll learn more about this process in Unit
Four.) The balance between complete fidelity of DNA replica
tion or repair and a low mutation rate has resulted in new
proteins that contribute to different phenotypes. Ultimately,
over long periods of time, this process leads to new species
and thus to the rich diversity of life on Earth today.
Replicating the Ends of DNA Molecules
For linear DNA, such as the DNA of eukaryotic chromosomes,
the usual replication machinery cannot complete the 5 ends
of daughter DNA strands because there is no 3 end of a preex
isting polynucleotide for DNA polymerase to add onto. This is
another consequence of the enzymes requirements. Even if an
Okazaki fragment can be started with an RNA primer hydrogen
bonded to the very end of the template strand, once that primer
is removed, it cannot be replaced with DNA because there is
no 3 end available for nucleotide addition (Figure 16.21). As
a result, repeated rounds of replication produce shorter and
shorter DNA molecules with uneven (staggered) ends.
Most prokaryotes have a circular chromosome, with
no ends, so the shortening of DNA does not occur. But
what protects the genes of linear eukaryotic chromosomes
from being eroded away during successive rounds of DNA
replication? Eukaryotic chromosomal DNA molecules have
special nucleotide sequences called telomeres at their ends
(Figure 16.22). Telomeres do not contain genes; instead, the
DNA typically consists of multiple repetitions of one short
nucleotide sequence. In each human telomere, for example,
the six-nucleotide sequence TTAGGG is repeated between
100 and 1,000 times.
Telomeres have two protective functions. First, specific
proteins associated with telomeric DNA prevent the stag
gered ends of the daughter molecule from activating the
cells systems for monitoring DNA damage. (Staggered ends
of a DNA molecule, which often result from double-strand
breaks, can trigger signal transduction pathways leading to
cell cycle arrest or cell death.) Second, telomeric DNA acts as
a kind of buffer zone that provides some protection against
the organisms genes shortening, somewhat like how the
plastic-wrapped ends of a shoelace slow down its unraveling.
Telomeres do not prevent the erosion of genes near the ends
of chromosomes; they merely postpone it.
378
CHAPTER 16 Nucleic Acids and Inheritance 379
5
End of
lagging strand
End of
parental strand
New leading strand
New lagging strand
RNA primer
Last fragment Next-to-last fragment
Removal of primers and
replacement with DNA
where a 3 end is available
Second round
of replication
Further rounds
of replication
3
5
3
5
3
5
3
Primer removed but
cannot be replaced
with DNA because
no 3 end available
for DNA polymerase
5
3
Ends of parental
DNA strands
Leading strand
Lagging strand
Shorter and shorter
daughter molecules
. Figure 16.21 Shortening of the ends of linear DNA
molecules. Here we follow the left end of one DNA molecule
through two rounds of replication. After the first round, the new
lagging strand is shorter than its template. After a second round,
both the leading and lagging strands have become shorter than the
original parental DNA. Although not shown here, the other ends of
these chromosomal DNA molecules (not shown) also become shorter.
As shown in Figure 16.21, telomeres become shorter dur
ing every round of replication. Thus, as expected, telomeric
DNA tends to be shorter in dividing somatic cells of older
individuals and in cultured cells that have divided many
times. It has been proposed that shortening of telomeres is
somehow connected to the aging process of certain tissues
and even to aging of the organism as a whole.
But what about germ cells, whose genome must persist
virtually unchanged from an organism to its offspring
over many generations? If the chromosomes of germ cells
became shorter in every cell cycle, essential genes would
eventually be missing from the gametes they produce.
However, this does not occur: An enzyme called telomerase
catalyzes the lengthening of telomeres in eukaryotic germ
1 om
. Figure 16.22 Telomeres. Eukaryotes have repetitive, noncoding
sequences called telomeres at the ends of their DNA. Telomeres are
stained orange in these mouse chromosomes (LM).
CONCEPT CHECK 16.2
1. What might happen during the replication of DNA if
topoisomerase is inhibited?
2. How do immortal cells cope with the shortening of
telomeres to be able to divide indefinitely?
3. MAKE CONNECTIONS What is the relationship between DNA
replication and the S phase of the cell cycle? See Figure 12.6.
4. VISUAL SKILLS If the DNA pol I in a given cell were non
functional, how would that affect the synthesis of a leading
strand? In the overview box in Figure 16.18, point out where
DNA pol I would normally function on the top leading strand.
For suggested answers, see Appendix A.
cells, thus restoring their original length and compensat
ing for the shortening that occurs during DNA replication.
This enzyme contains its own RNA molecule that it uses
as a template to artificially extend the leading strand,
allowing the lagging strand to maintain a given length.
Telomerase is not active in most human somatic cells, but
its activity varies from tissue to tissue. The activity of telom
erase in germ cells results in telomeres of maximum length
in the zygote.
Normal shortening of telomeres may protect organ
isms from cancer by limiting the number of divisions that
somatic cells can undergo. Cells from large tumors often
have unusually short telomeres, as we would expect for cells
that have undergone many cell divisions. Further shorten
ing would presumably lead to self-destruction of the tumor
cells. Telomerase activity is abnormally high in cancerous
somatic cells, suggesting that its ability to stabilize telomere
length may allow these cancer cells to persist. Many can
cer cells do seem capable of unlimited cell division, as do
immortal strains of cultured cells (see Concept 12.3). For
several years, researchers have studied inhibition of telomer
ase as a possible cancer therapy. While studies that inhibited
telomerase in mice with tumors have led to the death of
cancer cells, eventually the cells have restored the length of
their telomeres by an alternative pathway. This is an area
of ongoing research that may eventually yield useful cancer
treatments.
380 UNIT THREE The Genetic Basis of Life
single linear DNA molecule associated with a large number of
proteins. In E. coli, the chromosomal DNA consists of about
4.6 million nucleotide pairs, representing about 4,400 genes.
This is 100 times more DNA than is found in a typical virus,
but only about one-thousandth as much DNA as in a human
somatic cell. Even so, that is a tremendous amount of DNA to
be packaged in such a small container.
Stretched out, the DNA of an E. coli cell would measure
about a millimeter in length, 1,000 times longer than the
region it occupies in the cell. Within a bacterium, however,
certain proteins cause the chromosome to coil and super
coil, densely packing it so that it fills only part of the cell.
DNA double helix
(2 nm in diameter)
Histones
Nucleosome
(10 nm in diameter)
Histone tail
DNA
DNA, the Double Helix
Shown below is a ribbon model of DNA,
with each ribbon representing one of the
polynucleotide strands. The TEM shows a
molecule of naked (protein-free) DNA; the
double helix is 2 nm across.
Histones
Proteins called histones are responsi
ble for the main level of DNA packing
in interphase chromatin. More than a
fifth of a histones amino acids are
positively charged (Lys or Arg) and
therefore bind tightly to the
negatively charged DNA.
Four types of histones are most
common in chromatin. The histones
are very similar among eukaryotes,
probably reflecting their important
role in chromatin structure.
Nucleosomes in a 10-nm Fiber
In electron micrographs, unfolded
chromatin is roughly 10 nm in diame
ter (the 10-nm fiber). Such chromatin
resembles beads on a string (see the
TEM). Each bead is a nucleosome,
the basic unit of DNA packing; the
string between beads is called linker
DNA.
A nucleosome consists of DNA
wound twice around a protein core of
eight histones, two each of the four
main histone types. The amino end of
each histone (the histone tail) extends
outward from the nucleosome and
is involved in regulation of gene
expression.
In the cell cycle, the histones leave
the DNA only briefly during DNA
replication. Generally, they do the
same during the process of transcrip
tion, which requires access to the DNA
by transcription proteins.
Euchromatin/Heterochromatin
A recent technique called ChromEMT
allows scientists to visualize chromatin
in intact cells. ChromEMT and other
new techniques have shown that the
10-nm fiber is the basic constituent of
interphase chromatin.
During interphase, different regions
of a chromosome may exist as euchro
matin (below left) or heterochromatin
(below). In euchromatin, the 10-nm
fiber is loosely arranged in a more
open configuration than heterochro
matin; higher degrees of organization,
including the 30-nm fiber in one older
model, may exist in specific cells or at
certain times. (This is an area of very
active research.) The DNA in euchro
matin is accessible to the proteins that
carry out transcription, and its genes
can be expressed. In heterochromatin,
the 10-nm fiber is more densely
arranged and less accessible to these
proteins; genes in heterochromatin are
generally not expressed.
Euchromatin and heterochromatin
are organized into regions by other
proteins not shown here; this organi
zation is dynamic but disappears once
mitosis begins.
Heterochromatin (densely arranged 10-nm fiber) Euchromatin (loosely arranged 10-nm fiber)
. Figure 16.23 Exploring Chromatin Packing in a Eukaryotic Chromosome
CONCEPT 16.3
A chromosome consists of a DNA
molecule packed together with
proteins
Now lets examine how DNA is packaged into chromosomes,
the structures that carry genetic information. The main com
ponent of the genome in most bacteria is a double-stranded,
circular DNA molecule that is associated with specific pro
teins. A bacterial chromosome differs from a eukaryotic
chromosome in that a eukaryotic chromosome consists of a
CHAPTER 16 Nucleic Acids and Inheritance 381
In the cell, eukaryotic DNA is precisely combined with
a large amount of protein. The exact way in which this
complex of DNA and protein, called chromatin, fits into
the nucleus has long been debated. Figure 16.23 outlines
the current view of the organization of chromatin during
interphase and how it is condensed during mitosis into the
metaphase chromosome. Study this figure carefully before
reading further.
Chromatin undergoes striking changes in how densely it
is packed during the course of the cell cycle (see Figure 12.7).
In interphase cells stained for light microscopy, the
Loops
of DNA
(10-nm fiber)
Replicated
chromosome
(1,400 nm)
Condensin II
scaffold
Condensin I
Prophase
When mitosis begins, DNA replication
has already occurred, so each chromo
some consists of two sister chromatids.
During prophase, the chromatin of
each sister chromatid begins to
condense. Two related proteins called
condensin II and condensin I play
important roles. First, condensin II
proteins (red) bind to the 10-nm fiber
of DNA and form DNA loops that get
larger and larger. The condensin II
proteins form a central scaffold from
which the loops extend. As the loops
grow, the chromosome gets wider and
shorter. By the
end of prophase,
the chromosome
is half as long.
Prometaphase
When prometaphase begins, conden
sin I proteins (green) bind to DNA
outside the central scaffold, making
smaller loops (not shown) out of the
larger loops generated by condensin II.
The process continues, with more and
more loops extending outward, and
the chromosome getting denser,
shorter, and wider. The scaffold itself
also begins to twist into a helix
(suggested by the curved gray arrows),
allowing even more loops per given
length of chromosome.
Metaphase
At metaphase, the chromosome is at
its most dense, with the most loops
per turn, and therefore is at its shortest
length. The two sister chromatids are
fully condensed.
Sister chromatid
(700 nm)
Unlike the nucleus of a eukaryotic cell, this dense region of
DNA in a bacterium, called the nucleoid, is not bounded by
membrane (see Figure 7.5).
Each eukaryotic chromosome contains a single linear
DNA double helix that, in humans, averages about 1.5*108
nucleotide pairs. This is an enormous amount of DNA rela
tive to a chromosomes condensed length. If completely
stretched out, such a DNA molecule would be about 4 cm
long, thousands of times the diameter of a cell nucleusand
thats not even considering the DNA of the other 45 human
chromosomes!
Mastering Biology Animation: DNA Packing
chromatin usually appears as a diffuse mass within the
nucleus, with some denser clumps, including in regions of
centromeres and telomeres. The less compacted, more dis
persed interphase chromatin is called euchromatin (true
chromatin) to distinguish it from the more compacted,
denser-appearing heterochromatin (see Figure 16.23).
Recent research has clarified our understanding of chromatin
structure: For both types of chromatin, the basic organizing
unit is the 10-nm fibernucleosomes joined by linker DNA.
In heterochromatin, this 10-nm fiber is folded and bent
back on itself to a much greater degree than in euchromatin,
accounting for its denser appearance. Because heterochro
matin is so compacted, it is largely inaccessible to the pro
teins responsible for transcribing the genetic information, a
crucial early step in gene expression. In contrast, the looser
packing of euchromatin makes its DNA accessible to those
proteins, and the genes present in euchromatin are available
for transcription.
Early on, biologists assumed that interphase chroma
tin was a tangled mass in the nucleus, like a bowl of spa
ghetti, but this is far from the case. Although an interphase
chromosome lacks an obvious scaffold, there are proteins
that further organize the 10-nm fiber into larger compart
ments and smaller looped domains. Some of the looped
domains appear to be attached to the nuclear lamina, on
the inside of the nuclear envelope, and perhaps also to
fibers of the nuclear matrix. These attachments may help
organize regions of chromatin where genes are active.
The chromatin of each chromosome occupies a specific
restricted area within the interphase nucleus, and the chro
matin fibers of different chromosomes do not appear to be
entangled (Figure 16.24a).
As a cell prepares for mitosis, its chromatin becomes orga
nized into loops and coils, eventually condensing into a char
acteristic number of short, thick metaphase chromosomes
that are distinguishable from each other with the light micro
scope (Figure 16.24b).
The chromosome is a dynamic structure that is condensed,
loosened, modified, and remodeled as necessary for various
cell processes, including DNA replication, mitosis, meiosis, and
gene expression. Certain chemical modifications of histones
affect the state of chromatin condensation and also have mul
tiple effects on gene expression, as youll see in Concept 18.2.
In this chapter, you have learned how DNA molecules are
arranged in chromosomes and how DNA replication provides
the copies of genes that parents pass to offspring. However,
it is not enough that genes be copied and transmitted; the
information they carry must be used by the cell. In other
words, genes must also be expressed. In the next chapter, we
will examine how the cell expresses the genetic information
encoded in DNA.
UNIT THREE The Genetic Basis of Life
. Figure 16.24 Painting chromosomes. Researchers can treat
(paint) human chromosomes with molecular tags that cause each
chromosome pair to appear a different color.
5 om
(a) The ability to visually distinguish among chromosomes makes it
possible to see how the chromosomes are arranged in the interphase
nucleus. Each chromosome appears to occupy a specific territory
during interphase. In general, the two homologs of a pair are not
located together.
(b) These metaphase chromosomes have been painted so that the two
homologs of a pair are the same color. On the left is a spread of treated
chromosomes; on the right, they have been organized into a karyotype.
MAKE CONNECTIONS If you arrested a human cell in metaphase I
of meiosis and applied this technique, what would you observe? How
would this differ from what you would see in metaphase of mitosis?
Review Figure 13.8 and Figure 12.7.. De oefenexamen moet geschreven zijn in de Nederlandse taal. Onderin staan de antwoorden. Het aantal vragen dat het oefenexamen moet bevatten is 30.

Antwoord rapporteren