Essential Cell Biology 5th edition

206 CHAPTER 6 DNA Replication and Repair
new strand
5′ 3′
C A T T G
G T A A C G G T
3′ 5′
template strand
Figure 6–10 A new DNA strand is
synthesized
ECB5
in
e6.10/6.10
the 5ʹ-to-3ʹ direction.
At each step, the appropriate incoming
nucleoside triphosphate is selected by
forming base pairs with the next nucleotide
in the template strand: A with T, T with A,
C with G, and G with C. Each is added to
the 3ʹ end of the growing new strand, as
indicated.
5′
new
strand
P
P
P
P
C
C
3′
OH
A
G
incoming
nucleoside triphosphate
3′
5′ P P P OH
T
by the incoming deoxyribonucleoside triphosphate itself: hydrolysis
of one of its high-energy phosphate bonds fuels the reaction that links
the nucleotide monomer to the chain, releasing pyrophosphate (Figure
6–11). Pyrophosphate is further hydrolyzed to inorganic phosphate (P i ),
which makes the polymerization reaction effectively irreversible (see
Figure 3–42).
DNA polymerase does not dissociate from the DNA each time it adds a
new nucleotide to the growing strand; rather, it stays associated with the
DNA and moves along the template strand stepwise for many cycles of
the polymerization reaction (Movie 6.1). We will see later that a special
protein keeps the polymerase attached to DNA as it repeatedly adds new
nucleotides to the growing strand.
The Replication Fork Is Asymmetrical
The 5ʹ-to-3ʹ direction of the DNA polymerization reaction poses a problem
at the replication fork. As illustrated in Figure 5–2, the sugar–phosphate
backbone of each strand of a DNA double helix has a unique chemical
direction, or polarity, determined by the way each sugar residue is linked
to the next, and the two strands in the double helix are antiparallel; that
is, they run in opposite directions. As a consequence, at each replication
fork, one new DNA strand is being made on a template that runs in one
direction (3ʹ to 5ʹ), whereas the other new strand is being made on a
template that runs in the opposite direction (5ʹ to 3ʹ). The replication fork
is therefore asymmetrical (Figure 6–12). Figure 6–9A, however, makes it
look like both of the new DNA strands are growing in the same direction;
P P 5′ P P P P P
pyrophosphate
3′
OH
5′-to-3′
direction of
chain growth
3′
P
P
P
P
P
P
P
5′
3′ P P P P P P P 5′
template
strand
(A)
(C)
template
strand
5′
3′
5′
3′
new
strand
P
P
DNA
polymerase
(B)
nucleoside
triphosphate
INCOMING
NUCLEOSIDE
TRIPHOSPHATE PAIRS
WITH A BASE IN THE
TEMPLATE STRAND
DNA POLYMERASE
CATALYZES COVALENT
LINKAGE OF NUCLEOSIDE
TRIPHOSPHATE INTO
GROWING NEW STRAND
Figure 6–11 DNA polymerase adds a deoxyribonucleotide to the 3ʹ end of a growing DNA strand. (A) Nucleotides enter the
reaction as deoxyribonucleoside triphosphates. An incoming nucleoside triphosphate forms a base pair with its partner in the template
strand. It is then covalently attached to the free 3ʹ hydroxyl on the growing DNA strand. The new DNA strand is therefore synthesized
in the 5ʹ-to-3ʹ direction. The energy for the polymerization reaction comes from the hydrolysis of a high-energy phosphate bond in
the incoming nucleoside triphosphate and the release of pyrophosphate, which is subsequently hydrolyzed to yield two molecules of
inorganic phosphate (not shown). (B) The reaction is catalyzed by the enzyme DNA polymerase (light green). The polymerase guides
the incoming nucleoside triphosphate to the template strand and positions it such that its 5ʹ triphosphate will be able to react with the
3ʹ-hydroxyl group on the newly synthesized strand. The gray arrow indicates the direction of polymerase movement. (C) Structure of
DNA polymerase, as determined by x-ray crystallography, also showing the replicating DNA. The template strand is the longer, orange
strand, and the newly synthesized DNA strand is colored ECB5 red (Movie e6.11/6.11 6.1).