Page 39 - Genetics_From_Genes_to_Genomes_6th_FULL_Part2

198 Chapter 6 DNA Structure, Replication, and Recombination

Figure 6.21 DNA synthesis proceeds in a 5′-to-3′ Figure 6.22 Requirements of DNA polymerase. To
direction. The template strand is shown on the right in an synthesize DNA, DNA polymerase requires a single-stranded
antiparallel orientation to the new DNA strand under synthesis on DNA template, a primer that can be RNA or DNA, and free
the left. Here, a free molecule of dATP has formed hydrogen bonds deoxyribonucleotide triphosphates (dNTPs). DNA polymerase
with a complementary thymine base on the template strand. DNA adds nucleotides successively onto the 3′ end of the primer as
polymerase (yellow) cleaves dATP between the first and second instructed by the complementary nucleotides in the template.
phosphate groups. This cleavage releases the energy needed to
form a covalent phosphodiester bond between the terminal 3′-OH dNTPs
group on the preceding nucleotide to the first phosphate of the
dATP substrate. Pyrophosphate (PP i ) is released as a by-product. 5' 3' Synthesis
Primer
3' end of template
H
5' end of new strand
O H H H H Template
G C 3' 5'
H H
H H O
O
O H
H 2 C O P O
O P O CH 2
H O
O which DNA replication occurs inside a living cell. The entire
O H H
DNA polymerase H H molecular mechanism, illustrated in Fig. 6.23, has two
catalyzes covalent H H T A
bond formation H H O stages: initiation, during which proteins open up the dou-
with energy from O
newly paired OH H ble helix and prepare it for complementary base pairing,
nucleotide H 2 C O P O
triphosphate H O and elongation, during which proteins connect the correct
– O – O –
O O P O CH 2 H H sequence of nucleotides on both newly formed DNA dou-
– O P O P O O A T H H ble helixes.
O O H O
H H
{PP i } H O DNA replication is complicated by the strict biochemi-
OH H H 2 C O P O cal mechanism of polymerase function. DNA polymerase
5'-to-3' movement of H O
DNA polymerase can lengthen existing DNA chains only by adding nucleo-
H H
H H tides to the 3′ hydroxyl group of the DNA strand, as was
O – CH 2 G
O – P O O C O shown in Figs. 6.21 and 6.22. However, the antiparallel
O – P O O H H O
O strands of DNA unwind progressively at the two Y-shaped
P O H H 2 C O P O
– O
O H H H O areas called the replication forks in Fig. 6.23a. As a result,
OH
H H one newly synthesized strand (the leading strand) can grow
H H
G continuously into each of the opening forks. But the other
O
5' end of template new strand (the lagging strand), made at the same fork but
synthesized from the other template strand, can only be gen-
Many proteins in addition to DNA polymerase are re- erated in pieces called Okazaki fragments as more and
quired to replicate DNA. However, you will see below that more template is unwound at the fork (Fig. 6.23b). These
the most important features of DNA replication reflect three fragments must be joined together later in the process.
strict requirements for DNA polymerase action (Fig. 6.22): As Fig. 6.23 shows, DNA replication depends on the
(1) The four dNTPs. coordinated activity of many different proteins, including
(2) A single-stranded template. Double-stranded DNA two different DNA polymerases called pol I and pol III (pol
must be unwound, and DNA polymerase moves along the is short for polymerase). Pol III plays the major role in pro-
template strand in the 3′-to-5′ direction. ducing the new strands of complementary DNA, while pol
(3) A primer with a free 3′ hydroxyl group. DNA pol- I fills in the gaps between newly synthesized Okazaki seg-
ymerase adds nucleotides successively to the 3′ end of the ments. Other enzymes contribute to the initiation process:
growing DNA chain. (That is, DNA polymerase synthe- DNA helicase unwinds the double helix. A special group
sizes DNA only in the 5′-to-3′ direction.) However, DNA of single-stranded DNA binding proteins keep the DNA
polymerase cannot establish the first link in a new chain. helix open. An enzyme called primase generates RNA
Polymerization therefore must start with a primer, a short, primers to initiate DNA synthesis. During elongation, the
single-stranded molecule of DNA or RNA a few nucleo- DNA ligase enzyme welds together Okazaki fragments.
tides long that base pairs with part of the template strand. It took many years for biochemists and geneticists to
discover how the tight collaboration of many proteins
drives DNA replication. Today scientists think that pro-
DNA Replication Is a Tightly grammed molecular interactions of this kind underlie many
Regulated, Complex Process of the biochemical processes that occur in cells. In these
processes, a group of proteins, each performing a special-
The formation of phosphodiester bonds by DNA polymerase ized function, like the workers on an assembly line, coop-
is just one component of the highly coordinated process by erate in the manufacture of complex macromolecules.