1. (a) Key features of DNA structure (c) Space-filling model
Topic: DNA Replication
Aim: How does DNA replicate (copy) itself?
Figure 16.7a, c C T A G
0.34 nm
3.4 nm
(a) Key features of DNA structure
1 nm
(c) Space-filling model

2. History of DNA Structure Discovery
1962: Nobel Prize in Physiology and Medicine
Watson, J.D. and F.H. Crick, “Molecular Structure of Nucleic Acids: A Structure for Deoxynucleic Acids”. Nature 171 (1953), p. 738.
James D.
Watson
Francis H.
Crick
Maurice H. F.
Wilkins
What about?
Rosalind Franklin

3. The Structure of DNA
DNA is composed of four nucleotides, each containing: adenine, cytosine, thymine, or guanine.
The amounts of A = T, G = C, and purines = pyrimidines [Chargaff’s Rule].
DNA is a double-stranded helix with antiparallel strands [Watson and Crick].
Nucleotides in each strand are linked by 5’-3’ phosphodiester bonds
Bases on opposite strands are linked by hydrogen bonding: A with T, and G with C.

5. The Basic Principle: Base Pairing to a Template Strand
The relationship between structure and function is manifest in the double helix
Since the two strands of DNA are complementary each strand acts as a template for building a new strand in replication

6. DNA replication
The parent molecule unwinds, and two new daughter strands are built based on base-pairing rules
(a) The parent molecule has two complementary strands of DNA Each base is paired by hydrogen bonding with its specific partner, A with T and G with C.
(b) The first step in replication is separation of the two DNA strands.
(c) Each parental strand now serves as a template that determines the order of nucleotides along a new, complementary strand.
(d) The nucleotides are connected to form the sugar-phosphate backbones of the new strands Each “daughter” DNA molecule consists of one parental strand and one new strand. A C T G T T G A C A C T G T G A C A C T G A T G A C A C T G T G A C A C T G T G A C G C A T T A C G

7. DNA Replication is “Semi-conservative”
Each 2-stranded daughter molecule is only half new
One original strand was used as a template to make the new strand

8. DNA Replication
The copying of DNA is remarkable in its speed and accuracy
Involves unwinding the double helix and synthesizing two new strands.
More than a dozen enzymes and other proteins participate in DNA replication
The replication of a DNA molecule begins at special sites called origins of replication, where the two strands are separated

9. Origins of Replication
A eukaryotic chromosome may have hundreds or even thousands of replication origins
Replication begins at specific sites
where the two parental strands
separate and form replication
bubbles.
The bubbles expand laterally, as
DNA replication proceeds in both
directions.
Eventually, the replication
bubbles fuse, and synthesis of
the daughter strands is
complete. 1 2 3
Origin of replication
Bubble
Parental (template) strand
Daughter (new) strand
Replication fork
Two daughter DNA molecules
In eukaryotes, DNA replication begins at many sites along the giant
DNA molecule of each chromosome.
In this micrograph, three replication
bubbles are visible along the DNA of
a cultured Chinese hamster cell (TEM).
(b)
(a)
0.25 µm

10. Mechanism of DNA Replication
DNA replication is catalyzed by DNA polymerase which needs an RNA primer
RNA primase synthesizes primer on DNA strand
DNA polymerase adds nucleotides to the 3’ end of the growing strand

11. Mechanism of DNA Replication
Nucleotides are added by complementary base pairing with the template strand
The substrates, deoxyribonucleoside triphosphates, are hydrolyzed as added, releasing energy for DNA synthesis.

12. The Mechanism of DNA Replication
DNA synthesis on the leading strand is continuous
The lagging strand grows the same general direction as the leading strand (in the same direction as the Replication Fork). However, DNA is made in the 5’-to-3’ direction
Therefore, DNA synthesis on the lagging strand is discontinuous
DNA is added as short fragments (Okasaki fragments) that are subsequently ligated together

14. DNA polymerase I degrades the RNA primer and replaces it with DNA

15. The Mechanism of DNA Replication
Many proteins assist in DNA replication
DNA helicases unwind the double helix, the template strands are stabilized by other proteins
Single-stranded DNA binding proteins make the template available
RNA primase catalyzes the synthesis of short RNA primers, to which nucleotides are added.
DNA polymerase III extends the strand in the 5’-to-3’ direction
DNA polymerase I degrades the RNA primer and replaces it with DNA
DNA ligase joins the DNA fragments into a continuous daughter strand

16. Enzymes in DNA replication
Primase adds
short primer
to template strand
Helicase unwinds
parental double helix
Binding proteins
stabilize separate
strands
DNA polymerase III
binds nucleotides
to form new strands
DNA polymerase I (Exonuclease) removes RNA primer and inserts the correct bases
Ligase joins Okazaki
fragments and seals
other nicks in sugar-phosphate backbone

17. Replication Helicase protein binds to DNA sequences called
Primase protein makes a short segment of RNA
complementary to the DNA, a primer. 5’ 3’
Binding proteins prevent single strands from rewinding. 3’ 5’
Helicase protein binds to DNA sequences called
origins and unwinds DNA strands.

18. Replication DNA polymerase enzyme adds DNA nucleotides
Overall direction
of replication 5’ 3’
DNA polymerase enzyme adds DNA nucleotides
to the RNA primer.

19. Replication DNA polymerase enzyme adds DNA nucleotides5’
Overall direction
of replication 3’
DNA polymerase enzyme adds DNA nucleotides
to the RNA primer.
DNA polymerase proofreads bases added and
replaces incorrect nucleotides.

20. Replication Leading strand synthesis continues in a5’ 3’
Overall direction
of replication
Leading strand synthesis continues in a
5’ to 3’ direction.

21. Replication Leading strand synthesis continues in a3’ 5’
Overall direction
of replication
Okazaki fragment
Leading strand synthesis continues in a
5’ to 3’ direction.
Discontinuous synthesis produces 5’ to 3’ DNA
segments called Okazaki fragments.

22. Replication Leading strand synthesis continues in a
Overall direction
of replication 3’ 3’ 5’ 5’
Okazaki fragment 3’ 5’ 3’ 5’ 3’ 5’
Leading strand synthesis continues in a
5’ to 3’ direction.
Discontinuous synthesis produces 5’ to 3’ DNA
segments called Okazaki fragments.

23. Replication Leading strand synthesis continues in a3’ 3’ 5’ 5’ 3’ 5’ 3’ 5’ 3’ 3’ 5’ 5’
Leading strand synthesis continues in a
5’ to 3’ direction.
Discontinuous synthesis produces 5’ to 3’ DNA
segments called Okazaki fragments.

24. Replication Leading strand synthesis continues in a5’ 3’ 3’ 3’ 5’
Leading strand synthesis continues in a
5’ to 3’ direction.
Discontinuous synthesis produces 5’ to 3’ DNA
segments called Okazaki fragments.

25. Replication 3’ 5’ 5’ 5’ 3’
Exonuclease activity of DNA polymerase I removes RNA primers.

26. Replication Polymerase activity of DNA polymerase I fills the gaps.3’ 5’
Polymerase activity of DNA polymerase I fills the gaps.
Ligase forms bonds between sugar-phosphate backbone.

27. Replication Fork Overview