16.2 DNA Replication

Layout of the Eukaryote DNA

• Two DNA strands are antiparallel– Run in opposite

directions– 3’ (three prime) – 5’

(five prime)– 5’ (five prime) – 3’

(three prime)

DNA Replication

• Watson and Crick noted that the specific base pairing suggested a possible copying mechanism for genetic material

DNA Replication

• Since the two strands of DNA are complementary, each strand acts as a template for building a new strand in replication

• In DNA replication, the parent molecule unwinds, and two new daughter strands are built based on base-pairing rules

Fig. 16-9-1

A T

GC

T A

TA

G C

(a) Parent molecule

Fig. 16-9-2

A T

GC

T A

TA

G C

A T

GC

T A

TA

G C

(a) Parent molecule (b) Separation of strands

Fig. 16-9-3

A T

GC

T A

TA

G C

(a) Parent molecule

A T

GC

T A

TA

G C

(c) “Daughter” DNA molecules, each consisting of one parental strand and one new strand

(b) Separation of strands

A T

GC

T A

TA

G C

A T

GC

T A

TA

G C

Semiconservative Model

• Each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand

Fig. 16-10Parent cell

First replication

Second replication

(a) Conservative model

(b) Semiconserva- tive model

(c) Dispersive model

Matthew Meselson and Franklin Stahl

DNA in Prokaryotes and Eukaryotes

• Prokaryotes:– ring of chromosome– holds nearly all of

the cell’s genetic material

Prokaryote DNA Replication

• DNA replication begins at a single point and continues to replicate whole circular strand

• Replication goes in both directions around the DNA (begins with replication fork)

Fig. 16-12Origin of replication Parental (template) strand

Daughter (new) strand

Replication fork

Replication bubble

Two daughter DNA molecules

(a) Origins of replication in E. coli

Origin of replication Double-stranded DNA molecule

Parental (template) strandDaughter (new) strand

Bubble Replication fork

Two daughter DNA molecules

(b) Origins of replication in eukaryotes

0.5 µm

0.25 µm

Double-strandedDNA molecule

DNA Replication Overview

• DNA splits into two strands• Complementary base pairs fill in (A with T,

C with G)• Left with two DNA molecules

– Semiconservative model– Identical

Eukaryote DNA Replication

• Begins in hundreds of locations along the chromosome– Origins of replication

Initiation of DNA Replication

• Begins when the DNA molecule “unzips”– Replication fork– Replication “bubble”

• Hydrogen bonds between base pairs breaks

• Helicase• Single-strand binding proteins• Topoisomerase – relieves

pressure of DNA ahead of replication fork

Fig. 16-13

Topoisomerase

Helicase

PrimaseSingle-strand binding proteins

RNA primer

55

5 3

3

3

Synthesis of a New DNA Strand

• Each strand serves as a template for a new strand to form

• Primer of RNA– The primer is short (5–10 nucleotides long), and the 3 end

serves as the starting point for the new DNA strand

• Complimentary bases will attach• DNA polymerase

– E. coli – DNA polymerase III and DNA polymerase I– Humans – 11 different DNA polymerase molecules

Synthesis of a New DNA Strand

• RNA primer• Nucleoside

triphosphate– As each nucleotide is

added to the new strand, 2 phosphates are lost• Hydrolysis releases

energy to drive reaction

• Each nucleotide that is added to a growing DNA strand is a nucleoside triphosphate

• dATP supplies adenine to DNA and is similar to the ATP of energy metabolism

• The difference is in their sugars: dATP has deoxyribose while ATP has ribose

• As each monomer of dATP joins the DNA strand, it loses two phosphate groups as a molecule of pyrophosphate

Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Synthesis of a New DNA Strand

• Antiparallel Elongation– Remember 3’ – 5’ and 5’ – 3’

• Replication in the 3’ to 5’ direction ONLY– MEANING the NEW strand of DNA will form starting

with the 5’ end

• Leading strand (only 1 primer needed – moves toward the replication fork)

• Lagging strand (many primers needed – moves away from replication fork)

Fig. 16-16b1

Template strand

5

53

3

Fig. 16-16b2

Template strand

5

53

3

RNA primer 3 5

5

3

1

Fig. 16-16b3

Template strand

5

53

3

RNA primer 3 5

5

3

1

1

3

35

5

Okazaki fragment

Fig. 16-16b4

Template strand

5

53

3

RNA primer 3 5

5

3

1

1

3

35

5

Okazaki fragment

12

3

3

5

5

Fig. 16-16b5

Template strand

5

53

3

RNA primer 3 5

5

3

1

1

3

35

5

Okazaki fragment

12

3

3

5

5

12

3

3

5

5

Fig. 16-16b6

Template strand

5

53

3

RNA primer 3 5

5

3

1

1

3

35

5

Okazaki fragment

12

3

3

5

5

12

3

3

5

5

12

5

5

3

3

Overall direction of replication

Important Enzymes

• Helicase, single-strand binding protein, topoisomerase• Primase

– Synthesis of RNA primer

• DNA polymerase III (DNA pol III)– Add new bases to DNA strand

• DNA polymerase I (DNA pol I)– Removes and replaces RNA primer from 5’ end

• DNA ligase– Links Okazaki fragments and replaces RNA primer from 3’ end

Topoisomerase Video

• http://www.youtube.com/watch?v=EYGrElVyHnU

The Finished Product

• Each DNA molecule has one original strand and one new strand

• Molecules are identical

DNA Replication Video

• http://www.youtube.com/watch?v=teV62zrm2P0

Fig. 16-UN5

Repair of DNA

• DNA polymerase– Proofreads and repairs damaged/mismatched

DNA• Nuclease

– Removes section of DNA that is damaged– DNA polymerase and DNA ligase replace

missing portion

Telomeres

• Found at the ends of each chromosome• Contain no genes• Sequence that can be cut short and will

not affect normal functioning• TTAGGG• Telomerase lengthens telomeres in

gametes

Telomeres

• The shortening of telomeres might protect cells from cancerous growth by limiting the number of cell divisions

• There is evidence of telomerase activity in cancer cells, which may allow cancer cells to persist

16.3 A chromosome consists of a DNA molecule packed

together with proteins

Chromosomes

Chromosome Structure

• Bacterial chromosome– double-stranded– circular – small amount of protein

• Eukaryotic chromosomes – Linear DNA molecules – large amount of protein

• DNA in bacteria is “supercoiled” and found in a region of the cell called the nucleoid

Chromatin and Histones

• Chromatin is a complex of DNA and protein, and is found in the nucleus of eukaryotic cells

• Histones are proteins that are responsible for the first level of DNA packing in chromatin– Form a tight bond because DNA is negatively

charged and the histones have a positive charge

Fig. 16-21a

DNA double helix (2 nm in diameter)

Nucleosome(10 nm in diameter)

Histones Histone tailH1

DNA, the double helix Histones Nucleosomes, or “beads on a string” (10-nm fiber)

Fig. 16-21b

30-nm fiber

Chromatid (700 nm)

Loops Scaffold

300-nm fiber

Replicated chromosome (1,400 nm)

30-nm fiber Looped domains (300-nm fiber)

Metaphase chromosome

Chromosome Organization

• Chromatin is organized into fibers• 10-nm fiber

– DNA winds around histones to form nucleosome “beads”

– Nucleosomes are strung together• 30-nm fiber

– Interactions between nucleosomes cause the thin fiber to coil or fold into this thicker fiber

Chromosome Organization

• 300-nm fiber– The 30-nm fiber forms looped domains that

attach to proteins• Metaphase chromosome

– The looped domains coil further– The width of a chromatid is 700 nm

Euchromatin

• Most chromatin is loosely packed in the nucleus during interphase – Condenses prior to mitosis– Euchromatin

Heterochromatin

• During interphase, a few regions of chromatin (centromeres and telomeres) are highly condensed into heterochromatin– Dense packing of the heterochromatin makes

it difficult for the cell to express genetic information coded in these regions