DNA replication

Chapter 16

Summary of history Griffith Mice & Strep Transformation External DNA taken in by cell

Summary of history Hershey-Chase Bacteriophages Supported heredity information

was DNA

Bacteriophages

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Summary of history Franklin X-ray diffraction Double helix Watson-Crick Double helix model

Nucleic acid structure DNA deoxyribonucleic acid RNA ribonucleic acid Nucleotides

Nucleotide structure 1. 5 carbon sugar (ribose) 2. Phosphate 3. Nitrogenous base

Nucleotide structure

Nitrogenous base Purines (2 rings) Adenine(A) & Guanine(G) Pyrimidines (1 ring) Cytosine (C), Thymine (T) DNA only Uracil (U) RNA only

Phosphodiester bondLinks 2 sugars (nucleotides)

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Nucleic acids 5’ Phosphate group (5’C) at one end 3’ Hydroxyl group (3’C) at the other

end Sequence of bases is expressed in

the 5’ to 3’ direction GTCCAT 5’pGpTpCpCpApT---OH 3’

Double helix Complementary Sequence on one chain of DNA Determines sequence of other

chain

5’-ATTGCAT-3’

3’-TAACGTA-5’

Double Helix Complementary Purines pair with pyrimidines Diameter of base pairs are the

same Adenine (A) forms 2 hydrogen

bonds with Thymine (T) Guanine (G) forms 3 hydrogen

bonds with cytosine (C)

Double Helix Sugar-phosphates are the backbone Complementary Phosphodiester bonds Strands are antiparrellel Bases extend into interior of helix Base-pairs form to join the two

strands

Fig. 16-7

Hydrogen bond 3 end

5 end

3.4 nm

0.34 nm3 end

5 end

(b) Partial chemical structure(a) Key features of DNA structure

1 nm

Duplication DNA unzips-breaks hydrogen bonds New strand forms based on

existing strand Old strand is saved Compliment of new strand New DNA-one old strand & one new

strand Semiconservative replication

Fig. 16-9-3

A T

GC

T A

TA

G C

(a) Parent molecule

A T

GC

T A

TAG 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

TAG C

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Duplication study Meselson and Stahl Bacteria 14N and 15N Semiconservative method.

Fig. 16-10Parent cell

First replication

Second replication

(a) Conservative model

(b) Semiconserva- tive model

(c) Dispersive model

Summary

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Duplication Enzymes DNA helicase: Enzyme opens helix starts duplication Separates parental strands Single-strand binding protein: Binds to unpaired DNA After separation Stabilizes DNA

Duplication Enzymes DNA polymerases: Help lengthen new strand of DNA Adds new nucleotides strand Synthesis occurs only one direction 5’ to 3’ Adding new nucleotides to the

3’OH

Duplication Enzymes Primer: Section of RNA Complementary to the parental DNA Synthesis occurs only one direction 5’ to 3’ DNA primase: Enzyme creates the primer

Duplication Enzymes Topoisomerase: Relieves strain of unwinding DNA DNA pol1: Removes primers Replaces with DNA nucleotides DNA ligase: Creates phosphodiester bonds between

Okazaki fragments

Duplication OriC Origins of replication Starting point in DNA synthesis Replication is bidirectional Proceeds in both directions from origin 5’to 3’direction

Duplication E coli (bacteria) Circular DNA One origin Eurkaryotes Multiple origins

Duplication Replication bubble: Separation of strands of DNA Replication of DNA Replication fork: Y-shaped region End of replication bubble Site of active replication

Duplication

Duplication

Duplication Leading strand: DNA continuous 5’ to 3’ replication

(towards fork) Template is 3’ to 5’ Lagging strand: DNA duplicated in short segments

(away from fork) Okazaki fragments: Short stretches of new DNA-lagging side

Duplication

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Duplication Unzips (helicase, single-strand

binding protein, topoisomerase) Primer DNA polymerase (5’to3’) DNA ligase

Duplication

Fig. 16-14

A

C

T

G

G

G

GC

C C

C

C

A

A

AT

T

T

New strand 5 end

Template strand 3 end 5 end 3 end

3 end

5 end5 end

3 end

BaseSugar

Phosphate

Nucleoside triphosphate

Pyrophosphate

DNA polymerase

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Fig. 16-13

Topoisomerase

Helicase

PrimaseSingle-strand binding proteins

RNA primer

55

5 3

3

3

Fig. 16-15bOrigin of replication

RNA primer

“Sliding clamp”

DNA pol IIIParental DNA

3

5

5

5

5

5

5

3

3

3

Fig. 16-16a

OverviewOrigin of replication

Leading strand

Leading strand

Lagging strand

Lagging strand

Overall directions of replication

12

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Fig. 16-17

OverviewOrigin of replication

Leading strand

Leading strand

Lagging strand

Lagging strandOverall directions

of replication

Leading strand

Lagging strand

Helicase

Parental DNA

DNA pol III

Primer Primase

DNA ligase

DNA pol III

DNA pol I

Single-strand binding protein

5

3

5

5

5

5

3

3

3

313 2

4

Fig. 16-16Overview

Origin of replicationLeading strand

Leading strand

Lagging strand

Lagging strand

Overall directions of replication

Template strand

RNA primer

Okazaki fragment

Overall direction of replication

12

3

2

1

1

1

1

2

2

51

3

3

3

3

3

3

3

3

3

5

5

5

5

5

5

5

5

5

5

53

3

Duplication

Duplication

Duplication Telomers: Sequences at ends of chromosomes Short nucleotide sequences Repeated 100-1000 times Prevents 5’ end erosion Telomerase: Enzyme that lengthens telomers Usually in germ cells

Repairs Mismatched pair: Duplication error Enzymes remove error Nucleotide excision repair: Damaged section removed Nuclease New nucleotides fill gap Complement DNA section not damaged

Chromosome packaging Chromatin: Complex composed of DNA and proteins 40% DNA 60% protein Heterochromatin: More compacted chromatin Euchromatin: Loosely packed chromatin

Chromosome packaging Double helix Histones: proteins Nucleosome: DNA coiled around

8 histones (10nm) Nucleosomes then coil (30nm) Looped domains attach to

chromosome scaffold (300nm) Domains coil form chromosome

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