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 bond Links 2 sugars (nucleotides)

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 Two-ringed purine pairs with a one-ringed pyrimidine Diameter of base pairs are the same Adenine (A) forms two hydrogen bonds with Thymine (T) Guanine (G) forms three hydrogen bonds with cytosine (C)

Fig. 16-7 5 end Hydrogen bond 3 end 1 nm 3.4 nm 3 end 0.34 nm (a) Key features of DNA structure (b) Partial chemical structure

Double Helix Composed of 2 complementary phosphodiester strands Strands are antiparrellel Sugar-phosphates are the backbone Bases extend into interior of helix Base-pairs form to join the two strands

Duplication DNA unzips New strand forms based on existing strand Old strand is saved Compliment of the new strand New DNA-one old strand & one new strand Semiconservative replication

Fig. 16-9-3 A T A T A T A T C G C G C G C G T A T A T A T A A T A T A (a) Parent molecule (b) Separation of strands (c) “Daughter” DNA molecules, each consisting of one parental strand and one new strand

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

Fig. 16-10 (a) Conservative model (b) Semiconserva- tive model First replication Second replication Parent cell (a) Conservative model (b) Semiconserva- tive model (c) Dispersive model

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

Duplication 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 Parental DNA unwinding

Duplication Replication fork: Site of active replication

Duplication

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

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

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Duplication Unzips (helicase, single-strand binding protein, topoisomerase) Primer DNA polymerase (5’to3’) DNA ligase

Duplication

Nucleoside triphosphate Fig. 16-14 New strand 5 end Template strand 3 end 5 end 3 end Sugar A T A T Base Phosphate C G C G G C G C DNA polymerase 3 end A T A T 3 end C Pyrophosphate C Nucleoside triphosphate 5 end 5 end

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Fig. 16-13 Primase Single-strand binding proteins 3 Topoisomerase 5 RNA primer 5 5 3 Helicase

Fig. 16-15b Origin of replication 3 5 RNA primer 5 “Sliding clamp” DNA pol III Parental DNA 3 5 5 3 5

Overall directions of replication Fig. 16-16a Overview Origin of replication Leading strand Lagging strand Lagging strand 2 1 Leading strand Overall directions of replication

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Single-strand binding protein Overall directions of replication Fig. 16-17 Overview Origin of replication Leading strand Lagging strand Leading strand Lagging strand Single-strand binding protein Overall directions of replication Helicase Leading strand 5 DNA pol III 3 3 Primer Primase 5 Parental DNA 3 DNA pol III Lagging strand 5 DNA pol I DNA ligase 4 3 5 3 2 1 3 5

Overall directions of replication Fig. 16-16 Overview Origin of replication Leading strand Lagging strand Lagging strand 2 1 Leading strand Overall directions of replication 3 5 3 Template strand 5 3 RNA primer 3 5 1 5 Okazaki fragment 3 5 3 1 5 5 3 3 2 1 5 5 3 3 5 2 1 5 3 3 1 5 2 Overall direction of replication

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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