DNA - The Molecular Basis of Inheritance

James D. Watson & Francis H. Crick

• In 1953 presented the double helix model of DNA• Two primary sources of information:

– 1. Chargaff Rule: #A#T and #G#C. “A strange but possibly meaningless phenomenon”.

– 2. X-ray diffraction studies of Rosalind Franklin & Maurice H. F. Wilkins

DNA Structure• Conclusion-DNA is a helical structure with distinctive

regularities, 0.34 nm & 3.4 nm.

1962: Nobel Prize in Physiology and Medicine

James D.Watson

Francis H.Crick

Maurice H. F.Wilkins

What about?Rosalind Franklin

Watson, J.D. and F.H. Crick, “Molecular Structure of Nucleic Acids: A Structure for Deoxynucleic Acids”. Nature 171 (1953), p. 738.

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.

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

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

5 end

3 end

5 end

3 endHydrogen bond

0.34 nm

3.4 nm

1 nm

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.

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DNA Replication• DNA must replicate during each cell division• 3 alternative models for DNA replication were hypothesized:

– Semiconservative replication

– Conservative replication

– Dispersive replication

ConservativeSemi-conservative Dispersive

Meselson-Stahl Experiments• Labeled the nucleotides of

old strands with a heavy isotope of nitrogen (15N), new nucleotides were indicated by a lighter isotope (14N).

• The first replication in the 14N medium produced a band of hybrid (15N-14N) DNA, eliminating the conservative model.

• A second replication produced both light and hybrid DNA, eliminating the dispersive model and supporting the semiconservative model.

Bacteriacultured in mediumcontaining15N

DNA samplecentrifugedafter 20 min(after firstreplication)

DNA samplecentrifugedafter 40 min(after secondreplication)

Bacteriatransferred tomediumcontaining14N

Lessdense

Moredense

Conservativemodel

First replication

Semiconservativemodel

Second replication

Dispersivemodel

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

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

Origins of Replication• A eukaryotic chromosome may have hundreds or

even thousands of replication origins

Replication begins at specific siteswhere the two parental strandsseparate and form replicationbubbles.

The bubbles expand laterally, asDNA replication proceeds in bothdirections.

Eventually, the replicationbubbles fuse, and synthesis ofthe daughter strands iscomplete.

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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 giantDNA molecule of each chromosome.

In this micrograph, three replicationbubbles are visible along the DNA ofa cultured Chinese hamster cell (TEM).

(b)(a)

0.25 µm

Mechanism of DNA Replication

• DNA replication is catalyzed by DNA polymerase III which needs an RNA primer

• DNA polymerase III cannot initiate the synthesis of a polynucleotide, they can only add nucleotides to the 3 end

• The initial nucleotide strand is an RNA primer

• RNA primase synthesizes primer on DNA strand

• DNA polymerase adds nucleotides to the 3’ end of the growing strand

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

DNA polymerase III adds nucleotides to primer

Mechanism of DNA Replication• Nucleotides are added by complementary base pairing with the template strand• DNA always reads from 5’ end to 3’ end for transcription replication • During replication, new nucleotides are added to the free 3’ hydroxyl on the

growing strand• The nucleotides (deoxyribonucleoside triphosphates) are hydrolyzed as added,

releasing energy for DNA synthesis.

• The rate of elongation is about 500 nucleotides per second in bacteria and 50 per second in human cells

New strand5 end

Phosphate BaseSugar

Template strand3 end 5 end 3 end

5 end

3 end

5 end

3 end

Nucleosidetriphosphate

DNA polymerase

Pyrophosphate

The Mechanism of DNA Replication

• DNA synthesis on the leading strand is continuous

• Only one primer is needed for synthesis of the leading strand

• 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

• For synthesis of the lagging strand, each fragment (Okazaki) must be primed separately, then DNA fragments are sythesized and subsequently ligated together

Parental DNA

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Leading strand

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Okazakifragments

Lagging strand

DNA pol III

Templatestrand

Leading strand

Lagging strand

DNA ligase Templatestrand

Overall direction of replication

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

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3Parental DNA

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Overall direction of replication

DNA pol III

Replication fork

Leadingstrand

DNA ligase

Primase

OVERVIEW

PrimerDNA pol III

DNA pol I

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Laggingstrand

Leadingstrand

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Origin of replication

Enzymes in DNA replication

Helicase unwinds parental double helix

Binding proteinsstabilize separatestrands

DNA polymerase III binds nucleotides to form new strands

Ligase joins Okazaki fragments and seals other nicks in sugar-phosphate backbone

Primase adds short primer to template strand

DNA polymerase I (Exonuclease) removes RNA primer and inserts the correct bases

Binding proteins prevent single strands from rewinding.

Helicase protein binds to DNA sequences called origins and unwinds DNA strands.

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Primase protein makes a short segment of RNA complementary to the DNA, a primer.

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Replication

Overall directionof replication

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DNA polymerase III enzyme adds DNA nucleotides to the RNA primer.

Replication

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Overall directionof replication

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DNA polymerase proofreads bases added and replaces incorrect nucleotides.

Replication

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3’Overall directionof replication

Leading strand synthesis continues in a 5’ to 3’ direction.

Replication

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3’Overall directionof replication

Okazaki fragment

Leading strand synthesis continues in a 5’ to 3’ direction.

Discontinuous synthesis produces 5’ to 3’ DNA segments called Okazaki fragments.

Replication

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3’Overall directionof replication

Okazaki fragment

Leading strand synthesis continues in a 5’ to 3’ direction.

Discontinuous synthesis produces 5’ to 3’ DNA segments called Okazaki fragments.

Replication

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3’Overall directionof replication

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Leading strand synthesis continues in a 5’ to 3’ direction.

Discontinuous synthesis produces 5’ to 3’ DNA segments called Okazaki fragments.

Okazaki fragment

Replication

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Leading strand synthesis continues in a 5’ to 3’ direction.

Discontinuous synthesis produces 5’ to 3’ DNA segments called Okazaki fragments.

Replication

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

Replication

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Exonuclease activity of DNA polymerase I removes RNA primers.

Replication

Polymerase activity of DNA polymerase I fills the gaps.

Ligase forms bonds between sugar-phosphate backbone.

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Replication

Replication Fork Overview

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3Parental DNA

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Overall direction of replication

DNA pol III

Replication fork

Leadingstrand

DNA ligase

Primase

OVERVIEW

PrimerDNA pol III

DNA pol I

Laggingstrand

Laggingstrand

Leadingstrand

Leadingstrand

LaggingstrandOrigin of replication

Other Proteins That Assist DNA Replication• Helicase, topoisomerase, single-strand binding

protein are all proteins that assist DNA replication

Proofreading

• Mistakes during the initial pairing of template nucleotides and complementary nucleotides occur at a rate of one error per 100,000 base pairs.

• DNA polymerase proofreads each new nucleotide against the template nucleotide as soon as it is added and can correct errors

• If there is an incorrect pairing, the enzyme removes the wrong nucleotide and then resumes synthesis.

• Mismatched nucleotides that are missed by DNA polymerase or mutations that occur after DNA synthesis is completed can often be repaired

Mutations• Mismatch repair: ‘wrong’ inserted base can be removed• Excision repair: DNA may be damaged by chemicals,

radiation, etc. Mechanism to cut out and replace with correct bases

• Each cell continually monitors and repairs its genetic material, with 100 repair enzymes known in E. coli and more than 130 repair enzymes identified in humans.

• The final error rate is only one per ten billion nucleotides

• Because the human genome is so large, even at this rate, mutations add up. Each of us probably inherited 3-4 mutations!

Proofreading and Repairing DNA

• DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides

• In mismatch repair of DNA, repair enzymes correct errors in base pairing

• In nucleotide excision DNA repair nucleases cut out and replace damaged stretches of DNA

Nuclease

DNApolymerase

DNAligase

A thymine dimerdistorts the DNA molecule.1

A nuclease enzyme cutsthe damaged DNA strandat two points and thedamaged section isremoved.

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Repair synthesis bya DNA polymerasefills in the missingnucleotides.

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DNA ligase seals theFree end of the new DNATo the old DNA, making thestrand complete.

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DNA repair

Accuracy of DNA Replication

• The chromosome of E. coli bacteria contains about 5 million bases pairs

– Capable of copying this DNA in less than an hour

• The 46 chromosomes of a human cell contain about 6 BILLION base pairs of DNA!!

– Printed one letter (A,C,T,G) at a time…would fill up over 900 volumes of Campbell.

– Takes a cell a few hours to copy this DNA

– With amazing accuracy – an average of 1 per billion nucleotides

Replicating the Ends of DNA Molecules• The ends of eukaryotic chromosomal DNA get

shorter with each round of replication

End of parentalDNA strands

Leading strandLagging strand

Last fragment Previous fragment

RNA primer

Lagging strand

Removal of primers andreplacement with DNAwhere a 3 end is available

Primer removed butcannot be replacedwith DNA becauseno 3 end available

for DNA polymerase

Second roundof replication

New leading strand

New lagging strand 5

Further roundsof replication

Shorter and shorterdaughter molecules

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Telomeres• Eukaryotic chromosomal DNA molecules

have at their ends nucleotide sequences, called telomeres, that postpone the erosion of genes near the ends of DNA molecules

1 µm

Telomerases

• If the chromosomes of germ cells became shorter in every cell cycle essential genes would eventually be missing from the gametes they produce

• An enzyme called telomerase catalyzes the lengthening of telomeres in germ cells