Overview: Life’s Operating Instructions

• In 1953, James Watson and Francis Crick introduced an elegant double-helical model for the structure of deoxyribonucleic acid, or DNA

• DNA, the substance of inheritance, is the most celebrated molecule of our time

• Hereditary information is encoded in DNA and reproduced in all cells of the body

• This DNA program directs the development of biochemical, anatomical, physiological, and (to some extent) behavioral traits

The Search for the Genetic Material: Scientific Inquiry

• When Morgan’s group showed that genes are located on chromosomes, the two components of chromosomes—DNA and protein—became candidates for the genetic material

• The key factor in determining the genetic material was choosing appropriate experimental organisms

• The role of DNA in heredity was first discovered by studying bacteria and the viruses that infect them

Evidence That DNA Can Transform Bacteria

• The discovery of the genetic role of DNA began with research by Frederick Griffith in 1928

• Griffith worked with two strains of a bacterium, a pathogenic “S” strain and a harmless “R” strain

• When he mixed heat-killed remains of the pathogenic strain with living cells of the harmless strain, some living cells became pathogenic

• He called this phenomenon transformation, now defined as a change in genotype and phenotype due to assimilation of foreign DNA

Living S cells(control)

Living R cells(control)

Heat-killedS cells (control)

Mixture of heat-killedS cells and livingR cells

Mouse dies

Living S cellsare found in blood sample

Mouse healthy Mouse healthy Mouse dies

RESULTS

• In 1944, Oswald Avery, Maclyn McCarty, and Colin MacLeod announced that the transforming substance was DNA

• Their conclusion was based on experimental evidence that only DNA worked in transforming harmless bacteria into pathogenic bacteria

• Many biologists remained skeptical, mainly because little was known about DNA

Evidence That Viral DNA Can Program Cells

• More evidence for DNA as the genetic material came from studies of a virus that infects bacteria

• Such viruses, called bacteriophages (or phages), are widely used in molecular genetics research

Bacterialcell

Phagehead

Tail

Tail fiber

DNA

100

nm

• In 1952, Alfred Hershey and Martha Chase performed experiments showing that DNA is the genetic material of a phage known as T2

• To determine the source of genetic material in the phage, they designed an experiment showing that only one of the two components of T2 (DNA or protein) enters an E. coli cell during infection

• They concluded that the injected DNA of the phage provides the genetic information

Bacterial cell

Phage

DNA

Radioactiveprotein

Emptyprotein shell

PhageDNA

Radioactivity(phage protein)in liquid

Batch 1:Sulfur (35S)

RadioactiveDNA

Centrifuge

Pellet (bacterialcells and contents)

PelletRadioactivity(phage DNA)in pellet

Centrifuge

Batch 2:Phosphorus (32P)

Additional Evidence That DNA Is the Genetic Material

• In 1947, Erwin Chargaff reported that DNA composition varies from one species to the next

• This evidence of diversity made DNA a more credible candidate for the genetic material

• By the 1950s, it was already known that DNA is a polymer of nucleotides, each consisting of a nitrogenous base, a sugar, and a phosphate group

• Nucleotide monomers are made up of nucleosides and phosphate groups

• Nucleoside = nitrogenous base + sugar

• There are two families of nitrogenous bases:

– Pyrimidines have a single six-membered ring

– Purines have a six-membered ring fused to a five-membered ring

• In DNA, the sugar is deoxyribose

• In RNA, the sugar is ribose

Nitrogenous bases

Pyrimidines

Purines

Pentose sugars

CytosineC

Thymine (in DNA)T

Uracil (in RNA)U

AdenineA

GuanineG

Deoxyribose (in DNA) Ribose (in RNA)

Sugar–phosphatebackbone

5 end

Nitrogenousbases

Thymine (T)

Adenine (A)

Cytosine (C)

DNA nucleotidePhosphate

3 endGuanine (G)

Sugar (deoxyribose)

Building a Structural Model of DNA: Scientific Inquiry

• After most biologists became convinced that DNA was the genetic material, the challenge was to determine how its structure accounts for its role

• Maurice Wilkins and Rosalind Franklin were using a technique called X-ray crystallography to study molecular structure

• Franklin produced a picture of the DNA molecule using this technique

Franklin’s X-ray diffractionphotograph of DNA

Rosalind Franklin

• Franklin’s X-ray crystallographic images of DNA enabled Watson to deduce that DNA was helical

• The X-ray images also enabled Watson to deduce the width of the helix and the spacing of the nitrogenous bases

• The width suggested that the DNA molecule was made up of two strands, forming a double helix

• Watson and Crick built models of a double helix to conform to the X-rays and chemistry of DNA

• Franklin had concluded that there were two antiparallel sugar-phosphate backbones, with the nitrogenous bases paired in the molecule’s interior

• At first, Watson and Crick thought the bases paired like with like (A with A, and so on), but such pairings did not result in a uniform width

• Instead, pairing a purine with a pyrimidine resulted in a uniform width consistent with the X-ray

• Watson and Crick reasoned that the pairing was more specific, dictated by the base structures

• They determined that adenine paired only with thymine, and guanine paired only with cytosine

Purine + purine: too wide

Pyrimidine + pyrimidine: too narrow

Purine + pyrimidine: widthconsistent with X-ray data

Adenine (A) Thymine (T)

Guanine (G) Cytosine (C)

Sugar

Sugar

Sugar

Sugar

5 end

3 end

5 end

3 end

Space-filling modelPartial chemical structure

Hydrogen bond

Key features of DNA structure

0.34 nm

3.4 nm

1 nm

Many proteins work together in DNA replication and repair

• The relationship between structure and function is manifest in the double helix

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

The Basic Principle: Base Pairing to a Template Strand

• 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

Nucleotide Polymers

• Nucleotide polymers are linked together, building a polynucleotide

• Adjacent nucleotides are joined by covalent bonds that form between the –OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next

• These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages

• The sequence of bases along a DNA or mRNA polymer is unique for each gene

The DNA Double Helix

• A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix

• In the DNA double helix, the two backbones run in opposite 5´ to 3´ directions from each other, an arrangement referred to as antiparallel

• One DNA molecule includes many genes

• The nitrogenous bases in DNA form hydrogen bonds in a complementary fashion: A always with T, and G always with C

Sugar-phosphatebackbone

3 end5 end

Base pair (joined byhydrogen bonding)

Old strands

Nucleotideabout to beadded to anew strand

5 end

New strands

3 end

5 end3 end

5 end

DNA and Proteins as Tape Measres of Evolution

• The linear sequences of nucleotides in DNA molecules are passed from parents to offspring

• Two closely related species are more similar in DNA than are more distantly related species

• Molecular biology can be used to assess evolutionary kinship

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.

The first step in replication is separation of the two DNA strands.

Each parental strand now serves as a template that determines the order of nucleotides along a new, complementary strand.

The nucleotides are connected to form the sugar-phosphate back-bones of the new strands. Each “daughter” DNA molecule consists of one parental strand and one new strand.

• Watson and Crick’s semiconservative model of replication predicts that when a double helix replicates, each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand

• Competing models were the conservative model and the dispersive model

Conservative model. The two parental strands reassociate after acting as templates for new strands, thus restoring the parental double helix.

Semiconservative model. The two strands of the parental moleculeseparate, and each functions as a template for synthesis of a new, comple-mentary strand.

Dispersive model. Each strand of both daughter molecules contains a mixture of old and newly synthesized DNA.

Parent cellFirstreplication

Secondreplication

• Experiments by Meselson and Stahl supported the semiconservative model

• They labeled the nucleotides of the old strands with a heavy isotope of nitrogen, while any new nucleotides were labeled with a lighter isotope

• The first replication produced a band of hybrid 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: A Closer Look

• The copying of DNA is remarkable in its speed and accuracy

• More than a dozen enzymes and other proteins participate in DNA replication

Getting Started: Origins of Replication

• Replication begins at special sites called origins of replication, where the two DNA strands are separated, opening up a replication “bubble”

• A eukaryotic chromosome may have hundreds or even thousands of origins of replication

• Replication proceeds in both directions from each origin, until the entire molecule is copied

• At the end of each replication bubble is a replication fork, a Y-shaped region where new DNA strands are elongating

Origin 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

Elongating a New DNA Strand

• Enzymes called DNA polymerases catalyze the elongation of new DNA at a replication fork

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

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

New strand

5 end

Phosphate Base

Sugar

Template strand

3 end 5 end 3 end

5 end

3 end

5 end

3 end

Nucleosidetriphosphate

DNA polymerase

Pyrophosphate

Antiparallel Elongation

• The antiparallel structure of the double helix (two strands oriented in opposite directions) affects replication

• DNA polymerases add nucleotides only to the free 3end of a growing strand; therefore, a new DNA strand can elongate only in the 5to3direction

• Along one template strand of DNA, called the leading strand, DNA polymerase can synthesize a complementary strand continuously, moving toward the replication fork

• To elongate the other new strand, called the lagging strand, DNA polymerase must work in the direction away from the replication fork

• The lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase

Parental DNA

5

3

Leading strand

35

3

5

Okazakifragments

Lagging strand

DNA pol III

Templatestrand

Leading strand

Lagging strand

DNA ligase Templatestrand

Overall direction of replication

53

Primase joins RNAnucleotides into a primer.

Templatestrand

5 3

Overall direction of replication

RNA primer3

5

35

DNA pol III addsDNA nucleotides to the primer, formingan Okazaki fragment.

Okazakifragment

3

5

5

3

After reaching thenext RNA primer (not

shown), DNA pol IIIfalls off.

33

5

5

After the second fragment isprimed, DNA pol III adds DNAnucleotides until it reaches thefirst primer and falls off.

33

5

5

DNA pol I replaces the RNA with DNA,adding to the 3 endof fragment 2.

33

5

5

DNA ligase forms abond between the newestDNA and the adjacent DNAof fragment 1.

The lagging strand in the regionis now complete.

Other Proteins That Assist DNA Replication

• Helicase untwists the double helix and separates the template DNA strands at the replication fork

• Single-strand binding protein binds to and stabilizes single-stranded DNA until it can be used as a template

• Topoisomerase corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands

• Primase synthesizes an RNA primer at the 5 ends of the leading strand and the Okazaki fragments

• DNA pol III continuously synthesizes the leading strand and elongates Okazaki fragments

• DNA pol I removes primer from the 5 ends of the leading strand and Okazaki fragments, replacing primer with DNA and adding to adjacent 3 ends

• DNA ligase joins the 3 end of the DNA that replaces the primer to the rest of the leading strand and also joins the lagging strand fragments

5

3Parental DNA

3

5

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

The DNA Replication Machine as a Stationary Complex

• The proteins that participate in DNA replication form a large complex, a DNA replication “machine”

• The DNA replication machine is probably stationary during the replication process

• Recent studies support a model in which DNA polymerase molecules “reel in” parental DNA and “extrude” newly made daughter DNA molecules

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

• DNA can be damaged by chemicals, radioactive emissions, X-rays, UV light, and certain molecules (in cigarette smoke for example)

• In nucleotide excision repair, a nuclease cuts out and replaces damaged stretches of DNA

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

LE 16-17

DNA ligase

DNA polymerase

DNA ligase seals thefree end of the new DNAto the old DNA, making thestrand complete.

Repair synthesis bya DNA polymerasefills in the missingnucleotides.

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

A thymine dimerdistorts the DNA molecule.

Replicating the Ends of DNA Molecules

• Limitations of DNA polymerase create problems for the linear DNA of eukaryotic chromosomes

• The usual replication machinery provides no way to complete the 5 ends, so repeated rounds of replication produce shorter DNA molecules

LE 16-18

5

3

5

End of parentalDNA strands

5

3

Lagging strand

Last fragment

RNA primer

Leading strandLagging strand

Previous fragment

Primer removed butcannot be replacedwith DNA becauseno 3 end available

for DNA polymerase

5

3

Removal of primers andreplacement with DNAwhere a 3 end is available

Second roundof replication

5

3

3

Further roundsof replication

New leading strand

New leading strand

Shorter and shorterdaughter molecules

LE 16-19

1 µm

• Eukaryotic chromosomal DNA molecules have at their ends nucleotide sequences called telomeres

• Telomeres do not prevent the shortening of DNA molecules, but they do postpone the erosion of genes near the ends of DNA molecules

• It has been proposed that the shortening of telomeres is connected to aging

• If 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

• 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

A chromosome consists of a DNA molecule packed together with proteins

• The bacterial chromosome is a double-stranded, circular DNA molecule associated with a small amount of protein

• Eukaryotic chromosomes have linear DNA molecules associated with a large amount of protein

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

• 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

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)

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

• Chromatin is organized into fibers

• 10-nm fiber

– DNA winds around histones to form nucleosome “beads”

– Nucleosomes are strung together like beads on a string by linker DNA

• 30-nm fiber

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

• 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

• Most chromatin is loosely packed in the nucleus during interphase and condenses prior to mitosis

• Loosely packed chromatin is called euchromatin

• 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

• Histones can undergo chemical modifications that result in changes in chromatin organization

– For example, phosphorylation of a specific amino acid on a histone tail affects chromosomal behavior during meiosis

Animations and Videos

Bozeman - What is DNA?

Griffith's Experiment

Hershey-Chase Experiment

Meselson-Stahl Experiment – 1

Meselson-Stahl Experiment – 2

Bozeman - Meselson and Stahl Experiment

Structural Organization of the Chromosome

Replication of a Chromosome

DNA Structure and Replication

Structural Basis of DNA Replication

Animations and VideosDNA Replication Fork

How Nucleotides Are Added In DNA Replication

DNA Replication

Bidirectional Replication of DNA

Proofreading Function of DNA

Bozeman - DNA Replication

Addition and Deletion Mutations

Mutation by Base Substitution

Slipped-strand Mispairing

Thymine Dimers

Animations and Videos

Screening Mutations

Bozeman – Mutations

Genetic Testing - Sickle-Cell Anemia

Transposons: Shifting Segments of the Genome

Mechanism of Transposition

Telomerase – 1

Telomerase – 2

Chapter Quiz Questions – 1

Chapter Quiz Questions – 2

Who conducted the X-ray diffraction studies that were key to the discovery of the structure of DNA?

• Griffith• Franklin• Meselson and Stahl • Chargaff • McClintock

Who conducted the X-ray diffraction studies that were key to the discovery of the structure of DNA?

• Griffith• Franklin• Meselson and Stahl • Chargaff • McClintock

How do the leading and the lagging strands differ?• The leading strand is synthesized in the same

direction as the movement of the replication fork, whereas the lagging strand is synthesized in the opposite direction.

• The leading strand is synthesized at twice the rate of the lagging strand.

• The lagging strand is synthesized continuously, whereas the leading strand is synthesized in short fragments that are ultimately stitched together.

• The leading strand is synthesized by adding nucleotides to the 3' end of the growing strand, whereas the lagging strand is synthesized by adding nucleotides to the 5' end.

How do the leading and the lagging strands differ?• The leading strand is synthesized in the same

direction as the movement of the replication fork, whereas the lagging strand is synthesized in the opposite direction.

• The leading strand is synthesized at twice the rate of the lagging strand.

• The lagging strand is synthesized continuously, whereas the leading strand is synthesized in short fragments that are ultimately stitched together.

• The leading strand is synthesized by adding nucleotides to the 3' end of the growing strand, whereas the lagging strand is synthesized by adding nucleotides to the 5' end.

What kind of evidence about the structure of DNA came from each of the following branches of science?

• physics• chemistry• biology

What kind of evidence about the structure of DNA came from each of the following branches of science?

• physics: X-ray crystallography

• chemistry: The nature of ribose sugar, purines, and pyrimidines

• biology: Data from Chargaff on the ratios between A and T and so on

If the result of the Hershey and Chase experiment had been that radioactive sulfur (35S) was found inside the cells instead of radioactive phosphorus (32P), what could have been concluded?

If the result of the Hershey and Chase experiment had been that radioactive sulfur (35S) was found inside the cells instead of radioactive phosphorus (32P), what could have been concluded?

It would have been concluded that protein functions as the genetic material (this, of course, did not occur).

Define and diagram “semiconservative” as it applies to DNA replication.

Telomeres, or the ends of linear chromosomes, have special structure and function, even though they are noncoding. Describe their structure and function.

What enzyme does a gamete-producing cell include that compensates for replication-associated shortening?

• DNA polymerase II• ligase• telomerase• DNA nuclease• proofreading enzyme

What enzyme does a gamete-producing cell include that compensates for replication-associated shortening?

• DNA polymerase II• ligase• telomerase• DNA nuclease• proofreading enzyme

Which of the following is true of heterochromatin but not of euchromatin?

• It is accessible to enzymes needed for gene expression.• It becomes less tightly compacted after cell division.• It includes DNA primarily found in expressed genes.• It appears more pale when observed microscopically.• It remains tightly coiled at the G1 phase.

Which of the following is true of heterochromatin but not of euchromatin?

• It is accessible to enzymes needed for gene expression.• It becomes less tightly compacted after cell division.• It includes DNA primarily found in expressed genes.• It appears more pale when observed microscopically.• It remains tightly coiled at the G1 phase.

Which of the following results from Griffith’s experiment is an example of transformation?

• Mouse dies after being injected with living S cells.• Mouse is healthy after being injected with living R

cells.• Mouse is healthy after being injected with heat-killed

S cells.• Mouse dies after being injected with a mixture of

heat-killed S and living R cells.• In blood samples from the mouse in D, living S cells

were found.

Which of the following results from Griffith’s experiment is an example of transformation?

• Mouse dies after being injected with living S cells.• Mouse is healthy after being injected with living R cells.• Mouse is healthy after being injected with heat-killed

S cells.• Mouse dies after being injected with a mixture of heat-killed S and living R cells.• In blood samples from the mouse in D, living S cells were found.

Nitrogenous bases are paired in specific combinations. Which of the following does not provide evidence to support this conclusion?

• A purine-purine pair is too wide to account for the 2-nm diameter of the double helix.

• A pyrimidine-pyrimidine pair is too narrow to account for the 2-nm diameter of the double helix.

• The X-ray data suggested that the double helix had a uniform diameter.

• Whenever one strand of DNA has an A, the partner strand has a T.

• The pairs of nitrogenous bases are held together by hydrogen bonds.

Nitrogenous bases are paired in specific combinations. Which of the following does not provide evidence to support this conclusion?

• A purine-purine pair is too wide to account for the 2-nm diameter of the double helix.

• A pyrimidine-pyrimidine pair is too narrow to account for the 2-nm diameter of the double helix.

• The X-ray data suggested that the double helix had a uniform diameter.

• Whenever one strand of DNA has an A, the partner strand has a T.

• The pairs of nitrogenous bases are held together by hydrogen bonds.

Tables like the one shown here are useful for organizing sets of data representing a common set of values (in this case, percentages of A, G, C, and T) for a number of different samples (in this case, species).

Scientific Skills Exercise

Does the distribution of bases in sea urchin DNA and salmon DNA follow Chargaff’s rules?

• Yes, because the %A + %T is greater than the %G + %C in both species.

• No, because %A + %T does not equal %G + %C in both species.

• Yes, because the %A approximately equals the %T and the %G approximately equals the %C in both species.

• No, because %A is higher than %T and %G is higher than %C in both species.

Does the distribution of bases in sea urchin DNA and salmon DNA follow Chargaff’s rules?

• Yes, because the %A + %T is greater than the %G + %C in both species.

• No, because %A + %T does not equal %G + %C in both species.

• Yes, because the %A approximately equals the %T and the %G approximately equals the %C in both species.

• No, because %A is higher than %T and %G is higher than %C in both species.

What is the %T in wheat DNA?

• approximately 22%• approximately 23%• approximately 28%• approximately 45%

What is the %T in wheat DNA?

• approximately 22%• approximately 23%• approximately 28%• approximately 45%