180

10C H A P T E R Molecular Biology

of the Gene

B IG IDEAS

The Structure of theGenetic Material

(10.1–10.3)

A series of experimentsestablished DNA as the

molecule of heredity.

DNA Replication(10.4–10.5)

Each DNA strand can serve as a template for another.

The Flow of GeneticInformation from DNA to

RNA to Protein(10.6–10.16)

Genotype controls phenotypethrough the production of

proteins.

The Genetics of Virusesand Bacteria (10.17–10.23)

Viruses and bacteria are useful model systems for thestudy of molecular biology.

C G

C G

C G

C G

CG

CG

CG

AT

A T

A T

AT

A T

A T

C G

AT

181

The electron micrograph above shows herpesvirus, an infec-tious microbe that causes cold sores, genital herpes, chicken

pox, and other human diseases. In the micrograph, proteinspikes protrude from the exterior of the virus, while the geneticmaterial, colored orange, is visible inside the cell.

Once it enters the human body, a herpesvirus tumbles alonguntil it finds a suitable target cell, recognized when the virus’sspikes bind to protein receptor molecules on the cell’s surface. Theouter membrane of the virus then fuses with the plasma mem-brane of the cell, and the inner part of the virus enters the cell. Thevirus DNA, its genetic material, soon enters the nucleus. In thenuclei of certain nerve cells, the viral DNA can remain dormantfor long periods of time. Once activated, often under conditions ofphysical or emotional stress, the viral DNA hijacks the cell’s ownmolecules and organelles and uses them to produce new copies of

the virus. Virus production eventually causes host cells to burst.Such destruction causes the sores that are characteristic of herpesdiseases. The released viruses can then infect other cells.

Viruses share some of the characteristics of living organisms,but are generally not considered alive because they are not cellu-lar and cannot reproduce on their own. Because viruses havemuch less complex structures than cells, they are relatively easyto study on the molecular level. For this reason, we owe our firstglimpses of the functions of DNA, the molecule that controlshereditary traits, to the study of viruses.

This chapter is about molecular biology—the study of DNAand how it serves as the basis of heredity. We'll explore the struc-ture of DNA, how it replicates, and how it controls the cell by di-recting RNA and protein synthesis. We end with an examinationof the genetics of viruses and bacteria.

Tail

Tail fiber

DNA

TEM

300

,000

!

Head

Today, even schoolchildren have heard of DNA, and scientistsroutinely manipulate DNA in the laboratory and use it tochange the heritable characteristics of cells. Early in the 20thcentury, however, the precise identity of the molecular basis forinheritance was unknown. Biologists knew that genes were lo-cated on chromosomes and that the two chemical componentsof chromosomes were DNA and protein. Therefore, DNA andprotein were the likely candidates to be the genetic material.Until the 1940s, the case for proteins seemed stronger becauseproteins appeared to be more structurally complex: Proteinswere known to be made from 20 different amino acid buildingblocks, whereas DNA was known to be made from a mere fourkinds of nucleotides. It seemed to make sense that the morecomplex molecule would serve as the hereditary material. Biol-ogists finally established the role of DNA in heredity throughexperiments with bacteria and the viruses that infect them.This breakthrough ushered in the field of molecular biology,the study of heredity at the molecular level.

We can trace the discovery of the genetic role of DNA backto 1928. British medical officer Frederick Griffith was studyingtwo strains (varieties) of a bacterium: a harmless strain and apathogenic (disease-causing) strain that causes pneumonia.Griffith was surprised to find that when he killed the patho-genic bacteria and then mixed the bacterial remains with livingharmless bacteria, some living bacterial cells were converted tothe disease-causing form. Furthermore, all of the descendantsof the transformed bacteria inherited the newly acquired abil-ity to cause disease. Clearly, some chemical component of thedead bacteria could act as a “transforming factor” that broughtabout a heritable change in live bacteria.

Griffith’s work set the stage for a race to discover the identityof the transforming factor. In 1952, American biologists AlfredHershey and Martha Chase performed a very convincing set ofexperiments that showed DNA to be the genetic material of T2,a virus that infects the bacterium Escherichia coli (E. coli).Viruses that exclusively infect bacteria are called bacteriophages(“bacteria-eaters”), or phages for short. Figure 10.1A shows the

structure of phage T2, which consists solely of DNA(blue) and protein (gold). Resembling a lunar land-ing craft, T2 has a DNA-containing head and ahollow tail with six jointed protein fibers extend-ing from it. The fibers attach to the surface of asusceptible bacterium. Hershey and Chase knewthat T2 could reprogram its host cell to producenew phages, but they did not know which component—DNA orprotein—was responsible for this ability.

Hershey and Chase found the answer by devising an experi-ment to determine what kinds of molecules the phage trans-ferred to E. coli during infection. Their experiment used only afew relatively simple tools: chemicals containing radioactiveisotopes (see Module 2.4); a radioactivity detector; a kitchenblender; and a centrifuge, a device that spins test tubes to sepa-rate particles of different weights. (These are still basic tools ofmolecular biology.)

Hershey and Chase used different radioactive isotopes to label the DNA and protein in T2. First, they grew T2 with E. coliin a solution containing radioactive sulfur (bright yellow inFigure 10.1B). Protein contains sulfur but DNA does not, so asnew phages were made, the radioactive sulfur atoms were incor-porated only into the proteins of the bacteriophage. The re-searchers grew a separate batch of phages in a solution containingradioactive phosphorus (green). Because nearly all the phage’sphosphorus is in DNA, this labeled only the phage DNA.

Armed with the two batches of labeled T2, Hershey andChase were ready to perform the experiment outlined inFigure 10.1B. ! They allowed the two batches of T2 to infectseparate samples of nonradioactive bacteria. " Shortly afterthe onset of infection, they agitated the cultures in a blender toshake loose any parts of the phages that remained outside thebacterial cells. # Then, they spun the mixtures in a centrifuge.The cells were deposited as a pellet at the bottom of the cen-trifuge tubes, but phages and parts of phages, being lighter, re-mained suspended in the liquid. $ The researchers thenmeasured the radioactivity in the pellet and in the liquid.

Hershey and Chase found that when the bacteria had beeninfected with T2 phages containing labeled protein, the radio-activity ended up mainly in the liquid within the centrifugetube, which contained phages but not bacteria. This result sug-gested that the phage protein did not enter the cells. But whenthe bacteria had been infected with phages whose DNA wastagged, then most of the radioactivity was in the pellet of bac-terial cells at the bottom of the centrifuge tube. Furthermore,when these bacteria were returned to liquid growth medium,they soon lysed, or broke open, releasing new phages with ra-dioactive phosphorus in their DNA but no radioactive sulfurin their proteins.

Figure 10.1C outlines our current understanding—as origi-nally outlined by Hershey and Chase—of the replication cycleof phage T2. After the virus ! attaches to the host bacterialcell, it " injects its DNA into the host. Notice that virtually all

CHAPTER 10 Molecular Biology of the Gene182

The Structure of the Genetic MaterialS C I E N T I F I CD I S C O V E R Y 10.1 Experiments showed that DNA is the genetic material

! Figure 10.1A Phage T2

Phage

Bacterium

Radioactiveprotein

DNA

Centrifuge

The radioactivityis in the liquid

Emptyprotein shell

PhageDNA

Pellet

The radioactivity is in the pellet.

RadioactiveDNA

Hershey and Chase mixed radioactively labeled phages with bacteria. The phagesinfected the bacterial cells.

They agitated the cultures in a blender to separate the phages outside of the bacteria from the cells and their contents.

They centrifuged the mixture so that the bacteria formed a pelletat the bottom of the test tube.

Centrifuge

Pellet

Finally, they measured the radioactivity in the pellet and in the liquid.

Batch 1:Radioactiveproteinlabeled inyellow

Batch 2:RadioactiveDNA labeledin green

"! # $

183The Structure of the Genetic Material 183

●Radioactively labeled phage DNA, but not labeled protein, entered the hostcell during infection and directed the synthesis of new viruses.

! " #

$ The cell lyses andreleases the new phages.

The phage DNA directsthe host cell to make more phage DNA and proteins; new phages assemble.

The phage injects its DNA into the bacterium.

A phage attachesitself to a bacterial cell.

of the viral protein (yellow) is left outside (which is why the ra-dioactive protein did not show up in the host cells during theexperiment shown at the top of Figure 10.1B). Once injected,the viral DNA causes the bacterial cells to # produce newphage proteins and DNA molecules—indeed, complete newphages—which soon $ cause the cell to lyse, releasing thenewly produced phages. In agreement with the experimentalresults of Hershey and Chase, it is the viral DNA that containsthe instructions for making phages.

Once DNA was shown to be the molecule of heredity, un-derstanding its structure became the most important quest inbiology. In the next two modules, we’ll review the structure ofDNA and discuss how it was discovered.

What convinced Hershey and Chase that DNA, rather thanprotein, is the genetic material of phage T2?

?

! Figure 10.1B The Hershey-Chase experiment

! Figure 10.1C A phage replication cycle

Two representationsof a DNA polynucleotide

A

A

G

C

C

G C

G

G

TA

T

T

G C

T

T

A

A

TA

G

T

C

AH

N

ON

H

O

H3C

O–

P OO

O

O

O

C

CC

C

Phosphategroup

Sugar(deoxyribose)

HH

H

HH

Nitrogenous base(can be A, G, C, or T)

Thymine (T)

C

A

T

G

G

C

A

G

G

Sugar-phosphate backbone

DNA nucleotide

DNAnucleotide

Phosphate group

Nitrogenous base

Sugar

T

CH2

CC

C CA DNA double helix

Covalent bondjoiningnucleotides

CHAPTER 10 Molecular Biology of the Gene184

10.2 DNA and RNA are polymers of nucleotidesBy the time Hershey and Chase performed their experiments,much was already known about DNA. Scientists had identifiedall its atoms and knew how they were covalently bonded to oneanother. What was not understood was the specific arrange-ment of atoms that gave DNA its unique properties—the ca-pacity to store genetic information, copy it, and pass it fromgeneration to generation. However, only one year after Hersheyand Chase published their results, scientists figured out thethree-dimensional structure of DNA and the basic strategy ofhow it works. We will examine that momentous discovery inModule 10.3, but first, let’s look at the underlying chemicalstructure of DNA and its chemical cousin RNA.

Recall from Module 3.15 that DNA and RNA are nucleicacids, consisting of long chains (polymers) of chemical units(monomers) called nucleotides. Figure 10.2A shows fourrepresentations of various parts of the same molecule. At left isa view of a DNA double helix. One of the strands is opened up(center) to show two different views of an individual DNApolynucleotide, a nucleotide polymer (chain). The view on thefar right zooms into a single nucleotide from the chain. Each

type of DNA nucleotide has a differ-ent nitrogen-containing base: ade-

nine (A), cytosine (C), thymine(T), or guanine (G). Because

nucleotides can occur in a polynucleotide in any sequence andpolynucleotides vary in length from long to very long, thenumber of possible polynucleotides is enormous. The chainshown in this figure has the sequence ACTGG, only one ofmany possible arrangements of the four types of nucleotidesthat make up DNA.

Looking more closely at our polynucleotide, we see in thecenter of Figure 10.2A that each nucleotide consists of threecomponents: a nitrogenous base (in DNA: A, C, T, or G), asugar (blue), and a phosphate group (yellow). The nucleotidesare joined to one another by covalent bonds between thesugar of one nucleotide and the phosphate of the next. Thisresults in a sugar-phosphate backbone, a repeating patternof sugar-phosphate-sugar-phosphate. The nitrogenous basesare arranged like ribs that project from the backbone.

Examining a single nucleotide in even more detail (on theright in Figure 10.2A), you can see the chemical structure of itsthree components. The phosphate group has a phosphorusatom (P) at its center and is the source of the word acid innucleic acid. The sugar has five carbon atoms, shown in redhere for emphasis—four in its ring and one extending abovethe ring. The ring also includes an oxygen atom. The sugar iscalled deoxyribose because, compared with the sugar ribose, itis missing an oxygen atom. (Notice that the C atom in the

lower right corner of the ring is bonded to an H atom in-stead of to an —OH group, as it is in ribose; see Figure

10.2C. Hence, DNA is “deoxy”—which means“without an oxygen”—compared to RNA.)

! Figure 10.2A The structure of a DNA polynucleotide

Adenine

Ribose

Guanine

Uracil

Cytosine

Phosphate

185The Structure of the Genetic Material

! Figure 10.2B The nitrogenous bases of DNA

! Figure 10.2C An RNA nucleotide

The full name for DNA is deoxyribonucleic acid, with thenucleic portion of the word referring to DNA’s location in thenuclei of eukaryotic cells. Each nitrogenous base (thymine, inour example at the right in Figure 10.2A) has a single or doublering consisting of nitrogen and carbon atoms with variousfunctional groups attached. Recall from Module 3.2 that afunctional group is a chemical group that affects a molecule’sfunction by participating in specific chemical reactions. In thecase of DNA, the main role of the functional groups is to deter-mine which other kind of bases each base can hydrogen-bondwith. For example, the NH2 group hanging off cytosine is capa-ble of forming a hydrogen bond to the C=O group hangingoff guanine, but not with the NH2 group protruding from ade-nine. The chemical groups of the bases are therefore responsi-ble for DNA’s most important property, which you will learnmore about in the next module. In contrast to the acidic phos-phate group, nitrogenous bases are basic, hence their name.

The four nucleotides found in DNA differ only in the struc-ture of their nitrogenous bases (Figure 10.2B). At this point, thestructural details are not as important as the fact that the basesare of two types. Thymine (T) and cytosine (C) are single-ringstructures called pyrimidines. Adenine (A) and guanine (G)are larger, double-ring structures called purines. The one-letterabbreviations can be used either for the bases alone or for thenucleotides containing them.

What about RNA (Figure 10.2C)? As its name—ribonucleicacid—implies, its sugar is ribose rather than deoxyribose.Notice the ribose in the RNA nucleotide in Figure 10.2C;

unlike deoxyribose, the sugarring has an —OH group attached to the Catom at its lower-right corner. Anotherdifference between RNA and DNA isthat instead of thymine, RNA has a ni-trogenous base called uracil (U). (Youcan see the structure of uracil inFigure 10.2C; it is very similar tothymine.) Except for the presence of ribose and uracil, an RNA poly-nucleotide chain is identical to a DNApolynucleotide chain. Figure 10.2D is acomputer graphic of a piece of RNA polynucleotide about 20 nucleotides long. In this 3-D view, each sphere represents anatom, and notice that the color scheme is the same as in theother figures in this module. The yellow phosphate groups andblue ribose sugars make it easy to spot the sugar-phosphatebackbone.

In this module, we reviewed the structure of the nucleicacids DNA and RNA. In the next module, we’ll see how twoDNA polynucleotides join together in a molecule of DNA.

Compare and contrast DNA and RNA polynucleotides.?

Guanine (G)Cytosine (C) Adenine (A)Thymine (T)

N N

N NH

HH

H

N

N

N N

N N

H

NHH

H

O

H3C

H

CC

C COH

CC

C

C

C

H

C

C

C

O

PurinesPyrimidines

H

N

H

C

C

N

N

H

CC

C COH

H

NHH

H

N

ON

H

O

H

O–

P OO

OH

CH2

O

O

C

CC

C

Phosphategroup

Nitrogenous base(can be A, G, C, or U)

Sugar(ribose)

Uracil (U)O

C

C

C

C

H

HH

H

●Both are polymers of nucleotides consisting of a sugar, a nitrogenous base, anda phosphate. In RNA, the sugar is ribose; in DNA, it is deoxyribose. Both RNAand DNA have the bases A, G, and C, but DNA has a T and RNA has a U.

" Figure 10.2D A computermodel showing part of an RNApolynucleotide