Chapter 18

The Genetics of Virusesand Bacteria

1 µm

•Recall that bacteria are prokaryotes–Prokaryote = NO NUCLEUS = no nuclear membrane–Prokaryote = chromosome attached to cell membrane, DOES HAVE ORGANELLES–With cells much smaller and more simply organized than those of eukaryotes

•Viruses–Are smaller and simpler still

Figure 18.20.25 m

Virus

Animalcell

Bacterium

Animal cell nucleus

Microbial Model SystemsMicrobial Model Systems

•Viruses called bacteriophages

–Can infect and set in motion a genetic takeover of bacteria, such as Escherichia coli

Figure 18.10.5 m

VirusesViruses

Obligate Intracellular Obligate Intracellular ParasitesParasites

•A virus has a genome but can reproduce only within a host cell

•NOT LIVING

The Discovery of Viruses: The Discovery of Viruses: Scientific InquiryScientific Inquiry

•Tobacco mosaic disease

–Stunts the growth of tobacco plants and gives their leaves a mosaic coloration

Figure 18.3

•In the late 1800s

–Researchers hypothesized that a particle smaller than bacteria caused tobacco mosaic disease

•In 1935, Wendell Stanley

–Confirmed this hypothesis when he crystallized the infectious particle, now known as tobacco mosaic virus (TMV)

TMVTMV

Viruses

–Are very small infectious particles consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope

•Viral genomes may consist of

–Double- or single-stranded DNA

–Double- or single-stranded RNA

Capsids and EnvelopesCapsids and Envelopes

•A capsid

–Is the protein shell that encloses the viral genome

CAPSID

18 250 mm 70–90 nm (diameter)

20 nm 50 nm(b) Adenoviruses

RNADNACapsomere

Glycoprotein

TMV & Adenovirus

Capsids and EnvelopesCapsids and Envelopes

Envelopes

–Membranous coverings derived from the membrane of the host cell

Viral EnvelopesViral Envelopes

•Many animal viruses

–Have a membranous envelope

•Viral glycoproteins on the envelope

–Bind to specific receptor molecules on the surface of a host cell

A.K.A. phages

–Have the most complex capsids found among viruses

BacteriophagesBacteriophages

General Features of Viral General Features of Viral Reproductive CyclesReproductive Cycles

•Viruses are obligate intracellular parasites

–They can reproduce only within a host cell

•Each virus has a host range

–A limited number of host cells that it can infect

General Features of Viral General Features of Viral Reproductive CyclesReproductive Cycles

•Viruses use enzymes, ribosomes, and small molecules of host cells to synthesize progeny viruses

VIRUS

Capsid proteins

mRNA

Viral DNA

HOST CELL

Viral DNA

DNA

Capsid

Viral Reproductive Mechanisms

–Lytic cycle

Is a phage reproductive cycle that culminates in the death (lysis) of the host

–Lysogenic cycle

Replicates the phage genome without destroying the host

Lytic Cycle Lytic Cycle (Viral Reproduction)(Viral Reproduction)

1. DOCKING with the host receptor protein

2. PENETRATION of the viral nucleic acid into the host cytoplasm (Restriction Endonucleases, A.K.A. restriction enzymes break up host DNA)

3. BIOSYNTHESIS of the viral components

4. Assembly (MATURATION) of the viral components into complete viral units

RELEASE of the completed virus from the host cell

Phage assembly

Head Tails Tail fibers

Lysogenic CycleLysogenic Cycle

•Temperate phages

Are capable of using both the lytic & lysogenic cycles of reproduction

Lambda

ProphageProphage

When viral DNA is integrated into the bacterial chromosome (Plasmid)

RNA

Capsid

Envelope (withglycoproteins)

HOST CELL

Viral genome (RNA)

Template

Capsidproteins

Glyco-proteins

mRNA

Copy ofgenome (RNA)

ER

•Retroviruses, such as HIV, use the enzyme reverse transcriptase

–To copy their RNA genome into DNA, which can then be integrated into the host genome as a provirus (Integrates into host DNA)

HIV

Reversetranscriptase

Viral envelope

Capsid

Glycoprotein

RNA(two identicalstrands)

2 of each

Evolution of VirusesEvolution of Viruses

•Viruses do not really fit our definition of living organisms since viruses can reproduce only within cells

–They probably evolved after the first cells appeared, perhaps packaged as fragments of cellular nucleic acid

Viral Diseases in AnimalsViral Diseases in Animals

•Viruses may damage or kill cells

–By causing the release of hydrolytic enzymes from lysosomes

•Some viruses cause infected cells

–To produce toxins that lead to disease symptoms

Viral Diseases in AnimalsViral Diseases in Animals

•Viruses may damage or kill cells (Amount of damage depends on the ability of infected tissue to regenerate by mitosis)

-Respiratory tract epithelium repairs quickly from adenovirus infection

- Nerve tracts affected by polio virus is permanent

•Find host cells using “lock & key” fit with proteins on virus & host cell receptors

PrionsPrions

• Protein infectious particlesProtein infectious particles• Contain no RNA or DNAContain no RNA or DNA• Long incubation period (~10 years)Long incubation period (~10 years)

–Are slow-acting, virtually indestructible infectious proteins that cause brain diseases in mammals

–Propagate by converting normal proteins into the prion version

PrionsPrions

Prions

Prion

Normalprotein

Originalprion

Newprion

Many prions

Emerging VirusesEmerging Viruses

Are those that appear suddenly or suddenly come to the attention of medical scientists

3 processes contribute to emerging viruses

1. Mutation of existing viruses as RNA is not corrected by proofreading e.g. SARS

2. Spread from one host species to another e.g. Hanta Virus

3. Dissemination from a small isolated population e.g. HIV

Figure 18.11 A, B

(a) Young ballet students in Hong Kong wear face masks to protect themselves from the virus causing SARS.

(b) The SARS-causing agent is a coronavirus like this one (colorized TEM), so named for the “corona” of glycoprotein spikes protruding from the envelope.

SARS – Severe Acute Respiratory SARS – Severe Acute Respiratory SyndromeSyndrome

Emerging Viruses are NOT Emerging Viruses are NOT newnew

They are existing viruses that

•Mutate

•Spread to new host species

•Disseminate more widely in the host species

Small PoxSmall Pox

PolioPolio Polio

Herpes SimplexHerpes Simplex

HepatitisHepatitis

                          

Varicella Zoster Varicella Zoster – chicken pox– chicken pox

MumpsMumps

Measles - RubeolaMeasles - Rubeola

•Influenza Virus

•Rubella

•Parvo-virus

•Epstein Barr Virus

•Hanta Virus

•(HPV) Human Papilloma Virus

•(RSV) Respiratory Syncytial Virus

•Rabies

•Rhinovirus

•Rotavirus

•West Nile Virus

Other Viruses that affect Other Viruses that affect humanshumans

Viral Diseases in PlantsViral Diseases in Plants

•More than 2,000 types of viral diseases of plants are known

•Common symptoms of viral infection include

–Spots on leaves and fruits, stunted growth, and damaged flowers or roots

Viral Diseases in PlantsViral Diseases in Plants

•Plant viruses spread disease in two major modes

–Horizontal transmission, entering through damaged cell walls

–Vertical transmission, inheriting the virus from a parent

Viroids -Viroids -The Simplest Infectious AgentThe Simplest Infectious Agent

–Are circular RNA molecules that infect plants and disrupt their growth

BacteriaBacteria

•Rapid reproduction, mutation, and genetic recombination contribute to the genetic diversity of bacteria

•Bacteria allow researchers

–To investigate molecular genetics in the simplest true organisms

The Bacterial Genome and The Bacterial Genome and Its ReplicationIts Replication

•The bacterial chromosome

–Is usually a circular DNA molecule with few associated proteins

•In addition to the chromosome

–Many bacteria have plasmids, smaller circular DNA molecules that can replicate independently of the bacterial chromosome

The Bacterial Genome and The Bacterial Genome and Its ReplicationIts Replication

•Bacterial cells divide by binary fission

–Which is preceded by replication of the bacterial chromosome

Replicationfork

Origin of replication

Termination of replication

Binary Fission

Mutation and Genetic Recombination as Mutation and Genetic Recombination as Sources of Genetic VariationSources of Genetic Variation

•Since bacteria can reproduce rapidly

–New mutations can quickly increase a population’s genetic diversity

•Genetic diversity

–Can also arise by recombination of the DNA from two different bacterial cells

–Remember that prokaryotes don’t undergo meiosis or fertilization

Recombination in BacteriaRecombination in Bacteria

•Three processes bring bacterial DNA from different individuals together

–Transformation

–Transduction

–Conjugation

TransformationTransformation

Is the alteration of a bacterial cell’s genotype and phenotype by the uptake of naked, foreign DNA from the surrounding environment

TransductionTransduction

Phages carry bacterial genes from one host cell to another

Conjugation and PlasmidsConjugation and Plasmids

•Conjugation

–Is the direct transfer of genetic material between bacterial cells that are temporarily joined

Figure 18.17 Sex pilus 1 m

DNA transfer is one way

The F Plasmid and The F Plasmid and ConjugationConjugation

•Cells containing the F plasmid, designated F+ cells

–Function as DNA donors during conjugation

–Transfer plasmid DNA to an F recipient cell

Figure 18.18a

A cell carrying an F plasmid(an F+ cell) can form amating bridge with an F– celland transfer its F plasmid.

A single strand of the F plasmid breaks at a specific point (tip of blue arrowhead) and begins tomove into the recipient cell. As transfer continues, the donor plasmid rotates(red arrow).

2

DNA replication occurs inboth donor and recipientcells, using the single parental strands of the F plasmid as templates to synthesize complementary strands.

3

The plasmid in the recipient cell circularizes. Transfer and replication result in a compete F plasmid in each cell. Thus, both cells are now F+.

4

F Plasmid Bacterial chromosome

Bacterial chromosome

F+ cell

F+ cell

F+ cell

Mating bridge

1

F– cell

F Plasmid recombinationF Plasmid recombination

• Chromosomal genes can be transferred during Chromosomal genes can be transferred during conjugation wconjugation when the donor cell’s F factor is hen the donor cell’s F factor is integrated into the chromosomeintegrated into the chromosome

Hfr cellHfr cell• A cell with the F factor built into its chromosomeA cell with the F factor built into its chromosome

• The F factor of an Hfr cellThe F factor of an Hfr cell• Brings some chromosomal DNA along with it when Brings some chromosomal DNA along with it when

it is transferred to an Fit is transferred to an F–– cell cell

R plasmids and Antibiotic ResistanceR plasmids and Antibiotic Resistance

Confer resistance to various antibiotics

Transposition of Genetic Transposition of Genetic ElementsElements

•Transposable elements

–Can move around within a cell’s genome

–Are often called “jumping genes”

–Contribute to genetic shuffling in bacteria by folding the DNA

Insertion SequencesInsertion Sequences

•An insertion sequence contains a single gene for transposase

–An enzyme that catalyzes movement of the insertion sequence from one site to another within the genome

Figure 18.19a

(a) Insertion sequences, the simplest transposable elements in bacteria, contain a single gene that encodes transposase, which catalyzes movement within the genome. The inverted repeats are backward, upside-down versions of each other; only a portion is shown. The inverted repeat sequence varies from one type of insertion sequence to another.

Insertion sequence

Transposase geneInvertedrepeat

Invertedrepeat

3

5

3

5

A T C C G G T…

T A G G C C A …

A C C G G A T…

T G G C C T A …

TransposonsTransposons

•Bacterial transposons

–Also move about within the bacterial genome

–Have additional genes, such as those for antibiotic resistance

Figure 18.19b

(b) Transposons contain one or more genes in addition to the transposase gene. In the transposon shown here, a gene for resistance to an antibiotic is located between twin insertion sequences. The gene for antibiotic resistance is carried along as part of the transposon when the transposon is inserted at a new site in the genome.

Inverted repeats Transposase gene

Insertion sequence

Insertion sequence

Antibioticresistance gene

Transposon

5

3

5

3

Prokaryotic Gene Prokaryotic Gene ExpressionExpression

•Individual bacteria respond to environmental change by regulating their gene expression

•E. coli, a type of bacteria that lives in the human colon

–Can tune its metabolism to the changing environment and food sources

Response to the Response to the environmentenvironment

•This metabolic control occurs on two levels

–Adjusting the activity of metabolic enzymes already present

–Regulating the genes encoding the metabolic enzymes

Figure 18.20a, b

(a) Regulation of enzyme activity

Enzyme 1

Enzyme 2

Enzyme 3

Enzyme 4

Enzyme 5

Regulationof geneexpression

Feedbackinhibition

Tryptophan

Precursor

(b) Regulation of enzyme production

Gene 2

Gene 1

Gene 3

Gene 4

Gene 5

–

–

Feedback Inhibition

Operons: The Basic Operons: The Basic ConceptConcept

•In bacteria, genes are often clustered into operons, composed of

–An operator, an “on-off” switch

–A promoter

–Genes for metabolic enzymes

•An operon

–Is usually turned “on”

–Can be switched off by a protein called a repressor

Operon PartsOperon Parts

•The regulatory gene codes for the repressor protein.

•The promoter site is the attachment site for RNA polymerates.

•The operator site is the attachment site for the repressor protein.

•The structural genes code for the proteins.

•The repressor protein is different for each operon and is custom fit to the regulatory metabolite. Whether or not the repressor protein can bind to the operator site is determined by the type of operon.

•The regulatory metabolite is either the product of the reaction or the reactant depending on the type of operon.

Operon PartsOperon Parts

•The repressor protein is different for each operon and is custom fit to the regulatory metabolite. Whether or not the repressor protein can bind to the operator site is determined by the type of operon.

•The regulatory metabolite is either the product of the reaction or the reactant depending on the type of operon.

The The trptrp operon: regulated operon: regulated synthesis of repressible synthesis of repressible

enzymesenzymes

Figure 18.21a

(a) Tryptophan absent, repressor inactive, operon on. RNA polymerase attaches to the DNA at the promoter and transcribes the operon’s genes.

Genes of operon

Inactiverepressor

Protein

Operator

Polypeptides that make upenzymes for tryptophan synthesis

Promoter

Regulatorygene

RNA polymerase

Start codon Stop codon

Promoter

trp operon

5

3mRNA 5

trpDtrpE trpC trpB trpAtrpRDNA

mRNA

E D C B A

DNA

mRNA

Protein

Tryptophan(corepressor)

Active repressor

No RNA made

Tryptophan present, repressor active, operon off. As tryptophanaccumulates, it inhibits its own production by activating the repressor protein.

(b)

Figure 18.21b

Trp OperonTrp Operon

Repressible and Inducible Operons: Repressible and Inducible Operons: Two Types of Negative Gene Two Types of Negative Gene RegulationRegulation

•In a repressible operon

–Binding of a specific repressor protein to the operator shuts off transcription (Found in anabolic pathways)

•In an inducible operon

–Binding of an inducer to an innately inactive repressor inactivates the repressor and turns on transcription (Found in catabolic pathways)

Lac OperonLac Operon

The lac operon: regulated synthesis of inducible enzymes

Figure 18.22a

DNA

mRNA

ProteinActiverepressor

RNApolymerase

NoRNAmade

lacZlacl

Regulatorygene

Operator

Promoter

Lactose absent, repressor active, operon off. The lac repressor is innately active, and inthe absence of lactose it switches off the operon by binding to the operator.

(a)

5

3

Lac Operon “off”Lac Operon “off”

mRNA 5'

DNA

mRNA

Protein

Allolactose(inducer)

Inactiverepressor

lacl lacz lacY lacA

RNApolymerase

Permease Transacetylase-Galactosidase

5

3

(b) Lactose present, repressor inactive, operon on. Allolactose, an isomer of lactose, derepresses the operon by inactivating the repressor. In this way, the enzymes for lactose utilization are induced.

mRNA 5

lac operon

Figure 18.22b

Lac Operon “on”Lac Operon “on”

Types of OperonsTypes of Operons

• Inducible enzymesInducible enzymes• Usually function in catabolic pathwaysUsually function in catabolic pathways

• Repressible enzymesRepressible enzymes• Usually function in anabolic pathwaysUsually function in anabolic pathways