The Genetics of Viruses The Genetics of Viruses and Bacteriaand Bacteria

Microbial ModelsMicrobial Models

Viruses come in many shapes and sizes

Compare the size of a Eukaoryotic cell, Bacterial Cell and a Virus

Herpes Virus

Measles

Polio

Ebola Virus

Discovery of the VirusDiscovery of the Virus

Adolph Meyer a German Scientist studied Adolph Meyer a German Scientist studied the Tobacco Mosaic Virus.the Tobacco Mosaic Virus.

Thought it was caused by a very small Thought it was caused by a very small bacteria because it could not be viewed bacteria because it could not be viewed through the microscope.through the microscope.

Tobacco Mosaic Virus

Tobacco Mosaic Virus

Dimitri Ivanosky a Russian ScientistDimitri Ivanosky a Russian Scientist

Filtered the sap to get rid of the bacteria.Filtered the sap to get rid of the bacteria.

The plants still received the infection when The plants still received the infection when sprayed with the filtered sap.sprayed with the filtered sap.

Still thought the pathogen were very small Still thought the pathogen were very small bacteria.bacteria.

Martinus Beijerink a Dutch BotanistMartinus Beijerink a Dutch Botanist

Discovered that this infectious particle could Discovered that this infectious particle could reproduce.reproduce.

Sprayed plants with filtered sap and their sap Sprayed plants with filtered sap and their sap infected other plants.infected other plants.

Infection was not diluted on subsequent Infection was not diluted on subsequent infections.infections.

Could not grow outside the host in culture Could not grow outside the host in culture medium.medium.

Could not be inactivated with alcohol like Could not be inactivated with alcohol like bacteriabacteria

Wendell Stanley an American Wendell Stanley an American ScientistScientist

Finally crystallized Finally crystallized this infectious particle this infectious particle and viewed it under and viewed it under the electron the electron microscope.microscope.

Viral CompositionViral Composition

Capsid – protein coatCapsid – protein coat

Sometimes an envelope – glycoproteinsSometimes an envelope – glycoproteins

Nucleic acid – DNA or RNA. Never both. Nucleic acid – DNA or RNA. Never both. Can be single or double stranded.Can be single or double stranded.

Some have tail fibers – Bacteriophage T4Some have tail fibers – Bacteriophage T4

Viruses Are Obligate Intracellular Viruses Are Obligate Intracellular ParasitesParasites

They lack their own enzymes to perform They lack their own enzymes to perform metabolism and reproduction.metabolism and reproduction.

They utilize the host’s enzymatic They utilize the host’s enzymatic machinery to accomplish these tasks.machinery to accomplish these tasks.

Viruses have a Viruses have a host range or are host host range or are host specific.specific. Rabies infects more than one hostRabies infects more than one host Eukaryotic viruses are usually tissue specific.Eukaryotic viruses are usually tissue specific.

• Rhinoviruses, Adenoviruses, Herpes, HIVRhinoviruses, Adenoviruses, Herpes, HIV

Reproductive Cycles of VirusReproductive Cycles of Virus

Lytic CycleLytic Cycle – destroys the host cell – destroys the host cell Viral proteins are translated by host enzymes Viral proteins are translated by host enzymes

and new viral particles are produced.and new viral particles are produced. Viral particles are assembled and the host cell is Viral particles are assembled and the host cell is

lysed. Host cell death occurs.lysed. Host cell death occurs. Bacterial cells possess Bacterial cells possess restriction restriction

endonucleasesendonucleases that destroy foreign DNA. that destroy foreign DNA. The bacterial DNA is methylated to protect from The bacterial DNA is methylated to protect from

destruction.destruction.

Lytic Cycle

Lysogenic Cycle Can Be Used For Lysogenic Cycle Can Be Used For CloningCloning

Viruses can infect without destroying the host Viruses can infect without destroying the host cell.cell.

They integrate their DNA into the host cell and They integrate their DNA into the host cell and turn off their own genes.turn off their own genes.

These types of viruses are called These types of viruses are called temperate temperate viruses.viruses.

Bacterial cells that possess these viral genes are Bacterial cells that possess these viral genes are celled celled prophages.prophages.

Viral DNA can be replicated along with the host Viral DNA can be replicated along with the host cell’s DNA.cell’s DNA.

Lysogenic CycleLysogenic Cycle

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Lysogenic Viruses can be Triggered to Lysogenic Viruses can be Triggered to Become Lytic VirusesBecome Lytic Viruses

Radiation, chemicals or any host cell stress can Radiation, chemicals or any host cell stress can cause the virus to enter the lytic cycle and cause the virus to enter the lytic cycle and destroy the host cell.destroy the host cell.

Some prophages express prophage genes that Some prophages express prophage genes that alter the phenotype of the host cell.alter the phenotype of the host cell. Bacteria produce endotoxins that originate from viral Bacteria produce endotoxins that originate from viral

genes.(Diptheria, Scarlet Fever and Botulism)genes.(Diptheria, Scarlet Fever and Botulism)

Genes can be inserted into bacterial cells using Genes can be inserted into bacterial cells using viruses in a process called viruses in a process called Transduction.Transduction.

HIV Infection

HIV Life Cycle

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HIV Infection

RNA as Viral Genetic MaterialRNA as Viral Genetic Material

Messenger RNA serves as the template Messenger RNA serves as the template for new genetic material.for new genetic material.

Reverse transcriptaseReverse transcriptase produces DNA from produces DNA from mRNA.mRNA.

Newly made DNA integrates into the host Newly made DNA integrates into the host chromosome.chromosome.

Unlike prophages, proviruses never leave.Unlike prophages, proviruses never leave. The virus now is referred to as a The virus now is referred to as a provirusprovirus.. Viruses that do this are called retroviruses.Viruses that do this are called retroviruses.

The host’s RNA polymerase transcribes The host’s RNA polymerase transcribes viral RNA from the DNA. viral RNA from the DNA.

RNA serves as both a template and RNA serves as both a template and

mRNA.mRNA.

RNA viruses mutate more rapidly because RNA viruses mutate more rapidly because replication of RNA does not have to replication of RNA does not have to undergo the same proofreading steps as undergo the same proofreading steps as replicating DNA.replicating DNA.

Transduction

ViroidsViroids

ViroidsViroids are tiny molecules of naked are tiny molecules of naked circular RNA that infect plants.circular RNA that infect plants.

- only several hundred nucleotides long.- only several hundred nucleotides long.

- a molecule can be an infectious agent.- a molecule can be an infectious agent.

- disrupt metabolism by interferring with - disrupt metabolism by interferring with the host genome.the host genome.

PrionsPrionsPrions Prions are infectious proteins.are infectious proteins.

- cause degenerative brain diseases like - cause degenerative brain diseases like scrapes and Creutzfeldt-Jakob disease.scrapes and Creutzfeldt-Jakob disease.

- abnormal shaped brain proteins induce - abnormal shaped brain proteins induce normal proteins to assume an abnormal normal proteins to assume an abnormal shape propagating itself.shape propagating itself.

Prions

The Genetics of BacteriaThe Genetics of Bacteria Bacterial genomeBacterial genome

Circular double stranded DNA in the nucleoid region. Circular double stranded DNA in the nucleoid region. (remember prokaryotes do not have a nucleus)(remember prokaryotes do not have a nucleus)

Plasmids are in addition to the genomePlasmids are in addition to the genome• Circular double stranded DNACircular double stranded DNA• May carry extra chromosomal DNA called May carry extra chromosomal DNA called plasmids.plasmids.

Bacteria have about 4,300 genes, 500 x more than a Bacteria have about 4,300 genes, 500 x more than a virus but about 1/10virus but about 1/10thth of that of a typical eukaryotic of that of a typical eukaryotic cell.cell.

Divide by binary fissionDivide by binary fission DNA synthesis is bidirectional and can occur very DNA synthesis is bidirectional and can occur very

quickly.quickly.• E.coli can divide in 20 minutesE.coli can divide in 20 minutes

Genetic recombination of BacteriaGenetic recombination of Bacteria

TransformationTransformation Bacteria take up naked DNA from the environment.Bacteria take up naked DNA from the environment.

• If expressed this can change the phenotype of the bacterial If expressed this can change the phenotype of the bacterial cell.cell.

• Remember how the smooth strain of streptococcus Remember how the smooth strain of streptococcus pneumonia was transformed into the rough strain of pneumonia was transformed into the rough strain of streptococcus pneumonia.streptococcus pneumonia.

• Biotechnologist stimulate bacteria to take up foreign DNA Biotechnologist stimulate bacteria to take up foreign DNA with CaClwith CaCl22..

• Human genes like insulin can be transferred into bacteria Human genes like insulin can be transferred into bacteria and large quantities of insulin can be produced.and large quantities of insulin can be produced.

Genetic Recombination of BacteriaGenetic Recombination of Bacteria TransductionTransduction

Viruses (phages) are used to carry bacterial Viruses (phages) are used to carry bacterial genes from one host cell to another.genes from one host cell to another.

Two kinds of transductionTwo kinds of transduction• Generalized TransductionGeneralized Transduction

During the lytic cycle of the virus some of the host DNA During the lytic cycle of the virus some of the host DNA can be accidentally packaged in the viral particle.can be accidentally packaged in the viral particle.

When the virus infects a new host cell it injects the DNA When the virus infects a new host cell it injects the DNA from the previous host.from the previous host.

It is called generalized transduction because the It is called generalized transduction because the bacterial DNA is taken up randomly by the virus.bacterial DNA is taken up randomly by the virus.

Transduction

Genetic Recombination in BacteriaGenetic Recombination in Bacteria

Specialized TransductionSpecialized Transduction• Involved the lysogenic cycleInvolved the lysogenic cycle• The viral DNA integrates into the host bacterial cell The viral DNA integrates into the host bacterial cell

and is called a and is called a prophage.prophage.• The virus then enters the lytic cycle and The virus then enters the lytic cycle and

accidentally takes DNA that is flanking the accidentally takes DNA that is flanking the insertion site of the viral DNA.insertion site of the viral DNA.

• When the virus infects another host cell only When the virus infects another host cell only certain genes are transferred to the new host cell.certain genes are transferred to the new host cell.

Conjugation

Genetic Recombination in BacteriaGenetic Recombination in Bacteria

ConjugationConjugation Direct transfer of genetic material between bacteria.Direct transfer of genetic material between bacteria. Involves a Involves a sex pilussex pilus

• A bridge that forms between two cells.A bridge that forms between two cells. Involves the transfer of a small segment of DNA or a small Involves the transfer of a small segment of DNA or a small

circular segment of DNA called a plasmid containing genes that circular segment of DNA called a plasmid containing genes that code for the formation for the sex pili.code for the formation for the sex pili.

• The plasmid is called the The plasmid is called the F (fertility) factorF (fertility) factor• Bacteria that have the F factor are ( F Bacteria that have the F factor are ( F + + ) and are considered male.) and are considered male.

The f factor replicates and is donated to the recipient cell.The f factor replicates and is donated to the recipient cell.• The recipient cells are ( F The recipient cells are ( F - - ) and considered to be female.) and considered to be female.• The recipient cell becomes ( F The recipient cell becomes ( F + + ) when it receives the F factor.) when it receives the F factor.

When the F factor integrates into the main chromosome then the When the F factor integrates into the main chromosome then the cell is called an Hfr cell.cell is called an Hfr cell.

Hfr cells have the tendency to recombine with the host Hfr cells have the tendency to recombine with the host chromosome of another ( F chromosome of another ( F - - ) ) cell.cell.

Conjugation

Other types of PlasmidsOther types of Plasmids EpisomesEpisomes

A genetic element that can either exist as a plasmid A genetic element that can either exist as a plasmid or part of a bacterial chromosome.or part of a bacterial chromosome.

Usually beneficial to bacteria because: Usually beneficial to bacteria because: • it allows then to survive adverse conditionsit allows then to survive adverse conditions• F factors promote recombination which introduces new F factors promote recombination which introduces new

genes that can perhaps facilitate survival.genes that can perhaps facilitate survival. R PlasmidsR Plasmids

These plasmids carry genes for antibiotic resistance.These plasmids carry genes for antibiotic resistance. Bacteria can transfer antibiotic resistance from one Bacteria can transfer antibiotic resistance from one

cell to other by transferring the R plasmid.cell to other by transferring the R plasmid. Very dangerous antibiotic resistant bacteria have Very dangerous antibiotic resistant bacteria have

been created in hospitalsbeen created in hospitals

TransposonsTransposons

TransposonsTransposons Often called “jumping genes”Often called “jumping genes” Code for its own enzymes to excise itself from the genome and Code for its own enzymes to excise itself from the genome and

insert itself somewhere else.insert itself somewhere else. Transposons also copy themselves and insert the copy Transposons also copy themselves and insert the copy

somewhere else in the genome.somewhere else in the genome. Transposons can jump from a plasmid to the main chromosome Transposons can jump from a plasmid to the main chromosome

and visa versa.and visa versa. One main difference between genetic recombination through One main difference between genetic recombination through

transformation, transduction, conjugation and transposons are:transformation, transduction, conjugation and transposons are:• In transformation, transduction, conjugation depends on base In transformation, transduction, conjugation depends on base

pairing between homologous regions of DNA. Transposons do not pairing between homologous regions of DNA. Transposons do not require similar or identical sequences of DNA to pair with.require similar or identical sequences of DNA to pair with.

OperonsOperons

A mechanism that bacteria use to control their A mechanism that bacteria use to control their metabolic needs.metabolic needs.

A group of genes are either turned on or off A group of genes are either turned on or off depending the metabolic needs of the organism.depending the metabolic needs of the organism. Involve catabolic and anabolic pathways.Involve catabolic and anabolic pathways.

• Catabolic pathways break down substances and typically are Catabolic pathways break down substances and typically are turned off until the substance to be metabolized is present.turned off until the substance to be metabolized is present.

These are known as These are known as inducible operonsinducible operons

• Anabolic pathways are usually turned on until there is Anabolic pathways are usually turned on until there is enough product is made.enough product is made.

These are known as These are known as repressible operonsrepressible operons..

OperonsOperons Anatomy of a Repressible OperonAnatomy of a Repressible Operon

These operons are normally turned on until the repressor is These operons are normally turned on until the repressor is activated and binds to the operator to block RNA polymerase activated and binds to the operator to block RNA polymerase from binding to the promoter.from binding to the promoter.

OperatorOperator• regulatory switchregulatory switch• If a molecule is bound to the operator, then RNA polymerase cannot If a molecule is bound to the operator, then RNA polymerase cannot

bind to the promoter and mRNA cannot be transcribe and thus the bind to the promoter and mRNA cannot be transcribe and thus the protein product cannot be made.protein product cannot be made.

RepressorRepressor• The molecule that binds to the operator is the repressor.The molecule that binds to the operator is the repressor.

CorepressorCorepressor• Binds to the repressor and activates it so that it can bind to the Binds to the repressor and activates it so that it can bind to the

operator.operator. Regulatory GeneRegulatory Gene

• Synthesizes the repressor moleculeSynthesizes the repressor molecule

Trp operonTrp operon

Repessible operon present in E.coli that Repessible operon present in E.coli that synthesizes tryptophan.synthesizes tryptophan.

When enough tryptophan is made it acts as a When enough tryptophan is made it acts as a corepressor and binds to the repressor to and corepressor and binds to the repressor to and converts the repressor to its active form. converts the repressor to its active form.

The activated repressor binds to the operator The activated repressor binds to the operator and blocks RNA polymerase from binding to the and blocks RNA polymerase from binding to the promoter thus preventing transcription.promoter thus preventing transcription.

Trp operon

OperonsOperons Anatomy of a Inducible OperonAnatomy of a Inducible Operon

These operons are normally turned off until the repressor is These operons are normally turned off until the repressor is inactivated. At this point the repressor falls off the operator and inactivated. At this point the repressor falls off the operator and RNA polymerase and binds to the promoter.RNA polymerase and binds to the promoter.

OperatorOperator• regulatory switchregulatory switch• If a molecule is bound to the operator, then RNA polymerase cannot If a molecule is bound to the operator, then RNA polymerase cannot

bind to the promoter and mRNA cannot be transcribed and the bind to the promoter and mRNA cannot be transcribed and the protein product cannot be synthesized.protein product cannot be synthesized.

RepressorRepressor• The molecule that binds to the operator is the repressor.The molecule that binds to the operator is the repressor.

InducerInducer• Binds to the repressor and converts it to the inactive from and it falls Binds to the repressor and converts it to the inactive from and it falls

off the operator. off the operator. Regulatory GeneRegulatory Gene• Synthesizes the repressor moleculeSynthesizes the repressor molecule

lac operonlac operon

The The lac operon lac operon is only turned on when lactose is only turned on when lactose is present because it produces enzymes is present because it produces enzymes necessary to break down lactose.necessary to break down lactose.

It is an inducible operonIt is an inducible operon The inducer in allolactose which binds to the The inducer in allolactose which binds to the

repressor which is already bound to the operator repressor which is already bound to the operator and inactivates it.and inactivates it.

The inactivated repressor falls off the operator The inactivated repressor falls off the operator and the genes are transcribed by RNA and the genes are transcribed by RNA polymerase.polymerase.

lac operon

An Example of Positive Gene An Example of Positive Gene RegulationRegulation

E.coli would prefer to use glucose as an energy source. E.coli would prefer to use glucose as an energy source. It will produce the enzymes to break down lactose into its It will produce the enzymes to break down lactose into its

components galactose and glucose if glucose is not available.components galactose and glucose if glucose is not available. How does E.coli sense the glucose concentration and send a How does E.coli sense the glucose concentration and send a

message to the operon to produce or not produce the enzyme message to the operon to produce or not produce the enzyme necessary to break down lactose (Beta galactosidase)?necessary to break down lactose (Beta galactosidase)?

A molecule called A molecule called cyclic AMP(cAMP)cyclic AMP(cAMP) builds up when glucose is in builds up when glucose is in low concentrations.low concentrations.

cAMP binds to cAMP binds to cAMP receptor protein (CRPcAMP receptor protein (CRP)) and the cAMP/CRP and the cAMP/CRP complex binds to a site upstream from the promoter and bends the complex binds to a site upstream from the promoter and bends the DNA in such a way that it is easier for RNA polymerase to bind to DNA in such a way that it is easier for RNA polymerase to bind to the operon.the operon.

This stimulates transcription and is positive regulation.This stimulates transcription and is positive regulation. When there is an abundance of glucose the cAMP levels drop and When there is an abundance of glucose the cAMP levels drop and

the cAMP/CRP complex cannot form.the cAMP/CRP complex cannot form.

Up regulation of the lac operonUp regulation of the lac operon