Chapter 13

Ebolavirus

Nucleic acid surrounded by proteins Protein coat with capsomeres- capsomeres could be different proteins Envelope outside protein coat with spikes coming out Has its own enzyme During replication, it gets our cells to make the enzyme then captures it in the virus?

*General Characteristics of Viruses*

Obligatory intracellular parasites *Contain DNA or RNA* - Viruses can contain RNA as their genetic material whereas other organisms can only use double-stranded DNA No ribosomes No ATP-generating mechanism *Contain a protein coat* - Protein coat surrounds the DNA or RNA core *Most viruses infect only specific types of cells in one host* - Host cell- the cell that a virus infects *Host range is determined by specific host attachment sites and cellular factors necessary for viral replication* - Specific receptors on the cell membrane or cell wall - Host range- either a type of cell or a type of organism, determined by the attachment sites on the cells within the host For a virus to infect the host cell, the outer surface of the virus must chemically interact with specific receptor sites on the surface of the cell- held together by weak bonds, H-bonds, the combination of many attachment and receptor sites leads to a strong association between host cell virus

Parvoviridae don't need the details on all of these

Single-stranded DNA, nonenveloped viruses - Fifth disease - Anemia in immunocompromised patients

Flaviviridae

Single-stranded RNA, + strand, enveloped - Arboviruses can replicate in arthropods; include yellow fever, dengue, SLE, and West Nile viruses, - Hepatitis C virus Hepatitis- disease caused by various viruses, a condition of the liver that can be caused by different viruses

Picornaviridae

Single-stranded RNA, + strand, nonenveloped - Enterovirus - Poliovirus and coxsackievirus - Rhinovirus - Hepatitis A virus

Retroviridae

Single-stranded RNA, produce DNA - Use reverse transcriptase to produce DNA from viral genome - Lentivirus (HIV) - Oncogenic viruses - Includes all RNA tumor viruses

Orthomyxoviridae

Single-stranded RNA, − strand, multiple RNA strands - Influenzavirus

Growing Bacteriophages

Viruses must be grown in living cells - Bacteriophages form plaques on a lawn of bacteria - Mix phage and bacteria, plate bacteria evenly - Phage infectes bacteria, multiplies, lyse bacteria, infects more bacteria, repeats, form plaques - Original number of viruses quantified as plaque forming units

Cancer: Tumor Suppressor genes

* Tumor Suppressor Genes* - *encode proteins that in one way or another inhibit cell proliferation (brakes)* - *Loss of those proteins results in uncontrolled cell growth.* - *loss is caused by deletions or point mutations in the gene that prevents production of the protein or lead to production of a nonfunctional protein.* *The genetic material of viral genome that can cause a tumor is a viral oncogene* - *incorporates into the host cell DNA* Some viruses don't carry oncogenes but can activate an oncogene

*Bacterial defense systems against phage: Abortive Infection* slide 30

*Abortive Infection* - leads to death of the infected cell as a sacrifice to protect the surrounding clonal population from predation - Blocks Bacterial: - DNA replication - Transcription - Translation - Packaging of genome - Premature lysis of infected cell Bacteria just kill itself Get infected by a bacteriophage and stop its own replication and dies Altruistic

*Transduction*

*Another method of horizontal transmission of DNA* *Fragmented pieces of bacterial DNA are accidently packaged with phage DNA* They recombine with a host bacterial DNA in a position that allows them to be functional The DNA becomes part of the recipient bacterial cell DNA and replicates with the chromosome as the bacteria divides (not a lytic event) Accidental packaging of bacterial DNA into a bacteriophage rather than just bacteriophage DNA Horizontal transfer Conjugation- transfer of DNA via a plasmid through direct cell-to-cell contact Transformation- bacteria cell takes up a naked piece of DNA floating around that had come from a bacteria that had lysed

*Multiplication of Animal Viruses*

*Attachment: viruses attach to cell membrane via membrane protein receptors* - Receptor characteristics are an inherited trait; may differ human to human *Entry:* by receptor-mediated endocytosis or fusion - Endocytosis: cell membrane fold inward to form vesicles containing virus, Endocytosis: cell, virus attaches to it, cell membrane envelopes the virus, breaks off within the cell, virus is in a vesicle - entire virus enters the cell, bacteriophages- only part - Fusion: envelope which is similar in its components to the membrane of the animal host cell, will fuse together and the virus will move into the cell into the cytoplasm - Fusion: the envelope of enveloped viruses fuses with cell membrane and releases virus into cytoplasm *Uncoating:* Separation of viral nucleic acid from protein coat in vesicle - Capsid is digested by enzymes or released into cytoplasm - Protein coat has to be degraded when protein reaches the cytoplasm *Biosynthesis:* production of nucleic acid and proteins - Synthesize DNA in nucleus using viral enzymes and proteins in cytoplasm using host enzymes *Maturation:* Proteins transported into nucleus, nucleic acid and capsid proteins assemble *Release* Virus transported to plasma membrane and released by budding (enveloped viruses) or rupture Bacterial cell- all of this occurs in the cytoplasm Animal- nucleic acid- synthesized in nucleus, proteins synthesized in the cytoplasm, proteins transported into the nucleus to be packaged - so much being produce that it buds off, envelope surrounds protein coat OR fusion

*Prions*

*Proteinaceous infectious particle* Inherited and transmissible by ingestion, transplant, and surgical instruments - Spongiform encephalopathies: sheep scrapie, Creutzfeldt-Jakob disease, Gerstmann-Sträussler-Scheinker syndrome, fatal familial insomnia, mad cow disease *Caused by the conversion of a normal host glycoprotein into an infectious form* PrPC: normal cellular prion protein, on cell surface PrPSc: scrapie protein; accumulates in brain cells, forming plaques Not viruses Prions are proteins They are normal proteins that our body carries- important for the normal functioning of cells There is a change in the conformation of these proteins that make it into an infectious form, if they interact with other proteins of the same type, the other proteins will become malformed, will form plaques and death, mad cow disease

*Lytic cycle*

*Attachment:* attachment site on phage (tail fibers) interacts with specific receptor site on bacteria - Receptors on surface specific for a bacteriophage, attachment through these receptors *Penetration:* DNA is injected through a break in cell wall created by phage lysozyme, - a contracting a sheath drives a hollow tube into the bacterium: hypodermic needle - Lysozyme- breaks down peptidoglycan layer so that bacteriophage can inject DNA through cytoplasm *Biosynthesis: DNA reaches cytoplasm,* - bacterial (host) protein synthesis is stopped by interference with transcription and translation and bacterial DNA is degraded, - *Phage DNA synthesized using host nucleotides and enzymes* - Viral mRNA transcribed followed by protein synthesis - Protein synthesis to produce its own protein is stopped, transcription and translation is stopped, bacterial DNA fragments- cannot do anything for itself- can't make its own DNA or protein, the phage takes over and uses the bacterial machinery- nucleotides present, transcription and translation abilities *Maturation: all components are assembled into virions* - Occurs spontaneously, head and tail assembled, head is filled with DNA, attached to tail. *Release:* Host cell wall peptidoglycan is broken open by lysozyme causing osmotic lysis and release of the intact virus *Reinfection* Bacteriophage replicate in bacterial cell, bacteria burst and all the bacteria come out 3769-371

*The lytic cycle of a T-even bacteriophage.*

*Attachment:* phage attaches to host cell *Penetration:* phage penetrates host cell and injects its DNA *Biosynthesis:* phage DNA directs synthesis of viral components by the host cell *Maturation:* viral components are assembled into virions *Release:* host cell lyses, and new virions are released

Bacterial defense systems against phage

*Be aware of the fact that although bacteria seem simplistic bacteria have mechanisms and pathways for their own survival* *One of abilities has to do with protecting themselves from bacteriophage infection*

*Bacterial defense systems against phage: Blocking DNA Entry*

*Blocking DNA Entry* - Super infection exclusion systems (Sie) systems act to protect a lysogenized host from infection by other phages - typically phage encoded e.g. a phage encoded protein blocks the translocation of phage DNA into the cytoplasm (b) or - another blocks degradation of the peptidoglycan(c) Once a bacteriophage has inserted its DNA and the DNA becomes a prophage- part of the chromosome- there are genes in the bacteriophage DNA that block the infection of any other bacteriophage Bacteria is happy and continues to live with bacteriophage DNA inserted into its chromosome

*Virus Identification: Cytopathic effects* slide 9

*Cytopathic effects* changes in host cells that are caused by viral invasion - changes in cell morphology, in cell physiology, and the biosynthetic events - lysis of the host cell or when the cell dies without lysis due to an inability to reproduce - causes cells of a monolayer to deteriorate as they multiply, can lead to multiple nuclei in one cell rather than just one nucleus per cell Damage that individual viruses do to host cells Human cytomegalovirus- A tissue, B cells, D tissue changes morphologically *Inclusion bodies found in specific virally infected cells*- found in the cytoplasm or nucleus of some infected cells, sometime viral parts (nucleic acids or proteins in the process of being assembled into virions)- *can help identify the causative agent - can stain with an acidophilic or basophilic stain - Cowdry type A: Herpes simplex virus and Varicella zoster virus - Owl's eye appearance: Cytomegalovirus - Cowdry type B: Polio and Adenovirus - Paschen bodies in variola or small pox Example of cytopathic effects Inclusion bodies contain a lot of material Can identify the virus simply by looking at it and identifying the shapes They typically represent sites of viral multiplication in a bacterium or a eukaryotic cell and usually consist of viral capsid proteins, contain very little host protein, ribosomal components or DNA/RNA fragments 431

*Retroviruses* what they are why they are different from all other viruses the enzyme that is specific for those viruses

*Enveloped, single-stranded positive-sense RNA virus with a DNA intermediate* virus uses its own reverse transcriptase enzyme to produce DNA from its RNA genome *DNA incorporated into the host cell genome* by an integrase enzyme, - retroviral DNA is referred to as a provirus viral DNA (provirus) is translated and transcribed along with the cell's own genes, - Produces the proteins required to assemble new copies of the virus - the infection will persist indefinitely.

*Latent and Persistent Viral Infections*

*Latent: Virus remains in asymptomatic host cell for long periods* - *Cold sores (sunburn, fever), shingles (chickenpox virus)* *Persistent: Disease process occurs over a long period; generally is fatal* - Subacute sclerosing panencephalitis (measles virus) Shingles- people who have had chicken pox as children can get them as adults, stress involved

Virion Structure

*Nucleic acid:* DNA or RNA: double stranded, single stranded, linear, circular - RNA can be double-stranded in some cases *Capsid: protein coat* - *Capsomeres: subunits of the capsid* *Envelope: covers the capsid: lipids, proteins, carbs* - Some viruses have an envelope *Spikes: carbohydrate-protein complexes; may mediate binding to cells* - Some viruses have spikes

*Lysogenic cycle*

*Phage DNA is inserted* *Integrates into bacterial DNA (prophage)* Transcription of all other phage genes is repressed Since it is contained within the bacterial genome, it is replicated along with it. *Remains latent* *A spontaneous event, radiation, chemical, may lead to excision and start of the lytic cycle* DNA injected into the cytoplasm but it doesn't do anything, it is inserted into the bacteria's chromosome and doesn't do anything, just stays there - Piece of DNA that comes from a phage= prophage - Genes that express the proteins that will make up a bacteriophage are repressed - Bacteria divide by binary fission - Remains latent- just stays there - Periodically- an event that activates and prophage replicates, goes into lytic cycle and dies

*Bacterial defense systems against phage: Preventing Phage Attachment*

*Preventing Phage Attachment* - modifying receptor structure through mutation - concealing receptors with an additional physical barrier (protein, capsule or exopolysaccharide) - decrease in receptor availability through reversible switching (reduction in receptor expression) Mutate so that receptor changes or can make a capsule that can cover the receptor

*Bacterial defense systems against phage: Restriction-Modification Systems*

*Restriction-Modification Systems* - Destroys invading DNA - composed of a restriction endonuclease and a methyltransferase - Bacterial cell uses the restriction enzyme to cut the invading DNA of the virus at the specific recognition site of the enzyme. - methylase recognizes the same target site on the bacterial DNA as the restriction enzyme and adds a methyl group to a specific nucleotide in the restriction site. This blocks restriction enzyme cleavage (cutting the DNA) - Thus, viral DNA is restricted in the bacterial cell by the restriction enzyme, and the bacterial DNA is modified by the methylase to protect it from its own restriction enzyme. Bacteria are capable of determining when they have been infected Bacteria have enzymes that can degrade DNA When a bacteria gets infected by a phage DNA, these enzymes are expressed and they begin to degrade the phage DNA If you have enzymes that cut DNA and are not controlled, what stops them from cutting and degrading bacterial DNA? The bacteria attach another molecule, a methyl, to all of the parts of its own chromosome that block these enzymes from working Don't have to learn all of the details in these slides about bacterial defense systems

*Lysogenic Conversion by Prophages* slide 23 **

*The added genetic information provided by the DNA of a prophage may enable a bacterium to possess new genetic traits.* - *some bacteria become virulent only when infected themselves with a specific prophage* - The addition of new genetic info into a bacterial cell by a bacteriophage - Prophages can bring in certain genes that give an additional characteristic to the recipient lysogenized bacteria - Some of the new genetic traits result in a new virulence or increased ability to cause disease - Ability of bacteria to produce a disease depends upon the prophage *Bacterium. Phage. Gene Product. Phenotype* - Vibrio cholerae. CTX phage. cholerae toxin. cholera - Escherichia coli. lambda phage. shigalike toxin. hemorrhagic diarrhea - Clostridium botulinum. clostridial phages. botulinum toxin. botulism (food poisoning) - Corynebacterium diphtheriae. corynephage beta. diphtheria toxin. diphtheria - Streptococcus pyogenes. T12. erythrogenic toxins. scarlet fever know one example of lysogenic conversion - the host cell may exhibit new properties - organism can produce a toxin only when it carries the lysogenic phage, because the prophage carries the gene coding for the toxin - the toxin produced by Clostridium botulinum, which causes botulism, is encoded by a prophage gene

Cancer

*Two types of genes are responsible for cellular growth control; proto-oncogenes and tumor suppressor genes.* - *mutations in these genes can contribute to the development of cancer* - *Activated oncogenes can transform normal cells into cancerous cells.* *Proto-oncogenes promote cell growth in a controlled fashion* - *Mutations in proto-oncogenes result in (gain of function):* - *a constitutively acting protein product (no control of protein activity)* - *Movement of the gene to behind a different promoter that causes elevated expression of the gene* Some viruses can cause cancers- HPV- oncogenic viruses

*Taxonomy of Viruses*

*Viral species: a group of viruses sharing the same genetic information and ecological niche (host)* Genus names end in -virus Common names are used for species Subspecies are designated by a number Herpesviridae (Family) Herpesvirus (genus) Human Herpesvirus HHV-1, HHV-2, HHV-3 Retroviridae (Family) Lentivirus (genus) Human Immunodeficiency virus HIV-1, HIV-2 Names are written in italics with the first letter capitalized *Proper nouns in names should be capitalized; Semliki Forest virus, Polio virus, Ebola virus* Genus names end in virus Common names used for species Species is 3rd one down with numbers being strains

*Budding of an enveloped virus*

- Many animal viruses are surrounded by an envelope - Envelope proteins are coded for by virus genes - Envelope carbs and lipids synthesized by host and are incorporated into the host membrane - Virus pushes through membrane and part of it adheres to the virus and, voila, the virus has an envelope Release by budding: - viral capsid within host cell plasma membrane and viral protein within plasma membrane - bud forms - bud forms even more - envelope encloses and pinches off

*Replication of a DNA-Containing Animal Virus*

1. *Attachment:* virion attaches to host cell - a papovirus is a typical DNA-containing virus that attacks animal cells 2. *Entry and Uncoating:* virion enters cell, and its DNA is uncoated 3. A portion of viral DNA is transcribed, producing mRNA that encodes "early" viral proteins 4. *Biosynthesis:* viral DNA is replicated and some viral proteins are made 5. Late translation: capsid proteins are synthesized 6. *Maturation:* virions mature 7. *Release:* virions are released - viral replication in animals generally follows these steps: attachment, entry, uncoating, biosynthesis of nucleic acids and proteins, maturation, and release - knowledge of viral replication phases is important for drug development strategies, and for understanding disease pathology

*Transduction Process*

A phage infects the donor bacterial cell. Phage DNA and proteins are made, and the bacterial chromosome is broken into pieces. Occasionally pieces of bacterial DNA are packaged in a phage capsid. Then the donor cell lyses and releases phage particles containing bacterial DNA. A phage carrying bacterial DNA infects a new host cell, the recipient cell. Recombination can occur, producing a recombinant cell with a genotype different from both the donor and recipient cells. - Inserting from donor cell to recipient cell - Enters recipient DNA by recombination- piece of DNA with a certain nucleotide sequence homologous to a sequence within the bacterial chromosomal DNA, complementary nucleotides line up and piece of the new DNA is incorporated into the bacterial chromosome - Phage infection, fragmentation of DNA, accidental incorporation of bacterial DNA into phage, phage infects another cell, with permitting factors- homologous sequence- recombination will occur - Can transfer antibiotic resistance to a bacterial cell

Bacterial defense systems against phage, example

Attachment inhibition Attachment DNA entry blocking DNA injection injection DNA replication Restriction Modification Transcription and translation Assembly interference Assembly Lysis Abortive infection ** know this diagram Slide 32

Bacteriophage and animal viral multiplication compared.

Attachment: Bacteriophages- Tail fibers attach to cell wall proteins Animal Viruses- Attachment sites are plasma membrane proteins and glycoproteins Entry: Bacteriophages- Viral DNA is injected into host cell Animal Viruses- Capsid enters by receptor-mediated endocytosis or fusion Uncoating: Bacteriophages- Not required Animal Viruses- Enzymatic removal of capsid proteins Biosynthesis: Bacteriophages- In cytoplasm Animal Viruses- In nucleus (DNA viruses) or cytoplasm (RNA viruses) Chronic infection: (to biosynthesis) Bacteriophages- Lysogeny Animal Viruses- Latency; slow viral infections; cancer Release: Bacteriophages- Host cell is lysed Animal Viruses- Enveloped viruses bud out; non-enveloped viruses rupture plasma membrane Steps are the same but mechanisms are different- animals much more complex Both get attachment, entry, biosynthesis, chronic infection Both have receptors- cell wall or plasma proteins Chronic infection- An infection by a virus continues on and on and on Bacteria- Lysogeny- phage DNA injected into bacterial chromosome Animal- Virus may hang out for decades or DNA might be incorporated

Pathogenicity of Bacteriophages and Resistance of Bacteria

Bacteria and Bacteriophages have been co-evolving Phage mechanisms have evolved to overcome bacterial resistance. Therefore, there is a continuous evolutionary relationship between the *pathogenicity of Bacteriophages and the resistance of Bacteria (evolutionary arms race hypothesis)* Bacterial cell evolving pathways to protect against bacteriophages Phages evolving to get around those bacterial protections Dynamic, always changing

*Bacteriophage*

Binal (complex) viruses: neither helical nor polyhedral forms - pleomorphic (irregular shaped), or complex structures Structure: Capsid Nucleic acid- only DNA Sheath Tail fiber Baseplate Pin Once they insert their DNA into a bacteria, one of two pathways are followed: - *Lytic cycle: lytic bacteriophages* - *lyse (destroys) the host bacterium as a normal part of their life cycle* - *Lysogenic cycle: temperate bacteriophages* - *incorporates its DNA into the bacteria's DNA and become a noninfectious prophage.* Phage DNA integrates within the bacterial chromosome by recombination, becoming a prophage These viruses attach onto the bacteria surface/membrane through specific receptors and they insert their DNA Animal viruses- entire virus winds up in the cell and capsid has to be degraded for DNA to come out Bacteriophage is like a hypodermic needle- injects DNA

Chikungunya virus

Disease caused by the Chikungunya virus Spread from south asia To caribbean to south US

Virus Classification

Double or single-stranded DNA Double or single-stranded RNA RNA retroviruses Enveloped Spikes What disease it causes

Hepadnaviridae

Double-stranded DNA, enveloped viruses - Hepatitis B virus

Herpesviridae

Double-stranded DNA, enveloped viruses - Simplexvirus (HHV-1 and HHV-2) - Varicellovirus (HHV-3) - Lymphocryptovirus (HHV-4) - Cytomegalovirus (HHV-5) - Roseolovirus (HHV-6 and HHV-7) - Kaposi's sarcoma (HHV-8) Some herpesviruses can remain latent in host cells

Poxviridae

Double-stranded DNA, enveloped viruses -Orthopoxvirus (vaccinia and smallpox viruses) -Cowpox

Adenoviridae

Double-stranded DNA, nonenveloped viruses - Respiratory infections in humans - Tumors in animals

Specialized Transduction Process don't worry about this

During lysogenic life cycle, host DNA is accidentally excised when prophage is reactivated New virus genome contains host genes lying adjacent to the phage insertion site Can be packed into capsid along with viral DNA - infective virion: can infect a new host cell and will be able to replicate

*HIV*

HIV- enveloped virus, fuses with the cellular membrane, virus itself is incorporated, protein is broken down, envelope protein left at cell surface Virus has matrix and capsid protein that are digested when it enters the cell, releasing viral enzymes and viral RNA Reverse transcriptase- viral RNA, uses host nucleotides --> single-stranded DNA, reverse transcribed into double-stranded DNA - makes random errors during reverse transcription - then ssDNA is reverse transcribed into a dsDNA Integrase (comes in with virus) grabs double-stranded DNA, carries it into a nuclear pore into nucleus, finds host chromosome, makes a nick, and integrates viral DNA into cell genome/ chromosome- establishes life-long infection RNAP makes mRNA which code for different viral proteins and associated with ribosomes on RER, taken to cell surface, embeds in cell membrane, get cluster of envelope proteins on surface of infected cell, other mRNA allow for translation of other viral proteins which will be used to make up key components that virus will need- also transported to cell surface - buds off of cell surface- still not a mature virion- protease breaks up polypeptide chains allowing for them to coalesce and form structures that will make up mature virion that can go and infect other cells Integration --> transcription --> viral RNA leaves the nucleus --> translation --> virus proteins that virus will need --> protease cuts up the protein --> reconstruction allowing for them to coalesce and form the structures that make up the final mature virion which can go and infect other cells RNA to ssDNA to dsDNA to integration to synthesis of protein RNA to budding slide 47

Virus. Cancer Type. Mechanism Viruses that will cause cancer

Hepatitis B virus (HBV) Hepatocellular carcinoma Chronic inflammation Hepatitis C virus (HCV) Hepatocellular carcinoma Chronic inflammation Epstein-Barr virus (EBV)(HHV-4) Burkitt's lymphoma, Hodgkin's lumphoma, Post transplantation lymphoma, Nasopharyngeal carcinoma Oncogenic Human papillomavirus (HPV) Cervical cancer, Anal cancer, Penis cancer, Head and neck carcinoma Oncogenic Human T lymphotropic virus type I (HTLV-1) Adult T-cell leukemia Oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV) (HHV-8) Kaposi's sarcoma, Pleural effusion lymphoma, Multicentric Castleman's disease Oncogenic Oncogenic viruses- contain genes that will promote uncontrolled growth in our cells- genes that override the control mechanism of our cells growing normally

Phage plaques on a lawn of bacteria

If you were to take on a species of bacteria and create a lawn of bacteria and spread bacteria all over the plate and then add bacteriophage specific for that bacteria, you would get these holes- where the phage infected and lysed the bacteria Can determine specific type of bacteria or how many phages you have

*Retrovirus infection and reverse transcription*

Including HIV Intermediate step- (+) RNA is converted into DNA, not protein- done by reverse-transcriptase which is carried by the virus itself because our bodies do not contain this enzyme The (+) RNA is converted to DNA then duplicated and is now double-stranded DNA and can be incorporated into our chromosomes through integrase enzyme Animal virus DNA incorporated into our chromosomes is a provirus Put into the chromosome and is active- chronic and persists indefinitely like in AIDS

CRISPR-Cas System slide 30

Occurs in bacteria, can consider it a bacterial immune system Bacteria, when they are infected a bacteriophage, can protect themselves, take a piece of the bacteriophage DNA and insert it into its own chromosomes When another bacteriophage infects the bacterial cell later on, the bacteria can compare the sequence of DNA from the old bacteriophage to that of this new bacteriophage and use it as a memory to recognize it, know they are being infected, and can degrade that bacteriophage DNA

*The lysogenic cycle*

Phage DNA (double-stranded) 1. Phage attaches to host cell and injects DNA 2. Phage DNA circularizes and enters lytic cycle or lysogenic cycle Lytic Cycle 3a. New phage DNA and proteins are synthesized and assembled into virions 4a. Cell lyses, releasing phage virions Lysogenic Cycle 3b. Phage DNA integrates within the bacterial chromosome by recombination, becoming a prophage 4b. Lysogenic bacterium reproduce normally 5. Occasionally, the prophage may excise from the bacterial chromosome by another recombination event initiating a lytic cycle

Specialized Transduction don't worry about this too much

Phage DNA integrates into a very specific spot in the host chromosome. When viral DNA excises from the chromosome and enters the lytic phase some bacteria DNA is excised along with it Phage DNA will contain a new piece of bacterial DNA, which can undergo recombination Because the viral DNA integrates into a specific location the bacterial DNA removed and transferred will always be the same This is why it is called 'specialized' transduction.

Replication of Ebola Virus Replication of -strand RNA ??

RNA viruses don't follow the plan when it comes to nucleic acids All nucleic acids- DNA and RNA- have + or - strands (+) strand of DNA is read by the RNAP or DNAP, can be read by a ribosome, if it infects a cell, it can be read by a ribosome and produce all of the proteins it needs, cannot do (+) to (+) have to go from (+) to (-) back to (+), (+) strand does not need enzyme because can just be read by ribosome (-) strand cannot be read by a ribosome Ebola virus- has a (-) strand DNA, cannot be read, cannot be used to produce proteins, to get proteins has to be converted to a (+) strand, has to be an enzyme RNA-dependent-RNAP converts (-) to (+) which can be read by ribosome, enzyme comes from virus, to produce more RNA, have to go from (-) to (+) back to (-) again

Virus Identification: Serological Tests

Serological tests - *Detect antibodies against viruses* in a patient - *Use antibodies to identify viruses* in neutralization tests, and Western blot Identify them mainly by antibodies Serology test based on clumping of bacteria, viruses are too small to look for clumping so use tests like ELISA (detection of presence of antibody) or neutralization tests Neutralization- Take sample of unknown virus, add antibodies, try to infect host cells, if antibody interacts with unknown virus, the virus will not infect the cell

Virion Structure: shapes

a polyherdral virus - different sides to it - many-sides - capsid in shape of icosahedron - capsomeres- form an equilateral triangle a helical virus - resemble long rods that may be rigid or flexible - viral nucleic acid is found within a hollow, cylindrical capsid that has a helical structure an enveloped helical virus - protein coat, spikes come out of it - capsid of some viruses is covered by an envelope - roughly spherical

*Prophage*

inserted phage DNA, Phage DNA integrates within the bacterial chromosome by recombination, becoming a prophage when circle recombines with and becomes part of the circular bacterial DNA (lysogenic cycle) is not active: its genes aren't expressed, and it doesn't drive production of new phages. However, each time a host cell divides, the prophage is copied along with the host DNA, getting a free ride Under the right conditions, the prophage can become active and come back out of the bacterial chromosome, triggering the remaining steps of the lytic cycle (DNA copying and protein synthesis, phage assembly, and lysis).