Lecture 13-14

Agents that cause DNA damage induce lambda to ____ from the chromosome and enter a lytic cycle.

excise

__ encodes structural protein

gag

The genome map of retroviruses includes the genes __, __, __, and __.

gag, pol, env, R

RecA is normally involved in _____ ____ but can also act as a protease that inadvertently destroys the __ ____, allowing the cro protein to accumulate, activating lytic events.

genetic recombnation, cI repressor

What are some anatomic terms for a bacteriophage T4?

head, collar, tail, tail pins, endplate, tail fibers

With respect to prions, genetic information is contained in the ____.

host

Viral Classification is determined by ___ or ____ ___.

host and genome type.

For replication, virus particles must enter a ___ ___.

host cell

Viruses require ___ __ for propogation.

host cells

_____ ___ may be required for liberation of virions from the host cell.

host-lytic enzymes

The retrovirus called _____ _____ ____ causes AIDS.

human immunodeficiency virus

If the health of the bacterial cell is in jeopardy during the lysogenic cycle then, _____ will occur, sending the phage into the lytic pathway.

induction

Early genes are transcribed directly by RNApol-σ70, which is used to create proteins necessary for ___ ___ ____.

initial phase replication

Lambda can integrate into the host's genomes through a recombination event, utilizing the enzyme ____.

integrase

Lysogenic Cycle

integrate into host genome, replicating with the bacterium (prophage)

Besides classifying based on virus and genome in virion (DNA/RNA), David Baltimore also classified based on _______.

intermediates (reverse transcriptase)

Give a definition of plating efficiency.

is a measure of the number of colonies originating from single cells.

Complex viruses require _____ genomes to encode extra protein .

larger

Not all infections of animal host cells result in cell lysis or death; ____ or ___ infections are common.

latent and persistent infections

In a ____ ____, the virus replicates in the host and remain dormant until it decides to re-erupt.

latent infection (cold sores--herpesvirus)

The "One Step Growth Curve" begins with a _____ ____, where ___ ___, ___ ___, and ___ ___ are manufactured. This period is also known as ____ maturation.

latent period, early enzymes, nucleic acid, and protein coat, eclipse maturation

Bacteriophage are typically grown as ____ on lawns of cells (___ ___) or in ___ culture.

plaques, petri plates, liquid

__ encodes reverse transcriptase

pol

A _____ is used in some viruses that have genes that require this enzyme for replication.

polymerases

____ and ____ are the smallest known pathogens.

prions and viroids

Transformation of a gene that ___ or ____ the movement in the cell cycle could ruin cell cycle regulation leading to a tumor.

promotes, inhibits

The extracellular form of a prion is solely ____.

protein

Viroids lack ___-____ regions.

protein-encoding regions

In latent infections, virus tends to become ____ in nervous tissue.

quiescent

Specificity of viruses for particular hosts is mediated by ____ on the host cell ____.

receptors, surface

Viroid mechanism of action are unknown, but are though to function as a _____ ___, disrupting normal expression of proteins.

regulatory RNA

Lytic Cycle

replicate new virions

Animal viruses include all known modes of viral genome ____.

replication

RT is needed by the ______ to make a ___ intermediate as the packaged RNA is unable to act as mRNA.

retrovirus, DNA

______ and Class ____ viruses need reverse transcriptase.

retroviruses and Class VII

The retrovirus virion contains an enzyme, _____ _____, that copies the information from its RNA genome into DNA.

reverse transcriptase

______ _____ uses an RNA molecule as a template to produce a DNA molecule.

reverse transcriptase (RT)

Provirus

reverse transcriptase copy of the virus mRNA encoded into the host's DNA--> this section is called the provirus

What is a plaque-forming unit?

s a measure of the number of viruses capable of forming plaques per unit volume

The influenza virus is a ____ ____ virus.

segmented RNA virus

Prions and Viroids are ____-____.

self-replicating

When PrPSc accumulates, it causes symptoms including: ____, ____, and _____ _____.

shaking, tremors, pathological laughter

Class II is a ___-stranded ____ genome.

single stranded, DNA

Theoretically, each plaque is caused by the infection by a ___ ___ ___.

single virus partcile

Class VI is a ___-stranded ____ genome that replicates with ____ intermediate.

single, RNA, DNA intermediate

Class IV is a ___-stranded ____ genome plus ____.

single, RNA, sense

Class V is a ___-stranded ____ genome minus _____.

single, RNA, sense

All ___ -____ RNA is enveloped.

single-stranded RNA

The lambda injects genetic info into the cell that has ____-____ ends of ___ base pairs each. This allows the ends to re-cicularize once it is inside the cell since both of the ends are ______ to one another.

single-stranded, 12 bp, complementary

Viroids are _____ to the plant they infect.

specific

The cI, cII, and cIII _____ the cI protein, helping to push expression towards the _____ pathway.

stabilize, lysogenic

Most virons are _____; their symmetry is either ____ or _____.

symmetrical, helical, icosahedral

What events occur during the latent period of viral replication?

the period following the eclipse phase from the time of disappearance of the infecting virus to the appearance of infectious virus in the surroundings

Viruses of eukaryotes can often be grown in ___ ___ or in ____ organisms.

tissue culture, whole organisms

Genome replication for Class VII is _______ followed by _____ ______.

transcription followed by reverse transcription

Animal viruses may be carcinogenic through the process of _____, allowing a cell to become a tumor.

transformation

For some viruses, un-____ may be necessary.

uncoating

Some ____ ____ may be packaged for functions required early in the infection process.

viral enzymes

Membrane proteins are normally encoded on the ____ ___.

viral genome

No enzymatic activity occurs within the ____ package away from the host cells.

virion

How long does it take from the point of T4 infection until the bacteriophage lyses?

~25 minutes

Steps to Bacterial Virus Replication

(1) Attachment (adsorption) *protein coat remains outside (2) Penetration (injection) *viral DNA enters (3) Synthesis of nucleic acid and protein (4) Assembly and packaging (5) Release (lysis) *virions leave cell

How may have the viruses evolved to circumvent the host's endonucleases?

(1) Host endonnucleases only affect dsDNA, so ssDNA and RNA viruses are unaffected. (2) Modification may occur in the previous host (3) Virus-mediated modification (glucosylation or methylation) may inhibit restriction

Steps of Lambda Integration

(1) Lambda genome cyclizes at cohesive ends (2) Site-specific nuclease creates staggered ends of phage and host DNA (3) Integration of lambda DNA and closing of the gaps by DNA ligase

Steps to Calculating PFU

(1) Pour mixture (molten top agar, bacterial cells, and diluted phage suspension) onto solidified nutrient agar plate. (2)Incubate. (3) Result will include phage plaques and a lawn of host cells.

What are characteristics of a latent infection?

(1) Primary acute infection (2) Virus harbored in nervous tissue (3) Recurrent infections (4) Recurrence with trauma or stress (5) No virus production during latent stage

Retrovirus Replication

(1) entrance of ssRNA (virus particle) (2) uncoating (3) reverse transcription (4) travel to nucleus and integration into host DNA (5) Transcription (6) Encapsidation (7) Budding (8) Release

Overall structure of a retrovirus includes: (1) _____ and (2) ______

(1) two plus strand RNA genomes (2) includes reverse transcriptase protein

Viral Classification by genome type includes the classes of ____ and the ___ in the virion.

(Classes of Virus): (genome in virion) DNA viruses: ssDNA, dsDNA RNA viruses: ssRNA, dsRNA RNA <--> DNA viruses: ssRNA (retroviruses), dsDNA (Hepadnaviruses)

Distinguish between a + strand RNA virus and a - strand RNA virus.

--- + Sense RNA viruses: the viral RNA genome can be directly translated by the host cell to make viral proteins. There are no additional steps required (essentially straight mRNA) -- - Sense Strand: means that the ribonucleic acid strand is complementary to the viral mRNA, and therefore must first be converted to + sense RNA before the protein-building instructions can be carried out. So, essentially there are more steps.

What does the term "eclipse" refer to?

-phase during which the virion has entered the cell and before progeny virus are made. NO INFECTIOUS VIRUS are present during this phase -period in which virus gains control of host synthetic machinery and produce components required to assemble into virus

LambdaT4 is in class __ and has a ___-stranded ____ genome.

1, double-stranded, DNA

Rolling circle DNA replication involves the DNA polymerase binding to the __ __, displacing the __ end.

3' nick, displace 5' end

How does the attachment process contribute to virus-host specificity?

Attachment is a specific binding between viral capsid proteins and specific receptors on the host cellular surface. This specificity determines the host range of a virus.

Contrast the mechanisms by which animal viruses enter cells with those used by bacterial viruses.

Bacterial cell entry= have specific receptor sites on bacteria where specific attachment proteins bind, DNA from bacterial virus is injected Animal virus= bind to a specific receptor, fuses with membrane

How does the penetration stage in bacterial virus replication differ from that or many animal viruses?

Bacterial viral replication leaves the capsid out side of the cell and injects the DNA, while the animal viruses are pulled into the cell by endocytosis.

Another example of a complex virus is a _______ __.

Bacteriophage T4

During rolling circle DNA replication, the __ site is at the end of each lambda genome.

COS site

Why is it helpful to use a cell culture for viral research?

Growing viruses in cell cultures allowed preparation of purified viruses for the manufacture of vaccines.

Latent infections are caused by viruses including the ___ ___ ___ and the ____ ___ (___ ___ ___)

Herpes Simplex Virus Varicella virus (Alpha herpes viruses)

Going from Class I to Class VII, what are examples of animal viruses for each?

How Can Rats Play In Red Hats? (I) Herpesvirus (and pox virus) (II) Chicken Anemia Virus (III) Reoviruses (IV) Poliovirus (V) Influenza virus (and rabies virus) (VI) Retrovirus (VII) Hepatitis B Virus

What is an example of a virus that exhibits icosahedral symmetry?

Human Papilloma Virus

Differentiate between persistent and a latent viral infection.

Persistent infections are considered chronic infections that occurs over a long period of time, often with fatal consequences. Latent infections are "Trojan horses". These viruses invade host cells and remain dormant over a long period of time, producing no symptoms

What is an example of a temperate phage?

Phage Lambda

Virus numbers are calculated as ___ ___ ___.

Plaque Forming Units (PFU)

____ are clear zones that develop on lawns of host cells.

Plaques

____ _____ refers to the fact that normally only a small portion of the virions result in plaques. It is the portion of the particles that result in plaque formation.

Plating efficiency

What does it mean that the bacteriophage T4 genome is both circularly permuted and terminally redundant?

A bacteriophage T4 is "terminally redundant" because the ends of the bacteriophage have the same ends. Moreover, the bacteriophage T4 also is "circularly permuted" because if you take all genes and arrange them into the circle each phage head will become a full circle and include a little bit more.

How does the life cycle of a temperate bacteriophage differ from that of a retrovirus?

A temperate phage can integrate its genome into its host bacterium's chromosome, becoming a lysogen known as a prophage. A temperate phage is also able to undergo lytic life cycles, where the prophage is expressed, replicates the phage genome and produces phage progeny and the progeny phage leave the bacterium. The virulent phages have only lytic lifecycles and thus infection results in the host cell's death (due to lytic cell destruction-the phage replicates itself and then bursts the cell, releasing many copies). So, they are both the same in that they both require a host cell to reproduce. They both can have lytic lifecycles but only the temperate phage can "hitch a ride" in the host cell by integrating into the genome.

What is a bacteriophage?

A virus that infects bacteria by injecting genetic material, which they carry enclosed in an outer protein capsid.

Viral Classification by host includes the 3 classes: ___, ____, and _____.

Animal viruses, plant viruses, bacteriophage (or just phage)

_____ ____ refers to minor antigenic changes due to genetic mutations.

Antigenic Drift

_____ ___ refers to rearrangement of genome segments to produce different viruses.

Antigenic Shift

_____ ___ and _____ ___ are factors that make it necessary to get new flu shots every year

Antigenic Shift and Antigenic Drift

RT is needed by ___ ___ (DNA) viruses which replicated their genomes via an ___ intermediate.

Class VII, RNA

____ ___ have additional elements.

Complex Viruses

When the bacterial host is damaged, the ___ protein accumulates and activates promoters for phage DNA replication and bacterial cell lysis.

Cro

The lambda lytic cycle occurs when ___ is the dominant regulatory molecule. It results in the expressing of transcripts from __ and __.

Cro , PR and PL

The __ protein controls the ____ of the ___ events.

Cro, activation, lytic events

What are examples of some prion based diseases?

Crutzfeild-Jacobson Disease, BSE

The genome (in the virion) may be either ___ or ___, ___- or ____-stranded, ___ or _____.

DNA or RNA, double-stranded or single-stranded, linear or circular

The Viral Classification scheme was developed by ______ ______.

David Baltimore

Phage of ______ ___ have been identified as complex.

E. coli

____ ____ have membranes derived form the host plasma membranes.

Enveloped Virus

What is the difference between an enveloped and naked virus?

Enveloped: membranes are derived from the host plasma membrane, more common in animal viruses, membrane proteins are normally encoded on the viral genome composed of an envelope + nucleocapsid Naked Virus: composed of nucleocapsid (capsomers)

After the mRNA of the retrovirus is transcribed into DNA, ___s are attached to the DNA on each end.

LTRs (long terminal repeat on each end)

____ ___ are transcribed by RNApol associated with a phage-encoded sigma subunit.

Late genes

How does a virion differ from a cell?

No enzymatic activity occurs within a virion away from the host, a virion is composed of only nucleic acid, protein coat, and envelope (no organelles).

_____ may be produced by phage and target hosts nucleic acids.

Nucleases

___ is a mis-folded protein that affects more mis-folding.

PrPSc

__ protein is a normal neuronal protein.

PrPc

How does a prion induce disease?

Produce a surplus of PrPSc (misfolded proteins) in neural tissue.

__ is a terminal repeat region

R

The bacterial SOS defense system activates the protein ___.

RecA

____ ____ destroys the cI, the lambda repressor, resulting in Cro activation and entry into the lytic cycle.

RecA

_____ proteins exist outside of the host and recognize the animal virus envelope, allowing the capsid to enter.

Recognition

______ are RNA viruses that replicate through a DNA intermediate.

Retroviruses

Why must some types of viruses contain enzymes in the virion in order to mRNA to be produced?

Retroviruses require reverse transcriptase to make a DNA intermediate because the packaged RNA is unable to act as mRNA alone.

How does a virus differ from a plasmid?

Similar to viruses, plasmids are not considered by some to be a form of life. Unlike viruses, plasmids are naked DNA and do not encode genes necessary to encase the genetic material for transfer to a new host, though some classes of plasmids encode the sex pilus necessary for their own transfer.

Why do some viruses need to be uncoated after penetration while others do not?

THe viral capsid proteins must be removed, at least partly, to express and replicate the viral genome. -- DNA viruses, the capsid is routed to the nucleus prior to uncoating (these viruses uncoat and replicate completely in the cytoplasm). --RNA viruses typically lose the protective envelope and capsid proteins upon penetration into the cytoplasm. --Retroviruses- only an outer protein shell is removed and replication takes place inside a structured subviral particle

____ ____ have alternate life cycles whereby they can undergo the lytic cycle or the lysogenic cycle.

Temperate phage

What might be the advantage to be hosts of temperate viruses?

Temperature viruses reproduce without killing their host. Moreover, a temperate virus is 50,000 base pairs in size and does not require all the 50,000 base pairs for genes, so it can carry extra genes, making them good vectors for the host.

Give an example of a mechanism used by T4 to ensure that its genes rather than those of the host that are transcribed.

The T4 bacteriophage produces nuclease, which breaks down the hosts DNA. Moreover, the T4 bacteriophage also glycosylates its own phage DNA in order to make it resistant to the nuclease.

RNA polymerase does not have ___ ___, so mutations are possible in the RNA genome.

error checking

What events need to happen for lambda to become a prophage?

The phage must chose the lysogenic pathway in which the viral DNA is integrates into the host DNA, placing a "prophage" into the host's genome, which will appear in every cell resulting from cell division in the host.

Why are these viruses called "retroviruses?"

They go against the dogma of biology (DNA to RNA to protein). Instead, it is going from RNA to DNA.

What is an example of a virus that exhibits helical symmetry?

Tobacco Mosaic Virus

Cellular damage like __ ____, _____, _ ___, and DNA damaging ____, activates the bacteria; ____ defense system.

UV light, radiation, x rays, chemicals, SOS defense system

_____ are the extracellular form of a virus.

Virion

____ are small (~250-400 bases) circular ssRNA particles know to infect plants

Viroids

___ and ___ are produced, resulting in excision of the genome from the host chromosome.

Xis (Excisionase) and Int

When the bacterial host is healthy, cI accumulates and ____ promoters for integration of phage DNA into the host chromosome in the ______ cycle.

activates, lysogenic

Enveloped Viruses are most common in ____ ____.

animal viruses

Phage-encoded ___-___ shuts down early mRNA synthesis.

anti-sigma

What does att refer to in the lambda genome?

attachment site, it recognizes a specific place on the host genome to integrate

Viral plaques are analogous to ____ ____.

bacterial colonies

__ encodes envelope protein

env

Many animal viruses are ____, picking up portions of the host cytoplasmic membrane as they leave the cell.

enveloped

The __ protein is the lambda repressor.

cI

__ is degraded by RecA protease activity that occurs in response to DNA damages.

cI

Lack of __ favors that lytic cycle by allowing the activation of __ and __.

cI, PL, and PR

The lysogenic cycle occurs if enough __, ___, and __ are produced.

cI, cII, cIII

Upon integration of the Lambda phage into the host genome, only the ___ protein will be synthesized, preventing the production of any other protein. This commits the phage to the _____ cycle.

cI, lysogenic cycle

The __ protein, the lambda repressor, causes the _____ of the lambda ___ events.

cI, repression, lytic events

The nucleic acid that is surrounded by a protein coat is called the ___.

capsid

Capsids are made from subunits of one or more proteins called _______.

capsomers

_____ self-assemble into capsid structures.

capsomers

A "Naked Virus" is composed of ____, ____ __, and ____.

capsomers, nucleic acid, and capsid (composed of capsomers)

Some animal viruses are ______.

carcinogenic

The varicella virus causes ___ ___ and ____.

chicken pox, shingles

DNA replication of the bacteriophage T4 results in ____ _____ of the packaged genomes.

circular permutation

Genome replication for Class II is _____ _____, discard (__) strand.

classical semi-conservative, negative

Genome replication for Class I is ____ _____.

classical semiconservative

The single-stranded 12 bp ends are called ____ ___ (__)

cohesive ends (cos)

Recurrence of a latent virus occurs with a _____ immune system (stress).

compromised

In the circular permutation of T4 DNA, replicated genomes are joined together to form a large _____, which is then _____ into "headfuls" of DNA, resulting in _____ ____ _____.

concatemer, cleaved, repeated terminal sequences

Viral plaques form on a ____ ____ of tissues culture cells.

confluent monolayer

In the bacteriophage T4, 5-hydroxymethyl cytosine is substituted for ____, which is then ______, rendering T4 DN resistant to most _____ ______.

cytosine, glucosylated, restriction endonucleases

The choice made during the genetic switch depends on the ____ and ____ present.

environment and proteins present

Not all virions are ___ infectious.

equally

The ____ ___ is an accurate way of measuring virus infectivity.

plaque assay

When PrPSc accumulates and aggregates, it causes ____ to the host.

damage (PrPSc will take up space and energy of cell--lead to cell death)

RecA is secondly used to recognize where DNA is ___, where it will remove repressors so that the DNA may be repaired.

damaged

Class 1 is a ___-stranded ____ genome.

double stranded, DNA

Class VII is a ___-stranded ____ genome that replicates with ____ intermediate.

double, DNA, RNA intermediate

Class III is a ___-stranded ____ genome.

double, RNA

Animal viruses may be ____- or ___-stranded, ____, ____, or ___, ___ or ___.

double-/single- stranded, circular, segmented, or linear, DNA/RNA

What is thought to be the most common type of bacteriophage genome?

dsDNA

___ ___ are transcribed directly by host RNApol-σ70

early genes

Strategies exist for viral entry into host cells including ____ and __-___ ____.

endocytosis and tail-phaged penetration

Virus DNA may be restricted by host ______.

endonucleases

Lambda has a ____ genome, which it packs into a ____.

linear, capsid

A ____ is used to allow entry of the viral genome.

lysozyme

Examples of viral enzymes include: ____, _____, and __-___ ___.

lysozyme, polymerases, and host-lytic enzymes

What kinds of enzymes can be found within the virions of specific viruses?

lysozyme, polymerases, and host-lytic enzymes

____ ___ are transcribed by host RNApol that has been modified to recognize phage middle promoters by phage early proteins.

middle genes

The influenza virus undergoes frequent ______, especially in genes for _______ and ______ which are exposed on the viral coat.

mutagenesis, hemagglutinin, neuraminidase

Viroids have a ____ nucleic acid.

naked -(no capsid or other components)

When PrPSc only accumulates in the ____ ____.

nervous tissue

Prions are known to cause ______ _____ in animals.

neurological diseases

Moreover, the virus may itself encode ____ in the host, which will target the host's _____ ___. Those sneaky particles!

nucleases, modified DNA

An "Enveloped Virus" is composed of a ___ __, ____, and _____.

nucleic acid, capsid, and envelope

For some viruses, penetration of only the ____ ___ is needed. For others, ____ ____ may be required.

nucleic acid, packaged enzyme

Virions are the extracellular form which include the ____ ___ and normally a ____ ____ and possibly an outer ______.

nucleic acid, protein coat, envelope

_____ include the capsid and the nucleic acid.

nucleocapsids

The receptors on the surface of the host cell that dictate specificity for viruses also have other functions including ___ ___ and ___.

nutrient uptake and sex

Viruses are genetic elements with an ____ _____ replication cycle.

obligate intracellular

Genetic Switch

period when a phage must choose either a normal lytic pathway of growth or a lysogenic pathway

During a _____ _____, the animal virus replicates in the host cell and buds off throughout the life of the host cell.

persistent infection

_____-encoded ____ degrade host DNA.

phage-encoded nucleases