Chapter 6 Viruses

A viral genome can be

-DNA or RNA -Single or double stranded -Linear, circular, or segmented

What are the three ways that animals and plant host defend themselves?

-Genetic resistance -Immune system -RNA interference (RNAi)

International cmmittte on taxonomy of viruses based on 5 cirtera

-Genome composition -Capsid symmetry -Envelope -Size of virion -Host range

Contact and attachment are mediated by cell surface receptors such as

-LPS -OmpF -Tol C the previous two used to be a drug efflux complex -flagellar proteins

_____________ and _________ proposed the existence of viruses when they discovered infectious agents that passed through filters with pores too small for cells to pass.

Ivanovsky; Beijerinck

_______ may limit the bacterial numbers to levels that the human immune system can tolerate.

Phages

_________ earned the 1946 Nobel Prize in Chemistry for crystallizing viruses and thus reinforcing them as non living

Stanley

_________ viruses have complex multipart structures that elaborate delivery devices. For example, T4.

Tailed

How do retroviruses dictate the details of a replication cycle of an animal virus?

They use a reverse transcriptase to copy their genomic sequence into DNA for insertion in the host chromosome

How do RNA viruses dictate the details of a replication cycle of an animal virus?

They use an RNA-dependent RNA polymerase to transcribe their mRNA

How do DNA viruses dictate the details of a replication cycle of an animal virus?

They utilize some or all of the host replication machinery

group I

double stranded dna viruses

group iii

double stranded dna viruses

HPV is a ___________ virus that causes warts and, in some cases, cancer.

double-stranded DNA

A permanently integrated provirus transmitted from one human to another via the germ line is called an _________ virus.

endogenous

In some icosahedral viruses, the capsid is enclosed in an _______ that is derived from the cell membrane of the host organism. The envelope contains glycoprotein spies, which are encoded by the virus.

envelope

The capsid consists of a long tube of protein that possesses HELICAL symmetry. The capsid protein monomers surround the genome, which usually winds helically within the tube. Very in length, depending on genome size. Include bacteriophages as well as animal virus. Ex: TMV and Ebola with RNA genomes

filamentous

what is an example of a group II (single-stranded DNA virus)?

geminivirus

A virion possesses a ___________ of either DNA or RNA. The precise configuration of the genome varies with virus type.

genome

In 1971, David Baltimore proposed that the classes of viruses be distuingished by two main critera

genome compositon rna or dan route used to express mrna

The envelope contains ___________ spikes which are encoded by the virus. Some viruses contain _________ proteins between the envelope and the capsid.

glycoprotein; tegument

herpesviruses

group 1

hpv

group 1

bacteriophage M13

group 2

geminiviruses

group 2

coronavirus

group 4

ebola virus

group 5

rhabdovirus (rabies)

group 5

caulimoviruses

group 7

bacteriophage lambda

group I

The range of host species infected by a given virus is known as its ____________.

host range

Giant viruses have genomes that specify surprisingly large number of enzymes with ________ cell functions.

housekeeping

Where does assembly of new virions occur?

may occur in the cytoplasm or nucleus

An example of a human virus is the _________ virus.

measles

Bacteriophages and eukaryotic viruses convert marine organisms into dissolved organic molecules and particles. The organic particles settle to the benthos (marine sediment), where they provide carbon and _______ for corals and other marine life.

nitrogen (important for carbon and nitrogen cycling)

You can compare the phylogeny of viruses based on _______ or the genes of common ancestry in two genomes that share the same function. Otherwise, you can use a _______________ since viruses small genomes encode few proteins.

orthologs; proteomic classification

group vii

pararetroviruses dna reverse transcriping virus

Phage _______ may modulate immune system activity by suppressing T-cell activation and tumor formation. They may also attack ______.

particles; biofilms

______________ viruses remain in hosts where they may evolve traits that confer positive benefits in a virus-host mutualism.

persistent viruses

what is an example of group I virus?

phage lambda

Plaque assay is a method of culturing viruses in which single phages or virions each generate an isolated clearing of host cells. The plaques can be counted to enumerate the infectious virions in a suspension, called

plaque-forming units

Plate culture of viruses generate _________ or clearing zones, in a lawn of cells.

plaques

Infectious proteins that have an abnormal structure that alters conformation of other normal proteins

prions

A bacteriophage that integrates its genome into its bacterial host's genome is called a _________. Within a human cell, an integrated viral genome is called a provirus. It can even be transmitted via the germ line to future generations.

prophage

what is an example of a group IV (-) sense single-stranded RNA virus?

rabies virus

The genomes of large viruses show evidence of ______ evolution (evolutionary loss of genes) from a cellular origin, whereas genomes of small RNA viruses indicate they may have been built up from mere parts of a cell.

reductive

group vi

retrovirsues rna reverse transcribing viruses

what is an example of the group IV (+ sense single stranded RNA virus)?

rhinovirus

what is an example of the group III. double stranded RNA virus?

rotavirus

group ii

single stranded dna viruses

A _______________ replication cycle differs from lysis and lysogeny in that phage particles reproduce without destroying the host cell. Filamentous phages can extrude individual progeny through the cell envelope. Host cells grow slowly but do not die! Pretty amazing, I believe.

slow release

Batch culture of viruses generates a _____ curve.

step

A ________ phage such as phage lambda can infect lyse cells like a virulent phage, but it also has the unique ability to integrate its genome as a prophage. The phage is said to "lysogenize" the host, leading to a state called lysogen. where bacteriophage is not replicating and it can reactivate to become lytic.

temperate

A ______ is a noncellular particle that infects a host cell and directs it to produce progeny particles (more viruses)

virus

group iv

(+) sense single stranded rna viruses

group v

(-) sense single stranded rna viruses

How do oncogenic viruses cause cancer?

-Oncogenes like feline leukemia virus transform the host cells and change host proteins that control cell proliferation -Genome integration. Stimulate host cell devision and lead to growth of tumors -Cell cycle control: papillomaviruses express viral proteins that interact with host cell cycle controls and can stimulate uncontrolled growth

The siberian tundra reveals even more remarkable viruses

-pithovirus -mollivirus sibericum (contains parts of a ribosome)

how do viruses in genomes work? Ex: Coccolithus virus controls algae blooms

1. Acute virus attacks increasing host pop. density 2. Increase in rate of viral pathogen transmission 3. As host population declines, viruses look for new host and some host acquire resistance 4. Thus, virus can limit but not extinct population density

Lytic cycle of phage lambda

1. Cell synthesizes capsid proteins 2. Cell replicates phage DNA. DNA is packaged into capsids. 3. Phage lyses cell and progeny phages are released

These are the three forms of defense against bacteriophage infection

1. Genetic Resistance through altered receptor proteins 2. Restriction endonuclease that cleave viral DNA lacking methylation and add methyl groups to particular sequences 3. CRISPR integration of phage DNA sequences which is technically the "bacterial immune system"

Lytic replication cycle requires these steps

1. Host recognition and attachment 2. Genome entry 3. Assembly of phages 4. Exit and transmission

How does CRISPR work so bacteria can defend itself from phages

1. If bacterial enzymes are successful at destroying phage DNA, a piece of phage DNA gets copied as a spacer in host genome 2. If the bacterium runs into the same phage DNA, there is transcription of the spacers into CRISPR RNA. 3. Forms a Cas-crRNA complex 4. Cleaves phage DNA

Lysogenic cycle of a phage lambda

1. Phage DNA integrates into host genome to form prophage 2. Integrated phage DNA replicates with host genome UNTIL stress induces excision of phage DNA. 3. At that point, the phage recombines by re-joining the ends of its genome and enters the lytic cycle.

Here is the phage lambda reproductive cycle:

1. Phage attaches to host cell and inserts DNA and then the linear dsDNA circularizes 2. It can either go through a Lytic or lysogenic cyce 3. It releases its progeny

This is the mechanism behind slow release (an example is that of M13)

1. Phage inserts single-stranded DNA 2. Phage DNA forms a double-stranded circle 3. Cell replicates circular, stranded dna 4. Phages assemble and exit without lysis while the cell reproduces slowly

Small viruses have a small gene with less than ______ genes and the genes may actually overlap in seuence. Many small viral genomes consist of _______.

10; RNA

Icosahedral viruses are polyhedral with _______ identical triangular faces. Structure exhibits ROTATIONAL symmetry.

20

The giant viruses have genomes of double stranded DNA comprising of _______--________ genes. For example, the mimivirus is as large as bacteria and can be infected by smaller viruses called virophages.

300-2,500

___________ viruses rapidly kill their hosts and thus act as predators or parasites to limit host population density! They do it by: -Host death recycles nutrients back to the community -Surviving hosts have acquire resistance -Overall effect of the acute virome is to increase host diversity

Acute

___________ (phages) are viruses that infect bacteria. Their replication is observed as a plaque of lysed cells on a lawn of bacteria growing in a Petri dish.

Bacteriophages

As many as 20% of human cancers are caused by oncogenic viruses, such as ____________ (which causes lymphomas) and ___________ (which causes liver cancer).

Epstein-Barr virus; hepatitis C virus

Asymmetrical virus pox virus or vaccina has genomes containing over 200 genes and RNA segments are coated with nucleocapside proteins. They also have spike proteins of

H-hemaglutinin N-neuroaminadase

________ infects only humans while ____________ infects many species of birds and mammals.

HV; West Nile virus

Give an example of a RNA virus that lacks capsid symmetry? Instead, these RNA segments are coated with ___________ proteins.

Influenza viruses; nucleocapsid

_________________________- Within a host cell, the viral gene products direct the cell's enzymes to assemble progeny virions at "virus factories" called replication complexes.

Intracellular replication complex

How does bacteriphage counter attack from the bacterial host?

It carries an anti-CRISPR gene (Acr) which encodes a prtoein that blocks the host bacterial CRIPSR-cas from binding phage DNA

Poxviruses are large _________ viruses with genomes that contain over 200 genes. Their genome is surrounded by several layers. A core envelope studded with _______ proteins. An outer membrane. Also, they have a large number of accessory proteins needed for viral infections.

asymmetrical; spike

Two ways you can culture viruses

batch culture, plate culture

The protein __________ packages the viral genome and delivers it into the host cell. Different viruses make different types of capsids. Capsid types are either symmetrical or asymmetrical.

capsid

In marine ecosystems viruses cycle organic food molecules between multiple species. Marine bacteriophages and eukaryotic viruses infect numerous aquatic hosts. When the host organisms die, their organic matter provides both swimmers and bottom dwellers with _____ and ______ for growth.

carbon; nitrogen

what is an example of group 6 pararetroviruses (DNA reverse transcribing viruses)?

caulimovirus

The envelope proteins for the virion are inserted into a membrane of either the

cell; organelle

what is an example of group VI retroviruses (RNA reverse transcribing viruses)?

human immuno-deficiency virus

Where does translation of the virus occur?

in the cytoplasm

What is phage transcytosis?

the uptake of phages throughout our tissues

An example of a plant virus is the ________ (TMV).

tobacco mosaic virus.

The process of transferring host genes is known as

transduction

ability to infect a particular tissue type within a host

tropism

A _________, or virus particle-An inert particle that does not carry out any metabolism or energy conversion.

virion

The virus particle, or _______, generally consists of a viral genome (DNA or RNA) contained within a protein capsid.

virion

______________ are RNA molecules that infect plants. Also have: -No _________. -Replicated by host RNA polymerase -Catalytic ability -circular, single stranded

viroids

The sum of viral populations in an ecosystem is called the

virome