Microbiology6

Explain why some viruses contain enzymes within the virion and others do not.

In the example of retroviruses, the reverse transcriptase enzyme, which is critical for its replication is found within the virion itself. However, many other viruses do not carry enzymes simply because they use the host's cellular machinery to translate enzymes that they require.

The two events necessary to establish lysogeny for lambda phage are ________ and ________.

production of all late proteins must be prevented / a copy of the lambda virus genome must be integrated into the host chromosome

A cell that allows the complete replication cycle of a virus to take place is said to be a(n) ________.

permissive host

A clearing of no host cells among a lawn of growing host cells is known as a(n) ________, which in principle represents

plaque / one initial virion

Transmissible spongiform encephalopathies (TSEs) are caused by ________.

prions

The smallest unit that causes a detectable effect when added to a susceptible host is known as a(n) ________.

virus infectious unit

Avirulent prions consist largely of ________, whereas pathogenic prions have more ________ regions.

α-helices / β-sheet

Retroviruses 20) ______ A) may cause cancer. B) transcribe DNA from RNA template. C) include the virus that causes AIDS. D) do all of the above.

D

The simplest form of viral reproduction in RNA viruses is that which occurs with the 12) ______ A) negative-strand DNA viruses. B) negative-strand RNA viruses. C) positive-strand DNA viruses. D) positive-strand RNA viruses.

D

The virus repressor protein 18) ______ A) has different actions in different situations. B) does not control the prophage's lytic genes but does control the incoming genomes of the same virus. C) controls the prophage's lytic genes but not the incoming genomes of the same virus. D) controls both the lytic genes on the prophage and prevents an incoming virus of the same type.

D

A cell infected with T4 phage undergoes cell lysis because the virus codes for ________, which acts by ________.

T4 lysozyme / degrading the host's peptidoglycan layer

In the context of biogeochemical cycling, explain the role of bacteriophages and their impact on carbon cycling in the oceans.

Viruses that infect bacteria and lyse them are an integral part to cycling carbon in a system such as an ocean, where bacteria are abundant. This cell lysis frees up carbon stored in the cells as well as their cellular debris, which both provide a system with usable carbon substrates for others to use and proliferate.

Present in both animals and plants, ________ are incomplete and therefore require the presence of other active helper viruses.

defective, or satellite, viruses

Two chemical modifications of viral DNA that work to avoid host restriction mechanisms are ________ and ________.

glucosylation / methylation (either order)

Rod-shaped viruses have ________ symmetry, and spherical viruses have ________ symmetry.

helical / icosahedral

When a virus enters a host cell in which it can replicate, the process is called a(n) ________.

infection

16) The packaging mechanism of T4 DNA involves cutting of DNA from 16) ______ A) circular genetic elements. B) linear genetic elements. C) DNA concatemers. D) none of these; they are all transcribed directly from inserted viral DNA.

C

Explain viral replication in terms of an eclipse period, maturation, latent period, release, lysis, and burst size.

Figure 9.8 illustrates all five steps in the viral replication cycle. The first step involves the virus adsorbing to the host cell such that it becomes undetectable in the medium, termed an eclipse period. Once the genome has been injected into the host, maturation occurs of newly synthesized viral genomes as well as capsids. The time where replicated viruses remain in the host is called the latent period, which ends once the viruses are released. The host cell lyses, and the replicated viruses are released. If 18 viruses are released per host cell, then the burst size is 18.

Explain how to determine the number of plaque-forming units in a virus sample.

First, several plates containing the host are grown as a lawn on a suitable medium. Then different dilutions, often samples from a 10-fold serial dilution, are poured over the host cells. After incubation the number of plaques are counted, and the number of plaque forming units (pfu) per volume can then be calculated. Previously determined plating efficiency and the dilution factors must both be considered when calculating pfu per volume.

The process of copying information found in RNA into DNA is called ________.

reverse transcription

Explain the concept of a persistent infection in terms of a virus-infected cell.

Persistent viral infections occur when the host cell remains alive and continually produces more viruses. These conditions are especially common in animal cells when a persistent virus is coated with an envelope.

Regarding the viral membrane in an enveloped virus, the lipids are derived from the ________, and the proteins are encoded by ________.

host's cell membrane / viral genes

Viral proteins are categorized as early and late. Early proteins are ________, while late proteins include ________. 59)

necessary for replication of viral nucleic acid / those found in the protein coat

In viruses, genetic information flows from ________ to ________.

nucleic acid/ protein

A prophage replicates 17) ______ A) along with its host while the lytic genes are not expressed. B) along with its host while the lytic genes are expressed. C) independently of its host while the lytic genes are not expressed. D) independently of its host while the lytic genes are expressed.

A

Reverse transcriptase is a(n) 6) _______ A) RNA-dependent DNA polymerase. B) RNA-dependent RNA polymerase. C) DNA-dependent RNA polymerase. D) DNA-dependent DNA polymerase.

A

The primer for retrovirus reverse transcription is a specific 21) ______ A) tRNA encoded by the cell. B) nuclear tDNA. C) tRNA encoded by the virus. D) nuclear tRNA.

A

When packaged in the virion, the complete complex of nucleic acid and protein is known as the virus 24) ______ A) nucleocapsid. B) concatemer. C) capsid. D) envelope.

A

Which T bacteriophage has been studied most extensively? 15) ______ A) T4 B) T7 C) T2 D) T6

A

Which of the following are the hosts for most enveloped viruses? 25) ______ A) animals B) Archaea C) fungi D) Bacteria

A

Using T4 virions as a model, explain the concept of circular permutation.

A linear concatemer is first formed after recombination of several copies of the genome. An endonuclease then cuts out particular regions of the concatemer to form individual linear replicated genomes. Although the genomes will all contain the same genes, this circular permutation process generates the genes in a different sequence order.

Explain the difference between an enveloped virus and a naked virus.

A naked virus lacks an envelope and is called a nucleocapsid, because it contains only a nucleotide-based genome and capsid proteins. A virus containing a nucleocapsid enveloped within an additional lipid layer is called an enveloped virus.

What do viroids lack that viruses have, and how does this influence their ability to infect a host cell?

A viroids does not have a protein capsid covering and protecting its genome. This also means that viroids cannot actively infect a healthy host cell due to a lack of attaching structures. Viroids can, however, infect wounded cells. A viroid infection, for example, could occur after a plant cell wall has already been disrupted from an insect.

Explain the relationship between the terms virus particle, virion, and virus genome.

A virus particle is a broad term used to describe a virus at any stage of infection, whereas a virion is one single virus particle that is at an infectious state. They are metabolically inert in both cases and minimally contain a DNA- or RNA-based genome and a protein capsid layer. A viral genome is packaged within both a virus particle and a virion, containing a single or double stranded nucleotide sequence that serves as a template to produce viral transcripts and ultimately their proteins.

Why might a virus undergo lysogeny rather than the lytic cycle?

Answers will vary, but one idea discussed might be that lysogeny allows the virus to increase in numbers within a host. After cell lysis, expelled viruses then must attach to a new host to proliferate, and if the viral host is in low numbers, the rate of proliferation would likely be low relative to a lysogenic virus.

2) Viral replication occurs 2) _______ A) extracellularly. B) intracellularly. C) both intracellularly and extracellularly. D) either intracellularly or extracellularly, depending on the virus involved.

B

Bacteriophages' genomes are typically composed of 13) ______ A) single-stranded DNA. B) double-stranded DNA. C) double-stranded RNA. D) single-stranded RNA.

B

Viral size is generally measured in 3) _______ A) micrometers. B) nanometers. C) centimeters. D) picometers.

B

Viruses infecting ________ are typically the easiest to grow in the laboratory. 7) _______ A) plants B) prokaryotes C) fungi D) animals

B

Which statement is TRUE? 5) _______ A) The origins of the nucleic acid polymerases used by viruses are eukaryotic. B) Many viruses contain their own nucleic acid polymerases. C) Viruses do not contain their own nucleic acid polymerases. D) All viruses contain their own nucleic acid polymerases.

B

Describe the structure of the T4 virus, and explain this virus's attachment and penetration processes in terms of this structure.

The T4 phage has a very complex structure, containing a head, collar, tail, tail pins, an endplate, and tail fibers. The tail fibers bind to polysaccharides within a Gram negative cell envelope for attachment. When the tail fibers retract, the tail pins bind to the host so that the tail itself interacts with the cell wall. A viral enzyme then forms a small pore within the host, and once the tail's covering is contracted the viral dsDNA genome is inserted into the host's cytoplasm. This infection mechanism is illustrated in Figure 9.10 in the textbook.

Describe the process whereby dsDNA viruses are replicated.

The asymmetric processing of dsDNA amplification via rolling circle is highlighted in Figure 9.19 in the textbook. The two major steps involved are nicking of the dsDNA. The non-nicked strand uses a primer and polymerase to amplify the complementary strand as a concatemer.

The term "phage" is generally reserved for the viruses that infect ________.

bacteria

Lambda and other temperate viruses have an exceedingly complex genetic switch that ________.

controls whether the lytic or the lysogenic pathway is followed during infection

T4 bacteriophage contains 5-hydroxymethylcytosine that replaces ________ and is a protectant against ________.

cytosine in its genome / host defenses

Animal viruses are more easily lysed compared to prokaryotic cells, because animal host cells ________.

lack a cell wall

Bacteriophage Lambda integrates into an E. coli genome by the action of ________.

lambda integrase

Whether lambda phage undergoes the lytic or lysogenic cycle is dependent on the presence or absence of ________.

lambda repressor (cI protein)

Virions infecting some bacteria possess the enzyme ________ that makes a small hole in the bacterial cell wall, allowing the viral nucleic acid to enter.

lysozyme

Why is uncoating a step in the replication cycle of some animal viruses?

The genome is freely available for replication only once a virion is uncoated and its contents are exposed.

How does efficiency of plating affect plaque-forming units?

The issue of plating efficiency is that not every virus will be active at lysing the host in the medium. Consequently, the number of plaques observed is expected to be less than the actual number of viral particles in the plating. The plating efficiency therefore is required when counting plaque-forming units per volume plated to calculate the viral concentration (or titer).

Because a prion is composed entirely of protein, explain how the prion replicates.

The sheer presence of a pathogenic prion induces the refolding of avirulent prions into proteins that are infectious.

A virus that kills its host is said to be 14) ______ A) virulent or lysogenic, but not temperate. B) lysogenic. C) lytic or virulent. D) temperate.

C

All viral particles 8) _______ A) contain an envelope to prevent its degradation outside of a host. B) exhibit cell lysis under a particular condition. C) are metabolically inert. D) are smaller than bacterial cells.

C

What genome composition makes viruses most susceptible to destruction by prokaryotic restriction endonucleases? 27) ______ A) ssRNA B) ssDNA C) dsDNA D) dsRNA

C

10) Restriction is 10) ______ A) a general host mechanism to prevent virus particles from further infective action. B) the viral process whereby a host's DNA ceases normal functioning. C) the viral process whereby the virus prevents other viruses from entering the cell. D) a general host mechanism to prevent the invasion of foreign nucleic acid.

D

11) The Nobel Prize laureate David Baltimore is credited with the discovery of A) T-series viruses (such as T2, T4, etc.). B) parvoviruses. C) prions. D) retroviruses and reverse transcriptase.

D

26) Plant viruses can be difficult to work with because 26) ______ A) their study sometimes requires the use of the whole plant. B) plant viruses often require a break in the plant cell wall to initiate infection. C) plants typically grow much slower than bacteria. D) All of the above are factors.

D

A viroid 23) ______ A) is a small, circular ssRNA molecule. B) lacks protein-encoding genes. C) lacks a capsid. D) is characterized by all of the above.

D

An integrated stable genetic element in a eukaryotic cell 22) ______ A) is called a provirus. B) is analogous to the integration of phage DNA into a bacterial genome. C) can occur anywhere in the cellular DNA. D) is all of the above.

D

Cellular receptors may be composed of 9) _______ A) lipids. B) proteins. C) carbohydrates. D) combinations of any or all of the above.

D

Enveloped viral membranes are generally ________ with associated virus-specific ________. 4) _______ A) glycolipid bilayers / phospholipids B) protein bilayers / lipids C) lipid bilayers / phospholipids D) lipid bilayers / glycoproteins

D

Lambda is 19) ______ A) a temperate phage that infects Escherichia coli. B) replicated by the rolling circle mechanism. C) a linear double-stranded DNA phage. D) all of the above.

D

Viral replication is 1) _______ A) dependent on both the cell's chromosomes and the cell itself. B) independent of both the cell's chromosomes and the cell itself (although the cell does provide a convenient matrix for replication). C) dependent on the cell's chromosomes but independent of the cell itself. D) independent of the cell's chromosomes but dependent on the cell itself.

D

Describe the seven steps of retroviral replication.

Each of the seven steps is outlined in Figure 9.24 in the textbook. Once the retrovirus fuses to its host, the viral envelope is uncoated so that ssRNA is exposed. Reverse transcription then occurs to generate dsDNA that becomes integrated into the host's genome. The host's genome is transcribed into ssRNA along with the viral insert, and the viral mRNAs transcribed are encapsidated again to form more retroviruses. Progeny virions are released through a budding process within the host's cell membrane.

Describe the establishment and maintenance of the lysogenic state in the lambda phage.

Lambda phage, once circularized by matching its cohesive ends, integrates into an E. coli host genome by targeting the attλ gene in the host genome. The att gene in lambda's genome then base pairs with the complementary sequences found in the attλ gene, and the lambda genome is inserted in the presence of an integrase catalyst. After the lambda genome is established in the host's genome, it is maintained along with the E. coli genome through replication.

The Baltimore Classification System groups seven viral classes according to ________ and ________.

their genome composition / mRNA transcript synthesis method

The use of ________ has greatly enhanced research on most animal and many plant viruses.

tissue or cell cultures

The number of infectious plaque forming units (pfu) per volume of fluid is known as the ________.

titer