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BIMM 120 > Chapter 9 > Flashcards

Chapter 9 Flashcards

1
Q

What is a virus

A

A genetic element that cannot replicate independently of a living (host) cell. Viruses are not cells, no metabolism, and no ribosomes or translation. They are obligate intracellular parasites

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2
Q

What is virology

A

The study of viruses

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3
Q

What is a virus particle (virion)

A

The infectious form of a virus. It exists outside host and facilitates transmission from one host cell to another.

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4
Q

What is a virion composed of

A

They are composed of a nucleic acid genome surrounded by a protein coat and, in some cases, other layers of material such as a lipid membrane derived from the host cell

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5
Q

What kind of genomes do viruses have

A

They can have either double or single stranded DNA or RNA. Most are linear but some are circular

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6
Q

How have viral genes/genomes evolved

A

They have evolved to be compatible with the host’s genetic physiology

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7
Q

What is the host range

A

The host range is determined by the coevolution of virus and host. Ex. Influenza virus only infects certain types of epithelial cells of mammals and birds, bacterial viruses never infect animals or plants

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8
Q

What kind of genome do DNA viruses have

A

ssDNA or dsDNA

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9
Q

What kind of genome do RNA viruses have

A

ssRNA or dsRNA

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10
Q

What kind of genome do RNA and DNA viruses have

A

ssRNA (retrovirsues) and dsDNA (hepadnavriuses)

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11
Q

How was viruses classified

A

Viruses can be classified on the basis of the host they can infect. There is no overall evolutionary tree for virsues, they are more related to their hosts than to each other

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12
Q

How big are viruses

A

Most viruses are much smaller than prokaryotic cells, range from 0.02 to 0.3 um

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13
Q

How big are viral genomes

A

Most viral genomes are smaller than those of cells, smaller viruses contain only a few genes and many contain only 40-100 genes

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14
Q

What is the main components of the viral structure

A

The capsid, nucleocapsid, enveloped virus

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15
Q

What is the capsid

A

The protein shell that surrounds the genome in a virus particle. It is composed of capsomeres arranged in a precise and repetitive pattern around the nucleic acid genome. The capsid can self-assemble because of protein-protein interactions

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16
Q

What are capsomeres

A

They are the protein subunits of the capsid

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17
Q

What is the nucleocapsid

A

The complex of nucleic acid and protein forming the virion. The nucleic acid + capsid. Are highly symmetirc

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18
Q

What is the enveloped virus

A

It contains additional outer layers derived from the host-cell membrane (eukaryotic viruses)

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19
Q

What are the two types of symmetry found in nucleocapsids

A

Helical symmetry and isosahedral symmetry

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20
Q

What is helical symmetry

A

Found in rod-shaped viruses. The length of virus determined by length of nucleic acid genome, and the width of virus determined by size and packaging of protein subunits

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21
Q

What is icosahedral symmetry

A

Found in spherical viruses. Most efficient arrangement of protein sub units to make a closed shell

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22
Q

What are complex viruses

A

Virions composed of several parts, each with separate shapes and symmetries. Head, tail fibers, etc. Bacterial viruses often contain complicated structures

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23
Q

What are some enzymes that virions contain that are critical to infection

A

Lysozyme and Nucleic acid polymerase

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24
Q

What are lysozymes

A

They are used to make a hole in the cell wall and lyse the bacterial cell

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25
What are nucleic acid polymerases
Used for the replication of viral genomes, some that are not dsDNA and can perform rapid replication
26
Where can viruses replicate
Viruses can only replicate in coevolved host cells or organisms. Within their host range
27
What are bacterial viruses often called
Bacteriophage or phage
28
What is a titer
The number of infectious units per volume of fluid
29
What is a plaque assay
It is analogous to the bacterial colony, one way to measure virus infectivity
30
What are plaques
They are clear zones that develop on lawns of host cells. Lawn can be bacterial and each plaque results from initial infection by a single virus particle, then progeny viruses infect and lyse nearby cells, repeat cycle to make a clearing
31
How is a plaque assay performed
First a mixture containing molten top agar, bacterial cells, and diluted phage suspension are poured onto a solidified nutrient agar plate. It is then allowed to solidify, the bacteria and phages are sandwiched between the bottom nutrient agar and the top agar. The plates are incubated and then you can find phage plaques in the lawn of host cells afterwards
32
What are the 5 phases of viral replication
1. Attachment (adsorption) 2. Entry (penetration 3. Synthesis 4. Assembly 5. Release
33
Describe "attachment" in viral replication
It is the attachment of the virus to the susceptible host cell
34
Describe "entry" in viral replication
It is the penetration of the vriion or its nucleic acid
35
Describe "synthesis" in viral replication
Synthesis of virus nucliec acid (genome) and proteins by host cell metabolism as redirected by virus genes
36
Describe "assembly" in viral replication
Assembly of capsids and packaging of viral genomes into new virions (maturation), self-assembly
37
Describe "release" in viral replication
Release of mature virions from the host cell. The host cell is lysed
38
What are the general features of virus replication
Virus replication is typically characteriuzed by a "one-step" growth curve - compared to exponential growth.
39
What are the two phases in a virus replication growth curve
The latent period and the burst size
40
What is the latent period
Eclipse is the latent period after virus is added | Maturation is the assembly and release of virions
41
What is the burst size
The number of virions released, often about 100 viruses are all released at once and results in a sudden jump in the curve. Go from 1 to 100 cells in one step
42
Describe the viral attachment to the host cell
The attachment is highly specific. Viral proteins interact with receptors on the surface of a susceptible host. The receptors are normal host-cell features that carry out functions for the cell. These receptors include proteins, carbs, glycoproteins, lipids, lipoproteins, or complexes of these
43
What is a permissive cell
A host cell that allows the complete replication cycle of a virus to occur
44
Describe viral attachment and penetration of bacteriophage T4
Bacteriophage T4 is a virus of E.coli. Virions attach to cells via tail fibers that interact with polysaccharides on the E.coli cell envelope. The tail fibers retract and tail core makes contact with the E.coli cell wall. Lysozyme-like enzyme forms small pore in peptidoglycan and the tail sheath contracts and viral DNA passes into cytoplasm
45
What are the two defense mechanisms bacteria have to fight off viral infections
The CRISPR system and Restriction modification system
46
Describe the restriction-modification system
It is effective against double-stranded DNA viruses. There are restriction enzymes and modifications
47
What are restriction enzymes
Restriction endonucleases that cleave DNA at specific seqeunces. Can cleave the DNA of the incoming virus or transposons at certain sequences and voids cutting its own DNA
48
What is modification
Modification of host's own DNA at restriction enzyme recognition sites prevents cleavage of cell's own DNA by its own restriction enzymes
49
How have viral mechanisms evolved
Viral mechanisms have evolved to evade bacterial restriction systems
50
What are some viral mechanisms that have evolved to evade bacterial restriction systems
Chemical modification of viral DNA to block restriction enzyme activity and production of proteins that inhibit host cell restriction system
51
What are the two requirements of an infection
It must replicate the virus genome and make viral proteins
52
What is needed for production of viral nucleic acid and proteins
A viral messenger RNA (mRNA), for some RNA viruses the viral RNA itself is the mRNA and for others the transcriptional enzymes are contained in the virion or the virus can use the RNA polymerase of the host cell
53
What are viral proteins
They are proteins that are produced under the direction of viral mRNA and they require host cells ribosomes, tRNA, and energy to do so. A temporal program is required
54
What are early proteins
They are synthesized soon after infection, necessary for replication of virus nucliec acid, typically act catalytically, and are synthesized in smaller amounts
55
What are late proteins
They are synthesized later, include proteins of virus coat, typically structural components and are synthesized in larger amounts. Made after the genome has been copied
56
What type of viruses are more complex
Bacterial viruses tend to be more complex than animal viruses because they need to breach a cell wall, they have a tail and tail fibers that help them inject their genome across the cell wall
57
What are the two viral life cycles
Virulent mode and Temperate mode
58
Describe the virulent mode
Viruses lyse host cells after infection to release new virions
59
Describe the temperate mode
Viruses replicate their genomes in tandem with host genome without killing host. Temperate viruses can also switch to virulent (lytic) life cycle under certain conditions to lyse cell and release virions. Every time the host cell makes a progeny, it contains the viral genome hiding in the bacterial chromosome
60
How can the bacteriopahge T4 be divided into three parts
They have early, middle, and late genes
61
Describe the early and middle proteins
They are enzymes for DNA replication and transcription
62
Describe the late proteins
The head and tail proteins and enzymes required to release mature phage particles from the cell
63
Describe the process of bacteriophage T4 infecting a cell
The entire process takes about an hour to lyse a cell. Soon after infection the first mRNAs are made that code for the early proteins in order to replicate the genome first. Then the middle mRNA will make the middle proteins, and they might be involved in compacting or packing of the the DNA in the earliest stages of viral assembly. . Then the late mRNA and late proteins are involved with the structural proteins. All of these proteins are made and fit together as they are bouncing around in the cell, when they meet a compatible protein there will be self-assembly
64
What are temperate viruses
They can undergo a stable genetic relationship within the cell, but can also kill cells
65
For temperate viruses what is the lysogenic pathway
The state where most viral genes are not expressed and virus genome (prophage) is replicated in synchrony with host chromosome
66
What is a lysogen
A bacterium that contains a prophage. Under certain conditions lysogenic viruses can convert to a lytic pathway and begin to produce virions
67
For temperate viruses what is the lytic pathway
The viral DNA replicates, the coat proteins are synthesized and the virus particles are assembled. Then lysis occurs and all the virions are released from the lysed cell The lytic pathway can be turned on by the prophage under stress conditions
68
Describe bacteriophage lambda
It is a linear, dsDNA genome in virion and circularizes in the host cell. As a lysogen, phage genome DNA integrates into the E.coli chromosome at a SPECIFIC sequence, the lambda attachment site
69
Describe how the bacteriophage lambda integrates into the host cell genome
It can insert itself at a particular site of the chromosome called the lambda attachment site. The lambda genome circularizes at the cohesive ends when it enters the cell Site specific nucleases will create the staggered ends (overhangs/sticky ends) on the circular phage and the host DNA at the lambda attachment site. Then the integration of the lambda DNA and closing of gaps by DNA ligase can occur
70
What are the key elements that regulate the lytic vs lysogenic pathways in lambda
Two repressor proteins: cl protein (the lambda repressor) and the Cro repressor
71
Describe the cl protein (the lambda repressor)
It causes the repression of the lambda lytic events, if the cl repressor predominates, then the phage forms a lysogen
72
Describe the cro repressor
Controls activation of lytic events, if Cro predominates, it inhibits the ability of the lambda to form a lysogen and the phage enters the lytic pathway

BIMM 120 (17 decks)

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