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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
Q

What are nucleic acid polymerases

A

Used for the replication of viral genomes, some that are not dsDNA and can perform rapid replication

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26
Q

Where can viruses replicate

A

Viruses can only replicate in coevolved host cells or organisms. Within their host range

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27
Q

What are bacterial viruses often called

A

Bacteriophage or phage

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28
Q

What is a titer

A

The number of infectious units per volume of fluid

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29
Q

What is a plaque assay

A

It is analogous to the bacterial colony, one way to measure virus infectivity

30
Q

What are plaques

A

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
Q

How is a plaque assay performed

A

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
Q

What are the 5 phases of viral replication

A
  1. Attachment (adsorption)
  2. Entry (penetration
  3. Synthesis
  4. Assembly
  5. Release
33
Q

Describe “attachment” in viral replication

A

It is the attachment of the virus to the susceptible host cell

34
Q

Describe “entry” in viral replication

A

It is the penetration of the vriion or its nucleic acid

35
Q

Describe “synthesis” in viral replication

A

Synthesis of virus nucliec acid (genome) and proteins by host cell metabolism as redirected by virus genes

36
Q

Describe “assembly” in viral replication

A

Assembly of capsids and packaging of viral genomes into new virions (maturation), self-assembly

37
Q

Describe “release” in viral replication

A

Release of mature virions from the host cell. The host cell is lysed

38
Q

What are the general features of virus replication

A

Virus replication is typically characteriuzed by a “one-step” growth curve - compared to exponential growth.

39
Q

What are the two phases in a virus replication growth curve

A

The latent period and the burst size

40
Q

What is the latent period

A

Eclipse is the latent period after virus is added

Maturation is the assembly and release of virions

41
Q

What is the burst size

A

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
Q

Describe the viral attachment to the host cell

A

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
Q

What is a permissive cell

A

A host cell that allows the complete replication cycle of a virus to occur

44
Q

Describe viral attachment and penetration of bacteriophage T4

A

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
Q

What are the two defense mechanisms bacteria have to fight off viral infections

A

The CRISPR system and Restriction modification system

46
Q

Describe the restriction-modification system

A

It is effective against double-stranded DNA viruses. There are restriction enzymes and modifications

47
Q

What are restriction enzymes

A

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
Q

What is modification

A

Modification of host’s own DNA at restriction enzyme recognition sites prevents cleavage of cell’s own DNA by its own restriction enzymes

49
Q

How have viral mechanisms evolved

A

Viral mechanisms have evolved to evade bacterial restriction systems

50
Q

What are some viral mechanisms that have evolved to evade bacterial restriction systems

A

Chemical modification of viral DNA to block restriction enzyme activity and production of proteins that inhibit host cell restriction system

51
Q

What are the two requirements of an infection

A

It must replicate the virus genome and make viral proteins

52
Q

What is needed for production of viral nucleic acid and proteins

A

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
Q

What are viral proteins

A

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
Q

What are early proteins

A

They are synthesized soon after infection, necessary for replication of virus nucliec acid, typically act catalytically, and are synthesized in smaller amounts

55
Q

What are late proteins

A

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
Q

What type of viruses are more complex

A

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
Q

What are the two viral life cycles

A

Virulent mode and Temperate mode

58
Q

Describe the virulent mode

A

Viruses lyse host cells after infection to release new virions

59
Q

Describe the temperate mode

A

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
Q

How can the bacteriopahge T4 be divided into three parts

A

They have early, middle, and late genes

61
Q

Describe the early and middle proteins

A

They are enzymes for DNA replication and transcription

62
Q

Describe the late proteins

A

The head and tail proteins and enzymes required to release mature phage particles from the cell

63
Q

Describe the process of bacteriophage T4 infecting a cell

A

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
Q

What are temperate viruses

A

They can undergo a stable genetic relationship within the cell, but can also kill cells

65
Q

For temperate viruses what is the lysogenic pathway

A

The state where most viral genes are not expressed and virus genome (prophage) is replicated in synchrony with host chromosome

66
Q

What is a lysogen

A

A bacterium that contains a prophage. Under certain conditions lysogenic viruses can convert to a lytic pathway and begin to produce virions

67
Q

For temperate viruses what is the lytic pathway

A

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
Q

Describe bacteriophage lambda

A

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
Q

Describe how the bacteriophage lambda integrates into the host cell genome

A

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
Q

What are the key elements that regulate the lytic vs lysogenic pathways in lambda

A

Two repressor proteins: cl protein (the lambda repressor) and the Cro repressor

71
Q

Describe the cl protein (the lambda repressor)

A

It causes the repression of the lambda lytic events, if the cl repressor predominates, then the phage forms a lysogen

72
Q

Describe the cro repressor

A

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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