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Microbiology > Viruses, Viroids and Prions > Flashcards

Viruses, Viroids and Prions Flashcards

1
Q

What are the General characteristics of Viruses? What are viruses sensitive and not sensitive to?

A

General Characteristics of Viruses:
-Especially small (20- 200 nm)
-All are obligate intracellular parasites
-require living host cells to multiply
-contain very small genomes of either DNA or RNA
-Nucleic acid is enclosed in a protein coat capsid that surrounds the nucleic acid
- Coat or capsid is sometimes enclosed in a membrane envelope
-NO Ribosomes
-NO ATP-generating mechanism
-They are NOT sensitive to antibiotics
-They are sensitive to interferon-antiviral proteins produced by our immune system in response to viral infections

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2
Q

Compare the size of a virus vs bacteria.

A

Bacteria are larger than viruses
Bacteria cell can be 2um (2000 nm)
Virus can be 30 nm (picornavirus) or 200 nm (paramyxovirus)

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3
Q

What are viruses composed? What is a nucleocapsid? what are the characteristics of capsids?

A

The minimum composition of a virus particle:
1. A nucleic acid genome
-DNA or RNA
-single or double-stranded
-Linear or circular
-segmented or unsegmented (1 segment); on molecule or several
-Much, much smaller than single human chromosome
2. A protein capsid or coat
- Nucleocapsid- the genome plus the Capsid
-some viruses contain NO membranes, so in this way differ greatly from cells
-Capsids have highly ordered architecture with regular repeating subunits, and exhibit symmetry

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4
Q

What other components do some viruses also contain?

A

Some viruses also contain:
-Envelope or viral membrane:
taken from the host cell
-Membrane proteins:
some encoded by the virus
some belonging to the host
-a virus-encoded polymerase
an RNA polymerase or DNA polymerase
-other virus-encoded proteins

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5
Q

What is a Virion?

A

Virion: A complete, fully developed, infectious viral particle that is outside a host cell, where it is metabolically inactive

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6
Q

How are viruses visualized? What kind of technology are used. Which forms of microscopy can be used to see viruses ?

A

A typical virus is between 20 and 200 nm in size
-you can view viruses with Electron microscopy (TEM and Scanning) that are 0.2 nm and X-ray crystallography (0.05 nm, 0,5 Angstrom (A), Electron tunneling microscopy and atomic microscopy.
- You cannot view viruses with light microcopy (200 nm) or fluorescent microscopy. With Fluorescent microscopy, you can detect the virus but not have a clear image or see shape of virus.

(TEM lets you see internal structures)
-a carbon-carbon bond is 1.5 Angstroms

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7
Q

What size of viruses can be sen with TEM (transmission electron microsocpy0

A

TEM: see Viruses that are 30 nm in diameter

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8
Q

Explain how X-ray crystallography is used to visualize viruses ?

A

X-ray crystallography : process of detraining the atomic and molecular of crystal, as the creamy structure causes of a beam of X-rays to diffract in different directions.
a crystal of virus particles.
Process:
-proteins are dissolved in aqueous environment till supersaturated and precipitate as ordered crystals
-Then a complex computation is used to make a computer model of the atomic structure and crystalized virus (since there is no lens that exists to refocus scattered X-rays)
-(crystal–> Diffraction pattern–> Electron density map–> protein model)

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9
Q

What kind of virus naturally infects nematodes. Which ribbon model is used to observe this?

A

A ribbon model of the capsid of the ORSAY virus that naturally infects nematode.

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10
Q

How was the existence of viruses known before the advent of electron microscopy ?

A

Through FILTERABLE Agents- passed through bacteriological filters.
(Found that even after filtering out Bactria, there was still infectous agent (hence virus)

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11
Q

Describe how viruses are sharped and structured?

A

Virus classification by general morphology:
Shape:
polyhedral
helical
complex
envelope:
naked (NON-ENVELOPED)
ENVELOPED:
Spikes or no spikes

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12
Q

What odes polyhedral mean? What can bee seen in virion of a simple polyhedral virus? What are capsomeres?

A

Polyhedral- many sided
-virion of simple polyhedral virus capsomere, capsized)
Capsomeres: the protein subunits of the capsid: which may be composed of single type of protein or several types
-The capsid needs to be ordered symmetrically, so they can self-assemble.

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13
Q

What are the features of the icosahedron shape for viruses?

A

Icosahedron:
-Most polyhedral viruses are icosahedron
20 equilateral triangular faces and 12 corners

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14
Q

What is the morphology of a Helical Virus? What is an example of this>

A

Morphology of a helical virus:
-resemble long rods that may be rigid or flexible
-nucleic acid has a helical structure and is found within the hollow cyclindrical structure
Ex: EBOLA virus (is a helical virus)

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15
Q

What is an example of a complex virus? What are the components of this example>

A

Complex virus: viruses that does not fit description of other two shapes (of viruses)
Ex: T -even bacteriophage
(bacteriophage composed of Capsid (head) , DNA, sheath, Pin, Baseplate and Tail fiber
(t-even is 2, 46; t-odd is 1, 3, 7)

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16
Q

Wha kind of virus is Poxvirus? What are the components of poxvirus?

A

Poxvirus is a Complex Virus (very large virus)
components of poxvirus:
-envelope (surface tubules, outer membrane, innermembrane),
-Core envelope: core membrane and palisade layer
-Nucleoprotein
-Lateral body

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17
Q

What are the characteristic of Enveloped viruses? What is an example?

A

Enveloped Viruses
-roughly spherical
-enveloped helical (influenza virus) or enveloped polyhedral (ex: herpes virus) depending on capsid.

(This virus becomes spherical when it is packed into an envelope)
(Enveloped viruses: Have nucleic acid, capsomere, envelope with spikes)

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18
Q

What are spikes? What is it used for> Which viruses can have these spikes?

A

Spikes: carbohydrate-protein complexes that project from the surface of the membrane
Enveloped and non-enveloped viruses may or may not contain spikes
-Used by some viruses for Host attachment
- Can be used as a reliable means o microscopic identification
-some viral spikes trigger hemagglutination (RBC clumping).
Serum that neutralizes this reaction can be used for sub typing viruses (ex influenza virus) or determine a patient antibody titer.

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19
Q

What happens in a neutralization test? What happens to virus when serum is added?

A

Neutralization test: Have a virus that is mixed with Red blood cells and it will hemagluttinates. If you add serum, it blocks the virus and stops the hemagluttination (clumping)

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20
Q

Where does the virus envelope come from? How?

A

Virus envelope comes from HOSTt
1. have Viral capsid, and viral glycoproteins, and host cytoplasmic membrane
2. As the virus is assembling, some of the proteins that it synthesizes, are going to be put into membrane of host.
As viral capsid leaves host, it buds off and enclosed in membrane with viral proteins and host proteins)

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21
Q

How are viruses classified ? Descirbe the two ways

A

Viruses are classified
1. They are taxonomically classified into individual orders, families, and genera based on a variety physical and biological criteria.
(Viruses have FEWER classifications than bacteria)
2) They may also be placed into groups according to the type of genome in the virion (Baltimore classification scheme (1971)

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22
Q

Explain why viruses are excluded from the cellular tree of life. Is there a single viral phylogenetic tree?

A

Viruses are excluded from the cellular tree of life.
-There is NOT single viral phylogenetic tree because viruses have few genes and there is nothing you can compare them against

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23
Q

What are the seven classes of viruses in Baltimore’s Scheme?

A

Classification Is based the type of genome and how mRNA is produced
Classes:
I. Double-stranded DNA:
non-developed
enveloped
II. single-stranded DNA, ALL NON-enveloped
III. Double-stranded RNA,A ALL NON-enveloped
IV. Plus or postive (+) stranded RNA:
non-enveloped
enveloped
V. Minus or negative (-) stranded RNA, ALL enveloped one RNA molecule
multiple RNA molecules (sequenced DNA)
VI single-stranded RNA to DNA
VII. dsDNA to ssRNA to dsDNA

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24
Q

Explain how the 7 classes of viruses in Baltimore’s Scheme make mRNA and replicate the genome for new viral particles

A

REVIEW

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25
Q

Discuss the rules for Viral Nomenclature? How are different orders, families and genera named? How do you distinguish species vs subspecies. Give two main examples of subspecies?

A

Viral Nomenclature
Order names end in - ales
Family names end in -viridae
Genus names end in -virus
Descriptive common names are used for species
Subspecies are designated by a number
1. Human immunodeficiency virus 1 (HIV-1) is an Enveloped retrovirus that infects humans*
(not have genus )
2. Severe acute respiratory syndrome coronavirus 2* (SARS-CoV-2) is a coronavirus that infects humans
( coronavirus is genus name)
-Virus specific epithets are not used- no established binomial nomenclature
-Written in italics and first letter is capitalized
examples:
-Order Monoengavirales
-Family Paramyxoviride
-Genus Morbillivirus

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26
Q

What is viral species ?

A

Viral species: A group of viruses sharing the same genetic information and ecological niche (host)

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27
Q

Which Viral families are in class I ? What are their characteristics ?

A

Class I:
All families are Double stranded DNA
-Family Adenoviridae and Papovaviridae are Nonenveloped.
Family Poxviridiae and Herpesviridae are Enveloped

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28
Q

Which viral families are in class II? what are their characteristics?

A

Class II
Single stranded DNA
Family Parvoviridae is NON-Enveloped

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29
Q

Which Viral families are in class III? What are their characteristics?

A

Class III:
Double stranded RNA
Family Reoviridae is NON-ENVELOPED

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30
Q

Describe the viral families that are in class IV. What are the different characteristics?

A

Class IV:
ALL are Single-Stranded RNA, Positive strand
Families Picornaviridae and Caliciviridae are NON-ENVELOPED
Family Togaviridae, Flaviviridae, Coronaviridae, are ENVELOPED

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31
Q

Which viral families are in class V? What are their characteristics?

A

Class V
ALL families are Single stranded RNA, Negative strand
-Families Rhabdoviridae and Filoviridae and Paramyxoviridae have ONE strand of RNA, ENVELOPED
-Families Orthomyxoviridae, Bunyaviridae, and Arenaviridae have MULTIPLE Strands of RNA, ENVELOPED

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32
Q

Which Viral families are in class VI? What are the characteristics?

A

Class VI
Family Retroviridae is Single-Stranded RNA, produce DNA
- ENVELOPED

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33
Q

Describe the Viral families in class VII? Describe their characteristics

A

Class VII
Family Hepadnaviridae are Double-stranded DNA, use Reverse transcriptase, ENVELOPED

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34
Q

Describe the characteristics for Viral family Deltaviridae? What class is part of?

A

Class V
Family Deltaviridae
Characteristics :
Single stranded RNA, Negative strand
-One strand of RNA, ENVELOPED
-Virusoid or Satelite RNA
*Note Hepatitis D (Delta) is NOT a virus, but a virusoid

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35
Q

What is a bacteriophage? What are the properties of bacteriophages?

A

Bacteriophage: a virus that infects and replicates within bacteria
Properties of bacteriophages:
- replicate inside bacterial cells
- Consists of a protein coat that encapsulates a pieced of nucleic acid, which can be either double or single-stranded DNA or RNA
-Classified as either Virulent or Temperate

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36
Q

What is Virulent Phage?

A

Virulent phage- the end result of successful cell infection is the realist of PHAGE progeny

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37
Q

What is Temperate phage?

A

Temperate Phage: The end-result of successful cell infection can either be Release of Phage progeny OR the Formation of a prophage

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38
Q

What is a prophage?

A

Prophage: Bacteriophage whose DNA has entered the cell, is replicated in concert with the host genome. but its genes are indefinitely repressed by a phage encoded repressor protein

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39
Q

What is a Lysogen ?

A

Lysogen: Bacteria that carries a prophage

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40
Q

What is prophage induction?

A

Prophage induction- emergence of a prophage from its latent state

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41
Q

Whichproteons do the different phages (phage T4, lambda, and P1) attack to in lytic cycle?

A

Phages:
-Phage T4 attaches to a Porin protein
-Phage lambda attaches to a maltose transport protein
-P1 to a Calcium transporter

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42
Q

Describe the process of Lytic cycle of T-even bacteriophage? What occurs? When does the eclipse period happen in cycle?

A

Life Cycle of a T-even bacteriophage
1. Attachment: phage attaches to host cell
2. Entry: phage penetrates host cells and injects its DNA
3. Biosynthesis: Phage DNA. directs this synthesis of viral components by the host cells
4. Maturation: Viral components are assembled into visions
During steps 3-4 are ECLIPSE period
5. Release: Host cell lyses, and new visions are released

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43
Q

What is the order of how the phage DNA formed? what are the components?

A

Phage DNA:
start with Tail attaching to baseplate pin. Then sheath forms around tail and DNA is inserted into cashed, then Caspid with DNA will attach to tail (with sheath) and tail fibers attaching to tail, and cashed (head)

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44
Q

Describe what occurs in the Lysogenic cycle of Phage lambda. What occurs during this process?

A

Phage Lambda Lysogenic cycle
1. Phage attaches to bacterial cell wall and injects DNA
2. Phage DNA circularizes
3. Phage DNA integrates into bacterial chromosome to become a prophage
4. Cell division occurs
-Dormancy is maintained by a phage
protein that represses the expression of all phage genes except repressor gene
5. Dormant prophage is propagated indefinitely in progeny lysogenic cells

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45
Q

What are the different sites seen on lambda phage genome ?

A

Lambda phage genome
-cut sites, Head/tail genes, att site, recombination sites, immunity sites, DNA replication site, and lysis site.

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46
Q

Where does the prophage integrate at in the bacterial chromosomes?

A

The prophage integrates at specific sequence *(the att site) * in the bacterial chromosome

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47
Q

What is the integration site for bacteriophage 22 vs bacteriophage lambda?

A

Integration site for bacteriophage 22 is att P22
-integration site for bacteriophage lambda is att lamda

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48
Q

Explain what occurs in the induction of Lysogneic Bacterium?

A

Induction of a Lysogenic Bacterium (for Phage lambda)
1. Blockage of DNA synthesis (by UV irradiation, for example) causes a cascade of reactions that destroys the phage repressor
2. Phage genes are expressed and prophage excises from chromosome
3. Phage DNA replicates and directs synthesis of new phage particles
4. Lysis relates progeny phage

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49
Q

What are the specifics of Lambda induction?

A

lambda induction: various DNA damaging treatments INDUCE lambda prophages. Cellular repair of gapped DNA results in the accumulation of single-stranded DNA which binds and activates the E.coli Rec A protein. This activated protein then proteolytically cleaves the lambda repressor protein
-Efficient excision from bacterial genome requires a phage encoded protein

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50
Q

Why is it thought to be advantageous for the virus to exit lysogen following DNA damage?

A

REVIEW

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51
Q

What are the bacteriophages that can be lysogenic ?

A

Only certain bacteriophages can be lysogenic:
-Bacteriophage lambda
-bacteriophage P22 and many others

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52
Q

Describe the cascade that occurs in order to either cause lytic growth or activate DNA repair genes

A

Cascade
-UV light can cause damage in DNA strand and lead to break in DNA.
-This causes a protein called Rec A to become activated
-Activated Rec A will when Cleave Cl to for lytic growth OR cleave Lex A to activate DNA repair genes

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53
Q

Compare and contrast specialized transduction and generalized transduction? What do the different types of transduction require ?

A

Specialized transduction:
-prophage excises imperfectly, taking nearby DNA with it.
*Limited to few genes surrounding integration site *
requires LYSOGENY, integration of phage DNA into bacterial chromosome

Generalized transduction:
- as bacterial genome is degraded, some is packaged into phage
-Can transduce visually any gene in chromosome
-Does NOT require lysogeny

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54
Q

Describe the steps of Specialized Transduction? What occurs?

A

Specialized Transduction
-The virus carries a SPECIFIC gene or set of neighboring genes from a host to another host depending on where the att site is.
process:
1. Prophage exists in galactose-using host (containing gal gene)
2. Phage genome excises, carrying with it the adjacent gal gene from the host
3. Phage matures and cell lyses, releasing phage carrying gal gene
4. Phage infects a cell that cannot utilize galactose (lacking gal gene)
5. Along with the prophage, the bacterial gal gene, becomes integrated into the new host’s DNA.
6. Lysogenic cell can now metabolize galactose

55
Q

Describe what occurs in Generalized transduction. What is the process?

A

Generalized transduction : the virus carries a RANDOM gene or genes from a host to another host
process:
2. Phage DNA and proteins are made and then bacterial chromosome is broken into pieces
3. Occasionally during phage assembly, pieces of bacterial DNA are packaged in a phage caspid. Then the donor cell lyses and releases phage particles containing DNA
4. A phage carrying bacterial DNA infects new host cell, the recipient cell
5. Recombination can occur producing a recombinant cell with a genotype different from both donor and recipient cells.

56
Q

What is lysogenic conversion?

A

Lysognic conversion: the bacterium has a new property due to presence of the prophage
for example: a disease-causing bacterium may produce a toxin encoded on a gene in the prophage

57
Q

Discuss the bacterium that cause disease Cholera, hemorrhagic diarrhea, botulism/food poising a and Scarlett fever. Also include the bacteriophage and gene product that causes the disease listed above

A

Diseases:
* cholera: caused by bacterium Vibrio cholera and bacteriophage CTX phage. The gene product formed is cholera toxin
*Hemorrhagic diarrhea is caused by bacterium Escherichia coli and bacteriophage lambda phage. The gene product formed is the shiga-like toxin
*Botulism/food poisoning is caused by bacterium Clostridium botulinum and bacteriophage clostridial phages
The gene product formed is botulinum toxin
*scarlet fever is caused by bacterium Streptococcus pyogenes that have bacteriophage T12. The gene product formed are erthyogenic toxins

58
Q

What are the major structures of mammalian cell?

A

Major structures of mammalian cell:
-plasma membrane
-ribosomes
-nucleotides
-amino acids
-sugars
-DNA polymerases
-Golgi apparatus
-centriole
-nucleus
-endoplasmic reticulum
-lysosome
-mitochondrion

59
Q

What are the major steps of Virus multiplication ? Which step is unique to specific viruses ?

A

Steps of virus multiplication
1. Attachment to specific cell surface molecules
2. Entryof either the virus particle or its genome
3. Uncoating- separation of the viral nucleic acid from its protein coat
4. **Latent infection ** were the virus is present but produces few or no new viruses
5. Biosynthesis of nucleic acid and proteins
6. Maturation including assembly and incorporation of the genome into the cased
7. Release of many more viruses by budding (enveloped viruses) or lysis of the cell
*This latent infection, happens only in a few specific viruses; ex lambda bacteriophage, herpesviruses, retroviruses

60
Q

How does attachment differ for animal viruses compared to bacteriophages?

A

Attachment; a virus attaches to a specific receptor molecule on the cell surface
- in contrast to attachment for bacteriophages, animal viruses DO NOT have appendages like tail fibers of some bacteriophage and attachment sites for viruses are distributed over the SURFACE of the virus

61
Q

What are the kinds of receptors used for attachment in animal cells?

A

Attachment; animal cell surface receptors
-cell surface receptors are used for various viruses
Glycoproteins are also receptors
-these proteins have normal functions for the host that are hijacked by the virus.

62
Q

Describe the different ways of entry for viruses in mammalian cell. How do toga virus and herpes virus enter cell?

A

Entry:
-following virus attaches to host receptor
1) some enveloped and nonenveloped viruses enter by a variety of ENDOCYTIC methods
ex: togavirus enters by pinocytosis
2) Some noneveloped viruses insert their genome into the host cytoplasm through creation of a PORE in the Host plasma membrane or vesicle membrane.
-The virus has a pore-forming peptide in its capsid
-some enveloped viruses enter by FUSION
Ex: Herpesvirus enters by Fusion
(fusion of viral envelope and PM, and then capsid released into cytoplasm)

63
Q

How does the Poliovirus enter the cell?

A

Structural study showing the Poliovirus viral RNA directly translocating from the particle across the membrane, similar to bacteriophage

64
Q

Explain What uncoating and what occurs in the process

A

Uncoating; Separating of the viral nucleic acid from its protein coat
-process varies with type of virus and include…
1. Lysosomal enzymes degrade proteins of viral capsid
2. Virus encodes a specific enzyme for capsid degradation
3. Low pH of endosome triggers uncoating

REVIEW

65
Q

When it comes to animal cell nucleic acid biogenesis , what do mammalian cells lack?

A

In animal cell nucleic acid biogenesis:
mammalian cells lacks:
-RNA-dependent DNA polymerase
-RNA-dependent RNA polymerase

66
Q

Discuss the biosynthesis of viral nucleic acids, including what is required if a virus needs to make DNA from DNA; RNA from DNA; make RNA from RNA; make DNA from RNA

A

Biosynthesis of viral nucleic acids
-if a virus needs to…
make DNA from DNA,
it uses the host’s DNA-dependent DNA polymerase
-Unless its a CYTOPLASMIC virus, then it uses its OWN
To make RNA from DNA,
-it uses the host’s RNA polymerase
-unless its Cytoplasmic
To make RNA from RNA,
- if it is a POSITIVE strand virus, it can ENCODE its own polymerase
- if it is a NEGATIVE strand virus, it must BRING IN its own polymerase
To make DNA from RNA,
-it must BRING IN its own polymerase (reverse transcriptase)

67
Q

What occurs in the Multiplication of double stranded DNA (dsDNA) virus? How does it differ in Papoviridae/Adenoviridae, compared to Herpesviridae and Poxiviridae?

A

*For Adenoviridae and Papoviridae, Both Transcription and replication occur in the cell nucleus using cellular polymerases *
However, Herpesviridae uses a viral DNA polymerase in the Nucleus, while Poxviridae uses a viral DNA polymerase in the Cytoplasm
process:
1. attachment of vision to host cell
2. entry and uncoating (vision enter cell, its DNA is uncoated)
3. a portion of viral DNA is transcribed producing mrNA
4. Biosynthesis: viral DNA replicated and some viral proteins are made
5. late translation: capsid protons are made ‘
6 . maturation of visions
7. release of virions

68
Q

What occurring in the multiplication of +RNA virus (ex; Piconaviridae)

A

The + RNA genome serves as mRNA for the synthesis of new virus proteins, including the virus polymerase
-The virus polymerase (red) copies the +RNA into a - RNA and copies the -RNA into another +RNA
Viral genome is injected into the cytoplasm
process
1. Attachment of vision to host cell
2. Entry and uncoating; releasing viral RNA and proteins.
-the viral genome is injected into the cytoplasm
3. RNA replication by viral RNA-dependent RNA polymerase
4. Translation and synthesis of viral proteins
5. Maturation and release
*Piconaviridae: example of family that has + RNA virus *

69
Q

What occurs in the multiplication of
-RNA virus (Rhabodviridae) ?

A

Multiplication of -RNA virus
- RNA CANNOT be translated directly; viral polymerase must be carried within the virus
-Viral polymerase (blue) copies - RNA into + RNA for translation
-Viral polymerase copies the + RNA into more - RNA
- Rhabodiviridae is family of organisms that have -RNA virus
process:
1. Attachment
2. Entry and uncoating (releases viral RNA and proteins)
-Viral genome is injected into the cytoplasm
-virus polymerase is transported in with the genome
3. RNA replicate by viral RNA- dependent RNA polymerase (positive strand (mRNA) must first be transcribed from the - viral genome before proteins are made)
4. translation and synthesis of viral proteins
5. Maturation and release

70
Q

What occurs in the multiplication of doubles stranded RNA (dsRNA)?

A

Mutliplication of dsRNA virus (Reoviridae)
- Viral polymerase must be carried into the cell inside the virus
-The Double stranded RNA (dsRNA) stays inside the virus particle and Cannot be translated directly, so viral polymerase copies the dsRNA into mRNA and more dsRNA
process:
1. Attachment of capsid to host cell
2. Entry and uncoating (releases viral RNA and proteins)
virus does not completely uncoat
-virus polymerase is carried in with the genome
3. RNA replication by viral dependent RNA polymerase
-mRNA is produced inside the capsid and released into cytoplasm of the host
4. Translation and synthesis of viral proteins
-RNA polymerase initates the production of negative strand. The mRNA and - strands from the dsRNA that is incorporated as new viral genome
-dsRNA and polymerase are incorporated into the capsid
5. Maturation and relate

71
Q

What happens in the multiplication of Retroviridae? Why is a unique process?

A

Multiplication of a Retroviridae:
uses two identical + strands of RNA, has revere transcriptase (enzyme), envelope, capsid, host cell and virus.
process:
1. Retrovirus enters by fusion between attachment spikes and host cell receptors
2. *Uncoating releases the two viral strands and viral enzymes reverse transcriptase, integrate and protease
3. reverse transcriptase copes viral RNA to produce double-stranded DNA
4. The new viral DNA is transported into the host cell’s nucleus, where it is integrated into a host cell chromosome as a provirus by viral integrate. The provirus may be replicated when the host cell replicates
(DNA integrates into host genome)
5. Transcription of the provirus may also occur, producing RNA for new retrovirus genomes and RNA that encodes retrovirus capsid, enzymes, and envelope proteins
(virus DNA is transcribed like the host’s own genes)
6. Viral proteins are processed by viral protease. some of the viral proteins are moved to the host plasma membrane
7. Mature retrovirus leaves the host cell, acquiring an even lope and attachment spikes as it buds out.

72
Q

Explain what occurs in the one-step viral growth curve and what the periods are in the cycle? Why is it called this? what is MOI?

A

The One-step viral growth curve: describes the events that occur during reproduction of virus or (life cycle of virus)
-It is called one-step growth curve because it is on ONE replication cycle (1 life cycle)
Has diffrent periods:
-1. phase (at o minutes) where viruses contacts the cells
2.* Eclipse period: the time of synthesizing viral proteins and nucleic acids followed by maturation inside host cell
3. Then viruses are related form the host cell
4.* Acute infection period were there is a rapid onset of disease, short period of symptoms, quick resolution
MOI: multiplicity of infection
virus: virus number: host number

73
Q

Discuss why it is important to know how pathogenic viruses transcribes and replicates its genome

A

REVEIW this
do we have to know all info on Lisle 73 and 74?

74
Q

Compare the mutation rates seen in DNA synthesis and RNA synthesis ? Which has more variants per replication cycle (RNA or DNA ?)
Discuss the RNA polymerase of the Coraonvirus ?

A

Why does this matter: mutation rates
-DNA synthesis has a LOW error rate
DNA polymerases can “proofread:
-The cell has DNA-repair mechanisms
-RNA synthesis has a HIGH error rate
RNA polymerases CANNOT proofread
-NO known RNA repair mechanism is known
Therefore: RNA viruses produce more variants per replication cycle than DNA viruses
**Coronavirus RNA polymerase can proofread!

75
Q

What is the purpose of antiviral drug? what occurs if viruses make their own enzymes, vs use host cell enzymes?

A

We want antiviral drugs to INHIBIT viral replication
-If the virus makes and requires its own enzymes (such as an RNA-dependent DNA polymerase), then drugs against those enzymes may be effective treatments
-However, if virus uses the host cell enzymes to replicate, then drugs against those enzymes will be toxic to host cells as well

76
Q

What occurs during maturation?

A

Maturation: nucleic acids and capsids are assembled into complete virions–usualy spontaneous

77
Q

What are ways that virus can be released?

A

Release of virus:
-many viruses lyse the host cell
-also budding of an enveloped virus occur (budding does NOT result in host cell lysis)
(the surface of HIV is an envelope taken from the host cell plasma membrane)

78
Q

Describe the integration of animal viruses into the host genome. Which family of organisms will integrate into genome?

A

Some animal viruses integrate Into the genome (but not at specific sites)
-DNA from dsDNA (double-stranded) viruses normally enters the nucleus, circularizes, but does NOT integrate into the genome
-Some DNA viruses will integrate on rare occasions.
-Herpesviridae can resist and establish Latency without integration. However, certain herepsviridae do integrate at Low frequencies
-In many cervical cancers, the Human Papilloma virus (HPV), genome has been found integrated into the host cell genome, where certain viral proteins remain expressed and active.
-Retroviridae REQUIRES genome integration for its normal life cycle

79
Q

What is conditional integration and which organisms use it?

A

Conditional integration: Lambda (and certain other bacteriophages) have specialized mechanisms that allow them to integrate at SPECIFIC locations in the bacterial genome if the conditions are right

80
Q

Distinguish between Latent and persistent infections? Also discuss the illnesses or diseases that are examples of each

A

Certain viruses cause latent or persistent infections
*Latent infection: the virus remains asymptomatic in the host cell for LONG periods (often years)
-cold sores/fever blister (Herpes simplex virus)- inhabits nerve cells but cause No damage until activated (fevers or sunburn)
-fifty to 80 percent of US adults have oral herpes (HSV-1)
-Shingles (varicella zoster virus)- following Chickenpox, some virus enters nerve cells and remains latent. Later in life, changes in T-cell response can activate the virus producing the shingles rash along nerve where the virus was latent
*Persistent infection: Disease processes occurs over a Long period of time and is often FATAL
ex: subacute sclerosing panencephailts- rare progressive neurological disorder in children and young adults caused by measles virus

81
Q

Differentiate between the latent and persistent infection growth curves

A

Growth curves
persistent infection: Continuous, low-level virus production
Latent infection: No symptoms or virus produced for a long time

82
Q

What are examples of latent infections? Describe the virus, that causes disease, and the virus effect

A

Examples of Latent infections:
Virus:
*Herpes simplex 1 and 2 causes cold sores (disease) and virus effect: lesions in skin and mucosa
*HTLV-1 and 2 (retroviruses) will cause Leukemia (disease) and virus effect: increased white blood cell growth
*Varicella zoster virus (herpesvirus) cause Shingles (disease); virus effect: skin lesions

83
Q

What are examples of persistent infections? Include virus, disease and virus effect

A

Examples of persistent infections
Virus:
-Human papilloma virus (HPV) (papovirus) causes cervical cancer (disease); virus infect: increased cell growth
-HIV-1 and 2 (retrovirus) causes HIV/AIDS (disease) and virus effect: Decreased CD4+ T cells
-Hepatitis B virus (hepadnavirus) cause Liver cancer (disease) and virus effect; increased cell growth
-Rubella virus (togavirus) causes progressive encephalitis (disease); virus effect: rapid mental deterioration
-measles virus (paramyxovirus) causes subacute sclerosing panencephalitis (SSPE) (Disease) and virus effect; mental deterioration

84
Q

where must viruses be grown? What are examples?

A

Growing viruses in the laboratory
Viruses must be grown in living cells
-Bacteria for bacteriophages
-fungi for fungi viruses
-animals, animal tissues, or cultured animal cells (where the virus is grown) for animal viruses
-plants or cultured plant cell for plant viruses

85
Q

Discuss how bacteriophage is involved in the plaque method ? What occurs in this process?

A

Detection and Quantitation of bacteriophage by plaque method
-Bacteriophages can be grown either in suspensions of bacterial in liquid or solid media
- The concentration of a viral solution is usually expressed in terms of plaque-forming units (PFU)/ml
process;
1. mixture of unaffected bacterial cells and single layer of phage-infected cell are in melted agar
2. solidification of top agar layer immobilizes cells
3. Phage replicate in the infected cell. The cell lyses, releasing progeny that infect adjacent cells. These cells lyse and the cycle repeats
-Growth of uninfected bacteria creates an opaque lawn except at the location of original infected cell, where there is a plaque (hole) containing millions of phage

86
Q

What determines the phenotype of plaques being cloudy/turbid vs clear?

A

Depending on the virus, the plaques are either clear or cloudy/turbid.
phenotype:
Cloudy plaque: no cells in the hole (temperate phase)
Clear: some cells have been lysed (lytic phase)

87
Q

What are bacteriophage plaques?

A

bacteriophage plaques
-a phage causes plaques (clearings) in lawn of bacteria.
Each plaque was started by a single virus infection that spread to surrounding cells over time.

88
Q

What are animal and plant cell cultures used for? What is cell culture? What kind of cells are produced after cell culture?

A

Animal and plant cell cult can be used for viruses growth
Cell culture: cells grown in culture media in the lab
process:
1. tissue is treated with enzymes to separate the cells
2. Cells are suspended in culture medium
3. Normal cells or primary cells grow in a Monolayer across glass or plastic container. The transformed cells or continuous cell cultures Do NOT grow in a monolayer.
** transformed cells are also called cell lines or immortalized cells
(both transformed and normal cells are used to grow viruses in lab)

89
Q

Differentiate between primary cells and Cell lines?

A

Primary cells (normal cells) are derived from NORMAL tissues and have LIMITED growth capacity
-Cell lines (aka Transformed cells) are derived from Cancers and other abnormal tissues, but have UNLIMITED growth capacity
(there are more than 650 human cell lines)

90
Q

What are examples of human cell lines and what part of body part is affected?

A

Cell lines examples:
A-5449: lung carcinoma
MCF10A : mammary gland
HL-60 (myeloblast)
HEK (embryonic kidney )

91
Q

What are the most widely used human cell lines?

A

The most widely used human cell line is HeLa
HeLa cells have been used to study many viruses and have been critical to may scientific breakthroughs
(He La cells are easy to grow)
(He la cells- one of first immortalized cells used in cancer research)

92
Q

What is the Cytopathic Effect (CPE)? How is it used?

A

Cytopathic effect (CPE)
-many virus infections produce a cytopathic effect, characterized by round, swelling, detaching and dying of infected cells
-CPE can be detected and counted in a way similar to plaques on a lawn of bacteria and reported as PFU/ml
(PFU: plaque forming units)
-used as plaque assay

93
Q

What is the purpose of animal virus plaques?

A

Cultured mammalian cells can be used for plaque assays
-each plaque was started by a single virus infection that spread to surrounding cells over time
The cells are stained with a blue dye that stains only live cells

94
Q

What were chicken eggs used for when it comes to viruses ? Which virus specifically uses chicken eggs?

A

The GROWTH of Viruses used in embryonate chicken eggs
-once the most widely used method of isolating and growing virus
-Most influenza vaccine is made in chicken eggs each year
(in order for virus to effectively infect cells, they need to be injected into the right compartment of eggs)

(yolk sac, amniotic cavity, allatonic cavity, or choriallatonic membrane)

95
Q

What are animal hosts used for in term of viruses ? Which animals are used?

A

Animal hosts for human viruses
*some human pathogenic viruses can only be grown in animals. Scientists exhaust all other ways of trying to grow a virus before using such animals in research
- Mammals including mice, rhesus macaque monkeys and chimpanzees

96
Q

Provide examples of human viruses that cannot grow in animals or will not cause disease . Which virus can be grown in animals and are useful for studying the particular virus?

A

Some human viruses can’t grow in animals, or some can grow, BUT don’t cause disease
-Although chimpanzees can be infected with one of the two subspecies of HIV (HIV-1) , they are asymptomatic for the disease, and CANNOT be used to study effects of viral growth and disease treatments
-Simian AIDs (monkey) and feline AIDs develop disease within a few months and closely related to human AIDs. Thus provide models for studying AIDS.
-AIDS vaccines are tested in humans but can take years to determine effectiveness, because the disease progresses so slowly

97
Q

What are the different techniques used to study viruses ?

A

Virus identification (Not east to visualize)
*Observation of cytopathic effects (ex: cell shape, chromosome, or specific protein level changes, inclusion bodies, cell fusion )
*Viral culture: samples of a virus are added to different cell lines and tested for their ability to infect
Serological tests
-viral hemagglutination test (mix virus with blood to see if wit will agglutinate)
-Use ANTIBODIES from a patient’s serum against a panel of known viruses to identify the infecting virus (western blot or neutralization test)
*Nucleic acids
-PCR
-Sequencing (isolate DNA or nucleic acid and sequence it)
-RFLP- restriction fragment l linear polymorphism (digesting DNA)

98
Q

How can infected hosts cells be used to study viruses?

A

Infected host cells (eukaryotic or prokaryotic) can be cultured and grown, then the growth medium can be harvested as a source of virus. Viruses can be purified away from cellular proteins and organelles using centrifugation techniques

99
Q

What is host range (host tropism) ? What’s tissue tropism?

A

Host range (host tropism) the range of different species a virus can infect
Tissue tropism : the types of different tissues in an individual a virus can infect

100
Q

What determines the host range and tissue tropism? Where can restriction to virus tropism occur?

A

*specific host attachment sites
-due to differences in surface proteins
*Intracellular factors, such as host enzymes and antiviral defenses
-restriction to virus tropism are not just at the surface of the cell, but can occur at virtually any step of virus replication, maturation, and release form the cell

101
Q

What is tropism? Distinguish between cellular tropism, tissue tropism and host range. provide examples for each. How does virus tropism change?

A

tropism: what the virus is able infect
cellular tropism : type of cell in which a virus can infect
ex; HIV normally infects m macrophages but not neurons
tissue tropism: the types of tissues in an individual that a virus can infect
ex; Influenza virus normally infects lung tissue but not brain tissue
Host range ; aka host tropism describes the range of species that a virus can infect
ex: myxoma virus normally infects rabbits, but Not humans
-A virus’s tropism is strictly limited. it changes on evolutionary time scale

102
Q

What are the role of HA proteins in influenza A virus? What are the binding sites for influenza hemagglutinin protein?
REVIEW

A

Different HA proteins of influenza A virus bind different forms of sialic acid
binding sites for influenza hemagglutinin protein
-alpha 2, 6 linkages in human influenza
-alpha, 2, 3 linkages in Avian and some swine flu influenza
(changes in hemaglutinin protein recognize different linkages)

103
Q

What occurs in influenza virus tropism?

A

Influenza virus tropism
-Different HA proteins of influenza A virus bind different forms of sialic acid present in different places in each animal’s body

104
Q

Describe the host range seen in influenza virus ? Compare the host range to poliovirus

A

Influenza viruses have a BROAD host range. it can affect multiple species
-Poliovirus by contrast, has a Narrow host range of one species

105
Q

What are the effects of influenza A viruses ? How are the influenza viruses classified? What are their subtypes?

A

Human influenza A viruses cause seasonal epidemics of disease (know as flu season) almost every winter in the US
-Influenza virus are classified by their HA and NA proteins
HA—> Hemmmaglutinin
NA—> neuraminidase
-there are 17 different HA subtypes and 10 different NA subtypes
-Only three known subtypes of Human influenza virus: H1N1, H1N2, H3N2

106
Q

Describe the antigenic shift that occurs in Influenza virus and how this affects human population. Discuss the epidemic of influenza virus that occurred in 2009.

A

Model for antigenic shift in influenza virus
-Influenza A viruses are found in many different animals. sometimes viruses seen in one species can cross over and cause illness in another
(ex: human virus genes and avian virus genes can mix with swine virus genes to make triple reassortment )
-the 8 segments of the -RNA genome allows virus genes to mix and create a new influenza A virus, if viruses from two different species infect the same species.
-This virus will hav a mixture of the H an N antigens. This is known an antigenic shift. Term is applied specifically to influenza
-The 2009 H1N1 influenza virus was a quadruple reassortment virus: genes from flu viruses that circulated in European pigs, asian pigs, avian and human genes
-A new vaccine for flu must be made every year because new variants appear every year.

107
Q

What is the importance of virus surface proteins and its relationship with tissue tropism, host range, and host immune response

A

Importance of virus surface proteins;
-The virus surface proteins determine what Cell surface receptors the virus binds
-Whichever cells express the surface receptors determines TISSUE TROPISM, thus pathology (the tissue virus infects)
-Variation in the cell surface receptors determine the determine the host range, that is what species can be infected.
-Variations in virus surface proteins determine the effectiveness of the host immune response

108
Q

How do viral strains affect immunity? why do viruses mutate?

A

-immunity to one virus strain may confer immunity to another similar strain, but may NoT to a more distally-related virus.
-The virus mutates to vary its surface proteins a little, to evade immune response
-But viruses evolve to use different receptors, very, very slowly only on an evolutionary time scale

109
Q

What are oncogenes? How do they differ from protoncogenes? What kind of viruses are oncogenic for humans ?

A

Oncogene: a gene that has the potential to cause cancer
Most oncogenes begin as protoncogenes
Proto-oncogenes: normal genes that undergo cell division and apoptosis (inhibit apoptosis?)
The genetic material of oncogenic viruses become integrated into the host cell’s DNA
oncogenic viruses of humans are usually DNA viruses

110
Q

What are transformed cells? What are their characteristics?

A

Transformed cells acquire properties distinct from uninfected cells: increased growth, loss of contact inhibition, host-encoded tumor specific transplant antigens and (TSTA) on their cell surface and viral-encoded T-antigens

111
Q

What are tumor specific transplant antigens? What are T-antigens?

A

Tumor specific transplant antigens : (TSTA): a protein that is found only on cancer cells and NOT normal cells; these antigens can help body make an immune response against cancer cells.
T- antigens: protein that is produced by tumorigenic DNA viruses and that will transform normal cells into tumor cells

112
Q

Explain how oncogene can be activated by a retrovirus provirus

A

Activation of an oncogene by a retrovirus provirus
-during evolution, a retrovirus provirus might have integrated next to a host gene involved in cell growth control. if the virus activates that gene, it would become an oncogene capable of driving the formation of cancer
Thus, in the distant past these viruses have “picked up” oncogenes and now carry them other cells to cause cancer.

113
Q

Differentiate between Oncogenic DNA and RNA viruses. What are examples of of each ?

A

Oncogenic DNA viruses: carry genes unrelated to host that inactivate tumor suppressor genes
ex:
-Herpesviridae
-EBV (epstein Barr virus)
-Papovaridiae
-HPV (human papillomavirus)
-Hepadnaviridiae
- HBV (Hepatitis B virus)

Oncogenic RNA viruses; carry “TRUE” oncogenes related to host genes
-several examples in animals, but rare in humans
-Retroviruses
-HTLV-1
-HTLV-2

114
Q

What percent of viruses contribute to human cancers. What are the most common virus-associated cancers? how can they be prevented?

A

Only about 12% of human cancers are attributable to viruses
-The most common virus-associated cancers are:
*Cervical cancer (human papillomavirus, HPV)
-HPV types 16 and 18 cause 70% of cervical cancers
*Liver cancer (hepatitis B virus, Hepatitis C virus)
ALL of these are preventable with VACCINATION
-Girls and boys, age 11-26, should be vaccinated with a vaccine against four HPV serotypes, including HPV16.

115
Q

What are viroids? What are their characteristics?

A

Viroids:
NOT viruses
-**ONLY in Plants **
-short (300- 400 nucleotides)
-naked, infectious RNA
- 3-dimensional structure may protect it form cellular enzyme destruction
-encodes NO proteins and may cause disease by gene silencing
-May have evolved from introns
-replicated continuously by host RNA polymerase by rolling circle replication in the nucleus or chloroplast. They cut into viroid segments by viral RNA (act as ribozyme)

116
Q

What is a virusoid?

A

Virusoid: a viroid enclosed in a protein coat

117
Q

What is the only thing similar in humans to viroids and virusoids?

A

The only thing similar is Hepatitis Delta (NOT virusoid)

118
Q

Distinguish between virus, viroid, virusoid and prions

A

virus- can infect any cell, and have a protein coat called capsid (surrounds genetic material; DNA or RNA)
-Viroid is smaller than virus and does NOT have protein coat (naked single stranded RNA strand) , and only infect plants
virusoid: a viroid (single stranded, RNA) enclosed in protein coat
Prions are smaller than viroids and only composed of protein molecules

119
Q

Describe the Hepatitis D (delta ) virus ? what is another name for it? Why?

A

Hepatitis D (delta) virus is aka Satellite Virus
-Delta is a -RNA circle that makes one protein; the Delta antigen. It makes NO capsid. It requires co-infection with Hepatitis B; it is packaged and carried in the HBV particle
(it can only infect people who are also affected with hepatitis B virus)
(can be seen as virusoid?)

120
Q

What are prions? How do they compare to viruses?

A

Prions: Proteinaceous Infectious particles
-inherited and transmissible by ingestion, transplant, and surgical instruments
-Cause Spongiform encephalopathies: sheep scrapie, Creutzfedldt-Jakob disease, Gerstmann-Strausslaer-Scheinker syndrome, fatal familial insomnia, mad cow disease
Prions resemble viruses epidemiologically, but NOT viruses molecularly
(prions are abnormally mifolded shaped proteins that can transmit their misfolded shape onto normal proteins and cause disease
(prions can withstand autoclaving, and are extremely stable proteins)

121
Q

What are the two forms of prion proteins and how do they differ in structure?

A

Two forms of prion protein:
PrP^C : prion protein –> “cellular” normal (composed of alpha helices)
PrP^Sc : prion protein—> “scrapie” infectious (misfolded form composed of beta sheets)

122
Q

What does PrP^Sc form? How does it affect human body?

A

PrP^Sc forms fibrils: stacks of tightly bound proteins
-The fibrils cause neurological damage in the brain

123
Q

Explain the process of how a protein becomes infectious

A

How a protein can be infectious:
1. PrP^c (normal protein) produced by cells is secreted to the surface
2. PrP^Sc may be acquired or produced by an altered PrP^c gene
3. PrP^Sc reacts with PrP^c on the cell surface
4. PrP^Sc converted the PrP^c into PrP^Sc
5. The new PrP^Sc converts more PrP^c
6. The new PrP^Sc is taken in by endocytosis
7. PrP^Sc accumulates in endosomes
8. Prp^Sc continues to accumulate as the endoscope contents are transferred to the lysosomes. the result is cell death

124
Q

What virus can be seen in family Poxviridae? what class is this part of?

A

Family: poxiviridae
part of class I
SMALLPOX Virus*
(enveloped, large virus)

125
Q

What virus is seen in family Herpesviridae ? what Class?

A

Herpesviridae
-part of Class I
*Varicella Zoster Virus

126
Q

What virus is seen in family Papovaviridae? What class?

A

Papoviridae:
part of Class I
**Human Papilloma Virus (HPV) **

127
Q

Which virus is seen in Family Coronaviridae? What class it part of?

A

Coronaviridae
Class IV
**SARS-COV-2 *(SARS, MERS )
causes disease COVID-19

128
Q

Which virus is seen in family picornaviridae ? What class is apart of?

A

Picornaviridae:
Class IV
POLIOVIRUS

129
Q

What virus is in family Filoviridae ? What class ?

A

Filoviridae
Class V
*Ebola

130
Q

What virus is in family Paramyxoviridae? What class it apart of?

A

Paramyxoviridae
Class V
Measles*

131
Q

What virus is from family Orthomyxoviridae ? What class it apart of?

A

Orthomyxoviridae
Class V
*Influenza Virus

132
Q

What virus is in family Retroviridae? What class it apart of?

A

Retroviridae
Class VI
* HIV**
(causes disease AIDS)

133
Q

Which virus is in family Hepadnaviridae? what class it apart of?

A

Hepadnaviridae
Class VII
* Hepatitis B Virus*

134
Q

What are characteristics that are shared in each class (1-7) for families discussed in previous flashcards?

A

Class I: all are double stranded DNA
Class II: single stranded DNA (for family parvoviridae)
Class III: double stranded RNA (family reoviridae)
Class IV; all are + RNA and have polyhedral virion structure
Class V: all are -RNA, have envelopes and all are helical virion structure
Class VI: are + RNA for (family retroviridae–> HIV)
Class VII: gapped ds DNA (fmily hepadnaviridae—> Heaptits B virus)

Microbiology (18 decks)

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