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Basic Virology > Unit 1 > Flashcards

Unit 1 Flashcards

Impact of Viruses, Origins, Applications, Structure and Taxonomy (48 cards)

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1
Q

What is the political impact of viruses on mankind?

A

Air travel was restricted (HIV), mandatory inoculations during wars (Pox), intellectual property, birth rights, biochemical warfare

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2
Q

What is the economical impact of viruses on mankind?

A

Disease destroyed crops and animals thus destroying farmer lives, business closed due to fear and no manpower

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3
Q

What is the social impact of viruses on mankind?

A

HIV+ patients and homosexuals were treated differently, charities were created (March of Dimes)

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4
Q

What is the technological impact of viruses on mankind?

A

Improvements to research were made, heightened medical tools were made (Chamberland filter, EM)

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5
Q

What is a virus?

A

Latin: slimy liquid poison
Today: an extremely small obligate intracellular parasite

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6
Q

What are the two components of a virus?

A

proteins + nucleic acid

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7
Q

What tool was used to discover most viruses?

A

Chamberland filter

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8
Q

How was the first plant virus found?

A

Tobacco Mosaic Disease - Martinus Beijeirinick

A chamberland filter was used and it was discovered that the disease was filter passing –> soluble toxin

But when the experiment was repeated extensively, it was proven that the disease was able to multiply –> contagious living fluid

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9
Q

How was the first animal virus found?

A

Foot and Mouth Disease - Loeffler Frosch

A Chamberland filter was used and determined that FMD was filter passing

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10
Q

How was the first human virus found?

A

Yellow Fever - Walter Reed

Blood was extracted to obtain the serum that was passed through a Chamberland filter which was also filter passing. They injected the filtrate into a volunteer who contracted the disease.

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11
Q

How was the first bacterial virus found?

A

It was filtered goddammit - Frederick Twork

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12
Q

What defines life?

A
  1. growth/reproduction
  2. metabolism
  3. homeostasis
  4. evolution
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13
Q

What do viruses do not have in their genes?

A
  1. dna AND rna
  2. ribosomes
  3. cell membranes
  4. energy production
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14
Q

What are the virus origin hypotheses?

A
  1. The Panspermia Hypothesis
  2. The Escape Hypothesis
  3. The Reduction Hypothesis
  4. The Virus First Hypothesis (vers. 1)
  5. The Virst First Hypothesis (vers. 2)
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15
Q

What is the Panspermia Hypothesis?

A

“viruses rained down from space”

There is no evidence to support/refute this theory.

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16
Q

What is the Escape Hypothesis?

A

“viruses evolved from mobile genetic elements within cells that moved from within the genome of the cell and escaping to another cell”

Evidence?
45% of the human genome are transposable elements.
BUT there are few retroviruses like HIV. The rest are something completely different

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17
Q

What is a transposon (transposable element)?

A

A transposable element is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell’s genetic identity and genome size.

Two types:
1. DNA transposon: cut and paste of DNA segment with no RNA intermediates
2. Retrotransposon: copy and paste of DNA–>RNA–>DNA. There are long terminal repeat retrotransposons and non-ltr-retrotransposons.
HIV Genome is a homolog for ltrs in humans.

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18
Q

What is the Reduction Hypothesis?

A

“Viruses are remnants of cells that have progressively lost function over time to become obligate intracellular parasites.”

Evidence?
Mimivirus have 21% homologs to euk/prokaryotes and can also be infected by its own virus and contains mobile transpovirons. BUT: There are too many ORFans within their genome (no homologs)

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19
Q

What is the first version of the Virus First Hypothesis?

A

“All viruses arose from a LUCA before cells existed.”

Can be done through comparative genomics. BUT: There was no one LUCA for all viruses. There were many starting points.

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20
Q

What are the Classes of Viral Genes?

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A

I. Genes with closely related homologs in cells but detected in a narrow group of viruses.
II. Genes conserved within a major group of viruses that have relatively distant cellular homologs.
III. ORFans (viral genes with no known cellular homologs and no known function that are only detectable in closely related viruses)
IV. Virus-Specific Genes (Viral genes that are conserved in a broad group of viruses but have no detectable homolog)
V. Virus Hallmark Genes (Genes shared by many diverse groups of viruses with only distant homologs in cellular organisms)

21
Q

What class of viral gene would you use to find a LUCA?

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A

V. Virus Hallmark Genes (Genes shared by many diverse groups of viruses with only distant homologs in cellular organisms)

You need to use hallmark genes because then all viruses would have shared one distinct gene and since cells would have branched from viruses, then the cells would have similarities to these genes as well.

22
Q

What is the second version of the Virus First Hypothesis?

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A

“Viruses originated in a pre-cellular RNA WORLD from an assembly of self replicating elements present in IRON SULFUR RICH inorganic compartments in ancient hydrothermal vents.”

23
Q

What is the Viral Shunt Hypothesis?

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A

Nutrients from the lysis of microbes by bacteriophages actually provide food/fuel for the rest of the community.

24
Q

What is the viral shunt hypothesis as it applies to the ocean?

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A

Kill the Winner Hypothesis

Under limited resources, bacteriophages kill the dominant species so microbial diversity is in equilibrium.

25
What is the viral shunt hypothesis as it applies to all ecosystems?
Piggyback the Winner Hypothesis Bacteriophage lysogeny prevails when microbial abundance and grow rates are highest and this confers a competitive edge to microbes in maintaining their ecological niche because of superinfection immunity.
26
What is the environment of the gut in a 0-3 yr old child?
Kill the Winner Dynamics predominate with lytic phage killing abundant host cells to create a diverse microbial community most of which become PROPHAGES
27
What is the environment of the gut in an adult?
Piggy Back the Winner This is when equilibrium has been achieved and prophages will live across the gut until the environment becomes unfavorable.
28
What is BAM?
Bacteriophage Adherence to host Mucus An innate form of protection where the bacteriophages are in the lysogenic cycle within prophages that inherently protect us in our mucus from pathogens.
29
Explain the mutualism between the parasitoid wasps and a virus.
The virus acts as a vector to deliver wasp genes to the eggs that the wasps inject into an unwilling surrogate thus accommodating to the immune response that the surrogate will have to attack the eggs. (Endogenous Viral Elements).
30
Explain the mutualism between the plants and a virus.
Enhanced survival techniques against harsh environment because the virus wants the host to live so that it also has an environment to live in.
31
Explain the mutualism between our placenta and a virus.
The placenta is made from mushed together cells called synctiotrophoblasts. This process of mushing together is caused by a retrovirus that lives within us and has affected all placental mammals.
32
How are viruses applicable in molecular biology?
1. Discovery that DNA hold the genetic material. 2. Discovery of the first bacterial virus 3. Discovery of Reverse Transcriptase 4. Discovery of enhancers, promoters, and vectors 5. Discovery of introns and internal ribosome binding sites 6. Tracking of human immigration
33
What are ex vivo treatments?
A process where you grow gene edited cells outside of the body and replaced through injection. Use of a retrovirus would integrate the desired gene within the cells.
34
What can bacteriophages be used for today?
Biosorbent: where the phages would be upside down to see whether they can attach to a specific entity. Biosensors: where phages would be tagged by a color/luminescent and attach to antigen that the proteins on the virus are compatible too.
35
What are the different types of genomes a virus can have?
DNA: linear (ds/ss) and circular (ds/ss) RNA: linear (+ss/-ss/ds) and circular (+ss/-ss)
36
What is the difference between + sense and - sense?
+ sense is ribosome ready as it looks exactly like mRNA and can be translate directly. - sense must be transcribed to a + sense version in order for the strand to be translated to protein.
37
What is a monopartite genome as opposed to a multipartite genome?
Monopartite: non segmented gene where there is only one gene for the virus. Multipartite: segmented genes where there are many genes for the entire genome of the virus.
38
What kind of modifications (species of DNA/RNA) are there?
dsDNA: normal, proteins at both ends (5') ssDNA: protein at one end (5') ssRNA: normal, protein at one end, protein and poly A tail at either end, a methylated cap (5') and a methylated cap with a poly a tail (3') at either end. dsRNA: normal, 2 proteins at either end, and a methylated cap at the 5' end.
39
What kind of genes do viruses have?
1. genome replication 2. genome packing/assembly 3. regulation of infectious cycle 4. modulation of host defenses 5. cell to cell spread
40
What is the capsid for?
1. protection of the genome 2. recognition of viral nucleic acids for packing 3. delivery of the genome into the host
41
Genomes encode what 2 types of protein?
Nonstructural and structural
42
What are the two types of symmetry for capsids?
Helical: naked or enveloped Icosahedral: basically a d20. Must keep the 5:3:2 fold symmetry with 60 identical but asymmetrical subunits at minimum.
43
Holmes Classification System
Francis Holmes: Phagineae: bacteria infecting Phytophagineae: plant infecting Zoophagineae: animal infecting
44
LHT Classification System
Lwoff, Horne and Tournier Based on the structure of the virion 1. type of nucleic acid 2. type of capsid symmetry 3. presence of envelope 4. diameter of capsid and # of capsomers.
45
Baltimore Classification System
David Baltimore Based on genomic classes Class One: dsDNA->mRNA Class Two: ssDNA->dsDNA intermediate->mRNA Class Three: dsRNA->mRNA Class Four: +ssRNA->mRNA Class Five: -ssRNA->mRNA Class Six: +ssRNA->dsDNA intermediate ->mRNA Class Seven: gapped dsDNA->repaired dsDNA ->mRNA->proteins and gapped DNA
46
What are the traits we have in taxonomy now?
Biological Properties 1. Pathogenicity 2. Host Range 3. Epidemiology Sequence Relationships 1. Divergence 2. Phylogeny
47
What is the proposed taxonomy for the future?
Can be used for viral genome and metagenomic sequence data. Based on: 1. Phenotypes inferred from genome analysis 2. Sequence relatedness inferred from phylogeny, homology detection and divergence metrics Biological data not essential.
48
What are metagenomics?
the study of nucleic acids obtained directly from environmental samples (no biological or experimental characterization)

Basic Virology (4 decks)

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