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MicroEco > Lecture 10 - Virus Ecology I > Flashcards

Lecture 10 - Virus Ecology I Flashcards

1
Q

What are 4 statuses of viruses that are being debated about?

A

living or not, place on tree of life, how long they’ve existed, before LUCA?

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2
Q

Who discovered reverse transcriptase?

A

David Baltimore

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3
Q

What is one significant role of viruses that have a huge effect on all cellular organisms?

A

play a huge role in structuring microbial communities and populations

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4
Q

What are Pandora viruses?

A

giant viruses almost as large as cells (physically and genome-wise

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5
Q

What is the greatest source of biodiversity and most abundant biological entity on the planet?

A

viruses

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6
Q

What are 3 reasons why viruses are important?

A

helps in understanding an environment (microbiome) by looking at the virome; they are key components in evolution, important in medicine where vaccines have been made to different strains

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7
Q

Explain the theory that the eukaryotic nucleus comes from viruses

A

via “endosymbiosis” where an RNA cell during the RNA world gets infected by engulfing a primitive DNA and overtime, genetic info moved into the “nucleus”

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8
Q

What are 6 cellular functions people think that viral genes serve as a source for?

A

eukaryotic nucleus, transcription/translation machinery of mitochondrial genomes, proteins to form the immune system, embryo development, mammalian placenta formation, brain physiology

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9
Q

Explain the theory that viral genes provides proteins to form the immune system

A

viral proteins helps dampen the mother’s immune response during pregnancy as the fetus is seen as a foreign mass of cells which the immune system would normally attack

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10
Q

Explain the theory of during embryo development and formation of the placenta that viral genes are expressed

A

people have found that the “junk DNA” in our genome are actually viral DNA that is expressed during the formation of the placenta and embryonic development

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11
Q

What is the simplest definition of a virus?

A

molecular intracellular parasite

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12
Q

What are 3 ways that viral genomes are diverse?

A

DNA/RNA; single or double stranded; (+) or (–) sense

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13
Q

What does a virus consist of?

A

nucleic acid that is surrounded by a protein coat (some with internal or external membranes)

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14
Q

In what other 2 ways (other then genomically) are viruses diverse?

A

different symmetries and morphologies

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15
Q

What is one big way that viruses are different than cellular life?

A

all viruses are dependent on cellular life for translation

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16
Q

What are the 2 ways how viruses are classified?

A

Baltimore and Hierarchal

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17
Q

Which classification system is more commonly used?

A

Baltimore

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18
Q

What are the 4 steps of the hierarchal classification system?

A

RNA or DNA | symmetry of capsid | presence or absence of envelope | architecture of genome: double-stranded or (+)/(–) single-stranded

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19
Q

What is the Baltimore classification scheme based off of?

A

how the virus makes mRNA

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20
Q

How many groups are there in the Baltimore classification scheme?

A

7

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21
Q

What are the 2 different types of viral replication cycles?

A

Lytic and Lysogenic (temperate)

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22
Q

What is the lytic cycle?

A

leads to cell lysis = release of progeny virions

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23
Q

What is the lysogenic cycle?

A

virus integrates its genome into host cell genome = whenever cell replicates, the viral genome gets replicated too and passed down to daughter cells

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24
Q

If the cell becomes stressed and launches a stress response, how will the lysogenic virus exit the cell?

A

virus is able to cut itself out and revert back to a lytic-cycle lifestyle

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25
Q

What is the effect of lytic viruses on the environment?

A

they will kill host after infection and can structure a population over a short period of time

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26
Q

What is the effect of lysogenic viruses on the environment?

A

has an effect on shaping the host population for a longer period of time since it will be maintained within the cell

27
Q

In which type of environment are lysogenic viruses more prevalent in? (soil or aquatic)

A

soil

28
Q

In which type of environment are lytic viruses more prevalent in? (soil or aquatic)

A

aquatic

29
Q

How can the number of lytic viruses increase in any type of environment, soil and/or aquatic, and why?

A

if you add nutrients, lytic viruses will increase because if the cells are healthier = there will be more cells the virus can infect

30
Q

When looking at the Virus-to-Bacteria Ratio, why is the viral population higher in soil than in water?

A

there are other organisms present in soil (such as fungi, plants, etc) therefore the soil is more rich in the amount of cells a virus can infect

31
Q

Why is the Virus-to-Bacteria Ratio low in acidic environments?

A

low diversity

32
Q

What type of information could you learn about the bacterial population by knowing the Virus-to-Bacteria ratio of a population?

A

about the diversity of that environment

33
Q

What are plaque assays?

A

measures the quantity of infectious lytic viruses

34
Q

What does one plaque on the plaque assay plate represent?

A

one virus

35
Q

What are the 2 limitations of the plaque assay?

A

doesn’t measure lysogenic viruses and the other host cells in an environment

36
Q

What is a limitation of microscopy when studying viruses?

A

different results occur depending on who is observing

37
Q

What are the 2 common microscopy methods used to study viruses?

A

TEM (observe morphology) and epifluorescence

38
Q

What are the pros of culture Dependent viruses?

A

–

39
Q

What are the cons of culture Dependent viruses?

A

–

40
Q

What are the pros of culture INdependent viruses?

A

–

41
Q

What are the cons of culture INdependent viruses?

A

–

42
Q

What is a limitation with the use of metagenomics when studying viruses?

A

any viruses that are within a host cell will not be part of the viral metagenome but instead will be part of host metagenome

43
Q

What are the pros when it comes to sequencing?

A

quick, easy, and cheap (low-key)

44
Q

What are the cons when it comes to sequencing?

A

analyzing data is tedious and labor intensive

45
Q

What are the 4 ways that metagenomes are useful?

A

can discover new viruses, see the change in population over time, see the diversity of viruses and detect virus hallmark genes

46
Q

What is an example of a virus hallmark gene?

A

structural proteins

47
Q

Why is the role viruses in evolution more controversial than cell evolution?

A

viruses don’t have a fossil record (nothing we can use to date them back to) and they don’t have a universal genome

48
Q

What are the 3 competing concepts on the origin of viruses?

A

Escaped Genes model; Cell Degeneration model; Primordial Genes model

49
Q

What is the concept of the Escaped Genes model of virus origin?

A

viruses originated from cellular components (ie: RNA and other nucleic acid products) that escaped cellular control and hijacked the appropriate genes

50
Q

Is the Escaped Genes model a progressive or regressive theory? Why?

A

Progressive because they progressed from a gene into a virus

51
Q

What is the weakness of the Escaped Genes model?

A

where did the genes that encode for RNA dependent polymerases come from since no other cell encodes for them | no genetic similarity between cells and viruses, most viral genes don’t have a cellular counterpart

52
Q

What is the concept of the Cell Degeneration model?

A

viruses originated from cells then over time degenerated into viruses because it may have lost the ability to make proteins by itself | probably underwent a parasitic stage at one point

53
Q

Is the Cell Degeneration model a progressive or regressive theory?

A

regressive theory

54
Q

What is a weakness of the Cell Degeneration model?

A

inconsistent with genomic studies such as how can the prominence of genes without cellular counterparts exist?

55
Q

Why do some researchers hypothesize that viruses existed before LUCA in efforts to explain why the commonality between viruses and cells are not seen today?

A

if they existed prior or during LUCA = gave viruses enough time to evolve to be very different

56
Q

What is a strength of both the Escaped Genes model and Cell Degeneration model?

A

both are coming from cells and we know that viruses are dependent on cells

57
Q

What is a weakness of both the Escaped Genes model and the Cell Degeneration model?

A

lack of genetic similarity between viruses and cells

58
Q

What is the concept of the Primordial Genes model?

A

viruses originated from pre-cellular life (a pool of genetic elements) and invaded a new life form (cells) | viruses and LUCA evolved together during RNA world

59
Q

What is the weakness of the Primordial Genes model?

A

people have a hard time justifying the theory because viruses are dependent on cells = how can they precede cells if they’re dependent on them

60
Q

What is the strength of the Primordial Genes model?

A

DNA viruses do infect all 3 domains of life = can infer that they existed prior to the LUCA split || reverse transcriptase was used to

61
Q

Which model do biologists most resonate with and believe? Why?

A

Primordial Genes model because it would explain RNA viruses

62
Q

What are the sequence of events with the Primordial Genes model?

A

primordial genetic elements = engulfed by vesicle &raquo_space; start making proteins &raquo_space; reverse transcriptase RNA to DNA &raquo_space; stage of “giant viruses” &raquo_space; gives rise to bacteria, eukarya and archaea later down the line

63
Q

What is a viroid?

A

small pieces of RNA without protein coat or envelope

64
Q

What were the 2 primordial genetic elements?

A

viroids and ribozymes

MicroEco (10 decks)

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