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BIOL 240 Microbiology > Exam 2 > Flashcards

Exam 2 Flashcards

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Biology 101 flashcards
1
Q

What is a virus?

A

Small sub cellular particles that can replicate only within living host cells. Obligate intracellular parasite

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2
Q

Basic structure of a virus

A

RNA or DNA genome enclosed in a protein shell (capsid) which together are called the nucleocapsid. Some contain viral envelop, a membrane that surrounds the capsid

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3
Q

Who first found a virus?

A

Dimitri ivanovski in tobacco plants

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4
Q

Who found the cause of yellow fever?

A

Walter reed. Transmitted by mosquitos

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5
Q

What is the size of a virus?

A

10-100 nanometers

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6
Q

Range of nucleotides in viruses

A

Few thousand to 200,000

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7
Q

What are the four largest viruses and their size

A

Mimivirus- 400 nm
Megavirus chilensis- genome of 1.2 Mbp
Pandoravirus salinus- 2.47 Mbp
Pithovirus sibericum- 1.5 micrometers long and 500 nm wide

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8
Q

What are capsomeres?

A

Subunits of the capsid that are made of 1 or more polypeptides

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9
Q

Common shapes of the capsid and their structure

A

Helical morphology- capsomeres form a helix and the capsid resembles a hollow tube
Icosahedral morphology- capsomeres form a 20 sided polygon and each capsomeres makes up a face of the icosahedron

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10
Q

What do bacteriophages infect

A

Only bacteria, no plants or animals

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11
Q

What do enveloped bacteria infect

A

Animals, very few for plants or bacteria

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12
Q

Who discovered and coiled the term bacteriophages?

A

Felix d’Herelle

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13
Q

Host, structure, size, genome size, and genetic material of poliovirus

A 
Humans
Non-enveloped, icosahedral
30nm 
7,700bp
ssRNA
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14
Q

Host, structure, size, genome size, and genetic material of tobacco mosaic virus (TMV)

A 
Tobacco and related plants
Non-enveloped, helical
300x18 nm
6,400 bp
ssRNA
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15
Q

Host, structure, size, genome size, and genetic material of T4

A 
E. coli
Non-enveloped 
200x90 nm
170,000bp
dsDNA
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16
Q

Host, structure, size, genome size, and genetic material of variola virus

A 
Humans 
Enveloped, complex
300x250 nm
186,000bp
dsDNA
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17
Q

Host, structure, size, genome size, and genetic material of mimivirus

A 
Amoeba
Enveloped, complex
400nm
1,200,000bp
dsDNA
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18
Q

What is an viral enveloped made of?

A

Plasma membrane

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19
Q

How do viruses bind to a host cell?

A

Through the viral attachment protein on the surface of a virus and the receptor with which the attachment protein interacts. (spike like structure)

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20
Q

3 methods a virus enters a cell

A
  1. virus attaches to cell receptor –> endocytosis is initiated –> endosome forms with the virus inside –> nucleocapsid escapes to the cytoplasm and uncoats to release the genome
  2. virus attaches to the cell receptor –> conformational change in the attachment protein and bound receptor initiates membrane fusion –> viral envelop fuses with plasma membrane –> nucleocapsid enters the cytoplasm and uncoats to release the genome
  3. virus attaches to the cell receptor–> endocytosis is initiated –> endosome forms with virus inside –> low pH of endosome initiates fusion of the viral envelop with the endosome membrane and the nucleocapsids are released
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21
Q

Steps from viral entry into the cell to exiting the cell

A
  1. attaches to the cell
  2. entry and uncoating of the viral genome
  3. gene expression and protein production
  4. genome replication
  5. assembly and exit from the host cell
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22
Q

what are the 3 hypotheses about the origin of the virus?

A
  1. coevolution hypothesis- viruses may have originated prior to or at the same time as the primordial cell and have continued to coevolve with these hosts
  2. regressive hypothesis- viruses may represent a form of “life” that has lost some of its essential features and has become dependant on a host
  3. progressive hypothesis- viruses may have originated when genetic material in a cell gained functions that allowed the DNA or RNA to replicate and be transmitted in a semi-autonomous fashion
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23
Q

Types of bacteriophage replication

A
  1. lytic cycle- virus enters, replicates, and lyse host cell
  2. lysogenic cycle (temperature phage)- phage integrates their genome into host genome (prophage), prophage genome is replicated until stress occurs and then enters the lytic phase
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24
Q

general process of bacteriophage cultivation

A

Inoculate appropriate cells with virus, as the viruses are replicated the bacterial cells die (due to lysing), and the culture starts to turn from turbid to clear as the cells die. Afterwards the culture can be filtered to get rid of cell remains

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25
Q

what is plaque?

A

when host cells and viruses are plated on agar, small circles called plaque appear. these circles are dead cells

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26
Q

how are viruses purified?

A
  1. low speed centrifugation gets rid of whole and broken host cells
  2. transfer the supernatant (which contains the virus) into a new tube to be ultracentrifuged (differential centrifugation)
  3. viruses are collected at the bottom in a concentrated state
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27
Q

explain gradient centrifugation

A

it depends on the different densities of viral components. first a tube is filled with layers of decreasing concentration of sucrose, then viruses are added on top, this is centrifuged and the cell debris and intact viruses should be in different densities

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28
Q

what are the 4 types of viral quantification?

A
  1. direct count
  2. hemagglutination assay
  3. plaque assay
  4. endpoint assay
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29
Q

how does direct count of viruses work?

A

electron microscope is used to look at a known concentration and then scaled up to determine titer. this method doesn’t differentiate between infections and non-infectious

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30
Q

how does hemagglutination work?

A

some viruses stick to red blood cells and forms a gel mat. button shape means fewer viral particles are present. shield means theres a high number of viral particles. not all viruses do this and it doesn’t differentiate between viable/non-viable and doesn’t give an exact number

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31
Q

how does a plaque assay work?

A

virus is placed on target cell, plaques are counted and scaled to get original titer. can be used or phage and plant viruses

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32
Q

how does an endpoint assay work?

A
  • tissue culture infectious dose 50 (TCID50): amount of virus needed to produce a cytopathic effect in 50% of cultured cells
  • lethan dose 50 (LD50): amount of virus needed to kill 50% of test animal subjects
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33
Q

examples of how viruses were named

A
  • letter number combo
  • organism they infect
  • location discovered
  • appearance of virus
  • disease caused by virus
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34
Q

what is ICTV?

A

international committee on taxonomy of viruses. classify viruses in order, family, subfamily, genus, and species based on morphology, genome structure, biological features, disease caused, envelope, and genomes

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35
Q

what is the Baltimore classification system?

A

based on the mRNA production methods and separated into 7 classes:

  1. dsDNA genome
  2. ssDNA genome
  3. dsRNA genome
  4. ssRNA genome, positive sense
  5. ssRNA genome, negative sense
  6. ssRNA genome, DNA intermediate
  7. dsDNA genome, RNA intermediate
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36
Q

how are viruses identified?

A

first through electron microscopy, then nucleic acid analysis (PCR and reverse-transcriptase PCR)

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37
Q

name two virus like particles

A

viroids and prions

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38
Q

describe viroids

A
  • consist of only RNA
  • very small (less than 400 nucleotides)
  • lots of internal complementation (bases link together to form loops)
  • resistant to ribonuclease
  • only causes disease in plants so far
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39
Q

describe prions

A
  • proteinaceous infectious particles
  • no nucleic acids, no genes, just protein
  • responsible for transmissible spongiform encephalopathies (mad cow)
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40
Q

prion replication

A
  • still unclear

- idea: revolves around conversion of protein conformations from normal to abnormal (fibrils)

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41
Q

explain how CRISPR works

A
  1. transcription and translation of cas genes forming cas proteins
  2. transcription of CRISPR locus, forming the pre-crRNA transcript
  3. cas proteins cleave the pre-crRNA forming mature crRNA subunits
  4. other cas proteins interact with mature crRNA subunits, forming CRISPR-cas surveillance complexes (clusters of regularly interspaced short palindromic repeats)
  5. CRISPR-cas surveillance complex surveys calls for complementary phage DNA. once detected, the complementary sequences are aligned and the phage DNA is targeted for destruction
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42
Q

what are the 2 types of metabolism

A
  • catabolism (releases energy)

- anabolism (consumes energy)

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43
Q

what are the nutritional requirements of cells

A
  • macronutrients required by all cells: C,N,P,S,O

- micronutrients required by some cells: Fe, Cu, Na, Mg, Mn, and others

44
Q

what are the fundamentals of nutrition?

A
  1. energy source- photo (photosynthetic) or chemo (organic or inorganic)
  2. electrons- organo or litho
  3. carbon source- heterotroph (fixed organic) or autotroph (CO2)
45
Q

types of aerobic growth

A

obligate aerobes- require 02

microaerophiles- grow best in low levels of o2

46
Q

types of anaerobic growth

A

aerotolerant anaerobes- aren’t harmed by o2 but dont use it
obligate anaerobes- cannot grow when o2 is present
faculative anaerobes- can grow in the absence od o2 but grow better when it is present

47
Q

toxic oxygen species

A
  1. siglet oxygen- comes from photochemical reaction; product of peroxidase enzymes, defence is antioxidant such as caroenoid pigments
  2. superoxide anion- comes from one electron reduction of molecular oxygen, defence is superoxide dismutaase or superoxide reductase enzymes
  3. hydroxyl radical- comes from reduction of o2 during respiration, defence is antioxidant such as glutathione
  4. hydrogen peroxide- comes from reduction reactions, defence is catalase and peroxide enzymes
48
Q

how does temperature affect cells?

A

affects macromolecular structure, membrane fluidity, an enzyme function

49
Q

what is the temperature range for eukarya?

A

Psychrophiles (-15°-10), mesophiles (10-55), some thermophiles (55-~70)

50
Q

what is the temperature range for archaea?

A

psychrophiles, mesophiles, thermophiles, hyperthermophiles (-15-130+)

51
Q

what is the temperature range for bacteria

A

psychrophiles, mesophiles, thermophiles and some hyperthermophiles (~100)

52
Q

how to psychrophiles live?

A

higher proportion of unsaturated fatty acids in membrane phospholipids. enzymes denature at higher temperatures)

53
Q

what is psychrotolerance?

A

able to grow ~0-4 but optimal at 20-40

54
Q

what is selective media?

A

allows for isolation of microbes with specific properties

55
Q

what is differential media?

A

allows certain microbes to be recognized based on visual reactions in the medium

56
Q

what is enriched media?

A

used to increase the population of microbes with a specific property

57
Q

3 methods to obtain a pure culture

A
  1. streak plate method
  2. spread plate method
  3. pour plate method
58
Q

3 methods to quantify microbes

A
  1. direct count (known volume counted on microscope)
  2. viable cell count (serial dilutions and CFU counted)
  3. turbidity measurements (spectrophotometer)
59
Q

4 phases of mirobe’s growth curve

A
  1. lag phase- preparing for stead growth
  2. exponential phase- replicating at a constant and steady exponential rate
  3. stationary phase- replication has halted or equal to the death rate
  4. death phase- nutrients are depleted and waste levels are high, cells die at steady exponential rate
60
Q

what is continuous culture?

A

used to keep microbes in exponential growth in a limited but continuous flow of nutrients

61
Q

calculations from a growth curve

A

generation time- time to double the population in the exponential phase
growth rate- number of generations/unit of time (inverse of generation time)
growth yield- maximum population density and/or amount of cellular material produced by the culture

62
Q

what is filtration and possible problems that can result

A

filtration os the physical removal of microbes (0.2-0.45 micrometer pore size). problems can be that large particles clog the filter, viscous fluids don’t filter well, and unltafiltration (for viruses) require high pressure

63
Q

what is the common pore size for sterilization

A

0.2 micrometers and it is ideal when the material is heat or radiation sensitive

64
Q

what is varying pore size used for

A

to separate or distinguish organisms and to retrieve small cells from a mixture of large cells

65
Q

what is a depth filter

A

randomly overlapping fibers and is used as a “pre-filter”

66
Q

what is a conventional membrane filter?

A

polymer filter (0.45-0.22 micrometers): cellulose acetate or cellulose nitrate and the pore diameter is variable during production

67
Q

what are nucleopore filters?

A

thin polycarbonate film (~10 micrometers thick): radiation damage, cracks enlarged by chemical etching and has a consistent pore size. it is useful for microscopy as the filtered material is on a single surface plane

68
Q

describe what temperature manipulation does and some problems associated with it

A

it denatures proteins and nucleic acids and 100° kills most microbes while an autoclave adds pressure so that the liquid doesn’t evaporate. some problems are that it doesn’t kill hyperthermophiles, endospores can be created, and some materials can’t be heated

69
Q

describe an autoclave

A

creates steam under pressure (121°C and 15psi). efficiency is determined by destruction of endospores and vegetative cells

70
Q

what does pasteurization do?

A
  • destroys pathogens
  • kills 90-99% of other microbes but does not sterilize
  • increases shelf life
  • keeps flavour
71
Q

3 different pasteurization methods

A
  • High temp short time (HTST): 72°C for 15 seconds
  • ultrahigh temp (UHT): 135°C for less than 1 second
  • extended shelf life: filtration hen lower temp treatment
72
Q

explain freezing

A
  • damages cells by forming ice crystals
  • stops biochemical reactions
  • long-term preservation
73
Q

what is bacteriostatic?

A

growth inhibitory

74
Q

what is bacteriocidal?

A

kills cells

75
Q

what is bacteriolyic?

A

causes cell lysis

76
Q

disinfectant vs antiseptic

A

disinfectant- used on non-living surfaces to kill potentially infectious microbes
antiseptic- used on living tissue to kill potentially infectious microbes (usually topical)

77
Q

5 types of disinfectants/antiseptics

A
  1. alcohols: ethanol is an example and used in lab setting and hand sanitizer. targets membranes
  2. phenolic compounds: triclosan is an example and is added to cosmetics + soap. targets membranes
  3. oxidizing agents: sodium hypochlorite is an example and is added to pools
  4. benzalkonium chlorate: major ingredient in Lysol and targets membranes
  5. Glutaraldehyde: used to prepare biological specimens. targets crosslink proteins
78
Q

what are antimicrobics/antibiotics and how do they work?

A

antibiotics are antimicrobal agents produced by microbes. static, cidal, or lytic. work by disrupting essential functions that are necessary for growth and survival.

79
Q

who found the first antibiotic?

A

alexander fleming

80
Q

how do we measure effectiveness of killing microbes?

A

decimal reduction time: ime required to kill 90% of the target organism under specific conditions

81
Q

give example of broad-spectrum and narrow spectrum antibiotics and what they target

A

Broad-spectrum: -tetracyline, targets inhibition of protein synthesis
narrow-spectrum: -polymyxin B, disruption of cell outer membrane
-penecillin, inhibition of cell wall synthesis

82
Q

generally describe proteobacteria

A
  • very encountered bacteria
  • related to mitochondria
  • metabolically diverse (chemolithotrophs, chemoorganotrophs, phototrophs)
  • morphologically diverse
  • 5 phylogenic groups (alphs, beta, gamma, delta, epsilon)
83
Q

describe proteobacteria tree

A
  • all descend from 1 ancestor
  • epislon and delta lost photosynthetic ability and are chemoorganotrophs
  • alpha, beta, and gamma are from one common phototroph ancestor and are both chemolitho and chemoorgano
84
Q

what is anoxygenic photosynthesis?

A
  • photosynthesis is inhibited by o2

- colours determined by bacteriochlorophylls and carotenoids

85
Q

what are purple sulfur bacterial blooms?

A
  • photoautotrophs of gamma proteobacteria
  • oxidize H2S to S0 during photosynthetic CO2 reduction in anoxic lake water
  • stored in the periplasm and disappears when oxidized to sulfate
86
Q

what are methylotrophs?

A

-oxidize inorganic carbon compounds (1 carbon)

87
Q

what are mathanotrophs?

A
  • methylotrophs capable of oxidizing ethane into methanol
  • intracytoplasmic membranes
  • obligate c1 users
  • obligate aerobes, often microerophilic
  • found in soil and water and cattle rumen and swamps
88
Q

what are nitrifiers?

A

-use reduced nitrogen compounds as energy source (chemolithoautotrophs)

89
Q

subdivisions of nitrifiers

A
  1. nitrosocossus and nitrosomonas: ammonia oxidizer and ammonia monooxygenase
  2. nitrobacter and nitrospira: nitrite oxidizers and nitrite oxidase
90
Q

what are pseudomonas?

A
  • heterogenous group with evolving taxonomy
  • aerobic chemoorganoheterotrophs
  • nutritionally and ecologically versatile
  • some are fluorescent
91
Q

describe the metabolism, motility, cell wall, nucleus, mitochondria, and chloroplasts of fungi

A

heterotrophic, usually non-motile, chitin cell wall, nucleus and mitochondria present

92
Q

describe the metabolism, motility, cell wall, nucleus, mitochondria, and chloroplasts of protozoa

A

heterotrophic, cilia, flagella or pseudopods, no cell wall, nucleus and mitochondria present

93
Q

describe the metabolism, motility, cell wall, nucleus, mitochondria, and chloroplasts of slime molds

A

heterotrophic, pseudopods, no cell wall, nucleus and mitochondria present

94
Q

describe the metabolism, motility, cell wall, nucleus, mitochondria, and chloroplasts of algae

A

phototrophic, non-motile or flagella, cellulose cell wall, nucleus, mitochondria, and chloroplasts present

95
Q

what are saccharomyces ceerevisiae?

A

fungi used to make bread, beer, wine (yeast)

96
Q

name the 5 fungal categories

A
  1. chytridiomycota: early branching water molds
  2. zygomycota: bread mold (branch with black dot)
  3. glomeromycota: mycorrhizal fungi; important for plants
  4. ascomycota: spore shooters; cup/sac fungi, yeast
  5. basidiomycota: spore droppers, club fungi, typical mushrooom
97
Q

what are slime molds and 2 examples

A
  • individual cells that communicate and come together
  • Dictyostelium discodeum: model for studying ecology and cell-cell communication
  • physarum: fuses many cells into a continuous giant cell
98
Q

example of a algae species

A

chlamydomonas: has two flagella which are good for studying

99
Q

describe the saccharomyes life cycle (fungus)

A
  • can undergo meiosis to form an ascus
  • haploid mating types can fuse to reproduce sexually or be maintained asexually by mitosis
  • not limited to ascus form
  • budding off of smaller cells can occur or fission of identically sized cells
100
Q

describe the chlamydomonas life cycle (algae)

A
  • maintains a motile haploid state

- haploids can differentiate and fuse into diploids in bad conditions (spore formation)

101
Q

describe the dictyostelium life cycle

A
  • exists in a haploid unicellular form unless bad conditions which turns into a “slug” with a stalk and a fruiting body
  • spores form in the fruiting body
  • haploid cells can fuse into diploid macrocyst form
  • macrocyst form undergoes meiosis to generate more haploid cells
102
Q

evidence of the endosymbiotic theory

A
  • mitochondria and chloroplasts resemble bacteria in size and shape
  • double membranes
  • cell division with FtsZ
  • each has its own DNA and rRNA
  • circular chromosome
103
Q

what is rhytisma?

A

an ascomycete fungus that infects sycamores and maples (tar spots)

104
Q

what is phytophthora infestans?

A

causes potato blight

105
Q

what are cordyceps?

A

fungus that grows out of insects

106
Q

what are some benefits of eukaryal microbes?

A
  • primary producers provide energy (produce oxygen)
  • biodegraders recycle nutrients
  • come can degrade cellulose which recycles plant matter much better than animals

BIOL 240 Microbiology (3 decks)

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