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BIOL 322 > Topic 2: Microbial Diversity > Flashcards

Topic 2: Microbial Diversity Flashcards

1
Q

What are the survival strategies of microbes

A
  1. repair mechanisms
  2. metabolic flexibility
  3. heat/radioactivity resistance
  4. sleeping mode: reduces metabolic activity/energy use
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2
Q

define microbial DIVERSITY (3 factors)

A

relies on
1. species type
2. the number of species
3. the ecological diversity of species

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3
Q

what is species richness

A

number of variation among species

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4
Q

what do microorganisms comprise of

A

prokaryotes, viruses, viroids, filamentous fungus, yeast, microalgae, and protozoans

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5
Q

what is virus vs viroids

A

virus: has nucleic acids, RNA, and protein coat
infects all orgs.

Viroids: low molec RNA, no protein coat
infects only plants

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6
Q

what do soil bacteria play a role in

A

biogeochemical cycles (pathway of chemical cycling/nutrient cycling)

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7
Q

why is our diversity of soil microbes limited

A

human inability to study soil microbes
- cannot be cultured in standard lab (only 1% can be cultured and we cant assume it represent entire soil population)

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8
Q

what are thermophiles

A

thrive in extreme temp

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9
Q

what are psychrophiles

A

thrive in extreme temp

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10
Q

what are alkaliphiles/acidophiles

A

thrive in extreme pH ranges

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11
Q

what are barophiles

A

thrive in extreme pressures

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12
Q

what are halophiles, what is their gram, can they form spores, what type of photosynthesis do they use

A

thrive in high salinity
many shapes, gm-, non spore forming, obligate aerobes

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13
Q

what are radiophiles

A

thrive in high radiation

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14
Q

what are the survival mechanisms of thermophiles

A
  • change composition of amino acids/ membranes
  • add repair enzymes for heat damage
  • development of cell wall coatings
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15
Q

what are biochemical methods that assess microbial functional diversity

A
  1. plate counting
  2. Community Physiological profiling (CLPP)
  3. Fatty acid methyl ester analysis (FAME)
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16
Q

what is plate counting and whatre the disadvantages

A

plate counts the number of growing colonies from a culture

disadvantages:
- unculturable microbes arent present
- biased to fats growing microbes/ fungal species

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17
Q

what is CLPP and what are the disadvantages

A

tells morphology and gm+/gm- of microbe

disadvantages:
- represents only culturable fraction
- biased to fast growing organisms
- sensitive to inoculum density

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18
Q

what is FAME and what are its disadvantage

A

Morphology or how many cells are inside// also protein functions

Determined based off fatty acid grouping
sensitive to external environment

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19
Q

what is the extramural layer

A

slime layer (protect from loss of water/nutrients) and capsule (dense) which are external to bacterial cell wall

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20
Q

what are surface appendages

A

consists of flagella and pilli (project from cell surface)
important for motility/attachment

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21
Q

what is the cell envelope

A

combination of cell wall, inner cell membrane, (and outer wall only in gm-)

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22
Q

what is cytoplasmic inclusion

A

includes nucleoid, ribosomes, mesosomes, granules and plasmids of bacteria

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23
Q

why is glycocalyx on surface coating of bacterial cells

A

plays role in pathogenic resistance/ adhesion factor

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24
Q

what is fimbriae of bacterial cells

A

hair like structures on bacteria that partake in adhesion to other cells and surfaces

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25
Q

what are endospores

A

structure that allows bacterium to survive in unfavorable condition by reducing unessential metabolic activity but preserving just enough so the cell can grow and reproduce

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26
Q

what color do endospores stain

A

green

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27
Q

what does cryptobiotic mean in reference to endospores

A

endospores exhibit no signs of life
this makes them resistance to unfavorable changes in environment

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28
Q

do all bacteria exhibit endospore ability

A

no

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29
Q

what triggers spore formation

A

unfavorable environments that especially have a limitation in carbon supply

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30
Q

when does sporulation occur in the bacterial growth cycle

A

later log phages/ early stationary phase

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31
Q

what components help in sporulation

A

complete copy of chromosome, bare min proteins and chromosomes, high conc. of calcium bound to dipicolinic acid

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32
Q

what is the role of dipicolinic acid in sporulation

A

it binds free water molecules causing spore to be dehydrated
leads to heat resistance in core of macromolecules

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33
Q

is endospore production associated with gm+ or gm- bacteria?

A

gm+

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34
Q

what is glycocalyx in reference to gm+ and gm- cells

A

polysaccharide coating outer membrane of gm- cells
(or)
peptidoglycan layer of gm+ cells

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35
Q

what is streptococcus

A

gm+ bacteria that forms buildup of plaque on teeth
other bacteria adhere to slime layer–> mutants can grow

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36
Q

what is isotonicity

A

equal conc. of solute in and out of cell

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37
Q

what is hypertonicity

A

high conc. of solute causing cells to shrink

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38
Q

what is hypotonicity

A

low conc. of solute causing cells to swell

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39
Q

eukaryotic cell walls are made of

A

cellulose or chitin–> prevents bursting in hypotonic environment

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40
Q

Archaean cell walls are made of

A

polysaccharides and proteins (NO PEPTIDOGLYCAN)
-prevents bursting in hypotonic environment

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41
Q

bacterial cell walls are made of

A

peptidoglycans
prevents bursting in hypotonic environment

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42
Q

what are functions of the cell membrane

A
  1. selectively permeable membrane
  2. place where transport proteins are
  3. energy generating functions
  4. synthesis of phospholipids
  5. synthesis of murein
  6. secretion of extracytoplasmic proteins
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43
Q

what is murein, what does it do

A

peptidoglycan-> polymer of monomers that provide rigid support but also provides some permeability to solutes.

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44
Q

what is periplasmic space

A

space between plasma membrane and cell wall.

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45
Q

whats the difference between gm+ and gm- bacteria

A

gm+: thick peptidoglycan layer on the outside of bacterial cell wall –> interpeptide links easily degraded by antibiotics

gm-: thin peptidoglycan layer between 2 lipid bilayers, also covered by lipopolysaccharide (with lipid A) layer which makes it impermeable to antibiotics

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46
Q

what are porins

A

pore in gm- outer membrane
hydrophilic and allow exchange of nutrients/ also involved in pathogenesis

47
Q

what is the importance of interpeptide bridges

A

cross links make bacteria structurally strong against things like penicillin/cephalosporins (which degrade structural link)

48
Q

what are mycoplasmas

A

they lack cell walls which does not make bacteria gm+ or gm-

49
Q

what is bacilli

A

typical rod shaped bacteria

50
Q

what is vibrio

A

rod shaped bacteria but curved

51
Q

what is cocci

A

spherical shaped bacteria

52
Q

what is spirilla

A

spiral shaped bacteria

53
Q

what are proteobacteria

A

gm- bacteria that include
photoautotrophs, chemoautotrophs, heterotrophs

54
Q

what are hydrogenogenic CO oxidizers

A

bacteria that converts chemicals into H(g)
utilizes energy in the formation of hydrogen

proteobacteria

55
Q

what are neutrophillic

A

thrive in neutral pH (6.5-7.5)

proteobacteria

56
Q

what are mesophiles

A

grow in tolerant temperatures (not too hot nor cold)

57
Q

how do prokaryotes divide and why

A

binary fission due to lack of cytoskeleton
elongate and constrict in middle in favorable conditions

58
Q

what is the generation time for cell division

A

20 mins to 6 hours
more or less

59
Q

what is transformation (summary)

A

the integration of free naked DNA into prokaryotic chromosomes
process of horizontal gene transfer

60
Q

what is bacterial conjugation

A

process by which one bacterium transfers genetic material to another through direct contact from pilus

61
Q

what is donor bacterium

A

donates DNA sequence (fertility (f) factor) to recipient

62
Q

what is transduction

A

by which a virus transfers genetic material from one bacterium to another

63
Q

what is archaea cell wall LINKED by

A

ether linkage
maintains structure stability during extreme environments
makes pseudopeptidoglycan’s

64
Q

what are obligate anaerobes

A

bacteria that is killed by environmental conditions with oxygen

65
Q

what are sulfolobus
What are its properties

A

acidophiles, aerobic
thrive in high temps and low pH, typically live in sulfur rich environments

66
Q

what are methanogens

A

bacteria that form CH4 as a by product and is leading source of methane.
follow anaerobic respiration

67
Q

explain karyogenic evolution of the nucleus

A

nucleus evolved in a single lineage in which the cellular genome became enclosed within a membrane
- membrane formation mechanism is unspecified

68
Q

what is endokaryotic evolution of the nucleus

A

involved 2+ organisms invoking endosymbiosis or fusion to form nucleus

69
Q

explain the origin of mitochondria in eukaryotes

A

an event in which the ancestor of eukaryotes engulfed an alpha-proteobacterium.
the symbiont was then locked by its host and became a mitochondrion

70
Q

what is fully functional eukaryote

A

mitochondria with a genome and is responsible for generating energy through respiration

71
Q

what are mitochondrial relics in eukaryote

A

partial genome with an unknown function

72
Q

what are hydrogenosomes in eukaryotes

A

they have no genomes and generate energy by oxidation of a pyruvate

73
Q

what are eukaryotes with complete loss of mitochondria

A

have no mitochondria and arent functional

74
Q

what are the purpose of plastids

A

responsible for photosynthesis, storage of starch and synthesis of pigment

75
Q

what is the origin of plastids

A

event in which ancestor of Archaeplastida engulfed cyanobacterium, symbiont was trapped by its host and became a plastid

76
Q

what is primary and secondary symbiosis of plastids (chloroplast)

A

primary:
- green algae and red algae containing chloroplast evolve from engulfed cyanobacteria

secondary:
- green algae and red algae diverge and evolve independently

77
Q

what are protists

A

single celled colonial eukaryotes other than fungi

78
Q

what are protozoa

A

protists that are single celled heterotrophs

79
Q

what are purposes of fungi

A
  1. recycle biomass of wood/leaves that organisms cant digest
  2. produce antibiotics and food products
80
Q

what is mycorrhizae

A

fungal filaments the extend to roots of most plants
can be parasitic and pathogenic

81
Q

what is absorptive nutrition (traits of fungi)

A

secrete enzymes and absorb broken down nutrients

82
Q

what is hyphae (traits of fungi)

A

cell filaments that extend and to form branches and generate a mycelium (helps absorb organic matter)

83
Q

what are fungal walls made of

A

glucans, chitin, and glycoproteins

84
Q

what is sacchromyces cerevisae

A

single celled fungi (yeast)
makes up bakers yeast

85
Q

what is candida albicans

A

single celled fungi (yeast)
pathogenic

86
Q

how to fungus reproduce

A

through spores
- can be sexual (meiotic) or asexual (mitotic(
- can occur directly on fruiting bodies, hyphae, or sporangia

87
Q

what is Zygomycota

A

nonmotile spores
- grow in tropical/subtropical regions
-essential for carbon cycle as it decomposes soil, dung, and food types
- produces ethyl alcohol
- black bread mold

88
Q

what are basidiomycotan

A

typical mushrooms
- produce amanita phalloides that’s poisonous
- piptoporus:grow on trees
- starkish stinkhorn: attract insects

89
Q

what is Chlorophyta

A

green algae from chloroplast and grow in upper layer of water
- unicellular w/ flagella: Chlamydomonas (model for algae research)

-multicellular: volvox

90
Q

what is rhodophyta

A

red algae
phycoerythrin obscures chlorophyll making it red
- colonizes deep waters die to blue green light absorption

91
Q

what are heterokont (diatoms)

A

unicellular algae
found in aquatic habitats
have shell called frustule

92
Q

what is a virus

A

infection agent made of nucleic coat wrapped in protein coat called capsid

(bacteriophage)

93
Q

do viruses belong to any kingdon, why

A

no they do not,
they have no organelles, cytoplasm, or cell membrane (non-cellular)

94
Q

what is the virus-first/early hypothesis

A

hypothesis that states that viruses predated cells, contributing to the rise of cellular life

95
Q

what is the regressive/reduction hypothesis

A

states that viruses are remnants of cellular organisms

96
Q

what is the escape hypothesis

A

states that viruses were once part of genetic material, but escaped and evolved by pickpocketing genes using horizontal gene transfer (HGT)

97
Q

what is envelope in reference to viruses

A

flexible, membranous layer (lipids/capbs)
- used to identify viruses
- may have enzymatic activity
- may play a role in nucleic acid replication

98
Q

how do viruses recognize cells

A

viruses have a surface marker that match receptor site of cell,

causes specific attack processes

99
Q

what is helical symmetry in viruses

A

nucleic acid envelope by a hollow protein cylinder with helical shape

100
Q

what is isohedral symmetry of viruses

A

sort of spherical/rigid shape that gives protection to genome

101
Q

what is the virus replication cycle

A
  • attachment to host cell
  • penetration for viral entry
  • synthesis (nucleic acid/protein copies) made by cells machinery
  • assembly of viral components
  • release through lysis of cell
102
Q

what is the main difference between lysogenic and lytic infection

A

lysogenic-> has temperate stage/ phage dna is integrated in bacterial dna

lytic-> includes lysis of the cell/ no temperate stage

103
Q

what environment do phages best live in OUTSIDE the host cell

A

conditions with moisture and appropriate temp,
live longer on water resistant surfaces

104
Q

how long can cold virus last outside the cell

A

several days, but ability to infect declines with time

105
Q

how long can flu virus survive out the cell

A

several hours at low temp, can remain infectious for 24 hours

106
Q

how long can enteric viruses survive out the cell
name 2 enteric viruses we learnt

A

several weeks if conditions are suitable
enteric viruses include norovirus and hep A

107
Q

what is tobacco mosaic virus (TMV)

A

virus that infects plants –> mottled browning of tobacco leaves, and tomatoes

108
Q

what is avian/bird flu

A

influenza spread amongst birds, can infect humans (rare)

109
Q

how big is a virus (range)

A

seen under electron microscope–> range from 20-300 nanometers

110
Q

what acellular agents do viruses have

A

proteins and nucleic acid

111
Q

what acellular agents do viroids have

A

only RNA–> do not have protein coat and can only infect plants

112
Q

what acellular agents do satellites have

A

only nucleic acids, relies on helper virus for propogation

113
Q

1 gram of soil contains sufficient

A

DNA content

114
Q

what are phytoplankton

A

algae fused with photosynthetic bacteria–> involved as a biological pump

BIOL 322 (3 decks)

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