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Microbio > Bacteria and Archaea (3, 4, 5) > Flashcards

Bacteria and Archaea (3, 4, 5) Flashcards

1
Q

Bacterial cells: components outside cell wall

A

Have ONE of the following:
- slime layers
- capsules
- s-layers (proteins)
Protection, some movement, some adhesion

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2
Q

Capsules

A
  • usually composed of polysaccharides
  • well-organized and not easily removed from cell
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3
Q

slime layer

A
  • diffuse, unorganized, easy to remove
  • motility: helps cells glide
  • biofilms: community of microorganisms, work together
    • waste from one might fuel another
    • example: dental plaque
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4
Q

s-layers

A
  • protect from ions and pH fluctuations, osmotic stress
  • maintains shape and rigidity
  • adhesion
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5
Q

cytoplasmic structures

A
  • cytoplasm
    • ribosomes
    • nucleoid
    • plasmids
    • cytoskeletal proteins
    • inclusions
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6
Q

cytoskeletal proteins: functions

A

similar to those in eukaryotes
- cell division
- protein location and movement
- cell shape

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7
Q

FtsZ: homologue and function

A
  • found in many bacteria and archaea
  • homologue of tubulin (type of microtubule)
  • cell division
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8
Q

MreB: homologue and function

A
  • found in many rods and some archaea
  • homologue of actin (type of microfilament)
  • maintains cell shape
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9
Q

CreS: homologue and function

A
  • found in vibrio bacteria
  • homologue of keratin
  • creates comma shape by building up and inhibiting an area
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10
Q

common storage units: names and functions

A
  • poly-B-hydroxybutyrate (PHB) granules: carbon storage
  • polyphosphate granules: store phosphate
  • sulfur globules: store sulfur
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11
Q

microcompartments: names and functions

A
  • carboxysomes: carbon fixation (CO2 into fuel)
    • found in cyanobacteria
  • gas vacuoles: store gas for buoyancy
    • found in aquatic photosynthetic bacteria
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12
Q

Ribosomes in archaea and bacteria

A
  • type 70s
    • svedberg unit
  • antibiotics target ribosomes
  • since svedberg unit is different in bacteria than in eukaryotic cells, the antibiotics only impact bacterial cells
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13
Q

nucleoid region

A
  • irregularly-shaped
  • usually not membrane-bound
  • usually one chromosome
  • circular, double-stranded DNA
  • nucleoid-associated proteins (NAPS): coil DNA
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14
Q

plasmids

A
  • extrachromosomal DNA
    • found in bacteria and archaea
    • usually small, circular, closed DNA molecules
  • exist and replicate independently of chromosome
  • contain few genes that are non-essential but are of advantage to the organism
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15
Q

plasmids: 5 examples

A
  1. conjugative plasmids: transfer DNA from one cell to another
  2. R-plasmids: antibiotic resistance genes
  3. col plasmids: produce bacterioncins, which can kill other similar species
  4. virulence plasmids: carry virulence genes and cause disease
  5. metabolic plasmids: carry genes for enzymes, degradation
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16
Q

external structures: functions

A
  • protection
  • surface attachment
  • cell movement/motility
  • horizontal gene transfer
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17
Q

pili and fimbria: structure and function

A
  • short, thin, hair-like appendages
  • most mediate attachment to surfaces
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18
Q

Type IV pili

A

motility

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19
Q

Sex pili

A

conjugation

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20
Q

flagella: structure and function

A
  • threadlike, locomotor appendages
  • motility and attachment
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21
Q

patterns of flagella distribution

A
  1. monotrichous: polar flagellum, single, rod-shaped
  2. amphitrichous: one on both end
  3. lophotrichous: tuft
  4. peritrichous: surrounding cell
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22
Q

flagella: 3 parts

A
  1. filament
    - extends from cell surface to tip
    - hollow, rigid structure
    - composed of flagellin protein (some have sheath)
  2. hook
    - links filament to basal body
  3. basal body
    - intrecellular
    - flagellar motor
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23
Q

motility in archaea and bacteria

A
  • directed movement
  • chemotaxis
    • move in response to stimuli: temperature, light, oxygen, osmotic pressure, gravity
    • go to nutrients, away from danger, etc.
  • not all are motile
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24
Q

flagellar movement: 5 types

A

most common
1. swimming
2. swarming
other
3. spirochete
4. twitching
5. gliding

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25
Q

flagellar movement: swimming

A
  • flagellum rotates like a propellor
    • rapid (1100 revolutions/second)
  • counterclockwise: run
  • clockwise: tumble
    • detecting clues, chemotaxis “check-in”
  • proton motive force: gradient
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26
Q

Peritrichous flagella: swimming

A

run: form bundle and all rotate same direction
tumble: alternate rotational direction (every other flagella)

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27
Q

flagellar movement: swarming

A
  • usually peritrichous
  • multiple cells group together
  • form distinctive growth patterns
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28
Q

flagellar movement: spirochete

A
  • multiple flagella form axial fibril, which winds around cell
  • endoflagellum
  • corkscrew shape exhibits flexing and spinning forces
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29
Q

flagellar movement: twitching

A
  • type IV pili
  • short, intermittent, jerky motions
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30
Q

flagellar movement: gliding

A
  • slime (ATP or neck proteins)
  • smooth movement
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31
Q

bacterial endospore

A
  • complex, dormant structure formed by some bacteria
  • various locations
  • resistant to numerous environmental conditions
    • heat
    • radiation
    • chemicals
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32
Q

bacterial endospore: structure

A
  1. core: DNA and ribosomes
  2. inner membrane: like plasma membrane
  3. core wall: peptidoglycan
  4. cortex: peptidoglycan
  5. outer membrane
  6. coat: protection layer
  7. exosporium
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33
Q

sporulation (endospores): 7-step process

A
  • takes ~10 hours
    1. axial filament formation: DNA condenses to one side
    2. septum formation, forespore development: one side of cell walls off into a smaller compartment
    3. engulfment of forespore: mother cell “eats” forespore, creating multiple layers
    4. cortex formation: cortex develops
    5. coat synthesis: protein
    6. maturation process
    7. lysis of sporangeum: loses mother cell
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34
Q

poly-B-hydroxybutyrate granules (PHB)

A
  • storage inclusion
  • store carbon
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35
Q

polyphosphate granules

A
  • storage inclusion
  • store phosphate
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36
Q

sulfur globules

A
  • storage inclusion
  • store sulfur
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37
Q

carboxysomes

A
  • microcompartment
  • found in cyanobacteria
  • carbon fixation: CO2 into fuel
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38
Q

Gas vacuoles

A
  • microcompartment
  • store gas for buoyancy
  • found in aquatic, photosynthetic bacteria
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39
Q

plasmids

A
  • extrachromosomal DNA
  • found in bacteria and archaea
  • small, closed circular DNA molecules
  • exist and replicate independently of chromosome
  • contain few non-essential genes that are of advantage to organism
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40
Q

conjugative plasmids

A
  • transfer DNA from one cell to another
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41
Q

R-plasmids

A
  • antibiotic resistance genes
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42
Q

Col plasmids

A
  • produce bacteriocins, which can kill other similar species
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43
Q

virulence plasmids

A
  • carry virulence genes, cause disease
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44
Q

metabolic plasmids

A
  • carry genes for enzymes, degradation
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45
Q

3 parts of flagella

A
  1. filament: extends from cell surface to tip
    - hollow, rigid
    - composed of flagellin protein
    - some have sheath
  2. hook
    - connect filament to basal body
  3. basal body
    - intracellular
    - flagellar movement
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46
Q

formation of vegetative cells

A
  1. activation
  2. germination: environmental nutrients detected, spore swelling/rupture/absorption, increased metabolic activity
  3. outgrowth
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47
Q

Archaea: similarities with eukarya

A
  • replication, transcription, translation, & the proteins/enzymes involved in these processes
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48
Q

Archaea: similarities with bacteria

A
  • metabolism
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49
Q

Archaea: size and shape

A
  • commonly found as cocci and rods
  • can be bottle, square, elongated rod, tear, vibrio
  • 0.1-1.5 microns in size
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50
Q

archaeal cell envelope vs bacterial cell envelope

A
  • archaeal doesn’t have peptidoglycan
  • some have pseudomurein (sugar layer)
  • some have s-layer
  • capsules and slime membranes are rare
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51
Q

archaeal plasma membrane

A

composed of unique lipids
- branched hydrocarbons
- ether linkages (unlike ester in bacteria)
- stereochemistry differences
- some form monolayers (rather than bilayers like bacteria)

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52
Q

archaeal cell walls

A
  • lack peptidoglycan
  • may contain pseudomurein
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53
Q

archaea: cell wall types

A
  1. s-layer canopies
  2. protein sheath, s-layer
  3. s-layer, pseudomurein (like gram +)
  4. polysaccharide (like gram +)
  5. double membrane (like gram -)
54
Q

archaea: cytoplasm

A

similar to bacteria
- similar components
- ribosomes, nucleoid
- FtsZ

55
Q

archaea: nucleoid

A
  • irregularly shaped
  • usually not membrane bound
  • double stranded, circular
  • nucleoid proteins (NAPS) aid in supercoiling
56
Q

archaeal flagella: differences from bacteria

A
  • thinner
  • more than one type of flagellin protein
  • not hollow
57
Q

archaea: pili types

A

cannulae: cell-cell communication
hami: like a grappling hook

58
Q

archaeal DNA replication: similarities to eukarya

A

helicases, DNA polymerase

59
Q

archaeal DNA replication: similarities to bacteria

A
  • circular chromosome
  • plasmids
  • bidirectional
60
Q

archaeal transcription: similarities to eukarya

A

eukarya-like transcription machinery
- DNA polymerase
- TATA box-binding protein
- TFB
- similar elongation factors

61
Q

archaeal transcription: similarities to bacteria

A

regulation of transcription
- transcription regulators
- 70s ribosomes

62
Q

selenocysteine

A
  • coded for by UGA
  • protects from oxidative damage
63
Q

pyrrolysine

A
  • coded for by UAG
  • methanogenic characteristics
64
Q

archaea: protein secretion

A
  • sec system
  • tat system (unique to bacteria and archaea)
    • can transport folded proteins
65
Q

archaeal metabolism: 3 pathways

A
  1. emden-meyerhof pathways (glycolysis)
  2. 2 modified entner-doudoroff pathways
66
Q

archaeal metabolism: lacks

A
  • pyruvatedehydrogenase complex
    • pyruvate oxidoreductase
  • some lack TCA (krebs, citric acid cycle)
67
Q

thermostability of archaea

A
  • chaperones
  • reverse DNA gyrase
    • makes DNA more stable
  • 2003 discovery of strain 121
    • goegemma barossii, can withstand 121 degrees C
68
Q

archaeal taxonomy

A
  • 16 proposed phyla
  • 2 genera
    • sulfolobus
    • thermoproteas
  • 5 physiological groups
69
Q

genus sulfolobus

A
  • irregularly-lobed
  • aerobic
  • thermoacidophiles
    • 70-80 degrees celsius
    • pH 2-3
  • specialized ABC transporters
70
Q

genus thermoproteus

A
  • long, thin rods
  • anaerobic
  • thermoacidophiles
    • 75-100 degrees celsius
    • pH 3-4
  • reductive TCA cycle (reverse: CO2 + ATP-> acetyl coA
    • acetyl coA: makes fats, ATP, ADH
    • can be catabolized or used anabolically
71
Q

5 major physiological groups of archaea

A
  • methanogens
  • haloarchaea
  • thermoplasms
  • extreme thermophile
  • sulfur-reducing archaea
72
Q

methanogens

A
  • produce methane from CO2 via methanogenesis
  • rods, cocci, curved rods, irregular
  • unusual metabolism
73
Q

haloarchaea

A
  • aerobic
  • cubes, pyramids, rods, cocci
  • high salt requirements
    • requires at least 1.5 M NaCl
    • growth optima near 3.4 M NaCl
  • red to yellow pigment
74
Q

thermoplasms

A
  • thermoacidophiles lacking cell wall
    • thermoplasma: 59 degrees C, pH 1-2
    • picrophilus: 47-65 degrees C, can grow at pH zero
75
Q

extreme thermophile

A
  • motile by multiple flagella
  • 88-100 degrees C
  • strictly anaerobic
76
Q

sulfur-reducing archaea

A
  • irregular cocci cells
  • anaerobes
  • optimum 83 degrees C
  • reduce sulfate to sulfide
77
Q

uptake of nutrients: passive diffusion

A

doesn’t need transport proteins

78
Q

uptake of nutrients: facilitated diffusion

A

needs carrier protein

79
Q

active transport

A
  • requires energy
    • ATP
    • goes against concentration gradient
  • group translocation
  • primary and secondary active transport
80
Q

primary active transport

A
  • uses solute-binding proteins
  • unmodified solute
  • uses ATP to pull it in
81
Q

secondary active transport

A
  • uses ion gradients
  • no modification
  • cotransporter
    • symporter: 2 things in
    • antiporter: 1 in, 1 out
82
Q

group translocation

A
  • PEP (phosphenyl pyruvate) as energy
  • modification: phosphorylation
  • low to high concentration
  • phosphenol pyruvate: sugar phosphotransferase system (PTS)
    • phosphorelay: one molecule passes phosphate to the next
83
Q

key players in phosphorelay

A
  1. PEP
  2. Enzyme I
  3. HPr
  4. Enzyme II A
  5. Enzyme II B (phosphate stays here)
  6. Enzyme II C (conformational change so glucose can enter and become phosphorylated)
    End: glucose-6-phosphate or mannitol-1-phosphate
84
Q

iron uptake

A
  • complex transported into cells
  • siderophore: binds to iron and moves into cell
85
Q

culture media

A

solid or liquid medium used to grow, transport, and store microbes
- must contain all nutrients required for the organism to grow
- agar, broth

86
Q

culture media: supportive

A
  • many microorganisms
  • tryptic soy agar
87
Q

culture media: enriched

A
  • fastidious microorganisms with specific nutritional needs
    ex: blood agar
    • B-hemolytic colony
    • different levels of hemolysis
    • beta: most breakdown, alpha: partial breakdown, gamma: growth w/out breakdown
88
Q

culture media: selective

A
  • favors growth of some microorganisms and inhibits growth of others
    ex: MacConkey agar: lactose fermenters vs. non-fermenters
    ex: mannitol salt: selects gram +, differentiates mannitol perm
89
Q

Isolation of pure culture

A
  • population of cells arising from single cell
  • isolate colony in sterile media
  • spread & streak plate
90
Q

streak plate

A
  • mixed culture on a plate
  • each cell can form a separate colony
  • use single colony to create pure culture
    • divide plate into quadrants, drag sample to each area
    • spread evenly with sterile bent rod
91
Q

reproductive strategies

A
  • binary fission (most bacteria)
  • budding
  • multiple fission
  • spore formation
92
Q

binary fission steps

A
  1. cell elongates while chromosome replicates
  2. septum forms (FtsZ needed)
  3. new peptidoglycan between cells
  4. separation
93
Q

multiple fission

A
  • within cell envelope
  • progyny forms
94
Q

spore formation

A

forms filaments

95
Q

halotolerant

A

salinity of up to 3 M

96
Q

halophile

A

salinity between 0.2-3.5 M

97
Q

extreme halophile

A

salinity between 2-6 M

98
Q

acidophile

A

pH 0-5.5

99
Q

neutrophile

A

pH 5.5-8

100
Q

alkalophile

A

pH 8-11.5

101
Q

microbes and temperature

A
  • microbes cannot regulate their internal temperature
  • enzymes have optimal temperature requirements
102
Q

psychrophiles

A

0-20 degrees C

103
Q

psychrotrophs

A

0-35 degrees C

104
Q

mesophiles

A

20-45 degrees C

105
Q

thermophiles

A

45-85 degrees C

106
Q

hyperthermophiles

A

70-105 degrees C

107
Q

obligate anaerobe

A
  • cannot grow in presence of oxygen
  • grow at bottom of tube
108
Q

obligate aerobe

A
  • need oxygen to grow
  • grow at top of tube
109
Q

microaerophiles

A
  • need a little bit of oxygen
  • grow close to top
110
Q

facultative anaerobes

A
  • capable of growing in either condition
  • start with oxygen but can switch to fermentation if needed
111
Q

aerotolerant anaerobes

A
  • can grow under any condition
112
Q

microbes and pressure

A
  • microbes on land/water surface live at 1 atm
  • some live deep in sea at 600-1100 atm
113
Q

barotolerant

A

can live at high hydrostatic pressure

114
Q

barophilic

A

must live at high hydrostatic pressure

115
Q

bacterial cell cycle: steps

A
  • chromosome replication and partitioning
  • cytokineses
116
Q

chromosome replication and partitioning

A
  • replicates bidirectionally from origin
  • replisome (machinery involved in DNA replication)
  • terminus
117
Q

cytokinesis

A
  • separation
    • selection of site for septum formation
    • z-ring assembled, cell wall synthesizing machinery
    • constriction of cell
118
Q

z-ring assembly

A
  • protein FtsZ
  • MinCDE directs FtsZ: inhibits it from forming in regions where MinCDE is present
119
Q

cell growth

A
  • determined by peptidoglycan synthesis
  • UDP and bactoprenols
  • MurJ flippase, glycosyltransferase, transpeptidase
120
Q

UDP

A
  • part of cell growth
  • collects NAG and NAM and brings it to bactoprenol
121
Q

bactoprenol

A
  • part of cell growth
  • collects NAG and NAM and brings to MurJ
122
Q

MurJ flippase

A
  • part of cell growth
  • flips NAG and NAM to periplasmic side
123
Q

geogemma barossii

A
  • strain 121
  • can withstand 121 degrees celsius
124
Q

picrophilus

A
  • thermophile that can grow at pH zero
125
Q

glycosyltransferase (GT)

A

links NAG and NAM together during cell growth

126
Q

transpeptidase (TP)

A

links NAM together during cell growth

127
Q

growth curve stages

A
  1. lag
  2. exponential
  3. stationary
  4. death
  5. long-term stationary
128
Q

lag phase

A

taking in nutrients and preparing for binary fission

129
Q

exponential phase

A

binary fission

130
Q

stationary phase

A
  • plateau
  • threshold reached
  • waste buildup, need for O2
131
Q

death phase

A
  • natural selection
  • some cells can withstand toxic levels

Microbio (11 decks)

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