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BIOL 240 Microbiology > Topic 2 - Bacteria > Flashcards

Topic 2 - Bacteria Flashcards

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1
Q

possible morphology of bacteria

A

spherical (cocci)
rods (bacilli)
comma-shaped or slightly curved rods (vibrios)
spirals (spirilla)
varied/multiple shapes (pleiomorphic)

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2
Q

morphology term: spherical

A

cocci

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3
Q

morphology term: rod

A

bacilli

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4
Q

morphology term: comma-shaped

A

vibrios

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5
Q

morphology term: spiral

A

spirilla

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6
Q

morphology term: varied/multiple shapes

A

pleiomorphic

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7
Q

True or False: morphology is generally not good predictor of physiology, ecology, phylogeny

A

TRUE!

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8
Q

morphology can be determined by selection: (3)

A
  • nutrient uptake efficiency (surface-to-volume ratio)
  • spirals allow efficient swimming in viscous or turbulent fluids (i.e., near surfaces)
  • gliding motility (filaments)
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9
Q

some bacteria can also assume multicellular organization: (3 types of organization)

A
  • hyphae (branching filaments of cells)
  • mycelia (tufts of hyphae)
  • trichomes (smooth unbranched chains of cells)
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10
Q

cell sizes of prokaryotes

A

0.2 microns to > 700 microns in length/diameter
- very few large prokaryotes

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11
Q

cell sizes of eukaryotes

A

10 microns to >200microns
- minimum size due to minimum space for genome, proteins, ribosomes

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12
Q

bacterium up to 700 microns in diameter

A

Thiomargarita namibiensis

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13
Q

bacterium 200-700 microns x 80 microns

A

Epulopiscium fishelsoni

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14
Q

bacterium up to 2cm long

A

Thiomargarita magnifica

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15
Q

Epulopiscium fishelsoni

A

“guest at a banquet of a fish”
from surgeonfish gut
- uncultured
- identified by 16S rRNA seq
- related to Clostridium
- 700microns long!

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16
Q

advantages to being small?

A

higher surface-to-volume ratio
- greater rate of nutrient/waste exchange per unit volume
- supports higher metabolic rate
- supports faster growth rate, faster evolution

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17
Q

lower size limits

A
  • size reduction constrained by minimum complement of cellular structures
  • diameters < 0.15 microns unlikely
  • “very small” cells common in open marine environments (0.2 microns to 0.4 microns common)
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18
Q

What’s in bacteria’s cytoplasm?

A

DNA nucleoid
chromosome-packaging proteins
enzymes involved in DNA, RNA synthesis
regulatory factors
ribosomes
plasmids
enzymes for breaking down substrates
inclusion bodies
gas vesicles
magnetosomes
cytoskeletal structures

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19
Q

what are ribosomes used for?

A

translation

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20
Q

plasmid function

A

variable, encode non-chromosomal genes for variety of functions

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21
Q

inclusion bodies function

A

storage of carbon, phosphate, nitrogen, sulphur

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22
Q

gas vesicles function

A

buoyancy

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23
Q

magnetosomes function

A

orienting cell during movement

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24
Q

cytoskeletal structures function

A

guiding cell wall synthesis, cell division, possibly partitioning of chromosomes during replication

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25
Q

largest area in bacteria’s cytoplasm?

A

nucleoid region

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26
Q

how does DNA compress in bacterial nucleoids? (3)

A
  • use of cations (Mg2+, K+, Na+) to shield negative charges on sugar-phosphate (PO4-) backbone
  • small, positively charged proteins bind to chromosome to maintain condensed structure
  • topoisomerases modify DNA structure for “supercoiling”
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27
Q

___ membrane surrounds nucleoid

A

no

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28
Q

Do bacteria have histone proteins? What domains do?

A

No. Archaea and eukaryotes do.

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29
Q

other than nucleoid, what else is in cytoplasm?

A
  • “Stew” of macromolecules (e.g., tRNA, mRNA, proteins, ribosomes)
  • inclusion bodies (Storage) and microcompartments (protein compartments, except for magnetosome) might be present
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30
Q

List types of inclusion bodies (2) and microcompartments (3)!

A
  • sulfur globules (inclusion bodies)
  • polyhydroxybutyrate granules (PHB granules) (inclusion bodies)
  • gas vesicles (microcompartments)
  • carboxysomes (microcompartments)
  • magnetosomes (microcompartments)
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31
Q

sulfur globules

A
  • inclusion bodies
  • sulfur storage for energy
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32
Q

PHB granules

A
  • polyhydroxybutyrate granules
  • inclusion bodies
  • carbon storage (like bioplastic, accumulates in cell)
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33
Q

gas vesicles

A
  • microcompartments
  • buoyancy control; more = more buoyant
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34
Q

carboxysomes

A
  • microcompartments
  • location of carbon fixation reactions (RUBISCO)
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35
Q

magnetosomes

A
  • microcompartments
  • lipid around itself -> ORGANELLE associated with direction finding
  • ONLY in bacteria
  • arranged in chain that’s attracted to iron (stops at sediment or bottom of water, since these bacteria only need low oxygen)
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36
Q

what is bacterial cytoskeleton?

A

a series of internal proteins that helps to keeps everything in right place

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37
Q

bacteria - what cytoskeleton proteins are involved in cell wall synthesis in cell division? homologs? what do they do?

A

MreB (homolog of actin - microfilaments), spiral helix bands
- lets bacteria elongate (instead of being cocci)
FtsZ (homolog of tubulin - microtubules), need for cell division (Z-ring @ division plane)
- without it, no division, only grows longer and longer (filamentous)

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38
Q

bacteria - what other cytoskeletal proteins are involved in moving internal items? what homolog? what function?

A
  • ParM (partition protein) pushes plasmids into opposite cells by polymerization; (homolog of actin)
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39
Q

bacterial cell envelope

A

all layers surrounding cell cytoplasm, including (inside->outside): cell/plasma membrane, cell wall, and outer membrane (if present)

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40
Q

do all bacterial cells have a plasma membrane?

A

yes

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41
Q

roles of plasma membrane (3)

A
  • capturing energy
  • holding sensory systems
  • permeability barrier (but not structural)
42
Q

plasma membrane - capturing energy

A
  • electron transport chains create proton motive force (PMF) (make ATP)
  • can be used for respiration/photosynthesis
  • can be used to derive energy for motion (flagella)
43
Q

plasma membrane - holding sensory systems

A
  • embedded proteins can detect environment changes, alter gene expression in response
44
Q

plasma membrane - permeability barrier

Also: how is it chemically variable?

A

*not structural barrier
- usually made of phospholipid bilayer with embedded proteins
- hydrophobic core
- hydrophilic surfaces interact with either exterior or cytoplasm
- chemically variable due to changes in fatty acid groups attached to glycerol backbone
- connected by ESTER linkages

45
Q

bacteria - plasma membrane saturation/hopanoids

A

saturated - no double bonds, full with H
unsaturated - more fluidity (bends in fatty tail)

some have sterol-like molecules “hopanoids” to help stabilize across temp ranges

46
Q

how do things cross plasma membrane?

A
  • O2 and CO2 are small enough to diffuse
  • H2O go through aquaporin protein channels (osmosis)
  • facilitated diffusion and co-transport
47
Q

facilitated diffusion

A

protein channel moves particles by leveraging a conc gradient (no ATP)

48
Q

co-transport

A

AKA active transport (against a conc gradient)
- symport/antiport
- ATP needed

49
Q

symport vs antiport

A
  • both co-transport
  • symport: two diff things go in (one against, one with conc gradient)
  • antiport: one thing goes in, one goes out (in is against, out is with conc gradient)
50
Q

protein secretion

A
  • shipping proteins outside cell (uses ATP)
  • some proteins are tagged to be sent outside (threaded through membrane)
51
Q

where is periplasmic space?

A

behind outside membrane, before cell wall

52
Q

bacteria - cell wall

A
  • gives cell shape
  • protects against osmotic lysis/mechanical forces
  • matrix of crosslinked strands of peptidoglycan subunits
  • peptidoglycan subunits
53
Q

bacteria - cell wall peptidoglycan subunits

A
  • N-acetylmuramic acid (NAM) -> like NAG but with lactic acid
  • small peptide chain (linked to NAM) containing DAP
  • N-acetylglucosamine (NAG)

disaccharide backbone w/ peptide chain

54
Q

do peptides AND peptide crosslinks vary by species?

A

Yes

55
Q

DAP stands for? why is it special?

A

diaminopimelic acid
just in some gram negative bacterial cell wall (not used for much else so more resistant to other organisms breaking it)

56
Q

bacterial cell wall formation steps!

A

1) NAM is synthesized in cytoplasm and linked to UDP, then coupled to short peptide chain (pentapeptide precursor)
2) NAM is linked to bactoprenol through P-P
3) NAG is added to NAM
4) bactoprenol flips NAM-NAG to periplasm
5) disaccharide added to existing chain.
transpeptidase crosslinks pentapeptide precursor to another strand (leaves tetrapeptide)
6) bactoprenol flips back to cytoplasm

57
Q

cell wall can be degraded by

A

lysozyme and lysostaphin secretions

58
Q

how does lysozyme work?

A

cleaves backbone of peptidoglycan

59
Q

how does lysostaphin work?

A

acts on the crossbridge of certain Staphylococcus species

60
Q

“D”-amino acids are__?

A

unique to “bricks” in cell walls, D meaning it is an enantiomer; more resistant

61
Q

transglycosylation in bacterial cell wall building

A

connecting the two sugar groups (beta-1,4, glycosidic linkages)

62
Q

transpeptidation in bacterial cell wall building + what catalyst?

A

FtsI catalyzes transpeptidation - takes off fifth AA from pentapeptide precursor

63
Q

divisome meaning

A

enzymes associate with FtsZ and collectively called divisome to help with cell division

64
Q

without ____, cell CANNOT resist osmotic pressure changes?

A

cell wall

65
Q

if a lysozyme cuts peptidoglycan (bacterial cell wall), what happens in isotonic and hypotonic conditions?

A

isotonic: cell shape is lost, “protoplast”
hypotonic: water rushes in, internal pressure causes cell lysis (ruptured protoplast)

66
Q

how do beta-lactam antibiotics work?

A

prevent peptidoglycan crosslinking
(inhibits FtsI transpeptidation)

67
Q

antibiotic resistance, solution

A

some bacteria can produce enzymes to destroy the beta-lactam ring structure
-> add clavulanic acid, interfere with beta-lactamase so amoxicillin can act

68
Q

gram-positive cells characteristics

A
  • thick outer layer of peptidoglycan
  • narrow periplasmic space
  • negatively charged teichoic acids in peptidoglycan
  • lipoteichoic acid (LTA) keep it anchored down
69
Q

gram-negative cells characteristics

A
  • very thin layer of peptidoglycan
  • periplasmic space of varying width
  • outer membrane composed of lipopolysaccharide (LPS)
70
Q

LPS from a gram-negative cell can be harmful: why?

A

composed of:
- lipid A
- core polysaccharide
- O “outer” side chain of polysaccharides can vary (changed by microbes to evade host immune responses)

71
Q

gram stains were invented by?

A

Hans Christian Gram

72
Q

most bacteria are gram- ____

A

negative

73
Q

gram stain process

A
  • bacteria are stained with crystal violet
  • iodine (mordant) stabilizes crystal violet
  • alcohol may extract crystal violet (if gram-neg)
  • bacteria are stained with safranin

gram-positive = purple
gram-negative = pink

74
Q

why do gram-positive cells lock in crystal violet?

A

alcohol decolourization shrinks large pores in gram-positive cells

75
Q

alcohol removes ___________ in gram-negative cells, so more likely to lose initial crystal violet stain

A

outer membrane lipids

76
Q

how do nutrients get through bacterial cell wall? (gram-positive and gram-negative)

A

gram-positive: peptidoglycan layer has large pores throughout its matrix

gram-negative: have porins and TonB proteins in outer membrane
- transfer molecules into periplasmic space
- TonB uses proton motive force across cytoplasmic membrane

77
Q

how can molecules get out of a gram-negative cell’s periplasmic space?

A
  • some move from periplasm to outside directly (known as autotransporters and are rare)
  • some use single-step (never entering periplasm transport systems), e.g., type III secretion system like a syringe
78
Q

what grows similar to how a type III secretion system functions?

A

flagella!

79
Q

flagella

A

spiral, hollow, rigid filaments extending from cell surface
- locations and number vary across species

80
Q

flagella - monotrichous

A

one flagellum

81
Q

flagella - amphitrichous

A

two flagella (both poles)

82
Q

flagella - lophotrichous

A

“tuft” on one end

83
Q

flagella - peritrichous

A

all over (not polar)

84
Q

which types of flagella are polar?

A

monotrichous
amphitrichous
lophotrichous

85
Q

flagella’s 3 basic components

A
  • filament of multiple flagellin proteins (5-10microns)
  • hook protein portion (connects filament to basal body)
  • basal body (disk-like structure that turns filament like a propeller; anchored to periplasm, cell wall, plasma membrane, connected to cytoplasm
86
Q

flagella turn in different/same direction?

A

SAME direction! NO steering in bacteria

87
Q

how do flagella move (energy)?

A

derived from proton motive force (PMF)

88
Q

chemotaxis

A

chemoreceptor proteins temporally sense changes in conc of attractants or repellents (relating to flagella movement)

89
Q

how do polar flagella move?

A

front then back then front then back

90
Q

internal flagella

A

some spirochetes have flagella in periplasm
- as they spin, they rotate entire cell body like corkscrew

91
Q

nonflagellar motility

A
  • gliding motility - smooth sliding over surface
  • twitching motility - slow, jerky movement using pili that extend/attach/pull on surface
92
Q

“flagella” can also propel bacteria into adjacent cells through?

A

polymerization of actin in host cells

93
Q

Brownian motion

A

not real motility, just twitching

94
Q

adherence molecules

A
  • lets cell stick to surfaces
  • pili - fibers of pilin proteins, possess other proteins on tips for sticking
  • not same as sex pilus
95
Q

stalk

A
  • additional surface area!
  • has cytoplasm inside
  • some microbes will use an extension of cell envelope, tipped by a “holdfast” of polysaccharides
96
Q

capsules

A
  • thick layer of polysaccharides surrounding some cells (G+ve and -ve)
  • provides adhesion, defense against host immunity, protection against desiccation
  • can help bacteria form biofilms
97
Q

surface arrays (S-layers)

A
  • crystalline array of interlocking proteins
  • can protect cell against predation or infection with bacteriophages
  • in G+ve, -ve, and archaea
98
Q

what does bacterial classification depend on? (6)

A
  • DNA sequence
  • size/shape
  • Gram
  • colony morphology
  • presence of structures (e.g., capsules, endospores)
  • physiological/metabolic traits
99
Q

type strain =?

A

a referenced specimen deposited in a culture repository

100
Q

most bacteria are cultured. T/F

A

false! only ~1% are

101
Q

endospores

A

some bacteria can differentiate into endospores
- resistant to heat, radiation, acids, drying, UV, etc
- can stay dormant for at most 250+million years
- induced by limited nutrition (germinates rapidly under good conditions)
- GRAM POSITIVE (a lot of genes involved, so maybe that’s why it’s limited to specific phylogenetic goups)

involves: preparing thick protective protein coat over thickened peptidoglycan layer

BIOL 240 Microbiology (10 decks)

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