Topic 2 - Bacteria Flashcards
1
Q
possible morphology of bacteria
A
spherical (cocci)
rods (bacilli)
comma-shaped or slightly curved rods (vibrios)
spirals (spirilla)
varied/multiple shapes (pleiomorphic)
2
Q
morphology term: spherical
A
cocci
3
Q
morphology term: rod
A
bacilli
4
Q
morphology term: comma-shaped
A
vibrios
5
Q
morphology term: spiral
A
spirilla
6
Q
morphology term: varied/multiple shapes
A
pleiomorphic
7
Q
True or False: morphology is generally not good predictor of physiology, ecology, phylogeny
A
TRUE!
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)
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)
10
Q
cell sizes of prokaryotes
A
0.2 microns to > 700 microns in length/diameter
- very few large prokaryotes
11
Q
cell sizes of eukaryotes
A
10 microns to >200microns
- minimum size due to minimum space for genome, proteins, ribosomes
12
Q
bacterium up to 700 microns in diameter
A
Thiomargarita namibiensis
13
Q
bacterium 200-700 microns x 80 microns
A
Epulopiscium fishelsoni
14
Q
bacterium up to 2cm long
A
Thiomargarita magnifica
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!
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
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)
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
19
Q
what are ribosomes used for?
A
translation
20
Q
plasmid function
A
variable, encode non-chromosomal genes for variety of functions
21
Q
inclusion bodies function
A
storage of carbon, phosphate, nitrogen, sulphur
22
Q
gas vesicles function
A
buoyancy
23
Q
magnetosomes function
A
orienting cell during movement
24
Q
cytoskeletal structures function
A
guiding cell wall synthesis, cell division, possibly partitioning of chromosomes during replication
25
largest area in bacteria's cytoplasm?
nucleoid region
26
how does DNA compress in bacterial nucleoids? (3)
- 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"
27
___ membrane surrounds nucleoid
no
28
Do bacteria have histone proteins? What domains do?
No. Archaea and eukaryotes do.
29
other than nucleoid, what else is in cytoplasm?
- "Stew" of macromolecules (e.g., tRNA, mRNA, proteins, ribosomes)
- inclusion bodies (Storage) and microcompartments (protein compartments, except for magnetosome) might be present
30
List types of inclusion bodies (2) and microcompartments (3)!
- sulfur globules (inclusion bodies)
- polyhydroxybutyrate granules (PHB granules) (inclusion bodies)
- gas vesicles (microcompartments)
- carboxysomes (microcompartments)
- magnetosomes (microcompartments)
31
sulfur globules
- inclusion bodies
- sulfur storage for energy
32
PHB granules
- polyhydroxybutyrate granules
- inclusion bodies
- carbon storage (like bioplastic, accumulates in cell)
33
gas vesicles
- microcompartments
- buoyancy control; more = more buoyant
34
carboxysomes
- microcompartments
- location of carbon fixation reactions (RUBISCO)
35
magnetosomes
- 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)
36
what is bacterial cytoskeleton?
a series of internal proteins that helps to keeps everything in right place
37
bacteria - what cytoskeleton proteins are involved in cell wall synthesis in cell division? homologs? what do they do?
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)
38
bacteria - what other cytoskeletal proteins are involved in moving internal items? what homolog? what function?
- ParM (partition protein) pushes plasmids into opposite cells by polymerization; (homolog of actin)
39
bacterial cell envelope
all layers surrounding cell cytoplasm, including (inside->outside): cell/plasma membrane, cell wall, and outer membrane (if present)
40
do all bacterial cells have a plasma membrane?
yes
41
roles of plasma membrane (3)
- capturing energy
- holding sensory systems
- permeability barrier (but not structural)
42
plasma membrane - capturing energy
- 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
plasma membrane - holding sensory systems
- embedded proteins can detect environment changes, alter gene expression in response
44
plasma membrane - permeability barrier
Also: how is it chemically variable?
*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
bacteria - plasma membrane saturation/hopanoids
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
how do things cross plasma membrane?
- O2 and CO2 are small enough to diffuse
- H2O go through aquaporin protein channels (osmosis)
- facilitated diffusion and co-transport
47
facilitated diffusion
protein channel moves particles by leveraging a conc gradient (no ATP)
48
co-transport
AKA active transport (against a conc gradient)
- symport/antiport
- ATP needed
49
symport vs antiport
- 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
protein secretion
- shipping proteins outside cell (uses ATP)
- some proteins are tagged to be sent outside (threaded through membrane)
51
where is periplasmic space?
behind outside membrane, before cell wall
52
bacteria - cell wall
- gives cell shape
- protects against osmotic lysis/mechanical forces
- matrix of crosslinked strands of peptidoglycan subunits
- peptidoglycan subunits
53
bacteria - cell wall peptidoglycan subunits
- 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
do peptides AND peptide crosslinks vary by species?
Yes
55
DAP stands for? why is it special?
diaminopimelic acid
just in some gram negative bacterial cell wall (not used for much else so more resistant to other organisms breaking it)
56
bacterial cell wall formation steps!
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
cell wall can be degraded by
lysozyme and lysostaphin secretions
58
how does lysozyme work?
cleaves backbone of peptidoglycan
59
how does lysostaphin work?
acts on the crossbridge of certain Staphylococcus species
60
"D"-amino acids are__?
unique to "bricks" in cell walls, D meaning it is an enantiomer; more resistant
61
transglycosylation in bacterial cell wall building
connecting the two sugar groups (beta-1,4, glycosidic linkages)
62
transpeptidation in bacterial cell wall building + what catalyst?
FtsI catalyzes transpeptidation - takes off fifth AA from pentapeptide precursor
63
divisome meaning
enzymes associate with FtsZ and collectively called divisome to help with cell division
64
without ____, cell CANNOT resist osmotic pressure changes?
cell wall
65
if a lysozyme cuts peptidoglycan (bacterial cell wall), what happens in isotonic and hypotonic conditions?
isotonic: cell shape is lost, "protoplast"
hypotonic: water rushes in, internal pressure causes cell lysis (ruptured protoplast)
66
how do beta-lactam antibiotics work?
prevent peptidoglycan crosslinking
(inhibits FtsI transpeptidation)
67
antibiotic resistance, solution
some bacteria can produce enzymes to destroy the beta-lactam ring structure
-> add clavulanic acid, interfere with beta-lactamase so amoxicillin can act
68
gram-positive cells characteristics
- thick outer layer of peptidoglycan
- narrow periplasmic space
- negatively charged teichoic acids in peptidoglycan
- lipoteichoic acid (LTA) keep it anchored down
69
gram-negative cells characteristics
- very thin layer of peptidoglycan
- periplasmic space of varying width
- outer membrane composed of lipopolysaccharide (LPS)
70
LPS from a gram-negative cell can be harmful: why?
composed of:
- lipid A
- core polysaccharide
- O "outer" side chain of polysaccharides can vary (changed by microbes to evade host immune responses)
71
gram stains were invented by?
Hans Christian Gram
72
most bacteria are gram- ____
negative
73
gram stain process
- 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
why do gram-positive cells lock in crystal violet?
alcohol decolourization shrinks large pores in gram-positive cells
75
alcohol removes ___________ in gram-negative cells, so more likely to lose initial crystal violet stain
outer membrane lipids
76
how do nutrients get through bacterial cell wall? (gram-positive and gram-negative)
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
how can molecules get out of a gram-negative cell's periplasmic space?
- 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
what grows similar to how a type III secretion system functions?
flagella!
79
flagella
spiral, hollow, rigid filaments extending from cell surface
- locations and number vary across species
80
flagella - monotrichous
one flagellum
81
flagella - amphitrichous
two flagella (both poles)
82
flagella - lophotrichous
"tuft" on one end
83
flagella - peritrichous
all over (not polar)
84
which types of flagella are polar?
monotrichous
amphitrichous
lophotrichous
85
flagella's 3 basic components
- 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
flagella turn in different/same direction?
SAME direction! NO steering in bacteria
87
how do flagella move (energy)?
derived from proton motive force (PMF)
88
chemotaxis
chemoreceptor proteins temporally sense changes in conc of attractants or repellents (relating to flagella movement)
89
how do polar flagella move?
front then back then front then back
90
internal flagella
some spirochetes have flagella in periplasm
- as they spin, they rotate entire cell body like corkscrew
91
nonflagellar motility
- gliding motility - smooth sliding over surface
- twitching motility - slow, jerky movement using pili that extend/attach/pull on surface
92
"flagella" can also propel bacteria into adjacent cells through?
polymerization of actin in host cells
93
Brownian motion
not real motility, just twitching
94
adherence molecules
- lets cell stick to surfaces
- pili - fibers of pilin proteins, possess other proteins on tips for sticking
- not same as sex pilus
95
stalk
- additional surface area!
- has cytoplasm inside
- some microbes will use an extension of cell envelope, tipped by a "holdfast" of polysaccharides
96
capsules
- 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
surface arrays (S-layers)
- crystalline array of interlocking proteins
- can protect cell against predation or infection with bacteriophages
- in G+ve, -ve, and archaea
98
what does bacterial classification depend on? (6)
- DNA sequence
- size/shape
- Gram
- colony morphology
- presence of structures (e.g., capsules, endospores)
- physiological/metabolic traits
99
type strain =?
a referenced specimen deposited in a culture repository
100
most bacteria are cultured. T/F
false! only ~1% are
101
endospores
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
