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Main Concept 1 Microbial Form and Function
Chapter 2 of Brock Microbiology text with some
examples taken from other chapters
Emphasis on prokaryotic microbes-not eukaryotes or
subcellular microbes
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ARCHAEABACTERIA EUKARYA
Green nonsulfurbacteria
MitochondrionGram-positivebacteria
Proteobacteria
ChloroplastCyanobacteria
Green sulfurbacteria
Thermotoga
Thermodesulfobacterium
Aquifex
CrenarchaeotaThermoproteus
Pyrodictium
ThermococcusNitrosopumilus Pyrolobus
Methano-bacterium
EuryarchaeotaMethanosarcina
Thermoplasma
Methanopyrus
Extremehalophiles
Entamoebae Slimemolds
Animals
Fungi
Plants
Ciliates
Flagellates
Trichomonads
Microsporidia
Diplomonads
Macroorganisms
“Universal Tree” of Life-3 Domains
Only cellular systemsArchaea and Bacteria are prokaryotesEukarya are eukaryotes
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I. A Note on Microscopy
Key technique for analyzing cell structure
Covered mainly in lab
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Most Important Microscopic Test
The Gram stain
A differential staining technique
Most members of the Bacteria can be divided into two major groups called gram-positive and gram-negative
Gram-positive bacteria appear purple, and gram-negative bacteria appear red after staining
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II. Cells of Bacteria and Archaea
• 2.5 Cell Morphology
• 2.6 Cell Size and the Significance of Being
Small
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2.5 Cell Morphology
• Morphology = cell shape
• Major cell morphologies (Figure 2.11)• Coccus (pl. cocci): spherical or ovoid
• Rod: cylindrical shape (bacillus/bacilli)
• Spirillum: spiral shape
• Cells with unusual shapes• Spirochetes, appendaged bacteria, and filamentous
bacteria
• Many variations on basic morphological types
© 2015 Pearson Education, Inc. Figure 2.11
Coccus
Rod
Spirillum
Spirochete
Stalk Hypha
Filamentous bacteria
Budding and appendaged bacteria
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2.5 Cell Morphology
Morphology is descriptive but typically does not
predict physiology, ecology, phylogeny, etc. of a
prokaryotic cell
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Size range for prokaryotes: 0.2 µm to >700 µm
Most cultured rod-shaped bacteria are between 0.5 and 4.0 µm wide and < 15 µm long
Cellular organisms <0.15 µm in diameter are unlikely
Open oceans tend to contain small cells (0.2–0.4 µm in diameter)
Most prokaryotes are at the small end of the size range
2.6 Cell Size and the Significance of Being Small
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Why are most prokaryotic cells small?
Explained by square-cube rule
As cells get larger their internal volume grows faster than their surface area (cube > square)
So in larger cells there is relatively less plasma membrane to bring in nutrients for the cytoplasm
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Two prokaryotes notable for their large size
• Epulopiscium fishelsoni (Figure 2.12a and below)
• Thiomargarita namibiensis (Figure 2.12b)
2.6 Cell Size and the Significance of Being Small
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How does a large prokaryote such as Thiomargarita survive?
https://microbewiki.kenyon.edu/index.php/Thiomargarita_namibiensis
Bacteria are generally small which is favourable for rapid growth and efficient nutrient uptake (Jorgensen 2010). Nutrients are able to diffuse faster and are more effectively taken up in smaller cells. The primary mechanism of nutrient uptake in T. namibiensis is through diffusion without usage of special transport systems (Schulz 2002). Despite the large size of the microbe, nutrients are still capable of efficient diffusion throughout the organism due to the large central vacuoles which limit the volume of the effective cytoplasm. The large size of T. namibiensis is a result of its storage compartments for soluble electron donors and acceptors (Schulz 2002). With this adaptation, this bacterium does not need to be in constant contact with nutrients and are still capable of surviving for long periods of time. The occasional exposure to substrates allows T. namibiensis to uptake essential nutrients for storage in the central vacuoles. This adaptation is necessary for its habitat in oceanic sediments where nutrients are only available through occasional sediment re-suspensions (Schulz 2002).
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III. The Cytoplasmic Membrane and Transport(aka Plasma Membrane)
Three relevant sections of Chapter 2
• 2.7 Membrane Structure
• 2.8 Membrane Functions
• 2.9 Nutrient Transport
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2.7 Membrane Structure
• Cytoplasmic membrane or plasma membrane• Thin structure that surrounds the cell
• Vital barrier that separates cytoplasm from environment
• Highly selective permeable barrier; enables
concentration of specific metabolites and excretion of
waste products
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2.7 Membrane Structure
• Composition of membranes• Generic structure is phospholipid bilayer (Figure 2.14)
• Contain both hydrophobic and hydrophilic components
• Can exist in many different chemical forms as a result of
variation in the groups attached to the glycerol backbone
• Fatty acids or other lipids point inward to form
hydrophobic environment; hydrophilic portions remain
exposed to external environment or the cytoplasm
© 2015 Pearson Education, Inc. Figure 2.14
Fatty acids
Phosphate
Ethanolamine
Fatty acids
Hydrophilicregion
Hydrophobicregion
Hydrophilicregion
Glycerophosphates
Fatty acids
Glycerol
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2.7 Membrane Structure
• Cytoplasmic membrane (Figure 2.15)
• 8–10 nm wide
• Embedded proteins (integral/peripheral)
• Stabilized by hydrogen bonds and hydrophobic
interactions
• Mg2+ and Ca2+ help stabilize membrane by forming ionic
bonds with negative charges on the phospholipids
• Somewhat fluid
© 2015 Pearson Education, Inc. Figure 2.15
Phospholipids
6–8 nm
Integralmembraneproteins
Hydrophilicgroups
Hydrophobicgroups
Phospholipidmolecule
Out
In
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2.7 Membrane Structure
• Membrane proteins• Outer surface of cytoplasmic membrane can interact with a
variety of proteins that bind substrates or process large molecules for transport
• Inner surface of cytoplasmic membrane interacts with proteins involved in energy-yielding reactions and other important cellular functions
• Integral membrane proteins• Firmly embedded in the membrane
• Peripheral membrane proteins• One portion anchored in the membrane
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2.7 Membrane Structure
Archaeal membranes depart from “standard” model
• Ether linkages in phospholipids of Archaea (Figure 2.16)
• Bacteria and Eukarya that have ester linkages in
phospholipids
• Archaeal lipids lack fatty acids; have isoprenes instead
• Major lipids are glycerol diethers and tetraethers
(Figure 2.17a and b)
• Can exist as lipid monolayers, bilayers, or mixture
(Figure 2.17)
© 2015 Pearson Education, Inc. Figure 2.17
Phytanyl
Glycerol dietherCH3 groups
Isoprene unit
Biphytanyl
Diglycerol tetraethers
Crenarchaeol
Out Out
In In
Glycerophosphates
Phytanyl
Membrane protein
Lipid monolayer
Biphytanyl orcrenarchaeol
Lipid bilayer
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2.8 Membrane Function
• Permeability barrier (Figure 2.18)
• Polar and charged molecules must be transported
• Transport proteins accumulate solutes against the
concentration gradient
• Protein anchor
• Holds transport and other proteins in place
• Energy conservation
• Generation of proton motive force
© 2015 Pearson Education, Inc. Figure 2.18
Functions of the cytoplasmic membrane
Permeability barrier:Prevents leakage and functions as agateway for transport of nutrients into,and wastes out of, the cell
Protein anchor:Site of many proteins that participate intransport, bioenergetics, and chemotaxis
Energy conservation:Site of generation and dissipation of the proton motive force
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2.9 Nutrient Transport
• Carrier-mediated transport systems bring in
nutrients (Figure 2.19)
• Show saturation effect
• Highly specific
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2.9 Nutrient Transport
• Three major classes of transport systems in
prokaryotes based on mechanics (Figure 2.20)
• Simple transport
• Group translocation
• ABC system
• All require energy in some form, usually proton
motive force or ATP
© 2015 Pearson Education, Inc. Figure 2.20
Out In
R~
2
3
Transportedsubstance
P
P
ATP ADP + Pi
Simple transport:Driven by the energyin the proton motiveForce (H+ gradient)
Group translocation:Chemical modificationof the transportedsubstance driven byphosphoenolpyruvate
ABC transporter: Bindingproteins are involvedand energy comesfrom ATP.
1
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2.9 Nutrient Transport
• Three types of transport events are possible
based on directions: uniport, symport, and
antiport (Figure 2.21)
• Uniporters transport in one direction across the
membrane
• Symporters function as co-transporters
• Antiporters transport a molecule across the membrane
while simultaneously transporting another molecule in
the opposite direction
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2.9 Nutrient Transport
• Simple transport-example:
• Lac permease of Escherichia coli
• Lactose is transported into E. coli by the simple
transporter lac permease, a symporter
• Activity of lac permease is energy-driven by proton motive
force
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2.9 Nutrient Transport
• Example of Group Transport: phosphotransferase
(PTS) system in E. coli (Figure 2.22)
• Type of group translocation: substance transported is
chemically modified during transport across the
membrane
• Best-studied system
• Moves glucose, fructose, mannose, others
• Five cytoplasmic proteins required
• Energy derived from phosphoenolpyruvate (PEP)
© 2015 Pearson Education, Inc. Figure 2.22
Nonspecific components Specific components
Cytoplasmicmembrane
OutGlucose
Directionof glucosetransport
Glucose 6_PP
InDirection of P transfer
PPyruvate
PE P
EnzI
HPr EnzIIa
EnzIIb
EnzIIc
P
© 2015 Pearson Education, Inc.
2.9 Nutrient Transport
• ABC (ATP-binding cassette) systems (Figure 2.23)
• >200 different systems identified in prokaryotes
• Often involved in uptake of organic compounds (e.g., sugars,
amino acids), inorganic nutrients (e.g., sulfate, phosphate),
and trace metals
• Typically display high substrate specificity
• Gram-negatives employ periplasmic substrate-binding
proteins and ATP-driven transport proteins
• Gram-positives employ fixed substrate-binding proteins and
ATP-driven transport proteins
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IV. Cell Walls of Bacteria and Archaea
• 2.10 Peptidoglycan
• 2.11 LPS: The Outer Membrane
• 2.12 Archaeal Cell Walls
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2.10 Peptidoglycan-the Wonder Wall
• Gram-positives and gram-negatives have different
cell wall structure (Figure 2.24)
• Gram-negative cell wall
• Two layers: lipopolysaccharide (LPS) and
peptidoglycan
• Gram-positive cell wall
• One layer: peptidoglycan
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2.10 Peptidoglycan
• Peptidoglycan (Figure 2.25)
• Rigid layer that provides strength to cell wall
• Polysaccharide composed of:
• N-acetylglucosamine and N-acetylmuramic acid
• Amino acids-vary
• Cross-linked for strength
• Different cross-linking in gram-negative bacteria and
gram-positive bacteria (Figure 2.26)
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Peptidoglycan-(aka murein)a layer of sugars and amino acids linked together to form a chain-link type structure outside the cytoplasmic membrane.
NAG and NAM are the sugars
© 2015 Pearson Education, Inc. Figure 2.25
N-Acetylglucosamine N-Acetylmuramic acid
𝛃(1,4) 𝛃(1,4) 𝛃(1,4)
N-Acetyl group
Lysozyme-sensitivebondPeptide
cross-linksL-Alanine
D-Glutamic acid
Diaminopimelicacid
D-Alanine
Glyc
an te
trape
ptid
e
( M )( G )NAG and NAM
Non-proteinPeptide bond
Beta 1-4Glycoside inGram -)
© 2015 Pearson Education, Inc.
Unusual amino acids
Targets for antibiotics:
Penicillin, Vancomycin: block cross-bridge formation
See: https://www.asm.org/index.php/antibiotics-that-inhibit-bacterial-peptidoglycan-synthesis
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2.10 Peptidoglycan
• Gram-positive cell walls (Figure 2.27)
• Can contain up to 90% peptidoglycan
• Common to have teichoic acids (charged
carbohydrates) embedded in their cell wall for rigidity
• Wall teichoic acids-embedded in peptidoglycan only
• Lipoteichoic acids: extend to cytoplasmic membrane
and covalently bound to membrane lipids
© 2015 Pearson Education, Inc. Figure 2.27
Teichoic acid Peptidoglycan Lipoteichoicacid
Cytoplasmic membrane
Wall-associatedprotein
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2.10 Peptidoglycan-not present in all microbes• Some Bacteria have cell walls with a different
chemical structure that is not really Gram + or –(Mycobacteria) they are called “acid-fast”
• Some prokaryotes lack cell walls• Mycoplasmas• Group of pathogenic bacteria
• Thermoplasma• Species of Archaea
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2.11 LPS: The Outer Membrane
• Total cell wall contains ~10% peptidoglycan
• Most of cell wall composed of outer membrane,
aka lipopolysaccharide (LPS) layer• LPS consists of core polysaccharide and O-
polysaccharide and a membrane anchor (Lipid “A”)
(Figure 2.28)
• LPS replaces most of phospholipids in outer half of outer
membrane (Figure 2.29)
• Endotoxin: the toxic component of LPS
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O-specificpolysaccharide
Core polysaccharide
Lipid A Protein
Lipopolysaccharide (LPS)
Phospholipid
PorinPorin
Lipoprotein
Outer membrane
Periplasm
Cytoplasmicmembrane
8 nm
Out
Cellwall
Outer membrane
Periplasm
Cytoplasmicmembrane
PeptidoglycanPeptidoglycan
In
Figure 2.29
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2.11 LPS: The Outer Membrane
• Periplasm: space located between cytoplasmic
and outer membranes (Figure 2.29)
• ~15 nm wide
• Contents have gel-like consistency
• Houses many proteins
• Porins: channels for movement of hydrophilic
low-molecular-weight substances (Figure 2.29c)
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2.12 Archaeal Cell Walls
• Most Archaea have cell walls, some do not
• Same functions as in Bacteria
• When present, Archaeal walls are built differently
than Bacterial cell wall
• Highly variable but two main types
• Pseudopeptidoglycan (pseudomurein) or
• “S-layers”
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2.12 Archaeal Cell Walls
• Pseudomurein aka pseudopeptidoglycan
• Polysaccharide similar to peptidoglycan (Figure 2.30)
• Composed of N-acetylglucosamine and N-
acetylalosaminuronic acid (NAG and NAS)
• Beta 1-3 glycosides
• Found in cell walls of some Archaea including
Methanobacteria (methane producers)
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2.12 Archaeal Cell Walls
• S-Layers (Surface Layer)• “Most common” cell wall type among Archaea
• Consist of protein, glycoprotein or sugar
• Paracrystalline structure (Figure 2.31)
• Network of proteins/glycoproteins attached to outer
surface of plasma membrane
• Has openings or “pores”
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http://www.nature.com/nrmicro/journal/v13/n10/fig_tab/nrmicro3480_F1.html
Diagrams of wall structure
http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit1/prostruct/cw.html
More information on cell walls
Further reading if you want it
http://www.ucmp.berkeley.edu/archaea/archaea.html
More on the Archaea
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V. Other Cell Surface Structures and Inclusions
• 2.13 Cell Surface Structures (Glycocalyx)
• 2.14 Cell Inclusions
• 2.15 Gas Vesicles
• 2.16 Endospores
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2.13 Cell Surface Structures• Glycocalyx = capsules and slime layers• Polysaccharide layers, glycolipids, glycoproteins (Figure
2.32)
• May be thick or thin, rigid or flexible
• Assist in attachment to surfaces
• Protect against phagocytosis
• Resist desiccation
• External to cell
• In Gram + and –
• Not part of LPS outer membrane
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2.13 Cell Surface Structures
• Capsules and slime layers• Slime layer = unorganized, loosely attached, aka “slime
wall”
• Capsule = more organized, tighter, harder to remove
Exact composition, function, appearance is species-specific
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2.13 Cell Surface Structures
• Fimbriae• Filamentous protein structures for attachment
• curlin, adhesin
• Enable organisms to stick to surfaces or form pellicles
May enhance pathogenicity
Relatively thin and short
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2.13 Cell Surface Structures
• Pilus (pili) • Filamentous protein structures
• Pilin
• Not much different from fimbriae but typically longer and
thicker-term usually reserved for appendage with
specific known function
• Such as sex pilus of E. coli. Facilitate genetic exchange
between cells (conjugation)
• Type IV pili involved in twitching motility (grappling hook
motility)
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2.13 Cell Surface Structures
Sex pilus facilitates genetic exchange between cells
(conjugation)
Type IV pili involved in twitching motility (grappling hook
motility)
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2.14 Cell Inclusions
• Inclusions visible in many prokaryotic cells
• Solid or semi-solid aggregates
• Mostly used for storage of vital nutrients
• Minerals, carbohydrates
• Not membrane-bound
• Aka storage granule
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2.14 Cell Inclusions• Carbon storage polymers
• Poly-β-hydroxybutyric acid (PHB): lipid (Figure 2.35)
• Glycogen: glucose polymer
• Polyphosphates: accumulations of inorganic phosphate
(Figure 2.36a)
• Sulfur globules: composed of elemental sulfur (Figure
2.36b)
• Carbonate minerals: composed of barium, strontium, and
magnesium (Figure 2.37)
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2.14 Cell Inclusions• Magnetosomes: magnetic storage inclusions (Figure 2.38)
• These inclusions do have a membrane to enclose iron
magnetite crystals
• Magnetosomes orient cell in Earth’s magnetic field
• Helps organisms know up from down
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2.15 Gas Vesicles
• Gas vesicles• Confer buoyancy in
planktonic cells (Figure
2.39)
• Spindle-shaped, gas-filled
structures made of protein
(Figure 2.40)
• Impermeable to water
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2.15 Gas Vesicles
• Molecular structure
of gas vesicles
• Gas vesicles are
composed of two
proteins, GvpA and
GvpC (Figure 2.41)
• Function by
decreasing cell
density
© 2015 Pearson Education, Inc. Figure 14.4
Photosynthetic bacteria like this cyanobacterium usually have internal membranes
© 2015 Pearson Education, Inc. Figure 14.15
Others-like this green sulfur bacterium-utilize membrane-boundVesicles to house photosynthetic apparatus
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2.16 Endospores
• Endospores• Highly differentiated cells resistant to heat, harsh
chemicals, and radiation (Figure 2.42 )
• “Dormant” stage of bacterial life cycle (Figure 2.43) may
persist for decades in environment (soil)
• Ideal for dispersal via wind, water, or animal gut
• Present only in some gram-positive bacteria
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Endospore Formation•Endospore forms inside mother cell•Core is dormant, inert, minimal but alive•Several tough layers form a resistant shell around core•Chemical makeup of each layer is different•Small acid-soluble spore proteins (SASP) contribute to resistance
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YouTube version:
https://www.youtube.com/watch?v=7zCQLITFEb0
Note: dipicolinic acid
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VI. Microbial Locomotion
• 2.17 Flagella and Swimming Motility
• 2.18 Gliding Motility
• 2.19 Chemotaxis and Other Taxes
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2.17 Flagella and Swimming Motility
• Flagellum/flagella: extracellular structure that
assists in swimming
• Tend to be found on rods or spirals
• Cell may have 0, 1 or more
• Different arrangements: (a) peritrichous, (b) polar,
(c) lophotrichous (Figure 2.48) also amphitrichous
• Structurally very different from a eukaryotic flagellum
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2.17 Flagella and Swimming Motility
• Flagellar structure of Bacteria
• Consists of several components (Figure 2.51)
• Hollow filament composed of flagellin
• Move by rotation
• Hook region allows propeller action
• Powered by proton motive force
© 2015 Pearson Education, Inc. Figure 2.51
15–20 nm
Filament
Flagellin
LP
MS
HookOutermembrane(LPS)
L Ring
P Ring
Rod
PeptidoglycanPeriplasm
MS Ring
Basalbody
C Ring
Cytoplasmicmembrane
Fli proteins(motor switch)
Mot proteinMot protein
45 nm
Rod
MS Ring
C Ring
Mot protein
+ + + + + + + +
− − − − − − − −
© 2015 Pearson Education, Inc.
2.17 Flagella and Swimming Motility
• Flagellar structure of Archaea
• Archaellum
• More similar to bacterial pilus than flagellum
• Thinner, not hollow
• Probably powered by ATP
• No hook region
• Motility, recognition, attachment
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14.20 Spirochetes and atypical flagella
• Treponema pallidum and Borrelia burgdorferii are notable
• Spirochaetes• Gram-negative, motile, and coiled (Figure 14.49)
• Widespread in aquatic environments and in animals
• Have endoflagella: located in the periplasm of the cell (Figure 14.50)
© 2015 Pearson Education, Inc. Figure 14.50
Endoflagellum
Protoplasmiccylinder
Outersheath
Endoflagellum (rigid,rotates, attached to oneend of protoplasmiccylinder)
Outer sheath(flexible)
Protoplasmic cylinder(rigid, generally helical)
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2.18 Gliding Motility
• Gliding motility• Flagella-independent motility (Figure 2.56)
• Slower and smoother than swimming
• Movement typically occurs along long axis of cell
• Requires surface contact
• Mechanisms (not well understood)
• Excretion of polysaccharide slime
• Gliding-specific proteins
• Pili
© 2015 Pearson Education, Inc.
2.19 Chemotaxis and Other Taxes
• Taxis: directed movement in response to chemical
or physical gradients
• Chemotaxis: response to chemicals
• Phototaxis: response to light
• Aerotaxis: response to oxygen
• Osmotaxis: response to ionic strength
• Hydrotaxis: response to water
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2.19 Chemotaxis and Other Taxes
• Chemotaxis• Best studied in E. coli
• “Run and tumble” behavior (Figure 2.57)
• Attractants sensed by chemoreceptors
• http://web.biosci.utexas.edu/psaxena/
MicrobiologyAnimations/Animations/BacterialMotility/
PLAY_motility.html
© 2015 Pearson Education, Inc.
• Flagella rotate clockwise = tumble
• Flagella rotate counterclockwise = straight line run
• Controlled by simple molecular clock system in
cell
• With no chemotaxis tumbles and runs alternate so
that no net movement occurs: random walk
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• With chemotaxis, timing of clock is adjusted
• Runs are longer
• Produces net movement
• Chemotaxis works by controlling the rate of
switching between run and tumble-it re-sets clock
to favor run over tumble
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