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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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“Universal Tree” of Life-3 Domains
BACTERIA
ARCHAEA
Entamoebae
Green nonsulfur
bacteria
Mitochondrion
GramProteobacteria positive
bacteria
Chloroplast
Cyanobacteria
Euryarchaeota
Methanosarcina
MethanoExtreme
Crenarchaeota bacterium
halophiles
Thermoproteus
Slime
molds
Macroorganisms
Animals
Fungi
Plants
Ciliates
Thermoplasma
Pyrodictium
Thermococcus
Nitrosopumilus
Green sulfur
bacteria
EUKARYA
Pyrolobus
Flagellates
Methanopyrus
Trichomonads
Thermotoga
Microsporidia
Thermodesulfobacterium
Aquifex
Diplomonads
Only cellular systems
Archaea and Bacteria are prokaryotes
Eukarya 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 gramnegative 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
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Coccus
Rod
Spirillum
Spirochete
Stalk
Hypha
Budding and appendaged bacteria
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Filamentous bacteria
Figure 2.11
2.5 Cell Morphology
Morphology is descriptive but typically does not
predict physiology, ecology, phylogeny, etc. of a
prokaryotic cell
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2.6 Cell Size and the Significance of Being
Small
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
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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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Figure 2.13
2.6 Cell Size and the Significance of Being
Small
Two prokaryotes notable for their large size
• Epulopiscium fishelsoni (Figure 2.12a and
below)
• Thiomargarita namibiensis (Figure 2.12b)
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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
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Glycerol
Fatty acids
Phosphate
Ethanolamine
Hydrophilic
region
Fatty acids
Hydrophobic
region
Hydrophilic
region
Glycerophosphates
Fatty acids
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Figure 2.14
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
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Out
Phospholipids
Hydrophilic
groups
6–8 nm
Hydrophobic
groups
In
Integral
membrane
proteins
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Phospholipid
molecule
Figure 2.15
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)
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Ester
Bacteria
Eukarya
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Ether
Archaea
Figure 2.16
Phytanyl
CH3 groups
Glycerol diether
Isoprene unit
Biphytanyl
Diglycerol tetraethers
Crenarchaeol
Out
Out
Glycerophosphates
Phytanyl
Biphytanyl or
crenarchaeol
Membrane protein
In
Lipid bilayer
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In
Lipid monolayer
Figure 2.17
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
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Functions of the cytoplasmic membrane
Permeability barrier:
Prevents leakage and functions as a
gateway for transport of nutrients into,
and wastes out of, the cell
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Protein anchor:
Site of many proteins that participate in
transport, bioenergetics, and chemotaxis
Energy conservation:
Site of generation and dissipation of the
proton motive force
Figure 2.18
2.9 Nutrient Transport
• Carrier-mediated transport systems bring in
nutrients (Figure 2.19)
• Show saturation effect
• Highly specific
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Transporter saturated
Transport
Simple diffusion
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Figure 2.19
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
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Simple transport:
Driven by the energy
in the proton motive
Force (H+ gradient)
In
Out
Transported
substance
Group translocation:
Chemical modification
of the transported
substance driven by
phosphoenolpyruvate
P
R~ P
1
2
ABC transporter:
Binding
proteins are involved
and energy comes
from ATP.
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3
ATP
ADP + Pi
Figure 2.20
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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Figure 2.21
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)
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Glucose
Out
Cytoplasmic
membrane
Nonspecific components
PE
Specific components
Enz
IIc
P
Enz
I
HPr
Enz
IIa
Direction
of glucose
transport
Enz
IIb
Pyruvate
P
P
Direction of P transfer
In
P
Glucose 6_P
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Figure 2.22
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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Figure 2.23 (Gram -)
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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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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
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Figure 2.24
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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N-Acetylglucosamine ( G ) N-Acetylmuramic acid ( M )
NAG and NAM
N-Acetyl
group
Peptide
cross-links
Lysozymesensitive
bond
Glycan tetrapeptide
Non-protein
Peptide bond
L-Alanine
D-Glutamic acid
Diaminopimelic
acid
Beta 1-4
Glycoside in
Gram -)
D-Alanine
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Figure 2.25
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
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Peptidoglycan
cable
Wall-associated
protein
Teichoic acid
Cytoplasmic membrane
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Peptidoglycan Lipoteichoic
acid
Figure 2.27
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 Opolysaccharide 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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Figure 2.28
O-specific
polysaccharide
Core polysaccharide
Lipid A
Protein
Out
Lipopolysaccharide
(LPS)
Porin
Outer
membrane
8 nm
Cell
wall
Phospholipid
Periplasm
Peptidoglycan
Lipoprotein
Cytoplasmic
membrane
In
Outer membrane
Periplasm
Cytoplasmic
membrane
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Figure 2.29
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/nr
micro3480_F1.html
Diagrams of wall structure
http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit1/pro
struct/cw.html
More information on cell walls
http://www.ucmp.berkeley.edu/archaea/archaea.html
More on the Archaea
Further reading if you want it
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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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Cell Capsule
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Figure 2.32
2.13 Cell Surface Structures
• Fimbriae
• Filamentous protein structures for attachment
• curlin, adhesin
• Enable organisms to stick to surfaces or form pellicles
Relatively thin and short
May enhance
pathogenicity
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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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β-carbon
Polyhydroxyalkanoate
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Figure 2.35
Sulfur
Polyphosphate
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Figure 2.36
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
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Photosynthetic bacteria like this cyanobacterium usually
have internal membranes
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Figure 14.4
Others-like this green sulfur bacterium-utilize membrane-bound
Vesicles to house photosynthetic apparatus
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Figure 14.15
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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Figure 2.42
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
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15–20 nm
L
Filament
P
MS
Flagellin
Hook
Outer
membrane
(LPS)
L
Ring
Rod
P
Ring
Periplasm
Peptidoglycan
+ + ++
+ + ++
MS Ring
Basal
body
C Ring
−−−−
Cytoplasmic
membrane
Mot protein
−−−−
Fli proteins
(motor switch)
Mot protein
45 nm
Rod
MS Ring
Mot
protein
C Ring
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Figure 2.51
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
• 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)
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Endoflagellum (rigid,
rotates, attached to one
end of protoplasmic
cylinder)
Endoflagellum
Outer sheath
(flexible)
Protoplasmic
cylinder
Outer
sheath
Protoplasmic cylinder
(rigid, generally helical)
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Figure 14.50
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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
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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
• Bacteria respond to temporal, not spatial, difference in
chemical concentration
• “Run and tumble” behavior (Figure 2.57)
• Attractants sensed by chemoreceptors
• Run and tumble movement
• http://web.biosci.utexas.edu/psaxena/MicrobiologyAnim
ations/Animations/BacterialMotility/PLAY_motility.html
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• Flagella rotate clockwise = tumble
• Flagella rotate counterclockwise = straight line run
• With no chemotaxis tumbles and runs alternate so
that no net movement occurs: random walk
• With chemotaxis runs are longer
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Tumble
Attractant
Tumble
Run
Run
No attractant present: Random
walk
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Attractant present: Directed
movement
Figure 2.57