1. Cell Structure and Function in Bacteria and Archaea
Chapter 3
Cell Structure and Function in Bacteria and Archaea

2. I. Cell Shape and Size 3.1 Cell Morphology
3.2 Cell Size and the Significance of Smallness
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3. 3.1 Cell Morphology Morphology = cell shape
Major cell morphologies (Figure 3.1)
Coccus (pl. cocci): spherical or ovoid
Rod: cylindrical shape
Spirillum: spiral shape
Cells with unusual shapes
Spirochetes, appendaged bacteria, and filamentous bacteria
Many variations on basic morphological types
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4. Coccus Rod Spirillum Spirochete Stalk Hypha Budding and
Figure 3.1
Spirochete
Coccus
Stalk
Hypha
Rod
Budding and
appendaged bacteria
Figure 3.1 Representative cell morphologies of prokaryotes.
Spirillum
Filamentous bacteria
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5. 3.1 Cell Morphology
Morphology typically does not predict physiology, ecology, phylogeny, etc. of a prokaryotic cell
Selective forces may be involved in setting the morphology
Optimization for nutrient uptake (small cells and those with high surface-to-volume ratio)
Swimming motility in viscous environments or near surfaces (helical or spiral-shaped cells)
Gliding motility (filamentous bacteria)
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6. 3.2 Cell Size and the Significance of Smallness
Size range for prokaryotes: 0.2 µm to >700 µm in diameter
Most cultured rod-shaped bacteria are between 0.5 and 4.0 µm wide and <15 µm long
Examples of very large prokaryotes
Epulopiscium fishelsoni (Figure 3.2a)
Thiomargarita namibiensis (Figure 3.2b)
Size range for eukaryotic cells: 10 to >200 µm in diameter
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7. Figure 3.2 Figure 3.2 Some very large prokaryotes.
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8. 3.2 Cell Size and the Significance of Smallness
Surface-to-Volume Ratios, Growth Rates, and Evolution
Advantages to being small (Figure 3.3)
Small cells have more surface area relative to cell volume than large cells (i.e., higher S/V)
support greater nutrient exchange per unit cell volume
tend to grow faster than larger cells
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9. Surface Volume Surface Volume r = 1 m = 3 = 1.5
Figure 3.3
r = 1 m
r = 1 m
Surface area (4r2) = 12.6 m2 3 4
Volume ( r3) = 4.2 m3
Surface
= 3
Volume
r = 2 m
r = 2 m
Surface area = 50.3 m2
Volume = 33.5 m3
Figure 3.3 Surface area and volume relationships in cells.
Surface
= 1.5
Volume
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10. 3.2 Cell Size and the Significance of Smallness
Lower Limits of Cell Size
Cellular organisms <0.15 µm in diameter are unlikely
Open oceans tend to contain small cells (0.2–0.4 µm in diameter)
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11. II. The Cytoplasmic Membrane and Transport
3.4 Functions of the Cytoplasmic Membrane
3.5 Transport and Transport Systems
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12. 3.3 The Cytoplasmic Membrane in Bacteria and Archaea
Thin structure that surrounds the cell
6–8 nm thick
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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13. 3.3 The Cytoplasmic Membrane
Composition of Membranes
General structure is phospholipid bilayer (Figure 3.4)
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 point inward to form hydrophobic environment; hydrophilic portions remain exposed to external environment or the cytoplasm
Animation: Membrane Structure
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14. Glycerol Fatty acids Phosphate Ethanolamine Hydrophilic region
Figure 3.4
Glycerol
Fatty acids
Phosphate
Ethanolamine
Hydrophilic
region
Hydrophobic
Fatty acids
region
Figure 3.4 Phospholipid bilayer membrane.
Hydrophilic
region
Glycerophosphates
Fatty acids
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15. 3.3 The Cytoplasmic Membrane
Cytoplasmic Membrane (Figure 3.5)
6–8 nm wide
Embedded proteins
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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16. Out In Phospholipids Hydrophilic groups 6–8 nm Hydrophobic groups
Figure 3.5
Out
Phospholipids
Hydrophilic
groups
6–8 nm
Hydrophobic
groups In
Figure 3.5 Structure of the cytoplasmic membrane.
Integral
membrane
Phospholipid
proteins
molecule
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17. 3.3 The Cytoplasmic Membrane
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
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18. 3.3 The Cytoplasmic Membrane
Membrane Proteins (cont’d)
Integral membrane proteins
Firmly embedded in the membrane
Peripheral membrane proteins
One portion anchored in the membrane
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19. 3.3 The Cytoplasmic Membrane
Membrane-Strengthening Agents
Sterols
Rigid, planar lipids found in eukaryotic membranes Strengthen and stabilize membranes
Hopanoids
Structurally similar to sterols
Present in membranes of many Bacteria
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20. 3.3 The Cytoplasmic Membrane
Archaeal Membranes
Ether linkages in phospholipids of Archaea (Figure 3.6)
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 3.7a and b)
Can exist as lipid monolayers, bilayers, or mixture (Figure 3.7d and e)
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21. Ester Ether Bacteria Archaea Eukarya Figure 3.6
Figure 3.6 General structure of lipids.
Bacteria
Archaea
Eukarya
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22. CH3 groups Isoprene unit Glycerol diether Figure 3.7a Phytanyl
Figure 3.7 Major lipids of Archaea and the architecture of archaeal membranes.
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23. Diglycerol tetraethers
Figure 3.7b
Biphytanyl
Diglycerol tetraethers
Figure 3.7 Major lipids of Archaea and the architecture of archaeal membranes.
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24. Figure 3.7c
Crenarchaeol
Figure 3.7 Major lipids of Archaea and the architecture of archaeal membranes.
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25. Out In Glycerophosphates Phytanyl Membrane protein Lipid bilayer
Figure 3.7d
Out
Glycerophosphates
Phytanyl
Membrane protein In
Figure 3.7 Major lipids of Archaea and the architecture of archaeal membranes.
Lipid bilayer
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26. Out In Biphytanyl Lipid monolayer Figure 3.7e
Figure 3.7 Major lipids of Archaea and the architecture of archaeal membranes.
Lipid monolayer
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27. 3.4 Functions of the Cytoplasmic Membrane
Permeability Barrier (Figure 3.8)
Polar and charged molecules must be transported
Transport proteins accumulate solutes against the concentration gradient
Protein Anchor
Holds transport proteins in place
Energy Conservation
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28. Permeability barrier: Protein anchor: Energy conservation:
Figure 3.8
Permeability barrier:
Prevents leakage and functions
as a gateway for transport of
nutrients into, and wastes out
of, the cell
Protein anchor:
Site of many proteins that
participate in transport,
bioenergetics, and chemotaxis
Energy conservation:
Site of generation and use of the
proton motive force
Figure 3.8 The major functions of the cytoplasmic membrane.
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29. 3.5 Transport and Transport Systems
Carrier-Mediated Transport Systems (Figure 3.9)
Show saturation effect
Highly specific
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30. Transporter saturated with substrate
Figure 3.9
Transporter saturated
with substrate
Rate of solute entry
Transport
Figure 3.9 Transport versus diffusion.
Simple diffusion
External concentration of solute
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31. 3.5 Transport and Transport Systems
Three major classes of transport systems in prokaryotes (Figure 3.10)
Simple transport
Group translocation
ABC system
All require energy in some form, usually proton motive force or ATP
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32. Out In Simple transport: Driven by the energy in the proton motive
Figure 3.10 In
Simple transport:
Driven by the energy
in the proton motive
force
Out
Transported
substance
Group translocation:
Chemical modification
of the transported
substance driven by
phosphoenolpyruvate 1
Figure 3.10 The three classes of transport systems. 2
ABC transporter:
Periplasmic binding
proteins are involved
and energy comes
from ATP 3
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33. 3.5 Transport and Transport Systems
Three transport events are possible: uniport, symport, and antiport (Figure 3.11)
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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34. Out In Uniporter Antiporter Symporter Figure 3.11
Figure 3.11 Structure of membrane-spanning transporters and types of transport events.
Uniporter Antiporter Symporter
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35. 3.5 Transport and Transport Systems
Simple Transport:
Lac Permease of Escherichia coli (Figure 3.12)
Lactose is transported into E. coli by the simple transporter lac permease, a symporter
Activity of lac permease is energy driven
Other symporters, uniporters, and antiporters
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36. Figure 3.12
Out In
Figure 3.12 The lac permease of Escherichia coli and several other well-characterized simple transporters.
Sulfate
symporter
Potassium
uniporter
Phosphate
symporter
Sodium-proton
antiporter
Lac permease
(a symporter)
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37. 3.5 Transport and Transport Systems
The Phosphotransferase System in E. coli (Figure 3.13)
Type of group translocation: substance transported is chemically modified during transport across the membrane
Best-studied system
Moves glucose, fructose, and mannose
Five proteins required
Energy derived from phosphoenolpyruvate
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38. Figure 3.13
Glucose
Out
Cytoplasmic
membrane
Nonspecific components
Specific components
Enz
IIC
Direction
of glucose
transport PE
Enz
HPr
Enz
IIa
Enz
IIb
Pyruvate In
Figure 3.13 Mechanism of the phosphotransferase system of Escherichia coli.
Direction of P transfer
Glucose 6–P
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39. 3.5 Transport and Transport Proteins
ABC (ATP-Binding Cassette) Systems (Figure 3.14)
>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
Contain periplasmic binding proteins
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40. Out In Periplasm Peptidoglycan Periplasmic binding protein Transported
Figure 3.14
Peptidoglycan
Periplasmic
binding protein
Periplasm
Transported
substance
Out
Membrane-
spanning
transporter
Figure 3.14 Mechanism of an ABC transporter.
ATP-
hydrolyzing
protein In
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41. 3.5 Transport and Transport Proteins
Protein Export
Translocases: responsible for exporting proteins through and inserting into prokaryotic membranes
Sec translocase system: exports proteins and inserts integral membrane proteins into the membrane
Type III secretion system: common in pathogenic bacteria; secreted protein translocated directly into host
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42. III. Cell Walls of Prokaryotes
3.6 The Cell Wall of Bacteria: Peptidoglycan
3.7 The Outer Membrane
3.8 Cell Walls of Archaea
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43. 3.6 The Cell Wall of Bacteria: Peptidoglycan
Peptidoglycan (Figure 3.16)
Rigid layer that provides strength to cell wall
Polysaccharide composed of
N-acetylglucosamine and N-acetylmuramic acid
Amino acids
Lysine or diaminopimelic acid (DAP)
Cross-linked differently in gram-negative bacteria and gram-positive bacteria (Figure 3.17)
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44. Lysozyme- sensitive bond Diaminopimelic acid N-Acetylglucosamine
Figure 3.16
N-Acetylglucosamine
N-Acetylmuramic acid
N-Acetyl
group
Glycan tetrapeptide
Lysozyme-
sensitive
bond
Peptide
cross-links
Figure 3.16 Structure of the repeating unit in peptidoglycan, the glycan tetrapeptide.
L-Alanine
D-Glutamic acid
Diaminopimelic
acid
D-Alanine
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45. Figure 3.17 Polysaccharide backbone Interbridge Peptides
Escherichia coli
(gram-negative)
Staphylococcus aureus
(gram-positive)
Figure 3.17 Peptidoglycan in Escherichia coli and Staphylococcus aureus. Y
Peptide bonds X
Glycosidic bonds
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46. 3.6 The Cell Wall of Bacteria: Peptidoglycan
Gram-Positive Cell Walls (Figure 3.18)
Can contain up to 90% peptidoglycan
Common to have teichoic acids (acidic substances) embedded in the cell wall
Lipoteichoic acids: teichoic acids covalently bound to membrane lipids
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47. Figure 3.18
Peptidoglycan
cable
Ribitol
Teichoic acid
Peptidoglycan
Wall-associated
protein
Lipoteichoic
acid
Figure 3.18 Structure of the gram-positive bacterial cell wall.
Cytoplasmic membrane
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48. 3.6 The Cell Wall of Bacteria: Peptidoglycan
Prokaryotes That Lack Cell Walls
Mycoplasmas
Group of pathogenic bacteria
Thermoplasma
Species of Archaea
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49. 3.7 The Outer Membrane
Total cell wall contains ~10% peptidoglycan (Figure 3.20a)
Most of cell wall composed of outer membrane (aka lipopolysaccharide [LPS] layer)
LPS consists of core polysaccharide and O-polysaccharide
LPS replaces most of phospholipids in outer half of outer membrane
Endotoxin: the toxic component of LPS
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50. Figure 3.20a Out In Cell wall O-polysaccharide Core polysaccharide
Lipid A
Protein
Out
Lipopolysaccharide
(LPS)
Porin
Outer
membrane
8 nm
Cell
wall
Phospholipid
Peptidoglycan
Periplasm
Lipoprotein
Figure 3.20 The gram-negative cell wall.
Cytoplasmic
membrane In
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51. 3.7 The Outer Membrane
Porins: channels for movement of hydrophilic low-molecular weight substances (Figure 3.20b)
Periplasm: space located between cytoplasmic and outer membranes
~15 nm wide
Contents have gel-like consistency
Houses many proteins
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52. Figure 3.20b Periplasm Cytoplasmic membrane Outer membrane
Figure 3.20 The gram-negative cell wall.
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53. 3.7 The Outer Membrane
Structural differences between cell walls of gram-positive and gram-negative Bacteria are responsible for differences in the Gram stain reaction
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54. 3.8 Cell Walls of Archaea No peptidoglycan Typically no outer membrane
Pseudomurein
Polysaccharide similar to peptidoglycan (Figure 3.21)
Composed of N-acetylglucosamine and N-acetyltalosaminuronic acid
Found in cell walls of certain methanogenic Archaea
Cell walls of some Archaea lack pseudomurein
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55. group N-Acetylglucosamine N-Acetyltalosaminuronic acid
Figure 3.21
N-Acetyltalosaminuronic
acid
Lysozyme-insensitive
N-Acetyl
group
N-Acetylglucosamine
Figure 3.21 Pseudomurein.
Peptide
cross-links
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56. 3.8 Cell Walls of Archaea S-Layers
Most common cell wall type among Archaea
Consist of protein or glycoprotein
Paracrystalline structure (Figure 3.22)
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57. Figure 3.22
Figure 3.22 The S-layer.
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58. IV. Other Cell Surface Structures and Inclusions
3.10 Cell Inclusions
3.11 Gas Vesicles
3.12 Endospores
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59. 3.9 Cell Surface Structures
Capsules and Slime Layers
Polysaccharide layers (Figure 3.23)
May be thick or thin, rigid or flexible
Assist in attachment to surfaces
Protect against phagocytosis
Resist desiccation
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60. Cell Capsule Figure 3.23 Figure 3.23 Bacterial capsules.
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61. 3.9 Cell Surface Structures
Fimbriae
Filamentous protein structures (Figure 3.24)
Enable organisms to stick to surfaces or form pellicles
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62. Flagella Fimbriae Figure 3.24 Figure 3.24 Fimbriae.
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63. 3.9 Cell Surface Structures
Pili
Filamentous protein structures (Figure 3.25)
Typically longer than fimbriae
Assist in surface attachment
Facilitate genetic exchange between cells (conjugation)
Type IV pili involved in twitching motility
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64. Virus- covered pilus Figure 3.25 Figure 3.25 Pili.
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65. 3.10 Cell Inclusions Carbon storage polymers
Poly--hydroxybutyric acid (PHB): lipid (Figure 3.26)
Glycogen: glucose polymer
Polyphosphates: accumulations of inorganic phosphate (Figure 3.27)
Sulfur globules: composed of elemental sulfur
Magnetosomes: magnetic storage inclusions (Figure 3.28)
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66. Polyhydroxyalkanoate
Figure 3.26
-carbon
Figure 3.26 Poly-β-hydroxyalkanoates.
Polyhydroxyalkanoate
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67. Polyphosphate Sulfur Figure 3.27
Figure 3.27 Polyphosphate and sulfur storage products.
Sulfur
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68. Figure 3.28 Figure 3.28 Magnetotactic bacteria and magnetosomes.
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69. 3.11 Gas Vesicles Gas Vesicles
Confer buoyancy in planktonic cells (Figure 3.29)
Spindle-shaped, gas-filled structures made of protein (Figure 3.30)
Gas vesicle impermeable to water
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70. Figure 3.29 Figure 3.29 Buoyant cyanobacteria.
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71. Figure 3.30
Figure 3.30 Gas vesicles of the cyanobacteria Anabaena and Microcystis.
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72. 3.11 Gas Vesicles Molecular Structure of Gas Vesicles
Gas vesicles are composed of two proteins: GvpA and GvpC (Figure 3.31)
Function by decreasing cell density
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73. Ribs GvpA GvpC Figure 3.31 Figure 3.31 Gas vesicle architecture.
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74. 3.12 Endospores Endospores
Highly differentiated cells resistant to heat, harsh chemicals, and radiation (Figure 3.32)
“Dormant” stage of bacterial life cycle (Figure 3.33)
Ideal for dispersal via wind, water, or animal gut
Only present in some gram-positive bacteria
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75. Terminal Subterminal Central spores spores spores Figure 3.32
Figure 3.32 The bacterial endospore.
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76. Vegetative cell Developing spore Germination Sporulating cell
Figure 3.33
Vegetative cell
Developing spore
Germination
Sporulating cell
Figure 3.33 The life cycle of an endospore-forming bacterium.
Mature spore
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77. 3.12 Endospores Endospore Structure (Figure 3.35) Structurally complex
Contains dipicolinic acid
Enriched in Ca2+
Core contains small acid-soluble proteins (SASPs)
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78. Exosporium Spore coat Core wall Cortex DNA Figure 3.35
Figure 3.35 Structure of the bacterial endospore.
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79. 3.12 Endospores The Sporulation Process
Complex series of events (Figure 3.37)
Genetically directed
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80. Sporulation stages Vegetative cycle Figure 3.37 Coat Spore coat, Ca2
uptake, SASPs,
dipicolinic acid
Free endospore
Maturation,
cell lysis
Stage VI, VII
Growth
Stage V
Germination
Cortex
Vegetative
cycle
Sporulation
stages
Cell wall
Cytoplasmic
membrane
Cell
division
Asymmetric
cell division;
commitment
to sporulation,
Stage I
Stage IV
Cortex
formation
Figure 3.37 Stages in endospore formation.
Prespore
Septum
Engulfment
Mother cell
Stage III
Stage II
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81. V. Microbial Locomotion
3.13 Flagella and Motility
3.14 Gliding Motility
3.15 Microbial Taxes
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82. 3.13 Flagella and Motility
Flagellum (pl. flagella): structure that assists in swimming
Different arrangements: peritrichous, polar, lophotrichous (Figure 3.38)
Helical in shape
Animation: The Prokaryotic Flagellum
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83. Figure 3.38 Figure 3.38 Bacterial flagella.
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84. 3.13 Flagella and Motility Flagellar Structure
Consists of several components (Figure 3.41)
Filament composed of flagellin
Move by rotation
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85. Figure 3.41 L Filament P Flagellin MS Outer membrane (LPS) Hook L Ring
Rod
P Ring
Periplasm
Peptidoglycan
Figure 3.41 Structure and function of the flagellum in gram-negative Bacteria.
Rod
MS Ring
Basal
body
MS Ring
Mot
protein
C Ring
C Ring
Cytoplasmic
membrane
Mot protein
Fli proteins
(motor switch)
Mot protein
45 nm
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86. 3.13 Flagella and Motility Flagellar Synthesis
Several genes are required for flagellar synthesis and motility (Figure 3.43)
MS ring made first
Other proteins and hook made next
Filament grows from tip
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87. Figure 3.43 Filament synthesis Late hook Hook- filament junction Outer
membrane
Cap
Filament
Early hook
MS/C
ring
Motor (Mot)
proteins
P ring
L ring
Figure 3.43 Flagella biosynthesis.
Peptidoglycan
Cytoplasmic membrane
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88. 3.13 Flagella and Motility
Flagella increase or decrease rotational speed in relation to strength of the proton motive force
Differences in swimming motions (Figure 3.44)
Peritrichously flagellated cells move slowly in a straight line
Polarly flagellated cells move more rapidly and typically spin around
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89. Unidirectional flagella
Figure 3.44
Tumble—flagella
pushed apart
(CW rotation)
Bundled
flagella
(CCW rotation)
Flagella bundled
(CCW rotation)
Peritrichous
Reversible flagella
Figure 3.44 Movement in peritrichously and polarly flagellated prokaryotes.
CCW rotation
CW rotation
Unidirectional flagella
Cell
stops,
reorients
CW rotation
CW rotation
Polar
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90. 3.14 Gliding Motility Gliding Motility
Flagella-independent motility (Figure 3.46)
Slower and smoother than swimming
Movement typically occurs along long axis of cell
Requires surface contact
Mechanisms
Excretion of polysaccharide slime
Type IV pili
Gliding-specific proteins
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91. In Out Surface Cytoplasmic membrane Peptidoglycan Outer membrane
Figure 3.46 In
Cytoplasmic
membrane
Peptidoglycan
Outer
membrane
Figure 3.46 Gliding motility in Flavobacterium johnsoniae.
Out
Movement of outer
membrane proteins
Surface
Movement of cell
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92. 3.15 Microbial 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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93. 3.15 Microbial Taxes Chemotaxis Best studied in E. coli
Bacteria respond to temporal, not spatial, difference in chemical concentration
“Run and tumble” behavior (Figure 3.47)
Attractants and receptors sensed by chemoreceptors
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94. No attractant present: Random movement Attractant present:
Figure 3.47
Tumble
Attractant
Tumble
Run
Run
Figure 3.47 Chemotaxis in a peritrichously flagellated bacterium such as Escherichia coli.
No attractant present:
Random movement
Attractant present:
Directed movement
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95. 3.15 Microbial Taxes Measuring Chemotaxis (Figure 3.48)
Measured by inserting a capillary tube containing an attractant or a repellent in a medium of motile bacteria
Can also be seen under a microscope
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96. Control Attractant Repellent Attractant Cells per tube Control
Figure 3.48
Control
Attractant
Repellent
Attractant
Cells per tube
Control
Figure 3.48 Measuring chemotaxis using a capillary tube assay.
Repellent
Time
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