Structure and Function of Bacteria and Archaea

1
Structure and Function ofBacteria and Archaea
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4 Structure and Function of Bacteria and Archaea

• 4.1 Microscopy
• 4.2 Morphology of Bacteria and Archaea
• 4.3 Structure, Composition, and Cell Function
• 4.4 The Cell Envelope
• 4.5 Extracellular Layers

3
4 Structure and Function of Bacteria and Archaea

• Cest un grand progrè, monsieur.
• Louis Pasteur, 1881
• Microbiology did not become a scientific
  discipline until appropriate instruments and
  techniques were developed, especially quality
  microscopes.

4
4.1 Microscopy

• Magnification can be achieved by bringing objects
  closer to the eyes.
• The near point is the closest the object can be
  and remain in focus.
• Objects smaller than 0.1 mm cant be seen the
  image on the retina is too small. Prokaryotes
  typically are 0.001 mm.

5
Figure 4.1 How the human eye magnifies
6
4.1 Microscopy

• Microscopes are needed to magnify the specimens.
• A simple microscope is the same as a magnifying
  glass.
• Leeuwenhoeks simple microscopes could magnify
  200- to 300-fold, with great clarity.

7
4.1 Microscopy

• A compound light microscope has two lenses
  between the specimen and the eye.
• The objective lens is placed near the specimen,
  the eyepiece or ocular lens is next to the eye.

8
4.1 Microscopy

• The viewer focuses by adjusting the distance
  between the two lenses.
• A real image is produced in the ocular diaphragm.
  The viewer sees a virtual image.

9
Figure 4.2 Compound light microscope (A)
10
4.1 Microscopy

• The magnification power is determined by
  multiplying the power of the objective lens by
  the power of the ocular lens.
• Most microscopes have several objective lenses
  10? (low power), 60? (high, dry, power), and 100?
  (oil immersion).

11
Figure 4.2 Compound light microscope (B)
12
4.1 Microscopy

• Light from a light source is focused by a
  condenser lens, to provide high intensity light.
• The iris diaphragm in the condenser opens or
  closes to adjust intensity.

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4.1 Microscopy

• Maximum magnification possible with a light
  microscope is about 1000 to 2000?. Greater
  magnification doesnt provide greater detail of
  the specimenempty magnification.

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4.1 Microscopy

• Resolving power ability of an optical system to
  produce a detailed, accurate image of the
  specimen.
• Distance between two points that can be separated
  by the lens in forming the image.

15
Figure 4.3 Resolving power or resolution
16
4.1 Microscopy

• Resolving power
• l wavelength of light
• h refractive index
• sin q angular aperture
• The smaller the value of d, the greater the
  resolution.

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4.1 Microscopy

• The best resolution is obtained by
• Short wavelength light
• A medium with high refractive index
• High angular aperture

18
4.1 Microscopy

• The refractive index is a measure of the ability
  of a material to bend light.
• By increasing this, more light from the specimen
  enters the objective lens, increasing resolution.
• The crown glass used in lenses has a high
  refractive index (1.5).

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4.1 Microscopy

• Immersion oils of high refractive index can be
  used to create a continuous, high refractive
  index between the specimen and objective
  lenshomogeneous immersion.

20
Figure 4.4 Nonhomogeneous and homogeneous
immersion
21
4.1 Microscopy

• Resolution can be increased by increasing the
  size of the aperture, up to a point.
• The theoretical maximum for the sin of ? is 1.0.
• Maximum resolving power is about 0.2 µmgood for
  observing prokaryote cells, but not their
  internal structure.

22
4.1 Microscopy

• Lens aberrations
• Chromatic aberrationlight at different
  wavelengths is focused at different planes.
• Spherical aberrationlight that enters periphery
  of lens is focused at a different plane than
  light that enters center of lens.

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4.1 Microscopy

• These aberrations were common in early
  microscopes.
• Corrected by multicomponent lens systems.
• Development of these, plus condenser systems,
  took about 200 years. The light microscope was
  perfected in the late nineteenth century.

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Figure 4.5 Objective lens
25
4.1 Microscopy

• Refractive index of prokaryotes is about the same
  as waterthey are nearly invisible under the
  light microscope.
• Three approaches
• Stain the cells
• Modify microscope
• Use a fluorescent stain and microscope

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4.1 Microscopy

• Dyes and stains
• Positive stainingorganism or structure takes up
  a dye.
• Negative stainingstain the background.

27
4.1 Microscopy

• Most dyes are aniline dyesorganic salts from
  coal tar.
• Basic dyesthe chromatophore (pigmented portion)
  of dye molecule has a positive charge.
• E.g., crystal violet, methylene blue

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Figure 4.6 Dyes
29
4.1 Microscopy

• Acid dyeschromatophore has a negative charge.
• E.g., Congo red, eosin

30
4.1 Microscopy

• Simple stains
• A suspension of microorganisms is spread on a
  slide and heated gently to fix it to the
  slidecalled a smear.
• Stain is added to the smear, then rinsed off.
• A fixative allows the specimen to adhere.

31
Figure 4.7 Various stains used for bacteria and
archaea (A)
32
4.1 Microscopy

• Differential stains are used to distinguish one
  group from another.
• Example Gram staindistinguishes between
  gram-positive and gram-negative bacteria.

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Box 4.1 The Gram Stain
34
Figure 4.7 Various stains used for bacteria and
archaea (B)
35
4.1 Microscopy

• Some staining procedures allow identification of
  cell structures.
• Specific stains exist for bacterial endospores,
  flagella, capsules, DNA, and others.

36
Figure 4.7 Various stains used for bacteria and
archaea (C, D)
37
4.1 Microscopy

• An ordinary microscope is a brightfield
  microscopeentire field of view is illuminated.
• In darkfield microscopy, the cells are bright
  against a dark background. Can be used for living
  cells.
• Cells are observed in wet mountscoverslip is
  placed on a live suspension.

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Box 4.2 The Darkfield Microscope (Part 1)
39
Box 4.2 The Darkfield Microscope (Part 2)
40
4.1 Microscopy

• Phase contrast, or phase microscope amplifies the
  difference in refractive index between a cell and
  its aqueous environment.
• The cells appear dark against a bright
  background.
• Cells can be observed live.

41
Figure 4.8 Phase contrast microscopy
42
4.1 Microscopy

• Fluorescent dyes emit longer wavelength light
  when illuminated by short wavelength light.
• Example acridine orangestains nucleic acids.
  Under UV light, cells fluoresce green to orange.
• Cells can be observed on an opaque surface.

43
Figure 4.9 Fluorescence microscopy
44
4.1 Microscopy

• Other fluorescent dyes
• DAPI is specific for DNA.
• FM4-64 is lipophilic and stains membranes.
• Specific proteins can be stained with fluorescent
  protein tags.
• Cell molecules can be identified with fluorescent
  dye-labeled antibodies.

45
4.1 Microscopy

• In a fluorescent microscope, the short wavelength
  light is provided by a mercury lampUV, or a
  halogen lampnear UV.
• The light is incident, not transmitted through
  the specimen.

46
4.1 Microscopy

• A confocal scanning microscope illuminates the
  specimen with a laser beam.
• The light is focused on the specimen by the
  objective lens.
• Mirrors scan the laser beam across the specimen.
• Also called epifluorescence scanning microscopy
  when lit from above.

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Figure 4.10 Confocal Microscope (Part 1)
48
Figure 4.10 Confocal Microscope (Part 2)
49
Figure 4.11 Confocal laser microscopy
50
Figure 4.12 Natural community
51
4.1 Microscopy

• Light microscope useful magnification is 1000 to
  2000. It is limited by the properties of
  lightyou cant observe objects smaller than the
  wavelengths of the illuminating source.

52
4.1 Microscopy

• The transmission electron microscope creates very
  short wavelengths using a beam of electrons.
• Wavelength is controlled by voltage to the
  electron gun.
• The theoretical resolution is 2 Å (angstrom 1 Å
  1010 m)

53
Figure 4.13 Transmission electron microscope
(TEM)
54
4.1 Microscopy

• The TEM uses electromagnetic lenses to bend the
  electron beam for focusing.
• A vacuum is required for electron flow through
  the lenses.
• Image is formed by electrons bombarding a
  phosphorescent screen.
• An electron micrograph is taken of the screen.

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4.1 Microscopy

• TEM lenses are equivalent to light
  microscopecondenser, objective, and projector
  lenses.
• Electrons are the illuminating source and magnets
  replace optical lenses.

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Figure 4.14 Illumination in light and electron
microscopes (Part 1)
57
Figure 4.14 Illumination in light and electron
microscopes (Part 2)
58
Figure 4.14 Illumination in light and electron
microscopes (Part 3)
59
Figure 4.15 Resolution in light and electron
microscopy
60
4.1 Microscopy

• For TEM, cells are placed on a tiny grid of
  copper, and are stained with heavy metals.
• To observe internal cell structure, thin
  sectioning is required. Cells are first
  dehydrated, and embedded in a plastic resin.
• Embedded cells are sliced into thin sections with
  an ultramicrotome using a diamond knife.

61
Figure 4.16 Thin section of a gram-negative
bacterium
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4.1 Microscopy

• Scanning electron microscopeelectrons are the
  illuminating source, but electrons are not
  transmitted through the specimen.
• Incident electrons are back-scattered or
  reflected from the specimen.
• Specimen is prepared by critical point
  dryingwater is removed as vapor to prevent
  damage to cells. Specimen is then coated with a
  metal such as gold.

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4.1 Microscopy

• SEM has a greater depth of field than TEMall
  parts of the specimen remain in focus, image
  looks three-dimensional.

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Figure 4.17 Scanning electron microscope (SEM)
65
4.1 Microscopy

• SEM can be equipped with an x-ray analyzer to
  determine the elemental composition of organisms.
• Elements with atomic weights greater than 20 can
  be analyzed.

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Figure 4.18 SEM-elemental analysis of manganese
and iron
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4.1 Microscopy

• Atomic Force Microscopy (AFM)the specimen is
  scanned by a cantilevered probe.
• Provides extremely high-resolution images of
  cells and their structures.
• Resolution0.05 µm allows direct visualization
  of living biological material.

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Figure 4.19 Atomic force microscope
69
Figure 4.20 Atomic force microscopy
70
4.2 Morphology of Bacteria and Archaea

• Most Bacteria and Archaea are single-celled
• Some are multicellular formsmany cells living
  together.
• Some are pleomorphicexhibit different shapes
  within the culture.

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4.2 Morphology of Bacteria and Archaea

• Unicellular spherical organisms are called cocci.
• Random cell division in different planes produces
  grape-like clusters called staphylococcus.
• If cells divide along only one axis, and remain
  attached, a chain of cells results.

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Figure 4.21 Typical bacterial and archaeal
shapes (A, B, C)
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4.2 Morphology of Bacteria and Archaea

• Diplococcusa chain of only two cells.
• Streptococcoschain of many cells.
• Some cocci divide along two perpendicular axes to
  form a sheet of cells.
• Others divide along three axes to form a packet
  or sarcina of cells.

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Figure 4.21 Typical bacterial and archaeal
shapes (D, E)
75
Figure 4.22 Coccus and rod shape showing binary
transverse fission
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4.2 Morphology of Bacteria and Archaea

• Rod or bacillusmost common shape in prokaryotes.
• When cells divide along one axis, two daughter
  cells are produced. If they remain attached, a
  chain results.

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Figure 4.23 Bacilli, or rods
78
4.2 Morphology of Bacteria and Archaea

• Helix shapesless common
• Bent rod or vibrioshort helix.
• Spirillumlonger helical cell, rigid and
  unbending.
• Spirocheteflexible, changes shape during
  movement.

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Figure 4.24 Curved and helical cells
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4.2 Morphology of Bacteria and Archaea

• Variations on the basic shapes
• Prosthecate bacteria have appendages that are
  extensions of the cell.
• Most prokaryotes reproduce asexually by budding
  or transverse binary fission.

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Figure 4.25 Prosthecate bacterium
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4.2 Morphology of Bacteria and Archaea

• Actinobacteriarod-shaped produce long filaments
  of many cells.
• The filaments form branches and result in an
  extensive network of hundreds to thousands of
  cells called a mycelium.

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Figure 4.26 Mycelial bacterium
84
4.2 Morphology of Bacteria and Archaea

• Trichomecells form a chain, but cells have
  closer relationship than in other chains.
• Motility and other functions result from action
  of all cells of the trichome.
• Some cells are specialized, such as heterocysts
  where N-fixation occurs.
• Often found in cyanobacteria.

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Figure 4.27 Filamentous bacteria
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4.2 Morphology of Bacteria and Archaea

• Some bacteria form associations with other
  species to form metabolic aggregates with
  specialized metabolic functions.
• Examples biofilms, symbiotic relationships.

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4.2 Morphology of Bacteria and Archaea

• Most bacteria have characteristic and uniform
  cell size.
• Some are small0.2 µmMycoplasma
• Others can be largeThiomargarita ca. 700 µm in
  diameter Epulopiscium, in intestines of
  surgeonfish is larger than most protists.
• Cell size and shape is determined by genetics and
  nutritional state.

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4.3 Structure, Composition, and Cell Function

• Fine structure and ultrastructure refer to
  subcellular features best observed with electron
  microscopy.
• Cells are lysed (broken open) and the components
  separated by centrifugation. The components can
  be analyzed biochemically and with the electron
  microscope.

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4.3 Structure, Composition, and Cell Function

• Cytoplasmall cell components bounded by the cell
  membrane. It contains
• Intracellular enzymesbiosynthetic, catabolic,
  and repair enzymes.
• Small molecule poolsamino acids, nucleotides,
  ions, cofactors, etc.
• Macromolecules DNA, RNA, proteins.

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Figure 4.28 Cross section of bacterial cell
envelopes (Part 1)
91
Figure 4.28 Cross section of bacterial cell
envelopes (Part 2)
92
4.3 Structure, Composition, and Cell Function

• DNA
• Prokaryotic DNA is a circular double-stranded
  molecule strands held together by hydrogen bonds
  between the nucleotide bases.
• DNA appears as fibrous material in thin sections.
  Not bounded by a membrane, region is called a
  nucleoid or nuclear area.

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Figure 4.29 Appearance of DNA by electron
microscopy
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4.3 Structure, Composition, and Cell Function

• If the cell is gently lysed, DNA is released and
  appears as a coiled structure.
• Length is about 1 mm, 1,000 times longer than the
  cell!
• In the cell, the DNA is wound in supercoils,
  accomplished by special enzymes.

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Figure 4.30 DNA strands released from cell
96
Figure 4.31 Supercoiled DNA
97
4.3 Structure, Composition, and Cell Function

• Molecular weight of prokaryote DNA is 109 to 1010
  Da.
• Da Dalton mass of a hydrogen atom
• The DNA contains about 4 106 base pairs or four
  megabase pairs (4 MB).
• Some intracellular symbionts have much smaller
  genomes.

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4.3 Structure, Composition, and Cell Function

• Prokaryote cells may have more than one copy of
  the DNA in the cell, if the cells are growing and
  dividing rapidly.

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4.3 Structure, Composition, and Cell Function

• In addition to the genomic DNA, prokaryotic cells
  often contain extrachromosomal elements or
  plasmids.
• Plasmids are double-stranded DNA that contain
  features that may enhance the survival of the
  cell, (e.g., that allow them to degrade
  antibiotics, or specific carbon compounds).

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4.3 Structure, Composition, and Cell Function

• Genetic material can be transferred from one
  organism to another
• TransformationDNA is released when cell lyses,
  taken up by another cell.
• Conjugationtransfer occurs during cell-to-cell
  contact.
• Transductionviruses transfer the DNA to another
  cell.

101
4.3 Structure, Composition, and Cell Function

• Ribosomes sites of protein synthesis.
• TranslationmRNA carries message in nucleotides
  from DNA to the ribosome, where amino acids are
  linked to form proteins.

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Figure 4.32 Protein synthesis
103
4.3 Structure, Composition, and Cell Function

• Ribosomes have two subunits one 30S and one 50S
  total 70S.
• S Svedberg unit, or sedimentation density
• Ribosomes consist of protein and rRNA.

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Figure 4.33 Ribosome structure (Part 1)
105
Figure 4.33 Ribosome structure (Part 2)
106
4.3 Structure, Composition, and Cell Function

• Bacterial and archaeal ribosomes differ somewhat
  in structure, and thus respond differently to the
  same antibiotic.
• Some antibiotics inhibit protein synthesis in
  Bacteria, but not in Archaea.

107
4.3 Structure, Composition, and Cell Function

• Bacterial endosporea spore or resting stage
  formed within the cell.
• Dormant spore can survive extended periods of
  desiccation and high temperatures resist UV
  radiation and disinfection. Some survive up to 50
  years.
• Many soil bacteria form endospores.

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4.3 Structure, Composition, and Cell Function

• Endospores have low water content, high calcium
  ion content, and a unique compounddipicolinic
  acid.
• Dipicolinic acids are believed to form a chelate
  complex are responsible for heat resistance.

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Figure 4.34 Dipicolinate
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4.3 Structure, Composition, and Cell Function

• Endospores require a special stains such as
  malachite green followed by safranin.

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4.3 Structure, Composition, and Cell Function

• Endospore-formers have two growth phases
• Vegetative growthnormal growth and reproduction.
• Sporulationresponse to nutrient limitation,
  after other responses such as chemotaxis,
  motility, and synthesis of extracellular enzymes
  to obtain nutrients.

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Figure 4.35 Sporulation of an endospore-forming
bacterium
113
4.3 Structure, Composition, and Cell Function

• Stages of sporulation
• DNA is replicated and the two molecules separated
  by formation of a cell membrane.
• Membrane of one cell (the sporangium) grows
  around the other, which becomes the forespore.

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Figure 4.36 Sporulation process (A)
115
4.3 Structure, Composition, and Cell Function

• The spore develops four distinct layers that can
  be seen in thin sections.
• The endospore can survive long periods in the
  environment.
• Under appropriate conditions, the endospore
  germinatestakes up water and swells, breaks
  spore coat, releases calcium dipicolinate and
  begins to grow vegetatively.

116
Figure 4.36 Sporulation process (B, C)
117
4.3 Structure, Composition, and Cell Function

• Location of endospore and its shape are important
  in classification.
• Example Clostridium tetani produces a terminal
  endospore that is larger than the cell diameter.

118
Figure 4.37 Clostridium tetani
119
4.3 Structure, Composition, and Cell Function

• Gas vesicles are produced by some aquatic
  prokaryotes.
• Gas vesicles are clustered in areas called gas
  vacuoles.
• Gas vacuoles are found in several groups,
  including cyanobacteria, proteobacteria, green
  sulfur bacteria, and Archaea.

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Figure 4.38 Gas vacuoles and gas vesicles
121
4.3 Structure, Composition, and Cell Function

• Gas vesicles are analyzed by lysing the cell and
  centrifugationthe vesicles float to the surface.
• Each vesicle has a thin protein shell surrounding
  a hollow space.
• About half of the protein consists of hydrophobic
  amino acids, thought to be located on the inside,
  to prevent water from entering the vesicle.

122
Figure 4.39 Gas vesicles
123
4.3 Structure, Composition, and Cell Function

• Gases freely diffuse through the protein shell.
  Gases in the vesicle are the same as those in the
  environment. The rigid shell maintains its shape.
  
• The primary function is to provide buoyancy in
  aquatic habitats.
• The depth at which species are found is
  determined by cell density, determined by amount
  of cell volume occupied by gas vesicles.

124
Box 4.3 The Hammer, Cork, and Bottle Experiment
The Hammer, Cork, and Bottle Experiment
125
4.3 Structure, Composition, and Cell Function

• Intracellular reserve productsnutrient reserves,
  stored as polymers
• Glycogen
• Starch
• Poly-b-hydroxybutyric acid
• Neutral lipids/hydrocarbons
• Cyanophycin
• Polyphosphate (volutin)
• Elemental sulfur

126
4.3 Structure, Composition, and Cell Function

• Glycogen and starch are polymers of glucose can
  be degraded as energy and carbon sources.
• Poly-b-hydroxybutyric acid (PHB) lipids
  synthesized when nitrogen is low but excess
  carbon is available. Visible as granules in light
  microscopy. Only found in prokaryotes.

127
Figure 4.40 PHB granules
128
4.3 Structure, Composition, and Cell Function

• Neutral lipids or hydrocarbons are accumulated
  from the environment by some species.
• Cyanophycin is a copolymer of the amino acids
  aspartic acid and arginine. Contains nitrogen
  found only in cyanobacteria.

129
4.3 Structure, Composition, and Cell Function

• Volutin or metachromatic granules polymers of
  phosphate units, or polyphosphates.
• Volutin is synthesized by additions of phosphate
  units from ATP. May serve as an energy source,
  and reserve material for nucleic acid and
  phospholipid synthesis.

130
Figure 4.41 Polyphosphate granules
131
4.3 Structure, Composition, and Cell Function

• Some species store volutin when there is no
  nutrient limitation luxurious phosphate uptake.

132
4.3 Structure, Composition, and Cell Function

• Sulfur is stored as elemental sulfur granules by
  sulfur-oxidizing bacteria involved in the sulfur
  cycle.
• The granules are a source of energy when oxidized
  by filamentous sulfur bacteria or a source of
  electrons for photosynthetic bacteria.

133
Figure 4.42 Sulfur granules
134
4.4 The Cell Envelope

• The cell envelope the cell materials that
  surround the cytoplasm.
• The cytoplasmic membrane is present in all
  Bacteria and Archaea.
• Also includes cell wall, periplasmic space,
  outer membrane, surface appendages, and
  extracellular polymeric substances (EPSs).

135
Figure 4.43 Cell diagram
136
4.4 The Cell Envelope

• Cytoplasmic membrane, or cell membraneprimary
  boundary of the cytoplasm.
• The fluid mosaic model describes the nonrigid
  structure of the cell membrane, in which proteins
  can move about.

137
Figure 4.44 Bacterial cell membrane structure
138
4.4 The Cell Envelope

• Prokaryotic cell membranes are composed of
  phospholipids and membrane proteins.
• One type of phospholipid is phosphatidyl serine
  a bipolar molecule with a hydrophobic end.
• In an aqueous environment, phospholipids form a
  bilayer.

139
Figure 4.45 Phospholipid
140
4.4 The Cell Envelope

• Proteins are embedded in the phospholipid
  bilayer.
• Many are involved in the transport of substances
  across the membrane.
• Others are involved in energy harvesting, DNA
  replication, and protein export.

141
4.4 The Cell Envelope

• Sterols have a stabilizing effect on membranes.
• Mycoplasmas have sterols in the cell membrane
  (they have no cell walls) that are derived from
  their environment.
• Methanotrophic bacteria also have sterols in
  membranes specialized for oxidation of methane.
• Some cyanobacteria produce hopanoids.

142
Figure 4.46 Sterols and hopanoids
143
4.4 The Cell Envelope

• Archaeal cell membranes have a different
  composition than bacterial cell membranes.
• Bacterial membranes have glycerol-linked esters.
• Archaeal membranes have glycerol-linked ethers,
  plus isoprenoid side chains with repeating
  five-carbon units.

144
4.4 The Cell Envelope

• Two patterns are found in archaeal cell
  membranes
• A bilayertwo layers of glycerol diethers.
• A monolayer consisting of diglycerol tetraethers.

145
Figure 4.47 Archaeal cell membrane structure
(Part 1)
146
Figure 4.47 Archaeal cell membrane structure
(Part 2)
147
4.4 The Cell Envelope

• Functions of the cytoplasmic membrane
• Ultimate physical barrier between the cytoplasm
  and the environment.
• Selectively permeablewater and gases diffuse
  freely, sugars and amino acids do not.
• Many compounds are brought into the cell by
  special transport systems.

148
4.4 The Cell Envelope

• Cytoplasmic membrane also functions in DNA
  replication.
• DNA is attached to the membrane. After
  replication, the two DNA molecules are separated
  by synthesis of new cell membrane.

149
4.4 The Cell Envelope

• In some prokaryotes, the cell membrane extends
  into the cell.
• The internal membranes are used in photosynthesis
  in photosynthetic bacteria.
• Some bacteria that oxidize ammonia, nitrate, and
  methane, also have these intracytoplasmic
  membranes.

150
4.4 The Cell Envelope

• Most Bacteria and some Archaea have a cell walla
  polymeric mesh-like sack surrounding the cell
  membrane.
• Walls provide rigidity to prevent cell membrane
  from rupturing.
• Also provides characteristic size and shape.

151
4.4 The Cell Envelope

• The Mollicutes or mycoplasmas lack a cell wall.
• They have sterols or other compounds to stabilize
  the cell membrane.
• In this respect, they are similar to animal
  cells.
• They are unable to live in low solute
  environments.

152
4.4 The Cell Envelope

• Bacteria have peptidoglycan or murein in their
  cell walls.
• Archaea lack peptidoglycan, but some species have
  a related material called pseudomurein.

153
4.4 The Cell Envelope

• Peptidoglycans consist of amino sugars and amino
  acids.
• Glucosamine and muramic acid are joined together
  by b-1,4 linkages to form a chain (a glycan).
• The chains are cross-linked by peptides.

154
Figure 4.48 Cell walls of gram-positive and
gram-negative bacteria
155
4.4 The Cell Envelope

• Most bacteria have N-substituted acetyl groups
  N-acetylglucosamine (NAG) and N-acetylmuramic
  acid (NAM).
• One amino acid in the peptide is lycine, a
  diamino acidcontains two amino groups.
• A diamino acid must be present for cross-linking
  to occur.

156
Figure 4.49 Peptidoglycan of a gram-positive
bacterium
157
Figure 4.50 Diamino acids
158
4.4 The Cell Envelope

• Lysine and diaminopimelic acid are the most
  common diamino acids in the cross links.
• Diaminopimelic acid occurs only in the
  peptidoglycan of gram-negative bacteria.
• Some amino acids are never found in the peptide
  bridges.

159
4.4 The Cell Envelope

• Bacteria are divided into two groups based on the
  cells reactions to the Gram stain.
• The difference is due to the structure of the
  cell envelopes.
• Gram-negative bacteria have an additional layer
  called the outer membrane.

160
Figure 4.28 Cross section of bacterial cell
envelopes (Part 1)
161
Figure 4.28 Cross section of bacterial cell
envelopes (Part 2)
162
4.4 The Cell Envelope

• Gram-positive bacteria may have up to 50 layers
  of peptidoglycan, accounting for the much thicker
  walls than gram-negatives.
• Gram-positive cell walls contain teichoic acids
  and teichuronic acids.
• The negative charges of these molecules aid in
  forming a hydrophilic barrier to hydrophobic
  molecules in the environment.

163
Figure 4.51 Teichoic acids
164
Figure 4.51 Teichoic acids (Part 2)
165
Figure 4.52 Teichuronic acids
166
4.4 The Cell Envelope

• Gram-negative bacteria do not contain teichoic or
  teichuronic acids, but the cell walls are more
  complex.
• Peptidoglycan makes up a smaller proportion of
  the cell wall, but is covalently bonded to
  proteins in the outer membrane.

167
4.4 The Cell Envelope

• Archaea Only some methane-producing species have
  cell walls with pseudomurein.
• It contains N-acetylglucosamine (NAG), but
  N-acetyl-talosaminouronic acid (TAL) replaces the
  N-acetylmuramic acid (NAM) found in Bacteria.

168
Figure 4.53 Pseudomurein
169
4.4 The Cell Envelope

• Archaea consists of four major phyla
• Crenarchaeotahyperthermophiles.
• Euryarchaeotamethane-producing archaea and
  extreme halophiles.
• Nanoarchaeasmall parasites that live on other
  archaea.
• Korarchaeotahave never been isolated.

170
4.4 The Cell Envelope

• Cell wall composition may explain how some
  Archaea withstand extreme environments.
• Halophiles may not need the same rigid
  peptidoglycan walls that Bacteria have because
  they live in high osmotic concentrations.

171
4.4 The Cell Envelope

• Most prokaryotes live in hypotonic
  environmentsthe concentration of ions and
  molecules is greater inside the cell than
  outside.
• Cell membrane is permeable to water water tends
  to enter the cell by osmosis, and the cell
  swells.
• Osmotic pressure within the cell is called turgor
  pressure.

172
4.4 The Cell Envelope

• Cell walls prevent turgor pressure from
  stretching the membrane too far and rupturing the
  cellplasmoptysis.
• If the cell walls of Bacillus (gram-positive) are
  removed by lysozyme, which breaks down
  peptidoglycan, the cells will lyse in a hypotonic
  solution.
• If placed in an isotonic solution, the cells
  become spheroidalcalled protoplasts.

173
Figure 4.54 Protoplasts
174
4.4 The Cell Envelope

• If the peptidoglycan layer of gram-negative
  bacterial cell walls is removed, the cells form
  spheroplasts, which still have the outer membrane
  intact.

175
4.4 The Cell Envelope

• Because peptidoglycan is unique to the Bacteria,
  it is the target of some antibiotics.
• E.g., penicillins prevent synthesis of
  peptidoglycan.

176
4.4 The Cell Envelope

• An outer membrane surrounds the cell wall of
  gram-negative bacteria.
• Consists of two layers of lipids. Lipid A on
  outside has attached polysaccharides. Side chain
  O-polysaccharides or O-antigens vary with
  species.
• The lipid Apolysaccharide complex is called a
  lipopolysaccharide or LPS.

177
Figure 4.55 Outer membrane
178
Figure 4.56 Polysaccharide portion of LPS
179
4.4 The Cell Envelope

• The LPS that contains lipid A is called
  endotoxinit is toxic to many animals, including
  humans.
• Many gram-negative bacteria, including Salmonella
  and Yersinia pestis, are toxic because of this
  compound.
• Other species are nontoxic because the LPS lacks
  specific parts of the lipid A.

180
4.4 The Cell Envelope

• The outer membrane also contains many proteins.
• Brauns lipoprotein or LPP is structural, and
  aids in stabilizing the outer membrane by
  anchoring it to the cell wall.

181
Figure 4.57 Lipoprotein structure
182
4.4 The Cell Envelope

• Porins are membrane proteins that permit passage
  of small molecules.
• Porins are trimeric with three hydrophilic
  channels across the lipid bilayer.
• Porins are water-filled and allow diffusion of
  water-soluble nutrients. Passage of large
  molecules is limited.
• Some specialized porins allow entry of large
  molecules such as vitamin B12.

183
Figure 4.58 Porin
184
4.4 The Cell Envelope

• Periplasmic spacespace between cell membrane and
  outer membrane.
• Site of enzyme activitysynthesis of the cell
  wall occurs here.
• Binding proteins in the periplasmic space
  function in nutrient uptake. They combine
  reversibly with molecules to deliver them to the
  cell membrane.

185
4.4 The Cell Envelope

• Gram-positive bacteria may have a space that is
  functionally equivalent to the periplasmic space
  of gram-negatives.
• Gram-positives and archaea also have binding
  proteins.

186
4.5 Extracellular Layers

• Some prokaryotes have discrete layers external to
  the cell wall and/or outer membrane.
• Capsules, or extracellular polymeric substances
  (EPSs)
• Slime layers
• Sheaths
• Protein jackets, or S-layers

187
4.5 Extracellular Layers

• Capsules Extracellular polymeric substances
  (EPSs)constitute a physical barrier.
• Can aid in slowing desiccation, or prevent virus
  attack.

188
4.5 Extracellular Layers

• In some species, the capsule aids in attachment
  to a substrate.
• E.g., Streptococcus mutans attaches to dental
  enamel. Acid produced by fermentation of sucrose
  etches the enamel and can start cavities.

189
4.5 Extracellular Layers

• Capsules can be crucial to survival of organisms
  in their natural environments.
• Capsules of some species are virulence factors
  (e.g., Streptococcus pneumoniae)only capsulated
  strains are pathogenic. Unencapsulated cells are
  easily killed by phagocytes (white blood cells).

190
4.5 Extracellular Layers

• Capsules require special staining or other
  techniques for visualization.
• The Quellung reaction an antiserum is prepared
  from capsular material of S. pneumoniae and is
  used to stain the cells. The antiserumcapsule
  complex is thicker and more visible.

191
Figure 4.59 Capsule stain
192
4.5 Extracellular Layers

• Negative stains consist of insoluble particles,
  such as in India ink (nigrosin).
• The dark particles dont penetrate the capsule,
  which appears as an unstained halo around the
  cell.

193
Figure 4.60 Negative stain
194
4.5 Extracellular Layers

• Most capsules are composed of polysaccharides.
• Homopolymers (identical subunits)
• Dextrans (polymers of glucose)
• Levans (polymers of fructose or levulose)
• Found in capsules of lactic acid bacteria
  (Streptococcus and Lactobacillus spp.)

195
4.5 Extracellular Layers

• Heteropolymers (more than one type of subunit)
• Hyaluronic acidN-acetylglucosamine and
  glucuronic acid
• Some Streptococcus produce a glucoseglucuronic
  acid polymer.

196
4.5 Extracellular Layers

• Some capsules are composed of polypeptides.
• Some Bacillus spp. have capsules of D-glutamic
  acid polymers.
• D-stereoisomers of amino acids are found
  exclusively in capsules and cells walls of some
  bacteria. All other biological amino acids are
  L-stereoisomers.

197
Table 4.1 (Part 1)
198
Table 4.1 (Part 2)
199
4.5 Extracellular Layers

• Slime Layers
• Gliding bacteria, such as Cytophaga-Flavobacterium
  group, produce an EPS slime layer to aid in
  motility on a solid substrate.
• These bacteria degrade cellulose and chitin. As
  they glide over the surface, the cellulase and
  chitinase enzymes are kept close to the substrate.

200
Figure 4.61 Gliding motility
201
4.5 Extracellular Layers

• The sheathed bacteria produce a dense, highly
  organized external layer called a sheath.
• They grow in flowing water, and form filamentous
  chains. Sheath protects cells from turbulent
  water.
• Sheaths consist of polysaccharides, amino sugars,
  and amino acids.

202
Figure 4.62 Sheathed bacteria
203
4.5 Extracellular Layers

• Some Bacteria and Archaea produce protein jackets
  or S-layers.
• Function is poorly understood. In some Archaea it
  is the only external structure.
• Some Spirillum and cyanobacteria also have cell
  walls.
• Viruses adhere to the S-layer in some species.

204
Figure 4.63 S-layers
205
4.5 Extracellular Layers

• Flagella are long, flexible appendages for
  swimming.
• They act like a propellerthe cell moves through
  the water as the flagellum rotates.

206
Figure 4.64 Polar flagellum (monotrichous
flagellation)
207
4.5 Extracellular Layers

• Number and location of flagella are used in
  classification.
• Monotrichous polar flagellationone flagellum
  extending from one end of the cell.
• Lophotrichous polar flagellationtuft or bundle
  at one end of cell.

208
Figure 4.65 Polar flagellar tufts (lophotrichous
flagellation)
209
4.5 Extracellular Layers

• Peritrichous flagellationflagella from all
  locations on the cell surface.
• Some species move by mixed flagellationsome
  Vibrio produce polar flagella in water, but
  lateral flagella when grown on agar.

210
Figure 4.66 Peritrichous flagellation
211
4.5 Extracellular Layers

• Flagella have three main parts
• Basal structureanchors flagellum.
• Hookcurved section that connects filament to
  cell surface.
• Filamentextends into environment.

212
4.5 Extracellular Layers

• Basal structurea rod structure plus L, P, S, and
  M rings associated with cell envelope components.
• Rings function as part of a molecular motor that
  rotates the hook and filament.
• Motility provides selective advantage in seeking
  nutrients or other resources.

213
Figure 4.67 Flagellar structure (A)
214
4.5 Extracellular Layers

• Energy for flagellar rotation comes from the
  proton motive force (PMF).
• This energy is imparted to Mot proteins embedded
  in the cell membrane.
• Rate of rotation varies from 200 to 1,000 rpm.

215
4.5 Extracellular Layers

• Hook structurecontains FlgG proteinconnects rod
  of basal structure to the filament.
• Flagellar filamentcomposed of repeating subunits
  of the protein flagellin, helically wound with a
  hollow core.
• The filaments are curvedshape varies with
  species.

216
Figure 4.67 Flagellar structure (B)
217
Figure 4.67 Flagellar structure (B) (continued)
218
4.5 Extracellular Layers

• Tactic responses
• Chemotaxisprokaryotes swim toward or away from
  low-molecular-weight compounds.
• Positive chemotaxiscaused by chemical
  attractants such as amino acids and sugars.
• Negative chemotaxiscaused by repellant chemicals
  such as alcohols or heavy metals

219
4.5 Extracellular Layers

• Phototaxisresponse to light.
• Photosynthetic prokaryotes are attracted to
  wavelengths of light that are absorbed by
  photosynthetic pigments.
• Cells can also respond to light intensity to seek
  optimal conditions for growth and survival.

220
Figure 4.68 Phototaxis
221
4.5 Extracellular Layers

• Magnetotaxismagnetic bacteria swim to or away
  from the north or south magnetic poles.

222
4.5 Extracellular Layers

• Fimbriae, pili, or spinaeproteinaceous
  appendages, about 1 µm long.
• Protein subunits form a helix with a pore in the
  center.
• Some have a glycoprotein tipcalled adhesin, aids
  in adhesion.

223
Figure 4.69 Fimbriae (A, B)
224
4.5 Extracellular Layers

• Pili are usually considered a subset of fimbriae,
  typical of many enteric bacteria and pathogens.
• Some bacteria produce more than one type of
  fimbria or pili.
• Some bacterial viruses attach to particular types
  of fimbria or pili.

225
4.5 Extracellular Layers

• Some bacteria use pili to attach to surfaces or
  other cells.
• E. coli have a fertility (F) pilus used to attach
  cells during conjugationthe sex pilus.
• Pileated strains of Neisseria gonorrhoeae use
  pili to attach to endothelial cells of the human
  genitourinary tract.

226
4.5 Extracellular Layers

• Type I or P pilus of E. coli has a membrane
  anchor that provides support for the rod
  proteins. It may have special adhesin at the tip
  for cell attachment.
• In some Pseudomonas, pili are involved in
  extrustion of proteins from the cell.
• In myxobacteria, fimbriae are responsible for a
  type of motility called twitching.

227
Figure 4.70 Pili
228
4.5 Extracellular Layers

• Spinae are the largest appendages.
• In aquatic bacteria, spinae increase the surface
  area, allowing cells to remain suspended, or be
  carried by currents maintaining their position
  in the plankton.

229
Figure 4.69 Fimbriae (C)