the third chapter in microbiology 8th edition

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

2. Prokaryotes: two distinct domains
 The prokaryotes are divided into two very
distinct groups:
– Eubacteria
– Archaea
 Essential distinctive points are the cell wall
composition, the type of lipids synthesized by
the cells, and the structure of RNA
polymerase.

3. Major morphologies of bacterial cells
 Cocci (singular coccus) round cells
 Diplococci (when cocci divide and remains
together to form pairs
 Long chain cocci when cells adhere to each
other after repeated cell division in one plane
such as Streptococcus agalactiae
 Grapelike structure when they divide in random
planes such as Staphylococcus aureus

4. Major morphologies of bacterial cells
 Bacilli (singular bacillus) rod shaped cells and
differ in their length to width ratio
 Some they are arranged in chains such as
Bacillus megaterium
 Spirilla (singular spirillum) spiral shaped cells or
Spirochetes, flexible
 Comma shaped such as Vibrio cholera
 In addition to the basic shapes there are star
shaped cell, rectangular flat cells and triangular
cells
 Pleomorphic (do not have certain size or shape)

5. Bacterial morphology

6. 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
– Some small nanobacteria range from
0.2μm-0.05μm
– Examples of very large prokaryotes
Size range for eukaryotic cells: 10 to
>200 µm in diameter

7. Bacterial sizes

8. Cell Size and the Significance of Smallness
Surface-to-Volume Ratios, Growth
Rates, and Evolution
Advantages to being small
– 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

9. Cell Size and the Significance of Smallness

10. Elements of Microbial Structure
 Eukaryotic Cells
DNA enclosed in a membrane-bound nucleus
Cells are generally larger and more complex
Contain organelles

11. Elements of Microbial Structure
• Prokaryotic cell
No membrane-enclosed organelles, no
nucleus
Generally smaller than eukaryotic cells

12. Bacterial structure

13. Prokaryotes Vs Eukaryotes
 Single cell organisms. Discriminating
characteristics are:
– No defined nucleus (no nuclear
membrane) NUCLEOID
– Circular DNA. Bacterial cells are HAPLOID
(one single copy of the chromosome)
– Plasmids (can be found in yeast as well)
– No membrane bound organelles
– Presence of a CELL WALL
– 70S ribosomes
– Inclusion bodies (storage of C, P and
other)

14. The Cytoplasmic Membrane in Bacteria
 Cytoplasmic membrane:
– 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
– Transport of nutrients and waste products

15. Bacterial Cell Membranes
 The prokaryotic plasma membrane is not
only a selective barrier, but also the location
of a variety of crucial metabolic processes:
respiration, photosynthesis, and synthesis of
lipids and cell wall constituents. Consists
primarily of phospholipids and proteins
 Arranged as phospholipid bilayer with
scattered proteins. Phospholipids and
proteins move freely within the surface giving
rise to a fluid mosaic.

16. Fluid mosaic model
X
Membrane lipids are phospholipids
No Sterol such as cholesterol, instead bacteria has hapnoids

17. Phospholipid bilayer membrane

18. Composition of Membranes
– General structure is phospholipid bilayer
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

19. Cell membranes
 Membrane lipids are amphipathic with polar
and non-polar ends.
Two types of proteins
 Peripheral- are loosely associated to the
membrane and can be easily separated.
Generally they make up between 20 and
30% of the total membrane proteins
 Integral proteins- are amphipathic like the
lipids, much more strongly associated to the
membrane, and make up about 70 to 80% of
total proteins.

20. Archaeal membrane
 Can exist as lipid monolayers, bilayers, or
mixture
Bilayer
Monolayer

21. General structure of lipids
Ether linkages in phospholipids of Archaea
(Bacteria and Eukarya that have ester linkages in
phospholipids

22. Diether and tetraether
Major lipids are glycerol diethers and tetraethers

23. The Cytoplasmic Membrane
Archaeal Membranes
– Ether linkages in phospholipids of
Archaea (Bacteria and Eukarya that
have ester linkages in phospholipids
– Archaeal lipids lack fatty acids, have
isoprenes instead
– Major lipids are glycerol diethers and
tetraethers
– Can exist as lipid monolayers,
bilayers, or mixture

24. Membrane infoldings in bacteria
 Bacteria lack membrane bound organelle like
mitochondria, chloroplasts, etc…but some has
plasma membrane infoldings
 Plasma membrane infoldings are common and can
become extensive and complex in photosynthetic or
nitrogen fixing bacteria. They provide a larger
surface for greater metabolic activity

25. STORAGE GRANULES
 Bacteria exist in a very competitive environment
where nutrients are usually in SHORT SUPPLY, so
they tend to store up extra nutrients when possible.

26. Organic inclusion bodies
Glycogen- storage
of glucose polymers
 Poly-β-
hydroxybutyrate
(PHB) for lipid storage

27. Inclusion bodies
Inorganic inclusion bodies
Polyphosphate and sulfur granules.

28. Inorganic inclusion bodies
Magnetosomes include magnetic matter
(greigite, magnetite, pyrite)
Aquaspirillum magnetotacticum

29. Gas Vesicles
– Confer buoyancy in planktonic cells
Spindle-shaped, gas-filled structures made
of protein
– Gas vesicle impermeable to water
– Function by decreasing cell density
– Gas vacuole is another type of inclusion
body, are present in photosynthetic
bacteria and aquatic procaryotes
– Carboxysomes in photosynthetic bacteria
contain the enzyme Rubisco which is used
in CO2 fixation

30. Gas vesicles

31. Prokaryotic cytoskeleton
 Homologous of all eukaryotic cytoskeletal
elements (microfilaments, intermediate
filaments, and microtubules) have been
identified in bacteria. One homologous
identified in archaea.
 Structurally similar carry out similar functions:
cell division, protein localization, cell shape.

32. Ribosomes
 Prokaryotic ribosomes are very abundant in
the cell. Structurally and functionally similar
to eukaryotic ribosomes. They are the site of
protein synthesis and are composed of
protein and rRNA.
 Smaller than eukaryotic ribosomes. 70S
rather than 80S.
 Bacterial ribosomes consists of small (30S)
and large (50S) subunit

33. Ribosomes

34. Arrangement of DNA in Microbial Cells
 Genome
– A cell’s full complement of genes
 Prokaryotic cells generally have a single,
circular DNA molecule called a chromosome
– DNA aggregates to form the nucleoid region
Ruptured cell where the
chromosomes are located in
the nucleoid

35. Nucleoid
 Prokaryotic cells do not have a membrane
delimited nucleus and the prokaryotic
chromosome is located in an irregularly
shaped region called the nucleoid.
 Prokaryotes contain a single circle of double
stranded DNA but some have linear DNA,
and some (Vibrio cholerae and Borrellia
burgdorferi) have more than one
chromosome.
 DNA is packaged efficiently to fit inside the
cell.
 Bacteria do not use histones to package their
DNA

36. Plasmids

37. Plasmids
 Small double strand DNA molecules that
exist independently of the chromosome.
They can be linear, but the majority are
circular.
 They have relatively few genes, but they
confer a selective advantage to the bacteria
in certain environments.
 Plasmids replicate autonomously and can be
integrated in the chromosome (episomes).

38. Plasmids
 Conjugative plasmids: genes for the
construction of hair-like structures called sex
pili that help transfer of plasmids from cell to
cell during conjugation (F factor).
 Resistance factors: confer antibiotic
resistance. A single or as many as eight
resistance genes.
 Bacteriocin-encoding plasmids: coding for
bacteriocins that destroy other bacteria.
 Col plasmids: specifically kill Escherichia
coli (produce colicins)

39. Plasmids
 Virulence plasmids: encode factors that
make the bacteria more pathogenic and
more able to cause serious disease.
 Metabolic plasmids: carry genes for
enzymes that degrade specific substances
such as aromatic compounds (toluene),
pesticides, and sugars (lactose).

40. Cell wall- Bacteria
– Responsible for the shape of the cell
– Involved in virulence.
– Prevention of rupture due to osmotic
pressure changes
– Point of anchorage for structures.
– Antibiotics site of action.
– It consists of peptidoglycan

41. CELL WALL - Bacteria
Bacterial cell wall consists of
peptidoglycan
Bacteria are divided into two main
groups on the basis of their cell wall
structure:
Gram positive- stained blue
Gram negative- stained red

42. Cell walls of bacteria

43. Peptidoglycan
 Repeating disaccharide attached to
polypeptides to form a lattice.
 The disaccharide portion is made of
N-acetylglucosamine (NAG) and
N-acetylmuramic acid (NAM) linked to
adjacent rows by polypeptide chains.
 Some of the amino acids are D-isomers
rather than L. The presence of D-amino
acids protects against degradation by most
peptidases.

44. Structure of the repeating unit of
peptidoglycan

45. Structure of the repeating unit of
peptidoglycan
Note how glycosidic bonds confer strength on
peptidoglycan in the Y direction whereas peptide
bonds confer strength on the peptidoglycan in the X
direction
These bridges make the peptidoglycan porous and
elastic

46. Peptidoglycan in Escherichia coli and
Staphylococcus aureus.

47. Gram positive cell wall
 Can contain up to 90% peptidoglycan
 The Gram positive cell wall consists of a thick
layer of peptidoglycan that contains teichoic
acid.
 Teichoic acid is composed of polymers of
glycerol or ribitol joined by phosphate groups.
 The phosphate esters contain sugars or D-
alanine
 Teichoic acid is either covalently bound to the
peptidoglycan itself or to the cell membrane
lipids (in this case it is called lipoteichoic acid).
 Teichoic acid gives the outer wall negative
charge

48. Gram positive cell wall

49. Gram positive cell wall

50. The gram-negative cell wall
•Periplasm: space located between cytoplasmic and
outer membranes

51. Gram negative cell wall
 Total cell wall contains ~10% peptidoglycan
 Most of cell wall composed of outer membrane
(lipopolysaccharide [LPS] layer)
– LPS consists of core polysaccharide and
O-polysaccharide
– LPS replaces most of phospholipids in outer
 Periplasmic space ranges between 1nm to 71 nm. &
constitute up to 40% of the total cell volume.
 The peptidoglycan layer is generally very thin and in
some species, like Escherichia coli, it can be only
two sheet thick.
 The periplasm of Gram negative bacteria contains
enzymes important in nutrient acquisition, transport
or in energy conservation.

52. Gram negative outer membrane
The outer membrane of Gram negative
bacteria contains
LIPOPOLYSACCHARIDE
LPS is a large molecule consists of
lipids and polysaccharides attached to
each other by covalent bond
 (LPS), LPS consists of lipid A, core,
and O antigen or O polysaccharides
LPS is not a component of gram
positive bacteria

53. Gram negative outer membrane
 (LPS), LPS consists of lipid A, core, and O
antigen or O polysaccharides

54. Gram negative outer membrane
 O antigen:
– Functions as antigen. It elicits the immune
response but bacteria developed ways to
vary it thus avoiding the immune response
– Gives negative charge to bacterial
surfaces
– It stabilizes the outer membrane
– Restricts entry of antibiotics and toxic
substance that kill the bacteria

55. Gram negative outer membrane
Core:
• The Core domain always contains an
oligosaccharide component that attaches
directly to lipid A
Lipid A:
• Lipid portion of LPS is called lipid A
and is an endotoxin that causes fever
and shock

56. Gram negative outer membrane
 Functions of the outer membrane:
– Helps the cell to avoid phagocytosis and
complement
– Impermeable to certain antibiotic (e.g.
penicillin) and digestive enzymes,
detergents, heavy metals, bile salts and
certain dyes.
– Allows nutrients and other substances to
enter the cell through PORINS that form
channels.

57. Damage to cell wall
 Without the cell wall, bacterial cell will undergo lysis in
hypotonic solutions
 While bacterial cell will shrivels if it is in hypertonic solution
(plasmolysis).
Osmotic pressure summary

58. Damage to cell wall
 Lysozyme attack peptidoglycan by hydrolyzing the bond that
connect the NAG and NAM destroys the cell wall.
 Lysozyme treatment of gram positive in presence of hypotoinc
solution - result in complete loss of the cell wall with the
formation of protoplasts.
 Protoplast –removal of cell wall by enzymatic digestion
resulting in spherical cells
 Lysozyme treatment of gram negative- destruction is partial,
the peptidoglycan is lost but the outer membrane remains and
spheroplasts are formed. In hypotonic solution
 In hypotonic solution both spheroplasts and protoplast rupture
= osmotic lysis.

59. Cell Walls of Archaea
No peptidoglycan
Typically no outer membrane
Pseudomurein
– Polysaccharide similar to
peptidoglycan
Composed of N-acetylglucosamine
and N-acetyltalosaminuronic acid
Cell walls of some Archaea lack
pseudomurein

60. Pseudomurein

61. Archaeal cell wall
 Some archaea resemble gram positive but
they contain pseudomurine, as structure
similar to peptidoglycan that contain 1) L-
amino acid rather than D. 2) β(1-3) glycosidic
bond rather than and β(1-4).
 Some archaea resemble gram negative have
a layer of glycoprotein on the outside

62. Archaeal cell wall
 S-layer consists of proteins or glycoprotein

63. Bacterial structure

64. Cell Surface Structures
 Capsules and Slime Layers
– Polysaccharide layers May be
thick or thin, rigid or flexible
– Assist in attachment to
surfaces
– Protect against phagocytosis
– Resist desiccation
– May be TOXIC and may stop
immune system from working
properly (important in
virulence ‫اختباء‬
– Can be used as a source of
nutrition

65. Cell Surface Structures
Fimbriae
– Filamentous protein structures
– Enable organisms to stick to surfaces
or form pellicles

66. Cell Surface Structures
 Pili
– Filamentous protein structures
– Typically longer than fimbriae
– Assist in surface attachment
– Facilitate genetic exchange between cells
(conjugation)
– (1-10 per cell) hairlike structure
– Type IV pili involved in twitching motility

67. Flagella and motility
 Protein rods (hollow) that provide means for
movement to motile bacteria.
 Go through the cell wall and at the base they
have MOTOR that is driven by FLOW OF
PROTONS.
 The number and position of flagella is part of
the species genetic characteristics.
 The movement is described as RUN and
TUMBLE

68. Flagella
A: Monotrichous- one flagellum
B: Lophotrichous- a cluster of flagella at one or both ends
C: Amphitrichous-single flagellum at each pole
D: Peritrichous- flagella are spread over the whole cell

69. Structure and function of the flagellum
in gram-negative Bacteria
L ring connected to LPS
P ring connected to the
peptidoglycan
Ms ring connected to the inner
membrane (periplasmic side)
C ring connected to the inner
membrane (cytoplasmic side)

70. Flagella and Motility
 Flagellar Structure
– Consists of several components
– Filaments are hollow , cylinders and made out of
subunits called the flagellin , it ends with a capping
protein
– Hook and the basal body are wider
– The basal body is the most complex and consists to
four rings connected to central rod
– Move by rotation

71. Gliding Motility
 Gliding Motility
– Flagella-independent motility
– 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

72. Microbial Taxes
Taxis: directed movement in response
to chemical or physical gradients
‫الوسواط‬ ‫حركة‬
– Chemotaxis: response to chemicals
– Phototaxis: response to light
– Aerotaxis: response to oxygen
– Osmotaxis: response to ionic
strength
– Hydrotaxis: response to water

73. Endospores
 Spores are tough, dormant ‫خاملة‬ structure
 Bacteria form endospores when
environmental conditions become stressful
(lack of nutrients, lack of water etc)
 Mostly found in bacteria of the soil
 Formed during sporulation. Highly resistant
to heat, radiations, and chemicals. Can
survive for a very long time (100,000 y)
 It is a proper process of differentiation. The
vegetative cell converts to endospore in
stages.

74. The bacterial endospore

75. The life cycle of an endospore-forming
bacterium
 Sporulation can take up to 8 hours.
 Germination is much faster than sporulation
and takes only a few minutes

76. Endospores

77. Endospores.
 Endospores are composed of many layers.
 The outermost layer is called exosporium (thin
protein cover. Under there are spore coats
(endospore-specific proteins), cortex
(peptidoglycan), and core.
 Nucleoid is located in the core
 The DNA is protected by endospore-specific
proteins (SASP – small acid soluble protein)-
used as a carbon source during germination
 Dipicolinic acid synthesis result in increase
resistance to heat and promoting dormancy

78. https://www.youtube.com/v/7zCQLITFEb0
Sporulation and germination

79. Endospores

80. Protein secretion
 The membrane of procaryotes present a
considerable barrier to movement of large
molecules in or out of the cell.
 However, many structures of considerable
size are found outside the wall.
 Also exoenzymes and other proteins are
released by the cell in their environment.
 The process of releasing molecules outside
the cell is called protein secretion.

81. Sec-dependent pathway
 Major pathway in both Gram positive and Gram
negative bacteria
 It translocates proteins across the membrane or
integrates them in the membrane itself.
 The machinery of the Sec pathway recognizes a
hydrophobic N-terminal leader sequence (signal
peptide) on proteins destined for secretion, and
translocates proteins in an unfolded state, using
ATP hydrolysis and a proton gradient for energy
 while in Gram-negative bacteria they are
responsible for export of proteins into the
periplasm

82. Sec-dependent pathway

83. Two-arginine secretion (Tat)
 The machinery of the Tat secretion pathway
recognizes a motif rich in basic amino acid
residues (S-R-R-x-F-L-K) in the N-terminal
region of large co-factor containing proteins
and translocates the proteins in a folded
state using only a proton gradient as an
energy source
 Tat pathway moves proteins across the
plasma membrane then deliver it to type II, it
transports folded protein

84. Secretion in gram negative bacteria
 Six different secretion system have been
identified in Gram-negative bacteria
 In Gram-negative bacteria, some secreted
proteins are exported across the inner and
outer membranes in a single step via the
type I, type III, Type IV or type VI pathways
 Other proteins are first exported into the
periplasmic space via the universal Sec or
two-arginine (Tat) pathways and then
translocated across the outer membrane via
the type II, type V or less commonly, the type
I or type IV machinery

85. Bacterial secretion system
Summary of known bacterial secretion systems. In this simplified view
only the basics of each secretion system are sketched. HM: Host
membrane; OM: outer membrane; IM: inner membrane; MM:
mycomembrane; OMP: outer membrane protein; MFP: membrane fusion
protein. ATPases and chaperones are shown in yellow.

86. Transport and Transport Proteins
ABC (ATP-Binding Cassette) Systems
>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

87. Mechanism of an ABC transporter