Microbial Physiology Notes
Jan 23, 2024
Cell Wall: Bacteria vs Archaea
Does archaea have a cell wall? Some
Archaea
● unicellular organisms without
nuclei
● no organelles
● lacks peptidoglycan
● DNA is more similar to eukaryotes,
denotes lineage
● some live in extreme
environments, no oxygen
Pseudomurein
● made up of N- acetylglucosamine
and N-acetyltalosaminuronic acid
which is immune to lysozyme and
penicillin.
Other polysaccharide cell walls:
S-layers
● common type of cell wall in
archaea:
● a regularly structured crystalline
layer present on the surface of
archaea and many bacteria
● consist of interlocking molecules or
glycoprotein
● can form various symmetries,
including hexagonal, tetragonal or
trimeric
● can withstand osmotic pressure
● works as a molecular sieve,
allowing the passage of certain
molecules
● act as molecular ion traps
● perform roles in surface
recognition and maintenance of
shape
● protecting cell against ion and pH
fluctuations, osmotic stress,
degrading enzymes or predacious
bacteria
● promotes cell adhesion to surfaces
● contribute to virulence of bacteria
What are the S layers in the bacterial
cell envelope?
● composed of protein or
glycoprotein
● in Gram+ bacteria, s layer is
associated with peptidoglycan
surface
● in Gram - bacteria, it is associated
with the outer membrane layer
Arrangement of S layer
Archaea: attached to the cytoplasmic
membrane
Gram+ bacteria: beyond the peptidoglycan
Gram- bacteria; closely associated with
the lipopolysaccharide of the outer
membrane
Cytoplasmic Membrane
● surrounds the cytoplasm and
separates it from the environment
● chief role as the gatekeeper for
the entrance and exit of dissolved
substances
● selectively permeable where
nutrients are transported inwards
and waste products outwards
through membrane proteins
Bacterial Cytoplasmic Membrane
● made of phospholipid bilayer
containing embedded proteins
● hydrophobic component consists
of fatty acids
● hydrophilic side is composed of a
glycerol molecule containing
phosphate (bonded to it is one of
several other functional groups -
sugars, ethanolamine, or choline)
● ester linkages bond fatty acids to
glycerol
● only 8-10 nm wide
● some bacteria are strengthened by
sterol-like molecules called
hopanoids

*Integral membrane protein embedded in
the phospholipid bilayer; Peripheral
membrane protein is on the surface
Archaeal Cytoplasmic Membrane
● structurally similar to Bacteria and
Eukarya but the chemistry is
somewhat different
● ether bonds between glycerol and
a hydrophobic side chain that is
not a fatty acid
● hydrophobic region is formed from
repeating units of the five carbon
hydrocarbon isoprene
● the polar head groups in lipids can
be sugars, ethanolamine, or a
variety of other molecules
Archaea Lipid Monolayer
● archaeal phospholipid:
➢ L-glycerol
➢ ether linkage
➢ branched isoprene units
● bacterial phospholipid:
➢ D-glycerol
➢ ester linkage
➢ unbranched fatty acids
Cytoplasmic Membrane Functions
● permeability barrier: prevents
leakage and functions as a
gateway for transport of nutrients
into, and wastes out of, the cell
● protein anchor: site of proteins
that participate in transport,
bioenergetics, and chemotaxis
● energy conservation: site of
generation and dissipation of the
proton motive force
Cell Surface Structures
Bacterial Cell Structure - External
Structures
Capsule/Slime Layer
● Capsule - condensed layer that
closely surrounds the bacterium
● Slime layer - loosely adherent;
non-uniform in density and
thickness
● Capsule/slime layer is also called
the glycocalyx
Bacterial Capsules
● organized in a tight matrix that
exclude small particles and is
tightly attached to the cell surface
● known as the K-antigen
● a sharply defined, organized
structure (Pneumococcus)
● most are composed of
polysaccharides (Klebsiella
pneumoniae)
● a few capsules are polypeptides
(Bacillus anthracis)
Functions of Capsules
● offers protection from
desiccation, hydrophobic
toxic materials, and
bacterial viruses
● antiphagocytic, thus
contributes in its virulence
● protects against lysozymes
● it can help in attachment to
surfaces
● acts as receptors to
bacteriophages
Function Relevance
Prevention of Transmission
desiccation and survival
Adherence Colonization of
oral surfaces
Colonization of
indwelling
catheters
Bacteria-plant

interactions
Resistance to Complement-
nonspecific mediated
host immunity phagocytosis
Complement-
mediated
killing
Resistance to Poor antibody
specific host response to
immunity the capsule
Examples of Capsulated
Bacteria/Yeasts
Streptococcus pneumoniae (+)
Klebsiella pneumoniae (-)
Haemophilus influenzae (-)
Pseudomonas aeruginosa (-)
Neisseria meningitidis (-)
Cryptococcus neoformans (+)
*ABC transporters or atp-binding cassette
transporters are found in cell membrane
and aid in the entry of molecules*
*During binary fission, there is no capsule
yet, capsules are only produced due to the
environmental stressor and other such
factors.*
Capsular Serotyping: Quellung reaction
● Neufeld reaction
● use of specific antiserum against
capsular polysaccharide
● the gold standard technique for
serotyping Streptococcus
pneumoniae (pneumococcus)
● a microscopic "precipitin test" used
to identify pneumococci or to
determine the capsular serotype of
individual pneumococci isolates
● if the reaction is positive, the
capsule becomes opaque and
appears to enlarge
Slime Layer
● a loose network of polymers
extending outward from a cell
● this layer is more easily deformed
and loosely attached to the cell
surface
● easily recognized in colonies of
slime forming species such as the
lactic acid bacterium Leuconostoc
● Essential for the adherence of
microorganisms and subsequent
colonization
Slime Layer in Streptococcus
● The slime layer of Gram+
Streptococcus mutans allows it to
accumulate on tooth enamel (yuck
mouth and one of the causes of
cavities)
● Other bacteria in the mouth
become trapped in the slime and
form a biofilm and eventually a
buildup of plaque
*Slime layers are also produced through
membrane transporters, like capsule, but
with different chemical compositions*
Difference between Capsules and Slime
Layers
● Organization:
Capsule: Polysaccharide layer is
organized in a tight matrix that
excludes small particles such as
India ink; it is called a capsule.
Slime Layer: Polysaccharide layer
is more easily deformed, does not
exclude particles and is more
difficult to see.
● Adherence
Capsule: Adheres firmly to the cell
wall and some are even covalently
linked to peptidoglycan.
 Slime Layer: Loosely attached
and can be lost from the cell
surface.
● Role in Pathogenesis
Capsule: Capsule of pathogenic
Escherichia coli promotes
adherence to the brush border of
intestinal microvilli.
Slime Layer: Dextran slime layer
of Streptococcus mutans promotes
binding to tooth surfaces.
Surfaces Appendages
Fimbriae
● like the pili, these are thin (2-10 nm
in diameter) filamentous structures
made of protein
● shorter and straighter than flagella:
numerous
● enable cells to stick to surfaces,
including animal tissues in the
case of pathogenic bacteria or to
form pellicles (thin sheets of cells
on a liquid surfaces) or biofilms on
solid surfaces
● important virulence factors in
cell-to-surface adherence and cell
to cell adherence of oral bacteria
and pathogenesis of some oral and
systemic diseases
● *not all bacteria have one*
Pili
● similar to fimbriae, these are
typically longer and only one or a
few pili are present on the surface
of a cell
● can be receptors for certain types
of viruses
● It is for conjugation (conjugative or
sex pili F pilus) and adhesion (type
IV pili and other pili)
● pili also function in
twitching-motility
Type IV Pili
● implicates as key colonization and
virulence factors for certain human
pathogens
● mediate genetic transfer by
horizontal gene transfer (HGT)
● also widespread in Archaea
Hami
● a unique attachment structure
called a hamus that resembles a
tiny grappling hook
● structurally resemble type IV pili
except for their barbed terminus
● probably prevent cells from being
washed away in groundwater
flowage
● found in SM1 group of Archaea
(*found in extremely cold
environment*)
● less then 1 um in diameter
● live in a similar nutrient-limiting
habitat
Flagella
● also known as the H antigen
● tiny rotating machines that function
to push or pull the cell through a
liquid
● long thin appendages (15-20 nm
wide) free at one end and
anchored into the cell at the other
end
● not straight structures but helical
● can be anchored to a cell in
different location: polar flagellation,
peritrichous flagellation
Types of Flagellation
● peritrichous - flagella are inserted
around the cell surfaces (flagella
all over) (E. coli, Salmonella,
Bacillus spp.)
● amphitrichous - when a tuft of
flagella emerges from both poles of
the cell (Alkaligens faecalis)
● monotrichous/polar - single polar
flagellation at one end of the cell
(Vibrio cholerae)
 ● lophotrichous -a type of polar
flagellation wherein a group of
flagella may arise at one end of the
cell (Spirillum)
● amphilophotrichous - tuft of flagella
at both ends
Structure of Flagella
● Filament - main part of the flagella
which is made up of the protein
flagellin
● Hook - wider region at the base of
the filament; consists of a single
type of protein and connects the
filament to the flagellum motor in
the base
● Basal body - embedded in the
cytoplasmic membrane and cell
surface structure and connected to
the filament through the hook
● Flagellum motor - embedded in the
cytoplasmic membrane and the
cell wall
➢ central rod - passes
through a series of rings
➢ L ring - the outer ring, is
anchored in the outer
membrane (LPS)
➢ P ring - the 2nd ring, is
anchored in the
peptidoglycan layer
➢ MS and C rings - 3rd set of
rings, located within the
cytoplasmic membrane and
the cytoplasm, respectively
● Other proteins
➢ Mot proteins - surrounds
the inner ring and anchored
in the cytoplasmic
membrane and
peptidoglycan
➢ Fli proteins - function as the
motor switch, reversing the
direction of rotation of the
flagella in response to
intracellular signals.
Flagellum Motor’s Components
● rotor - consists of the central rod
and the L, P, C, and MS rings.
● stator - consists of mot proteins
that surround the rotor and function
to generate torque; where proton
translocation takes place
*a proton turbine model explains rotation
of the flagellum. protons, flowing through
the mot proteins, exert forces on charges
present on the c and ms rings, thereby
spinning the rotor.*
*speed is set by the protons*
Flagellar Biosynthesis
● approximately 20,000 flagellin
protein molecules are needed to
make one filament
● a flagellar filament grows not from
its base, but from its tip since it is
where the proteins are
● Synthesis begins with assembly of
MS and C rings in the cytoplasmic
membrane, followed by the other
rings , the hook, and the cap.
● Flagellin protein flows through the
hook to form the filament and is
guided into position by cap
proteins.