Microbial Physiology 3rd Class

University of Technology

Department of Applied Science

Biotechnology Division

3rd class
Produced by
Assistant prof. Wasnaa H. Mohammed
2017

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Microbial Physiology 3rd Class

Microbial physiology
The study of how the microbial cell functions biochemically. Includes the
study of microbial cell structure, microbial growth and microbial
metabolism.
1. Microbial Cell Morphology and Fine structure
A- Morphology of microbial cells:
Morphology includes the size, shape and arrangement of microbial cell.
However, these features vary with species of microorganisms.
1- Size and shape: The size, shape and arrangement of microbial cells vary
with species to which they belong. Bacteria are of about 0.1 to 60 x 6 μm in
size. However, there is variation in dimension of bacilli (5 x 0.4 -0.7 μm),
pseudomonads (0.4-0.7 μm diameter, 2-3 μm length) and microccoci (about
0.5 μm diameter).
The shape of bacterial cell determines by its rigid cell wall. Generally, the
bacterial cells are spherical (coccus, plural cocci which mean berries),
elongated rods (bacillus, plural bacilli), helical rods (Spirillum, plural spirilli),
pear-shaped (Pasteuria), lobed spheres (Sulfolobus), rods with squared ends
(Bacillus anthracis), rods with helically sculptured surface (Seliberia) and of
changing shape (pleomorphic), etc. The unicellular cyanobacterial cells are
usually spherical, some are elongated and multicellular (figure 1).

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Microbial Physiology 3rd Class

Figure 1: Bacteria come in a wide variety of shape.

2- Arrangement: The arrangements of cells are more complex in cocci than

bacilli. The arrangement of cells depends upon adherence of cells together
after the cell division (figure 1). Different forms of arrangement are given
below:
i. Coccus forms: there are several groups of cocci based on the number
and arrangement of cells.

a. Diplococcus: Cells divide in one plane and get attached permanently in

pairs.

b. Streptococcus: Cells divide in one plane and remain attached to forms a

linear chain of cells.

c. Tetracocci: Cells divide in two planes and form

group of four cells.

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Microbial Physiology 3rd Class

d. Staphylococci: Cells divide in three planes in

an irregular pattern producing bunches of cocci.

e. Sarcinae: Cells divide in three planes in regular pattern producing

bunches of cocci.

ii. Bacillus forms: There are a few groups of bacilli unlike cocci as the
former divide across their short arise.

a. Monobacillus: The single elongated cells freely

present in nature are monobacillus.

b. Diplobacillus: After division the cells

remain adhered and appear in paired form.

c. Streptobacillus: After
division the cells remain attached
in chain appearing like straws.

d. Coccobacillus: The oval cells looking like

cocci are called coccobacilli.

There is two meaning of bacillus, one is the form and the second is the genus.
For example the bacterium Bacillus anthracis causes anthrax disease.

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Microbial Physiology 3rd Class

iii. Spirilli forms:

a. Vibrioid: bacterial cells having less than one complete twist from vibrioid
shape e.g. Vibrio cholerae.
b. Helical: Cells that have more than one twist form a distinct helical shape
e.g. Spirillum ( with flagella).
iv. Other forms:
a. Pleomorphic: of changing forms e.g. Rhizobium, Mycoplasma, etc.
b. Trichomes : Cells divide in one plane forming a chain which has much
larger area of contact between the adjacent cells e.g. Baggiatoa, Saprospria.
c. Palisade: The cells are arranged laterally (side by side) to form a match
sticks like structure and at angles to one another e.g. Corynebacterium
diptheriae.
B- Structure of microbial cell
The structure of microbial cells reveals the composition and chemical
constituents building the cell wall, the components outside and internal to the
cell walls. Some of these structures are found only in certain species of
bacteria or fungi. Out of all these only cell wall is common to all microbial
cells. However, the cell wall structure differs in different microbial groups; for
example the prokaryotic cell wall differs from the eukaryotic cell wall and
Gram- positive bacteria from Gram-negative bacteria.
- Structure of prokaryotic bacterial cell:
Upon observation under microscope there reveal several structural
components outside and inside the cell wall (figure 2) which is explained
below:
1- Capsule: Some of bacterial cells are surrounded by the extracellular
polymeric substances which are commonly called capsule. It forms an
envelope around the cell wall and can be observed under light microscope
after special staining technique. The capsule is gelatinous polymer made up of
either polysaccharide (Klebsiella pneumoniae) polypeptide (B. anthracis) or
both. The polysaccharides may be of a single type of sugars
(homopolysaccharide) or several types of sugars (heteropolysaccharides). The
bacterial capsule is species specific and, therefore, can be used for
immunological differentiation of related species. Amount of these polymers
vary with bacterial species. It is sticky in nature and secreted from the inner
side of cell which gets firmly attached to the surface of cell wall. If the
substances are unorganized and loosely attached to cell wall, the capsule is

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Microbial Physiology 3rd Class

called slime layer. The fresh water and marine bacteria form trichomes which
are enclosed inside the gelatinous matrix called sheath. Sheath is also found in
cyanobacteria and algae.
Function of Capsule: Capsule may have a number of functions according to
bacterial species.
1- The capsule may prevent the attachment of bacteriophages.
2- It protects the bacterial cells against desiccation as it is hygroscopic and
contains water molecules.
3- It may survive in natural environment due to its sticky property. After
attachment they can grow on divers surfaces e.g. plant root surfaces, human
teeth and tissues (dental carries, respiratory tract), rocks in fast flowing
streams, etc.

4- They may inhibit the engulfment by WBCs (antiphagocytic feature) and,

therefore, contribute to virulence. Capsule protects from phagocytosis for
example the capsulated strains of Streptococcus pneumonia causes pneumonia
and uncapsulated strain is phagocytized.

5- S. mutans uses its capsules as a source of energy. Its breaks down the
sugars of capsule when stored energy is in low amount.

6- Capsule maintains the viscosity and inhibits the movement of nutrients

from the bacterial cell.

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Microbial Physiology 3rd Class

Figure 2: cross – section of a bacterium cell

2- Flagella: The motile bacterium may possess a flagellum (plural flagella).

The flagellum is hair like, helical and surface appendages emerging from the
cell wall. It is of 20-30 nm in diameter and 15 μm long. It provides various
types of motility to the bacterial cell. The flagella of prokaryotes are several
times thinner than that of eukaryotes.
In addition, the number and position of flagella vary (figure 3). The
arrangement may be monotrichous (a single polar flagellum e.g. V. cholera),
lophotrichous (a clusture of polar flagella e.g. Spirillum), amphitrichous
(flagella at both the end either singly or in clusture), cephalotrichous (two or
more flagella at one end of bacterial cell e.g. Pseudomonas), peritrichous (cell
surface evenly surrounded by several lateral flagella e.g. Proteus vulgaris) or
atrichous (cells devoid of flagella e.g. Lactobacillus).

Figure 3: Bacterial flagella.

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Microbial Physiology 3rd Class

Structure of flagella: A flagellum consists of three basic parts, the basal

body, hook and filament (figure 4).
a- Basal body: Isolated the basil body of a flagellum of E. coli and B. subtilis
and studied its fine structure and arrangement of rings. The basal body
attaches the flagellum to the cell wall and plasma membrane. It is composed
of a small central rod inserted into a series of rings. In Gram- negative bacteria
two pairs of rings, the proximal ring and the distal ring are connected by a
central rod. These two pairs of rings i.e. four rings are L-(lipopolysaccharide)
ring P- (peptidoglycan) ring, S- (super membrane) ring, and M- (membrane)
ring.
The outer pair of rings, L-ring and P-ring, are attached to respective
polysaccharide and peptidoglycan layer of cell wall, and the inner pair of rings
i.e. S-ring and M-ring are attached with cell membrane. The outer rings form a
bearing for the rod to pass through it. In Gram-positive bacteria only the distal
(inner) pair of rings is present. The S-ring is attached to inside thick layer of
peptidoglycan and M-ring is attached to cell membrane.
b. Hook: The hook is present outside the cell wall and connects filament to
the basal body. It consists of different proteins. The hook in Gram-positive
bacteria is slightly longer than the Gram-negative bacteria.

L ring

P ring

S ring
M ring
Figure 4: Flagellum structure in Gram- negative bacteria.

c. Filament or shaft: The outermost long region of the flagellum is called

filament or shaft. It has a constant diameter and is made up of globular
proteins, the flagellin. The flagellins are arranged in several chains that
intertwine and form helix around a hollow core. The proteins of flagella act to

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Microbial Physiology 3rd Class

identify certain pathogenic bacteria unlike eukaryotes, the filaments are not
covered by a membrane or sheath.
- Locomotion: There are four types of movement in bacteria. a. flagerllar
movement : bacterial flagella are motile and help in locomotion of bacterial
cells . Prokaryotic flagellum is semi rigid, helical rotor that moves the cell by
rotating from the basal body either clockwise or counter clockwise around its
axis. The helical waves are generated from the base to the tip of flagellum.
The rotating the flagellum forms a bundle that pushes against water and propel
the bacterium. The basal body acts as motor and cause rotation. Suggested that
a turning motion is generated between S-ring and M- ring, where the former
acts as a starter and the later acts as rotor. The P-ring and L-ring are just
bashings. The basal body gives a universal joint to the cell and allows
complete rotation of the hook and shaft both clockwise and counter clockwise.
The polar flagellum rotates anticlockwise but the cell rotates clockwise when
moving normally. Rotation of flagellum in anticlockwise direction results in
movement of bacterial cell in opposite direction. The peritrichous flagella as
trailing bundle also rotate in anticlockwise direction. Cells of spirilla possess a
non- helical tuft of polar flagella. The flagella rotate either at one end or both
and result in cell movement. There is coordination between the flagella of
both ends for rotation and movement of cell.
Energy is required for the movement of flagella. In eukaryotes, energy is
generated by ATP. The mechanism of energy generation for the movement of
prokaryotes flagella is not known. However, the basal body requires energy to
causes motion. Movement of ions between M-ring and S-ring possibly
energizes the flagellar motor.
b. Spirochaetial movement: The spirochaetes show several types of
movements such as flexing, spinning, free swimming and creeping as they are
flexible and helical bacteria lack flagella. Just within the cell envelope they
have flagella like structure which are known as periplasmic flagella or axial
fibrils or endoflagella. The axial fibrils are present in the space between inner
and outer membrane of cell envelope. The mechanism of motility is not
known. The axial fibrils rotate in periplasmic space and cause the rotation of
the opposite direction.
c. Gliding movement: some bacteria such as the species of cyanobactertia
(e.g. cytophaga) and mycoplasma show gliding movement when come in
contact with a solid surface. However, no organelles are associated with the
movement. Except mycoplasma, in others two gram-negative type cell walls
are present.

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d. Chemotaxis
Chemotaxis is the movement of bacteria towards chemical attraction and away
from chemical repellants. Bacteria are attracted towards the nutrients such as
sugar and amino acids, and are repelled by harmful substances and bacterial
wastes. They also respond to other environmental fluctuations such as
temperature, light, gravity, etc.
3. Pili and fimbriae
Pili and fimbriae are hair like appendages found on surface of cell wall in
gram-negative bacteria (e. g, Enterbacteriaceae, pseudomodaceae and
caulobacter). Eukaryotic cells lack pili. The term fimbriae are used for all hair
like structure covering the surface of the cell. Pili are genetically governed by
plasmids, the number of which varies from 3 to 5. The number of fimbriae is
around 1,000. However, a similar structure has also been observed only in
Corynebacterium renale, gram-positive bacterium. Pili differ from flagella in
being shorter and thinner, straight and less rigid. But they are in large number.
They occur either at poles of bacterial cell or evenly distributed over the
enteric surface of the cell. The pili are 0.2-20 um long with diameter of about
250 A°.
- Classes of Pili: According to the function pili are of two types:
a. Common pili which act to adhere the cell to surfaces , and b. Sex pili which
join the other bacterial cell for transfer of genome.
- Structure of Pili : both fimbriae and pili are like flagella as both are the
appendages on bacterial cell wall. They originate from cytoplasm that
protrudes outside after penetrating the peptidoglycan layer of cell wall.
fimbirae are made up of 100% protein called fimbrilin or pilin which consists
of about 163 amino acids. Fimbrilin has a molecular weight of about 16,000
Daltons. In addition, the sex pili are helical tubules consisting of a hollow core
(25-30A°). The sex pili are the cylinder of repeating protein units. Its
filamentous structure is governed by the sex factor (plasmid) of the bacterium
for example F Factor. Col I factor and R factor. As compared to fimbriae the
sex pili have greater diameter (65-135 A° diameter length up to 20 μm), and a
terminal knob of 150-800 A° diameter. There are two types of pili in E. coli
for example F-pili (determined by F factor) and I-pili (determined by Col I
factor) .
- Function of Pili : there are several functions of fimbirae and pili as given
below :
a. Bacteria containing fimbriae called fimbriate bacteria. Fimbriae have the
adhesive properties which attach the organism to the natural substrate or to the

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other organism. Fimbriea agglutinate the blood cells such as erythrocytes,

leucocyte, epithelial cells, etc.
b. Fimbriae are equipped with antigenic properties as they act as thermolabile
nonspecific agglutinogen.
c. Fimbriae affect the metabolic activity. The fim+ cells (cells containing
fimbriae) possess higher rate of metabolic activity than the Fim- cells (cells
devoid of fimbriae). Moreover, they function as aggregation organelles i.e.
they can form stellate aggregation on a static liquid medium.
d. The sex pili make contact between two cells, Since they possess hollow
-
core, they act as conjugation tube. The tip of pilus recognizes the female (F )
+
cell through which the genetic material of donor (F ) cell passes to the
recipient (female) cell. Only F-pili (not I-pili) contain axial hole.
4- The cell Wall (Outer Membrane)
The cell wall of bacteria is a semi rigid and complex structure present under
capsule and external to the plasma membrane. It is responsible for shape of
the cell. The cell wall protects the plasma membrane and the other
cytoplasmic inclusions from outer environment. It also protects the bacterial
cell from bursting when the osmotic pressure of cytoplasm is higher than that
of outside of cell wall. It provides support for attachment to the flagella. It
rescues the cell from antibodies and harmful chemicals.
The cell wall of gram-negative bacteria is comparatively thinner than the cell
wall of gram-positive bacteria. In addition, Chemical composition of cell wall
differs. Also cell walls of eukaryotic microorganisms (e.g. algae. fungi) differ
chemically from those of prokaryotes.
Chemical composition and cell wall characteristics
The cell wall of bacteria is made up of network of peptidoglycan. It is present
almost on all bacterial cell wall except halobacterium and halococcus.
Because these bacteria live in marine water which contains high salt
concentration the osmotic pressure of cytoplasm is more or less similar to
outside the cell environment.
Peptidoglycan determines the shape of the cell. It accounts for 40-80% of total
dry weight of cell. Its thickness is about 30-80 nm. It is insoluble and porous
polymer that provides rigidity. It is a mucopolysaccharide. However, its
chemical composition differs from species to species. It consists of repeating
disaccharide attached to chains of four or five amino acids. The
monosaccharide, N-acetylglucosamine (NAG) and N-acetylmuramic acid
(NAM) are linked by β-1, 4-glycosidic bond. These are related to glucose
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Microbial Physiology 3rd Class

attached with amino acid groups. The structural formulae of NAG and NAM
are shown in figure 5.
A tetrapeptide side chain containing four amino acid (L-alanine, D-glutamate,
L-lysine and D-alanine) was attached to each NAM. The third amino acid
varies with different bacteria and may be lysine, diaminopametic acid or
threonine. For example in E. coli instead of L-lysine (the third amino acid)
there is meso diaminopimelic acid. Due to extensive cross linking the
peptidoglycan becomes a rigid macromolecule of the cell wall.

Figure 5: Chemical structure of N-acetylglucosamine (NAG) and N- acetylmuramic acid

(NAM) linked together by β-1, 4 linkage.

i. Archaeobacteria: Structure and chemical composition of cell wall of

archaeobacteria differ from that of eubacteria. Many archaea have a well with
a single, thick homogeneous layer. Archaeal cell walls lack peptidoglycan and
posses no common cell wall polymer. Usually cell wall is composed of
proteins, glycoproteins or polysaccharides. Due to unusual chemical
composition the cell envelope show a high degree of resistance against cell
wall antibiotics and lytic agents.
Their walls chemistry varies from species to species but usually consists of
complex heteropolysaccharides; in Gram-positive archaeobacteria wells
consists of pseudomurein, methanochondroitin , or heteroplysaccharide and in
all Gram-negative archaeobacteria have cell envelopes which are composed of
crystalline protein or glycoprotein subunits. In most organism of
methanogenic branch and extreme thermophilic sulphur metabolizers, single
S-layers is found in cell envelope which provides remarkable resistance (
tolerate the extremes of environmental conditions such as high salt, low pH
and high temperature).

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Microbial Physiology 3rd Class

ii. Gram-positive bacteria: In most of Gram-positive bacteria, the cell wall

contains several layers of peptidoglycan which is inter-connected by side
chains and cross bridges. Peptidoglycan accounts for 40-90% of total dry
weight of cell wall. However, the thickness may vary with types of species
and provides rigidity to cell wall. The layers of peptidoglycan are thicker in
Gram-positive bacteria than that in Gram-negative bacteria (Table 1). In most
of Gram-positive bacteria peptidoglycan is associated with acidic polymers
containing phosphorus called teichoic acid or acidic polysaccharides. Teichoic
acids are hydrophilic, flexible and linear molecules. The presence of teichoic
acid makes easy to diagnose the bacteria serologically.
Teichoic acids are mainly of three types (a) ribitol teichoic acids (b) glycerol
teichoic acid, and (c) glucosylglycerol phosphate teichoic acid. The acids
are linked to layers of peptidoglycan of plasma membrane. The phosphate
groups provide negative charge which in turn controls the movement of
cation i.e. positive ions across the cells. Teichoic acids possibly play a role
in growth of bacterial cell by regulating the activity of an enzyme
autolysin. The acids prevent the extensive break down and possibly the
lysis of cell wall. They also store phosphorus.
The wall of most eubacteria contains very low amount of lipid except
mycobacterium and corynebacterium.
iii. Gram-negative bacteria: The cell envelope of gram-negative bacteria
consists of two unit membranes of 75 A° wide, separated by 100 A° wide
periplasmic space. Peptidoglycan is present in periplasmic space in Gram-
negative bacteria but in very low amount. They totally lack teichoic acids.
Peptidoglycan is situated in periplasmic space and covalently linked to
lipoproteins in the outer membrane. The periplasmic space is a space between
the outer membrane and plasma membrane which appears like gel and
contains a high amount of enzymes and transport proteins. Due to the presence
of low amount of peptidoglycan, the cell wall of Gram-negative bacteria can
easily be disintegrated (figure 6).

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Microbial Physiology 3rd Class

Figure 6: Structure and chemical composition and cell walls of Gram –negative and gram
positive bacteria.

The cell envelope of Gram-negative bacteria is a bilayer structure consisting

of mainly Apo proteins, lipopolysaccharides (LPS) and phospholipids.
The chemical constituents and arrangement are described in details as below:
a. Lipoproteins: Lipoproteins occur freely and in bound forms as well. In
lipoproteins of outer membrane, proteins bind to lipid non-covalently;
whereas in lipoproteins of plasma membrane, proteins bind to lipid covalently.
Lipoproteins together with matrix proteins form a complex which contains
diffusion channels. A diffusion channel is enclosed by three molecules of
matrix protein leaving a diameter of about 1.5-2nm.
b. Lipopolysaccharides (LPS): The outer membrane of Gram-negative
bacteria is covered by LPS which is made up of polysaccharides covalently
linked to lipid A. Lipid A: it consists of glucosamine, phosphate and fatty
acids.
c. Polysaccharide: the polysaccharide portion of LPS of salmonella cell wall is
composed of three important components, the inner core, the outer core and
the O-antigen side chain. Although the polysaccharide of LPS is also known
as O- polysaccharide. The O-antigen side chains in rough strains of Gram-
negative bacteria are absent; whereas the smooth strains of salmonella have
O-antigen side chains which may extend out the wall surface and attain about
30 nm length. These chains have antigenic property and, therefore, can be
distinguished serologically (e.g. species of salmonella). Its role is comparable
to that of teichoic acids in Gram-positive bacteria cell wall.
d. Matrix Proteins: the outer membrane of cell envelope doesn't warrant the
entry of all substances since the nutrients are to pass across the membrane. It
is impermeable only to macromolecules such as proteins, lipids, etc. The
permeability of outer membrane is due to the presence of proteins called

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Microbial Physiology 3rd Class

porins that from channels. The pornis are not specific and allow the small
molecules. Certain porins are specific and permit only the specific substances
such as vitamin B12 nucleotides. Porins also act as receptor sites for
bacteriophages and bacteriocins (the proteins produced by certain bacteria that
inhibit or kill the related species).
- Function of G –ve cell wall: following are the functions of the cell wall (the
outer membrane):
(a) Peptidoglycan provides structural integrity of cell by forming a rigid layer
in outer membrane. The matrix proteins to some extent also contribute to
structure with peptidoglycan.
(b) The cell envelope acts as barrier for diffusion to certain molecules across
the envelope.
(c) The matrix proteins act as receptor sites for bacteriophage and
bacteriocins.
(d) The O-antigen side chain of polysaccharide of LPS determines the antigen
specificity of Gram-negative bacteria.
Differences between cell walls of gram-positive and gram-negative bacteria
are given in table 1.
Table 1: Differences between cell walls of gram-positive and gram-negative bacteria.
Character

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Microbial Physiology 3rd Class

A typical cell wall

There are a few groups of microorganisms that have no cell walls. The
protoplasts are surrounded by only a cytoplasmic membrane, for example the
members of mollicutes (Mycoplasma and Ureoplasma). Due to the lack of
rigid cell wall the cell can take any shape cocci, filamentous, discs. However,
mycoplasmas are the smallest known microorganism. Like viruses they can
pass through the bacterial filters. Their plasma membrane is unique in having
lipids called sterols. Sterols possibly protect the cell from osmotic lysis.
The other example of a typical cell wall is the L-form of bacteria. The L-forms
are named after the Lister institute where they were discovered for the first
time. The L-forms are the small mutant bacteria containing defective cell
walls. This form can be produced by inducing the bacteria with certain
chemicals and antibiotics. Some L-forms after giving proper nutrition revert to
the original forms and the others are stable. The L-forms attain irregular
shape. It has been found when the protoplast of B. subtilis is placed in a 25%
gelatin medium and incubated at 26 C°; it reverts back to the normal walled
form.
The cell wall of Gram-positive bacteria is degraded when treated with
lysozyme. The cellular material is surrounded by plasma membrane. If
osmotic lysis does not occur the plasma membrane remains intact. These cells
devoid of cell wall are known as protoplast. In contrast the lysozymes destroy
the cell wall of Gram-negative bacteria only to some extent. Some of outer
membrane remains intact. Thus the cellular contact, plasma membrane and
remaining outer cell wall layer are jointly called spheroplast.
5. Plasma membrane (cell or cytoplasmic membrane):
The plasma membrane also called cell membrane or cytoplasmic membrane is
a structure situated just beneath the cell wall. However, no cell could be alive
without a plasma membrane. It consists of proteins (20-70%), lipids (28-80%),
oligosaccharides (1-5%) and water (20%). The plasma membrane consists of a
continuous bilayer of phospholipid molecules in which globular proteins are
embedded.
The plasma membrane is semifluid structure in which lipids and proteins are
arranged in a mosaic manner. The globular proteins are of two types; extrinsic
(peripheral) proteins and intrinsic (integral) proteins. The extrinsic protein is
soluble and, therefore. Dissociate from the membrane, while the intrinsic
protein is insoluble and could not (or rarely) dissociate. The intrinsic proteins
are partially embedded either on outer surface or on inner surface of the
bilayer and take part in lateral diffusion in lipid bilayer (figure 7).

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Microbial Physiology 3rd Class

The lipid matrix of membrane has fluidity that permits the membrane
components to move laterally. The membrane fluidity is due to the
hydrophobic interactions of lipids and proteins. The fluidity is important for a
number of membrane functions.
The presence of complex lipids becomes a key character of certain
microorganisms on the basis of which they can be identified. For example, the
cell wall of mycobacterium contains high amount of lipids such as waxes and
glycolipids which gives the bacterium a distinctive staining characteristic.

Figure 7: bacterial plasma membrane.

Function of Plasma Membrane:

The cytoplasmic membrane is the site of many metabolic activities as given
below:
a. The organic and inorganic nutrients are transported by permeases through
plasma membrane.
b. It consists of enzymes of biosynthetic pathways that synthesize different
components of the cell wall such as peptidoglycan, teichoic acids,
polysaccharides, lipopolysaccharides and phospholipids.
c. It possesses the attachment site for bacterial chromosome and plasmid
DNA.

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Microbial Physiology 3rd Class

d. The inner membrane invaginates to form mesosomes, a site for respiratory

activity. The plasma membrane contains about 200 respiratory proteins that
have been found to be responsible for the transport of H + ions.
e. It provides permeability barrier and thus prevent the escape of cellular
materials outside the cell, show selective permeability.
6- Mesosomes:
Mesosomes are the invaginated structures formed by the localized infoldings
of the plasma membrane. The invaginted structures comprise of vesicles,
Tubules of lamellar whorls. Generally mesosomes are found in association
with nuclear area or near the site of cell division. They are absent in
eukaryotes. The lamellae are formed by flat vesicles when arranged in
parallel. Some of the lamellae are connected to the cell membrane. The
lamellar whorl can be observed in Nitrobacter, Nitromonas and Nitrococcus.
The constriction does not cause the complete separation of tubules. However,
they are the special cell membrane components, the proteins of which differ
from the cell membrane.
The exact structure and function of
mesosomes are not known. However, it has
been suggest that these are artifacts (figure
8).
Figure 8: The bacterial mesosomes.

Moreover, mesosomes are supposed to take part in respiration but they

are not analogous to mitochondria because they lack outer membrane.
Respiratory enzymes have been found to be present in cell membrane. In the
vesicle of mesosomes the respiratory enzymes and the components of electron
transport such as ATPase, dehydrogenases, cytochrome are either absent or
present in low amount. In addition, mesosomes are supposed as a site for
synthesis of some of wall membranes.
Mesosomes might play a role in reproduction also. During binary fission a
cross wall is formed resulting in formation of two cells. Mesosomes begin the
formation of septum and attach bacterial DNA to the cell membrane. It
separates the bacterial DNA into each daughter cell. In addition, the infoldings
of mesosomes increase the surface area of plasma membrane that in turn
increases the absorption of nutrients.

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Microbial Physiology 3rd Class

7- Cytoplasm:
Cytoplasm of prokaryotes refers to the internal matrix of cell inside the
plasma membrane. Cytoplasm consists of water (80%), proteins,
carbohydrates, lipids, inorganic ions and certain low molecular components.
Cytoplasm is thick and semitransparent. The DNA molecules, ribosomes and
the other inclusions are the structure of cytoplasm. In certain cyanobacteria
gas vacuoles are found. The prokaryotic cytoplasm differs from the eukaryotic
cytoplasm.
i. Ribosomes: All living cell contains ribosomes which vary complex
structures made of protein and ribonucleic acid (RNA), act as site of protein
synthesis. Number of ribosomes represents high rate of protein synthesis and
vice versa. Cytoplasm of a prokaryotic cell contains about 10000 ribosomes
which account up to 30% of total dry weight of the cell. Presence of
ribosomes in high number gives the cytoplasm a granular appearance. The
eukaryotic ribosomes are found attached to cell membrane, whereas the
prokaryotic ribosomes are free in cytoplasm or loosely attached to the plasma
membrane. Prokaryotic ribosomes are smaller and less dense than eukaryotic
ribosomes. Ribosomes of prokaryotes are often called 70S ribosomes and that
of eukaryotes as 80S ribosomes. The letter S refers to Svedberg unit which
indicates the relative rate of sedimentation during ultracentrifugation.
Sedimentation rate depends on size, shape and weight of particles.
ii. Nucleoids (the bacterial chromosome): As in eukaryotes, in prokaryotes
also the basic dye stains the nuclear material and reveals as dense and
centrally located bodies of irregular outline. Upon observation with electron
microscope it was found that this central region is not separated from the
cytoplasm by a membrane and consists of nuclear structure besides; the DNA
fibrils. The eukaryotes contain a well-organized nucleus in which the genetic
material is enclosed by a nuclear membrane, whereas, the DNA material of
prokaryotes is not enclosed by any covering. Hence the bacterial chromosome
is known as chromatin bodies or nucleoids. The nucleoid is a single long
circular double stranded DNA molecule free from histone protein. The histone
is present in eukaryotes, therefore, results the eukaryotic DNA into the beaded
structures i.e. nucleosomes.
iii. Plasmids: during 1950s, working on conjugation process it was found that
maleness in bacteria is determined by a transmissible genetic element. When
male and female bacteria conjugate, every female is converted into a male.
This inherited property of male is called the F (fertility) factor which is
transmitted by cell to cell contact. Therefore, F is a separate genetic element.
In 1952, J. Lederberg coined the term plasmid as a genetic name for this
element. Hence the plasmids may be defined as a small circular, self-

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Microbial Physiology 3rd Class

replicating and double stranded DNA molecule present in bacterial cell,

in addition to bacterial chromosome. It replicates independently during cell
division and inherited by both of daughter cells. Therefore, its function is not
governed by the bacterial chromosome. Some important types of plasmid are
F factor, R plasmids, Col plasmids, virulence plasmids, metabolic plasmids.
vi. Granules or inclusions: this granules or inclusions also called storage
bodies. Bacteria store nutrients intra cellular in inclusions bodies during
periods of nutrient abundance, these bodies varying in size, number and
content.
Some types of inclusions bodies:
-Glycogen bodies (granules) and poly β hydroxyl – butyrate (PHB), this
granules source of Carbone (rich organic substance) and energy, it is have
single –layered membrane.
-Inorganic compound granules, this contains crystal of inorganic compound
are not enclosed by membrane, like:
a- Sulfur granules: of photosynthesis bacteria.
b-Meta chromatic granules: or poly phosphate granules, volutin granules, in
Corynebacterium and mycobacterium, an important source of building blocks
for nucleic acid and ATP, the stained redopurple by methylene blue so that
have been termed methachromatic granules.
-Lipid inclusions: Lipids are found in a high amount as source for energy, in
several species of Bacillus, Mycobacterium, and Spirillum.
-Magnetosomes: Magnetosomes are the intracellular chains of 40-50
magnetite (Fe3O4) Particles found in magnetotactic bacteria. Each iron particle
is a tiny magnet. Hence, the bacteria employ their magnetosomes to determine
northward and downward directions, also help them to swim to nutrient rich
sediments or locate the optimum depth in fresh water and marine habitats.
-Gas vesicles: Found in floating forms prokaryotic Microorganisms in lakes
and sea. These vesicles not found in flagellar microorganisms, they are gas-
filled structure which contains the same gas in which the organisms are
suspended. Gas vesicles provide buoyancy and keep the cell floating form.
8- Endospores:
Endospores are bacterial survival structures that are highly resistant to many
different types of chemical and environmental stresses and therefore enable
the survival of bacteria in environments that would be lethal for these
cells in their normal form. It has been proposed that endospore formation

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Microbial Physiology 3rd Class

has allowed for the survival of some bacteria for hundreds or millions of years
(e.g. in salt crystals).
Endospore formation (figure 9) is limited to several genera of Gram-positive
bacteria such as Bacillus and Clostridium. It's called endospore because it's
produced inside a cell and differs from reproductive spores in that only one
spore is formed per cell resulting in no net gain in cell number upon
endospore germination. The location of an endospore within a cell is species-
specific and can be used to determine the identity of a bacterium. Dipicolinic
acid is a chemical compound which composes 5% to 15% of the dry weight of
bacterial spores. It is implicated as responsible for the heat resistance of the
endospore.
The process of endospore formation is called sporulation or sporogenesis. It
occurs normally when growth of bacterium stop due to lack of nutrients,
sporulation is a complex process and occurs in several stages.

Figure 9: bacterial endospore.

Microbial Nutrition
All organisms extract energy from their environment. Producers (also called
autotrophs) extract energy from the nonliving environment, such as plants
capturing light energy from the sun or bacteria deriving chemical energy from
rocks. Consumers (also called heterotrophs), in contrast, obtain energy by
eating nutrients made by other organisms. Decomposers are consumers that
obtain nutrients from dead organisms. Fungi such as mushrooms are
decomposers. Like all other living things, microorganisms need to acquire
energy in order to survive figure 10.

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Microbial Physiology 3rd Class

Energy is required:
1) To maintain the structural integrity of the cell by repairing any damage to
its constituents.
2) To synthesis new cellular components such as nucleic acids,
polysaccharides and enzymes.
3) To transport certain substances into the cell from its surroundings.
4) For the cell to grow and multiply.
5) For cellular movement.
Microbial cell are structurally complex and carry out numerous functions. In
order to construct new cellular components and do cellular work, organisms
must have a supply of raw materials or nutrients and a source of energy. In
nature, particularly in a given environment, the distribution of microbes is
partly determined by the availability of specific nutrients required to support
their growth. Nutrients are substances used in biosynthesis and energy
release, therefore are required for microbial growth. Or all chemicals required
by microorganisms (and all other organisms) as raw material for their
metabolism and reproduction are called Nutrients. Nutrients can be classified
as mineral nutrients and growth factors.

A. The Common Nutrient requirements:

1- Mineral Nutrients The microbial mineral nutrients can be classified as
macro (major) nutrients, and micro (minor) nutrients or trace elements on the
basis of their amount required.
a. Macro or Major Mineral Nutrients
These are called macro mineral nutrients because they are required by
microorganisms in relatively large amount, the lack of which can limit growth.
The microbial cells contain water accounting for some 80-90% of their total
weight and, therefore, the water is always the major essential nutrient in
quantitative terms. The solid matter of cells contain, in addition to oxygen and

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Microbial Physiology 3rd Class

hydrogen (derivable metabolically from water), the other macro (major)

elements, namely, carbon, nitrogen, phosphorus, Sulphur, potassium,
magnesium, sodium, calcium and iron in order of decreasing abundance.
About 95% of cellular dry weight of microbial cells is accounted for only six
macro (major) elements (O, H, C, N, P and S). However, approximate
percentage of dry weight and general physiological functions of major mineral
nutrients are given in the table 2.
Table 2: Approximate percentage of dry weight and general physiological functions of
mineral nutrients
Element % of dry Physiological functions
(Nutrient) weight
Carbon (C) 50 Constituent of all organic cell materials
Oxygen(O) 20 Constituent of cellular water and most organic cell
materials; oxygen serves as an electron receptor in aerobic
respiration
Nitrogen (N) 14 Constituent of proteins, nucleic acids, coenzymes
Hydrogen (H) 8 Constituent of cellular water, organic cell materials
Sulphur (S) 1 Constituent of some amino acids (cysteine and methionine),
of some coenzymes (e.g., CoA, Co carboxylase)
Potassium (K) 1 Important inorganic cation in cells, cofactor for some
enzymatic reactions
Sodium (Na) 1 Important inorganic cations in cells, important in membrane
transport
Calcium (Ca) 0.5 Important inorganic cation in cells, cofactor for some
enzymatic reactions (e.g., reactions by proteinases). It is
essential component of endospores. Calcium concentrations
affect membrane permeability and play a critical role in
movement of flagella and cilia
Magnesium 0.5 Important inorganic cation in cells, cofactor for some
(Mg) enzymatic reactions sometimes replacing Mg. Magnesium
plays important role in protein synthesis; without the
ribosomal subunits do not associate and translation of
nucleic acids into protein is not possible
Iron (Fe) 0.2 Constituent of cytochromes and other haeme or non-haeme
proteins, cofactor for a number of enzymatic reactions
- Requirement for Carbon, hydrogen, Oxygen, and Electron
All organisms need C, H, O, and source of electrons. C is needed for
backbones of all organic molecules from which organisms are building. H and
O are also important elements found in organic molecules. Electrons are
needed for two reasons, the movement of electrons through electron transport
chains and during oxidation – reduction reactions can provide energy for in
cellular work also needed to reduce molecules during biosynthesis.
Organic compounds serve microorganisms (heterotrophs) as a source for:
- The required element of C, H, and O
- Energy

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Microbial Physiology 3rd Class

- Electrons for oxidation-reduction reactions or biosynthetic processes.

However, not all carbon sources provide energy or H, e.g., carbon dioxide
(CO2) as in Autotrophs use CO2 as carbon source, but this molecule does not
provide H or energy, many autotrophs use sunlight for energy via
photosynthesis, some autotrophs oxidize inorganic molecule to derive
electrons and energy.
Remarkably, microorganisms are extraordinary flexible with regard to their
carbon source, some will utilize a diverse array of carbon source, including
waxes, rubber, oil, etc.

- Requirement of Nitrogen, Phosphorus, and sulfur

To grow, microorganisms must be able to incorporate large quantities of
nitrogen, phosphorus and sulfur. Although these elements may be acquired
from organic molecules, microorganisms usually provided by inorganic
sources as well.
Nitrogen is needed for the synthesis of amino acid, purines, pyrimidines,
some carbohydrates and lipids, enzymes cofactors, and others. Most
phototrophs and many chemotrophs microorganisms reduce nitrate (NO3) to
ammonia (NH3) and incorporate the ammonia in a process known as
assimilatory nitrate reduction. A variety of bacteria (e.g. many cyanobacteria
and the symbiotic bacterium Rhizobium) can assimilate atmospheric nitrogen
(N2) by reducing it to ammonium (NH4+). This is called nitrogen fixation.
Phosphorus is present in nucleic acid, phospholipids, nucleotide like ATP,
several cofactors, some proteins, and other cell components. Almost all
microorganisms use inorganic phosphate as their phosphorus source and
incorporate it directly. Some Microorganisms utilize organophosphate. Low
phosphate levels actually limit microbial growth in many aquatic
environments. Some microbes, such as Escherichia coli, can use both organic
and inorganic phosphate.
Sulfur is needed for the synthesis of substances like the amino acid cysteine
and methionine, some carbohydrates, biotin, and thiamine. Most
microorganisms use sulfate (SO4) as a source of sulfur and reduce it by
assimilatory sulfate reduction; few microorganisms require a reduced form of
sulfur such as cysteine.

b - Micro or Minor Mineral Nutrients or Trace Elements

The microorganisms, in general do not use only macro (major) elements but
also others like cobalt, copper, manganese, molybdenum, nickel, selenium,
tungsten, vanadium and zinc which are required in residual fraction by
nearly all microorganisms. These elements are often referred to as minor
(micro) nutrients or trace elements table 3. The micronutrients required in
small amounts and usually not a growth limiting factor due to their ubiquitous

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 Microbial Physiology 3rd Class

nature. They are metals playing the role of cells catalysts and many of them
are play a structural role in various enzymes. The major micronutrients of
living systems and gives examples of enzymes in which each plays a role.
Some microorganisms.

Table 3: Micronutrients (trace elements) and their cellular functions

Micronutrient Cellular function

Cobalt (Co) Vitamin B12; transcarboxylase (propionic acid bacteria)
Copper (Cu) Respiration (cytochrome c oxidase); photosynthesis
Manganese (Mn) Acts as activator or various enzymes; and in the photolytic (water-
splitting) enzyme in oxygenic phototrophs (photosystem-II)
Molybdenum (Mo) Present in some Flavin-containing enzymes, nitrogenase, nitrate
reductase, sulphide oxidase, some format dehydrogenases
Nickel (Ni) Present in most hydrogenase enzymes; coenzyme F430 of
methanogenes; carbon monoxide Dehydrogenase; urease
Selenium (se) Occurs in format dehydrogenase; oxotransferases of
hyperthermophiles
Tungsten (W) In some format dehydrogenases; oxotransferased of
hyperthermophiles
Vanadium (V) Vanadium nitrogenase; bromoperoxidase
Zinc (Zn) In carbonic anhydrase; alcohol dehydrogenase; RNA and DNA
polymerases; many DNA-binding proteins

Finally, Microorganisms required a balance mixture of nutrients for normal

growth. If an essential nutrient is in short supply, microbial growth will be
limited regardless of the concentrations of other nutrients.

2. Growth Factors
Besides the mineral nutrients, the microorganisms need some organic
compounds. Most of the microorganisms are capable of synthesizing these
organic compounds from simpler carbon resources; others cannot and need
their supply from outside for their proper growth and development. Organic
nutrients of this type are known collectively as growth factors (essential
metabolites). Growth factors are organic compounds that are essential
cellular components or precursors of such components but cannot be
synthesized by the organism itself. And can be categorized into three groups.
1. Amino acids are needed for protein synthesis.
2. Purines and pyrimidines are needed for nucleic acid synthesis.
3. Vitamins are small organic molecules that usually make up all or part of
enzyme cofactors and are needed in only very small amounts to sustain
growth. Some important vitamins and their functions are summarized in the
table 4.

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Microbial Physiology 3rd Class

Table 4 : Vitamins and their Functions

Vitamins Function
Riboflavin (B2) Precursor of Flavin mononucleotide (FMN) and Flavin-adenine
dinucleotide (FAD) which are involved in electron transport
chain
Cobalamin (B12) Reduction of and transfer of single carbon fragments; synthesis
of deoxyribose
Biotin In fatty acid biosynthesis; in b-decarboxylation; in some CO2-
fixation reaction
p-Aminobenzoic acid Precursor of folic acid
Folic acid One-carbon metabolism; transfer of methyl group
Thiamine (B1) Transketolase; a-decarboxylations
Nicotinic acid (niacin) Precursor of Nicotinamide adenine dinucleotide (NAD+);
electron transfer in oxidation-reduction reactions
Lipoic acid Acyl group transfer in decarboxylations of Pyruvic acid and a-
ketoglutaric acid
Pantothenic acid Precursor of coenzyme A; activation acetyl and other acyl
derivastions
Vitamin B6 Amino acid and keto acid transformations
Vitamin K Electron transport; in synthesis of sphingolipids
Hydroxamates Solubilization of iron and transport into cell

B. Nutritional types of Microorganisms

Microorganisms can be grouped into nutritional classes based upon their
sources of Carbon, energy and electron:

Carbon Sources:
a- Autotrophs M.O.: Organisms that use CO2 as their principal source of
carbon.
b- Heterotrophs M.O.: Organisms that reduced performed organic molecules
as their carbon source.

Energy Sources:
a- phototrophs M.O: Use light as their energy source.
b- Chemotrophs M.O: obtain energy from oxidation of chemical compounds
(either organic or inorganic).

Electron sources:
a- Lithotrophus M.O.: use reduced inorganic substances as their electron
source.
b- Organotrophs M.O: extract electrons from reduced organic compounds.

Despite the great metabolic diversity seen in the microorganisms, most may
be placed in one of five nutritional classes based on the primary sources of
carbon, energy, and electrons as in table 5.

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 Microbial Physiology 3rd Class

Table 5: Major nutrition types of Microorganisms.

Nutritional Type Carbon Energy Electron Representative M.O.
Source Source Source
Photolithoautotrophy CO2 Light Inorganic e Purple and green sulfur
- donor bacteria, cyanobacteria
Photoorganoheterotr Organic Light Organic e - Purple nonsulfur
ophy carbon, but donor bacteria, green nonsulfur
CO2 may also bacteria
be used
Chemolithoautotrop CO2 Inorganic Inorganic e Sulfur –oxidization
hy chemicals - donor bacteria Hydrogen-
oxidizing bacteria
Chemolithoheterotro Organic Inorganic Inorganic e Some sulfur_oxidizing
phy Carbon but chemicals - donor bacteria
CO2 may also
be used
Chemoorganoheterot Organic carbon Organic Organic e Most nonphotosynthetic
rophy chemicals donor microbes , including
often same as Often same most pathogens , fungi
C source as C source

Although a particular species usually belongs to only one of the nutritional

classes, some show great metabolic flexibility and alter their metabolic
patterns in response to environmental changes (Mixotrophs). e.g., purple non
sulfur bacteria

C. Uptake of Nutrients by the cell

The first step in nutrient use is uptake of the required nutrients by the
microbial cell. Uptake mechanisms must be specific that is, the necessary
substances, and not others, must be acquired. Because microorganisms often
live in nutrient poor habitats, they must be able to transport nutrients from
dilute solutions into the cell against a concentration gradient. Finally, nutrient
molecules must pass through a selectively permeable plasma membrane that
prevents the free passage of most substances. Materials move into and out of
cells through either passive transport or active transport:
• Passive transport - movement of molecules from a more crowded to a less
crowded area WITHOUT the use of energy. Movement occurs when there are
unequal concentrations of a substance inside and outside of the cell.
• Active transport - movement of molecules from a less crowded to a more
crowded area WITH the use of energy. Molecules are "carried" into or out of
the cell using some of the cell's energy. Active transport is also characterized
by the carrier saturation effect at high solute concentration
Active and passive transport differ because: 1. Active transport makes use of
energy in the form of ATP whereas passive transport does not utilize any. 2.
Active transport involves the transfer of molecules or ions against a

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Microbial Physiology 3rd Class

concentration gradient whereas passive transport is the transfer along a

concentration gradient.

Microorganism’s uses of several different transport mechanisms include:

- Passive transport:
Passive diffusion
Facilitated diffusion

- Active transport:
Group translocation (primarily prokaryotes)
Membrane Bound Transport Systems
Binding Protein Transport System

- siderophores for iron uptake

- Endocytosis (Eukaryotes only)

Passive (Simple) diffusion: is the process in which molecules move from an

area of higher concentration to an area of lower concentration due to random
thermal energy. The rate of Passive diffusion is dependent on the size of the
concentration gradient between a cell exterior and its interior. Very Small
Molecules such as glycerol, H2O, O2, and CO2 often move across membranes
by passive diffusion. Large molecules must use another mechanism to be
transported across a membrane.

Facilitated diffusion: differs in that the rate of diffusion is increased by using

carrier molecules called permeases embedded in the plasma membrane.
Diffusion involving carrier protein is called Facilitated diffusion. Each
permease is specific for the particular molecule being transported.
Rate of diffusion increases as the concentration gradient increases, but the
process can become “saturated”, i.e., at a certain concentration all of the
permeases are bound with transport molecules. No metabolic energy input
required. After the solute molecule binds to the outside, the carrier may
change its conformation and release the molecule on the cell interior (figure
11). The carrier subsequently changes back to its original shape and is ready
to pick up another molecule, the process is reversible, i.e., if concentration is
higher in the cell, molecules will move out into the environment. Facilitated
diffusion is much more prominent in eukaryotic cells where it is used to
transport a variety of sugars and amino acids.

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Microbial Physiology 3rd Class

Figure 11: Facilitated diffusion involves the use of a protein to transport molecules across
the cell membrane.

Active transport: is carried out in at least three different ways in bacteria.

These include group translocation; membrane bound transport systems and
bidding protein transport systems. - Group translocation: is a type of active
transport because metabolic energy is used during uptake of the molecule
whereby molecules are chemically altered while being transported into the cell
(figure 12). Used by prokaryotes, not eukaryotes. Best example –
phosphoenolpyruvate : sugar transferase system (PTS).
PEP + sugar (outside) → pyruvate + sugar- phosphate (inside)

Figure 12: group translocation.

- Membrane Bound Transport Systems: In this type of transport system all

the proteins required for transport are firmly bound to the cell membranes. In
E. coli about 40% of the transport systems belong to this class, which includes
transport systems for sugars, ions and several amino acids.

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Microbial Physiology 3rd Class

- Binding Protein Transport System: The bacterial has special transport

problems arising from the presence of the cell wall and of the fluid filled
periplasmic space between the inner and outer membranes of the cell. Binding
proteins are present in the periplasmic space, and perhaps function in carrying
the solute across the space. The solute is then donated to another transport
receptor site at the surface of the inner membrane (plasma membrane).Binding
protein transport systems utilize ATP or a related compound.

Iron uptake: Iron uptake is made difficult by extreme insolubility of ferric

iron (Fe3+) and its derivatives, which leaves little free iron available for
transport many bacteria and fungi have overcome this difficulty by secreting
siderophores. Siderophores are low molecular weight organic molecules that
are able to complex with ferric iron and supply it to the cell. Microorganisms
have developed specialized transport system for siderophores, once
transported in molecule releases the iron ion which is reduced to its ferrous
form (Fe2+). Siderophore is recycled.

Endocytosis: is used to bring materials into

the cell from the outside, the cell takes up
solutes or particles by enclosing them in
vesicles pinched off from the plasma
membrane. In most cases the materials are
delivered to a lysosome where they are
digested Figure 13.
Figure 13: Endocytosis

Microbial Cultivation:
Cultivation is the process of propagating organisms by providing the
proper environmental conditions. The artificial culture of any organism
requires a supply of the necessary nutrients, together with appropriate
conditions such as temperature, pH and oxygen concentration. The nutrients
and conditions provided in the laboratory are usually a reflection of those
found in the organism’s natural habitat.
Cultivation Methods:
Two problems will be considered: 1) the choice of a suitable medium
and 2) the isolation of a bacterial organism in pure culture. The technique used
and the type of medium selected depend upon the nature of the investigation.
In general, three situations may be encountered: (1) One may need to raise a
growth of cells of a particular species that is on hand; (2) one may need to
determine the numbers and types of organisms present in a given material; or

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Microbial Physiology 3rd Class

(3) one may wish to isolate a particular type of microorganism from a natural
source.
Culture media: is a solid or liquid preparation used to grow, transport,
and store microorganisms. Must be containing the essential components
necessary for microbial growth as well as be useful in the identification and
characterization of microorganisms. Culture media can be classified on the
basis of several parameters: the chemical constitution from which they are
made, their physical nature, and their function (table 6)
Table 6: Types of Media

Physical nature Function type_____________

Liquid Defined (synthetic) Supportive (General purpose)
Semisolid Complex Enriched
Solid Selective Differential________
Two types of general purpose culture media:
- Synthetic (defined): all the components of the medium are known and
well defined, e.g., glucose –salts broth.
- Complex: one or more of the components are comprised of a chemically
unknown substance, e.g., tryptic soy broth.
Two types of enriched culture media:
- Selective: contain substances that favor the growth of one particular
microbe over another.
- Differential: contain substances that distinguish between different
groups of microbes.
Some enriched media can be both selective and differential, e.g.,
MacConkey’s agar.
Isolation of Microorganisms in Pure Culture
In order to study the properties of a given organism, it is necessary to
handle it in pure culture free of all other types of organisms. To do this, a
single cell must be isolated from all other cells and cultivated in such a
manner that its collective progeny also remain isolated. Several methods are
available.

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Microbial Physiology 3rd Class

1) Plating: Unlike cells in a liquid medium, cell in or on a gelled

medium are immobilized. Therefore, if few enough cells are placed in or on a
gelled medium, each cell will grow into an isolated colony.
2) Dilution: A much less reliable method. The suspension is serially
diluted, and samples of each dilution are plated. If only a few samples of a
particular dilution exhibit growth, it is presumed that some of the colonies
started from single cells.
Preservation of microbial cultures
Microbial cultures are preserved by storage at low temperatures, in order to
suspend growth processes. For short periods, most organisms can be kept at
refrigerator temperature (around 4 ◦C), but for longer-term storage, more
specialized treatment is necessary. Using deep freezing or freeze-drying,
cultures can be kept for many years, and then bring to life again and
recultured. Deep freezing requires rapid freezing to −70 ◦C to −95 ◦C, while
freeze-drying (lyophilization) involves freezing at slightly less extreme
temperatures and removing the water content under vacuum. Long-term
storage may be desirable to avoid the development of mutations or loss of cell
viability.
Microbial growth
Growth is the orderly increase in the sum of all the components of an
organism. Thus the increase in size that results when a cell takes up water or
lipid or polysaccharide is not true growth. Cell multiplication is a consequence
of growth; in unicellular organisms, growth leads to an increase in the number
of individuals making up a population or culture.
Growth is defined as an increase in cellular constituents and may result in an
increase in a microorganism's size, population number, or both.
Growth of a cell is the culmination of an ordered interplay among all of the
physiological activities of the cell. It is a complex process involving
1. Entrance of basic nutrients into the cell
2. Conversion of these compounds into energy and vital cell constituents
3. Replication of the chromosome
4. Increase in size and mass of the cell
5. Division of the cell into two daughter cells, each containing a copy of the
genome and other vital components.
Bacterial growth is the division of one bacterium into two daughter cells in a
process called binary fission. Providing no mutational event occurs the

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Microbial Physiology 3rd Class

resulting daughter cells are genetically identical to the original cell. Hence,
"local doubling" of the bacterial population occurs.
The prokaryotic cell cycle (binary fission):
The cell cycle is complete sequence of events extending from the formation of
a new cell through the next division. Most prokaryotes reproduce by binary
fission (figure 14), although some prokaryotes reproduce by budding,
fragmentation, and other means. Binary fission is a relatively simple type of
cell division: the cell elongates, replicates its chromosome, and separates the
newly formed DNA molecules so there is one chromosome in each half of the
cell. Finally, a septum (or cross wall) is formed at midcell, dividing the parent
cell into two progeny cell, each having its own chromosome and a
complement of other cellular constituents. Two pathways function during the
cell cycle: one pathway replicates and partitions the DNA into the progeny
cells, the other carries out cytokinesis (septum formation and formation of
progeny cells).

Figure 14: binary fission.

The Growth curve:

Binary fission and other cell division processes bring about an increase
in the number of cells in a population. Population growth is studied by
analyzing the growth curve of a microbial culture. When microorganisms are
cultivated in liquid medium, they usually are grown in a batch culture or
closed system- that is, they are incubated in a closed culture vessel with a
single batch of medium. Because no fresh medium is provided during
incubation, nutrient concentrations decline and concentrations of wastes
increase. The growth of microorganisms reproducing by binary fission can be
plotted as the logarithm of the number of viable cells versus the incubation
time. The resulting curve has four distinct phases (Figure 15).

33
Microbial Physiology 3rd Class

Figure 15: Microbial Growth Curve in closed system.

Lag phase: When microorganisms are introduced into fresh culture medium,
usually no immediate increase in cell number occurs, so this period is called
the lag phase. Although cell division does not take place right away and there
is no net increase in mass, the cell is synthesizing new components. A lag
phase prior to the start of cell division can be necessary for a variety of
reasons. The cell May be old and depleted of ATP, essential cofactors and
ribosomes; these must be synthesized before growth can begin. The medium
may be different from the one the microorganism was growing in previously.

34
Microbial Physiology 3rd Class

Here new enzymes would be needed to use different nutrients. Possibly the
microorganisms have been injured and require time to recover. Whatever the
causes, eventually the cells retool, replicate their DNA, begin to increase in
mass, and finally divide.
The lag phase varies considerably in length with the condition of the
microorganisms and the nature of the medium. This phase may be quite long
if the inoculum is from an old culture or one that has been refrigerated.
Inoculation of a culture into a chemically different medium also results in
longer lag phase. On the other hand, when a young, vigorously growing
exponential phase culture is transferred to fresh medium of the same
composition, the lag phase will be short or absent.
Exponential phase: During the exponential or log phase, microorganisms are
growing and dividing at the maximal rate possible given their genetic
potential, the nature of the medium, and the conditions under which they are
growing. Their rate of growth is constant during the exponential phase; that is,
the microorganisms are dividing and doubling in number at regular intervals.
Because each individual divides at a slightly different moment, the growth
curve rises smoothly rather than in discrete jumps. The population is most
uniform in terms of chemical and physiological properties during this phase;
therefore exponential phase cultures are usually used in biochemical and
physiological.
Exponential growth is balanced growth. That is, all cellular constituents
are manufactured at constant rates relative to each other. If nutrient levels or
other environmental conditions change, unbalanced growth results. This is
growth during which the rates of synthesis of cell components vary relative to
one another until a new balanced state is reached. Unbalanced growth is
readily observed in two types of experiments: shift –up, where a culture is
transferred from a nutritionally poor medium to a richer one; and shift-down,
where a culture is transferred from a rich medium to a poor one. In a shift –up
experiment, there is a lag while the cells first construct new ribosomes to
enhance their capacity for protein synthesis. This is followed by increases in
protein and DNA synthesis. Finally, the expected rise in reproductive rate
takes place. In a shift-down experiment, there is a lag in growth because cells
need time to make the enzyme required for the biosynthesis of unavailable
nutrients. Consequently cell division and DNA replication continue after the
shift –down, but net protein and RNA synthesis slow. The cells become
smaller and reorganize themselves metabolically until they are able to grow
again. Then balanced growth is resumed and the culture enters the exponential
phase. These shifts-up and shift-down experiments demonstrate that microbial
growth is under precise, coordinated control and responds quickly to changes
in environmental conditions.

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Microbial Physiology 3rd Class

The microbial growth is limited by the low concentration of a required

nutrient. The rate of growth also increases with nutrient concentration. At
sufficiently high nutrient levels the transport systems are saturated, and the
growth rate does not rise further with increasing nutrient concentration.
Stationary phase: Because this is a closed system, eventually population
growth stopped and growth curve becomes horizontal this stationary phase.
Usually is attained by bacteria at a population level of around 10 9 cells per ml.
Other microorganisms normally do not reach such high population densities;
protozoan and algal cultures often have maximum concentrations of about 10 6
cells per ml. Of course final population size depends on nutrient availability
and other factors, as well as the type of microorganism being cultured. In the
stationary phase the total number of viable microorganisms remains constant.
This may result from a balance between cell division and cell death, or the
population may simply stop to divide but remain metabolically active.
Microbial populations enter the stationary phase for several reasons.
One factor is nutrient limitation; if an essential nutrient is depleted, population
growth will slow. Aerobic organisms often are limited by O2 availability.
Oxygen is not very soluble and may be depleted so quickly that only the
surface of a culture will have an O2 concentration adequate for growth. The
cells beneath the surface will not be able to grow unless the culture is shaken
or aerated in another way. Population growth also may stop due to the
accumulation of toxic waste products. This factor seems to limit the growth of
many anaerobic cultures (cultures growing in the absence of O2). For example,
streptococci can produce so much lactic acid and other organic acids from
sugar fermentation that their medium becomes acidic and inhibited.
Streptococcal cultures also can enter the stationary phase due to depletion of
their sugar supply. Finally, there is some evidence that growth may stop when
a critical population level is reached.
Senescence and death: For many years, the decline in viable cells following
stationary cells was described simply as the death phase. It was assumed that
detrimental environmental changes like nutrient lack and the buildup of toxic
wastes caused permanent harm resulting in loss of viability. That is even when
bacterial cells were transferred to fresh medium, no cellular growth was
observed. Because loss of viability was often not accompanied by a loss in
total cell number, it was assumed that cells died but not lyse. This view is
currently under discussed. There are two alternative hypotheses. Some
microbiologist believes starving cells that show an exponential decline in
density have not irreversibly lost their ability to reproduce. Rather, they
suggest that microbes are temporarily unable to grow, at least under the
laboratory conditions used. This phenomenon, which the cells are called
viable but non culturable (VBNC), is thought to be the result of a genetic

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Microbial Physiology 3rd Class

response triggered in starving, stationary phase cells. Just as some bacteria

form spores as a survival mechanism, but others are able to become dormant
without changes in morphology. Once the appropriate conditions are
available, VBNC microbes resume growth. VBNC microorganisms could
cause a public health threat, as many assays that test for food and drinking
water safety are culture-based.
The second alternative to a simple death phase programmed cell death.
In contrast to the VBNC hypothesis whereby cells are genetically
programmed to survive, programmed cell death predicts that a fraction of the
microbial population is genetically programmed to commit suicide. In this
case, non culturable cells are dead and the nutrients that they leak enable the
eventual growth of those cells in the population that did not initiate suicide.
The dying cells are sacrifice themselves for the benefit of the larger
population.
Phase of prolonged decline:
Long-term growth experiments reveal that an exponential decline in
viability is sometimes replaced by a gradual decline in the number of
culturable cells. This decline can last months to years. During this time the
bacterial population continually evolves so that actively reproducing cells are
those best able to use the nutrients released by their dying brethren and best
able to tolerate the accumulated toxins. This dynamic process is marked by
successive waves of genetically distinct variants. Thus natural selection can be
observed within a single culture vessel (figure 16).

Figure 16: prolonged

Decline in Growth.

The continuous Culture of microorganisms:

In an open system, it is possible to grow microorganisms, a system with
constant environmental conditions maintained through continual provision of
nutrients and removal of wastes. The conditions are met in the laboratory by a
continuous culture system. A microbial population can be maintained in the
exponential growth phase and at a constant biomass concentration for
extended periods in a continuous culture system. Two major types of
continuous culture systems commonly are used:

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Microbial Physiology 3rd Class

1) chemostats
2) turbidostats
The chemostat: is constructed so that sterile medium is fed into the
culture vessel at the same rate as media containing microorganisms is
removed (figure 17.) The culture medium for a chemostat possesses an
essential nutrient (e.g., amino acid) in limiting quantities. Because one
nutrient is limiting, the growth rate is determined by the rate at which new
medium is fed into the growth chamber, and the final cell density depends on
the concentration of the limiting nutrients.

Figure 17: chemostat continuous culture.

The turbidostats: has a photocell that measures the absorbance or

turbidity of the culture in the growth vessel. The flow rate of media through
the vessel is automatically regulated to maintain a predetermined turbidity or
cell density. The turbidostat differs from the chemostat in several ways. The
dilution rate in a turbidostat varies rather than remaining constant, and its
culture medium contains all nutrients in excess. That is, none of the nutrients
is limiting. The turbidostats operates best at high dilution rated; the chemostat
is most stable and effective at lower dilution rated.
Continuous culture systems are very useful because they provide a
constant supply of cells in exponential phase and growing at a known rate.
They make possible the study of microbial growth at very low nutrient levels,
concentrations close to those present in natural environments. These systems
are essential for research in many areas- for example, in studies on
interactions between microbial species under environmental conditions
resembling those in freshwater lake or pond. Continuous systems also are used
in food and industrial microbiology.

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Microbial Physiology 3rd Class

Environmental Factors Affecting Growth:

A suitable growth medium must contain all the nutrients required by the
organism to be cultivated, and such factors as pH, temperature, and aeration
must be carefully controlled. The microbial growth also is greatly affected by
the chemical and physical nature of their surroundings. An understanding of
environmental effects aids in the control of microbial growth and the study of
the ecological distribution of microorganisms.
1) Nutrients: All microorganisms require the following nutrients to
grow, repair themselves, and to replicate:
(a) Carbon, Nitrogen, Sulfur, Phosphorus, and other Macro mineral nutrients.
(b) Various trace elements
(c) In addition, some microorganisms require various vitamins as well as
additional growth factors (e.g., specific amino acids)
(d) "Although we are concerned with ways microorganisms satisfy their own
nutritional needs, we can note that in satisfying such needs, they also help
recycle elements in the environment."
(e) Fastidious Microorganisms: microorganisms whose nutritional needs are
unusually complex are termed fastidious.
2) Hydrogen Ion Concentration (pH): Most organisms have a fairly
narrow optimal pH range. The optimal pH must be experimentally determined
for each species. Most organisms (Neutrophiles) grow best at a pH of 6.0–8.0,
although some kinds (Acidophiles ) have optima as low as pH 3.0 and others
(Alkaliphiles) have optima as high as pH 10.5.
Microorganisms regulate their internal pH over a wide range of external
pH values by pumping protons in or out of their cells. Acidophiles maintain an
internal pH of about 6.5 over an external range of 1.0–5.0; neutralophiles
maintain an internal pH of about 7.5 over an external range of 5.5–8.5; and
alkaliphiles maintain an internal pH of about 9.5 over an external range of
9.0–11.0. Internal pH is regulated by a set of proton transport systems in the
cytoplasmic membrane, including a primary, ATP-driven proton pump and a
Na+/H+ exchanger. A K+/H+ exchange system has also been proposed to
contribute to internal pH regulation in neutralophiles.
3) Temperature: Different microbial species vary widely in their
optimal temperature ranges for growth: Psychrophilic forms grow best at low
temperatures (15–20 °C); mesophilic forms grow best at 30–37 °C; and most
thermophilic forms grow best at 50–60 °C. Some organisms are
hyperthermophilic and can grow at well above the temperature of boiling
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Microbial Physiology 3rd Class

water, which exists under high pressure in the depths of the ocean. Most
organisms are mesophilic; 30 °C is optimal for many free-living forms, and
the body temperature of the host is optimal for warm-blooded animals (Figure
18).
Microorganisms share
with plants and animals the
heat-shock response, a synthesis
of a set of "heat-shock
proteins," when exposed to a
sudden rise in temperature
above the growth optimum.
These proteins appear to be
unusually heat-resistant and to
stabilize the heat-sensitive
proteins of the cell. Figure 18: Temperature and growth

4) Aeration: Many organisms are obligate aerobes, specifically

requiring oxygen as hydrogen acceptor; some are facultative, able to live
aerobically or anaerobically; and others are obligate anaerobes, requiring a
substance other than oxygen as hydrogen acceptor and being sensitive to
oxygen inhibition.
The supply of air to cultures of aerobes is a major technical problem.
Vessels are usually shaken mechanically to introduce oxygen into the
medium, or air is forced through the medium by pressure. The diffusion of
oxygen often becomes the limiting factor in growing aerobic bacteria; when a
cell concentration of 4–5 x 109/mL is reached, the rate of diffusion of oxygen
to the cells sharply limits the rate of further growth.
Obligate anaerobes, on the other hand, present the problem of oxygen
exclusion. Many methods are available for this: Reducing agents such as
sodium thioglycolate can be added to liquid cultures; the culture vessel can be
placed in a container from which the oxygen is removed by evacuation or by
chemical means; or the organism can be handled within an anaerobic glove-
box.
5) Ionic Strength & Osmotic Pressure: To a lesser extent, such
factors as osmotic pressure and salt concentration may have to be controlled.
For most organisms, the properties of ordinary media are satisfactory;
however, for marine forms and organisms adapted to growth in strong sugar
solutions, for example, these factors must be considered. Organisms requiring
high salt concentrations are called halophilic; those requiring high osmotic
pressures are called osmophilic.

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Microbial Physiology 3rd Class

Most bacteria are able to tolerate a wide range of external osmotic

pressures and ionic strengths because of their ability to regulate internal
osmolality and ion concentration. Osmolality is regulated by the active
transport of K+ ions into the cell; internal ionic strength is kept constant.
6) Light: Phototrophic organisms require light in order to carry out
photosynthesis. In the laboratory, care must be taken that light of the correct
wavelength is used, and that the source used does not also act as a heat source.
Fluorescent light produces little heat, but does not provide the wavelengths in
excess of 750 nm needed by purple and green photosynthetic bacteria.
Microbial Adaptation
Adaptation in biology; any feature in the structure or function of an organism
that allows it to survive and reproduce more effectively in its environment.
Much adaptation is inherited and is the result of many thousands of years of
evolution. It is thought to occur as a result of random variation in the genetic
make-up of organisms coupled with natural selection. Species become extinct
when they are no longer adapted to their environment.
Adaptation is the process whereby a population becomes better suited to
its habitat or better able to live in its habitats. This process takes place over
many generations, and is one of the basic phenomena of biology. Also, the
term adaptation may refer to a feature which is especially important for an
organism's survival. For example, the adaptation of horses' teeth to the
grinding of grass, or their ability to run fast and escape predators. Such
adaptations are produced in a variable population by the better suited forms
reproducing more successfully, that is, by natural selection.
Adaptedness is the state of being adapted: the degree to which an
organism is able to live and reproduce in a given set of habitats. An adaptive
trait is an aspect of the developmental pattern of the organism which enables
or enhances the probability of that organism surviving and reproducing.
Results of adaptation
Adaptation produces individuals whose genetically determined
characteristics allow them to survive and reproduce more effectively. Thus,
the Flavobacterium species that have evolved to eat nylon. Before nylon
existed in their environment there would have been no advantage to the ability
to digest it and turn it into useful chemical energy. Once it appeared in large
amounts a single bacterium with a mutation for nylon metabolism living in a
pool of nylon reproduced like mad, passing the gene on.

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Microbial Physiology 3rd Class

General principles of adaptation

The significance of an adaptation can only be understood in relation to
the total biology of the species.
Adaptation is, first of all, a process, rather than a physical part of a
body. The distinction may be seen in an internal parasite (such as a fluke),
where the bodily structure is greatly simplified, but nevertheless the organism
is highly adapted to its unusual environment. From this we see that adaptation
is not just a matter of visible traits: in such parasites critical adaptations take
place in the life-cycle, which is often quite complex. Many aspects of an
animal or plant can be correctly called adaptations, though there are always
some features whose function is in doubt.
Another great principle is that an organism must be viable at all
stages of its development and at all stages of its evolution. This is
obviously true, and it follows that there are constraints on the evolution of
development, behavior and structure of organisms. The main constraint is the
requirement that changes in the system during evolution should be relatively
small changes, because the body systems are so complex and interlinked.
All adaptations help organisms survive in their ecological. These adaptative
traits may be structural, behavioral or physiological.
Structural adaptations are physical features of an organism (shape, body
covering, defensive or offensive armament; and also the internal
organization).
Behavioral adaptations are composed of inherited behavior chains and/or the
ability to learn: behaviors may be inherited in detail, or a tendency for
learning may be inherited. Examples: searching for food, mating.
Physiological adaptations permit the organism to perform special functions
(making venom, phototropism); but also more general functions such as
growth and development, temperature regulation, ionic balance and other
aspects of homeostasis. Adaptation, then, affects all aspects of the life of an
organism.
Physiological adaption is a metabolic or physiologic adjustment within the
cell, or tissues, of an organism in response to an environmental stimulus
resulting in the improved ability of that organism to cope with its changing
environment. Unlike evolutionary adaptation which involves transgenerational
adjustment, physiological adaptation is generally narrow in scope and
involves response of an individual to a range of stimuli. e.g. the ability of
certain organisms to absorb nutrients under low oxygen tensions.

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Types of adaptation
1) Changes in habitat
Before Darwin, adaptation was seen as a fixed relationship between an
organism and its habitat. It was not appreciated that as the climate changed,
and as the habitat changed, so did the organisms. Also, habitats are subject to
changes in their organisms: for example, invasions of species from other
areas. The relative numbers of species in a given habitat are always changing.
Change is the rule, though much depends on the speed and degree of the
change.
When the habitat changes, three main things may happen to a resident
population: habitat tracking, genetic change or extinction. In fact, all three
things may occur in sequence. Of these three effects, only genetic change
brings about adaptation.
Habitat tracking
When a habitat changes, the most common thing to happen is that the
resident population moves to another locale which suits it; this is the typical
response of flying insects or oceanic organisms, who have wide (though not
unlimited) opportunity for movement. This common response is called habitat
tracking. It is one explanation put forward for the periods of apparent stasis in
the fossil record.
Genetic change
Genetic change is what occurs in a population when natural selection
acts on the genetic variability of the population. By this means, the population
adapts genetically to its circumstances. Genetic changes may result in visible
structures, or may adjust physiological activity in a way that suits the changed
habitat.
It is now clear that habitats and biota do frequently change. Therefore, it
follows that the process of adaptation is never finally complete. Over time, it
may happen that the environment changes little, and the species comes to fit
its surroundings better and better. On the other hand, it may happen that
changes in the environment occur relatively rapidly, and then the species
becomes less and less well adapted. Seen like this, adaptation is a genetic
tracking process, which goes on all the time to some extent, but especially
when the population cannot or does not move to another, less hostile area.
Also this process affects every species in a particular ecosystem.

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Microbial Physiology 3rd Class

2) Intimate relationships: co-adaptations

In co-evolution, where the existence of one species is tightly bound up
with the life of another species, new or 'improved' adaptations which occur in
one species are often followed by the appearance and spread of corresponding
features in the other species. There are many examples of this; the idea
emphasizes that the life and death of living things is intimately connected, not
just with the physical environment, but with the life of other species. These
relationships may continue on this way for millions of years, as has the
relationship between flowering plants and insects (pollination).
3) Internal adaptations
There are some important adaptations to do with the overall
coordination of the systems in the body. Such adaptations may have
significant consequences. Examples, in vertebrates, would be temperature
regulation, or improvements in brain function, or an effective immune system.
An example in plants would be the development of the reproductive system in
flowering plants.
Bacterial adaptation
Bacteria have been designed to be adaptable. Their surrounding layers
and the genetic information for these and other structures associated with a
bacterium are capable of alteration. Some alterations are reversible,
disappearing when the particular pressure is lifted. Other alterations are
maintained and can even be passed on to succeeding generations of bacteria.
The adaptation of bacteria to an antibacterial agent such as an antibiotic
can occur in two ways. The first method is known as inherent (or natural)
resistance. Gram-negative bacteria are often naturally resistant to penicillin,
for example. This is because these bacteria have another outer membrane,
which makes the penetration of penicillin to its target more difficult.
Sometimes when bacteria acquire resistance to an antibacterial agent, the
cause is a membrane alteration that has made the passage of the molecule into
the cell more difficult.
The second category of adaptive resistance is called acquired
resistance. This resistance is almost always due to a change in the genetic
make-up of the bacterial genome. Acquired resistance can occur because of
mutation or as a response by the bacteria to the selective pressure imposed by
the antibacterial agent. Once the genetic alteration that confers resistance is
present, it can be passed on to subsequent generations. Acquired adaptation
and resistance of bacteria to some clinically important antibiotics has become
a great problem in the last decade of the twentieth century.

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*Bacteria adapt to other environmental conditions as well. These

include adaptations to changes in temperature, pH, concentrations of ions such
as sodium, and the nature of the surrounding. An example of the latter is the
response shown by Vibrio parahaemolyticus to growth in a watery
environment versus a more viscous environment. In the more viscous setting,
the bacteria adapt by forming what are called swarmer cells. These cells adopt
a different means of movement, which is more efficient for moving over a
more solid surface. This adaptation is under tight genetic control, involving
the expression of multiple genes.
*Bacteria react to a sudden change in their environment by expressing
or repressing the expression of a whole loss of genes. This response changes
the properties of both the interior of the organism and its surface chemistry. A
well-known example of this adaptation is the so-called heat shock response
of Escherichia coli. The name derives from the fact that the response was first
observed in bacteria suddenly shifted to a higher growth temperature.
*Another adaptation exhibited by Vibrio parahaemolyticus, and a great
many other bacteria as well, is the formation of adherent populations on solid
surfaces. This mode of growth is called a biofilm. Adoption of a biofilm mode
of growth induces a many of changes, many involving the expression of
previously unexpressed genes. In addition, de-activation of actively
expressing genes can occur. Furthermore, the pattern of gene expression may
not be uniform throughout the biofilm. Bacteria within a biofilm and bacteria
found in other places, such as in a wound where oxygen is limited, grow and
divide at a far slower speed than the bacteria found in the test tube in the
laboratory. Such bacteria are able to adapt to the slower growth rate, once
again by changing their chemistry and gene expression pattern.

Control of Microorganisms Growth

• Important Terms:
1. Viability – ability to reproduce
2. Sterilization – absolute elimination of all microbes, any process that
destroys or removes all infectious organisms including endospores and
viruses.

3. Disinfection – destroys most microbes, not spores or some viruses. Any

physical process or application of any chemical that will kill the growing
microbial cells. These processes need not kill or inactivate endospores.

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Microbial Physiology 3rd Class

A disinfectant is a chemical capable of killing microbial cells. It should be

understood that if a chemical is referred to as a disinfectant, it is to be used
on inanimate objects and not to be used on body surfaces.

4. Antisepsis (antiseptic) – disinfection of living tissue. Those practices that

keep microorganism from entering the sterile tissues. The application of
these practices is referred to as aseptic technique. Antiseptics are those
chemicals that can be applied to tissue surfaces to kill or inhibit the growth
of microorganisms.

5. Germicide – Microbicidal agents are chemicals that will kill or destroy

microorganisms. Among the microbicidal agents are those that target specific
microorganisms including:
a. fungicidal agents which are designed to kill fungi.
b. bactericidal agents which are designed to kill bacteria.
c. sporicidal agents which are designed to destroy endospores.
d. viricidal agents which are designed to destroy viruses.

6. Antibiotic – substance that kills or reduces viability of microbes inside or on

the Surface of the body.

7. Microbiostasis refers to the inhibition of growth of microorganisms. This

does not mean that the organisms are killed simply but they are unable to grow.
Refrigeration and many antimicrobial drugs exert a microbistatic effect.
a. Bacteriostatic agents are chemicals that inhibit the growth of bacteria.
b. Fungistatic agents are chemicals that inhibit growth of fungi.

8. Aseptic – exclude entry of microbe.

9. Degerming – removal of transient microbes from an area, mechanical

removal.

10. Sanitization – reduce the number of microbes, not total elimination, any
mechanical process (scrubbing, rinsing, etc.) that reduces the microbial load
on a surface.
Sanitizers are chemical agents that assist in this task. These are usually soaps
or detergents.
12. Chemotherapy- use of chemical agents to kill or inhibit the growth of
microorganisms within the host tissue.

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Microbial Physiology 3rd Class

Control of Microorganisms by physical and chemical agents

Although most microorganisms are beneficial and necessary for human well-
being, microbial activities may have undesirable consequences, such as food
spoilage and disease. Therefore it is essential to be able to kill a wide variety
of microorganisms or inhibit their growth to minimize their destructive effects
(figure 19). The goal is twofold:
1- To destroy pathogens and prevent their transmission.
2- To reduce or eliminate microorganisms responsible for the contamination
of water, food, and other substances.
Microorganisms are not uniformly affected by physical and chemical
decontamination. Susceptibility to the effects of physical and chemical agents
depends upon the type of microorganism and at what stage in the
microorganism’s lifecycle they are exposed to the agent. When choosing
and applying a method of decontaminating materials, it is important that you
understand what type of organism is being targeted and the relative resistance
of that organism.
1. The target with the highest resistance is the bacterial endospores.
Endospores are ubiquitous in the environment. Many bacteria found in the soil
are capable of forming these structures. Introduced into deep wounds or
during surgical procedures, these spores can cause severe problems. Thus
surgical equipment and other materials used in invasive procedures need to be
decontaminated in such a way as to destroy these agents.
2. Targets with the moderate resistance include protist cysts, sexual fungal
spores, non-enveloped viruses (many enteric viruses including those
responsible for polio, Hepatitis A and Hepatitis E), Mycobacterium
tuberculosis, Staphylococcus aureus and members of the genus Pseudomonas.
3. Targets with the least resistance include vegetative cells of most microbes,
enveloped viruses (including those viruses responsible for AIDS and Hepatitis
B), and asexual fungal spores.

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Microbial Physiology 3rd Class

• The pattern of microbial death

A microbial population is not killed
instantly when exposed to a lethal agent.
Population death, like population growth,
is generally exponential or logarithmic that
is, the population will be reduced by the
same fraction at constant intervals (figure
20). When the population has been greatly
reduced, the rate of killing may slow due
to the survival of a more resistant strain of
the microorganism.
Figure 20: The Pattern of Microbial Death. An
exponential plot of the survivors versus the
minutes of exposure to heating at 121ͦ C. In this example the D121 value is 1 minute.

• Conditions influencing the effectiveness of antimicrobial agents

Distraction of microorganisms and inhibition of microbial growth are not
simple matters because the efficiency of an antimicrobial agent (an agent that
kills microbes or inhibits their growth) is affected by at least six factors.
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Microbial Physiology 3rd Class

A. Population size:
Because an equal fraction of microbial population is killed during each
interval, a larger population required a longer time to die than a smaller one.
This can be seen in the theoretical heat-killing experiment. Death is
logarithmic (Fig. 20)
B. Population composition:
The effectiveness of an agent varies greatly with the nature of the organisms
being treated because microorganisms differ markedly in susceptibility.
Bacterial endospores are much more resistant to most antimicrobial agents
than are vegetative forms, and younger cells are usually more readily
destroyed than mature organisms. Some species are able to withstand adverse
condition better than others. For instance, Mycobacterium tuberculosis, which
causes tuberculosis, is much more resistant to antimicrobial agents than most
other bacteria.
C. Concentration or intensity of an antimicrobial agent
Generally the more concentrated chemical agent or intense physical agent, the
more rapidly microorganisms are destroyed. However, agent effectiveness
usually is not directly related to concentration or intensity. Over a short range
a small increase in concentration leads to an exponential rise in effectiveness;
beyond a certain point, increase may not raise the killing rate much at all.
Sometimes an agent is more effective at lower concentrations. For example,
70% ethanol is more effective than 95% ethanol because its activity is
enhanced by the presence of water.
D. Duration of exposure (contact time):
The longer a population is exposed to a microbial agent, the more organisms
are killed (fig. 20). To achieve sterilization, exposure duration sufficient to
-6
reduce the probability of survival to 10 or less should be used.
E. Temperature:
An increase in the temperature at which a chemical acts often enhances its
activity. Frequently a lower concentration of disinfectant or sterilization agent
can be used at higher temperature.
F. Local environment:
The population to be controlled is not isolated but surrounded by
environmental factors that may either offer protections or aid in its
destruction. e.g., because heat kills more readily at an acidic PH, acidic foods
and beverages such as fruits and tomatoes are easier to pasteurize than foods
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Microbial Physiology 3rd Class

with higher PHs like milk. A second important environmental factor is organic
matter, which can protect microorganisms against heating and chemical
disinfectants.
• Use of Physical method in control
Heat and other physical agents are normally used to control microbial growth
and sterilize objects. The most frequently employed physical agents are Heat,
low temperature and radiation.
1-Heat
Fire and boiling water have been used for sterilization and disinfection. Either
moist or dry heat may be applied.
a. Moist heat readily kills viruses, bacteria, and fungi (table 7). Moist heat is
thought to kill by degrading nucleic acids and by denaturing enzymes and
other essential proteins. It may also disrupt cell membranes.
a1- Boiling water: Exposure to boiling water for 10 minutes is sufficient to
destroy vegetative cells and eukaryotic spores. Unfortunately the temperature
of boiling water (100 ͦ C or 212 ͦ F at sea level) is not high enough to destroy
bacteria endospores, which may survive hours of boiling. Therefore boiling
can be used for disinfection of drinking water and objects not harmed by
water, but boiling does not sterilize.
Table 7: Approximate Conditions for Moist Heat killing.

Organism Vegetative Cells Spores

Yeasts 5 minutes at 50-60°C 5 minutes at 70 -80 °C
Molds 30 minutes at 62°C 30 minutes at 80 °C
Bacteria* 10 minutes at 60 -70 2 to over 800 minutes at
°C 100°C
Viruses 30 minutes at 60°C
Condition for mesophilic bacteria

a2- Steam sterilization: In order to destroy bacteria endospores, moist heat

sterilization must be carried out at temperatures above 100 ͦ C, and this
requires the use of saturated steam under pressure is carried out with an
autoclave. Water is boiled to produce steam, which is released through the
jacket and into the autoclaves chamber. The air initially present in the
chamber is forced out until the chamber is filled with saturated steam and the
outlets are closed. Hot, saturated steam continues to enter until the chamber
reaches the desired temperature and pressure, usually 121 ͦ C and 15 pounds of
pressure. At this temperature saturated steam destroys all vegetative cells and
endospores in a small volume of liquid within 10 to 12 minute. Treatment is

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Microbial Physiology 3rd Class

continued for at least 15 minute to provide a margin of safety. Of course,

larger containers of liquid such as flasks require much longer treatment times.
Autoclave must be carried out properly or the processed material will not be
sterile. If all air has not been flushed out of the chamber, it will not reach 121 ͦ
C even though it may reach a pressure of 15 pounds. The chamber should not
be packed too lightly because the steam needs to circulate freely and contact
everything in the autoclave.
b. Pasteurization: Many substances, such as milk, are treated with controlled
heating at temperature well below boiling, a process known as pasteurization
in honor of its developer Louis Pasteur. In the 1860s the French wine
industry was plagues by the problem of wine spoilage, which made wine
storage and shipping difficult. Pasteur examined spoiled wine under the
microscope and detected microorganisms that looked like the bacteria
responsible for lactic acid and acetic acid fermentations. He then discovered
that a brief heating at 55 to 60 ͦ C would destroy these microorganisms and
preserve wine for long periods. In 1886 the German chemists adapted the
technique for preserving milk and reducing milk transmissible diseases. Milk
pasteurization was introduced into the United States in 1889. Milk, beer, and
many other beverages are now pasteurized. Pasteurization does not sterilize a
beverage, but it does kill any pathogens present and slows spoilage by
reducing the level of nonpathogenic spoilage microorganisms.

c. Dry heat sterilization: Many objects are best sterilized in the absence of
water by dry heat sterilization. Some items are sterilized by incineration. For
instance, inoculating loops, which are used routinely in the laboratory, can be
sterilized in a small, bench-top incinerator. Other items are sterilized in an
oven at 160 to 170 ͦ C for 2 to 3 hours. Microbial death apparently results from
the oxidation of cell constituents and denaturation of portions. Dry air heat is
less effective than moist heat. The spores of Clostridium botulinum, the cause
of botulism, are killed in 5 minutes at 121 ͦ C by moist heat but only after 2
hours at 160 ͦ C with dry heat. However, dry heat has some definite
advantages. It does not corrode glassware and metal instruments as moist heat
does, and it can be used to sterilize powders, oils, and similar items. Most
laboratories sterilize glassware and pipettes with dry heat. Despite these
advantages, dry heat sterilization is slow and not suitable for heat sensitive
materials like many plastic and under rubber items.

2- Low Temperature
Although our emphasis is on the destruction of microorganisms, often the
most convenient control technique is to inhibit their growth and reproduction
by the use of either freezing or refrigeration. This approach is particularly
important in food microbiology.
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 Microbial Physiology 3rd Class

a. Freezing items at -20 ͦ C or lower stops microbial growth because of the

low temperature and the absence of liquid water. Some microorganisms will
be killed by ice crystal disruption of cell membranes, but freezing does not
destroy all contaminating microbes. In fact, freezing is a very good method for
long –term storage of microbial samples when carried out properly, and many
laboratories have a low –temperature freezer for culture storage at -30 or – 70 ͦ
C. Because frozen food can contain many microorganisms, it should be
thawed in a refrigerator and consumed promptly in order to avoid spoilage and
pathogen growth.

b. Refrigeration greatly slows microbial growth and reproduction, but does

not stop it completely, fortunately most pathogens are mesophilic and do not
grow well at temperatures around 4 °C. Thus refrigeration is a good technique
only for shorter term storage age of food and other items.

3- Radiation

Microbiologists take advantage of the effects of ultraviolet and ionizing

radiation to sterilize or disinfect.
a. Ultraviolet (UV) radiation around 260 nm is quite lethal but does not
penetrate glass, dirt films, water, and other substances very effectively.
Because of this disadvantage, UV radiation is used as a sterilizing agent only
in a few specific situations. UV lamps are sometimes placed on the ceilings of
rooms or in biological safety cabinets to sterilize the air and any exposed
surfaces. Because UV radiation burns the skin and damages eyes, people
working in such areas must be certain the UV lamps are off when the areas are
in use.
b. Ionizing radiation is an excellent sterilizing agent and penetrates deep into
objects. It will destroy bacterial endospores and vegetative cells, both
prokaryotic and eukaryotic; however, ionizing radiation is not always
effective against viruses. Gamma radiation from a cobalt 60 source is used in
the cold sterilization of antibiotics, hormones, sutures, and plastic disposable
supplies such as syringes. Gamma radiation has also been used to sterilize and
pasteurize meat other food. Irradiation can eliminate the threat of such
pathogens as E.coli O157:h7, Staphylococcus aureus, and Campylobacter
jejuni. Based on the results of numerous studies, both the food and drug
administration and the WHO have approved food irradiation and declared it
safe. Currently irradiation is being used to treat poultry, beef, pork, veal, lamb,
fruits, vegetables, and spices.

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Microbial Physiology 3rd Class

• The use of mechanical methods:

1) Filtration:
Filtration is an excellent way to reduce the microbial population in solutions
of heat – sensitive material, and sometimes it can be used to sterilize solutions.
Rather than directly destroying contaminating microorganisms, the filter
simply removes them.

There are two types of filters:

a. Depth filters consist of fibrous or granular materials that have been bonded
into a thick layer filled with twisting channels of small diameter. The solution
containing microorganisms is sucked through this layer under vacuum, and
microbial cells are removed by physical screening or entrapment and also by
adsorption to the surface of the filter material.

b. Membrane filters have replaced depth filters for many purposes. These
circular filters are porous membranes, a little over 0.1 mm thick, made of
cellulose acetate, cellulose nitrate, polycarbonate, polyvinylidene fluoride, or
other synthetic materials. Although a wide variety of pore sizes are available,
membranes with pores about 0.2 μm in diameter are used to remove most
vegetative cells, but not viruses, from solutions ranging in volume from 1 ml
to many liters. The membranes are held in special holders (figure 21) and are
often preceded by depth filters made of glass fibers to remove larger particles
that might clog the membrane filter. The solution is pulled or forced through
the filter with a vacuum or with pressure from a syringe, collected in
previously sterilized containers. Membrane filters remove microorganisms by
screening them out much as a sieve separates large sand particles from small
ones. These filters are used to sterilize pharmaceuticals, ophthalmic solutions,
culture media, oils, antibiotics, and other heat – sensitive solutions.

Air also can be sterilized by filtration. Two common examples are surgical
masks and cotton plugs on culture vessels that let air in but keep
microorganisms out. Other important examples are laminar flow biological
safety cabinets, which employ high – efficiency particulate air (HEPA) filters
(a type of depth filter) to remove 99.97% of 0.3 μm particles. Laminar flow
biological safety cabinets or hoods force air through HEPA filters, and then
project a vertical curtain of sterile air across the cabinet opening. This protects
a worker from microorganisms being handled within the cabinet and prevents
contamination of the room (figure 22). A person uses these cabinets when
working with dangerous agents such as Mycobacterium tuberculosis and
tumor viruses. They are also employed in research labs and industries, such as
the pharmaceutical industry. When a sterile working surface is needed for
conducting assays, preparing media, examining tissue cultures, and the like.

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Microbial Physiology 3rd Class

Figure 21: Membrane filter Sterilization. The liquid to be sterilized in pumped through a
membrane filter and into sterile container. The inset shows a cross section of the filter and
its pores, which are too small for microbes to pass through.

Figure 22: A laminar Flow Biological Safety Cabinet. a) a Technician using potentially
hazardous material in a safety cabinet. b) A schematic diagram showing the airflow pattern.

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Microbial Physiology 3rd Class

• The Use of Chemical Agents in Control

Physical agents are generally used to sterilize objects. Chemicals, on the other
hand, are more often employed in disinfection and antisepsis. The proper use
of chemical agents is essential to laboratory and hospital safety. Chemicals
also are employed to prevent microbial growth in food, and certain chemicals
are used to treat infectious disease.
Many different chemicals are available for use as disinfectants, and each has
its own advantages and disadvantages. In selecting an agent, it is important to
keep in mind the characteristics of a desirable disinfectant. a) Ideally the
disinfectant must be effective against a wide variety of infectious agents
(gram-positive and gram – negative bacteria, acid –fast bacteria, bacterial
endospores, fungi, and viruses) at low concentrations and in the presence of
organic matter. b) Although the chemical must be toxic for infectious agents, it
should not be toxic to people or corrosive for common materials, in practice,
this balance between effectiveness and low toxicity for animals is hard to
achieve. Some chemicals are used despite their low effectiveness because they
are relatively nontoxic. The ideal c) disinfectant should be stable upon storage,
d) odorless or with a pleasant odor, e) soluble in water and lipids for
penetration into microorganisms, f) have a low surface tension so that it can
enter cracks in surfaces, and g) be relatively inexpensive.
One potentially serious problem is the overuse of antiseptics. For instance, the
antibacterial agent triclosan is found in products such as deodorants,
mouthwashes, soaps, cutting boards, and baby toys. Unfortunately, the
emergence of triclosan bacteria has become a problem. For example,
Pseudomonas actively pumps the antiseptic out of the cell. There is now
evidence that extensive use of triclosan also increases the frequency of
bacterial resistance to antibiotics. Thus overuse of antiseptics can have
unintended harmful consequences.

Some chemicals used as disinfectants and antiseptics;

a. Phenolics

Phenol was the first widely used antiseptic and disinfectant. In 1867
Joseph Lister employed it to reduce the risk of infection during surgery. Today
phenol and phenolics (phenol derivatives) such as cresols, xylenols, and
orthophenylphenol are used as disinfectants in laboratories and hospitals. The
commercial disinfectant Lysol is made of a mxture of phenolics. Phenolics act
by denaturing proteins and disrupting cell membranes. They have some
real advantages as disinfectants: phenolics are effective in the presence of
organic material, and remain active on surfaces long after application.
However, they have a disagreeable odor and can cause skin irritation.

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Microbial Physiology 3rd Class

b. Alcohols

Alcohols are among the most widely used disinfectants and antiseptics.
They are bacterial and fungicidal but not sporicidal; some liquid- containing
viruses are also destroyed. The two most popular alcohol germicides are
ethanol and isopropanol, usually used in about 70 to 80 % concentration. They
act by denaturing proteins and possibly by dissolving membrane lipids. A
10 to 15 minute soaking is sufficient to disinfect thermometers and small
instruments.

c. Halogens

A halogen is any of the five elements (fluorine, chlorine, bromine,

iodine, and astatine) in group VIIA (Group 17) of the periodic table. They
exist as diatomic molecules in the Free State and form salt like compounds
with sodium and most other metals. The halogens iodine and chlorine are
important antimicrobial agents. Iodine is used as a skin antiseptic and kills by
oxidizing cell constituents and iodinating cell proteins. At higher
concentrations, it may even kill some spores. Although it is an effective
antiseptic, the skin may be damaged, a stain is left, and iodine allergies can
result. More recently iodine has been complexed with an organic carrier to
form an iodophor. Iodophors are water soluble, stable, and nonstaining, and
release iodine slowly to minimize skin burns and irritation.
Chlorine is the usual disinfectant for municipal water supplies and swimming
pools and is also employed in the dairy and food industries. It may be applied
as chlorine gas, sodium hypochlorite, or calcium hypochlorite, all of which
yield hypochlorous acid (HCIO) and then atomic oxygen. The result is
oxidation of cellular materials and destruction of vegetative bacteria and
fungi, although not spores.
Cl2 + H2O HCl + HClO
Ca(OCl)2 + 2H2O Ca(OH)2 + 2HClO
HClO HCl + O

Death of almost all microorganisms usually occurs within 30 minute.

Since organic material interferes with chlorine action by reacting with
chlorine and its products, an excess of chlorine is added to ensure microbial
destruction. Chlorine is also an excellent disinfectant for individual use
because it is effective, inexpensive, and easy to employ. Small quantities of
drinking water can be disinfected with halazone tablets. Halazone slowly
releases chloride when added to water and disinfects it in about a half hour. It
is frequently used by campers lacking access to uncontaminated drinking
water.

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Chlorine solutions make very effective laboratory and household

disinfectants. An excellent disinfectant –detergent combination can be
prepared if a 1/40 dilution of household bleach is combined with a nonionic
detergent, such as a dishwashing detergent, to give a 0.8% detergent
concentration. This mixture will remove both dirt and bacteria.

d. Heavy Metals

For many years the ions of heavy metals such as mercury, silver, arsenic, zinc,
and copper were used as germicides. These have now been superseded by
other less toxic and more effective germicides (many heavy metals are more
bacteriostatic than bactericidal). There is little exception. In some hospitals, a
1%solution of silver nitrate is added to the eyes of infants to prevent
ophthalmic gonorrhea. Sliver sulfadiazine is used on burns. Copper sulfate is
an effective algicide in lakes and swimming pools.
Heavy metals combine with proteins, often with their sulfhydryl groups, and
inactivate them. They may also precipitate cell proteins.

e. Quaternary Ammonium compounds

They are detergents that have antimicrobial activity and are effective
disinfectants. Detergents are organic cleansing agents that are amphipathic,
having both polar hydrophilic and nonpolar hydrophobic components. The
hydrophilic portion of a quaternary ammonium compound is positively
charged quaternary nitrogen; thus quaternary ammonium compounds are
cationic detergents. Their antimicrobial activity is the result of their ability to
disrupt microbial membranes; they may also denature proteins.
Cationic detergents like benzalkonium chloride and cetypyridinium chloride
kill most bacteria but not M. tuberculosis or endospores. They have the
advantage of being stable and nontoxic but they are inactivated by hard water
and soap. Cationic detergents are often used disinfectants for food utensils and
small instruments and as skin antiseptics.

f. Aldehydes

Both of the commonly used aldehydes, formaldehyde and glutaraldehyde are

highly reactive molecules that combine with nucleic acid and proteins and
inactivate them, probably by cross- linking and alkylating molecules. They are
sporicidal and can be used as chemical sterilants. Formaldehyde is usually
dissolved in water or alcohol before use. A 2 % buffered solution of
glutaraldehyde is an effective disinfectant. It is less irritating than
formaldehyde and is used to disinfectant hospital and laboratory equipment.

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Microbial Physiology 3rd Class

Glutaraldehyde usually disinfects objects within about 10 minute but may

require as long as 12 hours to destroy all spores.

g. Sterilizing (by gases)

Many heat – sensitive items such as disposable plastic petri dishes and
syringes, heart – lung machine components, sutures, and catheters are
sterilized with ethylene oxide gas. Ethylene oxide (EtO) is both microbicidal
and sporicidal and kills by combining with cell proteins. It is a particularly
effective sterilizing agent because it rapidly penetrates packing materials, even
plastic warps.
Sterilization is carried out in a special ethylene oxide sterilizer, very much
resembling an autoclave in appearance, that controls the EtO concentration,
temperature, and humidity. Because pure EtO is explosive, it is usually
supplied in a 10 to 20 % concentration mixed with either CO 2 or
dichlorodifluoromethane. The ethylene oxide concentration, humidity, and
temperature influence the rate of sterilization. A clean object can be sterilized
if treated for 5 to 8 hours at 38 ° C or 3 to 4 hours at 54 ° C when the relative
humidity is maintained at 40 to 50 % and the EtO concentration at 700
mg/liter. Extensive aeration of the sterilized materials is necessary to remove
residual EtO because it is so toxic.
Betapropiolactone (BPL) is occasionally employed as a sterilizing gas. In the
liquid form it has been used to sterilize vaccines and sera. BPL decomposes to
an inactive form after several hours. It also destroys microorganisms more
readily than ethylene oxide but does not penetrate materials well and may be
carcinogenic. For these reasons, BPL has not been used as extensively as EtO.
Vaporized hydrogen peroxide can be used to decontaminate biological safety
cabinets, operating rooms, and other large places. These systems introduce
vaporized hydrogen peroxide into the enclosure for some time, depending on
the size of the enclosure and the materials within. Hydrogen peroxide is toxic
and kills a wide variety of microorganisms. However, during the course of
decontamination process, it breaks down to water and oxygen, both of which
are harmless. Other advantages of these systems are that they can be used at a
wide range of temperatures (4 to 80 ° C) and they do not damage most
materials.

• Chemotherapeutic Agents

The chemical discussed thus far are appropriate for use either on inanimate
objects or external host tissue. Chemotherapeutic agents are chemicals that
can be used internally to kill or inhibit the growth of microbes within host
tissues. They can be used internally because they have selective toxicity; that

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is, they target the microbe and do relatively little if any harm to host. Most
chemotherapeutic agents are antibiotic – chemicals synthesized by microbes
that are effective in controlling the growth of bacteria. Since the discovery of
the first antibiotics, pharmaceutical companies have developed numerous
derivatives and many synthetic antibiotics. Chemotherapeutic agents for
treating diseases caused by fungi, protists, and viruses have also been
developed.

Microbial Bioenergetics
Metabolism is the total of all chemical reaction that occur in cell. Metabolisms
are thousands of different reactions; most of them fall into of two general
categories:
Anabolism, sometimes also termed as biosynthesis, the reactions that
consume energy in order to build large molecules and cellular structures from
smaller and simpler one, they are endergonic reactions. It involve a series of
stapes (1) conversion of the organism’s carbon source into a set of small
molecules called precursor metabolites; (2) synthesis of monomers and other
building blocks (i.e., amino acids, nucleotides, simple carbohydrates, and
simple lipids) from precursor metabolites; (3) synthesis of macromolecules
(i.e., proteins, nucleic acids, complex carbohydrates, and complex lipids); and
(4) assembly of macromolecules into cellular structures.
Catabolism, is the opposite or complement of anabolism that involve the
breakdown of relatively large complex organic molecules into smaller and
simpler molecules and often release energy, they are exergonic reactions
Considerable metabolic diversity exists in the microbial world. However,
there are several biochemical principles common to all types of metabolism.
These are;(1) the use of ATP to store energy captured during exergonic
reactions so it is can be used to derive endergonic reaction; (2) the
organization of metabolic reactions into pathways and cycles;(3) the catalysis
of metabolic reactions by enzymes; and (4) the importance of oxidation –
reduction reactions in energy conservation.
Adenosine Triphosphate (Metabolic money)
In what way do cells extract energy from electrons of fuel compounds? To
answer this question, we must look more closely to the chief energy carrier
and powerhouse molecule Adenosine triphosphate(ATP), which also been
described as metabolic money because it can be earned, saved, spend, and
exchanged. This molecule provides connection between energy yielding
reactions (catabolism) and other cellular activities that require energy. Some

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clues to its energy storage behavior lie in its unique molecular structure. The
molecular structure of ATP first deduced by Lohman in 1930 and confirmed
by Alexander Todd et, al., in 1948, it is three - part molecule, consist of;
nitrogen base (adenine) linked to a 5 carbon sugar (ribose), with a chain of
three phosphate groups (figure 23). The two terminal phosphoryl groups are
highly energized, when ATP was utilize in anabolic processes the
phosphoanhydride bonds that link these groups together are break down or
hydrolyzes almost completely to produce adenosine diphosphate (ADP),
orthophosphate (Pi), and large amount of energy is released.
Adenosine PPP + H2O Adenosine PP (ADP)+ Pi + energy (- 7.3
Kcal)
Adenosine PP+ H2O Adenosine P (AMP) + Pi + energy (-
7.3Kcal)
Adenosine P + H2O Adenosine+ P + energy (-7.3 Kcal)

Figure 23: Structure of ATP, ADP, and AMP

The trapping of energy in form of ATP is called Phosphorylation; there are

three types of phosphorylation processes followed by living cells:
Photophosphorylation: It occurs in the presence of light in photosynthetic cells
with assistant of photo pigments (chlorophylls and carotenoids),which trap
photo energy from solar radiation that exited and release electrons from photo
pigments, these electrons pass through a series of electron carriers and
generates phosphate bonds in form of ATP.

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Microbial Physiology 3rd Class

Oxidative phosphorylation: Is the processes in which ATP is formed as a

-
result of the transfer of electrons (e ) that collected by certain electron carriers
like NAD, NADP, and FAD, and passed into electron transport chain (ETC),
located in the inner membrane of mitochondria in eukaryotic cells and in
-
plasma membrane in prokaryotic cells, finally the e combined with oxygen,
which act as final electron acceptor, the subsequent passage of electrons
though electron carriers release energy used to generate ATP from ADP. One
molecule of NAD generates three molecules of ATP when it enters the ETC,
however one molecule of FAD generates only two molecules of ATP, this is
due to the fact that FAD enters ETC later than NAD.
Substrate level phosphorylation: Is a type of metabolic reaction that results in
generation of ATP or guanosine triphosphate (GTP) by direct transfer and
donation of a phosphoryl group to ADP or GDP from phosphorylated reactive
intermediate, for example:
GTP + ADT ATP + GDP
Oxidation – Reduction Reactions
The release of energy from an energy source in bio-system normally involves
biological oxidation, fundamentally is the removal of electrons from various
substrates (electron donor), which thereby oxidized, and does not necessarily
-
involves oxygen. In living cells the removed e cannot be remain in a free state
there must be immediately transferred to other compounds or molecules
-
(electron acceptor), which thereby reduced. So oxidation is the loss of e , and
-
reduction is gain of e , an acceptor is oxidizing agent and the donor is
reducing agent.
Oxidation – reduction are always coupled so termed redox reaction. The
equilibrium constant for such reaction. In most cells oxidation of organic
substrates is accomplished by removal of hydrogen (dehydrogenation),
+ -
hydrogen atom provides one proton (H ) and one electron (e ). In living cells
enzymes involved in dehydrogenation processes are dehydrogenase enzymes,
these enzymes like other enzymes are highly specific for their respective
substrates, and all of these include coenzymes, which are less restricted; one
coenzyme may act in several different other Apoenzymes and reactions.
Dehydrogenises coenzymes (electron carriers), resemble shutter that are
alternately loaded and unloaded, repeatedly accepting and releasing e- and H
to facilitate the transfer of redox energy. Most of coenzymes transfer both e-
and H. The most common electron carriers are:
NAD; nicotinamide adenine dinucleotide

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Microbial Physiology 3rd Class

NADP; nicotinamide adenine dinucleotide phosphate

FAD; Flavin adenine dinucleotide
The essential portion of NAD and NADP is nicotinamide (Niacin, Vitamin
-
B3), the pyridine ring of this group accepts substrates H or e , and being
reduced to NADH and NADPH, the reduced form in turn transfers the
accepted hydrogen to second acceptor that is at low energy level and being re-
oxidized to NAD and NADP.
FAD, contain riboflavin (Vitamin B2), so far all vitamins are analogous part
of coenzymes, thus is common to several dehydrogenases, when reduced by
substrates hydrogen represented as FADH, the coenzyme very commonly re-
oxidized to FAD by transfer of hydrogen to an iron – bearing respiratory
pigments of cytochrome system.

The Thermodynamics and Bioenergetics

Energy may be most simply defined as the capacity to do work, the energy in
living cells which is termed as bioenergy, mostly trapped as ATP, and is used
to do cellular works like biosynthesis, transport, growth, and motility. The
flow of energy through organisms at cellular and molecular level termed
Bioenergetics; that concern with how organism extract energy from
surrounding environment and how this energy used to fuel the myriad of life.
To understand the basic concepts of bioenergetics some principles of
thermodynamics lows (is the study of energy transformation that describe the
relationships between thermal energy, or heat and other forms of energy, and
how energy affects matter). These principles facilitate a perception of how an
energy – producing and energy – utilizing reaction occurs within the same cell
and how the organism is able to accomplish various work functions.
The first law of thermodynamics: state the energy neither created nor
destroyed, but converted from one form to another, that the total amount of
energy in system remains constant, which confirm the principle of energy
conservation, such as, the plants do not produce energy but transform light
energy to chemical energy. The first low alone cannot explain why energy
released by a reaction and absorbed by other. Scientific explanation for this
phenomenon requires some knowledge of the second thermodynamics low,
which is about the quality of energy, it state that as energy is transferred or
transformed. In fact any discussion of energy must begin with definition of
Entropy (S); simply is the measure of disorder combined to system thermal
change, may be also considered as a measure of a system thermal energy that
is available.

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Chemical reactions classified as exergonic and endergonic based on free

energy, an exergonic reaction proceeds with a net release of energy, for the
overall reaction of cellular respiration,
C6H12O6 + 6O2 6CO2 + 6H2O

An endergonic reaction is one that absorbs free energy from its surroundings
and never proceeds spontaneously that requires input of energy for conversion
of CO2 and water to sugar.

6 CO2 + 6H2O C6H12O6

Photosynthesis
Microorganisms derive energy not only from the oxidation of inorganic and
organic compounds, but also from light energy, which they capture and use to
synthesize ATP and reducing power (e.g., NADPH). They harvest the energy
of sunlight and use it to power the synthesis of ATP. The conversion of solar
energy to chemical energy is called Photosynthesis. The general reaction of
photosynthesis can be summarized as follow:
6 CO2 + 12 H2X C6H12O6 + 12 X+ H2O
(X depends on the source of electron for reducing power and can be a number
of different compounds).
Usually a phototrophic organism reduces and incorporates CO 2.
Photosynthesis is one of the most significant metabolic processes on Earth
because almost all our energy is ultimately derived from solar energy. It
provides photosynthetic organisms with the ATP and reducing power
necessary to synthesize the organic material required for growth. In turn these
organisms serve as the base of most food chains in the biosphere. One type of
photosynthesis is also responsible for replenishing our supply of O 2, a
remarkable process carried out by a variety of organisms, both eukaryotic and
prokaryotic. Although photosynthesis is performed differently by different
organisms, the process always involves two reactions:
•Light - dependent reactions; are those reactions used to derive energy from
sunlight.
• Dark - dependent reactions; the reactions which use that energy to fix CO2.

The Role of Photosynthetic Pigments

Photosynthetic organisms are highly visible in their natural habitat because
they possess photo pigments, Chlorophylls and Carotenoids. Colored
pigments, used to capture light energy, these pigments vary in color because
they absorb different wavelengths of light.
The primary light – absorbing pigments are chlorophylls. Most photosynthetic
organisms, including an important group of bacteria called cyanobacteria, use

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Microbial Physiology 3rd Class

chlorophyll a. A different group of photosynthetic bacteria, the purple and

green bacteria, use bacteriochlorophyll. This absorbs wavelengths not
absorbed by chlorophyll a, enabling the green and purple bacteria to grow in
habitat where other photosynthetic organisms cannot.
The carotenoids are accessory pigments that increase the efficiency of light
utilization; they do this by absorbing wavelengths of lights not absorbed by
chlorophylls and transferring that energy to chlorophyll.
Chlorophyll and other light absorbing pigments are organized in protein
complex called Photosystem located in special photosynthetic membrane. In
cyanobacteria, these are found in stacked membrane called Thylakoids. Plants
and algae also have thylakoids, in the stroma of their chloroplasts; the
photosynthetic pigments in purple and green bacteria are either contained
within cytoplasmic membrane or within structure called Chlorosome attached
to the membrane.

Photophosphorylation
Within the photosystem there are two components that work together to
harvest energy, the antenna complex, is composed of hundreds of light –
gathering pigments (chlorophyll and accessory pigments), this complex act as
a funnel, capturing the energy of light and then transferring it to reaction-
center chlorophyll. When this chlorophyll absorbs that energy, one of its
electrons become excited, or raised to higher energy level, in a manner similar
to oxidative phosphorylation. The high energy electron is sequentially pass
along series of electron carriers in membrane embedded electron transport
chain, the flow of e- dawn an ETC that leads to the ultimate reduction of
NADH to NADPH. In addition this results in translocation of protons (H+)
across membrane, generating Proton motive force (PMF). ATP synthase
permits the flow of protons back across the membrane and uses the energy to
generate ATP. The high energy electron from reaction – center chlorophyll
that passes along the ETC may or may not be returned to their original source.
In cyclic photophosphorylation (a cyclical pathway), the chlorophyll molecule
regains the lost e- from water , In non – cyclical photophosphorylation, PMF is
produced, but in addition, high energy electrons are drawn off to generate
reducing power, electrons must still be returned to chlorophyll, but they must
come from a different source, such as hydrogen sulfide. (Figure 24).

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Microbial Physiology 3rd Class

Figure 24: Cyclical and non - cyclical Photosynthesis in Bacteria

Electron Source
Photosynthetic organisms require electron source to generate reducing power
in form of NADPH, the compound used to obtain electrons dictates whether or
not oxygen (O2) is evolved during photosynthesis.

Oxygenic Photosynthesis
When plants, algae, and cyanobacteria use non – cyclical
photophosphorylation to make reducing power, they use water as electrons
source that are returned to the chlorophyll. When electron extracted from
water proton and (O2) are released. It is because of oxygenic
photophosphorylation that obligate aerobes, including humans and other
animals are able to inhabit earth.

Un-oxygenic Photosynthesis
Un-oxygenic photosynthesis such as green and purple bacteria, lack the
sophisticated photosystem that the oxygenic photosynthetic organisms us to
generate NADPH. Instead they must use alternative mechanism such as
hydrogen sulfide, hydrogen gas, and reducing organic molecules. Because
water not used as electron source, un-oxygenic phototrophs do not evolve
(O2).
ATP and NADPH which produced from photophosphorylation processes have
short life spam so they must recycled by producer cells quickly because they
cannot store in cells as storage compounds, the cells overcome this situation
by auto fix of CO2 to high energy storage compounds.

Fixation of CO2 by Autotrophs

Autotrophs use CO2 as their only or principle carbon source and the reduction
and incorporation of CO2 Requires much energy. Many autotrophs obtain
energy by trapping light during photosynthesis, but some derive energy from
the oxidation of reduced electrons donors. Autotrophic CO2 fixation is crucial
to life on Earth because it provides the organic matter on which heterotrophs
depend.

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Microbial Physiology 3rd Class

Four different CO2 – fixation pathways have been identified in

microorganisms. Most autotrophs use the Calvin cycle, which is also called
the Calvin – Benson cycle or the Reductive Pentose Phosphate Cycle. The
Calvin cycle is found in photosynthetic eukaryotes and most photosynthetic
bacteria. It is absent in some obligatory anaerobes and microaerophilic
bacteria.

Anabolic Pathways – Synthesizing Subunit from Precursor Molecules

While prokaryotes as a group are highly diverse with respect to the
compounds they use for energy, they are remarkably similar when comparing
their biosynthetic processes. Using precursor metabolites, reducing power in
form of NADPH, and ATP, cells synthesize the necessary subunits using
specific anabolic pathways. Organisms that lack one or more enzymes in a
given pathway must have the end product of that pathway provided from an
external source. This is why fastidious bacteria such as the lactic acid bacteria
require many different growth factors. Once the subunits are either
synthesized or supplied, they can be assembled to make macromolecules.
Various different macromolecules can then be joined to form the structures
that make up the cell.

• Lipid Synthesis

Synthesis of lipids in microorganisms can be viewed as having two

essential components – Fatty acid synthesis and Glycerol synthesis.
Synthesis starts with the transfer of the acetyl group of acetyl-CoA to a
carrier protein called acyl carrier protein (ACP). This carrier serves to hold
the fatty acid chain as it elongated by progressively adding 2- carbon units.
When the newly synthesized fatty acid reaches its required length, usually
14, 16, or 18 carbons long, it is released from ACP. The glycerol
components are synthesized from glyceraldehyde 3 – phosphate.

• Amino Acids Synthesis

Proteins are composed of various combinations of 20 different amino

acids. Amino acids can be grouped into structurally related families that
share common pathway of biosynthesis. Some are synthesized from
precursor metabolites formed during glycolysis, while other are derived
from compounds of the TCA cycle.

⃰Glutamate
Although all amino acids are necessary for protein synthesis, glutamate is
especially important because it is used to form many other amino acids. In

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addition, its synthesis provides a mechanism for bacteria to incorporate

nitrogen into organic material.
Bacteria that synthesize glutamate use single – step reaction that
incorporates ammonia into precursor metabolites α - ketoglutarate,
produced in the TCA cycle (Figure 25a). Once glutamate has been
produced, its amino group can be transferred to other carbon compounds to
produce amino acids such as aspartate (Figure 25 b).
This transfer of amino group, a transamination, regenerates α -
ketoglutarate from glutamate. The α- ketoglutarate can then be used again
to incorporate more ammonia.

Figure 25: Glutamate synthesis in Microbial cell

Microbial Enzymes
Chemical reactions of life are organized and complex, but even when they are
highly organized cannot proceed without the tool of life, Enzymes, are
biological catalysts , designed to do the work of life , each enzyme has one
specific job to do. They are proteins act as catalysts, speed up a chemical
reaction without being altered during the reaction, this means enzymes can be
recycled and do not need to be made in large amount. This due to enzymes
lower the activation energy (the amount of energy necessary to push the
reactants over an energy barrier so that the reaction can proceed) needed to
derive biochemical reactions in normal cellular temperature, in this manner
cellular proteins are not damaged by excess heat for reaction.
Enzymes structure
Enzymes are globular proteins ranging in size from 1300 to millions Dalton,
with a thousands of amino acids are bounded together with covalent bonds
called peptide bonds, linked as polypeptide. Like all proteins an enzyme
exhibits levels of molecular complexity includes primary, secondary, and
tertiary structures, the larger enzymes exhibits quaternary organization (figure

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Microbial Physiology 3rd Class

26). The first three structural levels arise from polypeptide chains folding
process and. this folding cause the surface of apoenzyme acquire distinct tree
dimensional forms (3D) known as a “ native conformation”. The enzymes
native conformation which is essential for functional activity maintained and
stabilized by hydrogen and bisulfide bonds, disruption (breakage) of these
bonds lead to the loss of enzyme function known as denaturation. 3D
conformation relates to enzymes specificity cause the surface feature of the
tertiary structure provides a unique and specific site usually a crevices or
groove called the active site or catalytic site, which is small protein (include a
few amino acids) compared to the overall size of the protein molecule, used
for attachment and accepting of substrate that certain enzyme acted on.

Figure-26: Levels of Enzymes Structure

Cofactors and Coenzymes

Many enzymes are composed only of protein, sometimes referred as simple
enzymes. However some enzymes consist of protein (apoenzyme) and
nonprotein component (prosthetic groups). non protein portions are required
for participation in the catalytic reaction. The complete enzyme consisting of
apoenzyme and its prosthetic group called the holoenzyme. Prosthetic groups
fall into two major categories: Cofactors and Coenzymes.
Cofactors: are commonly metal ions, bind permanently or reversibly to the
enzyme, so most of trace elements used by living cells are primarily used as
cofactors to serve as structural or functional role, such elements include
magnesium, manganese, zinc, iron, copper, cobalt, and selenium. For example
2+
Mg needed for DNA polymerase to form a growing DNA molecule. Metal
cofactors participate in precise enzyme functions, in general help to form a
metal – bridge between enzyme and substrate that assists to bring active site
and substrates closely together or as an electron acceptor/donor in redox
reactions. In addition to these roles metals also bind directly to the enzyme to
stabilize it in the active conformation or perhaps to induce the formation of
active site.

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Microbial Physiology 3rd Class

Coenzymes: are small organic compounds works in conjugation with

apoenzyme, are present in cells in reasonably constant concentration and play
a dynamic role in metabolism, often derived of vitamins. Many important
coenzymes like Coenzyme A, NAD, NADP, and FAD are derived from
vitamin B complex, so vitamins are clearly important nutrients required as
growth factors in majority of living cells, in that vitamins deficiencies prevent
the complete holoenzymes from forming, which compromise both the
chemical reactions and structure or function dependent upon that reaction. The
general action of coenzymes is transmission of functional groups within
substrates that act as carrier of these groups so they are loosely attached to the
apoenzyme and can dissociate from the protein after products have been
formed, and some of them used in generation of energy throughout catabolic
pathways.
Classification of Enzymes
Enzymes can be classified in different ways, which based on many criteria,
the most common and followed classification categories are: (1) Location of
enzymes; In the basement of enzymes location in and site of activity, enzymes
generally divided into two main groups, Exoenzymes, these type of enzymes
after their initial biosynthesis inside cells are transported extracellularly where
they break down large food molecules and harmful chemicals like; cellulose,
amylase, and penicillinase. Endoenzymes, these enzymes are retained
intracellular and function there, most metabolic pathways enzymes are of this
variety. (2) Presence in the cell, enzymes are not all produced in equal
amounts or at equal rates, according to this criteria, two types of enzymes
figured in microbial cells, Constitutive enzymes, are always present
relatively in constant amounts regardless of the amount of their substrates,
such as the enzymes involved in utilizing of glucose, and, Inducible enzymes,
these enzymes not constantly present in cells ,they are selectively synthesis
depending on metabolic requirements, and when their specific substrates they
acted on are present. This property of selective synthesis prevents cells from
wasting energy and it is an important metabolic control that ceasing none
demands pathways. (3) Systematic classification, Despite the large number
and diversity of enzymes present in cells, they are classified as belonging to
one of six classes (includes other subclasses according to the type of reaction
catalyzed), recommended in 1973 by international union of biochemistry and
molecular biology (IUBMB), in this system the arbitrary name is end with the
suffix ase, and usually enzymes named using the prefix that related to the type
of chemical reaction they catalyze.

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Microbial Physiology 3rd Class

The systematic major classes of enzymes

Enzyme class catalyzed Example

Type of
reaction

Oxidoreductase Oxidation/reduction Lactate dehydrogenase

reactions Pyruvate + NADH + H ===
+
Lactate + NAD
Transferases Transfer of functional Hexokinase
groups Glucose + ATP === Glucose-6-
phosphate + ADP

Hydrolases Hydrolytic reactions glucose -6- phosphate

(Cleave bonds in Glucose- 6 –P + H2O === glucose
molecules with addition + Pi
of water)
Lyases Removal of a group Fumarate hydratase
from substrate (No L-malate ====== Fumarate + H2O
hydrolysis)
Isomerases Isomerization Aldose-1-epimerase
Reactions (change α-D-glucose ===== β -D-glucose
substrates into other
isomeric form)
Ligases The joining of two Glutamamine synthetase
molecules at the L-glutamate+ NH3 +ATP === L-
expense of bond glutamine + ADP +orthophosphate
energy in ATP and (pi)
removal of water

The Mechanism of Enzyme Reactions

It is important to keep in mind that enzymes speed up chemical reactions
without altering the energy barrier or equilibrium constant. If the reaction is
endergonic, the presence of enzyme will not shift its equilibrium so that more
products can be formed. Enzymes simply speed up the rate at which a reaction
speeds toward its final equilibrium. How do enzymes catalyze reactions? First
it must bind the substrate to form the enzyme – substrate complex (ES)
“transition state complex”
E + S ========= ES ======== P + E

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Microbial Physiology 3rd Class

Which resemble both substrate and product and falls between the process of
conversion of substrate to product, that many molecular changes occurs in this
level like, breakage, formation or rearrangement of bonds, and developments
of other changes. This state doesn’t take place if not supplied with amount of
energy equivalent to the activation energy which required to attain the
transition state which falls at the top of energy barrier that has to be overcome
and to complete the reaction. Presence of Enzyme accelerate the reaction by
lowering the activation energy, therefore more substrate molecules will have
sufficient energy to come together even though the equilibrium constant is
unchanged . In fact enzymes bring substrates together at their active site to
form the ES. An enzyme can interact with the substrate that acted on in two
general ways; it may be rigid and shaped to precisely fit the substrate so the
correct substrate binds specifically and is positioned properly in active site for
reaction. This mechanism referred to as Lock – and – key model (figure 27).
An enzyme also may be change shape when it binds the substrate so that the
active site surround and precisely fit the substrate, this has been called
Induced fit model. The formation of an ES complex can lower the activation
energy in many ways, in most cases, substrates are held in the active site by
weak interactions, such as hydrogen bonds and ionic bonds, as this
interaction achieved the enzyme may put stress on bonds that must be broken,
making it easier for the reaction to reach the transition state.

Figure-27: Lock – and – Key Model of Enzyme Function

The effect of environment conditions on enzymes activity

Enzymes activity varies greatly with the change in environmental factors. One
of the most important is the substrate concentration. Substrate concentration
(S) usually low within cells, at very low concentration , an enzyme make
product slowly because it seldom contract substrate molecules, if more
substrate molecules are present, the enzyme binds substrate more often, and
the reaction velocity (V), usually expressed in term of the rate of product
formation, greater than at a lower substrate concentration, the initial reaction

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velocity (V°), is proportional to substrate concentration so it's in 1st order

reaction thus, if more substrate molecules present, an enzyme binds more
often, under initial velocity that increase with substrate concentration.
Eventually further increase in substrate concentration does not affect the
reaction rate and the latter become constant “Zero order reaction” because the
available enzyme molecules are binding substrate and converting it to the
product as rapidly as possible. That is the enzyme is saturated with substrate
and operating at maximal velocity (Vmax). The resulting substrate
concentration curve. It is useful to know the substrate concentration an
enzyme needs to function adequately.
Usually the Michaelis – Menten (Km), the substrate concentration required
for the enzyme to achieve half maximal velocity, is used as a measure of the
apparent affinity of an enzyme for its substrate. The lower Km value, the
lower substrate concentration at which an enzyme catalyzes its reaction,
enzyme with a low Km value said to have a high affinity for their substrate.
Km value is not fixed value but varies according to substrate, temperature,
and pH (figure 28).
When the reciprocal values of S and V are used in plotting of V versus S, a
straight line curve is obtain as represented by Line weaver – Burk, used as
accurate determination of required substrate concentration for a certain
enzyme.

Figure 28: Michaelis –

Menten Kinetics of
Enzymes

Enzymes activity also affected by general environmental conditions, such as

with alteration in Temperature and pH (figure 29). Each enzyme works best at
certain optimal conditions which favor the most active conformation for the
enzyme molecule. Temperature has a major impact on reaction rate; each
enzyme has temperature optima for maximum activity. If temperature rises too
much above optimum, thermal agitation begins to disrupt the weak bonds that
stabilize the protein active conformation and the enzymes structure disrupted

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and its activity lost. This phenomenon known as denaturation. Enzymes

likewise function most rapidly at specific pH optimum, when the pH deviated
to greatly form an enzyme optimum activity slow and the enzyme may be
damaged. The temperature and pH optima of a microorganism’s enzymes
often reflect the temperature and pH of its habitat.

Figure 29: The Effect of pH and Temperature on Enzymes Activity

Allosteric Enzymes
Allosteric is derived from the Greek root allo, meaning “the other”. These are
regulatory enzymes; their catalytic activity depends upon non – covalent
binding of specific small molecules as ligands at a unique region of the
enzyme quite different and away from the active site known as regulatory
site, or allosteric site. Ligands binding can be either activators or inhibitors
(figure 30). Most allosterically regulated enzymes are constructed of two or
more polypeptide chain each subunit has its own active site, the allosteric site
are often located where subunits join. The ligands that bind at the allosteric
site are called allosteric effectors or modulators, binding of modulator to an
enzyme alter the 3D conformational structure of the active site and thus
affected the affinity for substrate, activator stabilizes the conformation that has
functional active site, while the binding of an inhibitor stabilize the inactive
form of the enzyme, so most of allosteric enzymes are key enzymes play a
major role in balancing the flow of traffic between anabolic and catabolic
pathways. For example, ATP binds to several catabolic enzymes allosterically,
inhibiting their activity by lowering their affinity for substrate. The substrate
saturation curve of these enzymes is often sigmoidal rather than hyperbolic.

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Microbial Physiology 3rd Class

Figure 30: Allosteric Regulation

Enzymes Inhibitors
An enzymes inhibitor is a molecule that binds to an enzyme and decreases its
activity. Since blocking an enzyme’s activity can kill a pathogen or correct a
metabolic imbalance. As many drugs and pharmaceutical compounds are
enzyme inhibitors, and much of metabolic pathways was determined by using
of inhibitors of specific enzymes. Inhibitors compounds can be bind to the free
enzyme or to the ES complex and affect the velocity of reaction. Several
classes of inhibitors are defined based on their reaction kinetics:

Types of enzymes inhibitors:

1. Reversible inhibitors
Reversible inhibitors attach to enzymes with non – covalent interactions such
as hydrogen bonds, hydrophobic interactions, and ionic bonds. Multiple weak
bonds between the inhibitors and the active site combine to produce strong
and specific binding, reversible inhibitors generally do not undergo chemical
reactions when bound to enzyme and can be easily removed by dilution and
dialysis.
There are two main kinds of reversible enzyme inhibitors, they are classified
according to the effect of the varying the concentration of the enzyme’s
substrate on the inhibitor.
• Competitive Inhibitors:
A competitive inhibitor is any compound which closely resembles the
chemical structure and molecular geometry of the substrate that competes with
the substrate for binding to free enzyme. The inhibitor may interact with the
enzyme at the active site, but no reaction takes place, or inhibitor is "stuck" on
the enzyme and prevents any substrate molecules from reacting with the

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enzyme. However, a competitive inhibition is usually reversible if sufficient

substrate molecules are available to ultimately displace the inhibitor.
Therefore, the amount of enzyme inhibition depends upon the inhibitor
concentration, substrate concentration, and the relative affinities of the
inhibitor and substrate for the active site (figure 31).

Figure 31:
Enzymes
reversible
inhibitors

• Non-competitive Inhibitors:
A noncompetitive inhibitor is a substance that interacts with the enzyme, but
usually not at the active site, reacts either remote from or very close to the
active site. The net effect of a non-competitive inhibitor is reduction the
activity and the enzyme reaction not proceed efficiently, but does not affected
the binding of substrate. This inhibition model are not influenced by
concentrations of the substrate as is the case for competitive inhibitor, and are
depends only on the concentration of inhibitors (figure 31).
2. Irreversible inhibitors
These inhibitors form strong covalent bonds with an enzyme that may act at,
near, or remote from the active site. Consequently, they may not be displaced
by the addition of excess substrate. In any case, the basic structure of the
enzyme is modified to the degree that it stops to work.
Since many enzymes contain sulfhydryl (-SH), alcohol, or acid groups as part
of their active sites, any chemical which can react with them acts as an
+ 2+ 2+
irreversible inhibitor. Heavy metals such as Ag , Hg , Pb have strong

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affinities for -SH groups. Oxalic and citric acid inhibit blood clotting by
forming complexes with calcium ions necessary for the enzyme metal ion
activator.
Regulation of Metabolic Pathways
The physiological integration of enzymes into metabolic pathways, which are
proceed in highly organized manner, so it's necessary to regulate the activity
of enzymes participates in pathways, most of regulatory behavior in cells
related to the key enzyme (Pacemaker), usually are allosteric enzyme, which
respond to various regulation signals, and control the flow of metabolic
pathways as cellular demands. Cells regulate these enzymes in two
procedures: long – term regulation, occurs by change the rate of de novo
(synthesis of complex molecules from simple molecules such
as sugars or amino acids) synthesis genetically, at either transcriptional or
translational level. Short – term regulation of an enzyme occurs through
modulation of the activity of key enzymes by activators and inhibitors. This is
referred to as feedback inhibition (figure 32). The end product of pathway is
feedback to reaction system that fits to allosteric site of key enzyme, by this
fitness enzyme distorted and can no longer bind to its substrates, this
attachment does not denature the enzyme and it's quite reversible.

Figure 32: Short-Term Regulation of Enzymes (Feed Back Inhibition)

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Microbial Physiology 3rd Class

Microbial Metabolism
Catabolic Pathways
Catabolism is the set of metabolic pathways that breaks down complex
compounds to simpler units, often supply material needed for biosynthesis,
including precursor metabolites, and reducing power.
Precursor metabolites serve as starting molecules for biosynthetic pathways.
Reducing power is used the carbon provided by the precursor metabolites, as
they are transformed into amino acids, nucleotides, and other small molecules
needed for synthesis of macromolecules .
Pathways that function both catabolically and anabolically are called
amphibolic pathways (Greek amphi, on both side).
The central catabolic (amphibolic) pathways that take place in microbial cells
are:
Glycolysis (glucose breaking down) and Tricarboxylic acid cycle (TCA).
Many of these reactions are freely reversible and can be used to synthesize or
degrade molecules depending on the nutrient available and the need of
microbe.
Glycolysis
Microorganisms employ several metabolic pathways to catabolize glucose
(fuel molecule) and other sugars. Because of this metabolic diversity their
metabolism is often confusing. To avoid confusion as much as possible, the
ways in which microorganism degrade sugars to pyruvate and similar
intermediates are introduced by focusing on only three routes: (1) Embden-
meyerhof pathway, (2) Pentose phosphate pathway, and (3) Entner –
Doudoroff pathway.
These three pathways collectively termed glycolytic pathways or glycolysis
[Greek glyco, sweet, and lysis, a loosening].
Glycolysis is the most important type of mechanism by which organism
obtains energy from organic compound in the absence of oxygen. As it occurs
in the absence of oxygen, there, it is also called anaerobic fermentation.

*The Embden-Meyerhof pathway (EMP)

The sequence anaerobic reactions from glucose to pyruvate is called Embden-
Meyerhof pathway, because the complete pathway were elucidated by Gustav
Embden (who gave the manner of cleavage of fructose 1, 6- diphosphate and
pattern of subsequent steps) and Otto Meyerhof (who confirmed Embden's
work and studied the energetic of glycolysis). It is an important amphibolic
pathway that provides several essential precursor metabolites, found in all
major groups of organisms, and occurs in the cytoplasmic matrix of
prokaryotes.
The pathway as a whole may be divided in to two phases (figure 33):
The six - carbon phase 6C (preliminary phase), in this phase energy is
consumed. The three – carbon phase 3C (energy conserving phase).
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Microbial Physiology 3rd Class

The EMP degrade one glucose to two pyruvates by the sequence of reactions,
and ATP , NADH are also produced. The yields of ATP and NADH may be
calculated by considering the two phase separately.

Figure 33: The Embden – Meyerhof Pathway (EMP)

* The Pentose Phosphate Pathway (PPP)

The Pentose phosphate pathway, also called Hexose monophosphate shunt
or Phosphogluconate pathway, a second glycolysis pathway, may be used at
the same time as either the EMP or the Entener- Doudoroff pathway. It can
operate either aerobically or anaerobically, is important in both biosynthesis
and catabolism and is the major source for NADPH require for anabolic
processes. There are two distinct phases in PPP; oxidative phase, the linear
portion of pathway carries out oxidation and decarboxylation of G-6-P,
producing 5C sugar ribulose – 5 – phosphate, CO2 and NADHs are generated
during these oxidations (figure 34). The overall reaction for this phase is:

3 G-6-P + 6 NADP + H2O 2 ribulose 5- phosphate + 3CO2+ 6

NADPH + 6H+

Ribulose 5- phosphate is then converted to a mixture of three, four, five, six,

and seven – carbon sugar phosphate in a series of non – oxidative reactions.
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Microbial Physiology 3rd Class

Two enzymes play a central role in non – oxidative subsequent

transformations:
Transketolase and Transaldolase, catalyze transfer of 2-C and 3-C
molecular fragments respectively. These enzymes create a reversible link
between PPP and EMP.

The overall result is that three G-6-P are converted to:

3 G-6-P + 6NADP + 3H2O 2 F-6-P + G3P + 3CO2 + 6
+
NADPH + H

The PPP is a good example of an amphibolic pathway as it has several

catabolic and anabolic functions that are summarized as follow:
1. NADPH from the pentose phosphate pathway serves as: a source of
electrons for the reduction of molecules during biosynthesis
2. The pathway produces two important precursor metabolites: Erythrose -4-
phosphate, which is used to synthesis aromatic amino acids and vitamin B6
(pyridoxal), and ribose 5 –phosphate, which is a major component of nucleic
acids. Note that when a microorganism growing on pentose carbon source, the
pathway in turn can function biosynthetically to supply hexose sugars (e,g.
glucose needed for biosynthesis of peptidoglycan).
3. Intermediates in the pathway may be used to produce ATP, G3P and F-6-P
from the pathway can enter the EMP and can be converted to pyruvate, as
ATP is produced by substrate – level phosphorylation. Pyruvate may be
oxidized in TCA to provide more energy.

Figure 34: The Pentose Phosphate Pathway (PPP)

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Microbial Physiology 3rd Class

*The Entner – Doudoroff Pathway (ED pathway)

Although the Embden – Meyerhof pathway is the most common rout for
conversion of hexoses to pyruvate, the Entner – Doudoroff pathway for
sugars breaking down is used by only prokaryotes, like some soil microbes,
such as Pseudomonas, Rhizobium, Azotobacter, and a few other gram-
negative bacteria. Very few gram-positive bacteria have this pathway, with the
intestinal bacterium Enterococcus faecalis being a rare exception.
The ED pathway catabolizes glucose to pyruvic acid using enzymes distinct
either from those used in EMP or PPP. The pathway begins with the same
reaction as the PPP, the formation of g-6-p, which is then converted to 6-
phosphogluconate (figure 35) Instead of being further oxidized, 6-
phosphogluconate is dehydrated to form 2-keto-3-deoxy-6-phosphogluconate
or KDPG, the key intermediate in this pathway. KDPG is then cleaved by
KDPG aldolase to pyruvate and G3P. The G3P is converted to pyruvate in
the EMP. If the Entner – Doudoroff pathway degrades glucose to pyruvate in
this way, a net yield 1 ATP for every one glucose molecule processed, as well
as 1 NADH and NADPH.

Figure 35: The Entner–

Doudoroff Pathway (ED
pathway)

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Microbial Physiology 3rd Class

The Tricarboxylic Acid Cycle (TCA Cycle)

The TCA also known as the citric acid cycle or Krebs cycle, is a series of
chemical reactions used by all aerobic organisms to generate energy through
the oxidation of acetate derived from carbohydrates, fats and proteins into CO2
and chemical energy in the form of ATP. In the glycolytic pathways, the
energy captured by the oxidation of glucose to pyruvate is limited to no more
than two ATP generated by substrate- level phosphorylation, so during the
aerobic respiration, the catabolic process continues by oxidizing pyruvate to
three CO2 through TCA cycle. The first step of this process employs a multi
enzyme system called pyruvate dehydrogenase complex. It oxidize, cleaves
and decarboxylate pyruvate to form two carbon- molecule, acetyl-coenzyme A
(acetyl-CoA), is the starting point for the cycle (figure 36).
In the first reaction acetyl-coA is condensed with a 4C intermediate,
oxaloacetate, to form citrate, a molecule with 6C. Citrate is rearranged to give
isocitrate, a more readily oxidized. Isocitrate is subsequently oxidized and
decarboxylated twice to yield -ketoglutarate (five carbons), and then succinyl-
CoA (four carbons), a molecule with a high - energy bond.
At this point two NADH molecules have been formed and two carbons lost
from the cycle as CO2. The cycle continues when succinyl-CoA is converted
to succinate. This involves breaking the high – energy bond in succinyl – CoA
and using the energy released to form one GTP by substrate-level
phosphorylation. GTP is also high – energy molecule and it is functionally
equivalent to ATP. Two oxidation steps follow, yielding one FADH and one
NADH. The last oxidation step regenerates oxaloacetate, and as long as there
is a supply of acetyl-CoA the cycle can repeat itself. The TCA cycle generates
two CO2 molecules, three NADH molecules, one FADH, and one GTP for
each acetyl-CoA molecule oxidized.
TCA cycle enzymes are widely distributed among microorganisms. In
prokaryotes, they are located in the cytoplasmic matrix. In eukaryotes, they
are found in the mitochondrial matrix. The complete cycle appears to be
functional in many aerobic bacteria and fungi. This is not surprising because
the cycle is such an important source of energy. Even those microorganisms
that lack the complete TCA cycle usually have most of the cycle enzymes,
because the TCA cycle is also a key source of carbon for use in biosynthesis.

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Figure 36: The

Tricarboxylic Acid
Cycle (TCA)

Respiration
Aerobic Respiration
Aerobic respiration is a series of enzymes – catalyzed reaction in which
electrons are transferred from fuel molecule such as glucose to oxygen as a
final electron acceptor. This pathway is the principal energy - yielding for
aerobic microorganisms, and it provides both ATP and metabolic
intermediates for many other pathways in the cell, including those of protein,
lipid, and carbohydrate synthesis.
Aerobic respiration in microorganisms can be summarized by an equation:
Glucose (C6H12O6) + 6O2 +38ADP + 38 Pi 6CO2 + 6H2O +
38ATP

The Respiratory Chain: (Electron Transport System)

We now come to energy chain, which is the final "processing mill" for
electron and hydrogen, and the major generator of ATP. Overall, the electron
transport system (ETS) consists of a chain of special redox carriers that
receive electrons from reduced carriers (NADH, FADH2) generated by TCA
cycle and glycolysis, and shuttle them in a sequential and orderly fashion. The
flow of electrons down this chain is highly energetic and gives off ATP at
various points. At its end, an enzyme catalyzes the final acceptances of
electrons and hydrogen by oxygen, producing water. Some variety exists from
one organism to another, but the principal compounds that carry out this
complex reaction are:

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Microbial Physiology 3rd Class

NADH dehydrogenase, flavoproteins, coenzyme Q (ubiquinone), and

cytochromes. These complex compounds contain a metal that readily
facilitates receiving and donating electrons (being reduced and oxidized).
The highly compartmentalized structure of the respiratory chain is an
important factor in its function. Not in that the electron transport carriers and
enzymes are embedded in the inner mitochondrial membrane in eukaryotes.
Bacteria carry them in the cell membrane (figure 37).

Elements of electron Transport (the energy cascade):

Although the biochemical details of this process are rather complicated, the
basic reaction consists of a number of redox reactions. In general the seven
carrier compounds and their enzymes are arranged in linear sequence and are
reduced and oxidized in turn.
The sequence of electron carriers in the respiratory chain of most aerobic
organisms is: (1) NADH dehydrogenase, (2) flavin mononucleotide (FMN),
(3) coenzyme Q, (4) cytochrome b, (5) cytochrome c1, (6) cytochrome c,
and (7) cytochrome aa3 (figure 37).
Conveyance of the NADHs from TCA cycle and glycolysis to the first carrier
sets in motion the remaining six steps. With each redox exchange, the energy
level of the reactant is lessened. The released energy is captured and used by
the ATP synthase complex station near the ETS.
Each NADH that enters electron transport gives rise to 3 ATPs. This coupling
of ATP to electron transport is termed oxidative phosphorylation. Since
FADH2 from the TCA cycle is metabolically equivalent to FMN, it releases
only enough energy to synthesize 2 ATPs.

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Microbial Physiology 3rd Class

Figure 37: Electron Transport System in Prokaryotes

The Theory of ATP formation by Oxidative Phosphorylation

What biochemical processes are involved in the coupling electron transport to
the production of ATP? As we know that in eukaryotes, the component of
electron transport is embedded in a precise sequence on mitochondrial
membrane. This stations essentially between two compartments: the inner
mitochondrial matrix, and the outer mitochondrial membrane and cytoplasm.
According to a widely accepted concept called the chemiosmotic hypothesis,
as the electron transport carriers shuttle electrons, they actively pump
hydrogen ions (protons) into the outer compartment of the mitochondrion.
This process set up a concentration gradient of hydrogen ions called the
proton motive force (PMF). The PMF also generates a difference in charge
between the outer membrane compartment (+) and the inner membrane
compartment (-). The potential energy inherent in such a separation of charge
can be harnessed to produce ATP (figure 38). Although the exact mechanism
is not completely understood, it appears that special pores penetrating the ATP
synthase complex transport hydrogen ions (protons) from outside
compartment back into the mitochondrial matrix. This process releases
sufficient free energy for the synthesis of ATP from an ADP and pi. Bacterial
ATP synthesis occurs by means of this same overall process. However,
bacteria have the ETS stationed in the cell membrane and the direction of the
proton movement is from the cytoplasm to the periplasmic space. In both cell
types, the chemiosmotic theory has been supported by test showing that the

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Microbial Physiology 3rd Class

oxidative phosphorylation is blocked if the mitochondrial or bacterial cell

membranes are disrupted.

Figure 38: ATP formation by

Oxidative Phosphorylation

Yield of ATPs from oxidative phosphorylation

The total of five NADHs (4 from TCA cycle and one from glycolysis) can be
used to synthesize:

15 ATPs from ETS (5 ×3 pre electron pair)

And
15 × 2 = 30 ATPs per glucose

The single FADH2 producing during the TCA cycle results in:
2 × 2 = 4 ATPs per glucose

Summary of aerobic respiration

(1) The total yield of ATP is 40 molecules: 4 from glycolysis, 2 from TCA
cycle, and 34 from electron transport.
However, since 2 ATPs were expended in early glycolysis, these have a
maximum of 38 ATPs. The actual number may be lower in certain eukaryotic
cell and bacteria.
(2) Six carbon dioxide molecules are generated during TCA cycle.
(3) Six oxygen molecules are consumed during electron transport.
(4) Six water molecules are reduced in electron transport and one in
glycolysis, but one is send in the TCA cycle, this leaves a net of 6.

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Microbial Physiology 3rd Class

Anaerobic respiration
Some bacteria have evolved an anaerobic respiratory system that function like
aerobic cytochrome system except that it utilizes oxygen containing salts,
rather than free oxygen, as the final electron acceptor. Of these, the nitrate
(NO3) and nitrite (NO2) reduction system are best known. The reaction in
species such as Escherichia coli is represented as:
Nitrite reductase
NO3 + H2 NO2 + H2O
Reduction here is the removal of oxygen from nitrate. A test for this reaction
is one of the best physiological tests in identifying bacteria.
Some species of Pseudomonas and Bacillus possess enzymes that can further
reduce nitrate to nitric oxide (NO), nitrous oxide (N2O), and even nitrogen gas
(N2). This process called denitrification is very important step in recycling
nitrogen in the biosphere. Other oxygen containing nutrients reduced
anaerobically by various bacteria are carbonates and sulfates. None of
anaerobic pathways produce as much ATP as aerobic respiration

Fermentation
Some chemoorganotrophic microbes do not respire because either they lack
electron transport chain or they repress the synthesis of electron transport
chain component under some conditions, making anaerobic respiration
impossible. Yet NADH produced by glycolysis pathway must still be oxidized
back to NAD. If NAD is not regenerated, oxidation of glyceraldehyde 3-
phosphate will stop and glycolysis will stop. Many microorganisms solve this
problem by slowing or stopping pyruvate dehydrogenase activity and using
pyruvate or one of its derivatives as an electron acceptor for reoxidation of
NADH in fermentation process (figure 39).

Figure 39: Reoxidation of NADH during Fermentation

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There are many kinds of fermentation, and they often characteristic of

particular microbial groups. Three unifying themes should be kept in mind
when microbial fermentation is examined:
(1) NADH is oxidized to NAD
(2) The electron acceptor is often either pyruvate or pyruvate derivatives.
(3) Oxidative phosphorylation cannot operate.
(4) ATP is generated exclusively by Substrate level phosphorylation, and
oxygen not participates.

Major pathways for fermentation of sugars

1- Alcoholic fermentation
2- Lactic acid fermentation: homolactic fermentative and heterolactic
fermentative
3- Propionate fermentation
4- Mixed acid fermentation
5- Formic acid fermentation
6- Butarate and acetone – butanol fermentation

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Microbial Physiology 3rd Class

Microbial physiology
References:

1- Burdon KL. A text book of Microbiology, 2PedP ed., Macnillan,2007.

2- Willey, et al. Microbiology, 7PthP.ed, McGraw-Hill, 2008.

3- Lewis, R. et al. Life, 6PthP ed. McGraw-Hill, 2007.

4- Albert, G. et al. Microbial physiology, 4PthP ed., wiley-liss, 2002.

5- Hogg, S. Essential Microbiology, the University of Glamorgan, UK. John

wiler &Sons, Ltd, 2005.

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