Microbial Physiology
e. Electron Transport Chain
A. Biochemical Pathways of Energy
Production
A series of enzymatically catalyzed
chemical reactions called biochemical
pathways store energy in
and release energy from organic molecules.
1. Carbohydrate Catabolism
Most of a cell's energy is produced from the
oxidation of carbohydrates.
Glucose is the most used carbohydrate.
The two major types of glucose catabolism
are respiration, in which glucose is
completely broken
down, and fermentation, in which it is
partially broken down.
a. Glycolysis
The most common pathway for the
oxidation
of glucose is glycolysis.
Pyruvic acid is the end-product.
Two ATP and two NADH molecules are
produced from one glucose molecule.
b. Alternatives to Glycolysis
The pentose phosphate pathway is used to
metabolize five-carbon sugars;
one ATP and 12 NADPH molecules are
produced from one glucose molecule.
The Entner-Doudoro0 pathway yields one
ATP and two NADPH molecules from one
glucose molecule.
c. Definition of Respiration
in aerobic respiration, O₂ functions as the
final electron acceptor.
In anaerobic respiration, the final electron
acceptor is an inorganic molecule other than
0₂.
d. The Krebs Cycle
Decarboxylation of pyruvic acid produces
one CO2molecule and one acetyl group.
Electrons are brought to the electron
transport chain by NADH.
The electron transport chain consists of
carriers, including flavoproteins,
cytochromes, and ubiquinones.
f. Chemiosmotic Mechanism of ATP
Energy produced from movement of the
protons back across the membrane is used
by ATP synthase.
In eukaryotes, electron carriers are located
on the inner mitochondrial membrane; in
prokaryotes, electron carriers are in the
plasma membrane.
g. Summary of Aerobic Respiration
In aerobic prokaryotes, 38 ATP molecules
can be produced from complete oxidation
of a glucose
molecule in glycolysis, the Krebs cycle, and
the electron transport chain.
In eukaryotes, 36 ATP molecules are
produced from complete oxidation of a
glucose molecule.
h. Anaerobic Respiration
The final electron acceptors in anaerobic
respiration include NOT , SO₄²—,And
CO,²—.
The total ATP yield is less than aerobic
respiration because only part of the Krebs
cycle operates
under anaerobic conditions.
i. Fermentation
Fermentation releases energy from sugars
or other organic molecules by oxidation.
O2is not required in fermentation.
Two ATP molecules are produced by
substrate-level phosphorylation.
i. Fermentation
The final electron acceptor is an organic
molecule.
In tactic acid fermentation, pyruvic acid is
reduced by NADH to lactic acid.
In alcohol fermentation, acetaldehyde is
reduced by NADH to produce ethanol.
Heterolactic fermentors can use the pentose
phosphate pathway to produce lactic acid
and ethanol.
2. Lipid Catabolism
Lipases hydrolyze lipids into glycerol and
fatty
acids.
3. Protein Catabolism
Before amino acids can be catabolized, they
must be converted to various substances
that enter the
Krebs cycle.
Transamination, decarboxylation, and
dehydrogenation reactions convert the
amino acids to be catabolized.
B. Biochemical Pathways of Energy Use
(Anabolism)
1. Biosynthesis of Polysaccharides
Glycogen is formed from ADPG.
UDPNAc (uridine diphospho-N-
acetyIgIucosamine) is the starting material
for the biosynthesis of peptidoglycan.
2. Biosynthesis of Lipids
Lipids are synthesized from faby acids and
glycerol.
Glycerol is derived from dihydroxyacetone
phosphate, and fatty acids are built from
acetyl CoA.
3. Biosynthesis of Amino Acids and
Proteins Amino Acids are required for
protein biosynthesis
All amino acids can be synthesized either
directly or indirectly from intermediates of
carbohydrate metabolism, particularly from
the Krebs cycle.
4. Biosynthesis of Purines and Pyrimidines
The sugars composing nucleotides are
derived from either the pentose phosphate
pathway or the Entner-Doudoroñ pathway.
Carbon and Nitrogen atoms from certain
amino acids form the backbones of the
purines and pyrimidines.
C. Integration of Metabolism
Anabolic and catabolic reactions are
integrated through a group of common
intermediates.
Such integrated pathways are referred to as
amphibolic pathways.
D. Summary of Energy Production
Sunlight is converted to chemical energy in
oxidation-reduction reactions carried by the
phototrophs
To produce energy, a cell needs an electron
donor (organic or inorganic), a system of
electron carriers, and a final electron
acceptor (organic or inorganic).
E. Nutritional Patterns Among Organisms
Phototrophs obtain energy by
photophosphorylation and fix carbon from
CO2 via the Calvin Benson cycle to
synthesize organic compounds.
Cyanobacteria are oxygenic phototrophs.
Green sulfur bacteria and purple sulfur
bacteria are anoxygenic phototrophs.
Photoheterotrophs use light as source of
energy and an organic compound for their
carbon source or electron donor.
Chemoautotrophs use inorganic compounds
as their energy source and carbon dioxide as
their carbon source.
Microbial Genetics
A. DNA Synthesis:
At the start of replication DNA is anchored
to the cell
membrane at a mesosome.
Replication is semi conservative.
DNA gyrase nicks between complimentary
strands to create 2 V shaped forks that
replicate in both directions at the same time.
DNA polymerase adds nucleotides to the 3 '
end of the continuously growing strand.
Okazaki fragments are synthesized in the 5 '
to 3 direction on the discontinuous strand
and are then joined to the previously
synthesized section by DNA ligase.
B. Bacterial Mutation:
1. Spontaneous mutations have no
identifiable cause and are rare.
2. Induced mutations are due to chemical
or physical mutagens e.g. UV light, nitrous
acid, base analogs etc.
3. Other mutations are caused by
transposable genetic elements.
Three major types of transposable elements
1. Insertion sequences
They are segments of DNA that encode
enzymes for site specific recombination and
have distinct nucleotides at their terminals.
2. Transposons
They are larger than insertion sequences,
code for protein synthesis and can induce
mutation the same way as insertion
sequences.
3. Transposable phages (Mu)
They can alternate between lytic and
lysogenic growth. During lysogeny.
They can insert themselves anywhere on the
bacterial chromosome, and later transpose
from one location to another, inactivating
the bacterial gene just as other transposable
elements.
C. Bacterial Recombination
1. Transformation
Donor cells lyse, a fragment of DNA is
released and passed into a recipient cell.
Enzyme dissolves one strand of the
fragment, and the other strand displaces a
homologous segment of the recipient's
DNA.
The recipient then has a recombinant DNA.
The displaced fragment is dissolved by an
enzyme.
Only competent cells can be transformed
and DNA of both organisms must be
similar.
Competence is the ability to take up DNA
from the environment.
2. Conjugation
It involves two live bacteria, donor and
recipient, with the transfer of genetic
material from a plasmid. The donor is F+,
has fertility factor and codes for sex pilus.
Once there is contact with the F - or
recipient, plasmid DNA begins to replicate
by the Rolling circle method.
3. Transduction
The transfer of genetic material from one
organism to another by a transducing phage.
a. There are two types of transducing
phages:
1) Lytic
The phage reproduces and causes the
bacterium to lyse.
This is a virulent phage.
2) Lysogenic
The phage codes for a repressor protein
which prevents its own
replication.
This is a temperate phage.
b. There are two types of transductions:
1.Generalized Transduction
A lytic virus uses the bacterial machinery to
make viruses.
The bacterium lyse and viral parts are
released.
2. Restricted or Specialized Transduction
When a bacterium with an integrated
prophage is induced to be lytic, the
phage DNA is excised.
Sometimes a piece of bacterial DNA
adjacent to the phage DNA remains
attached to the excised phage DNA.
Only genes adjacent to the phage can be
transduced.
Growth
Increase in the population of cells is called
a culture.
Cell division is by an asexual process called
binary fission, and the time it takes to
divide (double) is called generation time.
Growth of culture goes through four phases
with time, when plotted on a graph.
Growth Phases
1. Lag Phase
Organisms are adjusting to the environment
(little or no division).
They are synthesizing DNA, ribosomes and
enzymes to breakdown nutrients, and to be
used for growth.
2. Log or Logarithmic phase
Division is at a constant rate (generation
time) but varies with species, temperature
and media.
Cells are most susceptible to inhibitors.
3. Stationary phase
Dying and dividing organisms are at an
equilibrium.
Death is due to reduced nutrients, pH
changes, toxic waste and reduced oxygen.
Cells are smaller and have fewer ribosomes.
In some cases cells do not die but they are
not multiplying.
4. Death or Decline phase
The population is dying in a geometric
fashion so there are more deaths than new
cells.
Deaths are due to the factors in stationary
phase in addition to lytic enzymes that are
released when bacteria lyse.
Factors That Affect Microbial Growth
These environmental factors añect
microorganisms and play important roles in
the control of microorganisms in laboratory,
industrial, and hospital settings.
Availability of Osmotic
Nutrients Pressure
Moisture Barometric Pressure
Temperature Gaseous
Atmosphere
pH
Availability of Nutrients
All living organisms require nutrients —
various chemical compound use to sustain
life.
Energy sources
Sources of basic elements
C, O, H, N, P, S
Na, K, CI, Mg, Ca, Fe, I, Zn
Other Growth Factors
Other growth factors are organized into
three categories:
1. Purines and pyrimidines: required for
synthesis of nucleic acids (DNA and RNA)
2. Amino acids: required for the synthesis
of proteins
3. Vitamins: needed as coenzymes and
functional groups of certain enzymes
Terms Relating to Energy Sources

Phototrophs (organisms that use light as an
energy source)
Chemotrophs (organisms that use chemical
as energy source)
Terms Relation to Carbon Source
Autotrophs (organisms that use CO2 as a
carbon source)
Photoautotrophs
Heterotrophs (organisms that use organic
compounds as a carbon source)
Chemoheterotrophs
Moisture
Water is essential to all life on Earth.
Cells are composed of between 70 95%
water.
All living organisms require water to carry
out their normal metabolic processes, and
most will die in environments containing
too little moisture.
Desiccation — complete drying process
Some microbial stage can survive
desiccation.
Temperature
Optimum growth temperature — the
temperature at which the microorganisms
grows best
Minimum Growth Temperature - Below
this, the microorganisms cease to grow
Maximum Growth Temperature - Above
this, the microorganisms die
Temperature Range
Thermophiles — microorganisms that
grows at temperature of 50-60OC
Mesophiles — microorganisms that grow
best at moderate temperature of 20
40OC
Psychrophiles — prefer cold temperature of
10-20OC
Psychrotrophs — OGT is 4OC (refrigerator
temperature)
Psychrodurics — can tolerate or endure
very cold temperature of less than —4OC
pH
The term “pH” refers to the hydrogen ion
concentration of a solution and, thus, the
acidity or alkalinity of the solution.
Most microorganisms prefer a neutral or
slightly alkaline growth medium (pH 7.0—
7.4).
Osmotic Pressure
Osmotic pressure is the pressure that is
exerted on a cell membrane by solutions
both inside and outside the cell.
Isotonic
Hypotonic
Hypertonic
Barometric Pressure
Most bacteria are not añected by minor
changes in barometric pressure. Some
thrive at normal atmospheric pressure.
Gaseous Atmosphere
Oxygen serves as electron acceptor in
aerobic respiration. Bacteria can be divided
into the following groups based on their
oxygen requirements:
1. Obligate aerobe
Glucose is completely oxidized to CO2 and
H2O, requiring 21% oxygen.
2. Microaerophilic
The metabolic process is comparable to
obligate aerobes but requires 1-15%
oxygen.
3. Facultative anaerobe
In the absence of 02, glucose undergoes present alone or with other bacterial
glycolysis to pyruvic acid, and then species in a patient specimen.
fermentation takes place. e.g. Blood, Chocolate agar

4. Obligate anaerobe 2. Supportive media contain nutrients

Glucose undergoes glycolysis to pyruvic
acid, then fermentation or anaerobic
respiration in which oxygen is not the final
electron acceptor.
Some organisms use nitrate, sulfate or
carbonate.
5. Capnophile
Requires carbon dioxide to survive.
that support growth of most non-
fastidious organisms without giving
any organism a growth advantage.
3. Selective media contain one or more
agents that are inhibitory to all
organisms except those being
sought.
e.g. MacConkey agar, Eosin
methylene blue

Classification of Culture Media 4. Differential media employ some

A. Culture media according to consistency:
1. Liquid media are used for growth of pure
batch cultures.
2. Solidified media contain agar and are
used widely for the isolation of pure
cultures, for estimating viable bacterial
populations, and a variety of other
purposes.
factors that allows colonies of one
bacterial species or type to exhibit
certain metabolic or culture
characteristics that can be used to
distinguish them from other bacteria
growing on the same agar plate.

B. Culture media according to composition.

1. Chemically-defined (synthetic) medium
is one in which the exact
chemical composition is known.
2. Complex (undefined) medium is one in
which the exact chemical constitution of the
medium is not known. Also known as basal
medium.

C. Culture media according to their

function and use.

1. Enrichment media contain specific

nutrients required for the growth of
bacterial pathogens that may be