Microbiology Master Cheat Sheet
O1: Introduction to Microbiology
· Environmental Microbiology: The study of
microorganisms and their interaction with both living and
non-living components of the environment.
· Germ Theory: The theory that diseases are caused by
microorganisms.
· Microbiology: The study of microorganisms, viruses and
some multicellular parasites.
· Microorganisms: Organisms that must be viewed with
the aid of a microscope.
· Spontaneous generation: The theory that living things
arose form spontaneously from non-living components.
· Viruses: Non-living infectious molecules, consisting of
protein and genetic material. They are so small that they
must be viewed with an electron microscope.
Koch’s Postulates
· A microorganism that causes a disease must be found in all
cases.
· The microorganism must be isolated and purified.
· The isolated culture should cause the same disease in a
test subject.
· The microorganism should be recoverable from the test
subject.
Hershey-Chase Experiment
· Label one group of bacteriophages with radioactive sulfur
(S35). Sulfur is only found in proteins.
· Label another group of bacteriophages with radioactive
Phosphorous (P32). Phosphorous is only found in nucleic
acids, such as DNA.
· Allow bacteriophages to attach to bacteria.
· At the early stages of the infection detach bacteriophages
from bacteria by blending.
· Only P32 is found inside the bacterial cell demonstrating
that DNA and not protein was the genetic material.
How to study microbiology
· Read the textbook!
· Memorize your vocabulary – Make flash cards
· Construct a chart classifying all microorganisms you
encounter through out the semester.
· Make connections between the microorganisms you
encounter and the disease(s) they cause, their use in
industry, role in the environment and relation to other
organisms.
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02: Techniques in Microbiology
· Brightfield Microscopy: Image seen is from the light
passing directly through the specimen. Field without
specimen is “brighter” that that with it.
· Gram Stain: Gram positive and negative referrers to a
characteristic of cells to retain a specific stain typically
crystal violet or methylene blue.
· Aseptic Method: A method to ensure that a sample
remain pure. It does not contaminate the environment nor
become contaminated from the environment.
· Wet Mount Slide: A thin specimen immobilized on a slide
with water or stain added. The sample is overlaid with a
cover slip and excess stain removed.
Microbe Identification & Characterization
A culture can be identified and characterized using: Molecular
methods for DNA, RNA and protein I.D. and sequencing.
Microscopy: optical methods as in light microscopy, atomic
methods with electrons bombarding a sample and
fluorescence methods in which the sample is stained using
dyes that fluoresce when excited and emit a photon. Cell
culture is used to get a pure sample and characterize the
microbe physiology.
Pure Culture
Microbe (unknown or mixed sample)
· Using a sterile transfer or inoculation loop touch tip of
sample.
· Streak 3 quadrants of a Petri dish having selective media.
· Each quadrant touching just one point on the previous
quadrant (creating a dilution effect on the plate).
Correctly Streaked Plate
Note how each quadrant the
bacteria colonies become more
distinctive. The last streak (by
the end of the inoculation loop
shows individual colonies)
Microscopy – Slide Preparation
 03: Chemical Basis of Life 04: Prokaryotic and Eukaryotic Cells
· Chemical bonds store energy. Structure and Function
· For covalent bonds, the more electrons pairs shared, the Cell membrane: A lipid bilayer that surrounds the cells of
more energy is stored and the shorter the bond length. prokaryotes and eukaryotes. Typically it has proteins
· Ionic bond: forms when atoms lose or gain electrons embedded in or associated with the membrane. The
· Covalent bond: forms when atoms share electrons; very membrane acts a semi permeable barrier.
strong bonds Cell Wall: Most prokaryotes have a cell wall and some
· Atoms: eukaryotes. It serves as a ridged barrier to protect and give
o electrons: – charge, orbit nucleus form to the cell.
o neutrons: uncharged, in nucleus Ribosome: Is a protein complex that reads mRNA to make
o protons: + charge, in nucleus proteins. The ribosome in prokaryotes is smaller and less
· Molecules: complex then that of eukaryotes.
o formed from atoms Prokaryote: Made up of two Kingdoms: eubacteria and
o joined by chemical bonds (shared electrons) archaebacteria. It lacks a membrane bound organelles and
o molecular formula and structural formula no nucleus. They reproduce by binary fission and do not
· Organic Molecules/macromolecules: undergo meiosis.
o amino acids --> proteins Eukaryote: They posses membrane bound organelles and
o monosaccharides --> polysaccharides have a complex DNA structure. They reproduce via mitosis
o fatty acids --> lipid components or meiosis.
o nucleotides --> nucleic acids Organelle: A organelle is a structure within a eukaryotic cell.
Organic Chemicals It is differentiated and membrane bound, e.g. mitochondria.
· Classified by the functional groups: Histone: A protein with a basic charge that binds to
n Alcohols, R-OH chromosomes of eukaryotes.
n Aldehydes, R-CHO Eukaryote Cell Structure
n Ketones, R-CO-R Membrane bound organelles.
n Carboxylic Acids, R-COOH The nucleus contains the cells chromosomes.
n Amines, R-NH2 Eukaryote cell division: two type mitosis and meiosis.
n Thiols, R-SH Mitosis: involves the replication of the DNA and the cell
n Esters, R-COO-R’ splitting. This occurs in somatic cells. With the exception of
n Ethers, R-O-R’ mutations the two cells are identical.
n Amides, R-CONH2 Meiosis occurs in sexual reproduction (never in prokaryotes).
n Organic Phosphates, R-OPO32- The DNA reduces from diploid (2N) to haploid (1N). The
Law of Thermodynamics haploid cells (sperm, egg, germ cells) combine between
· First Law: The total energy of the universe is always parents to create a new and unique diploid cell (2N).
conserved. Energy can neither be created nor destroyed. Energy production is (predominantly) done in the
· Second Law: The universe tends towards maximum mitochondria.
disorder; the direction of all spontaneous processes Has cytoplasmic structures referred to as a cytoskeleton.
serves to increase the entropy of a system plus its
surroundings.
· DG: Change of free energy in a system. (DG=DH-TDS)
· DG <0: spontaneous reaction/exergonic
· DG >0: non-spontaneous reaction/endergonic
· DG =0: reaction at equilibrium
· DH: enthalpy, <0=exothermic, >0=endothermic
· T: the temperature in Kelvin
· DS: the net change in entropy
Chemical Reactions
· Coupled reactions: ATP hydrolysis can provide energy for
many biosynthesis reactions (i.e., the overall reaction will
have DG<0). The energy offered by ATP is stored in its Prokaryote Cell Structure
phosphate bonds. ATP hydrolysis breaks ATP into ADP and Has a cell membrane and (usually) a cell wall.
inorganic phosphate (Pi).
· Enzyme-catalyzed reactions: lower the free energy of
activation (Ea) but do not change DG.
Important Biochemical Molecules
· Organic molecules/macromolecules:
n Polysaccharides
o Monomer unit: monosaccharide
o store energy, structural function (plants=cellulose)
n Lipids
o Monomer unit (triglyceride): 3 fatty acids + glycerol
o Store energy, cellular membranes, steroid hormones
Typically single circular chromosome made up of DNA.
n Proteins:
Lipid bilayer membrane.
o Monomer unit: amino acids
No membrane bound organelles.
o Structural proteins, enzymes
Flagella used for motion, like a propeller.
n Nucleic Acids:
Replication by cell fission.
o Monomer unit: nucleotides
Two Kingdoms of prokaryotes: Eubacteria and Archaebacteria.
o Genetic material (RNA and DNA)
Genome is haploid having only one of each chromosome.
Reparatory enzymes located in the cytoplasmic membrane.

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 05: Microbial Metabolism
· Aerobic Respiration: chemical process were oxygen is
used to make energy from carbohydrates (sugars).
· Anabolism:In metabolism were simple biomolecules are
synthesized into the complex ones.
· ATP: Adenosine tri-phosphate. A high energy phosphate
molecule used to for energy for cellular processes.
· Catabolism: Metabolic breakdown of large biomolecules
to simpler molecules used by a living cell.
· Glycolysis: The process in which glucose (sugar) is
broken down to pyruvate acid. Glycolysis is one method
that cells use to produce energy.
· Kreb’s Cycle: Uses Acetyl-CoA to generate ATP, NADH
and FADH2. Water and CO2 are biproducts.
· Oxidative phosphorylation: The process in cell
metabolism by which respiratory enzymes synthesize ATP
from ADP .
· REDOX: Refers to oxidation reduction reactions.
Reduction is the acquisition of electrons and oxidation is
the loss or donation of electrons.
Kreb’s Cycle
Electron Transport System
The successive passage of electrons from one electron
carrier to another in a series of oxidation-reduction
reactions in the presence of oxygen for the production
of ATP. The electrons are donated to oxygen in the
final step. The oxidation-reduction reactions generate
the energy required for the production of ATP.
Glycolysis
Glycolysis pathway and energy production.
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06: Microbial Growth and Control
Autotroph: A microbe that uses only inorganic carbon
sources CO2 for nutrition.
Chemoautotroph: Uses chemical compounds as energy
source and inorganic carbon for nutrition.
Chemotroph: Acquires energy from REDOX reactions with
aerobic or anaerobic respiration or fermentation.
Heterotroph: A microbe that catabolizes (reduces) carbon
compounds from other organisms for nutrition e.g. protein,
amino acids, carbohydrates or fatty acids.
Obligate aerobes: Requires oxygen to be viable.
Obligate anaerobes: Requires an oxygen free environment
to be viable.
Photoautotroph: Are organisms such as plants, algae and
cyanobacteria that use water to reduce carbon dioxide and
produce oxygen. They use light for energy and inorganic
carbon.
Photoheterotroph: Uses light and organic carbon for energy
and nutrition.
Phototroph: Acquires energy from light.
Pure Cultures: Having cells that are only from one species
and derived from a CFU (colony forming unit) composed of a
single cell.
Quorum sensing: The process that bacteria use to respond
to changes in microbial density and use signal molecules and
receptors to communicate with the population.
Vitamins: organic molecules that used in small amount for
metabolism and are considered growth factors.
Types of Selective Media
· Defined media: has an exact amount of nutrients.
· Complex media: contains a variety of growth factors.
· Selective media: functions to either inhibit or favor the
growth of a particular microbe.
· Differential media: designed to distinguish different
groups of bacteria.
· Reducing media: used to culture anaerobes.
· Transport media: designed to transport specimens while
keeping them viable and uncontaminated.
Growth of Microbial Population
· Bacteria growth: logarithmic or exponential growth.
· The time it takes bacteria to go through an entire cycle of
binary fission is referred to as “doubling time”.
· A growth curve of bacteria in culture can be characterized by
four phases: Lag, Log, Stationary, and Death.
Lag Phase: microbes adjusting to new environment,
activating metabolism.
Log Phase: population actively growing.
Stationary Phase: microbe reproduction and death are
equal or balanced.
Death Phase: the rate of microbes dying is greater then
new cell production.
 07: Microbial Genetics and Biotechnology
· Chromosomes: Prokaryote chromosomes are usually
circular DNA strands associated with histone-like proteins
and RNA. They are localized in an area of the cell cytosol
referred to as the nucleoid. Some bacteria may also have
extrachromosomal DNA molecules called plasmids.
Plasmids have genes that confer non essential traits such
as antibiotic resistance or ability to conjugation.
· Eukaryotic chromosomes have histones associated with
them arranged in nucleosomes (beads of DNA).
Mitochondria and chloroplasts have DNA as well.
· Genetics: The study of genes and heredity. How traits are
transmitted from parents to offspring.
· Genome: The sum of all the genetic material in a cell (or
virus). Prokaryotes and eukaryotes use DNA as their
genetic material. Viruses use DNA or RNA as the carrier of
their genetic information.
· mRNA: Messenger RNA carries the genetic information
from the DNA to the ribosome where it is translated and t
by tRNA into chemical compounds as energy source and
inorganic carbon for nutrition.
· Restriction enzyme: Enzymes from bacteria that cleave
DNA at specific sequences. The ends of the DNA are either
sticky (they have a 4 nucleotide lip) or blunt ends.
· Semi conservative Replication: when DNA is copied
each newly synthesized strand remains associated with one
of the parental strands. The DNA is unwound by helicase
and the parental DNA copied in opposite directions in the 5’
to 3’ direction.
DNA Replication
· DNA replication is semiconservative process.
· DNA is copied from the 5’ to the 3’ direction.
· The process starts at the Origin (of replication)
· Chromosomal proteins are released exposing the DNA.
· DNA helicase unwinds or unzips a local regeion of DNA
breaking hydrogen bonds and exposing the two separate
strands.
· This opening is called the replication fork (think of a fork in
the road).
· DNA polymerase (an enzyme that matches a
complementary base to the one exposed) binds to the open
strand.
· Primase synthesizes a short complementary RNA molecule.
The RNA primer provides a 3’hydroxyl group for the DNA
polymerase to bind.
· The polymerase moves along the strand in the 5’ to 3’
direction.
· Because there are two strands that are antiparellel cells
synthesize new strand in two ways.
· The leading strand is synthesized continuously in a single
long chain of nucleotides.
· Lagging strand is synthesized in short segments that are
later joined.
Double stranded DNA unwinds
08: Classification of Microorganisms
· Binomial nomenclature: a Latin based two word organism
naming system often referred to as the “scientific name”.
The first word identifies the genus; the second often
describes a characteristic of the organisms.
· Cladistics: a branch of biology that determines the
evolutionary relationship between organisms. The basis is
“shared derived traits”.
· Cladogram: graphical representation of the information
compiled by cladistics. These are drawn to show different
hypotheses of relationships.
· Horizontal gene transfer: transfer of genes to an
organism that is not its offspring. Genetic engineering
would be an example of horizontal gene transfer.
· Molecular systematics: A branch of systematics that uses
molecular biology to group and classify organisms.
· mRNA: Messenger RNA carries the genetic information
from the DNA to the ribosome where it is translated.
· Phenotype: Refers to how an organism appears its
morphology.
· Phylogeny: The study of how organisms are genetically
related to each other.
· Ribosomal RNA: (rRNA) is a type of RNA that is main
component of the ribosome. rRNA is the most conserved
(least variable) gene known. The genes that encode rRNA
are refereed to as rDNA.
· Ribosome: is an organelle in cells that translates the
mRNA into proteins. Ribosomes are made up of: rRNA,
ribosomal proteins (RNP).
· Specific epithet: Is the second word in the scientific name
of an organism.
· Taxonomy: means to classify. Taxonomic units are known
as taxa and are a hierarchical structure.
· Vertical gene transfer: transfer of genes to an organism’s
offspring.
Taxonomic ranks: Domain, Kingdom, Phylum (plural, phyla),
Class, Order, Family, Genus and Species.

Transcription
Into mRNA

Ribosome Translates mRNA www.genome.gov

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 09: The Prokaryotes
Domains Bacteria and Archaea
· Mycoplasmas: Are Gram-negative, pleomorphic,
facultative anaerobes and obligate anaerobes. They do not
have cell walls and can cause pneumonia and urinary tract
infections.
· Nitrifying bacteria: oxidize NH2 to NO3 by a process
called nitrification. Alphaproteobacteria have nitrifying
bacteria.
· Vegetative Cell: Any cell except the reproductive cells.
· %G+C: the percentage of guanine plus cytosine that an
organism’s genome contains. Low G+C is a percentage
less then 50%. High G+C containing organisms are >
then 50%.
· Halophiles: Microbe that requires a high saline
concentration to live >9% NaCl.
· Methanogens: Obligate anaerobes that make methane
gas.
· Actinomycetes: Resemble fungi in that they make spores
and filaments. However they are bacteria.
· Nitrogen fixation: In cyanobacteria it is the reduction of
atmospheric N2 to NH3.
· Saprothophic: organism that obtains its nutrients from
non-living organic matter, usually dead and decaying plant
or animal matter.
· Archae: domain which includes all prokaryotic cells having
archaea rRNA sequences.
· Thermophiles: Microbes that require temperatures about
45°C to live.
Endospore Formation
The growth of microbes can be characterized by these
parameters:
Shapes of Bacteria
Shown are the different shapes that cocci and bacilli can
take.
Shapes are function of replication mechanism.
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10: The Eukaryotes
Fungi, Algae, Protozoa and Helminths
· Coenocytes: Multinucleate cells created by a delay in
cytokinesis, as can occur in some algae and fungi, following
mitosis.
· Schizogony: Asexual reproduction (protozoan
Plasmodium). Multiple mitoses form a multinucleate
schizont. This is followed by cytokinesis.
· Algae: typically reproduce ban an alternation of generations
in which a haploid thallus alternates with a diploid thallus.
· Chemoautotroph: Obtain nutrients by phagocytizing
bacteria and organic matter in decay and tissues of hosts.
Fungi, Protozoa, Algae, Water & Slime Molds
Major Characteristics
· Fungi: chemoheterotrophic eukaryotes that have cell walls
typically composed of chitin. Saprophytic and parasitic
organisms that lack chlorophyll and include molds, rusts,
mildews, smuts, mushrooms and yeast.
· Protozoa: Single-celled, eucaryotic microorganisms
without cell walls. Most protozoa are free-living although
many are parasitic. The majority of protozoa are aerobic or
facultatively anaerobic heterotrophs.
· Algae: Have cell walls with a diverse type of
polysaccharides. Most are unicellular or filamentous.
Phototrophic typically contain chlorophyll a and may have
accessory pigments. Most algae are aquatic and live in the
photic zone. Use sugar and starch as food reserves. 18S
rRNA sequences are similar to plants and so are considered
progenitors of plants.
· Water Mold: Have tubular cristae in their mitochondria.
Cell walls of cellulose. Spores have two flagella – one whip
like the other like tinsel. True diploid thalli. Example:
Phytophthora caused the great Irish potato famine of 1845.
· Slime Mold: Feed by phagocytizing organic debris and
bacteria. The thallus also called a plasmodium can have
millions of diploid nuclei. Cytoplasmic streaming distributes
the cells nutrients. When food or water is limiting the
plasmodium will divides into cytoplasmic units which make a
stalked sporangium. Meiosis occurs in the sporangia to
make haploid spores. If water is not limiting myxamoebae
make flagella a swim. Myxamoebae of opposite mating type
fuse to form a diploid zygote.
Review of Mitosis & Meiosis
· Meiosis: nuclear division that results in four nuclei with half
the number of chromosomes.
· Mitosis involves the nuclear replication that results in an
exact copy of the parent cell.
· There are typically four phases in mitosis: prophase,
metaphase, anaphase and telophase.
Modern Classification
 11: Viruses and Other Non-Living
Infectious Agents
· Virus: A small acellular infectious agent. It has one or
several pieces of nucleic acid, DNA or RNA. Viruses have
no cytoplasmic membrane but may have a envelope around
its capsid.ltinucleate cells created by a delay in cytokinesis,
as can occur in some algae and fungi, following mitosis.
· Capsid: The capsid is the protein coat that surrounds the
nucleic acid core of a virus. Capsids are composed of
capsomeres that bind together.
· Virion: A virus that in the extracellular state.
· Viroid: A small infectous particle composed only of RNA.
It causes diseases in plants.
· Bacteriophage: Are viruses that only infect bacteria.
· Viral Shapes: Three kinds, helical, polyhedral and
complex. Capsid of polyhedral virus is spherical. Capsid
of a helical virus is made up of capsomeres bonded in a
spiral to form a tube. Complex shapes include icosahedral
heads, helical tails and tail fibers.
· Viral Envelope: Some viruses have a membrane
(different from a cell’s membrane). A virion that has a
membrane is said to have an envelope.
· Naked virion: A virion without an envelope or
nonenveloped virus.
· Nucleocapsid: Viral nucleic acid surrounded by its capsid.
Lytic & Lysogenic Replication
· Attachment: virion binds to the host cell.
· Entry: the virion or its genome enters the host cell.
· Synthesis: nucleic acids and viral proteins are replicated
by the host cell’s enzymes and ribosomes.
· Assembly: new virions are put together within the host
cell.
· Release: The newly assembled virions are released from
the host cell either by lysis or budding.
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12: Principles of Disease and Epidemiology
· Epidemiology: Epidemiology is the study of the
determinants, distribution, and frequency of disease
· Epidemic : An epidemic occurs when there are significantly
more cases of the same disease than past experience would
have predicted.
· Sporadic Disease :When a disease occurs occasionally , at
irregular intervals, in a human population.
· Endemic Disease: When a disease occurs at a steady , low
level frequency at a moderately regular interval.
· Out Break : It is the sudden unexpected occurrence of a
disease, usually focally or in al limited segment of a
population.
· Pandemic: It is an increase in disease occurrence within a
large population over the entire world. E.g. AIDS.
· Symbiosis: symbiosis is the living together in close
association of two or more dissimilar organisms.
· Commensalism: It is the relationship in which one
organism, the commensal, benefits while the host is neither
harmed nor helped. It is like “eating on the same table”.
· Mutualism: It is the relationship in which both the partners
mutually benefit each other. They are metabolizing
dependant on each other.
· Pathogen: An organism capable of infecting a host,
multiplying and impairing the normal physiological activities
of the host , to such an extent that the individual suffers
abnormal changes in its body or dies.
· Infection: The manifestation caused by a pathogen in the
host is called infection.
Koch’s Postulates
· Same pathogen present in every case of disease
· Pathogen must be grown in pure culture
· Pathogen isolated from pure culture must cause disease in a
healthy host.
· Pathogen must be re-isolated from the inoculated animal,
who developed the disease.
Types of Carriers/Reservoirs
· Active carrier- An individual who has an overt clinical case
of the disease.
· Convalescent carrier-An individual who has recovered
from the disease but continues to harbor the disease causing
pathogen.
· Healthy carrier; An individual who harbors the infectious
organism but is not ill.
· Incubatory Carrier- an individual who is incubating the
organism in large numbers but not yet ill.
Mode of Transmission of infectious agent
· Airborne transmission-
· Contact transmission – a) direct contact & b) indirect
contact.
· Vehicle transmission. Vector borne
Major classification of symbiosis & examples
· Commensalism: (Latin com-together & Mensa, table) – e.
A relationship where one organism, the commensal benefits,
while host is neither harmed nor helped. E.g. E.coli lives in
the human colon & derives nutrients, warmth, & shelter, but
usually causes no disease to humans.
· Mutualism: Latin mutus-to lend. In this relationship, the
mutualist and host are metabolically dependant on each
other eg. Lichens are the association between fungi and
green algae. The fungus obtains its organic carbon from the
alga and in turn provides water and minerals to the alga.
· Parasitism: Relationship, when a symbiont either harms
or lives at the expense of another organism. Vibrio cholera
causing cholera in humans.
· Normal healthy state is a balance between host & pathogen,
with environment as the fulcrum, akin to a see saw. When
the pathogen wins, disease occurs.
 13: Innate Immunity
· Innate immunity or native immunity: It is the
resistance to infections which an individual possesses by
virtue of his genetic and constitutional make-up.
· Species immunity: refers to the total refractoriness to a
pathogen, shown by all the members of a species obtained
as their birthright.
· Racial immunity: Within a species, different races may
show differences in susceptibility to infections. This is
known as racial immunity, it is genetic in origin.
· Individual immunity: The difference in innate immunity
exhibited by different individuals in a race is known as
individual immunity. It is genetic in origin.
· Endocytosis: Process by which macromolecules contained
within the extracellular tissue fluid are internalized by cells.
· Pinocytosis: Cells take up fluid from the surrounding
medium it involves nonspecific cell invagination.
Innate Immune System
· The immune system comprises of two parallel but
interrelated systems, which work in harmony with each
other making them both more effective. These are Innate
immunity and Adaptive immunity.
· Innate immunity may be considered at the level of the
species, race or individual.
· Age, Hormonal levels & Nutrition are some factors which
influence the level of innate immunity in an individual.
· Various organs (eyes, nose, mouth, stomach, skin,
intestine, lungs, & reproductive organs) involved in innate
immunity protect the body from invading pathogens.
· Innate immune response shows following characteristics :
· Responses are Broad-Spectrum (non-specific).
· There is no memory or lasting protective immunity.
· There is a limited repertoire of recognition molecules.
· The responses are phylogenetically ancient.
Phagocytic Barriers
· Various cells internalize (endocytose) and break down
foreign macromolecules. Specialized cells such as blood
monocytes, neutrophils, and tissue macrophages
internalize i.e. phagocytose, kill and digest whole
microorganisms.
· Steps involved in phagocytosis are:
1. Chemotaxis & adherence of microbe to phagocyte.
2. Microbe is ingested by phagocyte.
3. Phagosomes are formed.
4. Phagolysosome is formed.
5. Microbe is ingested & digested with the help of
enzymes.
6. Residual body is formed which contains indigestible
materials.
7. Discharge of waste materials.
Mechanism of Innate Immunity
· Potential pathogens are encountered routinely, but only
rarely cause disease. The vast majority of microorganisms
are destroyed within minutes or hours by innate defenses.
· Innate immune response includes four barriers anatomical,
Physiological, Pagocytic & inflammatory barriers.
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14: Adaptive Immunity
· Adaptive immunity or acquired immunity: The
resistance that an individual acquires during life is known as
adaptive or acquired immunity. It is capable of recognizing
and selectively eliminating specific foreign microorganisms
and molecules.
· Active immunity: Active immunity is the resistance
developed by an individual as a result of an antigenic
stimulus. This involves the active functioning of person’s
immune system leading to the synthesis of antibodies
and/or the production of immunologically active cells.
· Passive immunity: The resistant that is transferred to a
recipient in a readymade form is known as passive
immunity. Here the recipient’s immune system plays no
active role. There is no antigenic stimulus; instead,
preformed antibodies are administered.
· Humoral immune response: Host defenses that are
mediated by antibody present in the plasma, lymph, and
tissue fluids. It protects against extracellular bacteria and
foreign molecules.
· Cell-mediated immune response: Host defenses that are
mediated by antigen-specific T cells and various non-specific
cells of the immune system. It protects against intracellular
bacteria, viruses, cancer & is responsible for graft rejection.
Maturation & Development of B-cells
1. B-lymphocytes mature within the bone marrow. Pluripotent
stem cell develops into progenitor B-cells.
Pro-B cells proliferate and differentiate into precursor B-cells.
Precursor B-cells develops into immature B-cells.
2. Inactive B cells before encountering the antigen are called
as naïve B-cells. Naïve B-cells after encountering antigen
become active B-cells.
3. T-helper cells primed by dendritic cells can interact with B
cells and stimulate antigen-specific antibody production.
4. Active B- cells express a unique antigen binding receptor on
its membrane i.e. antibody molecules. Binding of the antigen
to the antibody causes the cell to divide rapidly. Its progeny
differentiate into memory B cells and effector B-cells called
plasma B- cells.
5. Plasma B-cells secrete antigen specific antibodies that
destroy the pathogen.
6. Memory B cells have longer life span and continue to
express the same antibody as their parent naïve B cells.
Clonal Selection
§Clonal selection occurs when an antigen binds with a B-cell
whose membrane bound antibody molecules are specific for
epitopes on that antigen.
§Clonal selection of an antigen activated B-cell leads to a clone
of effector B-cells (plasma cells) and memory B-cells.
§Maturation & Clonal selection of T-cells takes place in similar
fashion as that of the B-cells.
Humoral & Cell-Mediated Immunity
§The responses carried out by B-lymphocytes are termed as
Humoral immune responses. And those carried out by T-
lymphocytes are termed as cell-mediated immune responses.
§Humoral immune responses are best suited for the
elimination of exogenous antigens; whereas cell mediated
immune response is best suited for the elimination of
endogenous antigens.
 15: Immunologic Disorders
· Hypersensitivity: an exaggerated immune response that
results in tissue damage and is manifested in the individual
on second exposure to the same antigen.
· Inflammation: -a localized protective response to tissue
injury or destruction. Acute inflammation is characterization
by pain, heat, swelling and redness in the injured area.
· Anaphylaxis: a sudden, severe, potentially fatal, systemic
allergic reaction that can involve various areas of the body
(such as the skin, respiratory tract, gastrointestinal tract,
and cardiovascular system).
· Autoimmune disease -When our immune system doesn't
work the way it is supposed to.
· Asthma: a chronic disease of the respiratory system in
which theairwayoccasionally constricts, becomes inflamed,
and is lined with excessive amounts of mucus, often in
response to one or more triggers
· Rheumatoid arthritis: a chronic, inflammatory auto
immune disorder that causes the immune system to attack
the .joints .It is a disabling and painful
inflammatorycondition, which can lead to substantial loss of
mobility due to pain and joint destruction.
· Mast cells: a resident cell of areolar connective tissuethat
contains many granules rich in histamine and heparin and
play an important protective role indefense against
pathogens
· Antibodies: Group of proteins which bind to antigen and
destroy it.
· Cytokines: a group of proteins that are used extensively
for inter-cell communication.
Types of Hypersensitivity
· Type-1is an allergic reaction provoked by reexposure to a
specific antigen and is mediated by IgE antibodies and
produced by immediate release of histamine,tryptase,
arachidonate and derivatives by basophils and mast cells
· Type-2: IgG and IgM antibodies bind to these antigens to
form complexes that activate the classical pathway of
complement of activation for eliminating cells
· Type-3: soluble immune complexes (aggregations of
antigens and IgG and IgM antibodies) form in the blood.
and are deposited in various tissues (typically the skin,
kidney and joints where they may trigger an immune
response.
· Type-4 It is a type of cell-mediated response and takes
days to develop.
Immunological Disorders
· When one or more of its components is missing in the
immune system the result is an immunodeficiency disorder.
· They can be inherited, acquired through infection or
produced unintentionally by drugs such as those used to
treat people with cancer or those who have received
transplants
Examples of Immunological Disorders
· SLE-antibodies made against self antigens.
· Diabetes-antibodies are made against pancreatic cells.
· Rheumatoid arthritis
· AIDS (HIV) that infects immune cells, namely the T cells
and disables the immune system.
· Latent AIDS infection the T cells and makes the person
susceptible to serious life threatening disease like cancer,
TB etc.
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16: Antibiotics
· Beta lactam- A beta-lactam ring or penam is a lactam with
a heteroatomic ring structure consisting of three carbon
atoms and one Nitrogen atom.
· Beta-lactam antibiotics- antibiotics having beta lactam
rings e.g. penicillin, cephalosporin.
· Penicillin- works by interfering with the synthesis of the
bacterial cell wall — a structure that is not found in
eukaryotes (see diagram below).
· Glycopeptides- Another group of proteins which work by
interfering with the synthesis of the protective cell wall in
microbes.
· Polymyxins- Polymyxin acts as an antibiotic by damaging
the cytoplasmic membrane of bacteria.
Categories of Antibiotics
· Bactericidal
· Usually antibiotic of choice
· Bacteriostatic
· Duration of treatment sufficient for host defenses
Cell Components that are Targets for
Antibiotics
· Cell walls-A rigid, protective structure which gives
microbial and plant cells their shape and limits the total
amount of liquid that can enter these cells.
· Cell membrane-All cells have these membranes. They
control what enters and exits the cells.
· Cellular Proteins: These are composed of a variety of
amino acids and play a variety of important roles in
microbial cells.
· Cellular Nucleic Acids: These are the building blocks of
RNA and DNA molecules. They are found in the nucleus of
microbial cells.
· Penicillin
The walls of bacteria are made of a complex polymeric
material called peptidoglycan. It contains both amino
acids and amino sugars
Penicillin binds to and inhibits enzymes needed for the
synthesis of the peptidoglycan wall.
Large scale production of antibiotics
· Most antibiotics are produced by staged fermentations in
which strains of microorganisms producing high yields are
grown under optimum conditions in nutrient media in
fermentation tanks.
· The mold is strained out of the fermentation broth.
· The antibiotic is removed from the broth by filtration,
precipitation, and other separation methods.
· Most antibiotics are produced by staged fermentations in
which strains of microorganisms producing high yields are
grown under optimum conditions in nutrient media in
fermentation tanks.
· The mold is strained out of the fermentation broth.
· The antibiotic is removed from the broth by filtration,
precipitation, and other separation methods.
 17: Skin and Eye Infections
· Epidermis: The epidermis is the outermost region of the
skin that is indirect contact with the outside world. It
consists of 5 distinct layers of cells, each with its own
structural characteristics.
· Dermis: The dermis region of the skin occurs
immediately deep to the epidermis and contains two layers.
The papillary region has ridges called papillae that are the
origns of finger prints. The reticular layer is under the
papillary layer.
· Hypodermis: The hypodermis lays deep to the dermis and
is not part of the skin.
· Layers of the Epidermis: The five layers of the epidermis
are: Stratum Corneum, Stratum Lucidum, Stratum
Granulosum, Stratum Spinosum, Stratum Basale
· Sebacceous Gland: The sebaceous glands are clustered
at around the stalk of the hair and secrete sebum that
waterproofs and protects the skin and hair.
· Sweat Gland: The sweat glands secrete sweat that cools
the body when it evaporates.
· Eye compartments: The eye has an anterior and
posterior segment. The anterior segmet is divided into
anterior and posterior compartments by the lens. Aqueous
humor flows from the posterior compartment to the
anterior compartment.
· Cornea: The outermost clear layer of the eye that provides
a significant portion of the optical power.
· Retina: A thin layer of cells lining the deep surface of the
globe that absorb photons and generate neural signals.
· Canal of Schleme: The very important opening in the
anterior chamber that drains aqueous humor produced in
the posterior chamber. Closure of this canal cause
blindness. (Glaucoma is very serious !!!)
· Iris: Segement of visible colored tissue containing muscles
that control the amount of light entering the eye.
· Pupil: Open space of the iris through which light passes.
· Lens: Biconcave structure that works with the cornea to
focus light on the retina.
Skin Structure
Eye Structure
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18: Nervous System Infections
· CNS: Central Nervous System includes the brain and spinal
cord surrounded by three layers of meninges: dura mater
(outermost), arachnoid mater and pia mater.
· PNS: The Peripheral nervous system is composed of cranial
nerves and spinal nerves. A plexus is a bundle of branching
nerves.
· Subarachnoid space: Is filled with cerebrospinal fluid
(CSF) which functions as a shock absorber and supplies
nutrients, oxygen and removes wastes.
· Petechiae: Small hemorrhages of blood vessels in the skin.
· Meningitis: Can be caused by a variety of organisms. And
involves the inflammation and cell death of the meninges.
Symptoms include fever, headache, sleepiness,
disorientation sometimes confusion and neuromuscular
complications.
· Neurons: one of two basic types of cells in the nervous
system. Neuron transmits electrical information from the
CNS to the body or from the body to the CNS. Information
is transmitted via the use of neurotransmitters.
· Neuroglia: One of two basic types of cells in the nervous
system. It acts as a supportive cell acts to insulate, give
nutrition and phagocytize microbes.
· Virulence Factors: Enzymes, toxins, cell structures that
affect the relative ability of a pathogen to infect, evade
destruction or detection and cause disease.
· Pathogenicity: A microbe’s ability to cause disease.
· Epidemiology: Study of the occurrence, distribution and
spread of diseases.
· Arboviruses: Enveloped, positive ssRNA viruses that are
transmitted by arthropods.
· Encephalitis: Is an inflammation of the brain.
· Zoonosis: Diseases spread from an animal host to
humans.
Meninges Structure & Function
Meninges: is a system of membranes that cover and
surround the central nervous system.
· Meninges are made up of three layers: dura mater,
arachnoid mater and the pia mater.
· Dura mater: is the strong and inflexible outermost layer of
the meninges tissue system. It is most close to the bone of
the skull and spinal column.
· Arachnoid mater: is between the two other meninges.
· Subarachnoid space: is a spider web like area between
the arachnoid and the pia mater. It is attached to the inside
of the dura and extends down to the pia mater.
Cerebrospinal fluid flows within the subarachnoid space.
· Pia mater: is a delicate innermost layer of the meninges.
It covers the brain all the way into the fissures.
Central Nervous System Structure
CNS includes the Brain
and spinal Cord.
Entire nervous system is made up of two basic types of
cells: neuroglia which are supportive cells and neurons
which carry signals as electrical signals to and from the
CNS.
 19: Cardiovascular, Lymphatic 20: Respiratory System infections
and Systemic Infections
Structures of the Respiratory System

Pneumococcal Pneumonia

· Main arteries are vessels that carry blood away from the · Pneumococci sometimes inhaled into the lungs from the
heart. pharynx.
· Pulmonary arteries carry it to the lungs and the aorta to · Phosphorylcholine triggers endocytosis the bacterium is
the body. Arteries connect to veins via capillaries. Veins protected by its unique capsule.
carry blood back to the heart. The major veins are: · This allows the bacteria to live in the lung cells eventually
pulmonary veins which carry blood from the lungs to the killing them.
heart, superior vena cava head neck and arms to heart and · The bacteria multiply in the alveoli damaging them and
inferior vena cava from the rest of the body to the heart. allowing erythrocytes and leukocytes and blood plasma to
· Blood is made up of serum, which is the liquid, and enter.
erythrocytes and platelets. When clotting proteins are · With this added fluid in the alveoli the lung is losses ability
taken out from serum the plasma remains. to transfer oxygen to the blood this causes the pneumonia.
· The atria and ventricles of heart are separated by valves
which prevent backflow of blood. Tuberculosis
· The wall of the heart is made up of an outer, fibrous
pericardium, muscular myocardium and inner endocardium.
· Blood flows in this sequence: venae cavae, right atrium,
atrioventricular valve, right ventricle, pulmonary semilunar
valve, pulmonary arteries, lungs, pulmonary veins, left
atrium, left atrioventricular valve, left ventricle, aortic
semilunar valve, aorta, arteries, capillaries, veins, venae
cavae.
Bacterial Cardiovascular and Systemic
Disease
· Septicemia is the presence of pathogens in the blood.
Lymphangitis is when lymphatic vessels become inflamed
due to septicemia. Bacterial septicemia or bacteremia is
the presence of relatively harmless bacteria in the blood.
Sometimes physicians use bacteremia and septicemia
interchangeably.
· Toxemia or blood poisoning is when bacteria at a specific
location releases toxins and can have systemic effects.
Living microbes release exotoxins which can disrupt or kill
cells of living tissue. Endotoxin is the lipid A part of
lipopolysaccharides, and is released from dying Gram
negative bacteria. It can trigger disseminated intravascular Tubercles: Small, hard lumps that are formed by the immune
coagulation, shock, inflammation, diarrhea, hemorrhaging system encasing the diseased cells. Collagen fibers enclose
and other advanced signs of septic shock. the lung cells. Infected cells in the center of the tubercle die
· Bacterial septicemia can trigger Petechiae and and release more bacteria. This results in caseous necrosis
osteomyelitis. which gives the lung a cheese like consistency.
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opportunists
 21: Digestive system Infections
· Gastrointestinal tract: A mucus lined tube extending
from the mouth to the anus. Includes the: mouth,
esophagus, stomach, small intestine, large intestine,
rectum and anus.
· Accessory digestive organs: Grind food or inject
digestive secretions. Include the: tongue, teeth, liver,
gallbladder and pancreas.
· Peritoneum: The membrane that covers and surrounds
most of the organs of the GI tract.
· Intestinal peristalsis: Is a series of coordinated
contractions by the smooth muscles of the intestine that
move undigested material into the large intestine.
· Gingivitis: inflammation of the gums it is a form of
periodontal disease.
· Caries: Second only to the common cold in the frequency
of this bacteria caused affliction. They usually look like
holes or pits in the teeth.
· Microbial antagonism: Microbiota that whose presence
prevents other bacteria from growing in the same place.
An example is in the intestine where the presence of
normal microbes protects the body from pathogens by out
competing them.
· Prophage: A virus that infects bacteria and can insert its
genome into the host’s chromosome or exist as a plasmid.
The prophage can upon proper stimulus begin replication
and production of virions.
· Shigatoxin: A toxin that binds specific target cells and
destroys the ability of ribosomes to synthesize proteins.
· Enteropathic bacteria: “Entero” refers to the intestine
(or gut). In naming bacteria that inhabit or cause disease
of the gut the naming conventions: enterohemorrhagic
bacteria cause bleeding in or of the intestine.
· Dysentery: infectious disease of the colon. Symptoms
include bloody, mucus-filled diarrhea and loss of fluids from
the body.
Digestive System
·
· The digestive system is divided into two segments.
Gastrointestinal Tract (GI) and Accessory Digestive Organs.
In this schematic the GI organs are in the blue the other in
green. GI tract is lined with a peritoneum. The Accessory
Organs are primary defined by function which is to grind
nutrients or inject digestive secretions like bile, salivary
amylase and others to help in the breakdown of food.
Bacterial Diseases of the Mouth
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22: Urogenital and
Sexually Transmitted Disease
· Kidney: The renal arteries and veins supply and drain blood
from the kidney respectively. The urine is produced in the
cortex, medulla, renal column, and pyramid. The functional
unit of the kidney that produces urine is called the nephron.
· Nephron: Within the Glomerular capsule the cellular
compnents of the blood are separated from the non-cellular
components of the blood, most of which are returned to the
blood. Besides removing waste, the nephrons help regulate
blood pressure and ion concentrations within the blood.
· Ureter: The ureter is a tube that drains the urine from the
kidney to the bladder.
· Bladder: Urine collects in the until 300 ml accumulates.
Upon mitriculation, the sphincters relax, the detrusor muscle
contracts, and urine streams through the internal urethral
orifice, prostate gland, through the external urethral orifice
and to ultimately out of the penile urethra.
· Prostate: Trouble with the prostate gland often involves
swelling. Swelling causes small amounts of urine to be
retained, which leads to further inflammation.
· Urethra: Only the upper portion of the urinary tract is
sterile; the urethra has a normal complement of microbiota
that prevent the colonization by harmful organisms.
(Lactobacillus, Staphylococcus, Streptococcus)
· Vagina: The vagina leads from outside the body to the
cervix. At times other than ovulation the vagina has an
acidic pH created by resident lactobacilli that feed on
glycogen secreted by the walls of the vagina. This
discourages infections.
· Cervix: The cervix leads from the vagina to the uterus, and
at times other than ovulation, is occluded by a plug of
mucus that prevent infections from entering the body cavity.
· Uterus: The uterus is the site of implantation of the
fertilized egg.
· Uterine Tubes: The fallopian tubes lead from ovaries to the
uterus. Note that the fallopian tubes are NOT connected to
the ovaries but rather are open to the entire body cavity. It
is therefore possible for an infection to enter abdomen cavity
directly from the vagina.
Reproductive System Structure
 23: Microbiology and the Environment
· Ecosystems: community of organisms and their physical &
chemical environment that functions as an ecological unit.
· Primary producers: The organisms which can accumulate
organic matter.
· Consumers: organisms that depend upon the organic
matter synthesized by the primary producers
· Mineralization: the process of organic matter
decomposition that releases simpler, inorganic compounds.
· Food web: a network of interlinked food chains
· Biogeochemical cycling: the recycling of essential elements
on earth by both biological and chemical processes.
· Nitrification: the aerobic process of ammonium ion
oxidation to nitrite and subsequent nitrite oxidation to
nitrate
· Denitrification:the process in which nitrate is used as an
oxidant by certain heterotrophs producing nitrogen gas and
nitrous oxide
Carbon Cycle
Nitrogen Cycle
Phosphorus Cycle
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24: Microbiology and Industry
· Industry: An industry is generally any grouping of
businesses that share a common method of generating
profits.
· Food microbiology: The field of science which deals with
microbes useful to man in the production of food or
bewerages.e.g.yeast is use din the leavening of bread.
· Biopesticides: microbes (viruses bacteria, and fungi) which
can be used for management of insect and nematodal pests
· Mycorhiza: The symbiotic association of the mycelium of a
fungus with the roots of certain plants such as conifers,
beeches or orchids
· Probiotics: live microorganisms administered in adequate
amounts which confer a beneficial health effect on the host".
Most probiotics are bacteria, which are small, single-celled
organisms. One yeast - Saccharomyces boulardii - also has
been evaluated as a probiotic.
· Bioremediation: to use biological organisms to solve an
environmental problem such as contaminated soil or
groundwater.
Microbes in Food
· In the home and in industry, microbes are used in the
production of fermented foods.
· Yeasts are used in the manufacture of beer and wine and for
the leavening of breads,
· Lactic acid bacteria are used to make yogurt, cheese, sour
cream, buttermilk and other fermented milk products.
· Vinegars are acetic acid fermentation.
· Other fermented foods include soy sauce, sauerkraut, dill
pickles, olives, salami, cocoa and black teas.
Vaccines
· Vaccines are substances derived from microorganisms used
to immunize against disease.
· The microbes that are the cause of infectious disease are
usually the ultimate source of vaccines. Thus, a version of
the diphtheria toxin (called toxoid) is used to immunize
against diphtheria, and parts of B. pertussis cells are used to
vaccinate against pertussis (whooping cough).
· The use of vaccines such as smallpox, polio, diphtheria,
tetanus and whooping cough has led to virtual elimination of
these diseases in regions of the world where the vaccines
have been deployed.
Bioremediation
· Micro organisms are responsible for getting rid of the waste
generated by industry and households. They detoxify acid
mine drainage and other toxins that we dump into the soil
and water
· Micro organisms help in waste water treatment
Microbes in Medicine
· Antibiotics are substances produced by microorganisms that
kill or inhibit other microbes which are used in the treatment
of infectious disease.
· Antibiotics are produced in nature by molds such as
Penicillium and bacteria such as Streptomyces and Bacillus
Microbes in Recovery of Oils
· Microbes like pseudomonas have been manipulated to
harbour plasmids containing genes which can degrade
hydrocarbons.
· Some microbes have the inherent capacity to degrade
hydrocarbons.
· Such organisms can degrade wide variety of aromatic,
polycyclic and aliphatic compounds in most petroleums.Thus
oil spill degradations work better.
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