BIO 003

Dr. Bamidele T. Odumosu

 Microbial Taxonomy
• Taxonomy can be defined as the biological
classification of living organisms into groups.
• It is applied to all-living entities taxonomy provides
a consistent means to classify name and identify
organisms.
• The common language that taxonomy provides
minimizes the confusion about names and allows
attention to center on more important scientific
issues and phenomena.
• Taxonomy consist of three separate
but interrelated parts namely;
Classification,
Nomenclature
Identification.
• Classification is the organization of organisms that share similar
morphologic, physiologic and genetic traits into specific groups or taxa.
The classification of microbes is based on how they look and what they
can do.

• Nomenclature is the assignment of names to taxa or taxonomic groups.

It is the naming of microorganisms according to established rules and
guidelines provide the accepted labels by which organisms are
universally recognized.
• Identification is the determination of taxon to which an isolate belongs.

• Identification is the practical use of classification criteria to distinguish

certain organisms from others, to verify the authenticity or utility of a
strain or a particular reaction, or to isolate and identify the organism
that causes a disease.
Classification Systems
• Classification system comprises of two
major parts.

• Natural and Phenetic (phenotypic)

classification
 Classification Systems
• Natural classification- it was first developed by
Linnaeus in 18th century on anatomical characteristic.
This is the classification of microorganisms into
groups based on members similarities which reflects
their biological nature.

• This approach does not necessarily provide

information on evolutionary relatedness in microbes
 Classification Systems
• Phenetic Classification – This system groups
microorganisms together based on overall similarities.
It is not dependent of phylogenetical analysis.

• For example motility and flagella are always

associated in particular organisms, it is reasonable to
suppose that flagella is involved in some types of
motility.
 Importance of taxonomy
• It allows scientists to organize huge amounts of
knowledge
• It allows scientists to make predictions and frame
hypotheses about organisms
• It places organisms into meaningful, useful groups,
with precise names, thus facilitating scientific
communication
• It is essential for accurate identification of organisms
Levels of classification.
• A group or “level” of classification
• Hierarchical; broad divisions are divided up
into smaller divisions:
– Kingdom (Not used by most bacteriologists)
– Phylum (Called “Division” by botanists)
– Class
– Order
– Family
– Genus (plural: Genera)
– Species (Both singular & plural)
Binomial Nomenclature of Microorganisms

• Microorganism names originate from four

different sources
• Descriptive – For example
• Staphylococcus aureus (grape-like cluster
of spheres, golden in color),
• Streptococcus viridans (chains of spheres,
green in colony color),
• Helicobacter pylori (spiral shaped rod at
the entrance to the duodenum)
 Binomial Nomenclature of Microorganisms
• Scientist’s names –
• Escherichia coli (Theodor Esherich),
• Erlichia (Paul Erlich),
• Nessieria (Albert Neisser),
• Listeria (Joseph Lister),
• Pasturella (Louis Pasteur ),
• Yersinia (AlexandreYersin),
• Bartonella (Alberto Barton) ,
• Morganella (H. de R. Morgan),
• Edwardsiella (P. R. Edwards
• Geographic places –
• Legionella longbeachiae (Long Beach, California),

• Pasturella tularensis (Tulare County, California),

• Pseudomonas fairmontensis (Fairmount Park,

Pennsylvania),

• Mycobacterium genavense (Geneva, Switzerland),

• Blastomyces brasiliensis (Brazil), Providencia spp.

(Brown University, Providence, RI)
• Organizations –
• Legionella (American Legion),

• Afipia felis (Air Force Institute of Pathology),

• Cedecea spp . (Centers for Disease Control),

• Bilophila wadsworthia (VA Wadsworth Medical Center

in Los Angeles)
 Rules of Nomenclature
• Use Binary Names - Binary names (invented by
Linnaeus), consisting of a generic name and a species
epithet (e.g., Escherichia coli ), must be used for all
microorganisms. Names of categories at or above the
genus level may be used alone, but species and
subspecies names
• (species names) may not be used. In other
words...never use a species name alone.
 Rules of Nomenclature
1. When to Capitalize
– The genus name (and above) is always capitalized, the
species name is never capitalized, e.g. Bacillus anthracis
2. When to Italicize - Names of all taxa (kingdoms,
phyla, classes, orders, families, genera, species, and
subspecies) are printed in italics and should be underlined
if handwritten
• E.g for typical specie
Bacillus anthracis or Bacillus anthracis
For family e.g Enterobacteriaceae, Pseudomonadaceae
3. When to use Initials
A specific epithet must be preceded by a generic name, written
out in full the first time it is used in a paper. Thereafter, the
generic name should be abbreviated to the initial capital letter
(e.g., E. coli ),
4. Common Names - Vernacular (common) names should be in
lowercase roman type, non-italic (e.g., streptococcus, brucella).
However when referring to the actual genus name (or above)
always capitalize and italicize.
5. Subspecies and Serovars
• For Salmonella , genus, species, and subspecies names should be

rendered in standard form: Salmonella enterica at first use,

S. enterica thereafter; Salmonella enterica subspecie. arizonae at
first use, S. enterica subsp. Arizonae thereafter.

6. Abbreviations for Species – use “sp.” for a particular species,

“spp.” for several species (“spp” stands for “species plural”). These
abbreviations are not italicized; e.g. Clostridium sp. or Clostridium
spp
 Defining Prokaryotic Species
• The basic taxonomic group in microbial
taxonomy is the species.
• Cannot use definition based on
interbreeding because procaryotes are
asexual.
• A prokaryotic species is collection of
strains that share many stable properties
and differ significantly from other groups
of strains
• Species as a collection of organisms that
share the same gene sequences that are
required for their cellular development also
known as core housekeeping genes
INTRODUCTION TO
MICROORGANISM
INTRODUCTION TO MICROORGANISM

• Bacteria are microscopic organisms that cannot be seen

with our naked eyes.

• They are found almost everywhere living freely or as a

pathogen

Pathogen are disease causing organisms

INTRODUCTION TO MICROORGANISM

• Bacteria appears in different shapes and sizes hence a

means of differentiating them into different categories
and families

• Some bacteria are motile with the use of flagella while

some are non-motile.

• They also appears in different shapes such as cocci, rod,

helical or curved shaped
 CLASSIFICATION OF BACTERIA (Shape)
• Bacillus (rod-shaped)
• Coccus (spherical)
• Spiral
Spirillum
Vibrio
Spirochete
23
CLASSIFICATION OF BACTERIA (Shape)
• Bacillus/Rod shaped bacteria:
Escherichia coli, Klebsiella
pneumonia, Pseudomonas
aeruginosa, lactobacillus spp

• Coccus/spherical shaped :
Staphylococcus aureus,
Micrococcus spp, Streptococcus
pyogenes, Enterococcus faecalis

• Spirila/Spiral shaped:

Vibrio cholera, Helicobacter pylori,

Campylobacter jejuni
CLASSIFICATION OF BACTERIA (Motility)
• Classification based on motility is based on certain
bacteria that has the ability to move with the use
of an appendage called Flagella.

• Flagella is the main structure for motility in

bacteria.

• There are different types of flagella available in

bacteria for motility
 Flagella
• Cytoplasmic appendages protruding
through cell wall.

• Thread or hair like structure- protein

flagellin

• Organ of locomotion

• All motile bacteria except spirochaetes

Arrangements/Types
Bacterial Cell Structure
Laboratory Demonstration of flagella:
• Electron microscopy

• Silver impregnation methods

• Dark field microscopy

• Special stains e.g Leifsons stain

( Leifson stain makes use of Potassium alum,
mercuric chloride, tannic acid)
GENERAL CHARACTERISTIC OF BACTERIA

• Bacteria are prokaryotic unicellular

microorganisms that are microscopic in
nature.
• A typical bacteria size is about 2-
8micrometer (µm) in length and 0.2-2 µm
in width
• They are found in abundant population
almost everywhere. Some bacteria are
harmful while some are beneficial to man.
 General Characteristic of Bacteria
• They are unicellular
• They lack defined organelles e.g golgi bodies
• They are microscopic
• Their cell wall is made up of peptidoglycan and
lipopolysaccharides
• They lack a well defined nucleus
• Their ribosomes is 70S type and is scattered in the
cytoplasmic matrix
• Most are heterotrophic
• True sexual reproduction is lacking
• The common method of multiplication is binary fission
• Motile bacteria possess one or more flagella
• The plasma membrane is invaginated to form mesosomes
 Classification Systems
• Classification of bacteria is to serves a variety of
different functions that can allow grouping of bacteria
into many different typing schemes

• Accurate and definitive microorganism identification,

including bacterial identification and pathogen
detection, is essential for correct disease diagnosis,
treatment of infection and trace-back of disease
outbreaks associated with microbial infections
• At present the typing schemes used by clinicians and clinical

microbiologists rely on phenotypic (physical appearances)

typing schemes.

• These schemes utilize the bacterial morphology and staining

properties of the organism, as well as O2 growth

requirements of the species combined with a variety of

biochemical tests. For clinicians, the environmental reservoir

of the organism, the vectors and means of transmission of the

pathogen are also of great importance.

Phenotypic classification

• Gram stain

• Bacterial morphology

• Growth Requirements

• Biochemical reactions

• Serologic systems

• Environmental Reservoirs.
FUNGI
• Fungi are large, diverse, and widespread
group of microorganisms, they are mostly
microscopic while others are macroscopic.
• Common types of fungi includes
Moulds
Mushrooms
Yeast
• They are either unicellular or multicellular.
• They eukaryotic and belong to the kingdom
Fungi
• multicellular, typically apically-elongating filamentous
organisms (the growth form of the great majority), in
which the filaments are called hyphae and have cell
walls composed of chitin and I-glucans.

• The yeasts can be individually microscopic in size, but

filamentous hyphae make up the commonly
encountered mould mycelium, as well as mildews,
rusts, smuts, cup fungi, mushrooms, puffballs, truffles
and morels.
 Moulds
Mould is a type of fungus that grows in multicellular
filaments called hyphae. These tubular branches have
multiple, genetically identical nuclei, yet form a
single organism, known as a colony.
They are typically found in damp, dark or steam-
filled areas
Reproduce through small spores, which can be
either sexual or asexual.
• Mould has a fuzzy appearance and can be an orange, green,
black, brown, pink or purple in color. Can be found in several
shapes.

• some molds are used in food production, for example,

Penicillium is used in the production of cheese and drug
formation e.g penicillin antibiotics, Neurospora in the
production of oncom, which is made from the by-product of
tofu.

• They can cause allergic reactions and respiratory problems

 Yeast
• Yeast is a type of fungus that grows as a single cell.
• Very common. Can be found on fruit and berries, in the
stomachs of mammals and on skin, among other places.
• The appear White and thready. Usually oval in shape.
• They are useful in Ethanol production, baking, vitamin
supplements, study of cell cycle.
• They can also cause infection in individuals with
compromised immune systems
• Most reproduce asexually through mitosis. Most common
form called “budding.”
mushrooms
• A mushroom (or toadstool) is the
fleshy, spore-bearing fruiting body of
a fungus, typically produced above
ground on soil or on its food source.
• Many species of mushrooms seemingly
appear overnight, growing or expanding
rapidly
 Types of Fungi
• Macroscopic fungi: They consist of
mushrooms and gill fungi
• Example Moulds

• Microscopic Fungi: They include

moulds and yeast
• Example yeast
 General Characteristic
• All are eukaryotic
• Most are filamentous
• Some are unicellular (yeast) while some are
multicellular
• Their cell wall is composed primarily of chitin
and glucans although the walls of some
species contain celluose
• Many reproduce both asesxually and
sexually
• Their nuclei are typically haploid and hyphal
compartments are often multinucleate
 General Characteristic
• All are achlorophyllous (they lack
chlorophyll pigment and are incapable of
photosynthesis)
• All are chemoheterotrophic (chemo-
organotrophic) meaning that they utilize
pre-existing organic sources of carbon in
their environment
 General Characteristic
• They possess characteristic range of storage
compounds e.g. tehalose, glycogen, sugar alcohols
and lipids
• They all produce spores which is the mode of
dispersal of these organisms.
• They may be free living or may form intimate
relationship with other organisms (parasitic or
mutualistic) or simply saprophytic
 Classification of fungi
• Fungi are classified according to their structure and
method of reproduction. Presently, then, the true
fungi which make up this monophyletic clade called
kingdom Fungi comprises the seven phyla:
• Chytridiomycota,
• Blastocladiomycota,
• Neocallimastigomycota,
• Microsporidia,
• Glomeromycota,
• Ascomycota and
• Basidiomycota.
 BASIDIOMYCOTA

Puffballs

Mushrooms

Shelf Fungi

Stinkhorns
Puffballs
Ascomycota
The phylum is commonly called the "sac

fungi“ because during sexual reproduction,

their sexual spores, the ascospores are

borne in a sac-like cell called an ascus.

They are the one of the largest phylum of

Fungi, with over 64,000 species.

Ascomycota
•Cup fungi
• Morels
• Truffles
• Yeast
• mildew
 Imperfect fungi (Deuteromycetes)
• Deuteromycetes (also known as Fungi Imperfecti because they
lacked a sexual cycle)

• Deuteromycota, are fungi which do not fit into the commonly

established taxonomic classifications of fungi or morphological
characteristics of sexual structures because their sexual form of
reproduction has never been observed; hence the name
"imperfect fungi." Only their asexual form of reproduction is
known, meaning that this group of fungi produces their spores
asexually, in the process called sporogenesis.
Deuteromycetes
 Protozoans
Giardia Amoeba
 PROTOZOA
• Protozoan are unicellular eukaryotes.
• Most species are free living, but all higher animals are
infected with one or more species of protozoa. Infections
range from asymptomatic to life threatening, depending
on the species and strain of the parasite and the
resistance of the host.

• Protozoa constitute a large group of about 65,000 species

 MORPHOLOGY
• Protozoa resembles animal cell because they contain

major cell organelles (including Nucleus, Mitochondria)

• Their organelles are highly specialized for feeding,

reproduction and movement

• The cytoplasm of protozoa are divided into an outer layer

called Ectoplasm and an inner layer called Endoplasm

 MORPHOLOGY
• The size of Protozoa is range between 3 to 300
micrometer.

• Few ciliate and Amoeba are larger enough to be seen

with naked eyes (they are about 4 to 5 mm).

• Except Sporozoates, all types of protozoa are motile either

through Flagella, cilia or Pseudopodia

• Have Eyespot that can detect change in light Respond to

light & learn by trial & error
Classification of Protozoa
Protozoa are classified on the basis of their
motility and method of reproduction
They are classified into Four main types
• Flagellates
• Ciliates
• Sarcodina
• Sporozoates
 Flagellates
Flagellates move by help of Flagella (a tail-like
structure ). The movement is whip like .

Example of Flagellates are.

• Trypanosoma, Leishmenia (blood pathogen) .

Giardia (intestinal parasite) .

Trichomonas (reproductive tract pathogen)

 Ciliates
• Ciliates protozoa movement is by cilia

• Some protozoa have special kind of cilia for

feeding and attachment.

• Most are harmless. Only one species

Balantidium coli is pathogenic for human,
causes a rare and severe form of Dysentery.
Cilia
Movement Using Flagella & Cilia
 Sarcodina
• Major loco-motor organelles in Sarcodina is
pseudopodia (Pseudo means false, podia means
Foot)

• Common example of Sarcodina is Amoeba

• Most species are harmless

• Entaemoba is a parasitic for human, causes

intestinal disease
 Sporozoates
• Sporozoates are the
only non-motile form
of protozoa.
• Sporozoates have
well developed
sexual and asexual
stages
• Entire group is
parasitic in nature
and are harmful
 Sporozoates
• Some common
examples of
Sporozoates and their
infections are
• Plasmodium (causative
agent of Malaria,
causes 100 to 300
million infection world
wide)
• Toxoplasma Gondii
(causes Toxoplasmosis)
Reproduction in Protozoa
• Protozoa can reproduce their off spring by
both Sexual and Asexual methods
• Asexual methods of reproduction are:
Budding
 Binary Fission
Schizogony or Multiple Fission
• Sexual Methods
 Conjugation
 Gametogony
Nutrition in Protozoa
• The following points highlight the top four
modes of nutrition in protozoa.
• The modes are:
• 1. Holozoic
• 2. Holophytic
• 3. Saprophytic
• 4. Parasitic.
 Holozoic method of feeding
• Circumvallation: Encircling the active prey
by pseudopodia. Example: Amoeba proteus
• Invagination: The prey is immotile, food cup
is formed and cytoplasm flows around to
engulf it. Example: Amoeba dubia
• Import: The prey is first killed by toxin and
taken in the cytoplasm by invagination.
Example: Amoeba
• Circumfluence: Food like algae is simply
drawn into the body e.g Amoeba
 HOLOPHYTIC
• (Holos = Whole + Phyton = Plant Origin)
Or Autotrophic (Photosynthesis):
• The chlorophyll-bearing flagellates or
phytomastigophores synthesize carbohydrates
from raw materials, water and carbon dioxide
using radiant energy from the sun. Example:
Euglena.
 SAPROPHYTIC
(Sapros = Rotten) or Saprozoic:
• Some protozoan’s cause disintegration of food
materials into smaller molecules outside their
body and subsist entirely on the dissolved
organic matters. The monosaccharide’s, amino
acids and other molecules are absorbed
through the body surface. Examples: Entam-
oeba histolytica, Gratium (a dinoflagellate),
 PARASITIC
• Parasitic protozoan’s are total or partial
parasites in different organs of the hosts and
obtain their food fully or partially from the
organs. The parasites either rob the food of its
host (Opalina, Gregarina, Nyctotherus, etc.) or
feed upon the tissues of the hosts (Plasmodium,
Entamoeba, etc.).
Disease Causative agent
MALARIA Plasmodium, (P. Falciparum, P.
Oval,P. Vivax, P.malariae)

Giardiasis (diarrhea) Giardia intestinalis

Amoebic Dysentery Entamoeba histolytica

Toxoplasmosis (immune Toxoplasma gondii

deficiency )
Cryptosporidiosis Cryptosporidia

Sleeping sickness Trypanosoma

Leishmmaniasis (kala-azar) Leishmania

VIRUS
 VIRUSES
• Viruses are small infectious agents that are
capable of replication only within a living cells
of other organisms such as bacteria, fungi or
human cells

• A virus can infect any living cell, when it is not

infecting any cells it becomes dormant hence a
virus can neither be classified as living or dead
cells because of this characteristic.
General characteristic of viruses
Viruses contain only a single type of nucleic acid
either DNA or RNA.

Viruses are host specific, they infect only a single

species and definite cells of the host organisms.

Viruses are effective in very small doses. They are

highly resistant to germicides, antibiotics and
extremes of physical conditions (pH, pressure,
salinity).
 Biological position of viruses
• Viruses lack a cytoplasmic membrane and
they do not have the basic component of a
cell. They can only replicate inside the
host cell. Outside the host cell, this makes
them to be non-living. Therefore, viruses
show characters of both living and non-
living.
Non-living Characters of Viruses:
• (a) They can be crystallized.

• (b) Outside the cell, they behave like inert

chemicals.

• (c) They do not show growth, development,

nutrition, reproduction, etc.

• (d) They can be precipitated

Living characters of viruses:
• (a) They multiply within host cells.

• (b) They possess genetic material, either DNA

or RNA.

• (c) There are definite races or strains.

• (d) They undergo mutations.

Structure of Virus.
They have simple structure. Virus is made up of nucleic
acid which is surrounded by a protein coat called
CAPSID.
A viral nucleic acid is either composed of DNA or RNA.
Virus capsid is made up of many identical protein sub
units called CAPSOMERE .
This protein coat is composed of a number of individual
protein molecules, which are arranged in a precise and
highly repetitive pattern around the nucleic acid
Structure of a virus
Viral structure
 CLASSIFICATION OF VIRUS
• Virus are classified based on the following
1. Type and structure of their nucleic acids (DNA or
RNA)
2. Methods of replication
3. Host range
4. Chemical and physical characteristics
They are not qualified for the normal taxonomic
classification for other living organisms because of
their unique nature that is different from other living
things
 CLASSIFICATION OF VIRUS
1. Taxonomic groups – family, subfamily,
genus and species
2. The names of virus family (family) are
italicized
End in Latin suffix – viridae
3. The genera (genus) end in the suffix –
virus
4. The species - English common name
Bacteriophage
• A bacteriophage , also known informally as
a phage
• Phage is a virus that infects and replicates
within a bacterium.
• Like other types of viruses, bacteriophages
vary a lot in their shape and genetic material
• Phage genetic material can consist of either
DNA or RNA, and can contain as few as four
genes or as many as several hundred
 Morphology
• They are called phages with designation (T2,
T4, T6 etc):
• They are Tadpole shaped
• Hexagonal head, cylindrical tail
• Head: contains nucleic acid (dsDNA or RNA)
surrounded by protein coat or capsid; 28-100 nm
size
• Tail: hollow core, surrounded by contractile
sheath and terminal base plate.
Spike: is used in attachment to the host
(bacterium)
BACTERIOPHAGE
Bacteriophage infections
• Bacteriophages, just like other viruses, must
infect a host cell in order to reproduce.

• The steps that make up the infection process

are collectively called the lifecycle of the phage

• They have types of lifecycle

• Lytic and Lysogenic

 LYTIC CYCLE

Intracellular multiplication of phage

• In the lytic cycle, a phage acts like a typical

virus: it hijacks its host cell and uses the cell's
resources to make lots of new phages, causing
the cell to lyse(burst) and die in the process.
 Temperate or Lysogenic cycle:

• The lysogenic cycle allows a phage to reproduce

without killing its host. Instead, it recombines
with a particular region of the bacterial
chromosome. This causes the phage DNA to be
integrated into the chromosome
 LYTIC CYCLE
• Replication can be considered under following
stages
• Adsorption
• Penetration
• Synthesis of phage components
• Assembly
• Maturation
• Release of progeny
 Adsorption (Life cycle contd)
• Phage particles come into contact with bacterial

cells by random collision

• Phage attaches to surface of susceptible

bacterium by its tail

• Adsorption: a specific process

 Adsorption (Life cycle contd)
• Depends on presence of complementary

chemical groups

• Rapid process; completed in minutes

• Bacterial receptor sites can be situated anywhere

• Transfection: experimental injection of phage

DNA
 Penetration (Life cycle contd)
Phage nucleic acid penetrates into bacterial cell

• Resembles injection through syringe

• Penetration facilitated by lysozyme producing

hole in bacterial cell wall

• After penetration, empty head and tail of phage:

shell or ghost on bacterial cell

• Lysis from without: Bacterial lysis without viral

multiplication
 Synthesis of phage components
(Life cycle contd)
• Early proteins: enzymes necessary for
building complex molecules

• Late proteins: including protein subunits

of phage head and tail

• Synthesis of bacterial protein, DNA and

RNA ceases
 Assembly, Maturation & Release
(Life cycle contd)
• Phage DNA, head protein and tail protein:
synthesised separately

• DNA condensed and ‘packaged’ into head •

Finally tail structures are added

• This assembly of phage components into

mature infective phage particle is known as
Maturation
 Assembly, Maturation & Release
(Life cycle contd)
• Bacterial cell wall weakens and assumes

spherical shape

• Phage enzymes cause bacterial cell wall to burst

or lyse • Daughter phages released

LYSOGENIC CYCLE
• The lysogenic cycle is When a phage infect a bacterial cell
and the phages only lyse a small fraction of the cells they
infect. Sometimes the phage DNA is incorporated into the
host’s chromosome and replicates along with the host
DNA. Once the viral DNA is incorporated into the host
genome, the viral DNA is called a prophage. During the
lysogenic state, the information contained in the
viral DNA is not expressed. But the prophage is copied
like the rest of the DNA and is passed on to every daughter
cell
 Viroid and Prions
• Viroid's are small non-protein‐coding RNAs that
infect, replicate and induce disease in higher plants

• Viroid's differ from viruses in fundamental aspects

that include structure, function and evolutionary
origin.

• Viroid's are not usually consider a form of life. Like

a virus, the viroid invades a cell, and takes over its
reproductive mechanisms
 Prions
• Prions are unique infectious agent that contains no
nucleic acid
• They contain protein in a misfolded form.
• If a prion enters a healthy organism, it causes an
existing protein to become mis-folded types
thereby converting them to prion form
• These newly formed prions can then go on to
convert more proteins themselves
 Prions diseases
• Encephalopathies in a variety of mammals

• Bovine spongiform encephalopathy (BSE, also known

as "mad cow disease") in cattle

• Creutzfeldt-Jakob Disease (CJD) in humans,

• Fatal Familial Insomnia

• Kuru

• All known prion diseases affect the structure of the brain

or other neural tissue and all are currently untreatable
and universally fatal
ALGAE
 ALGAE
• Algae are a diverse group of aquatic organisms that have the
ability to conduct photosynthesis "algae" includes prokaryotic
organisms — cyanobacteria, also known as blue-green algae
— as well as eukaryotic organisms

• They are simple plants that can range from the microscopic
(microalgae), to large seaweeds (macro-algae), such as giant
kelp more than one hundred feet in length. They lack true
roots, stems and leaves, and a vascular system to circulate
water and nutrients throughout their bodies many algae are
unicellular
 ALGAE
• Microalgae include both cyanobacteria,
(similar to bacteria, and formerly called
“blue-green algae”) as well as green, brown
and red algae. (There are more varieties of
microalgae, but these are the main ones.)
 ALGAE
• They also occur in a variety of forms and sizes. They can
exist as single, microscopic cells; they can be
macroscopic and multicellular; live in colonies; or take on
a leafy appearance as in the case of seaweeds such as
giant kelp.
• Algae are found in a range of aquatic habitats, both
freshwater and saltwater
• Algae belong to four types of Kingdoms
• Kingdom Plantae (e.g. chlorophytes a- green algae)
Kingdom Chromista (e.g. diatoms)
• Kingdom Protista (e.g. Euglenophytes)
• Kingdom Bacteria
 ALGAE
• They also occur in a variety of forms and sizes. They can
exist as single, microscopic cells; they can be
macroscopic and multicellular; live in colonies; or take on
a leafy appearance as in the case of seaweeds such as
giant kelp.
• Algae are found in a range of aquatic habitats, both
freshwater and saltwater
• Algae belong to four types of Kingdoms
• Kingdom Plantae (e.g. chlorophytes a- green algae)
Kingdom Chromista (e.g. diatoms)
• Kingdom Protista (e.g. Euglenophytes)
• Kingdom Bacteria
 REPRODUCTION
• Algae are capable of reproducing through asexual or
vegetative methods and via sexual reproduction.

• Algae asexual reproduction involves the production of a

motile spore, while vegetative methods include simple
cell division (mitosis) to produce identical offspring and
the fragmentation of a colony. Sexual reproduction
involves the union of gametes (produced individually in
each parent through meiosis).
 TYPES OF ALGAE
Diatoms
• Diatoms are a major group of microalgae, and are among
the most common types of phytoplankton. Diatoms
are unicellular, although they can form colonies in the
shape of filaments or ribbons (e.g. Fragilaria), fans
(e.g. Meridion), zigzags (e.g. Tabellaria), or stars
(e.g. Asterionella).
 DIATOMS
Diatoms are producers within the food chain. A unique
feature of diatom cells is that they are enclosed within a
cell wall made of silica (hydrated silicon dioxide) called
a frustule

Diatoms belong to a large group called the heterokonts,

including both autotrophs (e.g., golden algae, kelp)
and heterotrophs (e.g., water moulds). Individuals usually
lack flagella, but they are present in male gametes
 LICHENS
A lichen, or lichenized fungus, is actually two organisms functioning
as a single, stable unit. Lichens comprise a fungus living in a
symbiotic relationship with an alga or cyanobacterium (or both in
some instances).

Fungi are incapable of photosynthesis because they lack the green

pigment chlorophyll. On the other hand, algae and cyanobacteria
can conduct photosynthesis, similar to plants. So when a fungus
associates with an alga (usually from the green algae) or
cyanobacterium to form a lichen, it is providing itself with constant
access to a source of nourishment. Fungi often form a protective
cortex [or shell] with pigments that absorb ultraviolet light.
EXAMPLES OF LICHENS
 SEAWEEDS
Seaweeds or marine macroalgae are plant-like organisms that
generally live attached to rock or other hard substrata in
coastal areas. A number of seaweed species are edible, and
many are also of commercial importance to humans. Some are
used as fertilizers or as sources of polysaccharides

Two specific environmental requirements dominate

seaweed ecology. These are the presence of seawater (or at
least brackish water) and the presence of light sufficient to
drive photosynthesis.
 Archaea
Archaea are prokaryotic microscopic organism, they are
similar to bacteria in many respect but are different in
times of their genetic makeup. They were previously
classified as bacteria until after 1970, a new classification
that separates them from bacteria came up.

They also appear in different shapes similar to bacteria e.g.

spherical, rod, and spiral, rectangular or irregular shapes.
They are unicellular, while some exist as single cells, others
form filaments or clusters.
 Archaea are unicellular.
• As Bacteria, Archaea are mostly unicellular.
Archaeal forms
 Archaea
Their habitats includes extreme environments on the planet.
Some live near rift vents in the deep sea at temperatures well
over 100oC. Others live in hot springs or in extremely alkaline
or acid waters. They have been found thriving inside the
digestive tracts of cows, termites, and marine life where they
produce methane

They live in the anoxic muds of marshes and at the bottom of

the ocean, and even thrive in petroleum deposits deep
underground. They may be extremely abundant in
environments that are hostile to all other life forms.
EXAMPLES OF ARCHAEA

• Halophiles,

• Thermoacidophiles,

• Phyrolobus fumarii,

• Aeropyrum pernix

• Methanogen
 GENETIC
MATERIALS
 Nucleic Acids
• These are organic compounds that carry the instructions
for making all the proteins in an organism?

• They are molecules that allow organisms to transfer

genetic information from one generation to the next.
There are two types of nucleic acids: deoxyribonucleic
acid (better known as DNA) and ribonucleic acid (better
known as RNA).
 Nucleic Acids
• Nucleic acids are composed of nucleotide monomers linked
together. Nucleotides contain three parts
A Nitrogenous Base
A Five-Carbon Sugar
A Phosphate Group

Nucleotides are linked together to form polynucleotide chains.

Nucleotides are joined to one another by covalent bonds between
the phosphate of one and the sugar of another. These linkages are
called phosphodiester linkages. Phosphodiester linkages form the
sugar-phosphate backbone of both DNA and RNA.
 GENETIC INFORMATION
• What is a gene?

The gene is the functional unit

of genetic information in all life
forms including
microorganisms.
• Gene is present in all living things and are located
on the chromosome of living organism.
 NATURE OF DNA
• The genetic material of a cell or an organism refers to those
materials found in the nucleus, mitochondria and cytoplasm,
which play a fundamental role in determining the structure and
nature of cell substances, and capable of self-propagating and
variation
• The Deoxyribonucleic Acid (DNA) is the centre of genetic
information in the nucleic acid.
• The DNA carries the genetic blueprint for the cell while
Ribonucleic acid (RNA) is the intermediary molecule that
converts this blueprint into defined amino acid sequences in
protein
 Building blocks of DNA
• DNA has three types of chemical component: phosphate, a
sugar called deoxyribose, and four nitrogenous bases—
adenine, guanine, cytosine, and thymine. Two of the
bases, adenine and guanine, have a double-ring structure
characteristic of a type of chemical called a purine.

• The other two bases, cytosine and thymine, have a single-

ring structure of a type called a pyrimidine.
Each nucleotide is preferable called by the first letter of the
name of its base: A, G, C, and T
 Building blocks of DNA
• The chemical components of DNA are arranged into groups
called nucleotides, each composed of a phosphate group, a
deoxyribose sugar molecule, and any one of the four bases.

• DNA is composed of two side-by-side chains (“strands”) of

nucleotides twisted into the shape of a double helix.
 Building blocks of DNA
• In contrast to other molecule such as polysaccharides and
lipids, nucleic acids are informational macromolecules which
has proteins as its monomers.
• These protein monomers are called nucleotides consequently
DNA and RNA are called polynucleotides
• A nucleotide consist of pentose sugar, a nitrogen base and a
molecule of phosphate (PO4). The DNA contain a deoxyribose
sugar in addition to pentose sugar, nitrogen base and a
molecule of phosphate while RNA contains a ribose sugar
instead.
 Building blocks of DNA
• The nitrogen bases are either purines (adenine and
guanine) or pyrimidines (thymine, cytosine, and uracil)
which contain a single six-membered heterocyclic ring.
Guanine, adenine, and cytosine are present in both DNA
and RNA. With minor exceptions, thymine is present only
in DNA and uracil is present only in RNA
• The nitrogen bases are attached to the pentose sugar by
a glycosidic linkage between a carbon atom and a
nitrogen base. A nitrogen base attached to its sugar, but
lacking phosphate (PO4), is called a nucleoside.
Nucleotides are nucleosides that has one or more
phosphates.

• DNA is double stranded in the genome of a cell. A

genome is an organism’s complete set of DNA, including
all of its genes
• Each strand of DNA contains hundreds of thousands to

several millions of nucleotides linked together by

phosphodiester bonds. (Phosphodiester bond is

a bond between a two sugar groups and a phosphate

group; such bonds form the sugar-phosphate-sugar

backbone of DNA and RNA)

• DNA strands have specific base pairing which are
complementary to each other. Guanine (G) binds
with Cytosine (C) and Adenine (A) binds with
Thymine G + C, A + T

• That is, wherever a G is found in one strand, a C is

found in the other, and wherever a T is present in
one strand, its complementary strand has an A.
 TYPES OF RNA
• All RNA molecules are single-stranded they typically fold back
upon themselves in regions where complementary base
pairing is possible. When genes are expressed in an organism,
the information is usually stored in DNA and is transferred to
the ribonucleic acid (RNA).
Three types of RNA are involved in protein synthesis namely
1. Messenger RNA (mRNA)
2. Transfer RNA (tRNA)
3. Ribosomal RNA (rRNA)
• Messenger RNA (mRNA) is a single-stranded
molecule that carries the genetic information from
DNA to the ribosome, the protein-synthesizing
machine.

• Transfer RNAs (tRNAs) convert the genetic

information on mRNA into the language of proteins.

• Ribosomal RNAs (rRNAs) are important catalytic and

structural components of the ribosome.
• Transcription is the synthesis of ribonucleic acid (RNA)
using DNA as a template for the synthesis. It can also be
a form of transfer of information from DNA to RNA.

There are 3 major differences between RNA and DNA

RNA contains the sugar ribose instead of deoxyribose

RNA contains the base uracil instead of thymine

RNA is always single stranded except in certain viruses,

while DNA is double stranded
DNA Replication

C-G
A-T
Reactions of DNA
• In order for a DNA to fulfil its biological role, it
undergoes two kinds of reactions
• DNA Replication
• Gene expression
• DNA replication is the process by which a DNA
molecule is precisely duplicated, so that accurate
copies can be passed on progeny cells
• Gene expression is the process by which the
information stored in DNA is used to tell the cell
Thewhat
two steps of gene expression are called
to do
transcription and translation
DNA REPLICATION
• The first step in DNA replication is the separation
of dsDNA into single stands. The point of
separation is called replication forks or
replisomes. This is ensured by an enzyme called
DNA Helicase.
• DNA helicase is responsible for unwinding and
separation of strands

There are 3 major steps. INITIATION,

ELONGATION and TERMINATION
Complementary
base pairing

makes replication
possible

C-G
A-T
UNCOILING & UNZIPPING
Enzyme (-ase) breaks

weak

Hydrogen Bond

between bases
RNA PRIMASE • RNA primase is a enzyme that

copies a DNA template strand

by making an RNA strand

complementary to it

• It synthesized a short

segment of RNA called RNA

primer about 10 nucleotides

in 5′ to 3′ direction.
• The “topoisomerase” proteins surround the unzipping
strands and relax the twisting that might damage the
unwinding DNA. The cell prepares for the next step,
Elongation, by creating short sequences of RNA called
primers that provide a starting point of elongation. The gap
between two RNA primers is called Okazaki fragments.

• The RNA Primers are necessary for DNA Polymerase å to

bind Nucleotides to the 3' end of them. The daughter
strand is elongated with the binding of more DNA
nucleotides.
 Elongation
• With the primer as the starting point for the leading
strand, a new DNA strand grows one base at a time.
The existing strand is a template for the new strand.
For example, if the next base on the existing strand is
an A, the new strand receives a T. The enzyme DNA
polymerase controls elongation, which can occur
only in the leading direction. The lagging strand
unwinds in small sections that DNA polymerase
replicates in the leading direction.
 Termination step
• In the lagging strand
the DNA Polymerase I -
exonuclease- reads the
fragments and removes
the RNA Primers. The
gaps are closed with the
action of DNA
Polymerase and DNA
Ligase (adds phosphate in
the remaining gaps of the
phosphate - sugar
backbone).
Termination
• After elongation is complete, two new double helices

have replaced the original helix. During termination,

the last primer sequence must be removed from the

end of the lagging strand. This last portion of the

lagging strand is the telomere section, containing a

repeating non-coding sequence of bases. Finally,

enzymes called nucleases “proofread” the new double

helix structures and remove mispaired bases.

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Transcription and Translation
• Transcription is the process by which DNA is
copied (transcribed) to mRNA, which carries the
information needed for protein synthesis.
• This copy, called a messenger RNA (mRNA)
molecule, leaves the cell nucleus and enters the
cytoplasm, where it directs the synthesis of the
protein, which it encodes
Transcription and Translation
• Translation is the process of translating the sequence of a
messenger RNA (mRNA) molecule to a sequence of amino
acids during protein synthesis. The genetic code describes
the relationship between the sequence of base pairs in a
gene and the corresponding amino acid sequence that it
encodes.
• In the cell cytoplasm, the ribosome reads the sequence of
the mRNA in groups of three bases to assemble the
protein. E.g; AAT, GCG, TAT
 TRANSFER OF
GENETIC MATERIALS
IN PROKARYOTES
GENETIC TRANSFER
• Genetic transfer is the mechanism by which DNA is
transferred from a donor to a recipient. Once a
recipient acquired a new DNA from another source
(microorganism e,g bacteria), the recipient cell now
becomes a recombinant cell. Gene transfer in
bacteria is unidirectional from a donor cell to a
recipient cell and the donor usually gives only a
small part of its DNA to the recipient.
GENETIC TRANSFER
• Genetic transfer is the mechanism by which DNA is
transferred from a donor to a recipient. Once a
recipient acquired a new DNA from another source
(microorganism e,g bacteria), the recipient cell now
becomes a recombinant cell. Gene transfer in
bacteria is unidirectional from a donor cell to a
recipient cell and the donor usually gives only a
small part of its DNA to the recipient.
•In bacteria genetic transfer can
happen three ways:

• Transformation
• Transduction
• Conjugation
 Transformation
• Transformation is gene transfer resulting from the
uptake by a recipient cell of naked DNA from a donor
cell. Certain bacteria (e.g. Bacillus, Haemophilus,
Neisseria, Pneumococcus) can take up DNA from the
environment and the DNA that is taken Factor
up canaffecting
be
transformation
incorporated into the recipient’s chromosome.

1. DNA size
2. Competence of the recipient
 Competent cell in Transformation
Cells that are receptive to DNA transfer are termed competent
The process of becoming competent is largely unknown, but
requires protein synthesis
Competent cells permit DNA to pass through their cell walls
and membranes
This process is termed transformation and can lead to the
acquisition of new genes
Competent cells can be induced artificially and play an
important role in biotechnology
 TRANSDUCTION
• Transduction is the transfer of genetic information from a
donor to a recipient by way of a bacteriophage. The phage
coat protects the DNA in the environment so that
transduction, unlike transformation, is not affected by
nucleases in the environment. Not all phages can mediate
transduction. In most cases gene transfer is between members
of the same bacterial species. However, if a particular phage
has a wide host range then transfer between species can
occur. The ability of a phage to mediated transduction is
related to the life cycle of the phage.
 Types of Transduction
• Generalized Transduction – Generalized transduction is
transduction in which potentially any bacterial gene from the
donor can be transferred to the recipient.
• Specialized transduction – Specialized transduction is
transduction in which only certain donor genes can be
transferred to the recipient. Different phages may transfer
different genes but an individual phage can only transfer
certain genes. Specialized transduction is mediated by
lysogenic or temperate phage and the genes that get
transferred will depend on where the prophage has inserted
in the chromosome
 CONJUGATION

• Transfer of DNA from a donor to a recipient by direct

physical contact between the cells. In bacteria there are
two mating types a donor (male) and a recipient
(female) and the direction of transfer of genetic material
is one way; DNA is transferred from a donor to a
recipient via a genetic structure called pili.

•
Donor
The ability of a bacterium to be a donor is a consequence of
the presence in the cell of an extra piece of DNA called
the F factor or fertility factor or sex factor . The F factor is a
circular piece of DNA that can replicate autonomously in the
cell; it is an independent replicon. Extrachromosomal pieces of
DNA that can replicate autonomously are given the general
name of plasmids.
Recipient
The ability to act as a recipient is a consequence of the lack of
the F factor.
 MUTATION
• A mutation is a change that occurs in an organism DNA
sequence, either due to mistakes during the DNA is
What
replication or as the result of environmental factors such
is
as radiation (UV light), temperature etc.
Mutation
• This results in changes in the proteins that are
produce. This can be lethal or be of advantage to the
organism.

• Mutation leads to genetic variation withi species and can

also be inherited particularly if they have positive effect.
 Spontaneous Mutation
• What are spontaneous mutations?
• They are natural mutation that arise from a variety of
sources such as error during the process of DNA
replication, transposable genetic elements, phage
activities etc. It may occur as a result of various
environmental factors.

• spontaneous mutation are natural occurrence in

bacteria, fungi, virus, and even humans. The side effect
ay be good or bad
 EFFECT OF MUTATION
• Mutation can lead to a number of attributes both good
and bad. In most cases it results in damaging effect .
However for some beneficial effect in organism e.g

High resistance to antibiotic, temperature, salt etc

• In humans it can lead to cancer, sickle cell

TYPES OF MUTATION

• SUBSTITUTION

• INSERTION

• DELETION

• FRAMESHIFT
Substitution (point mutation)

• A substitution is a
mutation that occurs as
a result of of one base
for another . i.e a
change in a single base
such as switching an A
to a G
INSERTION
• Insertion are
mutation in
which extra base
pairs are
inserted into a
new place in the
DNA
 INVERSION
a DNA sequence of
nucleotides is
reversed. Inversions
can occur among a
few bases within a
gene or among
longer DNA
sequences that
contain several
genes.
 DELETION

• Deletions are

mutations in

which a section

of DNA is lost,

or deleted.
FRAMESHIFT
• Since protein-coding DNA is divided
into codons three bases long,
insertions and deletions can alter a
gene so that its message is no
longer correctly passed.
 INDUCED MUTATION
• Induced mutation are those that arise as a result of external
forces such as mutagens that are capable of causing mutation.

• Mutagens are chemical agents that can increase the rate of

mutation because they have the ability to change the genetic
nucleotides sequence in an organism.

• They have the ability to insert themselves in between DNA

sequences thereby causing either shift or deletion of the
sequence thereby leading to mutation. This type of mutation is
usually detrimental to the organism because it is not natural but
it was induced.
 Mutagenic agents
• Mutagenic agents are those chemical agents that can
cause mutation in organism.

• Examples include the following

• Acridine orange

• Ethidium bromide

• Ultral violet irradiations

• X-rays
 EXPRESSION OF MUTATION
• It leads to diversity among bacteria strains

• Mutation also alter the genotype and phenotype of

microorganism

• Organisms that acquire mutations are termed mutants

• Some mutants express their ability to be resistant to

antibiotics while some are known for extra ability Iike
degradation of waste in the environments