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Binomial nomenclature

In biology, binomial nomenclature is essential to integrate the naming system across life
sciences and therefore assign one particular unique name identifier for a particular species
across different languages. Binomial nomenclature is used especially by taxonomists in naming
or identifying a species of a particular organism.

It is used to come up with a scientific name for a species that is often based on the Greek or
Latin language. Although Latin is now a defunct language, the naming of organisms is still
being used in this language.

The scientific name of a species that is set by binomial nomenclature entails two parts: (1)
generic name (or genus name) and (2) specific name (or specific epithet). In this regard, the
scientific name is also referred to as the binomial name (or simply, binomial or binomen).

The generic name is the taxonomic genus. A genus is a rank in the classification system that
is generally below the family and above the species level. It is comprised of species with
common attributes. These attributes may be based on structural similarities or on phylogeny.

The second part of the binomial name is the specific name. In botanical nomenclature, the
second part is particularly referred to as the “specific epithet”. The second name (the specific
name or the specific epithet) sets a particular species apart from the rest of the species within
the genus.

History

The adoption of a system of binomial nomenclature is due to Swedish botanist and physician
Carolus Linnaeus (1707–1778) who attempted to describe the entire known natural world and
gave every species (mineral, vegetable or animal) a two-part name. However, binomial
nomenclature in various forms existed before Linnaeus, and was used by the Bauhins, who
lived nearly two hundred years before Linnaeus. Before Linnaeus, hardly anybody used
binomial nomenclature. After Linnaeus, almost everybody did.

The Science of Taxonomy

Taxonomy is the classification, description, identification, and naming of living organisms.

Classification is the practice of organizing organisms into different groups based on their
shared characteristics. The most famous early taxonomist was a Swedish botanist, zoologist,
and physician named Carolus Linnaeus (1701–1778). In 1735, Linnaeus published Systema
Naturae, an 11-page booklet in which he proposed the Linnaean taxonomy, a system of
categorizing and naming organisms using a standard format so scientists could discuss
organisms using consistent terminology. He continued to revise and add to the book, which
grew into multiple volumes.
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Value of binomial nomenclature

The value of the binomial nomenclature system derives primarily from its economy, its
widespread use, and the stability of names it generally favors:

 Every species can be unambiguously identified with just two words.

 The same name can be used all over the world, in all languages, avoiding difficulties of
translation.
 Although such stability as exists is far from absolute, the procedures associated with
establishing binomial nomenclature tend to favour stability. For example, when species
are transferred between genera (as not uncommonly happens as a result of new
knowledge), if possible the species descriptor is kept the same. Similarly if what were
previously thought to be distinct species are demoted from species to a lower rank,
former species names may be retained as infraspecific descriptors.

Despite the rules favoring stability and uniqueness, in practice a single species may have
several scientific names in circulation, depending largely on taxonomic point of view (see
synonymy).

A major source of instability is the resurrection of forgotten names, which can claim priority
of publication. In this case, however, conservation according to the nomenclature Codes is
possible.

Codes of nomenclature

From the mid nineteenth century onwards it became ever more apparent that a body of rules
was necessary to govern scientific names. In the course of time these became Nomenclature
Codes governing the naming of animals ( ICZN), plants (incl. Fungi, cyanobacteria) ( ICBN),
bacteria ( ICNB) and viruses. These Codes differ.

 For example, the ICBN, the plant Code does not allow tautonyms, whereas the ICZN,
the animal Code does allow tautonymy.
 The starting points, the time from which these Codes are in effect (retroactively), vary
from group to group. In botany the starting point will often be in 1753 (the year Carolus
Linnaeus first published Species Plantarum), in zoology in 1758. Bacteriology started
anew, with a starting point in 1980).

A BioCode has been suggested to replace several codes, although implementation is not in
sight. There also is debate concerning development of a PhyloCode to name clades of
phylogenetic trees, rather than taxa. Proponents of the PhyloCode use the name "Linnaean
Codes" for the joint existing Codes and "Linnaean taxonomy" for the scientific classification
that uses these existing Codes.

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Derivation of names

The genus name and species descriptor may come from any source whatsoever. Often they are
Latin words, but they may also come from Ancient Greek, from a place, from a person
(preferably a naturalist), a name from a local language, etc. In fact, taxonomists come up with
specific descriptors from a variety of sources, including inside-jokes and puns.

However, names are always treated grammatically as if they were a Latin sentence. For this
reason the name of a species is sometimes called its "Latin name," although this terminology
is frowned upon by biologists (and philologists), who prefer the phrase scientific name.

There is a separate list of Latin and Greek words commonly used in systematic names.

The genus name must be unique inside each kingdom. Species names are commonly reused,
and are usually an adjectival modifier to the genus name, which is a noun. Family names are
often derived from a common genus within the family.

Whittaker’s Five Kingdom

Evolving Trees of Life (Phylogenies)

With advances in technology, other scientists gradually made refinements to the Linnaean
system and eventually created new systems for classifying organisms. In the 1800s, there was
a growing interest in developing taxonomies that took into account the evolutionary
relationships, or phylogenies, of all different species of organisms on earth. One way to depict
these relationships is via a diagram called a phylogenetic tree (or tree of life). In these diagrams,
groups of organisms are arranged by how closely related they are thought to be. In early
phylogenetic trees, the relatedness of organisms was inferred by their visible similarities, such
as the presence or absence of hair or the number of limbs. Now, the analysis is more

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complicated. Today, phylogenic analyses include genetic, biochemical, and embryological

comparisons, as will be discussed later in this chapter.

Linnaeus’s tree of life contained just two main branches for all living things: the animal and
plant kingdoms. In 1866, Ernst Haeckel, a German biologist, philosopher, and physician,
proposed another kingdom, Protista, for unicellular organisms. He later proposed a fourth
kingdom, Monera, for unicellular organisms whose cells lack nuclei, like bacteria.

Nearly 100 years later, in 1969, American ecologist Robert Whittaker (1920–1980) proposed
adding another kingdom—Fungi—in his tree of life. Whittaker’s tree also contained a level of
categorization above the kingdom level—the empire or superkingdom level—to distinguish
between organisms that have membrane-bound nuclei in their cells (eukaryotes) and those that
do not (prokaryotes). Empire Prokaryota contained just the Kingdom Monera. The Empire
Eukaryota contained the other four kingdoms: Fungi, Protista, Plantae, and Animalia.
Whittaker’s five-kingdom tree was considered the standard phylogeny for many years.

Figure 1.1 shows how the tree of life has changed over time. Note that viruses are not found in
any of these trees. That is because they are not made up of cells and thus it is difficult to
determine where they would fit into a tree of life.

Fig 1.1

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THE CLASSIFICATION OF LIVING THINGS INTO FIVE KINGDOMS

The first person to divide living things into five broad kingdoms was North American ecologist
Robert Whittaker. This researcher proved in 1959 that fungi were not plant organisms -
previously it was thought that they were - and a decade later he proposed the creation of the
fungi kingdom to differentiate them from plants. Whittaker's theory was widely accepted
and the scientific community thereby added a new group to the previous four-kingdom
system, established by the American biologist Herbert Copeland in 1956.

Whitaker proposed that organisms should be broadly divided into kingdoms, based on certain
characters like the structure of the cell, mode of nutrition, the source of nutrition, interrelationship,
body organization, and reproduction. According to this system, there are five main kingdoms. They
are

Distinguishing Features of the Five Kingdoms

Kingdom Monera
These organisms are prokaryotic and unicellular. They do not have a well-defined nucleus and
also lack cell organelles. Some organisms show the presence of cell wall while there are others
without a cell wall. Consequently, some organisms are autotrophic and others are heterotrophic.
Examples include Bacteria, Cyanobacteria, and Mycoplasma.

Features of Monerans

1. They are typically unicellular organisms (but one group is mycelial).

2. Sap vacuoles do not occur. Instead, a gas vacuole may be present.

3. The predominant mode of nutrition is absorptive but some groups are photosynthetic
(holophytic) and chemosynthetic.

4. The organisms are non-motile or move by the beating of simple flagella or by gliding.

5. The genetic material in these organisms is the naked circular DNA.

6. A nuclear envelope is absent. Both, ribosomes and simple chromatophores, are the only
subcellular organelles in the cytoplasm.

Types of Monerans
Kingdom Monera is classified into three sub-kingdoms-

 Archaebacteria

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 Eubacteria

 Cyanobacteria

Kingdom Protista
Organisms grouped under Kingdom Protista are all unicellular, but eukaryotic organisms. These
are the simplest forms of eukaryotes that exhibit either autotrophic or heterotrophic mode of
nutrition. Some organisms have appendages such as cilia or flagella or pseudopodia to move
around. Some examples are Diatoms, Protozoans like Amoeba, Paramoecium

Features of Kingdom Protista:

1. They are primarily aquatic.

2. They form a link with the others dealing with plants, animals and fungi.

3. Also, they have a well-defined nucleus and other membrane-bound organelles.

4. Some have flagella or cilia.

5. They can reproduce asexually and sexually.

Sub-groups of Protista:

 Chrysophytes

 Dinoflagellates

 Euglenoids

 Slime Moulds

 Protozoans
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Kingdom Fungi
Heterotrophic, Multicellular and Eukaryotic organisms are grouped under Kingdom Fungi. Their
mode of nutrition is saprophytic as they use decaying organic matter as food. They have cell walls,
which are made up of a substance called Chitin. Fungi also form a symbiotic association with
some blue-green algae. Yeast, Mushroom, Aspergillus are examples of Fungi.

Features of Fungi:

1. The plant body of true fungi is a thallus. It may be non-mycelial or mycelial.

2. The cell wall of fungi is mainly made up of chitin and cellulose.

3. The fungi are achlorophyllous organisms. Hence, they cannot prepare their food. They live
as heterotrophs i.e., as parasites and saprophytes. Some forms live symbiotically with other
green forms.

4. The fungi either reproduce vegetatively, asexually or sexually.

Kingdom Plantae
These are Eukaryotic, Multicellular organisms with a cell wall that is made up of cellulose. They
are autotrophs and synthesize their own food through the process of photosynthesis. This kingdom
includes all plants.

Based on the body differentiation and presence or absence of specialized vascular tissue, Kingdom
Plantae is divided into different divisions, namely Thallophyta, Bryophyta, Pteridophyta,
Gymnosperms, and Angiosperms. Examples are Spirogyra, Lichens/algae,Ferns, Pines, and
Mango Plant etc.

Features of Plantae:

1. They have special organelles called chloroplasts.

2. They are autotrophic.

3. Reproduction can be asexual and sexual.

4. They show alternation of generation.

Kingdom Animalia
This Kingdom includes organisms that are Multicellular, Eukaryotic, without the presence of cell
wall. They have a heterotrophic mode of nutrition. They also exhibit great diversity. Some
organisms are simple while others have a complex body with specialized tissue differentiation and
body organs.

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The Animal Kingdom is divided into many phyla and classes. Some of the phyla
are Porifera, Coelenterata, Arthropoda, Echinodermata, Chordata etc. Examples – Hydra, Sea
anemone, crabs, Starfish, Monkeys etc.

Features of Animalia:

1. They are multicellular organisms that do not possess chlorophyll.

2. The mode of nutrition is heterotrophic i.e. they depend on other organisms for food.

3. They have muscle cells due to which they have the capability to contract and relax the body
parts.

4. Reproduction is sexual. However, asexual reproduction is also found in lower forms.

5. During development, the multicellular embryo is formed from the zygote.

6. They require oxygen for aerobic respiration.

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Three Domain Classification

Organism are now classify into three major domains
Archaebacteria: Thermophiles or heat loving bacteria
Eubacteria: Single cell organism without a well develop nucleus
Eukarya: All organism are well developed with nucleus in the cell.

Archea
Archaea can be spherical, rod, spiral, lobed, rectangular or irregular in shape. An unusual flat,
square-shaped species that lives in salty pools has also been discovered. Some exist as single
cells, others form filaments or clusters. Until the 1970s this group of microbes was classified

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as bacteria. These microorganisms physically resemble the bacteria but are genetically distinct
from the latter. Archaea are typically found inhabiting and thriving in extreme environmental
conditions. They include halophiles (archaea inhabiting extremely salty
environments), methanogens (archaea producing methane), and thermophiles (archaea that
thrive in scorching environments). Examples of archaea habitats are boiling hot springs and
geysers such as those found in Yellow Stone Park, USA and ice such as the Arctic and Antarctic
oceans, which remain frozen for most of the year.
Characteristics:
 Archaea or archaebacteria evolved separately from eubacteria and eukaryotes.
 They are similar to eubacteria in being prokaryotes and lacking a distinct nucleus.
However, they differ in terms of ribosomal structure, the presence of introns (in some
archaeal species), and membrane structure composition.
 They are similar to eukaryotes in ways that archaea possess genes and several
metabolic pathways that are more closely related to those of eukaryotes, notably,
the enzymes involved in transcription and translation.
 They are regarded to be living fossils and survivors of an ancient group of organisms
that bridged the gap in evolution between eubacteria and eukaryotes.
 Archaeal membrane is formed by lipids containing ether links. Contrastingly, bacterial
membranes are formed by lipids containing ester links.

 A large number of Archaea have a proteinaceous S-layer that is considered to be part

of the cell wall itself (unlike in Bacteria, where an S-layer is a structure in addition to
the cell wall)
 Archaea lack peptidoglycan, a few contain a substance with a similar chemical
structure, known as pseudomurein. Instead of NAM, it contains N-
acetylalosaminuronic acid (NAT) linked to NAG, with peptide interbridges to
increase strength.

Structures
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 Cannulae, a structure unique to archaea, have been discovered in some marine archaeal
strains. These hollow tube-like structures appear to connect cells after division,
eventually leading to a dense network composed of numerous cells and tubes. This
could serve as a means of anchoring a community of cells to a surface.
 Pili have been observed in archaea, composed of proteins most likely modified from
the bacterial pilin. The resulting tube-like structures have been shown to be used for
attachment to surfaces.
 The archaeal flagellum, while used for motility, differs so markedly from the bacterial
flagellum that it has been proposed to call it an “archaellum,” to differentiate it from
its bacterial counterpart.

Similarities to Bacteria

So, why were the archaea originally thought to be bacteria? Perhaps most importantly, they
lack a nucleus or other membrane-bound organelles, putting them into the prokaryotic category
(if you are using the traditional classification scheme). Most of them are unicellular, they have
70S sized ribosomes, they are typically a few micrometers in size, and they reproduce asexually
only. They are known to have many of the same structures that bacteria can have, such as
plasmids, inclusions, flagella, and pili. Capsules and slime layers have been found but appear
to be rare in archaea.

While archaea were originally isolated from extreme environments, such as places high in acid,
salt, or heat, earning them the name “extremophiles,” they have more recently been isolated
from all the places rich with bacteria: surface water, the ocean, human skin, soil, etc.

Archaeal Groups Inhabiting Different Extreme Habitats

Since archaea inhabit extreme habitats, they are called extremophiles. Within extremophiles,
there are different physiological categories or types of archaea like:
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1. Halophiles (live in extreme salt conditions like salt lakes, and brackish waters)
Example: Halobacterium spp.
2. Thermophiles (live in extremely high temperatures like hot springs and vents)
Example: Thermus aquaticus
3. Alkaliphiles (live in extreme alkaline conditions like marine hydrothermal systems)
Example: Thermococcus alcaliphilus is a marine archaea.
4. Acidophiles (live in extremely acidic conditions like dry hot soil and volcanic sites)
Example: Picrophilus torridus

Bacteria

Bacteria are defined as organisms that are microscopic, unicellular, independently

reproducing, and mostly free-living. Bacteria are ubiquitous in nature. They are structurally
simple but functionally complex organisms that form the basis of all life on earth. Most
bacteria, barring a few, are beneficial for their environment. They play a variety of important
roles in the ecosystem such as breaking down the toxic components, recycling the nutrients,
fixing nitrogen in the soil from the air, among many others.

The following is the list of characteristics of bacteria:

 Unicellular
 Free-living
 Independently reproducing
 Ubiquitous
 Prokaryotic
 Functionally Complex
 Structurally simple
 Divide by binary fission

Bacteria are microscopic, single-celled organisms belonging to Kingdom Monera that possess
a prokaryotic type of cell structure, which means their cells are non-compartmentalized, and
their DNA (usually circular) can be found throughout the cytoplasm rather than within a
membrane-bound nucleus. They reproduce by fission or by forming spores. They can
practically live everywhere. They can inhabit all kinds of environments, such as in soil, acidic
hot springs, radioactive waste, seawater, deep in the Earth’s crust, the stratosphere, and even
in the bodies of other organisms. Word origin: from Ancient Greek baktēria, meaning “rod”
or “stick”. Synonym: eubacteria.

1. Bacterial Classification based on Oxygen requirements

 Obligate Aerobes – They need oxygen for survival as they are incapable of respiring
anaerobically. For example, Pseudomonas aeruginosa, Mycobacterium tuberculosis

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 Obligate Anaerobes – They cannot grow in the presence of oxygen as they are
poisoned by it. For example, Clostridium perfringens, Clostridium botulinum
 Facultative Anaerobes – They can grow either with or without oxygen. They respire
aerobically in the presence of oxygen and can ferment in the absence of it. For example.,
Enterobacteriaceae group, Staphylococcus aureus
 Microaerophiles – They grow best in low oxygen concentrations. If the oxygen
concentrations are increased beyond a certain point, they get poisoned by it. For
example, Campylobacter jejuni, Helicobacter pylori
 Aerotolerant – They do not require oxygen for respiration. However, unlike obligate
anaerobes, they are not poisoned by oxygen. For example, Lactobacillus sp.

2) Bacterial classification according to the shape of the bodies of organisms

 Cocci – bacteria that are round shaped. For example,streptococcus

 Bacilli – rod-shaped bacteria, are generally 0.2 to 2 µm wide and 1 to 10 µm
long.,Bacillus subtilis
 Coccobacilli – Small rod-shaped bacteria that are often mistaken to appear like cocci.
Hence, they are named coccobacilli. Haemophilus influenzae
 Spirilla – bacteria with a spiral shape and a stiff body. Campylobacter jejuni
 Spirochetes – bacteria with a spiral shape and a flexible body. Treponema pallidum
 Fusiform – thick central body with tapering ends. F. nucleatum
 Vibrio – comma-shaped bacteria. V.cholerae

3) Bacterial classification according to the types of staining in microbiology.

 Gram-positive bacteria – They have the tendency to retain the crystal violet stain in
their cell walls due to their thick peptidoglycan layer. Hence, purple appearing bacteria
under the microscope are gram-positive. For example: Staphlococcus aureus
 Gram-negative bacteria – They do not retain the crystal violet stain during the
decolorization step of gram staining and get stained with the counterstain, safranin.
Hence, they appear pink when observed under the microscope. For Example
Escherichia coli
 Acid-fast bacteria – they are a group of bacteria that resist decolorization with strong
acids during the staining process. For example, Mycobacteria are acid-fast in nature
due to the high amount of mycolic acid present in their cell wall.

4) Bacterial classification according to the source of nutrition

 Heterotrophs – bacteria that derive their energy from organic compounds. For example,
lactic acid bacteria are used to make yogurt from milk by fermenting lactose.For
example, E.coli
 Chemoautotrophs – bacteria that derive their energy from inorganic compounds. They
are generally extremophiles. They feed on chemicals that are good electron donors,
such as hydrogen sulfide, sulfur, or iron. Like all autotrophs, chemoautotrophs are able

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to “fix” carbon. They take atoms of carbon from inorganic compounds, such as carbon
dioxide, and using it to make organic compounds such as sugars, proteins, and lipids.
For example, nitrobacter

Bacteria structure

The structure of bacteria can be discussed under the following heads.

1. Size

Bacteria are by far the smallest independently reproducing organisms. Most pathogenic
bacteria are 0.1 – 10 µm in size.

 The largest bacterium is Thiomargarita namibiensis that can reach up to a size of 0.75
mm.
 The smallest bacterium is Mycoplasma genitalium of size 200 to 300 nm.

2. Shape

As previously discussed, there are a variety of shapes of different bacteria. Some of the
common shapes of bacteria are named below.

 Coccus
 Bacillus
 Coccobacillus
 Spirilla
 Spirochete
 Fusiform
 Vibrio

3. Arrangement

Newly divided bacteria from certain genera have a special ability to stick together and form
peculiar arrangements. For example, Streptococci often arrange themselves in chains,
Staphylococci arrange themselves in irregular clusters, Diplococci can be seen arranging
themselves in pairs. These arrangements, however, should not be used for the purpose of
identification of bacteria.

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Algae

The algae are autotrophic protists that can be unicellular or multicellular. These organisms are
found in the supergroups Chromalveolata (dinoflagellates, diatoms, golden algae , and brown
algae ) and Archaeplastida (red algae and green algae).

Structure: Like protozoans, algae often have complex cell structures. For instance, algal cells
can have one or more chloroplasts that contain structures called pyrenoids to synthesize and
store starch .

The chloroplasts themselves differ in their number of membranes, indicative of secondary or

rare tertiary endosymbiotic events. Primary chloroplasts have two membranes—one from the
original cyanobacteria that the ancestral eukaryotic cell engulfed, and one from the plasma
membrane of the engulfing cell. Chloroplasts in some lineages appear to have resulted from
secondary endosymbiosis, in which another cell engulfed a green or red algal cell that already
had a primary chloroplast within it. The engulfing cell destroyed everything except the
chloroplast and possibly the cell membrane of its original cell, leaving three or four membranes
around the chloroplast.

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Different algal groups have different pigments, which are reflected in common names such as
red algae, brown algae, and green algae. Some algae , the seaweeds, are macroscopic and may
be confused with plants. Seaweeds can be red, brown, or green, depending on their
photosynthetic pigments. Green algae , in particular, share some important similarities with
land plants; however, there are also important distinctions. For example, seaweeds do not have
true tissues or organs like plants do. Additionally, seaweeds do not have a waxy cuticle to
prevent desiccation.

GENERAL CHARACTERSTICS OF ALGAE

1. Algae are the simplest multicellular plants. Some are unicellular eg. Chlamydomonas
2. Plant body: known as Thallus and they are avascular
3. Habitat: Algae are usually aquatic, either freshwater or marine and some are terresterial.
4. Algae are eukaryotic thallophytes.
5. Algae are photoautotrophs.
6. Storage form of food: Starch
7. Reproduction: Algae reproduce either by vegetative, asexual or sexual method
8. Vegetative method: fragmentation, hormogonia(Any vegetative part of the thallus
grows into a fresh new organism in this form.)
9. Asexual spore: zoospores(motile exposed spores containing two, four, or several
flagella), aplanospores(non motile spore), hypnospores(non motile,thick walled),
akinetes(lengthened thick-walled spore-like formations with ample food reserves).
10. Sexual method: isogamous(merger of two gametes that are physiologically and
morphologically identical, resulting in the formation of a zygote), anisogamous(uniting
gametes are physiologically and morphologically distinct), and oogamous(small motile
male gamete (sperm or antherozoids) is fertilised by a large non-motile female gamete
(egg or ovum) .

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CLASSIFICATION OF ALGAE

On the basis of photosynthetic pigments algae classified into three classes.

1. Chlorophyceae (green algae)

2. Phaeophyceae (brown algae)
3. Rhodophyceae (red algae).

1. Chlorophyceae (Green algae)

General characterstics of Chlorophyceae

 It is the largest class of algae

 They are commonly known as green Algae.
 Photosynthetic pigments: They possesses chlorophyll a, chlorophyll b and small
amount of β-carotenoids.
 The chloroplasts shows various shape ie. Spiral shape in Spirogyra, cup shaped in
Chlamydomonas, star shaped in Zygnema, girdle shaped in Ulothrix
 Habitat: Mostly freshwater (Spirogyra, Oedogonium, Chlamydomonas, Volvox, etc),
some are marine (Sargassum, Laminaria, etc) and some are parasitic (Polysiphonia,
Harvevella, Cephaleuros)
 Distribution: they are cosmopolitan in distribution
 They are unicellular as well as multicellular.
 Each cell is eukaryotic
 Thallus: their body structure, shape and size varies.

 Examples: Chlamydomonas: unicellular free living

 Volvox: colonial form
 Spirogyra: multicellular, unbranched filamentous form
 Ulva: multicellular, parenchymatous form

 Storage form of food: Starch

 Pyrenoids stores starch
 Cell wall has two layer: outer layer composed of pectose and inner layer is composed
of cellulose
 Reproduction: vegetative, asexual and sexual method
 Vegetative : fragmentation
 Asexual: asexual spore (akinete, aplanospore, azygospore)
 Sexual: isogamous, anisogamous, oogamous type gametic fusion

2. Phaeophyceae (Brown algae)

General characteristics of Phaeophyceae

 Pheophyceae are called commonly known as brown algae

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 Photosynthetic pigments: They possesses brown colored photosynthetic pigments

fucoxanthin and β-carotenoids in addition to chlorophyll a and c.
 Habitat: They are almost marine, very few are fresh water eg.
 Thallus: they are multicellular brown algae. No unicellular and colonial (motile or non-
motile) brown algae till known.
 Storage form of food: laminarin starch, manitol (alcohol) and some store iodine also.
 Reproduction: vegetative, asexual and sexual methods
 Vegetative: fragmentation.
 Asexual: asexual spores (motile zoospores).
 Sexual: isogamous or oogamous type gametic fusion.

3. Rhodophyceae (Red algae)

General characteristics of Rhodophyceae

 Rhodophyceae are commonly known as Red Algae

 Photosynthetic pigments: They possesses Red colored photosynthetic pigments r-
phycocyanin and r-phycoerythrin along with chlorophyll a, d, xanthophyll and β-
carotenoid
 Habitat: They are aquatic, mostly marine. Some are freshwater e.g. Batrachospermum.
 Thallus: Red algae show a variety of life forms-

 Examples: Unicellular- Porphyridium,

 multicellular- Goniotrichum,
 Parenchymatous- Porphyra,
 unicellular colonies-Chroothece,

 Storage form of food: Floridean starch and floridosides sugar.

 Reproduction: vegetative, asexual and sexual mode
 Vegetative: fragmentation
 Asexual reproduction: non- motile spores( akinete, aplanospore, azygospore)
 sexual reproduction: Oogamous.
 Some species shows Alternation of generations in their life cycle.

Importance:

 They are important ecologically and environmentally because they are responsible for
the production of approximately 70% of the oxygen and organic matter in aquatic
environments.
 Additionally, algae are the source for agar, agarose, and carrageenan, solidifying agents
used in laboratories and in food production. Agar is obtained from red algae such as
Gelidium and Gracilaria.

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 Although algae are typically not pathogenic, some produce toxins. Harmful algal
blooms, which occur when algae grow quickly and produce dense populations, can
produce high concentrations of toxins that impair liver and nervous-system function in
aquatic animals and humans.They are caused by diverse organisms, including toxic and
noxious phytoplankton, cyanobacteria, benthic algae, and macroalgae
 Crude oil and natural gas are the remnants of photosynthetic products of ancient algae,
which were subsequently modified by bacteria. The North Sea oil deposits are believed
to have been formed from coccolithophore algae (class Prymnesiophyceae), and the
Colorado oil shales by an alga similar to Botryococcus (a green alga).
 Algal extracts are commonly used in preparing foods and other products, and the
direct consumption of algae has existed for centuries in the diets of East Asian and
Pacific Island societies. The red alga nori, or laver (Porphyra), is the most important
commercial food alga.

Protozoa

The kingdom Protista, as defined by Whittaker’s five-kingdom scheme, is an artificial grouping

of over 64,000 different single-celled life forms that lack common evolutionary heritage; that
is to say, they are polyphyletic. In fact, the protists are unified only by what they lack: absent
is the level of tissue organization found in fungi, plants, and animals. The term protozoa [s.,
protozoan; Greek protos, first, and zoon, animal] has traditionally referred to
chemoorganotrophic protists, and protozoology generally refers to the study of protozoa. The
term algae can be used to describe photosynthetic protists. “Algae” was originally used to refer
to all “simple aquatic plants,” but this term has no phylogenetic utility.

Distribution:

Protists grow in a wide variety of moist habitats. Moisture is absolutely necessary for their
existence because they are susceptible to desiccation. Most protists are free living and inhabit
freshwater or marine environments. Many terrestrial chemoorganotrophic forms can be found
in decaying organic matter and in soil, where they are important in recycling the essential
elements nitrogen and phosphorus. Others are planktonic—floating free in lakes and oceans.
Planktonic microbes (both procaryotic and eucaryotic) are responsible for a majority of the
nutrient cycling that occurs in these ecosystems.

Characteristics

Nutrition : Photosynthetic protists are exclusively aerobic. Most photosynthetic forms are
photoautotrophic, obtaining energy from light and fixing CO2 to meet their carbon
requirements.

However, some are photoheterotrophic, using organic carbon rather than CO2.
Chemoheterotrophic protists can be holozoic or saprozoic. In holozoic nutrition, solid
nutrients such as bacteria are acquired by phagocytosis and the subsequent formation of

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phagocytic vacuoles. In saprozoic nutrition, soluble nutrients such as amino acids and sugars
cross the plasma membrane by endocytosis, diffusion, or carrier-mediated transport (facilitated
diffusion or active transport).

 Many protists are capable of encystment. During encystment, the organism de-
differentiates (becomes simpler in morphology) and develops into a resting stage called
a cyst. The cyst is a dormant form marked by the presence of a cell wall and by very
low metabolic activity.

Chrysophytes
Dianoflagellates
Euglenoids
Slime Moulds
Protozoans
All protozoans are heterotrophs and live as predators or parasites. They are believed to be
primitive relatives of animals. There are four major groups of protozoan:

 Flagellated Protozoans:

 Amoebid Protozoans:

 Sporozoans:

 Ciliated Protozoans:
 Structure

Most parasitic protozoa in humans are less than 50 μm in size. The smallest (mainly
intracellular forms) are 1 to 10 μm long, but Balantidium coli may measure 150 μm. Protozoa
are unicellular eukaryotes. As in all eukaryotes, the nucleus is enclosed in a membrane.

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In protozoa other than ciliates, the nucleus is vesicular, with scattered chromatin giving a
diffuse appearance to the nucleus, all nuclei in the individual organism appear alike.

One type of vesicular nucleus contains a more or less central body, called an endosome or
karyosome(meiosis specific structure). The endosome lacks DNA in the parasitic amoebas and
trypanosomes.

In the phylum Apicomplexa, on the other hand, the vesicular nucleus has one or more nucleoli
that contain DNA.

The ciliates have both a micronucleus and macronucleus, which appear quite homogeneous in
composition.( The macronucleus is the centre of all metabolic activities of the organism. The
micronucleus is a storage site for the germline genetic material of the organism.)

The organelles of protozoa have functions similar to the organs of higher animals. The plasma
membrane enclosing the cytoplasm also covers the projecting locomotory structures such as
pseudopodia, cilia, and flagella. The outer surface layer of some protozoa, termed a pellicle, is
sufficiently rigid to maintain a distinctive shape, as in the trypanosomes and Giardia. However,
these organisms can readily twist and bend when moving through their environment.

In most protozoa the cytoplasm is differentiated into ectoplasm (the outer, transparent layer)
and endoplasm (the inner layer containing organelles); the structure of the cytoplasm is most
easily seen in species with projecting pseudopodia, such as the amebas. Some protozoa have a
cytosome or cell “mouth” for ingesting fluids or solid particles. Contractile vacuoles for
osmoregulation occur in some, such as Naegleria and Balantidium. Many protozoa have
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subpellicular microtubules; in the Apicomplexa, which have no external organelles for

locomotion, these provide a means for slow movement.Many other structures occur in parasitic
protozoa, including the Golgi apparatus, mitochondria, lysosomes, food vacuoles, conoids in
the Apicomplexa, and other specialized structures. Electron microscopy is essential to visualize
the details of protozoal structure. From the point of view of functional and physiologic
complexity, a protozoan is more like an animal than like a single cell.

 Protozoan diseases range from very mild to life-threatening. Individuals whose

defenses are able to control but not eliminate a parasitic infection become carriers and
constitute a source of infection for others. In geographic areas of high prevalence, well-
tolerated infections are often not treated to eradicate the parasite because eradication
would lower the individual's immunity to the parasite and result in a high likelihood of
reinfection.
 Many protozoan infections that are inapparent or mild in normal individuals can be life-
threatening in immunosuppressed patients, particularly patients with acquired immune
deficiency syndrome (AIDS). Evidence suggests that many healthy persons harbor low
numbers of Pneumocystis carinii in their lungs. However, this parasite produces a
frequently fatal pneumonia in immunosuppressed patients such as those with AIDS.
 Toxoplasma gondii, a very common protozoan parasite, usually causes a rather mild
initial illness followed by a long-lasting latent infection. AIDS patients, however, can
develop fatal toxoplasmic encephalitis.
 Cryptosporidium was described in the 19th century, but widespread human infection
has only recently been recognized. Cryptosporidium is another protozoan that can
produce serious complications in patients with AIDS. Microsporidiosis in humans was
reported in only a few instances prior to the appearance of AIDS. It has now become a
more common infection in AIDS patients. As more thorough studies of patients with
AIDS are made, it is likely that other rare or unusual protozoan infections will be
diagnosed.
 Acanthamoeba species are free-living amebas that inhabit soil and water. Cyst stages
can be airborne. Serious eye-threatening corneal ulcers due to Acanthamoeba species
are being reported in individuals who use contact lenses. The parasites presumably are
transmitted in contaminated lens-cleaning solution. Amebas of the genus Naegleria,
which inhabit bodies of fresh water, are responsible for almost all cases of the usually
fatal disease primary amebic meningoencephalitis. The amebas are thought to enter the
body from water that is splashed onto the upper nasal tract during swimming or diving.
Human infections of this type were predicted before they were recognized and reported,
based on laboratory studies of Acanthamoeba infections in cell cultures and in animals.

Fungi

Microbiologists use the term fungus [pl., fungi; Latin fungus, mushroom] to describe
eucaryotic organisms that are spore-bearing, have absorptive nutrition, lack chlorophyll, and
reproduce sexually and asexually. According to the universal phylogenetic tree, fungi are
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members of the domain Eucarya. They are sometimes referred to as the true fungi or Eumycota
[Greek eu, true, andmykes, fungus]

porcini mushroom

DISTRIBUTION

Fungi are primarily terrestrial organisms, although a few are freshwater or marine. Many are
pathogenic and infect plants and animals. Fungi also form beneficial relationships with other
organisms. For example, the vast majority of vascular plant roots form associations (called
mycorrhizae) with fungi. Fungi also are found in the upper portions of many plants. These
endophytic fungi affect plant reproduction and palatability to herbivores. Lichens are
associations of fungi and photosynthetic protists or cyanobacteria.

Characteristics of Fungi

1. Morphology:

 Except for yeasts, which grow as single cells, most fungi grow as thread-like filaments.
The filaments are called hyphae (singular, hypha). Each hypha consists of one or more
cells surrounded by a tubular cell wall. A mass of hyphae make up the body of a fungus,
which is called a mycelium (plural, mycelia). Hyphae absorb nutrients from the
environment and transport them to other parts of the thallus (fungus body).

 The hyphae of most fungi are divided into cells by internal walls called septa (singular,
septum). Septa usually have little pores that are large enough to allow ribosomes,
mitochondria and sometimes nuclei to flow among cells. Hyphae that are divided into
cells are called septate hyphae. However, the hyphae of some fungi are not separated
by septa. Hyphae without septae are called coenocytic hyphae. Coenocytic hyphae are
big, multinucleated cells.

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2.Fungi lacks Chloroplast.

3.The fungal cell usually is encased in a cell wall of chitin. Chitin is a strong but flexible
nitrogen containing polysaccharide consisting of N-acetylglucosamine residues.

4.Cell membrane consists of ergosterol(it regulates permeability and fluidity)

5. Mode of nutrition:

 Fungi are organotropic heterotrophs.

 Mostly Fungi are saprophytic and some are Parasitic

6. Fungi grow best in acidic environment ( tolerate acidic pH).

7. Fungi can tolerate high sugar concentration and dry condition

8. Most of the fungi are Obligate aerobes (molds) and few are facultative anaerobes (yeasts)

9. Optimum temperature of growth for most saprophytic fungi is 20-30 C while (30-37) C for
parasitic fungi.

10. Growth rate of fungi is slower than that of bacteria.

11. Reproduction: both asexual (Axamorph) and sexual (Teliomorph) mode of reproduction

 Asexual methods: fragmentation, somatic budding, fission, asexual spore formation

 Sexual methods: gametic copulation, gamate-gametangium copulation, gametangium
copulation, somatic copulation and Spermatization.
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12. More than 20 species are responsible to cause severe systemic human infection, 35 species
causes less severe systemic disease or might causes cutaneous or sub cutaneous infection and
45 species causes superficial cutaneous infection.

13. Some fungi shows mutualistic relationship with higher plants, eg Mycorrhiza is symbiotic
associated with root of gymnosperm

Classification of Fungi
Kingdom Fungi are classified based on different modes. The different classification of fungi is
as follows:

Based on Mode of nutrition

On the basis of nutrition, kingdom fungi can be classified into 3 groups.

1. Saprophytic – The fungi obtain their nutrition by feeding on dead organic substances.
Examples: Rhizopus, Penicillium and Aspergillus.
2. Parasitic – The fungi obtain their nutrition by living on other living organisms (plants
or animals) and absorb nutrients from their host. Examples: Taphrina and Puccinia.
3. Symbiotic – These fungi live by having an interdependent relationship with other
species in which both are mutually benefited. Examples: Lichens and
mycorrhiza. Lichens are the symbiotic association between algae and fungi. Here both
algae and fungi are mutually benefited as fungi provide shelter for algae and in reverse
algae synthesis carbohydrates for fungi. Mycorrhiza is the symbiotic association
present between fungi and plants. Fungi improve nutrient uptake by plants, whereas,
plants provides organic molecules like sugar to the fungus.

Based on Spore Formation

Kingdom Fungi are classified into the following based on the formation of spores:

1. Zygomycetes – These are formed by the fusion of two different cells. The sexual spores
are known as zygospores, while the asexual spores are known as sporangiospores. The
hyphae are without the septa. Example – Mucor.
2. Ascomycetes – They are also called sac fungi. They can be coprophilous, decomposers,
parasitic or saprophytic. The sexual spores are called ascospores. Asexual reproduction
occurs by conidiospores. Example – Saccharomyces.
3. Basidiomycetes – Mushrooms are the most commonly found basidiomycetes and
mostly live as parasites(club fungi). Sexual reproduction occurs by basidiospores.
Asexual reproduction occurs by conidia, budding or fragmentation.
Example- Agaricus.
4. Deuteromycetes – They are otherwise called imperfect fungi as they do not follow the
regular reproduction cycle as the other fungi. They do not reproduce sexually. Asexual
reproduction occurs by conidia. Example – Trichoderma.

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Importance of fungi:

1. Fungi are important to humans in both beneficial and harmful ways. With bacteria and
a few other groups of chemoorganotrophic organisms, fungi act as decomposers, a role
of enormous significance. In this way carbon, nitrogen, phosphorus, and other critical
constituents of dead organisms are released and made available for living organisms.
2. On the other hand, fungi are a major cause of disease. Plants are particularly vulnerable
to fungal diseases because fungi can invade leaves through their stomates. Fungi also
cause many diseases of animals and humans. Aspergillus flavus cause diseases in
Poultry, swine, cattle, sheep, dogs. Candida albicans causes infection in humans.
3. Fungi, especially the yeasts, are essential to many industrial processes involving
fermentation. Examples include the making of bread, wine, and beer. Fungi also play a
major role in the preparation of some cheeses, soy sauce, and tofu; in the commercial
production of many organic acids (citric, gallic) and certain drugs (ergometrine,
cortisone); and in the manufacture of many antibiotics (penicillin, griseofulvin) and the
immunosuppressive drug cyclosporin.

Examples;

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 Penicillium notatum is used for production of

penicillin antibiotics
 Aspergillus niger is used for prodution of citric
acid
 Saccharomyces cerevisiae is used for alcohol
production

4. Fungi are important research tools in the study of fundamental biological processes.
Cytologists, geneticists, biochemists, biophysicists, and microbiologists regularly use
fungi in their research. The yeast Saccharomyces cerevisiae is the best understood
eucaryotic cell. It has been a valuable model organism in the study of cell biology,
genetics, and cancer. in their research.

Viruses are microscopic organisms that are known to be the connecting link between living
and non-living. These were not placed under the five-kingdom classification since they are
neither living nor dead. Hence, they form their own group.

Virus

Viruses were initially characterized as filterable agents capable of causing disease. Since that
time, advances in microscopy and scientific techniques have led to a better classification of
viruses and their properties. Electron microscopy has allowed us to visualize viruses in great
detail, while molecular and cellular assays have broadened our understanding of how viruses
function and are related to one another.

Common characteristics:

1. Viruses are Small in Size.

The smallest of viruses are about 20 nm in diameter, although influenza and the human
immunodeficiency virus have a more typical size, about 100 nm in diameter. However, some
viruses are significantly larger than 100 nm. Poxviruses, such as the variola virus that causes
smallpox, can approach 400 nm in length, and filoviruses, such as the dangerous Ebola virus
and Marburg virus, are only 80 nm in diameter but extend into long threads that can reach
lengths of over 1000 nm.

2. Viruses are obligate intracellular parasites, meaning that they are completely dependent
upon the internal environment of the cell to create new infectious virus particles, or virions.
3. Viruses, on the other hand, have genomes, or genetic material, that can be composed of
DNA or RNA (but not both). Genomes are not necessarily double-stranded, either; different
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virus types can also have single-stranded DNA (ssDNA) genomes, and viruses with RNA
genomes can be single-stranded or double-stranded. Any particular virus will only have one
type of nucleic acid genome, however, and so viruses are not encountered that have both
ssDNA and ssRNA genomes.
4. Capsid is the protective protein coat. It comprises many capsomeres, which are arranged
tightly together in repeating patterns. It is an impenetrable shell. Its main function is to help
introduce a viral genome into the host cell during infection. The structure of a capsid is what
gives symmetry to the virus. The structures can be cubical, helical, complex, or binal.
5. Some viruses even contain an envelope surrounding the nucleocapsid. It is a layer of
lipoprotein and glycoprotein, and the envelope results from the budding process from the
host cell. The proteins can also project out as telomeres such as neuraminidase and
haemagglutinin involved in binding virus to the host cells.

Structure of Viruses

Viruses vary in their structure. A virus particle consists of DNA or RNA within a protective
protein coat called a capsid. The shape of the capsid may vary from one type of virus to
another. The capsid is made from the proteins that are encoded by viral genes within their
genome.

The shape of the capsid serves as one basis for classification of viruses.

The capsid of the virus shown in Figure below is icosahedral. Virally coded proteins will self-
assemble to form a capsid. Some viruses have an envelope of phospholipids and proteins. The
envelope is made from portions of the host’s cell membrane. It surrounds the capsid and helps
protect the virus from the host’s immune system. The envelope may also have receptor
molecules that can bind with host cells. They make it easier for the virus to infect the cells.

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Diagram of a Cytomegalovirus. The capsid encloses the genetic material of the virus. The
envelope which surrounds the capsid is typically made from portions of the host cell
membranes (phospholipids and proteins). Not all viruses have a viral envelope.

Helical Viruses

Helical capsids are made up of a single type of protein subunit stacked around a central axis
to form a helical structure. The helix may have a hollow center, which makes it look like a
hollow tube. This arrangement results in rod-shaped or filamentous virions. These virions can
be anything from short and very rigid, to long and very flexible. The well-studied tobacco
mosaic virus (TMV) is an example of a helical virus, as seen in the Figure below.

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A helical virus, tobacco mosaic virus. Although their diameter may be very small, some helical
viruses can be quite long, as shown here. 1. Nucleic acid; 2. Viral protein units, 3. Capsid.
TMV causes tobacco mosaic disease in tobacco, cucumber, pepper, and tomato plants.

Icosahedral Viruses

Icosahedral capsid symmetry gives viruses a spherical appearance at low magnification, but
the protein subunits are actually arranged in a regular geometrical pattern, similar to a soccer
ball; they are not truly spherical. An icosahedral shape is the most efficient way of creating a
hardy structure from multiple copies of a single protein. This shape is used because it can be
built from a single basic unit protein which is used over and over again. This saves space in the
viral genome.

Adenovirus, an icosahedral virus. An icosahedron is a three-dimensional shape made up of 20

equilateral triangles. Viral structures are built of repeated identical protein subunits, making
the icosahedron the easiest shape to assemble using these subunits.

Complex Viruses

Complex viruses possess a capsid which is neither purely helical, nor purely icosahedral, and
which may have extra structures such as protein tails or a complex outer wall. Viral protein
subunits will self-assemble into a capsid, but the complex viruses DNA also codes for proteins
which help in building the viral capsid. Many phage viruses are complex-shaped; they have an
icosahedral head bound to a helical tail. The tail may have a base plate with protein tail fibers.
Some complex viruses do not have tail fibers.

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This “moon lander”-shaped complex virus infects Escherichia coli bacteria.

Enveloped Viruses

Some viruses are able to surround (envelop) themselves in a portion of the cell membrane of
their host. The virus can use either the outer membrane of the host cell, or an internal membrane
such as the nuclear membrane or endoplasmic reticulum. In this way the virus gains an outer
lipid bilayer known as a viral envelope. This membrane is studded with proteins coded for by
both the viral genome and the host genome. However, the lipid membrane itself and any
carbohydrates present come entirely from the host cell. The influenza virus, HIV, and the
varicella zoster virus (Figure below) are enveloped viruses.

An enveloped virus. Varicella zoster virus causes chicken pox and shingles.

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The viral envelope can give a virus some advantages over other capsid-only viruses. For
example, they have better protection from the host's immune system, enzymes and certain
chemicals. The proteins in the envelope can include glycoproteins, which act as
receptor molecules. These receptor molecules allow host cells to recognize and bind the
virions, which may result in easier uptake of the virion into the cell. Most enveloped viruses
depend on their envelopes to infect cells. However, because the envelope contains lipids, it
makes the virus more susceptible to inactivation by environmental agents, such as detergents
that disrupt lipids.

One classification scheme was developed in the 1970s by Nobel laureate David Baltimore. The
Baltimore classification system categorizes viruses based on the type of nucleic acid genome
and replication strategy of the virus. The system also breaks down single-stranded RNA viruses
into those that are positive strand (+) and negative strand (−). As will be further discussed in
the next chapter, positive-strand (also positive-sense or plus-strand) RNA is able to be
immediately translated into proteins; as such, messenger RNA (mRNA) in the cell is positive
strand. Negative-strand (also negative-sense or minus-strand) RNA is not translatable into
proteins; it first has to be transcribed into positive-strand RNA. Baltimore also took into
account viruses that are able to reverse transcribe, or create DNA from an RNA template,
which is something that cells are not capable of doing. Together, the seven classes are

Group I: These viruses contain double-stranded DNA in their genome. For example,
Adenovirus, and Poxvirus

Group II: These viruses have single-stranded DNA in their genome. For example Parvoviruses

Group III: They use double-stranded RNA as their genome. The 2 strands separate, and one of
them is used as a template for generating mRNA. For example Reoviruses

Group IV: They have single-stranded RNA in their genome with a positive sense of polarity.
Positive polarity means that the genomic RNA can serve directly as mRNA molecules. For
example,commom cold viruds

Group V: They have single-stranded RNA as their genome with a negative sense of polarity.
Negative polarity means that the sequence will be complementary to the mRNA strands. For
example Rabies virus

Group VI: They have two copies of single-stranded genomes that are converted using an
enzyme called reverse transcriptase, and the result is double-stranded DNA. For example,
Retroviruses

Group VII: These have partial double-stranded genomes and make single-stranded DNA
intermediaries that act as mRNA. For example, Hepadnaviruses.

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