BIO 102 Lecture Note Updated
BIO 102 Lecture Note Updated
COURSE OUTLINE
Basic characteristics, identification and classification of viruses, bacteria and fungi. A
generalized survey of the plant and animal kingdoms based mainly on the study of similarities
and differences in the external features. Ecological adaptations. Briefs on physiology to include
WEEK 10 REVISION
INTRODUCTION TO MICROBIAL WORLD
Microorganisms include all unicellular organisms, and so are extremely diverse. Archaea, and
Bacteria are microorganisms which were previously grouped together in the two domain system
as Prokaryotes, the other being the eukaryotes. The third domain Eukaryota includes all
multicellular organisms, and many unicellular protists and protozoans. Some protists are related
to animals and some to green plants. Many of the multicellular organisms are microscopic,
namely micro-animals, some fungi and some algae.
Microorganisms or microbes are microscopic organisms that exist as unicellular, multicellular, or
cell clusters. Microorganims are widespread in nature and are beneficial to life, but some can
cause serious harm. They can be divided into six major types: bacteria, archaea, fungi, protozoa,
algae, and viruses.
TYPES OF MICROORGANISMS
BACTERIA
Bacteria (single: bacterium) mostly are free-living organisms often consisting of one biological cell. They
constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria
were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit
soil, water, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Bacteria play a
vital role in many stages of the nutrient cycle by recycling nutrients and the fixation of nitrogen from the
atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the
putrefaction stage in this process. Bacteria provide the nutrients needed to sustain life by converting
dissolved compounds, such as hydrogen sulphide and methane, to energy. Most bacteria have not been
characterised and there are many species that cannot be grown in the laboratory. The study of bacteria is
known as bacteriology, a branch of microbiology.
Size of Bacteria:
Bacteria display a wide diversity of shapes and sizes. Bacterial cells are about are typically 0.5–5.0
micrometres in length. Among the smallest bacteria are members of the genus Mycoplasma, which
measure only 0.3 micrometres, as small as the largest viruses.
The three basic bacterial shapes are coccus (spherical), bacillus (rod-shaped), and spiral
(twisted), however pleomorphic bacteria can assume several shapes.
Cocci: Cocci bacteria can exist singly, in pairs (as diplococci), in groups of four (as tetrads), in
chains (as streptococci ), in clusters (as stapylococci ), or in cubes consisting of eight cells (as
sarcinae). Cocci may be oval, elongated, or flattened on one side. Cocci may remain attached
after cell division. These group characteristics are often used to help identify certain cocci.
The cocci are arranged in chains, as the cells divide in one plane.
3. Tetrads
The cocci are arranged in packets of four cells, as the cells divide in two plains.
4. Sarcinae
The cocci are arranged in a cuboidal manner, as the cells are formed by regular cell divisions in
three planes. Cocci that divide in three planes and remain in groups cube like groups of eight.
The cocci are arranged in grape-like clusters formed by irregular cell divisions in three plains.
1. Diplobacilli
Most bacilli appear as single rods. Diplobacilli appear in pairs after division.
2. Streptobacilli
The bacilli are arranged in chains, as the cells divide in one plane.
Examples: Streptobacillusmoniliformis
3. Coccobacilli
These are so short and stumpy that they appear ovoid. They look like coccus and bacillus.
4. Palisades
The bacilli bend at the points of division following the cell divisions, resulting in a palisade
arrangement resembling a picket fence and angular patterns that look like Chinese letters.
Example: Corynebacteriumdiphtheriae
Spirilla (or spirillum for a single cell) are curved bacteria which can range from a gently curved
shape to a corkscrew-like spiral. Many spirilla are rigid and capable of movement. A special
group of spirilla known as spirochetes are long, slender, and flexible.
pirilla (or spirillum for a single cell) are curved bacteria which can range from a gently
curved shape to a corkscrew-like spiral. Many spirilla are rigid and capable of
movement. A special group of spirilla known as spirochetes are long, slender, and
flexible.
1. Vibrio
They are comma-shaped bacteria with less than one complete turn or twist in the cell.
2. Spirilla
They have rigid spiral structure. Spirillum with many turns can superficially resemble
spirochetes. They do not have outer sheath and endoflagella, but have typical bacterial
flagella.
Example: Campylobacter jejuni, Helicobacter pylori, Spirillumwinogradskyi, etc.
3. Spirochetes
Spirochetes have a helical shape and flexible bodies. Spirochetes move by means of axial
filaments, which look like flagella contained beneath a flexible external sheath but lack
typical bacterial flagella.
Examples: Leptospira species
(Leptospirainterrogans), Treponemapallidum, Borreliarecurrentis, etc.
Biofilms:Bacteria often attach to surfaces and form dense aggregations called biofilms, and larger
formations known as microbial mats. These biofilms and mats can range from a few micrometres in
thickness to up to half a metre in depth, and may contain multiple species of bacteria, protists and
archaea. Bacteria living in biofilms display a complex arrangement of cells and extracellular components,
forming secondary structures, such as microcolonies, through which there are networks of channels to
enable better diffusion of nutrients. In natural environments, such as soil or the surfaces of plants, the
majority of bacteria are bound to surfaces in biofilms. Biofilms are also important in medicine, as these
structures are often present during chronic bacterial infections or in infections of implanted medical
devices, and bacteria protected within biofilms are much harder to kill than individual isolated bacteria.
IDENTIFICATION OF BACTERIA
Culture techniques: are designed to promote the growth and identify particular bacteria while
restricting the growth of the other bacteria in the sample. Often these techniques are designed for
specific specimens; for example, a sputum sample will be treated to identify organisms that
cause pneumonia, while stool specimens are cultured on selective media to identify organisms
that cause diarrhea while preventing growth of non-pathogenic bacteria. Specimens that are
normally sterile, such as blood, urine or spinal fluid, are cultured under conditions designed to
grow all possible organisms. Once a pathogenic organism has been isolated, it can be further
characterized by its morphology, growth patterns (such as aerobic or anaerobic growth), patterns
of hemolysis, and staining.
Molecular methods: Most bacteria have not been characterized and there are many species that
cannot be grown in the laboratory. Diagnostics using DNA-based tools, such as polymerase
chain reaction, are increasingly popular due to their specificity and speed, compared to culture-
based methods. These methods also allow the detection and identification of "viable but non-
culturable" cells that are metabolically active but non-dividing. However, even using these
improved methods, the total number of bacterial species is not known and cannot even be
estimated with any certainty. Following present classification, there are a little less than 9,300
known species of prokaryotes, which includes bacteria and archaea; but attempts to estimate the
true number of bacterial diversity have ranged from 107 to 109 total species—and even these
diverse estimates may be off by many orders of magnitude
VIRUSES
The microbial world consists not only of cellular organisms but also of acellular infectious
agents. The discipline of virology studies viruses; infectious agents composed simply of protein
and nucleic acid (viruses), RNA only (viroids and virusoids), or protein only (prions). Viruses
can exist in two phases: extracellular and intracellular. They possess few, if any, enzymes and
cannot reproduce outside of living cells. In the intracellular phase, viruses exist primarily as
replicating nucleic acids that induce host metabolism to synthesize viral components, from which
virions are assembled and eventually [Link] can infect either eucaryotic or procaryotic
cells. Viruses that infect bacteria are called bacteriophages, or phages for short.
CHARACTERISTICS OF VIRUSES
Viruses have a nucleic acid genome of either DNA or RNA and never both.
Viral genomes are very small, but genomes of different viruses range in size by over 100-
fold.
Viral genomes are associated with protein that at its simplest forms the virus particle, but
in some viruses this nucleoprotein is surrounded by further protein or a lipid bilayer.
Viruses are obligate interacellular parasites that can only reproduce in living cells.
Viruses’ possess the outermost proteins of the virus particle (capsid) which allow the
virus to recognize the correct host cell and gain entry into its cytoplasm.
SYSTEMIC CLASSIFICATION OF VIRUSES
Viruses are found throughout the world and infect all known organisms. Viruses cause a range of
different diseases and display a diversity of host range, morphology, and genetic makeup.
Bringing order to this huge diversity requires the designation of classification groups to permit
study of representative viruses that can inform us about their less well studied relatives.
All of the proposed classification schemes have different strengths and weaknesses but there is
now general consensus. Viruses were grouped according to their shared properties (not those of
their hosts) and the type of nucleic acid forming their genomes. Later the International
Committee on Taxonomy of Viruses was formed in 1966. However, viruses are not classified on
the basis of phylum or class, as their small genome size and high rate of mutation makes it
difficult to determine their ancestry beyond order. As such, the Baltimore classification is used to
supplement the more traditional hierarchy. The International Committee on Taxonomy of
Viruses has responsibility for assignment of new viruses to specific groupings.
Order (-virales)
Family (-viridae)
Subfamily (-virinae)
Genus (-virus)
Species (-virus)
NO2-BALTIMORE CLASSIFICATION ON THE BASIS OF VIRAL NUCLEIC ACIDS
The Baltimore system complements the ICTV system but focuses on the viral genome and the
process used to synthesize viral mRNA.
The Nobel Prize-winning biologist David Baltimore devised the Baltimore classification
system. The ICTV classification system is used in conjunction with the Baltimore classification
system in modern virus classification.
The Baltimore classification of viruses is based on the mechanism of mRNA production. Viruses
must generate mRNAs from their genomes to produce proteins and replicate themselves, but
different mechanisms are used to achieve this in each virus family.
The nucleic acid of a virus contains all the information needed to produce new virus particles.
Some of this information is used directly to make virion components and some to make
accessory proteins or to provide signals which allow the virus to subvert the biosynthetic
machinery of a cell and redirect it towards the production of virus.
Baltimore defines seven groups of viruses, with each commonly being referred to by the nature
of the virus genomes, it includes:
Class 1 contains all viruses that have double-stranded (ds) DNA genomes. In this class, the
designation of positive and negative sense is not meaningful since mRNAs may come from
either strand.
Class 2 contains viruses that have single-stranded (ss) DNA genomes. The DNA can be of
positive or negative sense, depending on the virus being studied.
Class 3 contains viruses that have dsRNA genomes. All known viruses of this type have
segmented genomes and mRNA is only synthesized from one template strand of each segment.
The process of transcription from a dsRNA genome can be envisioned as occurring using a
mechanism similar to that for transcription from a dsDNA genome.
Class 4 contains viruses with ssRNA genomes of the same (positive) sense as mRNA and which
can be translated. Synthesis of a complementary strand, generating a dsRNA intermediate,
precedes synthesis of mRNA.
Class 5 contains viruses that have ssRNA genomes which are complementary in base sequence
to the mRNA (negative-strand RNA viruses). Synthesis of mRNA requires novel virus-encoded
enzymes, and generation of new virus genomes requires the synthesis of a dsRNA intermediate,
the positive sense strand of which is used as a template for replication.
Class 6 contains viruses that have ssRNA genomes and which generate a dsDNA intermediate as
a prelude to replication, using an enzyme carried in the virion.
Class 7 More recently, it has been suggested that some viruses, termed reversiviruses, should be
transferred from class 1 into a new class 7. This is based on their replication from dsDNA
through a positive sense ssRNA intermediate back to dsDNA.
FUNGI
A fungus (plural:fungi ) is a member of the group of eukaryotic organisms that includes
microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These
organisms are classified as one of the traditional eukaryotic kingdoms, along with Animalia,
Plantae and either Protista or Protozoa.
A characteristic that places fungi in a different kingdom from plants, bacteria, and some protists
is chitin in their cell walls. Fungi, like animals, are heterotrophs that is they acquire their food by
absorbing dissolved molecules, typically by secreting digestive enzymes into their environment.
Fungi do not photosynthesize. Growth is their means of mobility, except for spores (a few of
which are flagellated), which may travel through the air or water. Fungi are the principal
decomposers in ecological systems. These and other differences place fungi in a single group of
related organisms, named the Eumycota (true fungi or Eumycetes).
The discipline of biology devoted to the study of fungi is known as mycology (from the Greek
word mykes meaning: mushroom). In the past mycology was regarded as a branch of botany,
although it is now known that fungi are genetically more closely related to animals than to
plants.
Placement into a division is based on the way in which the fungus reproduces sexually. The
shape and internal structure of the sporangia, which produce the spores, are the most useful
character for identifying these various major groups.
However, There are also two conventional groups which are not recognized as formal taxonomic
groups (that is polyphyletic groups); these are the Deuteromycota (fungi imperfecti), and the
lichens.
The Deuteromycota includes all fungi which have lost the ability to reproduce sexually. As a
result, it is not known for certain into which group they should be placed, and thus the
Deuteromycota becomes a convenient place to dump them until someone gets around to working
out their biology.
Before the introduction of molecular methods for phylogenetic analysis, taxonomists considered
fungi to be members of the plant kingdom because of similarities in lifestyle: both fungi and
plants are mainly immobile, and have similarities in general morphology and growth habitat.
Like plants, fungi often grow in soil and, in the case of mushrooms, form conspicuous fruit
bodies, which sometimes resemble plants such as mosses. The fungi are now considered a
separate kingdom, distinct from both plants and animals, from which they appear to have
diverged around one billion years ago. Some morphological, biochemical, and genetic features
are shared with other organisms, while others are unique to the fungi, clearly separating them
from the other kingdoms.
Shared features:
With animals: Fungi lack chloroplasts and are heterotrophic organisms and so require
preformed organic compounds as energy sources.
With plants: Fungi have a cell wall and [Link] reproduce by both sexual and
asexual means, and like basal plant groups (such as ferns and mosses) produce spores.
Similar to mosses and algae.
PLANT KINGDOM
Kingdom Plantae includes all the plants. They are eukaryotic, multicellular and autotrophic
organisms. The plant cell contains a rigid cell wall. Plants have chloroplast and chlorophyll
pigment, which is required for photosynthesis.
They make their own food and hence are called autotrophs.
These are multicellular eukaryotes. The plant cell contains the outer cell wall and a large
central vacuole.
They have different organelles for anchorage, reproduction, support and photosynthesis.
A plant kingdom is further classified into subgroups. Classification is based on the following
criteria:
Plant body: Presence or absence of a well-differentiated plant body. E.g. Root, Stem and
Leaves.
The plant kingdom has been classified into five subgroups according to the above-mentioned
criteria:
Thallophyta
Bryophyta
Pteridophyta
Gymnosperms
Angiosperms
Thallophytes: They lack a well-differentiated body structure and the plant body is thallus
like. They include plants with primitive and simple body structures. The plant body is
thallus, they may be filamentous, colonial, branched or unbranched. Examples include
green algae, red algae and brown algae. Common examples are Volvox, Fucus,
Spirogyra, Chara, Polysiphonia, Ulothrix, etc.
Bryophytes: They do not have vascular tissues. The plant body has root-like, stem-like
and leaf-like structures. Bryophytes are terrestrial plants but are known as “amphibians of
the plant kingdom” as they require water for sexual reproduction. They are present in
moist and shady places. Bryophyta includes mosses, hornworts and liverworts. Some of
the common examples are Marchantia, Funaria, Sphagnum, Antheoceros, etc.
Pteridophyta: Pteridophytes have a well-differentiated plant body into root, stem and
leaves. They have a vascular system for the conduction of water and other substances.
Some of the common examples are Selaginella, Equisetum, Pteris, etc.
Gymnosperms: They have a well-differentiated plant body and vascular tissues. They
bear naked seeds, i.e. seeds are not enclosed within a fruit. Some of the common
examples of gymnosperms are Cycas, Pinus, Ephedra, etc.
The kingdom Animalia, or Metazoa, includes all animals. Animals are multicellular, eukaryotic
organisms, which are heterotrophic, meaning they obtain nutrition from organic sources. Most
animals obtain nutrition by ingesting other organisms or decomposing organic material.
Animals can be divided broadly into vertebrates and invertebrates. Vertebrates have a backbone
or spine (vertebral column), and amount to less than five percent of all described animal species.
They include fish, amphibians, reptiles, birds and mammals. The remaining animals are the
invertebrates, which lack a backbone. The study of animals is called zoology.
Animals are living organism that are characterized by voluntary movement and depends on other
organism for their food. (The above statement seems simple but in a real sense the answer is
complex and requires an understanding of some rather hefty scientific concepts and terms. It's
easy to say, for instance, that a giraffe, a whale, or a dog is an animal. But when it comes down
to making a list of animal characteristics—identifying specific traits shared by all animals—it
gets complicated).
Over two million species have been described and many more are yet to be identified. Animals
are the most diverse form on earth. Their size ranges from about 30m long (whale) to
microscopic forms. They live in a vast range of habitat, from desert and arctic tundra to deep sea
floor.
CHARACTERISTICS OF ANIMALS
All living things need carbon to support the basic processes of life such as growth, development,
and reproduction. An organism can assimilate carbon from their environment in the form of
carbon dioxide (from the atmosphere) or inorganic compounds. They can ingest other organisms
and thus obtain carbon from the organic materials that make up other organism. The term
autotroph describes such organisms. An organism can obtain the carbon they need by getting it
from other living organisms that are made up of carbon-containing organic molecules. The term
heterotroph describes this type of organism, one that uses organic materials as a source of energy
for growth and development.
Green plants are autotrophs. They take energy from the sun and use it along with carbon
available in the atmosphere in the form of carbon dioxide to produce sugar, a simple organic
compound. In contrast, all animals are heterotrophs. They ingest plants and other organisms
as a way to get their carbon the energy they need to live.
Animals' bodies are made up of multiple cells. In most animals, those cells are organized into
different tissues that perform different functions. (For example, the roundworm C. elegans,
which is widely used in biology experiments, consists of exactly 1,031 cells, no more and no
less, while a human being is composed of literally trillions of cells.) However, it's important to
keep in mind that animals aren't the only multicellular organisms; that honor is also shared by
plants, fungi, and even some species of algae). During the development of an animal, cells
differentiate so they can perform specific functions. Groups of cells with similar specializations
that form a common function are referred to as a tissue. One exception to this is sponges
(Phylum Porifera) which do not posses tissues (they don't have muscles or nerves).
Most animals reproduce sexually through egg and sperm. This means genetic information is
crossed between individuals and variability between parents and offspring is maintained. There
are a few animals that are capable of asexual (non sexual) reproduction. These include, hydra,
sponges, planaria, wasps, bees e.t.c.
The terms diploid and haploid are used to describe how many copies of genetic material are
contained within a cell. In diploid cells, there are two full sets of the cell's genetic material, in
haploid cells; there is only one full set of the cell's genetic material. Most animals are made up of
diploid cells.
6. Animals do not possess rigid cell walls (plants do have rigid cell walls).
In plants, the cell wall provides structural support and protection for the cell. Some bacteria also
possess cell walls. Animals do not have cell walls.
7. Specialized Tissues
One of the most remarkable things about animals is how specialized their cells are. As these
organisms develop, what seem to be plain-vanilla "stem cells" diversify into four broad
biological categories: nervous tissues, connective tissues, muscle tissues, and epithelial tissues
(which line the organs and blood vessels). More advanced organisms display even more specific
levels of differentiation; the various organs of your body, for example, are made up of liver cells,
pancreatic cells, and dozens of other varieties. (The exceptions that proves the rule here are
sponges, which are technically animals but have virtually no differentiated cells.)
8. Symmetry
Most animals are symmetrical. The few asymmetrical animals have an arrangement of body parts
that cannot be divided into corresponding sections. Example is found in sponges which grow in
varied and irregular shapes. Symmetry animals could either be radial or bilateral.
Radially symmetrical animals have parts of the body which are arranged around the central point
i.e. their sensory organs are located around the circumference. They do not move efficiently.
They are sessile, float in water or crawl along the bottom of the sea. Examples are sea anemones,
jellyfish e.t.c
Bilaterally symmetrical animals are those that have body parts in which half is a mirror image of
the other e.g. human being, butterfly e.t.c. Bilateral symmetry animals possess the following
features;
Sub-groups of animals
All animals belong to the kingdom Animalia. Despite this broad classification, they are divided
into sub-groups based on some features.